Title: An 'Shiny' App for Exploring scRNA-seq Data Processed in
'Seurat'
Description: A simple, one-command package which runs an interactive dashboard capable of common visualizations for single cell RNA-seq. 'SeuratExplorer' requires a processed 'Seurat' object, which is saved as 'rds' or 'qs2' file.
Author: Yongchao Zhang [aut, cre]
Maintainer: Yongchao Zhang <zhangyongchao@nibs.ac.cn>
Diff between SeuratExplorer versions 0.1.4 dated 2026-03-30 and 0.1.6 dated 2026-06-17
SeuratExplorer-0.1.4/SeuratExplorer/inst |only SeuratExplorer-0.1.6/SeuratExplorer/DESCRIPTION | 14 SeuratExplorer-0.1.6/SeuratExplorer/MD5 | 70 SeuratExplorer-0.1.6/SeuratExplorer/NAMESPACE | 82 SeuratExplorer-0.1.6/SeuratExplorer/R/functions.R | 59 SeuratExplorer-0.1.6/SeuratExplorer/R/launch.R | 7 SeuratExplorer-0.1.6/SeuratExplorer/R/server.R | 863 +++-- SeuratExplorer-0.1.6/SeuratExplorer/R/ui.R | 1596 +++++++--- SeuratExplorer-0.1.6/SeuratExplorer/man/cellRatioPlot.Rd | 110 SeuratExplorer-0.1.6/SeuratExplorer/man/explorer_body_ui.Rd | 44 SeuratExplorer-0.1.6/SeuratExplorer/man/explorer_server.Rd | 50 SeuratExplorer-0.1.6/SeuratExplorer/man/explorer_sidebar_ui.Rd | 38 SeuratExplorer-0.1.6/SeuratExplorer/man/getColors.Rd | 48 SeuratExplorer-0.1.6/SeuratExplorer/man/get_counts_matrix.Rd | 38 SeuratExplorer-0.1.6/SeuratExplorer/man/get_data_matrix.Rd | 38 SeuratExplorer-0.1.6/SeuratExplorer/man/join_layers_if_needed.Rd | 38 SeuratExplorer-0.1.6/SeuratExplorer/man/launchSeuratExplorer.Rd | 62 SeuratExplorer-0.1.6/SeuratExplorer/man/prepare_gene_annotations.Rd | 44 SeuratExplorer-0.1.6/SeuratExplorer/man/server.Rd | 42 SeuratExplorer-0.1.6/SeuratExplorer/man/top_genes.Rd | 52 SeuratExplorer-0.1.6/SeuratExplorer/man/ui.Rd | 36 21 files changed, 2284 insertions(+), 1047 deletions(-)
More information about SeuratExplorer at CRAN
Permanent link
Title: Power Analyses using Monte Carlo Simulations
Description: Provides a general purpose simulation-based power analysis
API for routine and customized simulation experimental designs.
The package focuses exclusively on Monte Carlo simulation experiment variants of
(expected) prospective power analyses,
criterion analyses, compromise analyses, sensitivity analyses, and
a priori/post-hoc analyses. The default simulation experiment functions defined within the package
provide stochastic variants of the power analysis subroutines in
G*Power 3.1 (Faul, Erdfelder, Buchner, and Lang, 2009) <doi:10.3758/brm.41.4.1149>,
along with various other parametric and non-parametric power analysis
applications (e.g., mediation analyses) and support for Bayesian power analysis
by way of Bayes factors or posterior probability evaluations.
Additional functions for building
empirical power curves, reanalyzing simulation information, and
for increasing the precision of the resulting power
estimates are also included, each of which utilize similar API structures. [...truncated...]
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between Spower versions 0.6.3 dated 2026-05-21 and 0.6.4 dated 2026-06-17
DESCRIPTION | 8 - MD5 | 42 +++---- NAMESPACE | 1 R/Spower.R | 9 + inst/doc/SpowerIntro.R | 10 + inst/doc/SpowerIntro.Rmd | 14 ++ inst/doc/SpowerIntro.html | 36 +++--- inst/doc/SpowerIntro_logicals.html | 76 ++++++------- inst/doc/Spower_TypeSM.R | 3 inst/doc/Spower_TypeSM.Rmd | 23 ++-- inst/doc/Spower_TypeSM.html | 39 +++--- inst/doc/gpower_examples.R | 8 - inst/doc/gpower_examples.Rmd | 26 ++-- inst/doc/gpower_examples.html | 209 +++++++++++++++++++------------------ inst/gpower.rds |binary inst/intro.rds |binary inst/intro2.rds |binary inst/intro3.rds |binary tests/testthat/test-Spower.R | 42 +++++++ vignettes/SpowerIntro.Rmd | 14 ++ vignettes/Spower_TypeSM.Rmd | 23 ++-- vignettes/gpower_examples.Rmd | 26 ++-- 22 files changed, 361 insertions(+), 248 deletions(-)
Title: Automated Construction of R Data Packages from REDCap Projects
Description: Export all data, including metadata, from a REDCap (Research
Electronic Data Capture) Project via the REDCap API
<https://projectredcap.org/wp-content/resources/REDCapTechnicalOverview.pdf>.
The exported (meta)data will be processed and formatted into a stand-alone R
data package which can be installed and shared between researchers. Several
default reports are generated as vignettes in the resulting package.
Author: Peter DeWitt [aut, cre]
Maintainer: Peter DeWitt <peter.dewitt@cuanschutz.edu>
Diff between REDCapExporter versions 0.3.4 dated 2026-03-09 and 0.3.5 dated 2026-06-17
DESCRIPTION | 17 ++--- MD5 | 68 ++++++++++---------- NEWS.md | 29 +++++++- R/REDCapExporter-package.R | 3 R/build_r_data_package.R | 14 ++-- R/datasets.R | 8 +- R/keyring.R | 2 R/write.R | 11 +-- build/vignette.rds |binary data/avs_raw_core.rda |binary data/avs_raw_core_json.rda |binary data/avs_raw_metadata.rda |binary data/avs_raw_metadata_json.rda |binary data/avs_raw_project.rda |binary data/avs_raw_project_json.rda |binary data/avs_raw_record.rda |binary data/avs_raw_record_json.rda |binary data/avs_raw_user.rda |binary data/avs_raw_user_json.rda |binary inst/doc/api.Rmd | 34 +++++----- inst/doc/api.html | 73 ++++++++++----------- inst/doc/formatting.Rmd | 12 +-- inst/doc/formatting.html | 18 ++--- inst/doc/redcap2package.R | 9 ++ inst/doc/redcap2package.Rmd | 26 ++++--- inst/doc/redcap2package.html | 139 ++++++++++++++++++----------------------- man/REDCapExporter-package.Rd | 8 ++ man/REDCapExporter_keyring.Rd | 2 man/build_r_data_package.Rd | 8 +- man/example_data.Rd | 8 +- man/write_description_file.Rd | 8 +- tests/test-build_r_pkg.R | 10 +- vignettes/api.Rmd | 34 +++++----- vignettes/formatting.Rmd | 12 +-- vignettes/redcap2package.Rmd | 26 ++++--- 35 files changed, 307 insertions(+), 272 deletions(-)
More information about REDCapExporter at CRAN
Permanent link
Title: R Interface to the 'Uno' Nonlinear Optimization Solver
Description: Bindings to 'Uno' (Unifying Nonlinear Optimization), a C++ solver
for smooth nonlinearly constrained optimization. 'Uno' unifies Lagrange-Newton
methods, including sequential quadratic programming and interior-point
methods, by decomposing them into interacting building blocks
(constraint-relaxation, inequality-handling, Hessian, and globalization
strategies) that can be freely combined, either through options or through
presets that reproduce established solvers such as 'filterSQP' and 'IPOPT'.
The framework is described in Vanaret and Leyffer (2024)
<doi:10.48550/arXiv.2406.13454>.
Author: Balasubramanian Narasimhan [aut, cre],
Charlie Vanaret [aut, cph] ,
Sven Leyffer [aut, cph] ,
HiGHS development team [cph] ; see
inst/COPYRIGHTS)
Maintainer: Balasubramanian Narasimhan <naras@stanford.edu>
Diff between Uno versions 2.7.3-1 dated 2026-06-11 and 2.7.4 dated 2026-06-17
DESCRIPTION | 8 MD5 | 115 +++++----- NEWS.md | 22 + configure | 2 configure.win | 35 ++- inst/build_uno.sh | 10 inst/doc/Uno.html | 2 inst/tinytest/test_uno_solve.R | 36 ++- inst/uno/CMakeLists.txt | 8 inst/uno/README.md | 2 inst/uno/docs/developers/checklists.md | 5 inst/uno/docs/figures/logo.png |binary inst/uno/docs/options.md | 1 inst/uno/interfaces/AMPL/AMPLModel.cpp | 65 ++--- inst/uno/interfaces/AMPL/AMPLModel.hpp | 22 - inst/uno/interfaces/AMPL/README.md | 2 inst/uno/interfaces/AMPL/uno_ampl.cpp | 72 +++--- inst/uno/interfaces/C/README.md | 4 inst/uno/interfaces/C/Uno_C_API.cpp | 12 - inst/uno/interfaces/C/Uno_C_API.h | 5 inst/uno/interfaces/C/example/example_hs015.c | 5 inst/uno/interfaces/Fortran/README.md | 8 inst/uno/interfaces/Fortran/example_uno.f90 | 5 inst/uno/interfaces/Fortran/uno_c.f90 | 14 + inst/uno/interfaces/Fortran/uno_fortran.f90 | 77 +++--- inst/uno/pyproject.toml | 2 inst/uno/uno/Uno.cpp | 4 inst/uno/uno/ingredients/con_relax/relaxed_problems/ElasticVariables.cpp | 5 inst/uno/uno/ingredients/con_relax/relaxed_problems/l1RelaxedProblem.hpp | 6 inst/uno/uno/ingredients/hessian_models/qn/inverse/InverseLBFGSHessian.cpp | 17 - inst/uno/uno/ingredients/ineq/ipm/barrier_problems/PrimalDualInteriorPointProblem.hpp | 6 inst/uno/uno/ingredients/subproblem/Subproblem.hpp | 4 inst/uno/uno/ingredients/subproblem_solvers/BQPD/BQPDSolver.cpp | 7 inst/uno/uno/ingredients/subproblem_solvers/HiGHS/HiGHSSolver.hpp | 2 inst/uno/uno/ingredients/subproblem_solvers/MUMPS/MUMPSSolver.hpp | 2 inst/uno/uno/ingredients/subproblem_solvers/SSIDS/SSIDSSolver.hpp | 2 inst/uno/uno/linear_algebra/Vector.hpp | 44 +++ inst/uno/uno/linear_algebra/VectorView.hpp | 4 inst/uno/uno/model/FixedBoundsConstraintsModel.cpp | 4 inst/uno/uno/model/FixedBoundsConstraintsModel.hpp | 6 inst/uno/uno/model/HomogeneousEqualityConstrainedModel.cpp | 4 inst/uno/uno/model/HomogeneousEqualityConstrainedModel.hpp | 5 inst/uno/uno/optimization/OptimizationProblem.hpp | 5 inst/uno/uno/optimization/Result.hpp | 1 inst/uno/uno/options/Options.cpp | 3 inst/uno/uno/symbolic/IntegerRange.hpp |only inst/uno/uno/symbolic/Inverse.hpp | 4 inst/uno/uno/symbolic/Multiplication.hpp | 8 inst/uno/uno/symbolic/Range.hpp | 107 +++++---- inst/uno/uno/symbolic/ScalarMultiple.hpp | 10 inst/uno/uno/symbolic/Subtraction.hpp | 9 inst/uno/uno/symbolic/Sum.hpp | 8 inst/uno/uno/symbolic/Transpose.hpp | 4 inst/uno/uno/symbolic/Triangular.hpp | 16 - inst/uno/uno/symbolic/symbolic_traits.hpp | 17 + inst/uno/uno_default.opt | 2 inst/uno/unotest/unit_tests/ConcatenationTests.cpp | 8 src/dmumps_shim.c | 26 +- src/uno_binding.cpp | 8 59 files changed, 526 insertions(+), 371 deletions(-)
Title: "Node+Edge Betweenness Community Detection Algorithm for
'igraph' Objects"
Description: Implements the "Node + Edge Betweenness" community detection
algorithm for network analysis using 'igraph' objects. This algorithm
combines node degree and betweenness centrality measures to identify
communities within networks, with a gradient evident in social
partitioning. The package provides functions for implementation of the
algorithm, visualization, and analysis of the resulting community
structure along with the original dataset used in the publication.
Methods are based on results from Smith, Pittman and Xu (2026)
<doi:10.1002/cjs.70060>.
Author: Benjamin Smith [aut, cre] ,
Tyler Pittman [aut] ,
Wei Xu [aut]
Maintainer: Benjamin Smith <benyamin.smith@mail.utoronto.ca>
Diff between ig.degree.betweenness versions 0.2.0 dated 2025-06-24 and 0.2.1 dated 2026-06-17
DESCRIPTION | 67 ++++------ MD5 | 39 +++--- NAMESPACE | 50 ++++--- R/cluster_degree_betweenness.R | 10 - R/degree_balance.R |only R/ig.degree.betweenness-package.R |only R/lcd_graphs.R |only R/oncology_network.R | 36 ++--- R/plot_node_degrees.R | 222 +++++++++++++++++------------------ R/plot_simplified_edgeplot.R | 5 R/prep_unlabeled_graph.R | 4 R/zzz.R | 2 build |only inst/CITATION | 47 +++++-- man/cluster_degree_betweenness.Rd | 105 ++++++++-------- man/degree_balance.Rd |only man/figures |only man/ig.degree.betweenness-package.Rd |only man/lcd_graphs.Rd |only man/oncology_network.Rd | 8 - man/plot_node_degrees.Rd | 18 +- man/plot_simplified_edgeplot.Rd | 3 man/prep_unlabeled_graph.Rd | 3 23 files changed, 324 insertions(+), 295 deletions(-)
More information about ig.degree.betweenness at CRAN
Permanent link
Title: General Linear Blend Frequency Polygon Density Estimation
Description: Implements nonparametric density estimation with Averaged Shifted
Histogram (ASH), Linear Blend Frequency Polygon (LBFP), and General Linear
Blend Frequency Polygon (GLBFP) estimators. The package provides pointwise
and grid-based estimation workflows, sparse-prefix grid-count computation,
plotting helpers, and plug-in bandwidth selection. Methodological
background follows Scott (1992) <doi:10.1002/9780470316849>, Terrell and
Scott (1985) <doi:10.1080/01621459.1985.10477163>, and Carbon and
Duchesne (2024) <doi:10.1007/s10463-023-00883-5>.
Author: Aurelien Nicosia [aut, cre],
Thierry Duchesne [aut],
Michel Carbon [aut]
Maintainer: Aurelien Nicosia <aurelien.nicosia@mat.ulaval.ca>
Diff between GLBFP versions 0.5.1 dated 2026-06-16 and 0.5.2 dated 2026-06-17
DESCRIPTION | 26 MD5 | 16 NEWS.md | 4 inst/CITATION | 6 inst/doc/GLBFP_validation.html | 48 inst/doc/two-dimensional-density.R | 6 inst/doc/two-dimensional-density.Rmd | 8 inst/doc/two-dimensional-density.html | 1892 ---------------------------------- vignettes/two-dimensional-density.Rmd | 8 9 files changed, 72 insertions(+), 1942 deletions(-)
Title: Ebrahim-Farrington Goodness-of-Fit Test for Logistic Regression
Description: Implements the Ebrahim-Farrington goodness-of-fit test for logistic
regression models, particularly effective for sparse data and binary outcomes.
This test provides an improved alternative to the traditional Hosmer-Lemeshow
test by using a modified Pearson chi-square statistic with data-dependent
grouping. The test is based on Farrington (1996) theoretical framework but
simplified for practical implementation with binary data. Includes functions
for both the original Farrington test (for grouped data) and the new
Ebrahim-Farrington test (for binary data with automatic grouping), the
Directed Ebrahim-Farrington (DEF) test that targets calibration-shape
departures, and an ensemble that combines the DEF bases via the Cauchy
combination test. Also provides 'run.all.gof()', which runs a battery of
classical and modern goodness-of-fit and calibration tests (including
McCullagh, Osius-Rojek, le Cessie-van Houwelingen, Stute-Zhu, and the GiViTI
calibration test) in one call. For more details [...truncated...]
Author: Ebrahim Khaled Ebrahim [aut, cre]
Maintainer: Ebrahim Khaled Ebrahim <ebrahimkhaled@alexu.edu.eg>
Diff between ebrahim.gof versions 2.0.0 dated 2026-06-12 and 2.1.0 dated 2026-06-17
DESCRIPTION | 15 - MD5 | 28 +- NAMESPACE | 17 + NEWS.md | 56 +++++ R/cdef_gof.R |only R/run_all_gof.R | 319 ++++++++++++++++++++++++++++----- inst/WORDLIST | 131 ++++++------- inst/doc/ebrahim-farrington-intro.R | 2 inst/doc/ebrahim-farrington-intro.Rmd | 5 inst/doc/ebrahim-farrington-intro.html | 98 +++++----- man/cdef.gof.Rd |only man/deploy.gof.Rd |only man/gof.features.Rd |only man/plot.gof_battery.Rd |only man/print.gof_battery.Rd |only man/run.all.gof.Rd | 63 ++++-- tests/testthat/test-run-all-gof.R | 25 +- vignettes/ebrahim-farrington-intro.Rmd | 5 18 files changed, 557 insertions(+), 207 deletions(-)
Title: A 'dplyr' Back End for Databases
Description: A 'dplyr' back end for databases that allows you to work with
remote database tables as if they are in-memory data frames. Basic
features work with any database that has a 'DBI' back end; more
advanced features require 'SQL' translation to be provided by the
package author.
