Title: 'tint' is not 'Tufte'
Description: A 'tufte'-alike style for 'rmarkdown'.
A modern take on the 'Tufte' design for pdf and html vignettes,
building on the 'tufte' package with additional contributions
from the 'knitr' and 'ggtufte' package, and also acknowledging
the key influence of 'envisioned css'.
Author: Dirk Eddelbuettel [aut, cre] ,
Jonathan Gilligan [ctb]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between tint versions 0.1.4 dated 2022-11-01 and 0.1.5 dated 2025-03-27
ChangeLog | 24 ++++++ DESCRIPTION | 19 +++-- MD5 | 18 ++--- R/html.R | 6 - README.md | 6 - build/vignette.rds |binary inst/NEWS.Rd | 8 ++ inst/doc/tintHtmlIntro.html | 154 ++++++++++++++++++++++++++++++-------------- inst/doc/tintPdfIntro.pdf |binary man/tintHtml.Rd | 37 +++++++--- 10 files changed, 192 insertions(+), 80 deletions(-)
Title: Design of Experiments and Factorial Plans Utilities
Description: A number of functions to create and analyze factorial plans according to the Design of Experiments (DoE) approach, with the addition of some utility function to perform some statistical analyses. DoE approach follows the approach in "Design and Analysis of Experiments" by Douglas C. Montgomery (2019, ISBN:978-1-119-49244-3). The package also provides utilities used in the course "Analysis of Data and Statistics" at the University of Trento, Italy.
Author: Paolo Bosetti [aut, cre]
Maintainer: Paolo Bosetti <paolo.bosetti@unitn.it>
Diff between adas.utils versions 1.1.0 dated 2025-03-27 and 1.1.1 dated 2025-03-27
DESCRIPTION | 6 - MD5 | 16 ++- NEWS.md | 4 R/stats.R | 7 - README.md | 34 ++++---- inst/doc/adas.utils.html | 130 +++++++++++++++---------------- man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |only man/figures/README-unnamed-chunk-6-2.png |only man/ggTukey.data.frame.Rd | 2 10 files changed, 105 insertions(+), 94 deletions(-)
Title: Vertical Profiles of Biological Signals in Weather Radar Data
Description: 'R' implementation of the 'vol2bird' software for generating vertical profiles
of birds and other biological signals in weather radar data. See Dokter et al.
(2011) <doi:10.1098/rsif.2010.0116> for a paper describing the methodology.
Author: Anders Henja [aut] ,
Adriaan M. Dokter [aut, cre] ,
Alexander Tedeschi [ctb] ,
Tsung-Yu Lin [ctb] ,
Subranshu Maji [ctb] ,
Daniel Sheldon [ctb] ,
Bart Kranstauber [ctb] ,
Jurriaan H. Spaaks [ctb] ,
Lourens Veen [ctb] ,
Iwan Holleman [ctb] ,
Hidde Lei [...truncated...]
Maintainer: Adriaan M. Dokter <vol2birdr@cornell.edu>
Diff between vol2birdR versions 1.0.7 dated 2025-02-21 and 1.0.8 dated 2025-03-27
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- NAMESPACE | 1 + NEWS.md | 7 ++++++- R/install.R | 37 +++++++++++++++++++++++++++++++++++++ README.md | 41 ++++++++++++++++++++++------------------- man/mistnet_exists.Rd | 6 ++++++ man/mistnet_installed.Rd |only src/librsl/range.c | 8 ++++++-- src/libvol2bird/librsl.c | 3 --- src/libvol2bird/libvol2bird.c | 4 ++-- 11 files changed, 94 insertions(+), 40 deletions(-)
Title: Classical, Reloaded and Adaptive FastICA Algorithms
Description: Algorithms for classical symmetric and deflation-based FastICA, reloaded deflation-based FastICA algorithm and an algorithm for adaptive deflation-based FastICA using multiple nonlinearities. For details, see Miettinen et al. (2014) <doi:10.1109/TSP.2014.2356442> and Miettinen et al. (2017) <doi:10.1016/j.sigpro.2016.08.028>. The package is described in Miettinen, Nordhausen and Taskinen (2018) <doi:10.32614/RJ-2018-046>.
Author: Jari Miettinen [aut] ,
Klaus Nordhausen [aut, cre] ,
Hannu Oja [aut] ,
Sara Taskinen [aut]
Maintainer: Klaus Nordhausen <klausnordhausenr@gmail.com>
Diff between fICA versions 1.1-2 dated 2021-12-08 and 1.1-3 dated 2025-03-27
DESCRIPTION | 22 +++++++++++----------- MD5 | 7 ++++--- build |only inst/ChangeLog | 4 ++++ man/fICA-package.Rd | 19 ++++++------------- 5 files changed, 25 insertions(+), 27 deletions(-)
Title: Diagnostic Tools for Asymptotic Theory
Description: Leveraging Monte Carlo simulations, this package provides
tools for diagnosing regression models. It implements a parametric
bootstrap framework to compute statistics, generates diagnostic
envelopes to assess goodness-of-fit, and evaluates type I error
control for Wald tests. By simulating data under the assumption that
the model is true, it helps to identify model mis-specifications and
enhances the reliability of the model inferences.
Author: Alvaro Kothe [aut, cre, cph] ,
Alexandre Patriota [aut]
Maintainer: Alvaro Kothe <kothe65@gmail.com>
Diff between asympDiag versions 0.3.0 dated 2025-03-26 and 0.3.1 dated 2025-03-27
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/envelope.R | 6 ++++-- man/envelope.Rd | 1 - man/plot.AD_envelope.Rd | 2 +- tests/testthat/Rplots.pdf |binary tests/testthat/test-envelope.R | 18 ++++++++++++++++-- 7 files changed, 30 insertions(+), 15 deletions(-)
Title: Detection and Control of Tree-Ring Widths on Scanned Image
Sections
Description: Identification of ring borders on scanned image sections from dendrochronological samples. Processing of image reflectances to produce gray matrices and time series of smoothed gray values. Luminance data is plotted on segmented images for users to perform both: visual identification of ring borders or control of automatic detection. Routines to visually include/exclude ring borders on the R graphical devices, or automatically detect ring borders using a linear detection algorithm. This algorithm detects ring borders according to positive/negative extreme values in the smoothed time-series of gray values. Most of the in-package routines can be recursively implemented using the multiDetect() function.
Author: Wilson Lara [aut, cre] ,
Carlos Sierra [aut] ,
Felipe Bravo [aut]
Maintainer: Wilson Lara <wilarhen@gmail.com>
Diff between measuRing versions 0.5 dated 2018-02-20 and 0.5.1 dated 2025-03-27
DESCRIPTION | 27 ++- MD5 | 40 ++--- NEWS | 5 R/crossRings.R | 22 +- build/partial.rdb |binary inst/CITATION | 13 - man/colNarrow.Rd | 80 +++++----- man/crossRings.Rd | 104 +++++++------- man/dataSegments.Rd | 75 +++++----- man/grayDarker.Rd | 73 +++++---- man/graySmoothed.Rd | 69 ++++----- man/imageTogray.Rd | 104 +++++++------- man/lagIngray.Rd | 73 +++++---- man/linearDetect.Rd | 67 ++++----- man/multiDetect.Rd | 84 +++++------ man/plotSegments.Rd | 120 ++++++++-------- man/reduceList.Rd | 75 +++++----- man/ringBorders.Rd | 116 ++++++++------- man/ringDetect.Rd | 382 ++++++++++++++++++++++++++-------------------------- man/ringSelect.Rd | 128 ++++++++--------- man/ringWidths.Rd | 79 +++++----- 21 files changed, 883 insertions(+), 853 deletions(-)
Title: Simulation, Visualization and Comparison of Tumor Evolution Data
Description: Simulating, visualizing and comparing tumor clonal data by using simple commands. This aims at providing a tool to help researchers to easily simulate tumor data and analyze the results of their approaches for studying the composition and the evolutionary history of tumors.
Author: Aitor Sanchez-Ferrera [cre, aut]
,
Maitena Tellaetxe-Abete [aut] ,
Borja Calvo [aut]
Maintainer: Aitor Sanchez-Ferrera <aitor.sanchezf@ehu.eus>
Diff between GeRnika versions 1.0.0 dated 2024-09-04 and 1.1.0 dated 2025-03-27
GeRnika-1.0.0/GeRnika/data/hyperparameters.rda |only GeRnika-1.0.0/GeRnika/man/Node-class.Rd |only GeRnika-1.0.0/GeRnika/man/calc_clone_proportions.Rd |only GeRnika-1.0.0/GeRnika/man/dot-distribute_freqs.Rd |only GeRnika-1.0.0/GeRnika/man/get_clones.Rd |only GeRnika-1.0.0/GeRnika/man/get_genes.Rd |only GeRnika-1.0.0/GeRnika/man/get_parents.Rd |only GeRnika-1.0.0/GeRnika/man/hyperparameters.Rd |only GeRnika-1.0.0/GeRnika/man/phylotree_to_B.Rd |only GeRnika-1.0.0/GeRnika/man/phylotree_to_tree.Rd |only GeRnika-1.0.0/GeRnika/man/place_clones_space.Rd |only GeRnika-1.0.0/GeRnika/man/plot_p.Rd |only GeRnika-1.0.0/GeRnika/man/plot_phylotree.Rd |only GeRnika-1.1.0/GeRnika/DESCRIPTION | 6 GeRnika-1.1.0/GeRnika/MD5 | 62 -- GeRnika-1.1.0/GeRnika/NAMESPACE | 5 GeRnika-1.1.0/GeRnika/R/data.R | 74 +- GeRnika-1.1.0/GeRnika/R/generate_instances.R | 185 +---- GeRnika-1.1.0/GeRnika/R/phylotree_class.R | 65 -- GeRnika-1.1.0/GeRnika/R/tree.R | 32 - GeRnika-1.1.0/GeRnika/R/utils.R | 62 +- GeRnika-1.1.0/GeRnika/README.md | 134 ++-- GeRnika-1.1.0/GeRnika/build/vignette.rds |binary GeRnika-1.1.0/GeRnika/data/B_mats.rda |binary GeRnika-1.1.0/GeRnika/inst/doc/models.R | 25 GeRnika-1.1.0/GeRnika/inst/doc/models.Rmd | 617 ++++++++++---------- GeRnika-1.1.0/GeRnika/inst/doc/models.html | 395 ++++-------- GeRnika-1.1.0/GeRnika/inst/doc/usage.R | 68 +- GeRnika-1.1.0/GeRnika/inst/doc/usage.Rmd | 80 +- GeRnika-1.1.0/GeRnika/inst/doc/usage.html | 259 +++----- GeRnika-1.1.0/GeRnika/man/B_mats.Rd | 22 GeRnika-1.1.0/GeRnika/man/add_noise.Rd | 6 GeRnika-1.1.0/GeRnika/man/combine_trees.Rd | 14 GeRnika-1.1.0/GeRnika/man/create_F.Rd |only GeRnika-1.1.0/GeRnika/man/create_U.Rd | 28 GeRnika-1.1.0/GeRnika/man/equals.Rd | 8 GeRnika-1.1.0/GeRnika/man/find_common_subtrees.Rd | 10 GeRnika-1.1.0/GeRnika/vignettes/models.Rmd | 617 ++++++++++---------- GeRnika-1.1.0/GeRnika/vignettes/usage.Rmd | 80 +- 39 files changed, 1309 insertions(+), 1545 deletions(-)
Title: Visualization Package for CanvasXpress in R
Description: Enables creation of visualizations using the CanvasXpress framework
in R. CanvasXpress is a standalone JavaScript library for reproducible research
with complete tracking of data and end-user modifications stored in a single
PNG image that can be played back. See <https://www.canvasxpress.org> for more
information.
Author: Isaac Neuhaus [aut],
Connie Brett [aut, cre]
Maintainer: Connie Brett <connie@aggregate-genius.com>
Diff between canvasXpress versions 1.50.5 dated 2024-06-23 and 1.55.9 dated 2025-03-27
DESCRIPTION | 8 MD5 | 115 +- NEWS.md | 4 R/canvasXpress.R | 16 R/ggplot_as_list.R | 760 ++++++++++++---- R/internal_functionality.R | 11 README.md |only inst/README-known_issues.md | 2 inst/doc/additional_examples.Rmd | 2 inst/doc/additional_examples.html | 24 inst/doc/getting_started.Rmd | 24 inst/doc/getting_started.html | 44 inst/htmlwidgets/canvasXpress.js | 129 ++ inst/htmlwidgets/canvasXpress.yaml | 2 inst/htmlwidgets/lib/canvasXpress/canvasXpress.css | 831 +++++++++++++++--- inst/htmlwidgets/lib/canvasXpress/canvasXpress.min.js | 8 inst/shiny-examples/example2/server.R | 3 inst/ui-examples/cX-function.R.gz |binary tests/testthat/setup.R | 16 tests/testthat/test-other-bar-data-types.R | 6 tests/testthat/test-other-boxplot-grouping.R | 4 tests/testthat/test-other-color-setting.R | 16 tests/testthat/test-other-custom-events.R | 6 tests/testthat/test-other-cxHtmlPage.R | 4 tests/testthat/test-other-data-url.R | 4 tests/testthat/test-other-decorations.R | 26 tests/testthat/test-other-differentiated-groups.R | 12 tests/testthat/test-other-duplicated-labels.R | 8 tests/testthat/test-other-ggplot.R | 2 tests/testthat/test-other-ggplot_as_list.R | 17 tests/testthat/test-other-legend-position.R | 26 tests/testthat/test-other-legend-title.R | 32 tests/testthat/test-other-network-data-types.R | 12 tests/testthat/test-other-null-data.R | 20 tests/testthat/test-other-numeric-colorkey.R | 4 tests/testthat/test-other-piping.R | 27 tests/testthat/test-other-regression-lines.R | 14 tests/testthat/test-other-resizable.R | 10 tests/testthat/test-other-segregation-layout-change.R | 18 tests/testthat/test-other-segregation-ordering.R | 4 tests/testthat/test-other-segregation-title.R | 8 tests/testthat/test-other-segregation-tooltips.R | 4 tests/testthat/test-other-segregation-violin.R | 4 tests/testthat/test-other-table-view.R | 20 tests/testthat/test-other-toolbartype.R | 22 tests/testthat/test-other-zoom-disable.R | 28 tests/testthat/test-ui-area.R | 32 tests/testthat/test-ui-arealine.R | 4 tests/testthat/test-ui-bar.R | 12 tests/testthat/test-ui-boxplot.R | 8 tests/testthat/test-ui-heatmap.R | 4 tests/testthat/test-ui-kaplanmeier.R | 18 tests/testthat/test-ui-layout.R | 3 tests/testthat/test-ui-map.R | 30 tests/testthat/test-ui-radar.R | 4 tests/testthat/test-ui-sankey.R | 4 tests/testthat/test-ui-waterfall.R | 8 vignettes/additional_examples.Rmd | 2 vignettes/getting_started.Rmd | 24 59 files changed, 1811 insertions(+), 699 deletions(-)
Title: Multivariate Nonparametric Methods Based on Spatial Signs and
Ranks
Description: Test and estimates of location, tests of independence, tests of sphericity and several estimates of shape all based on spatial signs, symmetrized signs, ranks and signed ranks. For details, see Oja and Randles (2004) <doi:10.1214/088342304000000558> and Oja (2010) <doi:10.1007/978-1-4419-0468-3>.
Author: Seija Sirkia [aut],
Jari Miettinen [aut] ,
Klaus Nordhausen [cre, aut] ,
Hannu Oja [aut] ,
Sara Taskinen [aut]
Maintainer: Klaus Nordhausen <klausnordhausenr@gmail.com>
Diff between SpatialNP versions 1.1-5 dated 2021-12-08 and 1.1-6 dated 2025-03-27
DESCRIPTION | 24 ++++++++++++------------ MD5 | 7 ++++--- build |only inst/ChangeLog | 5 +++++ man/SpatialNP-package.Rd | 18 +++++++----------- 5 files changed, 28 insertions(+), 26 deletions(-)
Title: R Graphics Devices for 'Office' Vector Graphics Output
Description: Vector Graphics devices for 'Microsoft PowerPoint' and
'Microsoft Excel'. Functions extending package 'officer' are provided to
embed 'DrawingML' graphics into 'Microsoft PowerPoint' presentations and
'Microsoft Excel' workbooks.
Author: David Gohel [aut, cre],
ArData [cph],
Bob Rudis [ctb] ,
Francois Brunetti [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between rvg versions 0.3.4 dated 2024-08-27 and 0.3.5 dated 2025-03-27
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/ph_with_vg.R | 1 + src/Makevars.ucrt | 10 ++++++++-- tests/testthat/test-officer.R | 30 +++++++++++++++++++++++++++++- 6 files changed, 52 insertions(+), 11 deletions(-)
Title: Unified Framework for Numerical Optimizers
Description: Provides a unified object-oriented framework for numerical
optimizers in R. Allows for both minimization and maximization with any
optimizer, optimization over more than one function argument, measuring of
computation time, setting a time limit for long optimization tasks.
