Title: Paginate the HTML Output of R Markdown with CSS for Print
Description: Use the paged media properties in CSS and the JavaScript
library 'paged.js' to split the content of an HTML document into discrete
pages. Each page can have its page size, page numbers, margin boxes, and
running headers, etc. Applications of this package include books, letters,
reports, papers, business cards, resumes, and posters.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Romain Lesur [aut, cph] (<https://orcid.org/0000-0002-0721-5595>),
Brent Thorne [aut] (<https://orcid.org/0000-0002-1099-3857>),
Xianying Tan [aut] (<https://orcid.org/0000-0002-6072-3521>),
Christophe Dervieux [ctb] (<https://orcid.org/0000-0003-4474-2498>),
Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>),
RStudio, PBC [cph],
Adam Hyde [ctb] (paged.js in resources/js/),
Min-Zhong Lu [ctb] (resume.css in resources/css/),
Zulko [ctb] (poster-relaxed.css in resources/css/)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between pagedown versions 0.15 dated 2021-06-23 and 0.16 dated 2021-12-14
pagedown-0.15/pagedown/tests/test-travis |only pagedown-0.15/pagedown/tests/test-travis.R |only pagedown-0.16/pagedown/DESCRIPTION | 12 - pagedown-0.16/pagedown/MD5 | 30 ++-- pagedown-0.16/pagedown/NEWS.md | 18 ++ pagedown-0.16/pagedown/R/chrome.R | 9 - pagedown-0.16/pagedown/R/paged.R | 25 +-- pagedown-0.16/pagedown/README.md | 4 pagedown-0.16/pagedown/inst/resources/js/hooks.js | 153 +++++++++++++++++++++ pagedown-0.16/pagedown/inst/resources/lua/loft.lua | 27 +++ pagedown-0.16/pagedown/man/html_letter.Rd | 11 - pagedown-0.16/pagedown/tests/test-ci |only pagedown-0.16/pagedown/tests/test-ci.R |only 13 files changed, 243 insertions(+), 46 deletions(-)
Title: Interface to Unidata netCDF (Version 4 or Earlier) Format Data
Files
Description: Provides a high-level R interface to data files written using Unidata's netCDF library (version 4 or earlier), which are binary data files that are portable across platforms and include metadata information in addition to the data sets. Using this package, netCDF files (either version 4 or "classic" version 3) can be opened and data sets read in easily. It is also easy to create new netCDF dimensions, variables, and files, in either version 3 or 4 format, and manipulate existing netCDF files. This package replaces the former ncdf package, which only worked with netcdf version 3 files. For various reasons the names of the functions have had to be changed from the names in the ncdf package. The old ncdf package is still available at the URL given below, if you need to have backward compatibility. It should be possible to have both the ncdf and ncdf4 packages installed simultaneously without a problem. However, the ncdf package does not provide an interface for netcdf version 4 files.
Author: David Pierce <dpierce@ucsd.edu>
Maintainer: David Pierce <dpierce@ucsd.edu>
Diff between ncdf4 versions 1.18 dated 2021-11-26 and 1.19 dated 2021-12-14
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- R/ncdf4.R | 2 +- src/Makevars.ucrt |only 5 files changed, 13 insertions(+), 8 deletions(-)
Title: Extra Methods for Sparse Matrices
Description: Extends sparse matrix and vector classes from the 'Matrix' package by providing:
(a) Methods and operators that work natively on CSR formats (compressed sparse row,
a.k.a. 'RsparseMatrix') such as slicing/sub-setting, assignment, rbind(),
mathematical operators for CSR and COO such as addition ("+") or sqrt(), and methods such as diag();
(b) Multi-threaded matrix multiplication and cross-product for many <sparse, dense> types,
including the 'float32' type from 'float';
(c) Coercion methods between pairs of classes which are not present in 'Matrix',
such as 'dgCMatrix' -> 'ngRMatrix', as well as convenience conversion functions;
(d) Utility functions for sparse matrices such as sorting the indices or removing
zero-valued entries;
(e) Fast transposes that work by outputting in the opposite storage format;
(f) Faster replacements for many 'Matrix' methods for all sparse types, such as
slicing and elementwise multiplication.
(g) Convenience functions for sparse objects, such as 'mapSparse' or a shorter 'show' method.
Author: David Cortes [aut, cre, cph],
Dmitry Selivanov [cph],
Thibaut Goetghebuer-Planchon [cph] (Copyright holder of included
robinmap library),
Martin Maechler [cph] (Copyright holder of 'Matrix' package from which
some code was taken)
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between MatrixExtra versions 0.1.8 dated 2021-10-29 and 0.1.9 dated 2021-12-14
DESCRIPTION | 6 +-- MD5 | 14 ++++----- configure | 80 ++++++++++++++++++++++++++++++++++++++++++++-------- configure.ac | 31 +++++++++++++++++--- configure.win | 26 +++++++++++++++- src/Makevars.in | 2 - src/Makevars.win.in | 2 - src/matmul.cpp | 26 +++++++++++----- 8 files changed, 149 insertions(+), 38 deletions(-)
Title: Sparse Arrays and Multivariate Polynomials
Description: Sparse arrays interpreted as multivariate polynomials.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between spray versions 1.0-16 dated 2021-11-16 and 1.0-18 dated 2021-12-14
DESCRIPTION | 6 ++-- MD5 | 34 ++++++++++++------------- NAMESPACE | 2 + NEWS.md | 13 +++++++++ R/spray.R | 62 +++++++++++++++++++++++++++++++++++++--------- R/spray_ops.R | 20 +++++++++++++- build/spray.pdf |binary inst/doc/spray.pdf |binary man/Ops.spray.Rd | 2 + man/as.function.Rd | 7 +++-- man/constant.Rd | 21 ++++++++++++++- man/homog.Rd | 4 ++ man/ooom.Rd | 17 ++++++++---- man/print.Rd | 4 ++ man/spray.Rd | 7 ++++- man/subs.Rd | 13 ++++----- man/zero.Rd | 6 ++-- tests/testthat/test_aab.R | 5 ++- 18 files changed, 166 insertions(+), 57 deletions(-)
Title: Solving Mixed Model Equations in R
Description: Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures (e.g., heterogeneous and unstructured) and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms. Designed for genomic prediction and genome wide association studies (GWAS), particularly focused in the p > n problem (more coefficients to estimate than observations). Spatial models can also be fitted using the two-dimensional spline functionality available in sommer.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between sommer versions 4.1.4 dated 2021-07-29 and 4.1.5 dated 2021-12-14
sommer-4.1.4/sommer/man/spl2D.Rd |only sommer-4.1.5/sommer/CHANGELOG | 9 sommer-4.1.5/sommer/DESCRIPTION | 18 sommer-4.1.5/sommer/MD5 | 90 - sommer-4.1.5/sommer/NAMESPACE | 7 sommer-4.1.5/sommer/R/FUN_spatial.R | 698 +++++++--- sommer-4.1.5/sommer/R/FUN_spatial_two.R |only sommer-4.1.5/sommer/R/FUN_utils.R | 13 sommer-4.1.5/sommer/R/FUN_vsgvs.R | 80 - sommer-4.1.5/sommer/R/mmer.R | 160 +- sommer-4.1.5/sommer/R/predict.R | 219 +-- sommer-4.1.5/sommer/build/vignette.rds |binary sommer-4.1.5/sommer/data/DT_technow.RData |binary sommer-4.1.5/sommer/data/datalist | 2 sommer-4.1.5/sommer/inst/doc/v1.sommer.quick.start.R | 24 sommer-4.1.5/sommer/inst/doc/v1.sommer.quick.start.Rmd | 26 sommer-4.1.5/sommer/inst/doc/v1.sommer.quick.start.pdf |binary sommer-4.1.5/sommer/inst/doc/v2.sommer.changes.and.faqs.pdf |binary sommer-4.1.5/sommer/inst/doc/v3.sommer.qg.R | 120 + sommer-4.1.5/sommer/inst/doc/v3.sommer.qg.Rmd | 138 + sommer-4.1.5/sommer/inst/doc/v3.sommer.qg.pdf |binary sommer-4.1.5/sommer/inst/doc/v4.sommer.gxe.Rmd | 24 sommer-4.1.5/sommer/inst/doc/v4.sommer.gxe.pdf |binary sommer-4.1.5/sommer/inst/doc/v5.sommer.vs.lme4.pdf |binary sommer-4.1.5/sommer/inst/doc/v6.sommer.spatial.R |only sommer-4.1.5/sommer/inst/doc/v6.sommer.spatial.Rmd |only sommer-4.1.5/sommer/inst/doc/v6.sommer.spatial.pdf |only sommer-4.1.5/sommer/man/DT_technow.Rd | 6 sommer-4.1.5/sommer/man/GWAS.Rd | 16 sommer-4.1.5/sommer/man/GWAS2.Rd | 14 sommer-4.1.5/sommer/man/LD.decay.Rd | 2 sommer-4.1.5/sommer/man/bbasis.Rd |only sommer-4.1.5/sommer/man/build.HMM.Rd | 12 sommer-4.1.5/sommer/man/mmer.Rd | 16 sommer-4.1.5/sommer/man/mmer2.Rd | 18 sommer-4.1.5/sommer/man/sommer-package.Rd | 2 sommer-4.1.5/sommer/man/spl2Da.Rd |only sommer-4.1.5/sommer/man/spl2Db.Rd |only sommer-4.1.5/sommer/man/spl2Dmats.Rd |only sommer-4.1.5/sommer/man/tpsmmbwrapper.Rd |only sommer-4.1.5/sommer/src/RcppExports.cpp | 5 sommer-4.1.5/sommer/tests |only sommer-4.1.5/sommer/vignettes/v1.sommer.quick.start.Rmd | 26 sommer-4.1.5/sommer/vignettes/v1.sommer.quick.start.html | 72 - sommer-4.1.5/sommer/vignettes/v2.sommer.changes.and.faqs.html | 4 sommer-4.1.5/sommer/vignettes/v3.sommer.qg.Rmd | 138 + sommer-4.1.5/sommer/vignettes/v3.sommer.qg.html | 351 +++-- sommer-4.1.5/sommer/vignettes/v4.sommer.gxe.Rmd | 24 sommer-4.1.5/sommer/vignettes/v4.sommer.gxe.html | 26 sommer-4.1.5/sommer/vignettes/v5.sommer.vs.lme4.html | 4 sommer-4.1.5/sommer/vignettes/v6.sommer.spatial.Rmd |only sommer-4.1.5/sommer/vignettes/v6.sommer.spatial.html |only 52 files changed, 1551 insertions(+), 813 deletions(-)
Title: Bindings for the 'Geospatial' Data Abstraction Library
Description: Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4) and access to projection/transformation operations from the 'PROJ' library. Please note that 'rgdal' will be retired by the end of 2023, plan transition to sf/stars/'terra' functions using 'GDAL' and 'PROJ' at your earliest convenience. Use is made of classes defined in the 'sp' package. Raster and vector map data can be imported into R, and raster and vector 'sp' objects exported. The 'GDAL' and 'PROJ' libraries are external to the package, and, when installing the package from source, must be correctly installed first; it is important that 'GDAL' < 3 be matched with 'PROJ' < 6. From 'rgdal' 1.5-8, installed with to 'GDAL' >=3, 'PROJ' >=6 and 'sp' >= 1.4, coordinate reference systems use 'WKT2_2019' strings, not 'PROJ' strings. 'Windows' and 'macOS' binaries (including 'GDAL', 'PROJ' and their dependencies) are provided on 'CRAN'.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Tim Keitt [aut],
Barry Rowlingson [aut, ctb],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Daniel Baston [ctb],
Even Rouault [cph, ctb],
Frank Warmerdam [cph, ctb],
Jeroen Ooms [ctb],
Colin Rundel [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.5-27 dated 2021-09-16 and 1.5-28 dated 2021-12-14
ChangeLog | 2313 +++++++++++++------------- DESCRIPTION | 8 MD5 | 34 NEWS.md | 6 build/vignette.rds |binary configure | 18 inst/ChangeLog | 2313 +++++++++++++------------- inst/SVN_VERSION | 2 inst/doc/CRS_projections_transformations.R | 23 inst/doc/CRS_projections_transformations.Rmd | 26 inst/doc/CRS_projections_transformations.html | 1512 +--------------- inst/doc/OGR_shape_encoding.pdf |binary inst/doc/PROJ6_GDAL3.html | 1356 --------------- src/Makevars.ucrt | 30 tests/srs_rendering.Rout.save | 22 tests/test_enforce_xy.Rout.save | 136 + tests/test_proj.Rout.save | 14 vignettes/CRS_projections_transformations.Rmd | 26 18 files changed, 2893 insertions(+), 4946 deletions(-)
Title: Nanosecond-Resolution Time Support for R
Description: Full 64-bit resolution date and time functionality with
nanosecond granularity is provided, with easy transition to and from
the standard 'POSIXct' type. Three additional classes offer interval,
period and duration functionality for nanosecond-resolution timestamps.
Author: Dirk Eddelbuettel and Leonardo Silvestri
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between nanotime versions 0.3.4 dated 2021-11-24 and 0.3.5 dated 2021-12-14
ChangeLog | 9 +++++++++ DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- inst/NEWS.Rd | 7 +++++++ inst/doc/nanotime-introduction.pdf |binary src/Makevars.ucrt |only 6 files changed, 25 insertions(+), 8 deletions(-)
Title: Soil Database Interface
Description: A collection of functions for reading data from USDA-NCSS soil databases.
Author: Dylan Beaudette [aut],
Jay Skovlin [aut],
Stephen Roecker [aut],
Andrew Brown [aut, cre]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>
Diff between soilDB versions 2.6.9 dated 2021-12-03 and 2.6.10 dated 2021-12-14
soilDB-2.6.10/soilDB/DESCRIPTION | 6 soilDB-2.6.10/soilDB/MD5 | 62 +- soilDB-2.6.10/soilDB/NEWS.md | 8 soilDB-2.6.10/soilDB/R/SDA-spatial.R | 429 +++++++--------- soilDB-2.6.10/soilDB/R/SDA_coecoclass.R | 4 soilDB-2.6.10/soilDB/R/SDA_query.R | 3 soilDB-2.6.10/soilDB/R/SSURGO_spatial_query.R | 172 +++--- soilDB-2.6.10/soilDB/R/dbQueryNASIS.R | 2 soilDB-2.6.10/soilDB/R/fetchHenry.R | 26 soilDB-2.6.10/soilDB/R/get_component_from_SDA.R | 288 +++++----- soilDB-2.6.10/soilDB/R/mapunit_geom_by_ll_bbox.R | 43 - soilDB-2.6.10/soilDB/R/openNASISchannel.R | 5 soilDB-2.6.10/soilDB/R/simplfyFragmentData.R | 2 soilDB-2.6.10/soilDB/R/soilDB-package.R | 2 soilDB-2.6.10/soilDB/R/waterDayYear.R | 7 soilDB-2.6.10/soilDB/build/partial.rdb |binary soilDB-2.6.10/soilDB/data/gopheridge.rda |binary soilDB-2.6.10/soilDB/data/loafercreek.rda |binary soilDB-2.6.10/soilDB/data/mineralKing.rda |binary soilDB-2.6.10/soilDB/inst/WORDLIST |only soilDB-2.6.10/soilDB/man/SDA_query.Rd | 2 soilDB-2.6.10/soilDB/man/SDA_spatialQuery.Rd | 323 +++++------- soilDB-2.6.10/soilDB/man/SoilWeb_spatial_query.Rd | 4 soilDB-2.6.10/soilDB/man/dbConnectNASIS.Rd | 2 soilDB-2.6.10/soilDB/man/fetchHenry.Rd | 7 soilDB-2.6.10/soilDB/man/mapunit_geom_by_ll_bbox.Rd | 39 - soilDB-2.6.10/soilDB/man/processSDA_WKT.Rd | 26 soilDB-2.6.10/soilDB/man/simplifyFragmentData.Rd | 2 soilDB-2.6.10/soilDB/man/soilDB-package.Rd | 2 soilDB-2.6.10/soilDB/man/waterDayYear.Rd | 4 soilDB-2.6.10/soilDB/tests/testthat/test-fetchHenry.R | 3 soilDB-2.6.10/soilDB/tests/testthat/test-waterDayYear.R | 18 soilDB-2.6.9/soilDB/inst/_pkgdown.yml |only 33 files changed, 708 insertions(+), 783 deletions(-)
Title: Stock Assessment Methods Toolkit
Description: Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform data-rich fisheries.
'SAMtool' provides a conditioning model, assessment models of varying complexity with standardized reporting,
model-based management procedures, and diagnostic tools for evaluating assessments inside closed-loop simulation.
Author: Quang Huynh [aut, cre],
Tom Carruthers [aut],
Adrian Hordyk [aut]
Maintainer: Quang Huynh <quang@bluematterscience.com>
Diff between SAMtool versions 1.2.3 dated 2021-11-28 and 1.2.4 dated 2021-12-14
DESCRIPTION | 10 +++--- MD5 | 16 +++++----- NEWS.md | 4 ++ R/assess_VPA.R | 64 ++++++++++++++++++++++++++++++------------ R/assess_shortcut.R | 67 ++++++++++++++++++++++++++------------------- build/partial.rdb |binary inst/doc/SAMtool.html | 4 +- inst/include/ns/ns_VPA.hpp | 5 ++- man/VPA.Rd | 30 +++++++++++++++++++- 9 files changed, 136 insertions(+), 64 deletions(-)
Title: Interface to Geometry Engine - Open Source ('GEOS')
Description: Interface to Geometry Engine - Open Source ('GEOS') using the C 'API' for topology operations on geometries. Please note that 'rgeos' will be retired by the end of 2023, plan transition to sf functions using 'GEOS' at your earliest convenience. The 'GEOS' library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on 'CRAN'. ('rgeos' >= 0.5-1): Up to and including 'GEOS' 3.7.1, topological operations succeeded with some invalid geometries for which the same operations fail from and including 'GEOS' 3.7.2. The 'checkValidity=' argument defaults and structure have been changed, from default FALSE to integer default '0L' for 'GEOS' < 3.7.2 (no check), '1L' 'GEOS' >= 3.7.2 (check and warn). A value of '2L' is also provided that may be used, assigned globally using 'set_RGEOS_CheckValidity(2L)', or locally using the 'checkValidity=2L' argument, to attempt zero-width buffer repair if invalid geometries are found. The previous default (FALSE, now '0L') is fastest and used for 'GEOS' < 3.7.2, but will not warn users of possible problems before the failure of topological operations that previously succeeded. From 'GEOS' 3.8.0, repair of geometries may also be attempted using 'gMakeValid()', which may, however, return a collection of geometries of different types.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Colin Rundel [aut],
Edzer Pebesma [ctb],
Rainer Stuetz [ctb],
Karl Ove Hufthammer [ctb],
Patrick Giraudoux [ctb],
Martin Davis [cph, ctb],
Sandro Santilli [cph, ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgeos versions 0.5-8 dated 2021-09-22 and 0.5-9 dated 2021-12-14
ChangeLog | 22 +++++++++++++++++++ DESCRIPTION | 17 +++++++-------- MD5 | 16 +++++++------- NEWS.md | 6 ++++- configure | 18 ++++++++-------- inst/ChangeLog | 22 +++++++++++++++++++ inst/SVN_VERSION | 2 - src/Makevars.ucrt | 42 ++++++++++++++++++++++++++++++++++++-- tests/leak_by_exception.Rout.save | 22 ++----------------- 9 files changed, 118 insertions(+), 49 deletions(-)
Title: 'Rcpp' Bindings for the 'CCTZ' Library
Description: 'Rcpp' Access to the 'CCTZ' timezone library is provided. 'CCTZ' is
a C++ library for translating between absolute and civil times using the rules
of a time zone. The 'CCTZ' source code, released under the Apache 2.0 License,
is included in this package. See <https://github.com/google/cctz> for more
details.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppCCTZ versions 0.2.9 dated 2020-08-30 and 0.2.10 dated 2021-12-14
ChangeLog | 18 ++++++++++++++++++ DESCRIPTION | 11 ++++++----- MD5 | 9 +++++---- README.md | 2 +- inst/NEWS.Rd | 11 ++++++++++- src/Makevars.ucrt |only 6 files changed, 40 insertions(+), 11 deletions(-)
Title: Phylogenetic Reconstruction and Analysis
Description: Allows for estimation of phylogenetic trees and networks
using Maximum Likelihood, Maximum Parsimony, distance methods and
Hadamard conjugation. Offers methods for tree comparison, model
selection and visualization of phylogenetic networks as described in
Schliep et al. (2017) <doi:10.1111/2041-210X.12760>.
