Title: Statistical Methods for Graphs
Description: Contains statistical methods to analyze graphs, such as graph
parameter estimation, model selection based on the GIC (Graph Information
Criterion), statistical tests to discriminate two or more populations of
graphs (ANOGVA - Analysis of Graph Variability), correlation between
graphs, and clustering of graphs.
References: Takahashi et al. (2012) <doi:10.1371/journal.pone.0049949>,
Futija et al. (2017) <doi:10.3389/fnins.2017.00066>,
Fujita et al. (2017) <doi:10.1016/j.csda.2016.11.016>,
Tang et al. (2017) <doi:10.3150/15-BEJ789>,
Tang et al. (2017) <doi:10.1080/10618600.2016.1193505>,
Ghoshdastidar et al. (2017) <arXiv:1705.06168>,
Ghoshdastidar et al. (2017) <arXiv:1707.00833>,
Cerqueira et al. (2017) <doi:10.1109/TNSE.2017.2674026>,
Fraiman and Fraiman (2018) <doi:10.1038/s41598-018-23152-5>,
Fujita et al. (2019) <doi:10.1093/comnet/cnz028>.
Author: Diogo R. da Costa [aut],
Taiane C. Ramos [aut],
Grover E. Castro Guzman [aut],
Suzana S. Santos [aut],
Eduardo S. Lira [aut],
Andre Fujita [aut, cre]
Maintainer: Andre Fujita <andrefujita@usp.br>
Diff between statGraph versions 0.4.0 dated 2020-11-19 and 0.4.1 dated 2020-12-16
DESCRIPTION | 10 MD5 | 46 - NAMESPACE | 50 - R/statGraph-package.R | 7 R/statGraph.R | 1300 +++++++++++++++++++------------------- build/partial.rdb |binary man/GIC.Rd | 8 man/anogva.Rd | 10 man/cerqueira.Rd | 2 man/fast.graph.param.estimator.Rd | 14 man/fast.spectral.density.Rd | 9 man/fraiman.Rd | 2 man/gCEM.Rd | 39 - man/ghoshdastidar.Rd | 3 man/graph.acf.Rd | 2 man/graph.cluster.Rd | 10 man/graph.cor.test.Rd | 2 man/graph.entropy.Rd | 8 man/graph.model.selection.Rd | 10 man/graph.mult.scaling.Rd | 8 man/graph.param.estimator.Rd | 12 man/graph.test.Rd | 8 man/kmeans.graph.Rd | 16 man/statGraph-package.Rd | 7 24 files changed, 807 insertions(+), 776 deletions(-)
Title: Estimate Gaussian Mixture Vector Autoregressive Model
Description: Unconstrained and constrained maximum likelihood estimation of structural and reduced form
Gaussian mixture vector autoregressive (GMVAR) model, quantile residual tests, graphical diagnostics,
simulations, forecasting, and estimation of generalized impulse response function.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2016) <doi:10.1016/j.jeconom.2016.02.012>,
Savi Virolainen (2020) <arXiv:2007.04713>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between gmvarkit versions 1.3.0 dated 2020-12-16 and 1.3.1 dated 2020-12-16
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- NEWS.md | 4 ++++ R/loglikelihood.R | 7 ++++++- 4 files changed, 19 insertions(+), 9 deletions(-)
Title: A Collection of Useful Functions by John
Description: A set of general functions that I have used in various
projects and in other R packages. They support some miscellaneous operations
on data frames, matrices and vectors like adding a row on a ternary (3-value)
data.frame based on positive and negative vector-indicators, rearranging a
list of data.frames by rownames, pruning rows or columns of a data.frame
that contain only one specific value given by the user,
pruning and reordering a vector according to the common elements between its
names and elements of another given vector, finding the non-common elements
between two vectors (outer-section),
normalization of a vector, matrix or data.frame's numeric values in a specified range,
pretty printing of vector names and values in an R Markdown document.
Also included is a function that returns the statistics needed for plotting a ROC curve.
Author: John Zobolas [aut, cph, cre] (<https://orcid.org/0000-0002-3609-8674>)
Maintainer: John Zobolas <bblodfon@gmail.com>
Diff between usefun versions 0.4.7 dated 2020-06-10 and 0.4.8 dated 2020-12-16
DESCRIPTION | 8 ++-- MD5 | 14 ++++--- NAMESPACE | 2 + NEWS.md | 5 ++ R/operations.R | 74 +++++++++++++++++++++++++++++++++++++++ README.md | 8 ++-- man/dec_to_bin.Rd |only man/partial_permut.Rd |only tests/testthat/test-operations.R | 25 +++++++++++++ 9 files changed, 123 insertions(+), 13 deletions(-)
Title: 'DataSHIELD' Interface
Description: 'DataSHIELD' is an infrastructure and series of R packages that
enables the remote and 'non-disclosive' analysis of sensitive research data.
This package defines the API that is to be implemented by 'DataSHIELD' compliant
data repositories.
Author: Yannick Marcon [aut, cre] (<https://orcid.org/0000-0003-0138-2023>),
Amadou Gaye [ctb] (<https://orcid.org/0000-0002-1180-2792>),
Paul Burton [ctb]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Diff between DSI versions 1.1.0 dated 2020-05-18 and 1.1.1 dated 2020-12-16
DESCRIPTION | 6 +-- MD5 | 16 ++++---- R/DSObject.R | 3 + R/datashield.aggregate.R | 2 - R/datashield.assign.R | 6 +-- R/datashield.status.R | 86 +++++++++++++++++++++++++++++------------------ README.md | 10 +++-- build/DSI.pdf |binary man/dsGetInfo.Rd | 3 + 9 files changed, 80 insertions(+), 52 deletions(-)
Title: Variance Dispersion Graphs and Fraction of Design Space Plots
Description: Facilities for constructing variance dispersion graphs, fraction-
of-design-space plots and similar graphics for exploring the properties of
experimental designs. The design region is explored via random sampling, which
allows for more flexibility than traditional variance dispersion graphs. A
formula interface is leveraged to provide access to complex model formulae.
Graphics can be constructed simultaneously for multiple experimental designs
and/or multiple model formulae. Instead of using pointwise optimization to
find the minimum and maximum scaled prediction variance curves, which can be
inaccurate and time consuming, this package uses quantile regression as an
alternative.
Author: Pieter Schoonees [aut, cre, cph],
Niel le Roux [ctb]
Maintainer: Pieter Schoonees <schoonees@gmail.com>
Diff between vdg versions 1.2.0 dated 2016-10-18 and 1.2.1 dated 2020-12-16
DESCRIPTION | 16 MD5 | 78 +- NAMESPACE | 82 +- R/GJ54.R | 18 R/LHS.R | 210 +++--- R/meanspv.R | 224 +++--- R/plot.spv.R | 488 +++++++------- R/plot.spvforlist.R | 314 ++++----- R/plot.spvlist.R | 328 ++++----- R/plot.spvlistforlist.R | 332 ++++----- R/print.spv.R | 52 - R/print.spvforlist.R | 38 - R/print.spvlist.R | 40 - R/print.spvlistforlist.R | 36 - R/runif_cube.R | 46 - R/runif_sphere.R | 92 +- R/sampler.R | 106 +-- R/spv.R | 82 +- R/spv.data.frame.R | 166 ++-- R/spv.list.R | 156 ++-- R/spv.matrix.R | 166 ++-- R/stdrange.R | 62 - R/vdg-package.R | 82 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/vdg.R | 320 ++++----- inst/doc/vdg.Rnw | 1622 +++++++++++++++++++++++------------------------ inst/doc/vdg.pdf |binary man/GJ54.Rd | 35 - man/LHS.Rd | 131 +-- man/meanspv.Rd | 97 +- man/plot.spv.Rd | 368 ++++++---- man/print.spv.Rd | 72 +- man/runif_sphere.Rd | 99 +- man/sampler.Rd | 123 +-- man/spv.Rd | 187 +++-- man/stdrange.Rd | 55 - man/vdg-package.Rd | 89 +- vignettes/vdg.Rnw | 1622 +++++++++++++++++++++++------------------------ vignettes/vdg.bib | 654 +++++++++--------- 40 files changed, 4388 insertions(+), 4300 deletions(-)
Title: Tools at the Intersection of 'purrr' and 'dplyr'
Description: Some functions at the intersection of 'dplyr' and
'purrr' that formerly lived in 'purrr'.
Author: Lionel Henry [aut, cre],
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between purrrlyr versions 0.0.6 dated 2020-05-02 and 0.0.7 dated 2020-12-16
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- NEWS.md | 4 ++++ README.md | 4 +++- man/by_slice.Rd | 2 +- tests/testthat/helper-rows.R | 2 +- tests/testthat/test-dmap.R | 4 +--- tests/testthat/test-rows.R | 15 +++++++++------ 8 files changed, 32 insertions(+), 24 deletions(-)
Title: 'Opal' Data Repository Client and 'DataSHIELD' Utils
Description: Data integration Web application for biobanks by 'OBiBa'. 'Opal' is
the core database application for biobanks. Participant data, once
collected from any data source, must be integrated and stored in a central
data repository under a uniform model. 'Opal' is such a central repository.
It can import, process, validate, query, analyze, report, and export data.
'Opal' is typically used in a research center to analyze the data acquired at
assessment centres. Its ultimate purpose is to achieve seamless
data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal'
web services and to perform operations on the R server side. 'DataSHIELD'
administration tools are also provided.
Author: Yannick Marcon [aut, cre] (<https://orcid.org/0000-0003-0138-2023>),
Amadou Gaye [ctb] (<https://orcid.org/0000-0002-1180-2792>),
OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Diff between opalr versions 1.5.0 dated 2020-11-03 and 1.5.1 dated 2020-12-16
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/datashield.admin.r | 4 +++- build/vignette.rds |binary inst/doc/opal-files.html | 41 ++++------------------------------------- inst/doc/opal-projects.html | 41 ++++------------------------------------- inst/doc/opal-rsession.html | 41 ++++------------------------------------- 7 files changed, 24 insertions(+), 121 deletions(-)
Title: Morphometric Maps, Bone Landmarking and Cross Sectional Geometry
Description: Extract cross sections from long bone meshes at specified intervals along the diaphysis. Calculate two and three-dimensional morphometric maps, cross-sectional geometric parameters, and semilandmarks on the periosteal and endosteal contours of each cross section.
Author: Antonio Profico [aut, cre],
Luca Bondioli [aut],
Pasquale Raia [aut],
Julien Claude [ctb],
Paul O'Higgins [aut],
Damiano Marchi [aut]
Maintainer: Antonio Profico <antonio.profico@gmail.com>
Diff between morphomap versions 1.2 dated 2020-06-14 and 1.3 dated 2020-12-16
DESCRIPTION | 10 +++++----- MD5 | 34 ++++++++++++++++++---------------- NAMESPACE | 18 +++++++++++++++++- R/morphomap.R | 5 +++-- R/morphomap2Dmap.R | 2 +- R/morphomap3Dmap.R | 20 ++++++++++---------- R/morphomapAlignment.R |only R/morphomapCore.R | 22 +++++++++++++--------- R/morphomapMirror.R | 10 +++++----- R/morphomapPlotShape.R | 2 +- R/morphomapSegm.R | 10 +++++----- R/morphomapShape.R | 28 ++++++++++++++-------------- man/morphomap2Dmap.Rd | 2 +- man/morphomap3Dmap.Rd | 14 +++++++------- man/morphomapAlignment.Rd |only man/morphomapCore.Rd | 22 +++++++++++++--------- man/morphomapMirror.Rd | 10 +++++----- man/morphomapPlotShape.Rd | 2 +- man/morphomapSegm.Rd | 10 +++++----- 19 files changed, 124 insertions(+), 97 deletions(-)
Title: Functional Data Analysis
Description: These functions were developed to support functional data
analysis as described in Ramsay, J. O. and Silverman, B. W.
(2005) Functional Data Analysis. New York: Springer and in
Ramsay, J. O., Hooker, Giles, and Graves, Spencer (2009).
Functional Data Analysis with R and Matlab (Springer).
The package includes data sets and script files working many examples
including all but one of the 76 figures in this latter book. Matlab versions
are available by ftp from
<http://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/>.
Author: J. O. Ramsay <ramsay@psych.mcgill.ca> [aut,cre],
Spencer Graves <spencer.graves@effectivedefense.org> [ctb],
Giles Hooker <gjh27@cornell.edu> [ctb]
Maintainer: J. O. Ramsay <ramsay@psych.mcgill.ca>
Diff between fda versions 5.1.7 dated 2020-11-28 and 5.1.9 dated 2020-12-16
DESCRIPTION | 8 - MD5 | 16 +-- NEWS | 7 - R/fRegress.CV.R | 253 +++++++++++++++++++++++++-------------------------- R/fRegress.R | 6 + R/fRegress.double.R | 14 +- R/fRegress.stderr.R | 46 +++++---- R/fRegressArgCheck.R | 14 ++ man/fRegress.Rd | 132 ++++++++------------------ 9 files changed, 234 insertions(+), 262 deletions(-)
Title: Convert Statistical Objects into Tidy Tibbles
Description: Summarizes key information about statistical
objects in tidy tibbles. This makes it easy to report results, create
plots and consistently work with large numbers of models at once.
Broom provides three verbs that each provide different types of
information about a model. tidy() summarizes information about model
components such as coefficients of a regression. glance() reports
information about an entire model, such as goodness of fit measures
like AIC and BIC. augment() adds information about individual
observations to a dataset, such as fitted values or influence
measures.