Author: Lennart Oelschlaeger [aut, cre]
,
Marius Oetting [ctb]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between optimizeR versions 1.1.2 dated 2024-11-27 and 1.1.3 dated 2025-03-27
DESCRIPTION | 6 MD5 | 58 - NAMESPACE | 48 - NEWS.md | 222 ++--- R/debug.R | 198 ++--- R/legacy.R | 912 +++++++++++------------ R/objective.R | 828 ++++++++++----------- R/optimizeR-package.R | 64 - R/optimizer.R | 1300 ++++++++++++++++----------------- R/optimizer_dictionary.R | 176 ++-- R/parameter_spaces.R | 744 +++++++++--------- README.md | 618 +++++++-------- man/Objective.Rd | 524 ++++++------- man/Optimizer.Rd | 942 +++++++++++------------ man/ParameterSpaces.Rd | 436 +++++------ man/apply_optimizer.Rd | 88 +- man/define_optimizer.Rd | 308 +++---- man/new_optimizer.Rd | 190 ++-- man/optimizeR-package.Rd | 62 - man/optimizer_dictionary.Rd | 34 man/test_objective.Rd | 78 - man/test_optimizer.Rd | 102 +- man/validate_optimizer.Rd | 92 +- tests/testthat.R | 24 tests/testthat/_snaps/objective.md | 40 - tests/testthat/test-debug.R | 58 - tests/testthat/test-legacy.R | 432 +++++----- tests/testthat/test-objective.R | 186 ++-- tests/testthat/test-optimizer.R | 190 ++-- tests/testthat/test-parameter_spaces.R | 276 +++---- 30 files changed, 4623 insertions(+), 4613 deletions(-)
Title: Permutation Tests for Linear Models
Description: Linear model functions using permutation tests.
Author: Bob Wheeler [aut],
Marco Torchiano [aut, cre]
Maintainer: Marco Torchiano <marco.torchiano@polito.it>
Diff between lmPerm versions 2.1.0 dated 2016-08-02 and 2.1.4 dated 2025-03-27
DESCRIPTION | 17 +++++++++++--- MD5 | 16 ++++++------- README.md | 19 ++++++++++++++++ build/vignette.rds |binary inst/doc/lmPerm.pdf |binary man/multResp.Rd | 2 - man/poly.formula.Rd | 2 - src/lmPerm.c | 60 +++++++++++++++++++++++++++++++++++++++++++++++----- src/wheeler.h | 4 --- 9 files changed, 97 insertions(+), 23 deletions(-)
Title: Interface Between the 'JDemetra+' Cruncher and R, and Quality
Report Generator
Description: Tool for generating quality reports from cruncher outputs (and calculating series scores). The latest version of the cruncher can be downloaded here: <https://github.com/jdemetra/jwsacruncher/releases>.
Author: Tanguy Barthelemy [aut, cre, art],
Alain Quartier-la-Tente [aut] ,
Institut national de la statistique et des etudes economiques [cph]
,
Anna Smyk [aut]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between JDCruncheR versions 0.3.3 dated 2025-02-23 and 0.3.4 dated 2025-03-27
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 15 - R/QR_export.R | 26 +- R/QR_functions.R | 36 +- R/QR_matrix_classes.R | 6 R/extractQR.R | 648 ++++++++++++++++++++++++++++++-------------------- man/compute_score.Rd | 2 8 files changed, 459 insertions(+), 294 deletions(-)
Title: Summarise and Visualise Characteristics of Patients in the OMOP
CDM
Description: Summarise and visualise the characteristics of patients in data
mapped to the Observational Medical Outcomes Partnership (OMOP) common data
model (CDM).
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Mike Du [ctb] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [aut] ,
Marta Alcalde [aut]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between CohortCharacteristics versions 0.5.0 dated 2025-03-18 and 0.5.1 dated 2025-03-27
DESCRIPTION | 6 MD5 | 14 R/plotCohortAttrition.R | 18 inst/doc/summarise_characteristics.html | 600 ++++++++++---------- inst/doc/summarise_cohort_overlap.html | 220 +++---- inst/doc/summarise_cohort_timing.html | 220 +++---- inst/doc/summarise_large_scale_characteristics.html | 330 +++++------ tests/testthat/test-plotCohortAttrition.R | 3 8 files changed, 708 insertions(+), 703 deletions(-)
More information about CohortCharacteristics at CRAN
Permanent link
Title: Focused Information Criteria for Model Comparison
Description: Compares how well different models estimate a quantity of interest (the "focus") so that different models may be preferred for different purposes. Comparisons within any class of models fitted by maximum likelihood are supported, with shortcuts for commonly-used classes such as generalised linear models and parametric survival models. The methods originate from Claeskens and Hjort (2003) <doi:10.1198/016214503000000819> and Claeskens and Hjort (2008, ISBN:9780521852258).
Author: Christopher Jackson [cre, aut] ,
Gerda Claeskens [aut] ,
Howard Thom [ctb]
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between fic versions 1.0.0 dated 2019-04-13 and 1.0.1 dated 2025-03-27
fic-1.0.0/fic/vignettes/README.md |only fic-1.0.0/fic/vignettes/fic.rel |only fic-1.0.1/fic/DESCRIPTION | 12 fic-1.0.1/fic/MD5 | 88 ++-- fic-1.0.1/fic/NAMESPACE | 2 fic-1.0.1/fic/NEWS.md |only fic-1.0.1/fic/R/fic-package.R | 3 fic-1.0.1/fic/R/fic.R | 5 fic-1.0.1/fic/R/fic.survreg.R | 4 fic-1.0.1/fic/R/model_utils.R | 2 fic-1.0.1/fic/R/plot.fic.R | 38 + fic-1.0.1/fic/R/summary.R | 3 fic-1.0.1/fic/build/vignette.rds |binary fic-1.0.1/fic/inst/doc/fic.R | 222 +++++----- fic-1.0.1/fic/inst/doc/fic.Rnw | 6 fic-1.0.1/fic/inst/doc/fic.pdf |binary fic-1.0.1/fic/inst/doc/linear.R | 239 +++++------ fic-1.0.1/fic/inst/doc/linear.Rnw | 555 +++++++++++++-------------- fic-1.0.1/fic/inst/doc/linear.pdf |binary fic-1.0.1/fic/inst/doc/loss.R | 60 +- fic-1.0.1/fic/inst/doc/loss.pdf |binary fic-1.0.1/fic/inst/doc/multistate.R | 114 ++--- fic-1.0.1/fic/inst/doc/multistate.pdf |binary fic-1.0.1/fic/inst/doc/skewnormal.R | 174 ++++---- fic-1.0.1/fic/inst/doc/skewnormal.pdf |binary fic-1.0.1/fic/inst/doc/survival.R | 138 +++--- fic-1.0.1/fic/inst/doc/survival.pdf |binary fic-1.0.1/fic/man/all_inds.Rd | 2 fic-1.0.1/fic/man/birthwt.Rd | 6 fic-1.0.1/fic/man/fic-package.Rd | 22 + fic-1.0.1/fic/man/fic.Rd | 19 fic-1.0.1/fic/man/fic.coxph.Rd | 14 fic-1.0.1/fic/man/fic.flexsurvreg.Rd | 16 fic-1.0.1/fic/man/fic.glm.Rd | 16 fic-1.0.1/fic/man/fic.lm.Rd | 16 fic-1.0.1/fic/man/fic.msm.Rd | 16 fic-1.0.1/fic/man/fic.survreg.Rd | 20 fic-1.0.1/fic/man/fic_multi.Rd | 18 fic-1.0.1/fic/man/focus_fns.Rd | 3 fic-1.0.1/fic/man/ggplot_fic.Rd | 14 fic-1.0.1/fic/man/melanoma.Rd | 6 fic-1.0.1/fic/man/plot.fic.Rd | 18 fic-1.0.1/fic/tests/testthat/test_errors.R | 219 +++++----- fic-1.0.1/fic/tests/testthat/test_logistic.R | 205 +++++---- fic-1.0.1/fic/tests/testthat/test_plot.R |only fic-1.0.1/fic/vignettes/fic.Rnw | 6 fic-1.0.1/fic/vignettes/linear.Rnw | 555 +++++++++++++-------------- 47 files changed, 1503 insertions(+), 1353 deletions(-)
Title: Utilities for Interacting with the 'Posit Connect' Server API
Description: Provides a helpful 'R6' class and methods for interacting with
the 'Posit Connect' Server API along with some meaningful utility functions
for regular tasks. API documentation varies by 'Posit Connect' installation
and version, but the latest documentation is also hosted publicly at
<https://docs.posit.co/connect/api/>.
Author: Toph Allen [aut, cre],
Neal Richardson [aut],
Sean Lopp [aut],
Cole Arendt [aut],
Posit, PBC [cph, fnd]
Maintainer: Toph Allen <toph@posit.co>
Diff between connectapi versions 0.6.0 dated 2025-02-11 and 0.7.0 dated 2025-03-27
connectapi-0.6.0/connectapi/tests/testthat/2024.08.0/__api__/v1/oauth/integrations/credentials-f08930-POST.json |only connectapi-0.6.0/connectapi/tests/testthat/2024.08.0/__api__/v1/oauth/integrations/credentials-fe6213-POST.json |only connectapi-0.7.0/connectapi/DESCRIPTION | 9 connectapi-0.7.0/connectapi/MD5 | 61 +- connectapi-0.7.0/connectapi/NAMESPACE | 4 connectapi-0.7.0/connectapi/NEWS.md | 13 connectapi-0.7.0/connectapi/R/connect.R | 21 connectapi-0.7.0/connectapi/R/content.R | 34 + connectapi-0.7.0/connectapi/R/get.R | 228 +++++++++- connectapi-0.7.0/connectapi/R/page.R | 3 connectapi-0.7.0/connectapi/R/ptype.R | 16 connectapi-0.7.0/connectapi/inst/doc/customize-http.html | 4 connectapi-0.7.0/connectapi/inst/doc/getting-started.html | 4 connectapi-0.7.0/connectapi/man/Content.Rd | 13 connectapi-0.7.0/connectapi/man/ContentTask.Rd | 1 connectapi-0.7.0/connectapi/man/EnvironmentR6.Rd | 1 connectapi-0.7.0/connectapi/man/PositConnect.Rd | 22 connectapi-0.7.0/connectapi/man/Vanity.Rd | 1 connectapi-0.7.0/connectapi/man/VariantR6.Rd | 1 connectapi-0.7.0/connectapi/man/VariantSchedule.Rd | 1 connectapi-0.7.0/connectapi/man/VariantTask.Rd | 1 connectapi-0.7.0/connectapi/man/get_aws_content_credentials.Rd |only connectapi-0.7.0/connectapi/man/get_aws_credentials.Rd |only connectapi-0.7.0/connectapi/man/get_content_packages.Rd |only connectapi-0.7.0/connectapi/man/get_oauth_content_credentials.Rd | 11 connectapi-0.7.0/connectapi/man/get_oauth_credentials.Rd | 11 connectapi-0.7.0/connectapi/man/get_packages.Rd |only connectapi-0.7.0/connectapi/tests/testthat/2024.08.0/__api__/v1/content/8f37d6e0/packages.json |only connectapi-0.7.0/connectapi/tests/testthat/2024.08.0/__api__/v1/oauth/integrations/credentials-2877f7-POST.json |only connectapi-0.7.0/connectapi/tests/testthat/2024.08.0/__api__/v1/oauth/integrations/credentials-8dea8e-POST.json |only connectapi-0.7.0/connectapi/tests/testthat/2024.08.0/__api__/v1/oauth/integrations/credentials-b3e87e-POST.json |only connectapi-0.7.0/connectapi/tests/testthat/2024.08.0/__api__/v1/oauth/integrations/credentials-fe45b8-POST.json |only connectapi-0.7.0/connectapi/tests/testthat/Rplots.pdf |binary connectapi-0.7.0/connectapi/tests/testthat/test-connect.R | 15 connectapi-0.7.0/connectapi/tests/testthat/test-content.R | 20 connectapi-0.7.0/connectapi/tests/testthat/test-get.R | 113 ++++ connectapi-0.7.0/connectapi/tests/testthat/test-oauth.R | 82 +++ 37 files changed, 627 insertions(+), 63 deletions(-)
Title: Stratigraphic Paleobiology Modeling Pipelines
Description: The fossil record is a joint expression of ecological, taphonomic,
evolutionary, and stratigraphic processes (Holland and Patzkowsky, 2012, ISBN:978-0226649382).
This package allowing to simulate biological processes in the time domain
(e.g., trait evolution, fossil abundance), and examine how their expression
in the rock record (stratigraphic domain) is influenced based on
age-depth models, ecological niche models, and taphonomic effects.
Functions simulating common processes used in modeling trait evolution or
event type data such as first/last occurrences are provided and can be used
standalone or as part of a pipeline. The package comes with example
data sets and tutorials in several vignettes, which can be used as a
template to set up one's own simulation.
Author: Niklas Hohmann [aut, cre]
Maintainer: Niklas Hohmann <N.H.Hohmann@uu.nl>
Diff between StratPal versions 0.3.1 dated 2025-02-20 and 0.4.0 dated 2025-03-27
DESCRIPTION | 9 - MD5 | 64 +++++----- NAMESPACE | 4 NEWS.md | 8 + R/apply_niche.R | 204 ++++++++++++++++++-------------- R/apply_taphonomy.R | 130 +++++++++++--------- R/bounded_niche.R | 1 R/discrete_gradient.R |only R/discrete_niche.R |only R/snd_niche.R | 1 README.md | 10 + build/vignette.rds |binary inst/CITATION | 6 inst/WORDLIST | 14 ++ inst/doc/FossilSim_integration.R |only inst/doc/FossilSim_integration.Rmd |only inst/doc/FossilSim_integration.html |only inst/doc/StratPal.Rmd | 2 inst/doc/StratPal.html | 6 inst/doc/advanced_functionality.Rmd | 4 inst/doc/advanced_functionality.html | 10 + inst/doc/event_data.R | 2 inst/doc/event_data.Rmd | 4 inst/doc/event_data.html | 9 - man/apply_niche.Rd | 21 ++- man/apply_taphonomy.Rd | 6 man/bounded_niche.Rd | 1 man/discrete_gradient.Rd |only man/discrete_niche.Rd |only man/snd_niche.Rd | 1 tests/testthat/test_apply_niche.R | 9 + tests/testthat/test_apply_taphonomy.R | 9 + tests/testthat/test_discrete_gradient.R |only tests/testthat/test_discrete_niche.R |only vignettes/FossilSim_integration.Rmd |only vignettes/StratPal.Rmd | 2 vignettes/advanced_functionality.Rmd | 4 vignettes/event_data.Rmd | 4 38 files changed, 343 insertions(+), 202 deletions(-)
Title: Density, Cumulative and Quantile Functions of Quadratic Forms
Description: The computation of quadratic form (QF) distributions is often not trivial and it requires numerical routines. The package contains functions aimed at evaluating the exact distribution of quadratic forms (QFs) and ratios of QFs. In particular, we propose to evaluate density, quantile and distribution functions of positive definite QFs and ratio of independent positive QFs by means of an algorithm based on the numerical inversion of Mellin transforms.
Author: Aldo Gardini [aut, cre],
Fedele Greco [aut],
Carlo Trivisano [aut]
Maintainer: Aldo Gardini <aldo.gardini2@unibo.it>
Diff between QF versions 0.0.6 dated 2021-10-22 and 0.0.9 dated 2025-03-27
QF-0.0.6/QF/src/Makevars |only QF-0.0.6/QF/tools |only QF-0.0.9/QF/DESCRIPTION | 10 - QF-0.0.9/QF/MD5 | 42 +++--- QF-0.0.9/QF/NAMESPACE | 34 ++--- QF-0.0.9/QF/R/Distributions_QF.R | 6 QF-0.0.9/QF/R/Distributions_QF_ratio.R | 6 QF-0.0.9/QF/R/Distributions_depratio.R | 7 - QF-0.0.9/QF/R/MellinQF.R | 4 QF-0.0.9/QF/R/MellinQF_ratio.R | 6 QF-0.0.9/QF/cleanup |only QF-0.0.9/QF/configure |only QF-0.0.9/QF/configure.ac |only QF-0.0.9/QF/man/QF.Rd | 166 ++++++++++++------------- QF-0.0.9/QF/man/QF_ratio.Rd | 186 ++++++++++++++-------------- QF-0.0.9/QF/man/compute_MellinQF.Rd | 184 ++++++++++++++-------------- QF-0.0.9/QF/man/compute_MellinQF_ratio.Rd | 194 +++++++++++++++--------------- QF-0.0.9/QF/man/pQF_depratio.Rd | 104 ++++++++-------- QF-0.0.9/QF/man/print.MellinQF.Rd | 36 ++--- QF-0.0.9/QF/man/print.MellinQF_ratio.Rd | 36 ++--- QF-0.0.9/QF/src/Makevars.in |only QF-0.0.9/QF/src/Makevars.ucrt | 10 + QF-0.0.9/QF/src/Makevars.win | 17 +- QF-0.0.9/QF/src/get_mellin_QF.cpp | 6 QF-0.0.9/QF/src/get_mellin_QF_ratio.cpp | 2 25 files changed, 523 insertions(+), 533 deletions(-)
Title: Embedding and Clustering with Alignment for Spatial Datasets
Description: An efficient data integration method is provided for multiple spatial transcriptomics data with non-cluster-relevant effects such as the complex batch effects. It unifies spatial factor analysis simultaneously with spatial clustering and embedding alignment, requiring only partially shared cell/domain clusters across datasets. More details can be referred to Wei Liu, et al. (2023) <doi:10.1038/s41467-023-35947-w>.
