Title: Convenience Functions for Routine Data Exploration
Description: A series of shortcuts for routine tasks originally developed by
Rafael A. Irizarry to facilitate data exploration.
Author: Rafael A. Irizarry [aut, cre],
Michael I. Love [aut]
Maintainer: Rafael A. Irizarry <rafael_irizarry@dfci.harvard.edu>
Diff between rafalib versions 1.0.3 dated 2025-03-25 and 1.0.4 dated 2025-04-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NAMESPACE | 1 + R/popvar.R | 1 + 4 files changed, 8 insertions(+), 6 deletions(-)
Title: Calibration and Summarisation of Radiocarbon Dates
Description: Performs Bayesian non-parametric calibration of multiple related radiocarbon determinations, and summarises the calendar age information to plot their joint calendar age density (see Heaton (2022) <doi:10.1111/rssc.12599>).
Also models the occurrence of radiocarbon samples as a variable-rate (inhomogeneous) Poisson process, plotting the posterior estimate for the occurrence rate of the samples over calendar time, and providing information about potential change points.
Author: Timothy J Heaton [aut, cre, cph]
,
Sara Al-assam [aut, cph]
Maintainer: Timothy J Heaton <T.Heaton@leeds.ac.uk>
Diff between carbondate versions 1.0.1 dated 2024-01-31 and 1.1.0 dated 2025-04-07
DESCRIPTION | 8 MD5 | 94 +- NAMESPACE | 1 NEWS.md | 11 R/CalibrateSingleDetermination.R | 704 +++++++++---------- R/FindPosteriorMeanRate.R | 37 - R/FindPredictiveCalendarAgeDensity.R | 216 ++--- R/FindSummedProbabilityDistribution.R | 518 +++++++------- R/PPcalibrate.R | 2 R/PlotConvergenceData.R | 200 ++--- R/PlotNumberOfClusters.R | 106 +- R/PlotNumberOfInternalChanges.R | 94 +- R/PlotPosteriorChangePoints.R | 5 R/PlotPosteriorHeights.R | 5 R/PlotPosteriorMeanRate.R | 590 ++++++++------- R/PlotPredictiveCalendarAgeDensity.R | 691 +++++++++--------- R/PlotRateIndividualRealisation.R |only R/PolyaUrnBivarDirichlet.R | 794 ++++++++++----------- R/WalkerBivarDirichlet.R | 848 +++++++++++----------- R/check_arguments.R | 755 ++++++++++---------- R/data.R | 1036 ++++++++++++++-------------- README.md | 17 build/vignette.rds |binary inst/doc/Against_SPDs.R | 2 inst/doc/Against_SPDs.Rmd | 348 ++++----- inst/doc/Against_SPDs.html | 13 inst/doc/Independent_calibration.html | 13 inst/doc/Non-parametric-summed-density.R | 7 inst/doc/Non-parametric-summed-density.Rmd | 9 inst/doc/Non-parametric-summed-density.html | 83 +- inst/doc/Poisson-process-modelling.R | 55 + inst/doc/Poisson-process-modelling.Rmd | 669 ++++++++++-------- inst/doc/Poisson-process-modelling.html | 218 ++++- inst/doc/carbondate.html | 9 inst/doc/determining-convergence.R | 88 +- inst/doc/determining-convergence.Rmd | 276 +++---- inst/doc/determining-convergence.html | 17 man/FindPosteriorMeanRate.Rd | 9 man/PlotPosteriorChangePoints.Rd | 6 man/PlotPosteriorHeights.Rd | 6 man/PlotPosteriorMeanRate.Rd | 26 man/PlotPredictiveCalendarAgeDensity.Rd | 6 man/PlotRateIndividualRealisation.Rd |only man/figures/README-plot_density-1.png |binary man/figures/README-plot_mean_rate-1.png |binary vignettes/Against_SPDs.Rmd | 348 ++++----- vignettes/Non-parametric-summed-density.Rmd | 9 vignettes/Poisson-process-modelling.Rmd | 669 ++++++++++-------- vignettes/determining-convergence.Rmd | 276 +++---- 49 files changed, 5214 insertions(+), 4680 deletions(-)
Title: Bayesian Additive Regression Trees for Confounder Selection
Description: Fit Bayesian Regression Additive Trees (BART) models to
select true confounders from a large set of potential confounders and
to estimate average treatment effect. For more information, see Kim et
al. (2023) <doi:10.1111/biom.13833>.
Author: Yeonghoon Yoo [aut, cre]
Maintainer: Yeonghoon Yoo <yooyh.stat@gmail.com>
Diff between bartcs versions 1.2.2 dated 2024-05-01 and 1.3.0 dated 2025-04-07
DESCRIPTION | 8 MD5 | 53 +- NAMESPACE | 1 NEWS.md | 6 R/RcppExports.R | 56 +- R/bart.R | 338 +++++++-------- R/bartcs-package.R | 88 +-- R/plot.R | 162 +++---- R/separate_bart.R | 341 +++++++-------- R/single_bart.R | 318 +++++++------- R/summary.R | 296 ++++++------- R/synthetic_data.R |only R/trace_plot.R | 182 +++----- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 22 inst/doc/bartcs.R | 168 +++---- inst/doc/bartcs.Rmd | 298 ++++++------- inst/doc/bartcs.html | 1121 ++++++++++++++++++++++++-------------------------- man/bart.Rd | 378 ++++++++-------- man/bartcs-package.Rd | 108 ++-- man/plot.bartcs.Rd | 148 +++--- man/synthetic_data.Rd |only src/Models.cpp | 10 src/Models.h | 4 src/separate_bart.cpp | 19 src/single_bart.cpp | 19 vignettes/bartcs.Rmd | 298 ++++++------- vignettes/paper.html |only 29 files changed, 2225 insertions(+), 2217 deletions(-)
Title: Modeling and Inferring Gene Networks
Description: Analyzes gene expression
(time series) data with focus on the inference of gene networks.
In particular, GeneNet implements the methods of Schaefer and
Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
for learning large-scale gene association networks (including
assignment of putative directions).
Author: Juliane Schaefer [aut],
Rainer Opgen-Rhein [aut],
Korbinian Strimmer [aut, cre]
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>
Diff between GeneNet versions 1.2.16 dated 2021-11-14 and 1.2.17 dated 2025-04-07
DESCRIPTION | 23 ++++++++++++++--------- MD5 | 8 ++++---- NEWS | 23 ++++++++++++----------- data/ecoli.rda |binary man/ggm.estimate.pcor.Rd | 8 ++++---- 5 files changed, 34 insertions(+), 28 deletions(-)
Title: Estimation of Entropy, Mutual Information and Related Quantities
Description: Implements various estimators of entropy for discrete random
variables, including the shrinkage estimator by Hausser and Strimmer (2009),
the maximum likelihood and the Millow-Madow estimator, various Bayesian
estimators, and the Chao-Shen estimator. It also offers an R interface to the
NSB estimator. Furthermore, the package provides functions for estimating the
Kullback-Leibler divergence, the chi-squared divergence, mutual information,
and the chi-squared divergence of independence. It also computes the
G statistic and the chi-squared statistic and corresponding p-values.
Furthermore, there are functions for discretizing continuous random variables.
Author: Jean Hausser [aut],
Korbinian Strimmer [aut, cre]
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>
Diff between entropy versions 1.3.1 dated 2021-10-02 and 1.3.2 dated 2025-04-07
DESCRIPTION | 18 +++++++++++------- MD5 | 10 +++++----- NEWS | 11 ++++++++--- man/entropy.Dirichlet.Rd | 2 +- man/entropy.NSB.Rd | 2 +- man/entropy.Rd | 2 +- 6 files changed, 27 insertions(+), 18 deletions(-)
Title: Threshing and Reaping for Principal Components
Description: Defines the classes used to identify
outliers (threshing) and compute the number of significant principal
components and number of clusters (reaping) in a joint application
of PCA and hierarchical clustering. See Wang et al., 2018,
<doi:10.1186/s12859-017-1998-9>.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Thresher versions 1.1.4 dated 2024-04-28 and 1.1.5 dated 2025-04-07
DESCRIPTION | 16 +++++++++------- MD5 | 16 ++++++++-------- build/vignette.rds |binary data/savedSims.rda |binary inst/doc/Thresher.pdf |binary man/Reaper-class.Rd | 6 +++--- man/SimThresher-class.Rd | 2 +- man/Thresher-class.Rd | 12 ++++++------ man/matchLabels.Rd | 8 ++++---- 9 files changed, 31 insertions(+), 29 deletions(-)
Title: A Report Templating System
Description: Facilitating the creation of reproducible statistical
report templates. Once created, rapport templates can be exported to
various external formats (HTML, LaTeX, PDF, ODT etc.) with pandoc as the
converter backend.
Author: Aleksandar Blagotic [aut],
Gergely Daroczi [aut, cre]
Maintainer: Gergely Daroczi <daroczig@rapporter.net>
Diff between rapport versions 1.1 dated 2021-04-11 and 1.2 dated 2025-04-07
rapport-1.1/rapport/NEWS |only rapport-1.1/rapport/data/ius2008.R |only rapport-1.1/rapport/inst/CITATION |only rapport-1.2/rapport/DESCRIPTION | 19 +++--- rapport-1.2/rapport/MD5 | 21 +++---- rapport-1.2/rapport/NEWS.md |only rapport-1.2/rapport/R/export.R | 6 +- rapport-1.2/rapport/R/rapport.R | 82 ++++++++++++++--------------- rapport-1.2/rapport/R/template.R | 2 rapport-1.2/rapport/R/tpl-check.R | 2 rapport-1.2/rapport/data/ius2008.rda |only rapport-1.2/rapport/man/rapport-helpers.Rd | 78 +++++++++++++-------------- rapport-1.2/rapport/man/rapport-package.Rd | 9 +++ rapport-1.2/rapport/man/rapport.inputs.Rd | 2 14 files changed, 115 insertions(+), 106 deletions(-)
Title: Finding the Number of Significant Principal Components
Description: Implements methods to automate the Auer-Gervini graphical
Bayesian approach for determining the number of significant
principal components. Automation uses clustering, change points, or
simple statistical models to distinguish "long" from "short" steps
in a graph showing the posterior number of components as a function
of a prior parameter. See <doi:10.1101/237883>.
Author: Min Wang [aut],
Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between PCDimension versions 1.1.13 dated 2022-06-30 and 1.1.14 dated 2025-04-07
DESCRIPTION | 18 +++++++++++------- MD5 | 14 +++++++------- build/vignette.rds |binary data/spca.rda |binary inst/doc/PCDimension.pdf |binary man/agfun.Rd | 16 ++++++++-------- man/brokenStick.Rd | 2 +- man/spca-data.Rd | 4 ++-- 8 files changed, 29 insertions(+), 25 deletions(-)
Title: Modified Detecting Deviating Cells Algorithm in
Pharmacovigilance
Description: Methods for detecting signals related to (adverse event, medical
product e.g. drugs, vaccines) pairs, a data generation function for
simulating pharmacovigilance datasets, and various utility functions.
For more details please see Liu A., Mukhopadhyay R., and Markatou M.
<doi:10.48550/arXiv.2410.01168>.
Author: Anran Liu [aut, cre] ,
Raktim Mukhopadhyay [aut] ,
Marianthi Markatou [aut]
Maintainer: Anran Liu <anranliu@buffalo.edu>
Diff between MDDC versions 1.0.0 dated 2024-10-04 and 1.1.0 dated 2025-04-07
MDDC-1.0.0/MDDC/R/generate_contin_table_with_clustered_AE_with_tol.R.R |only MDDC-1.1.0/MDDC/DESCRIPTION | 8 - MDDC-1.1.0/MDDC/MD5 | 25 ++-- MDDC-1.1.0/MDDC/R/generate_contin_table_with_clustered_AE_with_tol.R |only MDDC-1.1.0/MDDC/R/mddc_mc.R | 24 +++- MDDC-1.1.0/MDDC/README.md | 15 +- MDDC-1.1.0/MDDC/build/vignette.rds |binary MDDC-1.1.0/MDDC/inst/WORDLIST |only MDDC-1.1.0/MDDC/inst/doc/Introduction_to_MDDC.R | 2 MDDC-1.1.0/MDDC/inst/doc/Introduction_to_MDDC.Rmd | 10 + MDDC-1.1.0/MDDC/inst/doc/Introduction_to_MDDC.html | 28 ++--- MDDC-1.1.0/MDDC/man/generate_contin_table_with_clustered_AE_with_tol.Rd | 2 MDDC-1.1.0/MDDC/man/mddc_mc.Rd | 15 ++ MDDC-1.1.0/MDDC/tests/testthat/test-report_drug_AE_pairs.R | 51 +++++++--- MDDC-1.1.0/MDDC/vignettes/Introduction_to_MDDC.Rmd | 10 + 15 files changed, 121 insertions(+), 69 deletions(-)
Title: A Flexible and Robust Sys.sleep() Replacement
Description: Provides a near drop-in replacement for base::Sys.sleep() that allows more types of input
to produce delays in the execution of code and can silence/prevent typical sources of error.
