Title: TVA Models in 'Stan' using 'R' and 'StanTVA'
Description: 'Stan' implementation of the Theory of Visual Attention (TVA; Bundesen, 1990; <doi:10.1037/0033-295X.97.4.523>) and numerous convenience functions for generating, compiling, fitting, and analyzing TVA models.
Author: Maximilian M. Rabe [aut, cre] ,
Soeren Kyllingsbaek [aut]
Maintainer: Maximilian M. Rabe <maximilian.rabe@uni-potsdam.de>
Diff between RStanTVA versions 0.3.0 dated 2025-05-08 and 0.3.2 dated 2025-12-16
DESCRIPTION | 13 - MD5 | 70 +++-- NAMESPACE | 7 R/tva.R | 490 +++++++++++++++++++++++++++------------ README.md | 4 build/partial.rdb |binary build/vignette.rds |only inst/StanTVA/tva.stan | 8 inst/doc |only man/alias-stantvafit-method.Rd | 2 man/coef-stantvafit-method.Rd | 2 man/extract-stantvafit-method.Rd | 2 man/fitted-stantvafit-method.Rd | 2 man/fixef-stantvafit-method.Rd | 2 man/logLik-stantvafit-method.Rd | 2 man/model_code.Rd | 2 man/names-stantvafit-method.Rd | 2 man/optimizing.Rd | 4 man/predict-stantvafit-method.Rd | 2 man/print-stantvafit-method.Rd | 2 man/ranef-stantvafit-method.Rd | 2 man/read_stantva_fit.Rd | 2 man/read_tva_data.Rd | 2 man/sampling.Rd | 3 man/show-stantvamodel-method.Rd | 2 man/stancsv2stantvafit.Rd | 2 man/stantva_model.Rd | 2 man/stantvacode-class.Rd | 2 man/stantvamodel-class.Rd | 2 man/summary-stantvafit-method.Rd | 2 man/tva_report.Rd | 2 man/write_stantva_fit.Rd | 2 man/write_stantva_model.Rd | 2 man/write_tva_data.Rd | 2 vignettes |only 35 files changed, 438 insertions(+), 207 deletions(-)
Title: Hazard of Multi-Stage Clonal Expansion Models
Description: Functions to calculate hazard and survival function of Multi-Stage Clonal Expansion Models used in cancer epidemiology. For the Two-Stage Clonal Expansion Model an exact solution is implemented assuming piecewise constant parameters, see Heidenreich, Luebeck, Moolgavkar (1997) <doi:10.1111/j.1539-6924.1997.tb00878.x>. Numerical solutions are provided for its extensions, see also Little, Vineis, Li (2008) <doi:10.1016/j.jtbi.2008.05.027>.
Author: Cristoforo Simonetto [aut, cre] ,
Jan Christian Kaiser [ctb]
Maintainer: Cristoforo Simonetto <cristoforo.simonetto@ph.tum.de>
This is a re-admission after prior archival of version 1.0.1 dated 2020-10-29
Diff between msce versions 1.0.1 dated 2020-10-29 and 1.0.2 dated 2025-12-16
msce-1.0.1/msce/man/msce.Rd |only msce-1.0.2/msce/DESCRIPTION | 27 - msce-1.0.2/msce/MD5 | 33 - msce-1.0.2/msce/R/RcppExports.R | 1 msce-1.0.2/msce/R/msce.R | 19 msce-1.0.2/msce/build/partial.rdb |only msce-1.0.2/msce/build/vignette.rds |binary msce-1.0.2/msce/inst/doc/msce.R | 9 msce-1.0.2/msce/inst/doc/msce.Rmd | 7 msce-1.0.2/msce/inst/doc/msce.html | 689 +++++++++++++++++++++-------- msce-1.0.2/msce/man/msce-package.Rd |only msce-1.0.2/msce/man/tsce.Rd | 3 msce-1.0.2/msce/src/Makevars | 1 msce-1.0.2/msce/src/Makevars.win | 1 msce-1.0.2/msce/src/RcppExports.cpp | 5 msce-1.0.2/msce/src/tsce.cpp | 1 msce-1.0.2/msce/tests/testthat.R | 7 msce-1.0.2/msce/tests/testthat/test_msce.R | 2 msce-1.0.2/msce/vignettes/msce.Rmd | 7 19 files changed, 593 insertions(+), 219 deletions(-)
Title: General Inverse Problem Platform
Description: Set of functions designed to solve inverse problems. The direct problem is used to calculate a cost function to be minimized.
Here are listed some papers using Inverse Problems solvers and sensitivity analysis:
(Jader Lugon Jr.; Antonio J. Silva Neto 2011) <doi:10.1590/S1678-58782011000400003>.
(Jader Lugon Jr.; Antonio J. Silva Neto; Pedro P.G.W. Rodrigues 2008) <doi:10.1080/17415970802082864>.
(Jader Lugon Jr.; Antonio J. Silva Neto; Cesar C. Santana 2008) <doi:10.1080/17415970802082922>.
Author: Jader Lugon Junior [aut, cre] ,
Antonio Jose Silva Neto [aut]
Maintainer: Jader Lugon Junior <jlugonjr@gmail.com>
Diff between gripp versions 0.2.20 dated 2019-08-24 and 0.2.21 dated 2025-12-16
DESCRIPTION | 16 + MD5 | 26 +- NAMESPACE | 21 +- R/cost.R | 4 R/invprob.R | 4 R/sensitivity.R | 4 R/synthetic.R | 4 build/vignette.rds |binary inst/doc/gripp_details.R | 4 inst/doc/gripp_details.html | 431 +++++++++++++++++++++++++++++++++++++------- man/cost.Rd | 2 man/invprob.Rd | 4 man/sensitivity.Rd | 2 man/synthetic.Rd | 2 14 files changed, 425 insertions(+), 99 deletions(-)
Title: Correlation-Based and Model-Based Predictor Pruning
Description: Provides functions for predictor pruning using association-based and model-based approaches. Includes corrPrune() for fast correlation-based pruning, modelPrune() for VIF-based regression pruning, and exact graph-theoretic algorithms (Eppstein–Löffler–Strash, Bron–Kerbosch) for exhaustive subset enumeration. Supports linear models, GLMs, and mixed models ('lme4', 'glmmTMB').
Author: Gilles Colling [aut, cre]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between corrselect versions 3.0.2 dated 2025-11-29 and 3.0.5 dated 2025-12-16
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deletions(-)
Title: "Risk Model Regression and Analysis with Complex Non-Linear
Models"
Description: Performs survival analysis using general non-linear models. Risk models can be the sum or product of terms. Each term is the product of exponential/linear functions of covariates. Additionally sub-terms can be defined as a sum of exponential, linear threshold, and step functions. Cox Proportional hazards <https://en.wikipedia.org/wiki/Proportional_hazards_model>, Poisson <https://en.wikipedia.org/wiki/Poisson_regression>, and Fine-Gray competing risks <https://www.publichealth.columbia.edu/research/population-health-methods/competing-risk-analysis> regression are supported. This work was sponsored by NASA Grants 80NSSC19M0161 and 80NSSC23M0129 through a subcontract from the National Council on Radiation Protection and Measurements (NCRP). The computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CNS-1006860, EPS-1006860, EPS-0919443, ACI-1440548, CHE-1726332, and NIH P20GM113109.
Author: Eric Giunta [aut, cre] ,
Amir Bahadori [ctb] ,
Dan Andresen [ctb] ,
Linda Walsh [ctb] ,
Benjamin French [ctb] ,
Lawrence Dauer [ctb] ,
John Boice Jr [ctb] ,
Kansas State University [cph],
NASA [fnd],
NCRP [fnd],
NRC [fnd]
Maintainer: Eric Giunta <egiunta@ksu.edu>
Diff between Colossus versions 1.4.5 dated 2025-12-07 and 1.4.6 dated 2025-12-16
DESCRIPTION | 6 MD5 | 110 ++++++++-------- NAMESPACE | 1 NEWS.md | 6 R/BasicRun.R | 163 ++++++++++++++++++++---- R/CaseControl_Regression.R | 42 ------ R/Cox_Regression.R | 50 ------- R/LogitRegression.R | 37 ----- R/Poisson_Regression.R | 92 ------------- R/RcppExports.R | 11 - R/SurvTypes.R | 21 ++- R/Utility.R | 165 ++++++++++++------------ R/utils-roxygen.R | 2 inst/doc/Alt_Run_Opt.html | 12 - inst/doc/Logistic.html | 56 ++++---- inst/doc/Matched_Case_Control.html | 36 ++--- inst/doc/SMR_Analysis.html | 12 - inst/doc/Starting-Description.html | 12 - inst/doc/Wald_and_Log_Bound.html | 46 +++--- man/CaseControlRun.Rd | 2 man/CoxRun.Rd | 2 man/CoxRunMulti.Rd | 2 man/LogisticRun.Rd | 2 man/PoisRun.Rd | 2 man/PoisRunJoint.Rd | 2 man/PoisRunMulti.Rd | 2 man/RelativeRisk.coxres.Rd | 4 man/gen_time_dep.Rd | 2 man/get_form.Rd | 6 man/plot.coxres.Rd | 4 src/Calc_Repeated.cpp | 31 ---- src/Calc_Repeated.h | 4 src/Main_Bound.cpp | 108 ++++++++++------ src/Main_Functions.cpp | 180 +++++++++++++------------- src/Main_Functions.h | 2 src/Main_Multi.cpp | 8 - src/Omnibus_Pieces.cpp | 109 ++++++++++++++-- src/Plot_Extensions.cpp | 6 src/Step_Calc.cpp | 208 ++++++++++++++++++------------- src/Step_Calc.h | 4 src/Subterms_Risk.cpp | 76 +++++++---- tests/testthat/test-Assigned.R | 31 ++-- tests/testthat/test-CaseControl.R | 12 - tests/testthat/test-Cox_Plot.R | 34 ++--- tests/testthat/test-Cox_Regression.R | 35 ++--- tests/testthat/test-Formula.R | 64 +++++---- tests/testthat/test-Gradient.R | 18 +- tests/testthat/test-Joint.R | 14 +- tests/testthat/test-Logbound.R | 59 ++++---- tests/testthat/test-Logit.R | 10 - tests/testthat/test-Multidose.R | 46 +++--- tests/testthat/test-Norm.R | 10 - tests/testthat/test-Omnibus.R | 52 +++---- tests/testthat/test-Poisson_Regression.R | 10 - tests/testthat/test-Poisson_Residual.R | 2 tests/testthat/test-Utility.R | 20 +- 56 files changed, 1093 insertions(+), 970 deletions(-)
Title: Chic and Sleek Functions for Beautiful Statisticians
Description: Because your linear models deserve better than console output.
A sleek color palette and kable styling to make your regression results look sharper than they are.
Includes support for Partial Least Squares (PLS) regression via both the SVD and NIPALS algorithms,
along with a unified interface for model fitting and fabulous LaTeX and console output formatting.
See the package website at
<https://finitesample.space/snazzier>.
Author: Aidan J. Wagner [aut, cre]
Maintainer: Aidan J. Wagner <JesusButForGayPeople@proton.me>
Diff between snazzieR versions 0.1.1 dated 2025-05-11 and 0.1.2 dated 2025-12-16
snazzieR-0.1.1/snazzieR/tests/testthat/test-format-pls.R |only snazzieR-0.1.2/snazzieR/.Rinstignore |only snazzieR-0.1.2/snazzieR/DESCRIPTION | 15 snazzieR-0.1.2/snazzieR/MD5 | 69 ++- snazzieR-0.1.2/snazzieR/NAMESPACE | 12 snazzieR-0.1.2/snazzieR/R/ANOVA.summary.table.R | 61 +-- snazzieR-0.1.2/snazzieR/R/NIPALS.pls.R | 28 - snazzieR-0.1.2/snazzieR/R/SVD.pls.R | 24 - snazzieR-0.1.2/snazzieR/R/colors.R | 55 +- snazzieR-0.1.2/snazzieR/R/cross.validation.R |only snazzieR-0.1.2/snazzieR/R/eigen.summary.R | 98 ++-- snazzieR-0.1.2/snazzieR/R/format.pls.R | 198 +++++----- snazzieR-0.1.2/snazzieR/R/model.summary.table.R | 96 +++- snazzieR-0.1.2/snazzieR/R/pls.summary.R |only snazzieR-0.1.2/snazzieR/R/ridge.regression.R |only snazzieR-0.1.2/snazzieR/R/ridge.summary.R |only snazzieR-0.1.2/snazzieR/R/snazzieR.theme.R | 25 + snazzieR-0.1.2/snazzieR/build/partial.rdb |binary snazzieR-0.1.2/snazzieR/build/vignette.rds |only snazzieR-0.1.2/snazzieR/inst/doc |only snazzieR-0.1.2/snazzieR/man/ANOVA.summary.table.Rd | 15 snazzieR-0.1.2/snazzieR/man/colors.Rd | 55 +- snazzieR-0.1.2/snazzieR/man/create_kfold_splits.Rd |only snazzieR-0.1.2/snazzieR/man/cv.mse.Rd |only snazzieR-0.1.2/snazzieR/man/eigen.summary.Rd | 12 snazzieR-0.1.2/snazzieR/man/fit.ridge.Rd |only snazzieR-0.1.2/snazzieR/man/kfold_cross_validation.Rd |only snazzieR-0.1.2/snazzieR/man/model.summary.table.Rd | 22 - snazzieR-0.1.2/snazzieR/man/optimize.cv.lambda.Rd |only snazzieR-0.1.2/snazzieR/man/pls.summary.Rd |only snazzieR-0.1.2/snazzieR/man/predict.ridge.model.Rd |only snazzieR-0.1.2/snazzieR/man/print.ridge.model.Rd |only snazzieR-0.1.2/snazzieR/man/ridge.regression.Rd |only snazzieR-0.1.2/snazzieR/man/ridge.summary.Rd |only snazzieR-0.1.2/snazzieR/man/snazzieR.theme.Rd | 25 + snazzieR-0.1.2/snazzieR/tests/testthat/test-nipals-pls.R | 135 ++++++ snazzieR-0.1.2/snazzieR/tests/testthat/test-pls-regression.R | 179 +++++++++ snazzieR-0.1.2/snazzieR/tests/testthat/test-ridge-regression.R |only snazzieR-0.1.2/snazzieR/tests/testthat/test-svd-pls.R | 181 +++++++++ snazzieR-0.1.2/snazzieR/vignettes |only 40 files changed, 966 insertions(+), 339 deletions(-)
Title: Choosing Sample Size for Evaluating a Diagnostic Test
Description: Calculates the sample size needed for evaluating a diagnostic test based on sensitivity, specificity, prevalence, and desired precision. Based on Buderer (1996) <doi:10.1111/j.1553-2712.1996.tb03538.x>.
Author: Mohamed Kamal [aut, cre]
Maintainer: Mohamed Kamal <mohamedkamalhospital@gmail.com>
Diff between SampleSizeDiagnostics versions 0.1.0 dated 2024-07-26 and 0.1.1 dated 2025-12-16
DESCRIPTION | 8 +- MD5 | 17 ++--- NEWS.md |only R/sample_size.R | 7 +- README.md | 111 +++++++++++++++++++++--------------- build/vignette.rds |binary inst/doc/SampleSizeDiagnostics.Rmd | 30 +++++++++ inst/doc/SampleSizeDiagnostics.html | 48 ++++++++++++--- man/SampleSizeDiagnostics.Rd | 7 +- vignettes/SampleSizeDiagnostics.Rmd | 30 +++++++++ 10 files changed, 183 insertions(+), 75 deletions(-)
More information about SampleSizeDiagnostics at CRAN
Permanent link
Title: Generate Generative Data for a Data Source
Description: Generative Adversarial Networks are applied to generate generative data for a data source. A generative model consisting of a generator and a discriminator network is trained. During iterative training the distribution of generated data is converging to that of the data source. Direct applications of generative data are the created functions for data evaluation, missing data completion and data classification. A software service for accelerated training of generative models on graphics processing units is available. Reference: Goodfellow et al. (2014) <doi:10.48550/arXiv.1406.2661>.
Author: Werner Mueller [aut, cre]
Maintainer: Werner Mueller <werner.mueller5@chello.at>
Diff between ganGenerativeData versions 2.1.4 dated 2024-12-12 and 2.1.6 dated 2025-12-16
DESCRIPTION | 10 - MD5 | 35 +++-- R/RcppExports.R | 40 +++--- R/dsInt.R | 10 - R/gdCalculateDensitiyValues.R | 17 +- R/gdPlotProjection.R | 44 +++---- R/gdTrain.R | 38 ++---- R/gdTrainGenerate.R | 107 +++++++++--------- R/keras_zip_lists.R |only man/ganGenerativeData-package.Rd | 21 +-- man/gdCalculateDensityValue.Rd | 8 - man/gdCalculateDensityValues.Rd | 9 - man/gdComplete.Rd | 4 man/gdGetRow.Rd | 2 man/gdKNearestNeighbors.Rd | 4 man/gdTrain.Rd | 13 +- src/density.h | 41 +++--- src/gdInt.cpp | 230 +++++++++++++++++++-------------------- src/vpTree.h | 90 +++++++-------- 19 files changed, 364 insertions(+), 359 deletions(-)
More information about ganGenerativeData at CRAN
Permanent link
Title: An Implementation of Dynamic TOPMODEL Hydrological Model in R
Description: An R implementation and enhancement of the Dynamic TOPMODEL semi-distributed hydrological model originally proposed by Beven and Freer (2001) <doi:10.1002/hyp.252>. The 'dynatop' package implements code for simulating models which can be created using the 'dynatopGIS' package.
