Title: Interface for 'Google Gemini' API
Description: Provides a comprehensive interface for Google Gemini API,
enabling users to access and utilize Gemini Large Language Model (LLM) functionalities directly from R.
This package facilitates seamless integration with Google Gemini, allowing for advanced language processing,
text generation, and other AI-driven capabilities within the R environment.
For more information, please visit <https://ai.google.dev/docs/gemini_api_overview>.
Author: Jinhwan Kim [aut, cre, cph] ,
Maciej Nasinski [ctb]
Maintainer: Jinhwan Kim <hwanistic@gmail.com>
Diff between gemini.R versions 0.6.1 dated 2024-12-10 and 0.8.0 dated 2025-02-05
DESCRIPTION | 10 ++--- MD5 | 38 +++++++++++++------ NAMESPACE | 14 +++++++ NEWS.md | 21 +++++++++- R/Urrecipe.R |only R/gemini.R | 70 ++++++++++++++++++++++++++++++++++-- R/gemini_audio.R |only R/gemini_chat.R | 15 +++++-- R/gemini_image.R | 75 ++++++++++++++++++++++++++++++++++++-- R/gen_tests.R |only R/vertex.R |only README.md | 83 +++++++++++++++++++++++++++++++++++++++---- inst/quarto |only inst/rstudio/addins.dcf | 5 ++ man/figures/testing.gif |only man/figures/vertex_audio.png |only man/figures/vertex_image.png |only man/figures/vertex_text.png |only man/gemini.Rd | 2 - man/gemini.vertex.Rd |only man/gemini_audio.Rd |only man/gemini_audio.vertex.Rd |only man/gemini_chat.Rd | 2 - man/gemini_image.Rd | 2 - man/gemini_image.vertex.Rd |only man/gen_tests.Rd |only man/token.vertex.Rd |only 27 files changed, 295 insertions(+), 42 deletions(-)
Title: R and C/C++ Wrappers to Run the Leiden find_partition() Function
Description: An R to C/C++ interface that runs the Leiden community
detection algorithm to find a basic partition (). It runs the
equivalent of the 'leidenalg' find_partition() function, which is
given in the 'leidenalg' distribution file
'leiden/src/functions.py'. This package includes the
required source code files from the official 'leidenalg'
distribution and functions from the R 'igraph'
package. The 'leidenalg' distribution is available from
<https://github.com/vtraag/leidenalg/>
and the R 'igraph' package is available from
<https://igraph.org/r/>.
The Leiden algorithm is described in the article by
Traag et al. (2019) <doi:10.1038/s41598-019-41695-z>.
Leidenbase includes code from the packages:
igraph version 0.9.8 with license GPL (>= 2),
leidenalg version 0.8.10 with license GPL 3.
Author: Brent Ewing [aut, cre],
Vincent Traag [ctb],
Gabor Csardi [ctb],
Tamas Nepusz [ctb],
Szabolcs Horvat [ctb],
Fabio Zanini [ctb]
Maintainer: Brent Ewing <bge@uw.edu>
Diff between leidenbase versions 0.1.31 dated 2024-09-25 and 0.1.32 dated 2025-02-05
DESCRIPTION | 6 +++--- MD5 | 6 +++--- build/vignette.rds |binary src/Makevars.ucrt | 43 +++++++++++++++++++++++++++++++++++-------- 4 files changed, 41 insertions(+), 14 deletions(-)
Title: Life and Fertility Tables Specially for Insects
Description: Life and Fertility Tables are appropriate to study the dynamics of
arthropods populations. This package provides utilities for constructing
Life Tables and Fertility Tables, related demographic parameters, and some
simple graphs of interest. It also offers functions to transform the
obtained data into a known format for better manipulation. This document is
based on the article by Maia, Luiz, and Campanhola "Statistical Inference on
Associated Fertility Life Table Parameters Using Jackknife Technique
Computational Aspects" (April 2000, Journal of Economic Entomology, Volume
93, Issue 2) <doi:10.1603/0022-0493-93.2.511>.
Author: Carlos Abimael Sarmiento Sanchez [aut, cre],
Lauro Soto Rojas [ctb],
Alejandro Corona Ambriz [ctb],
Gabriel Arcangel Rodriguez Yam [ctb],
Yolanda Franco Islas [ctb],
Noe Ramirez Negrete [ctb]
Maintainer: Carlos Abimael Sarmiento Sanchez <cass9918@hotmail.com>
Diff between Lifertable versions 0.0.1 dated 2024-02-29 and 0.1.0 dated 2025-02-05
DESCRIPTION | 31 ++- MD5 | 53 +++--- NEWS.md |only R/Insects.R | 23 +- R/PlotPseudoVals.R | 135 ++++++++--------- R/as.data.frame.lifertableCI.R | 8 - R/as.data.frame.lifertableLFT.R | 18 +- R/as.data.frame.lifertableParmEst.R | 76 +++++---- R/as.data.frame.lifertableTotEggs.R | 8 - R/lifertable.R | 162 +++++++++++++------- R/lifertable.groups.R | 258 +++++++++++++++++---------------- R/lifertable.individual.R | 156 ++++++++++--------- R/lifertable.jackknife.R | 5 R/plotDistrOvipos.R | 172 ++++++++++++---------- R/plotEggs.R | 18 +- R/plotSurvivalCurve.R | 150 +++++++++---------- build/partial.rdb |binary data/Insects.rda |binary man/Insects.Rd | 22 +- man/PlotPseudoVals.Rd | 9 - man/as.data.frame.lifertableCI.Rd | 8 - man/as.data.frame.lifertableLFT.Rd | 8 - man/as.data.frame.lifertableParmEst.Rd | 8 - man/as.data.frame.lifertableTotEggs.Rd | 8 - man/lifertable.Rd | 109 ++++++++----- man/plotDistrOvipos.Rd | 17 +- man/plotEggs.Rd | 18 +- man/plotSurvivalCurve.Rd | 6 28 files changed, 857 insertions(+), 629 deletions(-)
Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from
Model Outputs
Description: Compute marginal effects and adjusted predictions from statistical
models and returns the result as tidy data frames. These data frames are
ready to use with the 'ggplot2'-package. Effects and predictions can be
calculated for many different models. Interaction terms, splines and
polynomial terms are also supported. The main functions are ggpredict(),
ggemmeans() and ggeffect(). There is a generic plot()-method to plot the
results using 'ggplot2'.
Author: Daniel Luedecke [aut, cre] ,
Frederik Aust [ctb] ,
Sam Crawley [ctb] ,
Mattan S. Ben-Shachar [ctb] ,
Sean C. Anderson [ctb]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between ggeffects versions 2.1.0 dated 2025-01-20 and 2.2.0 dated 2025-02-05
ggeffects-2.1.0/ggeffects/R/johnson_neyman_numcat.R |only ggeffects-2.1.0/ggeffects/R/tp_label_hypothesis_categorical.R |only ggeffects-2.1.0/ggeffects/R/tp_label_hypothesis_formula.R |only ggeffects-2.1.0/ggeffects/R/tp_label_hypothesis_slopes.R |only ggeffects-2.1.0/ggeffects/R/tp_label_pairwise_categorical.R |only ggeffects-2.1.0/ggeffects/R/tp_label_pairwise_slopes.R |only ggeffects-2.1.0/ggeffects/tests/testthat/test-johnson_neyman_numcat.R |only ggeffects-2.1.0/ggeffects/tests/testthat/test-test_predictions.R |only ggeffects-2.2.0/ggeffects/DESCRIPTION | 25 ggeffects-2.2.0/ggeffects/LICENSE | 4 ggeffects-2.2.0/ggeffects/MD5 | 86 - ggeffects-2.2.0/ggeffects/NAMESPACE | 3 ggeffects-2.2.0/ggeffects/NEWS.md | 10 ggeffects-2.2.0/ggeffects/R/format.R | 12 ggeffects-2.2.0/ggeffects/R/ggemmeans_zi_predictions.R | 10 ggeffects-2.2.0/ggeffects/R/johnson_neyman.R | 484 ++------- ggeffects-2.2.0/ggeffects/R/pool_comparisons.R | 39 ggeffects-2.2.0/ggeffects/R/predict_response.R | 4 ggeffects-2.2.0/ggeffects/R/predict_zero_inflation.R | 9 ggeffects-2.2.0/ggeffects/R/print.R | 69 - ggeffects-2.2.0/ggeffects/R/test_predictions.R | 506 ---------- ggeffects-2.2.0/ggeffects/R/utils_test_predictions.R | 17 ggeffects-2.2.0/ggeffects/README.md | 35 ggeffects-2.2.0/ggeffects/inst/doc/content.Rmd | 9 ggeffects-2.2.0/ggeffects/inst/doc/content.html | 17 ggeffects-2.2.0/ggeffects/man/ggpredict.Rd | 4 ggeffects-2.2.0/ggeffects/man/install_latest.Rd | 80 - ggeffects-2.2.0/ggeffects/man/johnson_neyman.Rd | 30 ggeffects-2.2.0/ggeffects/man/predict_response.Rd | 4 ggeffects-2.2.0/ggeffects/man/print.Rd | 2 ggeffects-2.2.0/ggeffects/man/test_predictions.Rd | 23 ggeffects-2.2.0/ggeffects/tests/testthat/test-betareg.R | 2 ggeffects-2.2.0/ggeffects/tests/testthat/test-fixest.R | 6 ggeffects-2.2.0/ggeffects/tests/testthat/test-focal_only_random.R | 4 ggeffects-2.2.0/ggeffects/tests/testthat/test-ggaverage.R | 13 ggeffects-2.2.0/ggeffects/tests/testthat/test-glmmTMB.R | 1 ggeffects-2.2.0/ggeffects/tests/testthat/test-johnson_neyman.R | 177 --- ggeffects-2.2.0/ggeffects/tests/testthat/test-mgcv.R | 4 ggeffects-2.2.0/ggeffects/tests/testthat/test-parsnip.R | 7 ggeffects-2.2.0/ggeffects/tests/testthat/test-pool_comparisons.R | 4 ggeffects-2.2.0/ggeffects/tests/testthat/test-print_md.R | 2 ggeffects-2.2.0/ggeffects/tests/testthat/test-print_test_predictions-ordinal.R | 2 ggeffects-2.2.0/ggeffects/tests/testthat/test-print_test_predictions.R | 158 +-- ggeffects-2.2.0/ggeffects/tests/testthat/test-test_predictions-formula.R | 4 ggeffects-2.2.0/ggeffects/tests/testthat/test-test_predictions-mixed.R | 7 ggeffects-2.2.0/ggeffects/tests/testthat/test-test_predictions_emmeans.R | 68 - ggeffects-2.2.0/ggeffects/tests/testthat/test-vcov.R | 27 ggeffects-2.2.0/ggeffects/vignettes/content.Rmd | 9 48 files changed, 536 insertions(+), 1441 deletions(-)
Title: Methods to Analyse Signed Networks
Description: Methods for the analysis of signed networks. This includes
several measures for structural balance as introduced by Cartwright
and Harary (1956) <doi:10.1037/h0046049>, blockmodeling algorithms
from Doreian (2008) <doi:10.1016/j.socnet.2008.03.005>, various
centrality indices, and projections of signed two-mode networks
introduced by Schoch (2020) <doi:10.1080/0022250X.2019.1711376>.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david@schochastics.net>
Diff between signnet versions 1.0.4 dated 2024-01-08 and 1.0.5 dated 2025-02-05
DESCRIPTION | 8 MD5 | 46 NEWS.md | 4 R/blockmodel.R | 127 +- R/centrality_indices.R | 176 +-- R/complex_matrices.R | 400 +++---- R/laplace_matrix.R | 26 R/random_graphs.R | 190 ++- R/signed_triangles.R | 2154 ++++++++++++++++++++++++++++++++------- build/vignette.rds |binary inst/doc/blockmodeling.R | 2 inst/doc/blockmodeling.html | 221 +--- inst/doc/centrality.R | 2 inst/doc/centrality.html | 191 +-- inst/doc/complex_matrices.R | 4 inst/doc/complex_matrices.html | 175 +-- inst/doc/signed_2mode.html | 191 +-- inst/doc/signed_networks.html | 163 +- inst/doc/structural_balance.html | 173 +-- man/count_complex_triangles.Rd | 2 man/count_signed_triangles.Rd | 2 man/signed_blockmodel_general.Rd | 8 man/signed_triangles.Rd | 2 man/triad_census_signed.Rd | 2 24 files changed, 2886 insertions(+), 1383 deletions(-)
Title: Emax Model Analysis with 'Stan'
Description: Perform sigmoidal Emax model fit using 'Stan' in a formula notation, without writing 'Stan' model code.
Author: Kenta Yoshida [aut, cre] ,
Danielle Navarro [aut] ,
Trustees of Columbia University [cph]
Maintainer: Kenta Yoshida <yoshida.kenta.6@gmail.com>
Diff between rstanemax versions 0.1.7 dated 2024-12-06 and 0.1.8 dated 2025-02-05
rstanemax-0.1.7/rstanemax/src/Makevars.win |only rstanemax-0.1.8/rstanemax/DESCRIPTION | 16 rstanemax-0.1.8/rstanemax/MD5 | 22 rstanemax-0.1.8/rstanemax/NAMESPACE | 6 rstanemax-0.1.8/rstanemax/NEWS.md | 9 rstanemax-0.1.8/rstanemax/R/posterior_predict.R | 428 ++++++---- rstanemax-0.1.8/rstanemax/build/vignette.rds |binary rstanemax-0.1.8/rstanemax/inst/doc/emaxmodel.html | 129 +-- rstanemax-0.1.8/rstanemax/man/posterior_predict.Rd | 101 +- rstanemax-0.1.8/rstanemax/man/rstanemax-package.Rd | 2 rstanemax-0.1.8/rstanemax/tests/testthat/test-posterior_predict.R | 44 - rstanemax-0.1.8/rstanemax/tests/testthat/test-stan_emax_binary.R | 4 rstanemax-0.1.8/rstanemax/tests/testthat/test-tidybayes_integration.R |only 13 files changed, 488 insertions(+), 273 deletions(-)
Title: Lightweight Extension of the Base R Graphics System
Description: Lightweight extension of the base R graphics system, with support
for automatic legends, facets, themes, and various other enhancements.
