Title: Estimate Vaccine Effectiveness Based on Different Study Designs
Description: Provides tools for estimating vaccine effectiveness and
related metrics. The 'vaccineff_data' class manages key features for
preparing, visualizing, and organizing cohort data, as well as
estimating vaccine effectiveness. The results and model performance
are assessed using the 'vaccineff' class.
Author: David Santiago Quevedo [aut] ,
Zulma M. Cucunuba [aut] ,
International Development Research Center [fnd] ,
Geraldine Gomez Millan [ctb] ,
Pratik Gupte [ctb] ,
Erika J Cantor [ctb] ,
Santiago Loaiza [ctb] ,
Jaime Pavlich-Mariscal [ctb, cre] ,
Hugo Gr [...truncated...]
Maintainer: Jaime Pavlich-Mariscal <jpavlich@javeriana.edu.co>
Diff between vaccineff versions 1.0.1 dated 2025-10-02 and 1.0.3 dated 2026-07-29
DESCRIPTION | 18 +++++++++--------- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ build/vignette.rds |binary inst/doc/cohort_design.html | 40 +++++++++++++++++++--------------------- inst/doc/vaccineff.html | 10 ++++------ man/vaccineff-package.Rd | 8 ++++---- 7 files changed, 48 insertions(+), 46 deletions(-)
Title: Bayesian Spatial and Space-Time Linear Mixed Models
Description: Fits Bayesian linear mixed models for spatial and space-time data with fixed effects, independent and identically distributed (iid) grouped random effects, and structured latent processes. The formula interface supports first-order autoregressive (AR(1)) effects, dense Gaussian processes, nearest-neighbor Gaussian processes, proper and Leroux conditional autoregressive (CAR) effects, ordered directed acyclic graph autoregressive (DAGAR) effects, separable CAR-time and DAGAR-time effects, and spatially varying coefficients. The sampler uses sparse precision matrix calculations when available and includes post-fitting tools for latent process recovery, fitted values, prediction, pointwise log likelihoods, and posterior sample extraction. Method details include Datta et al. (2016) <doi:10.1080/01621459.2015.1044091>, Finley et al. (2019) <doi:10.1080/10618600.2018.1537924>, Datta et al. (2019) <doi:10.1214/19-BA1177>, and May and Finley (2025) <doi:10.1016/j.spasta.20 [...truncated...]
Author: Andrew O. Finley [aut, cre],
Sudipto Banerjee [ctb],
Abhirup Datta [ctb],
Paul B. May [ctb]
Maintainer: Andrew O. Finley <finleya@msu.edu>
Diff between stLMM versions 0.0.2 dated 2026-07-28 and 0.0.3 dated 2026-07-29
DESCRIPTION | 9 +++++---- MD5 | 14 +++++++------- README.md | 34 ++++++++++++++++++++-------------- inst/doc/v02-spatial-nngp.html | 2 +- src/stLMM_covariance.cpp | 5 ++--- src/stLMM_internal.h | 4 ++++ src/stLMM_predict.cpp | 2 +- src/stLMM_sampler.cpp | 26 +++++++++++++++----------- 8 files changed, 55 insertions(+), 41 deletions(-)
Title: Proportional Trimmed Mean
Description: Computes a proportional trimmed mean that resolves the
integer truncation problem of base R's mean(..., trim). When
k = trim * n is non-integer, a fractional discount (1 - delta) is
applied to boundary observations, where delta = k - floor(k).
The resulting estimator is continuous in alpha for any fixed n,
syntactically identical to mean(..., trim), and compatible with
the 'Statgraphics' implementation. See Gaviria Chaverra (2026)
<doi:10.32614/CRAN.package.sgmean>.
Author: Juan C. Gaviria-Chaverra [aut, cre]
Maintainer: Juan C. Gaviria-Chaverra <jcarlos.gaviria@udea.edu.co>
Diff between sgmean versions 0.1.0 dated 2026-06-03 and 0.1.1 dated 2026-07-29
DESCRIPTION | 40 ++++++---- MD5 | 15 ++- NEWS.md |only R/sgmean.R | 109 ++++++++++++++++++++++------ README.md | 72 +++++++++---------- inst/doc/sgmean-introduccion.Rmd | 144 +++++++++++++++++++------------------- inst/doc/sgmean-introduccion.html | 2 man/sgmean.Rd | 59 ++++++++++++--- vignettes/sgmean-introduccion.Rmd | 144 +++++++++++++++++++------------------- 9 files changed, 344 insertions(+), 241 deletions(-)
Title: JSS 'LaTeX'/'BibTeX' Style Checker
Description: Lints 'LaTeX'/'BibTeX' manuscripts against the Journal of Statistical
Software (JSS) style guide. Wraps the same 'Rust' rule engine used by the
standalone 'jsslint' binary, the browser/'WASM' build, and the 'Python'
binding, exposed to R via 'extendr'.
Author: Manuel Koller [aut, cre] ,
The authors of the vendored 'Rust' crates [cph]
Maintainer: Manuel Koller <kollerma@proton.me>
Diff between jsslintr versions 1.1.0-1 dated 2026-07-28 and 1.1.0-2 dated 2026-07-29
DESCRIPTION | 29 ++++++++++++++++++----------- MD5 | 12 ++++++++---- configure |only configure.win |only inst/AUTHORS |only src/Makevars | 13 ++++++++++--- src/Makevars.win | 11 ++++++++--- tools/generate-rust-authors.py |only tools/vendor-crate-archive.sh | 4 ++++ 9 files changed, 48 insertions(+), 21 deletions(-)
Title: Iterative Proportional Fitting
Description: Fast raking for survey weighting. The computational core
is written in Rust for speed. Supports multiple raking variables,
automatic variable selection, weight bounding, and comprehensive
diagnostics.
Author: Christopher T. Kenny [aut, cre]
Maintainer: Christopher T. Kenny <ctkenny@proton.me>
This is a re-admission after prior archival of version 0.0.1 dated 2026-07-09
Diff between ipf versions 0.0.1 dated 2026-07-09 and 0.0.3 dated 2026-07-29
DESCRIPTION | 8 MD5 | 17 NEWS.md |only R/data.R | 2 build/vignette.rds |binary man/anes24.Rd | 2 src/Makevars.in | 4 src/Makevars.win.in | 98 ++-- src/rust/Cargo.toml | 34 - src/rust/src/lib.rs | 1096 ++++++++++++++++++++++++++-------------------------- 10 files changed, 626 insertions(+), 635 deletions(-)
Title: Cayley Graph Analysis for Permutation Puzzles
Description: Implements algorithms for analyzing Cayley graphs of
permutation groups for the TopSpin puzzle. Provides methods for
cycle detection, state space exploration and finding optimal operation
sequences in permutation groups generated by shift and reverse
operations. Also provides rule-defined landmark states for probing
graphs too large to enumerate, and convex and non-convex hulls for
measuring the solid such states span. The method Iterative Cycle
Intersection (ICI) is described in Yuri Baramykov (2026)
<doi:10.48550/arXiv.2607.13219>.
Author: Yuri Baramykov [aut, cre]
Maintainer: Yuri Baramykov <lbsbmsu@mail.ru>
Diff between cayleyR versions 0.2.1 dated 2026-03-01 and 0.2.6 dated 2026-07-29
cayleyR-0.2.1/cayleyR/inst/examples/test_bfs_in_path.R |only cayleyR-0.2.1/cayleyR/inst/examples/test_sparse_bfs.R |only cayleyR-0.2.6/cayleyR/DESCRIPTION | 35 cayleyR-0.2.6/cayleyR/LICENSE | 4 cayleyR-0.2.6/cayleyR/MD5 | 160 ++- cayleyR-0.2.6/cayleyR/NAMESPACE | 38 cayleyR-0.2.6/cayleyR/NEWS.md | 63 + cayleyR-0.2.6/cayleyR/R/RcppExports.R | 136 ++ cayleyR-0.2.6/cayleyR/R/basic_ops_doc.R | 26 cayleyR-0.2.6/cayleyR/R/convex_hull_3d.R |only cayleyR-0.2.6/cayleyR/R/cycle_shortcut.R |only cayleyR-0.2.6/cayleyR/R/distance_methods.R |only cayleyR-0.2.6/cayleyR/R/enclosing_hull_3d.R |only cayleyR-0.2.6/cayleyR/R/find_best_random_combinations.R | 57 + cayleyR-0.2.6/cayleyR/R/find_path_bfs.R | 128 ++ cayleyR-0.2.6/cayleyR/R/find_path_iterative.R | 491 ++++++---- cayleyR-0.2.6/cayleyR/R/gpu.R | 4 cayleyR-0.2.6/cayleyR/R/graph_metrics.R |only cayleyR-0.2.6/cayleyR/R/human_algorithm.R |only cayleyR-0.2.6/cayleyR/R/human_algorithm_to.R |only cayleyR-0.2.6/cayleyR/R/human_navigation.R |only cayleyR-0.2.6/cayleyR/R/landmark_states.R |only cayleyR-0.2.6/cayleyR/R/path_utils.R | 33 cayleyR-0.2.6/cayleyR/R/short_path_bfs.R | 15 cayleyR-0.2.6/cayleyR/R/state_store.R |only cayleyR-0.2.6/cayleyR/R/state_utils.R | 16 cayleyR-0.2.6/cayleyR/README.md | 305 +++++- cayleyR-0.2.6/cayleyR/build |only cayleyR-0.2.6/cayleyR/inst/WORDLIST | 59 + cayleyR-0.2.6/cayleyR/inst/doc |only cayleyR-0.2.6/cayleyR/inst/examples/benchmark_cycle_shortcut.R |only cayleyR-0.2.6/cayleyR/inst/examples/benchmark_gpu_vs_cpu.R |only cayleyR-0.2.6/cayleyR/inst/examples/benchmark_human_algorithm_to.R |only cayleyR-0.2.6/cayleyR/inst/examples/benchmark_human_nav.R |only cayleyR-0.2.6/cayleyR/inst/examples/benchmark_n_moves.R |only cayleyR-0.2.6/cayleyR/inst/examples/benchmark_n_size.R |only cayleyR-0.2.6/cayleyR/inst/examples/benchmark_sort_by.R |only cayleyR-0.2.6/cayleyR/inst/examples/coord_diagnostics.R |only cayleyR-0.2.6/cayleyR/inst/examples/demo_graph_celestial.R |only cayleyR-0.2.6/cayleyR/inst/examples/demo_graph_spectral.R |only cayleyR-0.2.6/cayleyR/inst/examples/demo_graph_spectral_nobfs.R |only cayleyR-0.2.6/cayleyR/inst/examples/demo_landmark_network.R |only cayleyR-0.2.6/cayleyR/inst/examples/demo_landmark_paths.R |only cayleyR-0.2.6/cayleyR/inst/examples/graph_diameter.R |only cayleyR-0.2.6/cayleyR/inst/examples/landmark_distances.R |only cayleyR-0.2.6/cayleyR/inst/examples/landmark_hull_scan.R |only cayleyR-0.2.6/cayleyR/inst/examples/probe_human_table.R |only cayleyR-0.2.6/cayleyR/inst/examples/test_bh_in_path.R |only cayleyR-0.2.6/cayleyR/inst/examples/test_bh_path_coords.R |only cayleyR-0.2.6/cayleyR/inst/examples/test_human_algorithm.R |only cayleyR-0.2.6/cayleyR/inst/examples/test_human_navigation.R |only cayleyR-0.2.6/cayleyR/inst/examples/test_path.R | 26 cayleyR-0.2.6/cayleyR/inst/examples/test_sparse_bh.R |only cayleyR-0.2.6/cayleyR/man/apply_operations.Rd | 6 cayleyR-0.2.6/cayleyR/man/build_permutation_matrix.Rd | 1 cayleyR-0.2.6/cayleyR/man/cayleyR-package.Rd | 1 cayleyR-0.2.6/cayleyR/man/cayley_bfs_full.Rd |only cayleyR-0.2.6/cayleyR/man/cayley_graph_diameter.Rd |only cayleyR-0.2.6/cayleyR/man/compose_permutation_matrix.Rd | 1 cayleyR-0.2.6/cayleyR/man/convex_hull_3d.Rd |only cayleyR-0.2.6/cayleyR/man/create_state_store.Rd |only cayleyR-0.2.6/cayleyR/man/cycle_shortcut.Rd |only cayleyR-0.2.6/cayleyR/man/distance_methods.Rd |only cayleyR-0.2.6/cayleyR/man/enclosing_hull_3d.Rd |only cayleyR-0.2.6/cayleyR/man/find_best_match_human.Rd |only cayleyR-0.2.6/cayleyR/man/find_best_random_combinations.Rd | 33 cayleyR-0.2.6/cayleyR/man/find_path_bfs.Rd | 15 cayleyR-0.2.6/cayleyR/man/find_path_iterative.Rd | 22 cayleyR-0.2.6/cayleyR/man/generate_state.Rd | 10 cayleyR-0.2.6/cayleyR/man/human_algorithm.Rd |only cayleyR-0.2.6/cayleyR/man/human_algorithm_to.Rd |only cayleyR-0.2.6/cayleyR/man/human_phase1_navigate.Rd |only cayleyR-0.2.6/cayleyR/man/human_phase1_rank.Rd |only cayleyR-0.2.6/cayleyR/man/landmark_states.Rd |only cayleyR-0.2.6/cayleyR/man/openmp_threads.Rd |only cayleyR-0.2.6/cayleyR/man/reverse_prefix.Rd | 3 cayleyR-0.2.6/cayleyR/man/reverse_prefix_simple.Rd | 3 cayleyR-0.2.6/cayleyR/man/run_length.Rd |only cayleyR-0.2.6/cayleyR/man/shift_left.Rd | 3 cayleyR-0.2.6/cayleyR/man/shift_left_simple.Rd | 3 cayleyR-0.2.6/cayleyR/man/shift_right.Rd | 3 cayleyR-0.2.6/cayleyR/man/shift_right_simple.Rd | 3 cayleyR-0.2.6/cayleyR/man/short_path_bfs.Rd | 13 cayleyR-0.2.6/cayleyR/man/state_store_query.Rd |only cayleyR-0.2.6/cayleyR/man/store_add_from_df.Rd |only cayleyR-0.2.6/cayleyR/man/store_analyze_combos.Rd |only cayleyR-0.2.6/cayleyR/man/store_analyze_combos_gpu.Rd |only cayleyR-0.2.6/cayleyR/man/store_clear.Rd |only cayleyR-0.2.6/cayleyR/man/store_clear_opd.Rd |only cayleyR-0.2.6/cayleyR/man/store_collect_ops.Rd |only cayleyR-0.2.6/cayleyR/man/store_combos_for_state.Rd |only cayleyR-0.2.6/cayleyR/man/store_filter_middle.Rd |only cayleyR-0.2.6/cayleyR/man/store_find_best_match.Rd |only cayleyR-0.2.6/cayleyR/man/store_find_intersections.Rd |only cayleyR-0.2.6/cayleyR/man/store_get_meta.Rd |only cayleyR-0.2.6/cayleyR/man/store_get_state.Rd |only cayleyR-0.2.6/cayleyR/man/store_lookup.Rd |only cayleyR-0.2.6/cayleyR/man/store_reconstruct_path.Rd |only cayleyR-0.2.6/cayleyR/man/store_set_opd.Rd |only cayleyR-0.2.6/cayleyR/man/store_to_dataframe.Rd |only cayleyR-0.2.6/cayleyR/src/RcppExports.cpp | 467 +++++++++ cayleyR-0.2.6/cayleyR/src/cayley_utils.h | 39 cayleyR-0.2.6/cayleyR/src/celestial_coords.h |only cayleyR-0.2.6/cayleyR/src/coords.cpp | 132 +- cayleyR-0.2.6/cayleyR/src/cycle_shortcut.cpp |only cayleyR-0.2.6/cayleyR/src/graph_metrics.cpp |only cayleyR-0.2.6/cayleyR/src/human_algorithm.cpp |only cayleyR-0.2.6/cayleyR/src/short_path_bfs.cpp | 53 - cayleyR-0.2.6/cayleyR/src/state_store.cpp |only cayleyR-0.2.6/cayleyR/src/state_store.h |only cayleyR-0.2.6/cayleyR/tests/testthat/test-bidirectional-bfs.R | 10 cayleyR-0.2.6/cayleyR/tests/testthat/test-find-path-iterative.R | 59 + cayleyR-0.2.6/cayleyR/tests/testthat/test-graph-metrics.R |only cayleyR-0.2.6/cayleyR/tests/testthat/test-human-algorithm.R |only cayleyR-0.2.6/cayleyR/tests/testthat/test-state-store.R |only cayleyR-0.2.6/cayleyR/vignettes |only 116 files changed, 2028 insertions(+), 448 deletions(-)
Title: Brazilian Population Estimates
Description: Provides Brazilian municipality population estimates from official
and research sources, with functions to aggregate the data by state, health
region, sex, and age group.