Author: Wei Liu [aut, cre],
Yi Yang [aut],
Jin Liu [aut]
Maintainer: Wei Liu <liuweideng@gmail.com>
Diff between PRECAST versions 1.6.5 dated 2024-03-19 and 1.6.6 dated 2025-03-27
DESCRIPTION | 10 ++--- MD5 | 28 ++++++++-------- R/main.R | 2 - inst/doc/PRECAST.BreastCancer.html | 6 +-- inst/doc/PRECAST.DLPFC.html | 6 +-- inst/doc/PRECAST.DLPFC4.html | 6 +-- inst/doc/PRECAST.Simu.html | 10 ++--- man/AddAdjList.Rd | 2 - man/doHeatmap.Rd | 2 - man/drawFigs.Rd | 62 ++++++++++++++++++------------------- man/getAdj_fixedNumber.Rd | 2 - man/getAdj_reg.Rd | 2 - src/idrsc2.cpp | 4 +- src/utilMultIntcluster.cpp | 2 - src/wpca.cpp | 1 15 files changed, 72 insertions(+), 73 deletions(-)
Title: Summarise Patient-Level Drug Utilisation in Data Mapped to the
OMOP Common Data Model
Description: Summarise patient-level drug utilisation cohorts using data mapped
to the Observational Medical Outcomes Partnership (OMOP) common data model.
New users and prevalent users cohorts can be generated and their
characteristics, indication and drug use summarised.
Author: Marti Catala [aut, cre] ,
Mike Du [ctb] ,
Yuchen Guo [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Xintong Li [ctb] ,
Marta Alcalde-Herraiz [ctb] ,
Nuria Mercade-Besora [aut] ,
Xihang Chen [aut]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between DrugUtilisation versions 0.8.3 dated 2025-03-20 and 1.0.0 dated 2025-03-27
DrugUtilisation-0.8.3/DrugUtilisation/R/addDrugUse.R |only DrugUtilisation-0.8.3/DrugUtilisation/R/readConceptList.R |only DrugUtilisation-0.8.3/DrugUtilisation/R/summariseDrugUse.R |only DrugUtilisation-0.8.3/DrugUtilisation/man/addDailyDose.Rd |only DrugUtilisation-0.8.3/DrugUtilisation/man/addDrugUse.Rd |only DrugUtilisation-0.8.3/DrugUtilisation/man/addExposedTime.Rd |only DrugUtilisation-0.8.3/DrugUtilisation/man/addRoute.Rd |only DrugUtilisation-0.8.3/DrugUtilisation/man/dailyDoseCoverage.Rd |only DrugUtilisation-0.8.3/DrugUtilisation/man/readConceptList.Rd |only DrugUtilisation-0.8.3/DrugUtilisation/man/stratifyByUnit.Rd |only DrugUtilisation-0.8.3/DrugUtilisation/man/summariseDrugUse.Rd |only DrugUtilisation-0.8.3/DrugUtilisation/tests/testthat/test-readConceptList.R |only DrugUtilisation-1.0.0/DrugUtilisation/DESCRIPTION | 19 DrugUtilisation-1.0.0/DrugUtilisation/MD5 | 158 DrugUtilisation-1.0.0/DrugUtilisation/NAMESPACE | 8 DrugUtilisation-1.0.0/DrugUtilisation/NEWS.md | 12 DrugUtilisation-1.0.0/DrugUtilisation/R/addDrugUtilisation.R | 77 DrugUtilisation-1.0.0/DrugUtilisation/R/addIntersect.R | 16 DrugUtilisation-1.0.0/DrugUtilisation/R/benchmarkDrugUtilisation.R | 10 DrugUtilisation-1.0.0/DrugUtilisation/R/cohortUtilities.R | 149 DrugUtilisation-1.0.0/DrugUtilisation/R/dailyDose.R | 69 DrugUtilisation-1.0.0/DrugUtilisation/R/erafyCohort.R | 5 DrugUtilisation-1.0.0/DrugUtilisation/R/generateAtcCohortSet.R | 27 DrugUtilisation-1.0.0/DrugUtilisation/R/generateDrugUtilisationCohortSet.R | 66 DrugUtilisation-1.0.0/DrugUtilisation/R/generateIngredientCohortSet.R | 75 DrugUtilisation-1.0.0/DrugUtilisation/R/mockDrugUtilisation.R | 2 DrugUtilisation-1.0.0/DrugUtilisation/R/pattern.R | 131 DrugUtilisation-1.0.0/DrugUtilisation/R/plots.R | 36 DrugUtilisation-1.0.0/DrugUtilisation/R/require.R | 26 DrugUtilisation-1.0.0/DrugUtilisation/R/summariseDrugRestart.R | 14 DrugUtilisation-1.0.0/DrugUtilisation/R/summariseDrugUtilisation.R | 25 DrugUtilisation-1.0.0/DrugUtilisation/R/summariseIntersect.R | 90 DrugUtilisation-1.0.0/DrugUtilisation/R/tables.R | 59 DrugUtilisation-1.0.0/DrugUtilisation/R/validate.R | 2 DrugUtilisation-1.0.0/DrugUtilisation/inst/doc/create_cohorts.html | 78 DrugUtilisation-1.0.0/DrugUtilisation/inst/doc/drug_utilisation.html | 8361 +--------- DrugUtilisation-1.0.0/DrugUtilisation/man/addCumulativeDose.Rd | 2 DrugUtilisation-1.0.0/DrugUtilisation/man/addCumulativeQuantity.Rd | 2 DrugUtilisation-1.0.0/DrugUtilisation/man/addDaysExposed.Rd | 2 DrugUtilisation-1.0.0/DrugUtilisation/man/addDaysPrescribed.Rd | 2 DrugUtilisation-1.0.0/DrugUtilisation/man/addDrugRestart.Rd | 6 DrugUtilisation-1.0.0/DrugUtilisation/man/addDrugUtilisation.Rd | 7 DrugUtilisation-1.0.0/DrugUtilisation/man/addIndication.Rd | 8 DrugUtilisation-1.0.0/DrugUtilisation/man/addInitialDailyDose.Rd | 2 DrugUtilisation-1.0.0/DrugUtilisation/man/addInitialExposureDuration.Rd | 2 DrugUtilisation-1.0.0/DrugUtilisation/man/addInitialQuantity.Rd | 2 DrugUtilisation-1.0.0/DrugUtilisation/man/addNumberEras.Rd | 2 DrugUtilisation-1.0.0/DrugUtilisation/man/addNumberExposures.Rd | 2 DrugUtilisation-1.0.0/DrugUtilisation/man/addTimeToExposure.Rd | 2 DrugUtilisation-1.0.0/DrugUtilisation/man/addTreatment.Rd | 6 DrugUtilisation-1.0.0/DrugUtilisation/man/benchmarkDrugUtilisation.Rd | 10 DrugUtilisation-1.0.0/DrugUtilisation/man/cohortGapEra.Rd | 4 DrugUtilisation-1.0.0/DrugUtilisation/man/generateAtcCohortSet.Rd | 25 DrugUtilisation-1.0.0/DrugUtilisation/man/generateDrugUtilisationCohortSet.Rd | 26 DrugUtilisation-1.0.0/DrugUtilisation/man/generateIngredientCohortSet.Rd | 25 DrugUtilisation-1.0.0/DrugUtilisation/man/mockDrugUtilisation.Rd | 2 DrugUtilisation-1.0.0/DrugUtilisation/man/patternTable.Rd | 2 DrugUtilisation-1.0.0/DrugUtilisation/man/plotDrugRestart.Rd | 2 DrugUtilisation-1.0.0/DrugUtilisation/man/plotIndication.Rd | 6 DrugUtilisation-1.0.0/DrugUtilisation/man/plotProportionOfPatientsCovered.Rd | 4 DrugUtilisation-1.0.0/DrugUtilisation/man/plotTreatment.Rd | 2 DrugUtilisation-1.0.0/DrugUtilisation/man/requireDrugInDateRange.Rd | 6 DrugUtilisation-1.0.0/DrugUtilisation/man/requireIsFirstDrugEntry.Rd | 6 DrugUtilisation-1.0.0/DrugUtilisation/man/requireObservationBeforeDrug.Rd | 6 DrugUtilisation-1.0.0/DrugUtilisation/man/requirePriorDrugWashout.Rd | 6 DrugUtilisation-1.0.0/DrugUtilisation/man/summariseDoseCoverage.Rd | 2 DrugUtilisation-1.0.0/DrugUtilisation/man/summariseDrugRestart.Rd | 6 DrugUtilisation-1.0.0/DrugUtilisation/man/summariseDrugUtilisation.Rd | 8 DrugUtilisation-1.0.0/DrugUtilisation/man/summariseIndication.Rd | 8 DrugUtilisation-1.0.0/DrugUtilisation/man/summariseTreatment.Rd | 7 DrugUtilisation-1.0.0/DrugUtilisation/man/tableDoseCoverage.Rd | 4 DrugUtilisation-1.0.0/DrugUtilisation/man/tableDrugRestart.Rd | 9 DrugUtilisation-1.0.0/DrugUtilisation/man/tableDrugUtilisation.Rd | 9 DrugUtilisation-1.0.0/DrugUtilisation/man/tableIndication.Rd | 8 DrugUtilisation-1.0.0/DrugUtilisation/man/tableProportionOfPatientsCovered.Rd | 8 DrugUtilisation-1.0.0/DrugUtilisation/man/tableTreatment.Rd | 7 DrugUtilisation-1.0.0/DrugUtilisation/tests/testthat/test-addDrugUtilisation.R | 65 DrugUtilisation-1.0.0/DrugUtilisation/tests/testthat/test-erafyCohort.R | 1 DrugUtilisation-1.0.0/DrugUtilisation/tests/testthat/test-generateDrugUtilisationCohortSet.R | 45 DrugUtilisation-1.0.0/DrugUtilisation/tests/testthat/test-generatedIngredientCohortSet.R | 2 DrugUtilisation-1.0.0/DrugUtilisation/tests/testthat/test-plotProportionOfPatientsCovered.R | 9 DrugUtilisation-1.0.0/DrugUtilisation/tests/testthat/test-plots.R | 172 DrugUtilisation-1.0.0/DrugUtilisation/tests/testthat/test-require.R | 28 DrugUtilisation-1.0.0/DrugUtilisation/tests/testthat/test-summariseDrugRestart.R | 1 DrugUtilisation-1.0.0/DrugUtilisation/tests/testthat/test-summariseTreatment.R | 14 DrugUtilisation-1.0.0/DrugUtilisation/tests/testthat/test-tables.R | 14 86 files changed, 2007 insertions(+), 8114 deletions(-)
More information about DrugUtilisation at CRAN
Permanent link
Title: Design of Experiments and Factorial Plans Utilities
Description: A number of functions to create and analyze factorial plans according to the Design of Experiments (DoE) approach, with the addition of some utility function to perform some statistical analyses. DoE approach follows the approach in "Design and Analysis of Experiments" by Douglas C. Montgomery (2019, ISBN:978-1-119-49244-3). The package also provides utilities used in the course "Analysis of Data and Statistics" at the University of Trento, Italy.
Author: Paolo Bosetti [aut, cre]
Maintainer: Paolo Bosetti <paolo.bosetti@unitn.it>
Diff between adas.utils versions 1.0.0 dated 2024-12-18 and 1.1.0 dated 2025-03-27
DESCRIPTION | 8 - MD5 | 27 ++-- NAMESPACE | 12 ++ NEWS.md | 4 R/adas.utils-package.R | 9 + R/stats.R | 93 +++++++++++++++++ README.md | 2 inst/doc/adas.utils.R | 28 +++++ inst/doc/adas.utils.Rmd | 41 +++++++ inst/doc/adas.utils.html | 250 ++++++++++++++++++++++++++++------------------ man/ggTukey.Rd |only man/ggTukey.TukeyHSD.Rd |only man/ggTukey.data.frame.Rd |only tools/setup.Rmd | 11 +- tools/setup.nb.html | 15 +- vignettes/adas.utils.Rmd | 41 +++++++ 16 files changed, 419 insertions(+), 122 deletions(-)
Title: Target Diagram
Description: Implementation of target diagrams using 'lattice' and 'ggplot2' graphics. Target diagrams provide a graphical overview of the respective contributions of the unbiased RMSE and MBE to the total RMSE (Jolliff, J. et al., 2009. "Summary Diagrams for Coupled Hydrodynamic-Ecosystem Model Skill Assessment." Journal of Marine Systems 76: 64–82.)
Author: Oscar Perpinan Lamigueiro [cre, aut]
Maintainer: Oscar Perpinan Lamigueiro <oscar.perpinan@upm.es>
Diff between tdr versions 0.13 dated 2018-01-10 and 0.14 dated 2025-03-27
DESCRIPTION | 16 ++++++++-------- MD5 | 6 +++--- R/target_diagram.R | 18 ++++++++---------- man/targetDiagram.Rd | 14 +++++++------- 4 files changed, 26 insertions(+), 28 deletions(-)
Title: High-Dimensional Spatial Covariate-Augmented Overdispersed
Poisson Factor Model
Description: A spatial covariate-augmented overdispersed Poisson factor model is proposed to perform efficient latent representation learning method for high-dimensional large-scale spatial count data with additional covariates.
Author: Wei Liu [aut, cre],
Qingzhi Zhong [aut]
Maintainer: Wei Liu <liuwei8@scu.edu.cn>
Diff between SpaCOAP versions 1.2 dated 2024-05-27 and 1.3 dated 2025-03-27
SpaCOAP-1.2/SpaCOAP/README.md |only SpaCOAP-1.3/SpaCOAP/DESCRIPTION | 12 SpaCOAP-1.3/SpaCOAP/MD5 | 27 SpaCOAP-1.3/SpaCOAP/build/vignette.rds |binary SpaCOAP-1.3/SpaCOAP/inst/doc/mouseSpleen.R | 31 - SpaCOAP-1.3/SpaCOAP/inst/doc/mouseSpleen.Rmd | 41 - SpaCOAP-1.3/SpaCOAP/inst/doc/mouseSpleen.html | 782 +++++++++++++------------- SpaCOAP-1.3/SpaCOAP/inst/doc/simu.R | 2 SpaCOAP-1.3/SpaCOAP/inst/doc/simu.Rmd | 2 SpaCOAP-1.3/SpaCOAP/inst/doc/simu.html | 641 +++++++++++---------- SpaCOAP-1.3/SpaCOAP/src/Makevars | 2 SpaCOAP-1.3/SpaCOAP/src/Makevars.win | 2 SpaCOAP-1.3/SpaCOAP/src/spacoap.cpp | 3 SpaCOAP-1.3/SpaCOAP/vignettes/mouseSpleen.Rmd | 41 - SpaCOAP-1.3/SpaCOAP/vignettes/simu.Rmd | 2 15 files changed, 850 insertions(+), 738 deletions(-)
Title: Probabilistic Factor Analysis for Spatially-Aware Dimension
Reduction
Description: Probabilistic factor analysis for spatially-aware dimension reduction across multi-section spatial transcriptomics data with millions of spatial locations.
More details can be referred to Wei Liu, et al. (2023) <doi:10.1101/2023.07.11.548486>.
Author: Wei Liu [aut, cre],
Xiao Zhang [aut],
Jin Liu [aut]
Maintainer: Wei Liu <liuweideng@gmail.com>
Diff between ProFAST versions 1.5 dated 2025-03-20 and 1.6 dated 2025-03-27
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- inst/doc/CosMx.html | 4 ++-- inst/doc/FASTdlpfc.html | 4 ++-- inst/doc/FASTdlpfc2.html | 4 ++-- inst/doc/FASTsimu.html | 4 ++-- inst/doc/pbmc3k.html | 4 ++-- src/DR_removebatch.cpp | 3 +-- src/alignExp.cpp | 4 ++-- src/alignExps.cpp | 3 +-- src/profast.cpp | 6 ++---- 11 files changed, 30 insertions(+), 34 deletions(-)
Title: Asymptotic Covariance Matrices of Some BSS Mixing and Unmixing
Matrix Estimates
Description: Functions to compute the asymptotic covariance matrices of mixing and unmixing matrix estimates of the following blind source separation (BSS) methods: symmetric and squared symmetric FastICA, regular and adaptive deflation-based FastICA, FOBI, JADE, AMUSE and deflation-based and symmetric SOBI. Also functions to estimate these covariances based on data are available.
Author: Jari Miettinen [aut] ,
Klaus Nordhausen [cre, aut] ,
Hannu Oja [aut] ,
Sara Taskinen [aut]
Maintainer: Klaus Nordhausen <klausnordhausenr@gmail.com>
Diff between BSSasymp versions 1.2-3 dated 2021-12-10 and 1.2-4 dated 2025-03-27
DESCRIPTION | 24 ++++++++++++------------ MD5 | 7 ++++--- build |only inst/ChangeLog | 6 ++++++ man/BSSasymp-package.Rd | 19 +++++++------------ 5 files changed, 29 insertions(+), 27 deletions(-)
Title: Fast and Portable Character String Processing Facilities
Description: A collection of character string/text/natural language
processing tools for pattern searching (e.g., with 'Java'-like regular
expressions or the 'Unicode' collation algorithm), random string generation,
case mapping, string transliteration, concatenation, sorting, padding,
wrapping, Unicode normalisation, date-time formatting and parsing,
and many more. They are fast, consistent, convenient, and -
thanks to 'ICU' (International Components for Unicode) -
portable across all locales and platforms. Documentation about 'stringi' is
provided via its website at <https://stringi.gagolewski.com/> and
the paper by Gagolewski (2022, <doi:10.18637/jss.v103.i02>).