Author: David Robinson [aut],
Alex Hayes [aut, cre] (<https://orcid.org/0000-0002-4985-5160>),
Simon Couch [aut],
Indrajeet Patil [ctb] (<https://orcid.org/0000-0003-1995-6531>),
Derek Chiu [ctb],
Matthieu Gomez [ctb],
Boris Demeshev [ctb],
Dieter Menne [ctb],
Benjamin Nutter [ctb],
Luke Johnston [ctb],
Ben Bolker [ctb],
Francois Briatte [ctb],
Jeffrey Arnold [ctb],
Jonah Gabry [ctb],
Luciano Selzer [ctb],
Gavin Simpson [ctb],
Jens Preussner [ctb],
Jay Hesselberth [ctb],
Hadley Wickham [ctb],
Matthew Lincoln [ctb],
Alessandro Gasparini [ctb],
Lukasz Komsta [ctb],
Frederick Novometsky [ctb],
Wilson Freitas [ctb],
Michelle Evans [ctb],
Jason Cory Brunson [ctb],
Simon Jackson [ctb],
Ben Whalley [ctb],
Karissa Whiting [ctb],
Yves Rosseel [ctb],
Michael Kuehn [ctb],
Jorge Cimentada [ctb],
Erle Holgersen [ctb],
Karl Dunkle Werner [ctb] (<https://orcid.org/0000-0003-0523-7309>),
Ethan Christensen [ctb],
Steven Pav [ctb],
Paul PJ [ctb],
Ben Schneider [ctb],
Patrick Kennedy [ctb],
Lily Medina [ctb],
Brian Fannin [ctb],
Jason Muhlenkamp [ctb],
Matt Lehman [ctb],
Bill Denney [ctb] (<https://orcid.org/0000-0002-5759-428X>),
Nic Crane [ctb],
Andrew Bates [ctb],
Vincent Arel-Bundock [ctb] (<https://orcid.org/0000-0003-2042-7063>),
Hideaki Hayashi [ctb],
Luis Tobalina [ctb],
Annie Wang [ctb],
Wei Yang Tham [ctb],
Clara Wang [ctb],
Abby Smith [ctb] (<https://orcid.org/0000-0002-3207-0375>),
Jasper Cooper [ctb] (<https://orcid.org/0000-0002-8639-3188>),
E Auden Krauska [ctb] (<https://orcid.org/0000-0002-1466-5850>),
Alex Wang [ctb],
Malcolm Barrett [ctb] (<https://orcid.org/0000-0003-0299-5825>),
Charles Gray [ctb] (<https://orcid.org/0000-0002-9978-011X>),
Jared Wilber [ctb],
Vilmantas Gegzna [ctb] (<https://orcid.org/0000-0002-9500-5167>),
Eduard Szoecs [ctb],
Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>),
Angus Moore [ctb],
Nick Williams [ctb],
Marius Barth [ctb] (<https://orcid.org/0000-0002-3421-6665>),
Bruna Wundervald [ctb] (<https://orcid.org/0000-0001-8163-220X>),
Joyce Cahoon [ctb] (<https://orcid.org/0000-0001-7217-4702>),
Grant McDermott [ctb] (<https://orcid.org/0000-0001-7883-8573>),
Kevin Zarca [ctb],
Shiro Kuriwaki [ctb] (<https://orcid.org/0000-0002-5687-2647>),
Lukas Wallrich [ctb] (<https://orcid.org/0000-0003-2121-5177>),
James Martherus [ctb] (<https://orcid.org/0000-0002-8285-3300>),
Chuliang Xiao [ctb] (<https://orcid.org/0000-0002-8466-9398>),
Joseph Larmarange [ctb],
Max Kuhn [ctb],
Michal Bojanowski [ctb],
Hakon Malmedal [ctb],
Clara Wang [ctb],
Sergio Oller [ctb],
Luke Sonnet [ctb],
Jim Hester [ctb],
Cory Brunson [ctb],
Ben Schneider [ctb],
Bernie Gray [ctb] (<https://orcid.org/0000-0001-9190-6032>),
Mara Averick [ctb],
Aaron Jacobs [ctb],
Andreas Bender [ctb],
Sven Templer [ctb],
Paul-Christian Buerkner [ctb],
Matthew Kay [ctb],
Erwan Le Pennec [ctb],
Johan Junkka [ctb],
Hao Zhu [ctb],
Benjamin Soltoff [ctb],
Zoe Wilkinson Saldana [ctb],
Tyler Littlefield [ctb],
Charles T. Gray [ctb],
Shabbh E. Banks [ctb],
Serina Robinson [ctb],
Roger Bivand [ctb],
Riinu Ots [ctb],
Nicholas Williams [ctb],
Nina Jakobsen [ctb],
Michael Weylandt [ctb],
Lisa Lendway [ctb],
Karl Hailperin [ctb],
Josue Rodriguez [ctb],
Jenny Bryan [ctb],
Chris Jarvis [ctb],
Greg Macfarlane [ctb],
Brian Mannakee [ctb],
Drew Tyre [ctb],
Shreyas Singh [ctb],
Laurens Geffert [ctb],
Hong Ooi [ctb],
Henrik Bengtsson [ctb],
Eduard Szocs [ctb],
David Hugh-Jones [ctb],
Matthieu Stigler [ctb],
Hugo Tavares [ctb] (<https://orcid.org/0000-0001-9373-2726>),
R. Willem Vervoort [ctb],
Brenton M. Wiernik [ctb]
Maintainer: Alex Hayes <alexpghayes@gmail.com>
Diff between broom versions 0.7.2 dated 2020-10-20 and 0.7.3 dated 2020-12-16
broom-0.7.2/broom/R/gee.R |only broom-0.7.2/broom/R/lfe-tidiers.R |only broom-0.7.2/broom/R/mclogit.R |only broom-0.7.2/broom/R/scam-tidiers.R |only broom-0.7.2/broom/man/augment.felm.Rd |only broom-0.7.2/broom/man/glance.felm.Rd |only broom-0.7.2/broom/man/tidy.felm.Rd |only broom-0.7.2/broom/tests/testthat/test-gee.R |only broom-0.7.2/broom/tests/testthat/test-lfe.R |only broom-0.7.2/broom/tests/testthat/test-mclogit.R |only broom-0.7.3/broom/DESCRIPTION | 44 +-- broom-0.7.3/broom/MD5 | 66 ++--- broom-0.7.3/broom/NAMESPACE | 15 - broom-0.7.3/broom/NEWS.md | 21 + broom-0.7.3/broom/R/stats-glm-tidiers.R | 12 - broom-0.7.3/broom/R/stats-lm-tidiers.R | 28 +- broom-0.7.3/broom/R/stats-mlm-tidiers.R | 8 broom-0.7.3/broom/R/stats-summary-lm-tidiers.R |only broom-0.7.3/broom/R/utilities.R | 19 + broom-0.7.3/broom/README.md | 4 broom-0.7.3/broom/inst/doc/adding-tidiers.html | 45 +++ broom-0.7.3/broom/inst/doc/available-methods.html | 177 ++++++++------- broom-0.7.3/broom/inst/doc/bootstrapping.html | 45 +++ broom-0.7.3/broom/inst/doc/broom.html | 106 +++----- broom-0.7.3/broom/inst/doc/broom_and_dplyr.html | 106 +++----- broom-0.7.3/broom/inst/doc/kmeans.html | 41 +++ broom-0.7.3/broom/man/augment.glm.Rd | 4 broom-0.7.3/broom/man/augment.lm.Rd | 11 broom-0.7.3/broom/man/glance.glm.Rd | 4 broom-0.7.3/broom/man/glance.lm.Rd | 13 - broom-0.7.3/broom/man/glance.summary.lm.Rd |only broom-0.7.3/broom/man/glance.svyglm.Rd | 4 broom-0.7.3/broom/man/tidy.glm.Rd | 4 broom-0.7.3/broom/man/tidy.lm.Rd | 11 broom-0.7.3/broom/man/tidy.lm.beta.Rd | 4 broom-0.7.3/broom/man/tidy.mlm.Rd | 4 broom-0.7.3/broom/man/tidy.summary.lm.Rd |only broom-0.7.3/broom/tests/testthat/test-stats-lm.R | 1 broom-0.7.3/broom/tests/testthat/test-stats-mlm.R | 14 - broom-0.7.3/broom/tests/testthat/test-stats-summary-lm.R |only broom-0.7.3/broom/tests/testthat/test-utilities.R | 10 41 files changed, 481 insertions(+), 340 deletions(-)
Title: Biochemically Intuitive Generalized Loewe Model
Description: Response surface methods for drug synergy analysis. Available
methods include generalized and classical Loewe formulations as well as Highest
Single Agent methodology. Response surfaces can be plotted in an interactive
3-D plot and formal statistical tests for presence of synergistic effects are
available. Implemented methods and tests are described in the article
"BIGL: Biochemically Intuitive Generalized Loewe null model for prediction
of the expected combined effect compatible with partial agonism and antagonism"
by Koen Van der Borght, Annelies Tourny, Rytis Bagdziunas, Olivier Thas,
Maxim Nazarov, Heather Turner, Bie Verbist & Hugo Ceulemans (2017)
<doi:10.1038/s41598-017-18068-5>.
Author: Heather Turner, Annelies Tourny, Olivier Thas, Maxim Nazarov, Rytis Bagdziunas, Stijn Hawinkel
Maintainer: Maxim Nazarov <maxim.nazarov@openanalytics.eu>
Diff between BIGL versions 1.5.3 dated 2020-09-10 and 1.6.0 dated 2020-12-16
BIGL-1.5.3/BIGL/man/CPBootstrap.Rd |only BIGL-1.5.3/BIGL/man/bootstrapData.Rd |only BIGL-1.6.0/BIGL/DESCRIPTION | 14 BIGL-1.6.0/BIGL/MD5 | 103 ++-- BIGL-1.6.0/BIGL/NAMESPACE | 18 BIGL-1.6.0/BIGL/R/ResponseSurface-methods.R | 22 BIGL-1.6.0/BIGL/R/bootConfInt.R |only BIGL-1.6.0/BIGL/R/bootstrap.R | 384 ++++++--------- BIGL-1.6.0/BIGL/R/confInt-functions.R |only BIGL-1.6.0/BIGL/R/fitSurface.R | 218 ++++++-- BIGL-1.6.0/BIGL/R/generalizedLoewe.R | 43 + BIGL-1.6.0/BIGL/R/getd1d2.R |only BIGL-1.6.0/BIGL/R/harbronLoewe.R | 110 ++-- BIGL-1.6.0/BIGL/R/isobologram.R | 11 BIGL-1.6.0/BIGL/R/maxR-functions.R | 7 BIGL-1.6.0/BIGL/R/maxR.R |only BIGL-1.6.0/BIGL/R/meanR.R |only BIGL-1.6.0/BIGL/R/modelVar.R |only BIGL-1.6.0/BIGL/R/plotMeanVarFit.R |only BIGL-1.6.0/BIGL/R/plotReponseSurface.R | 24 BIGL-1.6.0/BIGL/R/predictOffAxis.R | 90 +-- BIGL-1.6.0/BIGL/R/predictResponseSurface.R |only BIGL-1.6.0/BIGL/R/scaleResids.R |only BIGL-1.6.0/BIGL/R/statistics.R | 396 +--------------- BIGL-1.6.0/BIGL/inst/NEWS | 4 BIGL-1.6.0/BIGL/inst/doc/analysis.R | 26 - BIGL-1.6.0/BIGL/inst/doc/analysis.Rmd | 59 +- BIGL-1.6.0/BIGL/inst/doc/analysis.html | 468 ++++++++++++------- BIGL-1.6.0/BIGL/inst/doc/methodology.Rmd | 137 +++++ BIGL-1.6.0/BIGL/inst/doc/methodology.html | 103 +++- BIGL-1.6.0/BIGL/man/addResids.Rd |only BIGL-1.6.0/BIGL/man/backscaleResids.Rd |only BIGL-1.6.0/BIGL/man/bootConfInt.Rd |only BIGL-1.6.0/BIGL/man/fitSurface.Rd | 36 + BIGL-1.6.0/BIGL/man/generalizedLoewe.Rd | 15 BIGL-1.6.0/BIGL/man/generateData.Rd | 31 + BIGL-1.6.0/BIGL/man/getCP.Rd |only BIGL-1.6.0/BIGL/man/getR.Rd |only BIGL-1.6.0/BIGL/man/getd1d2.Rd |only BIGL-1.6.0/BIGL/man/harbronLoewe.Rd | 15 BIGL-1.6.0/BIGL/man/maxR.Rd | 45 + BIGL-1.6.0/BIGL/man/meanR.Rd | 31 - BIGL-1.6.0/BIGL/man/modelVar.Rd |only BIGL-1.6.0/BIGL/man/outsidePoints.Rd | 7 BIGL-1.6.0/BIGL/man/plot.BIGLconfInt.Rd |only BIGL-1.6.0/BIGL/man/plot.ResponseSurface.Rd | 2 BIGL-1.6.0/BIGL/man/plotConfInt.Rd |only BIGL-1.6.0/BIGL/man/plotMeanVarFit.Rd |only BIGL-1.6.0/BIGL/man/predictOffAxis.Rd | 28 - BIGL-1.6.0/BIGL/man/predictResponseSurface.Rd |only BIGL-1.6.0/BIGL/man/predictVar.Rd |only BIGL-1.6.0/BIGL/man/print.summary.BIGLconfInt.Rd |only BIGL-1.6.0/BIGL/man/sampleResids.Rd |only BIGL-1.6.0/BIGL/man/scaleResids.Rd |only BIGL-1.6.0/BIGL/man/simulateNull.Rd | 10 BIGL-1.6.0/BIGL/man/summary.BIGLconfInt.Rd |only BIGL-1.6.0/BIGL/tests/testthat/helper_calls.R | 5 BIGL-1.6.0/BIGL/tests/testthat/helper_statistics.R | 13 BIGL-1.6.0/BIGL/tests/testthat/test_calls.R | 58 +- BIGL-1.6.0/BIGL/tests/testthat/test_confint.R |only BIGL-1.6.0/BIGL/tests/testthat/test_marginals.R | 2 BIGL-1.6.0/BIGL/tests/testthat/test_maxR.R | 3 BIGL-1.6.0/BIGL/tests/testthat/test_meanR.R | 7 BIGL-1.6.0/BIGL/tests/testthat/test_plotMeanVarFit.R |only BIGL-1.6.0/BIGL/tests/testthat/test_wrapper.R | 62 +- BIGL-1.6.0/BIGL/vignettes/analysis.Rmd | 59 +- BIGL-1.6.0/BIGL/vignettes/methodology.Rmd | 137 +++++ 67 files changed, 1621 insertions(+), 1182 deletions(-)
Title: Text Analysis Utilities
Description: Utilities for text analysis.
Author: Christian Buchta [aut],
Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>),
Ingo Feinerer [aut],
David Meyer [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between tau versions 0.0-22 dated 2020-12-03 and 0.0-23 dated 2020-12-16
tau-0.0-22/tau/man/translate.Rd |only tau-0.0-23/tau/DESCRIPTION | 6 +++--- tau-0.0-23/tau/MD5 | 4 ++-- tau-0.0-23/tau/man/ligatures.Rd |only 4 files changed, 5 insertions(+), 5 deletions(-)
Title: Fast Region-Based Association Tests on Summary Statistics
Description: An adaptation of classical region/gene-based association analysis
techniques to the use of summary statistics (P values and effect sizes)
and correlations between genetic variants as input. It is a tool to perform
the most popular and efficient gene-based tests using the results of genome-wide
association (meta-)analyses without having the original genotypes and
phenotypes at hand.
Author: Nadezhda M. Belonogova <belon@bionet.nsc.ru> and
Gulnara R. Svishcheva <gulsvi@bionet.nsc.ru>
with contributions from:
Seunggeun Lee (kernel functions), Pierre Lafaye de Micheaux ('davies' method),
Minghui Wang, Yiyuan Liu, Shizhong Han (simpleM function),
Yaowu Liu (ACAT function), Thomas Lumley ('kuonen' method),
and James O. Ramsay (functional data analysis functions)
Maintainer: Nadezhda M. Belonogova <belon@bionet.nsc.ru>
Diff between sumFREGAT versions 1.1.0 dated 2018-11-15 and 1.2.0 dated 2020-12-16
sumFREGAT-1.1.0/sumFREGAT/inst/doc |only sumFREGAT-1.1.0/sumFREGAT/inst/testfiles/CFH.scores.full.ref.vcf.gz |only sumFREGAT-1.1.0/sumFREGAT/inst/testfiles/CFH.scores.full.ref.vcf.gz.tbi |only sumFREGAT-1.2.0/sumFREGAT/ChangeLog |only sumFREGAT-1.2.0/sumFREGAT/DESCRIPTION | 12 sumFREGAT-1.2.0/sumFREGAT/MD5 | 55 sumFREGAT-1.2.0/sumFREGAT/NAMESPACE | 5 sumFREGAT-1.2.0/sumFREGAT/R/ACAT.R |only sumFREGAT-1.2.0/sumFREGAT/R/ACATO.R |only sumFREGAT-1.2.0/sumFREGAT/R/BT.R | 4 sumFREGAT-1.2.0/sumFREGAT/R/FLM.R | 4 sumFREGAT-1.2.0/sumFREGAT/R/MLR.R | 4 sumFREGAT-1.2.0/sumFREGAT/R/PCA.R | 4 sumFREGAT-1.2.0/sumFREGAT/R/SKAT.R | 4 sumFREGAT-1.2.0/sumFREGAT/R/SKATO.R | 246 ++-- sumFREGAT-1.2.0/sumFREGAT/R/check.R | 65 - sumFREGAT-1.2.0/sumFREGAT/R/genewise.R | 4 sumFREGAT-1.2.0/sumFREGAT/R/get.sumstat.R | 86 + sumFREGAT-1.2.0/sumFREGAT/R/minp.R | 74 + sumFREGAT-1.2.0/sumFREGAT/R/prep.score.files.R | 145 +- sumFREGAT-1.2.0/sumFREGAT/R/simpleM.R | 90 - sumFREGAT-1.2.0/sumFREGAT/R/sumSTAAR.R |only sumFREGAT-1.2.0/sumFREGAT/R/sumchi.R | 16 sumFREGAT-1.2.0/sumFREGAT/inst/testfiles/CFH.anno.phred.dat |only sumFREGAT-1.2.0/sumFREGAT/inst/testfiles/CFH.dat | 554 +++++----- sumFREGAT-1.2.0/sumFREGAT/inst/testfiles/CFH.scores.anno.vcf.gz |only sumFREGAT-1.2.0/sumFREGAT/inst/testfiles/CFH.scores.anno.vcf.gz.tbi |only sumFREGAT-1.2.0/sumFREGAT/inst/testfiles/CFH.scores.vcf.gz |binary sumFREGAT-1.2.0/sumFREGAT/inst/testfiles/CFH.scores.vcf.gz.tbi |binary sumFREGAT-1.2.0/sumFREGAT/inst/testfiles/ensembl.hg38.txt |only sumFREGAT-1.2.0/sumFREGAT/man/ACATO.rd |only sumFREGAT-1.2.0/sumFREGAT/man/gene-based_test_functions.rd | 113 +- sumFREGAT-1.2.0/sumFREGAT/man/prep.score.files.rd | 68 - sumFREGAT-1.2.0/sumFREGAT/man/sumFREGAT-package.rd | 5 sumFREGAT-1.2.0/sumFREGAT/man/sumSTAAR.rd |only 35 files changed, 892 insertions(+), 666 deletions(-)
Title: Workflow for Open Reproducible Code in Science
Description: Create reproducible and transparent research projects in 'R'.
This package is based on the Workflow for Open
Reproducible Code in Science (WORCS), a step-by-step procedure based on best
practices for
Open Science. It includes an 'RStudio' project template, several
convenience functions, and all dependencies required to make your project
reproducible and transparent. WORCS is explained in the tutorial paper
by Van Lissa, Brandmaier, Brinkman, Lamprecht, Struiksma, & Vreede (2020).
<doi:10.17605/OSF.IO/ZCVBS>.
Author: Caspar J. van Lissa [aut, cre]
(<https://orcid.org/0000-0002-0808-5024>),
Aaron Peikert [aut] (<https://orcid.org/0000-0001-7813-818X>),
Andreas M. Brandmaier [aut] (<https://orcid.org/0000-0001-8765-6982>)
Maintainer: Caspar J. van Lissa <c.j.vanlissa@uu.nl>
Diff between worcs versions 0.1.5 dated 2020-10-09 and 0.1.6 dated 2020-12-16
DESCRIPTION | 12 - MD5 | 63 +++-- NAMESPACE | 145 ++++++------- R/add_synthetic.R |only R/codebook.R | 7 R/descriptives.R | 23 -- R/github.R | 55 ++++ R/load_entrypoint.R |only R/save_load.R | 151 ++++++++++--- R/synthetic.R | 92 +++++++- R/worcs_project.R | 50 +++- build/vignette.rds |binary inst/doc/reproduce.R |only inst/doc/reproduce.Rmd |only inst/doc/reproduce.html |only inst/doc/setup-docker.R |only inst/doc/setup-docker.Rmd |only inst/doc/setup-docker.html |only inst/doc/setup.Rmd | 4 inst/doc/setup.html | 2 inst/doc/workflow.Rmd | 71 +++--- inst/doc/workflow.html | 79 ++++--- inst/rstudio/templates/project/resources/README.md | 45 ---- inst/rstudio/templates/project/worcs.dcf | 6 man/add_manuscript.Rd | 2 man/add_synthetic.Rd |only man/closed_data.Rd | 123 +++++------ man/codebook.Rd | 4 man/git_ignore.Rd |only man/git_update.Rd | 2 man/load_entrypoint.Rd |only man/notify_synthetic.Rd |only man/synthetic.Rd | 232 +++++++++++++-------- man/worcs_project.Rd | 11 tests/testthat/test-test-closed_data.R | 94 ++++---- vignettes/github_download.png |only vignettes/reproduce.Rmd |only vignettes/setup-docker.Rmd |only vignettes/setup.Rmd | 4 vignettes/workflow.Rmd | 71 +++--- 40 files changed, 846 insertions(+), 502 deletions(-)
Title: Procedures for Psychological, Psychometric, and Personality
Research
Description: A general purpose toolbox for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Functions for simulating and testing particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometric theory as well as publications in personality research. For more information, see the <https://personality-project.org/r/> web page.
