Title: Variational Bayes for Latent Patient Phenotypes in EHR
Description: Identification of Latent Patient Phenotype from Electronic Health Records (EHR) Data using Variational Bayes Gaussian Mixture Model for Latent Class Analysis and Variational Bayes regression for Biomarker level shifts, both implemented by Coordinate Ascent Variational Inference algorithms. Variational methods are used to enable Bayesian analysis of very large Electronic Health Records data. For VB GMM details see Bishop (2006,ISBN:9780-387-31073-2). For Logistic VB see Jaakkola and Jordan (2000) <doi:10.1023/A:1008932416310>. Please see preprint of JSS-submitted paper <doi:10.48550/arXiv.2512.14272>.
Author: Brian Buckley [aut, cre, cph] ,
Adrian O'Hagan [aut] ,
Marie Galligan [aut]
Maintainer: Brian Buckley <brian.buckley.1@ucdconnect.ie>
Diff between VBphenoR versions 1.0.0 dated 2025-09-15 and 1.1.0 dated 2025-12-17
VBphenoR-1.0.0/VBphenoR/man/examples/plots |only VBphenoR-1.0.0/VBphenoR/man/examples/vb_gmm_example_priors_orig.R |only VBphenoR-1.1.0/VBphenoR/DESCRIPTION | 11 VBphenoR-1.1.0/VBphenoR/MD5 | 30 - VBphenoR-1.1.0/VBphenoR/NEWS.md | 7 VBphenoR-1.1.0/VBphenoR/R/vb_gmm_cavi.R | 40 - VBphenoR-1.1.0/VBphenoR/R/vb_pheno.R | 16 VBphenoR-1.1.0/VBphenoR/README.md | 2 VBphenoR-1.1.0/VBphenoR/man/VBphenoR.Rd | 1 VBphenoR-1.1.0/VBphenoR/man/examples/vb_gmm_example_init.R | 246 +++------ VBphenoR-1.1.0/VBphenoR/man/examples/vb_gmm_example_priors.R | 258 +++++----- VBphenoR-1.1.0/VBphenoR/man/logit_CAVI.Rd | 108 ++-- VBphenoR-1.1.0/VBphenoR/man/run_Model.Rd | 7 VBphenoR-1.1.0/VBphenoR/man/vb_gmm_cavi.Rd | 110 ++-- 14 files changed, 420 insertions(+), 416 deletions(-)
Title: Use 'shiny' to Filter Data
Description: Provides an interface to 'shiny' inputs used for filtering vectors,
data.frames, and other objects. 'S7'-based implementation allows for seamless
extensibility.
Author: Josh Livingston [cre, aut]
Maintainer: Josh Livingston <joshwlivingston@gmail.com>
Diff between shinyfilters versions 0.1.0 dated 2025-12-17 and 0.2.0 dated 2025-12-17
DESCRIPTION | 8 +-- MD5 | 17 ++++--- NAMESPACE | 3 + NEWS.md | 20 +++++++++ R/dataframe.R | 104 ++++++++++++++++++++++++++++++++++++++++++++++++ R/filterInput.R | 12 ++++- R/updateFilterInput.R | 2 README.md | 13 ++++-- man/get_input_ids.Rd |only man/get_input_labels.Rd |only man/get_input_values.Rd |only 11 files changed, 161 insertions(+), 18 deletions(-)
Title: Reversion Mutation Detector for DNA Sequencing Data
Description: Reversion mutations are secondary mutations that reverse the deleterious effects of an original pathogenic mutation, partially or fully restoring the gene's function. The revert package detects reversion mutations for a specific pathogenic mutation from DNA-seq bam files.
Author: Hui Xiao [aut, cre],
Stephen Pettitt [aut],
Syed Haider [aut]
Maintainer: Hui Xiao <hui.xiao@icr.ac.uk>
Diff between revert versions 0.0.1 dated 2023-11-23 and 1.0.0 dated 2025-12-17
revert-0.0.1/revert/R/helpers.R |only revert-0.0.1/revert/inst/doc/Introduction.R |only revert-0.0.1/revert/inst/doc/Introduction.Rmd |only revert-0.0.1/revert/inst/doc/Introduction.html |only revert-0.0.1/revert/inst/extdata/toy_alignments_1.bam |only revert-0.0.1/revert/inst/extdata/toy_alignments_1.bam.bai |only revert-0.0.1/revert/inst/extdata/toy_alignments_2.bam |only revert-0.0.1/revert/inst/extdata/toy_alignments_2.bam.bai |only revert-0.0.1/revert/inst/extdata/toy_alignments_3.bam |only revert-0.0.1/revert/inst/extdata/toy_alignments_3.bam.bai |only revert-0.0.1/revert/vignettes/Introduction.Rmd |only revert-1.0.0/revert/DESCRIPTION | 36 revert-1.0.0/revert/MD5 | 66 revert-1.0.0/revert/NAMESPACE | 38 revert-1.0.0/revert/NEWS | 19 revert-1.0.0/revert/R/adjustIndels.R |only revert-1.0.0/revert/R/alignReadToRef.R |only revert-1.0.0/revert/R/alignSoftClippedRead.R |only revert-1.0.0/revert/R/annoPathogMutToCds.R |only revert-1.0.0/revert/R/callSingleRead.R |only revert-1.0.0/revert/R/cdsToGenome.R |only revert-1.0.0/revert/R/checkExonicSNV.R |only revert-1.0.0/revert/R/checkSpliceAcceptorSNV.R |only revert-1.0.0/revert/R/checkSpliceDonorSNV.R |only revert-1.0.0/revert/R/checkStartCodonSNV.R |only revert-1.0.0/revert/R/checkStopCodonSNV.R |only revert-1.0.0/revert/R/decodeCIGAR.R |only revert-1.0.0/revert/R/encodeCIGAR.R |only revert-1.0.0/revert/R/extractDetectionWindow.R |only revert-1.0.0/revert/R/gapShiftingPairwiseAlignment.R |only revert-1.0.0/revert/R/genomeToCds.R |only revert-1.0.0/revert/R/getCdsAndNoncds.R |only revert-1.0.0/revert/R/getGeneInfo.R |only revert-1.0.0/revert/R/getMutationsDistance.R |only revert-1.0.0/revert/R/getReversions.R | 1353 ++++++-------- revert-1.0.0/revert/R/leftAlignIndel.R |only revert-1.0.0/revert/R/parseCIGAR.R |only revert-1.0.0/revert/R/parseHGVS.R |only revert-1.0.0/revert/R/processPathogMut.R |only revert-1.0.0/revert/R/realignSingleRead.R |only revert-1.0.0/revert/R/scanAlnForRev.R |only revert-1.0.0/revert/R/trimCIGAR.R |only revert-1.0.0/revert/build/vignette.rds |binary revert-1.0.0/revert/inst/doc/help.R |only revert-1.0.0/revert/inst/doc/help.Rmd |only revert-1.0.0/revert/inst/doc/help.html |only revert-1.0.0/revert/inst/extdata/toy_data_1.bam |only revert-1.0.0/revert/inst/extdata/toy_data_1.bam.bai |only revert-1.0.0/revert/inst/extdata/toy_data_2.bam |only revert-1.0.0/revert/inst/extdata/toy_data_2.bam.bai |only revert-1.0.0/revert/inst/extdata/toy_data_3.bam |only revert-1.0.0/revert/inst/extdata/toy_data_3.bam.bai |only revert-1.0.0/revert/inst/extdata/toy_data_4.bam |only revert-1.0.0/revert/inst/extdata/toy_data_4.bam.bai |only revert-1.0.0/revert/inst/extdata/toy_data_5.bam |only revert-1.0.0/revert/inst/extdata/toy_data_5.bam.bai |only revert-1.0.0/revert/inst/extdata/toy_data_6.bam |only revert-1.0.0/revert/inst/extdata/toy_data_6.bam.bai |only revert-1.0.0/revert/inst/extdata/toy_data_6_reference.fa |only revert-1.0.0/revert/man/getReversions.Rd | 179 - revert-1.0.0/revert/vignettes/help.Rmd |only 61 files changed, 793 insertions(+), 898 deletions(-)
Title: Nitrogen Use Efficiency Toolkit on Numerics
Description: A comprehensive toolkit for calculating and visualizing Nitrogen Use Efficiency (NUE) indicators in agricultural research. The package implements 23 parameters categorized into fertilizer-based, plant-based, soil-based, isotope-based, ecology-based, and system-based indicators based on Congreves et al. (2021) <doi:10.3389/fpls.2021.637108>. Key features include vectorized calculations for paired-plot experimental designs, batch processing capabilities for handling large datasets, and built-in visualization tools using 'ggplot2'. Designed to streamline the workflow from raw agronomic data to publication-ready metrics and plots.
Author: Shubham Love [aut, cre]
Maintainer: Shubham Love <shubhamlove2101@gmail.com>
Diff between NUETON versions 0.1.0 dated 2023-11-13 and 0.2.0 dated 2025-12-17
DESCRIPTION | 13 ++--- MD5 | 106 ++++++++++++++++++++++++--------------------- NAMESPACE | 57 ++++++++++++++---------- R/AE.R | 76 ++++++++++++-------------------- R/IE.R | 53 ++++++++-------------- R/NBI.R | 48 ++++++-------------- R/NHI.R | 49 ++++++-------------- R/NP.R | 44 ++++++------------ R/NRE.R | 54 ++++++++-------------- R/NRE15.R | 44 ++++++------------ R/NUEFC.R | 44 ++++++------------ R/NUETON_doc.R |only R/NUEbal.R | 45 ++++++------------- R/NUEcrop.R | 47 ++++++------------- R/NUEsoil.R | 49 ++++++++------------ R/NUEyield.R | 41 ++++++----------- R/NUpE.R | 52 ++++++++-------------- R/NUtE.R | 49 ++++++-------------- R/NdfF.R | 47 ++++++------------- R/PE.R | 71 ++++++++++++------------------ R/PFP.R | 53 +++++++--------------- R/PNB.R | 47 ++++++------------- R/TNdfF.R | 69 +++++++++++------------------ R/VNF.R | 42 ++++++----------- R/calculate_all.R |only R/ecoNUE.R | 40 ++++++---------- R/sNBI.R | 44 +++++++----------- R/sNUE.R | 46 +++++++------------ R/viz_nue.R |only demo |only inst |only man/AE.Rd | 35 ++++---------- man/IE.Rd | 21 ++------ man/NBI.Rd | 24 ++-------- man/NHI.Rd | 18 ++----- man/NP.Rd | 20 ++------ man/NRE.Rd | 29 ++++-------- man/NRE15.Rd | 24 +++------- man/NUEFC.Rd | 22 ++------- man/NUETON-package.Rd |only man/NUEbal.Rd | 24 +++------- man/NUEcrop.Rd | 22 ++------- man/NUEsoil.Rd | 26 +++-------- man/NUEyield.Rd | 25 +++------- man/NUpE.Rd | 25 +++------- man/NUtE.Rd | 19 ++------ man/NdfF.Rd | 18 ++----- man/PE.Rd | 27 +++-------- man/PFP.Rd | 22 ++------- man/PNB.Rd | 24 +++------- man/TNdfF.Rd | 32 +++++-------- man/VNF.Rd | 21 ++------ man/calculate_nue_batch.Rd |only man/ecoNUE.Rd | 24 +++------- man/plot_nue_compare.Rd |only man/sNBI.Rd | 24 +++------- man/sNUE.Rd | 23 ++------- 57 files changed, 694 insertions(+), 1185 deletions(-)
Title: Retention Time Prediction in Liquid Chromatography
Description: A framework for predicting retention times in liquid
chromatography. Users can train custom models for specific
chromatography columns, predict retention times using existing models,
or adjust existing models to account for altered experimental
conditions. The provided functionalities can be accessed either via
the R console or via a graphical user interface. Related work: Bonini
et al. (2020) <doi:10.1021/acs.analchem.9b05765>.
Author: Tobias Schmidt [aut, cre, cph] ,
Christian Amesoeder [aut, cph] ,
Marian Schoen [aut, cph],
Fadi Fadil [ctb, cph] ,
Katja Dettmer [ths, cph] ,
Peter Oefner [ths, cph]
Maintainer: Tobias Schmidt <tobias.schmidt331@gmail.com>
Diff between FastRet versions 1.1.4 dated 2025-02-10 and 1.3.0 dated 2025-12-17
FastRet-1.1.4/FastRet/inst/mockdata |only FastRet-1.1.4/FastRet/man/getCDsFor1Molecule.Rd |only FastRet-1.1.4/FastRet/man/get_cache_dir.Rd |only FastRet-1.1.4/FastRet/man/ram_cache.Rd |only FastRet-1.1.4/FastRet/tests/testthat/Rplots.pdf |only FastRet-1.1.4/FastRet/tests/testthat/test-getCDsFor1Molecule.R |only FastRet-1.3.0/FastRet/DESCRIPTION | 43 FastRet-1.3.0/FastRet/MD5 | 118 FastRet-1.3.0/FastRet/NAMESPACE | 14 FastRet-1.3.0/FastRet/NEWS.md | 423 ++- FastRet-1.3.0/FastRet/R/app.R | 148 - FastRet-1.3.0/FastRet/R/data.R |only FastRet-1.3.0/FastRet/R/getcds.R | 724 +++-- FastRet-1.3.0/FastRet/R/plot.R | 167 - FastRet-1.3.0/FastRet/R/prepro.R | 315 +- FastRet-1.3.0/FastRet/R/server.R | 394 +- FastRet-1.3.0/FastRet/R/sm.R | 156 - FastRet-1.3.0/FastRet/R/train.R | 1391 +++++++--- FastRet-1.3.0/FastRet/R/ui.R | 149 - FastRet-1.3.0/FastRet/R/util.R | 450 +-- FastRet-1.3.0/FastRet/data/RP.rda |binary FastRet-1.3.0/FastRet/inst/WORDLIST | 37 FastRet-1.3.0/FastRet/inst/cachedata/CDs.rds |binary FastRet-1.3.0/FastRet/inst/extdata/Measurements_v8.xlsx |only FastRet-1.3.0/FastRet/man/CDFeatures.Rd | 8 FastRet-1.3.0/FastRet/man/CDNames.Rd | 12 FastRet-1.3.0/FastRet/man/RP.Rd | 25 FastRet-1.3.0/FastRet/man/adjust_frm.Rd | 111 FastRet-1.3.0/FastRet/man/analyzeCDNames.Rd | 15 FastRet-1.3.0/FastRet/man/as_canonical.Rd |only FastRet-1.3.0/FastRet/man/clip_predictions.Rd |only FastRet-1.3.0/FastRet/man/collect.Rd | 9 FastRet-1.3.0/FastRet/man/fastret_app.Rd | 5 FastRet-1.3.0/FastRet/man/getCDs.Rd | 11 FastRet-1.3.0/FastRet/man/get_predictors.Rd | 6 FastRet-1.3.0/FastRet/man/init_log_dir.Rd | 4 FastRet-1.3.0/FastRet/man/now.Rd | 9 FastRet-1.3.0/FastRet/man/plot_frm.Rd |only FastRet-1.3.0/FastRet/man/predict.frm.Rd | 25 FastRet-1.3.0/FastRet/man/preprocess_data.Rd | 56 FastRet-1.3.0/FastRet/man/read_retip_hilic_data.Rd | 43 FastRet-1.3.0/FastRet/man/read_rp_lasso_model_rds.Rd | 2 FastRet-1.3.0/FastRet/man/read_rp_xlsx.Rd | 10 FastRet-1.3.0/FastRet/man/read_rpadj_xlsx.Rd | 9 FastRet-1.3.0/FastRet/man/selective_measuring.Rd | 66 FastRet-1.3.0/FastRet/man/start_gui.Rd | 19 FastRet-1.3.0/FastRet/man/train_frm.Rd | 63 FastRet-1.3.0/FastRet/man/withLineEnd.Rd | 1 FastRet-1.3.0/FastRet/man/withSink.Rd | 1 FastRet-1.3.0/FastRet/man/withStopMessage.Rd | 1 FastRet-1.3.0/FastRet/man/withTimeout.Rd | 12 FastRet-1.3.0/FastRet/tests/testthat/test-adjust_frm.R | 152 - FastRet-1.3.0/FastRet/tests/testthat/test-createFolds.R |only FastRet-1.3.0/FastRet/tests/testthat/test-fit_gbtree.R | 98 FastRet-1.3.0/FastRet/tests/testthat/test-getCDs.R | 42 FastRet-1.3.0/FastRet/tests/testthat/test-get_param_grid.R |only FastRet-1.3.0/FastRet/tests/testthat/test-get_predictors.R |only FastRet-1.3.0/FastRet/tests/testthat/test-nearZeroVar.R |only FastRet-1.3.0/FastRet/tests/testthat/test-parLapply2.R |only FastRet-1.3.0/FastRet/tests/testthat/test-plot_frm.R | 15 FastRet-1.3.0/FastRet/tests/testthat/test-predict_frm-iat.R |only FastRet-1.3.0/FastRet/tests/testthat/test-predict_frm.R |only FastRet-1.3.0/FastRet/tests/testthat/test-preprocess_data.R | 71 FastRet-1.3.0/FastRet/tests/testthat/test-selective_measuring.R | 9 FastRet-1.3.0/FastRet/tests/testthat/test-train_frm-gbtree.R | 16 FastRet-1.3.0/FastRet/tests/testthat/test-train_frm-lasso.R | 35 FastRet-1.3.0/FastRet/tests/testthat/test-validate_inputdata.R |only 67 files changed, 3939 insertions(+), 1551 deletions(-)
Title: Power Calculation for Two-Way Factorial Designs
Description: The basic use of this package is with 3 sequential functions. First to generate a cell mean matrix. In case of a repeated measurements design also generate correlation and covariance matrices. This is followed by iterative experiment simulation. Finally, power is calculated from the simulated data. Features that may be considered in the model are interaction, measure correlation, non-normal and unbalanced designs distributions.
Author: Louis Macias [aut, cre, cph] ,
Silke Szymczak [aut]
Maintainer: Louis Macias <luisrmacias@gmail.com>
Diff between extraSuperpower versions 1.6.1 dated 2025-11-13 and 1.6.2 dated 2025-12-17
DESCRIPTION | 12 MD5 | 50 NAMESPACE | 68 - NEWS.md | 82 - R/data_summary_fplotting.R | 86 - README.md | 48 build/vignette.rds |binary inst/doc/eSp_balanced_design_powertest.R | 230 +-- inst/doc/eSp_balanced_design_powertest.html | 1645 +++++++++++++------------- man/calculate_mean_matrix.Rd | 270 ++-- man/effsize.Rd | 102 - man/exact_twoway_anova_power.Rd | 164 +- man/gencorrelationmat.Rd | 110 - man/gencovariancemat.Rd | 110 - man/graph_twoway_assumptions.Rd | 40 man/plot_powercurves.Rd | 126 - man/simulate_twoway_nrange.Rd | 186 +- man/test_power_overkn.Rd | 140 +- man/twoway_simulation_correlated.Rd | 166 +- man/twoway_simulation_independent.Rd | 138 +- man/twoway_simulation_testing.Rd | 126 - tests/testthat.R | 24 tests/testthat/test-data_summary_fplotting.R | 48 tests/testthat/test-effect_size_calculation.R | 194 +-- tests/testthat/test-gencovmat.R | 770 ++++++------ tests/testthat/test-graph_modelled_means_sd.R | 24 26 files changed, 2482 insertions(+), 2477 deletions(-)
More information about extraSuperpower at CRAN
Permanent link
Title: Approximate Bayesian Computation via Random Forests
Description: Performs Approximate Bayesian Computation (ABC) model choice and parameter inference via random forests.
Pudlo P., Marin J.-M., Estoup A., Cornuet J.-M., Gautier M. and Robert C. P. (2016) <doi:10.1093/bioinformatics/btv684>.
Raynal L., Marin J.-M., Pudlo P., Ribatet M., Robert C. P. and Estoup A. (2019) <doi:10.1093/bioinformatics/bty867>.
Author: Jean-Michel Marin [aut, cre],
Louis Raynal [aut],
Pierre Pudlo [aut],
Christian P. Robert [ctb],
Arnaud Estoup [ctb]
Maintainer: Jean-Michel Marin <jean-michel.marin@umontpellier.fr>
This is a re-admission after prior archival of version 1.9 dated 2022-08-09
Diff between abcrf versions 1.9 dated 2022-08-09 and 2.0 dated 2025-12-17
DESCRIPTION | 23 +++++++++------ MD5 | 29 ++++++++++--------- NAMESPACE | 1 README.md |only build/partial.rdb |binary man/abcrf.Rd | 7 ++-- man/covRegAbcrf.Rd | 8 ++--- man/densityPlot.Rd | 4 +- man/err.abcrf.Rd | 2 - man/err.regAbcrf.Rd | 4 +- man/plot.regAbcrf.Rd | 6 ++-- man/predict.abcrf.Rd | 6 ++-- man/predict.regAbcrf.Rd | 6 ++-- man/predictOOB.Rd | 6 ++-- man/regAbcrf.Rd | 6 ++-- man/variableImpPlot.Rd | 70 ++++++++++++++++++++++++------------------------ 16 files changed, 92 insertions(+), 86 deletions(-)
Title: eXtreme RuleFit
Description: An implementation of the RuleFit algorithm as described in
Friedman & Popescu (2008) <doi:10.1214/07-AOAS148>. eXtreme Gradient
Boosting ('XGBoost') is used to build rules, and 'glmnet' is used to
fit a sparse linear model on the raw and rule features. The result is
a model that learns similarly to a tree ensemble, while often offering
improved interpretability and achieving improved scoring runtime in
live applications. Several algorithms for reducing rule complexity are
provided, most notably hyperrectangle de-overlapping. All algorithms
scale to several million rows and support sparse representations to
handle tens of thousands of dimensions.
