Title: Versatile Curation of Table Metadata
Description: A YAML-based
mechanism for working with table metadata. Supports
compact syntax for creating, modifying, viewing, exporting,
importing, displaying, and plotting metadata coded as column
attributes. The 'yamlet' dialect is valid 'YAML' with
defaults and conventions chosen to improve readability.
See ?yamlet, ?decorate.data.frame and ?modify.default.
See ?read_yamlet ?write_yamlet, ?io_csv, and ?ggplot.decorated.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between yamlet versions 0.7.5 dated 2021-04-28 and 0.7.7 dated 2021-07-18
yamlet-0.7.5/yamlet/tests/figs |only yamlet-0.7.5/yamlet/tests/testthat/Rplots.pdf |only yamlet-0.7.7/yamlet/DESCRIPTION | 6 yamlet-0.7.7/yamlet/MD5 | 57 +- yamlet-0.7.7/yamlet/NAMESPACE | 2 yamlet-0.7.7/yamlet/R/data.frame.R |only yamlet-0.7.7/yamlet/R/package.R | 2 yamlet-0.7.7/yamlet/R/singularity.R | 11 yamlet-0.7.7/yamlet/inst/doc/yamlet-introduction.html | 475 +++++------------- yamlet-0.7.7/yamlet/man/as.data.frame.yamlet.Rd |only yamlet-0.7.7/yamlet/man/cell_value.Rd |only yamlet-0.7.7/yamlet/man/classified.data.frame.Rd | 1 yamlet-0.7.7/yamlet/man/decorate.character.Rd | 1 yamlet-0.7.7/yamlet/man/decorate.data.frame.Rd | 1 yamlet-0.7.7/yamlet/man/desolve.decorated.Rd | 1 yamlet-0.7.7/yamlet/man/ggplot.decorated.Rd | 1 yamlet-0.7.7/yamlet/man/io_csv.character.Rd | 1 yamlet-0.7.7/yamlet/man/io_csv.data.frame.Rd | 1 yamlet-0.7.7/yamlet/man/io_res.character.Rd | 1 yamlet-0.7.7/yamlet/man/io_table.character.Rd | 1 yamlet-0.7.7/yamlet/man/io_table.data.frame.Rd | 1 yamlet-0.7.7/yamlet/man/io_yamlet.character.Rd | 1 yamlet-0.7.7/yamlet/man/io_yamlet.data.frame.Rd | 1 yamlet-0.7.7/yamlet/man/is_parseable.default.Rd | 1 yamlet-0.7.7/yamlet/man/mimic.default.Rd | 1 yamlet-0.7.7/yamlet/man/modify.default.Rd | 1 yamlet-0.7.7/yamlet/man/promote.list.Rd | 1 yamlet-0.7.7/yamlet/man/read_yamlet.Rd | 1 yamlet-0.7.7/yamlet/man/resolve.decorated.Rd | 1 yamlet-0.7.7/yamlet/man/selected.default.Rd | 1 yamlet-0.7.7/yamlet/man/write_yamlet.Rd | 1 yamlet-0.7.7/yamlet/man/yamlet.Rd | 2 32 files changed, 207 insertions(+), 368 deletions(-)
Title: Extract, Analyze and Visualize Mutational Signatures for Genomic
Variations
Description: Genomic alterations including single nucleotide
substitution, copy number alteration, etc. are the major force for
cancer initialization and development. Due to the specificity of
molecular lesions caused by genomic alterations, we can generate
characteristic alteration spectra, called 'signature' (Wang, Shixiang,
et al. (2020) <DOI:10.1371/journal.pgen.1009557> & Alexandrov, Ludmil
B., et al. (2020) <DOI:10.1038/s41586-020-1943-3>). This package helps
users to extract, analyze and visualize signatures from genomic
alteration records, thus providing new insight into cancer study.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Ziyu Tao [aut] (<https://orcid.org/0000-0003-3272-1227>),
Huimin Li [aut] (<https://orcid.org/0000-0003-1683-9057>),
Tao Wu [aut] (<https://orcid.org/0000-0002-8999-9628>),
Xue-Song Liu [aut, ctb] (<https://orcid.org/0000-0002-7736-0077>),
Anand Mayakonda [ctb]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between sigminer versions 2.0.2 dated 2021-06-17 and 2.0.3 dated 2021-07-18
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- NEWS.md | 6 ++++++ R/generate_matrices.R | 19 +++++++++++++++++++ R/sig_tally.R | 1 + R/sigprofiler.R | 4 ++-- build/partial.rdb |binary inst/CITATION | 2 +- inst/doc/sigminer.html | 6 +++--- inst/extdata/human_hg19_gene_info.rds |only man/sigprofiler.Rd | 2 +- 11 files changed, 47 insertions(+), 20 deletions(-)
Title: PX-Web Data by API
Description: Function to read PX-Web data into R via API. The example code reads data from the three national statistical institutes, Statistics Norway, Statistics Sweden and Statistics Finland.