Author: Raphael Saldanha [aut, cre]
Maintainer: Raphael Saldanha <raphael.saldanha@fiocruz.br>
This is a re-admission after prior archival of version 0.6.3 dated 2025-09-03
Diff between brpop versions 0.6.3 dated 2025-09-03 and 0.7.0 dated 2026-07-29
brpop-0.6.3/brpop/tests/testthat/test-errors.R |only brpop-0.6.3/brpop/tests/testthat/test-pop_mun_consistency.R |only brpop-0.6.3/brpop/tests/testthat/test-pop_uf_consistency.R |only brpop-0.6.3/brpop/tests/testthat/test-regsaude_female_pop.R |only brpop-0.6.3/brpop/tests/testthat/test-regsaude_male_pop.R |only brpop-0.7.0/brpop/DESCRIPTION | 19 + brpop-0.7.0/brpop/MD5 | 131 ++++++------ brpop-0.7.0/brpop/NAMESPACE | 9 brpop-0.7.0/brpop/NEWS.md | 21 + brpop-0.7.0/brpop/R/data-download.R |only brpop-0.7.0/brpop/R/datasus2024_mun_female_pop.R | 24 -- brpop-0.7.0/brpop/R/datasus2024_mun_male_pop.R | 24 -- brpop-0.7.0/brpop/R/datasus_mun_female_pop.R | 22 -- brpop-0.7.0/brpop/R/datasus_mun_male_pop.R | 22 -- brpop-0.7.0/brpop/R/ibge_pop.R | 61 +++-- brpop-0.7.0/brpop/R/mun_female_pop_totals.R | 2 brpop-0.7.0/brpop/R/mun_male_pop_totals.R | 2 brpop-0.7.0/brpop/R/mun_pop_age.R | 6 brpop-0.7.0/brpop/R/mun_pop_totals.R | 6 brpop-0.7.0/brpop/R/mun_reg_saude.R | 9 brpop-0.7.0/brpop/R/mun_reg_saude_449.R | 9 brpop-0.7.0/brpop/R/mun_sex_pop.R | 2 brpop-0.7.0/brpop/R/regsaude_female_pop.R | 11 - brpop-0.7.0/brpop/R/regsaude_female_pop_totals.R | 12 - brpop-0.7.0/brpop/R/regsaude_male_pop.R | 11 - brpop-0.7.0/brpop/R/regsaude_male_pop_totals.R | 12 - brpop-0.7.0/brpop/R/regsaude_pop_age.R | 20 + brpop-0.7.0/brpop/R/regsaude_pop_totals.R | 29 +- brpop-0.7.0/brpop/R/regsaude_sex_pop.R | 20 + brpop-0.7.0/brpop/R/uf_female_pop_totals.R | 2 brpop-0.7.0/brpop/R/uf_male_pop_totals.R | 2 brpop-0.7.0/brpop/R/uf_pop_age.R | 6 brpop-0.7.0/brpop/R/uf_pop_totals.R | 6 brpop-0.7.0/brpop/R/uf_sex_pop.R | 2 brpop-0.7.0/brpop/R/ufrn_mun_female_pop.R | 24 -- brpop-0.7.0/brpop/R/ufrn_mun_male_pop.R | 24 -- brpop-0.7.0/brpop/R/utils-pipe.R | 5 brpop-0.7.0/brpop/R/zenodo_deposit.R | 2 brpop-0.7.0/brpop/README.md | 75 +++++- brpop-0.7.0/brpop/data/mun_reg_saude.rda |binary brpop-0.7.0/brpop/data/mun_reg_saude_449.rda |binary brpop-0.7.0/brpop/inst |only brpop-0.7.0/brpop/man/brpop-package.Rd | 10 brpop-0.7.0/brpop/man/datasus2024_mun_female_pop.Rd | 8 brpop-0.7.0/brpop/man/datasus2024_mun_male_pop.Rd | 8 brpop-0.7.0/brpop/man/datasus_mun_female_pop.Rd | 6 brpop-0.7.0/brpop/man/datasus_mun_male_pop.Rd | 6 brpop-0.7.0/brpop/man/ibge_pop.Rd | 51 ++-- brpop-0.7.0/brpop/man/mun_female_pop_totals.Rd | 2 brpop-0.7.0/brpop/man/mun_male_pop_totals.Rd | 2 brpop-0.7.0/brpop/man/mun_pop_age.Rd | 4 brpop-0.7.0/brpop/man/mun_pop_totals.Rd | 2 brpop-0.7.0/brpop/man/mun_reg_saude.Rd | 10 brpop-0.7.0/brpop/man/mun_reg_saude_449.Rd | 10 brpop-0.7.0/brpop/man/pipe.Rd | 3 brpop-0.7.0/brpop/man/regsaude_female_pop.Rd | 2 brpop-0.7.0/brpop/man/regsaude_female_pop_totals.Rd | 2 brpop-0.7.0/brpop/man/regsaude_male_pop.Rd | 2 brpop-0.7.0/brpop/man/regsaude_male_pop_totals.Rd | 2 brpop-0.7.0/brpop/man/regsaude_pop_age.Rd | 4 brpop-0.7.0/brpop/man/regsaude_pop_totals.Rd | 2 brpop-0.7.0/brpop/man/regsaude_sex_pop.Rd | 3 brpop-0.7.0/brpop/man/uf_female_pop_totals.Rd | 2 brpop-0.7.0/brpop/man/uf_male_pop_totals.Rd | 2 brpop-0.7.0/brpop/man/uf_pop_age.Rd | 4 brpop-0.7.0/brpop/man/uf_pop_totals.Rd | 2 brpop-0.7.0/brpop/man/ufrn_mun_female_pop.Rd | 8 brpop-0.7.0/brpop/man/ufrn_mun_male_pop.Rd | 8 brpop-0.7.0/brpop/tests/testthat/helper-fixtures.R |only brpop-0.7.0/brpop/tests/testthat/test-api-contracts.R |only brpop-0.7.0/brpop/tests/testthat/test-download-failures.R |only brpop-0.7.0/brpop/tests/testthat/test-ibge-pop.R |only 72 files changed, 445 insertions(+), 352 deletions(-)
Title: Rank-Clustered Estimation for Network Meta-Analysis
Description: An implementation of the RaCE-NMA (Rank-Clustered
Estimation for Network Meta-Analysis) model for post-hoc clustering
of treatments or interventions by rank in network meta-analysis
data. Functions for model estimation, assessment, and displaying
results are provided. For more details, see Pearce and Zhou (2025)
<doi:10.1017/rsm.2025.10049>.
Author: Michael Pearce [aut, cre, cph] ,
Shouhao Zhou [aut]
Maintainer: Michael Pearce <michaelpearce@reed.edu>
Diff between RaCE.NMA versions 1.0.3 dated 2026-06-02 and 1.1.0 dated 2026-07-29
DESCRIPTION | 12 +++++++----- MD5 | 23 ++++++++++++++++------- NEWS.md | 5 +++++ R/calculate_SUCRA_MNBT.R | 2 ++ R/clusterplot_ranks.R | 2 ++ R/cumulativeprobplot_ranks.R | 5 +++++ R/forestplot_muhat.R | 1 + R/traceplot_mu.R | 1 + tests |only 9 files changed, 39 insertions(+), 12 deletions(-)
Title: Extracting and Visualizing Output from 'jagsUI'
Description: Tools are provided to streamline Bayesian analyses in 'JAGS' using
the 'jagsUI' package. Included are functions for extracting output in
simpler format, functions for streamlining assessment of convergence, and
functions for producing summary plots of output. Also included is a
function that provides a simple template for running 'JAGS' from 'R'.
Referenced materials can be found at <DOI:10.1214/ss/1177011136>.
