Title: Access and Analyse 'VALD' Data via Our External 'APIs'
Description: Provides helper functions and wrappers to simplify authentication,
data retrieval, and result processing from the 'VALD' 'APIs'.
Designed to streamline integration for analysts and researchers working
with 'VALD's external 'APIs'.
For further documentation on integrating with 'VALD' 'APIs', see:
<https://support.vald.com/hc/en-au/articles/23415335574553-How-to-integrate-with-VALD-APIs>.
For a step-by-step guide to using this package, see:
<https://support.vald.com/hc/en-au/articles/48730811824281-A-guide-to-using-the-valdr-R-package>.
Author: Kieran Harrison [aut, cre],
VALD Support [ctb],
VALD [cph]
Maintainer: Kieran Harrison <k.harrison@vald.com>
Diff between valdr versions 3.0.0 dated 2026-04-22 and 4.0.0 dated 2026-09-02
DESCRIPTION | 6 MD5 | 73 + NAMESPACE | 8 R/config.R | 50 - R/dev |only R/dynamo_tests.R |only R/dynamo_tests_by_id.R |only R/forceframe_tests_by_id.R | 6 R/humantrak_reps_by_id.R |only R/humantrak_test_type_metrics.R |only R/humantrak_tests.R |only R/nordbord_tests_by_id.R | 4 R/profiles.R | 4 R/profiles_by_id.R |only R/session.R | 250 +++++- R/utils.R | 767 ++++++++++++++++++- man/dot-build_dynamo_asymmetries_df.Rd |only man/dot-build_dynamo_df.Rd |only man/dot-build_dynamo_ratios_df.Rd |only man/dot-build_dynamo_repetition_type_summaries_df.Rd |only man/dot-build_dynamo_repetitions_df.Rd |only man/dot-build_humantrak_df.Rd |only man/dot-build_humantrak_metric_groups_df.Rd |only man/dot-build_humantrak_repetition_counts_df.Rd |only man/dot-build_humantrak_repetitions_df.Rd |only man/dot-build_humantrak_summary_measurements_df.Rd |only man/dot-build_humantrak_test_type_metrics_df.Rd |only man/dot-build_profile_details_df.Rd |only man/dot-extract_nested_character_list.Rd |only man/get_dynamo_data.Rd |only man/get_dynamo_test_by_id.Rd |only man/get_dynamo_tests.Rd |only man/get_dynamo_tests_by_id.Rd |only man/get_dynamo_tests_only.Rd |only man/get_forceframe_repetitions_by_id.Rd | 2 man/get_forceframe_test_by_id.Rd | 2 man/get_forceframe_tests_by_id.Rd | 3 man/get_humantrak_data.Rd |only man/get_humantrak_repetitions_by_id.Rd |only man/get_humantrak_reps_by_id.Rd |only man/get_humantrak_test_type_metrics.Rd |only man/get_humantrak_test_type_metrics_only.Rd |only man/get_humantrak_tests.Rd |only man/get_humantrak_tests_only.Rd |only man/get_nordbord_test_by_id.Rd | 2 man/get_nordbord_tests_by_id.Rd | 3 man/get_nordbord_tests_only.Rd | 2 man/get_profile_by_id.Rd |only man/get_profiles_by_id.Rd |only man/get_profiles_groups_categories.Rd | 4 man/get_profiles_groups_categories_mapping.Rd | 13 man/load_credentials.Rd | 14 tests/testthat/test-12-dynamo-humantrak-builders.R |only tests/testthat/test-13-profile-by-id.R |only tests/testthat/test-14-dynamo-long-form.R |only tests/testthat/test-15-humantrak-relational.R |only tests/testthat/test-16-new-retrieval-visibility.R |only 57 files changed, 1107 insertions(+), 106 deletions(-)
Title: Plot Raster Map Tiles from Open Street Map and Other Sources
Description: Download and plot Open Street Map <https://www.openstreetmap.org/>,
Bing Maps <https://www.bing.com/maps> and other tiled map sources. Use to create
basemaps quickly and add hillshade to vector-based maps.
Author: Dewey Dunnington [aut, cre] ,
Timothee Giraud [ctb]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between rosm versions 0.3.1 dated 2026-01-21 and 0.3.2 dated 2026-09-02
DESCRIPTION | 8 +++---- MD5 | 10 ++++----- NEWS.md | 5 ++++ R/deprecated.R | 42 +++++++++++++++++++++++++++++---------- man/deprecated.Rd | 10 +++++++-- tests/testthat/test-deprecated.R | 32 +++++++++++++++++++++++++++-- 6 files changed, 84 insertions(+), 23 deletions(-)
Title: Read and Write ODS Files
Description: Read ODS (OpenDocument Spreadsheet) into R as data frame. Also support writing data frame into ODS file.
Author: Gerrit-Jan Schutten [aut],
Chung-hong Chan [aut, cre] ,
Peter Brohan [aut],
Detlef Steuer [aut] ,
Thomas J. Leeper [aut] ,
John Foster [ctb],
Sergio Oller [ctb],
Jim Hester [ctb] ,
Stephen Watts [ctb],
Arthur Katossky [ctb],
Stas Malavin [ctb],
Dunca [...truncated...]
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between readODS versions 2.3.5 dated 2026-04-13 and 2.3.6 dated 2026-09-02
DESCRIPTION | 8 MD5 | 26 +- NEWS.md | 4 README.md | 10 - src/cpp11.cpp | 8 src/get_sheet_names.cpp | 11 - src/is_ods.cpp | 3 src/read_flat_ods_.cpp | 9 src/read_ods_.cpp | 7 src/splice.cpp | 236 ++++++++------------------ src/splice.h | 11 - src/write_sheet_file_.cpp | 6 tests/testthat/test_read_ods.R | 4 tests/testthat/test_write_ods_append_update.R | 14 + 14 files changed, 141 insertions(+), 216 deletions(-)
Title: Read 'Blackrock-Microsystems' Files ('NEV', 'NSx')
Description: Loads 'Blackrock' <https://blackrockneurotech.com> neural signal
data files into the memory, provides utility tools to extract the data into
common formats such as plain-text 'tsv' and 'HDF5'.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between readNSx versions 0.0.7 dated 2026-05-23 and 0.1.0 dated 2026-09-02
readNSx-0.0.7/readNSx/R/hdf5-alternative.R |only readNSx-0.1.0/readNSx/DESCRIPTION | 14 readNSx-0.1.0/readNSx/MD5 | 32 readNSx-0.1.0/readNSx/NEWS.md | 29 readNSx-0.1.0/readNSx/R/bci2000.R | 8 readNSx-0.1.0/readNSx/R/blackrock.R | 11 readNSx-0.1.0/readNSx/R/cpp11.R | 40 readNSx-0.1.0/readNSx/R/hdf5.R | 652 +++++--------- readNSx-0.1.0/readNSx/R/nsx.R | 2 readNSx-0.1.0/readNSx/R/specifications.R | 2 readNSx-0.1.0/readNSx/R/validators.R | 2 readNSx-0.1.0/readNSx/build/vignette.rds |binary readNSx-0.1.0/readNSx/man/import_nsp.Rd | 14 readNSx-0.1.0/readNSx/src/Makevars |only readNSx-0.1.0/readNSx/src/cpp11.cpp | 122 ++ readNSx-0.1.0/readNSx/src/h5native.cpp |only readNSx-0.1.0/readNSx/tests/testthat/golden-hdf5r.h5 |only readNSx-0.1.0/readNSx/tests/testthat/test-h5-allocation.R | 85 - readNSx-0.1.0/readNSx/tests/testthat/test-h5.R |only readNSx-0.1.0/readNSx/tests/testthat/test-hdf5r-compat.R |only 20 files changed, 487 insertions(+), 526 deletions(-)
Title: Clustering Algorithm for Data Integration and Disease Subtyping
Description: Provides a robust approach for omics data integration and disease subtyping. PINSPlus is fast and supports the analysis of large datasets with hundreds of thousands of samples and features. The software automatically determines the optimal number of clusters and then partitions the samples in a way such that the results are robust against noise and data perturbation (Nguyen et al. (2019) <DOI: 10.1093/bioinformatics/bty1049>, Nguyen et al. (2017)<DOI: 10.1101/gr.215129.116>, Nguyen et al. (2021)<DOI: 10.3389/fonc.2021.725133>).
Author: Hung Nguyen [aut],
Bang Tran [aut],
Duc Tran [aut],
Tin Nguyen [aut],
Van-Dung Pham [cre]
Maintainer: Van-Dung Pham <dvp0001@wayne.edu>
Diff between PINSPlus versions 2.0.9 dated 2025-07-29 and 2.0.10 dated 2026-09-02
DESCRIPTION | 14 +- MD5 | 4 inst/doc/PINSPlus.html | 260 ++++++++++++++++++++++++------------------------- 3 files changed, 138 insertions(+), 140 deletions(-)
Title: NHDPlus Tools
Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
Author: David Blodgett [aut, cre] ,
Mike Johnson [aut] ,
Marc Weber [ctb] ,
Josh Erickson [ctb],
Lauren Koenig [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between nhdplusTools versions 1.5.1 dated 2026-07-27 and 1.5.2 dated 2026-09-02
nhdplusTools-1.5.1/nhdplusTools/build/vignette.rds |only nhdplusTools-1.5.1/nhdplusTools/inst/doc |only nhdplusTools-1.5.1/nhdplusTools/vignettes |only nhdplusTools-1.5.2/nhdplusTools/DESCRIPTION | 13 nhdplusTools-1.5.2/nhdplusTools/MD5 | 202 ++++------ nhdplusTools-1.5.2/nhdplusTools/NEWS.md | 5 nhdplusTools-1.5.2/nhdplusTools/R/A_nhdplusTools.R | 16 nhdplusTools-1.5.2/nhdplusTools/R/calc_network.R | 32 - nhdplusTools-1.5.2/nhdplusTools/R/discover_nhdplus.R | 11 nhdplusTools-1.5.2/nhdplusTools/R/downloading_tools.R | 38 - nhdplusTools-1.5.2/nhdplusTools/R/get_codes.R | 92 ---- nhdplusTools-1.5.2/nhdplusTools/R/get_drainage_area_estimates.R | 8 nhdplusTools-1.5.2/nhdplusTools/R/get_geoconnex.R | 24 - nhdplusTools-1.5.2/nhdplusTools/R/get_hydro.R | 61 --- nhdplusTools-1.5.2/nhdplusTools/R/get_network.R | 84 ---- nhdplusTools-1.5.2/nhdplusTools/R/get_nhdplus.R | 16 nhdplusTools-1.5.2/nhdplusTools/R/get_nhdplushr.R | 63 --- nhdplusTools-1.5.2/nhdplusTools/R/get_nldi.R | 83 ---- nhdplusTools-1.5.2/nhdplusTools/R/get_oaproc.R | 136 ------ nhdplusTools-1.5.2/nhdplusTools/R/get_path_lengths.R | 26 - nhdplusTools-1.5.2/nhdplusTools/R/get_paths.R | 47 -- nhdplusTools-1.5.2/nhdplusTools/R/get_vaa.R | 29 - nhdplusTools-1.5.2/nhdplusTools/R/index_nhdplus.R | 81 ---- nhdplusTools-1.5.2/nhdplusTools/R/map_nhdplus.R | 15 nhdplusTools-1.5.2/nhdplusTools/R/plot_nhdplus.R | 77 --- nhdplusTools-1.5.2/nhdplusTools/R/prep_nhdplus.R | 16 nhdplusTools-1.5.2/nhdplusTools/R/rebuild_topology.R | 19 nhdplusTools-1.5.2/nhdplusTools/R/rescale_catchments.R | 27 - nhdplusTools-1.5.2/nhdplusTools/R/run_plus_attributes.R | 14 nhdplusTools-1.5.2/nhdplusTools/R/subset_nhdplus.R | 91 ---- nhdplusTools-1.5.2/nhdplusTools/man/add_plus_network_attributes.Rd | 15 nhdplusTools-1.5.2/nhdplusTools/man/align_nhdplus_names.Rd | 12 nhdplusTools-1.5.2/nhdplusTools/man/calculate_arbolate_sum.Rd | 17 nhdplusTools-1.5.2/nhdplusTools/man/calculate_total_drainage_area.Rd | 17 nhdplusTools-1.5.2/nhdplusTools/man/disambiguate_flowline_indexes.Rd | 39 - nhdplusTools-1.5.2/nhdplusTools/man/discover_geoconnex_reference.Rd | 6 nhdplusTools-1.5.2/nhdplusTools/man/discover_nhdplus_id.Rd | 12 nhdplusTools-1.5.2/nhdplusTools/man/download_nhd.Rd | 10 nhdplusTools-1.5.2/nhdplusTools/man/download_nhdplushr.Rd | 13 nhdplusTools-1.5.2/nhdplusTools/man/download_nhdplusv2.Rd | 10 nhdplusTools-1.5.2/nhdplusTools/man/download_rf1.Rd | 5 nhdplusTools-1.5.2/nhdplusTools/man/download_wbd.Rd | 63 +-- nhdplusTools-1.5.2/nhdplusTools/man/get_3dhp.Rd | 41 -- nhdplusTools-1.5.2/nhdplusTools/man/get_DD.Rd | 15 nhdplusTools-1.5.2/nhdplusTools/man/get_DM.Rd | 16 nhdplusTools-1.5.2/nhdplusTools/man/get_UM.Rd | 16 nhdplusTools-1.5.2/nhdplusTools/man/get_UT.Rd | 14 nhdplusTools-1.5.2/nhdplusTools/man/get_catchment_characteristics.Rd | 5 nhdplusTools-1.5.2/nhdplusTools/man/get_characteristics_metadata.Rd | 10 nhdplusTools-1.5.2/nhdplusTools/man/get_drainage_area_estimates.Rd | 9 nhdplusTools-1.5.2/nhdplusTools/man/get_elev_along_path.Rd | 27 - nhdplusTools-1.5.2/nhdplusTools/man/get_flowline_index.Rd | 30 - nhdplusTools-1.5.2/nhdplusTools/man/get_geoconnex_reference.Rd | 20 nhdplusTools-1.5.2/nhdplusTools/man/get_levelpaths.Rd | 16 nhdplusTools-1.5.2/nhdplusTools/man/get_nhdphr.Rd | 22 - nhdplusTools-1.5.2/nhdplusTools/man/get_nhdplus.Rd | 14 nhdplusTools-1.5.2/nhdplusTools/man/get_nhdplushr.Rd | 24 - nhdplusTools-1.5.2/nhdplusTools/man/get_nldi_basin.Rd | 34 - nhdplusTools-1.5.2/nhdplusTools/man/get_nldi_feature.Rd | 5 nhdplusTools-1.5.2/nhdplusTools/man/get_nldi_index.Rd | 18 nhdplusTools-1.5.2/nhdplusTools/man/get_path_lengths.Rd | 14 nhdplusTools-1.5.2/nhdplusTools/man/get_path_members.Rd | 14 nhdplusTools-1.5.2/nhdplusTools/man/get_pathlength.Rd | 9 nhdplusTools-1.5.2/nhdplusTools/man/get_pfaf.Rd | 57 -- nhdplusTools-1.5.2/nhdplusTools/man/get_raindrop_trace.Rd | 18 nhdplusTools-1.5.2/nhdplusTools/man/get_sorted.Rd | 15 nhdplusTools-1.5.2/nhdplusTools/man/get_split_catchment.Rd | 54 -- nhdplusTools-1.5.2/nhdplusTools/man/get_streamlevel.Rd | 22 - nhdplusTools-1.5.2/nhdplusTools/man/get_streamorder.Rd | 16 nhdplusTools-1.5.2/nhdplusTools/man/get_terminal.Rd | 11 nhdplusTools-1.5.2/nhdplusTools/man/get_tocomid.Rd | 8 nhdplusTools-1.5.2/nhdplusTools/man/get_vaa.Rd | 14 nhdplusTools-1.5.2/nhdplusTools/man/get_vaa_names.Rd | 9 nhdplusTools-1.5.2/nhdplusTools/man/get_waterbody_index.Rd | 15 nhdplusTools-1.5.2/nhdplusTools/man/get_wb_outlet.Rd | 14 nhdplusTools-1.5.2/nhdplusTools/man/get_xs_point.Rd | 20 nhdplusTools-1.5.2/nhdplusTools/man/get_xs_points.Rd | 22 - nhdplusTools-1.5.2/nhdplusTools/man/make_node_topology.Rd | 20 nhdplusTools-1.5.2/nhdplusTools/man/make_standalone.Rd | 41 -- nhdplusTools-1.5.2/nhdplusTools/man/map_nhdplus.Rd | 16 nhdplusTools-1.5.2/nhdplusTools/man/navigate_network.Rd | 28 - nhdplusTools-1.5.2/nhdplusTools/man/navigate_nldi.Rd | 30 - nhdplusTools-1.5.2/nhdplusTools/man/plot_nhdplus.Rd | 65 --- nhdplusTools-1.5.2/nhdplusTools/man/prepare_nhdplus.Rd | 10 nhdplusTools-1.5.2/nhdplusTools/man/reexports.Rd | 2 nhdplusTools-1.5.2/nhdplusTools/man/rescale_catchment_characteristics.Rd | 158 +++---- nhdplusTools-1.5.2/nhdplusTools/man/subset_nhdplus.Rd | 76 --- nhdplusTools-1.5.2/nhdplusTools/man/subset_rpu.Rd | 9 nhdplusTools-1.5.2/nhdplusTools/man/subset_vpu.Rd | 9 nhdplusTools-1.5.2/nhdplusTools/tests/testthat.R | 8 90 files changed, 206 insertions(+), 2479 deletions(-)
Title: Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix
Operations
Description: Matrix eQTL is designed for fast eQTL analysis on large datasets.
Matrix eQTL can test for association between genotype
and gene expression using linear regression
with either additive or ANOVA genotype effects.
The models can include covariates to account for factors
as population stratification, gender, and clinical variables.
It also supports models with heteroscedastic and/or correlated errors,
false discovery rate estimation and
separate treatment of local (cis) and distant (trans) eQTLs.
For more details see Shabalin (2012) <doi:10.1093/bioinformatics/bts163>.
Author: Andrey A Shabalin [aut, cre]
Maintainer: Andrey A Shabalin <andrey.shabalin@gmail.com>
Diff between MatrixEQTL versions 2.3 dated 2019-12-22 and 2.4 dated 2026-09-02
DESCRIPTION | 11 MD5 | 10 NAMESPACE | 18 R/Matrix_eQTL_engine.R | 4341 ++++++++++++++++++++++++------------------------ inst/CITATION | 30 man/Matrix_eQTL_main.Rd | 4 6 files changed, 2208 insertions(+), 2206 deletions(-)
Title: Extension to 'ggplot2' for Plotting Stats
Description: Provides new statistics, new geometries and new positions for
'ggplot2' and a suite of functions to facilitate the creation of
statistical plots.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between ggstats versions 0.13.0 dated 2026-03-06 and 0.14.0 dated 2026-09-02
DESCRIPTION | 8 MD5 | 46 +-- NAMESPACE | 28 +- NEWS.md | 13 + R/deprecated.R | 204 ++++++++-------- R/ggcoef_model.R | 388 +++++++++++++++---------------- R/gglikert.R | 47 ++- R/weighted_quantile.R | 2 build/vignette.rds |binary inst/doc/ggcoef_model.html | 23 + inst/doc/stat_cross.html | 2 man/figures/README-unnamed-chunk-8-1.png |binary man/geom_connector.Rd | 4 man/ggcoef_model.Rd | 6 man/ggcoef_multicomponents.Rd | 310 ++++++++++++------------ man/gglikert.Rd | 20 + man/ggstats-package.Rd | 5 man/hex_bw.Rd | 5 man/pal_extender.Rd | 2 man/position_likert.Rd | 4 man/stat_cross.Rd | 2 man/stat_prop.Rd | 6 man/stat_weighted_mean.Rd | 2 tests/testthat/test-ggcoef_model.R | 16 - 24 files changed, 610 insertions(+), 533 deletions(-)
Title: Vectorised Computation of P-Values and Their Supports for
Several Discrete Statistical Tests
Description: Provides vectorised functions for computing p-values of various
common discrete statistical tests, as described e.g. in Agresti (2002)
<doi:10.1002/0471249688>, including their distributions. Exact and
approximate computation methods are provided. For exact ones, several
procedures of determining two-sided p-values are included, which are
outlined in more detail in Hirji (2006) <doi:10.1201/9781420036190>.
Author: Florian Junge [cre, aut] ,
Christina Kihn [aut],
Sebastian Doehler [ctb] ,
Guillermo Durand [ctb]
Maintainer: Florian Junge <diso.fbmn@h-da.de>
Diff between DiscreteTests versions 0.5.0 dated 2026-08-26 and 0.5.1 dated 2026-09-02
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ R/mann-whitney.R | 1 + src/mann_whitney.cpp | 10 +++++++--- 5 files changed, 24 insertions(+), 11 deletions(-)
Title: Run 'lavaan' Models from Keys Lists
Description: Specifying 'lavaan' models manually can be time consuming when
multiple similar models are required. The 'semFromKeys' package streamlines
the process of running 'lavaan' models by generating model code from simple
keys lists and running entire collections of models at once.
The package was inspired by the process used in the code for
Bainbridge, T. F., Ludeke, S. G., & Smillie, L. D. (2022)
<doi:10.1037/pspp0000395>.
The package also optionally checks that identical models have not been run
on the same data, which saves time when code needs to be run again.
Author: Timothy F. Bainbridge [aut, cre, cph]
Maintainer: Timothy F. Bainbridge <tfbainbridge@gmail.com>
Diff between semFromKeys versions 0.5.2 dated 2026-08-22 and 0.5.3 dated 2026-09-01
DESCRIPTION | 6 MD5 | 25 +- NEWS.md | 9 R/cache.clean.R | 142 +++++++------- R/cache.setup.R | 107 +++++----- R/sem.check.R | 13 + R/sem.cor.R | 362 +++++++++++++++++++++++++++--------- man/cache.clean.Rd | 40 ++- man/cache.setup.Rd | 71 +++---- man/sem.cor.Rd | 33 ++- tests/testthat/test-cache.clean.R | 86 ++++++++ tests/testthat/test-cache.setup.R |only tests/testthat/test-cfa.from.keys.R | 60 ++--- tests/testthat/test-sem.cor.R | 191 ++++++++++++++---- 14 files changed, 779 insertions(+), 366 deletions(-)
Title: Prior-Data Fitted Network Foundational Model for Tabular Data
Description: Provides a consistent API for classification and regression models
based on the 'TabPFN' model of Hollmann et al. (2025), "Accurate predictions
on small data with a tabular foundation model," Nature, 637(8045)
<doi:10.1038/s41586-024-08328-6>. The calculations are served via 'Python'
to train and predict the model.
Author: Max Kuhn [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between tabpfn versions 0.2.0 dated 2026-05-14 and 0.3.0 dated 2026-09-01
tabpfn-0.2.0/tabpfn/R/tabpfn-constructor.R |only tabpfn-0.2.0/tabpfn/R/tabpfn-predict.R |only tabpfn-0.3.0/tabpfn/DESCRIPTION | 16 - tabpfn-0.3.0/tabpfn/MD5 | 52 +++--- tabpfn-0.3.0/tabpfn/NAMESPACE | 2 tabpfn-0.3.0/tabpfn/NEWS.md | 19 ++ tabpfn-0.3.0/tabpfn/R/TabPFN-constructor.R |only tabpfn-0.3.0/tabpfn/R/TabPFN-fit.R | 103 ++++++++---- tabpfn-0.3.0/tabpfn/R/TabPFN-predict.R |only tabpfn-0.3.0/tabpfn/R/install.R |only tabpfn-0.3.0/tabpfn/R/misc.R | 52 +++++- tabpfn-0.3.0/tabpfn/R/zzz.R | 56 ++++++ tabpfn-0.3.0/tabpfn/README.md | 39 ++-- tabpfn-0.3.0/tabpfn/build/partial.rdb |binary tabpfn-0.3.0/tabpfn/inst/WORDLIST | 5 tabpfn-0.3.0/tabpfn/man/figures/README-boundaries-1.png |binary tabpfn-0.3.0/tabpfn/man/figures/logo.png |only tabpfn-0.3.0/tabpfn/man/install_tabpfn.Rd |only tabpfn-0.3.0/tabpfn/man/predict.tab_pfn.Rd | 80 +++++++-- tabpfn-0.3.0/tabpfn/man/reexports.Rd | 2 tabpfn-0.3.0/tabpfn/man/tab_pfn.Rd | 42 ++-- tabpfn-0.3.0/tabpfn/man/tabpfn-package.Rd | 7 tabpfn-0.3.0/tabpfn/man/tabpfn_initialize.Rd |only tabpfn-0.3.0/tabpfn/tests/testthat/_snaps/classification.md | 64 +++++-- tabpfn-0.3.0/tabpfn/tests/testthat/_snaps/regression.md | 80 +++++++-- tabpfn-0.3.0/tabpfn/tests/testthat/helper.R | 30 +++ tabpfn-0.3.0/tabpfn/tests/testthat/test-TabPFN-fit.R | 30 +++ tabpfn-0.3.0/tabpfn/tests/testthat/test-classification.R | 15 + tabpfn-0.3.0/tabpfn/tests/testthat/test-initialize.R |only tabpfn-0.3.0/tabpfn/tests/testthat/test-install.R |only tabpfn-0.3.0/tabpfn/tests/testthat/test-misc.R | 76 ++++++++ tabpfn-0.3.0/tabpfn/tests/testthat/test-regression.R | 81 +++++++++ 32 files changed, 704 insertions(+), 147 deletions(-)
Title: Soundscape Spectral Metrics
Description: Accessible and flexible implementation of spectral ecoacoustic indices. The functions were design to accommodate a variety of sampling designs. Users can tailor calculations by specifying spectrogram time bin size, amplitude thresholds and normality tests. By simplifying computation and standardizing reproducible methods, the package aims to support ecoacoustics studies.
Author: Arthur Igor da Fonseca-Freire [aut, cre, cph],
Weslley Geremias dos Santos [aut],
Lucas Rodriguez Forti [aut]
Maintainer: Arthur Igor da Fonseca-Freire <arthur.igorr@gmail.com>
Diff between Ruido versions 1.0.3 dated 2026-04-18 and 1.1.0 dated 2026-09-01
Ruido-1.0.3/Ruido/man/plotBGN.Rd |only Ruido-1.1.0/Ruido/DESCRIPTION | 16 Ruido-1.1.0/Ruido/MD5 | 48 - Ruido-1.1.0/Ruido/NAMESPACE | 60 - Ruido-1.1.0/Ruido/R/ACIspec.R |only Ruido-1.1.0/Ruido/R/ENTspec.R |only Ruido-1.1.0/Ruido/R/activity.R | 93 +- Ruido-1.1.0/Ruido/R/bgNoise.R | 152 ++- Ruido-1.1.0/Ruido/R/internalFunctions.R | 723 +++++++++++------- Ruido-1.1.0/Ruido/R/multActivity.R | 184 ++-- Ruido-1.1.0/Ruido/R/noise.matrix.R | 311 +++---- Ruido-1.1.0/Ruido/R/satBackup.R | 141 +-- Ruido-1.1.0/Ruido/R/singleSat.R | 137 +-- Ruido-1.1.0/Ruido/R/soundMat.R | 182 ++-- Ruido-1.1.0/Ruido/R/soundSat.R | 234 +++-- Ruido-1.1.0/Ruido/README.md | 27 Ruido-1.1.0/Ruido/data/sampleBGN.rda |binary Ruido-1.1.0/Ruido/man/ACIspec.Rd |only Ruido-1.1.0/Ruido/man/ENTspec.Rd |only Ruido-1.1.0/Ruido/man/activity.Rd | 25 Ruido-1.1.0/Ruido/man/bgNoise.Rd | 54 - Ruido-1.1.0/Ruido/man/multActivity.Rd | 56 - Ruido-1.1.0/Ruido/man/plot-noise.matrix-ANY-method.Rd | 10 Ruido-1.1.0/Ruido/man/plotNOISE.Rd |only Ruido-1.1.0/Ruido/man/satBackup.Rd | 14 Ruido-1.1.0/Ruido/man/singleSat.Rd | 61 - Ruido-1.1.0/Ruido/man/soundMat.Rd | 30 Ruido-1.1.0/Ruido/man/soundSat.Rd | 59 - 28 files changed, 1469 insertions(+), 1148 deletions(-)
Title: Simulate Models Based on the Generalized Linear Model
Description: Simulates regression models,
including both simple regression and generalized linear mixed
models with up to three level of nesting. Power simulations that are
flexible allowing the specification of missing data, unbalanced designs,
and different random error distributions are built into the package.
Author: Brandon LeBeau [aut, cre]
Maintainer: Brandon LeBeau <lebebr01+simglm@gmail.com>
Diff between simglm versions 0.8.9 dated 2022-02-07 and 1.0.0 dated 2026-09-01
simglm-0.8.9/simglm/R/simglm.r |only simglm-0.8.9/simglm/inst/shiny_examples |only simglm-0.8.9/simglm/man/parse_crossclass.Rd |only simglm-0.8.9/simglm/tests/testthat/test_crossclass.r |only simglm-1.0.0/simglm/DESCRIPTION | 17 simglm-1.0.0/simglm/LICENSE | 4 simglm-1.0.0/simglm/MD5 | 127 simglm-1.0.0/simglm/NAMESPACE | 27 simglm-1.0.0/simglm/NEWS.md | 165 simglm-1.0.0/simglm/R/corr_variables.r | 265 simglm-1.0.0/simglm/R/data_glm.r | 97 simglm-1.0.0/simglm/R/data_reg.r | 529 simglm-1.0.0/simglm/R/err_sim.r | 13 simglm-1.0.0/simglm/R/fixef_sim.r | 739 simglm-1.0.0/simglm/R/missing_data.r | 87 simglm-1.0.0/simglm/R/parse_formula.r | 515 simglm-1.0.0/simglm/R/pow_sim.r | 1119 - simglm-1.0.0/simglm/R/propensity.r |only simglm-1.0.0/simglm/R/rand_eff_sim.r | 78 simglm-1.0.0/simglm/R/simglm-package.r |only simglm-1.0.0/simglm/R/simglm_master_function.r | 110 simglm-1.0.0/simglm/R/util.r | 609 simglm-1.0.0/simglm/README.md | 13 simglm-1.0.0/simglm/build/vignette.rds |binary simglm-1.0.0/simglm/inst/doc/Propensity.R |only simglm-1.0.0/simglm/inst/doc/Propensity.Rmd |only simglm-1.0.0/simglm/inst/doc/Propensity.html |only simglm-1.0.0/simglm/inst/doc/simulation_arguments.R | 284 simglm-1.0.0/simglm/inst/doc/simulation_arguments.Rmd | 282 simglm-1.0.0/simglm/inst/doc/simulation_arguments.html | 9974 +++++----- simglm-1.0.0/simglm/inst/doc/spline_simulation.R |only simglm-1.0.0/simglm/inst/doc/spline_simulation.Rmd |only simglm-1.0.0/simglm/inst/doc/spline_simulation.html |only simglm-1.0.0/simglm/inst/doc/tidy_simulation.R | 69 simglm-1.0.0/simglm/inst/doc/tidy_simulation.Rmd | 75 simglm-1.0.0/simglm/inst/doc/tidy_simulation.html | 999 - simglm-1.0.0/simglm/man/aggregate_outcome_by_level.Rd |only simglm-1.0.0/simglm/man/compute_density_values.Rd |only simglm-1.0.0/simglm/man/compute_statistics.Rd | 19 simglm-1.0.0/simglm/man/extract_coefficients.Rd | 2 simglm-1.0.0/simglm/man/fit_propensity.Rd |only simglm-1.0.0/simglm/man/model_fit.Rd | 2 simglm-1.0.0/simglm/man/parse_correlation.Rd | 8 simglm-1.0.0/simglm/man/parse_multiplemember.Rd |only simglm-1.0.0/simglm/man/parse_power.Rd | 2 simglm-1.0.0/simglm/man/parse_varyarguments.Rd | 4 simglm-1.0.0/simglm/man/parse_varyarguments_w.Rd |only simglm-1.0.0/simglm/man/replicate_simulation.Rd | 4 simglm-1.0.0/simglm/man/robust_model.Rd |only simglm-1.0.0/simglm/man/sim_continuous2.Rd | 22 simglm-1.0.0/simglm/man/sim_factor2.Rd | 19 simglm-1.0.0/simglm/man/sim_ordinal2.Rd |only simglm-1.0.0/simglm/man/simglm-package.Rd |only simglm-1.0.0/simglm/man/simglm.Rd | 14 simglm-1.0.0/simglm/man/simulate_heterogeneity.Rd | 2 simglm-1.0.0/simglm/man/simulate_knot.Rd | 2 simglm-1.0.0/simglm/man/simulate_propensity.Rd |only simglm-1.0.0/simglm/man/transform_outcome.Rd | 4 simglm-1.0.0/simglm/tests/testthat/test_book_api_compatibility.r |only simglm-1.0.0/simglm/tests/testthat/test_correlation.r | 305 simglm-1.0.0/simglm/tests/testthat/test_data_generation.r | 40 simglm-1.0.0/simglm/tests/testthat/test_factor.r | 217 simglm-1.0.0/simglm/tests/testthat/test_fixef.r | 178 simglm-1.0.0/simglm/tests/testthat/test_heterogeneity.r | 29 simglm-1.0.0/simglm/tests/testthat/test_interactions.r | 105 simglm-1.0.0/simglm/tests/testthat/test_missing.r | 325 simglm-1.0.0/simglm/tests/testthat/test_mult-equations.r |only simglm-1.0.0/simglm/tests/testthat/test_multinomial.r |only simglm-1.0.0/simglm/tests/testthat/test_multiplemember.r |only simglm-1.0.0/simglm/tests/testthat/test_ordinal.r |only simglm-1.0.0/simglm/tests/testthat/test_poly_ns_bs.r | 235 simglm-1.0.0/simglm/tests/testthat/test_postprocess.r |only simglm-1.0.0/simglm/tests/testthat/test_power_struc.r | 103 simglm-1.0.0/simglm/tests/testthat/test_propensity.r |only simglm-1.0.0/simglm/tests/testthat/test_replication_one.r |only simglm-1.0.0/simglm/vignettes/Propensity.Rmd |only simglm-1.0.0/simglm/vignettes/simulation_arguments.Rmd | 282 simglm-1.0.0/simglm/vignettes/spline_simulation.Rmd |only simglm-1.0.0/simglm/vignettes/tidy_simulation.Rmd | 75 79 files changed, 10944 insertions(+), 7251 deletions(-)
Title: Semantic Factor Analysis of Language Model Embeddings
Description: Performs exploratory factor analysis on language model embeddings
of psychological scale items. Embeds item text with sentence transformers
or other language models, transforms the embeddings into item-by-item
similarity matrices, and extracts latent factor structure via standard
exploratory factor analysis, using several similarity transforms (atomic
reversed, SQuID centering, mean-centered Pearson) and fit diagnostics
tailored to embedding matrices (TEFI, RMSR, CAF, McDonald's omega).
Factor retention spans embedding-adapted parallel analysis, the empirical
Kaiser criterion, Velicer's minimum average partial, a comparison-data
misfit profile, and a calibrated learned rule that reports conformal
intervals. Further tools orient factor axes toward retrieved construct
terms by lexical target rotation, and audit whether a scale's items cover
their construct's semantic region without collecting responses. The
underlying methods are documented with full citations in the
corresponding functi [...truncated...]
Author: Devon Yanitski [aut, cre] ,
Chris Westbury [aut]
Maintainer: Devon Yanitski <dyanitsk@ualberta.ca>
Diff between semanticfa versions 0.1.1 dated 2026-07-03 and 0.5.0 dated 2026-09-01
DESCRIPTION | 28 ++- MD5 | 81 ++++++++-- NAMESPACE | 38 ++++ NEWS.md | 205 ++++++++++++++++++++++++++ R/bank.R |only R/cd.R |only R/coverage.R |only R/dimselect.R | 6 R/embed.R | 158 ++++++++++++++++++++ R/leximax.R |only R/naming.R |only R/pool.R |only R/region.R |only R/regions_multi.R |only R/retention.R | 249 +++++++++++++++++++++++++++++++- R/semk.R |only R/sfa.R | 74 ++++++++- README.md | 27 +++ build/vignette.rds |binary inst/doc/introduction.R | 2 inst/doc/introduction.Rmd | 13 + inst/doc/introduction.html | 275 ++++++++++++++++++++++++++++++++---- inst/doc/naming-factors.R |only inst/doc/naming-factors.Rmd |only inst/doc/naming-factors.html |only inst/python |only man/plot.sfa_coverage.Rd |only man/plot.sfa_coverage_battery.Rd |only man/sfa.Rd | 18 ++ man/sfa_build_bank.Rd |only man/sfa_build_region.Rd |only man/sfa_build_regions.Rd |only man/sfa_cd.Rd |only man/sfa_combine_banks.Rd |only man/sfa_coverage.Rd |only man/sfa_cross_matrix.Rd |only man/sfa_deletion_gaps.Rd |only man/sfa_dimselect.Rd | 6 man/sfa_ekc.Rd |only man/sfa_embedding_bank.Rd |only man/sfa_gaps.Rd |only man/sfa_leximax.Rd |only man/sfa_lexmap.Rd |only man/sfa_load_region.Rd |only man/sfa_map.Rd |only man/sfa_name.Rd |only man/sfa_nameability.Rd |only man/sfa_naming_instruction.Rd |only man/sfa_nfactors.Rd | 27 +++ man/sfa_pool.Rd |only man/sfa_reembed_region.Rd |only man/sfa_region_bank.Rd |only man/sfa_semk.Rd |only tests/testthat/fixtures |only tests/testthat/test-cd.R |only tests/testthat/test-coverage.R |only tests/testthat/test-leximax.R |only tests/testthat/test-naming-golden.R |only tests/testthat/test-naming.R |only tests/testthat/test-retention.R | 62 ++++++++ tests/testthat/test-semk.R |only vignettes/introduction.Rmd | 13 + vignettes/naming-factors.Rmd |only 63 files changed, 1187 insertions(+), 95 deletions(-)
Title: Bayesian Understanding for Mediator Selection Framework
Description: A collection of quantitative tools for selecting mediating effects within exploratory Bayesian mediation models. The package accommodates both continuous and dichotomous outcomes, including the dependent variables and the mediators for identifying and analyzing mediation pathways.
Author: Dingjing Shi [aut, cre],
Tansu Celikel [aut],
Chih-Chia Hsing [aut],
Dexin Shi [aut]
Maintainer: Dingjing Shi <dshi32@gatech.edu>
Diff between buzzMed versions 0.1.3 dated 2026-07-16 and 0.1.4 dated 2026-09-01
DESCRIPTION | 8 ++-- MD5 | 14 +++---- NEWS.md | 10 +++++ R/data.R | 98 +++++++++++++++++++++++++----------------------------- README.md | 2 - data/framing2.rda |binary inst/WORDLIST | 2 + man/framing2.Rd | 98 +++++++++++++++++++++++++----------------------------- 8 files changed, 116 insertions(+), 116 deletions(-)
Title: Double Machine Learning for Static Panel Models with Fixed
Effects
Description: The 'xtdml' package implements partially linear panel regression (PLPR) models with high-dimensional confounding variables and an exogenous treatment variable within the double machine learning framework. The package is used to estimate the structural parameter (treatment effect) in static panel data models with fixed effects using the approaches established in Clarke and Polselli (2025) <doi:10.1093/ectj/utaf011>. 'xtdml' follows the object-oriented architecture of 'DoubleML' (Bach et al., 2024) <doi:10.18637/jss.v108.i03> and uses the 'mlr3' ecosystem.
Author: Annalivia Polselli [aut, cre]
Maintainer: Annalivia Polselli <apolselli.econ@gmail.com>
Diff between xtdml versions 0.1.12 dated 2026-03-13 and 0.1.13 dated 2026-09-01
DESCRIPTION | 20 MD5 | 32 NAMESPACE | 97 - R/dataset.R | 247 ++- R/helper.R | 68 + R/xtdml_data.R | 97 + R/xtdml_main.R | 3260 +++++++++++++++++++++++++------------------------- R/xtdml_plr.R | 28 R/zzz.R | 6 README.md | 26 man/make_plpr_data.Rd | 143 +- man/xtdml.Rd | 550 ++++---- man/xtdml_data.Rd | 193 +- man/xtdml_plr.Rd | 226 +-- tests |only 15 files changed, 2673 insertions(+), 2320 deletions(-)
Title: Fast Enrichment Analysis via Circular Permutations
Description: Fast enrichment analysis for locally correlated statistics
via circular permutations.
The analysis can be performed at multiple significance thresholds
for both primary and auxiliary data sets with
efficient correction for multiple testing.
Author: Andrey A Shabalin [aut, cre] ,
Edwin J C G van den Oord [aut]
Maintainer: Andrey A Shabalin <andrey.shabalin@gmail.com>
Diff between shiftR versions 1.5 dated 2019-03-22 and 1.6 dated 2026-09-01
DESCRIPTION | 11 MD5 | 14 R/binary.R | 8 build/vignette.rds |binary inst/doc/intro.R | 12 inst/doc/intro.html | 742 +++++++++++++++++++++++++++++++-------------------- man/shiftrPrepare.Rd | 2 src/c_code.c | 16 - 8 files changed, 494 insertions(+), 311 deletions(-)
Title: Rapid Asynchronous and Distributed Computing
Description: Package to tackle large-scale problems asynchronously across
a distributed network. Employing a database centric model, rush
enables workers to communicate tasks and their results over a shared
'Redis' database. Key features include low task overhead, efficient
caching, and robust error handling. The package powers the
asynchronous optimization algorithms in the 'bbotk' and 'mlr3tuning'
packages.
Author: Marc Becker [cre, aut, cph]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between rush versions 1.2.1 dated 2026-07-24 and 1.3.0 dated 2026-09-01
DESCRIPTION | 8 - MD5 | 38 ++--- NAMESPACE | 1 NEWS.md | 5 R/Rush.R | 248 +++++++++++++++++++++++++++++-------- R/RushWorker.R | 69 ++++++++-- R/assertions.R | 21 +++ R/rush_plan.R | 12 + R/start_worker.R | 16 ++ inst/testthat/helper.R | 21 +++ man/Rush.Rd | 68 +++++++++- man/RushWorker.Rd | 19 ++ man/rush_assertions.Rd | 8 + man/rush_plan.Rd | 11 + man/start_worker.Rd | 8 + tests/testthat/helper.R | 19 ++ tests/testthat/test-Rush.R | 173 +++++++++++++++++++++++++ tests/testthat/test-RushWorker.R | 57 ++++++++ tests/testthat/test-rush_plan.R | 31 ++++ tests/testthat/test-start_worker.R | 13 + 20 files changed, 753 insertions(+), 93 deletions(-)
Title: Compact Inline Widgets for 'shiny' Apps
Description: Provides a basic set of compact widgets for 'shiny' apps which
occupy less space and can appear inline with surrounding text.
Author: Nick Davies [aut, cre]
Maintainer: Nick Davies <nicholas.davies@lshtm.ac.uk>
Diff between inshiny versions 0.1.4 dated 2026-03-31 and 0.1.5 dated 2026-09-01
DESCRIPTION | 11 MD5 | 59 +- NEWS.md | 25 + R/check.R | 4 R/helper.R | 28 + R/number.R | 4 R/select.R | 36 + R/text.R | 9 R/update.R | 34 + README.md | 3 build/vignette.rds |binary inst/doc/inshiny.Rmd | 16 inst/doc/inshiny.html | 25 - inst/www/inshiny/inshiny.css | 18 inst/www/inshiny/inshiny.js | 974 ++++++++++++++++++++++------------------ man/inline.Rd | 6 man/inline_link.Rd | 4 man/inline_switch.Rd | 2 man/inshiny-package.Rd | 5 tests/testthat/_snaps/check.md | 4 tests/testthat/_snaps/number.md | 4 tests/testthat/_snaps/select.md | 8 tests/testthat/_snaps/update.md | 83 ++- tests/testthat/apps |only tests/testthat/helper.R | 3 tests/testthat/test-dynamic.R |only tests/testthat/test-helper.R | 11 tests/testthat/test-text.R | 8 tests/testthat/test-update.R | 19 vignettes/images/vignette_3.jpg |only vignettes/inshiny.Rmd | 16 31 files changed, 896 insertions(+), 523 deletions(-)
Title: LUCID with Multiple Omics Data
Description: Implements Latent Unknown Clusters By Integrating Multi-omics Data
(LUCID; Peng (2019) <doi:10.1093/bioinformatics/btz667>) for integrative
clustering with exposures, multi-omics data, and health outcomes.
Supports three integration strategies: early, parallel, and serial.
Provides model fitting and tuning, lasso-type regularization for exposure
and omics feature selection, handling of missing data, including both
sporadic and complete-case patterns, prediction, and g-computation for
estimating causal effects of exposures, bootstrap inference for
uncertainty estimation, and S3 summary and plot methods. For the
multi-omics integration framework, see Jia (2024)
<https://journal.r-project.org/articles/RJ-2024-012/RJ-2024-012.pdf>.
For the missing-data imputation mechanism, see Jia (2024)
<doi:10.1093/bioadv/vbae123>.
Author: Qiran Jia [aut, cre] ,
Yinqi Zhao [aut] ,
David Conti [ths] ,
Jesse Goodrich [ctb]
Maintainer: Qiran Jia <qiranjia@usc.edu>
Diff between LUCIDus versions 3.1.0 dated 2026-03-11 and 3.2.0 dated 2026-09-01
LUCIDus-3.1.0/LUCIDus/R/00_stability_preload.R |only LUCIDus-3.1.0/LUCIDus/R/EM_all.R |only LUCIDus-3.1.0/LUCIDus/R/early_estep.R |only LUCIDus-3.1.0/LUCIDus/R/early_mstep.R |only LUCIDus-3.1.0/LUCIDus/R/em.R |only LUCIDus-3.1.0/LUCIDus/R/missing.R |only LUCIDus-3.1.0/LUCIDus/R/missing_utils.R |only LUCIDus-3.1.0/LUCIDus/R/pred_lucid.R |only LUCIDus-3.1.0/LUCIDus/R/predict_lucid_all.R |only LUCIDus-3.1.0/LUCIDus/R/summary_auxi_fxn_serial.R |only LUCIDus-3.1.0/LUCIDus/R/utility.R |only LUCIDus-3.1.0/LUCIDus/R/utils.R |only LUCIDus-3.1.0/LUCIDus/inst/tutorials |only LUCIDus-3.1.0/LUCIDus/man/Istep_Z.Rd |only LUCIDus-3.1.0/LUCIDus/man/check_and_stabilize_sigma.Rd |only LUCIDus-3.1.0/LUCIDus/man/check_convergence.Rd |only LUCIDus-3.1.0/LUCIDus/man/fill_data.Rd |only LUCIDus-3.1.0/LUCIDus/man/gen_ci.Rd |only LUCIDus-3.1.0/LUCIDus/man/plot.Rd |only LUCIDus-3.1.0/LUCIDus/man/safe_log_sum_exp.Rd |only LUCIDus-3.1.0/LUCIDus/man/safe_normalize.Rd |only LUCIDus-3.1.0/LUCIDus/man/safe_solve.Rd |only LUCIDus-3.1.0/LUCIDus/man/summarize_missing_stats.Rd |only LUCIDus-3.2.0/LUCIDus/DESCRIPTION | 11 LUCIDus-3.2.0/LUCIDus/MD5 | 250 +- LUCIDus-3.2.0/LUCIDus/NAMESPACE | 17 LUCIDus-3.2.0/LUCIDus/NEWS.md |only LUCIDus-3.2.0/LUCIDus/R/boot_lucid.R | 493 ++++ LUCIDus-3.2.0/LUCIDus/R/data.R | 75 LUCIDus-3.2.0/LUCIDus/R/density_helpers.R |only LUCIDus-3.2.0/LUCIDus/R/early_integration_em.R |only LUCIDus-3.2.0/LUCIDus/R/early_integration_family.R |only LUCIDus-3.2.0/LUCIDus/R/em_utils.R |only LUCIDus-3.2.0/LUCIDus/R/estimate_lucid.R |only LUCIDus-3.2.0/LUCIDus/R/g_computation_utility.R | 114 - LUCIDus-3.2.0/LUCIDus/R/input_validation.R |only LUCIDus-3.2.0/LUCIDus/R/lucid.R | 84 LUCIDus-3.2.0/LUCIDus/R/missing_data_diagnostics.R |only LUCIDus-3.2.0/LUCIDus/R/missing_data_em.R |only LUCIDus-3.2.0/LUCIDus/R/model_extractors.R |only LUCIDus-3.2.0/LUCIDus/R/outcome_utils.R |only LUCIDus-3.2.0/LUCIDus/R/parallel_estep.R | 394 --- LUCIDus-3.2.0/LUCIDus/R/parallel_mstep.R | 547 +---- LUCIDus-3.2.0/LUCIDus/R/plot_cluster_omic_profile.R |only LUCIDus-3.2.0/LUCIDus/R/plot_lucid.R | 210 -- LUCIDus-3.2.0/LUCIDus/R/predict_lucid.R |only LUCIDus-3.2.0/LUCIDus/R/stability_utils.R | 288 ++ LUCIDus-3.2.0/LUCIDus/R/summary.R | 1024 +++------- LUCIDus-3.2.0/LUCIDus/R/tune_lucid.R | 176 + LUCIDus-3.2.0/LUCIDus/build |only LUCIDus-3.2.0/LUCIDus/inst/doc |only LUCIDus-3.2.0/LUCIDus/man/analyze_missing_pattern.Rd | 40 LUCIDus-3.2.0/LUCIDus/man/boot_lucid.Rd | 43 LUCIDus-3.2.0/LUCIDus/man/check_imputation_quality.Rd | 55 LUCIDus-3.2.0/LUCIDus/man/check_na.Rd | 57 LUCIDus-3.2.0/LUCIDus/man/estimate_lucid.Rd | 175 + LUCIDus-3.2.0/LUCIDus/man/figures |only LUCIDus-3.2.0/LUCIDus/man/get_cluster_assignment.Rd |only LUCIDus-3.2.0/LUCIDus/man/get_selected_G.Rd |only LUCIDus-3.2.0/LUCIDus/man/get_selected_Z.Rd |only LUCIDus-3.2.0/LUCIDus/man/get_top_omics_features.Rd |only LUCIDus-3.2.0/LUCIDus/man/lucid.Rd | 38 LUCIDus-3.2.0/LUCIDus/man/plot.early_lucid.Rd |only LUCIDus-3.2.0/LUCIDus/man/plot.lucid_parallel.Rd |only LUCIDus-3.2.0/LUCIDus/man/plot.lucid_serial.Rd |only LUCIDus-3.2.0/LUCIDus/man/plot_cluster_omic_profile.Rd |only LUCIDus-3.2.0/LUCIDus/man/predict_lucid.Rd | 79 LUCIDus-3.2.0/LUCIDus/man/print.sumlucid_early.Rd | 12 LUCIDus-3.2.0/LUCIDus/man/print.sumlucid_parallel.Rd | 11 LUCIDus-3.2.0/LUCIDus/man/print.sumlucid_serial.Rd | 7 LUCIDus-3.2.0/LUCIDus/man/safe_impute.Rd | 47 LUCIDus-3.2.0/LUCIDus/man/sim_data.Rd | 33 LUCIDus-3.2.0/LUCIDus/man/simulated_HELIX_data.Rd | 32 LUCIDus-3.2.0/LUCIDus/man/summary.lucid_parallel.Rd | 10 LUCIDus-3.2.0/LUCIDus/man/summary.lucid_serial.Rd | 28 LUCIDus-3.2.0/LUCIDus/man/summary_lucid.Rd | 67 LUCIDus-3.2.0/LUCIDus/man/tune_lucid.Rd | 30 LUCIDus-3.2.0/LUCIDus/tests/testthat.R | 4 LUCIDus-3.2.0/LUCIDus/tests/testthat/helper-oracle.R |only LUCIDus-3.2.0/LUCIDus/tests/testthat/helper-sim.R |only LUCIDus-3.2.0/LUCIDus/tests/testthat/test-Serial-binary-missing.R | 7 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Title: Recursive Partitioning for Graded Response Models
Description: Provides methods for recursive partitioning based on the
'Graded Response Model' ('GRM'), extending the 'MOB' algorithm from the
'partykit' package. The package allows for fitting
'GRM' trees that partition the population into homogeneous
subgroups based on item response patterns and covariates.
Includes specialized plotting functions for visualizing 'GRM' trees
with different terminal node displays (threshold regions,
parameter profiles, and factor score distributions). The package also implements the Longitudinal GRMTree for detecting response shift in PROMs measured at two time points, embedding a constrained two-factor longitudinal GRM within recursive partitioning, with post-hoc characterization of recalibration and reprioritization. Random-forest ensembles (`grmforest()`) with permutation variable importance are available for both the cross-sectional and longitudinal trees.
For more details on the methods, see Samejima (1969) <doi:10.1002/J.2333-8504.1968.TB00153.X>, Komboz [...truncated...]
Author: Olayinka I. Arimoro [aut, cre] ,
Tolulope T. Sajobi [aut],
Lisa M. Lix [aut],
Matthew T. James [ctb],
Maria Santana [ctb],
Emmanuel Ugochukwu [ctb]
Maintainer: Olayinka I. Arimoro <olayinka.arimoro@ucalgary.ca>
Diff between grmtree versions 0.2.2 dated 2026-08-22 and 0.3.0 dated 2026-09-01
DESCRIPTION | 13 ++- MD5 | 42 ++++++------ NAMESPACE | 1 NEWS.md | 20 +++++- R/grmforest-varimp-final.R | 17 ++++- R/grmforest.R | 108 +++++++++++++++++++++++++++++---- R/longitudinal_grmtree.R | 57 +++++++++-------- README.md | 22 ++++++ inst/doc/GRMForest-implementation.R | 2 inst/doc/GRMForest-implementation.Rmd | 6 - inst/doc/GRMForest-implementation.html | 8 +- inst/doc/longitudinal-grmtree.R | 37 +++++++++++ inst/doc/longitudinal-grmtree.Rmd | 80 +++++++++++++++++++++++- inst/doc/longitudinal-grmtree.html | 85 +++++++++++++++++++++++-- man/grmforest.Rd | 41 +++++++++++- man/longitudinal_grmfit.Rd | 26 ++++--- man/longitudinal_grmtree.Rd | 3 man/varimp.Rd | 15 ++++ tests/testthat/test-grmforest.R | 24 +++++++ tests/testthat/test-varimp.R | 24 +++++++ vignettes/GRMForest-implementation.Rmd | 6 - vignettes/longitudinal-grmtree.Rmd | 80 +++++++++++++++++++++++- 22 files changed, 608 insertions(+), 109 deletions(-)
Title: Efficient Rolling Functions
Description: Fast rolling-window functions for numeric vectors.
Designed for efficient processing of environmental time-series data.
Author: Jonathan Callahan [aut, cre],
Hans Martin [aut]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between MazamaRollUtils versions 1.0.0 dated 2026-03-17 and 1.1.0 dated 2026-09-01
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More information about MazamaRollUtils at CRAN
Permanent link
Title: Basic Functions in Knowledge Space Theory Using Matrix
Representation
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework, which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kstMatrix' package
provides basic functionalities to generate, handle, and manipulate
knowledge structures and knowledge spaces. Opposed to the 'kst'
package, 'kstMatrix' uses matrix representations for knowledge
structures. Furthermore, 'kstMatrix' contains several knowledge spaces
obtained in the 1990s by the research group around Cornelia Dowling
through querying experts.
Author: Cord Hockemeyer [aut, cre],
Peter Steiner [aut],
Wai Wong [aut]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kstMatrix versions 2.3-4 dated 2026-07-15 and 3.0-0 dated 2026-09-01
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kstMatrix-3.0-0/kstMatrix/man/fractions.Rd | 8 kstMatrix-3.0-0/kstMatrix/man/kmSF2basis.Rd | 24 kstMatrix-3.0-0/kstMatrix/man/kmSR2basis.Rd | 24 kstMatrix-3.0-0/kstMatrix/man/kmSRdiagram.Rd |only kstMatrix-3.0-0/kstMatrix/man/kmSRvalidate.Rd | 7 kstMatrix-3.0-0/kstMatrix/man/kmassess.Rd | 4 kstMatrix-3.0-0/kstMatrix/man/kmassessbayesian.Rd | 4 kstMatrix-3.0-0/kstMatrix/man/kmassesshalfsplit.Rd | 4 kstMatrix-3.0-0/kstMatrix/man/kmassessinformative.Rd | 6 kstMatrix-3.0-0/kstMatrix/man/kmassessmentsimulation.Rd | 4 kstMatrix-3.0-0/kstMatrix/man/kmassessmultiplicative.Rd | 4 kstMatrix-3.0-0/kstMatrix/man/kmbasis.Rd | 30 kstMatrix-3.0-0/kstMatrix/man/kmbasisdiagram.Rd |only kstMatrix-3.0-0/kstMatrix/man/kmbasisfringe.Rd | 9 kstMatrix-3.0-0/kstMatrix/man/kmbasisneighbourhood.Rd | 9 kstMatrix-3.0-0/kstMatrix/man/kmclosure.Rd |only kstMatrix-3.0-0/kstMatrix/man/kmcolors.Rd | 12 kstMatrix-3.0-0/kstMatrix/man/kmdist.Rd | 7 kstMatrix-3.0-0/kstMatrix/man/kmdoubleequal.Rd | 6 kstMatrix-3.0-0/kstMatrix/man/kmeqreduction.Rd | 15 kstMatrix-3.0-0/kstMatrix/man/kmexpand.Rd |only kstMatrix-3.0-0/kstMatrix/man/kmfamset.Rd | 1 kstMatrix-3.0-0/kstMatrix/man/kmfringe.Rd | 9 kstMatrix-3.0-0/kstMatrix/man/kmgenerate.Rd | 10 kstMatrix-3.0-0/kstMatrix/man/kmgradations.Rd | 13 kstMatrix-3.0-0/kstMatrix/man/kmhasse.Rd |only kstMatrix-3.0-0/kstMatrix/man/kmheights.Rd |only kstMatrix-3.0-0/kstMatrix/man/kmiita2SR.Rd | 12 kstMatrix-3.0-0/kstMatrix/man/kmintersection.Rd |only kstMatrix-3.0-0/kstMatrix/man/kmintersectionclosure.Rd |only kstMatrix-3.0-0/kstMatrix/man/kmiswellgraded.Rd | 15 kstMatrix-3.0-0/kstMatrix/man/kmlearningpathmatrices.Rd |only kstMatrix-3.0-0/kstMatrix/man/kmlearningpaths.Rd | 31 kstMatrix-3.0-0/kstMatrix/man/kmmesh.Rd |only kstMatrix-3.0-0/kstMatrix/man/kmminimalfamset.Rd | 5 kstMatrix-3.0-0/kstMatrix/man/kmneighbourhood.Rd | 24 kstMatrix-3.0-0/kstMatrix/man/kmnotions.Rd | 12 kstMatrix-3.0-0/kstMatrix/man/kmprettyprint.Rd |only kstMatrix-3.0-0/kstMatrix/man/kmqspace.Rd |only kstMatrix-3.0-0/kstMatrix/man/kmrefine.Rd |only kstMatrix-3.0-0/kstMatrix/man/kmsetiselement.Rd | 5 kstMatrix-3.0-0/kstMatrix/man/kmsimulate.Rd | 10 kstMatrix-3.0-0/kstMatrix/man/kmspace.Rd | 39 kstMatrix-3.0-0/kstMatrix/man/kmstructure.Rd | 1 kstMatrix-3.0-0/kstMatrix/man/kmsubstructure.Rd |only kstMatrix-3.0-0/kstMatrix/man/kmsurmisefunction.Rd | 14 kstMatrix-3.0-0/kstMatrix/man/kmsurmiserelation.Rd | 10 kstMatrix-3.0-0/kstMatrix/man/kmsymmsetdiff.Rd | 5 kstMatrix-3.0-0/kstMatrix/man/kmtrivial.Rd | 24 kstMatrix-3.0-0/kstMatrix/man/kmunion.Rd |only kstMatrix-3.0-0/kstMatrix/man/kmunionclosure.Rd | 35 kstMatrix-3.0-0/kstMatrix/man/kmvalidate.Rd | 9 kstMatrix-3.0-0/kstMatrix/man/phsg.Rd | 8 kstMatrix-3.0-0/kstMatrix/man/plot.Rd | 87 kstMatrix-3.0-0/kstMatrix/man/readwrite.Rd | 8 kstMatrix-3.0-0/kstMatrix/man/xpl.Rd | 8 kstMatrix-3.0-0/kstMatrix/vignettes/SR.jpeg |only kstMatrix-3.0-0/kstMatrix/vignettes/emptyhead.jpeg |only kstMatrix-3.0-0/kstMatrix/vignettes/horizontal.jpeg |only kstMatrix-3.0-0/kstMatrix/vignettes/kstMatrix-Classes.png |only kstMatrix-3.0-0/kstMatrix/vignettes/kstMatrix.Rmd | 270 +- kstMatrix-3.0-0/kstMatrix/vignettes/neighbourhood.jpeg |only kstMatrix-3.0-0/kstMatrix/vignettes/neighbourhood2.png |only kstMatrix-3.0-0/kstMatrix/vignettes/space.jpeg |only 159 files changed, 2915 insertions(+), 1206 deletions(-)
Title: Improve the Coherence of Your Time Series Data
Description: 'R' version of 'G-Series', Statistics Canada's generalized system devoted
to the benchmarking and reconciliation of time series data. The methods
used in 'G-Series' essentially come from Dagum, E. B., and P. Cholette
(2006) <doi:10.1007/0-387-35439-5>.
Author: Michel Ferland [aut, cre],
Statistics Canada [cph, fnd]
Maintainer: Michel Ferland <michel.ferland@statcan.gc.ca>
Diff between gseries versions 3.0.2 dated 2025-06-18 and 3.0.3 dated 2026-09-01
DESCRIPTION | 10 MD5 | 86 +- NEWS.md | 20 R/benchmarking.R | 4 R/data.R | 2 R/plot_graphTable.R | 3 R/sysdata.rda |binary R/tsbalancing.R | 127 ++- R/tsraking.R | 2 R/utils-common.R | 2 README.md | 14 build/partial.rdb |binary build/vignette.rds |binary data/alternate_osqp_sequence.rda |binary data/default_osqp_sequence.rda |binary inst/doc/benchmarking-demo-script.R | 468 ++++++++----- inst/doc/benchmarking-demo-script.Rmd | 468 ++++++++----- inst/doc/benchmarking-demo-script.html | 858 ++++++++++++++----------- inst/doc/gseries.Rmd | 4 inst/doc/gseries.html | 6 inst/doc/osqp-settings-sequence-dataframe.html | 84 +- man/bench_graphs.Rd | 43 - man/benchmarking.Rd | 182 +++-- man/build_balancing_problem.Rd | 54 - man/build_raking_problem.Rd | 40 - man/gs.build_proc_grps.Rd | 92 +- man/gseries-package.Rd | 5 man/osqp_settings_sequence.Rd | 6 man/plot_benchAdj.Rd | 43 - man/plot_graphTable.Rd | 34 man/rkMeta_to_blSpecs.Rd | 16 man/stack_bmkDF.Rd | 14 man/stack_tsDF.Rd | 12 man/stock_benchmarking.Rd | 284 ++++---- man/time_values_conv.Rd | 4 man/tsDF_to_ts.Rd | 33 man/ts_to_bmkDF.Rd | 48 - man/ts_to_tsDF.Rd | 7 man/tsbalancing.Rd | 390 ++++++----- man/tsraking.Rd | 134 ++- man/tsraking_driver.Rd | 170 +++- man/unstack_tsDF.Rd | 42 - vignettes/benchmarking-demo-script.Rmd | 468 ++++++++----- vignettes/gseries.Rmd | 4 44 files changed, 2591 insertions(+), 1692 deletions(-)
Title: Create Upset Plots
Description: Create Upset plots using a combination of 'ggplot2' and 'patchwork'.
Author: Stevie Pederson [aut, cre] ,
Lachlan Baer [ctb]
Maintainer: Stevie Pederson <stephen.pederson.au@gmail.com>
Diff between SimpleUpset versions 0.1.5 dated 2026-06-30 and 0.1.6 dated 2026-09-01
DESCRIPTION | 8 +++--- MD5 | 8 +++--- NAMESPACE | 56 +++++++++++++++++++++++++-------------------- R/defaults.R | 4 +-- inst/doc/introduction.html | 18 +++++++------- 5 files changed, 51 insertions(+), 43 deletions(-)
Title: Production Function Estimation
Description: Implements the methods proposed by Olley, G.S. and Pakes, A. (1996) <doi:10.2307/2171831>, Levinsohn, J. and Petrin, A. (2003) <doi:10.1111/1467-937X.00246>, Ackerberg, D.A. and Caves, K. and Frazer, G. (2015) <doi:10.3982/ECTA13408> and Wooldridge, J.M. (2009) <doi:10.1016/j.econlet.2009.04.026> for structural productivity estimation.
Author: Gabriele Rovigatti [aut, cre]
Maintainer: Gabriele Rovigatti <gabriele.rovigatti@gmail.com>
Diff between prodest versions 1.0.1 dated 2018-06-19 and 1.0.2 dated 2026-09-01
prodest-1.0.1/prodest/inst/doc |only prodest-1.0.2/prodest/DESCRIPTION | 20 - prodest-1.0.2/prodest/MD5 | 54 ++-- prodest-1.0.2/prodest/NEWS | 25 + prodest-1.0.2/prodest/R/ClassMethods.R | 2 prodest-1.0.2/prodest/R/auxFun.R | 156 ++++++++++-- prodest-1.0.2/prodest/R/panelSim.R | 16 - prodest-1.0.2/prodest/R/prodestACF.R | 294 +++++++++++++++-------- prodest-1.0.2/prodest/R/prodestOPLP.R | 24 - prodest-1.0.2/prodest/README.md | 43 +-- prodest-1.0.2/prodest/data/chilean.rda |binary prodest-1.0.2/prodest/inst/CITATION | 49 ++- prodest-1.0.2/prodest/man/block.boot.resample.Rd | 68 ++--- prodest-1.0.2/prodest/man/checkM.Rd | 2 prodest-1.0.2/prodest/man/checkMD.Rd | 2 prodest-1.0.2/prodest/man/chilean.Rd | 77 ++---- prodest-1.0.2/prodest/man/gACF.Rd | 100 +++---- prodest-1.0.2/prodest/man/gOPLP.Rd | 2 prodest-1.0.2/prodest/man/lagPanel.Rd | 68 ++--- prodest-1.0.2/prodest/man/method-summary.Rd | 6 prodest-1.0.2/prodest/man/panelSim.Rd | 60 ++-- prodest-1.0.2/prodest/man/prodestACF.Rd | 12 prodest-1.0.2/prodest/man/prodestLP.Rd | 9 prodest-1.0.2/prodest/man/prodestOP.Rd | 16 - prodest-1.0.2/prodest/man/prodestROB.Rd | 4 prodest-1.0.2/prodest/man/prodestWRDG.Rd | 4 prodest-1.0.2/prodest/man/prodestWRDG_GMM.Rd | 4 prodest-1.0.2/prodest/man/weightM.Rd | 2 prodest-1.0.2/prodest/tests |only 29 files changed, 688 insertions(+), 431 deletions(-)
Title: Querying and Managing Large Biodiversity Occurrence Datasets
Description: Facilitates the gathering of biodiversity occurrence data
from disparate sources. Metadata is managed throughout the process to facilitate
reporting and enhanced ability to repeat analyses.
Author: Hannah L. Owens [aut, cre] ,
Cory Merow [aut] ,
Brian Maitner [aut] ,
Jamie M. Kass [aut] ,
Vijay Barve [aut] ,
Robert P. Guralnick [aut] ,
Damiano Oldoni [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/407>)
Maintainer: Hannah L. Owens <hannah.owens@gmail.com>
Diff between occCite versions 0.6.2 dated 2026-06-29 and 0.6.3 dated 2026-09-01
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Title: Lightweight Tables via JSON Specs and JavaScript
Description: A lightweight grammar of tables. Build a table by declaring a JSON
spec (titles, spanners, row groups, footnotes, formatting functions, etc.); a tiny
vanilla JavaScript runtime builds the HTML table from the spec on page
load. No 'sass', no 'V8', no 'htmlwidgets' — just base R and 'xfun'
('htmltools' is used only for the optional Shiny binding).
Author: Yihui Xie [aut, cre, cph]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between lt versions 0.3 dated 2026-08-19 and 0.4 dated 2026-09-01
DESCRIPTION | 10 +++--- MD5 | 28 ++++++++-------- NEWS.md | 6 +++ R/lt.R | 6 +++ R/render.R | 13 ++++++- R/tab.R | 41 ++++++++++++++++++++---- README.md | 4 +- inst/www/lt.js | 37 +++++++++++++++++++--- man/lt.Rd | 9 +++++ man/lt_footnote.Rd | 18 ++++++++++ man/lt_format.Rd | 8 ++++ man/lt_sub.Rd | 7 ++-- tests/test-ci/test-js.R | 75 +++++++++++++++++++++++++++++++++++++++++++-- tests/testit/test-render.R | 17 ++++++++++ tests/testit/test-tab.R | 44 ++++++++++++++++++++++++++ 15 files changed, 283 insertions(+), 40 deletions(-)
Title: Random Hazard Forests
Description: Random Hazard Forests (RHF) extend Random Survival
Forests (RSF) by directly estimating the hazard function and by
accommodating time-dependent covariates through counting-process
style inputs. The package fits tree ensembles for dynamic survival
prediction, returning hazard, cumulative hazard, integrated hazard,
and related performance summaries for training and test data. The
methods build on Random Survival Forests described by Ishwaran et
al. (2008) <doi:10.1214/08-AOAS169> and on nonparametric hazard
modeling with time-dependent covariates described by Lee et
al. (2021) <doi:10.1214/20-AOS2028>.
