Title: Confidence Estimation of Environmental State Classifications
Description: Functions for estimating and reporting multi-year averages and
corresponding confidence intervals and distributions. A potential use case
is reporting the chemical and ecological status of surface waters according
to the European Water Framework Directive.
Author: Willem van Loon [aut, cph],
Dennis Walvoort [aut, cre]
Maintainer: Dennis Walvoort <dennis.Walvoort@wur.nl>
Diff between confidence versions 1.1-2 dated 2017-07-01 and 1.1-3 dated 2025-07-04
DESCRIPTION | 22 MD5 | 29 - NAMESPACE | 4 R/confidence.R | 20 R/datasets.R | 144 +++--- R/utils.R | 1042 +++++++++++++++++++++++----------------------- build/vignette.rds |binary inst/NEWS.Rd | 63 +- inst/doc/confidence.R | 48 +- inst/doc/confidence.pdf |binary man/DCA.Rd | 28 - man/EQR.Rd | 28 - man/confidence-package.Rd | 22 man/metal.Rd | 32 - man/mya.Rd | 14 man/write_html.Rd |only 16 files changed, 750 insertions(+), 746 deletions(-)
Title: Interface to 'Python' Package 'StepMix'
Description: This is an interface for the 'Python' package
'StepMix'. It is a 'Python' package following the scikit-learn API for
model-based clustering and generalized mixture modeling (latent class/profile
analysis) of continuous and categorical data. 'StepMix' handles missing values
through Full Information Maximum Likelihood (FIML) and provides multiple stepwise
Expectation-Maximization (EM) estimation methods based on pseudolikelihood
theory. Additional features include support for covariates and distal outcomes,
various simulation utilities, and non-parametric bootstrapping, which allows
inference in semi-supervised and unsupervised settings. Software paper available
at <doi:10.18637/jss.v113.i08>.
Author: Eric Lacourse [aut],
Roxane de la Sablonniere [aut],
Charles-Edouard Giguere [aut, cre],
Sacha Morin [aut],
Robin Legault [aut],
Felix Laliberte [aut],
Zsusza Bakk [ctb]
Maintainer: Charles-Edouard Giguere <ce.giguere@gmail.com>
Diff between stepmixr versions 0.1.2 dated 2024-01-09 and 0.1.3 dated 2025-07-04
DESCRIPTION | 11 ++++++----- MD5 | 19 ++++++++++--------- inst |only man/bootstrap.Rd | 5 +++++ man/bootstrap_stats.Rd | 5 +++++ man/fit.Rd | 5 +++++ man/install.stepmix.Rd | 5 +++++ man/mixed_descriptor.Rd | 5 +++++ man/predict.Rd | 5 +++++ man/savefit.Rd | 5 +++++ man/stepmix.Rd | 5 +++++ 11 files changed, 56 insertions(+), 14 deletions(-)
Title: Automate the Delineation of Urban River Spaces
Description: Provides tools to automate the morphological delineation of
riverside urban areas, based on a method introduced in Forgaci (2018)
<doi:10.7480/abe.2018.31>. Delineation entails the identification of
corridor boundaries, segmentation of the corridor, and delineation of
the river space. The resulting delineation can be used to characterise
spatial phenomena that can be related to the river as a central element.
Author: Claudiu Forgaci [aut, cre, cph] ,
Francesco Nattino [aut] ,
Fakhereh Alidoost [ctb] ,
Meiert Willem Grootes [ctb] ,
Netherlands eScience Center [fnd]
Maintainer: Claudiu Forgaci <c.forgaci@tudelft.nl>
Diff between rcrisp versions 0.1.3 dated 2025-07-02 and 0.1.4 dated 2025-07-04
rcrisp-0.1.3/rcrisp/inst/doc/corridor-delineation.R |only rcrisp-0.1.3/rcrisp/inst/doc/corridor-delineation.Rmd |only rcrisp-0.1.3/rcrisp/inst/doc/corridor-delineation.html |only rcrisp-0.1.3/rcrisp/inst/doc/corridor-segmentation.R |only rcrisp-0.1.3/rcrisp/inst/doc/corridor-segmentation.Rmd |only rcrisp-0.1.3/rcrisp/inst/doc/corridor-segmentation.html |only rcrisp-0.1.3/rcrisp/inst/doc/getting-osm-data.R |only rcrisp-0.1.3/rcrisp/inst/doc/getting-osm-data.Rmd |only rcrisp-0.1.3/rcrisp/inst/doc/getting-osm-data.html |only rcrisp-0.1.3/rcrisp/inst/doc/method.R |only rcrisp-0.1.3/rcrisp/inst/doc/method.Rmd |only rcrisp-0.1.3/rcrisp/inst/doc/method.html |only rcrisp-0.1.3/rcrisp/inst/doc/network-preparation.R |only rcrisp-0.1.3/rcrisp/inst/doc/network-preparation.Rmd |only rcrisp-0.1.3/rcrisp/inst/doc/network-preparation.html |only rcrisp-0.1.3/rcrisp/inst/doc/riverspace-delineation.R |only rcrisp-0.1.3/rcrisp/inst/doc/riverspace-delineation.Rmd |only rcrisp-0.1.3/rcrisp/inst/doc/riverspace-delineation.html |only