Title: Bayesian Estimation of Nonlinear Data (BEND)
Description: Provides a set of models to estimate nonlinear longitudinal data using Bayesian estimation methods. These models include the: 1) Bayesian Piecewise Random Effects Model (Bayes_PREM()) which estimates a piecewise random effects (mixture) model for a given number of latent classes and a latent number of possible changepoints in each class, and can incorporate class and outcome predictive covariates (see Lamm (2022) <https://hdl.handle.net/11299/252533> and Lock et al., (2018) <doi:10.1007/s11336-017-9594-5>), 2) Bayesian Crossed Random Effects Model (Bayes_CREM()) which estimates a linear, quadratic, exponential, or piecewise crossed random effects models where individuals are changing groups over time (e.g., students and schools; see Rohloff et al., (2024) <doi:10.1111/bmsp.12334>), and 3) Bayesian Bivariate Piecewise Random Effects Model (Bayes_BPREM()) which estimates a bivariate piecewise random effects model to jointly model two related outcomes (e.g., reading and [...truncated...]
Author: Corissa T. Rohloff [aut, cre] ,
Rik Lamm [aut] ,
Yadira Peralta [aut] ,
Nidhi Kohli [aut] ,
Eric F. Lock [aut]
Maintainer: Corissa T. Rohloff <corissa.wurth@gmail.com>
Diff between BEND versions 1.0 dated 2024-03-23 and 1.1 dated 2025-09-23
DESCRIPTION | 19 +++++++++-------- MD5 | 14 ++++++------ NEWS.md | 8 ++++++- R/Bayes_BPREM.R | 11 ++++++++++ R/Bayes_CREM.R | 26 +++++++++++++---------- R/Bayes_PREM.R | 60 +++++++++++++++++++++++++++++++++++++++++++++++++++++++ R/summary_PREM.R | 2 - README.md | 8 +++++++ 8 files changed, 119 insertions(+), 29 deletions(-)
Title: Single-Cell Decomposition using Hierarchical Autoencoder
Description: Provides a fast and accurate pipeline for single-cell analyses.
The 'scDHA' software package can perform clustering, dimension reduction and visualization, classification, and time-trajectory inference on single-cell data (Tran et.al. (2021) <DOI:10.1038/s41467-021-21312-2>).
Author: Ha Nguyen [cre],
Duc Tran [aut],
Tin Nguyen [fnd],
Hao Chen [ctb]
Maintainer: Ha Nguyen <hvn0006@auburn.edu>
This is a re-admission after prior archival of version 1.2.2 dated 2024-04-02
Diff between scDHA versions 1.2.2 dated 2024-04-02 and 1.2.3 dated 2025-09-23
DESCRIPTION | 14 +-- MD5 | 16 +-- R/Analysis.R | 25 ++++- R/scDHA.R | 24 ++++- build/vignette.rds |binary inst/doc/Example.R | 152 ++++++++++++++++++------------------ inst/doc/Example.html | 211 +++++++++++++++++++++----------------------------- src/Makevars | 2 src/Makevars.win | 2 9 files changed, 221 insertions(+), 225 deletions(-)
Title: Non-Parametric Measures of Actigraphy Data
Description: Computes interdaily stability (IS), intradaily variability (IV) & the relative amplitude (RA) from actigraphy data as described in Blume et al. (2016) <doi: 10.1016/j.mex.2016.05.006> and van Someren et al. (1999) <doi: 10.3109/07420529908998724>. Additionally, it also computes L5 (i.e. the 5 hours with lowest average actigraphy amplitude) and M10 (the 10 hours with highest average amplitude) as well as the respective start times. The flex versions will also compute the L-value for a user-defined number of minutes. IS describes the strength of coupling of a rhythm to supposedly stable zeitgebers. It varies between 0 (Gaussian Noise) and 1 for perfect IS. IV describes the fragmentation of a rhythm, i.e. the frequency and extent of transitions between rest and activity. It is near 0 for a perfect sine wave, about 2 for Gaussian noise and may be even higher when a definite ultradian period of about 2 hrs is present. RA is the relative amplitude of a rhythm. Note that to ob [...truncated...]
Author: Christine Blume [aut, cre]
Maintainer: Christine Blume <christine.blume@unibas.ch>
This is a re-admission after prior archival of version 0.8 dated 2017-12-20
Diff between nparACT versions 0.8 dated 2017-12-20 and 0.9.0 dated 2025-09-23
nparACT-0.8/nparACT/R/nparACT-internal.R |only nparACT-0.8/nparACT/man/nparACT-package.Rd |only nparACT-0.8/nparACT/man/nparACT_ISIVfunctions.Rd |only nparACT-0.8/nparACT/man/nparACT_RAfunctions.Rd |only nparACT-0.8/nparACT/man/nparACT_auxfunctions1.Rd |only nparACT-0.8/nparACT/man/nparACT_auxfunctions2.Rd |only nparACT-0.8/nparACT/man/nparACT_base.Rd |only nparACT-0.8/nparACT/man/nparACT_base_loop.Rd |only nparACT-0.8/nparACT/man/nparACT_flex.Rd |only nparACT-0.8/nparACT/man/nparACT_flex_loop.Rd |only nparACT-0.9.0/nparACT/DESCRIPTION | 33 +++++--- nparACT-0.9.0/nparACT/MD5 | 43 +++++------ nparACT-0.9.0/nparACT/NAMESPACE | 13 ++- nparACT-0.9.0/nparACT/NEWS.md |only nparACT-0.9.0/nparACT/R/data.R |only nparACT-0.9.0/nparACT/R/nparACT_ISIVfunctions.R | 67 +++++++++-------- nparACT-0.9.0/nparACT/R/nparACT_RAfunctions.R | 81 ++++++++++----------- nparACT-0.9.0/nparACT/R/nparACT_auxfunctions1.R | 43 +++++++---- nparACT-0.9.0/nparACT/R/nparACT_auxfunctions2.R | 88 ++++++++++++----------- nparACT-0.9.0/nparACT/R/nparACT_base.R | 36 ++++----- nparACT-0.9.0/nparACT/R/nparACT_base_loop.R | 44 ++++++----- nparACT-0.9.0/nparACT/R/nparACT_flex.R | 39 +++++----- nparACT-0.9.0/nparACT/R/nparACT_flex_loop.R | 44 ++++++----- nparACT-0.9.0/nparACT/README.md |only nparACT-0.9.0/nparACT/build |only nparACT-0.9.0/nparACT/data/sleepstudy.rda |binary nparACT-0.9.0/nparACT/inst |only nparACT-0.9.0/nparACT/man/sleepstudy.Rd | 54 +++++--------- nparACT-0.9.0/nparACT/vignettes |only 29 files changed, 316 insertions(+), 269 deletions(-)
Title: Data Analysis for Censored Environmental Data
Description: Contains methods described by Dennis Helsel in
his book "Statistics for Censored Environmental Data
using Minitab and R" (2011) and courses and videos at
<https://practicalstats.com>. This package incorporates functions
of NADA and adds new functionality.
Author: Paul Julian [aut, cre],
Dennis Helsel [aut, cph],
Lopaka Lee [aut, cph]
Maintainer: Paul Julian <pauljulianphd@gmail.com>
This is a re-admission after prior archival of version 1.1.8 dated 2024-09-06
Diff between NADA2 versions 1.1.8 dated 2024-09-06 and 2.0.0 dated 2025-09-23
NADA2-1.1.8/NADA2/build/vignette.rds |only NADA2-1.1.8/NADA2/inst |only NADA2-1.1.8/NADA2/vignettes |only NADA2-2.0.0/NADA2/DESCRIPTION | 26 +- NADA2-2.0.0/NADA2/MD5 | 106 ++++++---- NADA2-2.0.0/NADA2/NAMESPACE | 46 +++- NADA2-2.0.0/NADA2/NEWS.md | 7 NADA2-2.0.0/NADA2/R/ATS.R | 311 ++++++++++++++++++------------ NADA2-2.0.0/NADA2/R/ATSmini.R | 5 NADA2-2.0.0/NADA2/R/Cadmium.R |only NADA2-2.0.0/NADA2/R/CuZn.R |only NADA2-2.0.0/NADA2/R/NADA_All.R |only NADA2-2.0.0/NADA2/R/NADA_icmle.R |only NADA2-2.0.0/NADA2/R/NADA_ken.R |only NADA2-2.0.0/NADA2/R/NADA_ros.R |only NADA2-2.0.0/NADA2/R/NADA_summary.R |only NADA2-2.0.0/NADA2/R/ROSci.R | 11 - NADA2-2.0.0/NADA2/R/ShePyrene.R |only NADA2-2.0.0/NADA2/R/TCEReg.R |only NADA2-2.0.0/NADA2/R/anosimPlot.R | 4 NADA2-2.0.0/NADA2/R/bestaic.R | 3 NADA2-2.0.0/NADA2/R/binaryClust.R | 53 ++++- NADA2-2.0.0/NADA2/R/binaryMDS.R | 2 NADA2-2.0.0/NADA2/R/cboxplot.R | 5 NADA2-2.0.0/NADA2/R/cenCompareCdfs.R | 6 NADA2-2.0.0/NADA2/R/cenpermanova.R | 1 NADA2-2.0.0/NADA2/R/censeaken.R | 217 ++++++++++---------- NADA2-2.0.0/NADA2/R/centrend.R | 1 NADA2-2.0.0/NADA2/R/centrendsea.R | 1 NADA2-2.0.0/NADA2/R/equivalent_n.R | 4 NADA2-2.0.0/NADA2/R/kenplot.R | 128 +++++------- NADA2-2.0.0/NADA2/R/ordranks.R | 1 NADA2-2.0.0/NADA2/build/partial.rdb |binary NADA2-2.0.0/NADA2/data/Cadmium.rda |only NADA2-2.0.0/NADA2/data/CuZn.rda |only NADA2-2.0.0/NADA2/data/ShePyrene.rda |only NADA2-2.0.0/NADA2/data/TCEReg.rda |only NADA2-2.0.0/NADA2/man/ATS.Rd | 4 NADA2-2.0.0/NADA2/man/ATSmini.Rd | 5 NADA2-2.0.0/NADA2/man/Cadmium.Rd |only NADA2-2.0.0/NADA2/man/CuZn.Rd |only NADA2-2.0.0/NADA2/man/EM.Rd |only NADA2-2.0.0/NADA2/man/MLEintvl.Rd |only NADA2-2.0.0/NADA2/man/Maclist.Rd |only NADA2-2.0.0/NADA2/man/Macmat.Rd |only NADA2-2.0.0/NADA2/man/NADAList.Rd |only NADA2-2.0.0/NADA2/man/NADAprobs.Rd |only NADA2-2.0.0/NADA2/man/ROSci.Rd | 10 NADA2-2.0.0/NADA2/man/ShePyrene.Rd |only NADA2-2.0.0/NADA2/man/TCEReg.Rd |only NADA2-2.0.0/NADA2/man/anosimPlot.Rd | 4 NADA2-2.0.0/NADA2/man/bestaic.Rd | 3 NADA2-2.0.0/NADA2/man/binaryClust.Rd | 20 + NADA2-2.0.0/NADA2/man/binaryMDS.Rd | 2 NADA2-2.0.0/NADA2/man/cenboxplot.Rd |only NADA2-2.0.0/NADA2/man/cenken.Rd |only NADA2-2.0.0/NADA2/man/cenpar.usr.Rd |only NADA2-2.0.0/NADA2/man/censeaken.Rd | 8 NADA2-2.0.0/NADA2/man/censtats.Rd |only NADA2-2.0.0/NADA2/man/censummary.Rd |only NADA2-2.0.0/NADA2/man/cenxyplot.Rd |only NADA2-2.0.0/NADA2/man/cohn.Rd |only NADA2-2.0.0/NADA2/man/equivalent_n.Rd | 3 NADA2-2.0.0/NADA2/man/hc_ppoints.Rd |only NADA2-2.0.0/NADA2/man/hc_ppoints_cen.Rd |only NADA2-2.0.0/NADA2/man/hc_ppoints_uncen.Rd |only NADA2-2.0.0/NADA2/man/kenplot.Rd | 9 NADA2-2.0.0/NADA2/man/ordranks.Rd | 1 NADA2-2.0.0/NADA2/man/pctCen.Rd |only NADA2-2.0.0/NADA2/man/print.NADAList.Rd |only NADA2-2.0.0/NADA2/man/rescaleP.Rd |only NADA2-2.0.0/NADA2/man/ros-class.Rd |only NADA2-2.0.0/NADA2/man/ros.Rd |only NADA2-2.0.0/NADA2/man/splitQual.Rd |only 74 files changed, 591 insertions(+), 416 deletions(-)
Title: Overlap Detection in n-Dimensional Space
Description: Uses support vector machines to identify a perfectly separating hyperplane (linear or curvilinear) between two entities in high-dimensional space. If this plane exists, the entities do not overlap. Applications include overlap detection in morphological, resource or environmental dimensions. More details can be found in: Brown et al. (2020) <doi:10.1111/2041-210X.13363> .
Author: Matilda Brown [aut, cre] ,
Greg Jordan [aut]
Maintainer: Matilda Brown <m.brown2@kew.org>
Diff between hyperoverlap versions 1.1.1 dated 2021-08-10 and 1.1.3 dated 2025-09-23
hyperoverlap-1.1.1/hyperoverlap/R/hyperoverlap.r |only hyperoverlap-1.1.1/hyperoverlap/man/hyperoverlap.Rd |only hyperoverlap-1.1.3/hyperoverlap/DESCRIPTION | 16 hyperoverlap-1.1.3/hyperoverlap/MD5 | 47 hyperoverlap-1.1.3/hyperoverlap/NAMESPACE | 25 hyperoverlap-1.1.3/hyperoverlap/NEWS.md | 13 hyperoverlap-1.1.3/hyperoverlap/R/hyperoverlap-class.R | 66 hyperoverlap-1.1.3/hyperoverlap/R/hyperoverlap-package.R |only hyperoverlap-1.1.3/hyperoverlap/R/hyperoverlap_detect.r | 442 hyperoverlap-1.1.3/hyperoverlap/R/hyperoverlap_lda.r | 374 hyperoverlap-1.1.3/hyperoverlap/R/hyperoverlap_pairs_plot.r | 75 hyperoverlap-1.1.3/hyperoverlap/R/hyperoverlap_plot.r | 104 hyperoverlap-1.1.3/hyperoverlap/R/hyperoverlap_set.r | 288 hyperoverlap-1.1.3/hyperoverlap/README.md | 26 hyperoverlap-1.1.3/hyperoverlap/build/partial.rdb |only hyperoverlap-1.1.3/hyperoverlap/build/vignette.rds |binary hyperoverlap-1.1.3/hyperoverlap/inst/doc/hyperoverlap-vignette.R | 132 hyperoverlap-1.1.3/hyperoverlap/inst/doc/hyperoverlap-vignette.Rmd | 216 hyperoverlap-1.1.3/hyperoverlap/inst/doc/hyperoverlap-vignette.html | 9559 +++++++++- hyperoverlap-1.1.3/hyperoverlap/man/hyperoverlap-class.Rd | 64 hyperoverlap-1.1.3/hyperoverlap/man/hyperoverlap-package.Rd |only hyperoverlap-1.1.3/hyperoverlap/man/hyperoverlap_detect.Rd | 82 hyperoverlap-1.1.3/hyperoverlap/man/hyperoverlap_lda.Rd | 82 hyperoverlap-1.1.3/hyperoverlap/man/hyperoverlap_pairs_plot.Rd | 54 hyperoverlap-1.1.3/hyperoverlap/man/hyperoverlap_plot.Rd | 46 hyperoverlap-1.1.3/hyperoverlap/man/hyperoverlap_set.Rd | 112 hyperoverlap-1.1.3/hyperoverlap/vignettes/hyperoverlap-vignette.Rmd | 216 27 files changed, 10552 insertions(+), 1487 deletions(-)
Title: Easily Create Presentation-Ready Display Tables
Description: Build display tables from tabular data with an easy-to-use
set of functions. With its progressive approach, we can construct
display tables with a cohesive set of table parts. Table values can be
formatted using any of the included formatting functions. Footnotes
and cell styles can be precisely added through a location targeting
system. The way in which 'gt' handles things for you means that you
don't often have to worry about the fine details.
Author: Richard Iannone [aut, cre] ,
Joe Cheng [aut],
Barret Schloerke [aut] ,
Ellis Hughes [aut] ,
Alexandra Lauer [aut] ,
JooYoung Seo [aut] ,
Ken Brevoort [aut] ,
Olivier Roy [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Richard Iannone <rich@posit.co>
Diff between gt versions 1.0.0 dated 2025-04-05 and 1.1.0 dated 2025-09-23
DESCRIPTION | 23 MD5 | 212 ++++---- NAMESPACE | 3 NEWS.md | 38 + R/cols_add.R | 18 R/cols_align.R | 19 R/cols_align_decimal.R | 9 R/cols_hide.R | 16 R/cols_label.R | 20 R/cols_merge.R | 32 + R/cols_move.R | 24 R/cols_units.R | 10 R/cols_width.R | 10 R/data_color.R | 61 ++ R/datasets.R | 8 R/dt_groups_rows.R | 4 R/dt_options.R | 3 R/dt_stub_df.R | 39 + R/export.R | 39 - R/fmt.R | 2 R/format_data.R | 119 ++++ R/gt.R | 44 + R/gtsave.R | 7 R/helpers.R | 178 ++++++ R/location_methods.R | 1 R/modify_rows.R | 7 R/nanoplot.R | 8 R/print.R | 2 R/quarto.R | 1 R/render_as_html.R | 10 R/resolver.R | 583 +++++++++++++++++++++- R/substitution.R | 20 R/tab_create_modify.R | 98 ++- R/tab_footnote.R | 115 ++++ R/tab_options.R | 23 R/tab_style.R | 54 +- R/text_transform.R | 24 R/utils.R | 79 ++- R/utils_color_contrast.R | 2 R/utils_render_common.R | 26 - R/utils_render_html.R | 883 ++++++++++++++++++++++++---------- R/utils_render_latex.R | 99 ++- R/utils_render_rtf.R | 4 R/utils_render_xml.R | 33 - R/z_utils_render_footnotes.R | 132 +++-- R/zzz.R | 9 data/films.rda |binary data/metro.rda |binary inst/graphics/test_image.jpeg |only inst/latex_unicode |only man/adjust_luminance.Rd | 1 man/as_word.Rd | 11 man/cell_borders.Rd | 1 man/cell_fill.Rd | 1 man/cell_text.Rd | 1 man/cells_stub.Rd | 86 ++- man/cols_add.Rd | 11 man/cols_align.Rd | 11 man/cols_align_decimal.Rd | 11 man/cols_hide.Rd | 11 man/cols_label.Rd | 11 man/cols_label_with.Rd | 11 man/cols_merge.Rd | 11 man/cols_merge_n_pct.Rd | 11 man/cols_merge_range.Rd | 11 man/cols_merge_uncert.Rd | 11 man/cols_move.Rd | 11 man/cols_move_to_end.Rd | 11 man/cols_move_to_start.Rd | 11 man/cols_nanoplot.Rd | 11 man/cols_unhide.Rd | 11 man/cols_units.Rd | 11 man/cols_width.Rd | 11 man/constants.Rd | 2 man/currency.Rd | 1 man/data_color.Rd | 25 man/default_fonts.Rd | 1 man/escape_latex.Rd | 1 man/films.Rd | 2 man/from_column.Rd | 1 man/google_font.Rd | 1 man/gt.Rd | 13 man/gt_latex_dependencies.Rd | 1 man/html.Rd | 1 man/latex.Rd |only man/md.Rd | 1 man/metro.Rd | 4 man/nanoplot_options.Rd | 1 man/pct.Rd | 1 man/px.Rd | 1 man/random_id.Rd | 1 man/row_group.Rd | 1 man/stub.Rd | 1 man/system_fonts.Rd | 1 man/tab_options.Rd | 21 man/tab_spanner.Rd | 2 man/tab_stubhead.Rd | 78 +-- man/unit_conversion.Rd | 1 tests/testthat/Rplots.pdf |binary tests/testthat/helper-gt_object.R | 2 tests/testthat/test-as_rtf.R |only tests/testthat/test-cols_add.R | 19 tests/testthat/test-cols_align.R | 20 tests/testthat/test-cols_hide.R | 27 + tests/testthat/test-cols_move.R | 57 ++ tests/testthat/test-cols_nanoplot.R | 38 + tests/testthat/test-cols_units.R | 19 tests/testthat/test-l_cols_merge.R | 94 +++ tests/testthat/test-rtf_table_parts.R | 39 + 109 files changed, 3207 insertions(+), 710 deletions(-)
Title: Finding Heterogeneous Treatment Effects
Description: The heterogeneous treatment effect estimation procedure
proposed by Imai and Ratkovic (2013)<DOI: 10.1214/12-AOAS593>.
The proposed method is applicable, for
example, when selecting a small number of most (or least)
efficacious treatments from a large number of alternative
treatments as well as when identifying subsets of the
population who benefit (or are harmed by) a treatment of
interest. The method adapts the Support Vector Machine
classifier by placing separate LASSO constraints over the
pre-treatment parameters and causal heterogeneity parameters of
interest. This allows for the qualitative distinction between
causal and other parameters, thereby making the variable
selection suitable for the exploration of causal heterogeneity.
The package also contains a class of functions, CausalANOVA,
which estimates the average marginal interaction effects (AMIEs)
by a regularized ANOVA as proposed by Egami and Imai (2019).
It contains a variety of regularization techniques to facilita [...truncated...]
