Title: Simulated Sampling Procedure for Community Ecology
Description: The Simulation-based Sampling Protocol (SSP) is an R package designed to estimate sampling effort in studies of ecological communities. It is based on the concept of pseudo-multivariate standard error (MultSE) (Anderson & Santana-Garcon, 2015, <doi:10.1111/ele.12385>) and the simulation of ecological data. The theoretical background is described in Guerra-Castro et al. (2020, <doi:10.1111/ecog.05284>).
Author: Edlin Guerra-Castro [aut, cre],
Maite Mascaro [aut],
Nuno Simoes [aut],
Juan Cruz-Motta [aut],
Juan Cajas [aut]
Maintainer: Edlin Guerra-Castro <edlinguerra@gmail.com>
Diff between SSP versions 1.0.1 dated 2020-03-28 and 1.0.2 dated 2025-04-24
DESCRIPTION | 15 - MD5 | 49 +-- NAMESPACE | 3 NEWS.md |only R/assempar.R | 99 +++++- R/datquality.R | 56 +++ R/ioptimum.R | 64 ++++ R/plot_ssp.R | 219 +++++++++------ R/sampsd.R | 68 ++++ R/simdata.R | 59 +++- R/summary_ssp.R | 51 +++ README.md | 43 +-- build/partial.rdb |only build/vignette.rds |binary inst/doc/SSP-guide.R | 12 inst/doc/SSP-guide.Rmd | 6 inst/doc/SSP-guide.html | 687 ++++++++++++++++++++++++++++++++++-------------- man/SSP-package.Rd | 11 man/assempar.Rd | 88 ++---- man/datquality.Rd | 120 ++------ man/figures |only man/ioptimum.Rd | 146 +++------- man/plot_ssp.Rd | 132 ++------- man/sampsd.Rd | 143 +++------ man/simdata.Rd | 102 ++----- man/summary_ssp.Rd | 116 ++------ vignettes/SSP-guide.Rmd | 6 27 files changed, 1367 insertions(+), 928 deletions(-)
Title: Forest Estimations and Dendrometric Computations
Description: Computation of dendrometric and structural
parameters from forest inventory data. The objective is to provide an
user-friendly R package for researchers, ecologists, foresters,
statisticians, loggers and others persons who deal with forest inventory
data. Useful conversion of angle value from degree to radian, conversion from
angle to slope (in percentage) and their reciprocals as well as principal
angle determination are also included. Position and dispersion parameters
usually found in forest studies are implemented. The package contains
Fibonacci series, its extensions and the Golden Number computation.
Useful references are Arcadius Y. J. Akossou, Soufianou Arzouma,
Eloi Y. Attakpa, Noël H. Fonton and Kouami Kokou (2013) <doi:10.3390/d5010099>
and W. Bonou, R. Glele Kakaï, A.E. Assogbadjo, H.N. Fonton, B. Sinsin (2009)
<doi:10.1016/j.foreco.2009.05.032> .
Author: Narcisse Yehouenou [aut, cre],
Information and Communication Technology for you ONG [fnd]
Maintainer: Narcisse Yehouenou <narcisstar211@gmail.com>
Diff between dendrometry versions 0.0.2 dated 2023-02-07 and 0.0.3 dated 2025-04-24
dendrometry-0.0.2/dendrometry/man/circum.Rd |only dendrometry-0.0.2/dendrometry/man/principal.Rd |only dendrometry-0.0.2/dendrometry/man/rad.Rd |only dendrometry-0.0.2/dendrometry/man/slope2angle.Rd |only dendrometry-0.0.3/dendrometry/DESCRIPTION | 12 dendrometry-0.0.3/dendrometry/MD5 | 84 dendrometry-0.0.3/dendrometry/NAMESPACE | 13 dendrometry-0.0.3/dendrometry/NEWS.md | 12 dendrometry-0.0.3/dendrometry/R/dendrometry.R | 1811 ++++++++++----- dendrometry-0.0.3/dendrometry/build/partial.rdb |binary dendrometry-0.0.3/dendrometry/build/vignette.rds |binary dendrometry-0.0.3/dendrometry/demo/dendro.R | 18 dendrometry-0.0.3/dendrometry/demo/volume.R | 54 dendrometry-0.0.3/dendrometry/inst/doc/dendrometry.R | 102 dendrometry-0.0.3/dendrometry/inst/doc/dendrometry.Rmd | 103 dendrometry-0.0.3/dendrometry/inst/doc/dendrometry.html | 293 +- dendrometry-0.0.3/dendrometry/man/Logging.Rd | 6 dendrometry-0.0.3/dendrometry/man/Tree.Rd | 13 dendrometry-0.0.3/dendrometry/man/adjWeibull.Rd |only dendrometry-0.0.3/dendrometry/man/angle2slope.Rd | 52 dendrometry-0.0.3/dendrometry/man/barkFactor.Rd |only dendrometry-0.0.3/dendrometry/man/basal.Rd | 40 dendrometry-0.0.3/dendrometry/man/basalContribution.Rd |only dendrometry-0.0.3/dendrometry/man/basal_i.Rd | 18 dendrometry-0.0.3/dendrometry/man/blackman.Rd | 2 dendrometry-0.0.3/dendrometry/man/dbh.Rd | 25 dendrometry-0.0.3/dendrometry/man/deg.Rd | 23 dendrometry-0.0.3/dendrometry/man/dendrometry-package.Rd | 8 dendrometry-0.0.3/dendrometry/man/densityRegen.Rd |only dendrometry-0.0.3/dendrometry/man/densityTree.Rd | 26 dendrometry-0.0.3/dendrometry/man/diameterMean.Rd | 10 dendrometry-0.0.3/dendrometry/man/distanceH.Rd | 18 dendrometry-0.0.3/dendrometry/man/factorize.Rd | 3 dendrometry-0.0.3/dendrometry/man/fiboRate.Rd | 78 dendrometry-0.0.3/dendrometry/man/fibonacci.Rd | 4 dendrometry-0.0.3/dendrometry/man/girard.Rd |only dendrometry-0.0.3/dendrometry/man/green.Rd | 2 dendrometry-0.0.3/dendrometry/man/height.Rd | 44 dendrometry-0.0.3/dendrometry/man/loreyHeight.Rd | 15 dendrometry-0.0.3/dendrometry/man/makedata.Rd | 17 dendrometry-0.0.3/dendrometry/man/param_i.Rd |only dendrometry-0.0.3/dendrometry/man/print.angle.Rd |only dendrometry-0.0.3/dendrometry/man/print.slope.Rd |only dendrometry-0.0.3/dendrometry/man/rfreq.Rd |only dendrometry-0.0.3/dendrometry/man/sampleSize.Rd | 21 dendrometry-0.0.3/dendrometry/man/skewness.Rd | 2 dendrometry-0.0.3/dendrometry/man/spNmReduce.Rd |only dendrometry-0.0.3/dendrometry/man/stacking.Rd | 3 dendrometry-0.0.3/dendrometry/man/volume.Rd | 8 dendrometry-0.0.3/dendrometry/vignettes/dendrometry.Rmd | 103 50 files changed, 1992 insertions(+), 1051 deletions(-)
Title: Nonparametric Bootstrap Test for Regression Monotonicity
Description: Implements nonparametric bootstrap tests for detecting monotonicity
in regression functions from Hall, P. and Heckman, N. (2000) <doi:10.1214/aos/1016120363>
Includes tools for visualizing results using Nadaraya-Watson kernel regression and supports
efficient computation with 'C++'.
Author: Dylan Huynh [aut, cre]
Maintainer: Dylan Huynh <dylanhuynh@utexas.edu>
Diff between MonotonicityTest versions 1.1 dated 2025-04-02 and 1.2 dated 2025-04-24
DESCRIPTION | 6 +++--- MD5 | 12 +++++++----- NAMESPACE | 5 ++++- R/main.R | 16 ++++++---------- R/monotonicity-result.R |only man/monotonicity_test.Rd | 10 ++-------- tests/testthat/Rplots.pdf |only tests/testthat/test-main.R | 5 +++++ 8 files changed, 27 insertions(+), 27 deletions(-)
More information about MonotonicityTest at CRAN
Permanent link
Title: Modern Database Engine for Complex Data Based on
Multi-Dimensional Arrays
Description: The modern database 'TileDB' introduces a powerful on-disk
format for storing and accessing any complex data based on multi-dimensional
arrays. It supports dense and sparse arrays, dataframes and key-values stores,
cloud storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression,
encryption and checksum filters, uses a fully multi-threaded implementation,
supports parallel I/O, data versioning ('time travel'), metadata and groups.
It is implemented as an embeddable cross-platform C++ library with APIs from
several languages, and integrations. This package provides the R support.
Author: TileDB, Inc. [aut, cph],
Isaiah Norton [cre]
Maintainer: Isaiah Norton <isaiah@tiledb.com>
Diff between tiledb versions 0.30.2 dated 2024-10-04 and 0.31.1 dated 2025-04-24
tiledb-0.30.2/tiledb/R/Init.R |only tiledb-0.31.1/tiledb/DESCRIPTION | 11 tiledb-0.31.1/tiledb/MD5 | 446 - tiledb-0.31.1/tiledb/NAMESPACE | 6 tiledb-0.31.1/tiledb/NEWS.md | 19 tiledb-0.31.1/tiledb/R/Array.R | 227 tiledb-0.31.1/tiledb/R/ArraySchema.R | 981 ++- tiledb-0.31.1/tiledb/R/ArraySchemaEvolution.R | 187 tiledb-0.31.1/tiledb/R/ArrowIO.R | 60 tiledb-0.31.1/tiledb/R/Attribute.R | 311 - tiledb-0.31.1/tiledb/R/BatchedQuery.R | 695 +- tiledb-0.31.1/tiledb/R/Config.R | 82 tiledb-0.31.1/tiledb/R/Ctx.R | 56 tiledb-0.31.1/tiledb/R/CurrentDomain.R | 65 tiledb-0.31.1/tiledb/R/DataFrame.R | 438 - tiledb-0.31.1/tiledb/R/Dim.R | 279 tiledb-0.31.1/tiledb/R/Domain.R | 174 tiledb-0.31.1/tiledb/R/Error.R | 4 tiledb-0.31.1/tiledb/R/Filestore.R | 74 tiledb-0.31.1/tiledb/R/Filter.R | 75 tiledb-0.31.1/tiledb/R/FilterList.R | 108 tiledb-0.31.1/tiledb/R/FragmentInfo.R | 183 tiledb-0.31.1/tiledb/R/Group.R | 417 - tiledb-0.31.1/tiledb/R/Matrix.R | 98 tiledb-0.31.1/tiledb/R/Metadata.R | 51 tiledb-0.31.1/tiledb/R/NDRectangle.R | 145 tiledb-0.31.1/tiledb/R/Object.R | 54 tiledb-0.31.1/tiledb/R/Query.R | 291 - tiledb-0.31.1/tiledb/R/QueryCondition.R | 375 - tiledb-0.31.1/tiledb/R/RcppExports.R | 4 tiledb-0.31.1/tiledb/R/SparseMatrix.R | 194 tiledb-0.31.1/tiledb/R/Stats.R | 18 tiledb-0.31.1/tiledb/R/Subarray.R | 27 tiledb-0.31.1/tiledb/R/TileDB-Package.R | 2 tiledb-0.31.1/tiledb/R/TileDBArray.R | 2814 +++++----- tiledb-0.31.1/tiledb/R/Utils.R | 365 - tiledb-0.31.1/tiledb/R/VFS.R | 327 - tiledb-0.31.1/tiledb/R/Version.R | 182 tiledb-0.31.1/tiledb/R/zzz.R |only tiledb-0.31.1/tiledb/README.md | 4 tiledb-0.31.1/tiledb/build/vignette.rds |binary tiledb-0.31.1/tiledb/configure.ac | 6 tiledb-0.31.1/tiledb/inst/doc/data-ingestion-from-sql.html | 2 tiledb-0.31.1/tiledb/inst/doc/documentation.html | 2 tiledb-0.31.1/tiledb/inst/doc/installation-options.html | 2 tiledb-0.31.1/tiledb/inst/doc/introduction.html | 6 tiledb-0.31.1/tiledb/inst/doc/introduction.md | 4 tiledb-0.31.1/tiledb/inst/doc/tiledb-mariadb-examples.html | 2 tiledb-0.31.1/tiledb/inst/pkgconfigtest |only tiledb-0.31.1/tiledb/inst/tinytest/test_arrayschema.R | 7 tiledb-0.31.1/tiledb/inst/tinytest/test_querycondition.R | 30 tiledb-0.31.1/tiledb/inst/tinytest/test_tiledbarray.R | 9 tiledb-0.31.1/tiledb/inst/tinytest/test_vfs.R | 111 tiledb-0.31.1/tiledb/man/array_consolidate.Rd | 9 tiledb-0.31.1/tiledb/man/array_vacuum.Rd | 16 tiledb-0.31.1/tiledb/man/as.vector.tiledb_config.Rd | 4 tiledb-0.31.1/tiledb/man/attrs-set-tiledb_array-method.Rd | 6 tiledb-0.31.1/tiledb/man/attrs-tiledb_array-ANY-method.Rd | 4 tiledb-0.31.1/tiledb/man/attrs-tiledb_array_schema-ANY-method.Rd | 14 tiledb-0.31.1/tiledb/man/attrs-tiledb_array_schema-character-method.Rd | 14 tiledb-0.31.1/tiledb/man/attrs-tiledb_array_schema-numeric-method.Rd | 14 tiledb-0.31.1/tiledb/man/cell_order-tiledb_array_schema-method.Rd | 5 tiledb-0.31.1/tiledb/man/config-tiledb_ctx-method.Rd | 4 tiledb-0.31.1/tiledb/man/datatype-tiledb_dim-method.Rd | 8 tiledb-0.31.1/tiledb/man/datatype-tiledb_domain-method.Rd | 4 tiledb-0.31.1/tiledb/man/datetimes_as_int64-set-tiledb_array-method.Rd | 9 tiledb-0.31.1/tiledb/man/datetimes_as_int64-tiledb_array-method.Rd | 12 tiledb-0.31.1/tiledb/man/dim.tiledb_array_schema.Rd | 12 tiledb-0.31.1/tiledb/man/dim.tiledb_dim.Rd | 8 tiledb-0.31.1/tiledb/man/dim.tiledb_domain.Rd | 10 tiledb-0.31.1/tiledb/man/dimensions-tiledb_array_schema-method.Rd | 14 tiledb-0.31.1/tiledb/man/dimensions-tiledb_domain-method.Rd | 10 tiledb-0.31.1/tiledb/man/domain-tiledb_array_schema-method.Rd | 9 tiledb-0.31.1/tiledb/man/domain-tiledb_dim-method.Rd | 6 tiledb-0.31.1/tiledb/man/dot-core_info.Rd |only tiledb-0.31.1/tiledb/man/dot-pkg_config.Rd |only tiledb-0.31.1/tiledb/man/extended-set-tiledb_array-method.Rd | 6 tiledb-0.31.1/tiledb/man/extended-tiledb_array-method.Rd | 9 tiledb-0.31.1/tiledb/man/filter_list-set-tiledb_dim-method.Rd | 2 tiledb-0.31.1/tiledb/man/filter_list-tiledb_array_schema-method.Rd | 4 tiledb-0.31.1/tiledb/man/filter_list-tiledb_attr-method.Rd | 9 tiledb-0.31.1/tiledb/man/filter_list-tiledb_dim-method.Rd | 4 tiledb-0.31.1/tiledb/man/fromSparseMatrix.Rd | 20 tiledb-0.31.1/tiledb/man/has_attribute.Rd | 2 tiledb-0.31.1/tiledb/man/is.anonymous.Rd | 4 tiledb-0.31.1/tiledb/man/is.anonymous.tiledb_dim.Rd | 6 tiledb-0.31.1/tiledb/man/is.integral-tiledb_domain-method.Rd | 4 tiledb-0.31.1/tiledb/man/is.sparse-tiledb_array_schema-method.Rd | 4 tiledb-0.31.1/tiledb/man/name-tiledb_attr-method.Rd | 4 tiledb-0.31.1/tiledb/man/name-tiledb_dim-method.Rd | 6 tiledb-0.31.1/tiledb/man/nfilters-tiledb_filter_list-method.Rd | 4 tiledb-0.31.1/tiledb/man/parse_query_condition.Rd | 14 tiledb-0.31.1/tiledb/man/query_condition-set-tiledb_array-method.Rd | 5 tiledb-0.31.1/tiledb/man/query_layout-set-tiledb_array-method.Rd | 11 tiledb-0.31.1/tiledb/man/query_layout-tiledb_array-method.Rd | 6 tiledb-0.31.1/tiledb/man/query_statistics-set-tiledb_array-method.Rd | 7 tiledb-0.31.1/tiledb/man/query_statistics-tiledb_array-method.Rd | 8 tiledb-0.31.1/tiledb/man/raw_dump-tiledb_array_schema-method.Rd | 2 tiledb-0.31.1/tiledb/man/return.array-set-tiledb_array-method.Rd | 4 tiledb-0.31.1/tiledb/man/return.array-tiledb_array-method.Rd | 4 tiledb-0.31.1/tiledb/man/return.data.frame-tiledb_array-method.Rd | 6 