Title: Fast and Robust Multi-Scale Graph Clustering
Description: A graph community detection algorithm that aims to be performant
on large graphs and robust, returning consistent results across runs.
SpeakEasy 2 (SE2), the underlying algorithm, is described in Chris Gaiteri,
David R. Connell & Faraz A. Sultan et al. (2023)
<doi:10.1186/s13059-023-03062-0>. The core algorithm is written in 'C',
providing speed and keeping the memory requirements low. This implementation
can take advantage of multiple computing cores without increasing memory
usage. SE2 can detect community structure across scales, making it a good
choice for biological data, which often has hierarchical structure. Graphs
can be passed to the algorithm as adjacency matrices using base 'R'
matrices, the 'Matrix' library, 'igraph' graphs, or any data that can be
coerced into a matrix.
Author: David Connell [aut, cre, cph] ,
Chris Gaiteri [cph] ,
Gabor Csardi [cph, ctb] ,
Tamas Nepusz [cph, ctb] ,
Szabolcs Horvat [cph, ctb] ,
Vincent Traag [cph, ctb] ,
Fabio Zanini [cph, ctb] ,
Daniel Noom [cph, ctb] ,
The igraph development team [cph] ,
F [...truncated...]
Maintainer: David Connell <david32@dcon.addy.io>
Diff between speakeasyR versions 0.1.8 dated 2025-09-30 and 0.1.9 dated 2026-10-19
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 6 ++++++ README.md | 2 +- build/vignette.rds |binary configure | 18 +++++++++--------- configure.ac | 2 +- configure.win | 2 +- inst/doc/speakeasyR.html | 12 +++--------- 9 files changed, 32 insertions(+), 32 deletions(-)
Title: Interface for Large Language Model APIs in R
Description: One interface to many large language model providers: a single
configuration object and a single calling function serve chat and embedding
models alike, so research code does not change when the provider does. The
same calls scale to multi-model and multi-condition studies. Small open
models can also run on the user's computer through 'llama.cpp', downloaded
only on request, with access to next-token probabilities.
Author: Ali Sanaei [aut, cre]
Maintainer: Ali Sanaei <sanaei@uchicago.edu>
Diff between LLMR versions 0.8.11 dated 2026-07-24 and 0.9.0 dated 2026-10-19
LLMR-0.8.11/LLMR/man/llm_methods_text.Rd |only LLMR-0.9.0/LLMR/DESCRIPTION | 19 LLMR-0.9.0/LLMR/MD5 | 149 ++++-- LLMR-0.9.0/LLMR/NAMESPACE | 21 LLMR-0.9.0/LLMR/NEWS.md | 208 ++++++++ LLMR-0.9.0/LLMR/R/LLMR.R | 233 +++++++--- LLMR-0.9.0/LLMR/R/LLMR_response.R | 18 LLMR-0.9.0/LLMR/R/LLM_chat_session.R | 43 + LLMR-0.9.0/LLMR/R/LLM_parallel_utils.R | 147 ++++-- LLMR-0.9.0/LLMR/R/LLM_robust_utils.R | 31 + LLMR-0.9.0/LLMR/R/audit_log.R | 86 ++- LLMR-0.9.0/LLMR/R/batch_api.R | 140 ++++-- LLMR-0.9.0/LLMR/R/errors_catalog.R |only LLMR-0.9.0/LLMR/R/generics.R | 8 LLMR-0.9.0/LLMR/R/generics_reset.R | 9 LLMR-0.9.0/LLMR/R/hash.R | 8 LLMR-0.9.0/LLMR/R/json_mode.R | 37 - LLMR-0.9.0/LLMR/R/local_install.R |only LLMR-0.9.0/LLMR/R/local_provider.R |only LLMR-0.9.0/LLMR/R/local_registry.R |only LLMR-0.9.0/LLMR/R/local_research.R |only LLMR-0.9.0/LLMR/R/local_server.R |only LLMR-0.9.0/LLMR/R/log_messages.R | 11 LLMR-0.9.0/LLMR/R/log_read.R | 135 ++++- LLMR-0.9.0/LLMR/R/render_messages.R | 78 +++ LLMR-0.9.0/LLMR/R/secrets.R | 5 LLMR-0.9.0/LLMR/R/stream.R | 200 ++++++-- LLMR-0.9.0/LLMR/R/tags_mode.R | 29 - LLMR-0.9.0/LLMR/R/tools.R | 141 ++++-- LLMR-0.9.0/LLMR/R/usage.R | 140 ++++-- LLMR-0.9.0/LLMR/README.md | 44 + LLMR-0.9.0/LLMR/build/vignette.rds |binary LLMR-0.9.0/LLMR/inst/ai/LLMR.md | 37 + LLMR-0.9.0/LLMR/inst/doc/local-models.R |only LLMR-0.9.0/LLMR/inst/doc/local-models.Rmd |only LLMR-0.9.0/LLMR/inst/doc/local-models.html |only LLMR-0.9.0/LLMR/man/call_llm.Rd | 41 + LLMR-0.9.0/LLMR/man/call_llm_par_structured.Rd | 10 LLMR-0.9.0/LLMR/man/call_llm_par_tags.Rd | 10 LLMR-0.9.0/LLMR/man/call_llm_stream.Rd | 25 - LLMR-0.9.0/LLMR/man/call_llm_tools.Rd | 12 LLMR-0.9.0/LLMR/man/diagnostics.Rd | 8 LLMR-0.9.0/LLMR/man/enable_structured_output.Rd | 4 LLMR-0.9.0/LLMR/man/figures |only LLMR-0.9.0/LLMR/man/llm_batch_fetch.Rd | 12 LLMR-0.9.0/LLMR/man/llm_batch_submit.Rd | 7 LLMR-0.9.0/LLMR/man/llm_chat_session.Rd | 5 LLMR-0.9.0/LLMR/man/llm_choice_probs.Rd |only LLMR-0.9.0/LLMR/man/llm_config.Rd | 12 LLMR-0.9.0/LLMR/man/llm_continue.Rd |only LLMR-0.9.0/LLMR/man/llm_failures.Rd | 16 LLMR-0.9.0/LLMR/man/llm_hash.Rd | 4 LLMR-0.9.0/LLMR/man/llm_judge.Rd | 4 LLMR-0.9.0/LLMR/man/llm_local_dir.Rd |only LLMR-0.9.0/LLMR/man/llm_local_install.Rd |only LLMR-0.9.0/LLMR/man/llm_local_model.Rd |only LLMR-0.9.0/LLMR/man/llm_local_models.Rd |only LLMR-0.9.0/LLMR/man/llm_local_ready.Rd |only LLMR-0.9.0/LLMR/man/llm_local_start.Rd |only LLMR-0.9.0/LLMR/man/llm_local_uninstall.Rd |only LLMR-0.9.0/LLMR/man/llm_log_enable.Rd | 21 LLMR-0.9.0/LLMR/man/llm_log_read.Rd | 15 LLMR-0.9.0/LLMR/man/llm_next_token.Rd |only LLMR-0.9.0/LLMR/man/llm_par_resume.Rd | 53 +- LLMR-0.9.0/LLMR/man/llm_render_template.Rd |only LLMR-0.9.0/LLMR/man/llm_request_from_log.Rd | 26 - LLMR-0.9.0/LLMR/man/llm_score.Rd |only LLMR-0.9.0/LLMR/man/llm_tokenize.Rd |only LLMR-0.9.0/LLMR/man/llm_usage.Rd | 23 LLMR-0.9.0/LLMR/man/llmr_response.Rd | 18 LLMR-0.9.0/LLMR/man/reset.Rd | 9 LLMR-0.9.0/LLMR/man/reset_llm_parallel.Rd | 17 LLMR-0.9.0/LLMR/man/setup_llm_parallel.Rd | 18 LLMR-0.9.0/LLMR/man/tool_calls.Rd | 8 LLMR-0.9.0/LLMR/tests/testthat/test-000-experiment-reporting.R | 11 LLMR-0.9.0/LLMR/tests/testthat/test-083-core.R | 15 LLMR-0.9.0/LLMR/tests/testthat/test-083-features.R | 7 LLMR-0.9.0/LLMR/tests/testthat/test-batch-ingestion.R |only LLMR-0.9.0/LLMR/tests/testthat/test-bugfixes.R | 77 +++ LLMR-0.9.0/LLMR/tests/testthat/test-error-catalog.R |only LLMR-0.9.0/LLMR/tests/testthat/test-experiment-templating.R |only LLMR-0.9.0/LLMR/tests/testthat/test-gemini-thinking-usage.R |only LLMR-0.9.0/LLMR/tests/testthat/test-judge-target.R |only LLMR-0.9.0/LLMR/tests/testthat/test-live-cheap.R | 23 LLMR-0.9.0/LLMR/tests/testthat/test-local-live.R |only LLMR-0.9.0/LLMR/tests/testthat/test-local.R |only LLMR-0.9.0/LLMR/tests/testthat/test-log-read-lines.R |only LLMR-0.9.0/LLMR/tests/testthat/test-meta.R |only LLMR-0.9.0/LLMR/tests/testthat/test-par-resume.R |only LLMR-0.9.0/LLMR/tests/testthat/test-price-table.R |only LLMR-0.9.0/LLMR/tests/testthat/test-replay-reissuable.R |only LLMR-0.9.0/LLMR/tests/testthat/test-stream-failures.R |only LLMR-0.9.0/LLMR/tests/testthat/test-timeout-and-hash.R |only LLMR-0.9.0/LLMR/tests/testthat/test-tool-arguments.R |only LLMR-0.9.0/LLMR/tests/testthat/test-usage-unknown.R |only LLMR-0.9.0/LLMR/vignettes/local-models.Rmd |only 96 files changed, 1904 insertions(+), 584 deletions(-)
Title: Distributed Online Goodness-of-Fit Tests for Distributed
Datasets
Description: Distributed Online Goodness-of-Fit Test can process the distributed datasets. The philosophy of the package is described in Guo G.(2024) <doi:10.1016/j.apm.2024.115709>.
Author: Guangbao Guo [aut, cre] ,
Di Chang [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between Dogoftest versions 0.4.2 dated 2026-10-12 and 0.4.3 dated 2026-10-19
DESCRIPTION | 6 +++--- MD5 | 13 +++++++++---- NAMESPACE | 3 +++ R/PECVM.R | 47 +++++++++++++++++++++++------------------------ R/data1.R |only R/simulate_power.R |only data/air_quality.rda |only man/PECVM.Rd | 7 +++++-- man/air_quality.Rd |only man/simulate_power.Rd |only 10 files changed, 43 insertions(+), 33 deletions(-)
Title: Load US Census Boundary and Attribute Data as 'tidyverse' and
'sf'-Ready Data Frames
Description: An integrated R interface to several United States Census Bureau
APIs (<https://www.census.gov/data/developers/data-sets.html>) and the US Census Bureau's
geographic boundary files. Allows R users to return Census and ACS data as
tidyverse-ready data frames, and optionally returns a list-column with feature geometry for mapping
and spatial analysis.
Author: Kyle Walker [aut, cre],
Matt Herman [aut],
Kris Eberwein [ctb]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between tidycensus versions 1.8.1 dated 2026-05-25 and 2.0.0 dated 2026-10-19
DESCRIPTION | 19 MD5 | 62 - NAMESPACE | 59 - NEWS.md | 14 R/acs.R | 234 ++++- R/census.R | 152 ++- R/estimates.R | 1220 ++++++++++++++++++++--------- R/fips_codes.R | 4 R/flows.R | 38 R/helpers.R | 83 + R/labels.R |only R/load_data.R | 292 ++---- R/popgroups.R | 14 R/pums.R | 8 R/request.R |only R/search_variables.R | 88 +- R/tidycensus-package.R | 1 R/utils.R | 161 +++ R/zzz.r | 5 man/get_acs.Rd | 42 man/get_decennial.Rd | 30 man/get_estimates.Rd | 33 man/get_flows.Rd | 28 man/get_pums.Rd | 6 man/load_variables.Rd | 35 man/pums_variables.Rd | 4 man/tidycensus-package.Rd | 1 tests/testthat/test-api-key.R | 81 + tests/testthat/test-estimates.R | 393 +++++++++ tests/testthat/test-helpers.R | 309 +++++++ tests/testthat/test-labels.R |only tests/testthat/test-national-geographies.R |only tests/testthat/test-postprocess.R |only tests/testthat/test-request.R |only tests/testthat/test-spatial-bind.R |only tests/testthat/test-utils.R |only 36 files changed, 2602 insertions(+), 814 deletions(-)
Title: Schema-Driven Machine Learning and Visualization
Description: Machine learning and visualization package with an 'S7' backend featuring
comprehensive type checking and validation, observable runs, and auditable outputs.
The functional API provides one-call access to supervised and unsupervised learning
through train(), cluster(), and decomp(). All configuration steps are performed using
setup functions and validated. A single call to train() can handle preprocessing,
decomposition, hyperparameter tuning, model stacking, and testing with nested resampling.
Supports 'data.frame', 'data.table', and 'tibble' inputs and parallel execution. Plot
methods for trained and resampled supervised models draw interactive figures through
'rtemis.draw'. Includes native implementations of SuperLearner, RuleFit, and Linear
Additive Trees, and supports conformal prediction. The package first appeared in
E.D. Gennatas (2017)
<https://repository.upenn.edu/entities/publication/d81892ea-3087-4b71-a6f5-739c58626d64>.
Author: E.D. Gennatas [aut, cre, cph]
Maintainer: E.D. Gennatas <gennatas@gmail.com>
Diff between rtemis versions 1.2.7 dated 2026-07-01 and 1.4.2 dated 2026-10-19
rtemis-1.2.7/rtemis/R/00_init.R |only rtemis-1.2.7/rtemis/R/01_ExecutionConfig.R |only rtemis-1.2.7/rtemis/R/02_Hyperparameters.R |only rtemis-1.2.7/rtemis/R/03_Metrics.R |only rtemis-1.2.7/rtemis/R/04_Preprocessor.R |only rtemis-1.2.7/rtemis/R/05_Resampler.R |only rtemis-1.2.7/rtemis/R/06_Tuner.R |only rtemis-1.2.7/rtemis/R/07_ClusteringConfig.R |only rtemis-1.2.7/rtemis/R/08_Clustering.R |only rtemis-1.2.7/rtemis/R/09_DecompositionConfig.R |only rtemis-1.2.7/rtemis/R/10_Decomposition.R |only rtemis-1.2.7/rtemis/R/11_Session.R |only rtemis-1.2.7/rtemis/R/12_Supervised.R |only rtemis-1.2.7/rtemis/R/13_MassUni.R |only rtemis-1.2.7/rtemis/R/14_Themes.R |only rtemis-1.2.7/rtemis/R/15_SuperConfig.R |only rtemis-1.2.7/rtemis/R/16_DecomposeConfig.R |only rtemis-1.2.7/rtemis/R/17_ClusterConfig.R |only rtemis-1.2.7/rtemis/R/18_CheckData.R |only rtemis-1.2.7/rtemis/R/19_S7utils.R |only rtemis-1.2.7/rtemis/R/data_xt_example.R |only rtemis-1.2.7/rtemis/R/draw_3Dscatter.R |only 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rtemis-1.4.2/rtemis/DESCRIPTION | 60 rtemis-1.4.2/rtemis/LICENSE |only rtemis-1.4.2/rtemis/MD5 | 722 + rtemis-1.4.2/rtemis/NAMESPACE | 172 rtemis-1.4.2/rtemis/NEWS.md |only rtemis-1.4.2/rtemis/R/005_HyperparameterCandidates.R |only rtemis-1.4.2/rtemis/R/009_DefaultPolicy.R |only rtemis-1.4.2/rtemis/R/010_Props.R |only rtemis-1.4.2/rtemis/R/015_ReferenceProps.R |only rtemis-1.4.2/rtemis/R/020_Props_read.R |only rtemis-1.4.2/rtemis/R/024_SchemaRules.R |only rtemis-1.4.2/rtemis/R/024_SchemaRules_result.R |only rtemis-1.4.2/rtemis/R/024_SemanticRules.R |only rtemis-1.4.2/rtemis/R/025_SchemaCatalog.R |only rtemis-1.4.2/rtemis/R/026_Defaults.R |only rtemis-1.4.2/rtemis/R/027_DefaultArtifact.R |only rtemis-1.4.2/rtemis/R/030_init.R |only rtemis-1.4.2/rtemis/R/040_DataFingerprint.R |only rtemis-1.4.2/rtemis/R/045_DataProfile.R |only rtemis-1.4.2/rtemis/R/047_IngestConfig.R |only rtemis-1.4.2/rtemis/R/048_PartitionConfig.R |only rtemis-1.4.2/rtemis/R/049_DeviceConfig.R |only rtemis-1.4.2/rtemis/R/050_ExecutionConfig.R |only rtemis-1.4.2/rtemis/R/060_Provenance.R |only rtemis-1.4.2/rtemis/R/061_DataRef.R |only rtemis-1.4.2/rtemis/R/065_Torch.R |only rtemis-1.4.2/rtemis/R/070_Hyperparameters.R |only rtemis-1.4.2/rtemis/R/075_HyperparametersSet.R |only rtemis-1.4.2/rtemis/R/080_Metrics.R |only rtemis-1.4.2/rtemis/R/090_Preprocessor.R |only rtemis-1.4.2/rtemis/R/100_Resampler.R |only rtemis-1.4.2/rtemis/R/110_Tuner.R |only rtemis-1.4.2/rtemis/R/115_MetaLearners.R |only rtemis-1.4.2/rtemis/R/120_ClusteringConfig.R |only rtemis-1.4.2/rtemis/R/130_ClusterConfig.R |only rtemis-1.4.2/rtemis/R/135_ClusteringMetrics.R |only rtemis-1.4.2/rtemis/R/140_Clustering.R |only rtemis-1.4.2/rtemis/R/150_DecompositionConfig.R |only rtemis-1.4.2/rtemis/R/160_DecomposeConfig.R |only rtemis-1.4.2/rtemis/R/165_DecompositionMetrics.R |only rtemis-1.4.2/rtemis/R/170_Decomposition.R |only rtemis-1.4.2/rtemis/R/180_Session.R |only rtemis-1.4.2/rtemis/R/190_SuperConfig.R |only rtemis-1.4.2/rtemis/R/200_Supervised.R |only rtemis-1.4.2/rtemis/R/210_MassUni.R |only rtemis-1.4.2/rtemis/R/230_CheckData.R |only rtemis-1.4.2/rtemis/R/240_S7utils.R |only rtemis-1.4.2/rtemis/R/250_Explanation.R |only rtemis-1.4.2/rtemis/R/260_PredictionRegion.R |only rtemis-1.4.2/rtemis/R/270_Diagnostics.R |only rtemis-1.4.2/rtemis/R/280_SupervisedReview.R |only rtemis-1.4.2/rtemis/R/285_AISupervisedReview.R |only rtemis-1.4.2/rtemis/R/290_SupervisedWriteup.R |only rtemis-1.4.2/rtemis/R/ai_review.R |only rtemis-1.4.2/rtemis/R/algorithmDB.R | 1020 +- rtemis-1.4.2/rtemis/R/bias_variance.R |only rtemis-1.4.2/rtemis/R/calibrate.R | 93 rtemis-1.4.2/rtemis/R/check_data.R | 145 rtemis-1.4.2/rtemis/R/check_input_data.R | 78 rtemis-1.4.2/rtemis/R/cluster.R | 173 rtemis-1.4.2/rtemis/R/cluster_CMeans.R | 20 rtemis-1.4.2/rtemis/R/cluster_DBSCAN.R | 21 rtemis-1.4.2/rtemis/R/cluster_GMM.R |only rtemis-1.4.2/rtemis/R/cluster_HOPACH.R |only rtemis-1.4.2/rtemis/R/cluster_PAM.R |only rtemis-1.4.2/rtemis/R/cluster_Spectral.R |only rtemis-1.4.2/rtemis/R/cluster_flexclust.R | 21 rtemis-1.4.2/rtemis/R/conditions.R | 3 rtemis-1.4.2/rtemis/R/conformal.R |only rtemis-1.4.2/rtemis/R/ddb.R | 18 rtemis-1.4.2/rtemis/R/decomp.R | 175 rtemis-1.4.2/rtemis/R/decomp_Autoencoder.R |only rtemis-1.4.2/rtemis/R/decomp_ICA.R | 123 rtemis-1.4.2/rtemis/R/decomp_Isomap.R | 9 rtemis-1.4.2/rtemis/R/decomp_MDS.R |only rtemis-1.4.2/rtemis/R/decomp_NMF.R | 195 rtemis-1.4.2/rtemis/R/decomp_PCA.R | 54 rtemis-1.4.2/rtemis/R/decomp_PCoA.R |only rtemis-1.4.2/rtemis/R/decomp_UMAP.R | 32 rtemis-1.4.2/rtemis/R/decomp_dist.R |only rtemis-1.4.2/rtemis/R/decomp_metrics.R |only rtemis-1.4.2/rtemis/R/decomp_tSNE.R | 21 rtemis-1.4.2/rtemis/R/draw_linad.R |only rtemis-1.4.2/rtemis/R/explain.R |only rtemis-1.4.2/rtemis/R/fit_predict.R |only rtemis-1.4.2/rtemis/R/fmt.R | 4 rtemis-1.4.2/rtemis/R/linad.R |only rtemis-1.4.2/rtemis/R/linad_forest.R |only rtemis-1.4.2/rtemis/R/massGLM.R | 10 rtemis-1.4.2/rtemis/R/metrics.R | 94 rtemis-1.4.2/rtemis/R/plot.SupervisedSession.R |only rtemis-1.4.2/rtemis/R/plot_confusion.R |only rtemis-1.4.2/rtemis/R/plot_learning.R |only rtemis-1.4.2/rtemis/R/plot_massglm.R |only rtemis-1.4.2/rtemis/R/plot_metric.R |only rtemis-1.4.2/rtemis/R/plot_roc.R |only rtemis-1.4.2/rtemis/R/plot_true_pred.R |only rtemis-1.4.2/rtemis/R/plot_varimp.R |only rtemis-1.4.2/rtemis/R/preprocess.R | 1687 ++- rtemis-1.4.2/rtemis/R/present.R | 527 - rtemis-1.4.2/rtemis/R/read.R | 108 rtemis-1.4.2/rtemis/R/read_config.R | 345 rtemis-1.4.2/rtemis/R/record.R |only rtemis-1.4.2/rtemis/R/reexports.R | 5 rtemis-1.4.2/rtemis/R/resample.R | 310 rtemis-1.4.2/rtemis/R/resolve_hyperparameters.R |only rtemis-1.4.2/rtemis/R/result_storage.R |only rtemis-1.4.2/rtemis/R/review.R |only rtemis-1.4.2/rtemis/R/roc_curve.R |only rtemis-1.4.2/rtemis/R/rtemis-package.R | 20 rtemis-1.4.2/rtemis/R/rtemis_color_system.R | 1 rtemis-1.4.2/rtemis/R/train.R | 1403 ++ rtemis-1.4.2/rtemis/R/train_BART.R |only rtemis-1.4.2/rtemis/R/train_CART.R | 335 rtemis-1.4.2/rtemis/R/train_ConditionalSuperLearner.R |only rtemis-1.4.2/rtemis/R/train_GAM.R | 170 rtemis-1.4.2/rtemis/R/train_GLM.R | 82 rtemis-1.4.2/rtemis/R/train_GLMNET.R | 248 rtemis-1.4.2/rtemis/R/train_GLMTree.R |only rtemis-1.4.2/rtemis/R/train_HAL.R |only rtemis-1.4.2/rtemis/R/train_Isotonic.R | 115 rtemis-1.4.2/rtemis/R/train_KNN.R |only rtemis-1.4.2/rtemis/R/train_LINAD.R |only rtemis-1.4.2/rtemis/R/train_LINADForest.R |only rtemis-1.4.2/rtemis/R/train_LightCART.R | 25 rtemis-1.4.2/rtemis/R/train_LightGBM.R | 328 rtemis-1.4.2/rtemis/R/train_LightRF.R | 181 rtemis-1.4.2/rtemis/R/train_LightRuleFit.R | 201 rtemis-1.4.2/rtemis/R/train_MARS.R |only rtemis-1.4.2/rtemis/R/train_MLP.R |only rtemis-1.4.2/rtemis/R/train_MetaLearner.R |only rtemis-1.4.2/rtemis/R/train_MonotonicHAL.R |only rtemis-1.4.2/rtemis/R/train_NNLS.R |only rtemis-1.4.2/rtemis/R/train_Ranger.R | 256 rtemis-1.4.2/rtemis/R/train_SPLS.R |only rtemis-1.4.2/rtemis/R/train_SVM.R | 176 rtemis-1.4.2/rtemis/R/train_StackedLearner.R |only rtemis-1.4.2/rtemis/R/train_TabNet.R | 54 rtemis-1.4.2/rtemis/R/tune.R | 13 rtemis-1.4.2/rtemis/R/tune_GridSearch.R | 1011 +- rtemis-1.4.2/rtemis/R/utils.R | 63 rtemis-1.4.2/rtemis/R/utils_art.R | 11 rtemis-1.4.2/rtemis/R/utils_async.R | 1131 ++ rtemis-1.4.2/rtemis/R/utils_audit_props.R |only rtemis-1.4.2/rtemis/R/utils_color.R | 802 - rtemis-1.4.2/rtemis/R/utils_data.R | 5 rtemis-1.4.2/rtemis/R/utils_data.table.R | 12 rtemis-1.4.2/rtemis/R/utils_date.R | 63 rtemis-1.4.2/rtemis/R/utils_df.R | 5 rtemis-1.4.2/rtemis/R/utils_exec.R | 96 rtemis-1.4.2/rtemis/R/utils_html.R | 235 rtemis-1.4.2/rtemis/R/utils_io.R | 29 rtemis-1.4.2/rtemis/R/utils_lightgbm.R | 2 rtemis-1.4.2/rtemis/R/utils_markdown.R |only rtemis-1.4.2/rtemis/R/utils_print.R | 18 rtemis-1.4.2/rtemis/R/utils_rt.R | 58 rtemis-1.4.2/rtemis/R/utils_strings.R | 19 rtemis-1.4.2/rtemis/R/utils_supervised.R | 217 rtemis-1.4.2/rtemis/R/validate_config.R |only rtemis-1.4.2/rtemis/R/validate_data.R |only rtemis-1.4.2/rtemis/R/write_config.R | 347 rtemis-1.4.2/rtemis/R/write_text.R |only rtemis-1.4.2/rtemis/R/writeup.R |only rtemis-1.4.2/rtemis/R/writeup_hyperparameters.R |only rtemis-1.4.2/rtemis/R/zzz.R | 51 rtemis-1.4.2/rtemis/R/zzz_model_plots.R |only rtemis-1.4.2/rtemis/R/zzzz_namespace_index.R |only rtemis-1.4.2/rtemis/README.md | 77 rtemis-1.4.2/rtemis/build |only rtemis-1.4.2/rtemis/inst/checks |only rtemis-1.4.2/rtemis/inst/profile |only rtemis-1.4.2/rtemis/inst/traits |only rtemis-1.4.2/rtemis/man/HyperparameterCandidates.Rd |only rtemis-1.4.2/rtemis/man/JSONSchema_to_S7.Rd |only rtemis-1.4.2/rtemis/man/S7_dispatcher_JSONSchema.Rd |only rtemis-1.4.2/rtemis/man/S7_to_JSONSchema.Rd |only rtemis-1.4.2/rtemis/man/ai_review.Rd |only rtemis-1.4.2/rtemis/man/applicable_metrics.Rd |only rtemis-1.4.2/rtemis/man/apply_decomp.Rd | 25 rtemis-1.4.2/rtemis/man/apply_preprocessor.Rd |only rtemis-1.4.2/rtemis/man/available_algorithms.Rd | 20 rtemis-1.4.2/rtemis/man/bias_variance.Rd |only rtemis-1.4.2/rtemis/man/calibrate.Rd | 60 rtemis-1.4.2/rtemis/man/check_data.Rd | 13 rtemis-1.4.2/rtemis/man/classification_metrics.Rd | 12 rtemis-1.4.2/rtemis/man/cluster.Rd | 27 rtemis-1.4.2/rtemis/man/conformal.Rd |only rtemis-1.4.2/rtemis/man/conformal_metrics.Rd |only rtemis-1.4.2/rtemis/man/data_fingerprint.Rd |only rtemis-1.4.2/rtemis/man/data_profile.Rd |only rtemis-1.4.2/rtemis/man/ddb_collect.Rd | 6 rtemis-1.4.2/rtemis/man/ddb_data.Rd | 10 rtemis-1.4.2/rtemis/man/decomp.Rd | 31 rtemis-1.4.2/rtemis/man/decomp_metrics.Rd |only rtemis-1.4.2/rtemis/man/decomposition_traits.Rd |only rtemis-1.4.2/rtemis/man/describe.Rd | 15 rtemis-1.4.2/rtemis/man/dot-drop_meta_keys.Rd |only rtemis-1.4.2/rtemis/man/dot-get_alg_name.Rd |only rtemis-1.4.2/rtemis/man/dot-get_clust_name.Rd |only rtemis-1.4.2/rtemis/man/dot-get_decom_name.Rd |only rtemis-1.4.2/rtemis/man/dot-list_to_ClusteringConfig.Rd |only rtemis-1.4.2/rtemis/man/dot-list_to_DecompositionConfig.Rd | 23 rtemis-1.4.2/rtemis/man/dot-list_to_Hyperparameters.Rd | 15 rtemis-1.4.2/rtemis/man/dot-list_to_PreprocessorConfig.Rd |only rtemis-1.4.2/rtemis/man/dot-list_to_ResamplerConfig.Rd | 12 rtemis-1.4.2/rtemis/man/dot-list_to_SuperConfig.Rd |only rtemis-1.4.2/rtemis/man/dot-list_to_SupervisedPreprocessorConfig.Rd |only rtemis-1.4.2/rtemis/man/dot-list_to_TunerConfig.Rd | 22 rtemis-1.4.2/rtemis/man/dot-supervised_algorithms.Rd |only rtemis-1.4.2/rtemis/man/draw_linad.Rd |only rtemis-1.4.2/rtemis/man/exc.Rd | 2 rtemis-1.4.2/rtemis/man/explain.Rd |only rtemis-1.4.2/rtemis/man/explanation_methods.Rd |only rtemis-1.4.2/rtemis/man/feature_names.Rd | 2 rtemis-1.4.2/rtemis/man/features.Rd | 2 rtemis-1.4.2/rtemis/man/fit_predict.Rd |only rtemis-1.4.2/rtemis/man/fitted_config.Rd |only rtemis-1.4.2/rtemis/man/get_factor_names.Rd | 2 rtemis-1.4.2/rtemis/man/get_learning_curve.Rd |only rtemis-1.4.2/rtemis/man/get_metrics.Rd |only rtemis-1.4.2/rtemis/man/get_varimp.Rd | 22 rtemis-1.4.2/rtemis/man/grapes-BC-grapes.Rd | 19 rtemis-1.4.2/rtemis/man/inc.Rd | 2 rtemis-1.4.2/rtemis/man/ingest.Rd |only rtemis-1.4.2/rtemis/man/inspect.Rd | 2 rtemis-1.4.2/rtemis/man/is_wire_hyperparameters_set.Rd |only rtemis-1.4.2/rtemis/man/numeric_features.Rd | 2 rtemis-1.4.2/rtemis/man/one_hot2factor.Rd | 2 rtemis-1.4.2/rtemis/man/outcome.Rd | 2 rtemis-1.4.2/rtemis/man/outcome_name.Rd | 2 rtemis-1.4.2/rtemis/man/partition.Rd |only rtemis-1.4.2/rtemis/man/plot_learning.Rd |only rtemis-1.4.2/rtemis/man/plot_manhattan.Rd | 73 rtemis-1.4.2/rtemis/man/plot_metric.Rd |only rtemis-1.4.2/rtemis/man/plot_roc.Rd | 38 rtemis-1.4.2/rtemis/man/plot_session.Rd |only rtemis-1.4.2/rtemis/man/plot_true_pred.Rd | 51 rtemis-1.4.2/rtemis/man/plot_varimp.Rd | 65 rtemis-1.4.2/rtemis/man/preprocess.Rd | 71 rtemis-1.4.2/rtemis/man/preprocessed.Rd | 2 rtemis-1.4.2/rtemis/man/present.Rd | 65 rtemis-1.4.2/rtemis/man/read.Rd | 8 rtemis-1.4.2/rtemis/man/read_config.Rd | 23 rtemis-1.4.2/rtemis/man/read_result.Rd |only rtemis-1.4.2/rtemis/man/reconstruct.Rd |only rtemis-1.4.2/rtemis/man/record.Rd |only rtemis-1.4.2/rtemis/man/reexports.Rd | 3 rtemis-1.4.2/rtemis/man/regression_metrics.Rd | 4 rtemis-1.4.2/rtemis/man/resample.Rd | 23 rtemis-1.4.2/rtemis/man/review.Rd |only