Author: Naoki Egami [aut, cre],
Marc Ratkovic [aut],
Kosuke Imai [aut]
Maintainer: Naoki Egami <naoki.egami5@gmail.com>
This is a re-admission after prior archival of version 1.2.0 dated 2019-11-20
Diff between FindIt versions 1.2.0 dated 2019-11-20 and 1.3.0 dated 2025-09-23
DESCRIPTION | 29 + MD5 | 40 +- R/CausalANOVA.R | 1 R/CausalANOVAFit.R | 3 R/ConditionalEffect.R | 1 R/FindIt-package.R | 6 R/SVMHet.R | 2 R/SceenINT.R | 328 +++++++++--------- R/cluster.R | 3 R/cv.CausalANOVA.R | 1 R/predict.FindIt.R | 849 ++++++++++++++++++++++++----------------------- R/test.CausalANOVA.R | 1 man/Carlson.Rd | 6 man/CausalANOVA.Rd | 1 man/ConditionalEffect.Rd | 1 man/FindIt-package.Rd | 6 man/FindIt.Rd | 2 man/GerberGreen.Rd | 6 man/LaLonde.Rd | 6 man/cv.CausalANOVA.Rd | 1 man/test.CausalANOVA.Rd | 1 21 files changed, 664 insertions(+), 630 deletions(-)
Title: Continuous Time Distance-Based and Network-Based Individual
Level Models for Epidemics
Description: Provides tools for simulating from continuous-time individual level models of disease transmission, and carrying out infectious disease data analyses with the same models. The epidemic models considered are distance-based and/or contact network-based models within Susceptible-Infectious-Removed (SIR) or Susceptible-Infectious-Notified-Removed (SINR) compartmental frameworks. <doi:10.18637/jss.v098.i10>.
Author: Waleed Almutiry [aut, cre],
Rob Deardon [aut, ths],
Vineetha Warriyar K. V. [ctb]
Maintainer: Waleed Almutiry <wkmtierie@qu.edu.sa>
This is a re-admission after prior archival of version 1.1.7 dated 2021-06-29
Diff between EpiILMCT versions 1.1.7 dated 2021-06-29 and 1.1.8 dated 2025-09-23
DESCRIPTION | 21 +++++++++++++-------- MD5 | 6 +++--- man/plot.epictmcmc.Rd | 46 +++++++++++++++++++++++----------------------- man/summary.epictmcmc.Rd | 42 +++++++++++++++++++++--------------------- 4 files changed, 60 insertions(+), 55 deletions(-)
Title: EM Algorithms for Estimating Item Response Theory Models
Description: Various Expectation-Maximization (EM) algorithms are implemented for item
response theory (IRT) models. The package includes IRT models for binary and ordinal
responses, along with dynamic and hierarchical IRT models with binary responses. The
latter two models are fitted using variational EM. The package also includes
variational network and text scaling models. The algorithms are described in Imai, Lo,
and Olmsted (2016) <DOI:10.1017/S000305541600037X>.
Author: Kosuke Imai [aut, cre],
James Lo [aut],
Jonathan Olmsted [aut]
Maintainer: Kosuke Imai <imai@harvard.edu>
Diff between emIRT versions 0.0.14 dated 2024-07-06 and 0.0.15 dated 2025-09-23
ChangeLog | 7 +++++++ DESCRIPTION | 24 +++++++++++++++++++----- MD5 | 10 +++++----- src/getEystar_dynIRT.cpp | 2 +- src/getEystar_hierIRT.cpp | 2 +- src/getEzstar_ordIRT.cpp | 2 +- 6 files changed, 34 insertions(+), 13 deletions(-)
Title: Datasets and Functions to Accompany Analisis De Datos Con R
Description: Datasets and functions to accompany the book 'Analisis de datos con el programa
estadistico R: una introduccion aplicada' by Salas-Eljatib (2021, ISBN: 9789566086109).
The package helps carry out data management, exploratory analyses, and model fitting.
Author: Christian Salas-Eljatib [aut, cre] ,
Nicolas Campos [ctb] ,
Joaquin Riquelme [ctb] ,
Nicolas Pino [ctb]
Maintainer: Christian Salas-Eljatib <cseljatib@gmail.com>
Diff between datana versions 1.1.3 dated 2025-09-02 and 1.1.4 dated 2025-09-23
DESCRIPTION | 34 +++++-- MD5 | 214 ++++++++++++++++++++++++----------------------- NAMESPACE | 4 R/assigncl.r | 65 ++++++++------ R/interp.r |only R/moda.r | 21 +++- R/obspredplot.r |only R/plotrend.r | 96 ++++++++++++--------- R/qqgauss.r |only R/simmeind.r |only R/smoothfit.r | 18 ++- R/tabtexanova.r | 3 R/tabtexdescstat.r | 21 ++-- R/tabtexregre.r | 3 R/valesta.r | 4 build/partial.rdb |binary data/aboutrsq.rda |binary data/aboutrsq2.rda |binary data/airnyc.rda |binary data/airnyc2.rda |binary data/annualppCities.rda |binary data/annualppCities2.rda |binary data/bears.rda |binary data/bears2.rda |binary data/bearsdepu.rda |binary data/bearsdepu2.rda |binary data/beetles.rda |binary data/beetles2.rda |binary data/cameratrap.rda |binary data/cameratrap2.rda |binary data/carAccidents.rda |binary data/caribou.rda |binary data/caribou2.rda |binary data/casen.rda |binary data/chicksw.rda |binary data/chicksw2.rda |binary data/co2temp.rda |binary data/corkoak.rda |binary data/corkoak2.rda |binary data/education.rda |binary data/election.rda |binary data/election2.rda |binary data/endfid2.rda |binary data/eucaleaf.rda |binary data/eucaleaf2.rda |binary data/eucaleafAll.rda |binary data/eucaleafAll2.rda |binary data/fdamage.rda |binary data/fdamage2.rda |binary data/fertiliza.rda |binary data/fertiliza2.rda |binary data/ficdiamgr.rda |binary data/ficdiamgr2.rda |binary data/fishgrowth.rda |binary data/fishgrowth2.rda |binary data/forestfire.rda |binary data/forestfire2.rda |binary data/gasoline.rda |binary data/gasoline2.rda |binary data/gdpcap.rda |binary data/hgrdfir.rda |binary data/hgrdfir2.rda |binary data/idahohd.rda |binary data/idahohd2.rda |binary data/imacec2.rda |binary data/landcover.rda |binary data/landcover2.rda |binary data/largetrees.rda |binary data/largetrees2.rda |binary data/leafw2.rda |binary data/lifexpect.rda |binary data/llancahue.rda |binary data/llancahue2.rda |binary data/maple.rda |binary data/papersdocstu.rda |binary data/pesohojas.rda |binary data/presenceIce.rda |binary data/president.rda |binary data/primarias.rda |binary data/pspLlancahue.rda |binary data/pspruca.rda |binary data/pspruca2.rda |binary data/ptaeda.rda |binary data/ptaeda2.rda |binary data/rainfallCA.rda |binary data/raulihg.rda |binary data/raulihg2.rda |binary data/rendesc2.rda |binary data/simce2.rda |binary data/sludge.rda |binary data/sludge2.rda |binary data/snaspe.rda |binary data/snaspe2.rda |binary data/soiltreat.rda |binary data/soiltreat2.rda |binary data/spataustria.rda |binary data/treevol.rda |binary data/treevol2.rda |binary data/treevolroble.rda |binary data/treevolroble2.rda |binary inst/CITATION | 8 - man/assigncl.Rd | 42 +++++---- man/datana-package.Rd | 6 - man/interp.Rd |only man/moda.Rd | 21 +++- man/obspredplot.Rd |only man/plotrend.Rd | 47 +++++----- man/qqgauss.Rd |only man/simmeind.Rd |only man/smoothfit.Rd | 15 +-- man/tabtexdescstat.Rd | 11 +- man/tabtexregre.Rd | 8 + 112 files changed, 367 insertions(+), 274 deletions(-)
Title: Create Lightweight Schema.org Descriptions of Data
Description: The goal of 'dataspice' is to make it easier for researchers to
create basic, lightweight, and concise metadata files for their datasets.
These basic files can then be used to make useful information available during
analysis, create a helpful dataset "README" webpage, and produce more complex
metadata formats to aid dataset discovery. Metadata fields are based on
the 'Schema.org' and 'Ecological Metadata Language' standards.
Author: Carl Boettiger [aut] ,
Scott Chamberlain [aut] ,
Auriel Fournier [aut] ,
Kelly Hondula [aut] ,
Anna Krystalli [aut] ,
Bryce Mecum [aut, cre] ,
Maelle Salmon [aut] ,
Kate Webbink [aut] ,
Kara Woo [aut] ,
Irene Steves [ctb]
Maintainer: Bryce Mecum <brycemecum@gmail.com>
Diff between dataspice versions 1.1.0 dated 2021-05-16 and 1.1.1 dated 2025-09-23
DESCRIPTION | 6 MD5 | 38 ++--- NEWS.md | 4 R/build_site.R | 11 - R/edit_file.R | 4 R/prep_access.R | 2 R/prep_attributes.R | 2 R/write_spice.R | 2 README.md | 22 -- build/vignette.rds |binary inst/doc/overview.Rmd | 2 inst/doc/overview.html | 275 +++++++++++++++++++++++++++++++++---- man/build_site.Rd | 4 man/edit_attributes.Rd | 2 man/prep_access.Rd | 6 man/prep_attributes.Rd | 2 man/write_spice.Rd | 2 tests/testthat/test-build_site.R | 20 ++ tests/testthat/test-eml_to_spice.R | 5 vignettes/overview.Rmd | 2 20 files changed, 327 insertions(+), 84 deletions(-)
Title: Analysis and Visualization of Circular Data
Description: Circumplex models, which organize constructs in a circle around two
underlying dimensions, are popular for studying interpersonal functioning,
mood/affect, and vocational preferences/environments. This package provides
tools for analyzing and visualizing circular data, including scoring
functions for relevant instruments and a generalization of the bootstrapped
structural summary method from Zimmermann & Wright (2017)
<doi:10.1177/1073191115621795> and functions for creating publication-ready
tables and figures from the results.
Author: Jeffrey Girard [aut, cre] ,
Johannes Zimmermann [aut] ,
Aidan Wright [aut]
Maintainer: Jeffrey Girard <me@jmgirard.com>
Diff between circumplex versions 1.0.1 dated 2025-07-28 and 1.0.2 dated 2025-09-23
DESCRIPTION | 8 MD5 | 148 - NAMESPACE | 84 NEWS.md | 10 R/circumplex-package.R | 56 R/example_data.R | 116 - R/instrument_oop.R | 434 ++-- R/ssm_analysis.R | 1064 +++++----- R/ssm_bootstrap.R | 164 - R/ssm_oop.R | 330 +-- R/ssm_plot.R | 4 R/ssm_table.R | 260 +- R/tidying_functions.R | 502 ++-- R/utils.R | 354 +-- inst/doc/intermediate-ssm-analysis.Rmd | 570 ++--- inst/doc/intermediate-ssm-analysis.html | 19 inst/doc/introduction-to-ssm-analysis.Rmd | 886 ++++---- inst/doc/introduction-to-ssm-analysis.html | 196 - inst/doc/using-instruments.Rmd | 304 +- inst/doc/using-instruments.html | 5 man/anchors.Rd | 60 man/aw2009.Rd | 60 man/circumplex-package.Rd | 94 man/csip.Rd | 54 man/figures/README-plot-1.png |binary man/figures/README-plot3-1.png |binary man/ggsave.Rd | 18 man/html_render.Rd | 56 man/igicr.Rd | 56 man/iip32.Rd | 58 man/iip64.Rd | 56 man/iipsc.Rd | 54 man/iis32.Rd | 56 man/iis64.Rd | 54 man/iitc.Rd | 54 man/instruments.Rd | 48 man/ipipipc.Rd | 52 man/ipsatize.Rd | 104 man/isc.Rd | 54 man/items.Rd | 60 man/jz2017.Rd | 84 man/norms.Rd | 62 man/octants.Rd | 42 man/poles.Rd | 42 man/quadrants.Rd | 42 man/raw_iipsc.Rd | 36 man/scales.Rd | 66 man/score.Rd | 124 - man/ssm_analyze.Rd | 300 +- man/ssm_parameters.Rd | 168 - man/ssm_score.Rd | 106 man/ssm_table.Rd | 124 - src/parameters.cpp | 2 tests/testthat.R | 8 tests/testthat/_snaps/ssm_plot/cross-zero-circle.svg | 12 tests/testthat/_snaps/ssm_plot/group-constrast-correlation-ssm.svg | 286 +- tests/testthat/_snaps/ssm_plot/many-circle-plots.svg | 26 tests/testthat/_snaps/ssm_plot/many-circle-repel.svg | 18 tests/testthat/_snaps/ssm_plot/many-curve-plots.svg | 452 ++-- tests/testthat/_snaps/ssm_plot/measure-contrast-circle-ssm.svg | 18 tests/testthat/_snaps/ssm_plot/measure-contrast-curve-ssm.svg | 312 +- tests/testthat/_snaps/ssm_plot/measure-contrast-ssm.svg | 182 - tests/testthat/_snaps/ssm_plot/single-group-correlation-ssm.svg | 12 tests/testthat/_snaps/ssm_plot/single-group-mean-ssm-no-palette.svg | 12 tests/testthat/_snaps/ssm_plot/single-group-mean-ssm.svg | 12 tests/testthat/test-RcppExport.R.R | 114 - tests/testthat/test-instrument_oop.R | 66 tests/testthat/test-ssm_analysis.R | 872 ++++---- tests/testthat/test-ssm_bootstrap.R | 64 tests/testthat/test-ssm_oop.R | 144 - tests/testthat/test-tidying_functions.R | 164 - tests/testthat/test-utils.R | 80 vignettes/intermediate-ssm-analysis.Rmd | 570 ++--- vignettes/introduction-to-ssm-analysis.Rmd | 886 ++++---- vignettes/using-instruments.Rmd | 304 +- 75 files changed, 6230 insertions(+), 6144 deletions(-)
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt' (<DOI:10.32614/CRAN.package.mlt>, <DOI:10.32614/CRAN.package.mlt.docreg>).
Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to
transformation models for clustered data is provided (Barbanti and Hothorn, 2022,
<DOI:10.1093/biostatistics/kxac048>). Multivariate conditional transformation models
(Klein et al, 2022, <DOI:10.1111/sjos.12501>) and shift-scale transformation models (Siegfried et al, 2023,
<DOI:10.1080/00031305.2023.2203177>) can be fitted as well. The package contains an implementation of
a doubly robust score test, [...truncated...]
Author: Torsten Hothorn [aut, cre] ,
Luisa Barbanti [ctb] ,
Sandra Siegfried [aut] ,
Lucas Kook [aut] ,
Susanne Dandl [ctb] ,
Brian Ripley [ctb],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Nadja Klein [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 1.2-3 dated 2025-06-18 and 1.2-4 dated 2025-09-23
tram-1.2-3/tram/demo/NAMI.Rout.save |only tram-1.2-3/tram/demo/SCI_ePolr.Rout.save |only tram-1.2-3/tram/demo/hcc.Rout.save |only tram-1.2-3/tram/demo/mtram.Rout.save |only tram-1.2-3/tram/demo/npb.Rout.save |only tram-1.2-3/tram/demo/npn.Rout.save |only tram-1.2-3/tram/demo/stram.Rout.save |only tram-1.2-3/tram/demo/survtram.Rout.save |only tram-1.2-3/tram/demo/tram.Rout.save |only tram-1.2-3/tram/demo/undernutrition.Rout.save |only tram-1.2-3/tram/inst/simulations/sim2d.Rout.save |only tram-1.2-3/tram/inst/simulations/sim5d.Rout.save |only tram-1.2-3/tram/tests/Coxph-Ex.Rout.save |only tram-1.2-3/tram/tests/Polr-Ex.R |only tram-1.2-3/tram/tests/Polr-Ex.Rout.save |only tram-1.2-3/tram/tests/Survreg-Ex.Rout.save |only tram-1.2-3/tram/tests/intercepts-Ex.Rout.save |only tram-1.2-3/tram/tests/mmlt-Ex.Rout.save |only tram-1.2-3/tram/tests/mtram-Ex.Rout.save |only tram-1.2-3/tram/tests/stram-Ex.Rout.save |only tram-1.2-4/tram/DESCRIPTION | 10 tram-1.2-4/tram/MD5 | 73 +- tram-1.2-4/tram/R/internal.R | 2 tram-1.2-4/tram/R/methods.R | 22 tram-1.2-4/tram/R/mmlt.R | 2 tram-1.2-4/tram/R/tram.R | 2 tram-1.2-4/tram/build/vignette.rds |binary tram-1.2-4/tram/demo/survtram.R | 589 -------------------- tram-1.2-4/tram/inst/NEWS.Rd | 8 tram-1.2-4/tram/inst/doc/NAMI.R | 12 tram-1.2-4/tram/inst/doc/NAMI.Rnw | 12 tram-1.2-4/tram/inst/doc/NAMI.pdf |binary tram-1.2-4/tram/inst/doc/mtram.R | 3 tram-1.2-4/tram/inst/doc/mtram.Rnw | 3 tram-1.2-4/tram/inst/doc/mtram.pdf |binary tram-1.2-4/tram/inst/doc/survtram.R |only tram-1.2-4/tram/inst/doc/survtram.Rnw |only tram-1.2-4/tram/inst/doc/survtram.pdf |only tram-1.2-4/tram/inst/doc/tram.R | 3 tram-1.2-4/tram/inst/doc/tram.Rnw | 3 tram-1.2-4/tram/inst/doc/tram.pdf |binary tram-1.2-4/tram/man/mmlt.Rd | 2 tram-1.2-4/tram/tests/bugfixes.R | 2 tram-1.2-4/tram/vignettes/COXME-margsurv-plot-1.pdf |only tram-1.2-4/tram/vignettes/HTECOX-DFS-plot-1.pdf |only tram-1.2-4/tram/vignettes/NAMI.Rnw | 12 tram-1.2-4/tram/vignettes/TVAR-DFS-plot-1.pdf |only tram-1.2-4/tram/vignettes/TVAR-iDFS-plot-1.pdf |only tram-1.2-4/tram/vignettes/mtram.Rnw | 3 tram-1.2-4/tram/vignettes/survtram.Rnw |only tram-1.2-4/tram/vignettes/survtram.bib |only tram-1.2-4/tram/vignettes/tram.Rnw | 3 52 files changed, 103 insertions(+), 663 deletions(-)
Title: Robust Multi-Model Subset Selection
Description: Efficient algorithms for generating ensembles of robust, sparse and diverse models via robust
multi-model subset selection (RMSS). The robust ensembles are generated by minimizing the sum of
the least trimmed square loss of the models in the ensembles under constraints for the size of
the models and the sharing of the predictors. Tuning parameters for the robustness, sparsity and
diversity of the robust ensemble are selected by cross-validation.
Author: Anthony Christidis [aut, cre],
Gabriela Cohen-Freue [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between RMSS versions 1.2.1 dated 2025-08-19 and 1.2.2 dated 2025-09-23
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 5 ++++- src/EnsembleModel.cpp | 16 ++++++++-------- 4 files changed, 19 insertions(+), 16 deletions(-)
Title: Analysis and Mining of Multilayer Social Networks
Description: Functions for the creation/generation and analysis of multilayer social networks <doi:10.18637/jss.v098.i08>.