Author: Matt Tyers [aut, cre]
Maintainer: Matt Tyers <matttyersstat@gmail.com>
Diff between jagshelper versions 0.4.2 dated 2026-06-07 and 0.4.3 dated 2026-07-29
DESCRIPTION | 8 +-- MD5 | 18 ++++---- NEWS.md | 4 + R/caterpillar.R | 79 +++++++++++++++++++++++++++++++++----- build/vignette.rds |binary inst/doc/jagshelper-vignette.html | 4 - man/caterpillar.Rd | 9 ++-- man/jagshelper-package.Rd | 4 - tests/testthat/Rplots.pdf |binary tests/testthat/test_jagshelper.R | 17 ++++++++ 10 files changed, 113 insertions(+), 30 deletions(-)
Title: Generate Tests from Examples Using 'roxygen' and 'testthat'
Description: Creates 'testthat' tests from 'roxygen' examples using simple tags.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between doctest versions 0.4.0 dated 2026-02-19 and 0.4.1 dated 2026-07-29
DESCRIPTION | 8 +- MD5 | 39 ++++++---- NAMESPACE | 1 NEWS.md | 5 + R/parse.R | 13 +++ build/vignette.rds |binary man/doctest-package.Rd | 5 + man/expect-tag.Rd | 2 man/expectRaw-tag.Rd | 2 man/snap-tag.Rd | 2 man/test_doctests.Rd | 6 - tests/testthat/_snaps/rd-roclet.md | 25 +++++- tests/testthat/_snaps/rd-roclet/palindrome.Rd | 1 tests/testthat/test-rd-roclet.R | 19 ++++ tests/testthat/testPackage/DESCRIPTION | 2 tests/testthat/testPackage/man/add.Rd |only tests/testthat/testPackage/man/grapes-plus-grapes.Rd |only tests/testthat/testPackage/man/palindrome.Rd |only tests/testthat/testPackage/man/safe_mean.Rd |only tests/testthat/testPackage/man/safe_var.Rd |only tests/testthat/testPackage/tests/testthat/test-doctest-%plus%.R |only tests/testthat/testPackage/tests/testthat/test-doctest-add.R |only tests/testthat/testPackage/tests/testthat/test-doctest-palindrome.R |only tests/testthat/testPackage/tests/testthat/test-doctest-palindrome_letters.R |only tests/testthat/testPackage/tests/testthat/test-doctest-safe_mean.R |only tests/testthat/testPackage/tests/testthat/test-doctest-safe_var.R |only 26 files changed, 98 insertions(+), 32 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') 'SQLite' Driver
Description: Provides a developer-facing interface to the 'Arrow' Database
Connectivity ('ADBC') 'SQLite' driver for the purposes of building high-level
database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is
an API standard for database access libraries that uses 'Arrow' for result
sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcsqlite versions 0.23.0-1 dated 2026-06-03 and 0.24.0-1 dated 2026-07-29
adbcsqlite-0.23.0-1/adbcsqlite/src/c/include/arrow-adbc/driver/bigquery.h |only adbcsqlite-0.23.0-1/adbcsqlite/src/c/include/arrow-adbc/driver/snowflake.h |only adbcsqlite-0.24.0-1/adbcsqlite/DESCRIPTION | 10 adbcsqlite-0.24.0-1/adbcsqlite/MD5 | 41 - adbcsqlite-0.24.0-1/adbcsqlite/man/adbcsqlite-package.Rd | 1 adbcsqlite-0.24.0-1/adbcsqlite/man/adbcsqlite.Rd | 2 adbcsqlite-0.24.0-1/adbcsqlite/src/c/driver/postgresql/bind_stream.h | 7 adbcsqlite-0.24.0-1/adbcsqlite/src/c/driver/postgresql/connection.cc | 122 ++- adbcsqlite-0.24.0-1/adbcsqlite/src/c/driver/postgresql/connection.h | 4 adbcsqlite-0.24.0-1/adbcsqlite/src/c/driver/postgresql/copy/writer.h | 343 +++++++++- adbcsqlite-0.24.0-1/adbcsqlite/src/c/driver/postgresql/database.cc | 22 adbcsqlite-0.24.0-1/adbcsqlite/src/c/driver/postgresql/database.h | 17 adbcsqlite-0.24.0-1/adbcsqlite/src/c/driver/postgresql/postgres_type.h | 15 adbcsqlite-0.24.0-1/adbcsqlite/src/c/driver/postgresql/statement.cc | 102 ++ adbcsqlite-0.24.0-1/adbcsqlite/src/c/driver/postgresql/statement.h | 13 adbcsqlite-0.24.0-1/adbcsqlite/src/c/driver/sqlite/sqlite.cc | 13 adbcsqlite-0.24.0-1/adbcsqlite/src/c/driver_manager/adbc_driver_manager.cc | 12 adbcsqlite-0.24.0-1/adbcsqlite/src/c/integration/shared_test/main.c | 12 adbcsqlite-0.24.0-1/adbcsqlite/src/c/integration/static_test/main.c | 2 adbcsqlite-0.24.0-1/adbcsqlite/src/c/validation/adbc_validation.h | 17 adbcsqlite-0.24.0-1/adbcsqlite/src/c/validation/adbc_validation_statement.cc | 328 ++++++--- adbcsqlite-0.24.0-1/adbcsqlite/src/c/vendor/toml++/toml.hpp | 5 adbcsqlite-0.24.0-1/adbcsqlite/tests/testthat/test-connection-profiles.R |only 23 files changed, 797 insertions(+), 291 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') 'PostgreSQL' Driver
Description: Provides a developer-facing interface to the 'Arrow' Database
Connectivity ('ADBC') 'PostgreSQL' driver for the purposes of building high-level
database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is
an API standard for database access libraries that uses 'Arrow' for result
sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcpostgresql versions 0.23.0-1 dated 2026-06-03 and 0.24.0-1 dated 2026-07-29
adbcpostgresql-0.23.0-1/adbcpostgresql/src/c/include/arrow-adbc/driver/bigquery.h |only adbcpostgresql-0.23.0-1/adbcpostgresql/src/c/include/arrow-adbc/driver/snowflake.h |only adbcpostgresql-0.24.0-1/adbcpostgresql/DESCRIPTION | 8 adbcpostgresql-0.24.0-1/adbcpostgresql/MD5 | 40 - adbcpostgresql-0.24.0-1/adbcpostgresql/man/adbcpostgresql-package.Rd | 1 adbcpostgresql-0.24.0-1/adbcpostgresql/man/adbcpostgresql.Rd | 2 adbcpostgresql-0.24.0-1/adbcpostgresql/src/c/driver/postgresql/bind_stream.h | 7 adbcpostgresql-0.24.0-1/adbcpostgresql/src/c/driver/postgresql/connection.cc | 122 ++- adbcpostgresql-0.24.0-1/adbcpostgresql/src/c/driver/postgresql/connection.h | 4 adbcpostgresql-0.24.0-1/adbcpostgresql/src/c/driver/postgresql/copy/writer.h | 343 +++++++++- adbcpostgresql-0.24.0-1/adbcpostgresql/src/c/driver/postgresql/database.cc | 22 adbcpostgresql-0.24.0-1/adbcpostgresql/src/c/driver/postgresql/database.h | 17 adbcpostgresql-0.24.0-1/adbcpostgresql/src/c/driver/postgresql/postgres_type.h | 15 adbcpostgresql-0.24.0-1/adbcpostgresql/src/c/driver/postgresql/statement.cc | 102 ++ adbcpostgresql-0.24.0-1/adbcpostgresql/src/c/driver/postgresql/statement.h | 13 adbcpostgresql-0.24.0-1/adbcpostgresql/src/c/driver/sqlite/sqlite.cc | 13 adbcpostgresql-0.24.0-1/adbcpostgresql/src/c/driver_manager/adbc_driver_manager.cc | 12 adbcpostgresql-0.24.0-1/adbcpostgresql/src/c/integration/shared_test/main.c | 12 adbcpostgresql-0.24.0-1/adbcpostgresql/src/c/integration/static_test/main.c | 2 adbcpostgresql-0.24.0-1/adbcpostgresql/src/c/validation/adbc_validation.h | 17 adbcpostgresql-0.24.0-1/adbcpostgresql/src/c/validation/adbc_validation_statement.cc | 328 ++++++--- adbcpostgresql-0.24.0-1/adbcpostgresql/src/c/vendor/toml++/toml.hpp | 5 22 files changed, 795 insertions(+), 290 deletions(-)
More information about adbcpostgresql at CRAN
Permanent link
Title: 'Shiny' User Interface for Multiple Source Capture Recapture
Models
Description: Implements user interfaces for log-linear models, Bayesian model averaging and
Bayesian Dirichlet process mixture models. See McIntyre, Fellows, Gutreuter and Hladik (2022) <doi:10.2196/32645>.
Author: Ian E. Fellows [aut, cre]
Maintainer: Ian E. Fellows <ian@fellstat.com>
This is a re-admission after prior archival of version 0.1.0 dated 2019-01-19
Diff between shinyrecap versions 0.1.0 dated 2019-01-19 and 0.2.0 dated 2026-07-29
DESCRIPTION | 24 +- MD5 | 100 +++++++--- NAMESPACE | 18 + R/extract_histories.R |only R/launch.R | 7 R/package.R | 8 R/power.R | 3 R/utils.R | 17 + inst/apps/capture_power/helpfiles |only inst/apps/capture_power/server.R | 18 + inst/apps/capture_power/ui.R | 24 +- inst/apps/extract_histories |only inst/apps/rcapture/helpfiles |only inst/apps/rcapture/import.R | 6 inst/apps/rcapture/server-dga.R | 332 ++++++++++++++++++++++++++++++---- inst/apps/rcapture/server-lcmcr.R | 178 +++++++++++++++++- inst/apps/rcapture/server-loglinear.R | 140 ++++++++++++++ inst/apps/rcapture/server-pairwise.R | 71 ++++++- inst/apps/rcapture/server.R | 91 ++++++++- inst/apps/rcapture/ui-dga.R | 40 +++- inst/apps/rcapture/ui-import.R | 9 inst/apps/rcapture/ui-intro.R | 77 ++----- inst/apps/rcapture/ui-lcmcr.R | 32 ++- inst/apps/rcapture/ui-loglinear.R | 32 ++- inst/apps/rcapture/ui-pairwise.R | 4 inst/apps/rcapture/ui.R | 31 ++- man/disaggregate.Rd | 7 man/extract_histories.Rd |only man/formatGraphs.Rd | 3 man/launchShinyPopSize.Rd | 5 man/lcmcrSample.Rd | 17 + man/shinyrecap-package.Rd | 5 man/simulateCapture.Rd | 3 man/simulateEstimates.Rd | 14 + man/simulateHeteroNormal.Rd | 3 man/srhelp.Rd |only tests/testthat/test-shinyrecap.R | 2 37 files changed, 1108 insertions(+), 213 deletions(-)
Title: Structural Breaks in Quantile Regression
Description: Methods for detecting structural breaks, determining the
number of breaks, and estimating break locations in linear quantile
regression, using one or multiple quantiles, based on Qu (2008) and
Oka and Qu (2011). Applicable to both time series and repeated
cross-sectional data. The main function is rq.break().
References for detailed theoretical and empirical explanations:
(1) Qu, Z. (2008). "Testing for Structural Change in Regression
Quantiles." Journal of Econometrics, 146(1), 170-184
<doi:10.1016/j.jeconom.2008.08.006>
(2) Oka, T., and Qu, Z. (2011). "Estimating Structural Changes in
Regression Quantiles." Journal of Econometrics, 162(2), 248-267
<doi:10.1016/j.jeconom.2011.01.005>.
Author: Zhongjun Qu [aut, cre],
Tatsushi Oka [aut],
Samuel Messer [ctb]
Maintainer: Zhongjun Qu <qu@bu.edu>
Diff between QR.break versions 1.0.2 dated 2025-04-23 and 1.0.3 dated 2026-07-29
DESCRIPTION | 15 +-- MD5 | 39 ++++---- NEWS.md | 24 +++++ R/dq.R | 16 ++- R/dq.test.0vs1.R | 238 +++++++++++++++++++++++++++++++------------------- R/dq.test.lvsl_1.R | 165 ++++++++++++++++++---------------- R/rq.break.R | 49 +++++++++- R/sq.R | 55 ++++++----- R/sq.test.0vs1.R | 207 +++++++++++++++++++++++++++---------------- R/sq.test.lvsl_1.R | 12 +- README.md | 6 - build |only inst |only man/dq.Rd | 21 +--- man/dq.test.0vs1.Rd | 38 +++++++ man/dq.test.lvsl_1.Rd | 6 + man/rq.break.Rd | 40 +++++++- man/sq.Rd | 28 +++-- man/sq.test.0vs1.Rd | 34 ++++++- man/sq.test.lvsl_1.Rd | 6 + vignettes |only 21 files changed, 658 insertions(+), 341 deletions(-)
Title: Profile Output Processing Tools for R
Description: Tools for examining Rprof profile output.
Author: Luke Tierney [aut, cre],
Riad Jarjour [aut]
Maintainer: Luke Tierney <luke-tierney@uiowa.edu>
Diff between proftools versions 0.99-3 dated 2020-07-08 and 0.99-4 dated 2026-07-29
proftools-0.99-3/proftools/vignettes/jsslogo.jpg |only proftools-0.99-4/proftools/DESCRIPTION | 16 +++++++++--- proftools-0.99-4/proftools/MD5 | 21 +++++++--------- proftools-0.99-4/proftools/README.md | 3 -- proftools-0.99-4/proftools/build/vignette.rds |binary proftools-0.99-4/proftools/inst/doc/proftools.R | 21 +++++++++------- proftools-0.99-4/proftools/inst/doc/proftools.Rnw | 8 +++--- proftools-0.99-4/proftools/inst/doc/proftools.pdf |binary proftools-0.99-4/proftools/man/printProfileCallGraph.Rd | 2 - proftools-0.99-4/proftools/man/proftools-package.Rd | 2 - proftools-0.99-4/proftools/vignettes/proftools.Rnw | 8 +++--- proftools-0.99-4/proftools/vignettes/proftools.bib | 2 - 12 files changed, 44 insertions(+), 39 deletions(-)
Title: Straightforward 'NetCDF' Metadata
Description: Extract metadata from 'NetCDF' data sources, these can be files, file handles or
servers. This package leverages and extends the lower level functions of the 'RNetCDF' package
providing a consistent set of functions that all return data frames. We introduce named concepts
of 'grid', 'axis' and 'source' which are all meaningful entities without formal definition in the
'NetCDF' library <https://www.unidata.ucar.edu/software/netcdf>. 'RNetCDF' matches the library
itself with only the named concepts of 'variables', 'dimensions' and 'attributes'.
Author: Michael Sumner [aut, cre, cph],
Tomas Remenyi [ctb],
Ben Raymond [ctb],
David Blodgett [ctb],
Milton Woods [ctb],
Patrick Van Laake [ctb]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between ncmeta versions 0.4.0 dated 2024-03-25 and 0.5.0 dated 2026-07-29
DESCRIPTION | 24 + MD5 | 68 ++--- NEWS.md | 8 R/nc-gridmapping.R | 39 +++ R/nc-prj.R | 18 + R/nc_axes.R | 4 R/nc_axis.R | 4 R/nc_coord.R | 416 +++++++++++++++++----------------- R/nc_dim.R | 9 R/nc_dimension.R | 5 R/nc_extended.R | 7 R/nc_grid.R | 19 + R/nc_inq_file.R | 11 R/nc_meta.R | 14 - R/nc_sources.R | 4 R/nc_var.R | 5 R/nc_variable.R | 12 README.md | 8 inst/extdata/dims_only.nc |only man/nc_axes.Rd | 7 man/nc_axis.Rd | 7 man/nc_coord_var.Rd | 98 ++++---- man/nc_dim.Rd | 13 - man/nc_dims.Rd | 8 man/nc_extended.Rd | 5 man/nc_gm_to_prj.Rd | 92 +++---- man/nc_grids.Rd | 9 man/nc_inq.Rd | 13 - man/nc_meta.Rd | 9 man/nc_prj_to_gridmapping.Rd | 72 ++--- man/nc_sources.Rd | 7 man/nc_var.Rd | 4 man/nc_vars.Rd | 5 man/ncmeta-package.Rd | 10 tests/testthat/test-gridmapping-prj.R | 19 + tests/testthat/test-no-vars.R |only 36 files changed, 624 insertions(+), 429 deletions(-)
Title: Filter Module for 'teal' Applications
Description: Data filtering module for 'teal' applications. Allows for
interactive filtering of data stored in 'data.frame' and
'MultiAssayExperiment' objects. Also displays filtered and unfiltered
observation counts.