Author: Grant McDermott [aut, cre] ,
Vincent Arel-Bundock [aut] ,
Achim Zeileis [aut] ,
Etienne Bacher [ctb]
Maintainer: Grant McDermott <gmcd@amazon.com>
Diff between tinyplot versions 0.2.1 dated 2024-08-26 and 0.3.0 dated 2025-02-05
tinyplot-0.2.1/tinyplot/R/aesthetics.R |only tinyplot-0.2.1/tinyplot/R/draw_elements.R |only tinyplot-0.3.0/tinyplot/DESCRIPTION | 21 tinyplot-0.3.0/tinyplot/MD5 | 114 + tinyplot-0.3.0/tinyplot/NAMESPACE | 61 tinyplot-0.3.0/tinyplot/NEWS.md | 178 ++ tinyplot-0.3.0/tinyplot/R/assertions.R | 17 tinyplot-0.3.0/tinyplot/R/by_aesthetics.R | 144 + tinyplot-0.3.0/tinyplot/R/draw_legend.R | 76 tinyplot-0.3.0/tinyplot/R/facet.R | 227 ++ tinyplot-0.3.0/tinyplot/R/get_saved_par.R | 4 tinyplot-0.3.0/tinyplot/R/lim.R | 32 tinyplot-0.3.0/tinyplot/R/sanitize.R | 89 - tinyplot-0.3.0/tinyplot/R/tinyAxis.R | 4 tinyplot-0.3.0/tinyplot/R/tinyplot.R | 782 ++++++---- tinyplot-0.3.0/tinyplot/R/tinyplot_add.R |only tinyplot-0.3.0/tinyplot/R/tinytheme.R |only tinyplot-0.3.0/tinyplot/R/tpar.R | 419 +++-- tinyplot-0.3.0/tinyplot/R/type_abline.R |only tinyplot-0.3.0/tinyplot/R/type_area.R | 34 tinyplot-0.3.0/tinyplot/R/type_boxplot.R | 185 +- tinyplot-0.3.0/tinyplot/R/type_density.R | 385 ++-- tinyplot-0.3.0/tinyplot/R/type_errorbar.R |only tinyplot-0.3.0/tinyplot/R/type_function.R |only tinyplot-0.3.0/tinyplot/R/type_glm.R |only tinyplot-0.3.0/tinyplot/R/type_histogram.R | 205 ++ tinyplot-0.3.0/tinyplot/R/type_hline.R |only tinyplot-0.3.0/tinyplot/R/type_jitter.R | 93 - tinyplot-0.3.0/tinyplot/R/type_lines.R |only tinyplot-0.3.0/tinyplot/R/type_lm.R |only tinyplot-0.3.0/tinyplot/R/type_loess.R |only tinyplot-0.3.0/tinyplot/R/type_pointrange.R | 65 tinyplot-0.3.0/tinyplot/R/type_points.R |only tinyplot-0.3.0/tinyplot/R/type_polygon.R |only tinyplot-0.3.0/tinyplot/R/type_polypath.R |only tinyplot-0.3.0/tinyplot/R/type_qq.R |only tinyplot-0.3.0/tinyplot/R/type_rect.R |only tinyplot-0.3.0/tinyplot/R/type_ribbon.R | 157 +- tinyplot-0.3.0/tinyplot/R/type_ridge.R |only tinyplot-0.3.0/tinyplot/R/type_rug.R |only tinyplot-0.3.0/tinyplot/R/type_segments.R |only tinyplot-0.3.0/tinyplot/R/type_spineplot.R |only tinyplot-0.3.0/tinyplot/R/type_spline.R |only tinyplot-0.3.0/tinyplot/R/type_summary.R |only tinyplot-0.3.0/tinyplot/R/type_text.R |only tinyplot-0.3.0/tinyplot/R/type_vline.R |only tinyplot-0.3.0/tinyplot/R/utils.R | 15 tinyplot-0.3.0/tinyplot/R/zzz.R | 41 tinyplot-0.3.0/tinyplot/README.md | 55 tinyplot-0.3.0/tinyplot/man/ci.Rd |only tinyplot-0.3.0/tinyplot/man/figures/README-quickstart4-1.png |binary tinyplot-0.3.0/tinyplot/man/figures/README-quickstart5-1.png |binary tinyplot-0.3.0/tinyplot/man/figures/README-quickstart_theme-1.png |only tinyplot-0.3.0/tinyplot/man/get_saved_par.Rd | 2 tinyplot-0.3.0/tinyplot/man/tinyAxis.Rd |only tinyplot-0.3.0/tinyplot/man/tinyplot-package.Rd | 2 tinyplot-0.3.0/tinyplot/man/tinyplot.Rd | 237 +-- tinyplot-0.3.0/tinyplot/man/tinyplot_add.Rd |only tinyplot-0.3.0/tinyplot/man/tinytheme.Rd |only tinyplot-0.3.0/tinyplot/man/tpar.Rd | 79 - tinyplot-0.3.0/tinyplot/man/type_abline.Rd |only tinyplot-0.3.0/tinyplot/man/type_boxplot.Rd |only tinyplot-0.3.0/tinyplot/man/type_density.Rd |only tinyplot-0.3.0/tinyplot/man/type_errorbar.Rd |only tinyplot-0.3.0/tinyplot/man/type_function.Rd |only tinyplot-0.3.0/tinyplot/man/type_glm.Rd |only tinyplot-0.3.0/tinyplot/man/type_histogram.Rd |only tinyplot-0.3.0/tinyplot/man/type_hline.Rd |only tinyplot-0.3.0/tinyplot/man/type_jitter.Rd |only tinyplot-0.3.0/tinyplot/man/type_lines.Rd |only tinyplot-0.3.0/tinyplot/man/type_lm.Rd |only tinyplot-0.3.0/tinyplot/man/type_loess.Rd |only tinyplot-0.3.0/tinyplot/man/type_points.Rd |only tinyplot-0.3.0/tinyplot/man/type_polygon.Rd |only tinyplot-0.3.0/tinyplot/man/type_polypath.Rd |only tinyplot-0.3.0/tinyplot/man/type_qq.Rd |only tinyplot-0.3.0/tinyplot/man/type_rect.Rd |only tinyplot-0.3.0/tinyplot/man/type_ribbon.Rd |only tinyplot-0.3.0/tinyplot/man/type_ridge.Rd |only tinyplot-0.3.0/tinyplot/man/type_rug.Rd |only tinyplot-0.3.0/tinyplot/man/type_segments.Rd |only tinyplot-0.3.0/tinyplot/man/type_spineplot.Rd |only tinyplot-0.3.0/tinyplot/man/type_spline.Rd |only tinyplot-0.3.0/tinyplot/man/type_summary.Rd |only tinyplot-0.3.0/tinyplot/man/type_text.Rd |only tinyplot-0.3.0/tinyplot/man/type_vline.Rd |only 86 files changed, 2538 insertions(+), 1185 deletions(-)
Title: Geometric Morphometric Analyses of 2D and 3D Landmark Data
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams [aut, cre],
Michael Collyer [aut],
Antigoni Kaliontzopoulou [aut],
Erica Baken [aut]
Maintainer: Dean Adams <dcadams@iastate.edu>
Diff between geomorph versions 4.0.9 dated 2024-11-15 and 4.0.10 dated 2025-02-05
geomorph-4.0.10/geomorph/DESCRIPTION | 8 geomorph-4.0.10/geomorph/MD5 | 23 - geomorph-4.0.10/geomorph/NEWS.md | 17 geomorph-4.0.10/geomorph/R/extended.pgls.r | 2 geomorph-4.0.10/geomorph/R/physignal.eigen.R | 38 +- geomorph-4.0.10/geomorph/build/vignette.rds |binary geomorph-4.0.10/geomorph/data/pupfish.ws.rda |binary geomorph-4.0.10/geomorph/inst/CITATION | 4 geomorph-4.0.10/geomorph/inst/doc/geomorph.digitize3D.html | 4 geomorph-4.0.10/geomorph/man/extended.pgls.Rd | 2 geomorph-4.0.10/geomorph/man/physignal.eigen.Rd | 18 geomorph-4.0.10/geomorph/tests/testthat/test-geomorph.R | 245 ++++++------- geomorph-4.0.9/geomorph/vignettes/cran-comments.md |only 13 files changed, 205 insertions(+), 156 deletions(-)
Title: Easy Study of Patient DICOM Data in Oncology
Description: Exploitation, processing and 2D-3D visualization of DICOM-RT files (structures, dosimetry, imagery) for medical physics and clinical research, in a patient-oriented perspective.
Author: Cathy Fontbonne [aut, cre] ,
Jean-Marc Fontbonne [aut] ,
Nathan Azemar [ctb]
Maintainer: Cathy Fontbonne <contact.espadon@lpccaen.in2p3.fr>
Diff between espadon versions 1.9.0 dated 2024-11-25 and 1.10.0 dated 2025-02-05
espadon-1.10.0/espadon/DESCRIPTION | 6 espadon-1.10.0/espadon/MD5 | 111 ++-- espadon-1.10.0/espadon/NAMESPACE | 3 espadon-1.10.0/espadon/R/RcppExports.R | 4 espadon-1.10.0/espadon/R/bin_from_roi.R | 31 - espadon-1.10.0/espadon/R/contour.R |only espadon-1.10.0/espadon/R/dicom_set_tag_value.R | 129 ----- espadon-1.10.0/espadon/R/display_3D_contour.R | 5 espadon-1.10.0/espadon/R/display_3D_mesh.R | 3 espadon-1.10.0/espadon/R/display_3D_sections.R | 3 espadon-1.10.0/espadon/R/display_3D_stack.R | 3 espadon-1.10.0/espadon/R/err_metrics_from_roi.R |only espadon-1.10.0/espadon/R/espadon_hidden.R | 5 espadon-1.10.0/espadon/R/export.R | 2 espadon-1.10.0/espadon/R/fan_beam.R | 8 espadon-1.10.0/espadon/R/fan_planar.R | 8 espadon-1.10.0/espadon/R/fan_sphere.R | 12 espadon-1.10.0/espadon/R/get_value_from_mesh.R | 25 espadon-1.10.0/espadon/R/histo_vol.R | 1 espadon-1.10.0/espadon/R/mesh_spheric_proj.R | 34 - espadon-1.10.0/espadon/R/nesting_bin.R | 6 espadon-1.10.0/espadon/R/nesting_cube.R | 15 espadon-1.10.0/espadon/R/orientation_create.R | 7 espadon-1.10.0/espadon/R/plot.R | 18 espadon-1.10.0/espadon/R/polyg.R | 234 --------- espadon-1.10.0/espadon/R/rt_chi_index.R | 2 espadon-1.10.0/espadon/R/rt_gamma_index.R | 2 espadon-1.10.0/espadon/R/rt_indices_from_roi.R | 4 espadon-1.10.0/espadon/R/struct_create.R | 6 espadon-1.10.0/espadon/R/toy_load_patient.R | 65 +- espadon-1.10.0/espadon/R/vol_abserror.R |only espadon-1.10.0/espadon/R/vol_error.R |only espadon-1.10.0/espadon/build/partial.rdb |binary espadon-1.10.0/espadon/build/stage23.rdb |binary espadon-1.10.0/espadon/inst/doc/espadon_overview.R | 317 ++++++------ espadon-1.10.0/espadon/inst/doc/espadon_overview.Rmd | 362 ++++++++------ espadon-1.10.0/espadon/inst/doc/espadon_overview.html | 462 ++++++++++-------- espadon-1.10.0/espadon/man/bin.from.roi.Rd | 6 espadon-1.10.0/espadon/man/display.3D.contour.Rd | 5 espadon-1.10.0/espadon/man/display.3D.mesh.Rd | 3 espadon-1.10.0/espadon/man/display.3D.sections.Rd | 3 espadon-1.10.0/espadon/man/display.3D.stack.Rd | 3 espadon-1.10.0/espadon/man/err.metrics.from.roi.Rd |only espadon-1.10.0/espadon/man/export.Rd | 2 espadon-1.10.0/espadon/man/fan.beam.Rd | 7 espadon-1.10.0/espadon/man/fan.planar.Rd | 7 espadon-1.10.0/espadon/man/fan.sphere.Rd | 11 espadon-1.10.0/espadon/man/get.value.from.mesh.Rd | 19 espadon-1.10.0/espadon/man/mesh.spheric.proj.Rd | 30 - espadon-1.10.0/espadon/man/rt.chi.index.Rd | 2 espadon-1.10.0/espadon/man/rt.gamma.index.Rd | 2 espadon-1.10.0/espadon/man/struct.create.Rd | 6 espadon-1.10.0/espadon/man/toy.load.patient.Rd | 2 espadon-1.10.0/espadon/man/vol.abserror.Rd |only espadon-1.10.0/espadon/man/vol.error.Rd |only espadon-1.10.0/espadon/src/RcppExports.cpp | 22 espadon-1.10.0/espadon/src/esplib.h | 1 espadon-1.10.0/espadon/src/getvaluefromijkC.cpp | 25 espadon-1.10.0/espadon/vignettes/espadon_overview.Rmd | 362 ++++++++------ espadon-1.9.0/espadon/R/roidata.R |only espadon-1.9.0/espadon/src/addcommonptC.cpp |only 61 files changed, 1150 insertions(+), 1261 deletions(-)
More information about CircNNTSRSymmetric at CRAN
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Title: Bayesian Knowledge Tracing Model
Description: Fitting, cross-validating, and predicting with Bayesian Knowledge Tracing (BKT) models. It is designed for analyzing educational datasets to trace student knowledge over time. The package includes functions for fitting BKT models, evaluating their performance using various metrics, and making predictions on new data. It provides the similar functionality as the Python package pyBKT authored by Zachary A. Pardos (zp@berkeley.edu) at <https://github.com/CAHLR/pyBKT>.
Author: Yuhao Yuan [aut, cre],
Biying Zhou [aut],
Feng Ji [aut]
Maintainer: Yuhao Yuan <yuanyuhaoapply@163.com>
Diff between BKT versions 0.0.1 dated 2025-01-30 and 0.1.0 dated 2025-02-05
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Estimation of Return Curves
Description: Estimates the p-probability return curve proposed by Murphy-Barltrop et al. (2023) <doi:10.1002/env.2797>. Implements pointwise and smooth estimation of the angular dependence function introduced by Wadsworth and Tawn (2013) <doi:10.3150/12-BEJ471>.
Author: Lidia Andre [aut, cre],
Callum Murphy-Barltrop [aut]
Maintainer: Lidia Andre <lidia.andre@unamur.be>
Diff between ReturnCurves versions 1.0 dated 2024-07-04 and 1.0.1 dated 2025-02-05
ReturnCurves-1.0.1/ReturnCurves/DESCRIPTION | 13 +++++++------ ReturnCurves-1.0.1/ReturnCurves/MD5 | 13 ++++++------- ReturnCurves-1.0.1/ReturnCurves/README.md | 5 ++++- ReturnCurves-1.0.1/ReturnCurves/build/partial.rdb |binary ReturnCurves-1.0.1/ReturnCurves/build/stage23.rdb |binary ReturnCurves-1.0.1/ReturnCurves/build/vignette.rds |binary ReturnCurves-1.0.1/ReturnCurves/inst/doc/ReturnCurves.pdf |binary ReturnCurves-1.0/ReturnCurves/build/ReturnCurves.pdf |only 8 files changed, 17 insertions(+), 14 deletions(-)
Title: Functional Programming Tools
Description: A complete and consistent functional programming toolkit for
R.