Author: Matteo Magnani [aut, cre],
Luca Rossi [aut] ,
Davide Vega [aut] ,
Obaida Hanteer [ctb]
Maintainer: Matteo Magnani <matteo.magnani@it.uu.se>
Diff between multinet versions 4.3 dated 2025-09-15 and 4.3.1 dated 2025-09-23
DESCRIPTION | 8 MD5 | 316 ++++++++--------- NEWS | 4 src/src/algorithms/components.ipp | 4 src/src/community/_impl/GMetaNetwork.cpp | 4 src/src/community/_impl/GMetaNetwork.hpp | 8 src/src/community/_impl/MLCPMCommunity.hpp | 6 src/src/community/_impl/MetaNetwork.hpp | 2 src/src/community/_impl/PillarCommunity.hpp | 6 src/src/community/_impl/abacus_utils.ipp | 22 - src/src/community/_impl/common.cpp | 2 src/src/community/_impl/common.hpp | 2 src/src/community/_impl/glouvain2_utils.cpp | 40 +- src/src/community/_impl/glouvain2_utils.hpp | 4 src/src/community/_impl/infomap_utils.hpp | 28 - src/src/community/_impl/louvain_utils.cpp | 18 src/src/community/_impl/louvain_utils.hpp | 4 src/src/community/_impl/mlcpm_utils.hpp | 16 src/src/community/_impl/mlcpm_utils.ipp | 24 - src/src/community/community_stats.hpp | 4 src/src/community/community_stats.ipp | 34 - src/src/community/label_propagation.ipp | 4 src/src/community/mlcpm.hpp | 4 src/src/community/mlcpm.ipp | 6 src/src/community/mlp.hpp | 18 src/src/community/modularity.ipp | 6 src/src/community/nmi.ipp | 2 src/src/community/omega_index.hpp | 2 src/src/community/omega_index.ipp | 32 - src/src/community/optimize_slices.cpp | 8 src/src/community/optimize_slices.hpp | 2 src/src/core/arules/bottom_up_search.cpp | 10 src/src/core/arules/bottom_up_search.hpp | 6 src/src/core/arules/eclat.cpp | 12 src/src/core/arules/eclat.hpp | 6 src/src/core/arules/freq_itemset.cpp | 4 src/src/core/arules/freq_itemset.hpp | 13 src/src/core/arules/generate_subsets.cpp | 12 src/src/core/arules/generate_subsets.hpp | 5 src/src/core/arules/intersect_tids.cpp | 12 src/src/core/arules/intersect_tids.hpp | 7 src/src/core/arules/join_items.cpp | 12 src/src/core/arules/join_items.hpp | 7 src/src/core/arules/read_transactions.cpp | 20 - src/src/core/arules/read_transactions.hpp | 6 src/src/core/attributes/date.hpp | 8 src/src/core/observers/UnionObserver.hpp | 2 src/src/core/propertymatrix/summarization.ipp | 6 src/src/core/stores/AttributeStore.hpp | 4 src/src/core/stores/AttributeStore.ipp | 4 src/src/core/stores/ObjectStore.hpp | 4 src/src/core/stores/ObjectStore.ipp | 4 src/src/core/stores/_impl/PtrSortedRandomSet.hpp | 12 src/src/core/stores/_impl/SharedPtrSortedRandomSet.hpp | 2 src/src/core/stores/_impl/SortedRandomBag.hpp | 60 +-- src/src/core/stores/_impl/SortedRandomBagEntry.hpp | 2 src/src/core/stores/_impl/SortedRandomSet.hpp | 54 +- src/src/core/stores/_impl/UnionSortedRandomSet.hpp | 2 src/src/core/stores/_impl/UniquePtrSortedRandomSet.hpp | 2 src/src/core/utils/CSVReader.cpp | 10 src/src/core/utils/CSVReader.hpp | 8 src/src/core/utils/Counter.hpp | 44 +- src/src/core/utils/NameIterator.cpp | 16 src/src/core/utils/NameIterator.hpp | 22 - src/src/core/utils/Stopwatch.hpp | 6 src/src/core/utils/hashing.hpp | 4 src/src/core/utils/math.ipp | 12 src/src/core/utils/random.cpp | 44 +- src/src/core/utils/random.hpp | 24 - src/src/core/utils/string.cpp | 2 src/src/core/utils/tuple.hpp | 10 src/src/core/utils/vector.cpp | 18 src/src/core/utils/vector.hpp | 10 src/src/core/utils/vector.ipp | 14 src/src/generation/ERModel.hpp | 4 src/src/generation/ERModel.ipp | 4 src/src/generation/PAModel.hpp | 8 src/src/generation/PAModel.ipp | 6 src/src/generation/communities.cpp | 58 +-- src/src/generation/communities.hpp | 28 - src/src/generation/erdos_renyi.cpp | 14 src/src/generation/erdos_renyi.hpp | 6 src/src/generation/evolve.hpp | 4 src/src/generation/evolve.ipp | 24 - src/src/generation/sample.ipp | 16 src/src/generation/standard_graphs.cpp | 22 - src/src/generation/standard_graphs.hpp | 20 - src/src/io/_impl/parser/mlpass1/actions.hpp | 4 src/src/io/_impl/parser/mlpass2/utility_functions.hpp | 8 src/src/io/_impl/read_common.cpp | 16 src/src/io/_impl/read_common.hpp | 38 +- src/src/io/_impl/write_common.hpp | 4 src/src/io/read_network.hpp | 4 src/src/measures/_impl/layer_utils.ipp | 4 src/src/measures/degree.hpp | 10 src/src/measures/degree.ipp | 34 - src/src/measures/degree_ml.hpp | 2 src/src/measures/degree_ml.ipp | 2 src/src/measures/distance.ipp | 22 - src/src/measures/order.hpp | 2 src/src/measures/order.ipp | 2 src/src/measures/size.hpp | 2 src/src/measures/size.ipp | 2 src/src/measures/strength.hpp | 4 src/src/networks/_impl/stores/EdgeStore.cpp | 4 src/src/networks/_impl/stores/EdgeStore.hpp | 4 src/src/networks/_impl/stores/LayerStore.cpp | 10 src/src/networks/_impl/stores/LayerStore.hpp | 8 src/src/networks/_impl/stores/MLECubeStore.cpp | 4 src/src/networks/_impl/stores/MLECubeStore.hpp | 2 src/src/networks/_impl/stores/VertexStore.cpp | 4 src/src/networks/_impl/stores/VertexStore.hpp | 4 src/src/objects/Dyad.cpp | 2 src/src/objects/Dyad.hpp | 4 src/src/objects/MultiplexClique.ipp | 16 src/src/objects/Path.hpp | 2 src/src/objects/PathLength.hpp | 6 src/src/objects/PathLength.ipp | 6 src/src/objects/Trail.hpp | 2 src/src/objects/Triad.cpp | 2 src/src/objects/Triad.hpp | 4 src/src/objects/Walk.cpp | 2 src/src/objects/Walk.hpp | 2 src/src/olap/ECube.cpp | 30 - src/src/olap/ECube.hpp | 28 - src/src/olap/MECube.cpp | 30 - src/src/olap/MECube.hpp | 28 - src/src/olap/MLCube.hpp | 64 +-- src/src/olap/MLCube.ipp | 122 +++--- src/src/olap/VCube.cpp | 34 - src/src/olap/VCube.hpp | 36 - src/src/olap/indexing.cpp | 12 src/src/olap/indexing.hpp | 6 src/src/olap/op/UniformDiscretization.hpp | 6 src/src/olap/op/UniformTemporalDiscretization.hpp | 6 src/src/olap/op/d-extension.ipp | 14 src/src/olap/op/slicing.hpp | 4 src/src/olap/op/slicing.ipp | 6 src/src/olap/sel/All.cpp | 4 src/src/olap/sel/All.hpp | 8 src/src/olap/sel/EntryIterator.hpp | 2 src/src/olap/sel/EntryIterator.ipp | 10 src/src/olap/sel/IndexIterator.cpp | 28 - src/src/olap/sel/IndexIterator.hpp | 26 - src/src/olap/sel/Indexes.cpp | 6 src/src/olap/sel/Indexes.hpp | 5 src/src/olap/sel/Range.cpp | 8 src/src/olap/sel/Range.hpp | 14 src/src/olap/sel/Set.cpp | 6 src/src/olap/sel/Set.hpp | 10 src/src/operations/_impl/add_predefined_subgraphs.hpp | 14 src/src/operations/_impl/add_predefined_subgraphs.ipp | 20 - src/src/operations/project.hpp | 2 src/src/operations/project.ipp | 4 src/src/operations/shuffle.hpp | 2 src/src/operations/shuffle.ipp | 6 src/src/operations/slice.cpp | 6 src/src/operations/slice.hpp | 2 src/src/utils/summary.cpp | 24 - 159 files changed, 1143 insertions(+), 1134 deletions(-)
Title: Design and Analyze Choice-Based Conjoint Experiments
Description: Design and evaluate choice-based conjoint survey experiments. Generate a variety of survey designs, including random designs, frequency-based designs, and D-optimal designs, as well as "labeled" designs (also known as "alternative-specific designs"), designs with "no choice" options, and designs with dominant alternatives removed. Conveniently inspect and compare designs using a variety of metrics, including design balance, overlap, and D-error, and simulate choice data for a survey design either randomly or according to a utility model defined by user-provided prior parameters. Conduct a power analysis for a given survey design by estimating the same model on different subsets of the data to simulate different sample sizes. Bayesian D-efficient designs using the 'cea' and 'modfed' methods are obtained using the 'idefix' package by Traets et al (2020) <doi:10.18637/jss.v096.i03>. Choice simulation and model estimation in power analyses are handled using the 'logitr' package by He [...truncated...]
Author: John Helveston [cre, aut, cph]
Maintainer: John Helveston <john.helveston@gmail.com>
Diff between cbcTools versions 0.6.3 dated 2025-08-21 and 0.6.4 dated 2025-09-23
DESCRIPTION | 6 MD5 | 36 +- NEWS.md | 5 R/choices.R | 1 R/design.R | 194 +++++++++++- R/design_greedy.R | 19 + R/input_checks.R | 53 +++ inst/CITATION | 2 inst/doc/choices.html | 7 inst/doc/design.R | 62 ++++ inst/doc/design.Rmd | 112 ++++++- inst/doc/design.html | 644 ++++++++++++++++++++++++------------------ inst/doc/getting-started.html | 205 ++++++------- inst/doc/power.html | 11 inst/doc/priors.html | 3 inst/doc/profiles.html | 1 man/cbc_design.Rd | 98 +++++- tests/testthat/test_design.R | 183 +++++++++++ vignettes/design.Rmd | 112 ++++++- 19 files changed, 1317 insertions(+), 437 deletions(-)
Title: Infrastructure for Computing with Basis Functions
Description: Some very simple infrastructure for basis functions.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between basefun versions 1.2-3 dated 2025-05-09 and 1.2-4 dated 2025-09-23
DESCRIPTION | 10 ++-- MD5 | 14 +++-- R/Bernstein.R | 103 +++++++++++++++++++++++++++---------------- build/partial.rdb |binary inst/NEWS.Rd | 10 ++++ man/Bernstein_basis.Rd | 5 +- tests/Bernstein-Ex.Rout.save | 12 ++--- tests/Rplots.pdf |only tests/bugfixes.R |only 9 files changed, 99 insertions(+), 55 deletions(-)
Title: Reads Fixed-Width ASCII Data Files (.txt or .dat) that Have
Accompanying Setup Files (.sps or .sas)
Description: Lets you open a fixed-width ASCII file (.txt or
.dat) that has an accompanying setup file (.sps or .sas). These file
combinations are sometimes referred to as .txt+.sps, .txt+.sas,
.dat+.sps, or .dat+.sas. This will only run in a txt-sps or txt-sas
pair in which the setup file contains instructions to open that text
file. It will NOT open other text files, .sav, .sas, or .por data
files. Fixed-width ASCII files with setup files are common in older
(pre-2000) government data.
Author: Jacob Kaplan [aut, cre]
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>
Diff between asciiSetupReader versions 2.5.2 dated 2024-08-16 and 2.5.3 dated 2025-09-23
DESCRIPTION | 11 +++++----- MD5 | 22 ++++++++++----------- NEWS.md | 4 +++ R/helper.R | 10 ++++----- R/parse_setup.R | 26 +++++++++++++++---------- R/read_ascii_setup.R | 4 +-- R/utils.R | 8 +++++-- build/vignette.rds |binary inst/doc/Introduction_to_asciiSetupReader.html | 7 +++--- inst/doc/making-an-sps-file.R | 12 +++++------ inst/doc/making-an-sps-file.html | 7 +++--- inst/doc/parsing-an-sps-or-sas-file.html | 7 +++--- 12 files changed, 68 insertions(+), 50 deletions(-)
More information about asciiSetupReader at CRAN
Permanent link
Title: Automatic Shift Detection using a Phylogenetic EM
Description: Implementation of the automatic shift detection method for
Brownian Motion (BM) or Ornstein–Uhlenbeck (OU) models of trait evolution on
phylogenies. Some tools to handle equivalent shifts configurations are also
available. See Bastide et al. (2017) <doi:10.1111/rssb.12206> and
Bastide et al. (2018) <doi:10.1093/sysbio/syy005>.
Author: Paul Bastide [aut, cre],
Mahendra Mariadassou [ctb]
Maintainer: Paul Bastide <paul.bastide@m4x.org>
Diff between PhylogeneticEM versions 1.8.0 dated 2025-02-14 and 1.8.1 dated 2025-09-23
DESCRIPTION | 6 - MD5 | 16 ++-- NEWS.md | 4 + build/vignette.rds |binary inst/doc/monkeys.R | 120 +++++++++++++++++------------------ inst/doc/monkeys.html | 162 +++++++++++++++++++++++++----------------------- inst/doc/tutorial.R | 38 +++++------ inst/doc/tutorial.html | 9 +- src/upward_downward.cpp | 2 9 files changed, 187 insertions(+), 170 deletions(-)
More information about PhylogeneticEM at CRAN
Permanent link
Title: Generalised Additive Extreme Value Models
Description: Methods for fitting various extreme value distributions with parameters of
generalised additive model (GAM) form are provided. For details of distributions
see Coles, S.G. (2001) <doi:10.1007/978-1-4471-3675-0>, GAMs see Wood, S.N. (2017)
<doi:10.1201/9781315370279>, and the fitting approach see Wood, S.N., Pya, N. &
Safken, B. (2016) <doi:10.1080/01621459.2016.1180986>. Details of how evgam works
and various examples are given in Youngman, B.D. (2022) <doi:10.18637/jss.v103.i03>.
Author: Ben Youngman [aut, cre]
Maintainer: Ben Youngman <b.youngman@exeter.ac.uk>
Diff between evgam versions 1.0.0 dated 2022-06-28 and 1.0.1 dated 2025-09-23
DESCRIPTION | 18 +++++++++++------- MD5 | 14 +++++++------- NEWS.md | 6 ++++++ R/generic.R | 4 ++-- build/partial.rdb |binary man/colplot.Rd | 4 ++-- src/Makevars | 14 +------------- src/Makevars.win | 14 +------------- 8 files changed, 30 insertions(+), 44 deletions(-)
Title: Non-Linear Dimensionality Reduction Visualization Tool
Description: A 'shiny' application for visualizing high-dimensional data
using non-linear dimensionality reduction (NLDR) techniques such as
t-SNE and UMAP. It provides an interactive platform to explore
high-dimensional datasets, diagnose the quality of the embeddings
using the 'quollr' package, and compare different NLDR methods.
Author: Divendra Yadav [aut, cre],
Ursula Laa [aut] ,
Jayani P. Gamage [aut] ,
Eun-Kyung Lee [aut]
Maintainer: Divendra Yadav <divendrasinghyadaviit@gmail.com>
Diff between polarisR versions 0.1.3 dated 2025-09-15 and 0.1.4 dated 2025-09-23
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NAMESPACE | 2 +- NEWS.md | 2 ++ R/server.R | 6 +++--- tests/testthat/test-app.R | 1 + 6 files changed, 15 insertions(+), 12 deletions(-)
Title: Order Constrained Solutions in k-Means Clustering
Description: Extends 'flexclust' with an R implementation of order constrained
solutions in k-means clustering (Steinley and Hubert, 2008, <doi:10.1007/s11336-008-9058-z>).
Author: Sebastian Krey [aut, cre],
Friedrich Leisch [aut],
Sebastian Hoffmeister [ctb]
Maintainer: Sebastian Krey <sebastian.dev@skrey.net>
Diff between ockc versions 1.1 dated 2022-12-23 and 1.1.1 dated 2025-09-23
DESCRIPTION | 20 ++++++++++---------- MD5 | 8 ++++---- NAMESPACE | 1 + man/bootockc.Rd | 4 ++-- man/ockc.Rd | 4 ++-- 5 files changed, 19 insertions(+), 18 deletions(-)
Title: Import, Manipulate and Explore the Results of an 'Antares'
Simulation
Description: Import, manipulate and explore results generated by 'Antares', a
powerful open source software developed by RTE (Réseau de Transport d’Électricité) to simulate and study electric power systems
(more information about 'Antares' here : <https://antares-simulator.org/>).
Author: Tatiana Vargas [aut, cre],
Jalal-Edine ZAWAM [aut],
Frederic Breant [ctb],
Francois Guillem [aut],
Benoit Thieurmel [aut],
Titouan Robert [aut],
Victor Perrier [ctb],
Etienne Sanchez [ctb],
Assil Mansouri [ctb],
Clement Berthet [ctb],
Kamel Kemiha [c [...truncated...]
Maintainer: Tatiana Vargas <tatiana.vargas@rte-france.com>
Diff between antaresRead versions 2.9.0 dated 2025-02-11 and 2.9.2 dated 2025-09-23
antaresRead-2.9.0/antaresRead/inst/referential_properties/properties_input_renewable.csv |only antaresRead-2.9.0/antaresRead/inst/referential_properties/properties_input_storage.csv |only antaresRead-2.9.0/antaresRead/inst/referential_properties/properties_input_storage_test.csv |only antaresRead-2.9.0/antaresRead/inst/referential_properties/properties_input_thermal.csv |only antaresRead-2.9.2/antaresRead/DESCRIPTION | 8 antaresRead-2.9.2/antaresRead/LICENSE | 2 antaresRead-2.9.2/antaresRead/MD5 | 304 antaresRead-2.9.2/antaresRead/NAMESPACE | 245 antaresRead-2.9.2/antaresRead/NEWS.md | 1429 +-- antaresRead-2.9.2/antaresRead/R/API-methods.R | 438 antaresRead-2.9.2/antaresRead/R/aggregateResult.R | 4434 +++++----- antaresRead-2.9.2/antaresRead/R/antaresRead-package.R | 14 antaresRead-2.9.2/antaresRead/R/asAntaresDataList.R | 140 antaresRead-2.9.2/antaresRead/R/asAntaresDataTable.R | 102 antaresRead-2.9.2/antaresRead/R/changeTimeStep.R | 410 antaresRead-2.9.2/antaresRead/R/copyToClipboard.R | 172 antaresRead-2.9.2/antaresRead/R/digest.R | 296 antaresRead-2.9.2/antaresRead/R/extractDataList.R | 206 antaresRead-2.9.2/antaresRead/R/getAreas.R | 186 antaresRead-2.9.2/antaresRead/R/getGeographicTrimming.R | 98 antaresRead-2.9.2/antaresRead/R/getLinks.R | 254 antaresRead-2.9.2/antaresRead/R/getNtcOutput.R | 48 antaresRead-2.9.2/antaresRead/R/giveSize.R | 500 - antaresRead-2.9.2/antaresRead/R/groupByDistrict.R | 170 antaresRead-2.9.2/antaresRead/R/hvdcModification.R | 226 antaresRead-2.9.2/antaresRead/R/importInput.R | 1049 +- antaresRead-2.9.2/antaresRead/R/importOutput.R | 2448 +++-- antaresRead-2.9.2/antaresRead/R/ponderateMcAggregation.R | 84 antaresRead-2.9.2/antaresRead/R/readAntares.R | 1920 ++-- antaresRead-2.9.2/antaresRead/R/readAntaresClusters.R | 182 antaresRead-2.9.2/antaresRead/R/readBindingConstraints.R | 788 - antaresRead-2.9.2/antaresRead/R/readClusterDesc.R | 658 - antaresRead-2.9.2/antaresRead/R/readIniFile.R | 330 antaresRead-2.9.2/antaresRead/R/readInputClusters.R | 498 - antaresRead-2.9.2/antaresRead/R/readInputTS.R | 390 antaresRead-2.9.2/antaresRead/R/readLayout.R | 374 antaresRead-2.9.2/antaresRead/R/read_st_constraints.R |only antaresRead-2.9.2/antaresRead/R/removeVirtualAreas.R | 1284 +- antaresRead-2.9.2/antaresRead/R/reorderCols.R | 100 antaresRead-2.9.2/antaresRead/R/setHvdcAreas.R | 110 antaresRead-2.9.2/antaresRead/R/setSimulationPath.R | 1439 +-- antaresRead-2.9.2/antaresRead/R/setSimulationPathAPI.R | 1036 +- antaresRead-2.9.2/antaresRead/R/showAliases.R | 196 antaresRead-2.9.2/antaresRead/R/simOptions.R | 118 antaresRead-2.9.2/antaresRead/R/subset.R | 264 antaresRead-2.9.2/antaresRead/R/thematic_trimming.R |only antaresRead-2.9.2/antaresRead/R/utils.R | 12 antaresRead-2.9.2/antaresRead/R/utils_api.R | 194 antaresRead-2.9.2/antaresRead/R/viewAntares.R | 108 antaresRead-2.9.2/antaresRead/R/zzz.R | 365 antaresRead-2.9.2/antaresRead/build/vignette.rds |binary antaresRead-2.9.2/antaresRead/inst/API/demo_api.R | 414 antaresRead-2.9.2/antaresRead/inst/API/demo_api_enr.R | 388 antaresRead-2.9.2/antaresRead/inst/ENR_cluster/test_clusters_enr.R | 184 antaresRead-2.9.2/antaresRead/inst/doc/antaresRead.Rmd | 316 antaresRead-2.9.2/antaresRead/inst/doc/antaresRead.html | 1028 +- antaresRead-2.9.2/antaresRead/inst/format_output/h5Struct.csv | 522 - antaresRead-2.9.2/antaresRead/inst/format_output/simulation_variables_names_by_support.csv | 20 