Author: Dawid Kaledkowski [aut] ,
Pawel Rucki [aut],
Aleksander Chlebowski [aut] ,
Andre Verissimo [aut] ,
Lluis Revilla Sancho [aut] ,
Dony Unardi [rev, cre],
Kartikeya Kirar [aut],
Marcin Kosinski [aut],
Chendi Liao [aut],
Andrew Bates [aut],
Mahmoud Halla [...truncated...]
Maintainer: Dony Unardi <unardid@gene.com>
Diff between teal.slice versions 0.8.1 dated 2026-07-02 and 0.8.2 dated 2026-07-29
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/FilterState.R | 3 +-- R/FilterStates.R | 2 +- R/FilteredDataset.R | 2 +- 6 files changed, 16 insertions(+), 13 deletions(-)
Title: Exploratory Web Apps for Analyzing Clinical Trials Data
Description: A 'shiny' based interactive exploration framework for
analyzing clinical trials data. 'teal' currently provides a dynamic
filtering facility and different data viewers. 'teal' 'shiny'
applications are built using standard 'shiny' modules.
Author: Dony Unardi [aut, cre],
Dawid Kaledkowski [aut] ,
Pawel Rucki [aut],
Aleksander Chlebowski [aut] ,
Andre Verissimo [aut] ,
Kartikeya Kirar [aut],
Vedha Viyash [aut],
Marcin Kosinski [aut],
Adrian Waddell [aut],
Nina Qi [rev],
Nikolas Burkoff [aut],
M [...truncated...]
Maintainer: Dony Unardi <unardid@gene.com>
Diff between teal versions 1.2.0 dated 2026-06-30 and 1.2.1 dated 2026-07-29
teal-1.2.0/teal/vignettes/blueprint_qmd |only teal-1.2.1/teal/DESCRIPTION | 8 ++-- teal-1.2.1/teal/MD5 | 18 +++++----- teal-1.2.1/teal/NEWS.md | 7 +++ teal-1.2.1/teal/R/module_teal.R | 6 +++ teal-1.2.1/teal/R/utils.R | 10 +---- teal-1.2.1/teal/R/zzz.R | 2 - teal-1.2.1/teal/build/vignette.rds |binary teal-1.2.1/teal/inst/WORDLIST | 2 - teal-1.2.1/teal/inst/doc/including-data-in-teal-applications.html | 6 +-- teal-1.2.1/teal/vignettes/teal-as-a-module.html |only 11 files changed, 34 insertions(+), 25 deletions(-)
Title: Sleep Data Filtering and Visualisation
Description: An online app and command-line utility to import, filter and visualise sleep data. Can be used with sleep data collected from any type of device (e.g. radar, sleep diary,...) as long as the data contains sleep onset and wake-up times for each sleep session.
Author: Daniel Thedie [aut, cre, cph]
Maintainer: Daniel Thedie <daniel.thedie@ed.ac.uk>
Diff between nocturn versions 1.1.3 dated 2026-06-22 and 1.2.0 dated 2026-07-29
nocturn-1.1.3/nocturn/tests/testthat/test-get_column_names.R |only nocturn-1.2.0/nocturn/DESCRIPTION | 14 nocturn-1.2.0/nocturn/MD5 | 225 ++++--- nocturn-1.2.0/nocturn/NAMESPACE | 4 nocturn-1.2.0/nocturn/NEWS.md | 290 +++++----- nocturn-1.2.0/nocturn/R/bedtimes_waketimes.R | 17 nocturn-1.2.0/nocturn/R/bland_altman.R |only nocturn-1.2.0/nocturn/R/colnames_accessors.R | 22 nocturn-1.2.0/nocturn/R/colnames_key.R | 40 + nocturn-1.2.0/nocturn/R/compliance.R | 47 + nocturn-1.2.0/nocturn/R/data_checks.R | 26 nocturn-1.2.0/nocturn/R/data_cleaning.R | 197 ++---- nocturn-1.2.0/nocturn/R/data_parsing.R |only nocturn-1.2.0/nocturn/R/data_tables.R | 38 - nocturn-1.2.0/nocturn/R/filtering.R | 50 - nocturn-1.2.0/nocturn/R/hypnogram.R | 8 nocturn-1.2.0/nocturn/R/load_data.R | 30 - nocturn-1.2.0/nocturn/R/sleep_bubbles.R | 13 nocturn-1.2.0/nocturn/R/sleep_clock.R | 9 nocturn-1.2.0/nocturn/R/sleep_distributions.R | 9 nocturn-1.2.0/nocturn/R/sleep_metrics.R | 44 - nocturn-1.2.0/nocturn/R/sleep_report.R | 18 nocturn-1.2.0/nocturn/R/sleep_spiral.R | 51 - nocturn-1.2.0/nocturn/R/time_utils.R | 41 + nocturn-1.2.0/nocturn/R/timeseries.R | 36 - nocturn-1.2.0/nocturn/R/timeseries_comparison.R |only nocturn-1.2.0/nocturn/README.md | 9 nocturn-1.2.0/nocturn/data/example_epochs.rda |binary nocturn-1.2.0/nocturn/data/example_epochs_v1.rda |binary nocturn-1.2.0/nocturn/data/example_sessions.rda |binary nocturn-1.2.0/nocturn/data/example_sessions_v1.rda |binary nocturn-1.2.0/nocturn/inst/shiny/Rmd/Bland-Altman.Rmd |only nocturn-1.2.0/nocturn/inst/shiny/Rmd/Bland-Altman_statistics.Rmd |only nocturn-1.2.0/nocturn/inst/shiny/Rmd/Comparison_timeseries.Rmd |only nocturn-1.2.0/nocturn/inst/shiny/Rmd/Epoch_timeseries.Rmd |only nocturn-1.2.0/nocturn/inst/shiny/Rmd/Hypnogram.Rmd |only nocturn-1.2.0/nocturn/inst/shiny/Rmd/Secondary_datasets.Rmd |only nocturn-1.2.0/nocturn/inst/shiny/Rmd/Session_timeseries.Rmd |only nocturn-1.2.0/nocturn/inst/shiny/Rmd/Sleep_bubbles.Rmd |only nocturn-1.2.0/nocturn/inst/shiny/Rmd/Sleep_clock.Rmd |only nocturn-1.2.0/nocturn/inst/shiny/Rmd/Sleep_onset_and_wakeup.Rmd |only nocturn-1.2.0/nocturn/inst/shiny/Rmd/Sleep_spiral.Rmd |only nocturn-1.2.0/nocturn/inst/shiny/Rmd/Sleep_times_distributions.Rmd |only nocturn-1.2.0/nocturn/inst/shiny/Rmd/text_intro_tab.Rmd | 2 nocturn-1.2.0/nocturn/inst/shiny/common.R | 8 nocturn-1.2.0/nocturn/inst/shiny/download_handlers.R | 27 nocturn-1.2.0/nocturn/inst/shiny/global.R | 1 nocturn-1.2.0/nocturn/inst/shiny/modal_dialogs.R |only nocturn-1.2.0/nocturn/inst/shiny/modules/annotation.R | 37 - nocturn-1.2.0/nocturn/inst/shiny/modules/bedtimes_waketimes.R | 14 nocturn-1.2.0/nocturn/inst/shiny/modules/bland-altman.R |only nocturn-1.2.0/nocturn/inst/shiny/modules/comparison-data.R |only nocturn-1.2.0/nocturn/inst/shiny/modules/comparison.R |only nocturn-1.2.0/nocturn/inst/shiny/modules/comparison_tables.R |only nocturn-1.2.0/nocturn/inst/shiny/modules/compliance.R | 37 - nocturn-1.2.0/nocturn/inst/shiny/modules/export_data.R | 1 nocturn-1.2.0/nocturn/inst/shiny/modules/filtering.R | 277 ++++++--- nocturn-1.2.0/nocturn/inst/shiny/modules/hypnogram.R | 11 nocturn-1.2.0/nocturn/inst/shiny/modules/input-epochs.R | 46 - nocturn-1.2.0/nocturn/inst/shiny/modules/input-sessions.R | 49 - nocturn-1.2.0/nocturn/inst/shiny/modules/input.R | 59 -- nocturn-1.2.0/nocturn/inst/shiny/modules/sleep_bubbles.R | 10 nocturn-1.2.0/nocturn/inst/shiny/modules/sleep_clock.R | 11 nocturn-1.2.0/nocturn/inst/shiny/modules/sleep_distributions.R | 12 nocturn-1.2.0/nocturn/inst/shiny/modules/sleep_regularity.R | 45 - nocturn-1.2.0/nocturn/inst/shiny/modules/sleep_spiral.R | 11 nocturn-1.2.0/nocturn/inst/shiny/modules/timeseries.R | 11 nocturn-1.2.0/nocturn/inst/shiny/modules/timeseries_comparison.R |only nocturn-1.2.0/nocturn/inst/shiny/modules/timeseries_sessions.R | 9 nocturn-1.2.0/nocturn/inst/shiny/plot_helpers.R | 60 +- nocturn-1.2.0/nocturn/inst/shiny/server.R | 3 nocturn-1.2.0/nocturn/inst/shiny/ui.R | 54 + nocturn-1.2.0/nocturn/inst/shiny/www/styles.css | 167 +++-- nocturn-1.2.0/nocturn/man/apply_adapters.Rd |only nocturn-1.2.0/nocturn/man/apply_rules.Rd |only nocturn-1.2.0/nocturn/man/circ_time_diff.Rd |only nocturn-1.2.0/nocturn/man/clean_epochs.Rd | 1 nocturn-1.2.0/nocturn/man/clean_sessions.Rd | 1 nocturn-1.2.0/nocturn/man/colnames_to_canonical.Rd |only nocturn-1.2.0/nocturn/man/dot-epochs_parser.Rd |only nocturn-1.2.0/nocturn/man/dot-sessions_parsers.Rd |only nocturn-1.2.0/nocturn/man/filter_by_age_range.Rd | 1 nocturn-1.2.0/nocturn/man/filter_by_night_range.Rd | 1 nocturn-1.2.0/nocturn/man/filter_by_sex.Rd | 1 nocturn-1.2.0/nocturn/man/filter_epochs_from_sessions.Rd | 1 nocturn-1.2.0/nocturn/man/get_col.Rd | 1 nocturn-1.2.0/nocturn/man/get_sessions_summary.Rd | 2 nocturn-1.2.0/nocturn/man/keep_longest.Rd |only nocturn-1.2.0/nocturn/man/load_batch.Rd | 3 nocturn-1.2.0/nocturn/man/load_epochs.Rd | 6 nocturn-1.2.0/nocturn/man/plot_bland_altman.Rd |only nocturn-1.2.0/nocturn/man/plot_sleep_bubbles.Rd | 1 nocturn-1.2.0/nocturn/man/plot_sleep_clock.Rd | 1 nocturn-1.2.0/nocturn/man/plot_timeseries_comparison.Rd |only nocturn-1.2.0/nocturn/man/plot_timeseries_sessions.Rd | 3 nocturn-1.2.0/nocturn/man/remove_sessions_no_sleep.Rd | 1 nocturn-1.2.0/nocturn/man/select_devices.Rd | 1 nocturn-1.2.0/nocturn/man/select_subjects.Rd | 1 nocturn-1.2.0/nocturn/man/set_colnames.Rd | 4 nocturn-1.2.0/nocturn/man/set_min_sleep_period.Rd | 1 nocturn-1.2.0/nocturn/man/set_min_time_in_bed.Rd | 1 nocturn-1.2.0/nocturn/man/set_session_sleep_onset_range.Rd | 1 nocturn-1.2.0/nocturn/man/set_session_start_time_range.Rd | 1 nocturn-1.2.0/nocturn/man/standardise_types.Rd |only nocturn-1.2.0/nocturn/man/time_diff.Rd | 2 nocturn-1.2.0/nocturn/tests/testthat/helper-data.R |only nocturn-1.2.0/nocturn/tests/testthat/test-bedtimes_waketimes.R | 2 nocturn-1.2.0/nocturn/tests/testthat/test-bland_altman.R |only nocturn-1.2.0/nocturn/tests/testthat/test-colnames_accessors.R |only nocturn-1.2.0/nocturn/tests/testthat/test-compliance.R | 10 nocturn-1.2.0/nocturn/tests/testthat/test-data_checks.R | 50 - nocturn-1.2.0/nocturn/tests/testthat/test-data_cleaning.R | 112 +++ nocturn-1.2.0/nocturn/tests/testthat/test-data_tables.R | 1 nocturn-1.2.0/nocturn/tests/testthat/test-filtering.R | 2 nocturn-1.2.0/nocturn/tests/testthat/test-module-bedtimes_waketimes.R | 15 nocturn-1.2.0/nocturn/tests/testthat/test-module-bland_altman.R |only nocturn-1.2.0/nocturn/tests/testthat/test-module-comparison_data.R |only nocturn-1.2.0/nocturn/tests/testthat/test-module-comparison_tables.R |only nocturn-1.2.0/nocturn/tests/testthat/test-module-compliance.R | 2 nocturn-1.2.0/nocturn/tests/testthat/test-module-filtering.R | 26 nocturn-1.2.0/nocturn/tests/testthat/test-module-hypnogram.R | 10 nocturn-1.2.0/nocturn/tests/testthat/test-module-input_epochs.R | 4 nocturn-1.2.0/nocturn/tests/testthat/test-module-input_sessions.R | 3 nocturn-1.2.0/nocturn/tests/testthat/test-module-sleep_bubbles.R | 13 nocturn-1.2.0/nocturn/tests/testthat/test-module-sleep_clock.R | 13 nocturn-1.2.0/nocturn/tests/testthat/test-module-sleep_distributions.R | 13 nocturn-1.2.0/nocturn/tests/testthat/test-module-sleep_regularity.R | 51 + nocturn-1.2.0/nocturn/tests/testthat/test-module-sleep_spiral.R | 13 nocturn-1.2.0/nocturn/tests/testthat/test-module-summary.R | 8 nocturn-1.2.0/nocturn/tests/testthat/test-module-timeseries.R | 13 nocturn-1.2.0/nocturn/tests/testthat/test-module-timeseries_comparison.R |only nocturn-1.2.0/nocturn/tests/testthat/test-module-timeseries_sessions.R | 13 nocturn-1.2.0/nocturn/tests/testthat/test-sleep_metrics.R | 22 133 files changed, 1385 insertions(+), 1247 deletions(-)
Title: Adaptive Trial Designs for Survival and Binary Endpoints
Description: Implements Goldilocks adaptive trial designs for time-to-event and
fixed-time binary endpoints. Outcomes are generated with a piecewise
exponential model, with conjugate Gamma priors used for predictive
imputation. Final analyses may use log-rank or Cox tests, Bayesian
piecewise-exponential inference, frequentist risk differences, or Bayesian
beta-binomial inference. The method closely follows Broglio and colleagues
<doi:10.1080/10543406.2014.888569> and supports simulation of design
operating characteristics.
