Title: Trellis Graphics for R
Description: A powerful and elegant high-level data visualization
system inspired by Trellis graphics, with an emphasis on
multivariate data. Lattice is sufficient for typical graphics needs,
and is also flexible enough to handle most nonstandard requirements.
See ?Lattice for an introduction.
Author: Deepayan Sarkar [aut, cre] ,
Felix Andrews [ctb],
Kevin Wright [ctb] ,
Neil Klepeis [ctb],
Johan Larsson [ctb] ,
Zhijian Wen [cph] ,
Paul Murrell [ctb],
Stefan Eng [ctb] ,
Achim Zeileis [ctb] ,
Alexandre Courtiol [ctb]
Maintainer: Deepayan Sarkar <deepayan.sarkar@r-project.org>
Diff between lattice versions 0.22-9 dated 2026-02-09 and 0.23-1 dated 2026-08-12
ChangeLog | 73 +++++++++++++++++++++++++++++++ DESCRIPTION | 11 ++-- MD5 | 57 ++++++++++++------------ NAMESPACE | 6 -- NEWS.md | 5 ++ R/common.R | 9 +++ R/levelplot.R | 2 R/panels.R | 30 ++++++------ R/parallel.R | 15 ------ R/settings.R | 11 ++-- R/xyplot.R | 10 ++-- build/vignette.rds |binary data/barley.rda |binary data/environmental.rda |binary data/ethanol.rda |binary data/melanoma.rda |binary data/singer.rda |binary inst/doc/grid.R | 2 inst/doc/grid.pdf |binary inst/po/en@quot/LC_MESSAGES/R-lattice.mo |binary man/Lattice.Rd | 2 man/axis.default.Rd | 4 - man/figures/logo-saturated.svg |only man/latticeParseFormula.Rd | 39 +++++++++------- man/llines.Rd | 1 man/panel.parallel.Rd | 22 ++++++--- man/prepanel.default.Rd | 22 ++++----- man/xyplot.Rd | 25 +++++++--- po/R-lattice.pot | 4 - tests/MASSch04.R | 42 +++++++++-------- 30 files changed, 247 insertions(+), 145 deletions(-)
Title: FastICA Algorithms to Perform ICA and Projection Pursuit
Description: Implementation of FastICA algorithm to perform Independent
Component Analysis (ICA) and Projection Pursuit.
Author: Jonathan L Marchini [aut],
Chris Heaton [aut],
Brian Ripley [aut, cre]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between fastICA versions 1.2-7 dated 2024-12-11 and 1.2-8 dated 2026-08-12
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/fastICA.Rd | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Functions for Kernel Smoothing Supporting Wand & Jones (1995)
Description: Functions for kernel smoothing (and density estimation)
corresponding to the book:
Wand, M.P. and Jones, M.C. (1995) "Kernel Smoothing".
Author: Matt Wand [aut],
Cleve Moler [ctb] ,
Brian Ripley [trl, cre, ctb]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between KernSmooth versions 2.23-26 dated 2025-01-01 and 2.23-27 dated 2026-08-12
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- man/bkde.Rd | 4 ++-- man/bkde2D.Rd | 4 ++-- man/bkfe.Rd | 4 ++-- man/dpih.Rd | 4 ++-- man/dpik.Rd | 4 ++-- man/dpill.Rd | 4 ++-- man/locpoly.Rd | 4 ++-- 9 files changed, 26 insertions(+), 26 deletions(-)
Title: Time Series Analysis and Computational Finance
Description: Time series analysis and computational finance.
Author: Adrian Trapletti [aut],
Kurt Hornik [aut, cre] ,
Blake LeBaron [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between tseries versions 0.10-62 dated 2026-07-13 and 0.10-63 dated 2026-08-11
ChangeLog | 4 ++++ DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- build/partial.rdb |binary man/irts-methods.Rd | 2 ++ man/portfolio.optim.Rd | 2 ++ man/terasvirta.test.Rd | 1 + man/white.test.Rd | 1 + 8 files changed, 20 insertions(+), 10 deletions(-)
Title: ODBC Database Access
Description: An ODBC database interface.
Author: Brian Ripley [aut, cre],
Michael Lapsley [aut]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between RODBC versions 1.3-26.1 dated 2025-12-15 and 1.3-26.2 dated 2026-08-11
ChangeLog | 5 +++++ DESCRIPTION | 11 ++++++----- MD5 | 30 +++++++++++++++--------------- build/vignette.rds |binary inst/doc/RODBC.pdf |binary inst/tests.R | 1 + tests/DB2.RR | 2 +- tests/Oracle.RR | 2 +- tests/SQLServer.RR | 2 +- tests/access.RR | 2 +- tests/excel.RR | 2 +- tests/mimer.RR | 2 +- tests/mysql-win.RR | 2 +- tests/mysql.RR | 2 +- tests/postgresql.RR | 2 +- tests/sqlite3.RR | 2 +- 16 files changed, 37 insertions(+), 30 deletions(-)
Title: An Interface to 'SUNDIALS' Ordinary Differential Equation (ODE)
Solvers
Description: Provides a way to call the functions in 'SUNDIALS' C ODE solving library (<https://computing.llnl.gov/projects/sundials>). Currently the serial version of ODE solver, 'CVODE', sensitivity calculator 'CVODES' and differential algebraic solver 'IDA' from the 'SUNDIALS' library are implemented. The package requires ODE to be written as an 'R' or 'Rcpp' function and does not require the 'SUNDIALS' library to be installed on the local machine.
Author: Satyaprakash Nayak [aut, cre, cph] ,
Lawrence Livermore National Security [cph],
Southern Methodist University [cph],
University of Maryland Baltimore County [cph]
Maintainer: Satyaprakash Nayak <satyaprakash.nayak@gmail.com>
Diff between sundialr versions 0.1.7 dated 2026-04-21 and 0.2.0 dated 2026-08-07
sundialr-0.1.7/sundialr/src/sundials-mod-7.6.0.tar.gz |only sundialr-0.1.7/sundialr/src/utils |only sundialr-0.2.0/sundialr/DESCRIPTION | 16 sundialr-0.2.0/sundialr/LICENSE | 2 sundialr-0.2.0/sundialr/MD5 | 123 +- sundialr-0.2.0/sundialr/NEWS.md | 20 sundialr-0.2.0/sundialr/R/RcppExports.R | 60 - sundialr-0.2.0/sundialr/R/zzz.R | 8 sundialr-0.2.0/sundialr/README.md | 138 +- sundialr-0.2.0/sundialr/build/vignette.rds |binary sundialr-0.2.0/sundialr/configure | 22 sundialr-0.2.0/sundialr/configure.ac | 2 sundialr-0.2.0/sundialr/inst/COPYRIGHTS | 12 sundialr-0.2.0/sundialr/inst/doc/my-vignette.Rmd | 4 sundialr-0.2.0/sundialr/inst/doc/my-vignette.html | 25 sundialr-0.2.0/sundialr/inst/examples/cv_Roberts_dns.r | 10 sundialr-0.2.0/sundialr/inst/examples/cvs_Roberts_dns.r | 28 sundialr-0.2.0/sundialr/inst/examples/cvsolve_1D.r | 7 sundialr-0.2.0/sundialr/inst/examples/ida_Roberts_dns.r | 70 - sundialr-0.2.0/sundialr/inst/include/arkode/arkode.h | 63 - sundialr-0.2.0/sundialr/inst/include/arkode/arkode_butcher_dirk.h | 8 sundialr-0.2.0/sundialr/inst/include/arkode/arkode_butcher_erk.h | 10 sundialr-0.2.0/sundialr/inst/include/arkode/arkode_lsrkstep.h | 3 sundialr-0.2.0/sundialr/inst/include/arkode/arkode_mristep.h | 4 sundialr-0.2.0/sundialr/inst/include/check_retval.h | 7 sundialr-0.2.0/sundialr/inst/include/cvode/cvode.h | 7 sundialr-0.2.0/sundialr/inst/include/cvodes/cvodes.h | 7 sundialr-0.2.0/sundialr/inst/include/jac_func.h |only sundialr-0.2.0/sundialr/inst/include/rhs_func.h | 4 sundialr-0.2.0/sundialr/inst/include/sundialr_capi.h |only sundialr-0.2.0/sundialr/inst/include/sundials/sundials_config.h | 46 sundialr-0.2.0/sundialr/inst/include/sundials/sundials_domeigestimator.h | 19 sundialr-0.2.0/sundialr/inst/include/sundials/sundials_logger.h | 38 sundialr-0.2.0/sundialr/inst/include/sundials/sundials_nonlinearsolver.h | 37 sundialr-0.2.0/sundialr/inst/include/sundials/sundials_profiler.h | 6 sundialr-0.2.0/sundialr/inst/include/sundials/sundials_profiler.hpp | 4 sundialr-0.2.0/sundialr/inst/include/sundials_err_handler.h | 43 sundialr-0.2.0/sundialr/inst/include/sundials_err_record.h |only sundialr-0.2.0/sundialr/inst/include/sundials_scope_guard.h |only sundialr-0.2.0/sundialr/inst/include/sundomeigest/sundomeigest_power.h | 31 sundialr-0.2.0/sundialr/inst/include/sunnonlinsol/sunnonlinsol_auto.h |only sundialr-0.2.0/sundialr/inst/include/sunnonlinsol/sunnonlinsol_fixedpoint.h | 24 sundialr-0.2.0/sundialr/inst/include/sunnonlinsol/sunnonlinsol_newton.h | 25 sundialr-0.2.0/sundialr/man/cvode.Rd | 17 sundialr-0.2.0/sundialr/man/cvodes.Rd | 20 sundialr-0.2.0/sundialr/man/cvsolve.Rd | 16 sundialr-0.2.0/sundialr/man/ida.Rd | 86 + sundialr-0.2.0/sundialr/src/Makevars.in | 3 sundialr-0.2.0/sundialr/src/RcppExports.cpp | 126 +- sundialr-0.2.0/sundialr/src/capi_register.cpp |only sundialr-0.2.0/sundialr/src/capi_test.cpp |only sundialr-0.2.0/sundialr/src/check_retval.cpp | 62 - sundialr-0.2.0/sundialr/src/cvode.cpp | 112 + sundialr-0.2.0/sundialr/src/cvodes.cpp | 269 +++- sundialr-0.2.0/sundialr/src/cvsolve.cpp | 562 +++++----- sundialr-0.2.0/sundialr/src/ida.cpp | 221 ++- sundialr-0.2.0/sundialr/src/rhs_func.cpp | 75 - sundialr-0.2.0/sundialr/src/scripts/cran_patches.sh |only sundialr-0.2.0/sundialr/src/scripts/sundials_download.sh | 4 sundialr-0.2.0/sundialr/src/sortTimes.cpp |only sundialr-0.2.0/sundialr/src/sortTimes.h |only sundialr-0.2.0/sundialr/src/sundialr_capi.cpp |only sundialr-0.2.0/sundialr/src/sundials-mod-7.8.0.tar.gz |only sundialr-0.2.0/sundialr/tests/testthat/test-callbacks.r |only sundialr-0.2.0/sundialr/tests/testthat/test-capi.r |only sundialr-0.2.0/sundialr/tests/testthat/test-cvode.r | 74 - sundialr-0.2.0/sundialr/tests/testthat/test-cvodes.r | 63 + sundialr-0.2.0/sundialr/tests/testthat/test-cvsolve.r |only sundialr-0.2.0/sundialr/tests/testthat/test-ida.r |only sundialr-0.2.0/sundialr/tools/cmake_call.sh | 129 -- sundialr-0.2.0/sundialr/tools/strip_sundials_tarball.sh |only sundialr-0.2.0/sundialr/vignettes/my-vignette.Rmd | 4 72 files changed, 1887 insertions(+), 889 deletions(-)
Title: Export Data Frames to Excel 'xlsx' Format
Description: Zero-dependency data frame to xlsx exporter based on 'libxlsxwriter'
<https://libxlsxwriter.github.io>. Fast and no Java or Excel required.
Author: Jeroen Ooms [aut] ,
Bill Denney [aut, cre] ,
John McNamara [cph] )
Maintainer: Bill Denney <wdenney@humanpredictions.com>
Diff between writexl versions 1.5.4 dated 2025-04-15 and 2.0.0 dated 2026-08-05
writexl-1.5.4/writexl/NEWS |only writexl-1.5.4/writexl/src/include |only writexl-1.5.4/writexl/src/libxlsxwriter/app.c |only writexl-1.5.4/writexl/src/libxlsxwriter/chart.c |only writexl-1.5.4/writexl/src/libxlsxwriter/chartsheet.c |only writexl-1.5.4/writexl/src/libxlsxwriter/comment.c |only writexl-1.5.4/writexl/src/libxlsxwriter/content_types.c |only writexl-1.5.4/writexl/src/libxlsxwriter/core.c |only writexl-1.5.4/writexl/src/libxlsxwriter/custom.c |only writexl-1.5.4/writexl/src/libxlsxwriter/drawing.c |only writexl-1.5.4/writexl/src/libxlsxwriter/format.c |only writexl-1.5.4/writexl/src/libxlsxwriter/hash_table.c |only writexl-1.5.4/writexl/src/libxlsxwriter/metadata.c |only writexl-1.5.4/writexl/src/libxlsxwriter/packager.c |only writexl-1.5.4/writexl/src/libxlsxwriter/relationships.c |only writexl-1.5.4/writexl/src/libxlsxwriter/shared_strings.c |only writexl-1.5.4/writexl/src/libxlsxwriter/styles.c |only writexl-1.5.4/writexl/src/libxlsxwriter/table.c |only writexl-1.5.4/writexl/src/libxlsxwriter/theme.c |only writexl-1.5.4/writexl/src/libxlsxwriter/utility.c |only writexl-1.5.4/writexl/src/libxlsxwriter/vml.c |only writexl-1.5.4/writexl/src/libxlsxwriter/workbook.c |only writexl-1.5.4/writexl/src/libxlsxwriter/worksheet.c |only writexl-1.5.4/writexl/src/libxlsxwriter/xmlwriter.c |only writexl-1.5.4/writexl/src/md5 |only writexl-1.5.4/writexl/src/minizip |only writexl-1.5.4/writexl/src/tmpfileplus |only writexl-2.0.0/writexl/DESCRIPTION | 25 writexl-2.0.0/writexl/LICENSE | 4 writexl-2.0.0/writexl/MD5 | 285 - writexl-2.0.0/writexl/NAMESPACE | 112 writexl-2.0.0/writexl/NEWS.md |only writexl-2.0.0/writexl/R/excel_types.R | 228 writexl-2.0.0/writexl/R/sheet_names.R |only writexl-2.0.0/writexl/R/sheet_visibility.R |only writexl-2.0.0/writexl/R/split_panes.R |only writexl-2.0.0/writexl/R/version.R | 33 writexl-2.0.0/writexl/R/write_xlsx.R | 493 +- writexl-2.0.0/writexl/R/xl_cell_general.R |only writexl-2.0.0/writexl/R/xl_chart.R |only writexl-2.0.0/writexl/R/xl_chart_axis.R |only writexl-2.0.0/writexl/R/xl_chart_extras.R |only writexl-2.0.0/writexl/R/xl_chart_format.R |only writexl-2.0.0/writexl/R/xl_chart_parts.R |only writexl-2.0.0/writexl/R/xl_chartsheet.R |only writexl-2.0.0/writexl/R/xl_comment.R |only writexl-2.0.0/writexl/R/xl_conditional.R |only writexl-2.0.0/writexl/R/xl_filter.R |only writexl-2.0.0/writexl/R/xl_format.R |only writexl-2.0.0/writexl/R/xl_image.R |only writexl-2.0.0/writexl/R/xl_merge.R |only writexl-2.0.0/writexl/R/xl_outline.R |only writexl-2.0.0/writexl/R/xl_page_setup.R |only writexl-2.0.0/writexl/R/xl_range.R |only writexl-2.0.0/writexl/R/xl_rich_string.R |only writexl-2.0.0/writexl/R/xl_sheet.R |only writexl-2.0.0/writexl/R/xl_sheet_view.R |only writexl-2.0.0/writexl/R/xl_table.R |only writexl-2.0.0/writexl/R/xl_validation.R |only writexl-2.0.0/writexl/R/xl_workbook.R |only writexl-2.0.0/writexl/build |only writexl-2.0.0/writexl/inst/AUTHORS | 10 writexl-2.0.0/writexl/inst/COPYRIGHT | 142 writexl-2.0.0/writexl/inst/WORDLIST | 92 writexl-2.0.0/writexl/inst/doc |only writexl-2.0.0/writexl/man/is_xl_comment.Rd |only writexl-2.0.0/writexl/man/is_xl_format.Rd |only writexl-2.0.0/writexl/man/write_xlsx.Rd | 132 writexl-2.0.0/writexl/man/writexl.Rd | 22 writexl-2.0.0/writexl/man/xl_cell_general.Rd |only writexl-2.0.0/writexl/man/xl_chart.Rd |only writexl-2.0.0/writexl/man/xl_chart_axis.Rd |only writexl-2.0.0/writexl/man/xl_chart_error_bars.Rd |only writexl-2.0.0/writexl/man/xl_chart_labels.Rd |only writexl-2.0.0/writexl/man/xl_chart_legend.Rd |only writexl-2.0.0/writexl/man/xl_chart_marker.Rd |only writexl-2.0.0/writexl/man/xl_chart_series.Rd |only writexl-2.0.0/writexl/man/xl_chart_table.Rd |only writexl-2.0.0/writexl/man/xl_chart_trendline.Rd |only writexl-2.0.0/writexl/man/xl_chartsheet.Rd |only writexl-2.0.0/writexl/man/xl_color.Rd |only writexl-2.0.0/writexl/man/xl_colrow_spec.Rd |only writexl-2.0.0/writexl/man/xl_comment.Rd |only writexl-2.0.0/writexl/man/xl_conditional.Rd |only writexl-2.0.0/writexl/man/xl_filter.Rd |only writexl-2.0.0/writexl/man/xl_filter_keep.Rd |only writexl-2.0.0/writexl/man/xl_format.Rd |only writexl-2.0.0/writexl/man/xl_format_groups.Rd |only writexl-2.0.0/writexl/man/xl_formula.Rd | 122 writexl-2.0.0/writexl/man/xl_image.Rd |only writexl-2.0.0/writexl/man/xl_merge.Rd |only writexl-2.0.0/writexl/man/xl_outline.Rd |only writexl-2.0.0/writexl/man/xl_page_setup.Rd |only writexl-2.0.0/writexl/man/xl_properties.Rd |only writexl-2.0.0/writexl/man/xl_rich_run.Rd |only writexl-2.0.0/writexl/man/xl_rich_string.Rd |only writexl-2.0.0/writexl/man/xl_sheet.Rd |only writexl-2.0.0/writexl/man/xl_sheet_view.Rd |only writexl-2.0.0/writexl/man/xl_table.Rd |only writexl-2.0.0/writexl/man/xl_table_column.Rd |only writexl-2.0.0/writexl/man/xl_validation.Rd |only writexl-2.0.0/writexl/man/xl_workbook.Rd |only writexl-2.0.0/writexl/src/Makevars | 31 writexl-2.0.0/writexl/src/libxlsxwriter/License.txt |only writexl-2.0.0/writexl/src/libxlsxwriter/include |only writexl-2.0.0/writexl/src/libxlsxwriter/src |only writexl-2.0.0/writexl/src/libxlsxwriter/third_party |only writexl-2.0.0/writexl/src/write_xlsx.c | 2309 +++++++++- writexl-2.0.0/writexl/tests/spelling.R | 2 writexl-2.0.0/writexl/tests/testthat.R | 16 writexl-2.0.0/writexl/tests/testthat/helper-xlsx.R |only writexl-2.0.0/writexl/tests/testthat/test-api-consistency.R |only writexl-2.0.0/writexl/tests/testthat/test-cell-general.R |only writexl-2.0.0/writexl/tests/testthat/test-cell-vector.R |only writexl-2.0.0/writexl/tests/testthat/test-format-cell.R |only writexl-2.0.0/writexl/tests/testthat/test-format-protect.R |only writexl-2.0.0/writexl/tests/testthat/test-format-workbook.R |only writexl-2.0.0/writexl/tests/testthat/test-format-worksheet.R |only writexl-2.0.0/writexl/tests/testthat/test-integration.R |only writexl-2.0.0/writexl/tests/testthat/test-libxlsxwriter-coverage.R |only writexl-2.0.0/writexl/tests/testthat/test-limits.R |only writexl-2.0.0/writexl/tests/testthat/test-na.R |only writexl-2.0.0/writexl/tests/testthat/test-performance.R | 25 writexl-2.0.0/writexl/tests/testthat/test-print.R |only writexl-2.0.0/writexl/tests/testthat/test-sheet-names.R |only writexl-2.0.0/writexl/tests/testthat/test-sheet-view.R |only writexl-2.0.0/writexl/tests/testthat/test-types.R | 327 + writexl-2.0.0/writexl/tests/testthat/test-xl_chart.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_chart_axis.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_chart_extras.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_chart_format.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_chart_parts.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_chartsheet.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_comment.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_conditional.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_filter.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_format.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_image.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_merge.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_outline.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_page_setup.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_range.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_rich_string.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_table.R |only writexl-2.0.0/writexl/tests/testthat/test-xl_validation.R |only writexl-2.0.0/writexl/vignettes |only 146 files changed, 3736 insertions(+), 674 deletions(-)
Title: Gene Set Analysis Toolkit WebGestaltR
Description: The web version WebGestalt <https://www.webgestalt.org> supports 12 organisms, 354 gene identifiers and 321,251 function categories. Users can upload the data and functional categories with their own gene identifiers. In addition to the Over-Representation Analysis, WebGestalt also supports Gene Set Enrichment Analysis and Network Topology Analysis. The user-friendly output report allows interactive and efficient exploration of enrichment results. The WebGestaltR package not only supports all above functions but also can be integrated into other pipeline or simultaneously analyze multiple gene lists.
