Title: Interface to the Penn Machine Learning Benchmarks Data
Repository
Description: Check available classification and regression data sets from the PMLB repository and download them.
The PMLB repository (<https://github.com/EpistasisLab/pmlbr>) contains a curated collection of data sets for evaluating and comparing machine learning algorithms.
These data sets cover a range of applications, and include binary/multi-class classification problems and
regression problems, as well as combinations of categorical, ordinal, and continuous features.
There are currently over 150 datasets included in the PMLB repository.
Author: Trang Le [aut, cre] ,
makeyourownmaker [aut] ,
Jason Moore [aut] ,
University of Pennsylvania [cph]
Maintainer: Trang Le <grixor@gmail.com>
Diff between pmlbr versions 0.2.3 dated 2025-02-19 and 0.3.0 dated 2025-02-27
pmlbr-0.2.3/pmlbr/R/data.R |only pmlbr-0.2.3/pmlbr/R/globals.R |only pmlbr-0.2.3/pmlbr/data |only pmlbr-0.2.3/pmlbr/man/classification_dataset_names.Rd |only pmlbr-0.2.3/pmlbr/man/regression_dataset_names.Rd |only pmlbr-0.3.0/pmlbr/DESCRIPTION | 9 - pmlbr-0.3.0/pmlbr/MD5 | 38 +++--- pmlbr-0.3.0/pmlbr/NAMESPACE | 5 pmlbr-0.3.0/pmlbr/NEWS.md | 4 pmlbr-0.3.0/pmlbr/R/list_datasets.R |only pmlbr-0.3.0/pmlbr/R/nearest.R | 104 +++++++++++------- pmlbr-0.3.0/pmlbr/R/pmlb.R | 40 +++++- pmlbr-0.3.0/pmlbr/R/zzz.R |only pmlbr-0.3.0/pmlbr/README.md | 51 +++++--- pmlbr-0.3.0/pmlbr/man/classification_datasets.Rd |only pmlbr-0.3.0/pmlbr/man/dataset_names.Rd | 24 ++-- pmlbr-0.3.0/pmlbr/man/fetch_data.Rd | 2 pmlbr-0.3.0/pmlbr/man/nearest_datasets-methods.Rd | 2 pmlbr-0.3.0/pmlbr/man/pmlb.Rd | 2 pmlbr-0.3.0/pmlbr/man/pmlb_metadata.Rd |only pmlbr-0.3.0/pmlbr/man/regression_datasets.Rd |only pmlbr-0.3.0/pmlbr/man/summary_stats.Rd | 35 ++---- pmlbr-0.3.0/pmlbr/tests |only 23 files changed, 186 insertions(+), 130 deletions(-)
Title: Working with Healthcare Databases
Description: A system for identifying diseases or events from healthcare databases and
preparing data for epidemiological studies. It includes capabilities not
supported by 'SQL', such as matching strings by 'stringr' style regular
expressions, and can compute comorbidity scores (Quan et al. (2005)
<doi:10.1097/01.mlr.0000182534.19832.83>) directly on a database server. The
implementation is based on 'dbplyr' with full 'tidyverse' compatibility.
Author: Kevin Hu [aut, cre, cph]
Maintainer: Kevin Hu <kevin.hu@bccdc.ca>
Diff between healthdb versions 0.3.1 dated 2024-05-22 and 0.4.0 dated 2025-02-27
DESCRIPTION | 8 MD5 | 38 +- NAMESPACE | 2 NEWS.md | 92 ++--- R/collapse_episode.R | 107 ------ R/collapse_episode_dataframe.R |only R/collapse_episode_sql.R |only R/fetch_var.R | 3 R/pool_case.R | 10 R/restrict_dates_sql.R | 5 build/partial.rdb |binary build/vignette.rds |binary inst/doc/healthdb.R | 43 +- inst/doc/healthdb.Rmd | 21 - inst/doc/healthdb.html | 579 ++++++++++++++++----------------- man/collapse_episode.Rd | 16 man/fetch_var.Rd | 2 man/pool_case.Rd | 2 tests/testthat/helper.R | 37 ++ tests/testthat/test-collapse_episode.R | 50 +- vignettes/healthdb.Rmd | 21 - 21 files changed, 503 insertions(+), 533 deletions(-)
Title: Download Data from Brazil's Population Census
Description: Easy access to data from Brazil's population censuses. The package
provides a simple and efficient way to download and read the data
sets and the documentation of all the population censuses taken in
and after 1960 in the country. The package is built on top of the
'Arrow' platform <https://arrow.apache.org/docs/r/>, which allows
users to work with larger-than-memory census data using 'dplyr'
familiar functions. <https://arrow.apache.org/docs/r/articles/arrow.html#analyzing-arrow-data-with-dplyr>.
Author: Rafael H. M. Pereira [aut, cre]
,
Rogerio J. Barbosa [aut] ,
Diego Rabatone Oliveira [ctb],
Neal Richardson [ctb],
Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between censobr versions 0.4.0 dated 2024-09-20 and 0.4.1 dated 2025-02-27
censobr-0.4.0/censobr/tests/tests_rafa/merge_household_notes.R |only censobr-0.4.0/censobr/tests/tests_rafa/merge_pdfs.R |only censobr-0.4.0/censobr/tests/tests_rafa/test_duckdb_merge.R |only censobr-0.4.0/censobr/tests/tests_rafa/test_duckdb_merge2.R |only censobr-0.4.0/censobr/tests/tests_rafa/test_duckdb_merge3.R |only censobr-0.4.1/censobr/DESCRIPTION | 14 - censobr-0.4.1/censobr/MD5 | 41 ++--- censobr-0.4.1/censobr/NEWS.md | 9 + censobr-0.4.1/censobr/R/merge_household.R | 74 ++++------ censobr-0.4.1/censobr/R/read_population.R | 12 - censobr-0.4.1/censobr/build/vignette.rds |binary censobr-0.4.1/censobr/inst/doc/censobr.R | 34 ++-- censobr-0.4.1/censobr/inst/doc/censobr.html | 8 - censobr-0.4.1/censobr/inst/doc/census_tracts_data.html | 8 - censobr-0.4.1/censobr/inst/doc/documentation.R | 39 ++--- censobr-0.4.1/censobr/inst/doc/documentation.Rmd | 11 - censobr-0.4.1/censobr/inst/doc/documentation.html | 22 +- censobr-0.4.1/censobr/inst/doc/larger_than_memory.R | 9 - censobr-0.4.1/censobr/inst/doc/larger_than_memory.Rmd | 12 - censobr-0.4.1/censobr/inst/doc/larger_than_memory.html | 51 ------ censobr-0.4.1/censobr/tests/tests_rafa/open_dictionary.R |only censobr-0.4.1/censobr/tests/tests_rafa/test_merge.R |only censobr-0.4.1/censobr/tests/testthat/test_read_population.R | 2 censobr-0.4.1/censobr/vignettes/documentation.Rmd | 11 - censobr-0.4.1/censobr/vignettes/larger_than_memory.Rmd | 12 - 25 files changed, 146 insertions(+), 223 deletions(-)
Title: Functions to Work with NCBI Accessions and Taxonomy
Description: Functions for assigning taxonomy to NCBI accession numbers and taxon IDs based on NCBI's accession2taxid and taxdump files. This package allows the user to download NCBI data dumps and create a local database for fast and local taxonomic assignment.
Author: Scott Sherrill-Mix [aut, cre]
Maintainer: Scott Sherrill-Mix <ssm@msu.edu>
Diff between taxonomizr versions 0.10.7 dated 2025-01-08 and 0.10.8 dated 2025-02-27
DESCRIPTION | 9 +++++---- MD5 | 16 ++++++++-------- R/taxa.R | 6 ++++-- README.md | 10 ++++++++++ inst/doc/usage.Rmd | 4 ++++ inst/doc/usage.html | 9 +++++++++ man/getTaxonomy.Rd | 5 ++++- tests/testthat/test_taxa.R | 44 ++++++++++++++++++++++++++++---------------- vignettes/usage.Rmd | 4 ++++ 9 files changed, 76 insertions(+), 31 deletions(-)
Title: Extensible Style-Sheet Language Transformations
Description: An extension for the 'xml2' package to transform XML documents
by applying an 'xslt' style-sheet.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between xslt versions 1.5.0 dated 2024-12-16 and 1.5.1 dated 2025-02-27
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 3 +++ src/Makevars.in | 2 +- src/Makevars.win | 2 +- 5 files changed, 12 insertions(+), 9 deletions(-)
Title: Statistical Hypothesis Testing Toolbox
Description: We provide a collection of statistical hypothesis testing procedures ranging from classical to modern methods for non-trivial settings such as high-dimensional scenario. For the general treatment of statistical hypothesis testing, see the book by Lehmann and Romano (2005) <doi:10.1007/0-387-27605-X>.
