Title: The 'jamovi' Analyses
Description: A suite of common statistical methods such as descriptives,
t-tests, ANOVAs, regression, correlation matrices, proportion tests,
contingency tables, and factor analysis. This package is also useable from
the 'jamovi' statistical spreadsheet (see <https://www.jamovi.org> for more
information).
Author: Ravi Selker [aut, cph],
Jonathon Love [aut, cre, cph],
Damian Dropmann [aut, cph],
Victor Moreno [ctb, cph],
Maurizio Agosti [ctb, cph],
Sebastian Jentschke [ctb, cph]
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmv versions 2.7.0 dated 2025-06-11 and 2.7.7 dated 2025-09-17
jmv-2.7.0/jmv/tests/testthat/testthat-problems.rds |only jmv-2.7.7/jmv/DESCRIPTION | 8 ++++---- jmv-2.7.7/jmv/MD5 | 13 ++++++------- jmv-2.7.7/jmv/R/ttestis.b.R | 2 ++ jmv-2.7.7/jmv/R/ttestones.b.R | 1 + jmv-2.7.7/jmv/R/ttestps.b.R | 2 +- jmv-2.7.7/jmv/tests/testthat/testerrors.R | 14 +++++++------- jmv-2.7.7/jmv/tests/testthat/testttestis.R | 4 ++-- 8 files changed, 23 insertions(+), 21 deletions(-)
Title: Investigating New Projection Pursuit Index Functions
Description: Projection pursuit is used to find interesting low-dimensional
projections of high-dimensional data by optimizing an index over all
possible projections. The 'spinebil' package contains methods to evaluate
the performance of projection pursuit index functions using tour methods.
A paper describing the methods can be found at <doi:10.1007/s00180-020-00954-8>.
Author: Ursula Laa [aut] ,
Dianne Cook [aut] ,
Tina Rashid Jafari [aut, cre]
Maintainer: Tina Rashid Jafari <tina.rashidjafari@gmail.com>
Diff between spinebil versions 0.1.6 dated 2025-07-11 and 1.0.4 dated 2025-09-17
spinebil-0.1.6/spinebil/NEWS |only spinebil-0.1.6/spinebil/R/indexFunctions.R |only spinebil-0.1.6/spinebil/R/samplingFunctions.R |only spinebil-0.1.6/spinebil/R/spinebil-package.R |only spinebil-0.1.6/spinebil/R/utils-tourr.R |only spinebil-0.1.6/spinebil/man/basisMatrix.Rd |only spinebil-0.1.6/spinebil/man/basisVector.Rd |only spinebil-0.1.6/spinebil/man/compareSmoothing.Rd |only spinebil-0.1.6/spinebil/man/distanceDist.Rd |only spinebil-0.1.6/spinebil/man/distanceToSp.Rd |only spinebil-0.1.6/spinebil/man/getIndexMean.Rd |only spinebil-0.1.6/spinebil/man/getTrace.Rd |only spinebil-0.1.6/spinebil/man/jitterAngle.Rd |only spinebil-0.1.6/spinebil/man/jitterPoints.Rd |only spinebil-0.1.6/spinebil/man/pipeData.Rd |only spinebil-0.1.6/spinebil/man/plotRotation.Rd |only spinebil-0.1.6/spinebil/man/plotSmoothingComparison.Rd |only spinebil-0.1.6/spinebil/man/plotTrace.Rd |only spinebil-0.1.6/spinebil/man/profileRotation.Rd |only spinebil-0.1.6/spinebil/man/scagIndex.Rd |only spinebil-0.1.6/spinebil/man/sinData.Rd |only spinebil-0.1.6/spinebil/man/spiralData.Rd |only spinebil-0.1.6/spinebil/man/squintAngleEstimate.Rd |only spinebil-0.1.6/spinebil/man/timeSequence.Rd |only spinebil-1.0.4/spinebil/DESCRIPTION | 12 + spinebil-1.0.4/spinebil/MD5 | 101 +++++++++------ spinebil-1.0.4/spinebil/NAMESPACE | 57 +++++--- spinebil-1.0.4/spinebil/NEWS.md |only spinebil-1.0.4/spinebil/R/distances.R | 46 ++---- spinebil-1.0.4/spinebil/R/index_functions.R |only spinebil-1.0.4/spinebil/R/index_mean.R |only spinebil-1.0.4/spinebil/R/index_noise_threshold.R |only spinebil-1.0.4/spinebil/R/index_scale.R |only spinebil-1.0.4/spinebil/R/rotation.R | 36 ++--- spinebil-1.0.4/spinebil/R/sample_size_effect.R |only spinebil-1.0.4/spinebil/R/sampling_functions.R |only spinebil-1.0.4/spinebil/R/smoothing.R | 50 +++---- spinebil-1.0.4/spinebil/R/spinebil_package.R |only spinebil-1.0.4/spinebil/R/timer.R | 8 - spinebil-1.0.4/spinebil/R/tracing.R | 44 +++--- spinebil-1.0.4/spinebil/R/utils.R | 6 spinebil-1.0.4/spinebil/R/utils_data.R |only spinebil-1.0.4/spinebil/R/utils_tourr.R |only spinebil-1.0.4/spinebil/README.md | 68 +--------- spinebil-1.0.4/spinebil/build |only spinebil-1.0.4/spinebil/inst/doc |only spinebil-1.0.4/spinebil/man/basis_matrix.Rd |only spinebil-1.0.4/spinebil/man/basis_nearby.Rd | 2 spinebil-1.0.4/spinebil/man/basis_vector.Rd |only spinebil-1.0.4/spinebil/man/compare_smoothing.Rd |only spinebil-1.0.4/spinebil/man/data_gen.Rd |only spinebil-1.0.4/spinebil/man/distance_dist.Rd |only spinebil-1.0.4/spinebil/man/distance_to_sp.Rd |only spinebil-1.0.4/spinebil/man/figures/README-example-1.png |binary spinebil-1.0.4/spinebil/man/figures/spinebil.png |only spinebil-1.0.4/spinebil/man/geodesic_info.Rd | 2 spinebil-1.0.4/spinebil/man/get_index_mean.Rd |only spinebil-1.0.4/spinebil/man/get_trace.Rd |only spinebil-1.0.4/spinebil/man/jitter_angle.Rd |only spinebil-1.0.4/spinebil/man/jitter_points.Rd |only spinebil-1.0.4/spinebil/man/noise_gen.Rd |only spinebil-1.0.4/spinebil/man/pipe_data.Rd |only spinebil-1.0.4/spinebil/man/plot_rotation.Rd |only spinebil-1.0.4/spinebil/man/plot_smoothing_comparison.Rd |only spinebil-1.0.4/spinebil/man/plot_trace.Rd |only spinebil-1.0.4/spinebil/man/ppi_mean.Rd |only spinebil-1.0.4/spinebil/man/ppi_noise_threshold.Rd |only spinebil-1.0.4/spinebil/man/ppi_samplesize_effect.Rd |only spinebil-1.0.4/spinebil/man/ppi_scale.Rd |only spinebil-1.0.4/spinebil/man/profile_rotation.Rd |only spinebil-1.0.4/spinebil/man/scag_index.Rd |only spinebil-1.0.4/spinebil/man/sin_data.Rd |only spinebil-1.0.4/spinebil/man/spinebil-package.Rd | 12 - spinebil-1.0.4/spinebil/man/spiral_data.Rd |only spinebil-1.0.4/spinebil/man/squint_angle_estimate.Rd |only spinebil-1.0.4/spinebil/man/step_fraction.Rd | 2 spinebil-1.0.4/spinebil/man/time_sequence.Rd |only spinebil-1.0.4/spinebil/vignettes |only 78 files changed, 214 insertions(+), 232 deletions(-)
Title: Rcpp Hidden Markov Model
Description: Collection of functions to evaluate sequences, decode hidden states and estimate parameters from a single or multiple sequences of a discrete time Hidden Markov Model. The observed values can be modeled by a multinomial distribution for categorical/labeled emissions, a mixture of Gaussians for continuous data and also a mixture of Poissons for discrete values. It includes functions for random initialization, simulation, backward or forward sequence evaluation, Viterbi or forward-backward decoding and parameter estimation using an Expectation-Maximization approach.
Author: Roberto A. Cardenas-Ovando [aut, cre],
Julieta Noguez [aut],
Claudia Rangel-Escareno [aut]
Maintainer: Roberto A. Cardenas-Ovando <robalecarova@gmail.com>
Diff between RcppHMM versions 1.2.2 dated 2017-11-21 and 1.2.2.1 dated 2025-09-17
DESCRIPTION | 27 +++++++++++++++++++-------- MD5 | 6 +++--- src/Makevars | 2 +- src/Makevars.win | 2 +- 4 files changed, 24 insertions(+), 13 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-10 0.1-10
Title: Analysis of Incubation Data
Description: Suite of functions to study animal incubation.
At the core of incR
lies an algorithm that allows for the scoring of
incubation behaviour. Additionally, several functions
extract biologically relevant metrics of incubation such as off-bout number
and off-bout duration - for a review of avian incubation studies,
see Nests, Eggs, and Incubation: New ideas about avian reproduction (2015)
edited by D. Charles Deeming and S. James Reynolds <doi:10.1093/acprof:oso/9780198718666.001.0001>.
Author: Pablo Capilla-Lasheras [aut, cre]
Maintainer: Pablo Capilla-Lasheras <pacapilla@gmail.com>
Diff between incR versions 2.1.0 dated 2023-04-18 and 2.1.1 dated 2025-09-17
DESCRIPTION | 10 MD5 | 35 - NAMESPACE | 1 NEWS.md | 4 R/inRt.R | 506 ++++++++--------- R/incRact.R | 136 ++-- R/incRplot.R | 158 ++--- R/incRprep.R | 164 ++--- R/incRscan.R | 2 R/incRscan_v3.R | 635 +++++++++++---------- README.md | 56 - build/vignette.rds |binary inst/doc/incR_pipeline.R | 216 +++---- inst/doc/incR_pipeline.html | 1278 ++++++++++++++++++++++---------------------- man/incR.Rd | 5 man/incRplot.Rd | 4 man/incRprep.Rd | 4 man/incRscan_v3.Rd |only man/incRt.Rd | 8 19 files changed, 1633 insertions(+), 1589 deletions(-)
Title: Interactively Explore Local Explanations with the Radial Tour
Description: Given a non-linear model, calculate the local explanation.
We purpose view the data space, explanation
space, and model residuals as ensemble graphic interactive on a shiny
application. After an observation of interest is identified, the normalized
variable importance of the local explanation is used as a 1D projection
basis. The support of the local explanation is then explored by changing
the basis with the use of the radial tour <doi:10.32614/RJ-2020-027>;
<doi:10.1080/10618600.1997.10474754>.