Author: Hadley Wickham [aut, cre] ,
Lionel Henry [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between purrr versions 1.0.2 dated 2023-08-10 and 1.0.4 dated 2025-02-05
DESCRIPTION | 23 ++-- LICENSE | 2 MD5 | 153 +++++++++++++++---------------- NAMESPACE | 33 ++++++ NEWS.md | 92 ++++++++++-------- R/deprec-when.R | 2 R/imap.R | 7 + R/keep.R | 8 - R/list-combine.R | 4 R/list-flatten.R | 4 R/list-modify.R | 5 - R/list-simplify.R | 8 - R/list-transpose.R | 25 +++-- R/modify-tree.R | 4 R/modify.R | 6 - R/pmap.R | 20 +++- R/progress-bars.R | 2 R/reduce.R | 68 +++++++------ R/superseded-map-df.R | 17 +++ R/superseded-transpose.R | 6 + R/utils.R | 2 README.md | 11 +- build/vignette.rds |binary inst/doc/base.R | 20 ++-- inst/doc/base.Rmd | 8 - inst/doc/base.html | 12 +- inst/doc/other-langs.Rmd | 2 inst/doc/other-langs.html | 2 man/accumulate.Rd | 2 man/figures/logo.png |binary man/imap.Rd | 5 - man/keep_at.Rd | 8 - man/list_assign.Rd | 7 - man/list_simplify.Rd | 6 - man/list_transpose.Rd | 6 - man/lmap.Rd | 2 man/map2.Rd | 2 man/map_depth.Rd | 8 - man/map_dfr.Rd | 17 +++ man/map_if.Rd | 2 man/modify.Rd | 2 man/modify_tree.Rd | 2 man/pmap.Rd | 10 +- man/progress_bars.Rd | 2 man/purrr-package.Rd | 6 - man/reduce.Rd | 33 ------ man/reduce_right.Rd | 31 ++++-- man/when.Rd | 2 src/backports.c | 10 ++ src/backports.h | 6 + src/conditions.c | 6 - src/map.c | 5 - src/pluck.c | 2 tests/testthat/_snaps/coerce.md | 56 +++++++++++ tests/testthat/_snaps/deprec-cross.md | 8 + tests/testthat/_snaps/deprec-prepend.md | 24 ++++ tests/testthat/_snaps/deprec-utils.md | 32 ++++++ tests/testthat/_snaps/deprec-when.md | 8 + tests/testthat/_snaps/every-some-none.md |only tests/testthat/_snaps/list-transpose.md | 16 +++ tests/testthat/_snaps/map-depth.md | 24 ++++ tests/testthat/_snaps/pluck.md | 16 +++ tests/testthat/test-adverb-auto-browse.R | 2 tests/testthat/test-coerce.R | 14 +- tests/testthat/test-deprec-cross.R | 2 tests/testthat/test-deprec-prepend.R | 15 --- tests/testthat/test-deprec-utils.R | 8 - tests/testthat/test-deprec-when.R | 2 tests/testthat/test-every-some-none.R | 4 tests/testthat/test-imap.R | 1 tests/testthat/test-list-transpose.R | 19 +++ tests/testthat/test-lmap.R | 1 tests/testthat/test-map-depth.R | 4 tests/testthat/test-modify.R | 1 tests/testthat/test-pluck.R | 4 tests/testthat/test-utils.R | 2 vignettes/base.Rmd | 8 - vignettes/other-langs.Rmd | 2 78 files changed, 669 insertions(+), 332 deletions(-)
Title: Simulating Diversification Dynamics
Description: Simulation of species diversification, fossil records, and phylogenies. While the literature on species birth-death simulators is extensive, including important software like 'paleotree' and 'APE', we concluded there were interesting gaps to be filled regarding possible diversification scenarios. Here we strove for flexibility over focus, implementing a large array of regimens for users to experiment with and combine. In this way, 'paleobuddy' can be used in complement to other simulators as a flexible jack of all trades, or, in the case of scenarios implemented only here, can allow for robust and easy simulations for novel situations. Environmental data modified from that in 'RPANDA': Morlon H. et al (2016) <doi:10.1111/2041-210X.12526>.
Author: Bruno do Rosario Petrucci [aut, cre]
,
Matheus Januario [aut] ,
Tiago Quental [aut]
Maintainer: Bruno do Rosario Petrucci <petrucci@iastate.edu>
Diff between paleobuddy versions 1.0.0 dated 2021-12-21 and 1.1.0 dated 2025-02-05
DESCRIPTION | 10 MD5 | 64 - NAMESPACE | 6 NEWS.md | 232 ++-- R/bd.sim.R | 58 - R/bd.sim.constant.R | 100 + R/bd.sim.general.R | 107 + R/bd.sim.traits.R |only R/bin.occurrences.R |only R/draw.sim.R | 391 ++++++- R/make.phylo.R | 507 ++++++++- R/paleobuddy.R | 8 R/phylo.to.sim.R | 4 R/rexp.musse.R |only R/sample.age.time.R | 8 R/sample.clade.R | 57 - R/sample.clade.traits.R |only R/sim.R | 12 R/traits.summary.R |only README.md | 8 build/vignette.rds |binary inst/CITATION |only inst/doc/overview.R | 245 +++- inst/doc/overview.Rmd | 220 +++ inst/doc/overview.html | 1713 ++++++++++++++++++++++++------- man/bd.sim.Rd | 43 man/bd.sim.traits.Rd |only man/bin.occurrences.Rd |only man/draw.sim.Rd | 146 ++ man/figures/README-unnamed-chunk-6-1.png |binary man/find.lineages.Rd | 6 man/make.phylo.Rd | 218 +++ man/paleobuddy.Rd | 17 man/sample.clade.Rd | 49 man/sample.clade.traits.Rd |only man/sim.Rd | 6 man/traits.summary.Rd |only vignettes/overview.Rmd | 220 +++ 38 files changed, 3707 insertions(+), 748 deletions(-)
Title: A Crew Launcher Plugin for AWS Batch
Description: In computationally demanding analysis projects,
statisticians and data scientists asynchronously
deploy long-running tasks to distributed systems,
ranging from traditional clusters to cloud services.
The 'crew.aws.batch' package extends the 'mirai'-powered
'crew' package with a worker launcher plugin for AWS Batch.
Inspiration also comes from packages 'mirai' by Gao (2023)
<https://github.com/shikokuchuo/mirai>,
'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>,
'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>,
'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>),
and 'batchtools' by Lang, Bischl, and Surmann (2017).
<doi:10.21105/joss.00135>.
Author: William Michael Landau [aut, cre]
,
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between crew.aws.batch versions 0.0.7 dated 2024-11-17 and 0.0.8 dated 2025-02-05
crew.aws.batch-0.0.7/crew.aws.batch/R/utils_options.R |only crew.aws.batch-0.0.7/crew.aws.batch/tests/testthat/test-utils_options.R |only crew.aws.batch-0.0.8/crew.aws.batch/DESCRIPTION | 8 crew.aws.batch-0.0.8/crew.aws.batch/MD5 | 38 +- crew.aws.batch-0.0.8/crew.aws.batch/NEWS.md | 7 crew.aws.batch-0.0.8/crew.aws.batch/R/crew_controller_aws_batch.R | 36 +- crew.aws.batch-0.0.8/crew.aws.batch/R/crew_launcher_aws_batch.R | 54 +-- crew.aws.batch-0.0.8/crew.aws.batch/R/crew_monitor_aws_batch.R | 160 ++++++---- crew.aws.batch-0.0.8/crew.aws.batch/R/crew_options_aws_batch.R | 61 ++- crew.aws.batch-0.0.8/crew.aws.batch/R/utils_time.R |only crew.aws.batch-0.0.8/crew.aws.batch/inst/WORDLIST | 1 crew.aws.batch-0.0.8/crew.aws.batch/man/crew_class_launcher_aws_batch.Rd | 41 -- crew.aws.batch-0.0.8/crew.aws.batch/man/crew_class_monitor_aws_batch.Rd | 12 crew.aws.batch-0.0.8/crew.aws.batch/man/crew_controller_aws_batch.Rd | 64 ++-- crew.aws.batch-0.0.8/crew.aws.batch/man/crew_definition_aws_batch.Rd | 6 crew.aws.batch-0.0.8/crew.aws.batch/man/crew_launcher_aws_batch.Rd | 28 + crew.aws.batch-0.0.8/crew.aws.batch/man/crew_monitor_aws_batch.Rd | 8 crew.aws.batch-0.0.8/crew.aws.batch/man/crew_options_aws_batch.Rd | 32 -- crew.aws.batch-0.0.8/crew.aws.batch/tests/monitor/test-monitor.R | 6 crew.aws.batch-0.0.8/crew.aws.batch/tests/testthat/test-crew_controller_aws_batch.R | 40 -- crew.aws.batch-0.0.8/crew.aws.batch/tests/testthat/test-crew_launcher_aws_batch.R | 20 - crew.aws.batch-0.0.8/crew.aws.batch/tests/testthat/test-utils_time.R |only 22 files changed, 327 insertions(+), 295 deletions(-)
More information about crew.aws.batch at CRAN
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Title: Targeted Maximum Likelihood Estimation for Two-Stage Study
Design
Description: An inverse probability of censoring weighted (IPCW) targeted maximum likelihood estimator (TMLE) for evaluating a marginal point treatment effect from data where some variables were collected on only a subset of participants using a two-stage design (or marginal mean outcome for a single arm study). A TMLE for conditional parameters defined by a marginal structural model (MSM) is also available.
Author: Susan Gruber [aut, cre],
Mark van der Laan [aut]
Maintainer: Susan Gruber <sgruber@TLrevolution.com>
Diff between twoStageDesignTMLE versions 1.0 dated 2024-09-05 and 1.0.1.2 dated 2025-02-05
DESCRIPTION | 8 +- MD5 | 22 ++++---- NAMESPACE | 3 + NEWS | 5 + R/Utils.R | 12 ++-- R/estimatePi.R |only R/twoStageTMLE.R | 111 ++++++++++++++++++++++++++++------------- R/twoStageTMLEMSM.R | 131 ++++++++++++++++++++++++++++++++----------------- build/partial.rdb |binary inst/CITATION | 2 man/estimatePi.Rd |only man/twoStageTMLE.Rd | 17 ++++-- man/twoStageTMLEmsm.Rd | 22 +++++--- 13 files changed, 222 insertions(+), 111 deletions(-)
More information about twoStageDesignTMLE at CRAN
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Title: Transfer of Hydrograph from Gauged to Ungauged Catchments
Description: A geomorphology-based hydrological modelling for transferring
streamflow measurements from gauged to ungauged catchments. Inverse
modelling enables to estimate net rainfall from streamflow measurements
following Boudhraâ et al. (2018) <doi:10.1080/02626667.2018.1425801>.
Resulting net rainfall is then estimated on the ungauged catchments
by spatial interpolation in order to finally simulate streamflow
following de Lavenne et al. (2016) <doi:10.1002/2016WR018716>.
Author: Alban de Lavenne [aut, cre] ,
Christophe Cudennec [ths] ,
Tom Loree [ctb],
Herve Squividant [ctb]
Maintainer: Alban de Lavenne <alban.delavenne@inrae.fr>
Diff between transfR versions 1.0.11 dated 2023-10-02 and 1.1.0 dated 2025-02-05
DESCRIPTION | 12 +-- MD5 | 50 +++++++------ NAMESPACE | 8 ++ R/as_transfr.R | 2 R/hdist.R | 96 ++++++++++++++++---------- R/mixr.R | 80 +++++++++++++-------- R/rsimilarity.R |only R/utils.R | 7 + R/weightr.R | 67 +++++++++--------- build/partial.rdb |binary build/vignette.rds |binary data/Blavet.rda |binary data/Oudon.rda |binary inst/doc/V01_get_started.html | 13 +-- inst/doc/V02_inputs_preparation_stars.html | 13 +-- inst/doc/V03_inputs_preparation_whitebox.Rmd | 2 inst/doc/V03_inputs_preparation_whitebox.html | 25 +++--- man/Blavet.Rd | 18 ++-- man/Oudon.Rd | 16 ++-- man/hdist.Rd | 13 ++- man/mixr.Rd | 19 +++-- man/rsimilarity.Rd |only man/weightr.Rd | 15 +++- src/Makevars |only src/Makevars.win |only src/gdist.f90 | 19 ++++- src/transfR.c | 4 - vignettes/V03_inputs_preparation_whitebox.Rmd | 2 28 files changed, 291 insertions(+), 190 deletions(-)
Title: Plot FTIR Spectra
Description: The goal of 'PlotFTIR' is to easily and quickly kick-start the production of journal-quality Fourier Transform Infra-Red (FTIR) spectral plots in R using 'ggplot2'. The produced plots can be published directly or further modified by 'ggplot2' functions.
L'objectif de 'PlotFTIR' est de démarrer facilement et rapidement la production des tracés spectraux de spectroscopie infrarouge à transformée de Fourier (IRTF) de qualité journal dans R à l'aide de 'ggplot2'. Les tracés produits peuvent être publiés directement ou modifiés davantage par les fonctions 'ggplot2'.
Author: Philip Bulsink [aut, cre] ,
Ulrich Makanda [trl] ,
His Majesty the King in Right of Canada, as represented by the Minister
of Natural Resources [cph]
Maintainer: Philip Bulsink <philip.bulsink@nrcan-rncan.gc.ca>
Diff between PlotFTIR versions 1.0.0 dated 2024-11-13 and 1.1.0 dated 2025-02-05
DESCRIPTION | 12 - MD5 | 69 ++++---- NAMESPACE | 2 NEWS.md | 15 + R/io.R | 53 ++++-- R/manipulations.R | 212 +++++++++++++++++++++++-- R/maths.R | 136 ++++++++++++++-- R/plot_ftir.R | 78 ++++++--- R/utils.R | 140 +++++----------- R/zzz.R |only README.md | 61 +++++-- inst/doc/plotting_ftir_spectra.R | 24 +- inst/doc/plotting_ftir_spectra.html | 48 ++--- man/add_band.Rd |only man/add_wavenumber_marker.Rd | 10 - man/check_ftir_data.Rd | 11 - man/conversion.Rd | 2 man/figures/README-basic_plot_en-1.png |binary man/figures/README-basic_plot_fr-1.png |binary man/figures/README-biodiesel_compress_en-1.png |binary man/figures/README-biodiesel_compress_fr-1.png |binary man/figures/README-biodiesel_labelled_en-1.png |binary man/figures/README-biodiesel_labelled_fr-1.png |binary man/figures/README-biodiesel_zoom_en-1.png |binary man/figures/README-biodiesel_zoom_fr-1.png |binary man/figures/README-stack_plot_en-1.png |binary man/figures/README-stack_plot_fr-1.png |binary man/highlight_sample.Rd |only man/intensity_type.Rd |only man/normalize_spectra.Rd | 3 man/plot_ftir.Rd | 15 + man/plot_ftir_core.Rd | 15 + man/plot_ftir_stacked.Rd | 15 + tests/testthat/test-manipulations.R | 149 +++++++++++++++++ tests/testthat/test-maths.R | 167 +++++++++++++++++-- tests/testthat/test-plot_ftir.R | 16 + tests/testthat/test-utils.R | 77 ++------- vignettes/peak_fitting.Rbak |only 38 files changed, 964 insertions(+), 366 deletions(-)
Title: Seamless 'Nonmem' Simulation Platform
Description: A complete and seamless 'Nonmem' simulation interface within R. Turns 'Nonmem' control streams into simulation control streams, executes them with specified simulation input data and returns the results. The simulation is performed by 'Nonmem', eliminating manual work and risks of re-implementation of models in other tools.