Author: Hadley Wickham [aut, cre],
Maximilian Girlich [aut],
Edgar Ruiz [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between dbplyr versions 2.5.2 dated 2026-02-13 and 2.6.0 dated 2026-06-17
dbplyr-2.5.2/dbplyr/R/build-sql.R |only dbplyr-2.5.2/dbplyr/R/db-escape.R |only dbplyr-2.5.2/dbplyr/R/explain.R |only dbplyr-2.5.2/dbplyr/R/lazy-join-query.R |only dbplyr-2.5.2/dbplyr/R/lazy-query.R |only dbplyr-2.5.2/dbplyr/R/lazy-select-query.R |only dbplyr-2.5.2/dbplyr/R/lazy-set-op-query.R |only dbplyr-2.5.2/dbplyr/R/pillar.R |only dbplyr-2.5.2/dbplyr/R/reexport.R |only dbplyr-2.5.2/dbplyr/R/simulate.R |only dbplyr-2.5.2/dbplyr/R/sql-expr.R |only dbplyr-2.5.2/dbplyr/R/test-frame.R |only dbplyr-2.5.2/dbplyr/R/testthat.R |only dbplyr-2.5.2/dbplyr/R/translate-sql-paste.R |only dbplyr-2.5.2/dbplyr/R/translate-sql-quantile.R |only dbplyr-2.5.2/dbplyr/inst/doc/backend-2.R |only dbplyr-2.5.2/dbplyr/inst/doc/backend-2.Rmd |only dbplyr-2.5.2/dbplyr/inst/doc/backend-2.html |only dbplyr-2.5.2/dbplyr/inst/doc/sql.R |only dbplyr-2.5.2/dbplyr/inst/doc/sql.Rmd |only dbplyr-2.5.2/dbplyr/inst/doc/sql.html |only dbplyr-2.5.2/dbplyr/man/db-quote.Rd |only dbplyr-2.5.2/dbplyr/man/memdb_frame.Rd |only dbplyr-2.5.2/dbplyr/man/reexports.Rd |only dbplyr-2.5.2/dbplyr/man/simulate_dbi.Rd |only dbplyr-2.5.2/dbplyr/man/testing.Rd |only dbplyr-2.5.2/dbplyr/man/win_over.Rd |only dbplyr-2.5.2/dbplyr/tests/testthat/_snaps/build-sql.md |only dbplyr-2.5.2/dbplyr/tests/testthat/_snaps/lazy-join-query.md |only dbplyr-2.5.2/dbplyr/tests/testthat/_snaps/lazy-select-query.md |only dbplyr-2.5.2/dbplyr/tests/testthat/_snaps/pillar.md |only dbplyr-2.5.2/dbplyr/tests/testthat/_snaps/tidyeval.md |only dbplyr-2.5.2/dbplyr/tests/testthat/_snaps/translate-sql-quantile.md |only dbplyr-2.5.2/dbplyr/tests/testthat/test-build-sql.R |only dbplyr-2.5.2/dbplyr/tests/testthat/test-db-escape.R |only dbplyr-2.5.2/dbplyr/tests/testthat/test-lazy-join-query.R |only dbplyr-2.5.2/dbplyr/tests/testthat/test-lazy-select-query.R |only dbplyr-2.5.2/dbplyr/tests/testthat/test-pillar.R |only dbplyr-2.5.2/dbplyr/tests/testthat/test-sql-expr.R |only dbplyr-2.5.2/dbplyr/tests/testthat/test-translate-sql-paste.R |only dbplyr-2.5.2/dbplyr/tests/testthat/test-translate-sql-quantile.R |only dbplyr-2.5.2/dbplyr/vignettes/backend-2.Rmd |only dbplyr-2.5.2/dbplyr/vignettes/sql.Rmd |only dbplyr-2.6.0/dbplyr/DESCRIPTION | 71 dbplyr-2.6.0/dbplyr/MD5 | 717 +++---- dbplyr-2.6.0/dbplyr/NAMESPACE | 439 ++-- dbplyr-2.6.0/dbplyr/NEWS.md | 129 + dbplyr-2.6.0/dbplyr/R/backend-.R | 476 +++- dbplyr-2.6.0/dbplyr/R/backend-access.R | 247 +- dbplyr-2.6.0/dbplyr/R/backend-adbc.R |only dbplyr-2.6.0/dbplyr/R/backend-db2.R |only dbplyr-2.6.0/dbplyr/R/backend-hana.R | 49 dbplyr-2.6.0/dbplyr/R/backend-hive.R | 89 dbplyr-2.6.0/dbplyr/R/backend-impala.R | 64 dbplyr-2.6.0/dbplyr/R/backend-jdbc.R |only dbplyr-2.6.0/dbplyr/R/backend-mssql.R | 914 ++++++--- dbplyr-2.6.0/dbplyr/R/backend-mysql.R | 275 +- dbplyr-2.6.0/dbplyr/R/backend-odbc.R | 57 dbplyr-2.6.0/dbplyr/R/backend-oracle.R | 358 ++- dbplyr-2.6.0/dbplyr/R/backend-postgres-old.R | 62 dbplyr-2.6.0/dbplyr/R/backend-postgres.R | 430 ++-- dbplyr-2.6.0/dbplyr/R/backend-redshift.R | 145 - dbplyr-2.6.0/dbplyr/R/backend-snowflake.R | 273 +- dbplyr-2.6.0/dbplyr/R/backend-spark-sql.R | 231 +- dbplyr-2.6.0/dbplyr/R/backend-sqlite.R | 165 + dbplyr-2.6.0/dbplyr/R/backend-teradata.R | 338 +-- dbplyr-2.6.0/dbplyr/R/backward-compatibility.R |only dbplyr-2.6.0/dbplyr/R/bind-queries.R |only dbplyr-2.6.0/dbplyr/R/data-cache.R | 18 dbplyr-2.6.0/dbplyr/R/data-lahman.R | 11 dbplyr-2.6.0/dbplyr/R/data-nycflights13.R | 33 dbplyr-2.6.0/dbplyr/R/db-io.R | 206 +- dbplyr-2.6.0/dbplyr/R/db-sql.R | 957 +++------- dbplyr-2.6.0/dbplyr/R/db.R | 126 - dbplyr-2.6.0/dbplyr/R/dbplyr.R | 2 dbplyr-2.6.0/dbplyr/R/escape.R | 244 +- dbplyr-2.6.0/dbplyr/R/ident.R | 42 dbplyr-2.6.0/dbplyr/R/import-standalone-obj-type.R | 2 dbplyr-2.6.0/dbplyr/R/join-by-compat.R | 75 dbplyr-2.6.0/dbplyr/R/join-cols-compat.R | 55 dbplyr-2.6.0/dbplyr/R/lazy-ops.R | 112 - dbplyr-2.6.0/dbplyr/R/memdb.R | 92 dbplyr-2.6.0/dbplyr/R/optimise-utils.R | 20 dbplyr-2.6.0/dbplyr/R/progress.R | 40 dbplyr-2.6.0/dbplyr/R/query-base.R |only dbplyr-2.6.0/dbplyr/R/query-join.R | 506 +++-- dbplyr-2.6.0/dbplyr/R/query-rf-join.R |only dbplyr-2.6.0/dbplyr/R/query-select.R | 428 +++- dbplyr-2.6.0/dbplyr/R/query-semi-join.R | 220 +- dbplyr-2.6.0/dbplyr/R/query-set-op.R | 174 - dbplyr-2.6.0/dbplyr/R/query-union.R |only dbplyr-2.6.0/dbplyr/R/query.R | 51 dbplyr-2.6.0/dbplyr/R/remote.R | 87 dbplyr-2.6.0/dbplyr/R/rows.R | 243 +- dbplyr-2.6.0/dbplyr/R/schema.R | 54 dbplyr-2.6.0/dbplyr/R/sql-build.R | 93 dbplyr-2.6.0/dbplyr/R/sql-clause.R | 139 - dbplyr-2.6.0/dbplyr/R/sql-dialect.R |only dbplyr-2.6.0/dbplyr/R/sql-glue.R |only dbplyr-2.6.0/dbplyr/R/sql-quote.R |only dbplyr-2.6.0/dbplyr/R/sql-superseded.R |only dbplyr-2.6.0/dbplyr/R/sql.R | 56 dbplyr-2.6.0/dbplyr/R/src-sql.R | 43 dbplyr-2.6.0/dbplyr/R/src_dbi.R | 121 - dbplyr-2.6.0/dbplyr/R/table-name.R | 73 dbplyr-2.6.0/dbplyr/R/tbl-lazy.R | 20 dbplyr-2.6.0/dbplyr/R/tbl-sql.R | 137 - dbplyr-2.6.0/dbplyr/R/tidyeval-across.R | 236 +- dbplyr-2.6.0/dbplyr/R/tidyeval.R | 181 + dbplyr-2.6.0/dbplyr/R/translate-sql-aggregate.R |only dbplyr-2.6.0/dbplyr/R/translate-sql-conditional.R | 87 dbplyr-2.6.0/dbplyr/R/translate-sql-cut.R | 32 dbplyr-2.6.0/dbplyr/R/translate-sql-helpers.R | 359 --- dbplyr-2.6.0/dbplyr/R/translate-sql-scalar.R |only dbplyr-2.6.0/dbplyr/R/translate-sql-string.R | 192 +- dbplyr-2.6.0/dbplyr/R/translate-sql-window.R | 251 +- dbplyr-2.6.0/dbplyr/R/translate-sql.R | 157 - 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dbplyr-2.6.0/dbplyr/tests/testthat/test-backend-.R | 215 +- dbplyr-2.6.0/dbplyr/tests/testthat/test-backend-access.R | 134 - dbplyr-2.6.0/dbplyr/tests/testthat/test-backend-adbc.R |only dbplyr-2.6.0/dbplyr/tests/testthat/test-backend-db2.R |only dbplyr-2.6.0/dbplyr/tests/testthat/test-backend-hana.R | 26 dbplyr-2.6.0/dbplyr/tests/testthat/test-backend-hive.R | 30 dbplyr-2.6.0/dbplyr/tests/testthat/test-backend-impala.R | 26 dbplyr-2.6.0/dbplyr/tests/testthat/test-backend-jdbc.R |only dbplyr-2.6.0/dbplyr/tests/testthat/test-backend-mssql.R | 678 ++++--- dbplyr-2.6.0/dbplyr/tests/testthat/test-backend-mysql.R | 175 - dbplyr-2.6.0/dbplyr/tests/testthat/test-backend-odbc.R | 33 dbplyr-2.6.0/dbplyr/tests/testthat/test-backend-oracle.R | 168 + dbplyr-2.6.0/dbplyr/tests/testthat/test-backend-postgres-old.R | 12 dbplyr-2.6.0/dbplyr/tests/testthat/test-backend-postgres.R | 413 ++-- dbplyr-2.6.0/dbplyr/tests/testthat/test-backend-redshift.R | 189 + dbplyr-2.6.0/dbplyr/tests/testthat/test-backend-snowflake.R | 509 ++++- dbplyr-2.6.0/dbplyr/tests/testthat/test-backend-spark-sql.R | 90 dbplyr-2.6.0/dbplyr/tests/testthat/test-backend-sqlite.R | 137 - dbplyr-2.6.0/dbplyr/tests/testthat/test-backend-teradata.R | 163 + dbplyr-2.6.0/dbplyr/tests/testthat/test-bind-queries.R |only dbplyr-2.6.0/dbplyr/tests/testthat/test-db-io.R | 25 dbplyr-2.6.0/dbplyr/tests/testthat/test-db-sql.R | 51 dbplyr-2.6.0/dbplyr/tests/testthat/test-db.R |only dbplyr-2.6.0/dbplyr/tests/testthat/test-escape.R | 119 - dbplyr-2.6.0/dbplyr/tests/testthat/test-ident.R | 13 dbplyr-2.6.0/dbplyr/tests/testthat/test-join-by-compat.R |only dbplyr-2.6.0/dbplyr/tests/testthat/test-memdb.R |only dbplyr-2.6.0/dbplyr/tests/testthat/test-query-join.R | 155 - dbplyr-2.6.0/dbplyr/tests/testthat/test-query-rf-join.R |only dbplyr-2.6.0/dbplyr/tests/testthat/test-query-select.R | 67 dbplyr-2.6.0/dbplyr/tests/testthat/test-query-semi-join.R | 49 dbplyr-2.6.0/dbplyr/tests/testthat/test-query-set-op.R | 26 dbplyr-2.6.0/dbplyr/tests/testthat/test-query-union.R |only dbplyr-2.6.0/dbplyr/tests/testthat/test-query.R |only dbplyr-2.6.0/dbplyr/tests/testthat/test-remote.R | 109 - dbplyr-2.6.0/dbplyr/tests/testthat/test-rows.R | 484 +++-- dbplyr-2.6.0/dbplyr/tests/testthat/test-schema.R | 26 dbplyr-2.6.0/dbplyr/tests/testthat/test-sql-build.R | 6 dbplyr-2.6.0/dbplyr/tests/testthat/test-sql-clause.R |only dbplyr-2.6.0/dbplyr/tests/testthat/test-sql-dialect.R |only dbplyr-2.6.0/dbplyr/tests/testthat/test-sql-glue.R |only dbplyr-2.6.0/dbplyr/tests/testthat/test-sql-quote.R |only dbplyr-2.6.0/dbplyr/tests/testthat/test-sql-superseded.R |only dbplyr-2.6.0/dbplyr/tests/testthat/test-sql.R | 30 dbplyr-2.6.0/dbplyr/tests/testthat/test-src_dbi.R | 15 dbplyr-2.6.0/dbplyr/tests/testthat/test-table-name.R | 34 dbplyr-2.6.0/dbplyr/tests/testthat/test-tbl-lazy.R | 20 dbplyr-2.6.0/dbplyr/tests/testthat/test-tbl-sql.R | 66 dbplyr-2.6.0/dbplyr/tests/testthat/test-tidyeval-across.R | 266 +- dbplyr-2.6.0/dbplyr/tests/testthat/test-tidyeval.R | 42 dbplyr-2.6.0/dbplyr/tests/testthat/test-translate-sql-aggregate.R |only dbplyr-2.6.0/dbplyr/tests/testthat/test-translate-sql-conditional.R | 325 ++- dbplyr-2.6.0/dbplyr/tests/testthat/test-translate-sql-cut.R | 176 - 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dbplyr-2.6.0/dbplyr/tests/testthat/test-verb-filter.R | 385 ++-- dbplyr-2.6.0/dbplyr/tests/testthat/test-verb-group_by.R | 98 - dbplyr-2.6.0/dbplyr/tests/testthat/test-verb-head.R | 30 dbplyr-2.6.0/dbplyr/tests/testthat/test-verb-joins.R | 844 +++++--- dbplyr-2.6.0/dbplyr/tests/testthat/test-verb-mutate.R | 391 ++-- dbplyr-2.6.0/dbplyr/tests/testthat/test-verb-pivot-longer.R | 125 - dbplyr-2.6.0/dbplyr/tests/testthat/test-verb-pivot-wider.R | 268 +- dbplyr-2.6.0/dbplyr/tests/testthat/test-verb-pull.R | 33 dbplyr-2.6.0/dbplyr/tests/testthat/test-verb-select.R | 333 +-- dbplyr-2.6.0/dbplyr/tests/testthat/test-verb-set-ops.R | 170 - dbplyr-2.6.0/dbplyr/tests/testthat/test-verb-slice.R | 120 - dbplyr-2.6.0/dbplyr/tests/testthat/test-verb-summarise.R | 197 +- dbplyr-2.6.0/dbplyr/tests/testthat/test-verb-uncount.R | 45 dbplyr-2.6.0/dbplyr/tests/testthat/test-verb-window.R | 34 dbplyr-2.6.0/dbplyr/tests/testthat/test-with-dialect.R |only dbplyr-2.6.0/dbplyr/vignettes/dbplyr.Rmd | 95 dbplyr-2.6.0/dbplyr/vignettes/new-backend.Rmd | 234 ++ dbplyr-2.6.0/dbplyr/vignettes/reprex.Rmd | 31 dbplyr-2.6.0/dbplyr/vignettes/setup/_mysql.Rmd | 17 dbplyr-2.6.0/dbplyr/vignettes/setup/_postgres.Rmd | 9 dbplyr-2.6.0/dbplyr/vignettes/translation-function.Rmd | 339 ++- dbplyr-2.6.0/dbplyr/vignettes/translation-verb.Rmd | 77 424 files changed, 19982 insertions(+), 14173 deletions(-)
Title: Global and Local Admixture Inference in Polyploids
Description: Provides functions to perform global (genome-wide) and local admixture inference
from bi- and multi-allelic marker dosages (discrete or continuous) in polyploid species.
Author: Simon Rio [aut, cre] ,
Tristan Mary-Huard [aut] ,
Franck Gauthier [aut]
Maintainer: Simon Rio <simon.rio@cirad.fr>
Diff between AdmixPoly versions 1.0.0 dated 2026-06-08 and 1.0.1 dated 2026-06-17
DESCRIPTION | 9 MD5 | 38 +- R/AdmixGlobal.R | 4 R/AdmixLocal.R | 43 +- R/RcppExports.R | 4 R/ReadHPA.R | 18 - R/ReadVCF.R | 15 - R/SimulatePop.R | 27 - inst/doc/AdmixPoly-vignette.html | 14 man/AdmixLocal.Rd | 8 src/AdmixGlobal.cpp | 308 ++++++++++++--------- src/AdmixLocal.cpp | 560 ++++++++++++++++++++------------------- src/AdmixPoly_types.h | 34 -- src/AdmixUtils.h | 388 +++++++++++++-------------- src/RcppExports.cpp | 19 - src/ReadFile.cpp | 221 ++++++++++----- src/SimulatePop.cpp | 199 ++++++++----- tests |only 18 files changed, 1056 insertions(+), 853 deletions(-)
Title: Ordered Panel
Description: The ordered panel methodology (Zezulinski et al 2025 <doi:10.1159/000545366>) provides a structured framework for identifying and organizing sets of biomarkers, such as genetic variants, that distinguish between positive and negative subjects in a study when only a training cohort is available. This approach is particularly useful in situations where an independent validation cohort does not yet exist, rendering conventional performance metrics such as the receiver operating characteristic (ROC) curve and area under the ROC curve (AUC) inappropriate or potentially misleading. The methodology emphasizes transparent construction and evaluation of ordered signatures of biomarkers, allowing investigators to examine operating characteristics without establishing predictive performance.
Author: Tingting Zhan [aut, cre] ,
Aejaz Sayeed [dtc]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between ordPanel versions 0.1.1 dated 2026-03-19 and 0.1.2 dated 2026-06-17
DESCRIPTION | 20 +++++++++++--------- MD5 | 6 +++--- build/partial.rdb |binary man/ordPanel-package.Rd | 6 ++++++ 4 files changed, 20 insertions(+), 12 deletions(-)
Title: Functional Guilds, Invasion Status, Endemism, and Rarity of Ants
Description: Provides functions for the analysis of ant communities, aiming to
standardize workflows in myrmecology. The package automates the assignment
of species to functional guilds based on trophic strategies, feeding
habits, and foraging behavior, using established classification frameworks
(Silva et al., 2015 <doi:10.7476/9788574554419>; Silvestre et al., 2003
<isbn:9588151236>; Delabie et al., 2000
<https://www.researchgate.net/publication/44961742_Sampling_Ground-Dwelling_Ants_Case_Studies_from_the_World%27s_Rain_Forests>),
and also includes a novel classification system implemented within the
package, developed from ant species occurring in urban environments.
It also includes routines to flag exotic species of Brazil (Vieira, 2025,
unpublished master's thesis), identify endemic species (Silva et al., 2025
<doi:10.37885/250920259>), and classify species rarity and rarity forms
of the Atlantic Forest (Silva et al., 2024 <doi:10.1016/j.biocon.2024.110640>).
The [...truncated...]
Author: Debora C. O. Goncalves [aut, cre],
Nathalia S. Silva [aut],
Rony P. S. Almeida [aut],
Livia P. Prado [aut],
Maria S. C. Morini [aut]
Maintainer: Debora C. O. Goncalves <debora_cog@outlook.com>
Diff between AntClassify versions 0.2.1 dated 2026-05-07 and 0.2.2 dated 2026-06-17
DESCRIPTION | 8 MD5 | 22 NAMESPACE | 2 R/antclassify.R | 18 R/antclassify_community.R | 91 ++-- R/assign_guild_ants.R | 91 +--- R/check_endemic_atlantic_ants.R | 62 +- R/check_exotic_ants.R | 65 +- R/check_rarity_atlantic_ants.R | 67 +-- inst/doc/antclassify_workflow.html | 819 ++++++++++++++++--------------------- man/antclassify.Rd | 12 man/antclassify_community.Rd | 8 12 files changed, 606 insertions(+), 659 deletions(-)
Title: Survey Instrument Workflows
Description: Supports survey research workflows built around a typed
instrument object (the sframe). Features include visual instrument
design via a browser-based builder or 'Shiny' studio, export to a
self-contained static HTML survey, an embeddable 'Shiny' module, SHA-256
integrity-checked serialisation to the '.sframe' format, multi-page survey
rendering, branching logic, response quality checking, scale scoring,
psychometric diagnostics, analysis-plan execution, model syntax planning,
an interactive response dashboard, codebook generation, and reproducible
HTML reporting.
Author: Mohammed Ali Sharafuddin [aut, cre]
Maintainer: Mohammed Ali Sharafuddin <mohammedali.page@gmail.com>
Diff between surveyframe versions 0.3.1 dated 2026-06-02 and 0.3.2 dated 2026-06-17
DESCRIPTION | 10 MD5 | 121 +- NAMESPACE | 18 NEWS.md | 54 + R/analysis_plan.R | 45 R/dashboard.R | 62 - R/google_sheets.R | 91 -- R/launch_studio.R | 2 R/model_layer.R | 16 R/psychometrics.R | 15 R/render_survey.R | 10 R/reporting.R | 137 ++- R/sf_branch.R | 2 R/sf_component_methods.R |only R/statistics_reports.R | 10 R/studio_builder.R | 20 R/survey_module.R | 4 build/vignette.rds |binary inst/CITATION | 16 inst/builder/survey_builder.html | 961 +++++++++++++++++++-- inst/doc/analysing-survey-responses.R | 46 - inst/doc/analysing-survey-responses.Rmd | 63 + inst/doc/analysing-survey-responses.html | 989 ++++++++++----------- inst/doc/deploying-and-collecting.R |only inst/doc/deploying-and-collecting.Rmd |only inst/doc/deploying-and-collecting.html |only inst/doc/efa-cfa-sem-pls-syntax.Rmd | 11 inst/doc/efa-cfa-sem-pls-syntax.html | 13 inst/doc/scale-reliability-validity.R | 23 inst/doc/scale-reliability-validity.Rmd | 36 inst/doc/scale-reliability-validity.html | 287 ++++-- inst/doc/surveybuilder-gui-overview.Rmd | 14 inst/doc/surveybuilder-gui-overview.html | 19 inst/doc/surveyframe.R | 96 +- inst/doc/surveyframe.Rmd | 167 +++ inst/doc/surveyframe.html | 1045 +++++++++++++++++++---- inst/extdata/surveyframe_input_types_demo.sframe | 991 ++++++++++++++++----- inst/extdata/tourism_services_demo.sframe | 710 +++++++++++++++ inst/shiny/app.R | 769 ++++++++++------ inst/shiny/dashboard/app.R | 9 inst/static_survey/collector_template.gs |only inst/static_survey/template.html | 45 inst/templates/report.qmd | 115 ++ man/format.sf_branch.Rd |only man/format.sf_check.Rd |only man/format.sf_choices.Rd |only man/format.sf_item.Rd |only man/format.sf_model.Rd |only man/format.sf_scale.Rd |only man/launch_dashboard.Rd | 26 man/launch_studio.Rd | 2 man/print.sf_branch.Rd |only man/print.sf_check.Rd |only man/print.sf_choices.Rd |only man/print.sf_item.Rd |only man/print.sf_model.Rd |only man/print.sf_scale.Rd |only man/render_survey.Rd | 10 man/sf_branch.Rd | 2 man/sframe_builder_validate_draft.Rd | 6 man/summary.sf_branch.Rd |only man/summary.sf_check.Rd |only man/summary.sf_choices.Rd |only man/summary.sf_item.Rd |only man/summary.sf_model.Rd |only man/summary.sf_scale.Rd |only man/survey_module_ui.Rd | 2 tests/testthat/test-component-methods.R |only vignettes/analysing-survey-responses.Rmd | 63 + vignettes/deploying-and-collecting.Rmd |only vignettes/efa-cfa-sem-pls-syntax.Rmd | 11 vignettes/scale-reliability-validity.Rmd | 36 vignettes/surveybuilder-gui-overview.Rmd | 14 vignettes/surveyframe.Rmd | 167 +++ 74 files changed, 5647 insertions(+), 1734 deletions(-)
Title: Principal Coordinates of Phylogenetic Structure
Description: Set of functions for analysis of Principal Coordinates of Phylogenetic Structure (PCPS).
Author: Vanderlei Julio Debastiani [aut, cre]
Maintainer: Vanderlei Julio Debastiani <vanderleidebastiani@yahoo.com.br>
Diff between PCPS versions 1.0.8 dated 2025-08-23 and 1.0.9 dated 2026-06-17
PCPS-1.0.8/PCPS/R/FUN.ADONIS.R |only PCPS-1.0.9/PCPS/DESCRIPTION | 19 +++-- PCPS-1.0.9/PCPS/MD5 | 16 ++-- PCPS-1.0.9/PCPS/NAMESPACE | 4 - PCPS-1.0.9/PCPS/R/FUN.ADONIS2.global.R |only PCPS-1.0.9/PCPS/R/FUN.ADONIS2.margin.R |only PCPS-1.0.9/PCPS/R/globals.R |only PCPS-1.0.9/PCPS/R/pcps.sig.R | 80 ++---------------------- PCPS-1.0.9/PCPS/R/select.pcpsmethod.R | 31 ++++----- PCPS-1.0.9/PCPS/man/pcps.sig.Rd | 102 ++++++++----------------------- PCPS-1.0.9/PCPS/man/select.pcpsmethod.Rd | 6 - 11 files changed, 76 insertions(+), 182 deletions(-)
Title: Information-Based Stability and Synchrony Measures
Description: Provides functions to compute a continuum of information-based measures for quantifying the temporal stability of populations, communities, and ecosystems, as well as their associated synchrony, based on species (or species assemblage) biomass, or other key variables. When biodiversity data are available, the package also enables the assessment of the corresponding diversity–stability and diversity–synchrony relationships. All measures are applicable in both temporal and spatial contexts. The theoretical and methodological background is detailed in Chao et al. (2025)
<doi:10.1101/2025.08.20.671203>.
Author: Anne Chao [aut, cre],
Yu-Ti Lee [aut],
Keng-Lei Lin [aut],
Po-Yen Chuang [aut]
Maintainer: Anne Chao <chao@stat.nthu.edu.tw>
Diff between iSTAY versions 1.0.0 dated 2025-10-28 and 1.1.0 dated 2026-06-17
iSTAY-1.0.0/iSTAY/data/Data_Jena_76_metapopulations.rda |only iSTAY-1.0.0/iSTAY/man/Data_Jena_76_metapopulations.Rd |only iSTAY-1.0.0/iSTAY/man/iStay_package.Rd |only iSTAY-1.1.0/iSTAY/DESCRIPTION | 37 iSTAY-1.1.0/iSTAY/MD5 | 34 iSTAY-1.1.0/iSTAY/R/Main_Function.R | 973 ++++++-- iSTAY-1.1.0/iSTAY/data/Data_Jena_76_community_populations.rda |only iSTAY-1.1.0/iSTAY/inst/doc/iStay.R | 397 ++- iSTAY-1.1.0/iSTAY/inst/doc/iStay.Rmd | 573 +++-- iSTAY-1.1.0/iSTAY/inst/doc/iStay.html | 1100 +++++----- iSTAY-1.1.0/iSTAY/man/Data_Jena_20_metacommunities.Rd | 2 iSTAY-1.1.0/iSTAY/man/Data_Jena_462_populations.Rd | 4 iSTAY-1.1.0/iSTAY/man/Data_Jena_76_community_populations.Rd |only iSTAY-1.1.0/iSTAY/man/Data_Jena_hierarchical_structure.Rd | 5 iSTAY-1.1.0/iSTAY/man/ggiSTAY_analysis.Rd | 198 + iSTAY-1.1.0/iSTAY/man/ggiSTAY_qprofile.Rd | 116 - iSTAY-1.1.0/iSTAY/man/iSTAY_Hier.Rd | 4 iSTAY-1.1.0/iSTAY/man/iSTAY_Multiple.Rd | 61 iSTAY-1.1.0/iSTAY/man/iSTAY_Single.Rd | 26 iSTAY-1.1.0/iSTAY/man/iSTAY_package.Rd |only iSTAY-1.1.0/iSTAY/vignettes/iStay.Rmd | 573 +++-- 21 files changed, 2734 insertions(+), 1369 deletions(-)
Title: Parse Eye-Tracking Data into Fixations
Description: Eye-tracking data must be transformed into fixations and saccades before it can be analyzed. This package provides a non-parametric speed-based approach to do this on a trial basis. The method is especially useful when there are large differences in data quality, as the thresholds are adjusted accordingly. The same pre-processing procedure can be applied to all participants, while accounting for individual differences in data quality. The method is described in van Renswoude et al. (2018) <doi:10.3758/s13428-017-0909-3>.
