Title: Create Pharmacometric Models
Description: Provides a user interface to create or modify pharmacometric
models for various modeling and simulation software platforms.
Author: Sebastien Bihorel [cre, aut]
Maintainer: Sebastien Bihorel <sb.pmlab@gmail.com>
Diff between pmxcode versions 0.1.4 dated 2024-10-19 and 0.2.0 dated 2025-02-28
pmxcode-0.1.4/pmxcode/man/get_mrg_individual_parm_code.Rd |only pmxcode-0.2.0/pmxcode/DESCRIPTION | 6 pmxcode-0.2.0/pmxcode/LICENSE | 2 pmxcode-0.2.0/pmxcode/MD5 | 36 pmxcode-0.2.0/pmxcode/NEWS.md | 7 pmxcode-0.2.0/pmxcode/R/golem_utils_ui.R | 30 pmxcode-0.2.0/pmxcode/R/new_model_server.R | 394 ++++++++-- pmxcode-0.2.0/pmxcode/R/new_model_ui.R | 9 pmxcode-0.2.0/pmxcode/R/utils_common.R | 28 pmxcode-0.2.0/pmxcode/R/utils_mrgsolve.R | 237 ++++-- pmxcode-0.2.0/pmxcode/R/utils_nonmem.R | 203 +++-- pmxcode-0.2.0/pmxcode/R/zzz.R | 3 pmxcode-0.2.0/pmxcode/inst/resources/labelunit_lib.json | 20 pmxcode-0.2.0/pmxcode/inst/resources/logit_variability_derivation.Rmd |only pmxcode-0.2.0/pmxcode/inst/resources/parm_lib.json | 4 pmxcode-0.2.0/pmxcode/inst/resources/rv_lib.json | 8 pmxcode-0.2.0/pmxcode/man/get_mrg_parms_code.Rd | 4 pmxcode-0.2.0/pmxcode/man/get_mrg_parms_code_minion.Rd |only pmxcode-0.2.0/pmxcode/man/replace_mrg_omega.Rd | 4 pmxcode-0.2.0/pmxcode/man/replace_mrg_param.Rd | 4 pmxcode-0.2.0/pmxcode/man/scale_value.Rd |only 21 files changed, 738 insertions(+), 261 deletions(-)
Title: Analyzing the Orientation of Maximum Horizontal Stress
Description: Models the direction of the maximum horizontal stress using
relative plate motion parameters. Statistical algorithms to evaluate
the modeling results compared with the observed data. Provides plots
to visualize the results. Methods described in Stephan et al. (2023)
<doi:10.1038/s41598-023-42433-2> and Wdowinski (1998)
<doi:10.1016/S0079-1946(98)00091-3>.
Author: Tobias Stephan [aut, cre]
Maintainer: Tobias Stephan <tobias.stephan1@yahoo.com>
Diff between tectonicr versions 0.4.5 dated 2025-02-26 and 0.4.6 dated 2025-02-28
tectonicr-0.4.5/tectonicr/tests/testthat/Rplots.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots1.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots10.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots11.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots12.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots13.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots14.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots15.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots16.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots17.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots18.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots19.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots2.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots20.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots21.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots22.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots23.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots24.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots25.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots26.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots27.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots3.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots4.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots5.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots6.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots7.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots8.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots9.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/test-coordinates.R |only tectonicr-0.4.5/tectonicr/tests/testthat/test-draw_eulerpole.R |only tectonicr-0.4.5/tectonicr/tests/testthat/test-misfit_shmax.R |only tectonicr-0.4.5/tectonicr/tests/testthat/test-model_shmax.R |only tectonicr-0.4.5/tectonicr/tests/testthat/test-nuvel1.R |only tectonicr-0.4.5/tectonicr/tests/testthat/test-rotation.R |only tectonicr-0.4.5/tectonicr/tests/testthat/test-various.R |only tectonicr-0.4.6/tectonicr/DESCRIPTION | 6 tectonicr-0.4.6/tectonicr/MD5 | 79 tectonicr-0.4.6/tectonicr/NEWS.md | 4 tectonicr-0.4.6/tectonicr/R/draw_eulerpole.R | 557 +- tectonicr-0.4.6/tectonicr/R/interpolation.R | 2039 ++++--- tectonicr-0.4.6/tectonicr/R/model_shmax.R | 1081 ++- tectonicr-0.4.6/tectonicr/R/pb_distance.R | 443 - tectonicr-0.4.6/tectonicr/R/plotting.R | 2719 +++++----- tectonicr-0.4.6/tectonicr/R/statistics.R | 2393 ++++---- tectonicr-0.4.6/tectonicr/R/various.R | 691 +- tectonicr-0.4.6/tectonicr/inst/doc/A_tectonicr.html | 4 tectonicr-0.4.6/tectonicr/inst/doc/B_datasets.html | 4 tectonicr-0.4.6/tectonicr/inst/doc/C_stress_trajectories.html | 4 tectonicr-0.4.6/tectonicr/inst/doc/D_statistics.html | 10 tectonicr-0.4.6/tectonicr/inst/doc/E_interpolation.html | 4 tectonicr-0.4.6/tectonicr/inst/doc/F_spatial.html | 8 tectonicr-0.4.6/tectonicr/man/PoR2Geo_azimuth.Rd | 4 tectonicr-0.4.6/tectonicr/man/PoR_azi.Rd | 4 tectonicr-0.4.6/tectonicr/man/PoR_map.Rd | 5 tectonicr-0.4.6/tectonicr/man/axes.Rd | 2 tectonicr-0.4.6/tectonicr/man/line_azimuth.Rd | 7 tectonicr-0.4.6/tectonicr/tests/testthat.R | 24 tectonicr-0.4.6/tectonicr/tests/testthat/test_that.R | 50 58 files changed, 5157 insertions(+), 4985 deletions(-)
Title: An R 'Pandoc' Writer
Description: Contains some functions catching all messages, 'stdout' and other
useful information while evaluating R code and other helpers to return user
specified text elements (like: header, paragraph, table, image, lists etc.)
in 'pandoc' markdown or several type of R objects similarly automatically
transformed to markdown format. Also capable of exporting/converting (the
resulting) complex 'pandoc' documents to e.g. HTML, 'PDF', 'docx' or 'odt'. This
latter reporting feature is supported in brew syntax or with a custom reference
class with a smarty caching 'backend'.
Author: Gergely Daroczi [aut, cre] ,
Roman Tsegelskyi [aut]
Maintainer: Gergely Daroczi <daroczig@rapporter.net>
Diff between pander versions 0.6.5 dated 2022-03-18 and 0.6.6 dated 2025-02-28
pander-0.6.5/pander/NEWS |only pander-0.6.6/pander/DESCRIPTION | 10 pander-0.6.6/pander/MD5 | 36 +- pander-0.6.6/pander/NAMESPACE | 1 pander-0.6.6/pander/NEWS.md |only pander-0.6.6/pander/R/S3.R | 3 pander-0.6.6/pander/R/convert.R | 2 pander-0.6.6/pander/R/helpers.R | 4 pander-0.6.6/pander/README.md | 4 pander-0.6.6/pander/build/vignette.rds |binary pander-0.6.6/pander/inst/README.brew | 4 pander-0.6.6/pander/inst/doc/evals.html | 425 ++++--------------------- pander-0.6.6/pander/inst/doc/knitr.html | 291 +---------------- pander-0.6.6/pander/inst/doc/pander.html | 374 +++------------------- pander-0.6.6/pander/inst/doc/pandoc_table.Rmd | 2 pander-0.6.6/pander/inst/doc/pandoc_table.html | 338 +------------------ pander-0.6.6/pander/man/Pandoc.convert.Rd | 2 pander-0.6.6/pander/man/splitLine.Rd | 4 pander-0.6.6/pander/src/RcppExports.cpp | 5 pander-0.6.6/pander/vignettes/pandoc_table.Rmd | 2 20 files changed, 231 insertions(+), 1276 deletions(-)
Title: Transfer Learning under Regularized Generalized Linear Models
Description: We provide an efficient implementation for two-step multi-source transfer learning algorithms in high-dimensional generalized linear models (GLMs). The elastic-net penalized GLM with three popular families, including linear, logistic and Poisson regression models, can be fitted. To avoid negative transfer, a transferable source detection algorithm is proposed. We also provides visualization for the transferable source detection results. The details of methods can be found in "Tian, Y., & Feng, Y. (2023). Transfer learning under high-dimensional generalized linear models. Journal of the American Statistical Association, 118(544), 2684-2697.".
Author: Ye Tian [aut, cre],
Yang Feng [aut]
Maintainer: Ye Tian <ye.t@columbia.edu>
Diff between glmtrans versions 2.0.0 dated 2022-02-08 and 2.1.0 dated 2025-02-28
DESCRIPTION | 11 +++---- MD5 | 32 ++++++++++---------- R/glmtrans.R | 49 +++++++++++++++++-------------- R/glmtrans_inf.R | 14 +++++---- R/models.R | 8 ++--- R/plot.glmtrans.R | 2 - R/predict.glmtrans.R | 10 +++--- R/source_detection.R | 69 +++++++++++++++++++++++++++++++-------------- build/vignette.rds |binary inst/doc/glmtrans-demo.R | 16 +++++----- inst/doc/glmtrans-demo.pdf |binary man/glmtrans.Rd | 35 ++++++++++++---------- man/glmtrans_inf.Rd | 6 +-- man/models.Rd | 12 +++---- man/plot.glmtrans.Rd | 2 - man/predict.glmtrans.Rd | 10 +++--- man/source_detection.Rd | 22 ++++++++------ 17 files changed, 170 insertions(+), 128 deletions(-)
More information about ConnectednessApproach at CRAN
Permanent link
Title: Sequence Symmetry Analysis Using the Observational Medical
Outcomes Partnership Common Data Model
Description: Calculating crude sequence ratio, adjusted sequence ratio and
confidence intervals using data mapped to the Observational Medical
Outcomes Partnership Common Data Model.
Author: Xihang Chen [aut, cre] ,
Tyman Stanford [aut] ,
Berta Raventos [aut] ,
Nicole Pratt [aut] ,
Ed Burn [aut] ,
Marti Catala [aut] ,
Danielle Newby [aut] ,
Nuria Mercade-Besora [aut] ,
Mike Du [aut] ,
Yuchen Guo [aut] ,
Kim Lopez [aut] ,
Marta Alcalde-He [...truncated...]
Maintainer: Xihang Chen <xihang.chen@ndorms.ox.ac.uk>
Diff between CohortSymmetry versions 0.2.1 dated 2025-02-12 and 0.2.2 dated 2025-02-28
DESCRIPTION | 22 +- MD5 | 18 - R/mockCohortSymmetry.R | 5 inst/doc/a01_Introduction.Rmd | 260 +++++++++++++------------- inst/doc/a01_Introduction.html | 14 - inst/doc/a02_Generate_a_sequence_cohort.html | 4 inst/doc/a03_Summarise_sequence_ratios.html | 2 inst/doc/a04_Visualise_sequence_ratios.html | 6 inst/doc/a05_Summarise_temporal_symmetry.html | 12 - vignettes/a01_Introduction.Rmd | 260 +++++++++++++------------- 10 files changed, 301 insertions(+), 302 deletions(-)
More information about CohortSymmetry at CRAN
Permanent link
Title: Miscellaneous (Stats) Helper Functions with Sane Defaults for
Reporting
Description: Helper functions that act as wrappers to more advanced statistical
methods with the advantage of having sane defaults for quick reporting.
Author: Gergely Daroczi [aut, cre] ,
Aleksandar Blagotic [aut]
Maintainer: Gergely Daroczi <daroczig@rapporter.net>
Diff between rapportools versions 1.1 dated 2022-03-21 and 1.2 dated 2025-02-28
rapportools-1.1/rapportools/inst/CITATION |only rapportools-1.2/rapportools/DESCRIPTION | 19 +++++++++++-------- rapportools-1.2/rapportools/MD5 | 13 ++++++------- rapportools-1.2/rapportools/NEWS | 26 +++++++++++++++----------- rapportools-1.2/rapportools/R/univar.R | 4 ++-- rapportools-1.2/rapportools/R/utils.R | 2 +- rapportools-1.2/rapportools/man/max.Rd | 2 +- rapportools-1.2/rapportools/man/min.Rd | 2 +- 8 files changed, 37 insertions(+), 31 deletions(-)
Title: Insurance Reserve Calculations
Description: Calculates insurance reserves and equivalence premiums using advanced numerical methods, including the Runge-Kutta algorithm and product integrals for transition probabilities. This package is useful for actuarial analyses and life insurance modeling, facilitating accurate financial projections.