Author: Graeme L. Hickey [aut, cre] ,
Ying Wan [aut],
Thevaa Chandereng [aut] ,
Becton, Dickinson and Company [cph],
Tim Kacprowski [ctb]
Maintainer: Graeme L. Hickey <graemeleehickey@gmail.com>
Diff between goldilocks versions 0.5.0 dated 2026-06-10 and 0.6.0 dated 2026-07-29
goldilocks-0.5.0/goldilocks/R/logrank_test.R |only goldilocks-0.5.0/goldilocks/inst/doc/broglio.R |only goldilocks-0.5.0/goldilocks/inst/doc/broglio.Rmd |only goldilocks-0.5.0/goldilocks/inst/doc/broglio.html |only goldilocks-0.5.0/goldilocks/vignettes/bayes-piecewise_cache |only goldilocks-0.5.0/goldilocks/vignettes/broglio.Rmd |only goldilocks-0.5.0/goldilocks/vignettes/single-arm_cache |only goldilocks-0.6.0/goldilocks/DESCRIPTION | 24 goldilocks-0.6.0/goldilocks/MD5 | 165 + goldilocks-0.6.0/goldilocks/NAMESPACE | 23 goldilocks-0.6.0/goldilocks/NEWS.md | 149 + goldilocks-0.6.0/goldilocks/R/RcppExports.R | 3 goldilocks-0.6.0/goldilocks/R/analyse_data.R | 598 ++++++ goldilocks-0.6.0/goldilocks/R/enrollment.R | 198 +- goldilocks-0.6.0/goldilocks/R/goldilocks.R | 34 goldilocks-0.6.0/goldilocks/R/haz_to_prop.R | 82 goldilocks-0.6.0/goldilocks/R/impute_data.R | 178 +- goldilocks-0.6.0/goldilocks/R/plot_enrollment.R |only goldilocks-0.6.0/goldilocks/R/plot_sim_decisions.R |only goldilocks-0.6.0/goldilocks/R/plot_sim_ocs.R |only goldilocks-0.6.0/goldilocks/R/posterior.R | 417 +++- goldilocks-0.6.0/goldilocks/R/prop_to_haz.R | 43 goldilocks-0.6.0/goldilocks/R/pwe.R | 235 +- goldilocks-0.6.0/goldilocks/R/randomization.R | 85 goldilocks-0.6.0/goldilocks/R/sim_comp_data.R | 200 +- goldilocks-0.6.0/goldilocks/R/sim_trials.R | 379 +++- goldilocks-0.6.0/goldilocks/R/summarise_sims.R | 36 goldilocks-0.6.0/goldilocks/R/survival_adapt.R | 860 ++++++---- goldilocks-0.6.0/goldilocks/R/test_final.R | 308 ++- goldilocks-0.6.0/goldilocks/R/test_stop_success.R | 187 +- goldilocks-0.6.0/goldilocks/R/trial_trace.R |only goldilocks-0.6.0/goldilocks/R/validation.R |only goldilocks-0.6.0/goldilocks/README.md | 67 goldilocks-0.6.0/goldilocks/build/vignette.rds |binary goldilocks-0.6.0/goldilocks/inst/doc/advent.R |only goldilocks-0.6.0/goldilocks/inst/doc/advent.Rmd |only goldilocks-0.6.0/goldilocks/inst/doc/advent.html |only goldilocks-0.6.0/goldilocks/inst/doc/architecture.R | 17 goldilocks-0.6.0/goldilocks/inst/doc/architecture.Rmd | 78 goldilocks-0.6.0/goldilocks/inst/doc/architecture.html | 74 goldilocks-0.6.0/goldilocks/inst/doc/bayes-piecewise.R | 43 goldilocks-0.6.0/goldilocks/inst/doc/bayes-piecewise.Rmd | 105 - goldilocks-0.6.0/goldilocks/inst/doc/bayes-piecewise.html | 353 ++-- goldilocks-0.6.0/goldilocks/inst/doc/bayesian-binary.R |only goldilocks-0.6.0/goldilocks/inst/doc/bayesian-binary.Rmd |only goldilocks-0.6.0/goldilocks/inst/doc/bayesian-binary.html |only goldilocks-0.6.0/goldilocks/inst/doc/decision-traces.R |only goldilocks-0.6.0/goldilocks/inst/doc/decision-traces.Rmd |only goldilocks-0.6.0/goldilocks/inst/doc/decision-traces.html |only goldilocks-0.6.0/goldilocks/inst/doc/single-arm.R | 55 goldilocks-0.6.0/goldilocks/inst/doc/single-arm.Rmd | 98 - goldilocks-0.6.0/goldilocks/inst/doc/single-arm.html | 206 +- goldilocks-0.6.0/goldilocks/inst/doc/technical-methods.R |only goldilocks-0.6.0/goldilocks/inst/doc/technical-methods.Rmd |only goldilocks-0.6.0/goldilocks/inst/doc/technical-methods.html |only goldilocks-0.6.0/goldilocks/inst/doc/two-arm.R |only goldilocks-0.6.0/goldilocks/inst/doc/two-arm.Rmd |only goldilocks-0.6.0/goldilocks/inst/doc/two-arm.html |only goldilocks-0.6.0/goldilocks/man/enrollment.Rd | 133 + goldilocks-0.6.0/goldilocks/man/goldilocks-package.Rd | 4 goldilocks-0.6.0/goldilocks/man/goldilocks.Rd | 22 goldilocks-0.6.0/goldilocks/man/plot_enrollment.Rd |only goldilocks-0.6.0/goldilocks/man/plot_sim_decisions.Rd |only goldilocks-0.6.0/goldilocks/man/plot_sim_ocs.Rd |only goldilocks-0.6.0/goldilocks/man/plot_sim_stopping.Rd |only goldilocks-0.6.0/goldilocks/man/plot_trial_trace.Rd |only goldilocks-0.6.0/goldilocks/man/ppwe.Rd | 20 goldilocks-0.6.0/goldilocks/man/print.goldilocks_trial.Rd |only goldilocks-0.6.0/goldilocks/man/prop_to_haz.Rd | 22 goldilocks-0.6.0/goldilocks/man/pwe_impute.Rd | 48 goldilocks-0.6.0/goldilocks/man/pwe_sim.Rd | 28 goldilocks-0.6.0/goldilocks/man/randomization.Rd | 22 goldilocks-0.6.0/goldilocks/man/sim_comp_data.Rd | 89 - goldilocks-0.6.0/goldilocks/man/sim_trials.Rd | 252 ++ goldilocks-0.6.0/goldilocks/man/summarise_sims.Rd | 8 goldilocks-0.6.0/goldilocks/man/summarise_trial_trace.Rd |only goldilocks-0.6.0/goldilocks/man/survival_adapt.Rd | 400 +++- goldilocks-0.6.0/goldilocks/tests/testthat/test-analyse_data.R | 625 ++++++- goldilocks-0.6.0/goldilocks/tests/testthat/test-enrollment.R | 130 + goldilocks-0.6.0/goldilocks/tests/testthat/test-haz_to_prop.R |only goldilocks-0.6.0/goldilocks/tests/testthat/test-impute_data.R |only goldilocks-0.6.0/goldilocks/tests/testthat/test-plot-enrollment.R |only goldilocks-0.6.0/goldilocks/tests/testthat/test-plot_sim_decisions.R |only goldilocks-0.6.0/goldilocks/tests/testthat/test-plot_sim_ocs.R |only goldilocks-0.6.0/goldilocks/tests/testthat/test-posterior.R | 435 ++++- goldilocks-0.6.0/goldilocks/tests/testthat/test-prop_to_haz.R | 49 goldilocks-0.6.0/goldilocks/tests/testthat/test-pwe.R | 239 ++ goldilocks-0.6.0/goldilocks/tests/testthat/test-randomization.R | 37 goldilocks-0.6.0/goldilocks/tests/testthat/test-sim_comp_data.R | 122 + goldilocks-0.6.0/goldilocks/tests/testthat/test-sim_trials.R | 368 ++++ goldilocks-0.6.0/goldilocks/tests/testthat/test-summarise_sims.R | 16 goldilocks-0.6.0/goldilocks/tests/testthat/test-survival_adapt.R | 640 ++++++- goldilocks-0.6.0/goldilocks/tests/testthat/test-test_final.R |only goldilocks-0.6.0/goldilocks/tests/testthat/test-trial_trace.R |only goldilocks-0.6.0/goldilocks/vignettes/advent.Rmd |only goldilocks-0.6.0/goldilocks/vignettes/architecture.Rmd | 78 goldilocks-0.6.0/goldilocks/vignettes/bayes-piecewise.Rmd | 105 - goldilocks-0.6.0/goldilocks/vignettes/bayesian-binary.Rmd |only goldilocks-0.6.0/goldilocks/vignettes/broglio.html |only goldilocks-0.6.0/goldilocks/vignettes/decision-traces.Rmd |only goldilocks-0.6.0/goldilocks/vignettes/single-arm.Rmd | 98 - goldilocks-0.6.0/goldilocks/vignettes/technical-methods.Rmd |only goldilocks-0.6.0/goldilocks/vignettes/two-arm.Rmd |only goldilocks-0.6.0/goldilocks/vignettes/vignette-sims.rda |binary 104 files changed, 6802 insertions(+), 2488 deletions(-)
More information about AlphaPowerHazard at CRAN
Permanent link
Title: Super Learner for Survival Prediction from Censored Data
Description: Several functions and S3 methods to construct a super learner in the presence of censored times-to-event and to evaluate its prognostic capacities.
Author: Yohann Foucher [aut, cre] ,
Camille Sabathe [aut]
Maintainer: Yohann Foucher <yohann.foucher@univ-poitiers.fr>
Diff between survivalSL versions 1.0 dated 2025-12-16 and 1.1 dated 2026-07-29
DESCRIPTION | 8 MD5 | 48 +-- NAMESPACE | 20 - R/LIB_COXen.R | 11 R/LIB_COXlasso.R | 16 - R/LIB_COXridge.R | 10 R/LIB_PHgompertz.R | 2 R/LIB_PLANN.R | 2 R/metrics.R | 749 ++++++++++++++++++++++++++--------------------- R/predict.libsl.R | 39 -- R/print.summary.libsl.R |only R/print.summary.sltime.R |only R/summary.libsl.R | 72 ++-- R/summary.sltime.R | 71 ++-- R/survivalSL.R | 217 +++++++++---- R/tuneCOXen.R | 82 ++++- R/tuneCOXlasso.R | 87 ++++- R/tuneCOXridge.R | 100 +++++- R/tunePHspline.R | 122 +++++-- R/tunePLANN.R | 183 +++++++---- README.md | 17 - man/summary.libsl.Rd | 6 man/summary.sltime.Rd | 8 man/survivalSL.Rd | 8 man/tunePHspline.Rd | 8 man/tunePLANN.Rd | 6 26 files changed, 1192 insertions(+), 700 deletions(-)
Title: Bayesian Deep Gaussian Processes using MCMC
Description: Performs Bayesian posterior inference for deep Gaussian
processes following Sauer, Gramacy, and Higdon (2023, <doi:10.48550/arXiv.2012.08015>).
See Sauer (2023, <http://hdl.handle.net/10919/114845>) for comprehensive
methodological details and <https://bitbucket.org/gramacylab/deepgp-ex/> for
a variety of coding examples. Models are trained through MCMC including
elliptical slice sampling of latent Gaussian layers and Metropolis-Hastings
sampling of kernel hyperparameters. Gradient-enhancement and gradient
predictions are offered following Booth (2026, <doi:10.48550/arXiv.2512.18066>).
