Title: Price Index Aggregation
Description: Most price indexes are made with a two-step procedure, where
period-over-period elementary indexes are first calculated for a collection
of elementary aggregates at each point in time, and then aggregated according
to a price index aggregation structure. These indexes can then be chained
together to form a time series that gives the evolution of prices with
respect to a fixed base period. This package contains a collection of
functions that revolve around this work flow, making it easy to build
standard price indexes, and implement the methods described by
Balk (2008, <doi:10.1017/CBO9780511720758>), von der Lippe (2007,
<doi:10.3726/978-3-653-01120-3>), and the CPI manual (2020,
<doi:10.5089/9781484354841.069>) and PPI manual
(2004, <doi:10.5089/9781589063044.069>) for bilateral price indexes.
Author: Steve Martin [aut, cre, cph]
Maintainer: Steve Martin <marberts@protonmail.com>
Diff between piar versions 0.10.1 dated 2026-07-30 and 0.11.0 dated 2026-10-12
piar-0.10.1/piar/LICENSE |only piar-0.11.0/piar/DESCRIPTION | 21 piar-0.11.0/piar/MD5 | 323 ++++---- piar-0.11.0/piar/NAMESPACE | 35 piar-0.11.0/piar/NEWS.md | 26 piar-0.11.0/piar/R/aggregate.piar_index.R | 45 - piar-0.11.0/piar/R/aggregation_structure.R | 6 piar-0.11.0/piar/R/as_aggregation_structure.R | 2 piar-0.11.0/piar/R/as_index.R | 3 piar-0.11.0/piar/R/back_period.R | 9 piar-0.11.0/piar/R/chain.R | 4 piar-0.11.0/piar/R/coerce-aggregation_structure.R | 23 piar-0.11.0/piar/R/coerce-index.R | 25 piar-0.11.0/piar/R/combine_classifications.R | 2 piar-0.11.0/piar/R/contrib.R | 2 piar-0.11.0/piar/R/cut.piar_aggregation_structure.R | 2 piar-0.11.0/piar/R/elementary_index.R | 44 - piar-0.11.0/piar/R/emean.R | 11 piar-0.11.0/piar/R/expand_classification.R | 6 piar-0.11.0/piar/R/extract.piar_index.R | 54 + piar-0.11.0/piar/R/geks_index.R | 15 piar-0.11.0/piar/R/gmean.R | 26 piar-0.11.0/piar/R/head.piar_index.R | 10 piar-0.11.0/piar/R/impute_prices.R | 20 piar-0.11.0/piar/R/index-class.R | 18 piar-0.11.0/piar/R/is.na.piar_index.R | 2 piar-0.11.0/piar/R/lag.piar_index.R |only piar-0.11.0/piar/R/levels.piar_aggregation_structure.R | 2 piar-0.11.0/piar/R/levels.piar_index.R | 2 piar-0.11.0/piar/R/mean.piar_index.R | 13 piar-0.11.0/piar/R/merge.piar_index.R | 2 piar-0.11.0/piar/R/outliers.R | 32 piar-0.11.0/piar/R/price_relative.R | 8 piar-0.11.0/piar/R/splice_index.R | 8 piar-0.11.0/piar/R/split.piar_index.R | 4 piar-0.11.0/piar/R/split_classification.R | 10 piar-0.11.0/piar/R/stack.piar_index.R | 2 piar-0.11.0/piar/R/time.piar_index.R | 2 piar-0.11.0/piar/R/transmute_weights.R | 46 - piar-0.11.0/piar/R/update.aggregation_structure.R | 2 piar-0.11.0/piar/R/update_weights.R | 11 piar-0.11.0/piar/R/utils.R | 99 -- piar-0.11.0/piar/R/weights.piar_aggregation_structure.R | 2 piar-0.11.0/piar/R/window.piar_index.R | 10 piar-0.11.0/piar/README.md | 117 +-- piar-0.11.0/piar/build/partial.rdb |binary piar-0.11.0/piar/build/vignette.rds |binary piar-0.11.0/piar/inst/REFERENCES.R |only piar-0.11.0/piar/inst/WORDLIST | 1 piar-0.11.0/piar/inst/doc/adjust-weights.R | 2 piar-0.11.0/piar/inst/doc/adjust-weights.Rmd | 5 piar-0.11.0/piar/inst/doc/adjust-weights.html | 2 piar-0.11.0/piar/inst/doc/contributions.R | 2 piar-0.11.0/piar/inst/doc/contributions.Rmd | 5 piar-0.11.0/piar/inst/doc/contributions.html | 259 +------ piar-0.11.0/piar/inst/doc/decomposing-indexes.R | 2 piar-0.11.0/piar/inst/doc/decomposing-indexes.Rmd | 63 - piar-0.11.0/piar/inst/doc/decomposing-indexes.html | 108 ++- piar-0.11.0/piar/inst/doc/imputation.R | 2 piar-0.11.0/piar/inst/doc/imputation.Rmd | 5 piar-0.11.0/piar/inst/doc/imputation.html | 2 piar-0.11.0/piar/inst/doc/index-number-formulas.R | 6 piar-0.11.0/piar/inst/doc/index-number-formulas.Rmd | 15 piar-0.11.0/piar/inst/doc/index-number-formulas.html | 157 ---- piar-0.11.0/piar/inst/doc/matrix-aggregation.R | 2 piar-0.11.0/piar/inst/doc/matrix-aggregation.Rmd | 5 piar-0.11.0/piar/inst/doc/matrix-aggregation.html | 114 --- piar-0.11.0/piar/inst/doc/multiple-baskets.R | 2 piar-0.11.0/piar/inst/doc/multiple-baskets.Rmd | 5 piar-0.11.0/piar/inst/doc/multiple-baskets.html | 2 piar-0.11.0/piar/inst/doc/multiple-data-sources.R | 2 piar-0.11.0/piar/inst/doc/multiple-data-sources.Rmd | 5 piar-0.11.0/piar/inst/doc/multiple-data-sources.html | 58 - piar-0.11.0/piar/inst/doc/multiple-dimensions.R | 23 piar-0.11.0/piar/inst/doc/multiple-dimensions.Rmd | 58 + piar-0.11.0/piar/inst/doc/multiple-dimensions.html | 126 +-- piar-0.11.0/piar/inst/doc/piar.R | 2 piar-0.11.0/piar/inst/doc/piar.Rmd | 16 piar-0.11.0/piar/inst/doc/piar.html | 359 ++-------- piar-0.11.0/piar/inst/doc/spatial-price-index.R | 2 piar-0.11.0/piar/inst/doc/spatial-price-index.Rmd | 5 piar-0.11.0/piar/inst/doc/spatial-price-index.html | 98 -- piar-0.11.0/piar/inst/doc/subperiods.R | 2 piar-0.11.0/piar/inst/doc/subperiods.Rmd | 5 piar-0.11.0/piar/inst/doc/subperiods.html | 34 piar-0.11.0/piar/inst/doc/superlative-aggregation.R | 2 piar-0.11.0/piar/inst/doc/superlative-aggregation.Rmd | 11 piar-0.11.0/piar/inst/doc/superlative-aggregation.html | 112 --- piar-0.11.0/piar/inst/tinytest/test-aggregate.R | 50 - piar-0.11.0/piar/inst/tinytest/test-aggregation-structure-attributes.R | 8 piar-0.11.0/piar/inst/tinytest/test-aggregation_structure.R | 8 piar-0.11.0/piar/inst/tinytest/test-as.ts.R | 2 piar-0.11.0/piar/inst/tinytest/test-as_index.R | 12 piar-0.11.0/piar/inst/tinytest/test-back_period.R | 6 piar-0.11.0/piar/inst/tinytest/test-chain.R | 22 piar-0.11.0/piar/inst/tinytest/test-coerce-aggregation-structure.R | 9 piar-0.11.0/piar/inst/tinytest/test-coerce-index.R | 6 piar-0.11.0/piar/inst/tinytest/test-combine_classifications.R | 6 piar-0.11.0/piar/inst/tinytest/test-contrib.R | 14 piar-0.11.0/piar/inst/tinytest/test-cut.R | 12 piar-0.11.0/piar/inst/tinytest/test-elemental_index.R | 10 piar-0.11.0/piar/inst/tinytest/test-expand_classification.R | 10 piar-0.11.0/piar/inst/tinytest/test-extract-index.R | 49 + piar-0.11.0/piar/inst/tinytest/test-geks_index.R | 12 piar-0.11.0/piar/inst/tinytest/test-gmean.R | 4 piar-0.11.0/piar/inst/tinytest/test-impute-prices.R | 18 piar-0.11.0/piar/inst/tinytest/test-index-attributes.R | 6 piar-0.11.0/piar/inst/tinytest/test-is.na.R | 4 piar-0.11.0/piar/inst/tinytest/test-known-values.R | 6 piar-0.11.0/piar/inst/tinytest/test-lag.R |only piar-0.11.0/piar/inst/tinytest/test-mean.R | 8 piar-0.11.0/piar/inst/tinytest/test-merge.R | 10 piar-0.11.0/piar/inst/tinytest/test-outliers.R | 8 piar-0.11.0/piar/inst/tinytest/test-splice_index.R | 18 piar-0.11.0/piar/inst/tinytest/test-split.R | 4 piar-0.11.0/piar/inst/tinytest/test-split_classification.R | 6 piar-0.11.0/piar/inst/tinytest/test-stack.R | 14 piar-0.11.0/piar/inst/tinytest/test-transmute_weights.R | 4 piar-0.11.0/piar/inst/tinytest/test-update.R | 6 piar-0.11.0/piar/inst/tinytest/test-window.R | 6 piar-0.11.0/piar/man/aggregate.piar_index.Rd | 36 - piar-0.11.0/piar/man/aggregation_structure.Rd | 2 piar-0.11.0/piar/man/as.data.frame.piar_index.Rd | 5 piar-0.11.0/piar/man/as.matrix.piar_aggregation_structure.Rd | 14 piar-0.11.0/piar/man/as.ts.piar_index.Rd | 7 piar-0.11.0/piar/man/back_period.Rd | 9 piar-0.11.0/piar/man/chain.Rd | 1 piar-0.11.0/piar/man/contrib.Rd | 1 piar-0.11.0/piar/man/elementary_index.Rd | 26 piar-0.11.0/piar/man/emean.Rd | 7 piar-0.11.0/piar/man/geks_index.Rd | 13 piar-0.11.0/piar/man/gmean.Rd | 18 piar-0.11.0/piar/man/head.piar_index.Rd | 5 piar-0.11.0/piar/man/impute_prices.Rd | 14 piar-0.11.0/piar/man/is.na.piar_index.Rd | 1 piar-0.11.0/piar/man/lag.piar_index.Rd |only piar-0.11.0/piar/man/levels.piar_index.Rd | 1 piar-0.11.0/piar/man/mean.piar_index.Rd | 10 piar-0.11.0/piar/man/merge.piar_index.Rd | 1 piar-0.11.0/piar/man/outliers.Rd | 28 piar-0.11.0/piar/man/piar-package.Rd | 4 piar-0.11.0/piar/man/price_relative.Rd | 2 piar-0.11.0/piar/man/splice_index.Rd | 8 piar-0.11.0/piar/man/split.piar_index.Rd | 3 piar-0.11.0/piar/man/split_classification.Rd | 4 piar-0.11.0/piar/man/stack.piar_index.Rd | 3 piar-0.11.0/piar/man/sub-.piar_index.Rd | 10 piar-0.11.0/piar/man/time.piar_index.Rd | 1 piar-0.11.0/piar/man/transmute_weights.Rd | 7 piar-0.11.0/piar/man/transmute_weights2.Rd | 17 piar-0.11.0/piar/man/update_weights.Rd | 11 piar-0.11.0/piar/man/window.piar_index.Rd | 2 piar-0.11.0/piar/vignettes/adjust-weights.Rmd | 5 piar-0.11.0/piar/vignettes/contributions.Rmd | 5 piar-0.11.0/piar/vignettes/decomposing-indexes.Rmd | 63 - piar-0.11.0/piar/vignettes/imputation.Rmd | 5 piar-0.11.0/piar/vignettes/index-number-formulas.Rmd | 15 piar-0.11.0/piar/vignettes/matrix-aggregation.Rmd | 5 piar-0.11.0/piar/vignettes/multiple-baskets.Rmd | 5 piar-0.11.0/piar/vignettes/multiple-data-sources.Rmd | 5 piar-0.11.0/piar/vignettes/multiple-dimensions.Rmd | 58 + piar-0.11.0/piar/vignettes/piar.Rmd | 16 piar-0.11.0/piar/vignettes/spatial-price-index.Rmd | 5 piar-0.11.0/piar/vignettes/subperiods.Rmd | 5 piar-0.11.0/piar/vignettes/superlative-aggregation.Rmd | 11 165 files changed, 1544 insertions(+), 2080 deletions(-)
Title: Read and Write 'Apache Iceberg' Tables
Description: A native client for 'Apache Iceberg', the open table format used by
'Snowflake', 'Databricks', 'BigQuery', 'AWS' and 'Dremio'. Rather than
reaching 'Iceberg' through a query engine such as 'DuckDB', this package
talks to it directly: it connects to REST and 'AWS Glue' catalogs, lists
namespaces and tables, reads the schema and partition specification of a
table, scans data with predicates and projections pushed down, travels back
through snapshot history, and appends new data. 'Apache Arrow' is the
interchange layer throughout, so scan results arrive in R without a
serialisation round trip. Built on 'iceberg-rust', the Apache-governed
'Rust' implementation, via 'extendr'.
Supports table spec versions 1 and 2; see the 'README' for the full matrix
of supported and unsupported features. This is a community package, not
affiliated with or endorsed by The Apache Software Foundation; 'Apache',
'Apache Iceberg' and 'Iceberg' are trademarks of The Apache Software
Foundation.
Author: Youzhi Yu [aut, cre],
The Apache Software Foundation [cph]
Maintainer: Youzhi Yu <yuyouzhi666@icloud.com>
Diff between icebergr versions 0.1.0 dated 2026-09-10 and 0.2.0 dated 2026-10-12
DESCRIPTION | 31 - LICENSE.note | 51 -- MD5 | 148 +++--- NEWS.md | 225 +++++++++ R/catalog.R | 226 ++++++++- R/extendr-wrappers.R | 4 R/filter.R | 172 ++++++ R/icebergr-package.R | 7 R/scan.R | 56 +- R/snapshots.R | 14 R/spec-support.R | 22 R/table.R | 22 R/utils.R | 70 ++ R/write.R | 174 ++++++- README.md | 347 ++------------ build/vignette.rds |binary inst/NOTICE | 4 inst/doc/catalog-configuration.R | 6 inst/doc/catalog-configuration.Rmd | 93 ++- inst/doc/catalog-configuration.html | 130 ++++- inst/doc/getting-started.R | 8 inst/doc/getting-started.Rmd | 48 + inst/doc/getting-started.html | 135 ++++- inst/doc/pushdown.R |only inst/doc/pushdown.Rmd |only inst/doc/pushdown.html |only inst/doc/table-format.R |only inst/doc/table-format.Rmd |only inst/doc/table-format.html |only inst/doc/time-travel.R |only inst/doc/time-travel.Rmd |only inst/doc/time-travel.html |only inst/doc/types.R |only inst/doc/types.Rmd |only inst/doc/types.html |only inst/doc/writing.R |only inst/doc/writing.Rmd |only inst/doc/writing.html |only man/figures |only man/icebergr-package.Rd | 8 man/icebergr_append.Rd | 13 man/icebergr_catalog.Rd | 44 + man/icebergr_create_table.Rd | 3 man/icebergr_properties.Rd | 2 man/icebergr_register_table.Rd | 28 + man/icebergr_scan.Rd | 32 - man/icebergr_table_exists.Rd | 6 src/Makevars.in | 6 src/rust/Cargo.lock | 813 ++++++++++++++++----------------- src/rust/Cargo.toml | 38 + src/rust/build.rs |only src/rust/src/arrow_bridge.rs | 12 src/rust/src/catalog.rs | 72 ++ src/rust/src/errors.rs | 258 ++++++++++ src/rust/src/lib.rs | 5 src/rust/src/panic.rs | 86 +++ src/rust/src/predicate.rs | 405 ++++++++++++---- src/rust/src/runtime.rs | 330 +++++++++++++ src/rust/src/scan.rs | 85 ++- src/rust/src/table.rs | 34 + src/rust/src/write.rs | 246 +++++++-- src/rust/vendor.tar.xz |binary tests/testthat/helper-icebergr.R | 47 + tests/testthat/test-case-sensitivity.R | 37 + tests/testthat/test-catalog.R | 19 tests/testthat/test-conditions.R | 26 + tests/testthat/test-confine.R |only tests/testthat/test-credentials.R |only tests/testthat/test-errors.R | 49 + tests/testthat/test-filter.R | 80 +++ tests/testthat/test-pushdown.R | 325 +++++++++++++ tests/testthat/test-roundtrip.R | 46 + tests/testthat/test-spec-support.R | 17 tests/testthat/test-time-travel.R | 72 ++ tests/testthat/test-types.R | 5 tools/config.R | 46 + tools/msrv.R | 61 ++ tools/vendor.R | 114 +++- vignettes/catalog-configuration.Rmd | 93 ++- vignettes/getting-started.Rmd | 48 + vignettes/pushdown.Rmd |only vignettes/table-format.Rmd |only vignettes/time-travel.Rmd |only vignettes/types.Rmd |only vignettes/vignette_reference.bib |only vignettes/writing.Rmd |only 86 files changed, 4274 insertions(+), 1330 deletions(-)
Title: Iterative Extrapolation of Species' Haplotype Accumulation
Curves for Genetic Diversity Assessment
Description: Performs iterative extrapolation of species' haplotype accumulation curves using a nonparametric stochastic (Monte Carlo) optimization method for assessment of specimen sampling completeness based on the approach of Phillips et al. (2015) <doi:10.1515/dna-2015-0008>, Phillips et al. (2019) <doi:10.1002/ece3.4757> and Phillips et al. (2020) <doi: 10.7717/peerj-cs.243>. 'HACSim' outputs a number of useful summary statistics of sampling coverage ("Measures of Sampling Closeness"), including an estimate of the likely required sample size (along with desired level confidence intervals) necessary to recover a given number/proportion of observed unique species' haplotypes. Any genomic marker can be targeted to assess likely required specimen sample sizes for genetic diversity assessment. The method is particularly well-suited to assess sampling sufficiency for DNA barcoding initiatives. Users can also simulate their own DNA sequences according to various models of nucleotide [...truncated...]
Author: Jarrett D. Phillips [aut, cre],
Steven H. French [ctb],
Navdeep Singh [ctb]
Maintainer: Jarrett D. Phillips <phillipsjarrett1@gmail.com>
Diff between HACSim versions 1.0.7-1 dated 2025-09-19 and 1.0.7-2 dated 2026-10-12
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- build/partial.rdb |binary 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Efficient Spatial Thinning of Species Occurrences
Description: Provides efficient geospatial thinning algorithms to reduce
the density of coordinate data while maintaining spatial
relationships. Implements K-D Tree and brute-force distance-based
thinning, as well as grid-based and precision-based thinning methods.
For more information on the methods, see Elseberg et al. (2012)
<https://hdl.handle.net/10446/86202>.
Author: Jorge Mestre-Tomas [aut, cre]
Maintainer: Jorge Mestre-Tomas <jorge.mestre.tomas@csic.es>
Diff between GeoThinneR versions 2.1.2 dated 2026-08-25 and 2.1.3 dated 2026-10-12
DESCRIPTION | 8 MD5 | 69 ++-- NAMESPACE | 63 +--- NEWS.md | 17 + R/GeoThinned_class.R | 9 R/distance_thinning.R | 78 ++++- R/grid_thinning.R | 2 R/precision_thinning.R | 2 R/thin_points.R | 1 R/thinning_algorithm.R | 15 - R/utils.R | 45 +-- build/vignette.rds |binary inst/CITATION | 28 - inst/doc/GeoThinneR.R | 23 + inst/doc/GeoThinneR.Rmd | 28 + inst/doc/GeoThinneR.html | 430 ++++++++++++++++-------------- man/GeoThinned.Rd | 203 ++++++-------- man/calculate_spatial_coverage.Rd | 69 ++-- man/caretta.Rd | 92 +++--- man/compute_nearest_neighbor_distances.Rd | 79 ++--- man/compute_neighbors_brute.Rd | 77 ++--- man/compute_neighbors_kdtree.Rd | 89 +++--- man/compute_neighbors_local_kdtree.Rd | 83 ++--- man/distance_thinning.Rd | 149 +++++----- man/estimate_k_max.Rd | 81 ++--- man/grid_thinning.Rd | 132 ++++----- man/is_lonlat.Rd | 61 ++-- man/lon_lat_to_cartesian.Rd | 53 +-- man/max_thinning_algorithm.Rd | 81 ++--- man/new_GeoThinned.Rd |only man/precision_thinning.Rd | 96 +++--- man/select_target_points.Rd | 88 +++--- man/thin_points.Rd | 255 ++++++++--------- man/thunnus.Rd | 72 ++--- tests/testthat/test-distance_thinning.R | 53 +++ vignettes/GeoThinneR.Rmd | 28 + 36 files changed, 1459 insertions(+), 1200 deletions(-)
Title: Local Large Language Model Inference Engine
Description: Enables R users to run large language models locally using 'GGUF' model files
and the 'llama.cpp' inference engine. Provides a complete R interface for loading models,
generating text completions, extracting vector representations, and streaming responses in real-time.
Includes grammar-constrained generation for structured output, text classification,
and retrieval-augmented generation (RAG) pipelines. Supports local inference without
requiring cloud APIs or internet connectivity, ensuring complete data privacy and
control. Based on the 'llama.cpp' project by Georgi Gerganov (2023) <https://github.com/ggml-org/llama.cpp>.
Author: Pawan Rama Mali [aut, cre, cph],
Georgi Gerganov [aut, cph] ,
The ggml authors [cph] ,
Jeffrey Quesnelle [ctb, cph] ,
Bowen Peng [ctb, cph] ,
pi6am [ctb] ,
Ivan Yurchenko [ctb] ,
Dirk Eddelbuettel [ctb, rev]
Maintainer: Pawan Rama Mali <prm@outlook.in>
Diff between edgemodelr versions 0.4.3 dated 2026-09-08 and 0.4.5 dated 2026-10-12
DESCRIPTION | 13 MD5 | 81 NEWS.md | 1003 ++- R/RcppExports.R | 8 R/api.R | 7316 ++++++++++++++-------------- R/edgemodelr-package.R | 42 R/ollama.R | 2 R/zzz.R | 2 inst/CITATION | 28 inst/examples/08_rag_pipeline.R | 650 +- man/edge_ask.Rd | 118 man/edge_chat_completion.Rd | 100 man/edge_classify.Rd | 102 man/edge_clean_cache.Rd | 90 man/edge_embeddings.Rd | 106 man/edge_extract.Rd | 102 man/edge_extract_batch.Rd | 102 man/edge_grammar_completion.Rd | 140 man/edge_index_documents.Rd | 112 man/edge_json_grammar.Rd | 70 man/edge_map.Rd | 102 man/edge_model_n_embd.Rd | 50 man/edge_search.Rd | 66 man/edge_serve.Rd | 108 man/edge_similarity.Rd | 58 man/edge_similarity_matrix.Rd | 56 src/Makevars | 14 src/Makevars.win | 8 src/RcppExports.cpp | 19 src/bindings.cpp | 152 src/ggml/ggml-common.h | 7 src/ggml/ggml.c | 10 tests/testthat.R | 8 tests/testthat/test-e2e-integration.R | 95 tests/testthat/test-error-handling.R | 27 tests/testthat/test-integration.R | 8 tests/testthat/test-malformed-model-files.R |only tests/testthat/test-model-loading.R | 13 tests/testthat/test-model-management.R | 16 tests/testthat/test-streaming.R | 22 tests/testthat/test-text-completion.R | 8 tests/testthat/test-utility-functions.R | 96 42 files changed, 5765 insertions(+), 5365 deletions(-)
Title: Data Science Infrastructure for Global Health
Description: Supports global health data analysis, including a
publication-ready 'ggplot2' theme, a 'flextable' defaults helper,
a thin pie chart wrapper, built-in regional country-code datasets
with a WHO region lookup helper, a geometric mean function for
indicator aggregation, an average annual rate of reduction function
for indicator progress tracking, direct age standardization against
the bundled WHO 2026 Standard Population, period life-table
construction, a snapshot helper for reproducible data pulls, and
convenience clients for the World Health Organization Global Health
Observatory (GHO) through its legacy OData API
<https://ghoapi.azureedge.net/api/> or the public WHO xMart OData API
<https://xmart-api-public.who.int/DATA_>, Global Health Estimates (GHE)
through WHO xMart, and
the United Nations Sustainable Development Goals (SDG) API
<https://unstats.un.org/SDGAPI/swagger/>.
Author: Shanlong Ding [aut, cre]
Maintainer: Shanlong Ding <dings@who.int>
Diff between DSIR versions 0.10.0 dated 2026-10-01 and 0.11.0 dated 2026-10-12
DESCRIPTION | 13 MD5 | 106 ++-- NAMESPACE | 85 +-- NEWS.md | 176 ++++--- R/DSIR-package.R | 69 +- R/age_standardize.R | 329 ++++++------- R/bind_indicators.R | 138 ++--- R/clean_metadata.R | 146 +++-- R/clean_schema.R | 126 ++--- R/data.R | 450 ++++++++---------- R/ghe.R |only R/gho.R | 507 +++++--------------- R/http.R | 45 + R/who_backend.R |only R/who_gho.R |only R/who_legacy.R |only README.md | 445 +++++++++++------ build/vignette.rds |binary data/who_std_pop.rda |binary inst/CITATION | 36 - inst/WORDLIST | 99 ++- inst/doc/DSIR.R | 350 ++++++-------- inst/doc/DSIR.Rmd | 273 +++++----- inst/doc/DSIR.html | 506 ++------------------ inst/doc/ghe-xmart.R |only inst/doc/ghe-xmart.Rmd |only inst/doc/ghe-xmart.html |only man/DSIR-package.Rd | 7 man/age_standardize.Rd | 209 ++++---- man/bind_indicators.Rd | 102 ++-- man/ghe_causes.Rd |only man/ghe_clean.Rd |only man/ghe_coverage.Rd |only man/ghe_data.Rd |only man/ghe_dimensions.Rd |only man/gho_clean.Rd | 185 +++---- man/gho_count.Rd | 148 +++-- man/gho_coverage.Rd | 170 +++--- man/gho_data.Rd | 171 ++++-- man/gho_dimensions.Rd | 98 ++- man/gho_has_data.Rd | 160 +++--- man/gho_indicators.Rd | 11 man/who_std_pop.Rd | 113 ++-- tests/testthat/helper-gho-cache.R | 27 - tests/testthat/helper-who-mock.R |only tests/testthat/test-age_standardize.R | 268 +++++----- tests/testthat/test-clean.R | 749 +++++++++++++++--------------- tests/testthat/test-ghe.R |only tests/testthat/test-gho-availability.R | 206 ++++---- tests/testthat/test-gho-backend.R |only tests/testthat/test-gho-catalog-cache.R | 150 +++--- tests/testthat/test-gho-dimensions.R | 219 ++++---- tests/testthat/test-gho-get-mock.R | 445 +++++++++-------- tests/testthat/test-gho.R | 4 tests/testthat/test-sdg-area-resolution.R | 145 ++--- tests/testthat/test-sdg-coverage.R | 258 +++++----- tests/testthat/test-sdg-indicators.R | 193 ++++--- tests/testthat/test-sdg-year-filter.R | 136 ++--- tests/testthat/test-who-html.R |only tests/testthat/test-who-xmart.R |only tests/testthat/test-who_std_pop.R | 75 +-- vignettes/DSIR.Rmd | 273 +++++----- vignettes/ghe-xmart.Rmd |only 63 files changed, 4087 insertions(+), 4334 deletions(-)
Title: Port of 'Dparser' Package
Description: A Scannerless GLR parser/parser generator. Note that GLR standing for "generalized LR", where L stands for "left-to-right" and
R stands for "rightmost (derivation)". For more information see <https://en.wikipedia.org/wiki/GLR_parser>. This parser is based on the Tomita
(1987) algorithm. (Paper can be found at <https://aclanthology.org/P84-1073.pdf>).
The original 'dparser' package documentation can be found at <https://dparser.sourceforge.net/>. This allows you to add mini-languages to R (like
rxode2's ODE mini-language Wang, Hallow, and James 2015 <DOI:10.1002/psp4.12052>) or to parse other languages like 'NONMEM' to automatically translate
them to R code. To use this in your code, add a LinkingTo dparser in your DESCRIPTION file and instead of using #include <dparse.h> use
#include <dparser.h>. This also provides a R-based port of the make_dparser <https://dparser.sourceforge.net/d/make_dparser.cat> command called
mkdparser(). Addition [...truncated...]
Author: Matthew Fidler [aut, cre],
John Plevyak [aut, cph]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between dparser versions 1.3.1-13 dated 2024-10-22 and 1.3.1-14 dated 2026-10-12
DESCRIPTION | 8 - MD5 | 40 +++++--- NAMESPACE | 6 - NEWS.md | 108 ++++++++++++++++++++++++ inst/ansic.test.g.d_parser.c |only man/dparser-package.Rd | 12 +- man/mkdparse.Rd | 12 +- src/dparse.h | 1 src/dparser.c | 2 src/dparser.h | 6 + src/dparser2.h | 1 src/dparserPtr.h | 3 src/lex.c | 9 +- src/parse.c | 57 ++++++++---- src/rdparse.c | 7 + src/util.c | 28 ++++-- src/write_tables.c | 45 ++++++---- tests/testthat/concurrent_parser.c |only tests/testthat/helper-concurrent.R |only tests/testthat/test-concurrent-dparse.R |only tests/testthat/test-mem-buf-read-large.R |only tests/testthat/test-mem-d-pass-negative.R |only tests/testthat/test-mem-dparse-unsigned.R |only tests/testthat/test-mem-new-D-Parser-negative.R |only tests/testthat/test-mem-rdparse-bad-file.R |only tests/testthat/test-mem-udparse-null.R |only 26 files changed, 268 insertions(+), 77 deletions(-)
Title: 'AV1' Video Encoding for Biological Microscopy Data
Description: Converts microscopy video and image data (H.264/H.265,
AVI/MJPEG, TIFF stacks) to the 'AV1' codec for compact storage, and
archives 16-bit image stacks and videos losslessly in the 'FFV1'
format. Encoding runs on the GPU via 'Vulkan' or 'VAAPI' when
available and falls back to the CPU through 'FFmpeg' and 'SVT-AV1'.
Whole experiment folders can be converted at once.
Author: Yuri Baramykov [aut, cre] ,
The Khronos Group Inc. [cph],
FFmpeg developers [cph]
Maintainer: Yuri Baramykov <lbsbmsu@mail.ru>
This is a re-admission after prior archival of version 0.1.3 dated 2026-03-23
Diff between AV1R versions 0.1.3 dated 2026-03-23 and 0.1.4 dated 2026-10-12
DESCRIPTION | 53 ++++------ MD5 | 98 ++++++++++++------ NAMESPACE | 2 NEWS.md | 11 ++ R/archive.R |only R/archive_video.R |only R/backend.R | 16 ++- R/convert.R | 57 ++++++---- R/quality.R | 17 ++- R/utils.R | 9 + README.md | 174 ++++++++++++++++++++++++++++++++- cleanup | 13 ++ cleanup.win |only configure | 29 +++++ configure.win | 26 ++++ inst/examples/benchmark_ffv1.R |only inst/examples/calibrate_vaapi_cqp.R | 17 --- inst/examples/profile_ffv1_shader.R |only man/AV1R-package.Rd | 10 + man/archive_tiff.Rd |only man/archive_video.Rd |only man/av1r_status.Rd | 3 man/detect_backend.Rd | 4 man/vulkan_available.Rd | 6 - man/vulkan_devices.Rd | 3 src/Makevars.in | 8 + src/Makevars.win.in | 8 + src/av1r_bindings.cpp | 62 +++++++++-- src/av1r_encode_vulkan.cpp | 14 +- src/av1r_ffv1_bindings.cpp |only src/av1r_ffv1_encoder.cpp |only src/av1r_ffv1_encoder.h |only src/av1r_ffv1_gpu.cpp |only src/av1r_ffv1_gpu.h |only src/av1r_ffv1_gpu_encoder.cpp |only src/av1r_ffv1_gpu_encoder.h |only src/av1r_ffv1_rangecoder.cpp |only src/av1r_ffv1_rangecoder.h |only src/av1r_ffv1_tables.h |only src/av1r_init.cpp | 11 +- src/av1r_memory.cpp | 7 + src/av1r_mkv_writer.cpp |only src/av1r_mkv_writer.h |only src/av1r_stderr_suppress.h | 7 + src/av1r_stream_encoder.h | 3 src/av1r_vk_instance.h |only src/av1r_vulkan_ctx.h | 5 src/ffv1_shaders |only tests/testthat/helper-device.R |only tests/testthat/test-archive-internal.R |only tests/testthat/test-archive-video.R |only tests/testthat/test-archive.R |only tests/testthat/test-backend.R | 8 - tests/testthat/test-batch-internal.R |only tests/testthat/test-compute-size.R | 4 tests/testthat/test-convert.R | 2 tests/testthat/test-ffmpeg.R | 21 +++ tests/testthat/test-ffv1.R |only tests/testthat/test-mkv.R |only tests/testthat/test-quality-internal.R | 2 tests/testthat/test-tiff.R | 42 ++++--- tests/testthat/test-utils.R | 8 + tools |only 63 files changed, 586 insertions(+), 174 deletions(-)
Title: Arc-Length Statistics: Goodness of Fit, Distributions and a
Bayesian Test
Description: Inference from the arc length of statistical functions. Three tools share one pure-C
back-end: a goodness-of-fit test based on the arc length of the probability plot, with an analytic
saddlepoint null and sensitivity to local density structure that the empirical-distribution tests
miss; two constructions that build a distribution from the arc length of its defining curve, the
arc-length generator and the quantile arc-length family estimated by L-moments; and a Bayesian
nonparametric arc-length goodness-of-fit test on the Dirichlet-process posterior. The same C sources
back the 'Python' package 'arcstat'.
Author: M. Theodor Loots [aut, cre]
Maintainer: M. Theodor Loots <theo.loots@gmail.com>
Diff between arcstat versions 0.3.0 dated 2026-09-14 and 0.3.1 dated 2026-10-12
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 11 +++++++++++ README.md | 12 ++++++++++++ src/arclen.c | 6 ++++++ tests/testthat/test-arclen.R | 13 +++++++++++++ 6 files changed, 50 insertions(+), 8 deletions(-)
Title: Tidy Tools for Chinese, Japanese and Korean Text
Description: A tidy toolkit for text that is written in Chinese, Japanese or
Korean. Most text tooling in R assumes that words are separated by
whitespace, which CJK writing does not use, so ordinary summaries of a text
column either treat a sentence as one undifferentiated blob or split it into
isolated characters. Word segmentation is a pluggable engine, with
dictionary-based segmentation for Chinese and Japanese supplied through
'ICU' and further engines registrable by the caller, because where a word
ends is a fact about a language and not about Unicode. 'tidycjk'
classifies characters by Unicode block, reports which script and which
language a text is written in, measures how much of a text is CJK, and
turns those measurements into tibbles that slot straight into a
'tidyverse' workflow. It also measures display width in terminal columns,
pads, truncates and wraps to a width rather than to a character
count, and normalises fullwidth and halfwidth forms surgically -- including
composing halfwidt [...truncated...]
Author: Youzhi Yu [aut, cre]
Maintainer: Youzhi Yu <yuyouzhi666@icloud.com>
Diff between tidycjk versions 0.1.0 dated 2026-09-09 and 0.2.0 dated 2026-10-11
DESCRIPTION | 46 ++- MD5 | 107 ++++++-- NAMESPACE | 14 + NEWS.md | 400 ++++++++++++++++++++++++++++++++ R/collate.R |only R/detect.R | 34 ++ R/nlp.R |only R/normalize.R | 189 ++++++++++++++- R/ranges.R | 322 ++++++++++++++++++++++---- R/segment.R | 289 ++++++++++++++++++++--- R/summary.R | 26 +- R/tidycjk-package.R | 95 +++++-- R/transliterate.R |only R/width.R | 238 ++++++++++++++++++- README.md | 316 +++++--------------------- build |only inst |only man/cjk_blocks.Rd | 60 ++-- man/cjk_char_counts.Rd | 8 man/cjk_detect_language.Rd | 8 man/cjk_jamo.Rd |only man/cjk_ngrams.Rd |only man/cjk_normalize.Rd |only man/cjk_pad.Rd | 5 man/cjk_ratio.Rd | 7 man/cjk_romanize.Rd |only man/cjk_script.Rd | 5 man/cjk_segment.Rd | 25 +- man/cjk_segmenters.Rd | 75 +++++- man/cjk_sentences.Rd |only man/cjk_simplify.Rd |only man/cjk_sort.Rd |only man/cjk_strip_punct.Rd |only man/cjk_summary.Rd | 6 man/cjk_tokens.Rd | 17 + man/cjk_truncate.Rd | 13 - man/cjk_width.Rd | 5 man/cjk_wrap.Rd |only man/figures |only man/has_cjk.Rd | 5 man/tidycjk-package.Rd | 111 +++++---- man/to_halfwidth.Rd | 9 man/to_hiragana.Rd |only tests/testthat/test-collate.R |only tests/testthat/test-detect.R | 64 +++++ tests/testthat/test-differential.R |only tests/testthat/test-invariants.R |only tests/testthat/test-nlp.R |only tests/testthat/test-normalize.R | 198 ++++++++++++++++ tests/testthat/test-ranges.R | 437 ++++++++++++++++++++++++++++++++++-- tests/testthat/test-segment.R | 313 +++++++++++++++++++++++++ tests/testthat/test-transliterate.R |only tests/testthat/test-width.R | 79 ++++++ tests/testthat/test-wrap.R |only vignettes |only 55 files changed, 2962 insertions(+), 564 deletions(-)
Title: Classes and Methods for Spatial Data
Description: Classes and methods for spatial
data; the classes document where the spatial location information
resides, for 2D or 3D data. Utility functions are provided, e.g. for
plotting data as maps, spatial selection, as well as methods for
retrieving coordinates, for subsetting, print, summary, etc. From this
version, 'rgdal', 'maptools', and 'rgeos' are no longer used at all,
see <https://r-spatial.org/r/2023/05/15/evolution4.html> for details.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [aut],
Barry Rowlingson [ctb],
Virgilio Gomez-Rubio [ctb],
Robert Hijmans [ctb],
Michael Sumner [ctb],
Don MacQueen [ctb],
Jim Lemon [ctb],
Finn Lindgren [ctb],
Josh O'Brien [ctb],
Joseph O'Rourke [ctb],
Patrick [...truncated...]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sp versions 2.2-3 dated 2026-07-19 and 2.2-4 dated 2026-10-11
DESCRIPTION | 6 - MD5 | 22 ++--- build/vignette.rds |binary inst/NEWS.Rd | 5 + inst/doc/csdacm.pdf |binary inst/doc/intro_sp.pdf |binary inst/doc/retiring_rgdal_geos_1.html | 2 inst/doc/sp_gallery.html | 43 +++++------ src/sp_xports.c | 1 tests/Rplots.pdf |binary tests/pass1.R | 20 ++--- tests/pass1.Rout.save | 138 +++--------------------------------- 12 files changed, 66 insertions(+), 171 deletions(-)
Title: A Shiny Dashboard Template Modular System with Chat Bot Support
Description: A template dashboard system with AI agent integrated.
Comes with default themes that can be customized.
Developers can upload modified templates on 'Github', and users can
easily download templates with 'RStudio' project wizard.
The key features of the default template include light and dark theme
switcher, resizing graphs, synchronizing inputs across sessions,
new notification system, fancy progress bars, and card-like flip
panels with back sides, as well as various of 'HTML' tool widgets.
Author: Zhengjia Wang [cph, aut, cre] ,
ColorlibHQ [cph] ,
Bootstrap contributors [ctb] ,
Twitter, Inc [cph] ,
Ivan Sagalaev [ctb, cph] ,
Rene Haas [ctb, cph] ,
Zeno Rocha [ctb, cph]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between shidashi versions 0.2.0 dated 2026-04-10 and 0.3.0 dated 2026-10-11
shidashi-0.2.0/shidashi/inst/builtin-templates/AdminLTE3-bare/ui.R |only shidashi-0.2.0/shidashi/inst/builtin-templates/AdminLTE3-bare/www/bootstrap/js/bootstrap.bundle.min.js.map |only shidashi-0.2.0/shidashi/inst/builtin-templates/bslib-bare/_rs_job.R |only shidashi-0.2.0/shidashi/inst/builtin-templates/bslib-bare/global.R |only shidashi-0.2.0/shidashi/inst/builtin-templates/bslib-bare/ui.R |only shidashi-0.2.0/shidashi/inst/builtin-templates/bslib-bare/www/shidashi/css/shidashi.css.map |only shidashi-0.3.0/shidashi/DESCRIPTION | 18 shidashi-0.3.0/shidashi/MD5 | 122 shidashi-0.3.0/shidashi/NAMESPACE | 12 shidashi-0.3.0/shidashi/NEWS.md | 117 shidashi-0.3.0/shidashi/R/aaa.R | 34 shidashi-0.3.0/shidashi/R/ask-user.R |only shidashi-0.3.0/shidashi/R/barebone.R | 28 shidashi-0.3.0/shidashi/R/chat-helpers.R | 115 shidashi-0.3.0/shidashi/R/chatbot.R | 29 shidashi-0.3.0/shidashi/R/colorpicker.R |only shidashi-0.3.0/shidashi/R/ellmer-helpers.R | 2 shidashi-0.3.0/shidashi/R/globals.R | 124 shidashi-0.3.0/shidashi/R/launcher.R |only shidashi-0.3.0/shidashi/R/mcp-catalog.R |only shidashi-0.3.0/shidashi/R/mcp-click.R |only shidashi-0.3.0/shidashi/R/mcp-handler.R | 1445 ++-------- shidashi-0.3.0/shidashi/R/mcp-http.R |only shidashi-0.3.0/shidashi/R/mcp-log.R |only shidashi-0.3.0/shidashi/R/mcp-module.R |only shidashi-0.3.0/shidashi/R/mcp-switch-module.R |only shidashi-0.3.0/shidashi/R/mcp-wrapper.R | 1096 ++++++- shidashi-0.3.0/shidashi/R/modules.R | 29 shidashi-0.3.0/shidashi/R/object-list.R |only shidashi-0.3.0/shidashi/R/render.R | 20 shidashi-0.3.0/shidashi/R/settings.R | 2 shidashi-0.3.0/shidashi/R/skill-parse.R | 115 shidashi-0.3.0/shidashi/R/skill-runner.R | 4 shidashi-0.3.0/shidashi/R/skill-wrapper.R | 516 ++- shidashi-0.3.0/shidashi/R/standalone-viewer.R | 6 shidashi-0.3.0/shidashi/R/zzz.R | 14 shidashi-0.3.0/shidashi/inst/builtin-templates/AdminLTE3-bare/www/shidashi/img/header-bg.png |binary shidashi-0.3.0/shidashi/inst/builtin-templates/bslib-bare/agents/skills/greet/SKILL.md | 2 shidashi-0.3.0/shidashi/inst/builtin-templates/bslib-bare/agents/tool-schema.yaml | 24 shidashi-0.3.0/shidashi/inst/builtin-templates/bslib-bare/modules/aiagent/agents.yaml | 2 shidashi-0.3.0/shidashi/inst/builtin-templates/bslib-bare/modules/demo/R/demo-ui.R | 110 shidashi-0.3.0/shidashi/inst/builtin-templates/bslib-bare/modules/demo/agents.yaml | 2 shidashi-0.3.0/shidashi/inst/builtin-templates/bslib-bare/modules/mcpsetup/R/mcpsetup-ui.R | 166 + shidashi-0.3.0/shidashi/inst/builtin-templates/bslib-bare/www/shidashi/css/shidashi.css | 2 shidashi-0.3.0/shidashi/inst/builtin-templates/bslib-bare/www/shidashi/img/header-bg.png |binary shidashi-0.3.0/shidashi/inst/builtin-templates/bslib-bare/www/shidashi/js/index.js | 16 shidashi-0.3.0/shidashi/inst/mcp-proxy/README.md |only shidashi-0.3.0/shidashi/inst/mcp-proxy/shidashi-proxy.mjs | 1341 ++++++++- shidashi-0.3.0/shidashi/inst/rave.yaml |only shidashi-0.3.0/shidashi/man/colormapSelectInput.Rd |only shidashi-0.3.0/shidashi/man/mcp_call_active.Rd |only shidashi-0.3.0/shidashi/man/mcp_click.Rd |only shidashi-0.3.0/shidashi/man/mcp_wrapper.Rd | 4 shidashi-0.3.0/shidashi/man/module_info.Rd | 19 shidashi-0.3.0/shidashi/man/objectListInput.Rd |only shidashi-0.3.0/shidashi/man/register_input_state.Rd |only shidashi-0.3.0/shidashi/man/register_io.Rd | 39 shidashi-0.3.0/shidashi/man/render.Rd | 5 shidashi-0.3.0/shidashi/man/renderPlot2.Rd |only shidashi-0.3.0/shidashi/man/render_hidden_output.Rd |only shidashi-0.3.0/shidashi/man/save_launcher.Rd |only shidashi-0.3.0/shidashi/man/skill_wrapper.Rd | 46 shidashi-0.3.0/shidashi/man/template_settings.Rd | 5 shidashi-0.3.0/shidashi/tests/testthat/helper-mcp.R |only shidashi-0.3.0/shidashi/tests/testthat/setup-cache.R |only shidashi-0.3.0/shidashi/tests/testthat/test-colorpicker.R |only shidashi-0.3.0/shidashi/tests/testthat/test-fastmap.R |only shidashi-0.3.0/shidashi/tests/testthat/test-input-hints.R |only shidashi-0.3.0/shidashi/tests/testthat/test-launcher.R |only shidashi-0.3.0/shidashi/tests/testthat/test-mcp-catalog.R |only shidashi-0.3.0/shidashi/tests/testthat/test-mcp-http.R |only shidashi-0.3.0/shidashi/tests/testthat/test-mcp-log.R |only shidashi-0.3.0/shidashi/tests/testthat/test-mcp-module.R |only shidashi-0.3.0/shidashi/tests/testthat/test-mcp-plugin.R |only shidashi-0.3.0/shidashi/tests/testthat/test-mcp-server-info.R |only shidashi-0.3.0/shidashi/tests/testthat/test-mcp-switch-module.R |only shidashi-0.3.0/shidashi/tests/testthat/test-object-list.R |only shidashi-0.3.0/shidashi/tests/testthat/test-query-ui.R |only shidashi-0.3.0/shidashi/tests/testthat/test-register-input.R |only shidashi-0.3.0/shidashi/tests/testthat/test-render.R |only shidashi-0.3.0/shidashi/tests/testthat/test-safe-observe.R |only shidashi-0.3.0/shidashi/tests/testthat/test-skill-parse.R | 64 shidashi-0.3.0/shidashi/tests/testthat/test-skill-runner.R | 15 shidashi-0.3.0/shidashi/tests/testthat/test-skill-wrapper.R | 231 + 84 files changed, 3883 insertions(+), 2058 deletions(-)
Title: Restricted Bridge Estimation
Description: Implements bridge regression with linear coefficient restrictions
using the local quadratic approximation described by Yuzbasi, Arashi and
Akdeniz (2021) <doi:10.1007/s00500-021-05763-9>. Provides coefficient paths,
cross-validation, prediction and coefficient extraction for restricted and
unrestricted linear models.
Author: Bahadir Yuzbasi [aut, cre],
Mohammad Arashi [aut],
Fikri Akdeniz [aut],
Jerome Friedman [ctb] ,
Trevor Hastie [ctb] ,
Robert Tibshirani [ctb]
Maintainer: Bahadir Yuzbasi <b.yzb@hotmail.com>
This is a re-admission after prior archival of version 1.0.2 dated 2020-02-29
Diff between rbridge versions 1.0.2 dated 2020-02-29 and 1.0.3 dated 2026-10-11
DESCRIPTION | 44 + MD5 | 90 ++- NAMESPACE | 1 NEWS.md |only R/RcppExports.R | 4 R/bridge.R | 126 +++-- R/cv.bridge.R | 183 +++++--- R/cv.rbridge.R | 263 +++++++---- R/methods.R | 879 +++++++++++++++++++++++---------------- R/rbridge.R | 196 +++++--- R/rbridge_info.R |only R/utilities.R | 33 + README.md |only build |only inst |only man/bridge.Rd | 131 ++++- man/coef.bridge.Rd | 48 +- man/coef.cv.bridge.Rd | 55 +- man/coef.cv.rbridge.Rd | 68 ++- man/coef.rbridge.Rd | 64 +- man/cv.bridge.Rd | 179 +++++-- man/cv.rbridge.Rd | 261 +++++++---- man/figures |only man/plot.cv.bridge.Rd | 49 +- man/plot.cv.rbridge.Rd | 53 ++ man/predict.bridge.Rd | 80 ++- man/predict.cv.bridge.Rd | 88 ++- man/predict.cv.rbridge.Rd | 104 +++- man/predict.rbridge.Rd | 93 ++-- man/rbridge.Rd | 201 +++++--- man/rbridge_info.Rd |only src/Main_functions.cpp | 427 +++++++----------- src/Makevars | 14 src/Makevars.win | 18 src/RcppExports.cpp | 16 tests/testthat/fixtures |only tests/testthat/helper-fixtures.R |only tests/testthat/test-engine.R |only tests/testthat/test-methods.R |only tests/testthat/test.R | 68 +-- vignettes |only 41 files changed, 2410 insertions(+), 1426 deletions(-)
Title: Bayesian Analysis of Finite Mixtures of Plackett-Luce Models for
Partial Rankings/Orderings
Description: Fit finite mixtures of Plackett-Luce models for partial top rankings/orderings within the Bayesian framework. It provides MAP point estimates via EM algorithm and posterior MCMC simulations via Gibbs Sampling. It also fits MLE as a special case of the noninformative Bayesian analysis with vague priors. In addition to inferential techniques, the package assists other fundamental phases of a model-based analysis for partial rankings/orderings, by including functions for data manipulation, simulation, descriptive summary, model selection and goodness-of-fit evaluation. Main references on the methods are Mollica and Tardella (2017) <doi:10.1007/s11336-016-9530-0> and Mollica and Tardella (2014) <doi:10.1002/sim.6224>.
Author: Cristina Mollica [aut, cre],
Luca Tardella [aut]
Maintainer: Cristina Mollica <cristina.mollica@uniroma1.it>
This is a re-admission after prior archival of version 2.2.0 dated 2025-06-30
Diff between PLMIX versions 2.2.0 dated 2025-06-30 and 2.2.1 dated 2026-10-11
PLMIX-2.2.0/PLMIX/src/dlb_sort.cpp |only PLMIX-2.2.1/PLMIX/DESCRIPTION | 24 +-- PLMIX-2.2.1/PLMIX/MD5 | 18 +- PLMIX-2.2.1/PLMIX/NAMESPACE | 86 +++++++----- PLMIX-2.2.1/PLMIX/NEWS | 3 PLMIX-2.2.1/PLMIX/R/PLMIXfunctions.R | 201 +++++++++++++++-------------- PLMIX-2.2.1/PLMIX/R/gibbsPLMIX_with_norm.R | 142 -------------------- PLMIX-2.2.1/PLMIX/man/plot.gsPLMIX.Rd | 8 - PLMIX-2.2.1/PLMIX/man/plot.mpPLMIX.Rd | 6 PLMIX-2.2.1/PLMIX/src/dbl_sort.cpp |only PLMIX-2.2.1/PLMIX/src/loglikPLMIX.cpp | 15 +- 11 files changed, 198 insertions(+), 305 deletions(-)
Title: Motif-Based Spectral Clustering of Weighted Directed Networks
Description: Tools for spectral clustering of weighted directed networks using motif
adjacency matrices. Methods perform well on large and sparse networks, and
random sampling methods for generating weighted directed networks are also
provided. Based on methodology detailed in Underwood, Elliott and Cucuringu
(2020) <doi:10.48550/arXiv.2004.01293>.
Author: William George Underwood [aut, cre]
Maintainer: William George Underwood <william.underwood@warwick.ac.uk>
Diff between motifcluster versions 0.2.3 dated 2022-11-18 and 0.2.4 dated 2026-10-11
DESCRIPTION | 14 ++++++------- MD5 | 32 +++++++++++++++---------------- NEWS.md | 4 +++ R/clustering.R | 4 +-- R/indicators.R | 22 ++++++++++----------- R/motifadjacency.R | 36 +++++++++++++++++------------------ R/sampling.R | 6 ++--- R/spectral.R | 8 +++---- R/utils.R | 12 +++++------ README.md | 4 +-- build/vignette.rds |binary inst/doc/motifcluster_vignette.R | 16 +++++++-------- inst/doc/motifcluster_vignette.Rmd | 5 +--- inst/doc/motifcluster_vignette.pdf |binary tests/testthat/test_motifadjacency.R | 12 +++++------ tests/testthat/test_spectral.R | 28 +++++++++++++-------------- vignettes/motifcluster_vignette.Rmd | 5 +--- 17 files changed, 105 insertions(+), 103 deletions(-)
Title: Identify Global Objects in R Expressions
Description: Identifies global ("unknown" or "free") objects in R expressions
by code inspection using various strategies (ordered, liberal,
conservative, or deep-first search). The objective of this package is to
make it as simple as possible to identify global objects for the purpose
of exporting them in parallel, distributed compute environments.
Author: Henrik Bengtsson [aut, cre, cph] ,
Davis Vaughan [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between globals versions 0.19.1 dated 2026-03-13 and 0.20.0 dated 2026-10-11
.Rinstignore |only DESCRIPTION | 19 MD5 | 91 ++-- NAMESPACE | 17 NEWS.md | 37 + R/Globals-class.R | 54 ++ R/call_find_globals_with_dotdotdot.R | 2 R/cleanup.R | 5 R/findGlobals.R | 56 -- R/findGlobalsDFS.R | 36 - R/globalsByName.R | 26 - R/globalsOf.R | 27 - R/packagesOf.R | 27 + R/utils.R | 6 inst/testme/_epilogue/002.undo-state.R | 4 inst/testme/_epilogue/995.detritus-connections.R | 19 inst/testme/_prologue/090.context.R | 9 inst/testme/deploy.R | 2 inst/testme/run.R | 516 ++++++++++++----------- inst/testme/test-Globals.R | 114 +++++ inst/testme/test-codetools-bug16.R | 33 + inst/testme/test-debug-trace-paths.R |only inst/testme/test-dotdotdot.R | 13 inst/testme/test-findGlobals,dfs.R | 16 inst/testme/test-findGlobals.R | 14 inst/testme/test-globalsByName.R | 33 + inst/testme/test-globalsOf.R | 51 ++ inst/testme/test-packagesOf.R |only man/Globals.Rd | 4 man/cleanup.Globals.Rd | 9 man/globalsOf.Rd | 7 man/packagesOf.Globals.Rd | 6 man/print.Globals.Rd |only tests/test-Globals.R | 1 tests/test-cleanup.R | 1 tests/test-codetools-bug16.R | 1 tests/test-conservative.R | 1 tests/test-debug-trace-paths.R |only tests/test-dotdotdot.R | 1 tests/test-findGlobals,dfs.R | 1 tests/test-findGlobals.R | 1 tests/test-formulas.R | 1 tests/test-globalsByName.R | 1 tests/test-globalsOf,locals.R | 1 tests/test-globalsOf.R | 1 tests/test-liberal.R | 1 tests/test-packagesOf.R |only tests/test-utils.R | 1 tests/test-walkAST.R | 1 tests/test-zzz.R | 1 50 files changed, 844 insertions(+), 424 deletions(-)
Title: Tools for Creating, Updating, and Analyzing Survey Replicate
Weights
Description: Provides tools for creating and working with survey replicate weights,
extending functionality of the 'survey' package from Lumley (2004) <doi:10.18637/jss.v009.i08>.
Implements bootstrap methods for complex surveys, including the generalized survey bootstrap
as described by Beaumont and Patak (2012) <doi:10.1111/j.1751-5823.2011.00166.x>.
Methods are provided for applying nonresponse adjustments to
both full-sample and replicate weights as described by
Rust and Rao (1996) <doi:10.1177/096228029600500305>.
Implements methods for sample-based calibration described by Opsomer and Erciulescu (2021)
<https://www150.statcan.gc.ca/n1/pub/12-001-x/2021002/article/00006-eng.htm>.
Diagnostic functions are included to compare weights and weighted estimates
from different sets of replicate weights.
Author: Ben Schneider [aut, cre]
Maintainer: Ben Schneider <benjamin.julius.schneider@gmail.com>
Diff between svrep versions 0.9.1 dated 2025-10-08 and 0.9.2 dated 2026-10-11
DESCRIPTION | 8 MD5 | 176 NEWS.md | 432 - R/accessor-functions.R | 222 R/add_inactive_replicates.R | 414 - R/as_bootstrap_design.R | 650 +- R/as_data_frame_with_weights.R | 262 R/as_jackknife_design.R | 1136 +-- R/calibrate_to_estimate.R | 790 +- R/calibrate_to_sample.R | 2 R/fays_generalized_replication.R | 17 R/generalized_bootstrap.R | 1626 ++--- R/libraries_data.R | 188 R/lou_vax_data.R | 216 R/make_bootstrap_weights.R | 1451 ++-- R/quadratic_forms.R | 3100 +++++----- R/redistribute_weights.R | 542 - R/rescale_replicates.R | 420 - R/shuffle_replicates.R | 170 R/stack_replicate_designs.R | 496 - R/subsample_replicates.R | 256 R/successive-difference-replication.R | 1100 +-- R/summarize_rep_weights.R | 658 +- R/svrep-package-options.R | 136 R/svrep-package.R | 78 R/svyby_repwts.R | 312 - R/variance-estimators.R | 466 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 20 inst/doc/bootstrap-replicates.Rmd | 1434 ++-- inst/doc/bootstrap-replicates.html | 23 inst/doc/sample-based-calibration.html | 2 inst/doc/two-phase-sampling.Rmd | 1928 +++--- inst/doc/two-phase-sampling.html | 21 man/add_inactive_replicates.Rd | 228 man/as_bootstrap_design.Rd | 368 - man/as_data_frame_with_weights.Rd | 130 man/as_fays_gen_rep_design.Rd | 420 - man/as_gen_boot_design.Rd | 660 +- man/as_random_group_jackknife_design.Rd | 462 - man/as_sdr_design.Rd | 346 - man/assign_hadamard_rows.Rd | 164 man/calibrate_to_estimate.Rd | 348 - man/calibrate_to_sample.Rd | 354 - man/draw_antal_tille_resample.Rd | 58 man/draw_doubled_half_sample.Rd | 52 man/estimate_boot_reps_for_target_cv.Rd | 270 man/estimate_boot_sim_cv.Rd | 220 man/get_design_quad_form.Rd | 400 - man/get_nearest_psd_matrix.Rd | 84 man/get_rep_scale_coefs.Rd | 152 man/get_rep_type.Rd | 84 man/ht_matrix_to_joint_probs.Rd | 52 man/is_psd_matrix.Rd | 86 man/libraries.Rd | 198 man/lou_pums_microdata.Rd | 108 man/lou_vax_survey.Rd | 62 man/lou_vax_survey_control_totals.Rd | 76 man/make_deville_tille_matrix.Rd | 124 man/make_doubled_half_bootstrap_weights.Rd | 248 man/make_fays_gen_rep_factors.Rd | 374 - man/make_gen_boot_factors.Rd | 388 - man/make_kernel_var_matrix.Rd | 176 man/make_ppswor_approx_matrix.Rd | 184 man/make_quad_form_matrix.Rd | 422 - man/make_rwyb_bootstrap_weights.Rd | 422 - man/make_sd_matrix.Rd | 78 man/make_sdr_replicate_factors.Rd | 132 man/make_twophase_quad_form.Rd | 618 - man/redistribute_weights.Rd | 136 man/rescale_replicates.Rd | 286 man/shuffle_replicates.Rd | 100 man/stack_replicate_designs.Rd | 140 man/subsample_replicates.Rd | 162 man/summarize_rep_weights.Rd | 194 man/svrep-package-options.Rd | 154 man/svrep-package.Rd | 5 man/svyby_repwts.Rd | 270 man/variance-estimators.Rd | 534 - tests/testthat/test-accessor-functions.R | 86 tests/testthat/test-add_inactive_replicates.R | 294 tests/testthat/test-doubled_half_bootstrap.R | 672 +- tests/testthat/test-fays-generalized-replication.R | 1134 +-- tests/testthat/test-quadratic-forms.R | 1708 ++--- tests/testthat/test-quadratic_forms_of_survey_design_objects.R | 544 - tests/testthat/test-rwyb_bootstrap.R | 796 +- vignettes/bootstrap-replicates.Rmd | 1434 ++-- vignettes/two-phase-sampling.Rmd | 1928 +++--- 89 files changed, 18978 insertions(+), 18899 deletions(-)
Title: Rolling Eigenanalysis
Description: Fast and efficient computation of rolling and expanding
eigenanalysis for time-series data. The 'rolleigen' package decomposes
the covariance matrix of the explanatory variables into eigenvalues
and eigenvectors to perform principal component analysis (Pearson,
1901, <doi:10.1080/14786440109462720>; Hotelling, 1933,
<doi:10.1037/h0071325>) and principal component regression (Massy,
1965, <doi:10.1080/01621459.1965.10480787>) over rolling and expanding
windows. For each window, the eigenvalues and eigenvectors are
computed from the covariance matrix and, optionally, ordered from the
largest to smallest eigenvalue to summarize the directions of greatest
variation in the data. A subset of leading components is then used to
fit a regression that mitigates collinearity in the explanatory
variables. Use cases include dimensionality reduction, factor
extraction, and regression on collinear explanatory variables. The
package supports rolling and expanding windows, weights, a [...truncated...]
Author: Jason Foster [aut, cre]
Maintainer: Jason Foster <jason.j.foster@gmail.com>
Diff between rolleigen versions 1.0.0 dated 2026-06-19 and 1.0.1 dated 2026-10-11
DESCRIPTION | 32 +- MD5 | 28 +- NAMESPACE | 6 NEWS.md | 8 R/rolleigen.R | 238 +++++++++--------- README.md | 176 ++++++------- build/partial.rdb |binary inst/include/rolleigen.h | 9 man/rolleigen-package.Rd | 46 +-- tests/testthat.R | 6 tests/testthat/helper-data.R | 60 ++-- tests/testthat/helper-eigen.R | 236 ++++++++++------- tests/testthat/helper-pcr.R | 552 +++++++++++++++++++++--------------------- tests/testthat/test-eigen.R | 105 +++++-- tests/testthat/test-pcr.R | 108 ++++---- 15 files changed, 843 insertions(+), 767 deletions(-)
Title: A Future API for Parallel Processing using 'callr'
Description: Implementation of the Future API <doi:10.32614/RJ-2021-048> on top of the 'callr' package. This allows you to process futures, as defined by the 'future' package, in parallel out of the box, on your local (Linux, macOS, Windows, ...) machine. Contrary to backends relying on the 'parallel' package (e.g. 'future::multisession') and socket connections, the 'callr' backend provided here can run more than 125 parallel R processes.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.callr versions 1.0.0 dated 2026-06-22 and 1.0.1 dated 2026-10-11
DESCRIPTION | 8 +-- MD5 | 70 ++++++++++++++++------------ NAMESPACE | 48 ++++++++++--------- NEWS.md | 19 +++++++ R/CallrFutureBackend-class.R | 42 +++++++++++++++- R/utils-debug.R | 3 - build/vignette.rds |binary inst/doc/future.callr.html | 18 ++++--- inst/testme/deploy.R | 21 ++------ inst/testme/run.R | 16 ++++++ inst/testme/test-callr,backend-validation.R |only inst/testme/test-callr,call-stack.R |only inst/testme/test-callr,cancel-interrupt.R |only inst/testme/test-callr,conditions.R |only inst/testme/test-callr,connections.R |only inst/testme/test-callr,timeout.R |only inst/testme/test-callr,worker-termination.R | 17 ++++++ inst/testme/test-utils.R | 18 +++++++ man/callr.Rd | 6 ++ tests/test-callr,backend-validation.R |only tests/test-callr,call-stack.R |only tests/test-callr,cancel-interrupt.R |only tests/test-callr,conditions.R |only tests/test-callr,connections.R |only tests/test-callr,launch-failure.R | 1 tests/test-callr,timeout.R |only tests/test-callr,worker-termination.R | 1 tests/test-demo.R | 1 tests/test-dotdotdot.R | 1 tests/test-future,labels.R | 1 tests/test-future,lazy.R | 1 tests/test-globals,formulas.R | 1 tests/test-globals,manual.R | 1 tests/test-globals,subassignment.R | 1 tests/test-globals,tricky.R | 1 tests/test-immediateCondition.R | 1 tests/test-nbrOfWorkers.R | 1 tests/test-plan.R | 1 tests/test-rng.R | 1 tests/test-stdout.R | 1 tests/test-utils.R | 1 tests/test-zzz,future_lapply.R | 1 42 files changed, 220 insertions(+), 83 deletions(-)
Title: File-Backed Array for Out-of-Memory Computation
Description: Stores large arrays in files to avoid occupying large
memories. Implemented with super fast gigabyte-level multi-threaded
reading/writing via 'OpenMP'. Supports multiple non-character data
types (double, float, complex, integer, logical, and raw).
Author: Zhengjia Wang [aut, cre, cph]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between filearray versions 0.2.3 dated 2026-08-21 and 0.2.4 dated 2026-10-11
DESCRIPTION | 8 MD5 | 55 ++-- NAMESPACE | 13 - NEWS.md | 16 + R/RcppExports.R | 36 ++ R/bind.R | 7 R/class-filearray.R | 193 +++++++++------ R/filearray-package.R | 6 R/lock.R | 423 +++++++++++++++++++++++++++++++++ R/method-map.R | 17 + R/methods-subsetAssign.R | 26 -- R/write.R | 149 +++++++++++ man/FileArray-class.Rd | 64 ++++ man/S3-filearray.Rd | 6 man/with_filelock.Rd |only src/RcppExports.cpp | 111 ++++++++ src/conversion.cpp | 6 src/core.cpp | 68 +++-- src/load.cpp | 13 - src/lock.cpp |only src/lock.h |only src/lockExports.cpp |only src/map.cpp | 63 +++- src/mapreduce.cpp | 25 + src/save.cpp | 2 src/serialize.cpp | 53 ++-- src/utils.cpp | 14 - tests/testthat/helper-lock.R |only tests/testthat/test-filelock.R |only tests/testthat/test-lock-process.R |only tests/testthat/test-lock.R |only tests/testthat/test-map.R | 111 ++++++++ tests/testthat/test-partition-create.R |only 33 files changed, 1268 insertions(+), 217 deletions(-)
Title: Machine Learning in R
Description: Interface to a large number of classification and regression
techniques, including machine-readable parameter descriptions. There
is also an experimental extension for survival analysis, clustering
and general, example-specific cost-sensitive learning. Generic
resampling, including cross-validation, bootstrapping and subsampling.
Hyperparameter tuning with modern optimization techniques, for single-
and multi-objective problems. Filter and wrapper methods for feature
selection. Extension of basic learners with additional operations
common in machine learning, also allowing for easy nested resampling.
Most operations can be parallelized.
Author: Bernd Bischl [aut] ,
Michel Lang [aut] ,
Lars Kotthoff [aut],
Patrick Schratz [aut] ,
Julia Schiffner [aut],
Jakob Richter [aut],
Zachary Jones [aut],
Giuseppe Casalicchio [aut] ,
Mason Gallo [aut],
Jakob Bossek [ctb] ,
Erich Studerus [ctb] ,
Leonard [...truncated...]
Maintainer: Martin Binder <mlr.developer@mb706.com>
Diff between mlr versions 2.19.3 dated 2025-08-22 and 2.19.4 dated 2026-10-11
mlr-2.19.3/mlr/tests/testthat/xgboost.model |only mlr-2.19.4/mlr/DESCRIPTION | 6 +- mlr-2.19.4/mlr/MD5 | 63 +++++++++++++-------------- mlr-2.19.4/mlr/NEWS.md | 11 ++++ mlr-2.19.4/mlr/R/ClassifTask.R | 2 mlr-2.19.4/mlr/R/ClusterTask.R | 2 mlr-2.19.4/mlr/R/CostSensTask.R | 10 +++- mlr-2.19.4/mlr/R/MultilabelTask.R | 2 mlr-2.19.4/mlr/R/RLearner_regr_km.R | 14 +++++- mlr-2.19.4/mlr/R/RegrTask.R | 2 mlr-2.19.4/mlr/R/SurvTask.R | 2 mlr-2.19.4/mlr/R/Task.R | 51 +-------------------- mlr-2.19.4/mlr/R/TuneControl.R | 25 ---------- mlr-2.19.4/mlr/R/TuneControlCMAES.R | 5 +- mlr-2.19.4/mlr/R/TuneControlDesign.R | 3 - mlr-2.19.4/mlr/R/TuneControlGenSA.R | 3 - mlr-2.19.4/mlr/R/TuneControlGrid.R | 3 - mlr-2.19.4/mlr/R/TuneControlIrace.R | 3 - mlr-2.19.4/mlr/R/TuneControlMBO.R | 3 - mlr-2.19.4/mlr/R/TuneControlRandom.R | 3 - mlr-2.19.4/mlr/R/TuneMultiCritControl.R | 2 mlr-2.19.4/mlr/R/batchmark.R | 8 +-- mlr-2.19.4/mlr/R/crossover.R | 2 mlr-2.19.4/mlr/R/datasets.R | 4 - mlr-2.19.4/mlr/R/getFeatureImportance.R | 2 mlr-2.19.4/mlr/build/partial.rdb |binary mlr-2.19.4/mlr/build/vignette.rds |binary mlr-2.19.4/mlr/man/Task.Rd | 62 +------------------------- mlr-2.19.4/mlr/man/TuneControl.Rd | 56 ------------------------ mlr-2.19.4/mlr/man/crossover.Rd | 4 + mlr-2.19.4/mlr/man/mlrFamilies.Rd | 4 + mlr-2.19.4/mlr/man/pid.task.Rd | 4 - mlr-2.19.4/mlr/tests/testthat/test_regr_km.R | 18 +++++++ 33 files changed, 135 insertions(+), 244 deletions(-)
Title: Nadaraya-Watson Kernel Regression
Description: Fast implementation of Nadaraya-Watson kernel regression for either univariate or multivariate responses, with one or more bandwidths. K-fold cross-validation is also performed.
Author: Michail Tsagris [aut, cre],
Christos Adam [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between kernreg versions 1.0 dated 2026-02-16 and 1.1 dated 2026-10-11
kernreg-1.0/kernreg/src/Makevars.win |only kernreg-1.1/kernreg/DESCRIPTION | 8 ++++---- kernreg-1.1/kernreg/MD5 | 5 ++--- kernreg-1.1/kernreg/src/kern_reg_cpp.cpp | 5 +---- 4 files changed, 7 insertions(+), 11 deletions(-)
Title: Grouped Hyper Data Frame
Description: Extensions of "hyper data frame" (from package 'spatstat.geom') with a grouping structure. The author has retired from academic research. Accordingly, this package should not be considered a validated tool for use in peer-reviewed publications or as the basis for grant applications. Backward compatibility with user-code published in <doi:10.1093/bioinformatics/btaf430> is not maintained in versions >= 0.4.0 (June 2026) of this package. The authors of those publications are the appropriate contacts for reproducibility inquiries.
Author: Tingting Zhan [aut, cre]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between groupedHyperframe versions 0.4.5 dated 2026-08-25 and 0.4.6 dated 2026-10-11
DESCRIPTION | 10 +++++----- MD5 | 3 ++- README.md |only 3 files changed, 7 insertions(+), 6 deletions(-)
More information about groupedHyperframe at CRAN
Permanent link
Title: Object-Oriented Implementation of Dose Escalation Designs
Description: Implements a wide range of dose escalation
designs. The focus is on model-based designs, ranging from classical and
modern continual reassessment methods (CRMs) based on dose-limiting toxicity
endpoints to dual-endpoint designs taking into account a biomarker/efficacy
outcome. Bayesian inference is performed via MCMC sampling in JAGS, and it is easy
to setup a new design with custom JAGS code. However, it is also possible to
implement 3+3 designs for comparison or models with non-Bayesian estimation.
The whole package is written in a modular form in the S4 class system, making it
very flexible for adaptation to new models, escalation or stopping rules.
Further details are presented in
Sabanés Bové et al. (2019) <doi:10.18637/jss.v089.i10>.
Author: Daniel Sabanes Bove [aut, cre] ,
Wai Yin Yeung [aut],
Burak Kuersad Guenhan [aut],
Giuseppe Palermo [aut],
Thomas Jaki [aut],
Jiawen Zhu [aut],
Ziwei Liao [aut],
Dimitris Kontos [aut],
Marlene Schulte-Goebel [aut],
Doug Kelkhoff [aut] ,
Oliver Boix [ [...truncated...]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@rconis.com>
Diff between crmPack versions 2.2.1 dated 2026-07-27 and 2.3.0 dated 2026-10-11
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Title: Structural Equation Modeling and Twin Modeling in R
Description: Quickly create, run, and report structural equation and twin models.
See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS.
Citations are:
* Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R. Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.
* Luis F.S. Castro-de-Araujo, Nathan A. Gillespie, Michael C. Neale, and Timothy Charles Bates (2026). umx version 4.5: Extending Twin and Path-Based SEM in R with CLPM, MR-DoC, Definition Variables, Onyx Integration, and Censored Distributions. Twin Research and Human Genetics, 1-6. <doi:10.1017/thg.2026.10056>.