Author: Øyvind Langsrud [aut, cre],
Jan Bruusgaard [aut],
Solveig Bjørkholt [ctb],
Susie Jentoft [ctb]
Maintainer: Øyvind Langsrud <oyl@ssb.no>
Diff between PxWebApiData versions 0.5.0 dated 2021-03-05 and 0.6.0 dated 2021-07-18
DESCRIPTION | 8 MD5 | 14 - NEWS.md | 6 R/ApiData.R | 43 ++-- build/vignette.rds |binary inst/doc/Introduction.html | 368 ++++++++---------------------------------- man/ApiData.Rd | 2 tests/testthat/test-ApiData.R | 2 8 files changed, 114 insertions(+), 329 deletions(-)
Title: Infrastructure for Manipulation Polynomial Matrices
Description: Implementation of class "polyMatrix" for storing a matrix of polynomials and implements
basic matrix operations; including a determinant and characteristic polynomial.
It is based on the package 'polynom' and uses a lot of its methods to implement matrix operations.
This package includes 3 methods of triangularization of polynomial matrices:
Extended Euclidean algorithm which is most classical but numerically unstable;
Sylvester algorithm based on LQ decomposition;
Interpolation algorithm is based on LQ decomposition and Newton interpolation.
Both methods are described in
D. Henrion & M. Sebek, Reliable numerical methods for polynomial matrix triangularization,
IEEE Transactions on Automatic Control (Volume 44, Issue 3, Mar 1999, Pages 497-508) <doi:10.1109/9.751344>
and in
Salah Labhalla, Henri Lombardi & Roger Marlin,
Algorithmes de calcule de la reduction de Hermite d'une matrice a coefficients polynomeaux,
Theoretical Computer Science (Volume 161, Issue 1-2, July 1996, Pages 69-92) <doi:10.1016/0304-3975(95)00090-9>.
Author: Tamas Prohle [aut],
Peter Prohle [aut],
Nikolai Ryzhkov [aut, cre] (<https://orcid.org/0000-0003-4896-280X>),
Ildiko Laszlo [aut] (<https://orcid.org/0000-0003-2324-8183>),
Ulas Onat Alakent [ctb]
Maintainer: Nikolai Ryzhkov <namezys@gmail.com>
Diff between polyMatrix versions 0.9.11 dated 2021-07-11 and 0.9.16 dated 2021-07-18
polyMatrix-0.9.11/polyMatrix/R/ops_substraction.R |only polyMatrix-0.9.16/polyMatrix/DESCRIPTION | 10 polyMatrix-0.9.16/polyMatrix/MD5 | 100 ++--- polyMatrix-0.9.16/polyMatrix/R/class_polyMatrix.R | 42 +- polyMatrix-0.9.16/polyMatrix/R/class_polyMatrixCharPolynomial.R | 8 polyMatrix-0.9.16/polyMatrix/R/method_adjoint.R | 20 - polyMatrix-0.9.16/polyMatrix/R/method_bind.R | 28 - polyMatrix-0.9.16/polyMatrix/R/method_charpolynom.R | 10 polyMatrix-0.9.16/polyMatrix/R/method_coef.R | 14 polyMatrix-0.9.16/polyMatrix/R/method_degree.R | 15 polyMatrix-0.9.16/polyMatrix/R/method_det.R | 4 polyMatrix-0.9.16/polyMatrix/R/method_diag.R | 24 - polyMatrix-0.9.16/polyMatrix/R/method_dim.R | 10 polyMatrix-0.9.16/polyMatrix/R/method_gcd.R | 6 polyMatrix-0.9.16/polyMatrix/R/method_inv.R | 10 polyMatrix-0.9.16/polyMatrix/R/method_is_zero.R | 106 ++--- polyMatrix-0.9.16/polyMatrix/R/method_lcm.R | 4 