tiledb-0.31.1/tiledb/man/return.matrix-set-tiledb_array-method.Rd | 4 tiledb-0.31.1/tiledb/man/return.matrix-tiledb_array-method.Rd | 4 tiledb-0.31.1/tiledb/man/return_as-set-tiledb_array-method.Rd | 11 tiledb-0.31.1/tiledb/man/return_as-tiledb_array-method.Rd | 15 tiledb-0.31.1/tiledb/man/save_allocation_size_preference.Rd | 5 tiledb-0.31.1/tiledb/man/save_return_as_preference.Rd | 30 tiledb-0.31.1/tiledb/man/selected_points-set-tiledb_array-method.Rd | 5 tiledb-0.31.1/tiledb/man/selected_points-tiledb_array-method.Rd | 9 tiledb-0.31.1/tiledb/man/selected_ranges-set-tiledb_array-method.Rd | 9 tiledb-0.31.1/tiledb/man/selected_ranges-tiledb_array-method.Rd | 9 tiledb-0.31.1/tiledb/man/show-tiledb_array_schema-method.Rd | 2 tiledb-0.31.1/tiledb/man/show-tiledb_config-method.Rd | 4 tiledb-0.31.1/tiledb/man/show-tiledb_dim-method.Rd | 2 tiledb-0.31.1/tiledb/man/strings_as_factors-set-tiledb_array-method.Rd | 5 tiledb-0.31.1/tiledb/man/strings_as_factors-tiledb_array-method.Rd | 8 tiledb-0.31.1/tiledb/man/sub-tiledb_array-ANY-method.Rd | 15 tiledb-0.31.1/tiledb/man/sub-tiledb_config-ANY-method.Rd | 4 tiledb-0.31.1/tiledb/man/sub-tiledb_filter_list-ANY-method.Rd | 4 tiledb-0.31.1/tiledb/man/subset-tiledb_array-ANY-ANY-ANY-method.Rd | 16 tiledb-0.31.1/tiledb/man/subset-tiledb_config-ANY-ANY-ANY-method.Rd | 4 tiledb-0.31.1/tiledb/man/tdb_collect-tiledb_array-method.Rd | 5 tiledb-0.31.1/tiledb/man/tdb_filter-tiledb_array-method.Rd | 5 tiledb-0.31.1/tiledb/man/tile-tiledb_dim-method.Rd | 8 tiledb-0.31.1/tiledb/man/tile_order-tiledb_array_schema-method.Rd | 5 tiledb-0.31.1/tiledb/man/tiledb-package.Rd | 1 tiledb-0.31.1/tiledb/man/tiledb_array-class.Rd | 57 tiledb-0.31.1/tiledb/man/tiledb_array.Rd | 80 tiledb-0.31.1/tiledb/man/tiledb_array_create.Rd | 6 tiledb-0.31.1/tiledb/man/tiledb_array_delete_fragments_list.Rd | 3 tiledb-0.31.1/tiledb/man/tiledb_array_get_non_empty_domain_from_index.Rd | 6 tiledb-0.31.1/tiledb/man/tiledb_array_get_non_empty_domain_from_name.Rd | 6 tiledb-0.31.1/tiledb/man/tiledb_array_is_open_for_reading.Rd |only tiledb-0.31.1/tiledb/man/tiledb_array_is_open_for_writing.Rd |only tiledb-0.31.1/tiledb/man/tiledb_array_open.Rd | 8 tiledb-0.31.1/tiledb/man/tiledb_array_schema.Rd | 25 tiledb-0.31.1/tiledb/man/tiledb_array_schema_check.Rd | 2 tiledb-0.31.1/tiledb/man/tiledb_array_schema_get_allows_dups.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_array_schema_get_capacity.Rd | 2 tiledb-0.31.1/tiledb/man/tiledb_array_schema_get_current_domain.Rd | 6 tiledb-0.31.1/tiledb/man/tiledb_array_schema_set_allows_dups.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_array_schema_set_capacity.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_array_schema_set_coords_filter_list.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_array_schema_set_current_domain.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_array_schema_set_enumeration_empty.Rd | 5 tiledb-0.31.1/tiledb/man/tiledb_array_schema_set_offsets_filter_list.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_array_schema_set_validity_filter_list.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_array_schema_version.Rd | 2 tiledb-0.31.1/tiledb/man/tiledb_attr.Rd | 10 tiledb-0.31.1/tiledb/man/tiledb_attribute_get_cell_val_num.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_config.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_config_as_built_json.Rd | 5 tiledb-0.31.1/tiledb/man/tiledb_config_load.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_config_save.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_ctx.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_ctx_set_tag.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_current_domain.Rd | 6 tiledb-0.31.1/tiledb/man/tiledb_dim.Rd | 6 tiledb-0.31.1/tiledb/man/tiledb_dim_get_cell_val_num.Rd | 2 tiledb-0.31.1/tiledb/man/tiledb_domain.Rd | 10 tiledb-0.31.1/tiledb/man/tiledb_filter.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_filter_get_option.Rd | 6 tiledb-0.31.1/tiledb/man/tiledb_filter_list.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_filter_list_get_max_chunk_size.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_filter_list_set_max_chunk_size.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_filter_set_option.Rd | 6 tiledb-0.31.1/tiledb/man/tiledb_filter_type.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_fragment_info.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_fragment_info_get_non_empty_domain_name.Rd | 2 tiledb-0.31.1/tiledb/man/tiledb_group.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_group_add_member.Rd | 9 tiledb-0.31.1/tiledb/man/tiledb_group_close.Rd | 3 tiledb-0.31.1/tiledb/man/tiledb_group_create.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_group_delete.Rd | 11 tiledb-0.31.1/tiledb/man/tiledb_group_delete_metadata.Rd | 6 tiledb-0.31.1/tiledb/man/tiledb_group_get_all_metadata.Rd | 3 tiledb-0.31.1/tiledb/man/tiledb_group_get_config.Rd | 3 tiledb-0.31.1/tiledb/man/tiledb_group_get_metadata.Rd | 6 tiledb-0.31.1/tiledb/man/tiledb_group_get_metadata_from_index.Rd | 3 tiledb-0.31.1/tiledb/man/tiledb_group_has_metadata.Rd | 6 tiledb-0.31.1/tiledb/man/tiledb_group_is_open.Rd | 3 tiledb-0.31.1/tiledb/man/tiledb_group_is_relative.Rd | 3 tiledb-0.31.1/tiledb/man/tiledb_group_member.Rd | 14 tiledb-0.31.1/tiledb/man/tiledb_group_member_count.Rd | 3 tiledb-0.31.1/tiledb/man/tiledb_group_member_dump.Rd | 9 tiledb-0.31.1/tiledb/man/tiledb_group_metadata_num.Rd | 3 tiledb-0.31.1/tiledb/man/tiledb_group_open.Rd | 7 tiledb-0.31.1/tiledb/man/tiledb_group_put_metadata.Rd | 6 tiledb-0.31.1/tiledb/man/tiledb_group_query_type.Rd | 6 tiledb-0.31.1/tiledb/man/tiledb_group_remove_member.Rd | 7 tiledb-0.31.1/tiledb/man/tiledb_group_set_config.Rd | 3 tiledb-0.31.1/tiledb/man/tiledb_group_uri.Rd | 3 tiledb-0.31.1/tiledb/man/tiledb_is_supported_fs.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_ndim-tiledb_array_schema-method.Rd | 12 tiledb-0.31.1/tiledb/man/tiledb_ndim-tiledb_dim-method.Rd | 8 tiledb-0.31.1/tiledb/man/tiledb_ndim-tiledb_domain-method.Rd | 10 tiledb-0.31.1/tiledb/man/tiledb_ndrectangle.Rd | 8 tiledb-0.31.1/tiledb/man/tiledb_ndrectangle_datatype.Rd | 10 tiledb-0.31.1/tiledb/man/tiledb_ndrectangle_datatype_by_ind.Rd | 10 tiledb-0.31.1/tiledb/man/tiledb_ndrectangle_dim_num.Rd | 10 tiledb-0.31.1/tiledb/man/tiledb_ndrectangle_get_range.Rd | 12 tiledb-0.31.1/tiledb/man/tiledb_ndrectangle_set_range.Rd | 10 tiledb-0.31.1/tiledb/man/tiledb_query.Rd | 8 tiledb-0.31.1/tiledb/man/tiledb_stats_dump.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_stats_raw_dump.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_version.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_vfs.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_vfs_close.Rd | 3 tiledb-0.31.1/tiledb/man/tiledb_vfs_copy_dir.Rd |only tiledb-0.31.1/tiledb/man/tiledb_vfs_copy_file.Rd | 2 tiledb-0.31.1/tiledb/man/tiledb_vfs_is_bucket.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_vfs_is_empty_bucket.Rd | 4 tiledb-0.31.1/tiledb/man/tiledb_vfs_read.Rd | 16 tiledb-0.31.1/tiledb/man/tiledb_vfs_sync.Rd | 3 tiledb-0.31.1/tiledb/man/tiledb_vfs_write.Rd | 11 tiledb-0.31.1/tiledb/src/Makevars.win | 9 tiledb-0.31.1/tiledb/src/RcppExports.cpp | 14 tiledb-0.31.1/tiledb/src/libtiledb.cpp | 8 tiledb-0.31.1/tiledb/src/nanoarrow.hpp | 2 tiledb-0.31.1/tiledb/src/shmem.cpp | 10 tiledb-0.31.1/tiledb/tests/pkgconfig-test.R |only tiledb-0.31.1/tiledb/tests/tinytest.R | 8 tiledb-0.31.1/tiledb/tools/buildTileDB.sh | 2 tiledb-0.31.1/tiledb/tools/ci/valgrind/buildTileDB.sh | 2 tiledb-0.31.1/tiledb/tools/fetchTileDBSrc.R | 4 tiledb-0.31.1/tiledb/tools/tiledbVersion.txt | 4 tiledb-0.31.1/tiledb/tools/winlibs.R | 24 tiledb-0.31.1/tiledb/vignettes/introduction.md | 4 228 files changed, 6571 insertions(+), 4709 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics
Description: A collection of functions to create spatial weights matrix
objects from polygon 'contiguities', from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial 'autocorrelation',
including global 'Morans I' and 'Gearys C' proposed by 'Cliff' and 'Ord'
(1973, ISBN: 0850860369) and (1981, ISBN: 0850860814), 'Hubert/Mantel'
general cross product statistic, Empirical Bayes estimates and
'Assunção/Reis' (1999) <doi:10.1002/(SICI)1097-0258(19990830)18:16%3C2147::AID-SIM179%3E3.0.CO;2-I> Index, 'Getis/Ord' G ('Getis' and 'Ord' 1992)
<doi:10.1111/j.1538-4632.1992.tb00261.x> and multicoloured
join count statistics, 'APLE' ('Li 'et al.' )
<doi:10.1111/j.1538-4632.2007.00708.x>, local 'Moran's I', 'Gearys C'
('Anselin' 1995) <doi:10.1111/j.1538-4632.1995.tb00338.x> and
'Getis/Ord' G ('Ord' and 'Getis' 1995)
< [...truncated...]
Author: Roger Bivand [cre, aut] ,
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assuncao [ctb],
Anil Bera [ctb],
Olaf Berke [ctb],
F. Guillaume Blanchet [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Steph [...truncated...]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spdep versions 1.3-10 dated 2025-01-20 and 1.3-11 dated 2025-04-24
spdep-1.3-10/spdep/inst/etc/misc/contiguity-myid.swm |only spdep-1.3-10/spdep/inst/etc/misc/contiguity-unique-id-islands.swm |only spdep-1.3-10/spdep/inst/etc/misc/contiguity-unique-id.swm |only spdep-1.3-10/spdep/inst/etc/misc/nc-contiguity-unique-id-island.swm |only spdep-1.3-10/spdep/inst/etc/misc/nc-contiguity-unique-id.swm |only spdep-1.3-11/spdep/DESCRIPTION | 8 - spdep-1.3-11/spdep/MD5 | 53 ++++------ spdep-1.3-11/spdep/NAMESPACE | 7 - spdep-1.3-11/spdep/NEWS.md | 12 +- spdep-1.3-11/spdep/R/SD.RStests.R | 21 ++- spdep-1.3-11/spdep/R/cat_durbin.R |only spdep-1.3-11/spdep/build/partial.rdb |binary spdep-1.3-11/spdep/build/vignette.rds |binary spdep-1.3-11/spdep/inst/doc/CO69.html | 6 - spdep-1.3-11/spdep/inst/doc/nb_sf.Rmd | 2 spdep-1.3-11/spdep/inst/doc/nb_sf.html | 33 +++--- spdep-1.3-11/spdep/inst/doc/sids.html | 16 +-- spdep-1.3-11/spdep/inst/doc/subgraphs.R | 13 +- spdep-1.3-11/spdep/inst/doc/subgraphs.Rmd | 13 +- spdep-1.3-11/spdep/inst/doc/subgraphs.html | 28 ++--- spdep-1.3-11/spdep/inst/tinytest/test_Durbin_factor.R |only spdep-1.3-11/spdep/man/SD.RStests.Rd | 15 ++ spdep-1.3-11/spdep/man/bhicv.Rd | 3 spdep-1.3-11/spdep/man/joincount.multi.Rd | 3 spdep-1.3-11/spdep/man/licd_multi.Rd | 3 spdep-1.3-11/spdep/man/localC.Rd | 2 spdep-1.3-11/spdep/man/mstree.Rd | 3 spdep-1.3-11/spdep/man/read.gwt2nb.Rd | 3 spdep-1.3-11/spdep/man/skater.Rd | 3 spdep-1.3-11/spdep/vignettes/nb_sf.Rmd | 2 spdep-1.3-11/spdep/vignettes/subgraphs.Rmd | 13 +- 31 files changed, 148 insertions(+), 114 deletions(-)
Title: Communicate with 'Ollama' to Run Large Language Models Locally
Description: Wraps the 'Ollama' <https://ollama.com> API, which can be used to
communicate with generative large language models locally.
Author: Johannes B. Gruber [aut, cre] ,
Maximilian Weber [aut, ctb]
Maintainer: Johannes B. Gruber <JohannesB.Gruber@gmail.com>
Diff between rollama versions 0.2.0 dated 2024-12-06 and 0.2.1 dated 2025-04-24
rollama-0.2.0/rollama/tests/testthat/_snaps |only rollama-0.2.1/rollama/DESCRIPTION | 6 rollama-0.2.1/rollama/MD5 | 47 +- rollama-0.2.1/rollama/NEWS.md | 7 rollama-0.2.1/rollama/R/chat.r | 37 +- rollama-0.2.1/rollama/R/embedding.r | 3 rollama-0.2.1/rollama/R/lib.R | 128 ++++--- rollama-0.2.1/rollama/R/models.r | 8 rollama-0.2.1/rollama/R/rollama-package.R | 7 rollama-0.2.1/rollama/R/utils.r | 19 - rollama-0.2.1/rollama/README.md | 309 +++++++------------ rollama-0.2.1/rollama/build/vignette.rds |binary rollama-0.2.1/rollama/inst/WORDLIST | 1 rollama-0.2.1/rollama/inst/doc/annotation.html | 5 rollama-0.2.1/rollama/inst/doc/hf-gguf.html | 5 rollama-0.2.1/rollama/inst/doc/image-annotation.html | 5 rollama-0.2.1/rollama/inst/doc/text-embedding.html | 5 rollama-0.2.1/rollama/man/ping_ollama.Rd | 4 rollama-0.2.1/rollama/man/pull_model.Rd | 7 rollama-0.2.1/rollama/man/query.Rd | 23 + rollama-0.2.1/rollama/man/rollama-options.Rd | 7 rollama-0.2.1/rollama/man/rollama-package.Rd | 2 rollama-0.2.1/rollama/tests/testthat.R | 1 rollama-0.2.1/rollama/tests/testthat/test-chat.R | 17 + rollama-0.2.1/rollama/tests/testthat/test-models.R | 6 25 files changed, 362 insertions(+), 297 deletions(-)
Title: Copula-Based Mixed Regression Models
Description: Estimation of 2-level factor copula-based regression models for clustered data where the response variable can be either discrete or continuous.