Author: Paul Smith [aut, cre] ,
Peter Metcalfe [aut]
Maintainer: Paul Smith <paul@waternumbers.co.uk>
Diff between dynatop versions 0.2.3 dated 2022-10-10 and 0.2.4 dated 2025-12-16
DESCRIPTION | 11 MD5 | 33 R/dynatop-package.R | 10 README.md | 8 build/partial.rdb |only build/vignette.rds |binary inst/doc/Channel_HRU.R | 2 inst/doc/Channel_HRU.html | 250 - inst/doc/Hillslope_HRU.html | 55 inst/doc/Notes_on_the_implementation_of_Dynamic_TOPMODEL.R | 2 inst/doc/Notes_on_the_implementation_of_Dynamic_TOPMODEL.html | 14 inst/doc/Selected_References.html | 24 inst/doc/The_Model_Object.R | 4 inst/doc/The_Model_Object.html | 294 - inst/doc/dynatop.R | 10 inst/doc/dynatop.html | 258 - man/dynatop-package.Rd | 23 vignettes/HRU.html | 1783 +++------- 18 files changed, 1191 insertions(+), 1590 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-08-24 1.1.1
2017-07-11 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-08-29 1.1.1
2017-07-13 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-04 0.4.5
2023-01-12 0.4.4
2020-09-29 0.4.3
2019-10-09 0.4.2
Title: Interpretable Boosted Linear Models
Description: Implements Interpretable Boosted Linear Models (IBLMs). These combine a conventional generalized linear model (GLM) with a machine learning component, such as XGBoost. The package also provides tools within for explaining and analyzing these models. For more details see Gawlowski and Wang (2025) <https://ifoa-adswp.github.io/IBLM/reference/figures/iblm_paper.pdf>.
Author: Karol Gawlowski [aut, cre, cph],
Paul Beard [aut]
Maintainer: Karol Gawlowski <Karol.Gawlowski@citystgeorges.ac.uk>
Diff between IBLM versions 1.0.1 dated 2025-11-19 and 1.0.2 dated 2025-12-16
DESCRIPTION | 11 - MD5 | 58 +++--- NEWS.md | 26 ++ R/create_beta_correction_plot_functions.R | 5 R/drop_xgb_data_params.R | 12 - R/explain_iblm.R | 25 -- R/extract_booster_shap.R | 12 + R/get_pinball_scores.R | 2 R/load_freMTPL2freq.R | 4 R/predict.R | 2 R/train_iblm_xgb.R | 116 ++++++------- R/train_xgb_as_per_iblm.R | 14 - README.md | 5 build |only inst |only man/beta_corrected_density.Rd | 5 man/beta_corrections_derive.Rd | 10 - man/create_beta_corrected_density.Rd | 124 ++++++------- man/create_beta_corrected_scatter.Rd | 108 ++++++------ man/create_bias_density.Rd | 104 +++++------ man/create_overall_correction.Rd | 90 +++++----- man/freMTPLmini.Rd | 98 +++++------ man/load_freMTPL2freq.Rd | 118 ++++++------- man/shap_to_onehot.Rd | 10 - man/train_iblm_xgb.Rd | 41 +--- man/train_xgb_as_per_iblm.Rd | 4 tests/testthat/test-explain_iblm.R | 267 +++++++++++++++++------------- tests/testthat/test-get_pinball_scores.R | 73 ++++---- tests/testthat/test-train_iblm.R | 63 ++++--- vignettes |only 30 files changed, 720 insertions(+), 687 deletions(-)
Title: Super Learner for Survival Prediction from Censored Data
Description: Several functions and S3 methods to construct a super learner in the presence of censored times-to-event and to evaluate its prognostic capacities.
Author: Yohann Foucher [aut, cre] ,
Camille Sabathe [aut]
Maintainer: Yohann Foucher <yohann.foucher@univ-poitiers.fr>
Diff between survivalSL versions 0.98 dated 2025-07-02 and 1.0 dated 2025-12-16
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NAMESPACE | 1 + R/metrics.R | 2 +- R/predict.sltime.R | 25 ++++++++++++++++++++----- README.md | 2 +- man/tuneRSF.Rd | 2 +- 7 files changed, 33 insertions(+), 17 deletions(-)
Title: Tidy Verbs for Fast Data Manipulation
Description: A toolkit of tidy data manipulation verbs with 'data.table' as the backend.
Combining the merits of syntax elegance from 'dplyr' and computing performance from 'data.table',
'tidyfst' intends to provide users with state-of-the-art data manipulation tools with least pain.
This package is an extension of 'data.table'. While enjoying a tidy syntax,
it also wraps combinations of efficient functions to facilitate frequently-used data operations.
Author: Tian-Yuan Huang [aut, cre]
Maintainer: Tian-Yuan Huang <huang.tian-yuan@qq.com>
Diff between tidyfst versions 1.8.2 dated 2025-05-07 and 1.8.3 dated 2025-12-16
DESCRIPTION | 6 ++--- MD5 | 26 ++++++++++----------- R/pairwise.R | 9 ++++--- build/vignette.rds |binary inst/doc/benchmark.html | 49 ++++++++++++++++++++--------------------- inst/doc/chinese_tutorial.html | 39 ++++++++++++++++---------------- inst/doc/english_tutorial.html | 3 +- inst/doc/example1_intro.html | 3 +- inst/doc/example2_join.html | 10 ++++---- inst/doc/example3_reshape.html | 3 +- inst/doc/example4_nest.html | 3 +- inst/doc/example5_fst.html | 3 +- inst/doc/example6_dt.html | 3 +- man/pairwise.Rd | 4 +-- 14 files changed, 85 insertions(+), 76 deletions(-)
Title: Common R Scripts and Utilities Used by the Statnet Project
Software
Description: Non-statistical utilities used by the software developed by the Statnet Project. They may also be of use to others.
Author: Pavel N. Krivitsky [aut, cre] ,
Skye Bender-deMoll [ctb],
Chad Klumb [ctb] ,
Michal Bojanowski [ctb]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>
Diff between statnet.common versions 4.12.0 dated 2025-05-30 and 4.13.0 dated 2025-12-16
DESCRIPTION | 10 +- MD5 | 27 ++++--- NAMESPACE | 13 +++ NEWS | 59 +++++++++++++--- NEWS.md | 34 +++++++-- R/formula.utilities.R | 118 ++++++++++++++++++++++++-------- R/misc.utilities.R | 161 +++++++++++++++++++++++++++++++++++++++++--- R/test.utilities.R |only build/stage23.rdb |binary inst/CITATION | 4 - man/enlist.Rd |only man/envir.Rd |only man/formula.utilities.Rd | 21 +++-- man/sign-set.Rd |only man/skip_if_not_checking.Rd |only man/split_len.Rd |only man/term_list.Rd | 57 ++++++++++++--- man/which_top_n.Rd |only 18 files changed, 409 insertions(+), 95 deletions(-)
More information about statnet.common at CRAN
Permanent link
Title: Identifies Package Differences
Description: Identifies differences between
versions of a package. Specifically, the functions help
determine if there are breaking changes from one package version
to the next. The package also includes a stability assessment,
to help you determine the overall stability of a package, or even
an entire repository.
Author: David Bosak [aut, cre],
Brian Varney [ctb],
Kevin Putschko [ctb]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between pkgdiff versions 1.0.0 dated 2025-11-24 and 1.0.1 dated 2025-12-16
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 6 +++++- tests/testthat/test-stability.R | 13 +++++++++---- tests/testthat/test-utilities.R | 20 +++++++++++++------- 5 files changed, 34 insertions(+), 19 deletions(-)
Title: Exact Multinomial Test: Goodness-of-Fit Test for Discrete
Multivariate Data
Description: Goodness-of-fit tests for discrete multivariate data. It is
tested if a given observation is likely to have occurred under
the assumption of an ab-initio model. Monte Carlo methods are provided to
make the package capable of solving high-dimensional problems.
Author: Uwe Menzel [aut, cre]
Maintainer: Uwe Menzel <uwemenzel@gmail.com>
Diff between EMT versions 1.3.1 dated 2024-03-26 and 1.3.2 dated 2025-12-16
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- NEWS | 1 + R/EMT.R | 2 ++ man/EMT-package.Rd | 2 +- 5 files changed, 14 insertions(+), 10 deletions(-)
Title: Make PX-Files in R
Description: Create PX-files from scratch or read and modify existing ones.
Includes a function for every PX keyword, making metadata manipulation
simple and human-readable.
Author: Johan Ejstrud [cre, aut],
Lars Pedersen [aut],
Statistics Greenland [cph]
Maintainer: Johan Ejstrud <johan@ejstrud.com>
Diff between pxmake versions 0.18.0 dated 2025-05-30 and 0.19.0 dated 2025-12-16
pxmake-0.18.0/pxmake/tests/testthat/test-50-px.R |only pxmake-0.19.0/pxmake/DESCRIPTION | 8 pxmake-0.19.0/pxmake/MD5 | 89 pxmake-0.19.0/pxmake/NAMESPACE | 2 pxmake-0.19.0/pxmake/NEWS.md | 18 pxmake-0.19.0/pxmake/R/data_df.R | 2 pxmake-0.19.0/pxmake/R/documentation.R | 2 pxmake-0.19.0/pxmake/R/globals.R | 2 pxmake-0.19.0/pxmake/R/helper_functions.R | 95 pxmake-0.19.0/pxmake/R/keywords.R | 14 pxmake-0.19.0/pxmake/R/metadata_df.R | 2 pxmake-0.19.0/pxmake/R/micro.R | 3 pxmake-0.19.0/pxmake/R/modify_data.R | 304 +- pxmake-0.19.0/pxmake/R/modify_languages.R | 4 pxmake-0.19.0/pxmake/R/modify_table1.R | 12 pxmake-0.19.0/pxmake/R/note_warning_error.R | 18 pxmake-0.19.0/pxmake/R/px.R | 11 pxmake-0.19.0/pxmake/R/px_base_tables.R | 4 pxmake-0.19.0/pxmake/R/px_file.R | 12 pxmake-0.19.0/pxmake/R/r_script.R | 2 pxmake-0.19.0/pxmake/README.md | 474 ++-- pxmake-0.19.0/pxmake/build/vignette.rds |binary pxmake-0.19.0/pxmake/data/px_keywords.rda |binary pxmake-0.19.0/pxmake/inst/doc/first-px-file.R | 92 pxmake-0.19.0/pxmake/inst/doc/first-px-file.html | 1013 ++++----- pxmake-0.19.0/pxmake/inst/doc/languages.R | 62 pxmake-0.19.0/pxmake/inst/doc/languages.html | 791 +++---- pxmake-0.19.0/pxmake/inst/doc/micro-files.R | 224 +- pxmake-0.19.0/pxmake/inst/doc/micro-files.html | 1115 +++++----- pxmake-0.19.0/pxmake/man/download_px_or_parquet_and_return_path.Rd |only pxmake-0.19.0/pxmake/man/get_data_table.Rd |only pxmake-0.19.0/pxmake/man/get_values_from_time_format.Rd | 4 pxmake-0.19.0/pxmake/man/px.Rd | 3 pxmake-0.19.0/pxmake/man/px_data.px.Rd | 7 pxmake-0.19.0/pxmake/man/px_official_statistics.px.Rd |only pxmake-0.19.0/pxmake/man/sort_data_table_by_order.Rd |only pxmake-0.19.0/pxmake/man/update_data_table.Rd |only pxmake-0.19.0/pxmake/man/validate_px_arguments.Rd | 3 pxmake-0.19.0/pxmake/man/validate_px_data_arguments.Rd | 5 pxmake-0.19.0/pxmake/tests/testthat.R | 24 pxmake-0.19.0/pxmake/tests/testthat/fixtures/px/MAP.px |only pxmake-0.19.0/pxmake/tests/testthat/fixtures/px/TIMEVAL_long.px |only pxmake-0.19.0/pxmake/tests/testthat/fixtures/px/TIMEVAL_short.px |only pxmake-0.19.0/pxmake/tests/testthat/test-00-helper_functions.R | 20 pxmake-0.19.0/pxmake/tests/testthat/test-49-px.R |only pxmake-0.19.0/pxmake/tests/testthat/test-50-px-urls.R |only pxmake-0.19.0/pxmake/tests/testthat/test-55-modify-data.R | 64 pxmake-0.19.0/pxmake/tests/testthat/test-55-modify-table1.R | 8 pxmake-0.19.0/pxmake/tests/testthat/test-56-modify-languages.R | 22 pxmake-0.19.0/pxmake/tests/testthat/test-58-timeval.R |only pxmake-0.19.0/pxmake/tests/testthat/test-59-map.R |only pxmake-0.19.0/pxmake/tests/testthat/test-60-px-pxsave-preserves.R | 6 52 files changed, 2428 insertions(+), 2113 deletions(-)
Title: Retrieving Oral Opioid Information
Description: Provides details such as Morphine Equivalent Dose (MED),
brand name and opioid content which are calculated of all oral opioids
authorized for sale by Health Canada and the FDA based on their Drug Identification Number (DIN) or National Drug Code (NDC).
MEDs are calculated based on recommendations by Canadian Institute for Health Information (CIHI) and Von Korff et al (2008)
and information obtained from Health Canada's Drug Product Database's monthly data dump or FDA Daily database for Canadian and US databases respectively.
Please note in no way should output from this package be a substitute for medical advise.
All medications should only be consumed on prescription from a licensed healthcare provider.
Author: Ankona Banerjee [aut, cre] ,
Erik Stricker [aut]
Maintainer: Ankona Banerjee <ankonanagpur@gmail.com>
Diff between OralOpioids versions 2.0.4 dated 2025-01-09 and 2.0.5 dated 2025-12-16
OralOpioids-2.0.4/OralOpioids/man/OralOpioids.Rd |only OralOpioids-2.0.5/OralOpioids/DESCRIPTION | 17 OralOpioids-2.0.5/OralOpioids/MD5 | 12 OralOpioids-2.0.5/OralOpioids/NEWS.md | 58 OralOpioids-2.0.5/OralOpioids/R/OralOpioids.R | 1280 +++++++-------- OralOpioids-2.0.5/OralOpioids/build/vignette.rds |binary OralOpioids-2.0.5/OralOpioids/inst/doc/OralOpioid.pdf |binary OralOpioids-2.0.5/OralOpioids/man/OralOpioids-package.Rd |only 8 files changed, 690 insertions(+), 677 deletions(-)
Title: Genetic Algorithm (GA) for Variable Selection from
High-Dimensional Data
Description: Provides a genetic algorithm for finding variable
subsets in high dimensional data with high prediction performance. The
genetic algorithm can use ordinary least squares (OLS) regression models or
partial least squares (PLS) regression models to evaluate the prediction
power of variable subsets. By supporting different cross-validation
schemes, the user can fine-tune the tradeoff between speed and quality of
the solution.
Author: David Kepplinger [aut, cre]
Maintainer: David Kepplinger <david.kepplinger@gmail.com>
Diff between gaselect versions 1.0.23 dated 2025-04-14 and 1.0.24 dated 2025-12-16
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- configure | 10 ++++------ configure.ac | 10 ++++------ 4 files changed, 16 insertions(+), 20 deletions(-)
Title: Create ToxPi Prioritization Models
Description: Enables users to build 'ToxPi' prioritization models and provides
functionality within the grid framework for plotting ToxPi graphs.
'toxpiR' allows for more customization than the 'ToxPi GUI'
(<https://toxpi.github.io/>) and integration into existing workflows for greater
ease-of-use, reproducibility, and transparency.
toxpiR package behaves nearly identically to the GUI; the package
documentation includes notes about all differences.
The vignettes download example files from
<https://github.com/ToxPi/ToxPi-example-files>.
Author: Jonathon F Fleming [aut, cre] ,
Dayne L Filer [aut, fnd] ,
Dillon T Lloyd [aut],
Preethi Thunga [aut] ,
Skylar W Marvel [aut],
Alison A Motsinger-Reif [fnd] ,
David M Reif [aut, fnd]
Maintainer: Jonathon F Fleming <jffleming0129@gmail.com>
Diff between toxpiR versions 1.3.0 dated 2024-09-12 and 1.3.1 dated 2025-12-16
DESCRIPTION | 26 MD5 | 42 NAMESPACE | 2 NEWS.md | 45 R/methods-TxpTransFunc.R | 5 R/txpImportGui.R | 260 ++--- R/utils.R | 43 build/vignette.rds |binary inst/doc/exportToGui.R | 106 +- inst/doc/exportToGui.html | 1725 ++++++++++++++++++------------------- inst/doc/exportToGui.rmd | 220 ++-- inst/doc/importFromGui.R | 122 +- inst/doc/importFromGui.Rmd | 192 ++-- inst/doc/importFromGui.html | 939 ++++++++++---------- inst/doc/introduction.R | 706 +++++++-------- inst/doc/introduction.Rmd | 1302 ++++++++++++++-------------- inst/doc/introduction.html | 2017 ++++++++++++++++++++++---------------------- man/toxpiR-package.Rd | 2 man/txpImportGui.Rd | 2 vignettes/exportToGui.rmd | 220 ++-- vignettes/importFromGui.Rmd | 192 ++-- vignettes/introduction.Rmd | 1302 ++++++++++++++-------------- 22 files changed, 4761 insertions(+), 4709 deletions(-)
Title: Cancer Registry Data Analysis and Visualisation
Description: Tools for basic and advance cancer statistics and graphics.