Author: Hemant Ishwaran [aut],
Udaya B. Kogalur [aut, cre]
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestRHF versions 2.0.0 dated 2026-08-28 and 2.0.3 dated 2026-09-01
DESCRIPTION | 8 - MD5 | 30 ++--- NEWS.md | 8 + R/auct.rhf.R | 111 +++++++++++++++++++- R/predict.rhf.R | 10 + R/predict.rhf.workhorse.R | 40 ++++++- R/rhf.R | 36 ++++++ R/rhf.workhorse.R | 10 + R/tune.treesize.rhf.R | 189 ++++++++++++++--------------------- R/utilities_additional.R | 17 +++ R/utilities_tdc.R | 248 ++++++++++++++++++++++++++++++++++++++++++++++ man/predict.rhf.Rd | 67 ++++++++---- man/rhf.Rd | 177 +++++++++++++++++++------------- man/tune.treesize.rhf.Rd | 61 ++++++++--- src/global.h | 1 src/processEnsemble.c | 50 +++++++++ 16 files changed, 806 insertions(+), 257 deletions(-)
More information about randomForestRHF at CRAN
Permanent link
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] ,
Christophe Dervieux [aut] ,
Jonathan McPherson [aut],
Javier Luraschi [aut],
Kevin Ushey [aut],
Aron Atkins [aut],
Hadley Wickham [aut],
Joe Cheng [aut],
Winston Chang [aut],
Richard Iannone [aut] ,
Andrew Dun [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rmarkdown versions 2.31 dated 2026-03-26 and 2.32 dated 2026-09-01
rmarkdown-2.31/rmarkdown/inst/rmd/latex |only rmarkdown-2.32/rmarkdown/DESCRIPTION | 15 rmarkdown-2.32/rmarkdown/LICENSE |only rmarkdown-2.32/rmarkdown/MD5 | 140 + rmarkdown-2.32/rmarkdown/NAMESPACE | 20 rmarkdown-2.32/rmarkdown/NEWS.md | 26 rmarkdown-2.32/rmarkdown/R/beamer_presentation.R | 99 - rmarkdown-2.32/rmarkdown/R/github_document.R | 14 rmarkdown-2.32/rmarkdown/R/html_dependencies.R | 22 rmarkdown-2.32/rmarkdown/R/html_document.R | 10 rmarkdown-2.32/rmarkdown/R/html_document_base.R | 5 rmarkdown-2.32/rmarkdown/R/html_fragment.R | 2 rmarkdown-2.32/rmarkdown/R/html_resources.R | 13 rmarkdown-2.32/rmarkdown/R/html_vignette.R | 2 rmarkdown-2.32/rmarkdown/R/ioslides_presentation.R | 20 rmarkdown-2.32/rmarkdown/R/md_document.R | 7 rmarkdown-2.32/rmarkdown/R/odt_document.R | 2 rmarkdown-2.32/rmarkdown/R/output_format.R | 2 rmarkdown-2.32/rmarkdown/R/pandoc.R | 26 rmarkdown-2.32/rmarkdown/R/pdf_document.R | 16 rmarkdown-2.32/rmarkdown/R/powerpoint_presentation.R | 3 rmarkdown-2.32/rmarkdown/R/render.R | 65 rmarkdown-2.32/rmarkdown/R/rtf_document.R | 2 rmarkdown-2.32/rmarkdown/R/slidy_presentation.R | 2 rmarkdown-2.32/rmarkdown/R/util.R | 12 rmarkdown-2.32/rmarkdown/R/word_document.R | 6 rmarkdown-2.32/rmarkdown/README.md | 6 rmarkdown-2.32/rmarkdown/build/vignette.rds |binary rmarkdown-2.32/rmarkdown/inst/CITATION | 4 rmarkdown-2.32/rmarkdown/inst/COPYING | 701 ---------- rmarkdown-2.32/rmarkdown/inst/doc/lua-filters.Rmd | 4 rmarkdown-2.32/rmarkdown/inst/doc/lua-filters.html | 4 rmarkdown-2.32/rmarkdown/inst/doc/rmarkdown.R | 2 rmarkdown-2.32/rmarkdown/inst/doc/rmarkdown.Rmd | 52 rmarkdown-2.32/rmarkdown/inst/doc/rmarkdown.html | 71 - rmarkdown-2.32/rmarkdown/inst/rmarkdown/lua/extract-data-uri.lua |only rmarkdown-2.32/rmarkdown/inst/rmarkdown/lua/latex-div.lua | 9 rmarkdown-2.32/rmarkdown/inst/rmarkdown/lua/number-sections.lua | 9 rmarkdown-2.32/rmarkdown/inst/rmarkdown/lua/pagebreak.lua | 10 rmarkdown-2.32/rmarkdown/inst/rmarkdown/lua/shared.lua | 16 rmarkdown-2.32/rmarkdown/inst/rmarkdown/templates/html_vignette/skeleton/skeleton.Rmd | 2 rmarkdown-2.32/rmarkdown/inst/rmd/ioslides/ioslides_presentation.lua | 8 rmarkdown-2.32/rmarkdown/inst/rmd/site/index.Rmd | 2 rmarkdown-2.32/rmarkdown/man/beamer_presentation.Rd | 4 rmarkdown-2.32/rmarkdown/man/context_document.Rd | 2 rmarkdown-2.32/rmarkdown/man/github_document.Rd | 2 rmarkdown-2.32/rmarkdown/man/html_document.Rd | 8 rmarkdown-2.32/rmarkdown/man/html_fragment.Rd | 4 rmarkdown-2.32/rmarkdown/man/html_vignette.Rd | 4 rmarkdown-2.32/rmarkdown/man/ioslides_presentation.Rd | 4 rmarkdown-2.32/rmarkdown/man/md_document.Rd | 4 rmarkdown-2.32/rmarkdown/man/metadata.Rd | 5 rmarkdown-2.32/rmarkdown/man/odt_document.Rd | 2 rmarkdown-2.32/rmarkdown/man/output_format.Rd | 2 rmarkdown-2.32/rmarkdown/man/output_metadata.Rd | 1 rmarkdown-2.32/rmarkdown/man/pandoc_available.Rd | 2 rmarkdown-2.32/rmarkdown/man/pdf_document.Rd | 4 rmarkdown-2.32/rmarkdown/man/powerpoint_presentation.Rd | 2 rmarkdown-2.32/rmarkdown/man/rmarkdown-package.Rd | 3 rmarkdown-2.32/rmarkdown/man/rtf_document.Rd | 2 rmarkdown-2.32/rmarkdown/man/slidy_presentation.Rd | 4 rmarkdown-2.32/rmarkdown/man/word_document.Rd | 4 rmarkdown-2.32/rmarkdown/tests/testthat/helpers.R | 20 rmarkdown-2.32/rmarkdown/tests/testthat/test-draft.R | 14 rmarkdown-2.32/rmarkdown/tests/testthat/test-html_dependencies.R | 47 rmarkdown-2.32/rmarkdown/tests/testthat/test-ioslides-figures.R |only rmarkdown-2.32/rmarkdown/tests/testthat/test-lua-filters.R | 34 rmarkdown-2.32/rmarkdown/tests/testthat/test-pandoc.R | 11 rmarkdown-2.32/rmarkdown/tests/testthat/test-pdf_document.R | 61 rmarkdown-2.32/rmarkdown/tests/testthat/test-resources.R | 65 rmarkdown-2.32/rmarkdown/tests/testthat/test-utils.R | 18 rmarkdown-2.32/rmarkdown/vignettes/lua-filters.Rmd | 4 rmarkdown-2.32/rmarkdown/vignettes/rmarkdown.Rmd | 52 73 files changed, 670 insertions(+), 1150 deletions(-)
Title: Feature Selection (Including Multiple Solutions) and Bayesian
Networks
Description: Many feature selection methods for a wide range of response variables, including minimal, statistically-equivalent and equally-predictive feature subsets. Bayesian network algorithms and related functions are also included. The package name 'MXM' stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin. References: a) Lagani, V. and Athineou, G. and Farcomeni, A. and Tsagris, M. and Tsamardinos, I. (2017). "Feature Selection with the R Package MXM: Discovering Statistically Equivalent Feature Subsets". Journal of Statistical Software, 80(7). <doi:10.18637/jss.v080.i07>. b) Tsagris, M., Lagani, V. and Tsamardinos, I. (2018). "Feature selection for high-dimensional temporal data". BMC Bioinformatics, 19:17. <doi:10.1186/s12859-018-2023-7>. c) Tsagris, M., Borboudakis, G., Lagani, V. and Tsamardinos, I. (2018). "Constraint-based causal discovery with mixed data". International Journal of Data Science and Analytics, 6(1): 19-30. <doi:10.1007/s41060-018-0097-y&g [...truncated...]
Author: Konstantina Biza [aut],
Ioannis Tsamardinos [aut, cph],
Vincenzo Lagani [aut, cph],
Giorgos Athineou [aut],
Michail Tsagris [aut],
Giorgos Borboudakis [ctb],
Anna Roumpelaki [ctb],
Stavros Papadopoulos [cre]
Maintainer: Stavros Papadopoulos <staurospapflor@gmail.com>
This is a re-admission after prior archival of version 1.5.5 dated 2022-08-25
Diff between MXM versions 1.5.5 dated 2022-08-25 and 1.5.8 dated 2026-09-01
DESCRIPTION | 30 - MD5 | 248 ++++----- NEWS |only R/MMPC.R | 2 R/MMPC.timeclass.R | 2 R/SES.timeclass.R | 2 R/beta.mod.R | 2 R/beta.reg.R | 2 R/beta.regs.R | 7 R/betamle.wei.R | 2 R/big.gomp.R | 2 R/censIndCR.R | 2 R/clogit.fsreg.R | 2 R/clogit.fsreg_2.R | 2 R/cond.regs.R | 2 R/corgraph.R | 2 R/cv.gomp.R | 2 R/dag_to_eg.R | 2 R/ebic.regs.R | 2 R/gee.condregs.R | 2 R/generatefolds.R | 10 R/glmm.condregs.R | 2 R/gomp.R | 2 R/mmhc.skel.R | 2 R/mmpc.or.R | 2 R/ordinal.reg.R | 2 R/perm.betaregs.R | 6 R/perm.mmpc.R | 2 R/perm.zipregs.R | 6 R/permCR.R | 2 R/rdag.R | 17 R/ridgereg.cv.R | 17 R/testIndGEEGamma.R | 2 R/testIndGEELogistic.R | 2 R/testIndGEENormLog.R | 2 R/testIndGEEPois.R | 2 R/testIndGEEReg.R | 2 R/testIndGLMMCR.R | 3 R/testIndGLMMGamma.R | 2 R/testIndGLMMLogistic.R | 2 R/testIndGLMMNB.R | 3 R/testIndGLMMNormLog.R | 2 R/testIndGLMMOrdinal.R | 2 R/testIndGLMMPois.R | 3 R/testIndGLMMReg.R | 2 R/testIndLMM.R | 3 R/wald.betaregs.R | 6 R/wald.mmpc.R | 2 R/waldCR.R | 2 R/zinb.mod.R | 2 R/zinb.reg.R | 2 R/zip.reg.R | 2 R/zip.regs.R | 6 build/partial.rdb |only build/vignette.rds |binary inst/COPYRIGHTS |only inst/doc/FS_guide.ltx | 4 inst/doc/FS_guide.pdf |binary inst/doc/MMPC_tutorial.R | 86 +-- inst/doc/MMPC_tutorial.Rmd | 28 - inst/doc/MMPC_tutorial.html | 724 +++++++++------------------- inst/doc/SES_KMVerrou_11_12.R | 10 inst/doc/SES_KMVerrou_11_12.Rmd | 21 inst/doc/SES_KMVerrou_11_12.html | 1006 ++++++++++++++------------------------- inst/doc/article.ltx | 16 inst/doc/article.pdf |binary inst/doc/guide.pdf |binary inst/extdata |only man/MXM-internal.Rd | 18 man/MXMCondIndTests.Rd | 2 man/SES.glmm.Rd | 22 man/bbc.Rd | 2 man/beta.mod.Rd | 2 man/beta.regs.Rd | 2 man/big.fbed.reg.Rd | 25 man/big.gomp.Rd | 16 man/censIndCR.Rd | 12 man/condis.Rd | 2 man/corfs.network.Rd | 2 man/cv.fbed.lmm.reg.Rd | 24 man/cv.gomp.Rd | 10 man/cv.ses.Rd | 2 man/dag2eg.Rd | 11 man/ebic.glmm.bsreg.Rd | 22 man/fbed.gee.reg.Rd | 22 man/fbed.glmm.reg.Rd | 19 man/generatefolds.Rd | 7 man/glmm.bsreg.Rd | 10 man/gomp.Rd | 2 man/is.dag.Rd | 2 man/local.mmhc.skel.Rd | 2 man/logiquant.regs.Rd | 2 man/mb.Rd | 2 man/mmhc.skel.Rd | 2 man/mmpc.glmm.model.Rd | 10 man/mmpc.glmm2.Rd | 8 man/mmpc.or.Rd | 2 man/mmpc.timeclass.model.Rd | 2 man/modeler.Rd | 2 man/nei.Rd | 2 man/ordinal.reg.Rd | 2 man/pc.or.Rd | 2 man/pc.sel.Rd | 2 man/pc.skel.Rd | 2 man/plotnetwork.Rd | 10 man/rdag.Rd | 7 man/read.big.data.Rd | 12 man/reg.fit.Rd | 2 man/ridge.plot.Rd | 2 man/ridge.reg.Rd | 2 man/ridgereg.cv.Rd | 9 man/ses.model.Rd | 2 man/sp.logiregs.Rd | 4 man/tc.plot.Rd | 2 man/testIndTobit.Rd | 4 man/topological_sort.Rd | 2 man/transitiveClosure.Rd | 2 man/undir.path.Rd | 2 man/wald.logisticregs.Rd | 2 man/zip.regs.Rd | 2 vignettes/FS_guide.ltx | 4 vignettes/JSS.bib | 4 vignettes/MMPC_tutorial.Rmd | 28 - vignettes/SES_KMVerrou_11_12.Rmd | 21 vignettes/article.ltx | 16 vignettes/athineou.bib | 43 - vignettes/biblio.bib | 8 127 files changed, 1096 insertions(+), 1708 deletions(-)
Title: Johnson-Neyman Analysis of Two- and Three-Way Interactions
Description: Reports and plots the conditional effect of each variable
involved in a multiplicative interaction across the range of its
moderators, together with the region over which that effect is
distinguishable from zero. Extends the classic framework of Johnson and
Neyman (1936) and Johnson and Fay (1950) <doi:10.1007/BF02288864> to
three-way interactions and to Bayesian models. The single entry point
JN() dispatches on the fitted object, with methods for lm()/glm()
models, 'lme4' models, 'RSiena' and 'multiSiena' results, and matrices
of posterior draws; support for further model classes is added by
writing one jn_input() method. Results are classed objects with print(),
summary() and plot() methods, and the figures carry data-density panels
showing how much empirical support each part of the moderator range has.
A detailed introduction can be found in Krause (2026)
<doi:10.48550/arXiv.2604.22051>.
Author: Robert W. Krause [aut, cre, cph]
Maintainer: Robert W. Krause <robert.w.krause@mailbox.org>
Diff between int3ract versions 1.0.7 dated 2026-05-05 and 2.0.0 dated 2026-09-01
int3ract-1.0.7/int3ract/R/JNK_bayes.R |only int3ract-1.0.7/int3ract/R/JNK_freq.R |only int3ract-2.0.0/int3ract/DESCRIPTION | 31 int3ract-2.0.0/int3ract/MD5 | 54 + int3ract-2.0.0/int3ract/NAMESPACE | 91 ++ int3ract-2.0.0/int3ract/NEWS.md | 145 +++- int3ract-2.0.0/int3ract/R/JN.R |only int3ract-2.0.0/int3ract/R/deprecated.R |only int3ract-2.0.0/int3ract/R/engine.R |only int3ract-2.0.0/int3ract/R/int3ract-package.R |only int3ract-2.0.0/int3ract/R/jn_input.R |only int3ract-2.0.0/int3ract/R/methods.R |only int3ract-2.0.0/int3ract/R/plot.R |only int3ract-2.0.0/int3ract/R/regions.R |only int3ract-2.0.0/int3ract/R/siena.R |only int3ract-2.0.0/int3ract/R/utils.R | 794 ------------------------ int3ract-2.0.0/int3ract/README.md | 158 +++- int3ract-2.0.0/int3ract/build |only int3ract-2.0.0/int3ract/inst/doc |only int3ract-2.0.0/int3ract/man/JN.Rd |only int3ract-2.0.0/int3ract/man/JNK_bayes.Rd | 139 ---- int3ract-2.0.0/int3ract/man/JNK_freq.Rd | 148 +--- int3ract-2.0.0/int3ract/man/as.data.frame.JN.Rd |only int3ract-2.0.0/int3ract/man/int3ract-package.Rd |only int3ract-2.0.0/int3ract/man/jn_input.Rd |only int3ract-2.0.0/int3ract/man/jn_plots.Rd |only int3ract-2.0.0/int3ract/man/jn_regions.Rd |only int3ract-2.0.0/int3ract/man/jn_save.Rd |only int3ract-2.0.0/int3ract/man/jn_style.Rd |only int3ract-2.0.0/int3ract/man/plot.JN.Rd |only int3ract-2.0.0/int3ract/man/print.JN.Rd |only int3ract-2.0.0/int3ract/man/print.JN_list.Rd |only int3ract-2.0.0/int3ract/man/reexports.Rd |only int3ract-2.0.0/int3ract/man/summary.JN.Rd |only int3ract-2.0.0/int3ract/tests |only int3ract-2.0.0/int3ract/vignettes |only 36 files changed, 477 insertions(+), 1083 deletions(-)
Title: Tools for Working with URLs and HTTP
Description: Useful tools for working with HTTP organised by HTTP verbs
(GET(), POST(), etc). Configuration functions make it easy to control
additional request components (authenticate(), add_headers() and so
on).
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between httr versions 1.4.8 dated 2026-02-13 and 1.4.9 dated 2026-09-01
DESCRIPTION | 8 ++--- MD5 | 68 ++++++++++++++++++++++----------------------- NEWS.md | 4 ++ R/http-verb.R | 4 +- build/vignette.rds |binary man/BROWSE.Rd | 16 +++++----- man/DELETE.Rd | 16 +++++----- man/GET.Rd | 16 +++++----- man/HEAD.Rd | 16 +++++----- man/PATCH.Rd | 16 +++++----- man/POST.Rd | 16 +++++----- man/PUT.Rd | 16 +++++----- man/VERB.Rd | 18 +++++------ man/add_headers.Rd | 16 +++++----- man/authenticate.Rd | 16 +++++----- man/config.Rd | 22 +++++++------- man/content.Rd | 16 +++++----- man/handle_pool.Rd | 1 man/http_error.Rd | 10 +++--- man/http_status.Rd | 10 +++--- man/httr-package.Rd | 5 +++ man/oauth1.0_token.Rd | 10 +++--- man/oauth2.0_token.Rd | 10 +++--- man/oauth_app.Rd | 10 +++--- man/oauth_endpoint.Rd | 10 +++--- man/oauth_service_token.Rd | 10 +++--- man/response.Rd | 10 +++--- man/set_config.Rd | 6 +-- man/set_cookies.Rd | 16 +++++----- man/stop_for_status.Rd | 10 +++--- man/timeout.Rd | 18 +++++------ man/use_proxy.Rd | 16 +++++----- man/user_agent.Rd | 16 +++++----- man/verbose.Rd | 16 +++++----- man/with_config.Rd | 6 +-- 35 files changed, 241 insertions(+), 233 deletions(-)
Title: Grammar of Graphics and Plot Helpers for Time Series
Visualization
Description: Extends the capabilities of 'ggplot2' by providing grammatical
elements and plot helpers designed for visualizing temporal patterns. The
package implements a grammar of temporal graphics, which leverages calendar
structures to highlight changes over time. The package also provides plot
helper functions to quickly produce commonly used time series graphics,
including time plots, season plots, and seasonal sub-series plots.
Author: Mitchell O'Hara-Wild [aut, cre] ,
Cynthia A. Huang [aut] ,
Matthew Kay [aut] ,
Rob Hyndman [aut] ,
Earo Wang [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between ggtime versions 0.2.0 dated 2026-02-09 and 1.0.0 dated 2026-09-01
ggtime-0.2.0/ggtime/man/figures/README-unnamed-chunk-2-1.png |only ggtime-0.2.0/ggtime/tests/testthat/_snaps/coord-calendar/inf-segment-and-hline.svg |only ggtime-0.2.0/ggtime/tests/testthat/_snaps/coord-loop/loop-ljust-0-5.svg |only ggtime-0.2.0/ggtime/tests/testthat/_snaps/coord-loop/loop-ljust-0.svg |only ggtime-0.2.0/ggtime/tests/testthat/_snaps/coord-loop/loop-ljust-1.svg |only ggtime-0.2.0/ggtime/tests/testthat/_snaps/coord-loop/radial-ljust-0-5.svg |only ggtime-0.2.0/ggtime/tests/testthat/_snaps/coord-loop/time-loop-ljust-0-5.svg |only ggtime-0.2.0/ggtime/tests/testthat/_snaps/coord-loop/time-loop-ljust-0.svg |only ggtime-0.2.0/ggtime/tests/testthat/_snaps/coord-loop/time-loop-ljust-1.svg |only ggtime-0.2.0/ggtime/tests/testthat/_snaps/coord-loop/time-loops-clip-loops-off.svg |only ggtime-1.0.0/ggtime/DESCRIPTION | 11 ggtime-1.0.0/ggtime/MD5 | 81 ++-- ggtime-1.0.0/ggtime/NAMESPACE | 22 + ggtime-1.0.0/ggtime/NEWS.md | 28 + ggtime-1.0.0/ggtime/R/coord-calendar.R |only ggtime-1.0.0/ggtime/R/coord-loop.R |only ggtime-1.0.0/ggtime/R/geom-time-line.R |only ggtime-1.0.0/ggtime/R/ggtime-package.R | 1 ggtime-1.0.0/ggtime/R/loop-cut.R |only ggtime-1.0.0/ggtime/R/plot-helpers.R | 22 - ggtime-1.0.0/ggtime/R/range-time.R |only ggtime-1.0.0/ggtime/R/scale-time.R |only ggtime-1.0.0/ggtime/R/transform.R |only ggtime-1.0.0/ggtime/R/utils.R | 200 ++++++++++ ggtime-1.0.0/ggtime/R/zzz.R |only ggtime-1.0.0/ggtime/README.md | 132 +++++- ggtime-1.0.0/ggtime/man/aes_nudge.Rd |only ggtime-1.0.0/ggtime/man/autoplot.dcmp_ts.Rd | 2 ggtime-1.0.0/ggtime/man/autoplot.tbl_cf.Rd | 4 ggtime-1.0.0/ggtime/man/autoplot.tbl_ts.Rd | 2 ggtime-1.0.0/ggtime/man/coord_calendar.Rd |only ggtime-1.0.0/ggtime/man/coord_loop.Rd |only ggtime-1.0.0/ggtime/man/figures/README-coordcalendar-1.png |only ggtime-1.0.0/ggtime/man/figures/README-coordloop-1.png |only ggtime-1.0.0/ggtime/man/figures/README-geomtimeline-1.png |only ggtime-1.0.0/ggtime/man/figures/README-scalemixtime-1.png |only ggtime-1.0.0/ggtime/man/geom_time_line.Rd |only ggtime-1.0.0/ggtime/man/gg_arma.Rd | 4 ggtime-1.0.0/ggtime/man/gg_lag.Rd | 3 ggtime-1.0.0/ggtime/man/gg_season.Rd | 3 ggtime-1.0.0/ggtime/man/gg_subseries.Rd | 3 ggtime-1.0.0/ggtime/man/gg_tsdisplay.Rd | 3 ggtime-1.0.0/ggtime/man/gg_tsresiduals.Rd | 5 ggtime-1.0.0/ggtime/man/ggtime-package.Rd | 3 ggtime-1.0.0/ggtime/man/reexports.Rd | 2 ggtime-1.0.0/ggtime/man/scale_mixtime.Rd |only ggtime-1.0.0/ggtime/man/scale_mixtime_continuous.Rd |only ggtime-1.0.0/ggtime/man/transform_warp.Rd |only ggtime-1.0.0/ggtime/tests/testthat/Rplots.pdf |only ggtime-1.0.0/ggtime/tests/testthat/_snaps/coord-calendar/flipped-pane-and-column-gaps.svg |only ggtime-1.0.0/ggtime/tests/testthat/_snaps/coord-calendar/granule-labels.svg |only ggtime-1.0.0/ggtime/tests/testthat/_snaps/coord-calendar/monthly-columns.svg |only ggtime-1.0.0/ggtime/tests/testthat/_snaps/coord-calendar/pane-and-column-gaps.svg |only ggtime-1.0.0/ggtime/tests/testthat/_snaps/coord-calendar/weekly-rows.svg |only ggtime-1.0.0/ggtime/tests/testthat/_snaps/coord-loop/annotations-span-the-panel.svg |only ggtime-1.0.0/ggtime/tests/testthat/_snaps/coord-loop/loops.svg |only ggtime-1.0.0/ggtime/tests/testthat/_snaps/coord-loop/radial.svg |only ggtime-1.0.0/ggtime/tests/testthat/_snaps/coord-loop/rects-and-ribbons-across-boundaries.svg |only ggtime-1.0.0/ggtime/tests/testthat/_snaps/coord-loop/time-loops.svg |only ggtime-1.0.0/ggtime/tests/testthat/test-coord-calendar.R |only ggtime-1.0.0/ggtime/tests/testthat/test-coord-loop.R |only ggtime-1.0.0/ggtime/tests/testthat/test-geom-time-line.R |only ggtime-1.0.0/ggtime/tests/testthat/test-loop-cut.R |only ggtime-1.0.0/ggtime/tests/testthat/test-scale-time.R |only 64 files changed, 446 insertions(+), 85 deletions(-)
Title: The Greatest Mathematician Since Antiquity
Description: Display a random fact about Carl Friedrich Gauss based on the
collection curated by Mike Cavers via the <https://web.archive.org/web/*/gaussfacts.com> site.
Author: Dirk Eddelbuettel [aut, cre] ,
Mike Cavers [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between gaussfacts versions 0.0.3 dated 2026-08-23 and 0.0.4 dated 2026-09-01
ChangeLog | 15 +++++++++++++++ DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/gaussfacts.R | 5 ++++- README.md | 4 ++-- inst/NEWS.Rd | 11 +++++++++-- man/gaussfact.Rd | 3 ++- 7 files changed, 43 insertions(+), 17 deletions(-)
Title: Import and Analysis of OMR Data from FormScanner
Description: Import data of tests and questionnaires from FormScanner. FormScanner is an open source software that converts scanned images to data using optical mark recognition (OMR) and it can be downloaded from <https://sourceforge.net/projects/formscanner/>. The spreadsheet file created by FormScanner is imported in a convenient format to perform the analyses provided by the package. These analyses include the conversion of multiple responses to binary (correct/incorrect) data, the computation of the number of corrected responses for each subject or item, scoring using weights,the computation and the graphical representation of the frequencies of the responses to each item and the report of the responses of a few subjects.
Author: Michela Battauz [aut, cre]
Maintainer: Michela Battauz <michela.battauz@uniud.it>
Diff between fsia versions 1.1.1 dated 2017-06-23 and 1.1.2 dated 2026-09-01
DESCRIPTION | 16 ++++++++++------ MD5 | 8 ++++---- inst/NEWS | 5 ++--- man/fsia-package.Rd | 4 ++-- man/report.Rd | 2 +- 5 files changed, 19 insertions(+), 16 deletions(-)
Title: Visualize and Improve Connectedness of Factors in Tables
Description: Visualize the connectedness of factors in two-way tables.
Perform two-way filtering to improve the degree of connectedness.
See Weeks & Williams (1964) <doi:10.1080/00401706.1964.10490188>.
Author: Kevin Wright [aut, cre]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between connected versions 1.1 dated 2025-03-05 and 1.2 dated 2026-09-01
DESCRIPTION | 13 LICENSE |only MD5 | 30 NAMESPACE | 16 NEWS.md | 16 R/data_documentation.R | 41 - R/functions.R | 712 ++++++++++++-------- build/vignette.rds |binary inst/doc/introduction_to_the_connected_package.R | 25 inst/doc/introduction_to_the_connected_package.Rmd | 37 - inst/doc/introduction_to_the_connected_package.html | 110 +-- man/con_concur.Rd | 7 man/con_filter.Rd | 2 man/con_view.Rd | 12 man/connected.Rd |only tests/testthat/test-functions.R | 136 +++ vignettes/introduction_to_the_connected_package.Rmd | 37 - 17 files changed, 739 insertions(+), 455 deletions(-)
Title: Time Series Methods Based on Growth Curves
Description: Provides tools for modelling and forecasting epidemic trajectories
using a dynamic Gompertz model within a state space framework, with the
Kalman filter for robust estimation of non-linear growth. Includes a
reinitialization feature to adapt to new waves, and a leading-indicator
extension that uses a related series moving ahead of the variable of
interest (e.g. cases ahead of hospitalisations) to improve short-horizon
forecasts, with model and lag selection via rolling-origin
cross-validation. Applicable to data at daily, monthly, quarterly, or
annual frequency, and to non-epidemic trajectories with similar dynamics,
such as innovation diffusion and product adoption. Includes functions for
data preprocessing, model fitting, forecast visualization, and accuracy
evaluation using standard error measures. Methods are described in Harvey
and Kattuman (2020) <doi:10.1162/99608f92.828f40de>, Harvey and Kattuman
(2021) <doi:10.1098/rsif.2021.0179>, and Ashby, Harvey, Kattuman, Tang [...truncated...]
Author: Michael Ashby [aut, cre],
Paul Kattuman [aut],
Andrew Harvey [aut],
Edwin Tang [aut],
Craig Thamotheram [aut],
Guglielmo Secchi [aut],
Cambridge Centre for Health Leadership & Enterprise, Cambridge Judge
Business School, University of Cambridge [fnd] [...truncated...]
Maintainer: Michael Ashby <mwa22@cam.ac.uk>
Diff between tsgc versions 0.0 dated 2024-08-26 and 2.0.0 dated 2026-09-01
tsgc-0.0/tsgc/R/SSModelBase.R |only tsgc-0.0/tsgc/R/SSModelDynGompertzReinit.R |only tsgc-0.0/tsgc/R/SSModelDynamicGompertz.R |only tsgc-0.0/tsgc/man/SSModelBase-class.Rd |only tsgc-0.0/tsgc/man/SSModelDynGompertzReinit-class.Rd |only tsgc-0.0/tsgc/man/forecast.peak.Rd |only tsgc-0.0/tsgc/man/forecast_peak.Rd |only tsgc-0.0/tsgc/man/plot_new_cases.Rd |only tsgc-0.0/tsgc/tests/testthat/test-ss_model_base.R |only tsgc-0.0/tsgc/tests/testthat/test-ss_model_dyn_gompertz_reinit.R |only tsgc-0.0/tsgc/tests/testthat/test-ss_model_dynamic_gompertz.R |only tsgc-2.0.0/tsgc/DESCRIPTION | 96 tsgc-2.0.0/tsgc/MD5 | 168 tsgc-2.0.0/tsgc/NAMESPACE | 186 tsgc-2.0.0/tsgc/NEWS.md | 108 tsgc-2.0.0/tsgc/R/SSModelDynGompertz.R |only tsgc-2.0.0/tsgc/R/SSModelLeadingIndicator.R |only tsgc-2.0.0/tsgc/R/accessorFns.R |only tsgc-2.0.0/tsgc/R/data.R | 220 tsgc-2.0.0/tsgc/R/filterResults.R | 906 +- tsgc-2.0.0/tsgc/R/filterResultsLI.R |only tsgc-2.0.0/tsgc/R/idx_calendar.R |only tsgc-2.0.0/tsgc/R/idx_series.R |only tsgc-2.0.0/tsgc/R/plotting.R | 1885 +++- tsgc-2.0.0/tsgc/R/utils.R | 1446 +++ tsgc-2.0.0/tsgc/README.md | 178 tsgc-2.0.0/tsgc/build/vignette.rds |binary tsgc-2.0.0/tsgc/data/england.rda |binary tsgc-2.0.0/tsgc/data/england_weather_2021.rda |only tsgc-2.0.0/tsgc/data/etrading_apps.rda |only tsgc-2.0.0/tsgc/data/gauteng_weather_2021.rda |only tsgc-2.0.0/tsgc/data/nintendo_sales.rda |only tsgc-2.0.0/tsgc/data/ukitaly.rda |only tsgc-2.0.0/tsgc/inst/doc/tsgc_vignette.R | 1103 +- tsgc-2.0.0/tsgc/inst/doc/tsgc_vignette.Rmd | 2791 +++++-- tsgc-2.0.0/tsgc/inst/doc/tsgc_vignette.html | 3854 ++++++---- tsgc-2.0.0/tsgc/man/FilterResults-class.Rd | 346 tsgc-2.0.0/tsgc/man/FilterResultsLI-class.Rd |only tsgc-2.0.0/tsgc/man/NCOL.idx_series.Rd |only tsgc-2.0.0/tsgc/man/Ptt.Rd |only tsgc-2.0.0/tsgc/man/SSModelDynamicGompertz-class.Rd | 190 tsgc-2.0.0/tsgc/man/SSModelLeadingIndicator-class.Rd |only tsgc-2.0.0/tsgc/man/alphahat.Rd |only tsgc-2.0.0/tsgc/man/argmax.Rd | 53 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tsgc-2.0.0/tsgc/tests/testthat/test-plotting.R | 429 - tsgc-2.0.0/tsgc/tests/testthat/test-ss_model_dyn_gompertz.R |only tsgc-2.0.0/tsgc/tests/testthat/test-ss_model_leading_indicator.R |only tsgc-2.0.0/tsgc/tests/testthat/test-utils.R | 433 + tsgc-2.0.0/tsgc/vignettes/book.bib | 238 tsgc-2.0.0/tsgc/vignettes/tsgc_replication_script.R |only tsgc-2.0.0/tsgc/vignettes/tsgc_vignette.Rmd | 2791 +++++-- 137 files changed, 13297 insertions(+), 5618 deletions(-)
Title: Spatial Concentration and Radius-Based Risk Calculations
Description: Provides computational building blocks for fixed-radius spatial
aggregation, weighted circle-placement problems, hotspot detection, and
polygon-based spatial summaries. The package focuses on efficient
determination of the sum of observations within a given radius, identifying
areas of high local concentration, and aggregating point data to polygon
geometries. These methods are useful for applications such as insurance,
urban analytics, environmental exposure analysis, and other spatial point
pattern workflows. The fixed-radius circle placement problem is discussed
by Chazelle and Lee (1986) <doi:10.1007/BF02238188>, and
related maximum covering problems are described by Church (1974)
<doi:10.1007/BF01942293>.
Author: Martin Haringa [aut, cre]
Maintainer: Martin Haringa <mtharinga@gmail.com>
Diff between spatialrisk versions 0.8.1 dated 2026-06-16 and 0.8.2 dated 2026-09-01
spatialrisk-0.8.1/spatialrisk/man/plot.Rd |only spatialrisk-0.8.2/spatialrisk/DESCRIPTION | 23 spatialrisk-0.8.2/spatialrisk/MD5 | 85 spatialrisk-0.8.2/spatialrisk/NAMESPACE | 3 spatialrisk-0.8.2/spatialrisk/NEWS.md | 64 spatialrisk-0.8.2/spatialrisk/R/RcppExports.R | 16 spatialrisk-0.8.2/spatialrisk/R/choropleth.R | 10 spatialrisk-0.8.2/spatialrisk/R/concentration_hotspot_indexed.R | 24 spatialrisk-0.8.2/spatialrisk/R/concentration_hotspot_pair_refine.R | 435 +++ spatialrisk-0.8.2/spatialrisk/R/deprecated-aliases.R | 4 spatialrisk-0.8.2/spatialrisk/R/deprecated_highest_concentration.R | 210 - spatialrisk-0.8.2/spatialrisk/R/highest_concentration_terra.R | 199 + spatialrisk-0.8.2/spatialrisk/R/hotspot-workflow.R | 342 ++ spatialrisk-0.8.2/spatialrisk/R/points_within_radius.R | 14 spatialrisk-0.8.2/spatialrisk/R/summarise_points_by_polygon.R | 4 spatialrisk-0.8.2/spatialrisk/R/utils.R | 102 spatialrisk-0.8.2/spatialrisk/build/partial.rdb |only spatialrisk-0.8.2/spatialrisk/build/vignette.rds |binary spatialrisk-0.8.2/spatialrisk/inst/benchmarks/benchmark-hotspot-500k.R | 2 spatialrisk-0.8.2/spatialrisk/inst/benchmarks/benchmark-hotspot-indexed.R | 2 spatialrisk-0.8.2/spatialrisk/inst/doc/fixed-radius-concentration.R | 111 spatialrisk-0.8.2/spatialrisk/inst/doc/fixed-radius-concentration.Rmd | 409 ++- spatialrisk-0.8.2/spatialrisk/inst/doc/fixed-radius-concentration.html | 905 +++++-- spatialrisk-0.8.2/spatialrisk/inst/doc/visualisation.R | 33 spatialrisk-0.8.2/spatialrisk/inst/doc/visualisation.Rmd | 123 - spatialrisk-0.8.2/spatialrisk/inst/doc/visualisation.html | 212 + spatialrisk-0.8.2/spatialrisk/man/choropleth.Rd | 10 spatialrisk-0.8.2/spatialrisk/man/concentration_hotspot.Rd | 127 - spatialrisk-0.8.2/spatialrisk/man/figures/README-unnamed-chunk-10-1.png |only spatialrisk-0.8.2/spatialrisk/man/highest_concentration.Rd | 87 spatialrisk-0.8.2/spatialrisk/man/mw_create.Rd | 10 spatialrisk-0.8.2/spatialrisk/man/neighborhood_gh_search.Rd | 44 spatialrisk-0.8.2/spatialrisk/man/plot.conc.Rd | 26 spatialrisk-0.8.2/spatialrisk/man/plot.neighborhood.Rd |only spatialrisk-0.8.2/spatialrisk/man/points_within_radius.Rd | 14 spatialrisk-0.8.2/spatialrisk/man/prepare_spatialrisk.Rd | 96 spatialrisk-0.8.2/spatialrisk/man/summarise_points_by_polygon.Rd | 4 spatialrisk-0.8.2/spatialrisk/src/RcppExports.cpp | 77 spatialrisk-0.8.2/spatialrisk/src/concentration_hotspot_indexed.cpp | 1196 +++++++++- spatialrisk-0.8.2/spatialrisk/tests/testthat/test-concentration-hotspot-indexed.R | 8 spatialrisk-0.8.2/spatialrisk/tests/testthat/test-concentration-hotspot-pair-refine.R | 315 ++ spatialrisk-0.8.2/spatialrisk/tests/testthat/test-hotspot-point-cell-bounds.R |only spatialrisk-0.8.2/spatialrisk/tests/testthat/test-hotspot-screening-bounds.R |only spatialrisk-0.8.2/spatialrisk/tests/testthat/test-hotspot-workflow-search-state.R |only spatialrisk-0.8.2/spatialrisk/tests/testthat/test_concentration_hotspot.R | 82 spatialrisk-0.8.2/spatialrisk/vignettes/fixed-radius-concentration.Rmd | 409 ++- spatialrisk-0.8.2/spatialrisk/vignettes/visualisation.Rmd | 123 - 47 files changed, 4540 insertions(+), 1420 deletions(-)
Title: Model Visualisation Toolbox for 'easystats' and 'ggplot2'
Description: Provides plotting utilities supporting packages in the 'easystats'
ecosystem (<https://github.com/easystats/easystats>) and some extra themes,
geoms, and scales for 'ggplot2'. Color scales are based on
<https://materialui.co/>.
References: Lüdecke et al. (2021) <doi:10.21105/joss.03393>.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, inv] ,
Indrajeet Patil [aut] ,
Mattan S. Ben-Shachar [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Remi Theriault [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Jeffrey R. Stevens [ctb] ,
Julius Bogomolo [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between see versions 0.14.1 dated 2026-06-29 and 0.14.2 dated 2026-09-01
DESCRIPTION | 20 ++- MD5 | 104 ++++++++++---------- NEWS.md | 29 ++++- R/geom_from_list.R | 1 R/plot.bayesfactor_models.R | 46 +++++--- R/plot.binned_residuals.R | 13 +- R/plot.check_collinearity.R | 14 +- R/plot.check_heteroscedasticity.R | 45 ++++++-- R/plot.check_homogeneity.R | 4 R/plot.check_model.R | 14 +- R/plot.check_normality.R | 45 +++++--- R/plot.check_outliers.R | 10 + R/plot.check_outliers.dots.R | 10 - R/plot.check_overdisp.R | 16 ++- R/plot.check_predictions.R | 46 +++++--- R/plot.compare_parameters.R | 2 R/plot.compare_performance.R | 10 + R/plot.estimate_density.R | 16 ++- R/plot.means_by_group.R | 14 ++ R/plot.p_function.R | 18 ++- R/plot.parameters_brms_meta.R | 10 + R/plot.parameters_model.R | 9 + R/plot.parameters_simulate.R | 11 +- R/plot.performance_simres.R | 14 +- R/plots.R | 2 man/plot.see_bayesfactor_models.Rd | 8 - man/plot.see_check_collinearity.Rd | 5 man/plot.see_check_heteroscedasticity.Rd | 5 man/plot.see_check_normality.Rd | 5 man/plot.see_check_outliers.Rd | 5 man/plot.see_compare_performance.Rd | 5 man/plot.see_dw_groupmeans.Rd | 2 man/plot.see_estimate_density.Rd | 5 man/plot.see_p_function.Rd | 5 man/plot.see_parameters_brms_meta.Rd | 5 man/plot.see_parameters_simulate.Rd | 5 man/plot.see_performance_simres.Rd | 5 man/print.see_performance_pp_check.Rd | 7 - man/see-package.Rd | 1 tests/testthat/test-plot.binned_residuals.R |only tests/testthat/test-plot.check_heteroscedasticity.R | 51 +++++++++ tests/testthat/test-plot.cluster_analysis.R | 14 ++ tests/testthat/test-plot.compare_performance.R | 15 ++ tests/testthat/test-plot.describe_distribution.R | 14 ++ tests/testthat/test-plot.dw_data_tabulate.R | 13 ++ tests/testthat/test-plot.easycormatrix.R | 14 ++ tests/testthat/test-plot.equivalence_test.R | 15 ++ tests/testthat/test-plot.p_function.R |only tests/testthat/test-plot.parameters_pca.R | 16 +++ tests/testthat/test-plot.parameters_simulate.R | 15 ++ tests/testthat/test-plot.point_estimates.R | 32 ++++++ tests/testthat/test-plot.rope.R | 32 ++++++ tests/testthat/test-vdiffr_check_model.R | 22 ++++ tests/testthat/test-vdiffr_check_predictions.R | 10 + 54 files changed, 642 insertions(+), 212 deletions(-)
Title: Hierarchical Bayesian Modeling of Decision-Making Tasks
Description: Fit an array of decision-making tasks with computational models in
a hierarchical Bayesian framework. Can perform hierarchical Bayesian analysis of
various computational models with a single line of coding
(Ahn et al., 2017) <doi:10.1162/CPSY_a_00002>.
Author: CCS Lab [cre],
Woo-Young Ahn [aut],
Nate Haines [aut],
Lei Zhang [aut],
Jinwoo Jeong [ctb],
Harhim Park [ctb],
Jaeyeong Yang [ctb],
Jethro Lee [ctb]
Maintainer: CCS Lab <ccsl.snu@gmail.com>
This is a re-admission after prior archival of version 1.2.1 dated 2022-09-23
Diff between hBayesDM versions 1.2.1 dated 2022-09-23 and 2.0.0 dated 2026-09-01
hBayesDM-1.2.1/hBayesDM/R/HDIofMCMC.R |only hBayesDM-1.2.1/hBayesDM/R/plotDist.R |only hBayesDM-1.2.1/hBayesDM/R/plotHDI.R |only hBayesDM-1.2.1/hBayesDM/R/plotInd.R |only hBayesDM-1.2.1/hBayesDM/R/printFit.R |only hBayesDM-1.2.1/hBayesDM/R/stanmodels.R |only hBayesDM-1.2.1/hBayesDM/inst/include |only hBayesDM-1.2.1/hBayesDM/man/HDIofMCMC.Rd |only hBayesDM-1.2.1/hBayesDM/man/plotDist.Rd |only hBayesDM-1.2.1/hBayesDM/man/plotHDI.Rd |only hBayesDM-1.2.1/hBayesDM/man/plotInd.Rd |only hBayesDM-1.2.1/hBayesDM/man/printFit.Rd |only hBayesDM-1.2.1/hBayesDM/src |only hBayesDM-1.2.1/hBayesDM/tools |only hBayesDM-2.0.0/hBayesDM/DESCRIPTION | 43 hBayesDM-2.0.0/hBayesDM/MD5 | 460 +++--- hBayesDM-2.0.0/hBayesDM/NAMESPACE | 85 - hBayesDM-2.0.0/hBayesDM/NEWS.md | 88 + hBayesDM-2.0.0/hBayesDM/R/alt_delta.R | 3 hBayesDM-2.0.0/hBayesDM/R/alt_gamma.R | 3 hBayesDM-2.0.0/hBayesDM/R/bandit2arm_delta.R | 4 hBayesDM-2.0.0/hBayesDM/R/bandit4arm2_kalman_filter.R | 3 hBayesDM-2.0.0/hBayesDM/R/bandit4arm_2par_lapse.R | 4 hBayesDM-2.0.0/hBayesDM/R/bandit4arm_4par.R | 4 hBayesDM-2.0.0/hBayesDM/R/bandit4arm_lapse.R | 4 hBayesDM-2.0.0/hBayesDM/R/bandit4arm_lapse_decay.R | 4 hBayesDM-2.0.0/hBayesDM/R/bandit4arm_singleA_lapse.R | 4 hBayesDM-2.0.0/hBayesDM/R/banditNarm_2par_lapse.R | 5 hBayesDM-2.0.0/hBayesDM/R/banditNarm_4par.R | 5 hBayesDM-2.0.0/hBayesDM/R/banditNarm_delta.R | 5 hBayesDM-2.0.0/hBayesDM/R/banditNarm_kalman_filter.R | 5 hBayesDM-2.0.0/hBayesDM/R/banditNarm_lapse.R | 5 hBayesDM-2.0.0/hBayesDM/R/banditNarm_lapse_decay.R | 5 hBayesDM-2.0.0/hBayesDM/R/banditNarm_singleA_lapse.R | 5 hBayesDM-2.0.0/hBayesDM/R/bart_ewmv.R | 3 hBayesDM-2.0.0/hBayesDM/R/bart_par4.R | 3 hBayesDM-2.0.0/hBayesDM/R/cgt_cm.R | 3 hBayesDM-2.0.0/hBayesDM/R/choiceRT_ddm.R | 7 hBayesDM-2.0.0/hBayesDM/R/choiceRT_ddm_single.R | 7 hBayesDM-2.0.0/hBayesDM/R/choiceRT_lba.R | 147 -- hBayesDM-2.0.0/hBayesDM/R/choiceRT_lba_single.R | 143 -- hBayesDM-2.0.0/hBayesDM/R/cra_exp.R | 2 hBayesDM-2.0.0/hBayesDM/R/cra_linear.R | 2 hBayesDM-2.0.0/hBayesDM/R/dbdm_prob_weight.R | 3 hBayesDM-2.0.0/hBayesDM/R/dd_cs.R | 4 hBayesDM-2.0.0/hBayesDM/R/dd_cs_single.R | 4 hBayesDM-2.0.0/hBayesDM/R/dd_exp.R | 4 hBayesDM-2.0.0/hBayesDM/R/dd_hyperbolic.R | 4 hBayesDM-2.0.0/hBayesDM/R/dd_hyperbolic_single.R | 4 hBayesDM-2.0.0/hBayesDM/R/extract_ic.R | 36 hBayesDM-2.0.0/hBayesDM/R/fit_cmdstan.R |only hBayesDM-2.0.0/hBayesDM/R/gng_m1.R | 3 hBayesDM-2.0.0/hBayesDM/R/gng_m2.R | 3 hBayesDM-2.0.0/hBayesDM/R/gng_m3.R | 3 hBayesDM-2.0.0/hBayesDM/R/gng_m4.R | 3 hBayesDM-2.0.0/hBayesDM/R/hBayesDM.R | 7 hBayesDM-2.0.0/hBayesDM/R/hBayesDM_model.R | 245 ++- hBayesDM-2.0.0/hBayesDM/R/hdi.R |only hBayesDM-2.0.0/hBayesDM/R/hgf_ibrb.R |only hBayesDM-2.0.0/hBayesDM/R/hgf_ibrb_single.R |only hBayesDM-2.0.0/hBayesDM/R/igt_orl.R | 4 hBayesDM-2.0.0/hBayesDM/R/igt_pvl_decay.R | 5 hBayesDM-2.0.0/hBayesDM/R/igt_pvl_delta.R | 5 hBayesDM-2.0.0/hBayesDM/R/igt_vpp.R | 5 hBayesDM-2.0.0/hBayesDM/R/peer_ocu.R | 3 hBayesDM-2.0.0/hBayesDM/R/plot.hBayesDM.R | 45 hBayesDM-2.0.0/hBayesDM/R/plot_dist.R |only hBayesDM-2.0.0/hBayesDM/R/plot_hdi.R |only hBayesDM-2.0.0/hBayesDM/R/plot_ind.R |only hBayesDM-2.0.0/hBayesDM/R/preprocess_funcs.R | 117 + hBayesDM-2.0.0/hBayesDM/R/print_fit.R |only hBayesDM-2.0.0/hBayesDM/R/prl_ewa.R | 2 hBayesDM-2.0.0/hBayesDM/R/prl_fictitious.R | 2 hBayesDM-2.0.0/hBayesDM/R/prl_fictitious_multipleB.R | 2 hBayesDM-2.0.0/hBayesDM/R/prl_fictitious_rp.R | 2 hBayesDM-2.0.0/hBayesDM/R/prl_fictitious_rp_woa.R | 2 hBayesDM-2.0.0/hBayesDM/R/prl_fictitious_woa.R | 2 hBayesDM-2.0.0/hBayesDM/R/prl_rp.R | 2 hBayesDM-2.0.0/hBayesDM/R/prl_rp_multipleB.R | 2 hBayesDM-2.0.0/hBayesDM/R/pstRT_ddm.R | 6 hBayesDM-2.0.0/hBayesDM/R/pstRT_rlddm1.R | 8 hBayesDM-2.0.0/hBayesDM/R/pstRT_rlddm6.R | 8 hBayesDM-2.0.0/hBayesDM/R/pst_Q.R | 5 hBayesDM-2.0.0/hBayesDM/R/pst_gainloss_Q.R | 3 hBayesDM-2.0.0/hBayesDM/R/ra_noLA.R | 4 hBayesDM-2.0.0/hBayesDM/R/ra_noRA.R | 4 hBayesDM-2.0.0/hBayesDM/R/ra_prospect.R | 4 hBayesDM-2.0.0/hBayesDM/R/rdt_happiness.R | 3 hBayesDM-2.0.0/hBayesDM/R/rhat.R | 24 hBayesDM-2.0.0/hBayesDM/R/settings.R | 8 hBayesDM-2.0.0/hBayesDM/R/task2AFC_sdt.R | 6 hBayesDM-2.0.0/hBayesDM/R/ts_par4.R | 4 hBayesDM-2.0.0/hBayesDM/R/ts_par6.R | 4 hBayesDM-2.0.0/hBayesDM/R/ts_par7.R | 4 hBayesDM-2.0.0/hBayesDM/R/ug_bayes.R | 4 hBayesDM-2.0.0/hBayesDM/R/ug_delta.R | 4 hBayesDM-2.0.0/hBayesDM/R/wcs_sql.R | 3 hBayesDM-2.0.0/hBayesDM/R/zzz.R | 9 hBayesDM-2.0.0/hBayesDM/inst/CITATION | 16 hBayesDM-2.0.0/hBayesDM/inst/extdata/hgf_ibrb_exampleData.txt |only hBayesDM-2.0.0/hBayesDM/inst/extdata/hgf_ibrb_single_exampleData.txt |only hBayesDM-2.0.0/hBayesDM/inst/plotting/plot_functions.R | 671 +++++----- hBayesDM-2.0.0/hBayesDM/inst/stan_files/alt_delta.stan | 123 - hBayesDM-2.0.0/hBayesDM/inst/stan_files/alt_gamma.stan | 141 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/bandit2arm_delta.stan | 100 - hBayesDM-2.0.0/hBayesDM/inst/stan_files/bandit4arm2_kalman_filter.stan | 216 +-- hBayesDM-2.0.0/hBayesDM/inst/stan_files/bandit4arm_2par_lapse.stan | 141 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/bandit4arm_4par.stan | 136 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/bandit4arm_lapse.stan | 153 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/bandit4arm_lapse_decay.stan | 173 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/bandit4arm_singleA_lapse.stan | 147 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/banditNarm_2par_lapse.stan | 141 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/banditNarm_4par.stan | 136 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/banditNarm_delta.stan | 107 - hBayesDM-2.0.0/hBayesDM/inst/stan_files/banditNarm_kalman_filter.stan | 212 +-- hBayesDM-2.0.0/hBayesDM/inst/stan_files/banditNarm_lapse.stan | 153 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/banditNarm_lapse_decay.stan | 173 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/banditNarm_singleA_lapse.stan | 147 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/bart_ewmv.stan | 144 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/bart_par4.stan | 126 + hBayesDM-2.0.0/hBayesDM/inst/stan_files/cgt_cm.stan | 182 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/choiceRT_ddm.stan | 95 - hBayesDM-2.0.0/hBayesDM/inst/stan_files/choiceRT_ddm_single.stan | 54 hBayesDM-2.0.0/hBayesDM/inst/stan_files/choiceRT_lba.stan | 224 +-- hBayesDM-2.0.0/hBayesDM/inst/stan_files/choiceRT_lba_single.stan | 168 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/cra_exp.stan | 143 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/cra_linear.stan | 139 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/dbdm_prob_weight.stan | 223 +-- hBayesDM-2.0.0/hBayesDM/inst/stan_files/dd_cs.stan | 130 + hBayesDM-2.0.0/hBayesDM/inst/stan_files/dd_cs_single.stan | 78 - hBayesDM-2.0.0/hBayesDM/inst/stan_files/dd_exp.stan | 102 - hBayesDM-2.0.0/hBayesDM/inst/stan_files/dd_hyperbolic.stan | 106 - hBayesDM-2.0.0/hBayesDM/inst/stan_files/dd_hyperbolic_single.stan | 67 hBayesDM-2.0.0/hBayesDM/inst/stan_files/gng_m1.stan | 184 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/gng_m2.stan | 204 +-- hBayesDM-2.0.0/hBayesDM/inst/stan_files/gng_m3.stan | 224 +-- hBayesDM-2.0.0/hBayesDM/inst/stan_files/gng_m4.stan | 263 ++- hBayesDM-2.0.0/hBayesDM/inst/stan_files/hgf_ibrb.stan |only hBayesDM-2.0.0/hBayesDM/inst/stan_files/hgf_ibrb_single.stan |only hBayesDM-2.0.0/hBayesDM/inst/stan_files/igt_orl.stan | 219 +-- hBayesDM-2.0.0/hBayesDM/inst/stan_files/igt_pvl_decay.stan | 138 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/igt_pvl_delta.stan | 142 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/igt_vpp.stan | 208 +-- hBayesDM-2.0.0/hBayesDM/inst/stan_files/peer_ocu.stan | 113 - hBayesDM-2.0.0/hBayesDM/inst/stan_files/prl_ewa.stan | 149 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/prl_fictitious.stan | 181 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/prl_fictitious_multipleB.stan | 201 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/prl_fictitious_rp.stan | 209 +-- hBayesDM-2.0.0/hBayesDM/inst/stan_files/prl_fictitious_rp_woa.stan | 197 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/prl_fictitious_woa.stan | 179 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/prl_rp.stan | 155 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/prl_rp_multipleB.stan | 163 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/pstRT_ddm.stan | 136 -- hBayesDM-2.0.0/hBayesDM/inst/stan_files/pstRT_rlddm1.stan | 192 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/pstRT_rlddm6.stan | 229 +-- hBayesDM-2.0.0/hBayesDM/inst/stan_files/pst_Q.stan | 112 - hBayesDM-2.0.0/hBayesDM/inst/stan_files/pst_gainloss_Q.stan | 112 - hBayesDM-2.0.0/hBayesDM/inst/stan_files/ra_noLA.stan | 93 - hBayesDM-2.0.0/hBayesDM/inst/stan_files/ra_noRA.stan | 97 - hBayesDM-2.0.0/hBayesDM/inst/stan_files/ra_prospect.stan | 115 - hBayesDM-2.0.0/hBayesDM/inst/stan_files/rdt_happiness.stan | 159 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/task2AFC_sdt.stan | 67 hBayesDM-2.0.0/hBayesDM/inst/stan_files/ts_par4.stan | 327 ++-- hBayesDM-2.0.0/hBayesDM/inst/stan_files/ts_par6.stan | 341 ++--- hBayesDM-2.0.0/hBayesDM/inst/stan_files/ts_par7.stan | 347 ++--- hBayesDM-2.0.0/hBayesDM/inst/stan_files/ug_bayes.stan | 185 +- hBayesDM-2.0.0/hBayesDM/inst/stan_files/ug_delta.stan | 126 - hBayesDM-2.0.0/hBayesDM/inst/stan_files/wcs_sql.stan | 201 +- hBayesDM-2.0.0/hBayesDM/man/alt_delta.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/alt_gamma.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/bandit2arm_delta.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/bandit4arm2_kalman_filter.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/bandit4arm_2par_lapse.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/bandit4arm_4par.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/bandit4arm_lapse.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/bandit4arm_lapse_decay.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/bandit4arm_singleA_lapse.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/banditNarm_2par_lapse.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/banditNarm_4par.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/banditNarm_delta.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/banditNarm_kalman_filter.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/banditNarm_lapse.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/banditNarm_lapse_decay.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/banditNarm_singleA_lapse.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/bart_ewmv.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/bart_par4.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/cgt_cm.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/choiceRT_ddm.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/choiceRT_ddm_single.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/choiceRT_lba.Rd | 30 hBayesDM-2.0.0/hBayesDM/man/choiceRT_lba_single.Rd | 30 hBayesDM-2.0.0/hBayesDM/man/cra_exp.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/cra_linear.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/dbdm_prob_weight.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/dd_cs.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/dd_cs_single.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/dd_exp.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/dd_hyperbolic.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/dd_hyperbolic_single.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/dot-hbayesdm_compile.Rd |only hBayesDM-2.0.0/hBayesDM/man/dot-hbayesdm_extract.Rd |only hBayesDM-2.0.0/hBayesDM/man/dot-hbayesdm_fit.Rd |only hBayesDM-2.0.0/hBayesDM/man/dot-hbayesdm_resolve_inits.Rd |only hBayesDM-2.0.0/hBayesDM/man/dot-hbayesdm_stan_file.Rd |only hBayesDM-2.0.0/hBayesDM/man/extract_ic.Rd | 3 hBayesDM-2.0.0/hBayesDM/man/gng_m1.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/gng_m2.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/gng_m3.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/gng_m4.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/hBayesDM_model.Rd | 9 hBayesDM-2.0.0/hBayesDM/man/hbayesdm-cmdstan.Rd |only hBayesDM-2.0.0/hBayesDM/man/hdi.Rd |only hBayesDM-2.0.0/hBayesDM/man/hgf_ibrb.Rd |only hBayesDM-2.0.0/hBayesDM/man/hgf_ibrb_single.Rd |only hBayesDM-2.0.0/hBayesDM/man/igt_orl.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/igt_pvl_decay.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/igt_pvl_delta.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/igt_vpp.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/peer_ocu.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/plot.hBayesDM.Rd | 8 hBayesDM-2.0.0/hBayesDM/man/plot_dist.Rd |only hBayesDM-2.0.0/hBayesDM/man/plot_hdi.Rd |only hBayesDM-2.0.0/hBayesDM/man/plot_ind.Rd |only hBayesDM-2.0.0/hBayesDM/man/print_fit.Rd |only hBayesDM-2.0.0/hBayesDM/man/prl_ewa.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/prl_fictitious.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/prl_fictitious_multipleB.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/prl_fictitious_rp.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/prl_fictitious_rp_woa.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/prl_fictitious_woa.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/prl_rp.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/prl_rp_multipleB.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/pstRT_ddm.Rd | 44 hBayesDM-2.0.0/hBayesDM/man/pstRT_rlddm1.Rd | 46 hBayesDM-2.0.0/hBayesDM/man/pstRT_rlddm6.Rd | 46 hBayesDM-2.0.0/hBayesDM/man/pst_Q.Rd | 44 hBayesDM-2.0.0/hBayesDM/man/pst_gainloss_Q.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/ra_noLA.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/ra_noRA.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/ra_prospect.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/rdt_happiness.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/task2AFC_sdt.Rd | 44 hBayesDM-2.0.0/hBayesDM/man/ts_par4.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/ts_par6.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/ts_par7.Rd | 42 hBayesDM-2.0.0/hBayesDM/man/ug_bayes.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/ug_delta.Rd | 41 hBayesDM-2.0.0/hBayesDM/man/wcs_sql.Rd | 42 hBayesDM-2.0.0/hBayesDM/tests/testthat/test_hgf_ibrb.R |only hBayesDM-2.0.0/hBayesDM/tests/testthat/test_hgf_ibrb_single.R |only hBayesDM-2.0.0/hBayesDM/tests/testthat/test_user_facing.R |only 251 files changed, 8571 insertions(+), 6836 deletions(-)
Title: Experimental Design and Randomization Methods for Biomedical and
Veterinary Research
Description: Provides reproducible methods for experimental design and
treatment allocation in biomedical, veterinary, agricultural, and clinical
research. Includes simple, fixed-block, variable-block, stratified,
stratified-block, cluster, matched-pair, restricted, minimization, and
covariate-adaptive randomization, together with completely randomized,
randomized-block, factorial, split-plot, Latin square, and crossover
designs. Also provides allocation summaries, balance diagnostics,
schedule export, and visualization. The methods are based on established
principles of randomization and experimental design; see Rosenberger and
Lachin (2015, ISBN:9781118742242) and Jones and Kenward (2014,
ISBN:9781439861424).
Author: Vinodhkumar Obli Rajendran [aut, cre],
Keerthi Aaradhana [aut]
Maintainer: Vinodhkumar Obli Rajendran <vinodhkumar.rajendran@gmail.com>
Diff between ExpDesignR versions 0.1.0 dated 2026-08-27 and 1.0.0 dated 2026-09-01
DESCRIPTION | 31 +- MD5 | 62 +++- NAMESPACE | 80 +++--- NEWS.md | 47 ++- R/block_randomization.R | 163 ++++++++---- R/cluster_randomization.R | 73 +---- R/covariate_adaptive_randomization.R |only R/designs_additional.R |only R/matched_pair_randomization.R |only R/minimization_randomization.R |only R/randomization_diagnostics.R |only R/randomization_utils.R |only R/restricted_randomization.R |only R/simple_randomization.R | 62 +--- R/stratified_block_randomization.R |only R/stratified_randomization.R | 107 ++------ R/variable_block_randomization.R |only R/zzz.R |only README.md | 53 +++- inst/doc/getting-started.R | 31 ++ inst/doc/getting-started.Rmd | 68 ++++- inst/doc/getting-started.html | 295 ++++++++++++++++++++++- man/balance_check.Rd |only man/block_randomization.Rd | 21 - man/cluster_randomization.Rd | 18 - man/completely_randomized_design.Rd |only man/covariate_adaptive_randomization.Rd |only man/export_schedule.Rd | 4 man/factorial_design.Rd |only man/matched_pair_randomization.Rd |only man/minimization_randomization.Rd |only man/randomization_diagnostics.Rd |only man/randomized_block_design.Rd |only man/restricted_randomization.Rd |only man/simple_randomization.Rd | 10 man/split_plot_design.Rd |only man/stratified_block_randomization.Rd |only man/stratified_randomization.Rd | 30 -- man/variable_block_randomization.Rd |only tests/testthat/test-block-randomization.R |only tests/testthat/test-core_randomization.R | 8 tests/testthat/test-matched-pair-randomization.R |only tests/testthat/test-phase1.R |only tests/testthat/test-randomization-diagnostics.R |only vignettes/getting-started.Rmd | 68 ++++- 45 files changed, 825 insertions(+), 406 deletions(-)
Title: Bayesian Adaptive Trial Simulator Software (BATSS) for
Generalised Linear Models
Description: Defines operating characteristics of Bayesian Adaptive Trials considering a generalised linear model response via Monte Carlo simulations of Bayesian GLM fitted via integrated Laplace approximations (INLA).
Author: Dominique-Laurent Couturier [aut, cre] ,
Liz Ryan [aut] ,
Rainer Puhr [aut],
Thomas Jaki [aut] ,
Stephane Heritier [aut]
Maintainer: Dominique-Laurent Couturier <dominique.couturier@mrc-bsu.cam.ac.uk>
Diff between BATSS versions 1.2.0 dated 2026-05-28 and 1.2.1 dated 2026-09-01
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/glm.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Import 'OpenStreetMap' Data as Simple Features or Spatial
Objects
Description: Download and import of 'OpenStreetMap' ('OSM') data as 'sf'
or 'sp' objects. 'OSM' data are extracted from the 'Overpass' web
server (<https://overpass-api.de/>) and processed with very fast 'C++'
routines for return to 'R'.
Author: Joan Maspons [aut, cre] ,
Mark Padgham [aut],
Bob Rudis [aut],
Robin Lovelace [aut],
Maelle Salmon [aut],
Andrew Smith [ctb],
James Smith [ctb],
Andrea Gilardi [ctb],
Enrico Spinielli [ctb],
Anthony North [ctb],
Martin Machyna [ctb],
Marcin Kalicinsk [...truncated...]
Maintainer: Joan Maspons <joanmaspons@gmail.com>
Diff between osmdata versions 0.4.0 dated 2026-06-15 and 0.4.1 dated 2026-09-01
DESCRIPTION | 17 ++++---- MD5 | 63 ++++++++++++++++-------------- NAMESPACE | 1 NEWS.md | 13 ++++++ R/elevation.R | 18 +++----- R/features.R | 2 R/get-osmdata-sf.R | 20 ++++++--- R/getbb.R | 3 + R/opq.R | 2 R/overpass-query.R | 52 +++++++++++++++++++------ R/zzz.R | 79 ++++++++++++++++++++++++-------------- README.md | 19 ++++++++- build/vignette.rds |binary inst/doc/osm-sf-translation.html | 4 - inst/doc/osmdata-sc.R | 7 --- inst/doc/osmdata-sc.Rmd | 16 ++----- inst/doc/osmdata-sc.html | 12 ++--- inst/doc/osmdata.R | 2 inst/doc/osmdata.Rmd | 2 inst/doc/osmdata.html | 11 ++--- inst/doc/query-split.html | 4 - man/add_osm_feature.Rd | 2 man/add_osm_features.Rd | 2 man/get_overpass_url.Rd | 3 - man/list_overpass_urls.Rd |only man/osm_elevation.Rd | 13 +++--- man/set_overpass_url.Rd | 26 ++++-------- tests/testthat/mock_no_user_agent |only tests/testthat/mock_user_agent |only tests/testthat/setup.R | 1 tests/testthat/test-osmdata.R | 17 ++++++++ vignettes/osmdata-sc.Rmd | 16 ++----- vignettes/osmdata.Rmd | 2 33 files changed, 261 insertions(+), 168 deletions(-)
Title: Cell Type Annotation Using Large Language Models
Description: Automated cell type annotation for single-cell RNA sequencing data
using consensus predictions from multiple large language models. Integrates
with Seurat objects and provides uncertainty quantification for annotations.
Supports various LLM providers including OpenAI, Anthropic, and Google.
For details see Yang et al. (2026) <doi:10.1038/s42003-026-10420-8>.
Author: Chen Yang [aut, cre, cph]
Maintainer: Chen Yang <cafferychen777@tamu.edu>
Diff between mLLMCelltype versions 2.0.7 dated 2026-07-21 and 2.0.8 dated 2026-09-01
DESCRIPTION | 6 +- MD5 | 42 +++++++------- NEWS.md | 17 +++++ R/anthropic_processor.R | 2 R/base_api_processor.R | 2 R/deepseek_processor.R | 3 - R/gemini_processor.R | 2 R/kimi_processor.R | 2 R/prompt_templates.R | 89 ++++++++++++++++++++---------- R/response_validation_utils.R | 15 +++++ inst/doc/advanced-features.html | 4 - inst/doc/consensus-principles.html | 4 - inst/doc/contributing-guide.html | 4 - inst/doc/faq.html | 4 - inst/doc/getting-started.html | 4 - inst/doc/installation.html | 4 - inst/doc/introduction.html | 4 - inst/doc/usage-tutorial.html | 4 - inst/doc/version-history.html | 4 - man/create_reasoning_annotation_prompt.Rd | 7 ++ tests/testthat/test-annotate-reasoning.R | 34 +++++++++++ tests/testthat/test-api-timeout.R |only tests/testthat/test-provider-deepseek.R |only 23 files changed, 183 insertions(+), 74 deletions(-)
Title: Knock Errors Off Nice Guesses
Description: Miscellaneous functions and data used in psychological research and teaching. Keng
currently has four built-in datasets, and could (1) scale a vector;
(2) divide a vector into three groups,
(3) compute the cut-off values of Pearson's r with known sample size;
(4) test the significance and compute the post-hoc power for Pearson's r with known sample size;
(5) conduct a priori power analysis and plan the sample size for Pearson's r;
(6) compare lm()'s fitted outputs using R-squared, f_squared, post-hoc power,
and PRE (Proportional Reduction in Error, also called partial R-squared or
partial Eta-squared); (7) calculate PRE from partial correlation, Cohen's f, or f_squared;
(8) conduct a priori power analysis and plan the sample size for one or a set of predictors in
regression analysis; (9) conduct post-hoc power analysis for one or a set of predictors in
regression analysis with known sample size; (10) randomly pick numbers for Chinese Super Lotto
and Double Color Balls; (11) assess cour [...truncated...]
Author: Qingyao Zhang [aut, cre]
Maintainer: Qingyao Zhang <qingyaozhang@outlook.com>
Diff between Keng versions 2026.3.19 dated 2026-03-19 and 2026.9.0 dated 2026-09-01
Keng-2026.3.19/Keng/R/data.R |only Keng-2026.9.0/Keng/DESCRIPTION | 10 - Keng-2026.9.0/Keng/MD5 | 67 ++++--- Keng-2026.9.0/Keng/NEWS.md | 4 Keng-2026.9.0/Keng/R/depress.R |only Keng-2026.9.0/Keng/R/depress1.R |only Keng-2026.9.0/Keng/R/depress2.R |only Keng-2026.9.0/Keng/R/depress3.R |only Keng-2026.9.0/Keng/R/pick_dcb.R | 5 Keng-2026.9.0/Keng/R/pick_sl.R | 120 ++++++------- Keng-2026.9.0/Keng/R/well.R |only Keng-2026.9.0/Keng/R/well1.R |only Keng-2026.9.0/Keng/R/well2.R |only Keng-2026.9.0/Keng/R/well3.R |only Keng-2026.9.0/Keng/README.md | 7 Keng-2026.9.0/Keng/build/vignette.rds |binary Keng-2026.9.0/Keng/data/depress.rda |binary Keng-2026.9.0/Keng/data/depress1.rda |only Keng-2026.9.0/Keng/data/depress2.rda |only Keng-2026.9.0/Keng/data/depress3.rda |only Keng-2026.9.0/Keng/data/well.rda |only Keng-2026.9.0/Keng/data/well1.rda |only Keng-2026.9.0/Keng/data/well2.rda |only Keng-2026.9.0/Keng/data/well3.rda |only Keng-2026.9.0/Keng/inst/doc/PRE.R | 22 +- Keng-2026.9.0/Keng/inst/doc/PRE.Rmd | 22 +- Keng-2026.9.0/Keng/inst/doc/PRE.html | 116 ++++++------- Keng-2026.9.0/Keng/inst/doc/assessCOA.html | 18 +- Keng-2026.9.0/Keng/inst/doc/partialRegression.R | 8 Keng-2026.9.0/Keng/inst/doc/partialRegression.Rmd | 34 +-- Keng-2026.9.0/Keng/inst/doc/partialRegression.html | 187 ++++++++++----------- Keng-2026.9.0/Keng/inst/doc/planSampleSize.R | 8 Keng-2026.9.0/Keng/inst/doc/planSampleSize.Rmd | 8 Keng-2026.9.0/Keng/inst/doc/planSampleSize.html | 35 ++- Keng-2026.9.0/Keng/man/depress.Rd | 79 ++++++-- Keng-2026.9.0/Keng/man/depress1.Rd |only Keng-2026.9.0/Keng/man/depress2.Rd |only Keng-2026.9.0/Keng/man/depress3.Rd |only Keng-2026.9.0/Keng/man/well.Rd |only Keng-2026.9.0/Keng/man/well1.Rd |only Keng-2026.9.0/Keng/man/well2.Rd |only Keng-2026.9.0/Keng/man/well3.Rd |only Keng-2026.9.0/Keng/tests/testthat/test-power_lm.R | 5 Keng-2026.9.0/Keng/vignettes/PRE.Rmd | 22 +- Keng-2026.9.0/Keng/vignettes/partialRegression.Rmd | 34 +-- Keng-2026.9.0/Keng/vignettes/planSampleSize.Rmd | 8 46 files changed, 444 insertions(+), 375 deletions(-)
Title: Actuarial Tools for Insurance Pricing Models
Description: Provides actuarial tools and building blocks for analysing,
modelling, refining, and validating insurance rating models. Designed to
support common GLM-based pricing tasks and the translation of statistical
model output into practical tariff structures. The package supports the
construction of insurance tariff classes using a data-driven approach, based
on the methodology of Antonio and Valdez
(2012) <doi:10.1007/s10182-011-0152-7>.
