Title: Bioinformatics Modeling with Recursion and Autoencoder-Based
Ensemble
Description: Tools for bioinformatics modeling using recursive transformer-inspired
architectures, autoencoders, random forests, XGBoost, and stacked ensemble models.
Includes utilities for cross-validation, calibration, benchmarking, and threshold
optimization in predictive modeling workflows. The methodology builds on ensemble
learning (Breiman 2001 <doi:10.1023/A:1010933404324>), gradient boosting (Chen and
Guestrin 2016 <doi:10.1145/2939672.2939785>), autoencoders (Hinton and Salakhutdinov
2006 <doi:10.1126/science.1127647>), and recursive transformer efficiency approaches
such as Mixture-of-Recursions (Bae et al. 2025 <doi:10.48550/arXiv.2507.10524>).
Author: MD. Arshad [aut, cre]
Maintainer: MD. Arshad <arshad10867c@gmail.com>
Diff between BioMoR versions 0.1.0 dated 2025-10-03 and 0.1.1 dated 2025-12-10
DESCRIPTION | 10 MD5 | 37 +- R/autoencoder.R | 4 R/train_biomor.R | 4 build/vignette.rds |binary inst/doc/biomor-autoencoder.R | 11 inst/doc/biomor-autoencoder.Rmd | 30 + inst/doc/biomor-autoencoder.html | 608 ++++++++++++++++------------------- inst/doc/biomor-benchmarking.R | 15 inst/doc/biomor-benchmarking.Rmd | 35 +- inst/doc/biomor-benchmarking.html | 654 +++++++++++++++++++------------------- inst/doc/biomor-intro.R | 14 inst/doc/biomor-intro.Rmd | 53 +-- inst/doc/biomor-intro.html | 59 +-- tests/testthat/test_benchmark.R | 4 tests/testthat/test_models.R | 11 tests/testthat/test_utils.R |only vignettes/biomor-autoencoder.Rmd | 30 + vignettes/biomor-benchmarking.Rmd | 35 +- vignettes/biomor-intro.Rmd | 53 +-- 20 files changed, 849 insertions(+), 818 deletions(-)
Title: Analysis of Moderation, Statistical Power, and Optimal Design
for Studies Detecting Difference and Equivalence
Description: Analysis of moderation (ANOMO) method conceptualizes
the difference and equivalence tests as a moderation problem to
test the difference and equivalence of
two estimates (e.g., two means or two effects).
Author: Zuchao Shen [aut, cre]
Maintainer: Zuchao Shen <zuchao.shen@gmail.com>
Diff between anomo versions 1.0.0 dated 2025-02-23 and 1.2.2 dated 2025-12-10
anomo-1.0.0/anomo/R/od.eq.2group.R |only anomo-1.0.0/anomo/R/power.eq.2group.R |only anomo-1.0.0/anomo/man/od.eq.2group.Rd |only anomo-1.0.0/anomo/man/power.eq.2group.Rd |only anomo-1.2.2/anomo/DESCRIPTION | 16 - anomo-1.2.2/anomo/MD5 | 32 +-- anomo-1.2.2/anomo/NAMESPACE | 5 anomo-1.2.2/anomo/R/mcci.R | 294 +++++++++++++++++++------------ anomo-1.2.2/anomo/R/od.1.eq.R |only anomo-1.2.2/anomo/R/plot.power.eq.R |only anomo-1.2.2/anomo/R/power.1.eq.R |only anomo-1.2.2/anomo/R/re.R | 8 anomo-1.2.2/anomo/build/vignette.rds |binary anomo-1.2.2/anomo/inst/doc/anomo.R | 46 +--- anomo-1.2.2/anomo/inst/doc/anomo.Rmd | 100 ++++------ anomo-1.2.2/anomo/inst/doc/anomo.html | 167 ++++++++--------- anomo-1.2.2/anomo/man/mcci.Rd | 80 +++++--- anomo-1.2.2/anomo/man/od.1.eq.Rd |only anomo-1.2.2/anomo/man/plot.power.eq.Rd |only anomo-1.2.2/anomo/man/power.1.eq.Rd |only anomo-1.2.2/anomo/man/re.Rd | 8 anomo-1.2.2/anomo/vignettes/anomo.Rmd | 100 ++++------ 22 files changed, 462 insertions(+), 394 deletions(-)
Title: Pull Spatial Layers from 'WDNR ArcGIS REST API'
Description: Functions for finding and pulling data from the
'Wisconsin Department of Natural Resources ArcGIS REST APIs'
<https://dnrmaps.wi.gov/arcgis/rest/services> and
<https://dnrmaps.wi.gov/arcgis2/rest/services>.
Author: Paul Frater [aut, cre] ,
Zac Driscoll [aut]
Maintainer: Paul Frater <paul.frater@wisconsin.gov>
Diff between wdnr.gis versions 0.1.6 dated 2025-10-13 and 0.1.7 dated 2025-12-10
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/wdnr.gis-package.R | 2 +- man/wdnr.gis-package.Rd | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-)
More information about spatialAtomizeR at CRAN
Permanent link
Title: Machine Coded Genetic Algorithms for Real-Valued Optimization
Problems
Description: Machine coded genetic algorithm (MCGA) is a fast tool for
real-valued optimization problems. It uses the byte
representation of variables rather than real-values. It
performs the classical crossover operations (uniform) on these
byte representations. Mutation operator is also similar to
classical mutation operator, which is to say, it changes a
randomly selected byte value of a chromosome by +1 or -1 with
probability 1/2. In MCGAs there is no need for
encoding-decoding process and the classical operators are
directly applicable on real-values. It is fast and can handle a
wide range of a search space with high precision. Using a
256-unary alphabet is the main disadvantage of this algorithm
but a moderate size population is convenient for many problems.
Package also includes multi_mcga function for multi objective
optimization problems. This function sorts the chromosomes
using their ranks calculated from the non-dominated sorting
algorithm.
Author: Mehmet Hakan Satman [aut, cre]
Maintainer: Mehmet Hakan Satman <mhsatman@istanbul.edu.tr>
Diff between mcga versions 3.0.7 dated 2023-11-27 and 3.0.9 dated 2025-12-10
DESCRIPTION | 14 +++++++++----- MD5 | 6 +++--- src/mcga.h | 2 +- src/multi_mcga.h | 2 +- 4 files changed, 14 insertions(+), 10 deletions(-)
Title: Parse Farm Credit Administration Call Report Data into Tidy Data
Frames
Description: Parses financial condition and performance data (Call Reports) for
institutions in the United States Farm Credit System. Contains functions for
downloading files from the Farm Credit Administration (FCA) Call Report
archive website and reading the files into tidy data frame format.
The archive website can be found at
<https://www.fca.gov/bank-oversight/call-report-data-for-download>.
Author: Michael Thomas [aut, cre],
Ivan Millanes [aut],
Ketchbrook Analytics [cph, fnd]
Maintainer: Michael Thomas <mthomas@ketchbrookanalytics.com>
Diff between fcall versions 0.1.5 dated 2025-11-19 and 0.1.6 dated 2025-12-10
DESCRIPTION | 6 +- MD5 | 10 +-- NEWS.md | 8 ++ R/download_data.R | 15 +++-- README.md | 152 ++++++++++++++++++++++++++------------------------- man/download_data.Rd | 7 +- 6 files changed, 111 insertions(+), 87 deletions(-)
Title: Network Scale-Up Models for Aggregated Relational Data
Description: Provides a variety of Network Scale-up Models for researchers to
analyze Aggregated Relational Data, through the use of Stan and 'glmmTMB'.
Also provides tools for model checking
In this version, the package implements models from
Laga, I., Bao, L., and Niu, X (2023) <doi:10.1080/01621459.2023.2165929>,
Zheng, T., Salganik, M. J., and Gelman, A. (2006) <doi:10.1198/016214505000001168>,
Killworth, P. D., Johnsen, E. C., McCarty, C., Shelley, G. A.,
and Bernard, H. R. (1998) <doi:10.1016/S0378-8733(96)00305-X>, and
Killworth, P. D., McCarty, C., Bernard, H. R., Shelley, G. A., and
Johnsen, E. C. (1998) <doi:10.1177/0193841X9802200205>.
Author: Ian Laga [aut, cre] ,
Owen G. Ward [aut],
Anna L. Smith [aut],
Benjamin Vogel [aut],
Jieyun Wang [aut],
Le Bao [aut],
Xiaoyue Niu [aut]
Maintainer: Ian Laga <ilaga25@gmail.com>
Diff between networkscaleup versions 0.1-2 dated 2024-02-25 and 0.2-1 dated 2025-12-10
networkscaleup-0.1-2/networkscaleup/man/networkscaleup-package.Rd |only networkscaleup-0.2-1/networkscaleup/DESCRIPTION | 41 networkscaleup-0.2-1/networkscaleup/MD5 | 192 ++- networkscaleup-0.2-1/networkscaleup/NAMESPACE | 14 networkscaleup-0.2-1/networkscaleup/R/aux_functions.R |only networkscaleup-0.2-1/networkscaleup/R/corr_perms.R |only networkscaleup-0.2-1/networkscaleup/R/correlatedStan.R | 255 ++--- networkscaleup-0.2-1/networkscaleup/R/cov_plots.R |only networkscaleup-0.2-1/networkscaleup/R/fit_ard.R |only networkscaleup-0.2-1/networkscaleup/R/killworth.R | 78 - networkscaleup-0.2-1/networkscaleup/R/make_ard.R |only networkscaleup-0.2-1/networkscaleup/R/networkscaleup-package.R | 3 networkscaleup-0.2-1/networkscaleup/R/overdispersed.R | 267 ++--- networkscaleup-0.2-1/networkscaleup/R/overdispersedStan.R | 135 +- networkscaleup-0.2-1/networkscaleup/R/plot_fitted.R |only networkscaleup-0.2-1/networkscaleup/R/rootogram.R |only networkscaleup-0.2-1/networkscaleup/R/scaling.R | 98 - networkscaleup-0.2-1/networkscaleup/R/surrogate.R |only networkscaleup-0.2-1/networkscaleup/README.md |only networkscaleup-0.2-1/networkscaleup/build/vignette.rds |binary networkscaleup-0.2-1/networkscaleup/inst/doc/ARD-Diagnostics.R |only networkscaleup-0.2-1/networkscaleup/inst/doc/ARD-Diagnostics.Rmd |only networkscaleup-0.2-1/networkscaleup/inst/doc/ARD-Diagnostics.html |only networkscaleup-0.2-1/networkscaleup/inst/doc/FittingNetworkScaleup.R | 91 - networkscaleup-0.2-1/networkscaleup/inst/doc/FittingNetworkScaleup.Rmd | 108 +- networkscaleup-0.2-1/networkscaleup/inst/doc/FittingNetworkScaleup.html | 505 +++++----- networkscaleup-0.2-1/networkscaleup/inst/inst |only networkscaleup-0.2-1/networkscaleup/inst/stan/Correlated_basic.stan | 100 - networkscaleup-0.2-1/networkscaleup/inst/stan/Correlated_x.stan | 106 +- networkscaleup-0.2-1/networkscaleup/inst/stan/Correlated_x_zglobal.stan | 114 +- networkscaleup-0.2-1/networkscaleup/inst/stan/Correlated_x_zsubpop.stan | 114 +- networkscaleup-0.2-1/networkscaleup/inst/stan/Correlated_x_zsubpop_zglobal.stan | 122 +- networkscaleup-0.2-1/networkscaleup/inst/stan/Correlated_zglobal.stan | 108 +- networkscaleup-0.2-1/networkscaleup/inst/stan/Correlated_zsubpop.stan | 108 +- networkscaleup-0.2-1/networkscaleup/inst/stan/Correlated_zsubpop_zglobal.stan | 116 +- networkscaleup-0.2-1/networkscaleup/inst/stan/Overdispersed_Stan.stan | 86 - networkscaleup-0.2-1/networkscaleup/inst/stan/Uncorrelated_basic.stan | 88 - networkscaleup-0.2-1/networkscaleup/inst/stan/Uncorrelated_x.stan | 96 - networkscaleup-0.2-1/networkscaleup/inst/stan/Uncorrelated_x_zglobal.stan | 104 +- networkscaleup-0.2-1/networkscaleup/inst/stan/Uncorrelated_x_zsubpop.stan | 106 +- networkscaleup-0.2-1/networkscaleup/inst/stan/Uncorrelated_x_zsubpop_zglobal.stan | 110 +- networkscaleup-0.2-1/networkscaleup/inst/stan/Uncorrelated_zglobal.stan | 98 - networkscaleup-0.2-1/networkscaleup/inst/stan/Uncorrelated_zsubpop.stan | 96 - networkscaleup-0.2-1/networkscaleup/inst/stan/Uncorrelated_zsubpop_zglobal.stan | 102 +- networkscaleup-0.2-1/networkscaleup/man/construct_pearson.Rd |only networkscaleup-0.2-1/networkscaleup/man/construct_rqr.Rd |only networkscaleup-0.2-1/networkscaleup/man/correlatedStan.Rd | 95 - networkscaleup-0.2-1/networkscaleup/man/cov_plots.Rd |only networkscaleup-0.2-1/networkscaleup/man/dispersion_metric.Rd |only networkscaleup-0.2-1/networkscaleup/man/figures |only networkscaleup-0.2-1/networkscaleup/man/fit_mle.Rd |only networkscaleup-0.2-1/networkscaleup/man/get_surrogate.Rd |only networkscaleup-0.2-1/networkscaleup/man/hang_rootogram_ard.Rd |only networkscaleup-0.2-1/networkscaleup/man/killworth.Rd | 32 networkscaleup-0.2-1/networkscaleup/man/log_mix_uniform.Rd |only networkscaleup-0.2-1/networkscaleup/man/make_ard.Rd |only networkscaleup-0.2-1/networkscaleup/man/make_ard_tidy.Rd |only networkscaleup-0.2-1/networkscaleup/man/networkscaleup.Rd |only networkscaleup-0.2-1/networkscaleup/man/overdispersed.Rd | 33 networkscaleup-0.2-1/networkscaleup/man/overdispersedStan.Rd | 37 networkscaleup-0.2-1/networkscaleup/man/plot_fitted.Rd |only networkscaleup-0.2-1/networkscaleup/man/residual_correlation.Rd |only networkscaleup-0.2-1/networkscaleup/man/residual_heatmap.Rd |only networkscaleup-0.2-1/networkscaleup/man/rqr_nbinom_logs.Rd |only networkscaleup-0.2-1/networkscaleup/man/rqr_pois_logs.Rd |only networkscaleup-0.2-1/networkscaleup/man/tw_group_corr_test.Rd |only networkscaleup-0.2-1/networkscaleup/src/Makevars.win | 5 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_basic.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_basic.h | 36 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_x.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_x.h | 40 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_x_zglobal.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_x_zglobal.h | 42 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_x_zsubpop.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_x_zsubpop.h | 42 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_x_zsubpop_zglobal.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_x_zsubpop_zglobal.h | 44 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_zglobal.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_zglobal.h | 40 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_zsubpop.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_zsubpop.h | 40 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_zsubpop_zglobal.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_zsubpop_zglobal.h | 42 networkscaleup-0.2-1/networkscaleup/src/stanExports_Overdispersed_Stan.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Overdispersed_Stan.h | 32 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_basic.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_basic.h | 30 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_x.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_x.h | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_x_zglobal.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_x_zglobal.h | 36 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_x_zsubpop.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_x_zsubpop.h | 36 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_x_zsubpop_zglobal.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_x_zsubpop_zglobal.h | 38 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_zglobal.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_zglobal.h | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_zsubpop.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_zsubpop.h | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_zsubpop_zglobal.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_zsubpop_zglobal.h | 36 networkscaleup-0.2-1/networkscaleup/vignettes/ARD-Diagnostics.Rmd |only networkscaleup-0.2-1/networkscaleup/vignettes/FittingNetworkScaleup.Rmd | 108 +- 103 files changed, 2607 insertions(+), 2478 deletions(-)
More information about networkscaleup at CRAN
Permanent link
Title: Likelihood Based Inference for ARIMA Modeling
Description: Estimating and analyzing auto regressive integrated moving average
(ARIMA) models. The primary function in this package is arima(), which fits
an ARIMA model to univariate time series data using a random restart
algorithm. This approach frequently leads to models that have model
likelihood greater than or equal to that of the likelihood obtained by
fitting the same model using the arima() function from the 'stats' package.
This package enables proper optimization of model likelihoods, which is a
necessary condition for performing likelihood ratio tests. This package
relies heavily on the source code of the arima() function of the 'stats'
package. For more information, please see Jesse Wheeler and Edward L.
Ionides (2025) <doi:10.1371/journal.pone.0333993>.
Author: Jesse Wheeler [aut, cre, cph],
Noel McAllister [aut],
Dhajanae Sylvertooth [aut],
Edward Ionides [ctb],
Brian Ripley [ctb] ,
R Core Team [cph]
Maintainer: Jesse Wheeler <jessewheeler@isu.edu>
Diff between arima2 versions 3.4.2 dated 2025-10-31 and 3.4.3 dated 2025-12-10
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 5 +++++ README.md | 4 ++-- man/figures/README-PlotARMAresults-1.png |binary man/figures/README-PlotARMAresults-2.png |binary 6 files changed, 17 insertions(+), 12 deletions(-)
Title: Data Validation Infrastructure
Description: Declare data validation rules and data quality indicators;
confront data with them and analyze or visualize the results.
The package supports rules that are per-field, in-record,
cross-record or cross-dataset. Rules can be automatically
analyzed for rule type and connectivity. Supports checks implied
by an SDMX DSD file as well. See also Van der Loo
and De Jonge (2018) <doi:10.1002/9781118897126>, Chapter 6
and the JSS paper (2021) <doi:10.18637/jss.v097.i10>.
Author: Mark van der Loo [cre, aut] ,
Edwin de Jonge [aut] ,
Paul Hsieh [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between validate versions 1.1.6 dated 2025-11-14 and 1.1.7 dated 2025-12-10
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS | 7 +++++++ R/compare.R | 4 ++-- inst/doc/JSS_3483.pdf |binary inst/doc/cookbook.Rmd | 4 +--- inst/doc/cookbook.html | 38 ++++++++++++++++++-------------------- inst/tinytest/test_validator.R | 6 +++--- man/cells.Rd | 2 +- man/compare.Rd | 2 +- vignettes/cookbook.Rmd | 4 +--- 11 files changed, 47 insertions(+), 46 deletions(-)
Title: Methods and Classes for the OMOP Common Data Model
Description: Provides definitions of core classes and methods used by analytic
pipelines that query the OMOP (Observational Medical Outcomes Partnership)
common data model.