Author: Russell S. Pierce [aut, cre],
Timothy Gann [aut]
Maintainer: Russell S. Pierce <russell.s.pierce@gmail.com>
Diff between naptime versions 1.3.0 dated 2017-02-23 and 1.3.1 dated 2025-04-07
naptime-1.3.0/naptime/build |only naptime-1.3.0/naptime/inst |only naptime-1.3.0/naptime/vignettes |only naptime-1.3.1/naptime/DESCRIPTION | 18 ++-- naptime-1.3.1/naptime/MD5 | 13 +-- naptime-1.3.1/naptime/NEWS.md | 6 + naptime-1.3.1/naptime/README.md | 131 +++++++++++++++++++---------------- naptime-1.3.1/naptime/man/naptime.Rd | 25 ++---- 8 files changed, 99 insertions(+), 94 deletions(-)
Title: Scores of Nominal Outlyingness (SONO)
Description: Computes scores of outlyingness for data sets consisting of nominal variables and includes various evaluation metrics for assessing performance of outlier identification algorithms producing scores of outlyingness. The scores of nominal outlyingness are computed based on the framework of Costa and Papatsouma (2025) <doi:10.48550/arXiv.2408.07463>.
Author: Efthymios Costa [aut, cre]
Maintainer: Efthymios Costa <efthymios.costa17@imperial.ac.uk>
Diff between SONO versions 1.1 dated 2025-03-22 and 1.2 dated 2025-04-07
DESCRIPTION | 8 +++++--- MD5 | 12 +++++++++--- README.md | 12 ++++++++++-- build/partial.rdb |binary build/vignette.rds |only inst/doc |only man/figures |only vignettes |only 8 files changed, 24 insertions(+), 8 deletions(-)
Title: Classes and Methods to Use Genetic Algorithms for Feature
Selection
Description: Defines classes and methods that can be used
to implement genetic algorithms for feature selection. The idea is
that we want to select a fixed number of features to combine into a
linear classifier that can predict a binary outcome, and can use a
genetic algorithm heuristically to select an optimal set of features.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between GenAlgo versions 2.2.0 dated 2020-10-15 and 2.2.1 dated 2025-04-07
DESCRIPTION | 16 +++++++++------- MD5 | 12 ++++++------ build/vignette.rds |binary data/gaTourResults.rda |binary data/tourData09.rda |binary inst/doc/genalg.pdf |binary man/maha.Rd | 2 +- 7 files changed, 16 insertions(+), 14 deletions(-)
Title: Clean and Analyze Continuous Glucose Monitor Data
Description: This code provides several different functions for cleaning and analyzing continuous glucose monitor data. Currently it works with 'Dexcom', 'iPro 2', 'Diasend', 'Libre', or 'Carelink' data. The cleandata() function takes a directory of CGM data files and prepares them for analysis. cgmvariables() iterates through a directory of cleaned CGM data files and produces a single spreadsheet with data for each file in either rows or columns. The column format of this spreadsheet is compatible with REDCap data upload. cgmreport() also iterates through a directory of cleaned data, and produces PDFs of individual and aggregate AGP plots. Please visit <https://github.com/childhealthbiostatscore/R-Packages/> to download the new-user guide.
Author: Tim Vigers [aut, cre]
Maintainer: Tim Vigers <timothy.vigers@cuanschutz.edu>
Diff between cgmanalysis versions 3.0.2 dated 2025-02-03 and 3.1.0 dated 2025-04-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/cgmvariables.R | 49 +++++++++++++++++++++++++++---------------------- R/cleandata.R | 17 +++++++++++++++-- 4 files changed, 48 insertions(+), 30 deletions(-)
Title: Classes and Methods for Training and Using Binary Prediction
Models
Description: Defines classes and methods to learn models and use them
to predict binary outcomes. These are generic tools, but we also
include specific examples for many common classifiers.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Modeler versions 3.4.7 dated 2025-01-08 and 3.4.8 dated 2025-04-07
DESCRIPTION | 10 +++++----- MD5 | 38 +++++++++++++++++++------------------- build/vignette.rds |binary inst/doc/Modeler.pdf |binary man/FittedModel-class.Rd | 2 +- man/FittedModel.Rd | 4 ++-- man/Modeler-class.Rd | 2 +- man/Modeler.Rd | 2 +- man/learn.Rd | 2 +- man/learnCCP.Rd | 2 +- man/learnKNN.Rd | 2 +- man/learnLR.Rd | 2 +- man/learnNNET.Rd | 2 +- man/learnNNET2.Rd | 2 +- man/learnPCALR.Rd | 2 +- man/learnRF.Rd | 2 +- man/learnRPART.Rd | 2 +- man/learnSVN.Rd | 2 +- man/learnSelectedLR.Rd | 2 +- man/learnTailRank.Rd | 2 +- 20 files changed, 41 insertions(+), 41 deletions(-)
Title: Spatial Visualization with ggplot2
Description: A collection of functions to visualize spatial data and models
on top of static maps from various online sources (e.g Google Maps and Stamen
Maps). It includes tools common to those tasks, including functions for
geolocation and routing.
Author: David Kahle [aut, cre] ,
Hadley Wickham [aut] ,
Scott Jackson [aut],
Mikko Korpela [ctb]
Maintainer: David Kahle <david@kahle.io>
Diff between ggmap versions 4.0.0 dated 2023-11-19 and 4.0.1 dated 2025-04-07
DESCRIPTION | 8 ++-- MD5 | 54 +++++++++++++-------------- NEWS.md | 13 ++++++ R/attach.R | 4 +- R/geocode.R | 9 ++-- R/geom_leg.R | 9 ++-- R/get_googlemap.R | 4 +- R/get_stadiamap.R | 2 - R/ggmap-package.R | 3 - R/inset.R | 4 +- R/qmplot.R | 5 +- R/route.R | 2 - README.md | 11 +++-- man/geocode.Rd | 9 ++-- man/geom_leg.Rd | 74 ++++++++++++++++++++++++++++--------- man/get_googlemap.Rd | 4 +- man/ggmap.Rd | 3 - man/inset.Rd | 4 +- man/legs2route.Rd | 2 - man/qmplot.Rd | 5 +- tools/README-faceting-1.png |binary tools/README-ggmap-1.png |binary tools/README-ggmap-layers-1.png |binary tools/README-ggmap-patchwork-1.png |binary tools/README-google_maps-1.png |binary tools/README-maptypes-1.png |binary tools/README-qmplot-1.png |binary tools/README-route_trek-1.png |binary 28 files changed, 141 insertions(+), 88 deletions(-)
Title: Dynamic Spectrogram Visualizations
Description: A set of tools to generate dynamic spectrogram visualizations in video format.
Author: Marcelo Araya-Salas [aut, cre]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
Diff between dynaSpec versions 1.0.2 dated 2024-09-29 and 1.0.3 dated 2025-04-07
DESCRIPTION | 6 MD5 | 8 NEWS.md | 7 README.md | 720 +++++++++++++++++++++++++++++++++------------------ data/canyon_wren.rda |binary 5 files changed, 493 insertions(+), 248 deletions(-)
Title: Classes and Methods for Cross Validation of "Class Prediction"
Algorithms
Description: Defines classes and methods to cross-validate various
binary classification algorithms used for "class prediction"
problems.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between CrossValidate versions 2.3.4 dated 2019-05-06 and 2.3.5 dated 2025-04-07
DESCRIPTION | 16 +++++++++------- MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/CrossVal.pdf |binary man/CrossVal.Rd | 4 ++-- 5 files changed, 15 insertions(+), 13 deletions(-)
Title: The Bimodality Index
Description: Defines the functions used to compute the
bimodal index as defined by Wang et al. (2009)
<https://pmc.ncbi.nlm.nih.gov/articles/PMC2730180/>,
<doi:10.4137/CIN.S2846>.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between BimodalIndex versions 1.1.9 dated 2019-05-06 and 1.1.11 dated 2025-04-07
DESCRIPTION | 16 +++++++++------- MD5 | 6 +++--- build/vignette.rds |binary inst/doc/bim.pdf |binary 4 files changed, 12 insertions(+), 10 deletions(-)
Title: 'tidyverse' Methods and 'ggplot2' Helpers for 'terra' Objects
Description: Extension of the 'tidyverse' for 'SpatRaster' and
'SpatVector' objects of the 'terra' package. It includes also new
'geom_' functions that provide a convenient way of visualizing 'terra'
objects with 'ggplot2'.
Author: Diego Hernangomez [aut, cre, cph]
,
Dewey Dunnington [ctb] ,
ggplot2 authors [cph] ,
Andrea Manica [ctb]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between tidyterra versions 0.7.0 dated 2025-02-03 and 0.7.1 dated 2025-04-07
DESCRIPTION | 12 MD5 | 92 +- NEWS.md | 9 R/geom_spat_contour.R | 972 ++++++++++++------------ R/geom_spat_contour_fill.R | 8 R/geom_spat_contour_text.R | 4 R/geom_spatraster.R | 1089 +++++++++++++-------------- R/geom_spatraster_rgb.R | 12 R/geom_spatvector.R | 330 ++++---- R/scales_cross_blended.R | 3 R/sysdata.rda |binary README.md | 17 build/partial.rdb |binary build/vignette.rds |binary data/cross_blended_hypsometric_tints_db.rda |binary data/grass_db.rda |binary data/hypsometric_tints_db.rda |binary data/princess_db.rda |binary data/volcano2.rda |binary inst/doc/tidyterra.Rmd | 2 inst/doc/tidyterra.html | 14 inst/doc/welcome.html | 16 inst/schemaorg.json | 23 man/figures/logo.png |binary man/geom_spat_contour.Rd | 14 man/geom_spatraster.Rd | 6 man/geom_spatraster_rgb.Rd | 322 ++++--- man/scale_cross_blended.Rd | 3 man/tidyterra-package.Rd | 1 tests/testthat/test-geom_spat_contour.R | 42 + tests/testthat/test-geom_spat_contour_fill.R | 42 + tests/testthat/test-geom_spat_contour_text.R | 52 + tests/testthat/test-geom_spatraster_1lyr.R | 24 tests/testthat/test-geom_spatraster_3lyr.R | 32 tests/testthat/test-geom_spatraster_rgb.R | 14 tests/testthat/test-stat_spatraster.R | 304 +++---- vignettes/aggregate-1.png |binary vignettes/aggregate-2.png |binary vignettes/contourfilled-1.png |binary vignettes/contourlines-1.png |binary vignettes/faceted-1.png |binary vignettes/hypso-1.png |binary vignettes/lux_ggplot-1.png |binary vignettes/rgb-1.png |binary vignettes/spatraster-example1-1.png |binary vignettes/spatraster-example2-1.png |binary vignettes/tidyterra.Rmd | 2 47 files changed, 1861 insertions(+), 1600 deletions(-)
Title: Deduplication Across Multiple Columns
Description: Duplicated data can exist in different rows and columns and user may need to
treat observations (rows) connected by duplicated data as one observation,
e.g. companies can belong to one family (and thus: be one company) by sharing
some telephone numbers. This package allows to find connected rows
based on data on chosen columns and collapse it into one row.
Author: Grzegorz Smolinski [aut, cre]
Maintainer: Grzegorz Smolinski <g.smolinski1@gmail.com>
Diff between dedupewider versions 0.1.0 dated 2021-10-28 and 0.1.1 dated 2025-04-07
DESCRIPTION | 8 LICENSE | 4 MD5 | 24 NEWS.md | 28 - R/dedupe_wide.R | 495 +++++++++---------- R/na_move.R | 3 build/vignette.rds |binary inst/doc/usage-and-algorithm-explained.R | 2 inst/doc/usage-and-algorithm-explained.html | 729 +++++++++++++++++++++++----- man/dedupe_wide.Rd | 135 ++--- man/na_move.Rd | 3 tests/testthat.R | 8 tests/testthat/test-dedupe_wide.R | 140 ++--- 13 files changed, 1036 insertions(+), 543 deletions(-)
More information about sdtm.terminology at CRAN
Permanent link
Title: 'PCATS' API Client
Description: Provides an R interface to the 'PCATS' API
<https://pcats.research.cchmc.org/api/__docs__/>,
allowing R users to submit tasks and retrieve results.