Author: Martin Haringa [aut, cre]
Maintainer: Martin Haringa <mtharinga@gmail.com>
Diff between insurancerating versions 0.8.1 dated 2026-07-30 and 0.8.2 dated 2026-09-01
insurancerating-0.8.1/insurancerating/man/autoplot.riskfactor_gam.Rd |only insurancerating-0.8.1/insurancerating/man/autoplot.tariff_segments.Rd |only insurancerating-0.8.1/insurancerating/man/relativities.Rd |only insurancerating-0.8.1/insurancerating/man/split_level.Rd |only insurancerating-0.8.2/insurancerating/DESCRIPTION | 14 insurancerating-0.8.2/insurancerating/MD5 | 232 insurancerating-0.8.2/insurancerating/NAMESPACE | 23 insurancerating-0.8.2/insurancerating/NEWS.md | 256 insurancerating-0.8.2/insurancerating/R/data_MTPL.R | 4 insurancerating-0.8.2/insurancerating/R/excess_loss.R | 7 insurancerating-0.8.2/insurancerating/R/gam_construct_tariff_classes.R | 686 + insurancerating-0.8.2/insurancerating/R/gam_riskfactor.R | 459 - insurancerating-0.8.2/insurancerating/R/model_add_prediction.R | 47 insurancerating-0.8.2/insurancerating/R/model_calibration.R |only insurancerating-0.8.2/insurancerating/R/model_get_data.R | 354 insurancerating-0.8.2/insurancerating/R/model_performance.R | 70 insurancerating-0.8.2/insurancerating/R/model_performance_bootstrap_coefficients.R |only insurancerating-0.8.2/insurancerating/R/model_performance_bootstrap_rmse.R | 91 insurancerating-0.8.2/insurancerating/R/model_performance_residuals.R | 45 insurancerating-0.8.2/insurancerating/R/model_rating_table.R | 1005 ++ insurancerating-0.8.2/insurancerating/R/model_rating_table_gt.R | 168 insurancerating-0.8.2/insurancerating/R/model_rating_table_plot.R | 196 insurancerating-0.8.2/insurancerating/R/model_refinement.R | 3740 +++++++++- insurancerating-0.8.2/insurancerating/R/model_refinement_audit.R |only insurancerating-0.8.2/insurancerating/R/model_refinement_plot.R | 440 + insurancerating-0.8.2/insurancerating/R/model_refinement_premium_change.R |only insurancerating-0.8.2/insurancerating/R/oud_model_refinement.R | 5 insurancerating-0.8.2/insurancerating/R/outlier_histogram.R | 2 insurancerating-0.8.2/insurancerating/R/portfolio_reduction_db.R |only insurancerating-0.8.2/insurancerating/R/time_period_to_months.R | 207 insurancerating-0.8.2/insurancerating/R/time_reduce.R | 295 insurancerating-0.8.2/insurancerating/R/time_rows_per_date.R | 191 insurancerating-0.8.2/insurancerating/R/truncated_distributions.R | 55 insurancerating-0.8.2/insurancerating/R/univariate.R | 251 insurancerating-0.8.2/insurancerating/R/utils.R | 133 insurancerating-0.8.2/insurancerating/R/utils_refinement.R | 457 + insurancerating-0.8.2/insurancerating/R/utils_univariate.R | 181 insurancerating-0.8.2/insurancerating/R/zzz.R | 2 insurancerating-0.8.2/insurancerating/build/vignette.rds |binary insurancerating-0.8.2/insurancerating/inst/doc/getting-started.R | 90 insurancerating-0.8.2/insurancerating/inst/doc/getting-started.Rmd | 322 insurancerating-0.8.2/insurancerating/inst/doc/getting-started.html | 570 - insurancerating-0.8.2/insurancerating/inst/doc/large-portfolios.R |only insurancerating-0.8.2/insurancerating/inst/doc/large-portfolios.Rmd |only insurancerating-0.8.2/insurancerating/inst/doc/large-portfolios.html |only insurancerating-0.8.2/insurancerating/inst/doc/model-validation.R | 112 insurancerating-0.8.2/insurancerating/inst/doc/model-validation.Rmd | 470 - insurancerating-0.8.2/insurancerating/inst/doc/model-validation.html | 606 + insurancerating-0.8.2/insurancerating/inst/doc/pricing-workflow-building-blocks.R | 167 insurancerating-0.8.2/insurancerating/inst/doc/pricing-workflow-building-blocks.Rmd | 555 - insurancerating-0.8.2/insurancerating/inst/doc/pricing-workflow-building-blocks.html | 810 +- insurancerating-0.8.2/insurancerating/inst/doc/refinement-workflow.R | 340 insurancerating-0.8.2/insurancerating/inst/doc/refinement-workflow.Rmd | 965 +- insurancerating-0.8.2/insurancerating/inst/doc/refinement-workflow.html | 1421 ++- insurancerating-0.8.2/insurancerating/man/MTPL.Rd | 2 insurancerating-0.8.2/insurancerating/man/MTPL2.Rd | 2 insurancerating-0.8.2/insurancerating/man/active_rows_by_date.Rd | 116 insurancerating-0.8.2/insurancerating/man/add_prediction.Rd | 47 insurancerating-0.8.2/insurancerating/man/add_rebasing.Rd |only insurancerating-0.8.2/insurancerating/man/add_relativities.Rd | 102 insurancerating-0.8.2/insurancerating/man/add_restriction.Rd | 183 insurancerating-0.8.2/insurancerating/man/add_shrinkage.Rd |only insurancerating-0.8.2/insurancerating/man/add_smoothing.Rd | 195 insurancerating-0.8.2/insurancerating/man/add_tariff_segments.Rd | 22 insurancerating-0.8.2/insurancerating/man/as_gt.Rd | 78 insurancerating-0.8.2/insurancerating/man/as_gt.refinement_audit.Rd |only insurancerating-0.8.2/insurancerating/man/audit_refinement.Rd |only insurancerating-0.8.2/insurancerating/man/autoplot.bootstrap_performance.Rd | 25 insurancerating-0.8.2/insurancerating/man/autoplot.check_residuals.Rd | 34 insurancerating-0.8.2/insurancerating/man/autoplot.factor_analysis.Rd | 90 insurancerating-0.8.2/insurancerating/man/autoplot.rating_refinement.Rd | 108 insurancerating-0.8.2/insurancerating/man/autoplot.rating_table.Rd | 134 insurancerating-0.8.2/insurancerating/man/autoplot.tariff_effect.Rd |only insurancerating-0.8.2/insurancerating/man/autoplot.truncated_severity.Rd | 12 insurancerating-0.8.2/insurancerating/man/bootstrap_coefficients.Rd |only insurancerating-0.8.2/insurancerating/man/bootstrap_performance.Rd | 71 insurancerating-0.8.2/insurancerating/man/bootstrap_rmse.Rd | 17 insurancerating-0.8.2/insurancerating/man/calibrate_model.Rd |only insurancerating-0.8.2/insurancerating/man/cash-.rating_table.Rd |only insurancerating-0.8.2/insurancerating/man/check_residuals.Rd | 11 insurancerating-0.8.2/insurancerating/man/construct_model_points.Rd | 3 insurancerating-0.8.2/insurancerating/man/construct_tariff_classes.Rd | 23 insurancerating-0.8.2/insurancerating/man/derive_tariff_segments.Rd | 164 insurancerating-0.8.2/insurancerating/man/edit_smoothing.Rd | 172 insurancerating-0.8.2/insurancerating/man/extract_model_data.Rd | 53 insurancerating-0.8.2/insurancerating/man/factor_analysis.Rd | 122 insurancerating-0.8.2/insurancerating/man/fit_gam.Rd | 18 insurancerating-0.8.2/insurancerating/man/fit_truncated_severity.Rd | 1 insurancerating-0.8.2/insurancerating/man/merge_date_ranges.Rd | 130 insurancerating-0.8.2/insurancerating/man/merge_date_ranges_db.Rd |only insurancerating-0.8.2/insurancerating/man/model_performance.Rd | 34 insurancerating-0.8.2/insurancerating/man/outlier_histogram.Rd | 2 insurancerating-0.8.2/insurancerating/man/period_to_months.Rd | 2 insurancerating-0.8.2/insurancerating/man/premium_change.Rd |only insurancerating-0.8.2/insurancerating/man/prepare_refinement.Rd | 74 insurancerating-0.8.2/insurancerating/man/rating_factors.Rd | 12 insurancerating-0.8.2/insurancerating/man/rating_grid.Rd | 201 insurancerating-0.8.2/insurancerating/man/rating_grid_db.Rd |only insurancerating-0.8.2/insurancerating/man/rating_table.Rd | 263 insurancerating-0.8.2/insurancerating/man/reduce.Rd | 2 insurancerating-0.8.2/insurancerating/man/refit.Rd | 86 insurancerating-0.8.2/insurancerating/man/relativity_specification.Rd |only insurancerating-0.8.2/insurancerating/man/rgammat.Rd | 21 insurancerating-0.8.2/insurancerating/man/risk_factor_gam.Rd | 146 insurancerating-0.8.2/insurancerating/man/riskfactor_gam.Rd | 37 insurancerating-0.8.2/insurancerating/man/rlnormt.Rd | 21 insurancerating-0.8.2/insurancerating/man/rmse.Rd | 36 insurancerating-0.8.2/insurancerating/man/rows_per_date.Rd | 8 insurancerating-0.8.2/insurancerating/man/set_reference_level.Rd | 39 insurancerating-0.8.2/insurancerating/man/split_periods_to_months.Rd | 103 insurancerating-0.8.2/insurancerating/man/split_relativities.Rd | 31 insurancerating-0.8.2/insurancerating/man/summary.bootstrap_coefficients.Rd |only insurancerating-0.8.2/insurancerating/man/summary.rating_refinement.Rd |only insurancerating-0.8.2/insurancerating/man/summary.refinement_audit.Rd |only 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insurancerating-0.8.2/insurancerating/tests/testthat/test_plot_axis_labels.R |only insurancerating-0.8.2/insurancerating/tests/testthat/test_portfolio_reduction_db.R |only insurancerating-0.8.2/insurancerating/tests/testthat/test_premium_change.R |only insurancerating-0.8.2/insurancerating/tests/testthat/test_rating_table_estimate_name.R |only insurancerating-0.8.2/insurancerating/tests/testthat/test_rating_table_ordering.R |only insurancerating-0.8.2/insurancerating/tests/testthat/test_time_utils.R | 362 insurancerating-0.8.2/insurancerating/tests/testthat/test_univariate.R | 36 insurancerating-0.8.2/insurancerating/vignettes/getting-started.Rmd | 322 insurancerating-0.8.2/insurancerating/vignettes/large-portfolios.Rmd |only insurancerating-0.8.2/insurancerating/vignettes/model-validation.Rmd | 470 - insurancerating-0.8.2/insurancerating/vignettes/pricing-workflow-building-blocks.Rmd | 555 - insurancerating-0.8.2/insurancerating/vignettes/refinement-workflow.Rmd | 965 +- 137 files changed, 18161 insertions(+), 5813 deletions(-)
More information about insurancerating at CRAN
Permanent link
Title: Probability Distributions with Certain or Uncertain Parameters
Description: Represents probability distributions with fixed or potentially
uncertain parameters, with tools to discretise, convolve, sample from and
summarise them.
Author: Sebastian Funk [aut, cre] ,
James M. Azam [aut] ,
Sam Abbott [aut]
Maintainer: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Diff between distspec versions 0.1.0 dated 2026-08-07 and 0.2.0 dated 2026-09-01
DESCRIPTION | 9 +- MD5 | 63 +++++++++-------- NAMESPACE | 8 ++ NEWS.md | 30 ++++++++ R/accessors.R | 1 R/as_dist_spec.R |only R/check.R | 16 ++-- R/constructors.R | 10 ++ R/discretise.R | 130 ++++++++++++++++++++++++++---------- R/dist_spec.R | 20 ++--- R/fixed.R | 24 ++++++ R/nonparametric.R | 6 + README.md | 11 +-- inst/design.md | 2 inst/doc/distspec.Rmd | 2 inst/doc/distspec.html | 2 man/NonParametric.Rd | 7 + man/as_dist_spec.Rd |only man/bound_dist.Rd | 20 +++-- man/discrete_pmf.Rd | 6 - man/discretise.Rd | 4 - man/distspec-package.Rd | 3 man/figures/logo.png |only man/figures/logo.svg |only man/has_uncertainty.Rd | 1 man/new_dist_spec.Rd | 20 ++++- man/plot.dist_spec.Rd | 2 man/validate_dist_spec.Rd | 2 tests/testthat/test-as_dist_spec.R |only tests/testthat/test-deprecation.R | 36 ++++++++- tests/testthat/test-dist_spec.R | 24 +++--- tests/testthat/test-fixed.R | 16 ++++ tests/testthat/test-nonparametric.R | 10 +- tests/testthat/test-validate.R | 8 +- vignettes/distspec.Rmd | 2 35 files changed, 350 insertions(+), 145 deletions(-)
Title: Extra Functionality for the 'xpose' Package
Description: Adding some at-present missing functionality, or functions
unlikely to be added to the base 'xpose' package. This includes some
diagnostic plots that have been missing in translation from 'xpose4',
but also some useful features that truly extend the capabilities of what
can be done with 'xpose'. These extensions include the concept of a set of
'xpose' objects, and diagnostics for likelihood-based models.
Author: John Prybylski [aut, cre, cph]
Maintainer: John Prybylski <jprybylski@gmail.com>
Diff between xpose.xtras versions 0.2.0 dated 2026-07-26 and 0.2.2 dated 2026-09-01
DESCRIPTION | 22 MD5 | 106 +-- NAMESPACE | 15 NEWS.md | 74 ++ R/bbr.R | 14 R/categorical.R | 2 R/colinearity.R | 13 R/covariates.R | 954 +++++++++++++++++++++++------- R/fixes.R | 239 ++++++- R/nlmixr2.R | 35 - R/nlmixr_examples.R | 128 ++-- R/utils.R | 380 +++++++++++ R/xp_xtras.R | 115 +++ R/xtra_pars.R | 27 R/xtra_plots.R | 119 +++ R/zzz.R | 105 ++- README.md | 12 data/pheno_base.rda |binary data/pheno_final.rda |binary data/pheno_saem.rda |binary data/pheno_set.rda |binary data/pkpd_m3.rda |binary data/vismo_dtmm.rda |binary data/vismo_pomod.rda |binary data/xpdb_set.rda |binary data/xpdb_x.rda |binary inst/WORDLIST | 4 inst/doc/a01-the-xp_xtra-object.html | 8 inst/doc/a02-xpose-sets.html | 49 - inst/doc/a03-useful_plots.html | 38 - inst/doc/a04-plot-output-and-options.html | 32 - man/derive_shk.Rd |only man/eta_vs_catcov.Rd | 23 man/eta_vs_contcov.Rd | 23 man/figures/README-m3_roc-1.png |binary man/get_cov_matrix.Rd | 13 man/grid_plots.Rd | 5 man/irep.Rd | 10 man/levelers.Rd | 19 man/nlmixr2_as_xtra.Rd | 10 man/normalize_etas.Rd |only man/patch_condn.Rd | 7 man/print.xpose_data.Rd |only man/recalc_shk.Rd |only man/shk_grid_plots.Rd |only man/shk_vs_catcov.Rd |only man/shk_vs_contcov.Rd |only man/xp_from_bbr.Rd | 11 man/xtras_data.Rd |only tests/testthat/helper-bbr.R | 13 tests/testthat/helper-nlmixr2_examples.R | 32 - tests/testthat/test-bbr.R | 22 tests/testthat/test-colinearity.R | 15 tests/testthat/test-covariates.R | 322 +++++++++- tests/testthat/test-fixes.R | 172 ++++- tests/testthat/test-utils.R | 184 +++++ tests/testthat/test-xp_xtras.R | 80 ++ tests/testthat/test-zzz.R | 124 +++ 58 files changed, 3019 insertions(+), 557 deletions(-)
Title: Text Extraction, Rendering and Converting of PDF Documents
Description: Utilities based on 'libpoppler' <https://poppler.freedesktop.org> for extracting
text, fonts, attachments and metadata from a PDF file. Also supports high quality rendering
of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for further
processing in R.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between pdftools versions 3.9.0 dated 2026-05-14 and 3.9.1 dated 2026-09-01
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 3 +++ tools/winlibs.R | 9 +++++---- 4 files changed, 14 insertions(+), 10 deletions(-)
Title: A Flexible Class for Messy Dates
Description: Contains a set of tools for constructing and coercing
into and from the "mdate" class.
This date class implements ISO 8601-2:2019(E) and
allows regular dates and times to be annotated
to express unspecified date or time components,
approximate or uncertain components,
ranges, and sets of dates.
The package therefore retains, represents, and reasons about data and time imprecision,
resolving to a single data/time only on demand.
This is useful for describing and analysing temporal information,
whether historical or recent, where date or time precision may vary.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb] ,
Jael Tan [ctb] ,
Nathan Werth [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between messydates versions 1.1.0 dated 2026-07-27 and 1.1.1 dated 2026-09-01
DESCRIPTION | 8 - MD5 | 21 ++-- NAMESPACE | 44 +++++---- NEWS.md | 23 ++++ R/coerce_to_messydate.R | 175 +++++++++++++++++++++++++++++++++++-- R/validate_input.R | 14 +- README.md | 15 ++- man/coerce_to.Rd | 19 ++++ man/figures/messydates_hexlogo.png |binary man/figures/messydates_v2c.png |only tests/testthat/test-coerce_from.R | 8 + tests/testthat/test-coerce_to.R | 77 +++++++++++++++- 12 files changed, 348 insertions(+), 56 deletions(-)
Title: Tree-Style Console Logger for Nested Processes
Description: Render nested process execution as a live, colored tree in the console, with tree connectors, status glyphs, and elapsed time per step. Nesting depth is tracked via frame exit handlers so it never desynchronizes, even when a step errors. Builds on the 'cli' package for console rendering.
Author: Ivan Sortino [aut, cre, cph]
Maintainer: Ivan Sortino <ivan.sortino97@gmail.com>
Diff between logtree versions 0.1.0 dated 2026-08-06 and 0.2.0 dated 2026-09-01
DESCRIPTION | 12 MD5 | 111 +- NAMESPACE | 7 NEWS.md | 171 +++ R/appenders.R | 316 +++++-- R/glyphs.R | 155 +++ R/leaves.R | 103 ++ R/logger-integration.R | 56 - R/run.R | 170 +++ R/sinks.R |only R/state.R | 139 +++ R/step.R | 629 +++++++++++++ R/summary.R | 176 +++ R/theme.R | 443 +++++++++ R/trace.R |only R/zzz.R | 12 README.md | 364 +------- build/vignette.rds |binary inst/doc/logtree.R | 255 ++++- inst/doc/logtree.Rmd | 892 ++++++++++++++++--- inst/doc/logtree.html | 1399 +++++++++++++++++++++++-------- man/figures/README-tree-color.svg | 120 +- man/figures/logo.png |binary man/layout_logtree.Rd | 19 man/logtree_logger.Rd | 7 man/logtree_mute.Rd |only man/logtree_reset.Rd | 5 man/logtree_sink.Rd |only man/logtree_sink_file.Rd | 62 + man/logtree_sink_memory.Rd |only man/logtree_sink_memory_events.Rd |only man/logtree_sink_remove.Rd |only man/logtree_sinks.Rd |only man/logtree_summary.Rd | 59 + man/logtree_theme.Rd | 251 +++++ man/logtree_threshold.Rd | 16 man/with_logging.Rd | 37 tests/testthat/_snaps/close-text.md |only tests/testthat/_snaps/connector-gap.md |only tests/testthat/_snaps/elapsed-slot.md |only tests/testthat/_snaps/glyph-gap.md |only tests/testthat/_snaps/preset-ci.md |only tests/testthat/_snaps/preset-minimal.md |only tests/testthat/_snaps/wrap.md |only tests/testthat/helper-clock.R | 16 tests/testthat/helper-mute.R |only tests/testthat/helper-sinks.R | 16 tests/testthat/helper-theme.R | 5 tests/testthat/helper-trace.R |only tests/testthat/test-appenders.R | 3 tests/testthat/test-close-text.R |only tests/testthat/test-connector-gap.R |only tests/testthat/test-elapsed-slot.R |only tests/testthat/test-glyph-gap.R |only tests/testthat/test-logger-integration.R | 12 tests/testthat/test-mute.R |only tests/testthat/test-onload.R | 8 tests/testthat/test-preset-ci.R |only tests/testthat/test-preset-minimal.R |only tests/testthat/test-sink-memory.R |only tests/testthat/test-sink-threshold.R |only tests/testthat/test-sinks.R |only tests/testthat/test-summary.R | 202 ++++ tests/testthat/test-theme.R | 136 +++ tests/testthat/test-timestamp.R |only tests/testthat/test-trace.R |only tests/testthat/test-warnings.R |only tests/testthat/test-wrap.R |only vignettes/concept-anatomy.svg |only vignettes/concept-elevation.svg |only vignettes/concept-frames.svg |only vignettes/concept-grouping.svg |only vignettes/logtree.Rmd | 892 ++++++++++++++++--- vignettes/routed-conditions.svg |only vignettes/timestamp-silver.svg |only 75 files changed, 5996 insertions(+), 1280 deletions(-)
Title: Track User-Defined Environment Names
Description: Set of functions to keep track and find objects in user-defined environments
by identifying environments by name --which cannot be retrieved with the built-in function environmentName().
The package also provides functionality to obtain simplified information about function calling chains
and to get an object's memory address.
Author: Daniel Mastropietro [aut, cre]
Maintainer: Daniel Mastropietro <mastropi@uwalumni.com>
Diff between envnames versions 0.4.1 dated 2020-12-08 and 0.4.2 dated 2026-09-01
DESCRIPTION | 19 MD5 | 37 - R/get_obj_address.r | 45 - R/get_obj_name.r | 60 +- R/obj_find.r | 2 build/vignette.rds |binary inst/doc/envnames.Rmd | 831 ++++++++++++++++++++++++---------- inst/doc/envnames.pdf |binary man/envnames-package.Rd | 19 man/get_obj_name.Rd | 18 man/testenv.Rd | 3 tests/testthat/_problems |only tests/testthat/test-get_env_names.r | 50 -- tests/testthat/test-get_obj_address.r | 7 tests/testthat/test-get_obj_name.r | 37 - tests/testthat/test-obj_find.r | 59 -- vignettes/envnames.Rmd | 831 ++++++++++++++++++++++++---------- 17 files changed, 1357 insertions(+), 661 deletions(-)
Title: Assessment of Regression Models Performance
Description: Utilities for computing measures to assess model quality,
which are not directly provided by R's 'base' or 'stats' packages.
These include e.g. measures like r-squared, intraclass correlation
coefficient (Nakagawa, Johnson & Schielzeth (2017)
<doi:10.1098/rsif.2017.0213>), root mean squared error or functions to
check models for overdispersion, singularity or zero-inflation and
more. Functions apply to a large variety of regression models,
including generalized linear models, mixed effects models and Bayesian
models. References: Lüdecke et al. (2021) <doi:10.21105/joss.03139>.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Remi Theriault [aut, ctb] ,
Vincent Arel-Bundock [ctb] ,
Martin J [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between performance versions 0.18.0 dated 2026-08-28 and 0.18.1 dated 2026-09-01
DESCRIPTION | 6 ++--- MD5 | 12 +++++----- NEWS.md | 10 ++++++++ R/binned_residuals.R | 32 ++++++++++++++++++++-------- man/binned_residuals.Rd | 9 ++++--- tests/testthat/test-binned_residuals.R | 15 +++++++++++++ tests/testthat/test-check_group_variation.R | 32 ++++++++++++++-------------- 7 files changed, 79 insertions(+), 37 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: Jose Pinheiro [aut] ,
Douglas Bates [aut] ,
Saikat DebRoy [ctb] ,
Deepayan Sarkar [ctb] ,
EISPACK authors [ctb] ,
Siem Heisterkamp [ctb] ,
Bert Van Willigen [ctb] ,
Johannes Ranke [ctb] ),
R Core Team [aut, cre]
Maintainer: R Core Team <R-core@R-project.org>
Diff between nlme versions 3.1-170 dated 2026-07-15 and 3.1-171 dated 2026-09-01
ChangeLog | 5 ++ DESCRIPTION | 8 ++-- MD5 | 92 ++++++++++++++++++++++++------------------------- build/partial.rdb |binary data/Alfalfa.rda |binary data/Assay.rda |binary data/BodyWeight.rda |binary data/Cefamandole.rda |binary data/Dialyzer.rda |binary data/Earthquake.rda |binary data/Fatigue.rda |binary data/Gasoline.rda |binary data/Glucose.rda |binary data/Glucose2.rda |binary data/Gun.rda |binary data/IGF.rda |binary data/Machines.rda |binary data/MathAchSchool.rda |binary data/MathAchieve.rda |binary data/Meat.rda |binary data/Milk.rda |binary data/Muscle.rda |binary data/Nitrendipene.rda |binary data/Oats.rda |binary data/Orthodont.rda |binary data/Ovary.rda |binary data/Oxboys.rda |binary data/Oxide.rda |binary data/PBG.rda |binary data/Phenobarb.rda |binary data/Pixel.rda |binary data/Quinidine.rda |binary data/Rail.rda |binary data/RatPupWeight.rda |binary data/Relaxin.rda |binary data/Remifentanil.rda |binary data/Soybean.rda |binary data/Spruce.rda |binary data/Tetracycline1.rda |binary data/Tetracycline2.rda |binary data/Wafer.rda |binary data/Wheat.rda |binary data/Wheat2.rda |binary data/bdf.rda |binary data/ergoStool.rda |binary tests/lme.R | 3 + tests/lme.Rout.save | 11 +++-- 47 files changed, 63 insertions(+), 56 deletions(-)
Title: Create Layout Plots of Biological Culture Plates and Microplates
Description: Enables users to create simple plots of biological culture plates as well as microplates. Both continuous and discrete values can be plotted onto the plate layout.
Author: Jan-Philipp Quast [aut, cre]
Maintainer: Jan-Philipp Quast <jpquast.software@gmail.com>
Diff between ggplate versions 0.3.1 dated 2026-05-11 and 0.4.0 dated 2026-09-01
DESCRIPTION | 10 MD5 | 101 +- NAMESPACE | 1 NEWS.md | 13 R/data.R | 50 + R/plate_plot.R | 188 ++++- README.md | 131 +++ data/border_colours.rda |only data/data_continuous_12.rda |binary data/data_continuous_1536.rda |binary data/data_continuous_1536_Aa.rda |binary data/data_continuous_24.rda |binary data/data_continuous_384.rda |binary data/data_continuous_48.rda |binary data/data_continuous_48_incomplete.rda |binary data/data_continuous_6.rda |binary data/data_continuous_96.rda |binary data/data_discrete_24.rda |binary data/data_discrete_6.rda |binary data/data_discrete_96.rda |binary man/border_colours.Rd |only man/data_continuous_12.Rd | 3 man/data_continuous_1536.Rd | 3 man/data_continuous_1536_Aa.Rd | 3 man/data_continuous_24.Rd | 3 man/data_continuous_384.Rd | 3 man/data_continuous_48.Rd | 3 man/data_continuous_48_incomplete.Rd | 4 man/data_continuous_6.Rd | 3 man/data_continuous_96.Rd | 3 man/data_discrete_24.Rd | 3 man/data_discrete_6.Rd | 3 man/data_discrete_96.Rd | 6 man/figures/README-24_well_plate_legend_n_row-1.png |binary man/figures/README-6_well_plot_new_colours-1.png |binary man/figures/README-6_well_plot_new_colours_no_legend-1.png |binary man/figures/README-discrete_96_well_plate-1.png |binary man/figures/README-discrete_96_well_plate_label-1.png |binary man/figures/README-resize_plot-1.png |binary man/figures/README-return_device_size-1.png |binary man/figures/README-standard_plot-1.png |binary man/figures/README-standard_plot_384_well_new_gradient-1.png |binary man/figures/README-standard_plot_384_well_new_limits-1.png |binary man/figures/README-standard_plot_384_well_new_limits_outlier-1.png |binary man/figures/README-standard_plot_48_empty_wells-1.png |binary man/figures/README-standard_plot_48_empty_wells_keep_na-1.png |binary man/figures/README-standard_plot_6_well-1.png |binary man/figures/README-standard_plot_labels-1.png |binary man/figures/README-standard_plot_labels_wells-1.png |binary man/figures/README-well_borders-1.png |only man/figures/README-well_borders_colour-1.png |only man/figures/README-well_borders_only-1.png |only man/plate_plot.Rd | 36 - tests/testthat/test-my-test.R | 347 ++++++++++ 54 files changed, 788 insertions(+), 129 deletions(-)
Title: Calculating Likelihoods by Pedigree Paring
Description: A fast and general implementation of the Elston-Stewart algorithm
that can calculate the likelihoods of large and complex pedigrees.
References for the Elston-Stewart algorithm are
Elston & Stewart (1971) <doi:10.1159/000152448>,
Lange & Elston (1975) <doi:10.1159/000152714> and
Cannings et al. (1978) <doi:10.2307/1426718>.
Author: James Dowty [aut, cre],
Kevin Wong [aut]
Maintainer: James Dowty <jgdowty@gmail.com>
Diff between clipp versions 1.1.1 dated 2022-07-12 and 1.2.0 dated 2026-09-01
DESCRIPTION | 8 MD5 | 18 - R/pedigree_loglikelihood.R | 2 R/pedigree_loglikelihood_g.R | 87 +++------ build/vignette.rds |binary inst/doc/using_clipp.R | 94 ++++----- inst/doc/using_clipp.Rmd | 2 inst/doc/using_clipp.html | 405 +++++++++++++++++++++---------------------- man/clipp-package.Rd | 1 vignettes/using_clipp.Rmd | 2 10 files changed, 305 insertions(+), 314 deletions(-)
Title: A S3 Class for Vectors of 64bit Integers
Description: Package 'bit64' provides serializable S3 atomic 64bit (signed) integers.
These are useful for handling database keys and exact counting in +-2^63.
WARNING: do not use them as replacement for 32bit integers, integer64 are not
supported for subscripting by R-core and they have different semantics when
combined with double, e.g. integer64 + double => integer64.
Class integer64 can be used in vectors, matrices, arrays and data.frames.
Methods are available for coercion from and to logicals, integers, doubles,
characters and factors as well as many elementwise and summary functions.
Many fast algorithmic operations such as 'match' and 'order' support inter-
active data exploration and manipulation and optionally leverage caching.
Author: Michael Chirico [aut, cre],
Jens Oehlschlaegel [aut],
Leonardo Silvestri [ctb],
Ofek Shilon [ctb],
Christian Ullerich [ctb]
Maintainer: Michael Chirico <michaelchirico4@gmail.com>
Diff between bit64 versions 4.8.4 dated 2026-08-20 and 4.8.6 dated 2026-09-01
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 6 ++++++ src/integer64.h | 6 +++++- 4 files changed, 17 insertions(+), 7 deletions(-)
Title: 'React Router' for 'shiny' Apps and 'Quarto'
Description: Provides a wrapper around the 'react-router-dom' 'React' library for use in
'Shiny' applications and 'Quarto' documents. Enables client-side routing with hash,
memory, and browser history strategies, nested routes, dynamic segments, data loaders,
actions, and navigation hooks.
Author: Felix Luginbuhl [aut, cre, cph] ,
Andryas Waurzenczak [ctb]
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>
Diff between reactRouter versions 0.2.0 dated 2026-05-10 and 0.2.1 dated 2026-09-01
DESCRIPTION | 6 +-- MD5 | 10 ++--- NEWS.md | 11 ++++++ README.md | 2 - inst/reactRouter/react-router-dom.js | 4 +- inst/reactRouter/react-router-dom.js.LICENSE.txt | 42 +++++++++++------------ 6 files changed, 43 insertions(+), 32 deletions(-)
Title: Adding Progress Bar to '*apply' Functions
Description: A lightweight package that adds
progress bar to vectorized R functions
('*apply'). The implementation can easily be added
to functions where showing the progress is
useful (e.g. bootstrap). The type and style of the
progress bar (with percentages or remaining time)
can be set through options.
Supports several parallel processing backends including mirai and future.
Author: Peter Solymos [aut, cre] ,
Zygmunt Zawadzki [aut],
Henrik Bengtsson [ctb],
R Core Team [cph, ctb]
Maintainer: Peter Solymos <psolymos@gmail.com>
Diff between pbapply versions 1.7-4 dated 2025-07-20 and 1.7-5 dated 2026-09-01
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ inst/WORDLIST | 1 - man/pbapply.Rd | 4 ++-- 5 files changed, 14 insertions(+), 11 deletions(-)
Title: Dense Neural Networks for Tabular Regression, Classification and
Survival
Description: Dense feed-forward neural networks (multilayer perceptrons)
for tabular regression, classification and survival analysis, with a
formula or x/y interface. Supports residual and gated hidden blocks,
batch normalization, per-layer dropout, learned cross-feature
interactions, exponential moving-average weights, learning-rate
schedules, internal bootstrap ensembles and Adam optimization. Survival
outcomes are trained with either a batch-wise Breslow-tie Cox partial
likelihood or a discrete-time inverse-probability-of-censoring-weighted
integrated Brier score. The numerical kernels are implemented natively
in C++ via 'RcppArmadillo', with no external deep learning framework
dependency (no 'torch' / 'libtorch'). Companion helpers provide k-fold
cross-validation, hyperparameter search and task-aware evaluation
metrics.
Author: Imad El Badisy [aut, cre]
Maintainer: Imad El Badisy <elbadisyimad@gmail.com>
Diff between densemlp versions 0.6.0 dated 2026-08-21 and 0.7.1 dated 2026-09-01
densemlp-0.6.0/densemlp/R/logging.R |only densemlp-0.6.0/densemlp/R/model_torch.R |only densemlp-0.6.0/densemlp/R/print.R |only densemlp-0.6.0/densemlp/R/training.R |only densemlp-0.6.0/densemlp/R/zzz.R |only densemlp-0.6.0/densemlp/inst/doc/getting-started.R |only densemlp-0.6.0/densemlp/inst/doc/getting-started.Rmd |only densemlp-0.6.0/densemlp/inst/doc/getting-started.pdf |only densemlp-0.6.0/densemlp/man/autoplot.densemlp_fit.Rd |only densemlp-0.6.0/densemlp/man/predict.densemlp_fit.Rd |only densemlp-0.6.0/densemlp/man/print.densemlp_fit.Rd |only densemlp-0.6.0/densemlp/tests/testthat/helper-torch.R |only densemlp-0.6.0/densemlp/tests/testthat/test-training-logging.R |only densemlp-0.6.0/densemlp/vignettes/getting-started.Rmd |only densemlp-0.7.1/densemlp/DESCRIPTION | 38 densemlp-0.7.1/densemlp/MD5 | 82 - densemlp-0.7.1/densemlp/NAMESPACE | 17 densemlp-0.7.1/densemlp/NEWS.md | 73 + densemlp-0.7.1/densemlp/R/RcppExports.R |only densemlp-0.7.1/densemlp/R/cv.R | 149 -- densemlp-0.7.1/densemlp/R/densemlp-package.R | 15 densemlp-0.7.1/densemlp/R/densemlp.R | 579 +++++++--- densemlp-0.7.1/densemlp/R/importance.R | 124 +- densemlp-0.7.1/densemlp/R/metrics.R | 142 +- densemlp-0.7.1/densemlp/R/plots.R | 52 densemlp-0.7.1/densemlp/R/predict.R | 204 ++- densemlp-0.7.1/densemlp/R/preprocess.R | 253 +--- densemlp-0.7.1/densemlp/R/tuning.R | 335 +---- densemlp-0.7.1/densemlp/R/utils.R | 168 -- densemlp-0.7.1/densemlp/README.md | 303 +---- densemlp-0.7.1/densemlp/build/vignette.rds |binary densemlp-0.7.1/densemlp/inst/WORDLIST |only densemlp-0.7.1/densemlp/inst/doc/densemlp-intro.R |only densemlp-0.7.1/densemlp/inst/doc/densemlp-intro.Rmd |only densemlp-0.7.1/densemlp/inst/doc/densemlp-intro.html |only densemlp-0.7.1/densemlp/man/cv_densemlp.Rd | 52 densemlp-0.7.1/densemlp/man/densemlp-package.Rd | 14 densemlp-0.7.1/densemlp/man/densemlp.Rd | 244 +++- densemlp-0.7.1/densemlp/man/densemlp_integrated_brier_score.Rd |only densemlp-0.7.1/densemlp/man/densemlp_metrics.Rd | 24 densemlp-0.7.1/densemlp/man/perm_importance.Rd | 41 densemlp-0.7.1/densemlp/man/plot.densemlp.Rd |only densemlp-0.7.1/densemlp/man/plot.densemlp_importance.Rd | 8 densemlp-0.7.1/densemlp/man/plot_history.Rd | 20 densemlp-0.7.1/densemlp/man/predict.densemlp.Rd |only densemlp-0.7.1/densemlp/man/tune_densemlp.Rd | 76 - densemlp-0.7.1/densemlp/src |only densemlp-0.7.1/densemlp/tests/testthat/test-cv.R | 70 - densemlp-0.7.1/densemlp/tests/testthat/test-densemlp.R | 350 ++++-- densemlp-0.7.1/densemlp/tests/testthat/test-features.R |only densemlp-0.7.1/densemlp/tests/testthat/test-metrics.R |only densemlp-0.7.1/densemlp/tests/testthat/test-plot-ncores.R |only densemlp-0.7.1/densemlp/tests/testthat/test-tuning.R | 54 densemlp-0.7.1/densemlp/vignettes/densemlp-intro.Rmd |only 54 files changed, 1854 insertions(+), 1633 deletions(-)
Title: An 'Shiny' App for Exploring scRNA-seq Data Processed in
'Seurat'
Description: A simple, one-command package which runs an interactive dashboard capable of common visualizations for single cell RNA-seq. 'SeuratExplorer' requires a processed 'Seurat' object, which is saved as 'rds' or 'qs2' file.
Author: Yongchao Zhang [aut, cre]
Maintainer: Yongchao Zhang <zhangyongchao@nibs.ac.cn>
Diff between SeuratExplorer versions 0.1.6 dated 2026-06-17 and 0.1.8 dated 2026-09-01
DESCRIPTION | 6 MD5 | 15 NAMESPACE | 3 R/functions.R | 76 +++ R/launch.R | 5 R/server.R | 841 +++++++++++++++++++++++++++++++++++++++----- R/ui.R | 440 +++++++++++++++-------- man/launchSeuratExplorer.Rd | 2 man/param_group_collapse.Rd |only 9 files changed, 1154 insertions(+), 234 deletions(-)
More information about SeuratExplorer at CRAN
Permanent link
Title: Poisson Fixed Effects Robust
Description: Computation of robust standard errors of Poisson fixed effects
models, following Wooldridge (1999).
Author: Evan Wright [aut, cre]
Maintainer: Evan Wright <enwright@umich.edu>
Diff between poisFErobust versions 2.0.0 dated 2020-02-17 and 2.0.1 dated 2026-09-01
DESCRIPTION | 9 ++++----- LICENSE | 2 +- MD5 | 10 +++++----- NEWS.md | 4 ++++ build/partial.rdb |binary man/pois.fe.robust.Rd | 29 +++++++++++------------------ 6 files changed, 25 insertions(+), 29 deletions(-)
Title: Contrast and Separation Metrics for Phonological Categories
Description: Computes and compares multiple measures of separation and overlap
between phonological categories (for example vowels or consonants) in
arbitrary multi-dimensional acoustic spaces such as formant values,
mel-frequency cepstral coefficients (MFCCs), duration, or learned
embeddings. The main entry point, phontrast(), reports several contrast
metrics in one call -- Jensen-Shannon divergence and distance (Lin, 1991)
<doi:10.1109/18.61115>, the Pillai-Bartlett trace, Bhattacharyya distance
and affinity, Mahalanobis distance, and proportional overlap -- globally or
by group on a common separation-oriented scale, with bootstrap confidence
intervals. Also provides utilities for preparing estimates for downstream
modelling such as generalized additive models and mixed-effects models.
Formerly released as 'phonJSD'.
Author: Grant M. Berry [aut, cre]
Maintainer: Grant M. Berry <berry.grant@gmail.com>
Diff between phontrast versions 2.4.0 dated 2026-08-21 and 2.4.1 dated 2026-09-01
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 16 ++++++++++++++++ R/pillai_bhatt.R | 20 ++++++++++++++------ tests/testthat/test-pillai-standardized.R | 17 +++++++++++++++++ 5 files changed, 54 insertions(+), 13 deletions(-)
Title: AAPOR Survey Outcome Rates
Description: Standardized survey outcome rate functions, including the response rate, contact rate, cooperation rate, and refusal rate. These outcome rates allow survey researchers to measure the quality of survey data using definitions published by the American Association for Public Opinion Research (AAPOR). For details on these standards, see AAPOR (2023) <https://aapor.org/wp-content/uploads/2024/03/Standards-Definitions-10th-edition.pdf>.
Author: Rafael Pilliard Hellwig [aut, cre] ,
Carl Ganz [rev],
Neal Richardson [rev]
Maintainer: Rafael Pilliard Hellwig <rafael.taph@gmail.com>
Diff between outcomerate versions 1.0.1 dated 2018-10-06 and 1.1.0 dated 2026-09-01
DESCRIPTION | 18 MD5 | 56 +-- NEWS.md | 25 + R/asserters.R | 144 ++++++- R/datasets.R | 37 +- R/eligibility_rate.R | 66 ++- R/helpers.R | 33 + R/outcomerate.R | 188 +++++++--- R/sysdata.rda |binary README.md | 134 ++++--- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 18 inst/REFERENCES.bib | 18 inst/WORDLIST | 28 - inst/doc/intro-to-outcomerate.R | 62 ++- inst/doc/intro-to-outcomerate.Rmd | 67 ++- inst/doc/intro-to-outcomerate.html | 532 +++++++++++++++++++---------- man/eligibility_rate.Rd | 46 +- man/fmat.Rd | 27 - man/middleearth.Rd | 9 man/outcomerate.Rd | 137 +++++-- tests/testthat/_snaps |only tests/testthat/spelling.R | 4 tests/testthat/test-aggregate-boundaries.R |only tests/testthat/test-e.R |only tests/testthat/test-helpers.R | 38 +- tests/testthat/test-params.R | 44 +- tests/testthat/test-rate.R | 15 tests/testthat/test-ur.R |only vignettes/intro-to-outcomerate.Rmd | 67 ++- 31 files changed, 1236 insertions(+), 577 deletions(-)
Title: Data from the US National Health and Nutrition Examination Study
Description: Body Shape and related measurements from the US National Health
and Nutrition Examination Survey (NHANES, 1999-2004). See
<https://www.cdc.gov/nchs/nhanes/index.html> for details.
Author: Randall Pruim [aut, cre]
Maintainer: Randall Pruim <rpruim@gmail.com>
Diff between NHANES versions 2.1.0 dated 2015-07-02 and 2.1.4 dated 2026-09-01
NHANES-2.1.0/NHANES/data/datalist |only NHANES-2.1.4/NHANES/DESCRIPTION | 19 +- NHANES-2.1.4/NHANES/MD5 | 15 - NHANES-2.1.4/NHANES/NAMESPACE | 3 NHANES-2.1.4/NHANES/R/datasets.R | 62 +++----- NHANES-2.1.4/NHANES/README.md | 3 NHANES-2.1.4/NHANES/data/NHANES.rda |binary NHANES-2.1.4/NHANES/data/NHANESraw.rda |binary NHANES-2.1.4/NHANES/man/NHANES.Rd | 253 ++++++++++++++++----------------- 9 files changed, 177 insertions(+), 178 deletions(-)
Title: Analyzing Wildlife Data with Detection Error
Description: Models for analyzing site occupancy and count data models
with detection error, including
single-visit based models (Lele et al. 2012 <doi:10.1093/jpe/rtr042>,
Moreno et al. 2010 <doi:10.1890/09-1073.1>,
Solymos et al. 2012 <doi:10.1002/env.1149>,
Denes et al. 2016 <doi:10.1111/1365-2664.12818>),
conditional distance sampling and time-removal models (QPAD)
(Solymos et al. 2013 <doi:10.1111/2041-210X.12106>,
Solymos et al. 2018 <doi:10.1650/CONDOR-18-32.1>),
and single bin QPAD (SQPAD) models
(Lele & Solymos 2025 <doi:10.1093/ornithapp/duaf078>).
Package development was supported by the
Alberta Biodiversity Monitoring Institute
and the Boreal Avian Modelling Project.
Author: Peter Solymos [aut, cre] ,
Monica Moreno [aut],
Subhash R. Lele [aut],
Steven L. Van Wilgenburg [ctb]
Maintainer: Peter Solymos <psolymos@gmail.com>
Diff between detect versions 0.5-1 dated 2026-01-08 and 0.5-2 dated 2026-09-01
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 1 + R/coef.svabu.R | 48 ++++++++++++++++++++++++++++-------------------- R/coef.svocc.R | 30 +++++++++++++++++------------- R/sqpad.R | 28 ++++++++++++++++++++++++++-- inst/WORDLIST | 3 +++ man/sqpad.Rd | 27 +++++++++++++++++++++------ 8 files changed, 107 insertions(+), 52 deletions(-)
Title: Highly Customizable, Parallelized Simulations of Frequentist
Confidence Clinical Trials
Description: Simulate one or many frequentist confidence clinical trials
based on a specified set of parameters. From a two-arm, single-stage
trial to a perpetually run Adaptive Platform Trial, this package
offers vast flexibility to customize your trial and observe
operational characteristics over thousands of instances.
Author: Freda Werdiger [aut, cre]
Maintainer: Freda Werdiger <freda.werdiger@unimelb.edu.au>
This is a re-admission after prior archival of version 0.1.0 dated 2025-10-25
Diff between confidenceSim versions 0.1.0 dated 2025-10-25 and 0.1.1 dated 2026-09-01
DESCRIPTION | 10 ++++---- MD5 | 15 ++++++------- NEWS.md |only R/trialDesignFns.R | 8 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/running-simulations-in-parallel.html | 30 +++++++++++++------------- man/getConfidenceFromBounds.Rd | 2 - man/getGSDesign.Rd | 6 ++--- 9 files changed, 36 insertions(+), 35 deletions(-)
Title: Make, Update, and Query Binary Causal Models
Description: Users can declare causal models over binary nodes, update beliefs about causal types given data, and calculate arbitrary queries. Updating is implemented in 'stan'. See Tietz, Medina, Syunyaev and Humphreys (2026) <doi:10.18637/jss.v117.i01>, Humphreys and Jacobs (2023) <doi:10.1017/9781316718636> and Pearl (2009) <doi:10.1017/CBO9780511803161>.
Author: Clara Bicalho [ctb],
Jasper Cooper [ctb],
Macartan Humphreys [aut] ,
Till Tietz [aut, cre] ,
Alan Jacobs [aut],
Merlin Heidemanns [ctb],
Lily Medina [aut] ,
Julio Solis [ctb],
Georgiy Syunyaev [aut] ,
Moritz Marbach [ctb]
Maintainer: Till Tietz <ttietz2014@gmail.com>
Diff between CausalQueries versions 1.4.5 dated 2026-01-29 and 1.4.6 dated 2026-09-01
DESCRIPTION | 10 +++---- MD5 | 42 +++++++++++++++++---------------- NEWS.md | 7 ++++- R/CausalQueries-package.R | 6 ++++ R/make_models.R | 5 +++ R/query_model.R | 5 +++ R/realise_outcomes.R | 4 ++- R/update_model.R | 8 +++++- build/partial.rdb |only inst/CITATION |only man/CausalQueries-package.Rd | 7 +++++ man/data_helpers.Rd | 13 +++------- man/get_all_data_types.Rd | 6 ++-- man/make_data_single.Rd | 6 ++-- man/make_model.Rd | 6 ++++ man/observe_data.Rd | 6 ++-- man/parents_to_int.Rd | 5 --- man/query_model.Rd | 6 ++++ man/set_confound.Rd | 6 ++-- man/set_prior_distribution.Rd | 6 ++-- man/set_restrictions.Rd | 6 ++-- man/update_model.Rd | 6 ++++ tests/testthat/test_update_model.R | 47 +++++++++++++++++++++++++++++++++++++ 23 files changed, 154 insertions(+), 59 deletions(-)
Title: Utilities to Output CDISC SDTM/ADaM XPT Files
Description: Tools to build CDISC compliant data sets and check for CDISC
compliance.
Author: Eli Miller [aut, cre] ,
Ben Straub [aut],
Zelos Zhu [aut],
Ethan Brockmann [aut],
Vedha Viyash [aut],
Andre Verissimo [aut],
Sophie Shapcott [aut],
Celine Piraux [aut],
Kangjie Zhang [aut],
Adrian Chan [aut],
Sadchla Mascary [aut],
Seunghyun Kim [aut [...truncated...]
Maintainer: Eli Miller <Eli.Miller@AtorusResearch.com>
Diff between xportr versions 0.5.0 dated 2026-01-13 and 0.6.0 dated 2026-08-31
DESCRIPTION | 11 MD5 | 86 ++-- NAMESPACE | 14 NEWS.md | 18 R/df_label.R | 8 R/format.R | 12 R/label.R | 13 R/length.R | 8 R/messages.R | 29 + R/metadata.R | 8 R/order.R | 16 R/support-test.R | 38 - R/type.R | 6 R/utils-xportr.R | 35 - R/write.R | 2 R/xportr-package.R | 6 R/xportr.R | 35 - README.md | 42 - build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/agency_standards.html | 88 ++-- inst/doc/deepdive.R | 161 +++---- inst/doc/deepdive.Rmd | 166 ++----- inst/doc/deepdive.html | 687 +++++++++++++------------------- inst/doc/options.R |only inst/doc/options.Rmd |only inst/doc/options.html |only inst/doc/xportr.R | 30 - inst/doc/xportr.Rmd | 32 - inst/doc/xportr.html | 40 - man/metadata.Rd | 8 man/xportr.Rd | 19 tests/testthat/_snaps/label.md | 36 + tests/testthat/test-label.R | 29 + tests/testthat/test-length.R | 220 ++++++++-- tests/testthat/test-messages.R | 52 +- tests/testthat/test-metadata.R | 148 +++--- tests/testthat/test-order.R | 26 - tests/testthat/test-support-for-tests.R | 16 tests/testthat/test-type.R | 42 - tests/testthat/test-utils-xportr.R | 26 - tests/testthat/test-write.R | 26 - tests/testthat/test-xportr.R | 16 vignettes/deepdive.Rmd | 166 ++----- vignettes/options.Rmd |only vignettes/xportr.Rmd | 32 - 46 files changed, 1202 insertions(+), 1252 deletions(-)
Title: Visualize R Data Structures with Trees
Description: A set of tools for inspecting and understanding R data
structures inspired by str(). Includes ast() for visualizing abstract
syntax trees, ref() for showing shared references, cst() for showing
call stack trees, and obj_size() for computing object sizes.
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between lobstr versions 1.2.1 dated 2026-04-04 and 1.2.2 dated 2026-08-31
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/size.R | 3 --- man/ast.Rd | 8 ++++---- man/lobstr-package.Rd | 5 +++++ man/ref.Rd | 8 ++++---- man/src.Rd | 8 ++++---- man/sxp.Rd | 8 ++++---- 9 files changed, 38 insertions(+), 32 deletions(-)
Title: Water Quality Assessment and Environmental Compliance in Brazil
Description: Tools to import, clean, validate, and analyze freshwater quality data
in Brazil. Implements water quality indices including the Water Quality Index
('WQI'/'IQA') using the weighted geometric mean following 'CETESB' methodology,
the Trophic State Index ('TSI'/'IET') after Carlson (1977)
<doi:10.4319/lo.1977.22.2.0361> and Lamparelli (2004)
<https://teses.usp.br/teses/disponiveis/41/41134/tde-20032006-075813/publico/TeseLamparelli2004.pdf>,
and the National Sanitation Foundation Water Quality Index ('NSF WQI', Brown
(1970)). The package also checks compliance with Brazilian standard 'CONAMA'
Resolution 357/2005
<https://conama.mma.gov.br/?id=450&option=com_sisconama&task=arquivo.download>
including the legal frequency rule (Art. 15, 80% conformity over six or more
samples per year), and provides seasonal analysis with regional flow-season
calendars, pollutant load computation, exceedance probability estimation, 'IET'
visualization, and multivariate 'PCA' tools f [...truncated...]
Author: Vinicius Saraiva Santos [aut, cre] ,
Fabricio Berton Zanchi [ctb]
Maintainer: Vinicius Saraiva Santos <vinisaraiva@gmail.com>
Diff between tikatuwq versions 0.9.0 dated 2026-06-09 and 0.10.0 dated 2026-08-31
DESCRIPTION | 32 - MD5 | 63 +- NAMESPACE | 2 NEWS.md | 18 R/analysis_text.R | 3 R/conama.R | 38 - R/io_clean.R | 19 R/iqa.R | 368 ++++++++++------ R/iqa_equations.R | 662 +++++++++++++++++++++--------- R/nsfwqi.R | 183 +++----- R/report.R | 3 R/seasonal.R | 54 +- R/utils_sanitize.R | 220 ++++++++- README.md | 200 +++------ inst/CITATION | 5 inst/doc/tikatuwq-methods.html | 46 +- inst/doc/tikatuwq-workflow.html | 30 - inst/doc/tikatuwq.html | 2 man/assign_season.Rd | 27 - man/classify_iqa.Rd | 11 man/conama_check.Rd | 14 man/iqa.Rd | 129 ++--- man/iqa_components.Rd |only man/normalize_param_names.Rd |only man/nsfwqi.Rd | 101 +--- man/render_report.Rd | 2 man/tikatuwq-package.Rd | 5 tests/testthat/test-iqa-cetesb-formulas.R |only tests/testthat/test-iqa-components.R |only tests/testthat/test-iqa-curves.R | 5 tests/testthat/test-iqa-geometric.R | 44 + tests/testthat/test-iqa-inema-benchmark.R |only tests/testthat/test-iqa-solids-tds.R |only tests/testthat/test-iqa-temperature.R |only tests/testthat/test-iqa.R | 16 tests/testthat/test-render_report.R | 21 36 files changed, 1419 insertions(+), 904 deletions(-)
Title: Assessing Risk Predictions for Clustered Data
Description: Assessing and comparing risk prediction rules for clustered data. The method is based on the paper: Rosner B, Qiu W, and Lee MLT.(2013) <doi: 10.1007/s10985-012-9240-6>.
Author: Bernard Rosner [aut, ctb],
Weiliang Qiu [aut, cre],
Meiling T. Lee [aut, ctb]
Maintainer: Weiliang Qiu <Weiliang.Qiu@gmail.com>
Diff between riskPredictClustData versions 0.2.6 dated 2018-11-28 and 0.2.7 dated 2026-08-31
DESCRIPTION | 9 MD5 | 14 NEWS | 215 +- R/functions.R | 2548 +++++++++++++++++------------------ man/print.class.riskPredict.Rd |only man/print.class.riskPredictDiff.Rd |only man/riskPredict.Rd | 264 +-- man/riskPredictDiff.Rd | 286 +-- man/summary.class.riskPredict.Rd |only man/summary.class.riskPredictDiff.Rd |only 10 files changed, 1702 insertions(+), 1634 deletions(-)
More information about riskPredictClustData at CRAN
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Title: Data-Derived Graph Construction Utilities
Description: Constructs data-derived graphs from numerical observations using
mutual, shared-neighbor, intersection, geodesic, radius, adaptive-radius,
and minimum-spanning-tree completion methods. Provides graph conversion,
pruning, diagnostics, spectral embedding, endpoint detection, and path
utilities. The implemented graph constructions include methods described by
Jarvis and Patrick (1973) <doi:10.1109/T-C.1973.223640>, Brito et al. (1997)
<doi:10.1016/S0167-7152(96)00213-1>, Berry and Sauer (2019)
<doi:10.3934/fods.2019001>, and Gower and Ross (1969)
<doi:10.2307/2346439>.
Author: Pawel Gajer [aut, cre],
Sunil Arya [ctb] ,
David M. Mount [ctb] ,
University of Maryland [cph] ,
Yixuan Qiu [ctb, cph] ,
Anna Araslanova [ctb, cph] ,
Gael Guennebaud [ctb, cph] ,
Jitse Niesen [ctb, cph] ,
Netherlands eScience Center [ctb, cph]
Maintainer: Pawel Gajer <pgajer@gmail.com>
Diff between dgraphs versions 0.1.0 dated 2026-08-20 and 0.2.0 dated 2026-08-31
dgraphs-0.1.0/dgraphs/R/graph_edit_distance.R |only dgraphs-0.1.0/dgraphs/man/adjlist.to.igraph.Rd |only dgraphs-0.1.0/dgraphs/man/calculate.edit.distances.Rd |only dgraphs-0.1.0/dgraphs/man/cpp.create.rknn.graphs.Rd |only dgraphs-0.1.0/dgraphs/man/create.distance.plot.Rd |only dgraphs-0.1.0/dgraphs/man/deprecated-radius-graph-constructors.Rd |only dgraphs-0.1.0/dgraphs/man/dist.to.knn.Rd |only dgraphs-0.1.0/dgraphs/man/euclidean.distance.Rd |only dgraphs-0.1.0/dgraphs/man/graph.adj.mat.Rd |only dgraphs-0.1.0/dgraphs/man/graph.edit.distance.Rd |only dgraphs-0.1.0/dgraphs/man/load.graph.data.Rd |only dgraphs-0.2.0/dgraphs/DESCRIPTION | 17 dgraphs-0.2.0/dgraphs/MD5 | 220 ++++------ dgraphs-0.2.0/dgraphs/NAMESPACE | 21 dgraphs-0.2.0/dgraphs/NEWS.md | 40 + dgraphs-0.2.0/dgraphs/R/as_igraph.R | 190 ++++++-- dgraphs-0.2.0/dgraphs/R/basic_graphs.R | 119 +++-- dgraphs-0.2.0/dgraphs/R/component_mst_connectivity.R | 37 - dgraphs-0.2.0/dgraphs/R/dgraphs-package.R | 1 dgraphs-0.2.0/dgraphs/R/divergences.R | 3 dgraphs-0.2.0/dgraphs/R/geodesic_distances.R | 5 dgraphs-0.2.0/dgraphs/R/geodesic_stats.R | 28 + dgraphs-0.2.0/dgraphs/R/graph_embedding_spectrum.R | 25 + dgraphs-0.2.0/dgraphs/R/graph_endpoint_geometry.R | 27 + dgraphs-0.2.0/dgraphs/R/graph_fixtures.R | 3 dgraphs-0.2.0/dgraphs/R/graph_pruning.R | 9 dgraphs-0.2.0/dgraphs/R/graph_summary_divergence.R | 24 + dgraphs-0.2.0/dgraphs/R/graph_utils.R | 60 ++ dgraphs-0.2.0/dgraphs/R/grid_graphs.R | 9 dgraphs-0.2.0/dgraphs/R/iknn_selection.R | 17 dgraphs-0.2.0/dgraphs/R/isometry_deviation.R | 9 dgraphs-0.2.0/dgraphs/R/local_extrema.R | 22 + dgraphs-0.2.0/dgraphs/R/path_geodesic_utils.R | 76 ++- dgraphs-0.2.0/dgraphs/R/path_graphs.R | 21 dgraphs-0.2.0/dgraphs/R/radius_graphs.R | 167 ------- dgraphs-0.2.0/dgraphs/R/threshold_distance_graph.R | 5 dgraphs-0.2.0/dgraphs/README.md | 11 dgraphs-0.2.0/dgraphs/build |only dgraphs-0.2.0/dgraphs/inst/doc |only dgraphs-0.2.0/dgraphs/man/as_igraph.Rd | 42 + dgraphs-0.2.0/dgraphs/man/build.iknn.graphs.and.selectk.Rd | 9 dgraphs-0.2.0/dgraphs/man/compare.adj.lists.Rd | 5 dgraphs-0.2.0/dgraphs/man/compare.paths.Rd | 7 dgraphs-0.2.0/dgraphs/man/compute.geodesic.stats.Rd | 13 dgraphs-0.2.0/dgraphs/man/compute.graph.diameter.Rd | 6 dgraphs-0.2.0/dgraphs/man/compute.graph.distance.Rd | 11 dgraphs-0.2.0/dgraphs/man/compute.graph.endpoint.scores.Rd | 13 dgraphs-0.2.0/dgraphs/man/compute.graph.summary.pmf.Rd | 5 dgraphs-0.2.0/dgraphs/man/compute.graph.summary.stability.Rd | 12 dgraphs-0.2.0/dgraphs/man/compute.stability.metrics.Rd | 10 dgraphs-0.2.0/dgraphs/man/compute.vertex.geodesic.stats.Rd | 12 dgraphs-0.2.0/dgraphs/man/convert.adjacency.list.to.adjacency.matrix.Rd | 6 dgraphs-0.2.0/dgraphs/man/convert.adjacency.to.edge.matrix.Rd | 5 dgraphs-0.2.0/dgraphs/man/convert.to.undirected.Rd | 5 dgraphs-0.2.0/dgraphs/man/convert.weighted.adjacency.matrix.to.adjacency.list.Rd | 5 dgraphs-0.2.0/dgraphs/man/count.edges.Rd | 4 dgraphs-0.2.0/dgraphs/man/create.bi.kNN.chain.graph.Rd | 6 dgraphs-0.2.0/dgraphs/man/create.bipartite.graph.Rd | 5 dgraphs-0.2.0/dgraphs/man/create.chain.graph.Rd | 6 dgraphs-0.2.0/dgraphs/man/create.chain.graph.with.offset.Rd | 4 dgraphs-0.2.0/dgraphs/man/create.circular.graph.Rd | 4 dgraphs-0.2.0/dgraphs/man/create.complete.graph.Rd | 5 dgraphs-0.2.0/dgraphs/man/create.empty.graph.Rd | 4 dgraphs-0.2.0/dgraphs/man/create.grid.graph.Rd | 10 dgraphs-0.2.0/dgraphs/man/create.path.graph.Rd | 6 dgraphs-0.2.0/dgraphs/man/create.path.graph.series.Rd | 6 dgraphs-0.2.0/dgraphs/man/create.plm.graph.Rd | 6 dgraphs-0.2.0/dgraphs/man/create.random.graph.Rd | 6 dgraphs-0.2.0/dgraphs/man/create.star.graph.Rd | 5 dgraphs-0.2.0/dgraphs/man/create.subgraph.Rd | 9 dgraphs-0.2.0/dgraphs/man/create.threshold.distance.graph.Rd | 5 dgraphs-0.2.0/dgraphs/man/detect.graph.endpoints.Rd | 16 dgraphs-0.2.0/dgraphs/man/detect.local.extrema.Rd | 12 dgraphs-0.2.0/dgraphs/man/dgraphs-package.Rd | 4 dgraphs-0.2.0/dgraphs/man/edge.diff.Rd | 6 dgraphs-0.2.0/dgraphs/man/estimate.geodesic.distances.Rd | 5 dgraphs-0.2.0/dgraphs/man/extract.edge.lengths.Rd | 6 dgraphs-0.2.0/dgraphs/man/extract.trajectory.edge.lengths.Rd | 6 dgraphs-0.2.0/dgraphs/man/generate.circle.graph.Rd | 6 dgraphs-0.2.0/dgraphs/man/geodesic.core.endpoints.Rd | 10 dgraphs-0.2.0/dgraphs/man/geodesic.disk.Rd | 6 dgraphs-0.2.0/dgraphs/man/geodesic.knn.Rd | 5 dgraphs-0.2.0/dgraphs/man/geodesic.knnx.Rd | 6 dgraphs-0.2.0/dgraphs/man/get.edge.weights.Rd | 6 dgraphs-0.2.0/dgraphs/man/get.shortest.path.Rd | 7 dgraphs-0.2.0/dgraphs/man/graph.connected.components.Rd | 5 dgraphs-0.2.0/dgraphs/man/graph.embedding.Rd | 6 dgraphs-0.2.0/dgraphs/man/graph.geodesic.distances.Rd | 6 dgraphs-0.2.0/dgraphs/man/graph.spectral.embedding.Rd | 6 dgraphs-0.2.0/dgraphs/man/graph.spectrum.Rd | 6 dgraphs-0.2.0/dgraphs/man/graph.summary.divergence.Rd | 10 dgraphs-0.2.0/dgraphs/man/identical.vertex.set.weighted.graph.similarity.Rd | 9 dgraphs-0.2.0/dgraphs/man/isometry.geodesic.diagnostics.Rd | 9 dgraphs-0.2.0/dgraphs/man/jensen.shannon.divergence.Rd | 4 dgraphs-0.2.0/dgraphs/man/join.graphs.Rd | 6 dgraphs-0.2.0/dgraphs/man/minh.limit.Rd | 7 dgraphs-0.2.0/dgraphs/man/nerve.graph.Rd | 5 dgraphs-0.2.0/dgraphs/man/path.dist.Rd | 5 dgraphs-0.2.0/dgraphs/man/path.length.Rd | 4 dgraphs-0.2.0/dgraphs/man/plot2D.colored.graph.Rd | 11 dgraphs-0.2.0/dgraphs/man/rm.self.loops.Rd | 4 dgraphs-0.2.0/dgraphs/man/shortest.path.Rd | 6 dgraphs-0.2.0/dgraphs/man/subdivide.path.Rd | 5 dgraphs-0.2.0/dgraphs/man/summary.rknn_graphs.Rd | 6 dgraphs-0.2.0/dgraphs/man/vertices.Rd | 12 dgraphs-0.2.0/dgraphs/man/wgraph.prune.long.edges.Rd | 10 dgraphs-0.2.0/dgraphs/src/Makevars | 4 dgraphs-0.2.0/dgraphs/src/Makevars.win | 4 dgraphs-0.2.0/dgraphs/src/adaptive_radius_graph_ann.cpp | 12 dgraphs-0.2.0/dgraphs/src/cpp_mstrees.cpp | 30 - dgraphs-0.2.0/dgraphs/src/iknn_graphs.cpp | 59 -- dgraphs-0.2.0/dgraphs/tests/dg7d-installed-self-containment.R | 9 dgraphs-0.2.0/dgraphs/tests/testthat/test-api-0.2.R |only dgraphs-0.2.0/dgraphs/tests/testthat/test-dg6c-path-geodesic-self-hosted.R | 20 dgraphs-0.2.0/dgraphs/tests/testthat/test-exported-examples.R |only dgraphs-0.2.0/dgraphs/tests/testthat/test-rknn-graphs.R | 90 +++- dgraphs-0.2.0/dgraphs/tests/testthat/test-self-hosted-graph-constructors.R | 42 + dgraphs-0.2.0/dgraphs/vignettes |only 118 files changed, 1390 insertions(+), 546 deletions(-)
Title: Model Diagnostics for Accelerated Failure Time Models
Description: A collection of model checking methods for semiparametric
accelerated failure time (AFT) models under the rank-based approach. For the
(computational) efficiency, Gehan's weight is used. It provides functions to
verify whether the observed data fit the specific model assumptions such as
a functional form of each covariate, a link function, and an omnibus test.
The p-value offered in this package is based on the Kolmogorov-type supremum
test and the variance of the proposed test statistics is estimated through
the re-sampling method. Furthermore, a graphical technique to compare the
shape of the observed residual to a number of the approximated realizations
is provided. See the following references; A general model-checking
procedure for semiparametric accelerated failure time models, Statistics and
Computing, 34 (3), 117 <doi:10.1007/s11222-024-10431-7>; Diagnostics for
semiparametric accelerated failure time models with R package 'afttest',
Journal of Statistical Software, to ap [...truncated...]
Author: Woojung Bae [aut, cre] ,
Dongrak Choi [aut] ,
Jun Yan [aut] ,
Sangwook Kang [aut]
Maintainer: Woojung Bae <matt.woojung@gmail.com>
Diff between afttest versions 4.5.3 dated 2026-03-22 and 4.6.1 dated 2026-08-31
DESCRIPTION | 12 +-- MD5 | 20 +++--- NAMESPACE | 54 +++++++++------- R/afttest.R | 156 ++++++++++++++++++++++++++++--------------------- README.md | 114 ++++++++++++++++++++++++++++++++--- inst/CITATION | 6 - inst/bib/afttest.bib | 6 - man/afttest-package.Rd | 1 man/afttest.Rd | 6 + man/afttest.aftgee.Rd | 13 ---- man/afttest.aftsrr.Rd | 18 ++--- 11 files changed, 261 insertions(+), 145 deletions(-)
Title: Weighted Dependence Measures
Description: Provides efficient implementations of weighted dependence measures
and related asymptotic tests for independence. Implemented measures are
the Pearson correlation, Spearman's rho, Kendall's tau, Blomqvist's beta,
Hoeffding's D, and Chatterjee's xi; see, e.g., Nelsen (2006)
<doi:10.1007/0-387-28678-0>, Hollander et al. (2015,
ISBN:9780470387375), and Chatterjee (2021)
<doi:10.1080/01621459.2020.1758115>.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between wdm versions 0.2.6 dated 2025-01-07 and 0.3.0 dated 2026-08-31
wdm-0.2.6/wdm/inst/test/test.cpp |only wdm-0.3.0/wdm/DESCRIPTION | 21 wdm-0.3.0/wdm/MD5 | 94 - wdm-0.3.0/wdm/NEWS.md | 8 wdm-0.3.0/wdm/R/RcppExports.R | 12 wdm-0.3.0/wdm/R/indep_test.R | 55 wdm-0.3.0/wdm/R/methods.R |only wdm-0.3.0/wdm/R/rank_wtd.R | 30 wdm-0.3.0/wdm/R/wdm-package.R | 5 wdm-0.3.0/wdm/R/wdm.R | 79 - wdm-0.3.0/wdm/README.md | 98 - wdm-0.3.0/wdm/build/partial.rdb |binary wdm-0.3.0/wdm/inst/CMakeLists.txt | 2 wdm-0.3.0/wdm/inst/cmake/buildTargets.cmake | 4 wdm-0.3.0/wdm/inst/cmake/compilerDefOpt.cmake | 4 wdm-0.3.0/wdm/inst/cmake/options.cmake | 4 wdm-0.3.0/wdm/inst/cmake/printInfo.cmake | 3 wdm-0.3.0/wdm/inst/include/mainpage.h | 67 - wdm-0.3.0/wdm/inst/include/wdm.hpp | 333 +++-- wdm-0.3.0/wdm/inst/include/wdm/bbeta.hpp | 46 wdm-0.3.0/wdm/inst/include/wdm/cxi.hpp |only wdm-0.3.0/wdm/inst/include/wdm/eigen.hpp | 146 +- wdm-0.3.0/wdm/inst/include/wdm/hoeffd.hpp | 175 +- wdm-0.3.0/wdm/inst/include/wdm/ktau.hpp | 136 +- wdm-0.3.0/wdm/inst/include/wdm/methods.hpp | 53 wdm-0.3.0/wdm/inst/include/wdm/nan_handling.hpp | 119 + wdm-0.3.0/wdm/inst/include/wdm/prho.hpp | 70 - wdm-0.3.0/wdm/inst/include/wdm/random.hpp | 145 +- wdm-0.3.0/wdm/inst/include/wdm/ranks.hpp | 369 ++--- wdm-0.3.0/wdm/inst/include/wdm/srho.hpp | 21 wdm-0.3.0/wdm/inst/include/wdm/utils.hpp | 769 ++++++------ wdm-0.3.0/wdm/inst/test/CMakeLists.txt | 73 + wdm-0.3.0/wdm/inst/test/install |only wdm-0.3.0/wdm/inst/test/test_cxi.cpp |only wdm-0.3.0/wdm/inst/test/test_eigen.cpp |only wdm-0.3.0/wdm/inst/test/test_estimators.cpp |only wdm-0.3.0/wdm/inst/test/test_headers.cpp |only wdm-0.3.0/wdm/inst/test/test_helpers.hpp |only wdm-0.3.0/wdm/inst/test/test_inference.cpp |only wdm-0.3.0/wdm/inst/test/test_input.cpp |only wdm-0.3.0/wdm/inst/test/test_ranks.cpp |only wdm-0.3.0/wdm/man/indep_test.Rd | 35 wdm-0.3.0/wdm/man/rank_wtd.Rd | 17 wdm-0.3.0/wdm/man/wdm-package.Rd | 10 wdm-0.3.0/wdm/man/wdm.Rd | 33 wdm-0.3.0/wdm/src/RcppExports.cpp | 28 wdm-0.3.0/wdm/src/wrappers.cpp | 50 wdm-0.3.0/wdm/tests/testthat/test_chatterjee.R |only wdm-0.3.0/wdm/tests/testthat/test_computations_unweighted.R | 37 wdm-0.3.0/wdm/tests/testthat/test_computations_weighted.R | 4 wdm-0.3.0/wdm/tests/testthat/test_indep_test.R | 2 wdm-0.3.0/wdm/tests/testthat/test_input_validation.R |only wdm-0.3.0/wdm/tests/testthat/test_matrix_interface.R |only wdm-0.3.0/wdm/tests/testthat/test_rank_wtd.R | 6 wdm-0.3.0/wdm/tests/testthat/test_wdm_interface.R | 2 55 files changed, 1776 insertions(+), 1389 deletions(-)
Title: Unsupervised Clustering of Individualized Survival Curves
Description: Tools for clustering individualized survival curves using the
Partitioning Around Medoids (PAM) algorithm, with monotonic enforcement,
optional smoothing, weighted distances (L1/L2), automatic K selection via
silhouette width, prediction for new curves, basic stability checks, and
plotting helpers. The method is described in El Badisy (2026)
<doi:10.1093/bioadv/vbag218>.