Author: Marti Catala [aut, cre] ,
Edward Burn [aut] ,
Mike Du [ctb] ,
Yuchen Guo [ctb] ,
Adam Black [ctb] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between omopgenerics versions 1.3.4 dated 2025-12-01 and 1.3.5 dated 2025-12-10
DESCRIPTION | 6 MD5 | 24 NEWS.md | 6 R/classCdmTable.R | 14 R/classCodelist.R | 83 ++- R/classCodelistWithDetails.R | 39 - R/classConceptSetExpression.R | 42 - R/compute.R | 114 ---- R/logger.R | 124 +++++ inst/doc/logging.html | 44 - inst/doc/summarised_result.html | 886 ++++++++++++++++++------------------ tests/testthat/test-classCodelist.R | 3 tests/testthat/test-logger.R | 3 13 files changed, 729 insertions(+), 659 deletions(-)
Title: Double Machine Learning for Static Panel Models with Fixed
Effects
Description: The 'xtdml' package implements partially linear panel regression (PLPR) models with high-dimensional confounding variables and an exogenous treatment variable within the double machine learning framework. The package is used to estimate the structural parameter (treatment effect) in static panel data models with fixed effects using the approaches established in Clarke and Polselli (2025) <doi:10.1093/ectj/utaf011>. 'xtdml' is built on the object-oriented package 'DoubleML' (Bach et al., 2024) <doi:10.18637/jss.v108.i03> using the 'mlr3' ecosystem.
Author: Annalivia Polselli [aut, cre]
Maintainer: Annalivia Polselli <apolselli.econ@gmail.com>
Diff between xtdml versions 0.1.9 dated 2025-11-12 and 0.1.10 dated 2025-12-10
DESCRIPTION | 10 +- MD5 | 26 ++--- NAMESPACE | 3 R/dataset.R | 5 - R/helper.R | 2 R/xtdml_data.R | 36 ++++--- R/xtdml_main.R | 183 +++++++++++++++++++++----------------- R/xtdml_plr.R | 20 +--- R/zzz.R | 39 ++++---- man/make_plpr_data.Rd | 4 man/xtdml.Rd | 82 ++++++++--------- man/xtdml_data.Rd | 32 ++++-- man/xtdml_data_from_data_frame.Rd | 8 - man/xtdml_plr.Rd | 21 ++-- 14 files changed, 249 insertions(+), 222 deletions(-)
Title: Integrative Analysis of Several Related Data Matrices
Description: A generalization of principal component analysis for integrative
analysis. The method finds principal components that describe single matrices
or that are common to several matrices. The solutions are sparse. Rank of
solutions is automatically selected using cross validation. The method is
described in Kallus et al. (2019) <doi:10.48550/arXiv.1911.04927>.
Author: Jonatan Kallus [aut],
Felix Held [ctb, cre]
Maintainer: Felix Held <felix.held@gmail.com>
Diff between mmpca versions 2.0.3 dated 2022-11-15 and 2.0.4 dated 2025-12-10
DESCRIPTION | 17 ++++++++--------- MD5 | 15 ++++++++------- NEWS.md | 6 +++++- README.md | 2 +- src/Makevars.in | 2 -- src/compile_commands.json |only src/fdf.cpp | 6 +++--- src/fdf.h | 8 ++++++++ src/optim.cpp | 1 + 9 files changed, 34 insertions(+), 23 deletions(-)
Title: Multilevel Latent Time Series Models with 'R' and 'Stan'
Description: Fit multilevel manifest or latent time-series models, including popular Dynamic Structural Equation Models (DSEM).
The models can be set up and modified with user-friendly functions and are fit to the data using 'Stan' for Bayesian inference.
Path models and formulas for user-defined models can be easily created with functions using 'knitr'.
Asparouhov, Hamaker, & Muthen (2018) <doi:10.1080/10705511.2017.1406803>.
Author: Kenneth Koslowski [aut, cre, cph] ,
Fabian Muench [aut] ,
Tobias Koch [aut] ,
Jana Holtmann [aut]
Maintainer: Kenneth Koslowski <kenneth.koslowski@uni-leipzig.de>
Diff between mlts versions 2.0.0 dated 2025-12-08 and 2.0.1 dated 2025-12-10
DESCRIPTION | 6 MD5 | 12 NEWS.md | 7 R/mlts_paths.R | 1630 +++++++++++++++++++++++----------------------- R/mlts_sim.R | 978 +++++++++++++-------------- R/mlts_standardized_btw.R | 685 +++++++++---------- R/prepare_data.R | 466 ++++++------- 7 files changed, 1911 insertions(+), 1873 deletions(-)
Title: Easily Convert GDP Data
Description: Convert GDP time series data from one unit to
another. All common GDP units are included, i.e. current and constant
local currency units, US$ via market exchange rates and international
dollars via purchasing power parities.
Author: Johannes Koch [aut, cre]
Maintainer: Johannes Koch <jokoch@pik-potsdam.de>
Diff between GDPuc versions 1.6.0 dated 2025-11-19 and 1.6.1 dated 2025-12-10
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ R/transform_user_input.R | 2 +- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Vectors Representing Random Variables
Description: Random vectors, called rvecs. An rvec holds
multiple draws, but tries to behave like a standard
R vector, including working well in data frames.
Rvecs are useful for analysing
output from a simulation or a Bayesian analysis.
Author: John Bryant [aut, cre],
Bayesian Demography Limited [cph]
Maintainer: John Bryant <john@bayesiandemography.com>
Diff between rvec versions 0.0.8 dated 2025-07-12 and 1.0.0 dated 2025-12-10
rvec-0.0.8/rvec/man/new_rvec.Rd |only rvec-0.0.8/rvec/tests/testthat/_snaps/plot |only rvec-1.0.0/rvec/DESCRIPTION | 15 rvec-1.0.0/rvec/MD5 | 142 +++--- rvec-1.0.0/rvec/NAMESPACE | 19 rvec-1.0.0/rvec/NEWS.md | 25 + rvec-1.0.0/rvec/R/aaa-rvec-classes.R |only rvec-1.0.0/rvec/R/as_list_col.R | 25 - rvec-1.0.0/rvec/R/atomic_to_rvec.R | 26 - rvec-1.0.0/rvec/R/check-functions.R | 75 +++ rvec-1.0.0/rvec/R/collapse_to_rvec.R | 25 - rvec-1.0.0/rvec/R/compare.R | 2 rvec-1.0.0/rvec/R/constructors.R | 145 +++++- rvec-1.0.0/rvec/R/distributions.R | 312 ++++--------- rvec-1.0.0/rvec/R/draws.R | 419 +++++++++++------ rvec-1.0.0/rvec/R/format.R | 48 +- rvec-1.0.0/rvec/R/if_else_rvec.R | 4 rvec-1.0.0/rvec/R/map_rvec.R | 4 rvec-1.0.0/rvec/R/matrixOps.R | 109 +--- rvec-1.0.0/rvec/R/missing.R | 30 - rvec-1.0.0/rvec/R/pool_draws.R |only rvec-1.0.0/rvec/R/rvec-package.R | 34 - rvec-1.0.0/rvec/R/rvec_to_rvec.R | 20 rvec-1.0.0/rvec/R/util.R | 8 rvec-1.0.0/rvec/R/vec_math.R | 6 rvec-1.0.0/rvec/README.md | 11 rvec-1.0.0/rvec/build/vignette.rds |binary rvec-1.0.0/rvec/inst/doc/vig1_overview.R | 21 rvec-1.0.0/rvec/inst/doc/vig1_overview.Rmd | 78 ++- rvec-1.0.0/rvec/inst/doc/vig1_overview.html | 104 ++-- rvec-1.0.0/rvec/man/as_list_col.Rd | 13 rvec-1.0.0/rvec/man/collapse_to_rvec.Rd | 25 - rvec-1.0.0/rvec/man/dbeta_rvec.Rd | 14 rvec-1.0.0/rvec/man/dbinom_rvec.Rd | 26 - rvec-1.0.0/rvec/man/dcauchy_rvec.Rd | 17 rvec-1.0.0/rvec/man/dchisq_rvec.Rd | 14 rvec-1.0.0/rvec/man/dexp_rvec.Rd | 14 rvec-1.0.0/rvec/man/df_rvec.Rd | 11 rvec-1.0.0/rvec/man/dgamma_rvec.Rd | 16 rvec-1.0.0/rvec/man/dgeom_rvec.Rd | 23 rvec-1.0.0/rvec/man/dhyper_rvec.Rd | 22 rvec-1.0.0/rvec/man/dlnorm_rvec.Rd | 16 rvec-1.0.0/rvec/man/dmultinom_rvec.Rd | 23 rvec-1.0.0/rvec/man/dnbinom_rvec.Rd | 28 - rvec-1.0.0/rvec/man/dnorm_rvec.Rd | 16 rvec-1.0.0/rvec/man/dpois_rvec.Rd | 24 - rvec-1.0.0/rvec/man/draws_all.Rd | 9 rvec-1.0.0/rvec/man/draws_ci.Rd | 11 rvec-1.0.0/rvec/man/draws_fun.Rd | 7 rvec-1.0.0/rvec/man/draws_median.Rd | 14 rvec-1.0.0/rvec/man/draws_min.Rd | 9 rvec-1.0.0/rvec/man/draws_quantile.Rd | 13 rvec-1.0.0/rvec/man/draws_sd.Rd |only rvec-1.0.0/rvec/man/dt_rvec.Rd | 14 rvec-1.0.0/rvec/man/dunif_rvec.Rd | 14 rvec-1.0.0/rvec/man/dweibull_rvec.Rd | 14 rvec-1.0.0/rvec/man/figures |only rvec-1.0.0/rvec/man/if_else_rvec.Rd | 4 rvec-1.0.0/rvec/man/map_rvec.Rd | 4 rvec-1.0.0/rvec/man/missing.Rd | 30 - rvec-1.0.0/rvec/man/new_rvec_blank.Rd |only rvec-1.0.0/rvec/man/new_rvec_deprecated.Rd |only rvec-1.0.0/rvec/man/pool_draws.Rd |only rvec-1.0.0/rvec/man/rvec-matrix-mult.Rd |only rvec-1.0.0/rvec/man/rvec-package.Rd | 25 - rvec-1.0.0/rvec/tests/testthat/test-check-functions.R | 48 ++ rvec-1.0.0/rvec/tests/testthat/test-constructors.R | 423 ++++++++++-------- rvec-1.0.0/rvec/tests/testthat/test-draws.R | 145 ++++++ rvec-1.0.0/rvec/tests/testthat/test-format.R | 2 rvec-1.0.0/rvec/tests/testthat/test-matrixOps.R | 130 +++++ rvec-1.0.0/rvec/tests/testthat/test-pool_draws.R |only rvec-1.0.0/rvec/tests/testthat/test-util.R | 8 rvec-1.0.0/rvec/vignettes/vig1_overview.Rmd | 78 ++- 73 files changed, 1824 insertions(+), 1187 deletions(-)
Title: J&J Innovative Medicine ADaM Test Data
Description: A set of Analysis Data Model (ADaM) datasets constructed by
modifying the ADaM datasets in the 'pharmaverseadam' package to meet J&J Innovative Medicine's
standard data structure for Clinical and Statistical Programming.
Author: David Munoz Tord [aut, cre],
Nicholas Masel [aut],
Joe Kovach [aut],
Mahesh Divakaran [ctb],
J&J Innovative Medicine [cph, fnd]
Maintainer: David Munoz Tord <david.munoztord@mailbox.org>
Diff between pharmaverseadamjnj versions 0.0.1 dated 2025-07-15 and 0.0.2 dated 2025-12-10
pharmaverseadamjnj-0.0.1/pharmaverseadamjnj/R/adaefmq.R |only pharmaverseadamjnj-0.0.1/pharmaverseadamjnj/data/adaefmq.rda |only pharmaverseadamjnj-0.0.1/pharmaverseadamjnj/man/adaefmq.Rd |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/DESCRIPTION | 10 - pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/MD5 | 73 +++++----- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/NEWS.md | 31 +--- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adae.R | 19 +- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adaeocmq.R |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adagocmq.R |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adcm.R | 7 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adeg.R | 7 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adex.R | 16 +- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adexsum.R | 4 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adlb.R | 19 +- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adpc.R |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adsl.R | 18 +- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adttesaf.R | 4 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/advs.R | 4 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/README.md | 28 +++ pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adae.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adaeocmq.rda |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adagocmq.rda |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adcm.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adeg.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adex.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adexsum.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adlb.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adpc.rda |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adsl.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adttesaf.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/advs.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/inst |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adae.Rd | 17 +- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adaeocmq.Rd |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adagocmq.Rd |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adcm.Rd | 5 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adeg.Rd | 5 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adex.Rd | 14 - pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adexsum.Rd | 2 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adlb.Rd | 17 +- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adpc.Rd |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adsl.Rd | 16 +- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adttesaf.Rd | 2 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/advs.Rd | 2 44 files changed, 179 insertions(+), 141 deletions(-)
More information about pharmaverseadamjnj at CRAN
Permanent link
Title: Download Radar Data for Biological Research
Description: Load polar volume and vertical profile data for
aeroecological research directly into R. With 'getRad' you can access
data from several sources in Europe and the US and standardize it to
facilitate further exploration in tools such as 'bioRad'.
Author: Bart Kranstauber [aut, cre] ,
Pieter Huybrechts [aut] ),
Peter Desmet [aut] ),
Cecilia Nilsson [ctb] ,
Alexander Tedeschi [ctb] ,
Hidde Leijnse [ctb] ,
Bart Hoekstra [ctb] ,
University of Amsterdam [cph] ,
Biodiversa+ [fnd]
Maintainer: Bart Kranstauber <b.kranstauber@uva.nl>
Diff between getRad versions 0.2.3 dated 2025-10-14 and 0.2.4 dated 2025-12-10
DESCRIPTION | 6 +- MD5 | 70 +++++++++++++++--------------- NEWS.md | 8 +++ R/get_pvol.R | 21 ++++----- R/get_pvol_de.R | 9 ++- R/get_pvol_dk.R | 3 - R/get_pvol_ee.R | 8 +-- R/get_pvol_nl.R | 71 +++++++++++++++++++++---------- R/get_pvol_se.R | 7 +-- R/get_pvol_us.R | 8 +-- R/get_vpts.R | 32 +++++-------- R/get_vpts_aloft.R | 11 ++-- R/get_vpts_coverage.R | 2 R/get_vpts_coverage_rmi.R | 8 +-- R/get_weather_radars.R | 33 ++++++++------ R/secrets.R | 16 ++---- R/utils.R | 43 +++++++++++------- R/utils_pvol.R | 2 README.md | 1 inst/doc/supported_sources.R | 2 inst/doc/supported_sources.Rmd | 2 inst/doc/supported_sources.html | 4 - man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/figures/README-example-3.png |binary man/figures/README-example-4.png |binary man/figures/README-vpts-1.png |binary man/get_weather_radars.Rd | 4 - tests/testthat/test-get_pvol.R | 6 +- tests/testthat/test-get_pvol_dk.R | 5 -- tests/testthat/test-get_pvol_nl.R | 57 +++++++++++++++++++----- tests/testthat/test-get_pvol_ro.R | 7 +-- tests/testthat/test-get_vpts_aloft.R | 29 +++++------- tests/testthat/test-get_weather_radars.R | 4 - tests/testthat/test-secrets.R | 8 +-- vignettes/supported_sources.Rmd | 2 36 files changed, 276 insertions(+), 213 deletions(-)
Title: Fit Multivariate Diversity-Interactions Models with Repeated
Measures
Description: An add-on package to 'DImodels' for the fitting of biodiversity and ecosystem function relationship study data with multiple ecosystem function responses and/or time points. This package uses the multivariate and repeated measures Diversity-Interactions (DI) methods developed by Kirwan et al. (2009) <doi:10.1890/08-1684.1>, Finn et al. (2013) <doi:10.1111/1365-2664.12041>, and Dooley et al. (2015) <doi:10.1111/ele.12504>.
Author: Laura Byrne [aut, cre] ,
Rishabh Vishwakarma [aut],
Rafael de Andrade Moral [aut],
Caroline Brophy [aut]
Maintainer: Laura Byrne <Laura.Byrne.Work@outlook.com>
Diff between DImodelsMulti versions 1.2.0 dated 2025-08-21 and 1.2.1 dated 2025-12-10
DESCRIPTION | 15 +- MD5 | 39 +++-- NAMESPACE | 1 R/DImodelsMulti_HelpFile.R | 6 R/DImulti_fit.R | 20 ++ R/DImulti_predict.R | 28 +++- R/DImulti_runApp.R |only README.md | 52 +++---- build/vignette.rds |binary inst/doc/DImulti_commonErrors.html | 5 inst/doc/DImulti_onTheta.html | 5 inst/doc/DImulti_prediction.html | 5 inst/doc/DImulti_workflow.Rmd | 3 inst/doc/DImulti_workflow.html | 12 + inst/shiny |only man/Belgium.Rd | 164 ++++++++++++------------ man/Belgium_MV.Rd | 252 ++++++++++++++++++------------------- man/Belgium_RM.Rd | 232 +++++++++++++++++----------------- man/DImodelsMulti.Rd | 6 man/DImulti.Rd | 6 man/DImultiApp.Rd |only vignettes/DImulti_workflow.Rmd | 3 22 files changed, 454 insertions(+), 400 deletions(-)
Title: Covariate-Based Covariance Functions for Nonstationary Spatial
Modeling
Description: Estimation, prediction, and simulation of nonstationary Gaussian process with modular covariate-based covariance functions.
Sources of nonstationarity, such as spatial mean, variance, geometric anisotropy, smoothness, and nugget, can be considered based on spatial characteristics.
An induced compact-supported nonstationary covariance function is provided, enabling fast and memory-efficient computations when handling densely sampled domains.