Author: Oskar Allerslev [aut, cre]
Maintainer: Oskar Allerslev <Oskar.m1660@gmail.com>
Diff between lifepack versions 0.0.8 dated 2025-01-29 and 0.1.0 dated 2025-02-28
DESCRIPTION | 10 +- MD5 | 33 +++++--- NAMESPACE | 2 R/RcppExports.R |only R/equiv_premium.R | 66 ++++++++--------- R/lifepack-package.R |only R/prodint.R | 40 +++------- R/reserve.R | 56 +++++++------- R/sreserve.R | 62 ++++++++-------- build/vignette.rds |binary inst/doc/lifepack-overview.Rmd | 136 ++++++++++++++++++------------------ man/prodint.Rd | 21 ++--- man/sreserve.Rd | 72 +++++++++---------- src |only tests/testthat/test-equiv_premium.R | 56 +++++++------- tests/testthat/test-reserve.R | 56 +++++++------- tests/testthat/test-sreserve.R | 56 +++++++------- vignettes/lifepack-overview.Rmd | 136 ++++++++++++++++++------------------ 18 files changed, 397 insertions(+), 405 deletions(-)
Title: Adapted Pair Correlation Function
Description: The adapted pair correlation function transfers the concept of the
pair correlation function from point patterns to patterns of objects of
finite size and irregular shape (e.g. lakes within a country). The pair
correlation function describes the spatial distribution of objects, e.g.
random, aggregated or regularly spaced. This is a reimplementation of the
method suggested by Nuske et al. (2009) <doi:10.1016/j.foreco.2009.09.050>
using the library 'GEOS'.
Author: Robert Nuske [aut, cre]
Maintainer: Robert Nuske <robert.nuske@mailbox.org>
Diff between apcf versions 0.3.1 dated 2024-06-13 and 0.3.2 dated 2025-02-28
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 3 +++ build/vignette.rds |binary configure | 18 +----------------- configure.ac | 18 +----------------- inst/doc/intro.html | 14 +++++++------- 7 files changed, 21 insertions(+), 50 deletions(-)
Title: Generalized Additive Extreme Value Models for Location, Scale
and Shape
Description: Fits generalized additive models for the location, scale and shape
parameters of a generalized extreme value response distribution. The
methodology is based on Rigby, R.A. and Stasinopoulos, D.M. (2005),
<doi:10.1111/j.1467-9876.2005.00510.x> and implemented using functions from
the 'gamlss' package <doi:10.32614/CRAN.package.gamlss>.
Author: Paul J. Northrop [aut, cre, cph],
Jennifer Ji [aut]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Diff between gamlssx versions 1.0.1 dated 2024-06-26 and 1.0.2 dated 2025-02-28
DESCRIPTION | 12 +++++------ MD5 | 33 ++++++++++++++++++------------- NAMESPACE | 1 NEWS.md |only R/GEVfamily.R | 10 ++++----- R/fitGEV.R | 10 +++++---- R/gamlssx-package.R | 1 R/gevExpInfo.R | 2 - README.md | 26 ++++++++++++------------ build/partial.rdb |binary man/GEV.Rd | 6 ++--- man/figures/README-unnamed-chunk-2-4.png |binary man/figures/README-unnamed-chunk-2-5.png |binary man/figures/README-unnamed-chunk-3-1.png |only man/figures/README-unnamed-chunk-4-1.png |only man/figures/README-unnamed-chunk-6-1.png |only man/figures/README-unnamed-chunk-7-1.png |only man/figures/README-unnamed-chunk-8-1.png |only man/fitGEV.Rd | 8 ++++--- man/gevExpInfo.Rd | 2 - tools |only 21 files changed, 62 insertions(+), 49 deletions(-)
Title: Fast Estimators for Design-Based Inference
Description: Fast procedures for small set of commonly-used, design-appropriate estimators with robust standard errors and confidence intervals. Includes estimators for linear regression, instrumental variables regression, difference-in-means, Horvitz-Thompson estimation, and regression improving precision of experimental estimates by interacting treatment with centered pre-treatment covariates introduced by Lin (2013) <doi:10.1214/12-AOAS583>.
Author: Graeme Blair [aut, cre],
Jasper Cooper [aut],
Alexander Coppock [aut],
Macartan Humphreys [aut],
Luke Sonnet [aut],
Neal Fultz [ctb],
Lily Medina [ctb],
Russell Lenth [ctb],
Molly Offer-Westort [ctb]
Maintainer: Graeme Blair <graeme.blair@gmail.com>
Diff between estimatr versions 1.0.4 dated 2024-03-31 and 1.0.6 dated 2025-02-28
DESCRIPTION | 14 ++-- MD5 | 32 +++++----- NEWS.md | 12 +++ R/S3_predict.R | 100 ++++++++++++++++++++++++-------- R/estimatr_lh_robust.R | 37 +++++++++-- R/estimatr_lm_lin.R | 47 +++++++++------ build/partial.rdb |binary man/estimatr.Rd | 1 man/lh_robust.Rd | 6 + man/lm_lin.Rd | 21 +++++- man/predict.lm_robust.Rd | 21 ++++++ tests/testthat/helper-se-types.R | 1 tests/testthat/test-lh-robust.R | 64 +++++++++++++++++++- tests/testthat/test-lm-cluster.R | 1 tests/testthat/test-lm-lin.R | 11 +++ tests/testthat/test-lm-robust_margins.R | 10 +-- tests/testthat/test-s3-methods.R | 64 ++++++++++++++++++-- 17 files changed, 353 insertions(+), 89 deletions(-)
Title: Methods to Analyse Seasonal Radial Tree Growth Data
Description: Methods for comparing different regression algorithms for
describing the temporal dynamics of secondary tree growth (xylem and
phloem). Users can compare the accuracy of the most common fitting methods
usually used to analyse xylem and phloem data, i.e., Gompertz function,
Double Gompertz function, General Additive Models (GAMs); and an algorithm
newly introduced to the field, i.e., Bayesian Regularised Neural Networks
(brnn). The core function of the package is XPSgrowth(), while the results
can be interpreted using implemented generic S3 methods, such as plot() and
summary().
Author: Jernej Jevsenak [aut, cre]
Maintainer: Jernej Jevsenak <jernej.jevsenak@gmail.com>
Diff between rTG versions 1.0.3 dated 2024-07-25 and 1.0.4 dated 2025-02-28
DESCRIPTION | 12 - MD5 | 18 +- NAMESPACE | 2 NEWS.md | 4 R/XPSgrowth.R | 162 ++++++++++++++---- man/XPSgrowth.Rd | 410 ++++++++++++++++++++++------------------------- man/data_dendrometers.Rd | 56 +++--- man/data_trees.Rd | 80 ++++----- man/double_gompertz.Rd | 60 +++--- man/parameters.Rd | 58 +++--- 10 files changed, 473 insertions(+), 389 deletions(-)
Title: Run Interruptible Code Asynchronously
Description: Takes an R expression and returns a Job object with a $stop() method
which can be called to terminate the background job. Also provides timeouts
and other mechanisms for automatically terminating a background job. The
result of the expression is available synchronously via $result or
asynchronously with callbacks or through the 'promises' package framework.
Author: Daniel P. Smith [aut, cre] ,
Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between jobqueue versions 1.4.1 dated 2025-02-21 and 1.5.1 dated 2025-02-28
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 5 +++++ R/process.r | 12 +++++++----- R/queue.r | 21 +++++++++++++-------- R/utils.r | 11 +++++++++++ R/validate.r | 5 +++-- R/worker.r | 31 ++++++++++++++++++------------- man/Queue.Rd | 8 ++++++-- man/Worker.Rd | 8 ++++++-- tests/testthat/test-process.r | 2 +- tests/testthat/test-queue.r | 4 ++++ 12 files changed, 89 insertions(+), 48 deletions(-)
Title: My Toolbox for Assisting Document Editing and Data Presenting
Description: The purpose of this package is to share a collection of functions the author wrote during weekends for managing
kitchen and garden tasks, e.g. making plant growth charts or Thanksgiving kitchen schedule charts, etc.
Functions might include but not limited to:
(1) aiding summarizing time related data;
(2) generating axis transformation from data; and
(3) aiding Markdown (with html output) and Shiny file editing.
Author: Y Hsu [aut, cre]
Maintainer: Y Hsu <yh202109@gmail.com>
Diff between mtb versions 0.1.8 dated 2022-10-20 and 0.1.9 dated 2025-02-28
DESCRIPTION | 14 MD5 | 42 - NEWS.md | 117 ++-- R/helper_timerelated.R | 148 ++--- R/helper_timerelated2.R | 246 ++++---- README.md | 180 +++--- build/vignette.rds |binary inst/doc/mtb_axis.R | 78 +- inst/doc/mtb_axis.html | 887 +++++++++++++++---------------- inst/doc/mtb_bill_summary.R | 66 +- inst/doc/mtb_bill_summary.html | 870 +++++++++++++++--------------- inst/doc/mtb_color.R | 58 +- inst/doc/mtb_color.html | 815 ++++++++++++++-------------- inst/doc/mtb_md.R | 48 - inst/doc/mtb_md.html | 787 +++++++++++++-------------- inst/doc/mtb_timerelated.R | 56 - inst/doc/mtb_timerelated.html | 837 ++++++++++++++--------------- man/figures/README-example_color_2-1.png |binary man/figures/README-example_color_2-2.png |binary man/time_plot_event.Rd | 6 man/time_plot_interval.Rd | 4 tests/testthat/test-helper_timerelated.R | 2 22 files changed, 2635 insertions(+), 2626 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley,
"Modern Applied Statistics with S" (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph],
Bill Venables [aut, cph],
Douglas M. Bates [ctb],
Kurt Hornik [trl] ,
Albrecht Gebhardt [trl] ,
David Firth [ctb]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between MASS versions 7.3-64 dated 2025-01-04 and 7.3-65 dated 2025-02-28
ChangeLog | 7 +- DESCRIPTION | 10 +- MD5 | 12 +-- build/partial.rdb |binary data/epil.rda |binary man/epil.Rd | 4 + tests/Examples/MASS-Ex.Rout.save | 134 +++++++++++++++++++-------------------- 7 files changed, 88 insertions(+), 79 deletions(-)
Title: Group Lasso and Elastic Net Solver for Generalized Linear Models
Description: Extremely efficient procedures for fitting the entire group lasso and group elastic net regularization path for GLMs, multinomial, the Cox model and multi-task Gaussian models. Similar to the R package 'glmnet' in scope of models, and in computational speed. This package provides R bindings to the C++ code underlying the corresponding Python package 'adelie'. These bindings offer a general purpose group elastic net solver,
a wide range of matrix classes that can exploit special structure
to allow large-scale inputs, and an assortment of
generalized linear model classes for fitting various types of data.
The package is an implementation of Yang, J. and Hastie, T. (2024) <doi:10.48550/arXiv.2405.08631>.
Author: James Yang [aut, cph],
Trevor Hastie [aut, cph, cre],
Balasubramanian Narasimhan [aut]
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between adelie versions 1.0.6 dated 2025-02-14 and 1.0.7 dated 2025-02-28
DESCRIPTION | 8 MD5 | 145 +- NAMESPACE | 1 R/constraints.R |only R/matrix.R | 3 R/solver.R | 2 R/state.R | 2 inst/adelie/adelie/__init__.py | 2 inst/adelie/adelie/matrix.py | 2 inst/adelie/adelie/src/include/adelie_core/constraint/constraint_base.hpp | 16 inst/adelie/adelie/src/include/adelie_core/constraint/constraint_box.ipp | 8 inst/adelie/adelie/src/include/adelie_core/constraint/constraint_linear.ipp | 28 inst/adelie/adelie/src/include/adelie_core/constraint/constraint_one_sided.ipp | 16 inst/adelie/adelie/src/include/adelie_core/io/io_snp_phased_ancestry.ipp | 22 inst/adelie/adelie/src/include/adelie_core/io/io_snp_unphased.ipp | 22 inst/adelie/adelie/src/include/adelie_core/io/utils.hpp | 25 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_constraint_base.hpp | 38 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_constraint_dense.hpp | 1 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_constraint_dense.ipp | 45 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_constraint_sparse.hpp | 1 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_constraint_sparse.ipp | 40 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_cov_base.hpp | 8 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_cov_block_diag.ipp | 25 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_cov_dense.ipp | 4 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_cov_lazy_cov.ipp | 57 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_cov_sparse.ipp | 11 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_base.hpp | 75 - inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_block_diag.hpp | 27 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_block_diag.ipp | 118 + inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_concatenate.hpp | 43 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_concatenate.ipp | 304 +++- inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_convex_gated_relu.hpp | 32 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_convex_gated_relu.ipp | 263 ++- inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_convex_relu.hpp | 32 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_convex_relu.ipp | 273 ++- inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_dense.ipp | 82 - inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_interaction.hpp | 29 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_interaction.ipp | 154 +- inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_kronecker_eye.hpp | 44 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_kronecker_eye.ipp | 302 ++-- inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_one_hot.hpp | 34 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_one_hot.ipp | 128 + inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_snp_phased_ancestry.hpp | 26 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_snp_phased_ancestry.ipp | 163 +- inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_snp_unphased.hpp | 24 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_snp_unphased.ipp | 109 - inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_sparse.hpp | 10 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_sparse.ipp | 92 - inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_standardize.hpp | 12 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_standardize.ipp | 77 - inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_subset.hpp | 25 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_subset.ipp | 155 +- inst/adelie/adelie/src/include/adelie_core/matrix/utils.hpp | 94 + inst/adelie/adelie/src/include/adelie_core/solver/solver_base.hpp | 42 inst/adelie/adelie/src/include/adelie_core/solver/solver_css_cov.hpp | 14 inst/adelie/adelie/src/include/adelie_core/solver/solver_gaussian_cov.hpp | 20 inst/adelie/adelie/src/include/adelie_core/solver/solver_gaussian_naive.hpp | 38 inst/adelie/adelie/src/include/adelie_core/solver/solver_glm_naive.hpp | 21 inst/adelie/adelie/src/include/adelie_core/state/state_base.ipp | 10 inst/adelie/adelie/src/include/adelie_core/util/omp.hpp |only inst/adelie/adelie/src/include/adelie_core/util/types.hpp | 8 inst/adelie/adelie/src/py_constraint.cpp | 22 inst/adelie/adelie/src/py_decl.hpp | 1 inst/adelie/adelie/src/py_matrix.cpp | 197 ++ inst/adelie/adelie/src/py_sklearn.cpp | 20 inst/adelie/adelie/src/py_solver.cpp | 14 inst/adelie/adelie/state.py | 6 inst/doc/adelie.R | 29 inst/doc/adelie.Rmd | 57 inst/doc/adelie.html | 703 +++++----- man/constraint.box.Rd |only man/grpnet.Rd | 2 src/rcpp_matrix.cpp | 10 src/rcpp_matrix.h | 114 + vignettes/adelie.Rmd | 57 75 files changed, 2890 insertions(+), 1754 deletions(-)
Title: Parse XML
Description: Bindings to 'libxml2' for working with XML data using a simple,
consistent interface based on 'XPath' expressions. Also supports XML schema
validation; for 'XSLT' transformations see the 'xslt' package.