Author: Bin Huang [aut] ,
Chen Chen [aut],
Michal Kouril [aut, cre]
Maintainer: Michal Kouril <michal.kouril@cchmc.org>
Diff between pcatsAPIclientR versions 1.2.0 dated 2025-03-11 and 1.3.0 dated 2025-04-07
DESCRIPTION | 8 +-- MD5 | 22 +++++----- NEWS.md | 6 ++ R/dynamicGP.R | 109 +++++++++++++++++++++++++++++------------------------ R/dynamicGP.cate.R | 39 ++++++++++++------ R/job_status.R | 32 +++++++++------ R/ploturl.R | 34 ++++++++++------ R/printgp.R | 33 +++++++++------- R/results.R | 33 ++++++++++------ R/staticGP.R | 90 +++++++++++++++++++++++-------------------- R/staticGP.cate.R | 39 ++++++++++++------ R/uploadfile.R | 33 ++++++++++------ 12 files changed, 284 insertions(+), 194 deletions(-)
More information about pcatsAPIclientR at CRAN
Permanent link
More information about groupedHyperframe.random at CRAN
Permanent link
More information about activityCounts at CRAN
Permanent link
Title: Animal Movement Modelling using Hidden Markov Models
Description: Provides tools for animal movement modelling using hidden Markov
models. These include processing of tracking data, fitting hidden Markov models
to movement data, visualization of data and fitted model, decoding of the state
process, etc. <doi:10.1111/2041-210X.12578>.
Author: Theo Michelot [aut, cre],
Roland Langrock [aut, ctb],
Toby Patterson [aut, ctb],
Brett McClintock [ctb],
Eric Rexstad [ctb]
Maintainer: Theo Michelot <theo.michelot@dal.ca>
Diff between moveHMM versions 1.9 dated 2023-05-08 and 1.10 dated 2025-04-07
DESCRIPTION | 34 +++++-- MD5 | 34 +++---- NAMESPACE | 1 R/moveData.R | 11 +- R/moveHMM.R | 14 +-- R/plotSat.R | 6 - R/splitAtGaps.R |only README.md | 6 - build/vignette.rds |binary inst/doc/moveHMM-custom-plots.pdf |binary inst/doc/moveHMM-example.pdf |binary inst/doc/moveHMM-guide.R | 162 +++++++++++++++++------------------ inst/doc/moveHMM-guide.pdf |binary inst/doc/moveHMM-starting-values.R | 94 ++++++++++---------- inst/doc/moveHMM-starting-values.pdf |binary man/moveData.Rd | 11 +- man/moveHMM.Rd | 14 +-- man/plotSat.Rd | 6 - man/splitAtGaps.Rd |only 19 files changed, 213 insertions(+), 180 deletions(-)
Title: Cluster Analysis via Random Partition Distributions
Description: Cluster analysis is performed using pairwise distance information and a random partition distribution. The method is
implemented for two random partition distributions. It draws samples and then obtains and plots clustering estimates.
An implementation of a selection algorithm is provided for the mass parameter of the partition distribution. Since
pairwise distances are the principal input to this procedure, it is most comparable to the hierarchical and k-medoids
clustering methods. The method is Dahl, Andros, Carter (2022+) <doi:10.1002/sam.11602>.
Author: David B. Dahl [aut, cre] ,
R. Jacob Andros [aut] ,
J. Brandon Carter [aut] ,
Alex Crichton [ctb] ,
Brendan Zabarauskas [ctb] ,
David B. Dahl [ctb] ,
David Tolnay [ctb] ,
Jim Turner [ctb] ,
Jorge Aparicio [ctb] ,
Josh Stone [ctb] ,
Mikhail Vorotilov [ [...truncated...]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between caviarpd versions 0.3.14 dated 2025-03-30 and 0.3.16 dated 2025-04-07
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 3 +++ src/rust/vendor.tar.gz |binary tools/build_rust_library.R | 36 ++++-------------------------------- 5 files changed, 14 insertions(+), 39 deletions(-)
Title: Time Dependent Shared Frailty Cox Model
Description: Fits time-dependent shared frailty Cox model (specifically the adapted Paik et al.'s Model) based on the paper "Centre-Effect on Survival After Bone Marrow Transplantation: Application of Time-Dependent Frailty Models", by C.M. Wintrebert, H. Putter, A.H. Zwinderman and J.C. van Houwelingen (2004) <doi:10.1002/bimj.200310051>.
Author: Alessandra Ragni [aut, cre] ,
Giulia Romani [aut],
Chiara Masci [aut]
Maintainer: Alessandra Ragni <alessandra.ragni@polimi.it>
Diff between TimeDepFrail versions 0.0.1 dated 2025-01-17 and 0.1.0 dated 2025-04-07
TimeDepFrail-0.0.1/TimeDepFrail/R/NodesWeightsQuadratureFomula.R |only TimeDepFrail-0.0.1/TimeDepFrail/R/base_hazard.R |only TimeDepFrail-0.0.1/TimeDepFrail/R/extractors.R |only TimeDepFrail-0.0.1/TimeDepFrail/R/params_se.R |only TimeDepFrail-0.0.1/TimeDepFrail/R/summary.R |only TimeDepFrail-0.0.1/TimeDepFrail/R/time_int_eval.R |only TimeDepFrail-0.0.1/TimeDepFrail/man/check.result.AdPaik.Rd |only TimeDepFrail-0.0.1/TimeDepFrail/man/check.structure_post_frailty_CI.Rd |only TimeDepFrail-0.0.1/TimeDepFrail/man/coefse.Rd |only TimeDepFrail-0.0.1/TimeDepFrail/man/frailty_sd.AdPaik.Rd |only TimeDepFrail-0.0.1/TimeDepFrail/man/n_nodes.Rd |only TimeDepFrail-0.0.1/TimeDepFrail/man/n_nodesG.Rd |only TimeDepFrail-0.0.1/TimeDepFrail/man/params_se.AdPaik.Rd |only TimeDepFrail-0.0.1/TimeDepFrail/man/plot_ll_1D.AdPaik.Rd |only TimeDepFrail-0.0.1/TimeDepFrail/man/plot_survival.Rd |only TimeDepFrail-0.0.1/TimeDepFrail/man/post_frailty.AdPaik.Rd |only TimeDepFrail-0.0.1/TimeDepFrail/man/post_frailty_CI.AdPaik.Rd |only TimeDepFrail-0.0.1/TimeDepFrail/man/summary.Rd |only TimeDepFrail-0.0.1/TimeDepFrail/man/survival.Rd |only TimeDepFrail-0.1.0/TimeDepFrail/DESCRIPTION | 6 TimeDepFrail-0.1.0/TimeDepFrail/MD5 | 143 ++-- TimeDepFrail-0.1.0/TimeDepFrail/NAMESPACE | 23 TimeDepFrail-0.1.0/TimeDepFrail/R/AdPaikModel.R | 133 ++-- TimeDepFrail-0.1.0/TimeDepFrail/R/Utils.R |only TimeDepFrail-0.1.0/TimeDepFrail/R/bas_hazard.R |only TimeDepFrail-0.1.0/TimeDepFrail/R/check.R | 129 ++-- TimeDepFrail-0.1.0/TimeDepFrail/R/check.result.R | 56 - TimeDepFrail-0.1.0/TimeDepFrail/R/coefse.R |only TimeDepFrail-0.1.0/TimeDepFrail/R/data.R | 8 TimeDepFrail-0.1.0/TimeDepFrail/R/extract_dummy_variables.R | 5 TimeDepFrail-0.1.0/TimeDepFrail/R/extractors.AdPaik.R |only TimeDepFrail-0.1.0/TimeDepFrail/R/frailty_sd.R | 278 ++------- TimeDepFrail-0.1.0/TimeDepFrail/R/params_se_CI.R |only TimeDepFrail-0.1.0/TimeDepFrail/R/plot.R | 292 ++++++---- TimeDepFrail-0.1.0/TimeDepFrail/R/posterior_frailty.R | 292 +++++++++- TimeDepFrail-0.1.0/TimeDepFrail/R/summary_and_print.R |only TimeDepFrail-0.1.0/TimeDepFrail/R/survival.R | 22 TimeDepFrail-0.1.0/TimeDepFrail/README.md | 8 TimeDepFrail-0.1.0/TimeDepFrail/man/AdPaikModel.Rd | 72 -- TimeDepFrail-0.1.0/TimeDepFrail/man/AdPaik_1D.Rd | 2 TimeDepFrail-0.1.0/TimeDepFrail/man/bas_hazard.Rd | 30 - TimeDepFrail-0.1.0/TimeDepFrail/man/bas_hazard_internal.Rd |only TimeDepFrail-0.1.0/TimeDepFrail/man/check.C_mult.Rd | 3 TimeDepFrail-0.1.0/TimeDepFrail/man/check.categories_params.Rd | 3 TimeDepFrail-0.1.0/TimeDepFrail/man/check.centre.Rd | 5 TimeDepFrail-0.1.0/TimeDepFrail/man/check.dataset.Rd | 3 TimeDepFrail-0.1.0/TimeDepFrail/man/check.flag_optimal_params.Rd | 3 TimeDepFrail-0.1.0/TimeDepFrail/man/check.formula_terms.Rd | 3 TimeDepFrail-0.1.0/TimeDepFrail/man/check.frailty_dispersion.Rd | 3 TimeDepFrail-0.1.0/TimeDepFrail/man/check.index.Rd | 3 TimeDepFrail-0.1.0/TimeDepFrail/man/check.pchtype_colorbg.Rd | 3 TimeDepFrail-0.1.0/TimeDepFrail/man/check.pos_frailty_sd.Rd | 3 TimeDepFrail-0.1.0/TimeDepFrail/man/check.poslegend.Rd | 3 TimeDepFrail-0.1.0/TimeDepFrail/man/check.post_frailty_centre.Rd | 3 TimeDepFrail-0.1.0/TimeDepFrail/man/check.range_params.Rd | 3 TimeDepFrail-0.1.0/TimeDepFrail/man/check.result.Rd | 65 +- TimeDepFrail-0.1.0/TimeDepFrail/man/check.structure_paramsCI.Rd | 3 TimeDepFrail-0.1.0/TimeDepFrail/man/check.structure_post_frailty_est.Rd | 3 TimeDepFrail-0.1.0/TimeDepFrail/man/check.structure_post_frailty_var.Rd | 3 TimeDepFrail-0.1.0/TimeDepFrail/man/check.time_axis.Rd | 3 TimeDepFrail-0.1.0/TimeDepFrail/man/check.value_post_frailty.Rd | 3 TimeDepFrail-0.1.0/TimeDepFrail/man/coef.AdPaik.Rd | 11 TimeDepFrail-0.1.0/TimeDepFrail/man/coefseAdPaik.Rd |only TimeDepFrail-0.1.0/TimeDepFrail/man/confint.AdPaik.Rd | 9 TimeDepFrail-0.1.0/TimeDepFrail/man/data_dropout.Rd | 2 TimeDepFrail-0.1.0/TimeDepFrail/man/extractAIC.AdPaik.Rd |only TimeDepFrail-0.1.0/TimeDepFrail/man/extract_dummy_variables.Rd | 3 TimeDepFrail-0.1.0/TimeDepFrail/man/extract_event_data.Rd | 3 TimeDepFrail-0.1.0/TimeDepFrail/man/frailty_Sd_internal.Rd |only TimeDepFrail-0.1.0/TimeDepFrail/man/frailty_sd.Rd | 37 - TimeDepFrail-0.1.0/TimeDepFrail/man/ll_AdPaik_1D.Rd | 3 TimeDepFrail-0.1.0/TimeDepFrail/man/ll_AdPaik_centre_1D.Rd | 3 TimeDepFrail-0.1.0/TimeDepFrail/man/ll_AdPaik_centre_eval.Rd | 3 TimeDepFrail-0.1.0/TimeDepFrail/man/ll_AdPaik_eval.Rd | 3 TimeDepFrail-0.1.0/TimeDepFrail/man/logLik.AdPaik.Rd |only TimeDepFrail-0.1.0/TimeDepFrail/man/nobs.AdPaik.Rd |only TimeDepFrail-0.1.0/TimeDepFrail/man/params_CI.Rd | 5 TimeDepFrail-0.1.0/TimeDepFrail/man/params_se.Rd |only TimeDepFrail-0.1.0/TimeDepFrail/man/plot.AdPaik.Rd |only TimeDepFrail-0.1.0/TimeDepFrail/man/plot_frailty_sd.Rd | 18 TimeDepFrail-0.1.0/TimeDepFrail/man/plot_ll_1D.Rd | 1 TimeDepFrail-0.1.0/TimeDepFrail/man/plot_post_frailty_est.Rd | 12 TimeDepFrail-0.1.0/TimeDepFrail/man/plot_post_frailty_var.Rd |only TimeDepFrail-0.1.0/TimeDepFrail/man/plot_survivalAdPaik.Rd |only TimeDepFrail-0.1.0/TimeDepFrail/man/post_frailty_CI_internal.Rd |only TimeDepFrail-0.1.0/TimeDepFrail/man/post_frailty_confint.Rd |only TimeDepFrail-0.1.0/TimeDepFrail/man/post_frailty_est.Rd |only TimeDepFrail-0.1.0/TimeDepFrail/man/post_frailty_internal.Rd |only TimeDepFrail-0.1.0/TimeDepFrail/man/post_frailty_var.Rd |only TimeDepFrail-0.1.0/TimeDepFrail/man/print.AdPaik.Rd |only TimeDepFrail-0.1.0/TimeDepFrail/man/print.summary.AdPaik.Rd |only TimeDepFrail-0.1.0/TimeDepFrail/man/summary.AdPaik.Rd | 37 - TimeDepFrail-0.1.0/TimeDepFrail/man/survivalAdPaik.Rd |only TimeDepFrail-0.1.0/TimeDepFrail/man/time_int_eval.Rd | 7 94 files changed, 992 insertions(+), 785 deletions(-)
Title: R Interface to the 'UNU.RAN' Random Variate Generators
Description: Interface to the 'UNU.RAN' library for Universal Non-Uniform RANdom variate generators.