rcrisp-0.1.3/rcrisp/inst/doc/valley-delineation.R |only rcrisp-0.1.3/rcrisp/inst/doc/valley-delineation.Rmd |only rcrisp-0.1.3/rcrisp/inst/doc/valley-delineation.html |only rcrisp-0.1.3/rcrisp/vignettes/corridor-delineation.Rmd |only rcrisp-0.1.3/rcrisp/vignettes/corridor-segmentation.Rmd |only rcrisp-0.1.3/rcrisp/vignettes/getting-osm-data.Rmd |only rcrisp-0.1.3/rcrisp/vignettes/method.Rmd |only rcrisp-0.1.3/rcrisp/vignettes/network-preparation.Rmd |only rcrisp-0.1.3/rcrisp/vignettes/riverspace-delineation.Rmd |only rcrisp-0.1.3/rcrisp/vignettes/valley-delineation.Rmd |only rcrisp-0.1.4/rcrisp/DESCRIPTION | 9 - rcrisp-0.1.4/rcrisp/MD5 | 72 +++++----- rcrisp-0.1.4/rcrisp/NEWS.md | 15 +- rcrisp-0.1.4/rcrisp/R/cache.R | 3 rcrisp-0.1.4/rcrisp/R/zzz.R | 2 rcrisp-0.1.4/rcrisp/README.md | 3 rcrisp-0.1.4/rcrisp/build/vignette.rds |binary rcrisp-0.1.4/rcrisp/inst/doc/vig_01-method.R |only rcrisp-0.1.4/rcrisp/inst/doc/vig_01-method.Rmd |only rcrisp-0.1.4/rcrisp/inst/doc/vig_01-method.html |only rcrisp-0.1.4/rcrisp/inst/doc/vig_02-getting-osm-data.R |only rcrisp-0.1.4/rcrisp/inst/doc/vig_02-getting-osm-data.Rmd |only rcrisp-0.1.4/rcrisp/inst/doc/vig_02-getting-osm-data.html |only rcrisp-0.1.4/rcrisp/inst/doc/vig_03-network-preparation.R |only rcrisp-0.1.4/rcrisp/inst/doc/vig_03-network-preparation.Rmd |only rcrisp-0.1.4/rcrisp/inst/doc/vig_03-network-preparation.html |only rcrisp-0.1.4/rcrisp/inst/doc/vig_04-valley-delineation.R |only rcrisp-0.1.4/rcrisp/inst/doc/vig_04-valley-delineation.Rmd |only rcrisp-0.1.4/rcrisp/inst/doc/vig_04-valley-delineation.html |only rcrisp-0.1.4/rcrisp/inst/doc/vig_05-corridor-delineation.R |only rcrisp-0.1.4/rcrisp/inst/doc/vig_05-corridor-delineation.Rmd |only rcrisp-0.1.4/rcrisp/inst/doc/vig_05-corridor-delineation.html |only rcrisp-0.1.4/rcrisp/inst/doc/vig_06-corridor-segmentation.R |only rcrisp-0.1.4/rcrisp/inst/doc/vig_06-corridor-segmentation.Rmd |only rcrisp-0.1.4/rcrisp/inst/doc/vig_06-corridor-segmentation.html |only rcrisp-0.1.4/rcrisp/inst/doc/vig_07-riverspace-delineation.R |only rcrisp-0.1.4/rcrisp/inst/doc/vig_07-riverspace-delineation.Rmd |only rcrisp-0.1.4/rcrisp/inst/doc/vig_07-riverspace-delineation.html |only rcrisp-0.1.4/rcrisp/man/figures/README-example-1.png |binary rcrisp-0.1.4/rcrisp/tests/testthat/test-cache.R | 4 rcrisp-0.1.4/rcrisp/vignettes/vig_01-method.Rmd |only rcrisp-0.1.4/rcrisp/vignettes/vig_02-getting-osm-data.Rmd |only rcrisp-0.1.4/rcrisp/vignettes/vig_03-network-preparation.Rmd |only rcrisp-0.1.4/rcrisp/vignettes/vig_04-valley-delineation.Rmd |only rcrisp-0.1.4/rcrisp/vignettes/vig_05-corridor-delineation.Rmd |only rcrisp-0.1.4/rcrisp/vignettes/vig_06-corridor-segmentation.Rmd |only rcrisp-0.1.4/rcrisp/vignettes/vig_07-riverspace-delineation.Rmd |only 65 files changed, 62 insertions(+), 46 deletions(-)
Title: Coloured Formatting for Columns
Description: Provides 'pillar' and 'colonnade' generics designed
for formatting columns of data using the full range of colours
provided by modern terminals.
Author: Kirill Mueller [aut, cre] ,
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between pillar versions 1.10.2 dated 2025-04-05 and 1.11.0 dated 2025-07-04
DESCRIPTION | 9 +++-- MD5 | 20 ++++++------- NEWS.md | 23 +++++++++++++++ R/shaft-.R | 9 +++++ R/sigfig.R | 35 +++++++++++++++++++--- R/utils.R | 5 ++- build/vignette.rds |binary inst/doc/printing.html | 4 +- tests/testthat/_snaps/format_decimal.md | 31 ++++++++++++++++++++ tests/testthat/test-format_decimal.R | 49 ++++++++++++++++++++++++++++++-- tests/testthat/test-ggplot2.R | 2 - 11 files changed, 161 insertions(+), 26 deletions(-)
Title: Visualizing Pedigrees with 'ggplot2' and 'plotly'
Description: Provides plotting functions for visualizing pedigrees in behavior genetics and kinship research. The package complements 'BGmisc' [Garrison et al. (2024) <doi:10.21105/joss.06203>] by rendering pedigrees using the 'ggplot2' framework and offers a modern alternative to the base-graphics pedigree plot in 'kinship2' [Sinnwell et al. (2014) <doi:10.1159/000363105>]. Features include support for duplicated individuals, complex mating structures, integration with simulated pedigrees, and layout customization.