Author: Philip Delff [aut, cre],
Brian Reilly [ctb],
Sanaya Shroff [ctb],
Boris Grinshpun [ctb]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMsim versions 0.1.5 dated 2024-11-14 and 0.1.6 dated 2025-02-05
NMsim-0.1.5/NMsim/tests/testthat/testReference/NMsim_03.rds |only NMsim-0.1.5/NMsim/tests/testthat/testReference/fnAppend_02.rds |only NMsim-0.1.5/NMsim/tests/testthat/testReference/fnAppend_03.rds |only NMsim-0.1.5/NMsim/tests/testthat/testReference/fnAppend_1.rds |only NMsim-0.1.6/NMsim/DESCRIPTION | 12 NMsim-0.1.6/NMsim/MD5 | 155 ++-- NMsim-0.1.6/NMsim/NAMESPACE | 3 NMsim-0.1.6/NMsim/NEWS.md | 58 + NMsim-0.1.6/NMsim/R/NMcreateMatLines.R | 104 +- NMsim-0.1.6/NMsim/R/NMexec.R | 95 -- NMsim-0.1.6/NMsim/R/NMexecDirectory.R | 8 NMsim-0.1.6/NMsim/R/NMreadSimModTab.R | 13 NMsim-0.1.6/NMsim/R/NMreplaceInits.R | 37 - NMsim-0.1.6/NMsim/R/NMrunWin.R | 93 +- NMsim-0.1.6/NMsim/R/NMsim.R | 356 +++++----- NMsim-0.1.6/NMsim/R/NMsimTestConf.R | 2 NMsim-0.1.6/NMsim/R/NMsim_EBE.R | 8 NMsim-0.1.6/NMsim/R/NMsim_NWPRI.R | 81 +- NMsim-0.1.6/NMsim/R/NMsim_VarCov.R | 1 NMsim-0.1.6/NMsim/R/NMsim_default.R | 9 NMsim-0.1.6/NMsim/R/NMsim_helpers.R | 56 + NMsim-0.1.6/NMsim/R/NMupdateInits.R | 6 NMsim-0.1.6/NMsim/R/NMupdateSizes.R |only NMsim-0.1.6/NMsim/R/NMwriteInits.R |only NMsim-0.1.6/NMsim/R/NWPRI_df.R | 1 NMsim-0.1.6/NMsim/R/modifyHelpers.R | 11 NMsim-0.1.6/NMsim/R/modifyModel.R |only NMsim-0.1.6/NMsim/R/pasteFuns.R |only NMsim-0.1.6/NMsim/R/prettyMatLines.R | 11 NMsim-0.1.6/NMsim/R/sampleParsSimpar.R | 2 NMsim-0.1.6/NMsim/R/simPopEtas.R | 21 NMsim-0.1.6/NMsim/R/zzz.R | 2 NMsim-0.1.6/NMsim/README.md | 5 NMsim-0.1.6/NMsim/inst/bash |only NMsim-0.1.6/NMsim/man/NMcreateMatLines.Rd | 23 NMsim-0.1.6/NMsim/man/NMexec.Rd | 53 - 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NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail/xgxr021_nmtranfail_input.rds |binary NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail_MetaData.rds |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/example1.csv |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/predu.cov |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/predu.ctl |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/predu.ext |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/predu.phi |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/predu.res |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/predu.tab |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/predu.vpd |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/predu.vpt |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/xgxr021.mod | 1 NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/xgxr021com.mod |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/xgxr032.mod | 36 - NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/xgxr051.mod |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/xgxr133.mod |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMcreateMatLines_01.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMcreateMatLines_02.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMcreateMatLines_03.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMseed_04.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_02.rds |binary NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_02b.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_07.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_EBE_03.rds |binary NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_NWPRI_01.rds |binary NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_NWPRI_01_OMEGAP.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_NWPRI_01_THETAPV.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_NWPRI_02.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_NWPRI_02_OMEGAP.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_NWPRI_02_THETAPV.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_inits_06.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_sizes_05.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMupdateSizes_01.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMupdateSizes_02.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMwriteInits_01.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMwriteInits_02.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMwriteInits_03.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMwriteInits_04.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMwriteInits_05.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMwriteInits_06.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/genPhiFile_01.rds |only NMsim-0.1.6/NMsim/tests/testthat/test_NMcreateMatLines.R |only NMsim-0.1.6/NMsim/tests/testthat/test_NMreadParsWide.R | 2 NMsim-0.1.6/NMsim/tests/testthat/test_NMreplaceInits.R |only NMsim-0.1.6/NMsim/tests/testthat/test_NMseed.R | 15 NMsim-0.1.6/NMsim/tests/testthat/test_NMsim.R | 150 ++++ NMsim-0.1.6/NMsim/tests/testthat/test_NMsim_NWPRI.R | 159 +++- NMsim-0.1.6/NMsim/tests/testthat/test_NMupdateSizes.R |only NMsim-0.1.6/NMsim/tests/testthat/test_NMwriteInits.R |only NMsim-0.1.6/NMsim/tests/testthat/test_genPhiFile.R |only 106 files changed, 1157 insertions(+), 589 deletions(-)
Title: Inference, Goodness-of-Fit and Forecast for Univariate Gaussian
Hidden Markov Models
Description: Inference, goodness-of-fit test, and prediction densities and intervals for univariate Gaussian Hidden Markov Models (HMM). The goodness-of-fit is based on a Cramer-von Mises statistic and uses parametric bootstrap to estimate the p-value. The description of the methodology is taken from Chapter 10.2 of Remillard (2013) <doi:10.1201/b14285>.
Author: Bouchra R. Nasri [aut, cre, cph],
Bruno N Remillard [aut, ctb, cph]
Maintainer: Bouchra R. Nasri <bouchra.nasri@umontreal.ca>
Diff between GaussianHMM1d versions 1.1.1 dated 2023-07-08 and 1.1.2 dated 2025-02-05
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/Sim.Markov.Chain.R | 9 +++++---- R/bootstrapfun.R | 6 +++--- man/Sim.Markov.Chain.Rd | 6 +++--- man/bootstrapfun.Rd | 3 +-- src/HMM_est_1d_new.c | 4 ++-- 7 files changed, 24 insertions(+), 24 deletions(-)
Title: Crew Launcher Plugins for Traditional High-Performance Computing
Clusters
Description: In computationally demanding analysis projects,
statisticians and data scientists asynchronously
deploy long-running tasks to distributed systems,
ranging from traditional clusters to cloud services.
The 'crew.cluster' package extends the 'mirai'-powered
'crew' package with worker launcher plugins for traditional
high-performance computing systems.
Inspiration also comes from packages 'mirai' by Gao (2023)
<https://github.com/shikokuchuo/mirai>,
'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>,
'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>,
'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>),
and 'batchtools' by Lang, Bischl, and Surmann (2017).
<doi:10.21105/joss.00135>.
Author: William Michael Landau [aut, cre]
,
Michael Gilbert Levin [aut] ,
Brendan Furneaux [aut] ,
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between crew.cluster versions 0.3.3 dated 2024-11-17 and 0.3.4 dated 2025-02-05
crew.cluster-0.3.3/crew.cluster/tests/sge/retries.R |only crew.cluster-0.3.4/crew.cluster/DESCRIPTION | 10 crew.cluster-0.3.4/crew.cluster/MD5 | 103 ++++------ crew.cluster-0.3.4/crew.cluster/NEWS.md | 4 crew.cluster-0.3.4/crew.cluster/R/crew_controller_lsf.R | 36 ++- crew.cluster-0.3.4/crew.cluster/R/crew_controller_pbs.R | 36 ++- crew.cluster-0.3.4/crew.cluster/R/crew_controller_sge.R | 36 ++- crew.cluster-0.3.4/crew.cluster/R/crew_controller_slurm.R | 36 ++- crew.cluster-0.3.4/crew.cluster/R/crew_launcher_cluster.R | 52 ++--- crew.cluster-0.3.4/crew.cluster/R/crew_launcher_lsf.R | 25 +- crew.cluster-0.3.4/crew.cluster/R/crew_launcher_pbs.R | 27 +- crew.cluster-0.3.4/crew.cluster/R/crew_launcher_sge.R | 25 +- crew.cluster-0.3.4/crew.cluster/R/crew_launcher_slurm.R | 25 +- crew.cluster-0.3.4/crew.cluster/R/crew_options_lsf.R | 61 +++-- crew.cluster-0.3.4/crew.cluster/R/crew_options_pbs.R | 62 +++--- crew.cluster-0.3.4/crew.cluster/R/crew_options_sge.R | 74 +++---- crew.cluster-0.3.4/crew.cluster/R/crew_options_slurm.R | 86 ++++---- crew.cluster-0.3.4/crew.cluster/R/utils_options.R | 12 - crew.cluster-0.3.4/crew.cluster/inst/WORDLIST | 1 crew.cluster-0.3.4/crew.cluster/man/crew_class_launcher_cluster.Rd | 35 +-- crew.cluster-0.3.4/crew.cluster/man/crew_class_launcher_lsf.Rd | 24 -- crew.cluster-0.3.4/crew.cluster/man/crew_class_launcher_pbs.Rd | 26 -- crew.cluster-0.3.4/crew.cluster/man/crew_class_launcher_sge.Rd | 24 -- crew.cluster-0.3.4/crew.cluster/man/crew_class_launcher_slurm.Rd | 24 -- crew.cluster-0.3.4/crew.cluster/man/crew_controller_lsf.Rd | 64 ++++-- crew.cluster-0.3.4/crew.cluster/man/crew_controller_pbs.Rd | 64 ++++-- crew.cluster-0.3.4/crew.cluster/man/crew_controller_sge.Rd | 64 ++++-- crew.cluster-0.3.4/crew.cluster/man/crew_controller_slurm.Rd | 64 ++++-- crew.cluster-0.3.4/crew.cluster/man/crew_launcher_cluster.Rd | 28 +- crew.cluster-0.3.4/crew.cluster/man/crew_launcher_lsf.Rd | 28 +- crew.cluster-0.3.4/crew.cluster/man/crew_launcher_pbs.Rd | 28 +- crew.cluster-0.3.4/crew.cluster/man/crew_launcher_sge.Rd | 28 +- crew.cluster-0.3.4/crew.cluster/man/crew_launcher_slurm.Rd | 28 +- crew.cluster-0.3.4/crew.cluster/man/crew_options_lsf.Rd | 34 --- crew.cluster-0.3.4/crew.cluster/man/crew_options_pbs.Rd | 35 --- crew.cluster-0.3.4/crew.cluster/man/crew_options_sge.Rd | 43 ---- crew.cluster-0.3.4/crew.cluster/man/crew_options_slurm.Rd | 50 +--- crew.cluster-0.3.4/crew.cluster/tests/sge/monitor.R | 4 crew.cluster-0.3.4/crew.cluster/tests/slurm/monitor.R | 4 crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_controller_lsf.R | 48 ---- crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_controller_pbs.R | 45 ---- crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_controller_sge.R | 51 ---- crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_controller_slurm.R | 46 ---- crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_launcher_cluster.R | 83 +------- crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_launcher_lsf.R | 11 - crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_launcher_pbs.R | 11 - crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_launcher_sge.R | 11 - crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_launcher_slurm.R | 11 - crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_options_lsf.R | 66 ------ crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_options_pbs.R | 70 ------ crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_options_sge.R | 78 ------- crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_options_slurm.R | 70 ------ crew.cluster-0.3.4/crew.cluster/tests/testthat/test-utils_options.R | 39 --- 53 files changed, 753 insertions(+), 1297 deletions(-)
Title: B-Spline Interpolation and Regression
Description: Build and use B-splines for interpolation and regression.
In case of regression, equality constraints as well as monotonicity
and/or positivity of B-spline weights can be imposed. Moreover,
knot positions (not only spline weights) can be part of
optimized parameters too. For this end, 'bspline' is able to calculate
Jacobian of basis vectors as function of knot positions. User is provided with
functions calculating spline values at arbitrary points. These
functions can be differentiated and integrated to obtain B-splines calculating
derivatives/integrals at any point. B-splines of this package can
simultaneously operate on a series of curves sharing the same set of
knots. 'bspline' is written with concern about computing
performance that's why the basis and Jacobian calculation is implemented in C++.
The rest is implemented in R but without notable impact on computing speed.
Author: Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between bspline versions 2.2.2 dated 2024-07-02 and 2.3.0 dated 2025-02-05
DESCRIPTION | 16 +++--- MD5 | 19 +++---- NAMESPACE | 1 NEWS.md | 9 +++ R/bspline.R | 103 ++++++++++++++++++++++++++++++----------- inst/unitTests/runit.bspline.R | 2 man/bspline.Rd | 16 +++--- man/dmat.Rd | 2 man/ibsp.Rd | 6 +- man/iknots.Rd | 4 + man/imat.Rd |only 11 files changed, 122 insertions(+), 56 deletions(-)
Title: R Session Information
Description: Query and print information about the current R session. It
is similar to 'utils::sessionInfo()', but includes more information
about packages, and where they were installed from.
Author: Gabor Csardi [cre],
Hadley Wickham [aut],
Winston Chang [aut],
Robert Flight [aut],
Kirill Mueller [aut],
Jim Hester [aut],
R Core team [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between sessioninfo versions 1.2.2 dated 2021-12-06 and 1.2.3 dated 2025-02-05
DESCRIPTION | 60 +++++++----------- MD5 | 39 ++++++------ NEWS.md | 34 ++++++++-- R/compare.R | 98 ++++++++++++++++++++++++++++--- R/github-actions.R |only R/mocks.r |only R/package-info.R | 8 ++ R/platform-info.R | 25 +++++++ R/printing.R | 2 R/session-info.R | 7 -- R/sessioninfo-package.R |only README.md | 24 ++++++- man/platform_info.Rd | 4 + man/session_diff.Rd | 28 +++++++- man/sessioninfo-package.Rd |only tests/testthat/_snaps/platform-info.md |only tests/testthat/test-dependent-packages.R | 32 ++-------- tests/testthat/test-diff.R | 57 +++++++----------- tests/testthat/test-os-name.R | 4 - tests/testthat/test-package-info.R | 20 +----- tests/testthat/test-platform-info.R | 21 +++++- tests/testthat/test-session-info.R | 38 +++++++++++- tests/testthat/test-warnings.R | 4 + 23 files changed, 345 insertions(+), 160 deletions(-)
Title: Geographically Weighted Non-Negative Principal Components
Analysis
Description: Implements a geographically weighted non-negative principal
components analysis, which consists of the fusion of geographically
weighted and sparse non-negative principal components analyses
<doi:10.17608/k6.auckland.9850826.v1>.
Author: Narumasa Tsutsumida [aut, cre]
Maintainer: Narumasa Tsutsumida <rsnaru.jp@gmail.com>
Diff between GWnnegPCA versions 0.0.4 dated 2020-11-18 and 0.0.5 dated 2025-02-05
DESCRIPTION | 32 ++++--- MD5 | 10 +- NAMESPACE | 19 ++-- R/gw_nsprcomp.R | 221 ++++++++++++++++++++++++++++++++++++----------------- man/gw_nsprcomp.Rd | 195 +++++++++++++++------------------------------- tests |only 6 files changed, 254 insertions(+), 223 deletions(-)
Title: Fishery Science Methods and Models
Description: Functions for applying a wide range of fisheries stock assessment methods.
Author: Gary A. Nelson [aut, cre]
Maintainer: Gary A. Nelson <gary.nelson@mass.gov>
Diff between fishmethods versions 1.12-1 dated 2023-04-27 and 1.13-1 dated 2025-02-05
DESCRIPTION | 13 ++- MD5 | 31 +++++---- NAMESPACE | 3 R/fm_telemetry.R | 5 + R/growth_LEP.R |only R/inverse_alk.R |only R/sbpr.R | 125 ++++++++++++++++++++++++++----------- R/ypr.R | 98 +++++++++++++++++++---------- data/hohe.rda |only data/lepdata.rda |only man/grotag.Rd | 7 +- man/growth_LEP.Rd |only man/hohe.Rd |only man/inverse_alk.Rd |only man/irm_cr.Rd | 4 - man/irm_h.Rd | 4 - man/lepdata.Rd |only man/sbpr.Rd | 53 ++++++++------- man/ypr.Rd | 21 +++--- src/TMB/fishmethods_TMBExports.cpp | 3 src/TMB/grow_LEP.hpp |only 21 files changed, 245 insertions(+), 122 deletions(-)
Title: Dynamical Assembly of Islands by Speciation, Immigration and
Extinction
Description: Simulates and computes the (maximum) likelihood of a dynamical
model of island biota assembly through speciation, immigration and
extinction. See Valente et al. (2015) <doi:10.1111/ele.12461>.
Author: Rampal S. Etienne [aut, cre] ,
Luis Valente [aut] ,
Albert B. Phillimore [aut] ,
Bart Haegeman [aut] ,
Joshua W. Lambert [aut] ,
Pedro Santos Neves [aut] ,
Shu Xie [aut] ,
Richel J.C. Bilderbeek [aut] ,
Hanno Hildenbrandt [aut] ,
Torsten Hauffe [ctb] [...truncated...]