Author: John Elizarraras [aut],
Jing Wang [aut],
Yuxing Liao [aut],
Eric Jaehnig [ctb],
Zhiao Shi [aut, cre],
Quanhu Sheng [ctb]
Maintainer: Zhiao Shi <zhiao.shi@gmail.com>
Diff between WebGestaltR versions 1.0.0 dated 2026-07-30 and 1.0.1 dated 2026-08-05
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 11 +++++++++++ src/Makevars.in | 11 +++++++++-- src/Makevars.win.in | 2 +- 5 files changed, 29 insertions(+), 11 deletions(-)
Title: Metabolomics and Spectral Data Analysis and Mining
Description: Provides methods for metabolomics and spectral data analysis,
including data import, preprocessing, visualization, univariate and
multivariate analysis, machine learning, feature selection, and pathway
analysis. The package supports analytical workflows for different data
types used in metabolomics and spectroscopy. Some optional functionality
uses the suggested packages 'cyjShiny' and 'specmine.datasets'. The package
'specmine.datasets' is maintained separately at
<https://github.com/PedroFontao/specmine.datasets>.
Author: Christopher Costa [aut],
Marcelo Maraschin [aut],
Miguel Rocha [aut],
Sara Cardoso [aut],
Telma Afonso [aut],
Bruno Pereira [aut],
Pedro Fontao [aut, cre],
C. Beleites [cph],
Jie Hao [cph]
Maintainer: Pedro Fontao <pedrofontao812004@gmail.com>
This is a re-admission after prior archival of version 3.1.6 dated 2021-09-21
Diff between specmine versions 3.1.6 dated 2021-09-21 and 3.1.8 dated 2026-08-05
specmine-3.1.6/specmine/README.md |only specmine-3.1.6/specmine/man/MAIT_identify_metabolites.Rd |only specmine-3.1.6/specmine/man/absorbance_to_transmittance.Rd |only specmine-3.1.6/specmine/man/apply_by_sample.Rd |only specmine-3.1.6/specmine/man/apply_by_variable.Rd |only specmine-3.1.6/specmine/man/background_correction.Rd |only specmine-3.1.6/specmine/man/boxplot_variables.Rd |only specmine-3.1.6/specmine/man/boxplot_vars_factor.Rd |only specmine-3.1.6/specmine/man/check_2d_dataset.Rd |only specmine-3.1.6/specmine/man/check_dataset.Rd |only specmine-3.1.6/specmine/man/clustering.Rd |only specmine-3.1.6/specmine/man/compare_regions_by_sample.Rd |only specmine-3.1.6/specmine/man/convert_to_factor.Rd |only specmine-3.1.6/specmine/man/correlation_test.Rd |only specmine-3.1.6/specmine/man/correlations_dataset.Rd |only specmine-3.1.6/specmine/man/correlations_test.Rd |only specmine-3.1.6/specmine/man/create_2d_dataset.Rd |only specmine-3.1.6/specmine/man/cubic_root_transform.Rd |only specmine-3.1.6/specmine/man/data_correction.Rd |only specmine-3.1.6/specmine/man/dendrogram_plot.Rd |only specmine-3.1.6/specmine/man/dendrogram_plot_col.Rd |only specmine-3.1.6/specmine/man/detect_nmr_peaks_from_dataset.Rd |only specmine-3.1.6/specmine/man/find_equal_samples.Rd |only specmine-3.1.6/specmine/man/first_derivative.Rd |only specmine-3.1.6/specmine/man/fold_change.Rd |only specmine-3.1.6/specmine/man/fold_change_var.Rd |only specmine-3.1.6/specmine/man/get_data.Rd |only specmine-3.1.6/specmine/man/get_data_as_df.Rd |only specmine-3.1.6/specmine/man/get_data_value.Rd |only specmine-3.1.6/specmine/man/get_data_values.Rd |only specmine-3.1.6/specmine/man/get_files_list_assay.Rd |only specmine-3.1.6/specmine/man/get_metadata.Rd |only specmine-3.1.6/specmine/man/get_metadata_value.Rd |only specmine-3.1.6/specmine/man/get_metadata_var.Rd |only specmine-3.1.6/specmine/man/get_sample_2d_data.Rd |only specmine-3.1.6/specmine/man/get_sample_names.Rd |only specmine-3.1.6/specmine/man/get_samples_names_spc.Rd |only specmine-3.1.6/specmine/man/get_type.Rd |only specmine-3.1.6/specmine/man/get_value_label.Rd |only specmine-3.1.6/specmine/man/get_x_values_as_num.Rd |only specmine-3.1.6/specmine/man/group_peaks.Rd |only specmine-3.1.6/specmine/man/heatmap_correlations.Rd |only specmine-3.1.6/specmine/man/hierarchical_clustering.Rd |only specmine-3.1.6/specmine/man/impute_nas_linapprox.Rd |only specmine-3.1.6/specmine/man/indexes_to_xvalue_interval.Rd |only specmine-3.1.6/specmine/man/is_spectra.Rd |only specmine-3.1.6/specmine/man/kmeans_clustering.Rd |only specmine-3.1.6/specmine/man/kmeans_plot.Rd |only specmine-3.1.6/specmine/man/kmeans_result_df.Rd |only specmine-3.1.6/specmine/man/kruskalTest_dataset.Rd |only specmine-3.1.6/specmine/man/ksTest_dataset.Rd |only specmine-3.1.6/specmine/man/linreg_all_vars.Rd |only specmine-3.1.6/specmine/man/linreg_coef_table.Rd |only specmine-3.1.6/specmine/man/linreg_pvalue_table.Rd |only specmine-3.1.6/specmine/man/linreg_rsquared.Rd |only specmine-3.1.6/specmine/man/linregression_onevar.Rd |only specmine-3.1.6/specmine/man/log_transform.Rd |only specmine-3.1.6/specmine/man/low_level_fusion.Rd |only specmine-3.1.6/specmine/man/mean_centering.Rd |only specmine-3.1.6/specmine/man/merge_datasets.Rd |only specmine-3.1.6/specmine/man/metadata_as_variables.Rd |only specmine-3.1.6/specmine/man/msc_correction.Rd |only specmine-3.1.6/specmine/man/multifactor_aov_all_vars.Rd |only specmine-3.1.6/specmine/man/multifactor_aov_pvalues_table.Rd |only specmine-3.1.6/specmine/man/multifactor_aov_varexp_table.Rd |only specmine-3.1.6/specmine/man/multiplot.Rd |only specmine-3.1.6/specmine/man/nmr_identification.Rd |only specmine-3.1.6/specmine/man/normalize.Rd |only specmine-3.1.6/specmine/man/normalize_samples.Rd |only specmine-3.1.6/specmine/man/num_samples.Rd |only specmine-3.1.6/specmine/man/num_x_values.Rd |only specmine-3.1.6/specmine/man/offset_correction.Rd |only specmine-3.1.6/specmine/man/pca_importance.Rd |only specmine-3.1.6/specmine/man/peaks_per_sample.Rd |only specmine-3.1.6/specmine/man/peaks_per_samples.Rd |only specmine-3.1.6/specmine/man/plot_2d_spectra.Rd |only specmine-3.1.6/specmine/man/plot_anova.Rd |only specmine-3.1.6/specmine/man/plot_fold_change.Rd |only specmine-3.1.6/specmine/man/plot_kruskaltest.Rd |only specmine-3.1.6/specmine/man/plot_kstest.Rd |only specmine-3.1.6/specmine/man/plot_peaks.Rd |only specmine-3.1.6/specmine/man/plot_regression_coefs_pvalues.Rd |only specmine-3.1.6/specmine/man/plot_spectra.Rd |only specmine-3.1.6/specmine/man/plot_spectra_simple.Rd |only specmine-3.1.6/specmine/man/plot_ttests.Rd |only specmine-3.1.6/specmine/man/plotvar_twofactor.Rd |only specmine-3.1.6/specmine/man/predict_samples.Rd |only specmine-3.1.6/specmine/man/read_Bruker_files.Rd |only specmine-3.1.6/specmine/man/read_Bruker_files_2d.Rd |only specmine-3.1.6/specmine/man/read_data_spc.Rd |only specmine-3.1.6/specmine/man/read_dataset_spc.Rd |only specmine-3.1.6/specmine/man/read_varian_2dspectra_raw.Rd |only specmine-3.1.6/specmine/man/read_varian_spectra_raw.Rd |only specmine-3.1.6/specmine/man/remove_peaks_interval.Rd |only specmine-3.1.6/specmine/man/remove_peaks_interval_sample_list.Rd |only specmine-3.1.6/specmine/man/replace_data_value.Rd |only specmine-3.1.6/specmine/man/replace_metadata_value.Rd |only specmine-3.1.6/specmine/man/savitzky_golay.Rd |only specmine-3.1.6/specmine/man/scaling.Rd |only specmine-3.1.6/specmine/man/scaling_samples.Rd |only specmine-3.1.6/specmine/man/set_metadata.Rd |only specmine-3.1.6/specmine/man/set_sample_names.Rd |only specmine-3.1.6/specmine/man/set_value_label.Rd |only specmine-3.1.6/specmine/man/set_x_label.Rd |only specmine-3.1.6/specmine/man/set_x_values.Rd |only specmine-3.1.6/specmine/man/shift_correction.Rd |only specmine-3.1.6/specmine/man/smoothing_interpolation.Rd |only specmine-3.1.6/specmine/man/snv_dataset.Rd |only specmine-3.1.6/specmine/man/stats_by_sample.Rd |only specmine-3.1.6/specmine/man/stats_by_variable.Rd |only specmine-3.1.6/specmine/man/sum_2d_dataset.Rd |only specmine-3.1.6/specmine/man/sum_dataset.Rd |only specmine-3.1.6/specmine/man/tTests_dataset.Rd |only specmine-3.1.6/specmine/man/transform_data.Rd |only specmine-3.1.6/specmine/man/transmittance_to_absorbance.Rd |only specmine-3.1.6/specmine/man/values_per_peak.Rd |only specmine-3.1.6/specmine/man/values_per_sample.Rd |only specmine-3.1.6/specmine/man/variables_as_metadata.Rd |only specmine-3.1.6/specmine/man/volcano_plot_fc_tt.Rd |only specmine-3.1.6/specmine/man/x_values_to_indexes.Rd |only specmine-3.1.6/specmine/man/xvalue_interval_to_indexes.Rd |only specmine-3.1.8/specmine/DESCRIPTION | 84 specmine-3.1.8/specmine/MD5 | 372 +--- specmine-3.1.8/specmine/NAMESPACE | 322 +-- specmine-3.1.8/specmine/NEWS.md |only specmine-3.1.8/specmine/R/DBSCAN_HDBSCAN.R |only specmine-3.1.8/specmine/R/GMM.R |only specmine-3.1.8/specmine/R/ICA.R |only specmine-3.1.8/specmine/R/MAIT_metabolite_identification.R | 267 +-- specmine-3.1.8/specmine/R/NMR_metabolite_identification.R | 235 +- specmine-3.1.8/specmine/R/PATHWAY_ANALYSIS.R | 649 ++++--- specmine-3.1.8/specmine/R/cluster_quality.R |only specmine-3.1.8/specmine/R/clustering.R | 238 +- specmine-3.1.8/specmine/R/compare_embeddings.R |only specmine-3.1.8/specmine/R/convert_chemospec.R | 19 specmine-3.1.8/specmine/R/feature_selection.R | 117 + specmine-3.1.8/specmine/R/filter_dataset.R | 598 ++++++ specmine-3.1.8/specmine/R/filters_flat.R | 138 - specmine-3.1.8/specmine/R/get_metabolights_study.R | 418 +++- specmine-3.1.8/specmine/R/globals.R |only specmine-3.1.8/specmine/R/graphics.R | 358 +--- specmine-3.1.8/specmine/R/init.R | 2 specmine-3.1.8/specmine/R/machinelearning.R | 694 +++++-- specmine-3.1.8/specmine/R/missing_values.R | 196 +- specmine-3.1.8/specmine/R/ms_functions.R | 110 - specmine-3.1.8/specmine/R/mzmatch_metabolite_identification.R |only specmine-3.1.8/specmine/R/nmr_id_utils.R | 2 specmine-3.1.8/specmine/R/pca.R | 730 ++++++-- specmine-3.1.8/specmine/R/peaklists.R | 116 + specmine-3.1.8/specmine/R/preprocessing.R | 169 + specmine-3.1.8/specmine/R/read.spc.modifed.R | 844 +-------- specmine-3.1.8/specmine/R/read_NMR_spectra.R | 873 +--------- specmine-3.1.8/specmine/R/read_dx.R | 110 + specmine-3.1.8/specmine/R/read_spc.R | 119 - specmine-3.1.8/specmine/R/reading_data.R | 230 ++ specmine-3.1.8/specmine/R/regression.R | 81 specmine-3.1.8/specmine/R/specmine-package.R |only specmine-3.1.8/specmine/R/spectra_options.R |only specmine-3.1.8/specmine/R/stats.R | 98 - specmine-3.1.8/specmine/R/structure.R | 519 +++-- specmine-3.1.8/specmine/R/t-sne.R |only specmine-3.1.8/specmine/R/umap.R |only specmine-3.1.8/specmine/R/univariate.R | 511 +++-- specmine-3.1.8/specmine/R/utils.R | 2 specmine-3.1.8/specmine/build/vignette.rds |binary specmine-3.1.8/specmine/inst/doc/dataset_2d_analysis.R | 90 - specmine-3.1.8/specmine/inst/doc/dataset_2d_analysis.html | 536 ++++-- specmine-3.1.8/specmine/man/aggregate_samples.Rd | 77 specmine-3.1.8/specmine/man/aov_all_vars.Rd | 78 specmine-3.1.8/specmine/man/aov_one_var.Rd |only specmine-3.1.8/specmine/man/apply_by_group.Rd | 62 specmine-3.1.8/specmine/man/apply_by_groups.Rd | 76 specmine-3.1.8/specmine/man/baseline_correction.Rd | 79 specmine-3.1.8/specmine/man/convert_chebi_to_kegg.Rd | 29 specmine-3.1.8/specmine/man/convert_from_chemospec.Rd | 46 specmine-3.1.8/specmine/man/convert_hmdb_to_kegg.Rd | 28 specmine-3.1.8/specmine/man/convert_keggpathway_2_reactiongraph.Rd | 28 specmine-3.1.8/specmine/man/convert_multiple_spcmnm_to_kegg.Rd | 29 specmine-3.1.8/specmine/man/count_missing_values.Rd | 39 specmine-3.1.8/specmine/man/count_missing_values_per_sample.Rd | 47 specmine-3.1.8/specmine/man/count_missing_values_per_variable.Rd | 47 specmine-3.1.8/specmine/man/create_dataset.Rd | 121 - specmine-3.1.8/specmine/man/create_pathway_with_reactions.Rd | 70 specmine-3.1.8/specmine/man/dataset_from_peaks.Rd | 65 specmine-3.1.8/specmine/man/feature_selection.Rd | 84 specmine-3.1.8/specmine/man/filter_feature_selection.Rd | 71 specmine-3.1.8/specmine/man/flat_pattern_filter.Rd | 83 specmine-3.1.8/specmine/man/get_MetabolitePath.Rd | 28 specmine-3.1.8/specmine/man/get_OrganismsCodes.Rd | 23 