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Title: Supplementary Idiomatic Utilities and Extensions
Description: Miscellaneous supplementary functions designed to follow idiomatic 'R' conventions. Some functions are simple wrappers that reduce repetitive code, while others address common tasks or extend existing 'R' functions.
Author: Luke Jenkins [aut, cre, cph]
Maintainer: Luke Jenkins <luke-jenkins-dev@outlook.com>
Diff between suppr versions 1.0.0 dated 2026-09-05 and 1.0.1 dated 2026-09-07
DESCRIPTION | 6 +- MD5 | 14 ++-- NEWS.md | 6 ++ README.md | 3 + src/repeated.c | 18 +++--- src/which_all_min_max.c | 28 --------- src/which_na.c | 29 ---------- tests/testthat/test-whichNA.r | 118 +++++++++++++++++++++--------------------- 8 files changed, 93 insertions(+), 129 deletions(-)
Title: Variational Seq2Seq Model with Lambda Transformer for Time
Series Analysis
Description: Probabilistic multivariate time series forecasting using a variational sequence-to-sequence model with Lambda-style temporal aggregation. Provides transformations, uncertainty estimates, diagnostics, and publication-ready plots.
Author: Giancarlo Vercellino [aut, cre]
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Diff between lambdaTS versions 1.1 dated 2022-02-20 and 2.0.0 dated 2026-09-07
DESCRIPTION | 28 ++++++++----- MD5 | 21 +++++++--- NAMESPACE | 40 ++++++------------- NEWS.md | 8 +++ R/internal.R |only R/main.R | 45 +++++++++------------- R/support.R | 95 +++++++++++++++++------------------------------ build |only inst |only man/lambdaTS-internal.Rd |only man/lambdaTS.Rd | 2 tests |only vignettes |only 13 files changed, 110 insertions(+), 129 deletions(-)
Title: Evaluating Heterogeneous Treatment Effects
Description: Provides various statistical methods for evaluating heterogeneous treatment effects (HTE) in randomized experiments. The package includes tools to estimate uniform confidence bands for estimation of the group average treatment effect sorted by generic machine learning algorithms (GATES). It also provides the tools to identify a subgroup of individuals who are likely to benefit from a treatment the most "exceptional responders" or those who are harmed by it. Detailed reference in Imai and Li (2023) <doi:10.48550/arXiv.2310.07973>.
Author: Michael Lingzhi Li [aut, cre],
Kosuke Imai [aut],
Jialu Li [ctb]
Maintainer: Michael Lingzhi Li <mili@hbs.edu>
Diff between evalHTE versions 0.1.1 dated 2026-02-03 and 0.2.0 dated 2026-09-07
DESCRIPTION | 15 LICENSE | 4 MD5 | 70 +- NAMESPACE | 79 +- NEWS.md | 19 R/GATE.R | 85 -- R/GATEcv.R | 127 +-- R/consist.test.R | 117 --- R/consistcv.test.R | 166 +---- R/het.test.R | 99 --- R/hetcv.test.R | 148 ---- R/hte_helpers.R | 216 +++--- R/hte_qoi.R | 272 ++++---- R/main.r | 580 +++++++++--------- README.md | 209 ++++++ build/vignette.rds |binary inst/doc/ACIC2016.R | 610 +++++++++---------- inst/doc/ACIC2016.html | 1347 +++++++++++++++++++++--------------------- man/GATE.Rd | 24 man/GATEcv.Rd | 25 man/URATE.Rd | 78 +- man/compute_qoi.Rd | 32 man/compute_qoi_user.Rd | 48 - man/consist.test.Rd | 24 man/consistcv.test.Rd | 25 man/estimate_hte.Rd | 128 +-- man/evaluate_hte.Rd | 38 - man/het.test.Rd | 22 man/hetcv.test.Rd | 23 man/plot.hte.Rd | 38 - man/plot_CI.hte.Rd | 42 - man/print.summary.hte.Rd | 38 - man/print.summary.test_hte.Rd | 38 - man/summary.hte.Rd | 46 - man/test_itr.Rd | 44 - tests |only 36 files changed, 2366 insertions(+), 2510 deletions(-)
Title: Course-Dependent Skill Structures
Description: Deriving skill structures from skill assignment
data for courses (sets of learning objects).
Author: Cord Hockemeyer [aut, cre]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between CDSS versions 0.3-1 dated 2026-04-27 and 1.0-0 dated 2026-09-07
CDSS-0.3-1/CDSS/R/cdss_binary_matrix_product.R |only CDSS-0.3-1/CDSS/R/cdss_close_ar.R |only CDSS-0.3-1/CDSS/R/cdss_csma2sf.R |only CDSS-0.3-1/CDSS/R/cdss_lo_csma2sf.R |only CDSS-0.3-1/CDSS/R/cdss_reduce_sf.R |only CDSS-0.3-1/CDSS/R/cdss_sa2ar_skill.R |only CDSS-0.3-1/CDSS/R/cdss_sa2sma.R |only CDSS-0.3-1/CDSS/R/cdss_sma2csma.R |only CDSS-0.3-1/CDSS/R/cdss_wf_read_skill_assignment.R |only CDSS-0.3-1/CDSS/man/cdss_binary_matrix_product.Rd |only CDSS-0.3-1/CDSS/man/cdss_close_ar.Rd |only CDSS-0.3-1/CDSS/man/cdss_csma2sf.Rd |only CDSS-0.3-1/CDSS/man/cdss_lo_csma2sf.Rd |only CDSS-0.3-1/CDSS/man/cdss_reduce_sf.Rd |only CDSS-0.3-1/CDSS/man/cdss_sa2ar_skill.Rd |only CDSS-0.3-1/CDSS/man/cdss_sa2sma.Rd |only CDSS-0.3-1/CDSS/man/cdss_sma2csma.Rd |only CDSS-0.3-1/CDSS/man/cdss_wf_read_skill_assignment.Rd |only CDSS-0.3-1/CDSS/vignettes/CDSS_Simplified_Workflow_Skills.png |only CDSS-0.3-1/CDSS/vignettes/CDSS_Workflow.png |only CDSS-1.0-0/CDSS/Changelog | 39 CDSS-1.0-0/CDSS/DESCRIPTION | 19 CDSS-1.0-0/CDSS/MD5 | 109 CDSS-1.0-0/CDSS/NAMESPACE | 13 CDSS-1.0-0/CDSS/R/CDSS-package.R | 24 CDSS-1.0-0/CDSS/R/cdss_lo_sa2af.R | 39 CDSS-1.0-0/CDSS/R/cdss_lo_sa2ar.R | 1 CDSS-1.0-0/CDSS/R/cdss_read_skill_assignment.R |only CDSS-1.0-0/CDSS/R/cdss_read_skll_assignments_csv.R | 7 CDSS-1.0-0/CDSS/R/cdss_read_skll_assignments_ods.R | 12 CDSS-1.0-0/CDSS/R/cdss_read_skll_assignments_xlsx.R | 7 CDSS-1.0-0/CDSS/R/cdss_sa2mu.R |only CDSS-1.0-0/CDSS/R/cdss_sa_compliance.R | 116 CDSS-1.0-0/CDSS/R/cdss_skill_sa2af.R |only CDSS-1.0-0/CDSS/R/cdss_skill_sa2ar.R |only CDSS-1.0-0/CDSS/R/cdss_tables2sa.R | 74 CDSS-1.0-0/CDSS/build/vignette.rds |binary CDSS-1.0-0/CDSS/inst/doc/CDSS.R | 94 CDSS-1.0-0/CDSS/inst/doc/CDSS.Rmd | 324 - CDSS-1.0-0/CDSS/inst/doc/CDSS.html | 2638 +++++++--- CDSS-1.0-0/CDSS/inst/extdata/ErroneousSkillAssignment.ods |binary CDSS-1.0-0/CDSS/man/CDSS.Rd | 24 CDSS-1.0-0/CDSS/man/cdss_circular_requirements.Rd | 8 CDSS-1.0-0/CDSS/man/cdss_lo_sa2af.Rd | 7 CDSS-1.0-0/CDSS/man/cdss_lo_sa2ar.Rd | 6 CDSS-1.0-0/CDSS/man/cdss_missing_los.Rd | 8 CDSS-1.0-0/CDSS/man/cdss_nonteaching_los.Rd | 8 CDSS-1.0-0/CDSS/man/cdss_read_skill_assignment.Rd |only CDSS-1.0-0/CDSS/man/cdss_read_skill_assignment_csv.Rd | 9 CDSS-1.0-0/CDSS/man/cdss_read_skill_assignment_ods.Rd | 11 CDSS-1.0-0/CDSS/man/cdss_read_skill_assignment_xlsx.Rd | 9 CDSS-1.0-0/CDSS/man/cdss_sa2mu.Rd |only CDSS-1.0-0/CDSS/man/cdss_sa_compliance.Rd | 12 CDSS-1.0-0/CDSS/man/cdss_sa_describes_sr.Rd | 6 CDSS-1.0-0/CDSS/man/cdss_skill_sa2af.Rd |only CDSS-1.0-0/CDSS/man/cdss_skill_sa2ar.Rd |only CDSS-1.0-0/CDSS/man/cdss_tables2sa.Rd | 7 CDSS-1.0-0/CDSS/vignettes/CDSS.Rmd | 324 - CDSS-1.0-0/CDSS/vignettes/CDSS_cache |only CDSS-1.0-0/CDSS/vignettes/Flowchart.png |only 60 files changed, 2629 insertions(+), 1326 deletions(-)