Author: S. Mason Garrison [aut, cre, cph]
Maintainer: S. Mason Garrison <garrissm@wfu.edu>
Diff between ggpedigree versions 0.7.0 dated 2025-06-09 and 0.8.0 dated 2025-07-04
ggpedigree-0.7.0/ggpedigree/man/computeCurvedMidpoint.Rd |only ggpedigree-0.8.0/ggpedigree/DESCRIPTION | 17 ggpedigree-0.8.0/ggpedigree/MD5 | 84 +- ggpedigree-0.8.0/ggpedigree/NAMESPACE | 27 ggpedigree-0.8.0/ggpedigree/NEWS.md | 19 ggpedigree-0.8.0/ggpedigree/R/calcConnectionsHelpers.R | 6 ggpedigree-0.8.0/ggpedigree/R/defaultPlotConfig.R | 65 + ggpedigree-0.8.0/ggpedigree/R/describeHelpers.R | 3 ggpedigree-0.8.0/ggpedigree/R/documentData.R | 28 ggpedigree-0.8.0/ggpedigree/R/ggPedigreeInteractive.R | 2 ggpedigree-0.8.0/ggpedigree/R/ggPhenotypeByDegree.R | 13 ggpedigree-0.8.0/ggpedigree/R/ggRelatednessMatrix.R | 20 ggpedigree-0.8.0/ggpedigree/R/ggpedigree.R | 346 ++++------ ggpedigree-0.8.0/ggpedigree/R/ggpedigreeHelpers.R |only ggpedigree-0.8.0/ggpedigree/R/processExtras.R | 3 ggpedigree-0.8.0/ggpedigree/README.md | 31 ggpedigree-0.8.0/ggpedigree/data/ASOIAF.rda |only ggpedigree-0.8.0/ggpedigree/inst/doc/v00_plots.R | 1 ggpedigree-0.8.0/ggpedigree/inst/doc/v00_plots.Rmd | 1 ggpedigree-0.8.0/ggpedigree/inst/doc/v00_plots.html | 17 ggpedigree-0.8.0/ggpedigree/inst/doc/v10_interactiveplots.html | 4 ggpedigree-0.8.0/ggpedigree/inst/doc/v20_matrix.html | 26 ggpedigree-0.8.0/ggpedigree/man/ASOIAF.Rd |only ggpedigree-0.8.0/ggpedigree/man/calculateConnections.Rd | 4 ggpedigree-0.8.0/ggpedigree/man/calculateCoordinates.Rd | 2 ggpedigree-0.8.0/ggpedigree/man/dot-addLabels.Rd | 5 ggpedigree-0.8.0/ggpedigree/man/dot-addNodes.Rd | 5 ggpedigree-0.8.0/ggpedigree/man/dot-addOverlay.Rd | 5 ggpedigree-0.8.0/ggpedigree/man/dot-addScales.Rd | 5 ggpedigree-0.8.0/ggpedigree/man/dot-addSelfSegment.Rd | 5 ggpedigree-0.8.0/ggpedigree/man/dot-adjustSpacing.Rd |only ggpedigree-0.8.0/ggpedigree/man/dot-computeCurvedMidpoint.Rd |only ggpedigree-0.8.0/ggpedigree/man/dot-restoreNames.Rd |only ggpedigree-0.8.0/ggpedigree/man/figures/README-basic-usage-1.png |only ggpedigree-0.8.0/ggpedigree/man/getDefaultPlotConfig.Rd | 25 ggpedigree-0.8.0/ggpedigree/man/getRelativeCoordinates.Rd | 2 ggpedigree-0.8.0/ggpedigree/man/ggPedigree.Rd | 13 ggpedigree-0.8.0/ggpedigree/man/ggPedigree.core.Rd | 12 ggpedigree-0.8.0/ggpedigree/man/ggPedigreeInteractive.Rd | 14 ggpedigree-0.8.0/ggpedigree/tests/testthat/Rplots.pdf |binary ggpedigree-0.8.0/ggpedigree/tests/testthat/test-defaultPlotConfig.R | 73 +- ggpedigree-0.8.0/ggpedigree/tests/testthat/test-documentData.R | 19 ggpedigree-0.8.0/ggpedigree/tests/testthat/test-ggPedigree.R | 20 ggpedigree-0.8.0/ggpedigree/tests/testthat/test-ggPedigreeInteractive.R | 6 ggpedigree-0.8.0/ggpedigree/tests/testthat/test-ggPhenotypeByDegree.R | 2 ggpedigree-0.8.0/ggpedigree/tests/testthat/test-ggRelatednessMatrix.R | 4 ggpedigree-0.8.0/ggpedigree/vignettes/v00_plots.Rmd | 1 47 files changed, 591 insertions(+), 344 deletions(-)
Title: Workflows for Health Technology Assessments in R using Discrete
EveNts
Description: Toolkit to support and perform discrete event simulations without
resource constraints in the context of health technology assessments (HTA).
The package focuses on cost-effectiveness modelling and aims to be submission-ready
to relevant HTA bodies in alignment with 'NICE TSD 15'
<https://www.sheffield.ac.uk/nice-dsu/tsds/patient-level-simulation>.
More details an examples can be found in the package website <https://jsanchezalv.github.io/WARDEN/>.
Author: Javier Sanchez Alvarez [aut, cre],
Gabriel Lemyre [ctb],
Valerie Aponte Ribero [ctb]
Maintainer: Javier Sanchez Alvarez <javiersanchezeco@gmail.com>
Diff between WARDEN versions 1.2.2 dated 2025-06-25 and 1.2.4 dated 2025-07-04
DESCRIPTION | 10 - MD5 | 34 ++- NAMESPACE | 13 + NEWS.md | 10 + R/calculator_f.R | 289 ++++++++++++++++++++++++++++++++ R/engine_helper_f.R | 82 ++++----- R/input_f.R | 85 +++++++++ R/results_summary_f.R | 10 - R/run_engine.R | 9 - R/run_sim.R | 3 R/run_sim_parallel.R | 2 inst/doc/example_ssd.html | 288 ++++++++++++++++---------------- man/adj_val.Rd |only man/qcond_gamma.Rd | 8 man/qcond_weibullPH.Rd |only man/qtimecov.Rd |only man/run_sim.Rd | 2 man/run_sim_parallel.Rd | 2 tests/testthat/test-input_f.R | 348 ++++++++++++++++++++++++++++++++++++++- tests/testthat/test_model_runs.R |only 20 files changed, 966 insertions(+), 229 deletions(-)
Title: Post-Selection Inference for Adjusted R Squared
Description: Conduct post-selection inference for regression coefficients in linear models after they have been selected by adjusted R squared. The p-values and confidence intervals are valid after model selection with the same data. This allows the user to use all data for both model selection and inference without losing control over the type I error rate. The provided tests are more powerful than data splitting, which bases inference on less data since it discards all information used for selection.