Thus it allows to build non-uniform random number generators from quite arbitrary
distributions. In particular, it provides an algorithm for fast numerical inversion
for distribution with given density function.
In addition, the package contains densities, distribution functions and quantiles
from a couple of distributions.
Author: Josef Leydold [aut, cre] ,
Wolfgang H"ormann [aut]
Maintainer: Josef Leydold <josef.leydold@wu.ac.at>
Diff between Runuran versions 0.40 dated 2024-10-04 and 0.41 dated 2025-04-07
DESCRIPTION | 8 MD5 | 51 +- NEWS | 7 build/partial.rdb |binary build/vignette.rds |binary configure | 788 +++++++++++++++++++++++-------------------- configure.ac | 2 inst/doc/Runuran.pdf |binary inst/include/Runuran.h | 16 inst/include/Runuran_ext.h | 10 man/Runuran-package.Rd | 4 man/hitro.new.Rd | 3 src/Makevars.in | 2 src/R_API_list.txt |only src/Runuran.c | 216 +++++------ src/Runuran.h | 16 src/Runuran_distr.c | 126 +++--- src/Runuran_ext.c | 12 src/Runuran_ext.h | 10 src/Runuran_pinv.c | 38 +- src/config.h.in | 46 +- src/mixture.c | 32 - src/performance.c | 52 +- src/verify.c | 26 - tests/run_testthat.R | 2 tests/testthat/test_distr.R | 1 vignettes/inputs/version.tex | 2 27 files changed, 791 insertions(+), 679 deletions(-)
Title: Reactive Transport Modelling in 1d, 2d and 3d
Description: Routines for developing models that describe reaction and advective-diffusive transport in one, two or three dimensions.
Includes transport routines in porous media, in estuaries, and in bodies with variable shape.
Author: Karline Soetaert [aut, cre] ,
Filip Meysman [aut]
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between ReacTran versions 1.4.3.1 dated 2017-08-15 and 1.4.3.2 dated 2025-04-07
ReacTran-1.4.3.1/ReacTran/inst/doc/ReacTran.rnw |only ReacTran-1.4.3.1/ReacTran/inst/doc/fortran |only ReacTran-1.4.3.1/ReacTran/vignettes/ReacTran.rnw |only ReacTran-1.4.3.2/ReacTran/DESCRIPTION | 20 ReacTran-1.4.3.2/ReacTran/MD5 | 37 ReacTran-1.4.3.2/ReacTran/NAMESPACE | 2 ReacTran-1.4.3.2/ReacTran/R/polar2cart.R | 2 ReacTran-1.4.3.2/ReacTran/R/tran.2D.R | 10 ReacTran-1.4.3.2/ReacTran/R/tran.3D.R | 68 - ReacTran-1.4.3.2/ReacTran/R/tran.volume.2D.R | 4 ReacTran-1.4.3.2/ReacTran/build/vignette.rds |binary ReacTran-1.4.3.2/ReacTran/inst/CITATION | 6 ReacTran-1.4.3.2/ReacTran/inst/doc/PDE.R | 454 ++++----- ReacTran-1.4.3.2/ReacTran/inst/doc/PDE.pdf |binary ReacTran-1.4.3.2/ReacTran/inst/doc/ReacTran.R | 834 ++++++++--------- ReacTran-1.4.3.2/ReacTran/inst/doc/ReacTran.Rnw |only ReacTran-1.4.3.2/ReacTran/inst/doc/ReacTran.pdf |binary ReacTran-1.4.3.2/ReacTran/man/ReacTran.Rd | 4 ReacTran-1.4.3.2/ReacTran/man/advection.Rd | 4 ReacTran-1.4.3.2/ReacTran/vignettes/ReacTran.Rnw |only ReacTran-1.4.3.2/ReacTran/vignettes/reactran-phase.pdf |binary 21 files changed, 707 insertions(+), 738 deletions(-)
Title: Partial LeAst Squares for Multiomic Analysis
Description: Contains tools for supervised analyses of incomplete, overlapping
multiomics datasets. Applies partial least squares in multiple steps to find
models that predict survival outcomes. See Yamaguchi et al. (2023)
<doi:10.1101/2023.03.10.532096>.
Author: Kevin R. Coombes [cre, aut],
Kyoko Yamaguchi [aut],
Salma Abdelbaky [aut]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between plasma versions 1.1.3 dated 2024-04-28 and 1.1.4 dated 2025-04-07
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ build/vignette.rds |binary data/mirESCA.rda |binary data/tfESCA.rda |binary inst/doc/plasma.pdf |binary man/01-MultiOmics.Rd | 4 ++-- man/02-fitCoxModel.Rd | 6 +++--- man/03-manyCoxModels.Rd | 6 +++--- man/04-plasma-class.Rd | 6 +++--- man/04-plasmaPredictions-class.Rd | 2 +- man/05-Contribution-class.Rd | 4 ++-- man/06-CombinedWeights-class.Rd | 2 +- 13 files changed, 31 insertions(+), 31 deletions(-)
Title: Bayesian Logistic Regression for Oncology Dose-Escalation Trials
Description: Bayesian logistic regression model with optional
EXchangeability-NonEXchangeability parameter modelling for flexible
borrowing from historical or concurrent data-sources. The safety model
can guide dose-escalation decisions for adaptive oncology Phase I
dose-escalation trials which involve an arbitrary number of
drugs. Please refer to Neuenschwander et al. (2008)
<doi:10.1002/sim.3230> and Neuenschwander et al. (2016)
<doi:10.1080/19466315.2016.1174149> for details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Lukas A. Widmer [aut],
Andrew Bean [aut],
Trustees of Columbia University [cph]
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between OncoBayes2 versions 0.9-1 dated 2025-03-17 and 0.9-2 dated 2025-04-07
DESCRIPTION | 8 - MD5 | 68 ++++---- NAMESPACE | 6 NEWS.md | 15 + R/OncoBayes2-package.R | 2 R/blrm_exnex.R | 57 +++---- R/blrm_trial.R | 16 +- R/example_combo2.R | 30 +-- R/example_combo3.R | 30 +-- R/example_single_agent.R | 8 - R/lodds.R | 4 R/posterior.R | 129 ++++++++++++---- R/summary.R | 10 - R/sysdata.rda |binary inst/doc/OncoBayes2.pdf |binary inst/doc/introduction.R | 2 inst/doc/introduction.Rmd | 4 inst/doc/introduction.html | 208 +++++++++++++++----------- inst/doc/map_approach.R | 2 inst/doc/map_approach.Rmd | 17 +- inst/doc/map_approach.html | 286 +++++++++++++++++------------------- inst/sbc/sbc_report.html | 304 +++++++++++++++++++-------------------- man/OncoBayes2.Rd | 2 man/blrm_exnex.Rd | 28 +-- man/draws-OncoBayes2.Rd | 26 ++- man/example-combo2.Rd | 30 +-- man/example-combo3.Rd | 30 +-- man/example-single-agent.Rd | 8 - man/lodds.Rd | 4 man/summary.blrm_trial.Rd | 8 - tests/testthat/test-blrm_trial.R | 14 + tests/testthat/test-posterior.R | 55 +++++++ vignettes/introduction.Rmd | 4 vignettes/map_approach.Rmd | 17 +- vignettes/settings-knitr.txt | 2 35 files changed, 817 insertions(+), 617 deletions(-)
Title: 'Rcpp' Integration for the 'mlpack' Library
Description: A fast, flexible machine learning library, written in C++, that
aims to provide fast, extensible implementations of cutting-edge
machine learning algorithms. See also Curtin et al. (2023)
<doi:10.21105/joss.05026>.
Author: Yashwant Singh Parihar [aut, ctb, cph],
Ryan Curtin [aut, ctb, cph, cre],
Dirk Eddelbuettel [aut, ctb, cph],
James Balamuta [aut, ctb, cph],
Bill March [ctb, cph],
Dongryeol Lee [ctb, cph],
Nishant Mehta [ctb, cph],
Parikshit Ram [ctb, cph],
James Cl [...truncated...]
Maintainer: Ryan Curtin <ryan@ratml.org>
Diff between mlpack versions 4.5.1 dated 2024-12-05 and 4.6.0 dated 2025-04-07
mlpack-4.5.1/mlpack/R/image_converter.R |only mlpack-4.5.1/mlpack/inst/include/stb |only mlpack-4.5.1/mlpack/man/image_converter.Rd |only mlpack-4.5.1/mlpack/src/image_converter.cpp |only mlpack-4.6.0/mlpack/DESCRIPTION | 19 mlpack-4.6.0/mlpack/LICENSE | 2 mlpack-4.6.0/mlpack/MD5 | 219 +-- mlpack-4.6.0/mlpack/NAMESPACE | 1 mlpack-4.6.0/mlpack/R/RcppExports.R | 4 mlpack-4.6.0/mlpack/inst/include/mlpack/base.hpp | 11 mlpack-4.6.0/mlpack/inst/include/mlpack/bindings/util/camel_case.hpp | 4 mlpack-4.6.0/mlpack/inst/include/mlpack/config.hpp | 65 - mlpack-4.6.0/mlpack/inst/include/mlpack/core.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/core/data/data.hpp | 1 mlpack-4.6.0/mlpack/inst/include/mlpack/core/data/image_info_impl.hpp | 4 mlpack-4.6.0/mlpack/inst/include/mlpack/core/data/image_resize_crop.hpp |only mlpack-4.6.0/mlpack/inst/include/mlpack/core/data/load_image.hpp | 28 mlpack-4.6.0/mlpack/inst/include/mlpack/core/data/load_image_impl.hpp | 25 mlpack-4.6.0/mlpack/inst/include/mlpack/core/data/save_image.hpp | 26 mlpack-4.6.0/mlpack/inst/include/mlpack/core/data/save_image_impl.hpp | 25 mlpack-4.6.0/mlpack/inst/include/mlpack/core/data/split_data.hpp | 254 ++-- mlpack-4.6.0/mlpack/inst/include/mlpack/core/data/string_algorithms.hpp | 97 - mlpack-4.6.0/mlpack/inst/include/mlpack/core/math/random.hpp | 4 mlpack-4.6.0/mlpack/inst/include/mlpack/core/stb |only mlpack-4.6.0/mlpack/inst/include/mlpack/core/tree/address.hpp | 10 mlpack-4.6.0/mlpack/inst/include/mlpack/core/tree/cellbound.hpp | 4 mlpack-4.6.0/mlpack/inst/include/mlpack/core/tree/cover_tree/cover_tree.hpp | 38 mlpack-4.6.0/mlpack/inst/include/mlpack/core/tree/hrectbound_impl.hpp | 16 mlpack-4.6.0/mlpack/inst/include/mlpack/core/tree/octree/octree.hpp | 45 mlpack-4.6.0/mlpack/inst/include/mlpack/core/tree/octree/octree_impl.hpp | 60 mlpack-4.6.0/mlpack/inst/include/mlpack/core/tree/rectangle_tree.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/core/tree/rectangle_tree/discrete_hilbert_value.hpp | 5 mlpack-4.6.0/mlpack/inst/include/mlpack/core/tree/rectangle_tree/discrete_hilbert_value_impl.hpp | 8 mlpack-4.6.0/mlpack/inst/include/mlpack/core/tree/rectangle_tree/hilbert_r_tree_auxiliary_information_impl.hpp | 8 mlpack-4.6.0/mlpack/inst/include/mlpack/core/tree/rectangle_tree/hilbert_r_tree_descent_heuristic_impl.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/core/tree/rectangle_tree/r_plus_plus_tree_auxiliary_information.hpp | 12 mlpack-4.6.0/mlpack/inst/include/mlpack/core/tree/rectangle_tree/r_plus_plus_tree_auxiliary_information_impl.hpp | 26 mlpack-4.6.0/mlpack/inst/include/mlpack/core/tree/rectangle_tree/r_plus_plus_tree_descent_heuristic.hpp | 8 mlpack-4.6.0/mlpack/inst/include/mlpack/core/tree/rectangle_tree/r_plus_tree_descent_heuristic.hpp | 10 mlpack-4.6.0/mlpack/inst/include/mlpack/core/tree/rectangle_tree/r_plus_tree_split.hpp | 13 mlpack-4.6.0/mlpack/inst/include/mlpack/core/tree/rectangle_tree/r_plus_tree_split_impl.hpp | 34 mlpack-4.6.0/mlpack/inst/include/mlpack/core/tree/rectangle_tree/r_star_tree_descent_heuristic_impl.hpp | 4 mlpack-4.6.0/mlpack/inst/include/mlpack/core/tree/rectangle_tree/r_star_tree_split.hpp | 4 mlpack-4.6.0/mlpack/inst/include/mlpack/core/tree/rectangle_tree/rectangle_tree.hpp | 108 + mlpack-4.6.0/mlpack/inst/include/mlpack/core/tree/rectangle_tree/rectangle_tree_impl.hpp | 173 +- mlpack-4.6.0/mlpack/inst/include/mlpack/core/tree/rectangle_tree/traits.hpp | 4 mlpack-4.6.0/mlpack/inst/include/mlpack/core/tree/rectangle_tree/typedef.hpp | 30 mlpack-4.6.0/mlpack/inst/include/mlpack/core/util/arma_traits.hpp | 63 - mlpack-4.6.0/mlpack/inst/include/mlpack/core/util/distr_param.hpp |only mlpack-4.6.0/mlpack/inst/include/mlpack/core/util/gitversion.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/core/util/io.hpp | 4 mlpack-4.6.0/mlpack/inst/include/mlpack/core/util/io_impl.hpp | 14 mlpack-4.6.0/mlpack/inst/include/mlpack/core/util/log.hpp | 3 mlpack-4.6.0/mlpack/inst/include/mlpack/core/util/timers.hpp | 4 mlpack-4.6.0/mlpack/inst/include/mlpack/core/util/timers_impl.hpp | 12 mlpack-4.6.0/mlpack/inst/include/mlpack/core/util/using.hpp | 74 - mlpack-4.6.0/mlpack/inst/include/mlpack/core/util/version.hpp | 4 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/augmented/tasks/add_impl.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/augmented/tasks/copy_impl.