rtemis-1.4.2/rtemis/man/roc_curve.Rd | 17 rtemis-1.4.2/rtemis/man/rtemis-package.Rd | 20 rtemis-1.4.2/rtemis/man/rtemis_conditions.Rd | 3 rtemis-1.4.2/rtemis/man/same_data.Rd |only rtemis-1.4.2/rtemis/man/se.Rd |only rtemis-1.4.2/rtemis/man/session_kind_colors.Rd |only rtemis-1.4.2/rtemis/man/session_timeline.Rd |only rtemis-1.4.2/rtemis/man/set_positive_class.Rd | 6 rtemis-1.4.2/rtemis/man/setup_ARFFIngest.Rd |only rtemis-1.4.2/rtemis/man/setup_ASWCriterion.Rd |only rtemis-1.4.2/rtemis/man/setup_Autoencoder.Rd |only rtemis-1.4.2/rtemis/man/setup_BART.Rd |only rtemis-1.4.2/rtemis/man/setup_Bootstrap.Rd |only rtemis-1.4.2/rtemis/man/setup_CART.Rd | 30 rtemis-1.4.2/rtemis/man/setup_CHCriterion.Rd |only rtemis-1.4.2/rtemis/man/setup_CMeans.Rd | 26 rtemis-1.4.2/rtemis/man/setup_CQR.Rd |only rtemis-1.4.2/rtemis/man/setup_CUDA.Rd |only rtemis-1.4.2/rtemis/man/setup_CVPlus.Rd |only rtemis-1.4.2/rtemis/man/setup_ClusterConfig.Rd | 18 rtemis-1.4.2/rtemis/man/setup_ConditionalSuperLearner.Rd |only rtemis-1.4.2/rtemis/man/setup_Custom.Rd |only rtemis-1.4.2/rtemis/man/setup_DBSCAN.Rd | 30 rtemis-1.4.2/rtemis/man/setup_DTAIngest.Rd |only rtemis-1.4.2/rtemis/man/setup_DecomposeConfig.Rd | 16 rtemis-1.4.2/rtemis/man/setup_DelimitedIngest.Rd |only rtemis-1.4.2/rtemis/man/setup_FutureExecution.Rd |only rtemis-1.4.2/rtemis/man/setup_GAM.Rd | 4 rtemis-1.4.2/rtemis/man/setup_GLM.Rd | 2 rtemis-1.4.2/rtemis/man/setup_GLMNET.Rd | 20 rtemis-1.4.2/rtemis/man/setup_GLMTree.Rd |only rtemis-1.4.2/rtemis/man/setup_GMM.Rd |only rtemis-1.4.2/rtemis/man/setup_GridSearch.Rd | 25 rtemis-1.4.2/rtemis/man/setup_GroupPartition.Rd |only rtemis-1.4.2/rtemis/man/setup_HAL.Rd |only rtemis-1.4.2/rtemis/man/setup_HOPACH.Rd |only rtemis-1.4.2/rtemis/man/setup_HardCL.Rd | 11 rtemis-1.4.2/rtemis/man/setup_ICA.Rd | 31 rtemis-1.4.2/rtemis/man/setup_Isomap.Rd | 18 rtemis-1.4.2/rtemis/man/setup_Isotonic.Rd | 4 rtemis-1.4.2/rtemis/man/setup_KFold.Rd |only rtemis-1.4.2/rtemis/man/setup_KMeans.Rd | 11 rtemis-1.4.2/rtemis/man/setup_KNN.Rd |only rtemis-1.4.2/rtemis/man/setup_LINAD.Rd |only rtemis-1.4.2/rtemis/man/setup_LINADForest.Rd |only rtemis-1.4.2/rtemis/man/setup_LOOCV.Rd |only rtemis-1.4.2/rtemis/man/setup_LightCART.Rd | 191 rtemis-1.4.2/rtemis/man/setup_LightGBM.Rd | 281 rtemis-1.4.2/rtemis/man/setup_LightRF.Rd | 229 rtemis-1.4.2/rtemis/man/setup_LightRuleFit.Rd | 279 rtemis-1.4.2/rtemis/man/setup_LinearSVM.Rd | 6 rtemis-1.4.2/rtemis/man/setup_MARS.Rd |only rtemis-1.4.2/rtemis/man/setup_MDS.Rd |only rtemis-1.4.2/rtemis/man/setup_MLP.Rd |only rtemis-1.4.2/rtemis/man/setup_MiraiExecution.Rd |only rtemis-1.4.2/rtemis/man/setup_ModalityStacking.Rd |only rtemis-1.4.2/rtemis/man/setup_MonotonicHAL.Rd |only rtemis-1.4.2/rtemis/man/setup_MultiASWCriterion.Rd |only rtemis-1.4.2/rtemis/man/setup_NMF.Rd | 17 rtemis-1.4.2/rtemis/man/setup_NNLS.Rd |only rtemis-1.4.2/rtemis/man/setup_NeuralGas.Rd | 11 rtemis-1.4.2/rtemis/man/setup_Nystrom.Rd |only rtemis-1.4.2/rtemis/man/setup_PAM.Rd |only rtemis-1.4.2/rtemis/man/setup_PAMK.Rd |only rtemis-1.4.2/rtemis/man/setup_PCA.Rd | 10 rtemis-1.4.2/rtemis/man/setup_PCoA.Rd |only rtemis-1.4.2/rtemis/man/setup_ParquetIngest.Rd |only rtemis-1.4.2/rtemis/man/setup_PredefinedPartition.Rd |only rtemis-1.4.2/rtemis/man/setup_Preprocessor.Rd | 176 rtemis-1.4.2/rtemis/man/setup_RDSIngest.Rd |only rtemis-1.4.2/rtemis/man/setup_RadialSVM.Rd | 8 rtemis-1.4.2/rtemis/man/setup_RandomPartition.Rd |only rtemis-1.4.2/rtemis/man/setup_Ranger.Rd | 51 rtemis-1.4.2/rtemis/man/setup_Resampler.Rd | 57 rtemis-1.4.2/rtemis/man/setup_SHAP.Rd |only rtemis-1.4.2/rtemis/man/setup_SPLS.Rd |only rtemis-1.4.2/rtemis/man/setup_SerialExecution.Rd |only rtemis-1.4.2/rtemis/man/setup_SpectralLaplace.Rd |only rtemis-1.4.2/rtemis/man/setup_SpectralLocal.Rd |only rtemis-1.4.2/rtemis/man/setup_SpectralRBF.Rd |only rtemis-1.4.2/rtemis/man/setup_SplitConformal.Rd |only rtemis-1.4.2/rtemis/man/setup_StratBoot.Rd |only rtemis-1.4.2/rtemis/man/setup_StratSub.Rd |only rtemis-1.4.2/rtemis/man/setup_SuperConfig.Rd | 56 rtemis-1.4.2/rtemis/man/setup_SuperConfigLive.Rd | 35 rtemis-1.4.2/rtemis/man/setup_SuperLearner.Rd |only rtemis-1.4.2/rtemis/man/setup_SupervisedPreprocessor.Rd |only rtemis-1.4.2/rtemis/man/setup_TabNet.Rd | 82 rtemis-1.4.2/rtemis/man/setup_TimePartition.Rd |only rtemis-1.4.2/rtemis/man/setup_UMAP.Rd | 19 rtemis-1.4.2/rtemis/man/setup_VariationalAutoencoder.Rd |only rtemis-1.4.2/rtemis/man/setup_XLSXIngest.Rd |only rtemis-1.4.2/rtemis/man/setup_tSNE.Rd | 40 rtemis-1.4.2/rtemis/man/shap_by_level.Rd |only rtemis-1.4.2/rtemis/man/shap_case.Rd |only rtemis-1.4.2/rtemis/man/shap_long.Rd |only rtemis-1.4.2/rtemis/man/to_json.Rd | 23 rtemis-1.4.2/rtemis/man/to_markdown.Rd |only rtemis-1.4.2/rtemis/man/train.Rd | 91 rtemis-1.4.2/rtemis/man/tune_over.Rd |only rtemis-1.4.2/rtemis/man/tuning_grid.Rd |only rtemis-1.4.2/rtemis/man/validate_config.Rd |only rtemis-1.4.2/rtemis/man/varimp_table.Rd |only rtemis-1.4.2/rtemis/man/write_config.Rd | 13 rtemis-1.4.2/rtemis/man/write_record.Rd |only rtemis-1.4.2/rtemis/man/write_result.Rd |only rtemis-1.4.2/rtemis/man/write_text.Rd |only rtemis-1.4.2/rtemis/man/writeup.Rd |only rtemis-1.4.2/rtemis/tests/ci |only rtemis-1.4.2/rtemis/tests/testthat-cran.R |only rtemis-1.4.2/rtemis/tests/testthat-fitting.R |only rtemis-1.4.2/rtemis/tests/testthat-general.R |only rtemis-1.4.2/rtemis/tests/testthat-supervised.R |only rtemis-1.4.2/rtemis/tests/testthat/_problems |only rtemis-1.4.2/rtemis/tests/testthat/fixtures |only rtemis-1.4.2/rtemis/tests/testthat/helper-decomposition.R |only rtemis-1.4.2/rtemis/tests/testthat/helper-execution.R |only rtemis-1.4.2/rtemis/tests/testthat/helper-torch.R |only rtemis-1.4.2/rtemis/tests/testthat/helper-varimp.R |only rtemis-1.4.2/rtemis/tests/testthat/test-model_plot_SupervisedSession.R |only rtemis-1.4.2/rtemis/tests/testthat/test-model_plot_boundary.R |only rtemis-1.4.2/rtemis/tests/testthat/test-model_plot_colors.R |only rtemis-1.4.2/rtemis/tests/testthat/test-model_plot_confusion.R |only rtemis-1.4.2/rtemis/tests/testthat/test-model_plot_learning.R |only rtemis-1.4.2/rtemis/tests/testthat/test-model_plot_massglm.R |only rtemis-1.4.2/rtemis/tests/testthat/test-model_plot_metric.R |only rtemis-1.4.2/rtemis/tests/testthat/test-model_plot_roc.R |only rtemis-1.4.2/rtemis/tests/testthat/test-model_plot_true_pred.R |only rtemis-1.4.2/rtemis/tests/testthat/test-model_plot_varimp.R |only rtemis-1.4.2/rtemis/tests/testthat/test-model_present.R |only rtemis-1.4.2/rtemis/tests/testthat/test-model_resampled_classification.R |only rtemis-1.4.2/rtemis/tests/testthat/test_AIReview.R |only rtemis-1.4.2/rtemis/tests/testthat/test_ArtifactInheritance.R |only rtemis-1.4.2/rtemis/tests/testthat/test_Autoencoder.R |only rtemis-1.4.2/rtemis/tests/testthat/test_BackendArguments.R |only rtemis-1.4.2/rtemis/tests/testthat/test_BiasVariance.R |only rtemis-1.4.2/rtemis/tests/testthat/test_CIGroups.R |only rtemis-1.4.2/rtemis/tests/testthat/test_Calibration.R | 426 rtemis-1.4.2/rtemis/tests/testthat/test_CandidateWire.R |only rtemis-1.4.2/rtemis/tests/testthat/test_CheckData.R | 96 rtemis-1.4.2/rtemis/tests/testthat/test_ChecksArtifact.R |only rtemis-1.4.2/rtemis/tests/testthat/test_ClusterConfig.R | 59 rtemis-1.4.2/rtemis/tests/testthat/test_Clustering.R | 773 + rtemis-1.4.2/rtemis/tests/testthat/test_ConfigProps.R |only rtemis-1.4.2/rtemis/tests/testthat/test_Conformal.R |only rtemis-1.4.2/rtemis/tests/testthat/test_DataFingerprint.R |only rtemis-1.4.2/rtemis/tests/testthat/test_DataProfile.R |only rtemis-1.4.2/rtemis/tests/testthat/test_DecomposeConfig.R | 64 rtemis-1.4.2/rtemis/tests/testthat/test_Decomposition.R | 724 + rtemis-1.4.2/rtemis/tests/testthat/test_DecompositionMetrics.R |only rtemis-1.4.2/rtemis/tests/testthat/test_DecompositionTraits.R |only rtemis-1.4.2/rtemis/tests/testthat/test_Defaults.R |only rtemis-1.4.2/rtemis/tests/testthat/test_ExecutionConfig.R | 317 rtemis-1.4.2/rtemis/tests/testthat/test_ExplainSupervised.R |only rtemis-1.4.2/rtemis/tests/testthat/test_Explanation.R |only rtemis-1.4.2/rtemis/tests/testthat/test_ExplanationMethods.R |only rtemis-1.4.2/rtemis/tests/testthat/test_ExternalStorage.R |only rtemis-1.4.2/rtemis/tests/testthat/test_GenericArgForcing.R |only rtemis-1.4.2/rtemis/tests/testthat/test_GetMetrics.R |only rtemis-1.4.2/rtemis/tests/testthat/test_Hyperparameters.R | 1155 ++ rtemis-1.4.2/rtemis/tests/testthat/test_HyperparametersSet.R |only 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rtemis-1.4.2/rtemis/tests/testthat/test_RecordDocuments.R |only rtemis-1.4.2/rtemis/tests/testthat/test_ReferenceProps.R |only rtemis-1.4.2/rtemis/tests/testthat/test_ResampledResults.R |only rtemis-1.4.2/rtemis/tests/testthat/test_Resampler.R | 254 rtemis-1.4.2/rtemis/tests/testthat/test_ResamplerCompatibility.R |only rtemis-1.4.2/rtemis/tests/testthat/test_ResolvedHyperparameters.R |only rtemis-1.4.2/rtemis/tests/testthat/test_ResultArrays.R |only rtemis-1.4.2/rtemis/tests/testthat/test_ResultRules.R |only rtemis-1.4.2/rtemis/tests/testthat/test_ResultValues.R |only rtemis-1.4.2/rtemis/tests/testthat/test_RuntimeState.R |only rtemis-1.4.2/rtemis/tests/testthat/test_SchemaCatalog.R |only rtemis-1.4.2/rtemis/tests/testthat/test_SchemaContract.R |only rtemis-1.4.2/rtemis/tests/testthat/test_SchemaRules.R |only rtemis-1.4.2/rtemis/tests/testthat/test_SemanticRules.R |only rtemis-1.4.2/rtemis/tests/testthat/test_SessionSidecar.R |only rtemis-1.4.2/rtemis/tests/testthat/test_Session_timeline.R |only rtemis-1.4.2/rtemis/tests/testthat/test_SuperConfig.R | 284 rtemis-1.4.2/rtemis/tests/testthat/test_SuperConfigLive.R | 68 rtemis-1.4.2/rtemis/tests/testthat/test_Supervised.R | 4740 +++++++++- rtemis-1.4.2/rtemis/tests/testthat/test_SupervisedReview.R |only rtemis-1.4.2/rtemis/tests/testthat/test_SupervisedWriteup.R |only rtemis-1.4.2/rtemis/tests/testthat/test_TrainPreflight.R |only rtemis-1.4.2/rtemis/tests/testthat/test_Tuner.R | 300 rtemis-1.4.2/rtemis/tests/testthat/test_ValidateConfig.R |only rtemis-1.4.2/rtemis/tests/testthat/test_ValidateConfigFixtures.R |only rtemis-1.4.2/rtemis/tests/testthat/test_VariableImportance.R |only rtemis-1.4.2/rtemis/tests/testthat/test_checks.R | 80 rtemis-1.4.2/rtemis/tests/testthat/test_draw.R | 674 - rtemis-1.4.2/rtemis/tests/testthat/test_fit_predict.R |only rtemis-1.4.2/rtemis/tests/testthat/test_massGLM.R | 38 rtemis-1.4.2/rtemis/tests/testthat/test_parallel_outer.R |only rtemis-1.4.2/rtemis/tests/testthat/test_read.R |only rtemis-1.4.2/rtemis/tests/testthat/test_shared_memory.R |only rtemis-1.4.2/rtemis/tests/testthat/test_to_json.R | 47 rtemis-1.4.2/rtemis/tests/testthat/test_tune_parallel.R |only 552 files changed, 23814 insertions(+), 4583 deletions(-)
Title: Download, Model and Analyze 'OpenStreetMap' Street Networks
Description: A 'tidyverse'-friendly toolkit, inspired by the 'OSMnx' 'Python'
library, to download, model, simplify, analyze and visualize street networks
and other geospatial features from 'OpenStreetMap'. Build routable graphs
from a place name, address, point or bounding box; simplify topology;
compute shortest paths, isochrones and urban metrics (intersection density,
circuity, street-orientation entropy, centrality); and export to 'sf',
'sfnetworks' and 'MapLibre'. Heavy graph computation is performed by a
bundled 'Rust' core.
Author: Andre Leite [aut, cre] ,
Marcos Wasiliew [aut] ,
Hugo Vasconcelos [aut] ,
Carlos Amorim [aut] ,
Diogo Bezerra [aut] ,
Julia Nascimento Barreto [aut] ,
StrategicProjects [cph, fnd],
The extendr authors [cph] ,
David Tolnay [cph] ,
Alex Crichton [cph] [...truncated...]
Maintainer: Andre Leite <leite@castlab.org>
Diff between osmnxr versions 0.1.1 dated 2026-07-05 and 0.1.2 dated 2026-10-19
DESCRIPTION | 37 +++++++---- LICENSE | 2 MD5 | 16 ++--- NAMESPACE | 1 NEWS.md | 10 +++ R/osm_graph.R | 137 ++++++++++++++++++++++++++++++++++++++++++++ README.md | 4 - man/osmnxr-package.Rd | 13 ++-- man/ox_union.Rd |only tests/testthat/test-union.R |only 10 files changed, 190 insertions(+), 30 deletions(-)
Title: Multi-Task Learning with Orthogonal Constraints
Description: Fits regularised multi-task learning models where relationships
between tasks are controlled via orthogonality or disjoint-support constraints.
Supports regression, binary classification, and censored survival data.
In survival mode, time-to-event outcomes are converted into binary labels at
user-defined thresholds, enabling the discovery of features with time-varying
effects that standard proportional-hazards models cannot detect.
Implements the penalty described in Vervier et al. (2014)
<https://hal.science/hal-00985654>.
Author: Kevin Vervier [aut, cre],
Novartis Pharma AG [cph, fnd]
Maintainer: Kevin Vervier <kevin.vervier@novartis.com>
Diff between orthoMTL versions 0.1.0 dated 2026-08-23 and 0.1.1 dated 2026-10-19
DESCRIPTION | 8 + MD5 | 12 +- NEWS.md | 25 +++++ R/nnmaxheap.R | 9 +- inst/doc/introduction.html | 66 +++++++-------- man/orthoMTL-package.Rd | 8 + tests/testthat/test-metrics.R | 179 +++++++++++++++++++++++++----------------- 7 files changed, 191 insertions(+), 116 deletions(-)
Title: Parallelize Common Functions via One Magic Function
Description: The futurize() function <doi:10.48550/arXiv.2601.17578> turns sequential map-reduce functions such as base::lapply(), purrr::map(), 'foreach::foreach() %do% { ... }' into concurrent alternatives, providing you with a simple, straightforward path to scalable parallel computing via the 'future' ecosystem <doi:10.32614/RJ-2021-048>. By combining this transpiler function with R's native pipe operator, you have a convenient way for speeding up iterative computations with minimal refactoring, e.g. 'lapply(xs, fcn) |> futurize()', 'purrr::map(xs, fcn) |> futurize()', and 'foreach::foreach(x = xs) %do% { fcn(x) } |> futurize()'. Other map-reduce packages that can be "futurized" are 'BiocParallel', 'plyr', 'crossmap', 'pbapply' packages. There is also support for a growing set of domain-specific packages on CRAN (e.g. 'boot', 'caret', 'DiceKriging', 'ez', 'fgsea', 'fwb', 'gamlss', 'glmmTMB', 'glmnet', 'kernelshap', 'lme4', 'metafor', 'mgcv', 'modelsummary', 'parameters', 'p [...truncated...]
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between futurize versions 1.0.0 dated 2026-06-12 and 1.1.0 dated 2026-10-19
futurize-1.0.0/futurize/.aspell |only futurize-1.0.0/futurize/README.md |only futurize-1.1.0/futurize/DESCRIPTION | 20 futurize-1.1.0/futurize/MD5 | 222 +++++----- futurize-1.1.0/futurize/NAMESPACE | 13 futurize-1.1.0/futurize/NEWS.md | 72 +++ futurize-1.1.0/futurize/R/000.bquote.R | 3 futurize-1.1.0/futurize/R/000.import-future.R |only futurize-1.1.0/futurize/R/000.import.R | 11 futurize-1.1.0/futurize/R/addons-BiocParallel.R | 2 futurize-1.1.0/futurize/R/addons-GSVA.R | 43 + futurize-1.1.0/futurize/R/addons-Sim.DiffProc.R | 12 futurize-1.1.0/futurize/R/addons-boot.R | 11 futurize-1.1.0/futurize/R/addons-foreach.R | 26 - futurize-1.1.0/futurize/R/addons-fwb.R | 11 futurize-1.1.0/futurize/R/addons-gamlss.R | 14 futurize-1.1.0/futurize/R/addons-lme4.R | 37 + futurize-1.1.0/futurize/R/addons-parameters.R | 10 futurize-1.1.0/futurize/R/addons-plyr.R | 55 ++ futurize-1.1.0/futurize/R/addons-rugarch.R | 13 futurize-1.1.0/futurize/R/addons-terra.R |only futurize-1.1.0/futurize/R/find_s3_method.R | 132 +++++ futurize-1.1.0/futurize/R/find_s4_method.R | 20 futurize-1.1.0/futurize/R/futurize.R | 38 + futurize-1.1.0/futurize/R/is_s3_generic.R | 3 futurize-1.1.0/futurize/R/make_addon_transpilers.R | 3 futurize-1.1.0/futurize/R/make_options_for_doFuture.R | 5 futurize-1.1.0/futurize/R/make_options_for_future.apply.R | 8 futurize-1.1.0/futurize/R/make_options_for_makeClusterFuture.R | 11 futurize-1.1.0/futurize/R/parse_call.R | 15 futurize-1.1.0/futurize/R/register_all_transpilers.R | 1 futurize-1.1.0/futurize/R/transpile.R | 155 ++++++ futurize-1.1.0/futurize/R/transpiler-hooks.R |only futurize-1.1.0/futurize/R/transpiler-unwrap.R | 7 futurize-1.1.0/futurize/R/utils-debug.R | 62 ++ futurize-1.1.0/futurize/R/utils.R | 3 futurize-1.1.0/futurize/R/vignette_engine.R | 3 futurize-1.1.0/futurize/R/zzz.R | 2 futurize-1.1.0/futurize/build/vignette.rds |binary futurize-1.1.0/futurize/inst/CITATION | 5 futurize-1.1.0/futurize/inst/WORDLIST | 4 futurize-1.1.0/futurize/inst/doc/futurize-11-apply.html | 33 - futurize-1.1.0/futurize/inst/doc/futurize-11-apply.md | 32 - futurize-1.1.0/futurize/inst/doc/futurize-81-GSVA.html | 23 - futurize-1.1.0/futurize/inst/doc/futurize-81-GSVA.md | 29 + futurize-1.1.0/futurize/inst/doc/futurize-81-terra.html |only futurize-1.1.0/futurize/inst/doc/futurize-81-terra.md |only futurize-1.1.0/futurize/inst/testme/test-api.R | 62 ++ futurize-1.1.0/futurize/inst/testme/test-doFuture-foreach_dofuture,errors.R | 58 -- futurize-1.1.0/futurize/inst/testme/test-doFuture-foreach_dofuture,globals.R | 134 ++---- futurize-1.1.0/futurize/inst/testme/test-doFuture-foreach_dofuture,nested_colon.R | 4 futurize-1.1.0/futurize/inst/testme/test-doFuture-foreach_dofuture,nested_dofuture.R | 4 futurize-1.1.0/futurize/inst/testme/test-doFuture-foreach_dofuture,rng.R | 4 futurize-1.1.0/futurize/inst/testme/test-doFuture-foreach_dofuture.R | 4 futurize-1.1.0/futurize/inst/testme/test-doFuture-times.R | 4 futurize-1.1.0/futurize/inst/testme/test-future.apply-future_lapply,RNG.R | 185 ++++---- futurize-1.1.0/futurize/inst/testme/test-future.apply-options,nested.R | 4 futurize-1.1.0/futurize/inst/testme/test-future.apply-stdout.R | 1 futurize-1.1.0/futurize/inst/testme/test-futurize-BiocParallel.R | 10 futurize-1.1.0/futurize/inst/testme/test-futurize-DESeq2.R | 32 + futurize-1.1.0/futurize/inst/testme/test-futurize-DiceKriging.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-GSVA.R | 68 ++- futurize-1.1.0/futurize/inst/testme/test-futurize-GenomicAlignments.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-Rsamtools.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-Sim.DiffProc.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-SimDesign.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-SingleCellExperiment.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-SuperLearner.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-TSP.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-base-stats.R | 8 futurize-1.1.0/futurize/inst/testme/test-futurize-boot.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-caret.R | 11 futurize-1.1.0/futurize/inst/testme/test-futurize-crossmap.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-duplicated-arguments.R |only futurize-1.1.0/futurize/inst/testme/test-futurize-ez.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-fgsea.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-foreach.R | 10 futurize-1.1.0/futurize/inst/testme/test-futurize-fwb.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-gamlss.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-glmmTMB.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-glmnet.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-kernelshap.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-lme4.R | 31 + futurize-1.1.0/futurize/inst/testme/test-futurize-metafor.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-mgcv.R | 19 futurize-1.1.0/futurize/inst/testme/test-futurize-modelsummary.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-parameters.R | 11 futurize-1.1.0/futurize/inst/testme/test-futurize-partykit.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-pbapply.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-pls.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-plyr-paropts.R |only futurize-1.1.0/futurize/inst/testme/test-futurize-plyr-sequential.R |only futurize-1.1.0/futurize/inst/testme/test-futurize-plyr.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-purrr.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-pvclust.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-riskRegression.R | 20 futurize-1.1.0/futurize/inst/testme/test-futurize-rugarch.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-sandwich.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-scater.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-scuttle.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-seriation.R | 10 futurize-1.1.0/futurize/inst/testme/test-futurize-shapr.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-stars.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-strucchange.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-sva.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-terra.R |only futurize-1.1.0/futurize/inst/testme/test-futurize-tm.R | 5 futurize-1.1.0/futurize/inst/testme/test-futurize-user-future-options.R |only futurize-1.1.0/futurize/inst/testme/test-futurize-vegan.R | 9 futurize-1.1.0/futurize/inst/testme/test-futurize-wrapped.R | 19 futurize-1.1.0/futurize/inst/testme/test-internals-make_options_for_nnn.R | 45 ++ futurize-1.1.0/futurize/man/figures/cran-terra-logo.webp |only futurize-1.1.0/futurize/man/futurize.Rd | 34 + futurize-1.1.0/futurize/man/transpile.Rd | 2 futurize-1.1.0/futurize/tests/test-futurize-duplicated-arguments.R |only futurize-1.1.0/futurize/tests/test-futurize-plyr-paropts.R |only futurize-1.1.0/futurize/tests/test-futurize-plyr-sequential.R |only futurize-1.1.0/futurize/tests/test-futurize-terra.R |only futurize-1.1.0/futurize/tests/test-futurize-user-future-options.R |only futurize-1.1.0/futurize/vignettes/futurize-11-apply.md | 32 - futurize-1.1.0/futurize/vignettes/futurize-81-GSVA.md | 29 + futurize-1.1.0/futurize/vignettes/futurize-81-terra.md |only 122 files changed, 1663 insertions(+), 540 deletions(-)
Title: Assessing False Discovery Rate Claims in Proteomics
Description: Provides scope, calibration and stability diagnostics to assess false discovery rate (FDR) claims in peptide and protein identification workflows based on target-decoy competition and related confidence measures. Includes the recomputed decoy ratio of the reported list, accepted decoy counts and local decoy support, threshold elasticity, posterior error probability (PEP) concordance with the decoys, equal-chance checks and p-value calibration, with an HTML report. If you used this package in your research, please cite the associated preprint <doi:10.64898/2026.04.16.718468>. Detailed examples of using this package can also be found on the GitHub repository (<https://github.com/Jacky11/diagFDR>).