Groups individual data, merges registry data and population data, calculates age-specific rate, age-standardized rate, cumulative risk, estimated annual percentage rate with standards error. Creates graphics across variable and
time, such as age-specific trends, bar chart and period-cohort trends.
Author: Mathieu Laversanne [aut, cre],
Jerome Vignat [aut],
Cancer Surveillance Unit [cph]
Maintainer: Mathieu Laversanne <laversannem@iarc.who.int>
Diff between Rcan versions 1.3.91 dated 2024-09-24 and 1.3.92 dated 2025-12-16
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/csu_trendCohortPeriod.R | 1 - R/helper.r | 3 --- build/partial.rdb |binary man/csu_eapc.Rd | 2 +- 6 files changed, 10 insertions(+), 14 deletions(-)
Title: Omics Data Process Toolbox
Description: Processing and analyzing omics data from genomics, transcriptomics, proteomics, and metabolomics platforms. It provides functions for preprocessing, normalization, visualization, and statistical analysis, as well as machine learning algorithms for predictive modeling. 'omicsTools' is an essential tool for researchers working with high-throughput omics data in fields such as biology, bioinformatics, and medicine.The QC-RLSC (quality control–based robust LOESS signal correction) algorithm is used for normalization. Dunn et al. (2011) <doi:10.1038/nprot.2011.335>.
Author: Yaoxiang Li [cre, aut]
Maintainer: Yaoxiang Li <liyaoxiang@outlook.com>
Diff between omicsTools versions 1.0.5 dated 2023-07-03 and 1.1.7 dated 2025-12-16
omicsTools-1.0.5/omicsTools/LICENSE |only omicsTools-1.0.5/omicsTools/R/mod_method_metadata.R |only omicsTools-1.0.5/omicsTools/inst/WORDLIST |only omicsTools-1.0.5/omicsTools/man/impute.Rd |only omicsTools-1.0.5/omicsTools/man/normalize.Rd |only omicsTools-1.0.5/omicsTools/tests/spelling.R |only omicsTools-1.0.5/omicsTools/tests/testthat/test-golem-recommended.R |only omicsTools-1.0.5/omicsTools/tests/testthat/test-golem_utils_server.R |only omicsTools-1.0.5/omicsTools/tests/testthat/test-golem_utils_ui.R |only omicsTools-1.0.5/omicsTools/tests/testthat/test-mod_imputation.R |only omicsTools-1.0.5/omicsTools/tests/testthat/test-mod_method_metadata.R |only omicsTools-1.0.5/omicsTools/tests/testthat/test-mod_qc_rlsc.R |only omicsTools-1.0.5/omicsTools/tests/testthat/test-mod_sample_sheet.R |only omicsTools-1.1.7/omicsTools/DESCRIPTION | 39 - omicsTools-1.1.7/omicsTools/MD5 | 106 ++- omicsTools-1.1.7/omicsTools/NAMESPACE | 199 ++++-- omicsTools-1.1.7/omicsTools/R/app_server.R | 13 omicsTools-1.1.7/omicsTools/R/app_ui.R | 87 ++ omicsTools-1.1.7/omicsTools/R/golem_utils_ui.R | 37 - omicsTools-1.1.7/omicsTools/R/mod_imputation.R | 12 omicsTools-1.1.7/omicsTools/R/mod_qc_rlsc.R | 6 omicsTools-1.1.7/omicsTools/R/mod_qtrap_qc.R |only omicsTools-1.1.7/omicsTools/R/mod_sample_sheet.R | 2 omicsTools-1.1.7/omicsTools/R/mod_vis_circos.R |only omicsTools-1.1.7/omicsTools/R/mod_vis_dot.R |only omicsTools-1.1.7/omicsTools/R/mod_vis_heatmap.R |only omicsTools-1.1.7/omicsTools/R/mod_vis_venn.R |only omicsTools-1.1.7/omicsTools/R/mod_vis_volcano.R |only omicsTools-1.1.7/omicsTools/R/run_app.R | 1 omicsTools-1.1.7/omicsTools/R/utils_batch_effect.R |only omicsTools-1.1.7/omicsTools/R/utils_feature.R |only omicsTools-1.1.7/omicsTools/R/utils_helpers.R | 145 ---- omicsTools-1.1.7/omicsTools/R/utils_impute.R |only omicsTools-1.1.7/omicsTools/R/utils_misc.R |only omicsTools-1.1.7/omicsTools/R/utils_normalize.R |only omicsTools-1.1.7/omicsTools/R/utils_outlier.R |only omicsTools-1.1.7/omicsTools/R/utils_qc_rsd.R |only omicsTools-1.1.7/omicsTools/R/utils_qtrap.R |only omicsTools-1.1.7/omicsTools/R/zzz.R | 32 omicsTools-1.1.7/omicsTools/README.md | 321 +++++++++- omicsTools-1.1.7/omicsTools/build |only omicsTools-1.1.7/omicsTools/inst/doc |only omicsTools-1.1.7/omicsTools/inst/golem-config.yml | 2 omicsTools-1.1.7/omicsTools/man/OmicsData-class.Rd |only omicsTools-1.1.7/omicsTools/man/calculate_cooks_distance.Rd |only omicsTools-1.1.7/omicsTools/man/calculate_lof.Rd |only omicsTools-1.1.7/omicsTools/man/calculate_measures.Rd |only omicsTools-1.1.7/omicsTools/man/calculate_qc_rsd.Rd |only omicsTools-1.1.7/omicsTools/man/check_and_sort_columns.Rd |only omicsTools-1.1.7/omicsTools/man/check_match.Rd |only omicsTools-1.1.7/omicsTools/man/combine_logical_tibbles.Rd |only omicsTools-1.1.7/omicsTools/man/convert_mrm_data.Rd |only omicsTools-1.1.7/omicsTools/man/convert_to_binary_matrix.Rd |only omicsTools-1.1.7/omicsTools/man/createOmicsData.Rd |only omicsTools-1.1.7/omicsTools/man/define_thresholds.Rd |only omicsTools-1.1.7/omicsTools/man/detect_duplicates.Rd |only omicsTools-1.1.7/omicsTools/man/ensure_enough_sets_for_upset.Rd |only omicsTools-1.1.7/omicsTools/man/figures |only omicsTools-1.1.7/omicsTools/man/flag_anomalies.Rd |only omicsTools-1.1.7/omicsTools/man/flag_underexpressed_features.Rd |only omicsTools-1.1.7/omicsTools/man/generate_data_with_anomalies.Rd |only omicsTools-1.1.7/omicsTools/man/generate_process_report.Rd |only omicsTools-1.1.7/omicsTools/man/handle_missing_values.Rd |only omicsTools-1.1.7/omicsTools/man/initialize_results_df.Rd |only omicsTools-1.1.7/omicsTools/man/internal_standard_normalize.Rd |only omicsTools-1.1.7/omicsTools/man/load_parse_sciex_txt.Rd |only omicsTools-1.1.7/omicsTools/man/ms1_annotation.Rd |only omicsTools-1.1.7/omicsTools/man/perform_batch_assessment.Rd |only omicsTools-1.1.7/omicsTools/man/perform_feature_selection.Rd |only omicsTools-1.1.7/omicsTools/man/pieDraw.Rd |only omicsTools-1.1.7/omicsTools/man/plot_distribution_measures.Rd |only omicsTools-1.1.7/omicsTools/man/plot_lipid_data_summary.Rd |only omicsTools-1.1.7/omicsTools/man/plot_met_data_summary.Rd |only omicsTools-1.1.7/omicsTools/man/plot_sample_measures.Rd |only omicsTools-1.1.7/omicsTools/man/pqn_normalize.Rd |only omicsTools-1.1.7/omicsTools/man/prepare_upset_data.Rd |only omicsTools-1.1.7/omicsTools/man/process_mrm_duplicates.Rd |only omicsTools-1.1.7/omicsTools/man/pvcaDraw.Rd |only omicsTools-1.1.7/omicsTools/man/qc_normalize.Rd |only omicsTools-1.1.7/omicsTools/man/transpose_df.Rd |only omicsTools-1.1.7/omicsTools/vignettes |only 81 files changed, 681 insertions(+), 321 deletions(-)
Title: Convert and Impute Dates to ISO 8601 Format and Reconcile Data
Sets
Description: Provides tools for converting and imputing date values to the ISO 8601
standard format and for reconciling differences between two versions of a
data set. The package automatically detects date patterns within data
frame columns and converts them to consistent ISO-formatted dates, with
optional imputation of missing day or month components based on
user-defined rules. It also includes functionality to identify inserted,
deleted, and updated records, as well as column- and value-level changes,
when comparing old and new versions of a data frame. Only one date format
may be applied within a single column.
Author: Lukasz Andrzejewski [aut, cre]
Maintainer: Lukasz Andrzejewski <lukasz.coding@gmail.com>
Diff between datetoiso versions 1.2.0 dated 2025-12-07 and 1.2.1 dated 2025-12-16
DESCRIPTION | 25 ++++++++++++++----------- MD5 | 4 ++-- NEWS.md | 4 ++++ 3 files changed, 20 insertions(+), 13 deletions(-)
Title: 'shiny' Application for Biological Dosimetry
Description: A tool to perform all different statistical tests and calculations
needed by Biological dosimetry Laboratories. Detailed documentation is
available in <https://biodosetools-team.github.io/documentation/>.
Author: Alfredo Hernandez [aut] ,
Anna Frances-Abellan [aut, cre] ,
David Endesfelder [aut],
Pere Puig [aut]
Maintainer: Anna Frances-Abellan <anna.frances@uab.cat>
Diff between biodosetools versions 3.7.1.2 dated 2025-12-04 and 3.7.2 dated 2025-12-16
DESCRIPTION | 6 ++-- MD5 | 18 ++++++------ R/calcs_interlab.R | 36 ++++++++++++++++++------ R/mod_fitting_server.R | 3 +- R/mod_interlab_server.R | 66 ++++++++++++++++++++++++++++---------------- inst/doc/interlab.html | 12 ++++---- inst/doc/micro-fitting.R | 2 - inst/doc/micro-fitting.Rmd | 2 - inst/doc/micro-fitting.html | 2 - vignettes/micro-fitting.Rmd | 2 - 10 files changed, 95 insertions(+), 54 deletions(-)
Title: Automatic Knowledge Classification
Description: A tidy framework for automatic knowledge classification and visualization. Currently, the core functionality of the framework is mainly supported by modularity-based clustering (community detection) in keyword co-occurrence network, and focuses on co-word analysis of bibliometric research. However, the designed functions in 'akc' are general, and could be extended to solve other tasks in text mining as well.
Author: Tian-Yuan Huang [aut, cre]
Maintainer: Tian-Yuan Huang <huang.tian-yuan@qq.com>
Diff between akc versions 0.9.9.1 dated 2025-02-25 and 0.9.9.2 dated 2025-12-16
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ R/keyword_merge.R | 2 +- build/vignette.rds |binary inst/doc/Benchmarking.html | 13 +++++++------ inst/doc/akc_vignette.html | 7 ++++--- inst/doc/tutorial_raw_text.html | 11 ++++++----- 7 files changed, 29 insertions(+), 25 deletions(-)
Title: Access to the 'RESOURCECODE' Hindcast Database
Description: Utility functions to download data from the 'RESOURCECODE'
hindcast database of sea-states, time series of sea-state parameters
and time series of 1D and 2D wave spectra. See
<https://resourcecode.ifremer.fr> for more details about the available
data. Also provides facilities to plot and analyse downloaded data,
such as computing the sea-state parameters from both the 1D and 2D
surface elevation variance spectral density.
Author: Nicolas Raillard [aut, cre]
Maintainer: Nicolas Raillard <nicolas.raillard@ifremer.fr>
Diff between resourcecode versions 0.5.0 dated 2025-11-10 and 0.5.1 dated 2025-12-16
DESCRIPTION | 12 MD5 | 86 - NAMESPACE | 98 +- NEWS.md | 4 R/RcppExports.R | 48 - R/orbital_speed.R | 160 +-- R/specta_data_ploting.R | 54 - R/spectral_data_download.R | 4 R/utils.R | 216 +++- README.md | 186 +-- build/vignette.rds |binary inst/CITATION | 22 inst/WORDLIST | 88 - inst/doc/resourcecode.R | 182 +-- inst/doc/resourcecode.Rmd | 318 +++--- inst/doc/resourcecode.html | 1179 ++++++++++++------------- man/compute_orbital_speeds.Rd | 82 - man/compute_sea_state_1d_spectrum.Rd | 78 - man/compute_sea_state_2d_spectrum.Rd | 82 - man/dispersion.Rd | 68 - man/fastTrapz.Rd | 52 - man/figures/README-bathymetry-1.png |binary man/figures/README-data_fetcher-1.png |binary man/get_1d_spectrum.Rd | 132 +- man/get_2d_spectrum.Rd | 108 +- man/get_parameters.Rd | 70 - man/grapes-nin-grapes.Rd | 46 man/jonswap.Rd | 92 - man/plot_2d_specta.Rd | 74 - man/resourcecode-package.Rd | 54 - man/rscd_dir.Rd | 46 man/rscd_freq.Rd | 48 - man/rscd_mapplot.Rd | 84 - man/zmcomp2metconv.Rd | 52 - tests/testthat/Rplots.pdf |binary tests/testthat/test-data_download.R | 8 tests/testthat/test-fractional_day_of_year.R | 296 +++--- tests/testthat/test-orbital_speed.R | 92 + tests/testthat/test-plots.R | 1 tests/testthat/test-spectral_data_processing.R | 138 +- tests/testthat/test-test_closest_point.R | 264 ++--- tests/testthat/test-test_cut_seasons.R | 144 +-- tests/testthat/test-test_utils.R | 53 + vignettes/resourcecode.Rmd | 318 +++--- 44 files changed, 2724 insertions(+), 2415 deletions(-)
Title: Geocoding for the Netherlands
Description: Interface to the open location server API of 'Publieke Diensten Op de Kaart' (<http://www.pdok.nl>). It offers geocoding, address suggestions and lookup of geographical objects. Included is an utility function for displaying leaflet tiles restricted to the Netherlands.
Author: Willy Tadema [aut],
Egge-Jan Polle [aut],
Edwin de Jonge [aut, cre] ,
Juris Breidaks [ctb]
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
This is a re-admission after prior archival of version 0.1.3 dated 2018-10-08
Diff between nlgeocoder versions 0.1.3 dated 2018-10-08 and 0.2.2 dated 2025-12-16
nlgeocoder-0.1.3/nlgeocoder/R/nl_queryresults.R |only nlgeocoder-0.2.2/nlgeocoder/DESCRIPTION | 21 nlgeocoder-0.2.2/nlgeocoder/MD5 | 50 nlgeocoder-0.2.2/nlgeocoder/NEWS.md |only nlgeocoder-0.2.2/nlgeocoder/R/addPdokTiles.R | 36 nlgeocoder-0.2.2/nlgeocoder/R/nl_free.R | 6 nlgeocoder-0.2.2/nlgeocoder/R/nl_geocode.R | 28 nlgeocoder-0.2.2/nlgeocoder/R/nl_lookup.R | 7 nlgeocoder-0.2.2/nlgeocoder/R/nl_reverse.R | 2 nlgeocoder-0.2.2/nlgeocoder/R/nl_suggest.R | 4 nlgeocoder-0.2.2/nlgeocoder/R/package.R | 18 nlgeocoder-0.2.2/nlgeocoder/build/vignette.rds |binary nlgeocoder-0.2.2/nlgeocoder/inst/doc/geocode.R | 32 nlgeocoder-0.2.2/nlgeocoder/inst/doc/geocode.Rmd | 4 nlgeocoder-0.2.2/nlgeocoder/inst/doc/geocode.html | 2263 ++++++----- nlgeocoder-0.2.2/nlgeocoder/man/addPdokTiles.Rd | 28 nlgeocoder-0.2.2/nlgeocoder/man/addresses.Rd | 8 nlgeocoder-0.2.2/nlgeocoder/man/nl_free.Rd | 28 nlgeocoder-0.2.2/nlgeocoder/man/nl_geocode.Rd | 51 nlgeocoder-0.2.2/nlgeocoder/man/nl_lookup.Rd | 6 nlgeocoder-0.2.2/nlgeocoder/man/nl_suggest.Rd | 13 nlgeocoder-0.2.2/nlgeocoder/man/nlgeocoder-package.Rd | 18 nlgeocoder-0.2.2/nlgeocoder/man/query.Rd | 11 nlgeocoder-0.2.2/nlgeocoder/tests/testthat/test-nl_geocode.R | 19 nlgeocoder-0.2.2/nlgeocoder/tests/testthat/test-nl_lookup.R | 10 nlgeocoder-0.2.2/nlgeocoder/tests/testthat/test-utf8.R | 1 nlgeocoder-0.2.2/nlgeocoder/vignettes/geocode.Rmd | 4 27 files changed, 1508 insertions(+), 1160 deletions(-)
Title: Mixture Autoregressive Models
Description: Model time series using mixture autoregressive (MAR)
models. Implemented are frequentist (EM) and Bayesian
methods for estimation, prediction and model
evaluation. See Wong and Li (2002)
<doi:10.1111/1467-9868.00222>, Boshnakov (2009)
<doi:10.1016/j.spl.2009.04.009>), and the extensive
references in the documentation.