Author: Klaus Schliep [aut, cre] (<https://orcid.org/0000-0003-2941-0161>),
Emmanuel Paradis [aut] (<https://orcid.org/0000-0003-3092-2199>),
Leonardo de Oliveira Martins [aut]
(<https://orcid.org/0000-0001-5247-1320>),
Alastair Potts [aut],
Tim W. White [aut],
Cyrill Stachniss [ctb],
Michelle Kendall [ctb],
Keren Halabi [ctb],
Richel Bilderbeek [ctb],
Kristin Winchell [ctb],
Liam Revell [ctb],
Mike Gilchrist [ctb],
Jeremy Beaulieu [ctb],
Brian O'Meara [ctb],
Long Qu [ctb]
Maintainer: Klaus Schliep <klaus.schliep@gmail.com>
Diff between phangorn versions 2.8.0 dated 2021-11-09 and 2.8.1 dated 2021-12-14
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- R/bootstrap.R | 11 ++++++----- R/fitch64.R | 1 - R/sankoff.R | 6 +++--- R/treeManipulation.R | 19 ++++++++++--------- inst/doc/AdvancedFeatures.html | 12 ++++++------ inst/doc/Ancestral.html | 12 ++++++------ inst/doc/IntertwiningTreesAndNetworks.html | 7 +++---- inst/doc/Networx.html | 11 +++++------ inst/doc/Trees.html | 12 ++++++------ vignettes/phangorn.bib | 2 +- 12 files changed, 60 insertions(+), 61 deletions(-)
Title: An R Interface to the 'ROPTLIB' Library for Riemannian Manifold
Optimization
Description: An R interface to version 0.3 of the 'ROPTLIB' optimization library
(see <https://www.math.fsu.edu/~whuang2/> for more information). Optimize real-
valued functions over manifolds such as Stiefel, Grassmann, and Symmetric
Positive Definite matrices. For details see Martin et. al. (2020) <doi:10.18637/jss.v093.i01>.
Note that the optional ldr package used in some of this package's examples can be obtained from either JSS
<https://www.jstatsoft.org/index.php/jss/article/view/v061i03/2886> or from the CRAN archives
<https://cran.r-project.org/src/contrib/Archive/ldr/ldr_1.3.3.tar.gz>.
Author: Kofi P. Adragni [aut, cph],
Sean R. Martin [aut, cre, cph],
Andrew M. Raim [aut, cph],
Wen Huang [aut, cph]
Maintainer: Sean R. Martin <sean.martin@jhuapl.edu>
Diff between ManifoldOptim versions 1.0.0 dated 2020-04-17 and 1.0.1 dated 2021-12-14
DESCRIPTION | 19 ++- MD5 | 50 +++++----- man/Manifold-definitions.Rd | 2 man/get.solver.params.Rd | 2 man/manifold.optim.Rd | 2 src/Manifolds/Grassmann/Grassmann.cpp | 28 ++--- src/Manifolds/L2Sphere/L2Sphere.cpp | 4 src/Manifolds/LowRank/LowRank.cpp | 40 ++++---- src/Manifolds/Manifold.cpp | 18 +-- src/Manifolds/SPDManifold.cpp | 24 ++-- src/Manifolds/SPDVariable.cpp | 2 src/Manifolds/Sphere/Sphere.cpp | 4 src/Manifolds/Stiefel/Stiefel.cpp | 64 ++++++------- src/Others/MyMatrix.cpp | 22 ++-- src/Others/def.h | 54 ++++++++++ src/Problems/ElasticCurvesRO/DriverElasticCurvesRO.cpp | 16 +-- src/Problems/ElasticCurvesRO/ElasticCurvesRO.cpp | 4 src/Problems/EucQuadratic/EucQuadratic.cpp | 4 src/Problems/GrassRQ/GrassRQ.cpp | 2 src/Problems/ObliqueTestSparsePCA/ObliqueTestSparsePCA.cpp | 18 +-- src/Problems/SPDMean/SPDMean.cpp | 10 +- src/Problems/StieBrockett/StieBrockett.cpp | 2 src/Problems/StieSoftICA/StieSoftICA.cpp | 4 src/Problems/StieSumBrockett/StieSumBrockett.cpp | 12 +- src/Problems/WeightedLowrank/WeightedLowRank.cpp | 20 ++-- src/Solvers/LRTRSR1.cpp | 2 26 files changed, 242 insertions(+), 187 deletions(-)
Title: R Interface to the 'DieHarder' RNG Test Suite
Description: The 'RDieHarder' package provides an R interface to
the 'DieHarder' suite of random number generators and tests that
was developed by Robert G. Brown and David Bauer, extending
earlier work by George Marsaglia and others. The 'DieHarder'
library code is included.
Author: Dirk Eddelbuettel, Robert G Brown, David Bauer
plus contributors to DieHarder
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RDieHarder versions 0.2.2 dated 2021-11-02 and 0.2.3 dated 2021-12-14
ChangeLog | 27 +++++++++++++++++++++ DESCRIPTION | 8 +++--- MD5 | 23 +++++++++--------- build/vignette.rds |binary configure | 38 +++++++++++++++--------------- configure.ac | 18 +++++++------- configure.win |only inst/doc/RDieHarder.pdf |binary src/dieharder.c | 4 +-- src/libdieharder/dieharder/libdieharder.h | 4 +-- src/libdieharder/kstest.c | 4 +-- src/libdieharder/rng_file_input.c | 8 +++--- src/libdieharder/rngs_gnu_r.c | 2 - 13 files changed, 82 insertions(+), 54 deletions(-)
Title: Pre-Commit Hooks
Description: Useful git hooks for R building on top of the multi-language
framework 'pre-commit' for hook management. This package provides git
hooks for common tasks like formatting files with 'styler' or spell
checking as well as wrapper functions to access the 'pre-commit'
executable.
Author: Lorenz Walthert
Maintainer: Lorenz Walthert <lorenz.walthert@icloud.com>
Diff between precommit versions 0.2.1 dated 2021-12-14 and 0.2.2 dated 2021-12-14
DESCRIPTION | 18 +- MD5 | 24 +-- NEWS.md | 11 + R/precommit-package.R | 6 R/release.R | 2 R/setup.R | 9 + R/testing.R | 2 R/utils.R | 4 inst/doc/available-hooks.html | 4 inst/hooks/exported/readme-rmd-rendered.R | 4 inst/pre-commit-config-pkg.yaml | 2 inst/pre-commit-config-proj.yaml | 2 tests/testthat/test-hooks.R | 184 ++++++++++++++---------------- 13 files changed, 144 insertions(+), 128 deletions(-)
Title: Tests of Multispecies Coalescent Gene Tree Simulator Output
Description: Statistical tests for validating multispecies coalescent gene tree simulators, using pairwise distances and rooted triple counts. Background is given by Allman, Banos, and Rhodes (2019) <arXiv:1908.01424>.
Author: Elizabeth Allman [aut, cre, cph],
Hector Banos [aut, cph],
John Rhodes [aut, cph]
Maintainer: Elizabeth Allman <e.allman@alaska.edu>
Diff between MSCsimtester versions 0.0.9 dated 2021-11-04 and 1.0.0 dated 2021-12-14
DESCRIPTION | 6 +++--- MD5 | 4 ++-- build/partial.rdb |binary 3 files changed, 5 insertions(+), 5 deletions(-)
Title: A Collection of Contrast Methods
Description: One degree of freedom contrasts for 'lm', 'glm', 'gls', and 'geese' objects.
Author: Alan O'Callaghan [cre],
Max Kuhn [aut],
Steve Weston [aut],
Jed Wing [aut],
James Forester [aut],
Thorn Thaler [aut]
Maintainer: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Diff between contrast versions 0.22 dated 2020-03-19 and 0.24.1 dated 2021-12-14
DESCRIPTION | 17 - MD5 | 32 +- NEWS.md | 5 R/contrast.lm.R | 270 ++++++++++----------- R/data.R | 12 R/gets.R | 26 +- R/misc.R | 71 +++-- R/model.frames.R | 555 ++++++++++++++++++++++---------------------- R/print.contrast.R | 120 ++++----- R/testStatistic.R | 97 ++++--- README.md | 14 - build/vignette.rds |binary inst/doc/contrast.html | 49 +++ tests/testthat/test-geese.R | 48 +-- tests/testthat/test-gls.R | 20 - tests/testthat/test-lm.R | 80 ++++-- tests/testthat/test-lme.R | 20 - 17 files changed, 765 insertions(+), 671 deletions(-)
Title: Geometric Tools Based on Balanced/Unbalanced Optimal Transport
Description: Includes a variety of methods to compute objects related to the 'Wasserstein distance' (also known as 'Kantorovich distance' or 'Earth-Mover distance'). The main effort of this package is to allow for computations of 'Wasserstein barycenter' using regularised, unregularised and stochastic methods. It also provides convenient wrappers to call the 'transport' package with more general inputs. Handy visual tools are provided to showcase, barycenters, animations of optimal transport geodesics and animations of principal components in the 'Wasserstein space'. It also includes tools to compute 'Kantorovich-Rubinstein' distances and barycenters.
Author: Florian Heinemann [aut, cre], Nicholas Bonneel [ctb]
Maintainer: Florian Heinemann <florian.heinemann@uni-goettingen.de>
Diff between WSGeometry versions 1.2 dated 2021-12-10 and 1.2.1 dated 2021-12-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/maaipm.cpp | 8 ++++---- src/umaaipm.cpp | 8 ++++---- 4 files changed, 14 insertions(+), 14 deletions(-)
Title: MCMC Sampling from 'TMB' Model Object using 'Stan'
Description: Enables all 'rstan' functionality for a 'TMB' model object, in particular MCMC sampling and chain visualization. Sampling can be performed with or without Laplace approximation for the random effects.
Author: Kasper Kristensen
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between tmbstan versions 1.0.2 dated 2019-05-18 and 1.0.3 dated 2021-12-14
DESCRIPTION | 13 +++++++------ MD5 | 4 ++-- src/Makevars | 6 +++++- 3 files changed, 14 insertions(+), 9 deletions(-)
Title: Tidy Common Workflow Language Tools and Workflows
Description: The Common Workflow Language <https://www.commonwl.org/> is an
open standard for describing data analysis workflows. This package takes
the raw Common Workflow Language workflows encoded in JSON or 'YAML'
and turns the workflow elements into tidy data frames or lists.
A graph representation for the workflow can be constructed and visualized
with the parsed workflow inputs, outputs, and steps. Users can embed the
visualizations in their 'Shiny' applications, and export them
as HTML files or static images.
Author: Jeffrey Grover [aut, cre] (<https://orcid.org/0000-0001-6246-1767>),
Soner Koc [aut] (<https://orcid.org/0000-0002-0772-6600>),
Nan Xiao [aut] (<https://orcid.org/0000-0002-0250-5673>),
Dennis Dean [aut] (<https://orcid.org/0000-0002-7621-9717>),
Seven Bridges Genomics [cph, fnd]
Maintainer: Jeffrey Grover <jeffrey.grover@sevenbridges.com>
Diff between tidycwl versions 1.0.5 dated 2020-10-19 and 1.0.6 dated 2021-12-14
DESCRIPTION | 21 - MD5 | 16 - NEWS.md | 10 R/parse.R | 22 + R/utils.R | 17 + README.md | 4 build/vignette.rds |binary inst/doc/tidycwl.html | 566 +++++++++++++++++++++++++++---------------------- man/tidycwl-package.Rd | 14 - 9 files changed, 386 insertions(+), 284 deletions(-)
Title: Client for Statistics Canada's Open Economic Data
Description: An easy connection with R to Statistics Canada's Web Data Service. Open economic data (formerly known as CANSIM tables, now identified by Product IDs (PID)) are accessible as a data frame, directly in the user's R environment.
Warin, Le Duc (2019) <doi:10.6084/m9.figshare.10544735>.
Author: Thierry Warin [aut, cre] (<https://orcid.org/0000-0002-5921-3428>),
Romain Le Duc [aut]
Maintainer: Thierry Warin <thierry.warin@hec.ca>
Diff between statcanR versions 0.2.1 dated 2021-03-03 and 0.2.3 dated 2021-12-14
statcanR-0.2.1/statcanR/man/figures/LOGO.png |only statcanR-0.2.1/statcanR/man/figures/logoSk.png |only statcanR-0.2.1/statcanR/man/statcanR-deprecated.Rd |only statcanR-0.2.3/statcanR/DESCRIPTION | 11 statcanR-0.2.3/statcanR/MD5 | 25 - statcanR-0.2.3/statcanR/NAMESPACE | 4 statcanR-0.2.3/statcanR/NEWS.md | 8 statcanR-0.2.3/statcanR/R/statCanR.R | 238 +++++++++++----- statcanR-0.2.3/statcanR/README.md | 54 ++- statcanR-0.2.3/statcanR/build/vignette.rds |binary statcanR-0.2.3/statcanR/inst/doc/statCanR.R | 3 statcanR-0.2.3/statcanR/inst/doc/statCanR.Rmd | 7 statcanR-0.2.3/statcanR/inst/doc/statCanR.html | 279 +------------------ statcanR-0.2.3/statcanR/man/figures/shiny.png |only statcanR-0.2.3/statcanR/man/statcan_download_data.Rd |only statcanR-0.2.3/statcanR/vignettes/statCanR.Rmd | 7 16 files changed, 275 insertions(+), 361 deletions(-)
Title: Text Tokenization using Byte Pair Encoding and Unigram Modelling
Description: Unsupervised text tokenizer allowing to perform byte pair encoding and unigram modelling.
Wraps the 'sentencepiece' library <https://github.com/google/sentencepiece> which provides a language independent tokenizer to split text in words and smaller subword units.
The techniques are explained in the paper "SentencePiece: A simple and language independent subword tokenizer and detokenizer for Neural Text Processing" by Taku Kudo and John Richardson (2018) <doi:10.18653/v1/D18-2012>.
Provides as well straightforward access to pretrained byte pair encoding models and subword embeddings trained on Wikipedia using 'word2vec',
as described in "BPEmb: Tokenization-free Pre-trained Subword Embeddings in 275 Languages" by Benjamin Heinzerling and Michael Strube (2018) <http://www.lrec-conf.org/proceedings/lrec2018/pdf/1049.pdf>.