Author: Marek Gagolewski [aut, cre, cph]
,
Bartek Tartanus [ctb],
Unicode, Inc. and others [ctb]
Maintainer: Marek Gagolewski <marek@gagolewski.com>
Diff between stringi versions 1.8.4 dated 2024-05-06 and 1.8.7 dated 2025-03-27
stringi-1.8.4/stringi/R/stringi-package.R |only stringi-1.8.4/stringi/man/about_stringi.Rd |only stringi-1.8.7/stringi/DESCRIPTION | 31 stringi-1.8.7/stringi/LICENSE | 2 stringi-1.8.7/stringi/MD5 | 436 +++---- stringi-1.8.7/stringi/NEWS | 9 stringi-1.8.7/stringi/R/ICU_settings.R | 2 stringi-1.8.7/stringi/R/compare.R | 2 stringi-1.8.7/stringi/R/encoding.R | 2 stringi-1.8.7/stringi/R/encoding_conversion.R | 4 stringi-1.8.7/stringi/R/encoding_detection.R | 2 stringi-1.8.7/stringi/R/encoding_management.R | 2 stringi-1.8.7/stringi/R/escape.R | 2 stringi-1.8.7/stringi/R/files.R | 2 stringi-1.8.7/stringi/R/install.R | 2 stringi-1.8.7/stringi/R/internal_prepare_arg.R | 2 stringi-1.8.7/stringi/R/internal_test.R | 2 stringi-1.8.7/stringi/R/join.R | 2 stringi-1.8.7/stringi/R/length.R | 2 stringi-1.8.7/stringi/R/locale.R | 2 stringi-1.8.7/stringi/R/locale_management.R | 2 stringi-1.8.7/stringi/R/opts.R | 2 stringi-1.8.7/stringi/R/pad.R | 2 stringi-1.8.7/stringi/R/random.R | 2 stringi-1.8.7/stringi/R/reverse.R | 2 stringi-1.8.7/stringi/R/search.R | 2 stringi-1.8.7/stringi/R/search_count_4.R | 2 stringi-1.8.7/stringi/R/search_count_bound.R | 2 stringi-1.8.7/stringi/R/search_detect_4.R | 2 stringi-1.8.7/stringi/R/search_extract_4.R | 2 stringi-1.8.7/stringi/R/search_extract_bound.R | 2 stringi-1.8.7/stringi/R/search_locate_4.R | 2 stringi-1.8.7/stringi/R/search_locate_bound.R | 2 stringi-1.8.7/stringi/R/search_match_4.R | 2 stringi-1.8.7/stringi/R/search_replace_4.R | 2 stringi-1.8.7/stringi/R/search_split_4.R | 2 stringi-1.8.7/stringi/R/search_split_bound.R | 2 stringi-1.8.7/stringi/R/search_startsendswith_4.R | 2 stringi-1.8.7/stringi/R/search_subset_4.R | 2 stringi-1.8.7/stringi/R/sort.R | 2 stringi-1.8.7/stringi/R/sprintf.R | 2 stringi-1.8.7/stringi/R/stats.R | 2 stringi-1.8.7/stringi/R/stringi_package.R |only stringi-1.8.7/stringi/R/sub.R | 2 stringi-1.8.7/stringi/R/time_calendar.R | 12 stringi-1.8.7/stringi/R/time_format.R | 2 stringi-1.8.7/stringi/R/time_symbols.R | 2 stringi-1.8.7/stringi/R/time_zone.R | 2 stringi-1.8.7/stringi/R/trans_casemap.R | 2 stringi-1.8.7/stringi/R/trans_normalization.R | 2 stringi-1.8.7/stringi/R/trans_other.R | 2 stringi-1.8.7/stringi/R/trans_transliterate.R | 2 stringi-1.8.7/stringi/R/trim.R | 2 stringi-1.8.7/stringi/R/utils.R | 2 stringi-1.8.7/stringi/R/wrap.R | 2 stringi-1.8.7/stringi/build/partial.rdb |binary stringi-1.8.7/stringi/configure | 549 +++++----- stringi-1.8.7/stringi/configure.ac | 19 stringi-1.8.7/stringi/configure.win | 2 stringi-1.8.7/stringi/man/about_arguments.Rd | 4 stringi-1.8.7/stringi/man/about_encoding.Rd | 6 stringi-1.8.7/stringi/man/about_locale.Rd | 6 stringi-1.8.7/stringi/man/about_search.Rd | 16 stringi-1.8.7/stringi/man/about_search_boundaries.Rd | 6 stringi-1.8.7/stringi/man/about_search_charclass.Rd | 4 stringi-1.8.7/stringi/man/about_search_coll.Rd | 6 stringi-1.8.7/stringi/man/about_search_fixed.Rd | 4 stringi-1.8.7/stringi/man/about_search_regex.Rd | 4 stringi-1.8.7/stringi/man/operator_add.Rd | 4 stringi-1.8.7/stringi/man/operator_compare.Rd | 2 stringi-1.8.7/stringi/man/stri_compare.Rd | 2 stringi-1.8.7/stringi/man/stri_count_boundaries.Rd | 4 stringi-1.8.7/stringi/man/stri_datetime_add.Rd | 10 stringi-1.8.7/stringi/man/stri_dup.Rd | 4 stringi-1.8.7/stringi/man/stri_duplicated.Rd | 2 stringi-1.8.7/stringi/man/stri_enc_detect2.Rd | 2 stringi-1.8.7/stringi/man/stri_enc_isascii.Rd | 2 stringi-1.8.7/stringi/man/stri_enc_isutf16.Rd | 2 stringi-1.8.7/stringi/man/stri_enc_isutf8.Rd | 2 stringi-1.8.7/stringi/man/stri_encode.Rd | 2 stringi-1.8.7/stringi/man/stri_extract_boundaries.Rd | 4 stringi-1.8.7/stringi/man/stri_flatten.Rd | 4 stringi-1.8.7/stringi/man/stri_locate.Rd | 4 stringi-1.8.7/stringi/man/stri_locate_boundaries.Rd | 8 stringi-1.8.7/stringi/man/stri_match.Rd | 4 stringi-1.8.7/stringi/man/stri_opts_brkiter.Rd | 2 stringi-1.8.7/stringi/man/stri_opts_collator.Rd | 6 stringi-1.8.7/stringi/man/stri_opts_fixed.Rd | 4 stringi-1.8.7/stringi/man/stri_opts_regex.Rd | 4 stringi-1.8.7/stringi/man/stri_order.Rd | 2 stringi-1.8.7/stringi/man/stri_rank.Rd | 2 stringi-1.8.7/stringi/man/stri_split_boundaries.Rd | 8 stringi-1.8.7/stringi/man/stri_split_lines.Rd | 6 stringi-1.8.7/stringi/man/stri_sub.Rd | 2 stringi-1.8.7/stringi/man/stri_sub_all.Rd | 2 stringi-1.8.7/stringi/man/stri_trans_casemap.Rd | 4 stringi-1.8.7/stringi/man/stri_trim.Rd | 4 stringi-1.8.7/stringi/man/stri_unique.Rd | 2 stringi-1.8.7/stringi/man/stri_wrap.Rd | 4 stringi-1.8.7/stringi/man/stringi-package.Rd |only stringi-1.8.7/stringi/src/Makevars.in | 2 stringi-1.8.7/stringi/src/Makevars.win | 2 stringi-1.8.7/stringi/src/icu74/i18n/collationdatabuilder.cpp | 9 stringi-1.8.7/stringi/src/icu74/i18n/collationiterator.h | 11 stringi-1.8.7/stringi/src/icu74/i18n/ucol.cpp | 6 stringi-1.8.7/stringi/src/install.libs.R.in | 2 stringi-1.8.7/stringi/src/stri_ICU_settings.cpp | 2 stringi-1.8.7/stringi/src/stri_brkiter.cpp | 2 stringi-1.8.7/stringi/src/stri_brkiter.h | 2 stringi-1.8.7/stringi/src/stri_bytesearch_matcher.h | 2 stringi-1.8.7/stringi/src/stri_callables.cpp |only stringi-1.8.7/stringi/src/stri_callables.h |only stringi-1.8.7/stringi/src/stri_collator.cpp | 4 stringi-1.8.7/stringi/src/stri_common.cpp | 2 stringi-1.8.7/stringi/src/stri_compare.cpp | 2 stringi-1.8.7/stringi/src/stri_container_base.cpp | 8 stringi-1.8.7/stringi/src/stri_container_base.h | 2 stringi-1.8.7/stringi/src/stri_container_bytesearch.cpp | 6 stringi-1.8.7/stringi/src/stri_container_bytesearch.h | 2 stringi-1.8.7/stringi/src/stri_container_charclass.h | 2 stringi-1.8.7/stringi/src/stri_container_double.h | 2 stringi-1.8.7/stringi/src/stri_container_integer.h | 2 stringi-1.8.7/stringi/src/stri_container_listint.cpp | 2 stringi-1.8.7/stringi/src/stri_container_listint.h | 2 stringi-1.8.7/stringi/src/stri_container_listraw.cpp | 2 stringi-1.8.7/stringi/src/stri_container_listraw.h | 2 stringi-1.8.7/stringi/src/stri_container_listutf8.cpp | 2 stringi-1.8.7/stringi/src/stri_container_listutf8.h | 2 stringi-1.8.7/stringi/src/stri_container_logical.h | 2 stringi-1.8.7/stringi/src/stri_container_regex.cpp | 2 stringi-1.8.7/stringi/src/stri_container_regex.h | 2 stringi-1.8.7/stringi/src/stri_container_usearch.cpp | 2 stringi-1.8.7/stringi/src/stri_container_usearch.h | 2 stringi-1.8.7/stringi/src/stri_container_utf16.cpp | 2 stringi-1.8.7/stringi/src/stri_container_utf16.h | 4 stringi-1.8.7/stringi/src/stri_container_utf8.cpp | 2 stringi-1.8.7/stringi/src/stri_container_utf8.h | 2 stringi-1.8.7/stringi/src/stri_container_utf8_indexable.cpp | 2 stringi-1.8.7/stringi/src/stri_container_utf8_indexable.h | 2 stringi-1.8.7/stringi/src/stri_cpp.txt | 1 stringi-1.8.7/stringi/src/stri_encoding_conversion.cpp | 19 stringi-1.8.7/stringi/src/stri_encoding_detection.cpp | 4 stringi-1.8.7/stringi/src/stri_encoding_management.cpp | 2 stringi-1.8.7/stringi/src/stri_escape.cpp | 2 stringi-1.8.7/stringi/src/stri_exception.cpp | 2 stringi-1.8.7/stringi/src/stri_exception.h | 5 stringi-1.8.7/stringi/src/stri_exports.h | 2 stringi-1.8.7/stringi/src/stri_external.h | 2 stringi-1.8.7/stringi/src/stri_interval.h | 2 stringi-1.8.7/stringi/src/stri_intvec.h | 2 stringi-1.8.7/stringi/src/stri_join.cpp | 4 stringi-1.8.7/stringi/src/stri_length.cpp | 2 stringi-1.8.7/stringi/src/stri_macros.h | 24 stringi-1.8.7/stringi/src/stri_messages.h | 14 stringi-1.8.7/stringi/src/stri_pad.cpp | 2 stringi-1.8.7/stringi/src/stri_prepare_arg.cpp | 6 stringi-1.8.7/stringi/src/stri_random.cpp | 2 stringi-1.8.7/stringi/src/stri_reverse.cpp | 2 stringi-1.8.7/stringi/src/stri_search_boundaries_count.cpp | 2 stringi-1.8.7/stringi/src/stri_search_boundaries_extract.cpp | 2 stringi-1.8.7/stringi/src/stri_search_boundaries_locate.cpp | 2 stringi-1.8.7/stringi/src/stri_search_boundaries_split.cpp | 2 stringi-1.8.7/stringi/src/stri_search_class_count.cpp | 2 stringi-1.8.7/stringi/src/stri_search_class_detect.cpp | 2 stringi-1.8.7/stringi/src/stri_search_class_extract.cpp | 2 stringi-1.8.7/stringi/src/stri_search_class_locate.cpp | 2 stringi-1.8.7/stringi/src/stri_search_class_replace.cpp | 2 stringi-1.8.7/stringi/src/stri_search_class_split.cpp | 2 stringi-1.8.7/stringi/src/stri_search_class_startsendswith.cpp | 2 stringi-1.8.7/stringi/src/stri_search_class_subset.cpp | 2 stringi-1.8.7/stringi/src/stri_search_class_trim.cpp | 2 stringi-1.8.7/stringi/src/stri_search_coll_count.cpp | 2 stringi-1.8.7/stringi/src/stri_search_coll_detect.cpp | 2 stringi-1.8.7/stringi/src/stri_search_coll_extract.cpp | 2 stringi-1.8.7/stringi/src/stri_search_coll_locate.cpp | 2 stringi-1.8.7/stringi/src/stri_search_coll_replace.cpp | 2 stringi-1.8.7/stringi/src/stri_search_coll_split.cpp | 2 stringi-1.8.7/stringi/src/stri_search_coll_startsendswith.cpp | 2 stringi-1.8.7/stringi/src/stri_search_coll_subset.cpp | 2 stringi-1.8.7/stringi/src/stri_search_common.cpp | 2 stringi-1.8.7/stringi/src/stri_search_fixed_count.cpp | 2 stringi-1.8.7/stringi/src/stri_search_fixed_detect.cpp | 2 stringi-1.8.7/stringi/src/stri_search_fixed_extract.cpp | 2 stringi-1.8.7/stringi/src/stri_search_fixed_locate.cpp | 2 stringi-1.8.7/stringi/src/stri_search_fixed_replace.cpp | 2 stringi-1.8.7/stringi/src/stri_search_fixed_split.cpp | 2 stringi-1.8.7/stringi/src/stri_search_fixed_startsendswith.cpp | 2 stringi-1.8.7/stringi/src/stri_search_fixed_subset.cpp | 2 stringi-1.8.7/stringi/src/stri_search_in.cpp | 2 stringi-1.8.7/stringi/src/stri_search_other_split.cpp | 2 stringi-1.8.7/stringi/src/stri_search_regex_count.cpp | 2 stringi-1.8.7/stringi/src/stri_search_regex_detect.cpp | 2 stringi-1.8.7/stringi/src/stri_search_regex_extract.cpp | 2 stringi-1.8.7/stringi/src/stri_search_regex_locate.cpp | 2 stringi-1.8.7/stringi/src/stri_search_regex_match.cpp | 2 stringi-1.8.7/stringi/src/stri_search_regex_replace.cpp | 2 stringi-1.8.7/stringi/src/stri_search_regex_split.cpp | 2 stringi-1.8.7/stringi/src/stri_search_regex_subset.cpp | 2 stringi-1.8.7/stringi/src/stri_sort.cpp | 4 stringi-1.8.7/stringi/src/stri_sprintf.cpp | 2 stringi-1.8.7/stringi/src/stri_stats.cpp | 4 stringi-1.8.7/stringi/src/stri_string8.cpp | 2 stringi-1.8.7/stringi/src/stri_string8.h | 2 stringi-1.8.7/stringi/src/stri_string8buf.h | 2 stringi-1.8.7/stringi/src/stri_stringi.cpp | 9 stringi-1.8.7/stringi/src/stri_stringi.h | 2 stringi-1.8.7/stringi/src/stri_sub.cpp | 2 stringi-1.8.7/stringi/src/stri_test.cpp | 2 stringi-1.8.7/stringi/src/stri_time_calendar.cpp | 3 stringi-1.8.7/stringi/src/stri_time_format.cpp | 2 stringi-1.8.7/stringi/src/stri_time_symbols.cpp | 2 stringi-1.8.7/stringi/src/stri_time_zone.cpp | 2 stringi-1.8.7/stringi/src/stri_trans_casemap.cpp | 2 stringi-1.8.7/stringi/src/stri_trans_normalization.cpp | 2 stringi-1.8.7/stringi/src/stri_trans_other.cpp | 2 stringi-1.8.7/stringi/src/stri_trans_transliterate.cpp | 2 stringi-1.8.7/stringi/src/stri_ucnv.cpp | 20 stringi-1.8.7/stringi/src/stri_ucnv.h | 4 stringi-1.8.7/stringi/src/stri_uloc.cpp | 2 stringi-1.8.7/stringi/src/stri_utils.cpp | 2 stringi-1.8.7/stringi/src/stri_wrap.cpp | 2 stringi-1.8.7/stringi/src/uconfig_local.h.in | 8 222 files changed, 906 insertions(+), 793 deletions(-)
Title: Blind Source Separation for Multivariate Spatial Data
Description: Blind source separation for multivariate spatial data based on simultaneous/joint diagonalization of (robust) local covariance matrices. This package is an implementation of the methods described in Bachoc, Genton, Nordhausen, Ruiz-Gazen and Virta (2020) <doi:10.1093/biomet/asz079>.