Author: Federico Blasi [aut, cre] ,
Reinhard Furrer [ctb]
Maintainer: Federico Blasi <federicoblasi@gmail.com>
Diff between cocons versions 0.1.4 dated 2024-12-12 and 0.1.5 dated 2025-12-10
DESCRIPTION | 15 - MD5 | 45 ++--- NEWS.md | 7 R/RcppExports.R | 10 + R/checkFunctions.R | 143 ++++++++++++++++- R/cocons.R | 21 ++ R/getFunctions.R | 103 ++++++++++-- R/methods.R | 62 +++++++ R/neg2loglikelihood.R | 10 - R/optim.R | 262 +++++++++++++++++++++++++++++--- R/profile.R | 5 inst/doc/cocons.pdf |binary man/GetNeg2loglikelihood.Rd | 2 man/GetNeg2loglikelihoodProfile.Rd | 2 man/GetNeg2loglikelihoodREML.Rd | 2 man/GetNeg2loglikelihoodTaper.Rd | 2 man/GetNeg2loglikelihoodTaperProfile.Rd | 2 man/coco.Rd | 5 man/cocoOptim.Rd | 15 - man/getBoundariesV4.Rd |only man/show-methods.Rd |only man/sumsmoothlone.Rd |only src/RcppExports.cpp | 14 + src/cocons_full.cpp | 96 +++++++++-- src/cocons_taper.cpp | 34 +++- 25 files changed, 743 insertions(+), 114 deletions(-)
Title: Text Mining Package
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut] ,
Kurt Hornik [aut, cre] ,
Artifex Software, Inc. [ctb, cph]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between tm versions 0.7-16 dated 2025-02-19 and 0.7-17 dated 2025-12-10
DESCRIPTION | 12 +++++------ MD5 | 50 +++++++++++++++++++++++------------------------ build/partial.rdb |binary build/vignette.rds |binary data/acq.rda |binary data/crude.rda |binary inst/doc/extensions.pdf |binary inst/doc/tm.pdf |binary man/Corpus.Rd | 2 - man/PCorpus.Rd | 4 +-- man/PlainTextDocument.Rd | 4 +-- man/SimpleCorpus.Rd | 2 - man/TextDocument.Rd | 2 - man/XMLSource.Rd | 2 - man/XMLTextDocument.Rd | 4 +-- man/foreign.Rd | 2 - man/matrix.Rd | 6 ++--- man/meta.Rd | 2 - man/plot.Rd | 3 +- man/readDOC.Rd | 2 - man/readPDF.Rd | 4 +-- man/readXML.Rd | 2 - man/removeWords.Rd | 2 - man/stemDocument.Rd | 1 man/termFreq.Rd | 2 - man/tokenizer.Rd | 8 +++---- 26 files changed, 59 insertions(+), 57 deletions(-)
Title: Store and Retrieve Data.frames in a Git Repository
Description: The git2rdata package is an R package for writing and reading
dataframes as plain text files. A metadata file stores important
information. 1) Storing metadata allows to maintain the classes of
variables. By default, git2rdata optimizes the data for file storage.
The optimization is most effective on data containing factors. The
optimization makes the data less human readable. The user can turn
this off when they prefer a human readable format over smaller files.
Details on the implementation are available in vignette("plain_text",
package = "git2rdata"). 2) Storing metadata also allows smaller row
based diffs between two consecutive commits. This is a useful feature
when storing data as plain text files under version control. Details
on this part of the implementation are available in
vignette("version_control", package = "git2rdata"). Although we
envisioned git2rdata with a git workflow in mind, you can use it in
combination with other version control systems like subversion [...truncated...]
Author: Thierry Onkelinx [aut, cre] ),
Floris Vanderhaeghe [ctb] ),
Peter Desmet [ctb] ),
Els Lommelen [ctb] ),
Research Institute for Nature and Forest [cph, fnd]
Maintainer: Thierry Onkelinx <thierry.onkelinx@inbo.be>
Diff between git2rdata versions 0.5.0 dated 2025-01-24 and 0.5.1 dated 2025-12-10
DESCRIPTION | 32 - MD5 | 133 +++---- NAMESPACE | 5 NEWS.md | 7 R/clean_data_path.R | 3 R/data_package.R | 47 +- R/datahash.R | 54 ++ R/is_git2rdata.R | 52 ++ R/is_git2rmeta.R | 57 ++- R/list_data.R | 46 +- R/meta.R | 350 ++++++++++++------ R/prune.R | 141 +++++-- R/read_vc.R | 146 +++---- R/recent_commit.R | 60 +-- R/reinstate.R |only R/relabel.R | 17 R/rename_variable.R | 24 - R/update_metadata.R | 54 ++ R/upgrade_data.R | 77 +++- R/verify_vc.R | 5 R/write_vc.R | 188 +++++++--- README.md | 62 ++- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 6 inst/Dockerfile |only inst/Rprofile.site |only inst/doc/efficiency.R | 25 - inst/doc/efficiency.Rmd | 25 - inst/doc/efficiency.html | 83 ++-- inst/doc/metadata.R | 9 inst/doc/metadata.Rmd | 9 inst/doc/metadata.html | 59 +-- inst/doc/plain_text.html | 75 ++-- inst/doc/split_by.html | 9 inst/doc/version_control.html | 85 ++-- inst/doc/workflow.R | 36 - inst/doc/workflow.Rmd | 42 +- inst/doc/workflow.html | 186 +++++---- man/git2rdata-package.Rd | 2 man/is_git2rdata.Rd | 4 man/is_git2rmeta.Rd | 4 man/list_data.Rd | 9 man/prune_meta.Rd | 9 man/read_vc.Rd | 13 man/recent_commit.Rd | 14 man/rm_data.Rd | 9 man/write_vc.Rd | 13 tests/testthat/setup_test_data.R | 27 + tests/testthat/test_a_basics.R | 372 +++++++++++++++++-- tests/testthat/test_b_is_git2rmeta.R | 157 +++++--- tests/testthat/test_b_prune.R | 56 ++ tests/testthat/test_b_special.R | 66 ++- tests/testthat/test_b_update.R | 18 tests/testthat/test_b_verify_vc.R | 9 tests/testthat/test_c_git.R | 561 +++++++++++++++++------------- tests/testthat/test_d_description.R | 52 +- tests/testthat/test_d_recent_commit.R | 167 ++++---- tests/testthat/test_d_relabel.R | 48 +- tests/testthat/test_e_data_package.R | 56 ++ tests/testthat/test_e_empty_label.R | 5 tests/testthat/test_e_non_ascii.R | 21 - tests/testthat/test_e_upgrade.R | 21 - tests/testthat/test_e_validate_metadata.R | 30 + tests/testthat/test_f_split_by.R | 55 ++ tests/testthat/test_g_rename_variable.R | 52 ++ vignettes/efficiency.Rmd | 25 - vignettes/metadata.Rmd | 9 vignettes/workflow.Rmd | 42 +- 69 files changed, 2673 insertions(+), 1462 deletions(-)
Title: Parse 'Tableau' Workbooks into Functional Data
Description: High-performance parsing of 'Tableau' workbook files into
tidy data frames and dependency graphs for other visualization tools
like R 'Shiny' or 'Power BI' replication.
Author: George Arthur [aut, cre]
Maintainer: George Arthur <prigasgenthian48@gmail.com>
Diff between twbparser versions 0.2.3 dated 2025-09-30 and 0.3.1 dated 2025-12-10
twbparser-0.2.3/twbparser/inst/extdata/test-for_zip.twbx |only twbparser-0.3.1/twbparser/DESCRIPTION | 6 twbparser-0.3.1/twbparser/MD5 | 52 - twbparser-0.3.1/twbparser/NAMESPACE | 14 twbparser-0.3.1/twbparser/NEWS.md | 70 - twbparser-0.3.1/twbparser/R/active-bindings.R |only twbparser-0.3.1/twbparser/R/calculated_fields.R | 35 twbparser-0.3.1/twbparser/R/datasources.R | 76 - twbparser-0.3.1/twbparser/R/insights.R |only twbparser-0.3.1/twbparser/R/published.R | 68 - twbparser-0.3.1/twbparser/R/twb_parser.R | 493 +++++----- twbparser-0.3.1/twbparser/R/utils.R | 20 twbparser-0.3.1/twbparser/README.md | 107 +- twbparser-0.3.1/twbparser/inst/doc/twbparser-intro.R | 87 - twbparser-0.3.1/twbparser/inst/doc/twbparser-intro.Rmd | 111 +- twbparser-0.3.1/twbparser/inst/doc/twbparser-intro.html | 222 ++-- twbparser-0.3.1/twbparser/inst/extdata/test_for_zip.twbx |only twbparser-0.3.1/twbparser/man/TwbParser.Rd | 2 twbparser-0.3.1/twbparser/man/extract_calculated_fields.Rd | 15 twbparser-0.3.1/twbparser/man/extract_datasource_details.Rd | 29 twbparser-0.3.1/twbparser/man/extract_named_connections.Rd | 14 twbparser-0.3.1/twbparser/man/twb_charts.Rd |only twbparser-0.3.1/twbparser/man/twb_colors.Rd |only twbparser-0.3.1/twbparser/man/twb_dashboard_filters.Rd |only twbparser-0.3.1/twbparser/man/twb_dashboard_summary.Rd |only twbparser-0.3.1/twbparser/man/twb_dashboards.Rd |only twbparser-0.3.1/twbparser/man/twb_page_composition.Rd |only twbparser-0.3.1/twbparser/man/twb_pages.Rd |only twbparser-0.3.1/twbparser/man/twb_pages_summary.Rd |only twbparser-0.3.1/twbparser/tests/testthat/test-active-bindings.R |only twbparser-0.3.1/twbparser/tests/testthat/test-calculated-fields.R |only twbparser-0.3.1/twbparser/tests/testthat/test-insights.R |only twbparser-0.3.1/twbparser/tests/testthat/test-overview.R |only twbparser-0.3.1/twbparser/tests/testthat/test-utils-extract_named_connections.R | 12 twbparser-0.3.1/twbparser/vignettes/twbparser-intro.Rmd | 111 +- 35 files changed, 863 insertions(+), 681 deletions(-)
Title: Tropical Cyclone (Hurricane, Typhoon) Spatial Hazard Modelling
Description: Methods for generating modelled parametric Tropical Cyclone (TC) spatial hazard fields and time series output at point locations from TC tracks. R's compatibility to simply use fast 'cpp' code via the 'Rcpp' package and the wide range spatial analysis tools via the 'terra' package makes it an attractive open source environment to study 'TCs'. This package estimates TC vortex wind and pressure fields using parametric equations originally coded up in 'python' by 'TCRM' <https://github.com/GeoscienceAustralia/tcrm> and then coded up in 'Cuda' 'cpp' by 'TCwindgen' <https://github.com/CyprienBosserelle/TCwindgen>.
Author: Julian O'Grady [aut, cre]
Maintainer: Julian O'Grady <julian.ogrady@csiro.au>
Diff between TCHazaRds versions 1.1.4 dated 2025-08-24 and 1.1.5 dated 2025-12-10
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/WindHazaRds.R | 32 ++++++++++++++++++++++++++------ README.md | 10 ++++++---- inst/doc/Introduction_to_TCHazaRds.R | 3 ++- inst/doc/Introduction_to_TCHazaRds.Rmd | 5 +++-- inst/doc/Introduction_to_TCHazaRds.html | 32 +++++++++++++++++++------------- man/update_Track.Rd | 3 ++- src/TCHazaRds.cpp | 16 ++++++++-------- vignettes/Introduction_to_TCHazaRds.Rmd | 5 +++-- 10 files changed, 82 insertions(+), 50 deletions(-)
Title: Posetic Data Analysis
Description: Build and manipulate partially ordered sets (posets), to perform some data analysis
on them and to implement multi-criteria decision making procedures. Several efficient ways for generating linear extensions are implemented, together with functions for building mutual ranking probabilities, incomparability, dominance and separation scores (Fattore, M., De Capitani, L., Avellone, A., Suardi, A. (2024). A fuzzy posetic toolbox for multi-criteria evaluation on ordinal data systems. ANNALS OF OPERATIONS RESEARCH <doi:10.1007/s10479-024-06352-3>).
Author: Alessandro Avellone [aut, cre],
Lucio De Capitani [aut],
Marco Fattore [aut]
Maintainer: Alessandro Avellone <alessandro.avellone@unimib.it>
Diff between poseticDataAnalysis versions 0.1.1 dated 2025-10-29 and 1.0.0 dated 2025-12-10
DESCRIPTION | 6 MD5 | 8 - src/lexicographicProductPOSet.cpp | 175 ++++++++++++++-------------- src/posetWrapper.cpp | 41 +++--- src/rwrapper.cpp | 234 +++++++++++++++++++------------------- 5 files changed, 232 insertions(+), 232 deletions(-)
More information about poseticDataAnalysis at CRAN
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Title: Toolkit for Analysis of Genomic Data
Description: A toolkit for analysis of genomic data. The 'misha' package
implements an efficient data structure for storing genomic data, and
provides a set of functions for data extraction, manipulation and
analysis. Some of the 2D genome algorithms were described in Yaffe and Tanay
(2011) <doi:10.1038/ng.947>.