polyMatrix-0.9.16/polyMatrix/R/method_predict.R | 12 polyMatrix-0.9.16/polyMatrix/R/method_proper.R | 27 - polyMatrix-0.9.16/polyMatrix/R/method_round.R | 48 +- polyMatrix-0.9.16/polyMatrix/R/method_show.R | 4 polyMatrix-0.9.16/polyMatrix/R/method_subscript.R | 45 +- polyMatrix-0.9.16/polyMatrix/R/method_trace.R | 2 polyMatrix-0.9.16/polyMatrix/R/method_zero_round.R | 133 +++--- polyMatrix-0.9.16/polyMatrix/R/ops.R |only polyMatrix-0.9.16/polyMatrix/R/ops_addition.R | 19 polyMatrix-0.9.16/polyMatrix/R/ops_matrix_mult.R | 11 polyMatrix-0.9.16/polyMatrix/R/ops_multiplication.R | 18 polyMatrix-0.9.16/polyMatrix/R/ops_subtraction.R |only polyMatrix-0.9.16/polyMatrix/R/parser.R | 2 polyMatrix-0.9.16/polyMatrix/R/polyMatrix-package.R |only polyMatrix-0.9.16/polyMatrix/man/GCD.Rd | 4 polyMatrix-0.9.16/polyMatrix/man/LCM.Rd | 2 polyMatrix-0.9.16/polyMatrix/man/adjoint.Rd | 10 polyMatrix-0.9.16/polyMatrix/man/cbind.Rd | 18 polyMatrix-0.9.16/polyMatrix/man/charpolynom.Rd | 24 - polyMatrix-0.9.16/polyMatrix/man/cofactor.Rd | 10 polyMatrix-0.9.16/polyMatrix/man/degree.Rd | 7 polyMatrix-0.9.16/polyMatrix/man/diag.Rd | 18 polyMatrix-0.9.16/polyMatrix/man/inv.Rd | 6 polyMatrix-0.9.16/polyMatrix/man/is.polyMatrix.Rd | 2 polyMatrix-0.9.16/polyMatrix/man/is.proper.Rd | 23 - polyMatrix-0.9.16/polyMatrix/man/is.zero.Rd | 33 - polyMatrix-0.9.16/polyMatrix/man/matrix.degree.Rd | 4 polyMatrix-0.9.16/polyMatrix/man/parse.polyMatrix.Rd | 3 polyMatrix-0.9.16/polyMatrix/man/parse.polynomial.Rd | 3 polyMatrix-0.9.16/polyMatrix/man/polyMatrix-Arith.Rd |only polyMatrix-0.9.16/polyMatrix/man/polyMatrix-class.Rd | 192 ---------- polyMatrix-0.9.16/polyMatrix/man/polyMatrix-mmult.Rd |only polyMatrix-0.9.16/polyMatrix/man/polyMatrix-package.Rd |only polyMatrix-0.9.16/polyMatrix/man/polyMatrix-subscript.Rd |only polyMatrix-0.9.16/polyMatrix/man/polyMatrix.Rd | 23 - polyMatrix-0.9.16/polyMatrix/man/polyMatrixCharPolynomial-class.Rd | 4 polyMatrix-0.9.16/polyMatrix/man/tr.Rd | 2 polyMatrix-0.9.16/polyMatrix/man/zero.round.Rd | 10 55 files changed, 499 insertions(+), 631 deletions(-)
Title: Rapid and Accurate Genetic Prediction Modeling for Genome-Wide
Association or Whole-Genome Sequencing Study Data
Description: Rapidly build accurate genetic prediction models for genome-wide association or whole-genome sequencing study data by smooth-threshold multivariate genetic prediction (STMGP) method. Variable selection is performed using marginal association test p-values with an optimal p-value cutoff selected by Cp-type criterion. Quantitative and binary traits are modeled respectively via linear and logistic regression models. A function that works through PLINK software (Purcell et al. 2007 <DOI:10.1086/519795>, Chang et al. 2015 <DOI:10.1186/s13742-015-0047-8>) <https://www.cog-genomics.org/plink2> is provided. Covariates can be included in regression model.