Author: Quentin Giai Gianetto [aut, cre]
Maintainer: Quentin Giai Gianetto <quentin.giaigianetto@pasteur.fr>
Diff between diagFDR versions 0.1.1 dated 2026-04-27 and 0.1.2 dated 2026-10-19
DESCRIPTION | 10 MD5 | 145 ++++++------ NAMESPACE | 6 NEWS.md |only R/alert_basis.R |only R/class_dfdr_tbl.R | 14 - R/dfdr_summary_headline.R | 9 R/diag_calibration.R | 115 ++++++++- R/diag_stability.R | 17 + R/flag_headline.R | 152 +++++++----- R/interpretation.R |only R/io_diann.R | 57 +++- R/io_mokapot.R | 23 + R/plots.R | 16 - R/render_report.R | 184 ++++++++------- R/run_all.R | 188 ++++++++++----- R/score_to_pvalue.R | 64 ++++- R/zzz.R | 2 inst/doc/diann.R | 12 - inst/doc/diann.Rmd | 20 + inst/doc/diann.html | 144 ++++++------ inst/doc/maxquant.Rmd | 2 inst/doc/maxquant.html | 34 +- inst/doc/mokapot.Rmd | 2 inst/doc/mokapot.html | 41 +-- inst/doc/mzid.html | 28 +- inst/doc/spectronaut.html | 26 +- inst/templates/dfdr_report.Rmd | 454 ++++++++++++++++++++++++++++++-------- man/add_pseudo_pvalues_to_list.Rd | 15 + man/as_dfdr_tbl.Rd | 19 + man/compete_max_score.Rd | 2 man/dfdr_alert_basis.Rd |only man/dfdr_bh_diagnostics.Rd | 16 - man/dfdr_bh_elasticity.Rd | 14 - man/dfdr_elasticity.Rd | 10 man/dfdr_equal_chance_qbands.Rd | 27 +- man/dfdr_headline.Rd | 10 man/dfdr_ipe.Rd |only man/dfdr_local_tail.Rd | 16 - man/dfdr_p_calibration.Rd | 16 - man/dfdr_p_interpretation.Rd |only man/dfdr_p_summary.Rd |only man/dfdr_pep_decoy_sanity.Rd | 14 - man/dfdr_pep_interpretation.Rd |only man/dfdr_pep_reliability.Rd | 29 +- man/dfdr_pep_reliability_tdc.Rd | 14 - man/dfdr_pep_summary.Rd |only man/dfdr_pi0_storey.Rd | 14 - man/dfdr_plot_cv.Rd | 10 man/dfdr_plot_equal_chance.Rd | 2 man/dfdr_plot_fdrhat_pi0.Rd | 8 man/dfdr_plot_p_calibration2.Rd | 8 man/dfdr_render_report.Rd | 2 man/dfdr_run_all.Rd | 53 +++- man/dfdr_run_jaccard.Rd | 6 man/dfdr_scope_disagreement.Rd | 8 man/dfdr_sumpep.Rd | 8 man/dfdr_write_report.Rd | 12 - man/diann_global_minrunq.Rd | 7 man/diann_global_precursor.Rd | 17 + man/diann_runxprecursor.Rd | 7 man/dot-bh_threshold.Rd | 2 man/flag_headline.Rd | 67 +++-- man/mokapot_competed_universe.Rd | 16 + man/mzid_parse_psms.Rd | 4 man/mzid_score_direction.Rd | 4 man/mzid_to_internal_score.Rd | 2 man/read_dfdr_maxquant_msms.Rd | 16 - man/read_dfdr_mzid.Rd | 12 - man/score_to_pvalue.Rd | 16 - man/spectronaut_runxprecursor.Rd | 3 man/tdc_qvalues.Rd | 2 tests |only vignettes/diann.Rmd | 20 + vignettes/maxquant.Rmd | 2 vignettes/mokapot.Rmd | 2 76 files changed, 1527 insertions(+), 770 deletions(-)
Title: Interactive 3D Visualization of Molecular Structures
Description: Provides an 'htmlwidgets' <https://www.htmlwidgets.org/> interface to 'NGL.js' <https://nglviewer.org/ngl/api/>.
'NGLVieweR' can be used to visualize and interact with protein databank ('PDB') and structural files in R and Shiny applications.
It includes a set of API functions to manipulate the viewer after creation in Shiny.
Author: Niels van der Velden [aut, cre],
Alexander Rose [cph] ,
three.js authors [cph] ,
Mol* contributors [cph] ,
Gregor Aisch [cph] ,
Cynthia Brewer [cph] ,
Mark Harrower [cph] ,
The Pennsylvania State University [cph] ,
Alexandru Mărășteanu [cph] ,
Miller [...truncated...]
Maintainer: Niels van der Velden <n.s.j.vandervelden@gmail.com>
Diff between NGLVieweR versions 1.4.0 dated 2024-11-22 and 1.5.0 dated 2026-10-19
NGLVieweR-1.4.0/NGLVieweR/inst/htmlwidgets/lib/NGL-2.0.0 |only NGLVieweR-1.5.0/NGLVieweR/DESCRIPTION | 58 NGLVieweR-1.5.0/NGLVieweR/MD5 | 131 NGLVieweR-1.5.0/NGLVieweR/NAMESPACE | 4 NGLVieweR-1.5.0/NGLVieweR/NEWS.md | 43 NGLVieweR-1.5.0/NGLVieweR/R/NGLVieweR-shiny.R | 2 NGLVieweR-1.5.0/NGLVieweR/R/NGLVieweR.R | 234 - NGLVieweR-1.5.0/NGLVieweR/R/NGLVieweR_example.R | 2 NGLVieweR-1.5.0/NGLVieweR/R/api.R | 106 NGLVieweR-1.5.0/NGLVieweR/R/colorByValue.R |only NGLVieweR-1.5.0/NGLVieweR/R/utils.R |only NGLVieweR-1.5.0/NGLVieweR/R/zzz.R |only NGLVieweR-1.5.0/NGLVieweR/README.md | 9 NGLVieweR-1.5.0/NGLVieweR/inst/COPYRIGHTS |only NGLVieweR-1.5.0/NGLVieweR/inst/doc/NGLVieweR.R | 30 NGLVieweR-1.5.0/NGLVieweR/inst/doc/NGLVieweR.Rmd | 72 NGLVieweR-1.5.0/NGLVieweR/inst/doc/NGLVieweR.html | 1577 ++++++---- NGLVieweR-1.5.0/NGLVieweR/inst/examples/multiStructureSelection/app.R | 27 NGLVieweR-1.5.0/NGLVieweR/inst/examples/updateFullscreen/app.R | 18 NGLVieweR-1.5.0/NGLVieweR/inst/htmlwidgets/NGLVieweR.js | 514 ++- NGLVieweR-1.5.0/NGLVieweR/inst/htmlwidgets/NGLVieweR.yaml | 7 NGLVieweR-1.5.0/NGLVieweR/inst/htmlwidgets/lib/NGL-2.5.0 |only NGLVieweR-1.5.0/NGLVieweR/inst/htmlwidgets/lib/helperFunctions.js | 93 NGLVieweR-1.5.0/NGLVieweR/man/NGLVieweR-shiny.Rd | 2 NGLVieweR-1.5.0/NGLVieweR/man/NGLVieweR.Rd | 21 NGLVieweR-1.5.0/NGLVieweR/man/NGLVieweR_example.Rd | 2 NGLVieweR-1.5.0/NGLVieweR/man/addRepresentation.Rd | 30 NGLVieweR-1.5.0/NGLVieweR/man/addSelection.Rd | 25 NGLVieweR-1.5.0/NGLVieweR/man/addStructure.Rd | 13 NGLVieweR-1.5.0/NGLVieweR/man/colorByValue.Rd |only NGLVieweR-1.5.0/NGLVieweR/man/reexports.Rd | 4 NGLVieweR-1.5.0/NGLVieweR/man/removeSelection.Rd | 6 NGLVieweR-1.5.0/NGLVieweR/man/setFocus.Rd | 18 NGLVieweR-1.5.0/NGLVieweR/man/setPosition.Rd | 8 NGLVieweR-1.5.0/NGLVieweR/man/setQuality.Rd | 15 NGLVieweR-1.5.0/NGLVieweR/man/setRock.Rd | 14 NGLVieweR-1.5.0/NGLVieweR/man/setRotation.Rd | 8 NGLVieweR-1.5.0/NGLVieweR/man/setScale.Rd | 8 NGLVieweR-1.5.0/NGLVieweR/man/setSpin.Rd | 14 NGLVieweR-1.5.0/NGLVieweR/man/setSuperpose.Rd | 3 NGLVieweR-1.5.0/NGLVieweR/man/snapShot.Rd | 10 NGLVieweR-1.5.0/NGLVieweR/man/stageParameters.Rd | 35 NGLVieweR-1.5.0/NGLVieweR/man/updateColor.Rd | 8 NGLVieweR-1.5.0/NGLVieweR/man/updateFocus.Rd | 10 NGLVieweR-1.5.0/NGLVieweR/man/updateFullscreen.Rd | 42 NGLVieweR-1.5.0/NGLVieweR/man/updateRepresentation.Rd | 8 NGLVieweR-1.5.0/NGLVieweR/man/updateRock.Rd | 10 NGLVieweR-1.5.0/NGLVieweR/man/updateSelection.Rd | 10 NGLVieweR-1.5.0/NGLVieweR/man/updateSpin.Rd | 10 NGLVieweR-1.5.0/NGLVieweR/man/updateStage.Rd | 12 NGLVieweR-1.5.0/NGLVieweR/man/updateVisibility.Rd | 8 NGLVieweR-1.5.0/NGLVieweR/man/updateZoomMove.Rd | 24 NGLVieweR-1.5.0/NGLVieweR/man/zoomMove.Rd | 15 NGLVieweR-1.5.0/NGLVieweR/tests |only NGLVieweR-1.5.0/NGLVieweR/vignettes/NGLVieweR.Rmd | 72 55 files changed, 2308 insertions(+), 1084 deletions(-)
Title: Estimate Parameters of Mixtures of Logistic Regressions
Description: Mixture of logistic regressions parameters (H)estimation with
(U)spectral methods. The main methods take d-dimensional inputs and a vector
of binary outputs, and return parameters according to the GLMs mixture model
(General Linear Model). For more details see chapter 3 in the PhD thesis of
Mor-Absa Loum: <https://theses.fr/2018SACLS299>, available here
<https://theses.hal.science/tel-01877796/document>.
Author: Benjamin Auder [aut, cre],
Mor-Absa Loum [aut]
Maintainer: Benjamin Auder <benjamin.auder@universite-paris-saclay.fr>
Diff between morpheus versions 1.0-5 dated 2026-05-21 and 1.0-6 dated 2026-10-19
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- NAMESPACE | 32 ++++++++++++++++++-------------- R/optimParams.R | 36 +++++++++++++++++++----------------- R/plot.R | 9 +++++---- build/partial.rdb |binary 6 files changed, 54 insertions(+), 47 deletions(-)
Title: Unified Access to Canadian Hydrometric Data
Description: Provides a unified interface for accessing diverse
web-published hydrometric data sources across Canada,
presenting users with consistent tabular output regardless
of the underlying data source.
Author: Sam Albers [aut, cre],
Emily Haughton [ctb] ,
Tula Foundation [fnd, cph],
Canada Water Agency [fnd]
Maintainer: Sam Albers <sam.albers@hakai.org>
Diff between hydrocan versions 0.0.1 dated 2026-06-16 and 0.0.2 dated 2026-10-19
DESCRIPTION | 17 ++++++--- MD5 | 14 ++++---- NEWS.md | 16 +++++++++ R/bc_aquarius.R |only R/hydrocan-package.R | 8 ++++ R/sysdata.rda |binary README.md | 65 ++++++++++++++++++++++---------------- man/hydrocan-package.Rd | 1 tests/testthat/test-bc-aquarius.R |only 9 files changed, 82 insertions(+), 39 deletions(-)
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Tim Gyger [aut],
Pascal Kuendig [aut],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the incl [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 1.7.4 dated 2026-08-23 and 1.8.0 dated 2026-10-19
gpboost-1.7.4/gpboost/tests/testthat/_snaps |only gpboost-1.8.0/gpboost/DESCRIPTION | 14 gpboost-1.8.0/gpboost/MD5 | 451 gpboost-1.8.0/gpboost/NAMESPACE | 10 gpboost-1.8.0/gpboost/R/GPModel.R | 879 gpboost-1.8.0/gpboost/R/gpb.Booster.R | 74 gpboost-1.8.0/gpboost/R/gpb.Dataset.R | 3 gpboost-1.8.0/gpboost/R/gpb.cv.R | 18 gpboost-1.8.0/gpboost/R/gpb.tune.num.threads.R |only gpboost-1.8.0/gpboost/R/gpboost.R | 6 gpboost-1.8.0/gpboost/R/utils.R | 184 gpboost-1.8.0/gpboost/configure.ac | 2 gpboost-1.8.0/gpboost/demo/generalized_linear_Gaussian_process_mixed_effects_models.R | 4 gpboost-1.8.0/gpboost/man/GPModel.Rd | 325 gpboost-1.8.0/gpboost/man/GPModel_shared_params.Rd | 430 gpboost-1.8.0/gpboost/man/fit.GPModel.Rd | 69 gpboost-1.8.0/gpboost/man/fit.Rd | 69 gpboost-1.8.0/gpboost/man/fitGPModel.Rd | 405 gpboost-1.8.0/gpboost/man/get_aux_pars.GPModel.Rd | 5 gpboost-1.8.0/gpboost/man/get_aux_pars.Rd | 5 gpboost-1.8.0/gpboost/man/get_coef.GPModel.Rd | 5 gpboost-1.8.0/gpboost/man/get_coef.Rd | 5 gpboost-1.8.0/gpboost/man/get_cov_pars.GPModel.Rd | 5 gpboost-1.8.0/gpboost/man/get_cov_pars.Rd | 5 gpboost-1.8.0/gpboost/man/gpb.cv.Rd | 6 gpboost-1.8.0/gpboost/man/gpb.get.default.num.threads.Rd |only gpboost-1.8.0/gpboost/man/gpb.get.num.threads.Rd |only gpboost-1.8.0/gpboost/man/gpb.set.default.num.threads.Rd |only gpboost-1.8.0/gpboost/man/gpb.set.num.threads.Rd |only gpboost-1.8.0/gpboost/man/gpb.train.Rd | 6 gpboost-1.8.0/gpboost/man/gpb.tune.num.threads.Rd |only gpboost-1.8.0/gpboost/man/gpb_shared_params.Rd | 6 gpboost-1.8.0/gpboost/man/gpboost.Rd | 6 gpboost-1.8.0/gpboost/man/set_optim_params.GPModel.Rd | 69 gpboost-1.8.0/gpboost/man/set_optim_params.Rd | 69 gpboost-1.8.0/gpboost/man/set_prediction_data.GPModel.Rd | 29 gpboost-1.8.0/gpboost/man/set_prediction_data.Rd | 29 gpboost-1.8.0/gpboost/man/summary.GPModel.Rd | 5 gpboost-1.8.0/gpboost/src/CG_utils.cpp | 1010 gpboost-1.8.0/gpboost/src/GP_utils.cpp | 120 gpboost-1.8.0/gpboost/src/Makevars.in | 121 gpboost-1.8.0/gpboost/src/Makevars.win | 121 gpboost-1.8.0/gpboost/src/Makevars.win.in | 121 gpboost-1.8.0/gpboost/src/SuiteSparse |only gpboost-1.8.0/gpboost/src/Vecchia_utils.cpp | 433 gpboost-1.8.0/gpboost/src/c_api.cpp | 136 gpboost-1.8.0/gpboost/src/cpu_topology.cpp |only gpboost-1.8.0/gpboost/src/gpboost_R.cpp | 147 gpboost-1.8.0/gpboost/src/gpboost_R.h | 117 gpboost-1.8.0/gpboost/src/include/Eigen/CholmodSupport |only gpboost-1.8.0/gpboost/src/include/Eigen/src/CholmodSupport |only gpboost-1.8.0/gpboost/src/include/GPBoost/CG_utils.h | 848 gpboost-1.8.0/gpboost/src/include/GPBoost/DF_utils.h | 6 gpboost-1.8.0/gpboost/src/include/GPBoost/GP_utils.h | 38 gpboost-1.8.0/gpboost/src/include/GPBoost/Vecchia_utils.h | 103 gpboost-1.8.0/gpboost/src/include/GPBoost/cov_fcts.h | 294 gpboost-1.8.0/gpboost/src/include/GPBoost/egpd_utils.h | 112 gpboost-1.8.0/gpboost/src/include/GPBoost/likelihoods.h |14198 +--------- gpboost-1.8.0/gpboost/src/include/GPBoost/likelihoods_aux_pars.h |only gpboost-1.8.0/gpboost/src/include/GPBoost/likelihoods_laplace.h |only gpboost-1.8.0/gpboost/src/include/GPBoost/likelihoods_predict.h |only gpboost-1.8.0/gpboost/src/include/GPBoost/optim_utils.h | 217 gpboost-1.8.0/gpboost/src/include/GPBoost/re_comp.h | 115 gpboost-1.8.0/gpboost/src/include/GPBoost/re_model.h | 139 gpboost-1.8.0/gpboost/src/include/GPBoost/re_model_template.h | 4276 ++- gpboost-1.8.0/gpboost/src/include/GPBoost/sparse_matrix_utils.h | 328 gpboost-1.8.0/gpboost/src/include/GPBoost/tweedie_utils.h | 98 gpboost-1.8.0/gpboost/src/include/GPBoost/type_defs.h | 14 gpboost-1.8.0/gpboost/src/include/GPBoost/utils.h | 244 gpboost-1.8.0/gpboost/src/include/LBFGS.h | 65 gpboost-1.8.0/gpboost/src/include/LBFGSpp/LineSearchBacktracking.h | 22 gpboost-1.8.0/gpboost/src/include/LBFGSpp/LineSearchNocedalWright.h | 77 gpboost-1.8.0/gpboost/src/include/LightGBM/c_api.h | 131 gpboost-1.8.0/gpboost/src/include/LightGBM/config.h | 2 gpboost-1.8.0/gpboost/src/include/LightGBM/utils/log.h | 16 gpboost-1.8.0/gpboost/src/include/LightGBM/utils/openmp_wrapper.h | 8 gpboost-1.8.0/gpboost/src/include/misc/optim_structs.hpp | 16 gpboost-1.8.0/gpboost/src/include/unconstrained/gd.hpp | 20 gpboost-1.8.0/gpboost/src/include/unconstrained/nm.hpp | 9 gpboost-1.8.0/gpboost/src/metric/regression_metric.hpp | 7 gpboost-1.8.0/gpboost/src/objective/objective_function.cpp | 1 gpboost-1.8.0/gpboost/src/re_model.cpp | 388 gpboost-1.8.0/gpboost/src/sparse_matrix_utils.cpp | 1115 gpboost-1.8.0/gpboost/src/treelearner/feature_histogram.hpp | 7 gpboost-1.8.0/gpboost/src/treelearner/voting_parallel_tree_learner.cpp | 8 gpboost-1.8.0/gpboost/tests/testthat.R | 10 gpboost-1.8.0/gpboost/tests/testthat/Rplots.pdf |binary gpboost-1.8.0/gpboost/tests/testthat/helper-num-threads.R |only gpboost-1.8.0/gpboost/tests/testthat/helper-tolerances.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_ar1_multifidelity.R | 989 gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_cg_convergence.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_combined_GP_random_effects.R | 572 gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_convergence_warnings.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_egpd.R | 178 gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_gaussian_process.R | 2915 -- gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_gaussian_process_cover_tree.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_gaussian_process_cuda.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_gaussian_process_fitc.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_gaussian_process_full_scale_tapering.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_gaussian_process_full_scale_vecchia.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_gaussian_process_prior_sampling.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_gaussian_process_space_time_ard.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_gaussian_process_state.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_gaussian_process_tapering.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_gaussian_process_vecchia.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_grouped_random_effects.R | 575 gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_non_Gaussian_data.R | 5986 ---- gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_non_Gaussian_data_asymmetric_laplace.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_non_Gaussian_data_count.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_non_Gaussian_data_covariance.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_non_Gaussian_data_families.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_non_Gaussian_data_fitc.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_non_Gaussian_data_full_scale_vecchia.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_non_Gaussian_data_large_data.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_non_Gaussian_data_space_time_ard.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_non_Gaussian_data_standard_errors.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_non_Gaussian_data_tapering.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_non_Gaussian_data_varying_shape.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_non_Gaussian_data_vecchia.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_non_Gaussian_data_zero_inflated.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_tweedie.R | 11 gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_tweedie_joint_varying_dispersion.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_weights.R |only gpboost-1.8.0/gpboost/tests/testthat/test_GPModel_zero_inflated_hurdle.R | 1338 gpboost-1.8.0/gpboost/tests/testthat/test_Grabit_mean-scale_regression.R | 5 gpboost-1.8.0/gpboost/tests/testthat/test_gpb.Booster.R | 30 gpboost-1.8.0/gpboost/tests/testthat/test_num_parallel_threads.R |only gpboost-1.8.0/gpboost/tests/testthat/test_z_GPBoost_algorithm.R | 1028 gpboost-1.8.0/gpboost/tests/testthat/test_z_GPBoost_algorithm_fitc.R |only gpboost-1.8.0/gpboost/tests/testthat/test_z_GPBoost_algorithm_full_scale_tapering.R |only gpboost-1.8.0/gpboost/tests/testthat/test_z_GPBoost_algorithm_gaussian_process.R |only gpboost-1.8.0/gpboost/tests/testthat/test_z_GPBoost_algorithm_large_data.R |only gpboost-1.8.0/gpboost/tests/testthat/test_z_GPBoost_algorithm_nesterov.R |only gpboost-1.8.0/gpboost/tests/testthat/test_z_GPBoost_algorithm_non_Gaussian_data.R | 1455 - gpboost-1.8.0/gpboost/tests/testthat/test_z_GPBoost_algorithm_non_Gaussian_data_combined.R |only gpboost-1.8.0/gpboost/tests/testthat/test_z_GPBoost_algorithm_non_Gaussian_data_duplicate_locations.R |only gpboost-1.8.0/gpboost/tests/testthat/test_z_GPBoost_algorithm_non_Gaussian_data_families.R |only gpboost-1.8.0/gpboost/tests/testthat/test_z_GPBoost_algorithm_non_Gaussian_data_gaussian_process.R |only gpboost-1.8.0/gpboost/tests/testthat/test_z_GPBoost_algorithm_non_Gaussian_data_gaussian_process_variants.R |only gpboost-1.8.0/gpboost/tests/testthat/test_z_GPBoost_algorithm_non_Gaussian_data_large_data.R |only gpboost-1.8.0/gpboost/tests/testthat/test_z_GPBoost_algorithm_non_Gaussian_data_reuse_learning_rates.R |only gpboost-1.8.0/gpboost/tests/testthat/test_z_GPBoost_algorithm_non_Gaussian_data_save_load.R |only gpboost-1.8.0/gpboost/tests/testthat/test_z_GPBoost_algorithm_non_Gaussian_data_tuning.R |only gpboost-1.8.0/gpboost/tests/testthat/test_z_GPBoost_algorithm_non_Gaussian_data_vecchia.R |only gpboost-1.8.0/gpboost/tests/testthat/test_z_GPBoost_algorithm_reuse_learning_rates.R |only gpboost-1.8.0/gpboost/tests/testthat/test_z_GPBoost_algorithm_save_load.R |only gpboost-1.8.0/gpboost/tests/testthat/test_z_GPBoost_algorithm_vecchia.R |only gpboost-1.8.0/gpboost/tests/testthat/test_z_GPBoost_algorithm_weights.R |only 148 files changed, 17416 insertions(+), 26122 deletions(-)
Title: Bayesian Dynamic Borrowing with Flexible Baseline Hazard
Function
Description: Allows Bayesian borrowing from a historical dataset for time-to-
event data. A flexible baseline hazard function is achieved via a piecewise
exponential likelihood with time varying split points and smoothing prior on the
historic baseline hazards. The method is described in Scott and Lewin (2026)
<doi:10.1093/biostatistics/kxag006>, and a paper focused on the software is
in Scott, Axillus, Lewin and Izmirlian (2026) <doi:10.48550/arXiv.2408.04327>.
Author: Darren Scott [aut],
Sophia Axillus [aut],
Grant Izmirlian [aut, cre]
Maintainer: Grant Izmirlian <grant.izmirlian@astrazeneca.com>
Diff between BayesFBHborrow versions 2.0.19 dated 2026-10-19 and 2.0.20 dated 2026-10-19
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- R/BayesFBHborrow.R | 4 +--- inst/doc/Using-BayesFBHborrow.pdf |binary vignettes/Using-BayesFBHborrow.bib | 2 +- vignettes/figures/fig-ggcs_KM_do.pdf |binary vignettes/figures/fig-p_gbcs_cndl_TrtEff_plot.pdf |binary vignettes/figures/fig-p_gbcs_cndl_haz_plot.pdf |binary vignettes/figures/fig-plot_cndl_haz_hst.pdf |binary vignettes/figures/fig-plot_cndl_haz_nb_wb.pdf |binary vignettes/figures/fig-trace.pdf |binary 11 files changed, 15 insertions(+), 17 deletions(-)
More information about BayesFBHborrow at CRAN
Permanent link
Title: Assessment of Agreement using the Total Deviation Index
Description: The total deviation index (TDI) is an unscaled statistical measure used to evaluate the deviation between paired quantitative measurements when assessing the extent of agreement between different raters. It describes a boundary such that a large specified proportion of the differences in paired measurements are within the boundary (Lin, 2000) <doi:10.1002/(SICI)1097-0258(20000130)19:2%3C255::AID-SIM293%3E3.0.CO;2-8>.
This R package implements some methodologies existing in the literature for TDI estimation and inference in the case of two raters.
Author: Anna Felip-Badia [aut, cre] ,
Sara Perez-Jaume [aut] ,
Josep L Carrasco [aut]
Maintainer: Anna Felip-Badia <annafelipibadia@gmail.com>
Diff between TDIagree versions 0.2.0 dated 2025-10-29 and 0.3.0 dated 2026-10-19
TDIagree-0.2.0/TDIagree/R/TDIagree.R |only TDIagree-0.3.0/TDIagree/DESCRIPTION | 22 TDIagree-0.3.0/TDIagree/MD5 | 50 - TDIagree-0.3.0/TDIagree/NAMESPACE | 108 +- TDIagree-0.3.0/TDIagree/NEWS.md |only TDIagree-0.3.0/TDIagree/R/TDI.Choudhary.NP.R | 198 ++--- TDIagree-0.3.0/TDIagree/R/TDI.Choudhary.P.R | 572 ++++++++++----- TDIagree-0.3.0/TDIagree/R/TDI.Escaramis.R | 299 +++---- TDIagree-0.3.0/TDIagree/R/TDI.Perez_Jaume_and_Carrasco.R | 28 TDIagree-0.3.0/TDIagree/R/TDI.R | 140 ++- TDIagree-0.3.0/TDIagree/R/TDIagree-package.R |only TDIagree-0.3.0/TDIagree/R/descriptive.plots.R | 126 +-- TDIagree-0.3.0/TDIagree/R/gt_tdi.R |only TDIagree-0.3.0/TDIagree/R/knit_print.tdi.R |only TDIagree-0.3.0/TDIagree/R/plot.tdi.R | 232 +++--- TDIagree-0.3.0/TDIagree/R/print.tdi.R | 254 ------ TDIagree-0.3.0/TDIagree/README.md |only TDIagree-0.3.0/TDIagree/build |only TDIagree-0.3.0/TDIagree/inst |only TDIagree-0.3.0/TDIagree/man/TDI.Rd | 56 - TDIagree-0.3.0/TDIagree/man/TDIagree-package.Rd | 14 TDIagree-0.3.0/TDIagree/man/descriptive.plots.Rd | 38 TDIagree-0.3.0/TDIagree/man/figures |only TDIagree-0.3.0/TDIagree/man/plot.tdi.Rd | 49 - TDIagree-0.3.0/TDIagree/man/print.tdi.Rd | 6 TDIagree-0.3.0/TDIagree/vignettes |only 26 files changed, 1113 insertions(+), 1079 deletions(-)
Title: Detect and Remove Chimeras from Amplicon Sequence Analysis Data
Description: Detect and remove chimeras from your amplicon sequence analysis
using reference-based or de novo approaches. The 'rchime' package
implements the 'VSEARCH' algorithms described in Rognes et al. (2016)
<doi:10.7717/peerj.2584>. 'VSEARCH' builds on the work of Edgar,R.C. et al.
(2011) <doi:10.1093/bioinformatics/btr381>.
Author: Sarah Westcott [aut] ,
Pat Schloss [cph, cre] ,
Torbjorn Rognes [cph],
Frederic Mahe [cph],
Tomas Flouri [cph],
Christopher Quince [cph],
Ben Nichols [cph]
Maintainer: Pat Schloss <pschloss@umich.edu>
Diff between rchime versions 0.1.2 dated 2026-08-21 and 0.1.3 dated 2026-10-19
rchime-0.1.2/rchime/inst/extdata/strollur_miseq_tiny.rds |only rchime-0.1.2/rchime/inst/extdata/strollur_multi_sample_small.rds |only rchime-0.1.2/rchime/inst/extdata/strollur_multi_sample_tiny.rds |only rchime-0.1.2/rchime/inst/extdata/strollur_reference.rds |only rchime-0.1.2/rchime/inst/extdata/strollur_single_sample.rds |only rchime-0.1.2/rchime/inst/extdata/strollur_single_sample_tiny.rds |only rchime-0.1.3/rchime/DESCRIPTION | 12 - rchime-0.1.3/rchime/MD5 | 32 +-- rchime-0.1.3/rchime/NAMESPACE | 7 rchime-0.1.3/rchime/NEWS.md | 5 rchime-0.1.3/rchime/R/generate_strollur_objects.R | 72 +++++--- rchime-0.1.3/rchime/R/rchime.R | 5 rchime-0.1.3/rchime/README.md | 28 +-- rchime-0.1.3/rchime/inst/doc/chimera_report.html | 2 rchime-0.1.3/rchime/inst/doc/denovo_based_detection.html | 40 ++-- rchime-0.1.3/rchime/inst/doc/reference_based_detection.html | 40 ++-- rchime-0.1.3/rchime/inst/extdata/test_abundance.rds |only rchime-0.1.3/rchime/inst/extdata/test_fasta.rds |only rchime-0.1.3/rchime/inst/extdata/test_single_abundance.rds |only rchime-0.1.3/rchime/man/rchime.Rd | 5 rchime-0.1.3/rchime/man/strollur_multi_sample_small.Rd |only rchime-0.1.3/rchime/tests/testthat/test-rchime_strollur.R | 89 ++++------ 22 files changed, 171 insertions(+), 166 deletions(-)
Title: Measuring Agreement Using Krippendorff's Alpha Coefficient
Description: Provides tools for applying Krippendorff's Alpha methodology <DOI:10.1080/19312450709336664>. Both the customary methodology and Hughes' methodology <DOI:10.1016/j.jspi.2024.106170> are supported, the former being preferred for larger datasets, the latter for smaller datasets. The framework supports common and user-defined distance functions, and can accommodate any number of units, any number of coders, and missingness. Interval estimation can be done in parallel for either methodology.
Author: John Hughes [aut, cre]
Maintainer: John Hughes <drjphughesjr@gmail.com>
Diff between krippendorffsalpha versions 2.0 dated 2022-10-25 and 2.0-3 dated 2026-10-19
krippendorffsalpha-2.0-3/krippendorffsalpha/COPYING | 2 krippendorffsalpha-2.0-3/krippendorffsalpha/DESCRIPTION | 20 ++++-- krippendorffsalpha-2.0-3/krippendorffsalpha/MD5 | 13 ++-- krippendorffsalpha-2.0-3/krippendorffsalpha/NAMESPACE | 30 ++++++---- krippendorffsalpha-2.0-3/krippendorffsalpha/R/krippendorff.R | 10 +-- krippendorffsalpha-2.0-3/krippendorffsalpha/R/zzz.R | 4 - krippendorffsalpha-2.0-3/krippendorffsalpha/man/krippendorffs.alpha.Rd | 4 - krippendorffsalpha-2.0/krippendorffsalpha/inst |only 8 files changed, 46 insertions(+), 37 deletions(-)
More information about krippendorffsalpha at CRAN
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Title: Linear Models for Sequence Count Data
Description: Provides scalable generalized linear and mixed effects models tailored for sequence count data analysis (e.g., analysis of 16S or RNA-seq data). Uses Dirichlet-multinomial sampling to quantify uncertainty in relative abundance or relative expression conditioned on observed count data.