specmine-3.1.8/specmine/man/get_cpd_names.Rd | 27 specmine-3.1.8/specmine/man/get_files_list_per_assay.Rd |only specmine-3.1.8/specmine/man/get_metabPaths_org.Rd | 25 specmine-3.1.8/specmine/man/get_metabolights_study.Rd | 44 specmine-3.1.8/specmine/man/get_metabolights_study_files_assay.Rd | 42 specmine-3.1.8/specmine/man/get_metabolights_study_metadata_assay.Rd | 39 specmine-3.1.8/specmine/man/get_metabolights_study_samples_files.Rd | 35 specmine-3.1.8/specmine/man/get_paths_with_cpds_org.Rd | 43 specmine-3.1.8/specmine/man/get_peak_values.Rd | 43 specmine-3.1.8/specmine/man/get_samples_names_dx.Rd | 34 specmine-3.1.8/specmine/man/get_x_label.Rd | 47 specmine-3.1.8/specmine/man/get_x_values_as_text.Rd | 47 specmine-3.1.8/specmine/man/impute_nas_knn.Rd | 55 specmine-3.1.8/specmine/man/impute_nas_mean.Rd | 41 specmine-3.1.8/specmine/man/impute_nas_median.Rd | 41 specmine-3.1.8/specmine/man/impute_nas_value.Rd | 46 specmine-3.1.8/specmine/man/merge_data_metadata.Rd | 73 specmine-3.1.8/specmine/man/metabolights_studies_list.Rd | 21 specmine-3.1.8/specmine/man/missingvalues_imputation.Rd | 66 specmine-3.1.8/specmine/man/multiClassSummary.Rd | 49 specmine-3.1.8/specmine/man/pathway_analysis.Rd | 69 specmine-3.1.8/specmine/man/pca_analysis_dataset.Rd | 77 specmine-3.1.8/specmine/man/pca_biplot.Rd | 84 specmine-3.1.8/specmine/man/pca_biplot3D.Rd | 59 specmine-3.1.8/specmine/man/pca_kmeans_plot2D.Rd | 103 - specmine-3.1.8/specmine/man/pca_kmeans_plot3D.Rd | 90 - specmine-3.1.8/specmine/man/pca_pairs_kmeans_plot.Rd | 68 specmine-3.1.8/specmine/man/pca_pairs_plot.Rd | 68 specmine-3.1.8/specmine/man/pca_plot_3d.Rd | 81 specmine-3.1.8/specmine/man/pca_robust.Rd | 81 specmine-3.1.8/specmine/man/pca_scoresplot2D.Rd | 106 - specmine-3.1.8/specmine/man/pca_scoresplot3D.Rd | 59 specmine-3.1.8/specmine/man/pca_scoresplot3D_rgl.Rd | 78 specmine-3.1.8/specmine/man/pca_screeplot.Rd | 92 - specmine-3.1.8/specmine/man/peak_detection2d.Rd | 79 specmine-3.1.8/specmine/man/read-spc.Rd | 79 specmine-3.1.8/specmine/man/read_csvs_folder.Rd | 41 specmine-3.1.8/specmine/man/read_data_csv.Rd | 71 specmine-3.1.8/specmine/man/read_data_dx.Rd | 38 specmine-3.1.8/specmine/man/read_dataset_csv.Rd | 141 - specmine-3.1.8/specmine/man/read_dataset_dx.Rd | 91 - specmine-3.1.8/specmine/man/read_metadata.Rd | 52 specmine-3.1.8/specmine/man/read_ms_spectra.Rd | 104 - specmine-3.1.8/specmine/man/read_multiple_csvs.Rd | 44 specmine-3.1.8/specmine/man/recursive_feature_elimination.Rd | 84 specmine-3.1.8/specmine/man/remove_data.Rd | 77 specmine-3.1.8/specmine/man/remove_data_variables.Rd | 55 specmine-3.1.8/specmine/man/remove_metadata_variables.Rd | 52 specmine-3.1.8/specmine/man/remove_samples.Rd | 54 specmine-3.1.8/specmine/man/remove_samples_by_na_metadata.Rd | 49 specmine-3.1.8/specmine/man/remove_samples_by_nas.Rd | 53 specmine-3.1.8/specmine/man/remove_variables_by_nas.Rd | 53 specmine-3.1.8/specmine/man/remove_x_values_by_interval.Rd | 45 specmine-3.1.8/specmine/man/specmine-package.Rd |only specmine-3.1.8/specmine/man/spectra_options.Rd | 34 specmine-3.1.8/specmine/man/subset_by_samples_and_xvalues.Rd | 84 specmine-3.1.8/specmine/man/subset_metadata.Rd | 49 specmine-3.1.8/specmine/man/subset_random_samples.Rd | 49 specmine-3.1.8/specmine/man/subset_samples.Rd | 54 specmine-3.1.8/specmine/man/subset_samples_by_metadata_values.Rd | 57 specmine-3.1.8/specmine/man/subset_x_values.Rd | 50 specmine-3.1.8/specmine/man/subset_x_values_by_interval.Rd | 51 specmine-3.1.8/specmine/man/summary_var_importance.Rd | 47 specmine-3.1.8/specmine/man/train_and_predict.Rd | 115 - specmine-3.1.8/specmine/man/train_classifier.Rd | 110 - specmine-3.1.8/specmine/man/train_models_performance.Rd | 129 - 255 files changed, 8188 insertions(+), 6893 deletions(-)
Title: Rank-Clustered Estimation for Network Meta-Analysis
Description: An implementation of the RaCE-NMA (Rank-Clustered
Estimation for Network Meta-Analysis) model for post-hoc clustering
of treatments or interventions by rank in network meta-analysis
data. Functions for model estimation, assessment, and displaying
results are provided. For more details, see Pearce and Zhou (2025)
<doi:10.1017/rsm.2025.10049>.
Author: Michael Pearce [aut, cre, cph] ,
Shouhao Zhou [aut]
Maintainer: Michael Pearce <michaelpearce@reed.edu>
Diff between RaCE.NMA versions 1.1.0 dated 2026-07-29 and 1.2.0 dated 2026-08-05
DESCRIPTION | 8 - MD5 | 87 +++++++++++--------- NEWS.md | 6 + R/calculate_Rhat.R | 4 R/calculate_SUCRA_MNBT.R | 8 + R/clusterplot_ranks.R | 4 R/cumulativeprobplot_ranks.R | 4 R/fit_raceNMA.R | 39 ++++++--- R/forestplot_muhat.R | 4 R/make_logdmvnorm.R |only R/mcmc_raceNMA.R | 84 +++++++++++++++----- R/sample_partition_correlation.R | 12 +- R/sample_partition_independence.R | 1 R/toy_data.R | 2 R/traceplot_K.R | 2 inst/doc/overview.Rmd | 2 inst/doc/overview.html | 2 inst/doc/reproducibility.R | 6 - inst/doc/reproducibility.Rmd | 8 - inst/doc/reproducibility.html | 8 - inst/doc/tutorial.R | 8 - inst/doc/tutorial.Rmd | 15 +-- inst/doc/tutorial.html | 104 ++++++++++++------------- man/calculate_Rhat.Rd | 4 man/calculate_SUCRA_MNBT.Rd | 2 man/clusterplot_ranks.Rd | 2 man/cumulativeprobplot_ranks.Rd | 2 man/fit_raceNMA.Rd | 2 man/forestplot_muhat.Rd | 2 man/make_logdmvnorm.Rd |only man/mcmc_raceNMA.Rd | 15 ++- man/sample_partition_correlation.Rd | 9 +- man/sample_partition_independence.Rd | 1 man/toy_data.Rd | 2 man/traceplot_K.Rd | 2 tests/testthat/test-calculate_Rhat.R | 10 ++ tests/testthat/test-calculate_SUCRA_MNBT.R | 43 ++++++++++ tests/testthat/test-clusterplot_ranks.R | 26 ++++++ tests/testthat/test-cumulativeprobplot_ranks.R | 18 ++++ tests/testthat/test-datasets.R |only tests/testthat/test-fit_raceNMA.R |only tests/testthat/test-forestplot_muhat.R | 26 ++++++ tests/testthat/test-mcmc_raceNMA.R | 36 +++++++- tests/testthat/test-sample_partition.R |only vignettes/overview.Rmd | 2 vignettes/reproducibility.Rmd | 8 - vignettes/tutorial.Rmd | 15 +-- 47 files changed, 450 insertions(+), 195 deletions(-)
Title: AI Agent Runtime
Description: An agent runtime that gives Large Language Models (LLMs)
from 'Anthropic' <https://www.anthropic.com/>, 'OpenAI'
<https://openai.com/>, 'Moonshot' <https://www.moonshot.ai/>, and
'Ollama' <https://ollama.com/> direct access to a live R session with
managed workspace state. Tools execute as R function calls with
provenance tracking, and a deterministic retrieval system keeps
relevant objects in context across turns. Three entry points: a
shell command-line interface (CLI), a console read-eval-print-loop
via chat(), and a Model Context Protocol (MCP) server via serve()
for external clients.
Author: Troy Hernandez [aut, cre] ,
Grant McDermott [ctb] ,
Jorge Krzyzaniak [ctb],
cornball.ai [cph]
Maintainer: Troy Hernandez <troy@cornball.ai>
Diff between corteza versions 0.7.0 dated 2026-06-26 and 0.7.1 dated 2026-08-05
DESCRIPTION | 12 MD5 | 139 +++--- NEWS.md | 117 +++++ R/agent_context.R | 1 R/archival-history-shim.R | 1 R/archival.R | 1 R/banner.R | 77 ++- R/chat-slash.R | 3 R/chat.R | 10 R/chunk.R | 1 R/cli-colors.R | 1 R/cli-ui.R | 32 - R/compact-turn.R | 1 R/config.R | 1 R/context-budget.R | 1 R/context-engine.R | 1 R/context-meter.R | 1 R/context.R | 1 R/deny.R | 1 R/diff-render.R | 1 R/dispatch.R | 1 R/format-elapsed.R | 1 R/handles.R | 1 R/heartbeat.R | 1 R/install-cli.R | 1 R/interrupt.R | 1 R/log.R | 1 R/matrix.R | 676 +++++++++++++++++++++++++---- R/matrix_crypto.R | 20 R/mcp-handler.R | 1 R/mcp-transport.R | 1 R/package-tools.R | 1 R/paths.R | 1 R/permissions.R | 1 R/plan-mode.R | 1 R/policy.R | 1 R/rate-limit.R | 1 R/registry.R | 1 R/render-md-ansi.R | 1 R/repl.R | 1 R/retrieval.R | 1 R/rstudio-addin.R | 1 R/schema.R | 1 R/serve.R | 1 R/session.R | 1 R/session_setup.R | 39 + R/skill.R | 5 R/spend.R | 1 R/subagent.R | 1 R/tasks.R | 1 R/tool-buffer.R | 1 R/tool-impl.R | 5 R/tools.R | 1 R/turn.R | 105 ++++ R/utils.R | 1 R/workspace.R | 1 build/partial.rdb |binary build/vignette.rds |binary inst/bin/corteza | 30 + inst/doc/configuration.html | 170 ++++--- inst/doc/configuration.md | 50 ++ inst/tinytest/test_banner.R | 27 - inst/tinytest/test_matrix.R | 851 +++++++++++++++++++++++++++++++++++-- inst/tinytest/test_session_setup.R | 75 +++ inst/tinytest/test_turn.R | 23 + inst/tinytest/test_web_search.R |only man/chat.Rd | 7 man/matrix_configure.Rd | 15 man/new_session.Rd | 17 man/session_setup.Rd | 11 vignettes/configuration.md | 50 ++ 71 files changed, 2225 insertions(+), 384 deletions(-)
Title: Neo4j to R
Description: The aim of neo2R is to provide simple and low level connectors
for querying neo4j graph databases (<https://neo4j.com/>).
The objects returned by the query functions are either lists or data.frames
with very little post-processing.
It allows fast processing of queries returning many records.
And it let the users handle post-processing according to the data model
and their needs.
Author: Patrice Godard [aut, cre, cph] ,
Eusebiu Marcu [ctb]
Maintainer: Patrice Godard <patrice.godard@gmail.com>
Diff between neo2R versions 3.0.0 dated 2026-05-18 and 3.1.1 dated 2026-08-05
DESCRIPTION | 8 +-- MD5 | 14 ++--- R/cypher.R | 125 ++++++++++++++++++++++++++++++++++++----------------- R/import_from_df.R | 29 +----------- R/startGraph.R | 23 ++++++++- man/cypher.Rd | 6 +- man/multicypher.Rd | 6 +- man/startGraph.Rd | 6 ++ 8 files changed, 133 insertions(+), 84 deletions(-)
Title: Morphological Analysis for Japanese
Description: Supports morphological analysis for Japanese by using
'MeCab' <https://taku910.github.io/mecab/>,
'Sudachi' <https://github.com/WorksApplications/Sudachi>,
'Chamame' <https://chamame.ninjal.ac.jp/>,
or 'Ginza' <https://github.com/megagonlabs/ginza>.
Can input a data.frame and obtain all results of 'MeCab' and the row
number of the original data.frame as a text id.
Author: Toshikazu Matsumura [aut, cre]
Maintainer: Toshikazu Matsumura <matutosi@gmail.com>
This is a re-admission after prior archival of version 0.9.7 dated 2024-08-01
Diff between moranajp versions 0.9.7 dated 2024-08-01 and 0.9.8 dated 2026-08-05
moranajp-0.9.7/moranajp/man/text_id_with_break.Rd |only moranajp-0.9.8/moranajp/DESCRIPTION | 10 moranajp-0.9.8/moranajp/MD5 | 42 +- moranajp-0.9.8/moranajp/NAMESPACE | 2 moranajp-0.9.8/moranajp/NEWS.md | 25 + moranajp-0.9.8/moranajp/R/clean_up.R | 5 moranajp-0.9.8/moranajp/R/make_group.R | 11 moranajp-0.9.8/moranajp/R/moranajp.R | 249 ++++++++++++++--- moranajp-0.9.8/moranajp/R/utils_id.R | 121 ++------ moranajp-0.9.8/moranajp/build/vignette.rds |binary moranajp-0.9.8/moranajp/inst/doc/bigram.R | 56 +-- moranajp-0.9.8/moranajp/inst/doc/bigram.html | 7 moranajp-0.9.8/moranajp/inst/doc/moranajp.R | 30 +- moranajp-0.9.8/moranajp/inst/doc/moranajp.html | 7 moranajp-0.9.8/moranajp/man/add_group.Rd | 6 moranajp-0.9.8/moranajp/man/add_sentence_no.Rd | 4 moranajp-0.9.8/moranajp/man/add_text_id.Rd | 6 moranajp-0.9.8/moranajp/man/eval_str.Rd |only moranajp-0.9.8/moranajp/man/make_groups.Rd | 17 - moranajp-0.9.8/moranajp/man/moranajp_all.Rd | 26 + moranajp-0.9.8/moranajp/man/remove_brk.Rd | 2 moranajp-0.9.8/moranajp/man/web_chamame.Rd | 90 ++++++ moranajp-0.9.8/moranajp/tests/testthat/test-moranajp.R | 10 23 files changed, 496 insertions(+), 230 deletions(-)
Title: Lookup for IP Address Information
Description: Enables the user to find the country, region, district, city, coordinates, zip code, time zone, ISP, domain name, connection type, area code, weather, Mobile Country Codes (MCC), Mobile Network Code (MNC), mobile brand name, elevation, usage type, address type, IAB category and Autonomous system number (ASN) that any IP address or hostname originates from. Supported IPv4 and IPv6.