Author: Ingmar Visser [aut, cre],
Daan van Renswoude [aut]
Maintainer: Ingmar Visser <i.visser@uva.nl>
This is a re-admission after prior archival of version 1.3 dated 2020-02-09
Diff between gazepath versions 1.3 dated 2020-02-09 and 1.4 dated 2026-06-17
DESCRIPTION | 23 +++++++++++------------ MD5 | 36 +++++++++++++++++++----------------- NEWS |only R/Eyelink.R | 4 ++-- R/GazePath.R | 10 +++++----- R/Interpolate.R | 4 ++-- R/Mould_vel.R | 2 +- R/Tobii.R | 4 ++-- R/comhull.R | 2 +- R/complete.R | 2 +- R/fixationANDsaccade.R | 4 ++-- R/plot.gazepath.R | 2 +- R/pnt.in.poly.R | 10 +++++----- R/summary.gazepath.R | 2 +- build |only data/eye_dat.RData |binary data/screen.RData |binary man/GUI.Rd | 4 +++- man/GazePath.Rd | 4 +++- man/gazepath-package.Rd | 14 ++++++++------ 20 files changed, 67 insertions(+), 60 deletions(-)
Title: Genetic Association Analysis
Description: This is a companion to Henry-Stewart talk by Zhao (2026, <doi:10.69645/FRFQ9519>),
which gathers information, metadata and scripts to showcase modern genetic analysis -- ranging from testing
of polymorphic variant(s) for Hardy-Weinberg equilibrium, association with traits using genetic and statistical
models, Bayesian implementation, power calculation in study design, and genetic annotation. It also covers
R integration with the Linux environment, GitHub, package creation and web applications. The earlier version
by Zhao (2009, <doi:10.69645/DCRY5578>) provides a brief introduction to these topics.
Author: Jing Hua Zhao [aut, cre] ,
Benjamin Altmann [ctb],
Brian Ripley [ctb]
Maintainer: Jing Hua Zhao <jinghuazhao@hotmail.com>
Diff between gaawr2 versions 0.0.7 dated 2026-03-10 and 0.0.8 dated 2026-06-17
gaawr2-0.0.7/gaawr2/inst/doc/index.html |only gaawr2-0.0.7/gaawr2/inst/scripts/cran.sh |only gaawr2-0.0.8/gaawr2/DESCRIPTION | 18 gaawr2-0.0.8/gaawr2/MD5 | 33 gaawr2-0.0.8/gaawr2/NEWS.md | 8 gaawr2-0.0.8/gaawr2/build/partial.rdb |binary gaawr2-0.0.8/gaawr2/build/vignette.rds |only gaawr2-0.0.8/gaawr2/data/DiaHealth.rda |binary gaawr2-0.0.8/gaawr2/data/diabetes.rda |binary gaawr2-0.0.8/gaawr2/inst/doc/gaawr2.R | 305 - gaawr2-0.0.8/gaawr2/inst/doc/gaawr2.Rmd | 572 --- gaawr2-0.0.8/gaawr2/inst/doc/gaawr2.html | 5749 ------------------------------- gaawr2-0.0.8/gaawr2/inst/doc/web.R | 146 gaawr2-0.0.8/gaawr2/inst/doc/web.Rmd | 320 - gaawr2-0.0.8/gaawr2/inst/doc/web.html | 1550 -------- gaawr2-0.0.8/gaawr2/man/DiaHealth.Rd | 2 gaawr2-0.0.8/gaawr2/man/diabetes.Rd | 2 gaawr2-0.0.8/gaawr2/man/gaawr2.Rd | 2 gaawr2-0.0.8/gaawr2/vignettes |only 19 files changed, 102 insertions(+), 8605 deletions(-)
Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services
<https://aws.amazon.com>. The functions handle building, signing, and
sending requests, and receiving responses. They are designed to help build
higher-level interfaces to individual services, such as Simple Storage
Service (S3).
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.common versions 0.8.9 dated 2026-02-17 and 0.8.10 dated 2026-06-17
DESCRIPTION | 8 +++---- MD5 | 32 ++++++++++++++--------------- NEWS.md | 7 ++++++ R/credential_providers.R | 5 +++- R/credentials.R | 12 +++++++--- R/handlers_restjson.R | 24 +++++---------------- R/signer_bearer.R | 11 ++++++++- R/signer_v1.R | 2 - R/signer_v4.R | 12 ++++++++++ man/locate_credentials.Rd | 4 ++- man/new_handlers.Rd | 10 ++++----- man/new_operation.Rd | 10 ++++----- man/new_request.Rd | 10 ++++----- man/new_service.Rd | 10 ++++----- man/send_request.Rd | 10 ++++----- src/populate.cpp | 2 - tests/testthat/test_credential_providers.R | 10 +++++++++ 17 files changed, 106 insertions(+), 73 deletions(-)
Title: Methods and Classes for the OMOP Common Data Model
Description: Provides definitions of core classes and methods used by analytic
pipelines that query the OMOP (Observational Medical Outcomes Partnership)
common data model.
Author: Marti Catala [aut, cre] ,
Edward Burn [aut] ,
Mike Du [ctb] ,
Yuchen Guo [ctb] ,
Adam Black [ctb] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between omopgenerics versions 1.3.7 dated 2026-03-07 and 1.4.0 dated 2026-06-17
DESCRIPTION | 8 MD5 | 660 - NAMESPACE | 594 - NEWS.md | 45 R/OMOPGenerics-package.R | 24 R/addSettings.R | 156 R/arrange.R | 60 R/assert.R | 1751 ++-- R/casting.R | 184 R/cdmFromTables.R | 208 R/cdmSelect.R | 100 R/classAchillesTable.R | 271 R/classCdmReference.R | 2242 ++--- R/classCdmSource.R | 304 R/classCdmTable.R | 472 - R/classCodeSearch.R |only R/classCodelist.R | 602 - R/classCodelistWithDetails.R | 333 R/classCohortTable.R | 1583 ++-- R/classConceptSetExpression.R | 459 - R/classOmopTable.R | 285 R/classReadOnly.R |only R/classSummarisedResult.R | 2100 ++--- R/cohortCodelist.R | 352 R/cohortCount.R | 166 R/columns.R | 506 - R/combineStrata.R | 92 R/compute.R | 215 R/documentationHelpers.R |only R/exportCodelist.R | 142 R/exportCodelistWithDetails.R |only R/exportConceptSetExpression.R | 144 R/exportSummarisedResult.R | 431 - R/filter.R | 660 + R/importCodelist.R | 113 R/importCodelistWithDetails.R |only R/importConceptSetExpression.R | 258 R/importSummarisedResult.R | 178 R/indexes.R | 534 - R/logger.R | 816 +- R/methodAttrition.R | 172 R/methodBind.R | 734 - R/methodCdmDisconnect.R | 114 R/methodCdmTableFromSource.R | 76 R/methodDropSourceTable.R | 175 R/methodDropTable.R | 66 R/methodInsertCdmTo.R | 79 R/methodInsertFromSource.R | 88 R/methodInsertTable.R | 179 R/methodListSourceTables.R | 87 R/methodReadSourceTable.R | 140 R/methodSettings.R | 242 R/methodSuppress.R | 474 - R/methodTidy.R | 184 R/omopDataFolder.R | 92 R/overwriteClasses.R | 860 +- R/pivot.R | 221 R/recordCohortAttrition.R | 293 R/resultType.R |only R/split.R | 628 - R/summary.R | 972 +- R/sysdata.rda |binary R/unite.R | 477 - R/utilities.R | 866 +- R/validate.R | 2336 +++--- README.md | 628 - build/vignette.rds |binary inst/Instructions.xlsx |only inst/WORDLIST | 92 inst/cohorts_for_mock/oa_desc.json | 176 inst/cohorts_for_mock/oa_no_desc.json | 174 inst/concepts_for_mock/oa_desc.json | 24 inst/concepts_for_mock/oa_no_desc.json | 24 inst/doc/cdm_reference.R | 54 inst/doc/cdm_reference.Rmd | 200 inst/doc/cdm_reference.html | 1187 +-- inst/doc/codelists.R | 156 inst/doc/codelists.Rmd | 207 inst/doc/codelists.html | 912 +- inst/doc/cohorts.R | 224 inst/doc/cohorts.Rmd | 444 - inst/doc/cohorts.html | 1324 +-- inst/doc/expanding_omopgenerics.R | 284 inst/doc/expanding_omopgenerics.Rmd | 598 - inst/doc/expanding_omopgenerics.html | 1318 +-- inst/doc/logging.R | 190 inst/doc/logging.Rmd | 276 inst/doc/logging.html | 1083 +- inst/doc/reexport.R | 12 inst/doc/reexport.Rmd | 202 inst/doc/reexport.html | 683 - inst/doc/summarised_result.R | 472 - inst/doc/summarised_result.Rmd | 898 +- inst/doc/summarised_result.html | 8686 +++++++++++------------ inst/doc/suppression.R | 94 inst/doc/suppression.Rmd | 190 inst/doc/suppression.html | 1019 +- inst/not_all_concept_sets/acetaminophen.json | 24 inst/not_all_concept_sets/cohort_def.json | 5706 +++++++-------- inst/not_all_concept_sets/influenza.json | 24 man/achillesColumns.Rd | 60 man/achillesTables.Rd | 48 man/addSettings.Rd | 102 man/additionalColumns.Rd | 96 man/assertCharacter.Rd | 89 man/assertChoice.Rd | 87 man/assertClass.Rd | 83 man/assertDate.Rd | 87 man/assertDoc.Rd |only man/assertList.Rd | 87 man/assertLogical.Rd | 81 man/assertNumeric.Rd | 99 man/assertTable.Rd | 95 man/assertTrue.Rd | 52 man/attrition.Rd | 34 man/attrition.cohort_table.Rd | 94 man/bind.Rd | 34 man/bind.cohort_table.Rd | 118 man/bind.summarised_result.Rd | 100 man/cash-.cdm_reference.Rd | 86 man/cash-set-.cdm_reference.Rd | 88 man/castDoc.Rd |only man/cdmAssignTableDoc.Rd |only man/cdmClasses.Rd | 34 man/cdmDisconnect.Rd | 76 man/cdmDoc.Rd |only man/cdmFromTables.Rd | 93 man/cdmIndexDoc.Rd |only man/cdmName.Rd | 93 man/cdmNameDoc.Rd |only man/cdmOrTableDoc.Rd |only man/cdmReference.Rd | 82 man/cdmSelect.Rd | 54 man/cdmSource.Rd | 88 man/cdmSourceType.Rd | 84 man/cdmTableDoc.Rd |only man/cdmTableFromSource.Rd | 50 man/cdmVersion.Rd | 84 man/cdmVersionArgumentDoc.Rd |only man/checkCohortRequirements.Rd | 86 man/cliCallDoc.Rd |only man/codelistDoc.Rd |only man/codelistWithDetailsDoc.Rd |only man/cohortCodelist.Rd | 148 man/cohortColumns.Rd | 54 man/cohortCount.Rd | 102 man/cohortDoc.Rd |only man/cohortTables.Rd | 50 man/cohortValidationChecksDoc.Rd |only man/collect.cdm_reference.Rd | 86 man/collect.cohort_table.Rd | 38 man/combineStrata.Rd | 54 man/compareOmopTableFields.Rd |only man/compute.cdm_table.Rd | 71 man/conceptCdmDoc.Rd |only man/conceptSetExpressionDoc.Rd |only man/createIndexes.Rd | 38 man/createLogFile.Rd | 70 man/createTableIndex.Rd | 38 man/dropSourceTable.Rd | 40 man/dropTable.Rd | 44 man/emptyAchillesTable.Rd | 52 man/emptyCdmReference.Rd | 51 man/emptyCodeSearch.Rd |only man/emptyCodelist.Rd | 36 man/emptyCodelistWithDetails.Rd | 36 man/emptyCohortTable.Rd | 98 man/emptyConceptSetExpression.Rd | 36 man/emptyDoc.Rd |only man/emptyOmopTable.Rd | 84 man/emptySummarisedResult.Rd | 48 man/emptyTableNameDoc.Rd |only man/estimateTypeChoices.Rd | 42 man/existingIndexes.Rd | 40 man/expectedIndexes.Rd | 40 man/exportCodeSearch.Rd |only man/exportCodelist.Rd | 44 man/exportCodelistWithDetails.Rd |only man/exportConceptSetExpression.Rd | 44 man/exportFileDoc.Rd |only man/exportSummarisedResult.Rd | 72 man/figures/lifecycle-deprecated.svg | 42 man/figures/lifecycle-experimental.svg | 42 man/figures/lifecycle-stable.svg | 58 man/figures/lifecycle-superseded.svg | 42 man/filterAdditional.Rd | 96 man/filterGroup.Rd | 96 man/filterResult.Rd |only man/filterSettings.Rd | 102 man/filterStrata.Rd | 96 man/getCohortId.Rd | 40 man/getCohortName.Rd | 40 man/getPersonIdentifier.Rd | 46 man/groupColumns.Rd | 94 man/importCodeSearch.Rd |only man/importCodelist.Rd | 43 man/importCodelistWithDetails.Rd |only man/importConceptSetExpression.Rd | 43 man/importFileDoc.Rd |only man/importSummarisedResult.Rd | 46 man/insertCdmTo.Rd | 42 man/insertFromSource.Rd | 44 man/insertTable.Rd | 100 man/isResultSuppressed.Rd | 80 man/isTableEmpty.Rd | 34 man/listSourceTables.Rd | 34 man/logMessage.Rd | 82 man/newAchillesTable.Rd | 42 man/newCdmReference.Rd | 99 man/newCdmSource.Rd | 38 man/newCdmTable.Rd | 42 man/newCodeSearch.Rd |only man/newCodelist.Rd | 37 man/newCodelistWithDetails.Rd | 39 man/newCohortTable.Rd | 144 man/newConceptSetExpression.Rd | 39 man/newLocalSource.Rd | 42 man/newOmopTable.Rd | 42 man/newReadOnlySource.Rd |only man/newSummarisedResult.Rd | 136 man/numberRecords.Rd | 72 man/numberSubjects.Rd | 72 man/omopCdmVersionDoc.Rd |only man/omopColumns.Rd | 72 man/omopDataFolder.Rd | 52 man/omopTableFields.Rd | 34 man/omopTables.Rd | 50 man/omopgenerics-package.Rd | 72 man/overwriteDoc.Rd |only man/pivotEstimates.Rd | 102 man/print.cdm_reference.Rd | 84 man/print.code_search.Rd |only man/print.codelist.Rd | 50 man/print.codelist_with_details.Rd | 56 man/print.concept_set_expression.Rd | 74 man/readSourceTable.Rd | 39 man/recordCohortAttrition.Rd | 124 man/recursiveDoc.Rd |only man/reexports.Rd | 38 man/resultColumns.Rd | 46 man/resultPackageVersion.Rd | 34 man/resultType.Rd |only man/searchStrategy.Rd |only man/settings.Rd | 34 man/settings.cohort_table.Rd | 106 man/settings.summarised_result.Rd | 96 man/settingsColumns.Rd | 98 man/sourceType.Rd | 34 man/splitAdditional.Rd | 106 man/splitAll.Rd | 110 man/splitGroup.Rd | 106 man/splitStrata.Rd | 108 man/statusIndexes.Rd | 42 man/strataColumns.Rd | 94 man/sub-sub-.cdm_reference.Rd | 86 man/sub-subset-.cdm_reference.Rd | 42 man/summariseLogFile.Rd | 84 man/summarisedResultDoc.Rd |only man/summary.cdm_reference.Rd | 82 man/summary.cdm_source.Rd | 46 man/summary.cohort_table.Rd | 92 man/summary.summarised_result.Rd | 86 man/suppress.Rd | 38 man/suppress.summarised_result.Rd | 120 man/tableName.Rd | 82 man/tableSource.Rd | 82 man/tidy.summarised_result.Rd | 106 man/tidyColumns.Rd | 96 man/tmpPrefix.Rd | 40 man/toSnakeCase.Rd | 46 man/transformToSummarisedResult.Rd | 108 man/uniqueId.Rd | 46 man/uniqueTableName.Rd | 42 man/uniteAdditional.Rd | 80 man/uniteGroup.Rd | 70 man/uniteStrata.Rd | 70 man/unusedDotsDoc.Rd |only man/validateAchillesTable.Rd | 63 man/validateAgeGroupArgument.Rd | 95 man/validateCdmArgument.Rd | 139 man/validateCdmTable.Rd | 53 man/validateCohortArgument.Rd | 163 man/validateCohortIdArgument.Rd | 137 man/validateColumn.Rd | 92 man/validateConceptSetArgument.Rd | 86 man/validateNameArgument.Rd | 89 man/validateNameLevel.Rd | 62 man/validateNameStyle.Rd | 105 man/validateNewColumn.Rd | 76 man/validateOmopTable.Rd | 63 man/validateResultArgument.Rd | 123 man/validateStrataArgument.Rd | 71 man/validateWindowArgument.Rd | 74 man/validationDoc.Rd |only tests/testthat.R | 24 tests/testthat/_snaps/utilities.md | 46 tests/testthat/setup.R | 360 tests/testthat/test-addSettings.R | 104 tests/testthat/test-assert.R | 768 +- tests/testthat/test-casting.R | 60 tests/testthat/test-cdmFromTables.R | 346 tests/testthat/test-cdmSelect.R | 20 tests/testthat/test-classCdmReference.R | 193 tests/testthat/test-classCdmSource.R | 120 tests/testthat/test-classCodeSearch.R |only tests/testthat/test-classCodelist.R | 206 tests/testthat/test-classCodelistWithDetails.R | 208 tests/testthat/test-classCohortTable.R | 1142 +-- tests/testthat/test-classConceptSetExpression.R | 382 - tests/testthat/test-classLocalSource.R | 14 tests/testthat/test-classReadOnly.R |only tests/testthat/test-classSummarisedResult.R | 993 +- tests/testthat/test-cohortCodelist.R | 418 - tests/testthat/test-columns.R | 148 tests/testthat/test-combineStrata.R | 54 tests/testthat/test-emptyObjects.R | 140 tests/testthat/test-exportCodelist.R | 104 tests/testthat/test-exportCodelistWithDetails.R |only tests/testthat/test-exportConceptSetExpression.R | 132 tests/testthat/test-exportSummarisedResult.R | 208 tests/testthat/test-filter.R | 434 - tests/testthat/test-importCodelist.R | 236 tests/testthat/test-importCodelistWithDetails.R |only tests/testthat/test-importConceptSetExpression.R | 382 - tests/testthat/test-importSummarisedResult.R | 321 tests/testthat/test-indexes.R |only tests/testthat/test-logger.R | 138 tests/testthat/test-methodBind.R | 564 - tests/testthat/test-methodCdmDisconnect.R | 36 tests/testthat/test-methodComputeTable.R | 56 tests/testthat/test-methodDropSourceTable.R | 234 tests/testthat/test-methodGetCdmSource.R | 6 tests/testthat/test-methodInsertFromSource.R | 38 tests/testthat/test-methodInsertTable.R | 34 tests/testthat/test-methodListSourceTables.R | 13 tests/testthat/test-methodReadSourceTable.R | 147 tests/testthat/test-methodSummary.R | 256 tests/testthat/test-methodSuppress.R | 510 - tests/testthat/test-methodTidy.R | 156 tests/testthat/test-omopDataFolder.R | 18 tests/testthat/test-overwriteClasses.R | 162 tests/testthat/test-pivot.R | 52 tests/testthat/test-prefix.R | 60 tests/testthat/test-recordCohortAttrition.R | 388 - tests/testthat/test-split.R | 297 tests/testthat/test-unite.R | 169 tests/testthat/test-utilities.R | 592 - tests/testthat/test-validate.R | 1030 +- vignettes/cdm_reference.Rmd | 200 vignettes/codelists.Rmd | 207 vignettes/cohorts.Rmd | 444 - vignettes/expanding_omopgenerics.Rmd | 598 - vignettes/logging.Rmd | 276 vignettes/reexport.Rmd | 202 vignettes/summarised_result.Rmd | 898 +- vignettes/suppression.Rmd | 190 356 files changed, 41637 insertions(+), 39167 deletions(-)
Title: Methods for Visualization of Computer Experiments Design and
Surrogate
Description: View 2D/3D sections, contour plots, mesh of excursion sets for computer experiments designs, surrogates or test functions.
Author: Yann Richet [aut, cre] ,
Yves Deville [aut],
Clement Chevalier [ctb]
Maintainer: Yann Richet <yann.richet@asnr.fr>
Diff between DiceView versions 3.2 dated 2026-05-19 and 4.0 dated 2026-06-17
DESCRIPTION | 13 +++++++------ MD5 | 31 +++++++++++++++++-------------- NAMESPACE | 9 +++++++++ R/Utils.R | 41 +++++++++++++++++++++++++++++++++-------- R/function.R | 4 ++-- R/mesh_set.R | 2 +- R/optim.R | 6 +++--- R/parview.R |only R/root.R | 4 ++-- man/Apply.function.Rd | 9 +-------- man/Vectorize.function.Rd | 8 +------- man/contourview.Rd | 2 -- man/filledcontourview.Rd | 2 -- man/parview.Rd |only man/roots.Rd | 2 +- man/safe_mclapply.Rd |only man/sectionview.Rd | 4 ---- man/sectionview3d.Rd | 2 -- 18 files changed, 77 insertions(+), 62 deletions(-)
Title: Necessary Condition Analysis
Description: Performs a Necessary Condition Analysis (NCA). (Dul, J. 2016. Necessary Condition Analysis (NCA). ''Logic and Methodology of 'Necessary but not Sufficient' causality." Organizational Research Methods 19(1), 10-52) <doi:10.1177/1094428115584005>.
NCA identifies necessary (but not sufficient) conditions in datasets, where x causes (e.g. precedes) y. Instead of drawing a regression line ''through the middle of the data'' in an xy-plot, NCA draws the ceiling line. The ceiling line y = f(x) separates the area with observations from the area without observations.
(Nearly) all observations are below the ceiling line: y <= f(x). The empty zone is in the upper left hand corner of the xy-plot (with the convention that the x-axis is ''horizontal'' and the y-axis is ''vertical'' and that values increase ''upwards'' and ''to the right''). The ceiling line is a (piecewise) linear non-decreasing line: a linear step function or a straight line. It indicates which level of x (e.g., an effort, [...truncated...]
Author: Jan Dul [aut],
Govert Buijs [cre]
Maintainer: Govert Buijs <buijs@rsm.nl>
Diff between NCA versions 5.0.1 dated 2026-04-28 and 5.0.2 dated 2026-06-17
DESCRIPTION | 8 +++---- MD5 | 26 +++++++++++----------- NEWS.md | 11 +++++++++ R/nca_difference.R | 57 ++++++++++++++++++++++++++++++-------------------- R/nca_normalize.R | 12 +++++++--- R/nca_plots.R | 2 - R/nca_power.R | 6 ++--- R/p_purity_helpers.R | 10 +++++--- R/p_purity_sql.R | 4 +-- R/p_scope.R | 8 +++---- R/p_utils.R | 18 ++++++++++++--- build/partial.rdb |binary man/NCA-package.Rd | 4 +-- man/nca_difference.Rd | 32 ++++++++++++++++++++-------- 14 files changed, 126 insertions(+), 72 deletions(-)
Title: Administrative Boundaries and Static Map Tiles for Spain
Description: Administrative boundaries of Spain at several levels
(Autonomous Communities and Cities, provinces, municipalities and
'NUTS'), based on 'GISCO' from 'Eurostat'
<https://ec.europa.eu/eurostat/web/gisco> and 'CartoBase ANE' from
'Instituto Geográfico Nacional' <https://www.ign.es/>. Includes tools
to download and process static map tiles and a 'leaflet' plugin for
Spanish public administration tile providers.