antaresRead-2.9.2/antaresRead/inst/format_output/tableOutput.csv | 502 - antaresRead-2.9.2/antaresRead/inst/format_output/tableOutput_aggreg.csv | 594 - antaresRead-2.9.2/antaresRead/inst/format_output/tableOutput_aggreg_v8.csv | 674 - antaresRead-2.9.2/antaresRead/inst/referential_properties/cluster_properties.csv |only antaresRead-2.9.2/antaresRead/inst/test_files/antares_version_files/antares_version_float.antares | 12 antaresRead-2.9.2/antaresRead/inst/test_files/antares_version_files/antares_version_float_2digit.antares | 12 antaresRead-2.9.2/antaresRead/inst/variables_selection |only antaresRead-2.9.2/antaresRead/man/API-methods.Rd | 139 antaresRead-2.9.2/antaresRead/man/aggregatate_mc_all.Rd | 130 antaresRead-2.9.2/antaresRead/man/antaresRead-package.Rd | 90 antaresRead-2.9.2/antaresRead/man/as.antaresDataList.Rd | 98 antaresRead-2.9.2/antaresRead/man/as.antaresDataTable.Rd | 70 antaresRead-2.9.2/antaresRead/man/changeTimeStep.Rd | 104 antaresRead-2.9.2/antaresRead/man/copyToClipboard.Rd | 88 antaresRead-2.9.2/antaresRead/man/dot-download_api_aggregate_result.Rd |only antaresRead-2.9.2/antaresRead/man/dot-filter_bindingConstraints_by_names.Rd |only antaresRead-2.9.2/antaresRead/man/dot-transform_antares_version.Rd | 36 antaresRead-2.9.2/antaresRead/man/dot-writeIni.Rd | 58 antaresRead-2.9.2/antaresRead/man/extractDataList.Rd | 56 antaresRead-2.9.2/antaresRead/man/figures/badge_api_no.svg | 38 antaresRead-2.9.2/antaresRead/man/figures/badge_api_ok.svg | 38 antaresRead-2.9.2/antaresRead/man/getAreas.Rd | 128 antaresRead-2.9.2/antaresRead/man/getGeographicTrimming.Rd | 42 antaresRead-2.9.2/antaresRead/man/getLinks.Rd | 178 antaresRead-2.9.2/antaresRead/man/getThematicTrimming.Rd |only antaresRead-2.9.2/antaresRead/man/hvdcModification.Rd | 64 antaresRead-2.9.2/antaresRead/man/list_thematic_variables.Rd |only antaresRead-2.9.2/antaresRead/man/mergeDigests.Rd | 46 antaresRead-2.9.2/antaresRead/man/ponderateMcAggregation.Rd | 60 antaresRead-2.9.2/antaresRead/man/read-ini.Rd | 122 antaresRead-2.9.2/antaresRead/man/readAntares.Rd | 476 - antaresRead-2.9.2/antaresRead/man/readAntaresAreas.Rd | 118 antaresRead-2.9.2/antaresRead/man/readAntaresClusters.Rd | 74 antaresRead-2.9.2/antaresRead/man/readAntaresSTClusters.Rd | 74 antaresRead-2.9.2/antaresRead/man/readBindingConstraints.Rd | 160 antaresRead-2.9.2/antaresRead/man/readClusterDesc.Rd | 198 antaresRead-2.9.2/antaresRead/man/readDigestFile.Rd | 40 antaresRead-2.9.2/antaresRead/man/readInputRES.Rd | 96 antaresRead-2.9.2/antaresRead/man/readInputTS.Rd | 234 antaresRead-2.9.2/antaresRead/man/readInputThermal.Rd | 128 antaresRead-2.9.2/antaresRead/man/readLayout.Rd | 100 antaresRead-2.9.2/antaresRead/man/readOptimCriteria.Rd | 62 antaresRead-2.9.2/antaresRead/man/read_storages_constraints.Rd |only antaresRead-2.9.2/antaresRead/man/removeVirtualAreas.Rd | 338 antaresRead-2.9.2/antaresRead/man/setAlias.Rd | 122 antaresRead-2.9.2/antaresRead/man/setHvdcAreas.Rd | 64 antaresRead-2.9.2/antaresRead/man/setSimulationPath.Rd | 408 antaresRead-2.9.2/antaresRead/man/setTimeoutAPI.Rd | 54 antaresRead-2.9.2/antaresRead/man/simOptions.Rd | 102 antaresRead-2.9.2/antaresRead/man/subset.antaresDataList.Rd | 100 antaresRead-2.9.2/antaresRead/man/summary.bindingConstraints.Rd | 40 antaresRead-2.9.2/antaresRead/man/viewAntares.Rd | 66 antaresRead-2.9.2/antaresRead/man/writeDigest.Rd | 46 antaresRead-2.9.2/antaresRead/tests/testthat.R | 34 antaresRead-2.9.2/antaresRead/tests/testthat/helper_init.R | 262 antaresRead-2.9.2/antaresRead/tests/testthat/test-.timeIdToDate.R | 118 antaresRead-2.9.2/antaresRead/tests/testthat/test-API.R | 46 antaresRead-2.9.2/antaresRead/tests/testthat/test-RemoveInputColumn.R | 88 antaresRead-2.9.2/antaresRead/tests/testthat/test-aggregateResult.R | 72 antaresRead-2.9.2/antaresRead/tests/testthat/test-aliases.R | 86 antaresRead-2.9.2/antaresRead/tests/testthat/test-asAntaresData.R | 140 antaresRead-2.9.2/antaresRead/tests/testthat/test-changeTimeStep.R | 102 antaresRead-2.9.2/antaresRead/tests/testthat/test-digest.R | 70 antaresRead-2.9.2/antaresRead/tests/testthat/test-extractDataList.R | 78 antaresRead-2.9.2/antaresRead/tests/testthat/test-getAreas.R | 106 antaresRead-2.9.2/antaresRead/tests/testthat/test-getGeographicTrimming.R | 30 antaresRead-2.9.2/antaresRead/tests/testthat/test-getLinks.R | 50 antaresRead-2.9.2/antaresRead/tests/testthat/test-getStartDate.R | 274 antaresRead-2.9.2/antaresRead/tests/testthat/test-giveSize.R | 348 antaresRead-2.9.2/antaresRead/tests/testthat/test-groupByDistrict.R | 50 antaresRead-2.9.2/antaresRead/tests/testthat/test-hvdcModification.R | 62 antaresRead-2.9.2/antaresRead/tests/testthat/test-importOutputForClusters.R | 237 antaresRead-2.9.2/antaresRead/tests/testthat/test-mcaggreg.R | 110 antaresRead-2.9.2/antaresRead/tests/testthat/test-opts-api.R | 80 antaresRead-2.9.2/antaresRead/tests/testthat/test-ponderate.R | 110 antaresRead-2.9.2/antaresRead/tests/testthat/test-ponderateMcAggregation.R | 26 antaresRead-2.9.2/antaresRead/tests/testthat/test-print.R | 86 antaresRead-2.9.2/antaresRead/tests/testthat/test-readAntares.R | 503 - antaresRead-2.9.2/antaresRead/tests/testthat/test-readAntaresClusters.R | 64 antaresRead-2.9.2/antaresRead/tests/testthat/test-readAntares_STclusters.R | 106 antaresRead-2.9.2/antaresRead/tests/testthat/test-readAntares_bc.R | 32 antaresRead-2.9.2/antaresRead/tests/testthat/test-readAntares_districts.R | 74 antaresRead-2.9.2/antaresRead/tests/testthat/test-readAntares_inputs.R | 128 antaresRead-2.9.2/antaresRead/tests/testthat/test-readAntares_mustRun.R | 154 antaresRead-2.9.2/antaresRead/tests/testthat/test-readAntares_time_columns.R | 64 antaresRead-2.9.2/antaresRead/tests/testthat/test-readBindingConstraints.R | 559 - antaresRead-2.9.2/antaresRead/tests/testthat/test-readClusterDesc.R | 755 - antaresRead-2.9.2/antaresRead/tests/testthat/test-readIni.R | 48 antaresRead-2.9.2/antaresRead/tests/testthat/test-readInputAPI.R | 38 antaresRead-2.9.2/antaresRead/tests/testthat/test-readInputClusters.R | 242 antaresRead-2.9.2/antaresRead/tests/testthat/test-readInputTS.R | 379 antaresRead-2.9.2/antaresRead/tests/testthat/test-readLayout.R | 84 antaresRead-2.9.2/antaresRead/tests/testthat/test-read_optim_criteria.R | 34 antaresRead-2.9.2/antaresRead/tests/testthat/test-read_st_constraints.R |only antaresRead-2.9.2/antaresRead/tests/testthat/test-removeVirtualAreas.R | 976 +- antaresRead-2.9.2/antaresRead/tests/testthat/test-setHvdcAreas.R | 48 antaresRead-2.9.2/antaresRead/tests/testthat/test-setSimulationPath.R | 558 - antaresRead-2.9.2/antaresRead/tests/testthat/test-subset_antaresDataList.R | 158 antaresRead-2.9.2/antaresRead/tests/testthat/test-thematic_timming.R |only antaresRead-2.9.2/antaresRead/tests/testthat/test-viewAntares.R | 90 antaresRead-2.9.2/antaresRead/vignettes/antaresRead.Rmd | 316 159 files changed, 21260 insertions(+), 19795 deletions(-)
Title: Hierarchical Multinomial Processing Tree Modeling
Description: User-friendly analysis of hierarchical multinomial processing tree (MPT)
models that are often used in cognitive psychology. Implements the latent-trait
MPT approach (Klauer, 2010) <DOI:10.1007/s11336-009-9141-0> and the beta-MPT
approach (Smith & Batchelder, 2010) <DOI:10.1016/j.jmp.2009.06.007> to model
heterogeneity of participants. MPT models are conveniently specified by an
.eqn-file as used by other MPT software and data are provided by a .csv-file
or directly in R. Models are either fitted by calling JAGS or by an MPT-tailored
Gibbs sampler in C++ (only for nonhierarchical and beta MPT models). Provides
tests of heterogeneity and MPT-tailored summaries and plotting functions.
A detailed documentation is available in Heck, Arnold, & Arnold (2018)
<DOI:10.3758/s13428-017-0869-7> and a tutorial on MPT modeling can be found
in Schmidt, Erdfelder, & Heck (2023) <DOI:10.1037/met0000561>.
Author: Daniel W. Heck [aut, cre] ,
Nina R. Arnold [aut, dtc],
Denis Arnold [aut],
Alexander Ly [ctb],
Marius Barth [ctb]
Maintainer: Daniel W. Heck <daniel.heck@uni-marburg.de>
Diff between TreeBUGS versions 1.5.0 dated 2023-05-21 and 1.5.3 dated 2025-09-23
DESCRIPTION | 21 - MD5 | 116 +++---- NEWS | 23 + R/BF_Rao_Blackwell.R | 12 R/TreeBUGS-package.R | 9 R/covariateHandling.R | 2 R/fitBetaMPT.R | 12 R/fitModel.R | 1 R/genDataBeta.R | 2 R/genDataMPT.R | 3 R/genDataTrait.R | 4 R/priorPredictive.R | 4 R/readEQN.R | 26 + R/thetaHandling.R | 31 + R/within_subject_EQN.R | 3 build/partial.rdb |binary build/vignette.rds |binary inst/doc/TreeBUGS_1_intro.R | 132 ++++---- inst/doc/TreeBUGS_1_intro.html | 113 +++---- inst/doc/TreeBUGS_2_extended.R | 94 ++--- inst/doc/TreeBUGS_2_extended.html | 89 ++--- man/BayesFactorMPT.Rd | 126 +++---- man/BayesFactorSlope.Rd | 154 ++++----- man/PPP.Rd | 66 ++-- man/TreeBUGS-package.Rd | 173 +++++----- man/arnold2013.Rd | 136 ++++---- man/betaMPT.Rd | 384 ++++++++++++------------ man/betaMPTcpp.Rd | 215 ++++++------- man/betweenSubjectMPT.Rd | 100 +++--- man/correlationPosterior.Rd | 176 +++++------ man/extendMPT.Rd | 66 ++-- man/genBetaMPT.Rd | 180 +++++------ man/genMPT.Rd | 116 +++---- man/genTraitMPT.Rd | 218 ++++++------- man/getGroupMeans.Rd | 92 ++--- man/getParam.Rd | 130 ++++---- man/getSamples.Rd | 72 ++-- man/marginalMPT.Rd | 276 ++++++++--------- man/plot.Rd | 100 +++--- man/plotDistribution.Rd | 68 ++-- man/plotFit.Rd | 80 ++--- man/plotFreq.Rd | 78 ++-- man/plotParam.Rd | 94 ++--- man/plotPrior.Rd | 122 +++---- man/plotPriorPost.Rd | 80 ++--- man/posteriorPredictive.Rd | 78 ++-- man/priorPredictive.Rd | 196 ++++++------ man/probitInverse.Rd | 78 ++-- man/readEQN.Rd | 185 ++++++----- man/simpleMPT.Rd | 195 ++++++------ man/summarizeMCMC.Rd | 40 +- man/summarizeMPT.Rd | 74 ++-- man/testHetChi.Rd | 124 +++---- man/testHetPerm.Rd | 150 ++++----- man/traitMPT.Rd | 604 +++++++++++++++++++------------------- man/transformedParameters.Rd | 88 ++--- man/withinSubjectEQN.Rd | 72 ++-- src/loglikMPT.cpp | 2 tests/testthat/test_readEQN.R | 34 +- 59 files changed, 3020 insertions(+), 2899 deletions(-)
Title: Fast Numerical Maximum Likelihood Estimation for Latent Markov
Models
Description: A variety of latent Markov models, including hidden Markov models, hidden semi-Markov models,
state-space models and continuous-time variants can be formulated and estimated within the same framework via directly maximising the likelihood function using the so-called forward algorithm.
Applied researchers often need custom models that standard software does not easily support.
Writing tailored 'R' code offers flexibility but suffers from slow estimation speeds.
We address these issues by providing easy-to-use functions (written in 'C++' for speed) for common tasks like the forward algorithm.
These functions can be combined into custom models in a Lego-type approach, offering up to 10-20 times faster estimation via standard numerical optimisers.
To aid in building fully custom likelihood functions, several vignettes are included that show how to simulate data from and estimate all the above model classes.
Author: Jan-Ole Koslik [aut, cre]
Maintainer: Jan-Ole Koslik <jan-ole.koslik@uni-bielefeld.de>
Diff between LaMa versions 2.0.5 dated 2025-06-15 and 2.0.6 dated 2025-09-23
LaMa-2.0.5/LaMa/vignettes/HSMMs_cache/html/model_muskox_f3388cfcf3579d554d515d003a6bde36.RData |only LaMa-2.0.5/LaMa/vignettes/HSMMs_cache/html/model_muskox_f3388cfcf3579d554d515d003a6bde36.rdb |only LaMa-2.0.5/LaMa/vignettes/HSMMs_cache/html/model_muskox_f3388cfcf3579d554d515d003a6bde36.rdx |only LaMa-2.0.5/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_7055ee4d964897bc47f386deee196cab.RData |only LaMa-2.0.5/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_7055ee4d964897bc47f386deee196cab.rdb |only LaMa-2.0.5/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_7055ee4d964897bc47f386deee196cab.rdx |only LaMa-2.0.5/LaMa/vignettes/State_space_models_cache/html/model_47c192ff81378d536c0ad61d2162b11c.RData |only LaMa-2.0.5/LaMa/vignettes/State_space_models_cache/html/model_47c192ff81378d536c0ad61d2162b11c.rdb |only LaMa-2.0.5/LaMa/vignettes/State_space_models_cache/html/model_47c192ff81378d536c0ad61d2162b11c.rdx |only LaMa-2.0.6/LaMa/DESCRIPTION | 6 LaMa-2.0.6/LaMa/MD5 | 148 +- LaMa-2.0.6/LaMa/NAMESPACE | 9 LaMa-2.0.6/LaMa/R/RcppExports.R | 4 LaMa-2.0.6/LaMa/R/decoding_functions.R | 15 LaMa-2.0.6/LaMa/R/forward_algorithms.R | 186 ++- LaMa-2.0.6/LaMa/R/helper_functions.R | 117 ++ LaMa-2.0.6/LaMa/R/model_matrix_functions.R | 564 +++++++++- LaMa-2.0.6/LaMa/R/qreml_functions.R | 422 ++++--- LaMa-2.0.6/LaMa/R/residual_functions.R | 26 LaMa-2.0.6/LaMa/R/sdreportMC.R | 44 LaMa-2.0.6/LaMa/R/tpm_functions.R | 219 +++ LaMa-2.0.6/LaMa/inst/doc/Continuous_time_HMMs.Rmd | 4 LaMa-2.0.6/LaMa/inst/doc/Continuous_time_HMMs.html | 16 LaMa-2.0.6/LaMa/inst/doc/HSMMs.Rmd | 2 LaMa-2.0.6/LaMa/inst/doc/HSMMs.html | 12 LaMa-2.0.6/LaMa/inst/doc/Inhomogeneous_HMMs.Rmd | 4 LaMa-2.0.6/LaMa/inst/doc/Inhomogeneous_HMMs.html | 18 LaMa-2.0.6/LaMa/inst/doc/Intro_to_LaMa.R | 8 LaMa-2.0.6/LaMa/inst/doc/Intro_to_LaMa.Rmd | 13 LaMa-2.0.6/LaMa/inst/doc/Intro_to_LaMa.html | 29 LaMa-2.0.6/LaMa/inst/doc/LaMa_and_RTMB.R | 11 LaMa-2.0.6/LaMa/inst/doc/LaMa_and_RTMB.Rmd | 17 LaMa-2.0.6/LaMa/inst/doc/LaMa_and_RTMB.html | 36 LaMa-2.0.6/LaMa/inst/doc/Longitudinal_data.Rmd | 2 LaMa-2.0.6/LaMa/inst/doc/Longitudinal_data.html | 16 LaMa-2.0.6/LaMa/inst/doc/MMMPPs.Rmd | 2 LaMa-2.0.6/LaMa/inst/doc/MMMPPs.html | 14 LaMa-2.0.6/LaMa/inst/doc/Penalised_splines.R | 14 LaMa-2.0.6/LaMa/inst/doc/Penalised_splines.Rmd | 14 LaMa-2.0.6/LaMa/inst/doc/Penalised_splines.html | 109 - LaMa-2.0.6/LaMa/inst/doc/Periodic_HMMs.Rmd | 5 LaMa-2.0.6/LaMa/inst/doc/Periodic_HMMs.html | 17 LaMa-2.0.6/LaMa/inst/doc/State_space_models.Rmd | 2 LaMa-2.0.6/LaMa/inst/doc/State_space_models.html | 10 LaMa-2.0.6/LaMa/man/forward_g.Rd | 2 LaMa-2.0.6/LaMa/man/gdeterminant.Rd | 2 LaMa-2.0.6/LaMa/man/generator.Rd | 1 LaMa-2.0.6/LaMa/man/grapes-sp-grapes.Rd |only LaMa-2.0.6/LaMa/man/make_matrices.Rd | 27 LaMa-2.0.6/LaMa/man/make_matrices_old.Rd |only LaMa-2.0.6/LaMa/man/minmax0_smooth.Rd |only LaMa-2.0.6/LaMa/man/penalty_uni.Rd |only LaMa-2.0.6/LaMa/man/plot.LaMaResiduals.Rd | 1 LaMa-2.0.6/LaMa/man/pred_matrix.Rd | 14 LaMa-2.0.6/LaMa/man/predict.LaMa_matrices.Rd | 17 LaMa-2.0.6/LaMa/man/process_hid_formulas.Rd |only LaMa-2.0.6/LaMa/man/pseudo_res.Rd | 12 LaMa-2.0.6/LaMa/man/qreml.Rd | 20 LaMa-2.0.6/LaMa/man/sdreportMC.Rd | 15 LaMa-2.0.6/LaMa/man/tpm.Rd | 1 LaMa-2.0.6/LaMa/man/tpm_cont.Rd | 1 LaMa-2.0.6/LaMa/man/tpm_emb.Rd | 1 LaMa-2.0.6/LaMa/man/tpm_emb_g.Rd | 1 LaMa-2.0.6/LaMa/man/tpm_g.Rd | 5 LaMa-2.0.6/LaMa/man/tpm_g2.Rd |only LaMa-2.0.6/LaMa/man/tpm_p.Rd | 3 LaMa-2.0.6/LaMa/src/RcppExports.cpp | 15 LaMa-2.0.6/LaMa/src/tpm_functions.cpp | 48 LaMa-2.0.6/LaMa/vignettes/Continuous_time_HMMs.Rmd | 4 LaMa-2.0.6/LaMa/vignettes/HSMMs.Rmd | 2 LaMa-2.0.6/LaMa/vignettes/HSMMs_cache/html/model_muskox_db5ee275b887b10204620537cc278451.RData |only LaMa-2.0.6/LaMa/vignettes/HSMMs_cache/html/model_muskox_db5ee275b887b10204620537cc278451.rdb |only LaMa-2.0.6/LaMa/vignettes/HSMMs_cache/html/model_muskox_db5ee275b887b10204620537cc278451.rdx |only LaMa-2.0.6/LaMa/vignettes/Inhomogeneous_HMMs.Rmd | 4 LaMa-2.0.6/LaMa/vignettes/Intro_to_LaMa.Rmd | 13 LaMa-2.0.6/LaMa/vignettes/LaMa_and_RTMB.Rmd | 17 LaMa-2.0.6/LaMa/vignettes/Longitudinal_data.Rmd | 2 LaMa-2.0.6/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_381c8978531f280149019df595b45f34.RData |only LaMa-2.0.6/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_381c8978531f280149019df595b45f34.rdb |only LaMa-2.0.6/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_381c8978531f280149019df595b45f34.rdx |only LaMa-2.0.6/LaMa/vignettes/MMMPPs.Rmd | 2 LaMa-2.0.6/LaMa/vignettes/Penalised_splines.Rmd | 14 LaMa-2.0.6/LaMa/vignettes/Periodic_HMMs.Rmd | 5 LaMa-2.0.6/LaMa/vignettes/State_space_models.Rmd | 2 LaMa-2.0.6/LaMa/vignettes/State_space_models_cache/html/model_39a632569c8d52d92ef4aa54d3616054.RData |only LaMa-2.0.6/LaMa/vignettes/State_space_models_cache/html/model_39a632569c8d52d92ef4aa54d3616054.rdb |only LaMa-2.0.6/LaMa/vignettes/State_space_models_cache/html/model_39a632569c8d52d92ef4aa54d3616054.rdx |only 87 files changed, 1762 insertions(+), 624 deletions(-)
Title: Elastic Functional Data Analysis
Description: Performs alignment, PCA, and modeling of multidimensional and
unidimensional functions using the square-root velocity framework
(Srivastava et al., 2011 <doi:10.48550/arXiv.1103.3817> and Tucker et al., 2014
<DOI:10.1016/j.csda.2012.12.001>). This framework allows for elastic
analysis of functional data through phase and amplitude separation.
Author: J. Derek Tucker [aut, cre] ,
Aymeric Stamm [ctb]
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between fdasrvf versions 2.4.0 dated 2025-06-27 and 2.4.1 dated 2025-09-23
DESCRIPTION | 10 +++++----- MD5 | 19 +++++++++++-------- NAMESPACE | 2 ++ NEWS.md | 6 ++++++ R/SqrtMedian.R | 16 ++++++++++++++-- R/horizFPNS.R |only R/plot.hfpns.R |only R/utils-pointwise.R | 2 +- R/utils.R | 8 ++++++++ README.md | 2 +- man/horizFPNS.Rd |only src/bayesian.cpp | 6 ++++-- 12 files changed, 52 insertions(+), 19 deletions(-)
Title: Analyzing Data with Cellwise Outliers
Description: Tools for detecting cellwise outliers and robust methods to analyze
data which may contain them. Contains the implementation of the algorithms described in
Rousseeuw and Van den Bossche (2018) <doi:10.1080/00401706.2017.1340909> (open access)
Hubert et al. (2019) <doi:10.1080/00401706.2018.1562989> (open access),
Raymaekers and Rousseeuw (2021) <doi:10.1080/00401706.2019.1677270> (open access),
Raymaekers and Rousseeuw (2021) <doi:10.1007/s10994-021-05960-5> (open access),
Raymaekers and Rousseeuw (2021) <doi:10.52933/jdssv.v1i3.18> (open access),
Raymaekers and Rousseeuw (2022) <doi:10.1080/01621459.2023.2267777> (open access)
Rousseeuw (2022) <doi:10.1016/j.ecosta.2023.01.007> (open access).