Author: Imad El Badisy [aut, cre]
Maintainer: Imad El Badisy <elbadisyimad@gmail.com>
Diff between unsurv versions 0.5.0 dated 2026-03-17 and 0.7.0 dated 2026-08-31
DESCRIPTION | 23 +-- MD5 | 29 ++-- NAMESPACE | 4 NEWS.md | 23 +++ R/compare.R |only R/zzz.R | 5 README.md | 57 +++---- inst/CITATION | 16 +- inst/doc/unsurv-intro.R | 109 ++++++++++++--- inst/doc/unsurv-intro.Rmd | 225 ++++++++++++++++++++++++------- inst/doc/unsurv-intro.html | 293 ++++++++++++++++++++++++++++++----------- inst/extdata |only man/autoplot.unsurv_compare.Rd |only man/dot-km_cluster_medians.Rd |only man/print.unsurv_compare.Rd |only man/unsurv-package.Rd | 2 man/unsurv_compare.Rd |only tests/testthat/test-compare.R |only vignettes/unsurv-intro.Rmd | 225 ++++++++++++++++++++++++------- 19 files changed, 760 insertions(+), 251 deletions(-)
Title: Authentication Helpers for 'Snowflake'
Description: Authentication helpers for 'Snowflake'.
It provides compatibility with authentication approaches supported
by the 'Snowflake Connector for Python' <https://pypi.org/project/snowflake-connector-python>
and the 'Snowflake CLI' <https://pypi.org/project/snowflake-cli>.
Author: Aaron Jacobs [aut],
E. David Aja [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: E. David Aja <david@posit.co>
Diff between snowflakeauth versions 0.2.2 dated 2026-02-25 and 0.3.0 dated 2026-08-31
DESCRIPTION | 6 +-- MD5 | 33 +++++++++++--------- NEWS.md | 13 ++++++++ R/config.R | 7 ++++ R/credentials.R | 40 ++++++++++++++++--------- R/externalbrowser.R | 20 +++++++----- R/keypair.R | 18 +++++++++-- R/oauth.R | 5 +-- R/oauth_authorization_code.R |only R/workload_identity.R | 5 +-- README.md | 3 + man/snowflake_connection.Rd | 3 + tests/testthat/connections.toml | 20 ++++++++++++ tests/testthat/test-config.R | 36 ++++++++++++++++++++++ tests/testthat/test-credentials.R |only tests/testthat/test-keypair.R | 39 ++++++++++++++++++++++++ tests/testthat/test-oauth-authorization-code.R |only tests/testthat/test-oauth.R | 35 +++++++++++++++++++++ tests/testthat/test-workload-identity.R | 18 ++++++----- 19 files changed, 246 insertions(+), 55 deletions(-)
Title: Detect and Remove Unwanted Variation using Negative Controls
Description: Implements the 'RUV' (Remove Unwanted Variation) algorithms. These algorithms attempt to adjust for systematic errors of unknown origin in high-dimensional data. The algorithms were originally developed for use with genomic data, especially microarray data, but may be useful with other types of high-dimensional data as well. These algorithms were proposed in Gagnon-Bartsch and Speed (2012) <doi:10.1093/nar/gkz433>, Gagnon-Bartsch, Jacob and Speed (2013), and Molania, et. al. (2019) <doi:10.1093/nar/gkz433>. The algorithms require the user to specify a set of negative control variables, as described in the references. The algorithms included in this package are 'RUV-2', 'RUV-4', 'RUV-inv', 'RUV-rinv', 'RUV-I', and RUV-III', along with various supporting algorithms.
Author: Johann Gagnon-Bartsch [aut, cre]
Maintainer: Johann Gagnon-Bartsch <johanngb@umich.edu>
Diff between ruv versions 0.9.7.1 dated 2019-08-30 and 0.9.7.2 dated 2026-08-31
DESCRIPTION | 16 ++++++++++------ MD5 | 30 +++++++++++++++--------------- R/ruv_shiny.R | 6 +++--- man/RUV2.Rd | 6 +++--- man/RUV4.Rd | 6 +++--- man/RUVI.Rd | 4 ++-- man/RUVIII.Rd | 4 ++-- man/RUVinv.Rd | 6 +++--- man/RUVrinv.Rd | 6 +++--- man/getK.Rd | 4 ++-- man/get_empirical_variances.Rd | 2 +- man/invvar.Rd | 2 +- man/randinvvar.Rd | 2 +- man/ruv-package.Rd | 6 +++--- man/sigmashrink.Rd | 4 ++-- man/variance_adjust.Rd | 4 ++-- 16 files changed, 56 insertions(+), 52 deletions(-)
Title: Road Network Projection
Description: Iterative least cost path and minimum spanning tree methods for projecting
forest road networks. The methods connect a set of target points to an existing
road network using 'igraph' <https://igraph.org> to identify least cost routes.
The cost of constructing a road segment between adjacent pixels is determined
by a user supplied weight raster and a weight function; options include the
average of adjacent weight raster values, and a function of the elevation
differences between adjacent cells that penalizes steep grades. These road
network projection methods are intended for integration into R workflows and
modelling frameworks used for forecasting forest change, and can be applied
over multiple time-steps without rebuilding a graph at each time-step.
Author: Sarah Endicott [aut, cre] ,
Kyle Lochhead [aut],
Josie Hughes [aut],
Patrick Kirby [aut],
Her Majesty the Queen in Right of Canada as represented by the Minister
of the Environment [cph] ,
Province of British Columbia [cph]
Maintainer: Sarah Endicott <sarah.endicott@ec.gc.ca>
This is a re-admission after prior archival of version 1.2.1 dated 2026-01-16
Diff between roads versions 1.2.1 dated 2026-01-16 and 1.2.2 dated 2026-08-31
DESCRIPTION | 22 + MD5 | 27 +- NEWS.md | 2 R/getDistFromSource.R | 403 +++++++++++++++++------------------ R/projectRoads.R | 7 README.md | 190 ++++++++-------- inst/WORDLIST |only inst/doc/ReconstructRoadHistory.html | 49 ++-- inst/doc/grade-penalty.html | 28 +- inst/doc/roads-vignette.html | 4 man/getDistFromSource.Rd | 17 - man/getLandingsFromTarget.Rd | 2 man/prepExData.Rd | 2 man/projectRoads.Rd | 7 man/roads-package.Rd | 3 15 files changed, 396 insertions(+), 367 deletions(-)
Title: 'KorAP' Web Service Client Package
Description: A client package that makes the 'KorAP' web service API accessible from R. The corpus analysis platform 'KorAP' has been developed as a scientific tool to make potentially large, stratified and multiply annotated corpora, such as the 'German Reference Corpus DeReKo' or the 'Corpus of the Contemporary Romanian Language CoRoLa', accessible for linguists to let them verify hypotheses and to find interesting patterns in real language use. The 'RKorAPClient' package provides access to 'KorAP' and the corpora behind it for user-created R code, as a programmatic alternative to the 'KorAP' web user-interface. You can learn more about 'KorAP' and use it directly on 'DeReKo' at <https://korap.ids-mannheim.de/>.
Author: Marc Kupietz [aut, cre],
Nils Diewald [ctb],
Leibniz Institute for the German Language [cph, fnd]
Maintainer: Marc Kupietz <kupietz@ids-mannheim.de>
Diff between RKorAPClient versions 1.2.1 dated 2025-10-09 and 1.3.0 dated 2026-08-31
RKorAPClient-1.2.1/RKorAPClient/man/KorAPConnection-class.Rd |only RKorAPClient-1.3.0/RKorAPClient/DESCRIPTION | 10 RKorAPClient-1.3.0/RKorAPClient/MD5 | 52 RKorAPClient-1.3.0/RKorAPClient/NAMESPACE | 167 - RKorAPClient-1.3.0/RKorAPClient/NEWS.md | 12 RKorAPClient-1.3.0/RKorAPClient/R/KorAPConnection.R | 55 RKorAPClient-1.3.0/RKorAPClient/R/collocationAnalysis.R | 1228 +++++++++- RKorAPClient-1.3.0/RKorAPClient/R/collocationScoreQuery.R | 66 RKorAPClient-1.3.0/RKorAPClient/man/KorAPConnection.Rd |only RKorAPClient-1.3.0/RKorAPClient/man/RKorAPClient-package.Rd | 5 RKorAPClient-1.3.0/RKorAPClient/man/association-score-functions.Rd | 4 RKorAPClient-1.3.0/RKorAPClient/man/auth-KorAPConnection-method.Rd | 2 RKorAPClient-1.3.0/RKorAPClient/man/clearAccessToken-KorAPConnection-method.Rd | 2 RKorAPClient-1.3.0/RKorAPClient/man/collocationAnalysis-KorAPConnection-method.Rd | 84 RKorAPClient-1.3.0/RKorAPClient/man/collocationScoreQuery-KorAPConnection-method.Rd | 10 RKorAPClient-1.3.0/RKorAPClient/man/corpusQuery-KorAPConnection-method.Rd | 2 RKorAPClient-1.3.0/RKorAPClient/man/defaultKorAPUrl.Rd |only RKorAPClient-1.3.0/RKorAPClient/man/fetchAll-KorAPQuery-method.Rd | 2 RKorAPClient-1.3.0/RKorAPClient/man/fetchAnnotations-KorAPQuery-method.Rd | 2 RKorAPClient-1.3.0/RKorAPClient/man/fetchNext-KorAPQuery-method.Rd | 2 RKorAPClient-1.3.0/RKorAPClient/man/hc_add_onclick_korap_search.Rd | 4 RKorAPClient-1.3.0/RKorAPClient/man/hc_freq_by_year_ci.Rd | 4 RKorAPClient-1.3.0/RKorAPClient/man/initialize-KorAPConnection-method.Rd | 7 RKorAPClient-1.3.0/RKorAPClient/man/persistAccessToken-KorAPConnection-method.Rd | 2 RKorAPClient-1.3.0/RKorAPClient/man/reexports.Rd | 12 RKorAPClient-1.3.0/RKorAPClient/man/synsemanticStopwords.Rd | 2 RKorAPClient-1.3.0/RKorAPClient/tests/testthat/test-collocations.R | 680 +++++ RKorAPClient-1.3.0/RKorAPClient/tests/testthat/test-fetchAnnotations.R | 9 RKorAPClient-1.3.0/RKorAPClient/tests/testthat/test-korapconnection-signature.R |only 29 files changed, 2208 insertions(+), 217 deletions(-)
Title: Density-Free RIF Decompositions for Unconditional Expectiles
Description: Implements a density-free recentered influence function (RIF)
regression framework for unconditional expectiles, and embeds it in a
two-sample Oaxaca-Blinder decomposition indexed continuously by the
expectile level. Unlike quantile-based RIF decompositions, which require
estimating an inverse density term at each quantile, the expectile RIF
depends only on primitive moments of the outcome distribution and
requires no density estimation, no bandwidth selection, and no kernel
smoothing. The package provides expectile estimation by iteratively
reweighted least squares, closed-form RIF construction, two-sample
composition/structure decomposition across a grid of expectile levels,
bootstrap-based inference, and plotting methods. The underlying
methodology is described in Ndoye (2025), "Semi-Nonparametric
Expectile RIF Regression for Distributional Decomposition," presented at
the 2025 World Congress of the Econometric Society, Seoul, Korea,
<https://www.econometricsociety.org/regional-a [...truncated...]
Author: Abdoul Aziz Ndoye [aut, cre]
Maintainer: Abdoul Aziz Ndoye <abdoulaziz1.ndoye@gmail.com>
Diff between rifexpectile versions 0.1.0 dated 2026-08-30 and 0.1.1 dated 2026-08-31
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/decompose.R | 2 ++ README.md | 7 ++++++- inst/doc/rifexpectile-intro.html | 6 +++--- 5 files changed, 18 insertions(+), 11 deletions(-)
Title: String Similarity Computation Using 'RapidFuzz'
Description: Provides a high-performance interface for calculating string similarities and distances, leveraging the efficient library 'RapidFuzz' <https://github.com/rapidfuzz/rapidfuzz-cpp>. This package integrates the 'C++' implementation, allowing 'R' users to access cutting-edge algorithms for fuzzy matching and text analysis. Supported metrics include Levenshtein, Damerau-Levenshtein, Hamming, Jaro, Jaro-Winkler, Longest Common Subsequence (LCS), Optimal String Alignment (OSA), Indel, Prefix, and Postfix distances and similarities, as well as multiple fuzzy matching ratios.
Author: Andre Leite [aut, cre],
Hugo Vaconcelos [aut],
Marcos Wasilew [aut],
Carlos Amorim [aut],
Diogo Bezerra [aut],
Max Bachmann [ctb],
Adam Cohen [ctb]
Maintainer: Andre Leite <leite@castlab.org>
Diff between RapidFuzz versions 1.1.0 dated 2026-04-07 and 1.1.1 dated 2026-08-31
DESCRIPTION | 14 +++++++------- MD5 | 20 +++++++++++--------- NEWS.md | 10 +++++++++- R/zzz.R | 2 +- README.md | 7 ++++--- build/vignette.rds |binary inst/doc/introduction.html | 6 +++--- man/figures |only src/rapidfuzz/details/GrowingHashmap.hpp | 2 ++ src/rapidfuzz/details/Range.hpp | 2 ++ src/rapidfuzz/details/types.hpp | 2 ++ 11 files changed, 41 insertions(+), 24 deletions(-)
Title: Prediction Rule Ensembles
Description: Fits prediction rule ensembles (PREs). Largely follows the
procedure for deriving PREs as described in Friedman & Popescu (2008;
<DOI:10.1214/07-AOAS148>), with adjustments and improvements described in
Fokkema (2020; <DOI:10.18637/jss.v092.i12>) and Fokkema & Strobl
(2020; <DOI:10.1037/met0000256>). The main function pre() derives
prediction rule ensembles consisting of rules and/or linear terms for
continuous, binary, count, multinomial, survival and multivariate
continuous responses. Function gpe() derives generalized prediction
ensembles, consisting of rules, hinge and linear functions of the
predictor variables.
Author: Marjolein Fokkema [aut, cre],
Benjamin Christoffersen [aut],
Giorgio Spadaccini [ctb]
Maintainer: Marjolein Fokkema <m.fokkema@fsw.leidenuniv.nl>
Diff between pre versions 1.0.9 dated 2026-06-09 and 1.1.0 dated 2026-08-31
DESCRIPTION | 22 MD5 | 128 NAMESPACE | 1 NEWS.md | 17 R/corplot.R |only R/cvpre.R |only R/explain.R |only R/get_modmat.R |only R/gpe.R | 3 R/interaction_H_statistics.R |only R/partial_dependence_plots.R |only R/pre.R | 4009 ---------- R/pre_S3_methods.R |only R/prune_pre.R |only R/rule_learners.R |only R/shap.R |only R/utils.R | 221 README.md | 188 build/vignette.rds |binary inst/README-figures/README-pairplot-1.png |binary inst/README-figures/README-singleplot-1.png |binary inst/README-figures/README-unnamed-chunk-9-1.png |only inst/doc/Missingness.Rmd | 9 inst/doc/Missingness.html | 42 inst/doc/Tuning.html | 12 inst/doc/relaxed.Rmd | 4 inst/doc/relaxed.html | 26 inst/doc/shap.R |only inst/doc/shap.Rmd |only inst/doc/shap.html |only inst/doc/speed.html | 22 man/RuleMats.Rd |only man/ShapleyMats.Rd |only man/bsnullinteract.Rd | 4 man/coef.gpe.Rd | 2 man/coef.pre.Rd | 4 man/corplot.Rd | 4 man/cvpre.Rd | 4 man/explain.Rd | 9 man/gpe_rules_pre.Rd | 2 man/importance.pre.Rd | 4 man/interact.Rd | 4 man/maxdepth_sampler.Rd | 2 man/pairplot.Rd | 4 man/plot.pre.Rd | 4 man/pre.Rd | 4 man/predict.pre.Rd | 4 man/print.gpe.Rd | 2 man/print.pre.Rd | 4 man/prune_pre.Rd | 2 man/rare_level_sampler.Rd | 2 man/shap.Rd |only man/singleplot.Rd | 4 man/summary.gpe.Rd | 2 man/summary.pre.Rd | 4 tests/testthat.R | 2 tests/testthat/helper.R | 13 tests/testthat/previous_results/PimaIndiansDiabetes_w_pre_LR.RDS |binary tests/testthat/previous_results/PimaIndiansDiabetes_w_pre_no_LR.RDS |binary tests/testthat/previous_results/SHAP.RDS |only tests/testthat/previous_results/SHAP_interact.RDS |only tests/testthat/previous_results/SHAP_marginal.RDS |only tests/testthat/previous_results/gpe_earth_binary.RDS |binary tests/testthat/previous_results/gpe_earth_binary_no_learn.RDS |binary tests/testthat/previous_results/gpe_fit1_binary.RDS |binary tests/testthat/previous_results/gpe_predict_binary_response.RDS |binary tests/testthat/previous_results/gpe_tree_binary_1.RDS |binary tests/testthat/previous_results/gpe_tree_binary_1_w_glm.RDS |binary tests/testthat/previous_results/gpe_tree_binary_2.RDS |binary tests/testthat/test_explain_and_shap.R |only tests/testthat/test_gpe.R | 18 tests/testthat/test_pre_misc.R | 9 vignettes/Missingness.Rmd | 9 vignettes/bib.bib | 63 vignettes/relaxed.Rmd | 4 vignettes/shap.Rmd |only 76 files changed, 616 insertions(+), 4281 deletions(-)
Title: Download and Manage Optional Package Data
Description: Manage optional data for your package. The data can be hosted anywhere, and you have to give a Uniform Resource Locator (URL) for each file. File integrity checks are supported. This is useful for package authors who need to ship more than the 5 Megabyte of data currently allowed by the the Comprehensive R Archive Network (CRAN). Download functions are supposed to be called by users in interactive sessions only.
Author: Tim Schaefer [aut, cre]
Maintainer: Tim Schaefer <ts+code@rcmd.org>
Diff between pkgfilecache versions 0.2.0 dated 2026-08-21 and 0.4.1 dated 2026-08-31
DESCRIPTION | 6 MD5 | 34 +++- NAMESPACE | 5 R/cli.R |only R/filecache.R | 216 ++++++++++++++++++++++++--- R/manifest.R |only exec |only inst/doc/pkgfilecache.R | 44 +++++ inst/doc/pkgfilecache.Rmd | 72 +++++++++ inst/doc/pkgfilecache.html | 220 +++++++++++++++++++--------- man/add_file_download_to_curl_pool.Rd |only man/derive_manifest_urls.Rd |only man/download_files_with_md5_mismatch.Rd | 8 - man/ensure_files_available.Rd | 14 + man/ensure_files_available_from_manifest.Rd |only man/manifest_cli.Rd |only man/manifest_cli_usage.Rd |only man/manifest_script.Rd |only man/read_manifest.Rd |only man/validate_manifest.Rd |only man/write_manifest_from_dir.Rd |only tests/testthat/test-filecache.R | 131 ++++++++++++++++ tests/testthat/test-manifest-cli.R |only tests/testthat/test-manifest.R |only vignettes/pkgfilecache.Rmd | 72 +++++++++ 25 files changed, 712 insertions(+), 110 deletions(-)
Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning.
The core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems, including
nominal, ordinal, numeric, censored as well as multivariate response
variables and arbitrary measurement scales of the covariates.
Based on conditional inference trees, cforest() provides an
implementation of Breiman's random forests. The function mob()
implements an algorithm for recursive partitioning based on
parametric models (e.g. linear models, GLMs or survival
regression) employing parameter instability tests for split
selection. Extensible functionality for visualizing tree-structured
regression models is available. The methods are described in
Hothorn et al. (2006) <doi:10.1198/106186006X133933>,
Zeileis et al. (2008) <d [...truncated...]
Author: Torsten Hothorn [aut, cre] ,
Kurt Hornik [aut] ,
Carolin Strobl [aut] ,
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between party versions 1.3-22 dated 2026-08-21 and 1.3-23 dated 2026-08-31
DESCRIPTION | 6 ++--- MD5 | 34 ++++++++++++++++---------------- build/partial.rdb |binary cleanup | 8 +++++++ inst/NEWS.Rd | 13 ++++++++++-- inst/doc/MOB.pdf |binary inst/doc/party.pdf |binary tests/Distributions.Rout.save | 4 +-- tests/LinearStatistic-regtest.Rout.save | 4 +-- tests/Predict-regtest.Rout.save | 4 +-- tests/RandomForest-regtest.R | 2 + tests/RandomForest-regtest.Rout.save | 11 +++------- tests/TestStatistic-regtest.Rout.save | 4 +-- tests/TreeGrow-regtest.Rout.save | 4 +-- tests/Utils-regtest.Rout.save | 4 +-- tests/bugfixes.R | 2 + tests/bugfixes.Rout.save | 11 +++------- tests/mob.Rout.save | 4 +-- 18 files changed, 65 insertions(+), 50 deletions(-)
Title: Optimal Binning and Weight of Evidence Framework for Modeling
Description: High-performance implementation of 37 optimal binning algorithms
(16 categorical, 21 numerical) for Weight of Evidence ('WoE') transformation,
credit scoring, and risk modeling. Includes advanced methods such as Mixed
Integer Linear Programming ('MILP'), Genetic Algorithms, Simulated Annealing,
and Monotonic Regression. Features automatic method selection based on
Information Value ('IV') maximization, strict monotonicity enforcement, and
efficient handling of large datasets via 'Rcpp'. Provides automated variable
screening by Information Value strength and bin ordering, and generation of
the equivalent 'SQL' 'CASE' expressions for in-database scoring. Fully
integrated with the 'tidymodels' ecosystem for building robust machine
learning pipelines.
Based on methods described in Siddiqi (2006) <doi:10.1002/9781119201731>
and Navas-Palencia (2020) <doi:10.48550/arXiv.2001.08025>.
Author: Jose Evandeilton Lopes [aut, cre, cph]
Maintainer: Jose Evandeilton Lopes <evandeilton@gmail.com>
Diff between OptimalBinningWoE versions 1.13.4 dated 2026-08-26 and 1.13.5 dated 2026-08-31
DESCRIPTION | 8 - MD5 | 14 +-- NEWS.md | 53 ++++++++++++ inst/doc/algorithms.html | 30 +++---- inst/doc/industrial-pipeline.html | 8 - inst/doc/introduction.html | 8 - tests/testthat/helper-germancredit.R | 149 ++++++++++++++++++++++++++++++++++- tests/testthat/test-obwoe-sql.R | 28 ++++++ 8 files changed, 262 insertions(+), 36 deletions(-)
More information about OptimalBinningWoE at CRAN
Permanent link
Title: The Nonparametric Classification Methods for Cognitive Diagnosis
Description: Statistical tools for analyzing cognitive diagnosis (CD) data collected from small settings using the nonparametric classification (NPCD) framework. The core methods of the NPCD framework includes the nonparametric classification (NPC) method developed by Chiu and Douglas (2013) <DOI:10.1007/s00357-013-9132-9> and the general NPC (GNPC) method developed by Chiu, Sun, and Bian (2018) <DOI:10.1007/s11336-017-9595-4> and Chiu and Köhn (2019) <DOI:10.1007/s11336-019-09660-x>. An extension of the NPCD framework included in the package is the nonparametric method for multiple-choice items (MC-NPC) developed by Wang, Chiu, and Koehn (2023) <DOI:10.3102/10769986221133088>. Functions associated with various extensions concerning the evaluation, validation, and feasibility of the CD analysis are also provided. These topics include the completeness of Q-matrix, Q-matrix refinement method, as well as Q-matrix estimation.
Author: Chia-Yi Chiu [aut, cph],
Weixuan Xiao [aut, cre],
Hans Friedrich Koehn [aut],
Yu Wang [aut],
Xiran Wen [aut]
Maintainer: Weixuan Xiao <wx2299@tc.columbia.edu>
Diff between NPCDTools versions 1.1.0 dated 2026-03-03 and 1.2.0 dated 2026-08-31
NPCDTools-1.1.0/NPCDTools/R/internal_functions.R |only NPCDTools-1.2.0/NPCDTools/DESCRIPTION | 12 NPCDTools-1.2.0/NPCDTools/MD5 | 30 NPCDTools-1.2.0/NPCDTools/NAMESPACE | 5 NPCDTools-1.2.0/NPCDTools/NEWS.md | 7 NPCDTools-1.2.0/NPCDTools/R/MCNPC.R |only NPCDTools-1.2.0/NPCDTools/R/NPC.R | 16 NPCDTools-1.2.0/NPCDTools/R/TSQE.R | 2 NPCDTools-1.2.0/NPCDTools/R/distractor.check.R | 34 NPCDTools-1.2.0/NPCDTools/R/internal.functions.R |only NPCDTools-1.2.0/NPCDTools/R/mcQ.generate.R |only NPCDTools-1.2.0/NPCDTools/R/mcdat.generate.R |only NPCDTools-1.2.0/NPCDTools/build/partial.rdb |binary NPCDTools-1.2.0/NPCDTools/inst/shiny/GNPC_app/app.R | 1973 +++++++++++--------- NPCDTools-1.2.0/NPCDTools/man/MCNPC.Rd |only NPCDTools-1.2.0/NPCDTools/man/NPC.Rd | 8 NPCDTools-1.2.0/NPCDTools/man/TSQE.Rd | 2 NPCDTools-1.2.0/NPCDTools/man/distractor.check.Rd | 6 NPCDTools-1.2.0/NPCDTools/man/mcQ.generate.Rd |only NPCDTools-1.2.0/NPCDTools/man/mcdat.generate.Rd |only 20 files changed, 1180 insertions(+), 915 deletions(-)
Title: Compute the Coefficient of Determination for Vector or Matrix
Outcomes
Description: Compute the coefficient of determination for outcomes in n-dimensions.
May be useful for multidimensional predictions (such as a multinomial model) or
calculating goodness of fit from latent variable models such as probabilistic
topic models like latent Dirichlet allocation or deterministic topic models
like latent semantic analysis. Based on Jones (2019)
<doi:10.48550/arXiv.1911.11061>.
Author: Tommy Jones [aut, cre] ,
Thomas Nagler [ctb]
Maintainer: Tommy Jones <jones.thos.w@gmail.com>
Diff between mvrsquared versions 0.1.5 dated 2023-07-14 and 0.1.6 dated 2026-08-31
mvrsquared-0.1.5/mvrsquared/man/mvrsquared.Rd |only mvrsquared-0.1.6/mvrsquared/DESCRIPTION | 15 mvrsquared-0.1.6/mvrsquared/MD5 | 28 - mvrsquared-0.1.6/mvrsquared/NEWS.md | 38 ++ mvrsquared-0.1.6/mvrsquared/R/RcppExports.R | 4 mvrsquared-0.1.6/mvrsquared/R/calc_rsquared.R | 59 ++- mvrsquared-0.1.6/mvrsquared/R/mvrsquared.R | 5 mvrsquared-0.1.6/mvrsquared/README.md | 1 mvrsquared-0.1.6/mvrsquared/build/vignette.rds |binary mvrsquared-0.1.6/mvrsquared/inst/WORDLIST | 1 mvrsquared-0.1.6/mvrsquared/inst/doc/getting_started_with_mvrsquared.R | 86 ++--- mvrsquared-0.1.6/mvrsquared/inst/doc/getting_started_with_mvrsquared.html | 31 - mvrsquared-0.1.6/mvrsquared/man/calc_rsquared.Rd | 11 mvrsquared-0.1.6/mvrsquared/man/mvrsquared-package.Rd |only mvrsquared-0.1.6/mvrsquared/src/RcppExports.cpp | 25 + mvrsquared-0.1.6/mvrsquared/src/calc_sum_squares_latent.cpp | 163 ++++++++-- 16 files changed, 324 insertions(+), 143 deletions(-)
Title: Monte Carlo Hypothesis Tests with Sequential Stopping
Description: Performs Monte Carlo hypothesis tests, allowing a couple of different sequential stopping boundaries. For example, a truncated sequential probability ratio test boundary (Fay, Kim and Hachey, 2007 <DOI:10.1198/106186007X257025>) and a boundary proposed by Besag and Clifford, 1991 <DOI:10.1093/biomet/78.2.301>. Gives valid p-values and confidence intervals on p-values.
Author: Michael P. Fay [aut, cre]
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between MChtest versions 1.0-3 dated 2019-05-16 and 1.0-4 dated 2026-08-31
ChangeLog | 8 ++++++++ DESCRIPTION | 14 +++++++++----- MD5 | 10 +++++----- inst/CITATION | 10 ++++------ man/MCbound.precalc1.Rd | 2 +- man/MCtest.Rd | 4 ++-- 6 files changed, 29 insertions(+), 19 deletions(-)
Title: L-Infinity Normalization and Dominant Community State Types
Description: Implements L-infinity normalization for compositional matrices,
assigns samples to dominant features, constructs truncated and
hierarchically refined dominant community state types, and computes
representative landmark profiles. The methods are described in the
accompanying publication <doi:10.48550/arXiv.2503.21543>. Bundled vaginal
and gut microbiome data support reproducible demonstrations of the package
interface; phenotype fields in the stratified gut subset are illustrative
and are not suitable for population-level inference.
Author: Pawel Gajer [aut, cre]
Maintainer: Pawel Gajer <pgajer@gmail.com>
Diff between linf versions 0.2.0 dated 2026-08-21 and 0.3.0 dated 2026-08-31
linf-0.2.0/linf/man/asv.to.linf.csts.Rd |only linf-0.2.0/linf/man/latex.linf.csts.Rd |only linf-0.2.0/linf/man/refine.linf.csts.iter.Rd |only linf-0.3.0/linf/DESCRIPTION | 9 linf-0.3.0/linf/MD5 | 42 linf-0.3.0/linf/NAMESPACE | 3 linf-0.3.0/linf/NEWS.md | 19 linf-0.3.0/linf/R/landmarks.R | 36 linf-0.3.0/linf/R/linf.R | 634 ++++----------- linf-0.3.0/linf/R/transfer_dcsts.R | 12 linf-0.3.0/linf/README.md | 5 linf-0.3.0/linf/data/valencia13k_dcst_depth2_merged.rda |binary linf-0.3.0/linf/data/valencia13k_dcst_depth3_merged.rda |binary linf-0.3.0/linf/inst/doc/linf-intro.html | 6 linf-0.3.0/linf/man/dcst.view.Rd | 16 linf-0.3.0/linf/man/linf.csts.Rd | 13 linf-0.3.0/linf/man/linf.landmarks.Rd | 16 linf-0.3.0/linf/man/normalize.linf.Rd | 10 linf-0.3.0/linf/man/print.linf.csts.Rd | 8 linf-0.3.0/linf/man/refine.linf.csts.Rd | 36 linf-0.3.0/linf/man/summary.linf.csts.Rd | 9 linf-0.3.0/linf/man/transfer.dcsts.Rd | 2 linf-0.3.0/linf/tests/testthat/test-api-cleanup.R |only linf-0.3.0/linf/tests/testthat/test-public-terminology.R | 3 24 files changed, 360 insertions(+), 519 deletions(-)
Title: HMM Toolkit for Inferring IBD Segments from SNP Genotypes
Description: Implements continuous-time hidden Markov models (HMMs) to
infer identity-by-descent (IBD) segments shared by two individuals
from their single-nucleotide polymorphism (SNP) genotypes. Provides
posterior probabilities at each marker (forward-backward algorithm),
prediction of IBD segments (Viterbi algorithm), and functions for
visualising results. Supports both autosomal data and X-chromosomal
data. The current model has two states, non-IBD and IBD1, and is
intended for unilineal relationships. The methodology and package are
described in Vigeland et al. (2026)
<doi:10.1016/j.fsigen.2025.103409>.
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between ibdfindr versions 0.3.1 dated 2025-08-18 and 0.4.0 dated 2026-08-31
ibdfindr-0.3.1/ibdfindr/tests/testthat/_snaps |only ibdfindr-0.4.0/ibdfindr/DESCRIPTION | 15 ibdfindr-0.4.0/ibdfindr/MD5 | 60 +- ibdfindr-0.4.0/ibdfindr/NAMESPACE | 17 ibdfindr-0.4.0/ibdfindr/NEWS.md | 13 ibdfindr-0.4.0/ibdfindr/R/computePR.R | 156 +++--- ibdfindr-0.4.0/ibdfindr/R/data.R | 4 ibdfindr-0.4.0/ibdfindr/R/findIBD.R | 21 ibdfindr-0.4.0/ibdfindr/R/findSegments.R | 29 - ibdfindr-0.4.0/ibdfindr/R/fitHMM.R | 127 +++-- ibdfindr-0.4.0/ibdfindr/R/ibdPosteriors.R | 15 ibdfindr-0.4.0/ibdfindr/R/plotIBD.R | 232 +++++----- ibdfindr-0.4.0/ibdfindr/R/prepForHMM.R | 71 ++- ibdfindr-0.4.0/ibdfindr/R/problemMarkers.R |only ibdfindr-0.4.0/ibdfindr/R/totalLoglik.R | 15 ibdfindr-0.4.0/ibdfindr/R/utils.R | 20 ibdfindr-0.4.0/ibdfindr/README.md | 41 + ibdfindr-0.4.0/ibdfindr/inst |only ibdfindr-0.4.0/ibdfindr/man/brothersX.Rd | 2 ibdfindr-0.4.0/ibdfindr/man/computePR.Rd | 74 +-- ibdfindr-0.4.0/ibdfindr/man/cousinsDemo.Rd | 2 ibdfindr-0.4.0/ibdfindr/man/figures/README-brothersX-plot-1.png |binary ibdfindr-0.4.0/ibdfindr/man/figures/README-cousinsDemo-plot-1.png |binary ibdfindr-0.4.0/ibdfindr/man/findIBD.Rd | 124 ++--- ibdfindr-0.4.0/ibdfindr/man/findSegments.Rd | 96 ++-- ibdfindr-0.4.0/ibdfindr/man/fitHMM.Rd | 161 +++--- ibdfindr-0.4.0/ibdfindr/man/ibdPosteriors.Rd | 90 +-- ibdfindr-0.4.0/ibdfindr/man/ibdfindr-package.Rd | 7 ibdfindr-0.4.0/ibdfindr/man/plotIBD.Rd | 3 ibdfindr-0.4.0/ibdfindr/man/problemMarkers.Rd |only ibdfindr-0.4.0/ibdfindr/man/totalLoglik.Rd | 64 +- ibdfindr-0.4.0/ibdfindr/tests/testthat/test-computePR.R |only ibdfindr-0.4.0/ibdfindr/tests/testthat/test-findIBD.R | 2 ibdfindr-0.4.0/ibdfindr/tests/testthat/test-hmm.R |only 34 files changed, 821 insertions(+), 640 deletions(-)
Title: Analysis of Evolutionary Diversification
Description: Methods for fitting macroevolutionary models to phylogenetic trees
Pennell (2014) <doi:10.1093/bioinformatics/btu181>.
Author: Luke Harmon [aut, cre],
Matthew Pennell [aut],
Chad Brock [aut],
Joseph Brown [aut],
Wendell Challenger [aut],
Jon Eastman [aut],
Rich FitzJohn [aut],
Rich Glor [aut],
Gene Hunt [aut],
Liam Revell [aut],
Graham Slater [aut],
Josef Uyeda [aut],
Jason [...truncated...]
Maintainer: Luke Harmon <lukeh@uidaho.edu>
Diff between geiger versions 2.0.11 dated 2023-04-03 and 2.0.12 dated 2026-08-31
ChangeLog | 68 DESCRIPTION | 45 MD5 | 136 - NAMESPACE | 343 ++-- R/TESTING.R | 1202 +++++++------- R/congruify.R | 910 +++++------ R/deprecated.R | 318 +-- R/disparity.R | 580 +++---- R/diversification.R | 496 +++--- R/edges.R | 452 ++--- R/examples.R | 222 +- R/glomogram.R | 312 +-- R/internal.R | 254 +-- R/likelihood.R | 862 +++++----- R/mecca.R | 3028 ++++++++++++++++++------------------- R/medusa.R | 2650 ++++++++++++++++---------------- R/plotting.R | 1446 ++++++++--------- R/postpred.R | 560 +++--- R/proposals.R | 1738 ++++++++++----------- R/rjmcmc.R | 552 +++--- R/simulation.R | 562 +++--- R/traits-fossil.R | 1538 +++++++++---------- R/traits.R | 2138 +++++++++++++------------- R/utilities-phylo.R | 3790 +++++++++++++++++++++++------------------------ R/utilities-print.R | 680 ++++---- R/utilities-stat.R | 316 +-- README.md | 62 inst/CITATION | 170 +- man/aicm.Rd | 86 - man/aicw.Rd | 66 man/aov.phylo.Rd | 116 - man/bd.ms.Rd | 152 - man/calibrate.mecca.Rd | 178 +- man/calibrate.rjmcmc.Rd | 88 - man/congruify.phylo.Rd | 110 - man/dcount.Rd | 86 - man/drop.extinct.Rd | 96 - man/dtt.Rd | 154 - man/fitContinuous.Rd | 394 ++-- man/fitContinuousMCMC.Rd | 212 +- man/fitDiscrete.Rd | 268 +-- man/gbresolve.Rd | 124 - man/geiger-data.Rd | 234 +- man/geiger-defunct.Rd | 157 - man/geiger-examples.Rd | 22 man/geiger-internal.Rd | 184 +- man/geiger-package.Rd | 48 man/load.rjmcmc.Rd | 116 - man/make.gbm.Rd | 148 - man/mecca.Rd | 296 +-- man/medusa.Rd | 172 +- man/name.check.Rd | 94 - man/nh.test.Rd | 152 - man/nodelabel.phylo.Rd | 254 +-- man/plot.medusa.Rd | 106 - man/pp.mcmc.Rd | 282 +-- man/r8s.phylo.Rd | 150 - man/ratematrix.Rd | 82 - man/rc.Rd | 116 - man/rescale.phylo.Rd | 178 +- man/rjmcmc.bm.Rd | 232 +- man/sim.bd.Rd | 90 - man/sim.bdtree.Rd | 116 - man/sim.char.Rd | 128 - man/startingpt.mecca.Rd | 132 - man/subset.phylo.Rd | 68 man/tips.Rd | 64 man/to.auteur.Rd | 70 man/treedata.Rd | 76 69 files changed, 15680 insertions(+), 15647 deletions(-)
Title: Fast Interpretable Greedy-Tree Sums for Tree Ensembles
Description: Flexible, interpretable machine learning algorithm for additive
tree sums (FIGS). Fits a sum of shallow classification and regression
trees (CART) by greedily minimizing residual impurity, growing a new
tree or deepening an existing one at each step, whichever reduces the
residuals most. Supports regression and two-class classification, variable
importance, bootstrap ensembling and seamless integration with 'parsnip'
and 'tidymodels' workflows. The method is described in Tan et al. (2023)
<doi:10.1073/pnas.2310151122>.
Author: Joao Paulo Assis Bonifacio [aut, cre, cph] ,
Geraldo Magela da Cruz Pereira [aut, cph] ,
Pedro Mambelli Fernandes [aut, cph] ,
Joao Vitor Andrade Alves de Souza [aut, cph]
Maintainer: Joao Paulo Assis Bonifacio <jpab.27@hotmail.com>
Diff between figsr versions 0.1.0 dated 2026-08-31 and 0.1.1 dated 2026-08-31
DESCRIPTION | 10 MD5 | 64 - NAMESPACE | 31 NEWS.md | 121 ++- R/bagging.R | 213 +++-- R/dials.R | 78 +- R/figs_tree.R | 525 +++++++------ R/fit_engine.R | 793 +++++++++++---------- R/plot.R | 400 +++++----- R/predict.R | 203 +++-- R/summary.R | 197 ++--- README.md | 147 ++- inst/WORDLIST | 3 inst/doc/figsr-intro.R | 55 + inst/doc/figsr-intro.Rmd | 175 +++- inst/doc/figsr-intro.html | 234 ++++-- man/bagging_figs.Rd | 88 +- man/figs.Rd | 143 ++- man/figs_tree.Rd | 85 +- man/figsr_importance.Rd | 72 - man/fit_figs.Rd | 106 +- man/max_splits.Rd | 42 - man/max_trees.Rd | 42 - man/plot.figsr_fit.Rd | 68 - man/predict.bagging_figs_fit.Rd | 52 - man/predict.figsr_fit.Rd | 58 - man/predict_figs.Rd | 53 - man/print.figsr_fit.Rd | 52 - man/summary.figsr_fit.Rd | 52 - man/update.figs_tree.Rd |only tests/testthat/test-classification-probabilities.R |only tests/testthat/test-deep-node-values.R |only tests/testthat/test-edge-cases.R |only tests/testthat/test-formula-interface.R |only tests/testthat/test-print-plot.R |only vignettes/figsr-intro.Rmd | 175 +++- 36 files changed, 2564 insertions(+), 1773 deletions(-)
Title: Escalation with Overdose Control
Description: An implementation of a variety of escalation with overdose control designs introduced by Babb, Rogatko and Zacks (1998) <doi:10.1002/(SICI)1097-0258(19980530)17:10%3C1103::AID-SIM793%3E3.0.CO;2-9>. It calculates the next dose as a clinical trial proceeds and performs simulations to obtain operating characteristics.
Author: Marcio A. Diniz [aut, cre, cph]
Maintainer: Marcio A. Diniz <marcio.diniz@mountsinai.org>
This is a re-admission after prior archival of version 0.3.0 dated 2020-06-07
Diff between ewoc versions 0.3.0 dated 2020-06-07 and 0.3.1 dated 2026-08-31
DESCRIPTION | 22 +++++++----- MD5 | 36 ++++++++++----------- NAMESPACE | 8 ++++ NEWS.md | 3 + R/classical_EWOC.R | 1 R/extended_EWOC.R | 3 + R/next_dose.R | 4 +- R/operating_characteristics.R | 39 ++++++++++++---------- R/pdlt.R | 3 + R/ph_EWOC.R | 1 R/plot.R | 15 +++++--- R/response.R | 5 ++ R/stop_rule.R | 28 ++++++++-------- README.md | 72 ++++++++++++++++++++++-------------------- man/opc.Rd | 6 +-- man/stop_rule.Rd | 2 - man/stop_rule_d1classical.Rd | 10 ++--- man/stop_rule_d1extended.Rd | 12 +++---- man/stop_rule_d1ph.Rd | 12 +++---- 19 files changed, 161 insertions(+), 121 deletions(-)
Title: Tools for General Maximum Likelihood Estimation
Description: Methods and functions for fitting maximum likelihood models in R. This package modifies and extends the 'mle' classes in the 'stats4' package.
Author: Ben Bolker [aut, cre] ,
R Development Core Team [aut],
Iago Gine-Vazquez [ctb]
Maintainer: Ben Bolker <bolker@mcmaster.ca>
Diff between bbmle versions 1.0.25.1 dated 2023-12-08 and 1.0.26 dated 2026-08-31
DESCRIPTION | 12 ++-- MD5 | 70 ++++++++++++++-------------- NAMESPACE | 4 - R/IC.R | 7 ++ R/confint.R | 14 +++-- R/mle.R | 110 ++++++++++++++++++++++++++++++-------------- R/mle2-methods.R | 2 R/predict.R | 2 R/profile.R | 8 ++- build/vignette.rds |binary inst/NEWS.Rd | 38 ++++++++++++++- inst/doc/mle2.R | 45 ++++++++++++------ inst/doc/mle2.Rnw | 15 ++---- inst/doc/mle2.pdf |binary inst/doc/quasi.pdf |binary inst/tinytest |only man/BIC-methods.Rd | 7 ++ man/ICtab.Rd | 42 ++++++++++------ man/mle2.Rd | 3 + man/pop_pred_samp.Rd | 3 - man/profile.mle-class.Rd | 9 ++- tests/BIC.R | 16 ++++++ tests/BIC.Rout.save | 25 ++++++++-- tests/ICtab.R | 10 +++- tests/ICtab.Rout.save | 21 +++++--- tests/binomtest1.R | 2 tests/binomtest1.Rout.save | 2 tests/formulatest.R | 8 +-- tests/formulatest.Rout.save | 8 +-- tests/mortanal.R | 6 +- tests/mortanal.Rout.save | 6 +- tests/optimx.R | 57 ++++++++++++++++++++++ tests/optimx.Rout.save | 65 ++++++++++++++++++++++++-- tests/startvals2.R | 6 +- tests/startvals2.Rout.save | 6 +- tests/tinytest.R |only vignettes/mle2.Rnw | 15 ++---- 37 files changed, 465 insertions(+), 179 deletions(-)
Title: Bayesian Averaging for Dynamic Panels
Description: Implements Bayesian model averaging for dynamic panels with weakly
exogenous regressors as described in the paper by
Moral-Benito (2013, <doi:10.1080/07350015.2013.818003>).
The package provides functions to estimate dynamic panel data models
and analyze the results of the estimation.
Author: Krzysztof Beck [aut],
Piotr Cukier [aut],
Marcin Dubel [aut, cre],
Mariusz Szczepanczyk [aut],
Mateusz Wyszynski [aut],
badp authors [cph]
Maintainer: Marcin Dubel <marcindubel@gmail.com>
Diff between badp versions 0.6.0 dated 2026-08-19 and 0.6.1 dated 2026-08-31
DESCRIPTION | 15 ++++++++++----- LICENSE | 4 ++-- MD5 | 6 +++--- NEWS.md | 5 +++++ 4 files changed, 20 insertions(+), 10 deletions(-)
Title: D-Vine Quantile Regression
Description: Implements D-vine quantile regression models with
parametric or nonparametric pair-copulas. See
Kraus and Czado (2017) <doi:10.1016/j.csda.2016.12.009> and
Schallhorn et al. (2017) <doi:10.48550/arXiv.1705.08310>.
Author: Thomas Nagler [aut, cre],
Dani Kraus [ctb]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between vinereg versions 0.12.1 dated 2025-12-10 and 0.13.0 dated 2026-08-31
DESCRIPTION | 7 MD5 | 68 ++--- NAMESPACE | 7 NEWS.md | 47 +++ R/cpit.R | 29 +- R/generics.R | 67 ++++- R/predict.vinereg.R | 19 - R/tools.R | 17 - R/vinereg-package.R |only R/vinereg.R | 105 +++++++- README.md | 116 +++++---- build/partial.rdb |only build/vignette.rds |binary inst/doc/abalone-example.R | 10 inst/doc/abalone-example.Rmd | 29 +- inst/doc/abalone-example.html | 389 ++++++++++++++----------------- inst/doc/bike-rental.R | 12 inst/doc/bike-rental.Rmd | 16 - inst/doc/bike-rental.html | 370 +++++++++++++++-------------- man/cll.Rd | 7 man/cpdf.Rd | 13 - man/cpit.Rd | 12 man/figures/README-unnamed-chunk-1-1.png |binary man/plot_effects.Rd | 14 - man/predict.vinereg.Rd | 11 man/vinereg-methods.Rd |only man/vinereg-package.Rd |only man/vinereg.Rd | 26 +- src/Makevars | 1 src/Makevars.win | 2 src/vinereg.cpp | 22 - tests/testthat/test-generics.R | 13 + tests/testthat/test-predict.R | 12 tests/testthat/test-test-cpit.R | 22 + tests/testthat/test-vinereg.R | 102 ++++++++ vignettes/abalone-example.Rmd | 29 +- vignettes/bike-rental.Rmd | 16 - 37 files changed, 986 insertions(+), 624 deletions(-)
Title: Stationary Vine Copula Models
Description: Provides functionality to fit and simulate from stationary vine
copula models for time series, see Nagler et al. (2022)
<doi:10.1016/j.jeconom.2021.11.015>.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between svines versions 0.2.7 dated 2025-06-12 and 0.3.0 dated 2026-08-31
svines-0.2.7/svines/src/Makevars |only svines-0.2.7/svines/src/Makevars.win |only svines-0.3.0/svines/DESCRIPTION | 18 - svines-0.3.0/svines/MD5 | 87 +++---- svines-0.3.0/svines/NEWS.md | 9 svines-0.3.0/svines/R/returns.R | 15 - svines-0.3.0/svines/R/standard_errors.R | 68 ++++- svines-0.3.0/svines/R/svine.R | 81 +++++- svines-0.3.0/svines/R/svine_methods.R | 22 - svines-0.3.0/svines/R/svinecop.R | 68 ++--- svines-0.3.0/svines/R/svinecop_methods.R | 39 +-- svines-0.3.0/svines/R/tools_select.R | 108 +++++++- svines-0.3.0/svines/README.md | 124 +++++----- svines-0.3.0/svines/build/partial.rdb |binary svines-0.3.0/svines/build/vignette.rds |only svines-0.3.0/svines/cleanup |only svines-0.3.0/svines/cleanup.win |only svines-0.3.0/svines/configure |only svines-0.3.0/svines/configure.win |only svines-0.3.0/svines/inst/CITATION |only svines-0.3.0/svines/inst/doc |only svines-0.3.0/svines/inst/include/svines/implementation/svine_selector.ipp | 54 +++- svines-0.3.0/svines/inst/include/svines/implementation/svinecop.ipp | 57 +++- svines-0.3.0/svines/inst/include/svines/svine_selector.hpp | 4 svines-0.3.0/svines/inst/include/svines/svinecop.hpp | 8 svines-0.3.0/svines/man/figures/README-unnamed-chunk-4-1.png |binary svines-0.3.0/svines/man/figures/README-unnamed-chunk-5-1.png |binary svines-0.3.0/svines/man/figures/README-unnamed-chunk-6-1.png |binary svines-0.3.0/svines/man/returns.Rd | 13 - svines-0.3.0/svines/man/svine.Rd | 18 + svines-0.3.0/svines/man/svine_bootstrap_models.Rd | 7 svines-0.3.0/svines/man/svine_dist.Rd | 10 svines-0.3.0/svines/man/svine_hessian.Rd | 13 - svines-0.3.0/svines/man/svine_loglik.Rd | 4 svines-0.3.0/svines/man/svine_pseudo_residuals.Rd | 14 - svines-0.3.0/svines/man/svine_scores.Rd | 10 svines-0.3.0/svines/man/svine_sim.Rd | 2 svines-0.3.0/svines/man/svinecop.Rd | 36 +- svines-0.3.0/svines/man/svinecop_dist.Rd | 14 - svines-0.3.0/svines/man/svinecop_hessian.Rd | 17 - svines-0.3.0/svines/man/svinecop_loglik.Rd | 4 svines-0.3.0/svines/man/svinecop_pseudo_residuals.Rd | 5 svines-0.3.0/svines/man/svinecop_scores.Rd | 11 svines-0.3.0/svines/man/svinecop_sim.Rd | 2 svines-0.3.0/svines/man/svines-package.Rd | 6 svines-0.3.0/svines/src/Makevars.in |only svines-0.3.0/svines/src/Makevars.win.in |only svines-0.3.0/svines/tests/testthat/test-discrete.R |only svines-0.3.0/svines/tests/testthat/test-svinecop.R | 5 svines-0.3.0/svines/vignettes |only 50 files changed, 658 insertions(+), 295 deletions(-)
Title: Minorization-Maximization via Assembly-Decomposition Technology
Description: A formula-driven framework for maximizing target functions
via the minorization-maximization (MM) algorithm. The package
represents the target as a symbolic expression tree, infers its
curvature via disciplined-convex-programming rules, and constructs
a separable surrogate at each iterate using only Jensen's
inequality and the supporting hyperplane. The driver maximizes the
surrogate via block-coordinate Newton with line search, falling
back to a multivariate step on any non-separable residue. A
formula interface accepts standard R expressions (including
`sum()` reductions and `X %*% theta` design-matrix products) so
statistical models such as Poisson regression can be written in
one line.
Author: Xifen Huang [aut],
Jinfeng Xu [aut],
Jiaqi Gu [aut, cre]
Maintainer: Jiaqi Gu <jiaqigu@usf.edu>
Diff between MMAD versions 3.0.0 dated 2026-07-07 and 3.0.1 dated 2026-08-31
DESCRIPTION | 9 - MD5 | 14 +- NAMESPACE | 10 + R/MMAD-package.R | 1 R/mmad_driver.R | 193 ++++++++++++++++++++++++++++++++++++-- man/mmad.Rd | 21 +++- man/mmad_fit-methods.Rd |only man/mmad_test.Rd |only tests/testthat/test-mmad_driver.R | 115 ++++++++++++++++++++++ 9 files changed, 338 insertions(+), 25 deletions(-)
Title: Mediation Analysis with Missing Data Using Bootstrap
Description: Four methods for mediation analysis with missing data: Listwise deletion, Pairwise deletion, Multiple imputation, and Two Stage Maximum Likelihood algorithm. For MI and TS-ML, auxiliary variables can be included. Bootstrap confidence intervals for mediation effects are obtained. The robust method is also implemented for TS-ML. Since version 1.4, bmem adds the capability to conduct power analysis for mediation models. Details about the methods used can be found in these articles. Zhang and Wang (2003) <doi:10.1007/s11336-012-9301-5>. Zhang (2014) <doi:10.3758/s13428-013-0424-0>.
Author: Zhiyong Zhang [aut, cre],
Lijuan Wang [aut]
Maintainer: Zhiyong Zhang <zhiyongzhang@nd.edu>
Diff between bmem versions 2.2 dated 2025-09-03 and 2.3 dated 2026-08-31
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/power.R | 12 ++++++------ inst/doc/MediationAnalysis.pdf |binary 4 files changed, 13 insertions(+), 13 deletions(-)
Title: Orchestration of Data Pipelines
Description: Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Author: Will Hipson [cre, aut, cph] ,
Ryan Garnett [aut, ctb, cph]
Maintainer: Will Hipson <will.e.hipson@gmail.com>
Diff between maestro versions 1.2.0 dated 2026-07-02 and 1.3.0 dated 2026-08-31
DESCRIPTION | 6 - MD5 | 49 +++++----- NAMESPACE | 2 NEWS.md | 6 + R/MaestroPipeline.R | 62 +++++++++++++ R/MaestroPipelineList.R | 104 +++++++++++++++++++++++ R/build_schedule.R | 1 R/build_schedule_entry.R | 24 ++++- R/maestro_tags.R | 35 +++++++ R/roxy_maestro.R | 37 ++++++++ inst/doc/maestro-1-quick-start.html | 2 inst/doc/maestro-3-advanced-scheduling.html | 4 inst/doc/maestro-4-directed-acyclic-graphs.html | 18 +-- inst/doc/maestro-4b-directed-acyclic-graphs.html | 38 ++++---- inst/doc/maestro-5-logging.html | 64 +++++++------- inst/doc/maestro-7-tag-reference.html | 24 +++++ inst/doc/maestro-7-tag-reference.qmd | 30 ++++++ inst/doc/maestro-8-conditionals.html | 38 ++++---- man/MaestroPipeline.Rd | 93 ++++++++++++++++++++ man/MaestroPipelineList.Rd | 20 ++++ man/maestro_tags.Rd | 37 ++++++++ tests/testthat/_snaps/fanout.md | 11 ++ tests/testthat/_snaps/get_slot_usage.md | 8 - tests/testthat/test-cascade.R |only tests/testthat/test-fanout.R | 33 +++++++ vignettes/maestro-7-tag-reference.qmd | 30 ++++++ 26 files changed, 658 insertions(+), 118 deletions(-)
Title: Curve Linear Regression via Dimension Reduction
Description: A new methodology for linear regression with both curve response
and curve regressors, which is described in Cho, Goude, Brossat and Yao
(2013) <doi:10.1080/01621459.2012.722900> and (2015)
<doi:10.1007/978-3-319-18732-7_3>. The key idea behind this methodology is
dimension reduction based on a singular value decomposition in a Hilbert
space, which reduces the curve regression problem to several scalar linear
regression problems.
Author: Amandine Pierrot [cre, aut],
Qiwei Yao [ctb],
Haeran Cho [ctb],
Yannig Goude [ctb],
Tony Aldon [ctb],
EDF [cph, fnd]
Maintainer: Amandine Pierrot <amandine.m.pierrot@gmail.com>
Diff between clr versions 0.1.2 dated 2019-07-29 and 0.1.3 dated 2026-08-31
clr-0.1.2/clr/data/datalist |only clr-0.1.3/clr/DESCRIPTION | 25 ++++++++++++++++++------- clr-0.1.3/clr/MD5 | 21 ++++++++++----------- clr-0.1.3/clr/NAMESPACE | 16 ++++++++++------ clr-0.1.3/clr/NEWS.md | 13 +++++++++++++ clr-0.1.3/clr/R/clr.R | 4 ++-- clr-0.1.3/clr/R/gb_load-data.R | 4 ++-- clr-0.1.3/clr/man/clr.Rd | 14 ++++++++++---- clr-0.1.3/clr/man/clust_test.Rd | 6 ++++-- clr-0.1.3/clr/man/clust_train.Rd | 6 ++++-- clr-0.1.3/clr/man/gb_load.Rd | 10 ++++++---- clr-0.1.3/clr/man/predict.clr.Rd | 10 ++++++++-- 12 files changed, 87 insertions(+), 42 deletions(-)
Title: Bayesian Estimation of Dynamic VAR Models using Stan
Description: Bayesian estimation of multilevel Vector Autoregression (VAR) models
using Stan. Supports Gaussian, Binary, and Ordinal (adjacent category) outcome
variables with random effects and customizable priors.
Author: Florian Metwaly [aut, cre, cph]
Maintainer: Florian Metwaly <f.j.metwaly@uva.nl>
Diff between bvarnet versions 1.0.1 dated 2026-06-13 and 1.0.2 dated 2026-08-31
DESCRIPTION | 19 + MD5 | 81 ++++---- NAMESPACE | 3 NEWS.md | 29 ++- R/bayes_factor.R | 129 +++++++++++-- R/bvar.R | 189 +++++++++++++------ R/download_models.R |only R/extract_param.R | 60 ++---- R/extractors.R | 77 +++++--- R/helpers.R | 298 +++++++++++++++++++++++++++---- R/set_priors.R | 13 + R/sim_bvarnet.R | 79 +++----- R/summary.R | 19 + R/to_stan_data.R | 131 +++++++++++-- R/utils.R |only R/zzz.R | 90 ++++++--- README.md | 45 +++- inst/COPYRIGHTS |only inst/doc/Missing-Data.Rmd | 160 +++------------- inst/doc/Missing-Data.html | 244 ++++++++----------------- man/bf_table.Rd | 12 + man/bvar.Rd | 48 ++++ man/bvarnet-package.Rd | 2 man/bvarnet_clear_model_cache.Rd |only man/bvarnet_model_cache_dir.Rd |only man/bvarnet_setup_models.Rd |only man/compare_to_truth.Rd | 6 man/extract_network_matrix.Rd | 10 - man/extract_param.Rd | 22 +- man/extract_random_effects.Rd | 22 ++ man/extract_temporal.Rd | 13 - man/figures |only man/set_priors.Rd | 15 + man/summary.bvarnet.Rd | 7 tests/testthat/helper-fixtures.R | 47 +++- tests/testthat/test-bayes_factor.R | 64 +++--- tests/testthat/test-download-models.R |only tests/testthat/test-draw-ordering.R |only tests/testthat/test-extract_param.R | 23 ++ tests/testthat/test-helpers.R | 192 +++++++++++++++++++ tests/testthat/test-input-validation.R | 29 +++ tests/testthat/test-prior-scaling.R |only tests/testthat/test-summary-extractors.R | 59 ++++++ tests/testthat/test-to_stan_data.R | 111 +++++++++++ tests/testthat/test-utils.R |only vignettes/Missing-Data.Rmd | 160 +++------------- vignettes/Missing-Data.Rmd.orig | 28 +- 47 files changed, 1728 insertions(+), 808 deletions(-)
Title: Bayesian Latent Space Model
Description: Provides a Bayesian latent space
model for complex networks, either weighted or unweighted.
Given an observed input graph, the estimates for the latent coordinates
of the nodes are obtained through a Bayesian MCMC algorithm.
The overall likelihood of the graph depends on a fundamental probability
equation, which is defined so that ties are more likely to exist
between nodes whose latent space coordinates are close.
The package is mainly based on the model by Hoff, Raftery and Handcock (2002)
<doi:10.1198/016214502388618906> and contains some extra features
(e.g., removal of the Procrustean step, weights implemented as
coefficients of the latent distances, 3D plots).
The original code related to the above model was retrieved from
<https://www2.stat.duke.edu/~pdh10/Code/hoff_raftery_handcock_2002_jasa/>.
Users can inspect the MCMC simulation, create and customize insightful
graphical representations or apply clustering techniques.
Author: Alberto Donizetti [aut, cre],
Francesca Ieva [ctb]
Maintainer: Alberto Donizetti <albe.donizetti@gmail.com>
Diff between BLSM versions 0.1.0 dated 2018-04-26 and 0.1.1 dated 2026-08-31
DESCRIPTION | 12 MD5 | 48 +- NAMESPACE | 50 +- NEWS.md | 10 R/RcppExports.R | 238 +++++------ R/blsm.R | 820 +++++++++++++++++++-------------------- R/data.R | 112 ++--- R/package.R | 102 ++-- README.md | 68 +-- man/BLSM.Rd | 92 ++-- man/Z_up.Rd | 58 +- man/alpha_up.Rd | 58 +- man/dst.Rd | 40 - man/estimate_latent_positions.Rd | 216 +++++----- man/example_adjacency_matrix.Rd | 28 - man/example_blsm_obj.Rd | 58 +- man/example_weights_matrix.Rd | 58 +- man/lpY.Rd | 50 +- man/lpYNODE.Rd | 58 +- man/lpz_dist.Rd | 46 +- man/lpz_distNODE.Rd | 46 +- man/mlpY.Rd | 46 +- man/plot_latent_positions.Rd | 70 +-- man/plot_traceplots_acf.Rd | 66 +-- man/proc_crr.Rd | 74 +-- 25 files changed, 1272 insertions(+), 1252 deletions(-)
Title: Interact with Peak Flow Data in the United Kingdom
Description: Obtain information on peak flow data from the National River Flow Archive (NRFA) in the United Kingdom, either from the Peak Flow Dataset files <https://nrfa.ceh.ac.uk/data/peak-flow-dataset> once these have been downloaded to the user's computer or using the NRFA's API. These files are in a format suitable for direct use in the 'WINFAP' software, hence the name of the package.
Author: Ilaria Prosdocimi [aut, cre] ,
Luke Shaw [aut]
Maintainer: Ilaria Prosdocimi <prosdocimi.ilaria@gmail.com>
Diff between winfapReader versions 0.1-7 dated 2026-02-20 and 0.1-7.1 dated 2026-08-31
DESCRIPTION | 8 ++++---- MD5 | 25 +++++++++++++------------ NAMESPACE | 26 ++++++++++++++------------ NEWS.md | 5 ++++- R/known_Oct1.R | 4 +++- R/readerFuncs.R | 27 ++++++++++++++------------- build/vignette.rds |binary data/known_Oct1.rda |binary inst/doc/winfapReader.R | 4 ---- inst/doc/winfapReader.Rmd | 4 ---- inst/doc/winfapReader.html | 12 ++++-------- man/known_Oct1.Rd | 2 +- vignettes/--find-assets.html |only vignettes/winfapReader.Rmd | 4 ---- 14 files changed, 57 insertions(+), 64 deletions(-)
Title: Community Ecology Package
Description: Ordination methods, diversity analysis and other
functions for community and vegetation ecologists.
Author: Jari Oksanen [aut, cre] ,
Gavin L. Simpson [aut] ,
F. Guillaume Blanchet [aut],
Roeland Kindt [aut],
Pierre Legendre [aut],
Peter R. Minchin [aut],
R.B. O'Hara [aut],
Peter Solymos [aut],
M. Henry H. Stevens [aut],
Eduard Szoecs [aut],
Helene Wagner [...truncated...]
Maintainer: Jari Oksanen <jhoksane@gmail.com>
Diff between vegan versions 2.7-5 dated 2026-05-25 and 2.7-6 dated 2026-08-31
DESCRIPTION | 6 +-- MD5 | 58 ++++++++++++++--------------- NEWS.md | 41 ++++++++++++++++++++ R/clamtest.R | 8 ++-- R/decorana.R | 4 +- R/make.cepnames.R | 17 +++++++- R/metaMDS.R | 11 ++--- R/ordimedian.R | 30 +++++++++------ R/ordispider.R | 4 -- R/ordisurf.R | 21 +++++++--- R/plot.decorana.R | 11 ++++- R/print.summary.clamtest.R | 6 ++- R/showvarparts.R | 2 - R/summary.clamtest.R | 8 ++-- R/summary.isomap.R | 1 R/tabasco.R | 13 ++++-- R/text.decorana.R | 8 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/FAQ-vegan.html | 18 +++++---- inst/doc/decision-vegan.pdf |binary inst/doc/diversity-vegan.pdf |binary inst/doc/intro-vegan.pdf |binary inst/doc/partitioning.pdf |binary man/make.cepnames.Rd | 38 ++++++++++++------- man/ordiArrowTextXY.Rd | 2 - man/tolerance.Rd | 34 ++++++++++++----- man/vegemite.Rd | 84 +++++++++++++++++++++---------------------- tests/vegan-tests.R | 26 +++++++++++-- tests/vegan-tests.Rout.save | 51 ++++++++++++++++++++++---- 30 files changed, 334 insertions(+), 168 deletions(-)
Title: Language Support for 'sylly' Package: English
Description: Adds support for the English language to the 'sylly' package. To ask for help, report bugs, suggest feature improvements, or discuss the global development of the package, please consider subscribing to the koRpus-dev mailing list (<https://korpusml.reaktanz.de>).
Author: Meik Michalke [aut, cre]
Maintainer: Meik Michalke <meik.michalke@hhu.de>
Diff between sylly.en versions 0.1-3 dated 2018-03-19 and 0.1-4 dated 2026-08-31
ChangeLog | 4 ++++ DESCRIPTION | 23 ++++++++--------------- MD5 | 23 ++++++++++++----------- R/hyph.en-data.R | 7 +++---- R/hyph.support-en.R | 10 +++++----- R/sylly.en-package.R | 35 +++++++++++++++++++---------------- README.md | 6 +++--- build |only inst/CITATION | 12 ++++++------ inst/NEWS.Rd | 7 +++++++ man/hyph.en.Rd | 13 ++++++------- man/hyph.support.en.Rd | 6 +++--- man/sylly.en-package.Rd | 29 +++++++++++++++++------------ 13 files changed, 93 insertions(+), 82 deletions(-)
Title: A Comprehensive and Intuitive R Package for Stepwise Regression
Analysis
Description: Stepwise regression is a statistical technique used for model selection. This package streamlines stepwise regression analysis by supporting multiple regression types(linear, Cox, logistic, Poisson, Gamma, and negative binomial), incorporating popular selection strategies(forward, backward, bidirectional, and subset), and offering essential metrics. It enables users to apply multiple selection strategies and metrics in a single function call, visualize variable selection processes, and export results in various formats. StepReg offers a data-splitting option to address potential issues with invalid statistical inference and a randomized forward selection option to avoid overfitting. We validated StepReg's accuracy using public datasets within the SAS software environment. For an interactive web interface, users can install the companion 'StepRegShiny' package. The methodology is described in Li et al. (2026) <doi:10.32614/RJ-2026-005>.
Author: Junhui Li [cre, aut] ,
Kai Hu [aut],
Xiaohuan Lu [aut],
Sushmita N Nayak [ctb, aut],
Cesar Bautista Sotelo [ctb, aut],
Michael A Lodato [ctb, aut],
Wenxin Liu [aut],
Lihua Julie Zhu [aut]
Maintainer: Junhui Li <junhui.li11@umassmed.edu>
Diff between StepReg versions 1.6.6 dated 2026-06-04 and 1.6.7 dated 2026-08-31
DESCRIPTION | 33 MD5 | 16 build/partial.rdb |only build/vignette.rds |binary inst/CITATION |only inst/doc/StepReg.R | 393 ---- inst/doc/StepReg.Rmd | 748 --------- inst/doc/StepReg.html | 3942 +++---------------------------------------------- man/StepReg-package.Rd | 15 vignettes/StepReg.Rmd | 748 --------- 10 files changed, 312 insertions(+), 5583 deletions(-)
Title: Species Sensitivity Distributions
Description: Species sensitivity distributions are cumulative probability
distributions which are fitted to toxicity concentrations for
different species as described by Posthuma et al. (2001)
<isbn:9781566705783>. The ssdtools package uses Maximum Likelihood to
fit distributions such as the gamma, log-logistic, log-normal and
log-normal log-normal mixture. Multiple distributions can be averaged
using Akaike Information Criteria. Confidence intervals on hazard
concentrations and proportions are produced by bootstrapping.
Author: Joe Thorley [aut, cre] ,
Rebecca Fisher [aut],
David Fox [aut],
Carl Schwarz [aut],
Angeline Tillmanns [ctb],
Seb Dalgarno [ctb] ,
Kathleen McTavish [ctb],
Heather Thompson [ctb],
Doug Spry [ctb],
Rick van Dam [ctb],
Graham Batley [ctb],
Ali Azizishi [...truncated...]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
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Title: Stagewise Generalized Estimating Equations
Description: Stagewise techniques implemented with Generalized Estimating Equations to handle individual, group, bi-level, and interaction selection. Stagewise approaches start with an empty model and slowly build the model over several iterations, which yields a 'path' of candidate models from which model selection can be performed. This 'slow brewing' approach gives stagewise techniques a unique flexibility that allows simple incorporation of Generalized Estimating Equations; see Vaughan, G., Aseltine, R., Chen, K., Yan, J., (2017) <doi:10.1111/biom.12669> for details.
Author: Gregory Vaughan [aut, cre],
Kun Chen [ctb],
Jun Yan [ctb]
Maintainer: Gregory Vaughan <gvaughan@bentley.edu>
Diff between sgee versions 0.6-0 dated 2018-01-08 and 0.6-2 dated 2026-08-31
ChangeLog | 460 +++++---- DESCRIPTION | 28 MD5 | 66 - R/bisee.R | 1212 ++++++++++++------------- R/deltaFinder.R | 84 - R/deltaValue.R | 86 - R/evaluateGEE.R | 506 +++++----- R/genCorMat.R | 250 ++--- R/genData.R | 581 +++++++----- R/gsee.R | 588 ++++++------ R/hisee.R | 1075 +++++++++++----------- R/isee.R | 1954 ++++++++++++++++++++--------------------- R/miniSim.R | 396 ++++---- R/plot.sgee.R | 644 ++++++------- R/print.sgee.R | 202 ++-- R/print.sgeeSummary.R | 186 +-- R/samplingDistCalculation.R | 262 ++--- R/see.R | 1279 +++++++++++++------------- R/sgee-package.R | 278 ++--- R/sgee.control.R | 268 ++--- R/subsample.R | 166 +-- R/summary.sgee.R | 670 +++++++------- inst/COPYRIGHT | 36 man/bisee.Rd | 71 + man/genData.Rd | 34 man/hisee.Rd | 36 man/isee.Rd | 69 + man/miniSim.Rd | 18 man/plot.sgee.Rd | 19 man/samplingDistCalculation.Rd | 18 man/see.Rd | 39 man/sgee-package.Rd | 16 man/sgee.control.Rd | 14 man/summary.sgee.Rd | 15 34 files changed, 5980 insertions(+), 5646 deletions(-)
Title: Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for univariate, multivariate, unsupervised, survival, competing risks, class imbalanced classification and quantile regression. New Mahalanobis splitting for correlated outcomes. Extreme random forests and randomized splitting. Suite of imputation methods for missing data. Fast random forests using subsampling. Confidence regions and standard errors for variable importance. New improved holdout importance. Case-specific importance. Minimal depth variable importance. Visualize trees on your Safari or Google Chrome browser. Anonymous random forests for data privacy.
Author: Hemant Ishwaran [aut],
Udaya B. Kogalur [aut, cre]
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 3.6.2 dated 2026-04-19 and 3.7.0 dated 2026-08-31
DESCRIPTION | 8 MD5 | 74 +-- NAMESPACE | 2 NEWS.md | 44 + R/generic.predict.rfsrc.R | 66 +- R/impute.learn.rfsrc.R | 346 ++++++++++++++- R/impute.rfsrc.R | 20 R/plot.survival.rfsrc.R | 450 ++++++++++++++----- R/rfsrc.R | 6 R/rfsrc.news.R | 2 R/utilities.R | 20 R/utilities_impute.R | 74 +++ R/utilities_impute_learn.R | 719 ++++++++++++++++++++++++++++++- R/utilities_survival.R | 1031 ++++++++++++++++++++++++++++++++++++++------- data/breast.rda |binary data/follic.rda |binary data/hd.rda |binary data/housing.rda |binary data/nutrigenomic.rda |binary data/pbc.rda |binary data/peakVO2.rda |binary data/vdv.rda |binary data/veteran.rda |binary data/wihs.rda |binary data/wine.rda |binary man/impute.learn.rfsrc.Rd | 383 +++++++++++----- man/impute.rfsrc.Rd | 26 - man/plot.survival.rfsrc.Rd | 299 +++++++++---- man/predict.rfsrc.Rd | 45 + man/rfsrc.Rd | 30 - src/entry.c | 7 src/entryGeneric.c | 6 src/processEnsemble.c | 56 +- src/rfsrc.c | 17 src/stack.c | 14 src/stackOutput.c | 128 +++-- src/tree.c | 270 ++++++++--- src/tree.h | 4 38 files changed, 3436 insertions(+), 711 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: Many Marks, Measures, Memberships, and Motifs for Networks
Description: Many tools for calculating network, node, or tie
marks, measures, motifs and memberships of many different types of networks.