Author: Hadley Wickham [aut],
Jim Hester [aut],
Jeroen Ooms [aut, cre],
Posit Software, PBC [cph, fnd],
R Foundation [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between xml2 versions 1.3.6 dated 2023-12-04 and 1.3.7 dated 2025-02-28
xml2-1.3.6/xml2/build/stage23.rdb |only xml2-1.3.6/xml2/build/xml2.pdf |only xml2-1.3.6/xml2/src/xml2_init.cpp |only xml2-1.3.7/xml2/DESCRIPTION | 25 ++-- xml2-1.3.7/xml2/LICENSE | 2 xml2-1.3.7/xml2/MD5 | 107 ++++++++---------- xml2-1.3.7/xml2/NEWS.md | 8 + xml2-1.3.7/xml2/R/as_xml_document.R | 2 xml2-1.3.7/xml2/R/format.R | 5 xml2-1.3.7/xml2/R/init.R | 4 xml2-1.3.7/xml2/R/paths.R | 4 xml2-1.3.7/xml2/R/utils.R | 22 +-- xml2-1.3.7/xml2/R/xml_missing.R | 2 xml2-1.3.7/xml2/R/xml_parse.R | 2 xml2-1.3.7/xml2/R/xml_serialize.R | 2 xml2-1.3.7/xml2/R/xml_write.R | 8 - xml2-1.3.7/xml2/README.md | 4 xml2-1.3.7/xml2/build/partial.rdb |only xml2-1.3.7/xml2/build/vignette.rds |binary xml2-1.3.7/xml2/cleanup | 2 xml2-1.3.7/xml2/configure | 21 +-- xml2-1.3.7/xml2/inst/doc/modification.html | 15 +- xml2-1.3.7/xml2/inst/include/xml2_types.h | 1 xml2-1.3.7/xml2/man/read_xml.Rd | 2 xml2-1.3.7/xml2/man/write_xml.Rd | 2 xml2-1.3.7/xml2/man/xml2-package.Rd | 2 xml2-1.3.7/xml2/src/Makevars.in | 2 xml2-1.3.7/xml2/src/Makevars.win | 30 +++-- xml2-1.3.7/xml2/src/connection.cpp | 3 xml2-1.3.7/xml2/src/connection.h | 3 xml2-1.3.7/xml2/src/init.c | 7 - xml2-1.3.7/xml2/src/xml2_doc.cpp | 5 xml2-1.3.7/xml2/src/xml2_init.c |only xml2-1.3.7/xml2/src/xml2_namespace.cpp | 8 - xml2-1.3.7/xml2/src/xml2_node.cpp | 3 xml2-1.3.7/xml2/src/xml2_output.cpp | 3 xml2-1.3.7/xml2/src/xml2_schema.cpp | 3 xml2-1.3.7/xml2/src/xml2_url.cpp | 3 xml2-1.3.7/xml2/src/xml2_utils.h | 8 - xml2-1.3.7/xml2/src/xml2_xpath.cpp | 3 xml2-1.3.7/xml2/tests/testthat/_snaps/xml_attr.md | 6 - xml2-1.3.7/xml2/tests/testthat/_snaps/xml_children.md | 6 - xml2-1.3.7/xml2/tests/testthat/_snaps/xml_find.md | 63 ++++++++++ xml2-1.3.7/xml2/tests/testthat/_snaps/xml_name.md | 6 - xml2-1.3.7/xml2/tests/testthat/_snaps/xml_parse.md | 27 ++++ xml2-1.3.7/xml2/tests/testthat/_snaps/xml_write.md | 18 ++- xml2-1.3.7/xml2/tests/testthat/test-xml_attr.R | 38 +++--- xml2-1.3.7/xml2/tests/testthat/test-xml_children.R | 2 xml2-1.3.7/xml2/tests/testthat/test-xml_find.R | 26 ++-- xml2-1.3.7/xml2/tests/testthat/test-xml_missing.R | 4 xml2-1.3.7/xml2/tests/testthat/test-xml_name.R | 2 xml2-1.3.7/xml2/tests/testthat/test-xml_namespaces.R | 6 - xml2-1.3.7/xml2/tests/testthat/test-xml_nodeset.R | 4 xml2-1.3.7/xml2/tests/testthat/test-xml_parse.R | 17 +- xml2-1.3.7/xml2/tests/testthat/test-xml_serialize.R | 2 xml2-1.3.7/xml2/tests/testthat/test-xml_write.R | 15 +- xml2-1.3.7/xml2/tools/winlibs.R | 6 - 57 files changed, 322 insertions(+), 249 deletions(-)
Title: General Modules for 'teal' Applications
Description: Prebuilt 'shiny' modules containing tools for viewing data,
visualizing data, understanding missing and outlier values within your
data and performing simple data analysis. This extends 'teal'
framework that supports reproducible research and analysis.
Author: Dawid Kaledkowski [aut, cre],
Pawel Rucki [aut],
Mahmoud Hallal [aut],
Ondrej Slama [ctb],
Maciej Nasinski [aut],
Konrad Pagacz [aut],
Nikolas Burkoff [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.modules.general versions 0.3.0 dated 2024-03-05 and 0.4.0 dated 2025-02-28
teal.modules.general-0.3.0/teal.modules.general/R/data.R |only teal.modules.general-0.3.0/teal.modules.general/data |only teal.modules.general-0.3.0/teal.modules.general/man/rADAE.Rd |only teal.modules.general-0.3.0/teal.modules.general/man/rADLB.Rd |only teal.modules.general-0.3.0/teal.modules.general/man/rADRS.Rd |only teal.modules.general-0.3.0/teal.modules.general/man/rADSL.Rd |only teal.modules.general-0.3.0/teal.modules.general/man/rADTTE.Rd |only teal.modules.general-0.3.0/teal.modules.general/vignettes/images |only teal.modules.general-0.4.0/teal.modules.general/DESCRIPTION | 63 teal.modules.general-0.4.0/teal.modules.general/MD5 | 257 +- teal.modules.general-0.4.0/teal.modules.general/NAMESPACE | 1 teal.modules.general-0.4.0/teal.modules.general/NEWS.md | 22 teal.modules.general-0.4.0/teal.modules.general/R/roxygen2_templates.R |only teal.modules.general-0.4.0/teal.modules.general/R/tm_a_pca.R | 295 +- teal.modules.general-0.4.0/teal.modules.general/R/tm_a_regression.R | 880 +++---- teal.modules.general-0.4.0/teal.modules.general/R/tm_data_table.R | 198 + teal.modules.general-0.4.0/teal.modules.general/R/tm_file_viewer.R | 19 teal.modules.general-0.4.0/teal.modules.general/R/tm_front_page.R | 67 teal.modules.general-0.4.0/teal.modules.general/R/tm_g_association.R | 117 - teal.modules.general-0.4.0/teal.modules.general/R/tm_g_bivariate.R | 393 +-- teal.modules.general-0.4.0/teal.modules.general/R/tm_g_distribution.R | 419 ++- teal.modules.general-0.4.0/teal.modules.general/R/tm_g_response.R | 132 - teal.modules.general-0.4.0/teal.modules.general/R/tm_g_scatterplot.R | 140 - teal.modules.general-0.4.0/teal.modules.general/R/tm_g_scatterplotmatrix.R | 127 - teal.modules.general-0.4.0/teal.modules.general/R/tm_missing_data.R | 658 +++-- teal.modules.general-0.4.0/teal.modules.general/R/tm_outliers.R | 398 ++- teal.modules.general-0.4.0/teal.modules.general/R/tm_t_crosstable.R | 114 teal.modules.general-0.4.0/teal.modules.general/R/tm_variable_browser.R | 189 - teal.modules.general-0.4.0/teal.modules.general/R/utils.R | 127 + teal.modules.general-0.4.0/teal.modules.general/R/zzz.R | 4 teal.modules.general-0.4.0/teal.modules.general/README.md | 18 teal.modules.general-0.4.0/teal.modules.general/build/vignette.rds |binary teal.modules.general-0.4.0/teal.modules.general/inst/WORDLIST | 5 teal.modules.general-0.4.0/teal.modules.general/inst/doc/decorate-module-output.R |only teal.modules.general-0.4.0/teal.modules.general/inst/doc/decorate-module-output.Rmd |only teal.modules.general-0.4.0/teal.modules.general/inst/doc/decorate-module-output.html |only teal.modules.general-0.4.0/teal.modules.general/inst/doc/teal-modules-general.R | 67 teal.modules.general-0.4.0/teal.modules.general/inst/doc/teal-modules-general.Rmd | 58 teal.modules.general-0.4.0/teal.modules.general/inst/doc/teal-modules-general.html | 121 - teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-association-plot.R | 36 teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-association-plot.Rmd | 39 teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-association-plot.html | 519 ++-- teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-bivariate-plot.R | 36 teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-bivariate-plot.Rmd | 39 teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-bivariate-plot.html | 1157 +++++----- teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-cross-table.R | 33 teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-cross-table.Rmd | 36 teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-cross-table.html | 196 - teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-data-table.R | 36 teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-data-table.Rmd | 43 teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-data-table.html | 137 - teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-outliers-module.R | 34 teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-outliers-module.Rmd | 41 teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-outliers-module.html | 301 +- teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-regression-plots.R | 36 teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-regression-plots.Rmd | 39 teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-regression-plots.html | 453 +-- teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-response-plot.R | 36 teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-response-plot.Rmd | 39 teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-response-plot.html | 673 ++--- teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-scatterplot-matrix.R | 37 teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-scatterplot-matrix.Rmd | 40 teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-scatterplot-matrix.html | 228 + teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-scatterplot.R | 45 teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-scatterplot.Rmd | 48 teal.modules.general-0.4.0/teal.modules.general/inst/doc/using-scatterplot.html | 658 ++--- teal.modules.general-0.4.0/teal.modules.general/man/figures |only teal.modules.general-0.4.0/teal.modules.general/man/select_decorators.Rd |only teal.modules.general-0.4.0/teal.modules.general/man/shared_params.Rd | 7 teal.modules.general-0.4.0/teal.modules.general/man/srv_decorate_teal_data.Rd |only teal.modules.general-0.4.0/teal.modules.general/man/tm_a_pca.Rd | 81 teal.modules.general-0.4.0/teal.modules.general/man/tm_a_regression.Rd | 79 teal.modules.general-0.4.0/teal.modules.general/man/tm_data_table.Rd | 47 teal.modules.general-0.4.0/teal.modules.general/man/tm_file_viewer.Rd | 11 teal.modules.general-0.4.0/teal.modules.general/man/tm_front_page.Rd | 46 teal.modules.general-0.4.0/teal.modules.general/man/tm_g_association.Rd | 74 teal.modules.general-0.4.0/teal.modules.general/man/tm_g_bivariate.Rd | 220 + teal.modules.general-0.4.0/teal.modules.general/man/tm_g_distribution.Rd | 84 teal.modules.general-0.4.0/teal.modules.general/man/tm_g_response.Rd | 72 teal.modules.general-0.4.0/teal.modules.general/man/tm_g_scatterplot.Rd | 70 teal.modules.general-0.4.0/teal.modules.general/man/tm_g_scatterplotmatrix.Rd | 66 teal.modules.general-0.4.0/teal.modules.general/man/tm_missing_data.Rd | 98 teal.modules.general-0.4.0/teal.modules.general/man/tm_outliers.Rd | 88 teal.modules.general-0.4.0/teal.modules.general/man/tm_t_crosstable.Rd | 72 teal.modules.general-0.4.0/teal.modules.general/man/tm_variable_browser.Rd | 72 teal.modules.general-0.4.0/teal.modules.general/tests/testthat/helper-TealAppDriver.R |only teal.modules.general-0.4.0/teal.modules.general/tests/testthat/helper-functions.R | 24 teal.modules.general-0.4.0/teal.modules.general/tests/testthat/helper-testing-depth.R |only teal.modules.general-0.4.0/teal.modules.general/tests/testthat/man |only teal.modules.general-0.4.0/teal.modules.general/tests/testthat/setup-logger.R |only teal.modules.general-0.4.0/teal.modules.general/tests/testthat/setup-options.R |only teal.modules.general-0.4.0/teal.modules.general/tests/testthat/test-examples.R |only teal.modules.general-0.4.0/teal.modules.general/tests/testthat/test-shinytest2-tm_a_pca.R |only teal.modules.general-0.4.0/teal.modules.general/tests/testthat/test-shinytest2-tm_a_regression.R |only teal.modules.general-0.4.0/teal.modules.general/tests/testthat/test-shinytest2-tm_data_table.R |only teal.modules.general-0.4.0/teal.modules.general/tests/testthat/test-shinytest2-tm_file_viewer.R |only teal.modules.general-0.4.0/teal.modules.general/tests/testthat/test-shinytest2-tm_front_page.R |only teal.modules.general-0.4.0/teal.modules.general/tests/testthat/test-shinytest2-tm_g_association.R |only teal.modules.general-0.4.0/teal.modules.general/tests/testthat/test-shinytest2-tm_g_bivariate.R |only teal.modules.general-0.4.0/teal.modules.general/tests/testthat/test-shinytest2-tm_g_distribution.R |only teal.modules.general-0.4.0/teal.modules.general/tests/testthat/test-shinytest2-tm_g_response.R |only teal.modules.general-0.4.0/teal.modules.general/tests/testthat/test-shinytest2-tm_g_scatterplot.R |only teal.modules.general-0.4.0/teal.modules.general/tests/testthat/test-shinytest2-tm_g_scatterplotmatrix.R |only teal.modules.general-0.4.0/teal.modules.general/tests/testthat/test-shinytest2-tm_misssing_data.R |only teal.modules.general-0.4.0/teal.modules.general/tests/testthat/test-shinytest2-tm_outliers.R |only teal.modules.general-0.4.0/teal.modules.general/tests/testthat/test-shinytest2-tm_t_crosstable.R |only teal.modules.general-0.4.0/teal.modules.general/tests/testthat/test-shinytest2-tm_variable_browser.R |only teal.modules.general-0.4.0/teal.modules.general/tests/testthat/test-tm_g_bivariate.R | 46 teal.modules.general-0.4.0/teal.modules.general/tests/testthat/test_g_expert_cl.R | 22 teal.modules.general-0.4.0/teal.modules.general/vignettes/decorate-module-output.Rmd |only teal.modules.general-0.4.0/teal.modules.general/vignettes/teal-modules-general.Rmd | 58 teal.modules.general-0.4.0/teal.modules.general/vignettes/using-association-plot.Rmd | 39 teal.modules.general-0.4.0/teal.modules.general/vignettes/using-bivariate-plot.Rmd | 39 teal.modules.general-0.4.0/teal.modules.general/vignettes/using-cross-table.Rmd | 36 teal.modules.general-0.4.0/teal.modules.general/vignettes/using-data-table.Rmd | 43 teal.modules.general-0.4.0/teal.modules.general/vignettes/using-outliers-module.Rmd | 41 teal.modules.general-0.4.0/teal.modules.general/vignettes/using-regression-plots.Rmd | 39 teal.modules.general-0.4.0/teal.modules.general/vignettes/using-response-plot.Rmd | 39 teal.modules.general-0.4.0/teal.modules.general/vignettes/using-scatterplot-matrix.Rmd | 40 teal.modules.general-0.4.0/teal.modules.general/vignettes/using-scatterplot.Rmd | 48 120 files changed, 6800 insertions(+), 4805 deletions(-)
More information about teal.modules.general at CRAN
Permanent link
Title: 'teal' Modules for Standard Clinical Outputs
Description: Provides user-friendly tools for creating and customizing
clinical trial reports. By leveraging the 'teal' framework, this
package provides 'teal' modules to easily create an interactive panel
that allows for seamless adjustments to data presentation, thereby
streamlining the creation of detailed and accurate reports.