Author: Jan Wijffels [aut, cre, cph] (R wrapper),
BNOSAC [cph] (R wrapper),
Google Inc. [ctb, cph] (Files at src/sentencepiece/src (Apache License,
Version 2.0),
The Abseil Authors [ctb, cph] (Files at src/third_party/absl (Apache
License, Version 2.0),
Google Inc. [ctb, cph] (Files at src/third_party/protobuf-lite (BSD-3
License)),
Kenton Varda (Google Inc.) [ctb, cph] (Files at
src/third_party/protobuf-lite: coded_stream.cc, extension_set.cc,
generated_message_util.cc, generated_message_util.cc,
message_lite.cc, repeated_field.cc, wire_format_lite.cc,
zero_copy_stream.cc, zero_copy_stream_impl_lite.cc,
google/protobuf/extension_set.h,
google/protobuf/generated_message_util.h,
google/protobuf/wire_format_lite.h,
google/protobuf/wire_format_lite_inl.h,
google/protobuf/message_lite.h, google/protobuf/repeated_field.h,
google/protobuf/io/coded_stream.h,
google/protobuf/io/zero_copy_stream_impl_lite.h,
google/protobuf/io/zero_copy_stream.h,
google/protobuf/stubs/common.h, google/protobuf/stubs/hash.h,
google/protobuf/stubs/once.h, google/protobuf/stubs/once.h.org
(BSD-3 License)),
Sanjay Ghemawat (Google Inc.) [ctb, cph] (Design of files at
src/third_party/protobuf-lite: coded_stream.cc, extension_set.cc,
generated_message_util.cc, generated_message_util.cc,
message_lite.cc, repeated_field.cc, wire_format_lite.cc,
zero_copy_stream.cc, zero_copy_stream_impl_lite.cc,
google/protobuf/extension_set.h,
google/protobuf/generated_message_util.h,
google/protobuf/wire_format_lite.h,
google/protobuf/wire_format_lite_inl.h,
google/protobuf/message_lite.h, google/protobuf/repeated_field.h,
google/protobuf/io/coded_stream.h,
google/protobuf/io/zero_copy_stream_impl_lite.h,
google/protobuf/io/zero_copy_stream.h (BSD-3 License)),
Jeff Dean (Google Inc.) [ctb, cph] (Design of files at
src/third_party/protobuf-lite: coded_stream.cc, extension_set.cc,
generated_message_util.cc, generated_message_util.cc,
message_lite.cc, repeated_field.cc, wire_format_lite.cc,
zero_copy_stream.cc, zero_copy_stream_impl_lite.cc,
google/protobuf/extension_set.h,
google/protobuf/generated_message_util.h,
google/protobuf/wire_format_lite.h,
google/protobuf/wire_format_lite_inl.h,
google/protobuf/message_lite.h, google/protobuf/repeated_field.h,
google/protobuf/io/coded_stream.h,
google/protobuf/io/zero_copy_stream_impl_lite.h,
google/protobuf/io/zero_copy_stream.h (BSD-3 License)),
Laszlo Csomor (Google Inc.) [ctb, cph] (Files at
src/third_party/protobuf-lite: io_win32.cc,
google/protobuf/stubs/io_win32.h (BSD-3 License)),
Wink Saville (Google Inc.) [ctb, cph] (Files at
src/third_party/protobuf-lite: message_lite.cc,
google/protobuf/wire_format_lite.h,
google/protobuf/wire_format_lite_inl.h,
google/protobuf/message_lite.h (BSD-3 License)),
Jim Meehan (Google Inc.) [ctb, cph] (Files at
src/third_party/protobuf-lite: structurally_valid.cc (BSD-3
License)),
Chris Atenasio (Google Inc.) [ctb, cph] (Files at
src/third_party/protobuf-lite: google/protobuf/wire_format_lite.h
(BSD-3 License)),
Jason Hsueh (Google Inc.) [ctb, cph] (Files at
src/third_party/protobuf-lite:
google/protobuf/io/coded_stream_inl.h (BSD-3 License)),
Anton Carver (Google Inc.) [ctb, cph] (Files at
src/third_party/protobuf-lite: google/protobuf/stubs/map_util.h
(BSD-3 License)),
Maxim Lifantsev (Google Inc.) [ctb, cph] (Files at
src/third_party/protobuf-lite: google/protobuf/stubs/mathlimits.h
(BSD-3 License)),
Susumu Yata [ctb, cph] (Files at src/third_party/darts_clone (BSD-3
License),
Daisuke Okanohara [ctb, cph] (File src/third_party/esaxx/esa.hxx (MIT
License)),
Yuta Mori [ctb, cph] (File src/third_party/esaxx/sais.hxx (MIT
License)),
Benjamin Heinzerling [ctb, cph] (Files
data/models/nl.wiki.bpe.vs1000.d25.w2v.txt,
data/models/nl.wiki.bpe.vs1000.d25.w2v.bin and
data/models/nl.wiki.bpe.vs1000.model (MIT License))
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between sentencepiece versions 0.1.2 dated 2020-06-08 and 0.2 dated 2021-12-14
sentencepiece-0.1.2/sentencepiece/src/sentencepiece/src/flags.cc |only sentencepiece-0.1.2/sentencepiece/src/sentencepiece/src/flags.h |only sentencepiece-0.1.2/sentencepiece/src/sentencepiece/src/flags_test.cc |only sentencepiece-0.1.2/sentencepiece/src/third_party/protobuf-lite/google/protobuf/inlined_string_field.h |only sentencepiece-0.1.2/sentencepiece/src/third_party/protobuf-lite/google/protobuf/io/coded_stream_inl.h |only sentencepiece-0.1.2/sentencepiece/src/third_party/protobuf-lite/google/protobuf/stubs/fastmem.h |only sentencepiece-0.1.2/sentencepiece/src/third_party/protobuf-lite/google/protobuf/stubs/io_win32.h |only sentencepiece-0.1.2/sentencepiece/src/third_party/protobuf-lite/google/protobuf/stubs/mathlimits.h |only sentencepiece-0.1.2/sentencepiece/src/third_party/protobuf-lite/google/protobuf/stubs/once.h.org |only sentencepiece-0.1.2/sentencepiece/src/third_party/protobuf-lite/google/protobuf/wire_format_lite_inl.h |only sentencepiece-0.2/sentencepiece/DESCRIPTION | 18 sentencepiece-0.2/sentencepiece/LICENSE.note | 2 sentencepiece-0.2/sentencepiece/MD5 | 375 sentencepiece-0.2/sentencepiece/NAMESPACE | 7 sentencepiece-0.2/sentencepiece/NEWS.md | 18 sentencepiece-0.2/sentencepiece/R/RcppExports.R | 16 sentencepiece-0.2/sentencepiece/R/bpemb.R | 217 sentencepiece-0.2/sentencepiece/R/pkg.R | 3 sentencepiece-0.2/sentencepiece/R/sentencepiece.R | 116 sentencepiece-0.2/sentencepiece/R/utils.R |only sentencepiece-0.2/sentencepiece/R/word2vec.R | 61 sentencepiece-0.2/sentencepiece/R/wordpiece.R | 3 sentencepiece-0.2/sentencepiece/README.md | 17 sentencepiece-0.2/sentencepiece/inst/models/nl-fr-dekamer-unigram.model |only sentencepiece-0.2/sentencepiece/inst/models/nl.wiki.bpe.vs1000.d25.w2v.bin |only sentencepiece-0.2/sentencepiece/man/BPEembed.Rd |only sentencepiece-0.2/sentencepiece/man/BPEembedder.Rd |only sentencepiece-0.2/sentencepiece/man/predict.BPEembed.Rd |only sentencepiece-0.2/sentencepiece/man/read_word2vec.Rd | 56 sentencepiece-0.2/sentencepiece/man/sentencepiece.Rd | 6 sentencepiece-0.2/sentencepiece/man/sentencepiece_decode.Rd | 11 sentencepiece-0.2/sentencepiece/man/sentencepiece_download_model.Rd | 7 sentencepiece-0.2/sentencepiece/man/sentencepiece_encode.Rd | 49 sentencepiece-0.2/sentencepiece/man/txt_remove_.Rd |only sentencepiece-0.2/sentencepiece/man/wordpiece_encode.Rd | 3 sentencepiece-0.2/sentencepiece/src/Makevars | 10 sentencepiece-0.2/sentencepiece/src/RcppExports.cpp | 63 sentencepiece-0.2/sentencepiece/src/rcpp_sentencepiece.cpp | 58 sentencepiece-0.2/sentencepiece/src/rcpp_wordpiece.cpp | 17 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/CMakeLists.txt | 57 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/bpe_model.cc | 32 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/bpe_model.h | 15 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/bpe_model_test.cc | 51 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/bpe_model_trainer.cc | 9 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/bpe_model_trainer.h | 10 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/bpe_model_trainer_test.cc | 70 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/builder.cc | 58 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/builder.h | 3 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/builder_test.cc | 77 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/builtin_pb/sentencepiece.pb.cc | 934 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/builtin_pb/sentencepiece.pb.h | 932 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/builtin_pb/sentencepiece_model.pb.cc | 3689 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/builtin_pb/sentencepiece_model.pb.h | 4536 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/char_model_test.cc | 5 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/char_model_trainer.cc | 10 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/char_model_trainer.h | 6 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/char_model_trainer_test.cc | 23 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/common.h | 15 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/compile_charsmap_main.cc | 17 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/error.cc | 59 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/filesystem.cc | 24 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/filesystem.h | 1 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/filesystem_test.cc | 18 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/freelist.h | 5 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/freelist_test.cc | 14 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/init.h |only sentencepiece-0.2/sentencepiece/src/sentencepiece/src/init_test.cc |only sentencepiece-0.2/sentencepiece/src/sentencepiece/src/model_factory.cc | 15 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/model_factory.h | 1 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/model_interface.cc | 86 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/model_interface.h | 101 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/model_interface_test.cc | 152 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/normalization_rule.h |199613 ++++++---- sentencepiece-0.2/sentencepiece/src/sentencepiece/src/normalizer.cc | 48 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/normalizer.h | 11 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/normalizer_test.cc | 32 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/pretokenizer_for_training.cc |only sentencepiece-0.2/sentencepiece/src/sentencepiece/src/pretokenizer_for_training.h |only sentencepiece-0.2/sentencepiece/src/sentencepiece/src/pretokenizer_for_training_test.cc |only sentencepiece-0.2/sentencepiece/src/sentencepiece/src/sentencepiece.proto |only sentencepiece-0.2/sentencepiece/src/sentencepiece/src/sentencepiece_model.proto |only sentencepiece-0.2/sentencepiece/src/sentencepiece/src/sentencepiece_processor.cc | 415 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/sentencepiece_processor.h | 301 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/sentencepiece_processor_test.cc | 610 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/sentencepiece_trainer.cc | 174 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/sentencepiece_trainer.h | 104 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/sentencepiece_trainer_test.cc | 367 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/spec_parser.h | 625 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/spm_decode_main.cc | 71 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/spm_encode_main.cc | 140 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/spm_export_vocab_main.cc | 33 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/spm_normalize_main.cc | 64 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/spm_train_main.cc | 283 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/test_main.cc | 12 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/testharness.cc | 38 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/testharness.h | 90 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/trainer_factory.cc | 24 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/trainer_factory.h | 4 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/trainer_factory_test.cc | 15 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/trainer_interface.cc | 324 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/trainer_interface.h | 59 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/trainer_interface_test.cc | 236 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/unicode_script.cc | 6 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/unicode_script_map.h | 4 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/unicode_script_test.cc | 4 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/unigram_model.cc | 491 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/unigram_model.h | 45 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/unigram_model_test.cc | 382 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/unigram_model_trainer.cc | 107 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/unigram_model_trainer.h | 12 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/unigram_model_trainer_test.cc | 49 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/util.cc | 133 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/util.h | 210 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/util_test.cc | 239 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/word_model.cc | 2 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/word_model_test.cc | 5 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/word_model_trainer.cc | 9 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/word_model_trainer.h | 6 sentencepiece-0.2/sentencepiece/src/sentencepiece/src/word_model_trainer_test.cc | 24 sentencepiece-0.2/sentencepiece/src/third_party/CMakeLists.txt | 8 sentencepiece-0.2/sentencepiece/src/third_party/absl/container |only sentencepiece-0.2/sentencepiece/src/third_party/absl/flags |only sentencepiece-0.2/sentencepiece/src/third_party/absl/memory |only sentencepiece-0.2/sentencepiece/src/third_party/absl/strings/ascii.h |only sentencepiece-0.2/sentencepiece/src/third_party/absl/strings/match.h |only sentencepiece-0.2/sentencepiece/src/third_party/absl/strings/numbers.h |only sentencepiece-0.2/sentencepiece/src/third_party/absl/strings/str_cat.h |only sentencepiece-0.2/sentencepiece/src/third_party/absl/strings/str_format.h |only sentencepiece-0.2/sentencepiece/src/third_party/absl/strings/str_join.h |only sentencepiece-0.2/sentencepiece/src/third_party/absl/strings/str_replace.h |only sentencepiece-0.2/sentencepiece/src/third_party/absl/strings/str_split.h |only sentencepiece-0.2/sentencepiece/src/third_party/absl/strings/string_view.h | 4 sentencepiece-0.2/sentencepiece/src/third_party/absl/strings/strip.h |only sentencepiece-0.2/sentencepiece/src/third_party/esaxx/esa.hxx | 250 sentencepiece-0.2/sentencepiece/src/third_party/esaxx/sais.hxx | 729 sentencepiece-0.2/sentencepiece/src/third_party/protobuf-lite/arena.cc | 408 sentencepiece-0.2/sentencepiece/src/third_party/protobuf-lite/arenastring.cc | 217 sentencepiece-0.2/sentencepiece/src/third_party/protobuf-lite/bytestream.cc | 4 sentencepiece-0.2/sentencepiece/src/third_party/protobuf-lite/coded_stream.cc | 552 sentencepiece-0.2/sentencepiece/src/third_party/protobuf-lite/common.cc | 126 sentencepiece-0.2/sentencepiece/src/third_party/protobuf-lite/extension_set.cc | 1365 sentencepiece-0.2/sentencepiece/src/third_party/protobuf-lite/generated_enum_util.cc |only sentencepiece-0.2/sentencepiece/src/third_party/protobuf-lite/generated_message_table_driven_lite.cc | 55 sentencepiece-0.2/sentencepiece/src/third_party/protobuf-lite/generated_message_util.cc | 212 sentencepiece-0.2/sentencepiece/src/third_party/protobuf-lite/google/protobuf/any.h |only sentencepiece-0.2/sentencepiece/src/third_party/protobuf-lite/google/protobuf/arena.h | 393 sentencepiece-0.2/sentencepiece/src/third_party/protobuf-lite/google/protobuf/arena_impl.h | 534 sentencepiece-0.2/sentencepiece/src/third_party/protobuf-lite/google/protobuf/arenastring.h | 602 sentencepiece-0.2/sentencepiece/src/third_party/protobuf-lite/google/protobuf/descriptor.h |only sentencepiece-0.2/sentencepiece/src/third_party/protobuf-lite/google/protobuf/extension_set.h | 777 sentencepiece-0.2/sentencepiece/src/third_party/protobuf-lite/google/protobuf/extension_set_inl.h |only sentencepiece-0.2/sentencepiece/src/third_party/protobuf-lite/google/protobuf/generated_enum_reflection.h |only 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Title: Testing and Plotting Procedures for Biostatistics
Description: Contains miscellaneous functions useful in biostatistics, mostly univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions intend to simplify user's life by shortening existing procedures or by implementing plotting functions that can be used with as many methods from different packages as possible.
Author: Maxime Herv<e9>
Maintainer: Maxime Herv<e9> <maxime.herve@univ-rennes1.fr>
Diff between RVAideMemoire versions 0.9-80 dated 2021-06-28 and 0.9-81 dated 2021-12-14
DESCRIPTION | 12 ++++++------ MD5 | 29 +++++++++++++++++------------ NAMESPACE | 9 ++++++--- NEWS | 7 +++++++ R/back.emmeans.R | 35 ++++++++++++++++++++--------------- R/elogis.R | 4 ++-- R/p.beta.R |only R/perm.anova.R | 4 ++-- R/plotresid.R | 28 ++++++++++++++++++++++++++++ R/quasibinomial.QAIC.R |only R/quasipoisson.QAIC.R |only R/zzz.R | 2 +- man/RVAideMemoire-package.Rd | 4 ++-- man/back.emmeans.Rd | 14 ++++++++++---- man/p.beta.Rd |only man/plotresid.Rd | 8 ++++---- man/quasibinomial.QAIC.Rd |only man/user.cont.Rd | 2 +- 18 files changed, 106 insertions(+), 52 deletions(-)
Title: Robust Estimation in Very Small Samples
Description: Implements the estimation techniques described in Rousseeuw &
Verboven (2002) <doi:10.1016/S0167-9473(02)00078-6> for the location and
scale of very small samples.
Author: Avraham Adler [aut, cph, cre] (<https://orcid.org/0000-0002-3039-0703>)
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between revss versions 1.0.1 dated 2020-11-10 and 1.0.2 dated 2021-12-14
DESCRIPTION | 9 ++++----- MD5 | 24 ++++++++++++------------ R/adm.R | 13 ++++++------- R/robLoc.R | 3 +++ R/robScale.R | 3 +++ README.md | 13 ++++++------- build/partial.rdb |binary inst/CITATION | 4 ++-- inst/NEWS.Rd | 16 +++++++++++++++- man/adm.Rd | 31 ++++++++++++++++--------------- man/robLoc.Rd | 12 +++++++----- man/robScale.Rd | 20 ++++++++++---------- tests/testthat/test-citation.R | 2 -- 13 files changed, 84 insertions(+), 66 deletions(-)
Title: Empirical Bayes Estimation and Inference
Description: Kiefer-Wolfowitz maximum likelihood estimation for mixture models
and some other density estimation and regression methods based on convex
optimization. See Koenker and Gu (2017) REBayes: An R Package for Empirical
Bayes Mixture Methods, Journal of Statistical Software, 82, 1--26,
<DOI:10.18637/jss.v082.i08>.
Author: Roger Koenker [aut, cre],
Jiaying Gu [ctb],
Ivan Mizera [ctb]
Maintainer: Roger Koenker <rkoenker@uiuc.edu>
Diff between REBayes versions 2.2 dated 2020-01-22 and 2.50 dated 2021-12-14
DESCRIPTION | 10 +- MD5 | 126 ++++++++++++++++++++++------------ NAMESPACE | 28 +++++++ R/B2mix.R |only R/BDGLmix.R |only R/BPmix.R |only R/GLVmix.R |only R/GLmix.R | 2 R/Gammamix.R | 4 - R/Guvenen.R | 2 R/KWPrimal.R |only R/Lfdr.R |only R/NPmix.R |only R/RLR.R |only R/WGLVmix.R | 34 +++++---- R/bball.R | 2 R/misc.R | 177 +++++++++++++++++++++++++++++++++++++++++++++++++ R/plot.GLVmix.R |only R/plot.WGLVmix.R |only R/predict.B2mix.R |only R/predict.Bmix.R | 7 - R/predict.GLVmix.R |only R/predict.GLmix.R | 5 - R/predict.Pmix.R | 4 - R/predict.WGLVmix.R |only build/vignette.rds |binary demo/00Index | 6 + demo/B2mix1.R |only demo/BPmix1.R |only demo/Bmmix1.R |only demo/Brown.R | 2 demo/NPmix1.R |only demo/RLR1.R |only demo/RLR2.R |only demo/WGLVmix1.R | 2 inst/ChangeLog | 109 ++++++++++++++++++++++++++++++ inst/Readme | 2 inst/doc/Bdecon.R | 4 - inst/doc/Bdecon.pdf |binary inst/doc/medde.R | 10 +- inst/doc/medde.pdf |binary inst/doc/rebayes.R | 36 ++++----- inst/doc/rebayes.pdf |binary man/B2mix.Rd |only man/BDGLmix.Rd |only man/BPmix.Rd |only man/Cosslett.Rd | 2 man/Finv.Rd |only man/GLVmix.Rd |only man/GLmix.Rd | 5 - man/Gammamix.Rd | 4 - man/Gompertzmix.Rd | 12 ++- man/Gosset.Rd | 6 + man/Guvenen.Rd | 8 +- man/KW2smooth.Rd |only man/KWPrimal.Rd |only man/KWsmooth.Rd |only man/Lfdr.Rd |only man/NPmix.Rd |only man/Norberg.Rd | 6 + man/RLR.Rd |only man/TLmix.Rd | 3 man/ThreshFDR.Rd |only man/Tncpmix.Rd | 3 man/WGLVmix.Rd | 10 ++ man/WGVmix.Rd | 13 +++ man/Weibullmix.Rd | 12 ++- man/bball.Rd | 2 man/bwKW.Rd |only man/bwKW2.Rd |only man/flies.Rd | 6 + man/medde.Rd | 14 +++ man/plot.GLVmix.Rd |only man/predict.B2mix.Rd |only man/predict.GLVmix.Rd |only man/predict.GLmix.Rd | 3 man/predict.Pmix.Rd | 3 man/predict.WGLVmix.Rd |only man/qKW.Rd |only man/qKW2.Rd |only man/rKW.Rd |only man/tacks.Rd | 6 + man/tannenbaum.Rd | 6 + man/velo.Rd | 6 + 84 files changed, 562 insertions(+), 140 deletions(-)
Title: Loading a JAGS Module for the Piecewise Exponential Distribution
Description: Load the Just Another Gibbs Sampling (JAGS) module 'pexm'. The module provides the tools to work with the Piecewise Exponential (PE) distribution in a Bayesian model with the corresponding Markov Chain Monte Carlo algorithm (Gibbs Sampling) implemented via JAGS. Details about the module implementation can be found in Mayrink et al. (2021) <doi:10.18637/jss.v100.i08>.
Author: Vinicius Mayrink [aut, cre] (<https://orcid.org/0000-0002-5683-8326>),
Joao Duarte [aut],
Fabio Demarqui [ctb] (<https://orcid.org/0000-0001-9236-1986>)
Maintainer: Vinicius Mayrink <vdinizm@gmail.com>
Diff between pexm versions 1.1.1 dated 2021-11-21 and 1.1.2 dated 2021-12-14
DESCRIPTION | 6 +++--- MD5 | 5 +++-- NEWS | 2 ++ src/Makevars.ucrt |only 4 files changed, 8 insertions(+), 5 deletions(-)
Title: Estimation of Tree-Based Item Response Models
Description: Helper functions and example data sets to facilitate the estimation of IRTree models from data with different shape and using different software.
Author: Zhaojun Li, Ivailo Partchev and Paul De Boeck
Maintainer: Ivailo Partchev <partchev@gmail.com>
Diff between irtrees versions 0.1.0 dated 2012-05-19 and 1.0.0 dated 2021-12-14
DESCRIPTION | 23 ++++++++-------- MD5 | 42 ++++++++++++++++++++++--------- NAMESPACE | 13 +++++++++ R/dendrify.R | 65 ++++++++++++++++++++++++------------------------ R/exogenize.R | 1 R/merm.R |only R/pretree.R |only build |only inst/CITATION | 4 +- inst/doc |only man/LtoL_multi.tree.Rd |only man/LtoL_single.tree.Rd |only man/LtoW_multi.tree.Rd |only man/LtoW_single.tree.Rd |only man/WtoL_multi.tree.Rd |only man/WtoL_single.tree.Rd |only man/WtoW_multi.tree.Rd |only man/WtoW_single.tree.Rd |only man/dendrify.Rd | 2 - man/exogenize.Rd | 2 - man/graph2mx.Rd |only man/irtrees.package.Rd | 2 - man/linlat.Rd | 2 - man/linresp.Rd | 2 - man/neslat.Rd | 2 - man/nesresp.Rd | 2 - man/tolong.Rd |only vignettes |only 28 files changed, 98 insertions(+), 64 deletions(-)
Title: Diet Estimated Trophic Levels
Description: Estimates fractional trophic level from quantitative and qualitative diet data and calculates electivity indices in R. Borstein (2020) <doi:10.1007/s10750-020-04417-5>.