Author: Karl Holub [aut, cre]
Maintainer: Karl Holub <karljholub@gmail.com>
Diff between xrf versions 0.3.0 dated 2025-12-04 and 0.3.1 dated 2025-12-17
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 1 - R/hyperrectangle_overlap.R | 21 ++++++++------------- tests/testthat/test_deoverlap.R | 2 +- 5 files changed, 18 insertions(+), 24 deletions(-)
Title: Computation and Plots of Influence Functions for Risk and
Performance Measures
Description: Computes the influence functions time series of the returns for the risk and
performance measures as mentioned in Chen and Martin (2018)
<https://www.ssrn.com/abstract=3085672>, as well as in Zhang et al. (2019)
<https://www.ssrn.com/abstract=3415903>. Also evaluates estimators influence
functions at a set of parameter values and plots them to display the shapes of
the influence functions.
Author: Anthony Christidis [aut, cre],
Shengyu Zhang [aut],
Douglas Martin [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
This is a re-admission after prior archival of version 1.2.4 dated 2021-10-14
Diff between RPEIF versions 1.2.4 dated 2021-10-14 and 1.2.5 dated 2025-12-17
DESCRIPTION | 31 +++++++++++++++------ MD5 | 70 ++++++++++++++++++++++++------------------------ NEWS.md | 4 ++ R/IF_DSR.R | 32 ++++++++++++--------- R/IF_ES.R | 32 ++++++++++++--------- R/IF_ESRatio.R | 32 ++++++++++++--------- R/IF_LPM.R | 32 ++++++++++++--------- R/IF_Mean.R | 34 +++++++++++++---------- R/IF_OmegaRatio.R | 32 ++++++++++++--------- R/IF_RachevRatio.R | 32 ++++++++++++--------- R/IF_SD.R | 33 ++++++++++++---------- R/IF_SR.R | 32 ++++++++++++--------- R/IF_SemiSD.R | 32 ++++++++++++--------- R/IF_SoR.R | 34 +++++++++++++---------- R/IF_VaR.R | 32 ++++++++++++--------- R/IF_VaRratio.R | 32 ++++++++++++--------- R/IF_robMean.R | 41 +++++++++++++++------------- R/InfluenceFunctions.R | 36 +++++++++++++----------- R/Nuisance_Parameters.R | 1 README.md | 5 ++- build/vignette.rds |binary man/IF.DSR.Rd | 32 ++++++++++++--------- man/IF.ES.Rd | 32 ++++++++++++--------- man/IF.ESratio.Rd | 32 ++++++++++++--------- man/IF.LPM.Rd | 32 ++++++++++++--------- man/IF.Mean.Rd | 34 +++++++++++++---------- man/IF.OmegaRatio.Rd | 32 ++++++++++++--------- man/IF.RachevRatio.Rd | 32 ++++++++++++--------- man/IF.Rd | 36 +++++++++++++----------- man/IF.SD.Rd | 33 ++++++++++++---------- man/IF.SR.Rd | 32 ++++++++++++--------- man/IF.SemiSD.Rd | 32 ++++++++++++--------- man/IF.SoR.Rd | 32 ++++++++++++--------- man/IF.VaR.Rd | 32 ++++++++++++--------- man/IF.VaRratio.Rd | 32 ++++++++++++--------- man/IF.robMean.Rd | 41 +++++++++++++++------------- 36 files changed, 619 insertions(+), 486 deletions(-)
Title: Robust Bayesian Meta-Analyses
Description: A framework for estimating ensembles of meta-analytic, meta-regression, and
multilevel models (assuming either presence or absence of the effect, heterogeneity,
publication bias, and moderators). The RoBMA framework uses Bayesian model-averaging to
combine the competing meta-analytic models into a model ensemble, weights
the posterior parameter distributions based on posterior model probabilities
and uses Bayes factors to test for the presence or absence of the
individual components (e.g., effect vs. no effect; Bartoš et al., 2022,
<doi:10.1002/jrsm.1594>; Maier, Bartoš & Wagenmakers, 2022,
<doi:10.1037/met0000405>; Bartoš et al., 2025, <doi:10.1037/met0000737>).
Users can define a wide range of prior distributions for the effect size, heterogeneity,
publication bias (including selection models and PET-PEESE), and moderator components.
The package provides convenient functions for summary, visualizations, and fit diagnostics.
Author: Frantisek Bartos [aut, cre] ,
Maximilian Maier [aut] ,
Eric-Jan Wagenmakers [ths] ,
Joris Goosen [ctb],
Matthew Denwood [cph] ,
Martyn Plummer [cph]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between RoBMA versions 3.6.0 dated 2025-09-10 and 3.6.1 dated 2025-12-17
DESCRIPTION | 6 MD5 | 109 ++++++------ NEWS.md | 7 R/datasets.R | 35 +++ R/plots.R | 4 R/summary.R | 84 ++++++++- R/utilities.R | 1 R/zcurve.R | 288 ++++++++++++++++++++++++-------- README.md | 21 +- build/partial.rdb |binary build/vignette.rds |binary data/Havrankova2025.RData |only data/Johnides2025.RData |only inst/REFERENCES.bib | 49 +++++ inst/doc/CustomEnsembles.html | 14 - inst/doc/Explanation.Rmd |only inst/doc/Explanation.html |only inst/doc/FastRoBMA.html | 4 inst/doc/HierarchicalBMA.html | 4 inst/doc/MedicineBMA.html | 14 - inst/doc/MedicineBiBMA.html | 4 inst/doc/MetaRegression.html | 4 inst/doc/MultilevelRoBMA.R |only inst/doc/MultilevelRoBMA.Rmd |only inst/doc/MultilevelRoBMA.html |only inst/doc/MultilevelRoBMARegression.R |only inst/doc/MultilevelRoBMARegression.Rmd |only inst/doc/MultilevelRoBMARegression.html |only inst/doc/ReproducingBMA.html | 14 - inst/doc/Tutorial.html | 10 - inst/doc/ZCurveDiagnostics.Rmd | 2 inst/doc/ZCurveDiagnostics.html | 79 ++++---- man/Havrankova2025.Rd |only man/Hoppen2025.Rd | 54 +++--- man/Johnides2025.Rd |only man/ManyLabs16.Rd | 54 +++--- man/RoBMA-package.Rd | 84 ++++----- man/RoBMA_options.Rd | 54 +++--- man/Wang2025.Rd | 56 +++--- man/Weingarten2018.Rd | 60 +++--- man/effect_sizes.Rd | 186 ++++++++++---------- man/forest.Rd | 144 ++++++++-------- man/hist.zcurve_RoBMA.Rd | 104 ++++++----- man/interpret.Rd | 42 ++-- man/lines.zcurve_RoBMA.Rd | 136 +++++++-------- man/plot.RoBMA.Rd | 218 ++++++++++++------------ man/plot.zcurve_RoBMA.Rd | 28 +++ man/plot_models.Rd | 164 +++++++++--------- man/print.RoBMA.Rd | 44 ++-- man/print.summary.RoBMA.Rd | 44 ++-- man/prior.Rd | 170 +++++++++--------- man/prior_PEESE.Rd | 156 ++++++++--------- man/prior_PET.Rd | 156 ++++++++--------- man/prior_none.Rd | 80 ++++---- man/prior_weightfunction.Rd | 124 ++++++------- man/sample_sizes.Rd | 120 ++++++------- man/set_default_priors.Rd | 150 ++++++++-------- man/standard_errors.Rd | 190 ++++++++++----------- man/weighted_multivariate_normal.Rd | 72 ++++---- vignettes/Explanation.Rmd |only vignettes/MultilevelRoBMA.Rmd |only vignettes/MultilevelRoBMARegression.Rmd |only vignettes/ZCurveDiagnostics.Rmd | 2 63 files changed, 1917 insertions(+), 1528 deletions(-)
Title: Observational Health Data Sciences and Informatics Report
Generator
Description: Extract results into R from the Observational Health Data Sciences and Informatics result database (see <https://ohdsi.github.io/Strategus/results-schema/index.html>) and generate reports/presentations via 'quarto' that summarize results in HTML format. Learn more about 'OhdsiReportGenerator' at <https://ohdsi.github.io/OhdsiReportGenerator/>.
Author: Jenna Reps [aut, cre],
Anthony Sena [aut]
Maintainer: Jenna Reps <jreps@its.jnj.com>
Diff between OhdsiReportGenerator versions 1.1.1 dated 2025-05-22 and 2.0.2 dated 2025-12-17
OhdsiReportGenerator-1.1.1/OhdsiReportGenerator/inst/templates/full-report/characterization/demographicsold.qmd |only OhdsiReportGenerator-1.1.1/OhdsiReportGenerator/man/getTargetCounts.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/DESCRIPTION | 14 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/MD5 | 212 - OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/NAMESPACE | 38 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/R/Backwards.R | 2 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/R/CharacterzationQueries.R | 1706 +++++++++- OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/R/CohortQueries.R | 385 ++ OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/R/Database.R |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/R/EstimationQueries.R | 1359 +++++++ OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/R/Generate.R | 18 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/R/Helpers.R | 29 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/R/OhdsiReportGenerator.R | 1 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/R/PredictionQueries.R | 1263 ++++++- OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/R/PredictionReport.R | 32 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/R/SummaryReports.R |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/R/TargetOutcomeInfo.R |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/inst/doc/ExampleCode.R | 6 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/inst/doc/ExampleCode.Rmd | 6 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/inst/doc/ExampleCode.html | 578 ++- OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/inst/exampledata/results.sqlite.zip |binary OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/inst/templates/full-report/causal_inference.qmd | 17 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/inst/templates/full-report/characterization.qmd | 35 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/inst/templates/full-report/characterization/demographics.qmd | 6 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/inst/templates/full-report/characterization/index_breakdown.qmd | 29 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/inst/templates/full-report/characterization/risk_factors.qmd | 34 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/inst/templates/full-report/cohort_incidence.qmd | 11 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/inst/templates/full-report/definitions.qmd | 37 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/inst/templates/full-report/main_template.qmd | 336 + OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/inst/templates/full-report/prediction.qmd | 8 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/inst/templates/patient-level-prediction-document/main.Rmd | 7 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/inst/templates/patient-level-prediction-document/model-design.Rmd | 144 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/inst/templates/patient-level-prediction-document/plp-outcome.Rmd | 2 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/inst/templates/patient-level-prediction-document/plp-participants.Rmd | 18 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/inst/templates/presentation/assure_presentation.qmd | 3 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/inst/templates/summary-templates |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/addTarColumn.Rd | 2 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/createPredictionReport.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/formatBinaryCovariateName.Rd | 2 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/generateFullReport.Rd | 8 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/generatePresentation.Rd | 6 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/generatePresentationMultiple.Rd | 4 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/generateSummaryPredictionReport.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getBinaryCaseSeries.Rd | 33 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getBinaryRiskFactors.Rd | 27 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCMEstimation.Rd | 14 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCaseBinaryFeatures.Rd | 30 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCaseContinuousFeatures.Rd | 28 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCaseCounts.Rd | 28 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCaseTargetBinaryFeatures.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCaseTargetCounts.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCharacterizationCohortBinary.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCharacterizationCohortContinuous.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCharacterizationDemographics.Rd | 11 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCharacterizationOutcomes.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCharacterizationTargets.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCmDiagnosticsData.Rd | 20 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCmMetaEstimation.Rd | 17 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCmNegativeControlEstimates.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCmOutcomes.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCmPropensityModel.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCmTable.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCmTargets.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCohortCounts.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCohortDefinitions.Rd | 5 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCohortInclusionRules.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCohortInclusionStats.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCohortInclusionSummary.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCohortMeta.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getCohortSubsetDefinitions.Rd | 5 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getContinuousCaseSeries.Rd | 27 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getContinuousRiskFactors.Rd | 27 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getDatabaseDetails.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getDechallengeRechallenge.Rd | 11 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getDechallengeRechallengeFails.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getExampleConnectionDetails.Rd | 2 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getFullPredictionPerformances.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getIncidenceOutcomes.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getIncidenceRates.Rd | 12 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getIncidenceTargets.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getOutcomeTable.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getPredictionAggregateTopPredictors.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getPredictionCohorts.Rd | 6 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getPredictionCovariates.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getPredictionDiagnosticTable.Rd | 6 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getPredictionDiagnostics.Rd | 13 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getPredictionHyperParamSearch.Rd | 6 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getPredictionIntercept.Rd | 6 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getPredictionLift.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getPredictionModelDesigns.Rd | 25 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getPredictionOutcomes.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getPredictionPerformanceTable.Rd | 21 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getPredictionPerformances.Rd | 7 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getPredictionTargets.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getPredictionTopPredictors.Rd | 11 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getSccsDiagnosticsData.Rd | 30 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getSccsEstimation.Rd | 15 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getSccsMetaEstimation.Rd | 16 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getSccsModel.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getSccsNegativeControlEstimates.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getSccsOutcomes.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getSccsTable.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getSccsTargets.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getSccsTimeToEvent.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getTargetBinaryFeatures.Rd | 44 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getTargetContinuousFeatures.Rd | 16 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getTargetTable.Rd |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/getTimeToEvent.Rd | 11 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/kableDark.Rd | 2 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/plotAgeDistributions.Rd | 10 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/plotCmEstimates.Rd | 11 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/plotSccsEstimates.Rd | 11 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/plotSexDistributions.Rd | 10 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/printReactable.Rd | 2 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/processCohorts.Rd | 5 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/man/removeSpaces.Rd | 2 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/tests/testthat/test-Backwards.R | 2 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/tests/testthat/test-CharacterizationQueries.R | 162 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/tests/testthat/test-CohortQueries.R | 85 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/tests/testthat/test-Database.R |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/tests/testthat/test-EstimationQueries.R | 389 ++ OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/tests/testthat/test-Generate.R | 8 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/tests/testthat/test-PredictionQueries.R | 161 OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/tests/testthat/test-TargetOutcomeInfo.R |only OhdsiReportGenerator-2.0.2/OhdsiReportGenerator/vignettes/ExampleCode.Rmd | 6 125 files changed, 6845 insertions(+), 909 deletions(-)
More information about OhdsiReportGenerator at CRAN
Permanent link
Title: Regularized PQL for Joint Selection in GLMMs
Description: Performs joint selection in Generalized Linear Mixed Models (GLMMs) using penalized likelihood methods. Specifically, the Penalized Quasi-Likelihood (PQL) is used as a loss function, and penalties are then augmented to perform simultaneous fixed and random effects selection. Regularized PQL avoids the need for integration (or approximations such as the Laplace's method) during the estimation process, and so the full solution path for model selection can be constructed relatively quickly.
Author: Francis K.C. Hui [aut, cre]
Maintainer: Francis K.C. Hui <fhui28@gmail.com>
Diff between rpql versions 0.8.2 dated 2025-07-26 and 0.8.3 dated 2025-12-17
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- build/partial.rdb |binary src/Makevars | 1 - src/Makevars.win | 1 - 5 files changed, 9 insertions(+), 11 deletions(-)
Title: A Cepstral Model for Covariate-Dependent Time Series
Description: Modeling associations between covariates and power spectra of replicated time series using a cepstral-based semiparametric framework. Implements a fast two-stage estimation procedure via Whittle likelihood and multivariate regression.The methodology is based on Li and Dong (2025) <doi:10.1080/10618600.2025.2473936>.
Author: Qi Xia [aut, cre],
Zeda Li [aut, ctb]
Maintainer: Qi Xia <xiaqi1010@gmail.com>
Diff between CepReg versions 0.1.2 dated 2025-09-19 and 0.1.3 dated 2025-12-17
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 1 - R/cepstral.R | 40 ++++++++++++++++++++++------------------ man/CepReg.Rd | 2 +- man/boot_effect.Rd | 6 +++--- man/rrr_get.Rd | 2 -- 7 files changed, 36 insertions(+), 35 deletions(-)
Title: Spatial Analysis with Misaligned Data Using Atom-Based
Regression Models
Description: Implements atom-based regression models (ABRM) for analyzing spatially
misaligned data. Provides functions for simulating misaligned spatial data,
preparing NIMBLE model inputs, running MCMC diagnostics, and comparing different
spatial analysis methods including dasymetric mapping. All main functions return
S3 objects with print(), summary(), and plot() methods for intuitive result exploration.
Methods are described in Nethery et al. (2023) <doi:10.1101/2023.01.10.23284410>.
Further methodological details and software implementation are described in Qian et al. (in review).
Author: Yunzhe Qian [aut, cre],
Rachel Nethery [aut],
Nancy Krieger [ctb] ,
Nykesha Johnson [ctb]
Maintainer: Yunzhe Qian <qyzanemos@gmail.com>
Diff between spatialAtomizeR versions 0.2.3 dated 2025-12-10 and 0.2.4 dated 2025-12-17
DESCRIPTION | 12 +- MD5 | 17 +-- NAMESPACE | 8 - R/nimble_model.R | 181 +++++++++++++++++++---------------- R/simulation.R | 22 +++- README.md | 2 inst/doc/getting-started.html | 4 man/Rmfnchypg_rcall.Rd |only man/dmfnchypg.Rd |only man/register_nimble_distributions.Rd | 9 - man/rmfnchypg.Rd |only 11 files changed, 145 insertions(+), 110 deletions(-)
More information about spatialAtomizeR at CRAN
Permanent link
Title: Robust Multi-Model Subset Selection
Description: Efficient algorithms for generating ensembles of robust, sparse and diverse models via robust
multi-model subset selection (RMSS). The robust ensembles are generated by minimizing the sum of
the least trimmed square loss of the models in the ensembles under constraints for the size of
the models and the sharing of the predictors. Tuning parameters for the robustness, sparsity and
diversity of the robust ensemble are selected by cross-validation.
Author: Anthony Christidis [aut, cre],
Gabriela Cohen-Freue [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between RMSS versions 1.2.2 dated 2025-09-23 and 1.2.3 dated 2025-12-17
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 5 ++++- src/Makevars.in | 2 +- src/Makevars.win | 2 +- 5 files changed, 14 insertions(+), 11 deletions(-)
Title: Greedy Set Cover
Description: A fast implementation of the greedy algorithm for the set cover problem using 'Rcpp'.
Author: Matthias Kaeding [aut, cre]
Maintainer: Matthias Kaeding <matthiaskaeding@posteo.de>
Diff between RcppGreedySetCover versions 0.1.0 dated 2018-01-24 and 0.1.1 dated 2025-12-17
DESCRIPTION | 17 ++-- LICENSE | 2 MD5 | 26 +++--- NAMESPACE | 10 +- NEWS.md | 14 +-- R/RcppExports.R | 14 +-- R/RcppGreedySetCover.R | 60 +++++++-------- R/greedySetCover.R | 148 +++++++++++++++++++------------------- README.md | 121 +++++++++++++++---------------- man/RcppGreedySetCover-package.Rd | 84 ++++++++++++--------- man/greedySetCover.Rd | 88 +++++++++++----------- src/RcppExports.cpp | 5 + src/set_cover0.cpp | 4 - tests |only 14 files changed, 305 insertions(+), 288 deletions(-)
More information about RcppGreedySetCover at CRAN
Permanent link
Title: Estimation of the Probability of Informed Trading
Description: A comprehensive bundle of utilities for the estimation of probability of informed trading models: original PIN in Easley and O'Hara (1992) and Easley et al. (1996); Multilayer PIN (MPIN) in Ersan (2016); Adjusted PIN (AdjPIN) in Duarte and Young (2009); and volume-synchronized PIN (VPIN) in Easley et al. (2011, 2012). Implementations of various estimation methods suggested in the literature are included. Additional compelling features comprise posterior probabilities, an implementation of an expectation-maximization (EM) algorithm, and PIN decomposition into layers, and into bad/good components. Versatile data simulation tools, and trade classification algorithms are among the supplementary utilities. The package provides fast, compact, and precise utilities to tackle the sophisticated, error-prone, and time-consuming estimation procedure of informed trading, and this solely using the raw trade-level data.