Author: Pavel Krupskii [aut, ctb, cph],
Bouchra R. Nasri [aut, ctb, cph],
Bruno N Remillard [aut, cre, cph]
Maintainer: Bruno N Remillard <bruno.remillard@hec.ca>
Diff between CopulaGAMM versions 0.4.1 dated 2023-11-30 and 0.6.5 dated 2025-04-24
DESCRIPTION | 8 - MD5 | 48 +++++----- NAMESPACE | 2 R/EstContinuous.R | 210 ++++++++++++++++++++++++++++++++++++----------- R/EstCopulaGAMM.R |only R/EstDiscrete.R | 71 +++++++++------ R/MAP.continuous.R | 16 +-- R/MAP.discrete.R | 7 + R/SimGenCluster.R | 16 +-- R/SimMultinomial.R | 9 +- R/coplik.R | 31 ++++-- R/dcop.R | 17 ++- R/invfunc.R | 4 R/margins.R | 25 +++-- R/predictContinuous.R | 6 - R/predictCopulaGAMM.R |only R/predictDiscrete.R | 3 data/normal.rda |binary data/out.normal.rda |binary man/EstContinuous.Rd | 20 ++-- man/EstCopulaGAMM.Rd |only man/EstDiscrete.Rd | 4 man/SimGenCluster.Rd | 4 man/SimMultinomial.Rd | 6 - man/dcop.Rd | 2 man/normal.Rd | 2 man/predictCopulaGAMM.Rd |only 27 files changed, 334 insertions(+), 177 deletions(-)
Title: Marker-Based Cell Type Purification for Single-Cell Sequencing
Data
Description: A common bioinformatics task in single-cell data analysis is to purify a cell type or cell population of interest from heterogeneous datasets. 'scGate' automatizes marker-based purification of specific cell populations, without requiring training data or reference gene expression profiles. Briefly, 'scGate' takes as input: i) a gene expression matrix stored in a 'Seurat' object and ii) a “gating model” (GM), consisting of a set of marker genes that define the cell population of interest. The GM can be as simple as a single marker gene, or a combination of positive and negative markers. More complex GMs can be constructed in a hierarchical fashion, akin to gating strategies employed in flow cytometry. 'scGate' evaluates the strength of signature marker expression in each cell using the rank-based method 'UCell', and then performs k-nearest neighbor (kNN) smoothing by calculating the mean 'UCell' score across neighboring cells. kNN-smoothing aims at compensating for the large degree of s [...truncated...]
Author: Massimo Andreatta [aut, cre] ,
Ariel Berenstein [aut] ,
Josep Garnica [aut],
Santiago Carmona [aut]
Maintainer: Massimo Andreatta <massimo.andreatta@unige.ch>
Diff between scGate versions 1.6.2 dated 2024-04-23 and 1.7.0 dated 2025-04-24
DESCRIPTION | 16 ++++++++-------- MD5 | 14 +++++++------- R/utils.R | 11 ++++++++++- build/vignette.rds |binary inst/NEWS.Rd | 6 ++++++ inst/doc/make.index.Rmd | 2 +- inst/doc/make.index.html | 2 +- vignettes/make.index.Rmd | 2 +- 8 files changed, 34 insertions(+), 19 deletions(-)
Title: Mating Environmental Designs
Description: In breeding experiments, mating environmental (ME) designs are very popular as mating designs are directly implemented in the field environment using block or row-column designs. Here, three functions are given related to three new methods which will generate mating diallel cross designs (Hinkelmann and Kempthorne, 1963<doi:10.2307/2333899>) or mating environmental (ME) designs along with design parameters, C matrix, eigenvalues (EVs), degree of fractionations (DF) and canonical efficiency factor (CEF). Another one function is added to check the properties of a given ME diallel cross design.
Author: Ashutosh Dalal [aut, cre],
Cini Varghese [aut, ctb],
Rajender Parsad [aut, ctb],
Mohd Harun [aut, ctb]
Maintainer: Ashutosh Dalal <ashutosh.dalal97@gmail.com>
Diff between MEDesigns versions 1.0.0 dated 2024-12-02 and 1.0.1 dated 2025-04-24
DESCRIPTION | 9 ++- MD5 | 13 +++- NAMESPACE | 3 + R/CheckME_Diallel.R | 2 R/MEBanalysis.R |only R/ME_CDC.R | 154 +++++++++++++++++----------------------------------- R/sysdata.rda |only data |only man/MEBanalysis.Rd |only man/MEdata.Rd |only 10 files changed, 70 insertions(+), 111 deletions(-)
Title: Unified Framework for Numerical Optimizers
Description: Provides a unified object-oriented framework for numerical
optimizers in R. Allows for both minimization and maximization with any
optimizer, optimization over more than one function argument, measuring of
computation time, setting a time limit for long optimization tasks.
Author: Lennart Oelschlaeger [aut, cre]
,
Marius Oetting [ctb]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between optimizeR versions 1.1.3 dated 2025-03-27 and 1.2.0 dated 2025-04-24
optimizeR-1.1.3/optimizeR/R/debug.R |only optimizeR-1.1.3/optimizeR/R/legacy.R |only optimizeR-1.1.3/optimizeR/man/apply_optimizer.Rd |only optimizeR-1.1.3/optimizeR/man/define_optimizer.Rd |only optimizeR-1.1.3/optimizeR/man/new_optimizer.Rd |only optimizeR-1.1.3/optimizeR/man/test_objective.Rd |only optimizeR-1.1.3/optimizeR/man/test_optimizer.Rd |only optimizeR-1.1.3/optimizeR/man/validate_optimizer.Rd |only optimizeR-1.1.3/optimizeR/tests/testthat/_snaps/legacy.md |only optimizeR-1.1.3/optimizeR/tests/testthat/test-debug.R |only optimizeR-1.1.3/optimizeR/tests/testthat/test-legacy.R |only optimizeR-1.2.0/optimizeR/DESCRIPTION | 14 optimizeR-1.2.0/optimizeR/MD5 | 48 optimizeR-1.2.0/optimizeR/NAMESPACE | 51 optimizeR-1.2.0/optimizeR/NEWS.md | 6 optimizeR-1.2.0/optimizeR/R/objective.R | 603 ++++- optimizeR-1.2.0/optimizeR/R/optimizeR-package.R | 59 optimizeR-1.2.0/optimizeR/R/optimizer.R | 1061 ++++++---- optimizeR-1.2.0/optimizeR/R/optimizer_dictionary.R | 202 + optimizeR-1.2.0/optimizeR/R/parameter_spaces.R | 30 optimizeR-1.2.0/optimizeR/README.md | 107 - optimizeR-1.2.0/optimizeR/man/Objective.Rd | 303 ++ optimizeR-1.2.0/optimizeR/man/Optimizer.Rd | 342 ++- optimizeR-1.2.0/optimizeR/man/ParameterSpaces.Rd | 18 optimizeR-1.2.0/optimizeR/man/figures/README-plot-ackley-1.png |binary optimizeR-1.2.0/optimizeR/man/optimizer_dictionary.Rd | 7 optimizeR-1.2.0/optimizeR/tests/testthat/_snaps/objective.md | 263 ++ optimizeR-1.2.0/optimizeR/tests/testthat/_snaps/optimizer.md |only optimizeR-1.2.0/optimizeR/tests/testthat/test-objective.R | 223 ++ optimizeR-1.2.0/optimizeR/tests/testthat/test-optimizer.R | 206 + optimizeR-1.2.0/optimizeR/tests/testthat/test-parameter_spaces.R | 8 31 files changed, 2605 insertions(+), 946 deletions(-)
Title: 'DT' Extension for CRUD (Create, Read, Update, Delete)
Applications in 'shiny'
Description: The core of this package is a function eDT() which enhances DT::datatable() such that it can be used to interactively modify data in 'shiny'. By the use of generic 'dplyr' methods it supports many types of data storage, with relational databases ('dbplyr') being the main use case.
Author: Jasper Schelfhout [aut, cre],
Maxim Nazarov [rev],
Daan Seynaeve [rev],
Lennart Tuijnder [rev],
Saar Junius [aut]
Maintainer: Jasper Schelfhout <jasper.schelfhout@openanalytics.eu>
Diff between editbl versions 1.2.0 dated 2025-03-31 and 1.3.0 dated 2025-04-24
DESCRIPTION | 12 - MD5 | 59 +++--- R/eDT.R | 195 +++++++++++++++++++-- R/utils.R | 11 - README.md | 18 + inst/NEWS | 19 +- inst/doc/howto_relational_db.R | 2 inst/doc/howto_relational_db.html | 6 inst/doc/howto_relational_db.rmd | 2 inst/doc/howto_relational_db_dm.html | 6 inst/doc/howto_row_level_access.html | 4 inst/doc/howto_switch_from_DT.html | 4 man/addButtons.Rd | 9 man/canXXXRowTemplate.Rd | 8 man/createButtons.Rd | 9 man/createCloneButtonHTML.Rd |only man/createCloneButtonHTML_shiny.Rd |only man/eDT.Rd | 11 + man/evalCanCloneRow.Rd |only man/evalCanDeleteRow.Rd | 2 man/evalCanEditRow.Rd | 2 man/initData.Rd | 13 + tests/testthat/test-utils.R | 30 +++ vignettes/howto_relational_db.rmd | 2 vignettes/screenshots/howto_relational_db_1.png |binary vignettes/screenshots/howto_relational_db_2.png |binary vignettes/screenshots/howto_relational_db_3.png |binary vignettes/screenshots/howto_relational_db_dm_1.png |binary vignettes/screenshots/howto_row_level_access_1.png |binary vignettes/screenshots/howto_row_level_access_2.png |binary vignettes/screenshots/howto_switch_from_DT_1.png |binary vignettes/screenshots/howto_switch_from_DT_2.png |binary 32 files changed, 336 insertions(+), 88 deletions(-)
Title: Generalized Propensity Score Estimation and Matching for
Multiple Groups
Description: Implements the Vector Matching algorithm to match multiple
treatment groups based on previously estimated generalized propensity
scores. The package includes tools for visualizing initial confounder
imbalances, estimating treatment assignment probabilities using various
methods, defining the common support region, performing matching across
multiple groups, and evaluating matching quality. For more details, see
Lopez and Gutman (2017) <doi:10.1214/17-STS612>.
Author: Mateusz Kolek [aut, cre, cph]
Maintainer: Mateusz Kolek <mati.kolek13@gmail.com>
Diff between vecmatch versions 1.0.3 dated 2025-03-28 and 1.1.0 dated 2025-04-24
DESCRIPTION | 9 +-- MD5 | 27 ++++++--- NEWS.md |only R/csregion.R | 30 ++++++++++ R/match_gps.R | 106 ++++++++++++++++++++++++-------------- R/methods.R | 15 +++++ README.md | 42 +++++++-------- build/vignette.rds |only inst/WORDLIST | 1 inst/doc |only man/csregion.Rd | 14 ++++- man/figures/unnamed-chunk-2-1.png |binary tests/testthat/test-csregion.R | 12 +++- tests/testthat/test-match_gps.R | 38 +++---------- vignettes |only 15 files changed, 190 insertions(+), 104 deletions(-)
Title: R Interface to the 'QuantLib' Library
Description: The 'RQuantLib' package makes parts of 'QuantLib' accessible from R
The 'QuantLib' project aims to provide a comprehensive software framework
for quantitative finance. The goal is to provide a standard open source library
for quantitative analysis, modeling, trading, and risk management of financial
assets.
Author: Dirk Eddelbuettel [aut, cre] ,
Khanh Nguyen [aut] ,
Terry Leitch [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RQuantLib versions 0.4.25 dated 2025-03-25 and 0.4.26 dated 2025-04-24
ChangeLog | 23 +++++++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- configure | 18 +++++++++--------- configure.ac | 2 +- data/tsQuotes.RData |binary data/vcube.RData |binary inst/NEWS.Rd | 8 ++++++++ inst/tinytest/test_schedule.R | 12 +++++++++--- src/Makevars.win | 18 ++++++++++++++---- 10 files changed, 77 insertions(+), 30 deletions(-)
Title: Search and Get Data from the I14Y Interoperability Platform of
Switzerland
Description: Search and download Swiss data and metadata from the I14Y
interoperability platform of Switzerland using its public APIs
<https://www.i14y.admin.ch/api/index.html>.
Author: Felix Luginbuhl [aut, cre, cph]
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>
Diff between I14Y versions 0.1.2 dated 2025-04-16 and 0.1.3 dated 2025-04-24
DESCRIPTION | 7 ++++--- MD5 | 4 ++-- NEWS.md | 4 ++++ 3 files changed, 10 insertions(+), 5 deletions(-)
Title: 'HiGHS' Optimization Solver
Description: R interface to 'HiGHS', an optimization solver for solving mixed integer
optimization problems with quadratic or linear objective and linear constraints.
Author: Florian Schwendinger [aut, cre],
Dirk Schumacher [aut],
Julian Hall [cph],
Ivet Galabova [cph],
Leona Gottwald [cph],
Michael Feldmeier [cph]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between highs versions 1.9.0-1 dated 2025-01-08 and 1.10.0-1 dated 2025-04-24
highs-1.10.0-1/highs/DESCRIPTION | 7 highs-1.10.0-1/highs/MD5 | 1038 +++++----- highs-1.10.0-1/highs/NAMESPACE | 60 highs-1.10.0-1/highs/NEWS.md | 5 highs-1.10.0-1/highs/R/RcppExports.R | 92 highs-1.10.0-1/highs/R/constants.R |only highs-1.10.0-1/highs/R/examples.R |only highs-1.10.0-1/highs/R/highs.R | 62 highs-1.10.0-1/highs/R/model-api.R |only highs-1.10.0-1/highs/R/options.R | 345 +-- highs-1.10.0-1/highs/R/smat.R | 9 highs-1.10.0-1/highs/R/solver-api.R |only highs-1.10.0-1/highs/README.md | 425 ++-- highs-1.10.0-1/highs/configure | 7 highs-1.10.0-1/highs/inst/HiGHS/CMakeLists.txt | 236 +- highs-1.10.0-1/highs/inst/HiGHS/FEATURES.md | 14 highs-1.10.0-1/highs/inst/HiGHS/MODULE.bazel | 2 highs-1.10.0-1/highs/inst/HiGHS/README.md | 70 highs-1.10.0-1/highs/inst/HiGHS/Version.txt | 2 highs-1.10.0-1/highs/inst/HiGHS/cmake/FindCUDAConf.cmake |only highs-1.10.0-1/highs/inst/HiGHS/cmake/cpp-highs.cmake | 145 + highs-1.10.0-1/highs/inst/HiGHS/cmake/dotnet.cmake | 2 highs-1.10.0-1/highs/inst/HiGHS/cmake/highs-config.cmake.in |only highs-1.10.0-1/highs/inst/HiGHS/cmake/python-highs.cmake | 2 highs-1.10.0-1/highs/inst/HiGHS/cmake/sources-python.cmake | 834 ++++---- highs-1.10.0-1/highs/inst/HiGHS/cmake/sources.cmake | 61 highs-1.10.0-1/highs/inst/HiGHS/extern/filereaderlp/reader.cpp | 11 highs-1.10.0-1/highs/inst/HiGHS/highs |only highs-1.10.0-1/highs/inst/HiGHS/meson.build | 7 highs-1.10.0-1/highs/inst/HiGHS/nuget/Highs.csproj | 2 highs-1.10.0-1/highs/inst/HiGHS/nuget/README.md | 2 highs-1.10.0-1/highs/inst/HiGHS/pyproject.toml | 20 highs-1.10.0-1/highs/inst/HiGHS/tests/test_highspy.py | 32 highs-1.10.0-1/highs/inst/build_highs.sh | 108 - highs-1.10.0-1/highs/inst/tinytest/test_model-api.R |only highs-1.10.0-1/highs/inst/tinytest/test_solver-api.R |only highs-1.10.0-1/highs/man/example_model.Rd |only highs-1.10.0-1/highs/man/example_solver.Rd |only highs-1.10.0-1/highs/man/hi_model_get_ncons.Rd |only highs-1.10.0-1/highs/man/hi_model_get_nvars.Rd |only highs-1.10.0-1/highs/man/hi_model_set_constraint_matrix.Rd |only highs-1.10.0-1/highs/man/hi_model_set_hessian.Rd |only highs-1.10.0-1/highs/man/hi_model_set_lhs.Rd |only highs-1.10.0-1/highs/man/hi_model_set_lower.Rd |only highs-1.10.0-1/highs/man/hi_model_set_ncol.Rd |only highs-1.10.0-1/highs/man/hi_model_set_nrow.Rd |only highs-1.10.0-1/highs/man/hi_model_set_objective.Rd |only highs-1.10.0-1/highs/man/hi_model_set_offset.Rd |only highs-1.10.0-1/highs/man/hi_model_set_rhs.Rd |only highs-1.10.0-1/highs/man/hi_model_set_sense.Rd |only highs-1.10.0-1/highs/man/hi_model_set_upper.Rd |only highs-1.10.0-1/highs/man/hi_model_set_vartype.Rd |only highs-1.10.0-1/highs/man/hi_new_model.Rd |only highs-1.10.0-1/highs/man/hi_new_solver.Rd |only highs-1.10.0-1/highs/man/hi_reset_global_scheduler.Rd |only highs-1.10.0-1/highs/man/hi_solver_add_cols.Rd |only highs-1.10.0-1/highs/man/hi_solver_add_rows.Rd |only highs-1.10.0-1/highs/man/hi_solver_add_vars.Rd |only highs-1.10.0-1/highs/man/hi_solver_change_constraint_bounds.Rd |only highs-1.10.0-1/highs/man/hi_solver_change_variable_bounds.Rd |only highs-1.10.0-1/highs/man/hi_solver_clear.Rd |only highs-1.10.0-1/highs/man/hi_solver_clear_model.Rd |only highs-1.10.0-1/highs/man/hi_solver_clear_solver.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_bool_option.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_constraint_bounds.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_constraint_matrix.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_dbl_option.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_int_option.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_lp_costs.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_num_col.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_num_row.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_option.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_options.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_sense.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_solution.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_str_option.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_variable_bounds.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_vartype.Rd |only highs-1.10.0-1/highs/man/hi_solver_infinity.Rd |only highs-1.10.0-1/highs/man/hi_solver_info.Rd |only highs-1.10.0-1/highs/man/hi_solver_run.Rd |only highs-1.10.0-1/highs/man/hi_solver_set_coeff.Rd |only highs-1.10.0-1/highs/man/hi_solver_set_constraint_bounds.Rd |only highs-1.10.0-1/highs/man/hi_solver_set_integrality.Rd |only highs-1.10.0-1/highs/man/hi_solver_set_objective.Rd |only highs-1.10.0-1/highs/man/hi_solver_set_offset.Rd |only highs-1.10.0-1/highs/man/hi_solver_set_option.Rd |only highs-1.10.0-1/highs/man/hi_solver_set_options.Rd |only highs-1.10.0-1/highs/man/hi_solver_set_sense.Rd |only highs-1.10.0-1/highs/man/hi_solver_set_variable_bounds.Rd |only highs-1.10.0-1/highs/man/hi_solver_status.Rd |only highs-1.10.0-1/highs/man/hi_solver_status_message.Rd |only highs-1.10.0-1/highs/man/hi_solver_write_basis.Rd |only highs-1.10.0-1/highs/man/hi_solver_write_model.Rd |only highs-1.10.0-1/highs/man/highs_write_model.Rd |only highs-1.10.0-1/highs/src/Makevars.in | 1 highs-1.10.0-1/highs/src/RcppExports.cpp | 300 ++ highs-1.10.0-1/highs/src/highs_interface.cpp | 319 ++- highs-1.9.0-1/highs/R/api.R |only highs-1.9.0-1/highs/R/model.R |only highs-1.9.0-1/highs/inst/HiGHS/app |only highs-1.9.0-1/highs/inst/HiGHS/docs |only highs-1.9.0-1/highs/inst/HiGHS/examples |only highs-1.9.0-1/highs/inst/HiGHS/extern/catch.hpp |only highs-1.9.0-1/highs/inst/HiGHS/highs-config.cmake.in |only highs-1.9.0-1/highs/inst/HiGHS/src |only highs-1.9.0-1/highs/man/hapi_new_model.Rd |only 107 files changed, 2730 insertions(+), 1490 deletions(-)
Title: Non-Negative Matrix Factorization for Single-Cell Omics
Description: A collection of methods to extract gene programs from single-cell gene expression data using non-negative matrix factorization (NMF). 'GeneNMF' contains functions to directly interact with the 'Seurat' toolkit and derive interpretable gene program signatures.