Author: Christoph Muehlmann [aut] ,
Mika Sipil<e4> [aut] ,
Claudia Cappello [aut] ,
Sandra De Iaco [aut] ,
Klaus Nordhausen [aut, cre] ,
Sara Taskinen [aut] ,
Joni Virta [aut]
Maintainer: Klaus Nordhausen <klausnordhausenR@gmail.com>
Diff between SpatialBSS versions 0.14-0 dated 2023-07-20 and 0.16-0 dated 2025-03-27
DESCRIPTION | 29 +- MD5 | 48 +-- R/RcppExports.R | 74 ++--- R/sbss.R | 6 R/utils.R | 56 ++- build/partial.rdb |binary build/vignette.rds |binary data |only inst/ChangeLog.txt | 12 inst/doc/SBSS.R | 15 + inst/doc/SBSS.Rmd | 533 ++++++++++++++++++++----------------- inst/doc/SBSS.pdf |binary man/SpatialBSS-package.Rd | 25 - man/coef.sbss.Rd | 62 ++-- man/local_covariance_matrix.Rd | 2 man/local_gss_covariance_matrix.Rd | 236 ++++++++-------- man/plot.sbss.Rd | 182 ++++++------ man/robsbss.Rd | 2 man/sbss.Rd | 394 ++++++++++++++------------- man/sbss_asymp.Rd | 2 man/sbss_boot.Rd | 2 man/spatial_kernel_matrix.Rd | 25 + man/veneto_weather.Rd |only src/RcppExports.cpp | 46 +++ src/k_mat.cpp | 103 ++++++- vignettes/SBSS.Rmd | 533 ++++++++++++++++++++----------------- 26 files changed, 1382 insertions(+), 1005 deletions(-)
Title: Analyse Activity and Sleep Behaviour
Description: Use behavioural variables to score activity and infer sleep from bouts of immobility.
It is primarily designed to score sleep in fruit flies from Drosophila Activity Monitor (TriKinetics) and Ethoscope data.
It implements sleep scoring using the "five-minute rule" (Hendricks et al. (2000) <DOI:10.1016/S0896-6273(00)80877-6>),
activity classification for Ethoscopes (Geissmann et al. (2017) <DOI:10.1371/journal.pbio.2003026>)
and a new algorithm to detect when animals are dead.
Author: Quentin Geissmann [aut, cre]
Maintainer: Quentin Geissmann <qgeissmann@gmail.com>
Diff between sleepr versions 0.3.0 dated 2018-10-30 and 0.3.1 dated 2025-03-27
sleepr-0.3.0/sleepr/README.md |only sleepr-0.3.1/sleepr/DESCRIPTION | 11 +++++------ sleepr-0.3.1/sleepr/MD5 | 15 +++++++-------- sleepr-0.3.1/sleepr/R/curate-dead-animals.R | 2 +- sleepr-0.3.1/sleepr/R/sleep-annotation.R | 6 +++--- sleepr-0.3.1/sleepr/man/bout_analysis.Rd | 6 +++--- sleepr-0.3.1/sleepr/man/curate_dead_animals.Rd | 15 ++++++++++----- sleepr-0.3.1/sleepr/man/motion_detectors.Rd | 8 ++++++-- sleepr-0.3.1/sleepr/man/sleep_annotation.Rd | 16 ++++++++++------ 9 files changed, 45 insertions(+), 34 deletions(-)
Title: Canonical Data Structure for Behavioural Data
Description: Implements an S3 class based on 'data.table' to store and process efficiently ethomics (high-throughput behavioural) data.
Author: Quentin Geissmann [aut, cre]
Maintainer: Quentin Geissmann <qgeissmann@gmail.com>
Diff between behavr versions 0.3.2 dated 2019-01-02 and 0.3.3 dated 2025-03-27
behavr-0.3.2/behavr/README.md |only behavr-0.3.3/behavr/DESCRIPTION | 11 +++++------ behavr-0.3.3/behavr/MD5 | 25 ++++++++++++------------- behavr-0.3.3/behavr/R/behavr.R | 14 +++++++------- behavr-0.3.3/behavr/R/bin-apply.R | 2 +- behavr-0.3.3/behavr/R/meta.R | 4 ++-- behavr-0.3.3/behavr/R/rejoin.R | 2 +- behavr-0.3.3/behavr/man/behavr.Rd | 16 ++++++++-------- behavr-0.3.3/behavr/man/bin_apply.Rd | 13 ++++++++++--- behavr-0.3.3/behavr/man/meta.Rd | 2 +- behavr-0.3.3/behavr/man/rejoin.Rd | 2 +- behavr-0.3.3/behavr/man/stitch_on.Rd | 3 +-- behavr-0.3.3/behavr/man/toy_activity_data.Rd | 10 ++++++++-- behavr-0.3.3/behavr/man/xmv.Rd | 2 +- 14 files changed, 58 insertions(+), 48 deletions(-)
Title: Connect to ODBC Compatible Databases (using the DBI Interface)
Description: A DBI-compatible interface to ODBC databases.
Author: Jim Hester [aut],
Hadley Wickham [aut, cre],
Oliver Gjoneski [aut],
lexicalunit [cph] ,
Google Inc. [cph] ,
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between odbc versions 1.6.0 dated 2025-02-28 and 1.6.1 dated 2025-03-27
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS.md | 5 +++++ R/utils.R | 17 +++++++++++++---- tests/testthat/helper.R | 6 ++++++ tests/testthat/test-dbi-connection.R | 1 + tests/testthat/test-driver-mysql.R | 2 ++ tests/testthat/test-driver-oracle.R | 2 ++ tests/testthat/test-driver-postgres.R | 3 ++- tests/testthat/test-driver-sql-server.R | 2 ++ tests/testthat/test-driver-sqlite.R | 2 ++ tests/testthat/test-odbc-connection.R | 2 ++ tests/testthat/test-utils.R | 8 +++++++- 13 files changed, 59 insertions(+), 21 deletions(-)
Title: Conditional Logistic Regression: A Two-Step Estimation Method
Description: Conditional logistic regression with longitudinal follow up and
individual-level random coefficients: A stable and efficient
two-step estimation method.
Author: Radu V. Craiu [aut],
Thierry Duchesne [aut, cre],
Daniel Fortin [aut],
Sophie Baillargeon [aut]
Maintainer: Thierry Duchesne <thierry.duchesne@mat.ulaval.ca>
Diff between TwoStepCLogit versions 1.2.5 dated 2016-03-21 and 1.2.6 dated 2025-03-27
DESCRIPTION | 32 ++++++++++++++++++++++++-------- MD5 | 18 +++++++++--------- R/Ts.estim.R | 8 ++++---- R/TwoStepCLogit.R | 4 ++-- R/internal.R | 2 +- inst/NEWS.Rd | 5 +++++ man/Ts.estim.Rd | 24 +++++++++++++++--------- man/TwoStepCLogit-package.Rd | 19 +++++++++---------- man/bison.Rd | 7 ++++--- man/ddim.Rd | 1 - 10 files changed, 73 insertions(+), 47 deletions(-)
Title: Tidy Integration of Large Language Models
Description: A tidy interface for integrating large language model (LLM) APIs such as 'Claude', 'Openai', 'Gemini','Mistral' and local models via 'Ollama' into R workflows. The package supports text and media-based interactions, interactive message history, batch request APIs, and a tidy, pipeline-oriented interface for streamlined integration into data workflows. Web services are available at <https://www.anthropic.com>, <https://openai.com>, <https://aistudio.google.com/>, <https://mistral.ai/> and <https://ollama.com>.
Author: Eduard Bruell [aut, cre],
Jia Zhang [ctb]
Maintainer: Eduard Bruell <eduard.bruell@zew.de>
Diff between tidyllm versions 0.3.2 dated 2025-03-07 and 0.3.4 dated 2025-03-27
tidyllm-0.3.2/tidyllm/tests/testthat/claude |only tidyllm-0.3.2/tidyllm/tests/testthat/deepseek |only tidyllm-0.3.2/tidyllm/tests/testthat/groq |only tidyllm-0.3.2/tidyllm/tests/testthat/mistral |only tidyllm-0.3.2/tidyllm/tests/testthat/mistral_embedding |only tidyllm-0.3.2/tidyllm/tests/testthat/ollama |only tidyllm-0.3.2/tidyllm/tests/testthat/ollama_embedding |only tidyllm-0.3.2/tidyllm/tests/testthat/openai |only tidyllm-0.3.2/tidyllm/tests/testthat/openai_embedding |only tidyllm-0.3.2/tidyllm/tests/testthat/openai_schema_multiple |only tidyllm-0.3.2/tidyllm/tests/testthat/openai_schema_single |only tidyllm-0.3.2/tidyllm/tests/testthat/perplexity |only tidyllm-0.3.2/tidyllm/tests/testthat/test_api_voyage.R |only tidyllm-0.3.2/tidyllm/tests/testthat/test_pdf_page_batch.R |only tidyllm-0.3.2/tidyllm/tests/testthat/voyage_embedding_text |only tidyllm-0.3.4/tidyllm/DESCRIPTION | 21 tidyllm-0.3.4/tidyllm/MD5 | 106 - tidyllm-0.3.4/tidyllm/NAMESPACE | 5 tidyllm-0.3.4/tidyllm/NEWS.md | 140 ++ tidyllm-0.3.4/tidyllm/R/APIProvider.R | 44 tidyllm-0.3.4/tidyllm/R/LLMMessage.R | 65 - tidyllm-0.3.4/tidyllm/R/api_azure_openai.R | 459 +++---- tidyllm-0.3.4/tidyllm/R/api_claude.R | 398 ++++-- tidyllm-0.3.4/tidyllm/R/api_deepseek.R | 34 tidyllm-0.3.4/tidyllm/R/api_gemini.R | 200 +-- tidyllm-0.3.4/tidyllm/R/api_groq.R | 481 +++++++ tidyllm-0.3.4/tidyllm/R/api_mistral.R | 406 ++++-- tidyllm-0.3.4/tidyllm/R/api_ollama.R | 142 +- tidyllm-0.3.4/tidyllm/R/api_openai.R | 641 +++++----- tidyllm-0.3.4/tidyllm/R/api_perplexity.R | 105 + tidyllm-0.3.4/tidyllm/R/message_retrieval.R | 1 tidyllm-0.3.4/tidyllm/R/perform_api_requests.R | 71 - tidyllm-0.3.4/tidyllm/R/tidyllm_schema.R | 240 ++- tidyllm-0.3.4/tidyllm/R/tools.R | 12 tidyllm-0.3.4/tidyllm/R/utilites.R | 1 tidyllm-0.3.4/tidyllm/R/zzz.R | 5 tidyllm-0.3.4/tidyllm/README.md | 2 tidyllm-0.3.4/tidyllm/inst/doc/tidyllm.R | 107 + tidyllm-0.3.4/tidyllm/inst/doc/tidyllm.Rmd | 188 +- tidyllm-0.3.4/tidyllm/inst/doc/tidyllm.html | 527 ++++---- tidyllm-0.3.4/tidyllm/man/azure_openai_chat.Rd | 46 tidyllm-0.3.4/tidyllm/man/check_groq_batch.Rd |only tidyllm-0.3.4/tidyllm/man/claude_chat.Rd | 15 tidyllm-0.3.4/tidyllm/man/fetch_groq_batch.Rd |only tidyllm-0.3.4/tidyllm/man/field_chr.Rd | 2 tidyllm-0.3.4/tidyllm/man/field_object.Rd |only tidyllm-0.3.4/tidyllm/man/list_groq_batches.Rd |only tidyllm-0.3.4/tidyllm/man/mistral_chat.Rd | 39 tidyllm-0.3.4/tidyllm/man/openai_chat.Rd | 4 tidyllm-0.3.4/tidyllm/man/send_azure_openai_batch.Rd | 35 tidyllm-0.3.4/tidyllm/man/send_claude_batch.Rd | 14 tidyllm-0.3.4/tidyllm/man/send_groq_batch.Rd |only tidyllm-0.3.4/tidyllm/man/send_mistral_batch.Rd | 33 tidyllm-0.3.4/tidyllm/man/tidyllm-package.Rd | 2 tidyllm-0.3.4/tidyllm/tests/testthat/test_api_claude.R | 122 + tidyllm-0.3.4/tidyllm/tests/testthat/test_api_deepseek.R | 26 tidyllm-0.3.4/tidyllm/tests/testthat/test_api_gemini.R | 77 - tidyllm-0.3.4/tidyllm/tests/testthat/test_api_groq.R | 41 tidyllm-0.3.4/tidyllm/tests/testthat/test_api_mistral.R | 112 - tidyllm-0.3.4/tidyllm/tests/testthat/test_api_ollama.R | 51 tidyllm-0.3.4/tidyllm/tests/testthat/test_api_openai.R | 168 -- tidyllm-0.3.4/tidyllm/tests/testthat/test_api_perplexity.R | 28 tidyllm-0.3.4/tidyllm/tests/testthat/test_message_retrieval.R | 88 - tidyllm-0.3.4/tidyllm/vignettes/tidyllm.Rmd | 188 +- 64 files changed, 3256 insertions(+), 2236 deletions(-)
Title: R We There Yet? Visualizing MCMC Convergence in Phylogenetics
Description: Implements various tests, visualizations, and metrics
for diagnosing convergence of MCMC chains in phylogenetics. It implements
and automates many of the functions of the AWTY package in the R
environment, as well as a host of other functions. Warren, Geneva, and Lanfear (2017), <doi:10.1093/molbev/msw279>.
Author: Dan Warren [aut, cre],
Anthony Geneva [aut],
Rob Lanfear [aut],
Luke Harmon [ctb],
April Wright [ctb],
Diego Mallo [ctb],
Klaus Schliep [ctb],
Kelly Luke [ctb],
Kendall Michelle [ctb],
Smith Martin [ctb]
Maintainer: Dan Warren <dan.l.warren@gmail.com>
Diff between rwty versions 1.0.2 dated 2019-02-15 and 1.0.3 dated 2025-03-27
rwty-1.0.2/rwty/build |only rwty-1.0.2/rwty/inst/doc |only rwty-1.0.2/rwty/vignettes |only rwty-1.0.3/rwty/DESCRIPTION | 26 +- rwty-1.0.3/rwty/MD5 | 159 ++++++--------- rwty-1.0.3/rwty/NAMESPACE | 110 ++++++----- rwty-1.0.3/rwty/R/analyze.rwty.R | 2 rwty-1.0.3/rwty/R/check.chains.R | 6 rwty-1.0.3/rwty/R/clade.freq.R | 56 +++-- rwty-1.0.3/rwty/R/combine.ptables.R | 2 rwty-1.0.3/rwty/R/cumulative.freq.R | 2 rwty-1.0.3/rwty/R/estimate.autocorr.m.R | 2 rwty-1.0.3/rwty/R/load.multi.R | 2 rwty-1.0.3/rwty/R/load.trees.R | 6 rwty-1.0.3/rwty/R/makeplot.acsf.cumulative.R | 6 rwty-1.0.3/rwty/R/makeplot.acsf.sliding.R | 2 rwty-1.0.3/rwty/R/makeplot.all.params.R | 2 rwty-1.0.3/rwty/R/makeplot.asdsf.R | 16 + rwty-1.0.3/rwty/R/makeplot.autocorr.R | 2 rwty-1.0.3/rwty/R/makeplot.pairs.R | 2 rwty-1.0.3/rwty/R/makeplot.param.R | 2 rwty-1.0.3/rwty/R/makeplot.pseudo.ess.R | 2 rwty-1.0.3/rwty/R/makeplot.splitfreq.matrix.R | 2 rwty-1.0.3/rwty/R/makeplot.splitfreqs.cumulative.R | 2 rwty-1.0.3/rwty/R/makeplot.splitfreqs.sliding.R | 10 - rwty-1.0.3/rwty/R/makeplot.topology.R | 2 rwty-1.0.3/rwty/R/makeplot.treespace.R | 2 rwty-1.0.3/rwty/R/parse.slide.clades.R |only rwty-1.0.3/rwty/R/print.rwty.chain.R | 2 rwty-1.0.3/rwty/R/slide.freq.R | 34 +-- rwty-1.0.3/rwty/R/topological.approx.ess.R | 2 rwty-1.0.3/rwty/R/topological.autocorr.R | 2 rwty-1.0.3/rwty/R/topological.pseudo.ess.R | 2 rwty-1.0.3/rwty/R/tree.dist.matrix.R | 179 +++++++++++++++--- rwty-1.0.3/rwty/R/treespace.R | 2 rwty-1.0.3/rwty/README.md |only rwty-1.0.3/rwty/inst/report.template.Rmd |only rwty-1.0.3/rwty/man/analyze.rwty.Rd | 32 ++- rwty-1.0.3/rwty/man/check.chains.Rd | 8 rwty-1.0.3/rwty/man/clade.freq.Rd | 6 rwty-1.0.3/rwty/man/combine.ptables.Rd | 8 rwty-1.0.3/rwty/man/cumulative.freq.Rd | 4 rwty-1.0.3/rwty/man/estimate.autocorr.m.Rd | 2 rwty-1.0.3/rwty/man/fungus.Rd | 4 rwty-1.0.3/rwty/man/load.multi.Rd | 6 rwty-1.0.3/rwty/man/load.trees.Rd | 19 + rwty-1.0.3/rwty/man/makeplot.acsf.cumulative.Rd | 9 rwty-1.0.3/rwty/man/makeplot.acsf.sliding.Rd | 9 rwty-1.0.3/rwty/man/makeplot.all.params.Rd | 17 + rwty-1.0.3/rwty/man/makeplot.asdsf.Rd | 16 + rwty-1.0.3/rwty/man/makeplot.autocorr.Rd | 16 + rwty-1.0.3/rwty/man/makeplot.pairs.Rd | 11 - rwty-1.0.3/rwty/man/makeplot.param.Rd | 17 + rwty-1.0.3/rwty/man/makeplot.pseudo.ess.Rd | 3 rwty-1.0.3/rwty/man/makeplot.splitfreq.matrix.Rd | 10 - rwty-1.0.3/rwty/man/makeplot.splitfreqs.cumulative.Rd | 16 + rwty-1.0.3/rwty/man/makeplot.splitfreqs.sliding.Rd | 16 + rwty-1.0.3/rwty/man/makeplot.topology.Rd | 19 + rwty-1.0.3/rwty/man/makeplot.treespace.Rd | 7 rwty-1.0.3/rwty/man/parse.slide.clades.Rd |only rwty-1.0.3/rwty/man/print.rwty.chain.Rd | 10 - rwty-1.0.3/rwty/man/salamanders.Rd | 4 rwty-1.0.3/rwty/man/slide.freq.Rd | 6 rwty-1.0.3/rwty/man/topological.approx.ess.Rd | 14 - rwty-1.0.3/rwty/man/topological.autocorr.Rd | 15 + rwty-1.0.3/rwty/man/topological.pseudo.ess.Rd | 5 rwty-1.0.3/rwty/man/tree.dist.matrix.Rd | 130 ++++++++++++- rwty-1.0.3/rwty/man/treespace.Rd | 6 rwty-1.0.3/rwty/tests |only 69 files changed, 701 insertions(+), 392 deletions(-)
Title: Wrappers for 'Open-Meteo' API
Description: Wrappers for the Application Programming Interface from the <https://open-meteo.com> project along with helper functions. The <https://open-meteo.com> project streamlines access to a range of publicly historical and forecast meteorology data from agencies across the world.