Title: Bayesian Forecasting with Large Vector Autoregressions
Description: Provides fast and efficient procedures for Bayesian estimation and forecasting using state-of-the-art Vector Autoregressions. This package includes the model proposed by Shang, Wang, Woźniak (2026) <doi:10.48550/arXiv.2608.28087> and Chan (2020) <doi:10.1080/07350015.2018.1451336>, that is, a Bayesian Vector Autoregression with Minnesota priors and a flexible structure of the error term specification. The latter includes: conditional multivariate normal or Student’s t distributions, as well as homoskedastic or heteroskedastic specifications with a common volatility modelled by centred or non-centred Stochastic Volatility. Additionally, the package facilitates predictive analyses using density forecasting and forecast-error variance decompositions. All this is complemented by simple workflows, useful plots and summary functions, and comprehensive documentation. The 'bvars' package aligns with R packages 'bsvars' by Woźniak (2026) <doi:10.32614/CRAN.package.bsvars>, 'bs [...truncated...]
Author: Rui Liu [aut] ,
Andres Ramirez Hassan [aut] ,
Tomasz Wozniak [aut, cre] ,
Fei Shang [ctb] , introduced
major code corrections and improvements),
Xiaolei Wang [ctb] )
Maintainer: Tomasz Wozniak <wozniak.tom@pm.me>
Diff between bvars versions 1.0 dated 2026-06-08 and 1.1 dated 2026-09-07
DESCRIPTION | 26 ++- MD5 | 40 +++-- NAMESPACE | 1 NEWS.md | 12 + R/bvars-package.R | 19 ++ R/forecast.R | 14 - R/specify_bvar.R | 6 README.md | 8 - build |only inst/tinytest |only man/bvars-package.Rd | 17 ++ man/reexports.Rd | 2 man/specify_bvar.Rd | 285 +++++++++++++++++------------------- man/specify_posterior_bvar.Rd | 144 +++++++++--------- man/specify_prior_bvar.Rd | 158 +++++++++---------- man/specify_starting_values_bvar.Rd | 218 +++++++++++++-------------- src/forecast_bvargig.cpp | 2 src/sample_ASigmaV.cpp | 5 src/sample_Omega.cpp | 31 ++- tests |only 20 files changed, 516 insertions(+), 472 deletions(-)
Title: BiMaU Miscellaneous
Description: Contains a function to plot publication-ready survival curves using the Kaplan-Meier method (1958) <doi:10.2307/2281868>, a function to format p-values, and a function to automatically select statistical tests for comparing continuous variables between groups, which are useful for repetitive analyses. BiMaU stands for the Biostatistics and Mathematics Research Unit at the Sant Joan de Déu - Pediatric Cancer Center Barcelona <https://github.com/BiMaU-PCCB>.
Author: Anna Felip-Badia [aut, cre] ,
Aleix Martin-Moral [aut] ,
Sara Perez-Jaume [aut]
Maintainer: Anna Felip-Badia <annafelipibadia@gmail.com>
Diff between BiMaUmisc versions 0.1.0 dated 2026-08-04 and 0.2.0 dated 2026-09-07
DESCRIPTION | 9 +++++---- MD5 | 10 ++++++---- NAMESPACE | 8 ++++++++ R/BiMaUmisc-package.R | 10 +++++++--- R/find.test.R |only man/BiMaUmisc-package.Rd | 11 ++++++++--- man/find.test.Rd |only 7 files changed, 34 insertions(+), 14 deletions(-)
Title: Time Feature Extrapolation Using Spectral Analysis and
Jack-Knife Resampling
Description: Proposes application of spectral analysis and jack-knife resampling for multivariate sequence forecasting using only base R functionality.
Author: Giancarlo Vercellino [aut, cre]
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Diff between spooky versions 1.4.0 dated 2022-08-13 and 2.0.0 dated 2026-09-07
DESCRIPTION | 29 +- MD5 | 17 - NAMESPACE | 31 -- NEWS.md | 14 - R/main.R | 703 +++++++++++++++++++--------------------------------------- build |only inst |only man/spooky.Rd | 54 +--- tests |only vignettes |only 10 files changed, 286 insertions(+), 562 deletions(-)
Title: Functions and Data Sets for "That's Weird: Anomaly Detection
Using R" by Rob J Hyndman
Description: All functions and data sets required for the examples in the book
Hyndman (2026) "That's Weird: Anomaly Detection Using R" <https://OTexts.com/weird/>.
All packages needed to run the examples are also loaded.
Author: Rob Hyndman [aut, cre, cph] ,
Torben Tvedebrink [ctb],
Posit Software, PBC [cph]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>
Diff between weird versions 3.0.0 dated 2026-07-06 and 3.1.0 dated 2026-09-07
weird-3.0.0/weird/R/dist_density.R |only weird-3.0.0/weird/man/dist_density.Rd |only weird-3.0.0/weird/tests/testthat/test_dist_density.R |only weird-3.1.0/weird/DESCRIPTION | 8 weird-3.1.0/weird/MD5 | 47 +- weird-3.1.0/weird/NAMESPACE | 113 +++---- weird-3.1.0/weird/NEWS.md | 97 +++--- weird-3.1.0/weird/R/dist_kde.R | 57 ++- weird-3.1.0/weird/R/gg_density.R | 14 weird-3.1.0/weird/R/hampel.R | 46 ++ weird-3.1.0/weird/R/hdr.R | 286 ++++++++++++++---- weird-3.1.0/weird/R/kde_bandwidth.R | 13 weird-3.1.0/weird/R/show_data.R | 35 +- weird-3.1.0/weird/README.md | 4 weird-3.1.0/weird/inst/doc/old-faithful.R | 25 - weird-3.1.0/weird/inst/doc/old-faithful.Rmd | 94 ++++- weird-3.1.0/weird/inst/doc/old-faithful.html | 63 ++- weird-3.1.0/weird/man/dist_kde.Rd | 4 weird-3.1.0/weird/man/figures/weird-hex.png |binary weird-3.1.0/weird/man/hampel_anomalies.Rd | 20 + weird-3.1.0/weird/man/hdr_regions.Rd |only weird-3.1.0/weird/man/kde_bandwidth.Rd | 10 weird-3.1.0/weird/man/weird-package.Rd | 2 weird-3.1.0/weird/tests/testthat/_snaps/hdr.md |only weird-3.1.0/weird/tests/testthat/test_hdr.R | 84 +++++ weird-3.1.0/weird/tests/testthat/test_kde_bandwidth.R | 13 weird-3.1.0/weird/vignettes/old-faithful.Rmd | 94 ++++- 27 files changed, 801 insertions(+), 328 deletions(-)
Title: Structured Screen-and-Select Variable Selection in Linear,
Generalized Linear, and Survival Models
Description: Performs variable selection using the structured screen-and-select (S3VS) framework in linear models, generalized linear models with binary data, and survival models such as the Cox model and accelerated failure time (AFT) model.