Author: Massimo Andreatta [aut, cre] ,
Santiago Carmona [aut]
Maintainer: Massimo Andreatta <massimo.andreatta@unige.ch>
Diff between GeneNMF versions 0.6.2 dated 2024-11-12 and 0.8.0 dated 2025-04-24
DESCRIPTION | 12 ++++---- MD5 | 16 +++++------ NAMESPACE | 1 R/main.R | 69 ++++++++++++++++++++++++++++++++++++++++--------- R/utils.R | 40 ++++++++++++++++++++++++++-- README.md | 2 - inst/NEWS.Rd | 16 +++++++++++ man/getMetaPrograms.Rd | 10 ++++--- man/runGSEA.Rd | 5 +++ 9 files changed, 137 insertions(+), 34 deletions(-)
Title: Functions for Calculating Fit-Robustness of CNA-Solutions
Description: Functions for automatically performing
a reanalysis series
on a data set using CNA, and for calculating the fit-robustness
of the resulting models, as described in
Parkkinen and Baumgartner (2021) <doi:10.1177/0049124120986200>.
Author: Veli-Pekka Parkkinen [aut, cre, cph],
Michael Baumgartner [aut, cph],
Mathias Ambuehl [aut, cph]
Maintainer: Veli-Pekka Parkkinen <parkkinenv@gmail.com>
Diff between frscore versions 0.4.1 dated 2024-06-11 and 0.5.0 dated 2025-04-24
DESCRIPTION | 8 MD5 | 29 - NAMESPACE | 2 NEWS.md | 11 R/causal_submodel.R | 2 R/frscore.R | 162 ++------- R/frscored_cna.R | 41 +- R/plot_submodel_network.R |only man/causal_submodel.Rd | 6 man/frscore.Rd | 25 - man/frscored_cna.Rd | 35 -- man/plot_submodel_network.Rd |only man/rean_cna.Rd | 21 + man/submodel_adjacencies_to_igraph.Rd |only tests/testthat/_snaps/frscore.md | 12 tests/testthat/_snaps/frscored_cna.md | 576 +++++++++++++++------------------- tests/testthat/test_frscored_cna.R | 47 ++ 17 files changed, 423 insertions(+), 554 deletions(-)
Title: Flexible, Extensible, & Reproducible Processing of Pupil Data
Description: Pupillometry offers a non-invasive window into the mind and has been used extensively as a psychophysiological readout of arousal signals linked with cognitive processes like attention, stress, and emotional states [Clewett et al. (2020) <doi:10.1038/s41467-020-17851-9>; Kret & Sjak-Shie (2018) <doi:10.3758/s13428-018-1075-y>; Strauch (2024) <doi:10.1016/j.tins.2024.06.002>]. Yet, despite decades of pupillometry research, many established packages and workflows to date unfortunately lack design patterns based on Findability, Accessibility, Interoperability, and Reusability (FAIR) principles [see Wilkinson et al. (2016) <doi:10.1038/sdata.2016.18>]. 'eyeris', on the other hand, follows a design philosophy that provides users with an intuitive, modular, performant, and extensible pupillometry data preprocessing framework out-of-the-box. 'eyeris' introduces a Brain Imaging Data Structure (BIDS)-like organization for derivative (i.e., preprocessed) pupillometry [...truncated...]
Author: Shawn Schwartz [aut, cre, cph]
,
Stanford Wu Tsai Human Performance Alliance [fnd],
Stanford Ric Weiland Graduate Fellowship [fnd],
Stanford Center for Mind, Brain, Computation and Technology [fnd],
NIH National Institute on Aging R01 AG065255 [fnd], [...truncated...]
Maintainer: Shawn Schwartz <stschwartz@stanford.edu>
Diff between eyeris versions 1.0.0 dated 2025-03-31 and 1.1.0 dated 2025-04-24
eyeris-1.0.0/eyeris/man/figures/interactive-reports-demo.gif |only eyeris-1.0.0/eyeris/man/figures/report_example_annotated-1.png |only eyeris-1.1.0/eyeris/DESCRIPTION | 55 +- eyeris-1.1.0/eyeris/LICENSE | 2 eyeris-1.1.0/eyeris/MD5 | 109 ++-- eyeris-1.1.0/eyeris/NAMESPACE | 4 eyeris-1.1.0/eyeris/NEWS.md | 49 + eyeris-1.1.0/eyeris/R/constants.R |only eyeris-1.1.0/eyeris/R/eyeris-package.R | 3 eyeris-1.1.0/eyeris/R/pipeline-bidsify.R | 11 eyeris-1.1.0/eyeris/R/pipeline-deblink.R | 35 + eyeris-1.1.0/eyeris/R/pipeline-detransient.R | 28 - eyeris-1.1.0/eyeris/R/pipeline-detrend.R | 27 - eyeris-1.1.0/eyeris/R/pipeline-epoch.R | 9 eyeris-1.1.0/eyeris/R/pipeline-glassbox.R | 268 +++++++--- eyeris-1.1.0/eyeris/R/pipeline-interpolate.R | 29 - eyeris-1.1.0/eyeris/R/pipeline-loadasc.R | 36 + eyeris-1.1.0/eyeris/R/pipeline-lpfilt.R | 30 - eyeris-1.1.0/eyeris/R/pipeline-zscore.R | 27 - eyeris-1.1.0/eyeris/R/plot.eyeris.R | 4 eyeris-1.1.0/eyeris/README.md | 76 +- eyeris-1.1.0/eyeris/build/partial.rdb |binary eyeris-1.1.0/eyeris/build/vignette.rds |binary eyeris-1.1.0/eyeris/inst/doc/anatomy.R | 1 eyeris-1.1.0/eyeris/inst/doc/anatomy.Rmd | 5 eyeris-1.1.0/eyeris/inst/doc/anatomy.html | 32 - eyeris-1.1.0/eyeris/inst/doc/complete-pipeline.R | 8 eyeris-1.1.0/eyeris/inst/doc/complete-pipeline.Rmd | 77 +- eyeris-1.1.0/eyeris/inst/doc/complete-pipeline.html | 131 +++- eyeris-1.1.0/eyeris/inst/doc/custom-extensions.Rmd | 2 eyeris-1.1.0/eyeris/inst/doc/custom-extensions.html | 27 - eyeris-1.1.0/eyeris/inst/doc/epoching-bids-reports.R | 4 eyeris-1.1.0/eyeris/inst/doc/epoching-bids-reports.Rmd | 8 eyeris-1.1.0/eyeris/inst/doc/epoching-bids-reports.html | 37 - eyeris-1.1.0/eyeris/inst/doc/reports.R | 8 eyeris-1.1.0/eyeris/inst/doc/reports.Rmd | 10 eyeris-1.1.0/eyeris/inst/doc/reports.html | 27 - eyeris-1.1.0/eyeris/man/bidsify.Rd | 11 eyeris-1.1.0/eyeris/man/deblink.Rd | 36 + eyeris-1.1.0/eyeris/man/detransient.Rd | 29 - eyeris-1.1.0/eyeris/man/detrend.Rd | 28 - eyeris-1.1.0/eyeris/man/epoch.Rd | 9 eyeris-1.1.0/eyeris/man/eyelink_asc_demo_dataset.Rd |only eyeris-1.1.0/eyeris/man/eyeris-package.Rd | 13 eyeris-1.1.0/eyeris/man/figures/README-timeseries-plot-1.png |only eyeris-1.1.0/eyeris/man/figures/README-timeseries-plot-2.png |only eyeris-1.1.0/eyeris/man/figures/README-unnamed-chunk-3-1.png |only eyeris-1.1.0/eyeris/man/figures/logo.png |binary eyeris-1.1.0/eyeris/man/glassbox.Rd | 77 +- eyeris-1.1.0/eyeris/man/interpolate.Rd | 30 - eyeris-1.1.0/eyeris/man/load_asc.Rd | 36 + eyeris-1.1.0/eyeris/man/lpfilt.Rd | 31 - eyeris-1.1.0/eyeris/man/plot.eyeris.Rd | 4 eyeris-1.1.0/eyeris/man/zscore.Rd | 28 - eyeris-1.1.0/eyeris/vignettes/anatomy.Rmd | 5 eyeris-1.1.0/eyeris/vignettes/complete-pipeline.Rmd | 77 +- eyeris-1.1.0/eyeris/vignettes/custom-extensions.Rmd | 2 eyeris-1.1.0/eyeris/vignettes/epoching-bids-reports.Rmd | 8 eyeris-1.1.0/eyeris/vignettes/reports.Rmd | 10 59 files changed, 1108 insertions(+), 505 deletions(-)
Title: Bayesian Inference for Neyman-Scott Point Processes
Description: The Bayesian MCMC estimation of parameters for Thomas-type cluster
point process with various inhomogeneities. It allows for inhomogeneity in
(i) distribution of parent points, (ii) mean number of points in a cluster,
(iii) cluster spread. The package also allows for the Bayesian MCMC
algorithm for the homogeneous generalized Thomas process. The cluster size
is allowed to have a variance that is greater or less than the expected
value (cluster sizes are over or under dispersed). Details are described in
Dvořák, Remeš, Beránek & Mrkvička (2022) <arXiv: 10.48550/arXiv.2205.07946>.
Author: Mrkvicka Tomas [aut],
Dvorak Jiri [aut],
Beranek Ladislav [aut],
Remes Radim [aut, cre],
Park Jaewoo [ctb],
Lee Sujeong [ctb]
Maintainer: Remes Radim <inrem@jcu.cz>
Diff between binspp versions 0.1.26 dated 2022-12-08 and 0.2.0 dated 2025-04-24
DESCRIPTION | 18 - MD5 | 32 +- NAMESPACE | 11 R/RcppExports.R | 39 ++ R/binspp-package.R | 114 ++++--- R/estgtp.R | 606 +++++++++++++++++++++--------------------- R/estinternsp.R |only build/partial.rdb |binary man/AuxVarGen.Rd |only man/binspp-package.Rd |only man/binspp.Rd | 7 man/coeff.Rd |only man/estinternsp.Rd |only man/pCClik2.Rd |only man/plot_conn.Rd |only man/print_outputs_internsp.Rd |only src/Makevars | 22 + src/Makevars.win |only src/RcppExports.cpp | 106 +++++++ src/STThomas.cpp |only src/header.h | 1 src/poit_updates.cpp | 3 22 files changed, 589 insertions(+), 370 deletions(-)
Title: Time Series Prediction with Integrated Tuning
Description: Time series prediction is a critical task in data analysis, requiring not only the selection of appropriate models, but also suitable data preprocessing and tuning strategies.
TSPredIT (Time Series Prediction with Integrated Tuning) is a framework that provides a seamless integration of data preprocessing, decomposition, model training, hyperparameter optimization, and evaluation.
Unlike other frameworks, TSPredIT emphasizes the co-optimization of both preprocessing and modeling steps, improving predictive performance.
It supports a variety of statistical and machine learning models, filtering techniques, outlier detection, data augmentation, and ensemble strategies.
More information is available in Salles et al. <doi:10.1007/978-3-662-68014-8_2>.
Author: Eduardo Ogasawara [aut, ths, cre]
,
Carla Pacheco [aut],
Cristiane Gea [aut],
Diogo Santos [aut],
Rebecca Salles [aut],
Vitoria Birindiba [aut],
Eduardo Bezerra [aut],
Esther Pacitti [aut],
Fabio Porto [aut],
CEFET/RJ [cph]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between tspredit versions 1.0.787 dated 2024-12-04 and 1.1.707 dated 2025-04-24
DESCRIPTION | 151 ++++++++++++++++++++++++------------------------- MD5 | 58 +++++++++--------- R/recursive_filter.R | 2 R/ts_aug_awareness.R | 2 R/ts_aug_awaresmooth.R | 2 R/ts_aug_flip.R | 2 R/ts_aug_jitter.R | 4 - R/ts_aug_none.R | 2 R/ts_aug_shrink.R | 2 R/ts_aug_stretch.R | 2 R/ts_aug_wormhole.R | 2 R/ts_fil_ema.R | 2 R/ts_fil_emd.R | 2 R/ts_fil_fft.R | 2 R/ts_fil_hp.R | 2 R/ts_fil_kalman.R | 2 R/ts_fil_lowess.R | 2 R/ts_fil_ma.R | 2 R/ts_fil_none.R | 2 R/ts_fil_qes.R | 2 R/ts_fil_remd.R | 2 R/ts_fil_seas_adj.R | 2 R/ts_fil_ses.R | 2 R/ts_fil_smooth.R | 2 R/ts_fil_spline.R | 2 R/ts_fil_wavelet.R | 4 - R/ts_fil_winsor.R | 2 R/ts_maintune.R | 4 - R/ts_norm_none.R | 2 README.md | 72 ++++++++++++++++------- 30 files changed, 186 insertions(+), 155 deletions(-)
Title: Semiparametric Likelihood Estimation with Errors in Variables
Description: Efficient regression analysis under general two-phase sampling, where Phase I includes error-prone data and Phase II contains validated data on a subset.
