Title: A Common Representation of Time Indices of Different Types
Description: Provides an easy-to-use tind class representing time indices
of different types (years, quarters, months, ISO 8601 weeks, dates,
time of day, date-time, and arbitrary integer/numeric indices).
Includes an extensive collection of functions for calendrical computations
(including business applications), index conversions, index parsing,
and other operations. Auxiliary classes representing time differences and
time intervals (with set operations and index matching functionality) are
also provided. All routines have been optimised for speed in order
to facilitate computations on large datasets. More details regarding
calendars in general and calendrical algorithms can be found in
"Calendar FAQ" by Claus Tøndering <https://www.tondering.dk/claus/calendar.html>.
Author: Grzegorz Klima [aut, cre, cph]
Maintainer: Grzegorz Klima <dever@post.pl>
Diff between tind versions 0.2 dated 2025-10-22 and 0.2.1 dated 2025-10-26
DESCRIPTION | 8 MD5 | 24 - R/methods.R | 1 build/vignette.rds |binary inst/doc/calendar.html | 750 +++++++++++++++++----------------- inst/doc/indices.R | 2 inst/doc/indices.html | 359 ++++++++-------- inst/po/en@quot/LC_MESSAGES/R-tind.mo |binary inst/po/pl/LC_MESSAGES/R-tind.mo |binary po/R-pl.po | 2 po/R-tind.pot | 6 src/tochar.c | 16 tests/testthat/test-12-coercion.R | 4 13 files changed, 585 insertions(+), 587 deletions(-)
Title: Initialization of Numerical Optimization
Description: Analysis of the initialization for numerical optimization of
real-valued functions, particularly likelihood functions of statistical
models. See <https://loelschlaeger.de/ino/> for more details.
Author: Lennart Oelschlaeger [aut, cre] ,
Marius Oetting [aut] ,
Dietmar Bauer [ctb]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between ino versions 1.1.1 dated 2025-10-21 and 1.2.0 dated 2025-10-26
ino-1.1.1/ino/data |only ino-1.1.1/ino/inst/doc/example_hmm.R |only ino-1.1.1/ino/inst/doc/example_hmm.Rmd |only ino-1.1.1/ino/inst/doc/example_hmm.html |only ino-1.1.1/ino/man/Nop_hmm.Rd |only ino-1.1.1/ino/vignettes/example_hmm.Rmd |only ino-1.1.1/ino/vignettes/figures/hmm-optimization-time-1.png |only ino-1.1.1/ino/vignettes/figures/hmm-plot-dax-data-1.png |only ino-1.2.0/ino/DESCRIPTION | 11 ino-1.2.0/ino/MD5 | 52 ino-1.2.0/ino/NAMESPACE | 158 ino-1.2.0/ino/NEWS.md | 4 ino-1.2.0/ino/R/autoplot.R | 672 +- ino-1.2.0/ino/R/ino-package.R | 213 ino-1.2.0/ino/R/nop.R | 3139 +++++------ ino-1.2.0/ino/README.md | 276 ino-1.2.0/ino/build/vignette.rds |binary ino-1.2.0/ino/inst/doc/ino.R | 310 - ino-1.2.0/ino/inst/doc/ino.Rmd | 922 +-- ino-1.2.0/ino/inst/doc/ino.html | 2119 +++---- ino-1.2.0/ino/man/Nop.Rd | 1509 ++--- ino-1.2.0/ino/man/autoplot.Nop.Rd | 132 ino-1.2.0/ino/man/figures/README-ackley_time-1.png |binary ino-1.2.0/ino/man/ino-package.Rd | 72 ino-1.2.0/ino/tests/testthat.R | 8 ino-1.2.0/ino/tests/testthat/test-nop.R | 490 - ino-1.2.0/ino/vignettes/figures/ino-estimated-mixtures-1.png |binary ino-1.2.0/ino/vignettes/figures/ino-faithful-plot-1.png |binary ino-1.2.0/ino/vignettes/figures/ino-plot-seconds-1.png |binary ino-1.2.0/ino/vignettes/ino.Rmd | 922 +-- ino-1.2.0/ino/vignettes/ref.bib | 265 31 files changed, 5603 insertions(+), 5671 deletions(-)
Title: Excerpt Structuring Comments from Your Code File and Set a Table
of Contents
Description: Ever read or wrote source files containing sectioning comments?
If these comments are markdown style section comments,
you can excerpt them and set a table of contents using the
'python' package 'excerpts' (<https://pypi.org/project/excerpts/>).