Implements scale models as a generalization of normalizations which account for uncertainty in scale (e.g., total abundances) as described in Nixon et al. (2025) <doi:10.1186/s13059-025-03609-3> and McGovern et al. (2025) <doi:10.1101/2025.08.05.668734>.
Author: Justin Silverman [aut, cre],
Greg Gloor [aut],
Kyle McGovern [aut, ctb]
Maintainer: Justin Silverman <JustinSilverman@psu.edu>
Diff between ALDEx3 versions 1.3.1 dated 2026-08-26 and 1.4.0 dated 2026-10-19
DESCRIPTION | 6 MD5 | 22 +-- NEWS.md | 9 + R/aldex.R | 3 R/blmm.R | 263 ++++++++++++++++++++++++++++++------- inst/doc/ALDEx3-mixed-effects.R | 2 inst/doc/ALDEx3-mixed-effects.Rmd | 170 ++++++++++++++++++----- inst/doc/ALDEx3-mixed-effects.html | 227 +++++++++++++++++++++---------- man/aldex.Rd | 3 man/blmm.Rd | 7 tests/testthat/test-blmm.R | 97 +++++++++++++ vignettes/ALDEx3-mixed-effects.Rmd | 170 ++++++++++++++++++----- 12 files changed, 766 insertions(+), 213 deletions(-)
Title: Missing Value Imputation for Accelerometer Data
Description: We present a statistical method for imputing missing values in accelerometer data. The methodology includes both parametric and semi-parametric multiple imputation under the zero-inflated Poisson lognormal model. It also offers several functions to preprocess accelerometer data before imputation. These include detecting wear and non-wear time, selecting valid days and subjects, and generating plots.
Author: Jung Ae Lee [aut, cre]
Maintainer: Jung Ae Lee <jungaeleeb@gmail.com>
Diff between accelmissing versions 2.2 dated 2025-05-30 and 2.4 dated 2026-10-19
DESCRIPTION | 10 ++++++---- MD5 | 12 ++++++------ R/ACCELMISSING.R | 34 +++++++++++++--------------------- data/acceldata.RData |binary data/acceldata2.RData |binary data/accelimp.RData |binary man/accelmissing-package.Rd | 4 ++-- 7 files changed, 27 insertions(+), 33 deletions(-)
Title: Analyzing the Survey of Consumer Finances
Description: Analyze public-use micro data from the Survey of Consumer Finances.
Provides tools to download prepared data files, construct replicate-weighted
multiply imputed survey designs, compute descriptive statistics and model
estimates, and produce plots and tables. Methods follow design-based inference
for complex surveys and pooling across multiple imputations. See the package
website and the code book for background.
Author: Joseph Cohen [aut, cre]
Maintainer: Joseph Cohen <joseph.cohen@qc.cuny.edu>
Diff between scf versions 1.0.10 dated 2026-05-21 and 1.2.0 dated 2026-10-19
scf-1.0.10/scf/R/scf_activate_theme.R |only scf-1.0.10/scf/R/scf_deflate.R |only scf-1.2.0/scf/DESCRIPTION | 8 scf-1.2.0/scf/MD5 | 219 ++- scf-1.2.0/scf/NAMESPACE | 25 scf-1.2.0/scf/NEWS | 76 + scf-1.2.0/scf/R/scf-package.R | 253 ++-- scf-1.2.0/scf/R/scf_MIcombine.R | 260 ++-- scf-1.2.0/scf/R/scf_axis_text_x.R | 5 scf-1.2.0/scf/R/scf_corr.R | 123 +- scf-1.2.0/scf/R/scf_design.R | 55 scf-1.2.0/scf/R/scf_download.R | 92 - scf-1.2.0/scf/R/scf_freq.R | 135 +- scf-1.2.0/scf/R/scf_glm.R | 203 +-- scf-1.2.0/scf/R/scf_implicates.R | 92 + scf-1.2.0/scf/R/scf_imports.R | 8 scf-1.2.0/scf/R/scf_load.R | 124 +- scf-1.2.0/scf/R/scf_logit.R | 103 - scf-1.2.0/scf/R/scf_mean.R | 190 +-- scf-1.2.0/scf/R/scf_median.R | 107 - scf-1.2.0/scf/R/scf_model_methods.R | 160 +- scf-1.2.0/scf/R/scf_nominal.R |only scf-1.2.0/scf/R/scf_ols.R | 147 +- scf-1.2.0/scf/R/scf_pctile_sum.R | 373 ++---- scf-1.2.0/scf/R/scf_percentile.R | 344 ++---- scf-1.2.0/scf/R/scf_plot_bbar.R | 75 - scf-1.2.0/scf/R/scf_plot_cbar.R | 88 - 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Title: Data Driven Smooth Tests
Description: Smooth tests are data driven (alternative hypothesis is dynamically selected based on data).
In this package you will find two groups of smooth of test: goodness-of-fit tests and
nonparametric tests for comparing distributions.
Among goodness-of-fit tests there are tests for exponent, Gaussian, Gumbel
and uniform distribution.
Among nonparametric tests there are tests for stochastic dominance,
k-sample test, test with umbrella alternatives and test for change-point problems.
Author: Przemyslaw Biecek [aut, cre],
Grzegorz Wylupek [aut]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between ddst versions 1.6.11 dated 2026-09-12 and 1.6.12 dated 2026-10-19
DESCRIPTION | 15 ++++--------- MD5 | 6 ++--- NEWS.md | 5 ++++ inst/doc/examples_all.html | 50 ++++++++++++++++++++++----------------------- 4 files changed, 38 insertions(+), 38 deletions(-)
Title: Templated Unified Library for Posterior Approximation in
Bayesian Hierarchical Models
Description: A general-purpose engine for fitting Bayesian hierarchical models
with spatial fields, temporal effects, spatially varying coefficients, and
multiple inference backends. Scalable spatial structure includes Hilbert
space approximate Gaussian processes (HSGP; Riutort-Mayol et al. 2023
<doi:10.1007/s11222-022-10167-2>), nearest-neighbor Gaussian processes
(NNGP; Datta et al. 2016 <doi:10.1080/01621459.2015.1044091>), intrinsic
conditional autoregressive models (ICAR; Besag, York, and Mollie 1991
<doi:10.1007/BF00116466>), the reparameterized Besag-York-Mollie model
(BYM2; Riebler et al. 2016 <doi:10.1177/0962280216660421>), and stochastic
partial differential equation fields (SPDE; Lindgren, Rue, and Lindstrom
2011 <doi:10.1111/j.1467-9868.2011.00777.x>). Temporal structure covers
random walks, autoregressive processes, and Gaussian processes. Inference
is tiered by correctness guarantee: exact Hamiltonian Monte Carlo with the
No-U-Turn sampler, Laplace and n [...truncated...]
Author: Gilles Colling [aut, cre, cph] ,
Frances Y. Kuo [ctb, cph] ,
Stephen Joe [ctb, cph] ,
Arm Limited [cph] ,
The Walnutpie Developers [cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between tulpa versions 0.6.0 dated 2026-09-24 and 0.7.5 dated 2026-10-19
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tulpa-0.7.5/tulpa/tests/testthat/test-joint-logpost-grad-kinds.R | 80 tulpa-0.7.5/tulpa/tests/testthat/test-joint-multi-hyperprior-blocks.R | 281 tulpa-0.7.5/tulpa/tests/testthat/test-joint-pareto-k-proposal.R | 372 tulpa-0.7.5/tulpa/tests/testthat/test-joint-placement-block-scale.R |only tulpa-0.7.5/tulpa/tests/testthat/test-joint-placement-mode.R |only tulpa-0.7.5/tulpa/tests/testthat/test-joint-placement-pass.R |only tulpa-0.7.5/tulpa/tests/testthat/test-kdiag-capture.R | 51 tulpa-0.7.5/tulpa/tests/testthat/test-kfold.R | 32 tulpa-0.7.5/tulpa/tests/testthat/test-laplace-beta-prior.R | 62 tulpa-0.7.5/tulpa/tests/testthat/test-laplace-beta.R | 47 tulpa-0.7.5/tulpa/tests/testthat/test-laplace-corr-re.R | 2 tulpa-0.7.5/tulpa/tests/testthat/test-laplace-eta-draws.R |only tulpa-0.7.5/tulpa/tests/testthat/test-laplace-exact-gradient.R | 343 tulpa-0.7.5/tulpa/tests/testthat/test-laplace-gp-dispatch.R | 70 tulpa-0.7.5/tulpa/tests/testthat/test-laplace-link-domain.R | 113 tulpa-0.7.5/tulpa/tests/testthat/test-laplace-mode-stationarity.R | 200 tulpa-0.7.5/tulpa/tests/testthat/test-laplace-offset-vcov.R | 2 tulpa-0.7.5/tulpa/tests/testthat/test-laplace-re-idx-zero.R |only tulpa-0.7.5/tulpa/tests/testthat/test-laplace-sample-clone.R | 31 tulpa-0.7.5/tulpa/tests/testthat/test-laplace-spatial-car-proper-hsgp.R | 2 tulpa-0.7.5/tulpa/tests/testthat/test-laplace-spatial-gp-spde-equiv.R | 2 tulpa-0.7.5/tulpa/tests/testthat/test-laplace-spatial-weights.R | 29 tulpa-0.7.5/tulpa/tests/testthat/test-laplace-spec-block-bym2.R | 4 tulpa-0.7.5/tulpa/tests/testthat/test-laplace-spec-block-icar.R | 4 tulpa-0.7.5/tulpa/tests/testthat/test-laplace-spec-builtin-family.R | 77 tulpa-0.7.5/tulpa/tests/testthat/test-laplace-spec-sparse-assembly.R |only tulpa-0.7.5/tulpa/tests/testthat/test-laplace-spec.R | 136 tulpa-0.7.5/tulpa/tests/testthat/test-laplace-weights.R | 2 tulpa-0.7.5/tulpa/tests/testthat/test-laplace_diagnostics.R | 124 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tulpa-0.7.5/tulpa/tests/testthat/test-nl-registry-axis-scope.R | 52 tulpa-0.7.5/tulpa/tests/testthat/test-nl-registry-refine.R |only tulpa-0.7.5/tulpa/tests/testthat/test-nl-required-fields.R | 92 tulpa-0.7.5/tulpa/tests/testthat/test-nl-single-block-prune.R | 177 tulpa-0.7.5/tulpa/tests/testthat/test-nl-weight-guard.R | 16 tulpa-0.7.5/tulpa/tests/testthat/test-nl-wtd-quantile-extend.R | 34 tulpa-0.7.5/tulpa/tests/testthat/test-nngp-cond-cores.R | 27 tulpa-0.7.5/tulpa/tests/testthat/test-nngp-coords-arity.R | 124 tulpa-0.7.5/tulpa/tests/testthat/test-nngp-doors.R |only tulpa-0.7.5/tulpa/tests/testthat/test-nngp-nc-grad.R | 135 tulpa-0.7.5/tulpa/tests/testthat/test-nngp-prior-scatter.R | 2 tulpa-0.7.5/tulpa/tests/testthat/test-nngp-row-neighbours.R | 41 tulpa-0.7.5/tulpa/tests/testthat/test-nngp-scatter-guards.R | 51 tulpa-0.7.5/tulpa/tests/testthat/test-nngp-twin.R | 50 tulpa-0.7.5/tulpa/tests/testthat/test-nuts-nan-gradient.R | 6 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tulpa-0.7.5/tulpa/tests/testthat/test-spde-kriging.R | 2 tulpa-0.7.5/tulpa/tests/testthat/test-spde-nc-transform.R | 62 tulpa-0.7.5/tulpa/tests/testthat/test-spde-nu-general.R | 148 tulpa-0.7.5/tulpa/tests/testthat/test-spde-nuts-joint.R | 168 tulpa-0.7.5/tulpa/tests/testthat/test-spde-nuts.R | 52 tulpa-0.7.5/tulpa/tests/testthat/test-spde-rational.R | 2 tulpa-0.7.5/tulpa/tests/testthat/test-spde-re-integrated.R | 60 tulpa-0.7.5/tulpa/tests/testthat/test-spde-re.R | 11 tulpa-0.7.5/tulpa/tests/testthat/test-spde.R | 9 tulpa-0.7.5/tulpa/tests/testthat/test-sprintf-messages.R |only tulpa-0.7.5/tulpa/tests/testthat/test-st-ar1-gp-density.R | 64 tulpa-0.7.5/tulpa/tests/testthat/test-st-hsgp-prior.R | 63 tulpa-0.7.5/tulpa/tests/testthat/test-st-iv-gmrf-mass.R | 100 tulpa-0.7.5/tulpa/tests/testthat/test-st-iv-margin-mass.R | 31 tulpa-0.7.5/tulpa/tests/testthat/test-st-nested.R | 72 tulpa-0.7.5/tulpa/tests/testthat/test-standalone-input-validation.R |only 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tulpa-0.7.5/tulpa/tests/testthat/test-temporal-frontdoor.R | 128 tulpa-0.7.5/tulpa/tests/testthat/test-temporal-gp-frontdoor.R | 73 tulpa-0.7.5/tulpa/tests/testthat/test-temporal-gp-parameterization.R | 6 tulpa-0.7.5/tulpa/tests/testthat/test-temporal-gp-period-units.R | 35 tulpa-0.7.5/tulpa/tests/testthat/test-temporal-grad-equiv.R | 219 tulpa-0.7.5/tulpa/tests/testthat/test-temporal-nested-readback.R |only tulpa-0.7.5/tulpa/tests/testthat/test-tgmrf-cpp.R | 4 tulpa-0.7.5/tulpa/tests/testthat/test-tgmrf-imh.R | 3 tulpa-0.7.5/tulpa/tests/testthat/test-tgmrf-laplace.R | 8 tulpa-0.7.5/tulpa/tests/testthat/test-tgmrf-nuts-joint.R | 1 tulpa-0.7.5/tulpa/tests/testthat/test-tgmrf-nuts.R | 1 tulpa-0.7.5/tulpa/tests/testthat/test-tgmrf-vi.R | 27 tulpa-0.7.5/tulpa/tests/testthat/test-tgmrf.R | 289 tulpa-0.7.5/tulpa/tests/testthat/test-threads.R | 51 tulpa-0.7.5/tulpa/tests/testthat/test-tri-solve-layout.R | 56 tulpa-0.7.5/tulpa/tests/testthat/test-truncated-gaussian.R | 26 tulpa-0.7.5/tulpa/tests/testthat/test-tulpa-agq-frontdoor.R | 61 tulpa-0.7.5/tulpa/tests/testthat/test-tulpa-entry-nested.R | 115 tulpa-0.7.5/tulpa/tests/testthat/test-tulpa-entry.R | 60 tulpa-0.7.5/tulpa/tests/testthat/test-tulpa-re-cov-frontdoor.R | 37 tulpa-0.7.5/tulpa/tests/testthat/test-tulpa-rpg.R | 19 tulpa-0.7.5/tulpa/tests/testthat/test-tulpa-spatial-frontdoor.R | 188 tulpa-0.7.5/tulpa/tests/testthat/test-tulpa-spatial-gp-frontdoor.R | 250 tulpa-0.7.5/tulpa/tests/testthat/test-tulpa-spatial-spde-frontdoor.R | 134 tulpa-0.7.5/tulpa/tests/testthat/test-tvc-gp.R | 37 tulpa-0.7.5/tulpa/tests/testthat/test-tvc-level-identification.R | 2 tulpa-0.7.5/tulpa/tests/testthat/test-tvc-nuts-frontdoor.R | 5 tulpa-0.7.5/tulpa/tests/testthat/test-tweedie.R | 53 tulpa-0.7.5/tulpa/tests/testthat/test-validate-mode.R |only tulpa-0.7.5/tulpa/tests/testthat/test-varcorr.R | 87 tulpa-0.7.5/tulpa/tests/testthat/test-varying-coef-accessors.R | 73 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Title: Disciplined Convex Optimization
Description: An object-oriented modeling language for disciplined
convex programming (DCP) as described in Fu, Narasimhan, and Boyd
(2020, <doi:10.18637/jss.v094.i14>). It allows the user to
formulate convex optimization problems in a natural way following
mathematical convention and DCP rules. The system analyzes the
problem, verifies its convexity, converts it into a canonical
form, and hands it off to an appropriate solver to obtain the
solution. This version uses the S7 object system for improved
performance and maintainability.
Author: Anqi Fu [aut, cre],
Balasubramanian Narasimhan [aut],
Steven Diamond [aut],
John Miller [aut],
Stephen Boyd [ctb]
Maintainer: Anqi Fu <anqif@alumni.stanford.edu>
Diff between CVXR versions 1.9.2 dated 2026-08-24 and 1.9.3 dated 2026-10-19
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CVXR-1.9.2/CVXR/R/195_reductions_complex2real_canonicalizers_aff_canon.R |only CVXR-1.9.2/CVXR/R/196_reductions_complex2real_canonicalizers_abs_canon.R |only CVXR-1.9.2/CVXR/R/197_reductions_complex2real_canonicalizers_pnorm_canon.R |only CVXR-1.9.2/CVXR/R/198_reductions_complex2real_canonicalizers_matrix_canon.R |only CVXR-1.9.2/CVXR/R/199_reductions_complex2real_canonicalizers_psd_canon.R |only CVXR-1.9.2/CVXR/R/200_reductions_complex2real_canonicalizers_soc_canon.R |only CVXR-1.9.2/CVXR/R/201_reductions_complex2real_canonicalizers_equality_canon.R |only CVXR-1.9.2/CVXR/R/202_reductions_complex2real_canonicalizers_inequality_canon.R |only CVXR-1.9.2/CVXR/R/203_reductions_complex2real_complex2real.R |only CVXR-1.9.2/CVXR/R/204_reductions_dgp2dcp_util.R |only CVXR-1.9.2/CVXR/R/205_reductions_dgp2dcp_canonicalizers_constant_canon.R |only CVXR-1.9.2/CVXR/R/206_reductions_dgp2dcp_canonicalizers_add_canon.R |only CVXR-1.9.2/CVXR/R/207_reductions_dgp2dcp_canonicalizers_div_canon.R |only CVXR-1.9.2/CVXR/R/208_reductions_dgp2dcp_canonicalizers_mul_canon.R |only CVXR-1.9.2/CVXR/R/209_reductions_dgp2dcp_canonicalizers_mulexpression_canon.R |only CVXR-1.9.2/CVXR/R/210_reductions_dgp2dcp_canonicalizers_power_canon.R |only CVXR-1.9.2/CVXR/R/211_reductions_dgp2dcp_canonicalizers_sum_canon.R |only CVXR-1.9.2/CVXR/R/212_reductions_dgp2dcp_canonicalizers_exp_canon.R |only CVXR-1.9.2/CVXR/R/213_reductions_dgp2dcp_canonicalizers_log_canon.R |only CVXR-1.9.2/CVXR/R/214_reductions_dgp2dcp_canonicalizers_prod_canon.R |only CVXR-1.9.2/CVXR/R/215_reductions_dgp2dcp_canonicalizers_trace_canon.R |only CVXR-1.9.2/CVXR/R/216_reductions_dgp2dcp_canonicalizers_pnorm_canon.R |only CVXR-1.9.2/CVXR/R/217_reductions_dgp2dcp_canonicalizers_norm1_canon.R |only CVXR-1.9.2/CVXR/R/218_reductions_dgp2dcp_canonicalizers_norm_inf_canon.R |only CVXR-1.9.2/CVXR/R/219_reductions_dgp2dcp_canonicalizers_geo_mean_canon.R |only CVXR-1.9.2/CVXR/R/220_reductions_dgp2dcp_canonicalizers_quad_form_canon.R |only CVXR-1.9.2/CVXR/R/221_reductions_dgp2dcp_canonicalizers_quad_over_lin_canon.R |only CVXR-1.9.2/CVXR/R/222_reductions_dgp2dcp_canonicalizers_xexp_canon.R |only CVXR-1.9.2/CVXR/R/223_reductions_dgp2dcp_canonicalizers_cumprod_canon.R |only CVXR-1.9.2/CVXR/R/224_reductions_dgp2dcp_canonicalizers_one_minus_pos_canon.R |only CVXR-1.9.2/CVXR/R/225_reductions_dgp2dcp_canonicalizers_eye_minus_inv_canon.R |only CVXR-1.9.2/CVXR/R/226_reductions_dgp2dcp_canonicalizers_pf_eigenvalue_canon.R |only CVXR-1.9.2/CVXR/R/227_reductions_dgp2dcp_canonicalizers_gmatmul_canon.R |only CVXR-1.9.2/CVXR/R/228_reductions_dgp2dcp_canonicalizers_dgp_canonicalizers.R |only CVXR-1.9.2/CVXR/R/229_reductions_dgp2dcp_canonicalizers_finite_set_canon.R |only CVXR-1.9.2/CVXR/R/230_reductions_dgp2dcp_dgp2dcp.R |only CVXR-1.9.2/CVXR/R/231_reductions_dnlp2smooth_canonicalizers_common_smooth_canons.R |only CVXR-1.9.2/CVXR/R/232_reductions_dnlp2smooth_canonicalizers_div_canon.R |only CVXR-1.9.2/CVXR/R/233_reductions_dnlp2smooth_canonicalizers_power_canon.R |only CVXR-1.9.2/CVXR/R/234_reductions_dnlp2smooth_canonicalizers_quad_over_lin_canon.R |only CVXR-1.9.2/CVXR/R/235_reductions_dnlp2smooth_canonicalizers_pnorm_canon.R |only CVXR-1.9.2/CVXR/R/236_reductions_dnlp2smooth_canonicalizers_geo_mean_canon.R |only CVXR-1.9.2/CVXR/R/237_reductions_dnlp2smooth_canonicalizers_rel_entr_canon.R |only CVXR-1.9.2/CVXR/R/238_reductions_dnlp2smooth_canonicalizers_kl_div_canon.R |only CVXR-1.9.2/CVXR/R/239_reductions_dnlp2smooth_canonicalizers_huber_canon.R |only CVXR-1.9.2/CVXR/R/240_reductions_dnlp2smooth_canonicalizers_log_sum_exp_canon.R |only CVXR-1.9.2/CVXR/R/241_reductions_dnlp2smooth_canonicalizers_smooth_canonicalizers.R |only CVXR-1.9.2/CVXR/R/242_reductions_dnlp2smooth_dnlp2smooth.R |only CVXR-1.9.2/CVXR/R/243_reductions_solvers_nlp_solvers_diff_engine_helpers.R |only CVXR-1.9.2/CVXR/R/244_reductions_solvers_nlp_solvers_diff_engine_converters.R |only CVXR-1.9.2/CVXR/R/245_reductions_solvers_nlp_solvers_diff_engine_registry.R |only CVXR-1.9.2/CVXR/R/246_reductions_solvers_nlp_solvers_diff_engine_c_problem.R |only CVXR-1.9.2/CVXR/R/247_reductions_dqcp2dcp_inverse.R |only CVXR-1.9.2/CVXR/R/248_reductions_dqcp2dcp_sets.R |only CVXR-1.9.2/CVXR/R/249_reductions_dqcp2dcp_tighten.R |only CVXR-1.9.2/CVXR/R/250_reductions_dqcp2dcp_dqcp2dcp.R |only CVXR-1.9.2/CVXR/R/251_reductions_discrete2mixedint_valinvec2mixedint.R |only CVXR-1.9.2/CVXR/R/252_transforms_partial_optimize.R |only CVXR-1.9.2/CVXR/R/253_transforms_scalarize.R |only CVXR-1.9.2/CVXR/R/254_reductions_solvers_bisection.R |only CVXR-1.9.2/CVXR/R/255_utilities_replace_quad_forms.R |only CVXR-1.9.2/CVXR/R/256_utilities_coeff_extractor.R |only CVXR-1.9.2/CVXR/R/257_utilities_perspective_utils.R |only CVXR-1.9.2/CVXR/R/258_reductions_dcp2cone_cone_matrix_stuffing.R |only CVXR-1.9.2/CVXR/R/259_reductions_cvx_attr2constr.R |only CVXR-1.9.2/CVXR/R/260_reductions_cone2cone_exact.R |only CVXR-1.9.2/CVXR/R/261_reductions_solvers_utilities.R |only CVXR-1.9.2/CVXR/R/262_reductions_solvers_solver.R |only CVXR-1.9.2/CVXR/R/263_reductions_solvers_nlp_solvers_nlp_solver.R |only CVXR-1.9.2/CVXR/R/264_reductions_solvers_nlp_solvers_uno_nlpif.R |only CVXR-1.9.2/CVXR/R/265_reductions_solvers_nlp_solvers_ipopt_nlpif.R |only CVXR-1.9.2/CVXR/R/266_reductions_solvers_nlp_solvers_knitro_nlpif.R |only CVXR-1.9.2/CVXR/R/267_reductions_solvers_nlp_solvers_copt_nlpif.R |only CVXR-1.9.2/CVXR/R/268_reductions_solvers_defines.R |only CVXR-1.9.2/CVXR/R/269_reductions_solvers_constant_solver.R |only CVXR-1.9.2/CVXR/R/270_reductions_solvers_qp_solvers_qp_solver.R |only CVXR-1.9.2/CVXR/R/271_reductions_solvers_conic_solvers_conic_solver.R |only CVXR-1.9.2/CVXR/R/272_reductions_solvers_conic_solvers_scs_conif.R |only CVXR-1.9.2/CVXR/R/273_reductions_solvers_conic_solvers_clarabel_conif.R |only CVXR-1.9.2/CVXR/R/274_reductions_solvers_conic_solvers_diffcp_conif.R |only CVXR-1.9.2/CVXR/R/275_reductions_solvers_conic_solvers_mosek_conif.R |only CVXR-1.9.2/CVXR/R/276_reductions_solvers_conic_solvers_gurobi_conif.R |only CVXR-1.9.2/CVXR/R/277_reductions_solvers_conic_solvers_cplex_conif.R |only CVXR-1.9.2/CVXR/R/278_reductions_solvers_conic_solvers_highs_conif.R |only CVXR-1.9.2/CVXR/R/279_reductions_solvers_conic_solvers_glpk_conif.R |only CVXR-1.9.2/CVXR/R/280_reductions_solvers_conic_solvers_glpk_mi_conif.R |only CVXR-1.9.2/CVXR/R/281_reductions_solvers_conic_solvers_ecos_conif.R |only CVXR-1.9.2/CVXR/R/282_reductions_solvers_conic_solvers_ecos_bb_conif.R |only CVXR-1.9.2/CVXR/R/283_reductions_solvers_conic_solvers_cvxopt_conif.R |only CVXR-1.9.2/CVXR/R/284_reductions_solvers_conic_solvers_scip_conif.R |only CVXR-1.9.2/CVXR/R/285_reductions_solvers_conic_solvers_xpress_conif.R |only CVXR-1.9.2/CVXR/R/286_reductions_solvers_qp_solvers_osqp_qpif.R |only CVXR-1.9.2/CVXR/R/287_reductions_solvers_qp_solvers_highs_qpif.R |only CVXR-1.9.2/CVXR/R/288_reductions_solvers_qp_solvers_gurobi_qpif.R |only CVXR-1.9.2/CVXR/R/289_reductions_solvers_qp_solvers_cplex_qpif.R |only CVXR-1.9.2/CVXR/R/290_reductions_solvers_qp_solvers_piqp_qpif.R |only CVXR-1.9.2/CVXR/R/291_reductions_solvers_qp_solvers_xpress_qpif.R |only CVXR-1.9.2/CVXR/R/292_reductions_solvers_solving_chain.R |only CVXR-1.9.2/CVXR/R/293_reductions_solvers_nlp_solving_chain.R |only CVXR-1.9.2/CVXR/R/294_zzz_R_specific_visualize_annotations.R |only CVXR-1.9.2/CVXR/R/295_zzz_R_specific_visualize_html.R |only CVXR-1.9.2/CVXR/R/296_zzz_R_specific_visualize.R |only CVXR-1.9.2/CVXR/R/297_zzz_R_specific_to_latex.R |only CVXR-1.9.2/CVXR/R/298_zzz_R_specific_solver_opts.R |only CVXR-1.9.2/CVXR/R/299_zzz_R_specific_exports.R |only CVXR-1.9.2/CVXR/R/300_zzz_R_specific_math_atoms.R |only CVXR-1.9.2/CVXR/R/301_zzz_R_specific_masking.R |only CVXR-1.9.2/CVXR/R/302_zzz_R_specific_aliases.R |only CVXR-1.9.2/CVXR/R/303_zzz_R_specific_data.R |only CVXR-1.9.2/CVXR/R/304_zzz_R_specific_grad_delta_attrs.R |only CVXR-1.9.2/CVXR/man/power.Rd |only CVXR-1.9.3/CVXR/DESCRIPTION | 14 CVXR-1.9.3/CVXR/MD5 | 1060 +++++----- CVXR-1.9.3/CVXR/NAMESPACE | 11 CVXR-1.9.3/CVXR/NEWS.md | 327 +++ CVXR-1.9.3/CVXR/R/001_zzz_R_specific_CVXR-package.R | 2 CVXR-1.9.3/CVXR/R/002_zzz_R_specific_globals.R | 18 CVXR-1.9.3/CVXR/R/005_zzz_R_specific_generics.R | 32 CVXR-1.9.3/CVXR/R/006_zzz_R_specific_utility.R | 98 CVXR-1.9.3/CVXR/R/007_utilities_performance_utils.R |only CVXR-1.9.3/CVXR/R/008_utilities_sign.R |only