Author: William Revelle [aut, cre] (<https://orcid.org/0000-0003-4880-9610>)
Maintainer: William Revelle <revelle@northwestern.edu>
Diff between psych versions 2.0.9 dated 2020-10-05 and 2.0.12 dated 2020-12-16
psych-2.0.12/psych/DESCRIPTION | 8 - psych-2.0.12/psych/MD5 | 93 ++++++++--------- psych-2.0.12/psych/NAMESPACE | 5 psych-2.0.12/psych/R/VSS.R | 2 psych-2.0.12/psych/R/bassAckward.R | 2 psych-2.0.12/psych/R/bassAckward.diagram.r | 22 +++- psych-2.0.12/psych/R/bestItems.r | 23 +++- psych-2.0.12/psych/R/cohen.d.R | 4 psych-2.0.12/psych/R/cor.ci.R | 4 psych-2.0.12/psych/R/densityBy.r | 142 ++++++++++++++++++++------ psych-2.0.12/psych/R/describe.R | 8 - psych-2.0.12/psych/R/describe.by.R | 2 psych-2.0.12/psych/R/error.bars.R | 9 + psych-2.0.12/psych/R/error.bars.by.R | 153 +++++++++++++++++++---------- psych-2.0.12/psych/R/esem.R | 4 psych-2.0.12/psych/R/fa.parallel.poly.R | 2 psych-2.0.12/psych/R/fa.poly.R | 2 psych-2.0.12/psych/R/fa.pooled.r |only psych-2.0.12/psych/R/faBy.R | 29 ++--- psych-2.0.12/psych/R/faCor.R | 2 psych-2.0.12/psych/R/mediate.r | 17 +-- psych-2.0.12/psych/R/misc.R | 2 psych-2.0.12/psych/R/print.psych.mediate.R | 23 ++-- psych-2.0.12/psych/R/print.psych.vss.R | 10 - psych-2.0.12/psych/R/reverse.code.R | 14 ++ psych-2.0.12/psych/R/scoreFast.r | 4 psych-2.0.12/psych/R/set.cor.R | 62 +++++++---- psych-2.0.12/psych/R/statsBy.r | 11 +- psych-2.0.12/psych/R/thurstone.R | 5 psych-2.0.12/psych/build/vignette.rds |binary psych-2.0.12/psych/inst/CITATION | 4 psych-2.0.12/psych/inst/News.Rd | 92 +++++++++++++---- psych-2.0.12/psych/inst/doc/intro.R | 64 ++++++------ psych-2.0.12/psych/inst/doc/intro.Rnw | 29 +++-- psych-2.0.12/psych/inst/doc/intro.pdf |binary psych-2.0.12/psych/inst/doc/overview.R |only psych-2.0.12/psych/inst/doc/overview.Rnw |only psych-2.0.12/psych/inst/doc/overview.pdf |only psych-2.0.12/psych/man/Garcia.Rd | 2 psych-2.0.12/psych/man/densityBy.Rd | 28 +++-- psych-2.0.12/psych/man/error.bars.by.Rd | 10 + psych-2.0.12/psych/man/fa.Rd | 16 ++- psych-2.0.12/psych/man/fa.lookup.Rd | 11 +- psych-2.0.12/psych/man/scrub.Rd | 14 +- psych-2.0.12/psych/man/statsBy.Rd | 4 psych-2.0.12/psych/man/thurstone.Rd | 16 ++- psych-2.0.12/psych/vignettes/intro.Rnw | 29 +++-- psych-2.0.12/psych/vignettes/overview.Rnw |only psych-2.0.9/psych/inst/doc/scoring.R |only psych-2.0.9/psych/inst/doc/scoring.Rnw |only psych-2.0.9/psych/inst/doc/scoring.pdf |only psych-2.0.9/psych/vignettes/scoring.Rnw |only 52 files changed, 637 insertions(+), 346 deletions(-)
Title: Interactive Analytic Networks
Description: Create interactive analytic networks. It joins the data analysis power of R to obtain coincidences, co-occurrences and correlations, and the visualization libraries of 'JavaScript' in one package. The methods are described in Escobar and Martinez-Uribe (2020) <doi:10.18637/jss.v093.i11>.
Author: Modesto Escobar <modesto@usal.es>,
David Barrios <metal@usal.es>,
Carlos Prieto <cprietos@usal.es>,
Luis Martinez-Uribe <lmartinez@usal.es>.
Maintainer: Modesto Escobar <modesto@usal.es>
Diff between netCoin versions 1.1.25 dated 2020-05-26 and 1.1.26 dated 2020-12-16
DESCRIPTION | 8 MD5 | 12 R/utils.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/netCoin.html | 735 ++++++++++++++++++++++---------------------------- inst/doc/surCoin.html | 672 +++++++++++++++++++-------------------------- 7 files changed, 625 insertions(+), 804 deletions(-)
Title: Learn Computer and Data Science using Algorithmic Trading
Description: Provide sets of functions and methods to learn and practice data science using idea of algorithmic trading.
Main goal is to process information within "Decision Support System" to come up with analysis or predictions.
There are several utilities such as dynamic and adaptive risk management using reinforcement learning
and even functions to generate predictions of price changes using pattern recognition deep regression learning.
Summary of Methods used: Awesome H2O tutorials: <https://github.com/h2oai/awesome-h2o>,
Market Type research of Van Tharp Institute: <https://www.vantharp.com/>,
Reinforcement Learning R package: <https://CRAN.R-project.org/package=ReinforcementLearning>.
Author: Vladimir Zhbanko
Maintainer: Vladimir Zhbanko <vladimir.zhbanko@gmail.com>
Diff between lazytrade versions 0.4.2 dated 2020-11-12 and 0.4.3 dated 2020-12-16
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 12 ++++++++++++ R/aml_make_model.R | 6 +++--- R/aml_test_model.R | 23 +++++++++-------------- R/mt_evaluate.R | 32 +++++--------------------------- R/mt_make_model.R | 18 ++++++++++-------- man/aml_test_model.Rd | 14 +++++++------- man/mt_evaluate.Rd | 6 ++++-- man/mt_make_model.Rd | 8 +++++--- 10 files changed, 67 insertions(+), 76 deletions(-)
Title: Genotype Plus Genotype-by-Environment Biplots
Description: Create biplots for GGE (genotype plus genotype-by-environment) and
GGB (genotype plus genotype-by-block-of-environments) models.
See Laffont et al. (2013) <doi:10.2135/cropsci2013.03.0178>.
Author: Kevin Wright [aut, cre] (<https://orcid.org/0000-0002-0617-8673>),
Jean-Louis Laffont [aut]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between gge versions 1.5 dated 2020-07-21 and 1.6 dated 2020-12-16
DESCRIPTION | 12 ++-- MD5 | 22 ++++----- NAMESPACE | 1 NEWS.md | 8 ++- R/gge.R | 7 ++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/gge_examples.Rmd | 4 - inst/doc/gge_examples.html | 109 +++++++++++++++++++++++++++++++++++++++------ man/gge.Rd | 2 tests/testthat/test_gge.R | 9 +-- vignettes/gge_examples.Rmd | 4 - 12 files changed, 136 insertions(+), 42 deletions(-)
Title: Feature Extraction from Biological Sequences
Description: Extracts features from biological sequences. It contains most features which are presented in related work and also includes features which have never been introduced before. It extracts numerous features from Nucleotide and Peptide sequences. Each feature converts the input sequences to discrete numbers in order to use them as predictors in machine learning models. There are many features and information which are hidden inside a sequence. Utilizing the package, users can convert biological sequences to discrete models based on chosen properties. References: 'iLearn' 'Z. Chen et al.' (2019) <DOI:10.1093/bib/bbz041>. 'iFeature' 'Z. Chen et al.' (2018) <DOI:10.1093/bioinformatics/bty140>. <https://CRAN.R-project.org/package=rDNAse>. 'PseKRAAC' 'Y. Zuo et al.' 'PseKRAAC: a flexible web server for generating pseudo K-tuple reduced amino acids composition' (2017) <DOI:10.1093/bioinformatics/btw564>. 'iDNA6mA-PseKNC' 'P. Feng et al.' 'iDNA6mA-PseKNC: Identifying DNA N6-methyladenosine sites by incorporating nucleotide physicochemical properties into PseKNC' (2019) <DOI:10.1016/j.ygeno.2018.01.005>. 'I. Dubchak et al.' 'Prediction of protein folding class using global description of amino acid sequence' (1995) <DOI:10.1073/pnas.92.19.8700>. 'W. Chen et al.' 'Identification and analysis of the N6-methyladenosine in the Saccharomyces cerevisiae transcriptome' (2015) <DOI:10.1038/srep13859>.
Author: Sare Amerifar
Maintainer: Sare Amerifar <sare.ameri.01@gmail.com>
Diff between ftrCOOL versions 0.1.0 dated 2020-08-31 and 1.1.0 dated 2020-12-16
ftrCOOL-0.1.0/ftrCOOL/R/APkNCTri.R |only ftrCOOL-0.1.0/ftrCOOL/R/APkNCdi.R |only ftrCOOL-0.1.0/ftrCOOL/R/AutoCorDiNuc.R |only ftrCOOL-0.1.0/ftrCOOL/R/AutoCorTriNuc.R |only ftrCOOL-0.1.0/ftrCOOL/R/CkSNUCpair.R |only ftrCOOL-0.1.0/ftrCOOL/R/CodonUsage.R |only ftrCOOL-0.1.0/ftrCOOL/R/DiNucIndex.R |only ftrCOOL-0.1.0/ftrCOOL/R/Dinuc2Binary.R |only ftrCOOL-0.1.0/ftrCOOL/R/ENUComposition.R |only ftrCOOL-0.1.0/ftrCOOL/R/ExpectedValKmerNUC.R |only ftrCOOL-0.1.0/ftrCOOL/R/G_Ccontent.R |only ftrCOOL-0.1.0/ftrCOOL/R/LocalPoSpKaaF.R |only ftrCOOL-0.1.0/ftrCOOL/R/LocalPoSpKnucF.R |only ftrCOOL-0.1.0/ftrCOOL/R/NUC2Binary.R |only ftrCOOL-0.1.0/ftrCOOL/R/NUCKpartComposition.R |only ftrCOOL-0.1.0/ftrCOOL/R/NovelPseKNC.R |only ftrCOOL-0.1.0/ftrCOOL/R/PSEkNCTri.R |only ftrCOOL-0.1.0/ftrCOOL/R/PSEkNCdi.R |only ftrCOOL-0.1.0/ftrCOOL/R/TriNucIndex.R |only ftrCOOL-0.1.0/ftrCOOL/R/kNUComposition.R |only ftrCOOL-0.1.0/ftrCOOL/R/maxORFlength.R |only ftrCOOL-0.1.0/ftrCOOL/inst/extdata/hs.fasta |only ftrCOOL-0.1.0/ftrCOOL/inst/extdata/non-hs.fasta |only ftrCOOL-0.1.0/ftrCOOL/inst/extdata/nuIdx2.csv |only ftrCOOL-0.1.0/ftrCOOL/inst/extdata/nuIdx3.csv |only ftrCOOL-0.1.0/ftrCOOL/inst/extdata/standardizeNUCidx2.csv |only ftrCOOL-0.1.0/ftrCOOL/inst/extdata/standardizeNUCidx3.csv |only ftrCOOL-0.1.0/ftrCOOL/man/APkNUCTri.Rd |only ftrCOOL-0.1.0/ftrCOOL/man/APkNUCdi.Rd |only ftrCOOL-0.1.0/ftrCOOL/man/AutoCorDiNuc.Rd |only ftrCOOL-0.1.0/ftrCOOL/man/AutoCorTriNuc.Rd |only ftrCOOL-0.1.0/ftrCOOL/man/CkSNUCpair.Rd |only ftrCOOL-0.1.0/ftrCOOL/man/CodonUsage.Rd |only ftrCOOL-0.1.0/ftrCOOL/man/DiNucIndex.Rd |only ftrCOOL-0.1.0/ftrCOOL/man/Dinuc2Binary.Rd |only ftrCOOL-0.1.0/ftrCOOL/man/ENUComposition.Rd |only ftrCOOL-0.1.0/ftrCOOL/man/ExpectedValKmerNUC.Rd |only ftrCOOL-0.1.0/ftrCOOL/man/GCcontent.Rd |only ftrCOOL-0.1.0/ftrCOOL/man/LocalPoSpKaaF.Rd |only ftrCOOL-0.1.0/ftrCOOL/man/LocalPoSpKnucF.Rd |only ftrCOOL-0.1.0/ftrCOOL/man/NUC2Binary.Rd |only ftrCOOL-0.1.0/ftrCOOL/man/NUCKpartComposition.Rd |only ftrCOOL-0.1.0/ftrCOOL/man/PSEkNCTri.Rd |only ftrCOOL-0.1.0/ftrCOOL/man/PSEkNCdi.Rd |only ftrCOOL-0.1.0/ftrCOOL/man/TriNucIndex.Rd |only ftrCOOL-0.1.0/ftrCOOL/man/kNUComposition.Rd |only ftrCOOL-0.1.0/ftrCOOL/man/maxORFlength.Rd |only ftrCOOL-0.1.0/ftrCOOL/man/novel_PseKNC.Rd |only ftrCOOL-0.1.0/ftrCOOL/tests/testthat/test_novelPseNuc.R |only ftrCOOL-1.1.0/ftrCOOL/DESCRIPTION | 8 ftrCOOL-1.1.0/ftrCOOL/MD5 | 533 ++++++---- ftrCOOL-1.1.0/ftrCOOL/NAMESPACE | 81 + ftrCOOL-1.1.0/ftrCOOL/R/AA2Binary.R | 16 ftrCOOL-1.1.0/ftrCOOL/R/AAKpartComposition.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/AAindex.R | 9 ftrCOOL-1.1.0/ftrCOOL/R/AAutoCor.R | 37 ftrCOOL-1.1.0/ftrCOOL/R/ANF_DNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/ANF_RNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/APAAC.R | 8 ftrCOOL-1.1.0/ftrCOOL/R/APkNUCTri_DNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/APkNUCdi_DNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/APkNUCdi_RNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/ASA.R |only ftrCOOL-1.1.0/ftrCOOL/R/AutoCorDiNUC_DNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/AutoCorDiNUC_RNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/AutoCorTriNUC_DNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/Blosum62.R | 9 ftrCOOL-1.1.0/ftrCOOL/R/CTD.R | 29 ftrCOOL-1.1.0/ftrCOOL/R/CTDC.R | 33 ftrCOOL-1.1.0/ftrCOOL/R/CTDD.R | 29 ftrCOOL-1.1.0/ftrCOOL/R/CTDT.R | 33 ftrCOOL-1.1.0/ftrCOOL/R/CkSAApair.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/CkSGAApair.R | 4 ftrCOOL-1.1.0/ftrCOOL/R/CkSNUCpair_DNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/CkSNUCpair_RNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/CodonFraction.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/CodonUsage_DNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/CodonUsage_RNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/DDE.R | 3 ftrCOOL-1.1.0/ftrCOOL/R/DiNUC2Binary_DNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/DiNUC2Binary_RNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/DiNUCindex_DNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/DiNUCindex_RNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/DisorderB.R |only ftrCOOL-1.1.0/ftrCOOL/R/DisorderC.R |only ftrCOOL-1.1.0/ftrCOOL/R/DisorderS.R |only ftrCOOL-1.1.0/ftrCOOL/R/EAAComposition.R | 37 ftrCOOL-1.1.0/ftrCOOL/R/EGAAComposition.R | 124 ++ ftrCOOL-1.1.0/ftrCOOL/R/EIIP.R | 15 ftrCOOL-1.1.0/ftrCOOL/R/ENUComposition_DNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/ENUComposition_RNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/EffectiveNumberOfCodon.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/ExpectedValKmerNUC_DNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/ExpectedValKmerNUC_RNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/ExpectedValueAA.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/ExpectedValueGAA.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/ExpectedValueGKmerAA.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/ExpectedValueKmerAA.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/GAAKpartComposition.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/G_Ccontent_DNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/G_Ccontent_RNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/GrpDDE.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/KNNPeptide.R |only ftrCOOL-1.1.0/ftrCOOL/R/KNNProtein.R |only ftrCOOL-1.1.0/ftrCOOL/R/LocalPoSpKAAF.R |only ftrCOOL-1.1.0/ftrCOOL/R/LocalPoSpKNUCF_DNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/LocalPoSpKNUCF_RNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/NCP_DNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/NCP_RNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/NUC2Binary_DNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/NUC2Binary_RNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/NUCKpartComposition_DNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/NUCKpartComposition_RNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/PCPseDNC.R |only ftrCOOL-1.1.0/ftrCOOL/R/PSEAAC.R | 7 ftrCOOL-1.1.0/ftrCOOL/R/PSEkNUCTri_DNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/PSEkNUCdi_DNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/PSEkNUCdi_RNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/PSSM.R |only ftrCOOL-1.1.0/ftrCOOL/R/PSTNPds.R |only ftrCOOL-1.1.0/ftrCOOL/R/PSTNPss_DNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/PSTNPss_RNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/PseEIIP.R | 14 ftrCOOL-1.1.0/ftrCOOL/R/PseKRAAC_T1.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/PseKRAAC_T10.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/PseKRAAC_T11.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/PseKRAAC_T12.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/PseKRAAC_T13.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/PseKRAAC_T14.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/PseKRAAC_T15.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/PseKRAAC_T16.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/PseKRAAC_T2.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/PseKRAAC_T3A.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/PseKRAAC_T3B.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/PseKRAAC_T4.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/PseKRAAC_T5.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/PseKRAAC_T6A.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/PseKRAAC_T6B.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/PseKRAAC_T7.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/PseKRAAC_T8.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/PseKRAAC_T9.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/QSOrder.R | 3 ftrCOOL-1.1.0/ftrCOOL/R/SAAC.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/SGAAC.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/SOCNumber.R | 3 ftrCOOL-1.1.0/ftrCOOL/R/SSEB.R |only ftrCOOL-1.1.0/ftrCOOL/R/SSEC.R |only ftrCOOL-1.1.0/ftrCOOL/R/SSES.R |only ftrCOOL-1.1.0/ftrCOOL/R/TorsionAngle.R |only ftrCOOL-1.1.0/ftrCOOL/R/TriNUCindex_DNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/codonAdaptionIndex.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/conjointTrKS.R | 4 ftrCOOL-1.1.0/ftrCOOL/R/conjointTriad.R | 5 ftrCOOL-1.1.0/ftrCOOL/R/fa.read.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/fickettScore.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/kAAComposition.R | 3 ftrCOOL-1.1.0/ftrCOOL/R/kGAAComposition.R | 5 ftrCOOL-1.1.0/ftrCOOL/R/kNUComposition_DNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/kNUComposition_RNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/maxORF.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/maxORF_RNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/maxORFlength_DNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/maxORFlength_RNA.R |only ftrCOOL-1.1.0/ftrCOOL/R/nameKmer.R | 4 ftrCOOL-1.1.0/ftrCOOL/R/needleman.