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
This is a re-admission after prior archival of version 2.0.1 dated 2021-08-04
Diff between excerptr versions 2.0.1 dated 2021-08-04 and 2.1.0 dated 2025-10-26
DESCRIPTION | 18 +- MD5 | 24 +- NEWS.md | 4 R/excerptr.R | 17 +- R/throw.R | 4 README.md | 33 ++-- build/vignette.rds |binary inst/NEWS.rd |only inst/doc/An_Introduction_to_excerptr.R | 72 ++++---- inst/doc/An_Introduction_to_excerptr.html | 242 +++++++++++++++++++----------- inst/vignettes_code |only man/excerptr-package.Rd | 11 + man/excerptr.Rd | 15 + man/throw.Rd | 5 14 files changed, 274 insertions(+), 171 deletions(-)
Title: Tools for Tidy Vowel Normalization
Description: An implementation of tidy speaker vowel normalization.
This includes generic functions for defining new normalization methods for
points, formant tracks, and Discrete Cosine Transform coefficients, as well
as convenience functions implementing established normalization methods.
References for the implemented methods are:
Johnson, Keith (2020) <doi:10.5334/labphon.196>
Lobanov, Boris (1971) <doi:10.1121/1.1912396>
Nearey, Terrance M. (1978) <https://sites.ualberta.ca/~tnearey/Nearey1978_compressed.pdf>
Syrdal, Ann K., and Gopal, H. S. (1986) <doi:10.1121/1.393381>
Watt, Dominic, and Fabricius, Anne (2002) <https://www.latl.leeds.ac.uk/article/evaluation-of-a-technique-for-improving-the-mapping-of-multiple-speakers-vowel-spaces-in-the-f1-f2-plane/>.
Author: Josef Fruehwald [cre, aut, cph]
Maintainer: Josef Fruehwald <JoFrhwld@gmail.com>
Diff between tidynorm versions 0.3.1 dated 2025-10-06 and 0.4.0 dated 2025-10-26
tidynorm-0.3.1/tidynorm/R/ops.R |only tidynorm-0.4.0/tidynorm/DESCRIPTION | 10 - tidynorm-0.4.0/tidynorm/MD5 | 74 +++++----- tidynorm-0.4.0/tidynorm/NAMESPACE | 2 tidynorm-0.4.0/tidynorm/NEWS.md | 15 ++ tidynorm-0.4.0/tidynorm/R/dct.R | 7 tidynorm-0.4.0/tidynorm/R/dct_norm.R | 50 +++--- tidynorm-0.4.0/tidynorm/R/norm.R | 53 +++---- tidynorm-0.4.0/tidynorm/R/options.R |only tidynorm-0.4.0/tidynorm/R/track_norm.R | 49 +++--- tidynorm-0.4.0/tidynorm/R/utils.R | 10 - tidynorm-0.4.0/tidynorm/README.md | 14 + tidynorm-0.4.0/tidynorm/inst/doc/dct.html | 10 - tidynorm-0.4.0/tidynorm/inst/doc/normalization-overview.html | 10 - tidynorm-0.4.0/tidynorm/inst/doc/normalizing_formant_tracks.html | 2 tidynorm-0.4.0/tidynorm/man/figures/README-norm-1.png |binary tidynorm-0.4.0/tidynorm/man/figures/README-rnorm-1.png |binary tidynorm-0.4.0/tidynorm/man/figures/README-unnorm-1.png |binary tidynorm-0.4.0/tidynorm/man/norm_barkz.Rd | 4 tidynorm-0.4.0/tidynorm/man/norm_dct_barkz.Rd | 4 tidynorm-0.4.0/tidynorm/man/norm_dct_deltaF.Rd | 4 tidynorm-0.4.0/tidynorm/man/norm_dct_generic.Rd | 4 tidynorm-0.4.0/tidynorm/man/norm_dct_lobanov.Rd | 4 tidynorm-0.4.0/tidynorm/man/norm_dct_nearey.Rd | 4 tidynorm-0.4.0/tidynorm/man/norm_dct_wattfab.Rd | 4 tidynorm-0.4.0/tidynorm/man/norm_deltaF.Rd | 4 tidynorm-0.4.0/tidynorm/man/norm_generic.Rd | 4 tidynorm-0.4.0/tidynorm/man/norm_lobanov.Rd | 4 tidynorm-0.4.0/tidynorm/man/norm_nearey.Rd | 4 tidynorm-0.4.0/tidynorm/man/norm_track_barkz.Rd | 4 tidynorm-0.4.0/tidynorm/man/norm_track_deltaF.Rd | 4 tidynorm-0.4.0/tidynorm/man/norm_track_generic.Rd | 4 tidynorm-0.4.0/tidynorm/man/norm_track_lobanov.Rd | 4 tidynorm-0.4.0/tidynorm/man/norm_track_nearey.Rd | 4 tidynorm-0.4.0/tidynorm/man/norm_track_wattfab.Rd | 4 tidynorm-0.4.0/tidynorm/man/norm_wattfab.Rd | 4 tidynorm-0.4.0/tidynorm/man/options.Rd |only tidynorm-0.4.0/tidynorm/man/tidynorm_options.Rd |only tidynorm-0.4.0/tidynorm/tests/testthat/test-options.R |only tidynorm-0.4.0/tidynorm/tests/testthat/test-reframes.R |only tidynorm-0.4.0/tidynorm/tests/testthat/test_reloc.R | 31 ++++ 41 files changed, 236 insertions(+), 173 deletions(-)
Title: Data Utilities for Congressional Research
Description: Provides easy-to-understand and consistent interfaces for
accessing data on the U.S. Congress. The functions in 'filibustr'
streamline the process for importing data on Congress into R, removing
the need to download and work from CSV files and the like. Data
sources include 'Voteview' (<https://voteview.com/>), the U.S. Senate
website (<https://www.senate.gov/>), and more.
Author: Max Feinleib [aut, cre, cph]
Maintainer: Max Feinleib <mhfeinleib@gmail.com>
Diff between filibustr versions 0.4.1 dated 2025-08-19 and 0.5.0 dated 2025-10-26
DESCRIPTION | 16 +-- MD5 | 47 +++++---- NEWS.md | 60 +++++++++++- R/build_url.R | 9 - R/get_les.R | 76 +++++++++------ R/get_voteview_member_votes.R | 1 R/get_voteview_members.R | 10 ++ R/utils_data_cleaning.R | 24 +++- R/utils_data_reading.R | 21 +++- README.md | 85 ++++++++--------- build/vignette.rds |only inst |only man/get_hvw_data.Rd | 4 man/get_les.Rd | 37 ++++--- man/get_senate_cloture_votes.Rd | 2 man/get_senate_sessions.Rd | 2 man/get_voteview_member_votes.Rd | 16 ++- man/get_voteview_members.Rd | 18 +++ man/get_voteview_parties.Rd | 18 +++ man/get_voteview_rollcall_votes.Rd | 18 +++ man/read_html_table.Rd | 4 tests/testthat/test-build_url.R | 20 +--- tests/testthat/test-get_hvw_data.R | 12 ++ tests/testthat/test-get_les.R | 179 +++++++++++++++++-------------------- vignettes |only 25 files changed, 421 insertions(+), 258 deletions(-)
Title: Algorithm for Searching the Space of Gaussian Directed Acyclic
Graph Models Through Moment Fractional Bayes Factors
Description: We propose an objective Bayesian algorithm for searching the space
of Gaussian directed acyclic graph (DAG) models. The algorithm uses moment
fractional Bayes factors (MFBF) and is suitable for learning sparse graphs.
The algorithm is implemented using Armadillo, an open-source C++ linear
algebra library.
Author: Davide Altomare [aut, cre],
Guido Consonni [aut],
Luca La Rocca [aut]
Maintainer: Davide Altomare <davide.altomare@gmail.com>
Diff between FBFsearch versions 1.2 dated 2022-08-08 and 1.3 dated 2025-10-26
DESCRIPTION | 25 - MD5 | 6 src/FBFsearch.cpp | 1264 +++++++++++++++++++++++------------------------------- src/FBFsearch_H.h | 30 - 4 files changed, 588 insertions(+), 737 deletions(-)
Title: Fast Approximation of Time-Varying Infectious Disease
Transmission Rates
Description: A fast method for approximating time-varying infectious disease
transmission rates from disease incidence time series and other
data, based on a discrete time approximation of an SEIR model, as
analyzed in Jagan et al. (2020) <doi:10.1371/journal.pcbi.1008124>.