Author: Misha Hoichman [aut],
Aviezer Lifshitz [aut, cre],
Eitan Yaffe [aut],
Amos Tanay [aut],
Weizmann Institute of Science [cph]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Diff between misha versions 4.3.12 dated 2025-08-31 and 5.3.1 dated 2025-12-10
misha-4.3.12/misha/R/compute.R |only misha-4.3.12/misha/R/db.R |only misha-4.3.12/misha/R/intervals.R |only misha-4.3.12/misha/R/track.R |only misha-4.3.12/misha/tests/testthat/test-gextract.R |only misha-4.3.12/misha/tests/testthat/test-gintervals.R |only misha-4.3.12/misha/tests/testthat/test-gtrack.import.R |only misha-5.3.1/misha/DESCRIPTION | 13 misha-5.3.1/misha/MD5 | 559 ++- misha-5.3.1/misha/NAMESPACE | 25 misha-5.3.1/misha/NEWS.md | 111 misha-5.3.1/misha/R/compute-analysis.R |only misha-5.3.1/misha/R/compute-bins.R |only misha-5.3.1/misha/R/compute-core.R |only misha-5.3.1/misha/R/compute-distribution.R |only misha-5.3.1/misha/R/compute-partition.R |only misha-5.3.1/misha/R/compute-sequence.R |only misha-5.3.1/misha/R/compute-utils.R |only misha-5.3.1/misha/R/db-attrs.R |only misha-5.3.1/misha/R/db-cache.R |only misha-5.3.1/misha/R/db-core.R |only misha-5.3.1/misha/R/db-create.R |only misha-5.3.1/misha/R/db-dir.R |only misha-5.3.1/misha/R/db-index.R |only misha-5.3.1/misha/R/db-management.R |only misha-5.3.1/misha/R/db-root.R |only misha-5.3.1/misha/R/intervals-annotation.R |only misha-5.3.1/misha/R/intervals-bigset.R |only misha-5.3.1/misha/R/intervals-core.R |only misha-5.3.1/misha/R/intervals-iterator.R |only misha-5.3.1/misha/R/intervals-liftover.R |only misha-5.3.1/misha/R/intervals-load-save.R |only misha-5.3.1/misha/R/intervals-management.R |only misha-5.3.1/misha/R/intervals-operations.R |only misha-5.3.1/misha/R/intervals-tracks.R |only misha-5.3.1/misha/R/intervals-utils.R |only misha-5.3.1/misha/R/misha-package.R | 34 misha-5.3.1/misha/R/neighbors.R |only misha-5.3.1/misha/R/pssm_utils.R |only misha-5.3.1/misha/R/sequence.R | 486 +++ misha-5.3.1/misha/R/track-2d.R | 20 misha-5.3.1/misha/R/track-array.R | 17 misha-5.3.1/misha/R/track-attr.R | 5 misha-5.3.1/misha/R/track-convert.R |only misha-5.3.1/misha/R/track-core.R |only misha-5.3.1/misha/R/track-create.R |only misha-5.3.1/misha/R/track-import.R |only misha-5.3.1/misha/R/track-liftover.R |only misha-5.3.1/misha/R/track-management.R |only misha-5.3.1/misha/R/track-modify.R |only misha-5.3.1/misha/R/track-var.R | 14 misha-5.3.1/misha/R/utils-memory.R |only misha-5.3.1/misha/R/utils.R | 21 misha-5.3.1/misha/R/vtrack.R | 749 ++++- misha-5.3.1/misha/R/zzz.R | 25 misha-5.3.1/misha/build/vignette.rds |binary misha-5.3.1/misha/inst/WORDLIST | 43 misha-5.3.1/misha/inst/doc/Database-Formats.R |only misha-5.3.1/misha/inst/doc/Database-Formats.Rmd |only misha-5.3.1/misha/inst/doc/Database-Formats.html |only misha-5.3.1/misha/inst/doc/Manual.R | 31 misha-5.3.1/misha/inst/doc/Manual.Rmd | 245 + misha-5.3.1/misha/inst/doc/Manual.html | 356 ++ misha-5.3.1/misha/man/directional-neighbors.Rd |only misha-5.3.1/misha/man/dot-misha.Rd | 2 misha-5.3.1/misha/man/gbins.quantiles.Rd | 2 misha-5.3.1/misha/man/gbins.summary.Rd | 2 misha-5.3.1/misha/man/gcis_decay.Rd | 2 misha-5.3.1/misha/man/gcompute_strands_autocorr.Rd | 2 misha-5.3.1/misha/man/gdb.convert_to_indexed.Rd |only misha-5.3.1/misha/man/gdb.create.Rd | 63 misha-5.3.1/misha/man/gdb.create_genome.Rd | 2 misha-5.3.1/misha/man/gdb.get_readonly_attrs.Rd | 2 misha-5.3.1/misha/man/gdb.info.Rd |only misha-5.3.1/misha/man/gdb.init.Rd | 13 misha-5.3.1/misha/man/gdb.mark_cache_dirty.Rd |only misha-5.3.1/misha/man/gdb.reload.Rd | 2 misha-5.3.1/misha/man/gdb.set_readonly_attrs.Rd | 2 misha-5.3.1/misha/man/gdir.cd.Rd | 2 misha-5.3.1/misha/man/gdir.create.Rd | 2 misha-5.3.1/misha/man/gdir.cwd.Rd | 2 misha-5.3.1/misha/man/gdir.rm.Rd | 2 misha-5.3.1/misha/man/gdist.Rd | 2 misha-5.3.1/misha/man/gextract.Rd | 2 misha-5.3.1/misha/man/gintervals.2d.Rd | 2 misha-5.3.1/misha/man/gintervals.2d.all.Rd | 2 misha-5.3.1/misha/man/gintervals.2d.band_intersect.Rd | 2 misha-5.3.1/misha/man/gintervals.2d.convert_to_indexed.Rd |only misha-5.3.1/misha/man/gintervals.Rd | 2 misha-5.3.1/misha/man/gintervals.all.Rd | 2 misha-5.3.1/misha/man/gintervals.annotate.Rd | 6 misha-5.3.1/misha/man/gintervals.as_chain.Rd |only misha-5.3.1/misha/man/gintervals.canonic.Rd | 2 misha-5.3.1/misha/man/gintervals.chrom_sizes.Rd | 2 misha-5.3.1/misha/man/gintervals.convert_to_indexed.Rd |only misha-5.3.1/misha/man/gintervals.coverage_fraction.Rd |only misha-5.3.1/misha/man/gintervals.covered_bp.Rd |only misha-5.3.1/misha/man/gintervals.diff.Rd | 2 misha-5.3.1/misha/man/gintervals.exists.Rd | 2 misha-5.3.1/misha/man/gintervals.force_range.Rd | 2 misha-5.3.1/misha/man/gintervals.import_genes.Rd | 2 misha-5.3.1/misha/man/gintervals.intersect.Rd | 2 misha-5.3.1/misha/man/gintervals.is.bigset.Rd | 2 misha-5.3.1/misha/man/gintervals.liftover.Rd | 62 misha-5.3.1/misha/man/gintervals.load.Rd | 2 misha-5.3.1/misha/man/gintervals.load_chain.Rd | 55 misha-5.3.1/misha/man/gintervals.ls.Rd | 2 misha-5.3.1/misha/man/gintervals.mapply.Rd | 2 misha-5.3.1/misha/man/gintervals.mark_overlaps.Rd |only misha-5.3.1/misha/man/gintervals.neighbors.Rd | 97 misha-5.3.1/misha/man/gintervals.normalize.Rd | 2 misha-5.3.1/misha/man/gintervals.path.Rd |only misha-5.3.1/misha/man/gintervals.quantiles.Rd | 2 misha-5.3.1/misha/man/gintervals.random.Rd |only misha-5.3.1/misha/man/gintervals.rbind.Rd | 2 misha-5.3.1/misha/man/gintervals.rm.Rd | 2 misha-5.3.1/misha/man/gintervals.save.Rd | 2 misha-5.3.1/misha/man/gintervals.summary.Rd | 2 misha-5.3.1/misha/man/gintervals.union.Rd | 2 misha-5.3.1/misha/man/gintervals.update.Rd | 2 misha-5.3.1/misha/man/giterator.cartesian_grid.Rd | 2 misha-5.3.1/misha/man/giterator.intervals.Rd | 2 misha-5.3.1/misha/man/glookup.Rd | 2 misha-5.3.1/misha/man/gpartition.Rd | 2 misha-5.3.1/misha/man/gquantiles.Rd | 2 misha-5.3.1/misha/man/gsample.Rd | 2 misha-5.3.1/misha/man/gscreen.Rd | 2 misha-5.3.1/misha/man/gsegment.Rd | 2 misha-5.3.1/misha/man/gseq.comp.Rd |only misha-5.3.1/misha/man/gseq.extract.Rd | 2 misha-5.3.1/misha/man/gseq.kmer.Rd |only misha-5.3.1/misha/man/gseq.pwm.Rd |only misha-5.3.1/misha/man/gseq.rev.Rd |only misha-5.3.1/misha/man/gseq.revcomp.Rd |only misha-5.3.1/misha/man/gsummary.Rd | 2 misha-5.3.1/misha/man/gtrack.convert.Rd | 2 misha-5.3.1/misha/man/gtrack.convert_to_indexed.Rd |only misha-5.3.1/misha/man/gtrack.create.Rd | 2 misha-5.3.1/misha/man/gtrack.create_dense.Rd | 2 misha-5.3.1/misha/man/gtrack.create_dirs.Rd | 2 misha-5.3.1/misha/man/gtrack.create_pwm_energy.Rd | 2 misha-5.3.1/misha/man/gtrack.create_sparse.Rd | 2 misha-5.3.1/misha/man/gtrack.exists.Rd | 2 misha-5.3.1/misha/man/gtrack.import.Rd | 2 misha-5.3.1/misha/man/gtrack.import_mappedseq.Rd | 2 misha-5.3.1/misha/man/gtrack.import_set.Rd | 2 misha-5.3.1/misha/man/gtrack.info.Rd | 6 misha-5.3.1/misha/man/gtrack.liftover.Rd | 53 misha-5.3.1/misha/man/gtrack.lookup.Rd | 2 misha-5.3.1/misha/man/gtrack.ls.Rd | 2 misha-5.3.1/misha/man/gtrack.modify.Rd | 2 misha-5.3.1/misha/man/gtrack.path.Rd |only misha-5.3.1/misha/man/gtrack.rm.Rd | 2 misha-5.3.1/misha/man/gtrack.smooth.Rd | 2 misha-5.3.1/misha/man/gvtrack.create.Rd | 399 +- misha-5.3.1/misha/man/gvtrack.filter.Rd |only misha-5.3.1/misha/man/gwilcox.Rd | 2 misha-5.3.1/misha/man/misha-package.Rd | 32 misha-5.3.1/misha/src/AggregationHelpers.h |only misha-5.3.1/misha/src/BinsManager.h | 11 misha-5.3.1/misha/src/BufferedFile.h | 113 misha-5.3.1/misha/src/CRC64.h |only misha-5.3.1/misha/src/Chain2Interval.cpp | 137 misha-5.3.1/misha/src/ChainIntervalConverter.cpp |only misha-5.3.1/misha/src/ChainIntervalConverter.h |only misha-5.3.1/misha/src/ConfigurationManager.cpp |only misha-5.3.1/misha/src/ConfigurationManager.h |only misha-5.3.1/misha/src/DataFrameUtils.cpp |only misha-5.3.1/misha/src/DataFrameUtils.h |only misha-5.3.1/misha/src/DnaPSSM.cpp | 190 + misha-5.3.1/misha/src/DnaPSSM.h | 8 misha-5.3.1/misha/src/Filter.cpp |only misha-5.3.1/misha/src/Filter.h |only misha-5.3.1/misha/src/FilterInterface.cpp |only misha-5.3.1/misha/src/FilterRegistry.cpp |only misha-5.3.1/misha/src/FilterRegistry.h |only misha-5.3.1/misha/src/GInterval.cpp | 49 misha-5.3.1/misha/src/GInterval.h | 6 misha-5.3.1/misha/src/GIntervalsBigSet1D.cpp | 105 misha-5.3.1/misha/src/GIntervalsBigSet1D.h | 34 misha-5.3.1/misha/src/GIntervalsBigSet2D.cpp | 101 misha-5.3.1/misha/src/GIntervalsBigSet2D.h | 34 misha-5.3.1/misha/src/GTrack2DImportContacts.cpp | 11 misha-5.3.1/misha/src/GTrackIntervalsFetcher.cpp | 3 misha-5.3.1/misha/src/GTrackIntervalsFetcher1D.h | 5 misha-5.3.1/misha/src/GTrackLiftover.cpp | 495 ++- misha-5.3.1/misha/src/GenomeChromKey.h | 47 misha-5.3.1/misha/src/GenomeIndex.cpp |only misha-5.3.1/misha/src/GenomeIndex.h |only misha-5.3.1/misha/src/GenomeIntervalUtils.cpp | 213 + misha-5.3.1/misha/src/GenomeSeqFetch.cpp | 179 + misha-5.3.1/misha/src/GenomeSeqFetch.h | 19 misha-5.3.1/misha/src/GenomeSeqMultiImport.cpp |only misha-5.3.1/misha/src/GenomeSeqRead.cpp | 39 misha-5.3.1/misha/src/GenomeSeqScorer.cpp | 50 misha-5.3.1/misha/src/GenomeSeqScorer.h | 7 misha-5.3.1/misha/src/GenomeTrack.cpp | 154 - misha-5.3.1/misha/src/GenomeTrack.h | 17 misha-5.3.1/misha/src/GenomeTrack1D.h | 35 misha-5.3.1/misha/src/GenomeTrackApply.cpp | 1 misha-5.3.1/misha/src/GenomeTrackArrayImport.cpp | 7 misha-5.3.1/misha/src/GenomeTrackArrays.cpp | 81 misha-5.3.1/misha/src/GenomeTrackArrays.h | 37 misha-5.3.1/misha/src/GenomeTrackCreateDense.cpp | 94 misha-5.3.1/misha/src/GenomeTrackCreateSparse.cpp | 16 misha-5.3.1/misha/src/GenomeTrackExtract.cpp | 191 + misha-5.3.1/misha/src/GenomeTrackFindNeighbors.cpp | 113 misha-5.3.1/misha/src/GenomeTrackFixedBin.cpp | 295 +- misha-5.3.1/misha/src/GenomeTrackFixedBin.h | 24 misha-5.3.1/misha/src/GenomeTrackImportWig.cpp | 96 misha-5.3.1/misha/src/GenomeTrackInMemory.cpp |only misha-5.3.1/misha/src/GenomeTrackInMemory.h |only misha-5.3.1/misha/src/GenomeTrackIndexedFormat.cpp |only misha-5.3.1/misha/src/GenomeTrackInfo.cpp | 55 misha-5.3.1/misha/src/GenomeTrackModify.cpp | 3 misha-5.3.1/misha/src/GenomeTrackScreener.cpp | 51 misha-5.3.1/misha/src/GenomeTrackSparse.cpp | 122 misha-5.3.1/misha/src/GenomeTrackSparse.h | 84 misha-5.3.1/misha/src/GenomeUtils.cpp | 20 misha-5.3.1/misha/src/GenomeUtils.h | 2 misha-5.3.1/misha/src/GenomeUtilsR.cpp | 346 ++ misha-5.3.1/misha/src/GseqString.cpp |only misha-5.3.1/misha/src/IntervVarProcessor.cpp |only misha-5.3.1/misha/src/IntervVarProcessor.h |only misha-5.3.1/misha/src/IntervalConverter.cpp |only misha-5.3.1/misha/src/IntervalConverter.h |only misha-5.3.1/misha/src/IntervalValidator.cpp |only misha-5.3.1/misha/src/IntervalValidator.h |only misha-5.3.1/misha/src/IntervalsIndex1D.cpp |only misha-5.3.1/misha/src/IntervalsIndex1D.h |only misha-5.3.1/misha/src/IntervalsIndex2D.cpp |only misha-5.3.1/misha/src/IntervalsIndex2D.h |only misha-5.3.1/misha/src/IntervalsIndexedFormat.cpp |only misha-5.3.1/misha/src/IntervalsLiftover.cpp | 591 ++++ misha-5.3.1/misha/src/KmerCounter.cpp | 91 misha-5.3.1/misha/src/KmerCounter.h | 20 misha-5.3.1/misha/src/MaskedBpCounter.cpp |only misha-5.3.1/misha/src/MaskedBpCounter.h |only misha-5.3.1/misha/src/PWMScorer.cpp | 1424 +++++++++ misha-5.3.1/misha/src/PWMScorer.h | 164 + misha-5.3.1/misha/src/PwmCoreParams.cpp |only misha-5.3.1/misha/src/PwmCoreParams.h |only misha-5.3.1/misha/src/Segment.h | 6 misha-5.3.1/misha/src/SequenceVarProcessor.cpp |only misha-5.3.1/misha/src/SequenceVarProcessor.h |only misha-5.3.1/misha/src/TrackExpressionParams.h |only misha-5.3.1/misha/src/TrackExpressionScanner.cpp | 54 misha-5.3.1/misha/src/TrackExpressionSparseIterator.cpp | 5 misha-5.3.1/misha/src/TrackExpressionTrackRectsIterator.cpp | 2 misha-5.3.1/misha/src/TrackExpressionVars.cpp | 1043 ++++--- misha-5.3.1/misha/src/TrackExpressionVars.h | 129 misha-5.3.1/misha/src/TrackIndex.cpp |only misha-5.3.1/misha/src/TrackIndex.h |only misha-5.3.1/misha/src/TrackVarProcessor.cpp |only misha-5.3.1/misha/src/TrackVarProcessor.h |only misha-5.3.1/misha/src/ValueVarProcessor.cpp |only misha-5.3.1/misha/src/ValueVarProcessor.h |only misha-5.3.1/misha/src/misha-init.cpp | 42 misha-5.3.1/misha/src/rdbinterval.cpp | 1455 +++------- misha-5.3.1/misha/src/rdbinterval.h | 245 + misha-5.3.1/misha/src/rdbutils.cpp | 104 misha-5.3.1/misha/src/rdbutils.h | 24 misha-5.3.1/misha/src/utils |only misha-5.3.1/misha/tests/testthat/helper-hic-data.R |only misha-5.3.1/misha/tests/testthat/helper-liftover.R |only misha-5.3.1/misha/tests/testthat/helper-pwm.R | 1 misha-5.3.1/misha/tests/testthat/helper-regression.R | 44 misha-5.3.1/misha/tests/testthat/helper-test_db.R |only misha-5.3.1/misha/tests/testthat/helper-track.R |only misha-5.3.1/misha/tests/testthat/setup-hic-test-data.R |only misha-5.3.1/misha/tests/testthat/setup.R | 16 misha-5.3.1/misha/tests/testthat/test-2d-hic-analysis.R |only misha-5.3.1/misha/tests/testthat/test-2d-parity.R |only misha-5.3.1/misha/tests/testthat/test-auto-config-stress.R |only misha-5.3.1/misha/tests/testthat/test-auto-config.R |only misha-5.3.1/misha/tests/testthat/test-chromid-ordering.R |only misha-5.3.1/misha/tests/testthat/test-db-cache-updates.R |only misha-5.3.1/misha/tests/testthat/test-db-format-conversion.R |only misha-5.3.1/misha/tests/testthat/test-db.R | 231 + misha-5.3.1/misha/tests/testthat/test-directional-neighbors.R |only misha-5.3.1/misha/tests/testthat/test-gbins.R | 2 misha-5.3.1/misha/tests/testthat/test-gcis_decay.R | 4 misha-5.3.1/misha/tests/testthat/test-gcluster.run.R | 2 misha-5.3.1/misha/tests/testthat/test-gdist.R | 2 misha-5.3.1/misha/tests/testthat/test-gextract1.R |only misha-5.3.1/misha/tests/testthat/test-gextract2.R |only misha-5.3.1/misha/tests/testthat/test-gextract3.R |only misha-5.3.1/misha/tests/testthat/test-gintervals-2d-indexed.R |only misha-5.3.1/misha/tests/testthat/test-gintervals-format-conversion.R |only misha-5.3.1/misha/tests/testthat/test-gintervals-multicontig-extended.R |only misha-5.3.1/misha/tests/testthat/test-gintervals.annotate.R | 11 misha-5.3.1/misha/tests/testthat/test-gintervals.canonic.R | 18 misha-5.3.1/misha/tests/testthat/test-gintervals.coverage.R |only misha-5.3.1/misha/tests/testthat/test-gintervals.intersect.R | 11 misha-5.3.1/misha/tests/testthat/test-gintervals.liftover-agg.R |only misha-5.3.1/misha/tests/testthat/test-gintervals.liftover-bin.R |only misha-5.3.1/misha/tests/testthat/test-gintervals.liftover-canonic.R |only misha-5.3.1/misha/tests/testthat/test-gintervals.mapply.R | 20 misha-5.3.1/misha/tests/testthat/test-gintervals.neighbors.R | 510 +++ misha-5.3.1/misha/tests/testthat/test-gintervals.normalize.R | 11 misha-5.3.1/misha/tests/testthat/test-gintervals.quantiles.R | 20 misha-5.3.1/misha/tests/testthat/test-gintervals.summary.R | 20 misha-5.3.1/misha/tests/testthat/test-gintervals1.R |only misha-5.3.1/misha/tests/testthat/test-gintervals2.R |only misha-5.3.1/misha/tests/testthat/test-giterator.cartesian_grid.R | 2 misha-5.3.1/misha/tests/testthat/test-giterator.intervals.R | 2 misha-5.3.1/misha/tests/testthat/test-glookup.R | 2 misha-5.3.1/misha/tests/testthat/test-gpartition.R | 20 misha-5.3.1/misha/tests/testthat/test-gquantiles.R | 2 misha-5.3.1/misha/tests/testthat/test-gsample.R | 2 misha-5.3.1/misha/tests/testthat/test-gscreen.R | 2 misha-5.3.1/misha/tests/testthat/test-gsegment.R | 11 misha-5.3.1/misha/tests/testthat/test-gseq.extract.R | 2 misha-5.3.1/misha/tests/testthat/test-gseq_pwm-parallel.R |only misha-5.3.1/misha/tests/testthat/test-gsummary.R | 2 misha-5.3.1/misha/tests/testthat/test-gtrack-format-conversion.R |only misha-5.3.1/misha/tests/testthat/test-gtrack-multicontig.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.array.R | 11 misha-5.3.1/misha/tests/testthat/test-gtrack.create.R | 89 misha-5.3.1/misha/tests/testthat/test-gtrack.create_dense.R | 53 misha-5.3.1/misha/tests/testthat/test-gtrack.import1.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.import2.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.import3.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.import4.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.import5.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.info.R | 29 misha-5.3.1/misha/tests/testthat/test-gtrack.liftover-agg.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.liftover-bin.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.liftover.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.lookup.R | 29 misha-5.3.1/misha/tests/testthat/test-gtrack.smooth.R | 41 misha-5.3.1/misha/tests/testthat/test-gtrack.var.R | 34 misha-5.3.1/misha/tests/testthat/test-gvtrack.filter.R |only misha-5.3.1/misha/tests/testthat/test-gwilcox.R | 11 misha-5.3.1/misha/tests/testthat/test-indexed-integration.R |only misha-5.3.1/misha/tests/testthat/test-kmer.R | 2 misha-5.3.1/misha/tests/testthat/test-liftover-autoscore-kent.R |only misha-5.3.1/misha/tests/testthat/test-liftover-best_source_cluster.R |only misha-5.3.1/misha/tests/testthat/test-liftover-hg19-hg38.R |only misha-5.3.1/misha/tests/testthat/test-liftover.R |only misha-5.3.1/misha/tests/testthat/test-masked.R |only misha-5.3.1/misha/tests/testthat/test-motifs.R | 11 misha-5.3.1/misha/tests/testthat/test-multicontig-edge-cases-errors.R |only misha-5.3.1/misha/tests/testthat/test-multifasta-import.R |only misha-5.3.1/misha/tests/testthat/test-path-functions.R |only misha-5.3.1/misha/tests/testthat/test-pwm-count-spatial-bidirect.R |only misha-5.3.1/misha/tests/testthat/test-pwm-count.R |only misha-5.3.1/misha/tests/testthat/test-pwm-indexed-gtrack-create.R |only misha-5.3.1/misha/tests/testthat/test-pwm-prego-regression.R |only misha-5.3.1/misha/tests/testthat/test-pwm-sliding-window.R |only misha-5.3.1/misha/tests/testthat/test-pwm-spatial.R |only misha-5.3.1/misha/tests/testthat/test-pwm.R | 277 + misha-5.3.1/misha/tests/testthat/test-random-genome.R |only misha-5.3.1/misha/tests/testthat/test-sequence.R | 1427 +++++++++ misha-5.3.1/misha/tests/testthat/test-track.attrs.R | 275 + misha-5.3.1/misha/tests/testthat/test-vtrack-coverage.R | 2 misha-5.3.1/misha/tests/testthat/test-vtrack-distance-edge.R |only misha-5.3.1/misha/tests/testthat/test-vtrack-max-pos.R |only misha-5.3.1/misha/tests/testthat/test-vtrack-neighbor-count.R |only misha-5.3.1/misha/tests/testthat/test-vtrack-new-funcs.R |only misha-5.3.1/misha/tests/testthat/test-vtrack-values-equivalence.R |only misha-5.3.1/misha/tests/testthat/test-vtrack-values.R |only misha-5.3.1/misha/tests/testthat/test-vtrack.R | 81 misha-5.3.1/misha/vignettes/Database-Formats.Rmd |only misha-5.3.1/misha/vignettes/Manual.Rmd | 245 + 365 files changed, 13370 insertions(+), 2986 deletions(-)
Title: Tools for Quantitative Risk Management
Description: Functions and data sets for reproducing selected results from
the book "Quantitative Risk Management: Concepts, Techniques and Tools".