Author: Nicholas Spyrison [aut, cre]
Maintainer: Nicholas Spyrison <spyrison@gmail.com>
Diff between cheem versions 0.4.1 dated 2025-08-26 and 0.4.2 dated 2025-09-17
cheem-0.4.1/cheem/inst/shiny_apps/cheem/rsconnect |only cheem-0.4.1/cheem/man/rnorm_from.Rd |only cheem-0.4.2/cheem/DESCRIPTION | 10 - cheem-0.4.2/cheem/MD5 | 44 +++--- cheem-0.4.2/cheem/NAMESPACE | 1 cheem-0.4.2/cheem/NEWS.md | 7 + cheem-0.4.2/cheem/R/0_util.r | 86 ++++++------- cheem-0.4.2/cheem/build/vignette.rds |binary cheem-0.4.2/cheem/inst/doc/getting-started-with-cheem.html | 10 - cheem-0.4.2/cheem/man/as_logical_index.Rd | 1 cheem-0.4.2/cheem/man/cheem.Rd | 2 cheem-0.4.2/cheem/man/color_scale_of.Rd | 1 cheem-0.4.2/cheem/man/contains_nonnumeric.Rd | 1 cheem-0.4.2/cheem/man/is_discrete.Rd | 1 cheem-0.4.2/cheem/man/is_diverging.Rd | 1 cheem-0.4.2/cheem/man/linear_tform.Rd | 1 cheem-0.4.2/cheem/man/logistic_tform.Rd | 1 cheem-0.4.2/cheem/man/problem_type.Rd | 1 cheem-0.4.2/cheem/man/radial_cheem_tour.Rd | 2 cheem-0.4.2/cheem/man/run_app.Rd | 2 cheem-0.4.2/cheem/man/sug_basis.Rd | 1 cheem-0.4.2/cheem/man/sug_manip_var.Rd | 1 cheem-0.4.2/cheem/tests/testthat/test-1_cheem_lists.R | 6 cheem-0.4.2/cheem/tests/testthat/test-2_visualization.r | 18 +- 24 files changed, 98 insertions(+), 100 deletions(-)
Title: Probabilistic Two Sample Mendelian Randomization
Description: Efficient statistical inference of two-sample MR (Mendelian Randomization) analysis.
It can account for the correlated instruments and the horizontal pleiotropy,
and can provide the accurate estimates of both causal effect and horizontal
pleiotropy effect as well as the two corresponding p-values. There are two main
functions in the 'PPMR' package. One is PMR_individual() for individual level data,
the other is PMR_summary() for summary data.
Author: Zhongshang Yuan [aut],
Xiang Zhou [aut],
Michael Kleinsasser [cre]
Maintainer: Michael Kleinsasser <mkleinsa@umich.edu>
Diff between PPMR versions 1.0 dated 2019-08-09 and 1.0.1 dated 2025-09-17
DESCRIPTION | 8 - MD5 | 28 ++--- NAMESPACE | 10 - R/RcppExports.R | 249 ++++++++++++++++++++++++++--------------------- R/data.R | 62 +++++------ README.md | 70 ++++++------- man/Exampleindividual.Rd | 42 ++++--- man/Examplesummary.Rd | 46 ++++---- man/PMR_individual.Rd | 150 ++++++++++++++++------------ man/PMR_summary.Rd | 151 +++++++++++++++------------- src/Makevars | 3 src/Makevars.win | 4 src/PMR_summary.cpp | 66 ++++++++++-- src/PPMR.cpp | 83 ++++++++++++++- src/RcppExports.cpp | 43 ++++---- 15 files changed, 614 insertions(+), 401 deletions(-)
Title: Deconvolution and Alignment of 1d NMR Spectra
Description: A framework for deconvolution, alignment and postprocessing
of 1-dimensional (1d) nuclear magnetic resonance (NMR) spectra, resulting in
a data matrix of aligned signal integrals. The deconvolution part uses the
algorithm described in Koh et al. (2009) <doi:10.1016/j.jmr.2009.09.003>.
The alignment part is based on functions from the 'speaq' package, described
in Beirnaert et al. (2018) <doi:10.1371/journal.pcbi.1006018> and Vu et al.
(2011) <doi:10.1186/1471-2105-12-405>. A detailed description and evaluation
of an early version of the package, 'MetaboDecon1D v0.2.2', can be found in
Haeckl et al. (2021) <doi:10.3390/metabo11070452>.
Author: Tobias Schmidt [aut, cre, cph],
Martina Haeckl [aut, cph],
Yanren Linda Hu [ctb],
Wolfram Gronwald [aut, cph]
Maintainer: Tobias Schmidt <tobias.schmidt331@gmail.com>
Diff between metabodecon versions 1.2.6 dated 2025-01-21 and 1.6.2 dated 2025-09-17
metabodecon-1.2.6/metabodecon/R/10_spec.R |only metabodecon-1.2.6/metabodecon/R/20_deconv.R |only metabodecon-1.2.6/metabodecon/R/30_align.R |only metabodecon-1.2.6/metabodecon/R/40_plot.R |only metabodecon-1.2.6/metabodecon/R/50_util.R |only metabodecon-1.2.6/metabodecon/R/60_data.R |only metabodecon-1.2.6/metabodecon/R/70_depr.R |only metabodecon-1.2.6/metabodecon/R/80_class.R |only metabodecon-1.2.6/metabodecon/R/90_testing.R |only metabodecon-1.2.6/metabodecon/man/metabodecon_classes.Rd |only metabodecon-1.2.6/metabodecon/tests/testthat/test-convert_sfr.R |only metabodecon-1.2.6/metabodecon/tests/testthat/test-convert_wsr.R |only metabodecon-1.2.6/metabodecon/tests/testthat/test-deconvolute_ispec.R |only metabodecon-1.2.6/metabodecon/tests/testthat/test-deconvolute_ispecs.R |only metabodecon-1.2.6/metabodecon/tests/testthat/test-init_lorentz_curves.R |only metabodecon-1.6.2/metabodecon/DESCRIPTION | 22 metabodecon-1.6.2/metabodecon/MD5 | 161 metabodecon-1.6.2/metabodecon/NAMESPACE 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metabodecon-1.6.2/metabodecon/man/calculate_lorentz_curves.Rd | 18 metabodecon-1.6.2/metabodecon/man/check_mdrb.Rd |only metabodecon-1.6.2/metabodecon/man/combine_peaks.Rd | 79 metabodecon-1.6.2/metabodecon/man/convert_pos.Rd | 5 metabodecon-1.6.2/metabodecon/man/datadir.Rd | 20 metabodecon-1.6.2/metabodecon/man/datadir_persistent.Rd | 6 metabodecon-1.6.2/metabodecon/man/datadir_temp.Rd | 6 metabodecon-1.6.2/metabodecon/man/deconvolute.Rd | 147 metabodecon-1.6.2/metabodecon/man/dohCluster.Rd | 44 metabodecon-1.6.2/metabodecon/man/download_example_datasets.Rd | 6 metabodecon-1.6.2/metabodecon/man/draw_spectrum.Rd | 94 metabodecon-1.6.2/metabodecon/man/evalwith.Rd | 5 metabodecon-1.6.2/metabodecon/man/gen_feat_mat.Rd | 18 metabodecon-1.6.2/metabodecon/man/generate_lorentz_curves.Rd |only metabodecon-1.6.2/metabodecon/man/get_data_dir.Rd | 5 metabodecon-1.6.2/metabodecon/man/get_ppm_range.Rd | 13 metabodecon-1.6.2/metabodecon/man/get_si_mat.Rd |only metabodecon-1.6.2/metabodecon/man/install_mdrb.Rd |only metabodecon-1.6.2/metabodecon/man/is_metabodecon_class.Rd | 48 metabodecon-1.6.2/metabodecon/man/make_spectrum.Rd | 7 metabodecon-1.6.2/metabodecon/man/metabodecon-package.Rd |only metabodecon-1.6.2/metabodecon/man/metabodecon_file.Rd | 5 metabodecon-1.6.2/metabodecon/man/plot_lorentz_curves_save_as_png.Rd | 12 metabodecon-1.6.2/metabodecon/man/plot_spectra.Rd | 14 metabodecon-1.6.2/metabodecon/man/plot_spectrum.Rd | 18 metabodecon-1.6.2/metabodecon/man/plot_spectrum_superposition_save_as_png.Rd | 4 metabodecon-1.6.2/metabodecon/man/plot_triplets.Rd | 6 metabodecon-1.6.2/metabodecon/man/print_methods.Rd | 29 metabodecon-1.6.2/metabodecon/man/read_spectra.Rd | 7 metabodecon-1.6.2/metabodecon/man/read_spectrum.Rd | 7 metabodecon-1.6.2/metabodecon/man/sap.Rd | 2 metabodecon-1.6.2/metabodecon/man/sim.Rd | 4 metabodecon-1.6.2/metabodecon/man/simulate_spectrum.Rd | 8 metabodecon-1.6.2/metabodecon/man/speaq_align.Rd | 32 metabodecon-1.6.2/metabodecon/man/tmpdir.Rd | 5 metabodecon-1.6.2/metabodecon/man/transp.Rd | 5 metabodecon-1.6.2/metabodecon/man/tree.Rd | 5 metabodecon-1.6.2/metabodecon/man/width.Rd | 5 metabodecon-1.6.2/metabodecon/tests/testthat/_snaps/draw_spectrum/draw-spectrum.svg | 6633 +++++----- metabodecon-1.6.2/metabodecon/tests/testthat/_snaps/plot_sfr |only metabodecon-1.6.2/metabodecon/tests/testthat/_snaps/plot_spectrum/plot-spectrum.svg | 5460 ++++---- metabodecon-1.6.2/metabodecon/tests/testthat/_snaps/plot_ws |only metabodecon-1.6.2/metabodecon/tests/testthat/test-aaa_Get_Started.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-align.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-as_decon.R | 270 metabodecon-1.6.2/metabodecon/tests/testthat/test-confirm_wshw.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-deconvolute.R | 91 metabodecon-1.6.2/metabodecon/tests/testthat/test-deconvolute_spectra.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-deconvolute_spectrum.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-draw_spectrum.R | 51 metabodecon-1.6.2/metabodecon/tests/testthat/test-enrich_sfr.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-enrich_wshw.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-evalwith.R | 2 metabodecon-1.6.2/metabodecon/tests/testthat/test-find_peaks_fast2.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-generate_lorentz_curves.R | 2 metabodecon-1.6.2/metabodecon/tests/testthat/test-get_names.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-get_right_borders_fast.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-get_sfr.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-get_si_mat.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-get_smopts.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-get_wshw.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-init_lc.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-install_mdrb.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-lorentz_int.R | 22 metabodecon-1.6.2/metabodecon/tests/testthat/test-plot_sfr.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-plot_spectrum.R | 121 metabodecon-1.6.2/metabodecon/tests/testthat/test-plot_ws.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-smooth_signals.R | 13 metabodecon-1.6.2/metabodecon/tests/testthat/test-speaq_align.R | 17 metabodecon-1.6.2/metabodecon/vignettes |only 108 files changed, 7807 insertions(+), 6080 deletions(-)
Title: Computationally Efficient Maximum Likelihood Identification of
Linear Dynamical Systems
Description: Provides implementations of computationally efficient maximum likelihood parameter estimation algorithms for models representing linear dynamical systems. Currently, two such algorithms (one offline and one online) are implemented for the single-output cumulative structural equation model with an additive-noise output measurement equation and assumptions of normality and independence. The corresponding scientific papers are referenced in the descriptions of the functions implementing these algorithms.
Author: Vytautas Dulskis [cre, aut],
Leonidas Sakalauskas [aut]
Maintainer: Vytautas Dulskis <vytautas.dulskis@gmail.com>
Diff between EMLI versions 0.2.0 dated 2022-11-20 and 0.3.0 dated 2025-09-17
DESCRIPTION | 10 +++++----- MD5 | 24 +++++++++++++----------- NAMESPACE | 1 + NEWS.md | 7 +++++++ R/calculate_likelihood.R | 6 +++--- R/estimate_parameters.R | 9 ++++++--- R/estimate_parameters_on.R |only R/evaluate_estimates.R | 4 ++-- R/generate_data.R | 8 ++++---- man/calculate_likelihood.Rd | 6 +++--- man/estimate_parameters.Rd | 9 ++++++--- man/estimate_parameters_on.Rd |only man/evaluate_estimates.Rd | 4 ++-- man/generate_data.Rd | 8 ++++---- 14 files changed, 56 insertions(+), 40 deletions(-)
Title: Access Colombian Data via APIs and Curated Datasets
Description: Provides a comprehensive interface to access diverse public data about
Colombia through multiple APIs and curated datasets. The package integrates
four different APIs: 'API-Colombia' for Colombian-specific data including
geography, culture, tourism, and government information; 'World Bank API'
for economic and demographic indicators; 'Nager.Date' for public holidays;
and 'REST Countries API' for general country information. The package enables
users to explore various aspects of Colombia such as geographic locations,
cultural attractions, economic indicators, demographic data, and public
holidays. Additionally, 'ColombiAPI' includes curated datasets covering
Bogota air stations, business and holiday dates, public schools, Colombian
coffee exports, cannabis licenses, Medellin rainfall, and malls in Bogota,
making it a comprehensive tool for exploring Colombia's multifaceted data
landscape. For more information on the APIs, see:
'API-Colombia' <https://api-colombia.com/>,
'Nager.Da [...truncated...]