Marks identify structural positions, measures quantify network properties,
memberships classify nodes into groups, and motifs tabulate substructure participation.
All functions operate with all classes of network data covered in 'manynet',
and on directed, undirected, multiplex, multimodal, signed, and other networks.
Author: James Hollway [cre, aut, ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between netrics versions 0.4.0 dated 2026-07-24 and 1.0.1 dated 2026-08-31
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Title: Tools for Multiple Imputation of Missing Data
Description: Tools to perform analyses and combine results from multiple-imputation datasets.
Author: Thomas Lumley [aut, cre]
Maintainer: Thomas Lumley <t.lumley@auckland.ac.nz>
Diff between mitools versions 2.4 dated 2019-04-26 and 2.7 dated 2026-08-31
mitools-2.4/mitools/NEWS |only mitools-2.7/mitools/DESCRIPTION | 15 +++++++++------ mitools-2.7/mitools/MD5 | 16 ++++++++-------- mitools-2.7/mitools/NAMESPACE | 1 + mitools-2.7/mitools/R/PV.R | 2 +- mitools-2.7/mitools/build/vignette.rds |binary mitools-2.7/mitools/data/smi.rda |binary mitools-2.7/mitools/inst/NEWZ |only mitools-2.7/mitools/inst/doc/smi.pdf |binary mitools-2.7/mitools/man/PV.Rd | 2 +- 10 files changed, 20 insertions(+), 16 deletions(-)
Title: Generate Optimal Designs of Accelerated Life Test using
PSO-Based Algorithm
Description: A computationally efficient solution for generating optimal experimental designs in Accelerated Life Testing (ALT). Leveraging a Particle Swarm Optimization (PSO)-based hybrid algorithm, the package identifies optimal test plans that minimize estimation variance under specified failure models and stress profiles. For more detailed, see Lee et al. (2025), Optimal Robust Strategies for Accelerated Life Tests and Fatigue Testing of Polymer Composite Materials <doi:10.1214/25-AOAS2075>.
Author: Hoai-Linh Hoang [aut, cre],
I-Chen Lee [aut],
Ping-Yang Chen [aut],
Ray-Bing Chen [aut],
Weng Kee Wong [aut]
Maintainer: Hoai-Linh Hoang <hoailinh.hoang17@gmail.com>
Diff between minimaxALT versions 1.0.3 dated 2025-12-23 and 1.0.4 dated 2026-08-31
minimaxALT-1.0.3/minimaxALT/R/common.R |only minimaxALT-1.0.3/minimaxALT/R/equivalence_theorem.R |only minimaxALT-1.0.3/minimaxALT/R/summary_methods.R |only minimaxALT-1.0.3/minimaxALT/inst/designs |only minimaxALT-1.0.3/minimaxALT/inst/figures |only minimaxALT-1.0.3/minimaxALT/man/check_equivalence_theorem.Rd |only minimaxALT-1.0.3/minimaxALT/tests/testthat/test-check-equivalence-theorem.R |only minimaxALT-1.0.3/minimaxALT/tests/testthat/test-locally-optimal-design-1factor.R |only minimaxALT-1.0.3/minimaxALT/tests/testthat/test-locally-optimal-design-2factor.R |only minimaxALT-1.0.4/minimaxALT/DESCRIPTION | 14 minimaxALT-1.0.4/minimaxALT/MD5 | 68 + minimaxALT-1.0.4/minimaxALT/NAMESPACE | 15 minimaxALT-1.0.4/minimaxALT/NEWS.md | 4 minimaxALT-1.0.4/minimaxALT/R/check_optimality.R |only minimaxALT-1.0.4/minimaxALT/R/extract_design.R |only minimaxALT-1.0.4/minimaxALT/R/helpers.R |only minimaxALT-1.0.4/minimaxALT/R/minimaxALT-package.R | 6 minimaxALT-1.0.4/minimaxALT/R/minimaxALT.R | 381 ++++------ minimaxALT-1.0.4/minimaxALT/R/plot.R |only minimaxALT-1.0.4/minimaxALT/R/print.R |only minimaxALT-1.0.4/minimaxALT/R/setup.R | 132 ++- minimaxALT-1.0.4/minimaxALT/R/summary.R |only minimaxALT-1.0.4/minimaxALT/build |only minimaxALT-1.0.4/minimaxALT/inst/doc |only minimaxALT-1.0.4/minimaxALT/man/check_optimality.Rd |only minimaxALT-1.0.4/minimaxALT/man/extract_design.Rd |only minimaxALT-1.0.4/minimaxALT/man/find_optimal_alt.Rd | 79 +- minimaxALT-1.0.4/minimaxALT/man/initialize_values.Rd | 30 minimaxALT-1.0.4/minimaxALT/man/minimaxALT-package.Rd | 2 minimaxALT-1.0.4/minimaxALT/man/plot.OptimalALT.Rd |only minimaxALT-1.0.4/minimaxALT/man/print.DesignInfo.Rd |only minimaxALT-1.0.4/minimaxALT/man/print.InitialValue.Rd |only minimaxALT-1.0.4/minimaxALT/man/print.OptimalALT.Rd |only minimaxALT-1.0.4/minimaxALT/man/print.OptimalityCheck.Rd |only minimaxALT-1.0.4/minimaxALT/man/print.PSOInfo.Rd |only minimaxALT-1.0.4/minimaxALT/man/pso_setting.Rd | 15 minimaxALT-1.0.4/minimaxALT/man/set_design_info.Rd | 10 minimaxALT-1.0.4/minimaxALT/man/summary.OptimalALT.Rd |only minimaxALT-1.0.4/minimaxALT/man/update_optimality_check.Rd |only minimaxALT-1.0.4/minimaxALT/src/psoMain.cpp | 144 ++- minimaxALT-1.0.4/minimaxALT/tests/testthat.R | 1 minimaxALT-1.0.4/minimaxALT/tests/testthat/helper-data.R |only minimaxALT-1.0.4/minimaxALT/tests/testthat/test-class.R |only minimaxALT-1.0.4/minimaxALT/tests/testthat/test-extract.R |only minimaxALT-1.0.4/minimaxALT/tests/testthat/test-models.R |only minimaxALT-1.0.4/minimaxALT/tests/testthat/test-multiple-factors.R |only minimaxALT-1.0.4/minimaxALT/tests/testthat/test-reproducibility.R |only minimaxALT-1.0.4/minimaxALT/vignettes |only 48 files changed, 487 insertions(+), 414 deletions(-)
Title: Lexicons for Text Analysis
Description: A collection of lexical hash tables, dictionaries, and word lists.
Author: Tyler Rinker [aut, cre, cph],
University of Notre Dame [dtc, cph],
Department of Knowledge Technologies [dtc, cph],
Unicode, Inc. [dtc, cph],
John Higgins [dtc, cph],
Grady Ward [dtc],
Heiko Possel [dtc],
Michal Boleslav Mechura [dtc, cph],
Bing Liu [...truncated...]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between lexicon versions 1.2.1 dated 2019-03-21 and 1.3.2 dated 2026-08-31
lexicon-1.2.1/lexicon/NEWS |only lexicon-1.2.1/lexicon/data/datalist |only lexicon-1.3.2/lexicon/DESCRIPTION | 10 lexicon-1.3.2/lexicon/MD5 | 338 +- lexicon-1.3.2/lexicon/NAMESPACE | 20 lexicon-1.3.2/lexicon/R/available_data.R | 100 lexicon-1.3.2/lexicon/R/cliches.R | 64 lexicon-1.3.2/lexicon/R/common_names.R | 24 lexicon-1.3.2/lexicon/R/constraining_loughran_mcdonald.R | 46 lexicon-1.3.2/lexicon/R/freq_first_names.R | 38 lexicon-1.3.2/lexicon/R/freq_last_names.R | 36 lexicon-1.3.2/lexicon/R/function_words.R | 29 lexicon-1.3.2/lexicon/R/grady_augmented.R | 32 lexicon-1.3.2/lexicon/R/hash_emoticons.R | 50 lexicon-1.3.2/lexicon/R/hash_grady_pos.R | 118 - lexicon-1.3.2/lexicon/R/hash_internet_slang.R | 40 lexicon-1.3.2/lexicon/R/hash_lemmas.R | 1120 ++++----- lexicon-1.3.2/lexicon/R/hash_nrc_emotion.R | 44 lexicon-1.3.2/lexicon/R/hash_sentiment_emojis.R | 362 +-- lexicon-1.3.2/lexicon/R/hash_sentiment_huliu.R | 62 lexicon-1.3.2/lexicon/R/hash_sentiment_jockers.R | 90 lexicon-1.3.2/lexicon/R/hash_sentiment_jockers_rinker.R | 52 lexicon-1.3.2/lexicon/R/hash_sentiment_loughran_mcdonald.R | 58 lexicon-1.3.2/lexicon/R/hash_sentiment_nrc.R | 70 lexicon-1.3.2/lexicon/R/hash_sentiment_senticnet.R | 66 lexicon-1.3.2/lexicon/R/hash_sentiment_sentiword.R | 58 lexicon-1.3.2/lexicon/R/hash_sentiment_slangsd.R | 78 lexicon-1.3.2/lexicon/R/hash_sentiment_socal_google.R | 54 lexicon-1.3.2/lexicon/R/hash_valence_shifters.R | 106 lexicon-1.3.2/lexicon/R/key_contractions.R | 32 lexicon-1.3.2/lexicon/R/key_corporate_social_responsibility.R | 54 lexicon-1.3.2/lexicon/R/key_grade.R | 32 lexicon-1.3.2/lexicon/R/key_ratings.R | 36 lexicon-1.3.2/lexicon/R/key_regressive_imagery.R | 126 - lexicon-1.3.2/lexicon/R/lexicon-package.R | 20 lexicon-1.3.2/lexicon/R/modal_loughran_mcdonald.R | 54 lexicon-1.3.2/lexicon/R/nrc_emotions.R | 70 lexicon-1.3.2/lexicon/R/pos_action_verb.R | 42 lexicon-1.3.2/lexicon/R/pos_df_irregular_nouns.R | 50 lexicon-1.3.2/lexicon/R/pos_df_pronouns.R | 44 lexicon-1.3.2/lexicon/R/pos_interjections.R | 24 lexicon-1.3.2/lexicon/R/pos_preposition.R | 20 lexicon-1.3.2/lexicon/R/profanity_alvarez.R | 26 lexicon-1.3.2/lexicon/R/profanity_arr_bad.R | 28 lexicon-1.3.2/lexicon/R/profanity_banned.R | 32 lexicon-1.3.2/lexicon/R/profanity_racist.R | 72 lexicon-1.3.2/lexicon/R/profanity_zac_anger.R | 34 lexicon-1.3.2/lexicon/R/sw_dolch.R | 36 lexicon-1.3.2/lexicon/R/sw_fry_100.R | 34 lexicon-1.3.2/lexicon/R/sw_fry_1000.R | 28 lexicon-1.3.2/lexicon/R/sw_fry_200.R | 34 lexicon-1.3.2/lexicon/R/sw_fry_25.R | 34 lexicon-1.3.2/lexicon/R/sw_jockers.R | 26 lexicon-1.3.2/lexicon/R/sw_loughran_mcdonald.R | 80 lexicon-1.3.2/lexicon/R/sw_lucene.R | 60 lexicon-1.3.2/lexicon/R/sw_mallet.R | 206 - lexicon-1.3.2/lexicon/R/sw_python.R | 86 lexicon-1.3.2/lexicon/R/utils.R | 152 - lexicon-1.3.2/lexicon/README.md | 652 ++--- lexicon-1.3.2/lexicon/data/cliches.rda |binary lexicon-1.3.2/lexicon/data/common_names.rda |binary lexicon-1.3.2/lexicon/data/constraining_loughran_mcdonald.rda |binary lexicon-1.3.2/lexicon/data/emojis_sentiment.rda |binary lexicon-1.3.2/lexicon/data/freq_first_names.rda |binary lexicon-1.3.2/lexicon/data/freq_last_names.rda |binary lexicon-1.3.2/lexicon/data/function_words.rda |binary lexicon-1.3.2/lexicon/data/grady_augmented.rda |binary lexicon-1.3.2/lexicon/data/hash_emojis.rda |binary lexicon-1.3.2/lexicon/data/hash_emojis_identifier.rda |binary lexicon-1.3.2/lexicon/data/hash_emoticons.rda |binary lexicon-1.3.2/lexicon/data/hash_grady_pos.rda |binary lexicon-1.3.2/lexicon/data/hash_internet_slang.rda |binary lexicon-1.3.2/lexicon/data/hash_lemmas.rda |binary lexicon-1.3.2/lexicon/data/hash_nrc_emotions.rda |binary lexicon-1.3.2/lexicon/data/hash_sentiment_emojis.rda |binary lexicon-1.3.2/lexicon/data/hash_sentiment_huliu.rda |binary lexicon-1.3.2/lexicon/data/hash_sentiment_jockers_rinker.rda |binary lexicon-1.3.2/lexicon/data/hash_sentiment_loughran_mcdonald.rda |binary lexicon-1.3.2/lexicon/data/hash_sentiment_nrc.rda |binary lexicon-1.3.2/lexicon/data/hash_sentiment_senticnet.rda |binary lexicon-1.3.2/lexicon/data/hash_sentiment_sentiword.rda |binary lexicon-1.3.2/lexicon/data/hash_sentiment_slangsd.rda |binary lexicon-1.3.2/lexicon/data/hash_sentiment_socal_google.rda |binary lexicon-1.3.2/lexicon/data/hash_valence_shifters.rda |binary lexicon-1.3.2/lexicon/data/key_contractions.rda |binary lexicon-1.3.2/lexicon/data/key_corporate_social_responsibility.rda |binary lexicon-1.3.2/lexicon/data/key_grade.rda |binary lexicon-1.3.2/lexicon/data/key_rating.rda |binary lexicon-1.3.2/lexicon/data/key_regressive_imagery.rda |binary lexicon-1.3.2/lexicon/data/modal_loughran_mcdonald.rda |binary lexicon-1.3.2/lexicon/data/nrc_emotions.rda |binary lexicon-1.3.2/lexicon/data/pos_action_verb.rda |binary lexicon-1.3.2/lexicon/data/pos_df_irregular_nouns.rda |binary lexicon-1.3.2/lexicon/data/pos_df_pronouns.rda |binary lexicon-1.3.2/lexicon/data/pos_interjections.rda |binary lexicon-1.3.2/lexicon/data/pos_preposition.rda |binary lexicon-1.3.2/lexicon/data/profanity_alvarez.rda |binary lexicon-1.3.2/lexicon/data/profanity_arr_bad.rda |binary lexicon-1.3.2/lexicon/data/profanity_banned.rda |binary lexicon-1.3.2/lexicon/data/profanity_racist.rda |binary lexicon-1.3.2/lexicon/data/profanity_zac_anger.rda |binary lexicon-1.3.2/lexicon/data/sw_dolch.rda |binary lexicon-1.3.2/lexicon/data/sw_fry_100.rda |binary lexicon-1.3.2/lexicon/data/sw_fry_1000.rda |binary lexicon-1.3.2/lexicon/data/sw_fry_200.rda |binary lexicon-1.3.2/lexicon/data/sw_fry_25.rda |binary lexicon-1.3.2/lexicon/data/sw_jockers.rda |binary lexicon-1.3.2/lexicon/data/sw_loughran_mcdonald_long.rda |binary lexicon-1.3.2/lexicon/data/sw_loughran_mcdonald_short.rda |binary lexicon-1.3.2/lexicon/data/sw_lucene.rda |binary lexicon-1.3.2/lexicon/data/sw_mallet.rda |binary lexicon-1.3.2/lexicon/data/sw_python.rda |binary lexicon-1.3.2/lexicon/inst/CITATION | 40 lexicon-1.3.2/lexicon/inst/dev_kit/test_valence_shifter.R | 100 lexicon-1.3.2/lexicon/man/available_data.Rd | 56 lexicon-1.3.2/lexicon/man/cliches.Rd | 84 lexicon-1.3.2/lexicon/man/common_names.Rd | 36 lexicon-1.3.2/lexicon/man/constraining_loughran_mcdonald.Rd | 66 lexicon-1.3.2/lexicon/man/emojis_sentiment.Rd | 90 lexicon-1.3.2/lexicon/man/freq_first_names.Rd | 50 lexicon-1.3.2/lexicon/man/freq_last_names.Rd | 48 lexicon-1.3.2/lexicon/man/function_words.Rd | 49 lexicon-1.3.2/lexicon/man/grady_augmented.Rd | 48 lexicon-1.3.2/lexicon/man/hash_emojis.Rd | 118 - lexicon-1.3.2/lexicon/man/hash_emojis_identifier.Rd | 120 - lexicon-1.3.2/lexicon/man/hash_emoticons.Rd | 70 lexicon-1.3.2/lexicon/man/hash_grady_pos.Rd | 94 lexicon-1.3.2/lexicon/man/hash_internet_slang.Rd | 54 lexicon-1.3.2/lexicon/man/hash_lemmas.Rd | 1136 +++++----- lexicon-1.3.2/lexicon/man/hash_nrc_emotions.Rd | 58 lexicon-1.3.2/lexicon/man/hash_sentiment_emojis.Rd | 88 lexicon-1.3.2/lexicon/man/hash_sentiment_huliu.Rd | 70 lexicon-1.3.2/lexicon/man/hash_sentiment_jockers.Rd | 48 lexicon-1.3.2/lexicon/man/hash_sentiment_jockers_rinker.Rd | 62 lexicon-1.3.2/lexicon/man/hash_sentiment_loughran_mcdonald.Rd | 80 lexicon-1.3.2/lexicon/man/hash_sentiment_nrc.Rd | 88 lexicon-1.3.2/lexicon/man/hash_sentiment_senticnet.Rd | 80 lexicon-1.3.2/lexicon/man/hash_sentiment_sentiword.Rd | 76 lexicon-1.3.2/lexicon/man/hash_sentiment_slangsd.Rd | 92 lexicon-1.3.2/lexicon/man/hash_sentiment_socal_google.Rd | 72 lexicon-1.3.2/lexicon/man/hash_valence_shifters.Rd | 88 lexicon-1.3.2/lexicon/man/key_contractions.Rd | 42 lexicon-1.3.2/lexicon/man/key_corporate_social_responsibility.Rd | 66 lexicon-1.3.2/lexicon/man/key_grade.Rd | 42 lexicon-1.3.2/lexicon/man/key_rating.Rd | 42 lexicon-1.3.2/lexicon/man/key_regressive_imagery.Rd | 142 - lexicon-1.3.2/lexicon/man/key_sentiment_jockers.Rd | 48 lexicon-1.3.2/lexicon/man/lexicon.Rd | 76 lexicon-1.3.2/lexicon/man/modal_loughran_mcdonald.Rd | 80 lexicon-1.3.2/lexicon/man/nrc_emotions.Rd | 90 lexicon-1.3.2/lexicon/man/pos_action_verb.Rd | 52 lexicon-1.3.2/lexicon/man/pos_df_irregular_nouns.Rd | 62 lexicon-1.3.2/lexicon/man/pos_df_pronouns.Rd | 56 lexicon-1.3.2/lexicon/man/pos_interjections.Rd | 38 lexicon-1.3.2/lexicon/man/pos_preposition.Rd | 30 lexicon-1.3.2/lexicon/man/profanity_alvarez.Rd | 46 lexicon-1.3.2/lexicon/man/profanity_arr_bad.Rd | 48 lexicon-1.3.2/lexicon/man/profanity_banned.Rd | 52 lexicon-1.3.2/lexicon/man/profanity_racist.Rd | 88 lexicon-1.3.2/lexicon/man/profanity_zac_anger.Rd | 50 lexicon-1.3.2/lexicon/man/sw_dolch.Rd | 52 lexicon-1.3.2/lexicon/man/sw_fry_100.Rd | 50 lexicon-1.3.2/lexicon/man/sw_fry_1000.Rd | 44 lexicon-1.3.2/lexicon/man/sw_fry_200.Rd | 50 lexicon-1.3.2/lexicon/man/sw_fry_25.Rd | 50 lexicon-1.3.2/lexicon/man/sw_jockers.Rd | 40 lexicon-1.3.2/lexicon/man/sw_loughran_mcdonald_long.Rd | 66 lexicon-1.3.2/lexicon/man/sw_loughran_mcdonald_short.Rd | 58 lexicon-1.3.2/lexicon/man/sw_lucene.Rd | 74 lexicon-1.3.2/lexicon/man/sw_mallet.Rd | 224 - lexicon-1.3.2/lexicon/man/sw_python.Rd | 102 171 files changed, 5336 insertions(+), 5174 deletions(-)
Title: A Functionally Oriented Interface for Integrating 'Julia' with R
Description: Allows to import functions and whole packages from 'Julia' in R.
Imported 'Julia' functions can directly be called as R functions.
Data structures can be translated between 'Julia' and R.
More details can also be found in the corresponding article
<doi:10.18637/jss.v101.i06>.
Author: Stefan Lenz [aut, cre] ,
Harald Binder [aut, ths] ,
Angelo D'Ambrosio [ctb] ,
June Choe [ctb] ,
Bjarke Hautop Kristensen [ctb]
Maintainer: Stefan Lenz <stefan-m-lenz@web.de>
Diff between JuliaConnectoR versions 1.1.5 dated 2026-01-08 and 1.1.6 dated 2026-08-31
DESCRIPTION | 16 ++++--- MD5 | 26 +++++------ R/connecting.R | 32 +++++++++----- R/main.R | 5 ++ R/writing.R | 32 ++++++++++---- inst/Julia/communicating.jl | 32 +++++++++++--- inst/Julia/evaluating.jl | 4 - inst/Julia/handling_dataframes.jl | 3 - inst/Julia/writing.jl | 32 +++++++------- inst/examples/iris-example/iris-example.R | 2 inst/examples/iris-example/iris-example.jl | 4 - man/JuliaConnectoR-package.Rd | 9 ++++ tests/testthat/helper.R | 9 ++++ tests/testthat/test.R | 64 +++++++++++++++++++++++++++-- 14 files changed, 202 insertions(+), 68 deletions(-)
More information about JuliaConnectoR at CRAN
Permanent link
Title: Functionalities for the 'INLA' Package
Description: Contain code to work with a C struct, in short cgeneric, to
define a Gaussian Markov random (GMRF) model. The cgeneric contain
code to specify GMRF elements such as the graph and the precision
matrix, and also the initial and prior for its parameters, useful for
model inference. It can be accessed from a C program and is the
recommended way to implement new GMRF models in the 'INLA' package
(<https://www.r-inla.org>). The 'INLAtools' implement functions to
evaluate each one of the model specifications from R. The implemented
functionalities leverage the use of 'cgeneric' models and provide a
way to debug the code as well to work with the prior for the model
parameters and to sample from it. The `generic0` can be used to
implement intrinsic models with the scaling as proposed in Sørbye &
Rue (2014) <doi:10.1016/j.spasta.2013.06.004>, and the required
constraints. A very useful functionality is the Kronecker product
method that creates a new model from multiple cgen [...truncated...]
Author: Elias Teixeira Krainski [cre, aut, cph] ,
Finn Lindgren [aut] ,
Haavard Rue’ [aut]
Maintainer: Elias Teixeira Krainski <elias.krainski@kaust.edu.sa>
Diff between INLAtools versions 0.1.4 dated 2026-05-04 and 0.1.5 dated 2026-08-31
DESCRIPTION | 10 - MD5 | 22 +- NAMESPACE | 18 + R/aaaaa.R | 2 R/cgeneric.R | 4 R/cgeneric_generic0.R | 2 R/cgeneric_get.R | 11 + R/kronecker.R | 39 +++- demo/kronecker.R | 4 man/cgeneric-class.Rd | 4 src/INLAtools.h | 56 +++-- src/cgeneric_kronecker.c | 444 +++++++++++++++++++++++------------------------ 12 files changed, 333 insertions(+), 283 deletions(-)
Title: Make 'ggplot2' Fully Accessible by Generating Alternative Text
Description: Generates concise alternative text for data visualizations created
with 'ggplot2'. Descriptions are produced by inspecting plot layers, labels,
scales, and facets, with support for multiple languages and alternative text
stored in plot metadata.
Author: Joseph Barbier [aut, cre, cph]
Maintainer: Joseph Barbier <joseph@ysunflower.com>
Diff between ggalttext versions 0.3.0 dated 2026-06-25 and 0.4.0 dated 2026-08-31
DESCRIPTION | 6 +- MD5 | 12 ++-- R/describe_helpers.R | 24 +++++++++ R/language.R | 3 + R/parse.R | 34 ++++++++++--- README.md | 26 ++++------ tests/testthat/test-generate-alt-text.R | 83 ++++++++++++++++++++++++++++++++ 7 files changed, 158 insertions(+), 30 deletions(-)
Title: Identifies Parameters in a Tree-Shaped SCM
Description: Implements the algorithm by Briefs and Bläser (2025) <https://openreview.net/forum?id=8PHOPPH35D>, based on the approach of Gupta and Bläser (2024) <doi:10.1609/aaai.v38i18.30023>. It determines, for a structural causal model (SCM) whose directed edges form a tree, whether each parameter is unidentifiable, 1-identifiable or 2-identifiable (other cases cannot occur), using a randomized algorithm with provable running time O(n^3 log^2 n).
Author: Yasmine Briefs [aut, cre],
Markus Blaeser [aut]
Maintainer: Yasmine Briefs <ybriefs@mpi-inf.mpg.de>
Diff between fasttreeid versions 1.0.1 dated 2025-11-18 and 1.0.2 dated 2026-08-31
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- src/algebra.h | 1 + src/random.cpp | 2 +- src/random.h | 1 + 5 files changed, 10 insertions(+), 8 deletions(-)
Title: Thermodynamic Calculations and Diagrams for Geochemistry
Description: An integrated set of tools for thermodynamic calculations in
aqueous geochemistry and geobiochemistry. Functions are provided for writing
balanced reactions to form species from user-selected basis species and for
calculating the standard molal properties of species and reactions, including
the standard Gibbs energy and equilibrium constant. Calculations of the
non-equilibrium chemical affinity and equilibrium chemical activity of species
can be portrayed on diagrams as a function of temperature, pressure, or
activity of basis species; in two dimensions, this gives a maximum affinity or
predominance diagram. The diagrams have formatted chemical formulas and axis
labels, and water stability limits can be added to Eh-pH, oxygen fugacity-
temperature, and other diagrams with a redox variable. The package has been
developed to handle common calculations in aqueous geochemistry, such as
solubility due to complexation of metal ions, mineral buffers of redox or pH,
and changing the basis spec [...truncated...]
Author: Jeffrey Dick [aut, cre]
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>
Diff between CHNOSZ versions 2.2.0 dated 2025-06-20 and 2.3.0 dated 2026-08-31
CHNOSZ-2.2.0/CHNOSZ/R/examples.R |only CHNOSZ-2.2.0/CHNOSZ/demo/gold.R |only CHNOSZ-2.2.0/CHNOSZ/demo/sum_S.R |only CHNOSZ-2.2.0/CHNOSZ/inst/TODO |only CHNOSZ-2.2.0/CHNOSZ/inst/extdata/OBIGT/SLOP98.csv |only CHNOSZ-2.2.0/CHNOSZ/inst/extdata/OBIGT/testing/IGEM.csv |only CHNOSZ-2.2.0/CHNOSZ/inst/tinytest/test-util.R |only CHNOSZ-2.2.0/CHNOSZ/src/count_letters.c |only CHNOSZ-2.3.0/CHNOSZ/DESCRIPTION | 8 CHNOSZ-2.3.0/CHNOSZ/MD5 | 284 - CHNOSZ-2.3.0/CHNOSZ/NAMESPACE | 12 CHNOSZ-2.3.0/CHNOSZ/R/AD.R | 4 CHNOSZ-2.3.0/CHNOSZ/R/JANAF.to.OBIGT.R |only CHNOSZ-2.3.0/CHNOSZ/R/add.OBIGT.R | 61 CHNOSZ-2.3.0/CHNOSZ/R/affinity.R | 42 CHNOSZ-2.3.0/CHNOSZ/R/basis.R | 5 CHNOSZ-2.3.0/CHNOSZ/R/diagram.R | 8 CHNOSZ-2.3.0/CHNOSZ/R/equilibrate.R | 4 CHNOSZ-2.3.0/CHNOSZ/R/info.R | 8 CHNOSZ-2.3.0/CHNOSZ/R/mosaic.R | 65 CHNOSZ-2.3.0/CHNOSZ/R/phosphorylate.R |only CHNOSZ-2.3.0/CHNOSZ/R/protein.info.R | 20 CHNOSZ-2.3.0/CHNOSZ/R/solubility.R | 78 CHNOSZ-2.3.0/CHNOSZ/R/subcrt.R | 67 CHNOSZ-2.3.0/CHNOSZ/R/thermo.R | 2 CHNOSZ-2.3.0/CHNOSZ/R/thermo.plot.R |only CHNOSZ-2.3.0/CHNOSZ/R/util.affinity.R | 106 CHNOSZ-2.3.0/CHNOSZ/R/util.data.R | 19 CHNOSZ-2.3.0/CHNOSZ/R/util.formula.R | 34 CHNOSZ-2.3.0/CHNOSZ/R/util.legend.R | 6 CHNOSZ-2.3.0/CHNOSZ/R/util.misc.R | 28 CHNOSZ-2.3.0/CHNOSZ/R/util.plot.R | 156 CHNOSZ-2.3.0/CHNOSZ/R/util.protein.R | 2 CHNOSZ-2.3.0/CHNOSZ/R/water.R | 2 CHNOSZ-2.3.0/CHNOSZ/README.md | 10 CHNOSZ-2.3.0/CHNOSZ/build/partial.rdb |binary CHNOSZ-2.3.0/CHNOSZ/build/vignette.rds |binary CHNOSZ-2.3.0/CHNOSZ/demo/00Index | 13 CHNOSZ-2.3.0/CHNOSZ/demo/ATP_hydrolysis.R |only CHNOSZ-2.3.0/CHNOSZ/demo/NaCl.R | 58 CHNOSZ-2.3.0/CHNOSZ/demo/Pourbaix.R | 2 CHNOSZ-2.3.0/CHNOSZ/demo/aluminum.R | 12 CHNOSZ-2.3.0/CHNOSZ/demo/arsenic.R | 81 CHNOSZ-2.3.0/CHNOSZ/demo/buffer.R | 2 CHNOSZ-2.3.0/CHNOSZ/demo/chalcocite.R |only CHNOSZ-2.3.0/CHNOSZ/demo/comproportionation.R | 9 CHNOSZ-2.3.0/CHNOSZ/demo/contour.R | 124 CHNOSZ-2.3.0/CHNOSZ/demo/demos.R |only CHNOSZ-2.3.0/CHNOSZ/demo/demos_png.R |only CHNOSZ-2.3.0/CHNOSZ/demo/examples.R |only CHNOSZ-2.3.0/CHNOSZ/demo/examples_png.R |only CHNOSZ-2.3.0/CHNOSZ/demo/glycinate.R | 1 CHNOSZ-2.3.0/CHNOSZ/demo/gold1.R |only CHNOSZ-2.3.0/CHNOSZ/demo/gold2.R |only CHNOSZ-2.3.0/CHNOSZ/demo/minsol.R | 38 CHNOSZ-2.3.0/CHNOSZ/demo/mosaic.R | 6 CHNOSZ-2.3.0/CHNOSZ/demo/neodymium.R |only CHNOSZ-2.3.0/CHNOSZ/demo/phosphorylate.R |only CHNOSZ-2.3.0/CHNOSZ/demo/potassium.R | 9 CHNOSZ-2.3.0/CHNOSZ/demo/references.R | 2 CHNOSZ-2.3.0/CHNOSZ/demo/saturation.R | 4 CHNOSZ-2.3.0/CHNOSZ/demo/sphalerite.R | 2 CHNOSZ-2.3.0/CHNOSZ/demo/sulfur.R |only CHNOSZ-2.3.0/CHNOSZ/demo/uranyl.R | 12 CHNOSZ-2.3.0/CHNOSZ/inst/CHECKLIST | 11 CHNOSZ-2.3.0/CHNOSZ/inst/NEWS.Rd | 457 + CHNOSZ-2.3.0/CHNOSZ/inst/doc/FAQ.R | 167 CHNOSZ-2.3.0/CHNOSZ/inst/doc/FAQ.Rmd | 196 CHNOSZ-2.3.0/CHNOSZ/inst/doc/FAQ.html | 2109 +++++-- CHNOSZ-2.3.0/CHNOSZ/inst/doc/OBIGT.R | 30 CHNOSZ-2.3.0/CHNOSZ/inst/doc/OBIGT.Rmd | 66 CHNOSZ-2.3.0/CHNOSZ/inst/doc/OBIGT.bib | 196 CHNOSZ-2.3.0/CHNOSZ/inst/doc/OBIGT.html | 4040 ++++++++++----- CHNOSZ-2.3.0/CHNOSZ/inst/doc/anintro.R | 108 CHNOSZ-2.3.0/CHNOSZ/inst/doc/anintro.Rmd | 63 CHNOSZ-2.3.0/CHNOSZ/inst/doc/anintro.html | 645 +- CHNOSZ-2.3.0/CHNOSZ/inst/doc/custom_data.html | 1207 +++- CHNOSZ-2.3.0/CHNOSZ/inst/doc/eos-regress.html | 209 CHNOSZ-2.3.0/CHNOSZ/inst/doc/multi-metal.R | 40 CHNOSZ-2.3.0/CHNOSZ/inst/doc/multi-metal.Rmd | 28 CHNOSZ-2.3.0/CHNOSZ/inst/doc/multi-metal.html | 2441 +++++---- CHNOSZ-2.3.0/CHNOSZ/inst/extdata/Berman/sympy.R | 4 CHNOSZ-2.3.0/CHNOSZ/inst/extdata/OBIGT/SLOP98-a.csv |only CHNOSZ-2.3.0/CHNOSZ/inst/extdata/OBIGT/SLOP98-b.csv |only CHNOSZ-2.3.0/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv | 107 CHNOSZ-2.3.0/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv | 213 CHNOSZ-2.3.0/CHNOSZ/inst/extdata/OBIGT/inorganic_liq.csv |only CHNOSZ-2.3.0/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv | 567 -- CHNOSZ-2.3.0/CHNOSZ/inst/extdata/OBIGT/organic_cr.csv | 7 CHNOSZ-2.3.0/CHNOSZ/inst/extdata/OBIGT/organic_gas.csv | 1 CHNOSZ-2.3.0/CHNOSZ/inst/extdata/misc/C-127.txt |only CHNOSZ-2.3.0/CHNOSZ/inst/extdata/misc/Fe-001.txt |only CHNOSZ-2.3.0/CHNOSZ/inst/extdata/misc/OBIGT_check.csv | 338 - CHNOSZ-2.3.0/CHNOSZ/inst/extdata/misc/S-004.txt |only CHNOSZ-2.3.0/CHNOSZ/inst/extdata/thermo/refs.csv | 114 CHNOSZ-2.3.0/CHNOSZ/inst/extdata/thermo/stoich.csv.xz |binary CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-AD.R | 39 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-EOSregress.R | 43 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-JANAF.to.OBIGT.R |only CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-S_liq.R |only CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-affinity.R | 31 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-diagram.R | 63 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-equilibrate.R | 6 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-logK.to.OBIGT.R | 49 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-makeup.R | 22 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-mix.R | 33 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-mod.buffer.R |only CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-mosaic.R | 22 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-nonideal.R | 13 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-phosphorylate.R |only CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-protein.info.R | 19 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-rank.affinity.R | 2 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-subcrt.R | 36 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-taxonomy.R |only CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-util.data.R | 26 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-util.expression.R | 30 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-util.formula.R |only CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-util.legend.R |only CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-util.misc.R |only CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-util.protein.R |only CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-util.units.R |only CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-util.water.R |only CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-water.R | 11 CHNOSZ-2.3.0/CHNOSZ/man/Berman.Rd | 10 CHNOSZ-2.3.0/CHNOSZ/man/CHNOSZ-package.Rd | 6 CHNOSZ-2.3.0/CHNOSZ/man/DEW.Rd | 4 CHNOSZ-2.3.0/CHNOSZ/man/EOSregress.Rd | 6 CHNOSZ-2.3.0/CHNOSZ/man/IAPWS95.Rd | 2 CHNOSZ-2.3.0/CHNOSZ/man/JANAF.to.OBIGT.Rd |only CHNOSZ-2.3.0/CHNOSZ/man/NaCl.Rd | 2 CHNOSZ-2.3.0/CHNOSZ/man/add.OBIGT.Rd | 12 CHNOSZ-2.3.0/CHNOSZ/man/affinity.Rd | 24 CHNOSZ-2.3.0/CHNOSZ/man/basis.Rd | 4 CHNOSZ-2.3.0/CHNOSZ/man/diagram.Rd | 22 CHNOSZ-2.3.0/CHNOSZ/man/equilibrate.Rd | 2 CHNOSZ-2.3.0/CHNOSZ/man/examples.Rd | 137 CHNOSZ-2.3.0/CHNOSZ/man/extdata.Rd | 48 CHNOSZ-2.3.0/CHNOSZ/man/ionize.aa.Rd | 6 CHNOSZ-2.3.0/CHNOSZ/man/logK.to.OBIGT.Rd | 9 CHNOSZ-2.3.0/CHNOSZ/man/mix.Rd | 4 CHNOSZ-2.3.0/CHNOSZ/man/mod.buffer.Rd | 6 CHNOSZ-2.3.0/CHNOSZ/man/mosaic.Rd | 26 CHNOSZ-2.3.0/CHNOSZ/man/nonideal.Rd | 18 CHNOSZ-2.3.0/CHNOSZ/man/phosphorylate.Rd |only CHNOSZ-2.3.0/CHNOSZ/man/protein.info.Rd | 10 CHNOSZ-2.3.0/CHNOSZ/man/solubility.Rd | 71 CHNOSZ-2.3.0/CHNOSZ/man/stack_mosaic.Rd | 8 CHNOSZ-2.3.0/CHNOSZ/man/subcrt.Rd | 30 CHNOSZ-2.3.0/CHNOSZ/man/thermo.Rd | 10 CHNOSZ-2.3.0/CHNOSZ/man/thermo.plot.Rd |only CHNOSZ-2.3.0/CHNOSZ/man/util.data.Rd | 6 CHNOSZ-2.3.0/CHNOSZ/man/util.formula.Rd | 2 CHNOSZ-2.3.0/CHNOSZ/man/util.legend.Rd | 10 CHNOSZ-2.3.0/CHNOSZ/man/util.plot.Rd | 71 CHNOSZ-2.3.0/CHNOSZ/man/util.protein.Rd | 2 CHNOSZ-2.3.0/CHNOSZ/man/util.water.Rd | 4 CHNOSZ-2.3.0/CHNOSZ/man/water.Rd | 22 CHNOSZ-2.3.0/CHNOSZ/src/H2O92D.f | 300 - CHNOSZ-2.3.0/CHNOSZ/vignettes/FAQ.Rmd | 196 CHNOSZ-2.3.0/CHNOSZ/vignettes/OBIGT.Rmd | 66 CHNOSZ-2.3.0/CHNOSZ/vignettes/OBIGT.bib | 196 CHNOSZ-2.3.0/CHNOSZ/vignettes/anintro.Rmd | 63 CHNOSZ-2.3.0/CHNOSZ/vignettes/multi-metal.Rmd | 28 CHNOSZ-2.3.0/CHNOSZ/vignettes/vig.bib | 8 164 files changed, 10330 insertions(+), 6336 deletions(-)
Title: A Byte-Pair-Encoding (BPE) Tokenizer for OpenAI's Large Language
Models
Description: A thin wrapper around the tiktoken-rs crate, allowing to encode text into Byte-Pair-Encoding (BPE) tokens and decode tokens back to text. This is useful to understand how Large Language Models (LLMs) perceive text.
Author: David Zimmermann-Kollenda [aut, cre],
Roger Zurawicki [aut] ,
Authors of the dependent Rust crates [aut]
Maintainer: David Zimmermann-Kollenda <david_j_zimmermann@hotmail.com>
Diff between rtiktoken versions 0.11.0.2 dated 2026-08-21 and 0.11.0.3 dated 2026-08-31
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ src/Makevars.in | 12 +++++++++--- src/Makevars.win.in | 13 +++++++++---- 5 files changed, 33 insertions(+), 14 deletions(-)
Title: Interface to the 'Pharmpy' 'Pharmacometrics' Library
Description: Interface to the 'Pharmpy' 'pharmacometrics' library. The 'Reticulate' package is used to interface Python from R.
Author: Rikard Nordgren [aut, cre, cph],
Stella Belin [aut, cph],
Mats O. Karlsson [sad],
Andrew C. Hooker [sad],
Xiaomei Chen [sad],
Sebastian Ueckert [sad] ,
Simon Buatois [rev],
Joao A. Abrantes [rev],
Emilie Schindler [rev],
F. Hoffmann-La Roche Ltd. [fn [...truncated...]
Maintainer: Rikard Nordgren <rikard.nordgren@uu.se>
Diff between pharmr versions 2.1.1 dated 2026-05-28 and 2.2.0 dated 2026-08-31
pharmr-2.1.1/pharmr/man/reset_indices_results.Rd |only pharmr-2.1.1/pharmr/man/set_unit.Rd |only pharmr-2.2.0/pharmr/DESCRIPTION | 16 pharmr-2.2.0/pharmr/MD5 | 77 pharmr-2.2.0/pharmr/NAMESPACE | 13 pharmr-2.2.0/pharmr/R/check_setup.R | 2 pharmr-2.2.0/pharmr/R/functions_wrapper.R | 2104 ++++------ pharmr-2.2.0/pharmr/R/install.R | 2 pharmr-2.2.0/pharmr/R/internals.R | 170 pharmr-2.2.0/pharmr/R/overloads.R | 7 pharmr-2.2.0/pharmr/R/utils.R | 28 pharmr-2.2.0/pharmr/R/zzz.R | 10 pharmr-2.2.0/pharmr/README.md | 2 pharmr-2.2.0/pharmr/man/add_administration.Rd |only pharmr-2.2.0/pharmr/man/add_arm.Rd |only pharmr-2.2.0/pharmr/man/add_observations.Rd |only pharmr-2.2.0/pharmr/man/annotate_unit.Rd |only pharmr-2.2.0/pharmr/man/calculate_bic.Rd | 12 pharmr-2.2.0/pharmr/man/calculate_epsilon_gradient_expression.Rd | 2 pharmr-2.2.0/pharmr/man/calculate_eta_gradient_expression.Rd | 2 pharmr-2.2.0/pharmr/man/convert_unit.Rd | 4 pharmr-2.2.0/pharmr/man/create_datainfo.Rd |only pharmr-2.2.0/pharmr/man/create_dataset_from_design.Rd |only pharmr-2.2.0/pharmr/man/create_symbol.Rd | 2 pharmr-2.2.0/pharmr/man/create_trial_design.Rd |only pharmr-2.2.0/pharmr/man/fit.Rd | 11 pharmr-2.2.0/pharmr/man/get_central_volume_and_clearance.Rd | 2 pharmr-2.2.0/pharmr/man/get_individual_prediction_expression.Rd | 2 pharmr-2.2.0/pharmr/man/get_observation_expression.Rd | 2 pharmr-2.2.0/pharmr/man/get_omegas.Rd | 2 pharmr-2.2.0/pharmr/man/get_population_prediction_expression.Rd | 2 pharmr-2.2.0/pharmr/man/get_sigmas.Rd | 2 pharmr-2.2.0/pharmr/man/get_thetas.Rd | 2 pharmr-2.2.0/pharmr/man/read_datainfo.Rd |only pharmr-2.2.0/pharmr/man/reset_dataset.Rd |only pharmr-2.2.0/pharmr/man/reset_index.Rd | 4 pharmr-2.2.0/pharmr/man/run_amd.Rd | 8 pharmr-2.2.0/pharmr/man/run_linearize.Rd | 12 pharmr-2.2.0/pharmr/man/run_qa.Rd | 6 pharmr-2.2.0/pharmr/man/run_retries.Rd | 8 pharmr-2.2.0/pharmr/man/set_covariates.Rd | 4 pharmr-2.2.0/pharmr/man/set_dataset.Rd | 8 pharmr-2.2.0/pharmr/man/set_index.Rd |only pharmr-2.2.0/pharmr/man/set_property.Rd | 2 pharmr-2.2.0/pharmr/man/write_datainfo.Rd |only pharmr-2.2.0/pharmr/tests/testthat/test-reset_index.R | 8 46 files changed, 1186 insertions(+), 1352 deletions(-)
Title: Predict and Map Oyster Growth Suitability from Environmental
Data
Description: Predicts spatial suitability for oyster growth from environmental
survey data using Analytic Hierarchy Process (AHP) weighted scoring.
Users supply sensor data from Acoustic Doppler Current Profilers (ADCP),
Conductivity-Temperature-Depth (CTD) sensors, bathymetric sonar, and
sidescan sonar, specify a target species, and receive per-location
suitability scores, a five-band 'GeoTIFF' heatmap for 'QGIS', contour
lines, and a formatted PDF or HTML report. Supports seventeen species across
global aquaculture regions, including Ostrea edulis, Magallana gigas,
Crassostrea virginica, Crassostrea hongkongensis, and thirteen further
species; see list_species(). Includes ocean acidification scoring via
in-house aragonite saturation state (Omega_arag) calculation using
Lueker et al. (2000) <doi:10.1016/S0304-4203(00)00022-0> and Mucci (1983)
<doi:10.1357/002224083788520153> equilibrium constants (no external
dependencies), variable impact diagnostics (variable_impact()), fine-scale
ha [...truncated...]
Author: T Tucker [aut, cre]
Maintainer: T Tucker <tristantucker48@gmail.com>
Diff between oystermapR versions 1.4.0 dated 2026-05-15 and 1.5.0 dated 2026-08-31
DESCRIPTION | 25 - MD5 | 192 +++++---- NAMESPACE | 6 NEWS.md | 88 ++++ R/anthropogenic.R | 16 R/aragonite.R |only R/area_summary.R |only R/backscatter.R | 38 - R/batch_compare.R | 20 - R/bayesian_update.R | 102 +++-- R/climate_projection.R | 31 - R/connectivity.R | 18 R/disease_risk.R | 20 - R/export_geotiff.R | 51 +- R/hab_risk.R | 22 - R/habitat_utils.R | 17 R/ingest_rasters.R | 9 R/ingest_sensors.R | 59 +- R/interpolation.R | 21 - R/larval_dispersal.R | 37 - R/planning.R | 32 - R/plot_tolerance.R |only R/predation_risk.R | 17 R/predict_oyster.R | 38 + R/report.R | 2 R/score_variables.R | 169 +++++++- R/seasonal_composite.R | 18 R/sediment_stability.R | 17 R/settlement.R | 18 R/spatial_smooth.R | 12 R/species_tolerances.R | 534 ++++++++++++++++++++++++++- R/summary_pdf.R | 11 R/survey_compare.R | 18 R/survey_qc.R | 30 - R/tidal_correction.R | 42 +- R/validate.R | 62 +-- R/variable_importance.R | 44 -- R/water_quality.R | 17 R/wave_exposure.R | 15 README.md | 183 ++++++++- inst/doc/example-bay-survey.R | 88 ++++ inst/doc/example-bay-survey.Rmd | 233 ++++++++++- inst/doc/example-bay-survey.html | 269 +++++++++++-- inst/extdata/example_bay_ctd.csv | 162 ++++---- inst/extdata/sample_survey.csv | 402 ++++++++++---------- man/add_intertidal_flag.Rd | 17 man/add_shellfish_classification.Rd | 17 man/add_suitability_ci.Rd | 10 man/analyse_connectivity.Rd | 14 man/area_summary.Rd |only man/assess_gear_feasibility.Rd | 11 man/auto_tidal_correct.Rd | 20 - man/calculate_aragonite.Rd |only man/classify_substrate_from_backscatter.Rd | 20 - man/compare_species.Rd | 20 - man/compare_surveys.Rd | 18 man/composite_seasonal.Rd | 14 man/correct_to_chart_datum.Rd | 22 - man/dot-auto_calculate_aragonite.Rd |only man/dot-estimate_cell_size_m.Rd |only man/dot-run_patch_analysis.Rd |only man/estimate_chlorophyll_from_backscatter.Rd | 18 man/export_contours.Rd | 9 man/export_geotiff.Rd | 23 - man/generate_report.Rd | 2 man/generate_summary_pdf.Rd | 11 man/get_tolerance_posteriors.Rd | 4 man/identify_resilient_sites.Rd | 9 man/interpolate_survey.Rd | 16 man/load_tolerance_update.Rd | 35 + man/merge_sensor_data.Rd | 19 man/permutation_importance.Rd | 20 - man/plot_tolerance.Rd |only man/predict_oyster.Rd | 31 - man/project_suitability.Rd | 20 - man/qc_survey_data.Rd | 25 - man/read_aanderaa_csv.Rd | 2 man/read_generic_csv.Rd | 14 man/read_nortek_adcp.Rd | 7 man/read_nortek_aquadopp.Rd | 2 man/read_rdi_adcp.Rd | 2 man/read_sonar_tif.Rd | 2 man/read_soundings_xyz.Rd | 7 man/reset_tolerance_update.Rd | 2 man/save_tolerance_update.Rd | 32 + man/score_anthropogenic_disturbance.Rd | 16 man/score_disease_risk.Rd | 15 man/score_economic_viability.Rd | 19 man/score_hab_risk.Rd | 22 - man/score_larval_connectivity.Rd | 30 - man/score_predation_risk.Rd | 17 man/score_sediment_stability.Rd | 17 man/score_settlement.Rd | 18 man/score_wave_exposure.Rd | 15 man/sensitivity_analysis.Rd | 24 - man/smooth_suitability.Rd | 12 man/spatial_block_cv.Rd | 27 - man/stack_surveys.Rd | 13 man/update_species_tolerances.Rd | 37 - man/validate_against_records.Rd | 25 - man/variable_impact.Rd |only vignettes/example-bay-survey.Rmd | 233 ++++++++++- 102 files changed, 2832 insertions(+), 1408 deletions(-)
Title: Optimal Two-Stage Designs for Ordered Categorical Outcomes
Description: Functions to design and simulate optimal two-stage randomized
controlled trials (RCTs) with ordered categorical outcomes, supporting
rank-based tests and group-sequential decision rules. Methods build on
classical and modern rank tests and two-stage/Group-Sequential designs,
e.g., Park (2025) <doi: 10.1371/journal.pone.0318211>. The functions
'rule()', 'op()' and 'design_table()' provide a single entry point for
constructing designs, evaluating their operating characteristics, and
tabulating several designs at once. The earlier functions, one for each
combination of test statistic and stopping rule, are retained and still
return the same values, but they are deprecated: each warns and names its
replacement, and they will be removed in the next version. Please see the
package reference manual and the vignette for details.
Author: Yeonhee Park [aut, cre],
Yudi Wang [aut],
Zhanpeng Xu [aut]
Maintainer: Yeonhee Park <yeonheepark@skku.edu>
Diff between OptOTrials versions 1.0.2 dated 2025-09-05 and 1.0.3 dated 2026-08-31
DESCRIPTION | 20 ++++-- MD5 | 116 ++++++++++++++++++++---------------- NAMESPACE | 30 +++++---- NEWS.md |only R/Decision_rule_M.F.R | 6 + R/Decision_rule_M.FS.R | 28 ++++++-- R/Decision_rule_M_1stage.R | 6 + R/Decision_rule_S.F.R | 10 ++- R/Decision_rule_S.FS.R | 35 ++++++++-- R/Decision_rule_S_1stage.R | 10 ++- R/Decision_rule_W.F.R | 6 + R/Decision_rule_W.FS.R | 26 ++++++-- R/Decision_rule_W_1stage.R | 6 + R/Proportional_odds_assumption.R | 43 ++++++++----- R/QR_fun.R | 4 + R/V_S.over.nk.R | 4 + R/W_W.R | 4 + R/deprecated.R |only R/effect-size.R |only R/op.1stage.R | 6 + R/op.F.R | 6 + R/op.FS.R | 15 +++- R/op.R |only R/p2_fun.R | 5 + R/p_minus.R | 4 + R/p_plus.R | 4 + R/pq_fun.R | 4 + R/print-methods.R |only R/rule.R |only R/ruleF.R | 24 ++++--- R/ruleFS.R | 90 ++++++++++++++------------- R/theta.R | 4 + R/utils-validate.R |only build/partial.rdb |binary build/vignette.rds |only inst |only man/Decision_rule_M.F.Rd | 38 ++++++++--- man/Decision_rule_M.FS.Rd | 44 +++++++++---- man/Decision_rule_M_1stage.Rd | 26 ++++++-- man/Decision_rule_S.F.Rd | 35 ++++++++-- man/Decision_rule_S.FS.Rd | 41 +++++++++--- man/Decision_rule_S_1stage.Rd | 26 ++++++-- man/Decision_rule_W.F.Rd | 35 ++++++++-- man/Decision_rule_W.FS.Rd | 41 +++++++++--- man/Decision_rule_W_1stage.Rd | 23 +++++-- man/OptOTrials-deprecated.Rd |only man/OptOTrials-package.Rd | 10 ++- man/Proportional_odds_assumption.Rd | 19 ++++- man/QR_fun.Rd | 12 ++- man/V_S.over.nk.Rd | 15 +++- man/W_W.Rd | 10 ++- man/design_table.Rd |only man/op.1stage.Rd | 34 ++++++++-- man/op.F.Rd | 39 +++++++++--- man/op.FS.Rd | 42 ++++++++++--- man/op.Rd |only man/p2_fun.Rd | 6 + man/p_minus.Rd | 10 ++- man/p_plus.Rd | 10 ++- man/pq_fun.Rd | 10 ++- man/rule.Rd |only man/ruleF.Rd | 34 ++++++++-- man/ruleFS.Rd | 34 ++++++++-- man/theta.Rd | 9 +- vignettes |only 65 files changed, 794 insertions(+), 325 deletions(-)
Title: Markov Decision Processes Toolbox
Description: The Markov Decision Processes (MDP) toolbox proposes functions related to the resolution of discrete-time Markov Decision Processes: finite horizon, value iteration, policy iteration, linear programming algorithms with some variants and also proposes some functions related to Reinforcement Learning.
Author: Iadine Chades [aut],
Guillaume Chapron [aut, cre],
Marie-Josee Cros [aut],
Frederick Garcia [aut],
Regis Sabbadin [aut]
Maintainer: Guillaume Chapron <gchapron@carnivoreconservation.org>
Diff between MDPtoolbox versions 4.0.3 dated 2017-03-03 and 4.0.4 dated 2026-08-31
DESCRIPTION | 32 ++++++++++++++++++++++++++------ MD5 | 4 ++-- man/mdp_example_forest.Rd | 2 +- 3 files changed, 29 insertions(+), 9 deletions(-)
Title: Advice on R Package Building
Description: Give advice about good practices when building R packages.
Advice includes functions and syntax to avoid, package structure, code
complexity, code formatting, etc.
Author: Mark Padgham [aut, cre] ,
Ascent Digital Services UK Limited [cph] ,
Karina Marks [aut] ,
Daniel de Bortoli [aut] ,
Gabor Csardi [aut],
Hannah Frick [aut],
Owen Jones [aut] ,
Hannah Alexander [aut],
Ana Simmons [ctb] ,
Fabian Scheipl [ctb] ,
Athanasi [...truncated...]
Maintainer: Mark Padgham <mark@ropensci.org>
Diff between goodpractice versions 1.1.0 dated 2026-06-05 and 1.2.0 dated 2026-08-31
goodpractice-1.1.0/goodpractice/tests/testthat/good_tidyverse/R/good_style.R |only goodpractice-1.1.0/goodpractice/tests/testthat/good_tidyverse/tests/testthat/test-good_style.R |only goodpractice-1.2.0/goodpractice/DESCRIPTION | 10 goodpractice-1.2.0/goodpractice/MD5 | 109 +++--- goodpractice-1.2.0/goodpractice/NAMESPACE | 36 +- goodpractice-1.2.0/goodpractice/NEWS.md | 179 +++++----- goodpractice-1.2.0/goodpractice/R/api.R | 92 +++++ goodpractice-1.2.0/goodpractice/R/chk_code_structure.R | 6 goodpractice-1.2.0/goodpractice/R/chk_description.R | 38 +- goodpractice-1.2.0/goodpractice/R/chk_lintr.R | 7 goodpractice-1.2.0/goodpractice/R/chk_rd.R | 2 goodpractice-1.2.0/goodpractice/R/chk_roxygen2.R | 8 goodpractice-1.2.0/goodpractice/R/chk_tidyverse.R | 22 - goodpractice-1.2.0/goodpractice/R/chk_urlchecker.R | 2 goodpractice-1.2.0/goodpractice/R/customization.R | 1 goodpractice-1.2.0/goodpractice/R/gp.R | 11 goodpractice-1.2.0/goodpractice/R/lists.R | 7 goodpractice-1.2.0/goodpractice/R/package.R | 1 goodpractice-1.2.0/goodpractice/R/prep_lintr.R | 1 goodpractice-1.2.0/goodpractice/R/prep_roxygen2.R | 3 goodpractice-1.2.0/goodpractice/R/prep_urlchecker.R | 2 goodpractice-1.2.0/goodpractice/R/print.R | 1 goodpractice-1.2.0/goodpractice/R/treesitter.R | 2 goodpractice-1.2.0/goodpractice/README.md | 99 +++-- goodpractice-1.2.0/goodpractice/build/vignette.rds |binary goodpractice-1.2.0/goodpractice/inst/doc/custom_checks.html | 6 goodpractice-1.2.0/goodpractice/inst/doc/goodpractice.Rmd | 4 goodpractice-1.2.0/goodpractice/inst/doc/goodpractice.html | 48 +- goodpractice-1.2.0/goodpractice/inst/doc/gp4developers.R |only goodpractice-1.2.0/goodpractice/inst/doc/gp4developers.Rmd |only goodpractice-1.2.0/goodpractice/inst/doc/gp4developers.html |only goodpractice-1.2.0/goodpractice/inst/skills |only goodpractice-1.2.0/goodpractice/man/all_check_groups.Rd | 10 goodpractice-1.2.0/goodpractice/man/all_checks.Rd | 10 goodpractice-1.2.0/goodpractice/man/checks.Rd | 3 goodpractice-1.2.0/goodpractice/man/checks_by_group.Rd | 10 goodpractice-1.2.0/goodpractice/man/customization.Rd | 7 goodpractice-1.2.0/goodpractice/man/default_checks.Rd | 10 goodpractice-1.2.0/goodpractice/man/describe_check.Rd | 10 goodpractice-1.2.0/goodpractice/man/describe_check_groups.Rd | 10 goodpractice-1.2.0/goodpractice/man/export_json.Rd | 6 goodpractice-1.2.0/goodpractice/man/failed_checks.Rd | 3 goodpractice-1.2.0/goodpractice/man/failed_positions.Rd | 7 goodpractice-1.2.0/goodpractice/man/goodpractice-package.Rd | 4 goodpractice-1.2.0/goodpractice/man/gp.Rd | 5 goodpractice-1.2.0/goodpractice/man/learn_skill_gp.Rd |only goodpractice-1.2.0/goodpractice/man/print.goodPractice.Rd | 6 goodpractice-1.2.0/goodpractice/man/results.Rd | 8 goodpractice-1.2.0/goodpractice/man/tidyverse_checks.Rd | 10 goodpractice-1.2.0/goodpractice/man/use_skill_gp.Rd |only goodpractice-1.2.0/goodpractice/tests/testthat/_snaps/describe-check.md | 3 goodpractice-1.2.0/goodpractice/tests/testthat/good_tidyverse/R/good-style_name.R |only goodpractice-1.2.0/goodpractice/tests/testthat/good_tidyverse/tests/testthat/test-good-style_name.R |only goodpractice-1.2.0/goodpractice/tests/testthat/helper-dotfiles.R |only goodpractice-1.2.0/goodpractice/tests/testthat/test-api.R | 8 goodpractice-1.2.0/goodpractice/tests/testthat/test-check-selection.R | 4 goodpractice-1.2.0/goodpractice/tests/testthat/test-gp.R | 45 -- goodpractice-1.2.0/goodpractice/tests/testthat/test-integrity.R | 3 goodpractice-1.2.0/goodpractice/tests/testthat/test-skill-gp.R |only goodpractice-1.2.0/goodpractice/tests/testthat/test-tidyverse.R | 17 goodpractice-1.2.0/goodpractice/vignettes/goodpractice.Rmd | 4 goodpractice-1.2.0/goodpractice/vignettes/gp4developers.Rmd |only 62 files changed, 597 insertions(+), 303 deletions(-)
Title: Generalized Additive Latent and Mixed Models
Description: Estimates generalized additive latent and
mixed models using maximum marginal likelihood,
as defined in Sorensen et al. (2023)
<doi:10.1007/s11336-023-09910-z>, which is an extension of Rabe-Hesketh and
Skrondal (2004)'s unifying framework for multilevel latent variable
modeling <doi:10.1007/BF02295939>. Efficient computation is done using sparse
matrix methods, Laplace approximation, and automatic differentiation. The
framework includes generalized multilevel models with heteroscedastic
residuals, mixed response types, factor loadings, smoothing splines,
crossed random effects, and combinations thereof. Syntax for model
formulation is close to 'lme4' (Bates et al. (2015)
<doi:10.18637/jss.v067.i01>) and 'PLmixed' (Rockwood and Jeon (2019)
<doi:10.1080/00273171.2018.1516541>).
Author: Oeystein Soerensen [aut, cre] ,
Douglas Bates [ctb],
Ben Bolker [ctb],
Martin Maechler [ctb],
Allan Leal [ctb],
Fabian Scheipl [ctb],
Steven Walker [ctb],
Simon Wood [ctb]
Maintainer: Oeystein Soerensen <oystein.sorensen@psykologi.uio.no>
Diff between galamm versions 0.4.0 dated 2025-12-21 and 0.4.1 dated 2026-08-31
DESCRIPTION | 14 MD5 | 231 +++++++-------- NAMESPACE | 50 +-- NEWS.md |only R/galamm-package.R | 2 README.md | 75 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/galamm.Rmd | 38 +- inst/doc/galamm.html | 113 +++---- inst/doc/glmm_factor.Rmd | 18 - inst/doc/glmm_factor.html | 68 ++-- inst/doc/latent_observed_interaction.Rmd | 12 inst/doc/latent_observed_interaction.html | 29 - inst/doc/lmm_factor.Rmd | 77 ++--- inst/doc/lmm_factor.html | 152 ++++----- inst/doc/lmm_heteroscedastic.Rmd | 6 inst/doc/lmm_heteroscedastic.html | 11 inst/doc/mixed_response.Rmd | 26 - inst/doc/mixed_response.html | 62 +--- inst/doc/optimization.Rmd | 12 inst/doc/optimization.html | 23 - inst/doc/posterior_sampling.Rmd | 2 inst/doc/posterior_sampling.html | 11 inst/doc/scaling.Rmd | 8 inst/doc/scaling.html | 23 - inst/doc/semiparametric.Rmd | 88 ++--- inst/doc/semiparametric.html | 188 ++++++------ man/VarCorr.Rd | 44 +- man/anova.galamm.Rd | 12 man/appraise.galamm.Rd | 44 +- man/coef.galamm.Rd | 44 +- man/cognition.Rd | 2 man/confint.galamm.Rd | 44 +- man/derivatives.galamm.Rd | 44 +- man/deviance.galamm.Rd | 44 +- man/diet.Rd | 2 man/draw.galamm.Rd | 12 man/epilep.Rd | 2 man/extract_optim_parameters.galamm.Rd | 4 man/factor_loadings.galamm.Rd | 44 +- man/family.galamm.Rd | 44 +- man/figures/README-unnamed-chunk-9-1.png |binary man/fitted.galamm.Rd | 44 +- man/fixef.Rd | 44 +- man/formula.galamm.Rd | 44 +- man/galamm-package.Rd | 11 man/galamm.Rd | 8 man/galammObject.Rd | 12 man/galamm_control.Rd | 8 man/gfam.Rd | 8 man/hsced.Rd | 2 man/latent_covariates.Rd | 2 man/latent_covariates_long.Rd | 2 man/lifespan.Rd | 2 man/llikAIC.Rd | 44 +- man/logLik.galamm.Rd | 44 +- man/model.frame.galamm.Rd | 44 +- man/mresp.Rd | 2 man/mresp_hsced.Rd | 2 man/nobs.galamm.Rd | 44 +- man/plot.galamm.Rd | 4 man/plot_smooth.galamm.Rd | 12 man/predict.galamm.Rd | 44 +- man/print.VarCorr.galamm.Rd | 44 +- man/print.galamm.Rd | 12 man/print.summary.galamm.Rd | 12 man/qqmath.galamm.Rd | 4 man/ranef.galamm.Rd | 44 +- man/residuals.galamm.Rd | 44 +- man/response.Rd | 44 +- man/sigma.galamm.Rd | 44 +- man/sl.Rd | 8 man/summary.galamm.Rd | 12 man/t2l.Rd | 8 man/vcov.galamm.Rd | 44 +- tests/testthat/_snaps/galamm-lmm.md | 16 - vignettes/galamm.Rmd | 38 +- vignettes/glmm_factor.Rmd | 18 - vignettes/glmm_factor_binomial_diagnostic-1.png |binary vignettes/glmm_factor_poisson_diagnostic-1.png |binary vignettes/latent-observed-smooth-1.png |binary vignettes/latent_observed_interaction.Rmd | 12 vignettes/lmm_factor.Rmd | 77 ++--- vignettes/lmm_factor_diagnostic_plot-1.png |binary vignettes/lmm_heteroscedastic.Rmd | 6 vignettes/mixed_response.Rmd | 26 - vignettes/optimization.Rmd | 12 vignettes/posterior_sampling.Rmd | 2 vignettes/scaling-glmm-plot-1.png |binary vignettes/scaling-hsced-plot-1.png |binary vignettes/scaling-lmm-plot-1.png |binary vignettes/scaling-semiparametric-binomial-plot-1.png |binary vignettes/scaling-semiparametric-gaussian-plot-1.png |binary vignettes/scaling.Rmd | 8 vignettes/semiparametric-gamm-binomial-1.png |binary vignettes/semiparametric-gamm4-binomial-1.png |binary vignettes/semiparametric-gaussian-by-factor1-1.png |binary vignettes/semiparametric-gaussian-by-factor2-1.png |binary vignettes/semiparametric-gaussian-factor-1.png |binary vignettes/semiparametric-gaussian-gamm-smooth1-1.png |binary vignettes/semiparametric-gaussian-gamm-smooth2-1.png |binary vignettes/semiparametric-gaussian-gamm-smooth2-2.png |binary vignettes/semiparametric-gaussian-gamm4-diagnostic-1.png |binary vignettes/semiparametric-gaussian-gamm4-smooth-1.png |binary vignettes/semiparametric-mixed-by-factor1-1.png |binary vignettes/semiparametric-mixed-by-factor2-1.png |binary vignettes/semiparametric-spaghetti-plot-1.png |binary vignettes/semiparametric.Rmd | 88 ++--- vignettes/unnamed-chunk-10-1.png |binary vignettes/unnamed-chunk-12-1.png |binary vignettes/unnamed-chunk-15-1.png |binary vignettes/unnamed-chunk-20-1.png |binary vignettes/unnamed-chunk-28-1.png |binary vignettes/unnamed-chunk-29-1.png |binary vignettes/unnamed-chunk-3-1.png |binary vignettes/unnamed-chunk-6-1.png |binary 117 files changed, 1365 insertions(+), 1410 deletions(-)
Title: String Interpolation for Documents, Reports and Apps
Description: Extra strength 'glue' for data-driven templates. String
interpolation for 'Shiny' apps or 'R Markdown' and 'knitr'-powered
'Quarto' documents, built on the 'glue' and 'whisker' packages.
Author: Garrick Aden-Buie [aut, cre] ,
Kushagra Gour [ctb] ,
The mustache.js community [ctb]
Maintainer: Garrick Aden-Buie <garrick@adenbuie.com>
This is a re-admission after prior archival of version 1.0.0 dated 2023-09-19
Diff between epoxy versions 1.0.0 dated 2023-09-19 and 1.0.1 dated 2026-08-31
DESCRIPTION | 11 +- MD5 | 108 ++++++++++++------------ NAMESPACE | 8 + NEWS.md | 5 + R/engines.R | 26 +++-- R/epoxy.R | 29 ++++-- R/epoxy_transform_html.R | 17 ++- R/epoxy_transform_inline.R | 64 +++++++------- R/epoxy_use.R | 8 + R/shiny.R | 40 ++++++-- R/transformers.R | 52 ++++++++--- R/utils-knitr.R | 4 R/utils.R | 19 +++- R/zzz.R | 5 - README.md | 2 build/vignette.rds |binary inst/doc/epoxy-report.Rmd | 4 inst/doc/epoxy-report.html | 17 ++- inst/doc/epoxy-script.html | 1 inst/doc/epoxy-shiny.html | 25 ++--- inst/doc/inline-reporting.Rmd | 4 inst/doc/inline-reporting.html | 13 +- inst/examples/word-list/server.R | 40 +++++--- inst/examples/word-list/ui.R | 46 +++++----- man/epoxy-package.Rd | 5 + man/epoxy.Rd | 4 man/epoxy_mustache.Rd | 4 man/epoxy_transform.Rd | 6 - man/epoxy_transform_html.Rd | 8 - man/epoxy_transform_inline.Rd | 10 +- man/epoxy_transform_one_shot.Rd | 2 man/epoxy_use.Rd | 2 man/fragments/setup.Rmd | 2 man/render_epoxy.Rd | 4 man/ui_epoxy_html.Rd | 6 - man/ui_epoxy_markdown.Rd | 10 +- man/ui_epoxy_mustache.Rd | 12 +- man/use_epoxy_knitr_engines.Rd | 2 tests/testthat/_snaps/epoxy_transform_inline.md | 6 - tests/testthat/_snaps/transformers.md | 2 tests/testthat/apps/no-shiny/app.R | 4 tests/testthat/helpers.R | 29 ++++-- tests/testthat/test-engines.R | 17 ++- tests/testthat/test-epoxy.R | 13 ++ tests/testthat/test-epoxy_transform_html.R | 16 ++- tests/testthat/test-epoxy_transform_inline.R | 4 tests/testthat/test-epoxy_use.R | 11 +- tests/testthat/test-shiny.R | 44 +++++++-- tests/testthat/test-shiny_ui_epoxy_html-list.R | 6 - tests/testthat/test-shiny_ui_epoxy_markdown.R | 1 tests/testthat/test-shiny_ui_epoxy_mustache.R | 1 tests/testthat/test-shiny_word-list.R | 1 tests/testthat/test-transformers.R | 33 ++++++- vignettes/epoxy-report.Rmd | 4 vignettes/inline-reporting.Rmd | 4 55 files changed, 501 insertions(+), 320 deletions(-)
Title: Extract Subsequences from GenBank Annotations
Description: Extraction of subsequences into FASTA files from GenBank annotations where gene names may vary among accessions. Borstein & O'Meara (2018) <doi:10.7717/peerj.5179>.