CVXR-1.9.3/CVXR/R/009_utilities_shape.R |only CVXR-1.9.3/CVXR/R/010_utilities_error.R |only CVXR-1.9.3/CVXR/R/011_utilities_power_tools.R |only CVXR-1.9.3/CVXR/R/012_utilities_grad.R |only CVXR-1.9.3/CVXR/R/013_utilities_solver_context.R |only CVXR-1.9.3/CVXR/R/014_utilities_psd_utils.R |only CVXR-1.9.3/CVXR/R/015_utilities_bounds.R |only CVXR-1.9.3/CVXR/R/016_settings.R |only CVXR-1.9.3/CVXR/R/017_lin_ops_LinOp.R |only CVXR-1.9.3/CVXR/R/018_lin_ops_LinOpVector.R |only CVXR-1.9.3/CVXR/R/019_lin_ops_RcppExports.R |only CVXR-1.9.3/CVXR/R/020_lin_ops_CVXcanon.R |only CVXR-1.9.3/CVXR/R/021_cvxcore_r_canonInterface.R |only CVXR-1.9.3/CVXR/R/022_zzz_R_specific_rcppUtils.R |only CVXR-1.9.3/CVXR/R/023_zzz_R_specific_sparse_utils.R |only CVXR-1.9.3/CVXR/R/024_zzz_R_specific_coll_utils.R |only CVXR-1.9.3/CVXR/R/025_interface_matrix_utilities.R |only CVXR-1.9.3/CVXR/R/026_lin_ops_lin_utils.R |only CVXR-1.9.3/CVXR/R/027_utilities_canonical.R |only CVXR-1.9.3/CVXR/R/028_expressions_expression.R |only CVXR-1.9.3/CVXR/R/029_expressions_leaf.R |only CVXR-1.9.3/CVXR/R/030_expressions_variable.R |only CVXR-1.9.3/CVXR/R/031_expressions_constants_constant.R |only CVXR-1.9.3/CVXR/R/032_expressions_constants_parameter.R |only CVXR-1.9.3/CVXR/R/033_expressions_constants_callback_param.R |only CVXR-1.9.3/CVXR/R/034_atoms_atom.R |only CVXR-1.9.3/CVXR/R/035_atoms_affine_affine_atom.R |only CVXR-1.9.3/CVXR/R/036_atoms_affine_conj.R |only CVXR-1.9.3/CVXR/R/037_atoms_affine_real.R |only CVXR-1.9.3/CVXR/R/038_atoms_affine_imag.R |only CVXR-1.9.3/CVXR/R/039_atoms_affine_wraps.R |only CVXR-1.9.3/CVXR/R/040_atoms_elementwise_elementwise.R |only CVXR-1.9.3/CVXR/R/041_atoms_axis_atom.R |only CVXR-1.9.3/CVXR/R/042_atoms_affine_axis_aff_atom.R |only CVXR-1.9.3/CVXR/R/043_atoms_affine_promote.R |only CVXR-1.9.3/CVXR/R/044_atoms_affine_unary_operators.R |only CVXR-1.9.3/CVXR/R/045_atoms_affine_add_expr.R |only CVXR-1.9.3/CVXR/R/046_atoms_affine_binary_operators.R |only CVXR-1.9.3/CVXR/R/047_atoms_affine_index.R |only CVXR-1.9.3/CVXR/R/048_atoms_affine_transpose.R |only CVXR-1.9.3/CVXR/R/049_atoms_affine_sum.R |only CVXR-1.9.3/CVXR/R/050_atoms_affine_reshape.R |only CVXR-1.9.3/CVXR/R/051_atoms_affine_diag.R |only CVXR-1.9.3/CVXR/R/052_atoms_affine_trace.R |only CVXR-1.9.3/CVXR/R/053_atoms_affine_partial_trace.R |only CVXR-1.9.3/CVXR/R/054_atoms_affine_partial_transpose.R |only CVXR-1.9.3/CVXR/R/055_atoms_affine_hstack.R |only CVXR-1.9.3/CVXR/R/056_atoms_affine_vstack.R |only CVXR-1.9.3/CVXR/R/057_atoms_affine_kron.R |only CVXR-1.9.3/CVXR/R/058_atoms_affine_upper_tri.R |only CVXR-1.9.3/CVXR/R/059_atoms_affine_conv.R |only CVXR-1.9.3/CVXR/R/060_atoms_affine_cumsum.R |only CVXR-1.9.3/CVXR/R/061_atoms_affine_diff.R |only CVXR-1.9.3/CVXR/R/062_atoms_affine_bmat.R |only CVXR-1.9.3/CVXR/R/063_atoms_elementwise_abs.R |only CVXR-1.9.3/CVXR/R/064_atoms_elementwise_exp.R |only CVXR-1.9.3/CVXR/R/065_atoms_elementwise_log.R |only CVXR-1.9.3/CVXR/R/066_atoms_elementwise_power.R |only CVXR-1.9.3/CVXR/R/067_atoms_elementwise_entr.R |only CVXR-1.9.3/CVXR/R/068_atoms_elementwise_huber.R |only CVXR-1.9.3/CVXR/R/069_atoms_elementwise_maximum.R |only CVXR-1.9.3/CVXR/R/070_atoms_elementwise_minimum.R |only CVXR-1.9.3/CVXR/R/071_atoms_elementwise_kl_div.R |only CVXR-1.9.3/CVXR/R/072_atoms_elementwise_rel_entr.R |only CVXR-1.9.3/CVXR/R/073_atoms_elementwise_log1p.R |only CVXR-1.9.3/CVXR/R/074_atoms_elementwise_xexp.R |only CVXR-1.9.3/CVXR/R/075_atoms_elementwise_logistic.R |only CVXR-1.9.3/CVXR/R/076_atoms_elementwise_square.R |only CVXR-1.9.3/CVXR/R/077_atoms_elementwise_pos.R |only CVXR-1.9.3/CVXR/R/078_atoms_elementwise_neg.R |only CVXR-1.9.3/CVXR/R/079_atoms_elementwise_inv_pos.R |only CVXR-1.9.3/CVXR/R/080_atoms_elementwise_scalene.R |only CVXR-1.9.3/CVXR/R/081_atoms_elementwise_loggamma.R |only CVXR-1.9.3/CVXR/R/082_atoms_elementwise_log_normcdf.R |only CVXR-1.9.3/CVXR/R/083_atoms_elementwise_normcdf.R |only CVXR-1.9.3/CVXR/R/084_atoms_elementwise_trig.R |only CVXR-1.9.3/CVXR/R/085_atoms_elementwise_hyperbolic.R |only CVXR-1.9.3/CVXR/R/086_atoms_elementwise_ceil.R |only CVXR-1.9.3/CVXR/R/087_atoms_elementwise_logic.R |only CVXR-1.9.3/CVXR/R/088_atoms_affine_vec.R |only CVXR-1.9.3/CVXR/R/089_atoms_total_variation.R |only CVXR-1.9.3/CVXR/R/090_atoms_sum_smallest.R |only CVXR-1.9.3/CVXR/R/091_atoms_harmonic_mean.R |only CVXR-1.9.3/CVXR/R/092_atoms_mixed_norm.R |only CVXR-1.9.3/CVXR/R/093_atoms_cvar.R |only CVXR-1.9.3/CVXR/R/094_atoms_ptp.R |only CVXR-1.9.3/CVXR/R/095_atoms_stats.R |only CVXR-1.9.3/CVXR/R/096_atoms_inv_prod.R |only CVXR-1.9.3/CVXR/R/097_atoms_norm1.R |only CVXR-1.9.3/CVXR/R/098_atoms_norm_inf.R |only CVXR-1.9.3/CVXR/R/099_atoms_pnorm.R |only CVXR-1.9.3/CVXR/R/100_atoms_max.R |only CVXR-1.9.3/CVXR/R/101_atoms_min.R |only CVXR-1.9.3/CVXR/R/102_atoms_norm.R |only CVXR-1.9.3/CVXR/R/103_atoms_geo_mean.R |only CVXR-1.9.3/CVXR/R/104_atoms_quad_form.R |only CVXR-1.9.3/CVXR/R/105_atoms_symbolic_quad_form.R |only CVXR-1.9.3/CVXR/R/106_atoms_quad_over_lin.R |only CVXR-1.9.3/CVXR/R/107_atoms_log_sum_exp.R |only CVXR-1.9.3/CVXR/R/108_atoms_sum_largest.R |only CVXR-1.9.3/CVXR/R/109_atoms_lambda_max.R |only CVXR-1.9.3/CVXR/R/110_atoms_sigma_max.R |only CVXR-1.9.3/CVXR/R/111_atoms_norm_nuc.R |only CVXR-1.9.3/CVXR/R/112_atoms_matrix_frac.R |only CVXR-1.9.3/CVXR/R/113_atoms_tr_inv.R |only CVXR-1.9.3/CVXR/R/114_atoms_lambda_sum_largest.R |only CVXR-1.9.3/CVXR/R/115_atoms_log_det.R |only CVXR-1.9.3/CVXR/R/116_atoms_cummax.R |only CVXR-1.9.3/CVXR/R/117_atoms_dotsort.R |only CVXR-1.9.3/CVXR/R/118_atoms_prod.R |only CVXR-1.9.3/CVXR/R/119_atoms_cumprod.R |only CVXR-1.9.3/CVXR/R/120_atoms_one_minus_pos.R |only CVXR-1.9.3/CVXR/R/121_atoms_eye_minus_inv.R |only CVXR-1.9.3/CVXR/R/122_atoms_pf_eigenvalue.R |only CVXR-1.9.3/CVXR/R/123_atoms_gmatmul.R |only CVXR-1.9.3/CVXR/R/124_atoms_perspective.R |only CVXR-1.9.3/CVXR/R/125_atoms_length.R |only CVXR-1.9.3/CVXR/R/126_atoms_condition_number.R |only CVXR-1.9.3/CVXR/R/127_atoms_gen_lambda_max.R |only CVXR-1.9.3/CVXR/R/128_atoms_dist_ratio.R |only CVXR-1.9.3/CVXR/R/129_atoms_sign.R |only CVXR-1.9.3/CVXR/R/130_zzz_R_specific_operators.R |only CVXR-1.9.3/CVXR/R/131_constraints_constraint.R |only CVXR-1.9.3/CVXR/R/132_constraints_zero.R |only CVXR-1.9.3/CVXR/R/133_constraints_nonpos.R |only CVXR-1.9.3/CVXR/R/134_constraints_cones.R |only CVXR-1.9.3/CVXR/R/135_constraints_second_order.R |only CVXR-1.9.3/CVXR/R/136_constraints_psd.R |only CVXR-1.9.3/CVXR/R/137_constraints_exponential.R |only CVXR-1.9.3/CVXR/R/138_constraints_power.R |only CVXR-1.9.3/CVXR/R/139_constraints_finite_set.R |only CVXR-1.9.3/CVXR/R/140_transforms_indicator.R |only CVXR-1.9.3/CVXR/R/141_problems_objective.R |only CVXR-1.9.3/CVXR/R/142_problems_problem.R |only CVXR-1.9.3/CVXR/R/143_problems_param_prob.R |only CVXR-1.9.3/CVXR/R/144_reductions_reduction.R |only CVXR-1.9.3/CVXR/R/145_reductions_eval_params.R |only CVXR-1.9.3/CVXR/R/146_reductions_flip_objective.R |only CVXR-1.9.3/CVXR/R/147_reductions_canonicalization.R |only CVXR-1.9.3/CVXR/R/148_reductions_subexpr_cache.R |only CVXR-1.9.3/CVXR/R/149_reductions_dcp2cone_dcp2cone.R |only CVXR-1.9.3/CVXR/R/150_reductions_dcp2cone_canonicalizers_abs_canon.R |only CVXR-1.9.3/CVXR/R/151_reductions_dcp2cone_canonicalizers_cummax_canon.R |only 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insertions(+), 1338 deletions(-)
Title: An Implementation of Z-Curves
Description: An implementation of z-curves - a method for estimating expected discovery
and replicability rates on the bases of test-statistics of published studies. The package
provides functions for fitting the density, EM, and censored EM version (Bartoš & Schimmack, 2022,
<doi:10.15626/MP.2021.2720>; Schimmack & Bartoš, 2023, <doi: 10.1371/journal.pone.0290084>),
as well as the original density z-curve (Brunner & Schimmack, 2020, <doi:10.15626/MP.2018.874>).
Furthermore, the package provides summarizing and plotting functions for the fitted z-curve objects.
See the aforementioned articles for more information about the z-curves, expected discovery
and replicability rates, validation studies, and limitations.
Author: Frantisek Bartos [aut, cre],
Ulrich Schimmack [aut]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between zcurve versions 2.4.6 dated 2026-01-21 and 2.4.7 dated 2026-10-19
DESCRIPTION | 10 - MD5 | 15 +- R/zcurve_EM.R | 84 ++++++++------ R/zcurve_density.R | 198 +++++++++++++++++++++++----------- build/partial.rdb |binary man/control_EM.Rd | 20 ++- man/control_density.Rd | 29 +++- man/control_density_v1.Rd | 20 ++- tests/testthat/test-density-reflect.R |only 9 files changed, 247 insertions(+), 129 deletions(-)
Title: Objective Bayesian Distribution Fitting
Description: Fits common univariate distributions using registered objective
Bayesian priors, including Jeffreys, reference, and maximal data information
priors, and supports user-defined distributions and priors through an
extensible model specification. Model-specific posterior propriety and
moment conditions are checked before computation when registered or supplied.
Exact simulation, marginalization, slice sampling, adaptive Metropolis, and
user-supplied posterior samplers share a common interface for summaries,
diagnostics, prediction, and pointwise log-likelihood evaluation.
A separate interface fits independently right-censored observations using
the registered complete-data priors, observed-data likelihood sampling or
data augmentation, with sufficient posterior-propriety checks. Optional
post-processing provides WAIC, PSIS-LOO, and DIC for observed-data likelihoods.
The reference-prior framework follows Bernardo (1979)
<doi:10.1111/j.2517-6161.1979.tb01066.x>.
Author: Pedro Luiz Ramos [aut, cre, cph]
Maintainer: Pedro Luiz Ramos <pedro.ramos@uc.cl>
Diff between fitdistrBayes versions 0.5.1 dated 2026-09-30 and 0.6.0 dated 2026-10-19
DESCRIPTION | 6 +- MD5 | 35 +++++++------ NEWS.md | 21 +++++++ R/criteria.R | 8 ++- R/dhillon.R |only R/fitcensBayes.R | 58 ++++++++++++++++------ R/fitdistrBayes.R | 17 +++++- README.md | 44 +++++++++++++--- inst/doc |only inst/examples/tutorial_dhillon.R |only inst/examples/tutorial_fitcensBayes.R | 16 +++++- inst/examples/tutorial_fitdistrBayes_all_models.R | 18 ++++++ man/Dhillon.Rd |only man/fitcensBayes.Rd | 18 +++++- man/fitcensBayes_models.Rd | 12 +++- man/fitdistrBayes.Rd | 21 ++++++- tests/censored-helpers.R | 1 tests/tests_censored_contracts.R | 2 tests/tests_censored_sampling.R | 4 - tests/tests_dhillon.R |only tests/tests_registry.R | 6 +- 21 files changed, 223 insertions(+), 64 deletions(-)
Title: Semi-Parametric Joint Modeling of Longitudinal and Survival Data
Description: Implements scalable joint models for large-scale competing risks time-to-event data with one or multiple longitudinal biomarkers using the efficient algorithms developed by Li et al. (2022) <doi:10.1155/2022/1362913> and <doi:10.1214/26-AOAS2218>.
The time-to-event process is modeled using a cause-specific Cox proportional hazards model
with time-fixed covariates, while longitudinal biomarkers are modeled
using linear mixed-effects models. The association between the longitudinal
and survival processes is captured through shared random effects. The
package enables analysis of large-scale biomedical data to model biomarker
trajectories, estimate their effects on event risks, and perform dynamic
prediction of future events based on patients' longitudinal histories.
Functions for simulating survival and longitudinal data for multiple
biomarkers are included, along with built-in example datasets. The package
also supports modeling a single biomarker with heterogeneous within-su [...truncated...]
Author: Shanpeng Li [aut, cre],
Ace Mejia-Sanchez [ctb],
Emily Ouyang [ctb],
Xinping Cui [ctb],
Gang Li [ctb]
Maintainer: Shanpeng Li <lishanpeng0913@ucla.edu>
Diff between FastJM versions 1.7.1 dated 2026-08-21 and 1.7.2 dated 2026-10-19
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Title: Dirichlet Regression
Description: Implements Dirichlet regression models.
Author: Marco Johannes Maier [cre, aut]
Maintainer: Marco Johannes Maier <marco_maier@posteo.de>
Diff between DirichletReg versions 0.7-3 dated 2026-10-16 and 0.7-4 dated 2026-10-19
DESCRIPTION | 8 ++--- MD5 | 14 ++++----- NEWS | 4 ++ build/partial.rdb |binary inst/NEWS.Rd | 5 +++ inst/NEWS.pdf |binary inst/doc/DirichletReg-vig.html | 4 +- tests/testthat/test-DR_data.R | 59 +++++++++++++---------------------------- 8 files changed, 41 insertions(+), 53 deletions(-)
Title: Bass-Ackwards Hierarchical Structural Analysis
Description: Implements Goldberg's (2006) <doi:10.1016/j.jrp.2006.01.001>
bass-ackwards method and modern descendants for hierarchical structural
analysis. Extracts solutions from 1 to k factors using principal
component analysis (PCA), exploratory factor analysis (EFA), or
exploratory structural equation modeling (ESEM) engines. It then
describes the hierarchy through the correlations between the factor
scores of different levels. It computes them with linear algebra from the
scoring weights and the correlation matrix the fit uses, so they are
exact for that matrix. Waller (2007) <doi:10.1016/j.jrp.2006.08.005>
showed, for principal components, that these correlations follow from
the correlation matrix alone. Includes the Forbes (2023) <doi:10.1037/met0000546> extension
for redundancy pruning and all-levels cross-correlations.
Author: Jeffrey M. Girard [aut, cre] ,
Miriam K. Forbes [cph] , CC-BY 4.0)
Maintainer: Jeffrey M. Girard <me@jmgirard.com>
Diff between ackwards versions 0.2.0 dated 2026-07-27 and 0.3.0 dated 2026-10-19
DESCRIPTION | 30 MD5 | 289 +-- NAMESPACE | 20 NEWS.md | 157 + R/ackwards.R | 433 +++- R/augment.R | 81 R/autoplot.R | 148 - R/boot_edges.R | 127 - R/check_items.R | 47 R/comparability.R | 160 - R/compute_edges.R | 37 R/data.R | 127 - R/engine_efa.R | 153 + R/engine_esem.R | 263 ++ R/engine_pca.R | 90 R/factor_labels.R | 30 R/factorability.R | 72 R/interpret.R | 26 R/label_template.R | 28 R/layout.R | 45 R/predict.R | 24 R/print.R | 18 R/prune.R | 212 +- R/suggest_k.R | 171 + R/summary.R | 41 R/tidy.R | 259 ++ R/utils.R | 266 ++ README.md | 148 - inst/doc/ackwards-engines.Rmd | 851 ++++++--- inst/doc/ackwards-engines.html | 925 ++++++---- inst/doc/ackwards-forbes.Rmd | 244 +- inst/doc/ackwards-forbes.html | 248 +- inst/doc/ackwards-forbes2023.Rmd | 206 +- inst/doc/ackwards-forbes2023.html | 216 +- inst/doc/ackwards-girard.Rmd | 293 +-- inst/doc/ackwards-girard.html | 288 +-- inst/doc/ackwards-interpret.Rmd | 251 +- inst/doc/ackwards-interpret.html | 168 - inst/doc/ackwards-intro.Rmd | 409 ++-- inst/doc/ackwards-intro.html | 393 ++-- inst/doc/ackwards-ordinal.Rmd | 227 +- inst/doc/ackwards-ordinal.html | 195 +- inst/doc/ackwards-suggest-k.Rmd | 335 +-- inst/doc/ackwards-suggest-k.html | 324 +-- inst/doc/ackwards-visualization.Rmd | 149 - inst/doc/ackwards-visualization.html | 229 +- man/ackwards.Rd | 372 ++-- man/augment.ackwards.Rd | 81 man/autoplot.Rd | 4 man/autoplot.ackwards.Rd | 130 - man/autoplot.comparability.Rd | 14 man/autoplot.suggest_k.Rd | 25 man/ba_layout.Rd | 45 man/bfi25.Rd | 23 man/boot_edges.Rd | 98 - man/check_items.Rd | 45 man/comparability.Rd | 144 - man/compute_edges.Rd | 39 man/factor_labels.Rd | 4 man/factorability.Rd | 74 man/figures/README-plot-1.png |binary man/forbes2023.Rd | 24 man/glance.ackwards.Rd | 22 man/label_template.Rd | 28 man/predict.ackwards.Rd | 24 man/print.ackwards.Rd | 2 man/prune.Rd | 182 + man/set_factor_labels.Rd | 26 man/sim16.Rd | 78 man/suggest_k.Rd | 148 - man/summary.ackwards.Rd | 14 man/tidy.ackwards.Rd | 151 + man/top_items.Rd | 26 tests/testthat/Rplots.pdf |binary tests/testthat/_problems |only tests/testthat/_snaps/print-snapshot.md | 291 +++ tests/testthat/fixtures/baseline-m89.rds |only tests/testthat/fixtures/forbes2023_oblique.rds |only tests/testthat/helper-data.R | 9 tests/testthat/test-baseline-m89.R |only tests/testthat/test-boot_edges.R | 8 tests/testthat/test-check-prose.R |only tests/testthat/test-comparability.R | 20 tests/testthat/test-compute_edges.R | 70 tests/testthat/test-docs-estimator-claims.R |only tests/testthat/test-efa.R | 6 tests/testthat/test-esem-rotation-starts.R |only tests/testthat/test-esem.R | 44 tests/testthat/test-factor-cor.R |only tests/testthat/test-forbes-fidelity.R | 120 + tests/testthat/test-missing.R | 67 tests/testthat/test-oblique-branches.R |only tests/testthat/test-oblique.R |only tests/testthat/test-partialled-edges.R |only tests/testthat/test-print-snapshot.R | 64 tests/testthat/test-prune.R | 30 tests/testthat/test-rotation.R |only tests/testthat/test-utils.R | 49 tests/testthat/test-vignette-rotation.R |only vignettes/ackwards-engines.Rmd | 851 ++++++--- vignettes/ackwards-forbes.Rmd | 244 +- vignettes/ackwards-forbes2023.Rmd | 206 +- vignettes/ackwards-girard.Rmd | 293 +-- vignettes/ackwards-interpret.Rmd | 251 +- vignettes/ackwards-intro.Rmd | 409 ++-- vignettes/ackwards-ordinal.Rmd | 227 +- vignettes/ackwards-suggest-k.Rmd | 335 +-- vignettes/ackwards-visualization.Rmd | 149 - vignettes/assets/ackwards-engines-fit-plot-1.png |binary vignettes/assets/ackwards-engines-rotation-plot-oblimin-1.png |only vignettes/assets/ackwards-engines-rotation-plot-varimax-1.png |only vignettes/assets/ackwards-forbes-drop-pruned-1.png |binary vignettes/assets/ackwards-forbes-drop-pruned-compressed-1.png |binary vignettes/assets/ackwards-forbes-drop-pruned-unlabeled-1.png |binary vignettes/assets/ackwards-forbes2023-pruned-diagram-1.png |binary vignettes/assets/ackwards-forbes2023-pruned-diagram-compressed-1.png |binary vignettes/assets/ackwards-girard-comparability-plot-1.png |binary vignettes/assets/ackwards-girard-hierarchy-plot-1.png |binary vignettes/assets/ackwards-intro-autoplot-1.png |binary vignettes/assets/ackwards-intro-suggest_k_plot-1.png |binary vignettes/assets/ackwards-ordinal-r-compare-1.png |binary vignettes/assets/ackwards-suggest-k-autoplot-1.png |binary vignettes/assets/ackwards-visualization-base-1.png |binary vignettes/assets/ackwards-visualization-colours-1.png |binary vignettes/assets/ackwards-visualization-cut-show-1.png |binary vignettes/assets/ackwards-visualization-direction-1.png |binary vignettes/assets/ackwards-visualization-drop-pruned-secondary-1.png |binary vignettes/assets/ackwards-visualization-drop-pruned-secondary-2.png |binary vignettes/assets/ackwards-visualization-edge-linewidth-1.png |binary vignettes/assets/ackwards-visualization-label-template-forbes-1.png |binary vignettes/assets/ackwards-visualization-level-labels-off-1.png |binary vignettes/assets/ackwards-visualization-level-labels-size-1.png |binary vignettes/assets/ackwards-visualization-magnitude-by-1.png |binary vignettes/assets/ackwards-visualization-manual-order-1.png |binary vignettes/assets/ackwards-visualization-mono-1.png |binary vignettes/assets/ackwards-visualization-no-arrows-1.png |binary vignettes/assets/ackwards-visualization-no-legend-1.png |binary vignettes/assets/ackwards-visualization-node-labels-1.png |binary vignettes/assets/ackwards-visualization-node-labels-multiline-1.png |binary vignettes/assets/ackwards-visualization-node-size-1.png |binary vignettes/assets/ackwards-visualization-primary-only-1.png |binary vignettes/assets/ackwards-visualization-pub-figure-1.png |binary vignettes/assets/ackwards-visualization-pub-figure-labeled-1.png |binary vignettes/assets/ackwards-visualization-show-items-1.png |binary vignettes/assets/ackwards-visualization-show-r-1.png |binary vignettes/assets/ackwards-visualization-show-r-digits-1.png |binary vignettes/assets/ackwards-visualization-sign-by-1.png |binary vignettes/assets/ackwards-visualization-sign-by-2.png |binary vignettes/assets/ackwards-visualization-suggest_k_plot-1.png |binary 149 files changed, 9311 insertions(+), 5708 deletions(-)
Title: Access the UNESCO Institute for Statistics API
Description: Retrieve data from the UNESCO Institute for Statistics (UIS) API
<https://api.uis.unesco.org/api/public/documentation/>. UIS provides public
access to more than 4,000 indicators focusing on education, science and
technology, culture, and communication.
Author: Christoph Scheuch [aut, cre, cph]
Maintainer: Christoph Scheuch <christoph@tidy-intelligence.com>
Diff between uisapi versions 0.1.1 dated 2025-10-02 and 0.1.2 dated 2026-10-19
DESCRIPTION | 14 ++++---- MD5 | 20 +++++------ NAMESPACE | 16 +++++---- NEWS.md | 9 +++-- R/perform_request.R | 2 - R/uis_bulk_files.R | 2 - R/uis_get.R | 4 +- README.md | 82 +++++++++++++++++++++++++----------------------- man/uis_get.Rd | 2 - man/uis_get_versions.Rd | 2 - man/uisapi-package.Rd | 11 ++++-- 11 files changed, 90 insertions(+), 74 deletions(-)
Title: Store and Transfer Amplicon Sequence Data
Description: Stores the data associated with your amplicon sequence analysis. This includes nucleotide sequences, abundance, sample and treatment assignments, taxonomic classifications, asv, otu and phylotype clusters, metadata, trees and various reports. It is designed to facilitate data analysis across multiple R packages with utility functions to read / write from 'mothur', 'qiime2', 'dada2', and 'phyloseq'.