Author: Georgi N. Boshnakov [aut, cre] ,
Davide Ravagli [aut]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between mixAR versions 0.22.8 dated 2023-12-18 and 0.22.9 dated 2025-12-16
DESCRIPTION | 22 MD5 | 19 NEWS.md | 166 +- R/fit_mixARreg.R | 172 +-- R/mixAR.R | 2802 +++++++++++++++++++++++++------------------------- README.md | 2 build/partial.rdb |binary inst/pkgdown.yml |only man/MixAR-class.Rd | 156 +- man/mixAR-internal.Rd | 58 - man/mixAR-package.Rd | 764 ++++++------- 11 files changed, 2086 insertions(+), 2075 deletions(-)
Title: Nested Cross Validation for the Relaxed Lasso and Other Machine
Learning Models
Description: Cross validation informed Relaxed LASSO (or more generally elastic net), gradient boosting machine ('xgboost'), Random Forest ('RandomForestSRC'), Oblique Random Forest ('aorsf'), Artificial Neural Network (ANN), Recursive Partitioning ('RPART') or step wise regression models are fit. Cross validation leave out samples (leading to nested cross validation) or bootstrap out-of-bag samples are used to evaluate and compare performances between these models with results presented in tabular or graphical means. Calibration plots can also be generated, again based upon (outer nested) cross validation or bootstrap leave out (out of bag) samples.
Note, at the time of this writing, in order to fit gradient boosting machine models one must install the packages 'DiceKriging' and 'rgenoud' using the install.packages() function.
For some datasets, for example when the design matrix is not of full rank, 'glmnet' may have very long run times when fitting the relaxed lasso model, from our experience [...truncated...]
Author: Walter K Kremers [aut, cre] ,
Nicholas B Larson [ctb]
Maintainer: Walter K Kremers <kremers.walter@mayo.edu>
Diff between glmnetr versions 0.6-2 dated 2025-08-19 and 0.6-3 dated 2025-12-16
glmnetr-0.6-2/glmnetr/R/nested.compare_250527.R |only glmnetr-0.6-2/glmnetr/R/nested.glmnetr_250804.R |only glmnetr-0.6-2/glmnetr/R/plot.cv.glmnetr_250503.R |only glmnetr-0.6-2/glmnetr/R/plot_perf_glmnetr_250525.R |only glmnetr-0.6-2/glmnetr/R/predict.cv.glmnetr_250804.R |only glmnetr-0.6-2/glmnetr/R/summary.cv.glmnetr_250818.R |only glmnetr-0.6-2/glmnetr/R/summary.nested.glmnetr_250525.R |only glmnetr-0.6-2/glmnetr/R/xgbm_tuned_240905.R |only glmnetr-0.6-3/glmnetr/DESCRIPTION | 14 ++-- glmnetr-0.6-3/glmnetr/MD5 | 46 ++++++++-------- glmnetr-0.6-3/glmnetr/R/nested.compare_251212.R |only glmnetr-0.6-3/glmnetr/R/nested.glmnetr_251215.R |only glmnetr-0.6-3/glmnetr/R/plot.cv.glmnetr_251212.R |only glmnetr-0.6-3/glmnetr/R/plot_perf_glmnetr_251212.R |only glmnetr-0.6-3/glmnetr/R/predict.cv.glmnetr_251212.R |only glmnetr-0.6-3/glmnetr/R/summary.cv.glmnetr_251212.R |only glmnetr-0.6-3/glmnetr/R/summary.nested.glmnetr_251212.R |only glmnetr-0.6-3/glmnetr/R/xgbm_tuned_251215.R |only glmnetr-0.6-3/glmnetr/build/vignette.rds |binary glmnetr-0.6-3/glmnetr/man/glmnetr.compcv.Rd | 2 glmnetr-0.6-3/glmnetr/man/nested.compare.Rd | 2 glmnetr-0.6-3/glmnetr/man/nested.glmnetr.Rd | 8 ++ glmnetr-0.6-3/glmnetr/man/plot.cv.glmnetr.Rd | 2 glmnetr-0.6-3/glmnetr/man/plot.glmnetr.Rd | 2 glmnetr-0.6-3/glmnetr/man/plot_perf_glmnetr.Rd | 2 glmnetr-0.6-3/glmnetr/man/predict.cv.glmnetr.Rd | 2 glmnetr-0.6-3/glmnetr/man/print.nested.glmnetr.Rd | 2 glmnetr-0.6-3/glmnetr/man/roundperf.Rd | 2 glmnetr-0.6-3/glmnetr/man/summary.cv.glmnetr.Rd | 2 glmnetr-0.6-3/glmnetr/man/summary.nested.glmnetr.Rd | 2 glmnetr-0.6-3/glmnetr/man/xgb.simple.Rd | 16 ----- glmnetr-0.6-3/glmnetr/man/xgb.tuned.Rd | 20 +----- 32 files changed, 50 insertions(+), 74 deletions(-)
Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from
Model Outputs
Description: Compute marginal effects and adjusted predictions from statistical
models and returns the result as tidy data frames. These data frames are
ready to use with the 'ggplot2'-package. Effects and predictions can be
calculated for many different models. Interaction terms, splines and
polynomial terms are also supported. The main functions are ggpredict(),
ggemmeans() and ggeffect(). There is a generic plot()-method to plot the
results using 'ggplot2'.
Author: Daniel Luedecke [aut, cre] ,
Frederik Aust [ctb] ,
Sam Crawley [ctb] ,
Mattan S. Ben-Shachar [ctb] ,
Sean C. Anderson [ctb]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between ggeffects versions 2.3.1 dated 2025-08-20 and 2.3.2 dated 2025-12-16
DESCRIPTION | 8 LICENSE | 4 MD5 | 16 - NEWS.md | 4 R/predict_zero_inflation.R | 5 build/vignette.rds |binary man/install_latest.Rd | 80 ++++----- tests/testthat/test-lmer.R | 300 +++++++++++++++++++++++++++++-------- tests/testthat/test-poly-zeroinf.R | 76 +++++++-- 9 files changed, 363 insertions(+), 130 deletions(-)
Title: Fast and Stable Fitting of Generalized Linear Models using
'RcppEigen'
Description: Fits generalized linear models efficiently using 'RcppEigen'. The iteratively reweighted least squares
implementation utilizes the step-halving approach of Marschner (2011) <doi:10.32614/RJ-2011-012> to help safeguard
against convergence issues.
Author: Jared Huling [aut, cre],
Douglas Bates [cph],
Dirk Eddelbuettel [cph],
Romain Francois [cph],
Yixuan Qiu [cph]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between fastglm versions 0.0.3 dated 2022-05-23 and 0.0.4 dated 2025-12-16
DESCRIPTION | 8 MD5 | 12 README.md | 2 build/vignette.rds |binary inst/doc/quick-usage-guide-to-the-fastglm-package.R | 10 inst/doc/quick-usage-guide-to-the-fastglm-package.html | 859 +++++++++-------- src/Makevars | 4 7 files changed, 510 insertions(+), 385 deletions(-)
Title: Simplification of scRNA-Seq Data by Merging Together Similar
Cells
Description: Aggregates large single-cell data into metacell dataset by merging together gene expression of very similar cells. 'SuperCell' uses 'velocyto.R' <doi:10.1038/s41586-018-0414-6> <https://github.com/velocyto-team/velocyto.R> for RNA velocity and 'WeightedCluster' <doi:10.12682/lives.2296-1658.2013.24> <https://mephisto.unige.ch/weightedcluster/> for weighted clustering on metacells. We also recommend installing 'scater' Bioconductor package <doi:10.18129/B9.bioc.scater> <https://bioconductor.org/packages/release/bioc/html/scater.html>.
Author: Mariia Bilous [aut],
Matei Teleman [cre]
Maintainer: Matei Teleman <matei.teleman@unil.ch>
Diff between SuperCell versions 1.0.1 dated 2024-10-25 and 1.1 dated 2025-12-16
DESCRIPTION | 27 -- MD5 | 15 - R/zzz.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/a_SuperCell.R | 4 inst/doc/a_SuperCell.html | 48 ++- inst/doc/b_Combined_vs_independent_sample_processing.R | 186 +++++++------- inst/doc/b_Combined_vs_independent_sample_processing.html | 3 9 files changed, 148 insertions(+), 135 deletions(-)
Title: Models for Non Linear Causality Detection in Time Series
Description: Models for non-linear time series analysis and causality detection. The main functionalities of this package consist of an implementation of the classical causality test (C.W.J.Granger 1980) <doi:10.1016/0165-1889(80)90069-X>, and a non-linear version of it based on feed-forward neural networks. This package contains also an implementation of the Transfer Entropy <doi:10.1103/PhysRevLett.85.461>, and the continuous Transfer Entropy using an approximation based on the k-nearest neighbors <doi:10.1103/PhysRevE.69.066138>. There are also some other useful tools, like the VARNN (Vector Auto-Regressive Neural Network) prediction model, the Augmented test of stationarity, and the discrete and continuous entropy and mutual information.
Author: Youssef Hmamouche [aut, cre]
Maintainer: Youssef Hmamouche <hmamoucheyussef@gmail.com>
Diff between NlinTS versions 1.4.5 dated 2021-02-01 and 1.4.6 dated 2025-12-16
DESCRIPTION | 12 ++++----- MD5 | 10 +++---- build/partial.rdb |binary src/RcppExports.cpp | 5 +++ src/dense.cpp | 69 ++++++++++++++++++++++++---------------------------- src/network.cpp | 2 - 6 files changed, 50 insertions(+), 48 deletions(-)
Title: An API Wrapper for 'DAWA' - 'The Danish Address Web API'
Description: Functions for interacting with all sections of
the official 'Danish Address Web API' (also known as 'DAWA')
<https://api.dataforsyningen.dk>. The development of this package is
completely independent from the government agency, Klimadatastyrelsen,
who maintains the API.
Author: Aleksander Bang-Larsen [aut, cre, cph] ,
Agency of Climate Data [ctb]
Maintainer: Aleksander Bang-Larsen <contact@aleksanderbl.dk>
Diff between dawaR versions 0.3.1 dated 2025-11-18 and 0.3.2 dated 2025-12-16
DESCRIPTION | 8 +++---- MD5 | 16 +++++++-------- NEWS.md | 6 +++++ R/status_check.R | 14 ++++++++----- README.md | 7 ++++++ inst/doc/status.html | 10 ++++----- tests/testthat/_snaps/get_data.md | 10 ++++----- tests/testthat/_snaps/status_check.md | 8 +++---- tests/testthat/test-autocomplete.R | 36 ++++++++++++++++++++++++++++++---- 9 files changed, 80 insertions(+), 35 deletions(-)
Title: Biostatistics and Clinical Data Analysis
Description: Biostatistical and clinical data analysis, including descriptive
statistics, exploratory data analysis, sample size and power calculations,
statistical inference, and data visualization. Normality tests are
implemented following Mishra et al. (2019) <doi:10.4103/aca.ACA_157_18>,
omnibus test procedures are based on Blanca et al. (2017)
<doi:10.3758/s13428-017-0918-2> and Field et al. (2012, ISBN:9781446200469),
while sample size and power calculation methods follow Chow et al. (2017)
<doi:10.1201/9781315183084>.
Author: Sebastian Quirarte-Justo [aut, cre] ,
Angela Carolina Montano-Ruiz [aut] ,
Jose Maria Torres-Arellano [aut] ,
Laboratorios Sophia S.A. de C.V. [cph, fnd]
Maintainer: Sebastian Quirarte-Justo <sebastian.quirarte@sophia.com.mx>
Diff between biostats versions 1.1.0 dated 2025-12-06 and 1.1.1 dated 2025-12-16
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 8 ++++++++ R/sample_size.R | 4 ++-- README.md | 17 +++++++++-------- man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-10-2.png |binary man/sample_size.Rd | 2 +- 8 files changed, 30 insertions(+), 21 deletions(-)
Title: Confirmatory Adaptive Clinical Trial Design and Analysis
Description: Design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints according to the methods described in the monograph by Wassmer and Brannath (2025) <doi:10.1007/978-3-031-89669-9>. This includes classical group sequential as well as multi-stage adaptive hypotheses tests that are based on the combination testing principle.
Author: Gernot Wassmer [aut] ,
Friedrich Pahlke [aut, cre] ,
Till Jensen [ctb],
Daniel Sabanes Bove [ctb] ,
Stephen Schueuerhuis [ctb] ,
Tobias Muetze [ctb]
Maintainer: Friedrich Pahlke <friedrich.pahlke@rpact.com>
Diff between rpact versions 4.2.1 dated 2025-07-24 and 4.3.0 dated 2025-12-16
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rpact-4.3.0/rpact/R/f_logger.R | 4 rpact-4.3.0/rpact/R/f_object_r_code.R | 342 ++++- rpact-4.3.0/rpact/R/f_parameter_set_utilities.R | 13 rpact-4.3.0/rpact/R/f_quality_assurance.R | 40 rpact-4.3.0/rpact/R/f_simulation_base_counts.R | 4 rpact-4.3.0/rpact/R/f_simulation_base_means.R | 21 rpact-4.3.0/rpact/R/f_simulation_base_rates.R | 32 rpact-4.3.0/rpact/R/f_simulation_base_survival.R | 32 rpact-4.3.0/rpact/R/f_simulation_calc_subjects_function.R | 4 rpact-4.3.0/rpact/R/f_simulation_enrichment.R | 16 rpact-4.3.0/rpact/R/f_simulation_enrichment_means.R | 5 rpact-4.3.0/rpact/R/f_simulation_enrichment_rates.R | 5 rpact-4.3.0/rpact/R/f_simulation_enrichment_survival.R | 5 rpact-4.3.0/rpact/R/f_simulation_multiarm.R | 45 rpact-4.3.0/rpact/R/f_simulation_multiarm_means.R | 5 rpact-4.3.0/rpact/R/f_simulation_multiarm_rates.R | 5 rpact-4.3.0/rpact/R/f_simulation_multiarm_survival.R | 5 rpact-4.3.0/rpact/R/f_simulation_performance_score.R | 4 rpact-4.3.0/rpact/R/f_simulation_plot.R | 4 rpact-4.3.0/rpact/R/f_simulation_utilities.R | 9 rpact-4.3.0/rpact/R/parameter_descriptions.R | 4 rpact-4.3.0/rpact/R/pkgname.R | 12 rpact-4.3.0/rpact/README.md | 77 - rpact-4.3.0/rpact/build/partial.rdb |binary rpact-4.3.0/rpact/build/vignette.rds |binary rpact-4.3.0/rpact/inst/doc/rpact_getting_started.Rmd | 138 -- rpact-4.3.0/rpact/inst/doc/rpact_getting_started.html | 136 -- rpact-4.3.0/rpact/inst/tests/testthat/test-rpact.R | 6 rpact-4.3.0/rpact/man/InstallationQualificationResult.Rd | 86 - rpact-4.3.0/rpact/man/MarkdownReporter.Rd | 72 - rpact-4.3.0/rpact/man/SimulationResultsCountData.Rd | 98 - rpact-4.3.0/rpact/man/checkInstallationQualificationStatus.Rd | 66 - rpact-4.3.0/rpact/man/disableStartupMessages.Rd | 54 rpact-4.3.0/rpact/man/enableStartupMessages.Rd | 54 rpact-4.3.0/rpact/man/fetch.ParameterSet.Rd | 92 - rpact-4.3.0/rpact/man/getClosedConditionalDunnettTestResults.Rd | 2 rpact-4.3.0/rpact/man/getDesignConditionalDunnett.Rd | 2 rpact-4.3.0/rpact/man/getDesignFisher.Rd | 11 rpact-4.3.0/rpact/man/getDesignGroupSequential.Rd | 14 rpact-4.3.0/rpact/man/getDesignInverseNormal.Rd | 9 rpact-4.3.0/rpact/man/getFutilityBounds.Rd |only rpact-4.3.0/rpact/man/getGroupSequentialProbabilities.Rd | 2 rpact-4.3.0/rpact/man/getParameterType.Rd | 68 - rpact-4.3.0/rpact/man/getSimulationCounts.Rd | 404 +++--- rpact-4.3.0/rpact/man/getSimulationSurvival.Rd | 21 rpact-4.3.0/rpact/man/getSystemIdentifier.Rd | 48 rpact-4.3.0/rpact/man/getTestLabel.Rd |only rpact-4.3.0/rpact/man/kableParameterSet.Rd | 106 - rpact-4.3.0/rpact/man/knit_print.FieldSet.Rd | 98 - rpact-4.3.0/rpact/man/param_doseLevels.Rd | 26 rpact-4.3.0/rpact/man/param_overdispersion_counts.Rd | 26 rpact-4.3.0/rpact/man/param_plannedCalendarTime.Rd | 26 rpact-4.3.0/rpact/man/param_typeOfShapeMeans.Rd | 42 rpact-4.3.0/rpact/man/param_typeOfShapeRates.Rd | 42 rpact-4.3.0/rpact/man/param_typeOfShapeSurvival.Rd | 42 rpact-4.3.0/rpact/man/plot.TrialDesignSummaries.Rd | 78 - rpact-4.3.0/rpact/man/print.FutilityBounds.Rd |only rpact-4.3.0/rpact/man/print.InstallationQualificationResult.Rd | 60 rpact-4.3.0/rpact/man/print.TrialDesignSummaries.Rd | 32 rpact-4.3.0/rpact/man/resetOptions.Rd | 60 rpact-4.3.0/rpact/man/rpact.Rd | 8 rpact-4.3.0/rpact/man/saveOptions.Rd | 52 rpact-4.3.0/rpact/man/setupPackageTests.Rd | 56 rpact-4.3.0/rpact/man/summary.FutilityBounds.Rd |only rpact-4.3.0/rpact/src/f_as251.cpp | 4 rpact-4.3.0/rpact/src/f_assertions.cpp | 4 rpact-4.3.0/rpact/src/f_assertions.h | 4 rpact-4.3.0/rpact/src/f_count_data_estimation.cpp | 4 rpact-4.3.0/rpact/src/f_design_fisher_combination_test.cpp | 4 rpact-4.3.0/rpact/src/f_design_group_sequential.cpp | 4 rpact-4.3.0/rpact/src/f_simulation_base_means.cpp | 4 rpact-4.3.0/rpact/src/f_simulation_base_rates.cpp | 4 rpact-4.3.0/rpact/src/f_simulation_base_survival.cpp | 17 rpact-4.3.0/rpact/src/f_simulation_survival_utilities.cpp | 4 rpact-4.3.0/rpact/src/f_simulation_survival_utilities.h | 4 rpact-4.3.0/rpact/src/f_utilities.cpp | 4 rpact-4.3.0/rpact/src/f_utilities.h | 4 rpact-4.3.0/rpact/src/rpact_types.h | 4 rpact-4.3.0/rpact/tests/testthat/test-pkgname.R | 6 rpact-4.3.0/rpact/vignettes/rpact_getting_started.Rmd | 138 -- 133 files changed, 3594 insertions(+), 2623 deletions(-)
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data. The package includes methods for spectral fitting: Wilson
(2021) <DOI:10.1002/mrm.28385>, Wilson (2025) <DOI:10.1002/mrm.30462> and
spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.