Author: Sarah Pirenne [aut, cre] ,
Gerda Claeskens [aut]
Maintainer: Sarah Pirenne <sarah.pirenne@kuleuven.be>
Diff between PoSIAdjRSquared versions 0.0.0.1 dated 2024-08-26 and 0.1.0 dated 2025-07-04
DESCRIPTION | 9 ++-- MD5 | 9 ++-- NAMESPACE | 2 + R/functions.R | 84 +++++++++++++++++++++++++++++++++++++++++++++ README.md | 66 ++++++++--------------------------- man/selective_inference.Rd |only 6 files changed, 111 insertions(+), 59 deletions(-)
More information about PoSIAdjRSquared at CRAN
Permanent link
Title: A Framework for Clustering Longitudinal Data
Description: A framework for clustering longitudinal datasets in a standardized way.
The package provides an interface to existing R packages for clustering longitudinal univariate trajectories, facilitating reproducible and transparent analyses.
Additionally, standard tools are provided to support cluster analyses, including repeated estimation, model validation, and model assessment.
The interface enables users to compare results between methods, and to implement and evaluate new methods with ease.
The 'akmedoids' package is available from <https://github.com/MAnalytics/akmedoids>.
Author: Niek Den Teuling [aut, cre] ,
Steffen Pauws [ctb],
Edwin van den Heuvel [ctb],
Koninklijke Philips N.V. [cph]
Maintainer: Niek Den Teuling <niek.den.teuling@philips.com>
Diff between latrend versions 1.6.1 dated 2024-05-15 and 1.6.2 dated 2025-07-04
DESCRIPTION | 19 +++++++++-------- MD5 | 44 ++++++++++++++++++++-------------------- R/generics.R | 5 ++-- R/latrend.R | 2 - R/methodDtwclust.R | 3 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/demo.html | 22 ++++++++++---------- inst/doc/implement.html | 8 +++---- inst/doc/simulation.html | 10 ++++----- man/latrend-package.Rd | 6 ++--- man/latrend.Rd | 2 - man/latrendBatch.Rd | 2 - man/latrendBoot.Rd | 2 - man/latrendCV.Rd | 2 - man/latrendRep.Rd | 2 - man/lcMethodDtwclust.Rd | 3 +- man/meanNA.Rd | 2 - man/plot-lcModel-method.Rd | 2 - man/plot-lcModels-method.Rd | 2 - man/update.lcModel.Rd | 2 - tests/testthat/setup-init.R | 2 - tests/testthat/test-plot.R | 48 ++++++++++++++++++++++---------------------- 23 files changed, 97 insertions(+), 93 deletions(-)
Title: ADaM in R Asset Library - Ophthalmology
Description: Aids the programming of Clinical Data Standards Interchange
Consortium (CDISC) compliant Ophthalmology Analysis Data Model (ADaM)
datasets in R. ADaM datasets are a mandatory part of any New Drug or
Biologics License Application submitted to the United States Food and
Drug Administration (FDA). Analysis derivations are implemented in
accordance with the "Analysis Data Model Implementation Guide" (CDISC
Analysis Data Model Team, 2021,
<https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package>).
Author: Edoardo Mancini [aut, cre] ,
Ritika Aggarwal [aut],
Jane Gao [aut],
William Holmes [aut],
Josie Jackson [aut],
Sonali Jain [aut],
Yuki Matsunaga [aut],
Gordon Miller [aut],
Rachel Linacre [aut],
Lucy Palmen [aut],
Nandini R Thampi [aut],
Aldrich Salv [...truncated...]
Maintainer: Edoardo Mancini <edoardo.mancini@roche.com>
Diff between admiralophtha versions 1.2.0 dated 2025-01-16 and 1.3.0 dated 2025-07-04
DESCRIPTION | 20 +-- MD5 | 50 ++++---- NEWS.md | 33 +++++ R/data.R | 16 +- data/admiralophtha_adoe.rda |binary inst/WORDLIST | 3 inst/doc/adbcva.R | 35 +++-- inst/doc/adbcva.Rmd | 39 +++--- inst/doc/adbcva.html | 259 ++++++++++++++++++++++++++++---------------- inst/doc/adoe.R | 103 +++++++++++++++-- inst/doc/adoe.Rmd | 124 +++++++++++++++++++-- inst/doc/adoe.html | 220 +++++++++++++++++++++++++++++++++---- inst/doc/advfq.Rmd | 2 inst/doc/advfq.html | 1 inst/doc/standards.Rmd | 7 + inst/doc/standards.html | 19 ++- inst/templates/ad_adbcva.R | 38 +++--- inst/templates/ad_adoe.R | 97 ++++++++++++---- inst/templates/ad_advfq.R | 4 man/admiralophtha_adbcva.Rd | 4 man/admiralophtha_adoe.Rd | 6 - man/admiralophtha_advfq.Rd | 6 - vignettes/adbcva.Rmd | 39 +++--- vignettes/adoe.Rmd | 124 +++++++++++++++++++-- vignettes/advfq.Rmd | 2 vignettes/standards.Rmd | 7 + 26 files changed, 962 insertions(+), 296 deletions(-)
Title: Query Composite Hypotheses
Description: Provides functions for the joint analysis of Q sets of
p-values obtained for the same list of items. This joint analysis is
performed by querying a composite hypothesis, i.e. an arbitrary
complex combination of simple hypotheses, as described in Mary-Huard
et al. (2021) <doi:10.1093/bioinformatics/btab592> and De Walsche et
al.(2023) <doi:10.1101/2024.03.17.585412>. In this approach, the
Q-uplet of p-values associated with each item is distributed as a
multivariate mixture, where each of the 2^Q components corresponds to
a specific combination of simple hypotheses. The dependence between
the p-value series is considered using a Gaussian copula function. A
p-value for the composite hypothesis test is derived from the
posterior probabilities.