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/augmented/tasks/sort_impl.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/ffn_impl.hpp | 13 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/layer/layer_types.hpp | 1 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/layer/linear_impl.hpp | 10 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/layer/linear_no_bias_impl.hpp | 8 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/layer/linear_recurrent.hpp |only mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/layer/linear_recurrent_impl.hpp |only mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/layer/lstm.hpp | 305 ++-- mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/layer/lstm_impl.hpp | 621 +++++----- mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/pixel_shuffle.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/layer/not_adapted/pixel_shuffle_impl.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/layer/recurrent_layer.hpp | 132 +- mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/layer/recurrent_layer_impl.hpp | 78 + mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/layer/serialization.hpp | 1 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/loss_functions/mean_absolute_percentage_error.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/loss_functions/mean_squared_error.hpp | 4 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/loss_functions/mean_squared_error_impl.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/loss_functions/multilabel_softmargin_loss.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/loss_functions/multilabel_softmargin_loss_impl.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/loss_functions/triplet_margin_loss.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/loss_functions/triplet_margin_loss_impl.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/rnn.hpp | 112 + mlpack-4.6.0/mlpack/inst/include/mlpack/methods/ann/rnn_impl.hpp | 343 +++-- mlpack-4.6.0/mlpack/inst/include/mlpack/methods/kde/kde_main.cpp | 4 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/lmnn/lmnn.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/lmnn/lmnn_impl.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/lmnn/lmnn_main.cpp | 4 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/local_coordinate_coding/local_coordinate_coding_main.cpp | 6 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/lsh/lsh_main.cpp | 9 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/nca/nca.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/nca/nca_impl.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/nca/nca_main.cpp | 3 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/neighbor_search/kfn_main.cpp | 10 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/neighbor_search/knn_main.cpp | 10 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/nmf/nmf_main.cpp | 4 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/perceptron/perceptron_main.cpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/radical/radical.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/radical/radical_impl.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/random_forest/bootstrap.hpp | 242 +++ mlpack-4.6.0/mlpack/inst/include/mlpack/methods/random_forest/random_forest.hpp | 50 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/random_forest/random_forest_impl.hpp | 194 +-- mlpack-4.6.0/mlpack/inst/include/mlpack/methods/range_search/range_search_main.cpp | 10 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/rann/krann_main.cpp | 14 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/reinforcement_learning/environment/acrobot.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/reinforcement_learning/environment/cart_pole.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/reinforcement_learning/environment/continuous_mountain_car.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/reinforcement_learning/environment/mountain_car.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/reinforcement_learning/environment/pendulum.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/reinforcement_learning/replay/random_replay.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/softmax_regression/softmax_regression_impl.hpp | 2 mlpack-4.6.0/mlpack/inst/include/mlpack/methods/sparse_coding/sparse_coding_main.cpp | 3 mlpack-4.6.0/mlpack/man/mlpack.Rd | 2 mlpack-4.6.0/mlpack/src/RcppExports.cpp | 12 mlpack-4.6.0/mlpack/tests/testthat/test-R_binding.R | 2 113 files changed, 2292 insertions(+), 1560 deletions(-)
Title: Excess Mortality
Description: Implementation of method for estimating excess mortality and other health related outcomes from weekly or daily count data described in Acosta and Irizarry (2021) "A Flexible Statistical Framework for Estimating Excess Mortality".
Author: Rafael A. Irizarry [aut, cre],
Rolando Acosta [aut],
Monica Robles-Fontan [aut],
Ferenci Tamas [ctb]
Maintainer: Rafael A. Irizarry <rafael_irizarry@dfci.harvard.edu>
Diff between excessmort versions 0.8.0 dated 2024-11-14 and 0.8.1 dated 2025-04-07
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/compute_expected.R | 7 ++++--- inst/doc/excessmort.R | 6 +++--- inst/doc/excessmort.html | 8 ++++---- 5 files changed, 19 insertions(+), 18 deletions(-)
Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
tree rearrangement;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of split support;
plotting the position of rogue taxa (Klopfstein & Spasojevic 2019)
<doi:10.1371/journal.pone.0212942>;
calculation of ancestor-descendant relationships,
of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013, Lemant et al. 2022)
<doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>;
artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph]
,
Emmanuel Paradis [cph] ,
Robert Noble [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeTools versions 1.13.0 dated 2025-01-10 and 1.13.1 dated 2025-04-07
DESCRIPTION | 6 MD5 | 24 NEWS.md | 5 R/DropTip.R | 6 R/parse_files.R | 2078 ++++++++++++++++++------------------ build/partial.rdb |binary inst/WORDLIST | 235 ++-- inst/doc/filesystem-navigation.html | 4 inst/doc/load-data.Rmd | 399 +++--- inst/doc/load-data.html | 96 + inst/doc/load-trees.html | 4 man/ReadCharacters.Rd | 2 vignettes/load-data.Rmd | 399 +++--- 13 files changed, 1672 insertions(+), 1586 deletions(-)
Title: Data Management and Analysis of Tests
Description: A system for the management, assessment, and psychometric analysis of data from educational and psychological tests.
Author: Gunter Maris [aut],
Timo Bechger [aut],
Jesse Koops [aut, cre],
Ivailo Partchev [aut]
Maintainer: Jesse Koops <jesse.koops@cito.nl>
Diff between dexter versions 1.5.0 dated 2024-07-05 and 1.6.0 dated 2025-04-07
dexter-1.5.0/dexter/man/coef.prms.Rd |only dexter-1.5.0/dexter/man/plot.prms.Rd |only dexter-1.5.0/dexter/man/plot.rim.Rd |only dexter-1.6.0/dexter/DESCRIPTION | 6 dexter-1.6.0/dexter/MD5 | 138 +- dexter-1.6.0/dexter/NAMESPACE | 14 dexter-1.6.0/dexter/NEWS.md | 16 dexter-1.6.0/dexter/R/RcppExports.R | 24 dexter-1.6.0/dexter/R/ability.R | 173 --- dexter-1.6.0/dexter/R/dexter.R | 49 dexter-1.6.0/dexter/R/dif.R | 17 dexter-1.6.0/dexter/R/equating.R | 33 dexter-1.6.0/dexter/R/fit_enorm.R | 111 +- dexter-1.6.0/dexter/R/individual_differences.R | 47 dexter-1.6.0/dexter/R/interaction_model.R | 90 - dexter-1.6.0/dexter/R/latent_cor.R | 196 ++- dexter-1.6.0/dexter/R/misc.R | 89 + dexter-1.6.0/dexter/R/misc_anon.R | 36 dexter-1.6.0/dexter/R/oplike.R | 5 dexter-1.6.0/dexter/R/param.R | 2 dexter-1.6.0/dexter/R/plausible_scores.R | 5 dexter-1.6.0/dexter/R/plausible_values.R | 22 dexter-1.6.0/dexter/R/plots.R | 58 - dexter-1.6.0/dexter/R/profile_analysis.R | 36 dexter-1.6.0/dexter/R/theta_functions.R | 64 - dexter-1.6.0/dexter/R/tia.R | 40 dexter-1.6.0/dexter/build/vignette.rds |binary dexter-1.6.0/dexter/inst/doc/DIF_vignette.html | 12 dexter-1.6.0/dexter/inst/doc/Equating.R | 124 -- dexter-1.6.0/dexter/inst/doc/Equating.Rmd | 124 -- dexter-1.6.0/dexter/inst/doc/Equating.html | 155 +- dexter-1.6.0/dexter/inst/doc/Plausible_Values.html | 18 dexter-1.6.0/dexter/inst/doc/Test_Individual_differences.html | 16 dexter-1.6.0/dexter/inst/doc/dexter.R | 12 dexter-1.6.0/dexter/inst/doc/dexter.Rmd | 8 dexter-1.6.0/dexter/inst/doc/dexter.html | 66 - dexter-1.6.0/dexter/inst/doc/profile-plots.html | 20 dexter-1.6.0/dexter/man/ability.Rd | 10 dexter-1.6.0/dexter/man/coef.enorm.Rd |only dexter-1.6.0/dexter/man/coef.inter.Rd |only dexter-1.6.0/dexter/man/fit_domains.Rd | 2 dexter-1.6.0/dexter/man/fit_enorm.Rd | 38 dexter-1.6.0/dexter/man/fit_inter.Rd | 4 dexter-1.6.0/dexter/man/latent_cor.Rd | 2 dexter-1.6.0/dexter/man/plausible_values.Rd | 4 dexter-1.6.0/dexter/man/plot.DIF_stats.Rd | 16 dexter-1.6.0/dexter/man/plot.enorm.Rd |only dexter-1.6.0/dexter/man/plot.inter.Rd |only dexter-1.6.0/dexter/src/RcppExports.cpp | 125 +- dexter-1.6.0/dexter/src/ability.cpp | 552 +++++----- dexter-1.6.0/dexter/src/ability.h | 11 dexter-1.6.0/dexter/src/binning.cpp |only dexter-1.6.0/dexter/src/enrm.cpp | 2 dexter-1.6.0/dexter/src/myomp.h | 9 dexter-1.6.0/dexter/src/priors.h | 4 dexter-1.6.0/dexter/src/pv.cpp | 19 dexter-1.6.0/dexter/src/shared.cpp | 11 dexter-1.6.0/dexter/src/shared.h | 6 dexter-1.6.0/dexter/src/simulation.cpp | 32 dexter-1.6.0/dexter/tests/testthat/test_ability.R | 2 dexter-1.6.0/dexter/tests/testthat/test_data_selection.R | 1 dexter-1.6.0/dexter/tests/testthat/test_database.R | 1 dexter-1.6.0/dexter/tests/testthat/test_elsym.R | 2 dexter-1.6.0/dexter/tests/testthat/test_enorm.R | 1 dexter-1.6.0/dexter/tests/testthat/test_interaction.R | 1 dexter-1.6.0/dexter/tests/testthat/test_latent_cor.R | 1 dexter-1.6.0/dexter/tests/testthat/test_p2p.R | 1 dexter-1.6.0/dexter/tests/testthat/test_plausible_scores.R | 1 dexter-1.6.0/dexter/tests/testthat/test_plausible_values.R | 26 dexter-1.6.0/dexter/tests/testthat/test_profiles.R | 1 dexter-1.6.0/dexter/tests/testthat/test_theta.R | 5 dexter-1.6.0/dexter/tests/testthat/test_tia.R | 1 dexter-1.6.0/dexter/vignettes/Equating.Rmd | 124 -- dexter-1.6.0/dexter/vignettes/dexter.Rmd | 8 74 files changed, 1561 insertions(+), 1288 deletions(-)
Title: Utilities for Interacting with the 'CTX' APIs
Description: Access chemical, hazard, bioactivity, and exposure data from the
Computational Toxicology and Exposure ('CTX') APIs
<https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-apis>.
'ctxR' was developed to streamline the process of accessing the information
available through the 'CTX' APIs without requiring prior knowledge of how to
use APIs. Most data is also available on the CompTox Chemical Dashboard
('CCD') <https://comptox.epa.gov/dashboard/> and other resources found at the
EPA Computational Toxicology and Exposure Online Resources
<https://www.epa.gov/comptox-tools>.