Author: Martin Wilson [cre, aut] ,
Yong Wang [ctb],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between spant versions 3.7.0 dated 2025-11-20 and 3.8.0 dated 2025-12-16
DESCRIPTION | 8 +- MD5 | 22 +++--- NEWS.md | 6 + R/fit_svs.R | 137 +++++++++++++++++++++++++++++++++----- R/fit_svs_edited.R | 131 +++++++++++++++++++++++++++++++++--- R/fmrs.R | 3 inst/cli_scripts/spant_fit_svs | 38 +++++++++- inst/doc/spant-intro.html | 132 ++++++++++++++++++------------------ inst/doc/spant-preprocessing.html | 4 - man/fit_svs.Rd | 9 ++ man/fit_svs_edited.Rd | 9 ++ man/mr_data2bids.Rd | 2 12 files changed, 384 insertions(+), 117 deletions(-)
Title: Weighted Subspace Random Forest for Classification
Description: A parallel implementation of Weighted Subspace Random Forest. The
Weighted Subspace Random Forest algorithm was proposed in the
International Journal of Data Warehousing and Mining by Baoxun Xu,
Joshua Zhexue Huang, Graham Williams, Qiang Wang, and Yunming Ye
(2012) <DOI:10.4018/jdwm.2012040103>. The algorithm can classify
very high-dimensional data with random forests built using small
subspaces. A novel variable weighting method is used for variable
subspace selection in place of the traditional random variable
sampling.This new approach is particularly useful in building
models from high-dimensional data.
Author: Qinghan Meng [aut],
He Zhao [aut, cre] ,
Graham J. Williams [aut] ,
Junchao Lv [aut],
Baoxun Xu [aut],
Joshua Zhexue Huang [aut]
Maintainer: He Zhao <Simon.Yansen.Zhao@gmail.com>
Diff between wsrf versions 1.7.30 dated 2023-01-06 and 1.7.31 dated 2025-12-16
wsrf-1.7.30/wsrf/src/Makevars |only wsrf-1.7.30/wsrf/src/Makevars.win |only wsrf-1.7.31/wsrf/DESCRIPTION | 19 wsrf-1.7.31/wsrf/MD5 | 14 wsrf-1.7.31/wsrf/README.md | 4 wsrf-1.7.31/wsrf/build/vignette.rds |binary wsrf-1.7.31/wsrf/inst/NEWS.Rd | 21 + wsrf-1.7.31/wsrf/inst/doc/wsrf-guide.R | 32 - wsrf-1.7.31/wsrf/inst/doc/wsrf-guide.html | 575 +++++++----------------------- 9 files changed, 199 insertions(+), 466 deletions(-)
Title: Tools for Calculating Allocations in Game Theory using Exact and
Approximated Methods
Description: The main objective of cooperative Transferable-Utility games (TU-games)
is to allocate a good among the agents involved. The package implements major
solution concepts including the Shapley value, Banzhaf value, and egalitarian
rules, alongside their extensions for structured games:
the Owen value and Banzhaf-Owen value for games with a priori unions, and the
Myerson value for communication games on networks. To address the inherent exponential
computational complexity of exact evaluation, the package offers both exact
algorithms and linear approximation methods based on sampling, enabling the
analysis of large-scale games. Additionally, it supports core set-based
solutions, allowing computation of the vertices and the centroid of the core.
Author: Maria D. Guillen [cre, aut] ,
Juan Carlos Goncalves [aut]
Maintainer: Maria D. Guillen <maria.guilleng@umh.es>
Diff between TUvalues versions 1.0.0 dated 2025-05-22 and 1.1.0 dated 2025-12-16
DESCRIPTION | 28 +++++---- MD5 | 68 ++++++++++++++-------- NAMESPACE | 12 ++++ R/banzhaf.R | 16 +++-- R/banzhaf_appro.R | 17 ++++- R/banzhaf_owen_appro.R | 24 ++++++-- R/banzhan_owen.R | 22 ++++--- R/centroid.R |only R/coalitions.R | 37 ++++++++---- R/coreVertex.R |only R/core_appro.R |only R/core_exact.R |only R/egalitarian.R | 12 ++-- R/egalitarian_unions.R |only R/equal_surplus_division.R | 26 +++++--- R/equal_surplus_division_unions.R |only R/myerson.R |only R/myerson_unions.R |only R/owen.R | 16 +++-- R/owen_appro.R | 27 +++++++-- R/owen_exact.R | 1 R/shapley.R | 21 ++++--- R/shapley_appro.R | 22 +++++-- R/shapley_exact.R | 2 man/banzhaf.Rd | 14 +++- man/banzhaf_appro.Rd | 52 +++++++++-------- man/banzhaf_owen.Rd | 21 +++++-- man/banzhaf_owen_appro.Rd | 14 +++- man/centroid.Rd |only man/coreVertex.Rd |only man/core_appro.Rd |only man/core_exact.Rd |only man/egalitarian.Rd | 3 + man/egalitarian_unions.Rd |only man/equal_surplus_division.Rd | 3 + man/equal_surplus_division_unions.Rd |only man/myerson.Rd |only man/myerson_unions.Rd |only man/owen.Rd | 15 ++++- man/owen_appro.Rd | 60 +++++++++++--------- man/owen_exact.Rd | 46 +++++++-------- man/shapley.Rd | 104 +++++++++++++++++++---------------- man/shapley_appro.Rd | 12 +++- 43 files changed, 441 insertions(+), 254 deletions(-)
Title: Simulation of Study Data
Description: Simulates data sets in order to explore modeling
techniques or better understand data generating processes. The user
specifies a set of relationships between covariates, and generates
data based on these specifications. The final data sets can represent
data from randomized control trials, repeated measure (longitudinal)
designs, and cluster randomized trials. Missingness can be generated
using various mechanisms (MCAR, MAR, NMAR).
Author: Keith Goldfeld [aut, cre] ,
Jacob Wujciak-Jens [aut]
Maintainer: Keith Goldfeld <keith.goldfeld@nyulangone.org>
Diff between simstudy versions 0.9.0 dated 2025-10-06 and 0.9.1 dated 2025-12-16
DESCRIPTION | 8 ++-- MD5 | 20 +++++----- R/generate_correlated_data.R | 19 +++++++-- build/vignette.rds |binary inst/doc/logisticCoefs.Rmd | 4 +- inst/doc/logisticCoefs.html | 4 +- inst/doc/simstudy.html | 2 - tests/testthat/helper-gen_def.R | 2 - tests/testthat/test-conditions.R | 48 +++++++++++++++++++++---- tests/testthat/test-generate_correlated_data.R | 7 ++- vignettes/logisticCoefs.Rmd | 4 +- 11 files changed, 81 insertions(+), 37 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>
Diff between nparACT versions 0.9.0 dated 2025-09-23 and 0.9.1 dated 2025-12-16
DESCRIPTION | 8 ++--- MD5 | 28 ++++++++++++-------- NAMESPACE | 4 ++ NEWS.md | 14 ++++++++++ R/nparACT-package.R |only R/nparACT_ISIVfunctions.R | 9 ++++-- R/nparACT_RAfunctions.R | 9 ++++-- R/nparACT_auxfunctions1.R | 15 ++++------ R/nparACT_auxfunctions2.R | 14 ++++++---- R/nparACT_base.R | 47 ++++++++++++++++++++++++++++++++- R/nparACT_base_loop.R | 47 ++++++++++++++++++++++++++++----- R/nparACT_flex.R | 57 ++++++++++++++++++++++++++++++++++++++-- R/nparACT_flex_loop.R | 64 ++++++++++++++++++++++++++++++++++++++++------ man/nparACT.Rd |only man/nparACT_base.Rd |only man/nparACT_base_loop.Rd |only man/nparACT_flex.Rd |only man/nparACT_flex_loop.Rd |only 18 files changed, 261 insertions(+), 55 deletions(-)
Title: Statistical Methods for Analysing Multivariate Abundance Data
Description: A set of tools for displaying, modeling and analysing
multivariate abundance data in community ecology. See
'mvabund-package.Rd' for details of overall package organization.
The package is implemented with the Gnu Scientific Library
(<http://www.gnu.org/software/gsl/>) and 'Rcpp'
(<http://dirk.eddelbuettel.com/code/rcpp.html>) 'R' / 'C++' classes.
Author: Yi Wang [aut],
Ulrike Naumann [aut],
Dirk Eddelbuettel [aut],
John Wilshire [aut],
David Warton [aut, cre],
Julian Byrnes [ctb],
Ralph dos Santos Silva [ctb, cph],
Jenni Niku [ctb],
Ian Renner [ctb],
Stephen Wright [ctb]
Maintainer: David Warton <David.Warton@unsw.edu.au>
Diff between mvabund versions 4.2.1 dated 2022-02-16 and 4.2.8 dated 2025-12-16
DESCRIPTION | 16 +++--- MD5 | 45 ++++++++++++------ NAMESPACE | 3 - R/anova.manyglm.R | 4 - R/block.to.bootID.R | 8 ++- R/default.plot.mvformula.R | 2 R/get_polys.R | 9 ++- R/manyany.R | 17 +++++-- R/manyglm.R | 6 +- R/traitglm.R | 2 README.md | 108 ++++++++++++++++++++++++++++++++++++++------- build |only inst |only man/coefplot.manyglm.Rd | 38 +++++---------- man/cv.glm1path.Rd | 2 man/figures |only man/spider.Rd | 11 ++-- src/Makevars | 3 - src/Makevars.win | 3 - src/anova.cpp | 15 ++---- vignettes |only 21 files changed, 198 insertions(+), 94 deletions(-)
Title: Linguistic Fuzzy Logic
Description: Various algorithms related to linguistic fuzzy logic: mining for linguistic fuzzy association
rules, composition of fuzzy relations, performing perception-based logical deduction (PbLD),
and forecasting time-series using fuzzy rule-based ensemble (FRBE). The package also contains basic
fuzzy-related algebraic functions capable of handling missing values in different styles (Bochvar,
Sobocinski, Kleene etc.), computation of Sugeno integrals and fuzzy transform.
Author: Michal Burda [aut, cre]
Maintainer: Michal Burda <michal.burda@osu.cz>
Diff between lfl versions 2.3.0 dated 2025-06-27 and 2.3.1 dated 2025-12-16
DESCRIPTION | 10 MD5 | 220 +++--- NEWS.md | 7 R/aggregateConsequents.R | 21 R/algebra.R | 33 R/algebraNA.R | 19 R/antecedents.R | 19 R/compose.R | 25 R/consequents.R | 19 R/ctx.R | 25 R/defuzz.R | 25 R/equidist.R | 23 R/equifreq.R | 26 R/evalfrbe.R | 21 R/exprs.R | 19 R/exprsDeprecated.R | 19 R/farules.R | 19 R/fcut.R | 45 - R/fire.R | 19 R/frbe.R | 35 - R/frbemodel.R | 19 R/fsets.R | 21 R/ft.R | 19 R/ftinv.R | 19 R/hedge.R | 21 R/horizon.R | 21 R/is.frbe.R | 21 R/is.specific.R | 19 R/lcut.R | 23 R/lfl-package.R | 25 R/lingexpr.R | 19 R/mase.R | 19 R/minmax.R | 23 R/mult.R | 19 R/pbld.R | 23 R/perceive.R | 27 R/print.ctx.R | 19 R/print.frbe.R | 19 R/quantifier.R | 21 R/rbcoverage.R | 21 R/reduce.R | 21 R/rmse.R | 19 R/rollapply.R | 19 R/searchrules.R | 63 + R/slicesDeprecated.R | 21 R/smape.R | 19 R/sugeno.R | 27 R/testers.R | 19 build/vignette.rds |binary configure | 1409 ++++++++++++++++++++++++++--------------- configure.ac | 8 inst/doc/main.pdf |binary man/aggregateConsequents.Rd | 2 man/algebra.Rd | 14 man/compose.Rd | 6 man/ctx.Rd | 6 man/defuzz.Rd | 6 man/equidist.Rd | 4 man/equifreq.Rd | 7 man/evalfrbe.Rd | 2 man/fcut.Rd | 24 man/frbe.Rd | 16 man/fsets.Rd | 2 man/hedge.Rd | 2 man/horizon.Rd | 2 man/is.frbe.Rd | 2 man/lcut.Rd | 4 man/lfl-package.Rd | 6 man/minmax.Rd | 4 man/pbld.Rd | 4 man/perceive.Rd | 8 man/quantifier.Rd | 2 man/rbcoverage.Rd | 2 man/reduce.Rd | 2 man/searchrules.Rd | 46 - man/slices.Rd | 2 man/sugeno.Rd | 8 src/algebra.cpp | 19 src/common.h | 21 src/common/Chain.h | 19 src/common/ChainCombiner.h | 19 src/common/Data.h | 19 src/exprs.cpp | 19 src/hedge.cpp | 19 src/mult.cpp | 19 src/reduce.cpp | 19 src/reduce/Reduce.h | 19 src/reduce/ReduceConfig.h | 19 src/reduce/Rule.h | 19 src/reduce/RuleQueue.h | 19 src/search.cpp | 19 src/search/AbstractExtension.h | 23 src/search/AbstractStorage.h | 19 src/search/Attribute.h | 23 src/search/BasicExtension.h | 23 src/search/BoundedStorage.h | 19 src/search/CombinationTrie.h | 19 src/search/Data.h | 19 src/search/DummyExtension.h | 23 src/search/IntervalStorage.h | 19 src/search/LiftExtension.h | 19 src/search/Rule.h | 19 src/search/RuleQueue.h | 19 src/search/Search.h | 19 src/search/SearchConfig.h | 27 src/search/Statistics.h | 19 src/search/Task.h | 19 src/search/TaskQueue.h | 19 src/search/TrieExtension.h | 19 src/search/UnlimitedStorage.h | 19 src/specificity.cpp | 19 111 files changed, 2726 insertions(+), 821 deletions(-)
Title: Wasserstein Regression and Inference
Description: Implementation of the methodologies described in 1) Alexander Petersen, Xi Liu and Afshin A. Divani (2021) <doi:10.1214/20-aos1971>, including global F tests, partial F tests, intrinsic Wasserstein-infinity bands and Wasserstein density bands, and 2) Chao Zhang, Piotr Kokoszka and Alexander Petersen (2022) <doi:10.1111/jtsa.12590>, including estimation, prediction, and inference of the Wasserstein autoregressive models.
Author: Xi Liu [aut, cre],
Chao Zhang [aut],
Matthew Coleman [aut],
Alexander Petersen [aut]
Maintainer: Xi Liu <xiliu@ucsb.edu>
Diff between WRI versions 0.2.0 dated 2022-07-08 and 0.2.1 dated 2025-12-16
DESCRIPTION | 18 +- MD5 | 30 +-- R/confidenceBands.R | 26 +-- R/globalFtest.R | 25 +-- R/partialFtest.R | 13 - R/simulate_quantile_curves.R | 2 R/wass_regress.R | 10 - README.md | 4 build/vignette.rds |binary inst/doc/WRI-vignette.R | 10 - inst/doc/WRI-vignette.html | 305 ++++++++++++++++++++-------------------- man/confidenceBands.Rd | 26 +-- man/globalFtest.Rd | 25 +-- man/partialFtest.Rd | 13 - man/simulate_quantile_curves.Rd | 2 man/wass_regress.Rd | 8 - 16 files changed, 265 insertions(+), 252 deletions(-)
Title: Global Univariate Minimization
Description: Global univariate minimization of Lipschitz functions is performed by using Pijavski method, which was published in Pijavski (1972) <DOI:10.1016/0041-5553(72)90115-2>.