Author: Diego Hernangomez [aut, cre, cph] ,
Eurostat [cph] ,
Instituto Geografico Nacional [cph] ,
Francisco J. Goerlich [ctb]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between mapSpain versions 1.1.0 dated 2026-03-26 and 1.2.0 dated 2026-06-17
DESCRIPTION | 37 MD5 | 363 +++--- NAMESPACE | 106 - NEWS.md | 271 ++-- R/addProviderEspTiles.R | 344 +++--- R/data.R | 494 ++++----- R/esp-cache.R | 721 ++++++------- R/esp-check-access.R | 146 -- R/esp-dict.R | 655 ++++++------ R/esp-get-attributions.R | 48 R/esp-get-can-box.R | 359 +++--- R/esp-get-capimun.R | 303 ++--- R/esp-get-ccaa-siane.R | 358 +++--- R/esp-get-ccaa.R | 276 ++--- R/esp-get-comarca.R | 124 -- R/esp-get-countries-siane.R | 194 +-- R/esp-get-grid-BDN.R | 90 - R/esp-get-grid-EEA.R | 86 - R/esp-get-grid-ESDAC.R | 162 +- R/esp-get-grid-MTN.R | 270 ++-- R/esp-get-gridmap.R | 58 - R/esp-get-hydrobasin.R | 230 +--- R/esp-get-hypsobath.R | 294 ++--- R/esp-get-landwater.R | 596 ++++------ R/esp-get-munic-siane.R | 336 ++---- R/esp-get-munic.R | 423 +++---- R/esp-get-nuts.R | 435 ++++---- R/esp-get-prov-siane.R | 277 +---- R/esp-get-prov.R | 285 ++--- R/esp-get-railway.R | 272 ++--- R/esp-get-roads.R | 232 +--- R/esp-get-simpl.R | 292 ++--- R/esp-get-spain-siane.R | 120 +- R/esp-get-spain.R | 163 +-- R/esp-get-stations.R | 77 - R/esp-get-tiles.R | 1050 ++++++++++--------- R/esp-make-provider.R | 227 ++-- R/esp-move-can.R | 312 ++--- R/esp-siane-bulk-download.R | 158 +- R/mapSpain-package.R | 17 R/sysdata.rda |binary R/utils-convert-names.R | 672 +++++------- R/utils-country.R | 15 R/utils-dict.R | 371 ++++-- R/utils-get-tiles.R | 439 +++----- R/utils-sf.R | 486 +++++--- R/utils-slippy.R | 184 +-- R/utils-url.R | 325 ++--- R/utils.R | 207 ++- README.md | 96 - build/partial.rdb |binary build/vignette.rds |binary data/esp_codelist.rda |binary data/esp_nuts_2024.rda |binary data/esp_tiles_providers.rda |binary data/pobmun25.rda |binary inst/CITATION | 34 inst/COPYRIGHTS | 156 +- inst/WORDLIST | 59 - inst/doc/imagery.html | 15 inst/doc/imagery.qmd | 10 inst/doc/mapSpain.html | 165 +-- inst/doc/mapSpain.qmd | 144 +- inst/schemaorg.json | 10 man/addProviderEspTiles.Rd | 146 +- man/esp_check_access.Rd | 2 man/esp_clear_cache.Rd | 118 +- man/esp_codelist.Rd | 210 ++- man/esp_dict.Rd | 188 +-- man/esp_get_can_box.Rd | 226 ++-- man/esp_get_capimun.Rd | 358 +++--- man/esp_get_ccaa.Rd | 326 +++--- man/esp_get_ccaa_siane.Rd | 302 ++--- man/esp_get_comarca.Rd | 305 ++--- man/esp_get_countries_siane.Rd | 236 ++-- man/esp_get_grid_BDN.Rd | 214 +-- man/esp_get_grid_EEA.Rd | 91 - man/esp_get_grid_ESDAC.Rd | 135 +- man/esp_get_grid_MTN.Rd | 246 ++-- man/esp_get_gridmap.Rd | 221 ++-- man/esp_get_hydrobasin.Rd | 234 ++-- man/esp_get_hypsobath.Rd | 306 ++--- man/esp_get_landwater.Rd | 303 ++--- man/esp_get_munic.Rd | 357 +++--- man/esp_get_munic_siane.Rd | 382 +++---- man/esp_get_nuts.Rd | 413 +++---- man/esp_get_prov.Rd | 324 ++--- man/esp_get_prov_siane.Rd | 286 ++--- man/esp_get_railway.Rd | 246 ++-- man/esp_get_roads.Rd | 204 +-- man/esp_get_simpl.Rd | 209 +-- man/esp_get_spain.Rd | 242 ++-- man/esp_get_spain_siane.Rd | 246 ++-- man/esp_get_tiles.Rd | 375 +++--- man/esp_make_provider.Rd | 139 +- man/esp_move_can.Rd | 160 +- man/esp_nuts_2024.Rd | 156 +- man/esp_set_cache_dir.Rd | 220 ++-- man/esp_siane_bulk_download.Rd | 200 +-- man/esp_tiles_providers.Rd | 311 ++--- man/figures/README-tile-1.png |binary man/figures/lifecycle-deprecated.svg | 42 man/figures/lifecycle-experimental.svg | 42 man/figures/lifecycle-stable.svg | 58 - man/figures/lifecycle-superseded.svg | 42 man/mapSpain-package.Rd | 72 - man/pobmun25.Rd | 78 - man/roxygen/meta.R | 31 tests/testthat.R | 8 tests/testthat/_snaps/addProviderEspTiles.md | 2 tests/testthat/_snaps/esp-cache.md | 4 tests/testthat/_snaps/esp-dict.md | 12 tests/testthat/_snaps/esp-get-can-box.md | 6 tests/testthat/_snaps/esp-get-capimun.md | 2 tests/testthat/_snaps/esp-get-ccaa-siane.md | 4 tests/testthat/_snaps/esp-get-ccaa.md | 8 tests/testthat/_snaps/esp-get-comarca.md | 2 tests/testthat/_snaps/esp-get-countries-siane.md | 2 tests/testthat/_snaps/esp-get-grid-BDN.md | 8 tests/testthat/_snaps/esp-get-grid-EEA.md | 2 tests/testthat/_snaps/esp-get-gridmap.md | 2 tests/testthat/_snaps/esp-get-hydrobasin.md | 4 tests/testthat/_snaps/esp-get-landwater.md | 2 tests/testthat/_snaps/esp-get-munic-siane.md | 2 tests/testthat/_snaps/esp-get-munic.md | 2 tests/testthat/_snaps/esp-get-nuts.md | 16 tests/testthat/_snaps/esp-get-railway.md | 2 tests/testthat/_snaps/esp-get-simpl.md | 2 tests/testthat/_snaps/esp-get-tiles.md | 8 tests/testthat/_snaps/esp-move-can.md | 4 tests/testthat/_snaps/utils-convert-names.md | 10 tests/testthat/_snaps/utils-country.md | 10 tests/testthat/_snaps/utils-get-tiles.md | 2 tests/testthat/_snaps/utils-sf.md | 4 tests/testthat/_snaps/utils-url.md | 4 tests/testthat/_snaps/utils.md | 24 tests/testthat/helpers.R |only tests/testthat/test-addProviderEspTiles.R | 50 tests/testthat/test-esp-cache.R | 389 +++---- tests/testthat/test-esp-check-access.R | 44 tests/testthat/test-esp-dict.R | 184 +-- tests/testthat/test-esp-get-attributions.R | 42 tests/testthat/test-esp-get-can-box.R | 32 tests/testthat/test-esp-get-capimun.R | 294 ++--- tests/testthat/test-esp-get-ccaa-siane.R | 332 ++---- tests/testthat/test-esp-get-ccaa.R | 142 +- tests/testthat/test-esp-get-comarca.R | 201 +-- tests/testthat/test-esp-get-countries-siane.R | 247 ++-- tests/testthat/test-esp-get-grid-BDN.R | 206 +-- tests/testthat/test-esp-get-grid-EEA.R | 8 tests/testthat/test-esp-get-grid-ESDAC.R | 107 - tests/testthat/test-esp-get-grid-MTN.R | 104 - tests/testthat/test-esp-get-gridmap.R | 144 +- tests/testthat/test-esp-get-hydrobasin.R | 253 ++-- tests/testthat/test-esp-get-hypsobath.R | 225 +--- tests/testthat/test-esp-get-landwater.R | 440 +++----- tests/testthat/test-esp-get-munic-siane.R | 303 ++--- tests/testthat/test-esp-get-munic.R | 236 ++-- tests/testthat/test-esp-get-nuts.R | 526 ++++----- tests/testthat/test-esp-get-prov-siane.R | 353 +++--- tests/testthat/test-esp-get-prov.R | 162 +- tests/testthat/test-esp-get-railway.R | 213 +-- tests/testthat/test-esp-get-roads.R | 209 +-- tests/testthat/test-esp-get-simpl.R | 190 +-- tests/testthat/test-esp-get-spain-siane.R | 141 +- tests/testthat/test-esp-get-spain.R | 114 +- tests/testthat/test-esp-get-stations.R | 160 +- tests/testthat/test-esp-get-tiles.R | 1248 +++++++++++------------ tests/testthat/test-esp-make-provider.R | 110 +- tests/testthat/test-esp-move-can.R | 408 +++---- tests/testthat/test-esp-siane-bulk-download.R | 105 - tests/testthat/test-utils-convert-names.R | 489 ++++----- tests/testthat/test-utils-country.R | 100 - tests/testthat/test-utils-dict.R | 154 +- tests/testthat/test-utils-get-tiles.R | 576 +++++----- tests/testthat/test-utils-sf.R | 209 +-- tests/testthat/test-utils-url.R | 425 +++---- tests/testthat/test-utils.R | 386 +++---- vignettes/basic2-1.png |binary vignettes/basic3-1.png |binary vignettes/giscoR-1.png |binary vignettes/imagery.qmd | 10 vignettes/mapSpain.qmd | 144 +- 183 files changed, 16776 insertions(+), 17448 deletions(-)
Title: Conditional Mutual Information Estimation for Multi-Omics Data
Description: The biases introduced in association measures, particularly mutual information,
are influenced by factors such as tumor purity, mutation burden, and hypermethylation.
This package provides the estimation of conditional mutual information (CMI) and its
statistical significance with a focus on its application to multi-omics data. Utilizing
B-spline functions (inspired by Daub et al. (2004) <doi:10.1186/1471-2105-5-118>), the package offers tools to estimate the association between heterogeneous multi-
omics data, while removing the effects of confounding factors. This helps to unravel complex
biological interactions. In addition, it includes methods to evaluate the statistical significance
of these associations, providing a robust framework for multi-omics data integration and
analysis. This package is ideal for researchers in computational biology, bioinformatics,
and systems biology seeking a comprehensive tool for understanding interdependencies in
omics data.
Author: Gaojianyong Wang [aut, cre]
Maintainer: Gaojianyong Wang <gjywang@gmail.com>
Diff between conMItion versions 0.3.1 dated 2026-05-26 and 0.4.0 dated 2026-06-17
DESCRIPTION | 6 MD5 | 14 - R/ComputePermutation.R | 282 +++++++++++++++++++++++++++---- man/CMIBiCondimat2matPermu.Rd | 5 man/CMIBiCondimat2vecPermu.Rd | 5 man/CMImat2matPermu.Rd | 7 man/CMImat2vecPermu.Rd | 5 man/permute_within_bins.Rd |only man/permute_within_two_condition_bins.Rd |only 9 files changed, 282 insertions(+), 42 deletions(-)
Title: Generate Citation File Format ('CFF') Metadata for R Packages
Description: Citation File Format ('CFF') version 1.2.0
<doi:10.5281/zenodo.5171937> is a human- and machine-readable file
format for software citation metadata. Core utilities generate, read,
write and validate Citation File Format metadata for R packages.
Author: Diego Hernangomez [aut, cre, cph] ,
Joao Martins [rev] ,
Scott Chamberlain [rev]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between cffr versions 1.4.0 dated 2026-05-04 and 1.4.1 dated 2026-06-17
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cffr-1.4.1/cffr/R/utils-schema.R | 601 - cffr-1.4.1/cffr/R/utils.R | 91 cffr-1.4.1/cffr/R/zzz.R | 26 cffr-1.4.1/cffr/README.md | 174 cffr-1.4.1/cffr/inst/CITATION | 134 cffr-1.4.1/cffr/inst/REFERENCES.bib | 499 - cffr-1.4.1/cffr/inst/WORDLIST | 6 cffr-1.4.1/cffr/inst/bash/citation-cff-pre-commit.sh | 72 cffr-1.4.1/cffr/inst/doc/bibtex-cff.R | 69 cffr-1.4.1/cffr/inst/doc/bibtex-cff.html | 178 cffr-1.4.1/cffr/inst/doc/bibtex-cff.qmd | 294 cffr-1.4.1/cffr/inst/doc/cffr.R | 26 cffr-1.4.1/cffr/inst/doc/cffr.html | 82 cffr-1.4.1/cffr/inst/doc/cffr.qmd | 81 cffr-1.4.1/cffr/inst/doc/joss-paper.html | 22 cffr-1.4.1/cffr/inst/doc/joss-paper.qmd | 61 cffr-1.4.1/cffr/inst/doc/r-cff.R | 70 cffr-1.4.1/cffr/inst/doc/r-cff.html | 120 cffr-1.4.1/cffr/inst/doc/r-cff.qmd | 146 cffr-1.4.1/cffr/inst/examples/CITATION_auto | 50 cffr-1.4.1/cffr/inst/examples/CITATION_basic | 46 cffr-1.4.1/cffr/inst/examples/CITATION_basic.cff | 48 cffr-1.4.1/cffr/inst/examples/CITATION_dx_doi | 28 cffr-1.4.1/cffr/inst/examples/CITATION_error.cff | 38 cffr-1.4.1/cffr/inst/examples/CITATION_rmarkdown | 100 cffr-1.4.1/cffr/inst/examples/CITATION_skeleton.cff | 16 cffr-1.4.1/cffr/inst/examples/CITATION_surveillance | 56 cffr-1.4.1/cffr/inst/examples/DESCRIPTION_basic | 32 cffr-1.4.1/cffr/inst/examples/DESCRIPTION_basic_plain_authors | 26 cffr-1.4.1/cffr/inst/examples/DESCRIPTION_basicdate | 34 cffr-1.4.1/cffr/inst/examples/DESCRIPTION_bioconductor | 134 cffr-1.4.1/cffr/inst/examples/DESCRIPTION_codeberg | 84 cffr-1.4.1/cffr/inst/examples/DESCRIPTION_gitlab | 156 cffr-1.4.1/cffr/inst/examples/DESCRIPTION_many_persons | 84 cffr-1.4.1/cffr/inst/examples/DESCRIPTION_many_urls | 38 cffr-1.4.1/cffr/inst/examples/DESCRIPTION_no_URL | 152 cffr-1.4.1/cffr/inst/examples/DESCRIPTION_no_encoding | 34 cffr-1.4.1/cffr/inst/examples/DESCRIPTION_posit_package_manager | 62 cffr-1.4.1/cffr/inst/examples/DESCRIPTION_r_universe | 216 cffr-1.4.1/cffr/inst/examples/DESCRIPTION_rgeos | 86 cffr-1.4.1/cffr/inst/examples/DESCRIPTION_surveillance | 212 cffr-1.4.1/cffr/inst/examples/DESCRIPTION_two_emails | 74 cffr-1.4.1/cffr/inst/examples/DESCRIPTION_twomaintainers | 106 cffr-1.4.1/cffr/inst/examples/DESCRIPTION_wrong_urls | 70 cffr-1.4.1/cffr/inst/examples/example.bib | 52 cffr-1.4.1/cffr/inst/examples/preferred-citation-book-missing.cff | 34 cffr-1.4.1/cffr/inst/examples/preferred-citation-book.cff | 40 cffr-1.4.1/cffr/inst/examples/preferred-citation-conference-paper-2.cff | 74 cffr-1.4.1/cffr/inst/examples/preferred-citation-conference-paper-missing.cff | 56 cffr-1.4.1/cffr/inst/examples/preferred-citation-conference-paper.cff | 94 cffr-1.4.1/cffr/inst/examples/preferred-citation-manual.cff | 82 cffr-1.4.1/cffr/inst/examples/preferred-citation-no-month.cff | 28 cffr-1.4.1/cffr/inst/examples/preferred-citation-no-vol.cff | 60 cffr-1.4.1/cffr/inst/examples/preferred-citation-pamphlet.cff | 58 cffr-1.4.1/cffr/inst/examples/preferred-citation-report-no-affiliation.cff | 58 cffr-1.4.1/cffr/inst/examples/preferred-citation-report-no-institution.cff | 60 cffr-1.4.1/cffr/inst/examples/preferred-citation-report.cff | 64 cffr-1.4.1/cffr/inst/examples/preferred-citation-unpublished.cff | 60 cffr-1.4.1/cffr/inst/examples/reprozip.cff | 282 cffr-1.4.1/cffr/inst/examples/smith-et-al.cff | 58 cffr-1.4.1/cffr/inst/examples/tidyverse-joss-paper.cff | 58 cffr-1.4.1/cffr/inst/examples/tidyverse-software.cff | 28 cffr-1.4.1/cffr/inst/extdata/SPDX_License_List.csv | 740 - 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More information about SelfControlledCohort at CRAN
Permanent link
Title: Algorithms and Data Structures for Large Single-Cell Expression
Matrices
Description: Single-cell datasets are growing in size, posing challenges
as well as opportunities for genomics researchers. 'ondisc' is an R
package that facilitates analysis of large-scale single-cell data
out-of-core on a laptop or distributed across tens to hundreds of
processors on a cluster or cloud. In both of these settings, 'ondisc'
requires only a few gigabytes of memory, even if the input data are tens
of gigabytes in size. 'ondisc' mainly is oriented toward single-cell
CRISPR screen analysis, but also can be used for single-cell differential
expression and single-cell co-expression analyses. 'ondisc' is powered by
several new, efficient algorithms for manipulating and querying large,
sparse expression matrices.
Author: Timothy Barry [aut, cre] ,
Songcheng Dai [ctb],
Yixuan Qiu [ctb],
Eugene Katsevich [aut, ths]
Maintainer: Timothy Barry <tbarry@hsph.harvard.edu>
This is a re-admission after prior archival of version 1.0.0 dated 2021-03-05
Diff between ondisc versions 1.0.0 dated 2021-03-05 and 1.3.5 dated 2026-06-17
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Title: Co-Clustering of Mixed Type Data
Description: Implementation of the co-clustering method for mixed type data proposed in M. Selosse, J. Jacques, C. Biernacki (2018) <https://hal.science/hal-01893457>. It consists in clustering simultaneously the rows (observations) and the columns (features) of a heterogeneous data set.
Author: Margot Selosse [aut],
Julien Jacques [aut, cre],
Christophe Biernacki [aut]
Maintainer: Julien Jacques <julien.jacques@univ-lyon2.fr>
This is a re-admission after prior archival of version 1.0.2 dated 2021-03-29
Diff between mixedClust versions 1.0.2 dated 2021-03-29 and 1.0.2.1 dated 2026-06-17
DESCRIPTION | 29 - MD5 | 14 build/vignette.rds |binary inst/doc/mixedClustLite.html | 960 ++++++++++++++++++++++++------------------- man/mixedCoclust.Rd | 49 -- src/Bos.cpp | 48 +- src/GaussianMulti.cpp | 32 - src/Makevars | 1 8 files changed, 632 insertions(+), 501 deletions(-)
Title: Analysis of Geostatistical Data using Bayes and Empirical Bayes
Methods
Description: Functions to fit geostatistical data. The data can be
continuous, binary or count data and the models implemented are
flexible. Conjugate priors are assumed on some parameters while
inference on the other parameters can be done through a full
Bayesian analysis of by empirical Bayes methods.
Author: Evangelos Evangelou [aut, cre],
Vivekananda Roy [aut]
Maintainer: Evangelos Evangelou <e.evangelou@maths.bath.ac.uk>
Diff between geoBayes versions 0.7.6 dated 2026-05-14 and 0.7.7 dated 2026-06-17
DESCRIPTION | 8 +++---- MD5 | 6 ++--- NEWS | 3 ++ src/modelfcns_link.f90 | 53 ++++++++++++++++++++++++++++++------------------- 4 files changed, 43 insertions(+), 27 deletions(-)
Title: Distributed Online Covariance Matrix Tests
Description: Distributed Online Covariance Matrix Tests 'Docovt' is a powerful tool designed to efficiently process and analyze distributed datasets. It enables users to perform covariance matrix tests in an online, distributed manner, making it highly suitable for large-scale data analysis. By leveraging advanced computational techniques, 'Docovt' ensures robust and scalable solutions for statistical analysis, particularly in scenarios where data is dispersed across multiple nodes or sources. This package is ideal for researchers and practitioners working with high-dimensional data, providing a flexible and efficient framework for covariance matrix estimation and hypothesis testing. The philosophy of 'Docovt' is described in Guo G.(2025) <doi:10.1016/j.physa.2024.130308>.
Author: Guangbao Guo [aut, cre] ,
Congfan Zhang [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between Docovt versions 0.3 dated 2025-09-03 and 0.6 dated 2026-06-17
DESCRIPTION | 11 ++++++----- MD5 | 53 ++++++++++++++++++++++++++++++++++------------------- NAMESPACE | 17 ++++++++++++++--- R/CLX.R | 18 ++++++++++++++---- R/DCLX.R |only R/DLC.R |only R/DPEC.R |only R/DPECO.R |only R/DPEF.R |only R/DSNET.R |only R/LC.R | 22 +++++++++++++++++++--- R/PEC.R | 26 +++++++++++++++++++++----- R/PECO.R | 22 ++++++++++++++-------- R/PEF.R | 23 +++++++++++++++++++---- R/SNET.R |only R/corneal.R | 2 +- build |only man/CLX.Rd | 13 ++++++++++--- man/COVID19.Rd | 7 +++---- man/DCLX.Rd |only man/DLC.Rd |only man/DPEC.Rd |only man/DPECO.Rd |only man/DPEF.Rd |only man/DSNET.Rd |only man/LC.Rd | 12 +++++++++--- man/PEC.Rd | 13 ++++++++++--- man/PECO.Rd | 15 +++++++++++---- man/PEF.Rd | 13 ++++++++++--- man/SNET.Rd |only man/cm13.Rd | 15 +++++++++++---- man/cmtwo.Rd | 7 +++++++ man/corneal.Rd | 8 ++++---- man/miRNA.Rd | 2 +- man/syk.Rd | 13 +++++++------ 35 files changed, 225 insertions(+), 87 deletions(-)
Title: Bayesian Dynamic Energy Budget Modelling
Description: Provides a Bayesian framework for Dynamic Energy Budget (DEB)
modelling via 'Stan'. Implements the standard DEB model of Kooijman
(2010, <doi:10.1017/CBO9780511805400>) as a state-space model with
Hamiltonian Monte Carlo inference (Carpenter et al., 2017,
<doi:10.18637/jss.v076.i01>). Includes individual-level growth models,
growth-reproduction models, hierarchical multi-individual models with
partial pooling, and toxicokinetic-toxicodynamic (TKTD) models for
ecotoxicology following the DEBtox framework (Jager et al., 2006,
<doi:10.1007/s10646-006-0060-x>). Supports prior specification from
biological knowledge, convergence diagnostics (Vehtari et al., 2021,
<doi:10.1214/20-BA1221>), posterior predictive checks, derived quantity
estimation, and visualisation via 'ggplot2'.