Author: Montasser Ghachem [aut, cre, cph] ,
Oguz Ersan [aut] ,
Alexandre Borentain [ctb]
Maintainer: Montasser Ghachem <montasser.ghachem@pinstimation.com>
Diff between PINstimation versions 0.1.2 dated 2023-03-20 and 0.2.0 dated 2025-12-17
PINstimation-0.1.2/PINstimation/man/vpin.Rd |only PINstimation-0.1.2/PINstimation/vignettes/file1bd06dfe606.html |only PINstimation-0.1.2/PINstimation/vignettes/file43fc2afa55e6.html |only PINstimation-0.1.2/PINstimation/vignettes/file45bc54564746.html |only PINstimation-0.1.2/PINstimation/vignettes/file45bc7db6775.html |only PINstimation-0.1.2/PINstimation/vignettes/file65943770f92.html |only PINstimation-0.1.2/PINstimation/vignettes/file659462e7f54.html |only PINstimation-0.2.0/PINstimation/DESCRIPTION | 42 PINstimation-0.2.0/PINstimation/MD5 | 124 PINstimation-0.2.0/PINstimation/NAMESPACE | 8 PINstimation-0.2.0/PINstimation/NEWS.md | 115 PINstimation-0.2.0/PINstimation/R/PINstimation-package.R |only PINstimation-0.2.0/PINstimation/R/PINstimation.R | 10 PINstimation-0.2.0/PINstimation/R/args_defaultvalues.R | 4 PINstimation-0.2.0/PINstimation/R/args_validation.R | 2 PINstimation-0.2.0/PINstimation/R/data_aggregation.R | 230 + PINstimation-0.2.0/PINstimation/R/data_simulation.R | 6 PINstimation-0.2.0/PINstimation/R/model_adjpin.R | 420 +- PINstimation-0.2.0/PINstimation/R/model_factorizations.R | 54 PINstimation-0.2.0/PINstimation/R/model_mpin.R | 4 PINstimation-0.2.0/PINstimation/R/model_mpin.ecm.R | 15 PINstimation-0.2.0/PINstimation/R/model_mpin.layers.R | 6 PINstimation-0.2.0/PINstimation/R/model_pin.R | 12 PINstimation-0.2.0/PINstimation/R/model_vpin.R | 1593 +++++++--- PINstimation-0.2.0/PINstimation/R/output_classes.R | 16 PINstimation-0.2.0/PINstimation/R/utilities_functions.R | 2 PINstimation-0.2.0/PINstimation/R/utilities_messages.R | 46 PINstimation-0.2.0/PINstimation/R/zzz.R | 17 PINstimation-0.2.0/PINstimation/README.md | 47 PINstimation-0.2.0/PINstimation/build/partial.rdb |binary PINstimation-0.2.0/PINstimation/build/vignette.rds |binary PINstimation-0.2.0/PINstimation/inst/REFERENCES.bib | 58 PINstimation-0.2.0/PINstimation/inst/doc/PINstimation.R | 15 PINstimation-0.2.0/PINstimation/inst/doc/PINstimation.html | 125 PINstimation-0.2.0/PINstimation/inst/doc/PINstimation.rmd | 89 PINstimation-0.2.0/PINstimation/inst/doc/parallel_processing.R | 7 PINstimation-0.2.0/PINstimation/inst/doc/parallel_processing.html | 45 PINstimation-0.2.0/PINstimation/inst/doc/parallel_processing.rmd | 19 PINstimation-0.2.0/PINstimation/inst/doc/sample_datasets.R | 4 PINstimation-0.2.0/PINstimation/inst/doc/sample_datasets.html | 168 - PINstimation-0.2.0/PINstimation/inst/doc/sample_datasets.rmd | 19 PINstimation-0.2.0/PINstimation/man/PINstimation-package.Rd | 44 PINstimation-0.2.0/PINstimation/man/adjpin.Rd | 2 PINstimation-0.2.0/PINstimation/man/estimate.vpin-class.Rd | 8 PINstimation-0.2.0/PINstimation/man/generatedata_mpin.Rd | 4 PINstimation-0.2.0/PINstimation/man/mpin_ecm.Rd | 2 PINstimation-0.2.0/PINstimation/man/mpin_ml.Rd | 2 PINstimation-0.2.0/PINstimation/man/pin.Rd | 2 PINstimation-0.2.0/PINstimation/man/pin_bayes.Rd | 2 PINstimation-0.2.0/PINstimation/man/pin_ea.Rd | 2 PINstimation-0.2.0/PINstimation/man/pin_gwj.Rd | 2 PINstimation-0.2.0/PINstimation/man/pin_yz.Rd | 2 PINstimation-0.2.0/PINstimation/man/trade_classification.Rd | 109 PINstimation-0.2.0/PINstimation/man/vpin_measures.Rd |only PINstimation-0.2.0/PINstimation/vignettes/PINstimation.rmd | 89 PINstimation-0.2.0/PINstimation/vignettes/file27c476425c2e.html |only PINstimation-0.2.0/PINstimation/vignettes/file27c4e8e731e.html |only PINstimation-0.2.0/PINstimation/vignettes/file2d684b8d2c9d.html |only PINstimation-0.2.0/PINstimation/vignettes/file2e90fba75a7.html |only PINstimation-0.2.0/PINstimation/vignettes/file5a9cbcd5a28.html |only PINstimation-0.2.0/PINstimation/vignettes/file6428180e76.html |only PINstimation-0.2.0/PINstimation/vignettes/file66a865435686.html |only PINstimation-0.2.0/PINstimation/vignettes/file6b704bf2e34.html |only PINstimation-0.2.0/PINstimation/vignettes/file6cd437287c94.html |only PINstimation-0.2.0/PINstimation/vignettes/file7b1021084bf9.html |only PINstimation-0.2.0/PINstimation/vignettes/file7b102f7be8a.html |only PINstimation-0.2.0/PINstimation/vignettes/file7b1077904f42.html |only PINstimation-0.2.0/PINstimation/vignettes/file7d14205f13e3.html |only PINstimation-0.2.0/PINstimation/vignettes/file7d14269d528.html |only PINstimation-0.2.0/PINstimation/vignettes/file7d145f274ac.html |only PINstimation-0.2.0/PINstimation/vignettes/file7d146e137ff.html |only PINstimation-0.2.0/PINstimation/vignettes/file7ff02f331c1e.html |only PINstimation-0.2.0/PINstimation/vignettes/file7ff0749b884.html |only PINstimation-0.2.0/PINstimation/vignettes/file9e7c2e3f161.html |only PINstimation-0.2.0/PINstimation/vignettes/images |only PINstimation-0.2.0/PINstimation/vignettes/parallel_processing.rmd | 19 PINstimation-0.2.0/PINstimation/vignettes/sample_datasets.rmd | 19 77 files changed, 2416 insertions(+), 1214 deletions(-)
Title: Climate Tools (Series Homogenization and Derived Products)
Description: Functions for the quality control, homogenization and missing data filling of climatological series and to obtain climatological summaries and grids from the results. Also functions to display wind-roses, meteograms, Walter&Lieth diagrams, and more.
Author: Jose A. Guijarro [aut, cre]
Maintainer: Jose A. Guijarro <jaguijarro21@gmail.com>
Diff between climatol versions 4.3-0 dated 2025-10-12 and 4.4-0 dated 2025-12-17
DESCRIPTION | 8 +- MD5 | 12 +-- NEWS | 10 ++ R/clihomog.R | 160 ++++++++++++++++++++++++++++------------------- man/datrestore.Rd | 8 +- man/rclimdex2climatol.Rd | 6 - man/weekendaccum.Rd | 38 +++++++---- 7 files changed, 148 insertions(+), 94 deletions(-)
Title: Network Analysis and Causal Inference Through Structural
Equation Modeling
Description: Estimate networks and causal relationships in complex systems through
Structural Equation Modeling. This package also includes functions for importing,
weight, manipulate, and fit biological network models within the
Structural Equation Modeling framework as outlined in the Supplementary Material of
Grassi M, Palluzzi F, Tarantino B (2022) <doi:10.1093/bioinformatics/btac567>.
Author: Mario Grassi [aut],
Fernando Palluzzi [aut],
Barbara Tarantino [cre]
Maintainer: Barbara Tarantino <barbara.tarantino01@universitadipavia.it>
Diff between SEMgraph versions 1.2.3 dated 2025-01-29 and 1.2.4 dated 2025-12-17
DESCRIPTION | 14 - MD5 | 75 +++++--- NAMESPACE | 1 NEWS.md | 86 +++++---- R/keggInteractome.R | 103 ++++++----- R/keggPathways.R | 26 +- R/semCluster.R | 4 R/semFit.R | 20 +- R/semLearn.R | 61 ++++-- R/semTools.R | 410 ++++++++++++++++++++++++++++++++++++++++++++++- R/semUtils.R | 410 ++++++++--------------------------------------- README.md | 88 ++++------ build/partial.rdb |binary build/vignette.rds |only data/ALSdata.RData |binary data/kegg.RData |binary data/kegg.pathways.RData |binary data/sachs.RData |binary inst |only man/SEMbap.Rd | 9 - man/SEMdag.Rd | 4 man/SEMdci.Rd | 41 ++-- man/SEMgsa.Rd | 22 +- man/SEMtree.Rd | 8 man/kegg.Rd | 21 +- man/kegg.pathways.Rd | 22 +- man/loadPathways.Rd |only man/modelSearch.Rd | 8 man/orientEdges.Rd | 2 man/properties.Rd | 4 man/resizeGraph.Rd | 9 - vignettes |only 32 files changed, 829 insertions(+), 619 deletions(-)
Title: Win Time Methods for Time-to-Event Data in Clinical Trials
Description: Performs an analysis of time-to-event clinical trial data using various "win time" methods,
including 'ewt', 'ewtr', 'rmt', 'ewtp', 'rewtp', 'ewtpr', 'rewtpr', 'max', 'wtr', 'rwtr', 'pwt', and 'rpwt'. These methods are used to calculate and compare
treatment effects on ordered composite endpoints. The package handles event times, event indicators, and treatment
arm indicators and supports calculations on observed and resampled data. Detailed explanations of each method and
usage examples are provided in "Use of win time for ordered composite endpoints in clinical trials," by Troendle et al.
(2024)<https://pubmed.ncbi.nlm.nih.gov/38417455/>. For more information, see the package documentation or the vignette titled "Introduction to wintime."
Author: James Troendle [aut, cre],
Samuel Lawrence [aut]
Maintainer: James Troendle <james.troendle@nih.gov>
Diff between wintime versions 0.4.1 dated 2025-08-28 and 0.4.2 dated 2025-12-17
DESCRIPTION | 6 MD5 | 12 - R/ewtpr.R | 426 ++++++++++++++++++++++------------------- R/rewtpr.R | 391 +++++++++++++++++++------------------ R/wintime.R | 21 +- build/vignette.rds |binary inst/doc/wintime_vignette.html | 5 7 files changed, 458 insertions(+), 403 deletions(-)
Title: Data for the 'Mastering Health Data Science Using R' Online
Textbook
Description: Contains ten datasets used in the chapters and exercises of Paul, Alice (2023) "Health Data Science in R" <https://alicepaul.github.io/health-data-science-using-r/>.
Author: Alice Paul [aut, cre],
Hannah Eglinton [aut],
Jialin Liu [ctb],
Joanna Walsh [aut],
Xinbei Yu [ctb]
Maintainer: Alice Paul <alice_paul@brown.edu>
Diff between HDSinRdata versions 0.1.3 dated 2024-12-04 and 0.3.0 dated 2025-12-17
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 4 ++-- R/mobility.R | 3 +-- R/pain.R | 4 ++-- R/tex_itop.R | 4 ++-- man/mobility.Rd | 3 +-- man/pain.Rd | 4 ++-- man/tex_itop.Rd | 4 ++-- 9 files changed, 24 insertions(+), 26 deletions(-)
Title: Tools for Fast Computing and Visualizing Euclidean Minimum
Spanning Trees
Description: Fast and easy computation of Euclidean Minimum Spanning Trees (EMST) from data,
relying on the R API for 'mlpack' - the C++ Machine Learning Library (Curtin et. al., 2013).
'emstreeR' uses the Dual-Tree Boruvka (March, Ram, Gray, 2010, <doi:10.1145/1835804.1835882>),
which is theoretically and empirically the fastest algorithm for computing an EMST. This package also provides
functions and an S3 method for readily visualizing Minimum Spanning Trees (MST) using either the
style of the 'base', 'scatterplot3d', or 'ggplot2' libraries; and functions to export the MST output to shapefiles.
Author: Allan Quadros [aut, cre],
Duncan Garmonsway [ctb]
Maintainer: Allan Quadros <allanvcq@gmail.com>
Diff between emstreeR versions 3.1.2 dated 2023-11-14 and 3.1.3 dated 2025-12-17
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/zzz.R | 2 +- README.md | 34 +++++++++++++++++++++++++--------- man/export_edges_to_shapefile.Rd | 2 +- man/export_vertices_to_shapefile.Rd | 2 +- 6 files changed, 38 insertions(+), 22 deletions(-)
Title: Analysis of Data from a Crossover Design with GEE
Description: Analyze data from a crossover design using generalized estimation equations (GEE), including carryover effects and various correlation structures based on the Kronecker product. It contains functions for semiparametric estimates of carry-over effects in repeated measures and allows estimation of complex carry-over effects. Related work includes: a) Cruz N.A., Melo O.O., Martinez C.A. (2023). "CrossCarry: An R package for the analysis of data from a crossover design with GEE". <doi:10.48550/arXiv.2304.02440>. b) Cruz N.A., Melo O.O., Martinez C.A. (2023). "A correlation structure for the analysis of Gaussian and non-Gaussian responses in crossover experimental designs with repeated measures". <doi:10.1007/s00362-022-01391-z> and c) Cruz N.A., Melo O.O., Martinez C.A. (2023). "Semiparametric generalized estimating equations for repeated measurements in cross-over designs". <doi:10.1177/09622802231158736>.
Author: Nelson Alirio Cruz Gutierrez [aut, cre, cph],
Oscar Orlando Melo [aut],
Carlos Alberto Martinez [aut],
Ricardo Alberich Marti [aut]
Maintainer: Nelson Alirio Cruz Gutierrez <nelson-alirio.cruz@uib.es>
Diff between CrossCarry versions 1.0.0 dated 2025-09-11 and 1.2.0 dated 2025-12-17
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- inst/CITATION | 15 ++++++++------- 3 files changed, 14 insertions(+), 13 deletions(-)
Title: Machine Learning-Assisted, Marker-Based Tool for Single-Cell and
Spatial Transcriptomics Annotation
Description: Annotates single-cell and spatial-transcriptomic (ST) data using marker datasets. Supports unified markers list ('Markers_list') creation from built-in databases (e.g., 'Cellmarker2', 'PanglaoDB', 'scIBD', 'TCellSI', 'PCTIT', 'PCTAM'), Seurat objects, or user-supplied Excel files. SlimR can predict calculation parameters by machine learning algorithms (e.g., 'Random Forest', 'Gradient Boosting', 'Support Vector Machine', 'Ensemble Learning'), and based on Markers_list, calculate gene expression of different cell types and predict annotation information, and calculate corresponding AUC and annotate it, then verify it. At the same time, it can calculate gene expression corresponding to the cell type to generate a reference map for manual annotation (e.g., 'Heat Map', 'Feature Plots', 'Combined Plots'). For more details, see Kabacoff (2020, ISBN:9787115420572).
Author: Zhaoqing Wang [aut, cre]
Maintainer: Zhaoqing Wang <zhaoqingwang@mail.sdu.edu.cn>
Diff between SlimR versions 1.0.8 dated 2025-10-08 and 1.0.9 dated 2025-12-17
DESCRIPTION | 10 - MD5 | 112 ++++++++++---------- NAMESPACE | 2 NEWS.md | 20 ++- R/Celltype_Annotation.R | 2 R/Celltype_Annotation_Combined.R | 2 R/Celltype_Annotation_Features.R | 2 R/Celltype_Annotation_Heatmap.R | 2 R/Celltype_Calculate.R | 2 R/Celltype_Verification.R | 2 R/Celltype_annotation_Cellmarker2.R | 2 R/Celltype_annotation_Excel.R | 46 +++++++- R/Celltype_annotation_PanglaoDB.R | 2 R/Celltype_annotation_Seurat.R | 2 R/Database_Markers_list_PCTAM.R |only R/Database_Markers_list_PCTIT.R |only R/Database_Markers_list_TCellSI.R | 4 R/Database_Markers_list_scIBD.R | 2 R/Markers_filter_Cellmarker2.R | 2 R/Markers_filter_PanglaoDB.R | 2 R/Probability_parameter.R | 19 +-- R/Read_excel_markers.R | 44 +++++-- R/Read_seurat_markers.R | 2 R/onattach.R | 4 README.md | 182 ++++++++++++++++++++------------- data/Markers_list_PCTAM.rda |only data/Markers_list_PCTIT.rda |only man/Cellmarker2.Rd | 2 man/Cellmarker2_raw.Rd | 2 man/Cellmarker2_table.Rd | 2 man/Celltype_Annotation.Rd | 4 man/Celltype_Annotation_Combined.Rd | 4 man/Celltype_Annotation_Features.Rd | 4 man/Celltype_Annotation_Heatmap.Rd | 4 man/Celltype_Calculate.Rd | 4 man/Celltype_Verification.Rd | 4 man/Celltype_annotation_Cellmarker2.Rd | 4 man/Celltype_annotation_Excel.Rd | 4 man/Celltype_annotation_PanglaoDB.Rd | 4 man/Celltype_annotation_Seurat.Rd | 4 man/Markers_filter_Cellmarker2.Rd | 4 man/Markers_filter_PanglaoDB.Rd | 4 man/Markers_list_PCTAM.Rd |only man/Markers_list_PCTIT.Rd |only man/Markers_list_TCellSI.Rd | 6 - man/Markers_list_scIBD.Rd | 4 man/PanglaoDB.Rd | 2 man/PanglaoDB_raw.Rd | 2 man/PanglaoDB_table.Rd | 2 man/Parameter_Calculate.Rd | 4 man/Read_excel_markers.Rd | 12 +- man/Read_seurat_markers.Rd | 4 man/calculate_cluster_variability.Rd | 2 man/calculate_expression_skewness.Rd | 2 man/estimate_batch_effect.Rd | 2 man/extract_dataset_features.Rd | 2 man/generate_training_data.Rd | 2 man/postprocess_parameters.Rd | 2 man/predict_optimal_parameters.Rd | 2 man/train_parameter_model.Rd | 2 60 files changed, 353 insertions(+), 222 deletions(-)
Title: Identify Relevant Clinical Codes and Evaluate Their Use
Description: Generate a candidate code list for the Observational Medical Outcomes Partnership (OMOP) common data model based on string matching. For a given search strategy, a candidate code list will be returned.