Author: Timothy C. Bates [aut, cre] ,
Luis De Araujo [ctb],
Nathan Gillespie [wit],
Hermine Maes [ctb],
Michael C. Neale [ctb],
Joshua N. Pritikin [ctb],
Brenton Wiernik [ctb],
Michael Zakharin [wit]
Maintainer: Timothy C. Bates <timothy.c.bates@gmail.com>
Diff between umx versions 4.65.0 dated 2026-05-18 and 4.80.0 dated 2026-10-11
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umx-4.80.0/umx/DESCRIPTION | 23 umx-4.80.0/umx/INSTALL | 1 umx-4.80.0/umx/MD5 | 961 +- umx-4.80.0/umx/NAMESPACE | 360 - umx-4.80.0/umx/NEWS.md | 106 umx-4.80.0/umx/R/TRHG_code.R | 3 umx-4.80.0/umx/R/build_run_modify.R | 3401 ---------- umx-4.80.0/umx/R/datasets.R | 190 umx-4.80.0/umx/R/double_entry.R |only umx-4.80.0/umx/R/fin_volatility_helper.R |only umx-4.80.0/umx/R/financial_functions.R | 1236 ++- umx-4.80.0/umx/R/fit_and_reporting.R | 2327 +++--- umx-4.80.0/umx/R/gh.R |only umx-4.80.0/umx/R/lavanify2ram.R | 39 umx-4.80.0/umx/R/misc_and_utility.R | 3332 +++++++-- umx-4.80.0/umx/R/package.R | 13 umx-4.80.0/umx/R/tmx.R | 132 umx-4.80.0/umx/R/umx-package.R |only umx-4.80.0/umx/R/umxAPA.R |only umx-4.80.0/umx/R/umxCLPM.R | 7 umx-4.80.0/umx/R/umxCloud.R |only umx-4.80.0/umx/R/umxCompare.R |only umx-4.80.0/umx/R/umxDoC.R | 34 umx-4.80.0/umx/R/umxDoCbyPath.R | 37 umx-4.80.0/umx/R/umxGSEM.R |only umx-4.80.0/umx/R/umxGSEM_std.R |only umx-4.80.0/umx/R/umxLISREL.R |only umx-4.80.0/umx/R/umxMRDoC.R | 8 umx-4.80.0/umx/R/umxMatrixFree.R | 1 umx-4.80.0/umx/R/umxMeasurementInvariance.R |only umx-4.80.0/umx/R/umxPower.R | 15 umx-4.80.0/umx/R/umxRAM.R |only umx-4.80.0/umx/R/umxRAM_DE.R |only umx-4.80.0/umx/R/umxRAM_GLM.R |only umx-4.80.0/umx/R/umxSummary.MxModel.R |only umx-4.80.0/umx/R/umx_ICA_report.R |only umx-4.80.0/umx/R/umx_build_high_level_models.R | 66 umx-4.80.0/umx/R/umx_build_polychoricMatrix3.R | 404 - umx-4.80.0/umx/R/umx_build_umxACE.R |only umx-4.80.0/umx/R/umx_build_umxACEv.R | 21 umx-4.80.0/umx/R/umx_build_umxCP.R |only umx-4.80.0/umx/R/umx_build_umxGxE.R |only umx-4.80.0/umx/R/umx_build_umxGxEbiv.R | 8 umx-4.80.0/umx/R/umx_build_umxIP.R |only umx-4.80.0/umx/R/umx_build_umxSexLim.R | 278 umx-4.80.0/umx/R/umx_build_umxSimplex.R | 14 umx-4.80.0/umx/R/umx_data.R |only umx-4.80.0/umx/R/umx_fit_stash_CIs.R | 4 umx-4.80.0/umx/R/umx_fit_umxFitIndices.R | 1 umx-4.80.0/umx/R/xmu.R | 1211 ++- umx-4.80.0/umx/R/xmuGSEM.R |only umx-4.80.0/umx/R/xmuWLS.R |only umx-4.80.0/umx/R/xmu_build_model_helpers.R |only umx-4.80.0/umx/R/xmu_make_top_twin_models.R | 47 umx-4.80.0/umx/R/xmu_robust_SB_savalei.R |only umx-4.80.0/umx/README.md | 15 umx-4.80.0/umx/build/partial.rdb |binary umx-4.80.0/umx/build/vignette.rds |only umx-4.80.0/umx/data/Anthro_LDSC.rda |only umx-4.80.0/umx/data/HSwls.rda |only umx-4.80.0/umx/data/Psych_LDSC.rda |only umx-4.80.0/umx/inst/CITATION | 4 umx-4.80.0/umx/inst/WORDLIST | 221 umx-4.80.0/umx/inst/doc |only umx-4.80.0/umx/man/Anthro_LDSC.Rd |only umx-4.80.0/umx/man/Fischbein_wt.Rd | 5 umx-4.80.0/umx/man/FishersMethod.Rd | 40 umx-4.80.0/umx/man/GFF.Rd | 5 umx-4.80.0/umx/man/HSwls.Rd |only umx-4.80.0/umx/man/Psych_LDSC.Rd |only umx-4.80.0/umx/man/RMSEA.MxModel.Rd | 37 umx-4.80.0/umx/man/RMSEA.Rd | 33 umx-4.80.0/umx/man/RMSEA.summary.mxmodel.Rd | 37 umx-4.80.0/umx/man/SE_from_p.Rd | 34 umx-4.80.0/umx/man/aic_weights.Rd |only umx-4.80.0/umx/man/bucks.Rd | 6 umx-4.80.0/umx/man/calculateStrictSb.Rd |only umx-4.80.0/umx/man/deg2rad.Rd | 20 umx-4.80.0/umx/man/dl_from_dropbox.Rd | 16 umx-4.80.0/umx/man/docData.Rd | 11 umx-4.80.0/umx/man/extractAIC.MxModel.Rd | 33 umx-4.80.0/umx/man/fin_options_Greeks.Rd |only umx-4.80.0/umx/man/fin_options_LeapSimulate.Rd |only umx-4.80.0/umx/man/fin_options_plotGreeks.Rd |only umx-4.80.0/umx/man/fin_options_teach.Rd |only umx-4.80.0/umx/man/fin_resolveVolatility.Rd |only umx-4.80.0/umx/man/fin_stock_CAGR.Rd |only umx-4.80.0/umx/man/fin_stock_justifiedPE.Rd |only umx-4.80.0/umx/man/fin_stock_target.Rd |only umx-4.80.0/umx/man/fin_stock_ticker.Rd |only umx-4.80.0/umx/man/fin_stock_valuation.Rd |only umx-4.80.0/umx/man/fin_tax_FIF.Rd |only umx-4.80.0/umx/man/fin_tax_NI.Rd |only umx-4.80.0/umx/man/fin_value_CAGR.Rd |only umx-4.80.0/umx/man/fin_value_CarryCost.Rd |only umx-4.80.0/umx/man/fin_value_NPV.Rd |only umx-4.80.0/umx/man/fin_value_interest.Rd |only umx-4.80.0/umx/man/fin_value_percent.Rd |only umx-4.80.0/umx/man/geometric_mean.Rd | 81 umx-4.80.0/umx/man/ggAddR.Rd | 36 umx-4.80.0/umx/man/gh_feature_branch.Rd |only umx-4.80.0/umx/man/gh_message_search.Rd |only umx-4.80.0/umx/man/gh_open_PR_url.Rd |only umx-4.80.0/umx/man/harmonic_mean.Rd | 58 umx-4.80.0/umx/man/install.OpenMx.Rd | 106 umx-4.80.0/umx/man/iqdat.Rd | 33 umx-4.80.0/umx/man/libs.Rd | 40 umx-4.80.0/umx/man/loadings.MxModel.Rd | 37 umx-4.80.0/umx/man/loadings.Rd | 37 umx-4.80.0/umx/man/mx_make.Rd |only umx-4.80.0/umx/man/noNAs.Rd | 51 umx-4.80.0/umx/man/oddsratio.Rd | 38 umx-4.80.0/umx/man/plot.MxLISRELModel.Rd | 65 umx-4.80.0/umx/man/plot.MxModel.Rd | 62 umx-4.80.0/umx/man/plot.MxModelTwinMaker.Rd | 36 umx-4.80.0/umx/man/plot.percent.Rd | 10 umx-4.80.0/umx/man/plot.umx_GWAS.Rd |only umx-4.80.0/umx/man/power.ACE.test.Rd | 70 umx-4.80.0/umx/man/print.percent.Rd | 10 umx-4.80.0/umx/man/prolific_anonymize.Rd | 57 umx-4.80.0/umx/man/prolific_check_ID.Rd | 59 umx-4.80.0/umx/man/prolific_read_demog.Rd | 55 umx-4.80.0/umx/man/prolific_scoring_stub.Rd |only umx-4.80.0/umx/man/qm.Rd | 39 umx-4.80.0/umx/man/rad2deg.Rd | 20 umx-4.80.0/umx/man/reliability.Rd | 40 umx-4.80.0/umx/man/residuals.MxModel.Rd | 37 umx-4.80.0/umx/man/tmx_genotypic_effect.Rd | 10 umx-4.80.0/umx/man/tmx_is.identified.Rd | 15 umx-4.80.0/umx/man/tmx_show.MxMatrix.Rd | 33 umx-4.80.0/umx/man/tmx_show.MxModel.Rd | 14 umx-4.80.0/umx/man/tmx_show.MxModelGSEM.Rd |only umx-4.80.0/umx/man/tmx_show.Rd | 33 umx-4.80.0/umx/man/tvars.Rd |only umx-4.80.0/umx/man/umx.Rd | 460 - umx-4.80.0/umx/man/umxACE.Rd | 69 umx-4.80.0/umx/man/umxACE_DE.Rd |only umx-4.80.0/umx/man/umxACE_GLM.Rd |only umx-4.80.0/umx/man/umxACEcov.Rd | 76 umx-4.80.0/umx/man/umxACEv.Rd | 68 umx-4.80.0/umx/man/umxAPA.Rd | 54 umx-4.80.0/umx/man/umxAlgebra.Rd | 17 umx-4.80.0/umx/man/umxBrownie.Rd | 20 umx-4.80.0/umx/man/umxCI.Rd | 37 umx-4.80.0/umx/man/umxCI_boot.Rd | 33 umx-4.80.0/umx/man/umxCLPM.Rd | 6 umx-4.80.0/umx/man/umxCP.Rd | 68 umx-4.80.0/umx/man/umxCloud.Rd |only umx-4.80.0/umx/man/umxCompare.Rd | 100 umx-4.80.0/umx/man/umxConfint.Rd | 37 umx-4.80.0/umx/man/umxCov2cor.Rd | 38 umx-4.80.0/umx/man/umxDiagnose.Rd | 10 umx-4.80.0/umx/man/umxDiffMZ.Rd | 65 umx-4.80.0/umx/man/umxDiscTwin.Rd | 63 umx-4.80.0/umx/man/umxDoC.Rd | 66 umx-4.80.0/umx/man/umxDoCp.Rd | 61 umx-4.80.0/umx/man/umxEFA.Rd | 49 umx-4.80.0/umx/man/umxEquate.Rd | 18 umx-4.80.0/umx/man/umxExamples.Rd | 4 umx-4.80.0/umx/man/umxExpCov.Rd | 33 umx-4.80.0/umx/man/umxExpMeans.Rd | 33 umx-4.80.0/umx/man/umxFactor.Rd | 67 umx-4.80.0/umx/man/umxFactorScores.Rd | 27 umx-4.80.0/umx/man/umxFitIndices.Rd | 33 umx-4.80.0/umx/man/umxFixAll.Rd | 21 umx-4.80.0/umx/man/umxGSEM.Rd |only umx-4.80.0/umx/man/umxGSEM_GWAS.Rd |only umx-4.80.0/umx/man/umxGSEM_dl_tutorial_files.Rd |only umx-4.80.0/umx/man/umxGSEM_label_ldsc.Rd |only umx-4.80.0/umx/man/umxGSEM_ldsc.Rd |only umx-4.80.0/umx/man/umxGSEM_munge.Rd |only umx-4.80.0/umx/man/umxGSEM_sim_snps.Rd |only umx-4.80.0/umx/man/umxGSEM_std.Rd |only umx-4.80.0/umx/man/umxGSEM_sumstats.Rd |only umx-4.80.0/umx/man/umxGetLatents.Rd | 20 umx-4.80.0/umx/man/umxGetManifests.Rd | 20 umx-4.80.0/umx/man/umxGetModel.Rd | 20 umx-4.80.0/umx/man/umxGetParameters.Rd | 24 umx-4.80.0/umx/man/umxGxE.Rd | 133 umx-4.80.0/umx/man/umxGxE_window.Rd | 72 umx-4.80.0/umx/man/umxGxEbiv.Rd | 61 umx-4.80.0/umx/man/umxHetCor.Rd | 91 umx-4.80.0/umx/man/umxIP.Rd | 69 umx-4.80.0/umx/man/umxJiggle.Rd | 21 umx-4.80.0/umx/man/umxLISREL.Rd |only umx-4.80.0/umx/man/umxLav2RAM.Rd | 35 umx-4.80.0/umx/man/umxMI.Rd | 29 umx-4.80.0/umx/man/umxMRDoC.Rd | 63 umx-4.80.0/umx/man/umxMatrix.Rd | 16 umx-4.80.0/umx/man/umxMeasurementInvariance.Rd |only umx-4.80.0/umx/man/umxModel.Rd | 191 umx-4.80.0/umx/man/umxModelNames.Rd | 35 umx-4.80.0/umx/man/umxModify.Rd | 20 umx-4.80.0/umx/man/umxParameters.Rd | 24 umx-4.80.0/umx/man/umxParan.Rd | 40 umx-4.80.0/umx/man/umxPath.Rd | 29 umx-4.80.0/umx/man/umxPlot.Rd | 46 umx-4.80.0/umx/man/umxPlotACE.Rd | 40 umx-4.80.0/umx/man/umxPlotACE_DE.Rd |only umx-4.80.0/umx/man/umxPlotACE_GLM.Rd |only umx-4.80.0/umx/man/umxPlotACEcov.Rd | 40 umx-4.80.0/umx/man/umxPlotACEv.Rd | 40 umx-4.80.0/umx/man/umxPlotCP.Rd | 48 umx-4.80.0/umx/man/umxPlotDoC.Rd | 40 umx-4.80.0/umx/man/umxPlotFun.Rd | 42 umx-4.80.0/umx/man/umxPlotGxE.Rd | 40 umx-4.80.0/umx/man/umxPlotGxEbiv.Rd | 40 umx-4.80.0/umx/man/umxPlotIP.Rd | 43 umx-4.80.0/umx/man/umxPlotPredict.Rd | 49 umx-4.80.0/umx/man/umxPlotSexLim.Rd | 43 umx-4.80.0/umx/man/umxPlotSimplex.Rd | 36 umx-4.80.0/umx/man/umxPower.Rd | 8 umx-4.80.0/umx/man/umxPrint_double_entry_data.Rd |only umx-4.80.0/umx/man/umxRAM.Rd | 104 umx-4.80.0/umx/man/umxRAM2Lav.Rd | 41 umx-4.80.0/umx/man/umxRAM_DE.Rd |only umx-4.80.0/umx/man/umxRAM_GLM.Rd |only umx-4.80.0/umx/man/umxReduce.Rd | 79 umx-4.80.0/umx/man/umxReduceACE.Rd | 65 umx-4.80.0/umx/man/umxReduceGxE.Rd | 65 umx-4.80.0/umx/man/umxRenameMatrix.Rd | 185 umx-4.80.0/umx/man/umxRotate.MxModelCP.Rd | 62 umx-4.80.0/umx/man/umxRotate.Rd | 33 umx-4.80.0/umx/man/umxRun.Rd | 21 umx-4.80.0/umx/man/umxSetParameters.Rd | 18 umx-4.80.0/umx/man/umxSexLim.Rd | 66 umx-4.80.0/umx/man/umxSimplex.Rd | 65 umx-4.80.0/umx/man/umxSummarizeTwinData.Rd | 75 umx-4.80.0/umx/man/umxSummary.MxDataStatic.Rd |only umx-4.80.0/umx/man/umxSummary.MxLISRELModel.Rd |only umx-4.80.0/umx/man/umxSummary.MxModel.Rd | 112 umx-4.80.0/umx/man/umxSummary.MxModelGLM.Rd |only umx-4.80.0/umx/man/umxSummary.Rd | 18 umx-4.80.0/umx/man/umxSummary.list.Rd |only umx-4.80.0/umx/man/umxSummaryACE.Rd | 65 umx-4.80.0/umx/man/umxSummaryACE_DE.Rd |only umx-4.80.0/umx/man/umxSummaryACE_GLM.Rd |only umx-4.80.0/umx/man/umxSummaryACEcov.Rd | 16 umx-4.80.0/umx/man/umxSummaryACEv.Rd | 65 umx-4.80.0/umx/man/umxSummaryCP.Rd | 16 umx-4.80.0/umx/man/umxSummaryDoC.Rd | 61 umx-4.80.0/umx/man/umxSummaryGxE.Rd | 16 umx-4.80.0/umx/man/umxSummaryGxEbiv.Rd | 65 umx-4.80.0/umx/man/umxSummaryIP.Rd | 16 umx-4.80.0/umx/man/umxSummaryMRDoC.Rd | 12 umx-4.80.0/umx/man/umxSummarySexLim.Rd | 66 umx-4.80.0/umx/man/umxSummarySimplex.Rd | 65 umx-4.80.0/umx/man/umxSuperModel.Rd | 26 umx-4.80.0/umx/man/umxThresholdMatrix.Rd | 21 umx-4.80.0/umx/man/umxTwinMaker.Rd | 81 umx-4.80.0/umx/man/umxTwoStage.Rd | 21 umx-4.80.0/umx/man/umxUnexplainedCausalNexus.Rd | 21 umx-4.80.0/umx/man/umxVersion.Rd | 44 umx-4.80.0/umx/man/umxWeightedAIC.Rd | 42 umx-4.80.0/umx/man/umx_APA_pval.Rd | 185 umx-4.80.0/umx/man/umx_ICA_report.Rd |only umx-4.80.0/umx/man/umx_aggregate.Rd | 44 umx-4.80.0/umx/man/umx_apply.Rd | 43 umx-4.80.0/umx/man/umx_array_shift.Rd | 35 umx-4.80.0/umx/man/umx_as_numeric.Rd | 59 umx-4.80.0/umx/man/umx_check.Rd | 33 umx-4.80.0/umx/man/umx_check_OS.Rd | 33 umx-4.80.0/umx/man/umx_check_model.Rd | 39 umx-4.80.0/umx/man/umx_check_names.Rd | 49 umx-4.80.0/umx/man/umx_check_parallel.Rd | 35 umx-4.80.0/umx/man/umx_complete_dollar.Rd |only umx-4.80.0/umx/man/umx_cont_2_quantiles.Rd | 68 umx-4.80.0/umx/man/umx_cor.Rd | 51 umx-4.80.0/umx/man/umx_data.Rd |only umx-4.80.0/umx/man/umx_detect_cores.Rd |only umx-4.80.0/umx/man/umx_explode.Rd | 22 umx-4.80.0/umx/man/umx_explode_twin_names.Rd | 26 umx-4.80.0/umx/man/umx_file_load_pseudo.Rd | 14 umx-4.80.0/umx/man/umx_find_object.Rd | 42 umx-4.80.0/umx/man/umx_fun_mean_sd.Rd | 189 umx-4.80.0/umx/man/umx_get_bracket_addresses.Rd | 189 umx-4.80.0/umx/man/umx_get_checkpoint.Rd | 40 umx-4.80.0/umx/man/umx_get_options.Rd | 39 umx-4.80.0/umx/man/umx_grep.Rd | 22 umx-4.80.0/umx/man/umx_has_CIs.Rd | 33 umx-4.80.0/umx/man/umx_has_been_run.Rd | 33 umx-4.80.0/umx/man/umx_has_means.Rd | 33 umx-4.80.0/umx/man/umx_has_square_brackets.Rd | 34 umx-4.80.0/umx/man/umx_is_GSEM.Rd |only umx-4.80.0/umx/man/umx_is_LISREL.Rd |only umx-4.80.0/umx/man/umx_is_MxData.Rd | 37 umx-4.80.0/umx/man/umx_is_MxMatrix.Rd | 33 umx-4.80.0/umx/man/umx_is_MxModel.Rd | 33 umx-4.80.0/umx/man/umx_is_RAM.Rd | 33 umx-4.80.0/umx/man/umx_is_class.Rd | 16 umx-4.80.0/umx/man/umx_is_cov.Rd | 35 umx-4.80.0/umx/man/umx_is_endogenous.Rd | 16 umx-4.80.0/umx/man/umx_is_exogenous.Rd | 16 umx-4.80.0/umx/man/umx_is_numeric.Rd | 16 umx-4.80.0/umx/man/umx_is_ordered.Rd | 16 umx-4.80.0/umx/man/umx_long2wide.Rd | 18 umx-4.80.0/umx/man/umx_lower.tri.Rd | 35 umx-4.80.0/umx/man/umx_lower2full.Rd | 63 umx-4.80.0/umx/man/umx_make.Rd | 209 umx-4.80.0/umx/man/umx_make_GxE_data.Rd |only umx-4.80.0/umx/man/umx_make_MR_data.Rd | 55 umx-4.80.0/umx/man/umx_make_TwinData.Rd | 134 umx-4.80.0/umx/man/umx_make_double_entry_data.Rd |only umx-4.80.0/umx/man/umx_make_fake_data.Rd | 71 umx-4.80.0/umx/man/umx_make_raw_from_cov.Rd | 55 umx-4.80.0/umx/man/umx_make_sql_from_excel.Rd | 18 umx-4.80.0/umx/man/umx_make_twin_data_nice.Rd | 18 umx-4.80.0/umx/man/umx_means.Rd | 38 umx-4.80.0/umx/man/umx_merge_randomized_columns.Rd | 51 umx-4.80.0/umx/man/umx_move_file.Rd | 14 umx-4.80.0/umx/man/umx_msg.Rd | 67 umx-4.80.0/umx/man/umx_names.Rd | 38 umx-4.80.0/umx/man/umx_open.Rd | 18 umx-4.80.0/umx/man/umx_open_CRAN_page.Rd | 35 umx-4.80.0/umx/man/umx_pad.Rd | 41 umx-4.80.0/umx/man/umx_polychoric.Rd | 57 umx-4.80.0/umx/man/umx_polypairwise.Rd | 66 umx-4.80.0/umx/man/umx_polytriowise.Rd | 63 umx-4.80.0/umx/man/umx_print.Rd | 35 umx-4.80.0/umx/man/umx_r_test.Rd | 34 umx-4.80.0/umx/man/umx_read_lower.Rd | 55 umx-4.80.0/umx/man/umx_rename.Rd | 51 umx-4.80.0/umx/man/umx_rename_file.Rd | 14 umx-4.80.0/umx/man/umx_reorder.Rd | 57 umx-4.80.0/umx/man/umx_residualize.Rd | 18 umx-4.80.0/umx/man/umx_rot.Rd | 23 umx-4.80.0/umx/man/umx_round.Rd | 38 umx-4.80.0/umx/man/umx_scale.Rd | 38 umx-4.80.0/umx/man/umx_scale_reliabilities.Rd |only umx-4.80.0/umx/man/umx_scale_wide_twin_data.Rd | 18 umx-4.80.0/umx/man/umx_score_scale.Rd | 59 umx-4.80.0/umx/man/umx_select_valid.Rd | 51 umx-4.80.0/umx/man/umx_set_auto_plot.Rd | 39 umx-4.80.0/umx/man/umx_set_auto_run.Rd | 35 umx-4.80.0/umx/man/umx_set_checkpoint.Rd | 50 umx-4.80.0/umx/man/umx_set_condensed_slots.Rd | 39 umx-4.80.0/umx/man/umx_set_cores.Rd | 68 umx-4.80.0/umx/man/umx_set_data_variance_check.Rd | 39 umx-4.80.0/umx/man/umx_set_dollar_symbol.Rd | 45 umx-4.80.0/umx/man/umx_set_optimization_options.Rd | 39 umx-4.80.0/umx/man/umx_set_optimizer.Rd | 58 umx-4.80.0/umx/man/umx_set_plot_file_suffix.Rd | 39 umx-4.80.0/umx/man/umx_set_plot_format.Rd | 39 umx-4.80.0/umx/man/umx_set_separator.Rd | 41 umx-4.80.0/umx/man/umx_set_silent.Rd | 39 umx-4.80.0/umx/man/umx_set_table_format.Rd | 39 umx-4.80.0/umx/man/umx_stack.Rd | 57 umx-4.80.0/umx/man/umx_standardize.Rd | 185 umx-4.80.0/umx/man/umx_str_chars.Rd | 22 umx-4.80.0/umx/man/umx_str_from_object.Rd | 22 umx-4.80.0/umx/man/umx_string_to_algebra.Rd | 189 umx-4.80.0/umx/man/umx_strings2numeric.Rd | 51 umx-4.80.0/umx/man/umx_tail.Rd |only umx-4.80.0/umx/man/umx_time.Rd | 28 umx-4.80.0/umx/man/umx_trim.Rd | 23 umx-4.80.0/umx/man/umx_tutorials.Rd |only umx-4.80.0/umx/man/umx_var.Rd | 38 umx-4.80.0/umx/man/umx_wide2long.Rd | 35 umx-4.80.0/umx/man/umx_wide2longTwinData.Rd | 22 umx-4.80.0/umx/man/umx_wide4lmer.Rd | 40 umx-4.80.0/umx/man/umx_write_to_clipboard.Rd | 14 umx-4.80.0/umx/man/umx_yj_wide_twin_data.Rd | 19 umx-4.80.0/umx/man/us_skinfold_data.Rd | 11 umx-4.80.0/umx/man/xgh_check_base_name.Rd |only umx-4.80.0/umx/man/xgh_get_current_branch.Rd |only umx-4.80.0/umx/man/xgh_git.Rd |only umx-4.80.0/umx/man/xmuCalculateSRMR.Rd |only umx-4.80.0/umx/man/xmuHasSquareBrackets.Rd | 185 umx-4.80.0/umx/man/xmuLabel.Rd | 23 umx-4.80.0/umx/man/xmuLabel_MATRIX_Model.Rd | 185 umx-4.80.0/umx/man/xmuLabel_Matrix.Rd | 185 umx-4.80.0/umx/man/xmuLabel_RAM_Model.Rd | 185 umx-4.80.0/umx/man/xmuMI.Rd | 185 umx-4.80.0/umx/man/xmuMakeOneHeadedPathsFromPathList.Rd | 185 umx-4.80.0/umx/man/xmuMakeTwoHeadedPathsFromPathList.Rd | 185 umx-4.80.0/umx/man/xmuMaxLevels.Rd | 185 umx-4.80.0/umx/man/xmuMinLevels.Rd | 185 umx-4.80.0/umx/man/xmuPropagateLabels.Rd | 185 umx-4.80.0/umx/man/xmuRAM2Ordinal.Rd | 189 umx-4.80.0/umx/man/xmuTwinSuper_Continuous.Rd | 185 umx-4.80.0/umx/man/xmuTwinSuper_NoBinary.Rd | 185 umx-4.80.0/umx/man/xmuTwinUpgradeMeansToCovariateModel.Rd | 185 umx-4.80.0/umx/man/xmuValues.Rd | 23 umx-4.80.0/umx/man/xmu_CI_merge.Rd | 191 umx-4.80.0/umx/man/xmu_CI_stash.Rd | 189 umx-4.80.0/umx/man/xmu_DF_to_mxData_TypeCov.Rd | 189 umx-4.80.0/umx/man/xmu_PadAndPruneForDefVars.Rd | 185 umx-4.80.0/umx/man/xmu_WLS_align_jacobian.Rd |only umx-4.80.0/umx/man/xmu_WLS_align_weight.Rd |only umx-4.80.0/umx/man/xmu_WLS_polycor_names.Rd |only umx-4.80.0/umx/man/xmu_ace_de_apply_censor_thresholds.Rd |only umx-4.80.0/umx/man/xmu_ace_de_parse_censor_meta.Rd |only umx-4.80.0/umx/man/xmu_ace_de_parse_censor_rule.Rd |only umx-4.80.0/umx/man/xmu_ace_de_release_binary_v1.Rd |only umx-4.80.0/umx/man/xmu_bracket_address2rclabel.Rd | 189 umx-4.80.0/umx/man/xmu_catml_df3_diagnostic.Rd |only umx-4.80.0/umx/man/xmu_catml_discrepancy_at_WLS.Rd |only umx-4.80.0/umx/man/xmu_catml_eval_model.Rd |only umx-4.80.0/umx/man/xmu_catml_implied_correlation.Rd |only umx-4.80.0/umx/man/xmu_catml_wls_v.Rd |only umx-4.80.0/umx/man/xmu_cell_is_on.Rd | 189 umx-4.80.0/umx/man/xmu_check_levels_identical.Rd | 185 umx-4.80.0/umx/man/xmu_check_needs_means.Rd | 185 umx-4.80.0/umx/man/xmu_check_variance.Rd | 185 umx-4.80.0/umx/man/xmu_clean_label.Rd | 185 umx-4.80.0/umx/man/xmu_compare_WLS.Rd |only umx-4.80.0/umx/man/xmu_compare_constraint_note.Rd |only umx-4.80.0/umx/man/xmu_compare_robust_ML.Rd |only umx-4.80.0/umx/man/xmu_custom_completer.Rd |only umx-4.80.0/umx/man/xmu_data_missing.Rd | 185 umx-4.80.0/umx/man/xmu_data_swap_a_block.Rd | 185 umx-4.80.0/umx/man/xmu_describe_data_WLS.Rd | 189 umx-4.80.0/umx/man/xmu_dot_define_shapes.Rd | 16 umx-4.80.0/umx/man/xmu_dot_make_paths.Rd | 217 umx-4.80.0/umx/man/xmu_dot_make_residuals.Rd | 217 umx-4.80.0/umx/man/xmu_dot_maker.Rd | 203 umx-4.80.0/umx/man/xmu_dot_mat2dot.Rd | 17 umx-4.80.0/umx/man/xmu_dot_move_ranks.Rd | 185 umx-4.80.0/umx/man/xmu_dot_rank.Rd | 12 umx-4.80.0/umx/man/xmu_dot_rank_str.Rd | 189 umx-4.80.0/umx/man/xmu_equate_threshold_values.Rd | 4 umx-4.80.0/umx/man/xmu_extract_column.Rd | 185 umx-4.80.0/umx/man/xmu_genomicmx_binary_url.Rd |only umx-4.80.0/umx/man/xmu_genomicmx_release_page_url.Rd |only umx-4.80.0/umx/man/xmu_get_CI.Rd | 189 umx-4.80.0/umx/man/xmu_gsem_expand_snp.Rd |only umx-4.80.0/umx/man/xmu_gsem_extract_snp_path.Rd |only umx-4.80.0/umx/man/xmu_gsem_prepare_WLS.Rd |only umx-4.80.0/umx/man/xmu_gsem_subset_covstruc.Rd |only umx-4.80.0/umx/man/xmu_has_summary_mxData.Rd |only umx-4.80.0/umx/man/xmu_invert_matrix.Rd |only umx-4.80.0/umx/man/xmu_is_gsem_covstruc.Rd |only umx-4.80.0/umx/man/xmu_is_ordinal_WLS.Rd |only umx-4.80.0/umx/man/xmu_is_wls.Rd |only umx-4.80.0/umx/man/xmu_lavaan_process_group.Rd | 185 umx-4.80.0/umx/man/xmu_make_TwinSuperModel.Rd | 191 umx-4.80.0/umx/man/xmu_make_bin_cont_pair_data.Rd | 199 umx-4.80.0/umx/man/xmu_make_mxData.Rd | 185 umx-4.80.0/umx/man/xmu_match.arg.Rd | 189 umx-4.80.0/umx/man/xmu_matrix_for_print.Rd |only umx-4.80.0/umx/man/xmu_mxData_summary.Rd |only umx-4.80.0/umx/man/xmu_mxRefModels.Rd |only umx-4.80.0/umx/man/xmu_mx_make_run.Rd |only umx-4.80.0/umx/man/xmu_name_from_lavaan_str.Rd | 189 umx-4.80.0/umx/man/xmu_openmx_engine_status.Rd |only umx-4.80.0/umx/man/xmu_openmx_install_message.Rd |only umx-4.80.0/umx/man/xmu_parse_completion_context.Rd |only umx-4.80.0/umx/man/xmu_path2twin.Rd | 185 umx-4.80.0/umx/man/xmu_path_regex.Rd | 189 umx-4.80.0/umx/man/xmu_print_algebras.Rd | 185 umx-4.80.0/umx/man/xmu_ram_de_apply_censor_thresholds.Rd |only umx-4.80.0/umx/man/xmu_ram_de_parse_censor_meta.Rd |only umx-4.80.0/umx/man/xmu_rclabel_2_bracket_address.Rd | 189 umx-4.80.0/umx/man/xmu_relevel_factors.Rd | 191 umx-4.80.0/umx/man/xmu_require_summary_mxData.Rd |only umx-4.80.0/umx/man/xmu_robust_ML_fit.Rd |only umx-4.80.0/umx/man/xmu_robust_WLS_fit.Rd |only umx-4.80.0/umx/man/xmu_safe_run_summary.Rd | 186 umx-4.80.0/umx/man/xmu_savalei_fit_cfi.Rd |only umx-4.80.0/umx/man/xmu_savalei_fit_rmsea.Rd |only umx-4.80.0/umx/man/xmu_savalei_fit_tli.Rd |only umx-4.80.0/umx/man/xmu_savalei_null_scaling_factor.Rd |only umx-4.80.0/umx/man/xmu_savalei_polycor_blocks.Rd |only umx-4.80.0/umx/man/xmu_savalei_scaling_factor.Rd |only umx-4.80.0/umx/man/xmu_set_sep_from_suffix.Rd | 189 umx-4.80.0/umx/man/xmu_show_fit_or_comparison.Rd | 187 umx-4.80.0/umx/man/xmu_simplex_corner.Rd | 185 umx-4.80.0/umx/man/xmu_standardize_ACE.Rd | 189 umx-4.80.0/umx/man/xmu_standardize_ACEcov.Rd | 189 umx-4.80.0/umx/man/xmu_standardize_ACEv.Rd | 189 umx-4.80.0/umx/man/xmu_standardize_CP.Rd | 189 umx-4.80.0/umx/man/xmu_standardize_IP.Rd | 189 umx-4.80.0/umx/man/xmu_standardize_LISREL.Rd |only umx-4.80.0/umx/man/xmu_standardize_RAM.Rd | 189 umx-4.80.0/umx/man/xmu_standardize_SexLim.Rd | 185 umx-4.80.0/umx/man/xmu_standardize_Simplex.Rd | 189 umx-4.80.0/umx/man/xmu_start_value_list.Rd | 185 umx-4.80.0/umx/man/xmu_starts.Rd | 185 umx-4.80.0/umx/man/xmu_summary_RAM_group_parameters.Rd | 185 umx-4.80.0/umx/man/xmu_threshold_id_RAM.Rd |only umx-4.80.0/umx/man/xmu_threshold_id_twin_check.Rd |only umx-4.80.0/umx/man/xmu_topo_sort.Rd |only umx-4.80.0/umx/man/xmu_twin_add_WeightMatrices.Rd | 185 umx-4.80.0/umx/man/xmu_twin_check.Rd | 189 umx-4.80.0/umx/man/xmu_twin_get_var_names.Rd | 185 umx-4.80.0/umx/man/xmu_twin_make_def_means_mats_and_alg.Rd | 185 umx-4.80.0/umx/man/xmu_twin_upgrade_selDvs2SelVars.Rd | 185 umx-4.80.0/umx/man/xmu_umxSummary_print_matrix.Rd |only umx-4.80.0/umx/man/xmu_update_covar.Rd | 191 umx-4.80.0/umx/man/xmu_utils_completeToken.Rd |only umx-4.80.0/umx/man/xmu_wls_block_diag.Rd |only umx-4.80.0/umx/man/xmu_wls_data_models.Rd |only umx-4.80.0/umx/man/xmu_wls_display_chi.Rd |only umx-4.80.0/umx/man/xmu_wls_extract_WV.Rd |only umx-4.80.0/umx/tests/testthat.R | 22 umx-4.80.0/umx/tests/testthat/Rplots.pdf |only umx-4.80.0/umx/tests/testthat/fixtures |only umx-4.80.0/umx/tests/testthat/test_GSEM_goldens.R |only umx-4.80.0/umx/tests/testthat/test_MLR_fit_and_compare.R |only umx-4.80.0/umx/tests/testthat/test_MxModel_residuals.r |only umx-4.80.0/umx/tests/testthat/test_SRMR-test.r |only umx-4.80.0/umx/tests/testthat/test_WLS_HSwls_catML_scale.R |only umx-4.80.0/umx/tests/testthat/test_WLS_Savalei_lavaan_parity.R |only umx-4.80.0/umx/tests/testthat/test_WLS_chi_consistency.R |only umx-4.80.0/umx/tests/testthat/test_WLS_lavaan.R |only umx-4.80.0/umx/tests/testthat/test_WLS_ordinal_robust.R |only umx-4.80.0/umx/tests/testthat/test_WLS_summary_compare_workflow.R |only umx-4.80.0/umx/tests/testthat/test_WLS_umxCompare_WLS_routing.R |only umx-4.80.0/umx/tests/testthat/test_WLS_umxSummary_WLS_routing.R |only umx-4.80.0/umx/tests/testthat/test_WLS_xmu_compare_WLS.R |only umx-4.80.0/umx/tests/testthat/test_data_HSwls.R |only umx-4.80.0/umx/tests/testthat/test_data_gxeData.R |only umx-4.80.0/umx/tests/testthat/test_datasets_in_umx.r |only umx-4.80.0/umx/tests/testthat/test_double_entry.r |only umx-4.80.0/umx/tests/testthat/test_fin_.r |only umx-4.80.0/umx/tests/testthat/test_lavaan.r | 21 umx-4.80.0/umx/tests/testthat/test_openmx_engine_status.R |only umx-4.80.0/umx/tests/testthat/test_plot.MxLISRELModel.r |only umx-4.80.0/umx/tests/testthat/test_prolific_scoring_stub.R |only umx-4.80.0/umx/tests/testthat/test_umxACE_GLM.R |only umx-4.80.0/umx/tests/testthat/test_umxACE_GLM_vs_threshold.R |only umx-4.80.0/umx/tests/testthat/test_umxAPA.r |only umx-4.80.0/umx/tests/testthat/test_umxAPA_pval.r |only umx-4.80.0/umx/tests/testthat/test_umxBuild_run_modify.r | 47 umx-4.80.0/umx/tests/testthat/test_umxCP.r | 32 umx-4.80.0/umx/tests/testthat/test_umxCloud.R |only umx-4.80.0/umx/tests/testthat/test_umxCompare_constraint_note.R |only umx-4.80.0/umx/tests/testthat/test_umxConfint.r | 2 umx-4.80.0/umx/tests/testthat/test_umxFactorScores.r | 2 umx-4.80.0/umx/tests/testthat/test_umxFitAndReporting.r | 205 umx-4.80.0/umx/tests/testthat/test_umxGSEM_dl_tutorial_files.R |only umx-4.80.0/umx/tests/testthat/test_umxGSEM_ldsc.R |only umx-4.80.0/umx/tests/testthat/test_umxGSEM_std.R |only umx-4.80.0/umx/tests/testthat/test_umxGxE.r |only umx-4.80.0/umx/tests/testthat/test_umxGxE_cov.R |only umx-4.80.0/umx/tests/testthat/test_umxLISREL.r |only umx-4.80.0/umx/tests/testthat/test_umxMeasurementInvariance.R |only umx-4.80.0/umx/tests/testthat/test_umxPath.r | 4 umx-4.80.0/umx/tests/testthat/test_umxPower.r | 2 umx-4.80.0/umx/tests/testthat/test_umxRAM_DE.R |only umx-4.80.0/umx/tests/testthat/test_umxRAM_GLM.R |only umx-4.80.0/umx/tests/testthat/test_umxRAM_etc.r | 57 umx-4.80.0/umx/tests/testthat/test_umxRAM_weight.R |only umx-4.80.0/umx/tests/testthat/test_umx_ACE_etc.r | 37 umx-4.80.0/umx/tests/testthat/test_umx_has_CI.r | 2 umx-4.80.0/umx/tests/testthat/test_umx_has_means.r | 8 umx-4.80.0/umx/tests/testthat/test_umx_lower2full.r | 19 umx-4.80.0/umx/tests/testthat/test_umx_make.R |only umx-4.80.0/umx/tests/testthat/test_umx_misc.r | 192 umx-4.80.0/umx/tests/testthat/test_umx_reorder.r | 2 umx-4.80.0/umx/tests/testthat/test_umx_score_scale.r | 88 umx-4.80.0/umx/tests/testthat/test_umx_set.r | 1 umx-4.80.0/umx/tests/testthat/test_umx_stack.R |only umx-4.80.0/umx/tests/testthat/test_uncertainty_reporting.R |only umx-4.80.0/umx/tests/testthat/test_xmu_make_mxData.r | 53 umx-4.80.0/umx/tests/testthat/test_xmu_safe_run_summary.r |only umx-4.80.0/umx/vignettes |only 579 files changed, 21897 insertions(+), 16980 deletions(-)
Title: Media File Preprocessing and Metadata for the 'tidyverse'
Description: Batch preprocessing and metadata extraction for audio,
video and image files, built on the command-line programs 'FFmpeg'
(<https://ffmpeg.org/>) and 'MediaInfo'
(<https://mediaarea.net/en/MediaInfo>). Trim, crop, scale, convert and
standardize files one at a time or across a whole directory, and read
container and stream metadata back as tibbles for use with the
'tidyverse'.
Author: Jeffrey Girard [aut, cre]
Maintainer: Jeffrey Girard <me@jmgirard.com>
Diff between tidymedia versions 0.2.1 dated 2026-10-10 and 0.2.2 dated 2026-10-11
DESCRIPTION | 6 MD5 | 112 ++++--- NAMESPACE | 1 NEWS.md | 79 +++++ R/cache.R | 42 ++ R/ffm.R | 82 +++++ R/ffm_batch.R | 110 +++++++ R/ffm_manifest.R | 6 R/ffmpeg.R | 242 +++++++++++++++-- R/program_management.R | 268 +++++++++++++++---- R/tidymedia-package.R | 6 R/timeout.R | 12 inst/doc/batch.html | 8 inst/doc/tidymedia.html | 24 - inst/doc/verification.R | 22 + inst/doc/verification.Rmd | 23 + inst/doc/verification.html | 19 - inst/doc/workflow.html | 14 man/ffm_batch.Rd | 28 + man/ffm_manifest.Rd | 6 man/ffm_run.Rd | 36 ++ man/ffmpeg_codecs.Rd | 1 man/ffmpeg_encoders.Rd | 1 man/find_ffmpeg.Rd | 17 - man/hardware_encoder.Rd | 1 man/has_encoder.Rd |only man/normalize_audio_batch.Rd | 7 man/program_status.Rd | 9 man/refresh_ffmpeg_capabilities.Rd | 21 + man/set_program.Rd | 8 man/tidymedia-package.Rd | 6 man/with_timeout.Rd | 12 tests/testthat/helper-media.R | 18 - tests/testthat/helper-program-config.R | 36 +- tests/testthat/helper-skip.R | 27 + tests/testthat/helper-timeout-sweep.R | 58 +++- tests/testthat/test-anonymize-video-batch.R | 6 tests/testthat/test-anonymize-video.R | 2 tests/testthat/test-audio-stream-normalize.R | 8 tests/testthat/test-convert-audio-batch.R | 2 tests/testthat/test-encoder-diagnosis.R |only tests/testthat/test-ffm-batch.R | 10 tests/testthat/test-ffm-manifest.R | 2 tests/testthat/test-ffm.R | 2 tests/testthat/test-ffmpeg.R | 4 tests/testthat/test-format-for-web-batch.R | 3 tests/testthat/test-has-encoder.R |only tests/testthat/test-input-path-front-door.R | 11 tests/testthat/test-location-portability.R |only tests/testthat/test-normalize-audio.R | 2 tests/testthat/test-program-management.R | 119 ++++---- tests/testthat/test-separate-av-multitrack.R | 72 ++++- tests/testthat/test-standardize-video-batch.R | 5 tests/testthat/test-timeout-refusal-blame.R | 5 tests/testthat/test-timeout-silence.R | 21 + tests/testthat/test-unguarded-argument-front-doors.R | 21 + tests/testthat/test-verify.R | 4 tests/testthat/test-video-codec.R | 1 vignettes/verification.Rmd | 23 + 59 files changed, 1355 insertions(+), 336 deletions(-)
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially
distributed animal population sampled with an array of passive detectors,
such as traps, or by searching polygons or transects. Models incorporating
distance-dependent detection are fitted by maximizing the likelihood.
Tools are included for data manipulation and model selection.
Author: Murray Efford [aut, cre] ,
Philipp Jund [ctb] ,
David Fletcher [ctb] ,
Yan Ru Choo [ctb]
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 5.4.3 dated 2026-05-27 and 5.5.1 dated 2026-10-11
secr-5.4.3/secr/R/telemetry.R |only secr-5.5.1/secr/DESCRIPTION | 13 secr-5.5.1/secr/MD5 | 154 secr-5.5.1/secr/NAMESPACE | 3 secr-5.5.1/secr/NEWS | 2258 +++++++------- secr-5.5.1/secr/R/RSE.R | 101 secr-5.5.1/secr/R/RcppExports.R | 32 secr-5.5.1/secr/R/addSightings.R | 151 secr-5.5.1/secr/R/addTelemetry.R | 627 ++-- secr-5.5.1/secr/R/autoini.R | 412 +- secr-5.5.1/secr/R/chatmarking.R |only secr-5.5.1/secr/R/derivedDcoef.R | 2 secr-5.5.1/secr/R/derivedDcw.R |only secr-5.5.1/secr/R/derivedDsurface.R | 479 +-- secr-5.5.1/secr/R/derivedMS.R | 13 secr-5.5.1/secr/R/fastsecrloglik.R | 669 ++-- secr-5.5.1/secr/R/fxi.R | 929 +++--- secr-5.5.1/secr/R/generalsecrloglik.R | 645 +++- secr-5.5.1/secr/R/homerange.R | 1454 ++++----- secr-5.5.1/secr/R/join2.R | 766 ++-- secr-5.5.1/secr/R/loglikhelperfn.R | 21 secr-5.5.1/secr/R/logmultinom.R | 89 secr-5.5.1/secr/R/makeStart.R | 52 secr-5.5.1/secr/R/methods.R | 121 secr-5.5.1/secr/R/plot.popn.R | 214 - secr-5.5.1/secr/R/preparedata.R | 126 secr-5.5.1/secr/R/regionN.R | 1297 ++++---- secr-5.5.1/secr/R/secr.design.MS.R | 1598 +++++----- secr-5.5.1/secr/R/secr.fit.R | 122 secr-5.5.1/secr/R/secr.refit.R | 212 - secr-5.5.1/secr/R/sim.capthist.R | 2311 +++++++-------- secr-5.5.1/secr/R/sim.detect.R | 6 secr-5.5.1/secr/R/summary.capthist.R | 591 +-- secr-5.5.1/secr/R/telemGH.R |only secr-5.5.1/secr/R/usagePlot.R | 271 - secr-5.5.1/secr/R/utility.R | 207 + secr-5.5.1/secr/R/verify.R | 2124 +++++++------ secr-5.5.1/secr/inst/doc/secr-datainput.pdf |binary secr-5.5.1/secr/inst/doc/secr-overview.Rmd | 1160 +++---- secr-5.5.1/secr/inst/doc/secr-overview.pdf |binary secr-5.5.1/secr/inst/extdata/telemetrydemo.txt |only secr-5.5.1/secr/man/AICcompatible.Rd | 145 secr-5.5.1/secr/man/RSE.Rd | 130 secr-5.5.1/secr/man/addTelemetry.Rd | 373 +- secr-5.5.1/secr/man/blackbear.Rd | 20 secr-5.5.1/secr/man/derivedMS.Rd | 10 secr-5.5.1/secr/man/details.Rd | 647 ++-- secr-5.5.1/secr/man/expected.n.Rd | 236 - secr-5.5.1/secr/man/homerange.Rd | 494 +-- secr-5.5.1/secr/man/read.telemetry.Rd | 137 secr-5.5.1/secr/man/region.N.Rd | 466 +-- secr-5.5.1/secr/man/secr-package.Rd | 368 +- secr-5.5.1/secr/man/secr.fit.Rd | 767 ++-- secr-5.5.1/secr/man/sighting.Rd | 30 secr-5.5.1/secr/man/usagePlot.Rd | 251 - secr-5.5.1/secr/man/userdist.Rd | 245 - secr-5.5.1/secr/man/verify.Rd | 257 - secr-5.5.1/secr/src/RcppExports.cpp | 121 secr-5.5.1/secr/src/autils.cpp | 2 secr-5.5.1/secr/src/detectfn.cpp | 30 secr-5.5.1/secr/src/poly.h | 4 secr-5.5.1/secr/src/prwifastproximity.cpp | 210 - secr-5.5.1/secr/src/prwisignal.cpp | 165 - secr-5.5.1/secr/src/prwisimple.cpp | 450 ++ secr-5.5.1/secr/src/prwisimplefxi.cpp | 85 secr-5.5.1/secr/src/secr.h | 14 secr-5.5.1/secr/src/sighting.cpp | 37 secr-5.5.1/secr/src/sightingchat.cpp | 247 - secr-5.5.1/secr/src/sightingexpectedmusk.cpp | 134 secr-5.5.1/secr/tests/testthat.R | 12 secr-5.5.1/secr/tests/testthat/telemetry_marking_ch.RDS |only secr-5.5.1/secr/tests/testthat/telemetry_marking_dx.RDS |only secr-5.5.1/secr/tests/testthat/telemetry_marking_q.RDS |only secr-5.5.1/secr/tests/testthat/telemetry_marking_sex.RDS |only secr-5.5.1/secr/tests/testthat/telemetry_metrescale.RDS |only secr-5.5.1/secr/tests/testthat/test-fixedpmix.R |only secr-5.5.1/secr/tests/testthat/test-getpmix.R |only secr-5.5.1/secr/tests/testthat/test-markresight.R | 18 secr-5.5.1/secr/tests/testthat/test-relativeD.R | 48 secr-5.5.1/secr/tests/testthat/test-signaldetector.R | 50 secr-5.5.1/secr/tests/testthat/test-start.R | 118 secr-5.5.1/secr/tests/testthat/test-telemetry.R |only secr-5.5.1/secr/tests/testthat/test-telemetrymarking.R |only secr-5.5.1/secr/tests/testthat/test-telemetrymarkingD.R |only secr-5.5.1/secr/tests/testthat/test-uselog.R |only secr-5.5.1/secr/vignettes/secr-overview.Rmd | 1160 +++---- 86 files changed, 14227 insertions(+), 12484 deletions(-)
Title: Object-Oriented Interface for Offline Change-Point Detection
Description: A collection of efficient implementations of popular offline change-point detection algorithms, featuring a consistent, object-oriented interface for practical use.
Author: Minh Long Nguyen [aut, cre],
Toby Hocking [aut],
Charles Truong [aut],
Huy Nhat Minh Nguyen [ctb]
Maintainer: Minh Long Nguyen <edelweiss611428@gmail.com>
Diff between rupturesRcpp versions 1.0.3 dated 2026-09-18 and 2.0.0 dated 2026-10-11
rupturesRcpp-1.0.3/rupturesRcpp/src/L1_cwMed.cpp |only rupturesRcpp-1.0.3/rupturesRcpp/src/L1_cwMed.h |only rupturesRcpp-1.0.3/rupturesRcpp/src/L2.cpp |only rupturesRcpp-1.0.3/rupturesRcpp/src/L2.h |only rupturesRcpp-1.0.3/rupturesRcpp/src/LinearL2.cpp |only rupturesRcpp-1.0.3/rupturesRcpp/src/LinearL2.h |only rupturesRcpp-1.0.3/rupturesRcpp/src/SIGMA.cpp |only rupturesRcpp-1.0.3/rupturesRcpp/src/SIGMA.h |only rupturesRcpp-1.0.3/rupturesRcpp/src/VAR.cpp |only rupturesRcpp-1.0.3/rupturesRcpp/src/VAR.h |only rupturesRcpp-1.0.3/rupturesRcpp/src/baseClass.h |only rupturesRcpp-2.0.0/rupturesRcpp/DESCRIPTION | 24 rupturesRcpp-2.0.0/rupturesRcpp/LICENSE |only rupturesRcpp-2.0.0/rupturesRcpp/MD5 | 62 +- rupturesRcpp-2.0.0/rupturesRcpp/NAMESPACE | 15 rupturesRcpp-2.0.0/rupturesRcpp/R/DynpR6.R |only rupturesRcpp-2.0.0/rupturesRcpp/R/PeltR6.R | 172 +++++- rupturesRcpp-2.0.0/rupturesRcpp/R/WindowR6.R | 283 +++++++++- rupturesRcpp-2.0.0/rupturesRcpp/R/binSegR6.R | 281 +++++++++ rupturesRcpp-2.0.0/rupturesRcpp/R/costFactoryR6.R |only rupturesRcpp-2.0.0/rupturesRcpp/R/costFuncR6.R | 239 ++++++++ rupturesRcpp-2.0.0/rupturesRcpp/R/zzz.R | 25 rupturesRcpp-2.0.0/rupturesRcpp/README.md | 264 +-------- rupturesRcpp-2.0.0/rupturesRcpp/man/Dynp.Rd |only rupturesRcpp-2.0.0/rupturesRcpp/man/PELT.Rd | 71 ++ rupturesRcpp-2.0.0/rupturesRcpp/man/Window.Rd | 127 +++- rupturesRcpp-2.0.0/rupturesRcpp/man/binSeg.Rd | 125 +++- rupturesRcpp-2.0.0/rupturesRcpp/man/costFactory.Rd |only rupturesRcpp-2.0.0/rupturesRcpp/man/costFunc.Rd | 68 ++ rupturesRcpp-2.0.0/rupturesRcpp/src/RcppExports.cpp | 44 + rupturesRcpp-2.0.0/rupturesRcpp/src/costs.cpp |only rupturesRcpp-2.0.0/rupturesRcpp/src/costs.h |only rupturesRcpp-2.0.0/rupturesRcpp/src/tmplBinSeg.cpp | 208 ++++++- rupturesRcpp-2.0.0/rupturesRcpp/src/tmplDynp.cpp |only rupturesRcpp-2.0.0/rupturesRcpp/src/tmplPelt.cpp | 187 +++++- rupturesRcpp-2.0.0/rupturesRcpp/src/tmplWindow.cpp | 277 ++++++++- rupturesRcpp-2.0.0/rupturesRcpp/tests/testthat/test-cost_Custom.R |only rupturesRcpp-2.0.0/rupturesRcpp/tests/testthat/test-cost_LinearL1.R |only rupturesRcpp-2.0.0/rupturesRcpp/tests/testthat/test-cost_LinearSIGMA.R |only rupturesRcpp-2.0.0/rupturesRcpp/tests/testthat/test-cost_costFactory.R |only rupturesRcpp-2.0.0/rupturesRcpp/tests/testthat/test-segModule_Dynp.R |only rupturesRcpp-2.0.0/rupturesRcpp/tests/testthat/test-segModule_PELT.R | 52 + rupturesRcpp-2.0.0/rupturesRcpp/tests/testthat/test-segModule_Window.R | 150 +++++ rupturesRcpp-2.0.0/rupturesRcpp/tests/testthat/test-segModule_binSeg.R | 150 +++++ 44 files changed, 2341 insertions(+), 483 deletions(-)
Title: A Legacy Package
Description: The author has retired from academic research. Accordingly, this package should not be considered a validated tool for use in peer-reviewed publications or as the basis for grant applications. Backward compatibility with user-code published in <doi:10.1186/s12859-023-05408-8>, <doi:10.1016/j.labinv.2023.100158> and <doi:10.1093/bioinformatics/btaf182> is not maintained in versions >= 0.4.0 (June 2026) of this package. The authors of those publications are the appropriate contacts for reproducibility inquiries.
Author: Tingting Zhan [aut, cre]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between Qindex versions 0.2.1 dated 2026-08-26 and 0.2.2 dated 2026-10-11
DESCRIPTION | 12 ++++++------ MD5 | 7 ++++--- R/0PACKAGE.R | 1 + README.md |only man/Qindex-package.Rd | 3 ++- 5 files changed, 13 insertions(+), 10 deletions(-)
Title: Generalized Additive Models with Hyper Column
Description: An interactive HTML widget of the perspective plot for generalized additive models; an alternative solution of the function mgcv::vis.gam(). This R package author has retired from academic research. Accordingly, this package should not be considered a validated tool for use in peer-reviewed publications or as the basis for grant applications. Backward compatibility with user-code published in <doi:10.1093/bioinformatics/btaf182> and <doi:10.1093/bioinformatics/btaf430> is not maintained in versions >= 0.3.0 (June 2026) of this package. The authors of those publications are the appropriate contacts for reproducibility inquiries.
Author: Tingting Zhan [aut, cre],
Erjia Cui [ctb]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between hyper.gam versions 0.3.3 dated 2026-08-25 and 0.3.4 dated 2026-10-11
DESCRIPTION | 10 +++++----- MD5 | 3 ++- README.md |only 3 files changed, 7 insertions(+), 6 deletions(-)
Title: Logistic Regression Trees
Description: A logistic regression tree is a decision tree with logistic regressions at its leaves. A particular stochastic expectation maximization algorithm is used to draw a few good trees, that are then assessed via the user's criterion of choice among BIC / AIC / test set Gini. The formal development is given in a PhD chapter, see Ehrhardt (2019) <https://github.com/adimajo/manuscrit_these/releases/>.
Author: Adrien Ehrhardt [aut, cre]
Maintainer: Adrien Ehrhardt <adrien.ehrhardt@polytechnique.edu>
This is a re-admission after prior archival of version 0.3.1 dated 2024-03-06
Diff between glmtree versions 0.3.1 dated 2024-03-06 and 0.4.0 dated 2026-10-11
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Title: Deal with Country Data in an Easy Way
Description: Wrangle country data more effectively and quickly.
This package contains functions to easily identify and convert country names,
download country information, merge country data from different sources,
and make quick world maps.
Author: Francesco Saverio Bellelli [aut, cre, cph]
Maintainer: Francesco Saverio Bellelli <fsabellelli@gmail.com>
Diff between countries versions 1.2.4 dated 2026-07-18 and 1.2.5 dated 2026-10-11
countries-1.2.4/countries/man/figures/unnamed-chunk-8-1.png |only countries-1.2.5/countries/DESCRIPTION | 8 - countries-1.2.5/countries/MD5 | 15 +- countries-1.2.5/countries/NEWS.md | 3 countries-1.2.5/countries/README.md | 27 ++-- countries-1.2.5/countries/data/country_reference_list.rda |binary countries-1.2.5/countries/data/country_reference_list_long.rda |binary countries-1.2.5/countries/inst/doc/auto_merge.html | 60 +++++----- countries-1.2.5/countries/inst/doc/dealing_with_names.html | 14 +- 9 files changed, 63 insertions(+), 64 deletions(-)
Title: Idealisation of Patch Clamp Recordings
Description: Implements the model-free multiscale idealisation approaches: Jump-Segmentation by MUltiResolution Filter (JSMURF), Hotz et al. (2013) <doi:10.1109/TNB.2013.2284063>, JUmp Local dEconvolution Segmentation filter (JULES), Pein et al. (2018) <doi:10.1109/TNB.2018.2845126>, and Heterogeneous Idealization by Local testing and DEconvolution (HILDE), Pein et al. (2021) <doi:10.1109/TNB.2020.3031202>. Further details on how to use them are given in Pein, Eltzner and Munk (2021) <doi:10.1007/s00249-021-01506-8>.
Author: Florian Pein [aut, cre],
Timo Aspelmeier [ctb]
Maintainer: Florian Pein <f.pein@lancaster.ac.uk>
Diff between clampSeg versions 1.3-0 dated 2026-10-08 and 1.3-1 dated 2026-10-11
ChangeLog | 8 ++++++++ DESCRIPTION | 6 +++--- MD5 | 8 ++++---- build/partial.rdb |binary tests/testthat/test_cacheLocation.R | 19 ++++++++++++++++--- 5 files changed, 31 insertions(+), 10 deletions(-)
Title: Health Geography Toolbox for Model-Based Analysis of Infections
Panel Data
Description: Within epidemic outbreaks, infections grow and decline differently between regions, and the velocity of spatial spread differs between countries. The swash library offers a set of model-based analyses for these topics. Spread velocity may be analysed with the Swash-Backwash Model for the Single Epidemic Wave by Cliff and Haggett (2006) <doi:10.1007/s10109-006-0027-8> and corresponding functions for bootstrap confidence intervals, country comparison, and visualization of results. Differences in epidemic growth between regions may be analysed using logistic growth models, exponential growth models, Hawkes processes and breakpoint analyses. Cluster and hotspot analyses can be conducted using neighborhood matrices. See Wieland (2020) <doi:10.18335/region.v7i2.324> for an application of some of the mentioned analysis methods. All functionalities are accessed by the class "infpan" for infections panel data defined in this package, which is built from a data.frame provided by the [...truncated...]
Author: Thomas Wieland [aut, cre]
Maintainer: Thomas Wieland <geowieland@googlemail.com>
Diff between swash versions 3.0.0 dated 2026-10-02 and 3.0.1 dated 2026-10-11
swash-3.0.0/swash/NEWS.md |only swash-3.0.1/swash/DESCRIPTION | 12 - swash-3.0.1/swash/MD5 | 24 +- swash-3.0.1/swash/NAMESPACE | 2 swash-3.0.1/swash/R/config.R | 6 swash-3.0.1/swash/R/growthmodels.R | 14 + swash-3.0.1/swash/R/stathelp.R | 30 ++- swash-3.0.1/swash/man/K4kant20260101gf_ch2007Poly.Rd | 2 swash-3.0.1/swash/man/exponential_growth.Rd | 30 ++- swash-3.0.1/swash/man/growth_initial.Rd | 29 ++- swash-3.0.1/swash/man/logistic_growth.Rd | 19 +- swash-3.0.1/swash/man/metrics.Rd | 6 swash-3.0.1/swash/man/swash-package.Rd | 166 +++++++++++++------ swash-3.0.1/swash/tests |only 14 files changed, 239 insertions(+), 101 deletions(-)
Title: Fast Spatial Species Accumulation Curves
Description: High-performance spatial species accumulation curves using
fixed-focus spatially constrained rarefaction, nearest-centroid expansion,
and nearest-neighbor walks with a C++ backend for speed. Supports Hill
numbers (q=0,1,2), beta diversity partitioning (turnover/nestedness) at
site and pooled resolution, coverage-based rarefaction and extrapolation
of alpha and beta diversity, phylogenetic diversity (PD; Faith's PD,
EvoHeritage, mean pairwise distance, mean nearest taxon distance),
functional diversity accumulation including aggregated functional
diversity and intraspecific trait variation, phylogenetic and functional
redundancy, interaction network accumulation, diversity-area
relationships (DAR), endemism-area curves, sampling-effort correction and
fragmentation analysis, species-area relationship (SAR) models based on
extreme value theory (EVT), and area-based richness extrapolation via the
total-species curve. Total richness is also estimated from frequency
counts, including the acc [...truncated...]
Author: Gilles Colling [aut, cre, cph] ,
Marius Muja [ctb, cph] ),
David G. Lowe [ctb, cph] ),
Jose Luis Blanco [ctb, cph] )
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between spacc versions 0.8.3 dated 2026-06-20 and 0.11.0 dated 2026-10-11
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Title: Interface to Global Biotic Interactions
Description: A programmatic interface to the web service methods
provided by Global Biotic Interactions ('GloBI')
(<https://www.globalbioticinteractions.org/>). 'GloBI' provides
access to spatial-temporal species interaction records from
sources all over the world. 'rglobi' provides methods to search
species interactions by location, interaction type, and
taxonomic name.
Author: Jorrit Poelen [aut, cre],
Stephen Gosnell [aut],
Sergey Slyusarev [aut],
Helen Waters [aut]
Maintainer: Jorrit Poelen <jhpoelen@jhpoelen.nl>
This is a re-admission after prior archival of version 0.3.4 dated 2023-10-06
Diff between rglobi versions 0.3.4 dated 2023-10-06 and 0.3.6 dated 2026-10-11
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Title: R Repositories Data
Description: Retrieve metadata about packages from repositories to explore
package dependencies, links between help pages, aliases, package
availability on a given date, and other repository-dependent outcome.
In addition, it provides access to information about the processes at CRAN.
This metadata can be used to help package maintainers and users navigate
changes to dependencies and with reproducibility.
Author: Lluis Revilla Sancho [aut, cre, cph]
Maintainer: Lluis Revilla Sancho <lluis.revilla@gmail.com>
Diff between repo.data versions 0.2.2 dated 2026-06-20 and 0.2.6 dated 2026-10-11
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Title: Policy Learning
Description: Package for learning and evaluating (subgroup) policies via doubly robust loss functions. Policy learning methods include doubly robust blip/conditional average treatment effect learning and sequential policy tree learning. Methods for (subgroup) policy evaluation include doubly robust cross-fitting and online estimation/sequential validation. See Nordland and Holst (2026) <doi:10.18637/jss.v116.i04> for documentation and references.
Author: Andreas Nordland [aut, cre],
Klaus Holst [aut]
Maintainer: Andreas Nordland <andreasnordland@gmail.com>
Diff between polle versions 1.6.6 dated 2026-10-10 and 1.6.7 dated 2026-10-11
DESCRIPTION | 11 - MD5 | 67 +++++----- NAMESPACE | 4 NEWS.md | 13 +- R/Q_function.R | 2 R/blip.R | 2 R/drql.R | 2 R/fit_functions.R | 2 R/g_function.R | 4 R/g_models.R | 163 ++++++++++++-------------- R/policy_eval.R | 2 R/policy_eval_online.R | 2 R/policy_learn.R | 4 R/q_models.R | 200 ++++++++++++++++---------------- R/sl_models.R | 125 +++++++++++++------- inst/doc/policy_data.html | 2 inst/doc/policy_eval.R | 6 inst/doc/policy_eval.Rmd | 8 - inst/doc/policy_eval.html | 47 +++---- inst/doc/policy_learn.html | 35 ++--- man/control_blip.Rd | 2 man/control_drql.Rd | 2 man/fit_g_functions.Rd | 2 man/g_model.Rd | 39 ++++-- man/policy_eval.Rd | 2 man/policy_eval_online.Rd | 2 man/policy_learn.Rd | 4 man/q_model.Rd | 48 +++++-- tests/testthat/test-Q-function.R | 3 tests/testthat/test-g_models.R | 74 +++++++++++ tests/testthat/test-policy_learn-blip.R | 15 +- tests/testthat/test-policy_learn-drql.R | 8 - tests/testthat/test-q_models.R | 74 +++++++++++ tests/testthat/test-q_sl.R |only vignettes/policy_eval.Rmd | 8 - 35 files changed, 607 insertions(+), 377 deletions(-)
Title: Fast and Efficient (Automated) Analysis of Sparse Omics Data
Description: A generalised data structure for fast and efficient loading and data munching of sparse omics data. The 'OmicFlow' requires an up-front validated metadata template from the user,
which serves as a guide to connect all the pieces together by aligning them into a single object that is defined as an 'omics' class.
Once this unified structure is established, users can perform manual subsetting, visualisation, and statistical analysis, or leverage the automated 'autoFlow' method to generate a comprehensive report.
Author: Alem Gusinac [aut, cre] ,
Thomas Ederveen [aut] ,
Annemarie Boleij [aut, fnd]
Maintainer: Alem Gusinac <alem.gusinac@gmail.com>
Diff between OmicFlow versions 1.6.0 dated 2026-05-19 and 1.7.0 dated 2026-10-11
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Title: Regularized Bayesian Estimator for Two-Level Latent Variable
Models
Description: Implements a regularized Bayesian estimator that optimizes the estimation
of between-group coefficients for multilevel latent variable models by minimizing
mean squared error (MSE) and balancing variance and bias. The package provides more reliable
estimates in scenarios with limited data, offering a robust solution for accurate
parameter estimation in two-level latent variable models. It is designed for
researchers in psychology, education, and related fields who face challenges in
estimating between-group effects under small sample sizes and low intraclass
correlation coefficients. The package includes comprehensive S3 methods for result
objects: print(), summary(), coef(), se(), vcov(), confint(), as.data.frame(),
dim(), length(), names(), and update() for enhanced usability and integration
with standard R workflows. Dashuk et al. (2025a) <doi:10.1017/psy.2025.10045>
derived the optimal regularized Bayesian estimator;
Dashuk et al. (2025b) <doi:10.1007/s41237-025-00264-7> [...truncated...]
Author: Valerii Dashuk [aut, cre],
Binayak Timilsina [aut],
Martin Hecht [aut],
Steffen Zitzmann [aut]
Maintainer: Valerii Dashuk <vadashuk@gmail.com>
Diff between MultiLevelOptimalBayes versions 0.0.4.0 dated 2025-09-23 and 0.1.0.0 dated 2026-10-11
DESCRIPTION | 9 MD5 | 34 - NEWS.md |only R/estimation-bayes.R | 661 +++++------------------------ R/mlob.R | 34 + README.md | 126 ++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/MultiLevelOptimalBayes-Intro.Rmd | 555 ++++++++++++------------ inst/doc/MultiLevelOptimalBayes-Intro.html | 260 +++++------ man/estimate_Bay_CV.Rd | 11 man/mlob.Rd | 18 man/ratio_moments.Rd |only man/ratio_se.Rd |only tests/testthat/helper-anova-moments.R |only tests/testthat/helper-reference-fits.R |only tests/testthat/helper-simulate-alcd.R |only tests/testthat/test-mlob.R | 19 tests/testthat/test-numeric-estimators.R |only tests/testthat/test-numeric-invariance.R |only tests/testthat/test-numeric-properties.R |only tests/testthat/test-numeric-reference.R |only vignettes/MultiLevelOptimalBayes-Intro.Rmd | 555 ++++++++++++------------ 23 files changed, 943 insertions(+), 1339 deletions(-)
More information about MultiLevelOptimalBayes at CRAN
Permanent link
Title: Mobility Network Analysis
Description: Implements the method to analyse weighted mobility networks or distribution networks as outlined in:
Block, P., Stadtfeld, C., & Robins, G. (2022) <doi:10.1016/j.socnet.2021.08.003>.
The purpose of the model is to analyse the structure of mobility,
incorporating exogenous predictors pertaining to individuals and locations
known from classical mobility analyses, as well as modelling emergent mobility
patterns akin to structural patterns known from the statistical analysis of social networks.
Version 2 runs the simulations in 'C++' (using 'Rcpp') and, besides stochastic
approximation (Robbins-Monro), can estimate parameters with Geyer-Thompson MCMC
maximum likelihood estimation.
Author: Per Block [cre, aut, cph] ,
Christoph Stadtfeld [aut] ,
Nico Keiser [aut] ,
Marion Hoffman [aut] ,
Jingying Wang [aut]
Maintainer: Per Block <block@soziologie.uzh.ch>
Diff between MoNAn versions 1.1.0 dated 2024-09-12 and 2.0.0 dated 2026-10-11
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Title: Calculation of Low Flow Statistics for Daily Stream Flow Data
Description: The "Manual on Low-flow Estimation and Prediction" (Gustard & Demuth (2009, ISBN:978-92-63-11029-9)), published by the World Meteorological Organisation, gives a comprehensive summary on how to analyse stream flow data focusing on low-flows. This packages provides functions to compute the described statistics and produces plots similar to the ones in the manual.
Author: Tobias Gauster [ctb, cre],
Gregor Laaha [aut] ,
Daniel Koffler [aut]
Maintainer: Tobias Gauster <t.gauster@gmail.com>
Diff between lfstat versions 0.9.13 dated 2025-09-04 and 0.9.15 dated 2026-10-11
DESCRIPTION | 11 +- MD5 | 10 +- NAMESPACE | 208 +++++++++++++++++++++++-------------------- NEWS.md | 6 + build/partial.rdb |binary tests/testthat/test-import.R | 9 + 6 files changed, 136 insertions(+), 108 deletions(-)
Title: Goodness-of-Fit and Calibration Tests for Logistic Regression
Description: Provides a unified battery of goodness-of-fit and calibration
tests for binary logistic regression, runnable in a single call via
'run.all.gof()'. Around twenty-five tests spanning five decades of
literature are aggregated and grouped by the departure each is built to
detect: global and standardized statistics, partition tests such as
Hosmer-Lemeshow, directed and covariate-space tests, smoothing and
resampling tests, and calibration tests. Each is obtained from its own
package where installed and attributed to its authors. The package also
implements the author's own procedures for sparse data, where the
Hosmer-Lemeshow test loses power: the omnibus Ebrahim-Farrington test
'ef.gof()', the directed 'edge.gof()' and its covariate-space variant
'cdef.gof()', the Cauchy-combination ensemble 'edges.gof()', 'DeepGOF-1'
(a pretrained convolutional statistic whose level comes from the analyst's
own parametric bootstrap rather than from the network), and 'legoft()'
(a frozen-weight combination [...truncated...]
Author: Ebrahim Khaled Ebrahim [aut, cre] ,
Jiawei Zhang [ctb, cph] ,
Jie Ding [ctb, cph] ,
Yuhong Yang [ctb, cph]
Maintainer: Ebrahim Khaled Ebrahim <ebrahimkhaled@alexu.edu.eg>
Diff between ebrahim.gof versions 2.9.0 dated 2026-10-01 and 2.10.0 dated 2026-10-11
DESCRIPTION | 19 MD5 | 122 NAMESPACE | 32 NEWS.md | 1988 +++++++------ R/bagoft_fast.R | 4 R/battery_summary.R |only R/calm_gof.R | 770 ++--- R/cdef_gof.R | 456 +-- R/cubic_calib_gof.R |only R/deepgof.R | 1371 ++++----- R/deepgof_certificate.R |only R/deepgof_plot.R |only R/def_ensemble_gof.R | 368 +- R/def_gof.R | 879 +++-- R/ebrahim.gof-package.R | 9 R/ebrahim_farrington_test.R | 807 +++-- R/edge_belt.R |only R/edge_gof.R | 451 ++- R/legoft.R | 498 +-- R/localize_gof.R |only R/localize_plot.R |only R/proj_gof.R | 428 +- R/run_all_external.R | 34 R/run_all_gof.R | 3897 +++++++++++++------------- R/shrink_gof.R | 444 +- README.md | 61 build/vignette.rds |binary inst/CITATION | 109 inst/doc/ebrahim-farrington-intro.Rmd | 6 inst/doc/ebrahim-farrington-intro.html | 97 inst/doc/ebrahim-gof-toolbox.R | 39 inst/doc/ebrahim-gof-toolbox.Rmd | 113 inst/doc/ebrahim-gof-toolbox.html | 435 ++ inst/doc/extensions.R |only inst/doc/extensions.Rmd |only inst/doc/extensions.html |only man/calm.gof.Rd | 6 man/cubic.calib.gof.Rd |only man/deepgof1.Rd | 5 man/deepgof1.external.Rd | 4 man/def.gof.Rd | 36 man/ebrahim.gof-package.Rd | 9 man/edge.belt.Rd |only man/edge.gof.Rd | 41 man/ef.gof.Rd | 157 - man/gof_certificate.Rd |only man/localize.external.Rd |only man/localize.gof.Rd |only man/plot.deepgof1.Rd |only man/plot.edge_gof.Rd |only man/plot.gof_battery.Rd | 7 man/plot.gof_localize.Rd |only man/print.gof_battery.Rd | 10 man/run.all.external.Rd | 10 man/run.all.gof.Rd | 104 man/shrink.gof.Rd | 6 man/summary.gof_battery.Rd |only tests/testthat/helper-ef-reference.R |only tests/testthat/test-battery-input.R |only tests/testthat/test-battery-summary.R |only tests/testthat/test-cubic-calib.R |only tests/testthat/test-deepgof-plot.R |only tests/testthat/test-deepgof1.R | 15 tests/testthat/test-def-gof.R | 480 +-- tests/testthat/test-ebrahim-farrington.R | 371 +- tests/testthat/test-edge-belt.R |only tests/testthat/test-edge-plot.R |only tests/testthat/test-ef-method.R | 47 tests/testthat/test-ef-paper.R |only tests/testthat/test-gof_certificate.R |only tests/testthat/test-localize.R |only tests/testthat/test-mccullagh-copas-algebra.R |only tests/testthat/test-na-exclude.R |only tests/testthat/test-run-all-external.R | 35 tests/testthat/test-run-all-gof.R | 644 ++-- vignettes/ebrahim-farrington-intro.Rmd | 6 vignettes/ebrahim-gof-toolbox.Rmd | 113 vignettes/extensions.Rmd |only 78 files changed, 8644 insertions(+), 6899 deletions(-)
Title: Data-Driven Locally Weighted Regression for Trend and
Seasonality in TS
Description: Various methods for the identification of trend and seasonal
components in time series (TS) are provided. Among them is a data-driven locally
weighted regression approach with automatically selected bandwidth for
equidistant short-memory time series. The approach is a
combination / extension of the algorithms by
Feng (2013) <doi:10.1080/02664763.2012.740626> and Feng, Y., Gries, T.,
and Fritz, M. (2020) <doi:10.1080/10485252.2020.1759598> and a brief
description of this new method is provided in the package documentation and in
more detail in Schulz (2026) <doi:10.32614/RJ-2026-025>.
Furthermore, the package allows its users to apply the base model of the
Berlin procedure, version 4.1, as described in Speth (2004) <https://www.destatis.de/DE/Methoden/Saisonbereinigung/BV41-methodenbericht-Heft3_2004.pdf?__blob=publicationFile>.
Permission to include this procedure was kindly provided by the Federal
Statistical Office of Germany.
Author: Yuanhua Feng [aut] ,
Dominik Schulz [aut, cre]
Maintainer: Dominik Schulz <dominik.schulz.r@gmail.com>
Diff between deseats versions 1.1.2 dated 2026-03-16 and 1.1.3 dated 2026-10-11
DESCRIPTION | 22 +- MD5 | 46 +++--- NAMESPACE | 60 ++++---- NEWS.md | 15 ++ R/AttachMessage.R | 3 R/class-s_semiarma.R | 19 ++ R/forecasting_functions.R | 2 README.md | 11 + build/vignette.rds |binary inst/CITATION |only inst/doc/deseats-workflow-example.html | 5 man/ENERGY.Rd | 56 +++---- man/GDP.Rd | 54 +++---- man/HOUSES.Rd | 54 +++---- man/RAINFALL.Rd | 52 +++---- man/RETAIL.Rd | 56 +++---- man/create_gain.Rd | 244 ++++++++++++++++----------------- man/deseats-package.Rd | 7 man/llin_decomp.Rd | 162 ++++++++++----------- man/plot-decomp-method.Rd | 130 ++++++++--------- man/plot-deseats_fc-method.Rd | 88 +++++------ man/plot-hfilter-method.Rd | 82 +++++------ man/predict-s_semiarma-method.Rd | 10 + man/run_decomposition.Rd | 58 +++---- tests/testthat/test-cores_prediction.R |only 25 files changed, 655 insertions(+), 581 deletions(-)
Title: Fast and Unified Synthetic Control Methods
Description: A unified 'Formula' interface to the Synthetic Control Method
(SCM) and related panel-data causal inference estimators: Synthetic
Difference-in-Differences (SDID), Generalized Synthetic Control (GSC),
Matrix Completion (MC), Time-Aware Synthetic Control (TASC), and Synthetic
Interventions (SI), together with an experimental-design variant.
Computational bottlenecks (quadratic programming, singular value
decomposition, and Kalman filtering) are implemented in 'C++' via
'RcppArmadillo'. Methods are described in Abadie, Diamond and Hainmueller
(2010) <doi:10.1198/jasa.2009.ap08746>, Arkhangelsky, Athey, Hirshberg,
Imbens and Wager (2021) <doi:10.1257/aer.20190159>, Xu (2017)
<doi:10.1017/pan.2016.2>, Athey, Bayati, Doudchenko, Imbens and Khosravi
(2021) <doi:10.1080/01621459.2021.1891924>, and Agarwal, Shah and Shen
(2025) <doi:10.1287/opre.2025.1590>.
Author: Yosuke Abe [aut, cre]
Maintainer: Yosuke Abe <yosuke.abe0507@gmail.com>
Diff between coresynth versions 0.5.0 dated 2026-08-25 and 1.0.1 dated 2026-10-11
DESCRIPTION | 6 MD5 | 104 NAMESPACE | 9 NEWS.md | 1973 +++--- R/RcppExports.R | 47 R/accessors.R | 23 R/broom.R | 713 +- R/conformal.R | 533 - R/coresynth-package.R | 11 R/export.R | 9 R/gsc.R | 137 R/mc.R | 233 R/plot.R | 1960 +++-- R/scm.R | 1104 ++- R/scm_fit.R | 1056 +-- R/scm_frontier.R |only R/scm_rank.R |only R/sdid.R | 1604 ++-- R/si.R | 1957 +++-- R/tasc.R | 18 R/utils.R | 323 README.md | 101 inst/doc/coresynth.Rmd | 307 inst/doc/coresynth.html | 15 man/coresynth-package.Rd | 10 man/figures/README-placebo-gaps-1.png |binary man/figures/README-plot-gap-1.png |binary man/figures/README-plot-trend-1.png |binary man/figures/README-plot-weights-1.png |binary man/gsc_boot.Rd | 5 man/mspe_ratio_pval.Rd | 24 man/plot.coresynth.Rd | 20 man/plot.scm_frontier.Rd |only man/plot.scm_placebo.Rd | 33 man/plot_data.Rd | 12 man/scm_balance_frontier.Rd |only man/scm_fit.Rd | 176 man/scm_inference.Rd | 90 man/scm_rank_pval.Rd |only man/sdid_inference.Rd | 4 man/soft_impute_cpp.Rd | 11 man/soft_impute_fe_cpp.Rd |only man/treated_outcomes.Rd | 15 src/RcppExports.cpp | 27 src/gsc.cpp | 34 src/inference.cpp | 30 src/mc.cpp | 107 src/optim.cpp | 149 src/scm.cpp | 244 src/sdid.cpp | 22 src/si.cpp | 14 src/tasc.cpp | 36 src/threads.h |only tests/testthat.R |only tests/testthat/test-integration.R |11156 +++++++++++++++++++--------------- tests/testthat/test-object-model.R | 25 vignettes/coresynth.Rmd | 307 57 files changed, 14527 insertions(+), 10267 deletions(-)
Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by
providing a high level interface to writing, styling and editing
worksheets.
Author: Jordan Mark Barbone [aut] ,
Jan Marvin Garbuszus [aut, cre],
Olivier Roy [ctb],
Paul Schmidt [ctb] ,
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 1.29 dated 2026-08-20 and 1.30 dated 2026-10-11
DESCRIPTION | 10 MD5 | 56 +-- NEWS.md | 22 + R/class-color.R | 10 R/class-workbook-wrappers.R | 21 - R/class-workbook.R | 491 ++++++++++++++------------- R/conditional_formatting.R | 57 +++ R/deprecate.R | 2 R/read.R | 2 R/utils.R | 20 + R/wb_styles.R | 2 R/write.R | 11 inst/WORDLIST | 1 man/col_widths-wb.Rd | 4 man/convertToExcelDate.Rd | 3 man/create_colors_xml.Rd | 2 man/openxlsx2-package.Rd | 1 man/wbWorkbook.Rd | 10 man/wb_add_conditional_formatting.Rd | 2 man/wb_base_colors.Rd | 4 man/wb_color.Rd | 10 man/wb_save.Rd | 17 man/write_xlsx.Rd | 4 src/helper_functions.cpp | 94 ++++- tests/testthat/test-class-workbook.R | 24 + tests/testthat/test-conditional_formatting.R | 491 +++++++++++++++++++++++++++ tests/testthat/test-read_sources.R | 4 tests/testthat/test-save.R | 57 +++ tests/testthat/test-write.R | 25 + 29 files changed, 1164 insertions(+), 293 deletions(-)
Title: Metrics of R Packages
Description: Static code analyses for R packages using the external code-tagging
libraries 'ctags' and 'gtags'. Static analyses enable packages to be
analysed very quickly, generally a couple of seconds at most. The package
also provides access to a database generating by applying the main function
to the full 'CRAN' archive, enabling the statistical properties of any package
to be compared with all other 'CRAN' packages.
Author: Mark Padgham [aut, cre] ,
Michael Sumner [ctb] ,
Jeffrey Hollister [ctb] ,
Egor Kotov [ctb]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between pkgstats versions 0.2.4 dated 2026-07-21 and 0.2.5 dated 2026-10-11
pkgstats-0.2.4/pkgstats/vignettes/installation.md |only pkgstats-0.2.4/pkgstats/vignettes/pkgstats.md |only pkgstats-0.2.5/pkgstats/DESCRIPTION | 14 +-- pkgstats-0.2.5/pkgstats/MD5 | 38 +++++---- pkgstats-0.2.5/pkgstats/NEWS.md | 6 + pkgstats-0.2.5/pkgstats/R/cran-data-archive.R | 45 +++++++---- pkgstats-0.2.5/pkgstats/R/cran-data-update.R | 47 ++++++++---- pkgstats-0.2.5/pkgstats/R/cran-data-utils.R |only pkgstats-0.2.5/pkgstats/R/pkgstats-summary.R | 3 pkgstats-0.2.5/pkgstats/build/vignette.rds |binary pkgstats-0.2.5/pkgstats/inst/doc/installation.html | 6 - pkgstats-0.2.5/pkgstats/inst/doc/pkgstats-data.html |only pkgstats-0.2.5/pkgstats/inst/doc/pkgstats-data.qmd |only pkgstats-0.2.5/pkgstats/inst/doc/pkgstats.html | 10 +- pkgstats-0.2.5/pkgstats/inst/extdata/pkgstats-col-types.csv |only pkgstats-0.2.5/pkgstats/tests/testthat/test-archive-trawl.R | 2 pkgstats-0.2.5/pkgstats/tests/testthat/test-col-types.R |only pkgstats-0.2.5/pkgstats/tests/testthat/test-cran-update.R | 2 pkgstats-0.2.5/pkgstats/tests/testthat/test-ctags.R | 2 pkgstats-0.2.5/pkgstats/tests/testthat/test-desc-stats.R | 2 pkgstats-0.2.5/pkgstats/tests/testthat/test-pkgstats.R | 2 pkgstats-0.2.5/pkgstats/tests/testthat/test-plot-network.R | 2 pkgstats-0.2.5/pkgstats/tests/testthat/test-summary.R | 2 pkgstats-0.2.5/pkgstats/vignettes/pkgstats-data.qmd |only 24 files changed, 116 insertions(+), 67 deletions(-)
Title: Identifies Package Differences
Description: Identifies differences between
versions of a package. Specifically, the functions help
determine if there are breaking changes from one package version
to the next. The package also includes a stability assessment,
to help you determine the overall stability of a package, or even
an entire repository.
Author: David Bosak [aut, cre],
Brian Varney [ctb],
Kevin Putschko [ctb]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between pkgdiff versions 1.0.4 dated 2026-07-14 and 1.0.5 dated 2026-10-11
DESCRIPTION | 11 MD5 | 44 +- NEWS.md | 5 R/pkgrepo.R | 17 R/utilities.R | 20 - build/vignette.rds |binary inst/doc/pkgdiff.R | 908 +++++++++++++++++++++++------------------------ man/pkg_cache.Rd | 18 man/pkg_diff.Rd | 18 man/pkg_info.Rd | 18 man/pkg_repo.Rd | 12 man/pkg_stability.Rd | 18 man/pkg_versions.Rd | 18 man/pkgdiff.Rd | 5 man/print.pcache.Rd | 18 man/print.pdiff.Rd | 18 man/print.pdiff_score.Rd | 18 man/print.pinfo.Rd | 18 man/print.prepo.Rd | 12 man/print.rbreak.Rd | 12 man/print.rstability.Rd | 12 man/repo_breakages.Rd | 12 man/repo_stability.Rd | 12 23 files changed, 634 insertions(+), 610 deletions(-)
Title: Spherical k-Means Clustering
Description: Algorithms to compute spherical k-means partitions.
Features several methods, including a genetic and a fixed-point
algorithm and an interface to the CLUTO vcluster program.
Author: Kurt Hornik [aut, cre] ,
Ingo Feinerer [aut] ,
Martin Kober [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between skmeans versions 0.2-20 dated 2026-03-26 and 0.2-21 dated 2026-10-11
DESCRIPTION | 9 ++++----- MD5 | 8 ++++---- R/skmeans.R | 21 --------------------- build/partial.rdb |binary man/skmeans.Rd | 20 -------------------- 5 files changed, 8 insertions(+), 50 deletions(-)
Title: Liquid Glass Design Themes for 'shiny' Applications
Description: Provides drop-in Liquid Glass themes for 'shiny'. Call
glass_theme() and pass the result as theme = to fluidPage(),
navbarPage(), or any 'bslib'-aware page function to get
translucent surfaces, backdrop blur, and system typography on
'Bootstrap' components. Includes light and dark presets with
runtime switching and an OS-following 'auto' mode, an iOS-style
intensity control from Ultra Clear to Tinted, optional
persistence of the look, named wallpaper scenes, helpers to
match 'ggplot2', 'plotly', 'gt', and 'DT' output to the glass pack,
a flatten mode for print and screenshots, and documented CSS tokens.
Author: Eric Anderson [aut, cre, cph]
Maintainer: Eric Anderson <eric.ray.anderson@gmail.com>
Diff between shinyglass versions 0.4.0 dated 2026-09-20 and 0.5.0 dated 2026-10-11
DESCRIPTION | 12 MD5 | 159 +- NAMESPACE | 3 NEWS.md | 239 +++ R/glass-accent.R | 35 R/glass-flatten.R | 10 R/glass-intensity.R | 48 R/glass-page.R | 47 R/glass-plots.R | 57 R/glass-react.R |only R/glass-theme.R | 409 ++++- R/glass-tokens.R | 124 + R/shinyglass-package.R | 166 +- README.md | 96 + build/vignette.rds |binary inst/WORDLIST | 43 inst/doc/compatibility.Rmd | 14 inst/doc/compatibility.html | 39 inst/doc/migrating.R |only inst/doc/migrating.Rmd |only inst/doc/migrating.html |only inst/doc/playground.Rmd | 7 inst/doc/playground.html | 5 inst/doc/shinychat.R |only inst/doc/shinychat.Rmd |only inst/doc/shinychat.html |only inst/doc/shinyglass.R |only inst/doc/shinyglass.Rmd |only inst/doc/shinyglass.html |only inst/doc/shinyreact.R |only inst/doc/shinyreact.Rmd |only inst/doc/shinyreact.html |only inst/doc/theming.R | 17 inst/doc/theming.Rmd | 56 inst/doc/theming.html | 69 inst/examples/_shared |only inst/examples/apple-glass-reference.R | 38 inst/examples/bslib-dashboard.R | 32 inst/examples/compat-glass.R |only inst/examples/demo-app.R | 28 inst/examples/inputs-gallery.R | 28 inst/examples/intensity-slider-demo.R | 6 inst/examples/shinychat-glass |only inst/examples/shinyreact-glass |only inst/js/glass-intensity-head.js |only inst/js/glass-ios27.js |only inst/js/shiny-glass.js | 539 +++++-- inst/js/shinyglass-react.js |only inst/scss/glass.scss | 2288 +++++++++++++++++++++++++++++--- man/dt_options_glass.Rd | 12 man/figures |only man/glass_accent_input.Rd | 24 man/glass_add_tokens.Rd | 9 man/glass_css_tokens.Rd | 11 man/glass_flatten.Rd | 8 man/glass_intensity_slider.Rd | 22 man/glass_page.Rd | 27 man/glass_page_react.Rd |only man/glass_plot_colors.Rd | 17 man/glass_plot_surface_input.Rd | 20 man/glass_preset_input.Rd | 20 man/glass_react_dependency.Rd |only man/glass_resolved_preset.Rd | 23 man/glass_scene_input.Rd | 20 man/glass_scenes.Rd | 13 man/glass_system_colors.Rd | 24 man/glass_theme.Rd | 91 + man/glass_theme_dependencies.Rd |only man/glass_theme_toggle.Rd | 23 man/glass_token_pack.Rd | 9 man/gt_theme_glass.Rd | 15 man/observe_glass.Rd | 37 man/observe_glass_accent.Rd | 30 man/observe_glass_intensity.Rd | 33 man/observe_glass_plot_surface.Rd | 42 man/observe_glass_preset_input.Rd | 33 man/observe_glass_scene.Rd | 41 man/observe_glass_theme_toggle.Rd | 33 man/plotly_glass.Rd | 14 man/shinyglass-package.Rd | 176 ++ man/theme_glass.Rd | 12 man/update_glass_theme.Rd | 27 tests/testthat/test-deploy-core5.R |only tests/testthat/test-glass-theme.R | 569 +++++++ tests/testthat/test-phone-preview.R |only tests/testthat/test-pkgdown-reference.R |only tests/testthat/test-shinyreact.R |only vignettes/compatibility.Rmd | 14 vignettes/migrating.Rmd |only vignettes/playground.Rmd | 7 vignettes/shinychat.Rmd |only vignettes/shinyglass.Rmd |only vignettes/shinyreact.Rmd |only vignettes/theming.Rmd | 56 94 files changed, 5454 insertions(+), 672 deletions(-)
Title: H3 Extension of 'DuckDB'
Description: Fast & memory-efficient functions to analyze and manipulate large
data sets. It leverages the fast analytical
capabilities of 'DuckDB' and its spatial extension (see <https://duckdb.org/community_extensions/extensions/h3>)
while maintaining compatibility with R’s spatial data ecosystem to
work with spatial vector data.
Author: Adrian Cidre Gonzalez [aut, cre] ,
Egor Kotov [aut] ,
Rafael H. M. Pereira [aut]
Maintainer: Adrian Cidre Gonzalez <adrian.cidre@gmail.com>
Diff between duckh3 versions 0.1.0 dated 2026-04-24 and 0.2.0 dated 2026-10-11
DESCRIPTION | 11 MD5 | 105 - NAMESPACE | 64 NEWS.md | 32 R/h3_extension.R | 224 +- R/h3_geom_to.R |only R/h3_get_resolution.R | 154 - R/h3_h3_to.R | 656 +++--- R/h3_hierarchy.R | 864 ++++---- R/h3_is.R | 460 ++-- R/h3_lonlat_to.R | 408 ++-- R/h3_points_to.R | 596 +++--- R/h3_templates.R | 679 ++++-- R/h3_vertex.R | 634 +++--- R/utils_not_exported.R | 494 +++-- README.md | 222 +- inst/extdata/example_pts.csv | 202 +- man/ddbh3_create_conn.Rd | 102 - man/ddbh3_geom_to.Rd |only man/ddbh3_get_child_pos.Rd | 174 - man/ddbh3_get_hierarchy.Rd | 374 +-- man/ddbh3_get_icosahedron_faces.Rd | 200 +- man/ddbh3_get_resolution.Rd | 182 - man/ddbh3_h3_to.Rd | 400 ++-- man/ddbh3_is.Rd | 342 +-- man/ddbh3_lonlat_to.Rd | 350 +-- man/ddbh3_points_to.Rd | 250 +- man/ddbh3_vertex.Rd | 390 +-- man/roxygen/templates/conn_null.R | 4 man/roxygen/templates/desc_formats.R | 8 man/roxygen/templates/h3.R | 4 man/roxygen/templates/h3vertex.R | 4 man/roxygen/templates/lat.R | 2 man/roxygen/templates/lon.R | 2 man/roxygen/templates/memory_limit_gb.R | 2 man/roxygen/templates/name.R | 8 man/roxygen/templates/nested.R | 6 man/roxygen/templates/new_column.R | 4 man/roxygen/templates/output.R | 20 man/roxygen/templates/overwrite.R | 4 man/roxygen/templates/quiet.R | 4 man/roxygen/templates/resolution.R | 4 man/roxygen/templates/returns_tbl.R | 18 man/roxygen/templates/threads.R | 2 man/roxygen/templates/x.R | 18 tests/testthat.R | 24 tests/testthat/setup.R | 22 tests/testthat/test-h3_geom_to.R |only tests/testthat/test-h3_get_resolution.R | 449 ++-- tests/testthat/test-h3_h3_to.R | 2114 ++++++++++----------- tests/testthat/test-h3_hierarchy.R | 3153 ++++++++++++++++---------------- tests/testthat/test-h3_is.R | 1814 +++++++++--------- tests/testthat/test-h3_lonlat_to.R | 1150 +++++------ tests/testthat/test-h3_points_to.R | 998 +++++----- tests/testthat/test-h3_vertex.R | 2400 ++++++++++++------------ 55 files changed, 10644 insertions(+), 10163 deletions(-)
Title: Meta Fuzzy Functions
Description: Implements Meta Fuzzy Functions (MFFs) for regression Tak and Ucan (2026) <doi:10.1016/j.asoc.2026.114592> by aggregating predictions from multiple base learners using membership weights learned in the prediction space of validation set. The package supports fuzzy and crisp meta-ensemble structures via Fuzzy C-Means (FCM) Tak (2018) <doi:10.1016/j.asoc.2018.08.009>, Possibilistic FCM (PFCM) Tak (2021) <doi:10.1016/j.ins.2021.01.024>, Gustafson–Kessel (GK) clustering, and k-means, and provides a workflow to (i) generate validation/test prediction matrices from common regression learners (linear and penalized regression via 'glmnet', random forests, gradient boosting with 'xgboost' and 'lightgbm'), (ii) fit cluster-wise meta fuzzy functions and compute membership-based weights, (iii) tune clustering-related hyperparameters (number of clusters/functions, fuzziness exponent, possibilistic regularization) via grid search on validation loss, and (iv) predict on new/test pre [...truncated...]