Please visit <https://www.ip2location.com> to learn more. You may also want to visit <https://lite.ip2location.com> for free database download.
This package requires 'IP2Location Python' module. At the terminal, please run 'pip install IP2Location' to install the module.
Author: Kai Wen Ooi [aut, cre],
IP2Location [cph]
Maintainer: Kai Wen Ooi <support@ip2location.com>
Diff between ip2location versions 8.1.3 dated 2023-05-02 and 8.1.4 dated 2026-08-05
DESCRIPTION | 14 ++--- LICENSE | 4 - MD5 | 16 +++--- NAMESPACE | 22 ++++---- R/IP2Location.R | 32 ++++++++---- README.md | 145 ++++++++++---------------------------------------------- man/get_all.Rd | 46 ++++++++--------- man/open.Rd | 40 +++++++-------- man/plot_map.Rd | 40 +++++++-------- 9 files changed, 140 insertions(+), 219 deletions(-)
Title: Predicting Invasion Probabilities from Phylogenetic Data and
Species Traits
Description: A phylogenetic modelling approach for predicting species invasion risk, out of
a given pool of local species where a subset is known to be invasive elsewhere.
The package uses phylogenetic signal estimation and phylogenetic linear and logistic models
to estimate probabilities of being invasive based on phylogeny and any set of additional
predictors. A ranking method is implemented to evaluate prioritisation strategies. A manuscript
describing these methods, by Shahar Dubiner and Tamar Guy-Haim, is in preparation.
Author: Shahar Dubiner [aut, cre]
Maintainer: Shahar Dubiner <dubiner@mail.tau.ac.il>
This is a re-admission after prior archival of version 0.1.0 dated 2026-07-21
Diff between invasible versions 0.1.0 dated 2026-07-21 and 0.1.1 dated 2026-08-05
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/predict_invasible.R | 8 +++++--- R/prepare_invasible.R | 2 +- man/predict_invasible.Rd | 8 +++++--- man/prepare_invasible.Rd | 2 +- 6 files changed, 20 insertions(+), 16 deletions(-)
Title: Convert Engineering 'DWG' Drawings to Auditable 'GeoJSON'
Description: Converts engineering 'DWG' drawings ('AutoCAD' 2013+ format) to
'GeoJSON' entirely in-process, with no 'CAD' software, 'LibreDWG', or
'GDAL' required. Wraps the pure-Rust 'dwg2geo' conversion core
<https://github.com/milkway/dwg2geo>: every feature carries resolved
'CAD' style metadata (layer, colour, line weight, text), skipped and
failed entities are reported with reasons, and the output is
deterministic: the same bytes always produce byte-identical 'GeoJSON'.
Coordinates are kept in the drawing's local system; the package never
guesses a coordinate reference system.
Author: Andre Leite [aut, cre]
Maintainer: Andre Leite <leite@castlab.org>
Diff between dwg2geo versions 0.2.3 dated 2026-08-04 and 0.2.4 dated 2026-08-05
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 10 ++++++++++ src/Makevars | 8 ++++++-- src/Makevars.win | 6 +++++- src/rust/Cargo.lock | 4 ++-- src/rust/src/lib.rs | 4 +++- src/rust/vendor.tar.xz |binary 8 files changed, 36 insertions(+), 16 deletions(-)
Title: Generic PK/PD Simulation Platform Campsis
Description: A generic, easy-to-use and intuitive
pharmacokinetic/pharmacodynamic (PK/PD) simulation platform based on
the R packages 'rxode2' and 'mrgsolve'. Campsis provides an
abstraction layer over the underlying processes of defining a PK/PD
model, assembling a custom dataset and running a simulation. The
package has a strong dependency on the R package 'campsismod', which
allows models to be read from and written to files, including through
a JSON-based interface, and to be adapted further on the fly in the R
environment. In addition, 'campsis' allows users to assemble datasets
in an intuitive manner, including via a JSON-based interface to import
Campsis datasets defined using formal JSON schemas distributed with
the package. Once the dataset is ready, the package prepares the
simulation, calls 'rxode2' or 'mrgsolve' (at the user's choice), and
returns the results for the given model, dataset and desired
simulation settings. The package itself is licensed under the GPL (>=
3); the JSON sc [...truncated...]
Author: Nicolas Luyckx [aut, cre]
Maintainer: Nicolas Luyckx <nicolas.luyckx@calvagone.com>
Diff between campsis versions 1.8.2 dated 2026-03-19 and 1.9.0 dated 2026-08-05
campsis-1.8.2/campsis/R/results_processing.R |only campsis-1.8.2/campsis/man/VPC.Rd |only campsis-1.8.2/campsis/man/applyAction.Rd |only campsis-1.8.2/campsis/man/applyCompartmentCharacteristics.Rd |only campsis-1.8.2/campsis/man/applyScenario.Rd |only campsis-1.8.2/campsis/man/assignDoseNumber.Rd |only campsis-1.8.2/campsis/man/checkIIandADDL.Rd |only campsis-1.8.2/campsis/man/computeIncrementalProgress.Rd |only campsis-1.8.2/campsis/man/dosingOnly.Rd |only campsis-1.8.2/campsis/man/dropOthers.Rd |only campsis-1.8.2/campsis/man/exportDelegate.Rd |only campsis-1.8.2/campsis/man/exportTableDelegate.Rd |only campsis-1.8.2/campsis/man/factorScenarios.Rd |only campsis-1.8.2/campsis/man/generateIIV.Rd |only campsis-1.8.2/campsis/man/generateIIV_.Rd |only campsis-1.8.2/campsis/man/getAvailableTimeUnits.Rd |only campsis-1.8.2/campsis/man/getCampsisOption.Rd |only campsis-1.8.2/campsis/man/getCampsisOptions.Rd |only campsis-1.8.2/campsis/man/getColumn.Rd |only campsis-1.8.2/campsis/man/getCompartmentMapping.Rd |only campsis-1.8.2/campsis/man/getCovariates.Rd |only campsis-1.8.2/campsis/man/getEventCovariates.Rd |only campsis-1.8.2/campsis/man/getFixedCovariates.Rd |only campsis-1.8.2/campsis/man/getIOVs.Rd |only campsis-1.8.2/campsis/man/getInitialConditions.Rd |only campsis-1.8.2/campsis/man/getOccasions.Rd |only campsis-1.8.2/campsis/man/getRandomSeedValue.Rd |only campsis-1.8.2/campsis/man/getSeed.Rd |only campsis-1.8.2/campsis/man/getSeedForDatasetExport.Rd |only campsis-1.8.2/campsis/man/getSeedForIteration.Rd |only campsis-1.8.2/campsis/man/getSeedForParametersSampling.Rd |only campsis-1.8.2/campsis/man/getSimulationEngineType.Rd |only campsis-1.8.2/campsis/man/getSplittingConfiguration.Rd |only campsis-1.8.2/campsis/man/getTimeVaryingCovariates.Rd |only campsis-1.8.2/campsis/man/getTimes.Rd |only campsis-1.8.2/campsis/man/importCampsismodToNamespace.Rd |only campsis-1.8.2/campsis/man/isEmptyBootstrap.Rd |only campsis-1.8.2/campsis/man/jsonToCampsisDataset.Rd |only campsis-1.8.2/campsis/man/jsonToCampsisSettings.Rd |only campsis-1.8.2/campsis/man/leftJoinIIV.Rd |only campsis-1.8.2/campsis/man/obsOnly.Rd |only campsis-1.8.2/campsis/man/onCI.Rd |only campsis-1.8.2/campsis/man/onCran.Rd |only campsis-1.8.2/campsis/man/openJSON.Rd |only campsis-1.8.2/campsis/man/output_function-class.Rd |only campsis-1.8.2/campsis/man/preprocessArmColumn.Rd |only campsis-1.8.2/campsis/man/preprocessDest.Rd |only campsis-1.8.2/campsis/man/preprocessDosing.Rd |only campsis-1.8.2/campsis/man/preprocessEvents.Rd |only campsis-1.8.2/campsis/man/preprocessIds.Rd |only campsis-1.8.2/campsis/man/preprocessOutfun.Rd |only campsis-1.8.2/campsis/man/preprocessOutvars.Rd |only campsis-1.8.2/campsis/man/preprocessReplicates.Rd |only campsis-1.8.2/campsis/man/preprocessScenarios.Rd |only campsis-1.8.2/campsis/man/preprocessSettings.Rd |only campsis-1.8.2/campsis/man/preprocessSlices.Rd |only campsis-1.8.2/campsis/man/preprocessTablefun.Rd |only campsis-1.8.2/campsis/man/processArmLabels.Rd |only campsis-1.8.2/campsis/man/processDropOthers.Rd |only campsis-1.8.2/campsis/man/processSimulateArguments.Rd |only campsis-1.8.2/campsis/man/removeInitialConditions.Rd |only campsis-1.8.2/campsis/man/reorderColumns.Rd |only campsis-1.8.2/campsis/man/repeatSchedule.Rd |only campsis-1.8.2/campsis/man/retrieveParameterValue.Rd |only campsis-1.8.2/campsis/man/sampleCovariatesList.Rd |only campsis-1.8.2/campsis/man/sampleDistributionAsTibble.Rd |only campsis-1.8.2/campsis/man/setSeed.Rd |only campsis-1.8.2/campsis/man/simulateDelegate.Rd |only campsis-1.8.2/campsis/man/simulateDelegateCore.Rd |only campsis-1.8.2/campsis/man/simulateScenarios.Rd |only campsis-1.8.2/campsis/man/standardiseTime.Rd |only campsis-1.8.2/campsis/man/toExplicitDistribution.Rd |only campsis-1.8.2/campsis/man/uniteColumns.Rd |only campsis-1.8.2/campsis/man/unwrapTreatment.Rd |only campsis-1.8.2/campsis/man/updateADDL.Rd |only campsis-1.8.2/campsis/man/updateAmount.Rd |only campsis-1.8.2/campsis/man/updateII.Rd |only campsis-1.8.2/campsis/man/updateRepeat.Rd |only campsis-1.8.2/campsis/tests/testthat/_snaps/testDefaultPlots |only campsis-1.8.2/campsis/tests/testthat/_snaps/testSimulateReplicates |only campsis-1.8.2/campsis/tests/testthat/testArm.R |only campsis-1.8.2/campsis/tests/testthat/testArms.R |only campsis-1.8.2/campsis/tests/testthat/testBootstrap.R |only campsis-1.8.2/campsis/tests/testthat/testCompilationError.R |only campsis-1.8.2/campsis/tests/testthat/testCovariate.R |only campsis-1.8.2/campsis/tests/testthat/testCovariates.R |only campsis-1.8.2/campsis/tests/testthat/testDataset.R |only campsis-1.8.2/campsis/tests/testthat/testDatasetExportParallelisation.R |only campsis-1.8.2/campsis/tests/testthat/testDefaultPlots.R |only campsis-1.8.2/campsis/tests/testthat/testDistribution.R |only campsis-1.8.2/campsis/tests/testthat/testDoseAdaptation.R |only campsis-1.8.2/campsis/tests/testthat/testEvent.R |only campsis-1.8.2/campsis/tests/testthat/testEvents.R |only campsis-1.8.2/campsis/tests/testthat/testJSONInterface.R |only campsis-1.8.2/campsis/tests/testthat/testObservations.R |only campsis-1.8.2/campsis/tests/testthat/testOccasion.R |only campsis-1.8.2/campsis/tests/testthat/testOccasions.R |only campsis-1.8.2/campsis/tests/testthat/testRepeatedSchedule.R |only campsis-1.8.2/campsis/tests/testthat/testScenario.R |only campsis-1.8.2/campsis/tests/testthat/testScenarios.R |only campsis-1.8.2/campsis/tests/testthat/testSeed.R |only campsis-1.8.2/campsis/tests/testthat/testSettings.R |only campsis-1.8.2/campsis/tests/testthat/testShowMethod.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateArguments.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateBioavailability.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateBolus.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateBolusInfusionSameCmt.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateDeclare.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateDoseAdaptation.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateDosingInfo.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateEvents.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateEventsLogic.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateIOV.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateInfusion.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateInit.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateLagTime.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateMinimalistModel.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateNoOmega.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateNocbLocf.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateOutvars.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateRUV.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateReplicates.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateScenarios.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateTSLD.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateTTEModels.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateTable.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateTimeVaryingCovariates.R |only campsis-1.8.2/campsis/tests/testthat/testSimulateWeirdCases.R |only campsis-1.8.2/campsis/tests/testthat/testTimeUtilities.R |only campsis-1.8.2/campsis/tests/testthat/testTreatment.R |only campsis-1.8.2/campsis/tests/testthat/testTreatmentEntry.R |only campsis-1.8.2/campsis/tests/testthat/testUtils.R |only campsis-1.9.0/campsis/DESCRIPTION | 33 campsis-1.9.0/campsis/MD5 | 894 +++---- campsis-1.9.0/campsis/NAMESPACE | 107 campsis-1.9.0/campsis/NEWS.md | 19 campsis-1.9.0/campsis/R/all_classes.R |only campsis-1.9.0/campsis/R/arm.R | 190 - campsis-1.9.0/campsis/R/arms.R | 126 - campsis-1.9.0/campsis/R/bootstrap.R | 94 campsis-1.9.0/campsis/R/campsis_metadata.R |only campsis-1.9.0/campsis/R/campsis_plot_helpers.R |only campsis-1.9.0/campsis/R/check.R | 93 campsis-1.9.0/campsis/R/covariate.R | 139 - campsis-1.9.0/campsis/R/covariates.R | 61 campsis-1.9.0/campsis/R/data.R | 1 campsis-1.9.0/campsis/R/dataset.R | 921 ++++--- campsis-1.9.0/campsis/R/dataset_config.R | 69 campsis-1.9.0/campsis/R/dataset_summary.R | 32 campsis-1.9.0/campsis/R/declare_settings.R | 18 campsis-1.9.0/campsis/R/default_plot.R | 251 +- campsis-1.9.0/campsis/R/default_settings.R | 115 campsis-1.9.0/campsis/R/deprecated_methods.R |only campsis-1.9.0/campsis/R/distribution.R | 365 +- campsis-1.9.0/campsis/R/dose_adaptation.R | 37 campsis-1.9.0/campsis/R/dose_adaptations.R | 11 campsis-1.9.0/campsis/R/event.R | 35 campsis-1.9.0/campsis/R/event_logic.R | 60 campsis-1.9.0/campsis/R/events.R | 26 campsis-1.9.0/campsis/R/generic.R | 249 +- campsis-1.9.0/campsis/R/global.R | 9 campsis-1.9.0/campsis/R/hardware_settings.R | 94 campsis-1.9.0/campsis/R/internal_settings.R | 11 campsis-1.9.0/campsis/R/json_interface.R | 100 campsis-1.9.0/campsis/R/nocb_settings.R | 25 campsis-1.9.0/campsis/R/observations.R | 104 campsis-1.9.0/campsis/R/observations_set.R | 26 campsis-1.9.0/campsis/R/occasion.R | 27 campsis-1.9.0/campsis/R/occasions.R | 24 campsis-1.9.0/campsis/R/outfun.R | 377 ++- campsis-1.9.0/campsis/R/outfun_core.R |only campsis-1.9.0/campsis/R/outfuns.R |only campsis-1.9.0/campsis/R/plan_setup.R | 28 campsis-1.9.0/campsis/R/progress_settings.R | 16 campsis-1.9.0/campsis/R/protocol.R | 18 campsis-1.9.0/campsis/R/repeated_schedule.R | 95 campsis-1.9.0/campsis/R/scatter_plot.R |only campsis-1.9.0/campsis/R/scenario.R | 79 campsis-1.9.0/campsis/R/scenario_action.R | 43 campsis-1.9.0/campsis/R/scenario_actions.R | 18 campsis-1.9.0/campsis/R/scenarios.R | 38 campsis-1.9.0/campsis/R/seed.R | 51 campsis-1.9.0/campsis/R/shaded_plot.R |only campsis-1.9.0/campsis/R/simulate.R | 1231 ++++++---- 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campsis-1.9.0/campsis/inst/doc/v01_dataset.Rmd | 42 