Author: Kyoungjae Lee [aut],
Lizhen Lin [aut],
Kisung You [aut, cre]
Maintainer: Kisung You <kisung.you@outlook.com>
Diff between SHT versions 0.1.8 dated 2022-11-03 and 0.1.9 dated 2025-02-27
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/package-SHT.R | 7 +++---- build/partial.rdb |binary src/Makevars | 12 +++++++++--- src/Makevars.win | 12 +++++++++--- src/cpp_eqdist_2014BG.cpp | 2 +- 8 files changed, 39 insertions(+), 24 deletions(-)
Title: Read Excel Files
Description: Import excel files into R. Supports '.xls' via the embedded
'libxls' C library <https://github.com/libxls/libxls> and '.xlsx' via
the embedded 'RapidXML' C++ library <https://rapidxml.sourceforge.net/>.
Works on Windows, Mac and Linux without external dependencies.
Author: Hadley Wickham [aut] ,
Jennifer Bryan [aut, cre] ,
Posit, PBC [cph, fnd] ,
Marcin Kalicinski [ctb, cph] ,
Komarov Valery [ctb, cph] ,
Christophe Leitienne [ctb, cph] ,
Bob Colbert [ctb, cph] ,
David Hoerl [ctb, cph] ,
Evan Miller [ctb, cph]
Maintainer: Jennifer Bryan <jenny@posit.co>
Diff between readxl versions 1.4.3 dated 2023-07-06 and 1.4.4 dated 2025-02-27
readxl-1.4.3/readxl/src/unix/config-solaris.h |only readxl-1.4.4/readxl/DESCRIPTION | 10 - readxl-1.4.4/readxl/MD5 | 71 +++++------ readxl-1.4.4/readxl/NEWS.md | 10 + readxl-1.4.4/readxl/R/cell-specification.R | 4 readxl-1.4.4/readxl/R/excel-sheets.R | 2 readxl-1.4.4/readxl/R/read_excel.R | 8 - readxl-1.4.4/readxl/README.md | 100 ++++++++-------- readxl-1.4.4/readxl/build/vignette.rds |binary readxl-1.4.4/readxl/inst/doc/cell-and-column-types.R | 6 readxl-1.4.4/readxl/inst/doc/cell-and-column-types.html | 58 ++++++--- readxl-1.4.4/readxl/inst/doc/sheet-geometry.R | 38 +++--- readxl-1.4.4/readxl/inst/doc/sheet-geometry.html | 14 +- readxl-1.4.4/readxl/inst/extdata/datasets.xls |binary readxl-1.4.4/readxl/inst/extdata/datasets.xlsx |binary readxl-1.4.4/readxl/inst/extdata/deaths.xls |binary readxl-1.4.4/readxl/man/cell-specification.Rd | 4 readxl-1.4.4/readxl/man/excel_sheets.Rd | 2 readxl-1.4.4/readxl/man/read_excel.Rd | 8 - readxl-1.4.4/readxl/src/libxls/ole.h | 4 readxl-1.4.4/readxl/src/libxls/xls.c | 22 +++ readxl-1.4.4/readxl/src/libxls/xlstool.c | 41 +++--- readxl-1.4.4/readxl/src/libxls/xlstypes.h | 4 readxl-1.4.4/readxl/src/unix/config-macos.h | 38 ++---- readxl-1.4.4/readxl/src/unix/config-unix.h | 43 ++---- readxl-1.4.4/readxl/src/unix/config.h | 2 readxl-1.4.4/readxl/src/utils.h | 25 +++- readxl-1.4.4/readxl/src/windows/config.h | 38 ++---- readxl-1.4.4/readxl/src/zip.cpp | 5 readxl-1.4.4/readxl/tests/testthat/_snaps/coercion.md | 32 ++++- readxl-1.4.4/readxl/tests/testthat/_snaps/col-names.md | 10 - readxl-1.4.4/readxl/tests/testthat/_snaps/col-types.md | 46 ++++--- readxl-1.4.4/readxl/tests/testthat/_snaps/dates.md | 6 readxl-1.4.4/readxl/tests/testthat/_snaps/problems.md | 15 +- readxl-1.4.4/readxl/tests/testthat/_snaps/read-excel.md | 68 ++++++---- readxl-1.4.4/readxl/tests/testthat/_snaps/sheets.md | 32 +++-- readxl-1.4.4/readxl/tests/testthat/test-geometry.R | 2 37 files changed, 433 insertions(+), 335 deletions(-)
Title: Tools for Matrix Algebra, Optimization and Inference
Description: Matrix is an universal and sometimes primary object/unit in applied mathematics and statistics. We provide a number of algorithms for selected problems in optimization and statistical inference. For general exposition to the topic with focus on statistical context, see the book by Banerjee and Roy (2014, ISBN:9781420095388).
Author: Kisung You [aut, cre]
Maintainer: Kisung You <kisung.you@outlook.com>
Diff between maotai versions 0.2.5 dated 2023-03-29 and 0.2.6 dated 2025-02-27
DESCRIPTION | 12 ++++++------ MD5 | 33 +++++++++++++++++++++++---------- NAMESPACE | 6 ++++++ NEWS.md | 4 ++++ R/RcppExports.R | 12 ++++++++++++ R/WLbarycenter.R |only R/WLpdist.R |only R/movMF_convert.R |only R/movMF_info.R |only R/movMF_reduce_greedy.R |only R/movMF_reduce_partitional.R |only R/package-maotai.R | 6 +++--- R/shortestpath.R | 4 ++-- R/zzz.R | 2 +- build/partial.rdb |binary man/WLbarycenter.Rd |only man/WLpdist.Rd |only man/movMF_convert.Rd |only man/movMF_info.Rd |only man/movMF_reduce_greedy.Rd |only man/movMF_reduce_partitional.Rd |only man/shortestpath.Rd | 2 +- src/RcppExports.cpp | 38 ++++++++++++++++++++++++++++++++++++++ src/cpp_WLvMF.cpp |only 24 files changed, 96 insertions(+), 23 deletions(-)
Title: Install R Packages or Download File from GitHub via the Proxy
Site
Description: When you want to install R package or download file from GitHub,
but you can't access GitHub, this package helps you install R packages or
download file from GitHub via the proxy website <https://gh-proxy.com/>
or <https://ghfast.top/>, which is in real-time sync with GitHub.