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between ColombiAPI versions 0.1.1 dated 2025-02-16 and 0.2.0 dated 2025-09-17
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Title: Compute Global Sensitivity Analysis Indices Using Optimal
Transport
Description: Computing Global Sensitivity Indices from given data using Optimal Transport, as defined in Borgonovo et al (2024) <doi:10.1287/mnsc.2023.01796>. You provide an input sample, an output sample, decide the algorithm, and compute the indices.
Author: Leonardo Chiani [aut, cre, cph] ,
Emanuele Borgonovo [rev],
Elmar Plischke [rev],
Massimo Tavoni [rev]
Maintainer: Leonardo Chiani <leonardo.chiani@polimi.it>
Diff between gsaot versions 1.1.0 dated 2025-07-18 and 1.1.1 dated 2025-09-17
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Title: Advanced Processing and Chart Generation from activPAL Events
Files
Description: Contains functions to generate pre-defined summary statistics from activPAL
events files <https://www.palt.com/>. The package also contains functions to produce informative
graphics that visualise physical activity behaviour and trends. This includes
generating graphs that align physical activity behaviour with additional time based
observations described by other data sets, such as sleep diaries and continuous glucose
monitoring data.
Author: Craig Speirs [aut, cre],
Kate Lyden [ctb],
Douglas Maxwell [ctb],
David Loudon [ctb]
Maintainer: Craig Speirs <craig@paltechnologies.com>
Diff between activPAL versions 0.1.3 dated 2019-07-18 and 0.1.4 dated 2025-09-17
DESCRIPTION | 9 ++++----- MD5 | 2 +- 2 files changed, 5 insertions(+), 6 deletions(-)
Title: Scatter Plot Combined with Ridgelines in 'ggplot2'
Description: The function combines a scatter plot with ridgelines to better visualise the distribution between sample groups. The plot is created with 'ggplot2'.
Author: Matthieu Bourgery [aut, cre]
Maintainer: Matthieu Bourgery <matthieu.bourgery@gmail.com>
This is a re-admission after prior archival of version 0.1.2 dated 2025-05-13
Diff between ggScatRidges versions 0.1.2 dated 2025-05-13 and 1.1.0 dated 2025-09-17
DESCRIPTION | 11 +++++------ MD5 | 8 ++++---- NAMESPACE | 4 +--- R/Scatter_ridges_function.R | 20 +++++++++----------- man/ggScatRidges.Rd | 8 ++++---- 5 files changed, 23 insertions(+), 28 deletions(-)
Title: Beta Kernel Process Modeling
Description: Implements the Beta Kernel Process (BKP) for nonparametric modeling of spatially varying binomial probabilities, together with its extension, the Dirichlet Kernel Process (DKP), for categorical or multinomial data.
The package provides functions for model fitting, predictive inference with uncertainty quantification, posterior simulation, and visualization in one-and two-dimensional input spaces.
Multiple kernel functions (Gaussian, Matern 5/2, and Matern 3/2) are supported, with hyperparameters optimized through multi-start gradient-based search.
For more details, see Zhao, Qing, and Xu (2025) <doi:10.48550/arXiv.2508.10447>.
Author: Jiangyan Zhao [cre, aut],
Kunhai Qing [aut],
Jin Xu [aut]
Maintainer: Jiangyan Zhao <zhaojy2017@126.com>
Diff between BKP versions 0.2.1 dated 2025-09-17 and 0.2.2 dated 2025-09-17
DESCRIPTION | 6 +++--- MD5 | 17 +++++++++-------- NEWS.md | 2 +- R/zzz.R |only README.md | 2 +- inst/CITATION | 2 +- inst/doc/vignettes.R | 6 ------ inst/doc/vignettes.Rmd | 10 ++-------- inst/doc/vignettes.pdf |binary vignettes/vignettes.Rmd | 10 ++-------- 10 files changed, 19 insertions(+), 36 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-08-01 1.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-08 1.0.2
2022-06-28 1.0.1
2022-02-07 1.0
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2018-06-15 1.0.0
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2021-06-25 1.0.2
2021-06-03 1.0.1
2021-05-04 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-03 1.0.3
2019-12-17 1.0.2
2019-02-18 1.0.1
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2021-08-04 0.1
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2022-06-06 1.1.4
2020-10-05 1.1.3
2020-02-13 1.1.2
2019-12-06 1.0.1
2019-12-06 1.1.1
2019-11-28 1.0.0
Title: Weibull Regression for a Right-Censored Endpoint with
Interval-Censored Covariate
Description: The function SurvRegCens() of this package allows estimation of a Weibull Regression for a right-censored endpoint, one interval-censored covariate, and an arbitrary number of non-censored covariates. Additional functions allow to switch between different parametrizations of Weibull regression used by different R functions, inference for the mean difference of two arbitrarily censored Normal samples, and estimation of canonical parameters from censored samples for several distributional assumptions. Hubeaux, S. and Rufibach, K. (2014) <doi:10.48550/arXiv.1402.0432>.
Author: Stanislas Hubeaux [aut, cre],
Kaspar Rufibach [aut]
Maintainer: Stanislas Hubeaux <stan.hubeaux@bluewin.ch>
Diff between SurvRegCensCov versions 1.7 dated 2023-09-27 and 1.8 dated 2025-09-17
DESCRIPTION | 23 ++++++++++----- MD5 | 24 +++++++-------- NAMESPACE | 70 +++++++++++++++++++++++----------------------- NEWS | 5 +++ build/vignette.rds |binary inst/doc/weibull.pdf |binary man/ConvertWeibull.Rd | 6 +-- man/NormalMeanDiffCens.Rd | 4 +- man/ParamSampleCens.Rd | 2 - man/SurvRegCens.Rd | 8 ++--- man/WeibullDiag.Rd | 6 +-- man/WeibullReg.Rd | 8 ++--- man/censorContVar.Rd | 2 - 13 files changed, 86 insertions(+), 72 deletions(-)
More information about SurvRegCensCov at CRAN
Permanent link
Title: Estimating Marginal Effects with Prognostic Covariate Adjustment
Description: Conduct power analyses and inference of marginal effects.
Uses plug-in estimation and influence functions to perform robust inference,
optionally leveraging historical data to increase precision with
prognostic covariate adjustment. The methods are described in
Højbjerre-Frandsen et al. (2025) <doi:10.48550/arXiv.2503.22284>.
Author: Mathias Lerbech Jeppesen [aut, cre],
Emilie Hojbjerre-Frandsen [aut],
Novo Nordisk A/S [cph]
Maintainer: Mathias Lerbech Jeppesen <mathiasljeppesen@outlook.com>
Diff between postcard versions 1.0.1 dated 2025-07-01 and 1.1.0 dated 2025-09-17
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Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-11 0.7.2
2020-10-30 0.7.1
2020-01-12 0.7
2019-05-24 0.6
2018-03-07 0.5
2017-05-07 0.4
2017-05-04 0.3
2017-03-02 0.2
2016-07-29 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-10 1.0
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2021-08-12 1.0.1
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2019-08-28 0.9.0
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2024-12-02 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-05 1.0.2
2019-04-26 1.0.1
2019-04-24 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-17 1.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-20 1.5
2020-10-06 1.4
2020-02-06 1.3
2020-02-01 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-02-22 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-10 0.3.4
2020-10-30 0.3.3
2020-01-12 0.3.2
2019-05-24 0.3.1
2019-05-14 0.3
2018-07-31 0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
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2019-12-06 1.2.1
2019-12-05 1.2.0
2019-09-05 1.1.0
2019-08-28 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-27 1.1.0
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2021-10-26 0.1
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2022-09-19 0.2.3
2022-01-28 0.2.1
2022-01-26 0.2
2021-10-06 0.1.4
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2021-06-11 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-28 1.1.2
2020-09-23 1.1.1
2020-09-17 1.0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-01-30 1.1.7
2022-01-07 1.1.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-06 1.1
2018-11-30 1.0
Title: Risk Regression Models and Prediction Scores for Survival
Analysis with Competing Risks
Description: Implementation of the following methods for event history analysis.
Risk regression models for survival endpoints also in the presence of competing
risks are fitted using binomial regression based on a time sequence of binary
event status variables. A formula interface for the Fine-Gray regression model
and an interface for the combination of cause-specific Cox regression models.
A toolbox for assessing and comparing performance of risk predictions (risk
markers and risk prediction models). Prediction performance is measured by the
Brier score and the area under the ROC curve for binary possibly time-dependent
outcome. Inverse probability of censoring weighting and pseudo values are used
to deal with right censored data. Lists of risk markers and lists of risk models
are assessed simultaneously. Cross-validation repeatedly splits the data, trains
the risk prediction models on one part of each split and then summarizes and
compares the performance across splits.
Author: Thomas Alexander Gerds [aut, cre],
Johan Sebastian Ohlendorff [aut],
Paul Blanche [ctb],
Rikke Mortensen [ctb],
Marvin Wright [ctb],
Nikolaj Tollenaar [ctb],
John Muschelli [ctb],
Ulla Brasch Mogensen [ctb],
Asbjoern Risom [ctb],
Brice Ozenne [aut]
Maintainer: Thomas Alexander Gerds <tag@biostat.ku.dk>
Diff between riskRegression versions 2025.05.20 dated 2025-05-20 and 2025.09.17 dated 2025-09-17
DESCRIPTION | 15 - MD5 | 61 ++--- NAMESPACE | 1 R/Brier.binary.R | 12 - R/CSC.R | 6 R/IPA.R | 10 R/IPACompute.R |only R/Score.R | 50 ++-- R/ate-pointEstimate.R | 8 R/ate.R | 39 ++- R/ate_initArgs.R | 6 R/calcSeCox.R | 8 R/computePerformance.R | 21 + R/coxLP.R | 8 R/iidCox.R | 25 +- R/predict.CauseSpecificCox.R | 2 R/predictCox.R | 9 R/predictRisk.R | 12 - R/print.Score.R | 26 +- R/summary.Score.R | 33 +- R/synthesize.R | 4 build/vignette.rds |binary inst/doc/IPA.html | 380 +++++++++++++++++---------------- man/CSC.Rd | 6 man/Score.Rd | 7 man/predictCox.Rd | 6 man/riskRegression-package.Rd | 3 src/Makevars | 20 - src/Makevars.win | 3 tests/testthat/test-iidCox.R | 6 tests/testthat/test-score-train-test.R | 131 +++++++---- tests/testthat/test-score.R | 22 - 32 files changed, 522 insertions(+), 418 deletions(-)
More information about riskRegression at CRAN
Permanent link
Title: Coloured Formatting for Columns
Description: Provides 'pillar' and 'colonnade' generics designed
for formatting columns of data using the full range of colours
provided by modern terminals.