Author: Branimir K. Hackenberger [aut, cre],
Tamara Djerdj [aut],
Domagoj K. Hackenberger [aut]
Maintainer: Branimir K. Hackenberger <branimir@sciom.hr>
Diff between BayesianDEB versions 0.1.4 dated 2026-04-21 and 0.2.1 dated 2026-06-17
DESCRIPTION | 11 MD5 | 127 ++-- NAMESPACE | 27 NEWS.md | 91 +++ R/BayesianDEB-package.R | 14 R/data_prep.R | 190 ++++++ R/debtox.R | 86 ++ R/diagnostics.R | 459 +++++++++++---- R/fit.R | 530 ++++++++++++++++- R/model_spec.R | 134 ++++ R/plot.R | 57 + R/ppc.R | 176 +++++ R/priors.R | 188 ++++++ R/utils.R | 21 README.md | 26 inst/CITATION | 2 inst/doc/case_study_eisenia_folsomia.R | 556 +++++++++--------- inst/doc/case_study_eisenia_folsomia.Rmd | 148 +++- inst/doc/case_study_eisenia_folsomia.html | 899 ++++++++++++++++++++++++------ inst/doc/getting_started.R | 171 +++-- inst/doc/getting_started.Rmd | 64 +- inst/doc/getting_started.html | 414 +++++++++++-- inst/stan/bdeb_debtox.stan | 2 inst/stan/bdeb_growth_repro.stan | 2 inst/stan/bdeb_hierarchical_growth.stan | 2 inst/stan/bdeb_individual_growth.stan | 2 man/BayesianDEB-package.Rd | 13 man/bdeb_derived.Rd | 25 man/bdeb_diagnose.Rd | 46 + man/bdeb_ec50.Rd | 15 man/bdeb_fit.Rd | 66 +- man/bdeb_loo.Rd | 13 man/bdeb_model.Rd | 7 man/bdeb_ppc.Rd | 14 man/bdeb_prior-methods.Rd |only man/bdeb_summary.Rd | 29 man/coef.bdeb_fit.Rd | 13 man/confint.bdeb_fit.Rd |only man/deb_fluxes.Rd | 5 man/figures |only man/fitted.bdeb_fit.Rd |only man/logLik.bdeb_fit.Rd |only man/nobs.bdeb_fit.Rd |only man/plot.bdeb_data.Rd |only man/plot.bdeb_diagnostics.Rd |only man/plot.bdeb_fit.Rd | 14 man/plot.bdeb_model.Rd |only man/plot.bdeb_ppc.Rd | 13 man/plot.bdeb_prediction.Rd |only man/plot_dose_response.Rd | 15 man/predict.bdeb_fit.Rd | 14 man/print.bdeb_data.Rd |only man/print.bdeb_diagnostics.Rd |only man/print.bdeb_fit.Rd |only man/print.bdeb_model.Rd |only man/print.bdeb_ppc.Rd |only man/print.bdeb_prediction.Rd |only man/repro_to_intervals.Rd | 8 man/residuals.bdeb_fit.Rd |only man/summary.bdeb_data.Rd |only man/summary.bdeb_diagnostics.Rd |only man/summary.bdeb_fit.Rd |only man/summary.bdeb_model.Rd |only man/summary.bdeb_prediction.Rd |only man/vcov.bdeb_fit.Rd |only tests/testthat/test-api-contracts.R | 6 tests/testthat/test-class-methods.R |only tests/testthat/test-deep-validation.R | 2 tests/testthat/test-diagnostics.R | 130 +++- tests/testthat/test-end-to-end.R | 2 tests/testthat/test-fit.R | 149 ++++ tests/testthat/test-input-validation.R |only tests/testthat/test-plot.R | 20 tests/testthat/test-ppc.R | 40 + tests/testthat/test-snapshot-regression.R | 4 vignettes/case_study_eisenia_folsomia.Rmd | 148 +++- vignettes/getting_started.Rmd | 64 +- 77 files changed, 4246 insertions(+), 1028 deletions(-)
Title: Generate Analysis Results Programmes Using ARS Metadata
Description: Analysis Results Standard (ARS), a foundational standard by CDISC
(Clinical Data Interchange Standards Consortium), provides a logical
data model for metadata describing all components to calculate Analysis
Results. <https://www.cdisc.org/standards/foundational/analysis-results-standard>
Using 'siera', ARS metadata is ingested (JSON or Excel format), producing
R programmes to generate Analysis Results Datasets (ARDs). Supports
arbitrary-depth table structures, multi-value conditions, data-driven
groupings, and CDISC-compliant ARD column stamping.
Author: Malan Bosman [aut, cre],
Clymb Clinical [cph, fnd]
Maintainer: Malan Bosman <malanbos@gmail.com>
Diff between siera versions 0.5.5 dated 2025-12-01 and 0.5.6 dated 2026-06-17
DESCRIPTION | 20 - LICENSE | 2 MD5 | 54 ++- NEWS.md | 11 R/DataSubsets.R | 30 +- R/loadADaM.R | 2 R/metadata.R | 96 +++--- R/readARS.R | 409 +++++++++++----------------- README.md | 9 inst/doc/Getting_started.html | 26 - inst/extdata/ADEXSUM.csv |only inst/extdata/cards_constructs.xlsx |binary inst/extdata/exampleARS_5.json |only inst/extdata/exampleARS_5.xlsx |only inst/extdata/exampleARS_6.json |only inst/extdata/exampleARS_6.xlsx |only man/dot-extract_lopa_ids.Rd |only man/dot-generate_adam_loading_code.Rd | 70 ++-- man/dot-generate_analysis_method_section.Rd | 76 ++--- man/dot-generate_analysis_set_code.Rd | 78 ++--- man/dot-generate_data_subset_code.Rd | 72 ++-- man/dot-generate_data_subset_condition.Rd | 52 +-- man/dot-generate_library_code.Rd | 32 +- man/dot-generate_program_header.Rd | 46 +-- man/dot-read_ars_json_metadata.Rd | 40 +- man/dot-read_ars_metadata.Rd | 40 +- man/dot-read_ars_xlsx_metadata.Rd | 40 +- tests/testthat/test-DataSubsets.R | 40 ++ tests/testthat/test-loadADaM.R | 22 + tests/testthat/test-metadata.R | 205 ++++++++++++++ tests/testthat/test-readARS.R | 281 +++++++++++++++++++ 31 files changed, 1152 insertions(+), 601 deletions(-)
Title: Basic Functions in Knowledge Space Theory Using Matrix
Representation
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework, which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kstMatrix' package
provides basic functionalities to generate, handle, and manipulate
knowledge structures and knowledge spaces. Opposed to the 'kst'
package, 'kstMatrix' uses matrix representations for knowledge
structures. Furthermore, 'kstMatrix' contains several knowledge spaces
developed by the research group around Cornelia Dowling through
querying experts.
Author: Cord Hockemeyer [aut, cre],
Peter Steiner [aut],
Wai Wong [aut]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kstMatrix versions 2.3-2 dated 2026-04-26 and 2.3-3 dated 2026-06-17
Changelog | 3 + DESCRIPTION | 10 ++-- MD5 | 96 +++++++++++++++++++++--------------------- NAMESPACE | 1 R/kmfamset.R | 4 - R/kmminimalfamset.R |only inst/doc/kstMatrix.Rmd | 13 +++-- inst/doc/kstMatrix.html | 13 +++-- man/cad.Rd | 2 man/fractions.Rd | 2 man/kmSF2basis.Rd | 12 ++--- man/kmSR2basis.Rd | 12 ++--- man/kmSRvalidate.Rd | 6 +- man/kmassess.Rd | 19 ++------ man/kmassessbayesian.Rd | 12 ++--- man/kmassesshalfsplit.Rd | 12 ++--- man/kmassessinformative.Rd | 12 ++--- man/kmassessmentsimulation.Rd | 12 ++--- man/kmassessmultiplicative.Rd | 12 ++--- man/kmbasis.Rd | 33 ++------------ man/kmbasisfringe.Rd | 14 +++--- man/kmbasisneighbourhood.Rd | 14 +++--- man/kmcolors.Rd | 13 +++-- man/kmdist.Rd | 6 +- man/kmdoubleequal.Rd | 9 ++- man/kmeqreduction.Rd | 6 +- man/kmfamset.Rd | 6 +- man/kmfringe.Rd | 14 +++--- man/kmgenerate.Rd | 4 - man/kmgradations.Rd | 14 +++--- man/kmiita2SR.Rd | 4 - man/kmiswellgraded.Rd | 6 +- man/kmlearningpaths.Rd | 14 +++--- man/kmminimalfamset.Rd |only man/kmneighbourhood.Rd | 14 +++--- man/kmnneighbourhood.Rd | 14 +++--- man/kmnotions.Rd | 6 +- man/kmsetiselement.Rd | 9 ++- man/kmspace.Rd | 6 +- man/kmstructure.Rd | 6 +- man/kmsurmisefunction.Rd | 12 ++--- man/kmsurmiserelation.Rd | 12 ++--- man/kmsymmsetdiff.Rd | 14 ++---- man/kmunionclosure.Rd | 12 ++--- man/kmvalidate.Rd | 6 +- man/phsg.Rd | 2 man/plot.Rd | 4 - man/readwrite.Rd | 2 man/xpl.Rd | 2 vignettes/kstMatrix.Rmd | 13 +++-- 50 files changed, 262 insertions(+), 282 deletions(-)
Title: Various Coefficients of Interrater Reliability and Agreement
Description: Coefficients of Interrater Reliability and Agreement for quantitative, ordinal and nominal data: ICC, Finn-Coefficient, Robinson's A, Kendall's W, Cohen's Kappa, ...
Author: Matthias Gamer [aut, cre],
Jim Lemon [aut],
Ian Fellows [aut],
Puspendra Singh [aut]
Maintainer: Matthias Gamer <matthias.gamer@uni-wuerzburg.de>
Diff between irr versions 0.84.1 dated 2019-01-26 and 0.85 dated 2026-06-17
CHANGES | 84 ++++++++++++++++-------------- DESCRIPTION | 30 ++++++---- MD5 | 26 ++++----- NAMESPACE | 32 +++++------ R/N2.cohen.kappa.R | 140 +++++++++++++++++++++++++------------------------- R/agree.R | 51 ++++++++++-------- R/icc.R | 20 +++---- R/kappam.fleiss.R | 24 ++++++-- R/kappam.light.R | 17 +++++- data/anxiety.rda |binary data/diagnoses.rda |binary data/video.rda |binary data/vision.rda |binary man/N2.cohen.kappa.Rd | 102 ++++++++++++++++++------------------ 14 files changed, 284 insertions(+), 242 deletions(-)
Title: Interface to the arXiv API
Description: An interface to the API for 'arXiv',
a repository of electronic preprints for
computer science, mathematics, physics, quantitative biology,
quantitative finance, and statistics.
Author: Karthik Ram [aut] ,
Karl Broman [aut, cre]
Maintainer: Karl Broman <broman@wisc.edu>
Diff between aRxiv versions 0.18 dated 2025-12-13 and 0.20 dated 2026-06-17
DESCRIPTION | 10 +- MD5 | 42 ++++++------ NEWS.md | 12 +++ R/aRxiv-package.R |only R/parse.R | 4 + R/query_terms-data.R | 2 README.md | 25 ++++--- build/vignette.rds |binary data/arxiv_cats.RData |binary data/query_terms.RData |binary inst/doc/aRxiv.R | 8 +- inst/doc/aRxiv.Rmd | 35 +++++++--- inst/doc/aRxiv.html | 129 +++++++++++++++++++------------------ man/aRxiv-package.Rd |only man/query_terms.Rd | 2 tests/testthat/test-arxiv_errors.R | 4 - tests/testthat/test-batches.R | 2 tests/testthat/test-clean.R | 2 tests/testthat/test-date_range.R | 2 tests/testthat/test-search.R | 6 - tests/testthat/test-sort.R | 4 - tests/testthat/test-toomany.R | 4 - vignettes/aRxiv.Rmd | 35 +++++++--- 23 files changed, 199 insertions(+), 129 deletions(-)
Title: Partial Least Squares Regression for Generalized Linear Models
Description: Provides (weighted) Partial least squares Regression for generalized linear models and repeated k-fold cross-validation of such models using various criteria <doi:10.48550/arXiv.1810.01005>. It allows for missing data in the explanatory variables. Bootstrap confidence intervals constructions are also available.
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between plsRglm versions 1.7.0 dated 2026-03-28 and 1.7.1 dated 2026-06-17
DESCRIPTION | 8 - MD5 | 170 ++++++++++++++------------- NAMESPACE | 2 NEWS.md | 9 + R/PLS_glm_wvc.R | 2 R/PLS_lm_wvc.R | 2 R/confints.bootpls.R | 32 +++-- R/confints2signifind.R |only R/cv.plsR.R | 2 R/cv.plsRglmmodel.default.R | 3 R/cv.plsRmodel.default.R | 3 R/cvtable.R | 2 R/datasets.R | 2 R/infcrit.dof.R | 3 R/kfolds2CVinfos_glm.R | 2 R/kfolds2CVinfos_lm.R | 2 R/kfolds2Chisq.R | 2 R/kfolds2Chisqind.R | 2 R/kfolds2Mclassed.R | 2 R/kfolds2Mclassedind.R | 2 R/kfolds2Press.R | 2 R/kfolds2Pressind.R | 2 R/kfolds2coeff.R | 2 R/plot.table.summary.cv.plsRglmmodel.R | 2 R/plot.table.summary.cv.plsRmodel.R | 2 R/plsR.R | 2 R/plsR.dof.R | 4 R/plsRglm.R | 2 R/predict.plsRglmmodel.R | 2 R/predict.plsRmodel.R | 2 R/print.coef.plsRglmmodel.R | 2 R/print.coef.plsRmodel.R | 2 R/print.cv.plsRglmmodel.R | 2 R/print.cv.plsRmodel.R | 2 R/print.plsRglmmodel.R | 2 R/print.plsRmodel.R | 2 R/print.summary.plsRglmmodel.R | 2 R/print.summary.plsRmodel.R | 2 R/summary.cv.plsRglmmodel.R | 2 R/summary.cv.plsRmodel.R | 2 R/summary.plsRglmmodel.R | 2 R/summary.plsRmodel.R | 2 R/utils_dof.R |only R/weighted_significance.R |only inst/CITATION | 2 inst/_pkgdown.yml | 2 inst/doc/getting-started.html | 47 ++++--- inst/doc/plsRglm.R | 52 +++----- inst/doc/plsRglm.Rmd | 52 +++----- inst/doc/plsRglm.html | 40 +++--- man/CorMat.Rd | 2 man/PLS_glm_wvc.Rd | 2 man/PLS_lm_wvc.Rd | 2 man/confints.bootpls.Rd | 4 man/confints2signifind.Rd |only man/cv.plsR.Rd | 2 man/cvtable.Rd | 2 man/kfolds2CVinfos_glm.Rd | 2 man/kfolds2CVinfos_lm.Rd | 2 man/kfolds2Chisq.Rd | 2 man/kfolds2Chisqind.Rd | 2 man/kfolds2Mclassed.Rd | 2 man/kfolds2Mclassedind.Rd | 2 man/kfolds2Press.Rd | 2 man/kfolds2Pressind.Rd | 2 man/kfolds2coeff.Rd | 2 man/plot.table.summary.cv.plsRglmmodel.Rd | 2 man/plot.table.summary.cv.plsRmodel.Rd | 2 man/plsR.Rd | 2 man/plsRglm.Rd | 2 man/predict.plsRglmmodel.Rd | 2 man/predict.plsRmodel.Rd | 2 man/print.coef.plsRglmmodel.Rd | 2 man/print.coef.plsRmodel.Rd | 2 man/print.cv.plsRglmmodel.Rd | 2 man/print.cv.plsRmodel.Rd | 2 man/print.plsRglmmodel.Rd | 2 man/print.plsRmodel.Rd | 2 man/print.summary.plsRglmmodel.Rd | 2 man/print.summary.plsRmodel.Rd | 2 man/summary.cv.plsRglmmodel.Rd | 2 man/summary.cv.plsRmodel.Rd | 2 man/summary.plsRglmmodel.Rd | 2 man/summary.plsRmodel.Rd | 2 man/weighted_significance.Rd |only tests/testthat/Rplots.pdf |binary tests/testthat/test-bootstrap-significance.R |only tests/testthat/test-cv-aliases.R |only tests/testthat/test-plsdof-fallback.R |only vignettes/plsRglm.Rmd | 52 +++----- 90 files changed, 311 insertions(+), 302 deletions(-)
Title: Harmonized Orphanhood Mortality Estimation
Description: Implements indirect demographic methods for estimating adult
mortality from orphanhood data. The package includes the standard
Brass and Hill (1973) method
<https://scholar.google.com/scholar_lookup?&title=Estimating%20Adult%20Mortality%20from%20Orphanhood&pages=111-23&publication_year=1973&author=Brass%2CW.&author=Hill.%2CK.>,
the regression-based approach developed by Timaeus (1992)
<https://pubmed.ncbi.nlm.nih.gov/12317481/>, and the adjustments
proposed by Luy (2012) <doi:10.1007/s13524-012-0101-4> for
low-mortality populations. A relational model is used to harmonize
estimates into comparable adult mortality indicators. The package
also provides diagnostic tools to assess the sensitivity of results
to assumptions about the mean age of childbearing and the choice of
model life table family.
Author: Tamara Vaz [aut, cre]
Maintainer: Tamara Vaz <tamaravaz.m@gmail.com>
Diff between HOME versions 0.1.0 dated 2026-06-02 and 0.1.1 dated 2026-06-17
DESCRIPTION | 10 MD5 | 43 NAMESPACE | 4 R/data.R |only R/om_diagnostics.R | 1052 ++++++++++++---------- build |only inst/doc |only inst/shiny/home_app/app.R | 1345 ++++++++++++++--------------- inst/shiny/home_app/rsconnect |only man/app_HOME.Rd | 6 man/dot-om_brass.Rd | 2 man/dot-om_luy.Rd | 2 man/dot-om_timaeus.Rd | 2 man/dot-resolve_inputs.Rd | 2 man/om_dashboard.Rd | 6 man/om_estimate_index.Rd | 146 +-- man/om_plot_linearity.Rd | 6 man/om_sensitivity.Rd | 24 man/om_sensitivity_family.Rd | 26 man/print.OrphanhoodSensitivity.Rd |only man/print.OrphanhoodSensitivityFamily.Rd |only man/summary.OrphanhoodSensitivity.Rd |only man/summary.OrphanhoodSensitivityFamily.Rd |only man/sysdata.Rd |only tests |only vignettes |only 26 files changed, 1422 insertions(+), 1254 deletions(-)
Title: Standardized Economic Reporting and Automated Dynamic Writing /
Synthèse d'Écrits Avec des Règles Automatisées et Dynamiques
Description: Provides tools for generating dynamic and standardized
economic narratives in R Markdown documents. The package is primarily
designed for French-language statistical and economic publications.
It includes functions to describe changes in levels, percentages,
trends, accelerations and short-term economic developments using
consistent linguistic rules. The package supports automated reporting
workflows and reproducible economic writing.
Fournit des outils permettant de générer des textes économiques
dynamiques et standardisés dans des documents R Markdown. Le package
est principalement conçu pour les publications statistiques et
économiques en français. Il propose des fonctions permettant de
décrire les évolutions de niveaux, de pourcentages, de tendances,
d'accélérations et les évolutions conjoncturelles à l'aide de règles
linguistiques homogènes. Le package facilite l'automatisation de la
rédaction et la reproductibilité des publications économiques.
Author: Alexandre Cazenave-Lacroutz [aut] ,
Jules Lejas [cre],
Direction de l'animation de la recherche, des etudes et des
statistiques [cph]
Maintainer: Jules Lejas <jules.lejas@gmail.com>
Diff between serad versions 0.2.0 dated 2026-06-02 and 0.2.1 dated 2026-06-17
DESCRIPTION | 6 +- MD5 | 20 +++---- R/gETa_nom_taux.R | 11 --- R/gETa_verbe_taux.R | 11 --- R/init_serad_en.R | 77 +++++++++++++++++++-------- R/init_serad_fr.R | 94 ++++++++++++++++++++-------------- inst/doc/serad.html | 8 +- tests/testthat/test-gETa_nom.R | 12 ++-- tests/testthat/test-gETa_nom_taux.R | 6 +- tests/testthat/test-gETa_verbe.R | 10 +-- tests/testthat/test-gETa_verbe_taux.R | 2 11 files changed, 145 insertions(+), 112 deletions(-)
Title: SQLite Interface for R
Description: Embeds the SQLite database engine in R and provides an
interface compliant with the DBI package. The source for the SQLite
engine and for various extensions is included.
System libraries will never be consulted because this package relies
on static linking for the plugins it includes; this also ensures a
consistent experience across all installations. Optionally, when
libcurl is available at build time, an experimental HTTP/HTTPS
virtual file system (VFS) can be enabled to allow read-only access
to remote immutable SQLite database files via URIs.
Author: Kirill Mueller [aut, cre] ,
Hadley Wickham [aut],
David A. James [aut],
Seth Falcon [aut],
D. Richard Hipp [ctb] ,
Dan Kennedy [ctb] ,
Joe Mistachkin [ctb] ,
SQLite Authors [ctb] ,
Liam Healy [ctb] ,
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between RSQLite versions 3.53.1 dated 2026-05-23 and 3.53.2 dated 2026-06-17
.aspell/DBI.rds |binary .aspell/defaults.R | 2 DESCRIPTION | 19 MD5 | 50 + NAMESPACE | 5 NEWS.md | 331 +++++------- R/SQLite.R | 111 +++- R/cpp11.R | 12 R/httpvfs.R |only R/httpvfs_config.R |only R/initExtension.R | 30 + README.md | 312 ++++++++--- cleanup |only cleanup.ucrt |only cleanup.win |only configure |only configure.win |only inst/WORDLIST | 8 man/initExtension.Rd | 18 man/sqliteHasHttpVFS.Rd |only man/sqliteHttpConfig.Rd |only man/sqliteHttpStats.Rd |only man/sqliteHttpVfsCompiled.Rd |only man/sqliteRemote.Rd |only src/DbConnection.cpp | 4 src/Makevars | 28 - src/cpp11.cpp | 24 src/ext-http.c |only src/has_http_vfs.cpp |only src/httpvfs_stats.cpp |only src/vendor/extensions/http.c |only src/vendor/extensions/uuid.c | 1 src/vendor/sqlite3/sqlite3.c | 874 ++++++++++++++++++++++++++------- src/vendor/sqlite3/sqlite3.h | 22 tests/testthat/helper-aspell.R |only tests/testthat/test-httpvfs-compiled.R |only tests/testthat/test-httpvfs-helpers.R |only tests/testthat/test-httpvfs.R |only 38 files changed, 1361 insertions(+), 490 deletions(-)
Title: Continuous Norming
Description: Generates continuous test norms in
psychometrics and biometrics, and analyzing model fit. The package offers
both distribution-free modeling using Taylor polynomials and parametric
modeling using the beta-binomial and the 'Sinh-Arcsinh' distribution.