Author: Edward Burn [aut, cre] ,
Marta Alcalde-Herraiz [aut] ,
Marti Catala [aut] ,
Xihang Chen [aut] ,
Nuria Mercade-Besora [aut] ,
Mike Du [aut] ,
Danielle Newby [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CodelistGenerator versions 3.5.0 dated 2025-04-10 and 4.0.0 dated 2025-12-17
CodelistGenerator-3.5.0/CodelistGenerator/R/CodelistFromCodelistWithDetails.R |only CodelistGenerator-3.5.0/CodelistGenerator/R/codesInUse.R |only CodelistGenerator-3.5.0/CodelistGenerator/R/drugCodes.R |only CodelistGenerator-3.5.0/CodelistGenerator/R/getDoseUnit.R |only CodelistGenerator-3.5.0/CodelistGenerator/R/getICD10StandardCodes.R |only CodelistGenerator-3.5.0/CodelistGenerator/R/getRoutes.R |only CodelistGenerator-3.5.0/CodelistGenerator/R/helperFunctions.R |only CodelistGenerator-3.5.0/CodelistGenerator/R/stratifyByRoute.R |only CodelistGenerator-3.5.0/CodelistGenerator/R/summariseUnmappedCodes.R |only CodelistGenerator-3.5.0/CodelistGenerator/R/tableUnmappedCodes.R |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a03_GenerateCandidateCodelist.R |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a03_GenerateCandidateCodelist.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a03_GenerateCandidateCodelist.html |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a04_GenerateVocabularyBasedCodelist.R |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a04_GenerateVocabularyBasedCodelist.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a04_GenerateVocabularyBasedCodelist.html |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a04b_icd_codes.R |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a04b_icd_codes.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a04b_icd_codes.html |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a05_ExtractCodelistFromJSONfile.R |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a05_ExtractCodelistFromJSONfile.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a05_ExtractCodelistFromJSONfile.html |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a06_CreateSubsetsFromCodelist.R |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a06_CreateSubsetsFromCodelist.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a06_CreateSubsetsFromCodelist.html |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a07_RunCodelistDiagnostics.R |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a07_RunCodelistDiagnostics.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a07_RunCodelistDiagnostics.html |only CodelistGenerator-3.5.0/CodelistGenerator/man/availableICD10.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/availableIngredients.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/buildAchillesTables.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/codesInUse.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/getConceptClassId.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/getDomains.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/getDoseForm.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/getDoseUnit.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/getICD10StandardCodes.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/getRelationshipId.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/getRouteCategories.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/getVocabVersion.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/getVocabularies.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/sourceCodesInUse.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/summariseUnmappedCodes.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/tableUnmappedCodes.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-codesInUse.R |only CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-findUnmappedCodes.R |only CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-getDoseUnit.R |only CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-getICD10StandardCodes.R |only CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-getRouteCategories.R |only CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-helperFunctions.R |only CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-restrictToCodesInUse.R |only CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-summariseUnmappedCodes.R |only CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-tableUnmappedCodes.R |only CodelistGenerator-3.5.0/CodelistGenerator/vignettes/a03_GenerateCandidateCodelist.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/vignettes/a04_GenerateVocabularyBasedCodelist.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/vignettes/a04b_icd_codes.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/vignettes/a05_ExtractCodelistFromJSONfile.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/vignettes/a06_CreateSubsetsFromCodelist.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/vignettes/a07_RunCodelistDiagnostics.Rmd |only CodelistGenerator-4.0.0/CodelistGenerator/DESCRIPTION | 56 CodelistGenerator-4.0.0/CodelistGenerator/MD5 | 459 +- CodelistGenerator-4.0.0/CodelistGenerator/NAMESPACE | 150 CodelistGenerator-4.0.0/CodelistGenerator/NEWS.md | 98 CodelistGenerator-4.0.0/CodelistGenerator/R/CodelistGenerator-package.R | 18 CodelistGenerator-4.0.0/CodelistGenerator/R/addConcepts.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/asCodelist.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/asCodelistWithDetails.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/asConceptSetExpression.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/availableATC.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/availableConceptClassIds.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/availableDomains.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/availableDoseForms.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/availableDoseUnits.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/availableDrugIngredients.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/availableRelationshipIds.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/availableRouteCategories.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/availableVocabularies.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/benchmarkCodelistGenerator.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/buildAchillesTables.R | 346 - CodelistGenerator-4.0.0/CodelistGenerator/R/checks.R | 166 CodelistGenerator-4.0.0/CodelistGenerator/R/codesFromConceptSet.R | 1146 +++-- CodelistGenerator-4.0.0/CodelistGenerator/R/compareCodelists.R | 256 - CodelistGenerator-4.0.0/CodelistGenerator/R/data.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/documentation_helper.R | 628 +-- CodelistGenerator-4.0.0/CodelistGenerator/R/excludeConcepts.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/functions.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/getATCCodes.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/getCandidateCodes.R | 389 +- CodelistGenerator-4.0.0/CodelistGenerator/R/getDescendants.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/getDrugIngredientCodes.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/getMappings.R | 270 - CodelistGenerator-4.0.0/CodelistGenerator/R/intersectCodelists.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/mockVocabRef.R | 876 ++-- CodelistGenerator-4.0.0/CodelistGenerator/R/runSearch.R | 1089 +++-- CodelistGenerator-4.0.0/CodelistGenerator/R/searchStrategy.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/stratify.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/stratifyByBrand.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/stratifyByConcept.R | 168 CodelistGenerator-4.0.0/CodelistGenerator/R/stratifyByDomain.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/stratifyByDoseForm.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/stratifyByDoseUnit.R | 231 - CodelistGenerator-4.0.0/CodelistGenerator/R/stratifyByRouteCategory.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/stratifyByVocabulary.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/subset.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/subsetOnDomain.R | 147 CodelistGenerator-4.0.0/CodelistGenerator/R/subsetOnDoseForm.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/subsetOnDoseUnit.R | 180 CodelistGenerator-4.0.0/CodelistGenerator/R/subsetOnIngredientRange.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/subsetOnRouteCategory.R | 171 CodelistGenerator-4.0.0/CodelistGenerator/R/subsetOnVocabulary.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/subsetToCodesInUse.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/summariseAchillesCodeUse.R | 451 +- CodelistGenerator-4.0.0/CodelistGenerator/R/summariseCodeUse.R | 1920 +++++----- CodelistGenerator-4.0.0/CodelistGenerator/R/summariseOrphanCodes.R | 395 +- CodelistGenerator-4.0.0/CodelistGenerator/R/sysdata.rda |binary CodelistGenerator-4.0.0/CodelistGenerator/R/tableAchillesCodeUse.R | 245 - CodelistGenerator-4.0.0/CodelistGenerator/R/tableCodeUse.R | 425 +- CodelistGenerator-4.0.0/CodelistGenerator/R/tableOrphanCodes.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/unionCodelists.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/utilities.R |only CodelistGenerator-4.0.0/CodelistGenerator/R/vocabUtilities.R | 622 --- CodelistGenerator-4.0.0/CodelistGenerator/README.md | 291 - CodelistGenerator-4.0.0/CodelistGenerator/build/vignette.rds |binary CodelistGenerator-4.0.0/CodelistGenerator/data |only CodelistGenerator-4.0.0/CodelistGenerator/inst/WORDLIST | 63 CodelistGenerator-4.0.0/CodelistGenerator/inst/cohorts_for_mock/oa_desc.json | 178 CodelistGenerator-4.0.0/CodelistGenerator/inst/cohorts_for_mock/oa_no_desc.json | 174 CodelistGenerator-4.0.0/CodelistGenerator/inst/cohorts_for_mock_dups/oa_desc.json | 176 CodelistGenerator-4.0.0/CodelistGenerator/inst/cohorts_for_mock_dups/oa_no_desc.json | 174 CodelistGenerator-4.0.0/CodelistGenerator/inst/cohorts_for_mock_with_exclude/oa_desc.json | 206 - CodelistGenerator-4.0.0/CodelistGenerator/inst/cohorts_for_mock_with_mapped/oa_desc.json | 178 CodelistGenerator-4.0.0/CodelistGenerator/inst/cohorts_for_mock_with_mapped/oa_no_desc.json | 174 CodelistGenerator-4.0.0/CodelistGenerator/inst/concepts_dbms/oa_desc.json | 24 CodelistGenerator-4.0.0/CodelistGenerator/inst/concepts_dbms/oa_no_desc.json | 24 CodelistGenerator-4.0.0/CodelistGenerator/inst/concepts_for_mock/arthritis_desc.json | 24 CodelistGenerator-4.0.0/CodelistGenerator/inst/concepts_for_mock/arthritis_no_desc.json | 24 CodelistGenerator-4.0.0/CodelistGenerator/inst/concepts_for_mock/arthritis_with_excluded.json | 38 CodelistGenerator-4.0.0/CodelistGenerator/inst/concepts_for_mock/codelist_with_details.json |only CodelistGenerator-4.0.0/CodelistGenerator/inst/concepts_for_mock_with_exclude/oa_desc.json | 24 CodelistGenerator-4.0.0/CodelistGenerator/inst/concepts_for_mock_with_exclude/oa_with_excluded.json | 38 CodelistGenerator-4.0.0/CodelistGenerator/inst/concepts_for_mock_with_exclude/oa_with_excluded2.json | 38 CodelistGenerator-4.0.0/CodelistGenerator/inst/concepts_for_mock_with_mapped/oa_desc.json | 24 CodelistGenerator-4.0.0/CodelistGenerator/inst/concepts_for_mock_with_mapped/oa_with_mapped.json | 24 CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a01_GettingOmopCdmVocabularies.R | 177 CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a01_GettingOmopCdmVocabularies.Rmd | 15 CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a01_GettingOmopCdmVocabularies.html | 978 ++--- CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a02_ExploreCDMvocabulary.R | 122 CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a02_ExploreCDMvocabulary.Rmd | 48 CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a02_ExploreCDMvocabulary.html | 862 ++-- CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a03_TypesOfCodelist.R |only CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a03_TypesOfCodelist.Rmd |only CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a03_TypesOfCodelist.html |only CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a04_GenerateCandidateCodelist.R |only CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a04_GenerateCandidateCodelist.Rmd |only CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a04_GenerateCandidateCodelist.html |only CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a05_GenerateVocabularyBasedCodelist.R |only CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a05_GenerateVocabularyBasedCodelist.Rmd |only CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a05_GenerateVocabularyBasedCodelist.html |only CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a06_ImportExport.R |only CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a06_ImportExport.Rmd |only CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a06_ImportExport.html |only CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a08_ManipulateCodelists.R |only CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a08_ManipulateCodelists.Rmd |only CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a08_ManipulateCodelists.html |only CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a09_RunCodelistDiagnostics.R |only CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a09_RunCodelistDiagnostics.Rmd |only CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a09_RunCodelistDiagnostics.html |only CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a10_CodelistGeneratorBenchmark.R |only CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a10_CodelistGeneratorBenchmark.Rmd |only CodelistGenerator-4.0.0/CodelistGenerator/inst/doc/a10_CodelistGeneratorBenchmark.html |only CodelistGenerator-4.0.0/CodelistGenerator/man/CodelistGenerator-package.Rd | 72 CodelistGenerator-4.0.0/CodelistGenerator/man/addConcepts.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/ageGroupDoc.Rd | 24 CodelistGenerator-4.0.0/CodelistGenerator/man/asCodelist.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/asCodelistWithDetails.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/asConceptSetExpression.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/associatedConceptClassIds.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/associatedDomains.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/associatedDoseForms.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/associatedDoseUnits.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/associatedDrugIngredients.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/associatedRelationshipIds.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/associatedRouteCategories.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/associatedVocabularies.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/availableATC.Rd | 67 CodelistGenerator-4.0.0/CodelistGenerator/man/availableConceptClassIds.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/availableDomains.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/availableDoseForms.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/availableDoseUnits.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/availableDrugIngredients.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/availableRelationshipIds.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/availableRouteCategories.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/availableVocabularies.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/benchmarkCodelistGenerator.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/byConceptDoc.Rd | 26 CodelistGenerator-4.0.0/CodelistGenerator/man/bySexDoc.Rd | 24 CodelistGenerator-4.0.0/CodelistGenerator/man/byYearDoc.Rd | 24 CodelistGenerator-4.0.0/CodelistGenerator/man/cdmDoc.Rd | 26 CodelistGenerator-4.0.0/CodelistGenerator/man/codelistNameDoc.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/codesFromCohort.Rd | 69 CodelistGenerator-4.0.0/CodelistGenerator/man/codesFromConceptSet.Rd | 88 CodelistGenerator-4.0.0/CodelistGenerator/man/compareCodelists.Rd | 119 CodelistGenerator-4.0.0/CodelistGenerator/man/countByDoc.Rd | 26 CodelistGenerator-4.0.0/CodelistGenerator/man/domainDoc.Rd | 30 CodelistGenerator-4.0.0/CodelistGenerator/man/doseFormDoc.Rd | 28 CodelistGenerator-4.0.0/CodelistGenerator/man/doseFormToRoute.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/doseUnitDoc.Rd | 28 CodelistGenerator-4.0.0/CodelistGenerator/man/dot-optionsDoc.Rd | 28 CodelistGenerator-4.0.0/CodelistGenerator/man/excludeConcepts.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/figures/README-unnamed-chunk-8-1.png |binary CodelistGenerator-4.0.0/CodelistGenerator/man/getATCCodes.Rd | 153 CodelistGenerator-4.0.0/CodelistGenerator/man/getCandidateCodes.Rd | 165 CodelistGenerator-4.0.0/CodelistGenerator/man/getDescendants.Rd | 75 CodelistGenerator-4.0.0/CodelistGenerator/man/getDrugIngredientCodes.Rd | 128 CodelistGenerator-4.0.0/CodelistGenerator/man/getMappings.Rd | 84 CodelistGenerator-4.0.0/CodelistGenerator/man/groupColumnDoc.Rd | 30 CodelistGenerator-4.0.0/CodelistGenerator/man/groupColumnStrataDoc.Rd | 32 CodelistGenerator-4.0.0/CodelistGenerator/man/headerDoc.Rd | 34 CodelistGenerator-4.0.0/CodelistGenerator/man/headerStrataDoc.Rd | 36 CodelistGenerator-4.0.0/CodelistGenerator/man/hideDoc.Rd | 30 CodelistGenerator-4.0.0/CodelistGenerator/man/hideStrataDoc.Rd | 32 CodelistGenerator-4.0.0/CodelistGenerator/man/includeDescendantsDoc.Rd | 28 CodelistGenerator-4.0.0/CodelistGenerator/man/ingredientRangeDoc.Rd | 32 CodelistGenerator-4.0.0/CodelistGenerator/man/intersectCodelists.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/keepOriginalDoc.Rd | 26 CodelistGenerator-4.0.0/CodelistGenerator/man/keepOriginalDocSubset.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/levelATCDoc.Rd | 26 CodelistGenerator-4.0.0/CodelistGenerator/man/levelICD10Doc.Rd | 26 CodelistGenerator-4.0.0/CodelistGenerator/man/minimumCountDoc.Rd | 24 CodelistGenerator-4.0.0/CodelistGenerator/man/mockVocabRef.Rd | 48 CodelistGenerator-4.0.0/CodelistGenerator/man/nameStyleDoc.Rd | 28 CodelistGenerator-4.0.0/CodelistGenerator/man/routeCategoryDoc.Rd | 28 CodelistGenerator-4.0.0/CodelistGenerator/man/searchStrategy.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/standardConceptDoc.Rd | 28 CodelistGenerator-4.0.0/CodelistGenerator/man/stratifyByBrand.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/stratifyByConcept.Rd | 82 CodelistGenerator-4.0.0/CodelistGenerator/man/stratifyByDomain.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/stratifyByDoseForm.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/stratifyByDoseUnit.Rd | 80 CodelistGenerator-4.0.0/CodelistGenerator/man/stratifyByRouteCategory.Rd | 80 CodelistGenerator-4.0.0/CodelistGenerator/man/stratifyByVocabulary.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/subsetOnDomain.Rd | 83 CodelistGenerator-4.0.0/CodelistGenerator/man/subsetOnDoseForm.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/subsetOnDoseUnit.Rd | 81 CodelistGenerator-4.0.0/CodelistGenerator/man/subsetOnIngredientRange.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/subsetOnRouteCategory.Rd | 81 CodelistGenerator-4.0.0/CodelistGenerator/man/subsetOnVocabulary.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/subsetToCodesInUse.Rd | 92 CodelistGenerator-4.0.0/CodelistGenerator/man/summariseAchillesCodeUse.Rd | 66 CodelistGenerator-4.0.0/CodelistGenerator/man/summariseCodeUse.Rd | 137 CodelistGenerator-4.0.0/CodelistGenerator/man/summariseCohortCodeUse.Rd | 162 CodelistGenerator-4.0.0/CodelistGenerator/man/summariseOrphanCodes.Rd | 98 CodelistGenerator-4.0.0/CodelistGenerator/man/tableAchillesCodeUse.Rd | 132 CodelistGenerator-4.0.0/CodelistGenerator/man/tableCodeUse.Rd | 150 CodelistGenerator-4.0.0/CodelistGenerator/man/tableCohortCodeUse.Rd | 165 CodelistGenerator-4.0.0/CodelistGenerator/man/tableDoc.Rd | 24 CodelistGenerator-4.0.0/CodelistGenerator/man/tableOrphanCodes.Rd | 144 CodelistGenerator-4.0.0/CodelistGenerator/man/tableStyleDoc.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/typeBroadDoc.Rd | 26 CodelistGenerator-4.0.0/CodelistGenerator/man/typeNarrowDoc.Rd | 24 CodelistGenerator-4.0.0/CodelistGenerator/man/typeTableDoc.Rd | 26 CodelistGenerator-4.0.0/CodelistGenerator/man/unionCodelists.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/vocabularyVersion.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/man/xDoc.Rd | 24 CodelistGenerator-4.0.0/CodelistGenerator/man/xDocCohort.Rd |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat.R | 24 CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/setup.R | 6 CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-addConcepts.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-asCodelist.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-asCodelistWithDetails.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-asConceptSetExpression.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-availableATC.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-availableConceptClassIds.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-availableDomains.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-availableDoseForms.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-availableDoseUnit.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-availableDrugIngredients.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-availableRelationshipIds.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-availableRouteCategories.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-availableVocabularies.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-buildAchillesTables.R | 113 CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-codesFrom.R | 365 - CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-compareCodelists.R | 310 - CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-data.R | 10 CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-dbms.R | 1219 +++--- CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-drugCodes.R | 342 + CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-excludeConcepts.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-getCandidateCodes.R | 841 ++-- CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-getMappings.R | 149 CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-intersectCodelists.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-mockVocabRef.R | 26 CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-searchStrategy.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-stratifyByBrand.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-stratifyByConcept.R | 100 CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-stratifyByDomain.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-stratifyByDoseForm.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-stratifyByDoseUnit.R | 21 CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-stratifyByRouteCategory.R | 78 CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-stratifyByVocabulary.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-subsetOnDomain.R | 150 CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-subsetOnDoseForm.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-subsetOnDoseUnit.R | 84 CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-subsetOnIngredientRange.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-subsetOnRouteCategory.R | 108 CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-subsetOnVocabulary.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-subsetToCodesInUse.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-summariseAchillesCodeUse.R | 180 CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-summariseCodeUse.R | 1892 +++++---- CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-summariseOrphanCodes.R | 105 CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-synthea_sql_server.R | 108 CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-tableAchillesCodeUse.R | 191 CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-tableCodeUse.R | 229 - CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-tableOrphanCodes.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-tidyWords.R | 24 CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-unionCodelists.R |only CodelistGenerator-4.0.0/CodelistGenerator/tests/testthat/test-vocabUtilities.R | 184 CodelistGenerator-4.0.0/CodelistGenerator/vignettes/a01_GettingOmopCdmVocabularies.Rmd | 15 CodelistGenerator-4.0.0/CodelistGenerator/vignettes/a02_ExploreCDMvocabulary.Rmd | 48 CodelistGenerator-4.0.0/CodelistGenerator/vignettes/a03_TypesOfCodelist.Rmd |only CodelistGenerator-4.0.0/CodelistGenerator/vignettes/a04_GenerateCandidateCodelist.Rmd |only CodelistGenerator-4.0.0/CodelistGenerator/vignettes/a05_GenerateVocabularyBasedCodelist.Rmd |only CodelistGenerator-4.0.0/CodelistGenerator/vignettes/a06_ImportExport.Rmd |only CodelistGenerator-4.0.0/CodelistGenerator/vignettes/a08_ManipulateCodelists.Rmd |only CodelistGenerator-4.0.0/CodelistGenerator/vignettes/a09_RunCodelistDiagnostics.Rmd |only CodelistGenerator-4.0.0/CodelistGenerator/vignettes/a10_CodelistGeneratorBenchmark.Rmd |only 325 files changed, 12964 insertions(+), 12487 deletions(-)
More information about CodelistGenerator at CRAN
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Title: Mechanistic Simulation of Species Range Dynamics
Description: Integrates population dynamics and dispersal into a
mechanistic virtual species simulator. The package can be used to
study the effects of environmental change on population growth and
range shifts. It allows for simple and straightforward definition of
population dynamics (including positive density dependence), extensive
possibilities for defining dispersal kernels, and the ability to
generate virtual ecologist data. Learn more about the 'rangr' at
<https://docs.ropensci.org/rangr/>.
Author: Katarzyna Markowska [aut, cre],
Lechoslaw Kuczynski [aut],
Tad Dallas [rev],
Joanne Potts [rev]
Maintainer: Katarzyna Markowska <katarzyna.markowska@amu.edu.pl>
Diff between rangr versions 1.0.7 dated 2025-05-26 and 1.0.8 dated 2025-12-17
DESCRIPTION | 48 +++++++++++++++++++++++++----------------------- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/disp.R | 4 ++-- R/initialise.R | 22 +++++++++++++--------- R/target_ids.R | 10 +++++----- inst/doc/rangr.html | 2 +- 7 files changed, 58 insertions(+), 46 deletions(-)
Title: Portfolio Management with R
Description: Tools for the practical management of financial
portfolios: backtesting investment and trading strategies,
computing profit/loss and returns, analysing trades,
handling lists of transactions, reporting, and more. The
package provides a small set of reliable, efficient and
convenient tools for processing and analysing
trade/portfolio data. The manual provides all the details;
it is available from
<https://enricoschumann.net/R/packages/PMwR/manual/PMwR.html>.
Examples and descriptions of new features are provided at
<https://enricoschumann.net/notes/PMwR/>.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between PMwR versions 1.1-0 dated 2025-10-19 and 1.2-0 dated 2025-12-17
DESCRIPTION | 8 +-- MD5 | 54 +++++++++++----------- NEWS | 12 ++++- R/internal.R | 2 R/rc.R | 46 +++++++++++++++++++ R/rebalance.R | 30 +++++++++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/An_overview_of_PMwR.Rnw | 4 - inst/doc/An_overview_of_PMwR.pdf |binary inst/doc/Computing_returns.Rnw | 4 - inst/doc/Computing_returns.pdf |binary inst/doc/Drawdowns_streaks.Rnw | 4 - inst/doc/Drawdowns_streaks.pdf |binary inst/doc/FinTeX.Rnw | 4 - inst/doc/FinTeX.pdf |binary inst/doc/pl_open_positions.Rnw | 4 - inst/doc/pl_open_positions.pdf |binary inst/doc/q32.Rnw | 4 - inst/doc/q32.pdf |binary inst/tinytest/test_rebalance.R | 91 ++++++++++++++++++++++++++++++++++---- man/rebalance.Rd | 15 +++--- vignettes/An_overview_of_PMwR.Rnw | 4 - vignettes/Computing_returns.Rnw | 4 - vignettes/Drawdowns_streaks.Rnw | 4 - vignettes/FinTeX.Rnw | 4 - vignettes/pl_open_positions.Rnw | 4 - vignettes/q32.Rnw | 4 - 28 files changed, 226 insertions(+), 80 deletions(-)
Title: Likelihood-Based Intrinsic Dimension Estimators
Description: Provides functions to estimate the intrinsic dimension of a dataset
via likelihood-based approaches. Specifically, the package implements the
'TWO-NN' and 'Gride' estimators and the 'Hidalgo' Bayesian mixture model.
In addition, the first reference contains an extended vignette on the usage of
the 'TWO-NN' and 'Hidalgo' models. References:
Denti (2023, <doi:10.18637/jss.v106.i09>);
Allegra et al. (2020, <doi:10.1038/s41598-020-72222-0>);
Denti et al. (2022, <doi:10.1038/s41598-022-20991-1>);
Facco et al. (2017, <doi:10.1038/s41598-017-11873-y>);
Santos-Fernandez et al. (2021, <doi:10.1038/s41598-022-20991-1>).