Author: Xinyuan Chu [aut, cre]
Maintainer: Xinyuan Chu <chuxinyuan@outlook.com>
Diff between ipkg versions 1.1.1 dated 2023-11-08 and 1.1.2 dated 2025-02-27
DESCRIPTION | 14 +-- LICENSE | 4 - MD5 | 14 +-- R/download_file.R | 190 +++++++++++++++++++++++++------------------------- R/install_github.R | 140 ++++++++++++++++++------------------ README.md | 82 ++++++++++----------- man/download_file.Rd | 2 man/install_github.Rd | 2 8 files changed, 224 insertions(+), 224 deletions(-)
More information about DistributionIV at CRAN
Permanent link
Title: Toolkit for Reduced Form and Structural Smooth Transition Vector
Autoregressive Models
Description: Penalized and non-penalized maximum likelihood estimation of smooth
transition vector autoregressive models with various types of transition weight
functions, conditional distributions, and identification methods. Constrained
estimation with various types of constraints is available. Residual based
model diagnostics, forecasting, simulations, and calculation of impulse
response functions, generalized impulse response functions, and generalized
forecast error variance decompositions. See
Heather Anderson, Farshid Vahid (1998) <doi:10.1016/S0304-4076(97)00076-6>,
Helmut Lütkepohl, Aleksei Netšunajev (2017) <doi:10.1016/j.jedc.2017.09.001>,
Markku Lanne, Savi Virolainen (2025) <doi:10.48550/arXiv.2403.14216>,
Savi Virolainen (2025) <doi:10.48550/arXiv.2404.19707>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between sstvars versions 1.1.3 dated 2025-01-30 and 1.1.4 dated 2025-02-27
DESCRIPTION | 16 ++--- MD5 | 116 ++++++++++++++++++++--------------------- NEWS.md | 15 +++++ R/GIRFandGFEVD.R | 17 ++++-- R/LSest.R | 40 +++++++------- R/MAINest.R | 22 ++++--- R/STVARconstruction.R | 7 +- R/argumentChecks.R | 4 - R/data.R | 10 ++- R/distributionFuns.R | 9 +-- R/jointSpectralRadius.R | 4 - R/loglikelihood.R | 4 - R/moreEst.R | 5 + R/pickParams.R | 6 +- R/plotMethods.R | 2 R/simulate.R | 33 +++++++---- R/sstvars.R | 17 +++--- README.md | 25 ++++---- data/usacpu.rda |binary inst/doc/sstvars-vignette.Rnw | 2 inst/doc/sstvars-vignette.pdf |binary man/GFEVD.Rd | 10 +-- man/GIRF.Rd | 32 ++++++----- man/STVAR.Rd | 5 + man/alt_stvar.Rd | 5 + man/bound_JSR.Rd | 2 man/bound_jsr_G.Rd | 4 - man/change_regime.Rd | 4 - man/check_params.Rd | 4 - man/diagnostic_plot.Rd | 4 - man/estim_LS.Rd | 9 ++- man/estim_NLS.Rd | 9 ++- man/filter_estimates.Rd | 1 man/fitSSTVAR.Rd | 5 + man/fitSTVAR.Rd | 12 ++-- man/fitbsSSTVAR.Rd | 3 - man/get_alpha_mt.Rd | 4 - man/get_residuals.Rd | 4 - man/in_paramspace.Rd | 4 - man/iterate_more.Rd | 6 +- man/loglikelihood.Rd | 4 - man/n_params.Rd | 4 - man/pick_Omegas.Rd | 6 +- man/plot_struct_shocks.Rd | 4 - man/predict.stvar.Rd | 4 - man/profile_logliks.Rd | 4 - man/reform_constrained_pars.Rd | 4 - man/regime_distance.Rd | 4 - man/reorder_B_columns.Rd | 1 man/simulate.stvar.Rd | 24 +++++--- man/simulate_from_regime.Rd | 4 - man/sstvars-package.Rd | 17 +++--- man/stand_t_dens.Rd | 9 +-- man/standard_errors.Rd | 4 - man/swap_B_signs.Rd | 1 man/swap_parametrization.Rd | 5 + man/usacpu.Rd | 18 +++--- vignettes/refs.bib | 12 +--- vignettes/sstvars-vignette.Rnw | 2 59 files changed, 342 insertions(+), 270 deletions(-)
Title: Tools for Working with Posterior Distributions
Description: Provides useful tools for both users and developers of packages
for fitting Bayesian models or working with output from Bayesian models.
The primary goals of the package are to:
(a) Efficiently convert between many different useful formats of
draws (samples) from posterior or prior distributions.
(b) Provide consistent methods for operations commonly performed on draws,
for example, subsetting, binding, or mutating draws.
(c) Provide various summaries of draws in convenient formats.
(d) Provide lightweight implementations of state of the art posterior
inference diagnostics. References: Vehtari et al. (2021)
<doi:10.1214/20-BA1221>.
Author: Paul-Christian Buerkner [aut, cre],
Jonah Gabry [aut],
Matthew Kay [aut],
Aki Vehtari [aut],
Mans Magnusson [ctb],
Rok Česnovar [ctb],
Ben Lambert [ctb],
Ozan Adiguezel [ctb],
Jacob Socolar [ctb],
Noa Kallioinen [ctb]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between posterior versions 1.6.0 dated 2024-07-03 and 1.6.1 dated 2025-02-27
DESCRIPTION | 10 +- MD5 | 66 +++++++++--------- NEWS.md | 11 +++ R/as_draws.R | 9 +- R/as_draws_array.R | 27 ++++--- R/convergence.R | 21 ++++- R/draws-index.R | 4 + R/misc.R | 1 R/nested_rhat.R | 22 +++--- R/pareto_smooth.R | 2 R/variables.R | 3 README.md | 132 ++++++++++++++++++++++-------------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 61 ++++++++++++++++ inst/doc/pareto_diagnostics.html | 2 inst/doc/rvar.html | 88 ++++++++++++------------ man/diagnostics.Rd | 7 + man/ess_basic.Rd | 2 man/ess_bulk.Rd | 2 man/ess_mean.Rd | 3 man/ess_quantile.Rd | 5 - man/ess_sd.Rd | 2 man/ess_tail.Rd | 2 man/mcse_quantile.Rd | 2 man/mcse_sd.Rd | 2 man/rhat.Rd | 2 man/rhat_basic.Rd | 2 man/rhat_nested.Rd | 10 +- man/u_scale.Rd | 6 + tests/testthat/test-as_draws.R | 22 ++++++ tests/testthat/test-convergence.R | 2 tests/testthat/test-pareto_smooth.R | 4 - tests/testthat/test-rstar.R | 4 + 34 files changed, 347 insertions(+), 191 deletions(-)
Title: Gaussian Process Classification as Described in Bachoc et al.
(2020)
Description: Parameter estimation and prediction of Gaussian Process Classifier models as described in Bachoc et al. (2020) <doi:10.1007/S10898-020-00920-0>. Important functions : gpcm(), predict.gpcm(), update.gpcm().
Author: Morgane Menz [aut, cre],
Celine Helbert [aut],
Victor Picheny [aut],
Francois Bachoc [aut],
Naoual Serraji [ctb]
Maintainer: Morgane Menz <morgane.menz@ifpen.fr>
Diff between GPCsign versions 0.1.0 dated 2024-09-23 and 0.1.1 dated 2025-02-27
DESCRIPTION | 6 +-- MD5 | 16 +++++----- R/gpcm.R | 64 ++++++++++++++++++++++++++++------------- R/gpcmStruct.R | 35 ++++++++++++++++------ R/logLik.R | 25 +++++++++++----- man/gpcm-class.Rd | 2 + man/gpcm.Rd | 6 ++- man/logLikFunc.Rd | 6 ++- tests/testthat/test-GPCmodel.R | 55 ++++++++++++++++++----------------- 9 files changed, 137 insertions(+), 78 deletions(-)
Title: A 'DuckDB'-Backed Version of 'dplyr'
Description: A drop-in replacement for 'dplyr', powered by 'DuckDB' for
performance. Offers convenient utilities for working with in-memory and
larger-than-memory data while retaining full 'dplyr' compatibility.
Author: Hannes Muehleisen [aut] ,
Kirill Mueller [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between duckplyr versions 1.0.0 dated 2025-02-07 and 1.0.1 dated 2025-02-27
duckplyr-1.0.0/duckplyr/R/compute_file.R |only duckplyr-1.0.0/duckplyr/R/io2.R |only duckplyr-1.0.0/duckplyr/man/compute_file.Rd |only duckplyr-1.0.0/duckplyr/tests/testthat/test-compute_file.R |only duckplyr-1.0.0/duckplyr/tests/testthat/test-io2.R |only duckplyr-1.0.1/duckplyr/DESCRIPTION | 12 duckplyr-1.0.1/duckplyr/MD5 | 70 +- duckplyr-1.0.1/duckplyr/NEWS.md | 25 + duckplyr-1.0.1/duckplyr/R/can_load_extension.R |only duckplyr-1.0.1/duckplyr/R/compute_csv.R |only duckplyr-1.0.1/duckplyr/R/compute_parquet.R |only duckplyr-1.0.1/duckplyr/R/duckplyr_df.R | 6 duckplyr-1.0.1/duckplyr/R/filter-rd.R | 2 duckplyr-1.0.1/duckplyr/R/filter.R | 2 duckplyr-1.0.1/duckplyr/R/read_csv_duckdb.R |only duckplyr-1.0.1/duckplyr/R/read_file_duckdb.R |only duckplyr-1.0.1/duckplyr/R/read_json_duckdb.R |only duckplyr-1.0.1/duckplyr/R/read_parquet_duckdb.R |only duckplyr-1.0.1/duckplyr/R/relational-duckdb.R | 6 duckplyr-1.0.1/duckplyr/R/relational.R | 2 duckplyr-1.0.1/duckplyr/R/zzz.R | 10 duckplyr-1.0.1/duckplyr/README.md | 6 duckplyr-1.0.1/duckplyr/inst/doc/developers.html | 176 ++----- duckplyr-1.0.1/duckplyr/inst/doc/extend.html | 8 duckplyr-1.0.1/duckplyr/inst/doc/fallback.html | 94 +-- duckplyr-1.0.1/duckplyr/inst/doc/large.R | 2 duckplyr-1.0.1/duckplyr/inst/doc/large.Rmd | 2 duckplyr-1.0.1/duckplyr/inst/doc/large.html | 4 duckplyr-1.0.1/duckplyr/inst/doc/limits.html | 239 +++------- duckplyr-1.0.1/duckplyr/inst/doc/prudence.html | 181 ++----- duckplyr-1.0.1/duckplyr/man/compute_csv.Rd |only duckplyr-1.0.1/duckplyr/man/compute_parquet.Rd |only duckplyr-1.0.1/duckplyr/man/filter.duckplyr_df.Rd | 2 duckplyr-1.0.1/duckplyr/man/read_csv_duckdb.Rd |only duckplyr-1.0.1/duckplyr/man/read_file_duckdb.Rd | 83 --- duckplyr-1.0.1/duckplyr/man/read_json_duckdb.Rd |only duckplyr-1.0.1/duckplyr/man/read_parquet_duckdb.Rd |only duckplyr-1.0.1/duckplyr/tests/testthat/_snaps/relational-duckdb.md | 10 duckplyr-1.0.1/duckplyr/tests/testthat/_snaps/relational.md | 7 duckplyr-1.0.1/duckplyr/tests/testthat/test-compute_csv.R |only duckplyr-1.0.1/duckplyr/tests/testthat/test-compute_parquet.R |only duckplyr-1.0.1/duckplyr/tests/testthat/test-read_csv_duckdb.R |only duckplyr-1.0.1/duckplyr/tests/testthat/test-read_json_duckdb.R |only duckplyr-1.0.1/duckplyr/tests/testthat/test-read_parquet_duckdb.R |only duckplyr-1.0.1/duckplyr/tests/testthat/test-relational-duckdb.R | 6 duckplyr-1.0.1/duckplyr/tests/testthat/test-relational.R | 4 duckplyr-1.0.1/duckplyr/vignettes/large.Rmd | 2 47 files changed, 378 insertions(+), 583 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrology and Water Quality
Data
Description: Collection of functions to help retrieve U.S. Geological Survey
and U.S. Environmental Protection Agency water quality and
hydrology data from web services. Data are discovered from
National Water Information System <https://waterservices.usgs.gov/> and <https://waterdata.usgs.gov/nwis>.