Author: Masao Ueki
Maintainer: Masao Ueki <uekimrsd@nifty.com>
Diff between stmgp versions 1.0.3 dated 2020-01-10 and 1.0.4 dated 2021-07-18
stmgp-1.0.3/stmgp/R/stplink1.0.3.R |only stmgp-1.0.4/stmgp/DESCRIPTION | 8 ++++---- stmgp-1.0.4/stmgp/MD5 | 13 +++++++------ stmgp-1.0.4/stmgp/NAMESPACE | 1 + stmgp-1.0.4/stmgp/NEWS.md | 2 ++ stmgp-1.0.4/stmgp/R/stplink1.0.4.R |only stmgp-1.0.4/stmgp/build/partial.rdb |binary stmgp-1.0.4/stmgp/man/stmgeplink.Rd |only stmgp-1.0.4/stmgp/man/stmgplink.Rd | 8 ++++++-- 9 files changed, 20 insertions(+), 12 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-14 0.3.5
2020-11-08 0.3.4
2020-09-11 0.3.1
2020-08-19 0.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-18 0.0.1
Title: Mappable Vector Library for Handling Large Datasets
Description: Mappable vector library provides convenient way to access large datasets on solid state drives. This bypasses limitation of physical memory size as well as limited bandwidth of database interfaces. Access speed depends on storage medium, so solid state drive is recommended, preferably with PCI Express (or M.2 nvme) interface. The data is memory mapped into R and then accessed using usual R list and array subscription operators. The layout of underlying MVL files is optimized for large datasets. The vectors are stored to guarantee alignment for vector intrinsics after memory map. The package is built on top of libMVL, which can be used as standalone C library. libMVL has simple C API making it easy to interchange of datasets with outside programs.
Author: Vladimir Dergachev [aut, cre] (<https://orcid.org/0000-0003-4708-6625>)
Maintainer: Vladimir Dergachev <support@altumrete.com>
Diff between RMVL versions 0.0.1.4 dated 2021-07-08 and 0.0.1.6 dated 2021-07-18
DESCRIPTION | 6 ++--- MD5 | 6 ++--- R/RMVL.R | 19 ++++++++-------- src/RlibMVL.c | 67 +++++++++++++++++++++++++++++++++++++++++++++++++++------- 4 files changed, 75 insertions(+), 23 deletions(-)
Title: Tabulate Descriptive Statistics in Multiple Formats
Description: Creates a table of descriptive statistics
for factor and numeric columns in a data frame. Displays
these by groups, if any. Highly customizable, with support
for 'html' and 'pdf' provided by 'kableExtra'. Respects
original column order, column labels, and factor level order.
See ?tablet.data.frame and vignettes.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between tablet versions 0.3.1 dated 2021-06-14 and 0.3.2 dated 2021-07-18
tablet-0.3.1/tablet/inst/shiny-examples/mesa/www/T-00-00.pdf |only tablet-0.3.2/tablet/DESCRIPTION | 6 tablet-0.3.2/tablet/MD5 | 16 tablet-0.3.2/tablet/NAMESPACE | 1 tablet-0.3.2/tablet/R/tablet.R | 29 tablet-0.3.2/tablet/inst/doc/tablet-introduction-html.html | 430 ----------- tablet-0.3.2/tablet/inst/doc/tablet-introduction-pdf.pdf |binary tablet-0.3.2/tablet/inst/shiny-examples/mesa/app.R | 49 - tablet-0.3.2/tablet/man/as_kable.tablet.Rd | 6 tablet-0.3.2/tablet/man/escape_latex.Rd |only 10 files changed, 90 insertions(+), 447 deletions(-)
Title: An Implementation of Matrix Mathematics
Description: An implementation of matrix mathematics wherein operations are performed "by name."
Author: Matthew Heun [aut, cre] (<https://orcid.org/0000-0002-7438-214X>)
Maintainer: Matthew Heun <matthew.heun@me.com>
Diff between matsbyname versions 0.4.18 dated 2021-06-03 and 0.4.19 dated 2021-07-18
matsbyname-0.4.18/matsbyname/tests/testthat/test_notation.R |only matsbyname-0.4.19/matsbyname/DESCRIPTION | 8 +- matsbyname-0.4.19/matsbyname/MD5 | 20 +++--- matsbyname-0.4.19/matsbyname/NEWS.md | 13 +++ matsbyname-0.4.19/matsbyname/R/Utilities.R | 5 - matsbyname-0.4.19/matsbyname/R/notation.R | 33 +++++----- matsbyname-0.4.19/matsbyname/inst/CITATION | 4 - matsbyname-0.4.19/matsbyname/inst/doc/applybyname-vignette.html | 4 - matsbyname-0.4.19/matsbyname/inst/doc/matsbyname.html | 4 - matsbyname-0.4.19/matsbyname/man/row-col-notation.Rd | 21 +++--- matsbyname-0.4.19/matsbyname/tests/testthat/test-notation.R |only matsbyname-0.4.19/matsbyname/tests/testthat/test_Utilities.R | 22 +++++- 12 files changed, 86 insertions(+), 48 deletions(-)