Author: Francesco Denti [aut, cre, cph] ,
Andrea Gilardi [aut]
Maintainer: Francesco Denti <francescodenti.personal@gmail.com>
Diff between intRinsic versions 1.1.1 dated 2025-09-24 and 1.1.2 dated 2025-12-17
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/compute_mus.R | 2 +- README.md | 4 ++-- build/partial.rdb |binary 6 files changed, 17 insertions(+), 13 deletions(-)
Title: Flux Estimation with Static Chamber Data
Description: Statistical analysis of static chamber concentration data for trace gas flux estimation.
Author: Asger Roer Pedersen [aut, cre]
Maintainer: Asger Roer Pedersen <arpstat@outlook.dk>
Diff between HMR versions 1.0.4 dated 2024-07-04 and 1.0.5 dated 2025-12-17
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- R/HMR.main.R | 4 +--- man/HMR.Rd | 4 ++-- 4 files changed, 12 insertions(+), 13 deletions(-)
Title: Easy and Efficient Batch Processing of Regression Models
Description: Easily processes batches of univariate or multivariate
regression models. Returns results in a tidy format and generates
visualization plots for straightforward interpretation (Wang,
Shixiang, et al. (2025) <DOI:10.1002/mdr2.70028>).
Author: Shixiang Wang [aut, cre] ,
Yun Peng [aut] ,
Chenyang Shu [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between bregr versions 1.3.0 dated 2025-09-22 and 1.3.1 dated 2025-12-17
DESCRIPTION | 10 - MD5 | 22 +- NEWS.md | 4 R/01-class.R | 2 README.md | 31 ++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/bregr-group-by.html | 11 - inst/doc/model-config.html | 39 ++-- inst/doc/quick-analyze-cancer-data.html | 21 +- inst/doc/save-model-file.html | 17 - inst/doc/supported-models.html | 308 ++++++++++++++++---------------- 12 files changed, 243 insertions(+), 222 deletions(-)
Title: Interface Between R and the OpenStreetMap-Based Routing Service
OSRM
Description: An interface between R and the 'OSRM' API. 'OSRM' is a routing
service based on 'OpenStreetMap' data. See <http://project-osrm.org/> for more
information. This package enables the computation of routes, trips, isochrones and
travel distances matrices (travel time and kilometric distance).
Author: Timothee Giraud [cre, aut] ,
Robin Cura [ctb] ,
Matthieu Viry [ctb] ,
Robin Lovelace [ctb]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between osrm versions 4.2.0 dated 2024-05-06 and 5.0.0 dated 2025-12-17
osrm-4.2.0/osrm/man/osrmIsometric.Rd |only osrm-5.0.0/osrm/DESCRIPTION | 19 - osrm-5.0.0/osrm/MD5 | 48 +-- osrm-5.0.0/osrm/NAMESPACE | 1 osrm-5.0.0/osrm/NEWS | 12 osrm-5.0.0/osrm/R/osrmIsochrone.R | 74 +++- osrm-5.0.0/osrm/R/osrmIsodistance.R | 95 +++--- osrm-5.0.0/osrm/R/osrmNearest.R | 50 +-- osrm-5.0.0/osrm/R/osrmRoute.R | 6 osrm-5.0.0/osrm/R/osrmTrip.R | 7 osrm-5.0.0/osrm/R/package.R | 2 osrm-5.0.0/osrm/R/utils.R | 30 + osrm-5.0.0/osrm/README.md | 151 +++++----- osrm-5.0.0/osrm/inst/tinytest/fill_grid_out.rds |binary osrm-5.0.0/osrm/inst/tinytest/test_internals_get_resolution.R |only osrm-5.0.0/osrm/inst/tinytest/test_osrmIsochrone.R | 41 +- osrm-5.0.0/osrm/inst/tinytest/test_osrmIsodistance.R | 44 +- osrm-5.0.0/osrm/inst/tinytest/test_osrmNearest.R | 3 osrm-5.0.0/osrm/man/figures/cov.png |only osrm-5.0.0/osrm/man/figures/iso.png |only osrm-5.0.0/osrm/man/figures/route.png |only osrm-5.0.0/osrm/man/figures/trip.png |only osrm-5.0.0/osrm/man/osrm.Rd | 2 osrm-5.0.0/osrm/man/osrmIsochrone.Rd | 16 - osrm-5.0.0/osrm/man/osrmIsodistance.Rd | 16 - osrm-5.0.0/osrm/man/osrmNearest.Rd | 7 osrm-5.0.0/osrm/man/osrmRoute.Rd | 3 osrm-5.0.0/osrm/man/osrmTrip.Rd | 3 28 files changed, 363 insertions(+), 267 deletions(-)
Title: 'JavaScript' Utilities for 'R'
Description: A collection of popular/useful JavaScript utilities, including the
terser minifier, sass compiler, typescript transpiler, and more.
Author: Andrew R. Johnson [aut, cre]
Maintainer: Andrew R. Johnson <andrew.johnson@arjohnsonau.com>
Diff between jsutils versions 0.1.0 dated 2025-11-06 and 0.2.0 dated 2025-12-17
jsutils-0.1.0/jsutils/inst/js/sass.1.93.3.js |only jsutils-0.1.0/jsutils/inst/js/terser.5.44.0.js |only jsutils-0.2.0/jsutils/DESCRIPTION | 9 jsutils-0.2.0/jsutils/MD5 | 35 +- jsutils-0.2.0/jsutils/NEWS.md |only jsutils-0.2.0/jsutils/R/esprima.R | 10 jsutils-0.2.0/jsutils/R/sass.R | 7 jsutils-0.2.0/jsutils/R/terser.R | 7 jsutils-0.2.0/jsutils/R/typescript.R | 7 jsutils-0.2.0/jsutils/R/versions.R | 4 jsutils-0.2.0/jsutils/README.md | 148 +++++----- jsutils-0.2.0/jsutils/inst/bundle/package-lock.json | 202 ++++++------- jsutils-0.2.0/jsutils/inst/bundle/package.json | 6 jsutils-0.2.0/jsutils/inst/js/esprima.4.0.1.js | 294 ++++++++++---------- jsutils-0.2.0/jsutils/inst/js/sass.1.97.0.js |only jsutils-0.2.0/jsutils/inst/js/terser.5.44.1.js |only jsutils-0.2.0/jsutils/man/esprima.Rd | 4 jsutils-0.2.0/jsutils/man/jsutils-package.Rd | 1 jsutils-0.2.0/jsutils/man/sass.Rd | 4 jsutils-0.2.0/jsutils/man/terser.Rd | 4 jsutils-0.2.0/jsutils/man/typescript.Rd | 4 21 files changed, 381 insertions(+), 365 deletions(-)
Title: General Unilateral Load Estimator for Two-Layer Latent Factor
Models
Description: Implements general unilateral loading estimator for two-layer latent factor models with smooth, element-wise factor transformations. We provide data simulation, loading estimation,finite-sample error bounds, and diagnostic tools for zero-mean and sub-Gaussian assumptions. A unified interface is given for evaluating estimation accuracy and cosine similarity. The philosophy of the package is described in Guo G. (2026) <doi:10.1016/j.apm.2025.116280>.
Author: Guangbao Guo [aut, cre]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between GulFM versions 0.1.2 dated 2025-10-28 and 0.2.0 dated 2025-12-17
DESCRIPTION | 6 +++--- MD5 | 11 +++++++++-- NAMESPACE | 1 + R/wholesale.R |only data |only man/Wine.Rd |only man/ionosphere.Rd |only man/wholesale.Rd |only 8 files changed, 13 insertions(+), 5 deletions(-)
Title: Estimate Aerosol Particle Collection Through Sample Lines
Description: Estimate ideal efficiencies of aerosol sampling through sample
lines. Functions were developed consistent with the approach described in
Hogue, Mark; Thompson, Martha; Farfan, Eduardo; Hadlock, Dennis, (2014),
"Hand Calculations for Transport of Radioactive Aerosols through Sampling
Systems" Health Phys 106, 5, S78-S87, <doi:10.1097/HP.0000000000000092>.
Author: Mark Hogue [aut, cre]
Maintainer: Mark Hogue <mark.hogue.chp@gmail.com>
Diff between AeroSampleR versions 0.2.0 dated 2023-01-05 and 0.3.0 dated 2025-12-17
AeroSampleR-0.2.0/AeroSampleR/man/AeroSampleR.Rd |only AeroSampleR-0.3.0/AeroSampleR/DESCRIPTION | 18 AeroSampleR-0.3.0/AeroSampleR/MD5 | 67 - AeroSampleR-0.3.0/AeroSampleR/NAMESPACE | 24 AeroSampleR-0.3.0/AeroSampleR/NEWS.md | 3 AeroSampleR-0.3.0/AeroSampleR/R/AeroSampleR-package.R | 20 AeroSampleR-0.3.0/AeroSampleR/R/bend_eff.R | 39 AeroSampleR-0.3.0/AeroSampleR/R/dat_for_plots.R | 36 AeroSampleR-0.3.0/AeroSampleR/R/particle_dist.R | 98 - AeroSampleR-0.3.0/AeroSampleR/R/probe_eff.R | 128 +- AeroSampleR-0.3.0/AeroSampleR/R/report_basic.R | 184 +-- AeroSampleR-0.3.0/AeroSampleR/R/report_cum_plots.R | 98 - AeroSampleR-0.3.0/AeroSampleR/R/report_log_mass.R | 114 +- AeroSampleR-0.3.0/AeroSampleR/R/report_plots.R | 150 +- AeroSampleR-0.3.0/AeroSampleR/R/set_params_1.R | 150 +- AeroSampleR-0.3.0/AeroSampleR/R/set_params_2.R | 124 +- AeroSampleR-0.3.0/AeroSampleR/R/tube_eff.R | 300 ++--- AeroSampleR-0.3.0/AeroSampleR/README.md | 2 AeroSampleR-0.3.0/AeroSampleR/build/partial.rdb |only AeroSampleR-0.3.0/AeroSampleR/build/vignette.rds |binary AeroSampleR-0.3.0/AeroSampleR/inst/doc/AeroSampleR_vignette.R | 30 AeroSampleR-0.3.0/AeroSampleR/inst/doc/AeroSampleR_vignette.Rmd | 9 AeroSampleR-0.3.0/AeroSampleR/inst/doc/AeroSampleR_vignette.html | 508 +++------- AeroSampleR-0.3.0/AeroSampleR/man/AeroSampleR-package.Rd |only AeroSampleR-0.3.0/AeroSampleR/man/bend_eff.Rd | 114 +- AeroSampleR-0.3.0/AeroSampleR/man/dat_for_plots.Rd | 58 - AeroSampleR-0.3.0/AeroSampleR/man/particle_dist.Rd | 98 - AeroSampleR-0.3.0/AeroSampleR/man/probe_eff.Rd | 82 - AeroSampleR-0.3.0/AeroSampleR/man/report_basic.Rd | 88 - AeroSampleR-0.3.0/AeroSampleR/man/report_cum_plots.Rd | 62 - AeroSampleR-0.3.0/AeroSampleR/man/report_log_mass.Rd | 62 - AeroSampleR-0.3.0/AeroSampleR/man/report_plots.Rd | 62 - AeroSampleR-0.3.0/AeroSampleR/man/set_params_1.Rd | 68 - AeroSampleR-0.3.0/AeroSampleR/man/set_params_2.Rd | 86 - AeroSampleR-0.3.0/AeroSampleR/man/tube_eff.Rd | 150 +- AeroSampleR-0.3.0/AeroSampleR/vignettes/AeroSampleR_vignette.Rmd | 9 36 files changed, 1409 insertions(+), 1632 deletions(-)
Title: Extra Twitter Bootstrap Components for Shiny
Description: Adds easy access to additional Twitter Bootstrap components to Shiny.
Author: Eric Bailey [aut],
Federico Marini [cre, ctb] ,
Jesse Koops [ctb]
Maintainer: Federico Marini <marinif@uni-mainz.de>
Diff between shinyBS versions 0.61.1 dated 2022-04-17 and 0.63.0 dated 2025-12-17
DESCRIPTION | 38 + MD5 | 137 +++--- NAMESPACE | 48 +- R/Alerts.R | 162 +++---- R/Buttons.R | 228 +++++----- R/Collapses.R | 142 +++--- R/Modals.R | 186 ++++---- R/Tooltips_and_Popovers.R | 330 +++++++-------- R/addPopover.R | 50 +- R/addTooltip.R | 48 +- R/bsAlert.R | 41 + R/bsButton.R | 110 ++--- R/bsCollapse.R | 86 ++-- R/bsCollapsePanel.R | 84 ++-- R/bsExample.R | 80 +-- R/bsModal.R | 105 ++--- R/bsPopover.R | 50 +- R/bsTooltip.R | 48 +- R/bsTypeahead.R |only R/closeAlert.R | 34 - R/createAlert.R | 60 +- R/misc.R | 84 +--- R/popify.R | 72 +-- R/removePopover.R | 34 - R/removeTooltip.R | 34 - R/tagManipulators.R |only R/tipify.R | 70 +-- R/toggleModal.R | 36 - R/updateButton.R | 72 +-- R/updateCollapse.R | 52 +- R/updateTypeahead.R |only inst/examples/Alerts/server.R | 44 +- inst/examples/Alerts/ui.R | 26 - inst/examples/Buttons/server.R | 98 ++-- inst/examples/Buttons/ui.R | 46 +- inst/examples/Collapses/server.R | 26 - inst/examples/Collapses/ui.R | 42 +- inst/examples/Modals/server.R | 66 +-- inst/examples/Modals/ui.R | 42 +- inst/examples/TooltipsandPopovers/server.R | 63 +-- inst/examples/TooltipsandPopovers/ui.R | 44 +- inst/tests/tipify_test.R | 70 +-- inst/tests/tipify_test2.R | 90 ++-- inst/www/bootstrap3-typeahead.js |only inst/www/shinyBS.css | 12 inst/www/shinyBS.js | 606 ++++++++++++++--------------- inst/www/typeahead_inputbinding.js |only man/Alerts.Rd | 196 ++++----- man/Buttons.Rd | 262 ++++++------ man/Collapses.Rd | 175 ++++---- man/Modals.Rd | 218 +++++----- man/Tooltips_and_Popovers.Rd | 269 ++++++------ man/addPopover.Rd | 107 ++--- man/addTooltip.Rd | 102 ++-- man/bsAlert.Rd | 65 +-- man/bsButton.Rd | 117 +++-- man/bsCollapse.Rd | 81 +-- man/bsCollapsePanel.Rd | 72 +-- man/bsExample.Rd | 63 +-- man/bsModal.Rd | 90 ++-- man/bsPopover.Rd | 102 ++-- man/bsTooltip.Rd | 91 ++-- man/bsTypeahead.Rd |only man/closeAlert.Rd | 66 +-- man/createAlert.Rd | 102 ++-- man/popify.Rd | 104 ++-- man/removePopover.Rd | 74 +-- man/removeTooltip.Rd | 74 +-- man/tipify.Rd | 92 ++-- man/toggleModal.Rd | 68 +-- man/updateButton.Rd | 118 +++-- man/updateCollapse.Rd | 88 ++-- man/updateTypeahead.Rd |only 73 files changed, 3391 insertions(+), 3201 deletions(-)
Title: Retrieve, Harmonise and Map Open Data Regarding the Italian
School System
Description: Compiles and displays the available data sets regarding the Italian school system, with a focus on the infrastructural aspects.
Input datasets are downloaded from the web, with the aim of updating everything to real time.
The functions are divided in four main modules, namely
'Get', to scrape raw data from the web
'Util', various utilities needed to process raw data
'Group', to aggregate data at the municipality or province level
'Map', to visualize the output datasets.
Author: Leonardo Cefalo [aut, cre] ,
Alessio Pollice [ctb, ths] ,
Paolo Maranzano [ctb]
Maintainer: Leonardo Cefalo <leonardo.cefalo@uniba.it>
Diff between SchoolDataIT versions 0.2.10 dated 2025-11-28 and 0.2.12 dated 2025-12-17
DESCRIPTION | 11 - MD5 | 52 ++--- NEWS.md | 12 + R/Get_AdmUnNames.R | 9 - R/Get_BroadBand.R | 2 R/Get_DB_MIUR.R | 53 +++--- R/Get_Invalsi_IS.R | 309 ++++++++++++++++------------------- R/Get_Registry.R | 6 R/Get_School2mun.R | 4 R/Get_nstud.R | 30 ++- R/Get_nteachers_prov.R | 11 - R/Group_teachers4stud.R | 2 R/Map_DB.R | 4 R/Map_Invalsi.R | 4 R/Map_School_Buildings.R | 4 R/Util_Check_nstud_availability.R | 8 README.md | 2 man/Get_AdmUnNames.Rd | 9 - man/Get_DB_MIUR.Rd | 7 man/Get_Invalsi_IS.Rd | 13 - man/Get_Registry.Rd | 2 man/Get_nteachers_prov.Rd | 15 - man/Group_teachers4stud.Rd | 2 man/Map_DB.Rd | 4 man/Map_Invalsi.Rd | 4 man/Map_School_Buildings.Rd | 4 man/Util_Check_nstud_availability.Rd | 6 27 files changed, 324 insertions(+), 265 deletions(-)
Title: eBird Data Extraction and Processing in R
Description: Extract and process bird sightings records from
eBird (<http://ebird.org>), an online tool for recording bird
observations. Public access to the full eBird database is via the
eBird Basic Dataset (EBD; see <http://ebird.org/ebird/data/download>
for access), a downloadable text file. This package is an interface to
AWK for extracting data from the EBD based on taxonomic, spatial, or
temporal filters, to produce a manageable file size that can be
imported into R.
Author: Matthew Strimas-Mackey [aut, cre] ,
Eliot Miller [aut],
Wesley Hochachka [aut],
Cornell Lab of Ornithology [cph]
Maintainer: Matthew Strimas-Mackey <mes335@cornell.edu>
Diff between auk versions 0.8.2 dated 2025-06-20 and 0.9.0 dated 2025-12-17
DESCRIPTION | 10 - MD5 | 142 +++++++++--------- NEWS.md | 4 R/auk-bbox.R | 8 - R/auk-bcr.R | 4 R/auk-breeding.R | 4 R/auk-complete.R | 4 R/auk-country.R | 4 R/auk-county.R | 4 R/auk-date.R | 12 - R/auk-distance.R | 4 R/auk-duration.R | 4 R/auk-filter.R | 16 +- R/auk-last-edited.R | 6 R/auk-observer.R | 4 R/auk-project.R | 4 R/auk-protocol.R | 4 R/auk-rollup.R | 8 - R/auk-species.R | 8 - R/auk-state.R | 4 R/auk-time.R | 4 R/auk-version.R | 6 R/auk-year.R | 10 - R/format-unmarked-occu.R | 6 R/process_barcharts.R | 3 R/read.R | 2 R/utils.R | 10 - build/vignette.rds |binary data/ebird_taxonomy.rda |binary inst/doc/auk.R | 78 +++++----- inst/doc/auk.Rmd | 82 +++++----- inst/doc/auk.html | 101 +++++++------ inst/doc/development.Rmd | 2 inst/doc/development.html | 7 inst/extdata/barchart-sample.txt | 248 +++++++++++++++++---------------- man/auk_bbox.Rd | 4 man/auk_bcr.Rd | 4 man/auk_breeding.Rd | 4 man/auk_complete.Rd | 4 man/auk_country.Rd | 4 man/auk_county.Rd | 4 man/auk_date.Rd | 12 - man/auk_distance.Rd | 4 man/auk_duration.Rd | 4 man/auk_extent.Rd | 4 man/auk_filter.Rd | 14 - man/auk_last_edited.Rd | 4 man/auk_observer.Rd | 4 man/auk_project.Rd | 4 man/auk_protocol.Rd | 4 man/auk_rollup.Rd | 8 - man/auk_species.Rd | 4 man/auk_state.Rd | 4 man/auk_time.Rd | 4 man/auk_year.Rd | 10 - man/format_unmarked_occu.Rd | 6 man/read_ebd.Rd | 2 tests/testthat/test_auk-ebd-version.r | 2 tests/testthat/test_auk-ebd.r | 168 +++++++++++----------- tests/testthat/test_auk-filter.r | 62 ++++---- tests/testthat/test_auk-keep-drop.r | 40 ++--- tests/testthat/test_auk-rollup.r | 8 - tests/testthat/test_auk-select.r | 14 - tests/testthat/test_auk-split.r | 6 tests/testthat/test_auk-unique.r | 20 +- tests/testthat/test_auk-zerofill.r | 4 tests/testthat/test_ebird-species.r | 1 tests/testthat/test_filters.r | 68 ++++----- tests/testthat/test_filters_sampling.r | 44 ++--- tests/testthat/test_unmarked.r | 28 +-- vignettes/auk.Rmd | 82 +++++----- vignettes/development.Rmd | 2 72 files changed, 750 insertions(+), 732 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library aiming towards
a good balance between speed and ease of use. It provides high-level syntax and
functionality deliberately similar to Matlab. It is useful for algorithm development
directly in C++, or quick conversion of research code into production environments.
It provides efficient classes for vectors, matrices and cubes where dense and sparse
matrices are supported. Integer, floating point and complex numbers are supported.
A sophisticated expression evaluator (based on template meta-programming) automatically
combines several operations to increase speed and efficiency. Dynamic evaluation
automatically chooses optimal code paths based on detected matrix structures.