Author: Joe Zhu [aut] ,
Jana Stoilova [aut],
Davide Garolini [aut],
Emily de la Rua [aut],
Abinaya Yogasekaram [aut],
Mahmoud Hallal [aut],
Dawid Kaledkowski [aut, cre],
Rosemary Li [aut],
Heng Wang [aut],
Pawel Rucki [aut],
Nikolas Burkoff [aut],
Konrad Pag [...truncated...]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.modules.clinical versions 0.9.1 dated 2024-04-27 and 0.10.0 dated 2025-02-28
DESCRIPTION | 58 MD5 | 319 NEWS.md | 25 R/argument_convention.R | 10 R/string_ops.R | 8 R/tm_a_gee.R | 100 R/tm_a_mmrm.R | 201 R/tm_g_barchart_simple.R | 110 R/tm_g_ci.R | 105 R/tm_g_forest_rsp.R | 157 R/tm_g_forest_tte.R | 160 R/tm_g_ipp.R | 100 R/tm_g_km.R | 101 R/tm_g_lineplot.R | 169 R/tm_g_pp_adverse_events.R | 151 R/tm_g_pp_patient_timeline.R | 107 R/tm_g_pp_therapy.R | 132 R/tm_g_pp_vitals.R | 93 R/tm_t_abnormality.R | 98 R/tm_t_abnormality_by_worst_grade.R | 107 R/tm_t_ancova.R | 96 R/tm_t_binary_outcome.R | 126 R/tm_t_coxreg.R | 135 R/tm_t_events.R | 112 R/tm_t_events_by_grade.R | 128 R/tm_t_events_patyear.R | 193 R/tm_t_events_summary.R | 252 R/tm_t_exposure.R | 98 R/tm_t_logistic.R | 97 R/tm_t_mult_events.R | 113 R/tm_t_pp_basic_info.R | 94 R/tm_t_pp_laboratory.R | 144 R/tm_t_pp_medical_history.R | 99 R/tm_t_pp_prior_medication.R | 135 R/tm_t_shift_by_arm.R | 104 R/tm_t_shift_by_arm_by_worst.R | 101 R/tm_t_shift_by_grade.R | 102 R/tm_t_smq.R | 112 R/tm_t_summary.R | 162 R/tm_t_summary_by.R | 112 R/tm_t_tte.R | 114 R/utils.R | 129 README.md | 18 build/vignette.rds |binary inst/WORDLIST | 7 inst/doc/decorate-module-output.R |only inst/doc/decorate-module-output.Rmd |only inst/doc/decorate-module-output.html |only inst/doc/generate_tmc_test_data.R | 3906 +++++----- inst/doc/generate_tmc_test_data.Rmd | 8 inst/doc/generate_tmc_test_data.html | 47 inst/doc/quickstart_substitute.html | 44 inst/doc/teal-modules-clinical.R |only inst/doc/teal-modules-clinical.Rmd | 25 inst/doc/teal-modules-clinical.html | 15 man/module_arguments.Rd | 11 man/select_decorators.Rd |only man/split_choices.Rd | 2 man/srv_decorate_teal_data.Rd |only man/teal.modules.clinical-package.Rd | 4 man/template_coxreg_m.Rd | 2 man/template_coxreg_u.Rd | 2 man/template_events_summary.Rd | 7 man/template_exposure.Rd | 2 man/template_forest_rsp.Rd | 21 man/template_forest_tte.Rd | 23 man/template_g_km.Rd | 4 man/template_g_lineplot.Rd | 7 man/template_summary.Rd | 9 man/tm_a_gee.Rd | 60 man/tm_a_mmrm.Rd | 70 man/tm_g_barchart_simple.Rd | 78 man/tm_g_ci.Rd | 75 man/tm_g_forest_rsp.Rd | 101 man/tm_g_forest_tte.Rd | 98 man/tm_g_ipp.Rd | 82 man/tm_g_km.Rd | 75 man/tm_g_lineplot.Rd | 87 man/tm_g_pp_adverse_events.Rd | 74 man/tm_g_pp_patient_timeline.Rd | 86 man/tm_g_pp_therapy.Rd | 83 man/tm_g_pp_vitals.Rd | 71 man/tm_t_abnormality.Rd | 73 man/tm_t_abnormality_by_worst_grade.Rd | 78 man/tm_t_ancova.Rd | 75 man/tm_t_binary_outcome.Rd | 90 man/tm_t_coxreg.Rd | 84 man/tm_t_events.Rd | 71 man/tm_t_events_by_grade.Rd | 74 man/tm_t_events_patyear.Rd | 117 man/tm_t_events_summary.Rd | 79 man/tm_t_exposure.Rd | 60 man/tm_t_logistic.Rd | 74 man/tm_t_mult_events.Rd | 82 man/tm_t_pp_basic_info.Rd | 64 man/tm_t_pp_laboratory.Rd | 71 man/tm_t_pp_medical_history.Rd | 71 man/tm_t_pp_prior_medication.Rd | 81 man/tm_t_shift_by_arm.Rd | 81 man/tm_t_shift_by_arm_by_worst.Rd | 78 man/tm_t_shift_by_grade.Rd | 75 man/tm_t_smq.Rd | 76 man/tm_t_summary.Rd | 72 man/tm_t_summary_by.Rd | 71 man/tm_t_tte.Rd | 83 tests/testthat/_snaps/tm_a_gee.md | 30 tests/testthat/_snaps/tm_a_mmrm.md | 16 tests/testthat/_snaps/tm_g_ci.md | 12 tests/testthat/_snaps/tm_g_forest_rsp.md | 55 tests/testthat/_snaps/tm_g_forest_tte.md | 61 tests/testthat/_snaps/tm_g_km.md | 15 tests/testthat/_snaps/tm_g_lineplot.md | 6 tests/testthat/_snaps/tm_t_abnormality.md | 32 tests/testthat/_snaps/tm_t_abnormality_by_worst_grade.md | 24 tests/testthat/_snaps/tm_t_ancova.md | 131 tests/testthat/_snaps/tm_t_binary_outcome.md | 114 tests/testthat/_snaps/tm_t_coxreg.md | 7 tests/testthat/_snaps/tm_t_events.md | 93 tests/testthat/_snaps/tm_t_events_by_grade.md | 33 tests/testthat/_snaps/tm_t_events_patyear.md | 50 tests/testthat/_snaps/tm_t_events_summary.md | 51 tests/testthat/_snaps/tm_t_exposure.md | 54 tests/testthat/_snaps/tm_t_logisitic.md | 9 tests/testthat/_snaps/tm_t_mult_events.md | 71 tests/testthat/_snaps/tm_t_pp_medical_history.md | 5 tests/testthat/_snaps/tm_t_shift_by_arm.md | 9 tests/testthat/_snaps/tm_t_shift_by_arm_by_worst.md | 9 tests/testthat/_snaps/tm_t_shift_by_grade.md | 14 tests/testthat/_snaps/tm_t_smq.md | 19 tests/testthat/_snaps/tm_t_summary.md | 104 tests/testthat/_snaps/tm_t_summary_by.md | 79 tests/testthat/_snaps/tm_t_tte.md | 35 tests/testthat/_snaps/utils.md | 2 tests/testthat/helper-TealAppDriver.R | 4 tests/testthat/test-examples.R | 17 tests/testthat/test-shinytest2-tm_a_gee.R |only tests/testthat/test-shinytest2-tm_a_mmrm.R |only tests/testthat/test-shinytest2-tm_g_barchart_simple.R |only tests/testthat/test-shinytest2-tm_g_ci.R |only tests/testthat/test-shinytest2-tm_g_forest_rsp.R |only tests/testthat/test-shinytest2-tm_g_forest_tte.R |only tests/testthat/test-shinytest2-tm_g_ipp.R |only tests/testthat/test-shinytest2-tm_g_km.R |only tests/testthat/test-shinytest2-tm_g_lineplot.R |only tests/testthat/test-shinytest2-tm_g_pp_adverse_events.R |only tests/testthat/test-shinytest2-tm_g_pp_patient_timeline.R |only tests/testthat/test-shinytest2-tm_g_pp_therapy.R |only tests/testthat/test-shinytest2-tm_g_pp_vitals.R |only tests/testthat/test-shinytest2-tm_t_abnormality.R |only tests/testthat/test-shinytest2-tm_t_abnormality_by_worst_grade.R |only tests/testthat/test-shinytest2-tm_t_ancova.R |only tests/testthat/test-shinytest2-tm_t_binary_outcome.R |only tests/testthat/test-shinytest2-tm_t_coxreg.R |only tests/testthat/test-shinytest2-tm_t_events.R |only tests/testthat/test-shinytest2-tm_t_events_by_grade.R |only tests/testthat/test-shinytest2-tm_t_events_patyear.R |only tests/testthat/test-shinytest2-tm_t_events_summary.R |only tests/testthat/test-shinytest2-tm_t_exposure.R |only tests/testthat/test-shinytest2-tm_t_logistic.R |only tests/testthat/test-shinytest2-tm_t_mult_events.R |only tests/testthat/test-shinytest2-tm_t_pp_basic_info.R |only tests/testthat/test-shinytest2-tm_t_pp_laboratory.R |only tests/testthat/test-shinytest2-tm_t_pp_medical_history.R |only tests/testthat/test-shinytest2-tm_t_pp_prior_medication.R |only tests/testthat/test-shinytest2-tm_t_shift_by_arm.R |only tests/testthat/test-shinytest2-tm_t_shift_by_arm_by_worst.R |only tests/testthat/test-shinytest2-tm_t_shift_by_grade.R |only tests/testthat/test-shinytest2-tm_t_smq.R |only tests/testthat/test-shinytest2-tm_t_summary.R |only tests/testthat/test-shinytest2-tm_t_summary_by.R |only tests/testthat/test-shinytest2-tm_t_tte.R |only tests/testthat/test-string_ops.R | 2 tests/testthat/test-tm_g_forest_rsp.R | 20 tests/testthat/test-tm_g_forest_tte.R | 18 tests/testthat/test-tm_g_lineplot.R | 2 tests/testthat/test-tm_t_events_patyear.R | 2 tests/testthat/test-tm_t_events_summary.R | 2 tests/testthat/test-tm_t_summary.R | 18 tests/testthat/test-utils.R | 1 vignettes/decorate-module-output.Rmd |only vignettes/generate_tmc_test_data.Rmd | 8 vignettes/teal-modules-clinical.Rmd | 25 182 files changed, 8607 insertions(+), 4705 deletions(-)
More information about teal.modules.clinical at CRAN
Permanent link
Title: Build and Raytrace 3D Scenes
Description: Render scenes using pathtracing. Build 3D scenes out of spheres, cubes, planes, disks, triangles, cones, curves, line segments, cylinders, ellipsoids, and 3D models in the 'Wavefront' OBJ file format or the PLY Polygon File Format. Supports several material types, textures, multicore rendering, and tone-mapping. Based on the "Ray Tracing in One Weekend" book series. Peter Shirley (2018) <https://raytracing.github.io>.