Author: Nihat Tak [aut, cre],
Sadik Coban [ctb]
Maintainer: Nihat Tak <nihattak@gmail.com>
Diff between MFF versions 0.2.4 dated 2026-08-31 and 0.2.5 dated 2026-10-11
DESCRIPTION | 8 +++--- MD5 | 22 +++++++++--------- NAMESPACE | 46 +++++++++++++++++++++++--------------- NEWS.md | 9 +++++++ R/mff.R | 5 ++-- R/tune.mff.R | 19 +++++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/mff-workflow.html | 4 +-- man/mff.Rd | 3 +- tests/testthat/test-mff-predict.R | 2 - tests/testthat/test-tune-mff.R | 36 +++++++++++++++++++++++++++++ 12 files changed, 109 insertions(+), 45 deletions(-)
Title: Measurement and Linear Hypothesis Models for Lambda Star
Description: Estimates intrinsic and captured noncentrality from parallel
measurements and evaluates the numerical parsimony functional for an
explicitly encoded hypothesis matrix, formula, or compatible linear model.
Includes common-case model comparisons, quantized entropy capacity,
controlled temperature integration, and explicit singularity diagnostics.
Uses manuscript projection estimates by default, with an explicit alternative
population estimator. Supports common nuisance adjustment and ordinary case
or cluster percentile bootstrap intervals, with diagnostics for undefined
estimates and preserved model coding.
Provides reusable row-bound design specifications and explicit conditional
term blocks, named linear restrictions, explicit predictor-grid contrasts,
and fixed or reevaluated basis recipes under a homogeneous isotropic
measurement-fluctuation assumption. Supports explicit known-reference
mean hypotheses and paired differences from parallel measurement pairs.
Encodes fixed person-by-oc [...truncated...]
Author: Mike Hammes [aut, cre, cph]
Maintainer: Mike Hammes <mike.hammes@mikehammes.name>
Diff between lambdastar versions 0.8.1 dated 2026-10-07 and 0.8.2 dated 2026-10-11
DESCRIPTION | 6 ++--- MD5 | 10 ++++---- NEWS.md | 13 ++++++++++ R/measurement.R | 13 ++++++---- README.md | 28 ++++++++++++++++++----- tests/cases/measurement.R | 55 ++++++++++++++++++++++++++++++++++++++++++++++ 6 files changed, 106 insertions(+), 19 deletions(-)
Title: Prophet Modelling Interface for 'fable'
Description: Allows prophet models from the 'prophet' package to be used in a tidy workflow with the modelling interface of 'fabletools'. This extends 'prophet' to provide enhanced model specification and management, performance evaluation methods, and model combination tools.
Author: Mitchell O'Hara-Wild [aut, cre],
Sean Taylor [ctb] ,
Ben Letham [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between fable.prophet versions 0.1.1 dated 2026-10-02 and 1.0.0 dated 2026-10-11
DESCRIPTION | 14 MD5 | 42 +- NAMESPACE | 3 NEWS.md | 30 ++ R/model.R | 462 ++++++++++++++++++++++++++----- R/prophet.R | 1 README.md | 85 +++-- inst/doc/intro.R | 24 + inst/doc/intro.Rmd | 42 ++ inst/doc/intro.html | 95 +++++- man/components.fbl_prophet.Rd | 5 man/fable.prophet-package.Rd | 1 man/figures/README-components-plot-1.png |binary man/figures/README-components-plot-2.png |binary man/figures/README-fable-1.png |binary man/figures/README-plot-1.png |binary man/forecast.fbl_prophet.Rd | 13 man/generate.fbl_prophet.Rd |only man/prophet.Rd | 83 +++++ man/refit.fbl_prophet.Rd |only man/tidy.fbl_prophet.Rd | 10 tests/testthat/test-prophet.R | 324 +++++++++++++++++++++ vignettes/intro.Rmd | 42 ++ 23 files changed, 1124 insertions(+), 152 deletions(-)
Title: Generalizability Theory for LLM Subjective Tasks
Description: Studies the reliability and generalizability of subjective
judgments produced by large language models (LLMs), including annotation,
rating, and structured LLM-as-a-judge tasks. Specifies evaluator, prompt,
generation, and repeated-run facets through crossed or explicitly nested
random sources with configurable item interactions. Fits univariate models,
joint Gaussian models, and joint discrete models for binary, ordinal, and
unordered categorical outcomes, with source-specific covariance. Gaussian
models use exact balanced likelihood; discrete models use a dense
first-order Laplace approximation with Gaussian latent random effects.
Supported balanced decision studies compare evaluator, prompt, and
replication allocations using observed Gaussian or explicitly requested
latent binary and ordinal reliability, with random or fixed facets after
Brennan (2001). Gaussian fits report asymptotic Wald standard errors for
their variance components and delta-method intervals for the coefficients; [...truncated...]
Author: Jin Liu [aut, cre, cph]
Maintainer: Jin Liu <Veronica.Liu0206@gmail.com>
Diff between Gtheory4LLM versions 0.2.0 dated 2026-10-04 and 0.5.0 dated 2026-10-10
DESCRIPTION | 22 - MD5 | 102 +++-- NAMESPACE | 20 + NEWS.md | 330 ++++++++++++++++ R/batch.R |only R/batch_reliability.R |only R/design.R | 90 ++++ R/diagnostics_stages.R | 14 R/discrete.R | 293 ++++++++++++--- R/discrete_dense.R | 6 R/discrete_mode.R | 25 - R/discrete_sparse.R | 27 + R/discrete_sparse_mode.R | 47 ++ R/family.R | 8 R/fit.R | 44 ++ R/gaussian.R | 50 ++ R/gaussian_engine.R | 31 + R/methods.R | 8 R/planning.R |only R/preflight.R | 490 +++++++++++++++++++++++-- R/reliability.R | 215 +++++++++-- R/report.R |only R/simulation.R |only R/visualization.R |only README.md | 120 +++++- build/vignette.rds |binary inst/doc/LLM-workflow.R | 49 ++ inst/doc/LLM-workflow.Rmd | 123 +++++- inst/doc/LLM-workflow.html | 739 ++++++++++++++++++++++++++------------ inst/doc/study-planning.R |only inst/doc/study-planning.Rmd |only inst/doc/study-planning.html |only man/Gtheory4LLM-package.Rd | 13 man/gt_batch.Rd |only man/gt_batch_dstudy.Rd |only man/gt_batch_reliability.Rd |only man/gt_control.Rd | 4 man/gt_design.Rd | 5 man/gt_diagnostics.Rd | 8 man/gt_dstudy.Rd | 89 ++++ man/gt_fit.Rd | 2 man/gt_fit_methods.Rd | 2 man/gt_pilot_plan.Rd |only man/gt_plan.Rd |only man/gt_preflight.Rd | 201 ++++++++++ man/gt_reliability.Rd | 71 +++ man/gt_report.Rd |only man/gt_simulate.Rd |only man/plot.gt_reliability.Rd |only tests/package-analysis-report.R |only tests/package-argument-parity.R | 6 tests/package-batch-reliability.R |only tests/package-batch.R |only tests/package-characterization.R | 157 +++++++- tests/package-discrete-safety.R | 95 ++++ tests/package-outcome-profile.R |only tests/package-planning.R |only tests/package-preflight.R | 136 ++++++ tests/package-reporting.R |only tests/package-simulation.R |only tests/package-smoke.R | 13 tests/package-standard-methods.R | 54 ++ tests/package-visualizations.R |only vignettes/LLM-workflow.Rmd | 123 +++++- vignettes/study-planning.Rmd |only 65 files changed, 3324 insertions(+), 508 deletions(-)
Title: Common Forms for Complex Hierarchical and Relational Data
Structures
Description: Generate common data forms for complex data suitable for conversions and
transmission by decomposition as paths or primitives. Paths are sequentially-linked records,
primitives are basic atomic elements and both can model many forms and be grouped into hierarchical
structures. The universal models 'SC0' (structural) and 'SC' (labelled, relational) are composed of
edges and can represent any hierarchical form. Specialist models 'PATH', 'ARC' and 'TRI' provide the
most common intermediate forms used for converting from one form to another. The methods are
inspired by the simplicial complex <https://en.wikipedia.org/wiki/Simplicial_complex> and
provide intermediate forms that relate spatial data structures to this mathematical construct.
Author: Michael D. Sumner [aut, cre],
John Corbett [ctb] ,
Simon Wotherspoon [ctb],
Kent Johnson [dtc],
Mark Padgham [aut]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between silicate versions 0.7.1 dated 2023-01-06 and 0.7.2 dated 2026-10-10
silicate-0.7.1/silicate/man/silicate.Rd |only silicate-0.7.1/silicate/tests/testthat/Rplots.pdf |only silicate-0.7.2/silicate/DESCRIPTION | 11 silicate-0.7.2/silicate/MD5 | 94 +- silicate-0.7.2/silicate/NAMESPACE | 83 +- silicate-0.7.2/silicate/NEWS.md | 27 silicate-0.7.2/silicate/R/000_cMESH.R | 4 silicate-0.7.2/silicate/R/00_arc.R | 6 silicate-0.7.2/silicate/R/00_coord.R | 28 silicate-0.7.2/silicate/R/00_edge.R | 11 silicate-0.7.2/silicate/R/00_node.R | 8 silicate-0.7.2/silicate/R/00_path.R | 520 ++++++------- silicate-0.7.2/silicate/R/00_segment.R | 6 silicate-0.7.2/silicate/R/00_triangle.R | 4 silicate-0.7.2/silicate/R/ARC-model.R | 4 silicate-0.7.2/silicate/R/PATH-model.R | 2 silicate-0.7.2/silicate/R/SC-model.R | 8 silicate-0.7.2/silicate/R/SC0-model.R | 36 silicate-0.7.2/silicate/R/TRI-model.R | 310 +++---- silicate-0.7.2/silicate/R/compact-indexes.R | 2 silicate-0.7.2/silicate/R/dplyr.R | 2 silicate-0.7.2/silicate/R/earcut.R | 2 silicate-0.7.2/silicate/R/get-projection.R | 1 silicate-0.7.2/silicate/R/plot.R | 1 silicate-0.7.2/silicate/R/print.R | 2 silicate-0.7.2/silicate/R/silicate-package.R | 8 silicate-0.7.2/silicate/R/spatial-builder.R | 4 silicate-0.7.2/silicate/R/triangles.R | 2 silicate-0.7.2/silicate/README.md | 76 - silicate-0.7.2/silicate/build/vignette.rds |binary silicate-0.7.2/silicate/inst/doc/silicate-data-model.R | 2 silicate-0.7.2/silicate/inst/doc/silicate-data-model.html | 127 +-- silicate-0.7.2/silicate/inst/doc/silicate_topology_01.R | 2 silicate-0.7.2/silicate/inst/doc/silicate_topology_01.html | 292 +++---- silicate-0.7.2/silicate/inst/misc/ARC-data.R | 4 silicate-0.7.2/silicate/man/ARC.Rd | 3 silicate-0.7.2/silicate/man/PATH.Rd | 3 silicate-0.7.2/silicate/man/TRI.Rd | 3 silicate-0.7.2/silicate/man/inlandwaters.Rd | 2 silicate-0.7.2/silicate/man/plot.SC.Rd | 3 silicate-0.7.2/silicate/man/print.sc.Rd | 4 silicate-0.7.2/silicate/man/sc_coord.Rd | 15 silicate-0.7.2/silicate/man/sc_object.Rd | 3 silicate-0.7.2/silicate/man/sc_segment.Rd | 3 silicate-0.7.2/silicate/man/silicate-package.Rd |only silicate-0.7.2/silicate/man/tri_area.Rd | 2 silicate-0.7.2/silicate/tests/testthat/test-counts.R |only silicate-0.7.2/silicate/tests/testthat/test-plot.R | 58 - silicate-0.7.2/silicate/tests/testthat/test-triangles.R | 2 silicate-0.7.2/silicate/tests/testthat/test-trip.R | 4 50 files changed, 970 insertions(+), 824 deletions(-)
Title: Run 'lavaan' Models from Keys Lists
Description: Specifying 'lavaan' models manually can be time consuming when
multiple similar models are required. The 'semFromKeys' package streamlines
the process of running 'lavaan' models by generating model code from simple
keys lists and running entire collections of models at once.
The package was inspired by the process used in the code for
Bainbridge, T. F., Ludeke, S. G., & Smillie, L. D. (2022)
<doi:10.1037/pspp0000395>.
The package also optionally checks that identical models have not been run
on the same data, which saves time when code needs to be run again.
Author: Timothy F. Bainbridge [aut, cre, cph]
Maintainer: Timothy F. Bainbridge <tfbainbridge@gmail.com>
Diff between semFromKeys versions 0.5.5 dated 2026-09-13 and 0.5.6 dated 2026-10-10
semFromKeys-0.5.5/semFromKeys/R/esem.from.mods.R |only semFromKeys-0.5.5/semFromKeys/man/esem.from.mods.Rd |only semFromKeys-0.5.6/semFromKeys/DESCRIPTION | 6 semFromKeys-0.5.6/semFromKeys/MD5 | 48 semFromKeys-0.5.6/semFromKeys/NEWS.md | 11 semFromKeys-0.5.6/semFromKeys/R/bifactor.from.keys.R | 181 +- semFromKeys-0.5.6/semFromKeys/R/cfa.from.keys.R | 170 +- semFromKeys-0.5.6/semFromKeys/R/efa.from.keys.R | 86 - semFromKeys-0.5.6/semFromKeys/R/esem.from.keys.r | 768 +++++++--- semFromKeys-0.5.6/semFromKeys/R/sem.check.R | 83 - semFromKeys-0.5.6/semFromKeys/R/sem.cor.R | 206 +- semFromKeys-0.5.6/semFromKeys/R/sem.path.R | 105 - semFromKeys-0.5.6/semFromKeys/man/bifactor.from.keys.Rd | 41 semFromKeys-0.5.6/semFromKeys/man/cfa.from.keys.Rd | 31 semFromKeys-0.5.6/semFromKeys/man/efa.from.keys.Rd | 32 semFromKeys-0.5.6/semFromKeys/man/esem.from.keys.Rd | 289 ++- semFromKeys-0.5.6/semFromKeys/man/sem.check.Rd | 4 semFromKeys-0.5.6/semFromKeys/man/sem.cor.Rd | 149 + semFromKeys-0.5.6/semFromKeys/man/sem.path.Rd | 166 +- semFromKeys-0.5.6/semFromKeys/tests/testthat/test-bifactor.from.keys.R | 43 semFromKeys-0.5.6/semFromKeys/tests/testthat/test-cache.clean.R | 9 semFromKeys-0.5.6/semFromKeys/tests/testthat/test-cfa.from.keys.R | 87 - semFromKeys-0.5.6/semFromKeys/tests/testthat/test-efa.from.keys.R | 22 semFromKeys-0.5.6/semFromKeys/tests/testthat/test-esem.from.keys.r | 127 + semFromKeys-0.5.6/semFromKeys/tests/testthat/test-esem.from.mods.R | 40 semFromKeys-0.5.6/semFromKeys/tests/testthat/test-sem.cor.R | 47 26 files changed, 1849 insertions(+), 902 deletions(-)
Title: Spline-Based Nonlinear Modeling for Multilevel and Longitudinal
Data
Description: Provides a unified framework for fitting, predicting, and
interpreting nonlinear relationships in single-level, multilevel, and
longitudinal regression models. Flexible functional forms are supported
using natural cubic splines ('splines'), B-splines ('splines'), and GAM
smooths ('mgcv'). Supports two-way and nested clustering via 'lme4',
automatic knot selection by AIC or BIC, multilevel R-squared
decomposition (marginal and conditional R-squared of Nakagawa and
Schielzeth (2013) <doi:10.1111/j.2041-210x.2012.00261.x>, extended to
random slopes as in Johnson (2014) <doi:10.1111/2041-210X.12225>, with
level-specific variance partitioning), a postestimation suite
returning first and second derivatives with confidence bands, turning
points and inflection regions, and a model comparison workflow
contrasting linear, polynomial, and spline fits by AIC, BIC, and
likelihood-ratio tests. Cluster heterogeneity in nonlinear effects is
supported via random-slope spline terms. Any 'lme [...truncated...]
Author: Subir Hait [aut, cre]
Maintainer: Subir Hait <haitsubi@msu.edu>
Diff between MultiSpline versions 0.2.0 dated 2026-04-16 and 0.3.0 dated 2026-10-10
DESCRIPTION | 26 +-- MD5 | 59 +++--- NAMESPACE | 1 NEWS.md | 175 +++++++++++++------- R/engine.R |only R/nl_compare.R | 68 +++----- R/nl_derivatives.R | 285 +++++++++++++++------------------ R/nl_fit.R | 169 +++++++++++++------ R/nl_het.R | 77 ++++----- R/nl_icc.R | 103 +++--------- R/nl_knots.R | 13 + R/nl_methods.R | 22 +- R/nl_plot.R | 32 ++- R/nl_predict.R | 398 +++++++++++++++++++---------------------------- R/nl_r2.R | 161 +++---------------- R/nl_summary.R | 5 R/nl_wald.R |only README.md | 338 +++++++-------------------------------- man/nl_compare.Rd | 39 ++-- man/nl_derivatives.Rd | 73 ++++++-- man/nl_fit.Rd | 108 +++++++----- man/nl_het.Rd | 47 +++-- man/nl_icc.Rd | 20 +- man/nl_knots.Rd | 28 ++- man/nl_plot.Rd | 30 ++- man/nl_predict.Rd | 80 ++++++--- man/nl_r2.Rd | 30 ++- man/nl_summary.Rd | 6 man/nl_turning_points.Rd | 32 ++- man/nl_wald.Rd |only tests |only 31 files changed, 1138 insertions(+), 1287 deletions(-)
Title: Multivariate Menu for Radiant: Business Analytics using R and
Shiny
Description: The Radiant Multivariate menu includes interfaces for perceptual
mapping, factor analysis, cluster analysis, and conjoint analysis. The
application extends the functionality in 'radiant.data'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.multivariate versions 1.6.8 dated 2026-01-10 and 1.6.9 dated 2026-10-10
DESCRIPTION | 10 +-- MD5 | 18 ++--- NAMESPACE | 140 ++++++++++++++++++++++++-------------------- NEWS.md | 5 + R/full_factor.R | 2 R/mds.R | 2 R/pre_factor.R | 2 R/prmap.R | 4 - README.md | 68 +-------------------- tests/testthat/test_stats.R | 14 ++-- 10 files changed, 113 insertions(+), 152 deletions(-)
More information about radiant.multivariate at CRAN
Permanent link
Title: Model Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Model menu includes interfaces for linear and logistic
regression, naive Bayes, neural networks, classification and regression trees,
model evaluation, collaborative filtering, decision analysis, and simulation.
The application extends the functionality in 'radiant.data'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.model versions 1.6.12 dated 2026-09-20 and 1.6.13 dated 2026-10-10
DESCRIPTION | 8 ++++---- MD5 | 25 +++++++++++++------------ NEWS.md | 6 ++++++ R/logistic.R | 16 +++++++++++++++- R/regress.R | 7 ++++++- inst/app/tools/analysis/logistic_ui.R | 17 +++++++++++++++-- inst/app/tools/analysis/regress_ui.R | 16 ++++++++++++++-- inst/app/tools/help/logistic.Rmd | 6 ++++++ inst/app/tools/help/logistic.md | 6 ++++++ inst/app/tools/help/regress.Rmd | 8 ++++++++ inst/app/tools/help/regress.md | 8 ++++++++ man/predict.logistic.Rd | 2 +- man/predict.regress.Rd | 2 +- tests/testthat/test_predict_interval.R |only 14 files changed, 103 insertions(+), 24 deletions(-)
Title: Stable Diffusion Image Generation
Description: Provides Stable Diffusion image generation using the 'ggmlR'
library, with no 'Python' or external API dependencies. Supports
text-to-image and image-to-image generation for SD 1.x, SD 2.x, 'SDXL',
Flux, and 'FLUX.2'. A single sd_generate() function handles the entire pipeline,
including sampling and high-resolution output. Features multi-GPU support,
a 'Shiny' GUI, and runs on CPU or 'Vulkan' GPU across Linux, macOS, and
Windows.
Author: Yuri Baramykov [aut, cre] ,
Georgi Gerganov [ctb, cph] ,
leejet [ctb, cph] ,
stduhpf [ctb] ,
Green-Sky [ctb] ,
wbruna [ctb] ,
akleine [ctb] ,
Martin Raiber [cph] ,
Rich Geldreich [cph] ,
RAD Game Tools [cph] ,
Valve Software [cph] ,
Alex Evans [cph] [...truncated...]
Maintainer: Yuri Baramykov <lbsbmsu@mail.ru>
Diff between sd2R versions 0.2.1 dated 2026-06-19 and 0.2.1.1 dated 2026-10-10
DESCRIPTION | 6 ++--- MD5 | 6 ++--- NEWS.md | 10 +++++++++ README.md | 66 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++- 4 files changed, 81 insertions(+), 7 deletions(-)
Title: Comparison of Bioregionalization Methods
Description: The main purpose of this package is to propose a transparent methodological framework to compare bioregionalization methods based on hierarchical and non-hierarchical clustering algorithms (Kreft & Jetz (2010) <doi:10.1111/j.1365-2699.2010.02375.x>) and network algorithms (Lenormand et al. (2019) <doi:10.1002/ece3.4718> and Leroy et al. (2019) <doi:10.1111/jbi.13674>).
Author: Maxime Lenormand [aut, cre] ,
Boris Leroy [aut] ,
Pierre Denelle [aut]
Maintainer: Maxime Lenormand <maxime.lenormand@inrae.fr>
Diff between bioregion versions 1.4.0 dated 2026-03-29 and 1.5.0 dated 2026-10-10
bioregion-1.4.0/bioregion/R/IHCT.R |only bioregion-1.4.0/bioregion/inst/CITATION |only bioregion-1.4.0/bioregion/inst/REFERENCES.bib |only bioregion-1.4.0/bioregion/man/figures/05_map_fish_bipartite_infomap.png |only bioregion-1.4.0/bioregion/man/figures/05_network_fish_basic.png |only bioregion-1.4.0/bioregion/man/figures/05_network_fish_bipartite_colored.png |only bioregion-1.4.0/bioregion/man/figures/05_network_fish_unipartite_weighted.png |only bioregion-1.4.0/bioregion/man/figures/comparison_Bray-Curtis.png |only bioregion-1.4.0/bioregion/man/figures/comparison_Jaccard.png |only bioregion-1.4.0/bioregion/man/figures/core_terms.svg |only bioregion-1.4.0/bioregion/man/figures/find_optimal_n.png |only bioregion-1.4.0/bioregion/man/figures/logo.svg |only bioregion-1.4.0/bioregion/man/figures/workflow.svg |only bioregion-1.4.0/bioregion/man/figures/workflow_network.png |only bioregion-1.4.0/bioregion/man/figures/workflow_network.svg |only bioregion-1.4.0/bioregion/man/figures/workflow_nonetwork.png |only bioregion-1.4.0/bioregion/man/figures/workflow_nonetwork.svg |only bioregion-1.4.0/bioregion/vignettes/journal-of-biogeography.csl |only bioregion-1.4.0/bioregion/vignettes/style_citation.csl |only bioregion-1.5.0/bioregion/DESCRIPTION | 14 bioregion-1.5.0/bioregion/MD5 | 92 - bioregion-1.5.0/bioregion/NAMESPACE | 2 bioregion-1.5.0/bioregion/R/RcppExports.R | 20 bioregion-1.5.0/bioregion/R/bioregion_colors.R | 129 + bioregion-1.5.0/bioregion/R/bioregion_metrics.R | 84 - bioregion-1.5.0/bioregion/R/bioregionalization_metrics.R | 735 ++++------ bioregion-1.5.0/bioregion/R/compare_bioregionalizations.R | 13 bioregion-1.5.0/bioregion/R/cut_tree.R | 3 bioregion-1.5.0/bioregion/R/find_optimal_n.R | 221 +-- bioregion-1.5.0/bioregion/R/generic_functions.R | 124 - bioregion-1.5.0/bioregion/R/hclu_diana.R | 6 bioregion-1.5.0/bioregion/R/hclu_hierarclust.R | 291 +++ bioregion-1.5.0/bioregion/R/hclu_optics.R | 17 bioregion-1.5.0/bioregion/R/ihct.R |only bioregion-1.5.0/bioregion/R/map_bioregions.R | 5 bioregion-1.5.0/bioregion/R/netclu_infomap.R | 2 bioregion-1.5.0/bioregion/R/nhclu_dbscan.R | 5 bioregion-1.5.0/bioregion/R/site_species_metrics.R | 229 +-- bioregion-1.5.0/bioregion/R/utils.R | 338 ++-- bioregion-1.5.0/bioregion/build/partial.rdb |binary bioregion-1.5.0/bioregion/build/vignette.rds |binary bioregion-1.5.0/bioregion/inst/doc/bioregion.Rmd | 4 bioregion-1.5.0/bioregion/inst/doc/bioregion.html | 6 bioregion-1.5.0/bioregion/man/bioregion_colors.Rd | 23 bioregion-1.5.0/bioregion/man/bioregion_metrics.Rd | 18 bioregion-1.5.0/bioregion/man/bioregionalization_metrics.Rd | 168 -- bioregion-1.5.0/bioregion/man/find_optimal_n.Rd | 50 bioregion-1.5.0/bioregion/man/hclu_hierarclust.Rd | 188 ++ bioregion-1.5.0/bioregion/man/hclu_optics.Rd | 15 bioregion-1.5.0/bioregion/man/ihct.Rd |only bioregion-1.5.0/bioregion/man/map_bioregions.Rd | 5 bioregion-1.5.0/bioregion/man/netclu_infomap.Rd | 2 bioregion-1.5.0/bioregion/man/nhclu_affprop.Rd | 8 bioregion-1.5.0/bioregion/man/nhclu_dbscan.Rd | 3 bioregion-1.5.0/bioregion/man/site_species_metrics.Rd | 82 - bioregion-1.5.0/bioregion/src/RcppExports.cpp | 70 bioregion-1.5.0/bioregion/src/ihct_trees.cpp |only bioregion-1.5.0/bioregion/vignettes/bioregion.Rmd | 4 58 files changed, 1729 insertions(+), 1247 deletions(-)
Title: Useful Wrappers Around Commonly Used Functions
Description: The main functionalities of 'wrappedtools' are:
adding backticks to variable names; rounding to desired precision
with special case for p-values;
selecting columns based on pattern and/or class and storing their position, name,
and backticked name; computing and formatting of descriptive statistics
(e.g. mean±SD), comparing groups and creating publication-ready tables with
descriptive statistics and p-values; creating specialized plots for
correlation matrices. Functions were mainly written for my own daily work or
teaching, but may be of use to others as well.
Author: Andreas Busjahn [cre, aut] ,
Franziska Eidloth [aut],
Bilal Asser [aut]
Maintainer: Andreas Busjahn <andreas@busjahn.net>
Diff between wrappedtools versions 0.9.9 dated 2025-09-04 and 0.10.0 dated 2026-10-10
DESCRIPTION | 16 MD5 | 120 - NAMESPACE | 80 NEWS.md | 144 - R/basefunctions.R | 128 - R/biotech.R | 240 +- R/clin_estimates.R | 300 +-- R/constants.R | 14 R/data.R | 6 R/descriptives.R | 49 R/pkgstart.R | 114 - R/plots.R | 100 - R/tests.R | 2728 ++++++++++++++--------------- README.md | 17 build/vignette.rds |binary inst/doc/wrappedtools.R | 16 inst/doc/wrappedtools.Rmd | 20 inst/doc/wrappedtools.html | 33 man/WINratio.Rd | 8 man/bt.Rd | 2 man/compare_n_numvars.Rd | 11 man/eGFR.Rd | 2 man/faketrial.Rd | 2 man/formatP.Rd | 12 man/glmCI.Rd | 2 man/logrange_1.Rd | 17 man/markSign.Rd | 2 man/pairwise_fisher_test.Rd | 4 man/pairwise_ordcat_test.Rd | 8 man/pairwise_t_test.Rd | 2 man/pairwise_wilcox_test.Rd | 6 man/plot_LB.Rd | 16 man/plot_MM.Rd | 16 man/se_median.Rd | 6 man/tab.search.Rd | 6 man/wrappedtools-package.Rd | 3 tests/testthat/test-FindVars.R | 17 tests/testthat/test-SEM.R | 6 tests/testthat/test-cat_desc_stats.R | 5 tests/testthat/test-compare2qualvars.R | 19 tests/testthat/test-compare_n_numvars.R | 34 tests/testthat/test-compare_n_qualvars.R | 6 tests/testthat/test-cortestR.R | 9 tests/testthat/test-formatP.R | 7 tests/testthat/test-glm_CI.R | 7 tests/testthat/test-ksnormal.R | 11 tests/testthat/test-logrange.R | 13 tests/testthat/test-markSign.R | 20 tests/testthat/test-meansd.R | 9 tests/testthat/test-meanse.R | 7 tests/testthat/test-median_cl_boot.R | 24 tests/testthat/test-median_quart.R | 10 tests/testthat/test-medianse.R | 7 tests/testthat/test-pairwise_fisher-test.R | 21 tests/testthat/test-pairwise_ordcat_test.R | 9 tests/testthat/test-pairwise_t_test.R | 9 tests/testthat/test-pairwise_wilcox_test.R | 11 tests/testthat/test-roundR.R | 5 tests/testthat/test-t_var_test.R | 7 tests/testthat/test-var_coeff.R | 6 vignettes/wrappedtools.Rmd | 20 61 files changed, 2242 insertions(+), 2307 deletions(-)
Title: Scorecard Development and Internal Ratings-Based Risk Parameters
Description: Builds points scorecards for binary targets (credit risk, fraud,
propensity) on the optimal binning and weight of evidence engine of
'OptimalBinningWoE', and takes them to the risk parameters of the internal
ratings-based (IRB) approach. Variables are selected through optimal
binning, eight admission rules, hold-out revalidation with frozen bins and
a consensus of 'glmnet', 'xgboost', 'lightgbm' and 'ranger' models weighted
by out-of-sample performance; the audit funnel never drops a candidate
from the report. The scorecard is fitted with an explicit, auditable scale
alignment (a log-odds regression on the raw score composed with the
points-to-double-the-odds map); cut-offs are swept with frozen cuts;
reject inference is reported as a sensitivity band; the population and
characteristic stability indices (PSI and CSI) are monitored with both the
fixed and the sample-size-adjusted threshold; and production SQL is
generated in fourteen dialects, with the agreement between R and SQL
verifi [...truncated...]
Author: Jose Evandeilton Lopes [aut, cre, cph]
Maintainer: Jose Evandeilton Lopes <evandeilton@gmail.com>
Diff between scorecraft versions 0.3.0 dated 2026-10-06 and 0.3.2 dated 2026-10-10
DESCRIPTION | 13 MD5 | 271 ++++++++++------- NAMESPACE | 60 +++ NEWS.md | 121 +++++++ R/RcppExports.R | 21 + R/apply.R | 8 R/bands.R |only R/bin.R | 6 R/capital.R | 24 - R/claims.R |only R/classing.R | 4 R/config.R | 52 ++- R/cpp.R | 26 + R/cutoff.R | 249 +++++++++++++--- R/data.R | 20 - R/db.R | 2 R/default.R | 2 R/detection.R |only R/ead.R | 82 ++--- R/ecl.R | 4 R/export.R | 48 ++- R/funnel.R | 4 R/irb-binning.R | 4 R/irb-params.R | 10 R/lgd.R | 67 ++-- R/maturity.R |only R/metrics.R | 85 ++++- R/mix-shift.R |only R/model.R | 4 R/monitor.R | 16 - R/operating.R |only R/overlap.R |only R/pd.R | 47 +-- R/rag.R |only R/score-cross.R |only R/scorecard.R | 106 +++++- R/scorecraft-package.R | 29 + R/segments.R |only R/select.R | 2 R/split.R | 6 R/sql.R | 7 R/study.R |only R/tiers.R |only R/triage.R | 6 R/uplift.R |only R/utils.R | 12 README.md | 7 build/partial.rdb |only build/vignette.rds |binary inst/WORDLIST | 73 ++++ inst/cheatsheet/scorecraft-cheatsheet.html | 274 ++++++++++++++++- inst/cheatsheet/scorecraft-cheatsheet.pdf |binary inst/doc/alignment-and-portfolio.Rmd | 11 inst/doc/alignment-and-portfolio.html | 11 inst/doc/coarse-classing.Rmd | 8 inst/doc/coarse-classing.html | 22 - inst/doc/score-studies.R |only inst/doc/score-studies.Rmd |only inst/doc/score-studies.html |only inst/doc/scorecraft.R | 5 inst/doc/scorecraft.Rmd | 24 + inst/doc/scorecraft.html | 447 +++++++++++++++-------------- man/scorecraft-package.Rd | 28 + man/scr_apply.Rd | 34 ++ man/scr_bands.Rd |only man/scr_capital.Rd | 4 man/scr_claims.Rd |only man/scr_coarse_classing.Rd | 2 man/scr_config.Rd | 2 man/scr_config_keys.Rd | 3 man/scr_core.Rd | 2 man/scr_demo_ead.Rd | 10 man/scr_demo_panel.Rd | 4 man/scr_demo_portfolio.Rd | 2 man/scr_demo_rates.Rd | 4 man/scr_detection.Rd |only man/scr_ead.Rd | 6 man/scr_ead_data.Rd | 14 man/scr_ead_downturn.Rd | 2 man/scr_ead_validate.Rd | 12 man/scr_ecl.Rd | 2 man/scr_elbe.Rd | 2 man/scr_export.Rd | 65 +++- man/scr_fetch.Rd | 2 man/scr_grades.Rd | 4 man/scr_irb_params.Rd | 4 man/scr_irb_rw.Rd | 2 man/scr_lgd.Rd | 8 man/scr_lgd_downturn.Rd | 2 man/scr_lgd_floor.Rd | 2 man/scr_lgd_pools.Rd | 4 man/scr_lgd_validate.Rd | 18 - man/scr_maturity.Rd |only man/scr_metrics.Rd | 20 + man/scr_migration.Rd | 2 man/scr_mix_shift.Rd |only man/scr_operating.Rd |only man/scr_overlap.Rd |only man/scr_pd_validate.Rd | 10 man/scr_rag.Rd |only man/scr_rag_plan.Rd |only man/scr_reasons.Rd | 2 man/scr_reject.Rd | 2 man/scr_sa_rw.Rd | 4 man/scr_score_cross.Rd |only man/scr_score_gains.Rd | 29 + man/scr_scorecard.Rd | 5 man/scr_segments.Rd |only man/scr_split.Rd | 4 man/scr_sql.Rd | 43 ++ man/scr_strategy.Rd | 121 ++++++- man/scr_tiers.Rd |only man/scr_triage.Rd | 2 man/scr_uplift.Rd |only man/scr_workout.Rd | 6 src/RcppExports.cpp | 20 + src/concordance.cpp | 2 src/correlation.cpp | 10 src/ecl.cpp | 2 src/tiers.cpp |only tests/testthat/helper-ead.R | 2 tests/testthat/helper-pd.R | 2 tests/testthat/helper-scorecraft.R | 30 + tests/testthat/test-audit-fixes.R | 2 tests/testthat/test-capital.R | 12 tests/testthat/test-claims.R |only tests/testthat/test-count-engine.R |only tests/testthat/test-cpp.R | 2 tests/testthat/test-cutoff.R | 281 ++++++++++++++++++ tests/testthat/test-detection.R |only tests/testthat/test-ead.R | 35 +- tests/testthat/test-export.R | 25 + tests/testthat/test-irb-core.R | 1 tests/testthat/test-lgd.R | 23 + tests/testthat/test-maturity.R |only tests/testthat/test-mix-shift.R |only tests/testthat/test-monitor.R | 38 ++ tests/testthat/test-operating.R |only tests/testthat/test-overlap.R |only tests/testthat/test-pd.R | 27 + tests/testthat/test-rag.R |only tests/testthat/test-runset.R | 2 tests/testthat/test-score-cross.R |only tests/testthat/test-scorecard.R | 77 ++++ tests/testthat/test-segments.R |only tests/testthat/test-split.R | 2 tests/testthat/test-study.R |only tests/testthat/test-tiers.R |only tests/testthat/test-triage-capital.R | 6 tests/testthat/test-triage-core.R | 4 tests/testthat/test-triage-lgd-ead.R | 6 tests/testthat/test-triage-pd.R | 4 tests/testthat/test-triage-production.R | 2 tests/testthat/test-uplift.R |only tests/testthat/test-utils.R | 9 vignettes/alignment-and-portfolio.Rmd | 11 vignettes/coarse-classing.Rmd | 8 vignettes/score-studies.Rmd |only vignettes/scorecraft.Rmd | 24 + 159 files changed, 2655 insertions(+), 808 deletions(-)
Title: Frequentist Dynamic Borrowing for Hybrid-Control Survival Trials
Description: Implements a class of likelihood-informed frequentist dynamic
borrowing methods for hybrid-control survival trials based on penalized
Cox partial likelihood estimation. Implements four
likelihood-informed penalty structures (precision-weighted L1,
smoothed integrated-gate, information-adaptive minimax concave penalty
(MCP), and likelihood-ratio-weighted L1), together with the adaptive
lasso borrowing approach of Li et al. (2023, <doi:10.1002/bimj.202100406>).
Provides conditional model-based standard errors and local plug-in
sandwich variance approximations, with smoothed penalties. Tools for design-stage lambda calibration
via simulation, including a two-stage coarse-fine grid search, drift-level
early stopping, and per-method tuning under both inference types, are also
provided. A simulation harness for evaluating type I error and statistical
power across population drift scenarios is included.
Author: Yusuke Yamaguchi [aut, cre]
Maintainer: Yusuke Yamaguchi <yamagubed@gmail.com>
Diff between fdb versions 0.2.0 dated 2026-10-04 and 0.2.2 dated 2026-10-10
DESCRIPTION | 8 MD5 | 56 +- NAMESPACE | 4 NEWS.md | 118 +++-- R/calibration.R | 6 R/censoring.R |only R/fdb-package.R | 17 R/fit_methods.R | 660 ++++++++++++++--------------- R/method_labels.R |only R/optimize_delta.R | 257 ++++++----- R/penalties.R | 366 ++++++++-------- R/simulate_data.R | 310 ++++++------- R/simulation.R | 14 R/study_wrapper.R | 2 README.md | 34 + inst/doc/fdb-intro.Rmd | 226 ++++----- inst/doc/fdb-intro.html | 21 man/add_ess_to_simulation_result.Rd | 4 man/calibrate_censor_rate.Rd |only man/compute_ess_from_raw.Rd | 4 man/fdb-package.Rd | 10 man/fit_P3_info_MCP.Rd | 14 man/method_labels.Rd |only man/run_simulation.Rd | 2 man/simulate_hybrid_cox.Rd | 10 tests/testthat/test-fit-methods.R | 164 +++---- tests/testthat/test-fixed-censoring.R |only tests/testthat/test-manuscript-penalties.R | 256 +++++------ tests/testthat/test-release-controls.R | 154 +++--- tests/testthat/test-simulation.R | 82 +-- tests/testthat/test-standardized-mcp.R |only vignettes/fdb-intro.Rmd | 226 ++++----- 32 files changed, 1568 insertions(+), 1457 deletions(-)
Title: Fast Compact Multilayer Perceptrons
Description: A small multilayer perceptron implementation for
'R'. It supports regression and classification, multiple hidden layers,
mini-batch training, adaptive moment estimation, stochastic gradient descent,
momentum, Nesterov acceleration, resilient backpropagation and limited-memory
quasi-Newton optimization, dropout, squared-weight regularization, early
stopping, convergence thresholds, gradient clipping, sample and class weights,
callback hooks,
target scaling and robust Huber loss for regression, 'Rcpp' forward-pass
kernels, formula interfaces, model evaluation with balanced classification
metrics, cross-validation, compact tuning, permutation importance, model
persistence helpers, and standard prediction methods. Methods follow
Rumelhart, Hinton and Williams (1986) <doi:10.1038/323533a0>, with
optimizers including Riedmiller and Braun (1993)
<doi:10.1109/ICNN.1993.298623>, Nocedal (1980)
<doi:10.1090/S0025-5718-1980-0572855-7>, and Kingma and Ba (2014)
<doi:10.48550/a [...truncated...]
Author: Feng Ji [aut, cre]
Maintainer: Feng Ji <f.ji@utoronto.ca>
Diff between neuralnetwork versions 0.1.1 dated 2026-09-06 and 0.1.4 dated 2026-10-10
DESCRIPTION | 16 MD5 | 60 +- NEWS.md | 75 +++ R/engine.R | 188 ++++++-- R/neuralnetwork.R | 779 ++++++++++++++++++++++++++---------- README.md | 45 +- inst/WORDLIST | 9 inst/doc/neuralnetwork.R | 37 + inst/doc/neuralnetwork.Rmd | 123 +++++ inst/doc/neuralnetwork.html | 588 ++++++++++++++++----------- man/compat.Rd | 77 ++- man/neuralnetwork-callbacks.Rd | 6 man/neuralnetwork-metrics.Rd | 73 ++- man/neuralnetwork-objects.Rd | 35 + man/neuralnetwork-package.Rd | 7 man/nn_cv.Rd | 20 man/nn_evaluate.Rd | 30 + man/nn_fit.Rd | 59 ++ man/nn_permutation_importance.Rd | 12 man/nn_save.Rd | 9 man/nn_tune.Rd | 18 man/plot.neuralnetwork.Rd | 8 man/predict.neuralnetwork.Rd | 9 man/print.neuralnetwork.Rd | 8 man/summary.neuralnetwork.Rd | 4 src/neuralnetwork.cpp | 8 tests/test-basic.R | 20 tests/test-classification-metrics.R |only tests/test-gradient-optimizers.R |only tests/test-inference.R |only tests/test-regression-data.R |only tests/test-selection-training.R |only tests/test-weighted-minibatches.R |only vignettes/neuralnetwork.Rmd | 123 +++++ 34 files changed, 1842 insertions(+), 604 deletions(-)
Title: A Graphical Interface to Perform STOCSY Analyses on NMR Data
Description: Launches a 'shiny' based application for Nuclear Magnetic Resonance (NMR) data importation and Statistical TOtal Correlation SpectroscopY (STOCSY) analyses in a full interactive approach. The theoretical background and applications of the STOCSY method are described by Cloarec, O., Dumas, M. E., Craig, A., Barton, R. H., Trygg, J., Hudson, J., Blancher, C., Gauguier, D., Lindon, J. C., Holmes, E. & Nicholson, J. (2005) <doi:10.1021/ac048630x>. Spectral alignment follows the interval correlation optimized shifting method of Savorani, F., Tomasi, G. & Engelsen, S. B. (2010) <doi:10.1016/j.jmr.2009.11.012>.
Author: Luiz Henrique Keng Queiroz Junior [aut, cre],
Vitor Mendes de Oliveira [aut],
Renan Ziemann Wilhelms [aut]
Maintainer: Luiz Henrique Keng Queiroz Junior <keng@ufg.br>
Diff between iSTATS versions 1.7 dated 2023-12-05 and 1.8 dated 2026-10-10
iSTATS-1.7/iSTATS/inst/app/global.R |only iSTATS-1.8/iSTATS/DESCRIPTION | 30 iSTATS-1.8/iSTATS/MD5 | 151 +- iSTATS-1.8/iSTATS/NAMESPACE | 7 iSTATS-1.8/iSTATS/NEWS |only iSTATS-1.8/iSTATS/R/alignment_regions.R |only iSTATS-1.8/iSTATS/R/icoshift.R |only iSTATS-1.8/iSTATS/R/icoshift_core.R |only iSTATS-1.8/iSTATS/R/icoshift_scal.R |only iSTATS-1.8/iSTATS/R/main.R | 103 + iSTATS-1.8/iSTATS/build |only iSTATS-1.8/iSTATS/inst/ICOSHIFT.md |only iSTATS-1.8/iSTATS/inst/app/Pretreatment_server.R | 686 +++++++--- iSTATS-1.8/iSTATS/inst/app/Pretreatment_ui.R | 5 iSTATS-1.8/iSTATS/inst/app/alignment_ui.R |only iSTATS-1.8/iSTATS/inst/app/example_data_server.R | 7 iSTATS-1.8/iSTATS/inst/app/functions.R | 1354 ++++++++++++++++++-- iSTATS-1.8/iSTATS/inst/app/plot_interativo_server.R | 373 ++--- iSTATS-1.8/iSTATS/inst/app/plot_interativo_ui.R | 176 +- iSTATS-1.8/iSTATS/inst/app/select_signals_server.R | 1098 +++++++--------- iSTATS-1.8/iSTATS/inst/app/select_signals_ui.R | 32 iSTATS-1.8/iSTATS/inst/app/server.R | 54 iSTATS-1.8/iSTATS/inst/app/session_state.R |only iSTATS-1.8/iSTATS/inst/app/stocsy_i_server.R | 607 +++----- iSTATS-1.8/iSTATS/inst/app/stocsy_i_ui.R | 4 iSTATS-1.8/iSTATS/inst/app/stocsy_is_server.R | 232 --- iSTATS-1.8/iSTATS/inst/app/stocsy_is_ui.R | 4 iSTATS-1.8/iSTATS/inst/app/stocsy_rt_server.R | 266 --- iSTATS-1.8/iSTATS/inst/app/stocsy_rt_ui.R | 4 iSTATS-1.8/iSTATS/inst/app/ui.R | 12 iSTATS-1.8/iSTATS/inst/app/uploader_server.R | 9 iSTATS-1.8/iSTATS/inst/app/uploader_server_CSV.R | 64 iSTATS-1.8/iSTATS/inst/app/uploader_server_Rdata.R | 3 iSTATS-1.8/iSTATS/inst/app/www/alignment_regions.js |only iSTATS-1.8/iSTATS/inst/app/www/istats1.gif |binary iSTATS-1.8/iSTATS/inst/app/www/suggest_regions.png |only iSTATS-1.8/iSTATS/man/iSTATS.Rd | 4 iSTATS-1.8/iSTATS/man/icoshift.Rd |only iSTATS-1.8/iSTATS/tests |only 39 files changed, 3256 insertions(+), 2029 deletions(-)
Title: Reproducible Cardiovascular Health Metric Scoring
Description: Provides a reproducible R implementation of the American Heart
Association Life's Essential 8 cardiovascular health scoring framework for
adult records from people aged 20 years or older. Calculates the eight
component scores and their unweighted composite score from available
component data using the 2022 adult definition described by Lloyd-Jones et
al. (2022)
<doi:10.1161/CIR.0000000000001078>.
Author: Carson Richardson [aut, cre, cph] ,
Amrik Khalsa [ctb] ,
Sara Conroy [ctb]
Maintainer: Carson Richardson <carson.richardson@outlook.com>
Diff between essential8 versions 0.1.0 dated 2026-09-03 and 0.2.0 dated 2026-10-10
DESCRIPTION | 35 + MD5 | 33 - NEWS.md | 19 R/diet-mepa.R | 47 +- R/essential8-package.R | 9 R/score-le8.R | 390 ++++++++++++---- README.md | 73 ++- inst/doc/essential8-get-started.R | 17 inst/doc/essential8-get-started.Rmd | 58 +- inst/doc/essential8-get-started.html | 70 ++- man/essential8-package.Rd | 9 man/score_le8.Rd | 48 +- tests/testthat/helper-adult-fixtures.R | 362 ++++++++------- tests/testthat/test-diet-mepa.R | 668 ++++++++++++++--------------- tests/testthat/test-score-le8-missing.R |only tests/testthat/test-score-le8-validation.R | 576 +++++++++++++------------ tests/testthat/test-score-le8.R | 4 vignettes/essential8-get-started.Rmd | 58 +- 18 files changed, 1475 insertions(+), 1001 deletions(-)
Title: R Interface to 'DuckDB' Database with Spatial Extension
Description: Fast and memory-efficient functions to analyze and manipulate large
spatial datasets. It leverages the fast analytical
capabilities of ‘DuckDB’ and its spatial extension (see
<https://duckdb.org/docs/stable/core_extensions/spatial/overview>)
while maintaining compatibility with R’s spatial data ecosystem to
work with spatial vector data.
Author: Adrian Cidre Gonzalez [aut, cre] ,
Egor Kotov [aut] ,
Rafael H. M. Pereira [aut]
Maintainer: Adrian Cidre Gonzalez <adrian.cidre@gmail.com>
Diff between duckspatial versions 1.2.1 dated 2026-07-04 and 1.3.0 dated 2026-10-10
DESCRIPTION | 14 MD5 | 133 +- NAMESPACE | 59 - NEWS.md | 40 R/crs_persistence.R | 7 R/db_extension.R | 49 R/db_utils.R | 6 R/ddbs_affine.R | 80 - R/ddbs_as_spatial.R | 2 R/ddbs_crs.R | 16 R/ddbs_dimensions_ops.R | 16 R/ddbs_extent_funs.R | 89 + R/ddbs_filter.R | 30 R/ddbs_interpolate_aw.R | 32 R/ddbs_join.R | 11 R/ddbs_measure.R | 88 - R/ddbs_mvt.R | 4 R/ddbs_ops_binary.R | 50 R/ddbs_ops_unary.R | 22 R/ddbs_ops_unary_line.R | 14 R/ddbs_predicates.R | 58 - R/ddbs_quadkey.R | 34 R/ddbs_templates.R | 65 - R/ddbs_union.R | 30 R/duckspatial-package.R | 1 R/duckspatial_df.R | 7 R/duckspatial_df_sf_methods.R | 7 R/io_read.R | 20 R/io_register.R | 40 R/io_write.R | 60 - R/io_write_dataset.R | 2 R/nanoarrow_methods.R | 74 + R/utils_not_exported.R | 204 ++- R/zzz.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/aw_interpolation.html | 40 inst/doc/benchmark.R | 711 ++++++------ inst/doc/benchmark.html | 329 +++-- inst/doc/benchmark.qmd | 1180 ++++++++++----------- inst/doc/duckspatial.html | 85 - inst/doc/spatial_joins.html | 11 man/as_nanoarrow_array_stream.duckspatial_df.Rd | 10 man/ddbs_default_conn.Rd | 21 man/ddbs_expand.Rd |only man/ddbs_filter.Rd | 5 man/ddbs_intersection_agg.Rd | 2 man/ddbs_join.Rd | 5 man/ddbs_measure_funs.Rd | 28 man/ddbs_predicate.Rd | 5 tests/testthat/test-crs-persistence.R | 41 tests/testthat/test-db_read.R | 13 tests/testthat/test-db_register.R | 49 tests/testthat/test-db_write.R | 146 ++ tests/testthat/test-ddbs_filter.R | 88 + tests/testthat/test-ddbs_join.R | 15 tests/testthat/test-ddbs_macros.R | 28 tests/testthat/test-ddbs_measure.R | 93 + tests/testthat/test-ddbs_ops_unary.R | 16 tests/testthat/test-ddbs_predicates.R | 170 +++ tests/testthat/test-ddbs_quadkey.R | 41 tests/testthat/test-duckspatial_df_dplyr_methods.R | 70 + tests/testthat/test-duckspatial_df_sf_methods.R | 8 tests/testthat/test-get_query_list.R | 106 + tests/testthat/test-import_view_to_connection.R | 3 tests/testthat/test-nanoarrow_methods.R | 116 +- tests/testthat/test-utils_not_exported.R |only vignettes/benchmark.qmd | 1180 ++++++++++----------- vignettes/data |only 69 files changed, 3787 insertions(+), 2194 deletions(-)
Title: Density Equality Testing
Description: Methods for testing the equality between groups of estimated
density functions. The package implements FDET (Fourier-based Density Equality
Testing) and MDET (Moment-based Density Equality Testing), two new approaches
introduced by the author. Both methods extend an earlier testing approach
by Delicado (2007), "Functional k-sample problem when data are density functions"
<doi:10.1007/s00180-007-0047-y>, which is referred to as DET (Density Equality
Testing) in this package for clarity. FDET compares groups of densities
based on their global shape using Fourier transforms, while MDET tests for
differences in distributional moments. All methods are described in Anarat,
Krutmann and Schwender (2026), "Testing for Differences in Extrinsic Skin Aging
Based on Density Functions" (Under revision).
Author: Akin Anarat [aut, cre]
Maintainer: Akin Anarat <akin.anarat@hhu.de>
Diff between denstest versions 1.0.1 dated 2026-06-25 and 1.0.2 dated 2026-10-10
DESCRIPTION | 10 ++-- MD5 | 21 ++++----- NAMESPACE | 1 NEWS.md | 6 ++ R/calculate_global_distances.R | 32 ++++++++++++++ R/compute_B.R | 36 +++++++++++++--- R/compute_D_residual.R | 8 ++- R/denscomp.R | 91 +++++++++++++++++++++++++++-------------- R/permutation_test.R | 51 +++++++++++++++++++++- R/split_into_groups.R |only man/compute_B.Rd | 4 - man/denscomp.Rd | 4 - 12 files changed, 203 insertions(+), 61 deletions(-)
Title: Bayesian Prior Elicitation, Diagnostics, and Regulatory
Reporting
Description: A toolkit for constructing, validating, and justifying Bayesian priors
in clinical trial settings. Implements expert elicitation via quantile
matching, the roulette method, and moment matching across six distribution
families, linear and logarithmic expert pooling, meta-analytic-predictive
(MAP) priors derived from historical trials, prior-data conflict
diagnostics including the Box p-value (with an exact prior predictive
option for selected prior and data combinations), an exploratory
surprisal (S-value) companion to it, surprise index, information
divergence, and Mahalanobis distance, sensitivity analyses with tornado
and influence heatmap plots, sceptical, robust, and power priors, and
automated prior justification reports. Includes a fully modular 'Shiny'
application for interactive use.
Methods based on O'Hagan et al. (2006, ISBN:9780470029886),
Box (1980) <doi:10.2307/2982063>,
Greenland (2023) <doi:10.1111/sjos.12625>,
Oakley and O'Hagan (2010) <https://tonyohagan [...truncated...]
Author: Ndoh Penn [aut, cre]
Maintainer: Ndoh Penn <ndohpenn9@gmail.com>
Diff between bayprior versions 0.3.2 dated 2026-08-19 and 0.4.0 dated 2026-10-10
bayprior-0.3.2/bayprior/vignettes/bayprior-introduction_files |only bayprior-0.3.2/bayprior/vignettes/robust-priors_files |only bayprior-0.3.2/bayprior/vignettes/sensitivity-analysis_files |only bayprior-0.4.0/bayprior/DESCRIPTION | 29 bayprior-0.4.0/bayprior/MD5 | 134 +- bayprior-0.4.0/bayprior/NAMESPACE | 7 bayprior-0.4.0/bayprior/NEWS.md | 96 + bayprior-0.4.0/bayprior/R/app_server.R | 65 - bayprior-0.4.0/bayprior/R/app_ui.R | 82 + bayprior-0.4.0/bayprior/R/bayprior-package.R | 28 bayprior-0.4.0/bayprior/R/conflict_sensitivity.R | 206 +++ bayprior-0.4.0/bayprior/R/elicitation.R | 11 bayprior-0.4.0/bayprior/R/globals.R | 4 bayprior-0.4.0/bayprior/R/map_prior.R |only bayprior-0.4.0/bayprior/R/mod_conflict.R | 76 + bayprior-0.4.0/bayprior/R/mod_elicitation.R | 45 bayprior-0.4.0/bayprior/R/mod_map_prior.R |only bayprior-0.4.0/bayprior/R/mod_report.R | 28 bayprior-0.4.0/bayprior/R/mod_roulette.R | 24 bayprior-0.4.0/bayprior/R/mod_welcome.R | 346 +++--- bayprior-0.4.0/bayprior/R/plotting.R | 17 bayprior-0.4.0/bayprior/R/prior_report.R | 54 - bayprior-0.4.0/bayprior/R/zzz_patches.R | 24 bayprior-0.4.0/bayprior/README.md | 64 + bayprior-0.4.0/bayprior/build/vignette.rds |binary bayprior-0.4.0/bayprior/inst/WORDLIST | 25 bayprior-0.4.0/bayprior/inst/app/www/custom.css | 370 +++++- bayprior-0.4.0/bayprior/inst/doc/bayprior-introduction.R | 13 bayprior-0.4.0/bayprior/inst/doc/bayprior-introduction.Rmd | 53 bayprior-0.4.0/bayprior/inst/doc/bayprior-introduction.html | 477 +++++--- bayprior-0.4.0/bayprior/inst/doc/conflict-diagnostics.R | 16 bayprior-0.4.0/bayprior/inst/doc/conflict-diagnostics.Rmd | 73 + bayprior-0.4.0/bayprior/inst/doc/conflict-diagnostics.html | 306 +++-- bayprior-0.4.0/bayprior/inst/doc/prior-elicitation.html | 28 bayprior-0.4.0/bayprior/inst/doc/regulatory-reporting.Rmd | 28 bayprior-0.4.0/bayprior/inst/doc/regulatory-reporting.html | 33 bayprior-0.4.0/bayprior/inst/doc/robust-priors.R | 52 bayprior-0.4.0/bayprior/inst/doc/robust-priors.Rmd | 144 ++ bayprior-0.4.0/bayprior/inst/doc/robust-priors.html | 536 ++++++---- bayprior-0.4.0/bayprior/inst/doc/sensitivity-analysis.html | 22 bayprior-0.4.0/bayprior/inst/doc/using-with-rstanarm-brms.R |only bayprior-0.4.0/bayprior/inst/doc/using-with-rstanarm-brms.Rmd |only bayprior-0.4.0/bayprior/inst/doc/using-with-rstanarm-brms.html |only bayprior-0.4.0/bayprior/inst/quarto/templates/prior_report/prior_report.qmd | 124 ++ bayprior-0.4.0/bayprior/man/bayprior.Rd | 28 bayprior-0.4.0/bayprior/man/historical_effect_sizes.Rd |only bayprior-0.4.0/bayprior/man/map_prior.Rd |only bayprior-0.4.0/bayprior/man/plot_tau_posterior.Rd |only bayprior-0.4.0/bayprior/man/prior_conflict.Rd | 47 bayprior-0.4.0/bayprior/man/prior_report.Rd | 7 bayprior-0.4.0/bayprior/man/resolve_tau_prior.Rd |only bayprior-0.4.0/bayprior/tests/testthat/_snaps/plots-snapshots/plot-tornado.svg | 31 bayprior-0.4.0/bayprior/tests/testthat/test-conflict.R | 92 + bayprior-0.4.0/bayprior/tests/testthat/test-map-prior.R |only bayprior-0.4.0/bayprior/tests/testthat/test-s-value.R |only bayprior-0.4.0/bayprior/tests/testthat/test-sensitivity.R | 290 +++++ bayprior-0.4.0/bayprior/vignettes/bayprior-introduction.Rmd | 53 bayprior-0.4.0/bayprior/vignettes/conflict-diagnostics.Rmd | 73 + bayprior-0.4.0/bayprior/vignettes/regulatory-reporting.Rmd | 28 bayprior-0.4.0/bayprior/vignettes/robust-priors.Rmd | 144 ++ bayprior-0.4.0/bayprior/vignettes/using-with-rstanarm-brms.Rmd |only 61 files changed, 3404 insertions(+), 1029 deletions(-)
Title: GC/LC-MS Data Analysis for Environmental Science
Description: Gas/Liquid Chromatography-Mass Spectrometer(GC/LC-MS) Data Analysis for Environmental Science. This package covered topics such molecular isotope ratio, matrix effects and Short-Chain Chlorinated Paraffins analysis etc. in environmental analysis.
Author: Miao YU [aut, cre] ,
Thanh Wang [ctb]
Maintainer: Miao YU <yufreecas@gmail.com>
Diff between enviGCMS versions 0.9.0 dated 2026-10-07 and 0.9.1 dated 2026-10-10
DESCRIPTION | 13 +-- MD5 | 62 ++++++++++------ NAMESPACE | 4 + NEWS.md | 20 +++++ R/RcppExports.R |only R/cleanmgf.R | 8 +- R/formula_engine.R |only R/general.R | 74 +++++++++---------- R/getmzrt.R | 8 +- R/hrmf.R | 24 +++--- R/io.R | 124 +++++++++++++++++++++++---------- R/mda.R | 16 ++-- README.md | 4 - inst/doc/GCMSDA.html | 4 - inst/doc/PooledQC.html | 24 +++--- man/HRMF.Rd | 8 +- man/checkGoldenRules.Rd |only man/cleanMGF.Rd | 2 man/findlipid.Rd | 2 man/findohc.Rd | 4 - man/findpfc.Rd | 2 man/getcsv.Rd | 6 - man/getformula.Rd | 23 +++++- man/getisotopologues.Rd | 6 + man/getpower.Rd | 4 - man/getrangecsv.Rd | 4 - man/plotcc.Rd | 4 - man/plothist.Rd | 4 - man/rcpp_check_golden_rules.Rd |only man/rcpp_decompose_mass.Rd |only man/rcpp_decompose_masses.Rd |only man/rcpp_get_molecule.Rd |only man/rcpp_score_isotopes.Rd |only man/scoreIsotopes.Rd |only src |only tests/testthat/test-formula-advanced.R |only 36 files changed, 281 insertions(+), 173 deletions(-)
Title: Bayesian Global Vector Autoregressions
Description: Estimation of Bayesian Global Vector Autoregressions (BGVAR) with different prior setups and the possibility to introduce stochastic volatility. Built-in priors include the Minnesota, the stochastic search variable selection and Normal-Gamma (NG) prior. For a reference see also Crespo Cuaresma, J., Feldkircher, M. and F. Huber (2016) "Forecasting with Global Vector Autoregressive Models: a Bayesian Approach", Journal of Applied Econometrics, Vol. 31(7), pp. 1371-1391 <doi:10.1002/jae.2504>. Post-processing functions allow for doing predictions, structurally identify the model with short-run or sign-restrictions and compute impulse response functions, historical decompositions and forecast error variance decompositions. Plotting functions are also available. The package has a companion paper: Boeck, M., Feldkircher, M. and F. Huber (2022) "BGVAR: Bayesian Global Vector Autoregressions with Shrinkage Priors in R", Journal of Statistical Software, Vol. 104(9), pp. 1-28 <doi:10.18 [...truncated...]
Author: Maximilian Boeck [aut, cre] ,
Martin Feldkircher [aut] ,
Florian Huber [aut] ,
Darjus Hosszejni [ctb]
Maintainer: Maximilian Boeck <maximilian.boeck@wu.ac.at>
Diff between BGVAR versions 2.5.9 dated 2025-09-22 and 2.7.0 dated 2026-10-10
DESCRIPTION | 14 MD5 | 59 + NEWS | 27 R/BGVAR.R | 120 ++- R/fevd.R | 25 R/hd.R | 27 R/helpers.R | 18 R/irf.R | 28 R/plot.R | 24 R/predict.R | 19 R/utils.R | 383 ++++++---- inst/doc/examples.html | 889 ++++++++++++------------ man/bgvar.Rd | 13 man/fevd.Rd | 3 src/BVAR_linear.cpp | 230 +++--- src/RcppExports.cpp | 2 src/gvar_stacking.cpp | 2 src/helper.cpp | 24 src/helper.h | 2 tests/testthat.R | 4 tests/testthat/helper-postprocessing.R |only tests/testthat/helper-prior-samplers.R |only tests/testthat/test-BGVAR.R | 193 +++++ tests/testthat/test-Rcpp-BVAR-linear.R |only tests/testthat/test-audit-fixes.R |only tests/testthat/test-fevd.R |only tests/testthat/test-forecast-evaluation.R |only tests/testthat/test-hd.R |only tests/testthat/test-higher-lags-trends.R |only tests/testthat/test-horseshoe.R |only tests/testthat/test-input-boundaries.R |only tests/testthat/test-irf.R |only tests/testthat/test-minnesota.R |only tests/testthat/test-normal-gamma-conditionals.R |only tests/testthat/test-normal-gamma.R |only tests/testthat/test-performance-equivalence.R |only tests/testthat/test-predict.R |only tests/testthat/test-prior-corrections.R |only tests/testthat/test-ssvs.R |only tests/testthat/test-stability.R |only 40 files changed, 1269 insertions(+), 837 deletions(-)
Title: Policy Learning
Description: Package for learning and evaluating (subgroup) policies via doubly robust loss functions. Policy learning methods include doubly robust blip/conditional average treatment effect learning and sequential policy tree learning. Methods for (subgroup) policy evaluation include doubly robust cross-fitting and online estimation/sequential validation. See Nordland and Holst (2026) <doi:10.18637/jss.v116.i04> for documentation and references.
Author: Andreas Nordland [aut, cre],
Klaus Holst [aut]
Maintainer: Andreas Nordland <andreasnordland@gmail.com>
Diff between polle versions 1.6.5 dated 2026-09-30 and 1.6.6 dated 2026-10-10
DESCRIPTION | 6 MD5 | 78 +++++----- NEWS.md | 16 ++ R/Q_function.R | 6 R/blip.R | 4 R/c_function.R | 47 +++++- R/estimate_target.R | 199 +++++++--------------------- R/fit_functions.R | 7 R/g_function.R | 8 - R/g_models.R | 25 +-- R/policy_data_functions.R | 48 +++++- R/policy_eval.R | 59 +++----- R/policy_eval_functions.R | 22 --- R/policy_eval_online.R | 4 R/q_models.R | 16 +- inst/doc/optimal_subgroup.html | 6 inst/doc/policy_data.html | 47 +++--- inst/doc/policy_eval.Rmd | 10 - inst/doc/policy_eval.html | 55 +++---- inst/doc/policy_learn.html | 43 ++---- inst/doc/right_censoring.html | 25 +-- man/g_model.Rd | 25 +-- man/get_g_functions.Rd | 8 - man/get_history.Rd | 16 +- man/get_q_functions.Rd | 6 man/policy_eval.Rd | 37 +---- man/policy_eval_online.Rd | 4 man/q_model.Rd | 16 +- tests/testthat/test-c_cox.R | 19 ++ tests/testthat/test-fit_c_functions.R | 197 +++++++++++++++++++++++++++ tests/testthat/test-fit_functions.R | 1 tests/testthat/test-g_models.R | 28 +-- tests/testthat/test-policy_data-functions.R | 43 ++---- tests/testthat/test-policy_eval-censoring.R | 98 +++++++++++++ tests/testthat/test-policy_eval-subgroup.R | 65 +++++++++ tests/testthat/test-policy_eval.R | 79 +++++------ tests/testthat/test-policy_learn-blip.R | 191 +++++++++++++------------- tests/testthat/test-q_glmnet.R | 8 - tests/testthat/test-q_models.R | 4 vignettes/policy_eval.Rmd | 10 - 40 files changed, 937 insertions(+), 649 deletions(-)
Title: Accessing the 'Wordbank' Database
Description: Connecting to 'Wordbank' <https://wordbank.stanford.edu>, an open
repository for developmental vocabulary data from the MacArthur-Bates
Communicative Development Inventories (Frank et al. 2017
<doi:10.1017/S0305000916000209>). Data are read from a versioned dataset
hosted on 'Redivis', so analyses can be pinned to a specific release.
Author: Mika Braginsky [aut, cre, cph],
Daniel Yurovsky [ctb],
Michael Frank [ctb],
Danielle Kellier [ctb],
Alvin Tan [ctb]
Maintainer: Mika Braginsky <mika.br@gmail.com>
This is a re-admission after prior archival of version 1.0.3 dated 2024-03-01
Diff between wordbankr versions 1.0.3 dated 2024-03-01 and 2.0.0 dated 2026-10-10
wordbankr-1.0.3/wordbankr/man/connect_to_wordbank.Rd |only wordbankr-1.0.3/wordbankr/man/get_common_table.Rd |only wordbankr-1.0.3/wordbankr/man/get_instrument_table.Rd |only wordbankr-1.0.3/wordbankr/man/get_wordbank_args.Rd |only wordbankr-2.0.0/wordbankr/DESCRIPTION | 37 wordbankr-2.0.0/wordbankr/MD5 | 80 - wordbankr-2.0.0/wordbankr/NAMESPACE | 3 wordbankr-2.0.0/wordbankr/NEWS.md | 79 - wordbankr-2.0.0/wordbankr/R/crossling.R | 59 - wordbankr-2.0.0/wordbankr/R/derived.R |only wordbankr-2.0.0/wordbankr/R/quantiles.R | 2 wordbankr-2.0.0/wordbankr/R/wordbankr.R | 830 ++++++--------- wordbankr-2.0.0/wordbankr/README.md | 104 + wordbankr-2.0.0/wordbankr/build/partial.rdb |only wordbankr-2.0.0/wordbankr/build/vignette.rds |binary wordbankr-2.0.0/wordbankr/inst/doc/wordbankr.R | 99 - wordbankr-2.0.0/wordbankr/inst/doc/wordbankr.Rmd | 58 - wordbankr-2.0.0/wordbankr/inst/doc/wordbankr.html | 301 +---- wordbankr-2.0.0/wordbankr/man/check_db_args.Rd |only wordbankr-2.0.0/wordbankr/man/get_administration_data.Rd | 41 wordbankr-2.0.0/wordbankr/man/get_aoa.Rd |only wordbankr-2.0.0/wordbankr/man/get_crossling_data.Rd | 12 wordbankr-2.0.0/wordbankr/man/get_crossling_items.Rd | 10 wordbankr-2.0.0/wordbankr/man/get_datasets.Rd | 32 wordbankr-2.0.0/wordbankr/man/get_embeddings.Rd |only wordbankr-2.0.0/wordbankr/man/get_instrument_data.Rd | 39 wordbankr-2.0.0/wordbankr/man/get_instruments.Rd | 14 wordbankr-2.0.0/wordbankr/man/get_item_data.Rd | 18 wordbankr-2.0.0/wordbankr/man/summarise_items.Rd | 10 wordbankr-2.0.0/wordbankr/man/wb_dataset.Rd |only wordbankr-2.0.0/wordbankr/man/wordbankr-package.Rd | 6 wordbankr-2.0.0/wordbankr/tests |only wordbankr-2.0.0/wordbankr/vignettes/wordbankr.Rmd | 58 - 33 files changed, 918 insertions(+), 974 deletions(-)
Title: Generate RNA-Seq Data from Gene-Gene Association Networks
Description: Methods to generate random gene-gene association networks and simulate RNA-seq data from them, as described in Grimes and Datta (2021) <doi:10.18637/jss.v098.i12>. Includes functions to generate random networks of any size and perturb them to obtain differential networks. Network objects are built from individual, overlapping modules that represent pathways. The resulting network has various topological properties that are characteristic of gene regulatory networks. RNA-seq data can be generated such that the association among gene expression profiles reflect the underlying network. A reference RNA-seq dataset can be provided to model realistic marginal distributions. Plotting functions are available to visualize a network, compare two networks, and compare the expression of two genes across multiple networks.
Author: Tyler Grimes [aut, cre],
Somnath Datta [aut]
Maintainer: Tyler Grimes <tyler.grimes@unf.edu>
This is a re-admission after prior archival of version 1.1.3 dated 2021-07-09
Diff between SeqNet versions 1.1.3 dated 2021-07-09 and 1.1.4 dated 2026-10-10
DESCRIPTION | 7 ++++--- MD5 | 29 +++++++++++++++++------------ NAMESPACE | 1 + R/data.R | 23 ++++++++++++----------- R/imports.R | 1 + R/plotting.R | 12 ++++++------ build/partial.rdb |binary build/vignette.rds |only data/reference.rda |binary inst/doc |only man/plot_gene_pair.Rd | 6 +++--- man/plot_modules.Rd | 2 +- man/plot_network.Rd | 2 +- man/plot_network_diff.Rd | 2 +- man/reference.Rd | 13 +++++++------ vignettes |only 16 files changed, 54 insertions(+), 44 deletions(-)
Title: Easy Handling Discrete Time Markov Chains
Description: Description: Functions and S4 classes to create, manage and analyse discrete
time Markov chains. Includes probabilistic analysis of chain structure
(state classification, hitting times, stationary distributions, spectral
and mixing diagnostics), statistical inference (maximum likelihood and
Bayesian estimation, tests of the Markov property, homogeneity, stationarity
and order, simulation), higher-order and multivariate chains, state
aggregation, and import/export to JSON, YAML and CSV. Basic support for
continuous time Markov chains is also provided; some of these functions
depend on the suggested 'ctmcd' package.
See Spedicato (2017) <doi:10.32614/RJ-2017-036>.
Author: Giorgio Alfredo Spedicato [aut, cre] ,
Tae Seung Kang [aut],
Sai Bhargav Yalamanchi [aut],
Mildenberger Thoralf [ctb] ,
Deepak Yadav [aut],
Ignacio Cordon [aut] ,
Vandit Jain [ctb],
Toni Giorgino [ctb] ,
Richel J.C. Bilderbeek [ctb] ,
Daniel Ebbert [ [...truncated...]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between markovchain versions 1.1.1 dated 2026-09-18 and 1.2 dated 2026-10-10
DESCRIPTION | 25 MD5 | 184 +- NAMESPACE | 40 NEWS.md | 65 R/RcppExports.R | 54 R/aggregateStates.R |only R/autoplot.R | 237 ++ R/chainTransforms.R |only R/classesAndMethods.R | 42 R/closestReversible.R |only R/ctmcProbabilistic.R | 2 R/dynamics.R |only R/fitHigherOrder.R | 231 ++ R/fitMTD.R |only R/fittingFunctions.R | 165 + R/generators.R |only R/graphExport.R |only R/higherOrderPredict.R |only R/hommc.R | 70 R/independenceTest.R |only R/markovchainFitAbsorbing.R | 75 R/mixingDiagnostics.R |only R/probabilistic.R | 202 ++ R/random.R | 308 +++ R/selectOrder.R |only R/sensitivity.R |only R/serialization.R |only R/spectralDiagnostics.R |only R/statisticalTests.R | 20 R/zzz.R | 3 build/partial.rdb |only inst/doc/an_introduction_to_markovchain_package.R | 464 ++++- inst/doc/an_introduction_to_markovchain_package.Rmd | 1612 +++++++++++++++---- inst/doc/an_introduction_to_markovchain_package.pdf |binary inst/doc/gsoc_2017_additions.R | 6 inst/doc/gsoc_2017_additions.html | 256 +-- inst/doc/gsoc_2017_additions.qmd | 174 +- inst/doc/higher_order_markov_chains.R | 106 + inst/doc/higher_order_markov_chains.html | 349 +++- inst/doc/higher_order_markov_chains.qmd | 190 ++ inst/extdata/README_berchtold_raftery.md |only inst/extdata/epileptic_seizures.csv |only inst/extdata/koeberg_wind.csv |only man/aggregateStates.Rd |only man/assessIndependence.Rd |only man/autoplot.markovchain.Rd | 39 man/birthDeath.Rd |only man/closestReversible.Rd |only man/dirichletChain.Rd |only man/fitHigherOrder.Rd | 49 man/fitMTD.Rd |only man/gamblersRuin.Rd |only man/higherOrderLogLik.Rd |only man/higherOrderPredict.Rd |only man/hittingProbabilities.Rd | 62 man/identityChain.Rd |only man/impliedTimescales.Rd |only man/is.reversible.Rd |only man/lazyChain.Rd |only man/markovchain-class.Rd | 10 man/markovchainFit.Rd | 97 - man/mergeWith.Rd |only man/mixingTime.Rd |only man/noofVisitsDist.Rd | 28 man/normalizedEntropyRate.Rd |only man/populationGeneticsModel.Rd |only man/predictHommc.Rd | 11 man/randomMarkovChain.Rd |only man/redistribute.Rd |only man/relaxationTime.Rd |only man/rmarkovchain.Rd | 9 man/rouwenhorst.Rd |only man/selectOrder.Rd |only man/sensitivity.Rd |only man/slem.Rd |only man/spectralGap.Rd |only man/statisticalTests.Rd | 7 man/subchain.Rd |only man/tauchen.Rd |only man/timeCorrelations.Rd |only man/toBoundedChain.Rd |only man/toDictionary.Rd |only man/toDot.Rd |only man/toFile.Rd |only man/toNthOrder.Rd |only man/topologicalEntropy.Rd |only man/urnModel.Rd |only src/RcppExports.cpp | 38 src/ctmcClassesAndMethods.cpp | 3 src/ctmcFittingFunctions.cpp | 22 src/ctmcProbabilistic.cpp | 9 src/fitMTD.cpp |only src/fittingFunctions.cpp | 768 +++++---- src/mapFitFunctions.h | 24 src/multinomCI.cpp | 4 src/probabilistic.cpp | 301 +++ src/utils.cpp | 13 tests/testthat/test-aggregateStates.R |only tests/testthat/test-assessIndependence.R |only tests/testthat/test-berchtold-raftery-2002.R |only tests/testthat/test-chainTransforms.R |only tests/testthat/test-closestReversible.R |only tests/testthat/test-ctmc-expectedtime-small.R |only tests/testthat/test-dynamics.R |only tests/testthat/test-fit-byrow-orientation.R |only tests/testthat/test-fit-list-methods.R |only tests/testthat/test-fitHigherOrder.R | 121 + tests/testthat/test-fitMTD.R |only tests/testthat/test-generators.R |only tests/testthat/test-graphExport.R |only tests/testthat/test-higherOrderLogLik.R |only tests/testthat/test-higherOrderPredict.R |only tests/testthat/test-markovchainFit-progress.R |only tests/testthat/test-mergeWith.R |only tests/testthat/test-mixingDiagnostics.R |only tests/testthat/test-predictHommc.R |only tests/testthat/test-random-generators.R |only tests/testthat/test-selectOrder.R |only tests/testthat/test-sensitivity.R |only tests/testthat/test-serialization.R |only tests/testthat/test-spectralDiagnostics.R |only tests/testthat/test-statisticalTests-revised.R | 15 tests/testthat/test-timeCorrelations.R |only tests/testthat/test-xml-summary.R |only tests/testthat/testByrowFalseEquivalence.R |only tests/testthat/testHittingProbabilities.R | 73 tests/testthat/testHittingSolvers.R |only tests/testthat/testMemorySafety.R |only tests/testthat/testNoofVisitsDist.R |only tests/testthat/testParallelRNG.R |only tests/testthat/testPredictKnownState.R |only tests/testthat/testSanitizeAbsorbing.R |only vignettes/an_introduction_to_markovchain_package.Rmd | 1612 +++++++++++++++---- vignettes/gsoc_2017_additions.qmd | 174 +- vignettes/higher_order_markov_chains.qmd | 190 ++ vignettes/markovchainBiblio.bib | 302 +++ 136 files changed, 7110 insertions(+), 1751 deletions(-)
Title: Fourier ARDL Methods: Quantile, Nonlinear, Multi-Threshold &
Unit Root Tests
Description: Implementation of ARDL methods for cointegration analysis with
structural breaks and asymmetric effects. Includes: (1) Fourier Quantile
ARDL (FQARDL), quantile regression with Fourier approximation following
the quantile ARDL of Cho, Kim and Shin (2015)
<doi:10.1016/j.jeconom.2015.05.003>; (2) Fourier Nonlinear ARDL (FNARDL),
asymmetric cointegration with partial sum decomposition following Shin,
Yu and Greenwood-Nimmo (2014) <doi:10.1007/978-1-4899-8008-3_9>;
(3) a deprecated Multi-Threshold NARDL (MTNARDL) function; (4) Fourier
unit root tests, ADF and KPSS tests with Fourier terms following Enders
and Lee (2012) <doi:10.1016/j.econlet.2012.04.081> and Becker, Enders and
Lee (2006) <doi:10.1111/j.1467-9892.2006.00478.x>. Features automatic lag
and frequency selection, Wald bounds statistics with the tables of
Pesaran, Shin and Smith (2001) <doi:10.1002/jae.616> (no verdict with
Fourier terms, for which the tables are not valid), recursive bootstrap
bound [...truncated...]
Author: Muhammad Alkhalaf [aut, cre, cph]
Maintainer: Muhammad Alkhalaf <muhammedalkhalaf@gmail.com>
Diff between fqardl versions 1.0.6 dated 2026-09-30 and 1.1.0 dated 2026-10-10
DESCRIPTION | 41 ++- MD5 | 60 +++-- NAMESPACE | 5 NEWS.md | 70 ++++++ R/ardl_boot_engine.R |only R/boot_fqardl.R |only R/bounds_test.R | 255 ++++++++++++++++------- R/fnardl.R | 354 +++++++++++++++++++++++++-------- R/fourier.R | 2 R/fqardl.R | 111 ++++++++-- R/funitroot.R | 19 - R/mtnardl.R | 182 ++++++++++++++-- README.md | 10 build |only man/bootstrap_bounds_test.Rd | 118 +++++++++-- man/bootstrap_nardl.Rd | 58 +++++ man/build_nardl_design.Rd |only man/decompose_multi_threshold.Rd | 10 man/fnardl.Rd | 116 ++++++++-- man/fourier_adf_test.Rd | 4 man/fourier_kpss_test.Rd | 4 man/fqardl-package.Rd | 13 - man/fqardl.Rd | 119 ++++++++--- man/generate_fourier_terms.Rd | 2 man/get_pss_critical_values.Rd | 18 + man/mtnardl.Rd | 107 ++++++++- man/perform_bounds_test.Rd | 75 +++++- man/perform_mtnardl_bounds.Rd | 21 + man/perform_nardl_bounds_test.Rd | 29 ++ man/plot.fqardl_mtnardl.Rd |only tests/testthat/test-bootstrap-1.1.0.R |only tests/testthat/test-mtnardl.R | 130 ++++++++++-- tests/testthat/test-regression-1.0.3.R | 2 tests/testthat/test-regression-1.0.6.R |only tests/testthat/test-size-mc.R |only 35 files changed, 1521 insertions(+), 414 deletions(-)
Title: Fourier Bootstrap ARDL Cointegration Test
Description: Implements the Fourier Bootstrap Autoregressive Distributed Lag
(FBARDL) bounds testing approach for cointegration analysis. Combines the
Pesaran, Shin and Smith (2001) <doi:10.1002/jae.616> ARDL bounds testing
framework with Fourier terms to capture smooth structural breaks, as in
Yilanci, Bozoklu and Gorus (2020) <doi:10.1016/j.scs.2020.102035>,
and recursive bootstrap critical values following McNown, Sam and Goh
(2018) <doi:10.1080/00036846.2017.1366643> and Bertelli, Vacca and Zoia
(2022) <doi:10.1016/j.econmod.2022.105987>, with the Fourier frequency
and the lags selected again in every bootstrap replication (a package
choice); finite-sample
bounds test critical values from Kripfganz and Schneider (2020)
<doi:10.1111/obes.12377> for models without Fourier terms. Features
include lag selection via AIC/BIC, Fourier frequency selection by minimum
SSR, long-run and short-run coefficient estimation and diagnostic tests.
Author: Muhammad Alkhalaf [aut, cre, cph]
Maintainer: Muhammad Alkhalaf <muhammedalkhalaf@gmail.com>
Diff between fbardl versions 1.1.0 dated 2026-09-30 and 1.2.0 dated 2026-10-10
DESCRIPTION | 29 +- MD5 | 25 + NEWS.md | 45 +++ R/ardl_boot_engine.R |only R/fbardl-package.R | 34 +- R/fbardl.R | 503 ++++++++++++++++++++++------------------ R/helpers.R | 460 ++++++++++++++++++++---------------- README.md | 54 ++-- build/partial.rdb |binary inst/CITATION | 2 man/fbardl-package.Rd | 47 +-- man/fbardl.Rd | 255 +++++++++++++------- tests/testthat/test-bootstrap.R |only tests/testthat/test-fbardl.R | 80 +++++- tests/testthat/test-size.R |only 15 files changed, 932 insertions(+), 602 deletions(-)
Title: Fast Estimators for Design-Based Inference
Description: Fast procedures for a small set of commonly-used,
design-appropriate estimators with robust standard errors and confidence
intervals. Includes estimators for linear regression, instrumental
variables regression, difference-in-means, Horvitz-Thompson estimation,
and regression improving precision of experimental estimates by
interacting treatment with centered pre-treatment covariates introduced by
Lin (2013) <doi:10.1214/12-AOAS583>. Fixed effects are absorbed by
alternating projections rather than by dummy expansion, and
Horvitz-Thompson variance is computed from the randomization declaration.
Author: Alexander Coppock [aut, cre],
Graeme Blair [aut],
Jasper Cooper [aut],
Luke Sonnet [aut],
Macartan Humphreys [ctb],
Neal Fultz [ctb],
Lily Medina [ctb],
Russell Lenth [ctb],
Molly Offer-Westort [ctb]
Maintainer: Alexander Coppock <acoppock@gmail.com>
Diff between estimatr versions 2.0.0 dated 2026-09-16 and 2.0.1 dated 2026-10-10
DESCRIPTION | 6 MD5 | 90 +- NAMESPACE | 2 NEWS.md | 133 ++ R/RcppExports.R | 4 R/S3_emmeans.R | 13 R/S3_tidy.R | 13 R/difference_in_means.R | 17 R/helper_fit.R | 279 ++++-- R/helper_misc.R | 146 +++ R/horvitz_thompson.R | 15 R/iv_robust.R | 79 + R/lh_robust.R | 41 R/lm_lin.R | 34 R/lm_robust.R | 13 README.md | 2 inst/doc/estimatr2.0.R | 2 inst/doc/estimatr2.0.Rmd | 16 inst/doc/estimatr2.0.html | 38 inst/doc/getting-started.html | 11 inst/doc/mathematical-notes.Rmd | 6 inst/doc/mathematical-notes.html | 77 + man/difference_in_means.Rd | 2 man/lm_lin.Rd | 21 man/lm_robust.Rd | 13 src/RcppExports.cpp | 9 src/lm_robust_helper.cpp | 316 ++++--- tests/testthat/fixtures/external_reference.rds |binary tests/testthat/helper-external.R | 54 + tests/testthat/test_blocked_variance.R | 72 - tests/testthat/test_degenerate.R | 1114 +++++++++++++++++++++++-- tests/testthat/test_difference_in_means.R | 169 +++ tests/testthat/test_errors.R | 32 tests/testthat/test_fe_leverage.R | 120 ++ tests/testthat/test_fixed_effects.R | 70 + tests/testthat/test_horvitz_thompson.R | 112 ++ tests/testthat/test_invariance.R | 64 + tests/testthat/test_iv_robust.R | 40 tests/testthat/test_lh_robust.R | 63 + tests/testthat/test_lm_lin.R | 55 + tests/testthat/test_lm_robust.R | 64 + tests/testthat/test_methods.R | 326 +++++++ tests/testthat/test_vs_clubsandwich.R | 27 tests/testthat/test_vs_fixest_plm.R | 62 + vignettes/estimatr2.0.Rmd | 16 vignettes/mathematical-notes.Rmd | 6 46 files changed, 3362 insertions(+), 502 deletions(-)
Title: Comprehensive ARDL: Panel, Bootstrap and Fourier Methods
Description: A unified framework for Autoregressive Distributed Lag (ARDL) modeling
and cointegration analysis. Implements Panel ARDL with Pooled Mean Group (PMG),
Mean Group (MG), and Dynamic Fixed Effects (DFE) estimators following
Pesaran, Shin and Smith (1999) <doi:10.1080/01621459.1999.10474156>.