Furthermore, new developments and auxiliary functions for Quantitative
Risk Management practice.
Author: Marius Hofert [aut, cre],
Kurt Hornik [aut],
Alexander J. McNeil [aut]
Maintainer: Marius Hofert <mhofert@hku.hk>
Diff between qrmtools versions 0.0-18 dated 2025-09-10 and 0.0-19 dated 2025-12-10
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- R/get_data.R | 23 +++++++++++++---------- inst/NEWS.Rd | 9 +++++++++ inst/doc/ARMA_GARCH_VaR.html | 4 ++-- inst/doc/VaR_bounds.html | 6 +++--- inst/doc/geometric_risk_measures.html | 4 ++-- man/get_data.Rd | 7 +++---- 9 files changed, 46 insertions(+), 35 deletions(-)
Title: Miscellaneous Statistical Functions Used in 'guide-R'
Description: Companion package for the manual
'guide-R : Guide pour l’analyse de données d’enquêtes avec R' available at
<https://larmarange.github.io/guide-R/>. 'guideR' implements miscellaneous
functions introduced in 'guide-R' to facilitate statistical analysis and
manipulation of survey data.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between guideR versions 0.7.0 dated 2025-11-26 and 0.8.0 dated 2025-12-10
DESCRIPTION | 12 MD5 | 59 +- NAMESPACE | 17 NEWS.md | 34 + R/gtsummary_tests.R | 41 ++ R/gtsummary_themes.R | 58 ++ R/mean_sd.R |only R/median_iqr.R |only R/plot_categorical.R |only R/plot_continuous.R |only R/plot_means.R |only R/plot_multiple_answers.R | 9 R/plot_proportions.R | 522 +++++++++++++++++--------- R/proportion.R | 29 - R/safe_pal.R |only R/svyoneway.R |only R/vdiffr-helper.R |only inst/WORDLIST | 6 man/gtsummary_test.Rd | 17 man/gtsummary_themes.Rd | 27 + man/mean_sd.Rd |only man/median_iqr.Rd |only man/plot_categorical.Rd |only man/plot_continuous.Rd |only man/plot_means.Rd |only man/plot_multiple_answers.Rd | 5 man/plot_proportions.Rd | 26 - man/safe_pal.Rd |only man/svyoneway.Rd |only tests/testthat/test-gtsummary-themes.R | 18 tests/testthat/test-mean_sd.R |only tests/testthat/test-median_iqr.R |only tests/testthat/test-observed_vs_theoretical.R | 6 tests/testthat/test-plot_categorical.R |only tests/testthat/test-plot_continuous.R |only tests/testthat/test-plot_inertia_from_tree.R | 5 tests/testthat/test-plot_means.R |only tests/testthat/test-plot_multiple_answers.R | 66 ++- tests/testthat/test-plot_proportions.R | 66 ++- tests/testthat/test-plot_trajectories.R | 29 + tests/testthat/test-svyoneway.R |only 41 files changed, 783 insertions(+), 269 deletions(-)
Title: Functions to Estimate Tree Volume and Phytomass in the Italian
Forest Inventory 2005
Description: Tabacchi et al. (2011) published a very detailed study producing a uniform system of functions to estimate tree volume and
phytomass components (stem, branches, stool). The estimates of the 2005 Italian forest inventory (<https://www.inventarioforestale.org/it/>)
are based on these functions. The study documents the domain of applicability of each function and the equations to quantify estimates
accuracies for individual estimates as well as for aggregated estimates. This package makes the functions available in the R environment.
Version 2 exposes two distinct functions for individual and summary estimates. To facilitate access to the functions, tree species
identification is now based on EPPO species codes (<https://data.eppo.int/>).
Author: Nicola Puletti [aut, cre] ,
Mirko Grotti [aut],
Roberto Scotti [aut]
Maintainer: Nicola Puletti <nicola.puletti@gmail.com>
Diff between ForIT versions 2.5.1 dated 2025-09-22 and 2.5.2 dated 2025-12-10
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 8 +++++++- R/ForIT_DataBase.R | 2 +- R/INFCtabulate.R | 2 +- R/INFCvpe.R | 5 ++--- R/INFCvpeSUM.R | 2 +- R/examples/INFCvpeSUM_e.R | 2 +- man/ForIT_DataBase.Rd | 2 +- man/INFCvpe.Rd | 2 +- man/INFCvpeSUM.Rd | 4 ++-- 11 files changed, 30 insertions(+), 25 deletions(-)
Title: Serialize Model Objects with a Consistent Interface
Description: Typically, models in 'R' exist in memory and can be saved via
regular 'R' serialization. However, some models store information in
locations that cannot be saved using 'R' serialization alone. The goal
of 'bundle' is to provide a common interface to capture this
information, situate it within a portable object, and restore it for
use in new settings.
Author: Julia Silge [aut, cre] ,
Simon Couch [aut],
Qiushi Yan [aut],
Max Kuhn [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Julia Silge <julia.silge@posit.co>
Diff between bundle versions 0.1.2 dated 2024-11-12 and 0.1.3 dated 2025-12-10
bundle-0.1.2/bundle/R/package.R |only bundle-0.1.2/bundle/man/bundle_description.Rd |only bundle-0.1.3/bundle/DESCRIPTION | 30 ++-- bundle-0.1.3/bundle/LICENSE | 2 bundle-0.1.3/bundle/MD5 | 86 ++++++----- bundle-0.1.3/bundle/NAMESPACE | 2 bundle-0.1.3/bundle/NEWS.md | 4 bundle-0.1.3/bundle/R/bundle-package.R |only bundle-0.1.3/bundle/R/bundle_bart.R | 6 bundle-0.1.3/bundle/R/bundle_embed.R | 6 bundle-0.1.3/bundle/R/bundle_keras.R | 19 +- bundle-0.1.3/bundle/R/bundle_parsnip.R | 6 bundle-0.1.3/bundle/R/bundle_stacks.R | 8 - bundle-0.1.3/bundle/R/bundle_torch.R | 19 +- bundle-0.1.3/bundle/R/bundle_workflows.R | 12 - bundle-0.1.3/bundle/R/bundle_xgboost.R | 38 +++-- bundle-0.1.3/bundle/R/utils.R | 12 - bundle-0.1.3/bundle/README.md | 64 +++----- bundle-0.1.3/bundle/build/vignette.rds |binary bundle-0.1.3/bundle/inst/doc/bundle.R | 48 +++--- bundle-0.1.3/bundle/inst/doc/bundle.Rmd | 94 +++++++++---- bundle-0.1.3/bundle/inst/doc/bundle.html | 83 ++++++----- bundle-0.1.3/bundle/man/bundle-package.Rd |only bundle-0.1.3/bundle/man/bundle_bart.Rd | 6 bundle-0.1.3/bundle/man/bundle_caret.Rd | 6 bundle-0.1.3/bundle/man/bundle_embed.Rd | 12 - bundle-0.1.3/bundle/man/bundle_h2o.Rd | 2 bundle-0.1.3/bundle/man/bundle_keras.Rd | 16 +- bundle-0.1.3/bundle/man/bundle_parsnip.Rd | 12 - bundle-0.1.3/bundle/man/bundle_stacks.Rd | 10 - bundle-0.1.3/bundle/man/bundle_torch.Rd | 12 - bundle-0.1.3/bundle/man/bundle_workflows.Rd | 18 +- bundle-0.1.3/bundle/man/bundle_xgboost.Rd | 20 +- bundle-0.1.3/bundle/man/figures/lifecycle-deprecated.svg |only bundle-0.1.3/bundle/man/figures/lifecycle-experimental.svg |only bundle-0.1.3/bundle/man/figures/lifecycle-stable.svg |only bundle-0.1.3/bundle/man/figures/lifecycle-superseded.svg |only bundle-0.1.3/bundle/tests/testthat.R | 4 bundle-0.1.3/bundle/tests/testthat/test_bundle_embed.R | 9 - bundle-0.1.3/bundle/tests/testthat/test_bundle_h2o.R | 25 ++- bundle-0.1.3/bundle/tests/testthat/test_bundle_keras.R | 24 ++- bundle-0.1.3/bundle/tests/testthat/test_bundle_parsnip.R | 6 bundle-0.1.3/bundle/tests/testthat/test_bundle_stacks.R | 8 - bundle-0.1.3/bundle/tests/testthat/test_bundle_torch.R | 24 +-- bundle-0.1.3/bundle/tests/testthat/test_bundle_workflows.R | 24 +-- bundle-0.1.3/bundle/tests/testthat/test_bundle_xgboost.R | 29 +++- bundle-0.1.3/bundle/tests/testthat/test_utils.R | 11 - bundle-0.1.3/bundle/vignettes/bundle.Rmd | 94 +++++++++---- 48 files changed, 536 insertions(+), 375 deletions(-)
Title: D-Vine Quantile Regression
Description: Implements D-vine quantile regression models with
parametric or nonparametric pair-copulas. See
Kraus and Czado (2017) <doi:10.1016/j.csda.2016.12.009> and
Schallhorn et al. (2017) <doi:10.48550/arXiv.1705.08310>.
Author: Thomas Nagler [aut, cre],
Dani Kraus [ctb]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between vinereg versions 0.11.0 dated 2025-01-11 and 0.12.1 dated 2025-12-10
DESCRIPTION | 10 +++--- MD5 | 22 ++++++------- NEWS.md | 6 +++ R/RcppExports.R | 4 +- R/vinereg.R | 10 +++--- README.md | 30 +++++++++--------- build/vignette.rds |binary inst/doc/abalone-example.html | 33 ++++++++++---------- inst/doc/bike-rental.html | 49 +++++++++++++++---------------- man/figures/README-unnamed-chunk-1-1.png |binary src/RcppExports.cpp | 11 +++--- src/vinereg.cpp | 27 ++++------------- 12 files changed, 99 insertions(+), 103 deletions(-)
Title: Visualise OMOP Results using 'shiny' Applications
Description: Visualise results obtained from analysing data mapped to the
Observational Medical Outcomes Partnership (OMOP) common data model using
'shiny' applications.
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Edward Burn [ctb] ,
Nuria Mercade-Besora [ctb] ,
Elin Rowlands [ctb] ,
Cecilia Campanile [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between OmopViewer versions 0.5.0 dated 2025-11-16 and 0.6.0 dated 2025-12-10
DESCRIPTION | 23 +++++----- MD5 | 38 ++++++++-------- NEWS.md | 12 +++++ R/appStatic.R | 52 ++++++++++++++--------- R/createServer.R | 8 ++- R/data.R | 4 - R/defaultPanels.R | 5 +- R/functions.R | 19 ++++++++ R/report.R |only R/sysdata.rda |binary data/omopViewerPanels.rda |binary data/omopViewerResults.rda |binary inst/brand/complement/darwin.yml | 2 inst/doc/edit_static_content.html | 2 inst/doc/export_static_app.html | 85 +++++++++++++++++++++++++++----------- inst/functions.R | 18 ++++++-- man/exportStaticApp.Rd | 7 +++ man/omopViewerPanels.Rd | 2 man/omopViewerResults.Rd | 2 tests/testthat/_snaps |only tests/testthat/test-choices.R | 2 21 files changed, 194 insertions(+), 87 deletions(-)
Title: Latent Binary Bayesian Neural Networks Using 'torch'
Description: Latent binary Bayesian neural networks (LBBNNs) are implemented using
'torch', an R interface to the LibTorch backend. Supports mean-field variational
inference as well as flexible variational posteriors using normalizing flows.
The standard LBBNN implementation follows Hubin and Storvik (2024) <doi:10.3390/math12060788>,
using the local reparametrization trick as in Skaaret-Lund et al. (2024)
<https://openreview.net/pdf?id=d6kqUKzG3V>. Input-skip connections are also supported,
as described in Høyheim et al. (2025) <doi:10.48550/arXiv.2503.10496>.
Author: Lars Skaaret-Lund [aut, cre],
Aliaksandr Hubin [aut],
Eirik Hoeyheim [aut]
Maintainer: Lars Skaaret-Lund <lars.skaaret-lund@nmbu.no>
Diff between LBBNN versions 0.1.1 dated 2025-12-01 and 0.1.2 dated 2025-12-10
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 11 +++++++---- R/LBBNN_Model.R | 3 ++- R/Layers.R | 12 +++++++++++- R/local_explanations.R | 4 +++- R/overwrite_functions.R | 7 +++---- R/plotting_graphs.R | 4 ++-- README.md | 3 +-- man/LBBNN_Linear.Rd | 5 ++++- man/figures/README-unnamed-chunk-6-1.png |binary man/predict.LBBNN_Net.Rd | 14 +++++++++++--- 12 files changed, 59 insertions(+), 34 deletions(-)
Title: Generalized Additive Models
Description: Functions for fitting and working with generalized additive models, as described in chapter 7 of "Statistical Models in S" (Chambers and Hastie (eds), 1991), and "Generalized Additive Models" (Hastie and Tibshirani, 1990).
Author: Trevor Hastie [aut, cre],
Balasubramanian Narasimhan [ctb]
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between gam versions 1.22-6 dated 2025-08-22 and 1.22-7 dated 2025-12-10
ChangeLog | 2 ++ DESCRIPTION | 10 +++++----- MD5 | 11 ++++++----- R/gam-package.R | 2 +- cleanup |only man/predict.gam.Rd | 2 +- src/sbart.c | 2 +- 7 files changed, 16 insertions(+), 13 deletions(-)
Title: Test Theory Analysis and Biclustering
Description: Implements comprehensive test data engineering methods as described in
Shojima (2022, ISBN:978-9811699856). Provides statistical techniques for
engineering and processing test data: Classical Test Theory (CTT) with
reliability coefficients for continuous ability assessment; Item Response
Theory (IRT) including Rasch, 2PL, and 3PL models with item/test information
functions; Latent Class Analysis (LCA) for nominal clustering; Latent Rank
Analysis (LRA) for ordinal clustering with automatic determination of cluster
numbers; Biclustering methods including infinite relational models for
simultaneous clustering of examinees and items without predefined cluster
numbers; and Bayesian Network Models (BNM) for visualizing inter-item
dependencies. Features local dependence analysis through LRA and biclustering,
parameter estimation, dimensionality assessment, and network structure
visualization for educational, psychological, and social science research.
Author: Koji Kosugi [aut, cre]
Maintainer: Koji Kosugi <kosugitti@gmail.com>
Diff between exametrika versions 1.7.0 dated 2025-11-22 and 1.8.0 dated 2025-12-10
DESCRIPTION | 6 +-- MD5 | 34 ++++++++++----------- NEWS.md | 71 ++++++++++++++++++++++++++++++++++++++++++++ R/00_EMclus.R | 28 ++++++++--------- R/00_GridSearch.R | 22 +++++++++---- R/00_exametrikaPlot.R | 6 ++- R/05_LCA.R | 11 ++++-- R/06_LRA.R | 13 ++++---- R/07_Biclustering.R | 30 ++++++++++-------- R/07_IRM.R | 36 +++++++++++++--------- R/10_LDB.R | 4 +- R/12_LRA_ordinal.R | 29 ++++++++--------- R/13_LRA_rated.R | 29 ++++++++--------- R/15_Biclustering_nominal.R | 22 +++++++------ R/16_Biclustering_ordinal.R | 24 ++++++++------ man/Biclustering_IRM.Rd | 8 +++- man/GridSearch.Rd | 3 + man/LRA.Rd | 4 +- 18 files changed, 242 insertions(+), 138 deletions(-)
Title: R Interface to the 'DataONE' REST API
Description: Provides read and write access to data and metadata from
the 'DataONE' network <https://www.dataone.org> of data repositories.
Each 'DataONE' repository implements a consistent repository application
programming interface. Users call methods in R to access these remote
repository functions, such as methods to query the metadata catalog, get
access to metadata for particular data packages, and read the data objects
from the data repository. Users can also insert and update data objects on
repositories that support these methods.