Author: Samuel R. Borstein <sam@borstein.com>
Maintainer: Samuel R. Borstein <sam@borstein.com>
Diff between dietr versions 1.1.2 dated 2021-11-23 and 1.1.3 dated 2021-12-14
dietr-1.1.2/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-16-1.pdf |only dietr-1.1.2/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-17-1.pdf |only dietr-1.1.2/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-17-2.pdf |only dietr-1.1.2/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-17-3.pdf |only dietr-1.1.2/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-17-4.pdf |only dietr-1.1.2/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-18-2.pdf |only dietr-1.1.2/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-18-3.pdf |only dietr-1.1.2/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-18-4.pdf |only dietr-1.1.2/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-3-1.pdf |only dietr-1.1.2/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-4-1.pdf |only dietr-1.1.2/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-4-2.pdf |only dietr-1.1.2/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-4-3.pdf |only dietr-1.1.2/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-4-4.pdf |only dietr-1.1.2/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-5-1.pdf |only dietr-1.1.2/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-5-2.pdf |only dietr-1.1.2/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-5-3.pdf |only dietr-1.1.2/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-5-4.pdf |only dietr-1.1.3/dietr/DESCRIPTION | 8 dietr-1.1.3/dietr/MD5 | 103 - dietr-1.1.3/dietr/NAMESPACE | 22 dietr-1.1.3/dietr/NEWS.md | 14 dietr-1.1.3/dietr/R/CompositeIndices.R | 288 ++-- dietr-1.1.3/dietr/R/ConvertFishbaseDiet.R | 92 - dietr-1.1.3/dietr/R/ConvertFishbaseFood.R | 84 - dietr-1.1.3/dietr/R/DataDoc.R | 206 +-- dietr-1.1.3/dietr/R/DietTroph.R | 258 +-- dietr-1.1.3/dietr/R/Electivity.R | 255 +-- dietr-1.1.3/dietr/R/FoodTroph.R | 220 +-- dietr-1.1.3/dietr/R/FullnessIndex.R | 76 - dietr-1.1.3/dietr/R/PlotElectivity.R | 102 - dietr-1.1.3/dietr/R/VacuityIndex.R | 56 dietr-1.1.3/dietr/R/pkgname.R | 70 - dietr-1.1.3/dietr/build/vignette.rds |binary dietr-1.1.3/dietr/data/Horn1982.RData |binary dietr-1.1.3/dietr/inst/CITATION | 30 dietr-1.1.3/dietr/inst/doc/dietr-vignette.R | 303 ++-- dietr-1.1.3/dietr/inst/doc/dietr-vignette.Rmd | 670 +++++----- dietr-1.1.3/dietr/inst/doc/dietr-vignette.pdf |binary dietr-1.1.3/dietr/man/Casaux1998.Rd | 66 dietr-1.1.3/dietr/man/CompositeIndices.Rd | 164 +- dietr-1.1.3/dietr/man/CortesPreyVals.Rd | 62 dietr-1.1.3/dietr/man/DietTroph.Rd | 208 +-- dietr-1.1.3/dietr/man/Electivity.Rd | 167 +- dietr-1.1.3/dietr/man/FishBasePreyVals.Rd | 66 dietr-1.1.3/dietr/man/FoodTroph.Rd | 120 - dietr-1.1.3/dietr/man/GastrosomaticIndex.Rd | 82 - dietr-1.1.3/dietr/man/Herichthys.Rd | 46 dietr-1.1.3/dietr/man/Horn1982.Rd | 60 dietr-1.1.3/dietr/man/PlotElectivity.Rd | 134 +- dietr-1.1.3/dietr/man/SebastesStomachs.Rd | 64 dietr-1.1.3/dietr/man/VacuityIndex.Rd | 82 - dietr-1.1.3/dietr/man/dietr.Rd | 76 - dietr-1.1.3/dietr/tests/testthat.R | 2 dietr-1.1.3/dietr/tests/testthat/test_ConvertFishbaseDiet.R | 24 dietr-1.1.3/dietr/tests/testthat/test_ConvertFishbaseFood.R | 28 dietr-1.1.3/dietr/tests/testthat/test_DietTroph.R | 92 - dietr-1.1.3/dietr/tests/testthat/test_FoodTroph.R | 24 dietr-1.1.3/dietr/vignettes/dietr-vignette.Rmd | 670 +++++----- dietr-1.1.3/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-18-1.pdf |binary dietr-1.1.3/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-19-1.pdf |only dietr-1.1.3/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-19-2.pdf |only dietr-1.1.3/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-19-3.pdf |only dietr-1.1.3/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-19-4.pdf |only 63 files changed, 2546 insertions(+), 2548 deletions(-)
Title: Estimations using Conley Standard Errors
Description: Functions calculating Conley (1999) <doi:10.1016/S0304-4076(98)00084-0> standard errors. The package started by merging and extending multiple packages and
other published scripts on this econometric technique. It strongly emphasizes computational optimization. Details are available in the function documentation and in
the vignette.
Author: Christian Düben [aut, cre],
Richard Bluhm [cph],
Luis Calderon [cph],
Darin Christensen [cph],
Timothy Conley [cph],
Thiemo Fetzer [cph],
Leander Heldring [cph]
Maintainer: Christian Düben <christian.dueben@uni-hamburg.de>
Diff between conleyreg versions 0.1.5 dated 2021-12-03 and 0.1.6 dated 2021-12-14
DESCRIPTION | 6 MD5 | 53 ++--- NEWS.md | 5 R/RcppExports.R | 12 + R/conleyreg.R | 81 +++++--- R/dist_mat.R | 27 ++ build/partial.rdb |binary inst/doc/conleyreg_introduction.Rmd | 36 +-- inst/doc/conleyreg_introduction.html | 43 ++-- man/conleyreg.Rd | 19 +- man/dist_mat.Rd | 33 ++- src/RcppExports.cpp | 53 +++++ src/XeeXhC.cpp | 10 - src/XeeXhC.h | 10 - src/XeeXhC_R.cpp | 10 - src/dist_mat.cpp | 10 - src/distance_functions.cpp | 10 - src/distance_functions.h | 10 - src/distance_matrices.cpp | 10 - src/distance_matrices.h | 10 - src/lp.cpp | 329 ++++++++++++++++++++++++++++++++++- src/lp_filling.cpp | 10 - src/lp_filling.h | 10 - src/lp_filling_R.cpp | 10 - src/ols.cpp | 287 ++++++++++++++++++++++++++++++ src/openmp_installed.cpp |only src/time_dist.cpp | 10 - vignettes/conleyreg_introduction.Rmd | 36 +-- 28 files changed, 985 insertions(+), 155 deletions(-)
Title: Supporting Functions for Packages Maintained by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>),
Wush Wu [ctb],
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brüggemann [ctb] (<https://orcid.org/0000-0002-5329-5987>),
Christophe Dervieux [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.28 dated 2021-11-04 and 0.29 dated 2021-12-14
xfun-0.28/xfun/inst/scripts/child_pids.sh |only xfun-0.29/xfun/DESCRIPTION | 6 +- xfun-0.29/xfun/MD5 | 43 ++++++++------- xfun-0.29/xfun/NAMESPACE | 6 ++ xfun-0.29/xfun/NEWS.md | 18 ++++++ xfun-0.29/xfun/R/api.R |only xfun-0.29/xfun/R/command.R | 27 +++++++++ xfun-0.29/xfun/R/github.R | 86 +++++++++++++++++++++++++----- xfun-0.29/xfun/R/io.R | 81 ++++++++++++++++++++++------ xfun-0.29/xfun/R/paths.R | 27 ++++++++- xfun-0.29/xfun/R/revcheck.R | 63 +++++++++------------ xfun-0.29/xfun/R/string.R | 7 ++ xfun-0.29/xfun/inst/doc/xfun.html | 11 ++- xfun-0.29/xfun/inst/scripts/child-pids.sh |only xfun-0.29/xfun/man/base_pkgs.Rd | 3 - xfun-0.29/xfun/man/download_file.Rd | 9 ++- xfun-0.29/xfun/man/existing_files.Rd |only xfun-0.29/xfun/man/github_releases.Rd | 26 +++++---- xfun-0.29/xfun/man/read_all.Rd |only xfun-0.29/xfun/man/rest_api.Rd |only xfun-0.29/xfun/man/retry.Rd | 3 - xfun-0.29/xfun/man/rev_check.Rd | 14 ++-- xfun-0.29/xfun/man/session_info.Rd | 3 - xfun-0.29/xfun/man/system3.Rd |only xfun-0.29/xfun/man/tinify.Rd | 3 - xfun-0.29/xfun/man/url_accessible.Rd | 15 +++-- 26 files changed, 326 insertions(+), 125 deletions(-)
Title: An R Package for Single-Index Quantile Regression
Description: Single-Index Quantile Regression is effective in some scenarios. We provides functions that allow users to fit Single-Index Quantile Regression model. It also provides functions to do prediction, estimate standard errors of the single-index coefficients via bootstrap, and visualize the estimated univariate function. Please see W., Y., Y. (2010) <doi:10.1016/j.jmva.2010.02.003> for details.
Author: Tianhai Zu [cre],
Yan Yu [aut]
Maintainer: Tianhai Zu <zuti@mail.uc.edu>
Diff between siqr versions 0.8.0 dated 2021-12-01 and 0.8.1 dated 2021-12-14
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- NAMESPACE | 2 ++ NEWS.md |only R/siqr.R | 27 +++++++++++++++------------ man/plot.siqr.Rd | 6 ++++-- 6 files changed, 30 insertions(+), 22 deletions(-)
Title: Clustering Algorithm for Data Integration and Disease Subtyping
Description: Provides a robust approach for omics data integration and disease subtyping. PINSPlus is fast and supports the analysis of large datasets with hundreds of thousands of samples and features. The software automatically determines the optimal number of clusters and then partitions the samples in a way such that the results are robust against noise and data perturbation (Nguyen et al. (2019) <DOI: 10.1093/bioinformatics/bty1049>, Nguyen et al. (2017)<DOI: 10.1101/gr.215129.116>, Nguyen et al. (2021)<DOI: 10.3389/fonc.2021.725133>).
Author: Hung Nguyen, Bang Tran, Duc Tran and Tin Nguyen
Maintainer: Hung Nguyen <hungnp@nevada.unr.edu>
Diff between PINSPlus versions 2.0.5 dated 2020-08-06 and 2.0.6 dated 2021-12-14
PINSPlus-2.0.5/PINSPlus/inst/doc/PINSPlus.pdf |only PINSPlus-2.0.5/PINSPlus/vignettes/PINSPlus.html |only PINSPlus-2.0.6/PINSPlus/DESCRIPTION | 12 PINSPlus-2.0.6/PINSPlus/MD5 | 33 - PINSPlus-2.0.6/PINSPlus/NAMESPACE | 1 PINSPlus-2.0.6/PINSPlus/R/perturbation-clustering-helpers.R | 100 ++++ PINSPlus-2.0.6/PINSPlus/R/perturbation-clustering.R | 18 PINSPlus-2.0.6/PINSPlus/R/subtyping-omics-data-helpers.R | 6 PINSPlus-2.0.6/PINSPlus/R/subtyping-omics-data.R | 255 +++++++++--- PINSPlus-2.0.6/PINSPlus/build/vignette.rds |binary PINSPlus-2.0.6/PINSPlus/inst/CITATION | 29 + PINSPlus-2.0.6/PINSPlus/inst/doc/PINSPlus.R | 50 +- PINSPlus-2.0.6/PINSPlus/inst/doc/PINSPlus.Rmd | 2 PINSPlus-2.0.6/PINSPlus/inst/doc/PINSPlus.html |only PINSPlus-2.0.6/PINSPlus/man/AML2004.Rd | 2 PINSPlus-2.0.6/PINSPlus/man/PerturbationClustering.Rd | 14 PINSPlus-2.0.6/PINSPlus/man/SubtypingOmicsData.Rd | 12 PINSPlus-2.0.6/PINSPlus/vignettes/PINSPlus.Rmd | 2 PINSPlus-2.0.6/PINSPlus/vignettes/PINSPlus.bib | 11 19 files changed, 431 insertions(+), 116 deletions(-)
Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting including the introduced here Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, color themes, Trellis graphics and a built-in help system. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, and generation and rendering of R markdown instructions for interpretative output.
Author: David Gerbing, The School of Business, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 4.0.8 dated 2021-11-18 and 4.1.4 dated 2021-12-14
DESCRIPTION | 8 MD5 | 114 +++++----- NAMESPACE | 2 NEWS | 62 +++++ R/ANOVA.R | 5 R/BarChart.R | 23 +- R/Correlation.R | 1 R/Density.R | 4 R/Histogram.R | 49 ++-- R/PieChart.R | 10 R/Plot.R | 23 +- R/Regression.R | 14 - R/bx.zstats.R | 1 R/cr.zmain.R | 7 R/dn.zmain.R | 34 ++- R/getColors.R | 11 - R/hst.stats.R | 8 R/param.zVBS.R | 4 R/pc.zmain.R | 26 -- R/pivot.R | 5 R/plt.zfill.R | 3 R/plt.zlattice.R | 10 R/plt.zmain.R | 27 +- R/plt.ztxt.R | 155 +++++++++++--- R/print.outall.R | 12 - R/reg.z1fitBasic.R | 8 R/reg.z1modelBasic.R | 15 - R/reg.zKfold.R | 2 R/ss.zfactor.R | 9 R/to.R | 15 + R/ttest.R | 5 R/zzz.R | 44 ++-- data/dataEmployee.rda |binary inst/doc/BarChart.html | 48 +--- inst/doc/Customize.html | 24 -- inst/doc/Extract.html | 104 ++++----- inst/doc/FactorAnalysis.html | 23 -- inst/doc/Histogram.html | 52 ++-- inst/doc/Means.Rmd | 2 inst/doc/Means.html | 102 +++------ inst/doc/Plot.R | 30 +- inst/doc/Plot.Rmd | 40 +-- inst/doc/Plot.html | 453 ++++++++++++++++--------------------------- inst/doc/Proportions.html | 5 inst/doc/ReadWrite.html | 14 - inst/doc/Regression.html | 411 ++++++++++++++++----------------------- inst/doc/Time.html | 115 +++------- inst/doc/pivot.R | 4 inst/doc/pivot.Rmd | 4 inst/doc/pivot.html | 266 ++++++++++++------------- inst/doc/utilities.html | 130 ++++++------ man/Density.Rd | 26 -- man/Histogram.Rd | 2 man/Plot.Rd | 9 man/to.Rd | 9 vignettes/Means.Rmd | 2 vignettes/Plot.Rmd | 40 +-- vignettes/pivot.Rmd | 4 58 files changed, 1292 insertions(+), 1343 deletions(-)
Title: Estimate Gaussian or Student's t Mixture Vector Autoregressive
Model
Description: Unconstrained and constrained maximum likelihood estimation of structural and reduced form
Gaussian mixture vector autoregressive, Student's t mixture vector autoregressive, and Gaussian and Student's t
mixture vector autoregressive models, quantile residual tests, graphical diagnostics,
simulations, forecasting, and estimation of generalized impulse response function and generalized
forecast error variance decomposition.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2016) <doi:10.1016/j.jeconom.2016.02.012>,
Savi Virolainen (2021) <arXiv:2007.04713>,
Savi Virolainen (2021) <arXiv:2109.13648>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between gmvarkit versions 2.0.0 dated 2021-11-22 and 2.0.1 dated 2021-12-14
DESCRIPTION | 8 - MD5 | 192 +++++++++++++++---------------- NEWS.md | 7 + R/GIRFandGFEVD.R | 14 +- R/GSMVARconstruction.R | 8 - R/MAINest.R | 2 R/argumentChecks.R | 4 R/data.R | 37 +++++ R/generateParams.R | 2 R/loglikelihood.R | 6 R/parameterReforms.R | 2 data/usamone.rda |only inst/doc/gmvarkit-vignette.pdf |binary man/GAfit.Rd | 2 man/GFEVD.Rd | 4 man/GIRF.Rd | 8 - man/GMVAR.Rd | 6 man/GSMVAR.Rd | 6 man/LR_test.Rd | 2 man/Wald_test.Rd | 2 man/add_data.Rd | 2 man/alt_gmvar.Rd | 2 man/alt_gsmvar.Rd | 2 man/change_parametrization.Rd | 6 man/change_regime.Rd | 6 man/check_constraints.Rd | 2 man/check_parameters.Rd | 6 man/cond_moment_plot.Rd | 2 man/cond_moments.Rd | 6 man/diagnostic_plot.Rd | 2 man/fitGMVAR.Rd | 4 man/fitGSMVAR.Rd | 4 man/form_boldA.Rd | 2 man/gdpdef.Rd | 2 man/get_alpha_mt.Rd | 2 man/get_boldA_eigens.Rd | 2 man/get_omega_eigens.Rd | 2 man/get_regime_autocovs.Rd | 2 man/get_regime_autocovs_int.Rd | 6 man/get_regime_means.Rd | 2 man/get_regime_means_int.Rd | 6 man/get_test_Omega.Rd | 6 man/get_unconstrained_structural_pars.Rd | 2 man/get_varying_h.Rd | 2 man/gmvar_to_sgmvar.Rd | 2 man/gsmvar_to_sgsmvar.Rd | 2 man/in_paramspace.Rd | 6 man/in_paramspace_int.Rd | 4 man/is_stationary.Rd | 6 man/iterate_more.Rd | 2 man/loglikelihood.Rd | 6 man/loglikelihood_int.Rd | 6 man/n_params.Rd | 4 man/pick_Am.Rd | 6 man/pick_Ami.Rd | 6 man/pick_Omegas.Rd | 6 man/pick_W.Rd | 6 man/pick_allA.Rd | 6 man/pick_all_phi0_A.Rd | 6 man/pick_alphas.Rd | 4 man/pick_df.Rd | 4 man/pick_lambdas.Rd | 6 man/pick_phi0.Rd | 6 man/pick_regime.Rd | 6 man/plot.gsmvarpred.Rd | 2 man/predict.gmvar.Rd | 2 man/predict.gsmvar.Rd | 2 man/print_std_errors.Rd | 2 man/profile_logliks.Rd | 2 man/quantile_residual_tests.Rd | 2 man/quantile_residuals.Rd | 2 man/quantile_residuals_int.Rd | 6 man/random_covmat.Rd | 2 man/random_ind.Rd | 4 man/random_ind2.Rd | 4 man/reform_constrained_pars.Rd | 6 man/reform_structural_pars.Rd | 6 man/regime_distance.Rd | 2 man/reorder_W_columns.Rd | 2 man/simulate.gsmvar.Rd | 2 man/simulateGMVAR.Rd | 2 man/smart_covmat.Rd | 2 man/smart_ind.Rd | 6 man/sort_W_and_lambdas.Rd | 4 man/sort_and_standardize_alphas.Rd | 2 man/sort_components.Rd | 6 man/standard_errors.Rd | 6 man/stmvar_to_gstmvar.Rd | 2 man/stmvarpars_to_gstmvar.Rd | 4 man/swap_W_signs.Rd | 2 man/swap_parametrization.Rd | 2 man/unWvec.Rd | 2 man/uncond_moments.Rd | 2 man/uncond_moments_int.Rd | 6 man/update_numtols.Rd | 2 man/usamone.Rd |only man/warn_df.Rd | 2 vignettes/refs.bib | 2 98 files changed, 325 insertions(+), 269 deletions(-)
Title: Sensitivities of Prices of Financial Options
Description: Methods to calculate sensitivities of financial option prices for
European, Asian, American and Digital Options options in the Black Scholes
model, and in more general jump diffusion models. Classical formulas are
implemented for European options in the Black Scholes Model, as is presented in
Hull, J. C. (2017). Options, Futures, and Other Derivatives, Global Edition
(9th Edition). Pearson. In the case of Asian options, Malliavin Monte Carlo
Greeks are implemented, see Hudde, A. & Rüschendorf, L. (2016). European and
Asian Greeks for exponential Lévy processes. <arXiv:1603.00920>.