Water quality data are obtained from the Water Quality Portal <https://www.waterqualitydata.us/>.
Author: Laura DeCicco [aut, cre] ,
Robert Hirsch [aut] ,
David Lorenz [aut],
Jordan Read [ctb],
Jordan Walker [ctb],
Lindsay Platt [ctb],
David Watkins [aut] ,
David Blodgett [aut] ,
Mike Johnson [aut] ,
Aliesha Krall [ctb] ,
Lee Stanish [ctb]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between dataRetrieval versions 2.7.17 dated 2024-10-31 and 2.7.18 dated 2025-02-27
DESCRIPTION | 16 - MD5 | 115 +++++------ NAMESPACE | 4 NEWS | 8 R/checkWQPdates.R | 4 R/constructNWISURL.R | 253 +++++++++++++----------- R/findNLDI.R | 43 +--- R/getWebServiceData.R | 163 +++++---------- R/importNGWMN_wml2.R | 54 ++--- R/importRDB1.R | 42 +--- R/importWQP.R | 36 ++- R/importWaterML1.R | 16 - R/readNGWMNdata.R | 53 ++--- R/readNWISdata.R | 171 +++++++++------- R/readNWISdv.R | 1 R/readNWISpCode.R | 25 +- R/readNWISsite.R | 16 - R/readNWISunit.R | 2 R/readWQPdata.R | 128 ++++++++++-- R/readWQPdots.R | 51 +--- R/readWQPqw.R | 19 + R/read_USGS_samples.R |only R/setAccess.R | 26 -- R/whatNWISdata.R | 13 - R/whatNWISsites.R | 15 - R/whatWQPdata.R | 117 +++++++---- R/whatWQPsites.R | 76 ++++--- build/vignette.rds |binary inst/CITATION | 7 inst/doc/dataRetrieval.R | 289 +++++++++++++-------------- inst/doc/dataRetrieval.Rmd | 7 inst/doc/dataRetrieval.html | 22 -- inst/doc/qwdata_changes.R | 12 - man/check_param.Rd |only man/constructNWISURL.Rd | 7 man/construct_USGS_sample_request.Rd |only man/countyCdLookup.Rd | 17 + man/create_NWIS_bib.Rd | 64 +++--- man/create_WQP_bib.Rd | 66 +++--- man/dataRetrieval.Rd | 1 man/findNLDI.Rd | 3 man/getWebServiceData.Rd | 8 man/importNGWMN.Rd | 19 + man/importWaterML1.Rd | 7 man/importWaterML2.Rd | 18 - man/readNWISpCode.Rd | 2 man/readWQPdata.Rd | 64 +++++- man/readWQPqw.Rd | 17 + man/readWQPsummary.Rd | 1 man/read_USGS_samples.Rd |only man/stateCdLookup.Rd | 14 + man/summarize_USGS_samples.Rd |only man/whatWQPdata.Rd | 8 man/wqpSpecials.Rd | 14 - man/wqp_check_status.Rd | 3 tests/manual |only tests/testthat/tests_general.R | 257 ------------------------ tests/testthat/tests_imports.R | 31 -- tests/testthat/tests_nldi.R | 322 +++++++++++++++---------------- tests/testthat/tests_samples.R |only tests/testthat/tests_userFriendly_fxns.R | 63 +++--- vignettes/dataRetrieval.Rmd | 7 62 files changed, 1388 insertions(+), 1429 deletions(-)
Title: Graphs and Tables for OMOP Results
Description: Provides methods to transform omop_result objects into
formatted tables and figures, facilitating the visualisation of study
results working with the Observational Medical Outcomes Partnership
(OMOP) Common Data Model.
Author: Marti Catala [aut] ,
Nuria Mercade-Besora [aut, cre]
,
Yuchen Guo [ctb] ,
Elin Rowlands [ctb] ,
Marta Alcalde-Herraiz [aut] ,
Edward Burn [ctb]
Maintainer: Nuria Mercade-Besora <nuria.mercadebesora@ndorms.ox.ac.uk>
Diff between visOmopResults versions 1.0.0 dated 2025-01-15 and 1.0.1 dated 2025-02-27
DESCRIPTION | 12 MD5 | 39 NAMESPACE | 1 R/formatEstimateName.R | 9 R/formatEstimateValue.R | 58 + R/fxTable.R | 198 ++-- R/visOmopTable.R | 32 R/visTable.R | 1 inst/doc/a01_tables.R | 3 inst/doc/a01_tables.Rmd | 14 inst/doc/a01_tables.html | 1284 +++++++++++++++--------------- inst/doc/a02_plots.html | 18 man/formatMinCellCount.Rd |only man/visOmopResults-package.Rd | 5 tests/testthat/test-formatEstimateName.R | 30 tests/testthat/test-formatEstimateValue.R | 6 tests/testthat/test-fxTable.R | 35 tests/testthat/test-plot.R | 20 tests/testthat/test-visOmopTable.R | 49 - tests/testthat/test-visTable.R | 14 vignettes/a01_tables.Rmd | 14 21 files changed, 1013 insertions(+), 829 deletions(-)
More information about visOmopResults at CRAN
Permanent link
Title: Central Limit Theorem 'shiny' Application
Description: A 'shiny' application estimating the operating characteristics of the Student's t-test by Student (1908) <doi:10.1093/biomet/6.1.1>, Welch's t-test by Welch (1947) <doi:10.1093/biomet/34.1-2.28>, and Wilcoxon test by Wilcoxon (1945) <doi:10.2307/3001968> in one-sample or two-sample cases, in settings defined by the user (conditional distribution, sample size per group, location parameter per group, nuisance parameter per group), using Monte Carlo simulations Malvin H. Kalos, Paula A. Whitlock (2008) <doi:10.1002/9783527626212>.
Author: Dominique-Laurent Couturier [aut, cre]
,
Nikita Mozgunov [aut] ,
Thomas Jaki [aut]
Maintainer: Dominique-Laurent Couturier <dominique.couturier@mrc-bsu.cam.ac.uk>
Diff between shinyCLT versions 0.9.3 dated 2025-01-29 and 0.9.4 dated 2025-02-27
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 2 ++ inst/app/plot_func.R | 2 +- 4 files changed, 9 insertions(+), 7 deletions(-)
Title: Easily Access and Maintain Time-Based Versioned Data
(Slowly-Changing-Dimension)
Description: A collection of functions that enable easy access and updating of a database of data over time.
More specifically, the package facilitates type-2 history for data-warehouses and provides a number
of Quality of life improvements for working on SQL databases with R.
For reference see Ralph Kimball and Margy Ross (2013, ISBN 9781118530801).