Examples can be found in the vignettes:
"DDC_examples", "MacroPCA_examples", "wrap_examples", "transfo_examples",
"DI_examples", "cellMCD_examples" , "Correspondence_analysis_examples",
and "cellwise_weights_examples".
Author: Jakob Raymaekers [aut, cre],
Peter Rousseeuw [aut],
Wannes Van den Bossche [ctb],
Mia Hubert [ctb]
Maintainer: Jakob Raymaekers <jakob.raymaekers@kuleuven.be>
Diff between cellWise versions 2.5.3 dated 2023-10-25 and 2.5.4 dated 2025-09-23
DESCRIPTION | 10 MD5 | 36 - R/cellHandler.R | 27 - R/cellMCD.R | 56 +- R/generateData.R | 7 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Correspondence_analysis_examples.html | 213 +++----- inst/doc/DDC_examples.html | 249 ++++----- inst/doc/DI_examples.html | 233 +++----- inst/doc/MacroPCA_examples.html | 247 ++++----- inst/doc/cellMCD_examples.R | 8 inst/doc/cellMCD_examples.html | 649 ++++++++++++------------- inst/doc/cellwise_weights_examples.html | 203 +++---- inst/doc/transfo_examples.html | 229 +++----- inst/doc/wrap_examples.html | 207 +++---- man/cellMCD.Rd | 4 src/LocScaleEstimators.cpp | 16 src/Main.cpp | 8 19 files changed, 1111 insertions(+), 1291 deletions(-)
Title: Analysis the Weather Data
Description: Functions are collected to analyse weather data for agriculture
purposes including to read weather records in multiple formats,
calculate extreme climate index. Demonstration data are included the
SILO daily climate data (licensed under CC BY 4.0, <https://www.longpaddock.qld.gov.au/silo/>).
Author: Bangyou Zheng [aut, cre]
Maintainer: Bangyou Zheng <bangyou.zheng@csiro.au>
Diff between weaana versions 0.1.1 dated 2021-09-27 and 0.3.0 dated 2025-09-23
DESCRIPTION | 18 MD5 | 55 NAMESPACE | 12 R/add_rh.R |only R/changeWeatherRecords.R | 1 R/climate_by_stage.R |only R/dew_point.R |only R/fileList.R | 112 R/mov.r | 207 - R/readWeatherRecords.r | 129 R/thermalTime.R | 4 R/thermaltime_hourly.R |only R/wcal.R | 290 - R/writeWeatherRecords.R | 51 README.md | 9 build |only inst/doc |only inst/extdata/README_extdata.txt |only inst/extdata/WeatherRecordsDemo1.met | 5117 ------------------------------- inst/extdata/WeatherRecordsDemo2.met | 5113 ------------------------------ inst/extdata/drill_-35_147.txt |only inst/extdata/ppd_72150.met |only inst/extdata/ppd_72150.txt |only man/add_rh.Rd |only man/climate_by_stages.Rd |only man/dp_mint.Rd |only man/mov.Rd |only man/mov.avg.Rd |only man/mov.max.Rd |only man/mov.min.Rd |only man/mov.sum.Rd |only man/tt_hourly_pp.Rd |only man/wcal-methods.Rd |only tests/testthat/test-add_rh.R |only tests/testthat/test-climate_by_stage.R |only tests/testthat/test-dew_point.R |only tests/testthat/test-readWeatherRecords.R | 19 tests/testthat/test-thermalTime.R | 10 tests/testthat/test-thermaltime_hourly.R |only vignettes |only 40 files changed, 561 insertions(+), 10586 deletions(-)
Title: Loading Screen for 'Shiny'
Description: Full screen and partial loading screens for 'Shiny' with spinners, progress bars, and notifications.
Author: John Coene [aut, cre],
Jinhwan Kim [ctb],
Victor Granda [ctb]
Maintainer: John Coene <jcoenep@gmail.com>
Diff between waiter versions 0.2.5 dated 2022-01-03 and 0.2.5.1 dated 2025-09-23
DESCRIPTION | 10 - MD5 | 42 +++--- build/vignette.rds |binary inst/doc/introduction.R | 2 inst/doc/introduction.html | 264 ++++++++++++++++++++++++------------------- man/Attendant.Rd | 74 ++++++------ man/attendantBar.Rd | 14 +- man/autoWaiter.Rd | 8 - man/garcon.Rd | 56 ++++----- man/hostess.Rd | 74 ++++++------ man/hostessLoader.Rd | 24 +-- man/httr_progress.Rd | 8 - man/spinners.Rd | 2 man/triggerWaiter.Rd | 2 man/waiter.Rd | 24 +-- man/waiterClass.Rd | 38 +++--- man/waiterTheme.Rd | 2 man/waitress.Rd | 4 man/waitressClass.Rd | 82 ++++++------- man/withProgressAttendant.Rd | 16 +- man/withProgressWaitress.Rd | 16 +- man/withWaiter.Rd | 6 22 files changed, 401 insertions(+), 367 deletions(-)
Title: Mappable Vector Library for Handling Large Datasets
Description: Mappable vector library provides convenient way to access large datasets. Use all of your data at once, with few limits. Memory mapped data can be shared between multiple R processes. Access speed depends on storage medium, so solid state drive is recommended, preferably with PCI Express (or M.2 nvme) interface or a fast network file system. The data is memory mapped into R and then accessed using usual R list and array subscription operators. Convenience functions are provided for merging, grouping and indexing large vectors and data.frames. The layout of underlying MVL files is optimized for large datasets. The vectors are stored to guarantee alignment for vector intrinsics after memory map. The package is built on top of libMVL, which can be used as a standalone C library. libMVL has simple C API making it easy to interchange datasets with outside programs. Large MVL datasets are distributed via Academic Torrents <https://academictorrents.com/collection/mvl-datasets>.
Author: Vladimir Dergachev [aut, cre]
Maintainer: Vladimir Dergachev <support@altumrete.com>
Diff between RMVL versions 1.1.0.1 dated 2024-09-14 and 1.1.0.2 dated 2025-09-23
DESCRIPTION | 11 MD5 | 18 - NAMESPACE | 2 R/RMVL.R | 75 +++++- man/mvl_close.Rd | 8 man/mvl_verify.Rd |only man/print.MVL_INDEX.Rd |only src/RlibMVL.c | 341 ++++++++++++++++++++++-------- src/libMVL.c | 448 ++++++++++++++++++++++++++++++++++++++-- src/libMVL.h | 100 ++++++++ tests/test_checksums1.R |only tests/test_checksums1.Rout.save |only 12 files changed, 866 insertions(+), 137 deletions(-)
Title: Preparing, Checking, and Submitting Articles to the 'R Journal'
Description: Create an 'R Journal' 'Rmarkdown' template article, that will
generate html and pdf versions of your paper. Check that the paper folder
has all the required components needed for submission.
Examples of 'R Journal' publications can be found at
<https://journal.r-project.org>.
Author: Mitchell O'Hara-Wild [aut],
Stephanie Kobakian [aut],
H. Sherry Zhang [aut],
Di Cook [aut, cre] ,
Simon Urbanek [aut],
Christophe Dervieux [aut]
Maintainer: Di Cook <dicook@monash.edu>
Diff between rjtools versions 1.0.18 dated 2025-01-23 and 1.0.18.1 dated 2025-09-23
DESCRIPTION | 13 +++++++------ MD5 | 26 +++++++++++++------------- R/check.R | 2 +- build/vignette.rds |binary data/keywords.rda |binary inst/doc/check_functions.html | 5 +++-- inst/doc/create_article.html | 5 +++-- inst/doc/format-details.html | 5 +++-- man/checks.Rd | 40 +++++++++++++++++++--------------------- man/create_article.Rd | 2 +- man/log_error.Rd | 12 ++++++------ man/rjournal_article.Rd | 10 +++++----- man/rjournal_issue.Rd | 4 ++-- man/zip_paper.Rd | 4 ++-- 14 files changed, 65 insertions(+), 63 deletions(-)
Title: Unicode Extensions for the 'rebus' Package
Description: Build regular expressions piece by piece using human readable code.
This package contains Unicode functionality, and is primarily intended to be
used by package developers.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between rebus.unicode versions 0.0-2 dated 2017-01-03 and 0.0-2.1 dated 2025-09-23
DESCRIPTION | 9 MD5 | 10 man/Unicode.Rd | 1441 ++++++++++++++++++++++++++++-------------- man/UnicodeGeneralCategory.Rd | 162 +++- man/UnicodeOperators.Rd | 7 man/UnicodeProperty.Rd | 156 +++- 6 files changed, 1224 insertions(+), 561 deletions(-)
Title: Regularized Bayesian Estimator for Two-Level Latent Variable
Models
Description: Implements a regularized Bayesian estimator that optimizes the estimation
of between-group coefficients for multilevel latent variable models by minimizing
mean squared error (MSE) and balancing variance and bias. The package provides more reliable
estimates in scenarios with limited data, offering a robust solution for accurate
parameter estimation in two-level latent variable models. It is designed for
researchers in psychology, education, and related fields who face challenges in
estimating between-group effects under small sample sizes and low intraclass
correlation coefficients. The package includes comprehensive S3 methods for result
objects: print(), summary(), coef(), se(), vcov(), confint(), as.data.frame(),
dim(), length(), names(), and update() for enhanced usability and integration
with standard R workflows. Dashuk et al. (2025a) <doi:10.1017/psy.2025.10045>
derived the optimal regularized Bayesian estimator;
Dashuk et al. (2025b) <doi:10.1007/s41237-025-00264-7> [...truncated...]
Author: Valerii Dashuk [aut, cre],
Binayak Timilsina [aut],
Martin Hecht [aut],
Steffen Zitzmann [aut]
Maintainer: Valerii Dashuk <vadashuk@gmail.com>
Diff between MultiLevelOptimalBayes versions 0.0.3.0 dated 2025-09-10 and 0.0.4.0 dated 2025-09-23
DESCRIPTION | 10 - MD5 | 18 +- R/methods.R | 2 R/mlob.R | 6 README.md | 4 build/partial.rdb |binary inst/doc/MultiLevelOptimalBayes-Intro.Rmd | 14 + inst/doc/MultiLevelOptimalBayes-Intro.html | 208 +++++++++++++++-------------- man/mlob.Rd | 6 vignettes/MultiLevelOptimalBayes-Intro.Rmd | 14 + 10 files changed, 155 insertions(+), 127 deletions(-)
More information about MultiLevelOptimalBayes at CRAN
Permanent link
Title: Swarm Intelligence Optimization
Description: A fast and flexible general-purpose implementation of Particle Swarm Optimization (PSO) and Differential Evolution (DE) for solving global minimization problems is provided. It is designed to handle complex optimization tasks with nonlinear, non-differentiable, and multi-modal objective functions defined by users. There are five types of PSO variants: Particle Swarm Optimization (PSO, Eberhart & Kennedy, 1995) <doi:10.1109/MHS.1995.494215>, Quantum-behaved particle Swarm Optimization (QPSO, Sun et al., 2004) <doi:10.1109/CEC.2004.1330875>, Locally convergent rotationally invariant particle swarm optimization (LcRiPSO, Bonyadi & Michalewicz, 2014) <doi:10.1007/s11721-014-0095-1>, Competitive Swarm Optimizer (CSO, Cheng & Jin, 2015) <doi:10.1109/TCYB.2014.2322602> and Double exponential particle swarm optimization (DExPSO, Stehlik et al., 2024) <doi:10.1016/j.asoc.2024.111913>. For the DE algorithm, six types in Storn, R. & Price, K. (1997) & [...truncated...]
Author: Ping-Yang Chen [aut, cre],
Ray-Bing Chen [aut],
Russell Eberhart [ctb],
Kennedy Kennedy [ctb],
Jun Sun [ctb],
Bin Feng [ctb],
Wenbo Xu [ctb],
Mohammad Reza Bonyadi [ctb],
Zbigniew Michalewicz [ctb],
Ran Cheng [ctb],
Yaochu Jin [ctb],
Milan Stehlik [c [...truncated...]
Maintainer: Ping-Yang Chen <pychen.ping@gmail.com>
Diff between globpso versions 1.3.0 dated 2025-03-19 and 1.3.1 dated 2025-09-23
DESCRIPTION | 10 +- MD5 | 16 +-- NAMESPACE | 28 +++--- README.md | 7 + man/diffevo.Rd | 204 ++++++++++++++++++++++++------------------------- man/getDEInfo.Rd | 108 ++++++++++++------------- man/globpso-package.Rd | 44 +++++----- src/deKernel.h | 10 +- src/psoKernel.h | 10 +- 9 files changed, 226 insertions(+), 211 deletions(-)
Title: Permutation-Based All-Resolutions Inference
Description: Computes the All-Resolution Inference method in the permutation framework, i.e., simultaneous lower confidence bounds for the number of true discoveries. <doi:10.1002/sim.9725>.
Author: Angela Andreella [aut, cre]
Maintainer: Angela Andreella <angela.andreella@unive.it>
Diff between pARI versions 1.1.2 dated 2024-09-06 and 1.1.3 dated 2025-09-23
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/lambdaOpt.R | 1 - inst/doc/intro.html | 2 +- src/Makevars | 1 - src/Makevars.win | 1 - src/lambdaCalibrate.cpp | 17 ++++++++++------- 7 files changed, 22 insertions(+), 22 deletions(-)
Title: Database for Experiment Dataset
Description: A 'SQLite' database is designed to store all information
of experiment-based data including metadata, experiment design,
managements, phenotypic values and climate records. The dataset can be
imported from an 'Excel' file.
Author: Bangyou Zheng [aut, cre]
Maintainer: Bangyou Zheng <bangyou.zheng@csiro.au>
Diff between expDB versions 0.1.0 dated 2021-10-08 and 0.3.0 dated 2025-09-23
DESCRIPTION | 16 ++--- MD5 | 13 ++-- NAMESPACE | 111 ++++++++++++++++++++-------------------- R/expdb_met.R | 26 ++++----- R/phenology.R |only README.md | 19 ++++++ inst/extdata/expdb_example.xlsx |binary man/approx_zadoks.Rd |only tests/testthat/test-phenology.R |only 9 files changed, 103 insertions(+), 82 deletions(-)
Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
tree rearrangement;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of split support;
plotting the position of rogue taxa (Klopfstein & Spasojevic 2019)
<doi:10.1371/journal.pone.0212942>;
calculation of ancestor-descendant relationships,
of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013, Lemant et al. 2022)
<doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>;
artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph] ,
Emmanuel Paradis [cph] ,
Robert Noble [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeTools versions 1.16.1 dated 2025-08-24 and 2.0.0 dated 2025-09-23
TreeTools-1.16.1/TreeTools/man/EnforceOutgroup.Rd |only TreeTools-1.16.1/TreeTools/man/SpectrumLegend.Rd |only TreeTools-2.0.0/TreeTools/DESCRIPTION | 22 TreeTools-2.0.0/TreeTools/MD5 | 289 TreeTools-2.0.0/TreeTools/NAMESPACE | 1013 +-- TreeTools-2.0.0/TreeTools/NEWS.md | 21 TreeTools-2.0.0/TreeTools/R/AddTip.R | 550 - TreeTools-2.0.0/TreeTools/R/Cherries.R |only TreeTools-2.0.0/TreeTools/R/ClusterTable.R | 250 TreeTools-2.0.0/TreeTools/R/Consensus.R | 297 TreeTools-2.0.0/TreeTools/R/ConsistentSplits.R | 84 TreeTools-2.0.0/TreeTools/R/Decompose.R | 330 - TreeTools-2.0.0/TreeTools/R/DropTip.R | 694 +- TreeTools-2.0.0/TreeTools/R/LongBranchScore.R | 150 TreeTools-2.0.0/TreeTools/R/MatchStrings.R | 66 TreeTools-2.0.0/TreeTools/R/PathLengths.R | 96 TreeTools-2.0.0/TreeTools/R/PhyToString.R | 286 TreeTools-2.0.0/TreeTools/R/RcppExports-manual.R | 64 TreeTools-2.0.0/TreeTools/R/RcppExports.R | 4 TreeTools-2.0.0/TreeTools/R/Reweight.R | 220 TreeTools-2.0.0/TreeTools/R/RoguePlot.R | 596 - TreeTools-2.0.0/TreeTools/R/SplitFunctions.R | 909 +- TreeTools-2.0.0/TreeTools/R/Splits.R | 1221 +-- TreeTools-2.0.0/TreeTools/R/Stemwardness.R | 6 TreeTools-2.0.0/TreeTools/R/Support.R | 347 - TreeTools-2.0.0/TreeTools/R/TopologyOnly.R | 84 TreeTools-2.0.0/TreeTools/R/TotalCopheneticIndex.R | 3 TreeTools-2.0.0/TreeTools/R/TreeNumber.R | 6 TreeTools-2.0.0/TreeTools/R/Treeness.R | 116 TreeTools-2.0.0/TreeTools/R/data.R | 180 TreeTools-2.0.0/TreeTools/R/helper_functions.R | 289 TreeTools-2.0.0/TreeTools/R/match.R | 13 TreeTools-2.0.0/TreeTools/R/mst.R | 3 TreeTools-2.0.0/TreeTools/R/parse_files.R | 1822 ++--- TreeTools-2.0.0/TreeTools/R/phylo.R | 644 +- TreeTools-2.0.0/TreeTools/R/split_analysis.R | 3 TreeTools-2.0.0/TreeTools/R/tree_descendants.R | 287 TreeTools-2.0.0/TreeTools/R/tree_display.R | 4 TreeTools-2.0.0/TreeTools/R/tree_generation.R | 1066 +-- TreeTools-2.0.0/TreeTools/R/tree_information.R | 11 TreeTools-2.0.0/TreeTools/R/tree_numbering.R | 1323 ++-- TreeTools-2.0.0/TreeTools/R/tree_properties.R | 1156 +-- TreeTools-2.0.0/TreeTools/R/tree_rearrangement.R | 1291 ++-- TreeTools-2.0.0/TreeTools/R/tree_shape.R | 23 TreeTools-2.0.0/TreeTools/build/partial.rdb |binary TreeTools-2.0.0/TreeTools/build/vignette.rds |binary TreeTools-2.0.0/TreeTools/inst/REFERENCES.bib | 734 +- TreeTools-2.0.0/TreeTools/inst/WORDLIST | 250 TreeTools-2.0.0/TreeTools/inst/apa-old-doi-prefix.csl | 3172 +++++----- TreeTools-2.0.0/TreeTools/inst/doc/filesystem-navigation.html | 4 TreeTools-2.0.0/TreeTools/inst/doc/load-data.Rmd | 428 - TreeTools-2.0.0/TreeTools/inst/doc/load-data.html | 4 TreeTools-2.0.0/TreeTools/inst/doc/load-trees.html | 4 TreeTools-2.0.0/TreeTools/inst/include/TreeTools/SplitList.h | 12 TreeTools-2.0.0/TreeTools/inst/include/TreeTools/n_cherries.h |only TreeTools-2.0.0/TreeTools/man/AddTip.Rd | 281 TreeTools-2.0.0/TreeTools/man/AncestorEdge.Rd | 106 TreeTools-2.0.0/TreeTools/man/Cherries.Rd |only TreeTools-2.0.0/TreeTools/man/CladisticInfo.Rd | 6 TreeTools-2.0.0/TreeTools/man/ClusterTable.Rd | 160 TreeTools-2.0.0/TreeTools/man/CollapseNode.Rd | 1 TreeTools-2.0.0/TreeTools/man/ConsensusWithout.Rd | 210 TreeTools-2.0.0/TreeTools/man/Decompose.Rd | 166 TreeTools-2.0.0/TreeTools/man/DescendantEdges.Rd | 170 TreeTools-2.0.0/TreeTools/man/DropTip.Rd | 281 TreeTools-2.0.0/TreeTools/man/EdgeAncestry.Rd | 124 TreeTools-2.0.0/TreeTools/man/EndSentence.Rd | 64 TreeTools-2.0.0/TreeTools/man/GenerateTree.Rd | 188 TreeTools-2.0.0/TreeTools/man/ImposeConstraint.Rd | 1 TreeTools-2.0.0/TreeTools/man/KeptPaths.Rd | 1 TreeTools-2.0.0/TreeTools/man/KeptVerts.Rd | 1 TreeTools-2.0.0/TreeTools/man/LeafLabelInterchange.Rd | 1 TreeTools-2.0.0/TreeTools/man/ListAncestors.Rd | 218 TreeTools-2.0.0/TreeTools/man/LongBranch.Rd | 127 TreeTools-2.0.0/TreeTools/man/MakeTreeBinary.Rd | 109 TreeTools-2.0.0/TreeTools/man/MatchEdges.Rd | 135 TreeTools-2.0.0/TreeTools/man/MatchStrings.Rd | 80 TreeTools-2.0.0/TreeTools/man/MatrixToPhyDat.Rd | 150 TreeTools-2.0.0/TreeTools/man/MorphoBankDecode.Rd | 58 TreeTools-2.0.0/TreeTools/man/NSplits.Rd | 169 TreeTools-2.0.0/TreeTools/man/NTip.Rd | 137 TreeTools-2.0.0/TreeTools/man/Neworder.Rd | 128 TreeTools-2.0.0/TreeTools/man/NodeNumbers.Rd | 111 TreeTools-2.0.0/TreeTools/man/PathLengths.Rd | 115 TreeTools-2.0.0/TreeTools/man/PhyToString.Rd | 212 TreeTools-2.0.0/TreeTools/man/ReadCharacters.Rd | 288 TreeTools-2.0.0/TreeTools/man/Renumber.Rd | 1 TreeTools-2.0.0/TreeTools/man/RenumberTips.Rd | 1 TreeTools-2.0.0/TreeTools/man/Reorder.Rd | 559 - TreeTools-2.0.0/TreeTools/man/Reweight.Rd | 156 TreeTools-2.0.0/TreeTools/man/RightmostCharacter.Rd | 72 TreeTools-2.0.0/TreeTools/man/RoguePlot.Rd | 3 TreeTools-2.0.0/TreeTools/man/RootTree.Rd | 191 TreeTools-2.0.0/TreeTools/man/SortTree.Rd | 1 TreeTools-2.0.0/TreeTools/man/SplitConsistent.Rd | 90 TreeTools-2.0.0/TreeTools/man/SplitFrequency.Rd | 185 TreeTools-2.0.0/TreeTools/man/Splits.Rd | 12 TreeTools-2.0.0/TreeTools/man/SplitsInBinaryTree.Rd | 159 TreeTools-2.0.0/TreeTools/man/Subsplit.Rd | 96 TreeTools-2.0.0/TreeTools/man/Subtree.Rd | 123 TreeTools-2.0.0/TreeTools/man/SupportColour.Rd | 4 TreeTools-2.0.0/TreeTools/man/TipLabels.Rd | 249 TreeTools-2.0.0/TreeTools/man/TipTimedTree.Rd | 1 TreeTools-2.0.0/TreeTools/man/TopologyOnly.Rd | 46 TreeTools-2.0.0/TreeTools/man/TreeIsRooted.Rd | 83 TreeTools-2.0.0/TreeTools/man/TreeShape.Rd | 320 - TreeTools-2.0.0/TreeTools/man/Treeness.Rd | 111 TreeTools-2.0.0/TreeTools/man/TrivialSplits.Rd | 96 TreeTools-2.0.0/TreeTools/man/TrivialTree.Rd | 125 TreeTools-2.0.0/TreeTools/man/Unquote.Rd | 64 TreeTools-2.0.0/TreeTools/man/brewer.Rd | 66 TreeTools-2.0.0/TreeTools/man/match.Splits.Rd | 121 TreeTools-2.0.0/TreeTools/man/match.multiPhylo.Rd | 144 TreeTools-2.0.0/TreeTools/man/sapply64.Rd | 164 TreeTools-2.0.0/TreeTools/src/RcppExports.cpp | 14 TreeTools-2.0.0/TreeTools/src/n_cherries.cpp |only TreeTools-2.0.0/TreeTools/tests/testthat/_snaps/RoguePlot/rogueplot-trees1.svg | 106 TreeTools-2.0.0/TreeTools/tests/testthat/_snaps/RoguePlot/rogueplot-trees2.svg | 82 TreeTools-2.0.0/TreeTools/tests/testthat/_snaps/Support/labelsplits-nameless.svg | 172 TreeTools-2.0.0/TreeTools/tests/testthat/_snaps/Support/labelsplits-names.svg | 148 TreeTools-2.0.0/TreeTools/tests/testthat/test-AddTip.R | 356 - TreeTools-2.0.0/TreeTools/tests/testthat/test-Cherries.R |only TreeTools-2.0.0/TreeTools/tests/testthat/test-ClusterTable.R | 274 TreeTools-2.0.0/TreeTools/tests/testthat/test-Decompose.R | 152 TreeTools-2.0.0/TreeTools/tests/testthat/test-DropTip.R | 504 - TreeTools-2.0.0/TreeTools/tests/testthat/test-LongBranchScore.R | 36 TreeTools-2.0.0/TreeTools/tests/testthat/test-MatchStrings.R | 26 TreeTools-2.0.0/TreeTools/tests/testthat/test-PathLengths.R | 70 TreeTools-2.0.0/TreeTools/tests/testthat/test-PhyToString.R | 150 TreeTools-2.0.0/TreeTools/tests/testthat/test-ReadTntTree.R | 290 TreeTools-2.0.0/TreeTools/tests/testthat/test-Reweight.R | 92 TreeTools-2.0.0/TreeTools/tests/testthat/test-RoguePlot.R | 336 - TreeTools-2.0.0/TreeTools/tests/testthat/test-SplitConsistent.R | 72 TreeTools-2.0.0/TreeTools/tests/testthat/test-SplitFunctions.R | 452 - TreeTools-2.0.0/TreeTools/tests/testthat/test-Splits.R | 1101 +-- TreeTools-2.0.0/TreeTools/tests/testthat/test-Support.R | 116 TreeTools-2.0.0/TreeTools/tests/testthat/test-TopologyOnly.R | 54 TreeTools-2.0.0/TreeTools/tests/testthat/test-Treeness.R | 38 TreeTools-2.0.0/TreeTools/tests/testthat/test-consensus.R | 220 TreeTools-2.0.0/TreeTools/tests/testthat/test-helper_functions.R | 22 TreeTools-2.0.0/TreeTools/tests/testthat/test-match.R | 58 TreeTools-2.0.0/TreeTools/tests/testthat/test-parsers.R | 426 - TreeTools-2.0.0/TreeTools/tests/testthat/test-split_analysis.R | 22 TreeTools-2.0.0/TreeTools/tests/testthat/test-tree_descendants.R | 2 TreeTools-2.0.0/TreeTools/tests/testthat/test-tree_generation.R | 438 - TreeTools-2.0.0/TreeTools/tests/testthat/test-tree_properties.R | 362 - TreeTools-2.0.0/TreeTools/tests/testthat/test-tree_rearrange.R | 830 +- TreeTools-2.0.0/TreeTools/tests/testthat/testdata/nonPreCons.nex | 48 TreeTools-2.0.0/TreeTools/vignettes/load-data.Rmd | 428 - 149 files changed, 17440 insertions(+), 17545 deletions(-)
Title: Simulate Package Installation and Attach
Description: Simulates the process of installing a package and then
attaching it. This is a key part of the 'devtools' package as it
allows you to rapidly iterate while developing a package.