Author: Nilotpal Sanyal [aut, cre],
Padmore N. Prempeh [aut]
Maintainer: Nilotpal Sanyal <nsanyal@utep.edu>
Diff between S3VS versions 1.0 dated 2026-01-13 and 1.1 dated 2026-09-07
DESCRIPTION | 18 +- MD5 | 47 +++-- NAMESPACE | 4 NEWS.md |only R/S3VS.R | 373 ++++++++++++++++++++++++-------------------- README.md | 316 ++++++++++++++++++++++++++++++++----- build/vignette.rds |binary inst/doc/S3VS_vignette.R | 2 inst/doc/S3VS_vignette.Rmd | 2 inst/doc/S3VS_vignette.pdf |binary man/S3VS.Rd | 11 - man/S3VS_GLM.Rd | 9 - man/S3VS_LM.Rd | 5 man/S3VS_SURV.Rd | 9 - man/VS_method.Rd | 5 man/VS_method_GLM.Rd | 14 - man/VS_method_LM.Rd | 7 man/VS_method_SURV.Rd | 12 - man/figures |only man/get_leadsets.Rd | 8 man/pred_S3VS_GLM.Rd | 2 man/pred_S3VS_LM.Rd | 2 man/pred_S3VS_SURV.Rd | 9 - vignettes/S3VS_vignette.Rmd | 2 24 files changed, 581 insertions(+), 276 deletions(-)
Title: Reduced Model Space Bayesian Model Averaging
Description: Implements Bayesian model averaging for settings with many
candidate regressors relative to the available sample size, including
cases where the number of regressors exceeds the number of observations.
By restricting attention to models with at most M regressors, the package
supports reduced model space inference, thereby preserving degrees of
freedom for estimation. It provides posterior summaries, Extreme Bounds
Analysis, model selection procedures, joint inclusion measures, and
graphical tools for exploring model probabilities, model size
distributions, and coefficient distributions. When the model space is too
large to enumerate, it can be explored by Markov chain Monte Carlo model
composition instead. The methodological approach follows Doppelhofer and
Weeks (2009) <doi:10.1002/jae.1046> and Madigan and York (1995)
<doi:10.2307/1403615>.
Author: Krzysztof Beck [aut, cre]
Maintainer: Krzysztof Beck <beckkrzysztof@gmail.com>
Diff between rmsBMA versions 0.1.2 dated 2026-03-14 and 0.2.0 dated 2026-09-07
rmsBMA-0.1.2/rmsBMA/man/figures |only rmsBMA-0.2.0/rmsBMA/DESCRIPTION | 15 rmsBMA-0.2.0/rmsBMA/MD5 | 106 - rmsBMA-0.2.0/rmsBMA/NAMESPACE | 7 rmsBMA-0.2.0/rmsBMA/NEWS.md |only rmsBMA-0.2.0/rmsBMA/R/bma.R | 141 +- rmsBMA-0.2.0/rmsBMA/R/coef_hist.R | 2 rmsBMA-0.2.0/rmsBMA/R/coef_to_full.R | 1 rmsBMA-0.2.0/rmsBMA/R/fast_ols.R | 4 rmsBMA-0.2.0/rmsBMA/R/fast_ols_HC.R | 4 rmsBMA-0.2.0/rmsBMA/R/fast_ols_const.R | 9 rmsBMA-0.2.0/rmsBMA/R/g_regression.R | 8 rmsBMA-0.2.0/rmsBMA/R/g_regression_fast.R | 8 rmsBMA-0.2.0/rmsBMA/R/g_regression_fast_HC.R | 8 rmsBMA-0.2.0/rmsBMA/R/g_regression_fast_const.R | 7 rmsBMA-0.2.0/rmsBMA/R/globals.R |only rmsBMA-0.2.0/rmsBMA/R/jointness.R | 10 rmsBMA-0.2.0/rmsBMA/R/mc3.R |only rmsBMA-0.2.0/rmsBMA/R/methods.R |only rmsBMA-0.2.0/rmsBMA/R/modelSpace.R | 1 rmsBMA-0.2.0/rmsBMA/R/model_matrix.R | 1 rmsBMA-0.2.0/rmsBMA/R/model_pmp.R | 87 - rmsBMA-0.2.0/rmsBMA/R/model_sizes.R | 80 - rmsBMA-0.2.0/rmsBMA/R/model_space.R | 177 ++ rmsBMA-0.2.0/rmsBMA/R/numeric_guards.R |only rmsBMA-0.2.0/rmsBMA/R/ols.R | 4 rmsBMA-0.2.0/rmsBMA/R/posterior_dens.R | 2 rmsBMA-0.2.0/rmsBMA/R/subset_design.R | 1 rmsBMA-0.2.0/rmsBMA/data/modelSpace.rda |binary rmsBMA-0.2.0/rmsBMA/inst/WORDLIST | 46 rmsBMA-0.2.0/rmsBMA/inst/doc/rmsBMA.R | 53 rmsBMA-0.2.0/rmsBMA/inst/doc/rmsBMA.Rmd | 136 ++ rmsBMA-0.2.0/rmsBMA/inst/doc/rmsBMA.html | 627 +++++++--- rmsBMA-0.2.0/rmsBMA/man/coef.bma.Rd |only rmsBMA-0.2.0/rmsBMA/man/coef_hist.Rd | 11 rmsBMA-0.2.0/rmsBMA/man/coef_to_full.Rd | 1 rmsBMA-0.2.0/rmsBMA/man/modelSpace.Rd | 1 rmsBMA-0.2.0/rmsBMA/man/model_matrix.Rd | 1 rmsBMA-0.2.0/rmsBMA/man/model_pmp.Rd | 11 rmsBMA-0.2.0/rmsBMA/man/model_sizes.Rd | 11 rmsBMA-0.2.0/rmsBMA/man/model_space.Rd | 38 rmsBMA-0.2.0/rmsBMA/man/posterior_dens.Rd | 3 rmsBMA-0.2.0/rmsBMA/man/print.bma.Rd |only rmsBMA-0.2.0/rmsBMA/man/print.model_space.Rd |only rmsBMA-0.2.0/rmsBMA/man/subset_design.Rd | 1 rmsBMA-0.2.0/rmsBMA/man/summary.bma.Rd |only rmsBMA-0.2.0/rmsBMA/man/summary.model_space.Rd |only rmsBMA-0.2.0/rmsBMA/tests/testthat/test-bma.R | 5 rmsBMA-0.2.0/rmsBMA/tests/testthat/test-fast_ols_const.R | 23 rmsBMA-0.2.0/rmsBMA/tests/testthat/test-g_regression_fast_const.R | 23 rmsBMA-0.2.0/rmsBMA/tests/testthat/test-mc3.R |only rmsBMA-0.2.0/rmsBMA/tests/testthat/test-model_pmp.R | 56 rmsBMA-0.2.0/rmsBMA/tests/testthat/test-model_sizes.R | 117 + rmsBMA-0.2.0/rmsBMA/tests/testthat/test-model_space.R | 6 rmsBMA-0.2.0/rmsBMA/tests/testthat/test-numeric-guards.R |only rmsBMA-0.2.0/rmsBMA/vignettes/references.bib | 11 rmsBMA-0.2.0/rmsBMA/vignettes/rmsBMA.Rmd | 136 ++ 57 files changed, 1530 insertions(+), 470 deletions(-)
Title: Extensible, Parallelizable Implementation of the Random Forest
Algorithm
Description: Scalable implementation of classification and regression forests, as described by Breiman (2001), <DOI:10.1023/A:1010933404324>.