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/nonStandardSeq.R | 2 ftrCOOL-1.1.0/ftrCOOL/R/readASAdir.R |only ftrCOOL-1.1.0/ftrCOOL/R/readDisDir.R |only ftrCOOL-1.1.0/ftrCOOL/R/readPSSMdir.R |only ftrCOOL-1.1.0/ftrCOOL/R/readTorsionDir.R |only ftrCOOL-1.1.0/ftrCOOL/R/readss2Dir.R |only ftrCOOL-1.1.0/ftrCOOL/R/revComp.R | 10 ftrCOOL-1.1.0/ftrCOOL/R/zSCALE.R | 4 ftrCOOL-1.1.0/ftrCOOL/inst/extdata/Carica_papaya101RNA.txt |only ftrCOOL-1.1.0/ftrCOOL/inst/extdata/Carica_papaya101RNATotal.txt |only ftrCOOL-1.1.0/ftrCOOL/inst/extdata/DI_DNA.csv |only ftrCOOL-1.1.0/ftrCOOL/inst/extdata/DI_RNA.csv |only ftrCOOL-1.1.0/ftrCOOL/inst/extdata/DNA_testing.txt |only ftrCOOL-1.1.0/ftrCOOL/inst/extdata/TRI_DNA.csv |only ftrCOOL-1.1.0/ftrCOOL/inst/extdata/eiip.csv |only ftrCOOL-1.1.0/ftrCOOL/inst/extdata/ncp.csv |only ftrCOOL-1.1.0/ftrCOOL/inst/extdata/neg2RNA.txt |only ftrCOOL-1.1.0/ftrCOOL/inst/extdata/negDNA.txt |only ftrCOOL-1.1.0/ftrCOOL/inst/extdata/negData.txt |only ftrCOOL-1.1.0/ftrCOOL/inst/extdata/pos2RNA.txt |only ftrCOOL-1.1.0/ftrCOOL/inst/extdata/posDNA.txt |only ftrCOOL-1.1.0/ftrCOOL/inst/extdata/posData.txt |only ftrCOOL-1.1.0/ftrCOOL/inst/extdata/testData.txt |only ftrCOOL-1.1.0/ftrCOOL/inst/extdata/testSeq2RNA.txt |only ftrCOOL-1.1.0/ftrCOOL/inst/testForder |only ftrCOOL-1.1.0/ftrCOOL/man/AA2Binary.Rd | 10 ftrCOOL-1.1.0/ftrCOOL/man/AAKpartComposition.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/AAindex.Rd | 9 ftrCOOL-1.1.0/ftrCOOL/man/AAutoCor.Rd | 6 ftrCOOL-1.1.0/ftrCOOL/man/ANF_DNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/ANF_RNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/APAAC.Rd | 8 ftrCOOL-1.1.0/ftrCOOL/man/APkNUCTri_DNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/APkNUCdi_DNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/APkNUCdi_RNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/ASA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/AutoCorDiNUC_DNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/AutoCorDiNUC_RNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/AutoCorTriNUC_DNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/BLOSUM62.Rd | 9 ftrCOOL-1.1.0/ftrCOOL/man/CTD.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/CTDC.Rd | 4 ftrCOOL-1.1.0/ftrCOOL/man/CTDD.Rd | 4 ftrCOOL-1.1.0/ftrCOOL/man/CTDT.Rd | 4 ftrCOOL-1.1.0/ftrCOOL/man/CkSAApair.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/CkSGAApair.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/CkSNUCpair_DNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/CkSNUCpair_RNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/CodonFraction.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/CodonUsage_DNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/CodonUsage_RNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/DDE.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/DiNUC2Binary_DNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/DiNUC2Binary_RNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/DiNUCindex_DNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/DiNUCindex_RNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/DisorderB.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/DisorderC.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/DisorderS.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/EAAComposition.Rd | 14 ftrCOOL-1.1.0/ftrCOOL/man/EGAAComposition.Rd | 12 ftrCOOL-1.1.0/ftrCOOL/man/EIIP.Rd | 12 ftrCOOL-1.1.0/ftrCOOL/man/ENUComposition_DNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/ENUComposition_RNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/EffectiveNumberCodon.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/ExpectedValKmerNUC_DNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/ExpectedValKmerNUC_RNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/ExpectedValueAA.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/ExpectedValueGAA.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/ExpectedValueGKmerAA.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/ExpectedValueKmerAA.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/GAAKpartComposition.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/G_Ccontent_DNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/G_Ccontent_RNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/GrpDDE.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/KNNPeptide.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/KNNProtein.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/LocalPoSpKAAF.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/LocalPoSpKNUCF_DNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/LocalPoSpKNUCF_RNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/NCP_DNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/NCP_RNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/NUC2Binary_DNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/NUC2Binary_RNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/NUCKpartComposition_DNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/NUCKpartComposition_RNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/PCPseDNC.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/PSEAAC.Rd | 6 ftrCOOL-1.1.0/ftrCOOL/man/PSEkNUCTri_DNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/PSEkNUCdi_DNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/PSEkNUCdi_RNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/PSSM.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/PSTNPds.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/PSTNPss_DNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/PSTNPss_RNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/PseEIIP.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/PseKRAAC_T1.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/PseKRAAC_T10.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/PseKRAAC_T11.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/PseKRAAC_T12.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/PseKRAAC_T13.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/PseKRAAC_T14.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/PseKRAAC_T15.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/PseKRAAC_T16.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/PseKRAAC_T2.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/PseKRAAC_T3A.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/PseKRAAC_T3B.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/PseKRAAC_T4.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/PseKRAAC_T5.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/PseKRAAC_T6A.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/PseKRAAC_T6B.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/PseKRAAC_T7.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/PseKRAAC_T8.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/PseKRAAC_T9.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/QSOrder.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/SAAC.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/SGAAC.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/SOCNumber.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/SSEB.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/SSEC.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/SSES.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/TorsionAngle.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/TriNUCindex_DNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/codonAdaptionIndex.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/conjointTriad.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/conjointTriadKS.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/fa.read.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/fickettScore.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/kAAComposition.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/kGAAComposition.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/kNUComposition_DNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/kNUComposition_RNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/maxORF.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/maxORF_RNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/maxORFlength_DNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/maxORFlength_RNA.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/nameKmer.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/needleman.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/nonStandardSeq.Rd | 2 ftrCOOL-1.1.0/ftrCOOL/man/readASAdir.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/readDisDir.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/readPSSMdir.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/readTorsionDir.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/readss2Dir.Rd |only ftrCOOL-1.1.0/ftrCOOL/man/revComp.Rd | 6 ftrCOOL-1.1.0/ftrCOOL/man/zSCALE.Rd | 4 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/Test_Torsion.R |only ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test-kNUComposition.R | 17 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_ANF.R |only ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_APkNCTri.R | 2 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_APkNCdi.R | 11 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_ASA.R |only ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_AutoCorDi.R | 164 ++- ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_AutoCorTri.R | 16 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_CTDC.R | 7 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_CTDT.R | 6 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_CkNUCpair.R | 16 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_DiNucIndex.R | 31 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_Dinuc2Binary.R | 16 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_Disorder.R |only ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_ENUCompos.R | 39 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_ExpectedValKmerNUC.R | 17 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_GCcontent.R | 32 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_KNNpeptide.R |only ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_KNNprotein.R |only ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_NCP.R |only ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_Nuc2Bin.R | 17 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_PCPseDNC.R |only ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_PSEAAC.R | 2 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_PSSM.R |only ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_PSTNPds.R |only ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_PSTNPss.R |only ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_PseEIIP.R | 5 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_PseKNCdi.R | 11 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_PsekNCTri.R | 2 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_SSE.R |only ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_TriNucIndex.R | 17 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_aautoCor.R | 4 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_codonUsage.R | 17 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_localPosAAFreq.R | 8 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_localPosNUCFreq.R |only ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_maxORF.R | 12 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_maxORFlen.R | 13 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_nuckpartComposition.R | 31 ftrCOOL-1.1.0/ftrCOOL/tests/testthat/test_revComp.R | 2 350 files changed, 1245 insertions(+), 614 deletions(-)
Title: Sequential Design for Deep Gaussian Processes using MCMC
Description: Performs model fitting and sequential design for deep Gaussian
processes following Sauer, Gramacy, and Higdon (2020) <arXiv:2012.08015>. Models
extend up to three layers deep; a one layer model is equivalent to typical Gaussian
process regression. Sequential design criteria include integrated mean-squared
error (IMSE), active learning Cohn (ALC), and expected
improvement (EI). Covariance structure is based on inverse exponentiated
squared euclidean distance. Applicable to noisy and deterministic functions.
Incorporates SNOW parallelization and utilizes C under the hood.
Author: Annie Sauer <anniees@vt.edu>
Maintainer: Annie Sauer <anniees@vt.edu>
Diff between deepgp versions 0.1.0 dated 2020-10-29 and 0.2.0 dated 2020-12-16
deepgp-0.1.0/deepgp/man/IMSPE.Rd |only deepgp-0.2.0/deepgp/DESCRIPTION | 25 deepgp-0.2.0/deepgp/MD5 | 36 - deepgp-0.2.0/deepgp/NAMESPACE | 10 deepgp-0.2.0/deepgp/R/deepgp-package.R | 48 - deepgp-0.2.0/deepgp/R/fit_models.R | 877 ++++++++++++++++------------- deepgp-0.2.0/deepgp/R/general.R | 21 deepgp-0.2.0/deepgp/R/seq_design.R | 150 ++-- deepgp-0.2.0/deepgp/README.md | 26 deepgp-0.2.0/deepgp/man/ALC.Rd | 14 deepgp-0.2.0/deepgp/man/EI.Rd | 9 deepgp-0.2.0/deepgp/man/IMSE.Rd |only deepgp-0.2.0/deepgp/man/deepgp-package.Rd | 48 - deepgp-0.2.0/deepgp/man/fit_one_layer.Rd | 33 - deepgp-0.2.0/deepgp/man/fit_three_layer.Rd | 55 + deepgp-0.2.0/deepgp/man/fit_two_layer.Rd | 32 - deepgp-0.2.0/deepgp/man/plot.Rd | 3 deepgp-0.2.0/deepgp/man/predict.Rd | 66 +- deepgp-0.2.0/deepgp/man/score.Rd | 8 deepgp-0.2.0/deepgp/src/imspe.c | 19 20 files changed, 816 insertions(+), 664 deletions(-)
More information about shinyfullscreen at CRAN
Permanent link
Title: Automatically Position Non-Overlapping Text Labels with
'ggplot2'
Description: Provides text and label geoms for 'ggplot2' that help to avoid
overlapping text labels. Labels repel away from each other and away from the
data points.
Author: Kamil Slowikowski [aut, cre] (<https://orcid.org/0000-0002-2843-6370>),
Alicia Schep [ctb] (<https://orcid.org/0000-0002-3915-0618>),
Sean Hughes [ctb] (<https://orcid.org/0000-0002-9409-9405>),
Trung Kien Dang [ctb] (<https://orcid.org/0000-0001-7562-6495>),
Saulius Lukauskas [ctb],
Jean-Olivier Irisson [ctb] (<https://orcid.org/0000-0003-4920-3880>),
Zhian N Kamvar [ctb] (<https://orcid.org/0000-0003-1458-7108>),
Thompson Ryan [ctb] (<https://orcid.org/0000-0002-0450-8181>),
Dervieux Christophe [ctb] (<https://orcid.org/0000-0003-4474-2498>),
Yutani Hiroaki [ctb],
Pierre Gramme [ctb],
Amir Masoud Abdol [ctb],
Malcolm Barrett [ctb] (<https://orcid.org/0000-0003-0299-5825>),
Robrecht Cannoodt [ctb] (<https://orcid.org/0000-0003-3641-729X>),
Michał Krassowski [ctb] (<https://orcid.org/0000-0002-9638-7785>)
Maintainer: Kamil Slowikowski <kslowikowski@gmail.com>
Diff between ggrepel versions 0.8.2 dated 2020-03-08 and 0.9.0 dated 2020-12-16
ggrepel-0.8.2/ggrepel/R/utilities-grid.R |only ggrepel-0.8.2/ggrepel/tools |only ggrepel-0.9.0/ggrepel/DESCRIPTION | 35 - ggrepel-0.9.0/ggrepel/MD5 | 50 - ggrepel-0.9.0/ggrepel/NAMESPACE | 6 ggrepel-0.9.0/ggrepel/NEWS.md | 164 ++++- ggrepel-0.9.0/ggrepel/R/RcppExports.R | 32 + ggrepel-0.9.0/ggrepel/R/geom-label-repel.R | 423 ++++++++------ ggrepel-0.9.0/ggrepel/R/geom-text-repel.R | 484 ++++++++++------- ggrepel-0.9.0/ggrepel/R/ggrepel-package.R | 8 ggrepel-0.9.0/ggrepel/R/position-nudge2.R |only ggrepel-0.9.0/ggrepel/R/utilities.R | 37 + ggrepel-0.9.0/ggrepel/README.md | 100 --- ggrepel-0.9.0/ggrepel/build/vignette.rds |binary ggrepel-0.9.0/ggrepel/inst/doc/ggrepel.R | 251 -------- ggrepel-0.9.0/ggrepel/inst/doc/ggrepel.Rmd | 366 +----------- ggrepel-0.9.0/ggrepel/inst/doc/ggrepel.html | 465 +--------------- ggrepel-0.9.0/ggrepel/man/figures |only ggrepel-0.9.0/ggrepel/man/geom_text_repel.Rd | 97 ++- ggrepel-0.9.0/ggrepel/man/ggplot2-ggproto.Rd | 5 ggrepel-0.9.0/ggrepel/man/ggrepel.Rd | 31 + ggrepel-0.9.0/ggrepel/src/RcppExports.cpp | 46 + ggrepel-0.9.0/ggrepel/src/repel_boxes.cpp | 341 ++++++++++- ggrepel-0.9.0/ggrepel/tests/testthat/test-grob-order.R |only ggrepel-0.9.0/ggrepel/tests/testthat/test-seed.R | 19 ggrepel-0.9.0/ggrepel/tests/testthat/test-to_unit.R | 26 ggrepel-0.9.0/ggrepel/vignettes/ggrepel.Rmd | 366 +----------- ggrepel-0.9.0/ggrepel/vignettes/style.css |only 28 files changed, 1403 insertions(+), 1949 deletions(-)
Title: Sparse Tables
Description: Fast Multiplication and Marginalization of Sparse Tables.
Author: Mads Lindskou [aut, cre]
Maintainer: Mads Lindskou <mads@math.aau.dk>
Diff between sparta versions 0.6.1 dated 2020-11-24 and 0.7.0 dated 2020-12-16
DESCRIPTION | 8 +++--- MD5 | 27 ++++++++++---------- NAMESPACE | 2 + NEWS.md | 12 +++++++++ R/RcppExports.R | 4 +-- R/api_sparta.R | 50 +++++++++++++++++++++++++------------- R/helpers_misc.R | 5 +++ R/helpers_sparta.R | 59 +++++++++++++++++++++++++++++++++++++++++++-- README.md | 6 ++-- man/equiv.Rd |only man/marg.Rd | 5 +++ man/merge.Rd | 3 -- man/sparta_unity_struct.Rd | 7 +++-- src/RcppExports.cpp | 9 +++--- src/merge.cpp | 19 ++++++++++---- 15 files changed, 161 insertions(+), 55 deletions(-)
Title: Variance Stabilizing Transformations for Single Cell UMI Data
Description: A normalization method for single-cell UMI count data using a
variance stabilizing transformation. The transformation is based on a
negative binomial regression model with regularized parameters. As part of the
same regression framework, this package also provides functions for
batch correction, and data correction. See Hafemeister and Satija 2019
<doi:10.1186/s13059-019-1874-1> for more details.