Author: Quinn Thomas [aut, cre, cph]
Maintainer: Quinn Thomas <rqthomas@vt.edu>
Diff between ropenmeteo versions 0.1 dated 2024-09-02 and 0.1.1 dated 2025-03-27
DESCRIPTION | 7 - MD5 | 12 +- NEWS.md | 7 + README.md | 6 - build/vignette.rds |binary inst/doc/example_usage.R | 28 +++--- inst/doc/example_usage.html | 199 +++++++++++++++++++++----------------------- 7 files changed, 131 insertions(+), 128 deletions(-)
Title: Demographic Analysis and Data Manipulation
Description: Perform tasks commonly encountered when
preparing and analysing demographic data.
Some functions are intended for end users, and
others for developers. Includes functions for
working with life tables.
Author: John Bryant [aut, cre],
Bayesian Demography Limited [cph]
Maintainer: John Bryant <john@bayesiandemography.com>
Diff between poputils versions 0.4.0 dated 2025-03-22 and 0.4.1 dated 2025-03-27
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 6 ++++++ src/lifetab.cpp | 9 +++++---- 4 files changed, 17 insertions(+), 10 deletions(-)
Title: Inference Based on Non-Probability Samples
Description: Statistical inference with non-probability samples when auxiliary information from external sources such as probability samples or population totals or means is available. The package implements various methods such as inverse probability (propensity score) weighting, mass imputation and doubly robust approach. Details can be found in: Chen et al. (2020) <doi:10.1080/01621459.2019.1677241>, Yang et al. (2020) <doi:10.1111/rssb.12354>, Kim et al. (2021) <doi:10.1111/rssa.12696>, Yang et al. (2021) <https://www150.statcan.gc.ca/n1/pub/12-001-x/2021001/article/00004-eng.htm> and Wu (2022) <https://www150.statcan.gc.ca/n1/pub/12-001-x/2022002/article/00002-eng.htm>.
Author: Lukasz Chrostowski [aut, ctb],
Maciej Beresewicz [aut, cre] ,
Piotr Chlebicki [aut, ctb]
Maintainer: Maciej Beresewicz <maciej.beresewicz@ue.poznan.pl>
Diff between nonprobsvy versions 0.1.1 dated 2024-11-14 and 0.2.0 dated 2025-03-27
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nonprobsvy-0.2.0/nonprobsvy/NAMESPACE | 84 nonprobsvy-0.2.0/nonprobsvy/NEWS.md | 244 ++ nonprobsvy-0.2.0/nonprobsvy/R/RcppExports.R | 4 nonprobsvy-0.2.0/nonprobsvy/R/boot_dr.R | 971 +++++----- nonprobsvy-0.2.0/nonprobsvy/R/boot_ipw.R | 263 +- nonprobsvy-0.2.0/nonprobsvy/R/boot_mi.R | 855 +------- nonprobsvy-0.2.0/nonprobsvy/R/check_balance.R |only nonprobsvy-0.2.0/nonprobsvy/R/control_inference.R | 121 - nonprobsvy-0.2.0/nonprobsvy/R/control_outcome.R | 124 - nonprobsvy-0.2.0/nonprobsvy/R/control_selection.R | 183 + nonprobsvy-0.2.0/nonprobsvy/R/data.R |only nonprobsvy-0.2.0/nonprobsvy/R/est_method_dr.R |only nonprobsvy-0.2.0/nonprobsvy/R/est_method_ipw.R |only nonprobsvy-0.2.0/nonprobsvy/R/internals.R | 168 - nonprobsvy-0.2.0/nonprobsvy/R/make_model_frame.R |only nonprobsvy-0.2.0/nonprobsvy/R/method_glm.R |only nonprobsvy-0.2.0/nonprobsvy/R/method_nn.R |only nonprobsvy-0.2.0/nonprobsvy/R/method_npar.R |only nonprobsvy-0.2.0/nonprobsvy/R/method_pmm.R |only nonprobsvy-0.2.0/nonprobsvy/R/method_ps.R |only nonprobsvy-0.2.0/nonprobsvy/R/methods.R |only nonprobsvy-0.2.0/nonprobsvy/R/methods_not_implemented.R |only nonprobsvy-0.2.0/nonprobsvy/R/nonprob.R | 215 +- nonprobsvy-0.2.0/nonprobsvy/R/nonprob_documentation.R |only nonprobsvy-0.2.0/nonprobsvy/R/nonprob_dr.R |only nonprobsvy-0.2.0/nonprobsvy/R/nonprob_ipw.R |only nonprobsvy-0.2.0/nonprobsvy/R/nonprob_mi.R |only nonprobsvy-0.2.0/nonprobsvy/R/prints.R | 333 ++- nonprobsvy-0.2.0/nonprobsvy/R/summary.R | 316 --- nonprobsvy-0.2.0/nonprobsvy/R/variance_ipw.R |only nonprobsvy-0.2.0/nonprobsvy/README.md | 298 +-- nonprobsvy-0.2.0/nonprobsvy/data |only nonprobsvy-0.2.0/nonprobsvy/inst/CITATION |only nonprobsvy-0.2.0/nonprobsvy/inst/WORDLIST | 47 nonprobsvy-0.2.0/nonprobsvy/inst/tinytest/_code_for_all_.R |only nonprobsvy-0.2.0/nonprobsvy/inst/tinytest/test_check_balance.R |only nonprobsvy-0.2.0/nonprobsvy/inst/tinytest/test_controls.R |only nonprobsvy-0.2.0/nonprobsvy/inst/tinytest/test_dr.R |only nonprobsvy-0.2.0/nonprobsvy/inst/tinytest/test_ipw.R |only nonprobsvy-0.2.0/nonprobsvy/inst/tinytest/test_ipw_boot.R |only nonprobsvy-0.2.0/nonprobsvy/inst/tinytest/test_methods.R | 296 --- nonprobsvy-0.2.0/nonprobsvy/inst/tinytest/test_mi.R |only nonprobsvy-0.2.0/nonprobsvy/inst/tinytest/test_mi_methods.R |only nonprobsvy-0.2.0/nonprobsvy/inst/tinytest/test_nonprob.R |only nonprobsvy-0.2.0/nonprobsvy/inst/tinytest/test_nonprob_unit_level.R |only nonprobsvy-0.2.0/nonprobsvy/inst/tinytest/test_simulations.R |only nonprobsvy-0.2.0/nonprobsvy/inst/tinytest/test_vars_selection.R |only nonprobsvy-0.2.0/nonprobsvy/man/admin.Rd |only nonprobsvy-0.2.0/nonprobsvy/man/check_balance.Rd |only nonprobsvy-0.2.0/nonprobsvy/man/confint.nonprob.Rd |only nonprobsvy-0.2.0/nonprobsvy/man/control_inf.Rd |only nonprobsvy-0.2.0/nonprobsvy/man/control_out.Rd |only nonprobsvy-0.2.0/nonprobsvy/man/control_sel.Rd |only nonprobsvy-0.2.0/nonprobsvy/man/figures |only nonprobsvy-0.2.0/nonprobsvy/man/jvs.Rd |only nonprobsvy-0.2.0/nonprobsvy/man/method_glm.Rd |only nonprobsvy-0.2.0/nonprobsvy/man/method_nn.Rd |only nonprobsvy-0.2.0/nonprobsvy/man/method_npar.Rd |only nonprobsvy-0.2.0/nonprobsvy/man/method_pmm.Rd |only nonprobsvy-0.2.0/nonprobsvy/man/method_ps.Rd |only nonprobsvy-0.2.0/nonprobsvy/man/nonprob.Rd | 295 +-- nonprobsvy-0.2.0/nonprobsvy/man/pop_size.Rd |only nonprobsvy-0.2.0/nonprobsvy/man/print.nonprob_summary.Rd |only nonprobsvy-0.2.0/nonprobsvy/man/summary.nonprob.Rd |only nonprobsvy-0.2.0/nonprobsvy/man/update.nonprob.Rd |only nonprobsvy-0.2.0/nonprobsvy/man/weights.nonprob.Rd |only nonprobsvy-0.2.0/nonprobsvy/src/RcppExports.cpp | 8 nonprobsvy-0.2.0/nonprobsvy/src/nonprobCV_cpp.cpp | 199 -- 115 files changed, 2340 insertions(+), 2852 deletions(-)
Title: ICS via a Shiny Application
Description: Performs Invariant Coordinate Selection (ICS) (Tyler, Critchley, Duembgen and Oja (2009) <doi:10.1111/j.1467-9868.2009.00706.x>) and especially ICS for multivariate outlier detection with application to quality control (Archimbaud, Nordhausen, Ruiz-Gazen (2018) <doi:10.1016/j.csda.2018.06.011>) using a shiny app.
Author: Aurore Archimbaud [aut] ,
Joris May [aut],
Klaus Nordhausen [aut, cre] ,
Anne Ruiz-Gazen [aut]
Maintainer: Klaus Nordhausen <klausnordhausenR@gmail.com>
Diff between ICSShiny versions 0.5 dated 2018-04-01 and 0.6 dated 2025-03-27
DESCRIPTION | 33 ++++++++++++++++++++++++++------- MD5 | 6 +++--- inst/ChangeLog | 4 ++++ man/ICSShiny.Rd | 9 ++++----- 4 files changed, 37 insertions(+), 15 deletions(-)
Title: Constructing Hierarchical Voronoi Tessellations and Overlay
Heatmaps for Data Analysis
Description: Facilitates building topology preserving maps for data analysis.
Author: Zubin Dowlaty [aut],
Mu Sigma, Inc. [cre]
Maintainer: "Mu Sigma, Inc." <ird.experiencelab@mu-sigma.com>
Diff between HVT versions 25.2.2 dated 2025-02-05 and 25.2.3 dated 2025-03-27
DESCRIPTION | 10 MD5 | 38 - R/clustHVT.R | 10 R/clusterPlot.R | 7 R/getOptimalCentroids.R | 5 R/global.R | 2 R/msm.R | 318 ++++++--- R/msm_plots.R | 1610 +++++++++++++++++++++++++++++++++++++++++------- R/plotAnimatedFlowmap.R | 649 ++++++++++--------- R/plotHVT.R | 4 R/plotStateTransition.R | 16 R/scoreHVT.R | 7 R/trainHVT.R | 39 - README.md | 18 build/vignette.rds |binary inst/doc/HVT.R | 6 inst/doc/HVT.Rmd | 13 inst/doc/HVT.html | 22 man/msm.Rd | 16 vignettes/HVT.Rmd | 13 20 files changed, 2115 insertions(+), 688 deletions(-)
Title: Quantify Compositional Variability Across Relative Abundance
Vectors
Description: Implements the statistic FAVA, an Fst-based Assessment of Variability across
vectors of relative Abundances, as well as a suite of helper functions which enable the
visualization and statistical analysis of relative abundance data. The 'FAVA' R package
accompanies the paper, “Quantifying compositional variability in microbial communities
with FAVA” by Morrison, Xue, and Rosenberg (2025) <doi:10.1073/pnas.2413211122>.
Author: Maike Morrison [aut, cre, cph]
Maintainer: Maike Morrison <maike.morrison@gmail.com>
Diff between FAVA versions 1.0.7 dated 2024-12-10 and 1.0.9 dated 2025-03-27
DESCRIPTION | 12 MD5 | 44 - NEWS.md | 10 R/boostrap_comparison.R | 954 ++++++++++++++++++++-------------------- R/data_documentation.R | 110 ++-- R/fava_functions.R | 5 R/helper_functions.R | 23 R/visualize_fava.R | 324 ++++++------- R/window_fava.R | 502 ++++++++++----------- README.md | 8 build/partial.rdb |binary man/bootstrap_fava.Rd | 4 man/fava.Rd | 144 +++--- man/fava_norm.Rd | 74 +-- man/gini_simpson.Rd | 64 +- man/gini_simpson_mean.Rd | 148 +++--- man/plot_relabund.Rd | 242 +++++----- man/window_fava.Rd | 118 ++-- man/xue_microbiome_sample.Rd | 56 +- man/xue_species_info.Rd | 48 +- man/xue_species_similarity.Rd | 46 - tests/testthat/test-bootstrap.R | 727 +++++++++++++++--------------- tests/testthat/test-fava.R | 48 +- 23 files changed, 1899 insertions(+), 1812 deletions(-)
Title: Fast Computation of Multivariate M-Estimators
Description: Implements the new algorithm for fast computation of M-scatter matrices using a partial Newton-Raphson procedure for several estimators. The algorithm is described in Duembgen, Nordhausen and Schuhmacher (2016) <doi:10.1016/j.jmva.2015.11.009>.
Author: Lutz Duembgen [aut] ,
Klaus Nordhausen [aut, cre] ,
Heike Schuhmacher [aut]
Maintainer: Klaus Nordhausen <klausnordhausenr@gmail.com>
Diff between fastM versions 0.0-4 dated 2018-05-24 and 0.0-5 dated 2025-03-27
DESCRIPTION | 26 ++++++++++++++++++++------ MD5 | 6 +++--- build/partial.rdb |binary inst/ChangeLog | 3 +++ 4 files changed, 26 insertions(+), 9 deletions(-)
Title: Statistical Combination of Diagnostic Tests
Description: A system for combining two diagnostic tests using various approaches
that include statistical and machine-learning-based methodologies.
These approaches are divided into four groups: linear combination
methods, non-linear combination methods, mathematical operators,
and machine learning algorithms. See
the <https://biotools.erciyes.edu.tr/dtComb/> website
for more information, documentation, and examples.