Author: Mark Seligman [aut, cre]
Maintainer: Mark Seligman <mseligman@suiji.org>
Diff between Rborist versions 0.3-11 dated 2025-02-02 and 0.3-12 dated 2026-09-07
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- build/vignette.rds |binary inst/doc/rborist.html | 1 + src/block.h | 1 + src/coreR.cc | 2 +- src/coreR.h | 2 +- src/dectree.cc | 2 ++ src/grove.h | 8 ++++---- 9 files changed, 22 insertions(+), 18 deletions(-)
Title: Pairwise Comparison Tools for Large Language Model-Based Writing
Evaluation
Description: Provides a unified framework for generating, submitting, and
analyzing pairwise comparisons of writing quality using large language
models (LLMs). The package supports live and/or batch evaluation workflows
across multiple providers ('OpenAI', 'Anthropic', 'Google Gemini',
'Together AI', and locally-hosted 'Ollama' models), includes bias-tested
prompt templates and a flexible template registry, and offers tools
for constructing forward and reversed comparison sets to analyze
consistency and positional bias. The package additionally supports
adaptive pairing workflows that iteratively select comparisons based on
model uncertainty to improve ranking efficiency. Results can be modeled
using frequentist or Bayesian Bradley–Terry–Luce models
(Bradley & Terry, 1952 <doi:10.2307/2334029>; see also
Caron & Doucet, 2012 <doi:10.1080/10618600.2012.638220>) or Elo rating methods (see
Clark et al., 2018 <doi:10.1371/journal.pone.0190393>) to derive
writing quality scores. [...truncated...]
Author: Sterett H. Mercer [aut, cre, cph]
Maintainer: Sterett H. Mercer <sterett.mercer@ubc.ca>
Diff between pairwiseLLM versions 1.1.0 dated 2025-12-22 and 1.3.1 dated 2026-09-07
pairwiseLLM-1.1.0/pairwiseLLM/R/batch_openai.R |only pairwiseLLM-1.1.0/pairwiseLLM/R/openai_parse.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-alternate_pair_order.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-anthropic_batch_api.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-anthropic_live.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-api_keys.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-bt_complete.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-check_positional_bias.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-data_import.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-elo_model.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-example_datasets.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-gemini-batch-api.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-gemini_live.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-llm_backends.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-llm_batch.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-ollama_live.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-openai_batch.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-openai_batch_api.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-openai_live.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-openai_parse.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-pairing.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-randomize_pair_order.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-read_samples.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-reverse_consistency.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-together_live.R |only pairwiseLLM-1.1.0/pairwiseLLM/tests/testthat/test-traits_template.R |only pairwiseLLM-1.3.1/pairwiseLLM/DESCRIPTION | 63 pairwiseLLM-1.3.1/pairwiseLLM/LICENSE | 2 pairwiseLLM-1.3.1/pairwiseLLM/MD5 | 472 pairwiseLLM-1.3.1/pairwiseLLM/NAMESPACE | 183 pairwiseLLM-1.3.1/pairwiseLLM/NEWS.md | 134 pairwiseLLM-1.3.1/pairwiseLLM/R/adaptive_benchmark_metrics.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/adaptive_btl_refit.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/adaptive_candidates.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/adaptive_constraints.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/adaptive_linking_calibration.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/adaptive_linking_phase_a.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/adaptive_logs.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/adaptive_persist.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/adaptive_print.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/adaptive_rank.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/adaptive_round_candidates.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/adaptive_run.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/adaptive_schemas.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/adaptive_select.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/adaptive_simulation_harness.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/adaptive_state.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/adaptive_step.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/adaptive_trueskill.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/adaptive_utility.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/anthropic_batch_api.R | 107 pairwiseLLM-1.3.1/pairwiseLLM/R/anthropic_live.R | 519 pairwiseLLM-1.3.1/pairwiseLLM/R/api_keys.R | 433 pairwiseLLM-1.3.1/pairwiseLLM/R/bayes_btl_mcmc.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/bayes_btl_mcmc_adaptive.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/bayes_btl_summarize.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/bt_helpers.R | 206 pairwiseLLM-1.3.1/pairwiseLLM/R/bt_model.R | 65 pairwiseLLM-1.3.1/pairwiseLLM/R/btl_mcmc_constraints.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/btl_mcmc_contracts.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/btl_mcmc_fit_contracts.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/btl_mcmc_ingest.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/btl_mcmc_model_variant.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/btl_mcmc_state.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/btl_mcmc_stopping.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/btl_mcmc_summaries.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/btl_mcmc_theta_summary_stubs.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/core_budget.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/cost_estimator.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/custom_id.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/data-example_writing.R | 87 pairwiseLLM-1.3.1/pairwiseLLM/R/data_import.R | 18 pairwiseLLM-1.3.1/pairwiseLLM/R/draws_sanitize.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/elo_model.R | 56 pairwiseLLM-1.3.1/pairwiseLLM/R/gemini_batch_api.R | 193 pairwiseLLM-1.3.1/pairwiseLLM/R/gemini_live.R | 732 - pairwiseLLM-1.3.1/pairwiseLLM/R/gemini_params.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/httr2_retry.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/llm_backends.R | 388 pairwiseLLM-1.3.1/pairwiseLLM/R/llm_batch.R | 138 pairwiseLLM-1.3.1/pairwiseLLM/R/llm_multi_batch.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/normalize_results.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/ollama_live.R | 559 pairwiseLLM-1.3.1/pairwiseLLM/R/openai_batch_api.R | 697 + pairwiseLLM-1.3.1/pairwiseLLM/R/openai_live.R | 588 pairwiseLLM-1.3.1/pairwiseLLM/R/openai_params.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/pairing.R | 75 pairwiseLLM-1.3.1/pairwiseLLM/R/pairwiseLLM-package.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/prompt_template.R | 10 pairwiseLLM-1.3.1/pairwiseLLM/R/reverse_consistency.R | 250 pairwiseLLM-1.3.1/pairwiseLLM/R/seed_helpers.R |only pairwiseLLM-1.3.1/pairwiseLLM/R/together_live.R | 566 pairwiseLLM-1.3.1/pairwiseLLM/R/traits.R | 32 pairwiseLLM-1.3.1/pairwiseLLM/R/utils-null-coalesce.R | 30 pairwiseLLM-1.3.1/pairwiseLLM/R/vertex_live.R |only pairwiseLLM-1.3.1/pairwiseLLM/README.md | 818 + pairwiseLLM-1.3.1/pairwiseLLM/build/partial.rdb |binary pairwiseLLM-1.3.1/pairwiseLLM/build/vignette.rds |binary pairwiseLLM-1.3.1/pairwiseLLM/data/example_writing_results.rda |only pairwiseLLM-1.3.1/pairwiseLLM/data/example_writing_samples1000.rda |only pairwiseLLM-1.3.1/pairwiseLLM/inst/CITATION | 8 pairwiseLLM-1.3.1/pairwiseLLM/inst/COPYRIGHTS |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/adaptive-linking-design.R |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/adaptive-linking-design.Rmd |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/adaptive-linking-design.html |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/adaptive-linking.R |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/adaptive-linking.Rmd |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/adaptive-linking.html |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/adaptive-pairing.R |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/adaptive-pairing.Rmd |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/adaptive-pairing.html |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/advanced-batch-workflows.R | 671 - pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/advanced-batch-workflows.Rmd | 1016 - pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/advanced-batch-workflows.html | 1844 +- pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/bayesian-btl.R |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/bayesian-btl.Rmd |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/bayesian-btl.html |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/data-and-prompts.R |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/data-and-prompts.Rmd |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/data-and-prompts.html |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/getting-started.R | 301 pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/getting-started.Rmd | 316 pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/getting-started.html | 1638 +- pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/model-compatibility.R |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/model-compatibility.Rmd |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/model-compatibility.html |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/prompt-template-bias.R | 572 pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/prompt-template-bias.Rmd | 1777 +- pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/prompt-template-bias.html | 6261 ++++------ pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/provider-controls-and-recovery.R |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/provider-controls-and-recovery.Rmd |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/provider-controls-and-recovery.html |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/within-set-adaptive-design.R |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/within-set-adaptive-design.Rmd |only pairwiseLLM-1.3.1/pairwiseLLM/inst/doc/within-set-adaptive-design.html |only pairwiseLLM-1.3.1/pairwiseLLM/inst/extdata/adaptive_linking_calibration_default.json |only pairwiseLLM-1.3.1/pairwiseLLM/inst/extdata/model_compatibility.csv |only pairwiseLLM-1.3.1/pairwiseLLM/inst/extdata/template_test_summary_all.csv | 152 pairwiseLLM-1.3.1/pairwiseLLM/inst/scripts |only pairwiseLLM-1.3.1/pairwiseLLM/inst/stan |only pairwiseLLM-1.3.1/pairwiseLLM/man/adaptive_get_logs.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/adaptive_item_log.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/adaptive_rank.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/adaptive_rank_resume.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/adaptive_rank_run_live.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/adaptive_rank_start.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/adaptive_results_history.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/adaptive_round_log.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/adaptive_step_log.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/alternate_pair_order.Rd | 12 pairwiseLLM-1.3.1/pairwiseLLM/man/anthropic_compare_pair_live.Rd | 481 pairwiseLLM-1.3.1/pairwiseLLM/man/anthropic_create_batch.Rd | 183 pairwiseLLM-1.3.1/pairwiseLLM/man/anthropic_download_batch_results.Rd | 29 pairwiseLLM-1.3.1/pairwiseLLM/man/anthropic_get_batch.Rd | 29 pairwiseLLM-1.3.1/pairwiseLLM/man/anthropic_poll_batch_until_complete.Rd | 29 pairwiseLLM-1.3.1/pairwiseLLM/man/build_anthropic_batch_requests.Rd | 291 pairwiseLLM-1.3.1/pairwiseLLM/man/build_bt_data.Rd | 27 pairwiseLLM-1.3.1/pairwiseLLM/man/build_btl_results_data.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/build_elo_data.Rd | 24 pairwiseLLM-1.3.1/pairwiseLLM/man/build_gemini_batch_requests.Rd | 278 pairwiseLLM-1.3.1/pairwiseLLM/man/build_openai_batch_requests.Rd | 260 pairwiseLLM-1.3.1/pairwiseLLM/man/build_prompt.Rd | 12 pairwiseLLM-1.3.1/pairwiseLLM/man/check_llm_api_keys.Rd | 116 pairwiseLLM-1.3.1/pairwiseLLM/man/check_positional_bias.Rd | 36 pairwiseLLM-1.3.1/pairwiseLLM/man/compute_reverse_consistency.Rd | 69 pairwiseLLM-1.3.1/pairwiseLLM/man/dot-parse_gemini_pair_response.Rd | 60 pairwiseLLM-1.3.1/pairwiseLLM/man/dot-together_api_key.Rd | 36 pairwiseLLM-1.3.1/pairwiseLLM/man/dot-vertex_api_key.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/ensure_only_ollama_model_loaded.Rd | 167 pairwiseLLM-1.3.1/pairwiseLLM/man/estimate_llm_pairs_cost.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/example_openai_batch_output.Rd | 4 pairwiseLLM-1.3.1/pairwiseLLM/man/example_writing_pairs.Rd | 4 pairwiseLLM-1.3.1/pairwiseLLM/man/example_writing_results.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/example_writing_samples.Rd | 4 pairwiseLLM-1.3.1/pairwiseLLM/man/example_writing_samples1000.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/figures |only pairwiseLLM-1.3.1/pairwiseLLM/man/fit_bayes_btl_mcmc.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/fit_bt_model.Rd | 18 pairwiseLLM-1.3.1/pairwiseLLM/man/fit_elo_model.Rd | 20 pairwiseLLM-1.3.1/pairwiseLLM/man/gemini_compare_pair_live.Rd | 358 pairwiseLLM-1.3.1/pairwiseLLM/man/gemini_create_batch.Rd | 35 pairwiseLLM-1.3.1/pairwiseLLM/man/gemini_download_batch_results.Rd | 29 pairwiseLLM-1.3.1/pairwiseLLM/man/gemini_get_batch.Rd | 29 pairwiseLLM-1.3.1/pairwiseLLM/man/gemini_poll_batch_until_complete.Rd | 29 pairwiseLLM-1.3.1/pairwiseLLM/man/get_prompt_template.Rd | 9 pairwiseLLM-1.3.1/pairwiseLLM/man/list_prompt_templates.Rd | 12 pairwiseLLM-1.3.1/pairwiseLLM/man/llm_compare_pair.Rd | 430 pairwiseLLM-1.3.1/pairwiseLLM/man/llm_download_batch_results.Rd | 125 pairwiseLLM-1.3.1/pairwiseLLM/man/llm_resume_multi_batches.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/llm_submit_pairs_batch.Rd | 411 pairwiseLLM-1.3.1/pairwiseLLM/man/llm_submit_pairs_multi_batch.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/load_adaptive_session.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/make_adaptive_judge_llm.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/make_pairs.Rd | 12 pairwiseLLM-1.3.1/pairwiseLLM/man/ollama_compare_pair_live.Rd | 433 pairwiseLLM-1.3.1/pairwiseLLM/man/openai_compare_pair_live.Rd | 305 pairwiseLLM-1.3.1/pairwiseLLM/man/openai_create_batch.Rd | 29 pairwiseLLM-1.3.1/pairwiseLLM/man/openai_download_batch_output.Rd | 29 pairwiseLLM-1.3.1/pairwiseLLM/man/openai_get_batch.Rd | 29 pairwiseLLM-1.3.1/pairwiseLLM/man/openai_poll_batch_until_complete.Rd | 29 pairwiseLLM-1.3.1/pairwiseLLM/man/openai_upload_batch_file.Rd | 29 pairwiseLLM-1.3.1/pairwiseLLM/man/pairwiseLLM.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/parse_anthropic_batch_output.Rd | 8 pairwiseLLM-1.3.1/pairwiseLLM/man/parse_gemini_batch_output.Rd | 120 pairwiseLLM-1.3.1/pairwiseLLM/man/parse_openai_batch_output.Rd | 222 pairwiseLLM-1.3.1/pairwiseLLM/man/print.adaptive_state.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/print.pairwiseLLM_cost_estimate.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/randomize_pair_order.Rd | 9 pairwiseLLM-1.3.1/pairwiseLLM/man/read_samples_df.Rd | 12 pairwiseLLM-1.3.1/pairwiseLLM/man/read_samples_dir.Rd | 24 pairwiseLLM-1.3.1/pairwiseLLM/man/register_prompt_template.Rd | 12 pairwiseLLM-1.3.1/pairwiseLLM/man/remove_prompt_template.Rd | 9 pairwiseLLM-1.3.1/pairwiseLLM/man/run_anthropic_batch_pipeline.Rd | 448 pairwiseLLM-1.3.1/pairwiseLLM/man/run_gemini_batch_pipeline.Rd | 337 pairwiseLLM-1.3.1/pairwiseLLM/man/run_openai_batch_pipeline.Rd | 38 pairwiseLLM-1.3.1/pairwiseLLM/man/sample_pairs.Rd | 12 pairwiseLLM-1.3.1/pairwiseLLM/man/sample_reverse_pairs.Rd | 16 pairwiseLLM-1.3.1/pairwiseLLM/man/save_adaptive_session.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/set_prompt_template.Rd | 12 pairwiseLLM-1.3.1/pairwiseLLM/man/submit_anthropic_pairs_live.Rd | 365 pairwiseLLM-1.3.1/pairwiseLLM/man/submit_gemini_pairs_live.Rd | 322 pairwiseLLM-1.3.1/pairwiseLLM/man/submit_llm_pairs.Rd | 391 pairwiseLLM-1.3.1/pairwiseLLM/man/submit_ollama_pairs_live.Rd | 337 pairwiseLLM-1.3.1/pairwiseLLM/man/submit_openai_pairs_live.Rd | 132 pairwiseLLM-1.3.1/pairwiseLLM/man/submit_together_pairs_live.Rd | 278 pairwiseLLM-1.3.1/pairwiseLLM/man/submit_vertex_pairs_live.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/summarize_adaptive.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/summarize_bt_fit.Rd | 21 pairwiseLLM-1.3.1/pairwiseLLM/man/summarize_items.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/summarize_refits.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/together_compare_pair_live.Rd | 318 pairwiseLLM-1.3.1/pairwiseLLM/man/trait_description.Rd | 19 pairwiseLLM-1.3.1/pairwiseLLM/man/validate_session_dir.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/vertex_compare_pair_live.Rd |only pairwiseLLM-1.3.1/pairwiseLLM/man/write_openai_batch_file.Rd | 69 pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/README.md |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/fixtures |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/helper-fit-contract.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/helper-fixtures.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/setup.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0001-api-keys.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0002-traits-template.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0003-data-import.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0004-read-samples.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0005-example-datasets.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0006-openai-parse.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0007-custom-id.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0008-seed-helpers.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0010-normalize-results.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0011-alternate-pair-order.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0012-check-positional-bias.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0013-pairing.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0014-cost-estimator.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0015-adaptive-schemas.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0015-bt-complete.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0016-adaptive-state.