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between DAISIE versions 4.4.1 dated 2023-10-21 and 4.5.0 dated 2025-02-05
DESCRIPTION | 10 - MD5 | 112 +++++++++++---------- NAMESPACE | 1 NEWS.md | 9 + R/DAISIE_ML1.R | 32 ++++-- R/DAISIE_ML_CS.R | 6 - R/DAISIE_ML_IW.R | 14 ++ R/DAISIE_SR_sim_core.R | 11 +- R/DAISIE_data.R | 40 +++++++ R/DAISIE_format_IW.R | 89 ++++++++++++++++ R/DAISIE_loglik_CS.R | 44 +++++++- R/DAISIE_loglik_IW.R | 11 +- R/DAISIE_loglik_high_lambda.R | 39 +++---- R/DAISIE_rates.R | 21 ++- R/DAISIE_sim_core_cr.R | 5 R/DAISIE_sim_core_cr_shift.R | 3 R/DAISIE_sim_core_time_dep.R | 3 R/DAISIE_sim_core_trait_dep.R | 3 R/DAISIE_sim_trait_dep.R | 6 - R/DAISIE_utils.R | 2 R/default_params_doc.R | 7 + build/partial.rdb |binary build/vignette.rds |binary data/frogs_sim_datalist.RData |only inst/doc/DAISIE_FAQs.Rmd |only inst/doc/DAISIE_FAQs.html |only man/DAISIE_ML.Rd | 10 + man/DAISIE_ML1.Rd | 29 +++-- man/DAISIE_ML2.Rd | 2 man/DAISIE_ML4.Rd | 2 man/DAISIE_ML_IW.Rd | 2 man/DAISIE_loglik_integrand.Rd | 2 man/DAISIE_loglik_integrate.Rd | 2 man/DAISIE_logp0.Rd |only man/DAISIE_plot_area.Rd | 2 man/DAISIE_sim_cr_shift.Rd | 4 man/DAISIE_sim_relaxed_rate.Rd | 4 man/DAISIE_sim_time_dep.Rd | 4 man/DAISIE_sim_trait_dep.Rd | 4 man/calc_next_timeval.Rd | 2 man/calc_next_timeval_shift.Rd | 2 man/default_params_doc.Rd | 8 + man/frogs_sim_datalist.Rd |only man/get_ana_rate.Rd | 2 man/get_ext_rate.Rd | 2 man/get_immig_rate.Rd | 2 man/update_max_rates.Rd | 2 man/update_rates.Rd | 2 src/DAISIE_loglik_rhs_FORTRAN.f95 | 22 ++-- src/Makevars | 1 src/Makevars.win | 1 tests/testthat/Rplots.pdf |binary tests/testthat/test-DAISIE_ML1.R | 72 +++++++++---- tests/testthat/test-DAISIE_ML2.R | 37 ++---- tests/testthat/test-DAISIE_format_IW.R | 32 +++--- tests/testthat/test-DAISIE_format_IW_full_stt.R | 6 - tests/testthat/test-DAISIE_format_IW_sampled_stt.R | 6 - tests/testthat/test-DAISIE_logp0.R |only tests/testthat/test-integration_DAISIE.R | 112 +++++++++++++++++++++ vignettes/DAISIE_FAQs.Rmd |only vignettes/Figure1.png |only 61 files changed, 625 insertions(+), 221 deletions(-)
Title: Collection of Helper Functions
Description: Provides a collection of lightweight helper functions (imps) both
for interactive use and for inclusion within other packages. These include
functions for minimal input assertions, visualising colour palettes,
quoting user input, searching rows of a data frame and capturing string
tokens.
Author: Tim Taylor [aut, cre, cph] ,
R Core Team [cph] ,
Toby Hocking [cph]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between ympes versions 1.7.0 dated 2024-11-27 and 1.8.0 dated 2025-02-05
DESCRIPTION | 6 +-- MD5 | 18 +++++----- NAMESPACE | 1 NEWS.md | 6 +++ R/fstrcapture.R | 78 +++++++++++++++++++++++++++++++++++++++++--- build/vignette.rds |binary inst/doc/ympes.Rmd | 6 +-- inst/doc/ympes.html | 91 +++++++++++++++++++++++++--------------------------- man/fstrcapture.Rd | 15 ++++++-- vignettes/ympes.Rmd | 6 +-- 10 files changed, 152 insertions(+), 75 deletions(-)
Title: Assess Study Cohorts Using a Common Data Model
Description: Phenotype study cohorts in data mapped to the
Observational Medical Outcomes Partnership Common Data Model. Diagnostics
are run at the database, code list, cohort, and population level to assess
whether study cohorts are ready for research.
Author: Edward Burn [aut, cre] ,
Marti Catala [aut] ,
Xihang Chen [aut] ,
Marta Alcalde-Herraiz [aut] ,
Albert Prats-Uribe [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between PhenotypeR versions 0.1.1 dated 2025-01-17 and 0.1.2 dated 2025-02-05
DESCRIPTION | 21 MD5 | 80 R/cohortDiagnostics.R | 2 R/matchedDiagnostics.R | 28 R/phenotypeR-package.R | 16 R/populationDiagnostics.R | 2 R/shinyDiagnostics.R | 4 R/utils-pipe.R | 28 README.md | 106 build/vignette.rds |binary inst/doc/a01_DatabaseDiagnostics.R | 38 inst/doc/a01_DatabaseDiagnostics.Rmd | 55 inst/doc/a01_DatabaseDiagnostics.html | 1125 ++++++ inst/doc/a02_CodelistDiagnostics.R | 24 inst/doc/a02_CodelistDiagnostics.Rmd | 31 inst/doc/a02_CodelistDiagnostics.html | 1811 ++++++++++ inst/doc/a03_CohortDiagnostics.R | 17 inst/doc/a03_CohortDiagnostics.Rmd | 17 inst/doc/a03_CohortDiagnostics.html | 4839 +++-------------------------- inst/doc/a04_MatchedDiagnostics.R | 43 inst/doc/a04_MatchedDiagnostics.Rmd | 51 inst/doc/a04_MatchedDiagnostics.html | 46 inst/doc/a05_PopulationDiagnostics.R | 51 inst/doc/a05_PopulationDiagnostics.Rmd | 63 inst/doc/a05_PopulationDiagnostics.html | 2040 ++++++++++-- inst/shiny/background.md | 8 inst/shiny/global.R | 139 inst/shiny/scripts/preprocess.R | 49 inst/shiny/server.R | 2004 ++++++------ inst/shiny/ui.R | 1287 +++---- man/pipe.Rd | 40 man/shinyDiagnostics.Rd | 9 tests/testthat/test-addCodelistAttribute.R | 2 tests/testthat/test-codelistDiagnostics.R | 2 tests/testthat/test-phenotypeDiagnostics.R | 2 tests/testthat/test-shinyDiagnostics.R | 6 vignettes/a01_DatabaseDiagnostics.Rmd | 55 vignettes/a02_CodelistDiagnostics.Rmd | 31 vignettes/a03_CohortDiagnostics.Rmd | 17 vignettes/a04_MatchedDiagnostics.Rmd | 51 vignettes/a05_PopulationDiagnostics.Rmd | 63 41 files changed, 7744 insertions(+), 6559 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 25.2.1 dated 2025-02-04 and 25.2.2 dated 2025-02-05
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ README.md | 12 ++++++------ inst/doc/HVT.R | 3 ++- inst/doc/HVT.Rmd | 15 +++++++++------ inst/doc/HVT.html | 37 +++++++++++++++++++++---------------- vignettes/HVT.Rmd | 15 +++++++++------ 7 files changed, 57 insertions(+), 45 deletions(-)
Title: Grouped Date Classes
Description: Provides a coherent interface and implementation for creating
grouped date classes. This package is part of the RECON
(<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Author: Tim Taylor [aut, cre]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between grates versions 1.4.0 dated 2025-01-17 and 1.4.1 dated 2025-02-05
DESCRIPTION | 12 - MD5 | 14 - NEWS.md | 4 README.md | 27 --- inst/doc/grates.R | 35 ---- inst/doc/grates.Rmd | 23 +- inst/doc/grates.html | 406 +++++++++++++++++++++++---------------------------- vignettes/grates.Rmd | 23 +- 8 files changed, 238 insertions(+), 306 deletions(-)
Title: Seasonal Adjustment of Weekly Data
Description: Perform seasonal adjustment of weekly data. The package provides a user-friendly interface for computing seasonally adjusted estimates of weekly data and includes functions for the creation of country-specific prior adjustment variables, as well as diagnostic tools to assess the quality of the adjustments. The method is described in more detail in Ginker (2023) <doi:10.13140/RG.2.2.12221.44000>.
Author: Tim Ginker [aut, cre, cph] ,
Jon Lachman [ctb]
Maintainer: Tim Ginker <tim.ginker@gmail.com>
Diff between boiwsa versions 1.1.2 dated 2024-09-23 and 1.1.3 dated 2025-02-05
DESCRIPTION | 20 + LICENSE | 4 MD5 | 73 +++--- NAMESPACE | 75 +++--- NEWS.md | 4 R/boiwsa.R | 71 ++++-- R/data.R | 96 ++++---- R/find_opt.R | 35 ++- R/find_outliers.R | 37 ++- R/fourier_vars.R | 182 ++++++++-------- R/generic_functions.R | 104 +++++++++ R/genhol.R | 146 ++++++------- R/my_ao.R | 94 ++++---- R/my_rosh.R | 138 ++++++------ R/plot_spec.R | 88 ++++---- R/simple_td.R | 138 ++++++------ README.md | 324 ++++++++++++++++++++++++++---- man/boiwsa.Rd | 136 ++++++------ man/dates_il.Rd | 50 ++-- man/figures/README-unnamed-chunk-10-1.png |only man/figures/README-unnamed-chunk-11-1.png |only man/figures/README-unnamed-chunk-12-1.png |only man/figures/README-unnamed-chunk-8-1.png |only man/find_opt.Rd | 96 ++++---- man/find_outliers.Rd | 104 ++++----- man/fourier_vars.Rd | 58 ++--- man/gasoline.data.Rd | 52 ++-- man/genhol.Rd | 74 +++--- man/holiday_dates_il.Rd | 48 ++-- man/lbm.Rd | 52 ++-- man/my_ao.Rd | 62 ++--- man/my_rosh.Rd | 62 ++--- man/plot.boiwsa.Rd | 34 +-- man/plot_spec.Rd | 50 ++-- man/predict.boiwsa.Rd |only man/print.Rd | 32 +- man/print.boiwsa.Rd | 34 +-- man/simple_td.Rd | 72 +++--- man/summary.Rd | 32 +- man/summary.boiwsa.Rd | 32 +- 40 files changed, 1560 insertions(+), 1149 deletions(-)
Title: Artificial Intelligence for Education
Description: In social and educational settings, the use of Artificial
Intelligence (AI) is a challenging task. Relevant data is often only
available in handwritten forms, or the use of data is restricted by
privacy policies. This often leads to small data sets. Furthermore, in
the educational and social sciences, data is often unbalanced in terms
of frequencies. To support educators as well as educational and social
researchers in using the potentials of AI for their work, this package
provides a unified interface for neural nets in 'PyTorch' to deal with
natural language problems. In addition, the package ships with a shiny
app, providing a graphical user interface. This allows the usage of
AI for people without skills in writing python/R scripts. The tools
integrate existing mathematical and statistical methods for dealing
with small data sets via pseudo-labeling (e.g. Cascante-Bonilla et al.
(2020) <doi:10.48550/arXiv.2001.06001>) and imbalanced data via the
creation of synthetic cases [...truncated...]
Author: Berding Florian [aut, cre] ,
Tykhonova Yuliia [aut] ,
Pargmann Julia [ctb] ,
Leube Anna [ctb] ,
Riebenbauer Elisabeth [ctb] ,
Rebmann Karin [ctb],
Slopinski Andreas [ctb]
Maintainer: Berding Florian <florian.berding@uni-hamburg.de>
Diff between aifeducation versions 1.0.1 dated 2025-01-28 and 1.0.2 dated 2025-02-05
aifeducation-1.0.1/aifeducation/R/sysdata.rda |only aifeducation-1.0.2/aifeducation/DESCRIPTION | 6 aifeducation-1.0.2/aifeducation/MD5 | 30 - aifeducation-1.0.2/aifeducation/NAMESPACE | 1 aifeducation-1.0.2/aifeducation/NEWS.md | 7 aifeducation-1.0.2/aifeducation/R/Studio_Classifier_Create.R | 2 aifeducation-1.0.2/aifeducation/R/Studio_FeatureExtractor_Create.R | 2 aifeducation-1.0.2/aifeducation/R/Studio_Tabs_DM_DataSetEditor.R | 2 aifeducation-1.0.2/aifeducation/R/data.R | 2 aifeducation-1.0.2/aifeducation/R/onLoad.R | 2 aifeducation-1.0.2/aifeducation/R/sustainability.R | 264 ++++++++++ aifeducation-1.0.2/aifeducation/README.md | 15 aifeducation-1.0.2/aifeducation/inst/studio_app/app.r | 2 aifeducation-1.0.2/aifeducation/man/get_alpha_3_codes.Rd |only aifeducation-1.0.2/aifeducation/man/matrix_to_array_c.Rd | 1 aifeducation-1.0.2/aifeducation/man/summarize_tracked_sustainability.Rd | 1 aifeducation-1.0.2/aifeducation/man/to_categorical_c.Rd | 1 17 files changed, 308 insertions(+), 30 deletions(-)
Title: Interpreted String Literals
Description: An implementation of interpreted string literals. Based on the
'glue' package by Hester & Bryan (2024) <doi:10.32614/CRAN.package.glue> but
with a focus on efficiency and simplicity at a cost of flexibility.
Author: Tim Taylor [aut, cre] ,
Jim Hester [aut] ,
Jennifer Bryan [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between super versions 0.0.4 dated 2024-12-16 and 0.0.5 dated 2025-02-05
DESCRIPTION | 6 MD5 | 26 +-- NEWS.md | 6 R/glue.R | 64 ++++---- R/trim.R | 12 - README.md | 32 +--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/super.R | 2 inst/doc/super.Rmd | 17 -- inst/doc/super.html | 101 ++++++-------- src/glue.c | 113 +++++++-------- src/trim.c | 370 ++++++++++++++++++++++++++-------------------------- vignettes/super.Rmd | 17 -- 14 files changed, 371 insertions(+), 395 deletions(-)
Title: Calculation of IBD Probabilities
Description: For biparental, three and four-way crosses Identity by Descent
(IBD) probabilities can be calculated using Hidden Markov Models and
inheritance vectors following Lander and Green
(<https://www.jstor.org/stable/29713>) and Huang
(<doi:10.1073/pnas.1100465108>). One of a series of statistical genetic
packages for streamlining the analysis of typical plant breeding experiments
developed by Biometris.