Author: Matthew B. Jones [aut, cre] ,
Peter Slaughter [aut] ,
Rob Nahf [aut],
Carl Boettiger [aut] ,
Chris Jones [aut] ,
Bryce Mecum [aut] ,
Jeanette Clark [aut] ,
Jordan Read [ctb] ,
Lauren Walker [aut] ,
Edmund Hart [ctb] ,
Scott Chamberlain [ctb] ,
Regent [...truncated...]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>
This is a re-admission after prior archival of version 2.2.2 dated 2022-06-10
Diff between dataone versions 2.2.2 dated 2022-06-10 and 2.3.0 dated 2025-12-10
DESCRIPTION | 41 +-- MD5 | 248 +++++++++---------- NEWS | 8 R/AbstractTableDescriber.R | 6 R/AuthenticationManager.R | 74 ++--- R/CNode.R | 87 +++--- R/CertificateManager.R | 41 +-- R/D1Client.R | 166 ++++++------ R/D1Node.R | 119 ++++----- R/D1Object.R | 28 +- R/MNode.R | 89 +++--- R/auth_request.R | 37 ++ R/dataone-defunct.R | 76 ++--- R/dataone-deprecated.R | 23 - R/dataone-package.R | 25 + README.md | 44 ++- build/vignette.rds |binary inst/WORDLIST | 158 +++++------- inst/doc/v01-dataone-overview.R | 64 ++-- inst/doc/v01-dataone-overview.Rmd | 2 inst/doc/v01-dataone-overview.html | 187 +++++++------- inst/doc/v02-dataone-federation.R | 22 - inst/doc/v02-dataone-federation.Rmd | 9 inst/doc/v02-dataone-federation.html | 158 ++++++------ inst/doc/v03-searching-dataone.R | 96 +++---- inst/doc/v03-searching-dataone.Rmd | 7 inst/doc/v03-searching-dataone.html | 210 ++++++++-------- inst/doc/v04-download-data.R | 106 ++++---- inst/doc/v04-download-data.Rmd | 2 inst/doc/v04-download-data.html | 209 ++++++++-------- inst/doc/v05-upload-data.R | 124 ++++----- inst/doc/v05-upload-data.html | 363 ++++++++++++++-------------- inst/doc/v06-update-package.R | 106 ++++---- inst/doc/v06-update-package.html | 201 ++++++++------- inst/doc/v07-known-issues.R | 40 +-- inst/doc/v07-known-issues.html | 165 ++++++------ man/AbstractTableDescriber-class.Rd | 20 - man/AuthenticationManager-class.Rd | 60 ++-- man/AuthenticationManager.Rd | 2 man/CNode-class.Rd | 32 +- man/CNode.Rd | 6 man/CertificateManager-class.Rd | 50 +-- man/CertificateManager.Rd | 8 man/D1Client-class.Rd | 32 +- man/D1Client-initialize.Rd | 2 man/D1Client.Rd | 6 man/D1Node-class.Rd | 28 +- man/D1Object-class.Rd | 16 - man/D1Object-initialize.Rd | 2 man/D1Object.Rd | 2 man/MNode-class.Rd | 29 +- man/MNode.Rd | 4 man/addData.Rd | 2 man/archive.Rd | 11 man/auth_delete.Rd | 2 man/auth_get.Rd | 2 man/auth_head.Rd | 10 man/auth_post.Rd | 2 man/auth_put.Rd | 2 man/auth_put_post_delete.Rd | 2 man/canRead.Rd | 2 man/convert.csv.Rd | 2 man/createDataPackage.Rd | 2 man/createObject.Rd | 7 man/d1IdentifierSearch.Rd | 2 man/d1SolrQuery.Rd | 2 man/data.tableAttributeNames.Rd | 10 man/data.tableAttributeOrientation.Rd | 10 man/data.tableAttributeStorageTypes.Rd | 10 man/data.tableAttributeTypes.Rd | 10 man/data.tableMissingValueCodes.Rd | 10 man/data.tableSkipLinesHeader.Rd | 8 man/dataone-defunct.Rd | 82 +++--- man/dataone-deprecated.Rd | 20 - man/dataone.Rd | 24 + man/downloadCert.Rd | 8 man/downloadObject.Rd | 8 man/echoCredentials.Rd | 2 man/encodeUrlPath.Rd | 2 man/encodeUrlQuery.Rd | 2 man/generateIdentifier.Rd | 11 man/getAuthMethod.Rd | 2 man/getAuthSubject.Rd | 2 man/getCN.Rd | 2 man/getCertExpires.Rd | 2 man/getCertLocation.Rd | 4 man/getChecksum.Rd | 2 man/getD1Object.Rd | 2 man/getDataObject.Rd | 12 man/getDataPackage.Rd | 6 man/getEndpoint.Rd | 2 man/getErrorDescription.Rd | 12 man/getFormat.Rd | 2 man/getMN.Rd | 4 man/getMNode.Rd | 6 man/getMNodeId.Rd | 2 man/getObject.Rd | 2 man/getPackage.Rd | 6 man/getSystemMetadata.Rd | 2 man/hasReservation.Rd | 4 man/isAuthValid.Rd | 8 man/isAuthorized.Rd | 4 man/isCertExpired.Rd | 2 man/is_windows.Rd |only man/listFormats.Rd | 4 man/listMemberNodes.Rd | 2 man/listNodes.Rd | 2 man/obscureCert.Rd | 6 man/query.Rd | 10 man/reserveIdentifier.Rd | 2 man/restoreCert.Rd | 6 man/setMNodeId.Rd | 2 man/setObsoletedBy.Rd | 6 man/setPublicAccess.Rd | 6 man/updateObject.Rd | 9 man/updateSystemMetadata.Rd | 9 man/uploadDataObject.Rd | 2 man/uploadDataPackage.Rd | 14 - tests/testthat/helper-base.R | 10 tests/testthat/test.AuthenticationManager.R | 14 - tests/testthat/test.CNode.R | 3 tests/testthat/test.ssl.R |only vignettes/v01-dataone-overview.Rmd | 2 vignettes/v02-dataone-federation.Rmd | 9 vignettes/v03-searching-dataone.Rmd | 7 vignettes/v04-download-data.Rmd | 2 126 files changed, 2106 insertions(+), 2018 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-11-25 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-10-31 1.0.3
2024-04-26 1.0.2
2024-03-15 1.0.1
2023-12-06 1.0.0
2023-05-07 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-08-26 0.9.5
2016-02-29 0.9.2
2016-01-22 0.9.1
2016-01-19 0.9
Title: Clustering of Weighted Data
Description: Clusters state sequences and weighted data. It provides an optimized weighted PAM algorithm as well as functions for aggregating replicated cases, computing cluster quality measures for a range of clustering solutions, sequence analysis typology validation using parametric bootstraps and plotting (fuzzy) clusters of state sequences. It further provides a fuzzy and crisp CLARA algorithm to cluster large database with sequence analysis, and a methodological framework for Robustness Assessment of Regressions using Cluster Analysis Typologies (RARCAT).
Author: Matthias Studer [aut, cre],
Leonard Roth [ctb]
Maintainer: Matthias Studer <matthias.studer@unige.ch>
Diff between WeightedCluster versions 1.8-1 dated 2024-12-10 and 2.0 dated 2025-12-10
DESCRIPTION | 19 ++- MD5 | 53 ++++++---- NAMESPACE | 14 +- NEWS | 10 ++ R/amemat.R |only R/bootclustrange.R | 3 R/clara_clustrange.R | 43 ++++++-- R/clustrangefamily.R | 2 R/rarcat.R |only R/wfcmdd.r | 169 +++++++++++++++++++---------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/BigDataSA.html | 39 ++++---- inst/doc/ClusterExternalValidSA.Rmd | 2 inst/doc/ClusterExternalValidSA.html | 37 ++++--- inst/doc/ClusterValidSA.html | 59 ++++++------ inst/doc/FuzzySA.Rmd | 2 inst/doc/FuzzySA.html | 60 ++++++------ inst/doc/RARCAT.R |only inst/doc/RARCAT.Rmd |only inst/doc/RARCAT.html |only inst/doc/WeightedCluster.pdf |binary inst/doc/WeightedClusterFR.Rnw | 6 - inst/doc/WeightedClusterFR.pdf |binary inst/doc/WeightedClusterPreview.pdf |binary man/rarcat.Rd |only vignettes/ClusterExternalValidSA.Rmd | 2 vignettes/FuzzySA.Rmd | 2 vignettes/RARCAT.Rmd |only vignettes/WeightedClusterFR.Rnw | 6 - vignettes/manual.bib | 3 31 files changed, 298 insertions(+), 233 deletions(-)
More information about WeightedCluster at CRAN
Permanent link
Title: R Interface to W3C Markup Validation Services
Description: R interface to a W3C Markup Validation service.
See <https://validator.w3.org/> for more information.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between W3CMarkupValidator versions 0.2-1 dated 2025-08-23 and 0.2-2 dated 2025-12-10
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/w3c.R | 31 ++++++++++++++++++++----------- man/w3c_markup_validate.Rd | 19 +++++++++++++++++-- 4 files changed, 43 insertions(+), 19 deletions(-)
More information about W3CMarkupValidator at CRAN
Permanent link
Title: Genome Interval Arithmetic
Description: Read and manipulate genome intervals and signals. Provides
functionality similar to command-line tool suites within R, enabling
interactive analysis and visualization of genome-scale data. Riemondy
et al. (2017) <doi:10.12688/f1000research.11997.1>.
Author: Jay Hesselberth [aut, cre] ,
Kent Riemondy [aut] ,
RNA Bioscience Initiative [fnd, cph]
Maintainer: Jay Hesselberth <jay.hesselberth@cuanschutz.edu>
Diff between valr versions 0.8.4 dated 2025-06-22 and 0.9.0 dated 2025-12-10
valr-0.8.4/valr/R/RcppExports.R |only valr-0.8.4/valr/R/globals.r |only valr-0.8.4/valr/inst/include/DataFrameBuilder.h |only valr-0.8.4/valr/inst/include/IntervalTree.h |only valr-0.8.4/valr/inst/include/IntervalTree_ext.h |only valr-0.8.4/valr/inst/include/genome.h |only valr-0.8.4/valr/inst/include/group_apply.h |only valr-0.8.4/valr/inst/include/grouped_dataframe.h |only valr-0.8.4/valr/inst/include/intervals.h |only valr-0.8.4/valr/inst/include/random.h |only valr-0.8.4/valr/inst/include/utils.h |only valr-0.8.4/valr/man/read_bigwig.Rd |only valr-0.8.4/valr/src/RcppExports.cpp |only valr-0.8.4/valr/src/init.c |only valr-0.8.4/valr/src/valr_utils.cpp |only valr-0.9.0/valr/DESCRIPTION | 24 valr-0.9.0/valr/MD5 | 217 ++-- valr-0.9.0/valr/NAMESPACE | 12 valr-0.9.0/valr/NEWS.md | 32 valr-0.9.0/valr/R/bed12_to_exons.r | 1 valr-0.9.0/valr/R/bed_absdist.r | 14 valr-0.9.0/valr/R/bed_closest.r | 8 valr-0.9.0/valr/R/bed_cluster.r | 5 valr-0.9.0/valr/R/bed_complement.r | 13 valr-0.9.0/valr/R/bed_coverage.R | 25 valr-0.9.0/valr/R/bed_fisher.r | 5 valr-0.9.0/valr/R/bed_flank.r | 5 valr-0.9.0/valr/R/bed_genomecov.R | 15 valr-0.9.0/valr/R/bed_glyph.r | 24 valr-0.9.0/valr/R/bed_intersect.r | 38 valr-0.9.0/valr/R/bed_jaccard.r | 24 valr-0.9.0/valr/R/bed_makewindows.r | 1 valr-0.9.0/valr/R/bed_map.r | 24 valr-0.9.0/valr/R/bed_merge.r | 13 valr-0.9.0/valr/R/bed_partition.r | 5 valr-0.9.0/valr/R/bed_projection.r | 68 - 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valr-0.9.0/valr/man/bed_subtract.Rd | 7 valr-0.9.0/valr/man/bed_window.Rd | 11 valr-0.9.0/valr/man/reexports.Rd |only valr-0.9.0/valr/src/bed12toexons.cpp | 147 +- valr-0.9.0/valr/src/closest.cpp | 327 +++--- valr-0.9.0/valr/src/complement.cpp | 134 +- valr-0.9.0/valr/src/coverage.cpp | 218 ++-- valr-0.9.0/valr/src/cpp11.cpp |only valr-0.9.0/valr/src/dist.cpp | 182 +-- valr-0.9.0/valr/src/flank.cpp | 183 +-- valr-0.9.0/valr/src/gcoverage.cpp | 167 ++- valr-0.9.0/valr/src/intersect.cpp | 210 ++-- valr-0.9.0/valr/src/makewindows.cpp | 145 +- valr-0.9.0/valr/src/merge.cpp | 207 ++- valr-0.9.0/valr/src/partition.cpp | 172 +-- valr-0.9.0/valr/src/random.cpp | 110 +- valr-0.9.0/valr/src/shuffle.cpp | 372 +++---- valr-0.9.0/valr/src/subtract.cpp | 184 ++- valr-0.9.0/valr/tests/testthat/_snaps/glyph/intersect-glyph-is-ok.svg | 78 - valr-0.9.0/valr/tests/testthat/_snaps/glyph/merge-glyph-is-ok.svg | 60 - valr-0.9.0/valr/tests/testthat/test-db.r | 8 valr-0.9.0/valr/tests/testthat/test_absdist.r | 89 - valr-0.9.0/valr/tests/testthat/test_bed12_to_exons.r | 1 valr-0.9.0/valr/tests/testthat/test_closest.r | 462 +++----- valr-0.9.0/valr/tests/testthat/test_cluster.r | 115 +- valr-0.9.0/valr/tests/testthat/test_complement.r | 236 +--- valr-0.9.0/valr/tests/testthat/test_coverage.r | 69 + valr-0.9.0/valr/tests/testthat/test_features.r | 2 valr-0.9.0/valr/tests/testthat/test_fisher.r | 21 valr-0.9.0/valr/tests/testthat/test_flank.r | 24 valr-0.9.0/valr/tests/testthat/test_genome.r | 26 valr-0.9.0/valr/tests/testthat/test_genomecov.R | 149 +- valr-0.9.0/valr/tests/testthat/test_glyph.r | 33 valr-0.9.0/valr/tests/testthat/test_groups.r | 8 valr-0.9.0/valr/tests/testthat/test_intersect.r | 464 ++++---- valr-0.9.0/valr/tests/testthat/test_jaccard.r | 52 - valr-0.9.0/valr/tests/testthat/test_makewindows.r | 51 valr-0.9.0/valr/tests/testthat/test_map.r | 172 +-- valr-0.9.0/valr/tests/testthat/test_merge.r | 193 +-- valr-0.9.0/valr/tests/testthat/test_partition.r | 307 ++--- valr-0.9.0/valr/tests/testthat/test_projection.r | 110 -- valr-0.9.0/valr/tests/testthat/test_random.r | 5 valr-0.9.0/valr/tests/testthat/test_reldist.r | 51 valr-0.9.0/valr/tests/testthat/test_shift.r | 58 - valr-0.9.0/valr/tests/testthat/test_shuffle.r | 70 - valr-0.9.0/valr/tests/testthat/test_slop.r | 101 - valr-0.9.0/valr/tests/testthat/test_sort.r | 253 ++-- valr-0.9.0/valr/tests/testthat/test_spacing.r | 30 valr-0.9.0/valr/tests/testthat/test_strands.r | 14 valr-0.9.0/valr/tests/testthat/test_subtract.r | 230 ++-- valr-0.9.0/valr/tests/testthat/test_tbls.r | 22 valr-0.9.0/valr/tests/testthat/test_types.R | 36 valr-0.9.0/valr/tests/testthat/test_utils.r | 33 valr-0.9.0/valr/tests/testthat/test_window.r | 27 valr-0.9.0/valr/vignettes/valr.Rmd | 52 - 119 files changed, 4295 insertions(+), 3905 deletions(-)
Title: Interactively Gate Points
Description: Interactively gate points on a scatter plot. Interactively drawn gates are
recorded and can be applied programmatically to reproduce results exactly. Programmatic gating is
based on the package gatepoints by Wajid Jawaid.
Author: Stefano Mangiola [aut],
Wajid Jawaid [ctb],
William Hutchison [cre, aut]
Maintainer: William Hutchison <hutchison.w@wehi.edu.au>
Diff between tidygate versions 1.0.14 dated 2024-09-17 and 1.0.19 dated 2025-12-10
DESCRIPTION | 25 ++-- MD5 | 20 +-- NAMESPACE | 7 + R/gate_app.R | 7 - R/methods.R | 80 ++++++++++++++- build/stage23.rdb |binary build/vignette.rds |binary inst/doc/introdution.R | 34 +++--- inst/doc/introdution.html | 236 ++++++++++++++++++++-------------------------- man/gate.Rd | 5 man/gate_interactive.Rd | 6 - 11 files changed, 234 insertions(+), 186 deletions(-)
Title: Develop and Use Modular Health Economic Models
Description: A template model module, tools to help find model modules
derived from this template and a programming syntax to use these
modules in health economic analyses. These elements are the
foundation for a prototype software framework for developing living
and transferable models and using those models in reproducible health
economic analyses. The software framework is extended by other R
libraries. For detailed documentation about the framework and how to
use it visit <https://www.ready4-dev.com/>. For a background to the
methodological issues that the framework is attempting to help solve,
see Hamilton et al. (2024) <doi:10.1007/s40273-024-01378-8>.