Vecchia approximation for faster
computation is implemented following Sauer, Cooper, and Gramacy
(2023, <doi:10.48550/arXiv.2204.02904>). Optional monotonic warpings are
implemented following Barnett et al. (2025, <doi:10.48550/arXiv.2408.01540>).
Downstream tasks include sequential design
through active learning Cohn/integrated mean squared error (ALC/IMSE; Sauer,
G [...truncated...]
Author: Annie S. Booth [aut, cre]
Maintainer: Annie S. Booth <annie_booth@vt.edu>
Diff between deepgp versions 1.2.1 dated 2026-02-09 and 1.2.2 dated 2026-07-29
DESCRIPTION | 12 +- MD5 | 54 ++++++------ R/RcppExports.R | 8 + R/checks.R | 14 +-- R/continue.R | 7 - R/deepgp-package.R | 5 - R/fit.R | 28 +++--- R/gibbs.R | 4 R/gibbs_vecchia.R | 2 R/krig.R | 84 ++++++++++++++----- R/mcmc.R | 23 +++-- R/plot.R | 18 ++-- R/predict.R | 36 ++++---- R/predict_vecchia.R | 23 +++-- R/sample.R | 12 +- R/trim.R | 10 +- R/vecchia.R | 15 ++- README.md | 14 ++- build/vignette.rds |binary inst/doc/deepgp.Rmd | 6 - inst/doc/deepgp.html | 146 +++++++++++++++++---------------- man/deepgp-package.Rd | 5 - src/RcppExports.cpp | 44 ++++++++++ src/cov.cpp | 204 +++++++++++++++++++++++++++++++++++++---------- src/cov.h | 7 + src/vecchia.cpp | 28 +++++- vignettes/deepgp.Rmd | 6 - vignettes/references.bib | 6 - 28 files changed, 554 insertions(+), 267 deletions(-)
Title: Bioequivalence Study Data Analysis
Description: Analyze bioequivalence study data with industrial strength. The statistical core is delegated to the 'sasLM' package, which reproduces 'SAS' PROC GLM output; this covers the analysis of variance, the least square means, and the confidence interval of a 2x2 crossover study. Sample size could be determined for various crossover designs, such as 2x2 design, 2x4 design, 4x4 design, Balaam design, Two-sequence dual design, and William design.
Reference: Chow SC, Liu JP. Design and Analysis of Bioavailability and Bioequivalence Studies. 3rd ed. (2009, ISBN:978-1-58488-668-6).
Author: Kyun-Seop Bae [aut, cre]
Maintainer: Kyun-Seop Bae <k@acr.kr>
This is a re-admission after prior archival of version 0.2.4 dated 2023-01-06
Diff between BE versions 0.2.4 dated 2023-01-06 and 0.3.0 dated 2026-07-29
BE-0.2.4/BE/R/sysdata.rda |only BE-0.3.0/BE/DESCRIPTION | 18 ++-- BE-0.3.0/BE/MD5 | 54 ++++++------- BE-0.3.0/BE/NAMESPACE | 34 ++++++-- BE-0.3.0/BE/R/BasicUtil.R | 20 ++-- BE-0.3.0/BE/R/be2x2.R | 6 - BE-0.3.0/BE/R/ci2mse.R | 1 BE-0.3.0/BE/R/hodges.R | 8 - BE-0.3.0/BE/R/plot2x2a.R | 2 BE-0.3.0/BE/R/powcv.R | 2 BE-0.3.0/BE/R/powmse.R | 2 BE-0.3.0/BE/R/scaledBound.R | 2 BE-0.3.0/BE/R/sscv.R | 2 BE-0.3.0/BE/R/ssscv.R | 2 BE-0.3.0/BE/R/test2x2.R | 163 +++++++++++++++------------------------- BE-0.3.0/BE/data |only BE-0.3.0/BE/inst/NEWS.Rd | 23 +++++ BE-0.3.0/BE/man/BE-package.Rd | 4 BE-0.3.0/BE/man/NCAResult4BE.Rd | 4 BE-0.3.0/BE/man/be2x2.Rd | 4 BE-0.3.0/BE/man/ci2mse.Rd | 2 BE-0.3.0/BE/man/cv2mse.Rd | 2 BE-0.3.0/BE/man/hodges.Rd | 2 BE-0.3.0/BE/man/pow2x2ci.Rd | 2 BE-0.3.0/BE/man/pow2x2mse.Rd | 4 BE-0.3.0/BE/man/powmse.Rd | 2 BE-0.3.0/BE/man/scaledBound.Rd | 4 BE-0.3.0/BE/man/ss2x2ci.Rd | 4 BE-0.3.0/BE/man/test2x2.Rd | 9 +- 29 files changed, 198 insertions(+), 184 deletions(-)
Title: Interactive Processing and Segmentation of Forest TLS
Point-Cloud Data
Description: Tools for the processing, segmentation, and analysis of terrestrial laser
scanning (TLS and MLS) forest point-cloud data. The package provides fast
voxel-based processing, classification of point clouds into forest
floor, understory, canopy, and woody components, and algorithms for
single-tree analysis and structural characterization. Methods are designed
to handle large and dense point-cloud datasets efficiently, supporting
applications in forest structure assessment, connectivity analysis, and
fire-risk evaluation. Input data are provided as '.xyz', '.txt', '.las', or '.laz' point-cloud files.
The circle-fitting routines used for diameter estimation are adapted, in
base R, from the 'conicfit' package (GPL-3) by Jose Gama, based on the
original algorithms and code by Nikolai Chernov.
For methodological details, see Ferrara and Arrizza (2025)
<https://hdl.handle.net/20.500.14243/533471> and Ferrara et al. (2018)
<doi:10.1016/j.agrformet.2018.04.008>.
Author: Roberto Ferrara [aut, cre] ,
Stefano Arrizza [ctb] ,
Nikolai Chernov [cph] ,
Jose Gama [ctb]
Maintainer: Roberto Ferrara <roberto.ferrara@cnr.it>
Diff between PiC versions 3.3.1 dated 2026-06-29 and 3.3.3 dated 2026-07-29
PiC-3.3.1/PiC/R/Forest_seg_v3_3_9.r |only PiC-3.3.3/PiC/DESCRIPTION | 37 +++++++-- PiC-3.3.3/PiC/MD5 | 24 +++--- PiC-3.3.3/PiC/NAMESPACE | 2 PiC-3.3.3/PiC/NEWS.md | 23 ++++++ PiC-3.3.3/PiC/R/Forest_seg_v3_3_10.r |only PiC-3.3.3/PiC/R/SegOne_v4_1_4.R | 21 ++--- PiC-3.3.3/PiC/R/Voxels.R | 6 - PiC-3.3.3/PiC/R/globals.r | 1 PiC-3.3.3/PiC/R/shared_utils.R | 130 ++++++++++++++++++++++++++++++++++- PiC-3.3.3/PiC/inst/WORDLIST | 2 PiC-3.3.3/PiC/man/Forest_seg.Rd | 2 PiC-3.3.3/PiC/man/PiC-package.Rd | 4 - PiC-3.3.3/PiC/man/Voxels.Rd | 10 ++ 14 files changed, 217 insertions(+), 45 deletions(-)
Title: Probabilistic Decomposition of Archaeological Palimpsests
Description: Probabilistic framework for the analysis of archaeological
palimpsests based on the Stratigraphic Entanglement Field (SEF).
Integrates spatial proximity, stratigraphic depth, chronological
overlap, and cultural similarity to estimate latent depositional
phases via diagonal Gaussian mixture Expectation-Maximisation (EM).
Provides the Stratigraphic Entanglement Index (SEI), Excavation
Stratigraphic Energy (ESE), and Palimpsest Dissolution Index (PDI)
for quantifying depositional coherence, detecting intrusive finds,
and measuring palimpsest formation. Includes simulation, diagnostics,
phase-count selection, publication-quality plots, and Geographic
Information System (GIS) export via 'sf'. Methods are described in Cocca (2026)
<https://github.com/enzococca/palimpsestr>.
Author: Enzo Cocca [aut, cre]
Maintainer: Enzo Cocca <enzo.ccc@gmail.com>
Diff between palimpsestr versions 0.24.0 dated 2026-07-25 and 0.24.1 dated 2026-07-29
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 13 +++++++++++++ R/export_report.R | 18 +++++++++++++++++- inst/doc/introduction.html | 26 +++++++++++++------------- tests/testthat/test-export-report.R | 33 +++++++++++++++++++++++++++++++++ 6 files changed, 84 insertions(+), 22 deletions(-)
Title: Download and Process 'DataSUS' Files
Description: Downloads and processes health microdata from Brazilian Unified
Health System ('DataSUS') information systems. It handles the compressed
'DBC' format internally and provides functions to organize variables and
add labels to categorical fields from mortality, live births, hospital
admissions, outpatient care, health facilities, and notifiable diseases
data. For details, see Saldanha et al. (2019)
<doi:10.1590/0102-311x00032419>.
Author: Raphael Saldanha [aut, cre] ,
Sidney da Silva Pereira Bissoli [ctb, cph] ,
Mark Adler [ctb, cph]
Maintainer: Raphael Saldanha <raphael.saldanha@fiocruz.br>
This is a re-admission after prior archival of version 2.3.1 dated 2024-06-18
Diff between microdatasus versions 2.3.1 dated 2024-06-18 and 3.0.0 dated 2026-07-29
microdatasus-2.3.1/microdatasus/man/microdatasus.Rd |only microdatasus-3.0.0/microdatasus/DESCRIPTION | 51 microdatasus-3.0.0/microdatasus/MD5 | 88 microdatasus-3.0.0/microdatasus/NAMESPACE | 6 microdatasus-3.0.0/microdatasus/NEWS.md | 115 microdatasus-3.0.0/microdatasus/R/datasus_download_helpers.R |only microdatasus-3.0.0/microdatasus/R/dbc_functions.R |only microdatasus-3.0.0/microdatasus/R/fetch_cadger.R |only microdatasus-3.0.0/microdatasus/R/fetch_datasus.R | 1530 ---- microdatasus-3.0.0/microdatasus/R/fetch_sigtab.R | 83 microdatasus-3.0.0/microdatasus/R/microdatasus.R | 19 microdatasus-3.0.0/microdatasus/R/process_cnes.R | 1167 ++- microdatasus-3.0.0/microdatasus/R/process_sia.R | 1556 ++-- microdatasus-3.0.0/microdatasus/R/process_sih.R | 3159 +++++----- microdatasus-3.0.0/microdatasus/R/process_sim.R | 246 microdatasus-3.0.0/microdatasus/R/process_sinan_chagas.R |only microdatasus-3.0.0/microdatasus/R/process_sinan_chikungunya.R | 1834 +++-- microdatasus-3.0.0/microdatasus/R/process_sinan_dengue.R | 1748 +++-- microdatasus-3.0.0/microdatasus/R/process_sinan_leishmaniose_tegumentar.R |only microdatasus-3.0.0/microdatasus/R/process_sinan_leishmaniose_visceral.R |only microdatasus-3.0.0/microdatasus/R/process_sinan_malaria.R | 645 +- microdatasus-3.0.0/microdatasus/R/process_sinan_zika.R | 558 + microdatasus-3.0.0/microdatasus/R/process_sinasc.R | 550 - microdatasus-3.0.0/microdatasus/R/sinan_chagas_sample.R |only microdatasus-3.0.0/microdatasus/R/sinan_leishmaniose_tegumentar_sample.R |only microdatasus-3.0.0/microdatasus/R/sinan_leishmaniose_visceral_sample.R |only microdatasus-3.0.0/microdatasus/R/zzz.R |only microdatasus-3.0.0/microdatasus/data/sinan_chagas_sample.rda |only microdatasus-3.0.0/microdatasus/data/sinan_leishmaniose_tegumentar_sample.rda |only microdatasus-3.0.0/microdatasus/data/sinan_leishmaniose_visceral_sample.rda |only microdatasus-3.0.0/microdatasus/data/tabNaturalidade.rda |binary microdatasus-3.0.0/microdatasus/inst/COPYRIGHTS |only microdatasus-3.0.0/microdatasus/man/fetch_cadger.Rd |only microdatasus-3.0.0/microdatasus/man/fetch_datasus.Rd | 155 microdatasus-3.0.0/microdatasus/man/fetch_sigtab.Rd | 24 microdatasus-3.0.0/microdatasus/man/microdatasus-package.Rd |only microdatasus-3.0.0/microdatasus/man/process_cnes.Rd | 36 microdatasus-3.0.0/microdatasus/man/process_sia.Rd | 50 microdatasus-3.0.0/microdatasus/man/process_sih.Rd | 32 microdatasus-3.0.0/microdatasus/man/process_sim.Rd | 26 microdatasus-3.0.0/microdatasus/man/process_sinan_chagas.Rd |only microdatasus-3.0.0/microdatasus/man/process_sinan_chikungunya.Rd | 27 microdatasus-3.0.0/microdatasus/man/process_sinan_dengue.Rd | 26 microdatasus-3.0.0/microdatasus/man/process_sinan_leishmaniose_tegumentar.Rd |only microdatasus-3.0.0/microdatasus/man/process_sinan_leishmaniose_visceral.Rd |only microdatasus-3.0.0/microdatasus/man/process_sinan_malaria.Rd | 24 microdatasus-3.0.0/microdatasus/man/process_sinan_zika.Rd | 25 microdatasus-3.0.0/microdatasus/man/process_sinasc.Rd | 27 microdatasus-3.0.0/microdatasus/man/read_dbc.Rd |only microdatasus-3.0.0/microdatasus/man/sinan_chagas_sample.Rd |only microdatasus-3.0.0/microdatasus/man/sinan_leishmaniose_tegumentar_sample.Rd |only microdatasus-3.0.0/microdatasus/man/sinan_leishmaniose_visceral_sample.Rd |only microdatasus-3.0.0/microdatasus/src |only microdatasus-3.0.0/microdatasus/tests/testthat/test-fetch_auxiliary_tables.R |only microdatasus-3.0.0/microdatasus/tests/testthat/test-fetch_datasus.R | 1316 +++- microdatasus-3.0.0/microdatasus/tests/testthat/test-process_functions.R | 75 microdatasus-3.0.0/microdatasus/tests/testthat/test-read_dbc.R |only 57 files changed, 8529 insertions(+), 6669 deletions(-)
Title: Clean and Harmonise 'Malawi Integrated Household Survey' Data
Description: An offline suite of tools to clean, aggregate, and harmonise data
from the 'Malawi Integrated Household Survey' ('IHS'), covering rounds two
through six (2004 to 2025). Provides crop-specific unit conversions,
stratified winsorization, consumer-price deflation, and automatic
cross-round harmonisation for complex survey designs.