Author: Paul Kruse [aut] ,
Caroline Ring [aut] ,
Madison Feshuk [cre] ,
Carter Thunes [ctb],
Jason Brown [ctb]
Maintainer: Madison Feshuk <feshuk.madison@epa.gov>
Diff between ctxR versions 1.1.1 dated 2025-04-01 and 1.1.2 dated 2025-04-07
DESCRIPTION | 18 MD5 | 16 NEWS.md | 6 build/vignette.rds |binary inst/doc/Bioactivity.html | 365 ++++----- inst/doc/Chemical.html | 1782 ++++++++++++++++++++++----------------------- inst/doc/Exposure.html | 568 +++++++------- inst/doc/Hazard.html | 1708 +++++++++++++++++++++---------------------- inst/doc/Introduction.html | 583 +++++++------- 9 files changed, 2564 insertions(+), 2482 deletions(-)
Title: Estimate Univariate Gaussian and Student's t Mixture
Autoregressive Models
Description: Maximum likelihood estimation of univariate Gaussian Mixture Autoregressive (GMAR),
Student's t Mixture Autoregressive (StMAR), and Gaussian and Student's t Mixture Autoregressive (G-StMAR) models,
quantile residual tests, graphical diagnostics, forecast and simulate from GMAR, StMAR and G-StMAR processes.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2015) <doi:10.1111/jtsa.12108>,
Mika Meitz, Daniel Preve, Pentti Saikkonen (2023) <doi:10.1080/03610926.2021.1916531>,
Savi Virolainen (2022) <doi:10.1515/snde-2020-0060>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between uGMAR versions 3.5.1 dated 2024-12-04 and 3.5.2 dated 2025-04-07
uGMAR-3.5.1/uGMAR/vignettes/figures/diagplotfit42gs.png |only uGMAR-3.5.1/uGMAR/vignettes/figures/diagplotfit42gsr.png |only uGMAR-3.5.1/uGMAR/vignettes/figures/figsimuexp.png |only uGMAR-3.5.1/uGMAR/vignettes/figures/pacfplot.png |only uGMAR-3.5.1/uGMAR/vignettes/figures/plotfit42gs.png |only uGMAR-3.5.1/uGMAR/vignettes/figures/predictfit42gs.png |only uGMAR-3.5.1/uGMAR/vignettes/figures/proflogfit42gs.png |only uGMAR-3.5.2/uGMAR/DESCRIPTION | 6 +- uGMAR-3.5.2/uGMAR/MD5 | 27 +++++------ uGMAR-3.5.2/uGMAR/NEWS.md | 5 ++ uGMAR-3.5.2/uGMAR/R/plotMethods.R | 6 +- uGMAR-3.5.2/uGMAR/inst/doc/uGMARpaper.Rnw | 34 +++++++-------- uGMAR-3.5.2/uGMAR/inst/doc/uGMARpaper.pdf |binary uGMAR-3.5.2/uGMAR/vignettes/figures/diagplotfit42gsr.pdf |only uGMAR-3.5.2/uGMAR/vignettes/figures/figsimuexp.pdf |only uGMAR-3.5.2/uGMAR/vignettes/figures/pacfplot.pdf |only uGMAR-3.5.2/uGMAR/vignettes/figures/plotfit42gs.pdf |only uGMAR-3.5.2/uGMAR/vignettes/figures/predictfit42gs.pdf |only uGMAR-3.5.2/uGMAR/vignettes/figures/proflogfit42gs.pdf |only uGMAR-3.5.2/uGMAR/vignettes/refs.bib | 19 ++++---- uGMAR-3.5.2/uGMAR/vignettes/uGMARpaper.Rnw | 34 +++++++-------- 21 files changed, 69 insertions(+), 62 deletions(-)
Title: The Tail-Rank Statistic
Description: Implements the tail-rank statistic for selecting biomarkers
from a microarray data set, an efficient nonparametric test focused
on the distributional tails. See
<https://gitlab.com/krcoombes/coombeslab/-/blob/master/doc/papers/tolstoy-new.pdf>.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between TailRank versions 3.2.2 dated 2022-05-03 and 3.2.4 dated 2025-04-07
DESCRIPTION | 14 ++++++++------ MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/betabinomial.pdf |binary inst/doc/tailrank.pdf |binary man/tr06-beta-binomial.Rd | 4 ++-- 6 files changed, 15 insertions(+), 13 deletions(-)
Title: Make PX-Files in R
Description: Create PX-files from scratch or read and modify existing ones.
Includes a function for every PX keyword, making metadata manipulation
simple and human-readable.
Author: Johan Ejstrud [cre, aut],
Lars Pedersen [aut],
Statistics Greenland [cph]
Maintainer: Johan Ejstrud <johan@ejstrud.com>
Diff between pxmake versions 0.16.0 dated 2025-03-04 and 0.17.0 dated 2025-04-07
DESCRIPTION | 12 - MD5 | 64 ++--- NEWS.md | 14 + R/classification.R | 25 +- R/data_df.R | 2 R/excel.R | 2 R/metadata_df.R | 9 R/modify_data.R | 57 ++++ R/modify_helpers.R | 2 R/modify_languages.R | 2 R/modify_variable1.R | 17 + R/note_warning_error.R | 20 + R/px_base_tables.R | 12 - R/px_file.R | 3 README.md | 3 inst/doc/first-px-file.html | 2 man/new_classification.Rd | 4 man/px_classification.Rd | 14 - man/px_classification_from_df.Rd | 4 man/px_data.px.Rd | 6 man/validate_px_classification_arguments.Rd | 4 tests/testthat/fixtures/classification/25-years_classes_strangely_formatted.agg | 8 tests/testthat/fixtures/classification/BRCH_BRCH_E.agg |only tests/testthat/fixtures/classification/BRCH_OFF_E.agg |only tests/testthat/fixtures/classification/PXVSBRCHE.vs |only tests/testthat/helper.R | 1 tests/testthat/test-00-note_warning_error.R | 21 + tests/testthat/test-10-classification.R | 51 ++++ tests/testthat/test-12-classification_save.R | 14 + tests/testthat/test-13-classification-inverse.R | 4 tests/testthat/test-51-pxsave.R | 16 + tests/testthat/test-55-modify-cells2.R | 20 + tests/testthat/test-55-modify-data.R | 120 ++++++++++ tests/testthat/test-55-modify-variables1.R | 11 tests/testthat/test-57-contvariable.R |only 35 files changed, 459 insertions(+), 85 deletions(-)
Title: Processing Hemispherical Canopy Images
Description: Import and classify canopy fish-eye images, estimate angular gap fraction and derive canopy attributes like leaf area index and openness. Additional information is provided in the study by Chianucci F., Macek M. (2023) <doi:10.1016/j.agrformet.2023.109470>.
Author: Francesco Chianucci [aut, cre]
,
Martin Macek [aut]
Maintainer: Francesco Chianucci <fchianucci@gmail.com>
Diff between hemispheR versions 1.1.4 dated 2024-04-05 and 1.1.6 dated 2025-04-07
DESCRIPTION | 10 ++--- MD5 | 30 ++++++++-------- NEWS.md | 6 +++ R/binarize_fisheye.R | 29 ++++++++++++++-- R/gapfrac_fisheye.R | 47 ++++++++++++++++++++------ README.md | 54 ++++++++++++++---------------- build/partial.rdb |binary man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-13-1.png |binary man/figures/README-unnamed-chunk-14-1.png |binary man/figures/README-unnamed-chunk-15-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary 16 files changed, 115 insertions(+), 61 deletions(-)
Title: Handling HL7 FHIR® Resources in R
Description: Useful tools for conveniently downloading FHIR resources in xml format
and converting them to R data.frames. The package uses FHIR-search to download bundles
from a FHIR server, provides functions to save and read xml-files containing such bundles
and allows flattening the bundles to data.frames using XPath expressions. FHIR® is the registered trademark
of HL7 and is used with the permission of HL7. Use of the FHIR trademark does not constitute endorsement of this product by HL7.
Author: Thomas Peschel [aut],
Julia Palm [aut, cre] ,
Jens Przybilla [aut],
Frank Meineke [aut]
Maintainer: Julia Palm <julia.palm@med.uni-jena.de>
Diff between fhircrackr versions 2.2.0 dated 2024-03-21 and 2.3.0 dated 2025-04-07
DESCRIPTION | 12 MD5 | 50 NAMESPACE | 3 NEWS.md | 24 R/download_resources.R | 118 +- R/flatten_resources.R | 2 R/miscellaneous.R | 215 +++ R/multiple_entries.R | 524 +++++++- build/vignette.rds |binary data/example_bundles6.rda |only data/example_bundles7.rda |only data/example_bundles_empty.rda |only inst/doc/downloadResources.html | 6 inst/doc/fhircrackr_intro.html | 6 inst/doc/flattenResources.R | 40 inst/doc/flattenResources.Rmd | 106 + inst/doc/flattenResources.html | 182 ++- inst/doc/recreateResources.html | 6 man/datasets_selfmade.Rd | 138 ++ man/fhir_collapse.Rd |only man/fhir_columns-methods.Rd | 2 man/fhir_is_empty-methods.Rd |only man/fhir_melt_all.Rd |only man/fhir_melt_internal.Rd |only man/fhir_search.Rd | 14 tests/testthat/_snaps/fhir_collapse.md |only tests/testthat/_snaps/fhir_crack.md | 1932 ++++++++++++++++----------------- tests/testthat/test_fhir_collapse.R |only tests/testthat/test_fhir_melt_all.R |only tests/testthat/test_fhir_search.R | 67 + vignettes/flattenResources.Rmd | 106 + 31 files changed, 2368 insertions(+), 1185 deletions(-)
Title: Classes and Methods for "Class Discovery" with Microarrays or
Proteomics
Description: Defines the classes used for "class discovery" problems
in the OOMPA project (<http://oompa.r-forge.r-project.org/>). Class
discovery primarily consists of unsupervised clustering methods with
attempts to assess their statistical significance.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between ClassDiscovery versions 3.4.5 dated 2024-04-28 and 3.4.8 dated 2025-04-07
DESCRIPTION | 16 +++---- MD5 | 34 +++++++-------- R/cd02-cluster.R | 2 build/vignette.rds |binary inst/doc/maha-test.pdf |binary inst/doc/oompa-cd.pdf |binary man/cd01-0-distanceMatrix.Rd | 10 ++-- man/cd02-0-plotColoredClusters.Rd | 8 +-- man/cd02-1-cluster3.Rd | 2 man/cd03-0-ClusterTest-class.Rd | 4 - man/cd03-2-hclust-class.Rd | 6 +- man/cd03-3-justClusters.Rd | 18 +++---- man/cd05-0-SamplePCA-class.Rd | 6 +- man/cd05-1-GenePCA-class.Rd | 2 man/cd06-0-aspectHeatmap.Rd | 50 +++++++++++----------- man/cd07-0-Mosaic-class.Rd | 18 +++---- tests/test02-cluster.R | 2 tests/test02-cluster.Rout.save | 86 +++++++++++++++++++------------------- 18 files changed, 133 insertions(+), 131 deletions(-)
More information about ClassDiscovery at CRAN
Permanent link
Title: Mixed Data Sampling Regression
Description: Methods and tools for mixed frequency time series data analysis.
Allows estimation, model selection and forecasting for MIDAS regressions.