campsis-1.9.0/campsis/inst/doc/v02_uncertainties.R | 6 campsis-1.9.0/campsis/inst/doc/v02_uncertainties.Rmd | 35 campsis-1.9.0/campsis/inst/doc/v03_covariates.R | 6 campsis-1.9.0/campsis/inst/doc/v03_covariates.Rmd | 115 campsis-1.9.0/campsis/inst/doc/v04_bioavailability.R | 6 campsis-1.9.0/campsis/inst/doc/v04_bioavailability.Rmd | 61 campsis-1.9.0/campsis/inst/doc/v05_lag_time.R | 6 campsis-1.9.0/campsis/inst/doc/v05_lag_time.Rmd | 61 campsis-1.9.0/campsis/inst/doc/v06_infusions.R | 6 campsis-1.9.0/campsis/inst/doc/v06_infusions.Rmd | 53 campsis-1.9.0/campsis/inst/doc/v07_iov.R | 6 campsis-1.9.0/campsis/inst/doc/v07_iov.Rmd | 30 campsis-1.9.0/campsis/inst/doc/v08_initial_conditions.R | 6 campsis-1.9.0/campsis/inst/doc/v08_initial_conditions.Rmd | 17 campsis-1.9.0/campsis/inst/doc/v09_dose_adaptation.R | 6 campsis-1.9.0/campsis/inst/doc/v09_dose_adaptation.Rmd | 21 campsis-1.9.0/campsis/inst/doc/v10_replicate_study.R | 6 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campsis-1.9.0/campsis/man/treatment_iov-class.Rd | 38 campsis-1.9.0/campsis/man/treatment_iovs-class.Rd | 18 campsis-1.9.0/campsis/man/undefined_distribution-class.Rd | 26 campsis-1.9.0/campsis/man/undefined_schedule-class.Rd | 18 campsis-1.9.0/campsis/man/uniform_distribution-class.Rd | 18 campsis-1.9.0/campsis/man/unite_columns.Rd |only campsis-1.9.0/campsis/man/unwrap_treatment.Rd |only campsis-1.9.0/campsis/man/update_addl.Rd |only campsis-1.9.0/campsis/man/update_amount.Rd |only campsis-1.9.0/campsis/man/update_ii.Rd |only campsis-1.9.0/campsis/man/update_repeat.Rd |only campsis-1.9.0/campsis/man/vec_restore.campsis_tbl.Rd |only campsis-1.9.0/campsis/man/vpcPlot.Rd | 55 campsis-1.9.0/campsis/man/vpc_plot.Rd |only campsis-1.9.0/campsis/man/vpc_plot.pi_campsis_tbl.Rd |only campsis-1.9.0/campsis/man/vpc_plot.std_campsis_tbl.Rd |only campsis-1.9.0/campsis/man/weeks.Rd | 34 campsis-1.9.0/campsis/man/years.Rd | 34 campsis-1.9.0/campsis/tests/testthat/_snaps/default_plots |only campsis-1.9.0/campsis/tests/testthat/_snaps/simulate_replicates |only campsis-1.9.0/campsis/tests/testthat/_snaps/vpc_plot |only campsis-1.9.0/campsis/tests/testthat/json_examples/settings_cts_example1.json |only campsis-1.9.0/campsis/tests/testthat/json_examples/settings_cts_example2.json |only campsis-1.9.0/campsis/tests/testthat/json_examples/settings_cts_example3.json |only campsis-1.9.0/campsis/tests/testthat/json_examples/settings_example_replicates.json |only campsis-1.9.0/campsis/tests/testthat/json_examples/settings_example_replicates_hardware.json |only campsis-1.9.0/campsis/tests/testthat/non_regression/full_uncertainty_cp.csv | 572 ++-- campsis-1.9.0/campsis/tests/testthat/test-arm.R |only campsis-1.9.0/campsis/tests/testthat/test-arms.R |only campsis-1.9.0/campsis/tests/testthat/test-bootstrap.R |only campsis-1.9.0/campsis/tests/testthat/test-compilation_error.R |only campsis-1.9.0/campsis/tests/testthat/test-covariate.R |only campsis-1.9.0/campsis/tests/testthat/test-covariates.R |only campsis-1.9.0/campsis/tests/testthat/test-dataset.R |only campsis-1.9.0/campsis/tests/testthat/test-dataset_export_parallelisation.R |only campsis-1.9.0/campsis/tests/testthat/test-default_plots.R |only campsis-1.9.0/campsis/tests/testthat/test-distribution.R |only campsis-1.9.0/campsis/tests/testthat/test-dose_adaptation.R |only campsis-1.9.0/campsis/tests/testthat/test-event.R |only campsis-1.9.0/campsis/tests/testthat/test-events.R |only campsis-1.9.0/campsis/tests/testthat/test-json_interface.R |only campsis-1.9.0/campsis/tests/testthat/test-observations.R |only campsis-1.9.0/campsis/tests/testthat/test-occasion.R |only campsis-1.9.0/campsis/tests/testthat/test-occasions.R |only campsis-1.9.0/campsis/tests/testthat/test-outfuns.R |only campsis-1.9.0/campsis/tests/testthat/test-plot_utils.R |only campsis-1.9.0/campsis/tests/testthat/test-repeated_schedule.R |only campsis-1.9.0/campsis/tests/testthat/test-scatter_plot.R |only campsis-1.9.0/campsis/tests/testthat/test-scenario.R |only campsis-1.9.0/campsis/tests/testthat/test-scenarios.R |only campsis-1.9.0/campsis/tests/testthat/test-seed.R |only campsis-1.9.0/campsis/tests/testthat/test-settings.R |only campsis-1.9.0/campsis/tests/testthat/test-shaded_plot.R |only campsis-1.9.0/campsis/tests/testthat/test-show_method.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_arguments.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_bioavailability.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_bolus.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_bolus_infusion_same_cmt.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_declare.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_dose_adaptation.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_dosing_info.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_events.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_events_logic.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_infusion.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_init.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_iov.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_lag_time.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_minimalist_model.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_no_omega.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_nocb_locf.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_outfun.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_outvars.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_replicates.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_ruv.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_scenarios.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_table.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_time_varying_covariates.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_tsld.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_tte_models.R |only campsis-1.9.0/campsis/tests/testthat/test-simulate_weird_cases.R |only campsis-1.9.0/campsis/tests/testthat/test-spaghetti_plot.R |only campsis-1.9.0/campsis/tests/testthat/test-time_utilities.R |only campsis-1.9.0/campsis/tests/testthat/test-treatment.R |only campsis-1.9.0/campsis/tests/testthat/test-treatment_entry.R |only campsis-1.9.0/campsis/tests/testthat/test-utils.R |only campsis-1.9.0/campsis/tests/testthat/test-vpc_plot.R |only campsis-1.9.0/campsis/vignettes/campsis.Rmd | 18 campsis-1.9.0/campsis/vignettes/resources/Targets_Squeletton/R/my_script.R | 28 campsis-1.9.0/campsis/vignettes/resources/Targets_Squeletton/_targets.R | 8 campsis-1.9.0/campsis/vignettes/resources/Targets_Squeletton_Parallel/R/my_script.R | 28 campsis-1.9.0/campsis/vignettes/resources/Targets_Squeletton_Parallel/_targets.R | 22 campsis-1.9.0/campsis/vignettes/v01_dataset.Rmd | 42 campsis-1.9.0/campsis/vignettes/v02_uncertainties.Rmd | 35 campsis-1.9.0/campsis/vignettes/v03_covariates.Rmd | 115 campsis-1.9.0/campsis/vignettes/v04_bioavailability.Rmd | 61 campsis-1.9.0/campsis/vignettes/v05_lag_time.Rmd | 61 campsis-1.9.0/campsis/vignettes/v06_infusions.Rmd | 53 campsis-1.9.0/campsis/vignettes/v07_iov.Rmd | 30 campsis-1.9.0/campsis/vignettes/v08_initial_conditions.Rmd | 17 campsis-1.9.0/campsis/vignettes/v09_dose_adaptation.Rmd | 21 campsis-1.9.0/campsis/vignettes/v10_replicate_study.Rmd | 22 campsis-1.9.0/campsis/vignettes/v11_scenarios.Rmd | 128 - campsis-1.9.0/campsis/vignettes/v12_time_varying_covariates.Rmd | 71 campsis-1.9.0/campsis/vignettes/v13_events.Rmd | 43 campsis-1.9.0/campsis/vignettes/v14_complex_pkpd_models.Rmd | 55 campsis-1.9.0/campsis/vignettes/v15_pkpd_model_library.Rmd | 98 campsis-1.9.0/campsis/vignettes/v16_progress_bar.Rmd | 69 campsis-1.9.0/campsis/vignettes/v17_run_simulation_in_parallel.Rmd | 224 - 590 files changed, 9636 insertions(+), 7404 deletions(-)
Title: R Interface for Apache Sedona
Description: R interface for 'Apache Sedona' based on 'sparklyr'
(<https://sedona.apache.org>).
Author: Apache Sedona [aut, cre],
Jia Yu [ctb, cph],
Yitao Li [aut, cph] ,
The Apache Software Foundation [cph],
RStudio [cph]
Maintainer: Apache Sedona <private@sedona.apache.org>
Diff between apache.sedona versions 1.9.0 dated 2026-04-23 and 1.9.1 dated 2026-08-05
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/dependencies.R | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: A Toolkit for Connecting R and Large Language Models
Description: A complete toolkit for connecting 'R' environments with Large
Language Models (LLMs). Provides utilities for describing 'R' objects,
package documentation, and workspace state in plain text formats
optimized for LLM consumption. Supports multiple workflows:
interactive copy-paste to external chat interfaces, programmatic tool
registration with 'ellmer' chat clients, batteries-included chat
applications via 'shinychat', and exposure to external coding agents
through the Model Context Protocol. Project configuration files enable
stable, repeatable conversations with project-specific context and
preferred LLM settings.
Author: Garrick Aden-Buie [aut, cre] ,
Simon Couch [aut] ,
Joe Cheng [aut],
Posit Software, PBC [cph, fnd],
Google [cph] ,
Microsoft [cph] ,
Jamie Perkins [cph]
Maintainer: Garrick Aden-Buie <garrick@adenbuie.com>
Diff between btw versions 1.3.0 dated 2026-07-02 and 1.4.0 dated 2026-08-05
btw-1.3.0/btw/inst/js/run-r/btw-icons.js |only btw-1.4.0/btw/DESCRIPTION | 44 - btw-1.4.0/btw/MD5 | 104 +-- btw-1.4.0/btw/NEWS.md | 22 btw-1.4.0/btw/R/btw-config.R |only btw-1.4.0/btw/R/btw_client.R | 24 btw-1.4.0/btw/R/btw_client_app.R | 160 +++-- btw-1.4.0/btw/R/edit_btw_md.R | 159 ++++- btw-1.4.0/btw/R/mcp.R | 2 btw-1.4.0/btw/R/task_create_btw_md.R | 2 btw-1.4.0/btw/R/tool-agent-custom.R | 19 btw-1.4.0/btw/R/tool-agent-subagent.R | 6 btw-1.4.0/btw/R/tool-docs-news.R | 2 btw-1.4.0/btw/R/tool-docs.R | 9 btw-1.4.0/btw/R/tool-env-df.R | 6 btw-1.4.0/btw/R/tool-files-edit.R | 4 btw-1.4.0/btw/R/tool-files-patch.R | 4 btw-1.4.0/btw/R/tool-files-read.R | 48 - btw-1.4.0/btw/R/tool-files-replace.R | 4 btw-1.4.0/btw/R/tool-files-search.R | 21 btw-1.4.0/btw/R/tool-files-write.R | 5 btw-1.4.0/btw/R/tool-git.R | 6 btw-1.4.0/btw/R/tool-pkg-src.R |only btw-1.4.0/btw/R/tool-run.R | 86 +- btw-1.4.0/btw/R/tool-skills.R | 38 + btw-1.4.0/btw/R/utils.R | 115 +++ btw-1.4.0/btw/exec/btw.R | 281 +++++++++ btw-1.4.0/btw/inst/cli-skill/r-btw-cli/SKILL.md | 23 btw-1.4.0/btw/inst/js/app/btw_app.css | 41 - btw-1.4.0/btw/inst/js/app/btw_app.js | 71 +- btw-1.4.0/btw/inst/js/run-r/btw-run-r.css | 508 +++++++++------- btw-1.4.0/btw/inst/js/run-r/btw-run-r.js | 514 +++-------------- btw-1.4.0/btw/man/btw-config.Rd |only btw-1.4.0/btw/man/btw_agent_tool.Rd | 6 btw-1.4.0/btw/man/btw_client.Rd | 72 ++ btw-1.4.0/btw/man/btw_skill_install_github.Rd | 3 btw-1.4.0/btw/man/btw_skill_install_package.Rd | 3 btw-1.4.0/btw/man/btw_tool_skill.Rd | 3 btw-1.4.0/btw/man/mcp.Rd | 2 btw-1.4.0/btw/man/use_btw_md.Rd | 28 btw-1.4.0/btw/tests/testthat/_snaps/btw_client.md | 4 btw-1.4.0/btw/tests/testthat/_snaps/edit_btw_md.md | 83 ++ btw-1.4.0/btw/tests/testthat/_snaps/tool-files-edit.md | 74 +- btw-1.4.0/btw/tests/testthat/_snaps/utils.md | 12 btw-1.4.0/btw/tests/testthat/helpers.R | 16 btw-1.4.0/btw/tests/testthat/test-btw_client_app.R |only btw-1.4.0/btw/tests/testthat/test-cli.R | 149 ++++ btw-1.4.0/btw/tests/testthat/test-edit_btw_md.R | 190 ++++++ btw-1.4.0/btw/tests/testthat/test-tool-agent-custom.R | 38 + btw-1.4.0/btw/tests/testthat/test-tool-docs.R | 3 btw-1.4.0/btw/tests/testthat/test-tool-files-read.R | 34 + btw-1.4.0/btw/tests/testthat/test-tool-files-write.R | 8 btw-1.4.0/btw/tests/testthat/test-tool-pkg-src.R |only btw-1.4.0/btw/tests/testthat/test-tool-run.R | 82 ++ btw-1.4.0/btw/tests/testthat/test-tool_skills.R | 82 ++ btw-1.4.0/btw/tests/testthat/test-utils.R | 187 ++++++ 56 files changed, 2413 insertions(+), 994 deletions(-)
Title: Colour Palettes for Data
Description: Colour palettes for data, based on some well known public data
sets. Includes helper functions to map absolute values to known palettes, and
capture the work of image colour mapping as raster data sets.
Author: Michael D. Sumner [aut, cre, cph],
Abigael Proctor [ctb] ,
Tomas Remenyi [ctb] ,
R Core Team and contributors worldwide [ctb]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between palr versions 0.4.0 dated 2023-11-06 and 0.5.0 dated 2026-08-05
palr-0.4.0/palr/R/element_pal.R |only palr-0.4.0/palr/R/palr-package.r |only palr-0.5.0/palr/DESCRIPTION | 19 - palr-0.5.0/palr/MD5 | 61 ++- palr-0.5.0/palr/NAMESPACE | 8 palr-0.5.0/palr/NEWS.md | 37 ++ palr-0.5.0/palr/R/bathy.R | 20 - palr-0.5.0/palr/R/data_pal.R | 10 palr-0.5.0/palr/R/dirty.R |only palr-0.5.0/palr/R/image_hex.R |only palr-0.5.0/palr/R/image_pal.R | 1 palr-0.5.0/palr/R/palr-package.R |only palr-0.5.0/palr/R/palr.R | 376 ++++++------------------ palr-0.5.0/palr/R/stretch.R |only palr-0.5.0/palr/R/utils.R | 2 palr-0.5.0/palr/README.md | 4 palr-0.5.0/palr/build/vignette.rds |binary palr-0.5.0/palr/data/chl.rda |only palr-0.5.0/palr/inst/doc/nasa_chla.Rmd | 2 palr-0.5.0/palr/inst/doc/nasa_chla.html | 11 palr-0.5.0/palr/inst/doc/palr.R | 2 palr-0.5.0/palr/inst/doc/palr.html | 15 palr-0.5.0/palr/inst/extdata |only palr-0.5.0/palr/man/bathy_deep_pal.Rd | 2 palr-0.5.0/palr/man/chl_pal.Rd | 16 - palr-0.5.0/palr/man/d_pal.Rd | 3 palr-0.5.0/palr/man/dirty_pal.Rd |only palr-0.5.0/palr/man/ice_pal.Rd | 15 palr-0.5.0/palr/man/image_hex.Rd |only palr-0.5.0/palr/man/oisst.Rd | 9 palr-0.5.0/palr/man/palr.Rd | 28 + palr-0.5.0/palr/man/sst_pal.Rd | 2 palr-0.5.0/palr/man/stretch_linear.Rd |only palr-0.5.0/palr/tests/testthat/test-basic.R | 93 ++--- palr-0.5.0/palr/tests/testthat/test-image_hex.R |only palr-0.5.0/palr/tests/testthat/test-missing.R | 19 - palr-0.5.0/palr/tests/testthat/test-stretch.R |only palr-0.5.0/palr/vignettes/nasa_chla.Rmd | 2 38 files changed, 335 insertions(+), 422 deletions(-)
Title: Reusable Data Viewer Module for 'shiny'
Description: Provides a reusable 'shiny' module for viewing tabular data with a searchable 'reactable' table and a variable summary sidebar built with 'bslib'.