Author: Sarah Westcott [aut] ,
Gregory Johnson [aut] ,
Pat Schloss [cph, cre]
Maintainer: Pat Schloss <pschloss@umich.edu>
Diff between strollur versions 0.1.3 dated 2026-07-02 and 0.1.4 dated 2026-10-19
DESCRIPTION | 14 MD5 | 416 +++--- NAMESPACE | 84 - NEWS.md | 53 R/RcppExports.R | 1178 ++++++++++++------- R/abundance.R | 30 R/add.R | 193 ++- R/assign.R | 187 ++- R/copy_dataset.R | 16 R/count.R | 40 R/export_dataset.R | 16 R/import_dataset.R | 41 R/is_equal.R | 16 R/load_dataset.R | 15 R/miseq_sop_example.R | 19 R/names.R | 47 R/new_dataset.R | 13 R/new_reference.R | 26 R/r6_strollur.R | 704 ++++++----- R/read_biom.R |only R/read_dada2.R | 9 R/read_fasta.R | 7 R/read_fastq.R |only R/read_mothur.R | 46 R/read_mothur_cons_taxonomy.R | 12 R/read_mothur_count.R | 12 R/read_mothur_list.R | 13 R/read_mothur_oligos.R | 12 R/read_mothur_rabund.R | 12 R/read_mothur_shared.R | 13 R/read_mothur_taxonomy.R | 12 R/read_phyloseq.R | 16 R/read_qiime2.R | 14 R/read_qiime2_feature_table.R | 13 R/read_qiime2_metadata.R | 5 R/read_qiime2_taxonomy.R | 4 R/read_quality.R |only R/report.R | 120 + R/save_dataset.R | 14 R/strollur_example.R | 4 R/summary.R | 34 R/taxonomy_table_format.R |only R/unpack_qiime2_artifact.R | 6 R/utils.R | 35 R/write_biom.R |only R/write_fasta.R | 14 R/write_fastq.R |only R/write_mothur.R | 18 R/write_mothur_cons_taxonomy.R | 10 R/write_mothur_count.R | 11 R/write_mothur_design.R | 10 R/write_mothur_list.R | 12 R/write_mothur_rabund.R | 12 R/write_mothur_shared.R | 12 R/write_phyloseq.R | 21 R/write_quality.R |only R/write_taxonomy.R | 11 README.md | 54 build/vignette.rds |binary inst/CITATION | 26 inst/doc/Accessing_Dataset.R | 118 + inst/doc/Accessing_Dataset.Rmd | 213 +-- inst/doc/Accessing_Dataset.html | 437 +++---- inst/doc/Data_Transfers.R | 17 inst/doc/Data_Transfers.Rmd | 29 inst/doc/Data_Transfers.html | 497 ++++---- inst/doc/Example_Analysis_Across_Software_Tools.R | 17 inst/doc/Example_Analysis_Across_Software_Tools.Rmd | 19 inst/doc/Example_Analysis_Across_Software_Tools.html | 23 inst/doc/Functions_for_Package_Developers.R | 49 inst/doc/Functions_for_Package_Developers.Rmd | 77 - inst/doc/Functions_for_Package_Developers.html | 593 ++++----- inst/doc/General_Importing.R | 70 - inst/doc/General_Importing.Rmd | 116 - inst/doc/General_Importing.html | 481 +++---- inst/doc/Importing_from_mothur.R | 38 inst/doc/Importing_from_mothur.Rmd | 89 - inst/doc/Importing_from_mothur.html | 171 +- inst/doc/Importing_from_phyloseq.R | 22 inst/doc/Importing_from_phyloseq.Rmd | 28 inst/doc/Importing_from_phyloseq.html | 91 - inst/doc/Importing_from_qiime2.R | 35 inst/doc/Importing_from_qiime2.Rmd | 63 - inst/doc/Importing_from_qiime2.html | 113 - inst/doc/strollur.Rmd | 2 inst/doc/strollur.html | 4 inst/extdata/final.opti_mcc.jclass.0.03.column.dist |only inst/extdata/miseq_sop.011.rds |only inst/extdata/miseq_sop.otu.biom |only inst/extdata/miseq_sop.rds |binary inst/extdata/miseq_tidy_bin_taxonomy.rds |only inst/extdata/tiny.fasta |only inst/extdata/tiny.fastq.gz |only inst/extdata/tiny.qual |only inst/include/strollur.h | 110 + man/abundance.Rd | 30 man/add.Rd | 112 + man/assign.Rd | 125 +- man/clear.Rd | 8 man/copy_dataset.Rd | 16 man/count.Rd | 44 man/export_dataset.Rd | 15 man/figures/strollur_overview.png |only man/get_bin_types.Rd | 6 man/has_sample.Rd | 6 man/has_sequence_strings.Rd | 6 man/import_dataset.Rd | 23 man/is_aligned.Rd | 6 man/is_equal.Rd | 16 man/load_dataset.Rd | 14 man/miseq_sop_example.Rd | 16 man/names.Rd | 48 man/new_dataset.Rd | 13 man/new_reference.Rd | 26 man/read_biom.Rd |only man/read_dada2.Rd | 17 man/read_fasta.Rd | 5 man/read_fastq.Rd |only man/read_mothur.Rd | 63 - man/read_mothur_cons_taxonomy.Rd | 14 man/read_mothur_count.Rd | 12 man/read_mothur_list.Rd | 13 man/read_mothur_oligos.Rd | 12 man/read_mothur_rabund.Rd | 10 man/read_mothur_shared.Rd | 13 man/read_mothur_taxonomy.Rd | 12 man/read_phyloseq.Rd | 19 man/read_qiime2.Rd | 17 man/read_qiime2_feature_table.Rd | 11 man/read_qiime2_metadata.Rd | 5 man/read_qiime2_taxonomy.Rd | 4 man/read_quality.Rd |only man/report.Rd | 80 - man/save_dataset.Rd | 16 man/sort_dataframe.Rd | 34 man/strollur.Rd | 618 +++++---- man/strollur_example.Rd | 6 man/summary.Rd | 27 man/taxonomy_table_format.Rd |only man/unpack_qiime2_artifact.Rd | 5 man/write_biom.Rd |only man/write_fasta.Rd | 13 man/write_fastq.Rd |only man/write_mothur.Rd | 26 man/write_mothur_cons_taxonomy.Rd | 10 man/write_mothur_count.Rd | 10 man/write_mothur_design.Rd | 10 man/write_mothur_list.Rd | 12 man/write_mothur_rabund.Rd | 12 man/write_mothur_shared.Rd | 12 man/write_phyloseq.Rd | 21 man/write_quality.Rd |only man/write_taxonomy.Rd | 10 man/xdev_abundance.Rd | 33 man/xdev_add_references.Rd | 44 man/xdev_add_report.Rd | 30 man/xdev_add_sequence_fastq_scores.Rd |only man/xdev_add_sequences.Rd | 35 man/xdev_assign_bin_representative_sequences.Rd | 21 man/xdev_assign_bin_taxonomy.Rd | 35 man/xdev_assign_bin_taxonomy_tidy.Rd |only man/xdev_assign_bins.Rd | 42 man/xdev_assign_sample_distances.Rd |only man/xdev_assign_sequence_abundance.Rd | 28 man/xdev_assign_sequence_quality_scores.Rd |only man/xdev_assign_sequence_taxonomy.Rd | 37 man/xdev_assign_sequence_taxonomy_tidy.Rd | 39 man/xdev_assign_treatments.Rd | 26 man/xdev_count.Rd | 59 man/xdev_get_abundances_by_sample.Rd | 10 man/xdev_get_alignment_length.Rd |only man/xdev_get_bin_abundances_by_sample.Rd |only man/xdev_get_by_sample.Rd | 20 man/xdev_get_list_vector.Rd | 8 man/xdev_get_sample_distances.Rd |only man/xdev_get_sequence_abundances_by_sample.Rd |only man/xdev_get_sequence_indexes_by_sample.Rd |only man/xdev_get_sequences.Rd | 16 man/xdev_has_bin_taxonomy.Rd |only man/xdev_has_sequence_taxonomy.Rd | 10 man/xdev_merge_bins.Rd | 21 man/xdev_merge_sequences.Rd | 23 man/xdev_names.Rd | 55 man/xdev_remove_bins.Rd | 26 man/xdev_remove_lineages.Rd | 16 man/xdev_remove_samples.Rd | 19 man/xdev_remove_sequences.Rd | 23 man/xdev_report.Rd | 57 man/xdev_set_abundance.Rd | 28 man/xdev_set_abundances.Rd | 27 man/xdev_set_dataset_name.Rd | 13 man/xdev_set_sequences.Rd | 21 src/RcppExports.cpp | 157 ++ src/abundtable.cpp | 27 src/dataset.cpp | 323 +++++ src/dataset.h | 9 src/rcpp_dataset.cpp | 32 src/rcpp_xint_xdev_functions.cpp | 442 +++++++ src/rcpp_xint_xdev_functions.h | 1164 ++++++++++++------ src/report.cpp | 18 tests/testthat/_snaps/r6_strollur.md | 24 tests/testthat/test-add.R | 120 + tests/testthat/test-assign.R | 27 tests/testthat/test-import.R | 15 tests/testthat/test-is_equal.R | 8 tests/testthat/test-r6_strollur.R | 289 +++- tests/testthat/test-read_biom.R |only tests/testthat/test-read_fasta.R | 28 tests/testthat/test-read_fastq.R |only tests/testthat/test-read_mothur.R | 13 tests/testthat/test-read_quality.R |only tests/testthat/test-report.R | 41 tests/testthat/test-save_load.R | 16 tests/testthat/test-summary.R | 27 tests/testthat/test-write_biom.R |only tests/testthat/test-write_fastq.R |only tests/testthat/test-write_mothur.R | 28 tests/testthat/test-write_quality.R |only tests/testthat/test-xint-xdev.R | 222 +++ vignettes/Accessing_Dataset.Rmd | 213 +-- vignettes/Data_Transfers.Rmd | 29 vignettes/Example_Analysis_Across_Software_Tools.Rmd | 19 vignettes/Functions_for_Package_Developers.Rmd | 77 - vignettes/General_Importing.Rmd | 116 - vignettes/Importing_from_mothur.Rmd | 89 - vignettes/Importing_from_phyloseq.Rmd | 28 vignettes/Importing_from_qiime2.Rmd | 63 - vignettes/strollur.Rmd | 2 228 files changed, 8454 insertions(+), 4967 deletions(-)
Title: Client for 'LaminDB'
Description: Interact with 'LaminDB'. 'LaminDB' is an open-source data
framework for biology. This package allows you to query and download
data from 'LaminDB' instances.
Author: Robrecht Cannoodt [aut, cre] ,
Luke Zappia [aut] ,
Data Intuitive [aut],
Lamin Labs [aut, cph]
Maintainer: Robrecht Cannoodt <robrecht@lamin.ai>
Diff between laminr versions 1.3.1 dated 2026-07-07 and 1.3.2 dated 2026-10-19
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ R/import.R | 1 - R/install.R | 2 +- R/lamindb.R | 11 +---------- R/require.R | 4 ++-- R/status.R | 1 - R/utils.R | 14 +++++++++++--- build/vignette.rds |binary man/require_module.Rd | 2 +- tests/testthat/test-import.R | 19 +++++++++++++++++++ tests/testthat/test-utils.R | 18 ++++++++++++++++++ tests/testthat/test-wrap-python.R | 9 +++++++++ 13 files changed, 77 insertions(+), 34 deletions(-)
Title: Distributed Online Covariance Matrix Tests
Description: Distributed Online Covariance Matrix Tests 'Docovt' is a
powerful tool designed to efficiently process and analyze distributed
datasets. It enables users to perform covariance matrix tests in an
online, distributed manner, making it highly suitable for large-scale
data analysis. By leveraging advanced computational techniques,
'Docovt' ensures robust and scalable solutions for statistical
analysis, particularly in scenarios where data is dispersed across
multiple nodes or sources. This package is ideal for researchers and
practitioners working with high-dimensional data, providing a flexible
and efficient framework for covariance matrix estimation and
hypothesis testing. The philosophy of 'Docovt' is described in
Guo G. (2025) <doi:10.1016/j.physa.2024.130308>.
Author: Guangbao Guo [aut, cre] ,
Congfan Zhang [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between Docovt versions 0.6 dated 2026-06-17 and 0.6.2 dated 2026-10-19
DESCRIPTION | 34 ++++-- MD5 | 52 +++++----- R/COVID19.R | 6 - R/DCLX.R | 143 ++++++++++++++++----------- R/DLC.R | 149 ++++++++++++++--------------- R/DPEC.R | 117 ++++++++++++++-------- R/DPECO.R | 233 ++++++++++++++++++++++++--------------------- R/DPEF.R | 118 ++++++++++++++--------- R/DSNET.R | 276 +++++++++++++++++++++++++++++++++++++++++++----------- R/PECO.R | 212 +++++++++++++++++++++++++---------------- R/SNET.R | 103 ++++++++++++-------- R/chr1qseg.R |only R/cm13.R | 57 ++++++----- R/corneal.R | 6 - build/partial.rdb |binary data/chr1qseg.rda |only data/datalist | 3 inst |only man/COVID19.Rd | 3 man/DCLX.Rd | 92 +++++++++++------- man/DLC.Rd | 86 +++++++++------- man/DPEC.Rd | 86 +++++++++------- man/DPECO.Rd | 92 ++++++++++-------- man/DPEF.Rd | 86 +++++++++------- man/DSNET.Rd | 50 +++++---- man/SNET.Rd | 60 ++++++++--- man/chr1qseg.Rd |only man/cm13.Rd | 54 +++++----- man/corneal.Rd | 3 29 files changed, 1306 insertions(+), 815 deletions(-)
Title: Generic PK/PD Simulation Platform Campsis
Description: A generic, easy-to-use and intuitive
pharmacokinetic/pharmacodynamic (PK/PD) simulation platform based on
the R packages 'rxode2' and 'mrgsolve'. Campsis provides an
abstraction layer over the underlying processes of defining a PK/PD
model, assembling a custom dataset and running a simulation. The
package has a strong dependency on the R package 'campsismod', which
allows models to be read from and written to files, including through
a JSON-based interface, and to be adapted further on the fly in the R
environment. In addition, 'campsis' allows users to assemble datasets
in an intuitive manner, including via a JSON-based interface to import
Campsis datasets defined using formal JSON schemas distributed with
the package. Once the dataset is ready, the package prepares the
simulation, calls 'rxode2' or 'mrgsolve' (at the user's choice), and
returns the results for the given model, dataset and desired
simulation settings. The package itself is licensed under the GPL (>=
3); the JSON sc [...truncated...]
Author: Nicolas Luyckx [aut, cre],
Calvagone [cph]
Maintainer: Nicolas Luyckx <nicolas.luyckx@lynxsoft.be>
Diff between campsis versions 1.9.2 dated 2026-09-24 and 1.9.3 dated 2026-10-19
DESCRIPTION | 14 MD5 | 175 +++++----- NAMESPACE | 2 NEWS.md | 4 R/dataset.R | 39 +- R/treatment_entry.R | 8 R/utilities.R | 4 README.md | 20 - inst/doc/campsis.Rmd | 2 inst/doc/campsis.html | 2 inst/doc/v01_dataset.R | 2 inst/doc/v01_dataset.Rmd | 2 inst/doc/v01_dataset.html | 2 inst/doc/v02_uncertainties.R | 2 inst/doc/v02_uncertainties.Rmd | 2 inst/doc/v02_uncertainties.html | 2 inst/doc/v03_covariates.R | 2 inst/doc/v03_covariates.Rmd | 2 inst/doc/v03_covariates.html | 2 inst/doc/v04_bioavailability.R | 2 inst/doc/v04_bioavailability.Rmd | 2 inst/doc/v04_bioavailability.html | 2 inst/doc/v05_lag_time.R | 2 inst/doc/v05_lag_time.Rmd | 2 inst/doc/v05_lag_time.html | 2 inst/doc/v06_infusions.R | 2 inst/doc/v06_infusions.Rmd | 2 inst/doc/v06_infusions.html | 2 inst/doc/v07_iov.R | 2 inst/doc/v07_iov.Rmd | 2 inst/doc/v07_iov.html | 2 inst/doc/v08_initial_conditions.R | 2 inst/doc/v08_initial_conditions.Rmd | 2 inst/doc/v08_initial_conditions.html | 2 inst/doc/v09_dose_adaptation.R | 2 inst/doc/v09_dose_adaptation.Rmd | 2 inst/doc/v09_dose_adaptation.html | 2 inst/doc/v10_replicate_study.R | 2 inst/doc/v10_replicate_study.Rmd | 2 inst/doc/v10_replicate_study.html | 2 inst/doc/v11_scenarios.R | 2 inst/doc/v11_scenarios.Rmd | 2 inst/doc/v11_scenarios.html | 2 inst/doc/v12_time_varying_covariates.R | 2 inst/doc/v12_time_varying_covariates.Rmd | 2 inst/doc/v12_time_varying_covariates.html | 2 inst/doc/v13_events.R | 2 inst/doc/v13_events.Rmd | 2 inst/doc/v13_events.html | 2 inst/doc/v14_complex_pkpd_models.R | 2 inst/doc/v14_complex_pkpd_models.Rmd | 2 inst/doc/v14_complex_pkpd_models.html | 2 inst/doc/v15_pkpd_model_library.R | 2 inst/doc/v15_pkpd_model_library.Rmd | 2 inst/doc/v15_pkpd_model_library.html | 2 inst/doc/v16_progress_bar.R | 2 inst/doc/v16_progress_bar.Rmd | 2 inst/doc/v16_progress_bar.html | 2 inst/doc/v17_run_simulation_in_parallel.R | 2 inst/doc/v17_run_simulation_in_parallel.Rmd | 2 inst/doc/v17_run_simulation_in_parallel.html | 2 inst/extdata/campsis.schema.json | 2 inst/extdata/campsis_scenarios.schema.json | 8 inst/extdata/campsis_settings.schema.json | 2 inst/extdata/campsismod.schema.json | 2 inst/extdata/no_sub_schemas/campsis_scenarios.schema.json | 2 man/preserve_column_levels.Rd | 1 man/remove_column_levels.Rd | 1 tests/testthat/json_examples/infusion_duration_bug_dataset.json |only tests/testthat/json_examples/infusion_duration_bug_model.json |only tests/testthat/non_regression/infusion_duration_bug_arm_conc.csv |only tests/testthat/test-simulate_infusion.R | 37 ++ vignettes/campsis.Rmd | 2 vignettes/v01_dataset.Rmd | 2 vignettes/v02_uncertainties.Rmd | 2 vignettes/v03_covariates.Rmd | 2 vignettes/v04_bioavailability.Rmd | 2 vignettes/v05_lag_time.Rmd | 2 vignettes/v06_infusions.Rmd | 2 vignettes/v07_iov.Rmd | 2 vignettes/v08_initial_conditions.Rmd | 2 vignettes/v09_dose_adaptation.Rmd | 2 vignettes/v10_replicate_study.Rmd | 2 vignettes/v11_scenarios.Rmd | 2 vignettes/v12_time_varying_covariates.Rmd | 2 vignettes/v13_events.Rmd | 2 vignettes/v14_complex_pkpd_models.Rmd | 2 vignettes/v15_pkpd_model_library.Rmd | 2 vignettes/v16_progress_bar.Rmd | 2 vignettes/v17_run_simulation_in_parallel.Rmd | 2 90 files changed, 263 insertions(+), 200 deletions(-)
Title: N-Power Fourier Deconvolution
Description: Implements the N-Power Fourier Deconvolution (NPFD) method for
nonparametric density deconvolution when observations are available from
a convolving distribution and the corresponding convolved distribution,
but no direct observations are available from the target distribution.
Functions are provided for deconvolution, construction of samples from
replicated mixed measurements, and spline-based density estimation.
The methodology is described in Anarat, Krutmann and Schwender (2026)
<doi:10.1186/s12859-026-06408-0>.
Author: Akin Anarat [aut, cre]
Maintainer: Akin Anarat <akin.anarat@hhu.de>
Diff between NPFD versions 1.0.1 dated 2026-06-07 and 1.0.2 dated 2026-10-19
DESCRIPTION | 15 +++++++++++---- MD5 | 19 +++++++++++-------- NAMESPACE | 2 ++ NEWS.md |only R/createSample.R | 47 +++++++++++++++++++++++++++++++++++++---------- R/deconvolve.R | 20 ++++++++++++++------ R/densprf.R | 46 ++++++++++++++++++++++++++++++---------------- build/partial.rdb |only inst/CITATION |only man/createSample.Rd | 26 +++++++++++++++++++++----- man/deconvolve.Rd | 6 +++++- man/densprf.Rd | 38 ++++++++++++++++++++++++++------------ 12 files changed, 157 insertions(+), 62 deletions(-)
Title: Model Confidence Set Procedure
Description: Implements the Model Confidence Set procedure of Hansen,
Lunde and Nason (2011) <doi:10.3982/ECTA5771> using bootstrap tests
of equal predictive ability. Includes loss functions for level,
volatility and quantile forecasts.
Author: Leopoldo Catania [aut, cre]
Maintainer: Leopoldo Catania <leopoldo.catania@econ.au.dk>
Diff between MCS versions 0.2.0 dated 2026-03-19 and 0.2.1 dated 2026-10-19
Changelog | 21 +++ DESCRIPTION | 21 +-- MD5 | 27 ++-- NAMESPACE | 5 R/ClassesMethods.R | 63 +++++----- R/LossFunctions.R | 199 ++++++++++++++++---------------- R/MCSprocedure.R | 307 +++++++++++++++++++------------------------------- R/internalFunctions.R | 237 ++++++++++++++++++++++++++++++++------ man/LossLevel.Rd | 21 +-- man/LossVaR.Rd | 59 ++++----- man/LossVol.Rd | 46 ++++--- man/MCSprocedure.Rd | 104 +++++++++------- man/SSM-class.Rd | 21 +-- man/SSM-methods.Rd | 22 +-- tests |only 15 files changed, 645 insertions(+), 508 deletions(-)
Title: Simulate Outcomes of a Latent State Reinforcement Learning Model
Description: Simulates outcomes of an updated version of the latent
state reinforcement learning model originally described in Cochran and Cisler
(2019) <doi:10.1371/journal.pcbi.1007331>. The package is designed to create
results under all reasonable experiment setups, including different
reinforcement schedules, number of cues, number of phases, and number of
options per trial. Participants can be simulated using either fixed
parameters or parameters drawn from a distribution.
Author: Martin Benada [aut, cre]
Maintainer: Martin Benada <martinibenada@gmail.com>
Diff between latentState versions 1.0.0 dated 2026-09-17 and 1.0.1 dated 2026-10-19
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/run.R | 4 +++- man/run.Rd | 3 +++ 4 files changed, 12 insertions(+), 7 deletions(-)
Title: False Discovery Exceedance Controlling Multiple Testing
Procedures
Description: Multiple testing procedures for heterogeneous and discrete tests as
described in Döhler and Roquain (2020) <doi:10.1214/20-EJS1771>. The main
algorithms of the paper are available as continuous, discrete and weighted
versions. They take as input the results of a test procedure from package
'DiscreteTests', or a set of observed p-values and their discrete support
under their nulls. A shortcut function to obtain such p-values and supports
is also provided, along with wrappers allowing to apply discrete procedures
directly to data.
Author: Sebastian Doehler [aut] ,
Florian Junge [aut, cre] ,
Etienne Roquain [ctb]
Maintainer: Florian Junge <diso.fbmn@h-da.de>
Diff between FDX versions 2.0.2 dated 2024-11-11 and 2.0.4 dated 2026-10-19
DESCRIPTION | 15 +++++----- MD5 | 18 ++++++------ NAMESPACE | 70 ++++++++++++++++++++++++++++---------------------- NEWS.md | 14 +++++++++- R/DGR_fun.R | 1 R/internal.R | 28 ++++++++++++++------ build/partial.rdb |binary man/FDX-package.Rd | 1 man/hist.FDX.Rd | 2 - src/kernel_weight.cpp | 2 - 10 files changed, 94 insertions(+), 57 deletions(-)
Title: Cayley Graph Analysis for Permutation Puzzles
Description: Analyzes Cayley graphs of permutation puzzles. Any puzzle
whose moves permute a fixed set of positions can be declared as a
permutation group, and the same tools then work on it: cycle
detection, state space exploration and path search. Two puzzles are
built in: TopSpin and Rubik's cubes of any size. The 3x3x3 is solved
by four human methods and by a two-phase search after Herbert
Kociemba; the 4x4x4 is solved by reduction.
The Iterative Cycle Intersection (ICI) method is described in Yuri
Baramykov (2026) <doi:10.48550/arXiv.2607.13219>.
Author: Yuri Baramykov [aut, cre] ,
Lucas Garron [ctb, cph] ,
cubing.js authors [cph]
Maintainer: Yuri Baramykov <lbsbmsu@mail.ru>
Diff between cayleyR versions 0.2.6 dated 2026-07-29 and 0.3.0 dated 2026-10-19
DESCRIPTION | 40 - MD5 | 386 ++++++++- NAMESPACE | 97 ++ NEWS.md | 74 + R/RcppExports.R | 523 ++++++++++++- R/analyze_combinations.R | 16 R/bidirectional_bfs.R | 60 + R/budget_ladder.R |only R/cayleyR-package.R | 3 R/cube_adi.R |only R/cube_astar.R |only R/cube_build_centres.R |only R/cube_centre_map.R |only R/cube_centres.R |only R/cube_check.R |only R/cube_colour.R |only R/cube_edge_map.R |only R/cube_kociemba.R |only R/cube_nnn.R |only R/cube_orbits.R |only R/cube_reduced.R |only R/cube_santa.R |only R/cube_solve.R |only R/cube_solve4.R |only R/cube_solve4_cascade.R |only R/cube_wide.R |only R/cycle_shortcut.R | 39 R/distance_methods.R | 95 ++ R/find_best_random_combinations.R | 32 R/find_path_bfs.R | 43 - R/find_path_iterative.R | 144 ++- R/generate_walk.R |only R/get_reachable_states_light.R | 26 R/graph_metrics.R | 62 + R/kociemba4_internals.R |only R/path_utils.R | 65 + R/perm_group.R |only R/short_path_bfs.R | 44 - R/sparse_bfs.R | 33 R/state_store.R | 90 +- R/state_utils.R | 62 + README.md | 407 ++++++++++ build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/cube-4x4.R |only inst/doc/cube-4x4.Rmd |only inst/doc/cube-4x4.html |only inst/doc/neural-solvers.R |only inst/doc/neural-solvers.Rmd |only inst/doc/neural-solvers.html |only inst/doc/permutation-groups.R |only inst/doc/permutation-groups.Rmd |only inst/doc/permutation-groups.html |only inst/doc/rubiks-cube.R |only inst/doc/rubiks-cube.Rmd |only inst/doc/rubiks-cube.html |only inst/examples/bench_coord12_bfs.R |only inst/examples/bench_coord12_bfs.cpp |only inst/examples/bench_cube3_encoding.R |only inst/examples/bench_cube3_sizes.R |only inst/examples/bench_full_face_shorten.R |only inst/examples/bench_goals2_coverage.R |only inst/examples/bench_handover.R |only inst/examples/bench_kociemba4.R |only inst/examples/bench_model_vs_schedule.R |only inst/examples/bench_orientation_cost.R |only inst/examples/bench_orientations.R |only inst/examples/bench_phase2_solutions.R |only inst/examples/bench_phase3_bonus.R |only inst/examples/bench_phase3_bonus2.R |only inst/examples/bench_phase3_branching.R |only inst/examples/bench_phase3_hash.R |only inst/examples/bench_phase3_prefill.R |only inst/examples/bench_phase3_prune_depth.R |only inst/examples/bench_phase3_saturation.R |only inst/examples/bench_phase3_select.R |only inst/examples/bench_phase3_true_distance.R |only inst/examples/bench_phase3_unbounded.R |only inst/examples/bench_phase3_width.R |only inst/examples/bench_prefilled_solve.R |only inst/examples/bench_reduce_budget.R |only inst/examples/bench_solve_scaling.R |only inst/examples/bench_where_time_goes.R |only inst/examples/build_phase_tables.R |only inst/examples/check_trainer_init.R |only inst/examples/demo_cube3_basic.R |only inst/examples/demo_cube3_cycles.R |only inst/examples/demo_cube3_path_iterative.R |only inst/examples/demo_cube3_solve.R |only inst/examples/demo_cube3_transformer.R |only inst/examples/demo_cube4_adi.R |only inst/examples/demo_cube4_branch5.R |only inst/examples/demo_cube4_branch_random.R |only inst/examples/demo_cube4_branch_tree.R |only inst/examples/demo_cube4_iterative_model.R |only inst/examples/demo_cube4_iterative_sweep.R |only inst/examples/demo_cube4_model.R |only inst/examples/demo_cube4_model_beam.R |only inst/examples/demo_cube4_model_cycles.R |only inst/examples/demo_cube4_model_deepen.R |only inst/examples/demo_cube4_model_depth.R |only inst/examples/demo_cube4_model_descent.R |only inst/examples/demo_cube4_model_variations.R |only inst/examples/demo_cube4_scout_branches.R |only inst/examples/demo_cube4_scout_moves.R |only inst/examples/demo_cube4_scout_resolve.R |only inst/examples/demo_cube4_solve.R |only inst/examples/demo_generate_walk.R |only inst/examples/diag_adi_failures.R |only inst/examples/diag_astar_profile.R |only inst/examples/diag_beam_loss.R |only inst/examples/diag_centre_coord.R |only inst/examples/diag_coord_candidates.R |only inst/examples/diag_cube3_q.R |only inst/examples/diag_encoding_cost.R |only inst/examples/diag_exact_centres.R |only inst/examples/diag_flat_vs_2d.R |only inst/examples/diag_goal_choice.R |only inst/examples/diag_goal_parity.R |only inst/examples/diag_handover_distance.R |only inst/examples/diag_hang_cube2.R |only inst/examples/diag_kociemba4_vs_solve4.R |only inst/examples/diag_layer_tables.R |only inst/examples/diag_model_pieces.R |only inst/examples/diag_orientation_equivalence.R |only inst/examples/diag_orientation_predictors.R |only inst/examples/diag_outer_only.R |only inst/examples/diag_pair_edges_stall.R |only inst/examples/diag_phase2_coord.R |only inst/examples/diag_phase2_short.R |only inst/examples/diag_phase3_ceiling.R |only inst/examples/diag_phase3_coord.R |only inst/examples/diag_phase3_from_scratch.R |only inst/examples/diag_phase3_parity.R |only inst/examples/diag_phase3_seeds.R |only inst/examples/diag_phase3_short.R |only inst/examples/diag_phase3_table.R |only inst/examples/diag_phase_generators.R |only inst/examples/diag_phase_handover_map.R |only inst/examples/diag_pll_bit_check.R |only inst/examples/diag_predict_overhead.R |only inst/examples/diag_reduced_nearby.R |only inst/examples/diag_score_batch.R |only inst/examples/diag_score_transfer.R |only inst/examples/diag_scramble_shape.R |only inst/examples/diag_scramble_vs_solve.R |only inst/examples/diag_short_path_lost.R |only inst/examples/diag_short_path_survey.R |only inst/examples/diag_stuck_seeds.R |only inst/examples/diag_trace_phase3.R |only inst/examples/diag_trace_phases.R |only inst/examples/kaggle_444_branch_notebook.R |only inst/examples/kaggle_444_cascade_notebook.R |only inst/examples/kaggle_444_kociemba_notebook.R |only inst/examples/kaggle_444_model_notebook.R |only inst/examples/kaggle_444_notebook.R |only inst/examples/predict_cube3_depth.R |only inst/examples/prof_cube4_kociemba.R |only inst/examples/profile_cube4_model.R |only inst/examples/test_cube3_transformer.R |only inst/examples/time_examples.R |only inst/examples/train_cube3_depth.R |only inst/examples/train_cube3_q.R |only inst/examples/train_cube3_q_online.R |only inst/examples/train_cube3_transformer.R |only inst/examples/train_cube4_cnn.R |only man/bidirectional_bfs.Rd | 34 man/cayley_bfs_full.Rd | 28 man/cayley_graph_diameter.Rd | 19 man/create_state_store.Rd | 19 man/cube_adi.Rd |only man/cube_adi_astar.Rd |only man/cube_adi_children.Rd |only man/cube_adi_encode_pieces.Rd |only man/cube_adi_keys.Rd |only man/cube_adi_load.Rd |only man/cube_adi_model.Rd |only man/cube_adi_save.Rd |only man/cube_adi_scramble.Rd |only man/cube_adi_solve.Rd |only man/cube_adi_targets.Rd |only man/cube_adi_train.Rd |only man/cube_alg_table.Rd |only man/cube_apply_word.Rd |only man/cube_build_lslice.Rd |only man/cube_central_moves.Rd |only man/cube_centre_counts.Rd |only man/cube_centre_cycles.Rd |only man/cube_centre_map_family.Rd |only man/cube_centre_positions.Rd |only man/cube_centre_shots.Rd |only man/cube_centre_structure.Rd |only man/cube_colours.Rd |only man/cube_edge_algs.Rd |only man/cube_edge_counts.Rd |only man/cube_edge_map.Rd |only man/cube_edge_map_family.Rd |only man/cube_edge_structure.Rd |only man/cube_empty_u_slice.Rd |only man/cube_expand_alg.Rd |only man/cube_expand_move.Rd |only man/cube_group.Rd |only man/cube_identity.Rd |only man/cube_is_colour_solved.Rd |only man/cube_is_reduced.Rd |only man/cube_kociemba.Rd |only man/cube_kociemba4.Rd |only man/cube_kociemba4_reduce.Rd |only man/cube_kociemba4_report.Rd |only man/cube_kociemba_init.Rd |only man/cube_kociemba_report.Rd |only man/cube_layer_move.Rd |only man/cube_lslice_cells.Rd |only man/cube_move_names.Rd |only man/cube_moves.Rd |only man/cube_nnn.Rd |only man/cube_orbits.Rd |only man/cube_orbits_family.Rd |only man/cube_pair_edges.Rd |only man/cube_piece_layout.Rd |only man/cube_pieces.Rd |only man/cube_pieces_home.Rd |only man/cube_predicates.Rd |only man/cube_progress.Rd |only man/cube_read_state.Rd |only man/cube_reduce_best.Rd |only man/cube_reduce_cpp.Rd |only man/cube_santa.Rd |only man/cube_santa_group.Rd |only man/cube_santa_move_names.Rd |only man/cube_santa_moves.Rd |only man/cube_santa_path.Rd |only man/cube_santa_perm.Rd |only man/cube_santa_state.Rd |only man/cube_slice_cells_cpp.Rd |only man/cube_slice_map.Rd |only man/cube_solve4.Rd |only man/cube_solve4_cascade.Rd |only man/cube_solve_centres.Rd |only man/cube_solve_cfop.Rd |only man/cube_solve_lbl.Rd |only man/cube_solve_m2.Rd |only man/cube_solve_old_pochmann.Rd |only man/cube_wide_turn.Rd |only man/cube_word_order.Rd |only man/cycle_shortcut.Rd | 17 man/distance_methods.Rd | 8 man/find_best_match_cube4_model.Rd |only man/find_best_random_combinations.Rd | 23 man/find_path_bfs.Rd | 9 man/find_path_iterative.Rd | 26 man/generate_state.Rd | 45 - man/generate_walk.Rd |only man/generate_walk_cpp.Rd |only man/get_reachable_states_light.Rd | 24 man/group_apply.Rd |only man/group_compose.Rd |only man/group_identity.Rd |only man/group_inverse_seq.Rd |only man/group_move_index.Rd |only man/group_moves.Rd |only man/group_order.Rd |only man/group_parse_word.Rd |only man/invert_path.Rd | 17 man/is_perm_group.Rd |only man/kociemba4_phases.Rd |only man/perm_group.Rd |only man/perm_group_intro.Rd |only man/print.perm_group.Rd |only man/short_path_bfs.Rd | 38 man/sparse_bfs.Rd | 38 man/store_analyze_combos.Rd | 28 man/store_group.Rd |only man/topspin_group.Rd |only man/validate_and_simplify_path.Rd | 26 src/RcppExports.cpp | 1071 +++++++++++++++++++++++++-- src/centre_table.h |only src/coords.cpp | 71 + src/cube_adi.cpp |only src/cube_algs.h |only src/cube_centres.h |only src/cube_centres5.h |only src/cube_centres_r.cpp |only src/cube_check_r.cpp |only src/cube_cubie.h |only src/cube_edges.h |only src/cube_nnn.h |only src/cube_nnn_r.cpp |only src/cube_orbits.h |only src/cube_orbits_r.cpp |only src/cube_reduce.h |only src/cube_search.h |only src/cube_solve.h |only src/cube_solve_cfop.h |only src/cube_solve_lbl.h |only src/cube_solve_m2.h |only src/cube_solve_old_pochmann.h |only src/cube_solve_r.cpp |only src/cycle_shortcut.cpp | 48 - src/generate_walk.cpp |only src/graph_metrics.cpp | 92 +- src/kociemba3.h |only src/kociemba4.h |only src/kociemba_core.h |only src/kociemba_r.cpp |only src/perm_group.h |only src/perm_group_r.cpp |only src/short_path_bfs.cpp | 49 - src/sparse_bfs.cpp | 29 src/state_store.cpp | 109 +- src/state_store.h | 29 tests/testthat.R | 31 tests/testthat/test-cube-adi.R |only tests/testthat/test-cube-algs.R |only tests/testthat/test-cube-basics.R |only tests/testthat/test-cube-build-centres.R |only tests/testthat/test-cube-centre-map.R |only tests/testthat/test-cube-centres.R |only tests/testthat/test-cube-colour.R |only tests/testthat/test-cube-edge-map.R |only tests/testthat/test-cube-kociemba.R |only tests/testthat/test-cube-kociemba4-gens2.R |only tests/testthat/test-cube-kociemba4-gens3.R |only tests/testthat/test-cube-kociemba4-goals2.R |only tests/testthat/test-cube-kociemba4-goals3.R |only tests/testthat/test-cube-kociemba4-phases.R |only tests/testthat/test-cube-kociemba4.R |only tests/testthat/test-cube-nnn.R |only tests/testthat/test-cube-orbits.R |only tests/testthat/test-cube-piece-encoding.R |only tests/testthat/test-cube-rotations.R |only tests/testthat/test-cube-santa.R |only tests/testthat/test-cube-solve4.R |only tests/testthat/test-cube-speffz.R |only tests/testthat/test-cube-wide.R |only tests/testthat/test-generate-walk.R |only vignettes/cube-4x4.Rmd |only vignettes/neural-solvers.Rmd |only vignettes/permutation-groups.Rmd |only vignettes/rubiks-cube.Rmd |only 340 files changed, 3772 insertions(+), 498 deletions(-)
Title: Conformal Prediction for Spatially and Spatio-Temporally
Dependent Data
Description: Provides distribution-free, model-agnostic prediction
intervals for spatially and spatio-temporally dependent data using
localized conformal calibration. Implements locally weighted split
conformal prediction for geostatistical (point-referenced) data based on
spatial-distance kernels, and a neighbourhood-weighted conformal
procedure for areal (lattice) data based on graph adjacency structures.