For American options, the Binomial Tree Method is implemented, as is presented
in Hull, J. C. (2017).
Author: Anselm Hudde [aut, cre] (<https://orcid.org/0000-0002-5652-2815>)
Maintainer: Anselm Hudde <anselmhudde@gmx.de>
Diff between greeks versions 0.4.0 dated 2021-11-16 and 0.4.1 dated 2021-12-14
DESCRIPTION | 18 +-- MD5 | 27 +++-- NAMESPACE | 30 ++--- R/Binomial_American_Greeks.R | 1 R/Malliavin_Asian_Greeks.R | 63 ++++-------- R/RcppExports.R | 16 +++ README.md |only man/Malliavin_Asian_Greeks.Rd | 216 +++++++++++++++++++++--------------------- src/RcppExports.cpp | 61 +++++++++++ src/calc_I.cpp |only src/calc_I_1.cpp | 6 - src/calc_I_2.cpp | 4 src/calc_I_3.cpp | 4 src/calc_XW.cpp |only src/make_BM.cpp |only src/rowCumsums.cpp |only tests |only 17 files changed, 257 insertions(+), 189 deletions(-)
Title: R Interface to COVID-19 Data Hub
Description: Provides a daily summary of COVID-19 cases, deaths, recovered, tests,
vaccinations, and hospitalizations for 230+ countries, 760+ regions,
and 12000+ administrative divisions of lower level.
Includes policy measures, mobility data, and geospatial identifiers.
Data source: COVID-19 Data Hub <https://covid19datahub.io>.
Author: Emanuele Guidotti [aut, cre] (<https://orcid.org/0000-0002-8961-6623>),
David Ardia [ctb] (<https://orcid.org/0000-0003-2823-782X>)
Maintainer: Emanuele Guidotti <emanuele.guidotti@unine.ch>
Diff between COVID19 versions 3.0.0 dated 2021-11-19 and 3.0.1 dated 2021-12-14
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/apple.R | 10 ++++++++++ R/covid19.R | 5 +++-- build/partial.rdb |binary man/covid19.Rd | 5 +++-- 7 files changed, 29 insertions(+), 13 deletions(-)
Title: Analyze Experimental High-Throughput (Omics) Data
Description: The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions.
Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc.
Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM) for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates).
Other functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc.
Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of large data-sets by combining very close values.
Many times large experimental datasets need some additional filtering, adequate functions are provided.
Batch reading (or writing) of sets of files and combining data to arrays is supported, too.
Convenient data normalization is supported in various different modes, parameter estimation via permutations or boot-strap as well as flexible testing of multiple pair-wise combinations using the framework of 'limma' is provided, too.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrMisc versions 1.7.0 dated 2021-10-28 and 1.8.0 dated 2021-12-14
DESCRIPTION | 6 MD5 | 26 - NAMESPACE | 2 R/appendNR.R |only R/filterNetw.R | 17 R/pairsAsPropensMatr.R |only R/readTabulatedBatch.R | 8 build/vignette.rds |binary inst/doc/wrMiscVignette1.R | 14 inst/doc/wrMiscVignette1.Rmd | 49 +- inst/doc/wrMiscVignette1.html | 945 ++++++++++++++++++++++-------------------- man/appendNR.Rd |only man/filterNetw.Rd | 5 man/pairsAsPropensMatr.Rd |only man/readTabulatedBatch.Rd | 14 vignettes/wrMiscVignette1.Rmd | 49 +- 16 files changed, 639 insertions(+), 496 deletions(-)
Title: Simulation of Simple and Complex Survival Data
Description: Simulation of simple and complex survival data including recurrent and multiple events and competing risks. See Moriña D, Navarro A. (2014) <doi:10.18637/jss.v059.i02> and Moriña D, Navarro A. (2017) <doi:10.1080/03610918.2016.1175621>.
Author: David Moriña Soler [aut, cre] (<https://orcid.org/0000-0001-5949-7443>),
Albert Navarro [aut]
Maintainer: David Moriña Soler <dmorina@ub.edu>
Diff between survsim versions 1.1.7 dated 2021-10-06 and 1.1.8 dated 2021-12-14
DESCRIPTION | 10 +++---- MD5 | 18 ++++++------ R/crisk.ncens.sim.R | 69 ++++++++++++++++++------------------------------- inst/CITATION | 20 ++++++++++++-- man/accum.Rd | 2 - man/crisk.sim.Rd | 2 - man/mult.ev.sim.Rd | 2 - man/rec.ev.sim.Rd | 2 - man/simple.surv.sim.Rd | 2 - man/survsim-package.Rd | 4 +- 10 files changed, 65 insertions(+), 66 deletions(-)
Title: Response Time Distributions
Description: Provides response time distributions (density/PDF,
distribution function/CDF, quantile function, and random
generation): (a) Ratcliff diffusion model (Ratcliff &
McKoon, 2008, <doi:10.1162/neco.2008.12-06-420>) based on C
code by Andreas and Jochen Voss and (b) linear ballistic
accumulator (LBA; Brown & Heathcote, 2008,
<doi:10.1016/j.cogpsych.2007.12.002>) with different
distributions underlying the drift rate.
Author: Henrik Singmann [aut, cre] (<https://orcid.org/0000-0002-4842-3657>),
Scott Brown [aut],
Matthew Gretton [aut],
Andrew Heathcote [aut],
Andreas Voss [ctb],
Jochen Voss [ctb],
Andrew Terry [ctb]
Maintainer: Henrik Singmann <singmann@gmail.com>
Diff between rtdists versions 0.11-2 dated 2020-03-06 and 0.11-4 dated 2021-12-14
DESCRIPTION | 6 MD5 | 86 - NAMESPACE | 94 - NEWS | 344 ++--- R/RcppExports.R | 38 R/deprecated.R | 54 R/diffusion.R | 989 +++++++------- R/lba.r | 1246 +++++++++--------- R/lba_race.R | 872 ++++++------ R/rr98-data.R | 182 +- R/rtdists-package.R | 50 R/single-lba.r | 1374 ++++++++++---------- R/speed_acc-data.R | 64 build/vignette.rds |binary inst/doc/reanalysis_rr98.R | 1406 ++++++++++---------- inst/doc/reanalysis_rr98.Rmd | 1870 +++++++++++++-------------- inst/doc/reanalysis_rr98.html | 2401 +++++++++++++++++------------------ inst/extdata/AUTHORS | 44 inst/extdata/lba-math.R | 344 ++--- man/Diffusion.Rd | 522 +++---- man/LBA-race.Rd | 316 ++-- man/LBA.Rd | 652 ++++----- man/deprecated.Rd | 50 man/rr98.Rd | 220 +-- man/rtdists-package.Rd | 60 man/single-LBA.Rd | 236 +-- man/speed_acc.Rd | 120 - src/RFastDM.cpp | 2 src/RcppExports.cpp | 5 tests/testthat.R | 6 tests/testthat/test-diffusion-bugs.R | 209 +-- tests/testthat/test-diffusion-math.R | 222 +-- tests/testthat/test-diffusion-rcpp.R | 268 +-- tests/testthat/test-diffusion.R | 340 ++-- tests/testthat/test-lba-bugs.R | 1360 +++++++++---------- tests/testthat/test-lba-math.R | 258 +-- tests/testthat/test-lba_basics.R | 1096 +++++++-------- tests/testthat/test-lba_input.R | 498 +++---- tests/testthat/test-lba_race-basic.R | 110 - tests/testthat/test-lba_race.R | 668 ++++----- tests/testthat/test-lba_race_input.R | 650 ++++----- tests/testthat/test-pdiffusion_rng.R | 288 ++-- tests/testthat/test-rrd.R | 84 - vignettes/reanalysis_rr98.Rmd | 1870 +++++++++++++-------------- 44 files changed, 10826 insertions(+), 10748 deletions(-)
Title: Utilities for the Forest Research Institute of the State
Baden-Wuerttemberg
Description: Miscellaneous utilities, tools and helper
functions for finding and searching files on disk, searching for and
removing R objects from the workspace.
These are utilities for packages
<https://CRAN.R-project.org/package=cleanr>,
<https://CRAN.R-project.org/package=document>,
<https://CRAN.R-project.org/package=fakemake>,
<https://CRAN.R-project.org/package=packager> and
<https://CRAN.R-project.org/package=rasciidoc>.
Does not import or depend on any third party package, but on core R
only (i.e. it may depend on packages with priority 'base').
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between fritools versions 2.5.0 dated 2021-12-07 and 3.0.0 dated 2021-12-14
DESCRIPTION | 6 MD5 | 50 ++++---- NAMESPACE | 1 NEWS.md | 20 +++ R/csv.R | 134 ++++++++++++++++++---- R/paths.R | 34 ++++- R/test_helpers.R | 10 + inst/NEWS.rd | 30 ++++ inst/runit_tests/runit-csv.R | 49 ++++---- inst/runit_tests/runit-paths.R | 40 ++++++ inst/source/R/csv.R | 134 ++++++++++++++++++---- inst/source/R/paths.R | 34 ++++- inst/source/R/test_helpers.R | 10 + inst/source/man/bulk_read_csv.Rd | 37 +++++- inst/source/man/bulk_write_csv.Rd | 1 inst/source/man/check_ascii_file.Rd |only inst/source/man/csv.Rd | 1 inst/source/man/csv2csv.Rd | 1 inst/source/man/is_running_on_fvafrcu_machines.Rd | 5 inst/source/man/paths.Rd | 10 + man/bulk_read_csv.Rd | 37 +++++- man/bulk_write_csv.Rd | 1 man/check_ascii_file.Rd |only man/csv.Rd | 1 man/csv2csv.Rd | 1 man/is_running_on_fvafrcu_machines.Rd | 5 man/paths.Rd | 10 + 27 files changed, 532 insertions(+), 130 deletions(-)
Title: Generation of Different Animated Christmas Cards
Description: Generation of different Christmas cards, most of them being
animated. Most of the cards can be generated in three languages (English,
Catalan and Spanish). The collection started in 2009.
Author: Jose Barrera-Gomez
Maintainer: Jose Barrera-Gomez <jose.barrera@isglobal.org>
Diff between christmas versions 1.0.0 dated 2019-12-13 and 1.1.0 dated 2021-12-14
christmas-1.0.0/christmas/R/xmas2008tree.R |only christmas-1.0.0/christmas/R/xmas2009caganer.R |only christmas-1.0.0/christmas/R/xmas2010text.R |only christmas-1.0.0/christmas/R/xmas2011health.R |only christmas-1.0.0/christmas/R/xmas2012snowkoch.R |only christmas-1.0.0/christmas/R/xmas2013neon.R |only christmas-1.0.0/christmas/R/xmas2014snowman.R |only christmas-1.0.0/christmas/R/xmas2015flag.R |only christmas-1.0.0/christmas/R/xmas2016epi.R |only christmas-1.0.0/christmas/R/xmas2017trees.R |only christmas-1.0.0/christmas/R/xmas2018galton.R |only christmas-1.0.0/christmas/R/xmas2019regression.R |only christmas-1.0.0/christmas/man/figures |only christmas-1.0.0/christmas/man/xmas2008tree.Rd |only christmas-1.0.0/christmas/man/xmas2009caganer.Rd |only christmas-1.0.0/christmas/man/xmas2010text.Rd |only christmas-1.0.0/christmas/man/xmas2011health.Rd |only christmas-1.0.0/christmas/man/xmas2012snowkoch.Rd |only christmas-1.0.0/christmas/man/xmas2013neon.Rd |only christmas-1.0.0/christmas/man/xmas2014snowman.Rd |only christmas-1.0.0/christmas/man/xmas2015flag.Rd |only christmas-1.0.0/christmas/man/xmas2016epi.Rd |only christmas-1.0.0/christmas/man/xmas2017trees.Rd |only christmas-1.0.0/christmas/man/xmas2018galton.Rd |only christmas-1.0.0/christmas/man/xmas2019regression.Rd |only christmas-1.1.0/christmas/DESCRIPTION | 19 +++--- christmas-1.1.0/christmas/MD5 | 63 ++++++++++---------- christmas-1.1.0/christmas/NAMESPACE | 25 ++++--- christmas-1.1.0/christmas/NEWS | 8 ++ christmas-1.1.0/christmas/R/christmas.R | 6 + christmas-1.1.0/christmas/R/xmascaganer.R |only christmas-1.1.0/christmas/R/xmasepitree.R |only christmas-1.1.0/christmas/R/xmasflag.R |only christmas-1.1.0/christmas/R/xmasgalton.R |only christmas-1.1.0/christmas/R/xmashealth.R |only christmas-1.1.0/christmas/R/xmasneon2014.R |only christmas-1.1.0/christmas/R/xmasregression.R |only christmas-1.1.0/christmas/R/xmassnowkoch.R |only christmas-1.1.0/christmas/R/xmassnowman.R |only christmas-1.1.0/christmas/R/xmastext.R |only christmas-1.1.0/christmas/R/xmastree.R |only christmas-1.1.0/christmas/R/xmastreeshape.R |only christmas-1.1.0/christmas/R/xmastreewire.R |only christmas-1.1.0/christmas/README.md | 2 christmas-1.1.0/christmas/man/christmas.Rd | 7 +- christmas-1.1.0/christmas/man/xmascaganer.Rd |only christmas-1.1.0/christmas/man/xmasepitree.Rd |only christmas-1.1.0/christmas/man/xmasflag.Rd |only christmas-1.1.0/christmas/man/xmasgalton.Rd |only christmas-1.1.0/christmas/man/xmashealth.Rd |only christmas-1.1.0/christmas/man/xmasneon2014.Rd |only christmas-1.1.0/christmas/man/xmasregression.Rd |only christmas-1.1.0/christmas/man/xmassnowkoch.Rd |only christmas-1.1.0/christmas/man/xmassnowman.Rd |only christmas-1.1.0/christmas/man/xmastext.Rd |only christmas-1.1.0/christmas/man/xmastree.Rd |only christmas-1.1.0/christmas/man/xmastreeshape.Rd |only christmas-1.1.0/christmas/man/xmastreewire.Rd |only 58 files changed, 73 insertions(+), 57 deletions(-)
Title: Manipulate SVG (Template) Files of Charts
Description: The purpose of this package is to manipulate SVG files that are templates of charts the user wants to produce.
In vector graphics one copes with x-/y-coordinates of elements (e.g. lines, rectangles, text). Their scale is often dependent on the program that is used to produce the graphics.
In applied statistics one usually has numeric values on a fixed scale (e.g. percentage values between 0 and 100) to show in a chart.
Basically, 'svgtools' transforms the statistical values into coordinates and widths/heights of the vector graphics.
This is done by stackedBar() for bar charts, by linesSymbols() for charts with lines and/or symbols (dot markers) and scatterSymbols() for scatterplots.
Author: Konrad Oberwimmer [aut, cre],
Christian Wimmer [aut],
Michael Bruneforth [ctb]
Maintainer: Konrad Oberwimmer <konrad.oberwimmer@iqs.gv.at>
Diff between svgtools versions 1.0.3 dated 2021-04-14 and 1.1.0 dated 2021-12-14
DESCRIPTION | 12 MD5 | 16 - NEWS | 14 R/svgtools.R | 715 +++++++++++++++++++++++++++++++++++++++++++++---- inst/doc/svgtools.html | 211 +------------- man/linesSymbols.Rd | 3 man/percentileBar.Rd | 114 +++---- man/referenceBar.Rd | 140 ++++----- man/scatterSymbols.Rd | 147 +++++----- 9 files changed, 907 insertions(+), 465 deletions(-)
Title: Import Files in the Triple-s (Standard Survey Structure) Format
Description: Tools to import survey files in the '.sss' (triple-s) format.
The package provides the function 'read.sss()' that reads the '.asc'
(or '.csv') and '.sss' files of a triple-s survey data file.
See also <https://www.triple-s.org/>.
Author: Andrie de Vries [aut, cre]
Maintainer: Andrie de Vries <apdevries@gmail.com>
Diff between sss versions 0.1-0 dated 2017-04-01 and 0.2.0 dated 2021-12-14
sss-0.1-0/sss/inst/doc/sss.Rnw |only sss-0.1-0/sss/inst/doc/sss.pdf |only sss-0.1-0/sss/man/getSSSrecord.Rd |only sss-0.1-0/sss/vignettes/sss.Rnw |only sss-0.1-0/sss/vignettes/sss.tex |only sss-0.2.0/sss/DESCRIPTION | 29 - sss-0.2.0/sss/MD5 | 74 +-- sss-0.2.0/sss/NAMESPACE | 1 sss-0.2.0/sss/NEWS | 43 + sss-0.2.0/sss/R/guess-asc-filename.R |only sss-0.2.0/sss/R/internal-csv.R | 33 - sss-0.2.0/sss/R/internal-xml.R | 73 +-- sss-0.2.0/sss/R/read-fwf.R | 37 - sss-0.2.0/sss/R/read-sss-metadata.R | 18 sss-0.2.0/sss/R/read-sss.R | 124 ++--- sss-0.2.0/sss/R/sss-package.R | 27 - sss-0.2.0/sss/build/vignette.rds |binary sss-0.2.0/sss/inst/WORDLIST |only sss-0.2.0/sss/inst/doc/sss.R | 40 - sss-0.2.0/sss/inst/doc/sss.Rmd |only sss-0.2.0/sss/inst/doc/sss.html |only sss-0.2.0/sss/inst/examples/example-read-sss.R | 10 sss-0.2.0/sss/inst/sampledata/sample-3.dat | 596 ------------------------- sss-0.2.0/sss/inst/sampledata/sample-4.asc |only sss-0.2.0/sss/inst/sampledata/sample-4.sss |only sss-0.2.0/sss/inst/sampledata/sample-5.asc |only sss-0.2.0/sss/inst/sampledata/sample-5.sss |only sss-0.2.0/sss/man/addQtext.Rd |only sss-0.2.0/sss/man/changeValues.Rd |only sss-0.2.0/sss/man/fast.read.fwf.Rd | 28 - sss-0.2.0/sss/man/figures |only sss-0.2.0/sss/man/getSSScodes.Rd |only sss-0.2.0/sss/man/namesMultiple.Rd |only sss-0.2.0/sss/man/parseSSSmetadata.Rd | 6 sss-0.2.0/sss/man/read.sss.Rd | 54 +- sss-0.2.0/sss/man/readSSSdata.Rd | 6 sss-0.2.0/sss/man/readSSSmetadata.Rd | 6 sss-0.2.0/sss/man/repN.Rd |only sss-0.2.0/sss/man/sss-package.Rd | 23 sss-0.2.0/sss/tests/spelling.R |only sss-0.2.0/sss/tests/testthat.R | 8 sss-0.2.0/sss/tests/testthat/test-1-metadata.R | 6 sss-0.2.0/sss/tests/testthat/test-2-read-fwf.R | 4 sss-0.2.0/sss/tests/testthat/test-3-sss.R | 4 sss-0.2.0/sss/tests/testthat/test-4-sample-2.R | 15 sss-0.2.0/sss/tests/testthat/test-5-sample-3.R | 10 sss-0.2.0/sss/tests/testthat/test-6-sample-4.R |only sss-0.2.0/sss/tests/testthat/test-7-sample-5.R |only sss-0.2.0/sss/vignettes/sss.Rmd |only 49 files changed, 405 insertions(+), 870 deletions(-)
Title: R Interface to 'FishBase'
Description: A programmatic interface to 'FishBase', re-written
based on an accompanying 'RESTful' API. Access tables describing over 30,000
species of fish, their biology, ecology, morphology, and more. This package also
supports experimental access to 'SeaLifeBase' data, which contains
nearly 200,000 species records for all types of aquatic life not covered by
'FishBase.'