Author: Vaidotas Zemlys-Balevicius [cre],
Virmantas Kvedaras [aut],
Vaidotas Zemlys-Balevicius [aut]
Maintainer: Vaidotas Zemlys-Balevicius <zemlys@gmail.com>
Diff between midasr versions 0.8 dated 2021-02-23 and 0.9 dated 2025-04-07
DESCRIPTION | 28 LICENCE | 2 MD5 | 138 +-- NAMESPACE | 7 NEWS | 21 R/deriv.R | 20 R/imidasreg.R | 235 ++--- R/lagspec.R | 362 ++++---- R/midas_nlpr.R | 1152 +++++++++++++------------- R/midas_nlpr_methods.R | 595 +++++++------ R/midas_qr_methods.R | 167 ++- R/midas_r_methods.R | 981 +++++++++++----------- R/midas_sp.R | 1026 ++++++++++++----------- R/midas_sp_methods.R | 605 +++++++------ R/midaslag.R | 272 +++--- R/midasqr.R | 304 +++--- R/midasr-package.R | 64 - R/midasreg.R | 1624 ++++++++++++++++++------------------ R/modsel.R | 1719 +++++++++++++++++++-------------------- R/nonparametric.R | 392 ++++---- R/simulate.R | 561 ++++++------ R/tests.R | 230 ++--- README.md | 3 demo/RV.R | 83 - demo/autoreg.R | 30 demo/imidasr.R | 26 demo/logRV.R | 106 +- demo/nlpr.R | 86 + demo/okun.R | 56 - demo/pl.R | 25 demo/single_index.R | 27 man/USrealgdp.Rd | 2 man/amweights.Rd | 5 man/average_forecast.Rd | 4 man/check_mixfreq.Rd | 4 man/deriv_tests.Rd | 3 man/fmls.Rd | 2 man/genexp.Rd | 7 man/genexp_gradient.Rd | 7 man/hAhr_test.Rd | 2 man/harstep.Rd | 6 man/harstep_gradient.Rd | 6 man/imidas_r.Rd | 40 man/midas_lstr_plain.Rd | 4 man/midas_lstr_sim.Rd | 19 man/midas_mmm_plain.Rd | 4 man/midas_mmm_sim.Rd | 19 man/midas_nlpr.Rd | 6 man/midas_pl_sim.Rd | 11 man/midas_qr.Rd | 6 man/midas_r.Rd | 8 man/midas_r_ic_table.Rd | 2 man/midas_r_plain.Rd | 4 man/midas_si_sim.Rd | 11 man/midas_sim.Rd | 2 man/midas_sp.Rd | 8 man/midas_u.Rd | 2 man/midasr-package.Rd | 10 man/mlsd.Rd | 43 man/nbetaMT.Rd | 3 man/nbetaMT_gradient.Rd | 3 man/nealmon.Rd | 6 man/oos_prec.Rd | 2 man/rvsp500.Rd | 7 man/select_and_forecast.Rd | 2 tests/testthat/test_methods.R | 106 +- tests/testthat/test_midas_nlpr.R | 361 ++++---- tests/testthat/test_midas_sp.R | 239 ++--- tests/testthat/test_midaslag.R | 127 +- tests/testthat/test_midasr.R | 548 ++++++------ 70 files changed, 6547 insertions(+), 6051 deletions(-)
Title: Estimation of Meiotic Recombination Rates Using Marey Maps
Description: Local recombination rates are graphically estimated across a genome using Marey maps.
Author: Gabriel Marais [aut] ,
Clement Rezvoy [aut],
Delphine Charif [aut],
Laurent Gueguen [aut],
Aurelie Siberchicot [ctb, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between MareyMap versions 1.3.7 dated 2024-01-23 and 1.3.10 dated 2025-04-07
DESCRIPTION | 24 ++++++++++++++++++------ MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/vignette.Rnw | 1 + inst/doc/vignette.pdf |binary vignettes/vignette.Rnw | 1 + 6 files changed, 25 insertions(+), 11 deletions(-)
Title: Unsupervised Learning Based Definition of Microbial Rare
Biosphere
Description: A tool to define rare biosphere. 'ulrb' solves the problem of the
definition of rarity by replacing arbitrary thresholds with an unsupervised machine
learning algorithm (partitioning around medoids, or k-medoids). This algorithm
works for any type of microbiome data, provided there is an abundance table.
For validation of this method to different abundance tables, see Pascoal et al, 2025.
This method also works for non-microbiome data.
Author: Francisco Pascoal [aut, cre] ,
Paula Branco [aut] ,
Luis Torgo [aut] ,
Rodrigo Costa [aut] ,
Catarina Magalhaes [aut]
Maintainer: Francisco Pascoal <fpascoal1996@gmail.com>
Diff between ulrb versions 0.1.5 dated 2024-06-18 and 0.1.6 dated 2025-04-07
DESCRIPTION | 12 +-- MD5 | 78 +++++++++++----------- R/check_CH.R | 3 R/check_DB.R | 6 - R/check_avgSil.R | 6 + R/define_rb.R | 31 ++++----- R/plot_ulrb.R | 67 ++++++++++++------- R/plot_ulrb_clustering.R | 59 ++++++++++++----- R/plot_ulrb_silhouette.R | 54 +++++++++++---- R/prepare_tidy_data.R | 11 +-- R/suggest_k.R | 2 README.md | 74 ++++++++++++--------- build/vignette.rds |binary inst/CITATION | 15 +++- inst/doc/eco-analysis.R | 4 - inst/doc/eco-analysis.Rmd | 4 - inst/doc/eco-analysis.html | 8 +- inst/doc/explore-classifications.R | 2 inst/doc/explore-classifications.Rmd | 6 + inst/doc/explore-classifications.html | 99 ++++++++++++++--------------- inst/doc/ulrb-vignet.R | 2 inst/doc/ulrb-vignet.Rmd | 12 +-- inst/doc/ulrb-vignet.html | 85 ++++++++++++------------ man/check_CH.Rd | 5 - man/check_DB.Rd | 7 +- man/check_avgSil.Rd | 5 - man/define_rb.Rd | 25 +++---- man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-3-2.png |binary man/figures/README-unnamed-chunk-4-1.png |only man/figures/README-unnamed-chunk-4-2.png |only man/plot_ulrb.Rd | 8 +- man/plot_ulrb_clustering.Rd | 7 +- man/plot_ulrb_silhouette.Rd | 13 ++- man/prepare_tidy_data.Rd | 10 +- man/suggest_k.Rd | 2 tests/testthat/test-plot_ulrb_clustering.R | 33 ++++++--- tests/testthat/test-plot_ulrb_silhouette.R | 30 +++++--- vignettes/eco-analysis.Rmd | 4 - vignettes/explore-classifications.Rmd | 6 + vignettes/ulrb-vignet.Rmd | 12 +-- 41 files changed, 464 insertions(+), 343 deletions(-)
Title: Sourcing Archaeological Materials by Chemical Composition
Description: Exploration and analysis of compositional data in the
framework of Aitchison (1986, ISBN: 978-94-010-8324-9). This package
provides tools for chemical fingerprinting and source tracking of
ancient materials.
Author: Nicolas Frerebeau [aut, cre] ,
Anne Philippe [aut] ,
Brice Lebrun [art] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between nexus versions 0.4.0 dated 2025-01-14 and 0.5.0 dated 2025-04-07
nexus-0.4.0/nexus/inst/tinytest/test_tools.R |only nexus-0.4.0/nexus/man/group_extract.Rd |only nexus-0.5.0/nexus/DESCRIPTION | 42 ++-- nexus-0.5.0/nexus/MD5 | 119 ++++++----- nexus-0.5.0/nexus/NAMESPACE | 2 nexus-0.5.0/nexus/NEWS.md | 10 nexus-0.5.0/nexus/R/AllGenerics.R | 17 - nexus-0.5.0/nexus/R/barplot.R | 22 +- nexus-0.5.0/nexus/R/bind.R |only nexus-0.5.0/nexus/R/chemistry.R | 9 nexus-0.5.0/nexus/R/coerce.R | 10 nexus-0.5.0/nexus/R/condense.R | 17 + nexus-0.5.0/nexus/R/describe.R | 38 ++- nexus-0.5.0/nexus/R/group.R | 49 ++-- nexus-0.5.0/nexus/R/hist.R | 2 nexus-0.5.0/nexus/R/mean.R | 24 +- nexus-0.5.0/nexus/R/nexus-internal.R | 18 + nexus-0.5.0/nexus/R/nexus-package.R | 2 nexus-0.5.0/nexus/R/outliers.R | 41 ++-- nexus-0.5.0/nexus/R/pca.R | 2 nexus-0.5.0/nexus/R/split.R | 84 ++------ nexus-0.5.0/nexus/README.md | 27 +- nexus-0.5.0/nexus/build/partial.rdb |binary nexus-0.5.0/nexus/build/vignette.rds |binary nexus-0.5.0/nexus/inst/doc/groups.Rmd | 1 nexus-0.5.0/nexus/inst/doc/groups.html | 213 ++++++++------------- nexus-0.5.0/nexus/inst/doc/nexus.Rmd | 1 nexus-0.5.0/nexus/inst/doc/nexus.html | 199 ++++++++----------- nexus-0.5.0/nexus/inst/examples/ex-outliers.R | 2 nexus-0.5.0/nexus/inst/examples/ex-split.R | 10 nexus-0.5.0/nexus/inst/fr |only nexus-0.5.0/nexus/inst/po |only nexus-0.5.0/nexus/inst/tinytest/test_chemistry.R |only nexus-0.5.0/nexus/inst/tinytest/test_coerce.R | 2 nexus-0.5.0/nexus/inst/tinytest/test_condense.R | 4 nexus-0.5.0/nexus/inst/tinytest/test_describe.R | 2 nexus-0.5.0/nexus/inst/tinytest/test_dist.R | 2 nexus-0.5.0/nexus/inst/tinytest/test_group.R | 26 +- nexus-0.5.0/nexus/inst/tinytest/test_mutators.R | 2 nexus-0.5.0/nexus/inst/tinytest/test_outliers.R | 2 nexus-0.5.0/nexus/inst/tinytest/test_pca.R | 2 nexus-0.5.0/nexus/inst/tinytest/test_plot.R | 2 nexus-0.5.0/nexus/inst/tinytest/test_replace.R | 2 nexus-0.5.0/nexus/inst/tinytest/test_simplex.R | 2 nexus-0.5.0/nexus/inst/tinytest/test_statistics.R | 12 - nexus-0.5.0/nexus/inst/tinytest/test_subset.R | 2 nexus-0.5.0/nexus/inst/tinytest/test_transform.R | 2 nexus-0.5.0/nexus/man/barplot.Rd | 3 nexus-0.5.0/nexus/man/bind.Rd | 15 - nexus-0.5.0/nexus/man/condense.Rd | 19 + nexus-0.5.0/nexus/man/detect_outlier.Rd | 6 nexus-0.5.0/nexus/man/figures/README-barplot-1.png |binary nexus-0.5.0/nexus/man/figures/README-lra-2.png |binary nexus-0.5.0/nexus/man/gmean.Rd | 8 nexus-0.5.0/nexus/man/group.Rd | 4 nexus-0.5.0/nexus/man/group_metadata.Rd | 4 nexus-0.5.0/nexus/man/group_split.Rd | 32 +-- nexus-0.5.0/nexus/man/group_subset.Rd |only nexus-0.5.0/nexus/man/mean.Rd | 10 nexus-0.5.0/nexus/man/nexus-package.Rd | 6 nexus-0.5.0/nexus/man/plot_outlier.Rd | 2 nexus-0.5.0/nexus/po |only nexus-0.5.0/nexus/vignettes/groups.Rmd | 1 nexus-0.5.0/nexus/vignettes/nexus.Rmd | 1 64 files changed, 589 insertions(+), 547 deletions(-)
Title: A Simple Graphical Representation of the Relative Occurrence and
Co-Occurrence of Events
Description: The unique function of this package allows representing in a single graph the relative occurrence and co-occurrence of events measured in a sample.
As examples, the package was applied to describe the occurrence and co-occurrence of different species of bacterial or viral symbionts infecting arthropods at the individual level. The graphics allows determining the prevalence of each symbiont and the patterns of multiple infections (i.e. how different symbionts share or not the same individual hosts).
We named the package after the famous painter as the graphical output recalls Mondrian’s paintings.
Author: Aurelie Siberchicot [aut, cre]
,
Delphine Charif [aut],
Gabriel Terraz [aut],
Fabrice Vavre [aut]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between Mondrian versions 1.1-1 dated 2024-01-19 and 1.1.2 dated 2025-04-07
DESCRIPTION | 20 ++++++++++++++------ MD5 | 4 ++-- inst/MondrianShiny/ui.R | 6 +++--- 3 files changed, 19 insertions(+), 11 deletions(-)
Title: An S4 Lattice-Based Package for the Representation of
Multivariate Data
Description: Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.
Author: Stephane Dray [aut] ,
Aurelie Siberchicot [aut, cre]
,
Jean Thioulouse [ctb] ,
Alice Julien-Laferriere [ctb]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between adegraphics versions 1.0-21 dated 2023-10-13 and 1.0-22 dated 2025-04-07
DESCRIPTION | 28 +- MD5 | 34 +- R/ADEg.Tr.R | 34 +- R/C1.density.R | 2 R/C1.gauss.R | 2 R/Tr.traject.R | 4 R/ade4-plot.R | 12 build/vignette.rds |binary inst/doc/FAQ.R |only inst/doc/FAQ.Rmd |only inst/doc/FAQ.html |only inst/doc/adegraphics.R | 26 +- inst/doc/adegraphics.Rmd | 25 +- inst/doc/adegraphics.html | 554 +++++++++++++++++++++------------------------- man/plot.inertia.Rd | 7 man/triangle.traject.Rd | 7 tests/ade4-functions.R | 6 tests/panelSpatial.R | 16 - vignettes/FAQ.Rmd |only vignettes/adegraphics.Rmd | 25 +- 20 files changed, 389 insertions(+), 393 deletions(-)
Title: High-Level Plotting Built Upon 'ggplot2' and Other Plotting
Packages
Description: Provides high-level API and a wide range of options to create stunning, publication-quality plots effortlessly.
It is built upon 'ggplot2' and other plotting packages, and is designed to be easy to use and to work seamlessly with 'ggplot2' objects.