Originally developed for achievement tests, it is applicable to a wide
range of mental, physical, or other test scores dependent on continuous or
discrete explanatory variables. The package provides several advantages:
It minimizes deviations from representativeness in subsamples, interpolates
between discrete levels of explanatory variables, and significantly reduces
the required sample size compared to conventional norming per age group.
cNORM enables graphical and analytical evaluation of model fit,
accommodates a wide range of scales including those with negative and
descending values, and as well supports conventional norming. It generates
norm tables including confidence intervals. Methods for addressing
representativeness issues are [...truncated...]
Author: Alexandra Lenhard [aut] ,
Wolfgang Lenhard [cre, aut] ,
Sebastian Gary [aut],
WPS Publisher [fnd]
Maintainer: Wolfgang Lenhard <wolfgang.lenhard@uni-wuerzburg.de>
Diff between cNORM versions 3.5.4 dated 2026-05-15 and 3.6.0 dated 2026-06-17
DESCRIPTION | 19 MD5 | 47 NAMESPACE | 10 NEWS.md | 25 R/betaBinomial.R | 232 ++ R/cNORM.R | 209 -- R/modelling.R | 966 +++------- R/preparation.R | 895 ++++----- R/raking.R | 163 - R/shash.R | 269 ++ R/utilities.R | 141 - README.md | 25 inst/doc/BetaBinomial.Rmd | 6 inst/doc/BetaBinomial.html | 18 inst/doc/WeightedRegression.html | 23 inst/doc/cNORM-Demo.R | 14 inst/doc/cNORM-Demo.Rmd | 24 inst/doc/cNORM-Demo.html | 241 +- inst/doc/sinh.html | 4 inst/shiny/app1/rsconnect/shinyapps.io/cnorm/app1.dcf |only inst/shiny/app2/rsconnect/shinyapps.io/cnorm/cNORM-Parametric.dcf | 2 man/autoselect.betabinomial.Rd |only man/autoselect.shash.Rd |only man/getGroups.Rd | 22 vignettes/BetaBinomial.Rmd | 6 vignettes/cNORM-Demo.Rmd | 24 26 files changed, 1812 insertions(+), 1573 deletions(-)
Title: Functions to Assist Design and Analysis of Agronomic Experiments
Description: Provides functions to aid in the design and analysis of
agronomic and agricultural experiments through easy access to
documentation and helper functions, especially for users who are
learning these concepts. While not required for most functionality,
this package enhances the `asreml` package which provides a
computationally efficient algorithm for fitting mixed models
using Residual Maximum Likelihood. It is a commercial package
that can be purchased as 'ASReml-R' from 'VSNi'
<https://vsni.co.uk/>, who will supply a zip file for local
installation/updating (see <https://asreml.kb.vsni.co.uk/>).
Author: Sharon Nielsen [aut],
Sam Rogers [aut, cre],
Annie Conway [aut],
Michael Mumford [ctb],
University of Adelaide [cph, fnd] ,
Grains Research and Development Corporation [cph, fnd]
Maintainer: Sam Rogers <biometrytraining@adelaide.edu.au>
Diff between biometryassist versions 1.4.0 dated 2026-02-03 and 1.5.0 dated 2026-06-17
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More information about biometryassist at CRAN
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Title: Materials for Introductory Course on Bayesian Learning
Description: Practicals, data sets, helper functions and interactive 'Shiny' apps
used in the introductory course on Bayesian inference at the
Valencia International Bayesian Summer School. Installing 'vibass' installs
all the other packages used during the course and downloads all necessary
materials for working off line.
Author: VIBASS Team [aut, cph],
Facundo Munoz [ctb, cre] ,
Carmen Armero [ctb] ,
Anabel Forte [ctb] ,
David Conesa [ctb] ,
Mark Brewer [ctb] ,
ORCID: <https://orcid.org/0000-0001-7559-389X>),
Virgilio Gomez-Rubio [ctb]
Maintainer: Facundo Munoz <facundo.munoz@cirad.fr>
Diff between vibass versions 1.0.3 dated 2025-09-10 and 1.0.4 dated 2026-06-17
DESCRIPTION | 11 ++++++----- MD5 | 34 +++++++++++++++++----------------- NEWS.md | 12 +++++++++++- R/zzz.R | 2 +- README.md | 10 +++++----- build/vignette.rds |binary inst/WORDLIST | 2 +- inst/doc/p1.html | 37 ++++++++++++++++++++----------------- inst/doc/p2count.html | 17 +++++++++-------- inst/doc/p2normal.html | 23 ++++++++++++----------- inst/doc/p3.html | 5 +++-- inst/doc/p4.html | 13 +++++++------ inst/doc/p5.html | 5 +++-- inst/doc/p6.Rmd | 2 +- inst/doc/p6.html | 9 +++++---- inst/doc/p7.html | 5 +++-- inst/doc/p8.html | 5 +++-- vignettes/p6.Rmd | 2 +- 18 files changed, 108 insertions(+), 86 deletions(-)
Title: Discover, Count and Score Emoji in Text
Description: A tidy toolkit for working with the emoji in any text column, such
as social-media posts, product reviews, chat logs or survey responses.
Unicode is awkward to handle and not every code point is an emoji, which
makes emoji statistics fiddly to obtain. 'tidyEmoji' extracts, counts,
categorises and sentiment-scores emoji with grapheme-aware detection (so
skin-tone and multi-person sequences stay intact), returning tidy data
frames that slot straight into a 'tidyverse' workflow. The bundled emoji
sentiment lexicon is from the Emoji Sentiment Ranking of Kralj Novak et al.
(2015) <doi:10.1371/journal.pone.0144296>, released under CC BY-SA 4.0.
Author: Youzhi Yu [aut, cre]
Maintainer: Youzhi Yu <yuyouzhi666@icloud.com>
Diff between tidyEmoji versions 0.1.1 dated 2023-08-19 and 0.2.0 dated 2026-06-17
tidyEmoji-0.1.1/tidyEmoji/man/emoji_tweets.Rd |only tidyEmoji-0.1.1/tidyEmoji/man/tidyEmoji.Rd |only tidyEmoji-0.2.0/tidyEmoji/DESCRIPTION | 28 tidyEmoji-0.2.0/tidyEmoji/MD5 | 66 tidyEmoji-0.2.0/tidyEmoji/NAMESPACE | 12 tidyEmoji-0.2.0/tidyEmoji/NEWS.md | 44 tidyEmoji-0.2.0/tidyEmoji/R/data.R | 65 tidyEmoji-0.2.0/tidyEmoji/R/emoji-categorize.R | 77 tidyEmoji-0.2.0/tidyEmoji/R/emoji-engine.R |only tidyEmoji-0.2.0/tidyEmoji/R/emoji-extraction.R | 121 - tidyEmoji-0.2.0/tidyEmoji/R/emoji-sentiment.R |only tidyEmoji-0.2.0/tidyEmoji/R/emoji-summary.R | 117 - tidyEmoji-0.2.0/tidyEmoji/R/tidyEmoji.R | 33 tidyEmoji-0.2.0/tidyEmoji/R/top-n-emojis.R | 124 - tidyEmoji-0.2.0/tidyEmoji/README.md | 233 +- tidyEmoji-0.2.0/tidyEmoji/build/partial.rdb |only tidyEmoji-0.2.0/tidyEmoji/build/vignette.rds |binary tidyEmoji-0.2.0/tidyEmoji/data/category_unicode_crosswalk.rda |binary tidyEmoji-0.2.0/tidyEmoji/data/emoji_sentiment_lexicon.rda |only tidyEmoji-0.2.0/tidyEmoji/data/emoji_unicode_crosswalk.rda |binary tidyEmoji-0.2.0/tidyEmoji/inst/doc/introduction.R | 147 + tidyEmoji-0.2.0/tidyEmoji/inst/doc/introduction.Rmd | 364 +++- tidyEmoji-0.2.0/tidyEmoji/inst/doc/introduction.html | 800 ++++++---- tidyEmoji-0.2.0/tidyEmoji/man/category_unicode_crosswalk.Rd | 18 tidyEmoji-0.2.0/tidyEmoji/man/emoji_categorize.Rd | 32 tidyEmoji-0.2.0/tidyEmoji/man/emoji_extract_nest.Rd | 31 tidyEmoji-0.2.0/tidyEmoji/man/emoji_extract_unnest.Rd | 29 tidyEmoji-0.2.0/tidyEmoji/man/emoji_filter.Rd |only tidyEmoji-0.2.0/tidyEmoji/man/emoji_frequency.Rd |only tidyEmoji-0.2.0/tidyEmoji/man/emoji_sentiment.Rd |only tidyEmoji-0.2.0/tidyEmoji/man/emoji_sentiment_lexicon.Rd |only tidyEmoji-0.2.0/tidyEmoji/man/emoji_summary.Rd | 37 tidyEmoji-0.2.0/tidyEmoji/man/emoji_tokens.Rd |only tidyEmoji-0.2.0/tidyEmoji/man/emoji_unicode_crosswalk.Rd | 22 tidyEmoji-0.2.0/tidyEmoji/man/tidyEmoji-package.Rd |only tidyEmoji-0.2.0/tidyEmoji/man/top_n_emojis.Rd | 51 tidyEmoji-0.2.0/tidyEmoji/tests/testthat/test-dimensions.R | 48 tidyEmoji-0.2.0/tidyEmoji/tests/testthat/test-edge-cases.R |only tidyEmoji-0.2.0/tidyEmoji/tests/testthat/test-extraction.R |only tidyEmoji-0.2.0/tidyEmoji/tests/testthat/test-frequency-categorize.R |only tidyEmoji-0.2.0/tidyEmoji/tests/testthat/test-sentiment.R |only tidyEmoji-0.2.0/tidyEmoji/vignettes/introduction.Rmd | 364 +++- 42 files changed, 1767 insertions(+), 1096 deletions(-)
Title: Calculate Slopes of Roads, Rivers and Trajectories
Description: Calculates the slope (longitudinal gradient or steepness)
of linear geographic features such as roads (for more details, see Ariza-López et al. (2019)
<doi:10.1038/s41597-019-0147-x>) and rivers (for more details, see Cohen et al. (2018)
<doi:10.1016/j.jhydrol.2018.06.066>). It can use local Digital Elevation Model (DEM)
data or download DEM data via the 'ceramic' package. The package also provides functions
to add elevation data to linestrings and visualize elevation profiles.
Author: Robin Lovelace [aut, cre, cph] ,
Rosa Felix [aut] ,
Joey Talbot [aut] ,
Goncalo Matos [aut] ,
Dan Olner [rev] ,
Andy Teucher [rev]
Maintainer: Robin Lovelace <rob00x@gmail.com>
This is a re-admission after prior archival of version 1.0.1 dated 2025-06-23
Diff between slopes versions 1.0.1 dated 2025-06-23 and 1.0.2 dated 2026-06-17
slopes-1.0.1/slopes/R/z.R |only slopes-1.0.1/slopes/data/dem_lisbon_raster.rda |only slopes-1.0.1/slopes/man/dem_lisbon_raster.Rd |only slopes-1.0.1/slopes/man/slopes-package.Rd |only slopes-1.0.1/slopes/man/z_value.Rd |only slopes-1.0.2/slopes/DESCRIPTION | 12 slopes-1.0.2/slopes/MD5 | 115 + slopes-1.0.2/slopes/NAMESPACE | 16 slopes-1.0.2/slopes/NEWS.md | 17 slopes-1.0.2/slopes/R/data.R | 163 -- slopes-1.0.2/slopes/R/palette.R |only slopes-1.0.2/slopes/R/plot_slope.R | 284 ++-- slopes-1.0.2/slopes/R/slope_get.R | 125 + slopes-1.0.2/slopes/R/slopes-package.R | 21 slopes-1.0.2/slopes/R/slopes.R | 633 +++------- slopes-1.0.2/slopes/R/z-functions.R |only slopes-1.0.2/slopes/README.md | 62 slopes-1.0.2/slopes/build/vignette.rds |binary slopes-1.0.2/slopes/inst/dem_lisbon.tif |only slopes-1.0.2/slopes/inst/doc/benchmark.R | 22 slopes-1.0.2/slopes/inst/doc/benchmark.Rmd | 29 slopes-1.0.2/slopes/inst/doc/benchmark.html | 204 +-- slopes-1.0.2/slopes/inst/doc/intro-to-slopes.html | 326 +++-- slopes-1.0.2/slopes/inst/doc/roadnetworkcycling.html | 395 +++--- slopes-1.0.2/slopes/inst/doc/slopes.R | 43 slopes-1.0.2/slopes/inst/doc/slopes.Rmd | 62 slopes-1.0.2/slopes/inst/doc/slopes.html | 251 ++- slopes-1.0.2/slopes/inst/doc/verification.R | 175 ++ slopes-1.0.2/slopes/inst/doc/verification.Rmd | 184 ++ slopes-1.0.2/slopes/inst/doc/verification.html | 481 +++++-- slopes-1.0.2/slopes/man/cyclestreets_route.Rd | 23 slopes-1.0.2/slopes/man/dem_lisbon.Rd |only slopes-1.0.2/slopes/man/distance_z.Rd |only slopes-1.0.2/slopes/man/elevation_add.Rd | 41 slopes-1.0.2/slopes/man/elevation_extract.Rd | 69 - slopes-1.0.2/slopes/man/elevation_get.Rd | 46 slopes-1.0.2/slopes/man/figures/README-elevationprofile-1.png |binary slopes-1.0.2/slopes/man/lisbon_road_network.Rd | 31 slopes-1.0.2/slopes/man/lisbon_road_segment.Rd | 24 slopes-1.0.2/slopes/man/lisbon_road_segment_3d.Rd |only slopes-1.0.2/slopes/man/lisbon_road_segment_xyz_mapbox.Rd |only slopes-1.0.2/slopes/man/lisbon_route.Rd | 27 slopes-1.0.2/slopes/man/lisbon_route_3d.Rd |only slopes-1.0.2/slopes/man/lisbon_route_xyz_mapbox.Rd |only slopes-1.0.2/slopes/man/magnolia_xy.Rd | 16 slopes-1.0.2/slopes/man/make_breaks.Rd |only slopes-1.0.2/slopes/man/make_colz.Rd |only slopes-1.0.2/slopes/man/make_pal.Rd |only slopes-1.0.2/slopes/man/plot_dz.Rd | 52 slopes-1.0.2/slopes/man/plot_slope.Rd | 50 slopes-1.0.2/slopes/man/route_to_segments.Rd |only slopes-1.0.2/slopes/man/sequential_dist.Rd | 29 slopes-1.0.2/slopes/man/sf_mid_ext_lonlat.Rd |only slopes-1.0.2/slopes/man/slope_distance.Rd |only slopes-1.0.2/slopes/man/slope_distance_mean.Rd |only slopes-1.0.2/slopes/man/slope_distance_weighted.Rd |only slopes-1.0.2/slopes/man/slope_matrices.Rd |only slopes-1.0.2/slopes/man/slope_matrix.Rd | 59 slopes-1.0.2/slopes/man/slope_matrix_mean.Rd |only slopes-1.0.2/slopes/man/slope_matrix_to_raster.Rd |only slopes-1.0.2/slopes/man/slope_matrix_weighted.Rd |only slopes-1.0.2/slopes/man/slope_raster.Rd | 54 slopes-1.0.2/slopes/man/slope_vector.Rd | 62 slopes-1.0.2/slopes/man/slope_xyz.Rd | 32 slopes-1.0.2/slopes/man/slope_xyz_simple.Rd |only slopes-1.0.2/slopes/man/slopes_palette.Rd |only slopes-1.0.2/slopes/tests/testthat/Rplots.pdf |only slopes-1.0.2/slopes/tests/testthat/test-get.R | 2 slopes-1.0.2/slopes/tests/testthat/test-palette.R |only slopes-1.0.2/slopes/tests/testthat/test-slopes.R | 6 slopes-1.0.2/slopes/vignettes/benchmark.Rmd | 29 slopes-1.0.2/slopes/vignettes/example-nl.png |only slopes-1.0.2/slopes/vignettes/slopes.Rmd | 62 slopes-1.0.2/slopes/vignettes/verification.Rmd | 184 ++ 74 files changed, 2416 insertions(+), 2102 deletions(-)
Title: Interface to the USA National 'Phenology' Network 'API'
Description: Programmatic interface to the Web Service methods provided by
the USA National 'Phenology' Network (<https://usanpn.org/>), which
includes data on various life history events that occur at specific
times.
Author: Jeff Switzer [aut, cre],
Scott Chamberlain [aut],
Lee Marsh [aut],
Kevin Wong [aut],
Eric R Scott [aut] ,
David LeBauer [ctb]
Maintainer: Jeff Switzer <jeff@usanpn.org>
Diff between rnpn versions 1.4.1 dated 2025-08-24 and 1.4.2 dated 2026-06-17
DESCRIPTION | 10 +++++----- MD5 | 26 +++++++++++++------------- NEWS.md | 2 ++ R/rnpn-package.R | 4 ++-- inst/CITATION | 10 +++++----- inst/doc/III_individual_phenometrics.html | 2 +- inst/doc/II_status_intensity.html | 2 +- inst/doc/IV_site_phenometrics.html | 2 +- inst/doc/I_introduction.html | 2 +- inst/doc/VIII_data_cleaning.html | 2 +- inst/doc/VII_combine_raster_point.html | 2 +- inst/doc/V_magnitude_phenometrics.html | 2 +- man/rnpn-package.Rd | 4 ++-- tests/testthat/test-npn-observations.R | 17 +++++++++++++++++ 14 files changed, 53 insertions(+), 34 deletions(-)
Title: Custom Formatted Console Messages with Timing Support
Description: A lightweight message system relying purely on base R. Comes with built-in and pre styled message types and provides an easy way to create custom messages. Supports individually styled and colored text as well as timing information. Designed to make console output more informative and visually organized.
Author: Tim Siebenmorgen [aut, cre, cph]
Maintainer: Tim Siebenmorgen <qol_package@proton.me>
Diff between printify versions 1.0.1 dated 2026-05-16 and 1.0.2 dated 2026-06-17
DESCRIPTION | 6 ++--- MD5 | 6 ++--- NEWS.md | 11 +++++++++ R/messages.R | 65 +++++++++++++++++++++++++++++++++-------------------------- 4 files changed, 54 insertions(+), 34 deletions(-)
Title: Clinical and Metabolic Biomarker Calculation Toolkit
Description: Computes specialist biomarker indices and risk scores for metabolic,
cardiovascular, renal, hepatic, inflammatory, frailty, and psychiatric
health assessment. Includes fasting and OGTT insulin sensitivity/resistance
indices, ASCVD/QRISK3/KFRE risk equations, liver and kidney markers,
frailty and comorbidity indices, biofluid marker panels, and utilities for
column mapping, normalization, imputation, and combined marker dispatch.
Author: Sufyan Suleman [aut, cre]
Maintainer: Sufyan Suleman <sufyansuleman@hotmail.com>
This is a re-admission after prior archival of version 0.1.2 dated 2026-05-19
Diff between HealthMarkers versions 0.1.2 dated 2026-05-19 and 0.1.4 dated 2026-06-17
DESCRIPTION | 36 ++------- MD5 | 60 ++++++++-------- NEWS.md | 118 +++++++++++++++++++++++++++++++- R/atherogenic_indices.R | 20 +++-- R/ckd_stage.R | 11 +- R/cvd_risk.R | 8 ++ R/fasting_is.R | 23 +++++- R/glycemic_markers.R | 17 ++-- R/kidney_kfre.R | 35 +++++---- R/liver_fat_markers.R | 7 + R/obesity_metrics.R | 21 ++--- R/ogtt_is.R | 19 +++-- R/renal_markers.R | 16 ++-- README.md | 87 ++++++++++++++--------- build/partial.rdb |binary inst/CITATION | 3 man/atherogenic_indices.Rd | 22 ++++- man/cvd_marker_aip.Rd | 9 ++ man/fasting_is.Rd | 9 ++ man/glycemic_markers.Rd | 8 +- man/kidney_failure_risk.Rd | 16 ++-- man/liver_fat_markers.Rd | 5 + man/ogtt_is.Rd | 9 +- man/renal_markers.Rd | 5 - tests/testthat/test-fasting_is.R | 15 +++- tests/testthat/test-frailty_index.R | 58 +++++++++++---- tests/testthat/test-glycemic_markers.R | 17 ++-- tests/testthat/test-kidney_kfre.R | 12 +++ tests/testthat/test-liver_fat_markers.R | 5 - tests/testthat/test-obesity_metrics.R | 6 + tests/testthat/test-ogtt_is.R | 13 +++ 31 files changed, 485 insertions(+), 205 deletions(-)
Title: Methods for Deliberation Analysis
Description: An implementation of deliberative reasoning index (DRI) and related
tools for analysis of deliberation survey data. Calculation of DRI, plot of
intersubjective correlations (IC), generation of large-language model (LLM)
survey data, and permutation tests are supported. Example datasets and a
graphical user interface (GUI) are also available to support analysis. For
more information, see Niemeyer and Veri (2022)
<doi:10.1093/oso/9780192848925.003.0007>. For an alternative version of this
dataset, see Niemeyer et al. (2024) <doi:10.1017/S0003055423000023>.
Author: Gustavo Kreia Umbelino [aut, cre] ,
Francesco Veri [aut] ,
Swiss National Science Foundation [fnd]
Maintainer: Gustavo Kreia Umbelino <gustavo.kreiaumbelino@zda.uzh.ch>
Diff between deliberr versions 0.1.0 dated 2025-12-19 and 0.1.3 dated 2026-06-17
DESCRIPTION | 9 MD5 | 18 - R/get_dri_llm_response.R | 221 +++++++++------- R/get_llm_response.R | 138 +++++++-- R/get_model_ids.R | 36 ++ inst/shiny/rsconnect/shinyapps.io/gumbelin/deliberr.dcf | 2 man/deliberr-package.Rd | 2 man/get_dri_llm_response.Rd | 35 ++ man/get_llm_response.Rd | 58 +++- man/get_model_ids.Rd | 8 10 files changed, 375 insertions(+), 152 deletions(-)
Title: Post-Translational Modification Enrichment, Integration, and
Matching Analysis
Description: Functions and mined database from 'UniProt' focusing on post-translational modifications to do single enrichment analysis (SEA) and protein set enrichment analysis (PSEA). Payman Nickchi, Uladzislau Vadadokhau, Mehdi Mirzaie, Marc Baumann, Amir Ata Saei, Mohieddin Jafari (2025) <doi:10.1002/pmic.202400238>.