Author: Samuel R. Borstein [aut, cre] ,
Brian O'Meara [aut]
Maintainer: Samuel R. Borstein <sam@borstein.com>
Diff between AnnotationBustR versions 1.3.0 dated 2020-09-24 and 2.0 dated 2026-08-31
DESCRIPTION | 40 +- MD5 | 58 +-- NAMESPACE | 2 R/AnnotationBust.R | 609 ++++++++++----------------------- R/DataDoc.R | 30 - R/FindLongestSeq.R | 67 ++- R/HelperFunctions.R |only R/MergeSearchTerms.R | 55 +- R/globals.R |only R/pkgname.R | 7 build/vignette.rds |binary data/cpDNAterms.RData |binary data/mtDNAterms.RData |binary data/mtDNAtermsPlants.RData |binary data/rDNAterms.RData |binary inst/CITATION | 39 -- inst/doc/AnnotationBustR-vignette.R | 12 inst/doc/AnnotationBustR-vignette.Rmd | 179 ++++----- inst/doc/AnnotationBustR-vignette.html | 604 ++++++++++++++++++++++---------- man/AnnotationBust.Rd | 90 ++-- man/AnnotationBustR.Rd | 7 man/FindLongestSeq.Rd | 12 man/MergeSearchTerms.Rd | 47 +- man/cpDNAterms.Rd | 8 man/mtDNAterms.Rd | 8 man/mtDNAtermsPlants.Rd | 6 man/rDNAterms.Rd | 8 tests/testthat/test_AnnotationBust.R | 34 - tests/testthat/test_FindLongestSeq.R | 14 tests/testthat/test_MergeSearchTerms.R | 33 - vignettes/AnnotationBustR-vignette.Rmd | 179 ++++----- 31 files changed, 1091 insertions(+), 1057 deletions(-)
More information about AnnotationBustR at CRAN
Permanent link
Title: A Compendium of Bayesian Statistical Routines Written in 'C++'
Description: This is a compendium of 'C++' routines useful for Bayesian statistics. We steal
other people's 'C++' code, repurpose it, and export it so developers of 'R'
packages can use it in their 'C++' code. We actually don't steal anything, or
claim that Thomas Bayes did, but copy code that is compatible with our GPL 3
licence, fully acknowledging the authorship of the original code.
Author: Tomasz Wozniak [aut, cre] ,
Xiaolei Wang [aut] ,
Longcan Li [aut] ,
Jianying Shelly Xie [aut] ,
Filip Reierson [aut] ,
Kenyon Ng [aut]
Maintainer: Tomasz Wozniak <wozniak.tom@pm.me>
Diff between StealLikeBayes versions 1.0 dated 2025-12-02 and 2.0 dated 2026-08-31
StealLikeBayes-1.0/StealLikeBayes/R/rnorm1_precision_sampler.R |only StealLikeBayes-1.0/StealLikeBayes/inst/tinytest/test_rnorm1_precision_sampler.R |only StealLikeBayes-1.0/StealLikeBayes/man/rnorm1_precision_sampler.Rd |only StealLikeBayes-1.0/StealLikeBayes/src/rnorm1_precision_sampler.cpp |only StealLikeBayes-1.0/StealLikeBayes/src/rnorm1_precision_sampler.h |only StealLikeBayes-2.0/StealLikeBayes/DESCRIPTION | 14 StealLikeBayes-2.0/StealLikeBayes/MD5 | 55 +- StealLikeBayes-2.0/StealLikeBayes/NAMESPACE | 4 StealLikeBayes-2.0/StealLikeBayes/NEWS.md | 11 StealLikeBayes-2.0/StealLikeBayes/R/rgennorm.R | 2 StealLikeBayes-2.0/StealLikeBayes/R/rgig1.R |only StealLikeBayes-2.0/StealLikeBayes/R/rig2.R |only StealLikeBayes-2.0/StealLikeBayes/R/rmvnorm1_precision_sampler.R |only StealLikeBayes-2.0/StealLikeBayes/R/sample_variances_horseshoe.R | 25 + StealLikeBayes-2.0/StealLikeBayes/R/sample_variances_normal_gamma.R | 19 StealLikeBayes-2.0/StealLikeBayes/README.md | 10 StealLikeBayes-2.0/StealLikeBayes/build |only StealLikeBayes-2.0/StealLikeBayes/inst/include/StealLikeBayes_RcppExports.h | 89 +++- StealLikeBayes-2.0/StealLikeBayes/inst/tinytest/test_rgig1.R |only StealLikeBayes-2.0/StealLikeBayes/inst/tinytest/test_rig2.R |only StealLikeBayes-2.0/StealLikeBayes/inst/tinytest/test_rmvnorm1_precision_sampler.R |only StealLikeBayes-2.0/StealLikeBayes/man/StealLikeBayes-package.Rd | 13 StealLikeBayes-2.0/StealLikeBayes/man/rgennorm.Rd | 2 StealLikeBayes-2.0/StealLikeBayes/man/rgig1.Rd |only StealLikeBayes-2.0/StealLikeBayes/man/rig2.Rd |only StealLikeBayes-2.0/StealLikeBayes/man/rmvnorm1_precision_sampler.Rd |only StealLikeBayes-2.0/StealLikeBayes/man/sample_variances_horseshoe.Rd | 24 - StealLikeBayes-2.0/StealLikeBayes/man/sample_variances_normal_gamma.Rd | 17 StealLikeBayes-2.0/StealLikeBayes/src/RcppExports.cpp | 200 +++++++--- StealLikeBayes-2.0/StealLikeBayes/src/rgig1.cpp |only StealLikeBayes-2.0/StealLikeBayes/src/rgig1.h |only StealLikeBayes-2.0/StealLikeBayes/src/rig2.cpp |only StealLikeBayes-2.0/StealLikeBayes/src/rig2.h |only StealLikeBayes-2.0/StealLikeBayes/src/rmvnorm1_precision_sampler.cpp |only StealLikeBayes-2.0/StealLikeBayes/src/rmvnorm1_precision_sampler.h |only StealLikeBayes-2.0/StealLikeBayes/src/sample_variances_horseshoe.cpp | 18 StealLikeBayes-2.0/StealLikeBayes/src/sample_variances_horseshoe.h | 4 StealLikeBayes-2.0/StealLikeBayes/src/sample_variances_normal_gamma.cpp | 25 - StealLikeBayes-2.0/StealLikeBayes/src/sample_variances_normal_gamma.h | 4 39 files changed, 396 insertions(+), 140 deletions(-)
More information about StealLikeBayes at CRAN
Permanent link
Title: Rational Approximations of Fractional Stochastic Partial
Differential Equations
Description: Functions that compute rational approximations of fractional elliptic stochastic partial differential equations. The package also contains functions for common statistical usage of these approximations. The main references for rSPDE are Bolin, Simas and Xiong (2023) <doi:10.1080/10618600.2023.2231051> for the covariance-based method and Bolin and Kirchner (2020) <doi:10.1080/10618600.2019.1665537> for the operator-based rational approximation. These can be generated by the citation function in R.
Author: David Bolin [cre, aut],
Alexandre Simas [aut],
Finn Lindgren [ctb]
Maintainer: David Bolin <davidbolin@gmail.com>
Diff between rSPDE versions 2.5.2 dated 2026-01-26 and 2.6.0 dated 2026-08-31
DESCRIPTION | 19 MD5 | 99 +-- NAMESPACE | 85 +- NEWS.md | 16 R/fractional.computations.R | 86 ++ R/fractional.operators.R | 14 R/hybrid.spde.R |only R/inla_rspde.R | 98 +-- R/inla_rspde_1d.R | 53 - R/inla_rspde_anisotropic.R | 24 R/inla_rspde_hybrid.R |only R/inla_rspde_intrinsic.R | 46 - R/inla_rspde_spacetime.R | 27 R/inla_safe.R |only R/inlabru_rspde.R | 108 +-- R/posterior_crossvalidation.R |only R/rSPDE-package.R | 13 R/rspde_lme.R | 419 ++++++++++-- R/util.R | 683 ++++++++++++++++++--- build/vignette.rds |binary demo |only inst/doc/rSPDE_package.html | 4 man/augment.rspde_lme.Rd | 2 man/bru_get_mapper.inla_rspde.Rd | 17 man/glance.rspde_lme.Rd | 4 man/hybrid.spde.Rd |only man/posterior_crossvalidation.Rd |only man/predict.hybrid_spde.Rd |only man/predict.inla_rspde_matern1d.Rd | 21 man/rSPDE-package.Rd | 3 man/rspde.anistropic2d.Rd | 9 man/rspde.hybrid.matern.Rd |only man/rspde.intrinsic.Rd | 11 man/rspde.make.A.Rd | 7 man/rspde.make.index.Rd | 20 man/rspde.matern.Rd | 9 man/rspde.matern.intrinsic.Rd | 9 man/rspde.matern1d.Rd | 9 man/rspde.metric_graph.Rd | 2 man/rspde.result.Rd | 17 man/rspde.spacetime.Rd | 18 man/rspde_lme.Rd | 7 man/rspde_safe_inla.Rd |only man/simulate.hybrid_spde.Rd |only man/spde.make.A.Rd | 5 man/spde.matern.operators.Rd | 7 man/summary.rspde_result.Rd | 17 man/update.CBrSPDEobj.Rd | 5 man/update.hybrid_spde.Rd |only man/update.rSPDEobj.Rd | 5 tests/testthat/setup.R |only tests/testthat/test.cgeneric_builtin.R |only tests/testthat/test.fem.R |only tests/testthat/test.inla_rspde.R |only tests/testthat/test.inlabru_rspde.R | 4 tests/testthat/test.posterior_crossvalidation.R |only tests/testthat/test.rspde_lme_optim_errors.R | 27 tests/testthat/test.rspde_lme_predict_precompute.R |only tests/testthat/test_hybrid_spde.R |only tests/testthat/test_inla_rspde_hybrid.R |only 60 files changed, 1476 insertions(+), 553 deletions(-)
Title: Bayesian Age-Period-Cohort Modeling and Prediction
Description: Bayesian Age-Period-Cohort Modeling and Prediction using efficient Markov Chain Monte Carlo Methods. This is the R version of the previous BAMP software as described in Volker Schmid and Leonhard Held (2007) <DOI:10.18637/jss.v021.i08> Bayesian Age-Period-Cohort Modeling and Prediction - BAMP, Journal of Statistical Software 21:8. This package includes checks of convergence using Gelman's R.
Author: Volker Schmid [aut, cre] ,
Florian Geressen [ctb],
Leonhard Held [ctb],
Evi Rainer [ctb],
Chris Kypridemos [aut]
Maintainer: Volker Schmid <volker.schmid@lmu.de>
Diff between bamp versions 2.2.0 dated 2026-06-21 and 3.0.0 dated 2026-08-31
DESCRIPTION | 16 - MD5 | 47 ++-- NAMESPACE | 3 NEWS.md | 42 ++++ R/bamp.R | 302 ++++++++++++++++++++++++++------ R/check_apc.R | 192 +++++++++++++++----- R/effects_apc.R | 187 +++++++++++++++---- R/pg_engine.R |only R/plot_apc.R | 65 ++++-- R/predict_apc.R | 80 ++++++-- R/print_apc.R | 15 + R/select_model.R |only README.md | 40 ++-- inst/CITATION | 2 inst/tinytest |only man/bamp.Rd | 133 +++++++++++++- man/checkConvergence.Rd | 30 ++- man/effects.apc.Rd | 51 +++++ man/plot.apc.Rd | 24 ++ man/selectModel.Rd |only src/bamp.cc | 5 src/block.cc | 2 src/init.c | 13 + src/pg_engine.c |only tests |only vignettes/publications/publications.Rmd | 8 26 files changed, 1010 insertions(+), 247 deletions(-)
Title: A High-Performance Taxonomic Database Interface
Description: Provides fast access to many commonly used taxonomic authorities
in a uniform Darwin Core format. Tables are read directly from
versioned Parquet snapshots, streamed from cloud storage or from a
local copy, and queried with familiar 'dplyr' verbs.
Author: Carl Boettiger [aut, cre] ,
Kari Norman [aut] ,
Jorrit Poelen [aut] ,
Scott Chamberlain [aut] ,
Noam Ross [ctb] ,
Mattia Ghilardi [ctb]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between taxadb versions 0.2.1 dated 2023-03-08 and 0.3.0 dated 2026-08-31
taxadb-0.2.1/taxadb/R/parse_schema.R |only taxadb-0.2.1/taxadb/R/taxadb_dir.R |only taxadb-0.2.1/taxadb/R/td_create.R |only taxadb-0.2.1/taxadb/R/tl_import.R |only taxadb-0.2.1/taxadb/inst/doc/backends.R |only taxadb-0.2.1/taxadb/inst/doc/backends.Rmd |only taxadb-0.2.1/taxadb/inst/doc/backends.html |only taxadb-0.2.1/taxadb/inst/extdata/common_itis_test.tsv.bz2 |only taxadb-0.2.1/taxadb/inst/extdata/dwc_itis_test.tsv.bz2 |only taxadb-0.2.1/taxadb/inst/extdata/prov.json |only taxadb-0.2.1/taxadb/inst/extdata/schema.json |only taxadb-0.2.1/taxadb/man/tl_import.Rd |only taxadb-0.2.1/taxadb/tests/testthat/test-tl_import.R |only taxadb-0.2.1/taxadb/vignettes/backends.Rmd |only taxadb-0.3.0/taxadb/DESCRIPTION | 39 - taxadb-0.3.0/taxadb/MD5 | 126 ++-- taxadb-0.3.0/taxadb/NAMESPACE | 26 taxadb-0.3.0/taxadb/NEWS.md | 152 +++++ taxadb-0.3.0/taxadb/R/build_col.R |only taxadb-0.3.0/taxadb/R/build_fishbase.R |only taxadb-0.3.0/taxadb/R/build_gbif.R |only taxadb-0.3.0/taxadb/R/build_itis.R |only taxadb-0.3.0/taxadb/R/build_ncbi.R |only taxadb-0.3.0/taxadb/R/build_ott.R |only taxadb-0.3.0/taxadb/R/build_utils.R |only taxadb-0.3.0/taxadb/R/clean_names.R | 7 taxadb-0.3.0/taxadb/R/filter_by.R | 25 taxadb-0.3.0/taxadb/R/filter_id.R | 4 taxadb-0.3.0/taxadb/R/fuzzy_filter.R | 6 taxadb-0.3.0/taxadb/R/get_ids.R | 5 taxadb-0.3.0/taxadb/R/get_names.R | 22 taxadb-0.3.0/taxadb/R/manifest.R |only taxadb-0.3.0/taxadb/R/providers.R |only taxadb-0.3.0/taxadb/R/taxa_tbl.R | 65 +- taxadb-0.3.0/taxadb/R/taxadb_source.R |only taxadb-0.3.0/taxadb/R/td_build.R |only taxadb-0.3.0/taxadb/R/td_connect.R | 137 +++-- taxadb-0.3.0/taxadb/R/td_download.R |only taxadb-0.3.0/taxadb/R/td_validate.R |only taxadb-0.3.0/taxadb/README.md | 366 ++++++++++---- taxadb-0.3.0/taxadb/build/vignette.rds |binary taxadb-0.3.0/taxadb/inst/WORDLIST | 54 +- taxadb-0.3.0/taxadb/inst/doc/data-sources.Rmd | 155 ++++- taxadb-0.3.0/taxadb/inst/doc/data-sources.html | 279 ++++++---- taxadb-0.3.0/taxadb/inst/extdata/common_itis_test.parquet |binary taxadb-0.3.0/taxadb/inst/extdata/dwc_itis_test.parquet |binary taxadb-0.3.0/taxadb/inst/scripts |only taxadb-0.3.0/taxadb/man/available_providers.Rd |only taxadb-0.3.0/taxadb/man/available_versions.Rd |only taxadb-0.3.0/taxadb/man/build_col.Rd |only taxadb-0.3.0/taxadb/man/build_dir.Rd |only taxadb-0.3.0/taxadb/man/build_fishbase.Rd |only taxadb-0.3.0/taxadb/man/build_gbif.Rd |only taxadb-0.3.0/taxadb/man/build_itis.Rd |only taxadb-0.3.0/taxadb/man/build_ncbi.Rd |only taxadb-0.3.0/taxadb/man/build_ott.Rd |only taxadb-0.3.0/taxadb/man/common_contains.Rd | 2 taxadb-0.3.0/taxadb/man/common_starts_with.Rd | 2 taxadb-0.3.0/taxadb/man/filter_by.Rd | 14 taxadb-0.3.0/taxadb/man/filter_common.Rd | 12 taxadb-0.3.0/taxadb/man/filter_id.Rd | 16 taxadb-0.3.0/taxadb/man/filter_name.Rd | 12 taxadb-0.3.0/taxadb/man/filter_rank.Rd | 12 taxadb-0.3.0/taxadb/man/fuzzy_filter.Rd | 4 taxadb-0.3.0/taxadb/man/get_ids.Rd | 4 taxadb-0.3.0/taxadb/man/get_names.Rd | 4 taxadb-0.3.0/taxadb/man/latest_version.Rd |only taxadb-0.3.0/taxadb/man/list_snapshots.Rd |only taxadb-0.3.0/taxadb/man/name_contains.Rd | 4 taxadb-0.3.0/taxadb/man/name_starts_with.Rd | 4 taxadb-0.3.0/taxadb/man/taxa_tbl.Rd | 22 taxadb-0.3.0/taxadb/man/taxadb_dir.Rd | 18 taxadb-0.3.0/taxadb/man/taxadb_provider_info.Rd |only taxadb-0.3.0/taxadb/man/taxadb_providers.Rd |only taxadb-0.3.0/taxadb/man/taxadb_repo.Rd |only taxadb-0.3.0/taxadb/man/taxadb_uri.Rd |only taxadb-0.3.0/taxadb/man/td_build.Rd |only taxadb-0.3.0/taxadb/man/td_connect.Rd | 49 + taxadb-0.3.0/taxadb/man/td_create.Rd | 68 -- taxadb-0.3.0/taxadb/man/td_disconnect.Rd | 6 taxadb-0.3.0/taxadb/man/td_download.Rd |only taxadb-0.3.0/taxadb/man/td_manifest.Rd |only taxadb-0.3.0/taxadb/man/td_validate.Rd |only taxadb-0.3.0/taxadb/man/td_write_metadata.Rd |only taxadb-0.3.0/taxadb/tests/testthat/test-clean_names.R | 3 taxadb-0.3.0/taxadb/tests/testthat/test-id-formats.R |only taxadb-0.3.0/taxadb/tests/testthat/test-taxadb_source.R |only taxadb-0.3.0/taxadb/tests/testthat/test-td_validate.R |only taxadb-0.3.0/taxadb/vignettes/data-sources.Rmd | 155 ++++- 89 files changed, 1307 insertions(+), 572 deletions(-)
Title: Sequential Poisson Sampling
Description: Sequential Poisson sampling is a variation of Poisson sampling for
drawing probability-proportional-to-size samples with a given number of
units, and is commonly used for price-index surveys. This package gives
functions to draw stratified sequential Poisson samples according to the
method by Ohlsson (1998, ISSN:0282-423X), as well as other order sample
designs by Rosén (1997, <doi:10.1016/S0378-3758(96)00186-3>), and generate
approximate bootstrap replicate weights according to the generalized
bootstrap method by Beaumont and Patak
(2012, <doi:10.1111/j.1751-5823.2011.00166.x>).
Author: Steve Martin [aut, cre, cph] ,
Justin Francis [ctb]
Maintainer: Steve Martin <marberts@protonmail.com>
Diff between sps versions 0.6.4 dated 2026-07-19 and 0.7.0 dated 2026-08-31
sps-0.6.4/sps/LICENSE |only sps-0.7.0/sps/DESCRIPTION | 14 - sps-0.7.0/sps/MD5 | 66 +++--- sps-0.7.0/sps/NEWS.md | 15 + sps-0.7.0/sps/R/expected_coverage.R | 6 sps-0.7.0/sps/R/inclusion_prob.R | 62 ++---- sps-0.7.0/sps/R/prop_allocation.R | 16 - sps-0.7.0/sps/R/sps.R | 74 ++----- sps-0.7.0/sps/R/sps_iterator.R | 9 sps-0.7.0/sps/R/sps_repweights.R | 37 +-- sps-0.7.0/sps/R/utils.R |only sps-0.7.0/sps/R/zzz.R | 7 sps-0.7.0/sps/README.md | 153 +++++++--------- sps-0.7.0/sps/build/partial.rdb |binary sps-0.7.0/sps/build/vignette.rds |binary sps-0.7.0/sps/inst/CITATION | 2 sps-0.7.0/sps/inst/REFERENCES.R |only sps-0.7.0/sps/inst/WORDLIST |only sps-0.7.0/sps/inst/doc/performance.Rmd |only sps-0.7.0/sps/inst/doc/performance.html |only sps-0.7.0/sps/inst/doc/sps.R | 8 sps-0.7.0/sps/inst/doc/sps.Rmd | 16 + sps-0.7.0/sps/inst/doc/sps.html | 208 ++++------------------ sps-0.7.0/sps/inst/doc/take-all.R | 2 sps-0.7.0/sps/inst/doc/take-all.Rmd | 18 + sps-0.7.0/sps/inst/doc/take-all.html | 13 - sps-0.7.0/sps/inst/tinytest/test-inclusion_prob.R | 1 sps-0.7.0/sps/inst/tinytest/test-sps.R | 19 +- sps-0.7.0/sps/inst/tinytest/test-zzz.R |only sps-0.7.0/sps/man/inclusion_prob.Rd | 13 - sps-0.7.0/sps/man/prop_allocation.Rd | 8 sps-0.7.0/sps/man/sps-package.Rd | 4 sps-0.7.0/sps/man/sps.Rd | 36 +-- sps-0.7.0/sps/man/sps_repweights.Rd | 33 +-- sps-0.7.0/sps/tests/spelling.R |only sps-0.7.0/sps/vignettes/performance.Rmd |only sps-0.7.0/sps/vignettes/performance.Rmd.orig |only sps-0.7.0/sps/vignettes/sps.Rmd | 16 + sps-0.7.0/sps/vignettes/take-all.Rmd | 18 + 39 files changed, 351 insertions(+), 523 deletions(-)
Title: Similarity Retrieval and Local Learning for Spectral
Chemometrics
Description: Functions for dissimilarity analysis and machine learning in complex
spectral data sets, including memory-based learning (MBL), optimal subset
search and selection, and retrieval-based modelling with model libraries.
Supports local learning, optimisation of spectral libraries, and
ensemble prediction from precomputed models. Most of these functions are
based on the methods presented in Ramirez-Lopez et al. (2013)
<doi:10.1016/j.geoderma.2012.12.014>, Ramirez-Lopez et al. (2026a)
<doi:10.1016/j.aca.2026.345682>, and Ramirez-Lopez et al. (2026b)
<doi:10.1016/j.aca.2026.345651>.
Author: Leonardo Ramirez-Lopez [aut, cre] ,
Antoine Stevens [aut, ctb] ,
Claudio Orellano [ctb]
Maintainer: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Diff between resemble versions 3.0.0 dated 2026-04-20 and 3.0.1 dated 2026-08-31
resemble-3.0.0/resemble/inst/doc/building-a-library-of-models-with-liblex.R |only resemble-3.0.0/resemble/inst/doc/building-a-library-of-models-with-liblex.html |only resemble-3.0.0/resemble/inst/doc/building-a-library-of-models-with-liblex.qmd |only resemble-3.0.0/resemble/inst/doc/classical-mbl.R |only resemble-3.0.0/resemble/inst/doc/classical-mbl.html |only resemble-3.0.0/resemble/inst/doc/classical-mbl.qmd |only resemble-3.0.0/resemble/inst/doc/dimensionality-reduction.R |only resemble-3.0.0/resemble/inst/doc/dimensionality-reduction.html |only resemble-3.0.0/resemble/inst/doc/dimensionality-reduction.qmd |only resemble-3.0.0/resemble/inst/doc/estimating-dissimilarity-between-spectra.R |only resemble-3.0.0/resemble/inst/doc/estimating-dissimilarity-between-spectra.html |only resemble-3.0.0/resemble/inst/doc/estimating-dissimilarity-between-spectra.qmd |only resemble-3.0.0/resemble/inst/doc/evolutionary-subset-search.R |only resemble-3.0.0/resemble/inst/doc/evolutionary-subset-search.html |only resemble-3.0.0/resemble/inst/doc/evolutionary-subset-search.qmd |only resemble-3.0.0/resemble/inst/doc/intro.R |only resemble-3.0.0/resemble/inst/doc/intro.html |only resemble-3.0.0/resemble/inst/doc/intro.qmd |only resemble-3.0.0/resemble/inst/doc/nearest-neighbor-search.R |only resemble-3.0.0/resemble/inst/doc/nearest-neighbor-search.html |only resemble-3.0.0/resemble/inst/doc/nearest-neighbor-search.qmd |only resemble-3.0.0/resemble/inst/doc/simple-global-models.R |only resemble-3.0.0/resemble/inst/doc/simple-global-models.html |only resemble-3.0.0/resemble/inst/doc/simple-global-models.qmd |only resemble-3.0.0/resemble/man/figures/mbl.png |only resemble-3.0.0/resemble/vignettes/building-a-library-of-models-with-liblex.qmd |only resemble-3.0.0/resemble/vignettes/classical-mbl.qmd |only resemble-3.0.0/resemble/vignettes/dimensionality-reduction.qmd |only resemble-3.0.0/resemble/vignettes/estimating-dissimilarity-between-spectra.qmd |only resemble-3.0.0/resemble/vignettes/evolutionary-subset-search.qmd |only resemble-3.0.0/resemble/vignettes/intro.qmd |only resemble-3.0.0/resemble/vignettes/nearest-neighbor-search.qmd |only resemble-3.0.0/resemble/vignettes/simple-global-models.qmd |only resemble-3.0.1/resemble/DESCRIPTION | 20 - resemble-3.0.1/resemble/MD5 | 123 +++++----- resemble-3.0.1/resemble/NAMESPACE | 2 resemble-3.0.1/resemble/NEWS.md | 9 resemble-3.0.1/resemble/R/AAA.R | 7 resemble-3.0.1/resemble/R/RcppExports.R | 12 resemble-3.0.1/resemble/R/diss_correlation.R | 16 - resemble-3.0.1/resemble/R/diss_evaluate.R | 10 resemble-3.0.1/resemble/R/diss_methods.R | 49 ++- resemble-3.0.1/resemble/R/gesearch.R | 15 - resemble-3.0.1/resemble/R/liblex.R | 29 +- resemble-3.0.1/resemble/R/local_helpers.R | 1 resemble-3.0.1/resemble/R/resemble.R | 17 - resemble-3.0.1/resemble/R/sid.R | 2 resemble-3.0.1/resemble/README.md | 58 +++- resemble-3.0.1/resemble/build/stage23.rdb |binary resemble-3.0.1/resemble/build/vignette.rds |binary resemble-3.0.1/resemble/inst/doc/aa-intro.R |only resemble-3.0.1/resemble/inst/doc/aa-intro.html |only resemble-3.0.1/resemble/inst/doc/aa-intro.qmd |only resemble-3.0.1/resemble/inst/doc/ab-dimensionality-reduction.R |only resemble-3.0.1/resemble/inst/doc/ab-dimensionality-reduction.html |only resemble-3.0.1/resemble/inst/doc/ab-dimensionality-reduction.qmd |only resemble-3.0.1/resemble/inst/doc/ac-estimating-dissimilarity-between-spectra.R |only resemble-3.0.1/resemble/inst/doc/ac-estimating-dissimilarity-between-spectra.html |only resemble-3.0.1/resemble/inst/doc/ac-estimating-dissimilarity-between-spectra.qmd |only resemble-3.0.1/resemble/inst/doc/ad-nearest-neighbor-search.R |only resemble-3.0.1/resemble/inst/doc/ad-nearest-neighbor-search.html |only resemble-3.0.1/resemble/inst/doc/ad-nearest-neighbor-search.qmd |only resemble-3.0.1/resemble/inst/doc/ae-simple-global-models.R |only resemble-3.0.1/resemble/inst/doc/ae-simple-global-models.html |only resemble-3.0.1/resemble/inst/doc/ae-simple-global-models.qmd |only resemble-3.0.1/resemble/inst/doc/af-classical-mbl.R |only resemble-3.0.1/resemble/inst/doc/af-classical-mbl.html |only resemble-3.0.1/resemble/inst/doc/af-classical-mbl.qmd |only resemble-3.0.1/resemble/inst/doc/ag-evolutionary-subset-search.R |only resemble-3.0.1/resemble/inst/doc/ag-evolutionary-subset-search.html |only resemble-3.0.1/resemble/inst/doc/ag-evolutionary-subset-search.qmd |only resemble-3.0.1/resemble/inst/doc/ah-building-a-library-of-models-with-liblex.R |only resemble-3.0.1/resemble/inst/doc/ah-building-a-library-of-models-with-liblex.html |only resemble-3.0.1/resemble/inst/doc/ah-building-a-library-of-models-with-liblex.qmd |only resemble-3.0.1/resemble/inst/logo.R | 2 resemble-3.0.1/resemble/man/diss_correlation.Rd | 15 - resemble-3.0.1/resemble/man/diss_cosine.Rd | 11 resemble-3.0.1/resemble/man/diss_euclidean.Rd | 11 resemble-3.0.1/resemble/man/diss_mahalanobis.Rd | 5 resemble-3.0.1/resemble/man/figures/mbl_example.png |only resemble-3.0.1/resemble/man/gesearch.Rd | 12 resemble-3.0.1/resemble/man/liblex.Rd | 27 +- resemble-3.0.1/resemble/man/mbl.Rd | 2 resemble-3.0.1/resemble/man/resemble-package.Rd | 16 - resemble-3.0.1/resemble/man/sid.Rd | 2 resemble-3.0.1/resemble/src/RcppExports.cpp | 11 resemble-3.0.1/resemble/src/diss_helpers.cpp | 17 + resemble-3.0.1/resemble/tests/setup.R |only resemble-3.0.1/resemble/vignettes/aa-intro.qmd |only resemble-3.0.1/resemble/vignettes/ab-dimensionality-reduction.qmd |only resemble-3.0.1/resemble/vignettes/ac-estimating-dissimilarity-between-spectra.qmd |only resemble-3.0.1/resemble/vignettes/ad-nearest-neighbor-search.qmd |only resemble-3.0.1/resemble/vignettes/ae-simple-global-models.qmd |only resemble-3.0.1/resemble/vignettes/af-classical-mbl.qmd |only resemble-3.0.1/resemble/vignettes/ag-evolutionary-subset-search.qmd |only resemble-3.0.1/resemble/vignettes/ah-building-a-library-of-models-with-liblex.qmd |only 96 files changed, 302 insertions(+), 199 deletions(-)
Title: Signal and Image Processing Toolbox for Analyzing Intracranial
Electroencephalography Data
Description: Implemented fast and memory-efficient Notch-filter,
Welch-periodogram, discrete wavelet spectrogram for minutes of
high-resolution signals, fast 3D convolution, image registration,
3D mesh manipulation; providing fundamental toolbox for intracranial
Electroencephalography (iEEG) pipelines.
Documentation and examples about 'RAVE' project are provided at
<https://rave.wiki>, and the paper by John F. Magnotti,
Zhengjia Wang, Michael S. Beauchamp (2020)
<doi:10.1016/j.neuroimage.2020.117341>; see 'citation("ravetools")' for
details.
Author: Zhengjia Wang [aut, cre] ,
John Magnotti [aut],
Michael Beauchamp [aut],
Trustees of the University of Pennsylvania [cph] ,
Karim Rahim [cph, ctb] ,
Thomas Possidente [cph, ctb] ,
Michael Prerau [cph, ctb] ,
Marcus Geelnard [ctb, cph] ,
Stefan Schlag [...truncated...]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ravetools versions 0.3.0 dated 2026-08-21 and 0.3.1 dated 2026-08-31
DESCRIPTION | 9 MD5 | 38 +- NEWS.md | 6 R/RcppExports.R | 4 R/aaa.R | 16 + R/vcg-collision.R | 249 ++++++++++++++++--- R/vcg.R | 51 +++ README.md | 62 ++++ build/vignette.rds |only inst/doc |only man/vcg_detect_collision.Rd | 196 ++++++++++++--- man/vcg_smooth.Rd | 5 src/RcppExports.cpp | 8 src/reg_linear.cpp | 6 src/reg_syn.cpp | 4 src/vcgCollision.cpp | 364 ++++++++++++++++++++++------ src/vcgCommon.cpp | 11 src/vcgCommon.h | 9 tests/testthat/test-vcg-collision.R | 460 +++++++++++++++++++++++++++--------- tests/testthat/test-vcg-mesh-io.R |only vignettes |only 21 files changed, 1203 insertions(+), 295 deletions(-)
Title: Administrative Boundaries and Static Map Tiles for Spain
Description: Administrative boundaries of Spain at several levels
(Autonomous Communities and Cities, provinces, municipalities and
'NUTS'), based on 'GISCO' from 'Eurostat'
<https://ec.europa.eu/eurostat/web/gisco> and 'CartoBase ANE' from
'Instituto Geográfico Nacional' <https://www.ign.es/>. Includes tools
to download and process static map tiles and a 'leaflet' plugin for
Spanish public administration tile providers.
Author: Diego Hernangomez [aut, cre, cph] ,
Eurostat [cph] ,
Instituto Geografico Nacional [cph] ,
Francisco J. Goerlich [ctb]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between mapSpain versions 1.2.0 dated 2026-06-17 and 1.2.1 dated 2026-08-31
mapSpain-1.2.0/mapSpain/tests/testthat/_snaps/esp-get-ccaa-siane.md |only mapSpain-1.2.0/mapSpain/tests/testthat/_snaps/esp-get-prov-siane.md |only mapSpain-1.2.0/mapSpain/tests/testthat/helpers.R |only mapSpain-1.2.1/mapSpain/DESCRIPTION | 10 mapSpain-1.2.1/mapSpain/MD5 | 341 +++++----- mapSpain-1.2.1/mapSpain/NAMESPACE | 8 mapSpain-1.2.1/mapSpain/NEWS.md | 63 - mapSpain-1.2.1/mapSpain/R/addProviderEspTiles.R | 9 mapSpain-1.2.1/mapSpain/R/data.R | 32 mapSpain-1.2.1/mapSpain/R/esp-cache.R | 52 - mapSpain-1.2.1/mapSpain/R/esp-check-access.R | 25 mapSpain-1.2.1/mapSpain/R/esp-dict.R | 41 - mapSpain-1.2.1/mapSpain/R/esp-get-attributions.R | 24 mapSpain-1.2.1/mapSpain/R/esp-get-can-box.R | 10 mapSpain-1.2.1/mapSpain/R/esp-get-capimun.R | 19 mapSpain-1.2.1/mapSpain/R/esp-get-ccaa-siane.R | 15 mapSpain-1.2.1/mapSpain/R/esp-get-ccaa.R | 13 mapSpain-1.2.1/mapSpain/R/esp-get-comarca.R | 21 mapSpain-1.2.1/mapSpain/R/esp-get-countries-siane.R | 27 mapSpain-1.2.1/mapSpain/R/esp-get-grid-BDN.R | 13 mapSpain-1.2.1/mapSpain/R/esp-get-grid-EEA.R | 8 mapSpain-1.2.1/mapSpain/R/esp-get-grid-ESDAC.R | 13 mapSpain-1.2.1/mapSpain/R/esp-get-grid-MTN.R | 14 mapSpain-1.2.1/mapSpain/R/esp-get-gridmap.R | 16 mapSpain-1.2.1/mapSpain/R/esp-get-hydrobasin.R | 7 mapSpain-1.2.1/mapSpain/R/esp-get-hypsobath.R | 10 mapSpain-1.2.1/mapSpain/R/esp-get-landwater.R | 35 - mapSpain-1.2.1/mapSpain/R/esp-get-munic-siane.R | 5 mapSpain-1.2.1/mapSpain/R/esp-get-munic.R | 11 mapSpain-1.2.1/mapSpain/R/esp-get-nuts.R | 19 mapSpain-1.2.1/mapSpain/R/esp-get-prov-siane.R | 7 mapSpain-1.2.1/mapSpain/R/esp-get-prov.R | 15 mapSpain-1.2.1/mapSpain/R/esp-get-railway.R | 31 mapSpain-1.2.1/mapSpain/R/esp-get-roads.R | 24 mapSpain-1.2.1/mapSpain/R/esp-get-simpl.R | 10 mapSpain-1.2.1/mapSpain/R/esp-get-spain-siane.R | 6 mapSpain-1.2.1/mapSpain/R/esp-get-spain.R | 11 mapSpain-1.2.1/mapSpain/R/esp-get-tiles.R | 56 - mapSpain-1.2.1/mapSpain/R/esp-make-provider.R | 2 mapSpain-1.2.1/mapSpain/R/esp-move-can.R | 16 mapSpain-1.2.1/mapSpain/R/esp-siane-bulk-download.R | 17 mapSpain-1.2.1/mapSpain/R/sysdata.rda |binary mapSpain-1.2.1/mapSpain/R/utils-convert-names.R | 20 mapSpain-1.2.1/mapSpain/R/utils-country.R | 18 mapSpain-1.2.1/mapSpain/R/utils-dict.R | 10 mapSpain-1.2.1/mapSpain/R/utils-get-tiles.R | 33 mapSpain-1.2.1/mapSpain/R/utils-sf.R | 24 mapSpain-1.2.1/mapSpain/R/utils-url.R | 83 +- mapSpain-1.2.1/mapSpain/R/utils.R | 75 +- mapSpain-1.2.1/mapSpain/README.md | 31 mapSpain-1.2.1/mapSpain/build/partial.rdb |binary mapSpain-1.2.1/mapSpain/build/vignette.rds |binary mapSpain-1.2.1/mapSpain/data/esp_codelist.rda |binary mapSpain-1.2.1/mapSpain/data/esp_nuts_2024.rda |binary mapSpain-1.2.1/mapSpain/data/esp_tiles_providers.rda |binary mapSpain-1.2.1/mapSpain/data/pobmun25.rda |binary mapSpain-1.2.1/mapSpain/inst/doc/imagery.html | 11 mapSpain-1.2.1/mapSpain/inst/doc/mapSpain.html | 35 - mapSpain-1.2.1/mapSpain/inst/doc/mapSpain.qmd | 34 mapSpain-1.2.1/mapSpain/inst/schemaorg.json | 4 mapSpain-1.2.1/mapSpain/man/addProviderEspTiles.Rd | 3 mapSpain-1.2.1/mapSpain/man/esp_clear_cache.Rd | 5 mapSpain-1.2.1/mapSpain/man/esp_codelist.Rd | 3 mapSpain-1.2.1/mapSpain/man/esp_dict.Rd | 16 mapSpain-1.2.1/mapSpain/man/esp_get_attributions.Rd |only mapSpain-1.2.1/mapSpain/man/esp_get_can_box.Rd | 8 mapSpain-1.2.1/mapSpain/man/esp_get_capimun.Rd | 68 - mapSpain-1.2.1/mapSpain/man/esp_get_ccaa.Rd | 49 - mapSpain-1.2.1/mapSpain/man/esp_get_ccaa_siane.Rd | 47 - mapSpain-1.2.1/mapSpain/man/esp_get_comarca.Rd | 47 - mapSpain-1.2.1/mapSpain/man/esp_get_countries_siane.Rd | 48 - mapSpain-1.2.1/mapSpain/man/esp_get_grid_BDN.Rd | 29 mapSpain-1.2.1/mapSpain/man/esp_get_grid_EEA.Rd | 9 mapSpain-1.2.1/mapSpain/man/esp_get_grid_ESDAC.Rd | 25 mapSpain-1.2.1/mapSpain/man/esp_get_grid_MTN.Rd | 26 mapSpain-1.2.1/mapSpain/man/esp_get_gridmap.Rd | 26 mapSpain-1.2.1/mapSpain/man/esp_get_hydrobasin.Rd | 29 mapSpain-1.2.1/mapSpain/man/esp_get_hypsobath.Rd | 29 mapSpain-1.2.1/mapSpain/man/esp_get_landwater.Rd | 27 mapSpain-1.2.1/mapSpain/man/esp_get_munic.Rd | 47 - mapSpain-1.2.1/mapSpain/man/esp_get_munic_siane.Rd | 46 - mapSpain-1.2.1/mapSpain/man/esp_get_nuts.Rd | 50 - mapSpain-1.2.1/mapSpain/man/esp_get_prov.Rd | 53 - mapSpain-1.2.1/mapSpain/man/esp_get_prov_siane.Rd | 50 - mapSpain-1.2.1/mapSpain/man/esp_get_railway.Rd | 25 mapSpain-1.2.1/mapSpain/man/esp_get_roads.Rd | 23 mapSpain-1.2.1/mapSpain/man/esp_get_simpl.Rd | 34 mapSpain-1.2.1/mapSpain/man/esp_get_spain.Rd | 45 - mapSpain-1.2.1/mapSpain/man/esp_get_spain_siane.Rd | 39 - mapSpain-1.2.1/mapSpain/man/esp_get_tiles.Rd | 26 mapSpain-1.2.1/mapSpain/man/esp_make_provider.Rd | 9 mapSpain-1.2.1/mapSpain/man/esp_move_can.Rd | 16 mapSpain-1.2.1/mapSpain/man/esp_nuts_2024.Rd | 7 mapSpain-1.2.1/mapSpain/man/esp_set_cache_dir.Rd | 17 mapSpain-1.2.1/mapSpain/man/esp_siane_bulk_download.Rd | 41 - mapSpain-1.2.1/mapSpain/man/esp_tiles_providers.Rd | 12 mapSpain-1.2.1/mapSpain/man/figures/README-tile-1.png |binary mapSpain-1.2.1/mapSpain/man/pobmun25.Rd | 3 mapSpain-1.2.1/mapSpain/man/roxygen/meta.R | 8 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/addProviderEspTiles.md | 6 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-cache.md | 20 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-dict.md | 31 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-attributions.md | 7 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-can-box.md | 14 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-capimun.md | 7 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-ccaa.md | 7 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-comarca.md | 23 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-countries-siane.md | 7 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-grid-BDN.md | 6 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-grid-EEA.md | 2 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-grid-ESDAC.md |only mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-grid-MTN.md |only mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-gridmap.md | 2 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-hydrobasin.md | 8 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-hypsobath.md |only mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-landwater.md | 16 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-munic-siane.md | 7 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-munic.md | 7 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-nuts.md | 28 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-prov.md | 7 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-railway.md | 4 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-roads.md |only mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-simpl.md | 2 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-tiles.md | 17 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-move-can.md | 6 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/utils-convert-names.md | 59 - mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/utils-country.md | 22 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/utils-dict.md | 2 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/utils-get-tiles.md | 28 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/utils-sf.md | 7 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/utils-url.md | 4 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/utils.md | 34 mapSpain-1.2.1/mapSpain/tests/testthat/helper.R |only mapSpain-1.2.1/mapSpain/tests/testthat/test-addProviderEspTiles.R | 7 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-cache.R | 216 ++++-- mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-check-access.R | 38 - mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-dict.R | 4 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-attributions.R | 2 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-can-box.R | 2 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-capimun.R | 26 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-ccaa-siane.R | 48 - mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-ccaa.R | 4 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-comarca.R | 21 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-countries-siane.R | 32 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-grid-BDN.R | 18 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-grid-EEA.R | 2 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-grid-ESDAC.R | 33 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-grid-MTN.R | 14 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-gridmap.R | 2 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-hydrobasin.R | 23 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-hypsobath.R | 31 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-landwater.R | 42 - mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-munic-siane.R | 24 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-munic.R | 9 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-nuts.R | 77 -- mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-prov-siane.R | 54 - mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-prov.R | 4 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-railway.R | 23 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-roads.R | 28 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-simpl.R | 16 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-spain-siane.R | 13 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-spain.R | 13 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-stations.R | 14 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-tiles.R | 155 ++-- mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-make-provider.R | 4 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-move-can.R | 16 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-siane-bulk-download.R | 24 mapSpain-1.2.1/mapSpain/tests/testthat/test-utils-convert-names.R | 6 mapSpain-1.2.1/mapSpain/tests/testthat/test-utils-country.R | 6 mapSpain-1.2.1/mapSpain/tests/testthat/test-utils-dict.R | 4 mapSpain-1.2.1/mapSpain/tests/testthat/test-utils-get-tiles.R | 92 +- mapSpain-1.2.1/mapSpain/tests/testthat/test-utils-sf.R | 21 mapSpain-1.2.1/mapSpain/tests/testthat/test-utils-url.R | 106 ++- mapSpain-1.2.1/mapSpain/tests/testthat/test-utils.R | 36 - mapSpain-1.2.1/mapSpain/vignettes/mapSpain.qmd | 34 mapSpain-1.2.1/mapSpain/vignettes/thematic-1.png |binary 176 files changed, 2282 insertions(+), 1931 deletions(-)
Title: Add Ipea Editorial Standards to 'ggplot2' Graphics
Description: Convenient functions to create 'ggplot2' graphics following the
editorial guidelines of the Institute for Applied Economic
Research (Ipea).
Author: Pedro Ferreira [aut, cre],
Pedro Jorge [aut],
Daniel Lima [aut],
Gustavo Coelho [aut],
Rafael H. M. Pereira [aut],
Lucas Mation [aut],
Fabio Vaz [ctb],
Ipea - Institue for Applied Economic Research [cph, fnd]
Maintainer: Pedro Ferreira <pedro.ferreira2@ipea.gov.br>
Diff between ipeaplot versions 0.5.4 dated 2026-07-09 and 1.0.0 dated 2026-08-31
ipeaplot |only 1 file changed
Title: Graph Drawing with Intelligent Placement (GRIP)
Description: Implements GRIP multiscale graph layout with a unified choice
between hop-count and geometry-aware edge-length graph metrics in 2D and
3D. Provides layout scoring, candidate
comparison, multiscale trace diagnostics, synthetic graph families,
and advanced experimental geodesic-KK utilities for weighted-layout
evaluation and polish. Based on Gajer and Kobourov (2002)
<doi:10.7155/jgaa.00052> and Gajer, Goodrich and Kobourov (2004)
<doi:10.1016/j.comgeo.2004.03.014>.
Author: Pawel Gajer [aut, cre]
Maintainer: Pawel Gajer <pgajer@gmail.com>
Diff between grip versions 0.1.3 dated 2026-08-21 and 0.2.0 dated 2026-08-31
grip-0.1.3/grip/R/deprecated_api.R |only grip-0.1.3/grip/man/deprecated-grip-api.Rd |only grip-0.1.3/grip/man/gmds.result.Rd |only grip-0.1.3/grip/man/grip.compare.layouts.Rd |only grip-0.1.3/grip/man/grip.optimize.edge.kk.layout.Rd |only grip-0.1.3/grip/man/grip.prepare.edge.kk.Rd |only grip-0.1.3/grip/man/grip.score.layout.Rd |only grip-0.2.0/grip/DESCRIPTION | 6 grip-0.2.0/grip/MD5 | 177 +- grip-0.2.0/grip/NAMESPACE | 93 - grip-0.2.0/grip/NEWS.md | 13 grip-0.2.0/grip/R/data-hmp_gc.R |only grip-0.2.0/grip/R/export_examples.R |only grip-0.2.0/grip/R/gmds_layout_interface.R | 61 grip-0.2.0/grip/R/graph_helpers.R | 640 ++++------ grip-0.2.0/grip/R/grip-0.2-migration.R |only grip-0.2.0/grip/R/grip_quality.R | 60 grip-0.2.0/grip/README.md | 15 grip-0.2.0/grip/data/hmp.gc.rda |only grip-0.2.0/grip/inst/doc/grip-examples.html | 12 grip-0.2.0/grip/inst/doc/grip-real-data.html | 188 +- grip-0.2.0/grip/inst/extdata/hmp_gc |only grip-0.2.0/grip/inst/extdata/hmp_u01_gc_coarse/PROVENANCE.md | 29 grip-0.2.0/grip/inst/extdata/hmp_u01_gc_coarse/vignette_results.rds |binary grip-0.2.0/grip/inst/extdata/vs_alternatives/BENCHMARK_PROVENANCE.md |only grip-0.2.0/grip/inst/extdata/vs_alternatives/benchmark_results.rds |binary grip-0.2.0/grip/inst/scripts |only grip-0.2.0/grip/man/build.weighted.misf.Rd | 10 grip-0.2.0/grip/man/compare.layouts.Rd | 9 grip-0.2.0/grip/man/cube_mask_pattern_helpers.Rd | 14 grip-0.2.0/grip/man/cylinder_surface_helpers.Rd | 22 grip-0.2.0/grip/man/edge.kk.Rd | 12 grip-0.2.0/grip/man/edge.length.density.stiffness.Rd | 7 grip-0.2.0/grip/man/edge.repulsive.stage.Rd | 12 grip-0.2.0/grip/man/edge.repulsive.state.Rd | 12 grip-0.2.0/grip/man/geodesic.kk.Rd | 9 grip-0.2.0/grip/man/geometry.diagnostics.Rd | 11 grip-0.2.0/grip/man/globalrep.weighted.grip.Rd | 11 grip-0.2.0/grip/man/graph.riemannian.star.structure.Rd | 9 grip-0.2.0/grip/man/graph_generators.Rd | 386 ------ grip-0.2.0/grip/man/grip-0.2-migration.Rd |only grip-0.2.0/grip/man/hmp.gc.Rd |only grip-0.2.0/grip/man/irregular_annulus_surface_helpers.Rd | 22 grip-0.2.0/grip/man/irregular_ball_solid_helpers.Rd | 24 grip-0.2.0/grip/man/irregular_double_torus_surface_helpers.Rd | 27 grip-0.2.0/grip/man/irregular_pair_of_pants_surface_helpers.Rd | 26 grip-0.2.0/grip/man/irregular_rectangle_surface_helpers.Rd | 71 - grip-0.2.0/grip/man/irregular_shell_solid_helpers.Rd | 25 grip-0.2.0/grip/man/irregular_sphere_surface_helpers.Rd | 22 grip-0.2.0/grip/man/irregular_torus_surface_helpers.Rd | 23 grip-0.2.0/grip/man/kary_tree_weighted_graph_helpers.Rd | 5 grip-0.2.0/grip/man/kernel.gram.gkk.Rd | 12 grip-0.2.0/grip/man/landmark.geodesic.kk.Rd | 11 grip-0.2.0/grip/man/mask_pattern_helpers.Rd | 11 grip-0.2.0/grip/man/menger_sponge_surface_helpers.Rd | 19 grip-0.2.0/grip/man/mesh_surface_helpers.Rd | 26 grip-0.2.0/grip/man/metric.mds.Rd | 7 grip-0.2.0/grip/man/misf.geodesic.kk.Rd | 14 grip-0.2.0/grip/man/occupied_mesh_surface_helpers.Rd | 26 grip-0.2.0/grip/man/perforated_grid_helpers.Rd | 12 grip-0.2.0/grip/man/porous_cube_surface_helpers.Rd | 62 grip-0.2.0/grip/man/prepare.edge.kk.Rd | 6 grip-0.2.0/grip/man/prepare.geodesic.kk.Rd | 6 grip-0.2.0/grip/man/prepare.graph.geodesic.mds.Rd | 6 grip-0.2.0/grip/man/prepare.landmark.geodesic.kk.Rd | 8 grip-0.2.0/grip/man/recursive_cube_mask_surface_helpers.Rd | 23 grip-0.2.0/grip/man/recursive_mask_grid_surface_helpers.Rd | 23 grip-0.2.0/grip/man/recursive_tetrahedron_mask_surface_helpers.Rd | 17 grip-0.2.0/grip/man/recursive_triangle_mask_surface_helpers.Rd | 19 grip-0.2.0/grip/man/repulsive.stage.Rd | 10 grip-0.2.0/grip/man/repulsive.state.Rd | 8 grip-0.2.0/grip/man/sampled_rectangle_surface_helpers.Rd | 46 grip-0.2.0/grip/man/score.geodesic.kk.Rd | 9 grip-0.2.0/grip/man/score.gmds.Rd | 9 grip-0.2.0/grip/man/score.landmark.geodesic.kk.Rd | 11 grip-0.2.0/grip/man/score.layout.Rd | 11 grip-0.2.0/grip/man/score.misf.geodesic.kk.Rd | 11 grip-0.2.0/grip/man/sierpinski_carpet_surface_helpers.Rd | 20 grip-0.2.0/grip/man/sierpinski_tetrahedron_surface_helpers.Rd | 16 grip-0.2.0/grip/man/sierpinski_triangle_surface_helpers.Rd | 18 grip-0.2.0/grip/man/sphere_surface_helpers.Rd | 23 grip-0.2.0/grip/man/tetrahedron_mask_helpers.Rd | 7 grip-0.2.0/grip/man/torus_surface_helpers.Rd | 22 grip-0.2.0/grip/man/triangle_mask_helpers.Rd | 7 grip-0.2.0/grip/man/triangulated_annulus_surface_helpers.Rd | 22 grip-0.2.0/grip/man/triangulated_pair_of_pants_surface_helpers.Rd | 24 grip-0.2.0/grip/man/triangulated_polyhedron_surface_helpers.Rd | 19 grip-0.2.0/grip/man/vicsek_surface_helpers.Rd | 22 grip-0.2.0/grip/man/weighted.grip.nd.Rd | 11 grip-0.2.0/grip/tests/testthat/test-edge-isometric-gkk.R | 52 grip-0.2.0/grip/tests/testthat/test-gmds-layout-interface.R | 2 grip-0.2.0/grip/tests/testthat/test-graph-helpers.R | 186 +- grip-0.2.0/grip/tests/testthat/test-hmp-gc.R |only grip-0.2.0/grip/tests/testthat/test-layout-metric-dispatch.R | 28 grip-0.2.0/grip/tests/testthat/test-layout-quality.R | 20 grip-0.2.0/grip/tests/testthat/test-public-api.R |only 96 files changed, 1190 insertions(+), 1795 deletions(-)
Title: Tools for Managing Classes on GitHub
Description: Interface for the GitHub API that enables efficient
management of courses on GitHub. It has a functionality for
managing organizations, teams, repositories, and users on GitHub
and helps automate most of the tedious and repetitive tasks
around creating and distributing assignments.
Author: Colin Rundel [aut, cre],
Mine Cetinkaya-Rundel [aut],
Therese Anders [ctb]
Maintainer: Colin Rundel <rundel@gmail.com>
Diff between ghclass versions 0.4.1 dated 2026-07-25 and 0.4.2 dated 2026-08-31
DESCRIPTION | 8 +- MD5 | 31 +++++---- NAMESPACE | 2 NEWS.md | 12 +++ R/github_token.R | 119 +++++++++++++++++++++++++++++++++++--- R/org_allows_forking.R | 5 + R/org_sitrep.R | 110 ++++++++++++++++++----------------- R/org_workflow_permissions.R | 5 + R/repo.R | 6 + R/repo_tree.R |only R/team_roster.R | 3 R/util_github.R | 8 ++ R/util_safely.R | 113 +++++++++++++++++++++++++----------- R/util_scopes.R |only man/github_token.Rd | 24 +++++++ man/repo_file.Rd | 12 +++ man/team_roster.Rd | 3 tests/testthat/test-util_scopes.R |only 18 files changed, 344 insertions(+), 117 deletions(-)
Title: An R Tool for Streamlining Database Joins
Description: Simplifies and automates the process of exploring and merging
data from relational databases. This package allows users to discover
table relationships, create a map of all possible joins, and generate
executable plans to merge data based on a structured metadata framework.
Author: Akshat Maurya [aut, cre],
David Shilane [aut]
Maintainer: Akshat Maurya <codingmaster902@gmail.com>
Diff between DBmaps versions 0.1.0 dated 2025-09-08 and 0.1.1 dated 2026-08-31
DESCRIPTION | 12 MD5 | 26 - NEWS.md | 13 R/generate_code.R | 14 R/join_plan.R | 158 +++---- R/map_joins.R | 48 +- build/vignette.rds |binary inst/doc/DBmaps-introduction.html | 633 ++++++++++++++---------------- inst/doc/defining-table-metadata.html | 417 +++++++++---------- inst/doc/discovering-join-paths.html | 229 +++++----- inst/doc/generating-aggregation-code.html | 231 +++++----- inst/doc/join-plan.html | 293 ++++++------- man/create_join_plan.Rd | 48 -- man/generate_aggregation_code.Rd | 9 14 files changed, 1033 insertions(+), 1098 deletions(-)
Title: Interactive Command-Line Menus
Description: Provides interactive command-line menu functionality with
single and multiple selection menus, keyboard navigation (arrow keys or
vi-style j/k), preselection, and graceful fallback for non-interactive
environments. Inspired by tools such as 'inquirer.js'
<https://github.com/SBoudrias/Inquirer.js>, 'pick'
<https://github.com/aisk/pick>, and 'survey'
<https://github.com/AlecAivazis/survey>. Designed to be lightweight and
easy to integrate into 'R' packages and scripts.
Author: Petr Čala [aut, cre]
Maintainer: Petr Čala <61505008@fsv.cuni.cz>
Diff between climenu versions 0.1.8 dated 2026-07-08 and 0.2.0 dated 2026-08-31
DESCRIPTION | 8 MD5 | 32 +-- NAMESPACE | 1 NEWS.md | 10 + R/checkbox.R | 113 ++++++++--- R/menu.R | 30 ++- R/select.R | 96 +++++++-- R/utils.R | 178 +++++++++++++++--- inst/doc/climenu.R | 29 ++- inst/doc/climenu.Rmd | 41 +++- inst/doc/climenu.html | 290 ++++++++++++++++-------------- man/checkbox.Rd | 29 ++- man/menu.Rd | 24 ++ man/select.Rd | 34 +++ tests/testthat/test-fallback.R | 30 +-- tests/testthat/test-labels-descriptions.R |only tests/testthat/test-render-frame.R |only vignettes/climenu.Rmd | 41 +++- 18 files changed, 704 insertions(+), 282 deletions(-)
Title: An Efficient and Deterministic Method for Identifying
Topological Domains in Genomes
Description: The 'TopDom' method identifies topological domains in genomes from Hi-C sequence data (Shin et al., 2016 <doi:10.1093/nar/gkv1505>). The authors published an implementation of their method as an R script (two different versions; also available in this package). This package originates from those original 'TopDom' R scripts and provides help pages adopted from the original 'TopDom' PDF documentation. It also provides a small number of bug fixes to the original code.
Author: Henrik Bengtsson [aut, cre, cph] ,
Hanjun Shin [aut, ctr, cph],
Harris Lazaris [ctr, cph] ,
Gangqing Hu [ctr, cph] ,
Xianghong Zhou [ctr]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between TopDom versions 0.10.1 dated 2021-05-06 and 0.10.2 dated 2026-08-31
TopDom-0.10.1/TopDom/NEWS |only TopDom-0.10.2/TopDom/.Rinstignore |only TopDom-0.10.2/TopDom/DESCRIPTION | 39 ++++++---- TopDom-0.10.2/TopDom/MD5 | 33 +++++--- TopDom-0.10.2/TopDom/NAMESPACE | 42 ++++++----- TopDom-0.10.2/TopDom/NEWS.md |only TopDom-0.10.2/TopDom/R/TopDom.R | 57 ++++++++++---- TopDom-0.10.2/TopDom/R/exdata.R | 15 ++- TopDom-0.10.2/TopDom/R/overlapScores.R | 8 +- TopDom-0.10.2/TopDom/README.md | 15 +-- TopDom-0.10.2/TopDom/build |only TopDom-0.10.2/TopDom/inst/CITATION | 80 +++++++++------------ TopDom-0.10.2/TopDom/inst/WORDLIST | 24 ++++++ TopDom-0.10.2/TopDom/man/TopDom-data.Rd | 15 ++- TopDom-0.10.2/TopDom/man/TopDom.Rd | 21 ++--- TopDom-0.10.2/TopDom/man/overlapScores.Rd | 8 +- TopDom-0.10.2/TopDom/tests/TopDom-options.R |only TopDom-0.10.2/TopDom/tests/countsPerRegion.R |only TopDom-0.10.2/TopDom/tests/ggplot.R |only TopDom-0.10.2/TopDom/tests/legacy-api.R |only TopDom-0.10.2/TopDom/tests/overlapScores-methods.R |only TopDom-0.10.2/TopDom/tests/readHiC.R |only TopDom-0.10.2/TopDom/tests/subsetByRegion.R |only TopDom-0.10.2/TopDom/tests/utils.R |only 24 files changed, 211 insertions(+), 146 deletions(-)
Title: Least Squares Sparse Principal Components Analysis
Description: Implements least-squares sparse principal component analysis with cardinality constraints. The package has an efficient C++ backend and provides functions for fitting, summarizing, comparing, and visualizing sparse principal component models. The approach follows Merola (2015) <doi:10.1111/anzs.12128> and Merola and Chen (2019) <doi:10.1016/j.jmva.2019.04.001>.
Author: Giovanni Maria Merola [aut, cre]
Maintainer: Giovanni Maria Merola <merolagio@gmail.com>
Diff between spca versions 1.1.1 dated 2026-07-10 and 1.1.3 dated 2026-08-31
spca-1.1.1/spca/R/helpers_and_validation.R |only spca-1.1.1/spca/R/utilities_and_cpp_wrappers.R |only spca-1.1.1/spca/inst/doc/spca_extended_vignette.R |only spca-1.1.1/spca/inst/doc/spca_extended_vignette.Rmd |only spca-1.1.1/spca/inst/doc/spca_extended_vignette.html |only spca-1.1.1/spca/man/figures/spca_Logo.png |only spca-1.1.1/spca/man/figures/spca_Logo_bordered.png |only spca-1.1.1/spca/man/show_contributions_spca.Rd |only spca-1.1.1/spca/vignettes/figures/spca_Logo.png |only spca-1.1.1/spca/vignettes/figures/spca_Logo_bordered.png |only spca-1.1.1/spca/vignettes/spca_extended_vignette.Rmd |only spca-1.1.3/spca/DESCRIPTION | 12 spca-1.1.3/spca/MD5 | 163 ++++--- spca-1.1.3/spca/NAMESPACE | 15 spca-1.1.3/spca/NEWS.md | 31 + spca-1.1.3/spca/R/Internal_utilities_and_cpp_wrappers.R |only spca-1.1.3/spca/R/accessors_for_obsolete.R |only spca-1.1.3/spca/R/compare_spca.R | 143 +++--- spca-1.1.3/spca/R/datasets.R | 4 spca-1.1.3/spca/R/imports.R | 2 spca-1.1.3/spca/R/methods_and_functions.R |only spca-1.1.3/spca/R/pca.R | 190 +-------- spca-1.1.3/spca/R/pca_methods.R |only spca-1.1.3/spca/R/plot.spca.R | 209 ++++------ spca-1.1.3/spca/R/print.spca.R | 35 - spca-1.1.3/spca/R/spca-package.R | 85 ++-- spca-1.1.3/spca/R/spca.R | 142 +++--- spca-1.1.3/spca/R/summary.spca.R | 40 - spca-1.1.3/spca/R/validation.R |only spca-1.1.3/spca/README.md | 52 +- spca-1.1.3/spca/build/vignette.rds |binary spca-1.1.3/spca/inst/doc/spca_extended.R |only spca-1.1.3/spca/inst/doc/spca_extended.Rmd |only spca-1.1.3/spca/inst/doc/spca_extended.html |only spca-1.1.3/spca/inst/doc/spca_intro.R | 3 spca-1.1.3/spca/inst/doc/spca_intro.Rmd | 22 - spca-1.1.3/spca/inst/doc/spca_intro.html | 104 ++-- spca-1.1.3/spca/man/aggregate_by_group.Rd | 90 ++-- spca-1.1.3/spca/man/change_loadings_sign_spca.Rd | 27 - spca-1.1.3/spca/man/change_sign.Rd |only spca-1.1.3/spca/man/change_weights_sign_spca.Rd |only spca-1.1.3/spca/man/compare_spca.Rd | 44 +- spca-1.1.3/spca/man/figures/README-pca_checks-1.png |binary spca-1.1.3/spca/man/figures/README-pca_checks-2.png |binary spca-1.1.3/spca/man/figures/README-pca_checks-3.png |only spca-1.1.3/spca/man/figures/spca_logo_octagon.png |only spca-1.1.3/spca/man/holzinger.Rd | 2 spca-1.1.3/spca/man/holzinger_scales.Rd | 4 spca-1.1.3/spca/man/is.spca.Rd | 14 spca-1.1.3/spca/man/new_spca.Rd | 16 spca-1.1.3/spca/man/pca.Rd | 11 spca-1.1.3/spca/man/plot.spca.Rd | 26 - spca-1.1.3/spca/man/print.spca.Rd | 18 spca-1.1.3/spca/man/qqplot_spca.Rd |only spca-1.1.3/spca/man/screeplot_spca.Rd |only spca-1.1.3/spca/man/show_correlations.Rd |only spca-1.1.3/spca/man/show_weights.Rd |only spca-1.1.3/spca/man/spca-package.Rd | 57 +- spca-1.1.3/spca/man/spca.Rd | 26 - spca-1.1.3/spca/man/spca_object.Rd | 32 + spca-1.1.3/spca/man/spca_screeplot.Rd | 40 - spca-1.1.3/spca/man/summary.spca.Rd | 22 - spca-1.1.3/spca/man/wachter_qqplot.Rd | 71 +-- spca-1.1.3/spca/src/pca.cpp | 34 - spca-1.1.3/spca/src/spca_fat.cpp | 46 +- spca-1.1.3/spca/src/spca_tall.cpp | 52 +- spca-1.1.3/spca/src/support_fat.cpp | 18 spca-1.1.3/spca/src/support_tall.cpp | 72 +-- spca-1.1.3/spca/src/utility_wrappers.cpp | 6 spca-1.1.3/spca/tests/testthat/helper-data.R | 12 spca-1.1.3/spca/tests/testthat/test-compare-plot.R | 84 ++-- spca-1.1.3/spca/tests/testthat/test-methods.R | 202 +++++++-- spca-1.1.3/spca/tests/testthat/test-new-spca.R | 4 spca-1.1.3/spca/tests/testthat/test-pca-plots.R | 140 ++++++ spca-1.1.3/spca/tests/testthat/test-pca.R | 6 spca-1.1.3/spca/tests/testthat/test-spca-power-methods.R | 2 spca-1.1.3/spca/tests/testthat/test-spca-selection.R | 2 spca-1.1.3/spca/tests/testthat/test-spca-structure.R | 10 spca-1.1.3/spca/tests/testthat/test-spca-validation.R | 4 spca-1.1.3/spca/vignettes/Extended_vignette_material/spca_JSS_article_results.rda |binary spca-1.1.3/spca/vignettes/figures/barplot-1.png |binary spca-1.1.3/spca/vignettes/figures/circplot-1.png |binary spca-1.1.3/spca/vignettes/figures/compare-1.png |binary spca-1.1.3/spca/vignettes/figures/groupplot-1.png |binary spca-1.1.3/spca/vignettes/figures/heatmap-1.png |binary spca-1.1.3/spca/vignettes/figures/intro-circular-1.png |binary spca-1.1.3/spca/vignettes/figures/intro-groups-1.png |binary spca-1.1.3/spca/vignettes/figures/intro-heatmap-1.png |binary spca-1.1.3/spca/vignettes/figures/intro-methods-1.png |binary spca-1.1.3/spca/vignettes/figures/intro-pca_checks-1.png |binary spca-1.1.3/spca/vignettes/figures/intro-pca_checks-2.png |binary spca-1.1.3/spca/vignettes/figures/intro-spca90-1.png |binary spca-1.1.3/spca/vignettes/figures/pca-1.png |binary spca-1.1.3/spca/vignettes/figures/qqplot-1.png |binary spca-1.1.3/spca/vignettes/figures/spca_logo_octagon.png |only spca-1.1.3/spca/vignettes/spca_extended.Rmd |only spca-1.1.3/spca/vignettes/spca_intro.Rmd | 22 - 97 files changed, 1320 insertions(+), 1148 deletions(-)
Title: SHAP Visualizations
Description: Visualizations for SHAP (SHapley Additive exPlanations), such
as waterfall plots, force plots, various types of importance plots,
dependence plots, and interaction plots. These plots act on a
'shapviz' object created from a matrix of SHAP values and a
corresponding feature dataset. Wrappers for the R packages 'xgboost',
'lightgbm', 'fastshap', 'shapr', 'h2o', 'treeshap', 'DALEX', and
'kernelshap' are added for convenience. By separating visualization
and computation, it is possible to display factor variables in graphs,
even if the SHAP values are calculated by a model that requires
numerical features. The plots are inspired by those provided by the
'shap' package in Python, but there is no dependency on it.
Author: Michael Mayer [aut, cre],
Adrian Stando [ctb]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between shapviz versions 0.10.3 dated 2025-10-13 and 0.10.4 dated 2026-08-31
shapviz-0.10.3/shapviz/man/figures/README-bee.svg |only shapviz-0.10.4/shapviz/DESCRIPTION | 10 shapviz-0.10.4/shapviz/MD5 | 72 - shapviz-0.10.4/shapviz/NEWS.md | 10 shapviz-0.10.4/shapviz/R/collapse_shap.R | 6 shapviz-0.10.4/shapviz/R/shapviz.R | 4 shapviz-0.10.4/shapviz/R/sv_dependence.R | 21 shapviz-0.10.4/shapviz/R/sv_dependence2D.R | 9 shapviz-0.10.4/shapviz/R/sv_force.R | 5 shapviz-0.10.4/shapviz/R/sv_importance.R | 2 shapviz-0.10.4/shapviz/R/sv_interaction.R | 5 shapviz-0.10.4/shapviz/R/sv_waterfall.R | 8 shapviz-0.10.4/shapviz/build/vignette.rds |binary shapviz-0.10.4/shapviz/data/miami.rda |binary shapviz-0.10.4/shapviz/inst/doc/basic_use.Rmd | 10 shapviz-0.10.4/shapviz/inst/doc/basic_use.html | 49 shapviz-0.10.4/shapviz/inst/doc/geographic.html | 15 shapviz-0.10.4/shapviz/inst/doc/multiple_output.html | 10 shapviz-0.10.4/shapviz/inst/doc/tidymodels.Rmd | 9 shapviz-0.10.4/shapviz/inst/doc/tidymodels.html | 37 shapviz-0.10.4/shapviz/man/collapse_shap.Rd | 6 shapviz-0.10.4/shapviz/man/figures/README-bee.png |only shapviz-0.10.4/shapviz/man/figures/README-dep.png |binary shapviz-0.10.4/shapviz/man/figures/README-force.svg | 507 ++++++++-- shapviz-0.10.4/shapviz/man/figures/README-imp.svg | 402 ++++++- shapviz-0.10.4/shapviz/man/figures/README-waterfall.svg | 495 ++++++++- shapviz-0.10.4/shapviz/man/figures/VIGNETTE-tidy-class-normal-dep1.png |binary shapviz-0.10.4/shapviz/man/figures/VIGNETTE-tidy-class-normal-imp.png |binary shapviz-0.10.4/shapviz/man/shapviz-package.Rd | 5 shapviz-0.10.4/shapviz/man/shapviz.Rd | 4 shapviz-0.10.4/shapviz/man/sv_dependence.Rd | 21 shapviz-0.10.4/shapviz/man/sv_dependence2D.Rd | 9 shapviz-0.10.4/shapviz/man/sv_force.Rd | 5 shapviz-0.10.4/shapviz/man/sv_importance.Rd | 4 shapviz-0.10.4/shapviz/man/sv_interaction.Rd | 7 shapviz-0.10.4/shapviz/man/sv_waterfall.Rd | 8 shapviz-0.10.4/shapviz/vignettes/basic_use.Rmd | 10 shapviz-0.10.4/shapviz/vignettes/tidymodels.Rmd | 9 38 files changed, 1431 insertions(+), 343 deletions(-)
Title: Functions for Pre-Processing Data for Multivariate Data
Visualisation using Tours
Description: This is a companion to the book Cook, D. and Laa, U. (2023) <https://dicook.github.io/mulgar_book/>
"Interactively exploring high-dimensional data and models in R".
by Cook and Laa. It contains useful functions for processing data in preparation for
visualising with a tour. There are also several sample data sets.
Author: Dianne Cook [aut, cre] ,
Ursula Laa [aut]
Maintainer: Dianne Cook <dicook@monash.edu>
Diff between mulgar versions 1.0.5 dated 2025-04-06 and 1.0.8 dated 2026-08-31
DESCRIPTION | 12 ++++++------ MD5 | 12 +++++++----- NEWS.md | 12 ++++++++++++ R/data.R | 13 +++++++++++++ R/pca.R | 4 +--- data/fake_trees.rda |only man/fake_trees.Rd |only man/mulgar-package.Rd | 1 + 8 files changed, 40 insertions(+), 14 deletions(-)
Title: Dynamic Multi-Species Size Spectrum Modelling
Description: A set of classes and methods to set up and run multi-species, trait
based and community size spectrum ecological models, focused on the marine
environment.