Author: Tyler Morgan-Wall [aut, cph, cre]
,
Syoyo Fujita [ctb, cph],
Melissa O'Neill [ctb, cph],
Vilya Harvey [ctb, cph]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between rayrender versions 0.38.8 dated 2025-02-07 and 0.38.10 dated 2025-02-28
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ src/matrix.cpp | 4 +++- src/simd.cpp | 3 ++- src/test-runner.cpp | 9 +++++++++ src/transform.cpp | 4 +++- src/vectypes.cpp | 6 +++++- 7 files changed, 33 insertions(+), 15 deletions(-)
Title: Easily Create Production-Ready Rich Text Format (RTF) Tables and
Figures
Description: Create production-ready Rich Text Format (RTF) tables and figures
with flexible format.
Author: Yilong Zhang [aut],
Siruo Wang [aut],
Simiao Ye [aut],
Fansen Kong [aut],
Brian Lang [aut],
Benjamin Wang [aut, cre],
Nan Xiao [ctb],
Madhusudhan Ginnaram [ctb],
Ruchitbhai Patel [ctb],
Huei-Ling Chen [ctb],
Peikun Wu [ctb],
Uday Preetham Palukuru [c [...truncated...]
Maintainer: Benjamin Wang <benjamin.wang@merck.com>
Diff between r2rtf versions 1.1.2 dated 2025-02-21 and 1.1.3 dated 2025-02-28
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 7 +++++++ R/content_create.R | 4 ++-- README.md | 11 ++++++++++- build/vignette.rds |binary 6 files changed, 28 insertions(+), 12 deletions(-)
Title: Evolutionary Diversity Metrics for Raster Data
Description: Phylogenetic Diversity (PD, Faith 1992), Evolutionary
Distinctiveness (ED, Isaac et al. 2007), Phylogenetic Endemism (PE,
Rosauer et al. 2009; Laffan et al. 2016), and Weighted Endemism (WE,
Laffan et al. 2016) for presence-absence raster. Faith, D. P. (1992)
<doi:10.1016/0006-3207(92)91201-3> Isaac, N. J. et al. (2007)
<doi:10.1371/journal.pone.0000296> Laffan, S. W. et al. (2016)
<doi:10.1111/2041-210X.12513> Rosauer, D. et al. (2009)
<doi:10.1111/j.1365-294X.2009.04311.x>.
Author: Gabriela Alves-Ferreira [aut, cre, cph]
,
Flavio M. M. Mota [aut] ,
Neander Marcel Heming [aut]
Maintainer: Gabriela Alves-Ferreira <gabriela-alves77@hotmail.com>
Diff between phyloraster versions 2.1.0 dated 2024-03-19 and 2.2.0 dated 2025-02-28
phyloraster-2.1.0/phyloraster/R/spp.ed.R |only phyloraster-2.1.0/phyloraster/tests/testthat/test-test-geophylo-ses.R |only phyloraster-2.2.0/phyloraster/DESCRIPTION | 35 phyloraster-2.2.0/phyloraster/MD5 | 106 - phyloraster-2.2.0/phyloraster/NAMESPACE | 3 phyloraster-2.2.0/phyloraster/NEWS.md | 14 phyloraster-2.2.0/phyloraster/R/branch.length.R | 94 - phyloraster-2.2.0/phyloraster/R/canape.rast.R |only phyloraster-2.2.0/phyloraster/R/delta.grid.R | 117 - phyloraster-2.2.0/phyloraster/R/df2rast.R | 70 phyloraster-2.2.0/phyloraster/R/geo.phylo.R | 906 +++++----- phyloraster-2.2.0/phyloraster/R/phylo.pres.R | 446 ++-- phyloraster-2.2.0/phyloraster/R/rast.ed.ses.R | 604 +++--- phyloraster-2.2.0/phyloraster/R/rast.pd.ses.R | 575 +++--- phyloraster-2.2.0/phyloraster/R/rast.pe.ses.R | 818 +++++---- phyloraster-2.2.0/phyloraster/R/rast.we.ses.R | 545 +++--- phyloraster-2.2.0/phyloraster/R/shp2rast.R | 169 - phyloraster-2.2.0/phyloraster/R/species.ed.R |only phyloraster-2.2.0/phyloraster/README.md | 116 - phyloraster-2.2.0/phyloraster/build/vignette.rds |binary phyloraster-2.2.0/phyloraster/inst/CITATION | 62 phyloraster-2.2.0/phyloraster/inst/doc/phyloraster-vignette.R | 95 - phyloraster-2.2.0/phyloraster/inst/doc/phyloraster-vignette.Rmd | 400 ++-- phyloraster-2.2.0/phyloraster/inst/doc/phyloraster-vignette.html | 644 +++---- phyloraster-2.2.0/phyloraster/man/canape.rast.Rd |only phyloraster-2.2.0/phyloraster/man/delta.grid.Rd | 7 phyloraster-2.2.0/phyloraster/man/dot-end.type.Rd |only phyloraster-2.2.0/phyloraster/man/dot-rast.ed.B.Rd | 4 phyloraster-2.2.0/phyloraster/man/dot-rast.geo.phylo.Rd | 4 phyloraster-2.2.0/phyloraster/man/dot-rast.pd.B.Rd | 4 phyloraster-2.2.0/phyloraster/man/dot-rast.pe.B.Rd | 44 phyloraster-2.2.0/phyloraster/man/geo.phylo.Rd | 9 phyloraster-2.2.0/phyloraster/man/geo.phylo.ses.Rd | 74 phyloraster-2.2.0/phyloraster/man/phylo.pres.Rd | 13 phyloraster-2.2.0/phyloraster/man/rast.ed.Rd | 19 phyloraster-2.2.0/phyloraster/man/rast.ed.ses.Rd | 65 phyloraster-2.2.0/phyloraster/man/rast.pd.Rd | 21 phyloraster-2.2.0/phyloraster/man/rast.pd.ses.Rd | 64 phyloraster-2.2.0/phyloraster/man/rast.pe.Rd | 19 phyloraster-2.2.0/phyloraster/man/rast.pe.ses.Rd | 84 phyloraster-2.2.0/phyloraster/man/rast.we.ses.Rd | 41 phyloraster-2.2.0/phyloraster/man/species.ed.Rd | 8 phyloraster-2.2.0/phyloraster/tests/testthat/test-branch.length.R | 32 phyloraster-2.2.0/phyloraster/tests/testthat/test-canape.rast.R |only phyloraster-2.2.0/phyloraster/tests/testthat/test-delta-grid.R | 146 - phyloraster-2.2.0/phyloraster/tests/testthat/test-geo.phylo.R | 389 ++-- phyloraster-2.2.0/phyloraster/tests/testthat/test-geophylo-ses.R |only phyloraster-2.2.0/phyloraster/tests/testthat/test-phylo-pres.R | 309 +-- phyloraster-2.2.0/phyloraster/tests/testthat/test-rast-ed-ses.R | 289 +-- phyloraster-2.2.0/phyloraster/tests/testthat/test-rast-ed.R | 116 - phyloraster-2.2.0/phyloraster/tests/testthat/test-rast-pd.R | 203 +- phyloraster-2.2.0/phyloraster/tests/testthat/test-rast-pe-rast-we.R | 46 phyloraster-2.2.0/phyloraster/tests/testthat/test-rast.pd.ses.R | 285 +-- phyloraster-2.2.0/phyloraster/tests/testthat/test-rast.pe.R | 229 +- phyloraster-2.2.0/phyloraster/tests/testthat/test-rast.pe.ses.R | 261 +- phyloraster-2.2.0/phyloraster/tests/testthat/test-shp2rast.R | 185 +- phyloraster-2.2.0/phyloraster/tests/testthat/test-species-ed.R | 64 phyloraster-2.2.0/phyloraster/vignettes/phyloraster-vignette.Rmd | 400 ++-- 58 files changed, 4782 insertions(+), 4471 deletions(-)
Title: Connect to ODBC Compatible Databases (using the DBI Interface)
Description: A DBI-compatible interface to ODBC databases.
Author: Jim Hester [aut],
Hadley Wickham [aut, cre],
Oliver Gjoneski [aut],
lexicalunit [cph] ,
Google Inc. [cph] ,
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between odbc versions 1.5.0 dated 2024-06-05 and 1.6.0 dated 2025-02-28
DESCRIPTION | 24 +- MD5 | 136 +++++++------ NAMESPACE | 7 NEWS.md | 51 +++++ R/RcppExports.R | 4 R/dbi-connection.R | 6 R/dbi-driver.R | 33 ++- R/dbi-result.R | 2 R/dbi-table.R | 6 R/driver-databricks.R | 102 +++++++--- R/driver-db2.R | 47 ++++ R/driver-netezza.R |only R/driver-oracle.R | 19 + R/driver-redshift.R | 199 ++++++++++++++++++- R/driver-snowflake.R | 120 ++++++++---- R/driver-sql-server.R | 48 ++++ R/odbc-config.R | 54 ++++- R/odbc-connection.R | 12 - R/odbc-package.R | 2 R/odbc.R | 2 R/utils.R | 290 ++++++++++++++++++++++------- README.md | 6 build/vignette.rds |binary inst/doc/benchmarks.R | 126 ++++++------ inst/doc/develop.Rmd | 171 ++++++++++++++--- inst/doc/develop.html | 203 ++++++++++++++++---- inst/doc/setup.R | 28 +- man/DBI-classes.Rd | 7 man/DBI-methods.Rd | 7 man/DBI-tables.Rd | 7 man/OdbcConnection.Rd | 13 - man/OdbcDriver.Rd | 4 man/OdbcResult.Rd | 7 man/SQLServer.Rd | 13 + man/databricks.Rd | 26 ++ man/dbConnect-OdbcDriver-method.Rd | 18 + man/dbListTables-OdbcConnection-method.Rd | 4 man/driver-Snowflake.Rd | 4 man/figures/logo.png |only man/odbc-package.Rd | 4 man/odbcConnectionColumns.Rd | 8 man/odbcDataType.Rd | 8 man/odbcListConfig.Rd | 27 ++ man/odbcSetTransactionIsolationLevel.Rd | 6 man/redshift.Rd |only man/snowflake.Rd | 25 ++ src/RcppExports.cpp | 9 src/connection.cpp | 10 - src/nanodbc/nanodbc.cpp | 136 ++++++++----- src/nanodbc/nanodbc.h | 15 + src/odbc_connection.cpp | 24 +- src/odbc_connection.h | 21 +- src/odbc_result.cpp | 39 ++- src/odbc_result.h | 5 tests/testthat/_snaps/Darwin |only tests/testthat/_snaps/Linux |only tests/testthat/_snaps/driver-databricks.md | 14 + tests/testthat/_snaps/driver-snowflake.md | 16 + tests/testthat/_snaps/odbc-config.md | 9 tests/testthat/_snaps/utils.md | 74 ++++++- tests/testthat/test-dbi-connection.R | 8 tests/testthat/test-driver-databricks.R | 30 ++- tests/testthat/test-driver-mysql.R | 5 tests/testthat/test-driver-oracle.R | 97 +++++++++ tests/testthat/test-driver-postgres.R | 5 tests/testthat/test-driver-redshift.R |only tests/testthat/test-driver-snowflake.R | 62 ++++-- tests/testthat/test-driver-sql-server.R | 55 +++++ tests/testthat/test-driver-sqlite.R | 1 tests/testthat/test-odbc-config.R | 6 tests/testthat/test-utils.R | 143 ++++++++++++-- vignettes/develop.Rmd | 171 ++++++++++++++--- 72 files changed, 2226 insertions(+), 615 deletions(-)
Title: Armadillo Client for the Armadillo Service
Description: A set of functions to manage data shared on a
'MOLGENIS Armadillo' server.