Author: Gleb Beliakov [aut, cre],
Gita Das [aut],
Jonathan Wells [ctb],
Hewlett-Packard Company [ctb],
Silicon Graphics Computer Systems Inc. [ctb]
Maintainer: Gleb Beliakov <gleb@deakin.edu.au>
Diff between Pijavski versions 1.0.3 dated 2020-10-22 and 1.0.5 dated 2025-12-16
Pijavski-1.0.3/Pijavski/src/Makevars |only Pijavski-1.0.3/Pijavski/src/Makevars.win |only Pijavski-1.0.5/Pijavski/DESCRIPTION | 9 ++++----- Pijavski-1.0.5/Pijavski/MD5 | 6 ++---- Pijavski-1.0.5/Pijavski/src/pijavski.cpp | 9 ++++++--- 5 files changed, 12 insertions(+), 12 deletions(-)
Title: Hamiltonian Monte Carlo and Other Gradient-Based MCMC Sampling
Algorithms for 'nimble'
Description: Provides gradient-based MCMC sampling algorithms for use with the MCMC engine provided by the 'nimble' package. This includes two versions of Hamiltonian Monte Carlo (HMC) No-U-Turn (NUTS) sampling, and (under development) Langevin samplers. The `NUTS_classic` sampler implements the original HMC-NUTS algorithm as described in Hoffman and Gelman (2014) <doi:10.48550/arXiv.1111.4246>. The `NUTS` sampler is a modern version of HMC-NUTS sampling matching the HMC sampler available in version 2.32.2 of Stan (Stan Development Team, 2023). In addition, convenience functions are provided for generating and modifying MCMC configuration objects which employ HMC sampling. Functionality of the 'nimbleHMC' package is described further in Turek, et al (2024) <doi: 10.21105/joss.06745>.
Author: Daniel Turek [aut, cre],
Perry de Valpine [aut],
Christopher Paciorek [aut]
Maintainer: Daniel Turek <danielturek@gmail.com>
Diff between nimbleHMC versions 0.2.3 dated 2024-12-18 and 0.2.4 dated 2025-12-16
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ R/HMC_configuration.R | 23 +++++++++++++++++------ R/HMC_samplers.R | 44 ++++++++++++++++++++++++++++---------------- man/buildHMC.Rd | 6 ++++-- man/nimbleHMC.Rd | 8 +++++--- tests/testthat/test-HMC.R | 29 +++++++++++++---------------- 7 files changed, 79 insertions(+), 55 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-07-16 0.1.1
2020-10-23 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-12-01 1.0.5
2021-07-17 1.0.2
Title: Estimated Marginal Means, aka Least-Squares Means
Description: Obtain estimated marginal means (EMMs) for many linear, generalized
linear, and mixed models. Compute contrasts or linear functions of EMMs,
trends, and comparisons of slopes. Plots and other displays.
Least-squares means are discussed, and the term "estimated marginal means"
is suggested, in Searle, Speed, and Milliken (1980) Population marginal means
in the linear model: An alternative to least squares means, The American
Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Author: Russell V. Lenth [aut, cph],
Julia Piaskowski [cre, aut],
Balazs Banfai [ctb],
Ben Bolker [ctb],
Paul Buerkner [ctb],
Iago Gine-Vazquez [ctb],
Maxime Herve [ctb],
Maarten Jung [ctb],
Jonathon Love [ctb],
Fernando Miguez [ctb],
Hannes Riebl [ctb],
Hen [...truncated...]
Maintainer: Julia Piaskowski <julia.piask@gmail.com>
Diff between emmeans versions 2.0.0 dated 2025-10-29 and 2.0.1 dated 2025-12-16
DESCRIPTION | 8 MD5 | 349 +-- NAMESPACE | 534 ++--- NEWS.md | 2749 ++++++++++++++--------------- R/0nly-internal.R | 1148 ++++++------ R/MCMC-support.R | 1426 +++++++-------- R/S4-classes.R | 252 +- R/aovlist-support.R | 412 ++-- R/betareg.support.R | 262 +- R/brms-support.R | 64 R/cld-emm.R | 516 ++--- R/contrast.R | 1262 ++++++------- R/countreg-support.R | 638 +++--- R/datasets.R | 690 +++---- R/eff-size.R | 322 +-- R/emm-contr.R | 1142 ++++++------ R/emm-example.R | 152 - R/emm-list.R | 764 ++++---- R/emmGrid-methods.R | 2203 +++++++++++------------ R/emmeans-package.R | 246 +- R/emmeans.R | 1652 ++++++++--------- R/emmip.R | 1151 ++++++------ R/emtrends.R | 540 ++--- R/factors.R | 764 ++++---- R/gam-support.R | 560 +++--- R/glht-support.R | 488 ++--- R/helpers.R | 1790 +++++++++---------- R/interfacing.R | 916 ++++----- R/lqm-support.R | 244 +- R/models.R | 62 R/multinom-support.R | 268 +- R/multiple-models.R | 372 +-- R/multiv.R | 480 ++--- R/nested.R | 853 ++++----- R/nonlin-support.R | 288 +-- R/ordinal-support.R | 828 ++++---- R/plot.emm.R | 1214 ++++++------- R/pwpp.R | 1106 +++++------ R/qdrg.R | 602 +++--- R/rbind.R | 386 ++-- R/ref-grid.R | 2562 +++++++++++++-------------- R/rms-support.R | 238 +- R/sommer-support.R | 132 - R/summary.R | 2983 ++++++++++++++++---------------- R/test.R | 1090 +++++------ R/transformations.R | 958 +++++----- R/wrappers.R | 256 +- R/xtable-method.R | 258 +- R/zzz.R | 332 +-- README.md | 246 +- build/vignette.rds |binary inst/css/clean-simple.css | 78 inst/doc/AQuickStart.R | 8 inst/doc/AQuickStart.Rmd | 430 ++-- inst/doc/AQuickStart.html | 668 +++---- inst/doc/FAQs.R | 28 inst/doc/FAQs.Rmd | 960 +++++----- inst/doc/FAQs.html | 1232 ++++++------- inst/doc/basics.R | 302 +-- inst/doc/basics.Rmd | 1454 +++++++-------- inst/doc/basics.html | 1992 ++++++++++----------- inst/doc/comparisons.R | 188 +- inst/doc/comparisons.Rmd | 736 +++---- inst/doc/comparisons.html | 1138 ++++++------ inst/doc/confidence-intervals.R | 138 - inst/doc/confidence-intervals.Rmd | 616 +++--- inst/doc/confidence-intervals.html | 1124 ++++++------ inst/doc/interactions.R | 172 - inst/doc/interactions.Rmd | 734 +++---- inst/doc/interactions.html | 1258 ++++++------- inst/doc/messy-data.R | 264 +- inst/doc/messy-data.Rmd | 1096 +++++------ inst/doc/messy-data.html | 1620 ++++++++--------- inst/doc/models.Rmd | 1112 +++++------ inst/doc/models.html | 2212 +++++++++++------------ inst/doc/predictions.R | 78 inst/doc/predictions.Rmd | 326 +-- inst/doc/predictions.html | 540 +++-- inst/doc/re-engineering-clds.R | 54 inst/doc/re-engineering-clds.html | 734 ++++--- inst/doc/re-engineering-clds.rmd | 472 ++--- inst/doc/sophisticated.R | 318 +-- inst/doc/sophisticated.Rmd | 954 +++++----- inst/doc/sophisticated.html | 1586 ++++++++--------- inst/doc/transformations.R | 402 ++-- inst/doc/transformations.Rmd | 1418 +++++++-------- inst/doc/transformations.html | 2052 +++++++++++----------- inst/doc/utilities.R | 180 - inst/doc/utilities.Rmd | 592 +++--- inst/doc/utilities.html | 1040 +++++------ inst/doc/vignette-topics.Rmd | 1606 ++++++++--------- inst/doc/vignette-topics.html | 2416 +++++++++++++------------ inst/doc/xplanations.R | 190 +- inst/doc/xplanations.Rmd | 784 ++++---- inst/doc/xplanations.html | 1174 ++++++------ inst/doc/xtending.R | 288 +-- inst/doc/xtending.Rmd | 1084 +++++------ inst/doc/xtending.html | 1838 +++++++++---------- inst/extexamples/as.mcmc-coda.R | 16 inst/extexamples/cld-multcomp.R | 14 inst/extexamples/glht-multcomp.R | 24 inst/extexamples/hpd.summary-coda.R | 18 inst/extexamples/mvregrid.R | 24 inst/extexamples/qdrg-biglm.R | 20 inst/extexamples/qdrg-coda.R | 14 inst/extexamples/qdrg-ordinal.R | 12 inst/extexamples/xtable.R | 6 man/CLD.emmGrid.Rd | 214 +- man/MOats.Rd | 94 - man/as.emmGrid.Rd | 132 - man/auto.noise.Rd | 124 - man/contrast.Rd | 466 ++-- man/eff_size.Rd | 248 +- man/emmGrid-class.Rd | 196 +- man/emmGrid-methods.Rd | 108 - man/emm_example.Rd | 66 man/emm_list-object.Rd | 208 +- man/emm_options.Rd | 446 ++-- man/emmc-functions.Rd | 462 ++-- man/emmeans-package.Rd | 200 +- man/emmeans.Rd | 508 ++--- man/emmip.Rd | 486 ++--- man/emmobj.Rd | 214 +- man/emtrends.Rd | 278 +- man/extending-emmeans.Rd | 712 +++---- man/feedlot.Rd | 102 - man/fiber.Rd | 82 man/glht-support.Rd | 152 - man/hpd.summary.Rd | 190 +- man/joint_tests.Rd | 392 ++-- man/make.tran.Rd | 392 ++-- man/manip-factors.Rd | 386 ++-- man/mcmc-support.Rd | 208 +- man/models.Rd | 18 man/mvcontrast.Rd | 162 - man/mvregrid.Rd | 102 - man/neuralgia.Rd | 86 man/nutrition.Rd | 102 - man/oranges.Rd | 94 - man/pigs.Rd | 68 man/plot.Rd | 322 +-- man/pwpm.Rd | 148 - man/pwpp.Rd | 242 +- man/qdrg.Rd | 272 +- man/rbind.emmGrid.Rd | 238 +- man/ref_grid.Rd | 932 ++++----- man/regrid.Rd | 260 +- man/summary.emmGrid.Rd | 994 +++++----- man/ubds.Rd | 80 man/untidy.Rd | 62 man/update.emmGrid.Rd | 562 +++--- man/wrappers.Rd | 126 - man/xtable.emmGrid.Rd | 128 - tests/testthat.R | 8 tests/testthat/test-contrast.R | 70 tests/testthat/test-emmeans.R | 62 tests/testthat/test-emtrends.R | 42 tests/testthat/test-nested.R | 74 tests/testthat/test-ref_grid.R | 188 +- tests/testthat/test-utility_functions.R |only vignettes/AQuickStart.Rmd | 430 ++-- vignettes/FAQs.Rmd | 960 +++++----- vignettes/basics.Rmd | 1454 +++++++-------- vignettes/comparisons.Rmd | 736 +++---- vignettes/confidence-intervals.Rmd | 616 +++--- vignettes/interactions.Rmd | 734 +++---- vignettes/messy-data.Rmd | 1096 +++++------ vignettes/models.Rmd | 1112 +++++------ vignettes/predictions.Rmd | 326 +-- vignettes/re-engineering-clds.rmd | 472 ++--- vignettes/sophisticated.Rmd | 954 +++++----- vignettes/transformations.Rmd | 1418 +++++++-------- vignettes/utilities.Rmd | 592 +++--- vignettes/vignette-topics.Rmd | 1606 ++++++++--------- vignettes/xplanations.Rmd | 784 ++++---- vignettes/xtending.Rmd | 1084 +++++------ 176 files changed, 52937 insertions(+), 52537 deletions(-)
Title: Supporting Functions for Packages Maintained by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] ,
Wush Wu [ctb],
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brueggemann [ctb] ,
Christophe Dervieux [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.54 dated 2025-10-30 and 0.55 dated 2025-12-16
DESCRIPTION | 8 ++--- MD5 | 50 ++++++++++++++++---------------- NAMESPACE | 1 R/app.R | 8 ++--- R/browser.R |only R/cache.R | 65 +++++++++++++++++++++++++----------------- R/image.R | 2 - R/record.R | 18 +++++++---- R/revcheck.R | 2 - R/zzz.R | 6 +++ inst/doc/xfun.Rmd | 2 - inst/doc/xfun.html | 18 +++++------ man/browser_print.Rd |only man/cache_exec.Rd | 11 +++---- man/cache_rds.Rd | 16 +++++----- man/download_cache.Rd | 4 +- man/github_releases.Rd | 4 +- man/mime_type.Rd | 4 +- man/news2md.Rd | 4 +- man/rest_api.Rd | 12 +++---- man/retry.Rd | 4 +- man/session_info.Rd | 4 +- man/shrink_images.Rd | 3 + man/system3.Rd | 4 +- tests/test-ci/test-cran.R | 2 - tests/test-cran/test-record.R | 9 +++++ vignettes/xfun.Rmd | 2 - 27 files changed, 152 insertions(+), 111 deletions(-)
Title: R Client for the VirusTotal API
Description: Provides a comprehensive R interface to the VirusTotal API (v2 and v3),
a Google service that analyzes files and URLs for viruses, worms, trojans and
other malware. Features include file/URL scanning, domain categorization,
passive DNS information, IP reputation analysis, and comment/voting systems.
Implements rate limiting, error handling, and response validation for robust
security analysis workflows.