Author: Rasmus Skytte Randloev [aut, cre, rev]
,
Marcus Munch Gruenewald [aut] ,
Lasse Engbo Christiansen [rev]
,
Sofia Myrup Otero [rev],
Kim Daniel Jacobsen [ctb],
Statens Serum Institut [cph, fnd]
Maintainer: Rasmus Skytte Randloev <rske@ssi.dk>
Diff between SCDB versions 0.5.0 dated 2025-02-03 and 0.5.1 dated 2025-02-27
DESCRIPTION | 38 + MD5 | 62 +- NEWS.md | 623 +++++++++++++-------------- R/Logger.R | 27 - R/connection.R | 11 R/create_index.R | 2 R/create_table.R | 4 R/db_joins.R | 4 R/digest_to_checksum.R | 13 R/get_table.R | 2 R/helpers.R | 2 R/id.R | 10 R/interlace.R | 8 R/locks.R | 9 R/update_snapshot.R | 66 +- inst/doc/benchmarks.html | 4 inst/doc/slowly-changing-dimension.R | 7 inst/doc/slowly-changing-dimension.Rmd | 7 inst/extdata/benchmarks.rds |binary man/Logger.Rd | 11 man/LoggerNull.Rd | 1 man/SCDB-package.Rd | 1 man/update_snapshot.Rd | 19 tests/testthat/helper-setup.R | 12 tests/testthat/setup.R | 9 tests/testthat/test-Logger.R | 4 tests/testthat/test-create_logs_if_missing.R | 2 tests/testthat/test-get_table.R | 4 tests/testthat/test-id.R | 2 tests/testthat/test-table_exists.R | 4 tests/testthat/test-update_snapshot.R | 38 + vignettes/slowly-changing-dimension.Rmd | 7 32 files changed, 555 insertions(+), 458 deletions(-)
Title: A Collection of Efficient and Extremely Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column and row wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions. References: a) Tsagris M., Papadakis M. (2018). Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1 <doi:10.7287/peerj.preprints.26605v1>. b) Tsagris M. and Papadakis M. (2018). Forward regression in R: from the extreme slow to the extreme fast. Journal of Data Science, 16(4): 771--780. <doi:10.6339/JDS.201810_16(4).00006>. c) Chatzipantsiou C., Dimitriadis M., Papadakis M. and Tsagris M. (2020). Extremely Efficient Permutation and Bootstrap Hypothesis Tests Using Hypothesis Tests Using R. Journal of Modern Applied Statistical Methods, 18(2), eP2898. <doi:10.48550/arXiv.1806.10947>. d) Tsagris M., Papadakis M., Alenazi A. and Alzeley O. (2024). Computationally Efficient Outlier Detection for High-Dimensional Data Using the [...truncated...]
Author: Manos Papadakis [aut, cre, cph],
Michail Tsagris [aut],
Marios Dimitriadis [aut],
Stefanos Fafalios [aut],
Matteo Fasiolo [aut],
Morgan Jacob [ctb],
Giorgos Borboudakis [aut],
John Burkardt [aut],
Changliang Zou [aut]
Maintainer: Manos Papadakis <rfastofficial@gmail.com>
Diff between Rfast versions 2.1.4 dated 2025-01-14 and 2.1.5 dated 2025-02-27
DESCRIPTION | 38 +++++++---------- MD5 | 37 ++++++++-------- NAMESPACE | 2 NEWS.md | 24 ++++++++++ R/ginis.R | 4 - R/random_values_simulation.R | 30 ++++++------- build/partial.rdb |binary inst/include/Rfast/Dist.h | 6 ++ inst/include/Rfast/matrix.hpp | 26 ++++++----- inst/include/Rfast/templates.h | 6 -- man/Rfast-package.Rd | 2 man/dcov.Rd | 3 + man/edist.Rd | 3 + man/pdcor.Rd | 3 + src/Dist.h |only src/Makevars.win | 2 src/dists.cpp | 90 ++++++++++++++++++++--------------------- src/energy.cpp | 13 +++-- src/rvmf.cpp | 8 +-- src/system_files.h | 1 20 files changed, 164 insertions(+), 134 deletions(-)
Title: Optimal Policy Learning
Description: Provides functions for optimal policy learning in socioeconomic applications helping users to learn the most effective policies based
on data in order to maximize empirical welfare. Specifically, 'OPL' allows to find "treatment assignment rules" that maximize the overall
welfare, defined as the sum of the policy effects estimated over all the policy beneficiaries. Documentation about 'OPL' is provided by
several international articles via Athey et al (2021, <doi:10.3982/ECTA15732>), Kitagawa et al (2018, <doi:10.3982/ECTA13288>),
Cerulli (2022, <doi:10.1080/13504851.2022.2032577>), the paper by Cerulli (2021, <doi:10.1080/13504851.2020.1820939>)
and the book by Gareth et al (2013, <doi:10.1007/978-1-4614-7138-7>).
Author: Federico Brogi [aut, cre],
Barbara Guardabascio [aut],
Giovanni Cerulli [aut]
Maintainer: Federico Brogi <federicobrogi@gmail.com>
Diff between OPL versions 1.0.1 dated 2025-02-17 and 1.0.2 dated 2025-02-27
DESCRIPTION | 6 MD5 | 42 ++-- R/make_cate.r | 302 +++++++++++++++++------------------ R/opl_dt_c.R | 17 + R/opl_lc_c.R | 1 R/opl_package.R |only R/opl_tb_c.R | 393 +++++++++++++++++++++++----------------------- inst/doc/make_cate.Rmd | 4 inst/doc/make_cate.html | 9 - inst/doc/opl_dt_c.Rmd | 4 inst/doc/opl_dt_c.html | 7 inst/doc/opl_lc_c.Rmd | 4 inst/doc/opl_lc_c.html | 7 inst/doc/opl_tb_c.Rmd | 3 inst/doc/opl_tb_c.html | 7 inst/doc/overlapping.Rmd | 3 inst/doc/overlapping.html | 7 man/OPL.Rd |only vignettes/make_cate.Rmd | 4 vignettes/opl_dt_c.Rmd | 4 vignettes/opl_lc_c.Rmd | 4 vignettes/opl_tb_c.Rmd | 3 vignettes/overlapping.Rmd | 3 23 files changed, 460 insertions(+), 374 deletions(-)
Title: Estimates and Plots Single-Level and Multilevel Latent Class
Models
Description: Efficiently estimates single- and multilevel latent class models with covariates, allowing for output visualization in all specifications. For more technical details, see Lyrvall et al (2023) <doi:10.48550/arXiv.2305.07276>.
Author: Roberto Di Mari [aut, cre],
Johan Lyrvall [aut],
Zsuzsa Bakk [ctb],
Jennifer Oser [ctb],
Jouni Kuha [ctb]
Maintainer: Roberto Di Mari <roberto.dimari@unict.it>
Diff between multilevLCA versions 2.0.0 dated 2025-02-04 and 2.0.1 dated 2025-02-27
DESCRIPTION | 8 MD5 | 10 R/MLCAfunctions.R | 7584 +++++++++++++++++++++++++++--------------------------- build/partial.rdb |binary data/dataIEA.rda |binary data/dataTOY.rda |binary 6 files changed, 3801 insertions(+), 3801 deletions(-)
Title: Tools for Reading SDMX Data and Metadata
Description: Set of classes and methods to read data and metadata documents
exchanged through the Statistical Data and Metadata Exchange (SDMX) framework,
currently focusing on the SDMX XML standard format (SDMX-ML).
Author: Emmanuel Blondel [aut, cre] ,
Matthieu Stigler [ctb] ,
Eric Persson [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between rsdmx versions 0.6-4 dated 2024-12-16 and 0.6-5 dated 2025-02-27
DESCRIPTION | 8 MD5 | 51 +- R/Class-SDMXDimension.R | 2 R/Class-SDMXRequestParams.R | 4 R/SDMX-methods.R | 3 R/SDMXCode-methods.R | 12 R/SDMXCompactData-methods.R | 3 R/SDMXConcepts-methods.R | 5 R/SDMXCrossSectionalData-methods.R | 3 R/SDMXData-methods.R | 34 + R/SDMXDimension-methods.R | 17 R/SDMXDotStatRequestBuilder-methods.R | 21 - R/SDMXMessageGroup-methods.R | 3 R/SDMXREST20RequestBuilder-methods.R | 23 - R/SDMXREST21RequestBuilder-methods.R | 39 + R/SDMXRequestParams-methods.R | 10 R/SDMXServiceProvider-methods.R | 81 ++- R/readSDMX.R | 16 README.md | 2 inst/extdata/SDMXCodelists_Example_hierarchical_2.1.xml |only man/SDMXDotStatRequestBuilder.Rd | 6 man/SDMXREST20RequestBuilder.Rd | 6 man/SDMXREST21RequestBuilder.Rd | 13 man/SDMXRequestParams.Rd | 193 ++++----- man/readSDMX.Rd | 327 ++++++++-------- tests/testthat/test_Codelists.R | 25 + tests/testthat/test_Main_Helpers.R | 35 + 27 files changed, 553 insertions(+), 389 deletions(-)
Title: Flood Extents and Duration along the Rivers Elbe and Rhine
Description: Raster based flood modelling internally using 'hyd1d', an R package
to interpolate 1d water level and gauging data. The package computes flood
extent and duration through strategies originally developed for 'INFORM',
an 'ArcGIS'-based hydro-ecological modelling framework. It does not provide
a full, physical hydraulic modelling algorithm, but a simplified, near real
time 'GIS' approach for flood extent and duration modelling. Computationally
demanding annual flood durations have been computed already and data
products were published by Weber (2022) <doi:10.1594/PANGAEA.948042>.