Author: Gustav Delius [cre, aut, cph] ,
Finlay Scott [aut, cph],
Julia Blanchard [aut, cph] ,
Ken Andersen [aut, cph] ,
Richard Southwell [ctb, cph]
Maintainer: Gustav Delius <gustav.delius@york.ac.uk>
Diff between mizer versions 3.3.0 dated 2026-08-24 and 3.4.0 dated 2026-08-31
mizer-3.3.0/mizer/inst/limit_cycle.R |only mizer-3.3.0/mizer/man/assertExtensionChain.Rd |only mizer-3.3.0/mizer/man/baseMizerClass.Rd |only mizer-3.3.0/mizer/man/clearExtensionChain.Rd |only mizer-3.3.0/mizer/man/compareExtensionChains.Rd |only mizer-3.3.0/mizer/man/defineExtensionClasses.Rd |only mizer-3.3.0/mizer/man/defineOrCheckClass.Rd |only mizer-3.3.0/mizer/man/dispatchExtensions.Rd |only mizer-3.3.0/mizer/man/formatExtensionChain.Rd |only mizer-3.3.0/mizer/man/getRegisteredExtensions.Rd |only mizer-3.3.0/mizer/man/isSuffixChain.Rd |only mizer-3.3.0/mizer/man/providesDispatchMethods.Rd |only mizer-3.3.0/mizer/man/registerExtension.Rd |only mizer-3.3.0/mizer/man/registerExtensions.Rd |only mizer-3.3.0/mizer/man/usesExtensionDispatch.Rd |only mizer-3.4.0/mizer/DESCRIPTION | 8 mizer-3.4.0/mizer/MD5 | 259 +-- mizer-3.4.0/mizer/NAMESPACE | 18 mizer-3.4.0/mizer/NEWS.md | 268 +++ mizer-3.4.0/mizer/R/ArraySpeciesBySize-class.R | 81 mizer-3.4.0/mizer/R/ArrayTimeBySpeciesBySize-class.R | 18 mizer-3.4.0/mizer/R/MizerParams-class.R | 230 +- mizer-3.4.0/mizer/R/MizerScan-class.R | 8 mizer-3.4.0/mizer/R/MizerSim-class.R | 84 - mizer-3.4.0/mizer/R/calibrate.R | 25 mizer-3.4.0/mizer/R/diffusion.R | 2 mizer-3.4.0/mizer/R/extension.R | 180 ++ mizer-3.4.0/mizer/R/generic_methods.R | 15 mizer-3.4.0/mizer/R/getSteadyResidual.R | 636 ++++++- mizer-3.4.0/mizer/R/helpers.R | 163 + mizer-3.4.0/mizer/R/indicator_functions.R | 100 + mizer-3.4.0/mizer/R/info_signals.R | 32 mizer-3.4.0/mizer/R/manipulate_species.R | 27 mizer-3.4.0/mizer/R/plots.R | 14 mizer-3.4.0/mizer/R/project.R | 45 mizer-3.4.0/mizer/R/project_methods.R | 48 mizer-3.4.0/mizer/R/rate_functions.R | 35 mizer-3.4.0/mizer/R/registerExtensions.R | 563 ------ mizer-3.4.0/mizer/R/saveParams.R | 95 - mizer-3.4.0/mizer/R/scanModel.R | 2 mizer-3.4.0/mizer/R/setFishing.R | 54 mizer-3.4.0/mizer/R/setMetadata.R | 9 mizer-3.4.0/mizer/R/species_params.R | 611 ++++++- mizer-3.4.0/mizer/R/steady.R | 145 + mizer-3.4.0/mizer/R/steadyNewton.R | 21 mizer-3.4.0/mizer/R/steadyState.R | 32 mizer-3.4.0/mizer/R/summary_methods.R | 26 mizer-3.4.0/mizer/R/upgrade.R | 20 mizer-3.4.0/mizer/R/validSpeciesParams.R | 21 mizer-3.4.0/mizer/R/zzz.R | 2 mizer-3.4.0/mizer/data/NS_params.rda |binary mizer-3.4.0/mizer/data/NS_sim.rda |binary mizer-3.4.0/mizer/inst/WORDLIST | 60 mizer-3.4.0/mizer/inst/doc/mizer_vignette.html | 4 mizer-3.4.0/mizer/inst/llms.txt | 24 mizer-3.4.0/mizer/inst/skills/analyse-and-plot/SKILL.md | 9 mizer-3.4.0/mizer/inst/skills/analyse-and-plot/quick-reference.md | 5 mizer-3.4.0/mizer/inst/skills/analyse-stability/SKILL.md | 12 mizer-3.4.0/mizer/inst/skills/build-model/SKILL.md | 7 mizer-3.4.0/mizer/inst/skills/calibrate-model/SKILL.md | 13 mizer-3.4.0/mizer/inst/skills/change-parameters/SKILL.md | 64 mizer-3.4.0/mizer/inst/skills/change-parameters/quick-reference.md | 2 mizer-3.4.0/mizer/inst/skills/create-extension-package/SKILL.md | 438 ++--- mizer-3.4.0/mizer/inst/skills/extend-mizer/SKILL.md | 157 + mizer-3.4.0/mizer/inst/skills/run-simulation/SKILL.md | 9 mizer-3.4.0/mizer/inst/skills/upgrade-extension-package |only mizer-3.4.0/mizer/inst/skills/upgrade-mizer-code/SKILL.md | 350 +++- mizer-3.4.0/mizer/inst/skills/upgrade-mizer-code/references/mizer-3.2.md | 11 mizer-3.4.0/mizer/inst/skills/upgrade-mizer-code/references/mizer-3.3.md | 840 ++++------ mizer-3.4.0/mizer/inst/skills/upgrade-mizer-code/references/mizer-3.4.md |only mizer-3.4.0/mizer/inst/skills/use-extension-packages/SKILL.md | 166 - mizer-3.4.0/mizer/man/MizerParams-class.Rd | 6 mizer-3.4.0/mizer/man/MizerScan.Rd | 8 mizer-3.4.0/mizer/man/MizerSim-class.Rd | 6 mizer-3.4.0/mizer/man/NOther.Rd | 5 mizer-3.4.0/mizer/man/addSpecies.Rd | 2 mizer-3.4.0/mizer/man/coerceToExtensionClass.Rd | 26 mizer-3.4.0/mizer/man/completeSpeciesParams.Rd | 88 - mizer-3.4.0/mizer/man/distanceSSLogN.Rd | 34 mizer-3.4.0/mizer/man/dot-hasSlot.Rd |only mizer-3.4.0/mizer/man/ensureExtensionNamespaces.Rd | 4 mizer-3.4.0/mizer/man/extensionRequirements.Rd | 6 mizer-3.4.0/mizer/man/extensionVersions.Rd | 2 mizer-3.4.0/mizer/man/extension_needs_upgrading.Rd | 4 mizer-3.4.0/mizer/man/getEncounter.Rd | 2 mizer-3.4.0/mizer/man/getMeanWeight.Rd | 52 mizer-3.4.0/mizer/man/getSteadyResidual.Rd | 137 + mizer-3.4.0/mizer/man/get_f0_default.Rd | 8 mizer-3.4.0/mizer/man/get_gamma_default.Rd | 8 mizer-3.4.0/mizer/man/indicator_functions.Rd | 1 mizer-3.4.0/mizer/man/initialNOther-set.Rd | 5 mizer-3.4.0/mizer/man/isSteady.Rd | 23 mizer-3.4.0/mizer/man/length_at_size.Rd |only mizer-3.4.0/mizer/man/mizerEncounter.Rd | 2 mizer-3.4.0/mizer/man/objectExtensions.Rd | 4 mizer-3.4.0/mizer/man/other_mort.Rd |only mizer-3.4.0/mizer/man/plotYield.Rd | 3 mizer-3.4.0/mizer/man/project.Rd | 30 mizer-3.4.0/mizer/man/projectUntilSettled.Rd | 7 mizer-3.4.0/mizer/man/reconcileSpeciesParams.Rd |only mizer-3.4.0/mizer/man/recordExtension.Rd | 32 mizer-3.4.0/mizer/man/runExtensionUpgrades.Rd | 2 mizer-3.4.0/mizer/man/saveParams.Rd | 23 mizer-3.4.0/mizer/man/setComponent.Rd | 5 mizer-3.4.0/mizer/man/setMetadata.Rd | 9 mizer-3.4.0/mizer/man/setRateFunction.Rd | 5 mizer-3.4.0/mizer/man/signal_defaulted_length_weight.Rd |only mizer-3.4.0/mizer/man/signal_removed_species_params.Rd |only mizer-3.4.0/mizer/man/simExtensionClass.Rd | 4 mizer-3.4.0/mizer/man/slot-set.Rd |only mizer-3.4.0/mizer/man/slot.Rd |only mizer-3.4.0/mizer/man/slotNames.Rd |only mizer-3.4.0/mizer/man/species_params.Rd | 64 mizer-3.4.0/mizer/man/species_size_range_mask.Rd |only mizer-3.4.0/mizer/man/summary.Rd | 16 mizer-3.4.0/mizer/man/upgrade_s4_to_s3.Rd |only mizer-3.4.0/mizer/man/validObject.Rd |only mizer-3.4.0/mizer/man/validSpeciesParams.Rd | 90 - mizer-3.4.0/mizer/tests/testthat/_snaps/indicator_functions.md | 8 mizer-3.4.0/mizer/tests/testthat/helper.R | 28 mizer-3.4.0/mizer/tests/testthat/test-ArraySpeciesBySize-class.R | 41 mizer-3.4.0/mizer/tests/testthat/test-ArrayTimeBySpeciesBySize-class.R | 14 mizer-3.4.0/mizer/tests/testthat/test-MizerParams-class.R | 10 mizer-3.4.0/mizer/tests/testthat/test-MizerSim-class.R | 25 mizer-3.4.0/mizer/tests/testthat/test-backwards_compatibility.R | 8 mizer-3.4.0/mizer/tests/testthat/test-calibrate.R | 22 mizer-3.4.0/mizer/tests/testthat/test-extension.R | 122 + mizer-3.4.0/mizer/tests/testthat/test-getOscillationModeSim.R | 2 mizer-3.4.0/mizer/tests/testthat/test-getSteadyResidual.R | 347 ++++ mizer-3.4.0/mizer/tests/testthat/test-indicator_functions.R | 68 mizer-3.4.0/mizer/tests/testthat/test-manipulate_species.R | 27 mizer-3.4.0/mizer/tests/testthat/test-plots.R | 11 mizer-3.4.0/mizer/tests/testthat/test-project.R | 37 mizer-3.4.0/mizer/tests/testthat/test-project_methods.R | 14 mizer-3.4.0/mizer/tests/testthat/test-project_n.R | 2 mizer-3.4.0/mizer/tests/testthat/test-registerExtensions.R | 293 --- mizer-3.4.0/mizer/tests/testthat/test-saveParams.R | 109 + mizer-3.4.0/mizer/tests/testthat/test-scanModel.R | 12 mizer-3.4.0/mizer/tests/testthat/test-second_order_summary.R | 12 mizer-3.4.0/mizer/tests/testthat/test-second_order_w.R | 2 mizer-3.4.0/mizer/tests/testthat/test-setFishing.R | 53 mizer-3.4.0/mizer/tests/testthat/test-species_params.R | 558 ++++++ mizer-3.4.0/mizer/tests/testthat/test-steady.R | 171 ++ mizer-3.4.0/mizer/tests/testthat/test-steadyState.R | 31 mizer-3.4.0/mizer/tests/testthat/test-upgrade.R | 20 145 files changed, 6072 insertions(+), 2766 deletions(-)
Title: Data Analysis for IP Addresses and Networks
Description: Classes and functions for working with IP (Internet Protocol)
addresses and networks, inspired by the Python 'ipaddress' module.
Offers full support for both IPv4 and IPv6 (Internet Protocol versions
4 and 6) address spaces. It is specifically designed to work well with
the 'tidyverse'.
Author: David Hall [aut, cre]
Maintainer: David Hall <david.hall.physics@gmail.com>
Diff between ipaddress versions 1.0.3 dated 2025-08-22 and 1.0.4 dated 2026-08-31
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS.md | 4 ++++ R/address_ranges.R | 4 ++-- build/vignette.rds |binary inst/doc/ip-data.html | 5 +++-- inst/doc/recipes.R | 4 ++-- inst/doc/recipes.html | 34 ++++++++++++++-------------------- inst/include/ipaddress/IpAddress.h | 1 + man/exclude_networks.Rd | 4 ++-- man/ip_to_binary.Rd | 8 ++++---- man/ip_to_bytes.Rd | 10 +++++----- man/ip_to_hex.Rd | 8 ++++---- man/ip_to_integer.Rd | 8 ++++---- man/ipaddress-package.Rd | 7 ++++++- 15 files changed, 69 insertions(+), 64 deletions(-)
Title: General Bivariate Copula Theory and Many Utility Functions
Description: Extensive functions for bivariate copula (bicopula) computations and related operations
for bicopula theory. The lower, upper, product, and select other bicopula are implemented along
with operations including the diagonal, survival copula, dual of a copula, co-copula, and
numerical bicopula density. Level sets, horizontal and vertical sections are supported. Numerical
derivatives and inverses of a bicopula are provided through which simulation is implemented.
Bicopula composition, convex combination, asymmetry extension, and products also are provided.
Support extends to the Kendall Function as well as the Lmoments thereof. Kendall Tau,
Spearman Rho and Footrule, Gini Gamma, Blomqvist Beta, Hoeffding Phi, Schweizer-
Wolff Sigma, tail dependency, tail order, skewness, and bivariate Lmoments are implemented, and
positive/negative quadrant dependency, left (right) increasing (decreasing) are available.
Other features include Kullback-Leibler Divergence, Vuong Procedure, spectral measure, [...truncated...]
Author: William Asquith [aut, cre]
Maintainer: William Asquith <william.asquith@ttu.edu>
Diff between copBasic versions 2.2.15 dated 2026-07-22 and 2.2.16 dated 2026-08-31
DESCRIPTION | 8 - MD5 | 41 +++++--- NEWS | 18 +++ R/CIRCcop.R | 9 + man/EuvCOP.Rd | 4 man/EvuCOP.Rd | 4 man/FGMcop.Rd | 6 - man/GLcop.Rd | 4 man/LzCOPpermsym.Rd | 4 man/MOcop.Rd | 2 man/derCOPinv.Rd | 60 ++++++------- man/figures/chck_wolfCOPtestCIRC_plot.jpg |only man/figures/chck_wolfCOPtestCIRC_plot.pdf |only man/figures/chck_wolfCOPtestCL_plotA.jpg |only man/figures/chck_wolfCOPtestCL_plotA.pdf |only man/figures/chck_wolfCOPtestCL_plotB.jpg |only man/figures/chck_wolfCOPtestCL_plotB.pdf |only man/footCOP.Rd | 6 - man/giniCOP.Rd | 138 +++++++++++++++--------------- man/hoefCOP.Rd | 24 +++-- man/joint.curvesCOP.Rd | 47 +++++----- man/joint.curvesCOP2.Rd | 23 ++--- man/wolfCOP.Rd | 2 man/wolfCOPtest.Rd | 42 ++++++--- man/wolfCOPtest_check.Rd |only 25 files changed, 249 insertions(+), 193 deletions(-)
Title: Cross-Entropy Clustering
Description: Splits data into Gaussian type clusters using the Cross-Entropy
Clustering ('CEC') method. This method allows for the simultaneous use of
various types of Gaussian mixture models, for performing the reduction of
unnecessary clusters, and for discovering new clusters by splitting them.
'CEC' is based on the work of Spurek, P. and Tabor, J. (2014)
<doi:10.1016/j.patcog.2014.03.006>.
Author: Kamieniecki Konrad [aut, cph],
Spurek Przemyslaw [ctb],
Simon Garnier [cre, ctb, cph]
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between CEC versions 0.11.3 dated 2026-02-04 and 0.12.0 dated 2026-08-31
CEC-0.11.3/CEC/R/tests.R |only CEC-0.11.3/CEC/inst |only CEC-0.11.3/CEC/tests/run.cec.tests.R |only CEC-0.12.0/CEC/DESCRIPTION | 27 +++--- CEC-0.12.0/CEC/MD5 | 110 ++++++++++++++------------ CEC-0.12.0/CEC/NEWS.md | 37 ++++++++ CEC-0.12.0/CEC/R/cec.R | 112 +++++++++++++++++++-------- CEC-0.12.0/CEC/R/cec.params.R | 9 -- CEC-0.12.0/CEC/R/init.centers.R | 12 ++ CEC-0.12.0/CEC/R/model.covariance.R | 2 CEC-0.12.0/CEC/R/plot.cec.R | 8 + CEC-0.12.0/CEC/R/utils.R | 23 ----- CEC-0.12.0/CEC/README.md | 4 CEC-0.12.0/CEC/man/cec.Rd | 27 +++++- CEC-0.12.0/CEC/src/cec_r.cpp | 104 ++++++++++++++----------- CEC-0.12.0/CEC/src/cec_r.h | 5 - CEC-0.12.0/CEC/src/cec_starter.cpp | 12 ++ CEC-0.12.0/CEC/src/cec_starter.h | 7 + CEC-0.12.0/CEC/src/cluster.h | 36 ++++---- CEC-0.12.0/CEC/src/cov.h | 81 ++++++++++++++----- CEC-0.12.0/CEC/src/exceptions.h | 12 -- CEC-0.12.0/CEC/src/models/cov_utils.cpp | 21 +++-- CEC-0.12.0/CEC/src/models/fixed_covariance.h | 4 CEC-0.12.0/CEC/src/models/model.h | 6 - CEC-0.12.0/CEC/src/parallel_starter.h | 56 ++++++++----- CEC-0.12.0/CEC/src/params.h | 10 +- CEC-0.12.0/CEC/src/r_ext_ptr.h | 4 CEC-0.12.0/CEC/src/r_params.cpp | 5 - CEC-0.12.0/CEC/src/r_utils.h | 6 - CEC-0.12.0/CEC/src/split_starter.cpp | 19 +++- CEC-0.12.0/CEC/src/split_starter.h | 2 CEC-0.12.0/CEC/src/starter.cpp | 29 +++++- CEC-0.12.0/CEC/src/starter.h | 7 - CEC-0.12.0/CEC/src/vec.h | 4 CEC-0.12.0/CEC/tests/testthat |only CEC-0.12.0/CEC/tests/testthat.R |only 36 files changed, 514 insertions(+), 287 deletions(-)
Title: Standardized Metrics Based on the CDC and WHO Growth Charts
Description: Calculation of sex- and age-standardized growth metrics using
the LMS method (lambda-mu-sigma). The package includes functions for the CDC
Growth Charts (cdc_z) and the WHO Charts (who_z). Because CDC recommends
using the WHO Charts for children under 24 months and the CDC Charts among
older children, there can be large differences at age 2.0 years. For example,
a girl weighing 9.9 kg would be at the WHO 10th percentile on the day before
her second birthday, but at the CDC 2nd percentile the following day.
The 'gradual_z' function reduces the differences among 2- to 5-year-olds
by taking a weighted average of the CDC and WHO z-scores.
Author: David Freedman [aut, cre] ,
Carrie Daymont [ctb]
Maintainer: David Freedman <DavidSFreedman@gmail.com>
Diff between cdcanthro versions 0.3.0 dated 2026-07-28 and 0.4.0 dated 2026-08-31
cdcanthro-0.3.0/cdcanthro/R/cdcanthro.R |only cdcanthro-0.3.0/cdcanthro/R/sysdata.rda |only cdcanthro-0.3.0/cdcanthro/man/cdcanthro.Rd |only cdcanthro-0.4.0/cdcanthro/DESCRIPTION | 49 ++++++++++++--------- cdcanthro-0.4.0/cdcanthro/MD5 | 28 +++++++----- cdcanthro-0.4.0/cdcanthro/NAMESPACE | 7 ++- cdcanthro-0.4.0/cdcanthro/NEWS.md | 22 ++++++++- cdcanthro-0.4.0/cdcanthro/R/cdc_z.R |only cdcanthro-0.4.0/cdcanthro/R/grad_Z.R |only cdcanthro-0.4.0/cdcanthro/R/utils-anthro.R |only cdcanthro-0.4.0/cdcanthro/R/who_z.R |only cdcanthro-0.4.0/cdcanthro/R/zzz.R |only cdcanthro-0.4.0/cdcanthro/data/NHanes.rda |binary cdcanthro-0.4.0/cdcanthro/data/cdc_ref_data.rda |binary cdcanthro-0.4.0/cdcanthro/data/who_ref_data.rda |only cdcanthro-0.4.0/cdcanthro/man/NHanes.Rd | 3 - cdcanthro-0.4.0/cdcanthro/man/cdc_ref_data.Rd | 2 cdcanthro-0.4.0/cdcanthro/man/cdc_z.Rd |only cdcanthro-0.4.0/cdcanthro/man/cdcanthro-package.Rd |only cdcanthro-0.4.0/cdcanthro/man/gradual_z.Rd |only cdcanthro-0.4.0/cdcanthro/man/who_ref_data.Rd |only cdcanthro-0.4.0/cdcanthro/man/who_z.Rd |only 22 files changed, 74 insertions(+), 37 deletions(-)
Title: Get Network Representation of an R Package
Description: Tools from the domain of graph theory can be used to quantify the complexity
and vulnerability to failure of a software package. That is the guiding philosophy
of this package. 'pkgnet' provides tools to analyze the dependencies between functions
in an R package and between its imported packages. See the pkgnet website for vignettes
and other supplementary information.
Author: Brian Burns [aut, cre],
James Lamb [aut],
Jay Qi [aut]
Maintainer: Brian Burns <brian.burns.opensource@gmail.com>
Diff between pkgnet versions 0.6.0 dated 2026-01-27 and 0.6.1 dated 2026-08-31
DESCRIPTION | 6 - MD5 | 16 ++-- NEWS.md | 11 +++ R/FunctionReporter.R | 79 +++++++++++++++++++----- README.md | 1 tests/testthat/test-DependencyReporter-class.R | 5 - tests/testthat/test-FunctionReporter-class.R | 49 +++++++++++--- tests/testthat/test-InheritanceReporter-class.R | 7 -- tests/testthat/test-plotting.R | 18 ----- 9 files changed, 124 insertions(+), 68 deletions(-)
Title: Topological Data Analysis: Mapper Algorithm
Description: The Mapper algorithm from Topological Data Analysis, the steps are as follows 1. Define a filter (lens) function on the data. 2. Perform clustering within each level set. 3. Generate a complex from the clustering results.
Author: ChiChien Wang [aut, cre, trl],
Paul Pearson [ctb],
Daniel Muellner [ctb],
Gurjeet Singh [ctb]
Maintainer: ChiChien Wang <kennywang2003@gmail.com>
Diff between MapperAlgo versions 1.1.0 dated 2026-04-13 and 1.2.0 dated 2026-08-31
DESCRIPTION | 15 +- MD5 | 33 ++--- NAMESPACE | 12 + R/Cluster.R | 17 -- R/ClusterMlr3.R |only R/GMapper.R | 2 R/GridSearch.R | 1 R/MapperAlgo.R | 52 ++++++-- R/MapperCorrelation.R | 3 R/Plotter.R | 264 ++++++++++++++++++++++++++++++++++++++++- README.md | 26 +--- inst/example/TestingFMapper.R | 9 - inst/example/TestingGMapper.R | 15 +- inst/example/TestingMapper.R | 40 ++++-- man/MapperAlgo.Rd | 7 - man/MapperCorrelation.Rd | 9 - man/MapperPlotter.Rd | 17 ++ man/MapperPlotter3D.Rd |only man/perform_clustering_mlr3.Rd |only 19 files changed, 412 insertions(+), 110 deletions(-)
Title: Progress Bar with Remaining Time Forecast Method
Description: A simple progress bar showing estimated remaining time.
Multiple forecast methods and user defined forecast method for
the remaining time are supported.
Author: Yangzhuoran Yang [aut, cre]
Maintainer: Yangzhuoran Yang <yangyangzhuoran@gmail.com>
This is a re-admission after prior archival of version 0.1.0 dated 2020-04-28
Diff between lazybar versions 0.1.0 dated 2020-04-28 and 0.1.1 dated 2026-08-31
lazybar-0.1.0/lazybar/R/lpblapply.R |only lazybar-0.1.1/lazybar/DESCRIPTION | 16 lazybar-0.1.1/lazybar/MD5 | 13 lazybar-0.1.1/lazybar/NAMESPACE | 1 lazybar-0.1.1/lazybar/NEWS.md | 11 lazybar-0.1.1/lazybar/R/LazyBar.R | 527 ++++++++++++++------------- lazybar-0.1.1/lazybar/README.md | 168 ++++---- lazybar-0.1.1/lazybar/man/lazyProgressBar.Rd | 2 8 files changed, 386 insertions(+), 352 deletions(-)
Title: Read Data from European Data Format (EDF and EDF+) Files
Description: Import physiologic data stored in
the European Data Format (EDF and EDF+) into R.
Both EDF and EDF+ files are supported. Discontinuous
EDF+ files are not yet supported.
Author: Andreas Henelius [aut, cre],
Finnish Institute of Occupational Health [cph]
Maintainer: Andreas Henelius <andreas.henelius@iki.fi>
Diff between edf versions 1.0.0 dated 2016-04-22 and 1.0.1 dated 2026-08-31
DESCRIPTION | 15 +++++++++------ LICENSE | 2 +- MD5 | 27 ++++++++++++++------------- R/edf.R | 7 +++---- R/read_edf.R | 6 +++--- build |only man/create.variable.name.Rd | 1 - man/edf.Rd | 26 +++++++++++++++++++++++--- man/edf.char.to.num.Rd | 1 - man/parse.edf.annotations.Rd | 1 - man/parse.edf.global.header.Rd | 1 - man/parse.edf.signal.header.Rd | 1 - man/parse.event.Rd | 1 - man/read.edf.Rd | 7 +++---- man/trim.end.Rd | 1 - 15 files changed, 56 insertions(+), 41 deletions(-)
Title: Calculate Distance Measures for DataFrames
Description: It provides functions that calculate Mahalanobis distance, Euclidean distance, Manhattan distance, Chebyshev distance, Hamming distance, Canberra distance, Minkowski dissimilarity (distance defined for p >= 1), Cosine dissimilarity, Bhattacharyya dissimilarity, Jaccard distance, Hellinger distance, Bray-Curtis dissimilarity, Sorensen-Dice dissimilarity between each pair of species in a list of data frames. These statistics are fundamental in various fields, such as cluster analysis, classification, and other applications of machine learning and data mining, where assessing similarity or dissimilarity between data is crucial. The package is designed to be flexible and easily integrated into data analysis workflows, providing reliable tools for evaluating distances in multidimensional contexts.
Author: Flavio Gioia [aut, cre]
Maintainer: Flavio Gioia <flaviogioia.fg@gmail.com>
Diff between cmahalanobis versions 1.0.0 dated 2025-09-14 and 1.1.0 dated 2026-08-31
DESCRIPTION | 13 MD5 | 117 NAMESPACE | 17 R/cmahalanobis.R | 8009 ++++++++++++---------- README.md |only inst/CITATION |only inst/rmarkdown/template_report_cbhattacharyya.Rmd | 577 + inst/rmarkdown/template_report_cbraycurtis.Rmd | 528 - inst/rmarkdown/template_report_ccanberra.Rmd | 523 - inst/rmarkdown/template_report_cchebyshev.Rmd | 508 - inst/rmarkdown/template_report_ccosine.Rmd | 514 - inst/rmarkdown/template_report_ceuclide.Rmd | 499 - inst/rmarkdown/template_report_chamming.Rmd | 509 - inst/rmarkdown/template_report_chellinger.Rmd | 566 + inst/rmarkdown/template_report_cjaccard.Rmd | 539 - inst/rmarkdown/template_report_cmahalanobis.Rmd | 560 + inst/rmarkdown/template_report_cmanhattan.Rmd | 516 - inst/rmarkdown/template_report_cminkowski.Rmd | 521 - inst/rmarkdown/template_report_csorensendice.Rmd | 506 - man/cbhattacharyya.Rd | 119 man/cbraycurtis.Rd | 120 man/ccanberra.Rd | 119 man/cchebyshev.Rd | 47 man/ccosine.Rd | 119 man/ceuclide.Rd | 49 man/chamming.Rd | 119 man/chellinger.Rd | 120 man/cjaccard.Rd | 121 man/cmahalanobis.Rd | 51 man/cmanhattan.Rd | 47 man/cminkowski.Rd | 49 man/csorensendice.Rd | 118 man/figures |only man/generate_report_cbhattacharyya.Rd | 39 man/generate_report_cbraycurtis.Rd | 39 man/generate_report_ccanberra.Rd | 43 man/generate_report_cchebyshev.Rd | 39 man/generate_report_ccosine.Rd | 105 man/generate_report_ceuclide.Rd | 39 man/generate_report_chamming.Rd | 106 man/generate_report_chellinger.Rd | 107 man/generate_report_cjaccard.Rd | 107 man/generate_report_cmahalanobis.Rd | 42 man/generate_report_cmanhattan.Rd | 38 man/generate_report_cminkowski.Rd | 45 man/generate_report_csorensendice.Rd | 39 man/pvaluescbatt.Rd | 110 man/pvaluescbrcu.Rd | 41 man/pvaluesccanb.Rd | 109 man/pvaluesccheb.Rd | 47 man/pvaluesccosi.Rd | 109 man/pvaluesceucl.Rd | 45 man/pvalueschamm.Rd | 111 man/pvalueschell.Rd | 109 man/pvaluescjacc.Rd | 110 man/pvaluescmaha.Rd | 48 man/pvaluescmanh.Rd | 45 man/pvaluescmink.Rd | 53 man/pvaluescsore.Rd | 109 tests/testthat.R | 24 tests/testthat/cmahalanobis.R | 7879 ++++++++++++--------- 61 files changed, 15704 insertions(+), 10253 deletions(-)
Title: Meta Fuzzy Functions
Description: Implements Meta Fuzzy Functions (MFFs) for regression Tak and Ucan (2026) <doi:10.1016/j.asoc.2026.114592> by aggregating predictions from multiple base learners using membership weights learned in the prediction space of validation set. The package supports fuzzy and crisp meta-ensemble structures via Fuzzy C-Means (FCM) Tak (2018) <doi:10.1016/j.asoc.2018.08.009>, Possibilistic FCM (PFCM) Tak (2021) <doi:10.1016/j.ins.2021.01.024>, Gustafson–Kessel (GK) clustering, and k-means, and provides a workflow to (i) generate validation/test prediction matrices from common regression learners (linear and penalized regression via 'glmnet', random forests, gradient boosting with 'xgboost' and 'lightgbm'), (ii) fit cluster-wise meta fuzzy functions and compute membership-based weights, (iii) tune clustering-related hyperparameters (number of clusters/functions, fuzziness exponent, possibilistic regularization) via grid search on validation loss, and (iv) predict on new/test pre [...truncated...]
Author: Nihat Tak [aut, cre],
Sadik Coban [ctb]
Maintainer: Nihat Tak <nihattak@gmail.com>
Diff between MFF versions 0.2.3 dated 2026-08-24 and 0.2.4 dated 2026-08-31
DESCRIPTION | 10 +- MD5 | 43 +++++----- NEWS.md | 17 ++++ R/MFF-package.R | 2 R/evaluate.R | 19 ++++ R/methods-mff.R | 92 ++++++++++++++++++++-- R/mff.R | 67 +++++++++++----- R/predict.mff.R | 29 ++++-- R/tune.mff.R | 158 ++++++++++++++++++++++++++++++-------- R/utils-clustering.R | 53 ++++++++++++ R/utils-validation.R |only inst/doc/mff-workflow.R | 4 inst/doc/mff-workflow.Rmd | 13 +++ inst/doc/mff-workflow.html | 88 ++++++++++++--------- man/MFF-package.Rd | 2 man/mff.Rd | 9 +- man/plot.mff.Rd | 26 ++++-- man/tune.mff.Rd | 12 ++ tests/testthat/test-evaluate.R | 7 + tests/testthat/test-methods-mff.R | 13 +++ tests/testthat/test-mff-predict.R | 47 +++++++++++ tests/testthat/test-tune-mff.R | 72 +++++++++++++++++ vignettes/mff-workflow.Rmd | 13 +++ 23 files changed, 649 insertions(+), 147 deletions(-)
Title: Loss Functions for Assessing Point Forecasts
Description: Implements consistent loss functions and the corresponding identification
functions for point forecasts, including those of the mean, the median,
quantiles, expectiles, moments and Huber functionals
(Gneiting T (2011) <doi:10.1198/jasa.2011.r10138>;
Fissler T, Ziegel JF (2016) <doi:10.1214/16-AOS1439>). Pointwise losses
and realised average scores are both available. Detailed documentation of
the functions' properties is included for facilitating the interpretation
of results.
Author: Hristos Tyralis [aut, cre] ,
Georgia Papacharalampous [aut]
Maintainer: Hristos Tyralis <montchrister@gmail.com>
Diff between scoringfunctions versions 1.1 dated 2025-03-03 and 1.2 dated 2026-08-30
DESCRIPTION | 30 +-- MD5 | 184 +++++++++++++-------- NAMESPACE | 27 ++- R/bmedian_rs.R |only R/bregman1_rs.R |only R/bregman2_rs.R |only R/bregman4_rs.R |only R/errorspread_sf.R | 2 R/expectile_if.R | 4 R/ghuber_rs.R |only R/ghuber_sf.R | 7 R/gpl1_rs.R |only R/gpl1_sf.R | 4 R/gpl2_rs.R |only R/gpl2_sf.R | 2 R/interval_sf.R | 2 R/linex_rs.R |only R/lqmean_rs.R |only R/lqquantile_rs.R |only R/maelog_rs.R |only R/maesd_rs.R |only R/meanexp_if.R |only R/meanpower_if.R |only R/mv_if.R | 2 R/nmoment_rs.R |only R/nmoment_sf.R | 2 R/obsweighted_rs.R |only R/powerweighted_if.R |only R/powerweighted_sf.R |only R/qlike.R |only R/serr_sf.R | 1 R/serrexp_rs.R |only R/serrexp_sf.R | 1 R/serrlog_rs.R |only R/serrlog_sf.R | 1 R/serrpower_rs.R |only R/serrpower_sf.R | 1 R/serrsq_rs.R |only R/serrsq_sf.R | 1 build/partial.rdb |binary inst/CITATION | 46 ++--- man/aerr_sf.Rd | 12 - man/aperr_sf.Rd | 14 + man/bmedian_rs.Rd |only man/bmedian_sf.Rd | 14 + man/bregman1_rs.Rd |only man/bregman1_sf.Rd | 20 +- man/bregman2_rs.Rd |only man/bregman2_sf.Rd | 21 +- man/bregman3_sf.Rd | 14 + man/bregman4_rs.Rd |only man/bregman4_sf.Rd | 14 + man/capping_function.Rd | 27 ++- man/errorspread_sf.Rd | 19 +- man/expectile_if.Rd | 6 man/expectile_rs.Rd | 11 - man/expectile_sf.Rd | 14 + man/ghuber_rs.Rd |only man/ghuber_sf.Rd | 60 ++++-- man/gpl1_rs.Rd |only man/gpl1_sf.Rd | 35 ++-- man/gpl2_rs.Rd |only man/gpl2_sf.Rd | 25 +- man/huber_rs.Rd | 27 +-- man/huber_sf.Rd | 19 +- man/hubermean_if.Rd | 27 ++- man/huberquantile_if.Rd | 36 ++-- man/interval_sf.Rd | 12 - man/linex_rs.Rd |only man/linex_sf.Rd | 31 ++- man/lqmean_rs.Rd |only man/lqmean_sf.Rd | 28 ++- man/lqquantile_rs.Rd |only man/lqquantile_sf.Rd | 25 ++ man/mae.Rd | 4 man/maelog_rs.Rd |only man/maelog_sf.Rd | 8 man/maesd_rs.Rd |only man/maesd_sf.Rd | 8 man/mape.Rd | 8 man/mean_if.Rd | 16 + man/meanexp_if.Rd |only man/meanlog_if.Rd | 37 +++- man/meanpower_if.Rd |only man/mre.Rd | 6 man/mse.Rd | 6 man/mspe.Rd | 6 man/msre.Rd | 6 man/mv_if.Rd | 19 +- man/mv_sf.Rd | 33 ++- man/nmoment_if.Rd | 29 +-- man/nmoment_rs.Rd |only man/nmoment_sf.Rd | 20 +- man/nse.Rd | 42 +++- man/obsweighted_rs.Rd |only man/obsweighted_sf.Rd | 20 +- man/powerweighted_if.Rd |only man/powerweighted_sf.Rd |only man/qlike.Rd |only man/quantile_if.Rd | 19 +- man/quantile_level.Rd | 32 +++ man/quantile_rs.Rd | 11 - man/quantile_sf.Rd | 14 + man/relerr_sf.Rd | 38 +++- man/scoringfunctions-package.Rd | 343 +++++++++++++++++++++++++++++++++------- man/serr_sf.Rd | 14 + man/serrexp_rs.Rd |only man/serrexp_sf.Rd | 39 +++- man/serrlog_rs.Rd |only man/serrlog_sf.Rd | 38 +++- man/serrpower_rs.Rd |only man/serrpower_sf.Rd | 35 ++-- man/serrsq_rs.Rd |only man/serrsq_sf.Rd | 26 +-- man/sperr_sf.Rd | 24 +- man/srelerr_sf.Rd | 25 ++ 116 files changed, 1245 insertions(+), 509 deletions(-)
More information about scoringfunctions at CRAN
Permanent link
Title: High-Dimensional Mediation Analysis
Description: Allows to estimate and test high-dimensional mediation effects based on advanced mediator screening and penalized regression techniques. Methods used in the package refer to Zhang H, Zheng Y, Hou L, Liu L, HIMA: An R Package for High-Dimensional Mediation Analysis. Journal of Data Science. (2025). <doi:10.6339/25-JDS1192>.
Author: Yinan Zheng [aut, cre] ,
Haixiang Zhang [aut],
Lifang Hou [aut],
Lei Liu [aut, cph]
Maintainer: Yinan Zheng <y-zheng@northwestern.edu>
This is a re-admission after prior archival of version 2.3.3 dated 2025-11-17
Diff between HIMA versions 2.3.3 dated 2025-11-17 and 2.3.4 dated 2026-08-30
DESCRIPTION | 12 +++---- MD5 | 20 +++++++------ NAMESPACE | 1 NEWS.md | 4 ++ R/HIMA-package.R | 5 +-- R/hima_classic.R | 2 - R/hima_dblasso.R | 10 +++++- R/utils.R | 67 ++++++++++++++++++++++++++++++++++++++++++++ inst/doc/hima-vignette.html | 9 +++-- man/HIMA-package.Rd | 2 - tests |only 11 files changed, 105 insertions(+), 27 deletions(-)
Title: Advanced and Fast Data Transformation
Description: A large C/C++-based package for advanced data transformation and
statistical computing in R that is extremely fast, class-agnostic, robust, and
programmer friendly. Core functionality includes a rich set of S3 generic grouped
and weighted statistical functions for vectors, matrices and data frames, which
provide efficient low-level vectorizations, OpenMP multithreading, and skip missing
values by default. These are integrated with fast grouping and ordering algorithms
(also callable from C), and efficient data manipulation functions. The package also
provides a flexible and rigorous approach to time series and panel data in R, fast
functions for data transformation and common statistical procedures, detailed
(grouped, weighted) summary statistics, powerful tools to work with nested data,
fast data object conversions, functions for memory efficient R programming, and
helpers to effectively deal with variable labels, attributes, and missing data. It
seamlessly supports base R objects/cla [...truncated...]
Author: Sebastian Krantz [aut, cre] ,
Matt Dowle [ctb],
Arun Srinivasan [ctb],
Morgan Jacob [ctb],
Dirk Eddelbuettel [ctb],
Laurent Berge [ctb],
Kevin Tappe [ctb],
Alina Cherkas [ctb],
Ivan Krylov [ctb],
R Core Team and contributors worldwide [ctb],
Martyn P [...truncated...]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between collapse versions 2.1.7 dated 2026-05-19 and 2.1.8 dated 2026-08-30
collapse-2.1.7/collapse/inst/doc/collapse_and_data.table.Rmd |only collapse-2.1.7/collapse/inst/doc/collapse_and_data.table.html |only collapse-2.1.7/collapse/inst/doc/collapse_and_dplyr.R |only collapse-2.1.7/collapse/inst/doc/collapse_and_dplyr.Rmd |only collapse-2.1.7/collapse/inst/doc/collapse_and_dplyr.html |only collapse-2.1.7/collapse/inst/doc/collapse_and_plm.Rmd |only collapse-2.1.7/collapse/inst/doc/collapse_and_plm.html |only collapse-2.1.7/collapse/inst/doc/collapse_intro.Rmd |only collapse-2.1.7/collapse/inst/doc/collapse_intro.html |only collapse-2.1.7/collapse/vignettes/collapse_and_data.table.Rmd |only collapse-2.1.7/collapse/vignettes/collapse_and_dplyr.Rmd |only collapse-2.1.7/collapse/vignettes/collapse_and_plm.Rmd |only collapse-2.1.7/collapse/vignettes/collapse_intro.Rmd |only collapse-2.1.8/collapse/DESCRIPTION | 8 - collapse-2.1.8/collapse/MD5 | 45 +++------ collapse-2.1.8/collapse/NEWS.md | 8 + collapse-2.1.8/collapse/build/partial.rdb |binary collapse-2.1.8/collapse/build/vignette.rds |binary collapse-2.1.8/collapse/inst/CITATION | 2 collapse-2.1.8/collapse/inst/doc/collapse_documentation.Rmd | 2 collapse-2.1.8/collapse/inst/doc/collapse_documentation.html | 6 - collapse-2.1.8/collapse/inst/doc/collapse_for_tidyverse_users.html | 4 collapse-2.1.8/collapse/inst/doc/collapse_object_handling.html | 4 collapse-2.1.8/collapse/man/collapse-documentation.Rd | 2 collapse-2.1.8/collapse/src/match.c | 3 collapse-2.1.8/collapse/src/programming.c | 49 ++++++++-- collapse-2.1.8/collapse/src/small_helper.c | 2 collapse-2.1.8/collapse/tests/testthat/test-fmatch.R | 25 +++++ collapse-2.1.8/collapse/tests/testthat/test-fslice.R | 20 ++++ collapse-2.1.8/collapse/vignettes/collapse_documentation.Rmd | 2 30 files changed, 128 insertions(+), 54 deletions(-)
Title: R Interface to the 'Uno' Nonlinear Optimization Solver
Description: Bindings to 'Uno' (Unifying Nonlinear Optimization), a C++ solver
for smooth nonlinearly constrained optimization. 'Uno' unifies Lagrange-Newton
methods, including sequential quadratic programming and interior-point
methods, by decomposing them into interacting building blocks
(constraint-relaxation, inequality-handling, Hessian, and globalization
strategies) that can be freely combined, either through options or through
presets that reproduce established solvers such as 'filterSQP' and 'IPOPT'.
The framework is described in Vanaret and Leyffer (2024)
<doi:10.48550/arXiv.2406.13454>.
Author: Balasubramanian Narasimhan [aut, cre],
Charlie Vanaret [aut, cph] ,
Sven Leyffer [aut, cph] ,
HiGHS development team [cph] ; see
inst/COPYRIGHTS)
Maintainer: Balasubramanian Narasimhan <naras@stanford.edu>
Diff between Uno versions 2.7.4 dated 2026-06-17 and 2.7.4-1 dated 2026-08-30
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 9 +++++++++ build/vignette.rds |binary inst/uno/uno/linear_algebra/VectorView.hpp | 1 + 5 files changed, 18 insertions(+), 8 deletions(-)
Title: Statistical Methods for Quantitative Finance
Description: Provides data and functions used in the book "Statistical Methods for Quantitative Finance"
by David Ardia (2026).
Author: David Ardia [aut, cre, cph, fnd] ,
Marius Hofert [ctb, cph] ,
Kurt Hornik [ctb, cph] ,
Alexander J. McNeil [ctb, cph] ,
Dries Cornilly [ctb, cph] was ported under GPL-2 | GPL-3),
Kris Boudt [ctb, cph] was ported under GPL-2 | GPL-3)
Maintainer: David Ardia <david.ardia.ch@gmail.com>
Diff between smqf versions 1.1-7 dated 2026-08-23 and 1.1-8 dated 2026-08-30
DESCRIPTION | 6 +- MD5 | 10 +-- NEWS.md | 52 ++++++++++++++++++++ tests/testthat/test-efficient-frontier.R | 80 +++++++++++++++++++++++++++---- tests/testthat/test-mvsk-portfolio.R | 1 tests/testthat/test-tail-dependence.R | 3 + 6 files changed, 135 insertions(+), 17 deletions(-)
Title: Interface to the SCIP Optimization Suite
Description: Provides an R interface to SCIP (Solving Constraint Integer Programs), a framework for mixed-integer
programming (MIP), mixed-integer nonlinear programming (MINLP), and constraint integer programming
(2025, <doi:10.48550/arXiv.2511.18580>). Supports linear, quadratic, SOS, indicator, and knapsack
constraints with continuous, binary, and integer variables. Includes a one-shot solver interface
and a model-building API for incremental problem construction.
Author: Balasubramanian Narasimhan [aut, cre] ,
SCIP Optimization Suite Authors [cph]
Maintainer: Balasubramanian Narasimhan <naras@stanford.edu>
Diff between scip versions 1.10.0-3 dated 2026-04-10 and 1.10.0-4 dated 2026-08-30
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 10 ++++++++++ build/vignette.rds |binary inst/scip/src/scip/githash.c | 2 +- inst/scip/src/scip/multiprecision.hpp | 1 + inst/soplex/src/soplex/basevectors.h | 2 ++ inst/soplex/src/soplex/git_hash.cpp | 2 +- inst/soplex/src/soplex/mpsinput.cpp | 1 + 9 files changed, 27 insertions(+), 13 deletions(-)
Title: Create, Manipulate and Query Parameter Terms
Description: Creates, manipulates, queries and repairs vectors of
parameter terms. Parameter terms are the labels used to reference
values in vectors, matrices and arrays. They represent the names in
coefficient tables and the column names in 'mcmc' and 'mcmc.list'
objects.
Author: Joe Thorley [aut, cre] ,
Kirill Mueller [aut] ,
Ayla Pearson [ctb] ,
Evan Amies-Galonski [ctb] ,
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between term versions 0.3.7 dated 2026-01-30 and 0.4.0 dated 2026-08-30
term-0.3.7/term/R/extras.R |only term-0.3.7/term/R/levels.R |only term-0.3.7/term/tests/testthat/out |only term-0.4.0/term/DESCRIPTION | 10 term-0.4.0/term/MD5 | 162 +++++++------- term-0.4.0/term/NAMESPACE | 41 ++- term-0.4.0/term/NEWS.md | 46 +++ term-0.4.0/term/R/as-data-frame.R | 7 term-0.4.0/term/R/as-term-rcrd.R | 4 term-0.4.0/term/R/chk.R | 28 +- term-0.4.0/term/R/complete-terms.R | 3 term-0.4.0/term/R/deprecated.R | 52 +--- term-0.4.0/term/R/format.R | 5 term-0.4.0/term/R/internal.R | 23 + term-0.4.0/term/R/namespace.R | 2 term-0.4.0/term/R/new-term-rcrd.R | 6 term-0.4.0/term/R/params.R | 4 term-0.4.0/term/R/pars.R | 16 - term-0.4.0/term/R/pdims.R | 4 term-0.4.0/term/R/set-pars.R | 45 +++ term-0.4.0/term/R/subset.R | 6 term-0.4.0/term/R/summary.R | 5 term-0.4.0/term/R/term.R | 8 term-0.4.0/term/R/tindex.R | 3 term-0.4.0/term/R/vec-cast-term.R | 2 term-0.4.0/term/R/vld.R | 4 term-0.4.0/term/man/NA_term_.Rd | 5 term-0.4.0/term/man/NA_term_rcrd_.Rd | 5 term-0.4.0/term/man/complete_terms.Rd | 2 term-0.4.0/term/man/deprecated.Rd | 14 - term-0.4.0/term/man/params.Rd | 4 term-0.4.0/term/man/pars.character.Rd | 10 term-0.4.0/term/man/pars.default.Rd | 10 term-0.4.0/term/man/pars.term.Rd | 18 - term-0.4.0/term/man/pars.term_rcrd.Rd | 10 term-0.4.0/term/man/pars_terms.Rd | 10 term-0.4.0/term/man/reexports.Rd | 4 term-0.4.0/term/man/set_pars.term_rcrd.Rd |only term-0.4.0/term/man/term-package.Rd | 1 term-0.4.0/term/man/term.Rd | 6 term-0.4.0/term/man/term_rcrd.Rd | 6 term-0.4.0/term/man/tindex.Rd | 6 term-0.4.0/term/man/valid_term.Rd | 4 term-0.4.0/term/man/vld_term.Rd | 7 term-0.4.0/term/tests/testthat/_snaps |only term-0.4.0/term/tests/testthat/test-anyduplicated.R | 20 + term-0.4.0/term/tests/testthat/test-as-term-rcrd.R | 93 ++++++-- term-0.4.0/term/tests/testthat/test-as-term.R | 75 +++++- term-0.4.0/term/tests/testthat/test-chk.R | 14 - term-0.4.0/term/tests/testthat/test-complete-terms.R | 41 +-- term-0.4.0/term/tests/testthat/test-consistent-term.R | 45 +++ term-0.4.0/term/tests/testthat/test-deprecated.R | 16 - term-0.4.0/term/tests/testthat/test-inconsistent-terms.R | 20 + term-0.4.0/term/tests/testthat/test-internal.R | 19 + term-0.4.0/term/tests/testthat/test-is-incomplete-terms.R | 14 - term-0.4.0/term/tests/testthat/test-new-term-rcrd.R | 33 ++ term-0.4.0/term/tests/testthat/test-normalize-terms.R | 15 + term-0.4.0/term/tests/testthat/test-npars.R | 15 - term-0.4.0/term/tests/testthat/test-npdims.R | 19 + term-0.4.0/term/tests/testthat/test-pars-terms.R | 18 + term-0.4.0/term/tests/testthat/test-pars.R | 83 +++++-- term-0.4.0/term/tests/testthat/test-pdims.R | 40 ++- term-0.4.0/term/tests/testthat/test-print.R | 26 +- term-0.4.0/term/tests/testthat/test-rep.R | 10 term-0.4.0/term/tests/testthat/test-repair-terms.R | 35 ++- term-0.4.0/term/tests/testthat/test-scalar-term.R | 5 term-0.4.0/term/tests/testthat/test-set-pars.R | 88 ++++--- term-0.4.0/term/tests/testthat/test-subset.R | 75 +++--- term-0.4.0/term/tests/testthat/test-summary.R | 5 term-0.4.0/term/tests/testthat/test-term-compat.R | 22 + term-0.4.0/term/tests/testthat/test-term-rcrd.R | 5 term-0.4.0/term/tests/testthat/test-term.R | 32 ++ term-0.4.0/term/tests/testthat/test-tindex.R | 26 +- term-0.4.0/term/tests/testthat/test-unique.R | 4 term-0.4.0/term/tests/testthat/test-utils.R | 2 term-0.4.0/term/tests/testthat/test-valid-term.R | 30 ++ term-0.4.0/term/tests/testthat/test-vld.R | 60 ++++- 77 files changed, 1079 insertions(+), 534 deletions(-)
Title: Manipulate MCMC Samples
Description: Functions and classes to store, manipulate and summarise
Monte Carlo Markov Chain (MCMC) samples. For more information see
Brooks et al. (2011) <isbn:978-1-4200-7941-8>.
Author: Joe Thorley [aut, cre] ,
Kirill Mueller [ctb] ,
Nadine Hussein [ctb] ,
Ayla Pearson [ctb] ,
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between mcmcr versions 0.6.2 dated 2025-01-23 and 0.7.0 dated 2026-08-30
mcmcr-0.6.2/mcmcr/R/parameters.R |only mcmcr-0.6.2/mcmcr/tests/testthat/test-parameters.R |only mcmcr-0.7.0/mcmcr/DESCRIPTION | 20 - mcmcr-0.7.0/mcmcr/MD5 | 204 ++++++------- mcmcr-0.7.0/mcmcr/NAMESPACE | 102 +++--- mcmcr-0.7.0/mcmcr/NEWS.md | 44 ++ mcmcr-0.7.0/mcmcr/R/as-mcmc.list.R | 10 mcmcr-0.7.0/mcmcr/R/as-mcmcarray.R | 8 mcmcr-0.7.0/mcmcr/R/as-mcmcr.R | 4 mcmcr-0.7.0/mcmcr/R/as-mcmcrs.R | 4 mcmcr-0.7.0/mcmcr/R/as-term.R | 4 mcmcr-0.7.0/mcmcr/R/bind-dimensions-n.R | 8 mcmcr-0.7.0/mcmcr/R/bind-dimensions.R | 27 + mcmcr-0.7.0/mcmcr/R/check.R | 23 + mcmcr-0.7.0/mcmcr/R/chk.R | 51 ++- mcmcr-0.7.0/mcmcr/R/coef.R | 192 ++++++++++-- mcmcr-0.7.0/mcmcr/R/combine-dimensions.R | 13 mcmcr-0.7.0/mcmcr/R/combine-samples.R | 14 mcmcr-0.7.0/mcmcr/R/converged.R | 42 ++ mcmcr-0.7.0/mcmcr/R/internal.R | 27 + mcmcr-0.7.0/mcmcr/R/mcmc-aperm.R | 5 mcmcr-0.7.0/mcmcr/R/mcmc-map.R | 8 mcmcr-0.7.0/mcmcr/R/mcmcr-package.R | 2 mcmcr-0.7.0/mcmcr/R/params.R | 8 mcmcr-0.7.0/mcmcr/R/pars.R | 25 + mcmcr-0.7.0/mcmcr/R/rhat.R | 12 mcmcr-0.7.0/mcmcr/R/sort.R | 4 mcmcr-0.7.0/mcmcr/R/split-chains.R | 4 mcmcr-0.7.0/mcmcr/R/subset.R | 68 +++- mcmcr-0.7.0/mcmcr/R/terms.R | 8 mcmcr-0.7.0/mcmcr/R/tidy.R | 19 + mcmcr-0.7.0/mcmcr/R/zero.R | 2 mcmcr-0.7.0/mcmcr/README.md | 22 - mcmcr-0.7.0/mcmcr/inst/JOSS/paper.bib | 6 mcmcr-0.7.0/mcmcr/inst/WORDLIST | 1 mcmcr-0.7.0/mcmcr/man/as.mcarray.Rd | 8 mcmcr-0.7.0/mcmcr/man/as.mcmcarray.Rd | 8 mcmcr-0.7.0/mcmcr/man/as.mcmcr.Rd | 12 mcmcr-0.7.0/mcmcr/man/as_nlist.mcmcr.Rd | 4 mcmcr-0.7.0/mcmcr/man/as_nlists.mcmcr.Rd | 4 mcmcr-0.7.0/mcmcr/man/bind_dimensions.Rd | 6 mcmcr-0.7.0/mcmcr/man/bind_dimensions_n.Rd | 6 mcmcr-0.7.0/mcmcr/man/bind_parameters.Rd | 6 mcmcr-0.7.0/mcmcr/man/coef.Rd | 20 + mcmcr-0.7.0/mcmcr/man/combine_dimensions.Rd | 6 mcmcr-0.7.0/mcmcr/man/combine_samples.Rd | 6 mcmcr-0.7.0/mcmcr/man/combine_samples_n.Rd | 6 mcmcr-0.7.0/mcmcr/man/figures/README-unnamed-chunk-2-1.png |binary mcmcr-0.7.0/mcmcr/man/figures/logo.png |binary mcmcr-0.7.0/mcmcr/man/fill_all.mcarray.Rd | 4 mcmcr-0.7.0/mcmcr/man/fill_all.mcmcarray.Rd | 4 mcmcr-0.7.0/mcmcr/man/fill_all.mcmcr.Rd | 4 mcmcr-0.7.0/mcmcr/man/fill_na.mcarray.Rd | 4 mcmcr-0.7.0/mcmcr/man/fill_na.mcmcarray.Rd | 4 mcmcr-0.7.0/mcmcr/man/fill_na.mcmcr.Rd | 4 mcmcr-0.7.0/mcmcr/man/is.mcarray.Rd | 8 mcmcr-0.7.0/mcmcr/man/is.mcmcarray.Rd | 8 mcmcr-0.7.0/mcmcr/man/is.mcmcr.Rd | 8 mcmcr-0.7.0/mcmcr/man/is.mcmcrs.Rd | 8 mcmcr-0.7.0/mcmcr/man/mcmc_aperm.Rd | 4 mcmcr-0.7.0/mcmcr/man/mcmc_map.Rd | 4 mcmcr-0.7.0/mcmcr/man/mcmcarray-object.Rd | 2 mcmcr-0.7.0/mcmcr/man/mcmcr-object.Rd | 2 mcmcr-0.7.0/mcmcr/man/mcmcr-package.Rd | 5 mcmcr-0.7.0/mcmcr/man/mcmcr_example.Rd | 2 mcmcr-0.7.0/mcmcr/man/mcmcrs-object.Rd | 2 mcmcr-0.7.0/mcmcr/man/mcmcrs.Rd | 8 mcmcr-0.7.0/mcmcr/man/params.Rd | 9 mcmcr-0.7.0/mcmcr/man/reexports.Rd | 20 - mcmcr-0.7.0/mcmcr/man/vld_mcmcr.Rd | 2 mcmcr-0.7.0/mcmcr/tests/testthat/test-aaa-deprecated.R | 47 ++ mcmcr-0.7.0/mcmcr/tests/testthat/test-aaa-zero.R | 12 mcmcr-0.7.0/mcmcr/tests/testthat/test-as-mcarray.R | 8 mcmcr-0.7.0/mcmcr/tests/testthat/test-as-mcmc.R | 7 mcmcr-0.7.0/mcmcr/tests/testthat/test-as-mcmcarray.R | 8 mcmcr-0.7.0/mcmcr/tests/testthat/test-as-mcmcr.R | 10 mcmcr-0.7.0/mcmcr/tests/testthat/test-as-term.R | 32 +- mcmcr-0.7.0/mcmcr/tests/testthat/test-bind-chains.R | 55 ++- mcmcr-0.7.0/mcmcr/tests/testthat/test-bind-dimensions-n.R | 6 mcmcr-0.7.0/mcmcr/tests/testthat/test-bind-dimensions.R | 11 mcmcr-0.7.0/mcmcr/tests/testthat/test-bind-iterations.R | 26 + mcmcr-0.7.0/mcmcr/tests/testthat/test-bind-parameters.R | 24 + mcmcr-0.7.0/mcmcr/tests/testthat/test-chk.R | 30 + mcmcr-0.7.0/mcmcr/tests/testthat/test-coef.R | 169 +++++++++- mcmcr-0.7.0/mcmcr/tests/testthat/test-combine-dimensions.R | 45 ++ mcmcr-0.7.0/mcmcr/tests/testthat/test-combine-samples-n.R | 65 +++- mcmcr-0.7.0/mcmcr/tests/testthat/test-converged.R | 16 - mcmcr-0.7.0/mcmcr/tests/testthat/test-esr.R | 193 ++++++++++-- mcmcr-0.7.0/mcmcr/tests/testthat/test-ess.R | 42 ++ mcmcr-0.7.0/mcmcr/tests/testthat/test-estimates.R | 101 +++++- mcmcr-0.7.0/mcmcr/tests/testthat/test-fill-all.R | 12 mcmcr-0.7.0/mcmcr/tests/testthat/test-fill-na.R | 12 mcmcr-0.7.0/mcmcr/tests/testthat/test-mcmc-aperm.R | 10 mcmcr-0.7.0/mcmcr/tests/testthat/test-mcmc-map.R | 69 +++- mcmcr-0.7.0/mcmcr/tests/testthat/test-npdims.R | 5 mcmcr-0.7.0/mcmcr/tests/testthat/test-nsims.R | 10 mcmcr-0.7.0/mcmcr/tests/testthat/test-pars.R | 11 mcmcr-0.7.0/mcmcr/tests/testthat/test-pdims.R | 25 + mcmcr-0.7.0/mcmcr/tests/testthat/test-rhat.R | 116 ++++++- mcmcr-0.7.0/mcmcr/tests/testthat/test-split-chains.R | 4 mcmcr-0.7.0/mcmcr/tests/testthat/test-subset.R | 35 +- mcmcr-0.7.0/mcmcr/tests/testthat/test-summary.R | 12 mcmcr-0.7.0/mcmcr/tests/testthat/test-tidy.R | 32 +- mcmcr-0.7.0/mcmcr/tests/testthat/test-vld.R | 6 104 files changed, 1866 insertions(+), 599 deletions(-)
Title: 'DEXi' Decision Tree Analysis and Visualization
Description: Provides a versatile toolkit for analyzing and visualizing 'DEXi' (Decision EXpert for education)
decision trees, facilitating multi-criteria decision analysis directly within R. Users can
read .dxi files, manipulate decision trees, and evaluate various scenarios. It supports sensitivity
analysis through Monte Carlo simulations, one-at-a-time approaches, and variance-based
methods, helping to discern the impact of input variations. Additionally, it includes functionalities
for generating sampling plans and an array of visualization options for decision trees and
analysis results. A distinctive feature is the synoptic table plot, aiding in the efficient
comparison of scenarios. Whether for in-depth decision modeling or sensitivity analysis, this
package stands as a comprehensive solution. Definition of sensitivity analyses available in
Carpani, Bergez and Monod (2012) <doi:10.1016/j.envsoft.2011.10.002> and detailed description of the package available in
Alaphilippe et al. (2025) [...truncated...]
Author: Roland Allart [aut],
Jacques-Eric Bergez [aut] ,
Marta Carpani [aut],
Herve Monod [aut] ,
Aude Alaphilippe [ctb] ,
Nicolas Cavan [ctb, cre],
INRAE [cph] )
Maintainer: Nicolas Cavan <nicolas.cavan@inrae.fr>
Diff between dexisensitivity versions 1.0.2 dated 2025-09-08 and 1.0.3 dated 2026-08-30
DESCRIPTION | 8 MD5 | 31 +-- NEWS.md | 6 R/data.R | 2 R/option.R | 28 ++ R/synoptique.R | 125 ++++++++++--- README.md | 2 inst/testdata/data_synoptic_graph_dexifruits_v1.rds |binary inst/testdata/data_synoptic_graph_dexifruits_v1_depth5.rds |only inst/testdata/data_synoptic_graph_masc2.rds |binary inst/testdata/data_synoptic_graph_missing_values_masc2.rds |binary man/create_list_synoptique.Rd | 19 + man/create_synoptique.Rd | 14 + man/dexisensitivity-package.Rd | 2 man/masc2.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/test-synoptique.R | 38 +++ 17 files changed, 218 insertions(+), 59 deletions(-)
More information about dexisensitivity at CRAN
Permanent link
Title: Health Geography Toolbox for Model-Based Analysis of Infections
Panel Data
Description: Within epidemic outbreaks, infections grow and decline differently between regions, and the velocity of spatial spread differs between countries. The swash library offers a set of model-based analyses for these topics. Spread velocity may be analysed with the Swash-Backwash Model for the Single Epidemic Wave and corresponding functions for bootstrap confidence intervals, country comparison, and visualization of results. Differences in epidemic growth between regions may be analysed using logistic growth models, exponential growth models, Hawkes processes and breakpoint analyses. All functionalities are accessed by the class "infpan" for infections panel data defined in this package, which is built from a data.frame provided by the user.
Author: Thomas Wieland [aut, cre]
Maintainer: Thomas Wieland <geowieland@googlemail.com>
Diff between swash versions 2.0.1 dated 2026-05-24 and 2.0.2 dated 2026-08-30
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 7 +++++-- R/swash.R | 22 ++++++++++++++++++---- build/partial.rdb |binary data/C19dNUTSdata.rda |binary data/COVID19Cases_geoRegion.rda |binary data/Infections.rda |binary data/Oesterreich_Faelle.rda |binary data/RKI_Corona_counties.rda |binary data/did_fatalities_splm_coef.rda |binary man/C19dNUTSdata.Rd | 2 +- 12 files changed, 39 insertions(+), 22 deletions(-)
Title: Estimation of Overlapping in Empirical Distributions
Description: Functions for estimating the overlapping area of two or more kernel density estimations from empirical data.
Author: Massimiliano Pastore [aut, cre],
Pierfrancesco Alaimo Di Loro [ctb],
Marco Mingione [ctb],
Antonio Calcagni' [ctb]
Maintainer: Massimiliano Pastore <massimiliano.pastore@unipd.it>
Diff between overlapping versions 2.4 dated 2026-02-19 and 2.5 dated 2026-08-30
DESCRIPTION | 8 +++--- MD5 | 25 ++++++++++++--------- NAMESPACE | 2 - NEWS.md | 59 ++++++++++++++++++++++++++++----------------------- R/boot.overlap.R | 9 +++++-- R/check.missing.R |only R/overlap.R | 4 +++ R/ovmult.R | 3 ++ R/perm.test.R | 6 ++--- inst |only man/boot.overlap.Rd | 22 ++++++++++++++++++- man/check.missing.Rd |only man/overlap.Rd | 6 +++++ man/ovmult.Rd | 8 ++++++ man/perm.test.Rd | 3 +- 15 files changed, 105 insertions(+), 50 deletions(-)
Title: Sequence Manipulation Utilities
Description: Tools for reading and writing biological sequences in multiple
formats, including 'FASTA', 'PHYLIP', 'CLUSTAL', 'STOCKHOLM', 'MEGA' and
'GenBank'. Supports interleaved and sequential layouts where applicable,
and reads or writes gzip, bzip2 and xz compressed files transparently.
Converts between formats, renames sequences via a two-column mapping,
summarizes sequence counts, lengths, GC content and ambiguous characters,
and manipulates sequence sets (e.g., filtering by patterns and computing
consensus sequences from alignments). Also includes functions to download
nucleotide records from NCBI by accession.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between seqmagick versions 0.1.8 dated 2026-01-31 and 0.1.9 dated 2026-08-30
.aspell |only DESCRIPTION | 23 MD5 | 129 NAMESPACE | 103 NEWS.md | 141 R/NCBI.R | 199 - R/aln.R | 62 R/bam2DNAStringSet.R | 76 R/consensus.R | 267 - R/fa_combine.R | 60 R/fa_conversion.R | 66 R/fas2phy.R | 34 R/filter.R | 141 R/get_id.R | 36 R/hamming.R | 230 - R/mega.r | 246 - R/phy2fas.R | 36 R/phylip.R | 16 R/read.R | 424 +- R/rename.R | 189 - R/renameTXT.R | 116 R/replaceInside.R | 121 R/seqlen.R | 71 R/seqmagick-package.R | 6 R/utilities.R | 31 R/write.R | 279 - README.md |only build/vignette.rds |binary inst/doc/seqmagick.R | 163 inst/doc/seqmagick.Rmd | 344 + inst/doc/seqmagick.html | 821 ++-- inst/extdata/AB115403.fa | 22 inst/extdata/AB115403.gb | 112 inst/extdata/HA.fas | 4612 ++++++++++++------------- inst/extdata/HA.phy | 202 - inst/extdata/mega/Chloroplast_Martin.meg | 5538 +++++++++++++++---------------- inst/extdata/mega/Crab_rRNA.meg | 256 - inst/extdata/mega/D-loop_Vigilant.meg | 152 inst/extdata/mega/Drosophila_Adh.meg | 468 +- man/bam2DNAStringSet.Rd | 44 man/bam2DNAStringSet2.Rd | 44 man/bs_aln.Rd | 62 man/bs_filter.Rd | 62 man/bs_hamming.Rd | 66 man/bs_rename.Rd | 56 man/consensus.Rd | 82 man/download_genbank.Rd | 68 man/fa_combine.Rd | 70 man/fa_conversion.Rd | 72 man/fa_filter.Rd | 74 man/fa_rename.Rd | 67 man/fa_summary.Rd |only man/fa_write.Rd | 66 man/fas2phy.Rd | 54 man/get_id.Rd | 58 man/msa-read.Rd | 4 man/phy2fas.Rd | 58 man/phy_read.Rd | 48 man/phy_write.Rd | 66 man/renameTXT.Rd | 54 man/replaceInside.Rd | 54 man/seqlen.Rd | 40 man/seqmagick-package.Rd | 7 tests |only vignettes/seqmagick.Rmd | 344 + vignettes/seqmagick.bib | 2 66 files changed, 9014 insertions(+), 8400 deletions(-)
Title: Inferential Methods for Multimodal and Other Networks
Description: A set of tools for testing networks.
It includes functions for univariate and multivariate conditional uniform graph
and quadratic assignment procedure testing, and network regression.
The package is a complement to
'Multimodal Political Networks' (2021, ISBN:9781108985000),
and includes various datasets used in the book.
Built on the 'manynet' package, all functions operate with matrices,
edge lists, and 'igraph', 'network', and 'tidygraph' objects,
and on one-mode and two-mode (bipartite) networks.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb] ,
Jael Tan [ctb] ,
Bernhard Bieri [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between migraph versions 1.6.8 dated 2026-07-31 and 1.7.0 dated 2026-08-30
migraph-1.6.8/migraph/man/mpn_cow.Rd |only migraph-1.7.0/migraph/DESCRIPTION | 10 migraph-1.7.0/migraph/MD5 | 74 +++--- migraph-1.7.0/migraph/NAMESPACE | 52 ++-- migraph-1.7.0/migraph/NEWS.md | 65 +++++ migraph-1.7.0/migraph/R/data_mpn.R | 179 ++++++++++++++- migraph-1.7.0/migraph/R/model_diffusion.R | 6 migraph-1.7.0/migraph/R/tutorial_run.R | 3 migraph-1.7.0/migraph/R/zzz.R |only migraph-1.7.0/migraph/data/mpn_DE_1990.rda |binary migraph-1.7.0/migraph/data/mpn_DE_2008.rda |binary migraph-1.7.0/migraph/data/mpn_IT_1990.rda |binary migraph-1.7.0/migraph/data/mpn_IT_2008.rda |binary migraph-1.7.0/migraph/data/mpn_UK_1990.rda |binary migraph-1.7.0/migraph/data/mpn_UK_2008.rda |binary migraph-1.7.0/migraph/data/mpn_bristol.rda |binary migraph-1.7.0/migraph/data/mpn_cow.rda |only migraph-1.7.0/migraph/data/mpn_cow_igo.rda |binary migraph-1.7.0/migraph/data/mpn_cow_trade.rda |binary migraph-1.7.0/migraph/data/mpn_elite_mex.rda |binary migraph-1.7.0/migraph/data/mpn_elite_usa_advice.rda |binary migraph-1.7.0/migraph/data/mpn_elite_usa_money.rda |binary migraph-1.7.0/migraph/data/mpn_evs_deu.rda |only migraph-1.7.0/migraph/data/mpn_evs_gbr.rda |only migraph-1.7.0/migraph/data/mpn_evs_ita.rda |only migraph-1.7.0/migraph/data/mpn_ryanair.rda |binary migraph-1.7.0/migraph/data/mpn_senate.rda |only migraph-1.7.0/migraph/data/mpn_senate_dem.rda |binary migraph-1.7.0/migraph/data/mpn_senate_over.rda |binary migraph-1.7.0/migraph/data/mpn_senate_rep.rda |binary migraph-1.7.0/migraph/man/make_play.Rd | 1 migraph-1.7.0/migraph/man/mpn_bristol.Rd | 22 - migraph-1.7.0/migraph/man/mpn_cow_combined.Rd |only migraph-1.7.0/migraph/man/mpn_cow_separate.Rd |only migraph-1.7.0/migraph/man/mpn_elite_mex.Rd | 2 migraph-1.7.0/migraph/man/mpn_elite_usa.Rd | 58 ++-- migraph-1.7.0/migraph/man/mpn_evs.Rd | 17 - migraph-1.7.0/migraph/man/mpn_evs_combined.Rd |only migraph-1.7.0/migraph/man/mpn_ryanair.Rd | 23 - migraph-1.7.0/migraph/man/mpn_senate.Rd |only migraph-1.7.0/migraph/man/mpn_senate112.Rd | 118 +++++---- migraph-1.7.0/migraph/tests/testthat/Rplots.pdf |binary migraph-1.7.0/migraph/tests/testthat/test-measure_over.R | 19 + migraph-1.7.0/migraph/tests/testthat/test-zzz.R |only 44 files changed, 473 insertions(+), 176 deletions(-)
Title: Native and Extensible R Driver for 'Zarr'
Description: The 'Zarr' specification is widely used to build libraries for the storage and retrieval of n-dimensional array data from data stores ranging from local file systems to the cloud. This package is a native 'Zarr' implementation in R with support for all required features of 'Zarr' version 3. It is designed to be extensible such that new stores, codecs and extensions can be added easily.