Author: Mikael Jagan [aut, cre] ,
David Earn [ctb]
Maintainer: Mikael Jagan <jaganmn@mcmaster.ca>
Diff between fastbeta versions 0.5.0 dated 2025-10-15 and 0.5.1 dated 2025-10-26
DESCRIPTION | 15 +++-- MD5 | 6 +- NAMESPACE | 22 ++++++-- inst/NEWS.Rd | 148 +++++++++++++++++++++++++++++++++-------------------------- 4 files changed, 113 insertions(+), 78 deletions(-)
Title: Factor-Augmented Regression Scenarios
Description: Provides a comprehensive framework in R for modeling and forecasting economic scenarios based on multi-level dynamic factor model. The package enables users to: (i) extract global and group-specific factors using a flexible multi-level factor structure; (ii) compute asymptotically valid confidence regions for the estimated factors, accounting for uncertainty in the factor loadings; (iii) obtain estimates of the parameters of the factor-augmented quantile regressions together with their standard deviations; (iv) recover full predictive conditional densities from estimated quantiles; (v) obtain risk measures based on extreme quantiles of the conditional densities; (vi) estimate the conditional density and the corresponding extreme quantiles when the factors are stressed.
Author: Gian Pietro Bellocca [aut, cre],
Ignacio Garron [aut],
Vladimir Rodriguez-Caballero [aut],
Esther Ruiz [aut]
Maintainer: Gian Pietro Bellocca <gbellocc@est-econ.uc3m.es>
Diff between FARS versions 0.6.1 dated 2025-10-08 and 0.7.0 dated 2025-10-26
FARS-0.6.1/FARS/R/eigen_sorted.R |only FARS-0.6.1/FARS/R/get_ellipsoids.R |only FARS-0.6.1/FARS/R/get_factors.R |only FARS-0.6.1/FARS/R/get_loadings.R |only FARS-0.6.1/FARS/R/get_mldfm_list.R |only FARS-0.6.1/FARS/R/get_mldfm_model.R |only FARS-0.6.1/FARS/R/get_quantile_levels.R |only FARS-0.6.1/FARS/R/get_quantiles.R |only FARS-0.6.1/FARS/R/get_residuals.R |only FARS-0.6.1/FARS/R/get_sigma_list.R |only FARS-0.6.1/FARS/R/get_stressed_factors.R |only FARS-0.6.1/FARS/R/q_reg.R |only FARS-0.6.1/FARS/man/eigen_sorted.Rd |only FARS-0.6.1/FARS/man/get_factors.Rd |only FARS-0.6.1/FARS/man/get_factors.mldfm.Rd |only FARS-0.6.1/FARS/man/get_loadings.Rd |only FARS-0.6.1/FARS/man/get_loadings.mldfm.Rd |only FARS-0.6.1/FARS/man/get_quantiles.Rd |only FARS-0.6.1/FARS/man/get_quantiles.fars.Rd |only FARS-0.6.1/FARS/man/get_residuals.Rd |only FARS-0.6.1/FARS/man/get_residuals.mldfm.Rd |only FARS-0.6.1/FARS/man/get_stressed_factors.Rd |only FARS-0.6.1/FARS/man/get_stressed_factors.fars.Rd |only FARS-0.6.1/FARS/man/q_reg.Rd |only FARS-0.6.1/FARS/man/shift.Rd |only FARS-0.7.0/FARS/DESCRIPTION | 6 FARS-0.7.0/FARS/MD5 | 107 +++---- FARS-0.7.0/FARS/NAMESPACE | 23 - FARS-0.7.0/FARS/R/canonical_correlation_analysis.R | 70 ++-- FARS-0.7.0/FARS/R/compute_fars.R | 146 +++------ FARS-0.7.0/FARS/R/compute_fpr_gamma.R | 43 +- FARS-0.7.0/FARS/R/compute_stressed_factors.R | 131 ++++---- FARS-0.7.0/FARS/R/create_scenario.R | 151 ++++------ FARS-0.7.0/FARS/R/fars_methods.R |only FARS-0.7.0/FARS/R/get_distribution.R | 16 - FARS-0.7.0/FARS/R/mldfm.R | 2 FARS-0.7.0/FARS/R/mldfm_methods.R |only FARS-0.7.0/FARS/R/mldfm_subsample_methods.R |only FARS-0.7.0/FARS/R/multiple_blocks.R | 14 FARS-0.7.0/FARS/R/plot.R | 86 ++--- FARS-0.7.0/FARS/R/print.R | 21 - FARS-0.7.0/FARS/R/scenario_methods.R |only FARS-0.7.0/FARS/R/single_block.R | 19 - FARS-0.7.0/FARS/R/summary.R | 48 --- FARS-0.7.0/FARS/inst/doc/Factor_Augmented_Regression_Scenarios_in_R.pdf |binary FARS-0.7.0/FARS/man/coef.fars.Rd |only FARS-0.7.0/FARS/man/compute_fars.Rd | 54 +-- FARS-0.7.0/FARS/man/compute_stressed_factors.Rd | 33 +- FARS-0.7.0/FARS/man/factors.Rd |only FARS-0.7.0/FARS/man/factors.mldfm.Rd |only FARS-0.7.0/FARS/man/fitted.fars.Rd |only FARS-0.7.0/FARS/man/fitted.mldfm.Rd |only FARS-0.7.0/FARS/man/get_distribution.Rd | 4 FARS-0.7.0/FARS/man/get_distribution.fars_density.Rd | 4 FARS-0.7.0/FARS/man/get_ellipsoids.Rd | 2 FARS-0.7.0/FARS/man/get_ellipsoids.fars_scenario.Rd | 2 FARS-0.7.0/FARS/man/get_mldfm_list.Rd | 2 FARS-0.7.0/FARS/man/get_mldfm_list.mldfm_subsample.Rd | 2 FARS-0.7.0/FARS/man/get_mldfm_model.Rd | 2 FARS-0.7.0/FARS/man/get_mldfm_model.mldfm_subsample.Rd | 2 FARS-0.7.0/FARS/man/get_quantile_levels.Rd | 2 FARS-0.7.0/FARS/man/get_quantile_levels.fars.Rd | 2 FARS-0.7.0/FARS/man/get_rq_model.Rd |only FARS-0.7.0/FARS/man/get_rq_model.fars.Rd |only FARS-0.7.0/FARS/man/get_sigma_list.Rd | 2 FARS-0.7.0/FARS/man/loadings.Rd |only FARS-0.7.0/FARS/man/loadings.mldfm.Rd |only FARS-0.7.0/FARS/man/mldfm.Rd | 1 FARS-0.7.0/FARS/man/multiple_blocks.Rd | 1 FARS-0.7.0/FARS/man/plot.fars.Rd | 13 FARS-0.7.0/FARS/man/predict.fars.Rd |only FARS-0.7.0/FARS/man/residuals.fars.Rd |only FARS-0.7.0/FARS/man/residuals.mldfm.Rd |only FARS-0.7.0/FARS/man/single_block.Rd | 1 FARS-0.7.0/FARS/man/summary.fars.Rd | 3 75 files changed, 452 insertions(+), 563 deletions(-)
Title: Conduct Simulation Study of Bayesian Optimal Interval Design
with BOIN-ET Family
Description: Bayesian optimal interval based on both efficacy and toxicity outcomes (BOIN-ET) design is a model-assisted oncology phase I/II trial design, aiming to establish an optimal biological dose accounting for efficacy and toxicity in the framework of dose-finding. Some extensions of BOIN-ET design are also available to allow for time-to-event efficacy and toxicity outcomes based on cumulative and pending data (time-to-event BOIN-ET: TITE-BOIN-ET), ordinal graded efficacy and toxicity outcomes (generalized BOIN-ET: gBOIN-ET), and their combination (TITE-gBOIN-ET). 'boinet' is a package to implement the BOIN-ET design family and supports the conduct of simulation studies to assess operating characteristics of BOIN-ET, TITE-BOIN-ET, gBOIN-ET, and TITE-gBOIN-ET, where users can choose design parameters in flexible and straightforward ways depending on their own application.
Author: Yusuke Yamaguchi [aut, cre],
Kentaro Takeda [aut]
Maintainer: Yusuke Yamaguchi <yamagubed@gmail.com>
Diff between boinet versions 1.4.0 dated 2025-06-26 and 1.5.0 dated 2025-10-26
DESCRIPTION | 12 MD5 | 17 NAMESPACE | 44 NEWS.md | 4 R/launch.shinyapp.R |only build/vignette.rds |binary inst/doc/gt_integration_vignette.html | 6337 ++++++++++++++----------------- inst/doc/quarto_workflow_vignette.html | 2717 ++++++------- inst/doc/result_formatting_vignette.html | 925 ++-- inst/shiny |only man/launch.shinyapp.Rd |only 11 files changed, 4808 insertions(+), 5248 deletions(-)
Title: Variational Bayes for Fast and Accurate Empirical Likelihood
Inference
Description: Computes the Gaussian variational approximation of the Bayesian
empirical likelihood posterior. This is an implementation of the function
found in Yu, W., & Bondell, H. D. (2023) <doi:10.1080/01621459.2023.2169701>.