Author: Ryan Harrison [aut, cre, cph]
Maintainer: Ryan Harrison <harrison.ryan.w@gmail.com>
Diff between shinydataviewer versions 0.1.0 dated 2026-04-09 and 0.2.0 dated 2026-08-04
DESCRIPTION | 11 +- MD5 | 56 +++++++------ NEWS.md | 12 ++ R/data_summary.R | 77 ++++++++++++++++--- R/data_viewer_assets.R | 40 +++++++++ R/mod_data_viewer.R | 26 ++++-- R/ui_components.R | 46 +++++++++++ README.md | 28 ++++++ build/vignette.rds |binary inst/WORDLIST | 2 inst/app/www/data-viewer.css | 93 ++++++++++++++++++++--- inst/doc/customization.R | 6 + inst/doc/customization.Rmd | 18 ++++ inst/doc/customization.html | 49 +++++++----- inst/doc/get-started.R | 3 inst/doc/get-started.Rmd | 10 ++ inst/doc/get-started.html | 9 +- inst/examples/upload-dataset |only man/data_viewer_card_ui.Rd | 7 + man/data_viewer_server.Rd | 2 man/data_viewer_ui.Rd | 7 + man/shinydataviewer-package.Rd | 5 + man/summarize_columns.Rd | 13 ++- tests/spelling.R |only tests/testthat/helper-load-package.R | 18 ---- tests/testthat/test-data-summary-edge-cases.R | 56 +++++++++++++ tests/testthat/test-module-server.R | 18 ++++ tests/testthat/test-ui-components.R | 105 ++++++++++++++++++++++++++ vignettes/customization.Rmd | 18 ++++ vignettes/get-started.Rmd | 10 ++ 30 files changed, 640 insertions(+), 105 deletions(-)
More information about shinydataviewer at CRAN
Permanent link
Title: Nonlinear Mixed Effects Models in Population PK/PD, Plot
Functions
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for
'ggplot2' plotting methods for 'nlmixr2' objects.
Author: Matthew Fidler [aut, cre] ,
Bill Denney [ctb] ,
Wenping Wang [aut],
Vipul Mann [aut]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2plot versions 5.0.2 dated 2026-06-11 and 5.1.0 dated 2026-08-04
nlmixr2plot-5.0.2/nlmixr2plot/R/nlmixr2PlotList.R |only nlmixr2plot-5.0.2/nlmixr2plot/tests/testthat/test-nlmixr2PlotList.R |only nlmixr2plot-5.1.0/nlmixr2plot/DESCRIPTION | 12 - nlmixr2plot-5.1.0/nlmixr2plot/MD5 | 34 +- nlmixr2plot-5.1.0/nlmixr2plot/NAMESPACE | 4 nlmixr2plot-5.1.0/nlmixr2plot/NEWS.md | 51 ++++ nlmixr2plot-5.1.0/nlmixr2plot/R/plot.bsv.R |only nlmixr2plot-5.1.0/nlmixr2plot/R/plot.nlmixr2.R | 108 ++++----- nlmixr2plot-5.1.0/nlmixr2plot/R/plot.nlmixr2AugPred.R | 69 +++--- nlmixr2plot-5.1.0/nlmixr2plot/R/vpcPlot.R | 114 ++++++++-- nlmixr2plot-5.1.0/nlmixr2plot/man/plot.nlmixr2AugPred.Rd | 6 nlmixr2plot-5.1.0/nlmixr2plot/man/plot.nlmixr2FitData.Rd | 19 + nlmixr2plot-5.1.0/nlmixr2plot/man/traceplot.Rd | 3 nlmixr2plot-5.1.0/nlmixr2plot/man/vpcPlot.Rd | 4 nlmixr2plot-5.1.0/nlmixr2plot/tests/testthat.R | 60 +++++ nlmixr2plot-5.1.0/nlmixr2plot/tests/testthat/test-gglist-integration.R |only nlmixr2plot-5.1.0/nlmixr2plot/tests/testthat/test-plots-bsv.R |only nlmixr2plot-5.1.0/nlmixr2plot/tests/testthat/test-plots-cens.R | 49 +++- nlmixr2plot-5.1.0/nlmixr2plot/tests/testthat/test-plots-multiple-endpoints.R | 18 + nlmixr2plot-5.1.0/nlmixr2plot/tests/testthat/test-plots.R | 26 +- nlmixr2plot-5.1.0/nlmixr2plot/tests/testthat/test-vpc-cens-cols.R |only 21 files changed, 422 insertions(+), 155 deletions(-)
Title: Save 'nlmixr2' Fits in a Format Readable Outside 'nlmixr2'
Description: Provides tools to save 'nlmixr2' fitted models in a portable format
readable outside of 'nlmixr2' and independent of the package version.
'nlmixr2' fits and compares nonlinear mixed-effects models in differential
equations with flexible dosing information commonly seen in pharmacokinetics
and pharmacodynamics (Almquist, Leander, and Jirstrand 2015
<doi:10.1007/s10928-015-9409-1>). Differential equation solving uses compiled
C code from the 'rxode2' package (Wang, Hallow, and James 2015
<doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2save versions 0.1.0 dated 2026-06-17 and 0.2.0 dated 2026-08-04
DESCRIPTION | 9 LICENSE | 4 MD5 | 77 NAMESPACE | 62 NEWS.md | 103 - R/RcppExports.R | 57 R/nlmixr2save-package.R | 10 R/save.R | 2782 +++++++++++++++++----------- R/simplify.R | 194 + README.md | 994 +++++----- build/vignette.rds |binary inst/doc/register-simulation-functions.R | 74 inst/doc/register-simulation-functions.Rmd | 258 +- inst/doc/register-simulation-functions.html | 915 ++++----- inst/doc/sharing-fits.R |only inst/doc/sharing-fits.Rmd |only inst/doc/sharing-fits.html |only inst/doc/uses.R | 78 inst/doc/uses.Rmd | 382 +-- inst/doc/uses.html | 1043 +++++----- inst/doc/version-tracking.R |only inst/doc/version-tracking.Rmd |only inst/doc/version-tracking.html |only man/colon-equals.Rd | 199 +- man/dot-assignParent.Rd | 48 man/dot-assignRestore.Rd | 44 man/dot-nlmixr2saveProps.Rd | 106 - man/loadFit.Rd | 38 man/nlmixr2saveInvalidate.Rd |only man/nlmixr2saveParFixedDf.Rd | 56 man/nlmixr2saveShare.Rd |only man/nlmixrDataSimplify.Rd | 79 man/saveFit.Rd | 149 - man/saveFitItem.Rd | 88 man/saveFitRandom.Rd | 60 src/RcppExports.cpp | 9 src/nlmixr2fix.cpp | 58 tests/testthat.R | 33 tests/testthat/test-save.R | 1416 ++++++++------ tests/testthat/test-simplify.R | 223 +- tests/testthat/test-vig-options.R |only vignettes/register-simulation-functions.Rmd | 258 +- vignettes/sharing-fits.Rmd |only vignettes/uses.Rmd | 382 +-- vignettes/version-tracking.Rmd |only 45 files changed, 5712 insertions(+), 4576 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD
Description: Fit and compare nonlinear mixed-effects models in differential
equations with flexible dosing information commonly seen in pharmacokinetics
and pharmacodynamics (Almquist, Leander, and Jirstrand 2015
<doi:10.1007/s10928-015-9409-1>). Differential equation solving is
by compiled C code provided in the 'rxode2' package
(Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Anne Keunecke [ctb],
Rik Schoemaker [ctb] ,
Justin Wilkins [ctb] ,
Wenping Wang [ctb],
Mirjam Trame [ctb],
John Harrold [ctb],
Bill Denney [ctb] ,
Theodoros Papathanasiou [ctb],
Richard Hooijmaijers [ctb],
Michael Wayne Ke [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2 versions 5.0.0 dated 2025-11-30 and 7.0.1 dated 2026-08-04
DESCRIPTION | 22 +++++---- MD5 | 14 +++--- NAMESPACE | 2 NEWS.md | 35 +++++++++++++++ R/nlmixr2CheckInstall.R | 55 +++++++++++++++++++++--- R/verse.R | 102 +++++++++++++++++++++++++-------------------- README.md | 83 +++++++++++------------------------- man/nlmixr2CheckInstall.Rd | 4 + 8 files changed, 192 insertions(+), 125 deletions(-)
Title: Survey Sampling Algorithms
Description: Fast implementations of survey sampling algorithms for
single-stage probability sampling from finite populations,
written in C.
Provides equal probability methods (simple random sampling,
systematic, Bernoulli), unequal probability methods (conditional
Poisson / maximum entropy, Sampford, Brewer, systematic PPS, Pareto,
sequential Poisson, Poisson, Chromy's minimum replacement,
multinomial), balanced sampling via the cube method, and
spatially balanced sampling via the local pivotal method and
spatially correlated Poisson sampling.
All sampling functions return design objects carrying sample
indices, inclusion probabilities, and design metadata. Generics
compute joint inclusion probabilities, pairwise expectations, and
sampling covariances for variance estimation. Mostly based on
algorithms from Tillé (2006, <doi:10.1007/0-387-34240-0>).
Author: Ahmadou Dicko [aut, cre] ,
Thomas Lumley [ctb],
Wilmer Prentius [ctb, cph] cube implementation from which src/cube.c was ported)
Maintainer: Ahmadou Dicko <mail@ahmadoudicko.com>
Diff between sondage versions 0.9.0 dated 2026-08-03 and 0.9.1 dated 2026-08-04
DESCRIPTION | 6 ++-- MD5 | 42 +++++++++++++++++----------------- R/balanced_wor.R | 2 - R/constructors.R | 4 +-- R/equal_prob.R | 2 - R/generics.R | 8 ++++-- R/register.R | 2 - R/unequal_prob.R | 6 ++-- README.md | 52 ++++++++++++++++--------------------------- inst/doc/custom-methods.html | 42 +++++++++++++++++----------------- inst/doc/sondage.Rmd | 2 - inst/doc/sondage.html | 6 +++- man/balanced_wor.Rd | 2 - man/equal_prob_wor.Rd | 2 - man/joint_expected_hits.Rd | 2 - man/joint_inclusion_prob.Rd | 2 - man/register_method.Rd | 2 - man/sampling_cov.Rd | 5 ++++ man/sondage_sample.Rd | 4 +-- man/unequal_prob_wor.Rd | 6 ++-- src/joint_probs.c | 12 +++++---- vignettes/sondage.Rmd | 2 - 22 files changed, 107 insertions(+), 106 deletions(-)
Title: LLM Wiki Engine
Description: Personal wiki engine with a large language model (LLM) as
research assistant. Supports guided sessions through a 'Claude Code'
<https://github.com/anthropics/claude-code> skill bundle and
autonomous research runs from R via autoresearch(). Results land in
a structured vault of markdown pages with 'YAML' frontmatter and
wikilinks, ready for hand-editing in your favourite editor
alongside the LLM. Vaults are seeded with 'CLAUDE.md' and
'AGENTS.md' so 'Claude Code', 'Codex'
<https://github.com/openai/codex>, and other agents share the same
operating instructions. Can adopt an existing 'Obsidian'
<https://obsidian.md/> vault in place via init_vault(adopt = TRUE).
Author: Troy Hernandez [aut, cre] ,
cornball.ai [cph]
Maintainer: Troy Hernandez <troy@cornball.ai>
Diff between pensar versions 0.6.4 dated 2026-06-24 and 0.7.0 dated 2026-08-04
DESCRIPTION | 8 - MD5 | 91 ++++++------ NAMESPACE | 1 NEWS.md | 54 +++++++ R/audits.R | 1 R/autoresearch.R | 1 R/autoresearch_backends.R | 1 R/autoresearch_program.R | 1 R/autoresearch_steps.R | 25 ++- R/backlinks.R | 1 R/db.R | 1 R/export.R | 7 R/git.R | 299 +++++++++++++++++++++++++++++++++++++++--- R/index.R | 1 R/ingest.R | 1 R/ingest_agent_context.R | 1 R/ingest_briefing.R | 1 R/ingest_repo.R | 1 R/ingest_url.R | 1 R/lint.R | 1 R/log.R | 1 R/manifest.R | 98 +++++++++++++ R/merge.R |only R/migrate.R | 1 R/outlinks.R | 1 R/parse.R | 1 R/pensar-package.R | 1 R/pensarignore.R | 1 R/registry.R | 1 R/retrieval.R | 1 R/show_page.R | 1 R/skills.R | 1 R/status.R | 20 ++ R/vault.R | 90 ++++++++++-- R/vault_graph.R | 1 R/wiki_write.R | 1 README.md | 7 build/partial.rdb |binary build/vignette.rds |binary inst/bin/pensar | 3 inst/scripts/merge.R |only inst/tinytest/test_git.R | 243 +++++++++++++++++++++++++++++++++- inst/tinytest/test_manifest.R | 81 +++++++++++ inst/tinytest/test_merge.R |only inst/tinytest/test_nested.R |only man/init_vault.Rd | 11 + man/status.Rd | 5 man/vault_commit.Rd | 41 ++++- man/vault_merge.Rd |only 49 files changed, 970 insertions(+), 139 deletions(-)
Title: Interface to the 'nanoarrow' 'C' Library
Description: Provides an 'R' interface to the 'nanoarrow' 'C' library and the
'Apache Arrow' application binary interface. Functions to import and
export 'ArrowArray', 'ArrowSchema', and 'ArrowArrayStream' 'C' structures
to and from 'R' objects are provided alongside helpers to facilitate zero-copy
data transfer among 'R' bindings to libraries implementing the 'Arrow' 'C'
data interface.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between nanoarrow versions 0.8.0-1 dated 2026-06-04 and 0.9.0 dated 2026-08-04
DESCRIPTION | 10 MD5 | 68 - NAMESPACE | 1 NEWS.md | 10 R/convert-array.R | 4 R/ipc.R | 24 R/nanoarrow-package.R | 7 configure | 21 man/as_nanoarrow_schema.Rd | 4 man/as_nanoarrow_schema.python.builtin.object.Rd | 2 man/convert_array.Rd | 6 man/example_ipc_stream.Rd | 4 man/infer_nanoarrow_ptype.Rd | 2 man/na_vctrs.Rd | 2 man/nanoarrow-package.Rd | 1 man/nanoarrow_version.Rd | 4 src/Makevars.ucrt | 18 src/Makevars.win | 18 src/flatcc.c | 9 src/flatcc/flatcc_endian.h | 2 src/flatcc/flatcc_types.h | 5 src/flatcc/flatcc_verifier.h | 4 src/flatcc/portable/flatcc_portable.h |only src/flatcc/portable/pstdint.h | 2 src/init.c | 2 src/nanoarrow.c | 430 ++++++ src/nanoarrow.h | 145 ++ src/nanoarrow.hpp | 8 src/nanoarrow_ipc.c | 1505 ++++++++++++++++++----- src/nanoarrow_ipc.h | 318 ++++ src/nanoarrow_ipc.hpp | 54 src/version.c | 8 tests/testthat/test-convert-array-stream.R | 96 + tests/testthat/test-convert-array.R | 75 + tests/testthat/test-ipc.R | 160 ++ tools/test_lz4.c |only 36 files changed, 2578 insertions(+), 451 deletions(-)
Title: Basis Expansions for Regression Modeling
Description: Provides various basis expansions for flexible regression modeling,
including random Fourier features (Rahimi & Recht, 2007)
<https://proceedings.neurips.cc/paper_files/paper/2007/file/013a006f03dbc5392effeb8f18fda755-Paper.pdf>,
exact kernel / Gaussian process feature maps, prior features for Bayesian
Additive Regression Trees (BART) (McCartan & Huang, 2026) <doi:10.48550/arXiv.2607.28844>,
and a helpful interface for n-way interactions. The provided functions may
be used within any modeling formula, allowing the use of kernel methods and
other basis expansions in modeling functions that do not otherwise support
them. Along with the basis expansions, a number of kernel functions are also
provided, which support kernel arithmetic to form new kernels. Basic ridge
regression functionality is included as well.
Author: Cory McCartan [aut, cre, cph]
Maintainer: Cory McCartan <mccartan@psu.edu>
Diff between bases versions 0.2.0 dated 2026-02-27 and 0.2.1 dated 2026-08-04
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NEWS.md | 5 +++++ R/b_bart.R | 27 ++++++++++++++++----------- R/b_gff.R | 4 ++-- R/b_rff.R | 2 +- README.md | 4 ++-- build/partial.rdb |binary build/vignette.rds |binary man/b_bart.Rd | 26 +++++++++++++++----------- man/b_gff.Rd | 2 +- man/bases-package.Rd | 7 ++++++- 12 files changed, 64 insertions(+), 45 deletions(-)
Title: Minimal R Documentation Generator
Description: A deterministic, dependency-free documentation generator for R
packages. Generates valid Rd files and NAMESPACE from 'roxygen2'-style comments
using only base R. Supports a strict subset of tags with no markdown parsing,
no inference magic, and explicit-only behavior.