Author: Christoph Hafemeister [aut, cre]
(<https://orcid.org/0000-0001-6365-8254>)
Maintainer: Christoph Hafemeister <christoph.hafemeister@nyu.edu>
Diff between sctransform versions 0.3.1 dated 2020-10-08 and 0.3.2 dated 2020-12-16
sctransform-0.3.1/sctransform/man/row_gmean_grouped.Rd |only sctransform-0.3.1/sctransform/man/row_mean_grouped.Rd |only sctransform-0.3.2/sctransform/DESCRIPTION | 7 sctransform-0.3.2/sctransform/MD5 | 37 - sctransform-0.3.2/sctransform/NAMESPACE | 5 sctransform-0.3.2/sctransform/NEWS.md | 17 sctransform-0.3.2/sctransform/R/RcppExports.R | 40 + sctransform-0.3.2/sctransform/R/denoise.R | 11 sctransform-0.3.2/sctransform/R/differential_expression.R | 191 ++++++++ sctransform-0.3.2/sctransform/R/fit.R | 2 sctransform-0.3.2/sctransform/R/plotting.R | 44 + sctransform-0.3.2/sctransform/R/utils.R | 58 -- sctransform-0.3.2/sctransform/R/vst.R | 79 +++ sctransform-0.3.2/sctransform/README.md | 7 sctransform-0.3.2/sctransform/man/correct.Rd | 4 sctransform-0.3.2/sctransform/man/diff_mean_test.Rd |only sctransform-0.3.2/sctransform/man/plot_model.Rd | 2 sctransform-0.3.2/sctransform/man/vst.Rd | 19 sctransform-0.3.2/sctransform/src/RcppExports.cpp | 136 ++++-- sctransform-0.3.2/sctransform/src/utils.cpp | 312 ++++++++++++-- sctransform-0.3.2/sctransform/tests/testthat/test_utils.R | 48 ++ 21 files changed, 854 insertions(+), 165 deletions(-)
Title: Junction Tree Inference
Description: Minimal and memory efficient implementation of the junction tree
algorithm using the Lauritzen-Spiegelhalter scheme;
S. L. Lauritzen and D. J. Spiegelhalter (1988)
<https://www.jstor.org/stable/2345762?seq=1>.
Author: Mads Lindskou [aut, cre]
Maintainer: Mads Lindskou <mads@math.aau.dk>
Diff between jti versions 0.5.2 dated 2020-11-24 and 0.6.0 dated 2020-12-16
DESCRIPTION | 6 MD5 | 20 NEWS.md | 10 R/api_compile.R | 28 + R/helper_charge.R | 22 R/helper_compile.R | 11 R/helper_jt.R | 51 +- R/sandbox.R | 948 +++---------------------------------------- README.md | 32 - man/compile.Rd | 36 + src/rooted_junction_tree.cpp | 28 + 11 files changed, 248 insertions(+), 944 deletions(-)
Title: Estimate Gaussian Mixture Vector Autoregressive Model
Description: Unconstrained and constrained maximum likelihood estimation of structural and reduced form
Gaussian mixture vector autoregressive (GMVAR) model, quantile residual tests, graphical diagnostics,
simulations, forecasting, and estimation of generalized impulse response function.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2016) <doi:10.1016/j.jeconom.2016.02.012>,
Savi Virolainen (2020) <arXiv:2007.04713>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between gmvarkit versions 1.2.3 dated 2020-11-03 and 1.3.0 dated 2020-12-16
DESCRIPTION | 11 - MD5 | 104 ++++++------ NAMESPACE | 1 NEWS.md | 16 + R/GIRF.R | 95 +++++------ R/GMVARconstruction.R | 87 ++++++++-- R/MAINest.R | 40 ++-- R/WaldAndLR.R | 29 +-- R/argumentChecks.R | 27 ++- R/diagnosticPlot.R | 8 R/generateParams.R | 6 R/geneticAlgorithm.R | 33 ++- R/loglikelihood.R | 114 +++++++++---- R/morePlots.R | 3 R/numericalDifferentiation.R | 14 - R/plotMethods.R | 10 - R/predictMethod.R | 4 R/quantileResidualTests.R | 23 ++ R/quantileResiduals.R | 39 +++- R/simulateGMVAR.R | 49 +---- R/standardErrors.R | 4 README.md | 23 +- inst/doc/intro-to-gmvarkit.Rmd | 17 +- inst/doc/intro-to-gmvarkit.html | 26 +-- man/GAfit.Rd | 20 +- man/GIRF.Rd | 29 +-- man/GMVAR.Rd | 19 ++ man/LR_test.Rd | 6 man/Wald_test.Rd | 10 + man/add_data.Rd | 2 man/alt_gmvar.Rd | 2 man/check_parameters.Rd | 20 ++ man/cond_moments.Rd | 13 + man/diagnostic_plot.Rd | 2 man/fitGMVAR.Rd | 28 +-- man/get_alpha_mt.Rd |only man/get_test_Omega.Rd | 13 + man/in_paramspace.Rd | 22 ++ man/in_paramspace_int.Rd | 13 + man/iterate_more.Rd | 20 ++ man/loglikelihood.Rd | 16 + man/loglikelihood_int.Rd | 16 + man/profile_logliks.Rd | 13 + man/quantile_residual_tests.Rd | 24 ++ man/quantile_residuals_int.Rd | 13 + man/random_ind2.Rd | 6 man/smart_ind.Rd | 6 man/standard_errors.Rd | 13 + man/swap_parametrization.Rd | 2 man/update_numtols.Rd |only tests/testthat/test_GIRF.R | 2 tests/testthat/test_loglikelihood.R | 13 + tests/testthat/test_quantileResiduals.R | 271 +++++++++++++++++--------------- vignettes/intro-to-gmvarkit.Rmd | 17 +- 54 files changed, 908 insertions(+), 506 deletions(-)
Title: Seismic Hypocenter Determination
Description: Hypocenter estimation and analysis of seismic data collected continuously, or in trigger mode. The functions organize other functions from RSEIS and GEOmap to help researchers pick, locate, and store hypocenters for detailed seismic investigation.
Author: Jonathan M. Lees [aut, cre],
Baptiste Auguie [ctb]
Maintainer: Jonathan M. Lees <jonathan.lees@unc.edu>
Diff between Rquake versions 2.4-0 dated 2016-08-20 and 2.4-4 dated 2020-12-16
Rquake-2.4-0/Rquake/R/ROTcovQUAKE.R |only Rquake-2.4-0/Rquake/R/rgl.ellipsoid.R |only Rquake-2.4-0/Rquake/R/rgl.ellipsoids.R |only Rquake-2.4-0/Rquake/R/rglGEOmapXY.R |only Rquake-2.4-0/Rquake/man/ROTcovQUAKE.Rd |only Rquake-2.4-0/Rquake/man/rgl.ellipsoid.Rd |only Rquake-2.4-0/Rquake/man/rgl.ellipsoids.Rd |only Rquake-2.4-0/Rquake/man/rglGEOmapXY.Rd |only Rquake-2.4-4/Rquake/DESCRIPTION | 15 +++--- Rquake-2.4-4/Rquake/MD5 | 38 ++++++--------- Rquake-2.4-4/Rquake/NAMESPACE | 1 Rquake-2.4-4/Rquake/R/Vlocate.R | 4 - Rquake-2.4-4/Rquake/R/XYlocate.R | 70 +++++++++++++++++++++++----- Rquake-2.4-4/Rquake/R/checkLOCATEinput.R |only Rquake-2.4-4/Rquake/data/ASW.vel.rda |binary Rquake-2.4-4/Rquake/data/LITHOS.vel.rda |binary Rquake-2.4-4/Rquake/data/StHelens4.vel.rda |binary Rquake-2.4-4/Rquake/data/coso_sta_LLZ.rda |binary Rquake-2.4-4/Rquake/data/fuj1.vel.rda |binary Rquake-2.4-4/Rquake/data/jap1.vel.rda |binary Rquake-2.4-4/Rquake/data/montserat.vel.rda |binary Rquake-2.4-4/Rquake/data/wu_coso.vel.rda |binary Rquake-2.4-4/Rquake/man/checkLOCATEinput.Rd |only Rquake-2.4-4/Rquake/man/euler_passive.Rd | 5 +- Rquake-2.4-4/Rquake/man/getEulers.Rd | 2 25 files changed, 89 insertions(+), 46 deletions(-)
Title: Data Base Backend for 'mlr3'
Description: Extends the 'mlr3' package with a backend to
transparently work with databases. Includes two extra backends:
One relies on relies on the abstraction of package 'dbplyr' to interact with
one of the many supported database management systems (DBMS). The other one
is specialized for package 'duckdb'.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3db versions 0.2.0 dated 2020-09-28 and 0.3.0 dated 2020-12-16
mlr3db-0.2.0/mlr3db/tests/testthat/test_basic_ops.R |only mlr3db-0.2.0/mlr3db/tests/testthat/test_train_predict.R |only mlr3db-0.3.0/mlr3db/DESCRIPTION | 23 +- mlr3db-0.3.0/mlr3db/MD5 | 38 ++-- mlr3db-0.3.0/mlr3db/NAMESPACE | 14 - mlr3db-0.3.0/mlr3db/NEWS.md | 13 + mlr3db-0.3.0/mlr3db/R/DataBackendDplyr.R | 87 +++------- mlr3db-0.3.0/mlr3db/R/DataBackendDuckDB.R |only mlr3db-0.3.0/mlr3db/R/as_duckdb_backend.R |only mlr3db-0.3.0/mlr3db/R/as_sqlite_backend.R | 81 ++++----- mlr3db-0.3.0/mlr3db/R/helper.R |only mlr3db-0.3.0/mlr3db/R/zzz.R | 6 mlr3db-0.3.0/mlr3db/README.md | 58 +++++- mlr3db-0.3.0/mlr3db/man/DataBackendDplyr.Rd | 34 +-- mlr3db-0.3.0/mlr3db/man/DataBackendDuckDB.Rd |only mlr3db-0.3.0/mlr3db/man/as_duckdb_backend.Rd |only mlr3db-0.3.0/mlr3db/man/as_sqlite_backend.Rd | 45 +++-- mlr3db-0.3.0/mlr3db/man/mlr3db-package.Rd | 17 + mlr3db-0.3.0/mlr3db/tests/testthat/helper.R | 12 + mlr3db-0.3.0/mlr3db/tests/testthat/test_as_duckdb_backend.R |only mlr3db-0.3.0/mlr3db/tests/testthat/test_as_sqlite_backend.R | 24 +- mlr3db-0.3.0/mlr3db/tests/testthat/test_dplyr.R |only mlr3db-0.3.0/mlr3db/tests/testthat/test_duckdb.R |only mlr3db-0.3.0/mlr3db/tests/testthat/test_reconnect.R | 54 ++---- mlr3db-0.3.0/mlr3db/tests/testthat/test_train_predict_dplyr.R |only mlr3db-0.3.0/mlr3db/tests/testthat/test_train_predict_duckdb.R |only 26 files changed, 283 insertions(+), 223 deletions(-)
Title: Markov Chain-Based Cost-Optimal Control Charts
Description: Functions for cost-optimal control charts with a focus on health care applications. Compared to assumptions in traditional control chart theory, here, we allow random shift sizes, random repair and random sampling times. The package focuses on X-bar charts with a sample size of 1 (representing the monitoring of a single patient at a time). The methods are described in Zempleni et al. (2004) <doi:10.1002/asmb.521>, Dobi and Zempleni (2019) <doi:10.1002/qre.2518> and Dobi and Zempleni (2019) <http://ac.inf.elte.hu/Vol_049_2019/129_49.pdf>.
Author: Balazs Dobi & Andras Zempleni
Maintainer: Balazs Dobi <dobib@cs.elte.hu>
Diff between Markovchart versions 1.1.0 dated 2020-11-07 and 1.1.1 dated 2020-12-16
Markovchart-1.1.0/Markovchart/R/Markovchart_functions_20200919.r |only Markovchart-1.1.1/Markovchart/DESCRIPTION | 6 +- Markovchart-1.1.1/Markovchart/MD5 | 12 ++-- Markovchart-1.1.1/Markovchart/NAMESPACE | 2 Markovchart-1.1.1/Markovchart/R/Markovchart_functions_20201216.r |only Markovchart-1.1.1/Markovchart/man/Markovchart.Rd | 27 +++++----- Markovchart-1.1.1/Markovchart/man/Markovcontour.Rd | 4 - Markovchart-1.1.1/Markovchart/man/Markovsim.Rd | 10 +-- 8 files changed, 32 insertions(+), 29 deletions(-)
Title: Imputation of High-Dimensional Count Data using Side Information
Description: Analysis, imputation, and multiple imputation of count data using covariates. LORI uses a log-linear Poisson model where main row and column effects, as well as effects of known covariates and interaction terms can be fitted. The estimation procedure is based on the convex optimization of the Poisson loss penalized by a Lasso type penalty and a nuclear norm. LORI returns estimates of main effects, covariate effects and interactions, as well as an imputed count table. The package also contains a multiple imputation procedure. The methods are described in Robin, Josse, Moulines and Sardy (2019) <arXiv:1703.02296v4>.
Author: Genevieve Robin [aut, cre]
Maintainer: Genevieve Robin <genevieve.robin@cnrs.fr>
Diff between lori versions 2.2.1 dated 2020-11-26 and 2.2.2 dated 2020-12-16
DESCRIPTION | 17 +++++++++-------- MD5 | 32 ++++++++++++++++++++++---------- R/altmin.R | 4 ++-- R/aravo.R |only R/cv.lori.R | 9 +++++++-- R/lori.R | 12 ++++++++++-- R/mi.lori.R | 6 +++++- R/pool.lori.R | 6 +++++- build |only data |only inst |only man/aravo.Rd |only man/cv.lori.Rd | 18 ++++++++++++++---- man/lori.Rd | 22 ++++++++++++++++++---- man/mi.lori.Rd | 12 ++++++++++-- man/pool.lori.Rd | 12 ++++++++++-- vignettes |only 17 files changed, 112 insertions(+), 38 deletions(-)
Title: Quickly Explore Your Data Using 'ggplot2' and 'table1' Summary
Tables
Description: Quickly and easily perform exploratory data analysis by uploading your
data as a 'csv' file. Start generating insights using 'ggplot2' plots and
'table1' tables with descriptive stats, all using an easy-to-use point and click
'Shiny' interface.
Author: Samer Mouksassi [aut, cre] (<https://orcid.org/0000-0002-7152-6654>),
Dean Attali [aut],
Benjamin Rich [aut] (provided summary stats tables tab code),
Michael Sachs [aut] (provided ggkm code)
Maintainer: Samer Mouksassi <samermouksassi@gmail.com>
Diff between ggquickeda versions 0.1.8 dated 2020-11-05 and 0.1.9 dated 2020-12-16
ggquickeda-0.1.8/ggquickeda/inst/shinyapp/img/snapshot2.gif |only ggquickeda-0.1.8/ggquickeda/inst/shinyapp/img/snapshot3.gif |only ggquickeda-0.1.9/ggquickeda/DESCRIPTION | 8 ggquickeda-0.1.9/ggquickeda/MD5 | 29 ggquickeda-0.1.9/ggquickeda/NEWS.md | 20 ggquickeda-0.1.9/ggquickeda/README.md | 33 ggquickeda-0.1.9/ggquickeda/inst/doc/AdditionalPlotsStats.html | 4 ggquickeda-0.1.9/ggquickeda/inst/doc/Visualizing_Summary_Data.html | 6 ggquickeda-0.1.9/ggquickeda/inst/doc/ggquickeda.html | 4 ggquickeda-0.1.9/ggquickeda/inst/shinyapp/global.R | 11 ggquickeda-0.1.9/ggquickeda/inst/shinyapp/img/snapshot1.gif |binary ggquickeda-0.1.9/ggquickeda/inst/shinyapp/img/snapshot3.1.png |only ggquickeda-0.1.9/ggquickeda/inst/shinyapp/img/snapshot4.1.png |binary ggquickeda-0.1.9/ggquickeda/inst/shinyapp/rsconnect/rstudio.studyexplorer.io/samer.mouksassi/ggquickeda.dcf | 4 ggquickeda-0.1.9/ggquickeda/inst/shinyapp/server.R | 1222 ++++++---- ggquickeda-0.1.9/ggquickeda/inst/shinyapp/ui.R | 466 +-- ggquickeda-0.1.9/ggquickeda/vignettes/nejmfigure.png |binary 17 files changed, 1103 insertions(+), 704 deletions(-)
Title: Additive and Multiplicative Effects Models for Networks and
Relational Data
Description: Analysis of dyadic network and relational data using additive and
multiplicative effects (AME) models. The basic model includes
regression terms, the covariance structure of the social relations model
(Warner, Kenny and Stoto (1979) <DOI:10.1037/0022-3514.37.10.1742>,
Wong (1982) <DOI:10.2307/2287296>), and multiplicative factor
models (Hoff(2009) <DOI:10.1007/s10588-008-9040-4>).
Several different link functions accommodate different
relational data structures, including binary/network data, normal
relational data, zero-inflated positive outcomes using a tobit model, ordinal relational data and data from
fixed-rank nomination schemes. Several of these link functions are
discussed in Hoff, Fosdick, Volfovsky and Stovel (2013)
<DOI:10.1017/nws.2013.17>. Development of this
software was supported in part by NIH grant R01HD067509.