Matrix decompositions are provided through integration with LAPACK, or one of its
high performance drop-in replacements (such as 'MKL' or 'OpenBLAS'). It can
automatically use 'OpenMP' multi-threading (parallelisation) to speed up
computationally expensive operations [...truncated...]
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
Doug Bates [aut] ,
Binxiang Ni [aut],
Conrad Sanderson [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 15.2.2-1 dated 2025-11-22 and 15.2.3-1 dated 2025-12-17
ChangeLog | 18 ++++ DESCRIPTION | 8 +- MD5 | 24 +++--- README.md | 36 +++++++++ configure | 18 ++-- configure.ac | 2 inst/NEWS.Rd | 10 ++ inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/current/armadillo_bits/Mat_meat.hpp | 66 ++++++++++------- inst/include/current/armadillo_bits/arma_version.hpp | 2 inst/include/current/armadillo_bits/op_repmat_meat.hpp | 20 +++-- inst/include/current/armadillo_bits/op_resize_meat.hpp | 2 13 files changed, 146 insertions(+), 60 deletions(-)
Title: Neighbourhood Functions for Local-Search Algorithms
Description: Neighbourhood functions are key components of
local-search algorithms such as Simulated Annealing or
Threshold Accepting. These functions take a solution and
return a slightly-modified copy of it, i.e. a neighbour.
The package provides a function neighbourfun() that
constructs such neighbourhood functions, based on
parameters such as admissible ranges for elements in a
solution. Supported are numeric and logical solutions.
The algorithms were originally created for
portfolio-optimisation applications, but can be used for
other models as well. Several recipes for neighbour
computations are taken from "Numerical Methods and
Optimization in Finance" by M. Gilli, D. Maringer and
E. Schumann (2019, ISBN:978-0128150658).
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between neighbours versions 0.1-3 dated 2023-09-21 and 0.1-5 dated 2025-12-17
ChangeLog | 18 ++++++++++++++++++ DESCRIPTION | 13 +++++++------ MD5 | 30 +++++++++++++++--------------- NEWS | 10 ++++++++++ R/neighbourfun.R | 6 +++++- README.md | 9 +++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/neighbours.Rnw | 5 ++--- inst/doc/neighbours.bib | 2 +- inst/doc/neighbours.pdf |binary inst/tinytest/test_neighbours.R | 32 ++++++++++++++++++++++++++++++-- man/neighbourfun.Rd | 4 ++-- tests/tinytest.R | 7 ++++--- vignettes/neighbours.Rnw | 5 ++--- vignettes/neighbours.bib | 2 +- 16 files changed, 102 insertions(+), 41 deletions(-)
Title: Diagnostics for Lists of Codes Based on Measurements
Description: Diagnostics of list of codes based on concepts from the domains measurement and observation. This package works for data mapped to the Observational Medical Outcomes Partnership Common Data Model.
Author: Edward Burn [aut] ,
Nuria Mercade-Besora [aut, cre] ,
Marta Alcalde-Herraiz [aut]
Maintainer: Nuria Mercade-Besora <nuria.mercadebesora@ndorms.ox.ac.uk>
Diff between MeasurementDiagnostics versions 0.1.0 dated 2025-07-29 and 0.2.0 dated 2025-12-17
MeasurementDiagnostics-0.1.0/MeasurementDiagnostics/R/plotMeasurementTimings.R |only MeasurementDiagnostics-0.1.0/MeasurementDiagnostics/R/tableMeasurementTimings.R |only MeasurementDiagnostics-0.1.0/MeasurementDiagnostics/R/utils.R |only MeasurementDiagnostics-0.1.0/MeasurementDiagnostics/man/pipe.Rd |only MeasurementDiagnostics-0.1.0/MeasurementDiagnostics/man/plotMeasurementTimings.Rd |only MeasurementDiagnostics-0.1.0/MeasurementDiagnostics/man/plotMeasurementValueAsNumeric.Rd |only MeasurementDiagnostics-0.1.0/MeasurementDiagnostics/man/tableMeasurementTimings.Rd |only MeasurementDiagnostics-0.1.0/MeasurementDiagnostics/man/tableMeasurementValueAsNumeric.Rd |only MeasurementDiagnostics-0.1.0/MeasurementDiagnostics/tests/testthat/test-plotMeasurementTimings.R |only MeasurementDiagnostics-0.1.0/MeasurementDiagnostics/tests/testthat/test-tableMeasurementTimings.R |only MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/DESCRIPTION | 22 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/MD5 | 90 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/NAMESPACE | 30 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/R/MeasurementDiagnostics-package.R |only MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/R/documentationHelpers.R | 196 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/R/mockMeasurementDiagnostics.R | 156 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/R/plotMeasurementSummary.R |only MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/R/plotMeasurementValueAsConcept.R | 136 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/R/plotMeasurementValueAsNumeric.R | 217 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/R/summariseCohortMeasurementUse.R | 129 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/R/summariseMeasurementUse.R | 1436 +- MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/R/tableMeasurementSummary.R |only MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/R/tableMeasurementValueAsConcept.R | 181 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/R/tableMeasurementValueAsNumeric.R | 196 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/README.md | 188 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/build/vignette.rds |binary MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/inst/doc/summariseMeasurementUse.R | 108 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/inst/doc/summariseMeasurementUse.Rmd | 180 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/inst/doc/summariseMeasurementUse.html | 4952 +++++----- MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/man/MeasurementDiagnostics-package.Rd |only MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/man/mockMeasurementDiagnostics.Rd | 74 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/man/plotDoc.Rd | 54 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/man/plotMeasurementSummary.Rd |only MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/man/plotMeasurementValueAsConcept.Rd | 106 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/man/plotMeasurementValueAsNumber.Rd |only MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/man/resultDoc.Rd | 24 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/man/summariseCohortMeasurementUse.Rd | 167 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/man/summariseMeasurementDoc.Rd | 90 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/man/summariseMeasurementUse.Rd | 164 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/man/tableDoc.Rd | 67 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/man/tableMeasurementSummary.Rd |only MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/man/tableMeasurementValueAsConcept.Rd | 126 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/man/tableMeasurementValueAsNumber.Rd |only MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/man/timeScaleDoc.Rd | 24 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/man/uniqueCombinationsDoc.Rd | 26 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/tests/testthat.R | 8 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/tests/testthat/setup.R | 575 - MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/tests/testthat/test-plotMeasurementSummary.R |only MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/tests/testthat/test-plotMeasurementValueAsConcept.R | 42 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/tests/testthat/test-plotMeasurementValueAsNumeric.R | 66 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/tests/testthat/test-summariseCohortMeasurementUse.R | 675 - MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/tests/testthat/test-summariseMeasurementUse.R | 668 - MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/tests/testthat/test-tableMeasurementSummary.R |only MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/tests/testthat/test-tableMeasurementValueAsConcept.R | 111 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/tests/testthat/test-tableMeasurementValueAsNumeric.R | 110 MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/vignettes/summariseMeasurementUse.Rmd | 180 56 files changed, 6147 insertions(+), 5427 deletions(-)
More information about MeasurementDiagnostics at CRAN
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Title: Multiplicative Interaction Models Diagnostics and Visualization
Description: Performs diagnostic tests of multiplicative interaction models and plots non-linear marginal effects of a treatment on an outcome across different values of a moderator.
Author: Jens Hainmueller [aut, ctb],
Jonathan Mummolo [aut, ctb],
Yiqing Xu [aut, cre],
Ziyi Liu [aut, ctb]
Maintainer: Yiqing Xu <yiqingxu@stanford.edu>
Diff between interflex versions 1.2.6 dated 2021-05-18 and 1.2.8 dated 2025-12-17
interflex-1.2.6/interflex/README.md |only interflex-1.2.8/interflex/DESCRIPTION | 20 ++++++++++---------- interflex-1.2.8/interflex/MD5 | 7 +++---- interflex-1.2.8/interflex/src/Makevars | 12 +----------- interflex-1.2.8/interflex/src/Makevars.win | 12 +----------- 5 files changed, 15 insertions(+), 36 deletions(-)
Title: Access Data from the 'Impect' API
Description: Pull data from the 'Impect' Customer API <https://glossary.impect.com/api-design>. The package can retrieve data such as events or match sums.
Author: Impect GmbH [cph],
Florian Schmitt [aut, cre],
Thomas Walentin [ctb]
Maintainer: Florian Schmitt <florian.schmitt@impect.com>
Diff between impectR versions 2.5.2 dated 2025-10-17 and 2.5.3 dated 2025-12-17
DESCRIPTION | 6 ++--- MD5 | 8 +++---- NEWS.md | 5 ++++ R/getPlayerIterationAverages.R | 42 ++++++++++++++++++++++++----------------- README.md | 6 ++--- 5 files changed, 40 insertions(+), 27 deletions(-)
More information about algebraic.dist at CRAN
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Title: Utilities for Handling Strings and Text
Description: Utilities for handling character vectors
that store human-readable text (either plain or with
markup, such as HTML or LaTeX). The package provides,
in particular, functions that help with the
preparation of plain-text reports, e.g. for expanding
and aligning strings that form the lines of such
reports. The package also provides generic functions for
transforming R objects to HTML and to plain text.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between textutils versions 0.4-2 dated 2025-04-01 and 0.4-3 dated 2025-12-17
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- NEWS | 4 ++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/btable.Rnw | 4 ++-- inst/doc/btable.pdf |binary vignettes/btable.Rnw | 4 ++-- 8 files changed, 21 insertions(+), 16 deletions(-)
Title: Translate CSS Selectors to XPath Expressions
Description: Translates a CSS selector into an equivalent XPath
expression. This allows us to use CSS selectors when working with
the XML package as it can only evaluate XPath expressions. Also
provided are convenience functions useful for using CSS selectors on
XML nodes. This package is a port of the Python package 'cssselect'
(<https://cssselect.readthedocs.io/>).
Author: Simon Potter [aut, trl, cre],
Simon Sapin [aut],
Ian Bicking [aut]
Maintainer: Simon Potter <simon@sjp.co.nz>
Diff between selectr versions 0.5-0 dated 2025-11-21 and 0.5-1 dated 2025-12-17
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/parser.R | 8 ++++---- inst/NEWS.Rd | 15 +++++++++++++++ tests/testthat/test-translation.R | 20 ++++++++++++++++++++ 5 files changed, 46 insertions(+), 11 deletions(-)
Title: Implements Pseudo-R2D2 Prior for Ordinal Regression
Description: Implements the pseudo-R2D2 prior for ordinal regression from the paper "Pseudo-R2D2 prior for high-dimensional ordinal regression" by Yanchenko (2025) <doi:10.1007/s11222-025-10667-x>. In particular, it provides code to evaluate the probability distribution function for the cut-points, compute the log-likelihood, calculate the hyper-parameters for the global variance parameter, find the distribution of McFadden's coefficient-of-determination, and fit the model in 'rstan'. Please cite the paper if you use these codes.
Author: Eric Yanchenko [aut, cre]
Maintainer: Eric Yanchenko <eyanchenko@aiu.ac.jp>
Diff between R2D2ordinal versions 1.0.1 dated 2025-03-18 and 1.0.2 dated 2025-12-17
DESCRIPTION | 8 MD5 | 26 +- R/functions.R | 68 +++-- R/ord_r2d2.R | 5 inst/doc/overview.html | 11 inst/stan/r2d2ord.stan | 6 man/dcut.Rd | 2 man/find_param.Rd | 2 man/llike.Rd | 2 man/ord_r2d2.Rd | 5 src/stanExports_r2d2ord.h | 150 ++++++++----- vignettes/overview_files/figure-html/unnamed-chunk-4-1.png |binary vignettes/overview_files/figure-html/unnamed-chunk-4-2.png |binary vignettes/overview_files/figure-html/unnamed-chunk-4-3.png |binary 14 files changed, 169 insertions(+), 116 deletions(-)
Title: Scraper for National Hockey League Data
Description: Scrapes and cleans data from the 'NHL' and 'ESPN' APIs into data.frames and lists. Wraps 125+ endpoints documented in <https://github.com/RentoSaijo/nhlscraper/wiki> from high-level multi-season summaries and award winners to low-level decisecond replays and bookmakers' odds, making them more accessible. Features cleaning and visualization tools, primarily for play-by-plays.
Author: Rento Saijo [aut, cre, cph] ,
Lars Skytte [ctb]
Maintainer: Rento Saijo <rentosaijo0527@gmail.com>
Diff between nhlscraper versions 0.4.0 dated 2025-11-30 and 0.4.1 dated 2025-12-17
DESCRIPTION | 6 +- MD5 | 42 +++++++-------- NEWS.md | 5 + R/Award.R | 30 +++++++---- R/Coach.R | 49 ++++++++++++------ R/Draft.R | 148 +++++++++++++++++++++++++++++++++++-------------------- R/ESPNGame.R | 1 R/ESPNOther.R | 17 ++++-- R/ESPNPlayer.R | 39 ++++++++------ R/ESPNTeam.R | 39 ++++++++------ R/Event.R | 18 ++++-- R/Franchise.R | 129 ++++++++++++++++++++++++++++++------------------ R/Game.R | 17 ++++-- R/Goalie.R | 152 +++++++++++++++++++++++++++++++++++++-------------------- R/League.R | 88 ++++++++++++++++++++++----------- R/Manager.R | 14 +++-- R/Official.R | 13 +++- R/Other.R | 39 ++++++++++---- R/Player.R | 28 +++++++--- R/Playoff.R | 35 ++++++++----- R/Skater.R | 109 ++++++++++++++++++++++++++++------------ R/Team.R | 71 +++++++++++++++++--------- 22 files changed, 706 insertions(+), 383 deletions(-)
Title: Translate Words or Sentences via Online Translators
Description: Useful functions to translate text for multiple languages using online translators.
For example, by translating error messages and descriptive analysis results into a language familiar
to the user, it enables a better understanding of the information, thereby reducing the barriers caused by language.
It offers several helper functions to query gene information to help interpretation of interested genes (e.g., marker genes, differential expression genes),
and provides utilities to translate 'ggplot' graphics. This package is not affiliated with any of the online translators.
The developers do not take responsibility for the invoice it incurs when using this package, especially for exceeding the free quota.
Author: Guangchuang Yu [aut, cre, cph] ,
Guannan Chen [ctb],
Difei Wang [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between fanyi versions 0.0.8 dated 2025-08-28 and 0.0.9 dated 2025-12-17
DESCRIPTION | 8 - MD5 | 16 +-- NAMESPACE | 2 NEWS.md | 4 R/deepseek.r | 195 ++++++++++++++++++++++++++++++-------------- R/qwen.r | 2 R/translate.r | 6 + man/set-translate-option.Rd | 2 man/translate.Rd | 2 9 files changed, 161 insertions(+), 76 deletions(-)
More information about customknitrender at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-09-17 1.1.0
2023-04-18 1.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-24 0.30.0
2024-11-10 0.29.0
2024-07-25 0.28.0
2023-04-05 0.27.1
2021-03-19 0.26.0
2020-02-05 0.24.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-06 0.1.4
2025-04-05 0.1.3
2025-02-18 0.1.2
2025-02-15 0.1.1
2024-12-19 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-22 0.3.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-11-17 1.0.6
2025-08-25 1.0.5
2025-04-28 1.0.4
2025-04-01 1.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-12-31 1.2
2015-10-02 1.1
2015-10-01 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-10-11 0.3.1
2023-11-15 0.3.0
2023-10-14 0.2.11
2023-08-22 0.2.10
2023-06-24 0.2.9
2023-04-14 0.2.8
Title: Running Local LLMs with 'llama.cpp' Backend
Description: Provides R bindings to the 'llama.cpp' library for running large language models.
The package uses a lightweight architecture where the C++ backend library is downloaded
at runtime rather than bundled with the package.
Package features include text generation, reproducible generation, and parallel inference.
Author: Eddie Yang [aut] ,
Yaosheng Xu [aut, cre]
Maintainer: Yaosheng Xu <xu2009@purdue.edu>
Diff between localLLM versions 1.0.1 dated 2025-10-15 and 1.1.0 dated 2025-12-17
localLLM-1.0.1/localLLM/src/Makevars |only localLLM-1.0.1/localLLM/src/Makevars.win |only localLLM-1.1.0/localLLM/DESCRIPTION | 23 localLLM-1.1.0/localLLM/MD5 | 73 localLLM-1.1.0/localLLM/NAMESPACE | 13 localLLM-1.1.0/localLLM/R/annotations.R |only localLLM-1.1.0/localLLM/R/api.R | 755 ++++++++-- localLLM-1.1.0/localLLM/R/capacity.R |only localLLM-1.1.0/localLLM/R/documentation.R |only localLLM-1.1.0/localLLM/R/hash_utils.R |only localLLM-1.1.0/localLLM/R/install.R | 12 localLLM-1.1.0/localLLM/R/ollama.R |only localLLM-1.1.0/localLLM/R/quick_llama.R | 290 ++- localLLM-1.1.0/localLLM/R/zzz.R | 4 localLLM-1.1.0/localLLM/README.md |only localLLM-1.1.0/localLLM/build |only localLLM-1.1.0/localLLM/inst |only localLLM-1.1.0/localLLM/man/annotation_sink_csv.Rd |only localLLM-1.1.0/localLLM/man/compute_confusion_matrices.Rd |only localLLM-1.1.0/localLLM/man/document_end.Rd |only localLLM-1.1.0/localLLM/man/document_start.Rd |only localLLM-1.1.0/localLLM/man/explore.Rd |only localLLM-1.1.0/localLLM/man/generate.Rd | 7 localLLM-1.1.0/localLLM/man/generate_parallel.Rd | 7 localLLM-1.1.0/localLLM/man/hardware_profile.Rd |only localLLM-1.1.0/localLLM/man/intercoder_reliability.Rd |only localLLM-1.1.0/localLLM/man/list_ollama_models.Rd |only localLLM-1.1.0/localLLM/man/quick_llama.Rd | 5 localLLM-1.1.0/localLLM/man/validate.Rd |only localLLM-1.1.0/localLLM/src/interface.cpp | 139 + localLLM-1.1.0/localLLM/tests/testthat/test-annotations.R |only localLLM-1.1.0/localLLM/tests/testthat/test-documentation.R |only localLLM-1.1.0/localLLM/tests/testthat/test-irr-comparison.R |only localLLM-1.1.0/localLLM/tests/testthat/test-ollama.R |only localLLM-1.1.0/localLLM/tests/testthat/test-quick-llama-helpers.R | 50 localLLM-1.1.0/localLLM/tests/testthat/test-validate.R |only localLLM-1.1.0/localLLM/vignettes |only 37 files changed, 1102 insertions(+), 276 deletions(-)
Title: Scientific Journal and Sci-Fi Themed Color Palettes for
'ggplot2'
Description: A collection of 'ggplot2' color palettes inspired by
plots in scientific journals, data visualization libraries,
science fiction movies, and TV shows.
Author: Nan Xiao [aut, cre, cph] ,
Joshua Cook [ctb],
Clara Jegousse [ctb],
Hui Chen [ctb],
Miaozhu Li [ctb],
iTerm2-Color-Schemes contributors [ctb, cph] ,
Winston Chang [ctb, cph]
Maintainer: Nan Xiao <me@nanx.me>
Diff between ggsci versions 4.1.0 dated 2025-10-25 and 4.2.0 dated 2025-12-17
DESCRIPTION | 6 - MD5 | 28 ++++---- NEWS.md | 11 +++ R/continuous-bs5.R | 36 ++++++----- R/continuous-material.R | 44 +++++++------ R/continuous-tw3.R | 44 +++++++------ R/discrete-cosmic.R | 15 ++-- R/discrete-uchicago.R | 4 - R/palettes-iterm.R | 152 ++++++++++++++++++++++++++++++++++++++++++++++++ build/vignette.rds |binary inst/doc/ggsci.Rmd | 2 inst/doc/ggsci.html | 2 man/pal_uchicago.Rd | 2 man/scale_uchicago.Rd | 2 vignettes/ggsci.Rmd | 2 15 files changed, 264 insertions(+), 86 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-12-03 1.2.6
2022-09-08 1.2.5
2021-09-22 1.2.4
2021-06-09 1.2.3
2021-05-13 1.2.2
2021-05-07 1.2.1
2021-03-10 1.2.0
2020-10-24 1.1.0
2020-06-19 1.0.5
2020-06-17 1.0.4
2020-03-16 1.0.3
2020-03-03 1.0.2
2019-12-17 1.0.1
2019-11-06 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-04-07 0.6.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-05-17 2.0.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-14 1.2.4
2021-06-09 1.2.3
2021-05-13 1.2.2
2021-05-06 1.2.1
2021-03-09 1.2.0
2020-10-23 1.1.0
2020-04-23 1.0.8
2020-03-16 1.0.7
2020-03-03 1.0.6
2020-03-02 1.0.5
2019-12-15 1.0.3
2019-10-28 1.0.1
2019-10-28 1.0.2
2019-07-03 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-01-26 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-12-15 1.1.0
2022-04-07 1.0.0
2022-01-15 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-08-21 0.99.7
2023-01-13 0.99.6
2022-11-20 0.99.3
2022-06-24 0.99.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-26 1.2.1
2023-12-17 1.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-04-14 0.3.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-30 1.1.3
2023-01-28 1.1.2
2021-05-13 1.1.1
2020-10-25 1.1.0
2020-01-13 1.0.1
2019-09-07 1.0
Title: Functions for University of Auckland Course STATS 201/208 Data
Analysis
Description: A set of functions used in teaching STATS 201/208 Data Analysis at
the University of Auckland. The functions are designed to make parts of R more
accessible to a large undergraduate population who are mostly not statistics
majors.