Author: Mohieddin Jafari [aut],
Payman Nickchi [aut, cre]
Maintainer: Payman Nickchi <payman.nickchi@gmail.com>
Diff between PEIMAN2 versions 1.0.2 dated 2026-02-15 and 1.1.0 dated 2026-06-17
DESCRIPTION | 8 MD5 | 41 ++- NAMESPACE | 4 R/database.R |only R/peiman.R | 274 ++++++++++++++----------- R/psea2mass.R | 158 +++++++------- R/runEnrichment.R | 202 +++++++++--------- R/runPSEA.R | 438 +++++++++++++++++++++-------------------- R/sea2mass.R | 101 ++++----- R/sysdata.rda |binary R/utility.R | 202 ++++++++++++------ README.md | 130 +++++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/PEIMAN2-vignette.html | 254 +++++++++++------------ man/getTaxonomyName.Rd | 7 man/load_peiman_database.Rd |only man/load_ptmlist.Rd |only man/peiman.Rd |only man/psea2mass.Rd | 7 man/runEnrichment.Rd | 14 + man/runPSEA.Rd | 8 man/sea2mass.Rd | 7 man/update_peiman_database.Rd |only 24 files changed, 1031 insertions(+), 824 deletions(-)
Title: Preparation, Checking and Post-Processing Data for PK/PD
Modeling
Description: Efficient tools for preparation, checking and post-processing of data in PK/PD (pharmacokinetics/pharmacodynamics) modeling, with focus on use of Nonmem, including consistency, traceability, and Nonmem compatibility of Data. Rigorously checks final Nonmem datasets. Implemented in 'data.table', but easily integrated with 'base' and 'tidyverse'.
Author: Philip Delff [aut, cre],
Brian Reilly [ctb],
Eric Anderson [ctb]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMdata versions 0.2.4 dated 2026-03-19 and 0.2.5 dated 2026-06-17
NMdata-0.2.4/NMdata/inst/examples/nonmem/input.ext |only NMdata-0.2.4/NMdata/inst/examples/nonmem/input.phi |only NMdata-0.2.4/NMdata/inst/examples/nonmem/xgxr001.ext |only NMdata-0.2.4/NMdata/inst/examples/nonmem/xgxr001.phi |only NMdata-0.2.4/NMdata/inst/examples/nonmem/xgxr003.phi |only NMdata-0.2.4/NMdata/inst/examples/nonmem/xgxr014.phi |only NMdata-0.2.4/NMdata/inst/examples/nonmem/xgxr018.phi |only NMdata-0.2.4/NMdata/inst/examples/nonmem/xgxr132.phi |only NMdata-0.2.4/NMdata/inst/examples/scripts |only NMdata-0.2.4/NMdata/man/figures/README-unnamed-chunk-3-1.png |only NMdata-0.2.4/NMdata/man/initsToExt.Rd |only NMdata-0.2.4/NMdata/tests/testthat/testData/data/xgxr12.csv |only NMdata-0.2.4/NMdata/tests/testthat/testData/data/xgxr12.rds |only NMdata-0.2.4/NMdata/tests/testthat/testData/data/xgxr12_meta.txt |only NMdata-0.2.4/NMdata/tests/testthat/testData/nonmem/pred030.ext |only NMdata-0.2.4/NMdata/tests/testthat/testData/nonmem/pred030.lst |only NMdata-0.2.4/NMdata/tests/testthat/testData/nonmem/pred030.phi |only NMdata-0.2.4/NMdata/tests/testthat/testData/nonmem/pred030.pnm |only NMdata-0.2.4/NMdata/tests/testthat/testData/nonmem/pred030.shk |only NMdata-0.2.4/NMdata/tests/testthat/testData/nonmem/pred030_res.txt |only NMdata-0.2.4/NMdata/tests/testthat/testData/nonmem/xgxr035.pnm |only NMdata-0.2.4/NMdata/tests/testthat/testData/nonmem/xgxr053.pnm |only NMdata-0.2.4/NMdata/tests/testthat/testData/nonmem/xgxr053_ETAS.msf |only NMdata-0.2.4/NMdata/tests/testthat/testData/nonmem/xgxr056.ext |only NMdata-0.2.4/NMdata/tests/testthat/testData/nonmem/xgxr056.lst |only NMdata-0.2.4/NMdata/tests/testthat/testData/nonmem/xgxr056.phi |only NMdata-0.2.4/NMdata/tests/testthat/testData/nonmem/xgxr056.shk |only NMdata-0.2.4/NMdata/tests/testthat/testData/nonmem/xgxr056.txt |only NMdata-0.2.4/NMdata/tests/testthat/testData/simulations/xgxr014_testsim1/xgxr014_testsim1.xml |only NMdata-0.2.4/NMdata/tests/testthat/testData/simulations/xgxr032_simpletab/xgxr032_simpletab.xml |only NMdata-0.2.4/NMdata/tests/testthat/testData/simulations/xgxr032_testsim1 |only NMdata-0.2.4/NMdata/tests/testthat/testOutput/NMwriteData_13.fst |only NMdata-0.2.4/NMdata/tests/testthat/testOutput/simulations |only NMdata-0.2.4/NMdata/tests/testthat/testOutput/stampedData_9.csv |only NMdata-0.2.4/NMdata/tests/testthat/testOutput/stampedData_9_meta.txt |only NMdata-0.2.4/NMdata/tests/testthat/testOutput/xgxr025_sd1 |only NMdata-0.2.4/NMdata/tests/testthat/testOutput/xgxr032_VarCov_1 |only NMdata-0.2.4/NMdata/tests/testthat/testReference/NMsim_VarCov_01a.rds |only NMdata-0.2.4/NMdata/tests/testthat/testReference/NMsim_VarCov_01b.rds |only NMdata-0.2.4/NMdata/tests/testthat/test_NMapplyFilters.R |only NMdata-0.2.5/NMdata/DESCRIPTION | 9 NMdata-0.2.5/NMdata/MD5 | 143 +-- NMdata-0.2.5/NMdata/NAMESPACE | 2 NMdata-0.2.5/NMdata/NEWS.md | 19 NMdata-0.2.5/NMdata/R/NMctl.R | 13 NMdata-0.2.5/NMdata/R/NMreadExt.R | 10 NMdata-0.2.5/NMdata/R/NMreadInits.R | 82 +- NMdata-0.2.5/NMdata/R/NMreadParsText.R | 31 NMdata-0.2.5/NMdata/R/NMreadPhi.R | 2 NMdata-0.2.5/NMdata/R/NMscanInput.R | 33 NMdata-0.2.5/NMdata/R/NMwriteData.R | 3 NMdata-0.2.5/NMdata/R/addTableStep.R | 9 NMdata-0.2.5/NMdata/R/dcastSe.R | 45 - NMdata-0.2.5/NMdata/R/deprecatedArg.R | 5 NMdata-0.2.5/NMdata/R/findCovs.R | 2 NMdata-0.2.5/NMdata/R/isSAME.R |only NMdata-0.2.5/NMdata/R/lapplydt.R | 6 NMdata-0.2.5/NMdata/R/reorder2.R |only NMdata-0.2.5/NMdata/R/setOrderList.R |only NMdata-0.2.5/NMdata/README.md | 90 +- NMdata-0.2.5/NMdata/man/NSAME.Rd |only NMdata-0.2.5/NMdata/man/dcastSe.Rd | 33 NMdata-0.2.5/NMdata/man/deprecatedArg.Rd | 5 NMdata-0.2.5/NMdata/man/elemsToExt.Rd |only NMdata-0.2.5/NMdata/man/findCovs.Rd | 2 NMdata-0.2.5/NMdata/man/isSAME.Rd |only NMdata-0.2.5/NMdata/man/lapplydt.Rd | 5 NMdata-0.2.5/NMdata/man/reorder2.Rd |only NMdata-0.2.5/NMdata/man/setOrderList.Rd |only NMdata-0.2.5/NMdata/tests/testthat/testOutput/NMwriteData10.rds |binary NMdata-0.2.5/NMdata/tests/testthat/testOutput/NMwriteData11.rds |binary NMdata-0.2.5/NMdata/tests/testthat/testOutput/NMwriteDataTmp.rds |binary NMdata-0.2.5/NMdata/tests/testthat/testOutput/NMwriteSection_07.mod | 1 NMdata-0.2.5/NMdata/tests/testthat/testOutput/pk.rds |binary NMdata-0.2.5/NMdata/tests/testthat/testOutput/reorder2_01.rds |only NMdata-0.2.5/NMdata/tests/testthat/testOutput/stampedData_08.rds |binary NMdata-0.2.5/NMdata/tests/testthat/testOutput/stampedData_08_meta.txt | 2 NMdata-0.2.5/NMdata/tests/testthat/testOutput/stampedData_09_meta.txt | 2 NMdata-0.2.5/NMdata/tests/testthat/testReference/NMreadInits_06_elems.rds |only NMdata-0.2.5/NMdata/tests/testthat/testReference/NMreadInits_06_lines.rds |only NMdata-0.2.5/NMdata/tests/testthat/testReference/NMreadInits_06_pars.rds |only NMdata-0.2.5/NMdata/tests/testthat/testReference/NMreadInits_07.rds |only NMdata-0.2.5/NMdata/tests/testthat/testReference/NMreadInits_08.rds |only NMdata-0.2.5/NMdata/tests/testthat/testReference/NMscanInput_04.rds |binary NMdata-0.2.5/NMdata/tests/testthat/test_NMreadExt.R | 6 NMdata-0.2.5/NMdata/tests/testthat/test_NMreadInits.R | 376 ++++++---- NMdata-0.2.5/NMdata/tests/testthat/test_NMreadParText.R | 48 + NMdata-0.2.5/NMdata/tests/testthat/test_NMscanInput.R | 62 + NMdata-0.2.5/NMdata/tests/testthat/test_NMwriteData.R | 2 NMdata-0.2.5/NMdata/tests/testthat/test_dcastSe.R | 18 NMdata-0.2.5/NMdata/tests/testthat/test_isSAME.R |only NMdata-0.2.5/NMdata/tests/testthat/test_reorder2.R |only NMdata-0.2.5/NMdata/tests/testthat/test_setOrderList.R |only 93 files changed, 704 insertions(+), 362 deletions(-)
Title: Interface for Large Language Model APIs in R
Description: Provides a unified interface to large language models across multiple
providers. Supports text generation, tidy data workflows, structured output
with optional JSON Schema validation, XML-like tag extraction, and embeddings.
Includes chat sessions, consistent error handling, and parallel batch tools.
Author: Ali Sanaei [aut, cre]
Maintainer: Ali Sanaei <sanaei@uchicago.edu>
Diff between LLMR versions 0.6.4 dated 2026-05-21 and 0.8.6 dated 2026-06-17
LLMR-0.6.4/LLMR/vignettes/demo.pdf |only LLMR-0.6.4/LLMR/vignettes/demo.pdf.asis |only LLMR-0.8.6/LLMR/DESCRIPTION | 15 LLMR-0.8.6/LLMR/MD5 | 204 ++- LLMR-0.8.6/LLMR/NAMESPACE | 52 LLMR-0.8.6/LLMR/NEWS.md | 501 ++++++- LLMR-0.8.6/LLMR/R/LLMR.R | 1005 ++++++++++----- LLMR-0.8.6/LLMR/R/LLMR_response.R | 125 + LLMR-0.8.6/LLMR/R/LLMR_tidy.R | 475 +++++-- LLMR-0.8.6/LLMR/R/LLM_chat_session.R | 168 ++ LLMR-0.8.6/LLMR/R/LLM_parallel_utils.R | 439 +++++- LLMR-0.8.6/LLMR/R/LLM_param_translate.R | 68 - LLMR-0.8.6/LLMR/R/LLM_robust_utils.R | 137 +- LLMR-0.8.6/LLMR/R/audit_log.R |only LLMR-0.8.6/LLMR/R/batch_api.R |only LLMR-0.8.6/LLMR/R/batch_mode.R |only LLMR-0.8.6/LLMR/R/generics.R |only LLMR-0.8.6/LLMR/R/generics_reset.R |only LLMR-0.8.6/LLMR/R/globalVariables.R | 8 LLMR-0.8.6/LLMR/R/hash.R |only LLMR-0.8.6/LLMR/R/json_mode.R | 259 +++ LLMR-0.8.6/LLMR/R/log_messages.R |only LLMR-0.8.6/LLMR/R/log_read.R |only LLMR-0.8.6/LLMR/R/logprobs.R |only LLMR-0.8.6/LLMR/R/preview.R |only LLMR-0.8.6/LLMR/R/render_messages.R |only LLMR-0.8.6/LLMR/R/replicate.R |only LLMR-0.8.6/LLMR/R/request_hash.R |only LLMR-0.8.6/LLMR/R/response_record.R |only LLMR-0.8.6/LLMR/R/secrets.R | 133 + LLMR-0.8.6/LLMR/R/stream.R |only LLMR-0.8.6/LLMR/R/tags_mode.R | 208 ++- LLMR-0.8.6/LLMR/R/tools.R |only LLMR-0.8.6/LLMR/R/usage.R |only LLMR-0.8.6/LLMR/README.md | 214 +-- LLMR-0.8.6/LLMR/build/vignette.rds |binary LLMR-0.8.6/LLMR/inst/ai |only LLMR-0.8.6/LLMR/inst/doc/about-schema.R | 27 LLMR-0.8.6/LLMR/inst/doc/about-schema.Rmd | 52 LLMR-0.8.6/LLMR/inst/doc/about-schema.html | 94 - LLMR-0.8.6/LLMR/inst/doc/chat-basics.R | 52 LLMR-0.8.6/LLMR/inst/doc/chat-basics.Rmd | 70 - LLMR-0.8.6/LLMR/inst/doc/chat-basics.html | 96 - LLMR-0.8.6/LLMR/inst/doc/experiments.R | 6 LLMR-0.8.6/LLMR/inst/doc/experiments.Rmd | 10 LLMR-0.8.6/LLMR/inst/doc/experiments.html | 16 LLMR-0.8.6/LLMR/inst/doc/interactive-calls.R |only LLMR-0.8.6/LLMR/inst/doc/interactive-calls.Rmd |only LLMR-0.8.6/LLMR/inst/doc/interactive-calls.html |only LLMR-0.8.6/LLMR/inst/doc/presidential_embeddings.R | 7 LLMR-0.8.6/LLMR/inst/doc/presidential_embeddings.Rmd | 9 LLMR-0.8.6/LLMR/inst/doc/presidential_embeddings.html | 11 LLMR-0.8.6/LLMR/inst/doc/quickstart.R |only LLMR-0.8.6/LLMR/inst/doc/quickstart.Rmd |only LLMR-0.8.6/LLMR/inst/doc/quickstart.html |only LLMR-0.8.6/LLMR/inst/doc/reproducibility-and-cost.R |only LLMR-0.8.6/LLMR/inst/doc/reproducibility-and-cost.Rmd |only LLMR-0.8.6/LLMR/inst/doc/reproducibility-and-cost.html |only LLMR-0.8.6/LLMR/inst/doc/tidy-and-structured.R | 51 LLMR-0.8.6/LLMR/inst/doc/tidy-and-structured.Rmd | 138 +- LLMR-0.8.6/LLMR/inst/doc/tidy-and-structured.html | 212 ++- LLMR-0.8.6/LLMR/inst/doc/trolley-dilemma-experiment.R |only LLMR-0.8.6/LLMR/inst/doc/trolley-dilemma-experiment.Rmd |only LLMR-0.8.6/LLMR/inst/doc/trolley-dilemma-experiment.html |only LLMR-0.8.6/LLMR/inst/examples/demo.qmd | 16 LLMR-0.8.6/LLMR/man/build_factorial_experiments.Rd | 6 LLMR-0.8.6/LLMR/man/cache_llm_call.Rd | 4 LLMR-0.8.6/LLMR/man/call_llm.Rd | 30 LLMR-0.8.6/LLMR/man/call_llm_broadcast.Rd | 6 LLMR-0.8.6/LLMR/man/call_llm_compare.Rd | 6 LLMR-0.8.6/LLMR/man/call_llm_par.Rd | 32 LLMR-0.8.6/LLMR/man/call_llm_par_tags.Rd |only LLMR-0.8.6/LLMR/man/call_llm_robust.Rd | 30 LLMR-0.8.6/LLMR/man/call_llm_stream.Rd |only LLMR-0.8.6/LLMR/man/call_llm_sweep.Rd | 7 LLMR-0.8.6/LLMR/man/call_llm_tools.Rd |only LLMR-0.8.6/LLMR/man/diagnostics.Rd |only LLMR-0.8.6/LLMR/man/enable_structured_output.Rd | 31 LLMR-0.8.6/LLMR/man/expand_llm_config.Rd |only LLMR-0.8.6/LLMR/man/get_batched_embeddings.Rd | 40 LLMR-0.8.6/LLMR/man/llm_agreement.Rd |only LLMR-0.8.6/LLMR/man/llm_api_key_env.Rd |only LLMR-0.8.6/LLMR/man/llm_batch_cancel.Rd |only LLMR-0.8.6/LLMR/man/llm_batch_fetch.Rd |only LLMR-0.8.6/LLMR/man/llm_batch_status.Rd |only LLMR-0.8.6/LLMR/man/llm_batch_submit.Rd |only LLMR-0.8.6/LLMR/man/llm_chat_session.Rd | 14 LLMR-0.8.6/LLMR/man/llm_config.Rd | 94 + LLMR-0.8.6/LLMR/man/llm_cross_design.Rd |only LLMR-0.8.6/LLMR/man/llm_failures.Rd |only LLMR-0.8.6/LLMR/man/llm_fn.Rd | 91 + LLMR-0.8.6/LLMR/man/llm_fn_structured.Rd | 33 LLMR-0.8.6/LLMR/man/llm_fn_tags.Rd |only LLMR-0.8.6/LLMR/man/llm_hash.Rd |only LLMR-0.8.6/LLMR/man/llm_judge.Rd |only LLMR-0.8.6/LLMR/man/llm_log_enable.Rd |only LLMR-0.8.6/LLMR/man/llm_log_read.Rd |only LLMR-0.8.6/LLMR/man/llm_logprobs.Rd |only LLMR-0.8.6/LLMR/man/llm_methods_text.Rd |only LLMR-0.8.6/LLMR/man/llm_mutate.Rd | 60 LLMR-0.8.6/LLMR/man/llm_mutate_structured.Rd | 30 LLMR-0.8.6/LLMR/man/llm_mutate_tags.Rd | 20 LLMR-0.8.6/LLMR/man/llm_par_resume.Rd |only LLMR-0.8.6/LLMR/man/llm_parse_rowpack_tags.Rd |only LLMR-0.8.6/LLMR/man/llm_preview.Rd |only LLMR-0.8.6/LLMR/man/llm_render_messages.Rd |only LLMR-0.8.6/LLMR/man/llm_replicate.Rd |only LLMR-0.8.6/LLMR/man/llm_request_from_log.Rd |only LLMR-0.8.6/LLMR/man/llm_request_hash.Rd |only LLMR-0.8.6/LLMR/man/llm_response_record.Rd |only LLMR-0.8.6/LLMR/man/llm_tool.Rd |only LLMR-0.8.6/LLMR/man/llm_usage.Rd |only LLMR-0.8.6/LLMR/man/llmr_response.Rd | 19 LLMR-0.8.6/LLMR/man/log_llm_error.Rd | 8 LLMR-0.8.6/LLMR/man/parse_embeddings.Rd | 6 LLMR-0.8.6/LLMR/man/print.llm_config.Rd |only LLMR-0.8.6/LLMR/man/report.Rd |only LLMR-0.8.6/LLMR/man/reset.Rd |only LLMR-0.8.6/LLMR/man/tool_calls.Rd |only LLMR-0.8.6/LLMR/tests/testthat/test-083-core.R |only LLMR-0.8.6/LLMR/tests/testthat/test-083-features.R |only LLMR-0.8.6/LLMR/tests/testthat/test-ai-capsule.R |only LLMR-0.8.6/LLMR/tests/testthat/test-audit-fixes-2.R |only LLMR-0.8.6/LLMR/tests/testthat/test-audit-fixes.R |only LLMR-0.8.6/LLMR/tests/testthat/test-batch_mode.R |only LLMR-0.8.6/LLMR/tests/testthat/test-bugfixes.R |only LLMR-0.8.6/LLMR/tests/testthat/test-call_llm.R | 25 LLMR-0.8.6/LLMR/tests/testthat/test-canonical-hash.R |only LLMR-0.8.6/LLMR/tests/testthat/test-generics.R |only LLMR-0.8.6/LLMR/tests/testthat/test-live-cheap.R |only LLMR-0.8.6/LLMR/tests/testthat/test-llm_fn.R | 7 LLMR-0.8.6/LLMR/tests/testthat/test-log-read.R |only LLMR-0.8.6/LLMR/tests/testthat/test-preview.R |only LLMR-0.8.6/LLMR/tests/testthat/test-render-messages.R |only LLMR-0.8.6/LLMR/tests/testthat/test-request-hash.R |only LLMR-0.8.6/LLMR/tests/testthat/test-response-record.R |only LLMR-0.8.6/LLMR/tests/testthat/test-usage.R |only LLMR-0.8.6/LLMR/vignettes/about-schema.Rmd | 52 LLMR-0.8.6/LLMR/vignettes/chat-basics.Rmd | 70 - 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Title: High-Level Modeling Functions with 'torch'
Description: Provides high-level modeling functions to define and train
models using the 'torch' R package. Models include linear, logistic,
and multinomial regression as well as multilayer perceptrons.
Author: Max Kuhn [aut, cre] ,
Daniel Falbel [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between brulee versions 0.6.0 dated 2025-09-01 and 1.0.0 dated 2026-06-17
DESCRIPTION | 20 MD5 | 150 +++- NAMESPACE | 50 + NEWS.md | 20 R/0_utils.R | 339 ++++++++-- R/autoint-fit.R |only R/autoint-predict.R |only R/autoplot.R | 17 R/checks.R | 293 ++++---- R/chronos2-fit.R |only R/chronos2-misc.R |only R/chronos2-predict.R |only R/coef.R | 18 R/convert_data.R | 18 R/linear_reg-fit.R | 289 +++----- R/linear_reg-predict.R | 46 - R/logistic_reg-fit.R | 333 ++++------ R/logistic_reg-predict.R | 47 - R/mlp-fit.R | 593 +++++++++-------- R/mlp-predict.R | 80 +- R/multinomial_reg-fit.R | 326 ++++----- R/multinomial_reg-predict.R | 42 - R/outcome_processing.R |only R/resnet-fit.R |only R/resnet-predict.R |only R/rln-fit.R |only R/rln-predict.R |only R/saint-fit.R |only R/saint-predict.R |only R/schedulers.R | 10 R/summary.R |only R/training_efficiency.R |only R/training_loop.R |only R/validation.R |only README.md | 12 inst/WORDLIST | 68 ++ inst/test_cuda_fix.R |only man/brulee-autoplot.Rd | 14 man/brulee-coefs.Rd | 8 man/brulee-package.Rd | 1 man/brulee_auto_int.Rd |only man/brulee_chronos.Rd |only man/brulee_linear_reg.Rd | 10 man/brulee_logistic_reg.Rd | 10 man/brulee_mlp.Rd | 17 man/brulee_multinomial_reg.Rd | 10 man/brulee_resnet.Rd |only man/brulee_rln.Rd |only man/brulee_saint.Rd |only man/matrix_to_dataset.Rd | 7 man/predict.brulee_auto_int.Rd |only man/predict.brulee_chronos.Rd |only man/predict.brulee_linear_reg.Rd | 2 man/predict.brulee_logistic_reg.Rd | 2 man/predict.brulee_mlp.Rd | 2 man/predict.brulee_multinomial_reg.Rd | 2 man/predict.brulee_resnet.Rd |only man/predict.brulee_rln.Rd |only man/predict.brulee_saint.Rd |only man/reexports.Rd | 6 man/schedule_decay_time.Rd | 3 man/summary.brulee.Rd |only man/training_efficiency.Rd |only tests/spelling.R | 13 tests/testthat.R | 9 tests/testthat/_snaps/autoint.md |only tests/testthat/_snaps/checks.md | 87 ++ tests/testthat/_snaps/chronos2-fit.md |only tests/testthat/_snaps/chronos2-misc.md |only tests/testthat/_snaps/chronos2-predict.md |only tests/testthat/_snaps/class-weight.md | 12 tests/testthat/_snaps/mlp-regression.md | 118 +-- tests/testthat/_snaps/saint.md |only tests/testthat/_snaps/schedulers.md | 20 tests/testthat/_snaps/set-optimizer.md |only tests/testthat/helper-chronos2.R |only tests/testthat/helper-output.R |only tests/testthat/test-autoint.R |only tests/testthat/test-check-mixture.R |only tests/testthat/test-checks.R | 124 +++ tests/testthat/test-chronos2-fit.R |only tests/testthat/test-chronos2-misc.R |only tests/testthat/test-chronos2-predict.R |only tests/testthat/test-class-weight.R | 150 ++-- tests/testthat/test-device-support.R |only tests/testthat/test-linear_reg-fit.R | 280 ++++---- tests/testthat/test-logistic_reg-fit.R | 410 ++++++------ tests/testthat/test-make-penalized-loss.R |only tests/testthat/test-mlp-activations.R | 73 +- tests/testthat/test-mlp-binary.R | 487 ++++++++------ tests/testthat/test-mlp-multinomial.R | 439 +++++++------ tests/testthat/test-mlp-regression.R | 997 ++++++++++++++++-------------- tests/testthat/test-multinomial_reg-fit.R | 413 ++++++------ tests/testthat/test-penalty-integration.R |only tests/testthat/test-penalty.R |only tests/testthat/test-resnet-binary.R |only tests/testthat/test-resnet-multinomial.R |only tests/testthat/test-resnet-regression.R |only tests/testthat/test-rln-regression.R |only tests/testthat/test-saint.R |only tests/testthat/test-schedulers.R | 204 +++--- tests/testthat/test-set-optimizer.R |only 102 files changed, 3786 insertions(+), 2915 deletions(-)
Title: 'tidyverse' Methods and 'ggplot2' Helpers for 'terra' Objects
Description: Provides methods from 'tidyverse' packages for 'SpatRaster'
and 'SpatVector' objects created with 'terra', plus 'ggplot2' 'geoms'
and scales for plotting those objects.