Author: Sarah Lotspeich [aut],
Ran Tao [aut, cre],
Joey Sherrill [prg],
Jiangmei Xiong [ctb]
Maintainer: Ran Tao <r.tao@vanderbilt.edu>
Diff between sleev versions 1.1.1 dated 2025-04-20 and 1.1.2 dated 2025-04-24
sleev-1.1.1/sleev/inst/doc/sleev_vignette.R |only sleev-1.1.1/sleev/inst/doc/sleev_vignette.Rmd |only sleev-1.1.1/sleev/inst/doc/sleev_vignette.pdf |only sleev-1.1.1/sleev/vignettes/sleev_vignette.Rmd |only sleev-1.1.2/sleev/DESCRIPTION | 11 ++++++----- sleev-1.1.2/sleev/MD5 | 14 +++++++------- sleev-1.1.2/sleev/build/vignette.rds |binary sleev-1.1.2/sleev/inst/article/sleev_vignette.pdf |binary sleev-1.1.2/sleev/inst/doc/sleev_vignette_file.Rnw |only sleev-1.1.2/sleev/inst/doc/sleev_vignette_file.pdf |only sleev-1.1.2/sleev/vignettes/sleev_vignette.pdf |only sleev-1.1.2/sleev/vignettes/sleev_vignette_file.Rnw |only 12 files changed, 13 insertions(+), 12 deletions(-)
Title: Reconstruction of Daily Data - Precipitation
Description: Applies quality control to daily precipitation observations;
reconstructs the original series by estimating precipitation in missing values; and
creates gridded datasets of daily precipitation.
Author: Roberto Serrano-Notivoli [aut, cre]
,
Adrian Huerta [aut] ,
Abel Centella [ctb]
Maintainer: Roberto Serrano-Notivoli <roberto.serrano@unizar.es>
Diff between reddPrec versions 2.0.4 dated 2025-03-09 and 3.0.0 dated 2025-04-24
DESCRIPTION | 35 ++++++-- MD5 | 66 ++++++++++++--- NAMESPACE | 41 +++++++++ R/eqc_Plot.R |only R/eqc_PrecisionRounding-get_dec_patterns.R |only R/eqc_PrecisionRounding-get_ndec.R |only R/eqc_PrecisionRounding.R |only R/eqc_SmallGaps-get_ngaps.R |only R/eqc_SmallGaps.R |only R/eqc_Truncation-get_lenght_borderline.R |only R/eqc_Truncation-get_ts_borderline.R |only R/eqc_Truncation.R |only R/eqc_Ts.R |only R/eqc_WeeklyCycle-get_wd_fraction.R |only R/eqc_WeeklyCycle.R |only R/fillData.R | 47 ++--------- R/gapFilling.R | 13 +-- R/gridPcp.R | 120 ++++++++++++++++++++++++----- R/hmg_Ts.R |only R/hmg_adjustment_ts.R |only R/hmg_build_ts.R |only R/hmg_cleaning_trend_ar1.R |only R/hmg_detection_ts.R |only R/hmg_indices_ts.R |only R/hmg_nearby_ts.R |only R/hmg_qc_hmg_ts.R |only R/learner_glm.R |only R/learner_nn.R |only R/learner_rf.R |only R/learner_svm.R |only R/learner_xgboost.R |only R/predday.R | 47 ++++++----- R/predpoint.R | 40 ++------- R/qcFirst.R | 41 ++------- R/qcLast.R | 47 +++-------- R/qcPrec.R | 10 +- R/stand_qq.R | 8 + inst |only man/eqc_Plot.Rd |only man/eqc_PrecisionRounding.Rd |only man/eqc_SmallGaps.Rd |only man/eqc_Truncation.Rd |only man/eqc_Ts.Rd |only man/eqc_WeeklyCycle.Rd |only man/gapFilling.Rd | 3 man/gridPcp.Rd | 54 +++++++++++-- man/hmg_Ts.Rd |only man/learner_glm.Rd |only man/learner_nn.Rd |only man/learner_rf.Rd |only man/learner_svm.Rd |only man/learner_xgboost.Rd |only man/qcPrec.Rd | 3 53 files changed, 366 insertions(+), 209 deletions(-)
Title: Fast PCA for Large Pedigrees
Description: Carry out principal component analysis (PCA) of very large pedigrees such as found
in breeding populations! This package, 'randPedPCA', exploits sparse matrices and randomised
linear algebra to deliver a gazillion-times speed-up compared to naive singular value decoposition (SVD)
(and eigen decomposition).
Author: Hanbin Lee [aut],
Hannes Becher [cre],
Ros Craddock [aut],
Gregor Gorjanc [aut]
Maintainer: Hannes Becher <h.becher@ed.ac.uk>
Diff between randPedPCA versions 1.0.0 dated 2025-04-24 and 1.0.1 dated 2025-04-24
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- inst/doc/pedigree-pca.html | 12 ++++++------ tests/testthat/Rplots.pdf |binary tests/testthat/test_rppca.R | 22 +++++++++++----------- 5 files changed, 26 insertions(+), 26 deletions(-)
Title: Retrieval-Augmented Generation (RAG) Workflows in R with Local
and Web Search
Description: Enables Retrieval-Augmented Generation (RAG) workflows in R by combining
local vector search using 'DuckDB' with optional web search via the 'Tavily' API.
Supports OpenAI- and Ollama-compatible embedding models, full-text and HNSW
(Hierarchical Navigable Small World) indexing, and modular large language model
(LLM) invocation. Designed for advanced question-answering, chat-based
applications, and production-ready AI pipelines. This package is the R
equivalent of the 'python' package 'RAGFlowChain' available at
<https://pypi.org/project/RAGFlowChain/>.
Author: Kwadwo Daddy Nyame Owusu Boakye [aut, cre]
Maintainer: Kwadwo Daddy Nyame Owusu Boakye <kwadwo.owusuboakye@outlook.com>
Diff between RAGFlowChainR versions 0.1.0 dated 2025-04-24 and 0.1.1 dated 2025-04-24
DESCRIPTION | 27 - MD5 | 14 NEWS.md |only R/create_rag_chain.R | 80 +++-- R/create_vectorstore.R | 481 ++++++++++++++----------------- man/create_vectorstore.Rd | 38 +- man/figures |only tests/testthat/test_create_rag_chain.R | 166 +++------- tests/testthat/test_create_vectorstore.R | 384 ++++++------------------ 9 files changed, 455 insertions(+), 735 deletions(-)
Title: Seamless 'Nonmem' Simulation Platform
Description: A complete and seamless 'Nonmem' simulation interface within R. Turns 'Nonmem' control streams into simulation control streams, executes them with specified simulation input data and returns the results. The simulation is performed by 'Nonmem', eliminating manual work and risks of re-implementation of models in other tools.
Author: Philip Delff [aut, cre],
Brian Reilly [ctb],
Sanaya Shroff [ctb],
Boris Grinshpun [ctb]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMsim versions 0.2.0 dated 2025-03-12 and 0.2.1 dated 2025-04-24
NMsim-0.2.0/NMsim/man/initsToExt.Rd |only NMsim-0.2.0/NMsim/tests/testthat/testReference/NMsim_VarCov_04.rds |only NMsim-0.2.1/NMsim/DESCRIPTION | 12 NMsim-0.2.1/NMsim/MD5 | 183 - NMsim-0.2.1/NMsim/NAMESPACE | 4 NMsim-0.2.1/NMsim/NEWS.md | 81 NMsim-0.2.1/NMsim/R/NMaddSamples.R |only NMsim-0.2.1/NMsim/R/NMcreateDoses.R | 6 NMsim-0.2.1/NMsim/R/NMcreateMatLines.R | 23 NMsim-0.2.1/NMsim/R/NMexec.R | 61 NMsim-0.2.1/NMsim/R/NMexecDirectory.R | 11 NMsim-0.2.1/NMsim/R/NMreadFilters.R | 1 NMsim-0.2.1/NMsim/R/NMreadInits.R | 1 NMsim-0.2.1/NMsim/R/NMreadSimModTab.R | 6 NMsim-0.2.1/NMsim/R/NMreplaceInits.R | 22 NMsim-0.2.1/NMsim/R/NMrunLin.R |only NMsim-0.2.1/NMsim/R/NMrunWin.R | 131 - NMsim-0.2.1/NMsim/R/NMsim.R | 43 NMsim-0.2.1/NMsim/R/NMsimCheckMod.R | 41 NMsim-0.2.1/NMsim/R/NMsim_EBE.R | 2 NMsim-0.2.1/NMsim/R/NMsim_NWPRI.R | 6 NMsim-0.2.1/NMsim/R/NMsim_VarCov.R | 55 NMsim-0.2.1/NMsim/R/NMsim_default.R | 2 NMsim-0.2.1/NMsim/R/NMsim_helpers.R | 31 NMsim-0.2.1/NMsim/R/NMsim_typical.R | 2 NMsim-0.2.1/NMsim/R/NMupdateSizes.R | 18 NMsim-0.2.1/NMsim/R/NMwriteInits.R | 20 NMsim-0.2.1/NMsim/R/addBlocks.R |only NMsim-0.2.1/NMsim/R/addEVID2.R | 269 -- NMsim-0.2.1/NMsim/R/callNonmemDirect.R |only NMsim-0.2.1/NMsim/R/cleaningPatterns.R |only NMsim-0.2.1/NMsim/R/completeCov.R | 2 NMsim-0.2.1/NMsim/R/expandCovs.R | 106 NMsim-0.2.1/NMsim/R/forestDefineCovs.R |only NMsim-0.2.1/NMsim/R/forestSummarize.R |only NMsim-0.2.1/NMsim/R/genPhiFile.R | 31 NMsim-0.2.1/NMsim/R/modifyModel.R | 49 NMsim-0.2.1/NMsim/R/readParsWide.R | 76 NMsim-0.2.1/NMsim/R/reportFailedRun.R | 6 NMsim-0.2.1/NMsim/R/samplePars.R |only NMsim-0.2.1/NMsim/R/sampleParsSimpar.R | 15 NMsim-0.2.1/NMsim/R/samplePars_mvrnorm.R |only NMsim-0.2.1/NMsim/R/samplePars_simpar.R |only NMsim-0.2.1/NMsim/R/simPopEtas.R | 11 NMsim-0.2.1/NMsim/R/summarizeCovs.R | 145 - NMsim-0.2.1/NMsim/R/typicalize.R | 2 NMsim-0.2.1/NMsim/README.md | 17 NMsim-0.2.1/NMsim/inst/examples/data/xgxr2covs.csv |only NMsim-0.2.1/NMsim/inst/examples/data/xgxr2covs.rds |only NMsim-0.2.1/NMsim/inst/examples/data/xgxr2covs_meta.txt |only NMsim-0.2.1/NMsim/inst/examples/nonmem/xgxr132.mod |only NMsim-0.2.1/NMsim/inst/examples/nonmem/xgxr134.coi |only NMsim-0.2.1/NMsim/inst/examples/nonmem/xgxr134.cor |only NMsim-0.2.1/NMsim/inst/examples/nonmem/xgxr134.cov |only NMsim-0.2.1/NMsim/inst/examples/nonmem/xgxr134.ext |only NMsim-0.2.1/NMsim/inst/examples/nonmem/xgxr134.lst |only NMsim-0.2.1/NMsim/inst/examples/nonmem/xgxr134.mod |only NMsim-0.2.1/NMsim/inst/examples/nonmem/xgxr134.phi |only NMsim-0.2.1/NMsim/inst/examples/nonmem/xgxr134.shk |only NMsim-0.2.1/NMsim/inst/examples/nonmem/xgxr134_etas.txt |only NMsim-0.2.1/NMsim/inst/examples/nonmem/xgxr134_res.txt |only NMsim-0.2.1/NMsim/man/NMaddSamples.Rd |only NMsim-0.2.1/NMsim/man/NMcreateMatLines.Rd | 8 NMsim-0.2.1/NMsim/man/NMreplaceInits.Rd | 2 NMsim-0.2.1/NMsim/man/NMrunLin.Rd | 2 NMsim-0.2.1/NMsim/man/NMsimCheckMod.Rd | 13 NMsim-0.2.1/NMsim/man/NMupdateSizes.Rd | 3 NMsim-0.2.1/NMsim/man/addBlocks.Rd |only NMsim-0.2.1/NMsim/man/addEVID2.Rd | 115 NMsim-0.2.1/NMsim/man/callNonmemDirect.Rd | 2 NMsim-0.2.1/NMsim/man/expandCovs.Rd | 55 NMsim-0.2.1/NMsim/man/forestDefineCovs.Rd |only NMsim-0.2.1/NMsim/man/forestSummarize.Rd |only NMsim-0.2.1/NMsim/man/genPhiFile.Rd | 12 NMsim-0.2.1/NMsim/man/modifyModel.Rd | 13 NMsim-0.2.1/NMsim/man/readParsWide.Rd | 29 NMsim-0.2.1/NMsim/man/samplePars.Rd |only NMsim-0.2.1/NMsim/man/simPopEtas.Rd | 16 NMsim-0.2.1/NMsim/man/simplePath.Rd |only NMsim-0.2.1/NMsim/man/summarizeCovs.Rd | 33 NMsim-0.2.1/NMsim/tests/testthat/testData/nonmem/NMsim/predu_sd2_NWPRI/NMsimData_predu_sd2_NWPRI.csv | 1202 +++++----- NMsim-0.2.1/NMsim/tests/testthat/testData/nonmem/NMsim/predu_sd2_NWPRI/NMsimData_predu_sd2_NWPRI.rds |binary NMsim-0.2.1/NMsim/tests/testthat/testData/nonmem/NMsim/predu_sd2_NWPRI/predu_sd2_NWPRI.mod | 12 NMsim-0.2.1/NMsim/tests/testthat/testData/nonmem/NMsim/predu_sd2_NWPRI_MetaData.rds |binary NMsim-0.2.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail/xgxr021_nmtranfail.lst | 2 NMsim-0.2.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail_MetaData.rds |binary NMsim-0.2.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr032_VarCov_1 |only NMsim-0.2.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr032_VarCov_1_MetaData.rds |only NMsim-0.2.1/NMsim/tests/testthat/testData/simres/xgxr134_forest1_MetaData.rds |only NMsim-0.2.1/NMsim/tests/testthat/testData/simres/xgxr134_forest1_ResultsData.fst |only NMsim-0.2.1/NMsim/tests/testthat/testReference/NMcreateDoses_16.rds |only NMsim-0.2.1/NMsim/tests/testthat/testReference/NMcreateMatLines_01.rds |binary NMsim-0.2.1/NMsim/tests/testthat/testReference/NMreadParsWide_01.rds |binary NMsim-0.2.1/NMsim/tests/testthat/testReference/NMsim_NWPRI_02.rds |binary NMsim-0.2.1/NMsim/tests/testthat/testReference/NMsim_NWPRI_02_OMEGAP.rds |binary NMsim-0.2.1/NMsim/tests/testthat/testReference/NMsim_VarCov_01.rds |only NMsim-0.2.1/NMsim/tests/testthat/testReference/addEVID2_17.rds |only NMsim-0.2.1/NMsim/tests/testthat/testReference/addEVID2_18.rds |only NMsim-0.2.1/NMsim/tests/testthat/testReference/samplePars_02.rds |only NMsim-0.2.1/NMsim/tests/testthat/testReference/samplePars_03.rds |only NMsim-0.2.1/NMsim/tests/testthat/testReference/summarizeCovs_01.rds |only NMsim-0.2.1/NMsim/tests/testthat/testReference/summarizeCovs_02.rds |only NMsim-0.2.1/NMsim/tests/testthat/test_NMcreateDoses.R | 9 NMsim-0.2.1/NMsim/tests/testthat/test_NMcreateMatLines.R | 11 NMsim-0.2.1/NMsim/tests/testthat/test_NMreadParsWide.R | 6 NMsim-0.2.1/NMsim/tests/testthat/test_NMsimCheckMod.R |only NMsim-0.2.1/NMsim/tests/testthat/test_NMsim_NWPRI.R | 12 NMsim-0.2.1/NMsim/tests/testthat/test_NMsim_VarCov.R |only NMsim-0.2.1/NMsim/tests/testthat/test_NMupdateSizes.R | 4 NMsim-0.2.1/NMsim/tests/testthat/test_addEVID2.R | 85 NMsim-0.2.1/NMsim/tests/testthat/test_genPhiFile.R | 1 NMsim-0.2.1/NMsim/tests/testthat/test_sampleParsSimpar.R | 68 NMsim-0.2.1/NMsim/tests/testthat/test_summarizeCovs.R |only 113 files changed, 1476 insertions(+), 1730 deletions(-)
Title: Mobility Oriented-Parity Metric
Description: A set of tools to perform multiple versions of the Mobility
Oriented-Parity metric. This multivariate analysis helps to characterize
levels of dissimilarity between a set of conditions of reference and another
set of conditions of interest. If predictive models are transferred to
conditions different from those over which models were calibrated (trained),
this metric helps to identify transfer conditions that differ
substantially from those of calibration. These tools are implemented
following principles proposed in Owens et al. (2013)
<doi:10.1016/j.ecolmodel.2013.04.011>, and expanded to obtain more detailed
results that aid in interpretation as in Cobos et al. (2024)
<doi:10.21425/fob.17.132916>.