Author: Troy Hernandez [aut, cre] ,
cornball.ai [cph]
Maintainer: Troy Hernandez <troy@cornball.ai>
Diff between tinyrox versions 0.4.0 dated 2026-06-24 and 0.4.1 dated 2026-08-04
DESCRIPTION | 8 +- MD5 | 18 +++-- NEWS.md | 7 ++ R/rd.R | 130 ++++++++++++++++++++++++++--------------- README.md | 28 ++++++++ inst/tinytest/test_rd.R | 152 ++++++++++++++++++++++++++++++++++++++++++++++++ man/document.Rd | 9 ++ man/escape_percent.Rd |only man/format_usage.Rd | 6 + man/generate_rd.Rd | 7 +- man/wrap_usage_arg.Rd |only 11 files changed, 302 insertions(+), 63 deletions(-)
Title: 'OpenAI' Compatible Speech-to-Text API Client
Description: A minimal-dependency R client for 'OpenAI'-compatible speech-to-text
APIs (see <https://developers.openai.com/api/reference/resources/audio>) with
optional local fallbacks. Supports 'OpenAI', local servers, and the
'whisper' package for local transcription.
Author: Troy Hernandez [aut, cre] ,
cornball.ai [cph]
Maintainer: Troy Hernandez <troy@cornball.ai>
Diff between stt.api versions 0.3.0 dated 2026-06-19 and 0.3.1 dated 2026-08-04
DESCRIPTION | 12 - LICENSE | 2 MD5 | 29 +++- NAMESPACE | 1 NEWS.md | 126 ++++++++++++++++++++ R/internal_api.R | 224 ++++++++++++++++++++++++++++++++---- R/internal_interop.R |only R/label_speakers.R |only R/stt.R | 170 +++++++++++++++++++++++++-- inst/audio |only inst/tinytest/test_diarize.R |only inst/tinytest/test_interop.R |only inst/tinytest/test_label_speakers.R |only man/dot-audio_data_uri.Rd |only man/dot-audio_mime.Rd |only man/dot-is_diarizing.Rd |only man/dot-parse_api_segments.Rd |only man/dot-validate_known_speakers.Rd |only man/label_speakers.Rd |only man/stt.Rd | 101 ++++++++++++++-- 20 files changed, 609 insertions(+), 56 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The vendored 'SUNDIALS'
'CVODE' sources and headers are released under the BSD-3-Clause license.
The information is available in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Aaron Collier [ctb] ,
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Ashley Crawford [ctb] ,
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Cleve Moler [ctb],
Cody J. Balos [ctb] ,
Dan Shumaker [ctb] ,
Dan [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 5.1.5 dated 2026-07-28 and 5.1.6 dated 2026-08-04
DESCRIPTION | 14 - MD5 | 43 ++-- NAMESPACE | 1 NEWS.md | 77 ++++++++ R/eventSens.R | 62 +++++- R/rxode2.R | 85 ++++++++- R/rxode2_md5.R | 2 inst/doc/rxode2-syntax.html | 26 +- inst/include/rxode2.h | 14 + inst/include/rxode2parseVer.h | 4 inst/include/rxode2ptr.h | 75 +++++++- inst/tools/workaround.R | 28 ++- man/rxEventSensLoadModel.Rd | 4 man/rxStripModelSrc.Rd |only src/init.c | 54 +++++ src/linCmt.cpp | 10 + src/par_solve.cpp | 240 ++++++++++++++++++++++++++ src/rx2api.c | 37 +++- src/rxode2_sundials_stan_compat.h | 15 + src/rxthreefry.cpp | 130 +++++++++++++- tests/testthat/test-event-sensitivities-api.R |only tests/testthat/test-plot.R | 18 + tests/testthat/test-random.R | 35 +++ tests/testthat/test-rxpre-cache-key.R |only 24 files changed, 889 insertions(+), 85 deletions(-)
Title: A Data-Centered Data Flow Manager
Description: A data manager meant to avoid manual storage/retrieval of
data to/from the file system. It builds one (or more) centralized
repository where R objects are stored with rich annotations,
including corresponding code chunks, and easily searched and
retrieved. See Napolitano (2017) <doi:10.1186/s12859-017-1510-6> for further
information.
Author: Francesco Napolitano [aut, cre]
Maintainer: Francesco Napolitano <franapoli@gmail.com>
This is a re-admission after prior archival of version 2.1.5 dated 2020-02-08
Diff between repo versions 2.1.5 dated 2020-02-08 and 2.1.7 dated 2026-08-04
DESCRIPTION | 22 - MD5 | 35 +- NEWS.md | 425 +++++++++++---------------- R/repo.R | 6 R/repo_private.R | 2 R/repo_public.R | 15 README.md | 58 ++- build/partial.rdb |only build/vignette.rds |binary inst/README-depgraph-1.png |binary inst/doc/index.R | 108 +++--- inst/doc/index.Rmd | 6 inst/doc/index.html | 707 ++++++++++++++++++++++++++------------------- man/repo-package.Rd | 5 man/repo_build.Rd | 9 man/repo_dependencies.Rd | 2 man/repo_open.Rd | 4 man/repo_pies.Rd | 4 vignettes/index.Rmd | 6 19 files changed, 762 insertions(+), 652 deletions(-)
Title: Matrix End-to-End Encryption Primitives
Description: 'Olm' and 'Megolm' encryption ratchet primitives for the
'Matrix' messaging protocol <https://matrix.org/>, wrapping the
'vodozemac' Rust crate. Provides device-key generation, one-time-key
management, 1:1 'Olm' sessions, and 'Megolm' group sessions. Pairs
with the 'mx.api' package, which handles 'Matrix' HTTP transport.
Author: Troy Hernandez [aut, cre] ,
cornball.ai [cph],
The Matrix.org Foundation C.I.C. [ctb, cph] ,
Authors of the dependency Rust crates [ctb]
Maintainer: Troy Hernandez <troy@cornball.ai>
Diff between mx.crypto versions 0.2.0 dated 2026-06-12 and 0.2.1 dated 2026-08-04
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 13 +++++++++++++ build/vignette.rds |binary tools/configure.R | 43 +++++++++++++++++++++++++++++++++---------- 5 files changed, 54 insertions(+), 18 deletions(-)
Title: Stateful Matrix Client Helpers
Description: Stateful helpers for building 'Matrix' (<https://matrix.org>)
chat clients in R. Builds on the low-level 'mx.api' Client-Server API
bindings, adding local configuration persistence, room resolution,
sync cursor handling, sync-event extraction, invite acceptance, a
conservative Markdown-to-HTML converter for formatted messages, and
'Olm'/'Megolm' end-to-end encryption orchestration over the optional
'mx.crypto' package.
Author: Troy Hernandez [aut, cre] ,
cornball.ai [cph]
Maintainer: Troy Hernandez <troy@cornball.ai>
Diff between mx.client versions 0.1.1 dated 2026-06-19 and 0.2.0 dated 2026-08-04
DESCRIPTION | 10 +- MD5 | 59 +++++++----- NAMESPACE | 5 + NEWS.md | 90 ++++++++++++++++++ R/config.R | 64 +++++++++++++ R/crypto.R | 131 +++++++++++++++++++++++++-- R/e2ee.R | 123 ++++++++++++++++++++++--- R/markdown.R | 167 +++++++++++++++++++++++++++++------ R/messages.R | 17 ++- R/profile.R |only R/tables.R |only R/transport.R | 104 ++++++++++++++++++--- build/partial.rdb |binary build/vignette.rds |binary inst/skills |only inst/tinytest/test_crypto.R | 11 +- inst/tinytest/test_e2ee.R | 120 ++++++++++++++++++++++++- inst/tinytest/test_markdown.R | 40 ++++++++ inst/tinytest/test_mx.client.R | 47 +++++++++ inst/tinytest/test_relogin.R | 7 + inst/tinytest/test_tables.R |only inst/tinytest/test_transport.R |only man/mx_crypto_claim_otks.Rd | 9 + man/mx_crypto_encrypt_for_devices.Rd | 14 ++ man/mx_crypto_handle_to_device.Rd | 32 +++++- man/mx_crypto_known_devices.Rd | 9 + man/mx_crypto_process_sync.Rd | 10 +- man/mx_crypto_room_key_payload.Rd | 15 ++- man/mx_extract_text_events.Rd | 6 + man/mx_markdown_to_html.Rd | 2 man/mx_pill_mentions.Rd | 15 +-- man/mx_send_table.Rd |only man/mx_set_displayname.Rd |only man/mx_table_html.Rd |only man/print.mx_client_config.Rd |only 35 files changed, 975 insertions(+), 132 deletions(-)
Title: Tidyverse-Friendly Introductory Linear Regression
Description: Datasets and wrapper functions for tidyverse-friendly introductory linear regression, used in "Statistical Inference via Data Science: A ModernDive into R and the Tidyverse" available at <https://moderndive.com/>.
Author: Albert Y. Kim [aut, cre] ,
Chester Ismay [aut] ,
Andrew Bray [ctb] ,
Delaney Moran [ctb],
Evgeni Chasnovski [ctb] ,
Will Hopper [ctb] ,
Benjamin S. Baumer [ctb] ,
Marium Tapal [ctb] ,
Wayne Ndlovu [ctb],
Catherine Peppers [ctb],
Annah Mutaya [ctb],
A [...truncated...]
Maintainer: Albert Y. Kim <albert.ys.kim@gmail.com>
Diff between moderndive versions 0.7.0 dated 2024-09-01 and 0.8.0 dated 2026-08-04
DESCRIPTION | 48 +- MD5 | 117 +++-- NAMESPACE | 13 NEWS.md | 19 R/datasets.R | 42 + R/geom_categorical_model.R | 21 R/get_correlation.R | 174 +++++-- R/moderndive.R | 12 R/plot_3d_regression.R |only R/regression_functions.R | 421 ++++++++++--------- R/view.R |only R/zzz.R |only build/partial.rdb |binary build/vignette.rds |binary data/pennies_resamples.rda |binary inst/doc/moderndive.R | 56 +- inst/doc/moderndive.Rmd | 2 inst/doc/moderndive.html | 61 +- inst/doc/paper.Rmd | 2 inst/doc/paper.pdf |binary man/MA_schools.Rd | 2 man/View.Rd |only man/early_january_2023_weather.Rd | 3 man/early_january_weather.Rd | 3 man/geom_categorical_model.Rd | 25 - man/geom_parallel_slopes.Rd | 8 man/get_correlation.Rd | 76 ++- man/get_regression_points.Rd | 38 - man/get_regression_summaries.Rd | 9 man/get_regression_table.Rd | 26 - man/house_prices.Rd | 4 man/ma_traffic_2020_vs_2019.Rd | 2 man/moderndive.Rd | 12 man/pennies_resamples.Rd | 2 man/pennies_sample.Rd | 2 man/plot_3d_regression.Rd |only man/reexports.Rd | 2 man/saratoga_houses.Rd | 4 man/spotify_52_original.Rd | 6 man/spotify_52_shuffled.Rd | 6 man/spotify_by_genre.Rd | 8 tests/testthat/_snaps |only tests/testthat/helper-utils.R | 4 tests/testthat/test-datasets.R |only tests/testthat/test-geom_categorical_model.R | 187 ++++++++ tests/testthat/test-geom_parallel_slopes.R | 51 ++ tests/testthat/test-get_correlation.R | 210 +++++++++ tests/testthat/test-get_regression_functions.R | 551 ++++++++++++++++++++++++- tests/testthat/test-plot_3d_regression.R |only tests/testthat/test-tidy_summary.R | 160 +++++++ tests/testthat/test-view.R |only vignettes/moderndive.Rmd | 2 vignettes/paper.Rmd | 2 vignettes/paper.html | 36 - vignettes/paper.md | 2 55 files changed, 1885 insertions(+), 546 deletions(-)
Title: A Fast and Lightweight Logging System for R, Based on 'log4j'
Description: Provides a fast, lightweight, object-oriented approach to
logging based on the widely-emulated 'log4j' system and etymology.
Loggers write messages to one or more destinations, such as the
console, a file, or a remote server, using a format you control.
Messages below the chosen severity threshold are discarded cheaply, so
logging calls can be left in production code.
Author: John Myles White [aut, cph],
Kenton White [ctb],
Kirill Mueller [ctb],
Aaron Jacobs [aut],
Posit Software, PBC [cph, fnd] ,
Hadley Wickham [cre]
Maintainer: Hadley Wickham <hadley@posit.co>
This is a re-admission after prior archival of version 0.4.4 dated 2024-10-12
Diff between log4r versions 0.4.4 dated 2024-10-12 and 0.5.0 dated 2026-08-04
log4r-0.4.4/log4r/R/create.logger.R |only log4r-0.4.4/log4r/R/level.logger.R |only log4r-0.4.4/log4r/R/logfile.logger.R |only log4r-0.4.4/log4r/R/logformat.logger.R |only log4r-0.4.4/log4r/R/loglevel.R |only log4r-0.4.4/log4r/man/create.logger.Rd |only log4r-0.4.4/log4r/man/levellog.Rd |only log4r-0.4.4/log4r/man/logfile.Rd |only log4r-0.4.4/log4r/man/logformat.Rd |only log4r-0.4.4/log4r/man/loglevel.Rd |only log4r-0.4.4/log4r/tests/testthat/test-loglevel.R |only log4r-0.4.4/log4r/tests/testthat/test-verbosity.R |only log4r-0.5.0/log4r/DESCRIPTION | 51 log4r-0.5.0/log4r/MD5 | 88 - log4r-0.5.0/log4r/NAMESPACE | 8 log4r-0.5.0/log4r/NEWS.md | 26 log4r-0.5.0/log4r/R/appenders.R | 129 +- log4r-0.5.0/log4r/R/deprecated.R |only log4r-0.5.0/log4r/R/layouts.R | 96 + log4r-0.5.0/log4r/R/level.R |only log4r-0.5.0/log4r/R/logfuncs.R | 90 - log4r-0.5.0/log4r/R/logger.R |only log4r-0.5.0/log4r/README.md | 51 log4r-0.5.0/log4r/build/vignette.rds |binary log4r-0.5.0/log4r/inst/doc/logging-beyond-local-files.R | 12 log4r-0.5.0/log4r/inst/doc/logging-beyond-local-files.Rmd | 6 log4r-0.5.0/log4r/inst/doc/logging-beyond-local-files.html | 13 log4r-0.5.0/log4r/inst/doc/performance.R | 19 log4r-0.5.0/log4r/inst/doc/performance.Rmd | 30 log4r-0.5.0/log4r/inst/doc/performance.html | 695 ++++++++++--- log4r-0.5.0/log4r/inst/doc/structured-logging.R | 4 log4r-0.5.0/log4r/inst/doc/structured-logging.Rmd | 6 log4r-0.5.0/log4r/inst/doc/structured-logging.html | 19 log4r-0.5.0/log4r/man/appenders.Rd | 14 log4r-0.5.0/log4r/man/figures |only log4r-0.5.0/log4r/man/http_appender.Rd | 11 log4r-0.5.0/log4r/man/layouts.Rd | 29 log4r-0.5.0/log4r/man/level.Rd | 36 log4r-0.5.0/log4r/man/log4r-deprecated.Rd |only log4r-0.5.0/log4r/man/log4r-package.Rd | 9 log4r-0.5.0/log4r/man/log_at.Rd |only log4r-0.5.0/log4r/man/logger.Rd | 25 log4r-0.5.0/log4r/man/syslog_appender.Rd | 18 log4r-0.5.0/log4r/man/tcp_appender.Rd | 19 log4r-0.5.0/log4r/src/log4r.c | 59 + log4r-0.5.0/log4r/tests/testthat/_snaps |only log4r-0.5.0/log4r/tests/testthat/test-acceptance.R | 8 log4r-0.5.0/log4r/tests/testthat/test-appenders.R | 30 log4r-0.5.0/log4r/tests/testthat/test-layouts.R | 7 log4r-0.5.0/log4r/tests/testthat/test-level.R |only log4r-0.5.0/log4r/vignettes/logging-beyond-local-files.Rmd | 6 log4r-0.5.0/log4r/vignettes/performance.Rmd | 30 log4r-0.5.0/log4r/vignettes/structured-logging.Rmd | 6 53 files changed, 1164 insertions(+), 486 deletions(-)
Title: Shared 'Shiny' Components for 'LLMR' Family Applications
Description: Reusable 'Shiny' user interface and server components from
which the graphical applications in the 'LLMR' package family are
assembled.