Relaxes the standard exchangeability assumption using spatial proximity,
following the localized conformal framework of Mao, Martin and Reich
(2024) <doi:10.1080/01621459.2022.2147531>. Includes comprehensive
spatial diagnostic tools to audit empirical coverage, conditional
spatial strata, and boundary proximity effects.
Author: Ahmed Sattar Jabbar [aut, cre]
Maintainer: Ahmed Sattar Jabbar <ahmed.state.me@gmail.com>
Diff between spconform versions 0.1.1 dated 2026-09-24 and 0.1.2 dated 2026-10-19
spconform-0.1.1/spconform/inst/benchmarks |only spconform-0.1.1/spconform/inst/scripts/code.Rmd |only spconform-0.1.1/spconform/inst/scripts/comprehensive_jss_comparisons.R |only spconform-0.1.1/spconform/inst/scripts/drone_sensing_outputs/table_drone_monte_carlo_100splits.tex |only spconform-0.1.1/spconform/inst/scripts/full_reproducible_script.R |only spconform-0.1.1/spconform/inst/scripts/satellite_sensing_outputs/table_satellite_latex.tex |only spconform-0.1.1/spconform/inst/scripts/sdss_conformal_simulation_study.R |only spconform-0.1.1/spconform/inst/scripts/tables_jss_manuscript.tex |only spconform-0.1.1/spconform/inst/scripts/verify_v010_execution_time.R |only spconform-0.1.2/spconform/DESCRIPTION | 10 spconform-0.1.2/spconform/MD5 | 106 spconform-0.1.2/spconform/NAMESPACE | 81 spconform-0.1.2/spconform/NEWS.md | 14 spconform-0.1.2/spconform/R/diagnose.R | 1087 ++++++---- spconform-0.1.2/spconform/R/methods.R | 76 spconform-0.1.2/spconform/R/scp_areal.R | 12 spconform-0.1.2/spconform/R/scp_geostatistical.R | 51 spconform-0.1.2/spconform/R/spconform-package.R | 36 spconform-0.1.2/spconform/R/utils.R | 7 spconform-0.1.2/spconform/README.md | 43 spconform-0.1.2/spconform/build/vignette.rds |binary spconform-0.1.2/spconform/inst/CITATION |only spconform-0.1.2/spconform/inst/doc/getting-help.R |only spconform-0.1.2/spconform/inst/doc/getting-help.Rmd | 413 +++ spconform-0.1.2/spconform/inst/doc/getting-help.html | 551 ++++- spconform-0.1.2/spconform/inst/doc/spconform-intro.Rmd | 374 +-- spconform-0.1.2/spconform/inst/doc/spconform-intro.html | 74 spconform-0.1.2/spconform/inst/scripts/baghdad_temperature_conformal_prediction.R | 246 +- spconform-0.1.2/spconform/inst/scripts/code.R | 86 spconform-0.1.2/spconform/inst/scripts/code.html | 283 +- spconform-0.1.2/spconform/inst/scripts/code.md | 804 ++++++- spconform-0.1.2/spconform/inst/scripts/figures |only spconform-0.1.2/spconform/inst/scripts/figures_html/areal_eval-1.png |only spconform-0.1.2/spconform/inst/scripts/figures_html/diagnostics-1.png |only spconform-0.1.2/spconform/inst/scripts/figures_html/fig2-1.png |only spconform-0.1.2/spconform/inst/scripts/figures_html/fig5-1.png |binary spconform-0.1.2/spconform/inst/scripts/figures_html/fig6-1.png |only spconform-0.1.2/spconform/inst/scripts/nc_sids_areal_study.R | 15 spconform-0.1.2/spconform/man/as.data.frame.spconform_diagnose.Rd |only spconform-0.1.2/spconform/man/boundary_diagnostics.Rd |only spconform-0.1.2/spconform/man/coverage_report.Rd | 19 spconform-0.1.2/spconform/man/diagnose.Rd | 44 spconform-0.1.2/spconform/man/plot.spconform_boundary.Rd |only spconform-0.1.2/spconform/man/plot.spconform_diagnose.Rd | 42 spconform-0.1.2/spconform/man/plot.spconform_strata.Rd |only spconform-0.1.2/spconform/man/predict.spconform.Rd | 52 spconform-0.1.2/spconform/man/print.spconform_boundary.Rd |only spconform-0.1.2/spconform/man/print.spconform_diagnose.Rd |only spconform-0.1.2/spconform/man/print.spconform_moran.Rd |only spconform-0.1.2/spconform/man/print.spconform_strata.Rd |only spconform-0.1.2/spconform/man/residuals.spconform.Rd | 52 spconform-0.1.2/spconform/man/scp_areal.Rd | 8 spconform-0.1.2/spconform/man/scp_geostatistical.Rd | 12 spconform-0.1.2/spconform/man/spatial_kernel_weights.Rd | 7 spconform-0.1.2/spconform/man/spatial_moran.Rd |only spconform-0.1.2/spconform/man/spconform-package.Rd | 29 spconform-0.1.2/spconform/man/strata_diagnostics.Rd |only spconform-0.1.2/spconform/tests/testthat.R | 8 spconform-0.1.2/spconform/tests/testthat/test-scp.R | 121 + spconform-0.1.2/spconform/vignettes/getting-help.Rmd | 413 +++ spconform-0.1.2/spconform/vignettes/spconform-intro.Rmd | 374 +-- 61 files changed, 3981 insertions(+), 1569 deletions(-)
Title: Access the Our World in Data Chart API
Description: Retrieve data from the Our World in Data (OWID) Chart API
<https://docs.owid.io/projects/etl/api/>. OWID provides public access to
more than 4,000 charts focusing on global problems such as poverty,
disease, hunger, climate change, war, existential risks, and inequality.
Author: Christoph Scheuch [aut, cre, cph]
Maintainer: Christoph Scheuch <christoph@tidy-intelligence.com>
Diff between owidapi versions 0.1.2 dated 2026-07-27 and 0.1.3 dated 2026-10-19
DESCRIPTION | 14 +++++----- MD5 | 10 +++---- NEWS.md | 8 +++++- R/perform_request.R | 2 - README.md | 64 ++++++++++++++++++++++++------------------------- man/owidapi-package.Rd | 11 ++++++-- 6 files changed, 60 insertions(+), 49 deletions(-)
Title: Seamless Access to OECD Official Development Assistance (ODA)
Data
Description: Access and Analyze Official Development Assistance (ODA) data using
the OECD API <https://gitlab.algobank.oecd.org/public-documentation/dotstat-migration/-/raw/main/OECD_Data_API_documentation.pdf>.
ODA data includes sovereign-level aid data such as key aggregates (DAC1), geographical
distributions (DAC2A), project-level data (CRS), and multilateral contributions (Multisystem).
Author: Christoph Scheuch [aut, cre, cph]
Maintainer: Christoph Scheuch <christoph@tidy-intelligence.com>
Diff between oecdoda versions 0.1.0 dated 2025-07-25 and 0.2.0 dated 2026-10-19
oecdoda-0.1.0/oecdoda/tests/testthat/test-oda_get_dac2.R |only oecdoda-0.2.0/oecdoda/DESCRIPTION | 14 +-- oecdoda-0.2.0/oecdoda/MD5 | 40 ++++----- oecdoda-0.2.0/oecdoda/NEWS.md | 16 +++ oecdoda-0.2.0/oecdoda/R/oda_get_crs.R | 16 ++- oecdoda-0.2.0/oecdoda/R/oda_get_dac1.R | 12 ++ oecdoda-0.2.0/oecdoda/R/oda_get_dac2a.R | 12 ++ oecdoda-0.2.0/oecdoda/R/oda_get_multisystem.R | 10 +- oecdoda-0.2.0/oecdoda/R/oda_list_filters.R | 6 - oecdoda-0.2.0/oecdoda/R/perform_request.R | 35 ++++++- oecdoda-0.2.0/oecdoda/R/zzz.R | 2 oecdoda-0.2.0/oecdoda/README.md | 37 ++++---- oecdoda-0.2.0/oecdoda/man/oda_get_crs.Rd | 10 +- oecdoda-0.2.0/oecdoda/man/oda_get_dac1.Rd | 10 +- oecdoda-0.2.0/oecdoda/man/oda_get_dac2a.Rd | 10 +- oecdoda-0.2.0/oecdoda/man/oda_get_multisystem.Rd | 10 +- oecdoda-0.2.0/oecdoda/man/oecdoda-package.Rd | 11 +- oecdoda-0.2.0/oecdoda/tests/testthat/test-oda_get_crs.R | 44 ++++++++-- oecdoda-0.2.0/oecdoda/tests/testthat/test-oda_get_dac1.R | 44 ++++++++-- oecdoda-0.2.0/oecdoda/tests/testthat/test-oda_get_dac2a.R |only oecdoda-0.2.0/oecdoda/tests/testthat/test-oda_get_multisystem.R | 26 +++++ oecdoda-0.2.0/oecdoda/tests/testthat/test-perform_request.R | 41 ++++++++- 22 files changed, 308 insertions(+), 98 deletions(-)
Title: American Psychological Association Thesis Templates for R
Markdown
Description: Facilitates writing computationally reproducible student theses in PDF format that conform to the American Psychological Association (APA) manuscript guidelines (6th Edition). The package currently provides two R Markdown templates for homework and theses at the Psychology Department of the University of Cologne. The package builds on the package 'papaja' but is tailored to the requirements of student theses and omits features for simplicity.
Author: Frederik Aust [aut, cre]
Maintainer: Frederik Aust <frederik.aust@uni-koeln.de>
Diff between apathe versions 0.1.0 dated 2025-10-10 and 0.1.1 dated 2026-10-19
DESCRIPTION | 14 ++-- LICENSE | 4 - MD5 | 15 ++-- R/imports.R |only R/uoc_psych_thesis_formats.R | 14 ++-- README.md | 8 +- inst/NEWS.md | 10 ++- inst/rmarkdown/templates/uoc-psych-homework/skeleton/skeleton.Rmd | 6 + inst/rmarkdown/templates/uoc-psych-thesis/skeleton/skeleton.Rmd | 31 +++++++++- 9 files changed, 73 insertions(+), 29 deletions(-)
Title: Portfolio Management with R
Description: Tools for the practical management of financial
portfolios: backtesting investment and trading strategies,
computing profit/loss and returns, analysing trades,
handling lists of transactions, reporting, and more. The
package provides a small set of reliable, efficient and
convenient tools for processing and analysing
trade/portfolio data. The manual provides all the details;
it is available from
<https://enricoschumann.net/R/packages/PMwR/manual/PMwR.html>.
Examples and descriptions of new features are provided at
<https://enricoschumann.net/notes/PMwR/>.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between PMwR versions 1.2-0 dated 2025-12-17 and 1.3-0 dated 2026-10-19
DESCRIPTION | 12 MD5 | 83 +++-- NEWS | 27 + R/btest.R | 2 R/pl.R | 107 +++++-- R/position.R | 24 + R/rc.R | 321 +++++++++++++++++----- R/rebalance.R | 4 R/streaks.R | 198 +++++++------ README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/An_overview_of_PMwR.R | 12 inst/doc/An_overview_of_PMwR.Rnw | 3 inst/doc/An_overview_of_PMwR.pdf |binary inst/doc/Computing_returns.R | 2 inst/doc/Computing_returns.pdf |binary inst/doc/Drawdowns_streaks.R | 2 inst/doc/Drawdowns_streaks.pdf |binary inst/doc/FinTeX.R | 2 inst/doc/FinTeX.Rnw | 6 inst/doc/FinTeX.pdf |binary inst/doc/PMwR.bib |only inst/doc/pl_open_positions.R | 2 inst/doc/pl_open_positions.Rnw | 8 inst/doc/pl_open_positions.pdf |binary inst/doc/q32.R | 2 inst/doc/q32.pdf |binary inst/doc/rc_return_constribution.R |only inst/doc/rc_return_constribution.Rnw |only inst/doc/rc_return_constribution.pdf |only inst/tinytest/test_btest_position.R | 43 ++ inst/tinytest/test_pl.R | 31 ++ inst/tinytest/test_pl_vprice.R | 21 - inst/tinytest/test_rc.R | 495 +++++++++++++++++++++++++++++++++- inst/tinytest/test_rc_btest.R |only inst/tinytest/test_streaks.R | 10 man/pl.Rd | 3 man/position.Rd | 23 + man/rc.Rd | 83 ++++- man/rebalance.Rd | 3 vignettes/.install_extras |only vignettes/An_overview_of_PMwR.Rnw | 3 vignettes/FinTeX.Rnw | 6 vignettes/PMwR.bib |only vignettes/pl_open_positions.Rnw | 8 vignettes/rc_return_constribution.Rnw |only 47 files changed, 1226 insertions(+), 322 deletions(-)
Title: Automated Eye Tracking Data Quality Determination for
Screen-Based Eye Trackers
Description: Compute common data quality metrics for accuracy, precision and data loss
for screen-based eye trackers. The package supports gaze input in screen pixels or
degrees and reports angular measures in degrees where appropriate. If you use this
package, please cite Niehorster, D.C., Nyström, M., Hessels, R.S., Benjamins, J.S.,
Andersson, R., and Hooge, I.T.C. (2026). The fundamentals of eye tracking, Part 7:
Determining data quality. Behavior Research Methods. <doi:10.3758/s13428-026-03039-4>.
Author: Diederick Niehorster [aut, cre, cph]
Maintainer: Diederick Niehorster <diederick_c.niehorster@humlab.lu.se>
Diff between ETDQualitizer versions 1.1.0 dated 2026-06-08 and 1.2.0 dated 2026-10-19
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NAMESPACE | 1 + R/ETDQualitizer.R | 18 +++++++++++++++++- man/frechet_median_on_sphere.Rd |only tests/testthat/test-data_quality_metrics.R | 5 +++++ 6 files changed, 31 insertions(+), 8 deletions(-)
Title: Non-Compartmental Analysis for Campsis Simulation Platform
Description: A flexible and user-friendly non-compartmental analysis (NCA)
toolkit designed to work seamlessly with simulated pharmacokinetic
data generated using the 'campsis' ecosystem. The package provides a
comprehensive framework to compute standard and custom NCA metrics,
including exposure (AUC), peak/trough concentrations, half-life and
time-above/below thresholds, with support for configurable time
windows and summary statistics. 'campsisnca' integrates tightly with
'campsis' and 'campsismod', enabling streamlined workflows from
simulation to analysis. In addition, the package provides a JSON-based
interface to define NCA analyses, metrics and options using formal
schemas, allowing analyses to be created, validated and executed
outside of R and facilitating reproducibility, automation and system
integration. The package also includes utilities for generating
formatted summary tables and exporting results in multiple formats
suitable for reporting. Trapezoidal rule implementation for AUC
ca [...truncated...]
Author: Nicolas Luyckx [aut, cre],
Calvagone [cph]
Maintainer: Nicolas Luyckx <nicolas.luyckx@lynxsoft.be>
Diff between campsisnca versions 1.7.2 dated 2026-09-24 and 1.7.3 dated 2026-10-19
DESCRIPTION | 10 +++++----- LICENSE.note | 2 +- MD5 | 8 ++++---- NEWS.md | 3 +++ README.md | 46 +++++++++++++++++++++++++++++++--------------- 5 files changed, 44 insertions(+), 25 deletions(-)
Title: 'A5' Discrete Global Grid System
Description: Bindings for the "A5 geospatial index"
<https://a5geo.org/>. 'A5' partitions the Earth's surface into
pentagonal cells across 31 resolution levels using an equal-area
projection onto a dodecahedron. Provides functions for indexing
coordinates to cells, traversing the cell hierarchy, computing cell
boundaries, and compacting/uncompacting cell sets. Powered by the
'A5' 'Rust' crate via 'extendr'.
Author: Hugh Graham [aut, cre],
belian.earth [cph],
Felix Palmer [ctb, cph] ,
Authors of the dependency Rust crates [cph]
Maintainer: Hugh Graham <hugh@belian.earth>
Diff between a5R versions 0.6.0 dated 2026-09-08 and 1.0.0 dated 2026-10-19
a5R-0.6.0/a5R/inst/hex |only a5R-0.6.0/a5R/man/a5_cell_area.Rd |only a5R-0.6.0/a5R/man/a5_cell_edge_length_avg.Rd |only a5R-0.6.0/a5R/man/a5_cell_to_children.Rd |only a5R-0.6.0/a5R/man/a5_cell_to_lonlat.Rd |only a5R-0.6.0/a5R/man/a5_cell_to_parent.Rd |only a5R-0.6.0/a5R/man/a5_compact.Rd |only a5R-0.6.0/a5R/man/a5_get_num_cells.Rd |only a5R-0.6.0/a5R/man/a5_get_num_children.Rd |only a5R-0.6.0/a5R/man/a5_lonlat_to_cell.Rd |only a5R-0.6.0/a5R/man/a5_uncompact.Rd |only a5R-0.6.0/a5R/man/figures/README-grid-plot-1.png |only a5R-0.6.0/a5R/man/figures/README-hierarchy-plot-1.png |only a5R-1.0.0/a5R/DESCRIPTION | 26 a5R-1.0.0/a5R/LICENSE.note |only a5R-1.0.0/a5R/MD5 | 234 ++++---- a5R-1.0.0/a5R/NAMESPACE | 55 + a5R-1.0.0/a5R/NEWS.md | 285 +++++++++ a5R-1.0.0/a5R/R/a5-info.R |only a5R-1.0.0/a5R/R/a5R-package.R | 32 - a5R-1.0.0/a5R/R/arrow.R | 196 +++++- a5R-1.0.0/a5R/R/boundary.R | 106 +++ a5R-1.0.0/a5R/R/c-api.R |only a5R-1.0.0/a5R/R/cell-base.R |only a5R-1.0.0/a5R/R/cell-list.R |only a5R-1.0.0/a5R/R/cell.R | 140 ++-- a5R-1.0.0/a5R/R/compact.R | 110 ++- a5R-1.0.0/a5R/R/covering-ops.R |only a5R-1.0.0/a5R/R/covering.R |only a5R-1.0.0/a5R/R/distance.R | 21 a5R-1.0.0/a5R/R/errors.R |only a5R-1.0.0/a5R/R/extendr-wrappers.R | 353 ++++++++++-- a5R-1.0.0/a5R/R/hierarchy.R | 287 ++++++++- a5R-1.0.0/a5R/R/indexing.R | 134 +++- a5R-1.0.0/a5R/R/info.R | 149 +---- a5R-1.0.0/a5R/R/migrate.R |only a5R-1.0.0/a5R/R/regions.R | 438 +++++++++++---- a5R-1.0.0/a5R/R/threads.R | 85 ++ a5R-1.0.0/a5R/R/traversal.R | 93 ++- a5R-1.0.0/a5R/R/utils.R | 187 ++++++ a5R-1.0.0/a5R/R/validity.R |only a5R-1.0.0/a5R/R/zzz.R | 4 a5R-1.0.0/a5R/README.md | 73 +- a5R-1.0.0/a5R/build/vignette.rds |binary a5R-1.0.0/a5R/inst/WORDLIST |only a5R-1.0.0/a5R/inst/doc/a5R.R | 92 +-- a5R-1.0.0/a5R/inst/doc/a5R.Rmd | 180 +++--- a5R-1.0.0/a5R/inst/doc/a5R.html | 279 +++++---- a5R-1.0.0/a5R/inst/doc/arrow-parquet.R | 63 +- a5R-1.0.0/a5R/inst/doc/arrow-parquet.Rmd | 161 +++-- a5R-1.0.0/a5R/inst/doc/arrow-parquet.html | 309 +++++----- a5R-1.0.0/a5R/inst/doc/coverings.R |only a5R-1.0.0/a5R/inst/doc/coverings.Rmd |only a5R-1.0.0/a5R/inst/doc/coverings.html |only a5R-1.0.0/a5R/inst/doc/internal-cell-representation.R | 32 - a5R-1.0.0/a5R/inst/doc/internal-cell-representation.Rmd | 149 ++++- a5R-1.0.0/a5R/inst/doc/internal-cell-representation.html | 246 ++++++-- a5R-1.0.0/a5R/inst/doc/multithreading.R | 39 - a5R-1.0.0/a5R/inst/doc/multithreading.Rmd | 137 ++-- a5R-1.0.0/a5R/inst/doc/multithreading.html | 195 ++++-- a5R-1.0.0/a5R/inst/doc/spatial-hierarchy.R |only a5R-1.0.0/a5R/inst/doc/spatial-hierarchy.Rmd |only a5R-1.0.0/a5R/inst/doc/spatial-hierarchy.html |only a5R-1.0.0/a5R/inst/doc/traversal-and-distance.R | 36 - a5R-1.0.0/a5R/inst/doc/traversal-and-distance.Rmd | 66 -- a5R-1.0.0/a5R/inst/doc/traversal-and-distance.html | 115 +-- a5R-1.0.0/a5R/inst/include |only a5R-1.0.0/a5R/man/a5R-package.Rd | 38 + a5R-1.0.0/a5R/man/a5_bbox.Rd |only a5R-1.0.0/a5R/man/a5_c_api.Rd |only a5R-1.0.0/a5R/man/a5_cell.Rd | 25 a5R-1.0.0/a5R/man/a5_cell_child.Rd |only a5R-1.0.0/a5R/man/a5_cell_children_range.Rd |only a5R-1.0.0/a5R/man/a5_cell_from_arrow.Rd | 10 a5R-1.0.0/a5R/man/a5_cell_list.Rd |only a5R-1.0.0/a5R/man/a5_cell_to_boundary.Rd | 23 a5R-1.0.0/a5R/man/a5_cell_to_boundary_xy.Rd |only a5R-1.0.0/a5R/man/a5_compaction.Rd |only a5R-1.0.0/a5R/man/a5_coordinates.Rd |only a5R-1.0.0/a5R/man/a5_covering.Rd |only a5R-1.0.0/a5R/man/a5_covering_from_arrow.Rd |only a5R-1.0.0/a5R/man/a5_covering_measures.Rd |only a5R-1.0.0/a5R/man/a5_covering_predicates.Rd |only a5R-1.0.0/a5R/man/a5_covering_stored.Rd |only a5R-1.0.0/a5R/man/a5_covering_to_supercells.Rd |only a5R-1.0.0/a5R/man/a5_errors.Rd |only a5R-1.0.0/a5R/man/a5_grid_disk.Rd | 32 - a5R-1.0.0/a5R/man/a5_hierarchy.Rd |only a5R-1.0.0/a5R/man/a5_info.Rd |only a5R-1.0.0/a5R/man/a5_is_valid.Rd |only a5R-1.0.0/a5R/man/a5_line_string_to_cells.Rd |only a5R-1.0.0/a5R/man/a5_linestring_to_cells.Rd | 39 - a5R-1.0.0/a5R/man/a5_migrate.Rd |only a5R-1.0.0/a5R/man/a5_polygon_to_cells.Rd | 80 ++ a5R-1.0.0/a5R/man/a5_resolution_stats.Rd |only a5R-1.0.0/a5R/man/a5_set_operations.Rd |only a5R-1.0.0/a5R/man/a5_set_threads.Rd |only a5R-1.0.0/a5R/man/a5_spatial_hierarchy.Rd |only a5R-1.0.0/a5R/man/a5_spherical_cap.Rd | 25 a5R-1.0.0/a5R/man/a5_threads.Rd | 55 + a5R-1.0.0/a5R/man/a5_to_arrow_table.Rd |only a5R-1.0.0/a5R/man/figures/README-nc-distance-1.png |only a5R-1.0.0/a5R/src/Makevars.in | 2 a5R-1.0.0/a5R/src/Makevars.win.in | 2 a5R-1.0.0/a5R/src/api.c |only a5R-1.0.0/a5R/src/entrypoint.c | 2 a5R-1.0.0/a5R/src/rust/Cargo.lock | 42 + a5R-1.0.0/a5R/src/rust/Cargo.toml | 6 a5R-1.0.0/a5R/src/rust/build.rs |only a5R-1.0.0/a5R/src/rust/src/arrow_ffi.rs |only a5R-1.0.0/a5R/src/rust/src/bbox.rs |only a5R-1.0.0/a5R/src/rust/src/boundary.rs | 192 +++++- a5R-1.0.0/a5R/src/rust/src/cell_info.rs | 50 + a5R-1.0.0/a5R/src/rust/src/cell_raw.rs | 430 ++++++++++---- a5R-1.0.0/a5R/src/rust/src/covering.rs |only a5R-1.0.0/a5R/src/rust/src/distance.rs | 70 +- a5R-1.0.0/a5R/src/rust/src/hierarchy.rs | 373 +++++++++++- a5R-1.0.0/a5R/src/rust/src/indexing.rs | 116 +-- a5R-1.0.0/a5R/src/rust/src/lib.rs | 11 a5R-1.0.0/a5R/src/rust/src/regions.rs | 276 +++------ a5R-1.0.0/a5R/src/rust/src/ring_check.rs |only a5R-1.0.0/a5R/src/rust/src/threading.rs | 81 ++ a5R-1.0.0/a5R/src/rust/src/traversal.rs | 80 +- a5R-1.0.0/a5R/src/rust/vendor.tar.xz |binary a5R-1.0.0/a5R/tests/testthat/_snaps/covering.md |only a5R-1.0.0/a5R/tests/testthat/fixtures |only a5R-1.0.0/a5R/tests/testthat/test-a5-info.R |only a5R-1.0.0/a5R/tests/testthat/test-arrow.R | 84 ++ a5R-1.0.0/a5R/tests/testthat/test-base-compat.R |only a5R-1.0.0/a5R/tests/testthat/test-bbox.R |only a5R-1.0.0/a5R/tests/testthat/test-boundary.R | 104 +++ a5R-1.0.0/a5R/tests/testthat/test-c-api.R |only a5R-1.0.0/a5R/tests/testthat/test-cell.R | 73 +- a5R-1.0.0/a5R/tests/testthat/test-compact.R | 100 ++- a5R-1.0.0/a5R/tests/testthat/test-covering-ops.R |only a5R-1.0.0/a5R/tests/testthat/test-covering-supercells.R |only a5R-1.0.0/a5R/tests/testthat/test-covering.R |only a5R-1.0.0/a5R/tests/testthat/test-descendants.R |only a5R-1.0.0/a5R/tests/testthat/test-distance.R | 71 +- a5R-1.0.0/a5R/tests/testthat/test-errors.R |only a5R-1.0.0/a5R/tests/testthat/test-hierarchy.R | 33 + a5R-1.0.0/a5R/tests/testthat/test-indexing.R | 15 a5R-1.0.0/a5R/tests/testthat/test-info.R | 5 a5R-1.0.0/a5R/tests/testthat/test-migrate.R |only a5R-1.0.0/a5R/tests/testthat/test-overhead.R |only a5R-1.0.0/a5R/tests/testthat/test-regions.R | 367 +++++++++--- a5R-1.0.0/a5R/tests/testthat/test-simplify.R |only a5R-1.0.0/a5R/tests/testthat/test-subcell.R |only a5R-1.0.0/a5R/tests/testthat/test-threads.R | 124 +++- a5R-1.0.0/a5R/tests/testthat/test-traversal.R | 117 +++- a5R-1.0.0/a5R/tests/testthat/test-validity.R |only a5R-1.0.0/a5R/vignettes/a5R.Rmd | 180 +++--- a5R-1.0.0/a5R/vignettes/arrow-parquet.Rmd | 161 +++-- a5R-1.0.0/a5R/vignettes/coverings.Rmd |only a5R-1.0.0/a5R/vignettes/internal-cell-representation.Rmd | 149 ++++- a5R-1.0.0/a5R/vignettes/multithreading.Rmd | 137 ++-- a5R-1.0.0/a5R/vignettes/spatial-hierarchy.Rmd |only a5R-1.0.0/a5R/vignettes/traversal-and-distance.Rmd | 66 -- 158 files changed, 6415 insertions(+), 2538 deletions(-)
Title: Single-Cell Network Propensity Matching
Description: Estimates and compares heterogeneous gene conditional-dependence
networks from single-cell expression data. A latent Gaussian mixture and
probit observation mechanism represent cellular heterogeneity and zero
observations. Protein interaction information supplies edge-specific prior
weights, while network propensity matching links cell clusters across
conditions and guides adaptation. Staged inference fixes correspondence after adaptation,
disables adaptation feedback, and jointly models matched network edges with
a four-state spike-and-slab prior for posterior group and directional
differential edge selection. Functions assess balance,
record criterion diagnostics, and visualize within-condition and
differential networks.