Author: Peter Hoff [aut, cre],
Bailey Fosdick [aut],
Alex Volfovsky [aut],
Yanjun He [ctb]
Maintainer: Peter Hoff <peter.hoff@duke.edu>
Diff between amen versions 1.3 dated 2017-05-24 and 1.4.4 dated 2020-12-16
amen-1.3/amen/R/rZ_rrl.R |only amen-1.3/amen/data/datalist |only amen-1.3/amen/inst/doc/amen.R |only amen-1.3/amen/inst/doc/amen.Rnw |only amen-1.3/amen/inst/doc/amen.pdf |only amen-1.3/amen/vignettes/amen.Rnw |only amen-1.4.4/amen/DESCRIPTION | 34 +- amen-1.4.4/amen/MD5 | 225 ++++++++++-------- amen-1.4.4/amen/NAMESPACE | 8 amen-1.4.4/amen/NEWS.md |only amen-1.4.4/amen/R/ame.R | 284 ++++++++++++++--------- amen-1.4.4/amen/R/ame_rep.R | 152 ++++++------ amen-1.4.4/amen/R/amen-package.R | 8 amen-1.4.4/amen/R/circplot.R | 11 amen-1.4.4/amen/R/design_array.R | 22 + amen-1.4.4/amen/R/gofstats.R | 9 amen-1.4.4/amen/R/ldZgbme.R |only amen-1.4.4/amen/R/plot.ame.R | 52 +++- amen-1.4.4/amen/R/precomputeX.R |only amen-1.4.4/amen/R/rSab_fc.R |only amen-1.4.4/amen/R/rSuv_fc.R |only amen-1.4.4/amen/R/rUV_fc.R | 26 -- amen-1.4.4/amen/R/rZ_bin_fc.R | 52 ++-- amen-1.4.4/amen/R/rZ_cbin_fc.R | 5 amen-1.4.4/amen/R/rZ_frn_fc.R | 2 amen-1.4.4/amen/R/rZ_nrm_fc.R | 4 amen-1.4.4/amen/R/rZ_ord_fc.R | 2 amen-1.4.4/amen/R/rZ_rrl_fc.R |only amen-1.4.4/amen/R/rZ_tob_fc.R |only amen-1.4.4/amen/R/raSab_bin_fc.R | 11 amen-1.4.4/amen/R/raSab_cbin_fc.R | 13 - amen-1.4.4/amen/R/raSab_frn_fc.R | 15 - amen-1.4.4/amen/R/rbeta_ab_fc.R | 112 ++++++--- amen-1.4.4/amen/R/rrho_fc.R |only amen-1.4.4/amen/R/rrho_mh.R | 19 + amen-1.4.4/amen/R/rs2_fc.R | 25 +- amen-1.4.4/amen/R/rwish.R | 4 amen-1.4.4/amen/R/simY_tob.R |only amen-1.4.4/amen/R/simZ.R | 11 amen-1.4.4/amen/R/summary.ame.R | 7 amen-1.4.4/amen/R/zscores.R | 7 amen-1.4.4/amen/README.md |only amen-1.4.4/amen/build/vignette.rds |binary amen-1.4.4/amen/inst/doc/binary_demo.R |only amen-1.4.4/amen/inst/doc/binary_demo.Rmd |only amen-1.4.4/amen/inst/doc/binary_demo.html |only amen-1.4.4/amen/inst/doc/diy_Poisson_demo.R |only amen-1.4.4/amen/inst/doc/diy_Poisson_demo.Rmd |only amen-1.4.4/amen/inst/doc/diy_Poisson_demo.html |only amen-1.4.4/amen/inst/doc/diy_binary_demo.R |only amen-1.4.4/amen/inst/doc/diy_binary_demo.Rmd |only amen-1.4.4/amen/inst/doc/diy_binary_demo.html |only amen-1.4.4/amen/inst/tutorial |only amen-1.4.4/amen/man/IR90s.Rd | 7 amen-1.4.4/amen/man/Xbeta.Rd | 1 amen-1.4.4/amen/man/YX_bin.Rd | 7 amen-1.4.4/amen/man/YX_bin_long.Rd | 5 amen-1.4.4/amen/man/YX_cbin.Rd | 7 amen-1.4.4/amen/man/YX_frn.Rd | 7 amen-1.4.4/amen/man/YX_nrm.Rd | 7 amen-1.4.4/amen/man/YX_ord.Rd | 7 amen-1.4.4/amen/man/YX_rrl.Rd | 7 amen-1.4.4/amen/man/addhealthc3.Rd | 5 amen-1.4.4/amen/man/addhealthc9.Rd | 5 amen-1.4.4/amen/man/addlines.Rd | 1 amen-1.4.4/amen/man/ame.Rd | 30 +- amen-1.4.4/amen/man/ame_rep.Rd | 23 - amen-1.4.4/amen/man/amen-package.Rd | 7 amen-1.4.4/amen/man/circplot.Rd | 27 +- amen-1.4.4/amen/man/coldwar.Rd | 9 amen-1.4.4/amen/man/comtrade.Rd | 9 amen-1.4.4/amen/man/design_array.Rd | 1 amen-1.4.4/amen/man/dutchcollege.Rd | 7 amen-1.4.4/amen/man/el2sm.Rd | 1 amen-1.4.4/amen/man/gofstats.Rd | 1 amen-1.4.4/amen/man/lazegalaw.Rd | 7 amen-1.4.4/amen/man/ldZgbme.Rd |only amen-1.4.4/amen/man/llsrmRho.Rd |only amen-1.4.4/amen/man/mhalf.Rd | 1 amen-1.4.4/amen/man/netplot.Rd | 1 amen-1.4.4/amen/man/plot.ame.Rd | 1 amen-1.4.4/amen/man/precomputeX.Rd |only amen-1.4.4/amen/man/rSab_fc.Rd |only amen-1.4.4/amen/man/rSuv_fc.Rd |only amen-1.4.4/amen/man/rUV_fc.Rd | 12 amen-1.4.4/amen/man/rUV_rep_fc.Rd | 1 amen-1.4.4/amen/man/rUV_sym_fc.Rd | 1 amen-1.4.4/amen/man/rZ_bin_fc.Rd | 1 amen-1.4.4/amen/man/rZ_cbin_fc.Rd | 1 amen-1.4.4/amen/man/rZ_frn_fc.Rd | 1 amen-1.4.4/amen/man/rZ_nrm_fc.Rd | 1 amen-1.4.4/amen/man/rZ_ord_fc.Rd | 1 amen-1.4.4/amen/man/rZ_rrl_fc.Rd | 3 amen-1.4.4/amen/man/rZ_tob_fc.Rd |only amen-1.4.4/amen/man/raSab_bin_fc.Rd | 7 amen-1.4.4/amen/man/raSab_cbin_fc.Rd | 7 amen-1.4.4/amen/man/raSab_frn_fc.Rd | 9 amen-1.4.4/amen/man/rbeta_ab_fc.Rd | 37 +- amen-1.4.4/amen/man/rbeta_ab_rep_fc.Rd | 1 amen-1.4.4/amen/man/rmvnorm.Rd | 1 amen-1.4.4/amen/man/rrho_fc.Rd |only amen-1.4.4/amen/man/rrho_mh.Rd | 12 amen-1.4.4/amen/man/rrho_mh_rep.Rd | 1 amen-1.4.4/amen/man/rs2_fc.Rd | 14 - amen-1.4.4/amen/man/rs2_rep_fc.Rd | 1 amen-1.4.4/amen/man/rwish.Rd | 3 amen-1.4.4/amen/man/sampsonmonks.Rd | 7 amen-1.4.4/amen/man/sheep.Rd | 7 amen-1.4.4/amen/man/simY_bin.Rd | 1 amen-1.4.4/amen/man/simY_frn.Rd | 1 amen-1.4.4/amen/man/simY_nrm.Rd | 1 amen-1.4.4/amen/man/simY_ord.Rd | 1 amen-1.4.4/amen/man/simY_rrl.Rd | 1 amen-1.4.4/amen/man/simY_tob.Rd |only amen-1.4.4/amen/man/simZ.Rd | 1 amen-1.4.4/amen/man/sm2el.Rd | 1 amen-1.4.4/amen/man/summary.ame.Rd | 1 amen-1.4.4/amen/man/xnet.Rd | 1 amen-1.4.4/amen/man/zscores.Rd | 5 amen-1.4.4/amen/vignettes/binary_demo.Rmd |only amen-1.4.4/amen/vignettes/binary_demo_cache |only amen-1.4.4/amen/vignettes/diy_Poisson_demo.Rmd |only amen-1.4.4/amen/vignettes/diy_Poisson_demo_cache |only amen-1.4.4/amen/vignettes/diy_binary_demo.Rmd |only amen-1.4.4/amen/vignettes/diy_binary_demo_cache |only 125 files changed, 893 insertions(+), 561 deletions(-)
Title: NPLS Regression with L1 Penalization
Description: Tools for performing variable selection in three-way data using N-PLS
in combination with L1 penalization, Selectivity Ratio and VIP scores.
The N-PLS model (Rasmus Bro, 1996 <DOI:10.1002/(SICI)1099-128X(199601)10:1%3C47::AID-CEM400%3E3.0.CO;2-C>)
is the natural extension of PLS (Partial Least Squares) to N-way structures, and tries
to maximize the covariance between X and Y data arrays. The package also adds
variable selection through L1 penalization, Selectivity Ratio and VIP scores.
Author: David Hervas
Maintainer: David Hervas <ddhervas@yahoo.es>
Diff between sNPLS versions 0.3.31 dated 2018-02-20 and 1.0.27 dated 2020-12-16
DESCRIPTION | 20 - MD5 | 35 +- NAMESPACE | 12 R/sNPLS_fit.R | 851 ++++++++++++++++++++++++++++++-------------------- man/SR.Rd |only man/bread.Rd | 4 man/cv_fit.Rd | 24 + man/cv_snpls.Rd | 29 + man/plot.cvsNPLS.Rd | 8 man/plot.repeatcv.Rd | 4 man/plot.sNPLS.Rd | 10 man/plot_T.Rd | 11 man/plot_U.Rd | 11 man/plot_Wj.Rd | 11 man/plot_Wk.Rd | 11 man/plot_time.Rd | 6 man/plot_variables.Rd | 6 man/repeat_cv.Rd | 28 + man/sNPLS.Rd | 133 ++++--- 19 files changed, 710 insertions(+), 504 deletions(-)
Title: Model-Based Sliced Inverse Regression
Description: An R package for dimension reduction based on finite Gaussian mixture modeling of inverse regression.
Author: Luca Scrucca [aut, cre] (<https://orcid.org/0000-0003-3826-0484>)
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>
Diff between msir versions 1.3.2 dated 2019-03-15 and 1.3.3 dated 2020-12-16
DESCRIPTION | 11 MD5 | 20 NEWS.md | 2 R/spinplot.R | 2 build/vignette.rds |binary inst/doc/msir.R | 55 inst/doc/msir.Rmd | 41 inst/doc/msir.html | 6396 +------------------------------------------ man/msir.Rd | 2 man/msir.permutation.test.Rd | 2 vignettes/msir.Rmd | 41 11 files changed, 304 insertions(+), 6268 deletions(-)
Title: Analysis and Visualisation of Benchmark Experiments
Description: Implements methods for post-hoc analysis and
visualisation of benchmark experiments, for 'mlr3' and beyond.
Author: Sonabend Raphael [cre, aut] (<https://orcid.org/0000-0001-9225-4654>),
Florian Pfisterer [aut] (<https://orcid.org/0000-0001-8867-762X>),
Michel Lang [ctb] (<https://orcid.org/0000-0001-9754-0393>),
Bernd Bischl [ctb] (<https://orcid.org/0000-0001-6002-6980>)
Maintainer: Sonabend Raphael <raphael.sonabend.15@ucl.ac.uk>
Diff between mlr3benchmark versions 0.1.0 dated 2020-11-19 and 0.1.1 dated 2020-12-16
DESCRIPTION | 6 MD5 | 33 ++-- NAMESPACE | 1 NEWS.md | 7 R/BenchmarkAggr.R | 218 +++++++++++++++------------ R/autoplot.BenchmarkAggr.R | 18 +- R/bibentries.R |only R/plots_cd.R | 11 - R/zzz.R | 2 README.md | 22 +- man/BenchmarkAggr.Rd | 69 ++++++-- man/as.BenchmarkAggr.Rd | 19 +- man/autoplot.BenchmarkAggr.Rd | 10 - man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-8-2.png |binary tests/testthat/test_BenchmarkAggr.R | 48 ++++- tests/testthat/test_autoplot_BenchmarkAggr.R | 1 18 files changed, 290 insertions(+), 175 deletions(-)
Title: Dynamic Hazard Models using State Space Models
Description: Contains functions that lets you fit dynamic hazard models using
state space models. The first implemented model is described in Fahrmeir
(1992) <doi:10.1080/01621459.1992.10475232> and Fahrmeir (1994)
<doi:10.1093/biomet/81.2.317>. Extensions hereof are available where the
Extended Kalman filter is replaced by an unscented Kalman filter and other
options including particle filters. The implemented particle filters support
more general state space models.
Author: Benjamin Christoffersen [cre, aut],
Alan Miller [cph],
Anthony Williams [cph],
Boost developers [cph],
R-core [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Diff between dynamichazard versions 0.6.6 dated 2019-10-14 and 0.6.7 dated 2020-12-16
DESCRIPTION | 8 MD5 | 92 +++---- NEWS.md | 4 build/vignette.rds |binary inst/doc/Bootstrap_illustration.pdf |binary inst/doc/Comparing_methods_for_logistic_models.pdf |binary inst/doc/Diagnostics.R | 116 +++++----- inst/doc/Diagnostics.Rmd | 12 - inst/doc/Diagnostics.pdf |binary inst/doc/Particle_filtering.pdf |binary inst/doc/ddhazard.R | 18 - inst/doc/ddhazard.pdf |binary man/PF_EM.Rd | 31 ++ man/PF_control.Rd | 24 +- man/PF_forward_filter.Rd | 64 ++++- man/ddhazard.Rd | 18 + man/ddhazard_boot.Rd | 13 - man/ddhazard_control.Rd | 30 +- man/ddsurvcurve.Rd | 6 man/get_cloud_means.Rd | 8 man/get_cloud_quantiles.Rd | 10 man/get_risk_obj.Rd | 11 man/get_survival_case_weights_and_data.Rd | 17 + man/hds.Rd | 6 man/logLik.PF_EM.Rd | 3 man/plot.PF_clouds.Rd | 18 + man/plot.ddhazard.Rd | 18 + man/plot.ddhazard_space_errors.Rd | 17 + man/predict.ddhazard.Rd | 14 - man/print.ddhazard_boot.Rd | 3 man/residuals.ddhazard.Rd | 8 man/static_glm.Rd | 22 + man/summary.ddhazard.Rd | 3 src/PF/PF_data.h | 2 src/arma_n_rcpp.h | 31 +- src/problem_data.h | 2 tests/testthat/helper.R | 4 tests/testthat/previous_results/PF_VARS_non_zero_mean_slope.RDS |binary tests/testthat/test_PF.R | 3 tests/testthat/test_SMA.R | 1 tests/testthat/test_UKF.R | 14 - tests/testthat/test_ddhazard_n_EKF.R | 4 tests/testthat/test_loglike.R | 4 tests/testthat/test_plot.R | 2 tests/testthat/test_predict.R | 2 tests/testthat/test_static_glm.R | 8 vignettes/Diagnostics.Rmd | 12 - 47 files changed, 431 insertions(+), 252 deletions(-)
Title: Bayesian Time-Stratified Population Analysis
Description: Provides advanced Bayesian methods to estimate
abundance and run-timing from temporally-stratified
Petersen mark-recapture experiments. Methods include
hierarchical modelling of the capture probabilities
and spline smoothing of the daily run size.