Author: Martin Boer [aut] ,
Bart-Jan van Rossum [aut, cre]
,
Wenhao Li [ctb] ,
Johannes Kruisselbrink [ctb]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenIBD versions 1.0.7 dated 2024-02-02 and 1.0.8 dated 2025-02-05
statgenIBD-1.0.7/statgenIBD/R/redundant |only statgenIBD-1.0.8/statgenIBD/DESCRIPTION | 12 statgenIBD-1.0.8/statgenIBD/MD5 | 90 ++++-- statgenIBD-1.0.8/statgenIBD/NEWS.md | 40 +-- statgenIBD-1.0.8/statgenIBD/R/IBDprob.R | 6 statgenIBD-1.0.8/statgenIBD/R/RcppExports.R | 2 statgenIBD-1.0.8/statgenIBD/R/getProbs.R | 2 statgenIBD-1.0.8/statgenIBD/R/readIBDs.R | 2 statgenIBD-1.0.8/statgenIBD/R/readRABBIT.R | 80 +----- statgenIBD-1.0.8/statgenIBD/R/writeFlapjack.R | 2 statgenIBD-1.0.8/statgenIBD/R/writeIBDs.R | 2 statgenIBD-1.0.8/statgenIBD/README.md | 21 - statgenIBD-1.0.8/statgenIBD/build/partial.rdb |binary statgenIBD-1.0.8/statgenIBD/build/vignette.rds |binary statgenIBD-1.0.8/statgenIBD/inst/doc/IBDCalculations.R | 22 - statgenIBD-1.0.8/statgenIBD/inst/doc/IBDCalculations.Rmd | 9 statgenIBD-1.0.8/statgenIBD/inst/doc/IBDCalculations.html | 132 ++++------ statgenIBD-1.0.8/statgenIBD/inst/doc/IBDFileFormat.R | 6 statgenIBD-1.0.8/statgenIBD/inst/doc/IBDFileFormat.html | 24 - statgenIBD-1.0.8/statgenIBD/inst/tinytest/example_magicreconstruct_ancestry.csv.gz |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/example_ped.csv |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popBC1S2 |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popBC1S2DH |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popBC3 |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popBC3DH |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popC3 |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popC3DH |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popC3S4 |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popC3S4DH |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popC4 |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popC4DH |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popC4S3 |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popC4S3DH |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popDH |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popF4 |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popF4DH |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/test_calcIBD.R | 11 statgenIBD-1.0.8/statgenIBD/inst/tinytest/test_readRABBIT.R | 31 ++ statgenIBD-1.0.8/statgenIBD/man/allGenoPlot.Rd | 24 - statgenIBD-1.0.8/statgenIBD/man/figures |only statgenIBD-1.0.8/statgenIBD/man/getProbs.Rd | 90 +++--- statgenIBD-1.0.8/statgenIBD/man/readRABBIT.Rd | 3 statgenIBD-1.0.8/statgenIBD/man/singleGenoPlot.Rd | 24 - statgenIBD-1.0.8/statgenIBD/man/statgenIBD-package.Rd | 2 statgenIBD-1.0.8/statgenIBD/man/summary.IBDprob.Rd | 66 ++--- statgenIBD-1.0.8/statgenIBD/man/writeFlapjack.Rd | 82 +++--- statgenIBD-1.0.8/statgenIBD/src/calcIBD.cpp | 2 statgenIBD-1.0.8/statgenIBD/vignettes/IBDCalculations.Rmd | 9 48 files changed, 410 insertions(+), 386 deletions(-)
Title: Small Count Rounding of Tabular Data
Description: A statistical disclosure control tool to protect frequency tables in cases where small values are sensitive. The function PLSrounding() performs small count rounding of necessary inner cells so that all small frequencies of cross-classifications to be published (publishable cells) are rounded. This is equivalent to changing micro data since frequencies of unique combinations are changed. Thus, additivity and consistency are guaranteed. The methodology is described in Langsrud and Heldal (2018) <https://www.researchgate.net/publication/327768398_An_Algorithm_for_Small_Count_Rounding_of_Tabular_Data>.
Author: Oeyvind Langsrud [aut, cre],
Johan Heldal [aut]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between SmallCountRounding versions 1.1.0 dated 2024-12-09 and 1.2.0 dated 2025-02-05
SmallCountRounding-1.1.0/SmallCountRounding/R/Extend0fromModelMatrixInput.R |only SmallCountRounding-1.2.0/SmallCountRounding/DESCRIPTION | 16 +++--- SmallCountRounding-1.2.0/SmallCountRounding/MD5 | 25 +++++----- SmallCountRounding-1.2.0/SmallCountRounding/NAMESPACE | 10 +++- SmallCountRounding-1.2.0/SmallCountRounding/NEWS.md | 11 ++++ SmallCountRounding-1.2.0/SmallCountRounding/R/PLSrounding.R | 22 ++++++++ SmallCountRounding-1.2.0/SmallCountRounding/R/reexport.R |only SmallCountRounding-1.2.0/SmallCountRounding/inst/doc/Introduction_to_SmallCountRounding.R | 16 +++--- SmallCountRounding-1.2.0/SmallCountRounding/inst/doc/Introduction_to_SmallCountRounding.Rmd | 2 SmallCountRounding-1.2.0/SmallCountRounding/inst/doc/Introduction_to_SmallCountRounding.html | 4 - SmallCountRounding-1.2.0/SmallCountRounding/man/PLSrounding.Rd | 20 ++++++++ SmallCountRounding-1.2.0/SmallCountRounding/man/SmallCountRounding-package.Rd | 1 SmallCountRounding-1.2.0/SmallCountRounding/man/reexports.Rd |only SmallCountRounding-1.2.0/SmallCountRounding/tests/testthat/test-PLSrounding.R | 2 SmallCountRounding-1.2.0/SmallCountRounding/vignettes/Introduction_to_SmallCountRounding.Rmd | 2 15 files changed, 95 insertions(+), 36 deletions(-)
More information about SmallCountRounding at CRAN
Permanent link
Title: A Template for Creating Reproducible 'shiny' Applications
Description: Create a skeleton 'shiny' application with create_template() that is
reproducible, can be saved and meets academic standards for attribution.
Forked from 'wallace'. Code is split into modules that are loaded and linked
together automatically and each call one function. Guidance pages explain
modules to users and flexible logging informs them of any errors. Options
enable asynchronous operations, viewing of source code, interactive maps and
data tables. Use to create complex analytical applications, following best
practices in open science and software development. Includes functions for
automating repetitive development tasks and an example application at
run_shinyscholar() that requires
install.packages("shinyscholar", dependencies = TRUE). A guide to developing
applications can be found on the package website.
Author: Simon E. H. Smart [aut, cre, cph],
Tim Lucas [aut] ,
Jamie M. Kass [ctb],
Gonzalo E. Pinilla-Buitrago [ctb],
Andrea Paz [ctb],
Bethany A. Johnson [ctb],
Valentina Grisales-Betancur [ctb],
Dean Attali [ctb],
Matthew E. Aiello-Lammens [ctb],
Cory Merow [...truncated...]
Maintainer: Simon E. H. Smart <simon.smart@cantab.net>
Diff between shinyscholar versions 0.2.4 dated 2025-01-29 and 0.2.5 dated 2025-02-05
DESCRIPTION | 6 ++-- MD5 | 44 +++++++++++++++++------------------ NEWS.md | 6 ++++ R/helper_functions.R | 2 - README.md | 2 - inst/app_skeleton/helper_functions.R | 2 - inst/app_skeleton/intro.Rmd | 8 +++--- inst/app_skeleton/server.Rmd | 10 +++++++ inst/app_skeleton/ui.Rmd | 10 ++++++- inst/shiny/Rmd/text_intro_tab.Rmd | 2 - inst/shiny/Rmd/userReport_intro.Rmd | 2 - inst/shiny/modules/core_intro.R | 2 - inst/shiny/modules/select_user.R | 4 ++- inst/shiny/server.R | 9 +++++++ inst/shiny/ui.R | 10 ++++++- tests/testthat/helper_data.R | 21 ++++++++++++++++ tests/testthat/helper_select_user.R | 16 ++++++++++++ tests/testthat/test-downloads.R | 7 +++++ tests/testthat/test-metadata.R | 3 ++ tests/testthat/test-plot_hist.R | 3 ++ tests/testthat/test-plot_scatter.R | 3 ++ tests/testthat/test-save_load.R | 12 +++++++++ tests/testthat/test-select_user.R | 14 +++++++++++ 23 files changed, 158 insertions(+), 40 deletions(-)
Title: Plot Function for Single-Case Data Frames
Description: Add-on for the 'scan' package that creates plots
from single-case data frames ('scdf'). It includes functions for styling
single-case plots, adding phase-based lines to indicate various statistical
parameters, and predefined themes for presentations and publications. More
information and in depth examples can be found in the online book
"Analyzing Single-Case Data with R and 'scan"
Jürgen Wilbert (2025) <https://jazznbass.github.io/scan-Book/>.
Author: Juergen Wilbert [aut, cre]
Maintainer: Juergen Wilbert <juergen.wilbert@uni-muenster.de>
Diff between scplot versions 0.4.0 dated 2024-06-29 and 0.5.0 dated 2025-02-05
scplot-0.4.0/scplot/R/forestplots.R |only scplot-0.4.0/scplot/R/private_scplot.R |only scplot-0.4.0/scplot/R/private_statline.R |only scplot-0.4.0/scplot/R/private_themes.R |only scplot-0.4.0/scplot/man/plot.sc_hplm.Rd |only scplot-0.4.0/scplot/man/plot.sc_tauu.Rd |only scplot-0.4.0/scplot/man/scplot.Rd |only scplot-0.5.0/scplot/DESCRIPTION | 16 +++--- scplot-0.5.0/scplot/MD5 | 44 ++++++++++-------- scplot-0.5.0/scplot/NAMESPACE | 7 ++ scplot-0.5.0/scplot/NEWS.md | 10 +++- scplot-0.5.0/scplot/R/add_legend.R | 29 +++++++++++- scplot-0.5.0/scplot/R/add_statline.R | 7 ++ scplot-0.5.0/scplot/R/as_ggplot.R | 68 +++++++++++++++-------------- scplot-0.5.0/scplot/R/private-forestplot.R |only scplot-0.5.0/scplot/R/private-scplot.R |only scplot-0.5.0/scplot/R/private-statline.R |only scplot-0.5.0/scplot/R/private-themes.R |only scplot-0.5.0/scplot/R/scplot-generic.R |only scplot-0.5.0/scplot/R/scplot-package.R | 2 scplot-0.5.0/scplot/R/scplot.R | 34 ++++++-------- scplot-0.5.0/scplot/R/scplot.sc_hplm.R |only scplot-0.5.0/scplot/R/scplot.sc_rand.R |only scplot-0.5.0/scplot/R/scplot.sc_tauu.R |only scplot-0.5.0/scplot/R/set_dataline.R | 24 +++++----- scplot-0.5.0/scplot/R/startup.R |only scplot-0.5.0/scplot/man/add_legend.Rd | 30 +++++++++++- scplot-0.5.0/scplot/man/add_statline.Rd | 5 +- scplot-0.5.0/scplot/man/scplot.sc_hplm.Rd |only scplot-0.5.0/scplot/man/scplot.sc_rand.Rd |only scplot-0.5.0/scplot/man/scplot.sc_tauu.Rd |only scplot-0.5.0/scplot/man/scplot.scdf.Rd |only scplot-0.5.0/scplot/man/set_dataline.Rd | 14 +++++ 33 files changed, 188 insertions(+), 102 deletions(-)
Title: Single-Case Data Analyses for Single and Multiple Baseline
Designs
Description: A collection of procedures for analysing, visualising,
and managing single-case data. These include piecewise linear regression
models, multilevel models, overlap indices ('PND', 'PEM', 'PAND', 'PET', 'tau-u',
'baseline corrected tau', 'CDC'), and randomization tests. Data preparation functions
support outlier detection, handling missing values, scaling, and custom transformations.
An export function helps to generate
html, word, and latex tables in a publication friendly style. More details can be
found in the online book 'Analyzing single-case data with R and scan', Juergen Wilbert (2025)
<https://jazznbass.github.io/scan-Book/>.
Author: Juergen Wilbert [cre, aut] ,
Timo Lueke [aut]
Maintainer: Juergen Wilbert <juergen.wilbert@uni-muenster.de>
Diff between scan versions 0.61.0 dated 2024-07-01 and 0.62.0 dated 2025-02-05
scan-0.61.0/scan/R/private_kendall_meta.R |only scan-0.61.0/scan/R/private_prepare_scdf.R |only scan-0.61.0/scan/R/private_regression.R |only scan-0.61.0/scan/R/private_utilities.R |only scan-0.62.0/scan/DESCRIPTION | 20 +- scan-0.62.0/scan/MD5 | 198 ++++++++++++----------- scan-0.62.0/scan/NAMESPACE | 17 - scan-0.62.0/scan/NEWS.md | 54 +++++- scan-0.62.0/scan/R/add_l2.R | 2 scan-0.62.0/scan/R/as_scdf.R | 20 +- scan-0.62.0/scan/R/between_smd.R |only scan-0.62.0/scan/R/cdc.R | 24 +- scan-0.62.0/scan/R/corrected_tau.R | 9 - scan-0.62.0/scan/R/deprec-ranks.R | 11 + scan-0.62.0/scan/R/deprec-shift.R | 4 scan-0.62.0/scan/R/deprec-smooth_cases.R | 2 scan-0.62.0/scan/R/deprec-standardize.R | 8 scan-0.62.0/scan/R/deprecated.R | 87 ---------- scan-0.62.0/scan/R/design.R | 32 +-- scan-0.62.0/scan/R/export.R | 31 ++- scan-0.62.0/scan/R/export.sc_hplm.R | 4 scan-0.62.0/scan/R/export.sc_pet.R | 19 +- scan-0.62.0/scan/R/export.sc_trend.R | 8 scan-0.62.0/scan/R/hplm.R | 56 +++--- scan-0.62.0/scan/R/ird.R | 7 scan-0.62.0/scan/R/mplm.R | 17 + scan-0.62.0/scan/R/nap.R | 8 scan-0.62.0/scan/R/outlier.R | 41 ++-- scan-0.62.0/scan/R/overlap.R | 13 - scan-0.62.0/scan/R/pand.R | 29 ++- scan-0.62.0/scan/R/pet.R | 25 +- scan-0.62.0/scan/R/plm.R | 20 +- scan-0.62.0/scan/R/plot.scdf.R | 5 scan-0.62.0/scan/R/plot_rand.R | 79 ++++++--- scan-0.62.0/scan/R/print.sc_bcsmd.R |only scan-0.62.0/scan/R/print.sc_hplm.R | 25 +- scan-0.62.0/scan/R/print.sc_pet.R | 11 + scan-0.62.0/scan/R/print.sc_tauu.R | 1 scan-0.62.0/scan/R/print.sc_trend.R | 2 scan-0.62.0/scan/R/private-kendall-meta.R |only scan-0.62.0/scan/R/private-prepare_scdf.R |only scan-0.62.0/scan/R/private-regression.R |only scan-0.62.0/scan/R/private-utilities.R |only scan-0.62.0/scan/R/private_check.R | 91 ++++++++-- scan-0.62.0/scan/R/private_kendall.R | 85 --------- scan-0.62.0/scan/R/private_options.R | 8 scan-0.62.0/scan/R/private_options_mc.R | 10 - scan-0.62.0/scan/R/rand_test.R | 96 ++++++++--- scan-0.62.0/scan/R/random_scdf.R | 7 scan-0.62.0/scan/R/rescale.R |only scan-0.62.0/scan/R/scan.R | 1 scan-0.62.0/scan/R/scdf-functions.R | 12 + scan-0.62.0/scan/R/scdf.R | 14 + scan-0.62.0/scan/R/scdf_attr.R | 5 scan-0.62.0/scan/R/select_phases.R | 6 scan-0.62.0/scan/R/set_vars.R | 4 scan-0.62.0/scan/R/smd.R | 2 scan-0.62.0/scan/R/style_plot.R | 5 scan-0.62.0/scan/R/subset.scdf.R | 2 scan-0.62.0/scan/R/tau_u.R | 159 ++++++++++-------- scan-0.62.0/scan/R/transform.scdf.R | 14 - scan-0.62.0/scan/R/trend.R | 49 ++--- scan-0.62.0/scan/inst/CITATION | 6 scan-0.62.0/scan/inst/shiny/server.R | 26 ++- scan-0.62.0/scan/inst/shiny/ui.R | 2 scan-0.62.0/scan/man/add_l2.Rd | 3 scan-0.62.0/scan/man/as.data.frame.scdf.Rd | 1 scan-0.62.0/scan/man/as_scdf.Rd | 1 scan-0.62.0/scan/man/between_smd.Rd |only scan-0.62.0/scan/man/cdc.Rd | 23 +- scan-0.62.0/scan/man/deprecated-functions.Rd | 42 ---- scan-0.62.0/scan/man/design.Rd | 4 scan-0.62.0/scan/man/export.Rd | 2 scan-0.62.0/scan/man/fill_missing.Rd | 1 scan-0.62.0/scan/man/hplm.Rd | 29 ++- scan-0.62.0/scan/man/ird.Rd | 12 + scan-0.62.0/scan/man/mplm.Rd | 9 - scan-0.62.0/scan/man/na.omit.scdf.Rd |only scan-0.62.0/scan/man/nap.Rd | 8 scan-0.62.0/scan/man/outlier.Rd | 39 ++-- scan-0.62.0/scan/man/overlap.Rd | 13 - scan-0.62.0/scan/man/pand.Rd | 27 +-- scan-0.62.0/scan/man/pem.Rd | 1 scan-0.62.0/scan/man/pet.Rd | 13 - scan-0.62.0/scan/man/plm.Rd | 10 - scan-0.62.0/scan/man/plot.scdf.Rd | 6 scan-0.62.0/scan/man/plot_rand.Rd | 9 - scan-0.62.0/scan/man/pnd.Rd | 1 scan-0.62.0/scan/man/rand_test.Rd | 49 ++++- scan-0.62.0/scan/man/ranks.Rd | 12 + scan-0.62.0/scan/man/rescale.Rd |only scan-0.62.0/scan/man/scdf.Rd | 7 scan-0.62.0/scan/man/select_cases.Rd | 1 scan-0.62.0/scan/man/select_phases.Rd | 6 scan-0.62.0/scan/man/set_vars.Rd | 5 scan-0.62.0/scan/man/shift.Rd | 5 scan-0.62.0/scan/man/smd.Rd | 2 scan-0.62.0/scan/man/smooth_cases.Rd | 3 scan-0.62.0/scan/man/standardize.Rd | 9 - scan-0.62.0/scan/man/style_plot.Rd | 2 scan-0.62.0/scan/man/subset.scdf.Rd | 2 scan-0.62.0/scan/man/tau_u.Rd | 36 ++-- scan-0.62.0/scan/man/transform.scdf.Rd | 13 - scan-0.62.0/scan/man/trend.Rd | 11 - scan-0.62.0/scan/man/truncate_phase.Rd | 1 scan-0.62.0/scan/tests/testthat/test-rand_test.R |only scan-0.62.0/scan/tests/testthat/test-scdf.R |only scan-0.62.0/scan/tests/testthat/test-tau.R |only scan-0.62.0/scan/tests/testthat/test-trend.R |only 109 files changed, 1065 insertions(+), 846 deletions(-)
Title: Analyzing Partial Rankings in Networks
Description: Implements methods for centrality related analyses of networks.