Author: Diego Hernangomez [aut, cre, cph] ,
Dewey Dunnington [ctb] ,
ggplot2 authors [cph] ,
Andrea Manica [ctb]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between tidyterra versions 1.1.0 dated 2026-03-11 and 1.2.0 dated 2026-06-17
tidyterra-1.1.0/tidyterra/man/group-by.SpatVector.Rd |only tidyterra-1.2.0/tidyterra/DESCRIPTION | 18 tidyterra-1.2.0/tidyterra/LICENSE | 4 tidyterra-1.2.0/tidyterra/MD5 | 519 +- tidyterra-1.2.0/tidyterra/NAMESPACE | 719 ++-- tidyterra-1.2.0/tidyterra/NEWS.md | 417 +- tidyterra-1.2.0/tidyterra/R/arrange-SpatVector.R | 153 tidyterra-1.2.0/tidyterra/R/as-coordinates.R | 137 tidyterra-1.2.0/tidyterra/R/as-sf.R | 163 tidyterra-1.2.0/tidyterra/R/as-spatraster.R | 487 +- tidyterra-1.2.0/tidyterra/R/as-spatvector.R | 150 tidyterra-1.2.0/tidyterra/R/as-tibble-Spat.R | 810 ++-- tidyterra-1.2.0/tidyterra/R/autoplot-Spat.R | 326 - tidyterra-1.2.0/tidyterra/R/bind-cols-SpatVector.R | 279 - tidyterra-1.2.0/tidyterra/R/bind-rows-SpatVector.R | 441 +- tidyterra-1.2.0/tidyterra/R/compare-spatrasters.R | 221 - tidyterra-1.2.0/tidyterra/R/complete-SpatVector.R |only tidyterra-1.2.0/tidyterra/R/count-tally-SpatVector.R | 496 +- tidyterra-1.2.0/tidyterra/R/data.R | 676 +-- tidyterra-1.2.0/tidyterra/R/distinct-SpatVector.R | 256 - tidyterra-1.2.0/tidyterra/R/drop-na-Spat.R | 366 +- tidyterra-1.2.0/tidyterra/R/expand-SpatVector.R |only tidyterra-1.2.0/tidyterra/R/fill-SpatVector.R | 163 tidyterra-1.2.0/tidyterra/R/filter-Spat.R | 383 +- tidyterra-1.2.0/tidyterra/R/fortify-Spat.R | 319 - tidyterra-1.2.0/tidyterra/R/geom-spat-contour-fill.R | 133 tidyterra-1.2.0/tidyterra/R/geom-spat-contour-text.R | 153 tidyterra-1.2.0/tidyterra/R/geom-spat-contour.R | 269 - tidyterra-1.2.0/tidyterra/R/geom-spatraster-rgb.R | 664 +-- tidyterra-1.2.0/tidyterra/R/geom-spatraster.R | 1074 ++---- tidyterra-1.2.0/tidyterra/R/geom-spatvector.R | 324 - tidyterra-1.2.0/tidyterra/R/glance-Spat.R | 272 - tidyterra-1.2.0/tidyterra/R/glimpse-Spat.R | 112 tidyterra-1.2.0/tidyterra/R/group-by-SpatVector.R | 372 +- tidyterra-1.2.0/tidyterra/R/group-data-SpatVector.R | 418 +- tidyterra-1.2.0/tidyterra/R/group-map-SpatVector.R |only tidyterra-1.2.0/tidyterra/R/group-nest-SpatVector.R |only tidyterra-1.2.0/tidyterra/R/group-split-SpatVector.R |only tidyterra-1.2.0/tidyterra/R/group-trim.SpatVector.R |only tidyterra-1.2.0/tidyterra/R/grouped-SpatVector.R | 66 tidyterra-1.2.0/tidyterra/R/is-regular-grid.R | 176 tidyterra-1.2.0/tidyterra/R/join-SpatVector.R | 68 tidyterra-1.2.0/tidyterra/R/join-cross.SpatVector.R |only tidyterra-1.2.0/tidyterra/R/mutate-Spat.R | 364 +- tidyterra-1.2.0/tidyterra/R/nest-SpatVector.R |only tidyterra-1.2.0/tidyterra/R/nest-join-SpatVector.R |only tidyterra-1.2.0/tidyterra/R/pivot-long-SpatVector.R | 291 - tidyterra-1.2.0/tidyterra/R/pivot-wide-SpatVector.R | 335 - tidyterra-1.2.0/tidyterra/R/pull-Spat.R | 228 - tidyterra-1.2.0/tidyterra/R/pull-crs.R | 266 - tidyterra-1.2.0/tidyterra/R/reframe-SpatVector.R |only tidyterra-1.2.0/tidyterra/R/relocate-Spat.R | 196 - tidyterra-1.2.0/tidyterra/R/rename-Spat.R | 267 - tidyterra-1.2.0/tidyterra/R/replace-na-Spat.R | 260 - tidyterra-1.2.0/tidyterra/R/required-pkgs-Spat.R | 124 tidyterra-1.2.0/tidyterra/R/rows-SpatVector.R |only tidyterra-1.2.0/tidyterra/R/rowwise-SpatVector.R | 268 - tidyterra-1.2.0/tidyterra/R/scales-coltab.R | 526 +- tidyterra-1.2.0/tidyterra/R/scales-cross-blended.R | 1548 ++++---- tidyterra-1.2.0/tidyterra/R/scales-grass.R | 1051 ++--- tidyterra-1.2.0/tidyterra/R/scales-hypso.R | 1503 +++----- tidyterra-1.2.0/tidyterra/R/scales-princess.R | 671 +-- tidyterra-1.2.0/tidyterra/R/scales-terrain.R | 490 +- tidyterra-1.2.0/tidyterra/R/scales-whitebox.R | 710 +-- tidyterra-1.2.0/tidyterra/R/scales-wiki.R | 639 +-- tidyterra-1.2.0/tidyterra/R/select-Spat.R | 244 - tidyterra-1.2.0/tidyterra/R/slice-Spat.R | 1507 ++++---- tidyterra-1.2.0/tidyterra/R/stat-spat-coordinates.R | 131 tidyterra-1.2.0/tidyterra/R/stat-spatraster.R | 376 +- tidyterra-1.2.0/tidyterra/R/summarise-SpatVector.R | 39 tidyterra-1.2.0/tidyterra/R/sysdata.rda |binary tidyterra-1.2.0/tidyterra/R/tidy-Spat.R | 363 +- tidyterra-1.2.0/tidyterra/R/tidyterra-package.R | 38 tidyterra-1.2.0/tidyterra/R/transmute-Spat.R | 236 - tidyterra-1.2.0/tidyterra/R/uncount-SpatVector.R |only tidyterra-1.2.0/tidyterra/R/unite-Spat.R |only tidyterra-1.2.0/tidyterra/R/utils-pipe.R | 29 tidyterra-1.2.0/tidyterra/R/utils.R | 327 + tidyterra-1.2.0/tidyterra/README.md | 160 tidyterra-1.2.0/tidyterra/build/partial.rdb |binary tidyterra-1.2.0/tidyterra/build/vignette.rds |binary tidyterra-1.2.0/tidyterra/data/cross_blended_hypsometric_tints_db.rda |binary tidyterra-1.2.0/tidyterra/data/grass_db.rda |binary tidyterra-1.2.0/tidyterra/data/hypsometric_tints_db.rda |binary tidyterra-1.2.0/tidyterra/data/princess_db.rda |binary tidyterra-1.2.0/tidyterra/data/volcano2.rda |binary tidyterra-1.2.0/tidyterra/inst/CITATION | 32 tidyterra-1.2.0/tidyterra/inst/WORDLIST | 26 tidyterra-1.2.0/tidyterra/inst/doc/tidyterra.html | 135 tidyterra-1.2.0/tidyterra/inst/doc/tidyterra.qmd | 199 - 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tidyterra-1.2.0/tidyterra/vignettes/fig-ex1-1.png |binary tidyterra-1.2.0/tidyterra/vignettes/fig-ex2-1.png |binary tidyterra-1.2.0/tidyterra/vignettes/paper.bib | 632 +-- tidyterra-1.2.0/tidyterra/vignettes/tidyterra.qmd | 199 - tidyterra-1.2.0/tidyterra/vignettes/welcome.qmd | 219 - 282 files changed, 33594 insertions(+), 34615 deletions(-)
Title: Download 'Eurostat' 'GISCO' Spatial Data
Description: Tools to download global and European spatial data from the
'Eurostat' 'GISCO' (Geographic Information System of the Commission)
data distribution <https://ec.europa.eu/eurostat/web/gisco>. The
package provides helpers for country boundaries, 'NUTS' regions,
administrative units, statistical units, transport networks, basic
service locations and other 'GISCO' datasets. This package is not
officially related to or endorsed by 'Eurostat'.
Author: Diego Hernangomez [aut, cre, cph] ,
Eurostat [cph] ,
EuroGeographics [cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between giscoR versions 1.1.0 dated 2026-03-28 and 1.1.1 dated 2026-06-17
DESCRIPTION | 36 MD5 | 299 ++++---- NAMESPACE | 124 +-- NEWS.md | 341 ++++----- R/data.R | 485 ++++++------- R/docs.R | 145 ++- R/gisco-address-api.R | 154 +--- R/gisco-attributions.R | 86 +- R/gisco-bulk-download.R | 224 +++--- R/gisco-cache.R | 726 +++++++++----------- R/gisco-check-access.R | 118 +-- R/gisco-get-airports.R | 194 ++--- R/gisco-get-cached-db.R | 639 ++++++++--------- R/gisco-get-census.R | 137 +-- R/gisco-get-coastal-lines.R | 221 ++---- R/gisco-get-communes.R | 265 +++---- R/gisco-get-countries.R | 416 +++++------ R/gisco-get-education.R | 263 +++---- R/gisco-get-grid.R | 258 +++---- R/gisco-get-healthcare.R | 192 ++--- R/gisco-get-lau.R | 298 +++----- R/gisco-get-metadata.R | 143 ++- R/gisco-get-nuts.R | 497 +++++-------- R/gisco-get-ports.R | 185 ++--- R/gisco-get-postal-codes.R | 247 ++---- R/gisco-get-unit-country.R | 154 +--- R/gisco-get-unit-nuts.R | 182 +---- R/gisco-get-unit-urban-audit.R | 231 ++---- R/gisco-get-units.R | 228 ++---- R/gisco-get-urban-audit.R | 298 +++----- R/gisco-id-api.R | 704 +++++++++---------- R/giscoR-package.R | 21 R/utils-country.R | 66 + R/utils-dataset.R |only R/utils-request.R |only R/utils-sf.R | 397 ++++++---- R/utils-units.R |only R/utils-url.R | 682 +++++++++--------- R/utils.R | 342 +++++---- README.md | 161 ++-- build/stage23.rdb |binary build/vignette.rds |binary data/gisco_coastal_lines.rda |binary data/gisco_countries_2024.rda |binary data/gisco_countrycode.rda |binary data/gisco_db.rda |binary data/gisco_nuts_2024.rda |binary inst/CITATION | 36 inst/COPYRIGHTS | 269 +++---- inst/REFERENCES.bib | 22 inst/WORDLIST | 11 inst/doc/giscoR.html | 299 ++++---- inst/doc/giscoR.qmd | 128 +-- inst/schemaorg.json | 10 man/chunks/address_api.Rmd | 50 - man/chunks/education_meta.Rmd | 24 man/chunks/healthcare_meta.Rmd | 20 man/figures/README-resolution-map-1.png |binary man/figures/README-thematic-map-1.png |binary man/figures/lifecycle-deprecated.svg | 42 - man/figures/lifecycle-experimental.svg | 42 - man/figures/lifecycle-stable.svg | 58 - man/figures/lifecycle-superseded.svg | 42 - man/giscoR-package.Rd | 69 + man/gisco_address_api.Rd | 364 ++++------ man/gisco_attributions.Rd | 194 ++--- man/gisco_bulk_download.Rd | 267 +++---- man/gisco_check_access.Rd | 42 - man/gisco_clear_cache.Rd | 117 +-- man/gisco_coastal_lines.Rd | 66 - man/gisco_countries_2024.Rd | 99 +- man/gisco_countrycode.Rd | 122 +-- man/gisco_db.Rd | 88 +- man/gisco_get_airports.Rd | 178 ++-- man/gisco_get_cached_db.Rd | 96 +- man/gisco_get_census.Rd | 136 +-- man/gisco_get_coastal_lines.Rd | 213 ++--- man/gisco_get_communes.Rd | 257 +++---- man/gisco_get_countries.Rd | 283 +++---- man/gisco_get_education.Rd | 250 +++--- man/gisco_get_grid.Rd | 244 +++--- man/gisco_get_healthcare.Rd | 265 +++---- man/gisco_get_lau.Rd | 263 +++---- man/gisco_get_metadata.Rd | 91 +- man/gisco_get_nuts.Rd | 362 +++++---- man/gisco_get_ports.Rd | 176 ++-- man/gisco_get_postal_codes.Rd | 202 ++--- man/gisco_get_unit.Rd | 305 ++++---- man/gisco_get_units.Rd | 221 +++--- man/gisco_get_urban_audit.Rd | 270 +++---- man/gisco_id_api.Rd | 363 +++++----- man/gisco_nuts_2024.Rd | 156 ++-- man/gisco_set_cache_dir.Rd | 225 +++--- man/roxygen/meta.R | 20 tests/testthat.R | 24 tests/testthat/_snaps/gisco-address-api.md | 6 tests/testthat/_snaps/gisco-attributions.md | 14 tests/testthat/_snaps/gisco-bulk-download.md | 4 tests/testthat/_snaps/gisco-cache.md | 4 tests/testthat/_snaps/gisco-get-cached-db.md | 8 tests/testthat/_snaps/gisco-get-coastal-lines.md | 4 tests/testthat/_snaps/gisco-get-communes.md | 4 tests/testthat/_snaps/gisco-get-countries.md | 4 tests/testthat/_snaps/gisco-get-lau.md | 4 tests/testthat/_snaps/gisco-get-metadata.md | 8 tests/testthat/_snaps/gisco-get-nuts.md | 6 tests/testthat/_snaps/gisco-get-postal-codes.md | 2 tests/testthat/_snaps/gisco-get-unit-country.md | 8 tests/testthat/_snaps/gisco-get-unit-nuts.md | 8 tests/testthat/_snaps/gisco-get-unit-urban-audit.md | 6 tests/testthat/_snaps/gisco-get-units.md | 2 tests/testthat/_snaps/gisco-get-urban-audit.md | 4 tests/testthat/_snaps/gisco-id-api.md | 22 tests/testthat/_snaps/utils-country.md | 10 tests/testthat/_snaps/utils-url.md | 16 tests/testthat/_snaps/utils.md | 25 tests/testthat/helpers.R |only tests/testthat/test-docs.R | 24 tests/testthat/test-gisco-address-api.R | 430 +++++------ tests/testthat/test-gisco-attributions.R | 34 tests/testthat/test-gisco-bulk-download.R | 182 +++-- tests/testthat/test-gisco-cache.R | 7 tests/testthat/test-gisco-check-access.R | 53 - tests/testthat/test-gisco-get-airports.R | 65 + tests/testthat/test-gisco-get-cached-db.R | 319 +++++--- tests/testthat/test-gisco-get-census.R | 104 ++ tests/testthat/test-gisco-get-coastal-lines.R | 77 +- tests/testthat/test-gisco-get-communes.R | 218 +++--- tests/testthat/test-gisco-get-countries.R | 99 +- tests/testthat/test-gisco-get-education.R | 121 ++- tests/testthat/test-gisco-get-grid.R | 59 + tests/testthat/test-gisco-get-healthcare.R | 94 ++ tests/testthat/test-gisco-get-lau.R | 239 +++--- tests/testthat/test-gisco-get-metadata.R | 79 +- tests/testthat/test-gisco-get-nuts.R | 119 +-- tests/testthat/test-gisco-get-ports.R | 66 + tests/testthat/test-gisco-get-postal-codes.R | 131 ++- tests/testthat/test-gisco-get-unit-country.R | 379 +++++----- tests/testthat/test-gisco-get-unit-nuts.R | 377 ++++------ tests/testthat/test-gisco-get-unit-urban-audit.R | 419 +++++------ tests/testthat/test-gisco-get-units.R | 161 ++-- tests/testthat/test-gisco-get-urban-audit.R | 164 ++-- tests/testthat/test-gisco-id-api.R | 87 +- tests/testthat/test-issues.R | 221 +++--- tests/testthat/test-utils-country.R | 193 ++--- tests/testthat/test-utils-sf.R | 212 ++--- tests/testthat/test-utils-units.R |only tests/testthat/test-utils-url.R | 205 ++++- tests/testthat/test-utils.R | 69 + vignettes/fig-africa-1.png |binary vignettes/fig-country-1.png |binary vignettes/fig-giscor-1.png |binary vignettes/giscoR.qmd | 128 +-- 153 files changed, 11390 insertions(+), 11154 deletions(-)
Title: A Collection of Functions for Directional Data Analysis
Description: A collection of functions for directional data (including massive data, with millions of observations) analysis.
Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included.
The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000).
Other references include:
a) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2018). "An elliptically symmetric angular Gaussian distribution". Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>.
b) Tsagris M. and Alenazi A. (2019). "Comparison of discriminant analysis methods on the sphere". Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>.
c) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2020). "Spherical regression models with general covariates and anisotropic errors". Statistics and Computing 30(1): 153--165. <doi:10.1007/s11222-019-09872 [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Christos Adam [aut],
Zehao Yu [aut],
Anamul Sajib [ctb],
Eli Amson [ctb],
Micah J. Waldstein [ctb],
Panagiotis Papastamoulis [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Directional versions 7.5 dated 2026-04-30 and 7.6 dated 2026-06-17
DESCRIPTION | 13 +++++----- MD5 | 54 ++++++++++++++++++++++----------------------- NAMESPACE | 4 +-- R/bic.mixpkbd.R | 2 - R/bic.mixspcauchy.R | 2 - R/bic.mixvmf.R | 2 - R/circpurka.reg.R | 20 +++++++++------- R/euclid.R | 11 +++------ R/euclid.inv.R | 15 +++++------- R/rESAGd.R | 50 ++++++++++++++++++++--------------------- R/rcircbeta.R | 4 +-- R/rcircexp.R | 2 - R/rcircpurka.R | 17 +++++--------- R/resag.R | 2 - R/riag.R | 2 - R/rmixpkbd.R | 2 - R/rmixspcauchy.R | 2 - R/rmixvmf.R | 2 - R/rpkbd.R | 8 +++--- R/rspml.R | 2 - R/sespc.mle.R | 17 ++++++++------ man/Directional-package.Rd | 4 +-- man/euclid.Rd | 4 +-- man/euclid.inv.Rd | 2 - man/gcpc.means.test.Rd | 3 +- man/rvonmises.Rd | 12 +++++----- man/spml.mle.Rd | 5 ++-- man/spml.reg.Rd | 6 +++-- 28 files changed, 134 insertions(+), 135 deletions(-)
Title: Dependent Mixture Models - Hidden Markov Models of GLMs and
Other Distributions in S4
Description: Fits latent (hidden) Markov models on mixed categorical and continuous (time series) data, otherwise known as dependent mixture models, see Visser & Speekenbrink (2010, <DOI:10.18637/jss.v036.i07>).
Author: Ingmar Visser [aut, cre],
Maarten Speekenbrink [aut]
Maintainer: Ingmar Visser <i.visser@uva.nl>
Diff between depmixS4 versions 1.5-2 dated 2026-06-03 and 1.5-3 dated 2026-06-17
DESCRIPTION | 8 - MD5 | 11 + NEWS | 6 + README | 2 inst/doc/depmixS4.pdf |binary tests/test4examples.R | 293 +++++++++++--------------------------------------- tools |only 7 files changed, 85 insertions(+), 235 deletions(-)
Title: Deal with Country Data in an Easy Way
Description: Wrangle country data more effectively and quickly.
This package contains functions to easily identify and convert country names,
download country information, merge country data from different sources,
and make quick world maps.
Author: Francesco Saverio Bellelli [aut, cre, cph]
Maintainer: Francesco Saverio Bellelli <fsabellelli@gmail.com>
Diff between countries versions 1.2.2 dated 2025-06-14 and 1.2.3 dated 2026-06-17
DESCRIPTION | 10 - MD5 | 24 ++-- NAMESPACE | 2 NEWS.md | 3 R/check_countries_api.R | 9 + R/country_info.R | 191 ++++++++++++++-------------------- R/list_fields.R | 3 README.md | 59 +++++----- inst/doc/auto_merge.html | 60 +++++----- inst/doc/dealing_with_names.html | 9 - man/country_info.Rd | 41 +++---- man/figures/unnamed-chunk-8-1.png |binary tests/testthat/test_function_output.R | 13 -- 13 files changed, 203 insertions(+), 221 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-02 1.1.1
2025-07-01 1.1.0
2023-08-18 1.0.6
2023-03-16 1.0.5
2023-01-30 1.0.4
2022-11-12 1.0.3
2022-10-13 1.0.2
2022-06-17 1.0.1
2022-06-09 1.0.0