Author: Kirill Mueller [aut, cre] ,
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between pillar versions 1.11.0 dated 2025-07-04 and 1.11.1 dated 2025-09-17
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NAMESPACE | 1 + NEWS.md | 9 ++++++--- R/glimpse.R | 15 +++++++++++---- R/tbl-format-setup.R | 4 ++++ README.md | 2 +- build/vignette.rds |binary inst/doc/printing.html | 4 ++-- man/scale_x_num.Rd | 10 ++++++---- tests/testthat/_snaps/tbl-format-header.md | 2 +- tests/testthat/_snaps/tbl-format-setup.md | 14 +++++++------- tests/testthat/helper-unknown-rows.R | 5 ++++- tests/testthat/test-format_decimal.R | 4 ++-- 14 files changed, 62 insertions(+), 42 deletions(-)
Title: Robust Image Rendering Support for 'ggplot2'
Description: A 'ggplot2' extension that enables robust image grobs in
panels and theme elements.
Author: Sebastian Carl [aut, cre, cph]
Maintainer: Sebastian Carl <mrcaseb@gmail.com>
Diff between ggpath versions 1.0.2 dated 2024-08-20 and 1.1.0 dated 2025-09-17
DESCRIPTION | 16 - LICENSE | 4 MD5 | 65 ++-- NAMESPACE | 39 +- NEWS.md | 10 R/build_grobs.R | 196 ++++++------ R/geom_from_path.R | 230 +++++++------- R/geom_lines.R | 353 ++++++++++------------ R/ggpath-package.R | 10 R/theme_element.R | 217 ++++++++----- R/utils.R |only R/zzz.R | 3 README.md | 443 +++++++++++++--------------- man/element_path.Rd | 46 +- man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/geom_from_path.Rd | 296 +++++++++--------- man/geom_lines.Rd | 287 +++++++++--------- man/ggpath-package.Rd | 78 ++-- tests/testthat.R | 8 tests/testthat/_snaps/geom_from_path/p1.svg | 129 ++++---- tests/testthat/_snaps/geom_lines/p1.svg | 199 ++++++------ tests/testthat/_snaps/geom_lines/p2.svg | 195 ++++++------ tests/testthat/_snaps/geom_lines/p3.svg | 195 ++++++------ tests/testthat/_snaps/geom_lines/p4.svg | 199 ++++++------ tests/testthat/_snaps/geom_lines/p5.svg | 181 +++++------ tests/testthat/_snaps/theme-elements/p1.svg | 103 +++--- tests/testthat/_snaps/theme-elements/p2.svg | 103 +++--- tests/testthat/_snaps/theme-elements/p3.svg | 152 ++++----- tests/testthat/test-geom_from_path.R | 98 +++--- tests/testthat/test-geom_lines.R | 118 +++---- tests/testthat/test-theme-elements.R | 42 +- 34 files changed, 2037 insertions(+), 1978 deletions(-)
Title: Scalable Joint Species Distribution Modeling
Description: A scalable and fast method for estimating joint Species Distribution Models (jSDMs) for big community data, including eDNA data. The package estimates a full (i.e. non-latent) jSDM with different response distributions (including the traditional multivariate probit model). The package allows to perform variation partitioning (VP) / ANOVA on the fitted models to separate the contribution of environmental, spatial, and biotic associations. In addition, the total R-squared can be further partitioned per species and site to reveal the internal metacommunity structure, see Leibold et al., <doi:10.1111/oik.08618>. The internal structure can then be regressed against environmental and spatial distinctiveness, richness, and traits to analyze metacommunity assembly processes. The package includes support for accounting for spatial autocorrelation and the option to fit responses using deep neural networks instead of a standard linear predictor. As described in Pichler & Hartig (2021) [...truncated...]
Author: Maximilian Pichler [aut, cre] ,
Florian Hartig [aut] ,
Wang Cai [ctb]
Maintainer: Maximilian Pichler <maximilian.pichler@biologie.uni-regensburg.de>
Diff between sjSDM versions 1.0.6 dated 2024-08-19 and 1.0.7 dated 2025-09-17
DESCRIPTION | 15 MD5 | 40 - NEWS.md | 9 R/anova.R | 24 - R/importance.R | 101 ++-- R/installation_help.R | 8 R/internalStructure.R | 231 ++++++++--- R/sjSDM.R | 4 R/sjSDM_cv.R | 5 build/stage23.rdb |binary build/vignette.rds |binary inst/doc/sjSDM_Introduction.Rmd | 8 inst/doc/sjSDM_Introduction.html | 24 - inst/python/sjSDM_py/__pycache__/dist_mvp.cpython-310.pyc |binary inst/python/sjSDM_py/__pycache__/model_sjSDM.cpython-310.pyc |binary inst/python/sjSDM_py/dist_mvp.py | 4 inst/python/sjSDM_py/model_sjSDM.py | 35 + man/installation_help.Rd | 8 tests/testthat/test-5-importance.R | 218 +++++----- vignettes/sjSDM_Introduction.Rmd | 8 vignettes/sjSDM_Introduction.orig | 8 21 files changed, 458 insertions(+), 292 deletions(-)
Title: Bootstrapping Helpers for Structural Equation Modelling
Description: A collection of helper functions for forming
bootstrapping confidence intervals and examining bootstrap
estimates in structural equation modelling. Currently
supports models fitted by the 'lavaan' package by
Rosseel (2012) <doi: 10.18637/jss.v048.i02>.
Author: Wendie Yang [aut, cre] ,
Shu Fai Cheung [aut]
Maintainer: Wendie Yang <1581075494q@gmail.com>
Diff between semboottools versions 0.1.0 dated 2025-04-01 and 0.1.1 dated 2025-09-17
DESCRIPTION | 12 MD5 | 8 NEWS.md | 78 +++++- README.md | 13 - man/hist_qq_boot.Rd | 662 ++++++++++++++++++++++++++-------------------------- 5 files changed, 424 insertions(+), 349 deletions(-)
Title: Helpers for Model Coefficients Tibbles
Description: Provides suite of functions to work with regression model
'broom::tidy()' tibbles. The suite includes functions to group
regression model terms by variable, insert reference and header rows
for categorical variables, add variable labels, and more.
Author: Joseph Larmarange [aut, cre] ,
Daniel D. Sjoberg [aut]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between broom.helpers versions 1.21.0 dated 2025-04-24 and 1.22.0 dated 2025-09-17
broom.helpers-1.21.0/broom.helpers/R/select_utilities.R |only broom.helpers-1.21.0/broom.helpers/man/dot-formula_list_to_named_list.Rd |only broom.helpers-1.21.0/broom.helpers/man/dot-generic_selector.Rd |only broom.helpers-1.21.0/broom.helpers/man/dot-select_to_varnames.Rd |only broom.helpers-1.22.0/broom.helpers/DESCRIPTION | 20 broom.helpers-1.22.0/broom.helpers/MD5 | 96 +- broom.helpers-1.22.0/broom.helpers/NAMESPACE | 8 broom.helpers-1.22.0/broom.helpers/NEWS.md | 17 broom.helpers-1.22.0/broom.helpers/R/broom.helpers-package.R | 2 broom.helpers-1.22.0/broom.helpers/R/custom_tidiers.R | 43 - broom.helpers-1.22.0/broom.helpers/R/model_get_assign.R | 13 broom.helpers-1.22.0/broom.helpers/R/model_get_contrasts.R | 10 broom.helpers-1.22.0/broom.helpers/R/model_get_model_frame.R | 9 broom.helpers-1.22.0/broom.helpers/R/model_get_model_matrix.R | 14 broom.helpers-1.22.0/broom.helpers/R/model_get_weights.R | 10 broom.helpers-1.22.0/broom.helpers/build/vignette.rds |binary broom.helpers-1.22.0/broom.helpers/data/supported_models.rda |binary broom.helpers-1.22.0/broom.helpers/inst/doc/broom-helpers.R | 2 broom.helpers-1.22.0/broom.helpers/inst/doc/broom-helpers.Rmd | 2 broom.helpers-1.22.0/broom.helpers/inst/doc/broom-helpers.html | 394 +++++----- broom.helpers-1.22.0/broom.helpers/man/model_get_assign.Rd | 3 broom.helpers-1.22.0/broom.helpers/man/model_get_contrasts.Rd | 3 broom.helpers-1.22.0/broom.helpers/man/model_get_model_matrix.Rd | 7 broom.helpers-1.22.0/broom.helpers/man/model_get_pairwise_contrasts.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/model_get_weights.Rd | 3 broom.helpers-1.22.0/broom.helpers/man/model_list_variables.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/select_helpers.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/supported_models.Rd | 1 broom.helpers-1.22.0/broom.helpers/man/tidy_add_estimate_to_reference_rows.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_add_header_rows.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_add_pairwise_contrasts.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_add_reference_rows.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_all_effects.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_avg_comparisons.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_avg_slopes.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_broom.Rd | 4 broom.helpers-1.22.0/broom.helpers/man/tidy_ggpredict.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_group_by.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_marginal_contrasts.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_marginal_predictions.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_margins.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_multgee.Rd | 6 broom.helpers-1.22.0/broom.helpers/man/tidy_parameters.Rd | 10 broom.helpers-1.22.0/broom.helpers/man/tidy_plus_plus.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_svy_vglm.Rd | 6 broom.helpers-1.22.0/broom.helpers/man/tidy_vgam.Rd | 6 broom.helpers-1.22.0/broom.helpers/man/tidy_with_broom_or_parameters.Rd | 9 broom.helpers-1.22.0/broom.helpers/man/tidy_zeroinfl.Rd | 6 broom.helpers-1.22.0/broom.helpers/tests/testthat/test-model_get_n.R | 25 broom.helpers-1.22.0/broom.helpers/tests/testthat/test-tidy_plus_plus.R | 36 broom.helpers-1.22.0/broom.helpers/vignettes/broom-helpers.Rmd | 2 51 files changed, 466 insertions(+), 333 deletions(-)
Title: R Interface to the A/B Street Transport System Simulation
Software
Description: Provides functions to convert origin-destination data,
represented as straight 'desire lines' in the 'sf' Simple Features
class system, into JSON files that can be directly imported into
A/B Street <https://www.abstreet.org>, a free and open source tool
for simulating urban transport systems and scenarios of change
<doi:10.1007/s10109-020-00342-2>.
Author: Robin Lovelace [aut, cre] ,
Nathanael Sheehan [aut] ,
Trevor Nederlof [aut],
Lucas Dias [ctb],
Dustin Carlino [aut]
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between abstr versions 0.4.1 dated 2021-11-30 and 0.4.2 dated 2025-09-17
DESCRIPTION | 29 MD5 | 90 +- NAMESPACE | 18 NEWS.md | 57 + R/ab_scenario.R | 680 +++++++++++----------- R/data.R | 12 R/montlake_buildings.R | 54 - R/montlake_od.R | 38 - R/montlake_zones.R | 32 - R/sao_paulo_activity_df_20.R | 124 ++-- R/utils-pipe.R | 38 - README.md | 538 +++++++++-------- build/vignette.rds |binary inst/doc/abstr.R | 96 +-- inst/doc/abstr.Rmd | 352 +++++------ inst/doc/abstr.html | 841 ++++++++++++++++++--------- inst/doc/activity.R | 234 +++---- inst/doc/activity.Rmd | 496 ++++++++-------- inst/doc/activity.html | 1002 ++++++++++++++++++++------------- inst/doc/montlake.R | 254 ++++---- inst/doc/montlake.Rmd | 452 +++++++------- inst/doc/montlake.html | 921 +++++++++++++++++++----------- inst/doc/pct_to_abstr.R | 404 ++++++------- inst/doc/pct_to_abstr.Rmd | 679 +++++++++++----------- inst/doc/pct_to_abstr.html | 1087 ++++++++++++++++++++++-------------- inst/extdata/activity_leeds.json | 188 +++--- inst/extdata/minimal_scenario.json | 86 +- inst/extdata/minimal_scenario2.json | 162 ++--- man/ab_json.Rd | 132 ++-- man/ab_save.Rd | 38 - man/ab_scenario.Rd | 180 ++--- man/ab_sf.Rd | 76 +- man/ab_time_normal.Rd | 64 +- man/figures/README-input-1.png |binary man/figures/README-outputplot-1.png |binary man/leeds_site_area.Rd | 26 man/montlake_buildings.Rd | 70 +- man/montlake_od.Rd | 60 - man/montlake_zones.Rd | 54 - man/pipe.Rd | 40 - man/sao_paulo_activity_df_20.Rd | 86 +- man/sao_paulo_activity_sf_20.Rd | 84 +- vignettes/abstr.Rmd | 352 +++++------ vignettes/activity.Rmd | 496 ++++++++-------- vignettes/montlake.Rmd | 452 +++++++------- vignettes/pct_to_abstr.Rmd | 679 +++++++++++----------- 46 files changed, 6443 insertions(+), 5410 deletions(-)
Title: Steve's Toy Data for Teaching About a Variety of Methodological,
Social, and Political Topics
Description: This is a collection of various kinds of data with broad uses for teaching.