Provides the bounds test of Pesaran, Shin and Smith (2001)
<doi:10.1002/jae.616> with the critical values of Kripfganz and Schneider
(2020) <doi:10.1111/obes.12377> and with recursive bootstrap critical
values following Bertelli, Vacca and Zoia (2022)
<doi:10.1016/j.econmod.2022.105987> and McNown, Sam and Goh (2018)
<doi:10.1080/00036846.2017.1366643>. Includes Quantile Nonlinear ARDL
(QNARDL) combining distributional and asymmetric effects based on Shin, Yu
and Greenwood-Nimmo (2014) <doi:10.1007/978-1-4899-8008-3_9>, Fourier ARDL
for modeling smooth structural breaks following Enders and Lee (2012)
<doi:10.1016/j.econlet.2012.04.081>, and Fourier (bootstrap [...truncated...]
Author: Muhammad Abdullah Alkhalaf [aut, cre] ,
Yeleazar Levchenko [ctb] )
Maintainer: Muhammad Abdullah Alkhalaf <muhammedalkhalaf@gmail.com>
Diff between ardlverse versions 2.0.3 dated 2026-09-30 and 2.1.0 dated 2026-10-10
ardlverse-2.0.3/ardlverse/man/dot-aardl_bootstrap.Rd |only ardlverse-2.0.3/ardlverse/man/dot-bootstrap_bounds.Rd |only ardlverse-2.0.3/ardlverse/man/dot-bounds_conclusion.Rd |only ardlverse-2.0.3/ardlverse/man/dot-mtnardl_bootstrap.Rd |only ardlverse-2.1.0/ardlverse/DESCRIPTION | 23 ardlverse-2.1.0/ardlverse/MD5 | 89 - ardlverse-2.1.0/ardlverse/NAMESPACE | 59 ardlverse-2.1.0/ardlverse/NEWS.md | 53 ardlverse-2.1.0/ardlverse/R/ardl_boot_engine.R |only ardlverse-2.1.0/ardlverse/R/augmented_ardl.R | 616 +++---- ardlverse-2.1.0/ardlverse/R/bootstrap_ardl.R | 417 ++-- ardlverse-2.1.0/ardlverse/R/ecm_tools.R |only ardlverse-2.1.0/ardlverse/R/fbnardl.R |only ardlverse-2.1.0/ardlverse/R/fourier_ardl.R | 4 ardlverse-2.1.0/ardlverse/R/mtnardl.R | 880 +++++----- ardlverse-2.1.0/ardlverse/R/panel_ardl.R | 8 ardlverse-2.1.0/ardlverse/R/panel_nardl.R | 4 ardlverse-2.1.0/ardlverse/R/qnardl.R | 8 ardlverse-2.1.0/ardlverse/R/rolling_ardl.R | 2 ardlverse-2.1.0/ardlverse/R/utils_formula.R |only ardlverse-2.1.0/ardlverse/R/zzz.R | 5 ardlverse-2.1.0/ardlverse/README.md | 34 ardlverse-2.1.0/ardlverse/build/partial.rdb |binary ardlverse-2.1.0/ardlverse/inst/replication/replicate_jasa.R | 8 ardlverse-2.1.0/ardlverse/man/aardl.Rd | 201 +- ardlverse-2.1.0/ardlverse/man/ardlverse-package.Rd | 18 ardlverse-2.1.0/ardlverse/man/boot_ardl.Rd | 190 +- ardlverse-2.1.0/ardlverse/man/dot-aardl_conclusion.Rd | 7 ardlverse-2.1.0/ardlverse/man/dot-aardl_critical_values.Rd | 4 ardlverse-2.1.0/ardlverse/man/dot-aardl_design.Rd |only ardlverse-2.1.0/ardlverse/man/dot-aardl_stats.Rd |only ardlverse-2.1.0/ardlverse/man/dot-boot_ardl_stats.Rd |only ardlverse-2.1.0/ardlverse/man/dot-compute_mt_multipliers.Rd | 12 ardlverse-2.1.0/ardlverse/man/dot-mt_decompose.Rd | 5 ardlverse-2.1.0/ardlverse/man/dot-mtnardl_bounds_conclusion.Rd | 3 ardlverse-2.1.0/ardlverse/man/dot-select_optimal_thresholds.Rd | 7 ardlverse-2.1.0/ardlverse/man/dot-test_regime_asymmetry.Rd | 14 ardlverse-2.1.0/ardlverse/man/fbnardl.Rd |only ardlverse-2.1.0/ardlverse/man/fourier_ardl.Rd | 4 ardlverse-2.1.0/ardlverse/man/mtnardl.Rd | 234 +- ardlverse-2.1.0/ardlverse/man/panel_ardl.Rd | 8 ardlverse-2.1.0/ardlverse/man/plot.boot_ardl.Rd |only ardlverse-2.1.0/ardlverse/man/plot.fbnardl.Rd |only ardlverse-2.1.0/ardlverse/man/pnardl.Rd | 4 ardlverse-2.1.0/ardlverse/man/print.boot_ardl.Rd |only ardlverse-2.1.0/ardlverse/man/qnardl.Rd | 6 ardlverse-2.1.0/ardlverse/man/rardl.Rd | 2 ardlverse-2.1.0/ardlverse/man/summary.boot_ardl.Rd |only ardlverse-2.1.0/ardlverse/tests/testthat/test-aardl.R | 55 ardlverse-2.1.0/ardlverse/tests/testthat/test-boot-engine.R |only ardlverse-2.1.0/ardlverse/tests/testthat/test-boot_ardl.R | 30 ardlverse-2.1.0/ardlverse/tests/testthat/test-fbnardl.R |only ardlverse-2.1.0/ardlverse/tests/testthat/test-mtnardl.R | 120 + ardlverse-2.1.0/ardlverse/tests/testthat/test-pmg-stata-parity.R | 2 ardlverse-2.1.0/ardlverse/tests/testthat/test-size-mc.R |only 55 files changed, 1897 insertions(+), 1239 deletions(-)
Title: Kernelized Stein Discrepancy for Goodness-of-Fit Tests and Stein
Sampling
Description: Provides Stein-discrepancy goodness-of-fit tests and
Stein-method-based sampling tools. The tests include kernel Stein
discrepancy U- and V-statistics following Liu et al. (2016)
<doi:10.48550/arXiv.1602.03253> and Chwialkowski et al. (2016)
<doi:10.48550/arXiv.1602.02964>, plus the finite set Stein discrepancy
test of Jitkrittum et al. (2017) <doi:10.48550/arXiv.1705.07673>. The
sampling tools include Stein thinning, Stein Points, Stein Point Markov
chain Monte Carlo, and Stein variational gradient descent following
Riabiz et al. (2022) <doi:10.48550/arXiv.2005.03952>, Chen et al. (2018)
<doi:10.48550/arXiv.1803.10161>, Chen et al. (2019)
<doi:10.48550/arXiv.1905.03673>, and Liu and Wang (2016)
<doi:10.48550/arXiv.1608.04471>. Gaussian mixture utilities are included
for constructing example targets, simulation, density evaluation, and
score callbacks.
Author: Junhao Gao [aut, cre],
Ery Arias-Castro [aut]
Maintainer: Junhao Gao <jug049@ucsd.edu>
Diff between steinsampling versions 0.1.2 dated 2026-09-07 and 0.1.3 dated 2026-10-10
steinsampling-0.1.2/steinsampling/man/cross_kernel.Rd |only steinsampling-0.1.2/steinsampling/man/densitygmm.Rd |only steinsampling-0.1.2/steinsampling/man/eval_kernel.Rd |only steinsampling-0.1.2/steinsampling/man/find_median_distance.Rd |only steinsampling-0.1.2/steinsampling/man/fmin_grid.Rd |only steinsampling-0.1.2/steinsampling/man/fmin_mc.Rd |only steinsampling-0.1.2/steinsampling/man/fmin_nm.Rd |only steinsampling-0.1.2/steinsampling/man/fssd_null_pvalue.Rd |only steinsampling-0.1.2/steinsampling/man/fssd_statistic.Rd |only steinsampling-0.1.2/steinsampling/man/grad_theta_v_kernel.Rd |only steinsampling-0.1.2/steinsampling/man/grad_x_kernel.Rd |only steinsampling-0.1.2/steinsampling/man/kernel_scale2.Rd |only steinsampling-0.1.2/steinsampling/man/ksd_u_bootstrap.Rd |only steinsampling-0.1.2/steinsampling/man/ksd_u_statistic.Rd |only steinsampling-0.1.2/steinsampling/man/ksd_v_bootstrap.Rd |only steinsampling-0.1.2/steinsampling/man/ksd_v_statistic.Rd |only steinsampling-0.1.2/steinsampling/man/mala.Rd |only steinsampling-0.1.2/steinsampling/man/print.SteinKernel.Rd |only steinsampling-0.1.2/steinsampling/man/print.stein_points.Rd |only steinsampling-0.1.2/steinsampling/man/print.svgd.Rd |only steinsampling-0.1.2/steinsampling/man/rgmm.Rd |only steinsampling-0.1.2/steinsampling/man/rwm.Rd |only steinsampling-0.1.2/steinsampling/man/sp_mcmc_eval_candidates.Rd |only steinsampling-0.1.2/steinsampling/man/summary.gmm.Rd |only steinsampling-0.1.2/steinsampling/man/summary.sp_mcmc.Rd |only steinsampling-0.1.2/steinsampling/man/summary.stein_points.Rd |only steinsampling-0.1.2/steinsampling/man/summary.svgd.Rd |only steinsampling-0.1.2/steinsampling/man/trace_mixed_kernel.Rd |only steinsampling-0.1.3/steinsampling/DESCRIPTION | 8 steinsampling-0.1.3/steinsampling/MD5 | 121 - steinsampling-0.1.3/steinsampling/NAMESPACE | 6 steinsampling-0.1.3/steinsampling/R/bootstrap.R | 30 steinsampling-0.1.3/steinsampling/R/fssd_test.R | 668 ++++----- steinsampling-0.1.3/steinsampling/R/gmm_model.R | 185 +- steinsampling-0.1.3/steinsampling/R/kernel_classes.R | 427 +++--- steinsampling-0.1.3/steinsampling/R/ksd_u_test.R | 143 +- steinsampling-0.1.3/steinsampling/R/ksd_v_test.R | 116 - steinsampling-0.1.3/steinsampling/R/stein_helpers.R | 116 - steinsampling-0.1.3/steinsampling/R/stein_point_mcmc.R | 451 ++---- steinsampling-0.1.3/steinsampling/R/stein_points.R | 698 ++++------ steinsampling-0.1.3/steinsampling/R/stein_points_alternative_kernel.R | 91 - steinsampling-0.1.3/steinsampling/R/stein_thinning.R | 132 - steinsampling-0.1.3/steinsampling/R/steinsampling-package.R | 71 - steinsampling-0.1.3/steinsampling/R/svgd.R | 96 - steinsampling-0.1.3/steinsampling/build |only steinsampling-0.1.3/steinsampling/man/compute_tau.Rd | 13 steinsampling-0.1.3/steinsampling/man/custom_stein_kernel.Rd | 37 steinsampling-0.1.3/steinsampling/man/fssd_components.Rd |only steinsampling-0.1.3/steinsampling/man/fssd_grad_kernel.Rd |only steinsampling-0.1.3/steinsampling/man/fssd_opt_test.Rd | 67 steinsampling-0.1.3/steinsampling/man/fssd_rand_test.Rd | 34 steinsampling-0.1.3/steinsampling/man/fssd_test.Rd | 62 steinsampling-0.1.3/steinsampling/man/get_score_evaluator.Rd | 14 steinsampling-0.1.3/steinsampling/man/gmm.Rd | 78 - steinsampling-0.1.3/steinsampling/man/kernel_operations.Rd |only steinsampling-0.1.3/steinsampling/man/kernel_scales.Rd |only steinsampling-0.1.3/steinsampling/man/ksd_matrix.Rd | 43 steinsampling-0.1.3/steinsampling/man/ksd_u_components.Rd |only steinsampling-0.1.3/steinsampling/man/ksd_u_test.Rd | 36 steinsampling-0.1.3/steinsampling/man/ksd_v_components.Rd |only steinsampling-0.1.3/steinsampling/man/ksd_v_test.Rd | 46 steinsampling-0.1.3/steinsampling/man/mcmc_transitions.Rd |only steinsampling-0.1.3/steinsampling/man/sp_mcmc.Rd | 122 + steinsampling-0.1.3/steinsampling/man/stein_codescent.Rd | 51 steinsampling-0.1.3/steinsampling/man/stein_kernel.Rd | 20 steinsampling-0.1.3/steinsampling/man/stein_kernel_imq_score.Rd | 29 steinsampling-0.1.3/steinsampling/man/stein_kernel_inverse_log.Rd | 18 steinsampling-0.1.3/steinsampling/man/stein_kernel_matrix.Rd | 12 steinsampling-0.1.3/steinsampling/man/stein_point_optimizers.Rd |only steinsampling-0.1.3/steinsampling/man/stein_points.Rd | 79 - steinsampling-0.1.3/steinsampling/man/stein_thinning.Rd | 48 steinsampling-0.1.3/steinsampling/man/steinsampling-package.Rd | 64 steinsampling-0.1.3/steinsampling/man/svgd.Rd | 41 steinsampling-0.1.3/steinsampling/tests/testthat/helper-test-utils.R | 6 steinsampling-0.1.3/steinsampling/tests/testthat/test-fssd.R | 26 steinsampling-0.1.3/steinsampling/tests/testthat/test-gof-scale-contract.R | 14 steinsampling-0.1.3/steinsampling/tests/testthat/test-kernels.R | 12 steinsampling-0.1.3/steinsampling/tests/testthat/test-ksd.R | 35 steinsampling-0.1.3/steinsampling/tests/testthat/test-optimizers-and-sampling.R | 21 steinsampling-0.1.3/steinsampling/tests/testthat/test-svgd-spmcmc.R | 13 80 files changed, 2350 insertions(+), 2050 deletions(-)
Title: Scientific Computation Using R
Description: A collection of undergraduate level mathematical routines for
quantitative work, covering calculus, distribution functions, random
variate generation, linear algebra, differential equations and
optimization, sized for one semester. The package is best studied with
its source open: every routine is short and written to be read.
Author: Kyun-Seop Bae [aut, cre]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between mathr versions 0.1.3 dated 2026-09-10 and 0.1.5 dated 2026-10-10
DESCRIPTION | 9 - MD5 | 341 +++++++++++++++++++++++++------------------------- R/Choose.R | 2 R/Dbeta.R | 2 R/Dbinom.R | 2 R/Dchisq.R | 2 R/Dec2Bin.R | 6 R/Df.R | 2 R/Dgamma.R | 2 R/Dlnorm.R | 2 R/Dnorm.R | 2 R/Dpois.R | 2 R/Dt.R | 2 R/EXP.R | 142 ++++++++++++-------- R/GAMMA.R | 2 R/Invbetai.R | 2 R/Invgammp.R | 2 R/LDLT.R | 2 R/LGAMMA.R | 2 R/LOG.R | 6 R/MachEps2.R | 2 R/MachEps3.R | 3 R/MachEps4.R | 3 R/NORM.R | 9 + R/NashSVD.R | 3 R/Optim0.R | 4 R/Pbeta.R | 2 R/Pbinom.R | 2 R/Pchisq.R | 2 R/Pf.R | 2 R/Pgamma.R | 2 R/Plnorm.R | 2 R/Pnorm.R | 2 R/PolyNom3.R | 4 R/Ppois.R | 2 R/Pt.R | 2 R/Qbeta.R | 2 R/Qbinom.R | 2 R/Qchisq.R | 2 R/Qf.R | 2 R/Qgamma.R | 2 R/Qlnorm.R | 2 R/Qnorm.R | 2 R/Qpois.R | 2 R/Qt.R | 2 R/Rbeta.R | 2 R/Rgamma.R | 8 - R/Rgamma0.R | 6 R/Rmvn.R | 2 R/Rnorm.R | 6 R/Run.test.R | 1 R/SQRT.R | 12 + R/Scalar1.R |only R/SymInv.R | 2 R/VMmin.R | 5 R/betacf.R | 2 R/betai.R | 2 R/betaiapprox.R | 12 - R/ellipse.R | 2 R/erf.R | 2 R/erfc.R | 2 R/erfccheb.R | 10 - R/evJacobi.R | 8 - R/gammln.R | 2 R/gammp.R | 2 R/gammpapprox.R | 12 - R/gammq.R | 2 R/gcf.R | 2 R/gser.R | 2 R/inverfc.R | 2 R/mlr.R | 4 R/romb.R | 4 R/run.p.R | 2 R/runifLC.R | 4 R/simps13.R | 2 R/simps38.R | 2 R/tableFactorial.R | 2 R/trapez0.R | 4 R/trapez1.R | 5 inst/NEWS.Rd | 203 +++++++++++++++++++++++++++++ man/Bin2Dec.Rd | 4 man/Chol.Rd | 8 - man/Choose.Rd | 6 man/DENORM.Rd | 4 man/Dbeta.Rd | 2 man/Dbinom.Rd | 4 man/Dchisq.Rd | 6 man/Dec2Bin.Rd | 6 man/Df.Rd | 6 man/Dgamma.Rd | 4 man/Dlnorm.Rd | 6 man/Dnorm.Rd | 5 man/Dpois.Rd | 4 man/Dt.Rd | 7 - man/EXP.Rd | 6 man/GAMMA.Rd | 7 - man/GQuad8.Rd | 2 man/GetP.Rd | 2 man/LDLT.Rd | 6 man/LGAMMA.Rd | 7 - man/LOG.Rd | 5 man/MachEps2.Rd | 2 man/MachEps3.Rd | 6 man/MachEps4.Rd | 6 man/NORM.Rd | 9 - man/NashSVD.Rd | 2 man/Optim0.Rd | 6 man/OuterProd.Rd | 6 man/Pbeta.Rd | 2 man/Pbinom.Rd | 6 man/Pchisq.Rd | 4 man/Pf.Rd | 6 man/Pgamma.Rd | 4 man/Plnorm.Rd | 8 - man/Pnorm.Rd | 8 - man/PolyNom3.Rd | 2 man/Ppois.Rd | 4 man/Pt.Rd | 8 - man/Qbeta.Rd | 4 man/Qbinom.Rd | 2 man/Qchisq.Rd | 6 man/Qf.Rd | 6 man/Qgamma.Rd | 4 man/Qlnorm.Rd | 10 - man/Qnorm.Rd | 12 + man/Qpois.Rd | 6 man/Qt.Rd | 10 - man/RK4.Rd | 4 man/Rbeta.Rd | 3 man/Rexp.Rd | 4 man/Rgamma.Rd | 3 man/Rgamma0.Rd | 3 man/Rmvn.Rd | 5 man/Rnorm.Rd | 3 man/Round.Rd | 2 man/Run.test.Rd | 7 - man/SQRT.Rd | 3 man/VMmin.Rd | 3 man/betacf.Rd | 4 man/betai.Rd | 6 man/betaiapprox.Rd | 6 man/conv.Rd | 6 man/conv0.Rd | 4 man/dc.Rd | 6 man/deconv.Rd | 6 man/deconv0.Rd | 4 man/ellipRange.Rd | 2 man/ellipse.Rd | 1 man/erf.Rd | 6 man/erfc.Rd | 6 man/erfccheb.Rd | 7 - man/evJacobi.Rd | 2 man/gammln.Rd | 4 man/gammp.Rd | 8 - man/gammpapprox.Rd | 8 - man/gammq.Rd | 8 - man/gcf.Rd | 6 man/gser.Rd | 6 man/invbetai.Rd | 12 + man/inverfc.Rd | 6 man/invgammp.Rd | 8 - man/mlr.Rd | 8 - man/romb.Rd | 8 - man/run.p.Rd | 8 - man/runifLC.Rd | 12 + man/sft.Rd | 2 man/simps13.Rd | 3 man/simps38.Rd | 3 man/tableFactorial.Rd | 4 man/trapez0.Rd | 4 man/trapez1.Rd | 5 tests/regression.R | 188 ++++++++++++++++++++++++++- 172 files changed, 1151 insertions(+), 460 deletions(-)
Title: Financial and Actuarial Mathematics for Life Contingencies
Description: Classes and methods that allow the user to manage life table,
actuarial tables (also multiple decrements tables). Moreover, functions to easily
perform demographic, financial and actuarial mathematics on life contingencies
insurances calculations are contained therein. See Spedicato (2013) <doi:10.18637/jss.v055.i10>.
Author: Giorgio Alfredo Spedicato [aut, cre] ,
Christophe Dutang [ctb] ,
Reinhold Kainhofer [ctb] ,
Kevin J Owens [ctb],
Ernesto Schirmacher [ctb],
Gian Paolo Clemente [ctb] ,
Ivan Williams [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between lifecontingencies versions 1.6.0 dated 2026-08-23 and 1.6.3 dated 2026-10-10
DESCRIPTION | 12 MD5 | 124 ++- NAMESPACE | 23 NEWS.md | 44 + R/0_dependencies.R | 41 - R/0_lifetableAndActuarialtableClassesAndMethods.R | 52 + R/1_mdtClassesAndMethods.R | 138 +++ R/3_demographicFunctions.R | 462 ++++++++----- R/5_actuarialFunctions.R | 174 ++-- R/6_randomGenerationFunctions.R | 206 ++--- R/7_tomarkovchain.R | 49 - R/8_mdtFunctions.R | 414 ++++++++++- R/9_demographicExtras.R |only R/RcppExports.R | 40 + R/zzz.R | 18 README.md | 2 build/vignette.rds |binary inst/doc/PensionPlanVal.html | 2 inst/doc/an_introduction_to_lifecontingencies_package.R | 137 --- inst/doc/an_introduction_to_lifecontingencies_package.Rnw | 300 +------- inst/doc/an_introduction_to_lifecontingencies_package.pdf |binary inst/doc/compute-detail.html | 2 inst/doc/demographic_analysis.R |only inst/doc/demographic_analysis.html |only inst/doc/demographic_analysis.qmd |only inst/doc/mortality_projection.pdf |binary inst/doc/multiple_decrement_tables.R |only inst/doc/multiple_decrement_tables.Rmd |only inst/doc/multiple_decrement_tables.html |only inst/doc/pensionfunding.html | 86 +- man/buildMdtFromIndependentRates.Rd |only man/endowment_trio.Rd | 7 man/exn.Rd | 49 + man/independentRatesFromMdt.Rd |only man/lifetable-class.Rd | 3 man/mdt-class.Rd | 12 man/mdtToLong.Rd |only man/median.Rd |only man/modalAge.Rd |only man/multidecrins.Rd | 74 +- man/multiple-life-probabilities.Rd | 3 man/other-demographic-functions.Rd | 18 man/plot-mdt-missing-method.Rd |only man/pxt.Rd | 36 - man/quantile.Rd |only man/rLifeContingencies.Rd | 25 man/rLifes.Rd | 8 man/rmdt.Rd | 6 man/varxn.Rd |only src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 172 ++++ src/pxtRcpp.cpp | 99 ++ src/simKernels.cpp |only tests/test-pxt-corner-cases_2.R |only tests/testthat/test-demographic-extras.R |only tests/testthat/test-demographic-functions-optimization.R |only tests/testthat/test-dxt-lifetable-vectorised.R |only tests/testthat/test-exn-aexn-vectorization.R |only tests/testthat/test-exn-definitions.R |only tests/testthat/test-legacy-actuarial.R | 2 tests/testthat/test-mdt-asdt-functions.R |only tests/testthat/test-mdt-s4-actuarial-long.R |only tests/testthat/test-native-memory-safety.R |only tests/testthat/test-optional-markovchain.R |only tests/testthat/test-published-australia-1932.R |only tests/testthat/test-published-destatis-germany.R |only tests/testthat/test-published-finan-ilt.R |only tests/testthat/test-published-grm80-spain.R |only tests/testthat/test-published-ireland-ilt14.R |only tests/testthat/test-published-life-expectancy.R |only tests/testthat/test-published-nchs-us2019.R |only tests/testthat/test-published-sult-ilt.R |only tests/testthat/test-pxt-corner-cases.R |only tests/testthat/test-pxt-fractional-regression-clean.R |only tests/testthat/test-pxt-lifetable-native.R |only tests/testthat/test-sim-vector-kernels.R |only tests/testthat/testMultipleDecrements.R | 88 ++ tests/testthat/testSimulationFunctions.R | 20 vignettes/an_introduction_to_lifecontingencies_package.Rnw | 300 +------- vignettes/demographic_analysis.qmd |only vignettes/lifecontingenciesBiblio.bib | 39 - vignettes/multiple_decrement_tables.Rmd |only 83 files changed, 2032 insertions(+), 1259 deletions(-)
More information about lifecontingencies at CRAN
Permanent link
Title: Classical Cultural Consensus Analysis
Description: Implements classical cultural consensus analysis with
formal, informal, and covariance agreement models, 'UCINET'-aligned
minimum-residual factor extraction, competence estimation, and
answer-key estimation. Based on the classical framework of Romney,
Weller, and Batchelder (1986)
<doi:10.1525/aa.1986.88.2.02a00020>, Romney, Batchelder, and
Weller (1987) <doi:10.1177/000276487031002003>, and Weller (2007)
<doi:10.1177/1525822X07303502>.
Author: Werner Hertzog [aut, cre]
Maintainer: Werner Hertzog <werner.hertzog@isek.uzh.ch>
Diff between Romney versions 0.1.0 dated 2026-05-20 and 0.1.1 dated 2026-10-10
DESCRIPTION | 19 +++- MD5 | 51 +++++++++--- NAMESPACE | 4 + NEWS.md |only R/agreement.R | 55 +++++++++++-- R/answer_key.R | 137 ++++++++++++++++++++++++++++------ R/consensus.R | 156 ++++++++++++++++++++++++++++++++------- R/simulate_data.R | 56 +++++++------- R/utils.R | 135 ++++++++++++++++++++++++++++----- README.md | 122 ++++++++++++++---------------- build |only inst/CITATION |only inst/doc |only inst/extdata/README.md |only inst/validation |only man/agreement_models.Rd | 41 +++++++++- man/answerkey_covariance.Rd |only man/answerkey_formal.Rd | 45 +++++++++-- man/answerkey_informal.Rd |only man/consensus.Rd | 83 ++++++++++++++++++-- man/simulate_consensus_data.Rd | 38 +++++++-- tests/testthat/helper-ucinet.R |only tests/testthat/test-agreement.R | 16 ++++ tests/testthat/test-answer-key.R | 91 ++++++++++++++++++++++ tests/testthat/test-consensus.R | 47 +++++++++++ tests/testthat/test-simulation.R |only tests/testthat/test-validation.R |only vignettes |only 28 files changed, 872 insertions(+), 224 deletions(-)
Title: Pattern Causality Analysis
Description: Infer causation from observational data through pattern causality analysis (PC), with original algorithm for time series data from Stavroglou et al. (2020) <doi:10.1073/pnas.1918269117>, as well as methodological extensions for spatial cross-sectional data introduced by Zhang & Wang (2025) <doi:10.1080/13658816.2025.2581207>, together with a systematic description proposed in Lyu et al. (2026) <doi:10.1016/j.compenvurbsys.2026.102435>.
Author: Wenbo Lyu [aut, cre, cph]
Maintainer: Wenbo Lyu <lyu.geosocial@gmail.com>
Diff between pc versions 0.2 dated 2026-04-10 and 0.3 dated 2026-10-10
DESCRIPTION | 13 - MD5 | 65 ++++-- NAMESPACE | 23 +- NEWS.md | 76 +++++--- R/Agenerics.R | 24 +- R/RcppExports.R | 20 +- R/dmi.R |only R/fnn.R | 6 R/formatoutput.R | 148 +++++++-------- R/internal_utility.R | 94 +++++----- R/ops.R | 138 +++++++------- R/pc-package.R | 8 R/pc.R | 214 +++++++++++----------- R/zzz.R | 7 README.md | 133 +++++++------- build |only inst/CITATION | 20 +- inst/case/abundance.csv |only inst/doc |only inst/include/pc.h | 2 inst/include/pc/distance.hpp | 117 ++++++++++-- inst/include/pc/dmi.hpp |only inst/include/pc/fnn.hpp | 16 + inst/include/pc/ksginfo.hpp |only inst/include/pc/neighbor.hpp | 31 +++ inst/include/pc/patcaus.hpp | 22 +- inst/include/pc/projection.hpp | 72 ++----- inst/include/pc/symdync.hpp | 10 - man/dmi.Rd |only man/fnn.Rd | 220 +++++++++++------------ man/ops.Rd | 258 +++++++++++++-------------- man/pc.Rd | 332 +++++++++++++++++------------------ src/DMI.cpp |only src/FNN.cpp | 67 +++---- src/PC.cpp | 385 +++++++++++++++++++++++++++++++++-------- src/RcppExports.cpp | 61 ++++-- vignettes |only 37 files changed, 1500 insertions(+), 1082 deletions(-)
Title: Exploratory Subgroup Identification in Survival and GLM Outcomes
Description: Implements statistical methods for exploratory subgroup
identification in clinical trials. Provides tools for identifying patient
subgroups with differential treatment effects using machine learning
approaches including Generalized Random Forests (GRF), LASSO
regularization, and exhaustive combinatorial search algorithms. Supports
survival endpoints (Cox proportional hazards), binary outcomes (log odds
ratio, log relative risk, risk difference), continuous outcomes (mean
difference), and count / rate outcomes (log incidence rate ratio via
Poisson, quasi-Poisson, or negative-binomial GLMs with optional
person-time offset). Features bootstrap bias correction using
infinitesimal jackknife methods to address selection bias in post-hoc
analyses. Designed for clinical researchers conducting exploratory
subgroup analyses in randomized controlled trials, particularly for
multi-regional clinical trials (MRCT) requiring regional consistency
evaluation. Methods are described in Leon et al. (2024) [...truncated...]
Author: Larry Leon [aut, cre]
Maintainer: Larry Leon <larry.leon.05@post.harvard.edu>
Diff between forestsearch versions 0.1.0 dated 2026-03-23 and 0.4.0 dated 2026-10-10
forestsearch-0.1.0/forestsearch/R/oc_analyses_gbsg.R |only forestsearch-0.1.0/forestsearch/man/default_fs_params.Rd |only forestsearch-0.1.0/forestsearch/man/default_grf_params.Rd |only forestsearch-0.1.0/forestsearch/man/extract_fs_estimates.Rd |only forestsearch-0.1.0/forestsearch/man/extract_grf_estimates.Rd |only forestsearch-0.1.0/forestsearch/man/run_forestsearch_analysis.Rd |only forestsearch-0.1.0/forestsearch/man/run_grf_analysis.Rd |only forestsearch-0.4.0/forestsearch/DESCRIPTION | 57 forestsearch-0.4.0/forestsearch/MD5 | 725 +- forestsearch-0.4.0/forestsearch/NAMESPACE | 665 + forestsearch-0.4.0/forestsearch/NEWS.md | 1687 ++++ forestsearch-0.4.0/forestsearch/R/Cox_estimation_helpers.R | 217 forestsearch-0.4.0/forestsearch/R/betaHhat_truth.R |only forestsearch-0.4.0/forestsearch/R/bootstrap_analysis_dofuture.R | 707 +- forestsearch-0.4.0/forestsearch/R/bootstrap_calculations_helpers.R | 186 forestsearch-0.4.0/forestsearch/R/bootstrap_dofuture_main.R | 728 +- forestsearch-0.4.0/forestsearch/R/bootstrap_summaries_helpers.R | 233 forestsearch-0.4.0/forestsearch/R/calibrate_glm_interaction.R |only forestsearch-0.4.0/forestsearch/R/calibrate_helpers.R |only forestsearch-0.4.0/forestsearch/R/calibrate_k_treat.R |only forestsearch-0.4.0/forestsearch/R/calibrate_null_correction.R |only forestsearch-0.4.0/forestsearch/R/compare_fs_subgroups.R |only forestsearch-0.4.0/forestsearch/R/compare_selection_rules.R |only forestsearch-0.4.0/forestsearch/R/compare_subgroup_sims.R |only forestsearch-0.4.0/forestsearch/R/consistency_resample.R |only forestsearch-0.4.0/forestsearch/R/cox_ahr_cde_wrapper.R | 64 forestsearch-0.4.0/forestsearch/R/cox_spline_fit.R | 22 forestsearch-0.4.0/forestsearch/R/create_summary_table.R | 23 forestsearch-0.4.0/forestsearch/R/cv_summary_tables.R | 66 forestsearch-0.4.0/forestsearch/R/dina.R |only forestsearch-0.4.0/forestsearch/R/dina_bagged.R |only forestsearch-0.4.0/forestsearch/R/dina_df.R |only forestsearch-0.4.0/forestsearch/R/dina_subgroup.R |only forestsearch-0.4.0/forestsearch/R/dina_subgroup_bootstrap.R |only forestsearch-0.4.0/forestsearch/R/dina_subgroup_refit.R |only forestsearch-0.4.0/forestsearch/R/explain_pareto_selection.R |only forestsearch-0.4.0/forestsearch/R/find_k_inter_main.R | 203 forestsearch-0.4.0/forestsearch/R/forestsearch_cross_validation.R | 1223 +++ forestsearch-0.4.0/forestsearch/R/forestsearch_helpers.R | 2330 ++++++ forestsearch-0.4.0/forestsearch/R/forestsearch_main.R | 3419 +++++++++- forestsearch-0.4.0/forestsearch/R/forestsearch_methods.R | 287 forestsearch-0.4.0/forestsearch/R/format_fs_details.R | 18 forestsearch-0.4.0/forestsearch/R/format_subgroup_summary_tables.R | 65 forestsearch-0.4.0/forestsearch/R/fpr_approximation.R |only forestsearch-0.4.0/forestsearch/R/fpr_calibration.R |only forestsearch-0.4.0/forestsearch/R/frontier_cis.R |only forestsearch-0.4.0/forestsearch/R/frontier_member_flags.R |only 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5 forestsearch-0.4.0/forestsearch/tests |only forestsearch-0.4.0/forestsearch/vignettes/forestsearch.Rmd | 485 + forestsearch-0.4.0/forestsearch/vignettes/survival-post-selection.qmd |only 463 files changed, 26734 insertions(+), 3676 deletions(-)
Title: Draw Network with Data
Description: Extends the 'ggplot2' plotting system to support network visualization. Inspired by the 'Method 1' in 'ggtree' (G Yu (2018) <doi:10.1093/molbev/msy194>), 'ggtangle' is designed to work with network associated data.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggtangle versions 0.1.3 dated 2026-09-24 and 0.1.4 dated 2026-10-09
DESCRIPTION | 6 +- MD5 | 16 ++++--- NAMESPACE | 1 NEWS.md | 11 +++++ R/cnet.r | 10 +++- R/graph.r | 83 ++++++++++++++++++++++++++++++++++++++- R/layout-readable.R |only inst/doc/ggtangle.html | 16 +++---- man/cnetplot.Rd | 8 +++ man/layout_cnet_category_rail.Rd |only 10 files changed, 129 insertions(+), 22 deletions(-)
Title: General Modules for 'teal' Applications
Description: Prebuilt 'shiny' modules containing tools for viewing data,
visualizing data, understanding missing and outlier values within your
data and performing simple data analysis. This extends 'teal'
framework that supports reproducible research and analysis.
Author: Dony Unardi [aut, cre],
Dawid Kaledkowski [aut],
Pawel Rucki [aut],
Mahmoud Hallal [aut],
Ondrej Slama [ctb],
Maciej Nasinski [aut],
Konrad Pagacz [aut],
Nikolas Burkoff [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dony Unardi <unardid@gene.com>
Diff between teal.modules.general versions 0.8.0 dated 2026-08-01 and 0.9.0 dated 2026-10-09
DESCRIPTION | 14 MD5 | 47 - NAMESPACE | 16 NEWS.md | 9 R/tm_g_distribution.R | 4 R/tm_g_scatterplot.R | 4 R/tm_missing_data.R | 2 R/tm_rmarkdown.R | 6 R/tm_variable_browser.R | 69 + build/vignette.rds |binary man/create_sparklines.Rd |only man/tm_tbl_summary.Rd | 11 tests/testthat/helper-picks.R | 49 - tests/testthat/man/create_sparklines.Rd |only tests/testthat/man/tm_tbl_summary.Rd | 11 tests/testthat/test-shinytest2-tm_a_pca_picks.R | 4 tests/testthat/test-shinytest2-tm_g_association_picks.R | 4 tests/testthat/test-shinytest2-tm_g_bivariate_picks.R | 14 tests/testthat/test-shinytest2-tm_g_distribution_picks.R | 8 tests/testthat/test-shinytest2-tm_g_response_picks.R | 8 tests/testthat/test-shinytest2-tm_g_scatterplot_picks.R | 18 tests/testthat/test-shinytest2-tm_g_scatterplotmatrix_picks.R | 22 tests/testthat/test-shinytest2-tm_t_crosstable_picks.R | 4 tests/testthat/test-shinytest2-tm_tbl_summary.R | 4 tests/testthat/test-tm_variable_browser.R | 347 ++++++---- vignettes/run_teal_app.R |only 26 files changed, 388 insertions(+), 287 deletions(-)
More information about teal.modules.general at CRAN
Permanent link
Title: Easy Publication-Ready Tables and Regression Analysis
Description: Streamlines the creation of descriptive frequency tables ('Table 1'),
diagnostic test accuracy evaluations (sensitivity, specificity, predictive values),
and multi-outcome regression summaries. Features a grammar for publication-ready epidemiological tables built on
design-aware effect measures, prevalence and odds ratio calculations, and seamless integration with 'flextable'
for exporting results to 'Microsoft Word' and 'PowerPoint'.
Author: Matheus Trabuco Gonzalez [aut, cre]
Maintainer: Matheus Trabuco Gonzalez <matheustrabucogonzalez@gmail.com>
Diff between SimtablR versions 1.2.0 dated 2026-02-21 and 3.1.1 dated 2026-10-09
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SimtablR-3.1.1/SimtablR/man/journal_style.Rd |only SimtablR-3.1.1/SimtablR/man/label.Rd |only SimtablR-3.1.1/SimtablR/man/list_engines.Rd |only SimtablR-3.1.1/SimtablR/man/list_journals.Rd |only SimtablR-3.1.1/SimtablR/man/measure.Rd |only SimtablR-3.1.1/SimtablR/man/missingness.Rd |only SimtablR-3.1.1/SimtablR/man/model-accessors.Rd |only SimtablR-3.1.1/SimtablR/man/model_info.Rd |only SimtablR-3.1.1/SimtablR/man/overall.Rd |only SimtablR-3.1.1/SimtablR/man/plot.simtab_diag.Rd |only SimtablR-3.1.1/SimtablR/man/print.simtab_rbind_tb.Rd |only SimtablR-3.1.1/SimtablR/man/print.simtab_result.Rd |only SimtablR-3.1.1/SimtablR/man/rbind.simtab_tb.Rd |only SimtablR-3.1.1/SimtablR/man/register_engine.Rd |only SimtablR-3.1.1/SimtablR/man/register_journal.Rd |only SimtablR-3.1.1/SimtablR/man/regtab.Rd | 344 - SimtablR-3.1.1/SimtablR/man/repro_manifest.Rd |only SimtablR-3.1.1/SimtablR/man/roc.Rd |only SimtablR-3.1.1/SimtablR/man/sensitivity.Rd |only SimtablR-3.1.1/SimtablR/man/set_design.Rd |only 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Title: General Unilateral Load Estimator for Two-Layer Latent Factor
Models
Description: Implements general unilateral loading estimator for two-layer latent factor models with smooth, element-wise factor transformations. We provide data simulation, loading estimation,finite-sample error bounds, and diagnostic tools for zero-mean and sub-Gaussian assumptions. A unified interface is given for evaluating estimation accuracy and cosine similarity. The philosophy of the package is described in Guo G. (2026) <doi:10.1016/j.apm.2025.116280>.
Author: Guangbao Guo [aut, cre]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between GulFM versions 0.5.0 dated 2026-01-07 and 0.5.1 dated 2026-10-09
DESCRIPTION | 6 +++--- MD5 | 6 ++++-- NAMESPACE | 1 + R/gul_factor_number.R |only man/gul_factor_number.Rd |only 5 files changed, 8 insertions(+), 5 deletions(-)
Title: Healthcare Analysis Methods
Description: Conducts analyses for healthcare program evaluations or intervention
studies. Calculates regression analyses for standard ordinary least squares
(OLS or linear) or logistic models. Performs regression models used for
causal modeling such as differences-in-differences (DID) and interrupted
time series (ITS) models. Provides limited interpretations of model
results and a ranking of variable importance in models. Performs
propensity score models, top-coding of model outcome variables, and
can return new data with the newly formed variables. Conducts Bayesian
analysis summaries and graphs, decision curve analysis, and produces some
Shewhart control charts. Also performs Cronbach's alpha for various scale
items (e.g., survey questions). See Github URL for examples in the README
file. For more details on the statistical methods, see
Allen & Yen (1979, ISBN:0-8185-0283-5),
Angrist & Pischke (2009, ISBN:9780691120355),
Cohen (1988, ISBN:0-8058-0283-5),
Gebski (2012) <doi:10.1017/S0 [...truncated...]
Author: Stephen Zuniga [aut, cre, cph]
Maintainer: Stephen Zuniga <rms.shiny@gmail.com>
Diff between ham versions 1.3.0 dated 2026-07-11 and 1.4.0 dated 2026-10-09
DESCRIPTION | 6 MD5 | 73 - NAMESPACE | 8 NEWS.md | 2 R/Bayes.R | 143 +- R/assess.R | 104 + R/data.R | 67 + R/importance.R | 2 R/interpret.R | 164 ++ R/itsEffect.R | 4 R/plot.Bayes.R | 396 ++++++- R/plot.assess.R | 1744 ++++++++++++++++++++++++++++++- R/plot.group.R | 34 R/print.interpret.R | 10 README.md | 435 ++++++- data/NHSN.rda |binary data/co2multi.rda |binary data/compapt.rda |only data/covshort.rda |only data/losvary.rda |only inst/doc/Bayes.R | 53 inst/doc/Bayes.Rmd | 137 ++ inst/doc/Bayes.html | 425 ++++--- inst/doc/ham-package.R | 39 inst/doc/ham-package.Rmd | 86 + inst/doc/ham-package.html | 1214 ++++++++++++--------- man/Bayes.Rd | 3 man/assess.Rd | 19 man/compapt.Rd |only man/covshort.Rd |only man/figures/README-plotDIDvary10-1.png |only man/figures/README-plotPPC1-1.png |binary man/figures/README-plotVary10-1.png |only man/figures/README-plotVary20-1.png |only man/figures/README-plotpartpred13-1.png |only man/figures/README-plotpartpred14-1.png |only man/figures/README-plotpartpred14b-1.png |only man/figures/README-plotreview04-1.png |only man/losvary.Rd |only man/plot.Bayes.Rd | 76 + man/plot.assess.Rd | 42 man/plot.group.Rd | 7 vignettes/Bayes.Rmd | 137 ++ vignettes/ham-package.Rmd | 86 + 44 files changed, 4493 insertions(+), 1023 deletions(-)
Title: Bayesian Quantile Regression with Lasso and Adaptive Lasso
Description: Markov chain Monte Carlo samplers for Bayesian quantile
regression, based on the asymmetric Laplace distribution and the
location-scale mixture representation of Kozumi and Kobayashi (2011)
<doi:10.1080/00949655.2010.496117>. A binary response and an observed
continuous response are both supported, each with three penalty layers
behind one interface: no penalty, following Benoit and Van den Poel (2012)
<doi:10.1002/jae.1216>; the Bayesian lasso, following Benoit, Al-Hamzawi
and Yu (2013) <doi:10.1007/s00180-013-0439-0>; and the Bayesian adaptive
lasso of Rubio Garcia (2023)
<https://soar.wichita.edu/entities/publication/a2f86232-4704-4ec2-b685-751e7b04ec42>.
In the binary family each is available as published and in a corrected
form, the default, in which every improper prior component is replaced by
a proper one so that the posterior exists unconditionally; the continuous
family ships the corrected form only. The continuous adaptive-lasso layer
at its default r [...truncated...]
Author: Fernando Rubio Garcia [aut, cre] ,
Mai Dao [ths] ,
Dries F. Benoit [ctb, cph] ,
Rahim Al-Hamzawi [ctb],
Keming Yu [ctb],
Dirk Van den Poel [ctb]
Maintainer: Fernando Rubio Garcia <j332v755@wichita.edu>
Diff between bbqr versions 0.1.0 dated 2026-09-08 and 0.2.0 dated 2026-10-09
DESCRIPTION | 11 MD5 | 39 +-- NEWS.md | 432 ++++++++++++++++++++++----------------- R/bbqr.R | 77 ++++++ R/fit-alasso.R | 10 R/fit-lasso.R | 10 R/fit-none.R | 10 R/internals.R | 114 ++++++++++ R/methods.R | 172 +++++++++++++-- inst/CITATION | 2 man/bbqr-package.Rd | 1 man/bbqr.Rd | 59 +++++ man/bbqr_alasso.Rd | 10 man/bbqr_lasso.Rd | 10 man/bbqr_none.Rd | 10 man/coef.bbqr.Rd | 35 ++- man/predict.bbqr.Rd | 50 ++++ man/summary.bbqr.Rd | 7 src/Makevars | 2 tests/testthat/test-methods.R | 130 ++++++++++- tests/testthat/test-separation.R |only 21 files changed, 926 insertions(+), 265 deletions(-)
Title: Clinical Trial Simulator
Description: Simulate phase II and/or phase III clinical trials. It supports various types of endpoints and adaptive strategies. Tools for carrying out graphical testing procedure and combination test under group sequential design are also provided.
Author: Han Zhang [cre, aut]
Maintainer: Han Zhang <zhangh.ustc@gmail.com>
Diff between TrialSimulator versions 1.35.8 dated 2026-09-04 and 1.39.0 dated 2026-10-09
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TrialSimulator-1.39.0/TrialSimulator/inst/doc/defineNonTimeToEventEndpoints.R | 2 TrialSimulator-1.39.0/TrialSimulator/inst/doc/defineNonTimeToEventEndpoints.Rmd | 2 TrialSimulator-1.39.0/TrialSimulator/inst/doc/defineNonTimeToEventEndpoints.html | 19 TrialSimulator-1.39.0/TrialSimulator/inst/doc/doseRanging.R | 2 TrialSimulator-1.39.0/TrialSimulator/inst/doc/doseRanging.Rmd | 2 TrialSimulator-1.39.0/TrialSimulator/inst/doc/doseRanging.html | 9 TrialSimulator-1.39.0/TrialSimulator/inst/doc/enrichmentDesign.R |only TrialSimulator-1.39.0/TrialSimulator/inst/doc/enrichmentDesign.Rmd |only TrialSimulator-1.39.0/TrialSimulator/inst/doc/enrichmentDesign.html |only TrialSimulator-1.39.0/TrialSimulator/inst/doc/fixedDesign.R | 2 TrialSimulator-1.39.0/TrialSimulator/inst/doc/fixedDesign.Rmd | 4 TrialSimulator-1.39.0/TrialSimulator/inst/doc/fixedDesign.html | 16 TrialSimulator-1.39.0/TrialSimulator/inst/doc/responseAdaptive.R | 2 TrialSimulator-1.39.0/TrialSimulator/inst/doc/responseAdaptive.Rmd | 4 TrialSimulator-1.39.0/TrialSimulator/inst/doc/responseAdaptive.html | 11 TrialSimulator-1.39.0/TrialSimulator/inst/doc/wrappers.R | 2 TrialSimulator-1.39.0/TrialSimulator/inst/doc/wrappers.Rmd | 2 TrialSimulator-1.39.0/TrialSimulator/man/Trials.Rd | 162 +- TrialSimulator-1.39.0/TrialSimulator/man/controller.Rd | 1 TrialSimulator-1.39.0/TrialSimulator/man/doNothing.Rd | 2 TrialSimulator-1.39.0/TrialSimulator/man/enrollment.Rd | 7 TrialSimulator-1.39.0/TrialSimulator/man/eventNumber.Rd | 6 TrialSimulator-1.39.0/TrialSimulator/man/getEnrichmentDesignOutput.Rd |only TrialSimulator-1.39.0/TrialSimulator/man/remove_arms.Rd | 130 ++ TrialSimulator-1.39.0/TrialSimulator/man/stop_followup.Rd | 6 TrialSimulator-1.39.0/TrialSimulator/man/summarizeMilestoneTime.Rd | 1 TrialSimulator-1.39.0/TrialSimulator/man/trial.Rd | 28 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/fixtures/doc_example1.R | 2 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/fixtures/doc_example2.R | 2 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/fixtures/doc_example3.R | 2 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/fixtures/setup_adaptiveDesign.R | 10 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/fixtures/setup_crossoverWashout.R | 1 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/fixtures/setup_doseRanging.R | 2 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/fixtures/setup_enrichmentDesign.R |only TrialSimulator-1.39.0/TrialSimulator/tests/testthat/fixtures/setup_filteredConditions.R | 4 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/fixtures/setup_fixedDesign.R | 2 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/fixtures/setup_responseAdaptive.R | 2 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/fixtures/setup_stopFollowupAccrual.R | 4 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/fixtures/setup_updateMilestone.R | 2 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-adaptive-mutations.R | 182 ++ TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-adaptive.R | 12 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-condition-arms.R |only TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-conditionalpower.R | 12 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-cpp-rollback.R | 6 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-crossover.R | 16 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-enroll-fastpath.R | 2 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-enroller.R | 6 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-eventnumberreestimation.R | 4 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-global-data.R |only TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-model-data.R |only TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-models.R | 12 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-ownership.R | 4 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-parallel.R | 13 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-progress-bar.R | 2 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-regimen.R | 14 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-run-guards.R | 18 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-tidy-run.R | 2 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-trajectory-truncation.R | 4 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-trial-core.R | 38 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-trials-methods.R | 10 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-unreachable-conditions.R | 4 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-update-milestone.R | 4 TrialSimulator-1.39.0/TrialSimulator/tests/testthat/test-utils.R | 7 TrialSimulator-1.39.0/TrialSimulator/vignettes/actionFunctions.Rmd | 92 + TrialSimulator-1.39.0/TrialSimulator/vignettes/adaptiveDesign.Rmd | 29 TrialSimulator-1.39.0/TrialSimulator/vignettes/conditionalPower.Rmd | 6 TrialSimulator-1.39.0/TrialSimulator/vignettes/crossoverAtMilestone.Rmd | 5 TrialSimulator-1.39.0/TrialSimulator/vignettes/crossoverWashout.Rmd | 5 TrialSimulator-1.39.0/TrialSimulator/vignettes/defineNonTimeToEventEndpoints.Rmd | 2 TrialSimulator-1.39.0/TrialSimulator/vignettes/doseRanging.Rmd | 2 TrialSimulator-1.39.0/TrialSimulator/vignettes/enrichmentDesign.Rmd |only TrialSimulator-1.39.0/TrialSimulator/vignettes/fixedDesign.Rmd | 4 TrialSimulator-1.39.0/TrialSimulator/vignettes/responseAdaptive.Rmd | 4 TrialSimulator-1.39.0/TrialSimulator/vignettes/wrappers.Rmd | 2 120 files changed, 1797 insertions(+), 768 deletions(-)
More information about TrialSimulator at CRAN
Permanent link
Title: 'teal' Modules for Standard Clinical Outputs
Description: Provides user-friendly tools for creating and customizing
clinical trial reports. By leveraging the 'teal' framework, this
package provides 'teal' modules to easily create an interactive panel
that allows for seamless adjustments to data presentation, thereby
streamlining the creation of detailed and accurate reports.
Author: Dony Unardi [aut, cre],
Joe Zhu [aut] ,
Jana Stoilova [aut],
Davide Garolini [aut],
Emily de la Rua [aut],
Abinaya Yogasekaram [aut],
Mahmoud Hallal [aut],
Dawid Kaledkowski [aut],
Rosemary Li [aut],
Heng Wang [aut],
Pawel Rucki [aut],
Nikolas Burkof [...truncated...]
Maintainer: Dony Unardi <unardid@gene.com>
Diff between teal.modules.clinical versions 0.13.0 dated 2026-07-02 and 0.14.0 dated 2026-10-09
DESCRIPTION | 19 MD5 | 301 ++-- NAMESPACE | 16 NEWS.md | 11 R/argument_convention.R | 118 - R/arm_ref_comp.R | 147 ++ R/teal.modules.clinical.R | 3 R/tm_a_gee.R | 383 ++--- R/tm_a_mmrm.R | 634 ++++----- R/tm_g_barchart_simple.R | 222 +-- R/tm_g_barchart_simple_picks.R |only R/tm_g_ci.R | 143 +- R/tm_g_ci_picks.R |only R/tm_g_forest_rsp.R | 500 +++---- R/tm_g_forest_tte.R | 443 +++--- R/tm_g_ipp.R | 410 ++---- R/tm_g_km.R | 492 +++---- R/tm_g_lineplot.R | 373 ++--- R/tm_g_pp_adverse_events.R | 381 ++--- R/tm_g_pp_patient_timeline.R | 664 ++++------ R/tm_g_pp_therapy.R | 479 +++---- R/tm_g_pp_vitals.R | 270 +--- R/tm_t_abnormality.R | 352 ++--- R/tm_t_abnormality_by_worst_grade.R | 396 ++--- R/tm_t_ancova.R | 381 ++--- R/tm_t_binary_outcome.R | 306 ++-- R/tm_t_coxreg.R | 516 +++---- R/tm_t_events.R | 274 +--- R/tm_t_events_by_grade.R | 291 ++-- R/tm_t_events_patyear.R | 378 ++--- R/tm_t_events_summary.R | 372 ++--- R/tm_t_exposure.R | 375 ++--- R/tm_t_glm_counts.R | 324 ++-- R/tm_t_logistic.R | 369 ++--- R/tm_t_mult_events.R | 203 +-- R/tm_t_pp_basic_info.R | 128 - R/tm_t_pp_laboratory.R | 387 ++--- R/tm_t_pp_medical_history.R | 212 +-- R/tm_t_pp_prior_medication.R | 262 +-- R/tm_t_shift_by_arm.R | 288 +--- R/tm_t_shift_by_arm_by_worst.R | 332 ++--- R/tm_t_shift_by_grade.R | 422 ++---- R/tm_t_smq.R | 270 +--- R/tm_t_summary.R | 203 +-- R/tm_t_summary_by.R | 324 ++-- R/tm_t_tte.R | 478 ++----- R/utils.R | 42 R/utils_picks.R |only R/zzz.R | 2 README.md | 2 build/vignette.rds |binary inst/WORDLIST | 6 inst/doc/decorate-module-output.R | 94 - inst/doc/decorate-module-output.Rmd | 94 - inst/doc/decorate-module-output.html | 332 ++--- inst/doc/generate_tmc_test_data.html | 4 inst/doc/quickstart_substitute.html | 10 inst/doc/teal-modules-clinical.R | 15 inst/doc/teal-modules-clinical.Rmd | 50 inst/doc/teal-modules-clinical.html | 70 - man/arm_bucket_values.Rd |only man/arm_ref_comp_observer_picks.Rd |only man/module_arguments.Rd | 118 - man/paramcd_title_from_anl.Rd |only man/template_coxreg_m.Rd | 2 man/template_laboratory.Rd | 4 man/template_shift_by_arm_by_worst.Rd | 6 man/tm_a_gee.Rd | 68 - man/tm_a_mmrm.Rd | 68 - man/tm_g_barchart_simple.Rd | 204 +-- man/tm_g_ci.Rd | 138 +- man/tm_g_forest_rsp.Rd | 81 - man/tm_g_forest_tte.Rd | 91 - man/tm_g_ipp.Rd | 105 - man/tm_g_km.Rd | 96 - man/tm_g_lineplot.Rd | 76 - man/tm_g_pp_adverse_events.Rd | 54 man/tm_g_pp_patient_timeline.Rd | 122 - man/tm_g_pp_therapy.Rd | 100 - man/tm_g_pp_vitals.Rd | 29 man/tm_t_abnormality.Rd | 78 - man/tm_t_abnormality_by_worst_grade.Rd | 80 - man/tm_t_ancova.Rd | 75 - man/tm_t_binary_outcome.Rd | 64 man/tm_t_coxreg.Rd | 91 - man/tm_t_events.Rd | 37 man/tm_t_events_by_grade.Rd | 39 man/tm_t_events_patyear.Rd | 86 - man/tm_t_events_summary.Rd | 71 - man/tm_t_exposure.Rd | 73 - man/tm_t_glm_counts.Rd | 69 - man/tm_t_logistic.Rd | 54 man/tm_t_mult_events.Rd | 39 man/tm_t_pp_basic_info.Rd | 18 man/tm_t_pp_laboratory.Rd | 54 man/tm_t_pp_medical_history.Rd | 25 man/tm_t_pp_prior_medication.Rd | 40 man/tm_t_shift_by_arm.Rd | 78 - man/tm_t_shift_by_arm_by_worst.Rd | 77 - man/tm_t_shift_by_grade.Rd | 97 - man/tm_t_smq.Rd | 58 man/tm_t_summary.Rd | 29 man/tm_t_summary_by.Rd | 65 man/tm_t_tte.Rd | 92 - tests/testthat/_snaps/tm_g_km.md | 21 tests/testthat/_snaps/tm_t_abnormality_by_worst_grade.md | 4 tests/testthat/_snaps/tm_t_coxreg.md | 6 tests/testthat/_snaps/tm_t_summary.md | 2 tests/testthat/_snaps/tm_t_tte.md | 4 tests/testthat/helper-TealAppDriver.R | 204 +++ tests/testthat/test-examples.R | 42 tests/testthat/test-shinytest2-teal_picks_playground.R |only tests/testthat/test-shinytest2-tm_a_gee.R | 118 - tests/testthat/test-shinytest2-tm_a_mmrm.R | 399 ++---- tests/testthat/test-shinytest2-tm_g_barchart_simple.R | 205 --- tests/testthat/test-shinytest2-tm_g_ci.R | 297 ++-- tests/testthat/test-shinytest2-tm_g_forest_rsp.R | 150 +- tests/testthat/test-shinytest2-tm_g_forest_tte.R | 235 ++- tests/testthat/test-shinytest2-tm_g_ipp.R | 176 +- tests/testthat/test-shinytest2-tm_g_km.R | 201 +-- tests/testthat/test-shinytest2-tm_g_lineplot.R | 164 +- tests/testthat/test-shinytest2-tm_g_pp_adverse_events.R | 181 +- tests/testthat/test-shinytest2-tm_g_pp_patient_timeline.R | 340 ++--- tests/testthat/test-shinytest2-tm_g_pp_therapy.R | 529 +++++-- tests/testthat/test-shinytest2-tm_g_pp_vitals.R | 111 - tests/testthat/test-shinytest2-tm_t_abnormality.R | 92 - tests/testthat/test-shinytest2-tm_t_abnormality_by_worst_grade.R | 85 - tests/testthat/test-shinytest2-tm_t_ancova.R | 142 +- tests/testthat/test-shinytest2-tm_t_binary_outcome.R | 91 - tests/testthat/test-shinytest2-tm_t_coxreg.R | 228 +-- tests/testthat/test-shinytest2-tm_t_events.R | 57 tests/testthat/test-shinytest2-tm_t_events_by_grade.R | 72 - tests/testthat/test-shinytest2-tm_t_events_patyear.R | 82 - tests/testthat/test-shinytest2-tm_t_events_summary.R | 80 - tests/testthat/test-shinytest2-tm_t_exposure.R | 106 - tests/testthat/test-shinytest2-tm_t_logistic.R | 117 - tests/testthat/test-shinytest2-tm_t_mult_events.R | 51 tests/testthat/test-shinytest2-tm_t_pp_basic_info.R | 45 tests/testthat/test-shinytest2-tm_t_pp_laboratory.R | 225 +-- tests/testthat/test-shinytest2-tm_t_pp_medical_history.R | 91 - tests/testthat/test-shinytest2-tm_t_pp_prior_medication.R | 116 - tests/testthat/test-shinytest2-tm_t_shift_by_arm.R | 122 - tests/testthat/test-shinytest2-tm_t_shift_by_arm_by_worst.R | 159 -- tests/testthat/test-shinytest2-tm_t_shift_by_grade.R | 156 -- tests/testthat/test-shinytest2-tm_t_smq.R | 130 - tests/testthat/test-shinytest2-tm_t_summary.R | 53 tests/testthat/test-shinytest2-tm_t_summary_by.R | 130 - tests/testthat/test-shinytest2-tm_t_tte.R | 144 -- tests/testthat/test-tm_g_lineplot.R | 5 tests/testthat/test-tm_t_glm_counts.R | 33 tests/testthat/test-tm_t_pp_laboratory.R |only tests/testthat/test-tm_t_summary.R | 1 tests/testthat/test-tm_t_summary_by.R | 28 tests/testthat/test-utils_picks.R |only vignettes/decorate-module-output.Rmd | 94 - vignettes/teal-modules-clinical.Rmd | 50 156 files changed, 10997 insertions(+), 12601 deletions(-)
More information about teal.modules.clinical at CRAN
Permanent link
Title: Qualification of R Software Installations
Description: Qualify R software installations using R Markdown as the foundation
for the Installation Qualification (IQ) and Operational Qualification (OQ) when
used in environments (such as regulated clinical trials) where such
processes may be required.
Author: Donnie Musgrove [aut, cre] ,
Graeme L. Hickey [aut] ,
Marc Schwartz [aut] ,
Alan Haynes [ctb],
Bryan Martin [ctb] ,
Medtronic Inc. [cph]
Maintainer: Donnie Musgrove <donniemusgrove@gmail.com>
Diff between rqualify versions 1.1.0 dated 2026-08-28 and 1.2.0 dated 2026-10-09
DESCRIPTION | 20 MD5 | 68 - NEWS.md | 30 R/check_validation_results.R | 71 - R/render_validation.R | 29 R/rqualify.R | 153 +- R/setup_pandoc_env.R | 46 R/setup_tinytex_env.R | 78 - R/setup_validation_dirs.R | 69 - R/validation_execution.R |only R/validation_result.R |only README.md | 24 inst/doc/rqualify-cran.R | 173 --- inst/doc/rqualify-cran.Rmd | 181 --- inst/doc/rqualify-cran.html | 183 --- inst/qualify_r/R-validation.Rmd | 1380 ++++++++++--------------- inst/qualify_r/R-validation.qmd | 252 ---- inst/qualify_r/example_success/CMDFile1Out.txt | 186 +-- inst/qualify_r/example_success/CMDFile2Out.txt | 90 - inst/qualify_r/example_success/CMDFile3Out.txt | 86 - inst/qualify_r/example_success/CMDFile4Out.txt | 86 - inst/qualify_r/example_success/CMDFile5Out.txt | 100 - inst/qualify_r/example_success/CMDFile6Out.txt | 268 ++-- inst/qualify_r/example_success/CMDFile7Out.txt | 818 +++++++------- man/rqualify.Rd | 114 +- tests/testthat.R | 24 tests/testthat/helper-validation.R |only tests/testthat/test-check_validation_results.R | 103 - tests/testthat/test-render-smoke.R |only tests/testthat/test-render_validation.R | 245 +--- tests/testthat/test-rqualify-orchestration.R | 284 +---- tests/testthat/test-rqualify.R | 12 tests/testthat/test-setup_pandoc_env.R | 80 - tests/testthat/test-setup_tinytex_env.R | 212 +-- tests/testthat/test-setup_validation_dirs.R | 41 tests/testthat/test-validation_execution.R |only tests/testthat/test-validation_result.R |only vignettes/rqualify-cran.Rmd | 181 --- 38 files changed, 2266 insertions(+), 3421 deletions(-)
Title: Parse Farm Credit Administration Call Report Data into Tidy Data
Frames
Description: Parses financial condition and performance data (Call Reports) for
institutions in the United States Farm Credit System. Contains functions for
downloading files from the Farm Credit Administration (FCA) Call Report
archive website and reading the files into tidy data frame format.
The archive website can be found at
<https://www.fca.gov/bank-oversight/call-report-data-for-download>.
Author: Michael Thomas [aut, cre],
Ivan Millanes [aut],
Ketchbrook Analytics [cph, fnd]
Maintainer: Michael Thomas <mthomas@ketchbrookanalytics.com>
Diff between fcall versions 0.1.6 dated 2025-12-10 and 0.1.7 dated 2026-10-09
DESCRIPTION | 12 LICENSE | 4 MD5 | 77 +- NAMESPACE | 18 NEWS.md | 157 ++--- R/compare_metadata.R | 278 ++++----- R/data.R | 306 +++++----- R/download_data.R | 370 +++++++----- R/process_data.R | 1006 ++++++++++++++++----------------- build/vignette.rds |binary inst/doc/data-structure.Rmd | 182 ++--- inst/doc/getting-started.Rmd | 164 ++--- man/RCB2__AssetCodeRCB2.Rd | 52 - man/RCB3__DebtMaturityCode.Rd | 52 - man/RCB__INV_CODE.Rd | 52 - man/RCF1__LOANSTATUS.Rd | 52 - man/RCF__LOANSTATUS.Rd | 52 - man/RCI2B__DerivCode.Rd | 52 - man/RCI2C__ExposureCode.Rd | 52 - man/RCI2D__DerivRMCode.Rd | 52 - man/RCO__ASSET_CODE.Rd | 52 - man/RCR3__RegCapCode.Rd | 52 - man/RCR7__RegCapCode.Rd | 52 - man/RID__CAP_CODE.Rd | 52 - man/RIE1__ACLCode.Rd | 52 - man/compare_files_content.Rd | 60 - man/compare_metadata.Rd | 114 +-- man/download_data.Rd | 165 ++--- man/file_metadata.Rd | 52 - man/get_codes_dict.Rd | 82 +- man/process_data.Rd | 94 +-- man/process_data_file.Rd | 105 +-- man/process_metadata_file.Rd | 89 +- man/read_data_file.Rd | 66 +- tests/testthat.R | 24 tests/testthat/test-compare_metadata.R | 176 ++--- tests/testthat/test-download_data.R |only tests/testthat/test-process_data.R | 264 +++----- vignettes/data-structure.Rmd | 182 ++--- vignettes/getting-started.Rmd | 164 ++--- 40 files changed, 2473 insertions(+), 2414 deletions(-)
Title: Statistical Tools Designed for End Users
Description: The statistical tools in this package do one of four things:
1) Enhance basic statistical functions with more
flexible inputs, smarter defaults, and richer, clearer, and ready-to-use
output (e.g., t.test2())
2) Produce publication-ready commonly needed figures with one line of code (e.g., plot_cdf())
3) Implement novel analytical tools developed by the authors (e.g., twolines())
4) Deliver niche functions of high value to the authors that are not easily
available elsewhere (e.g., clear(), convert_to_sql(), resize_images()).
Author: Uri Simonsohn [aut, cre]
Maintainer: Uri Simonsohn <urisohn@gmail.com>
Diff between statuser versions 0.3.1 dated 2026-06-24 and 0.4.0 dated 2026-10-09
DESCRIPTION | 6 MD5 | 51 +-- NAMESPACE | 1 NEWS.md | 18 + R/interprobe.R | 91 ++++-- R/interprobe_helpers.R | 148 ++++++++- R/lm2.R | 22 - R/round2.R |only R/stimulus_auxiliary.R | 43 +- R/t.test2.R | 1 R/table2.R | 10 R/text2.R | 1 R/zzz.R | 6 README.md | 13 build/partial.rdb |binary man/interprobe.Rd | 13 man/lm2.Rd | 19 + man/round2.Rd |only man/t.test2.Rd | 3 man/table2.Rd | 29 + man/text2.Rd | 13 tests/UNIT_TESTS.md | 6 tests/testthat/Rplots.pdf |binary tests/testthat/test-backend_equivalence.R | 3 tests/testthat/test-interprobe.R | 447 +++++++++++++++++++++++++++++- tests/testthat/test-lm2.R | 22 + tests/testthat/test-round2.R |only tests/testthat/test-stimulus.plot.R | 85 +++++ 28 files changed, 910 insertions(+), 141 deletions(-)
Title: Matrix-Variate Non-Gaussian Linear Regression Models
Description: Fits matrix-variate variance-gamma (MVVG) and matrix-variate normal-inverse-Gaussian (MVNIG) linear regression models using expectation-conditional maximization (ECM) algorithms. The models accommodate clustered matrix-valued responses, with unequal numbers of observations across subjects, correlated responses, skewness, and within-subject dependence. Functions are provided for model fitting, prediction, and subject-level influence assessment using approximate generalized Cook's distances. The package also includes motivating periodontal data from Gullah-speaking African Americans with Type-II diabetes. For details on the underlying matrix-variate distributions (MVVG and MVNIG), see Gallaugher and McNicholas (2019, <doi:10.1016/j.spl.2018.08.012>).
Author: Samuel Soon [aut, cre],
Dipankar Bandyopadhyay [aut],
Qingyang Liu [aut]
Maintainer: Samuel Soon <samksoon2@gmail.com>
Diff between MVNGmod versions 0.1.2 dated 2026-07-16 and 0.1.3 dated 2026-10-09
DESCRIPTION | 8 +++---- MD5 | 9 ++++---- NAMESPACE | 1 R/MVNGmod.R | 61 +++++++++++++++++++++++++++++++++++++++++++++++++++++++- man/MVVGmod.Rd | 2 - man/mod_hess.Rd |only 6 files changed, 71 insertions(+), 10 deletions(-)
Title: Bayesian Linear Mixed-Effects Models
Description: Maximum a posteriori estimation for linear and generalized linear mixed-effects models in a Bayesian setting, implementing the methods of Chung, et al. (2013) <doi:10.1007/s11336-013-9328-2>. Extends package 'lme4' (Bates, Maechler, Bolker, and Walker (2015) <doi:10.18637/jss.v067.i01>).
Author: Vincent Dorie [aut, cre] ,
Douglas Bates [ctb] ,
Martin Maechler [ctb] ,
Ben Bolker [ctb] ,
Steven Walker [ctb]
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between blme versions 1.0-7 dated 2026-01-10 and 1.0-8 dated 2026-10-09
ChangeLog | 19 +++- DESCRIPTION | 8 - MD5 | 43 ++++----- NAMESPACE | 1 R/blmer.R | 131 ++++++++++++++++++----------- R/control.R | 24 ++++- R/devFun.R | 47 ++++++++-- R/dist.R | 43 +++++++++ R/dist_independent_ts.R | 81 +++++++---------- R/dist_t.R | 8 + R/optimize.R | 19 ++-- R/parameters.R | 22 +++- R/priorEval.R | 4 build |only man/blmer.Rd | 9 + man/bmerDist-class.Rd | 23 +++++ tests/testthat/test-02-glmm.R | 29 ++++++ tests/testthat/test-04-fixef_errors.R | 6 + tests/testthat/test-05-covariance_errors.R | 8 + tests/testthat/test-07-lmm_fixef.R | 43 +++++++++ tests/testthat/test-08-lmm_covariance.R | 20 ++++ tests/testthat/test-09-glmm_priors.R | 26 ++++- tests/testthat/test-10-refit.R | 29 ++++++ 23 files changed, 492 insertions(+), 151 deletions(-)
Title: Dataset and Variable Picker and Merge Module for 'teal'
Applications
Description: Allows users to interactively select datasets, variables, and
values within 'teal' applications using a 'tidyselect'-style
interface. Selected picks can be merged and transformed into
analysis-ready data within 'teal' modules.
Author: Dawid Kaledkowski [aut] ,
Andre Verissimo [aut] ,
Marcin Kosinski [aut],
Lluis Revilla Sancho [aut] ,
Oriol Senan [aut] ,
Dony Unardi [rev, cre],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dony Unardi <unardid@gene.com>
Diff between teal.picks versions 0.3.0 dated 2026-07-30 and 0.3.1 dated 2026-10-09
DESCRIPTION | 23 - MD5 | 70 ++-- NAMESPACE | 3 NEWS.md | 16 + R/as_picks.R | 5 R/helpers.R | 75 +++++ R/module_merge.R | 6 R/module_picks.R | 67 +++- R/picks.R | 38 +- R/resolver.R | 34 +- R/teal.picks.R | 1 R/tm_merge.R | 2 R/zzz.R | 10 build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/teal-picks-in-teal.html | 4 inst/doc/teal-picks-standalone-shiny.html | 4 man/as.picks.Rd | 7 man/dot-determine_choices.Rd | 2 man/ensure_picks_datasets.Rd |only man/picks_datanames.Rd |only man/picks_module.Rd | 20 + tests/testthat.R | 2 tests/testthat/helper-shinytest2_options.R | 2 tests/testthat/test-as_picks.R | 58 ++-- tests/testthat/test-assertion.R | 34 +- tests/testthat/test-badge_dropdown.R | 2 tests/testthat/test-helper-shinytest2.R | 8 tests/testthat/test-helpers.R | 108 +++++-- tests/testthat/test-interaction.R | 10 tests/testthat/test-module_merge.R | 228 +++++++++++---- tests/testthat/test-module_picks.R | 239 ++++++++-------- tests/testthat/test-picks.R | 372 +++++++++++++++----------- tests/testthat/test-print.R | 40 +- tests/testthat/test-shinytest2-module_picks.R |only tests/testthat/test-tidyselect_helpers.R | 90 +++--- tests/testthat/test-tm_merge.R | 54 +-- tests/testthat/test-zzz.R |only 38 files changed, 1012 insertions(+), 623 deletions(-)
Title: Create Datasets with Hidden Images in Residual Plots
Description: Implements the "Residual (Sur)Realism" algorithm described by
Stefanski (2007) <doi:10.1198/000313007X190079> to generate datasets
that reveal hidden images or messages in their residual plots. It offers
both predefined datasets and tools to embed custom text or images
into residual structures. Allowing users to create intriguing visual
demonstrations for teaching model diagnostics.
Author: James Joseph Balamuta [aut, cre, cph]
Maintainer: James Joseph Balamuta <james.balamuta@gmail.com>
Diff between surreal versions 0.0.2 dated 2026-01-11 and 0.0.3 dated 2026-10-09
DESCRIPTION | 10 MD5 | 64 +++- NAMESPACE | 9 NEWS.md | 50 +++ R/data-documentation.R | 2 R/surreal-app.R | 6 R/surreal-decoys.R |only R/surreal-image.R | 269 +++++++++++------ R/surreal-path.R |only R/surreal-text.R | 82 ++++- R/surreal-trace.R |only R/surreal.R | 158 +++++++--- README.md | 39 ++ build/partial.rdb |binary inst/surreal-app/R |only inst/surreal-app/app.R | 608 +++++++++++++++++++++------------------ man/figures/app-surreal.png |only man/jackolantern_surreal_data.Rd | 2 man/plot.surreal_path.Rd |only man/plot.surreal_trace.Rd |only man/surreal_app.Rd | 6 man/surreal_decoys.Rd |only man/surreal_image.Rd | 1 man/surreal_image_points.Rd |only man/surreal_path.Rd |only man/surreal_text.Rd | 7 man/surreal_text_points.Rd |only man/surreal_trace.Rd |only tests |only 29 files changed, 876 insertions(+), 437 deletions(-)
Title: Vignettes for Analyzing Data using 'OlinkAnalyze'
Description: Exemplifying analysis of large-scale protein
data from the 'Olink platform', primarily relative protein expression
data that has been exported from
'Olink NPX Software', as well as QUANT data from 'Olink'.
QUANT data is log-transformed. Materials focus on reading data,
demonstrating data wrangling and quality control analysis,
performing statistical analysis and generating
figures to visualize the results of the statistical analysis.
The goal of this package is to guide users extract biological insights
from large-scale protein data run on the 'Olink platform'.
More information on 'Olink' data can be found at <https://olink.com/>.
Author: Kathleen Nevola [aut, cre] ,
Marianne Sandin [aut] ,
Jamey Guess [aut] ,
Simon Forsberg [aut] ,
Christoffer Cambronero [aut] ,
Pascal Pucholt [aut] ,
Boxi Zhang [aut] ,
Masoumeh Sheikhi [aut] ,
Klev Diamanti [aut] ,
Amrita Kar [aut] ,
Lei Conze [aut] [...truncated...]
Maintainer: Kathleen Nevola <biostattools@olink.com>
Diff between OlinkAnalyzeVignettes versions 1.0.1 dated 2026-06-08 and 1.1.0 dated 2026-10-09
DESCRIPTION | 10 MD5 | 34 NEWS.md | 7 build/vignette.rds |binary inst/doc/bridging_cross-product.R | 1342 ++++---- inst/doc/bridging_cross-product.html | 5329 +++++++++++++++++------------------ inst/doc/bridging_introduction.R | 1412 ++++----- inst/doc/bridging_introduction.Rmd | 16 inst/doc/bridging_introduction.html | 4863 +++++++++++++++---------------- inst/doc/lod.R | 654 ++-- inst/doc/lod.Rmd | 4 inst/doc/lod.html | 3658 ++++++++++++------------ inst/doc/outlier_exclusion.R | 938 +++--- inst/doc/outlier_exclusion.html | 1973 ++++++------ inst/doc/plate_randomizer.R | 292 - inst/doc/plate_randomizer.html | 2209 +++++++------- vignettes/bridging_introduction.Rmd | 16 vignettes/lod.Rmd | 4 18 files changed, 11393 insertions(+), 11368 deletions(-)
More information about OlinkAnalyzeVignettes at CRAN
Permanent link
Title: Circular Analyses Helper Functions
Description: Light-weight functions for computing descriptive statistics in different circular spaces (e.g., 2pi, 180, or 360 degrees), to handle angle-dependent biases, pad circular data, and more. Specifically aimed for psychologists and neuroscientists analyzing circular data. Basic methods are based on Jammalamadaka and SenGupta (2001) <doi:10.1142/4031>, removal of cardinal biases is based on the approach introduced in van Bergen, Ma, Pratte, & Jehee (2015) <doi:10.1038/nn.4150> and Chetverikov and Jehee (2023) <doi:10.1038/s41467-023-43251-w>.
Author: Andrey Chetverikov [aut, cre] ,
Eline Van Geert [ctb]
Maintainer: Andrey Chetverikov <andrey.chetverikov@uib.no>
Diff between circhelp versions 1.1 dated 2024-07-04 and 1.4.0 dated 2026-10-09
DESCRIPTION | 25 MD5 | 68 NAMESPACE | 129 NEWS.md | 69 R/circhelp-package.R | 50 R/data.R | 6 R/functions.R | 2986 ++++++++++------- README.md | 182 - build/circhelp.pdf |only build/stage23.rdb |binary build/vignette.rds |binary inst/WORDLIST |only inst/doc/cardinal_biases.R | 66 inst/doc/cardinal_biases.Rmd | 271 - inst/doc/cardinal_biases.html | 135 inst/doc/serial_dependence_with_density_asymmetry.R |only inst/doc/serial_dependence_with_density_asymmetry.Rmd |only inst/doc/serial_dependence_with_density_asymmetry.html |only man/Bae_Luck_2018_data.Rd | 6 man/angle_diff_rad.Rd | 7 man/circ_corr.Rd | 7 man/circ_lin_corr.Rd | 3 man/circ_loess.Rd | 1 man/circ_mean_rad.Rd | 7 man/circ_sd_rad.Rd | 7 man/circhelp-package.Rd | 5 man/density_asymmetry.Rd |only man/density_asymmetry_discrete.Rd |only man/get_boundary_preds.Rd | 17 man/pad_circ.Rd | 2 man/remove_cardinal_biases.Rd | 16 man/smoothed_circ_sd.Rd |only man/vm_kappa_to_circ_sd.Rd | 4 man/weighted_circ_mean.Rd | 6 man/weighted_sem.Rd | 2 tests/testthat.R | 2 tests/testthat/test-density-asymmetry.R |only tests/testthat/test-functions.R | 157 vignettes/cardinal_biases.Rmd | 271 - vignettes/serial_dependence_with_density_asymmetry.Rmd |only 40 files changed, 2776 insertions(+), 1731 deletions(-)
Title: Win Time Methods for Time-to-Event Data in Clinical Trials
Description: Performs an analysis of time-to-event clinical trial data using various "win time" methods,
including 'ewt', 'ewtr', 'rmt', 'ewtp', 'rewtp', 'ewtpr', 'rewtpr', 'max', 'wtr', 'rwtr', 'pwt', and 'rpwt'. These methods are used to calculate and compare
treatment effects on ordered composite endpoints. The package handles event times, event indicators, and treatment
arm indicators and supports calculations on observed and resampled data. Detailed explanations of each method and
usage examples are provided in "Use of win time for ordered composite endpoints in clinical trials," by Troendle et al.
(2024)<doi:10.1002/sim.10045>. For more information, see the package documentation or the vignette titled "Introduction to wintime."
Author: James Troendle [aut, cre],
Samuel Lawrence [aut]
Maintainer: James Troendle <james.troendle@nih.gov>
Diff between wintime versions 1.0.0 dated 2026-09-11 and 1.0.1 dated 2026-10-09
DESCRIPTION | 6 +-- MD5 | 10 ++--- R/bootstrap.R | 12 ++++++ R/ewt.R | 73 +++++++++++++++++++++++++++++++---------- R/rmt.R | 6 ++- inst/doc/wintime_vignette.html | 20 +++++------ 6 files changed, 89 insertions(+), 38 deletions(-)
Title: Sample Size Estimation for Bio-Equivalence Trials Through
Simulation
Description: Sample size estimation for bio-equivalence trials is supported through a simulation-based approach
that extends the Two One-Sided Tests (TOST) procedure. The methodology provides flexibility in
hypothesis testing, accommodates multiple treatment comparisons, and accounts for correlated endpoints.
Users can model complex trial scenarios, including parallel and crossover designs, intra-subject variability,
and different equivalence margins. Monte Carlo simulations enable accurate estimation of power and type I error
rates, ensuring well-calibrated study designs. The statistical framework builds on established methods for
equivalence testing and multiple hypothesis testing in bio-equivalence studies, as described in Schuirmann (1987)
<doi:10.1007/BF01068419>, Mielke et al. (2018) <doi:10.1080/19466315.2017.1371071>, Shieh (2022)
<doi:10.1371/journal.pone.0269128>, and Sozu et al. (2015) <doi:10.1007/978-3-319-22005-5>.
Comprehensive documentation and vignettes guid [...truncated...]
Author: Thomas Debray [aut, cre],
Tim Friede [ctb],
Johanna Munoz [ctb],
Dewi Amaliah [ctb],
Wei Wei [ctb],
Marian Mitroiu [ctb],
Scott McDonald [ctb],
Biogen Inc [cph, fnd] ,
Smart Data Analysis and Statistics B.V. [cph, fnd]
Maintainer: Thomas Debray <tdebray@fromdatatowisdom.com>
Diff between SimTOST versions 1.0.1 dated 2025-02-18 and 1.1.0 dated 2026-10-09
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Title: A Collection of Proteome Panels and Metadata
Description: It aggregates protein panel data and metadata for protein quantitative
trait locus (pQTL) analysis using 'pQTLtools' (<https://jinghuazhao.github.io/pQTLtools/>).
The package includes data from affinity-based panels such as 'Olink' (<https://olink.com/>)
and 'SomaScan' (<https://somalogic.com/>), as well as mass spectrometry-based panels from
'CellCarta' (<https://cellcarta.com/>), 'Seer' (<https://seer.bio/>) and 'SWATH-MS'
(<doi:10.15252/msb.20178126>). The metadata encompasses updated annotations
and publication details.
Author: Jing Hua Zhao [aut, cre] ,
Uwe Ligges [ctb],
Benjamin Altmann [ctb],
Brian Ripley [ctb]
Maintainer: Jing Hua Zhao <jinghuazhao@hotmail.com>
Diff between pQTLdata versions 0.6 dated 2026-03-09 and 0.7 dated 2026-10-09
DESCRIPTION | 14 ++--- MD5 | 71 +++++++++++++++------------- NEWS.md | 9 +++ R/caprion.R | 44 +++++++++++------ build/partial.rdb |binary build/vignette.rds |binary data/Olink_Explore_1536.rda |binary data/Olink_Explore_3072.rda |binary data/Olink_Explore_HT.rda |binary data/Olink_Target_96.rda |binary data/Olink_qPCR.rda |binary data/SomaScan11k.rda |binary data/SomaScan160410.rda |binary data/SomaScanV4.1.rda |binary data/caprion.rda |binary data/inf1.rda |binary data/scallop_inf1.rda |binary data/seer1980.rda |binary data/swath_ms.rda |binary inst/UniProt |only inst/doc/pQTLdata.html | 108 ++++++++++++++++++++++---------------------- inst/scripts/caprion.py |only inst/scripts/caprion2.R |only inst/scripts/cran.sh | 49 ++++++------------- inst/scripts/hg19Tables.R | 2 man/Olink_Explore_1536.Rd | 2 man/Olink_Explore_3072.Rd | 2 man/Olink_Explore_HT.Rd | 2 man/Olink_Target_96.Rd | 2 man/Olink_qPCR.Rd | 2 man/SomaScan11k.Rd | 2 man/SomaScan160410.Rd | 2 man/SomaScanV4.1.Rd | 2 man/caprion.Rd | 48 ++++++++++++------- man/inf1.Rd | 2 man/scallop_inf1.Rd | 2 man/seer1980.Rd | 2 man/swath_ms.Rd | 2 38 files changed, 194 insertions(+), 175 deletions(-)
Title: Estimation, Simulation and Reliability of Drifting Markov Models
Description: Performs the drifting Markov models (DMM) which are
non-homogeneous Markov models designed for modeling the heterogeneities of
sequences in a more flexible way than homogeneous Markov chains or even
hidden Markov models. In this context, we developed an R package dedicated to
the estimation, simulation and the exact computation of associated reliability
of drifting Markov models. The implemented methods are described in
Vergne, N. (2008), <doi:10.2202/1544-6115.1326> and
Barbu, V.S., Vergne, N. (2019) <doi:10.1007/s11009-018-9682-8> .