Author: Gaurav Sood [aut, cre]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between virustotal versions 0.3.0 dated 2025-09-02 and 0.5.0 dated 2025-12-16
virustotal-0.3.0/virustotal/tests/testthat/virustotal_api_key.enc |only virustotal-0.5.0/virustotal/DESCRIPTION | 36 +- virustotal-0.5.0/virustotal/MD5 | 117 ++++++--- virustotal-0.5.0/virustotal/NAMESPACE | 22 + virustotal-0.5.0/virustotal/NEWS.md | 57 ++++ virustotal-0.5.0/virustotal/R/domain_report.R | 116 ++++++-- virustotal-0.5.0/virustotal/R/errors.R |only virustotal-0.5.0/virustotal/R/file_report.R | 90 +++++- virustotal-0.5.0/virustotal/R/ip_report.R | 9 virustotal-0.5.0/virustotal/R/rate_limiting.R |only virustotal-0.5.0/virustotal/R/s3_classes.R |only virustotal-0.5.0/virustotal/R/scan_file.R | 65 +++-- virustotal-0.5.0/virustotal/R/security.R |only virustotal-0.5.0/virustotal/R/set_key.R | 70 ++++- virustotal-0.5.0/virustotal/R/utils.R |only virustotal-0.5.0/virustotal/R/virustotal.R | 129 ++++++---- virustotal-0.5.0/virustotal/R/zzz.R |only virustotal-0.5.0/virustotal/README.md | 4 virustotal-0.5.0/virustotal/inst/doc/using_virustotal.html | 4 virustotal-0.5.0/virustotal/man/add_comments.Rd | 12 virustotal-0.5.0/virustotal/man/as.data.frame.virustotal_response.Rd |only virustotal-0.5.0/virustotal/man/cleanup_temp_files.Rd |only virustotal-0.5.0/virustotal/man/create_safe_temp_dir.Rd |only virustotal-0.5.0/virustotal/man/domain_report.Rd | 31 +- virustotal-0.5.0/virustotal/man/file_report.Rd | 27 +- virustotal-0.5.0/virustotal/man/format_file_size.Rd |only virustotal-0.5.0/virustotal/man/get_domain_comments.Rd | 2 virustotal-0.5.0/virustotal/man/get_domain_relationship.Rd | 2 virustotal-0.5.0/virustotal/man/get_ip_info.Rd | 2 virustotal-0.5.0/virustotal/man/get_rate_limit_status.Rd |only virustotal-0.5.0/virustotal/man/init_rate_limit.Rd |only virustotal-0.5.0/virustotal/man/ip_report.Rd | 2 virustotal-0.5.0/virustotal/man/is_api_key_configured.Rd |only virustotal-0.5.0/virustotal/man/is_rate_limit_initialized.Rd |only virustotal-0.5.0/virustotal/man/is_safe_environment.Rd |only virustotal-0.5.0/virustotal/man/print.virustotal_domain_report.Rd |only virustotal-0.5.0/virustotal/man/print.virustotal_error.Rd |only virustotal-0.5.0/virustotal/man/print.virustotal_file_report.Rd |only virustotal-0.5.0/virustotal/man/print.virustotal_response.Rd |only virustotal-0.5.0/virustotal/man/rate-limiting.Rd |only virustotal-0.5.0/virustotal/man/rate_limit.Rd | 24 + virustotal-0.5.0/virustotal/man/rate_limit_legacy.Rd |only virustotal-0.5.0/virustotal/man/reset_rate_limit.Rd |only virustotal-0.5.0/virustotal/man/sanitize_domain.Rd |only virustotal-0.5.0/virustotal/man/sanitize_file_path.Rd |only virustotal-0.5.0/virustotal/man/sanitize_hash.Rd |only virustotal-0.5.0/virustotal/man/sanitize_ip.Rd |only virustotal-0.5.0/virustotal/man/sanitize_url.Rd |only virustotal-0.5.0/virustotal/man/scan_file.Rd | 25 + virustotal-0.5.0/virustotal/man/scan_url.Rd | 2 virustotal-0.5.0/virustotal/man/security-utilities.Rd |only virustotal-0.5.0/virustotal/man/set_key.Rd | 21 + virustotal-0.5.0/virustotal/man/summary.virustotal_response.Rd |only virustotal-0.5.0/virustotal/man/utilities.Rd |only virustotal-0.5.0/virustotal/man/validate_vt_response.Rd |only virustotal-0.5.0/virustotal/man/virustotal-classes.Rd |only virustotal-0.5.0/virustotal/man/virustotal-errors.Rd |only virustotal-0.5.0/virustotal/man/virustotal-package.Rd | 9 virustotal-0.5.0/virustotal/man/virustotal2_GET.Rd | 1 virustotal-0.5.0/virustotal/man/virustotal2_POST.Rd | 1 virustotal-0.5.0/virustotal/man/virustotal_GET.Rd | 1 virustotal-0.5.0/virustotal/man/virustotal_POST.Rd | 1 virustotal-0.5.0/virustotal/man/virustotal_auth_error.Rd |only virustotal-0.5.0/virustotal/man/virustotal_check.Rd | 16 + virustotal-0.5.0/virustotal/man/virustotal_domain_report.Rd |only virustotal-0.5.0/virustotal/man/virustotal_error.Rd |only virustotal-0.5.0/virustotal/man/virustotal_file_report.Rd |only virustotal-0.5.0/virustotal/man/virustotal_file_scan.Rd |only virustotal-0.5.0/virustotal/man/virustotal_info.Rd |only virustotal-0.5.0/virustotal/man/virustotal_ip_report.Rd |only virustotal-0.5.0/virustotal/man/virustotal_rate_limit_error.Rd |only virustotal-0.5.0/virustotal/man/virustotal_url_scan.Rd |only virustotal-0.5.0/virustotal/man/virustotal_validation_error.Rd |only virustotal-0.5.0/virustotal/man/virustotal_version.Rd |only virustotal-0.5.0/virustotal/tests/testthat/test-auth.R | 55 +++- virustotal-0.5.0/virustotal/tests/testthat/test-data-structures.R | 3 virustotal-0.5.0/virustotal/tests/testthat/test-domain-operations.R | 13 - virustotal-0.5.0/virustotal/tests/testthat/test-error-handling.R |only virustotal-0.5.0/virustotal/tests/testthat/test-file-operations.R | 34 +- virustotal-0.5.0/virustotal/tests/testthat/test-ip-operations.R | 4 virustotal-0.5.0/virustotal/tests/testthat/test-pkg-style.R | 2 virustotal-0.5.0/virustotal/tests/testthat/test-rate-limiting.R |only virustotal-0.5.0/virustotal/tests/testthat/test-url-operations.R | 4 83 files changed, 741 insertions(+), 272 deletions(-)
Title: Simulation and Prediction with Seasonal ARIMA Models
Description: Functions, classes and methods for time series modelling with ARIMA
and related models. The aim of the package is to provide consistent
interface for the user. For example, a single function autocorrelations()
computes various kinds of theoretical and sample autocorrelations. This is
work in progress, see the documentation and vignettes for the current
functionality. Function sarima() fits extended multiplicative seasonal
ARIMA models with trends, exogenous variables and arbitrary roots on the
unit circle, which can be fixed or estimated (for the algebraic basis for
this see <doi:10.48550/arXiv.2208.05055>, a paper on the methodology is being prepared).
Author: Georgi N. Boshnakov [aut, cre] ,
Jamie Halliday [aut]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between sarima versions 0.9.4 dated 2025-03-18 and 0.9.5 dated 2025-12-16
sarima-0.9.4/sarima/inst/auto |only sarima-0.9.5/sarima/DESCRIPTION | 17 sarima-0.9.5/sarima/MD5 | 41 sarima-0.9.5/sarima/NEWS.md | 977 ++++----- sarima-0.9.5/sarima/R/RcppExports.R | 62 sarima-0.9.5/sarima/R/fitTools.R | 1870 +++++++++--------- sarima-0.9.5/sarima/R/zzz.R | 32 sarima-0.9.5/sarima/build/partial.rdb |binary sarima-0.9.5/sarima/build/vignette.rds |binary sarima-0.9.5/sarima/inst/REFERENCES.bib | 236 +- sarima-0.9.5/sarima/inst/doc/garch_tests_example.R | 196 - sarima-0.9.5/sarima/inst/doc/garch_tests_example.Rnw | 2 sarima-0.9.5/sarima/inst/doc/garch_tests_example.pdf |binary sarima-0.9.5/sarima/inst/doc/white_noise_tests.R | 218 +- sarima-0.9.5/sarima/inst/doc/white_noise_tests.Rnw | 2 sarima-0.9.5/sarima/inst/doc/white_noise_tests.pdf |binary sarima-0.9.5/sarima/man/FisherInformation-methods.Rd | 200 - sarima-0.9.5/sarima/man/tsdiag.Sarima.Rd | 298 +- sarima-0.9.5/sarima/tests/testthat/test-armacalc.R | 458 ++-- sarima-0.9.5/sarima/tests/testthat/test-sarima-uar.R | 92 sarima-0.9.5/sarima/vignettes/garch_tests_example.Rnw | 2 sarima-0.9.5/sarima/vignettes/white_noise_tests.Rnw | 2 22 files changed, 2356 insertions(+), 2349 deletions(-)
Title: Multinomial Logit Models for Categorical Responses and Discrete
Choices
Description: Provides estimators for multinomial logit models in their
conditional logit (for discrete choices) and baseline logit variants
(for categorical responses), optionally with overdispersion or random
effects. Random effects models are estimated using the PQL technique
(based on a Laplace approximation) or the MQL technique (based on a
Solomon-Cox approximation). Estimates should be treated
with caution if the group sizes are small.
Author: Martin Elff [aut, cre]
Maintainer: Martin Elff <martin@elff.eu>
Diff between mclogit versions 0.9.6 dated 2022-10-27 and 0.9.15 dated 2025-12-16
mclogit-0.9.15/mclogit/DESCRIPTION | 40 mclogit-0.9.15/mclogit/MD5 | 69 - mclogit-0.9.15/mclogit/NAMESPACE | 8 mclogit-0.9.15/mclogit/R/blockMatrices.R | 71 + mclogit-0.9.15/mclogit/R/getSummary-mblogit.R | 196 +-- mclogit-0.9.15/mclogit/R/getSummary-mclogit.R | 21 mclogit-0.9.15/mclogit/R/mblogit.R | 518 ++++++-- mclogit-0.9.15/mclogit/R/mclogit-dispersion.R | 4 mclogit-0.9.15/mclogit/R/mclogit-fit.R | 5 mclogit-0.9.15/mclogit/R/mclogit-rebase.R |only mclogit-0.9.15/mclogit/R/mclogit.R | 138 +- mclogit-0.9.15/mclogit/R/mmclogit-fitPQLMQL.R | 231 ++- mclogit-0.9.15/mclogit/R/safeInverse.R |only mclogit-0.9.15/mclogit/R/zzz.R | 3 mclogit-0.9.15/mclogit/build/partial.rdb |binary mclogit-0.9.15/mclogit/build/vignette.rds |only mclogit-0.9.15/mclogit/data/Transport.rda |binary mclogit-0.9.15/mclogit/data/electors.rda |binary mclogit-0.9.15/mclogit/inst/ChangeLog | 1615 +++++++++++++++++++++++--- mclogit-0.9.15/mclogit/inst/ChangeLog-old |only mclogit-0.9.15/mclogit/inst/NEWS.Rd | 19 mclogit-0.9.15/mclogit/inst/doc |only mclogit-0.9.15/mclogit/man/dispersion.Rd | 96 + mclogit-0.9.15/mclogit/man/mblogit.Rd | 36 mclogit-0.9.15/mclogit/man/mclogit.Rd | 26 mclogit-0.9.15/mclogit/man/mclogit_control.Rd | 54 mclogit-0.9.15/mclogit/man/rebase.Rd |only mclogit-0.9.15/mclogit/man/simulate.Rd | 2 mclogit-0.9.15/mclogit/vignettes |only mclogit-0.9.6/mclogit/R/emmeans.R |only mclogit-0.9.6/mclogit/R/saveInverse.R |only 31 files changed, 2566 insertions(+), 586 deletions(-)
Title: Machine Learning Models and Tools
Description: Meta-package for statistical and machine learning with a unified
interface for model fitting, prediction, performance assessment, and
presentation of results. Approaches for model fitting and prediction of
numerical, categorical, or censored time-to-event outcomes include
traditional regression models, regularization methods, tree-based methods,
support vector machines, neural networks, ensembles, data preprocessing,
filtering, and model tuning and selection. Performance metrics are provided
for model assessment and can be estimated with independent test sets, split
sampling, cross-validation, or bootstrap resampling. Resample estimation
can be executed in parallel for faster processing and nested in cases of
model tuning and selection. Modeling results can be summarized with
descriptive statistics; calibration curves; variable importance; partial
dependence plots; confusion matrices; and ROC, lift, and other performance
curves.
Author: Brian J Smith [aut, cre]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>
Diff between MachineShop versions 3.9.0 dated 2025-06-09 and 3.9.1 dated 2025-12-16
DESCRIPTION | 12 MD5 | 22 - NEWS.md | 5 R/ML_XGBModel.R | 53 +-- R/resample.R | 2 R/varimp.R | 2 build/vignette.rds |binary inst/doc/UserGuide.html | 105 +++--- man/XGBModel.Rd | 14 tests/testthat/Rplots.pdf |binary tests/testthat/test-discrete-vars.R | 2 tests/testthat/test-survival.txt | 594 ++++++++++++++++++------------------ 12 files changed, 404 insertions(+), 407 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] ,
Shannon Haughton [aut],
Ellis Hughes [aut] ,
Alexandra Lauer [aut] ,
Romain Francois [aut],
JooYoung Seo [aut] ,
Ken Brevoort [aut] ,
Olivier Roy [aut],
Posit Software, PBC [cph, [...truncated...]
Maintainer: Richard Iannone <rich@posit.co>
Diff between gt versions 1.1.0 dated 2025-09-23 and 1.2.0 dated 2025-12-16
gt-1.1.0/gt/tests/testthat/test-l_tab_spanner_delim.R |only gt-1.2.0/gt/DESCRIPTION | 14 gt-1.2.0/gt/MD5 | 345 - gt-1.2.0/gt/NAMESPACE | 5 gt-1.2.0/gt/NEWS.md | 36 gt-1.2.0/gt/R/build_data.R | 4 gt-1.2.0/gt/R/data_color.R | 2 gt-1.2.0/gt/R/datasets.R | 10 gt-1.2.0/gt/R/dt_options.R | 2 gt-1.2.0/gt/R/dt_stub_df.R | 47 gt-1.2.0/gt/R/dt_summary.R | 8 gt-1.2.0/gt/R/dt_summary_cols.R |only gt-1.2.0/gt/R/export.R | 63 gt-1.2.0/gt/R/fmt.R | 128 gt-1.2.0/gt/R/fmt_date_time.R | 223 - gt-1.2.0/gt/R/fmt_number.R | 23 gt-1.2.0/gt/R/format_data.R | 968 +++- gt-1.2.0/gt/R/format_vec.R | 216 - gt-1.2.0/gt/R/gt-package.R | 2 gt-1.2.0/gt/R/gt.R | 22 gt-1.2.0/gt/R/helpers.R | 93 gt-1.2.0/gt/R/info_tables.R | 58 gt-1.2.0/gt/R/knitr-utils.R | 8 gt-1.2.0/gt/R/opts.R | 131 gt-1.2.0/gt/R/resolver.R | 44 gt-1.2.0/gt/R/substitution.R | 10 gt-1.2.0/gt/R/summary_columns.R |only gt-1.2.0/gt/R/tab_options.R | 21 gt-1.2.0/gt/R/topics.R | 50 gt-1.2.0/gt/R/utils.R | 21 gt-1.2.0/gt/R/utils_examples.R | 34 gt-1.2.0/gt/R/utils_render_grid.R | 401 + gt-1.2.0/gt/R/utils_render_html.R | 12 gt-1.2.0/gt/R/utils_render_latex.R | 526 ++ gt-1.2.0/gt/R/utils_render_rtf.R | 93 gt-1.2.0/gt/R/utils_render_xml.R | 300 - gt-1.2.0/gt/R/z_utils_render_footnotes.R | 143 gt-1.2.0/gt/R/zzz.R | 8 gt-1.2.0/gt/data/constants.rda |binary gt-1.2.0/gt/data/countrypops.rda |binary gt-1.2.0/gt/data/exibble.rda |binary gt-1.2.0/gt/data/gibraltar.rda |binary gt-1.2.0/gt/data/gtcars.rda |binary gt-1.2.0/gt/data/illness.rda |binary gt-1.2.0/gt/data/nuclides.rda |binary gt-1.2.0/gt/data/peeps.rda |binary gt-1.2.0/gt/data/photolysis.rda |binary gt-1.2.0/gt/data/pizzaplace.rda |binary gt-1.2.0/gt/data/reactions.rda |binary gt-1.2.0/gt/data/rx_addv.rda |binary gt-1.2.0/gt/data/rx_adsl.rda |binary gt-1.2.0/gt/data/sp500.rda |binary gt-1.2.0/gt/data/sza.rda |binary gt-1.2.0/gt/data/towny.rda |binary gt-1.2.0/gt/inst/latex_unicode/latex_unicode_conversion.txt | 2106 +++++----- gt-1.2.0/gt/man/countrypops.Rd | 6 gt-1.2.0/gt/man/data_color.Rd | 3 