Author: Carl Boettiger [cre, aut] (<https://orcid.org/0000-0002-1642-628X>),
Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>),
Duncan Temple Lang [aut],
Peter Wainwright [aut],
Kevin Cazelles [ctb] (<https://orcid.org/0000-0001-6619-9874>)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between rfishbase versions 3.1.10 dated 2021-11-10 and 4.0.0 dated 2021-12-14
rfishbase-3.1.10/rfishbase/R/list_fields.R |only rfishbase-3.1.10/rfishbase/R/sysdata.rda |only rfishbase-3.1.10/rfishbase/R/teardown-tests.R |only rfishbase-3.1.10/rfishbase/build |only rfishbase-3.1.10/rfishbase/data/fishbase.rda |only rfishbase-3.1.10/rfishbase/data/sealifebase.rda |only rfishbase-3.1.10/rfishbase/inst/doc |only rfishbase-3.1.10/rfishbase/man/db_delete.Rd |only rfishbase-3.1.10/rfishbase/man/default_db.Rd |only rfishbase-3.1.10/rfishbase/man/list_fields.Rd |only rfishbase-3.1.10/rfishbase/tests/testthat/test-db_create.R |only rfishbase-3.1.10/rfishbase/tests/testthat/test_list_fields.R |only rfishbase-3.1.10/rfishbase/vignettes |only rfishbase-4.0.0/rfishbase/DESCRIPTION | 13 rfishbase-4.0.0/rfishbase/MD5 | 151 +- rfishbase-4.0.0/rfishbase/NAMESPACE | 22 rfishbase-4.0.0/rfishbase/NEWS.md | 8 rfishbase-4.0.0/rfishbase/R/00-endpoint.R | 47 rfishbase-4.0.0/rfishbase/R/available_releases.R |only rfishbase-4.0.0/rfishbase/R/distribution.R | 36 rfishbase-4.0.0/rfishbase/R/fb_tbl.R | 108 - rfishbase-4.0.0/rfishbase/R/load_taxa.R | 20 rfishbase-4.0.0/rfishbase/R/local_db.R | 144 -- rfishbase-4.0.0/rfishbase/R/morpho_physio.R | 10 rfishbase-4.0.0/rfishbase/R/parquet_db.R |only rfishbase-4.0.0/rfishbase/R/population_dynamics.R | 10 rfishbase-4.0.0/rfishbase/R/refs.R | 2 rfishbase-4.0.0/rfishbase/R/reproduction.R | 20 rfishbase-4.0.0/rfishbase/R/rstudio_pane.R |only rfishbase-4.0.0/rfishbase/R/species.R | 4 rfishbase-4.0.0/rfishbase/R/synonyms.R | 10 rfishbase-4.0.0/rfishbase/R/trophic_ecology.R | 32 rfishbase-4.0.0/rfishbase/README.md | 571 ++-------- rfishbase-4.0.0/rfishbase/inst/WORDLIST | 16 rfishbase-4.0.0/rfishbase/inst/img |only rfishbase-4.0.0/rfishbase/inst/prov |only rfishbase-4.0.0/rfishbase/man/available_releases.Rd | 7 rfishbase-4.0.0/rfishbase/man/brains.Rd | 2 rfishbase-4.0.0/rfishbase/man/c_code.Rd | 4 rfishbase-4.0.0/rfishbase/man/country.Rd | 6 rfishbase-4.0.0/rfishbase/man/countrysub.Rd | 6 rfishbase-4.0.0/rfishbase/man/countrysubref.Rd | 4 rfishbase-4.0.0/rfishbase/man/db_dir.Rd |only rfishbase-4.0.0/rfishbase/man/diet.Rd | 6 rfishbase-4.0.0/rfishbase/man/diet_items.Rd | 27 rfishbase-4.0.0/rfishbase/man/distribution.Rd | 4 rfishbase-4.0.0/rfishbase/man/ecology.Rd | 3 rfishbase-4.0.0/rfishbase/man/ecosystem.Rd | 4 rfishbase-4.0.0/rfishbase/man/estimate.Rd | 4 rfishbase-4.0.0/rfishbase/man/fb_conn.Rd |only rfishbase-4.0.0/rfishbase/man/fb_import.Rd |only rfishbase-4.0.0/rfishbase/man/fb_tables.Rd |only rfishbase-4.0.0/rfishbase/man/fb_tbl.Rd |only rfishbase-4.0.0/rfishbase/man/fecundity.Rd | 6 rfishbase-4.0.0/rfishbase/man/fishbase_pane.Rd |only rfishbase-4.0.0/rfishbase/man/fooditems.Rd | 4 rfishbase-4.0.0/rfishbase/man/genetics.Rd | 4 rfishbase-4.0.0/rfishbase/man/introductions.Rd | 6 rfishbase-4.0.0/rfishbase/man/larvae.Rd | 6 rfishbase-4.0.0/rfishbase/man/length_freq.Rd | 4 rfishbase-4.0.0/rfishbase/man/length_length.Rd | 4 rfishbase-4.0.0/rfishbase/man/length_weight.Rd | 4 rfishbase-4.0.0/rfishbase/man/load_taxa.Rd | 2 rfishbase-4.0.0/rfishbase/man/maturity.Rd | 6 rfishbase-4.0.0/rfishbase/man/morphology.Rd | 2 rfishbase-4.0.0/rfishbase/man/morphometrics.Rd | 4 rfishbase-4.0.0/rfishbase/man/oxygen.Rd | 2 rfishbase-4.0.0/rfishbase/man/popchar.Rd | 4 rfishbase-4.0.0/rfishbase/man/popgrowth.Rd | 4 rfishbase-4.0.0/rfishbase/man/popqb.Rd | 4 rfishbase-4.0.0/rfishbase/man/predators.Rd | 4 rfishbase-4.0.0/rfishbase/man/ration.Rd | 4 rfishbase-4.0.0/rfishbase/man/references.Rd | 2 rfishbase-4.0.0/rfishbase/man/reproduction.Rd | 6 rfishbase-4.0.0/rfishbase/man/spawning.Rd | 6 rfishbase-4.0.0/rfishbase/man/species.Rd | 4 rfishbase-4.0.0/rfishbase/man/species_by_ecosystem.Rd | 4 rfishbase-4.0.0/rfishbase/man/speed.Rd | 4 rfishbase-4.0.0/rfishbase/man/stocks.Rd | 6 rfishbase-4.0.0/rfishbase/man/swimming.Rd | 6 rfishbase-4.0.0/rfishbase/man/validate_names.Rd | 3 rfishbase-4.0.0/rfishbase/tests/testthat.R | 3 rfishbase-4.0.0/rfishbase/tests/testthat/setup-test_db.R | 2 rfishbase-4.0.0/rfishbase/tests/testthat/teardown-tests.R |only rfishbase-4.0.0/rfishbase/tests/testthat/test_load_taxa.R | 4 rfishbase-4.0.0/rfishbase/tests/testthat/test_synonyms.R | 3 rfishbase-4.0.0/rfishbase/tests/testthat/test_trophic_ecology.R | 4 87 files changed, 511 insertions(+), 921 deletions(-)
Title: Pre-Commit Hooks
Description: Useful git hooks for R building on top of the multi-language
framework 'pre-commit' for hook management. This package provides git
hooks for common tasks like formatting files with 'styler' or spell
checking as well as wrapper functions to access the 'pre-commit'
executable.
Author: Lorenz Walthert
Maintainer: Lorenz Walthert <lorenz.walthert@icloud.com>
Diff between precommit versions 0.2.0 dated 2021-12-01 and 0.2.1 dated 2021-12-14
precommit-0.2.0/precommit/inst/bin |only precommit-0.2.0/precommit/inst/consistent-release-tag |only precommit-0.2.0/precommit/inst/hooks-config-to-inst |only precommit-0.2.0/precommit/inst/spell-check-exclude-to-config |only precommit-0.2.0/precommit/inst/spell-check-ordered-exclude.R |only precommit-0.2.0/precommit/man/has_persistent_R.cache.Rd |only precommit-0.2.0/precommit/tests/testthat/test-cache.R |only precommit-0.2.1/precommit/DESCRIPTION | 8 precommit-0.2.1/precommit/MD5 | 76 ++--- precommit-0.2.1/precommit/NEWS.md | 39 ++ precommit-0.2.1/precommit/R/cache.R | 48 --- precommit-0.2.1/precommit/R/exec.R | 18 + precommit-0.2.1/precommit/R/release.R | 2 precommit-0.2.1/precommit/R/roxygen2.R | 30 -- precommit-0.2.1/precommit/R/setup.R | 113 ++++++-- precommit-0.2.1/precommit/R/testing.R | 9 precommit-0.2.1/precommit/R/utils.R | 29 ++ precommit-0.2.1/precommit/inst/doc/available-hooks.Rmd | 25 - precommit-0.2.1/precommit/inst/doc/available-hooks.html | 19 - precommit-0.2.1/precommit/inst/doc/ci.Rmd | 84 ++++-- precommit-0.2.1/precommit/inst/doc/ci.html | 137 +++++++++- precommit-0.2.1/precommit/inst/hooks/exported/deps-in-desc.R | 4 precommit-0.2.1/precommit/inst/hooks/exported/parsable-R.R | 6 precommit-0.2.1/precommit/inst/hooks/exported/style-files.R | 22 + precommit-0.2.1/precommit/inst/pre-commit-config-pkg.yaml | 2 precommit-0.2.1/precommit/inst/pre-commit-config-proj.yaml | 2 precommit-0.2.1/precommit/man/git_init.Rd |only precommit-0.2.1/precommit/man/may_require_permanent_cache.Rd | 11 precommit-0.2.1/precommit/man/rev_read.Rd |only precommit-0.2.1/precommit/man/snippet_generate.Rd | 2 precommit-0.2.1/precommit/man/use_ci.Rd | 4 precommit-0.2.1/precommit/man/use_precommit.Rd | 7 precommit-0.2.1/precommit/tests/testthat/in/README.Rmd | 7 precommit-0.2.1/precommit/tests/testthat/test-conda.R | 4 precommit-0.2.1/precommit/tests/testthat/test-hook-roxygenize.R | 8 precommit-0.2.1/precommit/tests/testthat/test-hooks.R | 36 ++ precommit-0.2.1/precommit/tests/testthat/test-setup.R | 83 +++++- precommit-0.2.1/precommit/vignettes/available-hooks.Rmd | 25 - precommit-0.2.1/precommit/vignettes/ci.Rmd | 84 ++++-- 39 files changed, 677 insertions(+), 267 deletions(-)
Title: Read, Write and Edit xlsx Files
Description: Simplifies the creation of Excel .xlsx files by providing a
high level interface to writing, styling and editing worksheets.
Through the use of 'Rcpp', read/write times are comparable to the
'xlsx' and 'XLConnect' packages with the added benefit of removing the
dependency on Java.
Author: Philipp Schauberger [aut, cre],
Alexander Walker [aut],
Luca Braglia [ctb],
Joshua Sturm [ctb],
Jan Marvin Garbuszus [ctb],
Jordan Mark Barbone [ctb] (<https://orcid.org/0000-0001-9788-3628>)
Maintainer: Philipp Schauberger <philipp@schauberger.co.at>
Diff between openxlsx versions 4.2.4 dated 2021-06-16 and 4.2.5 dated 2021-12-14
openxlsx-4.2.4/openxlsx/man/createNamedRegion.Rd |only openxlsx-4.2.4/openxlsx/tests/testthat/test-style_replacing.R |only openxlsx-4.2.5/openxlsx/DESCRIPTION | 30 openxlsx-4.2.5/openxlsx/LICENSE | 4 openxlsx-4.2.5/openxlsx/MD5 | 375 openxlsx-4.2.5/openxlsx/NAMESPACE | 218 openxlsx-4.2.5/openxlsx/NEWS.md | 963 - openxlsx-4.2.5/openxlsx/R/CommentClass.R | 495 openxlsx-4.2.5/openxlsx/R/HyperlinkClass.R | 218 openxlsx-4.2.5/openxlsx/R/RcppExports.R | 288 openxlsx-4.2.5/openxlsx/R/StyleClass.R | 586 openxlsx-4.2.5/openxlsx/R/WorkbookClass.R | 8713 ++++----- openxlsx-4.2.5/openxlsx/R/asserts.R | 176 openxlsx-4.2.5/openxlsx/R/baseXML.R | 970 - openxlsx-4.2.5/openxlsx/R/borderFunctions.R | 1192 - openxlsx-4.2.5/openxlsx/R/build_workbook.R | 254 openxlsx-4.2.5/openxlsx/R/chartsheet_class.R | 110 openxlsx-4.2.5/openxlsx/R/class_definitions.R | 322 openxlsx-4.2.5/openxlsx/R/conditional_formatting.R | 1305 - openxlsx-4.2.5/openxlsx/R/data-fontSizeLookupTables.R | 20 openxlsx-4.2.5/openxlsx/R/helperFunctions.R | 1950 +- openxlsx-4.2.5/openxlsx/R/loadWorkbook.R | 2085 +- openxlsx-4.2.5/openxlsx/R/onUnload.R | 6 openxlsx-4.2.5/openxlsx/R/openXL.R | 211 openxlsx-4.2.5/openxlsx/R/openxlsx-package.R | 6 openxlsx-4.2.5/openxlsx/R/openxlsx.R | 333 openxlsx-4.2.5/openxlsx/R/openxlsxCoerce.R | 471 openxlsx-4.2.5/openxlsx/R/readWorkbook.R | 1216 - openxlsx-4.2.5/openxlsx/R/sheet_data_class.R | 204 openxlsx-4.2.5/openxlsx/R/utils.R | 110 openxlsx-4.2.5/openxlsx/R/workbook_column_widths.R | 394 openxlsx-4.2.5/openxlsx/R/workbook_read_workbook.R | 722 openxlsx-4.2.5/openxlsx/R/workbook_write_data.R | 610 openxlsx-4.2.5/openxlsx/R/worksheet_class.R | 552 openxlsx-4.2.5/openxlsx/R/wrappers.R | 9334 ++++------ openxlsx-4.2.5/openxlsx/R/writeData.R | 1104 - openxlsx-4.2.5/openxlsx/R/writeDataTable.R | 647 openxlsx-4.2.5/openxlsx/R/writexlsx.R | 194 openxlsx-4.2.5/openxlsx/R/zzz.R | 14 openxlsx-4.2.5/openxlsx/README.md | 92 openxlsx-4.2.5/openxlsx/build/vignette.rds 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insertions(+), 32847 deletions(-)
Title: R Interface to 'Mapbox' Web Services
Description: Includes support for 'Mapbox' Navigation APIs, including directions,
isochrones, and route optimization; the Search API for forward and reverse geocoding;
the Maps API for interacting with 'Mapbox' vector tilesets and visualizing
'Mapbox' maps in R; and the 'tippecanoe' tile-generation utility.
See <https://docs.mapbox.com/api/> for more information about the 'Mapbox' APIs.
Author: Kyle Walker [aut, cre]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between mapboxapi versions 0.3 dated 2021-11-08 and 0.3.1 dated 2021-12-14
DESCRIPTION | 8 +- LICENSE | 2 MD5 | 8 +- R/navigation.R | 192 +++++++++++++++++++++++++++++++++++++++------------- man/mb_isochrone.Rd | 9 +- 5 files changed, 160 insertions(+), 59 deletions(-)
Title: Flexible and Reproducible Label Designs
Description: An open-source R package to deploys flexible and reproducible labels using layers.
The 'huito' package is part of the 'inkaverse' project for developing different procedures and
tools used in plant science and experimental designs.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] (<https://orcid.org/0000-0002-0714-669X>),
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flavjack@gmail.com>
Diff between huito versions 0.1.0 dated 2021-12-01 and 0.1.1 dated 2021-12-14
DESCRIPTION | 20 ++++---- MD5 | 54 +++++++++++---------- NEWS.md | 8 +++ R/image_import.R | 2 R/include_image.R | 2 R/label_print.R | 53 +++++++++++---------- README.md | 6 ++ build/vignette.rds |binary inst/doc/germinar.R |only inst/doc/germinar.Rmd |only inst/doc/germinar.html |only inst/doc/huito.R | 84 +-------------------------------- inst/doc/huito.Rmd | 89 +++-------------------------------- inst/doc/huito.html | 20 +++++--- inst/doc/labels.R | 6 +- inst/doc/labels.Rmd | 10 ++-- inst/doc/labels.html | 102 ++++++++++++++++++++--------------------- inst/doc/stickers.R | 23 +++++---- inst/doc/stickers.Rmd | 36 +++++++++----- inst/doc/stickers.html | 46 +++++++++++------- man/image_import.Rd | 2 man/include_image.Rd | 2 man/label_print.Rd | 21 ++++---- vignettes/germinar.Rmd |only vignettes/huito.Rmd | 89 +++-------------------------------- vignettes/huito.zip |binary vignettes/huito/_doc.Rmd | 14 +---- vignettes/huito/huito-intro.md | 14 +---- vignettes/labels.Rmd | 10 ++-- vignettes/stickers.Rmd | 36 +++++++++----- 30 files changed, 298 insertions(+), 451 deletions(-)
Title: HTTP and WebSocket Server Library
Description: Provides low-level socket and protocol support for handling
HTTP and WebSocket requests directly from within R. It is primarily
intended as a building block for other packages, rather than making it
particularly easy to create complete web applications using httpuv alone.
httpuv is built on top of the libuv and http-parser C libraries, both of
which were developed by Joyent, Inc. (See LICENSE file for libuv and
http-parser license information.)
Author: Joe Cheng [aut],
Winston Chang [aut, cre],
RStudio, PBC [cph],
Hector Corrada Bravo [ctb],
Jeroen Ooms [ctb],
Andrzej Krzemienski [cph] (optional.hpp)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between httpuv versions 1.6.3 dated 2021-09-09 and 1.6.4 dated 2021-12-14
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS.md | 7 +++++++ README.md | 2 +- src/Makevars | 32 +++++++++++++++++++++++--------- 5 files changed, 40 insertions(+), 19 deletions(-)
Title: Resampling Methods for Triangular and Trapezoidal Fuzzy Numbers
Description: The classical (i.e. Efron's, see Efron and Tibshirani (1994, ISBN:978-0412042317) "An Introduction to the Bootstrap") bootstrap is widely used for both the real (i.e. "crisp") and fuzzy data.
The main aim of the algorithms implemented in this package is to overcome a problem with repetition of a few distinct values and to create fuzzy numbers, which are "similar" (but not the same) to values from the initial sample.
To do this, different characteristics of triangular/trapezoidal numbers are kept (like the value, the ambiguity, etc., see Grzegorzewski et al. <doi:10.2991/eusflat-19.2019.68>, Grzegorzewski et al. (2020) <doi:10.2991/ijcis.d.201012.003>, Grzegorzewski et al. (2020) <doi:10.34768/amcs-2020-0022>, Romaniuk and Hryniewicz (2019) <doi:10.1007/s00500-018-3251-5>).
Some additional procedures related to these resampling methods are also provided,
like calculation of the Bertoluzza et al.'s distance (aka the mid/spread distance, see Bertoluzza et al. (1995) "On a new class of distances between fuzzy numbers")
and estimation of the p-value of the one-sample bootstrapped test for the mean (see Lubiano et al. (2016, <doi:10.1016/j.ejor.2015.11.016>)).
Additionally, there are procedures which randomly generate trapezoidal fuzzy numbers using some well-known statistical distributions.
Author: Maciej Romaniuk [cre],
Przemyslaw Grzegorzewski [aut],
Olgierd Hryniewicz [aut]
Maintainer: Maciej Romaniuk <mroman@ibspan.waw.pl>
Diff between FuzzyResampling versions 0.3.0 dated 2021-11-22 and 0.3.1 dated 2021-12-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/SEResamplingMean.R | 4 ++++ README.md | 33 +++++++++++++++++---------------- 5 files changed, 33 insertions(+), 23 deletions(-)
More information about FuzzyResampling at CRAN
Permanent link
Title: Lyrics and Song Data for Taylor Swift's Discography
Description: A comprehensive resource for data on Taylor Swift songs. Data is
included for all officially released studio albums, extended plays (EPs),
and individual singles are included. Data comes from
'Genius' (lyrics) and 'Spotify' (song characteristics). Additional functions
are included for easily creating data visualizations with color palettes
inspired by Taylor Swift's album covers.