Author: Nicolas Vergne [aut, cre] ,
Corentin Lothode [aut] ,
Alexandre Seiller [aut],
Victor Mataigne [ctb],
Arnaud Lefebvre [ctb],
Annthomy Gilles [ctb],
Vlad Stefan Barbu [aut]
Maintainer: Nicolas Vergne <nicolas.vergne@univ-rouen.fr>
Diff between drimmR versions 1.0.3 dated 2026-02-12 and 1.0.4 dated 2026-10-09
DESCRIPTION | 9 +++++---- MD5 | 23 +++++++++++++++-------- NAMESPACE | 3 +-- NEWS.md | 12 ++++++++++++ R/allgenerics.R | 2 +- R/dmm.R | 13 ++++++++----- R/metrics.R | 12 ++++++++---- build/partial.rdb |binary build/vignette.rds |only inst/doc |only man/drimmR-package.Rd | 18 ++++++++++++++++++ vignettes |only 12 files changed, 68 insertions(+), 24 deletions(-)
Title: J&J Innovative Medicine ADaM Test Data
Description: A set of Analysis Data Model (ADaM) datasets constructed by
modifying the ADaM datasets in the 'pharmaverseadam' package to meet J&J Innovative Medicine's
standard data structure for Clinical and Statistical Programming.
Author: David Munoz Tord [aut, cre],
Nicholas Masel [aut],
Joe Kovach [aut],
Mahesh Divakaran [ctb],
Selvaraj Shanmugam [ctb],
Renfei Mao [ctb],
J&J Innovative Medicine [cph, fnd]
Maintainer: David Munoz Tord <david.munoztord@mailbox.org>
Diff between pharmaverseadamjnj versions 0.0.7 dated 2026-09-28 and 0.0.8 dated 2026-10-09
DESCRIPTION | 12 ++++++--- MD5 | 72 +++++++++++++++++++++++++++--------------------------- NEWS.md | 8 +++++- R/adae.R | 2 - R/adaecomp.R | 2 - R/adaeocmq.R | 2 - R/adagocmq.R | 2 - R/adcm.R | 2 - R/addili.R | 2 - R/addisp.R | 2 - R/adeg.R | 2 - R/adex.R | 2 - R/adexsum.R | 2 - R/adishum.R | 2 - R/adlb.R | 2 - R/adpc.R | 2 - R/adsl.R | 2 - R/adslcomp.R | 2 - R/adttesaf.R | 2 - R/advs.R | 2 - data/adae.rda |binary data/adaecomp.rda |binary data/adaeocmq.rda |binary data/adcm.rda |binary data/addili.rda |binary data/addisp.rda |binary data/adeg.rda |binary data/adex.rda |binary data/adexsum.rda |binary data/adishum.rda |binary data/adlb.rda |binary data/adpc.rda |binary data/adsl.rda |binary data/adslcomp.rda |binary data/adttesaf.rda |binary data/advs.rda |binary man/adlb.Rd | 2 - 37 files changed, 70 insertions(+), 58 deletions(-)
More information about pharmaverseadamjnj at CRAN
Permanent link
Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates graphics with
details from statistical tests included in the plots themselves. It
provides an easier syntax to generate information-rich plots for
statistical analysis of continuous (violin plots, scatterplots,
histograms, dot plots, dot-and-whisker plots) or categorical (pie and
bar charts) data. Currently, it supports the most common types of
statistical approaches and tests: parametric, nonparametric, robust,
and Bayesian versions of t-test/ANOVA, correlation analyses,
contingency table analysis, meta-analysis, and regression analyses.
References: Patil (2021) <doi:10.21105/joss.03167>.
Author: Indrajeet Patil [cre, aut, cph]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between ggstatsplot versions 1.1.1 dated 2026-08-25 and 1.1.2 dated 2026-10-09
DESCRIPTION | 32 +-- MD5 | 154 ++++++++--------- NAMESPACE | 18 +- NEWS.md | 8 R/0-utils.R | 5 R/combine-plots.R | 2 R/data.R | 29 +-- R/extract-stats.R | 28 ++- R/ggbarstats.R | 19 +- R/ggbetweenstats-helpers.R | 12 - R/ggbetweenstats.R | 49 +++-- R/ggcoefstats.R | 62 ++++--- R/ggcorrmat.R | 44 +++- R/ggdotplotstats.R | 25 +- R/gghistostats-helpers.R | 22 -- R/gghistostats.R | 25 +- R/ggpiestats.R | 61 ++++-- R/ggscatterstats.R | 22 +- R/ggstatsplot-package.R | 2 R/ggwithinstats.R | 12 + R/theme-ggstatsplot.R | 2 README.md | 74 ++++---- inst/doc/additional.Rmd | 66 +------ inst/doc/additional.html | 48 +---- inst/doc/ggstatsplot.Rmd | 12 + inst/doc/ggstatsplot.html | 22 +- man/Titanic_full.Rd | 4 man/bugs_long.Rd | 16 - man/combine_plots.Rd | 2 man/dot-grouped_list.Rd | 5 man/extract_stats.Rd | 29 ++- man/figures/README-customplot-1.png |binary man/figures/README-ggcorrmat1-1.png |binary man/figures/README-ggwithinstats2-1.png |binary man/ggbarstats.Rd | 69 ++++--- man/ggbetweenstats.Rd | 35 ++- man/ggcoefstats.Rd | 76 ++++---- man/ggcorrmat.Rd | 40 ++-- man/ggdotplotstats.Rd | 36 ++-- man/gghistostats.Rd | 26 +- man/ggpiestats.Rd | 65 ++++--- man/ggscatterstats.Rd | 22 +- man/ggstatsplot-package.Rd | 2 man/ggwithinstats.Rd | 35 ++- man/grouped_ggbarstats.Rd | 62 ++++--- man/grouped_ggbetweenstats.Rd | 39 ++-- man/grouped_ggcorrmat.Rd | 44 +++- man/grouped_ggdotplotstats.Rd | 43 +++- man/grouped_gghistostats.Rd | 39 ++-- man/grouped_ggpiestats.Rd | 54 +++--- man/grouped_ggscatterstats.Rd | 27 ++- man/grouped_ggwithinstats.Rd | 39 ++-- man/iris_long.Rd | 8 man/movies_long.Rd | 8 man/rmd-fragments/ggcoefstats_graphics.Rmd | 2 man/rmd-fragments/ggdotplotstats_graphics.Rmd | 4 man/theme_ggstatsplot.Rd | 2 tests/testthat.R | 3 tests/testthat/test-ggbetweenstats.R | 15 + tests/testthat/test-ggwithinstats.R | 16 + vignettes/additional.Rmd | 66 +------ vignettes/ggstatsplot.Rmd | 12 + vignettes/paper.bib | 21 -- vignettes/web_only/faq.Rmd | 229 +++++++++++++++++++------- vignettes/web_only/ggbarstats.Rmd | 62 +++++-- vignettes/web_only/ggbetweenstats.Rmd | 85 ++++++--- vignettes/web_only/ggcoefstats.Rmd | 80 +++++---- vignettes/web_only/ggcorrmat.Rmd | 59 ++++-- vignettes/web_only/ggdotplotstats.Rmd | 48 ++++- vignettes/web_only/gghistostats.Rmd | 67 ++++--- vignettes/web_only/ggpiestats.Rmd | 63 +++++-- vignettes/web_only/ggscatterstats.Rmd | 71 ++++---- vignettes/web_only/ggwithinstats.Rmd | 158 +++++++++++------ vignettes/web_only/interpretation.Rmd | 34 ++- vignettes/web_only/pairwise.Rmd | 67 ++++--- vignettes/web_only/paper.bib | 18 -- vignettes/web_only/principles.Rmd | 74 ++++---- vignettes/web_only/purrr_examples.Rmd | 126 ++++++-------- 78 files changed, 1832 insertions(+), 1230 deletions(-)
Title: Demonstration of Disease Freedom (DDF)
Description: Implements the formulae required to calculate freedom
from disease according to Cameron and Baldock (1998)
<doi:10.1016/S0167-5877(97)00081-0>. These are the
methods used at the Swedish national veterinary institute (SVA) to
evaluate the performance of our nation animal disease
surveillance programmes.
Author: Thomas Rosendal [aut, cre] ,
Petter Hopp [ctb]
Maintainer: Thomas Rosendal <trosendal@gmail.com>
Diff between freedom versions 1.0.1 dated 2020-09-08 and 1.1.1 dated 2026-10-09
DESCRIPTION | 22 +-- MD5 | 52 ++++--- NAMESPACE | 3 NEWS.md | 27 +++ R/data_gen.R | 73 +++++----- R/distribution.R | 9 - R/freedom-package.R |only R/herd_se.R | 101 ++++++++++---- R/risk.R | 25 ++- R/temporal_discounting.R | 13 + README.md | 5 build/vignette.rds |binary inst/doc/simple_prob_freedom.R | 6 inst/doc/simple_prob_freedom.html | 266 +++++++++++++++++-------------------- man/hse.Rd | 21 ++ man/hse_finite.Rd | 20 ++ man/rpert.Rd | 1 man/sysse.Rd | 10 - tests/EPHI.R |only tests/adjusted_risk.R |only tests/gen_data.R | 34 ++-- tests/hse.R |only tests/hse_finite.R |only tests/hse_infinite.R |only tests/multi_risk_herd_and_animal.R | 68 +++++---- tests/multirisk_test.R | 4 tests/pert.R |only tests/risk.R | 25 ++- tests/sample_data.R |only tests/sysse.R |only tests/sysse_finite.R |only tests/temporal_discounting.R |only tests/valid_proportion.R |only 33 files changed, 473 insertions(+), 312 deletions(-)
Title: In-Silico Knockout Experiments from Single-Cell Gene Regulatory
Networks
Description: A workflow based on 'scTenifoldNet' to perform in-silico knockout experiments using single-cell RNA sequencing (scRNA-seq) data from wild-type (WT) control samples as input. First, the package constructs a single-cell gene regulatory network (scGRN) and knocks out a target gene from the adjacency matrix of the WT scGRN by setting the gene’s outdegree edges to zero. Then, it compares the knocked out scGRN with the WT scGRN to identify differentially regulated genes, called virtual-knockout perturbed genes, which are used to assess the impact of the gene knockout and reveal the gene’s function in the analyzed cells. It also predicts the direction (up or down) of the response of each gene from the WT expression, and reads all knockouts of a network from a single heat kernel, which makes transcriptome-wide knockout screens practical.
Author: Daniel Osorio [aut, cre] ,
Yan Zhong [aut, ctb],
Guanxun Li [aut, ctb],
Qian Xu [aut, ctb],
Yongjian Yang [aut, ctb],
Yanan Tian [aut, ctb],
Robert Chapkin [aut, ctb],
Jianhua Huang [aut, ctb],
James J. Cai [aut, ctb, ths]
Maintainer: Daniel Osorio <dcosorioh@gmail.com>
Diff between scTenifoldKnk versions 1.1 dated 2026-09-02 and 2.0.0 dated 2026-10-09
DESCRIPTION | 12 +- MD5 | 29 ++++-- NAMESPACE | 13 ++ NEWS.md |only R/dRegulation.R | 74 ++++++++++++++- R/heatKernel.R |only R/perturbationMap.R |only R/plotKO.R | 22 +++- R/restoreSeed.R |only R/scTenifoldKnk.R | 216 ++++++++++++++++++++++++++++++--------------- man/dRegulation.Rd | 37 ++++++- man/heatKernel.Rd |only man/hkManifoldAlignment.Rd |only man/knockoutDirection.Rd |only man/perturbationMap.Rd |only man/plotKO.Rd | 3 man/scTenifoldKnk.Rd | 50 ++++++++-- tests |only 18 files changed, 345 insertions(+), 111 deletions(-)
Title: 'Rcpp' Bindings for the 'simdjson' Header-Only Library for
'JSON' Parsing
Description: The 'JSON' format is ubiquitous for data interchange, and the
'simdjson' library written by Daniel Lemire (and many contributors) provides a
high-performance parser for these files which by relying on parallel 'SIMD'
instruction manages to parse these files as faster than disk speed. See the
<doi:10.48550/arXiv.1902.08318> paper for more details about 'simdjson'. This
package parses 'JSON' from string, file, or remote URLs under a variety of
settings.
Author: Dirk Eddelbuettel [aut, cre] ,
Brendan Knapp [aut] ,
Daniel Lemire [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppSimdJson versions 0.1.15 dated 2026-01-14 and 0.1.16 dated 2026-10-09
ChangeLog | 118 DESCRIPTION | 10 MD5 | 67 R/RcppExports.R | 22 R/exported-utils.R | 5 R/fload.R | 2 R/fparse.R | 63 R/utils.R | 15 build/partial.rdb |binary inst/NEWS.Rd | 15 inst/include/RcppSimdJson/common.hpp | 118 inst/include/RcppSimdJson/deserialize.hpp | 112 inst/include/RcppSimdJson/deserialize/Type_Doctor.hpp | 15 inst/include/RcppSimdJson/deserialize/dataframe.hpp | 402 inst/include/RcppSimdJson/deserialize/matrix.hpp | 21 inst/include/RcppSimdJson/deserialize/scalar.hpp | 22 inst/include/RcppSimdJson/deserialize/simplify.hpp | 26 inst/include/RcppSimdJson/deserialize/vector.hpp | 35 inst/include/RcppSimdJson_RcppExports.h | 2 inst/include/simdjson.cpp |31756 +++- inst/include/simdjson.h |141442 ++++++++++++++---- inst/tinytest/test_fparse_fload.R | 1 inst/tinytest/test_misc.R | 8 inst/tinytest/test_query.R | 16 man/fparse.Rd | 3 man/parseExample.Rd | 10 man/release_json_memory.Rd |only man/simdjson-utilities.Rd | 3 src/Makevars | 3 src/Makevars.win | 3 src/RcppExports.cpp | 14 src/deserialize.cpp | 4 src/exported-utils.cpp | 22 src/internal-utils.cpp | 4 src/simdjson_example.cpp | 4 35 files changed, 144121 insertions(+), 30242 deletions(-)
Title: Gene Locus Plot with Gene Annotations
Description: Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots <doi:10.1093/bioadv/vbaf006>.
Author: Myles Lewis [aut, cre] ,
Tom Willis [ctb]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between locuszoomr versions 1.1.0 dated 2026-09-17 and 1.2.0 dated 2026-10-09
DESCRIPTION | 20 ++-- MD5 | 57 ++++++----- NAMESPACE | 18 --- NEWS.md | 8 + R/eqtl_plot.R | 4 R/eqtl_plotly.R |only R/genetrack_ly.R | 30 ++++-- R/gg_scatter.R | 11 +- R/link_LD.R | 2 R/link_eqtl.R | 16 ++- R/locus_plotly.R | 82 ++++++++++++---- R/overlay_plotly.R |only R/scatter_plotly.R | 9 - R/zoom.R | 218 +++++++++++++++++++++++++++++++++++---------- R/zoom_funcs.R | 17 +++ inst/doc/locuszoomr.R | 38 +++---- inst/doc/locuszoomr.Rmd | 42 ++++---- inst/doc/locuszoomr.html | 62 ++++++------ inst/doc/zoom_browser.R | 9 + inst/doc/zoom_browser.Rmd | 26 ++++- inst/doc/zoom_browser.html | 27 ++++- man/eqtl_plotly.Rd |only man/genetrack_ly.Rd | 6 + man/link_LD.Rd | 2 man/link_eqtl.Rd | 17 ++- man/locus_plotly.Rd | 31 ++++-- man/overlay_plotly.Rd |only man/zoom.Rd | 9 + vignettes/locuszoomr.Rmd | 42 ++++---- vignettes/zoom2.png |binary vignettes/zoom_browser.Rmd | 26 ++++- vignettes/zoom_eqtl.png |only 32 files changed, 548 insertions(+), 281 deletions(-)
Title: Explore and Analyse General Transit Feed Specification (GTFS)
Files with a Focus on Urban Mobility
Description: A bundle of methods to
harmonize GTFS and OSM data, enabling the integration and exploration
of different layers of transit data, starting with the planned
operations (GTFS), but also the infrastructure topology (OSM) and
real-time information (GTFS-RT).
Author: Goncalo F. Matos [aut, cre] ,
Rosa Felix [aut] ,
Miguel Relvas Pires [ctb]
Maintainer: Goncalo F. Matos <goncaloafmatos@tecnico.pt>
Diff between GTFShift versions 1.0.0 dated 2026-09-27 and 1.1.0 dated 2026-10-09
DESCRIPTION | 6 +- MD5 | 44 +++++++++-------- NAMESPACE | 6 ++ NEWS.md |only R/get_trip_speed_profile.R |only R/osm_utils.R | 26 ++++++++++ R/query_osm_bus_lanes.R | 14 +++-- R/query_osm_centerlines.R | 2 R/query_osm_shapes_match_routes.R | 1 R/query_osm_shapes_to_routes.R | 1 R/rt_extend_prioritisation.R | 4 + README.md | 15 ++++-- inst/WORDLIST | 1 inst/doc/GTFShift.R | 5 +- inst/doc/GTFShift.Rmd | 13 ++++- inst/doc/GTFShift.html | 16 +++--- man/get_trip_speed_profile.Rd |only man/osm_bus_lanes.Rd | 6 +- man/osm_centerlines.Rd | 2 man/rt_collect_protobuf.Rd | 1 man/rt_extend_prioritisation.Rd | 2 tests/testthat/test-get_trip_speed_profile.R |only tests/testthat/test-osm_utils.R | 34 +++++++++++++ tests/testthat/test-rt_extend_prioritisation.R | 62 ++++++++++++++++++++++++- vignettes/GTFShift.Rmd | 13 ++++- 25 files changed, 221 insertions(+), 53 deletions(-)
Title: Fuzzy and Non-Fuzzy Classifiers
Description: It provides classifiers which can be used for discrete variables and for continuous variables based on the Naive Bayes and Fuzzy Naive Bayes hypothesis. Those methods were developed by researchers belong to the 'Laboratory of Technologies for Virtual Teaching and Statistics (LabTEVE)' and 'Laboratory of Applied Statistics to Image Processing and Geoprocessing (LEAPIG)' at 'Federal University of Paraiba, Brazil'. They considered some statistical distributions and their papers were published in the scientific literature, as for instance, the Gaussian classifier using fuzzy parameters, proposed by 'Moraes, Ferreira and Machado' (2021) <doi:10.1007/s40815-020-00936-4>.
Author: Jodavid Ferreira [aut, cre] ,
Ronei Moraes [ctb] ,
Liliane Machado [ctb] ,
Arthur Ricardo [ctb],
Isaac Araujo [ctb]
Maintainer: Jodavid Ferreira <jodavid@protonmail.com>
Diff between FuzzyClass versions 0.1.7 dated 2025-09-03 and 0.2.0 dated 2026-10-09
DESCRIPTION | 16 MD5 | 103 +- NAMESPACE | 40 - NEWS.md | 20 R/DWFuzzyGammaNaiveBayes.R | 76 - R/DoubleWeightedFuzzyHiperGeometricNaiveBayes.R | 193 +--- R/ExpNBFuzzyParam.R | 127 --- R/FuzzyBayesRule.R | 54 - R/FuzzyBetaNaiveBayes.R | 66 - R/FuzzyBinomialNaiveBayes.R | 101 +- R/FuzzyExponentialNaiveBayes.R | 75 - R/FuzzyGammaNaiveBayes.R | 75 - R/FuzzyGaussianNaiveBayes.R | 97 +- R/FuzzyGeoNaiveBayes.R | 191 +--- R/FuzzyHiperGeometricNaiveBayes.R | 180 +--- R/FuzzyNaiveBayes.R | 271 ++---- R/FuzzyPoissonNaiveBayes.R | 82 -- R/FuzzyRuleBasedSystem.R | 53 - R/FuzzyTrapeNaiveBayes.R | 149 +-- R/FuzzyTriangNaiveBayes.R | 98 -- R/GauNBFuzzyParam.R | 123 --- R/PoiNBFuzzyParam.R | 135 --- R/functions.R | 935 +++++++++++++++--------- R/getMembershipsTrapezoidal.R | 1 README.md | 440 +++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/FuzzyClass.Rmd | 2 inst/doc/FuzzyClass.html | 6 inst/doc/index.Rmd | 2 inst/doc/index.html | 6 man/DWFuzzyGammaNaiveBayes.Rd | 2 man/DWFuzzyHipergeometricNaiveBayes.Rd | 2 man/ExpNBFuzzyParam.Rd | 18 man/FuzzyBayesRule.Rd | 2 man/FuzzyBetaNaiveBayes.Rd | 2 man/FuzzyBinomialNaiveBayes.Rd | 2 man/FuzzyClass-package.Rd | 8 man/FuzzyExponentialNaiveBayes.Rd | 2 man/FuzzyGammaNaiveBayes.Rd | 2 man/FuzzyGaussianNaiveBayes.Rd | 2 man/FuzzyGeoNaiveBayes.Rd | 2 man/FuzzyHipergeometricNaiveBayes.Rd | 2 man/FuzzyPoissonNaiveBayes.Rd | 2 man/FuzzyTrapezoidalNaiveBayes.Rd | 2 man/FuzzyTriangularNaiveBayes.Rd | 2 man/GauNBFuzzyParam.Rd | 18 man/PoiNBFuzzyParam.Rd | 18 man/figures/logo.png |binary man/figures/logo.svg |only tests/test_type.R | 72 + vignettes/FuzzyClass.Rmd | 2 vignettes/index.Rmd | 2 53 files changed, 1767 insertions(+), 2114 deletions(-)
Title: Interface to Download Meteorological (and Hydrological) Datasets
Description: Automatize downloading of meteorological and hydrological data from publicly available repositories:
OGIMET (<http://ogimet.com/index.phtml.en>),
University of Wyoming - atmospheric vertical profiling data (<http://weather.uwyo.edu/upperair/>),
Polish Institute of Meteorology and Water Management - National Research Institute (<https://danepubliczne.imgw.pl>),
and National Oceanic & Atmospheric Administration (NOAA).
This package also allows for searching geographical coordinates for each observation and calculate distances to the nearest stations.
Author: Bartosz Czernecki [aut, cre] ,
Arkadiusz Glogowski [aut] ,
Jakub Nowosad [aut] ,
IMGW-PIB [ctb]
Maintainer: Bartosz Czernecki <nwp@amu.edu.pl>
Diff between climate versions 1.4.1 dated 2026-09-18 and 1.4.2 dated 2026-10-09
DESCRIPTION | 6 MD5 | 8 NEWS.md | 5 R/meteo_shortening_imgw.R | 9 inst/doc/getstarted.html | 732 +++++++++++++++++++++++++++++++++------------- 5 files changed, 548 insertions(+), 212 deletions(-)
Title: Unify Dimensionality Reduction Results
Description: Dimensionality reduction is widely used in many domains for
analyzing and visualizing high-dimensional data. 'tidydr' provides uniform
output and is compatible with multiple methods, including 'prcomp',
'cmdscale', 'Rtsne', 'umap' and 'metaMDS'. Any function returning a numeric
matrix can also be used. The unified result can be visualized directly with
'ggplot2', and several methods can be run and compared in a single call.
Author: Guangchuang Yu [aut, cre, cph] ,
Shuangbin Xu [aut]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between tidydr versions 0.0.6 dated 2025-07-25 and 0.0.7 dated 2026-10-09
DESCRIPTION | 25 + MD5 | 68 ++--- NAMESPACE | 136 +++++----- NEWS.md | 175 +++++++++---- R/available_methods.R | 108 ++++---- R/dr-compare.R |only R/dr.R | 236 +++++++++++++---- R/element_line2.R | 110 ++++---- R/method-autoplot.R | 267 ++++++++++++-------- R/method-dr-extract.R | 292 ++++++++++++--------- R/method-drawDetails.R | 30 +- R/method-fortify.R | 117 ++++++-- R/silinfo.R | 432 ++++++++++++++++++++++++++++---- R/theme.R | 84 +++--- R/tidydr-package.R | 6 R/utilities.R | 34 +- README.md | 73 +++++ build/vignette.rds |binary inst/doc/tidydr.R | 97 +++++-- inst/doc/tidydr.Rmd | 237 ++++++++++++----- inst/doc/tidydr.html | 624 ++++++++++++++++++++++++++++------------------- man/available_methods.Rd | 46 +-- man/dr-extract.Rd | 59 ++-- man/dr.Rd | 77 +++-- man/dr_compare.Rd |only man/element_line2.Rd | 104 +++---- man/nk.Rd | 43 +++ man/reexports.Rd | 34 +- man/silinfo_widths.Rd |only man/theme_dr.Rd | 56 ++-- man/theme_noaxis.Rd | 40 +-- man/tidydr-package.Rd | 8 tests |only vignettes/tidydr.Rmd | 237 ++++++++++++----- 34 files changed, 2528 insertions(+), 1327 deletions(-)
Title: Stratigraphic Plug Alignment for Integrating Plug-Based and XRF
Data
Description: Implements the Stratigraphic Plug Alignment (SPA) procedure for
integrating sparsely sampled plug-based measurements (e.g., total organic
carbon, porosity, mineralogy) with high-resolution X-ray fluorescence
(XRF) geochemical data. SPA uses linear interpolation via the base
approx() function with constrained extrapolation (rule = 1) to preserve
stratigraphic order and avoid estimation beyond observed depths. The
method aligns all datasets to a common depth grid, enabling high-resolution
multivariate analysis and stratigraphic interpretation of core-based
datasets such as those from the Utica and Point Pleasant formations.
See R Core Team (2025)
<https://stat.ethz.ch/R-manual/R-devel/library/stats/html/stats-package.html>
and Omodolor (2025)
<http://rave.ohiolink.edu/etdc/view?acc_num=case175262671767524>
for methodological background and geological context.
Author: Hope E. Omodolor [aut] ,
Jeffrey M. Yarus [aut],
Roger H. French [cre]
Maintainer: Roger H. French <rxf131@case.edu>
Diff between spaAlign versions 0.0.6 dated 2026-01-07 and 0.0.7 dated 2026-10-09
DESCRIPTION | 25 ++-- MD5 | 16 +- NAMESPACE | 6 NEWS.md |only R/spa_align.R | 242 ++++++++++++++++++++-------------------- README.md |only man/figures |only man/spa_align.Rd | 136 +++++++++++----------- tests/testthat.R | 24 +-- tests/testthat/test-spa_align.R | 56 ++++----- 10 files changed, 258 insertions(+), 247 deletions(-)
Title: Reproducible Risk-Weighted Asset Calculations
Description: Provides transparent, deterministic and auditable calculations
of risk-weighted assets, own-funds requirements, interest-rate risk in the
banking book and related capital metrics. It supports canonical in-memory
tables and versioned spreadsheet datasets, strict validation, synthetic
reference profiles, bitemporal snapshots, calculation controls and
traceable regulatory source metadata. Methods are parameterised against
the European Parliament and Council (2013) Capital Requirements
Regulation <https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:32013R0575> and its
amending Regulation (EU) 2024/1623
<https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:32024R1623>. A granular analyst API exposes
individual formulae, domain views, controls, schemas and auditable
parameter overrides. The implementation is intended for
analytical, educational and model-validation use and does not constitute
legal or supervisory advice.
Author: Dimitrios Geromichalos [cre],
RiskDataScience GmbH [aut, cph]
Maintainer: Dimitrios Geromichalos <riskdatascience@web.de>
Diff between riskweightedassets versions 1.1.1 dated 2026-09-24 and 1.2.4 dated 2026-10-09
DESCRIPTION | 10 +- MD5 | 120 ++++++++++++++++++------------ NAMESPACE | 20 +++-- NEWS.md | 52 +++++++++++-- R/analyst_api.R | 7 + R/api.R | 5 + R/booleans.R |only R/contracts.R | 8 +- R/engine_credit.R | 39 ++++++++- R/engine_irrbb_icaap.R | 64 +++++++++------- R/excel_io.R | 6 + R/formula_api.R | 7 + R/formulas.R | 8 +- R/irb_contract.R |only R/pipeline.R | 5 - R/snapshot_time.R |only R/supporting_factors.R |only R/synthetic.R | 1 README.md | 21 ++++- build/vignette.rds |binary inst/CITATION | 2 inst/config/crr3_eu_2026_v1.yaml | 6 + inst/doc/complete-function-reference.R | 52 +++++++------ inst/doc/complete-function-reference.Rmd | 43 ++++++++++ inst/doc/complete-function-reference.html | 99 ++++++++++++++++++------ inst/doc/data-and-history.R | 6 - inst/doc/default-flags.Rmd |only inst/doc/default-flags.html |only inst/doc/getting-started.R | 16 ++-- inst/doc/irb-defaults.R |only inst/doc/irb-defaults.Rmd |only inst/doc/irb-defaults.html |only inst/doc/methodology-and-controls.R | 8 +- inst/doc/supporting-factors.R |only inst/doc/supporting-factors.Rmd |only inst/doc/supporting-factors.html |only man/analyze_credit_risk.Rd | 2 man/apply_credit_supporting_factors.Rd |only man/calculate_dataset.Rd | 2 man/calculate_tables.Rd | 7 + man/compare_calculation_views.Rd | 2 man/create_workspace.Rd | 2 man/failed_controls.Rd | 2 man/generate_synthetic_dataset.Rd | 2 man/infrastructure_supporting_factor.Rd |only man/irb_asset_correlation.Rd | 7 + man/irb_risk_weighted_assets.Rd |only man/official_snapshot.Rd | 9 ++ man/rwa_controls.Rd | 2 man/rwa_metric.Rd | 2 man/rwa_metrics.Rd | 2 man/rwa_result_table.Rd | 2 man/rwa_result_tables.Rd | 2 man/rwa_summary.Rd | 2 man/rwa_table_names.Rd | 2 man/rwa_validation.Rd | 2 man/sme_supporting_factor.Rd |only man/validate_dataset.Rd | 2 tests/testthat.R | 4 - tests/testthat/fixtures |only tests/testthat/helper-fixtures.R |only tests/testthat/helper-irrbb-reference.R |only tests/testthat/test-contracts-synthetic.R | 7 + tests/testthat/test-default-flags.R |only tests/testthat/test-e2e.R | 5 - tests/testthat/test-fixture-isolation.R |only tests/testthat/test-irb-default.R |only tests/testthat/test-irrbb-runtime.R |only tests/testthat/test-public-analyst-api.R | 16 +++- tests/testthat/test-snapshot-time.R |only tests/testthat/test-supporting-factors.R |only vignettes/complete-function-reference.Rmd | 43 ++++++++++ vignettes/default-flags.Rmd |only vignettes/irb-defaults.Rmd |only vignettes/supporting-factors.Rmd |only 75 files changed, 528 insertions(+), 205 deletions(-)
More information about riskweightedassets at CRAN
Permanent link
Title: Thematic Cartography
Description: Create and integrate thematic maps in your workflow. This package
helps to design various cartographic representations such as proportional
symbols, choropleth or typology maps. It also offers several functions to
display layout elements that improve the graphic presentation of maps
(e.g. scale bar, north arrow, title, labels). 'mapsf' maps 'sf' objects on
'base' graphics.
Author: Timothee Giraud [cre, aut] ,
Hugues Pecout [ctb] ,
Ronan Ysebaert [ctb] ,
Elina Marveaux [ctb] ,
Ian Fellows [cph] ,
Danielle Navarro [cph]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between mapsf versions 1.2.2 dated 2026-09-02 and 1.3.0 dated 2026-10-09
DESCRIPTION | 6 +-- MD5 | 44 ++++++++++++++-------------- NEWS.md | 8 +++++ R/deprecated.R | 2 - R/mf_annotation.R | 6 +++ R/mf_export.R | 4 +- R/mf_map.R | 31 +++++++++++--------- R/mf_map_utils.R | 7 +++- R/mf_prop_choro.R | 15 ++++++--- R/mf_prop_typo.R | 30 ++++++++++++------- R/mf_symb_choro.R | 16 ++++++---- R/mf_theme.R | 23 +++++++------- README.md | 21 +++++++------ inst/doc/mapsf.R | 16 +++++----- inst/doc/mapsf.Rmd | 36 +++++++++++------------ inst/doc/mapsf.html | 68 +++++++++++++++++++++----------------------- inst/tinytest/test_map_pc.R | 14 ++++----- inst/tinytest/test_map_pt.R | 4 +- inst/tinytest/test_map_sc.R | 2 - inst/tinytest/test_theme.R | 6 +-- man/mapsf-deprecated.Rd | 2 - man/mf_map.Rd | 27 +++++++++++------ vignettes/mapsf.Rmd | 36 +++++++++++------------ 23 files changed, 237 insertions(+), 187 deletions(-)
Title: Base Class and Methods for 'gson' Format
Description: Provides a lightweight container and exchange format for gene
set collections. A 'GSON' object stores which genes belong to which gene
set, together with gene set and gene names, the identifier types in use,
species, versions and source metadata. A collection can be built from data
frames, read from and written to the 'gson' JavaScript Object Notation
(JSON) format and the 'GMT' format, subset by gene set, merged across
sources, validated, and resolved to the web addresses of the databases it
comes from, so that a collection gathered by one package can be analysed
by another.
Author: Guangchuang Yu [aut, cre, cph]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between gson versions 0.2.1 dated 2026-08-04 and 0.2.2 dated 2026-10-09
DESCRIPTION | 24 MD5 | 61 NAMESPACE | 69 NEWS.md | 54 R/00-AllClasses.R | 109 - R/GMT.R | 127 - R/IO.R | 235 +- R/gson-package.R | 6 R/gson.R | 74 R/gsonList.R | 20 R/methods.R | 66 R/print.R | 81 R/union.R |only R/utilities.r | 98 - R/validate.R | 108 + README.md | 455 ++++- inst/extdata/wikipathways-20220310-gmt-Homo_sapiens.gmt | 1448 ++++++++-------- man/GSON-class.Rd | 86 man/IO.Rd | 58 man/extract.GSON.Rd | 24 man/gson-package.Rd | 10 man/gson.Rd | 119 - man/gsonList.Rd | 34 man/gson_union.Rd |only man/gson_url.Rd |only man/read-gmt.Rd | 68 man/show-methods.Rd | 42 man/validate_gson.Rd | 7 tests/testthat/test-constructors.R | 75 tests/testthat/test-io.R | 161 + tests/testthat/test-methods.R | 78 tests/testthat/test-union.R |only tests/testthat/test-url.R |only tests/testthat/test-validate.R | 113 + 34 files changed, 2573 insertions(+), 1337 deletions(-)
Title: Miscellaneous Functions for 'ggplot2'
Description: Provides a collection of 'ggplot2' extensions and utilities
for creating geometric layers, applying themes, working with legends,
and modifying plot objects.
Author: Guangchuang Yu [aut, cre, cph] ,
Shuangbin Xu [aut]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggfun versions 0.2.1 dated 2026-07-02 and 0.2.2 dated 2026-10-09
ggfun-0.2.1/ggfun/R/geom-volpoint.R |only ggfun-0.2.1/ggfun/man/geom_volpoint.Rd |only ggfun-0.2.1/ggfun/man/volplot.Rd |only ggfun-0.2.2/ggfun/DESCRIPTION | 8 ggfun-0.2.2/ggfun/MD5 | 119 +- ggfun-0.2.2/ggfun/NAMESPACE | 242 ++--- ggfun-0.2.2/ggfun/NEWS.md | 225 ++-- ggfun-0.2.2/ggfun/R/axis.R | 122 +- ggfun-0.2.2/ggfun/R/facet_set.R | 118 +- ggfun-0.2.2/ggfun/R/geom-bezier.R |only ggfun-0.2.2/ggfun/R/geom-hist.r | 150 +-- ggfun-0.2.2/ggfun/R/geom-scatter-rect.R | 180 +-- ggfun-0.2.2/ggfun/R/geom-xspline.R | 268 ++--- ggfun-0.2.2/ggfun/R/geom_cake.R | 224 ++-- ggfun-0.2.2/ggfun/R/geom_segment_c.R | 198 ++-- ggfun-0.2.2/ggfun/R/geom_triangle.R | 152 +-- ggfun-0.2.2/ggfun/R/get-legend.r | 46 ggfun-0.2.2/ggfun/R/ggelement.R | 289 +++--- ggfun-0.2.2/ggfun/R/ggfun-package.R | 6 ggfun-0.2.2/ggfun/R/gglegend.R | 96 +- ggfun-0.2.2/ggfun/R/keybox.R | 76 - ggfun-0.2.2/ggfun/R/method-ggplot-add.R | 386 +++----- ggfun-0.2.2/ggfun/R/method-identify.R | 128 +- ggfun-0.2.2/ggfun/R/operator.R | 226 ++-- ggfun-0.2.2/ggfun/R/reexport.R | 10 ggfun-0.2.2/ggfun/R/set_font.R | 133 +- ggfun-0.2.2/ggfun/R/theme.R | 334 +++---- ggfun-0.2.2/ggfun/R/treedata-function.R | 148 +-- ggfun-0.2.2/ggfun/R/utilities.R | 400 ++++---- ggfun-0.2.2/ggfun/R/zzz.R | 10 ggfun-0.2.2/ggfun/README.md | 4 ggfun-0.2.2/ggfun/build/vignette.rds |binary ggfun-0.2.2/ggfun/inst/doc/ggfun.R | 462 ++++----- ggfun-0.2.2/ggfun/inst/doc/ggfun.html | 1081 +++++++++++------------ ggfun-0.2.2/ggfun/inst/doc/ggfun.qmd | 13 ggfun-0.2.2/ggfun/inst/prototype/geom_rtile.r | 94 +- ggfun-0.2.2/ggfun/man/attacher.Rd | 46 ggfun-0.2.2/ggfun/man/element_blinds.Rd | 84 - ggfun-0.2.2/ggfun/man/element_roundrect.Rd | 106 +- ggfun-0.2.2/ggfun/man/facet_set.Rd | 42 ggfun-0.2.2/ggfun/man/geom_bezier.Rd |only ggfun-0.2.2/ggfun/man/geom_cake.Rd | 60 - ggfun-0.2.2/ggfun/man/geom_segment_c.Rd | 136 +- ggfun-0.2.2/ggfun/man/geom_triangle.Rd | 56 - ggfun-0.2.2/ggfun/man/geom_xspline.Rd | 308 +++--- ggfun-0.2.2/ggfun/man/get_aes_var.Rd | 44 ggfun-0.2.2/ggfun/man/ggbreak2ggplot.Rd | 40 ggfun-0.2.2/ggfun/man/ggfun-package.Rd | 58 - ggfun-0.2.2/ggfun/man/gglegend.Rd | 74 - ggfun-0.2.2/ggfun/man/ggrange.Rd | 70 - ggfun-0.2.2/ggfun/man/identify.Rd | 48 - ggfun-0.2.2/ggfun/man/is-ggbreak.Rd | 40 ggfun-0.2.2/ggfun/man/is.ggtree.Rd | 40 ggfun-0.2.2/ggfun/man/keybox.Rd | 58 - ggfun-0.2.2/ggfun/man/reexports.Rd | 38 ggfun-0.2.2/ggfun/man/set_font.Rd | 84 + ggfun-0.2.2/ggfun/man/theme_blinds.Rd | 90 - ggfun-0.2.2/ggfun/man/theme_nothing.Rd | 44 ggfun-0.2.2/ggfun/man/theme_stamp.Rd | 36 ggfun-0.2.2/ggfun/man/theme_transparent.Rd | 40 ggfun-0.2.2/ggfun/tests/testthat/test-operator.R | 22 ggfun-0.2.2/ggfun/tests/testthat/test-set-font.R | 130 ++ ggfun-0.2.2/ggfun/vignettes/ggfun.qmd | 13 63 files changed, 3980 insertions(+), 3775 deletions(-)
Title: Simulation and Data Analysis for Plant Breeders
Description: Provides tools for simulation of plant breeding programs
as described, for example, by Melchinger and Frisch
(2023) <doi:10.1007/s00122-023-04446-3>, prediction of
segregation variance (Osthushenrich, Frisch and Herzog
(2017) <doi:10.1371/journal.pone.0188839>), genomic
prediction (Hofheinz and Frisch (2014)
<doi:10.1534/g3.113.010025>), linkage disequilibrium
based haplotype construction, and planning of marker
assisted back crossing programs. It provides an integrated
framework for simulation and analysis of plant breeding
programs.
Author: Matthias Frisch [aut, cre],
Hans Peter Maurer [ctb],
Philipp Heilmann [ctb]
Maintainer: Matthias Frisch <matthias.frisch@uni-giessen.de>
Diff between SelectionTools versions 26.4 dated 2026-09-21 and 26.5 dated 2026-10-09
SelectionTools-26.4/SelectionTools/inst/doc/v-simmd.Rmd |only SelectionTools-26.4/SelectionTools/man/evaluate.genotype2.Rd |only SelectionTools-26.4/SelectionTools/vignettes/v-simmd.Rmd |only SelectionTools-26.5/SelectionTools/DESCRIPTION | 8 SelectionTools-26.5/SelectionTools/MD5 | 142 SelectionTools-26.5/SelectionTools/NAMESPACE | 3 SelectionTools-26.5/SelectionTools/R/SelectionTools01.R | 87 SelectionTools-26.5/SelectionTools/R/SelectionTools02.R | 19 SelectionTools-26.5/SelectionTools/R/SelectionTools03.R | 31 SelectionTools-26.5/SelectionTools/R/SelectionTools04.R | 99 SelectionTools-26.5/SelectionTools/R/SelectionTools05.R | 4 SelectionTools-26.5/SelectionTools/build/vignette.rds |binary SelectionTools-26.5/SelectionTools/data/masbc.input.rda |only SelectionTools-26.5/SelectionTools/inst/doc/v-cross.pdf |binary SelectionTools-26.5/SelectionTools/inst/doc/v-hapld.pdf |binary SelectionTools-26.5/SelectionTools/inst/doc/v-masbc.R |only SelectionTools-26.5/SelectionTools/inst/doc/v-masbc.Rnw |only SelectionTools-26.5/SelectionTools/inst/doc/v-masbc.pdf |only SelectionTools-26.5/SelectionTools/inst/doc/v-phase.R | 172 SelectionTools-26.5/SelectionTools/inst/doc/v-phase.Rnw | 1135 - SelectionTools-26.5/SelectionTools/inst/doc/v-phase.pdf |binary SelectionTools-26.5/SelectionTools/inst/doc/v-simbp.pdf |binary SelectionTools-26.5/SelectionTools/inst/doc/v-simmd.R | 322 SelectionTools-26.5/SelectionTools/inst/doc/v-simmd.Rnw |only SelectionTools-26.5/SelectionTools/inst/doc/v-simmd.pdf |binary SelectionTools-26.5/SelectionTools/man/DT_technow.Rd | 4 SelectionTools-26.5/SelectionTools/man/Md_technow.Rd | 4 SelectionTools-26.5/SelectionTools/man/Mf_technow.Rd | 8 SelectionTools-26.5/SelectionTools/man/append.population.Rd | 44 SelectionTools-26.5/SelectionTools/man/cross.Rd | 46 SelectionTools-26.5/SelectionTools/man/define.genome.Rd | 67 SelectionTools-26.5/SelectionTools/man/define.map.Rd | 38 SelectionTools-26.5/SelectionTools/man/evaluate.allele.Rd | 42 SelectionTools-26.5/SelectionTools/man/evaluate.allele.freq.Rd | 37 SelectionTools-26.5/SelectionTools/man/evaluate.allele.freq2.Rd | 77 SelectionTools-26.5/SelectionTools/man/evaluate.allele2.Rd | 42 SelectionTools-26.5/SelectionTools/man/evaluate.genotype.Rd | 71 SelectionTools-26.5/SelectionTools/man/gs.build.z.Rd | 14 SelectionTools-26.5/SelectionTools/man/init.population.Rd | 42 SelectionTools-26.5/SelectionTools/man/masbc.input.Rd |only SelectionTools-26.5/SelectionTools/man/read.vcf.Rd | 11 SelectionTools-26.5/SelectionTools/man/remove.all.populations.Rd | 5 SelectionTools-26.5/SelectionTools/man/reset.all.Rd | 2 SelectionTools-26.5/SelectionTools/man/rng.init.Rd | 44 SelectionTools-26.5/SelectionTools/man/sample.population.Rd | 22 SelectionTools-26.5/SelectionTools/man/st.STvcf.to.dataframe.Rd | 13 SelectionTools-26.5/SelectionTools/man/st.compact.data.set.Rd |only SelectionTools-26.5/SelectionTools/man/st.data.set.list.Rd |only SelectionTools-26.5/SelectionTools/man/st.data.set.remove.Rd |only SelectionTools-26.5/SelectionTools/man/st.data.set.remove.all.Rd |only SelectionTools-26.5/SelectionTools/man/st.dataframe.to.STvcf.Rd | 19 SelectionTools-26.5/SelectionTools/man/st.destroy.phase.Rd | 4 SelectionTools-26.5/SelectionTools/man/st.enrichment.Rd |only SelectionTools-26.5/SelectionTools/man/st.get.simpop.Rd | 4 SelectionTools-26.5/SelectionTools/man/st.get.simpop2.Rd | 4 SelectionTools-26.5/SelectionTools/man/st.keep.intersection.markers.Rd |only SelectionTools-26.5/SelectionTools/man/st.load.performance.data.Rd | 19 SelectionTools-26.5/SelectionTools/man/st.load.vcf.data.Rd | 123 SelectionTools-26.5/SelectionTools/man/st.marker.data.statistics.Rd | 52 SelectionTools-26.5/SelectionTools/man/st.markerdata.to.STvcf.Rd | 8 SelectionTools-26.5/SelectionTools/man/st.phase.Rd | 672 SelectionTools-26.5/SelectionTools/man/st.phase.v1.Rd |only SelectionTools-26.5/SelectionTools/man/st.read.map.df.Rd |only SelectionTools-26.5/SelectionTools/man/st.read.marker.data.df.Rd | 66 SelectionTools-26.5/SelectionTools/man/st.restrict.marker.Rd | 50 SelectionTools-26.5/SelectionTools/man/st.switch.error.Rd | 27 SelectionTools-26.5/SelectionTools/man/v-tropmaize-map.Rd | 7 SelectionTools-26.5/SelectionTools/man/v-tropmaize-phe.Rd | 7 SelectionTools-26.5/SelectionTools/man/v-tropmaize-pop.Rd | 7 SelectionTools-26.5/SelectionTools/man/v-tropmaize-vcf.Rd | 8 SelectionTools-26.5/SelectionTools/man/write.vcf.Rd | 11 SelectionTools-26.5/SelectionTools/src/MathLib12.c | 8 SelectionTools-26.5/SelectionTools/src/MathLib12.h | 3 SelectionTools-26.5/SelectionTools/src/SelectionTools01.c | 2027 ++ SelectionTools-26.5/SelectionTools/src/SelectionTools01a.h | 504 SelectionTools-26.5/SelectionTools/src/SelectionTools02.c | 55 SelectionTools-26.5/SelectionTools/src/SelectionTools03.c | 7345 +++++++--- SelectionTools-26.5/SelectionTools/src/SelectionToolsDataSet.h |only SelectionTools-26.5/SelectionTools/src/init.c | 27 SelectionTools-26.5/SelectionTools/vignettes/v-masbc.Rnw |only SelectionTools-26.5/SelectionTools/vignettes/v-phase.Rnw | 1135 - SelectionTools-26.5/SelectionTools/vignettes/v-simmd.Rnw |only 82 files changed, 9944 insertions(+), 4903 deletions(-)
More information about SelectionTools at CRAN
Permanent link
Title: Univariate GARCH Models
Description: Multiple flavors of the Generalized Autoregressive Conditional Heteroskedasticity (GARCH) model with a large choice of conditional distributions. Methods for specification, estimation, prediction, filtering, simulation, statistical testing and more. Represents a partial re-write and re-think of 'rugarch', making use of automatic differentiation for estimation.
Author: Alexios Galanos [aut, cre, cph]
Maintainer: Alexios Galanos <alexios@4dscape.com>
Diff between tsgarch versions 1.0.4 dated 2026-05-23 and 1.0.5 dated 2026-10-09
tsgarch-1.0.4/tsgarch/man/plot.Rd |only tsgarch-1.0.4/tsgarch/tests/longtests/test-backtest.R |only tsgarch-1.0.4/tsgarch/tests/longtests/test-prediction.R |only tsgarch-1.0.4/tsgarch/tests/longtests/test-profile.R |only tsgarch-1.0.5/tsgarch/DESCRIPTION | 6 tsgarch-1.0.5/tsgarch/MD5 | 124 ++- tsgarch-1.0.5/tsgarch/NAMESPACE | 9 tsgarch-1.0.5/tsgarch/NEWS.md | 191 +++++ tsgarch-1.0.5/tsgarch/R/RcppExports.R | 28 tsgarch-1.0.5/tsgarch/R/arma.R |only tsgarch-1.0.5/tsgarch/R/backtest.R | 52 + tsgarch-1.0.5/tsgarch/R/constraints.R | 12 tsgarch-1.0.5/tsgarch/R/equations.R | 51 + tsgarch-1.0.5/tsgarch/R/estimate.R | 110 +++ tsgarch-1.0.5/tsgarch/R/extractors.R | 55 + tsgarch-1.0.5/tsgarch/R/filter.R | 109 ++- tsgarch-1.0.5/tsgarch/R/initialization.R | 45 - tsgarch-1.0.5/tsgarch/R/methods.R | 236 ++++++ tsgarch-1.0.5/tsgarch/R/plot-arma.R |only tsgarch-1.0.5/tsgarch/R/predict.R | 207 +++++- tsgarch-1.0.5/tsgarch/R/print.R | 17 tsgarch-1.0.5/tsgarch/R/profile.R | 15 tsgarch-1.0.5/tsgarch/R/simulate.R | 372 ++++++++--- tsgarch-1.0.5/tsgarch/R/specification.R | 78 ++ tsgarch-1.0.5/tsgarch/R/tsgarch-package.R | 2 tsgarch-1.0.5/tsgarch/R/utilities.R | 70 +- tsgarch-1.0.5/tsgarch/build/partial.rdb |binary tsgarch-1.0.5/tsgarch/build/vignette.rds |binary tsgarch-1.0.5/tsgarch/inst/doc/arma_garch.R |only tsgarch-1.0.5/tsgarch/inst/doc/arma_garch.Rmd |only tsgarch-1.0.5/tsgarch/inst/doc/arma_garch.html |only tsgarch-1.0.5/tsgarch/inst/doc/benchmark.html | 42 - tsgarch-1.0.5/tsgarch/inst/doc/demonstration.html | 50 - tsgarch-1.0.5/tsgarch/inst/doc/garch_models.Rmd | 258 +++++++ tsgarch-1.0.5/tsgarch/inst/doc/garch_models.pdf |binary tsgarch-1.0.5/tsgarch/man/arma_coefficients.Rd |only tsgarch-1.0.5/tsgarch/man/arma_inverse_roots.Rd |only tsgarch-1.0.5/tsgarch/man/arma_irf.Rd |only tsgarch-1.0.5/tsgarch/man/arma_near_cancellation.Rd |only tsgarch-1.0.5/tsgarch/man/fitted.Rd | 15 tsgarch-1.0.5/tsgarch/man/garch_modelspec.Rd | 40 + tsgarch-1.0.5/tsgarch/man/plot.tsgarch.estimate.Rd | 94 ++ tsgarch-1.0.5/tsgarch/man/plot.tsgarch.newsimpact.Rd |only tsgarch-1.0.5/tsgarch/man/predict.Rd | 6 tsgarch-1.0.5/tsgarch/man/residuals.Rd | 16 tsgarch-1.0.5/tsgarch/man/simulate.Rd | 13 tsgarch-1.0.5/tsgarch/man/tsfilter.Rd | 5 tsgarch-1.0.5/tsgarch/man/tsgarch-package.Rd | 2 tsgarch-1.0.5/tsgarch/src/RcppExports.cpp | 73 +- tsgarch-1.0.5/tsgarch/src/TMB/aparchfun.hpp | 96 ++ tsgarch-1.0.5/tsgarch/src/TMB/cgarchfun.hpp | 93 ++ tsgarch-1.0.5/tsgarch/src/TMB/durbinlevinson.h |only tsgarch-1.0.5/tsgarch/src/TMB/egarchfun.hpp | 104 ++- tsgarch-1.0.5/tsgarch/src/TMB/fgarchfun.hpp | 96 ++ tsgarch-1.0.5/tsgarch/src/TMB/garchextra.h | 21 tsgarch-1.0.5/tsgarch/src/TMB/garchfun.hpp | 91 ++ tsgarch-1.0.5/tsgarch/src/TMB/gjrgarchfun.hpp | 102 ++- tsgarch-1.0.5/tsgarch/src/TMB/tsgarch_TMBExports.cpp | 1 tsgarch-1.0.5/tsgarch/src/simulation.cpp | 109 ++- tsgarch-1.0.5/tsgarch/tests/longtests/testthat |only tsgarch-1.0.5/tsgarch/tests/longtests/testthat.R |only tsgarch-1.0.5/tsgarch/tests/testthat/test-arma-diagnostics.R |only tsgarch-1.0.5/tsgarch/tests/testthat/test-arma.R |only tsgarch-1.0.5/tsgarch/tests/testthat/test-armax-dynamics.R |only tsgarch-1.0.5/tsgarch/tests/testthat/test-armax.R |only tsgarch-1.0.5/tsgarch/tests/testthat/test-estimation.R | 22 tsgarch-1.0.5/tsgarch/tests/testthat/test-filtering.R | 32 tsgarch-1.0.5/tsgarch/tests/testthat/test-simulation.R | 137 +++- tsgarch-1.0.5/tsgarch/vignettes/arma_garch.Rmd |only tsgarch-1.0.5/tsgarch/vignettes/garch_models.Rmd | 258 +++++++ 70 files changed, 3108 insertions(+), 457 deletions(-)
Title: Tidy Dataframes and Expressions with Statistical Details
Description: Utilities for producing dataframes with rich details for the
most common types of statistical approaches and tests: parametric,
nonparametric, robust, and Bayesian t-test, one-way ANOVA, correlation
analyses, contingency table analyses, and meta-analyses. The functions
are pipe-friendly and provide a consistent syntax to work with tidy
data. These dataframes additionally contain expressions with
statistical details, and can be used in graphing packages. This
package also forms the statistical processing backend for
'ggstatsplot'. References: Patil (2021) <doi:10.21105/joss.03236>.
Author: Indrajeet Patil [cre, aut, cph]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between statsExpressions versions 2.1.1 dated 2026-08-24 and 2.1.2 dated 2026-10-09
DESCRIPTION | 23 +-- MD5 | 117 ++++++++-------- NAMESPACE | 16 +- NEWS.md | 38 +++++ R/add-expression-col.R | 42 +++-- R/centrality-description.R | 5 R/contingency-table.R | 107 ++------------- R/data.R | 23 +-- R/helpers-easystats.R | 10 + R/long-to-wide-converter.R | 36 ++--- R/meta-analysis.R | 77 +++++----- R/one-sample-test.R | 3 R/oneway-anova.R | 52 ++----- R/pairwise-comparisons.R | 37 +---- R/pairwise-contingency-table.R | 1 R/switch-functions.R | 13 + R/tidy-model-expressions.R | 10 - R/two-sample-test.R | 130 +++--------------- README.md | 93 ++++++++++--- inst/doc/statsExpressions.R | 4 inst/doc/statsExpressions.Rmd | 11 - inst/doc/statsExpressions.html | 15 +- inst/doc/stats_details.Rmd | 34 ++-- inst/doc/stats_details.html | 206 ++++++++++++++++++++++++++--- man/add_expression_col.Rd | 48 ++++-- man/bugs_long.Rd | 12 - man/centrality_description.Rd | 45 +++++- man/contingency_table.Rd | 95 +++++++++++-- man/corr_test.Rd | 67 +++++++-- man/examples/examples-contingency-table.R |only man/examples/examples-two-sample-test.R |only man/extract_stats_type.Rd | 12 + man/figures/README-anova_parametric2-1.png |binary man/figures/README-anova_rob1-1.png |binary man/figures/README-centrality-1.png |binary man/figures/README-corr-1.png |binary man/figures/README-custom_expr-1.png |binary man/figures/README-gof-1.png |binary man/figures/README-metaanalysis-1.png |binary man/figures/README-t_one-1.png |binary man/figures/README-t_two-1.png |binary man/figures/README-t_two_paired1-1.png |binary man/iris_long.Rd | 6 man/long_to_wide_converter.Rd | 36 ++--- man/meta_analysis.Rd | 98 ++++++++++--- man/movies_long.Rd | 5 man/one_sample_test.Rd | 67 +++++++-- man/oneway_anova.Rd | 91 +++++++++--- man/pairwise_comparisons.Rd | 96 +++++++++---- man/pairwise_contingency_table.Rd | 64 +++++++-- man/rmd-fragments/contingency_table.Rmd | 9 + man/rmd-fragments/functionality.Rmd | 3 man/rmd-fragments/return.Rmd | 67 +++++++-- man/rmd-fragments/return_centrality.Rmd |only man/rmd-fragments/summary_intro.Rmd |only man/tidy_model_expressions.Rd | 11 + man/tidy_model_parameters.Rd | 10 + man/two_sample_test.Rd | 92 +++++++++--- vignettes/statsExpressions.Rmd | 11 - vignettes/stats_details.Rmd | 34 ++-- vignettes/web_only/dataframe_outputs.Rmd | 177 ------------------------ vignettes/web_only/return_value_schema.Rmd |only 62 files changed, 1365 insertions(+), 894 deletions(-)
More information about statsExpressions at CRAN
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Title: Convenient Plotting for the Modified Rankin Scale and Other
Ordinal Outcome Data
Description: Provides convenient tools for visualising ordinal outcome data following conventions within stroke research literature. It currently supports the "Grotta Bar" approach pioneered by The National Institute of Neurological Disorders and Stroke rt-PA Stroke Study Group (1995) <doi:10.1056/NEJM199512143332401> and Probability-Probability plots for visualising Desirability of Outcome Ranking (DOOR) scales with large numbers of categories proposed by Johns et al. (2026) <doi:10.1177/17474930261475853>.
Author: Hannah Johns [aut, cre] ,
Andreas Gammelgaard Damsbo [aut] ,
Florian van Leeuwen [aut]
Maintainer: Hannah Johns <dr.hannah.johns@gmail.com>
Diff between rankinPlot versions 1.1.0 dated 2023-01-30 and 1.2.0 dated 2026-10-09
DESCRIPTION | 30 +- MD5 | 22 +- NAMESPACE | 2 NEWS.md | 9 R/data.R | 20 + R/grottaBar.R | 556 ++++++++++++++++++++++++++++++++++++++--------------- R/pp_plot.R |only README.md | 9 data/alteplase.rda |binary data/remapcap.rda |only man/alteplase.Rd | 64 +++--- man/grottaBar.Rd | 206 ++++++++++++------- man/pp_plot.Rd |only man/remapcap.Rd |only 14 files changed, 648 insertions(+), 270 deletions(-)
Title: Estimation of Optimal Size for a Holdout Set for Updating a
Predictive Score
Description: Predictive scores must be updated with care, because actions taken on the basis of existing risk scores causes bias in risk estimates from the updated score. A holdout set is a straightforward way to manage this problem: a proportion of the population is 'held-out' from computation of the previous risk score. This package provides tools to estimate a size for this holdout set and associated errors. Comprehensive vignettes are included. Please see: Haidar-Wehbe S, Emerson SR, Aslett LJM, Liley J (2022) <doi:10.48550/arXiv.2202.06374> (in Annals of Applied Statistics) for details of methods.
Author: Sami Haidar-Wehbe [aut],
Sam Emerson [aut] ,
Louis Aslett [aut] ,
James Liley [cre, aut]
Maintainer: James Liley <james.liley@durham.ac.uk>
Diff between OptHoldoutSize versions 0.1.0.2 dated 2026-04-07 and 0.1.0.3 dated 2026-10-09
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ inst/doc/ASPRE_example.Rmd | 2 +- inst/doc/ASPRE_example.pdf |binary inst/doc/comparison_of_algorithms.pdf |binary inst/doc/simulated_example.pdf |binary vignettes/ASPRE_example.Rmd | 2 +- 8 files changed, 16 insertions(+), 12 deletions(-)
More information about OptHoldoutSize at CRAN
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Title: Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguous
Description: Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all of which have detailed examples in the vignette.
Author: Schaid Daniel [aut],
Jason P. Sinnwell [aut, cre]
Maintainer: Jason P. Sinnwell <sinnwell.jason@mayo.edu>
This is a re-admission after prior archival of version 1.9.9.1 dated 2026-09-10
Diff between haplo.stats versions 1.9.9.1 dated 2026-09-10 and 1.9.9.1 dated 2026-10-09
0 files changed
Title: R Toolkit for 'Databricks'
Description: Collection of utilities that improve using 'Databricks' from
R. Primarily functions that wrap specific 'Databricks' APIs
(<https://docs.databricks.com/api>), 'RStudio' connection pane
support, quality of life functions to make 'Databricks' simpler to
use.
Author: Zac Davies [aut, cre],
Rafi Kurlansik [aut],
Databricks [cph, fnd]
Maintainer: Zac Davies <zac@databricks.com>
Diff between brickster versions 0.2.14 dated 2026-07-24 and 0.2.15 dated 2026-10-09
brickster-0.2.14/brickster/vignettes/rmarkdown-databricks-notebook.R |only brickster-0.2.14/brickster/vignettes/rmarkdown-databricks-notebook.html |only brickster-0.2.15/brickster/DESCRIPTION | 6 brickster-0.2.15/brickster/MD5 | 154 ++--- brickster-0.2.15/brickster/NAMESPACE | 1 brickster-0.2.15/brickster/NEWS.md | 27 brickster-0.2.15/brickster/R/clusters.R | 192 ++++-- brickster-0.2.15/brickster/R/connection-pane.R | 123 +++- brickster-0.2.15/brickster/R/data-structures.R | 2 brickster-0.2.15/brickster/R/databricks-dbi.R | 161 ++--- brickster-0.2.15/brickster/R/databricks-dbplyr.R | 21 brickster-0.2.15/brickster/R/jobs.R | 97 +-- brickster-0.2.15/brickster/R/package-auth.R | 2 brickster-0.2.15/brickster/R/request-helpers.R | 58 + brickster-0.2.15/brickster/R/sql-query-execution.R | 131 +++- brickster-0.2.15/brickster/R/uc-volumes.R | 10 brickster-0.2.15/brickster/R/unity-catalog.R | 28 brickster-0.2.15/brickster/R/vector-search.R | 2 brickster-0.2.15/brickster/R/volume-fs.R | 125 ++-- brickster-0.2.15/brickster/README.md | 6 brickster-0.2.15/brickster/inst/doc/cluster-management.R | 22 brickster-0.2.15/brickster/inst/doc/cluster-management.Rmd | 50 + brickster-0.2.15/brickster/inst/doc/cluster-management.html | 169 +++-- brickster-0.2.15/brickster/inst/doc/managing-jobs.R | 16 brickster-0.2.15/brickster/inst/doc/managing-jobs.Rmd | 26 brickster-0.2.15/brickster/inst/doc/managing-jobs.html | 42 - brickster-0.2.15/brickster/inst/doc/remote-repl.Rmd | 9 brickster-0.2.15/brickster/inst/doc/remote-repl.html | 11 brickster-0.2.15/brickster/inst/doc/setup-auth.html | 5 brickster-0.2.15/brickster/inst/doc/sql-backend.Rmd | 19 brickster-0.2.15/brickster/inst/doc/sql-backend.html | 26 brickster-0.2.15/brickster/inst/doc/working-with-volumes.html | 5 brickster-0.2.15/brickster/man/databricks-dbplyr.Rd | 7 brickster-0.2.15/brickster/man/dbFetch-DatabricksResult-method.Rd | 4 brickster-0.2.15/brickster/man/dbWriteTable-DatabricksConnection-AsIs-data.frame-method.Rd | 6 brickster-0.2.15/brickster/man/dbWriteTable-DatabricksConnection-Id-data.frame-method.Rd | 6 brickster-0.2.15/brickster/man/dbWriteTable-DatabricksConnection-character-data.frame-method.Rd | 6 brickster-0.2.15/brickster/man/db_cluster_events.Rd | 51 + brickster-0.2.15/brickster/man/db_cluster_get.Rd | 2 brickster-0.2.15/brickster/man/db_cluster_list.Rd | 45 + brickster-0.2.15/brickster/man/db_jobs_get.Rd | 9 brickster-0.2.15/brickster/man/db_jobs_list.Rd | 28 brickster-0.2.15/brickster/man/db_jobs_runs_get.Rd | 10 brickster-0.2.15/brickster/man/db_jobs_runs_list.Rd | 20 brickster-0.2.15/brickster/man/db_list_all_pages.Rd |only brickster-0.2.15/brickster/man/db_perform_request.Rd | 1 brickster-0.2.15/brickster/man/db_perform_response.Rd | 1 brickster-0.2.15/brickster/man/db_req_error_body.Rd | 1 brickster-0.2.15/brickster/man/db_request.Rd | 1 brickster-0.2.15/brickster/man/db_request_json.Rd | 1 brickster-0.2.15/brickster/man/db_sql_fetch_inline.Rd |only brickster-0.2.15/brickster/man/db_sql_fetch_results.Rd | 9 brickster-0.2.15/brickster/man/db_sql_query.Rd | 4 brickster-0.2.15/brickster/man/db_volume_dir_delete.Rd | 9 brickster-0.2.15/brickster/man/db_volume_list.Rd | 14 brickster-0.2.15/brickster/man/db_write_table_volume.Rd | 11 brickster-0.2.15/brickster/tests/testthat/helper-sql-execution.R |only brickster-0.2.15/brickster/tests/testthat/test-auth-offline-helpers.R | 5 brickster-0.2.15/brickster/tests/testthat/test-clusters-offline-helpers.R | 131 +++- brickster-0.2.15/brickster/tests/testthat/test-clusters.R | 127 ++++ brickster-0.2.15/brickster/tests/testthat/test-connection-pane-offline-helpers.R |only brickster-0.2.15/brickster/tests/testthat/test-connection-pane-offline.R | 41 + brickster-0.2.15/brickster/tests/testthat/test-data-structures.R | 1 brickster-0.2.15/brickster/tests/testthat/test-databricks-dbi-offline-helpers.R | 200 ++++++ brickster-0.2.15/brickster/tests/testthat/test-databricks-dbi.R | 122 ++++ brickster-0.2.15/brickster/tests/testthat/test-databricks-dbplyr.R | 134 ++++ brickster-0.2.15/brickster/tests/testthat/test-jobs-offline-helpers.R | 169 +++-- brickster-0.2.15/brickster/tests/testthat/test-jobs.R | 44 + brickster-0.2.15/brickster/tests/testthat/test-request-helpers-offline-helpers.R |only brickster-0.2.15/brickster/tests/testthat/test-request-helpers.R | 4 brickster-0.2.15/brickster/tests/testthat/test-sql-execution-helpers-offline.R | 137 ++++ brickster-0.2.15/brickster/tests/testthat/test-sql-execution.R | 17 brickster-0.2.15/brickster/tests/testthat/test-uc-volumes.R | 12 brickster-0.2.15/brickster/tests/testthat/test-unity-catalog.R | 14 brickster-0.2.15/brickster/tests/testthat/test-vector-search.R | 12 brickster-0.2.15/brickster/tests/testthat/test-volume-field-types-offline-helpers.R |only brickster-0.2.15/brickster/tests/testthat/test-volumes-fs-offline-helpers.R | 298 +++++++++- brickster-0.2.15/brickster/tests/testthat/test-volumes-fs.R | 100 +++ brickster-0.2.15/brickster/vignettes/cluster-management.Rmd | 50 + brickster-0.2.15/brickster/vignettes/managing-jobs.Rmd | 26 brickster-0.2.15/brickster/vignettes/remote-repl.Rmd | 9 brickster-0.2.15/brickster/vignettes/sql-backend.Rmd | 19 82 files changed, 2742 insertions(+), 722 deletions(-)
Title: OMOP CDM DDL and Documentation Generator
Description: Generates the scripts required to create an Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) database and associated documentation for supported database platforms. Leverages the 'SqlRender' package to convert the Data Definition Language (DDL) script written in parameterized Structured Query Language (SQL) to the other supported dialects.
Author: Clair Blacketer [aut, cre]
Maintainer: Clair Blacketer <mblacke@its.jnj.com>
Diff between CommonDataModel versions 1.0.1 dated 2024-10-01 and 1.1.0 dated 2026-10-09
CommonDataModel-1.0.1/CommonDataModel/R/utils.R |only CommonDataModel-1.0.1/CommonDataModel/inst/csv/OMOP_CDM_Oncology_Ex_Field_Level.csv |only CommonDataModel-1.0.1/CommonDataModel/inst/csv/OMOP_CDM_Oncology_Ex_Table_Level.csv |only CommonDataModel-1.1.0/CommonDataModel/DESCRIPTION | 15 CommonDataModel-1.1.0/CommonDataModel/MD5 | 295 +- CommonDataModel-1.1.0/CommonDataModel/NAMESPACE | 11 CommonDataModel-1.1.0/CommonDataModel/NEWS.md | 6 CommonDataModel-1.1.0/CommonDataModel/R/CommonDataModel-package.R | 11 CommonDataModel-1.1.0/CommonDataModel/R/createDdl.R | 62 CommonDataModel-1.1.0/CommonDataModel/R/listSupportedVersions.R | 2 CommonDataModel-1.1.0/CommonDataModel/R/writeDDL.R | 39 CommonDataModel-1.1.0/CommonDataModel/README.md | 56 CommonDataModel-1.1.0/CommonDataModel/inst/csv/OMOP_CDMv5.3_Field_Level.csv | 808 +++---- CommonDataModel-1.1.0/CommonDataModel/inst/csv/OMOP_CDMv5.3_Table_Level.csv | 74 CommonDataModel-1.1.0/CommonDataModel/inst/csv/OMOP_CDMv5.4_Field_Level.csv | 1103 +++++----- CommonDataModel-1.1.0/CommonDataModel/inst/csv/OMOP_CDMv5.4_Table_Level.csv | 112 - CommonDataModel-1.1.0/CommonDataModel/inst/csv/OMOP_CDMv5.5_Field_Level.csv |only CommonDataModel-1.1.0/CommonDataModel/inst/csv/OMOP_CDMv5.5_Table_Level.csv |only CommonDataModel-1.1.0/CommonDataModel/inst/csv/OMOP_CDMv6.0_Field_Level.csv | 904 ++++---- CommonDataModel-1.1.0/CommonDataModel/inst/csv/OMOP_CDMv6.0_Table_Level.csv | 12 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/bigquery/OMOPCDM_bigquery_5.3_ddl.sql | 39 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/bigquery/OMOPCDM_bigquery_5.3_indices.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/duckdb/OMOPCDM_duckdb_5.3_ddl.sql | 39 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/duckdb/OMOPCDM_duckdb_5.3_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/hive/OMOPCDM_hive_5.3_ddl.sql | 39 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/hive/OMOPCDM_hive_5.3_indices.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/impala/OMOPCDM_impala_5.3_ddl.sql | 39 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/impala/OMOPCDM_impala_5.3_indices.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/iris |only CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/netezza/OMOPCDM_netezza_5.3_ddl.sql | 155 - CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/netezza/OMOPCDM_netezza_5.3_indices.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/oracle/OMOPCDM_oracle_5.3_ddl.sql | 39 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/oracle/OMOPCDM_oracle_5.3_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/pdw/OMOPCDM_pdw_5.3_ddl.sql | 111 - CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/pdw/OMOPCDM_pdw_5.3_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/postgresql/OMOPCDM_postgresql_5.3_ddl.sql | 39 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/postgresql/OMOPCDM_postgresql_5.3_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/redshift/OMOPCDM_redshift_5.3_ddl.sql | 183 - CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/redshift/OMOPCDM_redshift_5.3_indices.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/snowflake/OMOPCDM_snowflake_5.3_ddl.sql | 46 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/snowflake/OMOPCDM_snowflake_5.3_indices.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/spark/OMOPCDM_spark_5.3_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/spark/OMOPCDM_spark_5.3_ddl.sql | 193 - CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/spark/OMOPCDM_spark_5.3_indices.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/spark/OMOPCDM_spark_5.3_primary_keys.sql | 52 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/sql_server/OMOPCDM_sql_server_5.3_ddl.sql | 39 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/sql_server/OMOPCDM_sql_server_5.3_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/sqlite/OMOPCDM_sqlite_5.3_ddl.sql | 39 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/sqlite/OMOPCDM_sqlite_5.3_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/sqlite_extended/OMOPCDM_sqlite_extended_5.3_ddl.sql | 39 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/sqlite_extended/OMOPCDM_sqlite_extended_5.3_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/synapse/OMOPCDM_synapse_5.3_ddl.sql | 39 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.3/synapse/OMOPCDM_synapse_5.3_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/bigquery/OMOPCDM_bigquery_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/bigquery/OMOPCDM_bigquery_5.4_ddl.sql | 41 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/bigquery/OMOPCDM_bigquery_5.4_indices.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/bigquery/OMOPCDM_bigquery_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_ddl.sql | 47 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/duckdb/OMOPCDM_duckdb_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/hive/OMOPCDM_hive_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/hive/OMOPCDM_hive_5.4_ddl.sql | 47 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/hive/OMOPCDM_hive_5.4_indices.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/hive/OMOPCDM_hive_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/impala/OMOPCDM_impala_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/impala/OMOPCDM_impala_5.4_ddl.sql | 47 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/impala/OMOPCDM_impala_5.4_indices.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/impala/OMOPCDM_impala_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/iris |only CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/netezza/OMOPCDM_netezza_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/netezza/OMOPCDM_netezza_5.4_ddl.sql | 169 - CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/netezza/OMOPCDM_netezza_5.4_indices.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/netezza/OMOPCDM_netezza_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/oracle/OMOPCDM_oracle_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/oracle/OMOPCDM_oracle_5.4_ddl.sql | 47 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/oracle/OMOPCDM_oracle_5.4_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/oracle/OMOPCDM_oracle_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/pdw/OMOPCDM_pdw_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/pdw/OMOPCDM_pdw_5.4_ddl.sql | 125 - CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/pdw/OMOPCDM_pdw_5.4_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/pdw/OMOPCDM_pdw_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/postgresql/OMOPCDM_postgresql_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/postgresql/OMOPCDM_postgresql_5.4_ddl.sql | 47 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/postgresql/OMOPCDM_postgresql_5.4_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/postgresql/OMOPCDM_postgresql_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/redshift/OMOPCDM_redshift_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/redshift/OMOPCDM_redshift_5.4_ddl.sql | 199 - CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/redshift/OMOPCDM_redshift_5.4_indices.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/redshift/OMOPCDM_redshift_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/snowflake/OMOPCDM_snowflake_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/snowflake/OMOPCDM_snowflake_5.4_ddl.sql | 54 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/snowflake/OMOPCDM_snowflake_5.4_indices.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/snowflake/OMOPCDM_snowflake_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/spark/OMOPCDM_spark_5.4_constraints.sql | 4 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/spark/OMOPCDM_spark_5.4_ddl.sql | 212 - CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/spark/OMOPCDM_spark_5.4_indices.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/spark/OMOPCDM_spark_5.4_primary_keys.sql | 55 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sql_server/OMOPCDM_sql_server_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sql_server/OMOPCDM_sql_server_5.4_ddl.sql | 47 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sql_server/OMOPCDM_sql_server_5.4_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sql_server/OMOPCDM_sql_server_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sqlite/OMOPCDM_sqlite_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sqlite/OMOPCDM_sqlite_5.4_ddl.sql | 47 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sqlite/OMOPCDM_sqlite_5.4_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sqlite/OMOPCDM_sqlite_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sqlite_extended/OMOPCDM_sqlite_extended_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sqlite_extended/OMOPCDM_sqlite_extended_5.4_ddl.sql | 47 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sqlite_extended/OMOPCDM_sqlite_extended_5.4_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/sqlite_extended/OMOPCDM_sqlite_extended_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/synapse/OMOPCDM_synapse_5.4_constraints.sql | 2 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/synapse/OMOPCDM_synapse_5.4_ddl.sql | 47 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/synapse/OMOPCDM_synapse_5.4_indices.sql | 3 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.4/synapse/OMOPCDM_synapse_5.4_primary_keys.sql | 1 CommonDataModel-1.1.0/CommonDataModel/inst/ddl/5.5 |only CommonDataModel-1.1.0/CommonDataModel/inst/sql/sql_server/OMOP_CDM_indices_v5.5.sql |only CommonDataModel-1.1.0/CommonDataModel/man/CommonDataModel-package.Rd |only CommonDataModel-1.1.0/CommonDataModel/tests/testthat/setup.R | 82 CommonDataModel-1.1.0/CommonDataModel/tests/testthat/test-executeDdl.R | 2 119 files changed, 2725 insertions(+), 3389 deletions(-)
More information about CommonDataModel at CRAN
Permanent link
Title: Automated and Early Detection of Seasonal Epidemic Onset and
Burden Levels
Description: A powerful tool for automating the early detection of seasonal epidemic
onsets in time series data. It offers the ability to estimate growth rates
across consecutive time intervals, calculate the sum of cases (SoC) within
those intervals, and estimate seasonal onsets within user defined seasons.
With use of a disease-specific threshold it also offers the possibility to
estimate seasonal onset of epidemics.
Additionally it offers the ability to estimate burden levels for seasons
based on historical data. It is aimed towards epidemiologists,
public health professionals, and researchers seeking to identify and respond
to seasonal epidemics in a timely fashion.
Author: Sofia Myrup Otero [aut] ,
Kasper Schou Telkamp [aut] ,
Lasse Engbo Christiansen [aut, cre] ,
Rasmus Skytte Randloev [rev] ,
Statens Serum Institut, SSI [cph, fnd]
Maintainer: Lasse Engbo Christiansen <lsec@ssi.dk>
Diff between aedseo versions 1.1.0 dated 2026-01-23 and 1.2.0 dated 2026-10-09
DESCRIPTION | 8 MD5 | 99 +++--- NEWS.md | 17 + R/0_documentation.R | 40 ++ R/autoplot.R | 193 ++++++++----- R/combined_seasonal_output.R | 61 +++- R/consecutive_growth_warnings.R | 1 R/estimate_disease_threshold.R | 146 +++++++-- R/fit_growth_rate.R | 55 ++- R/fit_percentiles.R | 63 ++-- R/generate_seasonal_data.R | 82 +++++ R/historical_summary.R | 5 R/seasonal_burden_levels.R | 35 +- R/seasonal_onset.R | 145 +++++++-- R/summary.R | 118 ++------ R/to_time_series.R | 149 ++++++++-- README.md | 24 + build/vignette.rds |binary inst/CITATION |only inst/doc/aedseo.R | 124 +++++++- inst/doc/aedseo.Rmd | 205 ++++++++++++- inst/doc/aedseo.html | 338 ++++++++++++++++++++--- inst/doc/burden_levels.R | 9 inst/doc/burden_levels.Rmd | 20 - inst/doc/burden_levels.html | 48 +-- inst/doc/generate_seasonal_wave.html | 21 - inst/doc/multiple_waves.html | 7 inst/doc/seasonal_onset.Rmd | 6 inst/doc/seasonal_onset.html | 22 + man/aedseo-package.Rd | 1 man/autoplot.Rd | 11 man/combined_seasonal_output.Rd | 23 - man/estimate_disease_threshold.Rd | 47 ++- man/fit_growth_rate.Rd | 28 + man/fit_percentiles.Rd | 18 - man/generate_seasonal_data.Rd | 21 + man/seasonal_burden_levels.Rd | 16 - man/seasonal_onset.Rd | 20 - man/to_time_series.Rd | 29 + tests/testthat/test-combined_seasonal_output.R | 114 +++++++ tests/testthat/test-estimate_disease_threshold.R | 88 +++++ tests/testthat/test-fit_growth_rate.R | 28 + tests/testthat/test-fit_percentiles.R | 23 + tests/testthat/test-generate_seasonal_data.R | 126 ++++++++ tests/testthat/test-plot.R | 79 +++++ tests/testthat/test-seasonal_onset.R | 230 +++++++++++++++ tests/testthat/test-summary.R | 45 +++ tests/testthat/test-to_time_series.R | 57 +++ vignettes/aedseo.Rmd | 205 ++++++++++++- vignettes/burden_levels.Rmd | 20 - vignettes/seasonal_onset.Rmd | 6 51 files changed, 2696 insertions(+), 580 deletions(-)
Title: Create Common TLGs Used in Clinical Trials
Description: Table, Listings, and Graphs (TLG) library for common outputs
used in clinical trials.
Author: Joe Zhu [aut, cre] ,
Daniel Sabanes Bove [aut],
Jana Stoilova [aut],
Davide Garolini [aut] ,
Emily de la Rua [aut] ,
Abinaya Yogasekaram [aut] ,
Heng Wang [aut],
Francois Collin [aut],
Adrian Waddell [aut],
Pawel Rucki [aut],
Chendi Liao [aut],
Jenni [...truncated...]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between tern versions 0.9.12 dated 2026-09-29 and 0.9.13 dated 2026-10-09
tern-0.9.12/tern/man/h_miettinen_nurminen_var_est.Rd |only tern-0.9.13/tern/DESCRIPTION | 10 tern-0.9.13/tern/MD5 | 46 tern-0.9.13/tern/NAMESPACE | 44 tern-0.9.13/tern/NEWS.md | 16 tern-0.9.13/tern/R/prop_diff.R | 897 ++++--- tern-0.9.13/tern/R/prop_diff_test.R | 6 tern-0.9.13/tern/R/summarize_ancova.R | 5 tern-0.9.13/tern/R/utils.R | 38 tern-0.9.13/tern/build/partial.rdb |binary tern-0.9.13/tern/inst/doc/mantel_fleiss_criterion.html | 17 tern-0.9.13/tern/inst/doc/uncond_exact_prop_diff_ci.html | 2 tern-0.9.13/tern/man/escape_regex.Rd |only tern-0.9.13/tern/man/h_cmh_sato_var.Rd |only tern-0.9.13/tern/man/h_miettinen_nurminen_stratified_ci.Rd |only tern-0.9.13/tern/man/h_miettinen_nurminen_var.Rd |only tern-0.9.13/tern/man/h_prop_cmh.Rd |only tern-0.9.13/tern/man/h_prop_diff.Rd | 39 tern-0.9.13/tern/man/tern-package.Rd | 1 tern-0.9.13/tern/man/uniroot_catch_na.Rd |only tern-0.9.13/tern/tests/testthat/_snaps/prop_diff.md | 1242 +++++++++- tern-0.9.13/tern/tests/testthat/_snaps/summarize_ancova.md | 18 tern-0.9.13/tern/tests/testthat/_snaps/test_proportion_diff.md | 8 tern-0.9.13/tern/tests/testthat/helper-prop_diff.R |only tern-0.9.13/tern/tests/testthat/test-prop_diff.R | 271 +- tern-0.9.13/tern/tests/testthat/test-summarize_ancova.R | 31 tern-0.9.13/tern/tests/testthat/test-test_proportion_diff.R | 2 tern-0.9.13/tern/tests/testthat/test-utils.R | 15 28 files changed, 2238 insertions(+), 470 deletions(-)
Title: Search and Retrieve Data from Eurostat Database
Description: Eurostat is the statistical office of the European Union and provides high quality statistics for Europe.
Large set of the data is disseminated through the Eurostat database (<https://ec.europa.eu/eurostat/web/main/data/database>).
The tools are using the REST API with the Statistical Data and Metadata eXchange (SDMX) Web Services
(<https://ec.europa.eu/eurostat/web/user-guides/data-browser/api-data-access/api-detailed-guidelines/sdmx2-1>) to search and download data from
the Eurostat database using the SDMX standard.
Author: Matyas Meszaros [aut, cre],
Sebastian Weinand [ctb]
Maintainer: Matyas Meszaros <matyas.meszaros@ec.europa.eu>
Diff between restatapi versions 0.25.0 dated 2026-03-30 and 0.30.0 dated 2026-10-09
DESCRIPTION | 14 - MD5 | 48 +++--- NEWS.md | 15 + R/create_filter_table.R | 2 R/extract_data.R | 32 +--- R/extract_dsd.R | 32 ++-- R/filter_raw_data.R | 2 R/get_compressed_sdmx.R | 12 - R/get_eurostat_bulk.R | 96 ++++++------ R/get_eurostat_codelist.R | 8 - R/get_eurostat_data.R | 315 +++++++++++++++++++++-------------------- R/get_eurostat_dsd.R | 16 +- R/get_eurostat_raw.R | 128 ++++++++-------- R/get_eurostat_toc.R | 56 +++---- R/load_cfg.R | 22 ++ README.md | 34 +--- inst/tinytest/test_restatapi.R | 148 ++++++++++++------- man/dot-restatapi_env.Rd | 5 man/extract_data.Rd | 14 - man/extract_dsd.Rd | 14 - man/get_eurostat_bulk.Rd | 34 ++-- man/get_eurostat_data.Rd | 90 ++++++----- man/get_eurostat_raw.Rd | 24 +-- man/get_eurostat_toc.Rd | 2 man/load_cfg.Rd | 3 25 files changed, 618 insertions(+), 548 deletions(-)
Title: Getting Bibliographic Records from 'OpenAlex' Database Using
'DSL' API
Description: A set of tools to extract bibliographic content from
'OpenAlex' database using API <https://help.openalex.org/>.