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0016-elo-model.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0017-reverse-consistency.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0018-btl-mcmc-theta-summary-stubs.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0018-core-budget.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0019-schemas-and-utils.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0020-httr2-retry.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0021-btl-mcmc-core-helpers.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0022-bayes-btl-summarize-and-fit-contracts.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0023-btl-mcmc-summaries-helpers.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0024-btl-fit-contracts-and-adaptive-mcmc-helpers.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0025-btl-results-builder.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0026-documentation-contracts.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-0027-smoke-runner.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-2000-openai-live.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-2010-anthropic-live.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-2020-gemini-live.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-2021-vertex-live.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-2030-together-live.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-2040-ollama-live.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-2050-llm-backends.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-3000-llm-batch.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-3010-openai-batch.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-3020-openai-batch-api.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-3030-anthropic-batch-api.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-3040-gemini-batch-api.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-3050-llm-multi-batch.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-4000-openai-params-normalization.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-4001-openai-live-gpt5.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-4002-submit-llm-pairs-openai-service-tier.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-4003-openai-batch-gpt5.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-4004-llm-submit-pairs-batch-openai-gpt5.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5001-logs-constructors.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5002-state-constructor.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5003-entrypoints-scaffold.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5004-trueskill-state.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5005-trueskill-winprob.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5006-candidates.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5007-u0-utility.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5008-selector-basic.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5009-selector-caps-and-duplicates.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5010-selector-fallback-ladder.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5011-run-one-step-transactional.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5012-run-live-minimal.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5013-btl-refit-scheduling.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5014-stop-metrics-and-should-stop.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5015-run-live-stops-early.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5016-persist-save-load.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5016-reversal-on-repeat-invariant.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5017-resume-continues-run-live.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5018-print-and-summary.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5019-console-progress-and-refit-block.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5020-log-accessors-and-history.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5021-run-live-candidate-starvation-stop.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5022-selector-explore-metadata-consistency.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5023-round-log-required-fields.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5024-selector-pipeline-order.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5025-log-schema-ordering.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5026-adaptive-rank-wrapper.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5027-scaffold-unreachable.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5028-round-controller-routing.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5029-refit-summary-log-view.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5030-selection-btl-separation.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5031-refit-mcmc-settings-reporting.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5032-simulation-harness-determinism.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5033-simulation-scenarios-quotas-shortfalls.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5034-simulation-warmstart-coverage.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5035-simulation-anchors-linkmix.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5036-simulation-local-repeat-pressure.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5037-simulation-starvation-fallback.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5038-benchmark-report-only-guard.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5041-selection-controller-alignment.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5042-btl-refit-helpers-and-errors.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5043-logs-and-persist-edge-cases.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5044-benchmark-candidates-constraints-edges.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5045-adaptive-helper-branches.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5046-adaptive-schemas-validators.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5047-adaptive-run-persist-simulation-branches.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5048-linking-phase-a-artifacts.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5049-linking-candidates-round-routing.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5050-linking-refit-transforms.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5051-linking-invariant-guards.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5052-linking-calibration-harness.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5053-coverage-gap-helpers.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5054-low-coverage-helpers.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5055-adaptive-step-coverage.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5055-targeted-coverage-regressions.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5056-coverage-target-helpers.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5057-adaptive-rank-coverage-targets.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-5058-coverage-targets.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-6020-bayes-btl-mcmc-output.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-9001-integration-smoke.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-9002-linking-integration.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-9003-linking-regression-matrix.R |only pairwiseLLM-1.3.1/pairwiseLLM/tests/testthat/test-9004-linking-e2e-golden.R |only pairwiseLLM-1.3.1/pairwiseLLM/vignettes/adaptive-linking-design.Rmd |only pairwiseLLM-1.3.1/pairwiseLLM/vignettes/adaptive-linking.Rmd |only pairwiseLLM-1.3.1/pairwiseLLM/vignettes/adaptive-pairing.Rmd |only pairwiseLLM-1.3.1/pairwiseLLM/vignettes/advanced-batch-workflows.Rmd | 1016 - pairwiseLLM-1.3.1/pairwiseLLM/vignettes/bayesian-btl.Rmd |only pairwiseLLM-1.3.1/pairwiseLLM/vignettes/data-and-prompts.Rmd |only pairwiseLLM-1.3.1/pairwiseLLM/vignettes/getting-started.Rmd | 316 pairwiseLLM-1.3.1/pairwiseLLM/vignettes/model-compatibility.Rmd |only pairwiseLLM-1.3.1/pairwiseLLM/vignettes/prompt-template-bias.Rmd | 1777 +- pairwiseLLM-1.3.1/pairwiseLLM/vignettes/provider-controls-and-recovery.Rmd |only pairwiseLLM-1.3.1/pairwiseLLM/vignettes/within-set-adaptive-design.Rmd |only 361 files changed, 18962 insertions(+), 14206 deletions(-)
Title: Access Brazilian Public Health Data
Description: Provides easy access to Brazilian public health data from multiple
sources including VIGITEL (Surveillance of Risk Factors for Chronic Diseases
by Telephone Survey), PNS (National Health Survey), 'PNAD' Continua (Continuous
National Household Sample Survey), 'POF' (Household Budget Survey with food
security and consumption data), 'Censo Demografico' (population denominators
via 'SIDRA' API), SIM (Mortality Information System), SINASC (Live Birth
Information System), 'SIH' (Hospital Information System),
'SIA' (Outpatient Information System), 'SINAN' (Notifiable Diseases Surveillance),
'CNES' (National Health Facility Registry),
'SI-PNI' (National Immunization Program - aggregated 1994-2019 via FTP,
individual-level 'microdata' 2020+ via 'OpenDataSUS' API),
'SISAB' (Primary Care Health Information System - coverage indicators via
REST API), ANS ('Agencia Nacional de Saude Suplementar' - supplementary
health beneficiaries, consumer complaints, and financial statements),
'ANVISA' ('Agencia [...truncated...]