Author: Tristan Mary-Huard [aut, cre] ,
Annaig De Walsche [aut] ,
Franck Gauthier [ctb]
Maintainer: Tristan Mary-Huard <tristan.mary-huard@agroparistech.fr>
Diff between qch versions 2.0.0 dated 2024-03-29 and 2.1.0 dated 2025-07-04
DESCRIPTION | 17 - MD5 | 45 +- R/Data.R | 11 R/EM_functions.R | 503 ++++++++++++++++----------------- R/FastKerFDR_functions.R | 413 +++++++++++++++------------ R/GetHinfo.R | 218 ++++++++------ R/qch_fit.R | 358 ++++++++++++----------- R/qch_test.R | 259 ++++++++++------ inst |only man/Copula.Hconfig_gaussian_density.Rd | 12 man/EM_calibration_gaussian.Rd | 81 ++--- man/EM_calibration_gaussian_memory.Rd | 23 - man/EM_calibration_indep_memory.Rd | 6 man/FastKerFdr_signed.Rd | 75 +++- man/FastKerFdr_unsigned.Rd | 82 +++-- man/GetH1AtLeast.Rd | 62 ++-- man/GetH1Equal.Rd | 62 ++-- man/PvalSets_cor.Rd | 42 +- man/R.MLE.Rd | 6 man/R.MLE.memory.Rd | 12 man/f1_separation_signed.Rd | 64 ++-- man/gaussian_copula_density.Rd | 2 man/qch.fit.Rd | 15 man/qch.test.Rd | 20 - 24 files changed, 1316 insertions(+), 1072 deletions(-)
Title: Lean Analytics and Robust Exploration Sidekick
Description: Auxiliary package for better/faster analytics, visualization, data mining, and machine
learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling,
Marketing Mix Modeling (Robyn), Exploratory, API, and Scrapper, it helps the analyst or
data scientist to get quick and robust results, without the need of repetitive coding or
advanced R programming skills.
Author: Bernardo Lares [aut, cre]
Maintainer: Bernardo Lares <laresbernardo@gmail.com>
Diff between lares versions 5.3.0 dated 2025-06-25 and 5.3.1 dated 2025-07-04
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Title: SDTM Test Data for the 'Pharmaverse' Family of Packages
Description: A set of Study Data Tabulation Model (SDTM) datasets from the
Clinical Data Interchange Standards Consortium (CDISC) pilot project
used for testing and developing Analysis Data Model (ADaM) datasets
inside the pharmaverse family of packages. SDTM dataset specifications
are described in the CDISC SDTM implementation guide, accessible by
creating a free account on <https://www.cdisc.org/>.
Author: Edoardo Mancini [aut, cre] ,
Fanny Gautier [aut] ,
Gayatri G [aut],
Kangjie Zhang [aut],
Lina Patil [aut],
Pooja Kumari [aut],
Sadchla Mascary [aut],
Stefan Bundfuss [aut] ,
Tomoyuki Namai [aut],
Vinh Nguyen [aut],
Vladyslav Shuliar [aut] ,
Zelos Zhu [...truncated...]
Maintainer: Edoardo Mancini <edoardo.mancini@roche.com>
Diff between pharmaversesdtm versions 1.2.0 dated 2025-01-23 and 1.3.0 dated 2025-07-04
DESCRIPTION | 65 +++++++++------- MD5 | 166 ++++++++++++++++++++++------------------- NEWS.md | 42 ++++++++++ R/cm.R | 2 R/dm_metabolic.R |only R/eg.R | 18 +++- R/ex_vaccine.R | 4 R/face_vaccine.R | 7 + R/is_vaccine.R | 8 + R/lb.R | 51 ++++++++++++ R/lb_metabolic.R |only R/oe_ophtha.R | 8 + R/pc.R | 5 + R/pp.R | 14 +++ R/qs_metabolic.R |only R/qs_ophtha.R | 73 +++++++++++++----- R/rs_onco.R | 8 + R/rs_onco_ca125.R | 31 ++++--- R/rs_onco_imwg.R | 39 +++++---- R/rs_onco_irecist.R | 48 +++++++---- R/rs_onco_pcwg3.R |only R/rs_onco_recist.R | 33 ++++---- R/sc_ophtha.R | 5 + R/sdg_db.R | 10 +- R/smq_db.R | 12 +- R/supprs_onco_ca125.R | 18 ++-- R/supprs_onco_imwg.R | 18 ++-- R/tr_onco.R | 9 ++ R/tr_onco_recist.R | 45 ++++++----- R/tu_onco.R | 5 + R/tu_onco_recist.R | 37 +++++---- R/vs.R | 10 ++ R/vs_metabolic.R |only R/vs_peds.R | 8 + R/vs_vaccine.R | 5 + README.md | 15 --- data/cm.rda |binary data/dm_metabolic.rda |only data/eg.rda |binary data/ex_vaccine.rda |binary data/lb_metabolic.rda |only data/oe_ophtha.rda |binary data/qs_metabolic.rda |only data/qs_ophtha.rda |binary data/rs_onco_ca125.rda |binary data/rs_onco_imwg.rda |binary data/rs_onco_irecist.rda |binary data/rs_onco_pcwg3.rda |only data/rs_onco_recist.rda |binary data/sdg_db.rda |binary data/smq_db.rda |binary data/supprs_onco_ca125.rda |binary data/supprs_onco_imwg.rda |binary data/tr_onco_recist.rda |binary data/tu_onco_recist.rda |binary data/vs_metabolic.rda |only inst/WORDLIST | 147 ++++++++++++++++++++++++++++++++++++ inst/extdata/sdtms-specs.json | 31 +++++++ man/cm.Rd | 2 man/dm_metabolic.Rd |only man/eg.Rd | 18 +++- man/ex_vaccine.Rd | 4 man/face_vaccine.Rd | 7 + man/figures |only man/is_vaccine.Rd | 8 + man/lb.Rd | 51 ++++++++++++ man/lb_metabolic.Rd |only man/oe_ophtha.Rd | 8 + man/pc.Rd | 5 + man/pharmaversesdtm-package.Rd | 11 +- man/pp.Rd | 14 +++ man/qs_metabolic.Rd |only man/qs_ophtha.Rd | 73 +++++++++++++----- man/rs_onco.Rd | 8 + man/rs_onco_ca125.Rd | 31 ++++--- man/rs_onco_imwg.Rd | 39 +++++---- man/rs_onco_irecist.Rd | 48 +++++++---- man/rs_onco_pcwg3.Rd |only man/rs_onco_recist.Rd | 33 ++++---- man/sc_ophtha.Rd | 5 + man/sdg_db.Rd | 10 +- man/smq_db.Rd | 12 +- man/supprs_onco_ca125.Rd | 18 ++-- man/supprs_onco_imwg.Rd | 18 ++-- man/tr_onco.Rd | 9 ++ man/tr_onco_recist.Rd | 45 ++++++----- man/tu_onco.Rd | 5 + man/tu_onco_recist.Rd | 37 +++++---- man/vs.Rd | 10 ++ man/vs_metabolic.Rd |only man/vs_peds.Rd | 8 + man/vs_vaccine.Rd | 5 + 92 files changed, 1111 insertions(+), 428 deletions(-)
More information about pharmaversesdtm at CRAN
Permanent link
Title: Litter Analysis
Description: Data sets on various litter types like beach litter, riverain
litter, floating litter, and seafloor litter are rapidly growing. This
package offers a simple user interface to analyse these litter data in
a consistent and reproducible way. It also provides functions to
facilitate several kinds of litter analysis, e.g., trend analysis,
power analysis, and baseline analysis. Under the hood, these functions
are also used by the user interface. See Schulz et al. (2019)
<doi:10.1016/j.envpol.2019.02.030> for details. MS-Windows users are
advised to run 'litteR' in 'RStudio'. See our vignette: Installation manual
for 'RStudio' and 'litteR'.