Author: Carl J Schwarz <cschwarz.stat.sfu.ca@gmail.com> and
Simon J Bonner <sbonner6@uwo.ca>
Maintainer: Carl J Schwarz <cschwarz.stat.sfu.ca@gmail.com>
Diff between BTSPAS versions 2020.9.1 dated 2020-09-05 and 2021.1.1 dated 2020-12-16
DESCRIPTION | 8 MD5 | 96 NAMESPACE | 1 R/PredictivePosteriorPlot_TSPDE.R | 53 R/PredictivePosteriorPlot_TSPDE_WHChinook.R | 96 R/PredictivePosteriorPlot_TSPDE_WHChinook2.r | 7 R/PredictivePosteriorPlot_TSPDE_WHSteel.R | 52 R/PredictivePosteriorPlot_TSPNDE.R | 8 R/PredictivePosterior_TSPDE.R | 4 R/PredictivePosterior_TSPDE_WHChinook.R | 1 R/PredictivePosterior_TSPDE_WHChinook2.r | 1 R/PredictivePosterior_TSPNDE.R | 33 R/PredictivePosterior_TSPNDENP.R | 13 R/PredictivePosterior_TSPNDENPMarkAvail.R | 12 R/TimeStratPetersenDiagError.R | 24 R/TimeStratPetersenDiagErrorWHChinook.R | 24 R/TimeStratPetersenDiagErrorWHChinook2.R | 24 R/TimeStratPetersenDiagErrorWHChinook2_fit.R | 152 - R/TimeStratPetersenDiagErrorWHChinook_fit.R | 154 - R/TimeStratPetersenDiagErrorWHSteel.R | 40 R/TimeStratPetersenDiagErrorWHSteel_fit.R | 149 - R/TimeStratPetersenDiagError_fit.R | 116 - R/TimeStratPetersenNonDiagError.R | 73 R/TimeStratPetersenNonDiagErrorNP.R | 29 R/TimeStratPetersenNonDiagErrorNPMarkAvail.R | 31 R/TimeStratPetersenNonDiagErrorNPMarkAvail_fit.R | 145 - R/TimeStratPetersenNonDiagErrorNP_fit.R | 195 + R/TimeStratPetersenNonDiagError_fit.R | 158 - R/zzz.R | 2 build/vignette.rds |binary inst/NEWS.Rd | 12 inst/doc/a-Diagonal-model.html | 1960 ++++++++++++++++---- inst/doc/b-Diagonal-model-with-multiple-ages.html | 139 - inst/doc/c-Non-diagonal-model.html | 230 +- inst/doc/d-Non-diagonal-with-fall-back-model.html | 117 - inst/doc/e-Bias-from-incomplete-sampling.html | 216 +- inst/doc/f-Interpolating-run-earlier-and-later.html | 155 + man/TimeStratPetersenDiagErrorWHChinook_fit.Rd | 40 man/TimeStratPetersenDiagErrorWHSteel_fit.Rd | 32 man/TimeStratPetersenDiagError_fit.Rd | 40 man/TimeStratPetersenNonDiagErrorNPMarkAvail_fit.Rd | 25 man/TimeStratPetersenNonDiagErrorNP_fit.Rd | 27 man/TimeStratPetersenNonDiagError_fit.Rd | 27 vignettes/a-Diagonal-model.Rmd | 566 +++++ vignettes/b-Diagonal-model-with-multiple-ages.Rmd | 31 vignettes/c-Non-diagonal-model.Rmd | 62 vignettes/d-Non-diagonal-with-fall-back-model.Rmd | 29 vignettes/e-Bias-from-incomplete-sampling.Rmd | 32 vignettes/f-Interpolating-run-earlier-and-later.Rmd | 17 49 files changed, 3919 insertions(+), 1539 deletions(-)
Title: Geometric Shadow Calculations
Description: Functions for calculating: (1) shadow height, (2) logical shadow flag, (3) shadow footprint, (4) Sky View Factor and (5) radiation load. Basic required inputs include a polygonal layer of obstacle outlines along with their heights (i.e. "extruded polygons"), sun azimuth and sun elevation. The package also provides functions for related preliminary calculations: breaking polygons into line segments, determining azimuth of line segments, shifting segments by azimuth and distance, constructing the footprint of a line-of-sight between an observer and the sun, and creating a 3D grid covering the surface area of extruded polygons.
Author: Michael Dorman [aut, cre],
Evyatar Erell [ctb],
Itai Kloog [ctb],
Adi Vulkan [ctb],
Roger Bivand [ctb]
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>
Diff between shadow versions 0.6.9 dated 2020-10-10 and 0.7.0 dated 2020-12-16
shadow-0.6.9/shadow/inst/doc/introduction.pdf |only shadow-0.6.9/shadow/inst/doc/introduction.pdf.asis |only shadow-0.6.9/shadow/vignettes/introduction.pdf.asis |only shadow-0.7.0/shadow/DESCRIPTION | 8 ++++---- shadow-0.7.0/shadow/MD5 | 12 ++++++------ shadow-0.7.0/shadow/NEWS.md | 7 +++++-- shadow-0.7.0/shadow/build/vignette.rds |binary shadow-0.7.0/shadow/inst/doc/introduction2.pdf |only shadow-0.7.0/shadow/inst/doc/introduction2.pdf.asis |only shadow-0.7.0/shadow/vignettes/introduction2.pdf.asis |only 10 files changed, 15 insertions(+), 12 deletions(-)
Title: Hydro-Meteorology Time-Series
Description: Functions for the management and treatment of hydrology and
meteorology time-series stored in a 'Sqlite' data base.
Author: Pierre Chevallier [aut, cre]
Maintainer: Pierre Chevallier <pierre.chevallier@ird.fr>
Diff between htsr versions 1.0.4 dated 2020-11-25 and 1.1.0 dated 2020-12-16
htsr-1.0.4/htsr/R/d_exphts.R |only htsr-1.0.4/htsr/R/d_invent.R |only htsr-1.0.4/htsr/R/p_plothts.R |only htsr-1.0.4/htsr/man/d_exphts.Rd |only htsr-1.0.4/htsr/man/d_invent.Rd |only htsr-1.0.4/htsr/man/p_plothts.Rd |only htsr-1.1.0/htsr/DESCRIPTION | 10 - htsr-1.1.0/htsr/MD5 | 80 +++++---- htsr-1.1.0/htsr/R/d_convert_hydraccess.R | 9 - htsr-1.1.0/htsr/R/d_convert_weewx.R | 2 htsr-1.1.0/htsr/R/d_exp_hts.R | 4 htsr-1.1.0/htsr/R/d_inventory.R | 207 +++++++++++++----------- htsr-1.1.0/htsr/R/d_rem_hts.R | 3 htsr-1.1.0/htsr/R/d_sensor.R | 177 ++++++++++++-------- htsr-1.1.0/htsr/R/d_station.R | 177 ++++++++++++-------- htsr-1.1.0/htsr/R/d_table.R | 4 htsr-1.1.0/htsr/R/ds_exp_hts.R |only htsr-1.1.0/htsr/R/ds_inventory.R |only htsr-1.1.0/htsr/R/ds_sensor.R |only htsr-1.1.0/htsr/R/ds_station.R |only htsr-1.1.0/htsr/R/h_timestep.R | 2 htsr-1.1.0/htsr/R/h_wl_di.R |only htsr-1.1.0/htsr/R/hs_tstep.R |only htsr-1.1.0/htsr/R/p_bar.R | 2 htsr-1.1.0/htsr/R/p_line.R | 2 htsr-1.1.0/htsr/R/ps_plothts.R |only htsr-1.1.0/htsr/inst/doc/htsr-package.R | 5 htsr-1.1.0/htsr/inst/doc/htsr-package.Rmd | 91 +++++----- htsr-1.1.0/htsr/inst/doc/htsr-package.html | 43 ++-- htsr-1.1.0/htsr/inst/extdata/app_invent/app.R | 40 ++-- htsr-1.1.0/htsr/inst/extdata/app_plothts/app.R | 16 - htsr-1.1.0/htsr/inst/extdata/app_sensor |only htsr-1.1.0/htsr/inst/extdata/app_station |only htsr-1.1.0/htsr/inst/extdata/app_tstep |only htsr-1.1.0/htsr/inst/extdata/fichier_fhts.RData |only htsr-1.1.0/htsr/man/d_convert_hydraccess.Rd | 6 htsr-1.1.0/htsr/man/d_convert_weewx.Rd | 2 htsr-1.1.0/htsr/man/d_exp_hts.Rd | 4 htsr-1.1.0/htsr/man/d_inventory.Rd | 16 - htsr-1.1.0/htsr/man/d_sensor.Rd | 67 ++++--- htsr-1.1.0/htsr/man/d_station.Rd | 72 +++++--- htsr-1.1.0/htsr/man/d_table.Rd | 4 htsr-1.1.0/htsr/man/ds_exp_hts.Rd |only htsr-1.1.0/htsr/man/ds_inventory.Rd |only htsr-1.1.0/htsr/man/ds_sensor.Rd |only htsr-1.1.0/htsr/man/ds_station.Rd |only htsr-1.1.0/htsr/man/h_timestep.Rd | 2 htsr-1.1.0/htsr/man/h_wl_di.Rd |only htsr-1.1.0/htsr/man/hs_tstep.Rd |only htsr-1.1.0/htsr/man/p_bar.Rd | 2 htsr-1.1.0/htsr/man/p_line.Rd | 2 htsr-1.1.0/htsr/man/ps_plothts.Rd |only htsr-1.1.0/htsr/vignettes/htsr-package.Rmd | 91 +++++----- 53 files changed, 642 insertions(+), 500 deletions(-)
Title: Variable Selection for Gaussian Model-Based Clustering
Description: Variable selection for Gaussian model-based clustering as implemented in the 'mclust' package. The methodology allows to find the (locally) optimal subset of variables in a data set that have group/cluster information. A greedy or headlong search can be used, either in a forward-backward or backward-forward direction, with or without sub-sampling at the hierarchical clustering stage for starting 'mclust' models. By default the algorithm uses a sequential search, but parallelisation is also available.
Author: Nema Dean [aut] (<https://orcid.org/0000-0002-5080-2517>),
Adrian E. Raftery [aut],
Luca Scrucca [aut, cre] (<https://orcid.org/0000-0003-3826-0484>)
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>
Diff between clustvarsel versions 2.3.3 dated 2018-11-19 and 2.3.4 dated 2020-12-16
DESCRIPTION | 11 MD5 | 23 - NEWS.md |only R/bicreg.R | 5 R/clvarselgrfwd.R | 1 README.md |only build/vignette.rds |binary inst/doc/clustvarsel.R | 262 +++++++++++++- inst/doc/clustvarsel.Rmd | 54 ++ inst/doc/clustvarsel.html | 813 ++++++++++++++++++++------------------------ man/clustvarsel-internal.Rd | 6 man/clustvarsel.Rd | 19 - vignettes/clustvarsel.Rmd | 54 ++ vignettes/vignette.css |only 14 files changed, 754 insertions(+), 494 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-02-07 0.1.0
Title: Tidy Interface to 'data.table'
Description: A tidy interface to 'data.table' that is 'rlang' compatible,
giving users the speed of 'data.table' with the clean syntax of the tidyverse.
Author: Mark Fairbanks [aut, cre],
Tyson Barrett [ctb],
Ivan Leung [ctb],
Ross Kennedy [ctb],
Lionel Henry [ctb],
Matt Carlson [ctb],
Abdessabour Moutik [ctb]
Maintainer: Mark Fairbanks <mark.t.fairbanks@gmail.com>
Diff between tidytable versions 0.5.6 dated 2020-09-30 and 0.5.7 dated 2020-12-16
tidytable-0.5.6/tidytable/R/deprec-dt_verb.R |only tidytable-0.5.6/tidytable/R/zzz.R |only tidytable-0.5.6/tidytable/man/dt_verb.Rd |only tidytable-0.5.7/tidytable/DESCRIPTION | 8 tidytable-0.5.7/tidytable/MD5 | 136 +++----- tidytable-0.5.7/tidytable/NAMESPACE | 69 ---- tidytable-0.5.7/tidytable/NEWS.md | 23 + tidytable-0.5.7/tidytable/R/arrange.R | 9 tidytable-0.5.7/tidytable/R/arrange_across.R | 14 tidytable-0.5.7/tidytable/R/as_tidytable.R | 32 + tidytable-0.5.7/tidytable/R/bind.R | 20 - tidytable-0.5.7/tidytable/R/case.R | 9 tidytable-0.5.7/tidytable/R/complete.R | 8 tidytable-0.5.7/tidytable/R/count.R | 9 tidytable-0.5.7/tidytable/R/crossing.R | 65 +++ tidytable-0.5.7/tidytable/R/distinct.R | 16 tidytable-0.5.7/tidytable/R/drop_na.R | 9 tidytable-0.5.7/tidytable/R/expand.R | 6 tidytable-0.5.7/tidytable/R/expand_grid.R | 6 tidytable-0.5.7/tidytable/R/fill.R | 84 +--- tidytable-0.5.7/tidytable/R/filter.R | 9 tidytable-0.5.7/tidytable/R/get_dummies.R | 41 +- tidytable-0.5.7/tidytable/R/group_split.R | 10 tidytable-0.5.7/tidytable/R/ifelse.R | 19 - tidytable-0.5.7/tidytable/R/join.R | 45 -- tidytable-0.5.7/tidytable/R/map.R | 72 ---- tidytable-0.5.7/tidytable/R/map2.R | 72 ---- tidytable-0.5.7/tidytable/R/mutate.R | 33 + tidytable-0.5.7/tidytable/R/mutate_across.R | 64 +++ tidytable-0.5.7/tidytable/R/mutate_variants.R | 20 - tidytable-0.5.7/tidytable/R/n.R | 20 - tidytable-0.5.7/tidytable/R/nest.R | 9 tidytable-0.5.7/tidytable/R/pivot_longer.R | 17 - tidytable-0.5.7/tidytable/R/pivot_wider.R | 73 +--- tidytable-0.5.7/tidytable/R/pull.R | 9 tidytable-0.5.7/tidytable/R/relocate.R | 17 - tidytable-0.5.7/tidytable/R/rename.R | 9 tidytable-0.5.7/tidytable/R/rename_variants.R | 62 --- tidytable-0.5.7/tidytable/R/rename_with.R | 9 tidytable-0.5.7/tidytable/R/replace_na.R | 8 tidytable-0.5.7/tidytable/R/row_number.R | 8 tidytable-0.5.7/tidytable/R/select.R | 9 tidytable-0.5.7/tidytable/R/separate.R | 12 tidytable-0.5.7/tidytable/R/slice.R | 129 +++---- tidytable-0.5.7/tidytable/R/summarize.R | 17 - tidytable-0.5.7/tidytable/R/tidytable-package.R | 7 tidytable-0.5.7/tidytable/R/top_n.R | 8 tidytable-0.5.7/tidytable/R/transmute.R | 10 tidytable-0.5.7/tidytable/R/unite.R | 9 tidytable-0.5.7/tidytable/R/unnest.R | 33 - tidytable-0.5.7/tidytable/R/utils-general.R | 45 ++ tidytable-0.5.7/tidytable/README.md | 170 +++++----- tidytable-0.5.7/tidytable/man/as_dt.Rd |only tidytable-0.5.7/tidytable/man/as_tidytable.Rd | 7 tidytable-0.5.7/tidytable/man/complete..Rd | 4 tidytable-0.5.7/tidytable/man/figures/logo.png |binary tidytable-0.5.7/tidytable/man/mutate_if..Rd | 9 tidytable-0.5.7/tidytable/man/pivot_wider..Rd | 7 tidytable-0.5.7/tidytable/man/reexports.Rd | 3 tidytable-0.5.7/tidytable/man/rename_all..Rd | 17 - tidytable-0.5.7/tidytable/man/top_n..Rd | 3 tidytable-0.5.7/tidytable/man/unnest..Rd | 11 tidytable-0.5.7/tidytable/tests/testthat/test-distinct.R | 30 + tidytable-0.5.7/tidytable/tests/testthat/test-expand.R | 18 + tidytable-0.5.7/tidytable/tests/testthat/test-get_dummies.R | 24 - tidytable-0.5.7/tidytable/tests/testthat/test-mutate.R | 7 tidytable-0.5.7/tidytable/tests/testthat/test-mutate_variants.R | 30 + tidytable-0.5.7/tidytable/tests/testthat/test-pivot_wider.R | 18 + tidytable-0.5.7/tidytable/tests/testthat/test-rename.R | 9 tidytable-0.5.7/tidytable/tests/testthat/test-slice.R | 30 + tidytable-0.5.7/tidytable/tests/testthat/test-unnest.R | 9 71 files changed, 734 insertions(+), 1100 deletions(-)
Title: Datasets for 'spatstat'
Description: Contains all the datasets for the 'spatstat' package.
Author: Adrian Baddeley [aut, cre] (<https://orcid.org/0000-0001-9499-8382>),
Rolf Turner [aut] (<https://orcid.org/0000-0001-5521-5218>),
Ege Rubak [aut] (<https://orcid.org/0000-0002-6675-533X>)
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.data versions 1.5-2 dated 2020-11-12 and 1.7-0 dated 2020-12-16
DESCRIPTION | 8 ++++---- MD5 | 6 ++++-- data/concrete.rda |only inst/doc/packagesizes.txt | 3 ++- man/concrete.Rd |only 5 files changed, 10 insertions(+), 7 deletions(-)
Title: Database Interface and 'MariaDB' Driver
Description: Implements a 'DBI'-compliant interface to 'MariaDB'
(<https://mariadb.org/>) and 'MySQL' (<https://www.mysql.com/>)
databases.
Author: Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
Jeroen Ooms [aut] (<https://orcid.org/0000-0002-4035-0289>),
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between RMariaDB versions 1.0.10 dated 2020-08-27 and 1.0.11 dated 2020-12-16
DESCRIPTION | 10 +++--- MD5 | 25 ++++++++-------- NEWS.md | 14 ++++++++ R/coerce.R | 7 ++++ R/connect.R | 12 ++++++- R/default.R | 6 +++ README.md | 19 ++++-------- cleanup | 2 - configure | 53 +++++++++++++++++----------------- man/dbConnect-MariaDBDriver-method.Rd | 8 ++++- src/Makevars.win | 4 +- tests/testthat/helper-DBItest.R | 5 +++ tests/testthat/test-queries.R | 7 ++++ tests/testthat/testthat-problems.rds |only 14 files changed, 110 insertions(+), 62 deletions(-)
Title: Probabilistic Models to Analyze and Gaussianize Heavy-Tailed,
Skewed Data
Description: Lambert W x F distributions are a generalized framework to analyze
skewed, heavy-tailed data. It is based on an input/output system, where the
output random variable (RV) Y is a non-linearly transformed version of an input
RV X ~ F with similar properties as X, but slightly skewed (heavy-tailed).
The transformed RV Y has a Lambert W x F distribution. This package contains
functions to model and analyze skewed, heavy-tailed data the Lambert Way:
simulate random samples, estimate parameters, compute quantiles, and plot/
print results nicely. The most useful function is 'Gaussianize',
which works similarly to 'scale', but actually makes the data Gaussian.