My students, and academics like me who teach the same topics I teach, should find
this useful if their teaching workflow is also built around the R programming
language. The applications are multiple but mostly cluster on topics of statistical
methodology, international relations, and political economy.
Author: Steve Miller [aut, cre]
Maintainer: Steve Miller <steve@svmiller.com>
Diff between stevedata versions 1.6.0 dated 2025-07-18 and 1.7.0 dated 2025-09-17
DESCRIPTION | 6 ++-- MD5 | 57 ++++++++++++++++++++++++++------------------- NEWS.md | 15 +++++++++++ R/rd-GHR04.R | 16 ++++++++---- R/rd-Lipset59.R | 11 +++++--- R/rd-Weede84.R |only R/rd-mmb_war.R |only R/rd-stevesteps.R |only build/partial.rdb |binary data/DJIA.rda |binary data/ESS10NO.rda |binary data/GHR04.rda |binary data/PPGE.rda |binary data/USFAHR.rda |binary data/Weede84.rda |only data/chile88.rda |binary data/china_peace.rda |binary data/coffee_imports.rda |binary data/country_isocodes.rda |binary data/eu_ua_fta24.rda |binary data/mmb_war.rda |only data/rok_unga.rda |binary data/scb_regions.rda |binary data/states_war.rda |binary data/stevesteps.rda |only data/thatcher_approval.rda |binary data/turnips.rda |binary data/wb_groups.rda |binary data/wbd_example.rda |binary man/GHR04.Rd | 16 ++++++++---- man/Lipset59.Rd | 11 +++++--- man/Weede84.Rd |only man/mmb_war.Rd |only man/stevesteps.Rd |only 34 files changed, 87 insertions(+), 45 deletions(-)
Title: Sequential Trial Emulation
Description: Implementation of sequential trial emulation for the analysis of observational databases.
The 'SEQTaRget' software accommodates time-varying treatments and confounders, as well as binary
and failure time outcomes. 'SEQTaRget' allows to compare both static and dynamic strategies,
can be used to estimate observational analogs of intention-to-treat
and per-protocol effects, and can adjust for potential selection bias
induced by losses-to-follow-up. (Paper to come).
Author: Ryan O'Dea [aut, cre] ,
Alejandro Szmulewicz [aut] ,
Tom Palmer [aut] ,
Miguel Hernan [aut] ,
The President and Fellows of Harvard College [cph]
Maintainer: Ryan O'Dea <ryanodea@hsph.harvard.edu>
Diff between SEQTaRget versions 0.13.1 dated 2025-09-15 and 1.0.0 dated 2025-09-17
DESCRIPTION | 18 +++++++++++++----- MD5 | 24 ++++++++++++------------ NAMESPACE | 1 + R/SEQopts.R | 3 ++- R/SEQuential.R | 4 ++-- R/class_definitions.R | 2 +- README.md | 37 +++++++++++++++++++------------------ inst/doc/ITT.html | 2 +- inst/doc/SEQuential.html | 2 +- inst/doc/censoring.html | 2 +- inst/doc/doseresponse.html | 2 +- man/SEQopts.Rd | 2 +- man/SEQuential.Rd | 4 ++-- 13 files changed, 57 insertions(+), 46 deletions(-)
Title: Standardized Git Repository Data
Description: Obtain standardized data from multiple 'Git' services, including 'GitHub' and 'GitLab'.
Designed to be 'Git' service-agnostic, this package assists teams with activities spread across various
'Git' platforms by providing a unified way to access repository data.
Author: Maciej Banas [aut, cre],
Kamil Koziej [aut],
Karolina Marcinkowska [aut],
Matt Secrest [aut]
Maintainer: Maciej Banas <banasmaciek@gmail.com>
Diff between GitStats versions 2.3.5 dated 2025-08-18 and 2.3.6 dated 2025-09-17
GitStats-2.3.5/GitStats/inst/cache_workflow.R |only GitStats-2.3.5/GitStats/inst/example_workflow.R |only GitStats-2.3.5/GitStats/inst/get_commits_workflow.R |only GitStats-2.3.5/GitStats/inst/get_files_workflow.R |only GitStats-2.3.5/GitStats/inst/get_issues_workflow.R |only GitStats-2.3.5/GitStats/inst/get_orgs_workflow.R |only GitStats-2.3.5/GitStats/inst/get_repos_for_individual_users.R |only GitStats-2.3.5/GitStats/inst/get_repos_tree_workflow.R |only GitStats-2.3.5/GitStats/inst/get_repos_urls_workflow.R |only GitStats-2.3.5/GitStats/inst/get_storage_workflow.R |only GitStats-2.3.5/GitStats/inst/set_hosts.R |only GitStats-2.3.5/GitStats/inst/set_many_repos.R |only GitStats-2.3.5/GitStats/inst/set_tokens.R |only GitStats-2.3.5/GitStats/inst/verbose_workflow.R |only GitStats-2.3.5/GitStats/tests/testthat/_snaps/00-api-requests.md |only GitStats-2.3.6/GitStats/DESCRIPTION | 6 GitStats-2.3.6/GitStats/MD5 | 93 +--- GitStats-2.3.6/GitStats/NEWS.md | 13 GitStats-2.3.6/GitStats/R/EngineGraphQL.R | 58 +- GitStats-2.3.6/GitStats/R/EngineGraphQLGitHub.R | 231 +++++----- GitStats-2.3.6/GitStats/R/EngineGraphQLGitLab.R | 156 ++++-- GitStats-2.3.6/GitStats/R/EngineRest.R | 31 - GitStats-2.3.6/GitStats/R/EngineRestGitHub.R | 106 ++-- GitStats-2.3.6/GitStats/R/EngineRestGitLab.R | 129 +++-- GitStats-2.3.6/GitStats/R/GQLQueryGitHub.R | 17 GitStats-2.3.6/GitStats/R/GQLQueryGitLab.R | 17 GitStats-2.3.6/GitStats/R/GitHost.R | 124 +++-- GitStats-2.3.6/GitStats/R/GitHostGitHub.R | 7 GitStats-2.3.6/GitStats/R/GitHostGitLab.R | 32 - GitStats-2.3.6/GitStats/R/GitStats.R | 67 +- GitStats-2.3.6/GitStats/R/get_repos.R | 4 GitStats-2.3.6/GitStats/man/get_repos.Rd | 4 GitStats-2.3.6/GitStats/tests/testthat/_snaps/00-get_orgs-GitLab.md | 8 GitStats-2.3.6/GitStats/tests/testthat/_snaps/01-get_repos-GitHub.md | 30 - GitStats-2.3.6/GitStats/tests/testthat/_snaps/01-get_repos-GitLab.md | 6 GitStats-2.3.6/GitStats/tests/testthat/_snaps/02-get_commits-GitHub.md | 8 GitStats-2.3.6/GitStats/tests/testthat/_snaps/03-get_files_structure-GitLab.md | 2 GitStats-2.3.6/GitStats/tests/testthat/_snaps/04-get_files_content-GitHub.md | 2 GitStats-2.3.6/GitStats/tests/testthat/_snaps/04-get_files_content-GitLab.md | 4 GitStats-2.3.6/GitStats/tests/testthat/_snaps/helpers.md | 2 GitStats-2.3.6/GitStats/tests/testthat/helper-error-fixtures.R | 16 GitStats-2.3.6/GitStats/tests/testthat/helper-expect-responses.R | 10 GitStats-2.3.6/GitStats/tests/testthat/helper-expect-tables.R | 21 GitStats-2.3.6/GitStats/tests/testthat/helper-fixtures.R | 100 +++- GitStats-2.3.6/GitStats/tests/testthat/test-00-api-requests.R | 29 - GitStats-2.3.6/GitStats/tests/testthat/test-00-get_orgs-GitHub.R | 19 GitStats-2.3.6/GitStats/tests/testthat/test-00-get_orgs-GitLab.R | 20 GitStats-2.3.6/GitStats/tests/testthat/test-00-graphql_errors.R | 11 GitStats-2.3.6/GitStats/tests/testthat/test-01-get_repos-GitHub.R | 170 ++++--- GitStats-2.3.6/GitStats/tests/testthat/test-01-get_repos-GitLab.R | 17 GitStats-2.3.6/GitStats/tests/testthat/test-01-get_repos-GitStats.R | 2 GitStats-2.3.6/GitStats/tests/testthat/test-02-get_commits-GitHub.R | 41 + GitStats-2.3.6/GitStats/tests/testthat/test-03-get_files_structure-GitLab.R | 4 GitStats-2.3.6/GitStats/tests/testthat/test-04-get_files-REST-GitHub.R |only GitStats-2.3.6/GitStats/tests/testthat/test-04-get_files-REST-GitLab.R |only GitStats-2.3.6/GitStats/tests/testthat/test-06-get_issues-GitHub.R | 19 56 files changed, 1000 insertions(+), 636 deletions(-)
Title: Flexible, Extensible, & Reproducible Pupillometry Preprocessing
Description: Pupillometry offers a non-invasive window into the mind and has been used extensively as a psychophysiological readout of arousal signals linked with cognitive processes like attention, stress, and emotional states [Clewett et al. (2020) <doi:10.1038/s41467-020-17851-9>; Kret & Sjak-Shie (2018) <doi:10.3758/s13428-018-1075-y>; Strauch (2024) <doi:10.1016/j.tins.2024.06.002>]. Yet, despite decades of pupillometry research, many established packages and workflows to date lack design patterns based on Findability, Accessibility, Interoperability, and Reusability (FAIR) principles [see Wilkinson et al. (2016) <doi:10.1038/sdata.2016.18>]. 'eyeris' provides a modular, performant, and extensible preprocessing framework for pupillometry data with BIDS-like organization and interactive output reports [Esteban et al. (2019) <doi:10.1038/s41592-018-0235-4>; Gorgolewski et al. (2016) <doi:10.1038/sdata.2016.44>]. Development was supported, in part, by the S [...truncated...]