Author: Patrick Van Laake [aut, cre, cph]
Maintainer: Patrick Van Laake <patrick@vanlaake.net>
Diff between zarr versions 0.4.2 dated 2026-07-11 and 0.5.0 dated 2026-08-30
DESCRIPTION | 10 - MD5 | 69 +++++++----- NAMESPACE | 4 NEWS.md | 13 ++ R/api.R | 96 ++++++++++++++++- R/array.R | 228 +++++++++++++++++++++++++++++++++++------- R/array_builder.R | 13 +- R/chunking.R | 119 ++++++++++++++++++++-- R/chunking_regular.R | 33 +++++- R/codec.R | 20 +++ R/convention.R | 20 ++- R/group.R | 24 ---- R/node.R | 230 +++++-------------------------------------- R/sharding.R | 1 R/store.R | 52 +++++++++ R/store_local.R | 54 ++++++++-- R/store_memory.R | 34 +++++- R/store_s3.R |only R/utils.R | 57 ++++++++++ R/zarr.R | 19 --- R/zarr_object.R |only README.md | 16 +- man/chunk_grid_regular.Rd | 8 + man/chunk_grid_sharded.Rd | 5 man/chunking.Rd | 31 +++++ man/open_zarr.Rd | 27 +++-- man/optimal_chunking.Rd |only man/s3_list_dir.Rd |only man/zarr_array.Rd | 96 ++++++++++++++++- man/zarr_group.Rd | 6 - man/zarr_httpstore.Rd | 5 man/zarr_localstore.Rd | 80 ++++++++++++++ man/zarr_memorystore.Rd | 54 ++++++++++ man/zarr_node.Rd | 48 ++++---- man/zarr_object.Rd |only man/zarr_s3store.Rd |only man/zarr_store.Rd | 84 +++++++++++++++ tests/testthat/test-resize.R |only tests/testthat/test-zarr.R | 99 ++++++++++++++++++ 39 files changed, 1235 insertions(+), 420 deletions(-)
Title: Synthetic Experience Tracking Insurance Claims
Description: Creation of an individual claims simulator which generates various
features of non-life insurance claims. An initial set of test parameters,
designed to mirror the experience of an Auto Liability portfolio, were set
up and applied by default to generate a realistic test data set of
individual claims (see vignette). The simulated data set then allows
practitioners to back-test the validity of various reserving models and to
prove and/or disprove certain actuarial assumptions made in claims
modelling. The distributional assumptions used to generate this data set can
be easily modified by users to match their experiences. Reference: Avanzi B,
Taylor G, Wang M, Wong B (2020) "SynthETIC: an individual insurance claim
simulator with feature control" <doi:10.48550/arXiv.2008.05693>.
Author: Benjamin Avanzi [aut],
William Ho [aut],
Greg Taylor [aut],
Melantha Wang [aut, cre],
Bernard Wong [aut],
Patrick Laub [ctb]
Maintainer: Melantha Wang <wang.melantha@gmail.com>
Diff between SynthETIC versions 1.1.1 dated 2025-11-02 and 1.1.2 dated 2026-08-30
DESCRIPTION | 15 ++- MD5 | 18 ++-- NEWS.md | 29 ++++++ R/features_02a_claim_covariates.R | 37 +++++++- inst/doc/SynthETIC-covariates-demo.html | 135 +++++++++++++++----------------- inst/doc/SynthETIC-demo.html | 19 ++-- man/SynthETIC-package.Rd | 5 + man/claim_size_adj.Rd | 7 + man/simulate_covariates.Rd | 8 + tests |only 10 files changed, 172 insertions(+), 101 deletions(-)
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to safely and efficiently organize and execute
Monte Carlo simulation experiments in R.
The package controls the structure and back-end of Monte Carlo simulation experiments
by utilizing a generate-analyse-summarise workflow. The workflow safeguards against
common simulation coding issues, such as automatically re-simulating non-convergent results,
prevents inadvertently overwriting simulation files, catches error and warning messages
during execution, implicitly supports parallel processing with high-quality random number
generation, and provides tools for managing high-performance computing (HPC) array jobs
submitted to schedulers such as SLURM. For a pedagogical introduction to the package see
Sigal and Chalmers (2016) <doi:10.1080/10691898.2016.1246953>. For a more in-depth overview of
the package and its design philosophy see Chalmers and Adkins (2020) <doi:10.20982/tqmp.16.4.p248>.
Author: Phil Chalmers [aut, cre] ,
Matthew Sigal [ctb],
Ogreden Oguzhan [ctb],
Mikko Roenkkoe [aut],
Moritz Ketzer [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 2.26 dated 2026-07-27 and 2.27 dated 2026-08-30
DESCRIPTION | 12 +- MD5 | 62 +++++++------- NAMESPACE | 58 ++++++++----- NEWS.md | 12 ++ R/SimCollect.R | 71 +++++++++------- R/SimErrors.R | 8 + R/SimExtract.R | 4 R/SimWarnings.R | 8 + R/addMissing.R | 1 R/descript.R | 62 +++++++++----- R/functions.R | 4 R/runArraySimulation.R | 8 - R/runSimulation.R | 19 ++-- R/summary_functions.R | 1 R/util.R | 29 ++++++ inst/doc/Catch_errors.html | 27 +----- inst/doc/Fixed_obj_fun.html | 10 +- inst/doc/HPC-computing.html | 4 inst/doc/MultipleAnalyses.html | 4 inst/doc/Parallel-computing.html | 4 inst/doc/Saving-results.html | 50 +---------- inst/doc/SimDesign-intro.html | 163 +++++++++++++++------------------------ man/EDR.Rd | 2 man/SimCollect.Rd | 11 +- man/SimErrors.Rd | 6 + man/SimWarnings.Rd | 6 + man/addMissing.Rd | 2 man/descript.Rd | 25 ++++- man/runArraySimulation.Rd | 7 - man/runSimulation.Rd | 13 +-- tests/tests/test-02-aggregate.R | 16 +-- tests/tests/test-03-array.R | 94 ++++++++++++++++------ 32 files changed, 445 insertions(+), 358 deletions(-)
Title: Empirical Dynamic Modeling ('EDM')
Description: An implementation of 'EDM' algorithms based on research software developed at the Sugihara Lab ('UCSD/SIO'). Primary methods include 'Simplex' projection from Sugihara & May (1990) <doi:10.1038/344734a0>, Sequential locally-weighted global linear maps 'S-map': Sugihara (1994) <doi:10.1098/rsta.1994.0106>, Convergent cross mapping described in Sugihara et al. (2012) <doi:10.1126/science.1227079>, and, 'Multiview embedding' from Ye & Sugihara (2016) <doi:10.1126/science.aag0863>.
Author: Joseph Park [aut, cre] ,
George Sugihara [aut, ccp] ,
Ethan Deyle [aut] ,
The Regents of the University of California [cph]
Maintainer: Joseph Park <JosephPark@IEEE.org>
Diff between rEDM versions 2.0.1 dated 2026-07-30 and 2.0.2 dated 2026-08-30
DESCRIPTION | 8 - MD5 | 36 +++-- NEWS.md | 4 R/EDM_AppSweeps.R | 33 +++-- R/EDM_AuxFuncs.R | 167 ++++++++++++++++++--------- R/EDM_CCM.R | 89 +++++++++----- R/EDM_Embed.R | 76 +++++++++++- R/EDM_FileIO.R | 25 +++- R/EDM_Multiview.R | 5 R/EDM_Neighbors.R | 221 ++++++++++++++++++++++++++++++------ R/EDM_SMap.R | 191 +++++++++++++++++++++---------- R/EDM_Simplex.R | 86 ++++++++++---- inst/doc/rEDM-tutorial.html | 28 ++-- inst/extdata/Smplx_NeighborTies.csv |only man/Embed.Rd | 44 ++++--- man/PredictInterval.Rd | 4 man/PredictNonlinear.Rd | 4 man/RequireE.Rd |only man/SMap.Rd | 10 + man/Simplex.Rd | 20 ++- 20 files changed, 758 insertions(+), 293 deletions(-)
Title: True Random Numbers using RANDOM.ORG
Description: The true random number service provided by the RANDOM.ORG
website created by Mads Haahr samples atmospheric noise via radio tuned to
an unused broadcasting frequency together with a skew correction algorithm
due to John von Neumann. More background is available in the included
vignette based on an essay by Mads Haahr. In its current form, the package
offers functions to retrieve random integers, randomized sequences and
random strings.
Author: Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between random versions 0.2.6 dated 2017-02-05 and 0.2.7 dated 2026-08-30
ChangeLog | 65 +++++++++++++++++++++++++++++ DESCRIPTION | 19 +++++--- MD5 | 29 ++++++------- R/random.R | 6 +- README.md | 11 +++-- build/vignette.rds |binary inst/doc/random-essay.Rnw | 52 ++++++++++++----------- inst/doc/random-essay.pdf |binary inst/doc/random-intro.R | 9 +--- inst/doc/random-intro.Rnw | 15 ++++-- inst/doc/random-intro.pdf |binary man/random.Rd | 6 +- vignettes/auto |only vignettes/random-essay.Rnw | 52 ++++++++++++----------- vignettes/random-intro.Rnw | 15 ++++-- vignettes/random-intro.bib | 98 +++++++++++++++++++++++++++++++-------------- 16 files changed, 251 insertions(+), 126 deletions(-)
Title: Data Sets from the History of Statistics and Data Visualization
Description: The 'HistData' package provides a collection of small data sets
that are interesting and important in the history of statistics and data
visualization. The goal of the package is to make these available, both for
instructional use and for historical research. Some of these present interesting
challenges for graphics or analysis in R.
Author: Michael Friendly [aut, cre] ,
Stephane Dray [aut] ,
Peter Li [aut] ,
David Bellhouse [aut],
Hadley Wickham [ctb],
James Hanley [ctb],
Dennis Murphy [ctb],
Luiz Droubi [ctb],
James Riley [ctb],
Antoine de Falguerolles [ctb],
Monique Graf [ctb],
Nevill [...truncated...]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between HistData versions 1.0.0 dated 2025-11-30 and 1.1.0 dated 2026-08-30
DESCRIPTION | 18 +++++++------ MD5 | 48 ++++++++++++++++++++++++----------- NAMESPACE | 12 +++++--- NEWS.md | 11 ++++++++ R/Ebbinghaus.R |only R/Federalist.R |only R/Perozzo.R |only R/data-concepts.R | 29 +++++++++++++-------- build/partial.rdb |binary build/vignette.rds |binary data/Ebbinghaus.RData |only data/Federalist_corpus.RData |only data/Federalist_markers.RData |only data/Federalist_text.RData |only data/Perozzo.RData |only data/Pollen.RData |binary data/Quarrels.RData |binary inst/doc/HistData-Challenge.R |only inst/doc/HistData-Challenge.Rmd |only inst/doc/HistData-Challenge.html |only inst/doc/Snow_deaths-duplicates.html | 4 +- man/Cholera.Rd | 2 - man/Ebbinghaus.Rd |only man/Federalist.Rd |only man/Macdonell.Rd | 2 + man/Nightingale.Rd | 4 ++ man/Perozzo.Rd |only man/Quarrels.Rd | 7 ++--- man/Snow.Rd | 5 +++ man/figures/logo.png |binary vignettes/HistData-Challenge.Rmd |only vignettes/figures |only vignettes/histdata.bib |only 33 files changed, 95 insertions(+), 47 deletions(-)
Title: Estimate, Compare, and Visualize Healthcare Resource Utilization
for Real-World Evidence
Description: Tools to estimate, compare, and visualize healthcare resource utilization using
data derived from electronic health records or real-world evidence sources.
The package supports pre index and post index analysis, patient cohort comparison,
and customizable summaries and visualizations for clinical and health economics research.
Methods implemented are based on Scott et al. (2022) <doi:10.1080/13696998.2022.2037917>
and Xia et al. (2024) <doi:10.14309/ajg.0000000000002901>.
Author: Maheshkumar Umbarkar [aut, cre, cph],
Safiuddin Shoeb Syed [ctb]
Maintainer: Maheshkumar Umbarkar <maheshubr30@gmail.com>
Diff between hcruR versions 1.0.0 dated 2025-09-01 and 1.0.1 dated 2026-08-30
DESCRIPTION | 6 MD5 | 14 NEWS.md | 8 R/utils.R | 791 ++++++++++++++++++++++++++-------------------------- build/vignette.rds |binary inst/doc/hcruR.Rmd | 300 +++++++++---------- inst/doc/hcruR.html | 118 +++---- vignettes/hcruR.Rmd | 300 +++++++++---------- 8 files changed, 768 insertions(+), 769 deletions(-)
Title: Extra Themes, Scales and Geoms for 'ggplot2'
Description: Some extra themes, geoms, and scales for 'ggplot2'.
Provides 'ggplot2' themes and scales that replicate the look of plots
by Edward Tufte, Stephen Few, 'Fivethirtyeight', 'The Economist', 'Stata',
'Excel', and 'The Wall Street Journal', among others.
Provides 'geoms' for Tufte's box plot and range frame.
Author: Jeffrey B. Arnold [aut, cre] ,
Gergely Daroczi [ctb],
Bo Werth [ctb],
Brian Weitzner [ctb],
Joshua Kunst [ctb],
Baptiste Auguie [ctb],
Bob Rudis [ctb],
Hadley Wickham [ctb] ,
Justin Talbot [ctb] ,
Joshua London [ctb]
Maintainer: Jeffrey B. Arnold <jeffrey.arnold@gmail.com>
Diff between ggthemes versions 5.2.0 dated 2025-11-30 and 6.0.0 dated 2026-08-30
DESCRIPTION | 25 +- MD5 | 229 ++++++++++++------------- NAMESPACE | 125 ++++++++----- NEWS.md | 78 ++++++++ R/banking.R | 144 ++++++++++++++- R/canva.R | 5 R/colorblind.R | 23 +- R/economist.R | 5 R/excel.R | 13 - R/few.R | 9 R/geom-rangeframe.R | 23 +- R/hc.R | 10 - R/pander.R | 4 R/scales.R | 6 R/shapes.R | 9 R/stat-fivenumber.R | 12 - R/stata.R | 22 -- R/tableau.R | 29 ++- R/theme-foundation.R | 22 +- R/utils.R | 39 +++- R/wsj.R | 2 build/stage23.rdb |binary data/ggthemes_data.rda |binary inst/WORDLIST | 11 + inst/examples/ex-bank_slopes.R | 15 + inst/examples/ex-colorblind.R | 1 inst/examples/ex-excel_new_pal.R | 4 inst/examples/ex-geom_rangeframe.R | 9 inst/examples/ex-scale_linetype_stata.R | 6 man/bank_plot.Rd |only man/bank_slopes.Rd | 74 ++++++-- man/calc_pal.Rd | 4 man/calc_shape_pal.Rd | 4 man/circlefill_shape_pal.Rd | 12 - man/cleveland_shape_pal.Rd | 12 - man/colorblind.Rd | 19 +- man/economist_pal.Rd | 4 man/excel_new_pal.Rd | 12 - man/excel_pal.Rd | 8 man/few_pal.Rd | 4 man/figures/README-scale_color_tableau-1.png |binary man/figures/README-scale_colorblind-1.png |binary man/figures/README-theme_calc-1.png |binary man/figures/README-theme_clean-1.png |binary man/figures/README-theme_economist-1.png |binary man/figures/README-theme_excel-1.png |binary man/figures/README-theme_excel_new-1.png |binary man/figures/README-theme_few-1.png |binary man/figures/README-theme_fivethirtyeight-1.png |binary man/figures/README-theme_igray-1.png |binary man/figures/README-theme_par-1.png |binary man/figures/README-theme_solarized-1.png |binary man/figures/README-theme_solarized_dark-1.png |binary man/figures/README-theme_solid-1.png |binary man/figures/README-theme_stata-1.png |binary man/figures/README-theme_wsj-1.png |binary man/fivethirtyeight_pal.Rd | 4 man/gdocs_pal.Rd | 4 man/geom_rangeframe.Rd | 21 +- man/geom_tufteboxplot.Rd | 6 man/ggthemes-package.Rd | 8 man/hc_pal.Rd | 4 man/palette_pander.Rd | 4 man/ptol_pal.Rd | 4 man/scale_calc.Rd | 4 man/scale_color_tableau.Rd | 10 - man/scale_colour_gradient2_tableau.Rd | 16 + man/scale_colour_gradient_tableau.Rd | 10 - man/scale_economist.Rd | 4 man/scale_excel.Rd | 8 man/scale_excel_new.Rd | 8 man/scale_few.Rd | 4 man/scale_fivethirtyeight.Rd | 4 man/scale_gdocs.Rd | 4 man/scale_hc.Rd | 4 man/scale_linetype_stata.Rd | 10 - man/scale_pander.Rd | 4 man/scale_ptol.Rd | 4 man/scale_shape_calc.Rd | 4 man/scale_shape_circlefill.Rd | 12 - man/scale_shape_cleveland.Rd | 12 - man/scale_shape_tableau.Rd | 4 man/scale_shape_tremmel.Rd | 12 - man/scale_solarized.Rd | 4 man/scale_wsj.Rd | 4 man/smart_digits.Rd | 2 man/solarized_pal.Rd | 4 man/stat_fivenumber.Rd | 2 man/stata_linetype_pal.Rd | 4 man/tableau_color_pal.Rd | 10 - man/tableau_gradient_pal.Rd | 10 - man/tableau_shape_pal.Rd | 4 man/theme_base.Rd | 12 - man/theme_clean.Rd | 12 - man/theme_economist.Rd | 2 man/theme_excel.Rd | 4 man/theme_excel_new.Rd | 4 man/theme_foundation.Rd | 30 ++- man/theme_igray.Rd | 12 - man/theme_par.Rd | 12 - man/theme_solid.Rd | 12 - man/tremmel_shape_pal.Rd | 12 - man/wsj_pal.Rd | 4 tests/testthat/Rplots.pdf |only tests/testthat/test-banking.R | 96 ++++++++++ tests/testthat/test-canva.R | 2 tests/testthat/test-clean.R |only tests/testthat/test-colorblind.R | 22 ++ tests/testthat/test-economist.R | 12 + tests/testthat/test-excel.R | 19 ++ tests/testthat/test-geom-rangeframe.R | 65 +++++++ tests/testthat/test-hc.R | 2 tests/testthat/test-pander.R | 38 ++++ tests/testthat/test-scales.R |only tests/testthat/test-shapes.R | 11 + tests/testthat/test-tableau.R | 15 + tests/testthat/test-theme-foundation.R |only tests/testthat/test-wsj_pal.R | 2 118 files changed, 1169 insertions(+), 501 deletions(-)
Title: Matrices for Repeat-Sales Price Indexes
Description: Calculate the matrices in
Shiller (1991, <doi:10.1016/S1051-1377(05)80028-2>) that serve as the
foundation for many repeat-sales price indexes.
Author: Steve Martin [aut, cre, cph]
Maintainer: Steve Martin <marberts@protonmail.com>
Diff between rsmatrix versions 0.2.11 dated 2026-08-01 and 0.3.0 dated 2026-08-30
rsmatrix-0.2.11/rsmatrix/LICENSE |only rsmatrix-0.3.0/rsmatrix/DESCRIPTION | 12 -- rsmatrix-0.3.0/rsmatrix/MD5 | 24 ++-- rsmatrix-0.3.0/rsmatrix/NEWS.md | 6 + rsmatrix-0.3.0/rsmatrix/R/rs_matrix.R | 23 +--- rsmatrix-0.3.0/rsmatrix/R/rs_var.R | 19 +-- rsmatrix-0.3.0/rsmatrix/README.md | 134 ++++++++++-------------- rsmatrix-0.3.0/rsmatrix/build/partial.rdb |binary rsmatrix-0.3.0/rsmatrix/inst/CITATION | 2 rsmatrix-0.3.0/rsmatrix/inst/REFERENCES.R |only rsmatrix-0.3.0/rsmatrix/inst/doc/rsmatrix.html | 2 rsmatrix-0.3.0/rsmatrix/man/rs_matrix.Rd | 17 +-- rsmatrix-0.3.0/rsmatrix/man/rs_var.Rd | 15 -- rsmatrix-0.3.0/rsmatrix/man/rsmatrix-package.Rd | 4 14 files changed, 109 insertions(+), 149 deletions(-)
Title: Declarative Recipes for Staged Survey Weighting with
Recipe-Aware Replicate Variances
Description: Builds survey analysis weights by declaring the whole weighting
process as an ordered recipe of explicit adjustments and estimating it in a
single call. Steps include within-cluster selection, second-phase
subsampling for two-phase sampling, nonresponse adjustment by weighting
classes or response-propensity models (including machine-learning learners
with optional cross-fitting), calibration to known totals following Deville
and Sarndal (1992) <doi:10.2307/2290268> with optional model-assisted
calibration following Wu and Sitter (2001)
<doi:10.1198/016214501750333054>, adjustment of non-probability samples by
pseudo-weighting, mass imputation and doubly robust estimators, and
range-restricted trimming. Variances come from a recipe-aware bootstrap and
jackknife that resample or delete primary sampling units and re-apply the
entire cascade on each replicate, following Rao and Wu (1988)
<doi:10.1080/01621459.1988.10478591>, and are separated into first- and
second-phase [...truncated...]
Author: Juan Pablo Ferreira [aut, cre, cph] ,
Andres Gutierrez [aut]
Maintainer: Juan Pablo Ferreira <juanpablo.ferreira@fcea.edu.uy>
Diff between weightflow versions 1.1.0 dated 2026-08-19 and 1.2.0 dated 2026-08-29
DESCRIPTION | 46 - MD5 | 238 ++++--- NAMESPACE | 20 NEWS.md | 28 R/adjust-calibrate.R | 93 ++ R/adjust-ml.R | 8 R/adjust-nr-sensitivity.R |only R/adjust-poststrata.R | 69 ++ R/adjust-pseudoweight.R |only R/adjust-solve.R | 31 R/adjust-trim.R | 110 ++- R/adjustments.R | 35 - R/collect-propensities.R | 1 R/collect-step-detail.R | 16 R/data-defect.R |only R/disclosure-risk.R |only R/domain-summary.R | 43 + R/plots.R | 6 R/prep.R | 126 +++ R/print.R | 7 R/r-indicators.R | 9 R/recipe-io.R |only R/report-assets.R | 35 - R/report-cards.R | 441 ++++++++++--- R/report-helpers.R | 121 ++- R/report-narrative.R | 95 ++ R/report.R | 74 +- R/sae.R |only R/spec-steps-calibrate.R | 140 +++- R/spec-steps-cascade.R | 75 +- R/spec-steps-final.R | 171 ++++- R/spec-steps-subsample.R |only R/spec.R | 77 +- R/variance.R | 466 ++++++++++++-- R/weightflow-alerts.R |only R/weightflow-concepts.R | 20 README.md | 59 + build/vignette.rds |binary inst/WORDLIST | 68 ++ inst/doc/advanced-methods.html | 52 - inst/doc/calibration-totals.Rmd | 5 inst/doc/calibration-totals.html | 6 inst/doc/calibration.Rmd | 7 inst/doc/calibration.html | 32 inst/doc/inspecting-auditing.R |only inst/doc/inspecting-auditing.Rmd |only inst/doc/inspecting-auditing.html |only inst/doc/model-calibration.Rmd | 6 inst/doc/model-calibration.html | 7 inst/doc/nonprobability-samples.R |only inst/doc/nonprobability-samples.Rmd |only inst/doc/nonprobability-samples.html |only inst/doc/nonresponse-propensities.Rmd | 6 inst/doc/nonresponse-propensities.html | 13 inst/doc/preparing-the-sample.html | 76 +- inst/doc/quality-report.Rmd | 13 inst/doc/quality-report.html | 88 +- inst/doc/quickstart.html | 20 inst/doc/reference-survey.R |only inst/doc/reference-survey.Rmd |only inst/doc/reference-survey.html |only inst/doc/two-phase-sampling.R |only inst/doc/two-phase-sampling.Rmd |only inst/doc/two-phase-sampling.html |only inst/doc/validation-against-survey.R | 16 inst/doc/validation-against-survey.Rmd | 16 inst/doc/validation-against-survey.html | 16 inst/doc/variance-estimation.R | 19 inst/doc/variance-estimation.Rmd | 61 + inst/doc/variance-estimation.html | 896 +++------------------------ inst/doc/weightflow-in-production.R |only inst/doc/weightflow-in-production.Rmd |only inst/doc/weightflow-in-production.html |only inst/doc/weightflow.html | 36 - man/as_sae_input.Rd |only man/as_svydesign.Rd | 9 man/bootstrap_estimate.Rd | 35 - man/bootstrap_weights.Rd | 31 man/collect_propensities.Rd | 9 man/collect_replicate_weights.Rd | 20 man/collect_step_detail.Rd | 14 man/collect_weights.Rd | 10 man/data_defect.Rd |only man/disclosure_risk.Rd |only man/domain_summary.Rd | 23 man/jackknife_estimate.Rd | 26 man/jackknife_weights.Rd | 9 man/nr_sensitivity.Rd |only man/prep.Rd | 12 man/read_recipe.Rd |only man/reference_sample.Rd |only man/step_assert.Rd | 24 man/step_calibrate.Rd | 38 + man/step_drop_ineligible.Rd | 24 man/step_model_calibration.Rd | 30 man/step_nonresponse.Rd | 25 man/step_nr_sensitivity.Rd |only man/step_pseudoweight.Rd |only man/step_rescale.Rd | 24 man/step_round.Rd | 29 man/step_select_within.Rd | 30 man/step_subsample.Rd |only man/step_trim.Rd | 31 man/step_trim_calibrated.Rd | 39 + man/step_trim_weights.Rd | 25 man/step_unknown_eligibility.Rd | 24 man/two_phase_variance.Rd |only man/weight_factors.Rd | 10 man/weightflow-alerts.Rd |only man/weightflow-concepts.Rd | 21 man/weightflow-package.Rd | 4 man/weighting_alerts.Rd |only man/weighting_spec.Rd | 17 man/write_recipe.Rd |only tests/testthat/_snaps/snapshot.md | 22 tests/testthat/test-audit-2026-08b.R |only tests/testthat/test-audit-2026-08c.R |only tests/testthat/test-audit-2026-08d.R |only tests/testthat/test-audit-followups.R |only tests/testthat/test-audit-ronda2.R |only tests/testthat/test-audit-ronda2b.R |only tests/testthat/test-blindaje-reporte-en.R | 2 tests/testthat/test-calibrate-reference.R |only tests/testthat/test-data-defect.R |only tests/testthat/test-domain-gate-disclosure.R |only tests/testthat/test-fpc-ci.R |only tests/testthat/test-nr-sensitivity.R |only tests/testthat/test-pseudoweight.R |only tests/testthat/test-recipe-io.R |only tests/testthat/test-reference-sample.R |only tests/testthat/test-replication-card.R | 19 tests/testthat/test-report-reference-note.R |only tests/testthat/test-sae.R |only tests/testthat/test-step-id.R |only tests/testthat/test-subsample.R |only tests/testthat/test-trim-domain-and-alerts.R |only tests/testthat/test-unit-report-narrative.R | 2 tests/testthat/test-unit-spec-steps.R | 4 vignettes/calibration-totals.Rmd | 5 vignettes/calibration.Rmd | 7 vignettes/inspecting-auditing.Rmd |only vignettes/model-calibration.Rmd | 6 vignettes/nonprobability-samples.Rmd |only vignettes/nonresponse-propensities.Rmd | 6 vignettes/quality-report.Rmd | 13 vignettes/reference-survey.Rmd |only vignettes/two-phase-sampling.Rmd |only vignettes/validation-against-survey.Rmd | 16 vignettes/variance-estimation.Rmd | 61 + vignettes/weightflow-in-production.Rmd |only 150 files changed, 3377 insertions(+), 1498 deletions(-)
Title: Automatically Reduce Failing R Scripts to a Minimal Reproducible
Example
Description: Shrinks a failing R script to the smallest subset of statements
that still triggers the same error, using the delta debugging algorithm of
Zeller and Hildebrandt (2002) <doi:10.1109/32.988498>. Each candidate
reduction is evaluated in a separate R process, so dependencies between
statements and their side effects are respected. The result is a
one-minimal example, in which removing any remaining statement makes the
error disappear; this is the form most useful for bug reports and for
questions on community forums. When no statement can be removed, because
the failure is nested inside a function body, reduction continues within
the surviving statements. A general delta debugging routine and a
helper for reducing data frames to the rows that reproduce a failure are
also provided.
Author: Sandeep Bodduluri [aut, cph] ,
Sumanth Chandrupatla [aut, cre, cph]
Maintainer: Sumanth Chandrupatla <srchandr@uab.edu>
Diff between minex versions 0.1.0 dated 2026-07-16 and 0.2.0 dated 2026-08-29
DESCRIPTION | 32 +-- LICENSE | 2 MD5 | 71 ++++-- NAMESPACE | 4 NEWS.md | 61 +++++ R/cdd.R |only R/clipboard.R |only R/ddmin.R | 151 ++++++++++---- R/explain-prompt.R |only R/explain-verify.R |only R/explain.R |only R/hdd.R |only R/match.R |only R/minex.R | 368 ++++++++++++++++++++++++++++++----- R/oracle.R | 118 +++++------ R/parse-tree.R |only R/parse.R | 20 + R/print.R | 45 +++- R/reduce-rows.R | 12 - R/sweep.R |only R/trace.R |only R/truncate.R |only build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 23 ++ inst/doc/minex.html | 4 man/ddmin.Rd | 34 ++- man/explain_failure.Rd |only man/minex-package.Rd | 10 man/minex.Rd | 109 +++++++++- man/reduce_rows.Rd | 14 + tests/testthat.R | 14 + tests/testthat/test-auto-escalate.R |only tests/testthat/test-cdd.R |only tests/testthat/test-clipboard.R |only tests/testthat/test-ddmin.R | 77 +++++++ tests/testthat/test-explain-prompt.R |only tests/testthat/test-explain-verify.R |only tests/testthat/test-explain.R |only tests/testthat/test-hdd.R |only tests/testthat/test-match.R |only tests/testthat/test-minex.R | 220 ++++++++++++++++++++ tests/testthat/test-oracle.R |only tests/testthat/test-parse-error.R |only tests/testthat/test-parse-tree.R |only tests/testthat/test-print-axis.R |only tests/testthat/test-print.R |only tests/testthat/test-reduce-rows.R | 14 + tests/testthat/test-sweep.R |only tests/testthat/test-truncate.R |only 50 files changed, 1182 insertions(+), 221 deletions(-)
Title: Tools for Assessing Clustering
Description: A set of tools for evaluating clustering robustness using
proportion of ambiguously clustered pairs (Senbabaoglu et al. (2014)
<doi:10.1038/srep06207>), as well as similarity across methods
and method stability using element-centric clustering comparison (Gates et
al. (2019) <doi:10.1038/s41598-019-44892-y>). Additionally, this package
enables stability-based parameter assessment for graph-based clustering
pipelines typical in single-cell data analysis.
Author: Andi Munteanu [aut, cre],
Arash Shahsavari [aut],
Rafael Kollyfas [ctb],
Miguel Larraz Lopez de Novales [aut],
Liviu Ciortuz [ctb],
Irina Mohorianu [aut]
Maintainer: Andi Munteanu <am3019@cam.ac.uk>
Diff between ClustAssess versions 1.1.0 dated 2025-05-27 and 1.2.0 dated 2026-08-29
DESCRIPTION | 16 MD5 | 55 +- NAMESPACE | 6 NEWS.md | 26 + R/ECS.R | 87 ---- R/convert.R | 50 +- R/generics.R | 4 R/shiny-app.R | 29 + R/shiny-comparisons.R | 453 +++++++++++++++++----- R/shiny-feature-stability.R | 45 +- R/shiny-graph-clustering.R | 38 - R/shiny-info.R | 24 - R/shiny-sandbox.R | 31 - R/shiny-utils.R | 441 +++++++++++++++++---- R/stability-1-dim-reduction.R | 32 - R/stability-2-graph-construction.R | 54 -- R/stability-3-graph-clustering.R | 48 -- R/stability-based-parameter-assessment.R | 80 +-- R/utils.R | 86 ++++ README.md | 75 +-- man/add_metadata.Rd | 6 man/create_monocle_from_clustassess_app.Rd | 10 man/create_seurat_object_default.Rd | 6 man/plot_feature_overall_stability_incremental.Rd | 2 man/plot_n_neigh_ecs.Rd | 6 man/write_objects.Rd | 4 man/write_shiny_app.Rd | 8 src/optimise_snn.cpp | 32 - tests/testthat/test-calculate-markers.R |only 29 files changed, 1125 insertions(+), 629 deletions(-)
Title: Spatial Network Analysis
Description: Interface package for 'sala', the spatial network analysis library
from the 'depthmapX' software application. The R parts of the code are based
on the 'rdepthmap' package. Allows for the analysis of urban and
building-scale networks and provides metrics and methods usually found
within the Space Syntax domain. Methods in this package are described by K.
Al-Sayed, A. Turner, B. Hillier, S. Iida and A. Penn (2014) "Space Syntax
methodology", and also by A. Turner (2004)
<https://discovery.ucl.ac.uk/id/eprint/2651> "Depthmap 4: a researcher's
handbook".
Author: Petros Koutsolampros [cre, aut] ,
Fani Kostourou [ctb] ,
Kimon Krenz [ctb] ,
Alasdair Turner [ctb] ,
Tasos Varoudis [ctb] ,
Christian Sailer [ctb] ,
Eva Friedrich [ctb] ,
University College London [fnd, cph] ,
Spacelab UK [fnd]
Maintainer: Petros Koutsolampros <r-devel@pklampros.net>
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alcyon-0.9.0/alcyon/src/libs/salalib/agents/agent.hpp | 14 alcyon-0.9.0/alcyon/src/libs/salalib/agents/agentanalysis.cpp | 27 alcyon-0.9.0/alcyon/src/libs/salalib/agents/agentanalysis.hpp | 10 alcyon-0.9.0/alcyon/src/libs/salalib/agents/agentga.cpp | 7 alcyon-0.9.0/alcyon/src/libs/salalib/agents/agentprogram.cpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/alllinemap.cpp | 29 alcyon-0.9.0/alcyon/src/libs/salalib/analysisresult.hpp | 12 alcyon-0.9.0/alcyon/src/libs/salalib/attributemap.hpp | 12 alcyon-0.9.0/alcyon/src/libs/salalib/attributetable.cpp | 11 alcyon-0.9.0/alcyon/src/libs/salalib/attributetableindex.cpp | 5 alcyon-0.9.0/alcyon/src/libs/salalib/attributetableview.cpp | 3 alcyon-0.9.0/alcyon/src/libs/salalib/attributetableview.hpp | 7 alcyon-0.9.0/alcyon/src/libs/salalib/axialminimiser.cpp | 28 alcyon-0.9.0/alcyon/src/libs/salalib/axialmodules/axialintegration.cpp | 17 alcyon-0.9.0/alcyon/src/libs/salalib/axialmodules/axialintegration.hpp | 28 alcyon-0.9.0/alcyon/src/libs/salalib/axialmodules/axiallocal.cpp | 7 alcyon-0.9.0/alcyon/src/libs/salalib/axialmodules/axialstepdepth.cpp | 2 alcyon-0.9.0/alcyon/src/libs/salalib/axialpolygons.cpp | 31 alcyon-0.9.0/alcyon/src/libs/salalib/axialpolygons.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/connector.cpp | 29 alcyon-0.9.0/alcyon/src/libs/salalib/entityparsing.cpp | 6 alcyon-0.9.0/alcyon/src/libs/salalib/entityparsing.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/exportutils.cpp | 1 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/bsptree.cpp | 7 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/containerutils.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/exceptions.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/line4f.cpp | 1 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/pafmath.cpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/pafmath.hpp | 33 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/point2f.cpp | 1 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/poly.cpp | 1 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/readwritehelpers.hpp | 7 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/region4f.hpp | 2 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/simplematrix.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/stringutils.cpp | 10 alcyon-0.9.0/alcyon/src/libs/salalib/genlib/xmlparse.cpp | 7 alcyon-0.9.0/alcyon/src/libs/salalib/geometrygenerators.cpp | 3 alcyon-0.9.0/alcyon/src/libs/salalib/importtypedefs.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/importutils.cpp | 61 - 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alcyon-0.9.0/alcyon/src/libs/salalib/shapegraph.hpp | 36 alcyon-0.9.0/alcyon/src/libs/salalib/shapemap.cpp | 435 +++----- alcyon-0.9.0/alcyon/src/libs/salalib/shapemap.hpp | 62 - alcyon-0.9.0/alcyon/src/libs/salalib/shapemapgroupdata.cpp | 5 alcyon-0.9.0/alcyon/src/libs/salalib/spacepixel.cpp |only alcyon-0.9.0/alcyon/src/libs/salalib/spacepixel.hpp |only alcyon-0.9.0/alcyon/src/libs/salalib/sparksieve2.cpp | 1 alcyon-0.9.0/alcyon/src/libs/salalib/tidylines.cpp | 6 alcyon-0.9.0/alcyon/src/libs/salalib/tidylines.hpp | 2 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/extractlinkdata.hpp | 6 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/ivga.hpp | 9 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/ivgaangular.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/ivgametric.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/ivgatraversing.hpp | 2 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/ivgavisual.hpp | 2 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaangular.cpp | 5 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaangular.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaangulardepth.cpp | 2 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaangulardepth.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaangularopenmp.cpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaangularopenmp.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaangularshortestpath.cpp | 3 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaangularshortestpath.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaisovist.cpp | 5 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaisovist.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaisovistzone.cpp | 22 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgaisovistzone.hpp | 12 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametric.cpp | 17 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametric.hpp | 5 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametricdepth.cpp | 34 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametricdepth.hpp | 5 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametricdepthlinkcost.cpp | 3 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametricdepthlinkcost.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametricopenmp.cpp | 3 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametricopenmp.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametricshortestpath.cpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametricshortestpath.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametricshortestpathtomany.cpp | 5 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgametricshortestpathtomany.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgathroughvision.cpp | 7 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgathroughvision.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisualglobal.cpp | 6 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisualglobal.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisualglobaldepth.cpp | 2 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisualglobaldepth.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisualglobalopenmp.cpp | 10 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisualglobalopenmp.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisuallocal.cpp | 3 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisuallocal.hpp | 4 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisuallocaladjmatrix.cpp | 6 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisuallocaladjmatrix.hpp | 6 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisuallocalopenmp.cpp | 8 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisuallocalopenmp.hpp | 6 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisualshortestpath.cpp | 1 alcyon-0.9.0/alcyon/src/libs/salalib/vgamodules/vgavisualshortestpath.hpp | 4 alcyon-0.9.0/alcyon/src/process_link.cpp | 114 +- alcyon-0.9.0/alcyon/src/rcpp_LatticeMap.cpp |only alcyon-0.9.0/alcyon/src/rcpp_LatticeMap.hpp |only alcyon-0.9.0/alcyon/src/rcpp_metagraphdata.cpp | 12 alcyon-0.9.0/alcyon/tests/testthat/helper-loadMaps.R | 8 alcyon-0.9.0/alcyon/tests/testthat/test-LatticeMap.R |only alcyon-0.9.0/alcyon/tests/testthat/test-MetaGraph.R | 12 alcyon-0.9.0/alcyon/tests/testthat/test-agentanalysis.R | 14 alcyon-0.9.0/alcyon/tests/testthat/test-prepareVGA.R | 28 alcyon-0.9.0/alcyon/tests/testthat/test-segmentAnalysis.R | 94 + alcyon-0.9.0/alcyon/tests/testthat/test-vga.R | 64 - alcyon-0.9.0/alcyon/tests/testthat/test-vgaCpp.R | 64 - alcyon-0.9.0/alcyon/vignettes/agentAnalysis.Rmd | 10 alcyon-0.9.0/alcyon/vignettes/vga.Rmd | 8 255 files changed, 2579 insertions(+), 2089 deletions(-)
Title: Polished, Editable Tables and Statistical Results
Description: Sends supported 'R' objects to the 'Mellio' web app and creates
polished, editable statistical tables in 'R'. The 'mellio_open' interface
handles common hypothesis tests, model objects, model comparisons,
descriptive summaries, tabular data, plots, and image files. The
'melliotab' interface formats data frames, model summaries, correlation
matrices, and side-by-side comparison tables with APA-style numeric
formatting, confidence intervals, table notes, and optional significance
markers. Manual table helpers can copy or save 'melliotab' output as
'HTML', 'LaTeX', or 'Markdown' when file-based handoff is needed.
Payloads include package-version metadata to support reproducible
reporting and software citation.
Author: Melih Sahin [aut, cre]
Maintainer: Melih Sahin <nicomelpro@pm.me>
Diff between mellio versions 1.0.2 dated 2026-07-08 and 1.1.0 dated 2026-08-29
DESCRIPTION | 15 ++-- MD5 | 19 ++--- NAMESPACE | 4 + NEWS.md | 12 +++ R/bridge-edit.R | 33 +++++++++ R/bridge-extract-interactions.R |only R/bridge-payload.R | 7 ++ R/edit.R | 4 - man/mellio_payload.Rd | 19 +++-- tests/testthat/test-bridge.R | 130 ++++++++++++++++++++++++++++++++++++++ tests/testthat/test-mellio-open.R | 14 ++++ 11 files changed, 232 insertions(+), 25 deletions(-)
Title: Access 'Hugging Face' Models and Datasets
Description: Access models and datasets hosted on the 'Hugging Face' Hub
through its Inference Application Programming Interface (API). Run text
classification, embeddings, chat, translation, image, audio, and other
tasks from tidy 'R' workflows without installing 'Python' by default.
Results are returned as data frames or simple 'R' objects so they can be
composed with 'dplyr', 'tidyr', and related tooling. Helpers also support
Hub search, file download, provider discovery, and guarded uploads for
authenticated workflows.
Author: Alex Farach [aut, cre, cph],
Sam Terfa [aut, cph],
Jack Penzer [aut, cph]
Maintainer: Alex Farach <alexfarach@gmail.com>
Diff between huggingfaceR versions 2.1.0 dated 2026-06-30 and 2.2.0 dated 2026-08-29
huggingfaceR-2.1.0/huggingfaceR/tools |only huggingfaceR-2.2.0/huggingfaceR/DESCRIPTION | 12 huggingfaceR-2.2.0/huggingfaceR/MD5 | 50 +-- huggingfaceR-2.2.0/huggingfaceR/NAMESPACE | 1 huggingfaceR-2.2.0/huggingfaceR/NEWS.md | 66 ++++ huggingfaceR-2.2.0/huggingfaceR/R/auth.R | 82 +++-- huggingfaceR-2.2.0/huggingfaceR/R/batch.R | 10 huggingfaceR-2.2.0/huggingfaceR/R/defaults.R | 2 huggingfaceR-2.2.0/huggingfaceR/R/hub.R | 70 +++- huggingfaceR-2.2.0/huggingfaceR/R/multimodal.R | 22 - huggingfaceR-2.2.0/huggingfaceR/R/providers.R |only huggingfaceR-2.2.0/huggingfaceR/R/request.R | 139 +++++++-- huggingfaceR-2.2.0/huggingfaceR/R/text-tasks.R | 15 - huggingfaceR-2.2.0/huggingfaceR/R/utils.R | 10 huggingfaceR-2.2.0/huggingfaceR/R/zzz.R | 4 huggingfaceR-2.2.0/huggingfaceR/README.md | 44 ++ huggingfaceR-2.2.0/huggingfaceR/man/hf_clear_provider_cache.Rd |only huggingfaceR-2.2.0/huggingfaceR/man/hf_list_providers.Rd | 17 - huggingfaceR-2.2.0/huggingfaceR/man/hf_set_token.Rd | 10 huggingfaceR-2.2.0/huggingfaceR/man/hf_text_to_speech.Rd | 2 huggingfaceR-2.2.0/huggingfaceR/man/hf_whoami.Rd | 3 huggingfaceR-2.2.0/huggingfaceR/tests/testthat/test-auth.R | 149 ++++++---- huggingfaceR-2.2.0/huggingfaceR/tests/testthat/test-multimodal.R | 4 huggingfaceR-2.2.0/huggingfaceR/tests/testthat/test-providers.R |only huggingfaceR-2.2.0/huggingfaceR/tests/testthat/test-request.R | 15 - huggingfaceR-2.2.0/huggingfaceR/tests/testthat/test-text-tasks.R | 20 - 26 files changed, 548 insertions(+), 199 deletions(-)
Title: Add the 'dann' Model and the 'sub_dann' Model to the
'tidymodels' Ecosystem
Description: Provides model specifications and tuning parameters that make the
models in the 'dann' package available to the 'tidymodels' ecosystem.
Models based on Hastie (1996)
<https://web.stanford.edu/~hastie/Papers/dann_IEEE.pdf>.
Author: Greg McMahan [aut, cre]
Maintainer: Greg McMahan <gmcmacran@gmail.com>
Diff between tidydann versions 1.0.1 dated 2025-04-12 and 1.0.2 dated 2026-08-29
tidydann-1.0.1/tidydann/tests/testthat/testthat-problems.rds |only tidydann-1.0.2/tidydann/DESCRIPTION | 24 +- tidydann-1.0.2/tidydann/MD5 | 38 ++- tidydann-1.0.2/tidydann/NAMESPACE | 5 tidydann-1.0.2/tidydann/NEWS.md | 40 ++-- tidydann-1.0.2/tidydann/R/nearest_neighbor_adaptive.R | 98 ++++++++-- tidydann-1.0.2/tidydann/R/threads.R |only tidydann-1.0.2/tidydann/R/tunable.R | 75 +++++-- tidydann-1.0.2/tidydann/R/zzz.R | 20 +- tidydann-1.0.2/tidydann/README.md | 88 +++++--- tidydann-1.0.2/tidydann/man/check_args.nearest_neighbor_adaptive.Rd |only tidydann-1.0.2/tidydann/man/figures/README-Circle-1.png |binary tidydann-1.0.2/tidydann/man/matrix_diagonal.Rd | 13 - tidydann-1.0.2/tidydann/man/nearest_neighbor_adaptive.Rd | 48 +++- tidydann-1.0.2/tidydann/man/neighborhood.Rd | 19 + tidydann-1.0.2/tidydann/man/sphere.Rd | 12 - tidydann-1.0.2/tidydann/man/tidydann_set_threads.Rd |only tidydann-1.0.2/tidydann/man/tunable.nearest_neighbor_adaptive.Rd | 8 tidydann-1.0.2/tidydann/man/update.nearest_neighbor_adaptive.Rd | 46 +++- tidydann-1.0.2/tidydann/man/weighted.Rd | 11 - tidydann-1.0.2/tidydann/tests/testthat/setup.R |only tidydann-1.0.2/tidydann/tests/testthat/test_B_tunable.R | 66 ++++++ tidydann-1.0.2/tidydann/tests/testthat/test_D_threads.R |only 23 files changed, 431 insertions(+), 180 deletions(-)
Title: Self-Similarity Test for Normality
Description: Implements the Self-Similarity Test for Normality (SSTN), a new
statistical test designed to assess whether a given sample originates from
a normal distribution. The method exploits the self-similarity property of
the normal characteristic function by iteratively transforming and comparing
standardized empirical characteristic functions. The null distribution of
the test statistic is obtained via Monte Carlo simulation. Details of the
methodology are described in Anarat and Schwender (2026),
"A test for normality based on self-similarity", <doi:10.48550/arXiv.2604.03810>.
Author: Akin Anarat [aut, cre]
Maintainer: Akin Anarat <akin.anarat@hhu.de>
Diff between sstn versions 1.0.1 dated 2026-04-11 and 1.0.2 dated 2026-08-29
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS.md | 6 ++++++ R/asymptotic_calibration.R | 4 ++-- R/calibration_data.R | 4 ++-- R/sstn.R | 10 +++++----- R/sysdata.rda |binary inst/doc/Introduction_to_SSTN.R | 4 ++-- inst/doc/Introduction_to_SSTN.Rmd | 4 ++-- inst/doc/Introduction_to_SSTN.html | 26 ++++++++++++++++++-------- man/calibration_data.Rd | 4 ++-- man/sstn.Rd | 4 ++-- vignettes/Introduction_to_SSTN.Rmd | 4 ++-- 13 files changed, 58 insertions(+), 42 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. 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 0.2.0 dated 2026-08-06 and 0.2.2 dated 2026-08-29
DESCRIPTION | 20 MD5 | 24 NAMESPACE | 2 NEWS.md | 29 + R/fitdistrBayes.R | 619 ++++++++++++++++++++-- R/model_spec.R |only README.md | 14 inst/examples/teaching.R | 21 inst/examples/tutorial_fitdistrBayes_all_models.R | 69 ++ man/fitdistrBayes.Rd | 61 +- man/fitdistrBayes_model.Rd |only man/fitdistrBayes_routes.Rd | 5 tests/tests_extension_api.R |only tests/tests_registry.R | 16 tests/tests_weighted_lindley.R |only 15 files changed, 786 insertions(+), 94 deletions(-)
Title: Remedy for Violations of the Proportional Hazards Assumption in
Cox Proportional Hazards Models
Description: Remedying proportional hazards
assumption violations of a Cox proportional hazards model using
stepwise changepoint and time-varying coefficient methods based on
Cox (1972) <doi:10.1111/j.2517-6161.1972.tb00899.x> and Klein
and Moeschberger (1997) <doi:10.1007/978-1-4757-2728-9>.
Author: Hamin Kim [aut, cre]
Maintainer: Hamin Kim <haaamin@korea.ac.kr>
Diff between cox.rvph versions 0.1.5 dated 2026-08-19 and 0.2.0 dated 2026-08-29
DESCRIPTION | 8 +- MD5 | 12 ++- NAMESPACE | 2 R/cox.rvph.R | 191 +++++++++++++++++++++++++++++------------------- R/print.cox.rvph.R |only R/summary.cox.rvph.R |only man/cox.rvph.Rd | 108 ++++++++++----------------- man/print.cox.rvph.Rd |only man/summary.cox.rvph.Rd |only 9 files changed, 174 insertions(+), 147 deletions(-)
Title: Slide Automation for Tables, Listings and Figures
Description: The normal process of creating clinical study slides is that
a statistician manually type in the numbers from outputs and a
separate statistician to double check the typed in numbers. This
process is time consuming, resource intensive, and error prone.
Automatic slide generation is a solution to address these issues. It
reduces the amount of work and the required time when creating slides,
and reduces the risk of errors from manually typing or copying numbers
from the output to slides. It also helps users to avoid unnecessary
stress when creating large amounts of slide decks in a short time
window.
Author: Joe Zhu [cre, aut] ,
Heng Wang [aut],
Yinqi Zhao [aut],
Bo Ci [aut],
Liming Li [aut],
Laura Wang [ctb],
Xiaoli Duan [aut],
Stefan Pascal Thoma [aut],
Thomas Neitmann [ctb],
Miles Almond [aut],
Mahdi About [ctb],
Kai Lim [ctb],
Nolan Steed [ctb],
Daol [...truncated...]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between autoslider.core versions 0.3.2 dated 2026-01-12 and 0.3.3 dated 2026-08-29
autoslider.core-0.3.2/autoslider.core/man/decorate-VTableTree-method.Rd |only autoslider.core-0.3.2/autoslider.core/man/decorate-listing_df-method.Rd |only autoslider.core-0.3.3/autoslider.core/DESCRIPTION | 29 autoslider.core-0.3.3/autoslider.core/MD5 | 94 autoslider.core-0.3.3/autoslider.core/NAMESPACE | 18 autoslider.core-0.3.3/autoslider.core/NEWS.md | 5 autoslider.core-0.3.3/autoslider.core/R/decorate.R | 733 ++--- autoslider.core-0.3.3/autoslider.core/R/generate_output.R | 276 +- autoslider.core-0.3.3/autoslider.core/R/save_output.R | 480 +-- autoslider.core-0.3.3/autoslider.core/R/to_ft_funs.R | 884 +++--- autoslider.core-0.3.3/autoslider.core/R/to_slides.R | 786 +++--- autoslider.core-0.3.3/autoslider.core/README.md | 86 autoslider.core-0.3.3/autoslider.core/build/vignette.rds |binary autoslider.core-0.3.3/autoslider.core/inst/WORDLIST | 224 - autoslider.core-0.3.3/autoslider.core/inst/doc/adding_templates.html | 342 +- autoslider.core-0.3.3/autoslider.core/inst/doc/autoslideR.R | 88 autoslider.core-0.3.3/autoslider.core/inst/doc/autoslideR.Rmd | 1074 ++++---- autoslider.core-0.3.3/autoslider.core/inst/doc/autoslideR.html | 1275 ++++------ autoslider.core-0.3.3/autoslider.core/inst/doc/downstream.html | 193 - autoslider.core-0.3.3/autoslider.core/inst/doc/generate_placeholder_slides.html | 404 +-- autoslider.core-0.3.3/autoslider.core/inst/doc/mcp_server.R |only autoslider.core-0.3.3/autoslider.core/inst/doc/mcp_server.Rmd |only autoslider.core-0.3.3/autoslider.core/inst/doc/mcp_server.html |only autoslider.core-0.3.3/autoslider.core/inst/doc/opensource.html | 505 ++- autoslider.core-0.3.3/autoslider.core/inst/doc/tlg_templates.html | 524 ++-- autoslider.core-0.3.3/autoslider.core/inst/doc/use_LLM.html | 390 +-- autoslider.core-0.3.3/autoslider.core/inst/doc/using_formats.html | 402 +-- autoslider.core-0.3.3/autoslider.core/inst/mcp |only autoslider.core-0.3.3/autoslider.core/man/autoslider.core-package.Rd | 97 autoslider.core-0.3.3/autoslider.core/man/decorate.Rd | 39 autoslider.core-0.3.3/autoslider.core/man/decorate.VTableTree.Rd |only autoslider.core-0.3.3/autoslider.core/man/decorate.autoslider_error.Rd | 38 autoslider.core-0.3.3/autoslider.core/man/decorate.default.Rd | 38 autoslider.core-0.3.3/autoslider.core/man/decorate.ggplot.Rd | 69 autoslider.core-0.3.3/autoslider.core/man/decorate.grob.Rd | 69 autoslider.core-0.3.3/autoslider.core/man/decorate.gtsummary.Rd | 69 autoslider.core-0.3.3/autoslider.core/man/decorate.list.Rd | 62 autoslider.core-0.3.3/autoslider.core/man/decorate.listing_df.Rd |only autoslider.core-0.3.3/autoslider.core/man/decorate.tbl_roche_summary.Rd |only autoslider.core-0.3.3/autoslider.core/man/generate_outputs.Rd | 100 autoslider.core-0.3.3/autoslider.core/man/trial.Rd | 28 autoslider.core-0.3.3/autoslider.core/tests/testthat/_snaps/g_mean_slides/g_eg_test.new.svg |only autoslider.core-0.3.3/autoslider.core/tests/testthat/_snaps/g_mean_slides/g_lb_chg_test.new.svg |only autoslider.core-0.3.3/autoslider.core/tests/testthat/_snaps/g_mean_slides/g_lb_test.new.svg |only autoslider.core-0.3.3/autoslider.core/tests/testthat/_snaps/g_mean_slides/g_mean_general_test.new.svg |only autoslider.core-0.3.3/autoslider.core/tests/testthat/_snaps/g_mean_slides/g_mean_nounit_test.new.svg |only autoslider.core-0.3.3/autoslider.core/tests/testthat/_snaps/g_mean_slides/g_vs_test.new.svg |only autoslider.core-0.3.3/autoslider.core/tests/testthat/_snaps/save_output.md | 6 autoslider.core-0.3.3/autoslider.core/tests/testthat/l_ae_slide_SE.rds |only autoslider.core-0.3.3/autoslider.core/tests/testthat/t_ae_pt_slide_G34_X2PER_SE.rds |only autoslider.core-0.3.3/autoslider.core/tests/testthat/t_ae_pt_slide_X10PER_SE.rds |only autoslider.core-0.3.3/autoslider.core/tests/testthat/t_ae_pt_soc_slide_G34_X2PER_SE.rds |only autoslider.core-0.3.3/autoslider.core/tests/testthat/t_ae_pt_soc_slide_X10PER_SE.rds |only autoslider.core-0.3.3/autoslider.core/tests/testthat/t_ae_summ_slide_SE.rds |only autoslider.core-0.3.3/autoslider.core/tests/testthat/t_dd_slide_SE.rds |only autoslider.core-0.3.3/autoslider.core/tests/testthat/t_ds_slide_FAS.rds |only autoslider.core-0.3.3/autoslider.core/tests/testthat/test-ai-offline.R |only autoslider.core-0.3.3/autoslider.core/tests/testthat/test-gtsummary.R |only autoslider.core-0.3.3/autoslider.core/tests/testthat/test-save_output.R | 73 autoslider.core-0.3.3/autoslider.core/vignettes/autoslideR.Rmd | 1074 ++++---- autoslider.core-0.3.3/autoslider.core/vignettes/mcp_server.Rmd |only 61 files changed, 5405 insertions(+), 5169 deletions(-)
More information about autoslider.core at CRAN
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Title: Interventional Prediction Evaluation
Description: Provides methods to evaluate predictive performance of models that
estimate risks under hypothetical intervention scenarios
(interventional/causal/counterfactual predictions) with observational data
subject to treatment-outcome confounding. Inverse probability of treatment
weighting (IPTW) is used to construct a pseudopopulation in which all
individuals receive a specified intervention, enabling assessment of
agreement between predicted risks under the intervention and observed
outcomes in the pseudo-population corresponding to that intervention.
Supports interventions with binary or categorical treatment levels, applied
at a single time point. Performance measures supported are AUC (Area
Under the receiving operating characteristic Curve), Brier score,
observed-expected ratio, and calibration plots. Methods implemented in this
package are based on work by Keogh and Van Geloven (2024)
<DOI:10.1097/EDE.0000000000001713>.
Author: Jasper van Egeraat [aut, cre],
Nan van Geloven [aut, cph],
Ruth Keogh [aut, cph],
Leiden University Medical Center [fnd]
Maintainer: Jasper van Egeraat <j.w.a.van_egeraat@lumc.nl>
Diff between ipeval versions 0.1.0 dated 2026-05-06 and 0.1.1 dated 2026-08-29
DESCRIPTION | 32 - MD5 | 62 +- NAMESPACE | 1 NEWS.md | 7 R/bootstrap.R | 93 +-- R/helpers.R | 96 ++++ R/ip_score.R | 687 ++++++++++++++++++----------- R/ipc_weights.R | 31 - R/ipeval-package.R |only R/ipt_weights.R | 72 ++- R/metrics.R | 59 -- R/observed_score.R | 95 ++-- R/print.R | 333 +++++++++++--- README.md | 94 ++- build/partial.rdb |only build/vignette.rds |binary inst/doc/ipeval.Rmd | 8 inst/doc/ipeval.html | 91 ++- inst/doc/time-to-event.html | 159 ++++-- man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/ip_score.Rd | 231 ++++++--- man/ipeval-package.Rd |only man/observed_score.Rd | 38 + man/plot.ip_score.Rd |only tests/testthat/_snaps |only tests/testthat/test-helpers.R | 44 + tests/testthat/test-ip_score-categorical.R |only tests/testthat/test-ip_score.R | 241 +++++----- tests/testthat/test-ipc_weights.R | 110 +--- tests/testthat/test-ipt_weights.R | 18 tests/testthat/test-metrics.R | 148 +----- tests/testthat/test-observed_score.R | 23 tests/testthat/test-predict_CF.R |only tests/testthat/test-print.R |only vignettes/ipeval.Rmd | 8 36 files changed, 1777 insertions(+), 1004 deletions(-)
Title: Get Data for Brazilian Bonds (Tesouro Direto)
Description: Downloads and aggregates data for Brazilian government issued bonds directly from the website of Tesouro Direto <https://www.tesourodireto.com.br/>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between GetTDData versions 1.6.0 dated 2026-06-04 and 1.7.0 dated 2026-08-29
DESCRIPTION | 12 ++--- MD5 | 38 +++++++++------ NAMESPACE | 3 + NEWS.md | 11 ++++ R/download_td_file.R | 4 + R/globals.R | 1 R/gtdd_get_yield_curve.R | 3 - R/plots.R |only R/read_td_file.R | 48 ++++++++++++-------- R/td_get.R | 7 -- R/td_get_current.R | 53 ++++++++++++---------- R/utils.R | 74 ++++++++++++++++++++++++++++--- README.md | 13 +++++ man/figures/README-unnamed-chunk-3-1.png |only man/get_asset_info.Rd |only man/get_cache_folder.Rd | 5 +- man/get_td_names.Rd | 5 +- man/plot_td_series.Rd |only man/plot_yield_curve.Rd |only man/td_get_current.Rd | 14 ++++- tests/testthat/test-importing-data.R | 35 ++------------ tests/testthat/test-new-features.R |only tests/testthat/test-yc.R | 2 23 files changed, 218 insertions(+), 110 deletions(-)
Title: Supporting Functions for Packages Maintained by 'YuLab-SMU'
Description: Miscellaneous functions commonly used by 'YuLab-SMU'.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between yulab.utils versions 0.2.4 dated 2026-02-02 and 0.2.5 dated 2026-08-29
DESCRIPTION | 8 MD5 | 122 +++---- NAMESPACE | 198 ++++++----- NEWS.md | 314 +++++++++--------- R/bib-ggtree.R | 520 +++++++++++++++---------------- R/bib-knownledge.R | 649 +++++++++++++++++++-------------------- R/biorxiv.R | 88 ++--- R/cache.R | 444 +++++++++++++------------- R/combinations.R | 28 - R/concat.r | 261 +++++++++------ R/download.R | 160 ++++----- R/error-utils.r | 712 +++++++++++++++++++++---------------------- R/file.R | 314 +++++++++--------- R/install_zip.R | 134 ++++---- R/list.R | 62 +-- R/load-orgdb.r | 36 +- R/matrix-utils.R | 74 ++-- R/os.R | 194 +++++------ R/parse_ratio.R | 44 +- R/pkg-utils.R | 482 ++++++++++++++--------------- R/regexpr.R | 134 ++++---- R/scale.R | 28 - R/scihub-dl.R | 52 +-- R/str-utils.R | 214 ++++++------ R/sudo-install.R | 42 +- R/utilities.R | 108 +++--- R/yulab-msg.R | 206 ++++++------ R/yulab-utils-package.R | 6 R/zzz.R | 20 - inst/prototype/GEO.r | 66 +-- inst/prototype/sra.r | 24 - man/as_chunked_array.Rd |only man/c2.Rd | 14 man/check_directory.Rd | 10 man/check_file.Rd | 10 man/check_input.Rd | 10 man/check_packages.Rd | 10 man/check_range.Rd | 10 man/cran-bioc-pkg.Rd | 68 ++-- man/exec.Rd | 6 man/get_dependencies.Rd | 16 man/get_fun_from_pkg.Rd | 72 ++-- man/github-pkg.Rd | 16 man/has_internet.Rd | 6 man/install_zip.Rd | 48 +- man/install_zip_gh.Rd | 68 ++-- man/is.installed.Rd | 68 ++-- man/mat2df.Rd | 52 +-- man/mypkg.Rd | 66 +-- man/o.Rd | 66 +-- man/packageTitle.Rd | 16 man/pload.Rd | 16 man/read.cb.Rd | 58 +-- man/scihub-dl.Rd | 48 +- man/show_in_excel.Rd | 54 +-- man/str-detect.Rd | 8 man/str-extract.Rd | 8 man/str-starts-ends.Rd | 68 ++-- man/str_wrap.Rd | 58 +-- man/user_dir.Rd | 6 man/yread.Rd | 13 man/yulab.utils-package.Rd | 5 tests/testthat/test-concat.R |only 63 files changed, 3402 insertions(+), 3316 deletions(-)
Title: User-Friendly Tables with Color Helpers for Data Exploration
Description: Make it easy to deal with multiple cross-tables in data exploration, by
creating them, manipulating them, and adding color helpers to highlight deviations
(differences from totals, comparisons between lines or columns, contributions to
variance, odds ratios, etc.) and significance (confidence intervals, stars, etc.).
Create the same kind of tables for regression models, with a framework to compare
model effects with their crude/observed counterpart systematically.
All functions render data frames which can be easily manipulated.
All tables can be exported with formats and colors to 'Excel', html and markdown.
Author: Brice Nocenti [aut, cre]
Maintainer: Brice Nocenti <brice.nocenti@protonmail.com>
Diff between tabxplor versions 1.3.1 dated 2025-09-26 and 2.0.0 dated 2026-08-29
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Title: Encrypt and Decrypt Strings, R Objects and Files
Description: A consistent interface to encrypt and decrypt strings, R objects and files using symmetric and asymmetric key encryption.
Author: Komala Sheshachala Srikanth [aut, cre]
Maintainer: Komala Sheshachala Srikanth <sri.teach@gmail.com>
Diff between safer versions 0.2.2 dated 2026-03-24 and 0.2.3 dated 2026-08-29
DESCRIPTION | 9 +++-- MD5 | 11 +++---- NAMESPACE | 1 NEWS.md | 5 +++ R/keypair.R | 77 +++++++++++++++++++++++++++++++++++++++++++++------ man/read_keypair.Rd |only man/safer-package.Rd | 2 - 7 files changed, 87 insertions(+), 18 deletions(-)
Title: Tools for Developing R Packages Interfacing with 'Stan'
Description: Provides various tools for developers of R packages interfacing
with 'Stan' <https://mc-stan.org>, including functions to set up the required
package structure, S3 generics and default methods to unify function naming
across 'Stan'-based R packages, and vignettes with recommendations for
developers.
Author: Jonah Gabry [aut],
Ben Goodrich [aut],
Martin Lysy [aut],
Andrew Johnson [aut, cre],
Hamada S. Badr [ctb],
Marco Colombo [ctb],
Stefan Siegert [ctb],
Visruth Srimath Kandali [ctb],
Trustees of Columbia University [cph]
Maintainer: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Diff between rstantools versions 2.7.0 dated 2026-07-25 and 2.7.1 dated 2026-08-29
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 12 +++++++----- R/stanc_exceptions.R | 4 ++-- inst/doc/developer-guidelines.html | 2 +- inst/doc/minimal-rstan-package.html | 4 ++-- 6 files changed, 21 insertions(+), 19 deletions(-)
Title: Group Sequential Design
Description: Derives group sequential clinical trial designs and describes
their properties. Particular focus on time-to-event, binary, and
continuous outcomes. Largely based on methods described in
Jennison, Christopher and Turnbull, Bruce W., 2000,
"Group Sequential Methods with Applications to Clinical Trials"
ISBN: 0-8493-0316-8.
Author: Keaven Anderson [aut, cre],
Merck & Co., Inc., Rahway, NJ, USA and its affiliates [cph]
Maintainer: Keaven Anderson <keaven_anderson@merck.com>
Diff between gsDesign versions 3.10.1 dated 2026-07-19 and 3.11.0 dated 2026-08-29
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Title: Automatic Plotting and Theming of Many Graphs
Description: Visual exploration and presentation of networks should not be difficult.
This package includes functions for plotting networks and network-related metrics with sensible and pretty defaults.
It includes 'ggplot2'-based plot methods for many popular network package classes.
It also includes some novel layout algorithms, and options for straightforward, consistent themes.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between autograph versions 1.2.1 dated 2026-08-26 and 1.2.2 dated 2026-08-29
DESCRIPTION | 6 +-- MD5 | 26 ++++++------- NEWS.md | 14 +++++++ R/graph_aes.R | 21 +++++++++- R/graph_legends.R | 74 ++++++++++++++++++++++++------------- R/graph_nodes.R | 28 +++++++++----- R/graphr.R | 4 ++ R/grapht.R | 15 +++++++ R/zzz.R | 41 +++++++++++++++++--- man/plot_graphr.Rd | 4 ++ man/plot_grapht.Rd | 4 ++ tests/testthat/Rplots.pdf |binary tests/testthat/test-graphr.R | 86 +++++++++++++++++++++++++++++++++++++++++-- tests/testthat/test-grapht.R | 9 ++++ 14 files changed, 269 insertions(+), 63 deletions(-)
Title: The Uniform Manifold Approximation and Projection (UMAP) Method
for Dimensionality Reduction
Description: An implementation of the Uniform Manifold Approximation and
Projection dimensionality reduction by McInnes et al. (2018)
<doi:10.48550/arXiv.1802.03426>. It also provides means to transform new data and
to carry out supervised dimensionality reduction. An implementation of
the related LargeVis method of Tang et al. (2016) <doi:10.48550/arXiv.1602.00370>
is also provided. This is a complete re-implementation in R (and C++,
via the 'Rcpp' package): no Python installation is required. See the
uwot website (<https://github.com/jlmelville/uwot>) for more
documentation and examples.
Author: James Melville [aut, cre, cph],
Aaron Lun [ctb],
Mohamed Nadhir Djekidel [ctb],
Yuhan Hao [ctb],
Dirk Eddelbuettel [ctb],
Wouter van der Bijl [ctb],
Hugo Gruson [ctb]
Maintainer: James Melville <jlmelville@gmail.com>
Diff between uwot versions 0.2.4 dated 2025-11-10 and 0.2.5 dated 2026-08-29
uwot-0.2.4/uwot/inst/include/RcppPerpendicular.h |only uwot-0.2.5/uwot/DESCRIPTION | 9 uwot-0.2.5/uwot/MD5 | 89 ++++---- uwot-0.2.5/uwot/NEWS.md | 21 + uwot-0.2.5/uwot/R/neighbors.R | 43 ++++ uwot-0.2.5/uwot/R/nn_hnsw.R | 10 uwot-0.2.5/uwot/R/nn_nndescent.R | 21 + uwot-0.2.5/uwot/R/transform.R | 9 uwot-0.2.5/uwot/R/umap2.R | 11 - uwot-0.2.5/uwot/R/uwot.R | 139 +++++++++---- uwot-0.2.5/uwot/build/partial.rdb |binary uwot-0.2.5/uwot/build/vignette.rds |binary uwot-0.2.5/uwot/inst/include/pforr.h |only uwot-0.2.5/uwot/inst/include/uwot/connected_components.h | 4 uwot-0.2.5/uwot/inst/include/uwot/coords.h | 28 +- uwot-0.2.5/uwot/inst/include/uwot/epoch.h | 15 - uwot-0.2.5/uwot/inst/include/uwot/gradient.h | 33 +-- uwot-0.2.5/uwot/inst/include/uwot/optimize.h | 17 + uwot-0.2.5/uwot/inst/include/uwot/smooth_knn.h | 2 uwot-0.2.5/uwot/inst/include/uwot/tauprng.h | 3 uwot-0.2.5/uwot/inst/include/uwot/transform.h | 4 uwot-0.2.5/uwot/inst/include/uwot/update.h | 41 +-- uwot-0.2.5/uwot/man/lvish.Rd | 25 +- uwot-0.2.5/uwot/man/similarity_graph.Rd | 27 +- uwot-0.2.5/uwot/man/tumap.Rd | 25 +- uwot-0.2.5/uwot/man/umap.Rd | 25 +- uwot-0.2.5/uwot/man/umap2.Rd | 11 - uwot-0.2.5/uwot/src/Makevars | 1 uwot-0.2.5/uwot/src/nn_parallel.cpp | 4 uwot-0.2.5/uwot/src/perplexity.cpp | 4 uwot-0.2.5/uwot/src/r_uwot.cpp | 55 ++--- uwot-0.2.5/uwot/src/rparallel.h | 17 - uwot-0.2.5/uwot/src/smooth_knn.cpp | 4 uwot-0.2.5/uwot/src/transform.cpp | 4 uwot-0.2.5/uwot/tests/testthat/test_curve.R | 24 +- uwot-0.2.5/uwot/tests/testthat/test_epochs.R | 2 uwot-0.2.5/uwot/tests/testthat/test_errors.R | 36 +++ uwot-0.2.5/uwot/tests/testthat/test_fuzzy_simplicial_set.R | 38 +-- uwot-0.2.5/uwot/tests/testthat/test_knn_aff.R | 2 uwot-0.2.5/uwot/tests/testthat/test_neighbors.R | 68 +++--- uwot-0.2.5/uwot/tests/testthat/test_nndescent.R |only uwot-0.2.5/uwot/tests/testthat/test_output.R | 23 +- uwot-0.2.5/uwot/tests/testthat/test_perplexity.R | 20 - uwot-0.2.5/uwot/tests/testthat/test_saveload.R | 10 uwot-0.2.5/uwot/tests/testthat/test_smooth_knn_dists.R | 32 +- uwot-0.2.5/uwot/tests/testthat/test_supervised.R | 10 uwot-0.2.5/uwot/tests/testthat/test_transform.R | 4 47 files changed, 610 insertions(+), 360 deletions(-)