Author: Brant Deppa [aut] ,
James Curran [aut, cre] ,
Hannah Yun [ctb],
Rachel Fewster [ctb],
Russell Millar [ctb],
Ben Stevenson [ctb],
Andrew Balemi [ctb],
Chris Wild [ctb],
Sophie Jones [ctb],
Dineika Chandra [ctr],
Brendan McArdle [ctr]
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between s20x versions 3.1-40 dated 2023-08-21 and 3.2.1 dated 2025-12-17
s20x-3.1-40/s20x/data/fruitfly.df.rda |only s20x-3.2.1/s20x/DESCRIPTION | 15 + s20x-3.2.1/s20x/MD5 | 238 ++++++++++++++++++--------- s20x-3.2.1/s20x/NAMESPACE | 9 + s20x-3.2.1/s20x/R/casestudy.R |only s20x-3.2.1/s20x/R/ciReg.R | 86 ++++----- s20x-3.2.1/s20x/R/listCaseStudies.R |only s20x-3.2.1/s20x/R/openCaseStudy.R |only s20x-3.2.1/s20x/R/s20x-package.R | 2 s20x-3.2.1/s20x/inst/case_studies |only s20x-3.2.1/s20x/inst/extdata |only s20x-3.2.1/s20x/man/airpass.df.Rd | 28 +-- s20x-3.2.1/s20x/man/apples.df.Rd | 66 +++---- s20x-3.2.1/s20x/man/arousal.df.Rd | 40 ++-- s20x-3.2.1/s20x/man/autocorPlot.Rd | 72 ++++---- s20x-3.2.1/s20x/man/beer.df.Rd | 28 +-- s20x-3.2.1/s20x/man/body.df.Rd | 40 ++-- s20x-3.2.1/s20x/man/books.df.Rd | 46 ++--- s20x-3.2.1/s20x/man/boxqq.Rd | 88 +++++----- s20x-3.2.1/s20x/man/bursary.df.Rd | 36 ++-- s20x-3.2.1/s20x/man/butterfat.df.Rd | 62 +++---- s20x-3.2.1/s20x/man/camplake.df.Rd | 34 +-- s20x-3.2.1/s20x/man/casestudy.Rd |only s20x-3.2.1/s20x/man/chalk.df.Rd | 36 ++-- s20x-3.2.1/s20x/man/ciReg.Rd | 68 +++---- s20x-3.2.1/s20x/man/computer.df.Rd | 38 ++-- s20x-3.2.1/s20x/man/cooks20x.Rd | 104 +++++------ s20x-3.2.1/s20x/man/course.df.Rd | 58 +++--- s20x-3.2.1/s20x/man/course2way.df.Rd | 38 ++-- s20x-3.2.1/s20x/man/crossFactors.Rd | 122 +++++++------- s20x-3.2.1/s20x/man/crosstabs.Rd | 74 ++++---- s20x-3.2.1/s20x/man/diamonds.df.Rd | 32 +-- s20x-3.2.1/s20x/man/displayPairs.Rd | 142 ++++++++-------- s20x-3.2.1/s20x/man/eovcheck.Rd | 218 ++++++++++++------------- s20x-3.2.1/s20x/man/estimateContrasts.Rd | 122 +++++++------- s20x-3.2.1/s20x/man/fire.df.Rd | 32 +-- s20x-3.2.1/s20x/man/freq1way.Rd | 128 +++++++------- s20x-3.2.1/s20x/man/fruitfly.df.Rd | 64 +++---- s20x-3.2.1/s20x/man/getVersion.Rd | 38 ++-- s20x-3.2.1/s20x/man/house.df.Rd | 32 +-- s20x-3.2.1/s20x/man/incomes.df.Rd | 22 +- s20x-3.2.1/s20x/man/interactionPlots.Rd | 270 +++++++++++++++---------------- s20x-3.2.1/s20x/man/lakemary.df.Rd | 30 +-- s20x-3.2.1/s20x/man/larain.df.Rd | 26 +- s20x-3.2.1/s20x/man/layout20x.Rd | 66 +++---- s20x-3.2.1/s20x/man/levene.test.Rd | 80 ++++----- s20x-3.2.1/s20x/man/listCaseStudies.Rd |only s20x-3.2.1/s20x/man/mazda.df.Rd | 32 +-- s20x-3.2.1/s20x/man/mening.df.Rd | 30 +-- s20x-3.2.1/s20x/man/mergers.df.Rd | 24 +- s20x-3.2.1/s20x/man/modelcheck.Rd | 92 +++++----- s20x-3.2.1/s20x/man/mozart.df.Rd | 34 +-- s20x-3.2.1/s20x/man/multipleComp.Rd | 78 ++++---- s20x-3.2.1/s20x/man/nail.df.Rd | 34 +-- s20x-3.2.1/s20x/man/normcheck.Rd | 250 ++++++++++++++-------------- s20x-3.2.1/s20x/man/onewayPlot.Rd | 228 +++++++++++++------------- s20x-3.2.1/s20x/man/openCaseStudy.Rd |only s20x-3.2.1/s20x/man/oysters.df.Rd | 40 ++-- s20x-3.2.1/s20x/man/pairs20x.Rd | 68 +++---- s20x-3.2.1/s20x/man/peru.df.Rd | 40 ++-- s20x-3.2.1/s20x/man/predict20x.Rd | 126 +++++++------- s20x-3.2.1/s20x/man/predictCount.Rd | 76 ++++---- s20x-3.2.1/s20x/man/predictGLM.Rd | 76 ++++---- s20x-3.2.1/s20x/man/propslsd.new.Rd | 52 ++--- s20x-3.2.1/s20x/man/rain.df.Rd | 40 ++-- s20x-3.2.1/s20x/man/residPlot.Rd | 80 ++++----- s20x-3.2.1/s20x/man/rowdistr.Rd | 142 ++++++++-------- s20x-3.2.1/s20x/man/rr.Rd | 24 +- s20x-3.2.1/s20x/man/s20x-package.Rd | 1 s20x-3.2.1/s20x/man/seeds.df.Rd | 40 ++-- s20x-3.2.1/s20x/man/sheep.df.Rd | 30 +-- s20x-3.2.1/s20x/man/skewness.Rd | 60 +++--- s20x-3.2.1/s20x/man/skulls.df.Rd | 62 +++---- s20x-3.2.1/s20x/man/snapper.df.Rd | 46 ++--- s20x-3.2.1/s20x/man/soyabean.df.Rd | 40 ++-- s20x-3.2.1/s20x/man/stripqq.Rd | 80 ++++----- s20x-3.2.1/s20x/man/summary1way.Rd | 126 +++++++------- s20x-3.2.1/s20x/man/summary2way.Rd | 192 +++++++++++----------- s20x-3.2.1/s20x/man/summaryStats.Rd | 214 ++++++++++++------------ s20x-3.2.1/s20x/man/teach.df.Rd | 38 ++-- s20x-3.2.1/s20x/man/technitron.df.Rd | 44 ++--- s20x-3.2.1/s20x/man/thyroid.df.Rd | 42 ++-- s20x-3.2.1/s20x/man/toothpaste.df.Rd | 38 ++-- s20x-3.2.1/s20x/man/trendscatter.Rd | 164 +++++++++--------- s20x-3.2.1/s20x/man/zoo.df.Rd | 48 ++--- 85 files changed, 2830 insertions(+), 2731 deletions(-)
Title: Open-Source Software for 'Omic' Data Analysis and Visualization
Description: A tool for interactive exploration of the results from 'omics'
experiments to facilitate novel discoveries from high-throughput biology. The
software includes R functions for the 'bioinformatician' to deposit study
metadata and the outputs from statistical analyses (e.g. differential
expression, enrichment). These results are then exported to an interactive
JavaScript dashboard that can be interrogated on the user's local machine or
deployed online to be explored by collaborators. The dashboard includes
'sortable' tables, interactive plots including network visualization, and
fine-grained filtering based on statistical significance.
Author: Terrence Ernst [aut] ,
John Blischak [aut] ,
Paul Nordlund [aut] ,
Justin Moore [aut] ,
Joe Dalen [aut] ,
Akshay Bhamidipati [aut] ,
Brett Engelmann [aut, cre],
Marco Curado [aut] ,
Joe LoGrasso [aut] ,
Elyse Geoffroy [ctb],
AbbVie Inc. [cph, fnd]
Maintainer: Brett Engelmann <brett.engelmann@abbvie.com>
Diff between OmicNavigator versions 1.16.0 dated 2025-07-30 and 1.19.0 dated 2025-12-17
OmicNavigator-1.16.0/OmicNavigator/man/listStudies.Rd |only OmicNavigator-1.19.0/OmicNavigator/DESCRIPTION | 19 OmicNavigator-1.19.0/OmicNavigator/LICENSE | 4 OmicNavigator-1.19.0/OmicNavigator/MD5 | 281 OmicNavigator-1.19.0/OmicNavigator/NAMESPACE | 193 OmicNavigator-1.19.0/OmicNavigator/NEWS.md | 2006 +++--- OmicNavigator-1.19.0/OmicNavigator/R/add.R | 1472 ++--- OmicNavigator-1.19.0/OmicNavigator/R/app.R | 1062 +-- OmicNavigator-1.19.0/OmicNavigator/R/check.R | 1182 ++-- OmicNavigator-1.19.0/OmicNavigator/R/combine.R | 194 OmicNavigator-1.19.0/OmicNavigator/R/data.R | 388 - OmicNavigator-1.19.0/OmicNavigator/R/dropdowns.R |only OmicNavigator-1.19.0/OmicNavigator/R/export.R | 1180 +--- OmicNavigator-1.19.0/OmicNavigator/R/get.R | 1126 ++- OmicNavigator-1.19.0/OmicNavigator/R/import.R | 160 OmicNavigator-1.19.0/OmicNavigator/R/local.R | 222 OmicNavigator-1.19.0/OmicNavigator/R/overlaps.R | 245 OmicNavigator-1.19.0/OmicNavigator/R/plots.R | 1028 +-- OmicNavigator-1.19.0/OmicNavigator/R/print.R | 64 OmicNavigator-1.19.0/OmicNavigator/R/sanitize.R | 222 OmicNavigator-1.19.0/OmicNavigator/R/summary.R | 98 OmicNavigator-1.19.0/OmicNavigator/R/tests.R | 1046 +-- OmicNavigator-1.19.0/OmicNavigator/R/upset.R | 1411 ++-- OmicNavigator-1.19.0/OmicNavigator/R/utility.R | 448 - OmicNavigator-1.19.0/OmicNavigator/R/validate.R | 777 +- OmicNavigator-1.19.0/OmicNavigator/R/zzz.R | 207 OmicNavigator-1.19.0/OmicNavigator/README.md | 474 - OmicNavigator-1.19.0/OmicNavigator/build/partial.rdb |binary OmicNavigator-1.19.0/OmicNavigator/inst/CITATION | 46 OmicNavigator-1.19.0/OmicNavigator/inst/doc/OmicNavigatorAPI.R | 890 +-- OmicNavigator-1.19.0/OmicNavigator/inst/doc/OmicNavigatorAPI.Rnw | 1315 ++-- OmicNavigator-1.19.0/OmicNavigator/inst/doc/OmicNavigatorAPI.pdf |binary OmicNavigator-1.19.0/OmicNavigator/inst/doc/OmicNavigatorUsersGuide.R | 1034 +-- OmicNavigator-1.19.0/OmicNavigator/inst/doc/OmicNavigatorUsersGuide.Rnw | 2935 +++++----- OmicNavigator-1.19.0/OmicNavigator/inst/doc/OmicNavigatorUsersGuide.pdf |binary OmicNavigator-1.19.0/OmicNavigator/inst/extdata/description-fields-reserved.txt | 94 OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/backwardsCompatibility |only OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/testAdd.R | 331 - OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/testApp.R | 1109 +-- OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/testBackwardsCompatibility.R |only OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/testBugs.R | 462 - OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/testCheck.R | 1519 ++--- OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/testCombine.R | 268 OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/testDropdowns.R |only OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/testExport.R | 644 +- OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/testExtraMetadata.R | 278 OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/testGet.R | 1771 +++--- OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/testGetNumeric.R | 534 - OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/testImport.R | 536 + OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/testLibraries.R |only OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/testMetaAssays.R |only OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/testOverlaps.R | 90 OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/testPiecemeal.R | 364 - OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/testPlot.R | 2071 +++---- OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/testPrint.R | 58 OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/testSummary.R | 68 OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/testUpset.R | 1682 ++--- OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/testUtility.R | 98 OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/testValidate.R | 614 +- OmicNavigator-1.19.0/OmicNavigator/inst/tinytest/tinytestSettings.R | 18 OmicNavigator-1.19.0/OmicNavigator/man/Mm.c2.Rd | 70 OmicNavigator-1.19.0/OmicNavigator/man/OmicNavigator-package.Rd | 100 OmicNavigator-1.19.0/OmicNavigator/man/addAnnotations.Rd | 73 OmicNavigator-1.19.0/OmicNavigator/man/addAssays.Rd | 63 OmicNavigator-1.19.0/OmicNavigator/man/addBarcodes.Rd | 89 OmicNavigator-1.19.0/OmicNavigator/man/addEnrichments.Rd | 71 OmicNavigator-1.19.0/OmicNavigator/man/addEnrichmentsLinkouts.Rd | 122 OmicNavigator-1.19.0/OmicNavigator/man/addFeatures.Rd | 61 OmicNavigator-1.19.0/OmicNavigator/man/addMapping.Rd | 102 OmicNavigator-1.19.0/OmicNavigator/man/addMetaAssays.Rd |only OmicNavigator-1.19.0/OmicNavigator/man/addMetaFeatures.Rd | 71 OmicNavigator-1.19.0/OmicNavigator/man/addMetaFeaturesLinkouts.Rd | 129 OmicNavigator-1.19.0/OmicNavigator/man/addModels.Rd | 105 OmicNavigator-1.19.0/OmicNavigator/man/addObjects.Rd |only OmicNavigator-1.19.0/OmicNavigator/man/addOverlaps.Rd | 59 OmicNavigator-1.19.0/OmicNavigator/man/addPlots.Rd | 182 OmicNavigator-1.19.0/OmicNavigator/man/addReports.Rd | 65 OmicNavigator-1.19.0/OmicNavigator/man/addResults.Rd | 61 OmicNavigator-1.19.0/OmicNavigator/man/addResultsLinkouts.Rd | 129 OmicNavigator-1.19.0/OmicNavigator/man/addSamples.Rd | 61 OmicNavigator-1.19.0/OmicNavigator/man/addTests.Rd | 124 OmicNavigator-1.19.0/OmicNavigator/man/basal.vs.lp.Rd | 90 OmicNavigator-1.19.0/OmicNavigator/man/basal.vs.ml.Rd | 90 OmicNavigator-1.19.0/OmicNavigator/man/cam.BasalvsLP.Rd | 82 OmicNavigator-1.19.0/OmicNavigator/man/cam.BasalvsML.Rd | 82 OmicNavigator-1.19.0/OmicNavigator/man/combineStudies.Rd | 142 OmicNavigator-1.19.0/OmicNavigator/man/createStudy.Rd | 567 + OmicNavigator-1.19.0/OmicNavigator/man/exportStudy.Rd | 68 OmicNavigator-1.19.0/OmicNavigator/man/getAnnotations.Rd | 75 OmicNavigator-1.19.0/OmicNavigator/man/getAssays.Rd | 75 OmicNavigator-1.19.0/OmicNavigator/man/getBarcodeData.Rd | 83 OmicNavigator-1.19.0/OmicNavigator/man/getBarcodes.Rd | 75 OmicNavigator-1.19.0/OmicNavigator/man/getEnrichments.Rd | 97 OmicNavigator-1.19.0/OmicNavigator/man/getEnrichmentsAnnotations.Rd |only OmicNavigator-1.19.0/OmicNavigator/man/getEnrichmentsIntersection.Rd | 106 OmicNavigator-1.19.0/OmicNavigator/man/getEnrichmentsLinkouts.Rd | 85 OmicNavigator-1.19.0/OmicNavigator/man/getEnrichmentsModels.Rd |only OmicNavigator-1.19.0/OmicNavigator/man/getEnrichmentsNetwork.Rd | 64 OmicNavigator-1.19.0/OmicNavigator/man/getEnrichmentsStudies.Rd |only OmicNavigator-1.19.0/OmicNavigator/man/getEnrichmentsTable.Rd | 76 OmicNavigator-1.19.0/OmicNavigator/man/getEnrichmentsUpset.Rd | 84 OmicNavigator-1.19.0/OmicNavigator/man/getFavicons.Rd | 48 OmicNavigator-1.19.0/OmicNavigator/man/getFeatures.Rd | 59 OmicNavigator-1.19.0/OmicNavigator/man/getInstalledStudies.Rd | 48 OmicNavigator-1.19.0/OmicNavigator/man/getLinkFeatures.Rd | 55 OmicNavigator-1.19.0/OmicNavigator/man/getMapping.Rd | 75 OmicNavigator-1.19.0/OmicNavigator/man/getMetaAssays.Rd |only OmicNavigator-1.19.0/OmicNavigator/man/getMetaFeatures.Rd | 75 OmicNavigator-1.19.0/OmicNavigator/man/getMetaFeaturesLinkouts.Rd | 75 OmicNavigator-1.19.0/OmicNavigator/man/getMetaFeaturesTable.Rd | 57 OmicNavigator-1.19.0/OmicNavigator/man/getModels.Rd | 75 OmicNavigator-1.19.0/OmicNavigator/man/getNodeFeatures.Rd | 58 OmicNavigator-1.19.0/OmicNavigator/man/getObjects.Rd |only OmicNavigator-1.19.0/OmicNavigator/man/getOverlaps.Rd | 75 OmicNavigator-1.19.0/OmicNavigator/man/getPackageVersion.Rd | 41 OmicNavigator-1.19.0/OmicNavigator/man/getPlots.Rd | 75 OmicNavigator-1.19.0/OmicNavigator/man/getPlottingData.Rd | 195 OmicNavigator-1.19.0/OmicNavigator/man/getReportLink.Rd | 47 OmicNavigator-1.19.0/OmicNavigator/man/getReports.Rd | 75 OmicNavigator-1.19.0/OmicNavigator/man/getResults.Rd | 91 OmicNavigator-1.19.0/OmicNavigator/man/getResultsIntersection.Rd | 108 OmicNavigator-1.19.0/OmicNavigator/man/getResultsLinkouts.Rd | 75 OmicNavigator-1.19.0/OmicNavigator/man/getResultsModels.Rd |only OmicNavigator-1.19.0/OmicNavigator/man/getResultsStudies.Rd |only OmicNavigator-1.19.0/OmicNavigator/man/getResultsTable.Rd | 88 OmicNavigator-1.19.0/OmicNavigator/man/getResultsTests.Rd |only OmicNavigator-1.19.0/OmicNavigator/man/getResultsUpset.Rd | 69 OmicNavigator-1.19.0/OmicNavigator/man/getSamples.Rd | 75 OmicNavigator-1.19.0/OmicNavigator/man/getStudyMeta.Rd |only OmicNavigator-1.19.0/OmicNavigator/man/getTests.Rd | 79 OmicNavigator-1.19.0/OmicNavigator/man/getUpsetCols.Rd | 45 OmicNavigator-1.19.0/OmicNavigator/man/group.Rd | 80 OmicNavigator-1.19.0/OmicNavigator/man/importStudy.Rd | 44 OmicNavigator-1.19.0/OmicNavigator/man/installApp.Rd | 66 OmicNavigator-1.19.0/OmicNavigator/man/installStudy.Rd | 72 OmicNavigator-1.19.0/OmicNavigator/man/lane.Rd | 80 OmicNavigator-1.19.0/OmicNavigator/man/lcpm.Rd | 70 OmicNavigator-1.19.0/OmicNavigator/man/plotStudy.Rd | 135 OmicNavigator-1.19.0/OmicNavigator/man/removeStudy.Rd | 42 OmicNavigator-1.19.0/OmicNavigator/man/samplenames.Rd | 70 OmicNavigator-1.19.0/OmicNavigator/man/shared-add.Rd | 42 OmicNavigator-1.19.0/OmicNavigator/man/shared-data.Rd | 46 OmicNavigator-1.19.0/OmicNavigator/man/shared-dropdowns.Rd |only OmicNavigator-1.19.0/OmicNavigator/man/shared-get.Rd | 83 OmicNavigator-1.19.0/OmicNavigator/man/shared-upset.Rd | 66 OmicNavigator-1.19.0/OmicNavigator/man/startApp.Rd | 74 OmicNavigator-1.19.0/OmicNavigator/man/summary.onStudy.Rd | 46 OmicNavigator-1.19.0/OmicNavigator/man/validateStudy.Rd | 38 OmicNavigator-1.19.0/OmicNavigator/tests/tinytest.R | 8 OmicNavigator-1.19.0/OmicNavigator/vignettes/OmicNavigatorAPI.Rnw | 1315 ++-- OmicNavigator-1.19.0/OmicNavigator/vignettes/OmicNavigatorUsersGuide.Rnw | 2935 +++++----- 151 files changed, 23412 insertions(+), 21679 deletions(-)
Title: Vowel Covariation Tools
Description: Tools to support research on vowel covariation. Methods are provided to
support Principal Component Analysis workflows (as in Brand et al. (2021)
<doi:10.1016/j.wocn.2021.101096> and Wilson Black et al. (2023)
<doi:10.1515/lingvan-2022-0086>).