Author: Arnd Weber [aut, cre] ,
Stephan Rosenzweig [ctb],
Benjamin Eberhardt [ctb]
Maintainer: Arnd Weber <arnd.weber@bafg.de>
Diff between hydflood versions 0.5.9 dated 2024-10-07 and 0.5.10 dated 2025-02-27
DESCRIPTION | 10 ++++----- MD5 | 52 ++++++++++++++++++++++++------------------------- NEWS.md | 6 +++++ R/classifyToPNV.R | 2 - R/flood1.R | 1 R/flood2.R | 1 R/flood3.R | 1 R/flood3Points.R | 1 R/getDEM.R | 46 ++++++++++++++++++++++++++++++++++++++++--- R/hydSpatRaster.R | 2 - R/waterDepth.R | 1 build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 12 ++++++++++- inst/doc/hydflood.R | 30 ++++++++++++++-------------- inst/doc/hydflood.Rmd | 4 +-- inst/doc/hydflood.html | 20 ++++++++++++------ man/classifyToPNV.Rd | 2 - man/flood1.Rd | 1 man/flood2.Rd | 1 man/flood3.Rd | 1 man/flood3Points.Rd | 1 man/getDEM.Rd | 2 - man/hydSpatRaster.Rd | 2 - man/waterDepth.Rd | 1 vignettes/counts.Rdata |binary vignettes/hydflood.Rmd | 4 +-- 27 files changed, 138 insertions(+), 66 deletions(-)
Title: Efficient Outlier Detection for Large Time Series Databases
Description: Programs for detecting and cleaning outliers in single time series and in time series from homogeneous and heterogeneous databases using an Orthogonal Greedy Algorithm (OGA) for saturated linear regression models. The programs implement the procedures presented in the paper entitled "Efficient Outlier Detection for Large Time Series Databases" by Pedro Galeano, Daniel Peña and Ruey S. Tsay (2025), working paper, Universidad Carlos III de Madrid. Version 1.0.1 contains some improvements to the algorithm, so the results may vary slightly compared to those obtained with version 0.0.1.
Author: Pedro Galeano [aut, cre] ,
Daniel Pena [aut] ,
Ruey S. Tsay [aut]
Maintainer: Pedro Galeano <pedro.galeano@uc3m.es>
Diff between outliers.ts.oga versions 0.0.1 dated 2024-05-28 and 1.0.1 dated 2025-02-27
DESCRIPTION | 11 MD5 | 10 R/outliers.ts.oga.R | 651 +++++++++++++++++++++++++++------------------------- man/db_het_oga.Rd | 2 man/db_hom_oga.Rd | 2 man/single_oga.Rd | 2 6 files changed, 359 insertions(+), 319 deletions(-)
More information about outliers.ts.oga at CRAN
Permanent link
Title: A Lightweight Version of R Markdown
Description: Render R Markdown to Markdown (without using 'knitr'), and Markdown
to lightweight HTML or 'LaTeX' documents with the 'commonmark' package (instead
of 'Pandoc'). Some missing Markdown features in 'commonmark' are also
supported, such as raw HTML or 'LaTeX' blocks, 'LaTeX' math, superscripts,
subscripts, footnotes, element attributes, and appendices,
but not all 'Pandoc' Markdown features are (or will be) supported. With
additional JavaScript and CSS, you can also create HTML slides and articles.
This package can be viewed as a trimmed-down version of R Markdown and
'knitr'. It does not aim at rich Markdown features or a large variety of
output formats (the primary formats are HTML and 'LaTeX'). Book and website
projects of multiple input documents are also supported.
Author: Yihui Xie [aut, cre] ,
Tim Taylor [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between litedown versions 0.5 dated 2025-01-07 and 0.6 dated 2025-02-27
DESCRIPTION | 8 - LICENSE | 2 MD5 | 52 ++++----- NAMESPACE | 4 NEWS.md | 14 ++ R/format.R | 21 ++- R/fuse.R | 169 ++++++++++++++++++++++++------ R/mark.R | 17 ++- R/package.R | 32 ++++- R/preview.R | 17 +-- R/site.R | 25 ++-- R/utils.R | 221 ++++++++++++++++++++++++++++------------ README.md | 4 inst/doc/markdown-examples.html | 74 +++++++------ inst/doc/markdown-output.html | 26 +++- inst/doc/slides.html | 36 +++--- inst/examples/render-options.R | 6 - inst/resources/default.css | 20 ++- inst/resources/listing.css | 4 inst/resources/server.css | 5 inst/resources/server.js | 2 inst/resources/snap.css | 79 +++++++------- man/fuse_site.Rd | 2 man/get_context.Rd |only man/markdown_options.Rd | 6 - man/raw_text.Rd |only tests/examples.R | 2 tests/tests.Rout.save | 9 + 28 files changed, 581 insertions(+), 276 deletions(-)
Title: Non-Targeted Fluxomics on High-Resolution Mass-Spectrometry Data
Description: Identifying labeled compounds in a 13C-tracer experiment in
non-targeted fashion is a cumbersome process. This package facilitates
such type of analyses by providing high level quality control plots,
deconvoluting and evaluating spectra and performing a multitude of
tests in an automatic fashion. The main idea is to use changing
intensity ratios of ion pairs from peak list generated with 'xcms' as
candidates and evaluate those against base peak chromatograms and
spectra information within the raw measurement data automatically.
The functionality is described in Hoffmann et al. (2018)
<doi:10.1021/acs.analchem.8b00356>.
Author: Jan Lisec [aut, cre] ,
Friederike Hoffmann [aut]
Maintainer: Jan Lisec <jan.lisec@bam.de>
Diff between HiResTEC versions 0.62.3 dated 2024-02-26 and 0.63.1 dated 2025-02-27
HiResTEC-0.62.3/HiResTEC/R/CalcEnrichment.R |only HiResTEC-0.62.3/HiResTEC/R/CandidateBoxplot.R |only HiResTEC-0.62.3/HiResTEC/R/DetermineElementComposition.R |only HiResTEC-0.62.3/HiResTEC/R/EvaluateMassTargetedForFlux.R |only HiResTEC-0.62.3/HiResTEC/R/EvaluateSpectrum.R |only HiResTEC-0.62.3/HiResTEC/R/ExportHeuristicsTable.R |only HiResTEC-0.62.3/HiResTEC/R/RankCandidateList.R |only HiResTEC-0.62.3/HiResTEC/R/groupval.R |only HiResTEC-0.62.3/HiResTEC/man/mz_shift_corrector.Rd |only HiResTEC-0.62.3/HiResTEC/man/res_list.Rd |only HiResTEC-0.62.3/HiResTEC/man/sam.Rd |only HiResTEC-0.62.3/HiResTEC/man/xcms_cand.Rd |only HiResTEC-0.63.1/HiResTEC/DESCRIPTION | 20 + HiResTEC-0.63.1/HiResTEC/MD5 | 63 ++---- HiResTEC-0.63.1/HiResTEC/NAMESPACE | 7 HiResTEC-0.63.1/HiResTEC/NEWS.md |only HiResTEC-0.63.1/HiResTEC/R/DeconvoluteSpectrum.R | 69 +++--- HiResTEC-0.63.1/HiResTEC/R/EvaluateCandidate.R | 3 HiResTEC-0.63.1/HiResTEC/R/EvaluateCandidateListAgainstRawData.R | 48 ++-- HiResTEC-0.63.1/HiResTEC/R/EvaluatePairsFromXCMSSet.R | 105 ++++++---- HiResTEC-0.63.1/HiResTEC/R/GenerateCandXLSX.R | 30 +- HiResTEC-0.63.1/HiResTEC/R/GenerateQCPlots.R | 34 +-- HiResTEC-0.63.1/HiResTEC/R/HiResTEC-data.R | 31 +- HiResTEC-0.63.1/HiResTEC/R/HiResTEC-utils.R |only HiResTEC-0.63.1/HiResTEC/R/getMultipleBPC.R | 43 ++-- HiResTEC-0.63.1/HiResTEC/R/plotBPC.R | 38 +-- HiResTEC-0.63.1/HiResTEC/R/plotMID.R | 37 +-- HiResTEC-0.63.1/HiResTEC/README.md | 21 -- HiResTEC-0.63.1/HiResTEC/build |only HiResTEC-0.63.1/HiResTEC/data/raw.rda |only HiResTEC-0.63.1/HiResTEC/inst/doc |only HiResTEC-0.63.1/HiResTEC/man/DeconvoluteSpectrum.Rd | 30 +- HiResTEC-0.63.1/HiResTEC/man/EvaluateCandidateListAgainstRawData.Rd | 38 ++- HiResTEC-0.63.1/HiResTEC/man/EvaluatePairsFromXCMSSet.Rd | 73 ++++-- HiResTEC-0.63.1/HiResTEC/man/GenerateCandXLSX.Rd | 19 - HiResTEC-0.63.1/HiResTEC/man/GenerateQCPlots.Rd | 23 +- HiResTEC-0.63.1/HiResTEC/man/HiResTEC-data.Rd |only HiResTEC-0.63.1/HiResTEC/man/getMultipleBPC.Rd | 27 +- HiResTEC-0.63.1/HiResTEC/man/plotBPC.Rd | 24 +- HiResTEC-0.63.1/HiResTEC/man/plotMID.Rd | 24 +- HiResTEC-0.63.1/HiResTEC/vignettes |only 41 files changed, 464 insertions(+), 343 deletions(-)
Title: Regulatory Tables for Clinical Research
Description: Creates tables suitable for regulatory agency submission by
leveraging the 'gtsummary' package as the back end. Tables can be exported
to HTML, Word, PDF and more. Highly customized outputs are
available by utilizing existing styling functions from 'gtsummary' as
well as custom options designed for regulatory tables.