gt-1.2.0/gt/man/escape_latex.Rd | 12 gt-1.2.0/gt/man/fmt.Rd | 3 gt-1.2.0/gt/man/fmt_auto.Rd | 3 gt-1.2.0/gt/man/fmt_bins.Rd | 3 gt-1.2.0/gt/man/fmt_bytes.Rd | 15 gt-1.2.0/gt/man/fmt_chem.Rd | 3 gt-1.2.0/gt/man/fmt_country.Rd | 3 gt-1.2.0/gt/man/fmt_currency.Rd | 15 gt-1.2.0/gt/man/fmt_date.Rd | 3 gt-1.2.0/gt/man/fmt_datetime.Rd | 3 gt-1.2.0/gt/man/fmt_duration.Rd | 3 gt-1.2.0/gt/man/fmt_email.Rd | 3 gt-1.2.0/gt/man/fmt_engineering.Rd | 1 gt-1.2.0/gt/man/fmt_flag.Rd | 3 gt-1.2.0/gt/man/fmt_fraction.Rd | 3 gt-1.2.0/gt/man/fmt_icon.Rd | 3 gt-1.2.0/gt/man/fmt_image.Rd | 3 gt-1.2.0/gt/man/fmt_index.Rd | 3 gt-1.2.0/gt/man/fmt_integer.Rd | 14 gt-1.2.0/gt/man/fmt_markdown.Rd | 3 gt-1.2.0/gt/man/fmt_number.Rd | 14 gt-1.2.0/gt/man/fmt_number_si.Rd |only gt-1.2.0/gt/man/fmt_partsper.Rd | 3 gt-1.2.0/gt/man/fmt_passthrough.Rd | 3 gt-1.2.0/gt/man/fmt_percent.Rd | 15 gt-1.2.0/gt/man/fmt_roman.Rd | 3 gt-1.2.0/gt/man/fmt_scientific.Rd | 1 gt-1.2.0/gt/man/fmt_spelled_num.Rd | 3 gt-1.2.0/gt/man/fmt_tf.Rd | 3 gt-1.2.0/gt/man/fmt_time.Rd | 3 gt-1.2.0/gt/man/fmt_units.Rd | 3 gt-1.2.0/gt/man/fmt_url.Rd | 3 gt-1.2.0/gt/man/fmts.Rd | 10 gt-1.2.0/gt/man/grand_summary_rows.Rd | 1 gt-1.2.0/gt/man/gt-package.Rd | 2 gt-1.2.0/gt/man/gt.Rd | 12 gt-1.2.0/gt/man/locale.Rd | 25 gt-1.2.0/gt/man/opt_align_table_header.Rd | 3 gt-1.2.0/gt/man/opt_all_caps.Rd | 3 gt-1.2.0/gt/man/opt_css.Rd | 3 gt-1.2.0/gt/man/opt_footnote_marks.Rd | 1 gt-1.2.0/gt/man/opt_footnote_order.Rd |only gt-1.2.0/gt/man/opt_footnote_spec.Rd | 1 gt-1.2.0/gt/man/opt_horizontal_padding.Rd | 3 gt-1.2.0/gt/man/opt_interactive.Rd | 1 gt-1.2.0/gt/man/opt_row_striping.Rd | 3 gt-1.2.0/gt/man/opt_stylize.Rd | 1 gt-1.2.0/gt/man/opt_table_font.Rd | 3 gt-1.2.0/gt/man/opt_table_lines.Rd | 3 gt-1.2.0/gt/man/opt_table_outline.Rd | 3 gt-1.2.0/gt/man/opt_vertical_padding.Rd | 3 gt-1.2.0/gt/man/row_group_order.Rd | 1 gt-1.2.0/gt/man/rows-columns.Rd | 15 gt-1.2.0/gt/man/rows_add.Rd | 1 gt-1.2.0/gt/man/stub.Rd | 43 gt-1.2.0/gt/man/sub_large_vals.Rd | 3 gt-1.2.0/gt/man/sub_missing.Rd | 3 gt-1.2.0/gt/man/sub_small_vals.Rd | 3 gt-1.2.0/gt/man/sub_values.Rd | 3 gt-1.2.0/gt/man/sub_zero.Rd | 3 gt-1.2.0/gt/man/summary_columns.Rd |only gt-1.2.0/gt/man/summary_rows.Rd | 3 gt-1.2.0/gt/man/sza.Rd | 5 gt-1.2.0/gt/man/tab_options.Rd | 18 gt-1.2.0/gt/man/vec_fmt_bytes.Rd | 15 gt-1.2.0/gt/man/vec_fmt_currency.Rd | 15 gt-1.2.0/gt/man/vec_fmt_date.Rd | 3 gt-1.2.0/gt/man/vec_fmt_datetime.Rd | 3 gt-1.2.0/gt/man/vec_fmt_duration.Rd | 3 gt-1.2.0/gt/man/vec_fmt_engineering.Rd | 1 gt-1.2.0/gt/man/vec_fmt_fraction.Rd | 3 gt-1.2.0/gt/man/vec_fmt_index.Rd | 3 gt-1.2.0/gt/man/vec_fmt_integer.Rd | 13 gt-1.2.0/gt/man/vec_fmt_markdown.Rd | 3 gt-1.2.0/gt/man/vec_fmt_number.Rd | 13 gt-1.2.0/gt/man/vec_fmt_number_si.Rd |only gt-1.2.0/gt/man/vec_fmt_partsper.Rd | 3 gt-1.2.0/gt/man/vec_fmt_percent.Rd | 15 gt-1.2.0/gt/man/vec_fmt_roman.Rd | 3 gt-1.2.0/gt/man/vec_fmt_scientific.Rd | 1 gt-1.2.0/gt/man/vec_fmt_spelled_num.Rd | 3 gt-1.2.0/gt/man/vec_fmt_time.Rd | 3 gt-1.2.0/gt/tests/testthat/Rplots.pdf |binary gt-1.2.0/gt/tests/testthat/_snaps/cols_hide.md | 2 gt-1.2.0/gt/tests/testthat/_snaps/extract_body.md | 83 gt-1.2.0/gt/tests/testthat/helper-gt_object.R | 5 gt-1.2.0/gt/tests/testthat/helper-render_formats.R | 4 gt-1.2.0/gt/tests/testthat/helper-tab_info.R | 18 gt-1.2.0/gt/tests/testthat/helper-tab_style.R | 5 gt-1.2.0/gt/tests/testthat/helper.R | 111 gt-1.2.0/gt/tests/testthat/test-as_rtf.R | 51 gt-1.2.0/gt/tests/testthat/test-cols_add.R | 28 gt-1.2.0/gt/tests/testthat/test-cols_align.R | 250 - gt-1.2.0/gt/tests/testthat/test-cols_hide.R | 25 gt-1.2.0/gt/tests/testthat/test-cols_move.R | 279 - gt-1.2.0/gt/tests/testthat/test-cols_nanoplot.R | 32 gt-1.2.0/gt/tests/testthat/test-cols_units.R | 20 gt-1.2.0/gt/tests/testthat/test-fmt.R | 86 gt-1.2.0/gt/tests/testthat/test-gt_preview.R | 32 gt-1.2.0/gt/tests/testthat/test-l_cell_text_alignment.R |only gt-1.2.0/gt/tests/testthat/test-l_cols_align.R | 47 gt-1.2.0/gt/tests/testthat/test-l_cols_merge.R | 133 gt-1.2.0/gt/tests/testthat/test-l_cols_move.R | 30 gt-1.2.0/gt/tests/testthat/test-l_cols_width.R | 134 gt-1.2.0/gt/tests/testthat/test-l_fmt.R | 72 gt-1.2.0/gt/tests/testthat/test-l_fmt_currency.R | 74 gt-1.2.0/gt/tests/testthat/test-l_fmt_engineering.R | 48 gt-1.2.0/gt/tests/testthat/test-l_fmt_integer.R | 78 gt-1.2.0/gt/tests/testthat/test-l_fmt_markdown.R | 19 gt-1.2.0/gt/tests/testthat/test-l_fmt_missing.R | 34 gt-1.2.0/gt/tests/testthat/test-l_fmt_number.R | 94 gt-1.2.0/gt/tests/testthat/test-l_fmt_passthrough.R | 30 gt-1.2.0/gt/tests/testthat/test-l_fmt_percent.R | 94 gt-1.2.0/gt/tests/testthat/test-l_fmt_scientific.R | 50 gt-1.2.0/gt/tests/testthat/test-l_row_group_order.R | 8 gt-1.2.0/gt/tests/testthat/test-multicolumn_stub_latex.R |only gt-1.2.0/gt/tests/testthat/test-multicolumn_stub_na_handling.R |only gt-1.2.0/gt/tests/testthat/test-resolver.R | 2 gt-1.2.0/gt/tests/testthat/test-row_group_order.R | 43 gt-1.2.0/gt/tests/testthat/test-rtf_table_parts.R | 65 gt-1.2.0/gt/tests/testthat/test-stub_helper_multicolumn.R |only gt-1.2.0/gt/tests/testthat/test-tab_caption.R | 88 179 files changed, 5700 insertions(+), 3101 deletions(-)
Title: Interactively Visualize Structural Equation Modeling Diagrams
Description: It enables users to perform interactive and reproducible visualizations of path diagrams for structural equation modeling (SEM) and networks using interactive parameter visualization. Meta-data of figure outputs can be either reloaded, replayed or reproduced as objects with figure outputs or images.
Author: Seung Hyun Min [aut, cre]
Maintainer: Seung Hyun Min <seung.min@mail.mcgill.ca>
Diff between ggsem versions 0.2.4 dated 2025-02-02 and 0.9.6 dated 2025-12-16
ggsem-0.2.4/ggsem/R/launch.R |only ggsem-0.2.4/ggsem/R/utils.R |only ggsem-0.9.6/ggsem/DESCRIPTION | 20 ggsem-0.9.6/ggsem/MD5 | 71 ggsem-0.9.6/ggsem/NAMESPACE | 115 ggsem-0.9.6/ggsem/R/adjust_axis_range.R | 16 ggsem-0.9.6/ggsem/R/adjust_axis_space.R | 17 ggsem-0.9.6/ggsem/R/create_bundle.R |only ggsem-0.9.6/ggsem/R/csv_to_ggplot.R | 197 ggsem-0.9.6/ggsem/R/draw_annotations.R | 51 ggsem-0.9.6/ggsem/R/draw_lines.R | 457 ggsem-0.9.6/ggsem/R/draw_loops.R | 86 ggsem-0.9.6/ggsem/R/draw_points.R | 324 ggsem-0.9.6/ggsem/R/ggsem_app.R |only ggsem-0.9.6/ggsem/R/ggsem_builder.R |only ggsem-0.9.6/ggsem/R/ggsem_launch.R |only ggsem-0.9.6/ggsem/R/ggsem_silent.R |only ggsem-0.9.6/ggsem/R/globals.R |only ggsem-0.9.6/ggsem/R/metadata_to_ggplot.R |only ggsem-0.9.6/ggsem/R/reproduce_metadata.R |only ggsem-0.9.6/ggsem/R/save_fig.R | 38 ggsem-0.9.6/ggsem/R/utils_dot.R |only ggsem-0.9.6/ggsem/R/utils_geometry.R |only ggsem-0.9.6/ggsem/R/utils_graph.R |only ggsem-0.9.6/ggsem/R/utils_model.R |only ggsem-0.9.6/ggsem/README.md | 57 ggsem-0.9.6/ggsem/inst/sample_data |only ggsem-0.9.6/ggsem/inst/shiny/app.R |30732 ++++++++++++++++++-- ggsem-0.9.6/ggsem/man/add_group.Rd |only ggsem-0.9.6/ggsem/man/adjust_axis_range.Rd | 16 ggsem-0.9.6/ggsem/man/adjust_axis_space.Rd | 17 ggsem-0.9.6/ggsem/man/csv_to_ggplot.Rd | 147 ggsem-0.9.6/ggsem/man/draw_annotations.Rd | 17 ggsem-0.9.6/ggsem/man/draw_lines.Rd | 22 ggsem-0.9.6/ggsem/man/draw_loops.Rd | 16 ggsem-0.9.6/ggsem/man/draw_points.Rd | 16 ggsem-0.9.6/ggsem/man/figures |only ggsem-0.9.6/ggsem/man/ggsem.Rd | 116 ggsem-0.9.6/ggsem/man/ggsem_builder.Rd |only ggsem-0.9.6/ggsem/man/ggsem_launch.Rd |only ggsem-0.9.6/ggsem/man/ggsem_launch.default.Rd |only ggsem-0.9.6/ggsem/man/ggsem_launch.ggsem_builder.Rd |only ggsem-0.9.6/ggsem/man/ggsem_silent.Rd |only ggsem-0.9.6/ggsem/man/launch.Rd |only ggsem-0.9.6/ggsem/man/metadata_to_ggplot.Rd |only ggsem-0.9.6/ggsem/man/reproduce_network.Rd |only ggsem-0.9.6/ggsem/man/reproduce_sem.Rd |only ggsem-0.9.6/ggsem/man/save_figure.Rd | 28 ggsem-0.9.6/ggsem/man/set_type.Rd |only 49 files changed, 29104 insertions(+), 3472 deletions(-)
Title: Bayesian Variable Selection and Model Averaging using Bayesian
Adaptive Sampling
Description: Package for Bayesian Variable Selection and Model Averaging
in linear models and generalized linear models using stochastic or
deterministic sampling without replacement from posterior
distributions. Prior distributions on coefficients are
from Zellner's g-prior or mixtures of g-priors
corresponding to the Zellner-Siow Cauchy Priors or the
mixture of g-priors from Liang et al (2008)
<DOI:10.1198/016214507000001337>
for linear models or mixtures of g-priors from Li and Clyde
(2019) <DOI:10.1080/01621459.2018.1469992> in generalized linear models.
Other model selection criteria include AIC, BIC and Empirical Bayes
estimates of g. Sampling probabilities may be updated based on the sampled
models using sampling w/out replacement or an efficient MCMC algorithm which
samples models using a tree structure of the model space
as an efficient hash table. See Clyde, Ghosh and Littman (2010)
<DOI:10.1198/jcgs.2010.09049> for details on the sampling algorithms.
Uniform prior [...truncated...]
Author: Merlise Clyde [aut, cre, cph] ,
Michael Littman [ctb],
Joyee Ghosh [ctb],
Yingbo Li [ctb],
Betsy Bersson [ctb],
Don van de Bergh [ctb],
Quanli Wang [ctb]
Maintainer: Merlise Clyde <clyde@duke.edu>
Diff between BAS versions 1.7.5 dated 2024-11-28 and 2.0.0 dated 2025-12-16
BAS-1.7.5/BAS/R/glm_fit.R |only BAS-1.7.5/BAS/inst/CITATION |only BAS-1.7.5/BAS/src/glm_lpy.c |only BAS-1.7.5/BAS/tests/testthat/test-amcmc.R |only BAS-2.0.0/BAS/DESCRIPTION | 9 BAS-2.0.0/BAS/MD5 | 96 ++++---- BAS-2.0.0/BAS/NEWS.md | 32 ++ BAS-2.0.0/BAS/R/FPS-estimators.R |only BAS-2.0.0/BAS/R/bas_glm.R | 172 ++++++++++---- BAS-2.0.0/BAS/R/bas_lm.R | 133 +++++++++-- BAS-2.0.0/BAS/R/bayesglm_fit.R |only BAS-2.0.0/BAS/R/model_priors.R | 10 BAS-2.0.0/BAS/R/predict.R | 8 BAS-2.0.0/BAS/README.md | 12 - BAS-2.0.0/BAS/build/partial.rdb |binary BAS-2.0.0/BAS/build/vignette.rds |binary BAS-2.0.0/BAS/inst/doc/BAS-vignette.html | 185 +++++++-------- BAS-2.0.0/BAS/man/bas.glm.Rd | 40 ++- BAS-2.0.0/BAS/man/bas.lm.Rd | 54 +++- BAS-2.0.0/BAS/man/bayesglm.fit.Rd | 2 BAS-2.0.0/BAS/man/predict.bas.Rd | 8 BAS-2.0.0/BAS/src/Makevars | 3 BAS-2.0.0/BAS/src/bas.h | 76 +++++- BAS-2.0.0/BAS/src/bayesglm.c | 73 +----- BAS-2.0.0/BAS/src/bayesreg.c | 4 BAS-2.0.0/BAS/src/betapriorfamily.c | 29 ++ BAS-2.0.0/BAS/src/family.c | 11 BAS-2.0.0/BAS/src/glm_deterministic.c | 10 BAS-2.0.0/BAS/src/glm_fit.c | 187 ++++++++++++++-- BAS-2.0.0/BAS/src/glm_mcmc.c | 173 ++++++++++++-- BAS-2.0.0/BAS/src/glm_mcmc_grow.c |only BAS-2.0.0/BAS/src/glm_mcmcbas.c | 85 +++---- BAS-2.0.0/BAS/src/glm_sampleworep.c | 136 ++++++++++- BAS-2.0.0/BAS/src/glm_sampleworep_grow.c |only BAS-2.0.0/BAS/src/init.c | 28 +- BAS-2.0.0/BAS/src/lm_amcmc.c | 175 +++++++++++--- BAS-2.0.0/BAS/src/lm_amcmc_growable.c |only BAS-2.0.0/BAS/src/lm_mcmc.c | 161 +++++++++++-- BAS-2.0.0/BAS/src/lm_mcmc_grow.c |only BAS-2.0.0/BAS/src/lm_mcmcbas.c | 137 ++++++----- BAS-2.0.0/BAS/src/lm_sampleworep-grow.c |only BAS-2.0.0/BAS/src/lm_sampleworep.c | 172 +++++++++++--- BAS-2.0.0/BAS/src/model_probabilities.c | 119 +++++++++- BAS-2.0.0/BAS/src/resizeVectors.c |only BAS-2.0.0/BAS/src/tree_structures.c | 68 +++-- BAS-2.0.0/BAS/tests/testthat/Rplots.pdf |binary BAS-2.0.0/BAS/tests/testthat/test-bas-FPS.R |only BAS-2.0.0/BAS/tests/testthat/test-bas-amcmc.R |only BAS-2.0.0/BAS/tests/testthat/test-bas-glm.R | 68 +++++ BAS-2.0.0/BAS/tests/testthat/test-bas-lm.R | 14 - BAS-2.0.0/BAS/tests/testthat/test-bas_glm_growable.R |only BAS-2.0.0/BAS/tests/testthat/test-bas_lm_growable.R |only BAS-2.0.0/BAS/tests/testthat/test-bayesreg.R |only BAS-2.0.0/BAS/tests/testthat/test-family.R | 8 BAS-2.0.0/BAS/tests/testthat/test-glm-fit.R | 48 ++++ BAS-2.0.0/BAS/tests/testthat/test-model_probabilities.R |only BAS-2.0.0/BAS/tests/testthat/test-predict.R | 16 + BAS-2.0.0/BAS/vignettes/Dukelogo.jpg |only BAS-2.0.0/BAS/vignettes/custom.scss |only 59 files changed, 1893 insertions(+), 669 deletions(-)
Title: Immunoglobulin Clonal Lineage and Diversity Analysis
Description: Provides methods for high-throughput adaptive immune
receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In
particular, immunoglobulin (Ig) sequence lineage reconstruction,
lineage topology analysis, diversity profiling, amino acid property
analysis and gene usage.
Citations:
Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>,
Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.
Author: Susanna Marquez [cre, aut],
Namita Gupta [aut],
Nima Nouri [aut],
Ruoyi Jiang [aut],
Julian Zhou [aut],
Kenneth Hoehn [aut],
Daniel Gadala-Maria [ctb],
Edel Aron [ctb],
Cole Jensen [aut],
Gisela Gabernet [ctb],
Caroline Sullivan [ctb],
Hailong Meng [ [...truncated...]
Maintainer: Susanna Marquez <susanna.marquez@yale.edu>
Diff between alakazam versions 1.4.1 dated 2025-10-02 and 1.4.2 dated 2025-12-16
DESCRIPTION | 11 +++++++---- MD5 | 28 ++++++++++++++-------------- NEWS.md | 15 +++++++++++++++ R/Gene.R | 36 +++++++++++++++++++++++++++++------- R/Sequence.R | 2 +- README.md | 1 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/AminoAcids-Vignette.Rmd | 2 +- inst/doc/AminoAcids-Vignette.pdf |binary inst/doc/Diversity-Vignette.pdf |binary inst/doc/Fastq-Vignette.pdf |binary inst/doc/Files-Vignette.pdf |binary inst/doc/GeneUsage-Vignette.pdf |binary vignettes/AminoAcids-Vignette.Rmd | 2 +- 15 files changed, 69 insertions(+), 28 deletions(-)