It is particularly useful for creating complex plots with multiple layers, facets, and annotations.
It also provides a set of functions to create plots for specific types of data, such as Venn diagrams, alluvial diagrams, and phylogenetic trees.
The package is designed to be flexible and customizable, and to work well with the 'ggplot2' ecosystem.
The API can be found at <https://pwwang.github.io/plotthis/reference/index.html>.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>
Diff between plotthis versions 0.6.0 dated 2025-04-04 and 0.6.1 dated 2025-04-07
DESCRIPTION | 16 +++++++-------- MD5 | 10 ++++----- R/heatmap.R | 54 +++++++++++++++++++++++++++++++++++++++++++++++++-- R/manhattanplot.R | 28 +++++++++++++++++++++++++- man/Heatmap.Rd | 48 +++++++++++++++++++++++++++++++++++++++++++++ man/ManhattanPlot.Rd | 28 +++++++++++++++++++++++++- 6 files changed, 167 insertions(+), 17 deletions(-)
Title: Core Functions for Data Quality Assessment
Description: Perform data quality assessment ('DQA') of electronic health
records ('EHR'). Publication: Kapsner et al. (2021)
<doi:10.1055/s-0041-1733847>.
Author: Lorenz A. Kapsner [cre, aut] ,
Jonathan M. Mang [aut] ,
Helene Koester [ctb],
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen [cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between DQAstats versions 0.3.8 dated 2025-03-26 and 0.3.9 dated 2025-04-07
DESCRIPTION | 8 MD5 | 18 R/utils.R | 240 +++--- inst/doc/DQAstats2SHIPdataset.qmd | 1012 ++++++++++++++-------------- tests/testthat/_snaps/stats.md | 54 - tests/testthat/test-conformance.R | 308 ++++---- tests/testthat/test-datetime_restrictions.R | 239 +++--- tests/testthat/test-render_conformance.R | 332 ++++----- tests/testthat/test-stats.R | 9 vignettes/DQAstats2SHIPdataset.qmd | 1012 ++++++++++++++-------------- 10 files changed, 1621 insertions(+), 1611 deletions(-)
Title: Access Data from the Norwegian Parliament API
Description: Functions for retrieving general and specific data from the Norwegian Parliament,
through the Norwegian Parliament API at <https://data.stortinget.no>.
Author: Martin Soeyland [aut, cre]
Maintainer: Martin Soeyland <martin.soyland@stv.uio.no>
Diff between stortingscrape versions 0.4.0 dated 2025-03-07 and 0.4.1 dated 2025-04-07
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 6 ++++++ R/get_topics.R | 3 ++- build/vignette.rds |binary inst/doc/stortingscrape.Rmd | 2 +- inst/doc/stortingscrape.html | 8 ++++---- man/get_topics.Rd | 3 ++- vignettes/stortingscrape.Rmd | 2 +- 9 files changed, 27 insertions(+), 19 deletions(-)
More information about stortingscrape at CRAN
Permanent link
Title: Probabilistic Population Projection
Description: Generating population projections for all countries of the world using several probabilistic components, such as total fertility rate and life expectancy (Raftery et al., 2012 <doi:10.1073/pnas.1211452109>).
Author: Hana Sevcikova [aut, cre],
Adrian Raftery [aut],
Thomas Buettner [aut]
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between bayesPop versions 11.0-2 dated 2025-02-21 and 11.0-3 dated 2025-04-07
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/predict.pop.R | 10 ++++++---- 4 files changed, 17 insertions(+), 11 deletions(-)
Title: Densities and Sampling for the Skellam Distribution
Description: Functions for the Skellam distribution, including: density
(pmf), cdf, quantiles and regression.
Author: Jerry W. Lewis [aut],
Patrick E. Brown [aut],
Michail Tsagris [aut],
Montasser Ghachem [cre]
Maintainer: Montasser Ghachem <mg@pinstimation.com>
Diff between skellam versions 0.2.3 dated 2024-03-25 and 0.2.4 dated 2025-04-07
skellam-0.2.3/skellam/inst/doc/skellam.R |only skellam-0.2.3/skellam/inst/doc/skellam.pdf |only skellam-0.2.3/skellam/inst/doc/skellam.rnw |only skellam-0.2.3/skellam/vignettes/skellam.rnw |only skellam-0.2.4/skellam/DESCRIPTION | 31 + skellam-0.2.4/skellam/MD5 | 36 +- skellam-0.2.4/skellam/NEWS.md |only skellam-0.2.4/skellam/R/dskellam.r | 108 ++++++ skellam-0.2.4/skellam/R/dskellam.sp.r | 1 skellam-0.2.4/skellam/R/pskellam.r | 1 skellam-0.2.4/skellam/R/pskellam.sp.r | 1 skellam-0.2.4/skellam/R/qskellam.r | 1 skellam-0.2.4/skellam/R/rskellam.r | 1 skellam-0.2.4/skellam/R/skellam.mle.R | 73 ++++ skellam-0.2.4/skellam/R/skellam.reg.R | 67 +++- skellam-0.2.4/skellam/README.md |only skellam-0.2.4/skellam/build/vignette.rds |binary skellam-0.2.4/skellam/inst/doc/validate_skellam.R |only skellam-0.2.4/skellam/inst/doc/validate_skellam.Rmd |only skellam-0.2.4/skellam/inst/doc/validate_skellam.html |only skellam-0.2.4/skellam/man/skellam.Rd | 298 ++++++++----------- skellam-0.2.4/skellam/man/skellam.mle.Rd | 144 ++++----- skellam-0.2.4/skellam/man/skellam.reg.Rd | 126 ++++---- skellam-0.2.4/skellam/vignettes/validate_skellam.Rmd |only 24 files changed, 549 insertions(+), 339 deletions(-)
Title: Bayesian Modeling and Causal Inference for Multivariate
Longitudinal Data
Description: Easy-to-use and efficient interface for
Bayesian inference of complex panel (time series) data using dynamic
multivariate panel models by Helske and Tikka (2024)
<doi:10.1016/j.alcr.2024.100617>. The package supports joint modeling of
multiple measurements per individual, time-varying and time-invariant
effects, and a wide range of discrete and continuous distributions.
Estimation of these dynamic multivariate panel models is carried out via
'Stan'. For an in-depth tutorial of the package, see
(Tikka and Helske, 2024) <doi:10.48550/arXiv.2302.01607>.
Author: Santtu Tikka [aut, cre] ,
Jouni Helske [aut] ,
Nicholas Clark [rev],
Lucy D'Agostino McGowan [rev]
Maintainer: Santtu Tikka <santtuth@gmail.com>
Diff between dynamite versions 1.5.5 dated 2024-11-15 and 1.5.6 dated 2025-04-07
dynamite-1.5.5/dynamite/tests/testthat/Rplots.pdf |only dynamite-1.5.6/dynamite/DESCRIPTION | 6 dynamite-1.5.6/dynamite/MD5 | 147 dynamite-1.5.6/dynamite/NEWS.md | 5 dynamite-1.5.6/dynamite/R/as_data_frame.R | 278 dynamite-1.5.6/dynamite/R/as_data_table.R | 1634 +-- dynamite-1.5.6/dynamite/R/as_draws.R | 174 dynamite-1.5.6/dynamite/R/ci.R | 120 dynamite-1.5.6/dynamite/R/coef.R | 90 dynamite-1.5.6/dynamite/R/deprecated.R | 94 dynamite-1.5.6/dynamite/R/deterministic.R | 466 dynamite-1.5.6/dynamite/R/dynamice.R | 1000 +- dynamite-1.5.6/dynamite/R/dynamite-package.R | 542 - dynamite-1.5.6/dynamite/R/dynamite.R | 2478 ++--- dynamite-1.5.6/dynamite/R/dynamiteformula.R | 27 dynamite-1.5.6/dynamite/R/families.R | 278 dynamite-1.5.6/dynamite/R/fitted.R | 14 dynamite-1.5.6/dynamite/R/getters.R | 732 - dynamite-1.5.6/dynamite/R/lags.R | 11 dynamite-1.5.6/dynamite/R/latent_factor.R | 184 dynamite-1.5.6/dynamite/R/lfo.R | 712 - dynamite-1.5.6/dynamite/R/loo.R | 218 dynamite-1.5.6/dynamite/R/mcmc_diagnostics.R | 314 dynamite-1.5.6/dynamite/R/model_matrix.R | 10 dynamite-1.5.6/dynamite/R/ndraws.R | 54 dynamite-1.5.6/dynamite/R/nobs.R | 72 dynamite-1.5.6/dynamite/R/plot.R | 1314 +- dynamite-1.5.6/dynamite/R/predict.R | 3 dynamite-1.5.6/dynamite/R/predict_helpers.R | 3116 +++--- dynamite-1.5.6/dynamite/R/prepare_stan_input.R | 2 dynamite-1.5.6/dynamite/R/print.R | 214 dynamite-1.5.6/dynamite/R/random.R | 92 dynamite-1.5.6/dynamite/R/specials.R | 662 - dynamite-1.5.6/dynamite/R/splines.R | 196 dynamite-1.5.6/dynamite/R/stan_utilities.R | 35 dynamite-1.5.6/dynamite/R/stanblocks.R | 1920 +-- dynamite-1.5.6/dynamite/R/stanblocks_families.R | 4896 +++++----- dynamite-1.5.6/dynamite/R/summary.R | 60 dynamite-1.5.6/dynamite/R/update.R | 292 dynamite-1.5.6/dynamite/R/utilities.R | 956 + dynamite-1.5.6/dynamite/README.md | 24 dynamite-1.5.6/dynamite/build/vignette.rds |binary dynamite-1.5.6/dynamite/inst/CITATION | 66 dynamite-1.5.6/dynamite/inst/doc/dynamite.html | 240 dynamite-1.5.6/dynamite/inst/doc/dynamite.qmd | 4 dynamite-1.5.6/dynamite/inst/doc/dynamite_priors.html | 158 dynamite-1.5.6/dynamite/inst/doc/dynamite_priors.qmd | 12 dynamite-1.5.6/dynamite/inst/doc/dynamite_simulation.html | 23 dynamite-1.5.6/dynamite/inst/doc/dynamite_simulation.qmd | 493 - dynamite-1.5.6/dynamite/man/figures/README-unnamed-chunk-10-1.png |binary dynamite-1.5.6/dynamite/man/figures/README-unnamed-chunk-7-1.png |binary dynamite-1.5.6/dynamite/man/figures/README-unnamed-chunk-8-1.png |binary dynamite-1.5.6/dynamite/man/figures/README-unnamed-chunk-9-1.png |binary dynamite-1.5.6/dynamite/man/fitted.dynamitefit.Rd | 14 dynamite-1.5.6/dynamite/man/get_algorithm.Rd | 50 dynamite-1.5.6/dynamite/man/get_diagnostics.Rd | 50 dynamite-1.5.6/dynamite/man/get_draws.Rd | 54 dynamite-1.5.6/dynamite/man/get_elapsed_time.Rd | 50 dynamite-1.5.6/dynamite/man/get_max_treedepth.Rd | 50 dynamite-1.5.6/dynamite/man/get_model_code.Rd | 50 dynamite-1.5.6/dynamite/man/get_nchains.Rd | 50 dynamite-1.5.6/dynamite/man/get_ndraws.Rd | 50 dynamite-1.5.6/dynamite/man/get_pars_oi.Rd | 50 dynamite-1.5.6/dynamite/man/plot.dynamiteformula.Rd | 130 dynamite-1.5.6/dynamite/tests/testthat/test-cmdstanr.R | 1194 +- dynamite-1.5.6/dynamite/tests/testthat/test-edgecases.R | 1196 +- dynamite-1.5.6/dynamite/tests/testthat/test-extended.R | 76 dynamite-1.5.6/dynamite/tests/testthat/test-internals.R | 468 dynamite-1.5.6/dynamite/tests/testthat/test-lfactor.R | 348 dynamite-1.5.6/dynamite/tests/testthat/test-output.R | 1012 +- dynamite-1.5.6/dynamite/tests/testthat/test-scaling.R | 348 dynamite-1.5.6/dynamite/vignettes/dynamite.bib | 1460 +- dynamite-1.5.6/dynamite/vignettes/dynamite.qmd | 4 dynamite-1.5.6/dynamite/vignettes/dynamite_priors.qmd | 12 dynamite-1.5.6/dynamite/vignettes/dynamite_simulation.qmd | 493 - 75 files changed, 15766 insertions(+), 15881 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-17 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-03-14 0.5
2012-04-30 0.4
2012-03-26 0.3
2012-02-22 0.2
2011-06-05 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-24 2.0.0
2023-10-16 1.2.1
2023-01-09 1.1.0
2022-07-21 1.0.2
2020-01-08 0.7.0
2019-12-19 0.6.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-08 0.1.1
2019-02-27 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-04 0.3.1
2021-10-13 0.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-26 0.1.4
2020-02-07 0.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-15 2.2.16