Author: Mariska Slofstra [aut, cre] ,
Sido Haakma [aut] ,
Tommy de Boer [aut] ,
Fleur Kelpin [aut] ,
Morris Swertz [aut] ,
Tim Cadman [aut]
Maintainer: Mariska Slofstra <m.k.slofstra@umcg.nl>
Diff between MolgenisArmadillo versions 2.7.0 dated 2024-10-14 and 2.9.0 dated 2025-02-28
DESCRIPTION | 11 MD5 | 40 +- NAMESPACE | 9 NEWS.md | 3 R/package.R | 15 - R/subset.R | 186 +++++++++++- R/table.R | 7 R/utils.R | 8 build/vignette.rds |binary inst/doc/MolgenisArmadillo.html | 518 +++++++++++++++++++++++++----------- inst/doc/create_resources.Rmd | 32 -- inst/doc/create_resources.html | 414 +++++++++++++++++++++------- inst/doc/creating_data_subsets.html | 443 +++++++++++++++++++++++------- inst/doc/install_packages.html | 355 +++++++++++++++++++----- man/armadillo.subset.Rd | 7 tests/testthat/test-package.R | 93 ++---- tests/testthat/test-resource.R | 24 - tests/testthat/test-subset.R | 192 +++++++++++-- tests/testthat/test-table.R | 80 ++++- vignettes/create_resources.Rmd | 32 -- vignettes/create_resources.Rmd.orig | 4 21 files changed, 1817 insertions(+), 656 deletions(-)
More information about MolgenisArmadillo at CRAN
Permanent link
Title: Automatic Univariate Time Series Modelling of many Kinds
Description: Comprehensive analysis and forecasting
of univariate time series using automatic
time series models of many kinds.
Harvey AC (1989) <doi:10.1017/CBO9781107049994>.
Pedregal DJ and Young PC (2002) <doi:10.1002/9780470996430>.
Durbin J and Koopman SJ (2012) <doi:10.1093/acprof:oso/9780199641178.001.0001>.
Hyndman RJ, Koehler AB, Ord JK, and Snyder RD (2008) <doi:10.1007/978-3-540-71918-2>.
Gómez V, Maravall A (2000) <doi:10.1002/9781118032978>.
Pedregal DJ, Trapero JR and Holgado E (2024) <doi:10.1016/j.ijforecast.2023.09.004>.
Author: Diego J. Pedregal [aut, cre]
Maintainer: Diego J. Pedregal <Diego.Pedregal@uclm.es>
Diff between UComp versions 5.0.5 dated 2024-12-11 and 5.0.6 dated 2025-02-28
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/stats.h | 21 ++++++++++----------- 3 files changed, 16 insertions(+), 17 deletions(-)
Title: Regression Models with Break-Points / Change-Points Estimation
(with Possibly Random Effects)
Description: Fitting regression models where, in addition to possible linear terms, one or more covariates have segmented (i.e., broken-line or piece-wise linear) or stepmented (i.e. piece-wise constant) effects. Multiple breakpoints for the same variable are allowed.
The estimation method is discussed in Muggeo (2003, <doi:10.1002/sim.1545>) and
illustrated in Muggeo (2008, <https://www.r-project.org/doc/Rnews/Rnews_2008-1.pdf>). An approach for hypothesis testing is presented
in Muggeo (2016, <doi:10.1080/00949655.2016.1149855>), and interval estimation for the breakpoint is discussed in Muggeo (2017, <doi:10.1111/anzs.12200>).
Segmented mixed models, i.e. random effects in the change point, are discussed in Muggeo (2014, <doi:10.1177/1471082X13504721>).
Estimation of piecewise-constant relationships and changepoints (mean-shift models) is
discussed in Fasola et al. (2018, <doi:10.1007/s00180-017-0740-4>).
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>
Diff between segmented versions 2.1-3 dated 2024-10-25 and 2.1-4 dated 2025-02-28
DESCRIPTION | 8 MD5 | 66 +- NEWS | 9 R/plot.segmented.lme.r | 21 R/seg.Ar.fit.boot.r | 8 R/seg.def.fit.boot.r | 9 R/seg.glm.fit.boot.r | 20 R/seg.glm.fit.r | 6 R/seg.lm.fit.boot.r | 27 - R/seg.lm.fit.r | 21 R/seg.num.fit.boot.r | 17 R/segConstr.glm.fit.boot.r | 14 R/segConstr.lm.fit.boot.r | 16 R/segConstr.lm.fit.r | 22 R/segmented.glm.R | 23 R/segmented.lm.R | 33 - R/segmented.lme.r | 59 ++ R/segreg.r | 64 ++ R/step.glm.fit.boot.r | 1 R/step.glm.fit.r | 6 R/step.lm.fit.boot.r | 1 R/step.lm.fit.r | 6 R/step.num.fit.boot.r | 1 R/step.num.fit.r | 614 +++++++++++++------------- R/step.ts.fit.boot.r | 1 R/step.ts.fit.r | 6 R/stepmented.numeric.r | 1060 ++++++++++++++++++++++----------------------- R/stepmented.ts.R | 778 ++++++++++++++++----------------- R/stepreg.r | 8 man/plot.segmented.lme.Rd | 6 man/seg.Rd | 21 man/segmented-package.Rd | 4 man/segreg.Rd | 8 man/stepmented.Rd | 18 34 files changed, 1611 insertions(+), 1371 deletions(-)
Title: Regression Standardization for Causal Inference
Description: Contains more modern tools for causal inference using regression
standardization. Four general classes of models are implemented; generalized
linear models, conditional generalized estimating equation models,
Cox proportional hazards models, and shared frailty gamma-Weibull models.
Methodological details are described in Sjölander, A. (2016) <doi:10.1007/s10654-016-0157-3>.
Also includes functionality for doubly robust estimation for generalized linear models
in some special cases, and the ability to implement custom models.
Author: Michael C Sachs [aut, cre],
Arvid Sjoelander [aut],
Erin E Gabriel [aut],
Johan Sebastian Ohlendorff [aut],
Adam Brand [aut]
Maintainer: Michael C Sachs <sachsmc@gmail.com>
Diff between stdReg2 versions 1.0.1 dated 2024-09-13 and 1.0.3 dated 2025-02-28
DESCRIPTION | 10 MD5 | 37 +-- NAMESPACE | 1 NEWS.md | 9 R/coxph_methods.R | 39 ++- R/glm_methods.R | 48 +++- R/standardize_custom.R | 86 +++++++ README.md | 18 - inst/doc/custom.html | 2 inst/doc/overview.html | 360 +++++++++++++++----------------- man/standardize.Rd | 29 ++ man/standardize_coxph.Rd | 33 ++ man/standardize_gee.Rd | 30 ++ man/standardize_glm.Rd | 38 ++- man/standardize_glm_dr.Rd | 32 ++ man/standardize_level.Rd | 29 ++ man/standardize_parfrailty.Rd | 33 ++ man/tidy.std_custom.Rd |only tests/testthat/test-standardize.R | 2 tests/testthat/test-standardize_coxph.R | 21 + 20 files changed, 580 insertions(+), 277 deletions(-)
Title: Feature Stores for the 'diseasy' Framework
Description: Simple feature stores and tools for creating personalised feature stores.
'diseasystore' powers feature stores which can automatically link and aggregate features to a given stratification
level. These feature stores are automatically time-versioned (powered by the 'SCDB' package) and allows you to easily
and dynamically compute features as part of your continuous integration.
Author: Rasmus Skytte Randloev [aut, cre]
,
Kaare Graesboell [rev] ,
Kasper Schou Telkamp [rev] ,
Lasse Engbo Christiansen [rev]
,
Marcus Munch Gruenewald [rev] ,
Sofia Myrup Otero [rev],
Statens Serum Institut, SSI [cph, fnd]
Maintainer: Rasmus Skytte Randloev <rske@ssi.dk>
Diff between diseasystore versions 0.3.0 dated 2024-12-11 and 0.3.1 dated 2025-02-28
diseasystore-0.3.0/diseasystore/vignettes/vignette_data |only diseasystore-0.3.1/diseasystore/DESCRIPTION | 16 diseasystore-0.3.1/diseasystore/MD5 | 119 +- diseasystore-0.3.1/diseasystore/NAMESPACE | 1 diseasystore-0.3.1/diseasystore/NEWS.md | 323 +++---- diseasystore-0.3.1/diseasystore/R/0_R6_utils.R | 16 diseasystore-0.3.1/diseasystore/R/0_documentation.R | 142 ++- diseasystore-0.3.1/diseasystore/R/0_linters.R | 136 ++- diseasystore-0.3.1/diseasystore/R/2_FeatureHandler.R | 4 diseasystore-0.3.1/diseasystore/R/3_feature_store_helpers.R | 4 diseasystore-0.3.1/diseasystore/R/DiseasystoreBase.R | 255 +++-- diseasystore-0.3.1/diseasystore/R/DiseasystoreGoogleCovid19.R | 13 diseasystore-0.3.1/diseasystore/R/DiseasystoreSimulist.R | 6 diseasystore-0.3.1/diseasystore/R/drop_diseasystore.R | 11 diseasystore-0.3.1/diseasystore/R/grapes-.-grapes.R | 2 diseasystore-0.3.1/diseasystore/R/source_conn_helpers.R | 15 diseasystore-0.3.1/diseasystore/R/test_diseasystore.R | 133 ++ diseasystore-0.3.1/diseasystore/R/truncate_interlace.R | 6 diseasystore-0.3.1/diseasystore/README.md | 6 diseasystore-0.3.1/diseasystore/build/partial.rdb |binary diseasystore-0.3.1/diseasystore/build/vignette.rds |binary diseasystore-0.3.1/diseasystore/inst/WORDLIST | 64 + diseasystore-0.3.1/diseasystore/inst/doc/benchmarks.R | 198 ++-- diseasystore-0.3.1/diseasystore/inst/doc/benchmarks.Rmd | 136 ++- diseasystore-0.3.1/diseasystore/inst/doc/benchmarks.html | 5 diseasystore-0.3.1/diseasystore/inst/doc/diseasystore-ecdc-respiratory-viruses.R | 149 ++- diseasystore-0.3.1/diseasystore/inst/doc/diseasystore-ecdc-respiratory-viruses.Rmd | 81 + diseasystore-0.3.1/diseasystore/inst/doc/diseasystore-ecdc-respiratory-viruses.html | 49 - diseasystore-0.3.1/diseasystore/inst/doc/diseasystore-google-covid-19.R | 116 +- diseasystore-0.3.1/diseasystore/inst/doc/diseasystore-google-covid-19.Rmd | 50 - diseasystore-0.3.1/diseasystore/inst/doc/diseasystore-google-covid-19.html | 14 diseasystore-0.3.1/diseasystore/inst/doc/diseasystore.R | 38 diseasystore-0.3.1/diseasystore/inst/doc/diseasystore.Rmd | 38 diseasystore-0.3.1/diseasystore/inst/doc/diseasystore.html | 46 - diseasystore-0.3.1/diseasystore/inst/doc/extending-diseasystore-example.R | 446 +++++----- diseasystore-0.3.1/diseasystore/inst/doc/extending-diseasystore-example.html | 52 - diseasystore-0.3.1/diseasystore/inst/extdata/benchmarks.rds |binary diseasystore-0.3.1/diseasystore/man/DiseasystoreBase.Rd | 39 diseasystore-0.3.1/diseasystore/man/DiseasystoreEcdcRespiratoryViruses.Rd | 1 diseasystore-0.3.1/diseasystore/man/DiseasystoreGoogleCovid19.Rd | 1 diseasystore-0.3.1/diseasystore/man/DiseasystoreSimulist.Rd | 1 diseasystore-0.3.1/diseasystore/man/add_years.Rd | 2 diseasystore-0.3.1/diseasystore/man/age_on_date.Rd | 2 diseasystore-0.3.1/diseasystore/man/drop_diseasystore.Rd | 8 diseasystore-0.3.1/diseasystore/man/source_conn_helpers.Rd | 2 diseasystore-0.3.1/diseasystore/man/test_diseasystore.Rd | 5 diseasystore-0.3.1/diseasystore/tests/testthat/helper-setup.R | 90 +- diseasystore-0.3.1/diseasystore/tests/testthat/setup.R | 5 diseasystore-0.3.1/diseasystore/tests/testthat/test-0_R6_utils.R | 1 diseasystore-0.3.1/diseasystore/tests/testthat/test-0_documentation.R | 6 diseasystore-0.3.1/diseasystore/tests/testthat/test-0_linters.R | 20 diseasystore-0.3.1/diseasystore/tests/testthat/test-0_rd_files.R | 2 diseasystore-0.3.1/diseasystore/tests/testthat/test-DiseasystoreBase.R | 62 + diseasystore-0.3.1/diseasystore/tests/testthat/test-age_helpers.R | 12 diseasystore-0.3.1/diseasystore/tests/testthat/test-truncate_interlace.R | 4 diseasystore-0.3.1/diseasystore/vignettes/benchmarks.Rmd | 136 ++- diseasystore-0.3.1/diseasystore/vignettes/diseasystore-ecdc-respiratory-viruses.Rmd | 81 + diseasystore-0.3.1/diseasystore/vignettes/diseasystore-google-covid-19.Rmd | 50 - diseasystore-0.3.1/diseasystore/vignettes/diseasystore.Rmd | 38 59 files changed, 2107 insertions(+), 1151 deletions(-)
Title: Calibration, Validation, and Simulation of TKTD Models
Description: Eases the use of ecotoxicological effect models. Can simulate
common toxicokinetic-toxicodynamic (TK/TD) models such as
General Unified Threshold models of Survival (GUTS) and Lemna. It can
derive effects and effect profiles (EPx) from scenarios. It supports the
use of 'tidyr' workflows employing the pipe symbol. Time-consuming
tasks can be parallelized.