Author: Shawn Schwartz [aut, cre] ,
Mingjian He [ctb],
Haopei Yang [ctb],
Alice Xue [ctb],
Gustavo Santiago-Reyes [ctb]
Maintainer: Shawn Schwartz <shawn.t.schwartz@gmail.com>
Diff between eyeris versions 2.1.1 dated 2025-07-26 and 3.0.0 dated 2025-09-17
eyeris-2.1.1/eyeris/R/utils-alert.R |only eyeris-2.1.1/eyeris/man/alert.Rd |only eyeris-3.0.0/eyeris/DESCRIPTION | 16 eyeris-3.0.0/eyeris/MD5 | 254 eyeris-3.0.0/eyeris/NAMESPACE | 15 eyeris-3.0.0/eyeris/NEWS.md | 141 eyeris-3.0.0/eyeris/R/constants.R | 10 eyeris-3.0.0/eyeris/R/core-logging.R |only eyeris-3.0.0/eyeris/R/eyeris-package.R | 3 eyeris-3.0.0/eyeris/R/pipeline-bidsify.R | 2881 ++++------ eyeris-3.0.0/eyeris/R/pipeline-bin.R | 36 eyeris-3.0.0/eyeris/R/pipeline-confounds.R | 243 eyeris-3.0.0/eyeris/R/pipeline-deblink.R | 29 eyeris-3.0.0/eyeris/R/pipeline-detransient.R | 10 eyeris-3.0.0/eyeris/R/pipeline-detrend.R | 9 eyeris-3.0.0/eyeris/R/pipeline-downsample.R | 48 eyeris-3.0.0/eyeris/R/pipeline-epoch.R | 266 eyeris-3.0.0/eyeris/R/pipeline-glassbox.R | 504 - eyeris-3.0.0/eyeris/R/pipeline-handler.R | 74 eyeris-3.0.0/eyeris/R/pipeline-interpolate.R | 23 eyeris-3.0.0/eyeris/R/pipeline-loadasc.R | 79 eyeris-3.0.0/eyeris/R/pipeline-lpfilt.R | 25 eyeris-3.0.0/eyeris/R/pipeline-zscore.R | 46 eyeris-3.0.0/eyeris/R/plot.eyeris.R | 287 eyeris-3.0.0/eyeris/R/utils-baseline.R | 51 eyeris-3.0.0/eyeris/R/utils-checks.R | 128 eyeris-3.0.0/eyeris/R/utils-database.R |only eyeris-3.0.0/eyeris/R/utils-epoch.R | 110 eyeris-3.0.0/eyeris/R/utils-error_handler.R | 2 eyeris-3.0.0/eyeris/R/utils-eyelogger.R | 6 eyeris-3.0.0/eyeris/R/utils-gallery.R | 350 + eyeris-3.0.0/eyeris/R/utils-parquet-split.R |only eyeris-3.0.0/eyeris/R/utils-parsers.R | 32 eyeris-3.0.0/eyeris/R/utils-progress_bar.R | 9 eyeris-3.0.0/eyeris/R/utils-render_report.R | 160 eyeris-3.0.0/eyeris/R/utils-zip-cleanup.R |only eyeris-3.0.0/eyeris/R/utils-zip-gallery.R |only eyeris-3.0.0/eyeris/R/zzz.R | 35 eyeris-3.0.0/eyeris/README.md | 267 eyeris-3.0.0/eyeris/build/vignette.rds |binary eyeris-3.0.0/eyeris/inst/WORDLIST | 42 eyeris-3.0.0/eyeris/inst/doc/anatomy.html | 5 eyeris-3.0.0/eyeris/inst/doc/chunked-database-export.R |only eyeris-3.0.0/eyeris/inst/doc/chunked-database-export.Rmd |only eyeris-3.0.0/eyeris/inst/doc/chunked-database-export.html |only eyeris-3.0.0/eyeris/inst/doc/complete-pipeline.html | 65 eyeris-3.0.0/eyeris/inst/doc/custom-extensions.html | 5 eyeris-3.0.0/eyeris/inst/doc/database-guide.R |only eyeris-3.0.0/eyeris/inst/doc/database-guide.Rmd |only eyeris-3.0.0/eyeris/inst/doc/database-guide.html |only eyeris-3.0.0/eyeris/inst/doc/epoching-bids-reports.html | 137 eyeris-3.0.0/eyeris/inst/doc/internal-api.R |only eyeris-3.0.0/eyeris/inst/doc/internal-api.Rmd |only eyeris-3.0.0/eyeris/inst/doc/internal-api.html |only eyeris-3.0.0/eyeris/inst/doc/reports.html | 5 eyeris-3.0.0/eyeris/inst/www |only eyeris-3.0.0/eyeris/man/bidsify.Rd | 81 eyeris-3.0.0/eyeris/man/calculate_epoched_confounds.Rd | 2 eyeris-3.0.0/eyeris/man/check_column.Rd | 6 eyeris-3.0.0/eyeris/man/check_data.Rd | 4 eyeris-3.0.0/eyeris/man/check_duckdb.Rd |only eyeris-3.0.0/eyeris/man/check_epoch_manual_input_data.Rd | 4 eyeris-3.0.0/eyeris/man/check_epoch_manual_input_dfs.Rd | 6 eyeris-3.0.0/eyeris/man/check_epoch_msg_values.Rd | 4 eyeris-3.0.0/eyeris/man/check_pupil_cols.Rd | 2 eyeris-3.0.0/eyeris/man/check_start_end_timestamps.Rd | 6 eyeris-3.0.0/eyeris/man/cleanup_run_dir_images.Rd |only eyeris-3.0.0/eyeris/man/cleanup_source_figures_post_render.Rd |only eyeris-3.0.0/eyeris/man/cleanup_temp_database.Rd |only eyeris-3.0.0/eyeris/man/compute_baseline.Rd | 4 eyeris-3.0.0/eyeris/man/connect_eyeris_database.Rd |only eyeris-3.0.0/eyeris/man/create_epoch_images_zip.Rd |only eyeris-3.0.0/eyeris/man/create_table_name.Rd |only eyeris-3.0.0/eyeris/man/create_temp_eyeris_database.Rd |only eyeris-3.0.0/eyeris/man/detransient.Rd | 4 eyeris-3.0.0/eyeris/man/detrend.Rd | 4 eyeris-3.0.0/eyeris/man/disconnect_eyeris_database.Rd |only eyeris-3.0.0/eyeris/man/downsample.Rd | 2 eyeris-3.0.0/eyeris/man/draw_random_epochs.Rd | 6 eyeris-3.0.0/eyeris/man/epoch.Rd | 10 eyeris-3.0.0/eyeris/man/epoch_manually.Rd | 6 eyeris-3.0.0/eyeris/man/epoch_only_start_msg.Rd | 2 eyeris-3.0.0/eyeris/man/epoch_start_end_msg.Rd | 4 eyeris-3.0.0/eyeris/man/epoch_start_msg_and_limits.Rd | 2 eyeris-3.0.0/eyeris/man/export_confounds_to_csv.Rd | 29 eyeris-3.0.0/eyeris/man/extract_baseline_epochs.Rd | 8 eyeris-3.0.0/eyeris/man/extract_event_ids.Rd |only eyeris-3.0.0/eyeris/man/eyeris_db_collect.Rd |only eyeris-3.0.0/eyeris/man/eyeris_db_connect.Rd |only eyeris-3.0.0/eyeris/man/eyeris_db_disconnect.Rd |only eyeris-3.0.0/eyeris/man/eyeris_db_list_tables.Rd |only eyeris-3.0.0/eyeris/man/eyeris_db_read.Rd |only eyeris-3.0.0/eyeris/man/eyeris_db_reconstruct_from_chunks.Rd |only eyeris-3.0.0/eyeris/man/eyeris_db_split_for_sharing.Rd |only eyeris-3.0.0/eyeris/man/eyeris_db_summary.Rd |only eyeris-3.0.0/eyeris/man/eyeris_db_to_chunked_files.Rd |only eyeris-3.0.0/eyeris/man/eyeris_db_to_parquet.Rd |only eyeris-3.0.0/eyeris/man/figures/README-unnamed-chunk-3-1.png |binary eyeris-3.0.0/eyeris/man/filter_epochs.Rd | 2 eyeris-3.0.0/eyeris/man/find_baseline_structure.Rd | 6 eyeris-3.0.0/eyeris/man/get_block_numbers.Rd | 4 eyeris-3.0.0/eyeris/man/get_log_timestamp.Rd |only eyeris-3.0.0/eyeris/man/get_timestamps.Rd | 2 eyeris-3.0.0/eyeris/man/glassbox.Rd | 8 eyeris-3.0.0/eyeris/man/index_metadata.Rd | 8 eyeris-3.0.0/eyeris/man/interpolate.Rd | 2 eyeris-3.0.0/eyeris/man/is_binocular_object.Rd | 4 eyeris-3.0.0/eyeris/man/load_asc.Rd | 7 eyeris-3.0.0/eyeris/man/log_error.Rd |only eyeris-3.0.0/eyeris/man/log_info.Rd |only eyeris-3.0.0/eyeris/man/log_message.Rd |only eyeris-3.0.0/eyeris/man/log_success.Rd |only eyeris-3.0.0/eyeris/man/log_warn.Rd |only eyeris-3.0.0/eyeris/man/logging.Rd |only eyeris-3.0.0/eyeris/man/lpfilt.Rd | 2 eyeris-3.0.0/eyeris/man/make_gallery.Rd | 2 eyeris-3.0.0/eyeris/man/make_md_table.Rd | 6 eyeris-3.0.0/eyeris/man/make_md_table_multiline.Rd | 6 eyeris-3.0.0/eyeris/man/make_prog_summary_plot.Rd | 2 eyeris-3.0.0/eyeris/man/make_report.Rd | 4 eyeris-3.0.0/eyeris/man/merge_events_with_timeseries.Rd | 6 eyeris-3.0.0/eyeris/man/merge_temp_database.Rd |only eyeris-3.0.0/eyeris/man/pipeline_handler.Rd | 14 eyeris-3.0.0/eyeris/man/plot.eyeris.Rd | 14 eyeris-3.0.0/eyeris/man/plot_detrend_overlay.Rd | 2 eyeris-3.0.0/eyeris/man/plot_gaze_heatmap.Rd | 4 eyeris-3.0.0/eyeris/man/print_lightbox_img_html.Rd | 13 eyeris-3.0.0/eyeris/man/print_lightbox_img_html_legacy.Rd |only eyeris-3.0.0/eyeris/man/process_chunked_query.Rd |only eyeris-3.0.0/eyeris/man/process_eyeris_data.Rd | 2 eyeris-3.0.0/eyeris/man/read_eyeris_parquet.Rd |only eyeris-3.0.0/eyeris/man/run_bidsify.Rd | 27 eyeris-3.0.0/eyeris/man/save_detrend_plots.Rd | 7 eyeris-3.0.0/eyeris/man/save_progressive_summary_plots.Rd | 7 eyeris-3.0.0/eyeris/man/slice_epoch.Rd | 8 eyeris-3.0.0/eyeris/man/slice_epochs_no_limits.Rd | 8 eyeris-3.0.0/eyeris/man/slice_epochs_with_limits.Rd | 4 eyeris-3.0.0/eyeris/man/summarize_confounds.Rd | 6 eyeris-3.0.0/eyeris/man/write_csv_and_db.Rd |only eyeris-3.0.0/eyeris/man/write_eyeris_data_to_db.Rd |only eyeris-3.0.0/eyeris/man/zip_and_cleanup_source_figures.Rd |only eyeris-3.0.0/eyeris/man/zscore.Rd | 12 eyeris-3.0.0/eyeris/tests/testthat/test-binocular.R | 16 eyeris-3.0.0/eyeris/tests/testthat/test-chunked-processing.R |only eyeris-3.0.0/eyeris/tests/testthat/test-database.R |only eyeris-3.0.0/eyeris/tests/testthat/test-parallel-database.R |only eyeris-3.0.0/eyeris/tests/testthat/test-parquet-split.R |only eyeris-3.0.0/eyeris/tests/testthat/test-plot_gaze_heatmap.R | 6 eyeris-3.0.0/eyeris/vignettes/chunked-database-export.Rmd |only eyeris-3.0.0/eyeris/vignettes/database-guide.Rmd |only eyeris-3.0.0/eyeris/vignettes/internal-api.Rmd |only 151 files changed, 3599 insertions(+), 3226 deletions(-)
Title: Canonical Correlations and Tests of Independence
Description: A simple interface for multivariate correlation analysis that unifies various classical
statistical procedures including t-tests, tests in univariate and multivariate linear models,
parametric and nonparametric tests for correlation, Kruskal-Wallis tests, common approximate
versions of Wilcoxon rank-sum and signed rank tests, chi-squared tests of independence, score
tests of particular hypotheses in generalized linear models, canonical correlation analysis and
linear discriminant analysis.