Author: Dennis Walvoort [aut, cre, cph],
Willem van Loon [aut, cph],
Rijkswaterstaat - The Netherlands [cph, fnd, dtc]
Maintainer: Dennis Walvoort <dennis.Walvoort@wur.nl>
Diff between litteR versions 1.0.0 dated 2022-08-26 and 1.0.1 dated 2025-07-04
DESCRIPTION | 10 MD5 | 30 NEWS.md | 7 R/utils.R | 8 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/litteR-installation.Rmd | 2 inst/doc/litteR-installation.html | 32 inst/doc/litteR-manual.R | 40 inst/doc/litteR-manual.Rmd | 6 inst/doc/litteR-manual.html | 1780 +++++++++++--------------------------- man/is_natural_number.Rd | 2 man/list_duplicates.Rd | 6 vignettes/litteR-installation.Rmd | 2 vignettes/litteR-manual.Rmd | 6 16 files changed, 627 insertions(+), 1306 deletions(-)
Title: Visualisations for Generalized Additive Models
Description: Extension of the 'mgcv' package, providing visual tools for Generalized Additive Models that exploit the additive structure of such models, scale to large data sets and can be used in conjunction with a wide range of response distributions. The focus is providing visual methods for better understanding the model output and for aiding model checking and development beyond simple exponential family regression. The graphical framework is based on the layering system provided by 'ggplot2'.
Author: Matteo Fasiolo [aut, cre],
Raphael Nedellec [aut],
Yannig Goude [ctb],
Christian Capezza [ctb],
Simon N. Wood [ctb]
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>
Diff between mgcViz versions 0.2.0 dated 2025-04-11 and 0.2.1 dated 2025-07-04
DESCRIPTION | 13 MD5 | 16 NAMESPACE | 16 R/plotSlice.R | 2 R/shine.qqGam.R | 50 build/vignette.rds |binary inst/doc/mgcviz.R | 6 inst/doc/mgcviz.html | 9667 +++++++++++++++++++++++++++++++++++++++++++++++++-- man/shine.qqGam.Rd | 2 9 files changed, 9498 insertions(+), 274 deletions(-)
Title: Interval Censored Multi-State Models
Description: Allows for the non-parametric estimation of transition intensities in interval-censored
multi-state models using the approach of Gomon and Putter (2024) <doi:10.48550/arXiv.2409.07176> or
Gu et al. (2023) <doi:10.1093/biomet/asad073>.
Author: Daniel Gomon [aut, cre] ,
Hein Putter [aut]
Maintainer: Daniel Gomon <dgstatsoft@gmail.com>
Diff between icmstate versions 0.1.1 dated 2024-11-08 and 0.2.0 dated 2025-07-04
DESCRIPTION | 17 ++++--- MD5 | 63 +++++++++++++++++++++-------- NAMESPACE | 20 +++++++++ NEWS.md | 5 ++ R/Chapman_Kolmogorov.R |only R/Estep_smooth.R |only R/Mstep_smooth.R |only R/bbase.R |only R/crudeinit.R | 1 R/direct_from_observed_intervals.R | 1 R/interpolate_npfit.R | 55 ++++++++++++++++++++++--- R/npmsm.R | 9 +--- R/plot_methods.R | 34 +++++++++++++++ R/predict_tp.R |only R/probtrans_D.R | 4 + R/probtrans_coxph.R |only R/probtrans_subj_methods.R |only R/sim_weibmsm.R | 1 R/smoothmsm.R |only README.md | 20 +++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Overview.pdf |binary inst/doc/comparison-with-known-results.pdf |binary inst/doc/sim_msm.pdf |binary man/ChapKolm_fwd_smooth.Rd |only man/Estep_smooth.Rd |only man/Mstep_smooth.Rd |only man/baseline_intensities_from_coxmod.Rd |only man/bbase_D.Rd |only man/bbase_singletime.Rd |only man/expand_covariates_long_data.Rd |only man/extend_msfit.Rd |only man/figures |only man/npmsm.Rd | 8 +-- man/plot.probtrans.subjects.Rd |only man/plot.smoothmsm.Rd |only man/predict_tp.Rd |only man/print.summary.probtrans.subjects.Rd |only man/probtrans_coxph.Rd |only man/smoothmsm.Rd |only man/subject_specific_intensity_matrices.Rd |only man/subject_specific_intensity_matrix.Rd |only man/summary.probtrans.subjects.Rd |only man/trans_specific_risks.Rd |only tests/testthat/test-bbase.R |only tests/testthat/test-probtrans_coxph.R |only 47 files changed, 187 insertions(+), 51 deletions(-)
Title: Calibration Performance
Description: Plots calibration curves and computes statistics for assessing calibration performance. See De Cock Campo (2023) <doi:10.48550/arXiv.2309.08559> and Van Calster et al. (2016) <doi:10.1016/j.jclinepi.2015.12.005>.