Author: Marlon E. Cobos [aut, cre] ,
Hannah L. Owens [aut] ,
Jorge Soberon [aut] ,
A. Townsend Peterson [aut]
Maintainer: Marlon E. Cobos <manubio13@gmail.com>
Diff between mop versions 0.1.2 dated 2024-03-28 and 0.1.3 dated 2025-04-24
DESCRIPTION | 13 +++++++------ MD5 | 26 +++++++++++++------------- NEWS.md | 7 +++++++ R/helpers.R | 4 +--- R/mop.R | 9 +++++++-- README.md | 32 ++++++++++++++++++++++++++++++-- man/figures/README-load-1.png |binary man/figures/README-load-2.png |binary man/figures/README-plots-1.png |binary man/figures/README-plots-2.png |binary man/figures/README-plots-3.png |binary man/figures/README-plots-4.png |binary man/figures/README-plots-5.png |binary man/match_na_raster.Rd | 4 +--- 14 files changed, 66 insertions(+), 29 deletions(-)
Title: 'C++' Header Library for Ordinary Differential Equations
Description: A 'C++' header library for using the 'libsoda-cxx' library with R. The 'C++' header reimplements the 'lsoda' function from the 'ODEPACK' library for solving initial value problems for first order ordinary differential equations (Hindmarsh, 1982; <https://computing.llnl.gov/sites/default/files/ODEPACK_pub1_u88007.pdf>). The 'C++' header can be used by other R packages by linking against this package. The 'C++' functions can be called inline using 'Rcpp'. Finally, the package provides an 'ode' function to call from R.
Author: Mark Clements [aut, cre],
Dilawar Singh [ctb],
Heng Li [ctb],
Peter N. Brown [ctb],
George D. Byrne [ctb],
Alan C. Hindmarsh [ctb],
Cleve Moler [ctb],
Linda R. Petzold [ctb]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between lsoda versions 1.0 dated 2025-04-22 and 1.1 dated 2025-04-24
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/include/lsoda.h | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Lagrangian Multiplier Smoothing Splines for Smooth Function
Estimation
Description: Implements Lagrangian multiplier smoothing splines for flexible
nonparametric regression and function estimation. Provides tools for fitting,
prediction, and inference using a constrained optimization approach to
enforce smoothness.
Supports generalized linear models, Weibull accelerated failure time (AFT) models,
quadratic programming problems, and customizable arbitrary correlation structures.
Options for fitting in parallel are provided. The method builds upon the framework described
by Ezhov et al. (2018) <doi:10.1515/jag-2017-0029> using Lagrangian multipliers
to fit cubic splines. For more information on correlation structure estimation,
see Searle et al. (2009) <ISBN:978-0470009598>. For quadratic programming and
constrained optimization in general, see Nocedal & Wright (2006) <doi:10.1007/978-0-387-40065-5>.
For a comprehensive background on smoothing splines, see Wahba (1990)
<doi:10.1137/1.9781611970128> and Wood (2006) <ISBN:978-1584884743>
[...truncated...]
Author: Matthew Davis [aut, cre]
Maintainer: Matthew Davis <matthewlouisdavis@gmail.com>
Diff between lgspline versions 0.1.0 dated 2025-04-22 and 0.2.0 dated 2025-04-24
DESCRIPTION | 6 +- MD5 | 4 - tests/testthat/test-advanced.R | 83 +++++++++++++++++++++++------------------ 3 files changed, 53 insertions(+), 40 deletions(-)
Title: The Machine Learning and AI Modeling Companion to 'healthyR'
Description: Hospital machine learning and ai data analysis workflow tools, modeling, and automations.
This library provides many useful tools to review common administrative
hospital data. Some of these include predicting length of stay, and readmits.
The aim is to provide a simple and consistent verb framework that takes the
guesswork out of everything.
Author: Steven Sanderson [aut, cre, cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between healthyR.ai versions 0.1.0 dated 2024-09-11 and 0.1.1 dated 2025-04-24
DESCRIPTION | 6 MD5 | 64 ++--- NEWS.md | 494 +++++++++++++++++++-------------------- R/data-prep-c50.R | 3 R/data-prep-earth.R | 113 ++++---- R/data-prep-glmnet.R | 3 R/data-prep-knn.R | 3 R/data-prep-ranger.R | 5 R/data-prep-svm_poly.R | 3 R/data-prep-svm_rbf.R | 3 R/data-prep-xgboost.R | 3 R/get-juiced-data.R | 136 +++++----- R/hai-data-scale.R | 2 R/utils-mesh-generator.R | 2 README.md | 2 inst/doc/auto-kmeans.R | 26 +- inst/doc/auto-kmeans.html | 6 inst/doc/getting-started.html | 170 ++++++------- inst/doc/kmeans-umap.html | 30 +- man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/generate_mesh_data.Rd | 5 man/get_juiced_data.Rd | 6 man/hai_c50_data_prepper.Rd | 3 man/hai_data_scale.Rd | 2 man/hai_earth_data_prepper.Rd | 3 man/hai_glmnet_data_prepper.Rd | 3 man/hai_knn_data_prepper.Rd | 3 man/hai_ranger_data_prepper.Rd | 3 man/hai_svm_poly_data_prepper.Rd | 3 man/hai_svm_rbf_data_prepper.Rd | 3 man/hai_xgboost_data_prepper.Rd | 3 man/pca_your_recipe.Rd | 3 33 files changed, 588 insertions(+), 526 deletions(-)
Title: Package for Environmental Statistics, Including US EPA Guidance
Description: Graphical and statistical analyses of environmental data, with
focus on analyzing chemical concentrations and physical parameters, usually in
the context of mandated environmental monitoring. Major environmental
statistical methods found in the literature and regulatory guidance documents,
with extensive help that explains what these methods do, how to use them,
and where to find them in the literature. Numerous built-in data sets from
regulatory guidance documents and environmental statistics literature. Includes
scripts reproducing analyses presented in the book "EnvStats: An R Package for
Environmental Statistics" (Millard, 2013, Springer, ISBN 978-1-4614-8455-4,
<doi:10.1007/978-1-4614-8456-1>).
Author: Steven P. Millard [aut],
Alexander Kowarik [ctb, cre]
Maintainer: Alexander Kowarik <alexander.kowarik@statistik.gv.at>
Diff between EnvStats versions 3.0.0 dated 2024-08-24 and 3.1.0 dated 2025-04-24
EnvStats-3.0.0/EnvStats/man/htest.object.Rd |only EnvStats-3.0.0/EnvStats/man/print.htestEnvStats.Rd |only EnvStats-3.1.0/EnvStats/DESCRIPTION | 8 EnvStats-3.1.0/EnvStats/MD5 | 58 +- EnvStats-3.1.0/EnvStats/NAMESPACE | 10 EnvStats-3.1.0/EnvStats/NEWS | 25 + EnvStats-3.1.0/EnvStats/R/StatTestText.R | 49 +- EnvStats-3.1.0/EnvStats/R/chenTTest.R | 191 ++++----- EnvStats-3.1.0/EnvStats/R/geom_stripchart.R | 276 +++++++------- EnvStats-3.1.0/EnvStats/R/gofTestCensored.R | 2 EnvStats-3.1.0/EnvStats/R/print.R |only EnvStats-3.1.0/EnvStats/R/print.default.R |only EnvStats-3.1.0/EnvStats/R/print.htest.R |only EnvStats-3.1.0/EnvStats/R/print.htestEnvStats.R | 228 +++++------ EnvStats-3.1.0/EnvStats/R/signTest.R | 16 EnvStats-3.1.0/EnvStats/man/Distribution.df.Rd | 8 EnvStats-3.1.0/EnvStats/man/FcnsByCatEstDistParams.Rd | 1 EnvStats-3.1.0/EnvStats/man/chenTTest.Rd | 6 EnvStats-3.1.0/EnvStats/man/ciTableMean.Rd | 2 EnvStats-3.1.0/EnvStats/man/enparCensored.Rd | 4 EnvStats-3.1.0/EnvStats/man/geom_stripchart.Rd | 4 EnvStats-3.1.0/EnvStats/man/htest.htestEnvStats.object.Rd |only EnvStats-3.1.0/EnvStats/man/kendallSeasonalTrendTest.Rd | 8 EnvStats-3.1.0/EnvStats/man/kendallTrendTest.Rd | 8 EnvStats-3.1.0/EnvStats/man/print.Rd |only EnvStats-3.1.0/EnvStats/man/print.htest.htestEnvStats.Rd |only EnvStats-3.1.0/EnvStats/man/quantileTest.Rd | 8 EnvStats-3.1.0/EnvStats/man/rosnerTest.Rd | 2 EnvStats-3.1.0/EnvStats/man/serialCorrelationTest.Rd | 11 EnvStats-3.1.0/EnvStats/man/signTest.Rd | 182 ++++++++- EnvStats-3.1.0/EnvStats/man/stripChart.Rd | 8 EnvStats-3.1.0/EnvStats/man/twoSampleLinearRankTest.Rd | 8 EnvStats-3.1.0/EnvStats/man/varGroupTest.Rd | 8 EnvStats-3.1.0/EnvStats/man/zTestGevdShape.Rd | 8 34 files changed, 681 insertions(+), 458 deletions(-)
Title: Python-Based Extensions for Data Analytics Workflows
Description: Provides Python-based extensions to enhance data analytics workflows,
particularly for tasks involving data preprocessing and predictive modeling.
Includes tools for data sampling, transformation, feature selection,
balancing strategies (e.g., SMOTE), and model construction.
These capabilities leverage Python libraries via the reticulate interface,
enabling seamless integration with a broader machine learning ecosystem.
Supports instance selection and hybrid workflows that combine R and Python
functionalities for flexible and reproducible analytical pipelines.
The architecture is inspired by the Experiment Lines approach, which promotes
modularity, extensibility, and interoperability across tools.
More information on Experiment Lines is available in
Ogasawara et al. (2009) <doi:10.1007/978-3-642-02279-1_20>.
Author: Eduardo Ogasawara [aut, ths, cre]
,
Diego Salles [aut, ths],
Federal Center for Technological Education of Rio de Janeiro
[cph]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between daltoolboxdp versions 1.0.777 dated 2024-12-04 and 1.0.787 dated 2025-04-24
DESCRIPTION | 52 +++++++++++++++++++++++------------- MD5 | 35 +++++++++++++++++++++--- NAMESPACE | 5 +++ R/bal_oversampling.R | 3 -- R/bal_subsampling.R | 2 - R/globals.R |only R/sk_cla_gb.R |only README.md | 72 ++++++++++++++++++++++++++++++++++++++------------- inst/python/sklearn |only man/cla_gb.Rd |only 10 files changed, 124 insertions(+), 45 deletions(-)
Title: Scale Functions for Visualization
Description: Graphical scales map data to aesthetics, and provide methods
for automatically determining breaks and labels for axes and legends.
Author: Hadley Wickham [aut],
Thomas Lin Pedersen [cre, aut]
,
Dana Seidel [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between scales versions 1.3.0 dated 2023-11-28 and 1.4.0 dated 2025-04-24
DESCRIPTION | 24 +- LICENSE | 2 MD5 | 262 ++++++++++++++++-------------- NAMESPACE | 46 +++++ NEWS.md | 189 ++++++++++++--------- R/bounds.R | 53 ++++-- R/breaks-log.R | 88 ++++++++++ R/breaks-retired.R | 10 - R/breaks.R | 59 ++++++ R/colour-manip.R | 199 ++++++++++++++++++++-- R/colour-mapping.R | 168 ++++++++++++++----- R/colour-ramp.R | 16 - R/date-time.R | 7 R/full-seq.R | 11 + R/import-standalone-obj-type.R |only R/import-standalone-types-check.R |only R/label-bytes.R | 13 - R/label-compose.R |only R/label-currency.R | 66 +++++-- R/label-date.R | 55 ++++-- R/label-dictionary.R |only R/label-glue.R |only R/label-log.R | 53 ++++-- R/label-number-auto.R | 8 R/label-number-si.R | 8 R/label-number.R | 193 +++++++++++++++++----- R/label-ordinal.R | 27 ++- R/label-percent.R | 27 ++- R/label-pvalue.R | 25 +- R/label-scientific.R | 25 ++ R/label-wrap.R | 6 R/labels-retired.R | 45 +++-- R/pal-.R |only R/pal-area.R | 5 R/pal-brewer.R | 44 ++++- R/pal-dichromat.R | 11 - R/pal-gradient.R | 28 ++- R/pal-grey.R | 6 R/pal-hue.R | 12 + R/pal-linetype.R | 19 +- R/pal-manual.R | 31 +++ R/pal-rescale.R | 8 R/pal-shape.r | 5 R/pal-viridis.R | 11 + R/palette-registry.R |only R/range.R | 30 ++- R/scale-continuous.R | 43 ++++ R/scale-discrete.R | 27 ++- R/transform-compose.R | 15 + R/transform-date.R | 23 +- R/transform-numeric.R | 26 +- R/transform.R | 81 ++++++--- R/utils.R | 71 ++++++++ README.md | 44 ++--- build/partial.rdb |binary man/alpha.Rd | 8 man/breaks_exp.Rd |only man/breaks_extended.Rd | 6 man/breaks_log.Rd | 6 man/breaks_pretty.Rd | 6 man/breaks_timespan.Rd | 6 man/breaks_width.Rd | 6 man/col2hcl.Rd | 8 man/col_mix.Rd |only man/colour_manip.Rd |only man/comma.Rd | 27 ++- man/compose_label.Rd |only man/date_format.Rd | 6 man/dollar_format.Rd | 15 + man/figures/README-labels-1.png |binary man/figures/README-transforms-1.png |binary man/figures/README-unnamed-chunk-3-1.png |only man/figures/README-unnamed-chunk-4-1.png |only man/figures/logo.png |binary man/label_bytes.Rd | 30 ++- man/label_currency.Rd | 28 ++- man/label_date.Rd | 40 +++- man/label_dictionary.Rd |only man/label_glue.Rd |only man/label_log.Rd | 18 +- man/label_number.Rd | 29 ++- man/label_number_auto.Rd | 11 + man/label_number_si.Rd | 20 +- man/label_ordinal.Rd | 28 +-- man/label_parse.Rd | 3 man/label_percent.Rd | 24 +- man/label_pvalue.Rd | 10 - man/label_scientific.Rd | 6 man/label_wrap.Rd | 2 man/minor_breaks_log.Rd |only man/muted.Rd | 8 man/new_continuous_palette.Rd |only man/number.Rd | 27 ++- man/number_options.Rd |only man/ordinal_format.Rd | 21 -- man/pal_dichromat.Rd | 2 man/pal_div_gradient.Rd | 15 - man/pal_manual.Rd | 7 man/pal_seq_gradient.Rd | 7 man/palette-recommendations.Rd |only man/percent_format.Rd | 15 + man/pvalue_format.Rd | 11 - man/scales-package.Rd | 2 man/scientific_format.Rd | 7 man/train_continuous.Rd | 4 man/train_discrete.Rd | 11 + man/transform_boxcox.Rd | 8 man/unit_format.Rd | 11 - tests/testthat/_snaps/breaks-log.md |only tests/testthat/_snaps/colour-mapping.md | 77 ++++++++ tests/testthat/_snaps/label-bytes.md |only tests/testthat/_snaps/label-number.md | 4 tests/testthat/_snaps/pal-manual.md |only tests/testthat/_snaps/palette-registry.md |only tests/testthat/_snaps/scale-continuous.md |only tests/testthat/_snaps/trans-compose.md | 8 tests/testthat/_snaps/trans-numeric.md |only tests/testthat/_snaps/trans.md | 2 tests/testthat/_snaps/utils.md |only tests/testthat/test-bounds.R | 3 tests/testthat/test-breaks-log.R | 23 ++ tests/testthat/test-breaks.R | 18 ++ tests/testthat/test-colour-manip.R | 46 +++++ tests/testthat/test-colour-mapping.R | 88 +++++++--- tests/testthat/test-full-seq.R | 25 ++ tests/testthat/test-label-bytes.R | 12 - tests/testthat/test-label-compose.R |only tests/testthat/test-label-currency.R | 6 tests/testthat/test-label-date.R | 15 + tests/testthat/test-label-dictionary.R |only tests/testthat/test-label-glue.R |only tests/testthat/test-label-log.R | 1 tests/testthat/test-label-number.R | 60 ++++++ tests/testthat/test-label-ordinal.R | 1 tests/testthat/test-label-percent.R | 1 tests/testthat/test-label-pvalue.R | 1 tests/testthat/test-label-scientific.R | 1 tests/testthat/test-offset-by.R | 5 tests/testthat/test-pal-.R |only tests/testthat/test-pal-manual.R | 2 tests/testthat/test-palette-registry.R |only tests/testthat/test-range.R | 9 - tests/testthat/test-scale-continuous.R | 14 + tests/testthat/test-scale-discrete.R | 10 + tests/testthat/test-trans-compose.R | 5 tests/testthat/test-trans-date.R | 15 + tests/testthat/test-trans-numeric.R | 118 +++++++++---- tests/testthat/test-utils.R |only 148 files changed, 2482 insertions(+), 812 deletions(-)
Title: Computes Proximity in Large Sparse Matrices
Description: Computes proximity between rows or columns of large matrices efficiently in C++.