Author: Robert Schlicht [aut, cre]
Maintainer: Robert Schlicht <robert.schlicht@tu-dresden.de>
Diff between cctest versions 2.1.0 dated 2025-05-07 and 2.2.0 dated 2025-09-17
DESCRIPTION | 6 +- MD5 | 8 +-- R/cctest.R | 126 ++++++++++++++++++++++++++---------------------------- build/partial.rdb |binary man/cctest.Rd | 114 ++++++++++++++++++++++++++---------------------- 5 files changed, 130 insertions(+), 124 deletions(-)
Title: Beta Kernel Process Modeling
Description: Implements the Beta Kernel Process (BKP) for nonparametric modeling of spatially varying binomial probabilities, together with its extension, the Dirichlet Kernel Process (DKP), for categorical or multinomial data.
The package provides functions for model fitting, predictive inference with uncertainty quantification, posterior simulation, and visualization in one-and two-dimensional input spaces.
Multiple kernel functions (Gaussian, Matern 5/2, and Matern 3/2) are supported, with hyperparameters optimized through multi-start gradient-based search.
For more details, see Zhao, Qing, and Xu (2025) <doi:10.48550/arXiv.2508.10447>.
Author: Jiangyan Zhao [cre, aut],
Kunhai Qing [aut],
Jin Xu [aut]
Maintainer: Jiangyan Zhao <zhaojy2017@126.com>
Diff between BKP versions 0.2.0 dated 2025-09-16 and 0.2.1 dated 2025-09-17
DESCRIPTION | 6 ++-- MD5 | 16 ++++++------- NEWS.md | 6 ++++ README.md | 2 - inst/CITATION | 2 - inst/doc/vignettes.R | 6 ++++ inst/doc/vignettes.Rmd | 58 ++++++++++++++++++++++++++---------------------- inst/doc/vignettes.pdf |binary vignettes/vignettes.Rmd | 58 ++++++++++++++++++++++++++---------------------- 9 files changed, 88 insertions(+), 66 deletions(-)
Title: Develop a 'Telegram Bot' with R
Description: Provides a pure interface for the 'Telegram Bot API'
<http://core.telegram.org/bots/api>. In addition to the pure API
implementation, it features a number of tools to make the development of
'Telegram' bots with R easy and straightforward, providing an easy-to-use
interface that takes some work off the programmer.
Author: Ernest Benedito [aut, cre],
Chris Stefano [ctb]
Maintainer: Ernest Benedito <ebeneditos@gmail.com>
Diff between telegram.bot versions 3.0.0 dated 2022-09-07 and 3.0.1 dated 2025-09-17
DESCRIPTION | 8 MD5 | 226 - NAMESPACE | 104 NEWS.md | 190 - R/base.R | 216 - R/basefilter.R | 157 - R/bot.R | 3585 +++++++++++------------- R/callbackqueryhandler.R | 121 R/commandhandler.R | 257 - R/dispatcher.R | 329 +- R/errorhandler.R | 97 R/filters.R | 121 R/handler.R | 283 - R/inlinequeryresult.R | 101 R/messagehandler.R | 165 - R/replymarkup.R | 713 ++-- R/telegram.bot-package.R | 107 R/update.R | 427 +- R/updater.R | 481 +-- R/utils.R | 171 - R/webhook.R | 872 ++--- README.md | 424 +- build/vignette.rds |binary inst/doc/telegrambot-advanced-filters.R | 85 inst/doc/telegrambot-advanced-filters.Rmd | 213 - inst/doc/telegrambot-advanced-filters.html | 896 +++-- inst/doc/telegrambot-basic-functionalities.R | 96 inst/doc/telegrambot-basic-functionalities.Rmd | 210 - inst/doc/telegrambot-basic-functionalities.html | 925 +++--- inst/doc/telegrambot-building-a-bot.R | 68 inst/doc/telegrambot-building-a-bot.Rmd | 208 - inst/doc/telegrambot-building-a-bot.html | 901 +++--- inst/doc/telegrambot-introduction.R | 160 - inst/doc/telegrambot-introduction.Rmd | 360 +- inst/doc/telegrambot-introduction.html | 1113 +++---- inst/doc/telegrambot-set-a-proxy.R | 24 inst/doc/telegrambot-set-a-proxy.Rmd | 62 inst/doc/telegrambot-set-a-proxy.html | 743 ++-- inst/doc/telegrambot-the-add-operator.R | 108 inst/doc/telegrambot-the-add-operator.Rmd | 198 - inst/doc/telegrambot-the-add-operator.html | 845 ++--- man/BaseFilter.Rd | 86 man/Bot.Rd | 186 - man/CallbackQueryHandler.Rd | 44 man/CommandHandler.Rd | 116 man/Dispatcher.Rd | 64 man/ErrorHandler.Rd | 78 man/ForceReply.Rd | 66 man/Handler.Rd | 180 - man/InlineKeyboardButton.Rd | 104 man/InlineKeyboardMarkup.Rd | 124 man/InlineQueryResult.Rd | 88 man/KeyboardButton.Rd | 70 man/MessageFilters.Rd | 98 man/MessageHandler.Rd | 70 man/ReplyKeyboardMarkup.Rd | 116 man/ReplyKeyboardRemove.Rd | 110 man/TelegramObject-add.Rd | 126 man/TelegramObject.Rd | 86 man/Update.Rd | 76 man/Updater.Rd | 184 - man/Webhook.Rd | 298 - man/add_error_handler.Rd | 70 man/add_handler.Rd | 66 man/answerCallbackQuery.Rd | 76 man/answerInlineQuery.Rd | 130 man/bot_token.Rd | 54 man/check_update.Rd | 32 man/clean_updates.Rd | 24 man/deleteMessage.Rd | 54 man/deleteWebhook.Rd | 30 man/editMessageCaption.Rd | 94 man/editMessageReplyMarkup.Rd | 78 man/editMessageText.Rd | 102 man/effective_chat.Rd | 28 man/effective_message.Rd | 28 man/effective_user.Rd | 24 man/filtersLogic.Rd | 68 man/forwardMessage.Rd | 52 man/from_chat_id.Rd | 22 man/from_user_id.Rd | 22 man/getFile.Rd | 82 man/getMe.Rd | 28 man/getUpdates.Rd | 106 man/getUserProfilePhotos.Rd | 66 man/getWebhookInfo.Rd | 34 man/handle_update.Rd | 44 man/leaveChat.Rd | 36 man/running.Rd | 22 man/sendAnimation.Rd | 146 man/sendAudio.Rd | 152 - man/sendChatAction.Rd | 92 man/sendDocument.Rd | 138 man/sendLocation.Rd | 110 man/sendMessage.Rd | 124 man/sendPhoto.Rd | 130 man/sendSticker.Rd | 110 man/sendVideo.Rd | 154 - man/sendVideoNote.Rd | 122 man/sendVoice.Rd | 138 man/setWebhook.Rd | 132 man/set_token.Rd | 28 man/start_polling.Rd | 96 man/start_server.Rd | 98 man/stop_polling.Rd | 60 man/stop_server.Rd | 56 man/telegram.bot.Rd | 132 man/user_id.Rd | 54 vignettes/telegrambot-advanced-filters.Rmd | 213 - vignettes/telegrambot-basic-functionalities.Rmd | 210 - vignettes/telegrambot-building-a-bot.Rmd | 208 - vignettes/telegrambot-introduction.Rmd | 360 +- vignettes/telegrambot-set-a-proxy.Rmd | 62 vignettes/telegrambot-the-add-operator.Rmd | 198 - 114 files changed, 11819 insertions(+), 11716 deletions(-)
Title: Data Science Labs
Description: Datasets and functions that can be used for data analysis practice, homework and projects in data science courses and workshops. 26 datasets are available for case studies in data visualization, statistical inference, modeling, linear regression, data wrangling and machine learning.
Author: Rafael A. Irizarry [aut, cre],
Amy Gill [aut]
Maintainer: Rafael A. Irizarry <rafael_irizarry@dfci.harvard.edu>
Diff between dslabs versions 0.8.0 dated 2024-03-01 and 0.9.0 dated 2025-09-17
DESCRIPTION | 23 ++++++++++----- MD5 | 16 +++++++--- NAMESPACE | 1 R/fit_recommender_model.R |only R/results_us_election_2012.R |only build/partial.rdb |binary data/polls_us_election_2016.rda |binary data/results_us_election_2012.rda |only inst/script/make-polls_us_election_2016.R | 41 +++++++++++++++------------- inst/script/make-results_us_election_2012.R |only man/fit_recommender_model.Rd |only man/results_us_election_2012.Rd |only 12 files changed, 51 insertions(+), 30 deletions(-)
Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included. We further include functions for percentages (or proportions).
The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include:
a) Tsagris M.T., Preston S. and Wood A.T.A. (2011). "A data-based power transformation for compositional data". Fourth International International Workshop on Compositional Data Analysis. <doi:10.48550/arXiv.1106.1451>.
b) Tsagris M. (2014). "The k-NN algorithm for compositional data: a revised approach with and without zero values present". Journal of Data Science, 12(3): 519--534. <doi:10.6339/JDS.201407_12(3).0008>.
c) Tsagris M. (2015). "A novel, divergence based, regression for compositional data". Proceedings of the 28th Panhellenic Statistics Conference, 15-18 April 2015, Athens, Greece, 430--444. <doi:10.48550/arXiv.15 [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Abdulaziz Alenazi [ctb],
Christos Adam [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Compositional versions 7.7 dated 2025-08-18 and 7.8 dated 2025-09-17
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 2 +- R/mkde.R | 26 ++++++++++++++++---------- man/Compositional-package.Rd | 4 ++-- man/mkde.Rd | 5 ++++- 6 files changed, 32 insertions(+), 23 deletions(-)
Title: Algorithms for Quantitative Pedology
Description: The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps>. Components of the AQP project (aqp, soilD [...truncated...]