Author: Nils Kehrein [aut, cre],
Dirk Nickisch [aut],
Peter Vermeiren [aut],
Torben Wittwer [ctb],
Johannes Witt [ctb],
Andre Gergs [ctb]
Maintainer: Nils Kehrein <nils.kehrein@gmail.com>
Diff between cvasi versions 1.3.1 dated 2024-11-22 and 1.4.0 dated 2025-02-28
cvasi-1.3.1/cvasi/R/class-ScenarioSequence.R |only cvasi-1.3.1/cvasi/R/helper_functions.r |only cvasi-1.3.1/cvasi/src/algae_tktd.c |only cvasi-1.3.1/cvasi/tests/testthat/_snaps/verify_guts.md |only cvasi-1.3.1/cvasi/tests/testthat/lemna_helpers.R |only cvasi-1.3.1/cvasi/tests/testthat/test-simulate_AlgaeTKTD.R |only cvasi-1.3.1/cvasi/tests/testthat/test-simulate_Algae_simple.R |only cvasi-1.3.1/cvasi/tests/testthat/test-simulate_DEBtox.R |only cvasi-1.3.1/cvasi/tests/testthat/test-simulate_Weber.R |only cvasi-1.3.1/cvasi/tests/testthat/test-simulate_lemna_schmitt.R |only cvasi-1.3.1/cvasi/tests/testthat/test-simulate_lemna_setac.R |only cvasi-1.3.1/cvasi/tests/testthat/test-verify_guts.R |only cvasi-1.4.0/cvasi/DESCRIPTION | 17 cvasi-1.4.0/cvasi/MD5 | 205 ++-- cvasi-1.4.0/cvasi/NAMESPACE | 268 ++--- cvasi-1.4.0/cvasi/NEWS.md | 33 cvasi-1.4.0/cvasi/R/batch.R |only cvasi-1.4.0/cvasi/R/calibrate.R | 14 cvasi-1.4.0/cvasi/R/class-Transferable.R | 34 cvasi-1.4.0/cvasi/R/data.R | 53 - cvasi-1.4.0/cvasi/R/fx.R | 7 cvasi-1.4.0/cvasi/R/globals.R | 5 cvasi-1.4.0/cvasi/R/model-algae.R | 118 +- cvasi-1.4.0/cvasi/R/model-deb_abj.R | 28 cvasi-1.4.0/cvasi/R/model-deb_daphnia.R | 4 cvasi-1.4.0/cvasi/R/model-debtox.R | 33 cvasi-1.4.0/cvasi/R/model-guts_red.R | 57 - cvasi-1.4.0/cvasi/R/model-lemna_schmitt.R | 39 cvasi-1.4.0/cvasi/R/model-lemna_setac.R | 37 cvasi-1.4.0/cvasi/R/model-myriophyllum.R | 39 cvasi-1.4.0/cvasi/R/plotting.r | 4 cvasi-1.4.0/cvasi/R/sequence.R | 154 ++- cvasi-1.4.0/cvasi/R/set.R | 2 cvasi-1.4.0/cvasi/R/set_exposure.R | 11 cvasi-1.4.0/cvasi/R/set_transfer.R | 52 - cvasi-1.4.0/cvasi/R/set_window.R | 27 cvasi-1.4.0/cvasi/R/show.R | 41 cvasi-1.4.0/cvasi/R/simulate.R | 223 +++- cvasi-1.4.0/cvasi/R/solver.R | 13 cvasi-1.4.0/cvasi/data/minnow_it.rda |binary cvasi-1.4.0/cvasi/data/minnow_sd.rda |binary cvasi-1.4.0/cvasi/inst/doc/cvasi-1-manual.R | 10 cvasi-1.4.0/cvasi/inst/doc/cvasi-1-manual.Rmd | 14 cvasi-1.4.0/cvasi/inst/doc/cvasi-1-manual.html | 138 +- cvasi-1.4.0/cvasi/inst/doc/cvasi-2-howto.R | 50 - cvasi-1.4.0/cvasi/inst/doc/cvasi-2-howto.Rmd | 50 - cvasi-1.4.0/cvasi/inst/doc/cvasi-2-howto.html | 464 ++++++---- cvasi-1.4.0/cvasi/man/Algae-models.Rd | 14 cvasi-1.4.0/cvasi/man/Algae_Simple.Rd | 20 cvasi-1.4.0/cvasi/man/Algae_TKTD.Rd | 20 cvasi-1.4.0/cvasi/man/Algae_Weber.Rd | 20 cvasi-1.4.0/cvasi/man/DEB_abj.Rd | 11 cvasi-1.4.0/cvasi/man/DEBtox.Rd | 431 ++++----- cvasi-1.4.0/cvasi/man/GUTS_RED_IT.Rd | 11 cvasi-1.4.0/cvasi/man/GUTS_RED_SD.Rd | 11 cvasi-1.4.0/cvasi/man/Lemna-models.Rd | 14 cvasi-1.4.0/cvasi/man/Lemna_SETAC.Rd | 34 cvasi-1.4.0/cvasi/man/Lemna_Schmitt.Rd | 34 cvasi-1.4.0/cvasi/man/Macrophyte-models.Rd | 14 cvasi-1.4.0/cvasi/man/Myrio.Rd | 34 cvasi-1.4.0/cvasi/man/Myrio_log.Rd | 34 cvasi-1.4.0/cvasi/man/Transferable.Rd | 35 cvasi-1.4.0/cvasi/man/batch.Rd |only cvasi-1.4.0/cvasi/man/dmagna.Rd | 40 cvasi-1.4.0/cvasi/man/figures/lifecycle-deprecated.svg | 42 cvasi-1.4.0/cvasi/man/figures/lifecycle-experimental.svg | 42 cvasi-1.4.0/cvasi/man/figures/lifecycle-stable.svg | 58 - cvasi-1.4.0/cvasi/man/figures/lifecycle-superseded.svg | 42 cvasi-1.4.0/cvasi/man/import_morse.Rd | 144 +-- cvasi-1.4.0/cvasi/man/import_swash.Rd | 38 cvasi-1.4.0/cvasi/man/import_toxswa.Rd | 138 +- cvasi-1.4.0/cvasi/man/minnow_it.Rd | 28 cvasi-1.4.0/cvasi/man/minnow_sd.Rd | 27 cvasi-1.4.0/cvasi/man/plot.Rd | 72 - cvasi-1.4.0/cvasi/man/sequence.Rd | 37 cvasi-1.4.0/cvasi/man/set_bounds.Rd | 72 - cvasi-1.4.0/cvasi/man/set_exposure.Rd | 2 cvasi-1.4.0/cvasi/man/set_mode_of_action.Rd | 78 - cvasi-1.4.0/cvasi/man/set_transfer.Rd | 231 ++-- cvasi-1.4.0/cvasi/man/set_window.Rd | 15 cvasi-1.4.0/cvasi/man/simulate.Rd | 81 + cvasi-1.4.0/cvasi/man/simulate_batch.Rd | 7 cvasi-1.4.0/cvasi/man/solver.Rd | 87 - cvasi-1.4.0/cvasi/man/survival.Rd | 104 +- cvasi-1.4.0/cvasi/src/algae_TKTD.c |only cvasi-1.4.0/cvasi/tests/testthat/_snaps/verify-guts_red.md |only cvasi-1.4.0/cvasi/tests/testthat/class-DummyScenario.R | 8 cvasi-1.4.0/cvasi/tests/testthat/test-batch.R |only cvasi-1.4.0/cvasi/tests/testthat/test-cache.R | 4 cvasi-1.4.0/cvasi/tests/testthat/test-calibrate.R | 4 cvasi-1.4.0/cvasi/tests/testthat/test-clip.R | 12 cvasi-1.4.0/cvasi/tests/testthat/test-effect.R | 14 cvasi-1.4.0/cvasi/tests/testthat/test-epx.R | 3 cvasi-1.4.0/cvasi/tests/testthat/test-fx.R |only cvasi-1.4.0/cvasi/tests/testthat/test-has.R | 23 cvasi-1.4.0/cvasi/tests/testthat/test-model-algae.R |only cvasi-1.4.0/cvasi/tests/testthat/test-model-deb_abj.R |only cvasi-1.4.0/cvasi/tests/testthat/test-model-debtox.R |only cvasi-1.4.0/cvasi/tests/testthat/test-model-guts_red.R |only cvasi-1.4.0/cvasi/tests/testthat/test-model-lemna_schmitt.R |only cvasi-1.4.0/cvasi/tests/testthat/test-model-lemna_setac.R |only cvasi-1.4.0/cvasi/tests/testthat/test-model-myriophyllum.R |only cvasi-1.4.0/cvasi/tests/testthat/test-plotting.R |only cvasi-1.4.0/cvasi/tests/testthat/test-sequence.R | 122 +- cvasi-1.4.0/cvasi/tests/testthat/test-set.R | 56 - cvasi-1.4.0/cvasi/tests/testthat/test-set_bounds.R | 13 cvasi-1.4.0/cvasi/tests/testthat/test-set_exposure.R | 15 cvasi-1.4.0/cvasi/tests/testthat/test-set_param.R | 6 cvasi-1.4.0/cvasi/tests/testthat/test-set_transfer.R | 35 cvasi-1.4.0/cvasi/tests/testthat/test-show.R |only cvasi-1.4.0/cvasi/tests/testthat/test-simulate_batch.R | 10 cvasi-1.4.0/cvasi/tests/testthat/test-simulate_batch2.R |only cvasi-1.4.0/cvasi/tests/testthat/test-simulate_sequence.R | 7 cvasi-1.4.0/cvasi/tests/testthat/test-simulate_transfer.R | 157 +++ cvasi-1.4.0/cvasi/tests/testthat/test-solver.R | 91 - cvasi-1.4.0/cvasi/tests/testthat/test-verify-guts_red.R |only cvasi-1.4.0/cvasi/vignettes/cvasi-1-manual.Rmd | 14 cvasi-1.4.0/cvasi/vignettes/cvasi-2-howto.Rmd | 50 - 118 files changed, 2955 insertions(+), 2055 deletions(-)
Title: Get Basic Information from Chinese ID Number
Description: The Chinese ID number contains a lot of information,
this package helps you get the region, date of birth, age,
age based on year, gender, zodiac, constellation information from
the Chinese ID number.
Author: Xinyuan Chu [aut, cre]
Maintainer: Xinyuan Chu <chuxinyuan@outlook.com>
Diff between CNID versions 2.0.1 dated 2025-02-24 and 2.0.2 dated 2025-02-28
DESCRIPTION | 12 ++--- MD5 | 40 ++++++++--------- R/age.R | 5 +- R/age_by_year.R | 5 +- R/birth_date.R | 5 +- R/check_id.R | 5 +- R/cnid_info.R | 118 ++++++++++++++++++++++++++++++++--------------------- R/cstl.R | 5 +- R/gender.R | 5 +- R/region.R | 5 +- R/zodiac.R | 5 +- README.md | 7 ++- man/age.Rd | 5 +- man/age_by_year.Rd | 5 +- man/birth_date.Rd | 5 +- man/check_id.Rd | 5 +- man/cnid_info.Rd | 5 +- man/cstl.Rd | 5 +- man/gender.Rd | 5 +- man/region.Rd | 5 +- man/zodiac.Rd | 5 +- 21 files changed, 172 insertions(+), 90 deletions(-)
Title: Bayesian Structure and Causal Learning of Gaussian Directed
Graphs
Description: A collection of functions for structure learning of causal networks and estimation of joint causal effects from observational Gaussian data. Main algorithm consists of a Markov chain Monte Carlo scheme for posterior inference of causal structures, parameters and causal effects between variables.
References:
F. Castelletti and A. Mascaro (2021) <doi:10.1007/s10260-021-00579-1>,
F. Castelletti and A. Mascaro (2022) <doi:10.48550/arXiv.2201.12003>.
Author: Federico Castelletti [aut],
Alessandro Mascaro [aut, cre, cph]
Maintainer: Alessandro Mascaro <alessandro.mascaro@upf.edu>
Diff between BCDAG versions 1.1.2 dated 2025-01-30 and 1.1.3 dated 2025-02-28
BCDAG-1.1.2/BCDAG/tests/testthat/test-warnings-get_causaleffect.R |only BCDAG-1.1.2/BCDAG/tests/testthat/test-warnings-learn_DAG.R |only BCDAG-1.1.3/BCDAG/DESCRIPTION | 10 +++++----- BCDAG-1.1.3/BCDAG/MD5 | 8 +++----- BCDAG-1.1.3/BCDAG/NEWS.md | 3 +++ BCDAG-1.1.3/BCDAG/inst/doc/bcdag_learnDAG.html | 4 ++-- 6 files changed, 13 insertions(+), 12 deletions(-)
Title: Import Texts from Files in the 'Alceste' Format Using the 'tm'
Text Mining Framework
Description: Provides a 'tm' Source to create corpora from
a corpus prepared in the format used by the 'Alceste' application (i.e.
a single text file with inline meta-data). It is able to import both
text contents and meta-data (starred) variables.