Author: Tao Liu [aut, cre]
Maintainer: Tao Liu <25210690190@m.fudan.edu.cn>
Diff between scNPM versions 1.0.6 dated 2026-10-14 and 1.1.0 dated 2026-10-19
DESCRIPTION | 15 - MD5 | 46 ++- NEWS.md | 55 ++++ R/RcppExports.R | 8 R/differential_fdr.R | 300 ++++++++++++------------- R/group_fdr.R | 4 R/pairwise_matching.R |only R/run_scNPM.R | 159 ++++++++++--- R/sampler_progress.R |only R/zzz.R | 17 + README.md | 147 +++++++++--- inst/algorithm.md | 117 ++++++++- inst/examples/amd_workflow.R | 21 + man/run_scNPM.Rd | 108 +++++++-- man/scNPM-package.Rd | 17 + man/select_differential_edges.Rd | 2 man/select_group_edges.Rd | 2 src/RcppExports.cpp | 30 ++ src/freeze_consensus.h |only src/function_real.cpp | 202 +++++++++++++++- src/paired_prior.h |only tests/testthat/helper-threads.R |only tests/testthat/test-group-bfdr.R | 2 tests/testthat/test-paired-prior.R |only tests/testthat/test-pairwise-freeze-progress.R |only tests/testthat/test-pairwise-solver-fallback.R |only tests/testthat/test-reference-covariates.R | 4 tests/testthat/test-staged-fdr.R | 13 - 28 files changed, 944 insertions(+), 325 deletions(-)
Title: Direction-Aware Sufficient Condition Analysis
Description: Tests whether a high or low level of a condition is enough to
guarantee a high or low level of an outcome. Such a claim predicts that one
corner of the condition-outcome scatter plot is empty of observations. The
package estimates the boundary of that empty corner, its size as a share of
the scope (the effect size), a permutation test against random pairing, and
a threshold table giving the condition level that guarantees each outcome
level, in actual units, percentages, percentiles or standard deviations.
Each of the four directions (high or low condition, high or low outcome) is
stated as a claim and mapped to its empty corner. Because a condition can
rule out low outcomes while barely moving the average, results can be set
beside ordinary least-squares and median regression slopes, showing whether
the data hold an average effect, a sufficiency effect or both. Also
provides plots, influential-case diagnostics, scope-sensitivity and
resampling checks, random-data generation and power [...truncated...]
Author: Young Chan [aut, cre]
Maintainer: Young Chan <youngchanresearcher@gmail.com>
Diff between SCAtools versions 0.5.1 dated 2026-10-13 and 0.5.2 dated 2026-10-19
DESCRIPTION | 8 MD5 | 68 +++---- NEWS.md | 121 ++++++++++-- R/SCAtools-package.R | 8 R/analysis.R | 24 +- R/compare.R | 13 - R/corners.R | 19 +- R/magnitude.R | 10 - R/plots.R | 64 ++++-- R/resample.R | 4 R/results.R | 319 ++++++++++++++++++++++++++++++---- R/scales.R | 14 - R/simulation.R | 23 +- README.md | 10 - inst/docs/README_zh-TW.md | 5 inst/docs/sufficiency-logic.md | 2 man/SCAtools-package.Rd | 8 man/sca.Rd | 8 man/sca_analysis.Rd | 8 man/sca_compare.Rd | 10 - man/sca_corner_map.Rd | 4 man/sca_magnitude.Rd | 2 man/sca_power.Rd | 9 man/sca_powerplot.Rd | 4 man/sca_reference.Rd | 2 man/sca_relationship.Rd | 2 man/sca_resample.Rd | 2 man/sca_scope_sensitivity.Rd | 2 man/sca_table.Rd | 71 ++++++- man/sca_test_plot.Rd | 6 tests/testthat/test-adjust-resample.R | 43 +++- tests/testthat/test-api-0-5-0.R | 2 tests/testthat/test-critical.R |only tests/testthat/test-floor.R |only tests/testthat/test-magnitude.R | 2 tests/testthat/test-refusals.R | 2 36 files changed, 688 insertions(+), 211 deletions(-)
Title: Dynamic Model Averaging with Grid Search
Description: Perform dynamic model averaging with grid search as in Dangl and Halling (2012) <doi:10.1016/j.jfineco.2012.04.003> using parallel computing.
Author: Leopoldo Catania [aut, cre] ,
Nima Nonejad [ctb]
Maintainer: Leopoldo Catania <leopoldo.catania@econ.au.dk>
Diff between eDMA versions 1.5-4 dated 2025-05-12 and 1.5-5 dated 2026-10-19
eDMA-1.5-4/eDMA/README.md |only eDMA-1.5-5/eDMA/ChangeLog | 4 eDMA-1.5-5/eDMA/DESCRIPTION | 6 eDMA-1.5-5/eDMA/MD5 | 56 +-- eDMA-1.5-5/eDMA/NAMESPACE | 31 - eDMA-1.5-5/eDMA/R/BackTest.R | 51 +-- eDMA-1.5-5/eDMA/R/ClassMethods.R | 569 ++++++++++------------------------- eDMA-1.5-5/eDMA/R/Estimate.R | 224 ++++++------- eDMA-1.5-5/eDMA/R/Figures.R | 121 ++++--- eDMA-1.5-5/eDMA/R/Lag.R | 31 - eDMA-1.5-5/eDMA/R/RcppExports.R | 12 eDMA-1.5-5/eDMA/R/Utils.R | 22 - eDMA-1.5-5/eDMA/build/partial.rdb |binary eDMA-1.5-5/eDMA/man/BacktestDMA.Rd | 82 ++--- eDMA-1.5-5/eDMA/man/DMA-class.Rd | 205 +++++++----- eDMA-1.5-5/eDMA/man/DMA.Rd | 228 ++++++++------ eDMA-1.5-5/eDMA/man/Lag.Rd | 80 ++-- eDMA-1.5-5/eDMA/man/PowerSet.Rd | 60 +-- eDMA-1.5-5/eDMA/man/SimulateDLM.Rd | 126 +++---- eDMA-1.5-5/eDMA/man/eDMA-package.Rd | 2 eDMA-1.5-5/eDMA/src/Combinations.cpp | 155 ++------- eDMA-1.5-5/eDMA/src/Combinations.h | 8 eDMA-1.5-5/eDMA/src/Estimate.cpp | 369 ---------------------- eDMA-1.5-5/eDMA/src/Estimate.h | 2 eDMA-1.5-5/eDMA/src/EstimateCore.cpp |only eDMA-1.5-5/eDMA/src/EstimateCore.h |only eDMA-1.5-5/eDMA/src/Estimate_par.cpp | 392 ------------------------ eDMA-1.5-5/eDMA/src/RcppExports.cpp | 30 + eDMA-1.5-5/eDMA/src/Simulate.cpp | 54 +-- eDMA-1.5-5/eDMA/src/Utils.cpp | 15 eDMA-1.5-5/eDMA/tests |only 31 files changed, 985 insertions(+), 1950 deletions(-)
Title: Two- And Four-Parameter Beta Distributions and Classification
Accuracy and Consistency
Description: Functions for working with two- and four-parameter Beta
distributions and the closely related Beta-Binomial distribution, and for
estimating the accuracy and consistency of test-based classifications.
Includes d/p/q/r functions for four-parameter Beta distributions,
including parameterization by mean and variance; d/p/r functions for
Beta-Binomial distributions and for Lord's two-term approximation to the
compound Binomial distribution; moments of Beta, Binomial, Beta-Binomial,
and observed-score distributions; and method-of-moments fitting of two- and
four-parameter Beta true-score distributions. Classification accuracy and
consistency can be estimated with the 'Livingston and Lewis' approach
(Livingston and Lewis, 1995 <doi:10.1111/j.1745-3984.1995.tb00462.x>), the
'Hanson and Brennan' approach based on Lord's strong true-score theory
(Lord, 1965 <doi:10.1007/BF02289490>; Hanson, 1991
<https://files.eric.ed.gov/fulltext/ED344945.pdf>), and the multinomial
and compou [...truncated...]
Author: Haakon Eidem Haakstad [aut, cre]
Maintainer: Haakon Eidem Haakstad <h.e.haakstad@gmail.com>
Diff between betafunctions versions 1.9.0 dated 2024-03-06 and 2.0.0 dated 2026-10-19
DESCRIPTION | 62 - MD5 | 121 +-- NAMESPACE | 4 NEWS.md | 80 ++ R/betafunctions.R | 712 ++++++++---------- R/classification.R | 1547 ++++++++++++---------------------------- R/deprecated.R |only R/multinomial.R |only R/utils.R |only README.md | 72 + man/AUC.Rd | 3 man/Beta.2p.fit.Rd | 74 - man/Beta.tp.fit.Rd | 174 ++-- man/HB.CA.MC.Rd | 157 ++-- man/HB.CA.Rd | 161 ++-- man/HB.ROC.Rd | 168 ++-- man/HB.beta.tp.fit.Rd | 94 +- man/HB.tsm.Rd | 60 - man/LABMSU.Rd | 106 +- man/LL.CA.MC.Rd | 193 ++-- man/LL.CA.Rd | 217 ++--- man/Lords.k.Rd | 78 +- man/MC.out.tabular.Rd | 76 - man/MLA.Rd | 9 man/MLB.Rd | 9 man/MLM.Rd | 9 man/MN.CA.MC.Rd |only man/MN.CA.Rd |only man/MN.ROC.Rd |only man/R.ETL.Rd | 80 +- man/UABMSL.Rd | 106 +- man/afac.Rd | 56 - man/betabinomialmoments.Rd | 98 +- man/betafunctions-deprecated.Rd |only man/betamedian.Rd | 63 - man/betamode.Rd | 60 - man/binomialmoments.Rd | 74 - man/ccStats.Rd | 88 +- man/confmat.Rd | 82 +- man/dBeta.pBeta.Rd | 119 +-- man/dBeta.pBinom.Rd | 118 +-- man/dBeta.pGammaBinom.Rd | 123 +-- man/dBetaBinom.Rd | 70 - man/dBetaMS.Rd | 2 man/dBetacBinom.Rd | 69 - man/dGammaBinom.Rd | 79 +- man/dcBinom.Rd | 54 - man/dfac.Rd | 59 - man/gchoose.Rd | 58 - man/mdlfit.gfx.Rd | 128 +-- man/mdo.Rd | 95 +- man/observedmoments.Rd | 5 man/pBetaBinom.Rd | 74 - man/pGammaBinom.Rd | 75 + man/pcBinom.Rd | 61 - man/qBeta.4P.Rd | 5 man/qGammaBinom.Rd | 87 +- man/rBetaBinom.Rd | 68 - man/rBetaMS.Rd | 1 man/rBetacBinom.Rd | 74 - man/rGammaBinom.Rd | 67 - man/rcBinom.Rd | 66 - man/tsm.Rd | 94 +- tests |only 64 files changed, 3083 insertions(+), 3461 deletions(-)
Title: Optimal Density Estimation via Shimazaki-Shinomoto Method
Description: Implements the Shimazaki-Shinomoto method for optimizing the
bin width of histograms and the bandwidth of kernel density
estimators. The framework minimizes the expected Mean Integrated
Squared Error (MISE) and supports both 1D and 2D distributions, fixed
and locally adaptive estimators, bootstrap confidence intervals, and
'OpenMP'-accelerated 'C++' 'backends'. Ideally suited for
time-dependent rate estimation and identifying intrinsic data
structures. For more details see Shimazaki and Shinomoto (2007)
<doi:10.1162/neco.2007.19.6.1503> and Shimazaki and Shinomoto (2010)
<doi:10.1007/s10827-009-0180-4>.
Author: Daniil Popov [aut, cre]
Maintainer: Daniil Popov <popov.daniil@gmail.com>
Diff between sshist versions 0.2.4 dated 2026-07-17 and 0.2.6 dated 2026-10-19
DESCRIPTION | 33 ++- MD5 | 42 ++--- NEWS.md | 61 +++++++ R/RcppExports.R | 4 R/common.R | 13 + R/sshist.R | 2 R/sskernel.R | 90 ++++++++++ R/ssvkernel.R | 127 +-------------- README.md | 2 inst/WORDLIST | 13 - inst/doc/ggplot2_visualization.html | 10 - inst/doc/introduction.Rmd | 14 - inst/doc/introduction.html | 80 +++++---- man/sskernel2d.Rd | 4 man/ssvkernel.Rd | 5 src/RcppExports.cpp | 20 ++ src/sshist_algo.cpp | 298 ++++++++++++++++++++++++++++++++++++ tests/testthat/test-sskernel.R | 24 +- tests/testthat/test-sskernel_2d.R | 14 - tests/testthat/test-ssvkernel.R | 51 +++--- tests/testthat/test-ssvkernel_2d.R | 18 +- vignettes/introduction.Rmd | 14 - 22 files changed, 664 insertions(+), 275 deletions(-)
Title: Efficient MARCXML Processing and Record Querying
Description: Parses Machine-Readable Cataloging ('MARC 21') XML
<https://www.loc.gov/standards/marcxml/> into a canonical tidy long
representation while preserving leaders, control fields, data fields,
indicators, repeated fields, repeated subfields, and source order.
Provides in-memory reading, batched conversion to 'Parquet',
and reconstruction of MARCXML from canonical data.
Supports MARC-aware selection of complete records before materialisation
using native XML prefiltering, and after materialisation on canonical
tables and 'Arrow' datasets. Includes structural diagnostics for
in-memory and 'Arrow'-backed representations, optional recovery from
malformed MARC records, and local parallel processing.
Author: Lorenzo Isella [aut, cre]
Maintainer: Lorenzo Isella <lorenzo.isella@gmail.com>
Diff between marcxmlr versions 0.4.0 dated 2026-10-12 and 0.5.0 dated 2026-10-19
DESCRIPTION | 21 MD5 | 46 - NAMESPACE | 4 NEWS.md | 20 R/filtered-offset.R |only R/marc-query-screen.R |only R/marc-query.R |only R/marcxml-to-parquet.R | 34 R/read-marcxml.R | 37 README.md | 377 +++++++- build/vignette.rds |binary configure | 24 inst/doc/marcxmlr-workflow.R | 414 +++++++-- inst/doc/marcxmlr-workflow.Rmd | 721 +++++++++++----- inst/doc/marcxmlr-workflow.html | 1230 +++++++++++++++++++++-------- inst/extdata/gpo-cgp-part00-sample.xml |only man/marc_filter_records.Rd |only man/marc_has.Rd |only man/marcxml_to_parquet.Rd | 21 man/read_marcxml.Rd | 21 src/Makevars.win | 8 src/marcxml-expat-compat.h |only src/marcxml-native.c | 377 ++++++++ src/marcxml-offset-index.c |only src/marcxml-query-index.c |only tests/testthat/test-filtered-public-api.R |only tests/testthat/test-marc-query-ingestion.R |only tests/testthat/test-marc-query-public.R |only tests/testthat/test-read-marcxml.R | 9 vignettes/marcxmlr-workflow.Rmd | 721 +++++++++++----- 30 files changed, 3100 insertions(+), 985 deletions(-)
Title: Assessing the Integrity and Trustworthiness of Clinical Trials
Data
Description: The integrity package implements the IPD Integrity Tool, a
structured and transparent framework for evaluating the integrity of
individual participant data (IPD) from randomised trials (see Hunter et
al. (2024) <doi:10.1002/jrsm.1738> and <doi:10.1002/jrsm.1739>). It
supports users to identify potential issues, such as unusual data
patterns, implausible values, lack of expected correlations, date
violations, and inconsistencies. The package provides reproducible
workflows for screening, documenting and summarising integrity concerns,
and may be applied by evidence synthesists, editors, and others to
determine whether a randomised trial may be considered sufficiently
trustworthy to contribute to the evidence base that informs policy and
practice.
Author: Sol Libesman [aut, cre],
David Nguyen [aut],
Dario Strbenac [aut],
Jie Kang [aut],
Anna Lene Seidler [aut],
Kylie Hunter [aut]
Maintainer: Sol Libesman <sol.libesman@sydney.edu.au>
Diff between integrity versions 1.0.1 dated 2026-05-26 and 1.0.2 dated 2026-10-19
DESCRIPTION | 24 MD5 | 49 NAMESPACE | 3 NEWS.md | 23 R/checks.R | 671 ++-- R/prepare_data.R | 42 R/run_checks.R | 28 README.md | 4 build/vignette.rds |binary inst/doc/integrity.R | 344 +- inst/doc/integrity.Rmd | 862 ++--- inst/doc/integrity.html | 4765 +++++++++++++++--------------- inst/extdata/variables.yaml | 68 inst/scripts/about.txt | 2 man/private_differential_variability.Rd | 56 man/private_imbalance_day_intervention.Rd | 56 man/private_implausible_values.Rd | 52 man/private_prepare_data.Rd | 50 man/private_repeating_baseline.Rd | 52 man/private_terminal_digits.Rd | 53 man/private_unexpectedly_uncorrelated.Rd | 50 man/run_checks.Rd | 52 tests/regression.R |only tests/testthat.R | 24 tests/testthat/test-basic.R | 6 vignettes/integrity.Rmd | 862 ++--- 26 files changed, 4191 insertions(+), 4007 deletions(-)
Title: Quantifying Variable Change Induced by Administrative Boundary
Transformations
Description: Tools for auditing how analytic variables change when data
are transformed across administrative boundary systems. The package is
agnostic to data source, variable type, and administrative geography,
and is designed to quantify transformation-induced change without
attributing blame to any specific boundary definition or allocation
scheme.
Author: Phinn Markson [aut, cre]
Maintainer: Phinn Markson <markson.2@osu.edu>
Diff between geoDeltaAudit versions 0.1.0 dated 2026-05-13 and 0.1.1 dated 2026-10-19
geoDeltaAudit-0.1.0/geoDeltaAudit/man/figures/README-pressure-1.png |only geoDeltaAudit-0.1.1/geoDeltaAudit/DESCRIPTION | 6 geoDeltaAudit-0.1.1/geoDeltaAudit/MD5 | 25 + geoDeltaAudit-0.1.1/geoDeltaAudit/NEWS.md | 6 geoDeltaAudit-0.1.1/geoDeltaAudit/README.md | 137 +++++++--- geoDeltaAudit-0.1.1/geoDeltaAudit/build/vignette.rds |binary geoDeltaAudit-0.1.1/geoDeltaAudit/inst/doc/data-preparation.R |only geoDeltaAudit-0.1.1/geoDeltaAudit/inst/doc/data-preparation.Rmd |only geoDeltaAudit-0.1.1/geoDeltaAudit/inst/doc/data-preparation.html |only geoDeltaAudit-0.1.1/geoDeltaAudit/inst/doc/introduction.Rmd | 4 geoDeltaAudit-0.1.1/geoDeltaAudit/inst/doc/introduction.html | 12 geoDeltaAudit-0.1.1/geoDeltaAudit/inst/doc/proportionality_considerations.Rmd | 55 ++-- geoDeltaAudit-0.1.1/geoDeltaAudit/inst/doc/proportionality_considerations.html | 73 +++-- geoDeltaAudit-0.1.1/geoDeltaAudit/vignettes/data-preparation.Rmd |only geoDeltaAudit-0.1.1/geoDeltaAudit/vignettes/introduction.Rmd | 4 geoDeltaAudit-0.1.1/geoDeltaAudit/vignettes/proportionality_considerations.Rmd | 55 ++-- 16 files changed, 248 insertions(+), 129 deletions(-)
Title: Bayesian Dynamic Borrowing with Flexible Baseline Hazard
Function
Description: Allows Bayesian borrowing from a historical dataset for time-to-
event data. A flexible baseline hazard function is achieved via a piecewise
exponential likelihood with time varying split points and smoothing prior on the
historic baseline hazards. The method is described in Scott and Lewin (2026)
<doi:10.1093/biostatistics/kxag006>, and a paper focused on the software is
in Scott, Axillus, Lewin and Izmirlian (2026) <doi:10.48550/arXiv.2408.04327>.
Author: Darren Scott [aut],
Sophia Axillus [aut],
Grant Izmirlian [aut, cre]
Maintainer: Grant Izmirlian <grant.izmirlian@astrazeneca.com>
Diff between BayesFBHborrow versions 2.0.12 dated 2026-07-17 and 2.0.19 dated 2026-10-19
BayesFBHborrow-2.0.12/BayesFBHborrow/vignettes/bfbhb-gbcs-exmpls.rda |only BayesFBHborrow-2.0.12/BayesFBHborrow/vignettes/bfbhb-gbcs-nb-exmpl.rda |only BayesFBHborrow-2.0.12/BayesFBHborrow/vignettes/bfbhb-sim-exmpls.rda |only BayesFBHborrow-2.0.12/BayesFBHborrow/vignettes/borrowing_profile.eps |only BayesFBHborrow-2.0.12/BayesFBHborrow/vignettes/jsslogo.jpg |only BayesFBHborrow-2.0.19/BayesFBHborrow/DESCRIPTION | 8 BayesFBHborrow-2.0.19/BayesFBHborrow/MD5 | 56 BayesFBHborrow-2.0.19/BayesFBHborrow/NAMESPACE | 18 BayesFBHborrow-2.0.19/BayesFBHborrow/R/BayesFBHborrow.R | 4793 ++++++---- BayesFBHborrow-2.0.19/BayesFBHborrow/inst/doc/Using-BayesFBHborrow.R | 694 - BayesFBHborrow-2.0.19/BayesFBHborrow/inst/doc/Using-BayesFBHborrow.Rnw | 606 - BayesFBHborrow-2.0.19/BayesFBHborrow/inst/doc/Using-BayesFBHborrow.pdf |binary BayesFBHborrow-2.0.19/BayesFBHborrow/man/BayesFBHborrow.Rd | 112 BayesFBHborrow-2.0.19/BayesFBHborrow/man/MTE.Rd |only BayesFBHborrow-2.0.19/BayesFBHborrow/man/coef.BayesFBHborrow.Rd | 15 BayesFBHborrow-2.0.19/BayesFBHborrow/man/genBFBHBdat.Rd | 4 BayesFBHborrow-2.0.19/BayesFBHborrow/man/group_summary.Rd | 4 BayesFBHborrow-2.0.19/BayesFBHborrow/man/historical_data.Rd |only BayesFBHborrow-2.0.19/BayesFBHborrow/man/init_lambda_hyperparameters.Rd | 4 BayesFBHborrow-2.0.19/BayesFBHborrow/man/plot.BayesFBHborrow.Rd | 9 BayesFBHborrow-2.0.19/BayesFBHborrow/man/read_haz_mcmc_smpls.Rd | 50 BayesFBHborrow-2.0.19/BayesFBHborrow/man/rel_eff.Rd |only BayesFBHborrow-2.0.19/BayesFBHborrow/man/summary.BayesFBHborrow.Rd | 31 BayesFBHborrow-2.0.19/BayesFBHborrow/man/trial_data.Rd |only BayesFBHborrow-2.0.19/BayesFBHborrow/man/update.BayesFBHborrow.Rd | 125 BayesFBHborrow-2.0.19/BayesFBHborrow/man/xifinder.Rd | 4 BayesFBHborrow-2.0.19/BayesFBHborrow/vignettes/Using-BayesFBHborrow.Rnw | 606 - BayesFBHborrow-2.0.19/BayesFBHborrow/vignettes/Using-BayesFBHborrow.bib | 64 BayesFBHborrow-2.0.19/BayesFBHborrow/vignettes/figures |only BayesFBHborrow-2.0.19/BayesFBHborrow/vignettes/rdata |only 30 files changed, 4430 insertions(+), 2773 deletions(-)
More information about BayesFBHborrow at CRAN
Permanent link
Title: Data from the 'Access to Opportunities Project (AOP)'
Description: Download data from the 'Access to Opportunities Project (AOP)'. The
'aopdata' package brings annual estimates of access to employment,
health, education and social assistance services by transport mode,
as well as data on the spatial distribution of population, jobs,
health care, schools and social assistance facilities at a fine
spatial resolution for all cities included in the project. More
info on the 'AOP' website <https://www.ipea.gov.br/acessooportunidades/en/>.
Author: Rafael H. M. Pereira [aut, cre] ,
Daniel Herszenhut [aut] ,
Marcus Saraiva [aut] ,
Carlos Kaue Vieira Braga [aut] ,
Diego Bogado Tomasiello [ctb],
Joao Bazzo [ctb],
Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between aopdata versions 1.1.2 dated 2026-01-09 and 1.2.0 dated 2026-10-19
aopdata-1.1.2/aopdata/man/check_downloaded_obj.Rd |only aopdata-1.1.2/aopdata/tests/tests_rafa |only aopdata-1.2.0/aopdata/DESCRIPTION | 23 aopdata-1.2.0/aopdata/LICENSE | 4 aopdata-1.2.0/aopdata/MD5 | 139 - aopdata-1.2.0/aopdata/NAMESPACE | 9 aopdata-1.2.0/aopdata/NEWS.md | 310 +-- aopdata-1.2.0/aopdata/R/aopdata.R | 54 aopdata-1.2.0/aopdata/R/aopdata_dictionary.R | 74 aopdata-1.2.0/aopdata/R/download_metadata.R | 148 - aopdata-1.2.0/aopdata/R/read_access.R | 145 - aopdata-1.2.0/aopdata/R/read_grid.R | 9 aopdata-1.2.0/aopdata/R/read_landuse.R | 24 aopdata-1.2.0/aopdata/R/read_population.R | 24 aopdata-1.2.0/aopdata/R/utils.R | 1013 +++++----- aopdata-1.2.0/aopdata/README.md | 326 +-- aopdata-1.2.0/aopdata/build/vignette.rds |binary aopdata-1.2.0/aopdata/inst/CITATION | 56 aopdata-1.2.0/aopdata/inst/doc/access_inequality.R | 5 aopdata-1.2.0/aopdata/inst/doc/access_inequality.Rmd | 207 +- aopdata-1.2.0/aopdata/inst/doc/access_inequality.html | 10 aopdata-1.2.0/aopdata/inst/doc/access_maps.R | 7 aopdata-1.2.0/aopdata/inst/doc/access_maps.Rmd | 139 - aopdata-1.2.0/aopdata/inst/doc/access_maps.html | 14 aopdata-1.2.0/aopdata/inst/doc/aopdata.R | 24 aopdata-1.2.0/aopdata/inst/doc/aopdata.Rmd | 354 +-- aopdata-1.2.0/aopdata/inst/doc/aopdata.html | 27 aopdata-1.2.0/aopdata/inst/doc/data_dic_en.Rmd | 294 +- aopdata-1.2.0/aopdata/inst/doc/data_dic_en.html | 28 aopdata-1.2.0/aopdata/inst/doc/data_dic_pt.Rmd | 282 +- aopdata-1.2.0/aopdata/inst/doc/data_dic_pt.html | 98 aopdata-1.2.0/aopdata/inst/doc/landuse_maps.R | 5 aopdata-1.2.0/aopdata/inst/doc/landuse_maps.Rmd | 191 - aopdata-1.2.0/aopdata/inst/doc/landuse_maps.html | 14 aopdata-1.2.0/aopdata/inst/doc/population_maps.R | 5 aopdata-1.2.0/aopdata/inst/doc/population_maps.Rmd | 181 - aopdata-1.2.0/aopdata/inst/doc/population_maps.html | 11 aopdata-1.2.0/aopdata/man/abort_if_invalid.Rd |only aopdata-1.2.0/aopdata/man/aop_fetch.Rd |only aopdata-1.2.0/aopdata/man/aop_merge.Rd | 40 aopdata-1.2.0/aopdata/man/aop_request.Rd |only aopdata-1.2.0/aopdata/man/aopdata.Rd | 15 aopdata-1.2.0/aopdata/man/aopdata_dictionary.Rd | 60 aopdata-1.2.0/aopdata/man/classify_resp.Rd |only aopdata-1.2.0/aopdata/man/download_data.Rd | 14 aopdata-1.2.0/aopdata/man/download_metadata.Rd | 10 aopdata-1.2.0/aopdata/man/inform_failure.Rd |only aopdata-1.2.0/aopdata/man/load_data.Rd | 5 aopdata-1.2.0/aopdata/man/read_access.Rd | 82 aopdata-1.2.0/aopdata/man/read_grid.Rd | 3 aopdata-1.2.0/aopdata/man/read_landuse.Rd | 9 aopdata-1.2.0/aopdata/man/read_metadata.Rd |only aopdata-1.2.0/aopdata/man/read_population.Rd | 10 aopdata-1.2.0/aopdata/man/roxygen/templates/city.R | 4 aopdata-1.2.0/aopdata/man/roxygen/templates/geometry.R | 8 aopdata-1.2.0/aopdata/man/roxygen/templates/showProgress.R | 2 aopdata-1.2.0/aopdata/man/roxygen/templates/year.R | 2 aopdata-1.2.0/aopdata/man/select_mode_input.Rd | 12 aopdata-1.2.0/aopdata/tests/testthat.R | 16 aopdata-1.2.0/aopdata/tests/testthat/helper-aopdata.R |only aopdata-1.2.0/aopdata/tests/testthat/test_aopdata_dictionary.R | 55 aopdata-1.2.0/aopdata/tests/testthat/test_check_connection.R | 74 aopdata-1.2.0/aopdata/tests/testthat/test_read_access.R | 264 +- aopdata-1.2.0/aopdata/tests/testthat/test_read_grid.R | 118 - aopdata-1.2.0/aopdata/tests/testthat/test_read_landuse.R | 150 - aopdata-1.2.0/aopdata/tests/testthat/test_read_population.R | 149 - aopdata-1.2.0/aopdata/tests/testthat/test_utils.R | 490 ++++ aopdata-1.2.0/aopdata/vignettes/access_inequality.Rmd | 207 +- aopdata-1.2.0/aopdata/vignettes/access_maps.Rmd | 139 - aopdata-1.2.0/aopdata/vignettes/aopdata.Rmd | 354 +-- aopdata-1.2.0/aopdata/vignettes/data_dic_en.Rmd | 294 +- aopdata-1.2.0/aopdata/vignettes/data_dic_pt.Rmd | 282 +- aopdata-1.2.0/aopdata/vignettes/landuse_maps.Rmd | 191 - aopdata-1.2.0/aopdata/vignettes/population_maps.Rmd | 181 - aopdata-1.2.0/aopdata/vignettes/references.json | 80 75 files changed, 4131 insertions(+), 3443 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-10-02 0.8.1
2026-09-24 0.8.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-09-28 0.1.1
2026-09-27 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-09-17 1.0.4
2025-10-08 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-04 1.0