Functions are optimised for large sparse matrices using the Armadillo and Intel TBB libraries.
Among various built-in similarity/distance measures, computation of correlation,
cosine similarity, Dice coefficient and Euclidean distance is particularly fast.
Author: Kohei Watanabe [cre, aut, cph]
,
Robrecht Cannoodt [aut]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between proxyC versions 0.5.0 dated 2025-04-22 and 0.5.1 dated 2025-04-24
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 6 ++++++ inst/doc/measures.html | 4 ++-- src/linear.cpp | 6 ++++++ 5 files changed, 21 insertions(+), 9 deletions(-)
Title: Package for Sequence Analysis by Local Score
Description: Functionalities for calculating the local score and calculating statistical relevance (p-value) to find a local Score in a sequence of given distribution (S. Mercier and J.-J. Daudin (2001) <https://hal.science/hal-00714174/>) ; S. Karlin and S. Altschul (1990) <https://pmc.ncbi.nlm.nih.gov/articles/PMC53667/> ; S. Mercier, D. Cellier and F. Charlot (2003) <https://hal.science/hal-00937529v1/> ; A. Lagnoux, S. Mercier and P. Valois (2017) <doi:10.1093/bioinformatics/btw699> ).
Author: Sebastian Simon [aut],
Chris Verschelden [aut],
Charly Marty [aut],
David Robelin [aut, cre],
Sabine Mercier [aut],
Sebastien Dejean [aut],
The authors of Eigen the library for the included version of Eigen
[cph]
Maintainer: David Robelin <david.robelin@inrae.fr>
Diff between localScore versions 2.0.2 dated 2025-04-19 and 2.0.3 dated 2025-04-24
DESCRIPTION | 8 +- MD5 | 28 +++---- R/RcppExports.R | 21 ++++- build/vignette.rds |binary inst/doc/ExcursionsheightDocumentation.pdf |binary inst/doc/localScorePackageDocumentation.R | 3 inst/doc/localScorePackageDocumentation.Rmd | 3 inst/doc/localScorePackageDocumentation.pdf |binary man/daudin.Rd | 15 ++-- man/karlin.Rd | 11 +- man/maxPartialSumd.Rd | 8 +- man/mcc.Rd | 11 +- src/function_wrapper.cpp | 101 ++++++++++++++++++--------- tests/testthat/test-daudin.R | 49 ++++++++++++- vignettes/localScorePackageDocumentation.Rmd | 3 15 files changed, 180 insertions(+), 81 deletions(-)
Title: Client for 'LaminDB'
Description: Interact with 'LaminDB'. 'LaminDB' is an open-source data
framework for biology. This package allows you to query and download
data from 'LaminDB' instances.
Author: Robrecht Cannoodt [aut, cre] ,
Luke Zappia [aut] ,
Data Intuitive [aut],
Lamin Labs [aut, cph]
Maintainer: Robrecht Cannoodt <robrecht@lamin.ai>
Diff between laminr versions 1.0.1 dated 2025-03-18 and 1.1.0 dated 2025-04-24
laminr-1.0.1/laminr/inst/doc/welcome.qmd |only laminr-1.0.1/laminr/vignettes/cellxgene_basic.html |only laminr-1.0.1/laminr/vignettes/example_workflow.html |only laminr-1.0.1/laminr/vignettes/introduction.Rmd |only laminr-1.0.1/laminr/vignettes/laminr.Rmd |only laminr-1.0.1/laminr/vignettes/setup.Rmd |only laminr-1.0.1/laminr/vignettes/welcome.qmd |only laminr-1.1.0/laminr/DESCRIPTION | 20 +- laminr-1.1.0/laminr/MD5 | 79 ++++++----- laminr-1.1.0/laminr/NAMESPACE | 5 laminr-1.1.0/laminr/R/Artifact.R | 27 ++-- laminr-1.1.0/laminr/R/Collection.R | 4 laminr-1.1.0/laminr/R/Registry.R | 10 - laminr-1.1.0/laminr/R/Transform.R | 4 laminr-1.1.0/laminr/R/arguments.R |only laminr-1.1.0/laminr/R/checks.R | 12 + laminr-1.1.0/laminr/R/file_loaders.R | 6 laminr-1.1.0/laminr/R/import.R | 44 ++++-- laminr-1.1.0/laminr/R/install.R | 39 ++++- laminr-1.1.0/laminr/R/lamin_cli.R | 33 +++- laminr-1.1.0/laminr/R/lamindb.R | 77 ++++++----- laminr-1.1.0/laminr/R/laminr-package.R | 6 laminr-1.1.0/laminr/R/packages.R |only laminr-1.1.0/laminr/R/require.R |only laminr-1.1.0/laminr/R/save_active_file.R | 8 - laminr-1.1.0/laminr/R/utils.R | 21 +-- laminr-1.1.0/laminr/R/view.R | 34 ++++- laminr-1.1.0/laminr/R/wrap-python.R | 135 ++++++++++++++++++-- laminr-1.1.0/laminr/R/zzz.R | 2 laminr-1.1.0/laminr/README.md | 58 -------- laminr-1.1.0/laminr/build/vignette.rds |binary laminr-1.1.0/laminr/inst/doc/welcome.Rmd |only laminr-1.1.0/laminr/inst/doc/welcome.html | 116 ++++++++++++++--- laminr-1.1.0/laminr/man/figures |only laminr-1.1.0/laminr/man/import_module.Rd | 36 ++++- laminr-1.1.0/laminr/man/install_lamindb.Rd | 16 +- laminr-1.1.0/laminr/man/laminr-package.Rd | 2 laminr-1.1.0/laminr/man/require_module.Rd |only laminr-1.1.0/laminr/tests/testthat.R | 3 laminr-1.1.0/laminr/tests/testthat/setup.R | 28 +--- laminr-1.1.0/laminr/tests/testthat/test-Artifact.R |only laminr-1.1.0/laminr/tests/testthat/test-checks.R | 4 laminr-1.1.0/laminr/tests/testthat/test-import.R | 10 + laminr-1.1.0/laminr/tests/testthat/test-install.R | 14 +- laminr-1.1.0/laminr/vignettes/welcome.Rmd |only 45 files changed, 576 insertions(+), 277 deletions(-)
Title: Reproducible Data Science Environments with 'Nix'
Description: Simplifies the creation of reproducible data science environments
using the 'Nix' package manager, as described in
Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()`
function generates a complete description of the environment as a
`default.nix` file, which can then be built using 'Nix'. This results in
project specific software environments with pinned versions of R, packages,
linked system dependencies, and other tools. Additional helpers make it easy
to run R code in 'Nix' software environments for testing and production.
Author: Bruno Rodrigues [aut, cre] ,
Philipp Baumann [aut] ,
David Watkins [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/625>),
Jacob Wujiciak-Jens [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/62 [...truncated...]
Maintainer: Bruno Rodrigues <bruno@brodrigues.co>
Diff between rix versions 0.15.7 dated 2025-03-17 and 0.16.0 dated 2025-04-24
rix-0.15.7/rix/inst/extdata/result |only rix-0.16.0/rix/DESCRIPTION | 6 rix-0.16.0/rix/MD5 | 109 ++++---- rix-0.16.0/rix/NEWS.md | 25 +- rix-0.16.0/rix/R/fetchers.R | 3 rix-0.16.0/rix/R/nix_hash.R | 122 +++++++++- rix-0.16.0/rix/R/rix.R | 39 ++- rix-0.16.0/rix/R/rix_helpers.R | 85 ++++-- rix-0.16.0/rix/README.md | 15 - rix-0.16.0/rix/build/vignette.rds |binary rix-0.16.0/rix/inst/doc/b1-setting-up-and-using-rix-on-linux-and-windows.Rmd | 15 + rix-0.16.0/rix/inst/doc/b1-setting-up-and-using-rix-on-linux-and-windows.html | 12 rix-0.16.0/rix/inst/doc/b2-setting-up-and-using-rix-on-macos.Rmd | 8 rix-0.16.0/rix/inst/doc/b2-setting-up-and-using-rix-on-macos.html | 9 rix-0.16.0/rix/inst/doc/d1-installing-r-packages-in-a-nix-environment.R | 20 + rix-0.16.0/rix/inst/doc/d1-installing-r-packages-in-a-nix-environment.Rmd | 28 ++ rix-0.16.0/rix/inst/doc/d1-installing-r-packages-in-a-nix-environment.html | 92 ++++--- rix-0.16.0/rix/inst/doc/e-configuring-ide.Rmd | 22 + rix-0.16.0/rix/inst/doc/e-configuring-ide.html | 40 ++- rix-0.16.0/rix/inst/extdata/available_df.csv | 7 rix-0.16.0/rix/inst/extdata/default.nix | 16 - rix-0.16.0/rix/inst/extdata/run-pipeline.yaml | 2 rix-0.16.0/rix/man/renv2nix.Rd | 2 rix-0.16.0/rix/man/rix.Rd | 4 rix-0.16.0/rix/tests/testthat/_snaps/renv_helpers/default_datathin.nix | 12 rix-0.16.0/rix/tests/testthat/_snaps/renv_helpers/default_v0-14-0.nix | 12 rix-0.16.0/rix/tests/testthat/_snaps/renv_helpers/default_v0-15-5.nix | 12 rix-0.16.0/rix/tests/testthat/_snaps/renv_helpers/default_v0-17-3.nix | 12 rix-0.16.0/rix/tests/testthat/_snaps/renv_helpers/default_v1-0-7.nix | 12 rix-0.16.0/rix/tests/testthat/_snaps/rix-python/python_default.nix | 18 - rix-0.16.0/rix/tests/testthat/_snaps/rix/bioc-devel_default.nix | 12 rix-0.16.0/rix/tests/testthat/_snaps/rix/bleeding-edge_default.nix | 16 - rix-0.16.0/rix/tests/testthat/_snaps/rix/code_default.nix | 18 - rix-0.16.0/rix/tests/testthat/_snaps/rix/codium_default.nix | 18 - rix-0.16.0/rix/tests/testthat/_snaps/rix/date_default.nix | 16 - rix-0.16.0/rix/tests/testthat/_snaps/rix/frozen-edge_default.nix | 16 - rix-0.16.0/rix/tests/testthat/_snaps/rix/no_quarto_default.nix | 12 rix-0.16.0/rix/tests/testthat/_snaps/rix/one_git_default.nix | 12 rix-0.16.0/rix/tests/testthat/_snaps/rix/other_default.nix | 16 - rix-0.16.0/rix/tests/testthat/_snaps/rix/positron_default.nix | 16 - rix-0.16.0/rix/tests/testthat/_snaps/rix/r-devel-bioc-devel_default.nix | 12 rix-0.16.0/rix/tests/testthat/_snaps/rix/r-devel_default.nix | 12 rix-0.16.0/rix/tests/testthat/_snaps/rix/rstudio_default.nix | 16 - rix-0.16.0/rix/tests/testthat/_snaps/rix/yes_quarto_default.nix | 16 - rix-0.16.0/rix/tests/testthat/_snaps/tar_nix_ga/run-pipeline.yaml | 2 rix-0.16.0/rix/tests/testthat/result | 2 rix-0.16.0/rix/tests/testthat/test-available_r.R | 3 rix-0.16.0/rix/tests/testthat/test-fetchers.R | 17 + rix-0.16.0/rix/tests/testthat/test-rix-python.R | 46 +++ rix-0.16.0/rix/tests/testthat/testdata/remote-pkgs/gen_envs.R | 11 rix-0.16.0/rix/tests/testthat/testdata/remote-pkgs/mlr3_default.nix | 12 rix-0.16.0/rix/tests/testthat/testdata/remote-pkgs/mlr3_dups_default.nix | 12 rix-0.16.0/rix/vignettes/b1-setting-up-and-using-rix-on-linux-and-windows.Rmd | 15 + rix-0.16.0/rix/vignettes/b2-setting-up-and-using-rix-on-macos.Rmd | 8 rix-0.16.0/rix/vignettes/d1-installing-r-packages-in-a-nix-environment.Rmd | 28 ++ rix-0.16.0/rix/vignettes/e-configuring-ide.Rmd | 22 + 56 files changed, 805 insertions(+), 340 deletions(-)
Title: Tabular Data Suppression using Gaussian Elimination
Description: A statistical disclosure control tool to protect tables by suppression
using the Gaussian elimination secondary suppression algorithm
(Langsrud, 2024) <doi:10.1007/978-3-031-69651-0_6>. A suggestion is
to start by working with functions SuppressSmallCounts() and
SuppressDominantCells(). These functions use primary suppression functions for
the minimum frequency rule and the dominance rule, respectively. Novel
functionality for suppression of disclosive cells is also included. General
primary suppression functions can be supplied as input to the general working
horse function, GaussSuppressionFromData(). Suppressed frequencies can be
replaced by synthetic decimal numbers as described in
Langsrud (2019) <doi:10.1007/s11222-018-9848-9>.
Author: Oeyvind Langsrud [aut, cre] ,
Daniel Lupp [aut] ,
Hege Boevelstad [ctb] ,
Vidar Norstein Klungre [rev] ,
Statistics Norway [cph]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between GaussSuppression versions 0.9.6 dated 2025-03-12 and 1.0.0 dated 2025-04-24
DESCRIPTION | 10 MD5 | 40 NEWS.md | 13 R/FixRiskyIntervals.R | 8 R/GaussSuppressionFromData.R | 5 R/Intervals.R | 8 R/PackageSpecs.R | 4 build/vignette.rds |binary inst/doc/Magnitude_table_suppression.R | 26 inst/doc/Magnitude_table_suppression.Rmd | 49 inst/doc/Magnitude_table_suppression.html | 643 ++++++--- inst/doc/Small_count_frequency_table_suppression.R | 24 inst/doc/Small_count_frequency_table_suppression.Rmd | 45 inst/doc/Small_count_frequency_table_suppression.html | 622 +++++---- inst/doc/define_tables.html | 1202 +++++++++--------- man/ComputeIntervals.Rd | 2 man/GaussSuppressionFromData.Rd | 4 tests/testthat/test-FixRiskyIntervals.R | 2 vignettes/GaussKable.R | 8 vignettes/Magnitude_table_suppression.Rmd | 49 vignettes/Small_count_frequency_table_suppression.Rmd | 45 21 files changed, 1700 insertions(+), 1109 deletions(-)
More information about GaussSuppression at CRAN
Permanent link
Title: 'HiGHS' Plugin for the 'R' Optimization Infrastructure
Description: Enhances the 'R' Optimization Infrastructure ('ROI') package
with the quadratic solver 'HiGHS'. More information about
'HiGHS' can be found at <https://highs.dev>.
Author: Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between ROI.plugin.highs versions 1.0-3 dated 2023-07-06 and 1.0-4 dated 2025-04-24
ROI.plugin.highs-1.0-3/ROI.plugin.highs/tests |only ROI.plugin.highs-1.0-4/ROI.plugin.highs/DESCRIPTION | 9 +++++---- ROI.plugin.highs-1.0-4/ROI.plugin.highs/MD5 | 5 +++-- ROI.plugin.highs-1.0-4/ROI.plugin.highs/inst |only 4 files changed, 8 insertions(+), 6 deletions(-)
More information about ROI.plugin.highs at CRAN
Permanent link
Title: Heuristic Capacitated Vehicle Routing Problem Solver
Description: Implements the Clarke-Wright algorithm to find a quasi-optimal solution to the Capacitated Vehicle Routing Problem. See Clarke, G. and Wright, J.R. (1964) <doi:10.1287/opre.12.4.568> for details. The implementation is accompanied by helper functions to inspect its solution.