Author: Weichang Yu [aut] ,
Jeremy Lim [cre, aut]
Maintainer: Jeremy Lim <jeremy.lim@unimelb.edu.au>
Diff between VBel versions 1.1.0 dated 2024-12-05 and 1.1.6 dated 2025-10-26
DESCRIPTION | 11 +--- MD5 | 29 +++++------ NEWS.md |only R/RcppExports.R | 4 - R/compute-AEL-functions.R | 33 +++++------- R/compute-GVA-functions.R | 45 +++++++++-------- R/diagnostic-plot.R | 22 +++++--- README.md | 4 - build/partial.rdb |binary man/VBel-package.Rd | 15 +---- man/compute_AEL.Rd | 22 ++++---- man/compute_GVA.Rd | 43 +++++++++------- man/diagnostic_plot.Rd | 11 ++-- src/RcppExports.cpp | 8 +-- src/compute-AEL-functions-Rcpp.cpp | 96 +++++++++++-------------------------- src/compute-GVA-functions-Rcpp.cpp | 8 +-- 16 files changed, 159 insertions(+), 192 deletions(-)
Title: A Tidy Implementation of Heatmap
Description: This is a tidy implementation for heatmap. At the
moment it is based on the (great) package 'ComplexHeatmap'. The goal
of this package is to interface a tidy data frame with this powerful
tool. Some of the advantages are: Row and/or columns colour
annotations are easy to integrate just specifying one parameter
(column names). Custom grouping of rows is easy to specify providing
a grouped tbl. For example: df %>% group_by(...). Labels size
adjusted by row and column total number. Default use of Brewer and
Viridis palettes.
Author: Stefano Mangiola [aut, cre],
Anthony Papenfuss [ctb]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>
Diff between tidyHeatmap versions 1.12.2 dated 2025-07-22 and 1.12.3 dated 2025-10-26
tidyHeatmap-1.12.2/tidyHeatmap/man/check_if_counts_is_na.Rd |only tidyHeatmap-1.12.3/tidyHeatmap/DESCRIPTION | 8 tidyHeatmap-1.12.3/tidyHeatmap/MD5 | 23 tidyHeatmap-1.12.3/tidyHeatmap/R/deprecated_framework.R | 2 tidyHeatmap-1.12.3/tidyHeatmap/R/functions.R | 4 tidyHeatmap-1.12.3/tidyHeatmap/R/methods.R | 3 tidyHeatmap-1.12.3/tidyHeatmap/R/utilities.R | 45 tidyHeatmap-1.12.3/tidyHeatmap/R/validation.R | 17 tidyHeatmap-1.12.3/tidyHeatmap/build/stage23.rdb |binary tidyHeatmap-1.12.3/tidyHeatmap/inst/doc/introduction.R | 10 tidyHeatmap-1.12.3/tidyHeatmap/inst/doc/introduction.Rmd | 15 tidyHeatmap-1.12.3/tidyHeatmap/inst/doc/introduction.html | 733 +++++------- tidyHeatmap-1.12.3/tidyHeatmap/vignettes/introduction.Rmd | 15 13 files changed, 435 insertions(+), 440 deletions(-)
Title: Lightweight Wrapper to the 'ntfy.sh' Service
Description: The 'ntfy' (pronounce: notify) service is a simple HTTP-based pub-sub
notification service. It allows you to send notifications to your phone or
desktop via scripts from any computer, entirely without signup, cost or
setup. It's also open source if you want to run your own.
Visit <https://ntfy.sh> for more details.