Author: Hadley Wickham [aut],
Winston Chang [aut],
Jim Hester [aut],
Lionel Henry [aut, cre],
Posit Software, PBC [cph, fnd],
R Core team [ctb]
Maintainer: Lionel Henry <lionel@posit.co>
Diff between pkgload versions 1.4.0 dated 2024-06-28 and 1.4.1 dated 2025-09-23
DESCRIPTION | 14 +- LICENSE |only MD5 | 110 ++++++++-------- NEWS.md | 26 +++ R/compilation-db.R | 125 ++++++++++++------- R/dev-example.R | 27 ++-- R/dev-help.R | 30 +++- R/dev-meta.R | 4 R/dev-topic.R | 4 R/enc.R | 10 + R/imports-env.R | 54 +++++--- R/load-code.R | 26 ++- R/load-data.R | 12 + R/load-depends.R | 1 R/load-dll.R | 44 ++++-- R/load.R | 74 +++++++---- R/namespace-env.R | 78 +++++++---- R/package-deps.R | 17 +- R/package-env.R | 31 ++-- R/package.R | 22 +-- R/remove-s4-class.R | 21 ++- R/run-loadhooks.R | 18 +- R/shims.R | 35 +++-- R/source.R | 19 ++ R/unload.R | 20 ++- R/utils.R | 85 ++++++++---- R/withr-shims.R |only R/zzz.R | 11 - man/load_all.Rd | 18 ++ tests/testthat/test-depend.R | 11 + tests/testthat/test-dll.R | 22 ++- tests/testthat/test-examples.R | 19 ++ tests/testthat/test-extraction.R | 48 ++++--- tests/testthat/test-help.R | 49 ++++--- tests/testthat/test-imports.R | 1 tests/testthat/test-load-hooks.R | 12 - tests/testthat/test-load.R | 17 +- tests/testthat/test-metadata.R | 3 tests/testthat/test-namespace-env.R | 2 tests/testthat/test-namespace.R | 24 +-- tests/testthat/test-po.R | 15 +- tests/testthat/test-s4-export.R | 2 tests/testthat/test-s4-sort.R | 3 tests/testthat/test-s4-unload.R | 20 ++- tests/testthat/test-shim.R | 74 +++++++---- tests/testthat/testActiveBindings/R/bindings.r | 1 tests/testthat/testCollateAbsent/R/a.r | 2 tests/testthat/testCollateAbsent/R/b.r | 2 tests/testthat/testCollateAbsent/R/c.r | 2 tests/testthat/testCollateExtra/R/a.r | 2 tests/testthat/testCollateMissing/R/a.r | 2 tests/testthat/testCollateMissing/R/b.r | 2 tests/testthat/testHooks/R/a.r | 2 tests/testthat/testLibDynam/R/zzz.R | 3 tests/testthat/testLoadLazy/R/bindings.r | 1 tests/testthat/testS4import/R/all.r | 3 tests/testthat/testUnknownMacro/R/testUnknownMacro.R | 3 57 files changed, 819 insertions(+), 464 deletions(-)
Title: 'R' 'SDK' and Exporters for 'OpenTelemetry'
Description: 'OpenTelemetry' is a collection of tools,
'APIs', and 'SDKs' used to instrument, generate, collect, and export
telemetry data (metrics, logs, and traces) for analysis in order to
understand your software's performance and behavior.
This package contains the 'OpenTelemetry' 'SDK', and exporters.
Use this package to export traces, metrics, logs from instrumented
'R' code. Use the 'otel' package to instrument your 'R' code for
'OpenTelemetry'.
Author: Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd] ,
opentelemetry-cpp authors [ctb]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between otelsdk versions 0.2.0 dated 2025-09-10 and 0.2.1 dated 2025-09-23
DESCRIPTION | 9 +++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 8 ++++++++ R/docs.R | 3 ++- R/onload.R | 2 -- configure | 17 ++++++++++++++++- man/environmentvariables.Rd | 3 ++- src/Makevars.in | 8 +++++--- src/context.c | 2 +- tests/testthat/_snaps/current.md | 2 +- tests/testthat/test-meter-provider-stdout.R | 1 + tests/testthat/test-meter.R | 1 + tests/testthat/test-print.R | 1 + 13 files changed, 55 insertions(+), 26 deletions(-)
Title: Bayesian Hierarchical Multi-Subject Multiscale Analysis of
Functional MRI (fMRI) Data
Description: Package BHMSMAfMRI performs Bayesian hierarchical multi-subject multiscale analysis of fMRI data as described in Sanyal & Ferreira (2012) <DOI:10.1016/j.neuroimage.2012.08.041>, or other multiscale data, using wavelet-based prior that borrows strength across subjects and provides posterior smoothed images of the effect sizes and samples from the posterior distribution.
Author: Nilotpal Sanyal [aut, cre] ,
Marco A.R. Ferreira [aut]
Maintainer: Nilotpal Sanyal <nilotpal.sanyal@gmail.com>
Diff between BHMSMAfMRI versions 2.2 dated 2024-06-12 and 2.3 dated 2025-09-23
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/BHMSMAfMRIvignette.R | 14 +++++++------- inst/doc/BHMSMAfMRIvignette.pdf |binary man/BHMSMAfMRI-package.Rd | 4 ++-- src/BHMSMA.cpp | 2 +- 8 files changed, 27 insertions(+), 22 deletions(-)
Title: Functions for Atomic Force Microscope Force-Distance Curves
Analysis
Description: Set of functions for analyzing Atomic Force Microscope (AFM) force-distance curves. It allows to obtain the contact and unbinding points, perform the baseline correction, estimate the Young's modulus, fit up to two exponential decay function to a stress-relaxation / creep experiment, obtain adhesion energies. These operations can be done either over a single F-d curve or over a set of F-d curves in batch mode.
Author: Rafael Benitez [aut, cre],
Vicente Jose Bolos [aut],
Jose-Luis Toca-Herrera [aut]
Maintainer: Rafael Benitez <rabesua@uv.es>
Diff between afmToolkit versions 0.0.1 dated 2017-04-03 and 1.0.0 dated 2025-09-23
afmToolkit-0.0.1/afmToolkit/R/afmExpDecay.R |only afmToolkit-0.0.1/afmToolkit/README.md |only afmToolkit-0.0.1/afmToolkit/man/afmExpDecay.Rd |only afmToolkit-1.0.0/afmToolkit/DESCRIPTION | 26 afmToolkit-1.0.0/afmToolkit/MD5 | 94 - afmToolkit-1.0.0/afmToolkit/NAMESPACE | 7 afmToolkit-1.0.0/afmToolkit/R/afmBaselineCorrection.R | 333 ++--- afmToolkit-1.0.0/afmToolkit/R/afmContactPoint.R | 321 ++--- afmToolkit-1.0.0/afmToolkit/R/afmDetachPoint.R | 277 ++-- afmToolkit-1.0.0/afmToolkit/R/afmExtract.R | 583 ++++++---- afmToolkit-1.0.0/afmToolkit/R/afmHysteresis.R |only afmToolkit-1.0.0/afmToolkit/R/afmIndentation.R | 98 - afmToolkit-1.0.0/afmToolkit/R/afmReadJPK.R | 322 +++-- afmToolkit-1.0.0/afmToolkit/R/afmReadJPKFolder.R | 2 afmToolkit-1.0.0/afmToolkit/R/afmReadJPKMultiFolder.R |only afmToolkit-1.0.0/afmToolkit/R/afmReadJPKMultiIndent.R |only afmToolkit-1.0.0/afmToolkit/R/afmReadVeeco.R | 180 +-- afmToolkit-1.0.0/afmToolkit/R/afmReadVeecoFolder.R | 57 afmToolkit-1.0.0/afmToolkit/R/afmRelax.R |only afmToolkit-1.0.0/afmToolkit/R/afmStitch.R |only afmToolkit-1.0.0/afmToolkit/R/afmYoungModulus.R | 382 ++++-- afmToolkit-1.0.0/afmToolkit/R/afmZeroPointSlope.R | 218 ++- afmToolkit-1.0.0/afmToolkit/R/append.afmdata.R | 49 afmToolkit-1.0.0/afmToolkit/R/is.afmdata.R | 2 afmToolkit-1.0.0/afmToolkit/R/is.afmmulti.R |only afmToolkit-1.0.0/afmToolkit/R/plot.afmdata.R | 6 afmToolkit-1.0.0/afmToolkit/data/batchExperiment.RData |binary afmToolkit-1.0.0/afmToolkit/inst/force-save-JPK-multiIndent.txt.gz |only afmToolkit-1.0.0/afmToolkit/inst/veecoFolder/veeco_file4.txt.gz |binary afmToolkit-1.0.0/afmToolkit/man/afmAdhesionEnergy.Rd | 1 afmToolkit-1.0.0/afmToolkit/man/afmBaselineCorrection.Rd | 14 afmToolkit-1.0.0/afmToolkit/man/afmContactPoint.Rd | 16 afmToolkit-1.0.0/afmToolkit/man/afmDetachPoint.Rd | 16 afmToolkit-1.0.0/afmToolkit/man/afmExtract.Rd | 12 afmToolkit-1.0.0/afmToolkit/man/afmHysteresis.Rd |only afmToolkit-1.0.0/afmToolkit/man/afmIndentation.Rd | 1 afmToolkit-1.0.0/afmToolkit/man/afmReadJPK.Rd | 17 afmToolkit-1.0.0/afmToolkit/man/afmReadJPKFolder.Rd | 1 afmToolkit-1.0.0/afmToolkit/man/afmReadJPKMultiFolder.Rd |only afmToolkit-1.0.0/afmToolkit/man/afmReadJPKMultiIndent.Rd |only afmToolkit-1.0.0/afmToolkit/man/afmReadVeeco.Rd | 25 afmToolkit-1.0.0/afmToolkit/man/afmReadVeecoFolder.Rd | 5 afmToolkit-1.0.0/afmToolkit/man/afmRelax.Rd |only afmToolkit-1.0.0/afmToolkit/man/afmStitch.Rd |only afmToolkit-1.0.0/afmToolkit/man/afmYoungModulus.Rd | 31 afmToolkit-1.0.0/afmToolkit/man/afmZeroPointSlope.Rd | 11 afmToolkit-1.0.0/afmToolkit/man/afmdata.Rd | 1 afmToolkit-1.0.0/afmToolkit/man/afmexperiment.Rd | 1 afmToolkit-1.0.0/afmToolkit/man/append.afmdata.Rd | 1 afmToolkit-1.0.0/afmToolkit/man/batchExperiment.Rd | 7 afmToolkit-1.0.0/afmToolkit/man/is.afmdata.Rd | 3 afmToolkit-1.0.0/afmToolkit/man/is.afmexperiment.Rd | 1 afmToolkit-1.0.0/afmToolkit/man/is.afmmulti.Rd |only afmToolkit-1.0.0/afmToolkit/man/plot.afmdata.Rd | 1 afmToolkit-1.0.0/afmToolkit/man/summary.Rd | 1 afmToolkit-1.0.0/afmToolkit/man/windowedFit.Rd | 1 56 files changed, 1850 insertions(+), 1274 deletions(-)
Title: Connecting to Various Database Platforms
Description: An R 'DataBase Interface' ('DBI') compatible interface to various database platforms ('PostgreSQL', 'Oracle', 'Microsoft SQL Server',
'Amazon Redshift', 'Microsoft Parallel Database Warehouse', 'IBM Netezza', 'Apache Impala', 'Google BigQuery', 'Snowflake', 'Spark', 'SQLite',
and 'InterSystems IRIS'). Also includes support for fetching data as 'Andromeda' objects. Uses either 'Java Database Connectivity' ('JDBC') or
other 'DBI' drivers to connect to databases.