Author: Dylan Beaudette [aut, cre],
Pierre Roudier [aut, ctb],
Andrew Brown [aut, ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>
Diff between aqp versions 2.2 dated 2025-02-15 and 2.2-1 dated 2025-09-17
aqp-2.2-1/aqp/DESCRIPTION | 11 aqp-2.2-1/aqp/MD5 | 109 +++----- aqp-2.2-1/aqp/NAMESPACE | 3 aqp-2.2-1/aqp/NEWS.md | 12 aqp-2.2-1/aqp/R/NCSP.R | 100 ++++--- aqp-2.2-1/aqp/R/SoilProfileCollection-metadata.R | 3 aqp-2.2-1/aqp/R/accumulateDepths.R | 22 + aqp-2.2-1/aqp/R/aqp-package.R | 2 aqp-2.2-1/aqp/R/col2Munsell.R | 8 aqp-2.2-1/aqp/R/colorChart.R | 6 aqp-2.2-1/aqp/R/data-documentation.R | 6 aqp-2.2-1/aqp/R/evalMissingData.R | 10 aqp-2.2-1/aqp/R/fragmentClasses.R | 2 aqp-2.2-1/aqp/R/hzTransitionProbabilities.R | 2 aqp-2.2-1/aqp/R/mixMunsell.R | 4 aqp-2.2-1/aqp/R/mostLikelyHzSequence.R | 2 aqp-2.2-1/aqp/R/munsell2rgb.R | 14 - aqp-2.2-1/aqp/R/particleSizeClasses.R |only aqp-2.2-1/aqp/R/random_profile.R | 57 ++++ aqp-2.2-1/aqp/build/partial.rdb |binary aqp-2.2-1/aqp/build/vignette.rds |binary aqp-2.2-1/aqp/data/munsell.spectra.rda |binary aqp-2.2-1/aqp/data/munsell.spectra.wide.rda |binary aqp-2.2-1/aqp/data/munsellHuePosition.rda |binary aqp-2.2-1/aqp/inst/doc/Introduction-to-SoilProfileCollection-Objects.R | 2 aqp-2.2-1/aqp/inst/doc/Introduction-to-SoilProfileCollection-Objects.Rmd | 2 aqp-2.2-1/aqp/inst/doc/Introduction-to-SoilProfileCollection-Objects.html | 136 +++++----- aqp-2.2-1/aqp/inst/doc/Munsell-color-conversion.R | 2 aqp-2.2-1/aqp/inst/doc/Munsell-color-conversion.Rmd | 2 aqp-2.2-1/aqp/inst/doc/Munsell-color-conversion.html | 4 aqp-2.2-1/aqp/inst/doc/NCSP.R | 4 aqp-2.2-1/aqp/inst/doc/NCSP.Rmd | 4 aqp-2.2-1/aqp/inst/doc/NCSP.html | 12 aqp-2.2-1/aqp/inst/doc/label-placement.R | 19 - aqp-2.2-1/aqp/inst/doc/label-placement.Rmd | 20 - aqp-2.2-1/aqp/inst/doc/label-placement.html | 134 +++++---- aqp-2.2-1/aqp/man/NCSP.Rd | 28 -- aqp-2.2-1/aqp/man/accumulateDepths.Rd | 6 aqp-2.2-1/aqp/man/col2Munsell.Rd | 10 aqp-2.2-1/aqp/man/colorChart.Rd | 2 aqp-2.2-1/aqp/man/mixMunsell.Rd | 4 aqp-2.2-1/aqp/man/munsell.spectra.Rd | 4 aqp-2.2-1/aqp/man/munsell2rgb.Rd | 6 aqp-2.2-1/aqp/man/random_profile.Rd | 5 aqp-2.2-1/aqp/man/rgb2munsell.Rd | 10 aqp-2.2-1/aqp/man/rp.Rd |only aqp-2.2-1/aqp/tests/testthat/Rplots.pdf |binary aqp-2.2-1/aqp/tests/testthat/test-NCSP.R | 37 ++ aqp-2.2-1/aqp/tests/testthat/test-spec2Munsell.R | 42 +++ aqp-2.2-1/aqp/vignettes/Introduction-to-SoilProfileCollection-Objects.Rmd | 2 aqp-2.2-1/aqp/vignettes/Munsell-color-conversion.Rmd | 2 aqp-2.2-1/aqp/vignettes/NCSP.Rmd | 4 aqp-2.2-1/aqp/vignettes/label-placement.Rmd | 20 - aqp-2.2/aqp/R/unroll.R |only aqp-2.2/aqp/inst/_pkgdown.yml |only aqp-2.2/aqp/inst/doc/missing-data.R |only aqp-2.2/aqp/inst/doc/missing-data.Rmd |only aqp-2.2/aqp/inst/doc/missing-data.html |only aqp-2.2/aqp/man/unroll.Rd |only aqp-2.2/aqp/vignettes/missing-data.Rmd |only 60 files changed, 540 insertions(+), 356 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') Driver Manager
Description: Provides a developer-facing interface to 'Arrow' Database
Connectivity ('ADBC') for the purposes of driver development, driver
testing, and building high-level database interfaces for users. 'ADBC'
<https://arrow.apache.org/adbc/> is an API standard for database access
libraries that uses 'Arrow' for result sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcdrivermanager versions 0.19.0-1 dated 2025-07-20 and 0.20.0 dated 2025-09-17
DESCRIPTION | 6 MD5 | 38 - R/driver_void.R | 15 man/adbc_driver_load.Rd | 6 man/adbc_load_flags.Rd | 11 src/Makevars | 3 src/Makevars.win | 3 src/c/driver/postgresql/postgres_type.h | 18 src/c/driver/sqlite/sqlite.cc | 17 src/c/driver/sqlite/statement_reader.c | 56 ++ src/c/driver/sqlite/statement_reader.h | 6 src/c/driver_manager/adbc_driver_manager.cc | 522 ++++++++++++++++++++----- src/c/driver_manager/current_arch.h | 53 ++ src/c/include/arrow-adbc/adbc_driver_manager.h | 33 + src/c/vendor/nanoarrow/nanoarrow.c | 251 +++++++++++- src/c/vendor/nanoarrow/nanoarrow.h | 447 ++++++++++++++------- src/c/vendor/nanoarrow/nanoarrow.hpp | 473 +++++++++++++++------- src/init.c | 5 src/radbc.cc | 9 tests/testthat/test-driver_void.R | 5 20 files changed, 1508 insertions(+), 469 deletions(-)
More information about adbcdrivermanager at CRAN
Permanent link
Title: Price Index Aggregation
Description: Most price indexes are made with a two-step procedure, where
period-over-period elementary indexes are first calculated for a collection
of elementary aggregates at each point in time, and then aggregated according
to a price index aggregation structure. These indexes can then be chained
together to form a time series that gives the evolution of prices with
respect to a fixed base period. This package contains a collection of
functions that revolve around this work flow, making it easy to build
standard price indexes, and implement the methods described by
Balk (2008, <doi:10.1017/CBO9780511720758>), von der Lippe (2007,
<doi:10.3726/978-3-653-01120-3>), and the CPI manual (2020,
<doi:10.5089/9781484354841.069>) for bilateral price indexes.
Author: Steve Martin [aut, cre, cph]
Maintainer: Steve Martin <marberts@protonmail.com>
Diff between piar versions 0.8.2 dated 2025-03-19 and 0.8.3 dated 2025-09-17
piar-0.8.2/piar/R/elemental_index.R |only piar-0.8.2/piar/man/elemental_index.Rd |only piar-0.8.3/piar/DESCRIPTION | 13 piar-0.8.3/piar/MD5 | 259 +-- piar-0.8.3/piar/NAMESPACE | 6 piar-0.8.3/piar/NEWS.md | 39 piar-0.8.3/piar/R/aggregate.piar_index.R | 196 +- piar-0.8.3/piar/R/aggregation_structure-class.R | 25 piar-0.8.3/piar/R/aggregation_structure.R | 32 piar-0.8.3/piar/R/as_aggregation_structure.R | 10 piar-0.8.3/piar/R/as_index.R | 21 piar-0.8.3/piar/R/chain.R | 14 piar-0.8.3/piar/R/coerce-aggregation_structure.R | 22 piar-0.8.3/piar/R/coerce-index.R | 24 piar-0.8.3/piar/R/contrib.R | 82 - piar-0.8.3/piar/R/cut.piar_aggregation_structure.R | 14 piar-0.8.3/piar/R/elementary_index.R |only piar-0.8.3/piar/R/expand_classification.R | 17 piar-0.8.3/piar/R/extract.piar_index.R | 8 piar-0.8.3/piar/R/head.piar_index.R | 10 piar-0.8.3/piar/R/helpers.R | 145 +- piar-0.8.3/piar/R/impute_prices.R | 51 piar-0.8.3/piar/R/index-class.R | 41 piar-0.8.3/piar/R/is.na.piar_index.R | 2 piar-0.8.3/piar/R/levels.piar_index.R | 2 piar-0.8.3/piar/R/mean.piar_index.R | 87 - piar-0.8.3/piar/R/merge.piar_index.R | 6 piar-0.8.3/piar/R/split.piar_index.R | 32 piar-0.8.3/piar/R/split_classification.R | 10 piar-0.8.3/piar/R/stack.piar_index.R | 4 piar-0.8.3/piar/R/time.piar_index.R | 4 piar-0.8.3/piar/R/update.aggregation_structure.R | 16 piar-0.8.3/piar/R/weights.piar_aggregation_structure.R | 22 piar-0.8.3/piar/R/window.piar_index.R | 14 piar-0.8.3/piar/R/zzz.R |only piar-0.8.3/piar/README.md | 65 piar-0.8.3/piar/build/partial.rdb |binary piar-0.8.3/piar/build/vignette.rds |binary piar-0.8.3/piar/inst/doc/adjust-weights.R | 16 piar-0.8.3/piar/inst/doc/adjust-weights.Rmd | 24 piar-0.8.3/piar/inst/doc/adjust-weights.html | 94 - piar-0.8.3/piar/inst/doc/contributions.R | 6 piar-0.8.3/piar/inst/doc/contributions.Rmd | 12 piar-0.8.3/piar/inst/doc/contributions.html | 67 piar-0.8.3/piar/inst/doc/imputation.R | 2 piar-0.8.3/piar/inst/doc/imputation.Rmd | 20 piar-0.8.3/piar/inst/doc/imputation.html | 49 piar-0.8.3/piar/inst/doc/index-number-formulas.R | 40 piar-0.8.3/piar/inst/doc/index-number-formulas.Rmd | 64 piar-0.8.3/piar/inst/doc/index-number-formulas.html | 150 +- piar-0.8.3/piar/inst/doc/matrix-aggregation.R | 6 piar-0.8.3/piar/inst/doc/matrix-aggregation.Rmd | 22 piar-0.8.3/piar/inst/doc/matrix-aggregation.html | 88 - 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piar-0.8.3/piar/tests/test-making-price-indexes.Rout.save | 674 +++++----- piar-0.8.3/piar/tests/testthat/test-aggregate.R | 623 ++++++--- piar-0.8.3/piar/tests/testthat/test-aggregation-structure-attributes.R | 24 piar-0.8.3/piar/tests/testthat/test-as.ts.R | 7 piar-0.8.3/piar/tests/testthat/test-as_index.R | 47 piar-0.8.3/piar/tests/testthat/test-chain.R | 60 piar-0.8.3/piar/tests/testthat/test-coerce-aggregation-structure.R | 37 piar-0.8.3/piar/tests/testthat/test-coerce-index.R | 64 piar-0.8.3/piar/tests/testthat/test-contrib.R | 100 - piar-0.8.3/piar/tests/testthat/test-cut.R | 18 piar-0.8.3/piar/tests/testthat/test-elemental_index.R | 108 + piar-0.8.3/piar/tests/testthat/test-expand_classification.R | 105 + piar-0.8.3/piar/tests/testthat/test-extract-index.R | 107 + piar-0.8.3/piar/tests/testthat/test-impute-prices.R | 107 + piar-0.8.3/piar/tests/testthat/test-index-attributes.R | 28 piar-0.8.3/piar/tests/testthat/test-is.na.R | 21 piar-0.8.3/piar/tests/testthat/test-known-values.R | 16 piar-0.8.3/piar/tests/testthat/test-mean.R | 68 - piar-0.8.3/piar/tests/testthat/test-merge.R | 32 piar-0.8.3/piar/tests/testthat/test-split.R | 20 piar-0.8.3/piar/tests/testthat/test-split_classification.R | 37 piar-0.8.3/piar/tests/testthat/test-stack.R | 22 piar-0.8.3/piar/tests/testthat/test-update.R | 6 piar-0.8.3/piar/vignettes/adjust-weights.Rmd | 24 piar-0.8.3/piar/vignettes/contributions.Rmd | 12 piar-0.8.3/piar/vignettes/imputation.Rmd | 20 piar-0.8.3/piar/vignettes/index-number-formulas.Rmd | 64 piar-0.8.3/piar/vignettes/matrix-aggregation.Rmd | 22 piar-0.8.3/piar/vignettes/multiple-baskets.Rmd | 20 piar-0.8.3/piar/vignettes/multiple-data-sources.Rmd | 10 piar-0.8.3/piar/vignettes/multiple-dimensions.Rmd | 8 piar-0.8.3/piar/vignettes/piar.Rmd | 36 piar-0.8.3/piar/vignettes/subperiods.Rmd | 4 piar-0.8.3/piar/vignettes/superlative-aggregation.Rmd | 12 133 files changed, 3371 insertions(+), 2302 deletions(-)