Author: Jonathan Carroll [aut, cre] ,
Andrew Heiss [ctb] ,
Hadley Wickham [ctb]
Maintainer: Jonathan Carroll <rpkg@jcarroll.com.au>
Diff between ntfy versions 0.0.6 dated 2024-11-06 and 0.1.0 dated 2025-10-26
ntfy-0.0.6/ntfy/R/zzz.R |only ntfy-0.0.6/ntfy/inst |only ntfy-0.0.6/ntfy/man/get_image_path.Rd |only ntfy-0.0.6/ntfy/man/ntfy_auth.Rd |only ntfy-0.0.6/ntfy/man/ntfy_done_with_timing.Rd |only ntfy-0.0.6/ntfy/man/ntfy_password.Rd |only ntfy-0.0.6/ntfy/man/ntfy_server.Rd |only ntfy-0.0.6/ntfy/man/ntfy_username.Rd |only ntfy-0.0.6/ntfy/man/req_add_auth_if_needed.Rd |only ntfy-0.0.6/ntfy/man/req_add_image_if_needed.Rd |only ntfy-0.0.6/ntfy/tests/testthat/test-private_server.R |only ntfy-0.0.6/ntfy/tests/testthat/test-public_server.R |only ntfy-0.1.0/ntfy/DESCRIPTION | 26 + ntfy-0.1.0/ntfy/MD5 | 39 +- ntfy-0.1.0/ntfy/NEWS.md | 8 ntfy-0.1.0/ntfy/R/env.R | 64 ++-- ntfy-0.1.0/ntfy/R/ntfy.R | 268 +++++++++---------- ntfy-0.1.0/ntfy/R/tags.R | 5 ntfy-0.1.0/ntfy/README.md | 76 +---- ntfy-0.1.0/ntfy/man/ntfy-package.Rd | 2 ntfy-0.1.0/ntfy/man/ntfy_done.Rd | 29 +- ntfy-0.1.0/ntfy/man/ntfy_history.Rd | 2 ntfy-0.1.0/ntfy/man/ntfy_send.Rd | 6 ntfy-0.1.0/ntfy/man/ntfy_topic.Rd | 31 +- ntfy-0.1.0/ntfy/tests/testthat/_snaps |only ntfy-0.1.0/ntfy/tests/testthat/helpers.R |only ntfy-0.1.0/ntfy/tests/testthat/test-env.R |only ntfy-0.1.0/ntfy/tests/testthat/test-ntfy.R |only 28 files changed, 284 insertions(+), 272 deletions(-)
Title: Metabolic Pathway Completeness and Abundance Calculation
Description: Provides tools for analyzing metabolic pathway completeness, abundance, and transcripts
using KEGG Orthology (KO) data from (meta)genomic and (meta)transcriptomic studies.
Supports both completeness (presence/absence) and abundance-weighted analyses.
Includes built-in KEGG reference datasets. For more details see Li et al. (2023) <doi:10.1038/s41467-023-42193-7>.
Author: Liuyang Li [aut, cre]
Maintainer: Liuyang Li <cyanobacteria@yeah.net>
Diff between mclink versions 1.1 dated 2025-08-22 and 1.1.1 dated 2025-10-26
ChangeLog |only DESCRIPTION | 6 - MD5 | 11 +- R/mclink.R | 31 +++++-- R/read_and_process_KO_table.R | 2 README.md | 178 +++++++++++++++++++++++++++++++++++------- man/mclink.Rd | 32 +++++-- 7 files changed, 207 insertions(+), 53 deletions(-)
Title: A Repository of Bayesian Networks from the Academic Literature
Description: A collection of Bayesian networks (discrete, Gaussian, and conditional linear Gaussian) collated from recent academic literature. The 'bnRep_summary' object provides an overview of the Bayesian networks in the repository and the package documentation includes details about the variables in each network. A Shiny app to explore the repository can be launched with 'bnRep_app()' and is available online at <https://manueleleonelli.shinyapps.io/bnRep>. Reference: 'M. Leonelli' (2025) <doi:10.1016/j.neucom.2025.129502>.
Author: Manuele Leonelli [aut, cre, cph]
Maintainer: Manuele Leonelli <manuele.leonelli@ie.edu>
Diff between bnRep versions 0.0.5 dated 2025-07-23 and 0.0.6 dated 2025-10-26
DESCRIPTION | 6 +++--- MD5 | 23 +++++++++++++++++++---- R/airegulation1.R |only R/airegulation2.R |only R/airegulation3.R |only R/forest.R |only R/volleyball.R |only build/vignette.rds |binary data/airegulation1.rda |only data/airegulation2.rda |only data/airegulation3.rda |only data/bnRep_summary.rda |binary data/forest.rda |only data/volleyball.rda |only inst/doc/overview.html | 22 ++++++++++------------ man/airegulation1.Rd |only man/airegulation2.Rd |only man/airegulation3.Rd |only man/forest.Rd |only man/volleyball.Rd |only 20 files changed, 32 insertions(+), 19 deletions(-)
Title: Bayesian Regression for Dynamic Treatment Regimes
Description: Methods to estimate optimal dynamic treatment regimes using Bayesian
likelihood-based regression approach as described in
Yu, W., & Bondell, H. D. (2023) <doi:10.1093/jrsssb/qkad016>
Uses backward induction and dynamic programming theory for computing
expected values. Offers options for future parallel computing.