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut],
Adam Black [aut],
Observational Health Data Science and Informatics [cph],
Microsoft Inc. [cph] ,
PostgreSQL Global Development Group [cph] ,
Oracle Inc. [cph] ,
Amazon Inc. [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between DatabaseConnector versions 6.4.0 dated 2025-01-30 and 7.0.0 dated 2025-09-23
DatabaseConnector-6.4.0/DatabaseConnector/R/DbiDateFunctions.R |only DatabaseConnector-6.4.0/DatabaseConnector/java/org/ohdsi/databaseConnector/DebugRtoSqlTranslation.java |only DatabaseConnector-6.4.0/DatabaseConnector/java/org/ohdsi/databaseConnector/RFunctionToTranslate.java |only DatabaseConnector-6.4.0/DatabaseConnector/java/org/ohdsi/databaseConnector/RtoSqlTranslator.java |only DatabaseConnector-6.4.0/DatabaseConnector/man/dateAdd.Rd |only DatabaseConnector-6.4.0/DatabaseConnector/man/dateDiff.Rd |only DatabaseConnector-6.4.0/DatabaseConnector/man/dateFromParts.Rd |only DatabaseConnector-6.4.0/DatabaseConnector/man/day.Rd |only DatabaseConnector-6.4.0/DatabaseConnector/man/dbExecute-DatabaseConnectorConnection-character-method.Rd |only DatabaseConnector-6.4.0/DatabaseConnector/man/dbGetQuery-DatabaseConnectorConnection-character-method.Rd |only DatabaseConnector-6.4.0/DatabaseConnector/man/eoMonth.Rd |only DatabaseConnector-6.4.0/DatabaseConnector/man/lowLevelExecuteSql.Rd |only DatabaseConnector-6.4.0/DatabaseConnector/man/lowLevelQuerySql.Rd |only DatabaseConnector-6.4.0/DatabaseConnector/man/lowLevelQuerySqlToAndromeda.Rd |only DatabaseConnector-6.4.0/DatabaseConnector/man/month.Rd |only DatabaseConnector-6.4.0/DatabaseConnector/man/year.Rd |only DatabaseConnector-7.0.0/DatabaseConnector/DESCRIPTION | 18 DatabaseConnector-7.0.0/DatabaseConnector/MD5 | 120 +- DatabaseConnector-7.0.0/DatabaseConnector/NAMESPACE | 29 DatabaseConnector-7.0.0/DatabaseConnector/NEWS.md | 32 DatabaseConnector-7.0.0/DatabaseConnector/R/Andromeda.R | 274 +----- DatabaseConnector-7.0.0/DatabaseConnector/R/BulkLoad.R | 3 DatabaseConnector-7.0.0/DatabaseConnector/R/Compression.R | 2 DatabaseConnector-7.0.0/DatabaseConnector/R/Connect.R | 92 -- DatabaseConnector-7.0.0/DatabaseConnector/R/CtasHack.R | 33 DatabaseConnector-7.0.0/DatabaseConnector/R/DBI.R | 426 +++------ DatabaseConnector-7.0.0/DatabaseConnector/R/DataHash.R | 8 DatabaseConnector-7.0.0/DatabaseConnector/R/DatabaseConnector.R | 11 DatabaseConnector-7.0.0/DatabaseConnector/R/Drivers.R | 6 DatabaseConnector-7.0.0/DatabaseConnector/R/InsertTable.R | 116 +- DatabaseConnector-7.0.0/DatabaseConnector/R/ListTables.R | 38 DatabaseConnector-7.0.0/DatabaseConnector/R/LowLevelFunctions.R |only DatabaseConnector-7.0.0/DatabaseConnector/R/RStudio.R | 2 DatabaseConnector-7.0.0/DatabaseConnector/R/Sql.R | 454 +--------- DatabaseConnector-7.0.0/DatabaseConnector/R/backend-DatabaseConnector.R |only DatabaseConnector-7.0.0/DatabaseConnector/README.md | 7 DatabaseConnector-7.0.0/DatabaseConnector/inst/csv/jarChecksum.txt | 2 DatabaseConnector-7.0.0/DatabaseConnector/inst/doc/Connecting.pdf |binary DatabaseConnector-7.0.0/DatabaseConnector/inst/doc/DbiAndDbplyr.pdf |binary DatabaseConnector-7.0.0/DatabaseConnector/inst/doc/Querying.pdf |binary DatabaseConnector-7.0.0/DatabaseConnector/inst/java/DatabaseConnector.jar |binary DatabaseConnector-7.0.0/DatabaseConnector/java/DatabaseConnector.jardesc | 2 DatabaseConnector-7.0.0/DatabaseConnector/java/org/ohdsi/databaseConnector/BatchedInsert.java | 44 DatabaseConnector-7.0.0/DatabaseConnector/java/org/ohdsi/databaseConnector/BatchedQuery.java | 202 ++-- DatabaseConnector-7.0.0/DatabaseConnector/man/DatabaseConnector-package.Rd | 1 DatabaseConnector-7.0.0/DatabaseConnector/man/dbAppendTable-DatabaseConnectorConnection-character-method.Rd | 8 DatabaseConnector-7.0.0/DatabaseConnector/man/dbCreateTable-DatabaseConnectorConnection-method.Rd | 8 DatabaseConnector-7.0.0/DatabaseConnector/man/dbExecute-DatabaseConnectorDbiConnection-character-method.Rd |only DatabaseConnector-7.0.0/DatabaseConnector/man/dbExecute-DatabaseConnectorJdbcConnection-character-method.Rd |only DatabaseConnector-7.0.0/DatabaseConnector/man/dbGetQuery-DatabaseConnectorDbiConnection-character-method.Rd |only DatabaseConnector-7.0.0/DatabaseConnector/man/dbGetQuery-DatabaseConnectorJdbcConnection-character-method.Rd |only DatabaseConnector-7.0.0/DatabaseConnector/man/dbReadTable-DatabaseConnectorConnection-character-method.Rd | 15 DatabaseConnector-7.0.0/DatabaseConnector/man/dbRemoveTable-DatabaseConnectorConnection-ANY-method.Rd | 15 DatabaseConnector-7.0.0/DatabaseConnector/man/dbSendQuery-DatabaseConnectorDbiConnection-character-method.Rd | 4 DatabaseConnector-7.0.0/DatabaseConnector/man/dbSendQuery-DatabaseConnectorJdbcConnection-character-method.Rd | 4 DatabaseConnector-7.0.0/DatabaseConnector/man/dbSendStatement-DatabaseConnectorConnection-character-method.Rd | 4 DatabaseConnector-7.0.0/DatabaseConnector/man/dbWriteTable-DatabaseConnectorConnection-ANY-method.Rd | 8 DatabaseConnector-7.0.0/DatabaseConnector/man/downloadJdbcDrivers.Rd | 2 DatabaseConnector-7.0.0/DatabaseConnector/man/getAvailableJavaHeapSpace.Rd | 2 DatabaseConnector-7.0.0/DatabaseConnector/man/insertTable.Rd | 3 DatabaseConnector-7.0.0/DatabaseConnector/man/querySql.Rd | 11 DatabaseConnector-7.0.0/DatabaseConnector/man/reexports.Rd |only DatabaseConnector-7.0.0/DatabaseConnector/man/renderTranslateExecuteSql.Rd | 3 DatabaseConnector-7.0.0/DatabaseConnector/man/renderTranslateQueryApplyBatched.Rd | 14 DatabaseConnector-7.0.0/DatabaseConnector/man/renderTranslateQuerySql.Rd | 14 DatabaseConnector-7.0.0/DatabaseConnector/man/renderTranslateQuerySqlToAndromeda.Rd | 5 DatabaseConnector-7.0.0/DatabaseConnector/tests/testthat/dbplyrTestFunction.R | 210 ++-- DatabaseConnector-7.0.0/DatabaseConnector/tests/testthat/setup.R | 48 - DatabaseConnector-7.0.0/DatabaseConnector/tests/testthat/test-dbiConnection.R |only DatabaseConnector-7.0.0/DatabaseConnector/tests/testthat/test-dbplyr.R | 54 - DatabaseConnector-7.0.0/DatabaseConnector/tests/testthat/test-fetchResults.R | 4 DatabaseConnector-7.0.0/DatabaseConnector/tests/testthat/test-insertTable.R | 72 - DatabaseConnector-7.0.0/DatabaseConnector/tests/testthat/test-sendUpdates.R | 10 73 files changed, 972 insertions(+), 1468 deletions(-)
More information about DatabaseConnector at CRAN
Permanent link
Title: Optimal Bayesian Experimental Design using the ACE Algorithm
Description: Optimal Bayesian experimental design using the approximate coordinate exchange (ACE) algorithm.
Author: Antony M. Overstall [aut, cre],
David C. Woods [aut],
Maria Adamou & Damianos Michaelides [aut]
Maintainer: Antony M. Overstall <A.M.Overstall@soton.ac.uk>
Diff between acebayes versions 1.10 dated 2020-10-05 and 1.11 dated 2025-09-23
DESCRIPTION | 24 ++++++++++++++++----- MD5 | 12 +++++----- R/sysdata.rda |binary man/acebayes-package.Rd | 4 +-- man/overstallwoods.Rd | 53 ++++++++++++++++++++++++++---------------------- src/Makevars | 13 ----------- src/Makevars.win | 13 ----------- 7 files changed, 57 insertions(+), 62 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-06-07 0.3.0
2024-01-23 0.2.0
2023-11-27 0.1.9
2023-11-17 0.1.8
2023-11-06 0.1.6
2023-11-03 0.1.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-01 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-10-19 1.0.4
2023-01-12 1.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-05 0.2.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-12 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-01 0.1.2
2022-08-24 0.1.1
2021-07-21 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-15 0.0.8
2021-08-04 0.0.7
2021-02-26 0.0.6
2021-01-27 0.0.5
2021-01-22 0.0.4
2021-01-05 0.0.3
2020-12-17 0.0.2
2020-12-14 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-13 11.3.5.101
2020-12-21 11.3.0.1
2020-08-04 11.2.2.1
2020-06-23 11.2.2
2020-03-26 11.2.1
2019-12-10 11.2.0
2019-10-28 11.1.4.25
2018-09-14 10.11.1
Title: Multivariate Difference Between Two Groups
Description: Estimation of multivariate differences between two groups (e.g., multivariate sex differences) with regularized regression methods and predictive approach. See Ilmarinen et al. (2023) <doi:10.1177/08902070221088155>. Deconstructing difference score correlations (e.g., gender-equality paradox), see Ilmarinen & Lönnqvist (2024) <doi:10.1037/pspp0000508>.
Includes also tools that help in understanding difference score reliability, conditional intra-class correlations, tail-dependency, and heterogeneity of variance estimates. Package development was supported by the Academy of Finland research grant 338891.
Author: Ville-Juhani Ilmarinen [aut, cre]
Maintainer: Ville-Juhani Ilmarinen <vj.ilmarinen@gmail.com>
Diff between multid versions 1.0.1 dated 2025-09-04 and 1.0.2 dated 2025-09-23
DESCRIPTION | 8 MD5 | 15 NEWS.md | 5 R/data_documentation.R |only data |only inst/doc/multivariate_sex_differences_in_personality.R | 35 inst/doc/multivariate_sex_differences_in_personality.Rmd | 44 - inst/doc/multivariate_sex_differences_in_personality.html | 520 +++++++------- man/example_big5.Rd |only vignettes/multivariate_sex_differences_in_personality.Rmd | 44 - 10 files changed, 345 insertions(+), 326 deletions(-)
Title: Exporting Tools for 'rtables'
Description: Designed to create and display complex tables with R, the
'rtables' R package allows cells in an 'rtables' object to contain any
high-dimensional data structure, which can then be displayed with
cell-specific formatting instructions. Additionally, the
'rtables.officer' package supports export formats related to the
Microsoft Office software suite, including Microsoft Word ('docx') and
Microsoft PowerPoint ('pptx').
Author: Gabriel Becker [ctb],
Davide Garolini [aut] ,
Emily de la Rua [aut] ,
Abinaya Yogasekaram [aut] ,
Joe Zhu [aut, cre] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between rtables.officer versions 0.1.0 dated 2025-04-22 and 0.1.1 dated 2025-09-23
DESCRIPTION | 23 +++++---- MD5 | 28 ++++++------ NEWS.md | 5 ++ R/export_as_docx.R | 81 +++++++++++++++++++++++++++++++++-- R/theme_defaults.R | 4 + build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/export_rlistings.html | 9 ++- inst/doc/rtables.officer.html | 15 +++--- inst/docx_templates |only man/export_as_docx.Rd | 7 ++- man/tt_to_flextable.Rd | 4 + tests/testthat/test-export_as_docx.R | 52 +++++++++++++++++++++- tests/testthat/test-pagination.R | 10 ++-- 14 files changed, 189 insertions(+), 50 deletions(-)
More information about rtables.officer at CRAN
Permanent link
Title: Functions and C++ Header Files for Computation on Manifolds
Description: We provide a number of algorithms to estimate fundamental statistics including Fréchet mean and geometric median for manifold-valued data. Also, C++ header files are contained that implement elementary operations on manifolds such as Sphere, Grassmann, and others. See Bhattacharya and Bhattacharya (2012) <doi:10.1017/CBO9781139094764> if you are interested in statistics on manifolds, and Absil et al (2007, ISBN:9780691132983) on computational aspects of optimization on matrix manifolds.
Author: Kisung You [aut, cre]
Maintainer: Kisung You <kisung.you@outlook.com>
Diff between RiemBase versions 0.2.5 dated 2021-08-21 and 0.2.6 dated 2025-09-23
RiemBase-0.2.5/RiemBase/man/RiemBase-package.Rd |only RiemBase-0.2.6/RiemBase/DESCRIPTION | 14 ++++---- RiemBase-0.2.6/RiemBase/MD5 | 17 ++++------ RiemBase-0.2.6/RiemBase/R/RiemBase-package.R | 2 - RiemBase-0.2.6/RiemBase/R/init.R | 2 - RiemBase-0.2.6/RiemBase/README.md | 2 - RiemBase-0.2.6/RiemBase/build/partial.rdb |binary RiemBase-0.2.6/RiemBase/inst/include/manifolds/riem_04stiefel.h | 2 - RiemBase-0.2.6/RiemBase/src/Makevars | 1 RiemBase-0.2.6/RiemBase/src/Makevars.win | 1 10 files changed, 18 insertions(+), 23 deletions(-)
Title: Power and Sample Size for (Bio)Equivalence Studies
Description: Contains functions to calculate power and sample size for
various study designs used in bioequivalence studies. Use known.designs() to
see the designs supported. Power and sample size can be obtained based on
different methods, amongst them prominently the TOST procedure (two one-sided
t-tests). See README and NEWS for further information.
Author: Detlew Labes [aut, cre] ,
Helmut Schuetz [aut] ,
Benjamin Lang [aut]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>
Diff between PowerTOST versions 1.5-6 dated 2024-03-18 and 1.5-7 dated 2025-09-23
DESCRIPTION | 13 ++++--- MD5 | 40 ++++++++++++------------ NEWS.md | 8 ++++ R/helper.R | 20 +++++------- README.md | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/ABE.Rmd | 2 - inst/doc/ABE.html | 23 +++++++------ inst/doc/DP.html | 3 + inst/doc/Expected_Power_for_TOST.pdf |binary inst/doc/NI.html | 3 + inst/doc/PA.html | 17 +++++----- inst/doc/RSABE.Rmd | 58 +++++++++++++++++++---------------- inst/doc/RSABE.html | 13 ++++--- inst/doc/vignette.html | 5 +-- man/power.HVNTID.Rd | 12 +++++-- man/sampleN.HVNTID.Rd | 4 +- vignettes/ABE.Rmd | 2 - vignettes/RSABE.Rmd | 58 +++++++++++++++++++---------------- vignettes/RSABE.Rmd.orig | 12 +++++-- 21 files changed, 167 insertions(+), 128 deletions(-)
Title: Fast Alternatives to 'tidyverse' Functions
Description: A full set of fast data manipulation tools with a tidy
front-end and a fast back-end using 'collapse' and 'cheapr'.
Author: Nick Christofides [aut, cre]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between fastplyr versions 0.9.0 dated 2025-06-05 and 0.9.9 dated 2025-09-23
fastplyr-0.9.0/fastplyr/R/reconstruct.R |only fastplyr-0.9.9/fastplyr/DESCRIPTION | 10 fastplyr-0.9.9/fastplyr/MD5 | 124 fastplyr-0.9.9/fastplyr/NAMESPACE | 29 fastplyr-0.9.9/fastplyr/NEWS.md | 276 +- fastplyr-0.9.9/fastplyr/R/abc.R | 60 fastplyr-0.9.9/fastplyr/R/collapse_utils.R | 76 fastplyr-0.9.9/fastplyr/R/cpp11.R | 144 - fastplyr-0.9.9/fastplyr/R/desc.R | 46 fastplyr-0.9.9/fastplyr/R/df_utils.R | 2 fastplyr-0.9.9/fastplyr/R/exprs.R |only fastplyr-0.9.9/fastplyr/R/f_arrange.R | 15 fastplyr-0.9.9/fastplyr/R/f_count.R | 46 fastplyr-0.9.9/fastplyr/R/f_distinct.R | 8 fastplyr-0.9.9/fastplyr/R/f_duplicates.R | 11 fastplyr-0.9.9/fastplyr/R/f_expand.R | 60 fastplyr-0.9.9/fastplyr/R/f_fill.R | 38 fastplyr-0.9.9/fastplyr/R/f_filter.R | 10 fastplyr-0.9.9/fastplyr/R/f_group_by.R | 28 fastplyr-0.9.9/fastplyr/R/f_group_data.R | 3 fastplyr-0.9.9/fastplyr/R/f_join.R | 20 fastplyr-0.9.9/fastplyr/R/f_nest_by.R | 8 fastplyr-0.9.9/fastplyr/R/f_reframe.R | 4 fastplyr-0.9.9/fastplyr/R/f_rowwise.R | 16 fastplyr-0.9.9/fastplyr/R/f_select.R | 4 fastplyr-0.9.9/fastplyr/R/f_slice.R | 112 fastplyr-0.9.9/fastplyr/R/f_summarise.R | 339 +- fastplyr-0.9.9/fastplyr/R/f_ungroup.R |only fastplyr-0.9.9/fastplyr/R/fastplyr-package.R | 12 fastplyr-0.9.9/fastplyr/R/fastplyr_options.R |only fastplyr-0.9.9/fastplyr/R/group_collapse.R | 36 fastplyr-0.9.9/fastplyr/R/group_id.R | 15 fastplyr-0.9.9/fastplyr/R/group_unaware.R |only fastplyr-0.9.9/fastplyr/R/imports.R | 5 fastplyr-0.9.9/fastplyr/R/list_tidy.R | 9 fastplyr-0.9.9/fastplyr/R/re-exports.R |only fastplyr-0.9.9/fastplyr/R/rebuild.R |only fastplyr-0.9.9/fastplyr/R/remove_na.R | 26 fastplyr-0.9.9/fastplyr/R/tidy_utils.R | 938 ++----- fastplyr-0.9.9/fastplyr/README.md | 428 ++- fastplyr-0.9.9/fastplyr/man/f_arrange.Rd | 4 fastplyr-0.9.9/fastplyr/man/f_count.Rd | 10 fastplyr-0.9.9/fastplyr/man/f_distinct.Rd | 4 fastplyr-0.9.9/fastplyr/man/f_duplicates.Rd | 4 fastplyr-0.9.9/fastplyr/man/f_expand.Rd | 6 fastplyr-0.9.9/fastplyr/man/f_fill.Rd | 4 fastplyr-0.9.9/fastplyr/man/f_filter.Rd | 4 fastplyr-0.9.9/fastplyr/man/f_group_by.Rd | 14 fastplyr-0.9.9/fastplyr/man/f_nest_by.Rd | 8 fastplyr-0.9.9/fastplyr/man/f_rowwise.Rd | 4 fastplyr-0.9.9/fastplyr/man/f_slice.Rd | 26 fastplyr-0.9.9/fastplyr/man/f_ungroup.Rd |only fastplyr-0.9.9/fastplyr/man/fastplyr_options.Rd |only fastplyr-0.9.9/fastplyr/man/get_group_unaware_fns.Rd |only fastplyr-0.9.9/fastplyr/man/reexports.Rd |only fastplyr-0.9.9/fastplyr/man/remove_na.Rd | 6 fastplyr-0.9.9/fastplyr/src/cpp11.cpp | 301 +- fastplyr-0.9.9/fastplyr/src/expressions.cpp |only fastplyr-0.9.9/fastplyr/src/fastplyr.cpp | 800 ++---- fastplyr-0.9.9/fastplyr/src/fastplyr.h | 72 fastplyr-0.9.9/fastplyr/src/groups.cpp |only fastplyr-0.9.9/fastplyr/src/imports.cpp | 8 fastplyr-0.9.9/fastplyr/src/mask.cpp |only fastplyr-0.9.9/fastplyr/src/tidy.cpp | 1838 +++++--------- fastplyr-0.9.9/fastplyr/tests/testthat.R | 1 fastplyr-0.9.9/fastplyr/tests/testthat/test-df_utils.R | 3 fastplyr-0.9.9/fastplyr/tests/testthat/test-f_arrange.R | 1 fastplyr-0.9.9/fastplyr/tests/testthat/test-f_join.R |only fastplyr-0.9.9/fastplyr/tests/testthat/test-f_mutate.R |only fastplyr-0.9.9/fastplyr/tests/testthat/test-f_reframe.R |only fastplyr-0.9.9/fastplyr/tests/testthat/test-f_summarise.R | 158 + fastplyr-0.9.9/fastplyr/tests/testthat/test-tidy_utils.R |only 72 files changed, 2993 insertions(+), 3241 deletions(-)
Title: Extending the Range of Functions for Probability Distributions
Description: A consistent, unified and extensible
framework for estimation of parameters for probability distributions,
including parameter estimation procedures that allow for weighted samples;
the current set of distributions included are: the standard beta,
The four-parameter beta, Burr, gamma, Gumbel, Johnson SB and SU, Laplace,
logistic, normal, symmetric truncated normal, truncated normal,
symmetric-reflected truncated beta, standard symmetric-reflected truncated
beta, triangular, uniform, and Weibull distributions; decision criteria
and selections based on these decision criteria.
Author: Haizhen Wu [aut],
A. Jonathan R. Godfrey [aut],
Kondaswamy Govindaraju [aut],
Sarah Pirikahu [aut],
Oleksii Nikolaienko [cre, ctb]
Maintainer: Oleksii Nikolaienko <oleksii.nikolaienko@gmail.com>
Diff between ExtDist versions 0.7-3 dated 2025-06-09 and 0.7-4 dated 2025-09-23
DESCRIPTION | 8 ++--- MD5 | 14 +++++----- R/Normal_trunc_ab.R | 38 ++++++++++++++-------------- R/wmle.R | 2 - README.md | 6 +++- build/vignette.rds |binary inst/doc/ParaEst-and-DistSel-by-ExtDist.pdf |binary man/Normal_trunc_ab.Rd | 14 +++++----- 8 files changed, 43 insertions(+), 39 deletions(-)
Title: Lightweight Utilities for 'DIZ' R Package Development
Description: Lightweight utility functions used for the R package
development infrastructure inside the data integration centers ('DIZ')
to standardize and facilitate repetitive tasks such as setting up a
database connection or issuing notification messages and to avoid
redundancy.
Author: Jonathan M. Mang [aut, cre] ,
Lorenz A. Kapsner [aut] ,
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen, Germany [cph]
Maintainer: Jonathan M. Mang <jonathan.mang@uk-erlangen.de>
Diff between DIZtools versions 1.0.2 dated 2025-03-17 and 1.0.3 dated 2025-09-23
DESCRIPTION | 15 +++++++++------ MD5 | 10 +++++++--- NAMESPACE | 3 +++ R/get_package_names.R |only README.md | 7 ++----- man/calculate_check_digit.Rd |only man/get_package_names.Rd |only man/test_check_digit.Rd |only 8 files changed, 21 insertions(+), 14 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-21 0.4.1
2023-01-16 0.4.0
2022-11-16 0.3.1
2022-10-05 0.3.0
2022-05-11 0.2.1
2022-03-11 0.1.1
2021-11-22 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-03 3.3.4
2024-06-12 3.3.3
2024-03-09 3.3.2
2023-09-12 3.3.1
2023-03-03 3.3.0
2022-11-18 3.2.1
2022-10-01 3.2.0
Title: R Interface for 'TiddlyWiki'
Description: 'TiddlyWiki' is a unique non-linear notebook for capturing, organising and sharing complex information. 'rtiddlywiki' is a R interface of 'TiddlyWiki' <https://tiddlywiki.com> to create new tiddler from Rmarkdown file, and then put into a local 'TiddlyWiki' node.js server if it is available.
Author: Bangyou Zheng [aut, cre]
Maintainer: Bangyou Zheng <bangyou.zheng@csiro.au>
Diff between rtiddlywiki versions 0.1.0 dated 2022-07-05 and 0.5.0 dated 2025-09-23
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Title: Visualising How Nonlinear Dimension Reduction Warps Your Data
Description: To construct a model in 2-D space from 2-D nonlinear
dimension reduction data and then lift it to the high-dimensional
space. Additionally, provides tools to visualise the model overlay the
data in 2-D and high-dimensional space. Furthermore, provides
summaries and diagnostics to evaluate the nonlinear dimension
reduction layout.