Author: Shannon Pileggi [aut, cre, cph]
,
Daniel D. Sjoberg [aut]
Maintainer: Shannon Pileggi <shannon.pileggi@gmail.com>
Diff between gtreg versions 0.4.0 dated 2024-07-25 and 0.4.1 dated 2025-02-27
DESCRIPTION | 17 MD5 | 93 +- NAMESPACE | 224 ++-- NEWS.md | 7 R/add_overall.R | 477 +++++----- R/broom-helpers.R |only R/complete_ae_data.R | 512 +++++------ R/data.R | 60 - R/gtreg-package.R | 26 R/inline_text_tbl_ae.R | 160 +-- R/reexport.R | 334 +++---- R/selectors.R | 166 +-- R/tbl_ae.R | 398 ++++---- R/tbl_ae_count.R | 294 +++--- R/tbl_ae_focus.R | 420 ++++----- R/tbl_listing.R | 330 +++---- R/tbl_reg_summary.R | 152 +-- R/utils-tbl_ae.R | 689 +++++++-------- README.md | 305 +++--- build/vignette.rds |binary inst/WORDLIST | 42 inst/doc/further_documentation.R | 12 inst/doc/further_documentation.html | 542 +++++------ man/add_overall_tbl_ae.Rd | 228 ++--- man/df_adverse_events.Rd | 52 - man/df_patient_characteristics.Rd | 50 - man/dot-complete_ae_data.Rd | 136 +- man/gtreg-package.Rd | 62 - man/inline_text_tbl_ae.Rd | 94 +- man/reexports.Rd | 116 +- man/selectors.Rd | 136 +- man/style_xxx.Rd | 62 - man/tbl_ae.Rd | 242 ++--- man/tbl_ae_count.Rd | 188 ++-- man/tbl_ae_focus.Rd | 198 ++-- man/tbl_listing.Rd | 186 ++-- man/tbl_reg_summary.Rd | 198 ++-- tests/spelling.R | 6 tests/testthat.R | 8 tests/testthat/_snaps/style_xxx.md | 244 ++--- tests/testthat/test-add_overall.R | 444 ++++----- tests/testthat/test-complete_ae_data.R | 932 ++++++++++---------- tests/testthat/test-modify_header.R | 25 tests/testthat/test-style_xxx.R | 226 ++-- tests/testthat/test-tbl_ae.R | 1503 ++++++++++++++++----------------- tests/testthat/test-tbl_ae_count.R | 4 tests/testthat/test-tbl_ae_focus.R | 20 tests/testthat/test-utils-tbl_ae.R | 196 ++-- 48 files changed, 5420 insertions(+), 5396 deletions(-)
Title: 'DataSHIELD' 'Tidyverse' Clientside Package
Description: Implementation of selected 'Tidyverse' functions within 'DataSHIELD', an open-source federated analysis solution in R. Currently, 'DataSHIELD' contains very limited tools for data manipulation, so the aim of this package is to improve the researcher experience by implementing essential functions for data manipulation, including subsetting, filtering, grouping, and renaming variables. This is the clientside package which should be installed locally, and is used in conjuncture with the serverside package 'dsTidyverse' which is installed on the remote server holding the data. For more information, see <https://www.tidyverse.org/>, <https://datashield.org/> and <https://github.com/molgenis/ds-tidyverse>.
Author: Tim Cadman [aut, cre] ,
Mariska Slofstra [aut] ,
Stuart Wheater [aut],
Demetris Avraam [aut]
Maintainer: Tim Cadman <t.j.cadman@umcg.nl>
Diff between dsTidyverseClient versions 1.0.0 dated 2024-10-31 and 1.0.2 dated 2025-02-27
DESCRIPTION | 6 MD5 | 30 +- NEWS.md | 3 R/ds.case_when.R | 2 R/ds.filter.R | 2 R/utils.R | 6 README.md | 23 + build/vignette.rds |binary inst/doc/dstidyverse.Rmd | 173 +++++++---- inst/doc/dstidyverse.html | 615 +++++++++++++++++++---------------------- man/ds.case_when.Rd | 2 man/ds.filter.Rd | 2 tests/testthat/test-select.R | 4 tests/testthat/test-utils.R | 6 vignettes/dstidyverse.Rmd | 173 +++++++---- vignettes/dstidyverse.Rmd.orig | 6 16 files changed, 585 insertions(+), 468 deletions(-)
More information about dsTidyverseClient at CRAN
Permanent link
Title: 'DataSHIELD' 'Tidyverse' Serverside Package
Description: Implementation of selected 'Tidyverse' functions within 'DataSHIELD', an open-source federated analysis solution in R. Currently, DataSHIELD contains very limited tools for data manipulation, so the aim of this package is to improve the researcher experience by implementing essential functions for data manipulation, including subsetting, filtering, grouping, and renaming variables. This is the serverside package which should be installed on the server holding the data, and is used in conjuncture with the clientside package 'dsTidyverseClient' which is installed in the local R environment of the analyst. For more information, see <https://www.tidyverse.org/> and <https://datashield.org/>.
Author: Tim Cadman [aut, cre] ,
Mariska Slofstra [aut] ,
Stuart Wheater [aut],
Demetris Avraam [aut]
Maintainer: Tim Cadman <t.j.cadman@umcg.nl>
Diff between dsTidyverse versions 1.0.1 dated 2024-10-25 and 1.0.4 dated 2025-02-27
DESCRIPTION | 10 +++--- MD5 | 26 ++++++++--------- NEWS.md | 3 + R/caseWhenDS.R | 2 - R/distinctDS.R | 1 R/groupByDS.R | 1 R/ifElseDS.R | 2 - R/mutateDS.R | 25 +++++++++++++++- R/utils.R | 15 ++++----- README.md | 28 +++++++++++++++++- tests/testthat/_snaps/utils.md | 6 +-- tests/testthat/test-mutateDS.R | 62 +++++++++++++++++++++++++++++++++++++++++ tests/testthat/test-selectDS.R | 7 ++++ tests/testthat/test-utils.R | 4 +- 14 files changed, 155 insertions(+), 37 deletions(-)
Title: Code and Obtain Customized Planned Comparisons with 'appRiori'
Description: With 'appRiori' <doi:10.1177/25152459241293110>, users upload the research variables and the app guides them to the best set of comparisons fitting the hypotheses, for both main and interaction effects. Through a graphical explanation and empirical examples on reproducible data, it is shown that it is possible to understand both the logic behind the planned comparisons and the way to interpret them when a model is tested.