Author: Matthew Hamilton [aut, cre, cph] ,
Orygen [cph, fnd],
Australian Government Research Training Program [fnd],
VicHealth [fnd],
Victoria University [fnd]
Maintainer: Matthew Hamilton <matthew.hamilton1@monash.edu>
Diff between ready4 versions 0.1.18 dated 2024-09-30 and 0.1.19 dated 2025-12-10
DESCRIPTION | 35 +- MD5 | 422 +++++++++++++++--------------- NAMESPACE | 2 NEWS.md | 4 R/C4_Ready4Project.R |only R/fn_get.R | 72 +++-- R/fn_make.R | 8 R/fn_write.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 38 +- inst/MD_RMDs/index.Rmd | 54 +-- inst/MD_RMDs/index_Body.Rmd | 36 +- inst/MD_Rmarkdown/index.en.Rmarkdown | 56 +-- inst/doc/V_01.R | 2 inst/doc/V_01.Rmd | 162 +++++------ inst/doc/V_01.html | 2 inst/doc/V_02.R | 4 inst/doc/V_02.Rmd | 134 ++++----- inst/doc/V_02.html | 23 - inst/doc/V_03.Rmd | 98 +++--- inst/doc/V_03.html | 2 inst/doc/V_04.R | 4 inst/doc/V_04.Rmd | 8 inst/doc/V_04.html | 55 +-- inst/doc/V_05.R | 8 inst/doc/V_05.Rmd | 122 ++++---- inst/doc/V_05.html | 12 inst/doc/V_06.Rmd | 84 ++--- inst/doc/V_06.html | 2 inst/doc/V_07.Rmd | 78 ++--- inst/doc/V_07.html | 2 inst/doc/ready4.html | 2 man/Ready4Module-class.Rd | 32 +- man/Ready4Private-class.Rd | 32 +- man/Ready4Project-class.Rd |only man/Ready4Public-class.Rd | 32 +- man/add_lups.Rd | 64 ++-- man/add_references.Rd | 58 ++-- man/add_rows_from_fn_args.Rd | 50 +-- man/add_scroll_box.Rd | 58 ++-- man/add_vignette_links.Rd | 70 ++-- man/author-methods.Rd | 38 +- man/authorClasses-methods.Rd | 38 +- man/authorData-methods.Rd | 38 +- man/authorFunctions-methods.Rd | 38 +- man/authorReport-methods.Rd | 38 +- man/authorSlot-methods.Rd | 58 ++-- man/bind_tables_from_loc_files.Rd | 58 ++-- man/characterize-methods.Rd | 38 +- man/characterizeSlot-methods.Rd | 58 ++-- man/depict-methods.Rd | 38 +- man/depictSlot-methods.Rd | 58 ++-- man/deprecated.Rd | 30 +- man/dotdata.Rd | 30 +- man/enhance-methods.Rd | 38 +- man/enhanceSlot-methods.Rd | 58 ++-- man/examples/get_datasets_tb.R | 2 man/examples/get_from_lup_obj.R | 14 man/examples/get_gracefully.R | 78 ++--- man/examples/get_libraries_tb.R | 2 man/examples/get_methods.R | 2 man/examples/get_methods_tb.R | 2 man/examples/get_modules_tb.R | 2 man/examples/make_code_releases_tbl.R | 26 - man/examples/make_datasets_tb.R | 22 - man/examples/make_ds_releases_tbl.R | 2 man/examples/make_methods_tb.R | 8 man/examples/make_modules_tb.R | 8 man/examples/make_programs_tbl.R | 18 - man/examples/print_data.R | 10 man/examples/print_methods.R | 10 man/examples/print_modules.R | 10 man/examples/print_packages.R | 42 +- man/examples/procureSlot_Ready4Module.R | 4 man/examples/renewSlot_Ready4Module.R | 4 man/examples/write_to_copy_rmds.R | 12 man/examples/write_to_render_post.R | 56 +-- man/examples/write_ws.R | 6 man/exhibit-methods.Rd | 38 +- man/exhibitSlot-methods.Rd | 58 ++-- man/figures/lifecycle-archived.svg | 42 +- man/figures/lifecycle-defunct.svg | 42 +- man/figures/lifecycle-maturing.svg | 42 +- man/figures/lifecycle-questioning.svg | 42 +- man/figures/lifecycle-soft-deprecated.svg | 42 +- man/get_badge_urls.Rd | 52 +-- man/get_badges_lup.Rd | 52 +-- man/get_cls_extensions.Rd | 64 ++-- man/get_datasets_tb.Rd | 58 ++-- man/get_digits_from_text.Rd | 36 +- man/get_dv_fls_urls.Rd | 64 ++-- man/get_examples.Rd | 40 +- man/get_excluded_repos.Rd | 46 +-- man/get_fl_extension.Rd | 36 +- man/get_fl_id_from_dv_ls.Rd | 44 +-- man/get_fl_nm_from_path.Rd | 36 +- man/get_from_lup_obj.Rd | 80 ++--- man/get_functions_tb.Rd | 52 +-- man/get_generics.Rd | 58 ++-- man/get_gh_repos.Rd | 36 +- man/get_gracefully.Rd | 6 man/get_libraries_ls.Rd | 46 +-- man/get_libraries_tb.Rd | 50 +-- man/get_manual_urls.Rd | 46 +-- man/get_methods.Rd | 44 +-- man/get_methods_tb.Rd | 50 +-- man/get_modules_tb.Rd | 50 +-- man/get_mthd_titles.Rd | 52 +-- man/get_r4_obj_slots.Rd | 40 +- man/get_rds_from_dv.Rd | 3 man/get_source_code_urls.Rd | 46 +-- man/get_subroutine_repos.Rd | 46 +-- man/get_table_from_loc_file.Rd | 68 ++-- man/ingest-methods.Rd | 38 +- man/ingestSlot-methods.Rd | 58 ++-- man/investigate-methods.Rd | 38 +- man/investigateSlot-methods.Rd | 58 ++-- man/make_additions_tb.Rd | 58 ++-- man/make_code_releases_tbl.Rd | 162 +++++------ man/make_datasets_tb.Rd | 106 +++---- man/make_ds_releases_tbl.Rd | 74 ++--- man/make_dss_tb.Rd | 58 ++-- man/make_files_tb.Rd | 44 +-- man/make_fn_defaults_ls.Rd | 36 +- man/make_framework_pkgs_chr.Rd | 46 +-- man/make_libraries_ls.Rd | 52 +-- man/make_libraries_tb.Rd | 88 +++--- man/make_list_phrase.Rd | 36 +- man/make_local_path_to_dv_data.Rd | 44 +-- man/make_methods_tb.Rd | 98 +++--- man/make_modules_pkgs_chr.Rd | 58 ++-- man/make_modules_tb.Rd | 98 +++--- man/make_programs_tbl.Rd | 120 ++++---- man/make_prompt.Rd | 44 +-- man/manufacture-methods.Rd | 38 +- man/manufactureSlot-methods.Rd | 58 ++-- man/metamorphose-methods.Rd | 38 +- man/metamorphoseSlot-methods.Rd | 58 ++-- man/nseequals.Rd | 30 +- man/pipe.Rd | 30 +- man/print_data.Rd | 100 +++---- man/print_dss.Rd | 76 ++--- man/print_dvs.Rd | 82 ++--- man/print_methods.Rd | 124 ++++---- man/print_modules.Rd | 76 ++--- man/print_packages.Rd | 174 ++++++------ man/print_vignettes.Rd | 118 ++++---- man/procureSlot-methods.Rd | 70 ++-- man/prognosticate-methods.Rd | 38 +- man/prognosticateSlot-methods.Rd | 58 ++-- man/ratify-methods.Rd | 38 +- man/ratifySlot-methods.Rd | 58 ++-- man/ready4-package.Rd | 90 +++--- man/reckon-methods.Rd | 38 +- man/reckonSlot-methods.Rd | 58 ++-- man/remove_lbls_from_df.Rd | 36 +- man/renew-methods.Rd | 38 +- man/rowbind_all_tbs_in_r4_obj.Rd | 44 +-- man/rowbind_tbs_in_r4_obj.Rd | 48 +-- man/share-methods.Rd | 38 +- man/shareSlot-methods.Rd | 58 ++-- man/transform_chr_to_num.Rd | 36 +- man/transform_cls_type_ls.Rd | 36 +- man/update_libraries_ls.Rd | 52 +-- man/update_libraries_tb.Rd | 94 +++--- man/update_pt_fn_args_ls.Rd | 36 +- man/update_tb_r3.Rd | 94 +++--- man/write_all_tbs_in_tbs_r4_to_csvs.Rd | 76 ++--- man/write_blog_entries.Rd | 70 ++-- man/write_citation_cff.Rd | 70 ++-- man/write_conditional_tags.Rd | 76 ++--- man/write_dv_fl_to_loc.Rd | 106 +++---- man/write_env_objs_to_dv.Rd | 112 +++---- man/write_examples.Rd | 70 ++-- man/write_extra_pkgs_to_actions.Rd | 58 ++-- man/write_fls_from_dv.Rd | 88 +++--- man/write_fls_to_dv.Rd | 88 +++--- man/write_fls_to_repo.Rd | 112 +++---- man/write_from_tmp.Rd | 76 ++--- man/write_ingested_dv_fl.Rd | 106 +++---- man/write_library_metadata.Rd | 148 +++++----- man/write_new_credentials.Rd | 70 ++-- man/write_new_dirs.Rd | 58 ++-- man/write_new_files.Rd | 88 +++--- man/write_obj_with_prompt.Rd | 76 ++--- man/write_prj_outp_dirs.Rd | 70 ++-- man/write_tb_to_csv.Rd | 82 ++--- man/write_to_copy_rmds.Rd | 90 +++--- man/write_to_delete_dirs.Rd | 58 ++-- man/write_to_delete_fls.Rd | 64 ++-- man/write_to_dv_from_tbl.Rd | 82 ++--- man/write_to_dv_with_wait.Rd | 118 ++++---- man/write_to_edit_workflow.Rd | 64 ++-- man/write_to_force_links_in.Rd | 64 ++-- man/write_to_publish_dv_ds.Rd | 64 ++-- man/write_to_render_post.Rd | 134 ++++----- man/write_to_trim_html.Rd | 58 ++-- man/write_with_consent.Rd | 106 +++---- man/write_words.Rd | 70 ++-- man/write_ws.Rd | 66 ++-- tests/testthat.R | 24 - tests/testthat/setup.R | 10 tests/testthat/test-fn_get.R | 78 ++--- tests/testthat/test-fn_make.R | 136 ++++----- tests/testthat/test-fn_write.R | 120 ++++---- vignettes/V_01.Rmd | 162 +++++------ vignettes/V_02.Rmd | 134 ++++----- vignettes/V_03.Rmd | 98 +++--- vignettes/V_04.Rmd | 8 vignettes/V_05.Rmd | 122 ++++---- vignettes/V_06.Rmd | 84 ++--- vignettes/V_07.Rmd | 78 ++--- 213 files changed, 5910 insertions(+), 5886 deletions(-)
Title: Multivariate Imputation by Chained Equations
Description: Multiple imputation using Fully Conditional Specification (FCS)
implemented by the MICE algorithm as described in Van Buuren and
Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>. Each variable has
its own imputation model. Built-in imputation models are provided for
continuous data (predictive mean matching, normal), binary data (logistic
regression), unordered categorical data (polytomous logistic regression)
and ordered categorical data (proportional odds). MICE can also impute
continuous two-level data (normal model, pan, second-level variables).
Passive imputation can be used to maintain consistency between variables.
Various diagnostic plots are available to inspect the quality of the
imputations.
Author: Stef van Buuren [aut, cre],
Karin Groothuis-Oudshoorn [aut],
Gerko Vink [ctb],
Rianne Schouten [ctb],
Alexander Robitzsch [ctb],
Patrick Rockenschaub [ctb],
Lisa Doove [ctb],
Shahab Jolani [ctb],
Margarita Moreno-Betancur [ctb],
Ian White [ctb],
Phil [...truncated...]
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>
Diff between mice versions 3.18.0 dated 2025-05-27 and 3.19.0 dated 2025-12-10
DESCRIPTION | 20 ++++++--- MD5 | 26 +++++++----- NAMESPACE | 4 + NEWS.md | 33 +++++++++++++++ R/barnard.rubin.R | 11 +++-- R/predict_mi.R |only R/summary.R | 65 ++++++++++++++++++++++++------- R/tbc.R | 2 README.md | 2 build/partial.rdb |binary man/mice.Rd | 2 man/predict_mi.Rd |only man/tbc.Rd | 2 tests/testthat/test-banard.rubin.R |only tests/testthat/test-mice.impute.2l.bin.R | 2 tests/testthat/test-predict_mi.R |only 16 files changed, 130 insertions(+), 39 deletions(-)
Title: Hashmaps and Memoization (in-Memory Caching of Repeated
Computations)
Description: A simple in-memory, LRU cache that can be wrapped
around any function to memoize it. The cache is keyed on a hash
of the input data (using 'digest') or on pointer equivalence.
Also includes a generic hashmap object that can key on any object type.
Author: Peter Meilstrup [aut, cre]
Maintainer: Peter Meilstrup <peter.meilstrup@gmail.com>
Diff between memo versions 1.1.1 dated 2023-12-11 and 1.1.2 dated 2025-12-10
memo-1.1.1/memo/vignettes/README-woven.md |only memo-1.1.2/memo/DESCRIPTION | 24 +- memo-1.1.2/memo/MD5 | 38 +-- memo-1.1.2/memo/NAMESPACE | 1 memo-1.1.2/memo/NEWS | 6 memo-1.1.2/memo/R/cache.R | 16 - memo-1.1.2/memo/R/getPointer.R | 1 memo-1.1.2/memo/R/lru.R | 46 ++-- memo-1.1.2/memo/R/map.R | 7 memo-1.1.2/memo/build/vignette.rds |binary memo-1.1.2/memo/inst/doc/README.R | 2 memo-1.1.2/memo/inst/doc/README.html | 248 +++++++++++++++----------- memo-1.1.2/memo/man/lru_cache.Rd | 8 memo-1.1.2/memo/man/memo-package.Rd | 1 memo-1.1.2/memo/src/getPointer.c | 34 +++ memo-1.1.2/memo/src/vadr.c | 9 memo-1.1.2/memo/src/vadr.h | 7 memo-1.1.2/memo/tests/testthat/last.dump.rda |only memo-1.1.2/memo/tests/testthat/test-cache.R | 35 +++ memo-1.1.2/memo/tests/testthat/test-hashmap.R | 1 memo-1.1.2/memo/tests/testthat/test-lru.R | 8 21 files changed, 301 insertions(+), 191 deletions(-)
Title: Download Map Data from GISCO API - Eurostat
Description: Tools to download data from the GISCO (Geographic Information
System of the Commission) Eurostat database
<https://ec.europa.eu/eurostat/web/gisco>. Global and European map
data available. This package is in no way officially related to or
endorsed by Eurostat.