While the package includes the possibility to build more than 20 indices,
its main focus lies on index-free assessment of centrality via partial
rankings obtained by neighborhood-inclusion or positional dominance. These
partial rankings can be analyzed with different methods, including
probabilistic methods like computing expected node ranks and relative
rank probabilities (how likely is it that a node is more central than another?).
The methodology is described in depth in the vignettes and in
Schoch (2018) <doi:10.1016/j.socnet.2017.12.003>.
Author: David Schoch [aut, cre] ,
Julian Mueller [ctb]
Maintainer: David Schoch <david@schochastics.net>
Diff between netrankr versions 1.2.3 dated 2023-12-19 and 1.2.4 dated 2025-02-05
DESCRIPTION | 8 MD5 | 71 ++--- NAMESPACE | 4 NEWS.md | 5 R/approximate.ranks.R | 20 - R/comparable.pairs.R | 4 R/hyperbolic.index.R | 12 R/indirect.relations.R | 36 +- R/majorization.gap.R | 2 R/mcmc.rank.R | 12 R/neighborhood.inclusion.R | 2 R/netswan.R |only R/rank.analysis.R | 16 - R/spectral.gap.R | 2 README.md | 131 +++++----- build/vignette.rds |binary inst/doc/benchmarks.html | 53 +--- inst/doc/centrality_indices.R | 136 +++++----- inst/doc/centrality_indices.html | 267 ++++++++++---------- inst/doc/indirect_relations.html | 181 +++++++------- inst/doc/neighborhood_inclusion.html | 197 +++++++-------- inst/doc/partial_centrality.html | 197 +++++++-------- inst/doc/positional_dominance.html | 171 ++++++------- inst/doc/probabilistic_cent.html | 175 ++++++------- inst/doc/threshold_graph.html | 216 ++++++++-------- inst/doc/use_case.html | 398 +++++++++++++++---------------- man/majorization_gap.Rd | 2 man/neighborhood_inclusion.Rd | 2 man/netrankr-package.Rd | 2 man/swan_closeness.Rd |only man/swan_combinatory.Rd |only man/swan_connectivity.Rd |only man/swan_efficiency.Rd |only tests/testthat/test-hyperbolic.index.R | 10 tests/testthat/test_dominance.R | 4 tests/testthat/test_helpers.R | 10 tests/testthat/test_indices.R | 18 - tests/testthat/test_indirect_relations.R | 22 - tests/testthat/test_threshold_graph.R | 6 39 files changed, 1201 insertions(+), 1191 deletions(-)
Title: Estimation of Model-Based Predictions, Contrasts and Means
Description: Implements a general interface for model-based estimations
for a wide variety of models, used in the computation of
marginal means, contrast analysis and predictions. For a list of supported models,
see 'insight::supported_models()'.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut]
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between modelbased versions 0.8.9 dated 2024-10-26 and 0.9.0 dated 2025-02-05
modelbased-0.8.9/modelbased/R/get_marginaleffects.R |only modelbased-0.8.9/modelbased/R/visualisation_recipe.estimate_grouplevel.R |only modelbased-0.8.9/modelbased/R/visualisation_recipe.estimate_means.R |only modelbased-0.8.9/modelbased/R/visualisation_recipe.estimate_predicted.R |only modelbased-0.8.9/modelbased/R/visualisation_recipe.estimate_slopes.R |only modelbased-0.8.9/modelbased/man/figures/gganimate_figure.gif |only modelbased-0.8.9/modelbased/man/figures/unnamed-chunk-17-1.png |only modelbased-0.8.9/modelbased/man/figures/unnamed-chunk-18-1.png |only modelbased-0.8.9/modelbased/man/figures/unnamed-chunk-4-1.png |only modelbased-0.8.9/modelbased/man/figures/unnamed-chunk-6-1.png |only modelbased-0.8.9/modelbased/man/find_inversions.Rd |only modelbased-0.8.9/modelbased/man/get_marginaleffects.Rd |only modelbased-0.8.9/modelbased/tests/testthat/test-get_marginaleffects.R |only modelbased-0.9.0/modelbased/DESCRIPTION | 24 modelbased-0.9.0/modelbased/MD5 | 172 +- modelbased-0.9.0/modelbased/NAMESPACE | 22 modelbased-0.9.0/modelbased/NEWS.md | 62 modelbased-0.9.0/modelbased/R/clean_names.R | 15 modelbased-0.9.0/modelbased/R/data.R |only modelbased-0.9.0/modelbased/R/describe_nonlinear.R | 8 modelbased-0.9.0/modelbased/R/estimate_contrast_methods.R |only modelbased-0.9.0/modelbased/R/estimate_contrasts.R | 190 +- modelbased-0.9.0/modelbased/R/estimate_grouplevel.R | 6 modelbased-0.9.0/modelbased/R/estimate_means.R | 259 +++- modelbased-0.9.0/modelbased/R/estimate_predicted.R | 269 ++-- modelbased-0.9.0/modelbased/R/estimate_slopes.R | 186 -- modelbased-0.9.0/modelbased/R/format.R |only modelbased-0.9.0/modelbased/R/get_emcontrasts.R | 140 +- modelbased-0.9.0/modelbased/R/get_emmeans.R | 251 +-- modelbased-0.9.0/modelbased/R/get_emtrends.R | 98 - modelbased-0.9.0/modelbased/R/get_marginalcontrasts.R | 399 +++++- modelbased-0.9.0/modelbased/R/get_marginaleffects_type.R |only modelbased-0.9.0/modelbased/R/get_marginalmeans.R | 343 ++++- modelbased-0.9.0/modelbased/R/get_marginaltrends.R |only modelbased-0.9.0/modelbased/R/print.R | 77 - modelbased-0.9.0/modelbased/R/print_html.R |only modelbased-0.9.0/modelbased/R/print_md.R | 10 modelbased-0.9.0/modelbased/R/reexports.R | 4 modelbased-0.9.0/modelbased/R/reshape_grouplevel.R | 14 modelbased-0.9.0/modelbased/R/smoothing.R | 5 modelbased-0.9.0/modelbased/R/standardize_methods.R | 6 modelbased-0.9.0/modelbased/R/summary.R |only modelbased-0.9.0/modelbased/R/table_footer.R |only modelbased-0.9.0/modelbased/R/utils.R | 29 modelbased-0.9.0/modelbased/R/visualisation_matrix.R | 42 modelbased-0.9.0/modelbased/R/visualisation_recipe.R |only modelbased-0.9.0/modelbased/R/visualisation_recipe_internal.R |only modelbased-0.9.0/modelbased/R/zero_crossings.R | 36 modelbased-0.9.0/modelbased/R/zzz.R |only modelbased-0.9.0/modelbased/README.md | 374 +++-- modelbased-0.9.0/modelbased/build/partial.rdb |only modelbased-0.9.0/modelbased/build/vignette.rds |binary modelbased-0.9.0/modelbased/data |only modelbased-0.9.0/modelbased/inst/WORDLIST | 21 modelbased-0.9.0/modelbased/inst/doc/overview_of_vignettes.Rmd | 18 modelbased-0.9.0/modelbased/inst/doc/overview_of_vignettes.html | 25 modelbased-0.9.0/modelbased/man/coffee_data.Rd |only modelbased-0.9.0/modelbased/man/describe_nonlinear.Rd | 2 modelbased-0.9.0/modelbased/man/efc.Rd |only modelbased-0.9.0/modelbased/man/estimate_contrasts.Rd | 230 ++- modelbased-0.9.0/modelbased/man/estimate_expectation.Rd | 129 +- modelbased-0.9.0/modelbased/man/estimate_grouplevel.Rd | 2 modelbased-0.9.0/modelbased/man/estimate_means.Rd | 218 ++- modelbased-0.9.0/modelbased/man/estimate_slopes.Rd | 97 + modelbased-0.9.0/modelbased/man/figures/unnamed-chunk-10-1.png |binary modelbased-0.9.0/modelbased/man/figures/unnamed-chunk-11-1.png |binary modelbased-0.9.0/modelbased/man/figures/unnamed-chunk-13-1.png |binary modelbased-0.9.0/modelbased/man/figures/unnamed-chunk-14-1.png |binary modelbased-0.9.0/modelbased/man/figures/unnamed-chunk-15-1.png |binary modelbased-0.9.0/modelbased/man/figures/unnamed-chunk-16-1.png |binary modelbased-0.9.0/modelbased/man/figures/unnamed-chunk-3-1.png |binary modelbased-0.9.0/modelbased/man/figures/unnamed-chunk-5-1.png |binary modelbased-0.9.0/modelbased/man/figures/unnamed-chunk-7-1.png |binary modelbased-0.9.0/modelbased/man/figures/unnamed-chunk-8-1.png |binary modelbased-0.9.0/modelbased/man/figures/unnamed-chunk-9-1.png |binary modelbased-0.9.0/modelbased/man/fish.Rd |only modelbased-0.9.0/modelbased/man/get_emmeans.Rd | 383 ++++-- modelbased-0.9.0/modelbased/man/reexports.Rd | 3 modelbased-0.9.0/modelbased/man/visualisation_matrix.Rd | 33 modelbased-0.9.0/modelbased/man/visualisation_recipe.estimate_predicted.Rd | 332 ++--- modelbased-0.9.0/modelbased/man/zero_crossings.Rd | 14 modelbased-0.9.0/modelbased/tests/testthat/test-attributes_estimatefun.R |only modelbased-0.9.0/modelbased/tests/testthat/test-attributes_visualisation.R | 18 modelbased-0.9.0/modelbased/tests/testthat/test-brms-marginaleffects.R |only modelbased-0.9.0/modelbased/tests/testthat/test-brms.R | 15 modelbased-0.9.0/modelbased/tests/testthat/test-estimate_contrasts.R | 637 +++++++++- modelbased-0.9.0/modelbased/tests/testthat/test-estimate_contrasts_methods.R |only modelbased-0.9.0/modelbased/tests/testthat/test-estimate_expectation.R | 65 - modelbased-0.9.0/modelbased/tests/testthat/test-estimate_grouplevel.R | 2 modelbased-0.9.0/modelbased/tests/testthat/test-estimate_means.R | 426 +++++- modelbased-0.9.0/modelbased/tests/testthat/test-estimate_means_counterfactuals.R |only modelbased-0.9.0/modelbased/tests/testthat/test-estimate_means_mixed.R |only modelbased-0.9.0/modelbased/tests/testthat/test-estimate_predicted.R | 47 modelbased-0.9.0/modelbased/tests/testthat/test-estimate_slopes.R | 57 modelbased-0.9.0/modelbased/tests/testthat/test-g_computation.R |only modelbased-0.9.0/modelbased/tests/testthat/test-get_marginaltrends.R |only modelbased-0.9.0/modelbased/tests/testthat/test-glmmTMB.R | 95 + modelbased-0.9.0/modelbased/tests/testthat/test-mgcv.R | 67 - modelbased-0.9.0/modelbased/tests/testthat/test-ordinal.R |only modelbased-0.9.0/modelbased/tests/testthat/test-plot-facet.R |only modelbased-0.9.0/modelbased/tests/testthat/test-plot.R |only modelbased-0.9.0/modelbased/tests/testthat/test-predict-dpar.R |only modelbased-0.9.0/modelbased/tests/testthat/test-print.R |only modelbased-0.9.0/modelbased/tests/testthat/test-table_footer.R |only modelbased-0.9.0/modelbased/tests/testthat/test-transform_response.R |only modelbased-0.9.0/modelbased/tests/testthat/test-vcov.R |only modelbased-0.9.0/modelbased/tests/testthat/test-verbose.R |only modelbased-0.9.0/modelbased/tests/testthat/test-visualisation_recipe.R |only modelbased-0.9.0/modelbased/vignettes/overview_of_vignettes.Rmd | 18 109 files changed, 4017 insertions(+), 1978 deletions(-)
Title: Multi-Format Archive and Compression Support
Description: Bindings to 'libarchive' <http://www.libarchive.org> the
Multi-format archive and compression library. Offers R connections and
direct extraction for many archive formats including 'tar', 'ZIP',
'7-zip', 'RAR', 'CAB' and compression formats including 'gzip',
'bzip2', 'compress', 'lzma' and 'xz'.