Author: Sidney Bissoli [aut, cre]
Maintainer: Sidney Bissoli <sbissoli76@gmail.com>
Diff between healthbR versions 0.2.0 dated 2026-02-15 and 0.4.0 dated 2026-09-07
DESCRIPTION | 20 MD5 | 280 +-- NAMESPACE | 2 NEWS.md | 443 ++++- R/ans.R | 15 R/anvisa.R | 9 R/cnes.R | 9 R/cnes_data_internal.R | 556 +++---- R/pnadc.R | 212 +- R/pns.R | 395 ++-- R/pof.R | 396 ++--- R/sia.R | 159 +- R/sia_data_internal.R | 506 +++--- R/sih.R | 1142 ++++++++------ R/sih_data_internal.R | 540 +++--- R/sih_r2.R |only R/sim.R | 170 +- R/sinan.R | 9 R/sinan_data_internal.R | 594 +++---- R/sinasc.R | 9 R/sipni.R | 2455 ++++++++++++++++++------------- R/sipni_data_internal.R | 767 ++++----- R/sipni_dictionary_data.R |only R/sipni_r2.R |only R/sisab.R | 184 +- R/utils-cache.R | 1048 ++++++------- R/utils-download.R | 374 +++- R/utils-parallel.R | 37 R/utils-r2.R |only R/vigitel.R | 268 +-- README.md | 402 +++-- build/vignette.rds |binary inst/doc/healthbR.R | 52 inst/doc/healthbR.Rmd | 113 + inst/doc/healthbR.html | 182 +- inst/doc/healthbr-vs-microdatasus.R |only inst/doc/healthbr-vs-microdatasus.Rmd |only inst/doc/healthbr-vs-microdatasus.html |only inst/doc/sih-hospital-admissions.Rmd | 414 ++--- inst/doc/sih-hospital-admissions.html | 7 inst/doc/sipni-vaccination.R | 88 - inst/doc/sipni-vaccination.Rmd | 254 ++- inst/doc/sipni-vaccination.html | 496 +++--- inst/healthbr-data-integration.html |only inst/healthbr-data-integration.md |only man/ans_cache_status.Rd | 62 man/ans_clear_cache.Rd | 66 man/ans_data.Rd | 227 +- man/ans_info.Rd | 56 man/ans_operators.Rd | 104 - man/ans_variables.Rd | 76 man/ans_years.Rd | 74 man/anvisa_cache_status.Rd | 60 man/anvisa_clear_cache.Rd | 64 man/anvisa_data.Rd | 215 +- man/anvisa_info.Rd | 56 man/anvisa_types.Rd | 54 man/anvisa_variables.Rd | 72 man/cnes_cache_status.Rd | 14 man/cnes_clear_cache.Rd | 14 man/cnes_data.Rd | 21 man/cnes_dictionary.Rd | 14 man/cnes_info.Rd | 14 man/cnes_variables.Rd | 14 man/cnes_years.Rd | 14 man/healthbR-package.Rd | 7 man/pnadc_data.Rd | 8 man/pns_data.Rd | 8 man/pof_cache_status.Rd | 16 man/pof_clear_cache.Rd | 16 man/pof_data.Rd | 16 man/pof_dictionary.Rd | 16 man/pof_info.Rd | 16 man/pof_registers.Rd | 16 man/pof_variables.Rd | 16 man/pof_years.Rd | 16 man/sia_cache_status.Rd | 14 man/sia_clear_cache.Rd | 14 man/sia_data.Rd | 21 man/sia_dictionary.Rd | 14 man/sia_info.Rd | 14 man/sia_variables.Rd | 14 man/sia_years.Rd | 14 man/sih_cache_status.Rd | 15 man/sih_clear_cache.Rd | 15 man/sih_data.Rd | 100 + man/sih_dictionary.Rd | 15 man/sih_info.Rd | 15 man/sih_status.Rd |only man/sih_variables.Rd | 15 man/sih_years.Rd | 15 man/sim_cache_status.Rd | 14 man/sim_clear_cache.Rd | 14 man/sim_data.Rd | 21 man/sim_dictionary.Rd | 14 man/sim_info.Rd | 14 man/sim_variables.Rd | 14 man/sim_years.Rd | 14 man/sinan_cache_status.Rd | 16 man/sinan_clear_cache.Rd | 16 man/sinan_data.Rd | 23 man/sinan_dictionary.Rd | 16 man/sinan_diseases.Rd | 16 man/sinan_info.Rd | 16 man/sinan_variables.Rd | 16 man/sinan_years.Rd | 16 man/sinasc_cache_status.Rd | 14 man/sinasc_clear_cache.Rd | 14 man/sinasc_data.Rd | 21 man/sinasc_dictionary.Rd | 14 man/sinasc_info.Rd | 14 man/sinasc_variables.Rd | 14 man/sinasc_years.Rd | 14 man/sipni_cache_status.Rd | 15 man/sipni_clear_cache.Rd | 15 man/sipni_data.Rd | 120 + man/sipni_dictionary.Rd | 80 - man/sipni_info.Rd | 15 man/sipni_status.Rd |only man/sipni_variables.Rd | 30 man/sipni_years.Rd | 33 man/sisab_cache_status.Rd | 12 man/sisab_clear_cache.Rd | 12 man/sisab_data.Rd | 19 man/sisab_info.Rd | 12 man/sisab_variables.Rd | 12 man/sisab_years.Rd | 12 tests/testthat/helper.R | 64 tests/testthat/test-censo.R | 289 +++ tests/testthat/test-dbc_infrastructure.R | 39 tests/testthat/test-pnadc.R | 2076 +++++++++++++++++++------- tests/testthat/test-pns.R | 1175 ++++++++++++++ tests/testthat/test-pof.R | 2045 +++++++++++++++++++++++++ tests/testthat/test-sia.R | 245 +++ tests/testthat/test-sih-r2.R |only tests/testthat/test-sih.R | 1054 ++++++++----- tests/testthat/test-sim.R | 321 ++++ tests/testthat/test-sinan.R | 6 tests/testthat/test-sipni-r2.R |only tests/testthat/test-sipni.R | 1319 ++++++++++++++++ tests/testthat/test-sisab.R | 273 +++ tests/testthat/test-utils-download.R | 878 ++++++++--- tests/testthat/test-utils-parallel.R | 54 tests/testthat/test-vigitel.R | 601 +++++++ vignettes/healthbR.Rmd | 113 + vignettes/healthbr-vs-microdatasus.Rmd |only vignettes/sih-hospital-admissions.Rmd | 414 ++--- vignettes/sipni-vaccination.Rmd | 254 ++- 148 files changed, 18270 insertions(+), 8026 deletions(-)
Title: Defining Local Haplotype Variants for Use in Trait Association
and Trait Prediction Analyses
Description: A local haplotyping tool for use in trait association and trait prediction analyses pipelines.
'HaploVar' enables users take single nucleotide polymorphisms (SNPs) (in VCF
format) and a linkage disequilibrium (LD) matrix, calculate local haplotypes and format the
output to be compatible with a wide range of trait association and trait prediction tools.