Author: Diego Hernangomez [aut, cre, cph] ,
Eurostat [cph] ,
EuroGeographics [cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between giscoR versions 0.6.1 dated 2025-01-27 and 1.0.0 dated 2025-12-10
giscoR-0.6.1/giscoR/R/gisco_addressapi.R |only giscoR-0.6.1/giscoR/R/gisco_attributions.R |only giscoR-0.6.1/giscoR/R/gisco_bulk_download.R |only giscoR-0.6.1/giscoR/R/gisco_cache.R |only giscoR-0.6.1/giscoR/R/gisco_check_access.R |only giscoR-0.6.1/giscoR/R/gisco_clear_cache.R |only giscoR-0.6.1/giscoR/R/gisco_get_airports.R |only giscoR-0.6.1/giscoR/R/gisco_get_coastallines.R |only giscoR-0.6.1/giscoR/R/gisco_get_countries.R |only giscoR-0.6.1/giscoR/R/gisco_get_education.R |only giscoR-0.6.1/giscoR/R/gisco_get_grid.R |only giscoR-0.6.1/giscoR/R/gisco_get_healthcare.R |only giscoR-0.6.1/giscoR/R/gisco_get_lau.R |only giscoR-0.6.1/giscoR/R/gisco_get_nuts.R |only giscoR-0.6.1/giscoR/R/gisco_get_postalcodes.R |only giscoR-0.6.1/giscoR/R/gisco_get_units.R |only giscoR-0.6.1/giscoR/R/gisco_get_urban_audit.R |only giscoR-0.6.1/giscoR/R/utils_downloads.R |only giscoR-0.6.1/giscoR/R/utils_names.R |only giscoR-0.6.1/giscoR/data/gisco_coastallines.rda |only giscoR-0.6.1/giscoR/data/gisco_countries.rda |only giscoR-0.6.1/giscoR/data/gisco_nuts.rda |only giscoR-0.6.1/giscoR/man/chunks/addressapi.Rmd |only giscoR-0.6.1/giscoR/man/gisco_addressapi.Rd |only giscoR-0.6.1/giscoR/man/gisco_coastallines.Rd |only giscoR-0.6.1/giscoR/man/gisco_countries.Rd |only giscoR-0.6.1/giscoR/man/gisco_get.Rd |only giscoR-0.6.1/giscoR/man/gisco_get_coastallines.Rd |only giscoR-0.6.1/giscoR/man/gisco_get_postalcodes.Rd |only giscoR-0.6.1/giscoR/man/gisco_nuts.Rd |only giscoR-0.6.1/giscoR/tests/testthat/_snaps/gisco_attributions.md |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_addressapi.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_attributions.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_bulk_download.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_cache.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_airports.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_coastallines.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_communes.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_countries.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_education.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_grid.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_healthcare.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_lau.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_nuts.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_postalcodes.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_units.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_urban_audit.R |only giscoR-1.0.0/giscoR/DESCRIPTION | 29 giscoR-1.0.0/giscoR/MD5 | 230 +++- giscoR-1.0.0/giscoR/NAMESPACE | 34 giscoR-1.0.0/giscoR/NEWS.md | 274 ++++- giscoR-1.0.0/giscoR/R/data.R | 483 +++++----- giscoR-1.0.0/giscoR/R/docs.R |only giscoR-1.0.0/giscoR/R/gisco-address-api.R |only giscoR-1.0.0/giscoR/R/gisco-attributions.R |only giscoR-1.0.0/giscoR/R/gisco-bulk-download.R |only giscoR-1.0.0/giscoR/R/gisco-cache.R |only giscoR-1.0.0/giscoR/R/gisco-check-access.R |only giscoR-1.0.0/giscoR/R/gisco-get-airports.R |only giscoR-1.0.0/giscoR/R/gisco-get-cached-db.R |only giscoR-1.0.0/giscoR/R/gisco-get-census.R |only giscoR-1.0.0/giscoR/R/gisco-get-coastal-lines.R |only giscoR-1.0.0/giscoR/R/gisco-get-communes.R |only giscoR-1.0.0/giscoR/R/gisco-get-countries.R |only giscoR-1.0.0/giscoR/R/gisco-get-education.R |only giscoR-1.0.0/giscoR/R/gisco-get-grid.R |only giscoR-1.0.0/giscoR/R/gisco-get-healthcare.R |only giscoR-1.0.0/giscoR/R/gisco-get-lau.R |only giscoR-1.0.0/giscoR/R/gisco-get-metadata.R |only giscoR-1.0.0/giscoR/R/gisco-get-nuts.R |only giscoR-1.0.0/giscoR/R/gisco-get-ports.R |only giscoR-1.0.0/giscoR/R/gisco-get-postal-codes.R |only giscoR-1.0.0/giscoR/R/gisco-get-unit-country.R |only giscoR-1.0.0/giscoR/R/gisco-get-unit-nuts.R |only giscoR-1.0.0/giscoR/R/gisco-get-unit-urban-audit.R |only giscoR-1.0.0/giscoR/R/gisco-get-units.R |only giscoR-1.0.0/giscoR/R/gisco-get-urban-audit.R |only giscoR-1.0.0/giscoR/R/gisco-id-api.R |only giscoR-1.0.0/giscoR/R/giscoR-package.R | 9 giscoR-1.0.0/giscoR/R/utils-country.R |only giscoR-1.0.0/giscoR/R/utils-sf.R |only giscoR-1.0.0/giscoR/R/utils-url.R |only giscoR-1.0.0/giscoR/R/utils.R |only giscoR-1.0.0/giscoR/R/zzz.R |only giscoR-1.0.0/giscoR/README.md | 294 ++---- giscoR-1.0.0/giscoR/build/stage23.rdb |only giscoR-1.0.0/giscoR/build/vignette.rds |binary giscoR-1.0.0/giscoR/data/gisco_coastal_lines.rda |only giscoR-1.0.0/giscoR/data/gisco_countries_2024.rda |only giscoR-1.0.0/giscoR/data/gisco_countrycode.rda |binary giscoR-1.0.0/giscoR/data/gisco_db.rda |binary giscoR-1.0.0/giscoR/data/gisco_nuts_2024.rda |only giscoR-1.0.0/giscoR/inst/COPYRIGHTS | 186 ++- giscoR-1.0.0/giscoR/inst/WORDLIST | 65 - 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giscoR-1.0.0/giscoR/man/gisco_db.Rd | 37 giscoR-1.0.0/giscoR/man/gisco_get_airports.Rd | 133 -- giscoR-1.0.0/giscoR/man/gisco_get_cached_db.Rd |only giscoR-1.0.0/giscoR/man/gisco_get_census.Rd |only giscoR-1.0.0/giscoR/man/gisco_get_coastal_lines.Rd |only giscoR-1.0.0/giscoR/man/gisco_get_communes.Rd |only giscoR-1.0.0/giscoR/man/gisco_get_countries.Rd |only giscoR-1.0.0/giscoR/man/gisco_get_education.Rd | 131 +- giscoR-1.0.0/giscoR/man/gisco_get_grid.Rd | 63 - giscoR-1.0.0/giscoR/man/gisco_get_healthcare.Rd | 141 +- giscoR-1.0.0/giscoR/man/gisco_get_lau.Rd | 174 +-- giscoR-1.0.0/giscoR/man/gisco_get_metadata.Rd |only giscoR-1.0.0/giscoR/man/gisco_get_nuts.Rd | 175 ++- giscoR-1.0.0/giscoR/man/gisco_get_ports.Rd |only giscoR-1.0.0/giscoR/man/gisco_get_postal_codes.Rd |only giscoR-1.0.0/giscoR/man/gisco_get_unit.Rd |only giscoR-1.0.0/giscoR/man/gisco_get_units.Rd | 172 +-- giscoR-1.0.0/giscoR/man/gisco_get_urban_audit.Rd | 140 +- giscoR-1.0.0/giscoR/man/gisco_id_api.Rd |only giscoR-1.0.0/giscoR/man/gisco_nuts_2024.Rd |only giscoR-1.0.0/giscoR/man/gisco_set_cache_dir.Rd | 78 + giscoR-1.0.0/giscoR/man/roxygen |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/docs.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-address-api.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-attributions.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-bulk-download.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-cache.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-cached-db.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-coastal-lines.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-communes.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-countries.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-lau.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-metadata.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-nuts.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-postal-codes.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-unit-country.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-unit-nuts.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-unit-urban-audit.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-units.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-urban-audit.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-id-api.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/utils-country.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/utils-url.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/utils.md |only giscoR-1.0.0/giscoR/tests/testthat/test-docs.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-address-api.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-attributions.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-bulk-download.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-cache.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-check-access.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-airports.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-cached-db.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-census.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-coastal-lines.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-communes.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-countries.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-education.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-grid.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-healthcare.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-lau.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-metadata.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-nuts.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-ports.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-postal-codes.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-unit-country.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-unit-nuts.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-unit-urban-audit.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-units.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-urban-audit.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-id-api.R |only giscoR-1.0.0/giscoR/tests/testthat/test-issues.R |only giscoR-1.0.0/giscoR/tests/testthat/test-utils-country.R |only giscoR-1.0.0/giscoR/tests/testthat/test-utils-sf.R |only giscoR-1.0.0/giscoR/tests/testthat/test-utils-url.R |only giscoR-1.0.0/giscoR/tests/testthat/test-utils.R | 229 +++- giscoR-1.0.0/giscoR/vignettes/africa-1.png |binary giscoR-1.0.0/giscoR/vignettes/country-1.png |binary giscoR-1.0.0/giscoR/vignettes/giscoR-1.png |binary giscoR-1.0.0/giscoR/vignettes/giscoR.Rmd | 222 ++-- 195 files changed, 2356 insertions(+), 1941 deletions(-)
Title: Methods to Convert R Data to YAML and Back
Description: Implements the 'libyaml' 'YAML' 1.1 parser and emitter
(<https://pyyaml.org/wiki/LibYAML>) for R.
Author: Hadley Wickham [cre] ,
Shawn Garbett [ctb] ,
Jeremy Stephens [aut, ctb],
Kirill Simonov [aut],
Yihui Xie [ctb] ,
Zhuoer Dong [ctb],
Jeffrey Horner [ctb],
reikoch [ctb],
Will Beasley [ctb] ,
Brendan O'Connor [ctb],
Michael Quinn [ctb],
Charlie Gao [ct [...truncated...]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between yaml versions 2.3.11 dated 2025-11-28 and 2.3.12 dated 2025-12-10
yaml-2.3.11/yaml/inst/CHANGELOG |only yaml-2.3.11/yaml/inst/implicit.re |only yaml-2.3.11/yaml/inst/tests |only yaml-2.3.11/yaml/tests/RUnit.R |only yaml-2.3.12/yaml/DESCRIPTION | 72 +++++------ yaml-2.3.12/yaml/MD5 | 61 +++++---- yaml-2.3.12/yaml/NAMESPACE | 9 + yaml-2.3.12/yaml/NEWS.md |only yaml-2.3.12/yaml/R/as.yaml.R | 146 +++++++++++++++++++++- yaml-2.3.12/yaml/R/read_yaml.R | 85 +++++++++++-- yaml-2.3.12/yaml/R/verbatim_logical.R | 21 +++ yaml-2.3.12/yaml/R/write_yaml.R | 42 +++++- yaml-2.3.12/yaml/R/yaml-package.R |only yaml-2.3.12/yaml/R/yaml.load.R | 154 ++++++++++++++++++++++- yaml-2.3.12/yaml/R/yaml.load_file.R | 22 ++- yaml-2.3.12/yaml/README.md |only yaml-2.3.12/yaml/build |only yaml-2.3.12/yaml/inst/doc |only yaml-2.3.12/yaml/man/as.yaml.Rd | 155 ++++++++++++++---------- yaml-2.3.12/yaml/man/read_yaml.Rd | 97 +++++++++------ yaml-2.3.12/yaml/man/verbatim_logical.Rd | 49 +++---- yaml-2.3.12/yaml/man/write_yaml.Rd | 44 ++++-- yaml-2.3.12/yaml/man/yaml-package.Rd |only yaml-2.3.12/yaml/man/yaml.load.Rd | 200 +++++++++++++++++-------------- yaml-2.3.12/yaml/src/r_emit.c | 10 - yaml-2.3.12/yaml/src/r_ext.c | 8 - yaml-2.3.12/yaml/src/r_ext.h | 4 yaml-2.3.12/yaml/src/r_parse.c | 12 - yaml-2.3.12/yaml/tests/testthat |only yaml-2.3.12/yaml/tests/testthat.R |only yaml-2.3.12/yaml/vignettes |only 31 files changed, 842 insertions(+), 349 deletions(-)
Title: Variable Importance Plots
Description: A general framework for constructing variable importance plots from
various types of machine learning models in R. Aside from some standard model-
specific variable importance measures, this package also provides model-
agnostic approaches that can be applied to any supervised learning algorithm.
These include 1) an efficient permutation-based variable importance measure,
2) variable importance based on Shapley values (Strumbelj and Kononenko,
2014) <doi:10.1007/s10115-013-0679-x>, and 3) the variance-based
approach described in Greenwell et al. (2018) <doi:10.48550/arXiv.1805.04755>. A
variance-based method for quantifying the relative strength of interaction
effects is also included (see the previous reference for details).
Author: Brandon M. Greenwell [aut, cre] ,
Brad Boehmke [aut]
Maintainer: Brandon M. Greenwell <greenwell.brandon@gmail.com>
Diff between vip versions 0.4.2 dated 2025-12-02 and 0.4.3 dated 2025-12-10
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 +++- inst/tinytest/test_pkg_lightgbm.R | 3 +++ inst/tinytest/test_vi_firm.R | 3 +++ inst/tinytest/test_vi_permute.R | 3 +++ 6 files changed, 20 insertions(+), 9 deletions(-)
Title: Targeted Inference
Description: Various methods for targeted and semiparametric inference including
augmented inverse probability weighted (AIPW) estimators for missing data and
causal inference (Bang and Robins (2005) <doi:10.1111/j.1541-0420.2005.00377.x>),
variable importance and conditional average treatment effects (CATE)
(van der Laan (2006) <doi:10.2202/1557-4679.1008>),
estimators for risk differences and relative risks (Richardson et al. (2017)
<doi:10.1080/01621459.2016.1192546>), assumption lean inference for generalized
linear model parameters (Vansteelandt et al. (2022) <doi:10.1111/rssb.12504>).
Author: Klaus K. Holst [aut, cre],
Benedikt Sommer [aut],
Andreas Nordland [aut],
Christian B. Pipper [ctb]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between targeted versions 0.6 dated 2025-10-30 and 0.7 dated 2025-12-10
targeted-0.6/targeted/inst/doc/predictionclass.Rmd |only targeted-0.6/targeted/inst/doc/riskregression.Rmd |only targeted-0.6/targeted/inst/tinytest/test_test_sw.R |only targeted-0.6/targeted/vignettes/predictionclass.Rmd |only targeted-0.6/targeted/vignettes/riskregression.Rmd |only targeted-0.7/targeted/DESCRIPTION | 35 targeted-0.7/targeted/MD5 | 98 targeted-0.7/targeted/NAMESPACE | 6 targeted-0.7/targeted/NEWS.md | 54 targeted-0.7/targeted/R/RcppExports.R | 4 targeted-0.7/targeted/R/calibration.R | 10 targeted-0.7/targeted/R/cate.R | 6 targeted-0.7/targeted/R/cumhaz.R | 30 targeted-0.7/targeted/R/design.R | 134 - targeted-0.7/targeted/R/intsurv.R | 2 targeted-0.7/targeted/R/learner.R | 3 targeted-0.7/targeted/R/learner_sl.R | 2 targeted-0.7/targeted/R/learner_stratify.R | 2 targeted-0.7/targeted/R/learner_xgboost.R | 34 targeted-0.7/targeted/R/naivebayes.R | 51 targeted-0.7/targeted/R/riskreg.R | 2 targeted-0.7/targeted/R/targeted-package.R | 2 targeted-0.7/targeted/R/test_intersection_sw.R | 208 + targeted-0.7/targeted/R/truncatedscore.R | 7 targeted-0.7/targeted/build/partial.rdb |binary targeted-0.7/targeted/build/vignette.rds |binary targeted-0.7/targeted/inst/doc/predictionclass.R | 36 targeted-0.7/targeted/inst/doc/predictionclass.html | 1196 +++++----- targeted-0.7/targeted/inst/doc/predictionclass.qmd |only targeted-0.7/targeted/inst/doc/riskregression.R | 35 targeted-0.7/targeted/inst/doc/riskregression.html | 964 +++++--- targeted-0.7/targeted/inst/doc/riskregression.qmd |only targeted-0.7/targeted/inst/include/targeted_RcppExports.h | 8 targeted-0.7/targeted/inst/slowtest/test_sl.R | 50 targeted-0.7/targeted/inst/tinytest/test_cumhaz.R | 14 targeted-0.7/targeted/inst/tinytest/test_design.R | 198 + targeted-0.7/targeted/inst/tinytest/test_intersection_sw.R | 40 targeted-0.7/targeted/inst/tinytest/test_learner.R | 8 targeted-0.7/targeted/inst/tinytest/test_learner_glm.R | 2 targeted-0.7/targeted/inst/tinytest/test_learner_naivebayes.R | 6 targeted-0.7/targeted/inst/tinytest/test_learner_xgboost.R | 10 targeted-0.7/targeted/man/calibration.Rd | 2 targeted-0.7/targeted/man/design.Rd | 6 targeted-0.7/targeted/man/learner_xgboost.Rd | 25 targeted-0.7/targeted/man/naivebayes.Rd | 1 targeted-0.7/targeted/man/targeted-package.Rd | 5 targeted-0.7/targeted/man/test_intersection_sw.Rd | 42 targeted-0.7/targeted/man/test_zmax_onesided.Rd |only targeted-0.7/targeted/src/RcppExports.cpp | 17 targeted-0.7/targeted/src/target/include/target/dykstra.hpp | 9 targeted-0.7/targeted/src/target/src/dykstra.cpp | 17 targeted-0.7/targeted/src/utils_interface.cpp | 10 targeted-0.7/targeted/tests/tinytest.R | 4 targeted-0.7/targeted/vignettes/predictionclass.qmd |only targeted-0.7/targeted/vignettes/riskregression.qmd |only 55 files changed, 2170 insertions(+), 1225 deletions(-)
Title: RDF Library Bindings in R
Description: Provides methods to parse, query and serialize information
stored in the Resource Description Framework (RDF). RDF is described at <https://www.w3.org/TR/rdf-primer/>.
This package supports RDF by implementing an R interface to the Redland RDF C library,
described at <https://librdf.org/docs/api/index.html>. In brief, RDF provides a structured graph
consisting of Statements composed of Subject, Predicate, and Object Nodes.
Author: Matthew B. Jones [aut, cre] ,
Peter Slaughter [aut] ,
Jeroen Ooms [aut] ,
Carl Boettiger [aut] ,
Scott Chamberlain [ctb] ,
David Beckett [cph],
University of Bristol [cph],
Regents of the University of California [cph]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>
Diff between redland versions 1.0.17-18 dated 2024-02-23 and 1.0.17-19 dated 2025-12-10
DESCRIPTION | 22 ++++++++++++---------- MD5 | 21 +++++++++++++++------ NEWS | 7 +++++++ R/redland-package.R | 20 +++++++++++++------- build/vignette.rds |binary inst/Makefile |only inst/config.log |only inst/config.status |only inst/doc/redland_overview.html | 5 +++-- src/redland.c | 6 +++--- tools/Makefile |only tools/NEWS |only tools/README |only tools/aclocal.m4 |only tools/config.log |only tools/config.status |only 16 files changed, 53 insertions(+), 28 deletions(-)
Title: Selection of Linear Estimators
Description: Estimate the mean of a Gaussian vector, by choosing among a large collection of estimators,
following the method developed by Y. Baraud, C. Giraud and S. Huet (2014) <doi:10.1214/13-AIHP539>.
In particular it solves the problem of variable selection by choosing the best predictor among predictors emanating from different methods as lasso,
elastic-net, adaptive lasso, pls, randomForest. Moreover, it can be applied for choosing the tuning parameter in a Gauss-lasso procedure.
Author: Yannick Baraud [aut],
Christophe Giraud [aut],
Sylvie Huet [aut],
Benjamin Auder [cre]
Maintainer: Benjamin Auder <benjamin.auder@universite-paris-saclay.fr>
Diff between LINselect versions 1.1.5 dated 2023-12-07 and 1.1.6 dated 2025-12-10
DESCRIPTION | 19 +++++++++++++------ MD5 | 4 ++-- man/VARselect.Rd | 2 +- 3 files changed, 16 insertions(+), 9 deletions(-)
Title: DBI Package for the DuckDB Database Management System
Description: The DuckDB project is an embedded analytical data management
system with support for the Structured Query Language (SQL). This
package includes all of DuckDB and an R Database Interface (DBI)
connector.
Author: Hannes Muehleisen [aut] ,
Mark Raasveldt [aut] ,
Kirill Mueller [cre] ,
Stichting DuckDB Foundation [cph],
Apache Software Foundation [cph],
PostgreSQL Global Development Group [cph],
The Regents of the University of California [cph],
Cameron Desrocher [...truncated...]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between duckdb versions 1.4.2 dated 2025-11-17 and 1.4.3 dated 2025-12-10
DESCRIPTION | 6 MD5 | 48 - NEWS.md | 21 R/backend-dbplyr__duckdb_connection.R | 18 R/duckdb.R | 6 R/version.R | 2 src/altrepdataframe_relation.dd | 665 ------------- src/connection.dd | 666 ------------- src/convert.dd | 661 ------------- src/database.dd | 668 -------------- src/duckdb.tar.xz |binary src/include/rapi.hpp | 2 src/register.dd | 700 -------------- src/relational.dd | 709 -------------- src/reltoaltrep.dd | 761 --------------- src/rfuns.dd | 654 ------------- src/scan.dd | 664 ------------- src/statement.dd | 762 ---------------- src/transform.dd | 663 ------------- src/types.dd | 663 ------------- src/utils.cpp | 17 src/utils.dd | 671 -------------- tests/testthat/_snaps/error-handling.md | 2 tests/testthat/_snaps/sql.md | 7 tests/testthat/test-backend-dbplyr__duckdb_connection.R | 31 25 files changed, 107 insertions(+), 8960 deletions(-)