Author: Umberto Granziol [aut, cre],
Maximilian Rabe [aut] ,
Andrea Spoto [aut],
Giulio Vidotto [aut],
Marcello Gallucci [aut]
Maintainer: Umberto Granziol <umberto.granziol@unipd.it>
Diff between appRiori versions 0.0.5 dated 2024-02-13 and 0.0.6 dated 2025-02-27
DESCRIPTION | 8 ++++---- MD5 | 9 ++++++--- inst/CITATION |only inst/tutorial/tutorial0.html |only inst/tutorial/tutorial0.md | 2 +- inst/tutorial/welcome.html |only inst/tutorial/welcome.md | 8 +++++++- 7 files changed, 18 insertions(+), 9 deletions(-)
Title: Bayesian Multinomial Logistic Normal Regression
Description: Provides methods for fitting and inspection of Bayesian Multinomial Logistic Normal Models using MAP estimation and Laplace Approximation as developed in Silverman et. Al. (2022) <https://www.jmlr.org/papers/v23/19-882.html>. Key functionality is implemented in C++ for scalability. 'fido' replaces the previous package 'stray'.
Author: Justin Silverman [aut, cre],
Kim Roche [ctb],
Michelle Nixon [ctb]
Maintainer: Justin Silverman
<JustinSilverman@psu.edu>
Diff between fido versions 1.1.1 dated 2024-06-05 and 1.1.2 dated 2025-02-27
DESCRIPTION | 24 MD5 | 183 +-- NAMESPACE | 304 ++--- NEWS.md | 178 +- R/R2.R | 224 +-- R/RISK_CCFA.R | 112 - R/RcppExports.R | 1068 ++++++++--------- R/bassetfit_s3.R | 516 ++++---- R/driver-utils.R | 976 ++++++++-------- R/fido.R | 29 R/fido_transforms.R | 912 +++++++-------- R/fido_utils.R | 530 ++++---- R/fidofit_methods.R | 1744 ++++++++++++++--------------- R/fidofit_s3.R | 594 ++++----- R/fit_basset.R | 600 ++++----- R/fit_maltipoo.R | 404 +++--- R/fit_orthus.R | 554 ++++----- R/fit_pibble.R | 604 +++++----- R/generics_s3.R | 384 +++--- R/iqlr.R | 140 +- R/kernels.R | 78 - R/mallard-data.R | 30 R/mallard_family-data.R | 32 R/maltipoo_sim.R | 118 - R/maltipoofit_s3.R | 158 +- R/orthus_sim.R | 102 - R/orthus_transform_wrapper.R | 512 ++++---- R/pcrbias_mock-data.R | 80 - R/pibble_plotting.R | 382 +++--- R/pibble_sim.R | 96 - build/vignette.rds |binary inst/CITATION | 30 inst/doc/introduction-to-fido.Rmd | 948 +++++++-------- inst/doc/introduction-to-fido.html | 1740 ++++++++++++++-------------- inst/doc/mitigating-pcrbias.R | 30 inst/doc/mitigating-pcrbias.Rmd | 538 ++++---- inst/doc/mitigating-pcrbias.html | 1201 +++++++++---------- inst/doc/non-linear-models.R | 426 +++---- inst/doc/non-linear-models.Rmd | 710 +++++------ inst/doc/non-linear-models.html | 1474 ++++++++++++------------ inst/doc/orthus.R | 6 inst/doc/orthus.Rmd | 522 ++++---- inst/doc/orthus.html | 1292 ++++++++++----------- inst/doc/picking_priors.R | 50 inst/doc/picking_priors.Rmd | 412 +++--- inst/doc/picking_priors.html | 1421 +++++++++++------------ inst/extdata/Kashyap2013/README.txt | 2 inst/extdata/Kashyap2013/metabolites.csv | 974 ++++++++-------- inst/include/MultDirichletBoot.h | 1 inst/include/fidoGenerated.h |only man/RISK_CCFA.Rd | 44 man/RISK_CCFA_otu.Rd | 44 man/RISK_CCFA_sam.Rd | 44 man/RISK_CCFA_tax.Rd | 44 man/basset_fit.Rd | 166 +- man/conjugateLinearModel.Rd | 96 - man/fido_package.Rd | 66 - man/optimPibbleCollapsed.Rd | 334 ++--- man/orthus_fit.Rd | 194 +-- man/pibble_fit.Rd | 218 +-- man/predict.bassetfit.Rd | 106 - man/r2.Rd | 94 - man/uncollapsePibble.Rd | 196 +-- man/uncollapsePibble_sigmaKnown.Rd | 190 +-- src/ConjugateLinearModel.cpp | 13 tests/testthat.R | 12 tests/testthat/test-R2.R | 38 tests/testthat/test-baseFuns.R | 40 tests/testthat/test-basset.R | 372 +++--- tests/testthat/test-hessian.R | 120 - tests/testthat/test-hvp.R | 38 tests/testthat/test-ilr.R | 34 tests/testthat/test-iqlr.R | 34 tests/testthat/test-kernels.R | 26 tests/testthat/test-laplaceapproximation.R | 92 - tests/testthat/test-linesearch.R | 38 tests/testthat/test-maltipoo.R | 86 - tests/testthat/test-matdist.R | 156 +- tests/testthat/test-mongrelfit-methods.R | 98 - tests/testthat/test-multdirichletboot.R | 76 - tests/testthat/test-numCores.R | 26 tests/testthat/test-orthus-transforms.R | 156 +- tests/testthat/test-orthus.R | 94 - tests/testthat/test-pibble.R | 458 +++---- tests/testthat/test-sylvester-speedups.R | 108 - tests/testthat/test-transforms.R | 26 tests/testthat/test-utils.R | 68 - vignettes/bibliography.bib | 142 +- vignettes/introduction-to-fido.Rmd | 948 +++++++-------- vignettes/mitigating-pcrbias.Rmd | 538 ++++---- vignettes/non-linear-models.Rmd | 710 +++++------ vignettes/orthus.Rmd | 522 ++++---- vignettes/picking_priors.Rmd | 412 +++--- 93 files changed, 15382 insertions(+), 15380 deletions(-)
Title: Consensus OPLS for Multi-Block Data Fusion
Description: Merging data from multiple sources is a relevant approach for
comprehensively evaluating complex systems. However, the inherent problems
encountered when analyzing single tables are amplified with the generation
of multi-block datasets, and finding the relationships between data layers
of increasing complexity constitutes a challenging task. For that purpose,
a generic methodology is proposed by combining the strength of established
data analysis strategies, i.e. multi-block approaches and the Orthogonal
Partial Least Squares (OPLS) framework to provide an efficient tool for the
fusion of data obtained from multiple sources. The package enables quick
and efficient implementation of the consensus OPLS model for any horizontal
multi-block data structures (observation-based matching). Moreover, it
offers an interesting range of metrics and graphics to help to determine
the optimal number of components and check the validity of the model
through permutation tests. Interpretation tools incl [...truncated...]
Author: Celine Bougel [aut] ,
Julien Boccard [aut] ,
Florence Mehl [aut] ,
Marie Tremblay-Franco [fnd] ,
Mark Ibberson [fnd] ,
Van Du T. Tran [aut, cre]
Maintainer: Van Du T. Tran <thuong.tran@sib.swiss>
Diff between ConsensusOPLS versions 1.0.0 dated 2024-06-20 and 1.1.0 dated 2025-02-27
DESCRIPTION | 21 MD5 | 58 - NAMESPACE | 2 NEWS.md | 21 R/ConsensusOPLS.R | 234 +++++- R/ConsensusOPLSCV.R | 354 +++++---- R/DQ2.R | 61 - R/RVConsensusOPLS.R | 225 +++--- R/RVmodified.R | 10 R/VariableImportanceProjection.R | 24 R/koplsCenterK.R | 67 - R/koplsClassify.R | 11 R/koplsCrossValSet.R | 4 R/koplsDummy.R | 1 R/koplsKernel.R | 26 R/koplsModel.R | 196 ++--- R/koplsPredict.R | 149 ++-- R/koplsScale.R | 78 +- R/koplsSensSpec.R | 2 build/vignette.rds |binary inst/doc/ConsensusOPLS.R | 170 ++-- inst/doc/ConsensusOPLS.Rmd | 316 ++++++-- inst/doc/ConsensusOPLS.html | 1211 ++++++++++++++++++++-------------- man/ConsensusOPLS-class.Rd | 8 man/ConsensusOPLS-package.Rd | 1 man/ConsensusOPLS.Rd | 3 man/predict.Rd |only tests/testthat/test-ConsensusOPLS.R |only tests/testthat/test-RVConsensusOPLS.R | 253 ++++--- vignettes/ConsensusOPLS.Rmd | 316 ++++++-- vignettes/ConsensusOPLS.bib | 235 +++--- 31 files changed, 2479 insertions(+), 1578 deletions(-)