Author: De Cock Bavo [aut, cre],
Nieboer Daan [aut],
Van Calster Ben [aut],
Steyerberg Ewout [aut],
Vergouwe Yvonne [aut]
Maintainer: De Cock Bavo <bavo.decock@kuleuven.be>
Diff between CalibrationCurves versions 2.0.4 dated 2025-01-18 and 2.0.6 dated 2025-07-04
DESCRIPTION | 10 - MD5 | 26 +++-- NAMESPACE | 11 +- R/printFunction.R | 39 +++++++ R/rcspline.plot.noprint.R | 16 +-- R/valProbSurvival.R |only data/testDataSurvival.rda |only data/trainDataSurvival.rda |only inst/doc/CalibrationCurves.R | 11 ++ inst/doc/CalibrationCurves.Rmd | 57 +++++++++++ inst/doc/CalibrationCurves.html | 173 ++++++++++++++++++++++++++-------- man/print.SurvivalCalibrationCurve.Rd |only man/survivaltraindata.Rd |only man/val.prob.ci.2.Rd | 2 man/valProbSurvival.Rd |only man/valProbggplot.Rd | 2 vignettes/CalibrationCurves.Rmd | 57 +++++++++++ 17 files changed, 337 insertions(+), 67 deletions(-)
More information about CalibrationCurves at CRAN
Permanent link
Title: Bayesian Cost Effectiveness Analysis
Description: Produces an economic evaluation of a sample of suitable variables of
cost and effectiveness / utility for two or more interventions,
e.g. from a Bayesian model in the form of MCMC simulations.
This package computes the most cost-effective alternative and
produces graphical summaries and probabilistic sensitivity analysis,
see Baio et al (2017) <doi:10.1007/978-3-319-55718-2>.
Author: Gianluca Baio [aut, cre, cph] ,
Andrea Berardi [aut] ,
Anna Heath [aut] ,
Nathan Green [aut]
Maintainer: Gianluca Baio <g.baio@ucl.ac.uk>
Diff between BCEA versions 2.4.7 dated 2025-01-14 and 2.4.8 dated 2025-07-04
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Title: Comparing and Visualizing Differences Between Surveys
Description: Easily analyze and visualize differences between samples (e.g., benchmark comparisons, nonresponse comparisons in surveys) on three levels. The comparisons can be univariate, bivariate or multivariate. On univariate level the variables of interest of a survey and a comparison survey (i.e. benchmark) are compared, by calculating one of several difference measures (e.g., relative difference in mean), and an average difference between the surveys. On bivariate level a function can calculate significant differences in correlations for the surveys. And on multivariate levels a function can calculate significant differences in model coefficients between the surveys of comparison. All of those differences can be easily plotted and outputted as a table. For more detailed information on the methods and example use see Rohr, B., Silber, H., & Felderer, B. (2024). Comparing the Accuracy of Univariate, Bivariate, and Multivariate Estimates across Probability and Nonprobability Surveys with Po [...truncated...]
Author: Bjoern Rohr [aut, cre, cph],
Barbara Felderer [aut]
Maintainer: Bjoern Rohr <bjoern.rohr@gesis.org>
Diff between sampcompR versions 0.3.1.1 dated 2025-07-02 and 0.3.1.2 dated 2025-07-04
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 5 +++++ R/Multidiff_Plot.R | 14 +++++++++++++- 4 files changed, 24 insertions(+), 7 deletions(-)
Title: Transform Models into 'LaTeX' Equations
Description: The goal of 'equatiomatic' is to reduce the pain
associated with writing 'LaTeX' formulas from fitted models. The
primary function of the package, extract_eq(), takes a fitted model
object as its input and returns the corresponding 'LaTeX' code for the
model.
Author: Daniel Anderson [aut] ,
Andrew Heiss [aut] ,
Jay Sumners [aut],
Joshua Rosenberg [ctb] ,
Jonathan Sidi [ctb] ,
Ellis Hughes [ctb] ,
Thomas Fung [ctb] ,
Reza Norouzian [ctb] ,
Indrajeet Patil [ctb] ,
Quinn White [ctb] ,
David Kane [ctb],
Philippe Gros [...truncated...]
Maintainer: Philippe Grosjean <phgrosjean@sciviews.org>
Diff between equatiomatic versions 0.3.6 dated 2025-03-10 and 0.3.7 dated 2025-07-04
DESCRIPTION | 42 ++++++++++++++++++++++++------------- MD5 | 20 ++++++++--------- NEWS.md | 8 +++++++ R/extract_lhs.R | 15 ++++++++++++- inst/doc/lme4-lmer.html | 14 ++++++------ inst/doc/plotting-integration.R | 4 +-- inst/doc/plotting-integration.Rmd | 4 +-- inst/doc/plotting-integration.html | 4 +-- inst/doc/tests_and_coverage.html | 2 - man/equatiomatic-package.Rd | 2 + vignettes/plotting-integration.Rmd | 4 +-- 11 files changed, 78 insertions(+), 41 deletions(-)
Title: Marine Benthic Ecosystem Analysis
Description: Preprocessing tools and biodiversity measures
(species abundance, species richness, population heterogeneity and
sensitivity) for analysing marine benthic data. See Van Loon et al.
(2015) <doi:10.1016/j.seares.2015.05.002> for an application of
these tools.
Author: Dennis Walvoort [aut, cre, cph]
Maintainer: Dennis Walvoort <dennis.Walvoort@wur.nl>
Diff between benthos versions 1.3-8 dated 2022-08-22 and 1.3-9 dated 2025-07-04
DESCRIPTION | 10 MD5 | 38 R/benthos.R | 94 +- R/data_oosterschelde.R | 46 - R/indicators.R | 1950 ++++++++++++++++++++++---------------------- R/io.R | 2081 +++++++++++++++++++++++------------------------- R/utils.R | 2 build/vignette.rds |binary inst/NEWS.Rd | 82 + inst/doc/benthos.R | 18 inst/doc/benthos.html | 1309 +++++++++++++++--------------- man/benthos-package.Rd | 2 man/genus_to_species.Rd | 2 man/hill.Rd | 2 man/oosterschelde.Rd | 2 man/read_ambi.Rd | 15 man/read_iti.Rd | 22 man/read_taxa.Rd | 10 man/read_twn.Rd | 22 man/simpson.Rd | 4 20 files changed, 2865 insertions(+), 2846 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-15 1.0.0
2022-12-14 0.1.0
2022-09-01 0.0.1
Title: Constructing Hierarchical Voronoi Tessellations and Overlay
Heatmaps for Data Analysis
Description: Facilitates building topology preserving maps for data analysis.