Author: W. Jake Thompson [aut, cre, cph]
(<https://orcid.org/0000-0001-7339-0300>)
Maintainer: W. Jake Thompson <wjakethompson@gmail.com>
Diff between taylor versions 0.2.1 dated 2021-09-23 and 1.0.0 dated 2021-12-14
DESCRIPTION | 11 MD5 | 71 ++- NAMESPACE | 4 NEWS.md | 57 ++- R/data-checks.R | 27 - R/palette.R | 52 +- R/taylor-album-palettes.R | 7 R/taylor-package.R | 1 README.md | 65 +-- data/taylor_album_songs.rda |binary data/taylor_albums.rda |binary data/taylor_all_songs.rda |binary inst/WORDLIST | 2 inst/album-covers/red-tv.jpeg |only man/album_levels.Rd | 2 man/album_palettes.Rd | 4 man/color_palette.Rd | 15 man/figures/lifecycle-archived.svg |only man/figures/lifecycle-defunct.svg |only man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-maturing.svg |only man/figures/lifecycle-questioning.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/figures/logo.png |binary man/scale_albums.Rd | 6 man/taylor_album_songs.Rd | 2 man/taylor_albums.Rd | 2 man/taylor_all_songs.Rd | 2 tests/testthat/_snaps/ggplot2-color-scales/albums-correct-factor.svg | 186 +++++----- tests/testthat/_snaps/ggplot2-color-scales/albums-no-factor.svg | 186 +++++----- tests/testthat/_snaps/ggplot2-color-scales/albums-random-factor.svg | 186 +++++----- tests/testthat/_snaps/ggplot2-color-scales/albums-reverse-factor.svg | 186 +++++----- tests/testthat/_snaps/ggplot2-color-scales/red-tv-color-b.svg |only tests/testthat/_snaps/ggplot2-color-scales/red-tv-color-c.svg |only tests/testthat/_snaps/ggplot2-color-scales/red-tv-color-d.svg |only tests/testthat/_snaps/ggplot2-color-scales/red-tv-fill-b.svg |only tests/testthat/_snaps/ggplot2-color-scales/red-tv-fill-c.svg |only tests/testthat/_snaps/ggplot2-color-scales/red-tv-fill-d.svg |only tests/testthat/test-data-checks.R | 36 - tests/testthat/test-deprecation.R |only tests/testthat/test-ggplot2-color-scales.R | 24 + tests/testthat/test-palette.R | 55 ++ tests/testthat/test-print-palette-names.txt |only 45 files changed, 691 insertions(+), 498 deletions(-)
Title: Inbreeding-Purging Estimation in Pedigreed Populations
Description: Inbreeding-purging analysis of pedigreed populations, including the computation of the inbreeding coefficient, partial, ancestral and purged inbreeding coefficients, and measures of the opportunity of purging related to the individual reduction of inbreeding load.
In addition, functions to calculate the effective population size and other parameters relevant to population genetics are included.
See López-Cortegano E. (2021) <doi:10.1093/bioinformatics/btab599>.
Author: Eugenio López-Cortegano [aut, cre]
(<https://orcid.org/0000-0001-6914-6305>)
Maintainer: Eugenio López-Cortegano <elcortegano@gmail.com>
Diff between purgeR versions 1.3 dated 2021-08-18 and 1.4 dated 2021-12-14
DESCRIPTION | 8 +++--- MD5 | 51 ++++++++++++++++++++--------------------- NAMESPACE | 1 NEWS.md | 5 ++++ R/check.R | 2 + R/data.R | 8 +++--- R/expected.R | 26 +++++++++++++++++--- R/import.R |only R/sort.R | 2 - build/vignette.rds |binary data/arrui.rda |binary data/atlas.rda |binary data/dama.rda |binary data/darwin.rda |binary data/dorcas.rda |binary inst/doc/ip.Rmd | 2 - inst/doc/ip.html | 14 +++++------ inst/doc/purgeR-tutorial.Rmd | 2 - inst/doc/purgeR-tutorial.html | 16 ++++++------ man/arrui.Rd | 2 - man/atlas.Rd | 2 - man/dama.Rd | 2 - man/dorcas.Rd | 2 - man/exp_g.Rd | 6 ++++ tests/testthat/test_expected.R | 2 + vignettes/ip.Rmd | 2 - vignettes/purgeR-tutorial.Rmd | 2 - 27 files changed, 95 insertions(+), 62 deletions(-)
Title: Bayesian Meta-Analysis and Network Meta-Analysis
Description: Contains functions performing Bayesian inference for meta-analytic and network meta-analytic models through Markov chain Monte Carlo algorithm. Currently, the package implements Hui Yao, Sungduk Kim, Ming-Hui Chen, Joseph G. Ibrahim, Arvind K. Shah, and Jianxin Lin (2015) <doi:10.1080/01621459.2015.1006065> and Hao Li, Daeyoung Lim, Ming-Hui Chen, Joseph G. Ibrahim, Sungduk Kim, Arvind K. Shah, Jianxin Lin (2021) <doi:10.1002/sim.8983>. For maximal computational efficiency, the Markov chain Monte Carlo samplers for each model, written in C++, are fine-tuned. This software has been developed under the auspices of the National Institutes of Health and Merck & Co., Inc., Kenilworth, NJ, USA.
Author: Daeyoung Lim [aut, cre],
Ming-Hui Chen [ctb],
Sungduk Kim [ctb],
Joseph Ibrahim [ctb],
Arvind Shah [ctb],
Jianxin Lin [ctb]
Maintainer: Daeyoung Lim <daeyoung.lim@uconn.edu>
Diff between metapack versions 0.1.4 dated 2021-10-20 and 0.1.5 dated 2021-12-14
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 38 ++++++++++++++++++++++---------------- inst/doc/intro-to-metapack.html | 4 ++-- src/fmodel3.cpp | 13 +++++++------ src/fmodel3pp.cpp | 13 +++++++------ src/loglik_POCov.cpp | 6 ++++-- 7 files changed, 52 insertions(+), 42 deletions(-)
Title: Integrating Multiple Biomarker Responses in Aquatic Organisms
using Effect Size, Statistical Uncertainty, and Ecological
Relevance
Description: Compute and visualize the ps-index, a new integrated index for
multiple biomarker responses, as described in Pham & Sokolova
(2021, unpublished).
Author: Duy Nghia Pham [aut, cre] (<https://orcid.org/0000-0003-1349-1710>),
Inna M. Sokolova [aut] (<https://orcid.org/0000-0002-2068-4302>)
Maintainer: Duy Nghia Pham <nghiapham@yandex.com>
Diff between mbRes versions 0.1.1 dated 2021-09-02 and 0.1.2 dated 2021-12-14
DESCRIPTION | 13 ++++++++----- MD5 | 20 +++++++++++--------- NAMESPACE | 31 +++++++++---------------------- R/compare.R |only R/ggbar.R | 3 ++- R/mbRes-package.R | 23 ++++++++++++----------- R/mbr.R | 2 +- build/partial.rdb |binary data/sokolova2021.RData |binary man/compare.Rd |only man/mbRes-package.Rd | 8 +++++--- man/mbr.Rd | 2 +- 12 files changed, 49 insertions(+), 53 deletions(-)
Title: Item Pool Visualization
Description: Generate plots based on the Item Pool Visualization concept for
latent constructs. Item Pool Visualizations are used to display the
conceptual structure of a set of items (self-report or psychometric).
Dantlgraber, Stieger, & Reips (2019) <doi:10.1177/2059799119884283>.
Author: Nils Petras [aut, cre],
Michael Dantlgraber [aut],
Ulf-Dietrich Reips [ctb],
Matthias Bannert [ctb]
Maintainer: Nils Petras <nils.petras@mailbox.org>
Diff between IPV versions 0.1.1 dated 2020-03-04 and 0.2.0 dated 2021-12-14
DESCRIPTION | 15 MD5 | 91 +- NAMESPACE | 5 NEWS.md | 26 R/IPV.R | 50 - R/coord_facets.R | 44 - R/coord_items.R | 41 R/data.R | 20 R/facet_chart.R | 132 ++- R/input_excel.R | 56 + R/input_manual_process.R | 11 R/ipv_est.R |only R/item_chart.R | 91 ++ R/item_overview.R |only R/nested_chart.R | 365 ++++++-- R/rename.R |only README.md | 65 - build/vignette.rds |binary data/DSSEI.rda |binary data/HEXACO.rda |only data/SMTQ.rda |binary data/self_confidence.rda |binary inst/doc/ipv-vignette.R | 355 ++++---- inst/doc/ipv-vignette.Rmd | 609 +++++++++----- inst/doc/ipv-vignette.html | 1625 +++++++++++++++++++++++---------------- man/DSSEI.Rd | 166 ++- man/HEXACO.Rd |only man/IPV.Rd | 100 +- man/SMTQ.Rd | 134 +-- man/coord_facets.Rd | 123 +- man/coord_items.Rd | 131 +-- man/coord_nested.Rd | 226 ++--- man/cormat.Rd |only man/facet_chart.Rd | 280 +++--- man/figures/README-example-1.png |binary man/floads.Rd |only man/get_names.Rd |only man/get_xarrows.Rd |only man/ind_lav.Rd |only man/input_excel.Rd | 36 man/ipv_est.Rd |only man/item_chart.Rd | 309 ++++--- man/item_overview.Rd |only man/nested_chart.Rd | 539 +++++++----- man/plot_facets.Rd | 173 ++-- man/plot_items.Rd | 189 ++-- man/plot_nested.Rd | 251 +++--- man/rename.Rd |only man/rename_est.Rd |only man/rename_raw.Rd |only man/rename_raw_simple.Rd |only man/rename_simple.Rd |only man/rename_xarrow.Rd |only man/self_confidence.Rd | 130 +-- man/write_IPV_syntax.Rd |only vignettes/ipv-vignette.Rmd | 609 +++++++++----- 56 files changed, 4247 insertions(+), 2750 deletions(-)
Title: CRAN Task Views
Description: Infrastructure for task views to CRAN-style repositories: Querying task views and installing the associated
packages (client-side tools), generating HTML pages and storing task view information in the repository
(server-side tools).
Author: Achim Zeileis [aut, cre] (<https://orcid.org/0000-0003-0918-3766>),
Kurt Hornik [aut] (<https://orcid.org/0000-0003-4198-9911>)
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between ctv versions 0.8-5 dated 2018-05-17 and 0.9-0 dated 2021-12-14
ctv-0.8-5/ctv/NEWS |only ctv-0.8-5/ctv/inst/ctv/Bayesian.ctv |only ctv-0.8-5/ctv/inst/ctv/ChemPhys.ctv |only ctv-0.8-5/ctv/inst/ctv/ClinicalTrials.ctv |only ctv-0.8-5/ctv/inst/ctv/Cluster.ctv |only ctv-0.8-5/ctv/inst/ctv/DifferentialEquations.ctv |only ctv-0.8-5/ctv/inst/ctv/Distributions.ctv |only ctv-0.8-5/ctv/inst/ctv/Environmetrics.ctv |only ctv-0.8-5/ctv/inst/ctv/ExperimentalDesign.ctv |only ctv-0.8-5/ctv/inst/ctv/ExtremeValue.ctv |only ctv-0.8-5/ctv/inst/ctv/Finance.ctv |only ctv-0.8-5/ctv/inst/ctv/FunctionalData.ctv |only ctv-0.8-5/ctv/inst/ctv/Genetics.ctv |only ctv-0.8-5/ctv/inst/ctv/Graphics.ctv |only ctv-0.8-5/ctv/inst/ctv/HighPerformanceComputing.ctv |only ctv-0.8-5/ctv/inst/ctv/MachineLearning.ctv |only ctv-0.8-5/ctv/inst/ctv/MedicalImaging.ctv |only ctv-0.8-5/ctv/inst/ctv/MetaAnalysis.ctv |only ctv-0.8-5/ctv/inst/ctv/ModelDeployment.ctv |only ctv-0.8-5/ctv/inst/ctv/Multivariate.ctv |only ctv-0.8-5/ctv/inst/ctv/NaturalLanguageProcessing.ctv |only ctv-0.8-5/ctv/inst/ctv/NumericalMathematics.ctv |only ctv-0.8-5/ctv/inst/ctv/OfficialStatistics.ctv |only ctv-0.8-5/ctv/inst/ctv/Optimization.ctv |only ctv-0.8-5/ctv/inst/ctv/Pharmacokinetics.ctv |only ctv-0.8-5/ctv/inst/ctv/Phylogenetics.ctv |only ctv-0.8-5/ctv/inst/ctv/Psychometrics.ctv |only ctv-0.8-5/ctv/inst/ctv/ReproducibleResearch.ctv |only ctv-0.8-5/ctv/inst/ctv/Robust.ctv |only ctv-0.8-5/ctv/inst/ctv/SocialSciences.ctv |only ctv-0.8-5/ctv/inst/ctv/Spatial.ctv |only ctv-0.8-5/ctv/inst/ctv/SpatioTemporal.ctv |only ctv-0.8-5/ctv/inst/ctv/Survival.ctv |only ctv-0.8-5/ctv/inst/ctv/TimeSeries.ctv |only ctv-0.8-5/ctv/inst/ctv/WebTechnologies.ctv |only ctv-0.8-5/ctv/inst/ctv/gR.ctv |only ctv-0.8-5/ctv/inst/doc/ctv-howto.R |only ctv-0.8-5/ctv/inst/doc/ctv-howto.Rnw |only ctv-0.8-5/ctv/inst/doc/ctv-howto.pdf |only ctv-0.8-5/ctv/vignettes/ctv-howto.Rnw |only ctv-0.9-0/ctv/DESCRIPTION | 15 ctv-0.9-0/ctv/MD5 | 64 -- ctv-0.9-0/ctv/NEWS.md |only ctv-0.9-0/ctv/R/ctv-client.R | 21 ctv-0.9-0/ctv/R/ctv-md.R |only ctv-0.9-0/ctv/R/ctv-server.R | 428 +++++++++++-------- ctv-0.9-0/ctv/README.md |only ctv-0.9-0/ctv/build/vignette.rds |binary ctv-0.9-0/ctv/inst/ctv/Econometrics.ctv | 164 ++++--- ctv-0.9-0/ctv/inst/ctv/Econometrics.md |only ctv-0.9-0/ctv/inst/doc/ctv-howto.Rmd |only ctv-0.9-0/ctv/inst/doc/ctv-howto.html |only ctv-0.9-0/ctv/man/ctv-client.Rd | 28 - ctv-0.9-0/ctv/man/ctv-server.Rd | 55 +- ctv-0.9-0/ctv/man/figures |only ctv-0.9-0/ctv/tests/read-all.R | 2 ctv-0.9-0/ctv/vignettes/ctv-howto.Rmd |only 57 files changed, 426 insertions(+), 351 deletions(-)
Title: Techniques for Evaluating Clustering
Description: The design of this package allows us to run different clustering packages and compare the results between them, to determine which algorithm behaves best from the data provided.
Author: Luis Alfonso Perez Martos [aut, cre]
Maintainer: Luis Alfonso Perez Martos <lapm0001@gmail.com>
Diff between Clustering versions 1.7.4 dated 2021-12-08 and 1.7.5 dated 2021-12-14
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/app.R | 3 --- R/validation.R | 16 ++++++++-------- inst/shiny/clustering/server.R | 23 ++++++++++++----------- tests/testthat/test-clustering.R | 10 +++++----- 6 files changed, 34 insertions(+), 36 deletions(-)
Title: Bayesian Multivariate GARCH Models
Description: Fit Bayesian multivariate GARCH models using 'Stan' for full Bayesian inference. Generate (weighted) forecasts for means, variances (volatility) and correlations. Currently DCC(P,Q), CCC(P,Q), pdBEKK(P,Q), and BEKK(P,Q) parameterizations are implemented, based either on a multivariate gaussian normal or student-t distribution. DCC and CCC models are based on Engle (2002) <doi:10.1198/073500102288618487> and Bollerslev (1990). The BEKK parameterization follows Engle and Kroner (1995) <doi:10.1017/S0266466600009063> while the pdBEKK as well as the estimation approach for this package is described in Rast et al. (2020) <doi:10.31234/osf.io/j57pk>. The fitted models contain 'rstan' objects and can be examined with 'rstan' functions.
Author: Philippe Rast [aut, cre] (<https://orcid.org/0000-0003-3630-6629>),
Stephen Martin [aut] (<https://orcid.org/0000-0001-8085-2390>)
Maintainer: Philippe Rast <rast.ph@gmail.com>
Diff between bmgarch versions 1.0.1 dated 2021-06-14 and 1.1.0 dated 2021-12-14
bmgarch-1.0.1/bmgarch/inst/include/meta_header.hpp |only bmgarch-1.0.1/bmgarch/man/dot-print.summary.arma.Rd |only bmgarch-1.0.1/bmgarch/src/init.cpp |only bmgarch-1.0.1/bmgarch/src/stan_files |only bmgarch-1.0.1/bmgarch/tools |only bmgarch-1.1.0/bmgarch/DESCRIPTION | 22 bmgarch-1.1.0/bmgarch/MD5 | 95 +- bmgarch-1.1.0/bmgarch/NAMESPACE | 1 bmgarch-1.1.0/bmgarch/NEWS.md | 7 bmgarch-1.1.0/bmgarch/R/bmgarch.R | 91 +- bmgarch-1.1.0/bmgarch/R/forecasting_gq.R | 20 bmgarch-1.1.0/bmgarch/R/lfocv.R | 3 bmgarch-1.1.0/bmgarch/R/model_weights.R | 16 bmgarch-1.1.0/bmgarch/R/print.R | 59 + bmgarch-1.1.0/bmgarch/R/stanmodels.R | 62 - bmgarch-1.1.0/bmgarch/README.md | 571 ++++++++-------- bmgarch-1.1.0/bmgarch/build/partial.rdb |binary bmgarch-1.1.0/bmgarch/configure |only bmgarch-1.1.0/bmgarch/configure.win |only bmgarch-1.1.0/bmgarch/inst/include/stan_meta_header.hpp |only bmgarch-1.1.0/bmgarch/inst/stan |only bmgarch-1.1.0/bmgarch/man/bmgarch.Rd | 7 bmgarch-1.1.0/bmgarch/man/dot-get_stan_summary.Rd | 4 bmgarch-1.1.0/bmgarch/man/dot-print.summary.means.Rd |only bmgarch-1.1.0/bmgarch/man/print.summary.bmgarch.Rd | 2 bmgarch-1.1.0/bmgarch/man/supported_models.Rd | 2 bmgarch-1.1.0/bmgarch/src/Makevars | 22 bmgarch-1.1.0/bmgarch/src/Makevars.win | 23 bmgarch-1.1.0/bmgarch/src/RcppExports.cpp |only bmgarch-1.1.0/bmgarch/src/stanExports_BEKKMGARCH.cc |only bmgarch-1.1.0/bmgarch/src/stanExports_BEKKMGARCH.h |only bmgarch-1.1.0/bmgarch/src/stanExports_CCCMGARCH.cc |only bmgarch-1.1.0/bmgarch/src/stanExports_CCCMGARCH.h |only bmgarch-1.1.0/bmgarch/src/stanExports_DCCMGARCH.cc |only bmgarch-1.1.0/bmgarch/src/stanExports_DCCMGARCH.h |only bmgarch-1.1.0/bmgarch/src/stanExports_forecastBEKK.cc |only bmgarch-1.1.0/bmgarch/src/stanExports_forecastBEKK.h |only bmgarch-1.1.0/bmgarch/src/stanExports_forecastCCC.cc |only bmgarch-1.1.0/bmgarch/src/stanExports_forecastCCC.h |only bmgarch-1.1.0/bmgarch/src/stanExports_forecastDCC.cc |only bmgarch-1.1.0/bmgarch/src/stanExports_forecastDCC.h |only bmgarch-1.1.0/bmgarch/src/stanExports_pdBEKKMGARCH.cc |only bmgarch-1.1.0/bmgarch/src/stanExports_pdBEKKMGARCH.h |only 43 files changed, 553 insertions(+), 454 deletions(-)
Title: Alternate DEA Package
Description: The meaning of adea is "alternate DEA". This package is devoted to provide the alternative method of DEA described in the paper entitled "Stepwise Selection of Variables in DEA Using Contribution Load", by F. Fernandez-Palacin, M. A. Lopez-Sanchez and M. Munoz-Marquez. Pesquisa Operacional 38 (1), pg. 1-24, 2018. <doi:10.1590/0101-7438.2018.038.01.0031>.