Author: Jeremy Lim [aut, cre],
Weichang Yu [aut]
Maintainer: Jeremy Lim <jeremylim23@gmail.com>
Diff between BayesRegDTR versions 1.0.1 dated 2025-06-27 and 1.1.1 dated 2025-10-26
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 10 ++++++++++ R/BayesLinRegDTR.model.fit.R | 8 ++++---- tests/testthat/test-BayesLinRegDTR_model_fit.R | 4 ++-- 5 files changed, 24 insertions(+), 14 deletions(-)
Title: Probabilistic Regression Trees
Description: Implementation of Probabilistic Regression Trees (PRTree),
providing functions for model fitting and prediction, with specific adaptations
to handle missing values. The main computations are implemented in 'Fortran'
for high efficiency. The package is based on the PRTree methodology described in
Alkhoury et al. (2020), "Smooth and Consistent Probabilistic Regression Trees"
<https://proceedings.neurips.cc/paper_files/paper/2020/file/8289889263db4a40463e3f358bb7c7a1-Paper.pdf>.
Details on the treatment of missing data and implementation aspects are presented in
Prass, T.S.; Neimaier, A.S.; Pumi, G. (2025), "Handling Missing Data in Probabilistic Regression Trees:
Methods and Implementation in R" <doi:10.48550/arXiv.2510.03634>.
Author: Alisson Silva Neimaier [aut] ,
Taiane Schaedler Prass [aut, ths, cre]
Maintainer: Taiane Schaedler Prass <taianeprass@gmail.com>
Diff between PRTree versions 1.0.1 dated 2025-10-18 and 1.0.2 dated 2025-10-26
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/misc.R | 2 +- inst/news.md | 8 +++++++- src/prtree.f90 | 11 ++++++----- src/prtree_types.f90 | 1 + 6 files changed, 24 insertions(+), 16 deletions(-)
Title: Nonparametric Missing Value Imputation using Random Forest
Description: The function 'missForest' in this package is used to
impute missing values particularly in the case of mixed-type
data. It uses a random forest (via 'ranger' or 'randomForest') trained on the observed values of
a data matrix to predict the missing values. It can be used to
impute continuous and/or categorical data including complex
interactions and non-linear relations. It yields an out-of-bag
(OOB) imputation error estimate without the need of a test set
or elaborate cross-validation. It can be run in parallel to
save computation time.
Author: Daniel J. Stekhoven [aut, cre]
Maintainer: Daniel J. Stekhoven <stekhoven@nexus.ethz.ch>
Diff between missForest versions 1.5 dated 2022-04-14 and 1.6.1 dated 2025-10-26
missForest-1.5/missForest/inst/doc/missForest_1.5.R |only missForest-1.5/missForest/inst/doc/missForest_1.5.Rnw |only missForest-1.5/missForest/inst/doc/missForest_1.5.pdf |only missForest-1.5/missForest/vignettes/missForest_1.5.Rnw |only missForest-1.6.1/missForest/DESCRIPTION | 42 missForest-1.6.1/missForest/MD5 | 36 missForest-1.6.1/missForest/NAMESPACE | 34 missForest-1.6.1/missForest/NEWS.md |only missForest-1.6.1/missForest/R/globals.R |only missForest-1.6.1/missForest/R/missForest.R | 839 ++++++++++----- missForest-1.6.1/missForest/README.md | 163 ++ missForest-1.6.1/missForest/build/partial.rdb |only missForest-1.6.1/missForest/build/vignette.rds |binary missForest-1.6.1/missForest/inst/CITATION | 60 - missForest-1.6.1/missForest/inst/REFERENCES.bib |only missForest-1.6.1/missForest/inst/doc/missForest_1.6.R |only missForest-1.6.1/missForest/inst/doc/missForest_1.6.Rmd |only missForest-1.6.1/missForest/inst/doc/missForest_1.6.html |only missForest-1.6.1/missForest/man/missForest-package.Rd | 37 missForest-1.6.1/missForest/man/missForest.Rd | 288 ++--- missForest-1.6.1/missForest/man/mixError.Rd | 71 - missForest-1.6.1/missForest/man/nrmse.Rd | 58 - missForest-1.6.1/missForest/man/prodNA.Rd | 46 missForest-1.6.1/missForest/man/varClass.Rd | 22 missForest-1.6.1/missForest/vignettes/missForest_1.6.Rmd |only 25 files changed, 1129 insertions(+), 567 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-08 0.9.6
2024-10-14 0.9.5
2020-06-06 0.9.2