Author: Vitumbiko Kayuni [aut, cre]
Maintainer: Vitumbiko Kayuni <vitumbikokayuni@gmail.com>
Diff between ihsMW versions 1.0.0 dated 2026-07-08 and 1.1.1 dated 2026-07-29
DESCRIPTION | 15 MD5 | 105 NEWS.md | 126 R/ihs_aggregate.R | 36 R/ihs_clean.R | 80 R/ihs_convert.R | 355 - R/ihs_crosswalk_check.R | 63 R/ihs_deflate.R | 89 R/ihs_harmonise.R | 66 R/ihs_merge.R | 44 R/ihs_panel_ids.R | 36 R/ihs_report.R | 34 R/ihs_search.R | 34 R/ihs_svydesign.R | 33 R/utils.R | 12 R/zzz.R | 3 README.md | 109 build/vignette.rds |binary inst/doc/getting-started.R | 64 inst/doc/getting-started.Rmd | 59 inst/doc/getting-started.html | 102 inst/doc/harmonisation.R | 12 inst/doc/harmonisation.Rmd | 29 inst/doc/harmonisation.html | 79 inst/doc/ihsMW-user-guide.R |only inst/doc/ihsMW-user-guide.Rmd |only inst/doc/ihsMW-user-guide.html |only inst/doc/survey-weights.R | 3 inst/doc/survey-weights.Rmd | 3 inst/doc/survey-weights.html | 5 inst/extdata/ihs_crosswalk.csv |12405 ++++++++++++++++++------------------ inst/extdata/mw_cpi_annual.csv | 45 man/figures |only man/ihs_aggregate.Rd | 37 man/ihs_clean.Rd | 27 man/ihs_convert_units.Rd | 62 man/ihs_crosswalk_check.Rd | 27 man/ihs_deflate.Rd | 44 man/ihs_harmonise.Rd | 38 man/ihs_merge.Rd | 26 man/ihs_panel_ids.Rd | 29 man/ihs_report.Rd | 33 man/ihs_search.Rd | 11 man/ihs_standardize_missing.Rd | 26 man/ihs_svydesign.Rd | 35 man/ihs_winsorize.Rd | 28 tests/testthat/test-ihs_convert.R |only tests/testthat/test-ihs_deflate.R | 56 tests/testthat/test-ihs_merge.R | 29 tests/testthat/test-ihs_panel_ids.R | 14 tests/testthat/test-utils.R | 15 vignettes/getting-started.Rmd | 59 vignettes/harmonisation.Rmd | 29 vignettes/ihsMW-user-guide.Rmd |only vignettes/survey-weights.Rmd | 3 55 files changed, 8263 insertions(+), 6411 deletions(-)
Title: Procedures for Gaussian and Non Gaussian Geostatistical (Large)
Data Analysis
Description: Functions for Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data analysis are provided for a) (fast) simulation of random fields, b) inference for random fields using standard likelihood and a likelihood approximation method called weighted composite likelihood based on pairs and b) prediction using (local) best linear unbiased prediction. Weighted composite likelihood can be very efficient for estimating massive datasets. Both regression and spatial (temporal) dependence analysis can be jointly performed. Flexible covariance models for spatial and spatial-temporal data on Euclidean domains and spheres are provided. There are also many useful functions for plotting and performing diagnostic analysis. Different non Gaussian random fields can be considered in the analysis. Among them, random fields with marginal distributions such as Skew-Gaussian, Student-t, Tukey-h, Sin-Arcsin, Two-piece, Weibull, Gamma, Log-Gaussian, Binomial, Negative Binomial and Poisson. Se [...truncated...]
Author: Moreno Bevilacqua [aut, cre, cph],
Victor Morales-Onate [ctb],
Francisco Cuevas-Pacheco [ctb],
Christian Caamano-Carrillo [ctb]
Maintainer: Moreno Bevilacqua <moreno.bevilacqua89@gmail.com>
Diff between GeoModels versions 2.2.6 dated 2026-07-16 and 2.2.7 dated 2026-07-29
GeoModels-2.2.6/GeoModels/R/GeoFit.r |only GeoModels-2.2.6/GeoModels/man/GeoTest_supp.Rd |only GeoModels-2.2.7/GeoModels/DESCRIPTION | 8 GeoModels-2.2.7/GeoModels/MD5 | 50 GeoModels-2.2.7/GeoModels/NAMESPACE | 2 GeoModels-2.2.7/GeoModels/R/GeoCompositeLik2.R | 184 ++ GeoModels-2.2.7/GeoModels/R/GeoFit.R |only GeoModels-2.2.7/GeoModels/R/GeoFit2.R | 563 ++------ GeoModels-2.2.7/GeoModels/R/GeoIndCompositeLik2.R | 154 +- GeoModels-2.2.7/GeoModels/R/GeoSimcond.R | 971 +++++++++++---- GeoModels-2.2.7/GeoModels/R/GeoTest.r | 603 ++++++--- GeoModels-2.2.7/GeoModels/R/GeoTestIndependence.R |only GeoModels-2.2.7/GeoModels/R/GeoTestIsotropy.R | 683 +++++++--- GeoModels-2.2.7/GeoModels/R/GeoTestsupp_space.R | 762 ++++++++--- GeoModels-2.2.7/GeoModels/R/GeoVarest.R | 137 +- GeoModels-2.2.7/GeoModels/R/GeoVarestbootstrap.R | 39 GeoModels-2.2.7/GeoModels/R/Utility_cov.R | 4 GeoModels-2.2.7/GeoModels/man/GeoFit2.Rd | 97 + GeoModels-2.2.7/GeoModels/man/GeoTestIndependence.Rd |only GeoModels-2.2.7/GeoModels/man/GeoTestIsotropy.Rd | 239 ++- GeoModels-2.2.7/GeoModels/man/GeoTests.Rd | 484 +++---- GeoModels-2.2.7/GeoModels/man/GeoTestsupp_space.Rd |only GeoModels-2.2.7/GeoModels/man/GeoVarest.Rd | 7 GeoModels-2.2.7/GeoModels/src/2F1_v2.c | 353 ++--- GeoModels-2.2.7/GeoModels/src/CompositeLikelihood2.c | 280 +++- GeoModels-2.2.7/GeoModels/src/CompositeLikelihoodCond2.c | 33 GeoModels-2.2.7/GeoModels/src/Distributions.c | 506 ++++++- GeoModels-2.2.7/GeoModels/src/header.h | 9 GeoModels-2.2.7/GeoModels/src/skewgaussian_gibbs.c | 396 ++++-- 29 files changed, 4345 insertions(+), 2219 deletions(-)
Title: Sensitivity Analysis Using the Trimmed Means Estimator
Description: Sensitivity analysis using the trimmed means estimator.
Author: Audinga-Dea Hazewinkel [aut, cre] ,
Tom Palmer [aut] ,
Kate Tilling [aut] ,
Kaitlin Wade [aut] ,
Jack Bowden [aut]
Maintainer: Audinga-Dea Hazewinkel <dea.hazew@gmail.com>
Diff between tmsens versions 0.3.1 dated 2024-08-29 and 0.4.0 dated 2026-07-29
DESCRIPTION | 21 ++--- MD5 | 18 ++-- NEWS.md | 18 ++++ R/TM_bias.R | 99 ++++++------------------ R/tmF.R | 203 ++++++++++++++++++++++++++++---------------------- inst/CITATION | 4 man/summary.tm.Rd | 6 - man/tm.Rd | 9 +- man/tm_bias.Rd | 12 +- man/tmsens-package.Rd | 1 10 files changed, 201 insertions(+), 190 deletions(-)
Title: Tools for Joint Sentiment and Topic Analysis of Textual Data
Description: A framework that joins topic modeling and sentiment analysis of
textual data. The package implements a fast Gibbs sampling estimation of
Latent Dirichlet Allocation (Griffiths and Steyvers (2004)
<doi:10.1073/pnas.0307752101>) and Joint Sentiment/Topic Model (Lin, He,
Everson and Ruger (2012) <doi:10.1109/TKDE.2011.48>). It offers a variety of
helpers and visualizations to analyze the result of topic modeling. The
framework also allows enriching topic models with dates and externally
computed sentiment measures. A flexible aggregation scheme enables the
creation of time series of sentiment or topical proportions from the enriched
topic models. Moreover, a novel method jointly aggregates topic proportions
and sentiment measures to derive time series of topical sentiment.
Author: Olivier Delmarcelle [aut, cre] ,
Samuel Borms [ctb] ,
Chengua Lin [cph] ,
Yulan He [cph] ,
Jose Bernardo [cph] ,
David Robinson [cph] ),
Julia Silge [cph] , ORCID:
<https://orcid.org/0000-0002-3671-836X>)
Maintainer: Olivier Delmarcelle <delmarcelle.olivier@gmail.com>
Diff between sentopics versions 0.7.6 dated 2025-10-15 and 0.7.7 dated 2026-07-29
DESCRIPTION | 9 ++--- MD5 | 62 +++++++++++++++++++------------------- NEWS.md | 4 ++ R/conversions.R | 1 R/functions.R | 1 R/methods.R | 4 +- R/models.R | 16 ++++++--- R/timeSeries.R | 2 - R/utils.R | 16 +++++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/Basic_usage.R | 1 inst/doc/Basic_usage.Rmd | 2 - inst/doc/Basic_usage.html | 2 - inst/doc/Topical_time_series.R | 1 inst/doc/Topical_time_series.Rmd | 3 + inst/doc/Topical_time_series.html | 6 +-- man/JST.Rd | 3 + man/LDAvis.Rd | 1 man/chainsDistances.Rd | 1 man/melt.sentopicmodel.Rd | 1 man/plot.multiChains.Rd | 1 man/plot.sentopicmodel.Rd | 1 man/rJST.Rd | 3 + man/sentiment_series.Rd | 1 src/Makevars | 2 - src/Makevars.win | 2 - tests/testthat.R | 6 +-- tests/testthat/Rplots.pdf |binary tests/testthat/test-utils.R | 6 +++ vignettes/Basic_usage.Rmd | 2 - vignettes/Topical_time_series.Rmd | 3 + 32 files changed, 104 insertions(+), 59 deletions(-)
Title: Create Non-Confidential Multi-Resolution Grids
Description: The need for anonymization of individual survey responses often leads to many suppressed grid cells in a regular grid. Here we provide functionality for creating multi-resolution gridded data, respecting the confidentiality rules, such as a minimum number of units and dominance by one or more units for each grid cell. The functions also include the possibility for contextual suppression of data. For more details see Skoien et al. (2025) <doi:10.48550/arXiv.2410.17601>.
Author: Jon Olav Skoien [aut, cre],
Nicolas Lampach [aut]
Maintainer: Jon Olav Skoien <jon.skoien@gmail.com>
Diff between MRG versions 0.3.29 dated 2026-06-24 and 0.3.30 dated 2026-07-29
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/gridData2.R | 20 +++++++++----------- R/inspireID.R | 7 ++++--- 4 files changed, 19 insertions(+), 20 deletions(-)
Title: Graphics in the Context of Analyzing High-Throughput Data
Description: Additional options for making graphics in the context of analyzing high-throughput data are available here.
This includes automatic segmenting of the current device (eg window) to accommodate multiple new plots,
automatic checking for optimal location of legends in plots, small histograms to insert as legends,
histograms re-transforming axis labels to linear when plotting log2-transformed data,
a violin-plot <doi:10.1080/00031305.1998.10480559> function for a wide variety of input-formats,
principal components analysis (PCA) <doi:10.1080/14786440109462720> with bag-plots <doi:10.1080/00031305.1999.10474494>
to highlight and compare the center areas for groups of samples,
generic MA-plots (differential- versus average-value plots) <doi:10.1093/nar/30.4.e15>,
staggered count plots and generation of mouse-over interactive html pages.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrGraph versions 1.3.16 dated 2026-06-11 and 1.3.17 dated 2026-07-29
DESCRIPTION | 11 ++-- MD5 | 20 ++++----- R/VolcanoPlotW.R | 38 +++++++++-------- R/plotLinReg.R | 25 ++++++----- R/staggerdCountsPlot.R | 15 ++++-- R/vioplotW.R | 37 +++++++++------- build/vignette.rds |binary inst/doc/wrGraphVignette1.html | 91 +++++++++++++++++++++-------------------- man/plotLinReg.Rd | 2 man/staggerdCountsPlot.Rd | 5 +- man/vioplotW.Rd | 4 + 11 files changed, 136 insertions(+), 112 deletions(-)
Title: Randomization Inference for Randomized Experiments
Description: Randomization inference procedures for simple and complex randomized designs, including multi-armed trials, as described in Gerber and Green (2012, ISBN: 978-0393979954). Users formally describe their randomization procedure and test statistic. The randomization distribution of the test statistic under some null hypothesis is efficiently simulated.