Author: Lukas Schneiderbauer [aut, cre, cph]
Maintainer: Lukas Schneiderbauer <lukas.schneiderbauer@gmail.com>
Diff between heumilkr versions 0.2.0 dated 2024-04-01 and 0.3.0 dated 2025-04-24
heumilkr-0.2.0/heumilkr/R/plumber.R |only heumilkr-0.3.0/heumilkr/DESCRIPTION | 8 - heumilkr-0.3.0/heumilkr/MD5 | 43 +++---- heumilkr-0.3.0/heumilkr/NEWS.md | 30 ++++- heumilkr-0.3.0/heumilkr/R/autoplot.R | 50 ++++++++ heumilkr-0.3.0/heumilkr/R/clarke_wright.R | 52 ++++----- heumilkr-0.3.0/heumilkr/R/cpp11.R | 4 heumilkr-0.3.0/heumilkr/R/cvrplib.R | 49 +++++--- heumilkr-0.3.0/heumilkr/R/heumilkr_solution.R | 2 heumilkr-0.3.0/heumilkr/README.md | 3 heumilkr-0.3.0/heumilkr/build/partial.rdb |binary heumilkr-0.3.0/heumilkr/build/vignette.rds |binary heumilkr-0.3.0/heumilkr/inst/doc/clarke_wright_performance.html | 4 heumilkr-0.3.0/heumilkr/man/autoplot.heumilkr_solution.Rd |only heumilkr-0.3.0/heumilkr/man/clarke_wright.Rd | 9 + heumilkr-0.3.0/heumilkr/man/clarke_wright_cvrplib.Rd | 10 + heumilkr-0.3.0/heumilkr/man/plot.heumilkr_solution.Rd |only heumilkr-0.3.0/heumilkr/src/clarke_wright.cpp | 13 -- heumilkr-0.3.0/heumilkr/src/cpp11.cpp | 8 - heumilkr-0.3.0/heumilkr/src/routing_state.cpp | 57 ++++++++-- heumilkr-0.3.0/heumilkr/tests/testthat/helper-hedgehog.R | 4 heumilkr-0.3.0/heumilkr/tests/testthat/test-autoplot.R | 30 ++--- heumilkr-0.3.0/heumilkr/tests/testthat/test-clarke_wright.R | 50 ++++++++ heumilkr-0.3.0/heumilkr/tests/testthat/test-cvrplib.R | 1 24 files changed, 286 insertions(+), 141 deletions(-)
Title: Helpers for Model Coefficients Tibbles
Description: Provides suite of functions to work with regression model
'broom::tidy()' tibbles. The suite includes functions to group
regression model terms by variable, insert reference and header rows
for categorical variables, add variable labels, and more.
Author: Joseph Larmarange [aut, cre] ,
Daniel D. Sjoberg [aut]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between broom.helpers versions 1.20.0 dated 2025-03-06 and 1.21.0 dated 2025-04-24
DESCRIPTION | 9 MD5 | 97 +++--- NAMESPACE | 11 NEWS.md | 13 R/custom_tidiers.R | 65 ++++ R/model_get_assign.R | 6 R/model_get_coefficients_type.R | 6 R/model_get_contrasts.R | 6 R/model_get_model_frame.R | 9 R/model_get_model_matrix.R | 6 R/model_get_nlevels.R | 6 R/model_get_terms.R | 6 R/model_get_weights.R | 6 R/model_get_xlevels.R | 6 R/model_identify_variables.R | 8 R/model_list_variables.R | 2 R/tidy_add_term_labels.R | 28 + R/tidy_disambiguate_terms.R | 3 R/tidy_group_by.R | 6 R/tidy_plus_plus.R | 12 README.md | 4 build/vignette.rds |binary data/supported_models.rda |binary inst/WORDLIST | 4 inst/doc/broom-helpers.R | 12 inst/doc/broom-helpers.Rmd | 19 + inst/doc/broom-helpers.html | 530 +++++++++++++++++----------------- man/model_get_assign.Rd | 3 man/model_get_coefficients_type.Rd | 3 man/model_get_contrasts.Rd | 3 man/model_get_model_frame.Rd | 3 man/model_get_model_matrix.Rd | 3 man/model_get_nlevels.Rd | 3 man/model_get_terms.Rd | 3 man/model_get_weights.Rd | 3 man/model_get_xlevels.Rd | 3 man/model_identify_variables.Rd | 3 man/supported_models.Rd | 1 man/tidy_add_term_labels.Rd | 3 man/tidy_broom.Rd | 1 man/tidy_multgee.Rd | 1 man/tidy_parameters.Rd | 1 man/tidy_plus_plus.Rd | 3 man/tidy_svy_vglm.Rd |only man/tidy_vgam.Rd | 1 man/tidy_with_broom_or_parameters.Rd | 1 man/tidy_zeroinfl.Rd | 1 tests/testthat/test-add_term_labels.R | 15 tests/testthat/test-tidy_plus_plus.R | 22 + vignettes/broom-helpers.Rmd | 19 + 50 files changed, 639 insertions(+), 340 deletions(-)
Title: Efficient Spatial Thinning of Species Occurrences
Description: Provides efficient geospatial thinning algorithms to reduce
the density of coordinate data while maintaining spatial
relationships. Implements K-D Tree and brute-force distance-based
thinning, as well as grid-based and precision-based thinning methods.
For more information on the methods, see Elseberg et al. (2012)
<https://hdl.handle.net/10446/86202>.
Author: Jorge Mestre-Tomas [aut, cre]
Maintainer: Jorge Mestre-Tomas <jorge.mestre.tomas@csic.es>
Diff between GeoThinneR versions 1.1.0 dated 2024-10-03 and 2.0.0 dated 2025-04-24
GeoThinneR-1.1.0/GeoThinneR/R/brute_force_thinning.R |only GeoThinneR-1.1.0/GeoThinneR/R/kd_tree_thinning.R |only GeoThinneR-1.1.0/GeoThinneR/R/max_thinning_algorithm.R |only GeoThinneR-1.1.0/GeoThinneR/R/rounding_hashing_thinning.R |only GeoThinneR-1.1.0/GeoThinneR/man/assign_coords_to_grid.Rd |only GeoThinneR-1.1.0/GeoThinneR/man/brute_force_thinning.Rd |only GeoThinneR-1.1.0/GeoThinneR/man/figures/README-unnamed-chunk-3-1.png |only GeoThinneR-1.1.0/GeoThinneR/man/figures/README-unnamed-chunk-5-1.png |only GeoThinneR-1.1.0/GeoThinneR/man/figures/README-unnamed-chunk-7-1.png |only GeoThinneR-1.1.0/GeoThinneR/man/kd_tree_thinning.Rd |only GeoThinneR-1.1.0/GeoThinneR/man/long_lat_to_cartesian.Rd |only GeoThinneR-1.1.0/GeoThinneR/man/rounding_hashing_thinning.Rd |only GeoThinneR-1.1.0/GeoThinneR/src |only GeoThinneR-1.1.0/GeoThinneR/tests/testthat/test-brute_force_thinning.R |only GeoThinneR-1.1.0/GeoThinneR/tests/testthat/test-kd_tree_thinning.R |only GeoThinneR-1.1.0/GeoThinneR/tests/testthat/test-rounding_hashing_thinning.R |only GeoThinneR-2.0.0/GeoThinneR/DESCRIPTION | 16 GeoThinneR-2.0.0/GeoThinneR/LICENSE | 4 GeoThinneR-2.0.0/GeoThinneR/MD5 | 86 GeoThinneR-2.0.0/GeoThinneR/NAMESPACE | 37 GeoThinneR-2.0.0/GeoThinneR/NEWS.md | 28 GeoThinneR-2.0.0/GeoThinneR/R/GeoThinned_class.R |only GeoThinneR-2.0.0/GeoThinneR/R/data.R | 68 GeoThinneR-2.0.0/GeoThinneR/R/distance_thinning.R |only GeoThinneR-2.0.0/GeoThinneR/R/grid_thinning.R | 40 GeoThinneR-2.0.0/GeoThinneR/R/precision_thinning.R | 17 GeoThinneR-2.0.0/GeoThinneR/R/thin_points.R | 237 +- GeoThinneR-2.0.0/GeoThinneR/R/thinning_algorithm.R |only GeoThinneR-2.0.0/GeoThinneR/R/utils.R | 192 +- GeoThinneR-2.0.0/GeoThinneR/README.md | 178 - GeoThinneR-2.0.0/GeoThinneR/build/vignette.rds |binary GeoThinneR-2.0.0/GeoThinneR/data/caretta.rda |binary GeoThinneR-2.0.0/GeoThinneR/data/thunnus.rda |only GeoThinneR-2.0.0/GeoThinneR/inst/doc/GeoThinneR.R | 238 +- GeoThinneR-2.0.0/GeoThinneR/inst/doc/GeoThinneR.Rmd | 395 ++-- GeoThinneR-2.0.0/GeoThinneR/inst/doc/GeoThinneR.html | 948 +++++----- GeoThinneR-2.0.0/GeoThinneR/man/GeoThinned.Rd |only GeoThinneR-2.0.0/GeoThinneR/man/calculate_spatial_coverage.Rd |only GeoThinneR-2.0.0/GeoThinneR/man/caretta.Rd | 33 GeoThinneR-2.0.0/GeoThinneR/man/compute_nearest_neighbor_distances.Rd |only GeoThinneR-2.0.0/GeoThinneR/man/compute_neighbors_brute.Rd |only GeoThinneR-2.0.0/GeoThinneR/man/compute_neighbors_kdtree.Rd |only GeoThinneR-2.0.0/GeoThinneR/man/compute_neighbors_local_kdtree.Rd |only GeoThinneR-2.0.0/GeoThinneR/man/distance_thinning.Rd |only GeoThinneR-2.0.0/GeoThinneR/man/estimate_k_max.Rd |only GeoThinneR-2.0.0/GeoThinneR/man/figures/README-GeoThinneR_summary.png |only GeoThinneR-2.0.0/GeoThinneR/man/grid_thinning.Rd | 21 GeoThinneR-2.0.0/GeoThinneR/man/lon_lat_to_cartesian.Rd |only GeoThinneR-2.0.0/GeoThinneR/man/max_thinning_algorithm.Rd | 26 GeoThinneR-2.0.0/GeoThinneR/man/precision_thinning.Rd | 12 GeoThinneR-2.0.0/GeoThinneR/man/select_target_points.Rd |only GeoThinneR-2.0.0/GeoThinneR/man/thin_points.Rd | 127 - GeoThinneR-2.0.0/GeoThinneR/man/thunnus.Rd |only GeoThinneR-2.0.0/GeoThinneR/tests/testthat/test-GeoThinned_class.R |only GeoThinneR-2.0.0/GeoThinneR/tests/testthat/test-distance_thinning.R |only GeoThinneR-2.0.0/GeoThinneR/tests/testthat/test-grid_thinning.R | 18 GeoThinneR-2.0.0/GeoThinneR/tests/testthat/test-precision_thinning.R | 8 GeoThinneR-2.0.0/GeoThinneR/tests/testthat/test-thin_points.R | 120 - GeoThinneR-2.0.0/GeoThinneR/tests/testthat/test-thinning_algorithm.R |only GeoThinneR-2.0.0/GeoThinneR/tests/testthat/test-utils.R | 30 GeoThinneR-2.0.0/GeoThinneR/vignettes/GeoThinneR.Rmd | 395 ++-- 61 files changed, 1983 insertions(+), 1291 deletions(-)
Title: Estimate and Manipulate Age-Depth Models
Description: Estimate age-depth models from stratigraphic and sedimentological data,
and transform data
between the time and stratigraphic domain.
Author: Niklas Hohmann [aut, cre]
Maintainer: Niklas Hohmann <N.H.Hohmann@uu.nl>
Diff between admtools versions 0.4.0 dated 2024-10-03 and 0.5.0 dated 2025-04-24
admtools-0.4.0/admtools/data/CarboCATLite_data.rda |only admtools-0.5.0/admtools/DESCRIPTION | 8 admtools-0.5.0/admtools/MD5 | 100 +++++--- admtools-0.5.0/admtools/NAMESPACE | 36 +++ admtools-0.5.0/admtools/NEWS.md | 8 admtools-0.5.0/admtools/R/T_and_L_unit_handling.R | 135 +++++++++++- admtools-0.5.0/admtools/R/adm_to_ddc.R |only admtools-0.5.0/admtools/R/flip_ddc.R |only admtools-0.5.0/admtools/R/get_total_thickness.R | 7 admtools-0.5.0/admtools/R/get_total_thicknesses.R |only admtools-0.5.0/admtools/R/plot.ddc.R |only admtools-0.5.0/admtools/R/section_names.R |only admtools-0.5.0/admtools/R/sedrate_gen_helpers.R | 63 +++++ admtools-0.5.0/admtools/R/strat_to_time.fossils.R |only admtools-0.5.0/admtools/R/strat_to_time.taxonomy.R |only admtools-0.5.0/admtools/R/summary.R | 22 + admtools-0.5.0/admtools/R/time_to_strat.fossils.R |only admtools-0.5.0/admtools/R/time_to_strat.taxonomy.R |only admtools-0.5.0/admtools/R/tp_to_ddc.R |only admtools-0.5.0/admtools/README.md | 4 admtools-0.5.0/admtools/build/vignette.rds |binary admtools-0.5.0/admtools/data/CarboCatLite_data.rda |only admtools-0.5.0/admtools/inst/CITATION | 6 admtools-0.5.0/admtools/inst/WORDLIST | 17 + admtools-0.5.0/admtools/inst/doc/FossilSim_integration.R |only admtools-0.5.0/admtools/inst/doc/FossilSim_integration.Rmd |only admtools-0.5.0/admtools/inst/doc/FossilSim_integration.html |only admtools-0.5.0/admtools/inst/doc/adm_from_sedrate.Rmd | 6 admtools-0.5.0/admtools/inst/doc/adm_from_sedrate.html | 24 +- admtools-0.5.0/admtools/inst/doc/adm_from_trace_cont.html | 12 - admtools-0.5.0/admtools/inst/doc/admtools.R | 3 admtools-0.5.0/admtools/inst/doc/admtools.Rmd | 7 admtools-0.5.0/admtools/inst/doc/admtools.html | 6 admtools-0.5.0/admtools/inst/doc/admtools_doc.Rmd | 56 ++++ admtools-0.5.0/admtools/inst/doc/admtools_doc.html | 84 +++++++ admtools-0.5.0/admtools/inst/doc/correlation.R |only admtools-0.5.0/admtools/inst/doc/correlation.Rmd |only admtools-0.5.0/admtools/inst/doc/correlation.html |only admtools-0.5.0/admtools/man/adm_to_ddc.Rd |only admtools-0.5.0/admtools/man/flip_ddc.Rd |only admtools-0.5.0/admtools/man/get_L_unit.Rd | 2 admtools-0.5.0/admtools/man/get_L_units.Rd |only admtools-0.5.0/admtools/man/get_T_unit.Rd | 4 admtools-0.5.0/admtools/man/get_section_names.Rd |only admtools-0.5.0/admtools/man/get_total_thickness.Rd | 2 admtools-0.5.0/admtools/man/get_total_thicknesses.Rd |only admtools-0.5.0/admtools/man/plot.ddc.Rd |only admtools-0.5.0/admtools/man/plot.timelist.Rd | 32 +- admtools-0.5.0/admtools/man/sed_rate_from_matrix.Rd | 8 admtools-0.5.0/admtools/man/sed_rate_gen_from_bounds.Rd | 17 + admtools-0.5.0/admtools/man/sed_rate_gen_gamma.Rd |only admtools-0.5.0/admtools/man/set_L_unit.Rd | 4 admtools-0.5.0/admtools/man/set_L_units.Rd |only admtools-0.5.0/admtools/man/set_T_unit.Rd | 6 admtools-0.5.0/admtools/man/set_section_names.Rd |only admtools-0.5.0/admtools/man/strat_to_time.fossils.Rd |only admtools-0.5.0/admtools/man/strat_to_time.taxonomy.Rd |only admtools-0.5.0/admtools/man/summary.ddc.Rd |only admtools-0.5.0/admtools/man/time_to_strat.fossils.Rd |only admtools-0.5.0/admtools/man/time_to_strat.taxonomy.Rd |only admtools-0.5.0/admtools/man/tp_to_ddc.Rd |only admtools-0.5.0/admtools/tests/testthat/test_flip_ddc.R |only admtools-0.5.0/admtools/tests/testthat/test_strat_to_time.R | 17 + admtools-0.5.0/admtools/tests/testthat/test_time_to_strat.R | 17 + admtools-0.5.0/admtools/vignettes/FossilSim_integration.Rmd |only admtools-0.5.0/admtools/vignettes/adm_from_sedrate.Rmd | 6 admtools-0.5.0/admtools/vignettes/admtools.Rmd | 7 admtools-0.5.0/admtools/vignettes/admtools_doc.Rmd | 56 ++++ admtools-0.5.0/admtools/vignettes/correlation.Rmd |only 69 files changed, 672 insertions(+), 110 deletions(-)