Author: Joshua Wilson Black [aut, cre, cph] ,
James Brand [aut]
Maintainer: Joshua Wilson Black <joshua.black@canterbury.ac.nz>
Diff between nzilbb.vowels versions 0.4.2 dated 2025-12-04 and 0.4.3 dated 2025-12-17
DESCRIPTION | 10 ++++----- MD5 | 14 ++++++------- NAMESPACE | 3 -- NEWS.md | 6 +++++ R/correlation_plots.R | 32 +++++++++++++------------------ man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-2-2.png |binary man/plot_correlation_counts.Rd | 6 ++--- 8 files changed, 36 insertions(+), 35 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-14 1.5.6
2024-09-12 1.5.5
2024-08-18 1.5.4
2024-06-23 1.5.3
2024-06-04 1.5.2
2024-04-10 1.5.1
2024-02-05 1.5.0
2024-01-15 1.4.13
2023-12-15 1.4.12
2023-12-08 1.4.11
2023-10-28 1.4.10
2023-09-03 1.4.9
2023-08-24 1.4.8
2023-08-07 1.4.7
2023-04-29 1.4.6
2023-02-15 1.4.5
2023-01-09 1.4.4
2022-12-08 1.4.3
2022-10-16 1.4.2
2022-09-25 1.4.1
2022-09-08 1.4.0
2022-08-23 1.3.4
2022-07-04 1.3.3
2022-06-23 1.3.2
2022-05-23 1.3.1
2022-02-21 1.3.0
2021-12-13 1.2.5
2021-10-18 1.2.4
2021-10-05 1.2.2
2021-09-23 1.2.1
2021-09-20 1.2.0
2021-08-23 1.1.0
2021-08-17 1.0.0
2021-07-22 0.3.0
2021-06-17 0.2.0
2021-05-19 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-14 2.3.11
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to safely and efficiently organize and execute
Monte Carlo simulation experiments in R.
The package controls the structure and back-end of Monte Carlo simulation experiments
by utilizing a generate-analyse-summarise workflow. The workflow safeguards against
common simulation coding issues, such as automatically re-simulating non-convergent results,
prevents inadvertently overwriting simulation files, catches error and warning messages
during execution, implicitly supports parallel processing with high-quality random number
generation, and provides tools for managing high-performance computing (HPC) array jobs
submitted to schedulers such as SLURM. For a pedagogical introduction to the package see
Sigal and Chalmers (2016) <doi:10.1080/10691898.2016.1246953>. For a more in-depth overview of
the package and its design philosophy see Chalmers and Adkins (2020) <doi:10.20982/tqmp.16.4.p248>.
Author: Phil Chalmers [aut, cre] ,
Matthew Sigal [ctb],
Ogreden Oguzhan [ctb],
Mikko Roenkkoe [aut],
Moritz Ketzer [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 2.21 dated 2025-09-18 and 2.22 dated 2025-12-17
DESCRIPTION | 12 +- MD5 | 64 ++++++----- NEWS.md | 18 +++ R/PBA.R | 28 +++- R/SimExtract.R | 22 +++ R/SimResults.R | 18 ++- R/SimSolve.R | 3 R/analysis.R | 50 ++++++++ R/runSimulation.R | 214 ++++++++++++++++++++++++++++++++++---- R/util.R | 2 R/zzz.R | 6 + inst/doc/Catch_errors.html | 10 - inst/doc/Fixed_obj_fun.html | 10 - inst/doc/HPC-computing.html | 4 inst/doc/MultipleAnalyses.html | 4 inst/doc/Parallel-computing.html | 4 inst/doc/Saving-results.html | 4 inst/doc/SimDesign-intro.html | 4 man/PBA.Rd | 6 - man/SimExtract.Rd | 4 man/SimResults.Rd | 13 +- man/SimSolve.Rd | 2 man/new_PushbulletNotifier.Rd | 2 man/new_TelegramNotifier.Rd | 2 man/runArraySimulation.Rd | 12 ++ man/runSimulation.Rd | 147 ++++++++++++++++++++++++-- tests/tests/test-04-prepare.R |only tests/tests/test-seeds_cruncher |only tests/tests/test-seeds_cruncher_1 |only tests/tests/test.rds |only 30 files changed, 565 insertions(+), 100 deletions(-)
Title: R Interface to 'FishBase'
Description: A programmatic interface to 'FishBase', re-written
based on an accompanying 'RESTful' API. Access tables describing over 30,000
species of fish, their biology, ecology, morphology, and more. This package also
supports experimental access to 'SeaLifeBase' data, which contains
nearly 200,000 species records for all types of aquatic life not covered by
'FishBase.'
Author: Carl Boettiger [cre, aut] ,
Scott Chamberlain [aut] ,
Duncan Temple Lang [aut],
Peter Wainwright [aut],
Kevin Cazelles [ctb] ,
Guohuan Su [ctb]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between rfishbase versions 5.0.1 dated 2025-01-12 and 5.0.2 dated 2025-12-17
DESCRIPTION | 22 ++-- MD5 | 14 +- NEWS.md | 11 ++ R/fb_tbl.R | 179 +++++++++++++++++----------------- R/load_taxa.R | 215 ++++++++++++++++++++++++++--------------- README.md | 13 +- inst/WORDLIST | 3 tests/testthat/test_endpoint.R | 14 -- 8 files changed, 278 insertions(+), 193 deletions(-)
Title: Machinery for Processing Random Effect Formulas
Description: Takes formulas including random-effects components (formatted as in 'lme4', 'glmmTMB', etc.) and processes them. Includes various helper functions.
Author: Ben Bolker [aut, cre] ,
Anna Ly [ctb]
Maintainer: Ben Bolker <bolker@mcmaster.ca>
Diff between reformulas versions 0.4.2 dated 2025-10-28 and 0.4.3 dated 2025-12-17
DESCRIPTION | 23 ++++++++++++++--------- MD5 | 13 ++++++++----- NAMESPACE | 13 +++++++++++++ NEWS.md | 4 ++++ R/VarCorr.R |only build/partial.rdb |binary man/formatVC.Rd |only man/format_sdvar.Rd |only man/no_specials.Rd | 1 + 9 files changed, 40 insertions(+), 14 deletions(-)
Title: Bayesian Reconstruction of Disease Outbreaks by Combining
Epidemiologic and Genomic Data
Description: Bayesian reconstruction of disease outbreaks using epidemiological
and genetic information. Jombart T, Cori A, Didelot X, Cauchemez S, Fraser
C and Ferguson N. 2014. <doi:10.1371/journal.pcbi.1003457>. Campbell, F,
Cori A, Ferguson N, Jombart T. 2019. <doi:10.1371/journal.pcbi.1006930>.
Author: Thibaut Jombart [aut],
Finlay Campbell [aut, cre],
Rich Fitzjohn [aut],
Gerry Tonkin-Hill [ctb],
Kristjan Eldjarn [ctb],
Alexis Robert [ctb]
Maintainer: Finlay Campbell <finlaycampbell93@gmail.com>
Diff between outbreaker2 versions 1.1.3 dated 2022-05-23 and 1.1.4 dated 2025-12-17
DESCRIPTION | 11 LICENSE | 2 MD5 | 180 NEWS.md | 13 R/bind_to_function.R | 2 R/create_config.R | 55 R/create_param.R | 2 R/custom_likelihoods.R | 6 R/custom_moves.R | 8 R/doc_data.R | 68 R/get_cpp_api.R | 36 R/internals.R | 25 R/outbreaker.R | 22 R/outbreaker_chains_methods.R | 23 R/outbreaker_data.R | 9 R/outbreaker_move.R | 4 R/package.R | 14 R/palettes.R | 82 README.md | 16 build/vignette.rds |binary inst/CITATION | 33 inst/doc/Rcpp_API.R | 6 inst/doc/Rcpp_API.html | 240 - inst/doc/customisation.R | 89 inst/doc/customisation.Rmd | 6 inst/doc/customisation.html | 2029 +++++----- inst/doc/introduction.R | 53 inst/doc/introduction.html | 1100 ++--- inst/doc/overview.R | 6 inst/doc/overview.html | 211 - man/bind_to_function.Rd | 2 man/create_config.Rd | 54 man/create_param.Rd | 2 man/custom_likelihoods.Rd | 6 man/custom_moves.Rd | 8 man/get_cpp_api.Rd | 36 man/outbreaker.Rd | 22 man/outbreaker_chains.Rd | 14 man/outbreaker_data.Rd | 6 man/outbreaker_package.Rd | 14 man/palettes.Rd | 52 src/likelihoods.cpp | 34 tests/testthat.R | 8 tests/testthat/test_binding.R | 116 tests/testthat/test_priors.R | 254 - vignettes/customisation.Rmd | 6 vignettes/customisation_cache/html/run_new_move_201bee2736c15bd01aff7d66538c46bd.RData |binary vignettes/customisation_cache/html/run_new_move_201bee2736c15bd01aff7d66538c46bd.rdb |binary vignettes/customisation_cache/html/run_new_move_201bee2736c15bd01aff7d66538c46bd.rdx |binary vignettes/customisation_cache/html/run_null_model_8771832d87831190a82188fc37cef737.RData |binary vignettes/customisation_cache/html/run_null_model_8771832d87831190a82188fc37cef737.rdb |binary vignettes/customisation_cache/html/run_null_model_8771832d87831190a82188fc37cef737.rdx |binary vignettes/customisation_cache/html/run_wt_770f6e5ae6cc9263e7c7c554c148a8b2.RData |binary vignettes/customisation_cache/html/run_wt_770f6e5ae6cc9263e7c7c554c148a8b2.rdb |binary vignettes/customisation_cache/html/run_wt_770f6e5ae6cc9263e7c7c554c148a8b2.rdx |binary vignettes/figs-customisation/null_net-1.png |binary vignettes/figs-customisation/null_trees-1.png |binary vignettes/figs-customisation/res_new_move-1.png |binary vignettes/figs-customisation/res_new_move-2.png |binary vignettes/figs-customisation/res_null_diag-1.png |binary vignettes/figs-customisation/res_null_diag-2.png |binary vignettes/figs-customisation/res_null_model-1.png |binary vignettes/figs-customisation/res_null_model-2.png |binary vignettes/figs-customisation/res_null_model-3.png |binary vignettes/figs-customisation/res_null_priors-1.png |binary vignettes/figs-customisation/res_null_priors-2.png |binary vignettes/figs-customisation/res_wt-1.png |binary vignettes/figs-customisation/res_wt-2.png |binary vignettes/figs-customisation/res_wt-3.png |binary vignettes/figs-customisation/traces_custom_priors-4.png |binary vignettes/figs-customisation/traces_custom_priors-5.png |binary vignettes/figs-customisation/wt_net-1.png |binary vignettes/figs-introduction/basic_trace-1.png |binary vignettes/figs-introduction/basic_trace_burn-1.png |binary vignettes/figs-introduction/config2-1.png |binary vignettes/figs-introduction/config2-2.png |binary vignettes/figs-introduction/many_plots-1.png |binary vignettes/figs-introduction/many_plots-2.png |binary vignettes/figs-introduction/many_plots-3.png |binary vignettes/figs-introduction/many_plots-4.png |binary vignettes/figs-introduction/many_plots-5.png |binary vignettes/figs-introduction/traces-1.png |binary vignettes/figs-introduction/traces-2.png |binary vignettes/figs-introduction/traces-3.png |binary vignettes/introduction_cache/html/__packages | 2 vignettes/introduction_cache/html/config2_a6e218c734814a74f6d109430a70e31f.RData |binary vignettes/introduction_cache/html/config2_a6e218c734814a74f6d109430a70e31f.rdb |binary vignettes/introduction_cache/html/config2_a6e218c734814a74f6d109430a70e31f.rdx |binary vignettes/introduction_cache/html/first_run_262464f50c8d3b374ad1083b0ea73503.RData |binary vignettes/introduction_cache/html/first_run_262464f50c8d3b374ad1083b0ea73503.rdb |binary vignettes/introduction_cache/html/first_run_262464f50c8d3b374ad1083b0ea73503.rdx |binary 91 files changed, 2626 insertions(+), 2361 deletions(-)
Title: Read and Write 'Parquet' Files
Description: Self-sufficient reader and writer for flat 'Parquet' files.
Can read most 'Parquet' data types. Can write many 'R' data types,
including factors and temporal types. See docs for limitations.
Author: Gabor Csardi [aut, cre],
Hannes Muehleisen [aut, cph] ,
Google Inc. [cph],
Apache Software Foundation [cph],
Posit Software, PBC [cph],
RAD Game Tools [cph],
Valve Software [cph],
Tenacious Software LLC [cph],
Facebook, Inc. [cph]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between nanoparquet versions 0.4.2 dated 2025-02-22 and 0.4.3 dated 2025-12-17
DESCRIPTION | 14 - MD5 | 76 +++--- NEWS.md | 4 R/arrow-schema.R | 47 ++-- R/infer-parquet-schema.R | 52 ++-- R/options.R | 29 +- R/parquet-column-types.R | 168 +++++++------- R/parquet-metadata.R | 218 +++++++++---------- R/porcelain.R | 184 ++++++++-------- R/read-parquet.R | 231 ++++++++++---------- R/schema.R | 160 +++++++++----- R/utils.R | 29 +- R/write-parquet.R | 96 +++++--- inst/WORDLIST | 10 src/RParquetReader.cpp | 2 src/lib/bytebuffer.h | 2 src/rwrapper.cpp | 1 tests/testthat.R | 1 tests/testthat/helper.R | 20 + tests/testthat/test-parquet-schema.R | 2 tests/testthat/test-porcelain.R | 43 ++- tests/testthat/test-pypolars.R | 7 tests/testthat/test-read-parquet-2.R | 64 +++-- tests/testthat/test-read-parquet-3.R | 68 ++++-- tests/testthat/test-read-parquet-4.R | 35 ++- tests/testthat/test-read-parquet-5.R | 81 ++++--- tests/testthat/test-read-parquet-row-group.R | 8 tests/testthat/test-read-parquet.R | 88 +++++-- tests/testthat/test-rle.R | 2 tests/testthat/test-utils.R | 2 tests/testthat/test-write-encodings-2.R | 27 +- tests/testthat/test-write-encodings.R | 26 +- tests/testthat/test-write-parquet-2.R | 94 ++++++-- tests/testthat/test-write-parquet-3.R | 90 ++++--- tests/testthat/test-write-parquet-4.R | 154 +++++++++++-- tests/testthat/test-write-parquet-compression.R | 14 + tests/testthat/test-write-parquet-row-groups.R | 5 tests/testthat/test-write-parquet-statistics.R | 271 +++++++++++++++--------- tests/testthat/test-write-parquet.R | 25 +- 39 files changed, 1532 insertions(+), 918 deletions(-)
Title: The Tidymodels Extension for Time Series Modeling
Description: The time series forecasting framework for use with the 'tidymodels' ecosystem.
Models include ARIMA, Exponential Smoothing, and additional time series models
from the 'forecast' and 'prophet' packages. Refer to "Forecasting Principles & Practice, Second edition"
(<https://otexts.com/fpp2/>).
Refer to "Prophet: forecasting at scale"
(<https://research.facebook.com/blog/2017/02/prophet-forecasting-at-scale/>.).
Author: Matt Dancho [aut, cre],
Business Science [cph]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between modeltime versions 1.3.2 dated 2025-08-28 and 1.3.3 dated 2025-12-17
DESCRIPTION | 17 MD5 | 34 NEWS.md | 9 R/modeltime-fit-workflowset.R | 1 R/modeltime-refit.R | 1 R/parsnip-arima_boost.R | 3 R/utils-control-par.R | 7 R/utils-xgboost.R | 12 build/vignette.rds |binary inst/doc/getting-started-with-modeltime.html | 1666 +++++++++------------- man/adam_reg.Rd | 16 man/arima_boost.Rd | 4 man/exp_smoothing.Rd | 14 man/prophet_boost.Rd | 4 man/temporal_hierarchy.Rd | 2 tests/testthat/test-algo-arima_boost-Arima.R | 41 tests/testthat/test-algo-arima_boost-auto_arima.R | 42 tests/testthat/test-algo-prophet_boost.R | 42 18 files changed, 860 insertions(+), 1055 deletions(-)
Title: Imputation Estimator from Borusyak, Jaravel, and Spiess (2021)
Description: Estimates Two-way Fixed Effects difference-in-differences/event-study models using the imputation-based approach proposed by Borusyak, Jaravel, and Spiess (2021).
Author: Kyle Butts [aut, cre]
Maintainer: Kyle Butts <buttskyle96@gmail.com>
Diff between didimputation versions 0.3.0 dated 2022-08-25 and 0.5.0 dated 2025-12-17
didimputation-0.3.0/didimputation/R/RcppExports.R |only didimputation-0.3.0/didimputation/R/didimputation-package.R |only didimputation-0.3.0/didimputation/R/utils-pipe.R |only didimputation-0.3.0/didimputation/R/utils.R |only didimputation-0.3.0/didimputation/R/zzz.R |only didimputation-0.3.0/didimputation/inst/CITATION |only didimputation-0.3.0/didimputation/man/pipe.Rd |only didimputation-0.3.0/didimputation/src |only didimputation-0.5.0/didimputation/DESCRIPTION | 33 didimputation-0.5.0/didimputation/MD5 | 31 didimputation-0.5.0/didimputation/NAMESPACE | 4 didimputation-0.5.0/didimputation/R/did_imputation.R | 369 +++++----- didimputation-0.5.0/didimputation/README.md | 274 +++---- didimputation-0.5.0/didimputation/inst/references.bib | 90 +- didimputation-0.5.0/didimputation/man/did_imputation.Rd | 65 + didimputation-0.5.0/didimputation/man/figures/README-plot-compare-1.png |binary didimputation-0.5.0/didimputation/man/figures/README-plot-df-het-1.png |binary didimputation-0.5.0/didimputation/man/figures/README-plot-es-1.png |binary didimputation-0.5.0/didimputation/tests/testthat/test-did_imputation.R | 80 +- 19 files changed, 524 insertions(+), 422 deletions(-)
Title: Compute Expected Shortfall and Value at Risk for Continuous
Distributions
Description: Compute expected shortfall (ES) and Value at Risk (VaR) from a
quantile function, distribution function, random number generator,
probability density function, or data. ES is also known as Conditional
Value at Risk (CVaR). Virtually any continuous distribution can be
specified. The functions are vectorized over the arguments. The
computations are done directly from the definitions, see e.g. Acerbi and
Tasche (2002) <doi:10.1111/1468-0300.00091>. Some support for GARCH models
is provided, as well.
Author: Georgi N. Boshnakov [aut, cre]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between cvar versions 0.5 dated 2022-11-03 and 0.6 dated 2025-12-17
cvar-0.5/cvar/vignettes/auto |only cvar-0.6/cvar/DESCRIPTION | 31 +-- cvar-0.6/cvar/MD5 | 42 ++-- cvar-0.6/cvar/NAMESPACE | 2 cvar-0.6/cvar/NEWS.md | 16 + cvar-0.6/cvar/R/VaR.R | 273 +++++++++++++++++++++----------- cvar-0.6/cvar/R/cvar-package.R | 78 +++++---- cvar-0.6/cvar/R/garch.R | 9 - cvar-0.6/cvar/README.md | 7 cvar-0.6/cvar/build/partial.rdb |binary cvar-0.6/cvar/build/vignette.rds |binary cvar-0.6/cvar/inst/doc/Guide_cvar.Rnw | 2 cvar-0.6/cvar/inst/doc/Guide_cvar.pdf |binary cvar-0.6/cvar/inst/pkgdown.yml |only cvar-0.6/cvar/man/ES.Rd | 63 ++++--- cvar-0.6/cvar/man/GarchModel.Rd | 1 cvar-0.6/cvar/man/VaR.Rd | 33 ++- cvar-0.6/cvar/man/cvar-package.Rd | 73 +++++--- cvar-0.6/cvar/man/predict.garch1c1.Rd | 1 cvar-0.6/cvar/man/sim_garch1c1.Rd | 2 cvar-0.6/cvar/tests/testthat/test-VaR.R | 85 +++++++++ cvar-0.6/cvar/vignettes/Guide_cvar.Rnw | 2 cvar-0.6/cvar/vignettes/REFERENCES.bib | 2 23 files changed, 492 insertions(+), 230 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-06-08 0.5.2
2025-05-16 0.4.0
2025-04-16 0.3.0
2025-02-25 0.2.0
2024-11-14 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-12-06 0.3.3
2025-10-10 0.3.2
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2025-01-23 0.2.0
2024-11-19 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-07-04 0.1.3
2022-09-30 0.1.2
2021-11-06 0.1.1
2021-02-22 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-28 3.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-27 0.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-12-06 0.1.4
2025-11-14 0.1.1
2025-10-30 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-12-14 1.1.2
2023-06-30 1.1.0
2021-09-18 1.0.0
2021-02-03 0.2.3
2020-07-08 0.2.2
2020-07-06 0.2.1
2020-05-15 0.2.0
2020-03-02 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
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