A do-it-yourself toolkit allows users to define their own Lambert W x
'MyFavoriteDistribution' and use it in their analysis right away.
Author: Georg M. Goerg [aut, cre]
Maintainer: Georg M. Goerg <im@gmge.org>
Diff between LambertW versions 0.6.5 dated 2020-06-08 and 0.6.6 dated 2020-12-16
DESCRIPTION | 19 +++---- MD5 | 28 +++++----- NEWS.md | 22 +++++--- R/0_W.R | 107 ++++++++++++++++++++-------------------- R/LambertW-package.R | 6 +- R/datasets.R | 2 README.md | 35 +++++++++++-- build/vignette.rds |binary inst/doc/lambertw-overview.R | 12 +--- inst/doc/lambertw-overview.Rmd | 31 ++++------- inst/doc/lambertw-overview.html | 69 +++++++++++-------------- man/LambertW-package.Rd | 6 +- man/W.Rd | 46 ++++++++--------- man/datasets.Rd | 2 vignettes/lambertw-overview.Rmd | 31 ++++------- 15 files changed, 214 insertions(+), 202 deletions(-)
Title: Statistical Analysis for Random Objects and Non-Euclidean Data
Description: Provides implementation of statistical methods for random objects
lying in various metric spaces, which are not necessarily linear spaces.
The core of this package is Fréchet regression for random objects with
Euclidean predictors, which allows one to perform regression analysis
for non-Euclidean responses under some mild conditions.
Examples include distributions in L^2-Wasserstein space,
covariance matrices endowed with power metric (with Frobenius metric
as a special case), Cholesky and log-Cholesky metrics.
References: Petersen, A., & Müller, H.-G. (2019) <doi:10.1214/17-AOS1624>.
Author: Yaqing Chen [aut, cre],
Alvaro Gajardo [aut],
Jianing Fan [aut],
Qixian Zhong [aut],
Paromita Dubey [aut],
Kyunghee Han [aut],
Satarupa Bhattacharjee [aut],
Hans-Georg Müller [cph, ths, aut]
Maintainer: Yaqing Chen <yaqchen@ucdavis.edu>
Diff between frechet versions 0.1.0 dated 2020-06-19 and 0.2.0 dated 2020-12-16
DESCRIPTION | 12 - MD5 | 57 ++++--- NAMESPACE | 2 NEWS | 13 + R/CovFMean.R | 4 R/CovFPowerDist.R |only R/CreateDensity.R | 6 R/DenFMean.R | 44 ++++- R/DistCholesky.R |only R/GFRCovCholesky.R | 77 +++++---- R/GFRCovPower.R | 8 - R/GloCovReg.R | 4 R/GloDenReg.R | 9 - R/GloWassReg.R | 10 - R/LFRCov.R | 24 ++- R/LFRCovCholesky.R | 92 ++++++----- R/LFRCovPower.R | 37 ++-- R/LocCovReg.R | 4 R/LocDenReg.R | 397 +++++++++++++++++++++++++++++++++------------------ R/LocWassReg.R | 107 +++++++++---- R/dist4cov.R |only R/dist4den.R |only R/plot.denReg.R | 4 README.md |only man/CovFMean.Rd | 4 man/CreateDensity.Rd | 6 man/DenFMean.Rd | 17 +- man/GloCovReg.Rd | 4 man/GloDenReg.Rd | 11 + man/LocCovReg.Rd | 4 man/LocDenReg.Rd | 36 ++-- man/dist4cov.Rd |only man/dist4den.Rd |only 33 files changed, 632 insertions(+), 361 deletions(-)
Title: Plot ForestGEO Data
Description: To help you access, transform, analyze, and
visualize ForestGEO data, we developed a collection of R packages
(<https://forestgeo.github.io/fgeo/>). This package, in particular,
helps you to plot ForestGEO data. To learn more about ForestGEO visit
<https://forestgeo.si.edu/>.
Author: Mauro Lepore [aut, ctr, cre] (<https://orcid.org/0000-0002-1986-7988>),
CTFS-ForestGEO [cph, fnd]
Maintainer: Mauro Lepore <maurolepore@gmail.com>
Diff between fgeo.plot versions 1.1.9 dated 2019-06-18 and 1.1.10 dated 2020-12-16
DESCRIPTION | 12 +-- MD5 | 58 +++++++-------- NEWS.md | 4 - R/autoplot-sp_elev.R | 20 ++--- R/autoplot.fgeo_habitat.R | 2 R/autoplot_by_species.R | 10 +- R/plot_dbh_bubles_by_quadrat.R | 16 ++-- R/plot_tag_status_by_subquadrat.R | 24 +++--- R/sp_elev.R | 16 ++-- R/suffix_match.R | 4 - README.md | 26 ++---- inst/WORDLIST | 28 +++---- man/autoplot.fgeo_habitat.Rd | 24 +++--- man/autoplot.sp_elev.Rd | 114 ++++++++++++++++++++---------- man/autoplot_by_species.sp_elev.Rd | 76 +++++++++++++------- man/elev.Rd | 34 +++++--- man/fgeo.plot-package.Rd | 4 - man/figures/README-fgeo.plot-sp-1.png |binary man/figures/README-unnamed-chunk-1-1.png |binary man/header_dbh_bubbles.Rd | 5 - man/header_tag_status.Rd | 5 - man/plot_dbh_bubbles_by_quadrat.Rd | 43 +++++++---- man/plot_tag_status_by_subquadrat.Rd | 59 ++++++++++----- man/sp.Rd | 35 +++++---- man/sp_elev.Rd | 42 ++++++----- man/theme_dbh_bubbles.Rd | 45 ++++++----- man/theme_default.Rd | 13 +-- man/theme_tag_status.Rd | 56 ++++++++------ tests/testthat/test-autoplot_by_species.R | 2 tests/testthat/test-sp_elev.R | 4 - 30 files changed, 452 insertions(+), 329 deletions(-)
Title: An Advanced Guide to Trade Policy Analysis
Description: On-disk embedded database with SQL versions of the original
datasets from Yotov, et al (2016, ISBN: 978-92-870-4367-2) and functions to
report regressions with clustered robust standard errors.
Author: Mauricio Vargas [aut, cre] (<https://orcid.org/0000-0003-1017-7574>),
Alexey Kravchenko [ths],
The United Nations [dtc, cph, fnd]
Maintainer: Mauricio Vargas <mvargas@dcc.uchile.cl>
Diff between yotover versions 0.1 dated 2020-11-05 and 0.3.2 dated 2020-12-16
yotover-0.1/yotover/inst/paper.log |only yotover-0.1/yotover/inst/paper.md |only yotover-0.1/yotover/inst/paper.pdf |only yotover-0.3.2/yotover/DESCRIPTION | 16 ++-- yotover-0.3.2/yotover/MD5 | 34 ++++----- yotover-0.3.2/yotover/NAMESPACE | 1 yotover-0.3.2/yotover/R/attach.R | 2 yotover-0.3.2/yotover/R/chapter1.R | 37 +++++----- yotover-0.3.2/yotover/R/chapter2.R | 2 yotover-0.3.2/yotover/R/connections.R | 8 +- yotover-0.3.2/yotover/R/download.R | 48 ++++---------- yotover-0.3.2/yotover/R/remove.R |only yotover-0.3.2/yotover/R/utils.R | 8 -- yotover-0.3.2/yotover/man/yotov_db_delete.Rd | 2 yotover-0.3.2/yotover/man/yotov_model_summary.Rd | 6 - yotover-0.3.2/yotover/man/yotov_model_summary2.Rd | 6 - yotover-0.3.2/yotover/man/yotov_model_summary3.Rd | 6 - yotover-0.3.2/yotover/tests/testthat/test-01-download.R | 2 yotover-0.3.2/yotover/tests/testthat/test-02-tables.R | 26 +++---- yotover-0.3.2/yotover/tests/testthat/test-03-connection.R | 4 - 20 files changed, 93 insertions(+), 115 deletions(-)
Title: Maximum Likelihood Shrinkage using Generalized Ridge or Least
Angle Regression Methods
Description: Functions are provided to calculate and display ridge TRACE diagnostics for
a variety of shrinkage Paths. TRACEs identify the m-Extent of shrinkage most likely,
under Normal-theory, to produce optimally biased estimates of beta-coefficients with
minimum MSE Risk. The unr.ridge() function implements the "Unrestricted Path"
introduced in Obenchain (2020) <arXiv:2005.14291>. This Shrinkage-Path is more
efficient than the Paths used by the qm.ridge(), aug.lars() and uc.lars() functions.
Optimally biased predictions can be made using RXpredict() for all six types of
RXshrink linear model estimation methods. Functions MLboot(), MLcalc(), MLhist() and
MLtrue() provide insights into the true bias and MSE risk characteristics of non-linear
Shrinkage estimators. Functions unr.aug() and unr.biv() augment the calculations made
by unr.ridge() to provide plots of the bivariate confidence ellipses corresponding to
any of the p*(p-1) possible pairs of shrunken regression coefficients. The correct.signs()
function provides estimates with "correct" numerical signs when ill-conditioned (nearly
multicollinear) models yield OLS estimates that disagree with the signs of the observed
correlations between the y-outcome and the selected x-predictor variables. Finally, the
YonX() function displays Shrinkage statistics and graphics for "simple" linear regression
(p = 1) models.
Author: Bob Obenchain
Maintainer: Bob Obenchain <wizbob@att.net>
Diff between RXshrink versions 1.4.3 dated 2020-11-01 and 1.5 dated 2020-12-16
DESCRIPTION | 12 +++++++----- MD5 | 15 +++++++++------ NAMESPACE | 4 ++++ R/YonX.R |only man/RXshrink-package.Rd | 8 +++++--- man/YonX.Rd |only man/internal.Rd | 21 ++++++++++++++++++--- man/plot.YonX.Rd |only man/unr.aug.Rd | 4 ++-- man/unr.ridge.Rd | 9 +++++---- 10 files changed, 50 insertions(+), 23 deletions(-)
Title: API Client for Fantasy Football League Platforms
Description: Helps access various Fantasy Football APIs by handling authentication and
rate-limiting, forming appropriate calls, and returning tidy
dataframes which can be easily connected to other data sources.
Author: Tan Ho [aut, cre]
Maintainer: Tan Ho <tan@tanho.ca>
Diff between ffscrapr versions 1.2.0 dated 2020-11-27 and 1.2.1 dated 2020-12-16
DESCRIPTION | 6 MD5 | 108 +++++----- NEWS.md | 7 R/flea_players.R | 2 R/flea_userleagues.R | 2 R/sleeper_api.R | 2 R/sleeper_userleagues.R | 1 README.md | 32 +- inst/doc/fleaflicker_basics.R | 6 inst/doc/fleaflicker_basics.Rmd | 8 inst/doc/fleaflicker_basics.html | 82 +++---- inst/doc/fleaflicker_getendpoint.R | 6 inst/doc/fleaflicker_getendpoint.Rmd | 8 inst/doc/fleaflicker_getendpoint.html | 2 inst/doc/mfl_basics.R | 6 inst/doc/mfl_basics.Rmd | 8 inst/doc/mfl_basics.html | 100 ++++----- inst/doc/mfl_getendpoint.R | 6 inst/doc/mfl_getendpoint.Rmd | 8 inst/doc/mfl_getendpoint.html | 2 inst/doc/sleeper_basics.R | 5 inst/doc/sleeper_basics.Rmd | 7 inst/doc/sleeper_basics.html | 88 ++++---- inst/doc/sleeper_getendpoint.R | 6 inst/doc/sleeper_getendpoint.Rmd | 8 inst/doc/sleeper_getendpoint.html | 38 +-- man/fleaflicker_players.Rd | 2 man/fleaflicker_userleagues.Rd | 2 man/sleeper_getendpoint.Rd | 2 tests/testthat/api.myfantasyleague.com/2019/export-5ddec2.R |only tests/testthat/api.myfantasyleague.com/2019/export-d2d913.R |only tests/testthat/api.myfantasyleague.com/2020/export-5b11ff.R | 71 ++---- tests/testthat/api.myfantasyleague.com/2020/export-6788e2.R | 51 +--- tests/testthat/api.myfantasyleague.com/2020/export-96a6d5.R | 59 +---- tests/testthat/api.myfantasyleague.com/2020/export-c43c8e.R |only tests/testthat/api.myfantasyleague.com/2020/export-ca73a0.R | 71 ++---- tests/testthat/api.myfantasyleague.com/2020/export-ccd01d.R | 71 ++---- tests/testthat/api.sleeper.app/v1/league/386236959468675072.R | 81 ++----- tests/testthat/api.sleeper.app/v1/league/521379020332068864/users.R | 79 ++----- tests/testthat/api.sleeper.app/v1/league/522458773317046272.R | 79 ++----- tests/testthat/api.sleeper.app/v1/league/522458773317046272/rosters.R | 30 +- tests/testthat/api.sleeper.app/v1/league/522458773317046272/users.R | 79 ++----- tests/testthat/api.sleeper.app/v1/league/633501761776197632 |only tests/testthat/api.sleeper.app/v1/players/nfl |only tests/testthat/api.sleeper.app/v1/players/nfl.R | 77 ++----- tests/testthat/api.sleeper.app/v1/user/202892038360801280/leagues/nfl/2020.R | 79 ++----- tests/testthat/api.sleeper.app/v1/user/solarpool.R | 80 ++----- tests/testthat/test-ff_transactions.R | 2 tests/testthat/www.fleaflicker.com/api/FetchLeagueBoxscore-d3c59c.R |only tests/testthat/www.fleaflicker.com/api/FetchLeagueRosters-e56db7.R | 51 +--- tests/testthat/www.fleaflicker.com/api/FetchLeagueRules-43d23d.R | 51 +--- tests/testthat/www.fleaflicker.com/api/FetchLeagueScoreboard-750fd2.R |only tests/testthat/www.fleaflicker.com/api/FetchLeagueStandings-fdba0d.R |only vignettes/fleaflicker_basics.Rmd | 8 vignettes/fleaflicker_getendpoint.Rmd | 8 vignettes/mfl_basics.Rmd | 8 vignettes/mfl_getendpoint.Rmd | 8 vignettes/sleeper_basics.Rmd | 7 vignettes/sleeper_getendpoint.Rmd | 8 59 files changed, 748 insertions(+), 870 deletions(-)
Title: Base de Datos de Facil Acceso del Censo 2017 de Chile (2017
Chilean Census Easy Access Database)
Description: Provee un acceso conveniente a mas de 17 millones de registros
de la base de datos del Censo 2017. Los datos fueron importados desde
el DVD oficial del INE usando el Convertidor REDATAM creado por Pablo De
Grande y ademas se proporcionan los mapas que acompanian a estos
datos. Esta paquete esta documentado intencionalmente en castellano
asciificado para que funcione sin problema en diferentes plataformas.
(Provides convenient access to more than 17 million records from the
Chilean Census 2017 database. The datasets were imported from the official
DVD provided by the Chilean National Bureau of Statistics by using the
REDATAM converter created by Pablo De Grande and in addition it includes the
maps accompanying these datasets.)
Author: Mauricio Vargas [aut, cre] (<https://orcid.org/0000-0003-1017-7574>),
Juan Correa [ctb],
Instituto Nacional de Estadisticas (INE) [dtc]
Maintainer: Mauricio Vargas <mvargas@dcc.uchile.cl>
Diff between censo2017 versions 0.1 dated 2020-11-11 and 0.2 dated 2020-12-16
censo2017-0.1/censo2017/build |only censo2017-0.1/censo2017/inst/doc |only censo2017-0.1/censo2017/vignettes |only censo2017-0.2/censo2017/DESCRIPTION | 10 ++--- censo2017-0.2/censo2017/MD5 | 24 +++++------- censo2017-0.2/censo2017/NEWS.md |only censo2017-0.2/censo2017/R/connect.R | 24 +++++++----- censo2017-0.2/censo2017/R/connection-pane.R | 3 + censo2017-0.2/censo2017/R/download.R | 13 +++--- censo2017-0.2/censo2017/README.md | 31 ++++++++++++++++ censo2017-0.2/censo2017/man/censo_descargar_base.Rd | 10 ++--- censo2017-0.2/censo2017/man/censo_estado.Rd | 4 +- censo2017-0.2/censo2017/man/censo_tabla.Rd | 6 +-- censo2017-0.2/censo2017/tests/testthat/test-02-tables.R | 6 ++- 14 files changed, 83 insertions(+), 48 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-01 0.3.8
2020-09-15 0.3.7
2020-05-25 0.3.6
2020-03-21 0.3.5
2020-02-24 0.3.4
2020-01-08 0.3.3
2019-10-26 0.3.2
2019-09-27 0.3.1
2019-09-09 0.3.0
2019-03-28 0.2.9
2019-03-26 0.2.8
2019-03-07 0.2.7
2019-02-24 0.2.6
2018-09-10 0.2.5
2018-08-27 0.2.4
2018-06-16 0.2.3
2018-05-09 0.2.2
2018-04-24 0.2.0
2018-04-24 0.2.1
2018-03-01 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-06 1.0-6
2020-01-07 1.0-4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-04-09 0.0.8-10
2015-03-12 0.0.8-8
2015-02-22 0.0.8-6
2014-09-29 0.0.8-3
2014-08-26 0.0.8-1
2014-06-25 0.0.7
2014-04-24 0.0.6
2013-12-11 0.0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-01-13 0.0.3-5
2014-08-26 0.0.3-4
2014-06-25 0.0.3-3
2014-04-25 0.0.3-2
2013-05-30 0.0.2-1
2013-05-28 0.0.2
2012-08-31 0.0.1