Author: Massimo Aria [aut, cre, cph] ,
Corrado Cuccurullo [ctb] ,
Trang Le [aut] ,
June Choe [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between openalexR versions 3.1.0 dated 2026-07-02 and 3.1.1 dated 2026-10-09
openalexR-3.1.0/openalexR/man/oa_email.Rd |only openalexR-3.1.1/openalexR/DESCRIPTION | 10 openalexR-3.1.1/openalexR/MD5 | 45 +- openalexR-3.1.1/openalexR/NAMESPACE | 1 openalexR-3.1.1/openalexR/NEWS.md | 50 ++ openalexR-3.1.1/openalexR/R/coro.R | 10 openalexR-3.1.1/openalexR/R/oa2df.R | 15 openalexR-3.1.1/openalexR/R/oa_fetch.R | 159 +++++-- openalexR-3.1.1/openalexR/R/oa_snowball.R | 2 openalexR-3.1.1/openalexR/R/simplify.R | 97 ++++ openalexR-3.1.1/openalexR/R/utils.R | 96 +++- openalexR-3.1.1/openalexR/README.md | 84 +--- openalexR-3.1.1/openalexR/data/oa2df_coverage.rda |binary openalexR-3.1.1/openalexR/man/oa_fetch.Rd | 9 openalexR-3.1.1/openalexR/man/oa_generate.Rd | 2 openalexR-3.1.1/openalexR/man/oa_request.Rd | 7 openalexR-3.1.1/openalexR/man/oa_snowball.Rd | 7 openalexR-3.1.1/openalexR/man/openalexR-package.Rd | 2 openalexR-3.1.1/openalexR/man/show_authors.Rd | 3 openalexR-3.1.1/openalexR/man/show_works.Rd | 5 openalexR-3.1.1/openalexR/tests/testthat/test-oa2df.R | 44 ++ openalexR-3.1.1/openalexR/tests/testthat/test-oa_fetch.R | 245 +++++++++++- openalexR-3.1.1/openalexR/tests/testthat/test-oa_snowball.R | 4 openalexR-3.1.1/openalexR/tests/testthat/test-simplify.R | 105 +++++ 24 files changed, 813 insertions(+), 189 deletions(-)
Title: ICESat-2 Data Analysis for Land and Vegetation
Description: Provides tools for downloading, reading, processing, visualizing,
and exporting NASA's ICESat-2 ATL03 (Global Geolocated Photon
Data) and ATL08 (Land and Vegetation Height) products. Supports
photon- and segment-level analysis, spatial sampling, gridding,
statistical and machine-learning modeling, and integration with
'Google Earth Engine' (<https://earthengine.google.com/>) for
wall-to-wall mapping of vegetation structure and other land
attributes.
Author: Carlos Alberto Silva [aut, cph, cre],
Caio Hamamura [aut, cph],
Cesar Alvites [aut, ctb],
Alexander J. Gaskins [aut, ctb],
Sunil Arya [ctb, cph] ),
David Mount [ctb, cph] ),
University of Maryland [cph] ),
Chuck Gantz [ctb] ,
Cole Krehbiel [ctb]
Maintainer: Carlos Alberto Silva <c.silva@ufl.edu>
Diff between ICESat2VegR versions 0.0.4 dated 2026-10-06 and 0.0.6 dated 2026-10-09
ICESat2VegR-0.0.4/ICESat2VegR/inst/proj |only ICESat2VegR-0.0.6/ICESat2VegR/DESCRIPTION | 6 ICESat2VegR-0.0.6/ICESat2VegR/MD5 | 33 ICESat2VegR-0.0.6/ICESat2VegR/R/zzz.R | 27 ICESat2VegR-0.0.6/ICESat2VegR/cleanup.ucrt | 32 ICESat2VegR-0.0.6/ICESat2VegR/configure.win |12284 +++++----- ICESat2VegR-0.0.6/ICESat2VegR/src/Makevars.in | 15 ICESat2VegR-0.0.6/ICESat2VegR/src/Makevars.ucrt | 15 ICESat2VegR-0.0.6/ICESat2VegR/src/Makevars.ucrt.in | 19 ICESat2VegR-0.0.6/ICESat2VegR/src/gdal_bindings.h | 12 ICESat2VegR-0.0.6/ICESat2VegR/tests/testthat/test-gdal-proj.R |only 11 files changed, 6178 insertions(+), 6265 deletions(-)
Title: Group Response Adaptive Randomization for Clinical Trials
Description: Implements group response-adaptive randomization procedures, which include standard (non-group) response-adaptive randomization methods as special cases. The package also handles delayed and missing responses, which broadens its use in real-world trials. It offers functions for simulating a variety of response-adaptive randomization procedures, to help guide the choice of design for a clinical trial, including the doubly adaptive biased coin design and the multi-arm efficient randomized adaptive design (ERADE), k-arm optimal target allocations, group sequential monitoring, and a function that computes allocation probabilities for an ongoing trial. For details of the methods and algorithms, see the following references:
Wei, L. J. (1979) <doi:10.1214/aos/1176344614>;
Wei, L. J. and Durham, S. (1978) <doi:10.1080/01621459.1978.10480109>;
Durham, S. D., Flournoy, N. and Li, W. (1998) <doi:10.2307/3315771>;
Ivanova, A., Rosenberger, W. F., Durham, S. D. and Flournoy, N. ( [...truncated...]
Author: Guannan Zhai [aut, cre],
Feifang Hu [aut, ths]
Maintainer: Guannan Zhai <guannanzhai1996@gmail.com>
Diff between grouprar versions 0.1.0 dated 2024-03-04 and 0.2.0 dated 2026-10-09
grouprar-0.1.0/grouprar/man/DBCD_bin.Rd |only grouprar-0.2.0/grouprar/DESCRIPTION | 45 grouprar-0.2.0/grouprar/MD5 | 55 grouprar-0.2.0/grouprar/NAMESPACE | 9 grouprar-0.2.0/grouprar/NEWS.md |only grouprar-0.2.0/grouprar/R/groupRAR_complement.R | 416 +++--- grouprar-0.2.0/grouprar/R/groupRAR_functions.R | 1264 ++++++++++----------- grouprar-0.2.0/grouprar/R/groupRAR_tools.R |only grouprar-0.2.0/grouprar/build |only grouprar-0.2.0/grouprar/inst |only grouprar-0.2.0/grouprar/man/Bai.Hu.Shen.Urn.Rd | 82 - grouprar-0.2.0/grouprar/man/BirthDeathUrn.Rd | 75 - grouprar-0.2.0/grouprar/man/CRDesign.Rd | 65 - grouprar-0.2.0/grouprar/man/DBCD_Bin.Rd |only grouprar-0.2.0/grouprar/man/DBCD_Cont.Rd | 113 + grouprar-0.2.0/grouprar/man/DLRule.Rd | 68 - grouprar-0.2.0/grouprar/man/GDLRule.Rd | 72 - grouprar-0.2.0/grouprar/man/Group.DBCD_Bin.Rd | 143 +- grouprar-0.2.0/grouprar/man/Group.DBCD_Cont.Rd | 107 + grouprar-0.2.0/grouprar/man/Group.dyldDBCD_Bin.Rd | 141 +- grouprar-0.2.0/grouprar/man/Group.dyldDBCD_Cont.Rd | 118 + grouprar-0.2.0/grouprar/man/PolyaUrn.Rd | 74 - grouprar-0.2.0/grouprar/man/RPWRule.Rd | 68 - grouprar-0.2.0/grouprar/man/WeiUrn.Rd | 75 - grouprar-0.2.0/grouprar/man/dyldDBCD_Bin.Rd | 119 + grouprar-0.2.0/grouprar/man/dyldDBCD_Cont.Rd | 115 + grouprar-0.2.0/grouprar/man/grouprar_package.Rd | 77 - grouprar-0.2.0/grouprar/man/nextAlloc.Rd |only grouprar-0.2.0/grouprar/man/print.grouprar.Rd |only grouprar-0.2.0/grouprar/man/sqMonitor.Rd |only grouprar-0.2.0/grouprar/tests |only 31 files changed, 1847 insertions(+), 1454 deletions(-)
Title: Interactive Plotting for Funnel, Sigma, and Statistical Process
Control Charts
Description: Generate interactive funnel plots, multi-indicator sigma charts,
and statistical process control ('SPC') charts. Chart calculation and plotting
use JavaScript, allowing dynamic charts without a Shiny server. For more details
see Spiegelhalter (2004) <doi:10.1002/sim.1970> and Pfadt & Wheeler (1995)
<doi:10.1901/jaba.1995.28-349>.
Author: Andrew R. Johnson [aut, cre] ,
Healthcare Quality Intelligence Unit [aut]
Maintainer: Andrew R. Johnson <andrew.johnson@arjohnsonau.com>
Diff between controlcharts versions 0.0.19 dated 2026-08-04 and 0.0.23 dated 2026-10-09
DESCRIPTION | 20 MD5 | 58 NAMESPACE | 4 R/aaa.R | 2 R/funnel.R | 42 R/misc.R |only R/print.R | 11 R/spc.R | 75 - R/util.R | 269 +++- R/zzz.R | 3 inst/doc/aesthetic_options.html | 32 inst/doc/chart_types.html | 158 +- inst/doc/getting_started.html | 4 inst/doc/outlier_detection.html | 40 inst/htmlwidgets/funnel.yaml | 3 inst/htmlwidgets/lib/MISC |only inst/htmlwidgets/lib/PBIFUN/PBIFUN.js | 1409 ++++++++++++------------ inst/htmlwidgets/lib/PBISPC/PBISPC.js | 475 +++++--- inst/htmlwidgets/lib/UTILS/commonUtils.js | 143 +- inst/htmlwidgets/lib/UTILS/headlessUtils.js | 40 inst/htmlwidgets/lib/UTILS/interactiveUtils.css |only inst/htmlwidgets/lib/UTILS/interactiveUtils.js | 126 ++ inst/htmlwidgets/misc.js |only inst/htmlwidgets/misc.yaml |only inst/htmlwidgets/spc.yaml | 3 man/funnel.Rd | 11 man/misc-shiny.Rd |only man/misc.Rd |only man/misc_default_settings.Rd |only man/spc.Rd | 17 tests/testthat/test-export-html.R |only tests/testthat/test-knit-print.R |only tests/testthat/test-misc-html.R |only tests/testthat/test-misc.R |only tests/testthat/test-spc-indicators.R |only tests/testthat/test-tooltips.R |only vignettes/articles/interactive_charts.Rmd | 7 37 files changed, 1815 insertions(+), 1137 deletions(-)
Title: Bimodal GEV Distribution with Location Parameter
Description: Density, distribution function, quantile function random generation and estimation of bimodal GEV distribution given in Otiniano et al. (2023) <doi:10.1007/s10651-023-00566-7>. This new generalization of the well-known GEV (Generalized Extreme Value) distribution is useful for modeling heterogeneous bimodal data from different areas.
Author: Thiago do Rego Sousa [aut, cre],
Yasmin Lirio [aut],
Cira Etheowalda Guevara Otiniano [aut]
Maintainer: Thiago do Rego Sousa <thiagodoregosousa@gmail.com>
Diff between bgev versions 0.2 dated 2025-11-05 and 0.3 dated 2026-10-09
bgev-0.2/bgev/R/bgev_functions.R |only bgev-0.2/bgev/man/bgev-package.Rd |only bgev-0.2/bgev/man/bgev.mle.Rd |only bgev-0.2/bgev/man/bgev.support.Rd |only bgev-0.2/bgev/man/distCheck.Rd |only bgev-0.2/bgev/man/likbgev.Rd |only bgev-0.3/bgev/DESCRIPTION | 34 ++++-- bgev-0.3/bgev/MD5 | 39 +++++-- bgev-0.3/bgev/NAMESPACE | 22 +++- bgev-0.3/bgev/NEWS.md |only bgev-0.3/bgev/R/bgev_distribution.R |only bgev-0.3/bgev/R/bgev_domain.R |only bgev-0.3/bgev/R/bgev_estimation.R |only bgev-0.3/bgev/R/dist_check.R | 123 ++++++++++++++---------- bgev-0.3/bgev/README.md |only bgev-0.3/bgev/build/partial.rdb |binary bgev-0.3/bgev/build/vignette.rds |only bgev-0.3/bgev/inst |only bgev-0.3/bgev/man/bgev.Rd |only bgev-0.3/bgev/man/bgev_log_likelihood.Rd |only bgev-0.3/bgev/man/bgev_mle.Rd |only bgev-0.3/bgev/man/bgev_profile_likelihood.Rd |only bgev-0.3/bgev/man/bgev_start_using_quantiles.Rd |only bgev-0.3/bgev/man/bgev_support.Rd |only bgev-0.3/bgev/man/bgev_valid_params.Rd |only bgev-0.3/bgev/man/dist_check.Rd |only bgev-0.3/bgev/tests |only bgev-0.3/bgev/vignettes |only 28 files changed, 144 insertions(+), 74 deletions(-)
Title: Quantifying (Animal) Sound Degradation
Description: Intended to facilitate acoustic analysis of (animal) sound propagation experiments, which typically aim to quantify changes in signal structure when transmitted in a given habitat by broadcasting and re-recording animal sounds at increasing distances. The package offers a workflow with functions to prepare the data set for analysis as well as to calculate and visualize several degradation metrics, including blur ratio, signal-to-noise ratio, excess attenuation and envelope correlation among others (Dabelsteen et al 1993 <doi:10.1121/1.406682>).
Author: Marcelo Araya-Salas [aut, cre] ,
Michael Mahoney [rev] ,
Dena Clink [rev]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
This is a re-admission after prior archival of version 2.1.7 dated 2026-07-24
Diff between baRulho versions 2.1.7 dated 2026-07-24 and 2.2.0 dated 2026-10-09
DESCRIPTION | 7 MD5 | 134 +-- NEWS.md | 16 R/add_noise.R | 83 +- R/align_test_files.R | 57 + R/attenuation.R | 42 - R/auto_realign.R | 68 + R/baRulho-package.R | 17 R/blur_ratio.R | 59 + R/detection_distance.R | 80 +- R/envelope_correlation.R | 46 + R/excess_attenuation.R | 76 +- R/find_markers.R | 82 ++ R/internal_functions.R | 72 +- R/manual_realign.R | 131 +++ R/master_est-data.R | 15 R/master_sound_file.R | 81 +- R/noise_profile.R | 91 ++ R/plot_aligned_sounds.R | 115 ++- R/plot_blur_ratio.R | 97 ++ R/plot_degradation.R | 130 ++- R/set_reference_sounds.R | 92 ++ R/signal_to_noise_ratio.R | 103 ++ R/spcc.R | 44 + R/spectrum_blur_ratio.R | 69 + R/spectrum_correlation.R | 50 + R/spot_ambient_noise.R | 61 + R/synth_sounds.R | 119 ++- R/tail_to_signal_ratio.R | 97 ++ R/template_params.R | 81 +- R/test_sounds_est-data.R | 14 README.md | 121 ++- build/vignette.rds |binary data/master_est.rda |binary data/test_sounds_est.rda |binary inst/doc/align_test_sounds.R | 1 inst/doc/align_test_sounds.Rmd | 17 inst/doc/align_test_sounds.html | 522 ++++---------- inst/doc/quantify_degradation.Rmd | 25 inst/doc/quantify_degradation.html | 1293 +++++++++++++++---------------------- man/add_noise.Rd | 109 ++- man/align_test_files.Rd | 85 +- man/attenuation.Rd | 38 - man/auto_realign.Rd | 102 ++ man/baRulho-package.Rd | 24 man/blur_ratio.Rd | 133 ++- man/detection_distance.Rd | 165 +++- man/envelope_correlation.Rd | 122 ++- man/excess_attenuation.Rd | 119 ++- man/find_markers.Rd | 108 ++- man/manual_realign.Rd | 195 ++++- man/master_est.Rd | 14 man/master_sound_file.Rd | 102 ++ man/noise_profile.Rd | 126 ++- man/plot_aligned_sounds.Rd | 187 +++-- man/plot_blur_ratio.Rd | 187 +++-- man/plot_degradation.Rd | 234 ++++-- man/set_reference_sounds.Rd | 126 ++- man/signal_to_noise_ratio.Rd | 169 +++- man/spcc.Rd | 119 ++- man/spectrum_blur_ratio.Rd | 138 ++- man/spectrum_correlation.Rd | 126 ++- man/spot_ambient_noise.Rd | 85 +- man/synth_sounds.Rd | 136 ++- man/tail_to_signal_ratio.Rd | 139 ++- man/test_sounds_est.Rd | 14 vignettes/align_test_sounds.Rmd | 17 vignettes/quantify_degradation.Rmd | 25 68 files changed, 4793 insertions(+), 2559 deletions(-)
Title: Infrastructure for Interacting with GPUs
Description: Compiling, managing, and dispatching functions to GPUs. Will compile tooling for successfully detected frameworks, currently limited to: 'OpenCL' (<https://www.khronos.org/opencl/resources>), 'CUDA' (<https://docs.nvidia.com/cuda/>), and 'Metal' (<https://developer.apple.com/documentation/metal>).
Author: Nicholas Cooley [aut, cre]
Maintainer: Nicholas Cooley <npcooley@gmail.com>
Diff between ardea versions 0.0.9 dated 2026-10-08 and 0.1.1 dated 2026-10-09
DESCRIPTION | 6 - MD5 | 21 ++-- NAMESPACE | 3 R/utils.R | 39 ++++++++ build/vignette.rds |binary inst/doc/introduction_to_ardea.R | 81 ++++++++++-------- inst/doc/introduction_to_ardea.Rmd | 85 ++++++++++--------- inst/doc/introduction_to_ardea.html | 161 +++++++++++++++++++----------------- man/metal_compiler_is_available.Rd |only man/metal_make_program.Rd | 8 + man/simple_wrapper.Rd | 12 ++ vignettes/introduction_to_ardea.Rmd | 85 ++++++++++--------- 12 files changed, 296 insertions(+), 205 deletions(-)
Title: R Interface for the 'STATcube' REST API and Open Government Data
Description: Import data from the 'STATcube' REST API or from the open data
portal of Statistics Austria. This package includes a client for API
requests as well as parsing utilities for data which originates from
'STATcube'. Documentation about 'STATcubeR' is provided by several vignettes
included in the package as well as on the public 'pkgdown' page at
<https://statistikat.github.io/STATcubeR/>.
Author: Bernhard Meindl [ctb, cre],
Alexander Kowarik [ctb] ,
Gregor de Cillia [aut]
Maintainer: Bernhard Meindl <Bernhard.Meindl@statistik.gv.at>
Diff between STATcubeR versions 1.0.0 dated 2024-11-29 and 1.0.1 dated 2026-10-09
DESCRIPTION | 15 +- MD5 | 80 +++++------ NAMESPACE | 10 + NEWS.md | 21 +++ R/browse.R | 2 R/error.R | 7 - R/od_cache.R | 2 R/od_list.R | 197 ++++++++++++++++++++++------ R/od_resource.R | 21 ++- R/od_revisions.R | 4 R/od_table.R | 4 R/od_table_save.R | 2 R/od_utils.R | 58 ++++++++ R/other_endpoints.R | 10 + R/recoder.R | 2 R/sc_data.R | 8 - R/schema.R | 5 R/schema_db.R | 8 - R/table.R | 57 ++++++++ R/table_custom.R | 43 +++--- R/table_saved.R | 4 R/tabulate.R | 8 - inst/json_examples/accomodation.json | 12 - man/od_cache.Rd | 2 man/od_catalogue.Rd | 2 man/od_list.Rd | 11 + man/od_resource.Rd | 8 + man/od_revisions.Rd | 2 man/od_server_reachable.Rd |only man/od_table.Rd | 2 man/od_table_class.Rd | 86 ++++++------ man/od_table_save.Rd | 2 man/other_endpoints.Rd | 2 man/sc_data.Rd | 218 +++++++++++++------------------ man/sc_last_error.Rd | 2 man/sc_recoder.Rd | 243 +++++++++++++++++------------------ man/sc_schema.Rd | 10 - man/sc_server_reachable.Rd |only man/sc_table.Rd | 2 man/sc_table_class.Rd | 177 ++++++++++++------------- man/sc_table_custom.Rd | 40 +++-- man/sc_tabulate.Rd | 9 - 42 files changed, 851 insertions(+), 547 deletions(-)
Title: Gene Analysis Toolkit
Description: Provides features for searching, converting, analyzing, plotting, and exporting data effortlessly by inputting feature IDs. Enables easy retrieval of feature information, conversion of ID types, gene enrichment analysis, publication-level figures, group interaction plotting, and result export in one Excel file for seamless sharing and communication.
Author: Yunze Liu [aut, cre]
Maintainer: Yunze Liu <jieandze1314@gmail.com>
Diff between genekitr versions 1.2.8 dated 2024-09-06 and 1.3.0 dated 2026-10-09
ChangeLog | 25 DESCRIPTION | 23 MD5 | 70 - NAMESPACE | 226 ++-- R/asEnrichdat.R | 2 R/expoSheet.R | 123 +- R/genGSEA.R | 39 R/genInfo.R | 14 R/genORA.R | 2 R/getPubmed.R | 272 ++--- R/importCP.R | 448 ++++---- R/importPanther.R | 139 +- R/importShinygo.R | 70 - R/ploTheme.R | 8 R/plotEnrich.R | 2063 +++++++++++++++++++-------------------- R/plotEnrichAdv.R | 14 R/plotGSEA.R | 1174 +++++++++++----------- R/plotVenn.R | 22 R/plotVolcano.R | 250 ++-- R/transID.R | 9 R/transProbe.R | 52 R/utilities.R | 54 - R/zzz.R | 2 README.md | 2 data/biocOrg_name.rda |binary data/deg.rda |binary data/ensOrg_name.rda |binary data/geneList.rda |binary data/hsapiens_probe_platform.rda |binary data/keggOrg_name.rda |binary data/msig_category.rda |binary data/msig_org.rda |binary man/genGSEA.Rd | 3 man/plotEnrich.Rd | 2 man/plotVenn.Rd | 7 man/plotVolcano.Rd | 6 36 files changed, 2604 insertions(+), 2517 deletions(-)
Title: Suess and Laws Corrections for Marine Stable Carbon Isotope Data
Description: Generates region-specific Suess and Laws corrections for
stable carbon isotope data from marine organisms collected between 1850 and 2025. Version
0.1.7 of 'SuessR' contains four built-in regions: the Bering Sea ('Bering Sea'), the
Aleutian archipelago ('Aleutian Islands'), the Gulf of Alaska ('Gulf of Alaska'), and the
subpolar North Atlantic ('Subpolar North Atlantic'). Users can supply their own environmental
data for regions currently not built into the package to generate corrections for those regions.
Author: Casey Clark [cre, aut],
Mattias Cape [aut],
Mark Shapley [aut],
Franz Mueter [aut],
Bruce Finney [aut],
Nicole Misarti [aut]
Maintainer: Casey Clark <casey.t.clark@gmail.com>
Diff between SuessR versions 0.1.6 dated 2025-02-20 and 0.1.7 dated 2026-10-09
DESCRIPTION | 12 ++++++------ LICENSE | 2 +- MD5 | 18 +++++++++--------- NEWS.md | 5 +++++ R/SuessR_Package.R | 6 +++--- R/SuessR_Reference_Data.R | 4 ++-- data/SuessR_Reference_Data.RData |binary man/SuessR.Rd | 2 +- man/SuessR.custom.Rd | 4 ++-- man/SuessR.reference.data.Rd | 4 ++-- 10 files changed, 31 insertions(+), 26 deletions(-)
Title: Forest Carbon Sequestration and Potential Productivity
Calculation
Description: Include assessing site classes based on the stand height growth and establishing a nonlinear mixed-effect biomass model under different site classes based on the whole stand model to achieve more accurate estimation of carbon sequestration. In particular, a carbon sequestration potential productivity calculation method based on the potential mean annual increment is proposed. This package is applicable to both natural forests and plantations. It can quantitatively assess stand’s potential productivity, realized productivity, and possible improvement under certain site, and can be used in many aspects such as site quality assessment, tree species suitability evaluation, and forest degradation evaluation. Reference: Lei X, Fu L, Li H, et al (2018) <doi:10.11707/j.1001-7488.20181213>. Fu L, Sharma R P, Zhu G, et al (2017) <doi:10.3390/f8040119>.
Author: Liyong Fu [aut],
Shirong Liu [aut],
Shouzheng Tang [aut],
Guangshuang Duan [aut],
Zhong Wang [aut],
Linyan Feng [aut],
Dongbo Xie [aut],
Yuanyuan Han [aut, cre]
Maintainer: Yuanyuan Han <jackhanyuan@foxmail.com>
Diff between forestat versions 1.1.0 dated 2023-10-10 and 1.2.0 dated 2026-10-08
DESCRIPTION | 10 MD5 | 64 - NAMESPACE | 1 NEWS.md | 96 - R/birch_and_larch_and_picea_data.R |only R/class_plot.R | 186 +-- R/degraded_forest_grade.R | 174 +- R/degraded_forest_preprocess.R | 190 +-- R/forestData.R | 36 R/plot.R | 366 +++--- R/plot_1.R | 42 R/plot_2.R | 42 R/plot_3.R | 42 R/potential_productivity.R | 168 +- R/realized_productivity.R | 154 +- R/summary.R | 186 +-- R/tree_1.R | 28 R/tree_2.R | 28 R/tree_3.R | 28 R/util.R | 1657 ++++++++++++++------------- build/vignette.rds |binary data/birch.rda |only data/larch.rda |only data/picea.rda |only inst/CITATION | 50 inst/doc/forestat.Rmd | 1386 +++++++++++------------ inst/doc/forestat.html | 2195 ++++++++++++++++++------------------- man/FittingEvaluationIndex.Rd |only man/birch.Rd |only man/class.plot.Rd | 2 man/larch.Rd |only man/picea.Rd |only man/plot.forestData.Rd | 2 man/potential.productivity.Rd | 2 man/realized.productivity.Rd | 2 man/summary.forestData.Rd | 2 vignettes/forestat.Rmd | 1386 +++++++++++------------ 37 files changed, 4327 insertions(+), 4198 deletions(-)
Title: Quantify the Compositional Stability of Each Community Based on
a Single Sampling Event
Description: Quantify the stability of each community based on the beta
diversity between communities gathered in a single sampling event rather
than a series of continuous sampling activities.
Author: Yu Gao [aut, cre, cph, fnd]
Maintainer: Yu Gao <gaoyu19920914@gmail.com>
Diff between betaStability versions 0.0.4 dated 2026-06-05 and 0.1.0 dated 2026-10-08
DESCRIPTION | 18 +- MD5 | 73 +++++----- NAMESPACE | 80 ++++++----- NEWS | 10 + R/betaStability.R | 28 ++-- R/calcStability.R | 35 +++-- R/data.R |only R/gamPred.R | 8 - R/gdmPred.R | 8 - R/glmPred.R | 8 - R/linearPred.R | 6 R/mlPred.R | 8 - R/plotStability.R | 264 +++++++++++++++++++++++++++++++-------- R/rfPred.R | 8 - R/utils.R | 3 R/xgboostPred.R | 8 - build/vignette.rds |binary data |only inst/doc/quickstart.R | 30 +++- inst/doc/quickstart.Rmd | 35 ++++- inst/doc/quickstart.html | 206 ++++++++++++++++++------------ inst/doc/rioja_examples.html | 60 ++++---- inst/doc/vegan_examples.R | 13 + inst/doc/vegan_examples.Rmd | 16 ++ inst/doc/vegan_examples.html | 87 +++++++----- man/betaStability.Rd | 4 man/calcStability.Rd | 10 + man/gamPred.Rd | 5 man/gdmPred.Rd | 5 man/glmPred.Rd | 4 man/linearPred.Rd | 4 man/mlPred.Rd | 4 man/plotStability.Rd | 38 ++++- man/rfPred.Rd | 4 man/varecoords.Rd |only man/xgboostPred.Rd | 11 + tests/testthat/test-linearPred.R | 17 ++ vignettes/quickstart.Rmd | 35 ++++- vignettes/vegan_examples.Rmd | 16 ++ 39 files changed, 826 insertions(+), 343 deletions(-)
Title: Mixed-Effect Models, with or without Spatial Random Effects
Description: Inference based on models with or without spatially-correlated random effects, multivariate responses, or non-Gaussian random effects (e.g., Beta). Variation in residual variance (heteroscedasticity) can itself be represented by a mixed-effect model. Both classical geostatistical models (Rousset and Ferdy 2014 <doi:10.1111/ecog.00566>), and Markov random field models on irregular grids (as considered in the 'INLA' package, <https://www.r-inla.org>), can be fitted, with distinct computational procedures exploiting the sparse matrix representations for the latter case and other autoregressive models. Laplace approximations are used for likelihood or restricted likelihood. Penalized quasi-likelihood and other variants discussed in the h-likelihood literature (Lee and Nelder 2001 <doi:10.1093/biomet/88.4.987>) are also implemented.
Author: Francois Rousset [aut, cre, cph] ,
Jean-Baptiste Ferdy [aut, cph],
Alexandre Courtiol [aut]
Maintainer: Francois Rousset <francois.rousset@umontpellier.fr>
Diff between spaMM versions 4.7.0 dated 2026-09-09 and 4.7.17 dated 2026-10-08
DESCRIPTION | 10 MD5 | 144 ++++----- NAMESPACE | 2 R/COMPoisson.R | 4 R/HLCor_body.R | 15 R/HLFactorList.R | 2 R/HLfit_Internals.R | 63 ++- R/HLfit_b_internals.R | 7 R/HLfit_loop.R | 2 R/LMLTslots.R | 2 R/augZXy_obj.R | 2 R/betabin.R | 2 R/betaresp.R | 2 R/confint.R | 12 R/corrHLfit-internals.R | 4 R/corrHLfit_body.R | 10 R/corrPars.R | 3 R/determine_spprec.R | 94 +++-- R/extractors.R | 48 ++- R/fit_as_ZX.R | 6 R/fitme_body.R | 8 R/fitme_fitmv_internals.R | 9 R/fitmecorrHLfit_body_internals.R | 85 +++-- R/fitmv.R | 2 R/fitmv_body.R | 8 R/geo_info.R | 14 R/get_inits_by_glm.R | 33 +- R/locoptim.R | 6 R/makeLowerUpper.R | 8 R/negbin1.R | 2 R/negbin2.R | 2 R/numInfo.R | 27 + R/pois4mlogit.R | 125 ++++--- R/preprocess.R | 51 --- R/preprocess_MV.R | 27 - R/preprocess_internals.R | 134 ++++++-- R/profile.R | 4 R/sXaug_Matrix_CHM_Hess.R | 124 ++++--- R/sXaug_Matrix_QRP_CHM.R | 82 +++-- R/sXaug_sparsePrecisions.R | 134 ++++---- R/spaMM.data.R | 4 R/update.HL.R | 4 inst/NEWS.Rd | 31 + inst/doc/multinomial-logit.Rmd | 145 +++------ inst/doc/multinomial-logit.html | 383 +++++++++++------------- man/CauchyCorr.Rd | 2 man/Gryphon.Rd | 4 man/HLfit.Rd | 1 man/extractors.Rd | 5 man/fitmv.Rd | 2 man/fixed.Rd | 4 man/mapMM.Rd | 2 man/pois4mlogit.Rd | 17 - man/random-effects.Rd | 3 man/remove_fixef.Rd | 2 man/seaMask.Rd | 4 man/spaMM-internal.Rd | 1 man/spaMM.Rd | 2 man/update.Rd | 2 src/PLS.cpp | 4 src/PLS.h | 6 src/RcppExports.cpp | 6 tests/testthat/extralong/test-composite-extra.R | 7 tests/testthat/extralong/test-mv-extra.R | 2 tests/testthat/test-COMPoisson.R | 8 tests/testthat/test-adjacency-corrMatrix.R | 43 +- tests/testthat/test-adjacency-long.R | 15 tests/testthat/test-corrFamilies.R | 8 tests/testthat/test-dhglm.R | 2 tests/testthat/test-obsInfo.R | 3 tests/testthat/test-pois4mlogit.R | 25 + vignettes/multinomial-logit.Rmd | 145 +++------ vignettes/rdIntZ-1.png |binary 73 files changed, 1214 insertions(+), 997 deletions(-)
Title: Rendering Graphs as Coherent Spatial Objects in 'ggplot2'
Description: An interface for rendering 'igraph' objects as 'ggplot2' graphics
within a normalized coordinate space. 'RGraphSpace' implements new
geometries that treat a graph as a single coherent object, synchronizing
node and edge layers under standard aesthetic mappings. Node features are
resolved on demand, supporting high-dimensional data without expanding
node tables. Spatial alignment is available at the pixel level,
with node coordinates anchored to pixel centers through a half-pixel
offset, enabling precise node positioning over external reference frames
such as images and maps. Core functionality builds on 'igraph', 'ggplot2',
and 'tidygraph'; optional geometry and large raster-background
images use 'sf' and 'terra' when installed.
Author: Flavio Gabriel Carazza-Kessler [aut] ,
Jonathan Andre Back [aut] ,
Lana Bazan Peters Querne [aut] ,
Victor Henrique Apolonio dos Santos [aut] ,
Vinicius Chagas [ctb],
Mauro Antonio Alves Castro [aut, cre]
Maintainer: Mauro Antonio Alves Castro <mauro.a.castro@gmail.com>
Diff between RGraphSpace versions 1.5.2 dated 2026-08-24 and 1.5.7 dated 2026-10-08
RGraphSpace-1.5.2/RGraphSpace/inst/NEWS.Rd |only RGraphSpace-1.5.7/RGraphSpace/DESCRIPTION | 71 RGraphSpace-1.5.7/RGraphSpace/MD5 | 131 - RGraphSpace-1.5.7/RGraphSpace/NAMESPACE | 65 RGraphSpace-1.5.7/RGraphSpace/NEWS.md |only RGraphSpace-1.5.7/RGraphSpace/R/annotation-gspace.R | 172 +- RGraphSpace-1.5.7/RGraphSpace/R/geom-edgespace.R | 550 +++---- RGraphSpace-1.5.7/RGraphSpace/R/geom-nodespace.R | 100 - RGraphSpace-1.5.7/RGraphSpace/R/gspace-accessors.R | 423 ++--- RGraphSpace-1.5.7/RGraphSpace/R/gspace-addition.R | 737 +++++---- RGraphSpace-1.5.7/RGraphSpace/R/gspace-attributes.R |only RGraphSpace-1.5.7/RGraphSpace/R/gspace-checks.R | 64 RGraphSpace-1.5.7/RGraphSpace/R/gspace-classes.R | 146 + RGraphSpace-1.5.7/RGraphSpace/R/gspace-coercion.R | 26 RGraphSpace-1.5.7/RGraphSpace/R/gspace-constructor.R | 662 +++----- RGraphSpace-1.5.7/RGraphSpace/R/gspace-features.R | 44 RGraphSpace-1.5.7/RGraphSpace/R/gspace-generics.R | 20 RGraphSpace-1.5.7/RGraphSpace/R/gspace-geometry.R | 208 +- RGraphSpace-1.5.7/RGraphSpace/R/gspace-ggplot-constructor.R | 33 RGraphSpace-1.5.7/RGraphSpace/R/gspace-glyph-accessors.R |only RGraphSpace-1.5.7/RGraphSpace/R/gspace-glyph-collection.R |only RGraphSpace-1.5.7/RGraphSpace/R/gspace-glyph-constructor.R |only RGraphSpace-1.5.7/RGraphSpace/R/gspace-glyph-legend.R |only RGraphSpace-1.5.7/RGraphSpace/R/gspace-methods.R | 182 +- RGraphSpace-1.5.7/RGraphSpace/R/gspace-misc.R | 64 RGraphSpace-1.5.7/RGraphSpace/R/gspace-normalize.R | 208 +- RGraphSpace-1.5.7/RGraphSpace/R/gspace-subscript.R | 31 RGraphSpace-1.5.7/RGraphSpace/R/gspace-subset.R | 179 +- RGraphSpace-1.5.7/RGraphSpace/R/gspace-themes.R | 45 RGraphSpace-1.5.7/RGraphSpace/R/gspace-transform-rawcoords.R |only RGraphSpace-1.5.7/RGraphSpace/R/gspace-transform.R | 386 ++--- RGraphSpace-1.5.7/RGraphSpace/R/gspace-validation.R | 769 +++++----- RGraphSpace-1.5.7/RGraphSpace/R/zzz.R |only RGraphSpace-1.5.7/RGraphSpace/inst/CITATION | 23 RGraphSpace-1.5.7/RGraphSpace/inst/doc/RGraphSpace.R | 14 RGraphSpace-1.5.7/RGraphSpace/inst/doc/RGraphSpace.Rmd | 28 RGraphSpace-1.5.7/RGraphSpace/inst/doc/RGraphSpace.html | 93 - RGraphSpace-1.5.7/RGraphSpace/man/GraphSpace-accessors.Rd | 108 - RGraphSpace-1.5.7/RGraphSpace/man/GraphSpace-attributes.Rd |only RGraphSpace-1.5.7/RGraphSpace/man/GraphSpace-class.Rd | 9 RGraphSpace-1.5.7/RGraphSpace/man/GraphSpace-methods.Rd | 75 RGraphSpace-1.5.7/RGraphSpace/man/GraphSpace-subscript.Rd | 5 RGraphSpace-1.5.7/RGraphSpace/man/GraphSpace-transform.Rd | 40 RGraphSpace-1.5.7/RGraphSpace/man/RGraphSpace-package.Rd | 18 RGraphSpace-1.5.7/RGraphSpace/man/StatEdgeSpace.Rd | 7 RGraphSpace-1.5.7/RGraphSpace/man/StatNodeSpace.Rd | 7 RGraphSpace-1.5.7/RGraphSpace/man/annotation_gspace_image.Rd | 26 RGraphSpace-1.5.7/RGraphSpace/man/as.GraphSpace.Rd | 15 RGraphSpace-1.5.7/RGraphSpace/man/deprecated-attr.Rd |only RGraphSpace-1.5.7/RGraphSpace/man/geom_edgespace.Rd | 82 - RGraphSpace-1.5.7/RGraphSpace/man/geom_nodespace.Rd | 52 RGraphSpace-1.5.7/RGraphSpace/man/geometry-methods.Rd | 59 RGraphSpace-1.5.7/RGraphSpace/man/ggplot-GraphSpace.Rd | 4 RGraphSpace-1.5.7/RGraphSpace/man/glyph_collection.Rd |only RGraphSpace-1.5.7/RGraphSpace/man/glyph_legend.Rd |only RGraphSpace-1.5.7/RGraphSpace/man/glyph_list.Rd |only RGraphSpace-1.5.7/RGraphSpace/man/glyph_mode.Rd |only RGraphSpace-1.5.7/RGraphSpace/man/glyph_proto.Rd |only RGraphSpace-1.5.7/RGraphSpace/man/gs_add_edges.Rd | 38 RGraphSpace-1.5.7/RGraphSpace/man/gs_add_nodes.Rd | 22 RGraphSpace-1.5.7/RGraphSpace/man/gs_compute.Rd |only RGraphSpace-1.5.7/RGraphSpace/man/gs_features-utils.Rd | 20 RGraphSpace-1.5.7/RGraphSpace/man/gs_subset.Rd | 7 RGraphSpace-1.5.7/RGraphSpace/man/inject_nodespace.Rd | 2 RGraphSpace-1.5.7/RGraphSpace/man/normalizeGraphSpace-methods.Rd | 7 RGraphSpace-1.5.7/RGraphSpace/man/plot.GraphSpace.Rd | 9 RGraphSpace-1.5.7/RGraphSpace/man/plotGraphSpace-methods.Rd | 16 RGraphSpace-1.5.7/RGraphSpace/man/sfshape_ngons.Rd | 13 RGraphSpace-1.5.7/RGraphSpace/man/sfshape_stars.Rd | 3 RGraphSpace-1.5.7/RGraphSpace/man/summary-GraphSpace-method.Rd | 9 RGraphSpace-1.5.7/RGraphSpace/man/theme_gspace.Rd | 10 RGraphSpace-1.5.7/RGraphSpace/man/updateGraphSpace.Rd | 8 RGraphSpace-1.5.7/RGraphSpace/tests/testthat.R | 2 RGraphSpace-1.5.7/RGraphSpace/tests/testthat/test-RGraphSpace.R | 650 ++++++++ RGraphSpace-1.5.7/RGraphSpace/vignettes/RGraphSpace.Rmd | 28 75 files changed, 4090 insertions(+), 2735 deletions(-)
Title: Calculate Fetch and Wave Exposure for Lake Sampling Points
Description: Calculates fetch (open water distance) and wave exposure metrics
for lake sampling points. Downloads lake boundaries from 'OpenStreetMap',
calculates directional fetch using a ray-casting approach, and optionally
integrates National Hydrography Dataset ('NHD') data
<https://www.usgs.gov/national-hydrography> for hydrological context
including outlet and inlet locations. Can estimate lake depth from surface
area using empirical relationships, and integrate historical weather data
for cumulative wave energy calculations. Includes an optional interactive
'shiny' application for visualization.
Author: Jeremy Lynch Farrell [aut, cre]
Maintainer: Jeremy Lynch Farrell <farrej2@rpi.edu>
Diff between lakefetch versions 0.1.3 dated 2026-03-20 and 0.1.14 dated 2026-10-08
DESCRIPTION | 13 MD5 | 97 +++-- NEWS.md | 479 +++++++++++++++++++++++++---- R/bathymetry.R | 75 ---- R/data.R | 59 ++- R/fetch_core.R | 126 ++++++- R/globals.R | 4 R/lake_sources.R | 439 +++++++++++++++++++++----- R/nhd_integration.R | 48 +- R/shiny_app.R | 357 +++++++++++++++------ R/visualization.R | 135 +++++--- R/weather_integration.R | 44 +- R/zzz.R | 6 README.md | 349 ++++++++++++--------- data/adirondack_sites.rda |binary data/example_lake.rda |binary data/wisconsin_lakes.rda |binary inst/CITATION | 2 inst/WORDLIST | 124 +++++-- inst/doc/getting-started.R | 35 +- inst/doc/getting-started.Rmd | 47 +- inst/doc/getting-started.html | 44 +- inst/examples/example_workflow.R | 4 inst/extdata/sample_sites.csv | 4 man/add_lake_context.Rd | 7 man/add_lake_depth.Rd | 5 man/add_weather_context.Rd | 23 + man/adirondack_sites.Rd | 5 man/assign_sites_to_lakes.Rd | 18 - man/create_ray_geometries.Rd | 5 man/example_lake.Rd | 53 +-- man/fetch_calculate.Rd | 14 man/get_lake_boundary.Rd | 49 ++ man/lakefetch-package.Rd | 5 man/plot_fetch_bars.Rd | 5 man/plot_fetch_map.Rd | 21 - man/plot_fetch_rose.Rd | 24 - man/wisconsin_lakes.Rd | 5 tests/testthat/Rplots.pdf |only tests/testthat/_problems |only tests/testthat/helper-geometries.R | 5 tests/testthat/test-bathymetry.R |only tests/testthat/test-fetch-integration.R |only tests/testthat/test-fetch_core.R | 53 +++ tests/testthat/test-lake-sources-helpers.R |only tests/testthat/test-lake-sources-mocked.R |only tests/testthat/test-nhd-helpers.R |only tests/testthat/test-nhd-mocked.R |only tests/testthat/test-options.R | 2 tests/testthat/test-package-init.R |only tests/testthat/test-shiny-helpers.R |only tests/testthat/test-spatial-standards.R |only tests/testthat/test-weather-helpers.R |only tests/testthat/test-weather-mocked.R |only tests/testthat/testthat-problems.rds |only vignettes/getting-started.Rmd | 47 +- 56 files changed, 2024 insertions(+), 813 deletions(-)
Title: In-Line Documentation for R
Description: Generate your Rd documentation, 'NAMESPACE' file, and
collation field using specially formatted comments. Writing
documentation in-line with code makes it easier to keep your
documentation up-to-date as your requirements change. 'roxygen2' is
inspired by the 'Doxygen' system for C++.
Author: Hadley Wickham [aut, cre, cph] ,
Peter Danenberg [aut, cph],
Gabor Csardi [aut],
Manuel Eugster [aut, cph],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between roxygen2 versions 8.1.0 dated 2026-08-04 and 8.1.1 dated 2026-10-08
DESCRIPTION | 10 ++--- MD5 | 32 ++++++++-------- NEWS.md | 9 ++++ R/collate.R | 2 - R/namespace.R | 5 ++ R/object-from-call.R | 3 + R/rd-inherit.R | 5 +- R/rd-usage.R | 5 ++ R/tag-parser.R | 1 build/vignette.rds |binary man/update_collate.Rd | 2 - tests/testthat/test-markdown-code.R | 3 + tests/testthat/test-namespace.R | 19 +++++++-- tests/testthat/test-object-from-call.R | 11 +++++ tests/testthat/test-rd-include-rmd.R | 2 + tests/testthat/test-rd-inherit.R | 65 +++++++++++++++++++++++++++++++++ tests/testthat/test-rd-usage.R | 14 +++---- 17 files changed, 149 insertions(+), 39 deletions(-)
Title: Load 'Overture' Datasets as 'dbplyr' and 'sf'-Ready Data Frames
Description: An integrated R interface to the 'Overture' API
(<https://docs.overturemaps.org/>). Allows R users to return 'Overture' data as
'dbplyr' data frames or materialized 'sf' spatial data frames.
Author: Arthur Gailes [aut, cre, cph]
Maintainer: Arthur Gailes <agailes1@gmail.com>
Diff between overtureR versions 0.2.5 dated 2025-04-21 and 0.3.1 dated 2026-10-08
overtureR-0.2.5/overtureR/tests/testthat/test-bbox.R |only overtureR-0.2.5/overtureR/tests/testthat/test-class.R |only overtureR-0.2.5/overtureR/tests/testthat/test-mem_test.R |only overtureR-0.2.5/overtureR/tests/testthat/test-st_filter.R |only overtureR-0.3.1/overtureR/DESCRIPTION | 19 overtureR-0.3.1/overtureR/LICENSE | 4 overtureR-0.3.1/overtureR/MD5 | 91 + overtureR-0.3.1/overtureR/NAMESPACE | 8 overtureR-0.3.1/overtureR/NEWS.md | 204 +++ overtureR-0.3.1/overtureR/R/as_overture.R | 57 overtureR-0.3.1/overtureR/R/collect.R | 110 + overtureR-0.3.1/overtureR/R/get_theme_from_type.R | 80 - overtureR-0.3.1/overtureR/R/latest_overture_release.R |only overtureR-0.3.1/overtureR/R/open_curtain.R | 653 +++++++---- overtureR-0.3.1/overtureR/R/record_overture.R | 331 ++++- overtureR-0.3.1/overtureR/R/sf_as_dbplyr.R | 146 +- overtureR-0.3.1/overtureR/R/sf_methods.R |only overtureR-0.3.1/overtureR/R/stac.R |only overtureR-0.3.1/overtureR/R/stage_conn.R | 176 +- overtureR-0.3.1/overtureR/R/utils.R | 100 + overtureR-0.3.1/overtureR/README.md | 39 overtureR-0.3.1/overtureR/build/vignette.rds |binary overtureR-0.3.1/overtureR/inst/WORDLIST |only overtureR-0.3.1/overtureR/inst/skills |only overtureR-0.3.1/overtureR/man/as_overture.Rd | 33 overtureR-0.3.1/overtureR/man/clear_overture_cache.Rd |only overtureR-0.3.1/overtureR/man/collect.overture_call.Rd | 15 overtureR-0.3.1/overtureR/man/config_extensions.Rd | 28 overtureR-0.3.1/overtureR/man/figures/README-counties-1.png |binary overtureR-0.3.1/overtureR/man/figures/README-record-1.png |binary overtureR-0.3.1/overtureR/man/latest_overture_release.Rd |only overtureR-0.3.1/overtureR/man/open_curtain.Rd | 60 - overtureR-0.3.1/overtureR/man/overture_releases.Rd |only overtureR-0.3.1/overtureR/man/overture_sf_methods.Rd |only overtureR-0.3.1/overtureR/man/overture_types.Rd |only overtureR-0.3.1/overtureR/man/record_overture.Rd | 70 - overtureR-0.3.1/overtureR/man/sf_as_dbplyr.Rd | 15 overtureR-0.3.1/overtureR/man/stage_conn.Rd | 11 overtureR-0.3.1/overtureR/tests/testthat.R | 24 overtureR-0.3.1/overtureR/tests/testthat/_snaps |only overtureR-0.3.1/overtureR/tests/testthat/fixtures |only overtureR-0.3.1/overtureR/tests/testthat/helper.R |only overtureR-0.3.1/overtureR/tests/testthat/test-live.R |only overtureR-0.3.1/overtureR/tests/testthat/test-open_curtain.R |only overtureR-0.3.1/overtureR/tests/testthat/test-record.R | 272 +++- overtureR-0.3.1/overtureR/tests/testthat/test-sf_methods.R |only overtureR-0.3.1/overtureR/tests/testthat/test-sql_builders.R |only overtureR-0.3.1/overtureR/tests/testthat/test-stac.R |only overtureR-0.3.1/overtureR/tests/testthat/test-stage_conn.R |only 49 files changed, 1741 insertions(+), 805 deletions(-)
Title: Create Custom Research Compendiums
Description: Provides functions to create and manage research compendiums for data analysis. Research compendiums are a standard and intuitive folder structure for organizing the digital materials of a research project, which can significantly improve reproducibility. The package offers several compendium structure options that fit different research project as well as the ability of duplicating the folder structure of existing projects or implementing custom structures. It also simplifies the use of version control.
Author: Marcelo Araya-Salas [aut, cre] ,
Andrea Yure Arriaga Madrigal [aut]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
Diff between sketchy versions 1.0.5 dated 2025-01-16 and 1.0.6 dated 2026-10-08
DESCRIPTION | 20 +- MD5 | 61 ++++---- NAMESPACE | 8 - NEWS.md | 51 +++++++ R/add_to_gitignore.R | 85 ++++------- R/check_urls.R | 11 - R/compendiums-data.R | 8 - R/internal_functions.R | 43 +++++ R/load_packages.R | 156 +++++++++------------ R/make_compendium.R | 140 +++++++++++++++---- R/open_wd.R | 9 - R/print_skeleton.R | 211 ++++++----------------------- R/sketchy-package.R | 11 - R/spot_unused_files.R | 126 ++++++++++------- R/sysdata.rda |binary README.md | 341 ++++++++++++++++++++++------------------------- data/compendiums.rda |binary inst/CITATION | 22 ++- man/add_to_gitignore.Rd | 6 man/check_urls.Rd | 9 - man/compendiums.Rd | 11 - man/figures |only man/load_packages.Rd | 35 +++- man/make_compendium.Rd | 36 +++- man/open_wd.Rd | 4 man/print_skeleton.Rd | 15 -- man/sketchy-package.Rd | 7 man/spot_unused_files.Rd | 26 +-- tests |only 29 files changed, 764 insertions(+), 688 deletions(-)
Title: Weighted NPMLE for Recurrent Events with a Competing Terminal
Event
Description: Provides regression modeling and prediction for the marginal
mean of recurrent events in the presence of a competing terminal event
using the weighted nonparametric maximum likelihood estimator (wNPMLE)
of Bellach and Kosorok (2026)
<doi:10.48550/arXiv.2605.25934>. Two classes of transformation
models are implemented: Box-Cox transformation models and logarithmic
transformation models. These extend the proportional means model of
Ghosh and Lin (2002) <doi:10.17615/pt0g-y207> and the transformation
model framework of Zeng and Lin (2006)
<doi:10.1093/biomet/93.3.627>. Parameter estimation is performed using
automatic differentiation through the Template Model Builder (TMB)
framework. Standard errors are computed using sandwich variance
estimators that account for estimation of the inverse-probability
censoring weights following Bellach, Kosorok, Rüschendorf and Fine
(2019) <doi:10.1080/01621459.2017.1401540>.
Author: Anna Bellach [aut, cre]
Maintainer: Anna Bellach <abellach.biostat@gmail.com>
Diff between wnpmle versions 0.1.2 dated 2026-06-18 and 0.1.3 dated 2026-10-08
DESCRIPTION | 11 MD5 | 42 ++- NAMESPACE | 3 NEWS.md |only R/helpers.R | 92 ++++++- R/methods.R | 134 ++++++++-- R/readmission_prep.R |only R/wnpmle-package.R | 2 R/wnpmle_fit.R | 49 +-- build/partial.rdb |only inst/doc/wnpmle.R | 130 +++++----- inst/doc/wnpmle.Rmd | 482 +++++++++++++++++++++------------------ inst/doc/wnpmle.html | 432 ++++++++++++++++++++-------------- inst/extdata |only inst/tmb/corr_BC_tmb.cpp |only inst/tmb/corr_log_tmb.cpp |only inst/tmb/score_BC_tmb.cpp |only inst/tmb/score_log_tmb.cpp |only man/plot_loglik.Rd | 7 man/predict.wnpmle.Rd | 32 ++ man/readmission_prep.Rd |only man/summary.wnpmle.Rd | 8 man/wnpmle-package.Rd | 71 ++--- man/wnpmle_fit.Rd | 4 tests/testthat/test-wnpmle.R | 17 + vignettes/loglik_readmission.png |only vignettes/wnpmle.Rmd | 482 +++++++++++++++++++++------------------ 27 files changed, 1202 insertions(+), 796 deletions(-)
Title: A Unified Tidy Interface to R's Machine Learning Ecosystem
Description: Provides a unified tidyverse-compatible interface to R's machine
learning ecosystem - from data ingestion to model publishing. The tl_read()
family reads data from files ('CSV', 'Excel', 'Parquet', 'JSON'), databases
('SQLite', 'PostgreSQL', 'MySQL', 'BigQuery'), and cloud sources ('S3',
'GitHub', 'Kaggle'). The tl_model() function wraps established
implementations from 'glmnet', 'randomForest', 'xgboost', 'e1071', 'rpart',
'gbm', 'nnet', 'cluster', 'dbscan', and others with consistent function
signatures and tidy tibble output. Results flow into unified 'ggplot2'-based
visualization and optional formatted 'gt' tables via the tl_table() family.
The underlying algorithms are unchanged; 'tidylearn' simply makes them
easier to use together. Access raw model objects via the $fit slot for a
supervised method, or $fit$model for an unsupervised one.
Methods include random forests Breiman (2001) <doi:10.1023/A:1010933404324>,
LASSO regression Tibshirani (1996) <doi:10.1111/j.2517-6161 [...truncated...]
Author: Cesaire Tobias [aut, cre]
Maintainer: Cesaire Tobias <cesaire@sheetsolved.com>
Diff between tidylearn versions 0.5.0 dated 2026-09-02 and 0.6.0 dated 2026-10-08
DESCRIPTION | 16 MD5 | 476 +- NAMESPACE | 2 NEWS.md | 5235 ++++++++++++++++++++++-------- R/cloud-cost.R | 78 R/cloud-endpoint.R | 53 R/coefficients.R |only R/compute-advisor.R | 176 - R/compute-detection.R | 81 R/core.R | 621 +++ R/diagnostics.R | 455 +- R/integration.R | 818 +++- R/interactions.R | 910 ++++- R/metrics.R | 1683 ++++++--- R/model-selection.R | 521 ++ R/pipeline.R | 333 + R/preprocessing.R | 396 +- R/read-backends.R | 817 +++- R/read.R | 799 +++- R/supervised-classification.R | 462 +- R/supervised-deep-learning.R | 381 +- R/supervised-neural-networks.R | 897 ++--- R/supervised-regression.R | 367 +- R/supervised-regularization.R | 591 ++- R/supervised-svm.R | 201 - R/supervised-trees.R | 1916 +++++++--- R/supervised-xgboost.R | 971 ++++- R/tables.R | 544 ++- R/tuning.R | 1661 +++++++-- R/unsupervised-clustering.R | 178 - R/unsupervised-dbscan.R | 130 R/unsupervised-distance.R | 404 ++ R/unsupervised-hclust.R | 119 R/unsupervised-market-basket.R | 1319 ++++--- R/unsupervised-mds.R | 119 R/unsupervised-pca.R | 62 R/unsupervised-validation.R | 206 - R/utils.R | 810 ++++ R/visualization.R | 1174 +++++- R/workflows.R | 658 ++- README.md | 28 inst/doc/automl.R | 24 inst/doc/automl.Rmd | 71 inst/doc/automl.html | 141 inst/doc/compute-backends.Rmd | 11 inst/doc/compute-backends.html | 12 inst/doc/data-ingestion.R | 8 inst/doc/data-ingestion.Rmd | 8 inst/doc/data-ingestion.html | 24 inst/doc/diagnostics.R | 20 inst/doc/diagnostics.Rmd | 33 inst/doc/diagnostics.html | 192 - inst/doc/getting-started.R | 4 inst/doc/getting-started.Rmd | 14 inst/doc/getting-started.html | 38 inst/doc/integration-workflows.R | 2 inst/doc/integration-workflows.Rmd | 2 inst/doc/integration-workflows.html | 19 inst/doc/market-basket.R | 24 inst/doc/market-basket.Rmd | 50 inst/doc/market-basket.html | 429 -- inst/doc/reporting.R | 6 inst/doc/reporting.Rmd | 50 inst/doc/reporting.html | 1288 +++++-- inst/doc/supervised-learning.R | 8 inst/doc/supervised-learning.Rmd | 22 inst/doc/supervised-learning.html | 30 inst/doc/tuning-and-pipelines.R | 2 inst/doc/tuning-and-pipelines.Rmd | 17 inst/doc/tuning-and-pipelines.html | 57 inst/doc/unsupervised-learning.R | 8 inst/doc/unsupervised-learning.Rmd | 22 inst/doc/unsupervised-learning.html | 72 inst/examples/unified_workflow.R | 14 inst/security/threat-model.md | 22 man/calc_validation_metrics.Rd | 15 man/compare_clusterings.Rd | 3 man/create_cluster_dashboard.Rd | 11 man/figures/logo.png |binary man/filter_rules_by_item.Rd | 7 man/find_related_items.Rd | 7 man/inspect_rules.Rd | 14 man/optimal_hclust_k.Rd | 5 man/plot_cluster_comparison.Rd | 2 man/plot_clusters.Rd | 6 man/plot_dendrogram.Rd | 4 man/plot_knn_dist.Rd | 2 man/predict.tidylearn_model.Rd | 16 man/predict.tidylearn_stratified.Rd | 14 man/print.tidylearn_data.Rd | 1 man/recommend_products.Rd | 8 man/standardize_data.Rd | 6 man/suggest_eps.Rd | 5 man/summarize_rules.Rd | 3 man/tidy_apriori.Rd | 25 man/tidy_clara.Rd | 11 man/tidy_dbscan.Rd | 19 man/tidy_dist.Rd | 3 man/tidy_gap_stat.Rd | 10 man/tidy_gower.Rd | 4 man/tidy_hclust.Rd | 4 man/tidy_kmeans.Rd | 1 man/tidy_mds.Rd | 4 man/tidy_pam.Rd | 16 man/tidy_pca.Rd | 4 man/tidy_rules.Rd | 10 man/tidy_silhouette.Rd | 5 man/tidylearn-coefficients.Rd |only man/tidylearn-read.Rd | 24 man/tl_anomaly_aware.Rd | 23 man/tl_auto_interactions.Rd | 12 man/tl_auto_ml.Rd | 77 man/tl_calc_classification_metrics.Rd | 66 man/tl_calculate_pr_auc.Rd | 13 man/tl_check_assumptions.Rd | 16 man/tl_check_gpu.Rd | 16 man/tl_cloud_allow_host.Rd | 9 man/tl_coefficients.Rd |only man/tl_compare_cv.Rd | 39 man/tl_compare_pipeline_models.Rd | 4 man/tl_compute_advisor.Rd | 21 man/tl_cv.Rd | 27 man/tl_dashboard.Rd | 8 man/tl_default_param_grid.Rd | 23 man/tl_detect_outliers.Rd | 8 man/tl_diagnostic_dashboard.Rd | 4 man/tl_evaluate.Rd | 26 man/tl_explore.Rd | 13 man/tl_extract_importance.Rd | 3 man/tl_fit_boost.Rd | 14 man/tl_fit_deep.Rd | 11 man/tl_fit_elastic_net.Rd | 6 man/tl_fit_forest.Rd | 3 man/tl_fit_lasso.Rd | 6 man/tl_fit_nn.Rd | 4 man/tl_fit_regularized.Rd | 27 man/tl_fit_ridge.Rd | 6 man/tl_fit_svm.Rd | 5 man/tl_fit_tree.Rd | 4 man/tl_fit_xgboost.Rd | 15 man/tl_get_best_model.Rd | 10 man/tl_get_importance_regularized.Rd | 44 man/tl_interaction_effects.Rd | 31 man/tl_model.Rd | 99 man/tl_pipeline.Rd | 16 man/tl_plot_deep_architecture.Rd | 11 man/tl_plot_importance_comparison.Rd | 20 man/tl_plot_importance_regularized.Rd | 4 man/tl_plot_interaction.Rd | 34 man/tl_plot_model.Rd | 4 man/tl_plot_model_comparison.Rd | 7 man/tl_plot_partial_dependence.Rd | 7 man/tl_plot_svm_boundary.Rd | 10 man/tl_plot_tree.Rd | 2 man/tl_plot_tuning_results.Rd | 9 man/tl_plot_xgboost_importance.Rd | 16 man/tl_plot_xgboost_shap_dependence.Rd | 7 man/tl_plot_xgboost_shap_summary.Rd | 6 man/tl_plot_xgboost_tree.Rd | 9 man/tl_predict_xgboost.Rd | 5 man/tl_prepare_data.Rd | 34 man/tl_read.Rd | 52 man/tl_read_bigquery.Rd | 25 man/tl_read_csv.Rd | 7 man/tl_read_db.Rd | 13 man/tl_read_dir.Rd | 29 man/tl_read_excel.Rd | 11 man/tl_read_github.Rd | 32 man/tl_read_json.Rd | 24 man/tl_read_kaggle.Rd | 32 man/tl_read_mysql.Rd | 28 man/tl_read_parquet.Rd | 10 man/tl_read_postgres.Rd | 31 man/tl_read_rdata.Rd | 22 man/tl_read_rds.Rd | 17 man/tl_read_s3.Rd | 26 man/tl_read_sqlite.Rd | 12 man/tl_read_tsv.Rd | 7 man/tl_read_zip.Rd | 38 man/tl_reduce_dimensions.Rd | 13 man/tl_run_pipeline.Rd | 5 man/tl_semisupervised.Rd | 43 man/tl_split.Rd | 9 man/tl_step_selection.Rd | 13 man/tl_stratified_models.Rd | 27 man/tl_table.Rd | 2 man/tl_table_clusters.Rd | 7 man/tl_table_coefficients.Rd | 31 man/tl_table_comparison.Rd | 12 man/tl_table_confusion.Rd | 6 man/tl_table_importance.Rd | 2 man/tl_table_loadings.Rd | 2 man/tl_table_metrics.Rd | 5 man/tl_table_variance.Rd | 2 man/tl_test_interactions.Rd | 5 man/tl_test_model_difference.Rd | 12 man/tl_transfer_learning.Rd | 15 man/tl_tune_deep.Rd | 28 man/tl_tune_grid.Rd | 154 man/tl_tune_nn.Rd | 18 man/tl_tune_random.Rd | 45 man/tl_tune_xgboost.Rd | 47 man/tl_xgboost_shap.Rd | 20 man/visualize_rules.Rd | 19 tests/testthat/test-cloud-cost.R | 72 tests/testthat/test-cloud-guards.R | 46 tests/testthat/test-coefficients.R |only tests/testthat/test-compute-advisor.R | 146 tests/testthat/test-compute-detection.R | 129 tests/testthat/test-compute-routing.R | 27 tests/testthat/test-core.R | 883 +++++ tests/testthat/test-degenerate-specs.R | 8 tests/testthat/test-diagnostics.R | 220 + tests/testthat/test-examples.R | 68 tests/testthat/test-integration.R | 772 ++++ tests/testthat/test-interactions.R |only tests/testthat/test-leakage-and-guards.R | 14 tests/testthat/test-metrics-correctness.R | 540 ++- tests/testthat/test-metrics.R | 379 ++ tests/testthat/test-pipeline.R | 501 ++ tests/testthat/test-predict-contract.R | 206 + tests/testthat/test-preprocessing.R | 437 ++ tests/testthat/test-read.R | 1332 +++++++ tests/testthat/test-supervised-backends.R |only tests/testthat/test-supervised-predict.R | 2 tests/testthat/test-supervised.R | 925 +++++ tests/testthat/test-tables.R | 390 ++ tests/testthat/test-tuning.R | 1650 +++++++++ tests/testthat/test-unsupervised.R | 1434 ++++++++ tests/testthat/test-visualization.R | 884 +++++ tests/testthat/test-workflows.R | 289 + vignettes/automl.Rmd | 71 vignettes/compute-backends.Rmd | 11 vignettes/data-ingestion.Rmd | 8 vignettes/diagnostics.Rmd | 33 vignettes/getting-started.Rmd | 14 vignettes/integration-workflows.Rmd | 2 vignettes/market-basket.Rmd | 50 vignettes/reporting.Rmd | 50 vignettes/supervised-learning.Rmd | 22 vignettes/tuning-and-pipelines.Rmd | 17 vignettes/unsupervised-learning.Rmd | 22 242 files changed, 34190 insertions(+), 8997 deletions(-)
Title: External Control Borrowing for Rare Disease Trials
Description: Implements causal inference methods for incorporating external
control data into randomized controlled trials (RCTs) with longitudinal
outcomes. Provides an analysis module supporting weighting-based methods
such as inverse probability weighting (IPW) and augmented inverse
probability weighting (AIPW), difference-in-differences (DID), and
synthetic control approaches for borrowing external control information,
as well as a simulation module for generating trial and external control
data, evaluating estimator performance via Monte Carlo studies, and
conducting power analyses for sample size determination. Methods are
based on Zhou et al. (2025) <doi:10.1093/jrsssa/qnae075> and
Zhou et al. (2024) <doi:10.1080/10543406.2024.2330209>.
Author: Lei Shi [aut],
Matt Secrest [cre, aut] ,
Herbert Pang [aut],
Chen Chen [aut],
Jiawen Zhu [aut],
Genentech, Inc. [cph]
Maintainer: Matt Secrest <secrmatt@gmail.com>
Diff between rdborrow versions 0.0.4.2 dated 2026-10-01 and 0.0.5.0 dated 2026-10-08
DESCRIPTION | 15 - MD5 | 152 ++++++------ NAMESPACE | 4 NEWS.md | 42 +++ R/analysis_OLE_class.R | 30 +- R/analysis_class.R | 27 +- R/analysis_primary_class.R | 25 + R/data.R | 41 +++ R/did_ec_aipw.R | 64 ++++- R/did_ec_ipw.R | 43 ++- R/did_ec_or.R | 70 ++++- R/ec_aipw.R | 111 +++++--- R/ec_ipw.R | 56 +++- R/method_class.R | 238 ++++++++++++++++++ R/package.R | 4 R/rdborrow-package.R | 7 R/run_analysis.R | 27 +- R/run_simulation.R | 14 - R/scm.R | 205 +++++++++++----- R/simulate_outcome_from_model.R | 1 R/simulate_trial.R | 2 R/simulation_class.R | 29 +- README.md | 4 data/SyntheticDataII.rda |only inst/WORDLIST | 13 + inst/doc/OLE_analysis_workflow.R | 6 inst/doc/OLE_analysis_workflow.Rmd | 14 + inst/doc/OLE_analysis_workflow.html | 49 ++- inst/doc/OLE_simulation_workflow.html | 4 inst/doc/introduction.Rmd | 16 - inst/doc/introduction.html | 24 + inst/doc/primary_analysis_workflow.R | 2 inst/doc/primary_analysis_workflow.Rmd | 12 inst/doc/primary_analysis_workflow.html | 26 +- inst/doc/primary_simulation_workflow.R | 4 inst/doc/primary_simulation_workflow.Rmd | 8 inst/doc/primary_simulation_workflow.html | 24 - man/SyntheticData.Rd | 22 + man/SyntheticDataII.Rd |only man/aaa-rdborrow-package.Rd | 7 man/did_ec_aipw.Rd | 36 ++ man/did_ec_ipw.Rd | 28 +- man/did_ec_or.Rd | 25 + man/ec_aipw.Rd | 48 ++- man/ec_ipw.Rd | 24 + man/estimate.Rd | 7 man/run_analysis.Rd | 25 + man/run_simulation.Rd | 2 man/scm.Rd | 33 ++ man/setup_analysis_OLE.Rd | 29 +- man/setup_analysis_primary.Rd | 30 +- man/setup_simulation_OLE.Rd | 10 man/setup_simulation_primary.Rd | 7 man/simulation_OLE_obj-class.Rd | 2 man/simulation_primary_obj-class.Rd | 2 tests/testthat/helper-analysis.R |only tests/testthat/helper-independent.R |only tests/testthat/helper-ole.R |only tests/testthat/test-analysis_OLE_class.R | 13 + tests/testthat/test-analysis_class.R | 278 ++++++++++++++++++++++ tests/testthat/test-analysis_primary_class.R | 6 tests/testthat/test-data.R |only tests/testthat/test-did_ec_aipw.R |only tests/testthat/test-did_ec_ipw.R |only tests/testthat/test-did_ec_or.R |only tests/testthat/test-ec_aipw.R |only tests/testthat/test-ec_ipw.R |only tests/testthat/test-full_pipeline_did_ec_aipw.R | 5 tests/testthat/test-full_pipeline_did_ec_ipw.R | 5 tests/testthat/test-full_pipeline_did_ec_or.R | 3 tests/testthat/test-full_pipeline_ec_aipw.R | 8 tests/testthat/test-full_pipeline_ec_ipw.R | 6 tests/testthat/test-full_pipeline_scm.R | 3 tests/testthat/test-method_class.R | 163 ++++++++++++ tests/testthat/test-run_analysis.R | 226 +++++++++++++++++ tests/testthat/test-run_simulation.R | 46 +++ tests/testthat/test-scm.R |only tests/testthat/test-simulate_outcome_from_model.R | 11 tests/testthat/test-simulation_class.R | 71 +++++ vignettes/OLE_analysis_workflow.Rmd | 14 + vignettes/introduction.Rmd | 16 - vignettes/primary_analysis_workflow.Rmd | 12 vignettes/primary_simulation_workflow.Rmd | 8 83 files changed, 2160 insertions(+), 484 deletions(-)
Title: Partial Dependence Plots
Description: A general framework for constructing partial dependence (i.e.,
marginal effect) plots from various types of machine learning models
in R.
Author: Brandon M. Greenwell [aut, cre]
Maintainer: Brandon M. Greenwell <greenwell.brandon@gmail.com>
Diff between pdp versions 0.8.3 dated 2026-01-23 and 0.10.0 dated 2026-10-08
pdp-0.10.0/pdp/DESCRIPTION | 30 +- pdp-0.10.0/pdp/MD5 | 145 +++------- pdp-0.10.0/pdp/NAMESPACE | 29 -- pdp-0.10.0/pdp/NEWS.md | 142 ++++++++++ pdp-0.10.0/pdp/R/data.R | 90 +++--- pdp-0.10.0/pdp/R/exemplar.R | 40 ++ pdp-0.10.0/pdp/R/get_predictions.R | 162 +++--------- pdp-0.10.0/pdp/R/get_task.R | 13 pdp-0.10.0/pdp/R/get_training_data.R | 6 pdp-0.10.0/pdp/R/pardep.R | 209 +++++++-------- pdp-0.10.0/pdp/R/partial.R | 323 ++++++++++++++---------- pdp-0.10.0/pdp/R/pdp-package.R | 22 - pdp-0.10.0/pdp/R/plot.R |only pdp-0.10.0/pdp/R/plotPartial.R | 172 ++++++------ pdp-0.10.0/pdp/R/pred_grid.R | 17 - pdp-0.10.0/pdp/R/utils.R | 31 +- pdp-0.10.0/pdp/README.md | 134 +++++---- pdp-0.10.0/pdp/build/vignette.rds |binary pdp-0.10.0/pdp/data/pima.RData |binary pdp-0.10.0/pdp/inst/doc/faster-pdp.R |only pdp-0.10.0/pdp/inst/doc/faster-pdp.Rmd |only pdp-0.10.0/pdp/inst/doc/faster-pdp.html |only pdp-0.10.0/pdp/inst/doc/ice-curves.R |only pdp-0.10.0/pdp/inst/doc/ice-curves.Rmd |only pdp-0.10.0/pdp/inst/doc/ice-curves.html |only pdp-0.10.0/pdp/inst/doc/pdp.R |only pdp-0.10.0/pdp/inst/doc/pdp.Rmd |only pdp-0.10.0/pdp/inst/doc/pdp.html |only pdp-0.10.0/pdp/inst/tinytest/test_batch_size.R |only pdp-0.10.0/pdp/inst/tinytest/test_issues.R |only pdp-0.10.0/pdp/inst/tinytest/test_pkg_MASS.R | 16 - pdp-0.10.0/pdp/inst/tinytest/test_pkg_gbm.R |only pdp-0.10.0/pdp/inst/tinytest/test_pkg_party.R | 24 - pdp-0.10.0/pdp/inst/tinytest/test_pkg_stats.R | 16 - pdp-0.10.0/pdp/inst/tinytest/test_pkg_xgboost.R | 18 - pdp-0.10.0/pdp/inst/tinytest/test_plot.R |only pdp-0.10.0/pdp/man/boston.Rd | 36 +- pdp-0.10.0/pdp/man/exemplar.Rd | 21 + pdp-0.10.0/pdp/man/partial.Rd | 90 ++++-- pdp-0.10.0/pdp/man/pdp-package.Rd | 21 - pdp-0.10.0/pdp/man/pima.Rd | 51 ++- pdp-0.10.0/pdp/man/plot.partial.Rd |only pdp-0.10.0/pdp/man/plotPartial.Rd | 24 + pdp-0.10.0/pdp/man/trellis.last.object.Rd | 2 pdp-0.10.0/pdp/src/PartialGBM.cpp | 14 - pdp-0.10.0/pdp/vignettes/faster-pdp.Rmd |only pdp-0.10.0/pdp/vignettes/ice-curves.Rmd |only pdp-0.10.0/pdp/vignettes/pdp.Rmd |only pdp-0.8.3/pdp/R/autoplot.R |only pdp-0.8.3/pdp/R/topPredictors.R |only pdp-0.8.3/pdp/inst/doc/pdp-approximate.Rnw |only pdp-0.8.3/pdp/inst/doc/pdp-approximate.pdf |only pdp-0.8.3/pdp/inst/doc/pdp-intro.Rnw |only pdp-0.8.3/pdp/inst/doc/pdp-intro.pdf |only pdp-0.8.3/pdp/inst/doc/pdp-link-function.Rnw |only pdp-0.8.3/pdp/inst/doc/pdp-link-function.pdf |only pdp-0.8.3/pdp/man/autoplot.partial.Rd |only pdp-0.8.3/pdp/man/topPredictors.Rd |only pdp-0.8.3/pdp/vignettes/pdf |only pdp-0.8.3/pdp/vignettes/pdp-approximate.Rnw |only pdp-0.8.3/pdp/vignettes/pdp-intro.Rnw |only pdp-0.8.3/pdp/vignettes/pdp-link-function.Rnw |only pdp-0.8.3/pdp/vignettes/rmd |only 63 files changed, 1035 insertions(+), 863 deletions(-)
Title: Download Crypto Currency Data from 'CoinMarketCap' and
'CoinGecko'
Description: Retrieves crypto currency information and historical prices as well as information on the exchanges they are listed on. Historical data contains daily open, high, low and close values for all crypto currencies. The package draws on two complementary sources: 'CoinMarketCap' <https://coinmarketcap.com> (primary, via the 'crypto_*' functions) and 'CoinGecko' <https://www.coingecko.com> (secondary, via the 'cg_*' functions). Both sources are queried without an 'API' key; the two function families return tibbles with identical column conventions so downstream pipelines work on either source.
Author: Sebastian Stoeckl [aut, cre] ,
Jesse Vent [ctb]
Maintainer: Sebastian Stoeckl <sebastian.stoeckl@uni.li>
Diff between crypto2 versions 2.0.5 dated 2025-09-11 and 3.0.0 dated 2026-10-08
DESCRIPTION | 21 MD5 | 78 + NAMESPACE | 26 NEWS.md | 291 ++++-- R/cg_daily.R |only R/cg_extras.R |only R/cg_history.R |only R/cg_info.R |only R/cg_list.R |only R/cg_listings.R |only R/cg_recover.R |only R/crypto_crosswalk.R |only R/crypto_global_quotes.R | 2 R/crypto_history.R | 65 + R/crypto_info.R | 67 - R/crypto_listings.R | 444 +++++----- R/globals.R | 7 README.md | 231 ++--- build |only inst/CITATION | 6 inst/WORDLIST | 56 + inst/doc |only inst/extdata |only man/cg_history.Rd |only man/cg_history_by_id.Rd |only man/cg_id_mapping.Rd |only man/cg_info.Rd |only man/cg_list.Rd |only man/cg_listings.Rd |only man/crypto_crosswalk.Rd |only man/crypto_listings.Rd | 244 ++--- man/exchange_info.Rd | 118 +- man/safeFromJSON.Rd | 36 tests/testthat/helper-cg.R |only tests/testthat/test-cg-anomalies.R |only tests/testthat/test-cg-daily.R |only tests/testthat/test-cg-endpoints.R |only tests/testthat/test-cg-helpers.R |only tests/testthat/test-cg-listings.R |only tests/testthat/test-cg-mapping.R |only tests/testthat/test-cg-recover.R |only tests/testthat/test-cg-schema.R |only tests/testthat/test-cg-vs-cmc.R |only tests/testthat/test-crosswalk.R |only tests/testthat/test-crypto-info.R | 9 tests/testthat/test-listings.R | 145 ++- tests/testthat/test_data/crypto_history_reference.rds |binary tests/testthat/test_data/d9e71308b8f7d2956f6151a2ebf9423d.json | 2 tests/testthat/test_data/ex_info_reference.rds |binary tests/testthat/test_data/fcce7d762bbee082f65c377f184cd541.json | 2 tools |only vignettes |only 52 files changed, 1126 insertions(+), 724 deletions(-)
Title: Construct and Compare scGRN from Single-Cell Transcriptomic Data
Description: A workflow based on machine learning methods to construct and compare single-cell gene regulatory networks (scGRN) using single-cell RNA-seq (scRNA-seq) data collected from different conditions. Uses principal component regression, tensor decomposition, and manifold alignment, to accurately identify even subtly shifted gene expression programs. See <doi:10.1016/j.patter.2020.100139> for more details.
Author: Daniel Osorio [aut, cre] ,
Yan Zhong [aut, ctb],
Guanxun Li [aut, ctb],
Jianhua Huang [aut, ctb],
James Cai [aut, ctb, ths]
Maintainer: Daniel Osorio <dcosorioh@gmail.com>
Diff between scTenifoldNet versions 1.4 dated 2026-08-04 and 1.4.3 dated 2026-10-08
scTenifoldNet-1.4.3/scTenifoldNet/DESCRIPTION | 13 scTenifoldNet-1.4.3/scTenifoldNet/MD5 | 40 scTenifoldNet-1.4.3/scTenifoldNet/NAMESPACE | 14 scTenifoldNet-1.4.3/scTenifoldNet/R/checkMemory.R |only scTenifoldNet-1.4.3/scTenifoldNet/R/dRegulation.R | 16 scTenifoldNet-1.4.3/scTenifoldNet/R/makeNetworks.R | 4 scTenifoldNet-1.4.3/scTenifoldNet/R/pcNet.R | 774 ++++++---- scTenifoldNet-1.4.3/scTenifoldNet/R/restoreSeed.R |only scTenifoldNet-1.4.3/scTenifoldNet/R/scTenifoldNet.R | 32 scTenifoldNet-1.4.3/scTenifoldNet/R/tensorDecomposition.R | 11 scTenifoldNet-1.4.3/scTenifoldNet/README.md | 50 scTenifoldNet-1.4.3/scTenifoldNet/man/checkMemory.Rd |only scTenifoldNet-1.4.3/scTenifoldNet/man/dRegulation.Rd | 6 scTenifoldNet-1.4.3/scTenifoldNet/man/makeNetworks.Rd | 2 scTenifoldNet-1.4.3/scTenifoldNet/man/pcNet.Rd | 119 - scTenifoldNet-1.4.3/scTenifoldNet/man/scTenifoldNet.Rd | 7 scTenifoldNet-1.4.3/scTenifoldNet/man/tensorDecomposition.Rd | 5 scTenifoldNet-1.4.3/scTenifoldNet/tests/testthat/test-checkMemory.R |only scTenifoldNet-1.4.3/scTenifoldNet/tests/testthat/test-dRegulation.R |only scTenifoldNet-1.4.3/scTenifoldNet/tests/testthat/test-pcNet.R | 38 scTenifoldNet-1.4/scTenifoldNet/R/RcppExports.R |only scTenifoldNet-1.4/scTenifoldNet/man/pcNetCoreRcpp.Rd |only scTenifoldNet-1.4/scTenifoldNet/src |only scTenifoldNet-1.4/scTenifoldNet/tests/testthat/test-pcNetRcpp.R |only 24 files changed, 727 insertions(+), 404 deletions(-)
Title: SQL Parsing, Analysis and Dialect Translation
Description: Parse, tokenize, validate, format, analyze and translate SQL
between more than 30 dialects ('PostgreSQL', 'MySQL', 'BigQuery',
'Snowflake', 'DuckDB', 'T-SQL', and others) using the 'polyglot-sql'
Rust crate <https://github.com/tobilg/polyglot>, a Rust port of the
'SQLGlot' 'Python' library. All processing happens locally in the R
session; no database connection, 'Python' runtime or external service
is required. Includes column-level lineage, structural query
analysis, query optimization, 'AST' diffing and 'OpenLineage' facet
generation.
Author: Andre Leite [aut, cre] ,
Marcos Wasiliew [aut] ,
Hugo Vasconcelos [aut] ,
Carlos Amorim [aut] ,
Diogo Bezerra [aut] ,
Julia Nascimento Barreto [aut] ,
Tobias Mueller [cph] ),
Toby Mao [cph] ,
The authors of the vendored Rust dependencies [cph]
Maintainer: Andre Leite <leite@castlab.org>
Diff between polyglotSQL versions 0.1.1 dated 2026-09-27 and 0.1.2 dated 2026-10-08
DESCRIPTION | 21 +++++++---- MD5 | 19 +++++----- NEWS.md | 18 ++++++++++ README.md | 2 + inst/doc/getting-started.html | 2 - man/polyglotSQL-package.Rd | 7 ++- src/Makevars.in | 3 + src/entrypoint.c | 64 ++++++++++++++++++++++++++++++++++++ src/rust/Cargo.toml | 9 +++-- tests/testthat/test-compiled-code.R |only tools/config.R | 48 ++++++++++++++++++++++++++- 11 files changed, 168 insertions(+), 25 deletions(-)
Title: Generalized Latent Markov Models
Description: Latent Markov models for longitudinal continuous and categorical data. See Bartolucci, Pandolfi, Pennoni (2017)<doi:10.18637/jss.v081.i04>.
Author: Francesco Bartolucci [aut, cre],
Silvia Pandolfi [aut],
Fulvia Pennoni [aut],
Luca Brusa [ctb],
Alessio Farcomeni [ctb],
Alessio Serafini [ctb]
Maintainer: Francesco Bartolucci <francesco.bartolucci@unipg.it>
Diff between LMest versions 3.2.8 dated 2026-01-14 and 4.0.0 dated 2026-10-08
DESCRIPTION | 16 +++-- MD5 | 72 ++++++++++++++++--------- NAMESPACE | 24 ++------ R/backward_Multinom.R |only R/comp_PI.R |only R/comp_Piv.R |only R/comp_sc_PI.R |only R/comp_sc_Piv.R |only R/design_matrices.R |only R/est_LM_cat_multinom.R |only R/forward_Multinom.R |only R/mc_multinom.R |only R/print.R | 26 +++++++++ R/summary.LM_cat_multinom.R |only R/summary.mc_multinom.R |only build/vignette.rds |binary inst/doc/vignetteLMest.R | 32 ++++++++++- inst/doc/vignetteLMest.Rmd | 69 ++++++++++++++++++------ inst/doc/vignetteLMest.html | 122 ++++++++++++++++++++++++++++---------------- man/LMbasic-class.Rd | 2 man/LMest-package.Rd | 8 +- man/RLMSlong.Rd | 2 man/bootstrap.Rd | 6 +- man/data_employment_sim.Rd | 2 man/data_heart_sim.Rd | 8 +- man/data_market_sim.Rd | 6 +- man/design_matrices.Rd |only man/draw.Rd | 6 -- man/est_LM_cat_multinom.Rd |only man/est_lm_cov_latent.Rd | 6 +- man/est_lm_cov_manifest.Rd | 3 - man/lmest.Rd | 8 +- man/lmestCont.Rd | 8 +- man/lmestMc.Rd | 10 +-- man/lmestSearch.Rd | 4 - man/mc_multinom.Rd |only man/print.Rd | 9 ++- man/summary.Rd | 6 +- src/LMest_init.c | 38 +++++++++---- src/backward.f |only src/backward_multinom.f |only src/comp_PI.f |only src/comp_Piv.f |only src/comp_sc_PI.f |only src/comp_sc_Piv.f |only src/forward.f |only src/forward_multinom.f |only vignettes/vignetteLMest.Rmd | 69 ++++++++++++++++++------ 48 files changed, 378 insertions(+), 184 deletions(-)
Title: Fast Survival Analysis and Simulation for Clinical Trials
Description: Provides fast alternatives to standard survival analysis functions
in the 'survival' package, together with tools for time-to-event trial
simulation and sequential analysis. The estimation and testing functions
cover a single-time-point Kaplan-Meier estimator (survfit_fast()), log-rank
tests including weighted and stratified variants (survdiff_fast()), a
closed-form hazard ratio estimator based on the Pike-Halley Estimator method
(coxph_fast()), restricted mean survival time (rmst_fast()), window mean
survival time (wmst_fast()), milestone survival comparison
(milestone_fast()), median survival time (medsurv_fast()), the max-combo
test (maxcombo_fast()), the robust modestly-weighted log-rank test
(rmw_fast()), the weighted Kaplan-Meier (Pepe-Fleming) test (wkm_fast()),
the average hazard with survival weight (ahsw_fast()), and the
Kalbfleisch-Prentice average hazard ratio (ahr_fast()). The simulation
layer generates individual patient data (simdata_fast()), determines the
calendar time [...truncated...]