Author: Jayani P. Gamage [aut, cre] ,
Dianne Cook [aut] ,
Paul Harrison [aut] ,
Michael Lydeamore [aut] ,
Thiyanga S. Talagala [aut]
Maintainer: Jayani P. Gamage <jayanilakshika76@gmail.com>
Diff between quollr versions 0.3.7 dated 2025-07-22 and 0.3.13 dated 2025-09-23
quollr-0.3.13/quollr/DESCRIPTION | 8 quollr-0.3.13/quollr/MD5 | 156 - quollr-0.3.13/quollr/NAMESPACE | 8 quollr-0.3.13/quollr/NEWS.md | 4 quollr-0.3.13/quollr/R/2d.R | 79 quollr-0.3.13/quollr/R/data.R | 2 quollr-0.3.13/quollr/R/data_preprocessing.R | 22 quollr-0.3.13/quollr/R/highd.R | 27 quollr-0.3.13/quollr/R/link_plots.R | 14 quollr-0.3.13/quollr/R/model.R | 41 quollr-0.3.13/quollr/R/parameters.R | 18 quollr-0.3.13/quollr/R/prediction.R | 94 quollr-0.3.13/quollr/R/projection.R | 4 quollr-0.3.13/quollr/R/util.R | 10 quollr-0.3.13/quollr/data/scurve_model_obj.rda |binary quollr-0.3.13/quollr/data/scurve_plts.rda |binary quollr-0.3.13/quollr/inst/doc/quollr1quickstart.R | 4 quollr-0.3.13/quollr/inst/doc/quollr1quickstart.Rmd | 4 quollr-0.3.13/quollr/inst/doc/quollr1quickstart.html | 137 - quollr-0.3.13/quollr/inst/doc/quollr2dataprocessing.html | 5 quollr-0.3.13/quollr/inst/doc/quollr3hexbin.R | 12 quollr-0.3.13/quollr/inst/doc/quollr3hexbin.Rmd | 12 quollr-0.3.13/quollr/inst/doc/quollr3hexbin.html | 43 quollr-0.3.13/quollr/inst/doc/quollr4algo.R | 6 quollr-0.3.13/quollr/inst/doc/quollr4algo.Rmd | 6 quollr-0.3.13/quollr/inst/doc/quollr4algo.html | 99 quollr-0.3.13/quollr/inst/doc/quollr5summary.R | 16 quollr-0.3.13/quollr/inst/doc/quollr5summary.Rmd | 16 quollr-0.3.13/quollr/inst/doc/quollr5summary.html | 73 quollr-0.3.13/quollr/inst/doc/quollr6bestbinwidth.html | 7 quollr-0.3.13/quollr/inst/doc/quollr7bestfit.html | 7 quollr-0.3.13/quollr/man/assign_data.Rd | 6 quollr-0.3.13/quollr/man/augment.Rd | 23 quollr-0.3.13/quollr/man/augment.highd_vis_model.Rd |only quollr-0.3.13/quollr/man/calc_bins_y.Rd | 6 quollr-0.3.13/quollr/man/comb_all_data_model_error.Rd | 3 quollr-0.3.13/quollr/man/compute_mean_density_hex.Rd | 4 quollr-0.3.13/quollr/man/find_low_dens_hex.Rd | 8 quollr-0.3.13/quollr/man/find_non_empty_bins.Rd | 6 quollr-0.3.13/quollr/man/fit_highd_model.Rd | 10 quollr-0.3.13/quollr/man/gen_centroids.Rd | 6 quollr-0.3.13/quollr/man/gen_diffbin1_errors.Rd | 4 quollr-0.3.13/quollr/man/gen_edges.Rd | 2 quollr-0.3.13/quollr/man/glance.Rd | 20 quollr-0.3.13/quollr/man/glance.highd_vis_model.Rd |only quollr-0.3.13/quollr/man/group_hex_pts.Rd |only quollr-0.3.13/quollr/man/hex_binning.Rd | 6 quollr-0.3.13/quollr/man/merge_hexbin_centroids.Rd |only quollr-0.3.13/quollr/man/merge_hexbin_mean.Rd |only quollr-0.3.13/quollr/man/scurve_model_obj.Rd | 2 quollr-0.3.13/quollr/man/show_error_link_plots.Rd | 3 quollr-0.3.13/quollr/man/tri_bin_centroids.Rd | 2 quollr-0.3.13/quollr/src/2d.cpp | 4 quollr-0.3.13/quollr/src/Makevars | 3 quollr-0.3.13/quollr/tests/testthat/_snaps/2d.md | 71 quollr-0.3.13/quollr/tests/testthat/_snaps/geom_hexgrid/geom-hexgrid-basic-with-selected-bin-centroids.svg | 1010 ++++++++-- quollr-0.3.13/quollr/tests/testthat/_snaps/geom_trimesh/geom-trimesh-basic-with-selected-bin-centroids.svg | 557 +++++ quollr-0.3.13/quollr/tests/testthat/_snaps/highd.md | 28 quollr-0.3.13/quollr/tests/testthat/_snaps/link_plots.md | 56 quollr-0.3.13/quollr/tests/testthat/_snaps/model.md | 78 quollr-0.3.13/quollr/tests/testthat/_snaps/parameters.md | 57 quollr-0.3.13/quollr/tests/testthat/_snaps/prediction.md | 48 quollr-0.3.13/quollr/tests/testthat/_snaps/projection.md | 30 quollr-0.3.13/quollr/tests/testthat/_snaps/projection/2-d-projection-from-langevitour.svg | 352 +++ quollr-0.3.13/quollr/tests/testthat/test-2d.R | 27 quollr-0.3.13/quollr/tests/testthat/test-data_processing.R | 1 quollr-0.3.13/quollr/tests/testthat/test-geom_hexgrid.R | 2 quollr-0.3.13/quollr/tests/testthat/test-geom_trimesh.R | 3 quollr-0.3.13/quollr/tests/testthat/test-highd.R | 2 quollr-0.3.13/quollr/tests/testthat/test-link_plots.R | 9 quollr-0.3.13/quollr/tests/testthat/test-model.R | 14 quollr-0.3.13/quollr/tests/testthat/test-parameters.R | 8 quollr-0.3.13/quollr/tests/testthat/test-prediction.R | 22 quollr-0.3.13/quollr/tests/testthat/test-projection.R | 2 quollr-0.3.13/quollr/tests/testthat/test-util.R | 10 quollr-0.3.13/quollr/vignettes/quollr1quickstart.Rmd | 4 quollr-0.3.13/quollr/vignettes/quollr3hexbin.Rmd | 12 quollr-0.3.13/quollr/vignettes/quollr4algo.Rmd | 6 quollr-0.3.13/quollr/vignettes/quollr5summary.Rmd | 16 quollr-0.3.13/quollr/vignettes/quollr7bestfit_files/figure-html/unnamed-chunk-3-1.png |binary quollr-0.3.7/quollr/man/extract_hexbin_centroids.Rd |only quollr-0.3.7/quollr/man/extract_hexbin_mean.Rd |only quollr-0.3.7/quollr/man/find_pts.Rd |only 83 files changed, 2530 insertions(+), 947 deletions(-)
Title: High-Level Plotting Built Upon 'ggplot2' and Other Plotting
Packages
Description: Provides high-level API and a wide range of options to create stunning, publication-quality plots effortlessly.
It is built upon 'ggplot2' and other plotting packages, and is designed to be easy to use and to work seamlessly with 'ggplot2' objects.
It is particularly useful for creating complex plots with multiple layers, facets, and annotations.
It also provides a set of functions to create plots for specific types of data, such as Venn diagrams, alluvial diagrams, and phylogenetic trees.
The package is designed to be flexible and customizable, and to work well with the 'ggplot2' ecosystem.
The API can be found at <https://pwwang.github.io/plotthis/reference/index.html>.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>
Diff between plotthis versions 0.7.4 dated 2025-08-23 and 0.8.0 dated 2025-09-23
DESCRIPTION | 8 ++-- MD5 | 31 +++++++++-------- NAMESPACE | 1 R/barplot.R | 85 ++++++++++++++++++++++++------------------------ R/corplot.R | 37 ++++++++++++++++---- R/dotplot.R | 2 + R/gsea.R | 1 R/heatmap.R | 4 +- R/jitterplot.R |only R/network.R | 11 ++++-- R/velocityplot.R | 7 +++ man/BarPlotAtomic.Rd | 2 - man/BarPlotGrouped.Rd | 2 - man/BarPlotSingle.Rd | 2 - man/JitterPlotAtomic.Rd |only man/barplot.Rd | 4 +- man/dotplot.Rd | 2 + man/jitterplot.Rd |only 18 files changed, 123 insertions(+), 76 deletions(-)
Title: Network Analysis and Visualization
Description: Collection of functions for fast manipulation, handling, and analysis of large-scale
networks based on family and social data. Functions are utility functions used to manipulate data
in three "formats": sparse adjacency matrices, pedigree trio family data, and pedigree family data.
When possible, the functions should be able to handle millions of data points quickly for use in combination
with data from large public national registers and databases.
Kenneth Lange (2003, ISBN:978-8181281135).
Author: Claus Thorn Ekstroem [aut, cre],
Bendix Carstensen [ctb]
Maintainer: Claus Thorn Ekstroem <ekstrom@sund.ku.dk>
Diff between networkR versions 0.1.4 dated 2025-09-21 and 0.1.5 dated 2025-09-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/RcppExports.R | 2 +- man/make_parental_chain.Rd | 2 +- src/cluster_parental_chains.cpp | 15 +++++++-------- 5 files changed, 17 insertions(+), 18 deletions(-)
Title: Plots for Compositional Data
Description: Provides a collection of easy-to-use functions for creating
visualizations of compositional data using 'ggplot2'. Includes support
for common plotting techniques in compositional data analysis.
Author: Marc Comas-Cufi [aut, cre]
Maintainer: Marc Comas-Cufi <mcomas@imae.udg.edu>
Diff between coda.plot versions 0.1.9 dated 2025-04-20 and 0.1.10 dated 2025-09-23
DESCRIPTION | 15 +++--- MD5 | 16 +++--- NAMESPACE | 5 +- R/clr_ciplot.R | 13 +++-- R/coda.plot.R | 3 - R/ternary_diagram.R | 114 ++++++++++++++++++++++++++++++++++++++++--------- R/zzz.R | 34 +++++++++++++- man/clr_biplot.Rd | 7 ++- man/ternary_diagram.Rd | 3 - 9 files changed, 161 insertions(+), 49 deletions(-)
Title: An Interface to the 'Arctos' Database
Description: Performs requests to the 'Arctos' API to download data. Provides a
set of builder classes for performing complex requests, as well as a set of
simple functions for automating many common requests and workflows. More
information about 'Arctos' can be found in
Cicero et al. (2024) <doi:10.1371/journal.pone.0296478> or on their website
<https://arctosdb.org/>.
Author: Harlan R. Williams [aut, cre],
Marlon E. Cobos [aut],
Jocelyn P. Colella [aut],
Michelle S. Koo [aut],
Vijay Barve [aut]
Maintainer: Harlan R. Williams <harlanrhwilliams@gmail.com>
Diff between ArctosR versions 0.1.2 dated 2025-09-15 and 0.1.3 dated 2025-09-23
ArctosR-0.1.2/ArctosR/tests/testthat/save_csv_test.json |only ArctosR-0.1.2/ArctosR/tests/testthat/test.json |only ArctosR-0.1.3/ArctosR/DESCRIPTION | 8 ArctosR-0.1.3/ArctosR/MD5 | 31 ArctosR-0.1.3/ArctosR/NAMESPACE | 1 ArctosR-0.1.3/ArctosR/NEWS.md | 6 ArctosR-0.1.3/ArctosR/R/frontend.R | 35 ArctosR-0.1.3/ArctosR/R/utils.R | 2 ArctosR-0.1.3/ArctosR/build/vignette.rds |binary ArctosR-0.1.3/ArctosR/inst/doc/example.R | 194 +- ArctosR-0.1.3/ArctosR/inst/doc/example.Rmd | 113 + ArctosR-0.1.3/ArctosR/inst/doc/example.html | 962 ++++++------ ArctosR-0.1.3/ArctosR/inst/doc/overview.R | 252 +-- ArctosR-0.1.3/ArctosR/inst/doc/overview.html | 1195 ++++++++-------- ArctosR-0.1.3/ArctosR/man/get_request_url.Rd |only ArctosR-0.1.3/ArctosR/tests/testthat/test-frontend.R | 21 ArctosR-0.1.3/ArctosR/vignettes/example.Rmd | 113 + ArctosR-0.1.3/ArctosR/vignettes/figures |only 18 files changed, 1656 insertions(+), 1277 deletions(-)
Title: Matching Algorithms in R and C++
Description: Computes matching algorithms quickly using Rcpp.
Implements the Gale-Shapley Algorithm to compute the stable
matching for two-sided markets, such as the stable marriage
problem and the college-admissions problem. Implements Irving's
Algorithm for the stable roommate problem. Implements the top
trading cycle algorithm for the indivisible goods trading problem.
Author: Jan Tilly [aut, cre],
Nick Janetos [aut]
Maintainer: Jan Tilly <jantilly@gmail.com>
Diff between matchingR versions 1.3.3 dated 2021-05-25 and 2.0.0 dated 2025-09-23
matchingR-1.3.3/matchingR/R/deprecated.R |only matchingR-1.3.3/matchingR/man/matchingR-deprecated.Rd |only matchingR-1.3.3/matchingR/man/matchingR-package.Rd |only matchingR-2.0.0/matchingR/DESCRIPTION | 17 matchingR-2.0.0/matchingR/MD5 | 41 matchingR-2.0.0/matchingR/NEWS.md | 72 - matchingR-2.0.0/matchingR/R/RcppExports.R | 7 matchingR-2.0.0/matchingR/R/galeshapley.R | 2 matchingR-2.0.0/matchingR/R/matchingR.R | 2 matchingR-2.0.0/matchingR/README.md | 59 - matchingR-2.0.0/matchingR/build/vignette.rds |binary matchingR-2.0.0/matchingR/inst/doc/matchingR-intro.R | 14 matchingR-2.0.0/matchingR/inst/doc/matchingR-intro.Rmd | 36 matchingR-2.0.0/matchingR/inst/doc/matchingR-intro.html | 666 ++++++------ matchingR-2.0.0/matchingR/man/cpp_wrapper_galeshapley.Rd | 2 matchingR-2.0.0/matchingR/man/galeShapley.marriageMarket.Rd | 2 matchingR-2.0.0/matchingR/src/Makevars | 1 matchingR-2.0.0/matchingR/src/galeshapley.cpp | 58 - matchingR-2.0.0/matchingR/src/roommate.cpp | 2 matchingR-2.0.0/matchingR/src/toptradingcycle.cpp | 2 matchingR-2.0.0/matchingR/tests/testthat/test_galeshapley.R | 6 matchingR-2.0.0/matchingR/vignettes/bibliography.bib | 2 matchingR-2.0.0/matchingR/vignettes/matchingR-intro.Rmd | 36 23 files changed, 577 insertions(+), 450 deletions(-)
Title: Scientific Journal and Sci-Fi Themed Color Palettes for
'ggplot2'
Description: A collection of 'ggplot2' color palettes inspired by
plots in scientific journals, data visualization libraries,
science fiction movies, and TV shows.
Author: Nan Xiao [aut, cre, cph] ,
Joshua Cook [ctb],
Clara Jegousse [ctb],
Hui Chen [ctb],
Miaozhu Li [ctb],
iTerm2-Color-Schemes contributors [ctb, cph] ,
Winston Chang [ctb, cph]
Maintainer: Nan Xiao <me@nanx.me>
Diff between ggsci versions 3.2.0 dated 2024-06-17 and 4.0.0 dated 2025-09-23
ggsci-3.2.0/ggsci/inst/logo |only ggsci-4.0.0/ggsci/DESCRIPTION | 26 - ggsci-4.0.0/ggsci/MD5 | 182 +++++----- ggsci-4.0.0/ggsci/NAMESPACE | 16 ggsci-4.0.0/ggsci/NEWS.md | 26 + ggsci-4.0.0/ggsci/R/discrete-aaas.R | 21 - ggsci-4.0.0/ggsci/R/discrete-atlassian.R |only ggsci-4.0.0/ggsci/R/discrete-bmj.R | 21 - ggsci-4.0.0/ggsci/R/discrete-cosmic.R | 21 - ggsci-4.0.0/ggsci/R/discrete-d3.R | 19 - ggsci-4.0.0/ggsci/R/discrete-flatui.R | 19 - ggsci-4.0.0/ggsci/R/discrete-frontiers.R | 30 - ggsci-4.0.0/ggsci/R/discrete-futurama.R | 21 - ggsci-4.0.0/ggsci/R/discrete-igv.R | 23 - ggsci-4.0.0/ggsci/R/discrete-iterm.R |only ggsci-4.0.0/ggsci/R/discrete-jama.R | 21 - ggsci-4.0.0/ggsci/R/discrete-jco.R | 21 - ggsci-4.0.0/ggsci/R/discrete-lancet.R | 21 - ggsci-4.0.0/ggsci/R/discrete-locuszoom.R | 21 - ggsci-4.0.0/ggsci/R/discrete-nejm.R | 21 - ggsci-4.0.0/ggsci/R/discrete-npg.R | 21 - ggsci-4.0.0/ggsci/R/discrete-observable.R | 21 - ggsci-4.0.0/ggsci/R/discrete-primer.R |only ggsci-4.0.0/ggsci/R/discrete-rickandmorty.R | 21 - ggsci-4.0.0/ggsci/R/discrete-simpsons.R | 21 - ggsci-4.0.0/ggsci/R/discrete-startrek.R | 21 - ggsci-4.0.0/ggsci/R/discrete-tron.R | 30 - ggsci-4.0.0/ggsci/R/discrete-uchicago.R | 19 - ggsci-4.0.0/ggsci/R/discrete-ucscgb.R | 21 - ggsci-4.0.0/ggsci/R/examples.R |only ggsci-4.0.0/ggsci/R/palettes-iterm.R |only ggsci-4.0.0/ggsci/R/palettes.R | 33 + ggsci-4.0.0/ggsci/R/staticimports.R |only ggsci-4.0.0/ggsci/R/utils.R | 75 ---- ggsci-4.0.0/ggsci/README.md | 12 ggsci-4.0.0/ggsci/build/vignette.rds |binary ggsci-4.0.0/ggsci/inst/WORDLIST | 7 ggsci-4.0.0/ggsci/inst/doc/ggsci.R | 36 + ggsci-4.0.0/ggsci/inst/doc/ggsci.Rmd | 66 ++- ggsci-4.0.0/ggsci/inst/doc/ggsci.html | 156 +++++--- ggsci-4.0.0/ggsci/man/example_plots.Rd |only ggsci-4.0.0/ggsci/man/figures/README-ggsci-aaas-1.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-atlassian-1.png |only ggsci-4.0.0/ggsci/man/figures/README-ggsci-bmj-1.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-bs5-1.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-cosmic-1.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-cosmic-2.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-cosmic-3.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-d3-1.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-flatui-1.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-frontiers-1.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-futurama-1.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-igv-1.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-iterm-1.png |only ggsci-4.0.0/ggsci/man/figures/README-ggsci-jama-1.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-jco-1.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-lancet-1.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-locuszoom-1.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-material-1.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-nejm-1.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-npg-1.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-observable-1.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-primer-1.png |only ggsci-4.0.0/ggsci/man/figures/README-ggsci-rickandmorty-1.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-simpsons-1.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-startrek-1.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-tron-1.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-tw3-1.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-uchicago-1.png |binary ggsci-4.0.0/ggsci/man/figures/README-ggsci-ucscgb-1.png |binary ggsci-4.0.0/ggsci/man/figures/logo.png |binary ggsci-4.0.0/ggsci/man/ggsci-package.Rd | 4 ggsci-4.0.0/ggsci/man/iterm_palettes.Rd |only ggsci-4.0.0/ggsci/man/pal_atlassian.Rd |only ggsci-4.0.0/ggsci/man/pal_iterm.Rd |only ggsci-4.0.0/ggsci/man/pal_primer.Rd |only ggsci-4.0.0/ggsci/man/scale_aaas.Rd | 21 - ggsci-4.0.0/ggsci/man/scale_atlassian.Rd |only ggsci-4.0.0/ggsci/man/scale_bmj.Rd | 21 - ggsci-4.0.0/ggsci/man/scale_cosmic.Rd | 21 - ggsci-4.0.0/ggsci/man/scale_d3.Rd | 19 - ggsci-4.0.0/ggsci/man/scale_flatui.Rd | 19 - ggsci-4.0.0/ggsci/man/scale_frontiers.Rd | 30 - ggsci-4.0.0/ggsci/man/scale_futurama.Rd | 21 - ggsci-4.0.0/ggsci/man/scale_igv.Rd | 23 - ggsci-4.0.0/ggsci/man/scale_iterm.Rd |only ggsci-4.0.0/ggsci/man/scale_jama.Rd | 21 - ggsci-4.0.0/ggsci/man/scale_jco.Rd | 21 - ggsci-4.0.0/ggsci/man/scale_lancet.Rd | 21 - ggsci-4.0.0/ggsci/man/scale_locuszoom.Rd | 21 - ggsci-4.0.0/ggsci/man/scale_nejm.Rd | 21 - ggsci-4.0.0/ggsci/man/scale_npg.Rd | 21 - ggsci-4.0.0/ggsci/man/scale_observable.Rd | 21 - ggsci-4.0.0/ggsci/man/scale_primer.Rd |only ggsci-4.0.0/ggsci/man/scale_rickandmorty.Rd | 21 - ggsci-4.0.0/ggsci/man/scale_simpsons.Rd | 21 - ggsci-4.0.0/ggsci/man/scale_startrek.Rd | 21 - ggsci-4.0.0/ggsci/man/scale_tron.Rd | 30 - ggsci-4.0.0/ggsci/man/scale_uchicago.Rd | 19 - ggsci-4.0.0/ggsci/man/scale_ucscgb.Rd | 21 - ggsci-4.0.0/ggsci/vignettes/ggsci.Rmd | 66 ++- 101 files changed, 545 insertions(+), 1070 deletions(-)