Author: Serra Ilayda Yerlitas [aut, ctb],
Serra Bersan Gengec [aut, ctb],
Necla Kochan [aut, ctb],
Gozde Erturk Zararsiz [aut, ctb],
Selcuk Korkmaz [aut, ctb],
Gokmen Zararsiz [aut, ctb, cre]
Maintainer: Gokmen Zararsiz <gokmen.zararsiz@gmail.com>
Diff between dtComb versions 1.0.5 dated 2025-03-19 and 1.0.6 dated 2025-03-27
dtComb-1.0.5/dtComb/data/laparoscopy.rda |only dtComb-1.0.5/dtComb/man/laparoscopy.Rd |only dtComb-1.0.6/dtComb/DESCRIPTION | 6 - dtComb-1.0.6/dtComb/MD5 | 80 +++++++++--------- dtComb-1.0.6/dtComb/R/data.R | 30 +++--- dtComb-1.0.6/dtComb/R/dtComb.R | 16 ++- dtComb-1.0.6/dtComb/R/linComb.R | 40 ++++----- dtComb-1.0.6/dtComb/R/mathComb.R | 39 ++++---- dtComb-1.0.6/dtComb/R/mlComb.R | 6 - dtComb-1.0.6/dtComb/R/nonlinComb.R | 4 dtComb-1.0.6/dtComb/R/plotComb.R | 12 +- dtComb-1.0.6/dtComb/R/predict.dtComb.R | 6 - dtComb-1.0.6/dtComb/R/standardization.R | 4 dtComb-1.0.6/dtComb/build/vignette.rds |binary dtComb-1.0.6/dtComb/data/laparotomy.rda |only dtComb-1.0.6/dtComb/inst/doc/vignettedtComb.R | 14 +-- dtComb-1.0.6/dtComb/inst/doc/vignettedtComb.Rnw | 16 +-- dtComb-1.0.6/dtComb/inst/doc/vignettedtComb.pdf |binary dtComb-1.0.6/dtComb/man/allMethods.Rd | 4 dtComb-1.0.6/dtComb/man/dtComb.Rd | 15 ++- dtComb-1.0.6/dtComb/man/exampleData2.Rd | 8 + dtComb-1.0.6/dtComb/man/exampleData3.Rd | 4 dtComb-1.0.6/dtComb/man/helper_PCL.Rd | 6 - dtComb-1.0.6/dtComb/man/helper_PT.Rd | 6 - dtComb-1.0.6/dtComb/man/helper_TS.Rd | 6 - dtComb-1.0.6/dtComb/man/helper_minimax.Rd | 6 - dtComb-1.0.6/dtComb/man/helper_minmax.Rd | 6 - dtComb-1.0.6/dtComb/man/laparotomy.Rd |only dtComb-1.0.6/dtComb/man/linComb.Rd | 10 +- dtComb-1.0.6/dtComb/man/mathComb.Rd | 18 ++-- dtComb-1.0.6/dtComb/man/mlComb.Rd | 6 - dtComb-1.0.6/dtComb/man/nonlinComb.Rd | 4 dtComb-1.0.6/dtComb/man/plotComb.Rd | 6 - dtComb-1.0.6/dtComb/man/predict.dtComb.Rd | 6 - dtComb-1.0.6/dtComb/man/std.train.Rd | 4 dtComb-1.0.6/dtComb/man/transform_math.Rd | 20 ++-- dtComb-1.0.6/dtComb/tests/testthat/test-linComb.R | 6 - dtComb-1.0.6/dtComb/tests/testthat/test-mathComb.R | 4 dtComb-1.0.6/dtComb/tests/testthat/test-mlComb.R | 4 dtComb-1.0.6/dtComb/tests/testthat/test-nonlinComb.R | 4 dtComb-1.0.6/dtComb/tests/testthat/test-predComb.R | 6 - dtComb-1.0.6/dtComb/tests/testthat/test-standardize.R | 6 - dtComb-1.0.6/dtComb/vignettes/vignettedtComb.Rnw | 16 +-- 43 files changed, 233 insertions(+), 221 deletions(-)
Title: High-Dimensional Covariate-Augmented Overdispersed Poisson
Factor Model
Description: A covariate-augmented overdispersed Poisson factor model is proposed to jointly perform a high-dimensional Poisson factor analysis and estimate a large coefficient matrix for overdispersed count data.
More details can be referred to Liu et al. (2024) <doi:10.1093/biomtc/ujae031>.
Author: Wei Liu [aut, cre],
Qingzhi Zhong [aut]
Maintainer: Wei Liu <liuweideng@gmail.com>
Diff between COAP versions 1.2 dated 2024-05-01 and 1.3 dated 2025-03-27
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/main.R | 2 +- build/vignette.rds |binary inst/doc/COAPsimu.html | 41 ++++++++++++++++++++++++----------------- src/coap_R1.cpp | 4 ++-- 6 files changed, 36 insertions(+), 29 deletions(-)
Title: Bayesian Seemingly Unrelated Regression Models in
High-Dimensional Settings
Description: Bayesian seemingly unrelated regression with general variable selection and dense/sparse covariance matrix. The sparse seemingly unrelated regression is described in Bottolo et al. (2021) <doi:10.1111/rssc.12490>, the software paper is in Zhao et al. (2021) <doi:10.18637/jss.v100.i11>, and the model with random effects is described in Zhao et al. (2024) <doi:10.1093/jrsssc/qlad102>.
Author: Marco Banterle [aut],
Zhi Zhao [aut, cre],
Leonardo Bottolo [ctb],
Sylvia Richardson [ctb],
Waldir Leoncio [ctb],
Alex Lewin [aut],
Manuela Zucknick [aut]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Diff between BayesSUR versions 2.2-1 dated 2024-06-30 and 2.3-0 dated 2025-03-27
DESCRIPTION | 10 - MD5 | 33 +++-- NEWS.md | 7 + R/BayesSUR.R | 6 - R/plotEstimator.R | 244 +++++++++++++++++++++++++------------------ README.md | 71 +++++++----- build/vignette.rds |binary configure | 18 +-- data/exampleGDSC.rda |binary inst/CITATION | 6 - inst/doc/BayesSUR-RE.R | 4 inst/doc/BayesSUR-RE.Rmd | 69 +++++++----- inst/doc/BayesSUR-RE.html | 108 ++++++++++--------- man/figures/figureS.png |only src/HRR_Chain.cpp | 88 ++++++++++----- src/SUR_Chain.cpp | 258 +++++++++++++++++++++++++++++++++++++--------- src/drive.cpp | 3 vignettes/BayesSUR-RE.Rmd | 69 +++++++----- 18 files changed, 644 insertions(+), 350 deletions(-)
Title: Spatial Analysis in Archaeology from Refitting Fragments
Description: Methods to analyse spatial units in archaeology from the relationships between refitting fragmented objects scattered in these units (e.g. stratigraphic layers). Graphs are used to model archaeological observations. The package is mainly based on the 'igraph' package for graph analysis. Functions can: 1) create, manipulate, and simulate fragmentation graphs, 2) measure the cohesion and admixture of archaeological spatial units, and 3) characterise the topology of a specific set of refitting relationships. Empirical datasets are provided as examples. Documentation about 'archeofrag' is provided by the vignette included in this package, by the accompanying scientific papers: Plutniak (2021, Journal of Archaeological Science, <doi:10.1016/j.jas.2021.105501>) and Plutniak (2022, Journal of Open Source Software, <doi:10.21105/joss.04335>). This package is complemented by a companion GUI application available at <https://analytics.huma-num.fr/Sebastien.Plutniak/archeofrag/> [...truncated...]
Author: Sebastien Plutniak [aut, cre]
Maintainer: Sebastien Plutniak <sebastien.plutniak@posteo.net>
Diff between archeofrag versions 1.1.0 dated 2025-03-07 and 1.2.0 dated 2025-03-27
DESCRIPTION | 8 MD5 | 60 + NEWS.md | 5 R/frag.get.parameters.R | 4 R/frag.graph.reduce.R | 165 ++++- R/frag.layers.admixture.R | 8 R/frag.layers.cohesion.R | 15 R/frag.simul.compare.R | 6 R/frag.simul.process.R | 23 R/frag.simul.summarise.R | 2 TODO | 34 - data/BoutDesVergnes.RData |binary data/Chauzeys.RData |binary data/CuzoulCave.RData |binary data/CuzoulSouth.RData |binary data/Eaton.RData |only data/FontJuvenal.RData |binary data/Fumane.RData |only data/GrandeRivoire.RData |binary data/LiangAbu.RData |binary data/TaiCave.RData |binary data/TaiSouth.RData |binary inst/doc/archeofrag-vignette.html | 916 +++++++++++++++++------------ man/CuzoulCave.Rd | 2 man/Eaton.Rd |only man/Fumane.Rd |only man/LiangAbu.Rd | 4 man/frag.get.parameters.Rd | 10 man/frag.graph.reduce.Rd | 23 man/frag.simul.process.Rd | 4 tests/testthat/test-frag.graph.reduce.R | 44 + tests/testthat/test-frag.simul.compare.R | 9 tests/testthat/test-frag.simul.summarise.R | 6 33 files changed, 864 insertions(+), 484 deletions(-)
Title: Latent Interaction (and Moderation) Analysis in Structural
Equation Models (SEM)
Description: Estimation of interaction (i.e., moderation) effects between latent variables
in structural equation models (SEM).
The supported methods are:
The constrained approach (Algina & Moulder, 2001).
The unconstrained approach (Marsh et al., 2004).
The residual centering approach (Little et al., 2006).
The double centering approach (Lin et al., 2010).
The latent moderated structural equations (LMS) approach (Klein & Moosbrugger, 2000).
The quasi-maximum likelihood (QML) approach (Klein & Muthén, 2007) (temporarily unavailable)
The constrained- unconstrained, residual- and double centering- approaches
are estimated via 'lavaan' (Rosseel, 2012), whilst the LMS- and QML- approaches
are estimated via 'modsem' it self. Alternatively model can be
estimated via 'Mplus' (Muthén & Muthén, 1998-2017).
References:
Algina, J., & Moulder, B. C. (2001).
<doi:10.1207/S15328007SEM0801_3>.
"A note on estimating the Jöreskog-Yang model for latent variable interaction using 'LISREL' 8. [...truncated...]
Author: Kjell Solem Slupphaug [aut, cre]
,
Mehmet Mehmetoglu [ctb] ,
Matthias Mittner [ctb]
Maintainer: Kjell Solem Slupphaug <slupphaugkjell@gmail.com>
Diff between modsem versions 1.0.6 dated 2025-01-20 and 1.0.7 dated 2025-03-27
modsem-1.0.6/modsem/man/coef_modsem_da.Rd |only modsem-1.0.6/modsem/man/vcov_modsem_da.Rd |only modsem-1.0.7/modsem/DESCRIPTION | 8 modsem-1.0.7/modsem/MD5 | 78 - modsem-1.0.7/modsem/NAMESPACE | 5 modsem-1.0.7/modsem/R/calc_se_da.R | 53 - modsem-1.0.7/modsem/R/check_model_da.R | 37 modsem-1.0.7/modsem/R/construct_matrices_da.R | 5 modsem-1.0.7/modsem/R/generics.R | 40 modsem-1.0.7/modsem/R/generics_modsem_da.R | 24 modsem-1.0.7/modsem/R/method_settings_da.R | 4 modsem-1.0.7/modsem/R/model_da.R | 28 modsem-1.0.7/modsem/README.md | 19 modsem-1.0.7/modsem/build/partial.rdb |binary modsem-1.0.7/modsem/build/vignette.rds |binary modsem-1.0.7/modsem/inst/doc/customizing.R | 74 - modsem-1.0.7/modsem/inst/doc/customizing.html | 235 ----- modsem-1.0.7/modsem/inst/doc/higher_order_interactions.R | 94 +- modsem-1.0.7/modsem/inst/doc/higher_order_interactions.html | 231 ----- modsem-1.0.7/modsem/inst/doc/interaction_two_etas.R | 68 - modsem-1.0.7/modsem/inst/doc/interaction_two_etas.html | 249 ----- modsem-1.0.7/modsem/inst/doc/lavaan.R | 32 modsem-1.0.7/modsem/inst/doc/lavaan.html | 205 ---- modsem-1.0.7/modsem/inst/doc/lms_qml.R | 84 - modsem-1.0.7/modsem/inst/doc/lms_qml.html | 240 ----- modsem-1.0.7/modsem/inst/doc/methods.R | 44 - modsem-1.0.7/modsem/inst/doc/methods.html | 225 ----- modsem-1.0.7/modsem/inst/doc/modsem.R | 172 +-- modsem-1.0.7/modsem/inst/doc/modsem.html | 260 ------ modsem-1.0.7/modsem/inst/doc/observed_lms_qml.R | 106 +- modsem-1.0.7/modsem/inst/doc/observed_lms_qml.Rmd | 19 modsem-1.0.7/modsem/inst/doc/observed_lms_qml.html | 433 ++++------ modsem-1.0.7/modsem/inst/doc/plot_interactions.R | 32 modsem-1.0.7/modsem/inst/doc/plot_interactions.html | 253 ----- modsem-1.0.7/modsem/inst/doc/quadratic.R | 48 - modsem-1.0.7/modsem/inst/doc/quadratic.html | 215 ---- modsem-1.0.7/modsem/inst/doc/simple_slopes.R | 82 - modsem-1.0.7/modsem/inst/doc/simple_slopes.html | 226 ----- modsem-1.0.7/modsem/man/modsem_coef.Rd |only modsem-1.0.7/modsem/man/modsem_nobs.Rd |only modsem-1.0.7/modsem/man/modsem_vcov.Rd |only modsem-1.0.7/modsem/tests/testthat/test_zero_variance_indicator_lms.R |only modsem-1.0.7/modsem/vignettes/observed_lms_qml.Rmd | 19 43 files changed, 952 insertions(+), 2995 deletions(-)
Title: Calculate Bark Beetle Phenology Using Different Models
Description: Calculate the bark beetle phenology based on raster data or
point-related data. There are multiple models implemented for two bark
beetle species. The models can be customized and their submodels (onset of
infestation, beetle development, diapause initiation, mortality) can be
combined. The following models are available in the package:
PHENIPS-Clim (first-time release in this package),
PHENIPS (Baier et al. 2007) <doi:10.1016/j.foreco.2007.05.020>,
RITY (Ogris et al. 2019) <doi:10.1016/j.ecolmodel.2019.108775>,
CHAPY (Ogris et al. 2020) <doi:10.1016/j.ecolmodel.2020.109137>,
BSO (Jakoby et al. 2019) <doi:10.1111/gcb.14766>,
Lange et al. (2008) <doi:10.1007/978-3-540-85081-6_32>,
Jönsson et al. (2011) <doi:10.1007/s10584-011-0038-4>.
The package may be expanded by models for other bark beetle species in the
future.
Author: Jakob Jentschke [aut, cre],
FVA BW, Abt. Waldschutz [cph, fnd]
Maintainer: Jakob Jentschke <jakob.jentschke@forst.bwl.de>
Diff between barrks versions 1.1.0 dated 2025-03-03 and 1.1.1 dated 2025-03-27
DESCRIPTION | 8 MD5 | 20 NEWS.md | 82 +- R/model-lange.R | 644 +++++++++++------------ R/model-phenips-clim.R | 1190 +++++++++++++++++++++---------------------- R/model-phenips.R | 1035 ++++++++++++++++++------------------- R/plot-development-diagram.R | 814 ++++++++++++++--------------- R/utils-doc.R | 170 +++--- R/utils.R | 346 ++++++------ build/partial.rdb |binary inst/doc/storage.R | 24 11 files changed, 2188 insertions(+), 2145 deletions(-)
Title: Teaching Hydrological Modelling with the GR Rainfall-Runoff
Models ('Shiny' Interface Included)
Description: Add-on package to the 'airGR' package that simplifies its use and is aimed at being used for teaching hydrology. The package provides 1) three functions that allow to complete very simply a hydrological modelling exercise 2) plotting functions to help students to explore observed data and to interpret the results of calibration and simulation of the GR ('Génie rural') models 3) a 'Shiny' graphical interface that allows for displaying the impact of model parameters on hydrographs and models internal variables.
Author: Olivier Delaigue [aut, cre] ,
Laurent Coron [aut] ,
Pierre Brigode [aut] ,
Guillaume Thirel [aut]
Maintainer: Olivier Delaigue <airGR@inrae.fr>
Diff between airGRteaching versions 0.3.4 dated 2025-02-11 and 0.3.5 dated 2025-03-27
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- NEWS.md | 9 +++++++++ build/partial.rdb |binary inst/ShinyGR/www/tab_about.md | 4 ++-- inst/ShinyGR/www/tab_about.rmd | 4 ++-- inst/ShinyGR/www/tab_fun.md | 4 ++-- inst/ShinyGR/www/tab_fun.rmd | 4 ++-- inst/doc/get_started.html | 8 ++++---- inst/doc/v00_teaching_hydrology.html | 24 ++++++++++++------------ inst/doc/v01_EN_flow_reconstruction.html | 12 ++++++------ inst/doc/v01_FR_flow_reconstruction.html | 12 ++++++------ inst/doc/v02_EN_flow_forecasting.html | 16 ++++++++-------- inst/doc/v02_FR_flow_forecasting.html | 16 ++++++++-------- inst/doc/v03_EN_impact_CC_flow.html | 12 ++++++------ inst/doc/v03_FR_impact_CC_flow.html | 12 ++++++------ 16 files changed, 92 insertions(+), 83 deletions(-)
Title: Support for Parallel Computation, Logging, and Function
Automation
Description: Support for parallel computation with progress bar, and option to stop or proceed on errors. Also provides logging to console and disk,
and the logging persists in the parallel threads. Additional functions support function call automation with delayed execution (e.g. for executing functions in
parallel).
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between ParallelLogger versions 3.3.1 dated 2024-08-23 and 3.4.0 dated 2025-03-27
DESCRIPTION | 10 - MD5 | 42 ++--- NAMESPACE | 3 NEWS.md | 16 ++ R/Appenders.R | 6 R/Args.R | 10 - R/Cluster.R | 114 ++++++++++++++ R/Layouts.R | 18 +- R/Loggers.R | 2 R/Logging.R | 10 + R/ParallelLogger.R | 2 R/ShinyApps.R | 2 inst/doc/Logging.R | 320 +++++++++++++++++++++--------------------- inst/doc/Logging.pdf |binary inst/doc/Parallel.Rmd | 2 inst/doc/Parallel.pdf |binary man/getPhysicalMemory.Rd |only man/getThreadNumber.Rd |only man/makeCluster.Rd | 7 tests/testthat/test-args.R | 12 + tests/testthat/test-cluster.R | 61 +++----- tests/testthat/test-layouts.R | 18 +- vignettes/Parallel.Rmd | 2 23 files changed, 404 insertions(+), 253 deletions(-)
More information about ParallelLogger at CRAN
Permanent link
Title: Analysis of Bivariate Survival Data Based on Copulas
Description: Simulating bivariate survival data from copula models.