Author: Gosuke Homma [aut, cre]
Maintainer: Gosuke Homma <my.name.is.gosuke@gmail.com>
Diff between FastSurvival versions 1.0.0 dated 2026-09-29 and 1.1.0 dated 2026-10-08
DESCRIPTION | 18 - MD5 | 230 +++++++++++-------- NAMESPACE | 2 NEWS.md | 237 ++++++++++++++++++++ R/FastSurvival-package.R | 17 + R/RcppExports.R | 12 - R/ahr_fast.R | 7 R/ahsw_fast.R | 7 R/analysis_fast.R | 205 +++++++++++++++-- R/check_presorted.R |only R/check_time_event.R | 7 R/coxph_fast.R | 40 +-- R/cutoff_fast.R |only R/kmcurve_fast.R | 4 R/maxcombo_fast.R | 10 R/medsurv_fast.R | 2 R/milestone_fast.R | 17 + R/pairwise_fast.R | 144 +++++------- R/rmst_fast.R | 8 R/rmw_fast.R | 2 R/sim_key.R |only R/simdata_fast.R | 149 +++++++++++- R/simdata_fast_id_sub.R |only R/simsummary_fast.R | 4 R/survdiff_fast.R | 7 R/survfit_fast.R | 10 R/switch_fast.R |only R/wkm_fast.R | 2 R/wmst_fast.R | 2 README.md | 108 ++++++--- build/vignette.rds |binary inst/WORDLIST | 20 + inst/doc/FastSurvival.R | 2 inst/doc/FastSurvival.Rmd | 28 +- inst/doc/FastSurvival.html | 128 +++++------ inst/doc/compare-logrank-rmst.R | 8 inst/doc/compare-logrank-rmst.Rmd | 12 - inst/doc/compare-logrank-rmst.html | 30 +- inst/doc/correlated-pfs-os-gsd.R | 110 +++------ inst/doc/correlated-pfs-os-gsd.Rmd | 173 ++++++-------- inst/doc/correlated-pfs-os-gsd.html | 267 +++++++++++------------ inst/doc/external-data.R |only inst/doc/external-data.Rmd |only inst/doc/external-data.html |only inst/doc/group-sequential-design.R | 199 ++++++++++------- inst/doc/group-sequential-design.Rmd | 233 +++++++++++--------- inst/doc/group-sequential-design.html | 325 ++++++++++++++++------------ inst/doc/investigate-freidlin-and-korn.R | 39 +-- inst/doc/investigate-freidlin-and-korn.Rmd | 61 ++--- inst/doc/investigate-freidlin-and-korn.html | 148 ++++++------ inst/doc/mrct-regional-consistency.R | 3 inst/doc/mrct-regional-consistency.Rmd | 22 - inst/doc/mrct-regional-consistency.html | 157 ++++++------- inst/doc/multi-arm-pairwise.R | 30 +- inst/doc/multi-arm-pairwise.Rmd | 54 +++- inst/doc/multi-arm-pairwise.html | 76 ++++-- inst/doc/speed-comparison.Rmd | 48 +++- inst/doc/speed-comparison.html | 59 ++++- inst/doc/treatment-switching.R |only inst/doc/treatment-switching.Rmd |only inst/doc/treatment-switching.html |only inst/doc/validation.R | 42 +++ inst/doc/validation.Rmd | 135 +++++++++-- inst/doc/validation.html | 187 +++++++++++----- man/FastSurvival-package.Rd | 17 + man/ahr_fast.Rd | 3 man/ahsw_fast.Rd | 8 man/analysis_fast.Rd | 95 ++++++-- man/coxph_fast.Rd | 37 +-- man/cutoff_fast.Rd |only man/maxcombo_fast.Rd | 11 man/medsurv_fast.Rd | 3 man/milestone_fast.Rd | 8 man/pairwise_fast.Rd | 36 ++- man/rmst_fast.Rd | 6 man/rmw_fast.Rd | 3 man/simdata_fast.Rd | 111 ++++++++- man/simsummary_fast.Rd | 4 man/survdiff_fast.Rd | 5 man/survfit_fast.Rd | 10 man/switch_fast.Rd |only man/wkm_fast.Rd | 3 man/wmst_fast.Rd | 3 src/RcppExports.cpp | 58 ++++ src/analysis_loop_core.cpp | 19 + src/cutoff_core.cpp |only src/simdata_core_full.cpp | 29 ++ src/simdata_core_id.cpp | 299 +++++++++++++++++++++++++ src/wkm_core.cpp | 16 + tests/testthat/test-ahr_fast.R | 12 + tests/testthat/test-ahsw_fast.R | 7 tests/testthat/test-analysis_fast.R | 158 +++++++++++++ tests/testthat/test-coxph_fast.R | 9 tests/testthat/test-cutoff_fast.R |only tests/testthat/test-gen_scenario_fast.R |only tests/testthat/test-kmcurve_fast.R | 7 tests/testthat/test-maxcombo_fast.R | 7 tests/testthat/test-medsurv_fast.R | 7 tests/testthat/test-milestone_fast.R | 38 +++ tests/testthat/test-pairwise_fast.R | 71 +++++- tests/testthat/test-plot.scenario_fast.R |only tests/testthat/test-print.ahr_fast.R |only tests/testthat/test-print.ahsw_fast.R |only tests/testthat/test-print.maxcombo_fast.R |only tests/testthat/test-print.medsurv_fast.R |only tests/testthat/test-print.rmst_fast.R |only tests/testthat/test-print.rmw_fast.R |only tests/testthat/test-print.scenario_fast.R |only tests/testthat/test-print.survfit_fast.R |only tests/testthat/test-print.wkm_fast.R |only tests/testthat/test-print.wmst_fast.R |only tests/testthat/test-rmst_fast.R | 8 tests/testthat/test-rmw_fast.R | 7 tests/testthat/test-simdata_fast.R | 91 +++++++ tests/testthat/test-simdata_fast_id.R | 144 ++++++++++++ tests/testthat/test-survdiff_fast.R | 23 + tests/testthat/test-survfit_fast.R | 5 tests/testthat/test-switch_fast.R |only tests/testthat/test-wkm_fast.R | 61 ++++- tests/testthat/test-wmst_fast.R | 7 vignettes/FastSurvival.Rmd | 28 +- vignettes/compare-logrank-rmst.Rmd | 12 - vignettes/correlated-pfs-os-gsd.Rmd | 173 ++++++-------- vignettes/external-data.Rmd |only vignettes/group-sequential-design.Rmd | 233 +++++++++++--------- vignettes/investigate-freidlin-and-korn.Rmd | 61 ++--- vignettes/mrct-regional-consistency.Rmd | 22 - vignettes/multi-arm-pairwise.Rmd | 54 +++- vignettes/speed-comparison.Rmd | 48 +++- vignettes/treatment-switching.Rmd |only vignettes/validation.Rmd | 135 +++++++++-- 131 files changed, 4261 insertions(+), 1798 deletions(-)
Title: Read and Manipulate Video Subtitles
Description: A collection of functions to read, write and manipulate video
subtitles. Supported formats include 'srt', 'subrip', 'sub', 'subviewer',
'microdvd', 'ssa', 'ass', 'substation', 'vtt', and 'webvtt'.
Author: Francois Keck [aut, cre, cph] ,
Bob Rudis [ctb] ,
Alban Sagouis [ctb]
Maintainer: Francois Keck <francois.keck@gmail.com>
Diff between subtools versions 1.1.0 dated 2026-03-24 and 1.1.1 dated 2026-10-08
DESCRIPTION | 8 +-- MD5 | 26 +++++------ NEWS.md | 6 ++ R/read_subtitles.R | 58 +++++++++++++++++++----- R/utils_regexes.R | 42 ++++++++++++++++++ README.md | 77 +++++++++++++++++++++++---------- build/vignette.rds |binary inst/doc/subtools-text-analysis.html | 6 +- man/as_subtitle.Rd | 2 man/read_subtitles.Rd | 12 +++-- tests/testthat/_snaps/unnest_tokens.md | 2 tests/testthat/test_read.R | 16 ++++++ tests/testthat/test_unnest_tokens.R | 2 tests/testthat/test_utils_regex.R | 2 14 files changed, 197 insertions(+), 62 deletions(-)
Title: Tidy Tools for Joinpoint Regression Models
Description: Provides tools to fit joinpoint regression models with a log-linear specification by levels of one or two categorical variable(s) using the grid-search method. It includes functions to estimate the Annual Percent Change (APC) and the Average Annual Percent Change (AAPC), along with their 95% confidence intervals, and to generate formatted summary tables and plots of results.
Author: Tamara Ricardo [aut, cre]
Maintainer: Tamara Ricardo <tamararicardo83@gmail.com>
Diff between joinpointR versions 1.1.0 dated 2026-07-20 and 2.0.0 dated 2026-10-08
joinpointR-1.1.0/joinpointR/R/as_ft_jp.R |only joinpointR-1.1.0/joinpointR/R/get_aapc.R |only joinpointR-1.1.0/joinpointR/R/get_apc.R |only joinpointR-1.1.0/joinpointR/R/model_jp.R |only joinpointR-1.1.0/joinpointR/R/summary_jp.R |only joinpointR-1.1.0/joinpointR/R/utils.R |only joinpointR-1.1.0/joinpointR/inst/doc/introduction.R |only joinpointR-1.1.0/joinpointR/inst/doc/introduction.Rmd |only joinpointR-1.1.0/joinpointR/inst/doc/introduction.html |only joinpointR-1.1.0/joinpointR/man/get_aapc.Rd |only joinpointR-1.1.0/joinpointR/man/get_apc.Rd |only joinpointR-1.1.0/joinpointR/man/jp_to_ft.Rd |only joinpointR-1.1.0/joinpointR/man/summary_jp.Rd |only joinpointR-1.1.0/joinpointR/vignettes/introduction.Rmd |only joinpointR-2.0.0/joinpointR/DESCRIPTION | 27 joinpointR-2.0.0/joinpointR/LICENSE | 4 joinpointR-2.0.0/joinpointR/MD5 | 61 - joinpointR-2.0.0/joinpointR/NAMESPACE | 32 joinpointR-2.0.0/joinpointR/NEWS.md | 46 - joinpointR-2.0.0/joinpointR/R/bic_jp.R |only joinpointR-2.0.0/joinpointR/R/clean_jp_data.R |only joinpointR-2.0.0/joinpointR/R/get_summary.R |only joinpointR-2.0.0/joinpointR/R/gg_jpoint.R | 600 ++++++++++------- joinpointR-2.0.0/joinpointR/R/globals.R | 2 joinpointR-2.0.0/joinpointR/R/hiv_data.R | 22 joinpointR-2.0.0/joinpointR/R/model_jp_grid.R |only joinpointR-2.0.0/joinpointR/R/plot_cbpal.R |only joinpointR-2.0.0/joinpointR/R/scale_cbpal_color.R |only joinpointR-2.0.0/joinpointR/R/sysdata.rda |only joinpointR-2.0.0/joinpointR/README.md | 178 ++--- joinpointR-2.0.0/joinpointR/build/vignette.rds |binary joinpointR-2.0.0/joinpointR/data/hiv_data.rda |binary joinpointR-2.0.0/joinpointR/inst/doc/Introduction.R |only joinpointR-2.0.0/joinpointR/inst/doc/Introduction.Rmd |only joinpointR-2.0.0/joinpointR/inst/doc/Introduction.html |only joinpointR-2.0.0/joinpointR/man/bic_jp.Rd |only joinpointR-2.0.0/joinpointR/man/clean_jp_data.Rd |only joinpointR-2.0.0/joinpointR/man/figures/logo.png |binary joinpointR-2.0.0/joinpointR/man/get_summary.Rd |only joinpointR-2.0.0/joinpointR/man/gg_jpoint.Rd | 193 ++--- joinpointR-2.0.0/joinpointR/man/hiv_data.Rd | 54 - joinpointR-2.0.0/joinpointR/man/model_jp.Rd | 214 +++--- joinpointR-2.0.0/joinpointR/man/plot_cbpal.Rd |only joinpointR-2.0.0/joinpointR/man/scale_cbpal.Rd |only joinpointR-2.0.0/joinpointR/man/summary.model_jp.Rd |only joinpointR-2.0.0/joinpointR/tests |only joinpointR-2.0.0/joinpointR/vignettes/Introduction.Rmd |only 47 files changed, 782 insertions(+), 651 deletions(-)
Title: Amazon Web Services Software Development Kit
Description: Interface to Amazon Web Services <https://aws.amazon.com>,
including storage, database, and compute services, such as 'Simple
Storage Service' ('S3'), 'DynamoDB' 'NoSQL' database, and 'Lambda'
functions-as-a-service.
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws versions 0.10.0 dated 2026-06-01 and 0.11.0 dated 2026-10-08
paws-0.10.0/paws/man/panorama.Rd |only paws-0.11.0/paws/DESCRIPTION | 25 paws-0.11.0/paws/MD5 | 565 +- paws-0.11.0/paws/NAMESPACE | 19 paws-0.11.0/paws/R/paws.R | 2315 ++++++++--- paws-0.11.0/paws/man/accessanalyzer.Rd | 4 paws-0.11.0/paws/man/account.Rd | 9 paws-0.11.0/paws/man/acm.Rd | 29 paws-0.11.0/paws/man/acmpca.Rd | 4 paws-0.11.0/paws/man/apigateway.Rd | 4 paws-0.11.0/paws/man/apigatewaymanagementapi.Rd | 4 paws-0.11.0/paws/man/apigatewayv2.Rd | 4 paws-0.11.0/paws/man/appfabric.Rd | 4 paws-0.11.0/paws/man/applicationautoscaling.Rd | 4 paws-0.11.0/paws/man/applicationcostprofiler.Rd | 4 paws-0.11.0/paws/man/applicationinsights.Rd | 4 paws-0.11.0/paws/man/appmesh.Rd | 4 paws-0.11.0/paws/man/appregistry.Rd | 4 paws-0.11.0/paws/man/apprunner.Rd | 4 paws-0.11.0/paws/man/appstream.Rd | 4 paws-0.11.0/paws/man/arczonalshift.Rd | 4 paws-0.11.0/paws/man/athena.Rd | 4 paws-0.11.0/paws/man/auditmanager.Rd | 4 paws-0.11.0/paws/man/augmentedairuntime.Rd | 4 paws-0.11.0/paws/man/autoscaling.Rd | 4 paws-0.11.0/paws/man/autoscalingplans.Rd | 4 paws-0.11.0/paws/man/backup.Rd | 20 paws-0.11.0/paws/man/backupgateway.Rd | 4 paws-0.11.0/paws/man/batch.Rd | 7 paws-0.11.0/paws/man/bedrock.Rd | 16 paws-0.11.0/paws/man/bedrockagent.Rd | 15 paws-0.11.0/paws/man/bedrockagentcore.Rd | 6 paws-0.11.0/paws/man/bedrockagentcorecontrol.Rd | 48 paws-0.11.0/paws/man/bedrockagentruntime.Rd | 14 paws-0.11.0/paws/man/bedrockdataautomation.Rd | 4 paws-0.11.0/paws/man/bedrockdataautomationruntime.Rd | 4 paws-0.11.0/paws/man/bedrockruntime.Rd | 5 paws-0.11.0/paws/man/billing.Rd | 15 paws-0.11.0/paws/man/billingconductor.Rd | 6 paws-0.11.0/paws/man/braket.Rd | 6 paws-0.11.0/paws/man/budgets.Rd | 4 paws-0.11.0/paws/man/chatbot.Rd | 4 paws-0.11.0/paws/man/cleanroomsml.Rd | 4 paws-0.11.0/paws/man/cloud9.Rd | 4 paws-0.11.0/paws/man/cloudcontrolapi.Rd | 4 paws-0.11.0/paws/man/clouddirectory.Rd | 6 paws-0.11.0/paws/man/cloudformation.Rd | 6 paws-0.11.0/paws/man/cloudfront.Rd | 4 paws-0.11.0/paws/man/cloudfrontkeyvaluestore.Rd | 4 paws-0.11.0/paws/man/cloudhsm.Rd | 4 paws-0.11.0/paws/man/cloudhsmv2.Rd | 4 paws-0.11.0/paws/man/cloudsearch.Rd | 4 paws-0.11.0/paws/man/cloudsearchdomain.Rd | 4 paws-0.11.0/paws/man/cloudtrail.Rd | 70 paws-0.11.0/paws/man/cloudtraildataservice.Rd | 4 paws-0.11.0/paws/man/cloudwatch.Rd | 51 paws-0.11.0/paws/man/cloudwatchapplicationsignals.Rd | 13 paws-0.11.0/paws/man/cloudwatchinternetmonitor.Rd | 4 paws-0.11.0/paws/man/cloudwatchlogs.Rd | 19 paws-0.11.0/paws/man/cloudwatchobservabilityaccessmanager.Rd | 4 paws-0.11.0/paws/man/cloudwatchrum.Rd | 4 paws-0.11.0/paws/man/codeartifact.Rd | 4 paws-0.11.0/paws/man/codebuild.Rd | 4 paws-0.11.0/paws/man/codecatalyst.Rd | 4 paws-0.11.0/paws/man/codecommit.Rd | 6 paws-0.11.0/paws/man/codeconnections.Rd | 4 paws-0.11.0/paws/man/codedeploy.Rd | 4 paws-0.11.0/paws/man/codeguruprofiler.Rd | 4 paws-0.11.0/paws/man/codegurureviewer.Rd | 4 paws-0.11.0/paws/man/codegurusecurity.Rd | 4 paws-0.11.0/paws/man/codepipeline.Rd | 4 paws-0.11.0/paws/man/codestarconnections.Rd | 4 paws-0.11.0/paws/man/codestarnotifications.Rd | 4 paws-0.11.0/paws/man/cognitoidentity.Rd | 4 paws-0.11.0/paws/man/cognitoidentityprovider.Rd | 14 paws-0.11.0/paws/man/cognitosync.Rd | 4 paws-0.11.0/paws/man/comprehend.Rd | 4 paws-0.11.0/paws/man/comprehendmedical.Rd | 4 paws-0.11.0/paws/man/computeoptimizer.Rd | 4 paws-0.11.0/paws/man/configservice.Rd | 9 paws-0.11.0/paws/man/connect.Rd | 40 paws-0.11.0/paws/man/connectcampaignservice.Rd | 4 paws-0.11.0/paws/man/connectcampaignservicev2.Rd | 4 paws-0.11.0/paws/man/connectcases.Rd | 4 paws-0.11.0/paws/man/connectcontactlens.Rd | 6 paws-0.11.0/paws/man/connectparticipant.Rd | 8 paws-0.11.0/paws/man/connectwisdomservice.Rd | 4 paws-0.11.0/paws/man/controltower.Rd | 4 paws-0.11.0/paws/man/costandusagereportservice.Rd | 4 paws-0.11.0/paws/man/costexplorer.Rd | 4 paws-0.11.0/paws/man/customerprofiles.Rd | 13 paws-0.11.0/paws/man/datapipeline.Rd | 4 paws-0.11.0/paws/man/datazone.Rd | 6 paws-0.11.0/paws/man/dax.Rd | 4 paws-0.11.0/paws/man/detective.Rd | 4 paws-0.11.0/paws/man/devopsguru.Rd | 4 paws-0.11.0/paws/man/directconnect.Rd | 14 paws-0.11.0/paws/man/directoryservice.Rd | 4 paws-0.11.0/paws/man/dlm.Rd | 4 paws-0.11.0/paws/man/docdb.Rd | 4 paws-0.11.0/paws/man/docdbelastic.Rd | 4 paws-0.11.0/paws/man/drs.Rd | 24 paws-0.11.0/paws/man/dynamodb.Rd | 5 paws-0.11.0/paws/man/dynamodbstreams.Rd | 4 paws-0.11.0/paws/man/ebs.Rd | 4 paws-0.11.0/paws/man/ec2.Rd | 50 paws-0.11.0/paws/man/ec2instanceconnect.Rd | 4 paws-0.11.0/paws/man/ecr.Rd | 4 paws-0.11.0/paws/man/ecrpublic.Rd | 4 paws-0.11.0/paws/man/ecs.Rd | 4 paws-0.11.0/paws/man/efs.Rd | 4 paws-0.11.0/paws/man/eks.Rd | 10 paws-0.11.0/paws/man/elasticache.Rd | 4 paws-0.11.0/paws/man/elasticbeanstalk.Rd | 36 paws-0.11.0/paws/man/elasticsearchservice.Rd | 4 paws-0.11.0/paws/man/elb.Rd | 6 paws-0.11.0/paws/man/elbv2.Rd | 6 paws-0.11.0/paws/man/emr.Rd | 9 paws-0.11.0/paws/man/emrcontainers.Rd | 8 paws-0.11.0/paws/man/emrserverless.Rd | 4 paws-0.11.0/paws/man/entityresolution.Rd | 4 paws-0.11.0/paws/man/eventbridge.Rd | 4 paws-0.11.0/paws/man/eventbridgepipes.Rd | 4 paws-0.11.0/paws/man/eventbridgescheduler.Rd | 4 paws-0.11.0/paws/man/finspace.Rd | 4 paws-0.11.0/paws/man/finspacedata.Rd | 4 paws-0.11.0/paws/man/firehose.Rd | 4 paws-0.11.0/paws/man/fis.Rd | 4 paws-0.11.0/paws/man/fms.Rd | 4 paws-0.11.0/paws/man/forecastqueryservice.Rd | 4 paws-0.11.0/paws/man/forecastservice.Rd | 4 paws-0.11.0/paws/man/frauddetector.Rd | 4 paws-0.11.0/paws/man/fsx.Rd | 4 paws-0.11.0/paws/man/glacier.Rd | 4 paws-0.11.0/paws/man/globalaccelerator.Rd | 4 paws-0.11.0/paws/man/glue.Rd | 45 paws-0.11.0/paws/man/gluedatabrew.Rd | 4 paws-0.11.0/paws/man/guardduty.Rd | 19 paws-0.11.0/paws/man/health.Rd | 5 paws-0.11.0/paws/man/healthlake.Rd | 23 paws-0.11.0/paws/man/iam.Rd | 8 paws-0.11.0/paws/man/iamrolesanywhere.Rd | 4 paws-0.11.0/paws/man/identitystore.Rd | 17 paws-0.11.0/paws/man/imagebuilder.Rd | 86 paws-0.11.0/paws/man/inspector.Rd | 6 paws-0.11.0/paws/man/inspector2.Rd | 14 paws-0.11.0/paws/man/ivs.Rd | 7 paws-0.11.0/paws/man/ivschat.Rd | 6 paws-0.11.0/paws/man/ivsrealtime.Rd | 4 paws-0.11.0/paws/man/kafka.Rd | 9 paws-0.11.0/paws/man/kafkaconnect.Rd | 5 paws-0.11.0/paws/man/kendra.Rd | 4 paws-0.11.0/paws/man/kendraranking.Rd | 4 paws-0.11.0/paws/man/keyspaces.Rd | 4 paws-0.11.0/paws/man/kinesis.Rd | 10 paws-0.11.0/paws/man/kinesisanalytics.Rd | 4 paws-0.11.0/paws/man/kinesisanalyticsv2.Rd | 4 paws-0.11.0/paws/man/kms.Rd | 4 paws-0.11.0/paws/man/lakeformation.Rd | 4 paws-0.11.0/paws/man/lambda.Rd | 7 paws-0.11.0/paws/man/lexmodelbuildingservice.Rd | 4 paws-0.11.0/paws/man/lexmodelsv2.Rd | 33 paws-0.11.0/paws/man/lexruntimeservice.Rd | 4 paws-0.11.0/paws/man/lexruntimev2.Rd | 4 paws-0.11.0/paws/man/licensemanager.Rd | 4 paws-0.11.0/paws/man/licensemanagerlinuxsubscriptions.Rd | 4 paws-0.11.0/paws/man/licensemanagerusersubscriptions.Rd | 4 paws-0.11.0/paws/man/lightsail.Rd | 5 paws-0.11.0/paws/man/locationservice.Rd | 4 paws-0.11.0/paws/man/lookoutequipment.Rd | 4 paws-0.11.0/paws/man/machinelearning.Rd | 4 paws-0.11.0/paws/man/macie2.Rd | 4 paws-0.11.0/paws/man/managedgrafana.Rd | 4 paws-0.11.0/paws/man/marketplacecatalog.Rd | 6 paws-0.11.0/paws/man/marketplacecommerceanalytics.Rd | 4 paws-0.11.0/paws/man/marketplaceentitlementservice.Rd | 4 paws-0.11.0/paws/man/marketplacemetering.Rd | 8 paws-0.11.0/paws/man/memorydb.Rd | 4 paws-0.11.0/paws/man/mq.Rd | 5 paws-0.11.0/paws/man/mturk.Rd | 4 paws-0.11.0/paws/man/mwaa.Rd | 4 paws-0.11.0/paws/man/neptune.Rd | 4 paws-0.11.0/paws/man/neptunedata.Rd | 4 paws-0.11.0/paws/man/networkfirewall.Rd | 12 paws-0.11.0/paws/man/networkmanager.Rd | 4 paws-0.11.0/paws/man/omics.Rd | 4 paws-0.11.0/paws/man/opensearchingestion.Rd | 4 paws-0.11.0/paws/man/opensearchservice.Rd | 12 paws-0.11.0/paws/man/opensearchserviceserverless.Rd | 4 paws-0.11.0/paws/man/organizations.Rd | 30 paws-0.11.0/paws/man/paymentcryptographycontrolplane.Rd | 4 paws-0.11.0/paws/man/paymentcryptographydataplane.Rd | 6 paws-0.11.0/paws/man/pcaconnectorad.Rd | 4 paws-0.11.0/paws/man/personalize.Rd | 4 paws-0.11.0/paws/man/personalizeevents.Rd | 4 paws-0.11.0/paws/man/personalizeruntime.Rd | 4 paws-0.11.0/paws/man/pi.Rd | 4 paws-0.11.0/paws/man/pinpoint.Rd | 4 paws-0.11.0/paws/man/pinpointemail.Rd | 4 paws-0.11.0/paws/man/pinpointsmsvoice.Rd | 4 paws-0.11.0/paws/man/pinpointsmsvoicev2.Rd | 8 paws-0.11.0/paws/man/polly.Rd | 4 paws-0.11.0/paws/man/pricing.Rd | 4 paws-0.11.0/paws/man/prometheusservice.Rd | 6 paws-0.11.0/paws/man/proton.Rd | 4 paws-0.11.0/paws/man/quicksight.Rd | 71 paws-0.11.0/paws/man/ram.Rd | 4 paws-0.11.0/paws/man/rds.Rd | 4 paws-0.11.0/paws/man/rdsdataservice.Rd | 8 paws-0.11.0/paws/man/recyclebin.Rd | 4 paws-0.11.0/paws/man/redshift.Rd | 8 paws-0.11.0/paws/man/redshiftdataapiservice.Rd | 5 paws-0.11.0/paws/man/redshiftserverless.Rd | 4 paws-0.11.0/paws/man/rekognition.Rd | 45 paws-0.11.0/paws/man/resiliencehub.Rd | 4 paws-0.11.0/paws/man/resourceexplorer.Rd | 4 paws-0.11.0/paws/man/resourcegroups.Rd | 4 paws-0.11.0/paws/man/resourcegroupstaggingapi.Rd | 4 paws-0.11.0/paws/man/route53.Rd | 4 paws-0.11.0/paws/man/route53domains.Rd | 4 paws-0.11.0/paws/man/route53profiles.Rd | 4 paws-0.11.0/paws/man/route53recoverycluster.Rd | 4 paws-0.11.0/paws/man/route53recoverycontrolconfig.Rd | 4 paws-0.11.0/paws/man/route53recoveryreadiness.Rd | 4 paws-0.11.0/paws/man/route53resolver.Rd | 10 paws-0.11.0/paws/man/s3.Rd | 26 paws-0.11.0/paws/man/s3control.Rd | 4 paws-0.11.0/paws/man/s3outposts.Rd | 4 paws-0.11.0/paws/man/s3tables.Rd | 4 paws-0.11.0/paws/man/sagemaker.Rd | 12 paws-0.11.0/paws/man/sagemakeredgemanager.Rd | 4 paws-0.11.0/paws/man/sagemakerfeaturestoreruntime.Rd | 9 paws-0.11.0/paws/man/sagemakergeospatialcapabilities.Rd | 4 paws-0.11.0/paws/man/sagemakermetrics.Rd | 4 paws-0.11.0/paws/man/sagemakerruntime.Rd | 4 paws-0.11.0/paws/man/savingsplans.Rd | 4 paws-0.11.0/paws/man/schemas.Rd | 4 paws-0.11.0/paws/man/secretsmanager.Rd | 4 paws-0.11.0/paws/man/securityhub.Rd | 14 paws-0.11.0/paws/man/securitylake.Rd | 4 paws-0.11.0/paws/man/serverlessapplicationrepository.Rd | 4 paws-0.11.0/paws/man/servicecatalog.Rd | 4 paws-0.11.0/paws/man/servicediscovery.Rd | 4 paws-0.11.0/paws/man/servicequotas.Rd | 4 paws-0.11.0/paws/man/ses.Rd | 4 paws-0.11.0/paws/man/sesv2.Rd | 24 paws-0.11.0/paws/man/sfn.Rd | 4 paws-0.11.0/paws/man/shield.Rd | 4 paws-0.11.0/paws/man/simpledb.Rd | 4 paws-0.11.0/paws/man/sns.Rd | 8 paws-0.11.0/paws/man/sqs.Rd | 4 paws-0.11.0/paws/man/ssm.Rd | 12 paws-0.11.0/paws/man/ssmcontacts.Rd | 4 paws-0.11.0/paws/man/ssmincidents.Rd | 4 paws-0.11.0/paws/man/ssmsap.Rd | 4 paws-0.11.0/paws/man/sso.Rd | 4 paws-0.11.0/paws/man/ssoadmin.Rd | 4 paws-0.11.0/paws/man/ssooidc.Rd | 6 paws-0.11.0/paws/man/storagegateway.Rd | 4 paws-0.11.0/paws/man/sts.Rd | 12 paws-0.11.0/paws/man/support.Rd | 14 paws-0.11.0/paws/man/supportapp.Rd | 4 paws-0.11.0/paws/man/swf.Rd | 4 paws-0.11.0/paws/man/synthetics.Rd | 4 paws-0.11.0/paws/man/telconetworkbuilder.Rd | 4 paws-0.11.0/paws/man/textract.Rd | 4 paws-0.11.0/paws/man/timestreamquery.Rd | 4 paws-0.11.0/paws/man/timestreamwrite.Rd | 4 paws-0.11.0/paws/man/transcribeservice.Rd | 5 paws-0.11.0/paws/man/translate.Rd | 4 paws-0.11.0/paws/man/verifiedpermissions.Rd | 4 paws-0.11.0/paws/man/voiceid.Rd | 4 paws-0.11.0/paws/man/vpclattice.Rd | 4 paws-0.11.0/paws/man/waf.Rd | 4 paws-0.11.0/paws/man/wafregional.Rd | 4 paws-0.11.0/paws/man/wafv2.Rd | 8 paws-0.11.0/paws/man/wellarchitected.Rd | 35 paws-0.11.0/paws/man/workdocs.Rd | 4 paws-0.11.0/paws/man/workmail.Rd | 4 paws-0.11.0/paws/man/workmailmessageflow.Rd | 4 paws-0.11.0/paws/man/workspaces.Rd | 28 paws-0.11.0/paws/man/workspacesweb.Rd | 4 paws-0.11.0/paws/man/xray.Rd | 4 paws-0.11.0/paws/tests |only 284 files changed, 3676 insertions(+), 1417 deletions(-)
Title: Optimizing Acoustic Signal Detection
Description: Facilitates the automatic detection of acoustic signals,
providing functions to diagnose and optimize the performance of detection
routines. Detections from other software can also be explored and optimized.
This package has been peer-reviewed by rOpenSci.
Araya-Salas et al. (2022) <doi:10.1101/2022.12.13.520253>.
Author: Marcelo Araya-Salas [aut, cre] ,
Alec L. Robitaille [rev] ,
Sam Lapp [rev]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
Diff between ohun versions 1.0.4 dated 2025-10-22 and 1.0.5 dated 2026-10-08
DESCRIPTION | 13 + MD5 | 121 ++++++++--------- NAMESPACE | 3 NEWS.md | 15 ++ R/consensus_detection.R | 21 +-- R/diagnose_detection.R | 30 ++-- R/energy_detector.R | 28 ++-- R/get_envelopes.R | 17 +- R/get_templates.R | 11 - R/internal_functions.R | 169 ++++++++++++++++-------- R/label_detection.R | 29 ++-- R/label_spectro.R | 63 ++++----- R/merge_overlaps.R | 9 - R/ohun-package.R | 7 - R/optimize_energy_detector.R | 34 ++--- R/optimize_template_detector.R | 10 - R/plot_detection.R | 16 +- R/reassemble_detection.R | 23 ++- R/split_acoustic_data.R | 34 ++--- R/summarize_acoustic_data.R | 9 - R/summarize_diagnostic.R | 17 +- R/summarize_reference.R | 8 - R/template_correlator.R | 20 +- R/template_detector.R | 95 ++++++++++--- README.md | 88 +++++++++++- build/vignette.rds |binary data/lbh1.rda |binary data/lbh2.rda |binary data/lbh_reference.rda |binary inst/doc/energy_based_detection.R | 32 +++- inst/doc/energy_based_detection.Rmd | 69 +++++----- inst/doc/energy_based_detection.html | 224 +++++++++++++++++---------------- inst/doc/intro_to_ohun.R | 13 - inst/doc/intro_to_ohun.Rmd | 59 ++++---- inst/doc/intro_to_ohun.html | 188 +++++++++++++++------------ inst/doc/template_based_detection.R | 8 - inst/doc/template_based_detection.Rmd | 43 +++--- inst/doc/template_based_detection.html | 216 ++++++++++++++++--------------- man/consensus_detection.Rd | 20 +- man/diagnose_detection.Rd | 16 +- man/energy_detector.Rd | 16 +- man/envelopes.Rd |only man/get_envelopes.Rd | 7 - man/get_templates.Rd | 7 - man/label_detection.Rd | 6 man/label_spectro.Rd | 16 +- man/merge_overlaps.Rd | 6 man/ohun.Rd | 4 man/optimize_energy_detector.Rd | 12 - man/optimize_template_detector.Rd | 6 man/plot_detection.Rd | 14 +- man/print.envelopes.Rd | 9 - man/reassemble_detection.Rd | 6 man/split_acoustic_data.Rd | 10 - man/summarize_acoustic_data.Rd | 2 man/summarize_diagnostic.Rd | 9 - man/summarize_reference.Rd | 8 - man/template_correlator.Rd | 12 - man/template_detector.Rd | 13 + vignettes/energy_based_detection.Rmd | 69 +++++----- vignettes/intro_to_ohun.Rmd | 59 ++++---- vignettes/template_based_detection.Rmd | 43 +++--- 62 files changed, 1185 insertions(+), 927 deletions(-)
Title: Unidimensional Item Response Theory Modeling
Description: Fit unidimensional item response theory (IRT) models to test
data, which includes both dichotomous and polytomous items, calibrate
pretest item parameters, estimate examinees' abilities, and examine
the IRT model-data fit on item-level in different ways as well as provide
useful functions related to IRT analyses such as differential item
functioning analysis.
In addition, the package provides a set of classical test theory functions
for computing item- and test-level statistics (e.g., item difficulty, item-total
correlation, and coefficient alpha) and for scoring and analyzing selected-response
item data.
The bring.flexmirt() and write.flexmirt() functions were written by modifying
the read.flexmirt() function (Pritikin & Falk (2020) <doi:10.1177/0146621620929431>).
The bring.bilog() and bring.parscale() functions were written by modifying the read.bilog()
and read.parscale() functions, respectively (Weeks (2010) <doi:10.18637/jss.v035.i12>).
The bisection() function wa [...truncated...]
Author: Hwanggyu Lim [aut, cre],
Craig S. Wells [ctb],
James Howard [ctb],
Joshua Pritikin [ctb],
Jonathan P Weeks [ctb],
Jorge Gonzalez [ctb],
David Magis [ctb]
Maintainer: Hwanggyu Lim <hglim83@gmail.com>
Diff between irtQ versions 1.3.0 dated 2026-10-05 and 1.3.1 dated 2026-10-08
DESCRIPTION | 8 MD5 | 114 +- NAMESPACE | 1 NEWS.md | 117 ++ R/cac_rud.R | 8 R/catsib.R | 14 R/ctt.R | 69 + R/ctt_alpha.R | 24 R/ctt_distr.R | 25 R/ctt_item.R | 88 +- R/find_cut.R | 18 R/irtQ-package.R | 10 R/irtfit.R | 1587 +++++++++++++++++++-------------------- R/lwrc.R | 5 R/pcd2.R | 21 R/plot_irtfit.R | 4 R/rdif.R | 2 R/reval_mst.R | 56 + R/ripd.R | 4 R/run_mst.R | 381 ++++----- R/score_resp.R | 18 R/shape_df.R | 18 R/simMST.R | 5 R/simdat.R | 3 R/traceline.R | 6 README.md | 861 ++++++++++----------- inst/doc/irtQ.Rmd | 11 inst/doc/irtQ.html | 20 man/catsib.Rd | 3 man/ctt.Rd | 24 man/ctt_alpha.Rd | 26 man/ctt_distr.Rd | 8 man/ctt_item.Rd | 9 man/figures/README-example-2.png |binary man/figures/README-example-3.png |binary man/figures/README-example-4.png |binary man/figures/README-example-5.png |binary man/figures/README-example-6.png |binary man/figures/README-example-7.png |binary man/find_cut.Rd | 6 man/irtQ-package.Rd | 10 man/lwrc.Rd | 5 man/pcd2.Rd | 21 man/rdif.Rd | 2 man/reval_mst.Rd | 30 man/ripd.Rd | 4 man/run_mst.Rd | 76 + man/score_resp.Rd | 4 man/simMST.Rd | 5 man/traceline.Rd | 234 ++--- tests/testthat/test-cac_rud.R |only tests/testthat/test-ctt.R | 94 ++ tests/testthat/test-ctt_distr.R | 40 tests/testthat/test-dif.R | 22 tests/testthat/test-irtfit.R |only tests/testthat/test-reval_mst.R |only tests/testthat/test-run_mst.R |only tests/testthat/test-score_resp.R | 29 tests/testthat/test-shape_df.R |only tests/testthat/test-simdat.R |only vignettes/irtQ.Rmd | 11 61 files changed, 2367 insertions(+), 1794 deletions(-)
Title: Insect Ecology Data Analysis Toolkit
Description: A collection of analytical tools for insect ecology research,
currently covering age-stage, two-sex life table analysis,
dose-response bioassays, temperature-dependent development and insect
phenology prediction. The life table module follows the age-stage,
two-sex life table theory of Chi (1988) <doi:10.1093/ee/17.1.26> and
Chi et al. (2020) <doi:10.1127/entomologia/2020/0936>. It supports
fast batch processing of multi-group datasets, validates raw 'csv'
data, computes cohort size, mean fecundity, age-stage survival rates,
age-specific survival, age-specific fecundity, life expectancy, and
derived population parameters (net reproductive rate, intrinsic and
finite rates of increase, mean generation time), simultaneously
generates age-stage survival curves for all groups, and exports all
tabular results and plots to 'Excel' in a single run. The bioassay
module estimates lethal concentrations by the traditional and the
weighted (improved) linear regression methods and by pro [...truncated...]
Author: Wangyao Li [aut, cre, cph],
Yongsheng Zhang [aut],
Huan Yu [aut]
Maintainer: Wangyao Li <1561941342@qq.com>
Diff between insectecol versions 1.1.1 dated 2026-10-05 and 1.1.2 dated 2026-10-08
DESCRIPTION | 8 MD5 | 116 +-- NAMESPACE | 1 R/check_data.R | 7 R/emergence_calc.R | 12 R/emergence_export.R | 23 R/emergence_main.R | 122 ++- R/emergence_plot.R | 6 R/font.R | 451 ++++++++++++- R/gdd_calc.R | 14 R/gdd_export.R | 74 +- R/gdd_fit.R | 52 + R/gdd_main.R | 136 ++-- R/gdd_plot.R | 162 ++++ R/lc50_data.R | 6 R/lc50_export.R | 125 +-- R/lc50_export_auto.R | 438 ++++++------- R/lc50_main.R | 104 ++- R/lc50_plot.R | 139 ++-- R/lifetable_bootstrap.R | 1004 +++++++++++++++--------------- R/lifetable_calculate.R | 352 +++++----- R/lifetable_data.R | 10 R/lifetable_export.R | 277 ++++---- R/lifetable_indicators.R | 224 +++++- R/lifetable_main.R | 792 +++++++++++++---------- R/lifetable_plot.R | 326 +++++---- R/plot_path.R |only README.md | 62 + inst/CITATION | 2 man/calc_ex.Rd | 11 man/calc_exj.Rd |only man/calc_r.Rd | 15 man/emergence_analyze.Rd | 72 +- man/emergence_calc.Rd | 12 man/emergence_export.Rd | 2 man/emergence_export_plot.Rd | 2 man/figures/emergence.png |binary man/figures/gdd.png |binary man/figures/lc50.png |binary man/gdd_analyze.Rd | 92 +- man/gdd_calc.Rd | 14 man/gdd_export.Rd | 2 man/gdd_export_plot.Rd | 37 - man/gdd_plot.Rd | 10 man/lc50_analyze.Rd | 69 +- man/lc50_export.Rd | 4 man/lc50_export_auto.Rd | 4 man/lc50_plot.Rd | 7 man/lifeTable_analyze.Rd | 92 ++ man/lifeTable_boot_test.Rd | 4 man/lifeTable_bootstrap.Rd | 4 man/lifeTable_calculate.Rd | 7 man/lifeTable_calculate_all.Rd | 9 man/lifeTable_export.Rd | 31 man/lifeTable_plot.Rd | 21 tests/testthat/test-emergence.R | 21 tests/testthat/test-gdd.R | 79 ++ tests/testthat/test-lc50.R | 28 tests/testthat/test-life_table.R | 189 +++++ tests/testthat/twosex_ptw_example.csv |only tests/testthat/twosex_ptw_exj_example.txt |only 61 files changed, 3775 insertions(+), 2108 deletions(-)
Title: Statistical Consistency Checker for Published Research Results
Description: A conservative, assumption-aware statistical consistency checker
for already-extracted research-results text. Parses test statistics, effect
sizes, and confidence intervals across multiple citation styles including
American Psychological Association (APA), Harvard, Frontiers, PLOS ONE,
Scientific Reports, Nature Human Behaviour, PeerJ, eLife, PNAS, and others.
Recomputes effect sizes using all plausible variants when design is ambiguous,
and validates internal consistency. Supports t-tests, F-tests/ANOVA,
correlations, chi-square, z-tests, regression, and nonparametric tests.
Explicitly tracks all assumptions and uncertainty in output. Detects decision
errors (significance reversals) similar to 'statcheck'. From v0.4.0 file
extraction is no longer part of the package — pair with an external extractor
(e.g., 'docpluck' at <https://docpluck.app>) and pass the resulting text
to check_text(). Note: this package is under active development and results
should be independently verified. [...truncated...]
Author: Gilad Feldman [aut, cre]
Maintainer: Gilad Feldman <giladfel@gmail.com>
Diff between effectcheck versions 0.2.3 dated 2026-03-25 and 0.7.17 dated 2026-10-08
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effectcheck-0.7.17/effectcheck/tests/testthat/test-v0713-uncaptioned-table-rows.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v0714-ci-verdict-premise.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v0714-generalized-eta2.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v0714-mediation-direct-vs-acme.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v0714-omnibus-contrast-undecided.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v0714-quoted-restatement.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v0714-welch-backsolved-n.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v0717-welch-stated-n-kept.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v074-paragraph-chunking.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v074-separator-review.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v075-dual-p-and-legend.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v075-locale-conflict.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v075-mean-diff-ci.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v075-methods-resample-count.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v076-docpluck-consumer-canary.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v076-docpluck-contract.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v076-outbox-0813-defects.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v078-ci-engine-labelling.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v079-chisq-n-backsolve-is-not-verification.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v079-ci-method-label-honesty.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v079-ci-severity-tiers.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v079-ci-symmetry-on-correlations.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v079-corr-bare-r-adopts-matched-df.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v079-corr-matched-df-is-ambiguous-not-resolved.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v079-corr-n-provenance-reaches-output.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v079-design-ambiguous-action-scope.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v079-estimate-outside-ci.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-v079-robust-family-nsource-undefined.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-version-fallback-honesty.R |only effectcheck-0.7.17/effectcheck/tests/testthat/test-z-u-effects.R |only effectcheck-0.7.17/effectcheck/vignettes/effectcheck.Rmd | 51 310 files changed, 21539 insertions(+), 4323 deletions(-)
Title: Read, Write, and Modify TOML Files
Description: Simple toolkit for working with TOML text. Based on tomledit which
allows for modifying TOML while preserving order, comments,and whitespace.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between toml versions 1.1.0 dated 2026-04-13 and 1.2.0 dated 2026-10-08
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 3 +++ R/tomledit.R | 2 +- 4 files changed, 10 insertions(+), 7 deletions(-)
Title: Parameter Converter and Calculator for Health Technology
Assessment
Description: An interactive 'shiny' application for Health Technology
Assessment (HTA) parameter estimation. Converts between rates,
probabilities, odds, and hazard ratios (HR); extrapolates survival
curves (Exponential, Weibull, Log-Logistic); fits probabilistic
sensitivity analysis (PSA) distributions (Beta, Gamma, LogNormal,
Dirichlet) via the method of moments; calculates incremental
cost-effectiveness ratios (ICERs), net monetary benefit (NMB),
value-based pricing, and budget impact; adjusts costs for inflation,
discounting, and purchasing power parity (PPP) across 30 countries;
and adjusts background mortality using life-table methods. Designed
for researchers building cost-effectiveness and budget-impact models
who need auditable, formula-documented parameter transformations.
Methods include Zhang and Yu (1998)
<doi:10.1001/jama.280.19.1690> for odds ratio (OR) to relative
risk (RR) conversion and Chinn (2000, Statistics in Medicine, 19,
3127-3131) for effect-size transformations.
Author: Abhijit Pakhare [aut, cre],
Soumya Jain [aut],
Anvita Malhotra [aut],
Shivansh Verma [aut],
Biju Somen [aut],
Oshima Sachin [aut],
Beena Joshi [aut],
Ankur Joshi [aut]
Maintainer: Abhijit Pakhare <drpakhare@gmail.com>
Diff between ParCC versions 1.4.0 dated 2026-03-30 and 1.4.1 dated 2026-10-08
DESCRIPTION | 22 ++++++++-- MD5 | 28 +++++++------ NEWS.md | 19 +++++++++ R/mod_batch.R | 1 R/mod_core_conv.R | 67 ++++++++++++++++++++------------ R/mod_diagnostic.R | 18 +++++--- R/mod_home.R | 20 ++++++++- R/mod_hr_converter.R | 75 ++++++++++++++++++++++++------------ R/mod_psa.R | 2 R/mod_report.R | 72 +++++++++++++++++++++++++++++++--- R/mod_static_pages.R | 61 +++++++++++++++++++++++++++++ R/parcc_helpers.R | 7 ++- README.md | 13 ++++-- man/figures |only tests/testthat/test-hr-conversion.R | 21 +++++++--- 15 files changed, 331 insertions(+), 95 deletions(-)
Title: Ensemble Platform for Species Distribution Modeling
Description: Functions for species distribution modelling, to calibrate, evaluate, and project
species-environment relationships across space and time using multiple modelling algorithms and
ensemble forecasting. It accommodates diverse ecological data types (presence-only, presence-absence,
counts, multi-class abundance, or relative/absolute abundance) within a unified modelling workflow
which includes cross-validation schemes, pseudo-absence selection strategies, expanded model
parametrization options, a dozen of algorithms, and tools for exploring and visualizing outputs.
Author: Maya Gueguen [aut, cre] ,
Helene Blancheteau [aut],
Remi Lemaire-Patin [aut],
Wilfried Thuiller [aut]
Maintainer: Maya Gueguen <maya.gueguen@univ-grenoble-alpes.fr>
Diff between biomod2 versions 4.3-4-6 dated 2026-05-23 and 4.3-4-7 dated 2026-10-08
biomod2-4.3-4-6/biomod2/man/predict.bm.Rd |only biomod2-4.3-4-6/biomod2/man/predict.em.Rd |only biomod2-4.3-4-7/biomod2/DESCRIPTION | 33 +-- biomod2-4.3-4-7/biomod2/MD5 | 149 ++++++-------- biomod2-4.3-4-7/biomod2/R/BIOMOD_EnsembleForecasting.R | 33 ++- biomod2-4.3-4-7/biomod2/R/BIOMOD_FormatingData.R | 13 - biomod2-4.3-4-7/biomod2/R/BIOMOD_Modeling.R | 28 ++ biomod2-4.3-4-7/biomod2/R/BIOMOD_Projection.R | 64 +++--- biomod2-4.3-4-7/biomod2/R/biomod2_classes_0.R | 24 -- biomod2-4.3-4-7/biomod2/R/biomod2_classes_1.R | 84 +++---- biomod2-4.3-4-7/biomod2/R/biomod2_classes_3.R | 30 +- biomod2-4.3-4-7/biomod2/R/biomod2_classes_4.R | 80 ++----- biomod2-4.3-4-7/biomod2/R/biomod2_classes_5.R | 27 -- biomod2-4.3-4-7/biomod2/R/biomod2_internal.R | 106 ++++++--- biomod2-4.3-4-7/biomod2/R/bm_BinaryTransformation.R | 2 biomod2-4.3-4-7/biomod2/R/bm_FindOptimStat.R | 4 biomod2-4.3-4-7/biomod2/R/bm_ModelingOptions.R | 32 --- biomod2-4.3-4-7/biomod2/R/bm_PlotEvalBoxplot.R | 4 biomod2-4.3-4-7/biomod2/R/bm_PlotEvalMean.R | 4 biomod2-4.3-4-7/biomod2/R/bm_PlotRangeSize.R | 6 biomod2-4.3-4-7/biomod2/R/bm_PlotResponseCurves.R | 2 biomod2-4.3-4-7/biomod2/R/bm_PlotVarImpBoxplot.R | 2 biomod2-4.3-4-7/biomod2/R/bm_PseudoAbsences.R | 6 biomod2-4.3-4-7/biomod2/R/bm_RunModelsLoop.R | 34 ++- biomod2-4.3-4-7/biomod2/R/bm_SampleBinaryVector.R | 2 biomod2-4.3-4-7/biomod2/R/bm_Tuning.R | 55 +---- biomod2-4.3-4-7/biomod2/README.md | 8 biomod2-4.3-4-7/biomod2/build/partial.rdb |binary biomod2-4.3-4-7/biomod2/build/vignette.rds |binary biomod2-4.3-4-7/biomod2/inst/CITATION |only biomod2-4.3-4-7/biomod2/inst/doc/news.Rmd | 18 + biomod2-4.3-4-7/biomod2/inst/doc/news.html | 30 ++ biomod2-4.3-4-7/biomod2/man/BIOMOD.ensemble.models.out.Rd | 10 biomod2-4.3-4-7/biomod2/man/BIOMOD.formated.data.PA.Rd | 8 biomod2-4.3-4-7/biomod2/man/BIOMOD.formated.data.Rd | 8 biomod2-4.3-4-7/biomod2/man/BIOMOD.models.options.Rd | 10 biomod2-4.3-4-7/biomod2/man/BIOMOD.models.out.Rd | 10 biomod2-4.3-4-7/biomod2/man/BIOMOD.options.dataset.Rd | 8 biomod2-4.3-4-7/biomod2/man/BIOMOD.options.default.Rd | 8 biomod2-4.3-4-7/biomod2/man/BIOMOD.projection.out.Rd | 10 biomod2-4.3-4-7/biomod2/man/BIOMOD.rangesize.out.Rd | 10 biomod2-4.3-4-7/biomod2/man/BIOMOD.stored.data.Rd | 10 biomod2-4.3-4-7/biomod2/man/BIOMOD_EnsembleForecasting.Rd | 14 - biomod2-4.3-4-7/biomod2/man/BIOMOD_EnsembleModeling.Rd | 14 - biomod2-4.3-4-7/biomod2/man/BIOMOD_FormatingData.Rd | 14 - biomod2-4.3-4-7/biomod2/man/BIOMOD_LoadModels.Rd | 14 - biomod2-4.3-4-7/biomod2/man/BIOMOD_Modeling.Rd | 23 +- biomod2-4.3-4-7/biomod2/man/BIOMOD_Projection.Rd | 14 - biomod2-4.3-4-7/biomod2/man/BIOMOD_RangeSize.Rd | 14 - biomod2-4.3-4-7/biomod2/man/biomod2_ensemble_model.Rd | 10 biomod2-4.3-4-7/biomod2/man/biomod2_model.Rd | 10 biomod2-4.3-4-7/biomod2/man/bm_BinaryTransformation.Rd | 38 +-- biomod2-4.3-4-7/biomod2/man/bm_CrossValidation.Rd | 38 +-- biomod2-4.3-4-7/biomod2/man/bm_FindOptimStat.Rd | 42 +-- biomod2-4.3-4-7/biomod2/man/bm_MakeFormula.Rd | 38 +-- biomod2-4.3-4-7/biomod2/man/bm_ModelAnalysis.Rd | 50 ++-- biomod2-4.3-4-7/biomod2/man/bm_ModelingOptions.Rd | 43 ++-- biomod2-4.3-4-7/biomod2/man/bm_PlotEvalBoxplot.Rd | 50 ++-- biomod2-4.3-4-7/biomod2/man/bm_PlotEvalMean.Rd | 50 ++-- biomod2-4.3-4-7/biomod2/man/bm_PlotRangeSize.Rd | 50 ++-- biomod2-4.3-4-7/biomod2/man/bm_PlotResponseCurves.Rd | 50 ++-- biomod2-4.3-4-7/biomod2/man/bm_PlotVarImpBoxplot.Rd | 50 ++-- biomod2-4.3-4-7/biomod2/man/bm_PseudoAbsences.Rd | 38 +-- biomod2-4.3-4-7/biomod2/man/bm_RangeSize.Rd | 38 +-- biomod2-4.3-4-7/biomod2/man/bm_RunModelsLoop.Rd | 38 +-- biomod2-4.3-4-7/biomod2/man/bm_SRE.Rd | 38 +-- biomod2-4.3-4-7/biomod2/man/bm_SampleBinaryVector.Rd | 38 +-- biomod2-4.3-4-7/biomod2/man/bm_SampleFactorLevels.Rd | 38 +-- biomod2-4.3-4-7/biomod2/man/bm_Tuning.Rd | 56 ++--- biomod2-4.3-4-7/biomod2/man/bm_VariablesImportance.Rd | 38 +-- biomod2-4.3-4-7/biomod2/man/getters.bm.Rd | 6 biomod2-4.3-4-7/biomod2/man/getters.out.Rd | 6 biomod2-4.3-4-7/biomod2/man/load_stored_object.Rd | 4 biomod2-4.3-4-7/biomod2/man/predict2.bm.Rd | 36 +-- biomod2-4.3-4-7/biomod2/man/predict2.em.Rd | 16 - biomod2-4.3-4-7/biomod2/man/setters.Rd | 6 biomod2-4.3-4-7/biomod2/vignettes/news.Rmd | 18 + 77 files changed, 1033 insertions(+), 979 deletions(-)
Title: Draw from Sequence of 'My Man' Posts by Kevin Kruse
Description: Starting on the afternoon of July 17, 2026, Kevin Kruse fired off an astonishing
array of 'BlueSky' replies to an initial post of his featuring a certain government figure:
<https://bsky.app/profile/did:plc:cnpe7qvcyjrhm6w7w7e4atur/post/3mqum4mxsuk2g>. This lasted a week and generated
nearly seven hundred posts. A second wave started on August 12, 2026, with this post:
<https://bsky.app/profile/kevinmkruse.bsky.social/post/3mstvbjpagc2a>. A third wave started on August 17, 2026,
with <https://bsky.app/profile/kevinmkruse.bsky.social/post/3mtcpiw7gi22j>. A fourth wave started on August 27,
2026, with <https://bsky.app/profile/kevinmkruse.bsky.social/post/3mu3pugs2yk2f>. A fifth wave ran on August 30,
2026, beginning with <https://bsky.app/profile/kevinmkruse.bsky.social/post/3mudbzy5ksk25>. A sixth wave started
September 4, 2026, with <https://bsky.app/profile/kevinmkruse.bsky.social/post/3muparqtdkk2w>. A seventh wave
started September 12, 2026, wi [...truncated...]
Author: Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between myman versions 0.1.0 dated 2026-09-27 and 0.10.0 dated 2026-10-08
ChangeLog | 114 +++++++++++ DESCRIPTION | 15 - MD5 | 16 - NAMESPACE | 2 R/myman.R | 42 +++- README.md | 23 +- inst/NEWS.Rd | 23 ++ inst/myman/myman.csv | 490 +++++++++++++++++++++++++++++++++++++++++++++++++++ man/myman.Rd | 31 ++- 9 files changed, 714 insertions(+), 42 deletions(-)
Title: Microdata Infrastructure Tools for Firm-Level Microdata Research
Description: Supports the full analysis pipeline for researchers working with
firm-level microdata. Provides data tools for panel preparation (import,
outlier detection, classification harmonization), analytical methods
(production function estimation, capital stock measurement, markups,
intensity measures, distributions, regression, clustering), and disclosure
tools for tagging outputs with dominance and observation counts before
aggregation and publication.
Production function estimation implements methods by Ackerberg, Caves and
Frazer (2015) <doi:10.3982/ECTA13408>, Levinsohn and Petrin (2003)
<doi:10.1111/1467-937X.00246>, Wooldridge (2009)
<doi:10.1016/j.econlet.2009.04.026>, Petrin, Poi and Levinsohn (2004)
<doi:10.1177/1536867X0400400202>, and Arellano and Bond (1991)
<doi:10.2307/2297968> with the "too many instruments" correction by
Roodman (2009) <doi:10.1111/j.1468-0084.2008.00542.x>. Markup estimation
follows De Loecker and Warzynski (2012) <doi:1 [...truncated...]
Author: Daniele Aglio [aut],
Eric Bartelsman [aut],
Mirja Haelbig [aut],
Marco Miorandi [aut],
Johanna Weiss [aut, cre],
Alessandro Zona Mattioli [aut],
Julian Diaz-Acosta [ctb],
Alberto Ferreira [ctb],
Javier Miranda [ctb],
Marcelo Piemonte Ribeiro [ctb],
Re [...truncated...]
Maintainer: Johanna Weiss <johanna.weiss@iwhesl.onmicrosoft.com>
Diff between mditools versions 0.1.0 dated 2026-08-20 and 0.1.1 dated 2026-10-08
DESCRIPTION | 16 + MD5 | 85 +++++----- NAMESPACE | 54 +++--- NEWS.md |only R/hier_levels.R |only R/mdi_acf_prodest.R | 4 R/mdi_aggregate.R | 32 ++- R/mdi_clustering.R | 18 +- R/mdi_hier_apply.R | 2 R/mdi_import_data.R | 54 +++++- R/mdi_jointdist.R | 17 +- R/mdi_make_conc.R | 289 +++++++++++------------------------ R/mdi_outlier.R | 4 R/mdi_regress.R | 2 R/mditools-package.R | 7 R/utils.R | 47 +++++ README.md | 6 man/check_dt.Rd |only man/hier_levels.Rd |only man/mdi_acf_prodest.Rd | 22 +- man/mdi_aggregate.Rd | 75 +++++---- man/mdi_clustering.Rd | 130 ++++++++------- man/mdi_cs_prodest.Rd | 26 +-- man/mdi_disclose_crit.Rd | 76 ++++----- man/mdi_disclose_reg_tab.Rd | 48 +++-- man/mdi_dpgmm_prodest.Rd | 14 - man/mdi_estimate_markup.Rd | 10 - man/mdi_estimate_prodfun.Rd | 66 ++++--- man/mdi_hier_apply.Rd | 48 ++--- man/mdi_import_data.Rd | 70 +++++--- man/mdi_intensity.Rd | 8 man/mdi_jointdist.Rd | 45 +++-- man/mdi_lp_prodest.Rd | 18 +- man/mdi_make_conc.Rd | 44 +++-- man/mdi_ols_prodest.Rd | 14 - man/mdi_outlier.Rd | 12 - man/mdi_pim_capital.Rd | 26 +-- man/mdi_regress.Rd | 106 ++++++------ man/mdi_transition.Rd | 12 - man/mdi_wdrg_prodest.Rd | 6 man/mditools-package.Rd | 8 man/panel_lag_L.Rd |only tests/testthat/test-mdi_aggregate.R | 19 ++ tests/testthat/test-mdi_clustering.R | 37 ++++ tests/testthat/test-mdi_make_conc.R | 111 +++++++++++++ tests/testthat/test-mdi_outlier.R | 4 46 files changed, 996 insertions(+), 696 deletions(-)
Title: Read and Write General Transit Feed Specification (GTFS) Files
Description: Tools for the development of packages related to General
Transit Feed Specification (GTFS) files. Establishes a standard for
representing GTFS feeds using R data types. Provides fast and flexible
functions to read and write GTFS feeds while sticking to this
standard. Defines a basic 'gtfs' class which is meant to be extended
by packages that depend on it. And offers utility functions that
support checking the structure of GTFS objects.
Author: Daniel Herszenhut [aut] ,
Flavio Poletti [aut, cre],
Mark Padgham [aut],
Rafael H. M. Pereira [rev] ,
Tom Buckley [rev],
Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Flavio Poletti <flavio.poletti@hotmail.ch>
Diff between gtfsio versions 1.2.1 dated 2026-05-20 and 1.2.2 dated 2026-10-08
DESCRIPTION | 8 +++--- MD5 | 34 ++++++++++++++-------------- NEWS.md | 7 +++++ R/import_gtfs.R | 13 ++++++++-- inst/doc/gtfsio.html | 3 +- inst/extdata/macosx.zip |only inst/extdata/na_strings.zip |only inst/reference/create_gtfs_reference_data.R | 13 ++++++---- inst/tinytest/test_import_gtfs.R | 19 +++++++++++++++ man/assert_gtfs.Rd | 4 +-- man/check_field_class.Rd | 6 ++-- man/check_field_exists.Rd | 6 ++-- man/check_file_exists.Rd | 6 ++-- man/export_gtfs.Rd | 4 +-- man/gtfsio-package.Rd | 1 man/gtfsio_error.Rd | 4 +-- man/import_gtfs.Rd | 7 +++-- man/new_gtfs.Rd | 4 +-- man/parent_function_error.Rd | 4 +-- 19 files changed, 92 insertions(+), 51 deletions(-)
Title: Visually Exploring Random Forests
Description: Graphic elements for exploring Random Forests using the
'randomForest' or 'randomForestSRC' package for survival, regression
and classification forests and 'ggplot2' package plotting. Implements
visualizations of the methods described in Breiman (2001)
<doi:10.1023/A:1010933404324> and Ishwaran, Kogalur, Blackstone, and
Lauer (2008) <doi:10.1214/08-AOAS169>.
Author: John Ehrlinger [aut, cre]
Maintainer: John Ehrlinger <john.ehrlinger@gmail.com>
Diff between ggRandomForests versions 3.5.3 dated 2026-09-11 and 3.5.4 dated 2026-10-08
DESCRIPTION | 8 MD5 | 57 +- NEWS.md | 81 +++ R/gg_partial.R | 9 R/gg_partial_rfsrc.R | 67 ++- R/gg_partial_varpro.R | 4 R/gg_udependent.R | 30 + R/kaplan.R | 31 - R/nelson.R | 84 +++ R/plot.gg_partial.R | 116 ++++- R/utils.R | 82 ++- inst/doc/ggRandomForests-classification.html | 45 +- inst/doc/ggRandomForests-regression.html | 53 +- inst/doc/ggRandomForests-survival.html | 61 +- inst/doc/ggRandomForests.html | 21 inst/doc/uvarpro.html | 21 inst/doc/varpro.html | 41 + man/gg_partial.Rd | 9 man/gg_partial_rfsrc.Rd | 20 man/gg_partial_varpro.Rd | 4 man/gg_udependent.Rd | 13 man/nelson.Rd | 18 man/plot.gg_partial.Rd | 7 man/plot.gg_partial_rfsrc.Rd | 19 tests/testthat/_snaps/snapshots/gg-partial-categorical.svg |only tests/testthat/_snaps/snapshots/gg-partial-rfsrc-categorical-survival.svg |only tests/testthat/_snaps/snapshots/gg-partial-rfsrc-continuous-survival-by-group.svg |only tests/testthat/test_gg_partial.R | 212 ++++++++++ tests/testthat/test_gg_udependent.R | 42 + tests/testthat/test_kaplan_nelson.R | 172 +++++++- tests/testthat/test_snapshots.R | 43 ++ 31 files changed, 1109 insertions(+), 261 deletions(-)
More information about ggRandomForests at CRAN
Permanent link
Title: 'Amazon Web Services' Compute Services
Description: Interface to 'Amazon Web Services' compute services,
including 'Elastic Compute Cloud' ('EC2'), 'Lambda'
functions-as-a-service, containers, batch processing, and more
<https://aws.amazon.com/>.
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.compute versions 0.10.0 dated 2026-05-31 and 0.11.0 dated 2026-10-08
DESCRIPTION | 11 MD5 | 571 - NAMESPACE | 36 R/apprunner_interfaces.R | 222 R/apprunner_operations.R | 111 R/apprunner_service.R | 4 R/batch_interfaces.R | 300 R/batch_operations.R | 265 R/batch_service.R | 7 R/braket_interfaces.R | 102 R/braket_operations.R | 51 R/braket_service.R | 8 R/computeoptimizer_interfaces.R | 168 R/computeoptimizer_operations.R | 100 R/computeoptimizer_service.R | 4 R/ec2_interfaces.R | 4851 +++------- R/ec2_operations.R | 4064 ++++++-- R/ec2_service.R | 52 R/ec2instanceconnect_interfaces.R | 12 R/ec2instanceconnect_operations.R | 6 R/ec2instanceconnect_service.R | 4 R/ecr_interfaces.R | 348 R/ecr_operations.R | 174 R/ecr_service.R | 6 R/ecrpublic_interfaces.R | 138 R/ecrpublic_operations.R | 69 R/ecrpublic_service.R | 6 R/ecs_interfaces.R | 462 R/ecs_operations.R | 319 R/ecs_service.R | 4 R/eks_interfaces.R | 444 R/eks_operations.R | 425 R/eks_service.R | 10 R/elasticbeanstalk_interfaces.R | 237 R/elasticbeanstalk_operations.R | 338 R/elasticbeanstalk_service.R | 38 R/emrcontainers_interfaces.R | 158 R/emrcontainers_operations.R | 154 R/emrcontainers_service.R | 8 R/emrserverless_interfaces.R | 132 R/emrserverless_operations.R | 66 R/emrserverless_service.R | 4 R/imagebuilder_interfaces.R | 462 R/imagebuilder_operations.R | 950 + R/imagebuilder_service.R | 86 R/lambda_interfaces.R | 506 - R/lambda_operations.R | 476 R/lambda_service.R | 9 R/lightsail_interfaces.R | 976 -- R/lightsail_operations.R | 544 - R/lightsail_service.R | 5 R/proton_interfaces.R | 522 - R/proton_operations.R | 261 R/proton_service.R | 4 R/serverlessapplicationrepository_interfaces.R | 78 R/serverlessapplicationrepository_operations.R | 42 R/serverlessapplicationrepository_service.R | 4 R/sysdata.rda |only man/apprunner.Rd | 4 man/batch.Rd | 7 man/batch_cancel_job.Rd | 4 man/batch_cancel_jobs.Rd |only man/batch_create_compute_environment.Rd | 7 man/batch_register_job_definition.Rd | 4 man/batch_terminate_job.Rd | 4 man/batch_terminate_jobs.Rd |only man/batch_terminate_service_job.Rd | 2 man/batch_terminate_service_jobs.Rd |only man/batch_update_compute_environment.Rd | 8 man/braket.Rd | 6 man/computeoptimizer.Rd | 4 man/computeoptimizer_put_recommendation_preferences.Rd | 11 man/ec2.Rd | 50 man/ec2_allocate_hosts.Rd | 3 man/ec2_associate_application_status_check.Rd |only man/ec2_attach_image_watermark.Rd |only man/ec2_authorize_security_group_ingress.Rd | 2 man/ec2_batch_modify_ipam_routing_policy_registrations.Rd |only man/ec2_cancel_capacity_reservation.Rd | 11 man/ec2_copy_image.Rd | 2 man/ec2_copy_snapshot.Rd | 2 man/ec2_copy_volumes.Rd | 8 man/ec2_create_application_status_check.Rd |only man/ec2_create_capacity_reservation_cancellation_quote.Rd |only man/ec2_create_capacity_reservation_date_change_quote.Rd |only man/ec2_create_capacity_reservation_fleet.Rd | 4 man/ec2_create_client_vpn_endpoint.Rd | 5 man/ec2_create_fleet.Rd | 4 man/ec2_create_flow_logs.Rd | 7 man/ec2_create_image.Rd | 21 man/ec2_create_interruptible_capacity_reservation_allocation.Rd | 5 man/ec2_create_ipam_internet_registry_association.Rd |only man/ec2_create_ipam_routing_policy_registration.Rd |only man/ec2_create_placement_group.Rd | 3 man/ec2_create_replace_root_volume_task.Rd | 17 man/ec2_create_traffic_mirror_filter_rule.Rd | 2 man/ec2_create_transit_gateway_policy_table_entry.Rd |only man/ec2_create_vpc_endpoint.Rd | 16 man/ec2_delete_application_status_check.Rd |only man/ec2_delete_client_vpn_endpoint_authorization_policy.Rd |only man/ec2_delete_ipam_internet_registry_association.Rd |only man/ec2_delete_ipam_routing_policy_registration.Rd |only man/ec2_delete_placement_group.Rd | 2 man/ec2_delete_transit_gateway_policy_table_entry.Rd |only man/ec2_describe_account_vpc_encryption_control.Rd |only man/ec2_describe_application_status.Rd |only man/ec2_describe_application_status_check_associations.Rd |only man/ec2_describe_application_status_checks.Rd |only man/ec2_describe_capacity_reservation_cancellation_quotes.Rd |only man/ec2_describe_capacity_reservation_date_change_quotes.Rd |only man/ec2_describe_capacity_reservation_topology.Rd | 2 man/ec2_describe_images.Rd | 9 man/ec2_describe_instance_status.Rd | 1 man/ec2_describe_ipam_internet_registry_associations.Rd |only man/ec2_describe_placement_groups.Rd | 2 man/ec2_describe_volumes_modifications.Rd | 5 man/ec2_describe_vpc_endpoints.Rd | 2 man/ec2_detach_image_watermark.Rd |only man/ec2_disable_application_status_check_suppression.Rd |only man/ec2_disassociate_application_status_check.Rd |only man/ec2_enable_application_status_check_suppression.Rd |only man/ec2_enable_ipam_internet_registry_association.Rd |only man/ec2_get_client_vpn_endpoint_authorization_policy.Rd |only man/ec2_get_ipam_discovered_routes.Rd |only man/ec2_get_ipam_internet_registry_association_asns.Rd |only man/ec2_get_ipam_internet_registry_association_cidrs.Rd |only man/ec2_get_ipam_route_origin_authorizations.Rd |only man/ec2_get_ipam_route_protection_findings.Rd |only man/ec2_get_ipam_routing_policy_registration_deltas.Rd |only man/ec2_get_ipam_routing_policy_registrations.Rd |only man/ec2_get_spot_placement_scores.Rd | 7 man/ec2_get_transit_gateway_policy_table_entries.Rd | 13 man/ec2_modify_account_vpc_encryption_control.Rd |only man/ec2_modify_application_status_check.Rd |only man/ec2_modify_capacity_reservation.Rd | 11 man/ec2_modify_client_vpn_endpoint.Rd | 5 man/ec2_modify_client_vpn_endpoint_authorization_policy.Rd |only man/ec2_modify_ipam_routing_policy_registration.Rd |only man/ec2_modify_transit_gateway_policy_table_entry.Rd |only man/ec2_modify_vpc_endpoint_payer_responsibility.Rd |only man/ec2_replace_image_instance_type_specification.Rd |only man/ec2_revoke_security_group_ingress.Rd | 2 man/ec2_update_interruptible_capacity_reservation_allocation.Rd | 9 man/ec2_validate_security_group_quotas_for_interface.Rd |only man/ec2instanceconnect.Rd | 4 man/ecr.Rd | 4 man/ecrpublic.Rd | 4 man/ecs.Rd | 4 man/ecs_create_daemon.Rd | 11 man/ecs_create_express_gateway_service.Rd | 30 man/ecs_create_service.Rd | 5 man/ecs_list_daemons.Rd | 2 man/ecs_register_daemon_task_definition.Rd | 12 man/ecs_update_daemon.Rd | 11 man/ecs_update_express_gateway_service.Rd | 22 man/ecs_update_service.Rd | 5 man/eks.Rd | 10 man/eks_activate_certificate_authority.Rd |only man/eks_cancel_update.Rd |only man/eks_create_certificate_authority.Rd |only man/eks_create_cluster.Rd | 11 man/eks_delete_certificate_authority.Rd |only man/eks_describe_certificate_authority.Rd |only man/eks_list_certificate_authorities.Rd |only man/eks_update_cluster_config.Rd | 13 man/eks_update_cluster_version.Rd | 7 man/elasticbeanstalk.Rd | 36 man/elasticbeanstalk_associate_environment_operations_role.Rd | 5 man/elasticbeanstalk_create_application_version.Rd | 23 man/elasticbeanstalk_create_configuration_template.Rd | 12 man/elasticbeanstalk_create_environment.Rd | 18 man/elasticbeanstalk_describe_account_attributes.Rd | 6 man/elasticbeanstalk_describe_applications.Rd | 2 man/elasticbeanstalk_describe_configuration_settings.Rd | 4 man/elasticbeanstalk_describe_environment_health.Rd | 2 man/elasticbeanstalk_describe_environment_resources.Rd | 12 man/elasticbeanstalk_describe_environments.Rd | 8 man/elasticbeanstalk_describe_events.Rd | 18 man/elasticbeanstalk_describe_instances_health.Rd | 10 man/elasticbeanstalk_disassociate_environment_operations_role.Rd | 5 man/elasticbeanstalk_list_platform_branches.Rd | 5 man/elasticbeanstalk_list_platform_versions.Rd | 5 man/elasticbeanstalk_list_tags_for_resource.Rd | 4 man/elasticbeanstalk_rebuild_environment.Rd | 10 man/elasticbeanstalk_request_environment_info.Rd | 4 man/elasticbeanstalk_restart_app_server.Rd | 4 man/elasticbeanstalk_retrieve_environment_info.Rd | 4 man/elasticbeanstalk_terminate_environment.Rd | 12 man/elasticbeanstalk_update_application.Rd | 2 man/elasticbeanstalk_update_environment.Rd | 18 man/elasticbeanstalk_update_tags_for_resource.Rd | 4 man/emrcontainers.Rd | 8 man/emrcontainers_create_managed_endpoint.Rd | 5 man/emrcontainers_create_virtual_cluster.Rd | 10 man/emrcontainers_delete_security_configuration.Rd |only man/emrcontainers_delete_virtual_cluster.Rd | 2 man/emrcontainers_describe_virtual_cluster.Rd | 2 man/emrcontainers_list_virtual_clusters.Rd | 2 man/emrcontainers_update_virtual_cluster.Rd |only man/emrserverless.Rd | 4 man/imagebuilder.Rd | 86 man/imagebuilder_cancel_image_creation.Rd | 6 man/imagebuilder_cancel_lifecycle_execution.Rd | 7 man/imagebuilder_create_component.Rd | 12 man/imagebuilder_create_container_recipe.Rd | 25 man/imagebuilder_create_distribution_configuration.Rd | 13 man/imagebuilder_create_image.Rd | 25 man/imagebuilder_create_image_pipeline.Rd | 35 man/imagebuilder_create_image_recipe.Rd | 26 man/imagebuilder_create_infrastructure_configuration.Rd | 33 man/imagebuilder_create_lifecycle_policy.Rd | 23 man/imagebuilder_create_workflow.Rd | 22 man/imagebuilder_delete_component.Rd | 2 man/imagebuilder_delete_container_recipe.Rd | 2 man/imagebuilder_delete_distribution_configuration.Rd | 2 man/imagebuilder_delete_image_pipeline.Rd | 2 man/imagebuilder_delete_infrastructure_configuration.Rd | 2 man/imagebuilder_delete_lifecycle_policy.Rd | 4 man/imagebuilder_delete_workflow.Rd | 2 man/imagebuilder_distribute_image.Rd | 23 man/imagebuilder_get_component.Rd | 6 man/imagebuilder_get_component_policy.Rd | 4 man/imagebuilder_get_distribution_configuration.Rd | 4 man/imagebuilder_get_image.Rd | 6 man/imagebuilder_get_image_pipeline.Rd | 4 man/imagebuilder_get_image_policy.Rd | 4 man/imagebuilder_get_image_recipe.Rd | 6 man/imagebuilder_get_image_recipe_policy.Rd | 4 man/imagebuilder_get_infrastructure_configuration.Rd | 4 man/imagebuilder_get_lifecycle_execution.Rd | 9 man/imagebuilder_get_lifecycle_policy.Rd | 4 man/imagebuilder_get_marketplace_resource.Rd | 6 man/imagebuilder_get_workflow.Rd | 6 man/imagebuilder_get_workflow_execution.Rd | 6 man/imagebuilder_get_workflow_step_execution.Rd | 8 man/imagebuilder_import_component.Rd | 16 man/imagebuilder_import_disk_image.Rd | 16 man/imagebuilder_import_vm_image.Rd | 17 man/imagebuilder_list_component_build_versions.Rd | 12 man/imagebuilder_list_components.Rd | 15 man/imagebuilder_list_container_recipes.Rd | 6 man/imagebuilder_list_distribution_configurations.Rd | 4 man/imagebuilder_list_image_build_versions.Rd | 6 man/imagebuilder_list_image_packages.Rd | 10 man/imagebuilder_list_image_pipeline_images.Rd | 4 man/imagebuilder_list_image_pipelines.Rd | 4 man/imagebuilder_list_image_recipes.Rd | 4 man/imagebuilder_list_image_scan_finding_aggregations.Rd | 11 man/imagebuilder_list_image_scan_findings.Rd | 14 man/imagebuilder_list_images.Rd | 12 man/imagebuilder_list_infrastructure_configurations.Rd | 4 man/imagebuilder_list_lifecycle_execution_resources.Rd | 14 man/imagebuilder_list_lifecycle_executions.Rd | 10 man/imagebuilder_list_lifecycle_policies.Rd | 11 man/imagebuilder_list_waiting_workflow_steps.Rd | 10 man/imagebuilder_list_workflow_build_versions.Rd | 6 man/imagebuilder_list_workflow_executions.Rd | 4 man/imagebuilder_list_workflow_step_executions.Rd | 4 man/imagebuilder_list_workflows.Rd | 14 man/imagebuilder_put_component_policy.Rd | 2 man/imagebuilder_put_container_recipe_policy.Rd | 4 man/imagebuilder_put_image_policy.Rd | 4 man/imagebuilder_put_image_recipe_policy.Rd | 2 man/imagebuilder_retry_image.Rd | 9 man/imagebuilder_send_workflow_step_action.Rd | 16 man/imagebuilder_start_image_pipeline_execution.Rd | 6 man/imagebuilder_start_resource_state_update.Rd | 19 man/imagebuilder_update_distribution_configuration.Rd | 8 man/imagebuilder_update_image_pipeline.Rd | 30 man/imagebuilder_update_infrastructure_configuration.Rd | 26 man/imagebuilder_update_lifecycle_policy.Rd | 16 man/lambda.Rd | 7 man/lambda_add_permission.Rd | 14 man/lambda_create_capacity_provider.Rd | 8 man/lambda_create_event_source_mapping.Rd | 24 man/lambda_create_function.Rd | 22 man/lambda_delete_resource_policy.Rd |only man/lambda_get_durable_execution.Rd | 4 man/lambda_get_resource_policy.Rd |only man/lambda_invoke.Rd | 4 man/lambda_invoke_with_response_stream.Rd | 16 man/lambda_list_durable_executions_by_function.Rd | 2 man/lambda_list_layer_versions.Rd | 8 man/lambda_list_layers.Rd | 8 man/lambda_publish_layer_version.Rd | 8 man/lambda_put_resource_policy.Rd |only man/lambda_update_capacity_provider.Rd | 8 man/lambda_update_event_source_mapping.Rd | 34 man/lambda_update_function_code.Rd | 21 man/lambda_update_function_configuration.Rd | 4 man/lightsail.Rd | 5 man/lightsail_create_distribution.Rd | 15 man/lightsail_create_relational_database.Rd | 4 man/lightsail_get_profile.Rd |only man/lightsail_update_distribution.Rd | 17 man/proton.Rd | 4 man/serverlessapplicationrepository.Rd | 4 tests/testthat.R |only tests/testthat/test_apprunner.R | 14 tests/testthat/test_batch.R | 9 tests/testthat/test_braket.R | 2 tests/testthat/test_computeoptimizer.R | 3 tests/testthat/test_ec2.R | 366 tests/testthat/test_ec2instanceconnect.R | 2 tests/testthat/test_ecr.R | 7 tests/testthat/test_ecrpublic.R | 4 tests/testthat/test_ecs.R | 10 tests/testthat/test_eks.R | 7 tests/testthat/test_elasticbeanstalk.R | 10 tests/testthat/test_emrcontainers.R | 5 tests/testthat/test_emrserverless.R | 3 tests/testthat/test_imagebuilder.R | 17 tests/testthat/test_lambda.R | 7 tests/testthat/test_lightsail.R | 2 tests/testthat/test_proton.R | 10 tests/testthat/test_serverlessapplicationrepository.R | 3 316 files changed, 12014 insertions(+), 9639 deletions(-)
Title: Idealisation of Patch Clamp Recordings
Description: Implements the model-free multiscale idealisation approaches: Jump-Segmentation by MUltiResolution Filter (JSMURF), Hotz et al. (2013) <doi:10.1109/TNB.2013.2284063>, JUmp Local dEconvolution Segmentation filter (JULES), Pein et al. (2018) <doi:10.1109/TNB.2018.2845126>, and Heterogeneous Idealization by Local testing and DEconvolution (HILDE), Pein et al. (2021) <doi:10.1109/TNB.2020.3031202>. Further details on how to use them are given in Pein, Eltzner and Munk (2021) <doi:10.1007/s00249-021-01506-8>.
Author: Florian Pein [aut, cre],
Timo Aspelmeier [ctb]
Maintainer: Florian Pein <f.pein@lancaster.ac.uk>
This is a re-admission after prior archival of version 1.2-0 dated 2025-06-27
Diff between clampSeg versions 1.2-0 dated 2025-06-27 and 1.3-0 dated 2026-10-08
clampSeg-1.2-0/clampSeg/build/vignette.rds |only clampSeg-1.2-0/clampSeg/inst/doc |only clampSeg-1.2-0/clampSeg/vignettes |only clampSeg-1.3-0/clampSeg/ChangeLog | 51 +++++++ clampSeg-1.3-0/clampSeg/DESCRIPTION | 17 +- clampSeg-1.3-0/clampSeg/MD5 | 54 ++----- clampSeg-1.3-0/clampSeg/build/partial.rdb |only clampSeg-1.3-0/clampSeg/inst/CITATION | 16 ++ clampSeg-1.3-0/clampSeg/man/clampSeg-package.Rd | 62 +++++---- clampSeg-1.3-0/clampSeg/man/createLocalList.Rd | 32 +++- clampSeg-1.3-0/clampSeg/man/deconvolveLocally.Rd | 14 +- clampSeg-1.3-0/clampSeg/man/getCritVal.Rd | 47 +++++- clampSeg-1.3-0/clampSeg/man/hilde.Rd | 82 ++++++++---- clampSeg-1.3-0/clampSeg/man/improveSmallScales.Rd | 50 ++++--- clampSeg-1.3-0/clampSeg/man/jsmurf.Rd | 53 +++++-- clampSeg-1.3-0/clampSeg/man/jules.Rd | 53 +++++-- clampSeg-1.3-0/clampSeg/man/lowpassFilter.Rd | 19 ++ clampSeg-1.3-0/clampSeg/man/stepDetection.Rd | 44 ++++-- clampSeg-1.3-0/clampSeg/tests/testthat.R | 7 - clampSeg-1.3-0/clampSeg/tests/testthat/test_cacheLocation.R |only 20 files changed, 414 insertions(+), 187 deletions(-)
Title: Word and Document Vector Models
Description: Create dense vector representation of words and documents using 'quanteda'. Implements Word2vec (Mikolov et al., 2013) <doi:10.48550/arXiv.1310.4546>, Doc2vec (Le & Mikolov, 2014) <doi:10.48550/arXiv.1405.4053> and Latent Semantic Analysis (Deerwester et al., 1990) <doi:10.1002/(SICI)1097-4571(199009)41:6%3C391::AID-ASI1%3E3.0.CO;2-9>.