A full functional on-line and interactive version is available at
<https://knuth.uca.es/shiny/DEA/>.
Author: Fernando Fernandez-Palacin [aut]
(<https://orcid.org/0000-0002-3525-2924>),
Manuel Munoz-Marquez [aut, cre]
(<https://orcid.org/0000-0003-4157-8784>)
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Diff between adea versions 1.1.6 dated 2021-09-07 and 1.2.1 dated 2021-12-14
ChangeLog | 4 ++++ DESCRIPTION | 17 ++++++++++------- MD5 | 31 ++++++++++++++++++------------- R/adea-package.R | 4 ++-- R/adea_hierarchical.R | 1 + R/cardealers4.R | 2 +- build/vignette.rds |binary data/spanishuniversities2018.rda |binary demo/00Index | 4 +++- demo/cardealers.R |only demo/spanishuniversities2018.R |only inst/doc/adea_load_leverage.html | 4 ++-- inst/doc/adea_variable_selection.html | 30 ++++++++++++++++-------------- inst/doc/cadea.html | 4 ++-- man/adea-package.Rd | 4 ++-- man/cardealers4.Rd | 2 +- tests |only 17 files changed, 62 insertions(+), 45 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics
Description: A collection of functions to create spatial weights matrix
objects from polygon 'contiguities', from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial 'autocorrelation',
including global 'Morans I' and 'Gearys C' proposed by 'Cliff' and 'Ord'
(1973, ISBN: 0850860369) and (1981, ISBN: 0850860814), 'Hubert/Mantel'
general cross product statistic, Empirical Bayes estimates and
'Assunção/Reis' (1999) <doi:10.1002/(SICI)1097-0258(19990830)18:16%3C2147::AID-SIM179%3E3.0.CO;2-I> Index, 'Getis/Ord' G ('Getis' and 'Ord' 1992)
<doi:10.1111/j.1538-4632.1992.tb00261.x> and multicoloured
join count statistics, 'APLE' ('Li 'et al.' )
<doi:10.1111/j.1538-4632.2007.00708.x>, local 'Moran's I', 'Gearys C'
('Anselin' 1995) <doi:10.1111/j.1538-4632.1995.tb00338.x> and
'Getis/Ord' G ('Ord' and 'Getis' 1995)
<doi:10.1111/j.1538-4632.1995.tb00912.x>,
'saddlepoint' approximations ('Tiefelsdorf' 2002)
<doi:10.1111/j.1538-4632.2002.tb01084.x> and exact tests
for global and local 'Moran's I' ('Bivand et al.' 2009)
<doi:10.1016/j.csda.2008.07.021> and 'LOSH' local indicators
of spatial heteroscedasticity ('Ord' and 'Getis')
<doi:10.1007/s00168-011-0492-y>. The implementation of most of
the measures is described in 'Bivand' and 'Wong' (2018)
<doi:10.1007/s11749-018-0599-x>.
'spdep' >= 1.1-1 corresponds to 'spatialreg' >= 1.1-1, in which the model
fitting functions are deprecated and pass through to 'spatialreg', but
will mask those in 'spatialreg'. From versions 1.2-1, the functions will
be made defunct in 'spdep'.
For now 'spatialreg' only has functions from 'spdep', where they are shown
as deprecated. 'spatialreg' only loads the namespace of 'spdep'; if you
attach 'spdep', the same functions in the other package will be masked.
Some feed through adequately, others do not.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assunção [ctb],
Olaf Berke [ctb],
Andrew Bernat [ctb],
Guillaume Blanchet [ctb],
Eric Blankmeyer [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Stéphane Dray [ctb],
Virgilio Gómez-Rubio [ctb],
Martin Gubri [ctb],
Rein Halbersma [ctb],
Elias Krainski [ctb],
Pierre Legendre [ctb],
Nicholas Lewin-Koh [ctb],
Angela Li [ctb],
Hongfei Li [ctb],
Jielai Ma [ctb],
Abhirup Mallik [ctb, trl],
Giovanni Millo [ctb],
Werner Mueller [ctb],
Hisaji Ono [ctb],
Josiah Parry [ctb] (<https://orcid.org/0000-0001-9910-865X>),
Pedro Peres-Neto [ctb],
Gianfranco Piras [ctb],
Markus Reder [ctb],
Jeff Sauer [ctb],
Michael Tiefelsdorf [ctb],
René Westerholt [ctb],
Levi Wolf [ctb],
Danlin Yu [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spdep versions 1.1-12 dated 2021-11-09 and 1.1-13 dated 2021-12-14
ChangeLog | 920 ++++--- DESCRIPTION | 19 MD5 | 37 NAMESPACE | 10 NEWS.md | 10 R/geary.R | 10 R/lisa_perm.R | 56 R/localC.R |only R/nb2listw.R | 2 R/poly2nb.R | 46 build/partial.rdb |binary inst/ChangeLog | 4669 ++++++++++++++++++++++---------------- inst/doc/CO69.html | 1365 ----------- inst/doc/nb.html | 1331 ---------- inst/doc/nb_igraph.html | 1287 ---------- inst/doc/nb_sf.html | 1311 ---------- inst/doc/sids.html | 1369 ----------- inst/tinytest/test_poly2nb_snap.R |only man/localC.Rd |only man/localmoran.Rd | 10 man/poly2nb.Rd | 8 21 files changed, 3705 insertions(+), 8755 deletions(-)
Title: Article Formats for R Markdown
Description: A suite of custom R Markdown formats and templates for
authoring journal articles and conference submissions.
Author: JJ Allaire [aut],
Yihui Xie [aut] (<https://orcid.org/0000-0003-0645-5666>),
Christophe Dervieux [aut, cre]
(<https://orcid.org/0000-0003-4474-2498>),
RStudio [cph, fnd],
R Foundation [aut, cph],
Hadley Wickham [aut],
Journal of Statistical Software [aut, cph],
Ramnath Vaidyanathan [aut, cph],
Association for Computing Machinery [aut, cph],
Carl Boettiger [aut, cph],
Elsevier [aut, cph],
Karl Broman [aut, cph],
Kirill Mueller [aut, cph],
Bastiaan Quast [aut, cph],
Randall Pruim [aut, cph],
Ben Marwick [aut, cph],
Charlotte Wickham [aut, cph],
Oliver Keyes [aut, cph],
Miao Yu [aut, cph],
Daniel Emaasit [aut, cph],
Thierry Onkelinx [aut, cph],
Alessandro Gasparini [aut, cph]
(<https://orcid.org/0000-0002-8319-7624>),
Marc-Andre Desautels [aut, cph],
Dominik Leutnant [aut, cph] (<https://orcid.org/0000-0003-3293-2315>),
MDPI [aut, cph],
Taylor and Francis [aut, cph],
Oğuzhan Öğreden [aut] (<https://orcid.org/0000-0002-9949-3348>),
Dalton Hance [aut],
Daniel Nüst [aut, cph] (<https://orcid.org/0000-0002-0024-5046>),
Petter Uvesten [aut, cph],
Elio Campitelli [aut, cph] (<https://orcid.org/0000-0002-7742-9230>),
John Muschelli [aut, cph] (<https://orcid.org/0000-0001-6469-1750>),
Alex Hayes [aut] (<https://orcid.org/0000-0002-4985-5160>),
Zhian N. Kamvar [aut, cph] (<https://orcid.org/0000-0003-1458-7108>),
Noam Ross [aut, cph] (<https://orcid.org/0000-0002-2136-0000>),
Robrecht Cannoodt [aut, cph] (<https://orcid.org/0000-0003-3641-729X>,
rcannood),
Duncan Luguern [aut],
David M. Kaplan [aut, ctb] (<https://orcid.org/0000-0001-6087-359X>,
dmkaplan2000),
Sebastian Kreutzer [aut] (<https://orcid.org/0000-0002-0734-2199>),
Shixiang Wang [aut, ctb] (<https://orcid.org/0000-0001-9855-7357>),
Jay Hesselberth [aut, ctb] (<https://orcid.org/0000-0002-6299-179X>),
Alfredo Hernández [ctb] (<https://orcid.org/0000-0002-2660-4545>),
Stefano Coretta [ctb] (<https://orcid.org/0000-0001-9627-5532>,
stefanocoretta),
Greg Macfarlane [ctb] (gregmacfarlane),
Matthias Templ [ctb] (<https://orcid.org/0000-0002-8638-5276>,
matthias-da),
Alvaro Uzaheta [ctb] (auzaheta),
JooYoung Seo [ctb] (<https://orcid.org/0000-0002-4064-6012>),
Callum Arnold [ctb] (arnold-c)
Maintainer: Christophe Dervieux <cderv@rstudio.com>
Diff between rticles versions 0.21 dated 2021-09-11 and 0.22 dated 2021-12-14
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Title: Database Interface and 'MySQL' Driver for R
Description: Legacy 'DBI' interface to 'MySQL' / 'MariaDB' based on old code
ported from S-PLUS. A modern 'MySQL' client based on 'Rcpp' is available
from the 'RMariaDB' package.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between RMySQL versions 0.10.22 dated 2021-06-22 and 0.10.23 dated 2021-12-14
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ configure | 2 +- src/Makevars.ucrt | 1 + src/Makevars.win | 5 +++-- 6 files changed, 18 insertions(+), 12 deletions(-)
Title: Tool for Diagnosis of Tables Joins and Complementary Join
Features
Description: Tool for diagnosing table joins. It combines the speed
`data.table`, the flexibility of `dplyr`, and the diagnosis and features of
the `merge` command in `Stata`.
Author: R.Andres Castaneda [aut, cre]
Maintainer: R.Andres Castaneda <acastanedaa@worldbank.org>
Diff between joyn versions 0.1.3 dated 2021-04-28 and 0.1.4 dated 2021-12-14
joyn-0.1.3/joyn/R/data.R |only joyn-0.1.3/joyn/R/sysdata.rda |only joyn-0.1.3/joyn/man/x1.Rd |only joyn-0.1.3/joyn/man/x2.Rd |only joyn-0.1.3/joyn/man/x3.Rd |only joyn-0.1.3/joyn/man/x4.Rd |only joyn-0.1.3/joyn/man/y1.Rd |only joyn-0.1.3/joyn/man/y2.Rd |only joyn-0.1.3/joyn/man/y3.Rd |only joyn-0.1.3/joyn/man/y4.Rd |only joyn-0.1.4/joyn/DESCRIPTION | 8 - joyn-0.1.4/joyn/MD5 | 54 +++---- joyn-0.1.4/joyn/NAMESPACE | 8 - joyn-0.1.4/joyn/NEWS.md | 12 + joyn-0.1.4/joyn/R/freq_table.R | 5 joyn-0.1.4/joyn/R/is_id.R | 3 joyn-0.1.4/joyn/R/merge.R | 148 ++++++++++++--------- joyn-0.1.4/joyn/R/possible_ids.R | 5 joyn-0.1.4/joyn/R/update_values.R | 2 joyn-0.1.4/joyn/README.md | 105 ++++++-------- joyn-0.1.4/joyn/build/vignette.rds |binary joyn-0.1.4/joyn/inst/doc/advanced-use.html | 4 joyn-0.1.4/joyn/inst/doc/general-use.Rmd | 42 +++++ joyn-0.1.4/joyn/inst/doc/general-use.html | 60 +++++--- joyn-0.1.4/joyn/man/freq_table.Rd | 5 joyn-0.1.4/joyn/man/is_id.Rd | 3 joyn-0.1.4/joyn/man/merge.Rd | 15 +- joyn-0.1.4/joyn/man/possible_ids.Rd | 5 joyn-0.1.4/joyn/tests/testthat/test-freq_table.R | 42 +++++ joyn-0.1.4/joyn/tests/testthat/test-is_id.R | 37 +++++ joyn-0.1.4/joyn/tests/testthat/test-merge.R | 42 +++++ joyn-0.1.4/joyn/tests/testthat/test-possible_ids.R | 37 +++++ joyn-0.1.4/joyn/vignettes/general-use.Rmd | 42 +++++ 33 files changed, 490 insertions(+), 194 deletions(-)
Title: Gaussian Graphical Models with Nonconvex Regularization
Description: Estimate Gaussian graphical models with nonconvex penalties <doi:10.31234/osf.io/ad57p>,
including the atan Wang and Zhu (2016) <doi:10.1155/2016/6495417>,
seamless L0 Dicker, Huang, and Lin (2013) <doi:10.5705/ss.2011.074>,
exponential Wang, Fan, and Zhu <doi:10.1007/s10463-016-0588-3>,
smooth integration of counting and absolute deviation Lv and Fan (2009) <doi:10.1214/09-AOS683>,
logarithm Mazumder, Friedman, and Hastie (2011) <doi:10.1198/jasa.2011.tm09738>,
Lq, smoothly clipped absolute deviation Fan and Li (2001) <doi:10.1198/016214501753382273>,
and minimax concave penalty Zhang (2010) <doi:10.1214/09-AOS729>. There are also extensions
for computing variable inclusion probabilities, multiple regression coefficients, and
statistical inference <doi:10.1214/15-EJS1031>.
Author: Donald Williams [aut, cre]
Maintainer: Donald Williams <drwwilliams@ucdavis.edu>
Diff between GGMncv versions 2.0.0 dated 2020-11-16 and 2.1.0 dated 2021-12-14
GGMncv-2.0.0/GGMncv/build/GGMncv.pdf |only GGMncv-2.0.0/GGMncv/man/ggm_compare.Rd |only GGMncv-2.1.0/GGMncv/DESCRIPTION | 22 GGMncv-2.1.0/GGMncv/MD5 | 111 + GGMncv-2.1.0/GGMncv/NAMESPACE | 117 + GGMncv-2.1.0/GGMncv/R/GGMncv-package.R |only GGMncv-2.1.0/GGMncv/R/coef.ggmncv.R | 159 +- GGMncv-2.1.0/GGMncv/R/confirm_edges.R |only GGMncv-2.1.0/GGMncv/R/datasets.R | 51 GGMncv-2.1.0/GGMncv/R/derivative.R | 236 ++- GGMncv-2.1.0/GGMncv/R/desparsify.R | 172 +- GGMncv-2.1.0/GGMncv/R/eip.R | 357 ++--- GGMncv-2.1.0/GGMncv/R/gen_net.R |only GGMncv-2.1.0/GGMncv/R/ggm_compare.R | 258 ++- GGMncv-2.1.0/GGMncv/R/ggmncv.R | 358 ++++- GGMncv-2.1.0/GGMncv/R/helpers.R | 618 +++------ GGMncv-2.1.0/GGMncv/R/htf.R | 105 + GGMncv-2.1.0/GGMncv/R/inference.R | 266 ++- GGMncv-2.1.0/GGMncv/R/kl.R |only GGMncv-2.1.0/GGMncv/R/lw_estimator.R |only GGMncv-2.1.0/GGMncv/R/nct.R |only GGMncv-2.1.0/GGMncv/R/pen_function.R | 173 +- GGMncv-2.1.0/GGMncv/R/plot_graph.R |only GGMncv-2.1.0/GGMncv/R/predict.R | 115 - GGMncv-2.1.0/GGMncv/R/score_binary.R |only GGMncv-2.1.0/GGMncv/README.md | 1440 ++++++++++----------- GGMncv-2.1.0/GGMncv/build/partial.rdb |binary GGMncv-2.1.0/GGMncv/build/vignette.rds |only GGMncv-2.1.0/GGMncv/configure.ac | 2 GGMncv-2.1.0/GGMncv/data/bfi.rda |only GGMncv-2.1.0/GGMncv/inst/REFERENCES.bib | 841 +++++++----- GGMncv-2.1.0/GGMncv/inst/doc |only GGMncv-2.1.0/GGMncv/man/GGMncv-package.Rd |only GGMncv-2.1.0/GGMncv/man/bfi.Rd |only GGMncv-2.1.0/GGMncv/man/boot_eip.Rd | 80 - GGMncv-2.1.0/GGMncv/man/coef.ggmncv.Rd | 120 + GGMncv-2.1.0/GGMncv/man/compare_edges.Rd |only GGMncv-2.1.0/GGMncv/man/confirm_edges.Rd |only GGMncv-2.1.0/GGMncv/man/constrained.Rd | 86 - GGMncv-2.1.0/GGMncv/man/desparsify.Rd | 52 GGMncv-2.1.0/GGMncv/man/figures/cpu_time.png |only GGMncv-2.1.0/GGMncv/man/figures/p_dist.png |only GGMncv-2.1.0/GGMncv/man/figures/qqplot.png |only GGMncv-2.1.0/GGMncv/man/gen_net.Rd |only GGMncv-2.1.0/GGMncv/man/get_graph.Rd |only GGMncv-2.1.0/GGMncv/man/ggmncv.Rd | 477 ++++-- GGMncv-2.1.0/GGMncv/man/head.eip.Rd |only GGMncv-2.1.0/GGMncv/man/inference.Rd | 132 + GGMncv-2.1.0/GGMncv/man/kl_mvn.Rd |only GGMncv-2.1.0/GGMncv/man/ledoit_wolf.Rd |only GGMncv-2.1.0/GGMncv/man/nct.Rd |only GGMncv-2.1.0/GGMncv/man/penalty_derivative.Rd | 92 - GGMncv-2.1.0/GGMncv/man/penalty_function.Rd | 90 - GGMncv-2.1.0/GGMncv/man/plot.eip.Rd | 6 GGMncv-2.1.0/GGMncv/man/plot.ggmncv.Rd | 84 - GGMncv-2.1.0/GGMncv/man/plot.graph.Rd |only GGMncv-2.1.0/GGMncv/man/plot.penalty_derivative.Rd | 58 GGMncv-2.1.0/GGMncv/man/plot.penalty_function.Rd | 58 GGMncv-2.1.0/GGMncv/man/predict.ggmncv.Rd | 89 - GGMncv-2.1.0/GGMncv/man/print.nct.Rd |only GGMncv-2.1.0/GGMncv/man/score_binary.Rd |only GGMncv-2.1.0/GGMncv/src/RcppExports.cpp | 5 GGMncv-2.1.0/GGMncv/vignettes |only 63 files changed, 3942 insertions(+), 2888 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-01 4.0
2021-01-20 3.3.2
2020-06-02 3.3.1
2020-05-08 3.3
2020-01-09 3.2
2019-10-23 3.1.0
2019-07-13 3.0.3
2019-05-02 3.0.2
2019-03-20 3.0.1
2019-03-07 3.0.0
2018-12-14 2.0.1
2018-12-06 2.0.0
2018-06-25 1.1.5
2018-04-19 1.1.4
2018-03-20 1.1.3
2018-03-19 1.1.2
2017-08-28 1.1.1
2017-08-16 1.1
2017-01-16 1.0