Author: Alexander Coppock [aut, cre]
Maintainer: Alexander Coppock <acoppock@gmail.com>
Diff between ri2 versions 0.4.1 dated 2025-10-14 and 0.5.0 dated 2026-07-29
DESCRIPTION | 16 MD5 | 52 +- NAMESPACE | 21 NEWS.md | 22 R/conduct_ri.R | 316 +++++------- R/conduct_ri_ATE.R | 258 +++++----- R/conduct_ri_f.R | 241 ++++----- R/conduct_ri_test_function.R | 42 + R/potential_outcomes.R |only R/reexports.R | 43 + R/ri_ci.R |only build/vignette.rds |binary inst/doc/ri2_vignette.R | 284 ++++++++++- inst/doc/ri2_vignette.Rmd | 368 +++++++++++++-- inst/doc/ri2_vignette.html | 754 ++++++++++++++++++++++--------- man/conduct_ri.Rd | 46 - man/figures/README-ri-example-1.png |only man/reexports.Rd | 14 man/ri2-package.Rd | 14 man/ri_ci.Rd |only tests/testthat/test-blocked.R | 2 tests/testthat/test-fixes.R |only tests/testthat/test-potential-outcomes.R |only vignettes/ri2_vignette.Rmd | 368 +++++++++++++-- vignettes/ri2_vignette_cache |only vignettes/ri2_vignette_files |only 26 files changed, 2068 insertions(+), 793 deletions(-)
Title: Statistical Tools for Covariance Analysis
Description: Covariance is of universal prevalence across various disciplines within statistics.
We provide a rich collection of geometric and inferential tools for convenient analysis of
covariance structures, topics including distance measures, mean covariance estimator,
covariance hypothesis test for one-sample and two-sample cases, and covariance estimation.
For an introduction to covariance in multivariate statistical analysis,
see Schervish (1987) <doi:10.1214/ss/1177013111>.
Author: Kyoungjae Lee [aut],
Lizhen Lin [ctb],
Kisung You [aut, cre]
Maintainer: Kisung You <kisung.you@outlook.com>
Diff between CovTools versions 0.5.6 dated 2025-09-21 and 0.5.7 dated 2026-07-29
CovTools-0.5.6/CovTools/src/rcpp_expm.cpp |only CovTools-0.5.7/CovTools/DESCRIPTION | 12 - CovTools-0.5.7/CovTools/MD5 | 71 ++++----- CovTools-0.5.7/CovTools/NAMESPACE | 1 CovTools-0.5.7/CovTools/NEWS.md | 19 ++ CovTools-0.5.7/CovTools/R/BDiagTest1.mxPBF.R | 14 + CovTools-0.5.7/CovTools/R/CovDist.R | 17 +- CovTools-0.5.7/CovTools/R/CovEst.hardPD.R | 128 ++++++++++++----- CovTools-0.5.7/CovTools/R/CovMean.R | 16 +- CovTools-0.5.7/CovTools/R/CovTest1.2014Srivastava.R | 9 + CovTools-0.5.7/CovTools/R/DiagTest1.2011Cai.R | 19 +- CovTools-0.5.7/CovTools/R/DiagTest1.2015Lan.R | 11 - CovTools-0.5.7/CovTools/R/PreEst.2014An.R | 94 +++++++++--- CovTools-0.5.7/CovTools/R/PreEst.2014Banerjee.R | 103 +++++++++---- CovTools-0.5.7/CovTools/R/PreEst.2017Lee.R | 108 +++++++++++--- CovTools-0.5.7/CovTools/R/PreEst.glasso.R | 88 +++++++---- CovTools-0.5.7/CovTools/R/RcppExports.R | 4 CovTools-0.5.7/CovTools/R/auxiliary.R | 46 +++++- CovTools-0.5.7/CovTools/R/fns.covest.R | 58 +++++-- CovTools-0.5.7/CovTools/R/fns.dist.R | 81 ++++++---- CovTools-0.5.7/CovTools/R/fns.mean.R | 35 ++++ CovTools-0.5.7/CovTools/R/package-CovTools.R | 2 CovTools-0.5.7/CovTools/build/partial.rdb |binary CovTools-0.5.7/CovTools/man/BDiagTest1.mxPBF.Rd | 5 CovTools-0.5.7/CovTools/man/CovDist.Rd | 6 CovTools-0.5.7/CovTools/man/CovEst.hardPD.Rd | 11 + CovTools-0.5.7/CovTools/man/CovMean.Rd | 6 CovTools-0.5.7/CovTools/man/CovTest1.2014Srivastava.Rd | 3 CovTools-0.5.7/CovTools/man/DiagTest1.2011Cai.Rd | 2 CovTools-0.5.7/CovTools/man/DiagTest1.2015Lan.Rd | 2 CovTools-0.5.7/CovTools/man/PreEst.2014An.Rd | 5 CovTools-0.5.7/CovTools/man/PreEst.2014Banerjee.Rd | 2 CovTools-0.5.7/CovTools/man/PreEst.2017Lee.Rd | 9 - CovTools-0.5.7/CovTools/src/RcppExports.cpp | 13 - CovTools-0.5.7/CovTools/src/rcpp_preest.cpp | 20 ++ CovTools-0.5.7/CovTools/tests |only 36 files changed, 724 insertions(+), 296 deletions(-)
Title: Download Data from Brazil's Population Census
Description: Easy access to data from Brazil's population censuses. The package
provides a simple and efficient way to download and read the data
sets and the documentation of all the population censuses taken in
and after 1960 in the country. The package is built on top of the
'Arrow' platform <https://arrow.apache.org/docs/r/>, which allows
users to work with larger-than-memory census data using 'dplyr'
familiar functions. <https://arrow.apache.org/docs/r/articles/arrow.html#analyzing-arrow-data-with-dplyr>.
Author: Rafael H. M. Pereira [aut, cre] ,
Rogerio J. Barbosa [aut] ,
Diego Rabatone Oliveira [ctb],
Neal Richardson [ctb],
Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between censobr versions 0.5.0 dated 2025-07-06 and 0.6.0 dated 2026-07-29
DESCRIPTION | 13 LICENSE | 2 MD5 | 90 +++--- NEWS.md | 58 ++-- R/cache.R | 2 R/censobr.R | 2 R/data_dictionary.R | 54 ++- R/docs_interview_manual.R | 2 R/docs_questionnaire.R | 2 R/onLoad.R | 2 R/read_emigration.R | 2 R/read_families.R | 2 R/read_households.R | 2 R/read_mortality.R | 7 R/read_population.R | 2 R/read_tracts.R | 10 README.md | 38 +- build/vignette.rds |binary inst/doc/censobr.R | 206 +++++++------- inst/doc/censobr.Rmd | 8 inst/doc/censobr.html | 119 +------- inst/doc/census_tracts_data.R | 294 ++++++++++----------- inst/doc/census_tracts_data.Rmd | 16 - inst/doc/census_tracts_data.html | 473 +++------------------------------- inst/doc/documentation.html | 4 inst/doc/larger_than_memory.R | 92 +++--- inst/doc/larger_than_memory.html | 66 ---- man/censobr.Rd | 9 man/censobr_cache.Rd | 8 man/data_dictionary.Rd | 37 +- man/get_censobr_cache_dir.Rd | 8 man/interview_manual.Rd | 6 man/questionnaire.Rd | 2 man/read_emigration.Rd | 12 man/read_families.Rd | 12 man/read_households.Rd | 12 man/read_mortality.Rd | 17 - man/read_population.Rd | 12 man/read_tracts.Rd | 2 man/set_censobr_cache_dir.Rd | 8 tests/tests_rafa/aaaaaa.R |only tests/tests_rafa/s3_test.R |only tests/tests_rafa/test_rafa.R | 6 tests/testthat/test_read_tracts.R | 24 + tests/testthat/test_z_censobr_cache.R | 2 vignettes/censobr.Rmd | 8 vignettes/census_tracts_data.Rmd | 16 - 47 files changed, 643 insertions(+), 1126 deletions(-)
Title: Visualizing Categorical Data
Description: Visualization techniques, data sets, summary and inference
procedures aimed particularly at categorical data. Special
emphasis is given to highly extensible grid graphics. The
package was package was originally inspired by the book
"Visualizing Categorical Data" by Michael Friendly and is
now the main support package for a new book,
"Discrete Data Analysis with R" by Michael Friendly and
David Meyer (2015).
Author: David Meyer [aut, cre] ,
Achim Zeileis [aut] ,
Kurt Hornik [aut] ,
Florian Gerber [ctb],
Michael Friendly [aut]
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between vcd versions 1.4-13 dated 2024-09-16 and 1.4-14 dated 2026-07-29
DESCRIPTION | 14 ++++---- MD5 | 68 ++++++++++++++++++++-------------------- R/assoc.R | 2 + R/coindep_test.R | 2 - R/loddsratio.R | 10 ++--- R/shadings.R | 20 +++++------ build/partial.rdb |binary build/vignette.rds |binary data/Butterfly.rda |binary data/Employment.rda |binary data/Federalist.rda |binary data/HorseKicks.rda |binary data/Hospital.rda |binary data/Lifeboats.rda |binary data/MSPatients.rda |binary data/PreSex.rda |binary data/RepVict.rda |binary data/Rochdale.rda |binary data/Saxony.rda |binary data/Suicide.rda |binary data/UKSoccer.rda |binary data/WeldonDice.rda |binary data/WomenQueue.rda |binary inst/NEWS.Rd | 11 ++++++ inst/doc/residual-shadings.R | 2 - inst/doc/residual-shadings.Rnw | 8 ++-- inst/doc/residual-shadings.pdf |binary inst/doc/strucplot.R | 2 - inst/doc/strucplot.Rnw | 2 - inst/doc/strucplot.pdf |binary man/Bundesliga.Rd | 2 - man/Bundestag2005.Rd | 2 - vignettes/residual-shadings.Rnw | 8 ++-- vignettes/strucplot.Rnw | 2 - vignettes/vcd.bib | 31 ++++++++++-------- 35 files changed, 99 insertions(+), 87 deletions(-)
Title: Genome-Wide Nucleic Acid Melting Temperature Profiling and
Multi-Omics Integration
Description: Accurate calculation of nucleic acid melting temperature (Tm) is fundamental to many molecular biology applications, and this software scales Tm analysis from individual sequences to genome‑wide thermodynamic profiling. This package extends Tm analysis from simple sequence level computation to comprehensive genome-wide thermodynamic profiling. It takes multiple input formats including sequence strings, FASTA files, genomic coordinates. The implementation provides three Tm calculation methods: the Wallace rule (Thein & Wallace, 1986), empirical GC‑content formulas (Marmur, 1962; Schildkraut, 2010; Wetmur, 1991; Untergasser, 2012; von Ahsen, 2001), and nearest‑neighbor thermodynamics (Breslauer, 1986; Sugimoto, 1996; Allawi, 1998; SantaLucia, 2004; Freier, 1986; Xia, 1998; Chen, 2012; Bommarito, 2000; Turner, 2010; Sugimoto, 1995; Allawi, 1997; SantaLucia, 2005). Corrections are supported for salt ions (SantaLucia, 1996, 1998; Owczarzy, 2004, 2008) and for chemical conditions such as [...truncated...]
Author: Junhui Li [cre, aut] ,
Lihua Julie Zhu [aut]
Maintainer: Junhui Li <ljh.biostat@gmail.com>
Diff between TmCalculator versions 1.0.7 dated 2026-06-25 and 1.0.8 dated 2026-07-29
DESCRIPTION | 8 +-- MD5 | 10 ++-- inst/doc/genome_wide_tm_ecoli.R | 1 inst/doc/genome_wide_tm_ecoli.Rmd | 44 ++++++++++++++------ inst/doc/genome_wide_tm_ecoli.html | 79 ++++++++++++++++++++++--------------- vignettes/genome_wide_tm_ecoli.Rmd | 44 ++++++++++++++------ 6 files changed, 119 insertions(+), 67 deletions(-)
Title: Hazard Function Estimation in Survival Analysis
Description: Produces a smooth estimate of the hazard
function for censored data.
Author: S original by Kenneth Hess [aut],
R port by R. Gentleman [aut],
David Winsemius [cre, ctb],
Ken Beath [ctb]
Maintainer: David Winsemius <dwinsemius@comcast.net>
Diff between muhaz versions 1.2.6.4 dated 2021-04-21 and 1.2.6.5 dated 2026-07-29
DESCRIPTION | 30 ++++++++++++++++++++++++------ MD5 | 8 +++++--- NEWS.md |only R/all.R | 2 +- README.md |only man/muhaz.object.Rd | 7 +++++-- 6 files changed, 35 insertions(+), 12 deletions(-)
Title: Bayesian Nonparametric Sensitivity Analysis of Multiple Testing
Procedures for p Values
Description: Bayesian Nonparametric sensitivity analysis of multiple testing procedures for p values with arbitrary dependencies, based on the Dirichlet process prior distribution.
Author: George Karabatsos [aut, cre]
Maintainer: George Karabatsos <gkarabatsos1@gmail.com>
Diff between bnpMTP versions 1.0.0 dated 2025-09-24 and 1.0.1 dated 2026-07-29
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- R/bnpMTPfunction.R | 16 ++++++++++------ build |only man/bnpMTP.Rd | 7 +++++-- 5 files changed, 23 insertions(+), 15 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-12-18 0.5.2
2025-09-23 0.5.0
2022-07-05 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-07-17 0.1.5