Author: Zubin Dowlaty [aut, cre],
Mu Sigma, Inc. [cph]
Maintainer: Zubin Dowlaty <zubin.dowlaty@mu-sigma.com>
Diff between HVT versions 25.2.4 dated 2025-06-10 and 25.2.5 dated 2025-07-04
DESCRIPTION | 26 ++- MD5 | 13 - NEWS.md |only R/plotAnimatedFlowmap.R | 356 +++++++++++++++++++++------------------------ README.md | 2 build/vignette.rds |binary inst/doc/HVT.html | 2 man/plotAnimatedFlowmap.Rd | 28 --- 8 files changed, 206 insertions(+), 221 deletions(-)
Title: Functions to Assist Design and Analysis of Agronomic Experiments
Description: Provides functions to aid in the design and analysis of
agronomic and agricultural experiments through easy access to
documentation and helper functions, especially for users who are
learning these concepts. While not required for most functionality,
this package enhances the `asreml` package which provides a
computationally efficient algorithm for fitting mixed models
using Residual Maximum Likelihood. It is a commercial package
that can be purchased as 'asreml-R' from 'VSNi'
<https://vsni.co.uk/>, who will supply a zip file for local
installation/updating (see <https://asreml.kb.vsni.co.uk/>).
Author: Sharon Nielsen [aut],
Sam Rogers [aut, cre],
Annie Conway [aut],
University of Adelaide [cph, fnd] ,
Grains Research and Development Corporation [cph, fnd]
Maintainer: Sam Rogers <biometrytraining@adelaide.edu.au>
Diff between biometryassist versions 1.3.0 dated 2025-06-11 and 1.3.1 dated 2025-07-04
DESCRIPTION | 6 ++-- MD5 | 24 ++++++++-------- NEWS.md | 7 ++++ R/create_buffers.R | 41 ++++++++++++++--------------- R/use_template.R | 18 +++++------- build/vignette.rds |binary inst/doc/installing-asreml-r.html | 5 ++- man/add_buffers.Rd | 20 +++++++++++++- man/create_buffers.Rd | 2 - man/use_template.Rd | 18 +++++------- tests/testthat/_snaps/utility_functions.md | 34 ++++++++++++------------ tests/testthat/test-resplot.R | 15 +++------- tests/testthat/test-variogram.r | 3 -- 13 files changed, 104 insertions(+), 89 deletions(-)
More information about biometryassist at CRAN
Permanent link
Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by
providing a high level interface to writing, styling and editing
worksheets.
Author: Jordan Mark Barbone [aut] ,
Jan Marvin Garbuszus [aut, cre],
Olivier Roy [ctb],
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 1.16 dated 2025-06-05 and 1.17 dated 2025-07-04
DESCRIPTION | 6 MD5 | 77 ++- NEWS.md | 13 R/RcppExports.R | 88 ---- R/baseXML.R | 8 R/class-workbook-wrappers.R | 5 R/class-workbook.R | 37 - R/class-worksheet.R | 4 R/converters.R | 2 R/helper-functions.R | 2 R/openxlsx2-package.R | 28 + R/pugixml.R | 74 --- R/read.R | 16 R/standardize.R | 4 R/wb_load.R | 6 R/write.R | 37 + R/xl_open.R | 10 build/vignette.rds |binary inst/doc/conditional-formatting.html | 104 +++-- inst/doc/openxlsx2_style_manual.html | 8 man/openxlsx2-package.Rd | 29 + man/wbWorkbook.Rd | 4 man/wb_data.Rd | 3 man/wb_open.Rd | 4 man/wb_to_df.Rd | 2 man/xl_open.Rd | 9 src/RcppExports.cpp | 297 +-------------- src/helper_functions.cpp | 48 +- src/load_workbook.cpp | 9 src/openxlsx2.h | 12 src/openxlsx2_types.h | 5 src/pugi.cpp | 510 ++++++++++---------------- src/write_file.cpp | 90 +--- src/xlsb.cpp | 559 ++++++++++++++--------------- src/xlsb_defines.h | 276 -------------- src/xlsb_flags.h |only src/xlsb_funs.h | 106 ++--- tests/testthat/test-pugi_cpp.R | 69 +-- tests/testthat/test-pugixml.R | 2 tests/testthat/test-read_from_created_wb.R | 14 40 files changed, 997 insertions(+), 1580 deletions(-)
Title: Tables and Graphs for Mixed Models for Repeated Measures (MMRM)
Description: Mixed models for repeated measures (MMRM) are a popular
choice for analyzing longitudinal continuous outcomes in randomized
clinical trials and beyond; see for example Cnaan, Laird and Slasor
(1997)
<doi:10.1002/(SICI)1097-0258(19971030)16:20%3C2349::AID-SIM667%3E3.0.CO;2-E>.
This package provides an interface for fitting MMRM within the 'tern'
<https://cran.r-project.org/package=tern> framework by Zhu et al.
(2023) and tabulate results easily using 'rtables'
<https://cran.r-project.org/package=rtables> by Becker et al. (2023).
It builds on 'mmrm' <https://cran.r-project.org/package=mmrm> by
Sabanés Bové et al. (2023) for the actual MMRM computations.
Author: Daniel Sabanes Bove [aut],
Joe Zhu [aut, cre] ,
Godwin Yung [aut],
Francois Collin [aut],
Julia Dedic [aut],
Jana Stoilova [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between tern.mmrm versions 0.3.2 dated 2024-09-23 and 0.3.3 dated 2025-07-04
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