Author: Milan Bouchet-Valat [aut, cre]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>
Diff between tm.plugin.alceste versions 1.1.1 dated 2024-03-06 and 1.1.2 dated 2025-02-28
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 3 +++ R/readAlceste.R | 2 +- man/AlcesteSource.Rd | 4 ++-- man/readAlceste.Rd | 2 +- 6 files changed, 16 insertions(+), 13 deletions(-)
More information about tm.plugin.alceste at CRAN
Permanent link
Title: L1-Penalized Multinomial Regression with Statistical Inference
Description: We aim for fitting a multinomial regression model with Lasso penalty and doing statistical inference (calculating confidence intervals of coefficients and p-values for individual variables). It implements 1) the coordinate descent algorithm to fit an l1-penalized multinomial regression model (parameterized with a reference level); 2) the debiasing approach to obtain the inference results, which is described in "Tian, Y., Rusinek, H., Masurkar, A. V., & Feng, Y. (2024). L1‐Penalized Multinomial Regression: Estimation, Inference, and Prediction, With an Application to Risk Factor Identification for Different Dementia Subtypes. Statistics in Medicine, 43(30), 5711-5747."
Author: Ye Tian [aut, cre],
Henry Rusinek [aut],
Arjun V. Masurkar [aut],
Yang Feng [aut]
Maintainer: Ye Tian <ye.t@columbia.edu>
Diff between pemultinom versions 0.1.0 dated 2023-02-16 and 0.1.1 dated 2025-02-28
DESCRIPTION | 13 +-- MD5 | 20 ++--- NAMESPACE | 3 R/RcppExports.R | 12 +-- R/cv.pemultinom.R | 66 ++++++++++++----- R/debiased_lasso.R | 115 +++++++++++++++++++++++------ R/funcs.R | 112 +++++++++++++++++++++++++---- man/cv.pemultinom.Rd | 20 +++-- man/debiased_lasso.Rd | 44 ++++++++--- src/RcppExports.cpp | 51 ++++++------- src/test_cpp.cpp | 193 ++++++++++++++++++++++++++++++-------------------- 11 files changed, 452 insertions(+), 197 deletions(-)
Title: Methods for Analysing 'EQ-5D' Data and Calculating 'EQ-5D' Index
Scores
Description: EQ-5D is a popular health related quality of life instrument used
in the clinical and economic evaluation of health care. Developed by the
EuroQol group <https://euroqol.org/>, the instrument consists of two
components: health state description and evaluation. For the description
component a subject self-rates their health in terms of five dimensions;
mobility, self-care, usual activities, pain/discomfort, and
anxiety/depression using either a three-level (EQ-5D-3L,
<https://euroqol.org/information-and-support/euroqol-instruments/eq-5d-3l/>) or a five-level
(EQ-5D-5L, <https://euroqol.org/information-and-support/euroqol-instruments/eq-5d-5l/>)
scale. Frequently the scores on these five dimensions are converted to a
single utility index using country specific value sets, which can be used
in the clinical and economic evaluation of health care as well as in
population health surveys. The eq5d package provides methods to calculate
index scores from a subject's dimension [...truncated...]
Author: Fraser Morton [aut, cre],
Jagtar Singh Nijjar [aut]
Maintainer: Fraser Morton <fraser.morton@glasgow.ac.uk>
Diff between eq5d versions 0.15.6 dated 2025-01-16 and 0.15.7 dated 2025-02-28
DESCRIPTION | 12 ++-- MD5 | 66 +++++++++++----------- NAMESPACE | 2 NEWS.md | 8 ++ R/data.R | 13 ++-- R/eq5d.R | 4 - R/eq5d3l.R | 14 ++-- R/eq5dcf.R | 2 R/eq5dds.R | 2 R/eq5dlfs.R | 2 R/eq5dlss.R | 2 R/eq5dy3l.R | 2 R/eqhpg.R | 2 R/eqhsdi.R | 2 R/eqpchc.R | 2 R/eqshannon.R | 2 R/helpers.R | 2 R/imports.R | 2 R/sysdata.rda |binary inst/doc/eq5d.html | 118 ++++++++++++++++++++-------------------- man/VT.Rd | 15 ++--- man/eq5d-package.Rd | 2 tests/testthat/test-eq5d.R | 37 ++++++++++++ tests/testthat/test-eq5d5l.R | 10 +++ tests/testthat/test-eq5dcf.R | 10 +++ tests/testthat/test-eq5dds.R | 10 +++ tests/testthat/test-eq5dlfs.R | 10 +++ tests/testthat/test-eq5dlss.R | 10 +++ tests/testthat/test-eq5dy3l.R | 12 +++- tests/testthat/test-eqhpg.R | 10 +++ tests/testthat/test-eqhsdi.R | 12 +++- tests/testthat/test-eqpchc.R | 9 +++ tests/testthat/test-eqshannon.R | 10 +++ tests/testthat/test-helpers.R | 9 +++ 34 files changed, 292 insertions(+), 133 deletions(-)
Title: Bayesian Vector Heterogeneous Autoregressive Modeling
Description: Tools to model and forecast multivariate time series
including Bayesian Vector heterogeneous autoregressive (VHAR) model
by Kim & Baek (2023) (<doi:10.1080/00949655.2023.2281644>).
'bvhar' can model Vector Autoregressive (VAR), VHAR, Bayesian VAR (BVAR), and Bayesian VHAR (BVHAR) models.
Author: Young Geun Kim [aut, cre, cph]
,
Changryong Baek [ctb]
Maintainer: Young Geun Kim <ygeunkimstat@gmail.com>
Diff between bvhar versions 2.2.1 dated 2025-02-25 and 2.2.2 dated 2025-02-28
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ R/misc-r.R | 2 +- README.md | 2 +- inst/doc/shrinkage.R | 3 +-- inst/doc/shrinkage.Rmd | 3 +-- inst/doc/stochastic-volatility.R | 3 +-- inst/doc/stochastic-volatility.Rmd | 3 +-- vignettes/shrinkage.Rmd | 3 +-- vignettes/stochastic-volatility.Rmd | 3 +-- 11 files changed, 25 insertions(+), 27 deletions(-)
Title: Bayesian Inference and Model Selection for Stochastic Epidemics
Description: Bayesian analysis for stochastic extensions of non-linear
dynamic systems using advanced computational algorithms. Described in Bouranis, L., Demiris, N., Kalogeropoulos, K., and Ntzoufras, I. (2022) <doi:10.48550/arXiv.2211.15229>.
Author: Lampros Bouranis [aut, cre, cph]
,
European Union [fnd]
Maintainer: Lampros Bouranis <bernadette.aueb@gmail.com>
Diff between Bernadette versions 1.1.5 dated 2024-01-12 and 1.1.6 dated 2025-02-28
DESCRIPTION | 18 MD5 | 20 NAMESPACE | 94 R/aggregate_contact_matrix.R | 87 R/countries_contact_matrix.R | 4 R/misc.R | 14 inst/doc/Bernadette.html | 2 inst/stan/igbm.stan | 19 man/priors.Rd | 3 src/Makevars.win | 2 src/stanExports_igbm.h | 5110 +++++++++++++++++++------------------------ 11 files changed, 2466 insertions(+), 2907 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-14 0.2.3
2022-03-11 0.2.2
2019-10-12 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-14 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-22 0.1.0
Title: Extended Joint Models for Longitudinal and Time-to-Event Data
Description: Fit joint models for longitudinal and time-to-event data under the Bayesian approach. Multiple longitudinal outcomes of mixed type (continuous/categorical) and multiple event times (competing risks and multi-state processes) are accommodated. Rizopoulos (2012, ISBN:9781439872864).
Author: Dimitris Rizopoulos [aut, cre]
,
Pedro Miranda Afonso [aut],
Grigorios Papageorgiou [aut]
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between JMbayes2 versions 0.5-0 dated 2024-05-30 and 0.5-2 dated 2025-02-28
DESCRIPTION | 16 ++-- MD5 | 17 ++--- NAMESPACE | 15 +++- R/accuracy_measures.R | 152 +++++++++++++++++++++++++++++++--------------- R/accuracy_measures_Cox.R |only R/basic_methods.R | 5 - man/JMbayes2.Rd | 4 - man/accuracy.Rd | 15 +++- man/jm.Rd | 6 + man/predict.Rd | 5 + 10 files changed, 157 insertions(+), 78 deletions(-)
Title: Flexible Mixture Modeling
Description: A general framework for finite mixtures of regression
models using the EM algorithm is implemented. The E-step and all
data handling are provided, while the M-step can be supplied by the
user to easily define new models. Existing drivers implement
mixtures of standard linear models, generalized linear models and
model-based clustering.
Author: Bettina Gruen [aut, cre] ,
Friedrich Leisch [aut] ,
Deepayan Sarkar [ctb] ,
Frederic Mortier [ctb],
Nicolas Picard [ctb]
Maintainer: Bettina Gruen <Bettina.Gruen@R-project.org>
Diff between flexmix versions 2.3-19 dated 2023-03-16 and 2.3-20 dated 2025-02-28
DESCRIPTION | 6 +++--- MD5 | 22 ++++++++++++---------- NAMESPACE | 2 ++ R/multcomp.R |only build/vignette.rds |binary data/Mehta.RData |binary inst/NEWS.Rd | 7 +++++++ inst/doc/bootstrapping.pdf |binary inst/doc/flexmix-intro.pdf |binary inst/doc/mixture-regressions.pdf |binary inst/doc/regression-examples.pdf |binary man/flxglht.Rd |only man/whiskey.Rd | 4 ++-- 13 files changed, 26 insertions(+), 15 deletions(-)
Title: Flexible Cluster Algorithms
Description: The main function kcca implements a general framework for
k-centroids cluster analysis supporting arbitrary distance measures
and centroid computation. Further cluster methods include hard
competitive learning, neural gas, and QT clustering. There are
numerous visualization methods for cluster results (neighborhood
graphs, convex cluster hulls, barcharts of centroids, ...), and
bootstrap methods for the analysis of cluster stability.
Author: Friedrich Leisch [aut] ,
Evgenia Dimitriadou [ctb],
Lena Ortega Menjivar [ctb] ,
Dominik Ernst [ctb] ,
Bettina Gruen [ctb, cre]
Maintainer: Bettina Gruen <Bettina.Gruen@R-project.org>
Diff between flexclust versions 1.4-2 dated 2024-04-27 and 1.5.0 dated 2025-02-28
DESCRIPTION | 21 ++++++++++++++------- MD5 | 30 ++++++++++++++++-------------- R/AAA-classes.R | 5 +++-- R/bclust.R | 4 ++-- R/bootstrap.R | 24 +----------------------- R/boxplot.R | 6 +++--- R/conversion.R | 14 +++++++------- R/family.R | 7 +++++-- R/histogram.R | 2 +- R/kcca.R | 14 +++++++++++--- R/shadow.R | 4 ++-- R/stepflexclust.R | 4 ++-- build |only inst/NEWS.Rd |only man/bclust.Rd | 2 +- man/info.Rd | 10 +++++----- man/kcca.Rd | 21 ++++++++++++--------- 17 files changed, 85 insertions(+), 83 deletions(-)
Title: Regression Spline Functions and Classes
Description: Constructs basis functions of B-splines, M-splines,
I-splines, convex splines (C-splines), periodic splines,
natural cubic splines, generalized Bernstein polynomials,
their derivatives, and integrals (except C-splines)
by closed-form recursive formulas.
It also contains a C++ head-only library integrated with Rcpp.
See Wang and Yan (2021) <doi:10.6339/21-JDS1020> for details.
Author: Wenjie Wang [aut, cre] ,
Jun Yan [aut]
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between splines2 versions 0.5.3 dated 2024-07-08 and 0.5.4 dated 2025-02-28
DESCRIPTION | 6 - MD5 | 78 ++++++++++++------------ NEWS.md | 13 ++++ R/bSpline.R | 2 R/bernsteinPoly.R | 2 R/cSpline.R | 2 R/deriv.R | 2 R/extract.R | 2 R/iSpline.R | 2 R/knots.R | 2 R/mSpline.R | 2 R/makepredictcall.R | 2 R/misc.R | 2 R/naturalSpline.R | 2 R/plot.R | 6 + R/predict.R | 2 R/print.R | 2 R/splines2-package.R | 2 R/update.R | 2 R/zzz.R | 2 README.md | 40 ++++++------ build/vignette.rds |binary inst/CITATION | 4 - inst/doc/splines2-intro.html | 11 +-- inst/doc/splines2-wi-rcpp.html | 9 +- inst/include/splines2Armadillo.h | 2 inst/include/splines2Armadillo/BSpline.h | 2 inst/include/splines2Armadillo/BernsteinPoly.h | 2 inst/include/splines2Armadillo/CSpline.h | 2 inst/include/splines2Armadillo/ISpline.h | 2 inst/include/splines2Armadillo/MSpline.h | 2 inst/include/splines2Armadillo/NaturalSpline.h | 21 ++---- inst/include/splines2Armadillo/NaturalSplineK.h | 2 inst/include/splines2Armadillo/PeriodicSpline.h | 2 inst/include/splines2Armadillo/SplineBase.h | 2 inst/include/splines2Armadillo/common.h | 2 inst/include/splines2Armadillo/utils.h | 2 inst/tinytest/test-naturalSpline.R | 18 ++++- inst/tinytest/test-plot.R | 6 + src/splines2_export.cpp | 2 40 files changed, 149 insertions(+), 119 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-24 0.2.0
2020-06-03 0.1.30.3
2020-05-26 0.1.30.1
2018-05-23 0.1.30
2018-05-17 0.1.25
2017-04-03 0.1.14
2016-10-28 0.1.3
2016-10-26 0.1.2
2016-08-10 0.0.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-22 0.1