The local haplotypes are calculated from the LD matrix using a clustering algorithm called
density-based spatial clustering of applications with noise (DBSCAN) (Ester et al., 1996)
<ISBN: 1577350049>.
Author: Tessa MacNish [aut, cre] ,
Hawlader Al-Mamun [ctb],
Thomas Bergmann [ctb],
Mitchell Bestry [ctb],
Jacob Marsh [ctb],
David Edwards [ctb]
Maintainer: Tessa MacNish <tessamacnish@gmail.com>
Diff between HaploVar versions 0.1.1 dated 2025-07-21 and 0.1.2 dated 2026-09-07
DESCRIPTION | 14 +++++++------- MD5 | 14 +++++++------- R/define_haplotypes.R | 7 ++++--- R/haplotype_variants.R | 4 ++-- inst/doc/introduction.R | 12 +++++++++--- inst/doc/introduction.Rmd | 27 ++++++++++++++++++++++----- inst/doc/introduction.html | 39 ++++++++++++++++++++++++++++++--------- vignettes/introduction.Rmd | 27 ++++++++++++++++++++++----- 8 files changed, 103 insertions(+), 41 deletions(-)
Title: Interface to the 'HDF5' Binary Data Format
Description: 'HDF5' is a data model, library and file format for storing
and managing large amounts of data. This package provides a nearly
feature complete, object oriented wrapper for the 'HDF5' API
<https://support.hdfgroup.org/documentation/hdf5/latest/_r_m.html> using R6 classes.
Additionally, functionality is added so that 'HDF5' objects behave very
similar to their corresponding R counterparts.
Author: Holger Hoefling [aut, cre],
Mario Annau [aut],
Novartis Institute for BioMedical Research [cph]
Maintainer: Holger Hoefling <hhoeflin@gmail.com>
Diff between hdf5r versions 1.3.12 dated 2025-01-20 and 1.3.15 dated 2026-09-07
hdf5r-1.3.12/hdf5r/src/patch_1.10.6 |only hdf5r-1.3.15/hdf5r/DESCRIPTION | 6 hdf5r-1.3.15/hdf5r/MD5 | 31 hdf5r-1.3.15/hdf5r/NEWS.md | 12 hdf5r-1.3.15/hdf5r/R/R6Classes_H5T.R | 2 hdf5r-1.3.15/hdf5r/build/vignette.rds |binary hdf5r-1.3.15/hdf5r/configure | 1793 ++++++++++--------- hdf5r-1.3.15/hdf5r/configure.ac | 18 hdf5r-1.3.15/hdf5r/inst/Release_checks.md | 35 hdf5r-1.3.15/hdf5r/inst/doc/hdf5r.R | 2 hdf5r-1.3.15/hdf5r/inst/doc/hdf5r.html | 36 hdf5r-1.3.15/hdf5r/src/Makevars.in | 2 hdf5r-1.3.15/hdf5r/src/convert.c | 9 hdf5r-1.3.15/hdf5r/src/patches |only hdf5r-1.3.15/hdf5r/tests/testthat/test-h5p.R | 12 hdf5r-1.3.15/hdf5r/tests/testthat/test-zzz-DataSet.R | 9 hdf5r-1.3.15/hdf5r/tests/testthat/test-zzz-H5Group.R | 11 17 files changed, 1140 insertions(+), 838 deletions(-)
Title: A Grammar of Graphics Implementation of Biplots
Description: A 'ggplot2' based implementation of biplots, giving a representation of a dataset in
a two dimensional space accounting for the greatest variance, together with variable vectors
showing how the data variables relate to this space. It provides a
replacement for stats::biplot(), but with many enhancements to control the analysis and
graphical display. It implements
biplot and scree plot methods which can be used with the results of prcomp(), princomp(),
FactoMineR::PCA(), ade4::dudi.pca() or MASS::lda() and can be customized using 'ggplot2' techniques.
Author: Vincent Q. Vu [aut] ,
Michael Friendly [aut, cre] ,
Aghasi Tavadyan [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between ggbiplot versions 0.6.2 dated 2024-01-08 and 0.6.5 dated 2026-09-07
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Title: Evaluating Individualized Treatment Rules
Description: Provides various statistical methods for evaluating
Individualized Treatment Rules under randomized data. The provided
metrics include Population Average Value (PAV), Population Average
Prescription Effect (PAPE), Area Under Prescription Effect Curve
(AUPEC). It also provides the tools to analyze Individualized
Treatment Rules under budget constraints. Detailed reference in Imai
and Li (2023) <doi:10.1080/01621459.2021.1923511>.
Author: Michael Lingzhi Li [aut, cre],
Kosuke Imai [aut],
Jialu Li [ctb],
Xiaolong Yang [ctb]
Maintainer: Michael Lingzhi Li <mili@hbs.edu>
Diff between evalITR versions 1.0.0 dated 2023-08-25 and 1.1.0 dated 2026-09-07
DESCRIPTION | 20 +-- MD5 | 88 +++++++------- NEWS.md | 6 R/GATE.R | 58 ++------- R/GATEcv.R | 91 ++------------ R/consist.test.R | 83 ++----------- R/consistcv.test.R | 129 ++------------------- R/gates_inference.R |only R/het.test.R | 68 ++--------- R/hetcv.test.R | 114 ++---------------- R/itr_helpers.R | 9 - R/main.r | 18 +- build/vignette.rds |binary inst/doc/cv_multiple_alg.R | 2 inst/doc/cv_multiple_alg.html | 73 +++++------ inst/doc/cv_single_alg.R | 2 inst/doc/cv_single_alg.html | 16 +- inst/doc/install.R | 28 ++-- inst/doc/paper_alg1.R | 2 inst/doc/sample_split.R | 2 inst/doc/sample_split.html | 20 +-- inst/doc/sample_split_caret.R | 16 +- inst/doc/sample_split_caret.html | 44 +++---- inst/doc/user_itr.R | 2 inst/doc/user_itr.html | 14 +- inst/doc/user_itr_algs.R | 2 inst/doc/user_itr_algs.html | 72 +++++------ man/GATE.Rd | 89 +++++++------- man/GATEcv.Rd | 27 ++-- man/consist.test.Rd | 92 +++++++------- man/consistcv.test.Rd | 99 ++++++++-------- man/figures/README-caret_model-1.png |binary man/figures/README-caret_model-2.png |binary man/figures/README-compare_itr_aupec-1.png |binary man/figures/README-compare_itr_model_summary-1.png |binary man/figures/README-est_extract-1.png |binary man/figures/README-multiple_plot-1.png |binary man/figures/README-sl_plot-1.png |binary man/figures/README-sp_plot-1.png |binary man/figures/README-user_itr_aupec-1.png |binary man/figures/README-user_itr_gate-1.png |binary man/het.test.Rd | 88 +++++++------- man/hetcv.test.Rd | 95 +++++++-------- man/test_itr.Rd | 4 tests/testthat/test-gates-variance.R |only tests/testthat/test-high_level.R | 3 46 files changed, 574 insertions(+), 902 deletions(-)
Title: Bayesian Emulation of Computer Programs
Description: Allows one to estimate the output of a computer program,
as a function of the input parameters, without actually running it.
The computer program is assumed to be a Gaussian process, whose
parameters are estimated using Bayesian techniques that give a PDF of
expected program output. This PDF is conditional on a training set
of runs, each consisting of a point in parameter space and the model
output at that point. The emphasis is on complex codes that take
weeks or months to run, and that have a large number of undetermined
input parameters; many climate prediction models fall into this
class. The emulator essentially determines Bayesian posterior
estimates of the PDF of the output of a model, conditioned on results
from previous runs and a user-specified prior linear model. The
package includes functionality to evaluate quadratic forms
efficiently.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between emulator versions 1.2-24 dated 2024-03-22 and 1.3-0 dated 2026-09-07
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