Author: Jim Hester [aut] ,
Gabor Csardi [aut, cre],
Ondrej Holy [cph] ,
RStudio [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between archive versions 1.1.10 dated 2024-11-08 and 1.1.11 dated 2025-02-05
DESCRIPTION | 8 ++-- MD5 | 60 +++++++++++++++++----------------- NEWS.md | 4 ++ R/archive.R | 14 +++++-- R/archive_extract.R | 4 +- R/archive_read.R | 4 +- R/archive_write.R | 6 +-- R/archive_write_dir.R | 4 +- R/archive_write_files.R | 4 +- R/cpp11.R | 24 ++++++------- R/file_read.R | 4 +- R/file_write.R | 4 +- man/archive.Rd | 4 +- man/archive_extract.Rd | 5 ++ man/archive_read.Rd | 5 ++ man/archive_write.Rd | 5 ++ man/archive_write_files.Rd | 6 ++- man/file_connections.Rd | 18 +++++++++- src/archive.cpp | 6 ++- src/archive_extract.cpp | 5 ++ src/archive_read.cpp | 6 +++ src/archive_write.cpp | 6 +++ src/archive_write_direct.cpp | 6 +++ src/archive_write_files.cpp | 5 ++ src/cpp11.cpp | 48 +++++++++++++-------------- src/r_archive.h | 1 tests/testthat/helper-mock.R |only tests/testthat/helpers.R |only tests/testthat/test-archive.R | 20 +++++++++++ tests/testthat/test-archive_extract.R | 17 +++++++++ tests/testthat/test-archive_read.R | 1 tests/testthat/test-archive_write.R | 2 + 32 files changed, 209 insertions(+), 97 deletions(-)
Title: Bayesian Penalized Quantile Regression
Description: The quantile varying coefficient model is robust to data heterogeneity,
outliers and heavy-tailed distributions in the response variable. In addition,
it can flexibly model dynamic patterns of regression coefficients through
nonparametric varying coefficient functions. In this package, we have implemented
the Gibbs samplers of the penalized Bayesian quantile varying coefficient model with
spike-and-slab priors [Zhou et al.(2023)]<doi:10.1016/j.csda.2023.107808> for efficient
Bayesian shrinkage estimation, variable selection and statistical inference. In particular,
valid Bayesian inferences on sparse quantile varying coefficient functions can be validated
on finite samples. The Markov Chain Monte Carlo (MCMC) algorithms of the proposed
and alternative models can be efficiently performed by using the package.
Author: Kun Fan [aut],
Cen Wu [aut, cre],
Jie Ren [aut],
Fei Zhou [aut]
Maintainer: Cen Wu <wucen@ksu.edu>
Diff between pqrBayes versions 1.0.4 dated 2025-01-24 and 1.0.5 dated 2025-02-05
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- README.md | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Performs Quality Control, Data Normalization, and Batch Effect
Correction for 'NanoString nCounter' Data
Description: Provides quality control (QC), normalization, and batch
effect correction operations for 'NanoString nCounter' data, Talhouk
et al. (2016) <doi:10.1371/journal.pone.0153844>. Various metrics are
used to determine which samples passed or failed QC. Gene expression
should first be normalized to housekeeping genes, before a
reference-based approach is used to adjust for batch effects. Raw
NanoString data can be imported in the form of Reporter Code Count
(RCC) files.
Author: Derek Chiu [aut, cre] ,
Aline Talhouk [aut] ,
Samuel Leung [aut]
Maintainer: Derek Chiu <dchiu@bccrc.ca>
Diff between nanostringr versions 0.4.2 dated 2024-06-11 and 0.5.0 dated 2025-02-05
DESCRIPTION | 10 ++-- MD5 | 32 ++++++------- NEWS.md | 6 ++ R/NanoStringQC.R | 2 R/normalize_pools.R | 36 ++++++++------ R/normalize_random.R | 20 ++++---- R/read_rcc.R | 2 R/utils.R | 1 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Overview.R | 2 inst/doc/Overview.Rmd | 102 ------------------------------------------ inst/doc/Overview.html | 106 ++++++-------------------------------------- man/normalize_pools.Rd | 4 - man/normalize_random.Rd | 10 ++-- tests/testthat/test-order.R | 5 -- vignettes/Overview.Rmd | 102 ------------------------------------------ 17 files changed, 87 insertions(+), 353 deletions(-)
Title: Kaplan-Meier Plot with 'ggplot2'
Description: The function 'jskm()' creates publication quality Kaplan-Meier plot with at risk tables below. 'svyjskm()' provides plot for weighted Kaplan-Meier estimator.
Author: Jinseob Kim [aut, cre] ,
yoonkyoung Chun [aut],
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jskm versions 0.5.8 dated 2025-01-08 and 0.5.10 dated 2025-02-05
DESCRIPTION | 11 - MD5 | 22 +-- NAMESPACE | 2 NEWS.md | 10 + R/adjustedLR.R |only R/jskm.R | 366 +++++++++++++++++++++++++++++++++-------------------- R/svyjskm.R | 4 inst/doc/jskm.R | 2 inst/doc/jskm.Rmd | 2 inst/doc/jskm.html | 175 ++----------------------- man/adjusted.LR.Rd |only man/jskm.Rd | 2 vignettes/jskm.Rmd | 2 13 files changed, 284 insertions(+), 314 deletions(-)
Title: Corrected Test Statistics for Comparing Machine Learning Models
on Correlated Samples
Description: Calculate a set of corrected test statistics for cases when samples
are not independent, such as when classification accuracy values are obtained
over resamples or through k-fold cross-validation, as proposed by Nadeau and Bengio (2003) <doi:10.1023/A:1024068626366>
and presented in Bouckaert and Frank (2004) <doi:10.1007/978-3-540-24775-3_3>.
Author: Trent Henderson [cre, aut]
Maintainer: Trent Henderson <then6675@uni.sydney.edu.au>
Diff between correctR versions 0.2.1 dated 2024-03-13 and 0.3.1 dated 2025-02-05
DESCRIPTION | 10 LICENSE | 2 MD5 | 42 - NAMESPACE | 14 R/correctR.R | 20 R/kfold_ttest.R | 152 ++--- R/repkfold_ttest.R | 198 +++--- R/resampled_ttest.R | 158 ++--- R/zzz.R | 10 README.md | 101 +-- build/vignette.rds |binary inst/doc/correctR.R | 92 +-- inst/doc/correctR.Rmd | 252 ++++---- inst/doc/correctR.html | 1100 +++++++++++++++++++------------------- man/correctR.Rd | 20 man/kfold_ttest.Rd | 82 +- man/repkfold_ttest.Rd | 94 +-- man/resampled_ttest.Rd | 86 +- tests/testthat.R | 24 tests/testthat/helper-core_data.R | 24 tests/testthat/test-correctR.R | 30 - vignettes/correctR.Rmd | 252 ++++---- 22 files changed, 1377 insertions(+), 1386 deletions(-)
Title: Diverse Cluster Ensemble in R
Description: Performs cluster analysis using an ensemble clustering
framework, Chiu & Talhouk (2018) <doi:10.1186/s12859-017-1996-y>.
Results from a diverse set of algorithms are pooled together using
methods such as majority voting, K-Modes, LinkCluE, and CSPA. There
are options to compare cluster assignments across algorithms using
internal and external indices, visualizations such as heatmaps, and
significance testing for the existence of clusters.
Author: Derek Chiu [aut, cre],
Aline Talhouk [aut],
Johnson Liu [ctb, com]
Maintainer: Derek Chiu <dchiu@bccrc.ca>
Diff between diceR versions 2.2.0 dated 2024-01-22 and 3.0.0 dated 2025-02-05
DESCRIPTION | 24 ++-- MD5 | 46 ++++---- NEWS.md | 7 + R/algorithms.R | 35 ++++-- R/consensus_cluster.R | 7 + R/consensus_evaluate.R | 78 ++++++-------- R/dice.R | 21 ++- R/graphs.R | 136 ++++++++++++++++++------ R/utils.R | 9 + README.md | 33 ++++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/overview.R | 28 +++-- inst/doc/overview.Rmd | 25 +++- inst/doc/overview.html | 175 ++++++++++++++++++++++---------- man/dice.Rd | 15 +- man/min_fnorm.Rd | 1 tests/testthat.R | 8 + tests/testthat/test-consensus_cluster.R | 18 +-- tests/testthat/test-consensus_funs.R | 6 - tests/testthat/test-dice.R | 100 ++++++++++++++---- tests/testthat/test-graphs.R | 19 ++- tests/testthat/test-utils.R | 2 vignettes/overview.Rmd | 25 +++- 24 files changed, 555 insertions(+), 263 deletions(-)
Title: Estimate Real-Time Case Counts and Time-Varying Epidemiological
Parameters
Description: Estimates the time-varying reproduction number,
rate of spread, and doubling time using a range of open-source tools
(Abbott et al. (2020) <doi:10.12688/wellcomeopenres.16006.1>), and
current best practices (Gostic et al. (2020)
<doi:10.1101/2020.06.18.20134858>). It aims to help users avoid some
of the limitations of naive implementations in a framework that is
informed by community feedback and is actively supported.
Author: Sam Abbott [aut] ,
Joel Hellewell [aut] ,
Katharine Sherratt [aut],
Katelyn Gostic [aut],
Joe Hickson [aut],
Hamada S. Badr [aut] ,
Michael DeWitt [aut] ,
James M. Azam [aut] ,
Robin Thompson [ctb],
Sophie Meakin [ctb],
James Munday [ctb],
Nikos Boss [...truncated...]
Maintainer: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Diff between EpiNow2 versions 1.6.1 dated 2024-10-31 and 1.7.0 dated 2025-02-05
EpiNow2-1.6.1/EpiNow2/inst/stan/data/generation_time.stan |only EpiNow2-1.6.1/EpiNow2/man/create_complete_cases.Rd |only EpiNow2-1.7.0/EpiNow2/DESCRIPTION | 6 EpiNow2-1.7.0/EpiNow2/MD5 | 386 EpiNow2-1.7.0/EpiNow2/NAMESPACE | 7 EpiNow2-1.7.0/EpiNow2/NEWS.md | 45 EpiNow2-1.7.0/EpiNow2/R/checks.R | 38 EpiNow2-1.7.0/EpiNow2/R/create.R | 417 EpiNow2-1.7.0/EpiNow2/R/deprecated.R | 12 EpiNow2-1.7.0/EpiNow2/R/dist_spec.R | 228 EpiNow2-1.7.0/EpiNow2/R/epinow-internal.R | 10 EpiNow2-1.7.0/EpiNow2/R/epinow.R | 64 EpiNow2-1.7.0/EpiNow2/R/estimate_infections.R | 114 EpiNow2-1.7.0/EpiNow2/R/estimate_secondary.R | 101 EpiNow2-1.7.0/EpiNow2/R/estimate_truncation.R | 17 EpiNow2-1.7.0/EpiNow2/R/extract.R | 55 EpiNow2-1.7.0/EpiNow2/R/fit.R | 6 EpiNow2-1.7.0/EpiNow2/R/get.R | 17 EpiNow2-1.7.0/EpiNow2/R/opts.R | 342 EpiNow2-1.7.0/EpiNow2/R/plot.R | 23 EpiNow2-1.7.0/EpiNow2/R/preprocessing.R |only EpiNow2-1.7.0/EpiNow2/R/regional_epinow.R | 36 EpiNow2-1.7.0/EpiNow2/R/report.R | 34 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EpiNow2-1.7.0/EpiNow2/inst/doc/estimate_infections_workflow.html | 87 EpiNow2-1.7.0/EpiNow2/inst/doc/estimate_secondary.Rmd | 4 EpiNow2-1.7.0/EpiNow2/inst/doc/estimate_secondary.html | 12 EpiNow2-1.7.0/EpiNow2/inst/doc/estimate_truncation.Rmd | 4 EpiNow2-1.7.0/EpiNow2/inst/doc/estimate_truncation.html | 4 EpiNow2-1.7.0/EpiNow2/inst/doc/gaussian_process_implementation_details.Rmd | 46 EpiNow2-1.7.0/EpiNow2/inst/doc/gaussian_process_implementation_details.html | 51 EpiNow2-1.7.0/EpiNow2/inst/extdata/example_estimate_infections.rds |binary EpiNow2-1.7.0/EpiNow2/inst/extdata/example_regional_epinow.rds |binary EpiNow2-1.7.0/EpiNow2/inst/stan/data/backcalc.stan | 4 EpiNow2-1.7.0/EpiNow2/inst/stan/data/delays.stan | 46 EpiNow2-1.7.0/EpiNow2/inst/stan/data/estimate_infections_params.stan |only EpiNow2-1.7.0/EpiNow2/inst/stan/data/estimate_secondary_params.stan |only EpiNow2-1.7.0/EpiNow2/inst/stan/data/gaussian_process.stan | 20 EpiNow2-1.7.0/EpiNow2/inst/stan/data/observation_model.stan | 23 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|only EpiNow2-1.7.0/EpiNow2/inst/stan/functions/rt.stan | 80 EpiNow2-1.7.0/EpiNow2/inst/stan/functions/secondary.stan | 14 EpiNow2-1.7.0/EpiNow2/inst/stan/simulate_infections.stan | 121 EpiNow2-1.7.0/EpiNow2/inst/stan/simulate_secondary.stan | 110 EpiNow2-1.7.0/EpiNow2/man/Distributions.Rd | 4 EpiNow2-1.7.0/EpiNow2/man/add_breakpoints.Rd |only EpiNow2-1.7.0/EpiNow2/man/add_horizon.Rd |only EpiNow2-1.7.0/EpiNow2/man/apply_default_cdf_cutoff.Rd | 3 EpiNow2-1.7.0/EpiNow2/man/apply_zero_threshold.Rd |only EpiNow2-1.7.0/EpiNow2/man/c.dist_spec.Rd | 7 EpiNow2-1.7.0/EpiNow2/man/check_na_setting_against_data.Rd | 2 EpiNow2-1.7.0/EpiNow2/man/check_reports_valid.Rd | 2 EpiNow2-1.7.0/EpiNow2/man/clean_regions.Rd | 2 EpiNow2-1.7.0/EpiNow2/man/collapse.Rd | 11 EpiNow2-1.7.0/EpiNow2/man/create_clean_reported_cases.Rd | 23 EpiNow2-1.7.0/EpiNow2/man/create_obs_model.Rd | 3 EpiNow2-1.7.0/EpiNow2/man/create_shifted_cases.Rd | 37 EpiNow2-1.7.0/EpiNow2/man/create_stan_data.Rd | 25 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Title: Classes and Methods for "Class Comparison" Problems on
Microarrays
Description: Defines the classes used for "class comparison" problems
in the OOMPA project (<http://oompa.r-forge.r-project.org/>). Class
comparison includes tests for differential expression; see Simon's
book for details on typical problem types.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between ClassComparison versions 3.3.2 dated 2024-08-17 and 3.3.5 dated 2025-02-05
ClassComparison-3.3.2/ClassComparison/tests/testDiff.R |only ClassComparison-3.3.2/ClassComparison/tests/testDiff.Rout.save |only ClassComparison-3.3.5/ClassComparison/DESCRIPTION | 8 ++++---- ClassComparison-3.3.5/ClassComparison/MD5 | 10 ++++------ ClassComparison-3.3.5/ClassComparison/R/cc01-ttest.R | 4 ++-- ClassComparison-3.3.5/ClassComparison/R/cc03-fastlm.R | 4 ++-- ClassComparison-3.3.5/ClassComparison/inst/doc/oompa-cc.pdf |binary 7 files changed, 12 insertions(+), 14 deletions(-)
More information about ClassComparison at CRAN
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