Estimation of the association parameter in copula models.
Two different ways to estimate the association parameter in copula models are implemented.
A goodness-of-fit test for a given copula model is implemented.
See Emura, Lin and Wang (2010) <doi:10.1016/j.csda.2010.03.013> for details.
Author: Takeshi Emura [aut, cre]
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between Copula.surv versions 1.8 dated 2025-01-31 and 1.9 dated 2025-03-27
DESCRIPTION | 8 ++++---- MD5 | 10 +++++++--- R/Weib.reg.cBB1.0.R |only R/simu.BB1.R | 3 ++- R/simu.BB1reg.R |only man/Weib.reg.cBB1.0.Rd |only man/simu.BB1.Rd | 6 +++--- man/simu.BB1reg.Rd |only 8 files changed, 16 insertions(+), 11 deletions(-)
Title: Some Useful Functions for Statistics and Visualization
Description: Offers a range of utilities and functions for everyday programming tasks. 1.Data
Manipulation. Such as grouping and merging, column splitting, and character expansion. 2.File
Handling. Read and convert files in popular formats. 3.Plotting Assistance. Helpful utilities
for generating color palettes, validating color formats, and adding transparency.
4.Statistical Analysis. Includes functions for pairwise comparisons and multiple testing
corrections, enabling perform statistical analyses with ease. 5.Graph Plotting, Provides
efficient tools for creating doughnut plot and multi-layered doughnut plot; Venn diagrams,
including traditional Venn diagrams, upset plots, and flower plots; Simplified functions for
creating stacked bar plots, or a box plot with alphabets group for multiple comparison group.
Author: Chen Peng [aut, cre]
Maintainer: Chen Peng <pengchen2001@zju.edu.cn>
Diff between pcutils versions 0.2.7 dated 2024-11-27 and 0.2.8 dated 2025-03-27
DESCRIPTION | 33 +++++++------- MD5 | 16 +++--- NAMESPACE | 2 NEWS.md | 11 ++++ R/l_tools.R | 52 ++++++++++++++++++++++ R/plots.R | 91 ++++++++++++++++++++++++++++++++++----- README.md | 2 man/check_directory_structure.Rd |only man/get_legend2.Rd |only man/gghuan2.Rd | 15 ++++-- 10 files changed, 183 insertions(+), 39 deletions(-)
Title: A Simple and Robust JSON Parser and Generator for R
Description: A reasonably fast JSON parser and generator, optimized for statistical
data and the web. Offers simple, flexible tools for working with JSON in R, and
is particularly powerful for building pipelines and interacting with a web API.
The implementation is based on the mapping described in the vignette (Ooms, 2014).
In addition to converting JSON data from/to R objects, 'jsonlite' contains
functions to stream, validate, and prettify JSON data. The unit tests included
with the package verify that all edge cases are encoded and decoded consistently
for use with dynamic data in systems and applications.
Author: Jeroen Ooms [aut, cre] ,
Duncan Temple Lang [ctb],
Lloyd Hilaiel [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between jsonlite versions 1.9.1 dated 2025-03-03 and 2.0.0 dated 2025-03-27
DESCRIPTION | 8 - MD5 | 197 +++++++++++++------------- NEWS | 9 + R/apply_by_pages.R | 28 +-- R/as.scalar.R | 14 - R/asJSON.AAAgeneric.R | 2 R/asJSON.AsIs.R | 2 R/asJSON.Date.R | 4 R/asJSON.NULL.R | 2 R/asJSON.POSIXt.R | 16 -- R/asJSON.array.R | 24 +-- R/asJSON.character.R | 12 - R/asJSON.complex.R | 14 - R/asJSON.data.frame.R | 38 ++--- R/asJSON.difftime.R | 5 R/asJSON.factor.R | 2 R/asJSON.function.R | 7 R/asJSON.json.R | 2 R/asJSON.list.R | 30 ++- R/asJSON.logical.R | 18 +- R/asJSON.numeric.R | 29 +-- R/asJSON.raw.R | 5 R/asJSON.sf.R | 18 -- R/base64.R | 17 +- R/cleannames.R | 5 R/collapse.R | 16 +- R/collapse_object.R | 4 R/deparse_vector.R | 18 +- R/fixNativeSymbol.R | 3 R/flatten.R | 8 - R/fromJSON.R | 26 +-- R/is.recordlist.R | 10 - R/is.scalarlist.R | 10 - R/json_gzip.R | 8 - R/list_to_vec.R | 4 R/loadpkg.R | 5 R/null_to_na.R | 2 R/num_to_char.R | 18 +- R/pack.R | 80 +++++----- R/parseJSON.R | 4 R/prettify.R | 15 + R/print.R | 10 - R/push_parser.R | 4 R/raw_to_json.R | 8 - R/rbind_pages.R | 9 - R/read_json.R | 4 R/serializeJSON.R | 4 R/simplify.R | 101 ++++++------- R/simplifyDataFrame.R | 41 ++--- R/stop.R | 2 R/stream.R | 60 +++---- R/toJSON.R | 67 ++++++-- R/unbox.R | 16 +- R/unescape_unicode.R | 15 + R/utf8conv.R | 2 R/warn_keep_vec_names.R | 5 inst/doc/json-aaquickstart.html | 2 inst/doc/json-mapping.pdf |binary man/fromJSON.Rd | 2 man/prettify.Rd | 2 src/Makevars | 7 src/collapse_pretty.c | 35 +++- src/prettify.c | 1 src/row_collapse.c | 4 src/yajl/yajl_gen.c | 13 + tests/testthat.R | 7 tests/testthat/flatten.R | 13 - tests/testthat/helper-toJSON.R | 2 tests/testthat/test-fromJSON-NA-values.R | 21 +- tests/testthat/test-fromJSON-array.R | 71 ++++----- tests/testthat/test-fromJSON-dataframe.R | 68 ++++---- tests/testthat/test-fromJSON-datasets.R | 10 - tests/testthat/test-fromJSON-date.R | 34 +--- tests/testthat/test-fromJSON-matrix.R | 52 +++--- tests/testthat/test-libjson-escaping.R | 22 +- tests/testthat/test-libjson-large.R | 18 -- tests/testthat/test-libjson-utf8.R | 33 +--- tests/testthat/test-libjson-validator.R | 18 -- tests/testthat/test-network-Github.R | 96 ++++++------ tests/testthat/test-serializeJSON-S4.R | 28 +-- tests/testthat/test-serializeJSON-datasets.R | 17 -- tests/testthat/test-serializeJSON-functions.R | 21 +- tests/testthat/test-serializeJSON-types.R | 24 +-- tests/testthat/test-toJSON-AsIs.R | 20 +- tests/testthat/test-toJSON-Date.R | 33 ++-- tests/testthat/test-toJSON-NA-values.R | 17 -- tests/testthat/test-toJSON-NULL-values.R | 28 +-- tests/testthat/test-toJSON-POSIXt.R | 107 ++++++-------- tests/testthat/test-toJSON-complex.R | 36 ++-- tests/testthat/test-toJSON-dataframe.R | 29 +-- tests/testthat/test-toJSON-factor.R | 10 - tests/testthat/test-toJSON-indent.R |only tests/testthat/test-toJSON-keep-vec-names.R | 25 +-- tests/testthat/test-toJSON-logical.R | 34 ++-- tests/testthat/test-toJSON-matrix.R | 14 - tests/testthat/test-toJSON-numeric.R | 48 +++--- tests/testthat/test-toJSON-raw.R | 9 - tests/testthat/test-toJSON-sf.R | 16 +- tests/testthat/test-toJSON-zerovec.R | 42 ++--- tests/testthat/test_rbind_pages.R | 19 +- 100 files changed, 1072 insertions(+), 1123 deletions(-)
Title: Utilities for Graphical Rendering and Fonts Management
Description: Tools are provided to compute metrics of formatted strings
and to check the availability of a font. Another set of functions is
provided to support the collection of fonts from 'Google Fonts' in a
cache. Their use is simple within 'R Markdown' documents and 'shiny'
applications but also with graphic productions generated with the
'ggiraph', 'ragg' and 'svglite' packages or with tabular productions
from the 'flextable' package.
Author: David Gohel [aut, cre],
Hadley Wickham [aut],
Lionel Henry [aut],
Jeroen Ooms [aut] ,
Yixuan Qiu [ctb],
R Core Team [cph] ,
ArData [cph],
RStudio [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between gdtools versions 0.4.1 dated 2024-11-04 and 0.4.2 dated 2025-03-27
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ README.md | 26 +++++++++++++++++++++++++- src/Makevars.in | 6 +++--- src/Makevars.win | 17 +++++++++++++---- 6 files changed, 53 insertions(+), 16 deletions(-)
Title: A Collection of Outlier Ensemble Algorithms
Description: Ensemble functions for outlier/anomaly detection. There is a new ensemble method proposed using
Item Response Theory. Existing outlier ensemble methods from Schubert et al (2012) <doi:10.1137/1.9781611972825.90>,
Chiang et al (2017) <doi:10.1016/j.jal.2016.12.002> and Aggarwal and Sathe (2015) <doi:10.1145/2830544.2830549>
are also included.
Author: Sevvandi Kandanaarachchi [aut, cre]
Maintainer: Sevvandi Kandanaarachchi <sevvandik@gmail.com>
Diff between outlierensembles versions 0.1.2 dated 2025-02-22 and 0.1.3 dated 2025-03-27
DESCRIPTION | 11 +++--- MD5 | 40 ++++++++++++++---------- R/Y-data.R |only R/Yfaithful-data.R |only R/greedy_ensemble.R | 2 + R/icwa_ensemble.R | 2 + R/irt_ensemble.R | 2 + R/max_thres_mean_ensembles.R | 6 +++ README.md | 54 ++++++++++++++++++++------------- build/vignette.rds |binary data |only inst/doc/outlierensembles.R | 34 +++++++++++--------- inst/doc/outlierensembles.Rmd | 34 +++++++++++--------- inst/doc/outlierensembles.html | 67 ++++++++++++++++++++--------------------- man/Y.Rd |only man/Yfaithful.Rd |only man/average_ensemble.Rd | 2 + man/greedy_ensemble.Rd | 2 + man/icwa_ensemble.Rd | 2 + man/irt_ensemble.Rd | 2 + man/max_ensemble.Rd | 2 + man/threshold_ensemble.Rd | 2 + vignettes/outlierensembles.Rmd | 34 +++++++++++--------- 23 files changed, 177 insertions(+), 121 deletions(-)
More information about outlierensembles at CRAN
Permanent link
Title: Inferring Cell-Specific Gene Regulatory Network
Description: An R package for inferring cell-type specific gene regulatory network from single-cell RNA data.
Author: Meng Xu [aut, cre]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between inferCSN versions 1.0.8 dated 2024-08-24 and 1.1.6 dated 2025-03-27
inferCSN-1.0.8/inferCSN/R/performance_evaluation.R |only inferCSN-1.0.8/inferCSN/R/sparse_regression.R |only inferCSN-1.0.8/inferCSN/man/calculate_acc.Rd |only inferCSN-1.0.8/inferCSN/man/fit_sparse_regression.Rd |only inferCSN-1.0.8/inferCSN/man/plot_weight_distribution.Rd |only inferCSN-1.0.8/inferCSN/src/README.cpp |only inferCSN-1.0.8/inferCSN/src/tableToMatrix.cpp |only inferCSN-1.1.6/inferCSN/DESCRIPTION | 18 inferCSN-1.1.6/inferCSN/MD5 | 111 - inferCSN-1.1.6/inferCSN/NAMESPACE | 28 inferCSN-1.1.6/inferCSN/R/RcppExports.R | 173 ++ inferCSN-1.1.6/inferCSN/R/import.R | 42 inferCSN-1.1.6/inferCSN/R/inferCSN.R | 219 +- inferCSN-1.1.6/inferCSN/R/meta_cells.R |only inferCSN-1.1.6/inferCSN/R/network_evaluation.R |only inferCSN-1.1.6/inferCSN/R/network_sift.R | 81 - inferCSN-1.1.6/inferCSN/R/network_visualization.R | 135 - inferCSN-1.1.6/inferCSN/R/plotting_functions.R | 147 + inferCSN-1.1.6/inferCSN/R/single_network.R |only inferCSN-1.1.6/inferCSN/R/sparse_regression_model.R |only inferCSN-1.1.6/inferCSN/R/subsampling.R |only inferCSN-1.1.6/inferCSN/R/utils.R | 589 ++++--- inferCSN-1.1.6/inferCSN/README.md | 6 inferCSN-1.1.6/inferCSN/inst |only inferCSN-1.1.6/inferCSN/man/as_matrix.Rd | 29 inferCSN-1.1.6/inferCSN/man/calculate_accuracy.Rd |only inferCSN-1.1.6/inferCSN/man/calculate_auc.Rd | 31 inferCSN-1.1.6/inferCSN/man/calculate_auprc.Rd |only inferCSN-1.1.6/inferCSN/man/calculate_auroc.Rd |only inferCSN-1.1.6/inferCSN/man/calculate_f1.Rd |only inferCSN-1.1.6/inferCSN/man/calculate_ji.Rd |only inferCSN-1.1.6/inferCSN/man/calculate_metrics.Rd |only inferCSN-1.1.6/inferCSN/man/calculate_precision.Rd |only inferCSN-1.1.6/inferCSN/man/calculate_recall.Rd |only inferCSN-1.1.6/inferCSN/man/calculate_si.Rd |only inferCSN-1.1.6/inferCSN/man/coef.srm.Rd | 5 inferCSN-1.1.6/inferCSN/man/figures/logo.svg | 1111 ++++---------- inferCSN-1.1.6/inferCSN/man/filter_sort_matrix.Rd | 2 inferCSN-1.1.6/inferCSN/man/fit_srm.Rd |only inferCSN-1.1.6/inferCSN/man/grapes-ss-grapes.Rd |only inferCSN-1.1.6/inferCSN/man/inferCSN.Rd | 78 inferCSN-1.1.6/inferCSN/man/log_message.Rd | 20 inferCSN-1.1.6/inferCSN/man/matrix_to_table.Rd |only inferCSN-1.1.6/inferCSN/man/meta_cells.Rd |only inferCSN-1.1.6/inferCSN/man/network_format.Rd | 11 inferCSN-1.1.6/inferCSN/man/network_sift.Rd | 13 inferCSN-1.1.6/inferCSN/man/normalization.Rd | 4 inferCSN-1.1.6/inferCSN/man/pearson_correlation.Rd |only inferCSN-1.1.6/inferCSN/man/plot_all_metrics.Rd |only inferCSN-1.1.6/inferCSN/man/plot_coefficient.Rd |only inferCSN-1.1.6/inferCSN/man/plot_coefficients.Rd |only inferCSN-1.1.6/inferCSN/man/plot_edges_comparison.Rd |only inferCSN-1.1.6/inferCSN/man/plot_histogram.Rd |only inferCSN-1.1.6/inferCSN/man/plot_network_heatmap.Rd | 29 inferCSN-1.1.6/inferCSN/man/plot_static_networks.Rd | 8 inferCSN-1.1.6/inferCSN/man/predict.srm.Rd | 5 inferCSN-1.1.6/inferCSN/man/prepare_binary_predictions.Rd |only inferCSN-1.1.6/inferCSN/man/print.srm.Rd | 8 inferCSN-1.1.6/inferCSN/man/simulate_sparse_matrix.Rd |only inferCSN-1.1.6/inferCSN/man/single_network.Rd | 48 inferCSN-1.1.6/inferCSN/man/sparse_cor.Rd |only inferCSN-1.1.6/inferCSN/man/sparse_regression.Rd | 112 + inferCSN-1.1.6/inferCSN/man/split_indices.Rd |only inferCSN-1.1.6/inferCSN/man/subsampling.Rd |only inferCSN-1.1.6/inferCSN/man/table_to_matrix.Rd | 2 inferCSN-1.1.6/inferCSN/man/weight_sift.Rd |only inferCSN-1.1.6/inferCSN/src/CDL012SquaredHingeSwaps.cpp | 56 inferCSN-1.1.6/inferCSN/src/Grid2D.cpp | 50 inferCSN-1.1.6/inferCSN/src/Interface.cpp | 86 - inferCSN-1.1.6/inferCSN/src/RcppExports.cpp | 109 + inferCSN-1.1.6/inferCSN/src/filter_sort_matrix.cpp |only inferCSN-1.1.6/inferCSN/src/include/CD.h | 8 inferCSN-1.1.6/inferCSN/src/include/network_format.h |only inferCSN-1.1.6/inferCSN/src/matrix_to_table.cpp |only inferCSN-1.1.6/inferCSN/src/network_evaluation.cpp |only inferCSN-1.1.6/inferCSN/src/network_format.cpp |only inferCSN-1.1.6/inferCSN/src/sparseCovCor.cpp |only inferCSN-1.1.6/inferCSN/src/split_indices.cpp |only inferCSN-1.1.6/inferCSN/src/table_to_matrix.cpp |only inferCSN-1.1.6/inferCSN/src/weight_sift.cpp |only 80 files changed, 1859 insertions(+), 1515 deletions(-)