Author: Kohei Watanabe [aut, cre, cph] ,
Jan Wijffels [aut] ,
BNOSAC [cph] ,
Max Fomichev [ctb, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between wordvector versions 0.6.4 dated 2026-09-10 and 0.6.5 dated 2026-10-08
DESCRIPTION | 8 - MD5 | 32 ++++--- NAMESPACE | 13 ++ NEWS.md | 7 + R/as.doc2vec.R | 97 ++++++++++++++++------ R/as.word2vec.R | 31 +++---- R/doc2vec.R | 6 - R/lsa.R | 21 ++-- R/object-builder.R |only R/utils.R | 25 +++++ R/word2vec.R | 94 --------------------- R/wordvector.R |only inst/WORDLIST | 6 + man/as.textmodel_doc2vec.Rd | 14 ++- man/check_model.Rd |only tests/testthat/test-as.doc2vec.R | 153 ++++++++++++++++++++++++++++------- tests/testthat/test-as.word2vec.R | 7 + tests/testthat/test-lsa.R | 16 ++- tests/testthat/test-object-builder.R |only 19 files changed, 326 insertions(+), 204 deletions(-)
Title: Access Nature Media Repositories
Description: Streamline searching, downloading and formatting of nature media files (e.g. audios, photos) from online repositories. The package offers functions for obtaining media metadata from online repositories, downloading associated media files and updating data sets with new records.
Author: Marcelo Araya-Salas [aut, cre] ,
Jorge Elizondo-Calvo [aut] ,
Alejandro Rico-Guevara [aut] ,
Hugo Gruson [rev] ,
Eric R Scott [rev]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
Diff between suwo versions 0.2.1 dated 2026-04-20 and 0.2.2 dated 2026-10-08
DESCRIPTION | 25 MD5 | 91 +- NAMESPACE | 1 NEWS.md | 133 ++- R/access_wikiaves.R |only R/download_media.R | 33 R/find_duplicates.R | 43 - R/internal_functions.R | 392 ++++++++++- R/map_locations.R | 72 ++ R/query_gbif.R | 2 R/query_macaulay.R | 3 R/query_wikiaves.R | 248 +++++-- R/query_xenocanto.R | 131 +++ R/remove_duplicates.R | 7 R/sysdata.rda |binary R/template_params.R | 5 R/update_metadata.R | 62 + README.md | 208 +++--- build/vignette.rds |binary inst/CITATION | 8 inst/doc/suwo.Rmd | 815 ++++++++++++------------ inst/doc/suwo.html | 949 ++++++++++++---------------- inst/figures/logo.png |binary man/access_wikiaves.Rd |only man/download_media.Rd | 16 man/figures/logo.png |binary man/find_duplicates.Rd | 8 man/map_locations.Rd | 21 man/query_gbif.Rd | 1 man/query_wikiaves.Rd | 166 ++-- man/query_xenocanto.Rd | 64 + man/remove_duplicates.Rd | 7 man/template_params.Rd | 5 man/update_metadata.Rd | 53 + tests/testthat/test_download_media.R | 6 tests/testthat/test_internals.R | 4 tests/testthat/test_query_gbif.R | 2 tests/testthat/test_query_inaturalist.R | 2 tests/testthat/test_query_wikiaves.R | 40 - tests/testthat/test_query_xenocanto.R | 38 + tests/testthat/test_update_metadata.R | 27 tests/testthat/test_wikiaves_helpers.R |only vignettes/precompile.R | 10 vignettes/query_function_summary.txt | 10 vignettes/references.bib |only vignettes/suwo.Rmd | 815 ++++++++++++------------ vignettes/suwo.Rmd.orig | 88 ++ vignettes/workflow_diagram.png |binary vignettes/xenocanto_annotations_queries.rds |only 49 files changed, 2839 insertions(+), 1772 deletions(-)
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 1.0.1 dated 2026-09-07 and 1.1.0 dated 2026-10-08
DESCRIPTION | 6 MD5 | 15 + NAMESPACE | 254 ++++++++++++++++----------------- NEWS.md | 24 +-- R/character.r | 32 ++++ README.md | 12 - man/rm.prefix.Rd |only src/prefix_suffix.c |only src/suppr-package.c | 4 tests/testthat/test-rm.prefix_suffix.r |only 10 files changed, 197 insertions(+), 150 deletions(-)
Title: The Q Approach to Consensus Building
Description: Implements a workflow based on Q method to support
consensus-building processes. It prepares participant rankings, selects
and fits group perspectives, calculates consensus priority scores,
validates results by bootstrap resampling, and produces publication-ready
figures. The underlying method is described by Geschke et al. (2022)
"The Q approach to consensus building: integrating diverse perspectives
to guide decision-making" <doi:10.32942/X2F59S>.
Author: Jonas Geschke [aut, cre]
Maintainer: Jonas Geschke <hallo@qapproach.app>
Diff between qapproach versions 0.1.1 dated 2026-09-22 and 0.1.2 dated 2026-10-08
DESCRIPTION | 6 MD5 | 57 + NAMESPACE | 4 NEWS.md | 52 + R/analysis.R | 89 +- R/api-documentation.R | 22 R/validation.R | 483 +++++++++++-- R/visualization.R | 1084 ++++++++++++++++++++++++++++++ inst/COPYRIGHTS |only inst/doc/qapproach.pdf |binary inst/extdata |only man/agreement_across_levels.Rd |only man/plot_hierarchical_levels.Rd |only man/plot_sdg_cps.Rd |only man/plot_sdg_diamonds.Rd |only man/qapproach-bootstrap.Rd | 3 man/qapproach.Rd | 19 man/validate.Rd | 17 man/validation_cps.Rd | 7 man/validation_means.Rd | 23 tests/testthat/Rplots.pdf |only tests/testthat/test-bootstrap-alignment.R | 2 tests/testthat/test-prepare-rankings.R | 12 tests/testthat/test-validation-api.R | 200 +++++ tests/testthat/test-visualization-api.R | 170 ++++ 25 files changed, 2097 insertions(+), 153 deletions(-)
Title: 'Amazon Web Services' Security, Identity, & Compliance Services
Description: Interface to 'Amazon Web Services' security, identity, and
compliance services, including the 'Identity & Access Management'
('IAM') service for managing access to services and resources, and
more <https://aws.amazon.com/>.
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.security.identity versions 0.10.0 dated 2026-05-31 and 0.11.0 dated 2026-10-08
DESCRIPTION | 11 MD5 | 580 +++--- NAMESPACE | 36 R/accessanalyzer_interfaces.R | 207 -- R/accessanalyzer_operations.R | 117 - R/accessanalyzer_service.R | 6 R/account_interfaces.R | 102 - R/account_operations.R | 166 + R/account_service.R | 9 R/acm_interfaces.R | 299 ++- R/acm_operations.R | 845 +++++++++- R/acm_service.R | 29 R/acmpca_interfaces.R | 105 - R/acmpca_operations.R | 73 R/acmpca_service.R | 4 R/cleanroomsml_interfaces.R | 309 +-- R/cleanroomsml_operations.R | 177 +- R/cleanroomsml_service.R | 4 R/clouddirectory_interfaces.R | 393 +--- R/clouddirectory_operations.R | 198 +- R/clouddirectory_service.R | 6 R/cloudhsm_interfaces.R | 120 - R/cloudhsm_operations.R | 60 R/cloudhsm_service.R | 4 R/cloudhsmv2_interfaces.R | 108 - R/cloudhsmv2_operations.R | 54 R/cloudhsmv2_service.R | 6 R/cognitoidentity_interfaces.R | 126 - R/cognitoidentity_operations.R | 69 R/cognitoidentity_service.R | 6 R/cognitoidentityprovider_interfaces.R | 793 +++------ R/cognitoidentityprovider_operations.R | 799 +++++++-- R/cognitoidentityprovider_service.R | 16 R/cognitosync_interfaces.R | 99 - R/cognitosync_operations.R | 51 R/cognitosync_service.R | 4 R/detective_interfaces.R | 141 - R/detective_operations.R | 87 - R/detective_service.R | 6 R/directoryservice_interfaces.R | 480 +---- R/directoryservice_operations.R | 240 +- R/directoryservice_service.R | 4 R/fms_interfaces.R | 225 -- R/fms_operations.R | 126 - R/fms_service.R | 4 R/guardduty_interfaces.R | 663 +++---- R/guardduty_operations.R | 814 ++++++++- R/guardduty_service.R | 21 R/iam_interfaces.R | 835 +++------ R/iam_operations.R | 703 ++++++-- R/iam_service.R | 10 R/iamrolesanywhere_interfaces.R | 180 -- R/iamrolesanywhere_operations.R | 90 - R/iamrolesanywhere_service.R | 4 R/identitystore_interfaces.R | 144 - R/identitystore_operations.R | 259 ++- R/identitystore_service.R | 17 R/inspector2_interfaces.R | 510 ++---- R/inspector2_operations.R | 452 ++++- R/inspector2_service.R | 14 R/inspector_interfaces.R | 192 -- R/inspector_operations.R | 119 - R/inspector_service.R | 6 R/kms_interfaces.R | 282 +-- R/kms_operations.R | 164 + R/kms_service.R | 4 R/macie2_interfaces.R | 486 +---- R/macie2_operations.R | 243 +- R/macie2_service.R | 6 R/pcaconnectorad_interfaces.R | 117 - R/pcaconnectorad_operations.R | 75 R/pcaconnectorad_service.R | 4 R/ram_interfaces.R | 210 -- R/ram_operations.R | 105 - R/ram_service.R | 4 R/secretsmanager_interfaces.R | 132 - R/secretsmanager_operations.R | 69 R/secretsmanager_service.R | 4 R/securityhub_interfaces.R | 754 +++----- R/securityhub_operations.R | 698 ++++++-- R/securityhub_service.R | 16 R/securitylake_interfaces.R | 186 -- R/securitylake_operations.R | 93 - R/securitylake_service.R | 4 R/shield_interfaces.R | 216 -- R/shield_operations.R | 108 - R/shield_service.R | 4 R/sso_interfaces.R | 21 R/sso_operations.R | 12 R/sso_service.R | 4 R/ssoadmin_interfaces.R | 456 +---- R/ssoadmin_operations.R | 244 +- R/ssoadmin_service.R | 4 R/ssooidc_interfaces.R | 24 R/ssooidc_operations.R | 12 R/ssooidc_service.R | 6 R/sts_interfaces.R | 66 R/sts_operations.R | 63 R/sts_service.R | 12 R/sysdata.rda |only R/verifiedpermissions_interfaces.R | 204 -- R/verifiedpermissions_operations.R | 102 - R/verifiedpermissions_service.R | 4 R/waf_interfaces.R | 462 +---- R/waf_operations.R | 231 +- R/waf_service.R | 4 R/wafregional_interfaces.R | 486 +---- R/wafregional_operations.R | 243 +- R/wafregional_service.R | 4 R/wafv2_interfaces.R | 370 +--- R/wafv2_operations.R | 347 +++- R/wafv2_service.R | 8 man/accessanalyzer.Rd | 4 man/account.Rd | 9 man/account_get_primary_email_update_status.Rd |only man/account_send_phone_number_verification.Rd |only man/account_verify_phone_number.Rd |only man/acm.Rd | 29 man/acm_create_acme_domain_validation.Rd |only man/acm_create_acme_endpoint.Rd |only man/acm_create_acme_external_account_binding.Rd |only man/acm_delete_acme_domain_validation.Rd |only man/acm_delete_acme_endpoint.Rd |only man/acm_delete_acme_external_account_binding.Rd |only man/acm_describe_acme_account.Rd |only man/acm_describe_acme_domain_validation.Rd |only man/acm_describe_acme_endpoint.Rd |only man/acm_describe_acme_external_account_binding.Rd |only man/acm_get_acme_external_account_binding_credentials.Rd |only man/acm_list_acme_accounts.Rd |only man/acm_list_acme_domain_validations.Rd |only man/acm_list_acme_endpoints.Rd |only man/acm_list_acme_external_account_bindings.Rd |only man/acm_list_certificate_domain_validations.Rd |only man/acm_list_certificates.Rd | 3 man/acm_list_tags_for_resource.Rd |only man/acm_request_certificate.Rd | 4 man/acm_revoke_acme_account.Rd |only man/acm_revoke_acme_external_account_binding.Rd |only man/acm_tag_resource.Rd |only man/acm_untag_resource.Rd |only man/acm_update_acme_domain_validation.Rd |only man/acm_update_acme_endpoint.Rd |only man/acm_update_certificate_options.Rd | 6 man/acmpca.Rd | 4 man/acmpca_create_certificate_authority.Rd | 2 man/acmpca_update_certificate_authority.Rd | 2 man/cleanroomsml.Rd | 4 man/clouddirectory.Rd | 6 man/cloudhsm.Rd | 4 man/cloudhsmv2.Rd | 4 man/cognitoidentity.Rd | 4 man/cognitoidentityprovider.Rd | 14 man/cognitoidentityprovider_admin_delete_software_token.Rd |only man/cognitoidentityprovider_admin_get_user_auth_factors.Rd |only man/cognitoidentityprovider_admin_initiate_auth.Rd | 6 man/cognitoidentityprovider_admin_link_provider_for_user.Rd | 4 man/cognitoidentityprovider_create_identity_provider.Rd | 7 man/cognitoidentityprovider_create_user_import_job.Rd | 7 man/cognitoidentityprovider_create_user_pool.Rd | 25 man/cognitoidentityprovider_create_user_pool_client.Rd | 2 man/cognitoidentityprovider_create_user_pool_domain.Rd | 9 man/cognitoidentityprovider_create_user_pool_replica.Rd |only man/cognitoidentityprovider_delete_user_pool_replica.Rd |only man/cognitoidentityprovider_describe_terms_by_client.Rd |only man/cognitoidentityprovider_get_client_token.Rd |only man/cognitoidentityprovider_get_provisioned_limit.Rd |only man/cognitoidentityprovider_initiate_auth.Rd | 6 man/cognitoidentityprovider_list_user_pool_replicas.Rd |only man/cognitoidentityprovider_update_identity_provider.Rd | 7 man/cognitoidentityprovider_update_provisioned_limit.Rd |only man/cognitoidentityprovider_update_user_pool.Rd | 13 man/cognitoidentityprovider_update_user_pool_client.Rd | 2 man/cognitoidentityprovider_update_user_pool_domain.Rd | 5 man/cognitoidentityprovider_update_user_pool_replica.Rd |only man/cognitosync.Rd | 4 man/detective.Rd | 4 man/directoryservice.Rd | 4 man/fms.Rd | 4 man/guardduty.Rd | 19 man/guardduty_create_custom_detection_rule_association.Rd |only man/guardduty_create_custom_detection_rule_org_configuration.Rd |only man/guardduty_create_filter.Rd | 7 man/guardduty_create_investigation.Rd |only man/guardduty_delete_custom_detection_rule_association.Rd |only man/guardduty_delete_custom_detection_rule_org_configuration.Rd |only man/guardduty_get_custom_detection_rule.Rd |only man/guardduty_get_custom_detection_rule_association.Rd |only man/guardduty_get_custom_detection_rule_org_configuration.Rd |only man/guardduty_get_investigation.Rd |only man/guardduty_list_custom_detection_rule_associations.Rd |only man/guardduty_list_custom_detection_rule_org_configurations.Rd |only man/guardduty_list_custom_detection_rules.Rd |only man/guardduty_list_investigations.Rd |only man/guardduty_update_custom_detection_rule_association.Rd |only man/guardduty_update_custom_detection_rule_org_configuration.Rd |only man/guardduty_update_filter.Rd | 7 man/iam.Rd | 8 man/iam_acquire_role.Rd |only man/iam_create_service_specific_credential.Rd | 4 man/iam_get_account_properties.Rd |only man/iam_get_role_template_version.Rd |only man/iam_list_service_specific_credentials.Rd | 2 man/iam_put_account_properties.Rd |only man/iam_simulate_custom_policy.Rd | 11 man/iam_simulate_principal_policy.Rd | 13 man/iamrolesanywhere.Rd | 4 man/identitystore.Rd | 17 man/identitystore_create_group.Rd | 4 man/identitystore_create_group_membership.Rd | 8 man/identitystore_create_user.Rd | 4 man/identitystore_delete_group.Rd | 12 man/identitystore_delete_group_membership.Rd | 8 man/identitystore_delete_user.Rd | 12 man/identitystore_describe_group.Rd | 8 man/identitystore_describe_group_membership.Rd | 8 man/identitystore_describe_identity_store.Rd |only man/identitystore_describe_user.Rd | 8 man/identitystore_get_group_id.Rd | 4 man/identitystore_get_group_membership_id.Rd | 8 man/identitystore_get_user_id.Rd | 4 man/identitystore_is_member_in_groups.Rd | 8 man/identitystore_list_group_memberships.Rd | 10 man/identitystore_list_group_memberships_for_member.Rd | 8 man/identitystore_list_groups.Rd | 8 man/identitystore_list_identity_stores.Rd |only man/identitystore_list_users.Rd | 8 man/identitystore_update_group.Rd | 17 man/identitystore_update_identity_store.Rd |only man/identitystore_update_user.Rd | 12 man/inspector.Rd | 6 man/inspector2.Rd | 14 man/inspector2_create_connector.Rd |only man/inspector2_delete_connector.Rd |only man/inspector2_get_configuration.Rd | 9 man/inspector2_list_connector_scan_configurations.Rd |only man/inspector2_list_connectors.Rd |only man/inspector2_update_configuration.Rd | 12 man/inspector2_update_connector.Rd |only man/inspector2_update_connector_scan_configuration.Rd |only man/inspector_create_assessment_target.Rd | 2 man/inspector_create_assessment_template.Rd | 2 man/inspector_get_assessment_report.Rd | 2 man/inspector_list_assessment_targets.Rd | 2 man/kms.Rd | 4 man/kms_derive_shared_secret.Rd | 2 man/macie2.Rd | 4 man/pcaconnectorad.Rd | 4 man/ram.Rd | 4 man/secretsmanager.Rd | 4 man/securityhub.Rd | 14 man/securityhub_create_connector.Rd |only man/securityhub_delete_connector.Rd |only man/securityhub_describe_standards.Rd | 8 man/securityhub_disable_security_hub_feature_v2.Rd |only man/securityhub_disable_security_hub_v2.Rd | 2 man/securityhub_enable_security_hub_feature_v2.Rd |only man/securityhub_get_connector.Rd |only man/securityhub_get_enabled_standards.Rd | 5 man/securityhub_get_remediations_v2.Rd |only man/securityhub_list_connectors.Rd |only man/securityhub_list_connectors_v2.Rd | 5 man/securityhub_list_exposures_by_remediation_v2.Rd |only man/securityhub_list_free_trial_statuses_v2.Rd |only man/securityhub_list_security_control_definitions.Rd | 5 man/securityhub_update_connector.Rd |only man/securitylake.Rd | 4 man/shield.Rd | 4 man/sso.Rd | 4 man/ssoadmin.Rd | 4 man/ssoadmin_update_instance.Rd | 7 man/ssooidc.Rd | 6 man/sts.Rd | 12 man/sts_assume_role.Rd | 5 man/sts_assume_role_with_saml.Rd | 5 man/sts_assume_role_with_web_identity.Rd | 5 man/sts_assume_root.Rd | 9 man/sts_get_federation_token.Rd | 5 man/sts_get_session_token.Rd | 5 man/verifiedpermissions.Rd | 4 man/waf.Rd | 4 man/wafregional.Rd | 4 man/wafv2.Rd | 8 man/wafv2_associate_web_acl.Rd | 1 man/wafv2_create_rule_group.Rd | 5 man/wafv2_create_web_acl.Rd | 5 man/wafv2_disassociate_web_acl.Rd | 1 man/wafv2_get_revenue_statistics.Rd |only man/wafv2_get_revenue_statistics_summary.Rd |only man/wafv2_get_revenue_statistics_time_series.Rd |only man/wafv2_get_web_acl_for_resource.Rd | 1 man/wafv2_list_settlement_records.Rd |only man/wafv2_update_rule_group.Rd | 5 man/wafv2_update_web_acl.Rd | 5 tests/testthat.R |only tests/testthat/test_accessanalyzer.R | 4 tests/testthat/test_account.R | 4 tests/testthat/test_acm.R | 13 tests/testthat/test_acmpca.R | 4 tests/testthat/test_cleanroomsml.R | 8 tests/testthat/test_clouddirectory.R | 10 tests/testthat/test_cloudhsm.R | 2 tests/testthat/test_cloudhsmv2.R | 6 tests/testthat/test_cognitoidentity.R | 2 tests/testthat/test_cognitoidentityprovider.R | 2 tests/testthat/test_cognitosync.R | 4 tests/testthat/test_detective.R | 8 tests/testthat/test_directoryservice.R | 8 tests/testthat/test_fms.R | 2 tests/testthat/test_guardduty.R | 41 tests/testthat/test_iam.R | 19 tests/testthat/test_iamrolesanywhere.R | 6 tests/testthat/test_identitystore.R | 10 tests/testthat/test_inspector.R | 9 tests/testthat/test_inspector2.R | 25 tests/testthat/test_kms.R | 6 tests/testthat/test_macie2.R | 16 tests/testthat/test_pcaconnectorad.R | 6 tests/testthat/test_ram.R | 7 tests/testthat/test_secretsmanager.R | 4 tests/testthat/test_securityhub.R | 57 tests/testthat/test_securitylake.R | 6 tests/testthat/test_shield.R | 7 tests/testthat/test_sso.R | 2 tests/testthat/test_ssoadmin.R | 6 tests/testthat/test_ssooidc.R | 2 tests/testthat/test_sts.R | 2 tests/testthat/test_verifiedpermissions.R | 4 tests/testthat/test_waf.R | 15 tests/testthat/test_wafregional.R | 15 tests/testthat/test_wafv2.R | 2 331 files changed, 11874 insertions(+), 8867 deletions(-)
More information about paws.security.identity at CRAN
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Title: 'Amazon Web Services' Machine Learning Services
Description: Interface to 'Amazon Web Services' machine learning services,
including 'SageMaker' managed machine learning service, natural
language processing, speech recognition, translation, and more
<https://aws.amazon.com/machine-learning/>.
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.machine.learning versions 0.10.0 dated 2026-05-30 and 0.11.0 dated 2026-10-08
paws.machine.learning-0.10.0/paws.machine.learning/R/panorama_interfaces.R |only paws.machine.learning-0.10.0/paws.machine.learning/R/panorama_operations.R |only paws.machine.learning-0.10.0/paws.machine.learning/R/panorama_service.R |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_create_application_instance.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_create_job_for_devices.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_create_node_from_template_job.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_create_package.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_create_package_import_job.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_delete_device.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_delete_package.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_deregister_package_version.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_describe_application_instance.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_describe_application_instance_details.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_describe_device.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_describe_device_job.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_describe_node.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_describe_node_from_template_job.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_describe_package.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_describe_package_import_job.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_describe_package_version.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_list_application_instance_dependencies.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_list_application_instance_node_instances.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_list_application_instances.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_list_devices.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_list_devices_jobs.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_list_node_from_template_jobs.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_list_nodes.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_list_package_import_jobs.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_list_packages.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_list_tags_for_resource.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_provision_device.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_register_package_version.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_remove_application_instance.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_signal_application_instance_node_instances.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_tag_resource.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_untag_resource.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/man/panorama_update_device_metadata.Rd |only paws.machine.learning-0.10.0/paws.machine.learning/tests/testthat/test_panorama.R |only paws.machine.learning-0.11.0/paws.machine.learning/DESCRIPTION | 18 paws.machine.learning-0.11.0/paws.machine.learning/MD5 | 643 +- paws.machine.learning-0.11.0/paws.machine.learning/NAMESPACE | 37 paws.machine.learning-0.11.0/paws.machine.learning/R/augmentedairuntime_interfaces.R | 30 paws.machine.learning-0.11.0/paws.machine.learning/R/augmentedairuntime_operations.R | 15 paws.machine.learning-0.11.0/paws.machine.learning/R/augmentedairuntime_service.R | 4 paws.machine.learning-0.11.0/paws.machine.learning/R/bedrock_interfaces.R | 656 +- paws.machine.learning-0.11.0/paws.machine.learning/R/bedrock_operations.R | 443 + paws.machine.learning-0.11.0/paws.machine.learning/R/bedrock_service.R | 16 paws.machine.learning-0.11.0/paws.machine.learning/R/bedrockagent_interfaces.R | 502 -- paws.machine.learning-0.11.0/paws.machine.learning/R/bedrockagent_operations.R | 500 +- paws.machine.learning-0.11.0/paws.machine.learning/R/bedrockagent_service.R | 15 paws.machine.learning-0.11.0/paws.machine.learning/R/bedrockagentcore_interfaces.R | 410 - paws.machine.learning-0.11.0/paws.machine.learning/R/bedrockagentcore_operations.R | 338 + paws.machine.learning-0.11.0/paws.machine.learning/R/bedrockagentcore_service.R | 6 paws.machine.learning-0.11.0/paws.machine.learning/R/bedrockagentcorecontrol_interfaces.R | 1122 ++-- paws.machine.learning-0.11.0/paws.machine.learning/R/bedrockagentcorecontrol_operations.R | 1506 +++++- paws.machine.learning-0.11.0/paws.machine.learning/R/bedrockagentcorecontrol_service.R | 48 paws.machine.learning-0.11.0/paws.machine.learning/R/bedrockagentruntime_interfaces.R | 226 paws.machine.learning-0.11.0/paws.machine.learning/R/bedrockagentruntime_operations.R | 260 - paws.machine.learning-0.11.0/paws.machine.learning/R/bedrockagentruntime_service.R | 14 paws.machine.learning-0.11.0/paws.machine.learning/R/bedrockdataautomation_interfaces.R | 162 paws.machine.learning-0.11.0/paws.machine.learning/R/bedrockdataautomation_operations.R | 81 paws.machine.learning-0.11.0/paws.machine.learning/R/bedrockdataautomation_service.R | 4 paws.machine.learning-0.11.0/paws.machine.learning/R/bedrockdataautomationruntime_interfaces.R | 36 paws.machine.learning-0.11.0/paws.machine.learning/R/bedrockdataautomationruntime_operations.R | 18 paws.machine.learning-0.11.0/paws.machine.learning/R/bedrockdataautomationruntime_service.R | 4 paws.machine.learning-0.11.0/paws.machine.learning/R/bedrockruntime_interfaces.R | 70 paws.machine.learning-0.11.0/paws.machine.learning/R/bedrockruntime_operations.R | 63 paws.machine.learning-0.11.0/paws.machine.learning/R/bedrockruntime_service.R | 5 paws.machine.learning-0.11.0/paws.machine.learning/R/comprehend_interfaces.R | 510 -- paws.machine.learning-0.11.0/paws.machine.learning/R/comprehend_operations.R | 255 - paws.machine.learning-0.11.0/paws.machine.learning/R/comprehend_service.R | 6 paws.machine.learning-0.11.0/paws.machine.learning/R/comprehendmedical_interfaces.R | 156 paws.machine.learning-0.11.0/paws.machine.learning/R/comprehendmedical_operations.R | 78 paws.machine.learning-0.11.0/paws.machine.learning/R/comprehendmedical_service.R | 4 paws.machine.learning-0.11.0/paws.machine.learning/R/forecastqueryservice_interfaces.R | 12 paws.machine.learning-0.11.0/paws.machine.learning/R/forecastqueryservice_operations.R | 6 paws.machine.learning-0.11.0/paws.machine.learning/R/forecastqueryservice_service.R | 4 paws.machine.learning-0.11.0/paws.machine.learning/R/forecastservice_interfaces.R | 330 - paws.machine.learning-0.11.0/paws.machine.learning/R/forecastservice_operations.R | 189 paws.machine.learning-0.11.0/paws.machine.learning/R/forecastservice_service.R | 4 paws.machine.learning-0.11.0/paws.machine.learning/R/frauddetector_interfaces.R | 435 - paws.machine.learning-0.11.0/paws.machine.learning/R/frauddetector_operations.R | 219 paws.machine.learning-0.11.0/paws.machine.learning/R/frauddetector_service.R | 4 paws.machine.learning-0.11.0/paws.machine.learning/R/lexmodelbuildingservice_interfaces.R | 225 paws.machine.learning-0.11.0/paws.machine.learning/R/lexmodelbuildingservice_operations.R | 126 paws.machine.learning-0.11.0/paws.machine.learning/R/lexmodelbuildingservice_service.R | 4 paws.machine.learning-0.11.0/paws.machine.learning/R/lexmodelsv2_interfaces.R | 630 -- paws.machine.learning-0.11.0/paws.machine.learning/R/lexmodelsv2_operations.R | 333 - paws.machine.learning-0.11.0/paws.machine.learning/R/lexmodelsv2_service.R | 32 paws.machine.learning-0.11.0/paws.machine.learning/R/lexruntimeservice_interfaces.R | 30 paws.machine.learning-0.11.0/paws.machine.learning/R/lexruntimeservice_operations.R | 15 paws.machine.learning-0.11.0/paws.machine.learning/R/lexruntimeservice_service.R | 4 paws.machine.learning-0.11.0/paws.machine.learning/R/lexruntimev2_interfaces.R | 36 paws.machine.learning-0.11.0/paws.machine.learning/R/lexruntimev2_operations.R | 18 paws.machine.learning-0.11.0/paws.machine.learning/R/lexruntimev2_service.R | 4 paws.machine.learning-0.11.0/paws.machine.learning/R/lookoutequipment_interfaces.R | 261 - paws.machine.learning-0.11.0/paws.machine.learning/R/lookoutequipment_operations.R | 147 paws.machine.learning-0.11.0/paws.machine.learning/R/lookoutequipment_service.R | 4 paws.machine.learning-0.11.0/paws.machine.learning/R/machinelearning_interfaces.R | 168 paws.machine.learning-0.11.0/paws.machine.learning/R/machinelearning_operations.R | 84 paws.machine.learning-0.11.0/paws.machine.learning/R/machinelearning_service.R | 4 paws.machine.learning-0.11.0/paws.machine.learning/R/personalize_interfaces.R | 396 - paws.machine.learning-0.11.0/paws.machine.learning/R/personalize_operations.R | 213 paws.machine.learning-0.11.0/paws.machine.learning/R/personalize_service.R | 4 paws.machine.learning-0.11.0/paws.machine.learning/R/personalizeevents_interfaces.R | 15 paws.machine.learning-0.11.0/paws.machine.learning/R/personalizeevents_operations.R | 15 paws.machine.learning-0.11.0/paws.machine.learning/R/personalizeevents_service.R | 4 paws.machine.learning-0.11.0/paws.machine.learning/R/personalizeruntime_interfaces.R | 18 paws.machine.learning-0.11.0/paws.machine.learning/R/personalizeruntime_operations.R | 9 paws.machine.learning-0.11.0/paws.machine.learning/R/personalizeruntime_service.R | 4 paws.machine.learning-0.11.0/paws.machine.learning/R/polly_interfaces.R | 60 paws.machine.learning-0.11.0/paws.machine.learning/R/polly_operations.R | 30 paws.machine.learning-0.11.0/paws.machine.learning/R/polly_service.R | 6 paws.machine.learning-0.11.0/paws.machine.learning/R/rekognition_interfaces.R | 450 - paws.machine.learning-0.11.0/paws.machine.learning/R/rekognition_operations.R | 279 - paws.machine.learning-0.11.0/paws.machine.learning/R/rekognition_service.R | 50 paws.machine.learning-0.11.0/paws.machine.learning/R/sagemaker_interfaces.R | 2270 +++------- paws.machine.learning-0.11.0/paws.machine.learning/R/sagemaker_operations.R | 1538 ++++-- paws.machine.learning-0.11.0/paws.machine.learning/R/sagemaker_service.R | 12 paws.machine.learning-0.11.0/paws.machine.learning/R/sagemakeredgemanager_interfaces.R | 15 paws.machine.learning-0.11.0/paws.machine.learning/R/sagemakeredgemanager_operations.R | 9 paws.machine.learning-0.11.0/paws.machine.learning/R/sagemakeredgemanager_service.R | 4 paws.machine.learning-0.11.0/paws.machine.learning/R/sagemakerfeaturestoreruntime_interfaces.R | 47 paws.machine.learning-0.11.0/paws.machine.learning/R/sagemakerfeaturestoreruntime_operations.R | 122 paws.machine.learning-0.11.0/paws.machine.learning/R/sagemakerfeaturestoreruntime_service.R | 9 paws.machine.learning-0.11.0/paws.machine.learning/R/sagemakergeospatialcapabilities_interfaces.R | 114 paws.machine.learning-0.11.0/paws.machine.learning/R/sagemakergeospatialcapabilities_operations.R | 57 paws.machine.learning-0.11.0/paws.machine.learning/R/sagemakergeospatialcapabilities_service.R | 4 paws.machine.learning-0.11.0/paws.machine.learning/R/sagemakermetrics_interfaces.R | 12 paws.machine.learning-0.11.0/paws.machine.learning/R/sagemakermetrics_operations.R | 6 paws.machine.learning-0.11.0/paws.machine.learning/R/sagemakermetrics_service.R | 4 paws.machine.learning-0.11.0/paws.machine.learning/R/sagemakerruntime_interfaces.R | 18 paws.machine.learning-0.11.0/paws.machine.learning/R/sagemakerruntime_operations.R | 34 paws.machine.learning-0.11.0/paws.machine.learning/R/sagemakerruntime_service.R | 4 paws.machine.learning-0.11.0/paws.machine.learning/R/sysdata.rda |only paws.machine.learning-0.11.0/paws.machine.learning/R/textract_interfaces.R | 150 paws.machine.learning-0.11.0/paws.machine.learning/R/textract_operations.R | 77 paws.machine.learning-0.11.0/paws.machine.learning/R/textract_service.R | 6 paws.machine.learning-0.11.0/paws.machine.learning/R/transcribeservice_interfaces.R | 247 - paws.machine.learning-0.11.0/paws.machine.learning/R/transcribeservice_operations.R | 201 paws.machine.learning-0.11.0/paws.machine.learning/R/transcribeservice_service.R | 7 paws.machine.learning-0.11.0/paws.machine.learning/R/translate_interfaces.R | 111 paws.machine.learning-0.11.0/paws.machine.learning/R/translate_operations.R | 57 paws.machine.learning-0.11.0/paws.machine.learning/R/translate_service.R | 6 paws.machine.learning-0.11.0/paws.machine.learning/R/voiceid_interfaces.R | 162 paws.machine.learning-0.11.0/paws.machine.learning/R/voiceid_operations.R | 87 paws.machine.learning-0.11.0/paws.machine.learning/R/voiceid_service.R | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/augmentedairuntime.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrock.Rd | 16 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrock_batch_delete_advanced_prompt_optimization_job.Rd | 6 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrock_create_advanced_prompt_optimization_job.Rd | 20 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrock_create_custom_model.Rd | 13 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrock_get_account_data_retention.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrock_get_advanced_prompt_optimization_job.Rd | 6 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrock_list_advanced_prompt_optimization_jobs.Rd | 12 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrock_put_account_data_retention.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrock_stop_advanced_prompt_optimization_job.Rd | 6 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagent.Rd | 15 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagent_create_agent.Rd | 7 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagent_create_data_source.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagent_create_vpc_configuration.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagent_delete_resource_policy.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagent_delete_vpc_configuration.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagent_get_flow.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagent_get_flow_version.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagent_get_prompt.Rd | 8 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagent_get_resource_policy.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagent_get_vpc_configuration.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagent_list_vpc_configurations.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagent_put_resource_policy.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcore.Rd | 6 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcore_create_ab_test.Rd | 5 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcore_create_event.Rd | 10 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcore_delete_capacity_provider_session.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcore_delete_memory_record.Rd | 8 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcore_get_memory_record.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcore_ingest_data.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcore_invoke_agent_runtime.Rd | 11 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcore_invoke_harness.Rd | 18 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcore_start_batch_evaluation.Rd | 14 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcore_start_browser_session.Rd | 3 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcore_start_code_interpreter_session.Rd | 3 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcore_start_recommendation.Rd | 8 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol.Rd | 48 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_add_dataset_examples.Rd | 2 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_batch_put_gateway_rate_limits.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_create_agent_runtime.Rd | 12 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_create_api_key_credential_provider.Rd | 10 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_create_browser.Rd | 3 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_create_capacity_provider.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_create_code_interpreter.Rd | 3 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_create_configuration_bundle.Rd | 3 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_create_consent_portal.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_create_dataset.Rd | 10 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_create_dataset_version.Rd | 2 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_create_gateway_rate_limit.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_create_gateway_target.Rd | 9 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_create_harness.Rd | 7 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_create_harness_endpoint.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_create_memory.Rd | 3 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_create_online_evaluation_config.Rd | 13 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_create_payment_connector.Rd | 7 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_create_payment_manager.Rd | 5 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_create_policy.Rd | 7 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_delete_agent_runtime.Rd | 8 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_delete_agent_runtime_endpoint.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_delete_capacity_provider.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_delete_consent_portal.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_delete_dataset.Rd | 7 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_delete_dataset_examples.Rd | 2 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_delete_gateway_rate_limit.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_delete_harness.Rd | 8 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_delete_harness_endpoint.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_delete_memory.Rd | 2 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_get_capacity_provider.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_get_consent_portal.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_get_dataset.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_get_gateway_rate_limit.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_get_harness.Rd | 8 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_get_harness_endpoint.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_get_policy_generation.Rd | 2 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_list_agen_runt_vers_by_capa_prov.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_list_capacity_providers.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_list_consent_portals.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_list_dataset_examples.Rd | 6 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_list_datasets.Rd | 2 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_list_gateway_rate_limits.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_list_harness_endpoints.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_list_harness_versions.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_list_harnesses.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_list_policy_generation_assets.Rd | 2 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_rotate_payment_connector_credentials.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_start_policy_generation.Rd | 6 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_update_agent_runtime.Rd | 10 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_update_api_key_credential_provider.Rd | 13 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_update_capacity_provider.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_update_configuration_bundle.Rd | 13 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_update_consent_portal.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_update_dataset.Rd | 2 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_update_dataset_examples.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_update_gateway.Rd | 8 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_update_gateway_rate_limit.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_update_gateway_target.Rd | 9 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_update_harness.Rd | 7 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_update_harness_endpoint.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_update_memory.Rd | 3 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_update_online_evaluation_config.Rd | 9 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_update_payment_manager.Rd | 5 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentcorecontrol_update_policy.Rd | 7 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentruntime.Rd | 14 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentruntime_agentic_retrieve_stream.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentruntime_check_ingested_document_acl.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentruntime_get_document_content.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentruntime_get_ingested_document_acl.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentruntime_invoke_agent.Rd | 5 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentruntime_retrieve.Rd | 5 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentruntime_retrieve_and_generate.Rd | 5 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockagentruntime_retrieve_and_generate_stream.Rd | 5 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockdataautomation.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockdataautomationruntime.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockruntime.Rd | 5 paws.machine.learning-0.11.0/paws.machine.learning/man/bedrockruntime_invoke_guardrail_checks.Rd |only paws.machine.learning-0.11.0/paws.machine.learning/man/comprehend.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/comprehendmedical.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/forecastqueryservice.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/forecastservice.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/frauddetector.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/lexmodelbuildingservice.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/lexmodelsv2.Rd | 33 paws.machine.learning-0.11.0/paws.machine.learning/man/lexmodelsv2_create_bot_locale.Rd | 5 paws.machine.learning-0.11.0/paws.machine.learning/man/lexmodelsv2_create_resource_policy_statement.Rd | 2 paws.machine.learning-0.11.0/paws.machine.learning/man/lexmodelsv2_update_bot_locale.Rd | 5 paws.machine.learning-0.11.0/paws.machine.learning/man/lexruntimeservice.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/lexruntimev2.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/lookoutequipment.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/machinelearning.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/personalize.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/personalizeevents.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/personalizeruntime.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/polly.Rd | 4 paws.machine.learning-0.11.0/paws.machine.learning/man/rekognition.Rd | 45 paws.machine.learning-0.11.0/paws.machine.learning/man/rekognition_create_stream_processor.Rd | 6 paws.machine.learning-0.11.0/paws.machine.learning/man/rekognition_delete_stream_processor.Rd | 5 paws.machine.learning-0.11.0/paws.machine.learning/man/rekognition_describe_stream_processor.Rd | 6 paws.machine.learning-0.11.0/paws.machine.learning/man/rekognition_get_media_analysis_job.Rd | 5 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More information about paws.machine.learning at CRAN
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Title: Latent Variable Analysis
Description: Fit a variety of latent variable models, including confirmatory
factor analysis, structural equation modeling and latent growth curve models.
Author: Yves Rosseel [aut, cre] ,
Terrence D. Jorgensen [aut] ,
Luc De Wilde [aut],
Daniel Oberski [ctb],
Jarrett Byrnes [ctb],
Leonard Vanbrabant [ctb],
Victoria Savalei [ctb],
Ed Merkle [ctb],
Michael Hallquist [ctb],
Mijke Rhemtulla [ctb],
Myrsini Katsika [...truncated...]
Maintainer: Yves Rosseel <Yves.Rosseel@UGent.be>
Diff between lavaan versions 0.7-2 dated 2026-07-16 and 0.7-3 dated 2026-10-08
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lavaan-0.7-3/lavaan/R/lav_model_vcov.R | 253 +- lavaan-0.7-3/lavaan/R/lav_model_wls.R | 25 lavaan-0.7-3/lavaan/R/lav_modification.R | 2 lavaan-0.7-3/lavaan/R/lav_msg.R | 12 lavaan-0.7-3/lavaan/R/lav_muthen1984.R | 234 + lavaan-0.7-3/lavaan/R/lav_mvnorm_cluster.R | 270 +- lavaan-0.7-3/lavaan/R/lav_mvnorm_cluster_kernels.R | 54 lavaan-0.7-3/lavaan/R/lav_mvnorm_cluster_missing.R | 74 lavaan-0.7-3/lavaan/R/lav_mvnorm_cluster_missing_louis.R | 24 lavaan-0.7-3/lavaan/R/lav_mvnorm_cluster_rs.R | 72 lavaan-0.7-3/lavaan/R/lav_mvnorm_missing_h1.R | 4 lavaan-0.7-3/lavaan/R/lav_mvreg_cluster.R | 88 lavaan-0.7-3/lavaan/R/lav_object_check_version.R | 24 lavaan-0.7-3/lavaan/R/lav_object_generate.R | 16 lavaan-0.7-3/lavaan/R/lav_object_inspect.R | 221 + lavaan-0.7-3/lavaan/R/lav_object_inspect_constraints.R |only lavaan-0.7-3/lavaan/R/lav_object_inspect_sampstat.R |only lavaan-0.7-3/lavaan/R/lav_object_methods.R | 94 lavaan-0.7-3/lavaan/R/lav_object_post_check.R | 94 lavaan-0.7-3/lavaan/R/lav_object_summary.R | 27 lavaan-0.7-3/lavaan/R/lav_objective.R | 4 lavaan-0.7-3/lavaan/R/lav_optim_gn.R | 14 lavaan-0.7-3/lavaan/R/lav_optim_noniter.R | 39 lavaan-0.7-3/lavaan/R/lav_optim_noniter_vcov.R |only lavaan-0.7-3/lavaan/R/lav_options.R | 354 ++ lavaan-0.7-3/lavaan/R/lav_options_default.R | 36 lavaan-0.7-3/lavaan/R/lav_options_estimator.R | 589 ++++ lavaan-0.7-3/lavaan/R/lav_options_mimic.R | 22 lavaan-0.7-3/lavaan/R/lav_options_se.R | 14 lavaan-0.7-3/lavaan/R/lav_partable.R | 82 lavaan-0.7-3/lavaan/R/lav_partable_bounds.R | 102 lavaan-0.7-3/lavaan/R/lav_partable_constraints.R | 13 lavaan-0.7-3/lavaan/R/lav_partable_dv.R |only lavaan-0.7-3/lavaan/R/lav_partable_flat.R | 26 lavaan-0.7-3/lavaan/R/lav_partable_marker.R | 184 + lavaan-0.7-3/lavaan/R/lav_partable_random.R | 8 lavaan-0.7-3/lavaan/R/lav_partable_unrestricted.R | 15 lavaan-0.7-3/lavaan/R/lav_partable_utils.R | 54 lavaan-0.7-3/lavaan/R/lav_partable_vnames.R | 6 lavaan-0.7-3/lavaan/R/lav_pml_utils.R | 7 lavaan-0.7-3/lavaan/R/lav_predict.R | 251 +- lavaan-0.7-3/lavaan/R/lav_predict_mdist.R | 4 lavaan-0.7-3/lavaan/R/lav_predict_y.R | 12 lavaan-0.7-3/lavaan/R/lav_print.R | 290 +- lavaan-0.7-3/lavaan/R/lav_representation_lisrel.R | 331 ++ lavaan-0.7-3/lavaan/R/lav_representation_ram.R | 33 lavaan-0.7-3/lavaan/R/lav_rescale.R |only lavaan-0.7-3/lavaan/R/lav_residuals.R | 27 lavaan-0.7-3/lavaan/R/lav_sam_step0.R | 132 - lavaan-0.7-3/lavaan/R/lav_sam_step1.R | 96 lavaan-0.7-3/lavaan/R/lav_sam_step1_local.R | 737 +++++- lavaan-0.7-3/lavaan/R/lav_sam_step2.R | 195 + lavaan-0.7-3/lavaan/R/lav_sam_step2_se.R | 124 - lavaan-0.7-3/lavaan/R/lav_sam_utils.R | 855 ++++++- lavaan-0.7-3/lavaan/R/lav_samplestats.R | 449 +++ lavaan-0.7-3/lavaan/R/lav_samplestats_gamma.R | 604 +++-- lavaan-0.7-3/lavaan/R/lav_samplestats_gamma_recipe.R | 26 lavaan-0.7-3/lavaan/R/lav_samplestats_icov.R | 4 lavaan-0.7-3/lavaan/R/lav_samplestats_igamma.R | 6 lavaan-0.7-3/lavaan/R/lav_samplestats_wls_2l_cat.R | 4 lavaan-0.7-3/lavaan/R/lav_samplestats_wls_obs.R | 20 lavaan-0.7-3/lavaan/R/lav_scores.R | 2 lavaan-0.7-3/lavaan/R/lav_sem_js.R |only lavaan-0.7-3/lavaan/R/lav_sem_js_deriv.R |only lavaan-0.7-3/lavaan/R/lav_sem_miiv.R | 587 ++++ lavaan-0.7-3/lavaan/R/lav_sem_miiv_utils.R | 518 ++++ lavaan-0.7-3/lavaan/R/lav_standardize.R | 6 lavaan-0.7-3/lavaan/R/lav_start.R | 111 lavaan-0.7-3/lavaan/R/lav_syntax.R | 17 lavaan-0.7-3/lavaan/R/lav_syntax_parser.R | 29 lavaan-0.7-3/lavaan/R/lav_syntax_parser_open.R | 48 lavaan-0.7-3/lavaan/R/lav_test.R | 65 lavaan-0.7-3/lavaan/R/lav_test_LRT.R | 224 + lavaan-0.7-3/lavaan/R/lav_test_browne.R | 120 - lavaan-0.7-3/lavaan/R/lav_test_fmg.R | 4 lavaan-0.7-3/lavaan/R/lav_test_hayakawa.R | 88 lavaan-0.7-3/lavaan/R/lav_test_net.R |only lavaan-0.7-3/lavaan/R/lav_test_satorra_bentler.R | 34 lavaan-0.7-3/lavaan/R/lav_test_utils.R | 37 lavaan-0.7-3/lavaan/R/lav_test_yuan_bentler.R | 11 lavaan-0.7-3/lavaan/R/lav_utils.R | 92 lavaan-0.7-3/lavaan/R/lav_vcov_hc.R |only lavaan-0.7-3/lavaan/R/xxx_efa.R | 9 lavaan-0.7-3/lavaan/R/xxx_lavaan.R | 206 + lavaan-0.7-3/lavaan/R/xxx_sam.R | 340 ++ lavaan-0.7-3/lavaan/README.md | 14 lavaan-0.7-3/lavaan/inst/rbm_sem.R | 4 lavaan-0.7-3/lavaan/inst/understanding_lavaan_internals.R | 2 lavaan-0.7-3/lavaan/man/bootstrap.Rd | 2 lavaan-0.7-3/lavaan/man/cfa.Rd | 18 lavaan-0.7-3/lavaan/man/efa.Rd | 14 lavaan-0.7-3/lavaan/man/estimator_iv.Rd | 79 lavaan-0.7-3/lavaan/man/estimator_js.Rd |only lavaan-0.7-3/lavaan/man/fitMeasures.Rd | 102 lavaan-0.7-3/lavaan/man/growth.Rd | 16 lavaan-0.7-3/lavaan/man/lavEffects.Rd | 8 lavaan-0.7-3/lavaan/man/lavH1.Rd |only lavaan-0.7-3/lavaan/man/lavInspect.Rd | 421 ++- lavaan-0.7-3/lavaan/man/lavListInspect.Rd | 12 lavaan-0.7-3/lavaan/man/lavNames.Rd | 43 lavaan-0.7-3/lavaan/man/lavOptions.Rd | 515 +++- lavaan-0.7-3/lavaan/man/lavPredict.Rd | 29 lavaan-0.7-3/lavaan/man/lavResiduals.Rd | 15 lavaan-0.7-3/lavaan/man/lavTestLRT.Rd | 69 lavaan-0.7-3/lavaan/man/lavTestNET.Rd |only lavaan-0.7-3/lavaan/man/lav_constraints.Rd | 8 lavaan-0.7-3/lavaan/man/lav_export_estimation.Rd | 4 lavaan-0.7-3/lavaan/man/lav_partable.Rd | 6 lavaan-0.7-3/lavaan/man/lav_scores.Rd | 2 lavaan-0.7-3/lavaan/man/lavaan-class.Rd | 14 lavaan-0.7-3/lavaan/man/lavaan.Rd | 8 lavaan-0.7-3/lavaan/man/mimic.Rd | 59 lavaan-0.7-3/lavaan/man/model.syntax.Rd | 82 lavaan-0.7-3/lavaan/man/parameterEstimates.Rd | 16 lavaan-0.7-3/lavaan/man/sam.Rd | 163 + lavaan-0.7-3/lavaan/man/sem.Rd | 18 lavaan-0.7-3/lavaan/man/simulateData.Rd | 19 lavaan-0.7-3/lavaan/man/standardizedSolution.Rd | 22 168 files changed, 13012 insertions(+), 3096 deletions(-)
Title: Predicting Invasion Probabilities from Phylogenetic Data and
Species Traits
Description: A phylogenetic modelling approach for predicting species invasion risk, out of
a given pool of local species where a subset is known to be invasive elsewhere.
The package uses phylogenetic signal estimation and phylogenetic linear and logistic models
to estimate probabilities of being invasive based on phylogeny and any set of additional
predictors. A ranking method is implemented to evaluate prioritisation strategies. A manuscript
describing these methods, by Shahar Dubiner and Tamar Guy-Haim, is in preparation.
Author: Shahar Dubiner [aut, cre]
Maintainer: Shahar Dubiner <dubiner@mail.tau.ac.il>
Diff between invasible versions 0.1.1 dated 2026-08-05 and 1.0.0 dated 2026-10-08
DESCRIPTION | 6 MD5 | 14 - R/globals.R | 3 R/invasion_signal.R | 154 +++++++-------- R/predict_invasible.R | 355 ++++++++++++++++++----------------- R/prepare_invasible.R | 465 +++++++++++++++++++++++++++++++++++++++-------- man/predict_invasible.Rd | 8 man/prepare_invasible.Rd | 56 ++++- 8 files changed, 705 insertions(+), 356 deletions(-)
Title: The Gauss Hypergeometric Function
Description: The Gaussian hypergeometric function for complex numbers.
Author: Robin K. S. Hankin [aut, cre] ,
Richard D. Morey [ctb]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between hypergeo versions 1.2-14 dated 2025-03-24 and 1.2-15 dated 2026-10-08
hypergeo-1.2-14/hypergeo/inst/doc/hypergeometric.R |only hypergeo-1.2-14/hypergeo/inst/doc/hypergeometric.Rnw |only hypergeo-1.2-14/hypergeo/inst/doc/hypergeometric.pdf |only hypergeo-1.2-14/hypergeo/tests/aaa.R |only hypergeo-1.2-14/hypergeo/tests/aab.R |only hypergeo-1.2-14/hypergeo/vignettes/hypergeometric.Rnw |only hypergeo-1.2-15/hypergeo/DESCRIPTION | 28 +++-- hypergeo-1.2-15/hypergeo/MD5 | 77 ++++++++----- hypergeo-1.2-15/hypergeo/NAMESPACE | 5 hypergeo-1.2-15/hypergeo/NEWS.md |only hypergeo-1.2-15/hypergeo/R/RcppExports.R |only hypergeo-1.2-15/hypergeo/R/complex_gamma.R | 47 ++------ hypergeo-1.2-15/hypergeo/R/hypergeo.R | 100 +++++++----------- hypergeo-1.2-15/hypergeo/README.md |only hypergeo-1.2-15/hypergeo/build/partial.rdb |only hypergeo-1.2-15/hypergeo/build/vignette.rds |binary hypergeo-1.2-15/hypergeo/inst/CITATION |only hypergeo-1.2-15/hypergeo/inst/doc/hypergeo.R |only hypergeo-1.2-15/hypergeo/inst/doc/hypergeo.Rnw |only hypergeo-1.2-15/hypergeo/inst/doc/hypergeo.pdf |only hypergeo-1.2-15/hypergeo/inst/include |only hypergeo-1.2-15/hypergeo/man/buhring.Rd | 2 hypergeo-1.2-15/hypergeo/man/complex_gamma.Rd | 12 +- hypergeo-1.2-15/hypergeo/man/cpp.Rd |only hypergeo-1.2-15/hypergeo/man/f15.1.20.Rd |only hypergeo-1.2-15/hypergeo/man/f15.3.1.Rd | 10 + hypergeo-1.2-15/hypergeo/man/f15.3.3.Rd | 7 + hypergeo-1.2-15/hypergeo/man/f15.5.1.Rd | 2 hypergeo-1.2-15/hypergeo/man/figures |only hypergeo-1.2-15/hypergeo/man/genhypergeo.Rd | 14 ++ hypergeo-1.2-15/hypergeo/man/gosper.Rd | 2 hypergeo-1.2-15/hypergeo/man/hypergeo-package.Rd | 40 +++---- hypergeo-1.2-15/hypergeo/man/hypergeo.Rd | 2 hypergeo-1.2-15/hypergeo/man/hypergeo_A_nonpos_int.Rd | 6 - hypergeo-1.2-15/hypergeo/man/hypergeo_contfrac.Rd | 2 hypergeo-1.2-15/hypergeo/man/hypergeo_cover1.Rd | 8 - hypergeo-1.2-15/hypergeo/man/hypergeo_powerseries.Rd | 5 hypergeo-1.2-15/hypergeo/man/is.nonpos.Rd | 7 - hypergeo-1.2-15/hypergeo/man/residue.Rd | 10 - hypergeo-1.2-15/hypergeo/man/wolfram.Rd | 6 - hypergeo-1.2-15/hypergeo/src |only hypergeo-1.2-15/hypergeo/tests/testthat |only hypergeo-1.2-15/hypergeo/tests/testthat.R |only hypergeo-1.2-15/hypergeo/vignettes/hypergeo.Rnw |only hypergeo-1.2-15/hypergeo/vignettes/hypergeometric.bib | 29 ++++- 45 files changed, 232 insertions(+), 189 deletions(-)
Title: Grammar of Graphics for SQL
Description: Allows you to write queries that combine SQL (Structured Query
Language) data retrieval with visualization specifications in a single,
composable syntax. The 'ggsql' package binds directly with the 'ggsql' 'Rust'
library and allows you to set up readers and writers and execute queries
against it. The package also offers 'knitr' and 'shiny' integration allowing
the user to use 'ggsql' in both frameworks.
Author: Thomas Lin Pedersen [aut, cre] ,
George Stagg [aut] ,
Teun van den Brand [aut] ,
Posit, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between ggsql versions 0.3.3 dated 2026-06-03 and 0.5.2 dated 2026-10-08
ggsql-0.3.3/ggsql/R/vega-versions.R |only ggsql-0.3.3/ggsql/inst/htmlwidgets/ggsql_vega.css |only ggsql-0.3.3/ggsql/inst/htmlwidgets/ggsql_vega.js |only ggsql-0.3.3/ggsql/inst/htmlwidgets/lib/vega |only ggsql-0.3.3/ggsql/inst/htmlwidgets/lib/vega-embed |only ggsql-0.3.3/ggsql/inst/htmlwidgets/lib/vega-lite |only ggsql-0.3.3/ggsql/src/rust/vendor.tar.xz.sha256 |only ggsql-0.5.2/ggsql/DESCRIPTION | 12 ggsql-0.5.2/ggsql/MD5 | 78 ggsql-0.5.2/ggsql/NAMESPACE | 5 ggsql-0.5.2/ggsql/NEWS.md | 29 ggsql-0.5.2/ggsql/R/aaa.R | 1 ggsql-0.5.2/ggsql/R/engine.R | 43 ggsql-0.5.2/ggsql/R/extendr-wrappers.R | 8 ggsql-0.5.2/ggsql/R/hep-version.R |only ggsql-0.5.2/ggsql/R/render.R | 140 - ggsql-0.5.2/ggsql/R/shiny.R | 8 ggsql-0.5.2/ggsql/R/spec.R | 17 ggsql-0.5.2/ggsql/R/widget.R | 77 ggsql-0.5.2/ggsql/R/writer.R | 94 - ggsql-0.5.2/ggsql/R/zzz.R | 8 ggsql-0.5.2/ggsql/README.md | 28 ggsql-0.5.2/ggsql/inst/doc/engine.html | 1207 +++++++++---- ggsql-0.5.2/ggsql/inst/doc/ggsql.html | 1205 +++++++++--- ggsql-0.5.2/ggsql/inst/htmlwidgets/ggsql_hep.js |only ggsql-0.5.2/ggsql/inst/htmlwidgets/lib/hephaestus-svg |only ggsql-0.5.2/ggsql/man/figures/README-unnamed-chunk-2-1.svg | 2 ggsql-0.5.2/ggsql/man/figures/README-unnamed-chunk-3-1.svg | 2 ggsql-0.5.2/ggsql/man/figures/README-unnamed-chunk-4-1.svg |only ggsql-0.5.2/ggsql/man/ggsql_render.Rd | 11 ggsql-0.5.2/ggsql/man/ggsql_save.Rd | 19 ggsql-0.5.2/ggsql/man/ggsql_widget.Rd |only ggsql-0.5.2/ggsql/man/svg_writer.Rd |only ggsql-0.5.2/ggsql/man/vegalite_writer.Rd | 10 ggsql-0.5.2/ggsql/src/Makevars.win.in | 4 ggsql-0.5.2/ggsql/src/rust/Cargo.lock | 692 ++++++- ggsql-0.5.2/ggsql/src/rust/Cargo.toml | 8 ggsql-0.5.2/ggsql/src/rust/build-env-win.sh | 3 ggsql-0.5.2/ggsql/src/rust/src/lib.rs | 75 ggsql-0.5.2/ggsql/tests/testthat/test-engine.R | 77 ggsql-0.5.2/ggsql/tests/testthat/test-spec.R | 27 ggsql-0.5.2/ggsql/tests/testthat/test-validate.R | 2 ggsql-0.5.2/ggsql/tests/testthat/test-writer.R | 81 ggsql-0.5.2/ggsql/tools/build-hep-assets.mjs |only ggsql-0.5.2/ggsql/tools/config.R | 17 ggsql-0.5.2/ggsql/tools/update-hephaestus.sh |only ggsql-0.5.2/ggsql/tools/vendor.R | 50 47 files changed, 3120 insertions(+), 920 deletions(-)
Title: Automatic Generation of Exams in R
Description: Automatic generation of exams based on exercises in Markdown or LaTeX format,
possibly including R code for dynamic generation of exercise elements.
Exercise types include single-choice and multiple-choice questions, arithmetic problems,
string questions, and combinations thereof (cloze). Output formats include standalone
files (PDF, HTML, Docx, ODT, ...), Moodle XML, QTI 1.2, QTI 2.1, Blackboard, Canvas, OpenOlat, ILIAS, TestVision,
Particify, ARSnova, Kahoot!, Grasple, and TCExam. In addition to fully customizable PDF exams, a standardized PDF format
(NOPS) is provided that can be printed, scanned, and automatically evaluated.
Author: Achim Zeileis [aut, cre] ,
Bettina Gruen [aut] ,
Friedrich Leisch [aut] ,
Nikolaus Umlauf [aut] ,
Niels Smits [aut] ,
Dominik Ernst [ctb] ,
Patrik Keller [ctb],
Reto Stauffer [ctb] ,
Kenji Sato [ctb] ,
Florian Wickelmaier [ctb],
Sebastian Bachler [ct [...truncated...]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between exams versions 2.4-4 dated 2026-07-31 and 2.4-5 dated 2026-10-08
DESCRIPTION | 12 +++++------- MD5 | 21 +++++++++++---------- NEWS.md | 17 +++++++++++++++++ R/exams2ilias.R | 2 ++ R/read_metainfo.R | 2 +- README.md |only inst/doc/exams.Rnw | 2 +- inst/doc/exams.pdf |binary inst/doc/exams2.pdf |binary man/exams2ilias.Rd | 18 +++++++++++++----- man/include_tikz.Rd | 2 +- vignettes/exams.Rnw | 2 +- 12 files changed, 52 insertions(+), 26 deletions(-)
Title: Estimate and Manipulate Age-Depth Models
Description: Estimate age-depth models from stratigraphic and sedimentological data,
and transform data
between the time and stratigraphic domain.
Author: Niklas Hohmann [aut] ,
Emilia Jarochowska [cre]
Maintainer: Emilia Jarochowska <e.jarochowska@uni-muenster.de>
Diff between admtools versions 0.6.0 dated 2025-05-20 and 0.7.0 dated 2026-10-08
DESCRIPTION | 21 ++++++++------ MD5 | 30 ++++++++++---------- NEWS.md | 6 ++++ R/strat_to_time.fossils.R | 4 +- README.md | 10 ++++-- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 6 ++-- inst/doc/FossilSim_integration.html | 5 ++- inst/doc/adm_from_sedrate.html | 15 +++++----- inst/doc/adm_from_trace_cont.html | 15 +++++----- inst/doc/adm_plotting.html | 5 ++- inst/doc/admtools.html | 15 +++++----- inst/doc/admtools_doc.html | 1 inst/doc/correlation.html | 7 ++-- man/admtools-package.Rd | 53 +++++++++++++++++++----------------- 16 files changed, 109 insertions(+), 84 deletions(-)
Title: Estimate Permutation p-Values for Random Forest Importance
Metrics
Description: Estimate significance of importance metrics for a Random Forest
model by permuting the response variable. Produces null distribution of
importance metrics for each predictor variable and p-value of observed.
Provides summary and visualization functions for 'randomForest' results.
Author: Eric Archer [aut, cre]
Maintainer: Eric Archer <eric.ivan.archer@gmail.com>
Diff between rfPermute versions 2.5.5 dated 2025-06-10 and 2.5.6 dated 2026-10-08
DESCRIPTION | 25 ++++++------- MD5 | 30 ++++++++-------- NAMESPACE | 13 ++++--- R/confusionMatrix.R | 8 ++-- R/importance.R | 6 +-- R/plotImpPreds.R | 2 - R/plotInbag.R | 86 ++++++++++++++++++++++++++++++++++++----------- R/plotNull.R | 4 +- R/plotPredictedProbs.R | 2 - R/plotProximity.R | 10 ++--- R/plotTrace.R | 8 ++-- R/rfPermute.R | 3 + R/rfROC.R |only README.md | 11 +++++- man/plotInbag.Rd | 5 +- man/rfPermute-package.Rd | 5 ++ man/rfROC.Rd |only 17 files changed, 147 insertions(+), 71 deletions(-)
Title: JSON Graphics Device
Description: A graphics device that translates R plotting operations into JSON
and streams them over a local connection to an external display
application. The device acts as a pure recorder with no rendering
dependencies; all rendering occurs in that application (e.g. a 'VS Code'
extension or a web browser). Official display applications are available
from the project homepage.
Author: Grant McDermott [aut, cre],
Tatsuya Shima [aut],
Dave Gamble [cph] ,
cJSON contributors [cph]
Maintainer: Grant McDermott <contact@grantmcdermott.com>
Diff between jgd versions 0.2.0 dated 2026-09-27 and 0.2.1 dated 2026-10-08
DESCRIPTION | 7 +- MD5 | 7 +- NEWS.md | 9 ++ tests/testthat/helper-mock-server.R | 110 ++++++++++++++++++++++-------------- tests/testthat/test-mock-server.R |only 5 files changed, 86 insertions(+), 47 deletions(-)
Title: Data Only Package to 'healthyR'
Description: Provides data for functions typically used in the 'healthyR' package.
Author: Steven Sanderson [aut, cre, cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between healthyR.data versions 1.2.0 dated 2025-01-12 and 1.2.1 dated 2026-10-08
DESCRIPTION | 12 MD5 | 53 +-- NEWS.md | 12 R/meta-get-cms-data.R | 9 README.md | 322 ++++++++++++++++++++- man/current_asc_data.Rd | 38 +- man/current_asc_oas_cahps_data.Rd | 38 +- man/current_comp_death_data.Rd | 38 +- man/current_hai_data.Rd | 38 +- man/current_hcahps_data.Rd | 38 +- man/current_hosp_data.Rd | 38 +- man/current_hvbp_data.Rd | 38 +- man/current_ipfqr_data.Rd | 38 +- man/current_maternal_data.Rd | 38 +- man/current_medicare_hospital_spending_data.Rd | 38 +- man/current_oqr_oas_cahps_data.Rd | 38 +- man/current_outpatient_imaging_efficiency_data.Rd | 38 +- man/current_payments_data.Rd | 38 +- man/current_pch_hai_hospital_data.Rd | 38 +- man/current_pch_hcahps_data.Rd | 38 +- man/current_pch_oncology_measures_hospital_data.Rd | 38 +- man/current_pch_outcomes_data.Rd | 38 +- man/current_timely_and_effective_care_data.Rd | 38 +- man/current_unplanned_hospital_visits_data.Rd | 40 +- man/current_va_data.Rd | 38 +- man/get_cms_meta_data.Rd | 7 man/get_provider_meta_data.Rd | 4 tests |only 28 files changed, 748 insertions(+), 433 deletions(-)
Title: Functions and Utilities for Jordan
Description: Provides core functions and utilities for packages and other code
developed by Jordan Mark Barbone.
Author: Jordan Mark Barbone [aut, cph, cre]
Maintainer: Jordan Mark Barbone <jmbarbone@gmail.com>
Diff between fuj versions 0.2.2 dated 2025-04-23 and 0.3.0 dated 2026-10-08
DESCRIPTION | 16 +- MD5 | 139 ++++++++++++-------- NAMESPACE | 92 +++++++++++++ NEWS.md | 88 ++++++++++++ R/arithmetic.R | 14 +- R/attributes.R | 6 R/colons.R | 50 +++---- R/condition.R | 204 ++++++++++++++++++++---------- R/conditions-fuj.R |only R/conditions.R |only R/data-frame.R | 88 +++++++----- R/delay.R |only R/encode.R |only R/extract.R | 14 +- R/flip.R | 7 - R/fs.R | 105 ++++++++++++++- R/fuj-package.R | 22 ++- R/hot.R |only R/if-null.R | 2 R/include.R | 51 ++++--- R/list.R | 10 + R/match-arg.R |only R/match.R | 34 ++--- R/muffle.R | 9 - R/names.R | 10 - R/namespace.R | 251 +++++++++++++++++++++++++++---------- R/negate.R |only R/os.R | 17 +- R/package.R |only R/paste.R | 4 R/progress.R |only R/struct.R | 13 + R/utils.R | 51 ++++++- R/vap.R |only R/verbose.R | 29 +--- R/yes-no.R | 54 +++---- README.md | 55 ++++++-- inst/WORDLIST | 5 man/alias_extract.Rd | 2 man/collapse.Rd | 4 man/conditions.Rd |only man/delay.Rd |only man/encode.Rd |only man/exattr.Rd | 2 man/fp.Rd | 59 +++++++- man/fuj-package.Rd | 5 man/hot.Rd |only man/if_null.Rd | 2 man/include.Rd | 38 ++--- man/list0.Rd | 5 man/match_arg.Rd |only man/match_ext.Rd | 18 +- man/muffle.Rd | 2 man/negate.Rd |only man/new_condition.Rd | 56 +++++--- man/op.fuj.Rd | 6 man/quick_df.Rd | 10 - man/require_namespace.Rd | 37 +++++ man/struct.Rd | 15 +- man/vap.Rd |only man/verbose.Rd | 8 - tests/spelling.R | 3 tests/testthat.R | 3 tests/testthat/_snaps/namespace.md |only tests/testthat/_snaps/vap.md |only tests/testthat/test-colons.R | 10 - tests/testthat/test-condition.R | 26 +++ tests/testthat/test-conditions.R |only tests/testthat/test-data-frame.R | 36 ++++- tests/testthat/test-delay.R |only tests/testthat/test-encode.R |only tests/testthat/test-fs.R | 64 ++++++--- tests/testthat/test-hot.R |only tests/testthat/test-if-null.R | 1 tests/testthat/test-include.R | 10 - tests/testthat/test-list.R | 8 + tests/testthat/test-match-arg.R |only tests/testthat/test-muffle.R | 4 tests/testthat/test-namespace.R | 79 +++++++++-- tests/testthat/test-negate.R |only tests/testthat/test-progress.R |only tests/testthat/test-vap.R |only tests/testthat/test-verbose.R | 32 +++- tests/testthat/test-yes-no.R | 82 ++++++------ 84 files changed, 1444 insertions(+), 623 deletions(-)
Title: A Toolbox for Manipulating and Assessing Colors and Palettes
Description: Carries out mapping between assorted color spaces including RGB, HSV, HLS,
CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar CIELAB.
Qualitative, sequential, and diverging color palettes based on HCL colors
are provided along with corresponding ggplot2 color scales.
Color palette choice is aided by an interactive app (with either a Tcl/Tk
or a shiny graphical user interface) and shiny apps with an HCL color picker and a
color vision deficiency emulator. Plotting functions for displaying
and assessing palettes include color swatches, visualizations of the
HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation
functions include: desaturation, lightening/darkening, mixing, and
simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly).
Details can be found on the project web page at <https://colorspace.R-Forge.R-project.org/>
and in the accompanying scientific paper: Zeileis et al. (2020, Journal of Statistical
Software, <doi:10.18637/ [...truncated...]
Author: Ross Ihaka [aut],
Paul Murrell [aut] ,
Kurt Hornik [aut] ,
Jason C. Fisher [aut] ,
Reto Stauffer [aut] ,
Claus O. Wilke [aut] ,
Claire D. McWhite [aut] ,
Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between colorspace versions 2.1-3 dated 2026-07-12 and 2.1-4 dated 2026-10-08
DESCRIPTION | 12 ++++++------ MD5 | 24 ++++++++++++------------ NEWS.md | 12 ++++++++++++ R/choose_palette.R | 2 +- inst/doc/colorspace.R | 6 +++--- inst/doc/colorspace.Rmd | 12 ++++++------ inst/doc/colorspace.html | 26 +++++++++++++------------- inst/doc/hcl-colors.Rnw | 2 +- inst/doc/hcl-colors.pdf |binary inst/hclwizard/html/R.html | 4 ++-- inst/hclwizard/html/RReg.html | 2 +- vignettes/colorspace.Rmd | 12 ++++++------ vignettes/hcl-colors.Rnw | 2 +- 13 files changed, 64 insertions(+), 52 deletions(-)
Title: Wrangle Large Simulation Studies
Description: An 'R6' class to set up, run, monitor, collate, and debug large simulation studies comprising many small independent replications and treatment configurations. Parallel processing, reproducibility, fault- and error-tolerance, and ability to resume an interrupted or timed-out simulation study are built in.
Author: Pavel N. Krivitsky [aut, cre]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>
Diff between piecemeal versions 0.2.0 dated 2026-03-11 and 0.3.0 dated 2026-10-08
piecemeal-0.2.0/piecemeal/inst/examples/post.R |only piecemeal-0.2.0/piecemeal/inst/examples/run.R |only piecemeal-0.2.0/piecemeal/inst/examples/setup.R |only piecemeal-0.2.0/piecemeal/tests/testthat/test-piecemeal.R |only piecemeal-0.3.0/piecemeal/DESCRIPTION | 10 piecemeal-0.3.0/piecemeal/MD5 | 50 piecemeal-0.3.0/piecemeal/NAMESPACE | 28 piecemeal-0.3.0/piecemeal/NEWS | 67 piecemeal-0.3.0/piecemeal/NEWS.md | 61 piecemeal-0.3.0/piecemeal/R/Piecemeal.R | 456 +++-- piecemeal-0.3.0/piecemeal/R/consolidate.R | 19 piecemeal-0.3.0/piecemeal/build/stage23.rdb |binary piecemeal-0.3.0/piecemeal/build/vignette.rds |binary piecemeal-0.3.0/piecemeal/inst/doc/piecemeal.R | 43 piecemeal-0.3.0/piecemeal/inst/doc/piecemeal.Rmd | 100 - piecemeal-0.3.0/piecemeal/inst/doc/piecemeal.html | 882 +++++----- piecemeal-0.3.0/piecemeal/inst/examples/2file |only piecemeal-0.3.0/piecemeal/inst/examples/3file |only piecemeal-0.3.0/piecemeal/inst/examples/README.md | 60 piecemeal-0.3.0/piecemeal/man/Piecemeal.Rd | 810 +++++---- piecemeal-0.3.0/piecemeal/man/piecemeal-package.Rd | 2 piecemeal-0.3.0/piecemeal/tests/testthat/test-autorun.R |only piecemeal-0.3.0/piecemeal/tests/testthat/test-cli.R |only piecemeal-0.3.0/piecemeal/tests/testthat/test-cluster.R |only piecemeal-0.3.0/piecemeal/tests/testthat/test-concurrent-status.R |only piecemeal-0.3.0/piecemeal/tests/testthat/test-consolidation.R | 42 piecemeal-0.3.0/piecemeal/tests/testthat/test-test-debug.R |only piecemeal-0.3.0/piecemeal/tests/testthat/test-vignette.R | 129 + piecemeal-0.3.0/piecemeal/tests/testthat/test-worker-results.R | 55 piecemeal-0.3.0/piecemeal/vignettes/piecemeal.Rmd | 100 - 30 files changed, 1887 insertions(+), 1027 deletions(-)
Title: DDI with R
Description: Useful functions for various DDI (Data Documentation Initiative)
related inputs and outputs. Converts data files to and from DDI, SPSS,
Stata, SAS, R and Excel, including user declared missing values.
Author: Adrian Dusa [aut, cre, cph]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between DDIwR versions 0.21 dated 2026-09-12 and 0.22 dated 2026-10-08
DESCRIPTION | 6 MD5 | 46 +- NAMESPACE | 5 R/DDIwR_package.R | 4 R/exportCodebook.R | 47 +- R/internals.R | 91 +++- R/metadataDialog.R |only R/metadataProjection.R |only R/metadataSession.R |only R/metadataSnapshot.R |only R/metadataSweepImport.R |only R/parallel.R |only R/readstat_internal.R | 69 ++- inst/ChangeLog | 15 man/DDIwRParallel.Rd |only man/DDIwR_internal.Rd | 7 man/DDIwR_package.Rd | 4 man/exportCodebook.Rd | 19 man/metadataSweepCapture.Rd |only man/metadataSweepImport.Rd |only src/Makevars.in | 12 src/Makevars.win | 12 src/init.c | 21 src/metadata_snapshot.c |only src/metadata_text.c |only src/metadata_text.h |only src/sc_parallel_read.c | 8 src/variable_analysis.c |only src/variable_analysis.h |only src/variable_threads.c |only src/variable_threads.h |only src/xmlvars.c | 996 ++++++++++++-------------------------------- 32 files changed, 588 insertions(+), 774 deletions(-)
Title: Tools for Easier Analysis of Meteorological Fields
Description: Many useful functions and extensions for dealing with
meteorological data in the tidy data framework. Extends 'ggplot2' for
better plotting of scalar and vector fields and provides commonly used
analysis methods in the atmospheric sciences.
Author: Elio Campitelli [cre, aut]
Maintainer: Elio Campitelli <eliocampitelli@gmail.com>
Diff between metR versions 0.18.3 dated 2025-12-09 and 0.19.0 dated 2026-10-08
DESCRIPTION | 10 MD5 | 247 +++---- NAMESPACE | 41 - NEWS.md | 513 +++++++-------- R/ConvertLongitude.R | 81 +- R/Derivate.R | 497 ++++++++------ R/EOF.R | 349 +++++----- R/EOF_methods.R | 202 +++-- R/FitLm.R | 229 +++--- R/FitWave.R | 149 ++-- R/GeostrophicWind.R | 54 - R/GetSMNData.R | 12 R/GetTopography.R | 209 ++++-- R/IdealGas.R | 154 ++-- R/Impute2D.R | 141 ++-- R/ImputeEOF.R | 324 +++++---- R/Interpolate.R | 257 ++++--- R/MakeBreaks.R | 149 +++- R/MaskLand.R | 67 + R/ReadNetCDF.R | 823 +++++++++++++----------- R/RepeatCircular.R | 84 +- R/Smooth2D.R | 95 +- R/Tajectory.R | 273 ++++--- R/WaveFlux.R | 280 +++++--- R/WriteNetCDF.R | 145 ++-- R/arrowGrob.R | 136 ++- R/as-discretised-scale.R | 26 R/coriolis.R | 10 R/cross.R | 23 R/geom_arrow.R | 597 ++++++++++------- R/geom_contour2.r | 290 ++++---- R/geom_contour_fill.R | 78 +- R/geom_contour_tanaka.R | 416 +++++++----- R/geom_label_contour.R | 279 ++++---- R/geom_relief.R | 290 ++++---- R/geom_shadow.R | 329 +++++---- R/geom_streamline.R | 956 ++++++++++++++++------------ R/geom_text_contour.R | 278 ++++---- R/guide_colorstrip.R | 931 ++++++++++++++++----------- R/helpfunctions.R | 527 ++++++++------- R/label-placement.R | 352 +++++----- R/label-scales.R | 43 - R/reverselog_trans.R | 16 R/rk4.R | 50 - R/scale-unbinned.R | 403 ++++++----- R/scale_divergent.R | 56 + R/scale_longitude.R | 147 ++-- R/scale_vector.R | 41 - R/season.R | 132 ++- R/small_funs.R | 76 +- R/standard_atmosphere.R | 442 +++++++----- R/stat_contour2.r | 741 ++++++++++++--------- R/stat_contour_fill.R | 616 +++++++++--------- R/stat_na.R | 96 +- R/stat_subset.R | 48 - R/textContourGrob.R | 600 +++++++++-------- R/theme_fields.R | 49 - R/zzz.R | 59 + README.md | 7 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Visualization-tools.html | 31 inst/doc/Working-with-data.html | 36 - man/Anomaly.Rd | 8 man/Derivate.Rd | 8 man/EOF.Rd | 8 man/FitLm.Rd | 24 man/GeostrophicWind.Rd | 8 man/Impute2D.Rd | 2 man/ImputeEOF.Rd | 5 man/JumpBy.Rd | 8 man/Mag.Rd | 14 man/MakeBreaks.Rd | 57 + man/Percentile.Rd | 8 man/ReadNetCDF.Rd | 2 man/WaveFlux.Rd | 45 - man/WrapCircular.Rd | 24 man/discretised_scale.Rd | 2 man/geom_arrow.Rd | 26 man/geom_contour2.Rd | 42 - man/geom_contour_fill.Rd | 26 man/geom_contour_tanaka.Rd | 2 man/geom_relief.Rd | 28 man/geom_streamline.Rd | 31 man/geom_text_contour.Rd | 30 man/guide_colourstrip.Rd | 24 man/logic.Rd | 10 man/map_labels.Rd | 26 man/metR.Rd | 5 man/reverselog_trans.Rd | 24 man/scale_divergent.Rd | 26 man/scale_longitude.Rd | 26 man/scale_stroke.colour_continuous.Rd | 2 man/standard_atmosphere.Rd | 2 man/stat_na.Rd | 26 man/stat_subset.Rd | 26 man/thermodynamics.Rd | 10 man/waves.Rd | 10 tests/testthat.R | 4 tests/testthat/era5_timestamp.nc |only tests/testthat/test-GetTopography.R | 22 tests/testthat/test-ReadNetCDF.R | 157 ++-- tests/testthat/test-Smooth2D.R | 24 tests/testthat/test-breaks.R | 35 - tests/testthat/test-derivate.R | 228 +++--- tests/testthat/test-eof.R | 151 ++-- tests/testthat/test-fitlm.R | 112 +-- tests/testthat/test-imputeeof.R | 57 + tests/testthat/test-interpolate.R | 49 - tests/testthat/test-season.R | 37 - tests/testthat/test-smallfun.R | 55 - tests/testthat/test-thermodynamics.R | 86 +- tests/testthat/test-trajectory.R | 46 - tests/testthat/test-vis-arrow.R | 56 - tests/testthat/test-vis-contour2.R | 121 +-- tests/testthat/test-vis-contour_fill.R | 88 +- tests/testthat/test-vis-discretised-scale.R | 53 - tests/testthat/test-vis-geom-relief.R | 78 +- tests/testthat/test-vis-guide_colorstrip.R | 41 - tests/testthat/test-vis-streamline.R | 109 ++- tests/testthat/test-vis-text-contour.R | 157 ++-- tests/testthat/test-waveflux.R | 9 tests/testthat/test-waves.R | 27 tests/testthat/test_text_contour.R | 1 tests/testthat/tests.R | 33 125 files changed, 9654 insertions(+), 7399 deletions(-)
Title: Random Effects Latent Class Analysis
Description: Fits standard and random effects latent class models. The single level random effects model is described in Qu et al <doi:10.2307/2533043> and the two level random effects model in Beath and Heller <doi:10.1177/1471082X0800900302>. Examples are given for their use in diagnostic testing.
Author: Ken Beath [aut, cre]
Maintainer: Ken Beath <ken@kjbeath.id.au>
Diff between randomLCA versions 1.1-4 dated 2024-09-23 and 1.1-5 dated 2026-10-07
randomLCA-1.1-4/randomLCA/inst/doc/randomLCA-package.pdf |only randomLCA-1.1-4/randomLCA/inst/doc/randomLCA-package.pdf.asis |only randomLCA-1.1-4/randomLCA/vignettes/randomLCA-package.pdf.asis |only randomLCA-1.1-5/randomLCA/DESCRIPTION | 13 - randomLCA-1.1-5/randomLCA/MD5 | 32 ++-- randomLCA-1.1-5/randomLCA/NAMESPACE | 8 - randomLCA-1.1-5/randomLCA/R/bestlca.R | 78 +++++----- randomLCA-1.1-5/randomLCA/R/fitFixed.R | 36 +--- randomLCA-1.1-5/randomLCA/R/outcomeProbs.R | 6 randomLCA-1.1-5/randomLCA/R/randomLCA.R | 23 +- randomLCA-1.1-5/randomLCA/R/refit.randomLCA.R | 24 ++- randomLCA-1.1-5/randomLCA/build/partial.rdb |binary randomLCA-1.1-5/randomLCA/build/vignette.rds |binary randomLCA-1.1-5/randomLCA/inst/NEWS | 8 + randomLCA-1.1-5/randomLCA/inst/doc/randomLCA-package.html |only randomLCA-1.1-5/randomLCA/inst/doc/randomLCA-package.html.asis |only randomLCA-1.1-5/randomLCA/man/outcomeProbs.Rd | 2 randomLCA-1.1-5/randomLCA/man/randomLCA.Rd | 4 randomLCA-1.1-5/randomLCA/vignettes/randomLCA-package.Rmd |only randomLCA-1.1-5/randomLCA/vignettes/randomLCA-package.bib |only randomLCA-1.1-5/randomLCA/vignettes/randomLCA-package.html.asis |only 21 files changed, 127 insertions(+), 107 deletions(-)
Title: Venn Diagram
Description: Generate Venn plots, summary tables, and ellipse paths for polygon clipping.
Provides direct access to subsets of interest and offers flexible customization of Venn diagrams.
Summary tables are also available when Venn diagram visualization is not suitable.
Author: Joon-Keat Lai [aut, cre, cph]
Maintainer: Joon-Keat Lai <p10911004@gmail.com>
Diff between venny versions 0.0.3 dated 2026-05-27 and 0.0.4 dated 2026-10-07
DESCRIPTION | 16 ++++++------ MD5 | 23 ++++++++++------- NEWS.md | 44 ++++++++++++++++++++++----------- R/params.R | 14 ++++++---- R/utils.R | 27 +++++++++++++------- R/venny.R | 5 ++- README.md | 57 +++++++++++++++++++++++--------------------- build |only inst |only man/venn_summary.Rd | 2 - man/venny.Rd | 2 - tests/testthat/test-venny.R | 13 ++++------ vignettes |only 13 files changed, 119 insertions(+), 84 deletions(-)
Title: Model-Robust Standardization in Cluster-Randomized Trials
Description: Implements model-robust standardization for cluster-randomized trials (CRTs). Provides functions that standardize user-specified regression models to estimate marginal treatment effects. The targets include the cluster-average and individual-average treatment effects, with utilities for variance estimation and example simulation datasets. Methods are described in Li, Tong, Fang, Cheng, Kahan, and Wang (2025) <doi:10.1002/sim.70270>.
Author: Jiaqi Tong [aut],
Changjun Li [aut, cre],
Xi Fang [aut],
Chao Cheng [aut],
Bingkai Wang [aut],
Fan Li [aut]
Maintainer: Changjun Li <changjun.li@yale.edu>
Diff between MRStdCRT versions 0.1.1 dated 2025-11-11 and 0.1.2 dated 2026-10-07
DESCRIPTION | 6 MD5 | 25 R/MRStdCRT_fit.R | 97 +-- R/MRStdCRT_point.R | 135 +++-- R/validate.R |only README.md | 2 build/vignette.rds |binary inst/doc/introduction.R |only inst/doc/introduction.Rmd | 124 +++- inst/doc/introduction.html | 1180 +++++++++++++++++++++++---------------------- man/MRStdCRT_fit.Rd | 13 man/MRStdCRT_point.Rd | 8 man/summary.MRS_obj.Rd | 5 tests |only vignettes/introduction.Rmd | 124 +++- 15 files changed, 963 insertions(+), 756 deletions(-)