Author: Ali Sanaei [aut, cre]
Maintainer: Ali Sanaei <sanaei@uchicago.edu>
Diff between LLMR.shiny versions 0.1.1 dated 2026-07-21 and 0.1.2 dated 2026-08-04
LLMR.shiny-0.1.1/LLMR.shiny/R/cost.R |only LLMR.shiny-0.1.1/LLMR.shiny/man/cost_add_usage.Rd |only LLMR.shiny-0.1.1/LLMR.shiny/man/cost_empty.Rd |only LLMR.shiny-0.1.1/LLMR.shiny/man/cost_set_plan.Rd |only LLMR.shiny-0.1.1/LLMR.shiny/man/cost_tile.Rd |only LLMR.shiny-0.1.1/LLMR.shiny/man/github_remote_for.Rd |only LLMR.shiny-0.1.1/LLMR.shiny/man/is_auth_error.Rd |only LLMR.shiny-0.1.1/LLMR.shiny/man/llmr_error_banner.Rd |only LLMR.shiny-0.1.1/LLMR.shiny/man/null-coalesce.Rd |only LLMR.shiny-0.1.1/LLMR.shiny/man/pkg_available.Rd |only LLMR.shiny-0.1.2/LLMR.shiny/DESCRIPTION | 21 LLMR.shiny-0.1.2/LLMR.shiny/MD5 | 82 +- LLMR.shiny-0.1.2/LLMR.shiny/NAMESPACE | 18 LLMR.shiny-0.1.2/LLMR.shiny/NEWS.md | 39 + LLMR.shiny-0.1.2/LLMR.shiny/R/LLMR.shiny-package.R | 4 LLMR.shiny-0.1.2/LLMR.shiny/R/display.R | 193 ++++- LLMR.shiny-0.1.2/LLMR.shiny/R/guards.R | 60 - LLMR.shiny-0.1.2/LLMR.shiny/R/io.R | 104 ++ LLMR.shiny-0.1.2/LLMR.shiny/R/keys.R | 44 - LLMR.shiny-0.1.2/LLMR.shiny/R/persona_selector.R | 56 + LLMR.shiny-0.1.2/LLMR.shiny/R/runners.R | 157 +++- LLMR.shiny-0.1.2/LLMR.shiny/R/theme.R |only LLMR.shiny-0.1.2/LLMR.shiny/R/usage.R |only LLMR.shiny-0.1.2/LLMR.shiny/README.md | 183 ++++- LLMR.shiny-0.1.2/LLMR.shiny/man/LLMR.shiny-package.Rd | 4 LLMR.shiny-0.1.2/LLMR.shiny/man/annotate_demo_result.Rd | 15 LLMR.shiny-0.1.2/LLMR.shiny/man/as_display_table.Rd | 20 LLMR.shiny-0.1.2/LLMR.shiny/man/build_llm_config.Rd | 25 LLMR.shiny-0.1.2/LLMR.shiny/man/build_runner.Rd | 9 LLMR.shiny-0.1.2/LLMR.shiny/man/demo_banner_ui.Rd | 4 LLMR.shiny-0.1.2/LLMR.shiny/man/demo_runner.Rd | 18 LLMR.shiny-0.1.2/LLMR.shiny/man/extract_token_counts.Rd | 5 LLMR.shiny-0.1.2/LLMR.shiny/man/figures/logo.png |binary LLMR.shiny-0.1.2/LLMR.shiny/man/guess_column.Rd |only LLMR.shiny-0.1.2/LLMR.shiny/man/help_tip.Rd |only LLMR.shiny-0.1.2/LLMR.shiny/man/install_guidance_ui.Rd | 2 LLMR.shiny-0.1.2/LLMR.shiny/man/is_demo_result.Rd | 6 LLMR.shiny-0.1.2/LLMR.shiny/man/llmr_theme.Rd |only LLMR.shiny-0.1.2/LLMR.shiny/man/persona_selector_server.Rd | 15 LLMR.shiny-0.1.2/LLMR.shiny/man/persona_selector_ui.Rd | 2 LLMR.shiny-0.1.2/LLMR.shiny/man/provider_default_model.Rd | 2 LLMR.shiny-0.1.2/LLMR.shiny/man/provider_registry.Rd | 16 LLMR.shiny-0.1.2/LLMR.shiny/man/shell_context.Rd | 7 LLMR.shiny-0.1.2/LLMR.shiny/man/shell_sidebar.Rd | 15 LLMR.shiny-0.1.2/LLMR.shiny/man/text_block_output.Rd |only LLMR.shiny-0.1.2/LLMR.shiny/man/usage_add.Rd |only LLMR.shiny-0.1.2/LLMR.shiny/man/usage_empty.Rd |only LLMR.shiny-0.1.2/LLMR.shiny/man/usage_set_plan.Rd |only LLMR.shiny-0.1.2/LLMR.shiny/man/usage_tile.Rd |only LLMR.shiny-0.1.2/LLMR.shiny/tests/testthat/test-guess-column.R |only LLMR.shiny-0.1.2/LLMR.shiny/tests/testthat/test-persona-selector.R | 40 - LLMR.shiny-0.1.2/LLMR.shiny/tests/testthat/test-substrate.R | 347 ++++++++-- LLMR.shiny-0.1.2/LLMR.shiny/tests/testthat/test-ui-helpers.R |only 53 files changed, 1185 insertions(+), 328 deletions(-)
Title: Estimate Gaussian and Student's t Mixture Vector Autoregressive
Models
Description: Unconstrained and constrained maximum likelihood estimation of structural and reduced form
Gaussian mixture vector autoregressive, Student's t mixture vector autoregressive, and Gaussian and Student's t
mixture vector autoregressive models, quantile residual tests, graphical diagnostics,
simulations, forecasting, and estimation of generalized impulse response function and generalized
forecast error variance decomposition.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2016) <doi:10.1016/j.jeconom.2016.02.012>,
Savi Virolainen (2025) <doi:10.1080/07350015.2024.2322090>,
Savi Virolainen (in press) <doi:10.1016/j.ecosta.2025.09.003>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@gmail.com>
Diff between gmvarkit versions 2.2.1 dated 2025-10-06 and 2.2.2 dated 2026-08-04
DESCRIPTION | 12 ++++++------ MD5 | 22 +++++++++++----------- NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/gmvarkit-vignette.R | 2 -- inst/doc/gmvarkit-vignette.pdf |binary man/cond_moments.Rd | 8 ++++---- man/get_regime_autocovs.Rd | 8 ++++---- man/get_regime_means.Rd | 8 ++++---- man/gmvarkit-package.Rd | 7 ++++++- man/uncond_moments.Rd | 8 ++++---- vignettes/refs.bib | 2 +- 12 files changed, 44 insertions(+), 37 deletions(-)
Title: Publication-Ready Forest Plots with 'ggplot2'
Description: Transform model coefficients into flexible forest
plots using 'ggplot2'. Provides helpers to standardize
coefficient data from a range of modelling workflows and render
publication-ready forest plots with a consistent interface.
Author: Carson Richardson [aut, cre, cph]
Maintainer: Carson Richardson <carson.richardson@outlook.com>
Diff between ggforestplotR versions 0.3.0 dated 2026-07-07 and 0.3.1 dated 2026-08-04
DESCRIPTION | 6 ++--- MD5 | 16 +++++++------- NEWS.md | 7 ++++++ R/add_forest_table.R | 17 ++++++++++----- R/as_forest_data.R | 6 +++-- R/ggforestplot.R | 8 ++++--- R/utils.R | 5 ++++ build/vignette.rds |binary tests/testthat/test-forest-table.R | 40 ++++++++++++++++++++++++++++++++----- 9 files changed, 78 insertions(+), 27 deletions(-)
Title: Bayesian Treed Distributed Lag Models
Description: Estimation of distributed lag models (DLMs) based on a Bayesian additive regression trees framework. Includes several extensions of DLMs: treed DLMs and distributed lag mixture models (Mork and Wilson, 2023) <doi:10.1111/biom.13568>; treed distributed lag nonlinear models (Mork and Wilson, 2022) <doi:10.1093/biostatistics/kxaa051>; heterogeneous DLMs (Mork, et. al., 2024) <doi:10.1080/01621459.2023.2258595>; monotone DLMs (Mork and Wilson, 2024) <doi:10.1214/23-BA1412>. The package also includes visualization tools and a 'shiny' interface to check model convergence and to help interpret results.
Author: Daniel Mork [aut, cre, cph] ,
Seongwon Im [aut] ,
Ander Wilson [aut]
Maintainer: Daniel Mork <dmork@hsph.harvard.edu>
Diff between dlmtree versions 1.1.1 dated 2026-02-02 and 1.2.0 dated 2026-08-04
dlmtree-1.1.1/dlmtree/man/dlmtreeGPFixedGaussian.Rd |only dlmtree-1.1.1/dlmtree/man/dlmtreeGPGaussian.Rd |only dlmtree-1.1.1/dlmtree/man/dlmtreeHDLMGaussian.Rd |only dlmtree-1.1.1/dlmtree/man/dlmtreeHDLMMGaussian.Rd |only dlmtree-1.1.1/dlmtree/man/dlmtreeTDLMFixedGaussian.Rd |only dlmtree-1.1.1/dlmtree/man/dlmtreeTDLMNestedGaussian.Rd |only dlmtree-1.1.1/dlmtree/man/dlmtreeTDLM_cpp.Rd |only dlmtree-1.1.1/dlmtree/src/dlmtreeGPFixedGaussian.cpp |only dlmtree-1.1.1/dlmtree/src/dlmtreeGPGaussian.cpp |only dlmtree-1.1.1/dlmtree/src/dlmtreeHDLMGaussian.cpp |only dlmtree-1.1.1/dlmtree/src/dlmtreeHDLMMGaussian.cpp |only dlmtree-1.1.1/dlmtree/src/dlmtreeTDLMFixedGaussian.cpp |only dlmtree-1.1.1/dlmtree/src/dlmtreeTDLMNestedGaussian.cpp |only dlmtree-1.1.1/dlmtree/src/dlmtreeTDLM_cpp.cpp |only dlmtree-1.2.0/dlmtree/DESCRIPTION | 6 dlmtree-1.2.0/dlmtree/MD5 | 52 +--- dlmtree-1.2.0/dlmtree/NEWS.md | 12 + dlmtree-1.2.0/dlmtree/R/RcppExports.R | 52 ---- dlmtree-1.2.0/dlmtree/R/control.R | 1 dlmtree-1.2.0/dlmtree/R/dlmtree.R | 44 +++ dlmtree-1.2.0/dlmtree/R/estDLM.R | 2 dlmtree-1.2.0/dlmtree/man/dlmtree.Rd | 3 dlmtree-1.2.0/dlmtree/man/dlmtreeMixtures.Rd |only dlmtree-1.2.0/dlmtree/man/dlmtreeNested.Rd |only dlmtree-1.2.0/dlmtree/man/dlmtreeShared.Rd |only dlmtree-1.2.0/dlmtree/src/Fncs.cpp | 6 dlmtree-1.2.0/dlmtree/src/Node.cpp | 47 +++- dlmtree-1.2.0/dlmtree/src/Node.h | 1 dlmtree-1.2.0/dlmtree/src/RcppExports.cpp | 78 +----- dlmtree-1.2.0/dlmtree/src/dlmtreeMixtures.cpp |only dlmtree-1.2.0/dlmtree/src/dlmtreeNested.cpp |only dlmtree-1.2.0/dlmtree/src/dlmtreeShared.cpp |only dlmtree-1.2.0/dlmtree/src/modelCtr.h | 52 ++-- dlmtree-1.2.0/dlmtree/src/modelEst.cpp | 186 ++++++---------- dlmtree-1.2.0/dlmtree/src/monotdlnm_Cpp.cpp | 40 +++ dlmtree-1.2.0/dlmtree/src/tdlmm_Cpp.cpp | 45 +++ dlmtree-1.2.0/dlmtree/src/tdlnm_Cpp.cpp | 61 +++-- 37 files changed, 374 insertions(+), 314 deletions(-)
Title: Interface to 'the CAVD DataSpace'
Description: Provides a convenient API interface to access immunological data
within 'the CAVD DataSpace'(<https://dataspace.cavd.org>), a data sharing
and discovery tool that facilitates exploration of HIV immunological data
from pre-clinical and clinical HIV vaccine studies.
Author: Ju Yeong Kim [aut],
Sean Hughes [rev],
Jason Taylor [aut, cre],
Helen Miller [aut],
Kellie MacPhee [rev],
CAVD DataSpace [cph]
Maintainer: Jason Taylor <jmtaylor@fredhutch.org>
Diff between DataSpaceR versions 1.0.0 dated 2026-06-26 and 1.0.1 dated 2026-08-04
DataSpaceR-1.0.0/DataSpaceR/inst/doc/Accessing_CDS_DAASH.Rmd |only DataSpaceR-1.0.0/DataSpaceR/inst/doc/Accessing_CDS_DAASH.html |only DataSpaceR-1.0.0/DataSpaceR/vignettes/Accessing_CDS_DAASH.Rmd |only DataSpaceR-1.0.0/DataSpaceR/vignettes/Accessing_CDS_DAASH.Rmd.orig |only DataSpaceR-1.0.1/DataSpaceR/DESCRIPTION | 8 DataSpaceR-1.0.1/DataSpaceR/MD5 | 82 - DataSpaceR-1.0.1/DataSpaceR/NAMESPACE | 1 DataSpaceR-1.0.1/DataSpaceR/NEWS.md | 6 DataSpaceR-1.0.1/DataSpaceR/R/DataSpaceConnection.R | 77 + DataSpaceR-1.0.1/DataSpaceR/R/DataSpaceDaash.R | 4 DataSpaceR-1.0.1/DataSpaceR/R/DataSpaceR.R | 4 DataSpaceR-1.0.1/DataSpaceR/R/DataSpaceStudies.R | 30 DataSpaceR-1.0.1/DataSpaceR/R/helpers.R | 118 ++ DataSpaceR-1.0.1/DataSpaceR/README.md | 13 DataSpaceR-1.0.1/DataSpaceR/build/vignette.rds |binary DataSpaceR-1.0.1/DataSpaceR/inst/doc/DataSpaceR.Rmd | 433 ------- DataSpaceR-1.0.1/DataSpaceR/inst/doc/DataSpaceR.html | 547 +--------- DataSpaceR-1.0.1/DataSpaceR/inst/doc/DataSpace_DAASH.Rmd |only DataSpaceR-1.0.1/DataSpaceR/inst/doc/DataSpace_DAASH.html |only DataSpaceR-1.0.1/DataSpaceR/inst/doc/Monoconal_Antibody_Data.Rmd | 6 DataSpaceR-1.0.1/DataSpaceR/inst/doc/Monoconal_Antibody_Data.html | 8 DataSpaceR-1.0.1/DataSpaceR/inst/doc/Publication_Data.Rmd | 16 DataSpaceR-1.0.1/DataSpaceR/inst/doc/Publication_Data.html | 64 - DataSpaceR-1.0.1/DataSpaceR/inst/doc/Studies_Groups.Rmd |only DataSpaceR-1.0.1/DataSpaceR/inst/doc/Studies_Groups.html |only DataSpaceR-1.0.1/DataSpaceR/inst/doc/Virus_Name_Mapping_Tables.Rmd | 2 DataSpaceR-1.0.1/DataSpaceR/inst/doc/Virus_Name_Mapping_Tables.html | 4 DataSpaceR-1.0.1/DataSpaceR/man/DataSpaceConnection.Rd | 413 ++++--- DataSpaceR-1.0.1/DataSpaceR/man/DataSpaceDaash.Rd | 217 ++- DataSpaceR-1.0.1/DataSpaceR/man/DataSpaceDonors.Rd | 153 +- DataSpaceR-1.0.1/DataSpaceR/man/DataSpaceGroups.Rd | 139 +- DataSpaceR-1.0.1/DataSpaceR/man/DataSpaceMabs.Rd | 160 +- DataSpaceR-1.0.1/DataSpaceR/man/DataSpaceStudies.Rd | 180 +-- DataSpaceR-1.0.1/DataSpaceR/tests/testthat/setup.R | 2 DataSpaceR-1.0.1/DataSpaceR/tests/testthat/test-connection.R | 8 DataSpaceR-1.0.1/DataSpaceR/tests/testthat/test-daash.R | 8 DataSpaceR-1.0.1/DataSpaceR/tests/testthat/test-mabs-donors.R | 28 DataSpaceR-1.0.1/DataSpaceR/vignettes/DataSpaceR.Rmd | 433 ------- DataSpaceR-1.0.1/DataSpaceR/vignettes/DataSpaceR.Rmd.orig | 136 -- DataSpaceR-1.0.1/DataSpaceR/vignettes/DataSpace_DAASH.Rmd |only DataSpaceR-1.0.1/DataSpaceR/vignettes/DataSpace_DAASH.Rmd.orig |only DataSpaceR-1.0.1/DataSpaceR/vignettes/Monoconal_Antibody_Data.Rmd | 6 DataSpaceR-1.0.1/DataSpaceR/vignettes/Monoconal_Antibody_Data.Rmd.orig | 4 DataSpaceR-1.0.1/DataSpaceR/vignettes/Publication_Data.Rmd | 16 DataSpaceR-1.0.1/DataSpaceR/vignettes/Studies_Groups.Rmd |only DataSpaceR-1.0.1/DataSpaceR/vignettes/Studies_Groups.Rmd.orig |only DataSpaceR-1.0.1/DataSpaceR/vignettes/Virus_Name_Mapping_Tables.Rmd | 2 DataSpaceR-1.0.1/DataSpaceR/vignettes/precompile.R | 3 48 files changed, 1174 insertions(+), 2157 deletions(-)
Title: Biomonitoring and Bioassessment Calculations
Description: An aid for manipulating data associated with biomonitoring and bioassessment. Calculations include metric calculation, marking of excluded taxa,
subsampling, and multimetric index calculation. Targeted communities are benthic macroinvertebrates, fish, periphyton, and coral. As described in the Revised Rapid Bioassessment Protocols (Barbour et al. 1999) <https://archive.epa.gov/water/archive/web/html/index-14.html>.
Author: Erik W. Leppo [aut, cre] ,
Jen Stamp [ctb],
John van Sickles [ctb],
Ben Block [ctb]
Maintainer: Erik W. Leppo <Erik.Leppo@tetratech.com>
Diff between BioMonTools versions 1.3.1 dated 2026-07-22 and 1.3.2 dated 2026-08-04
DESCRIPTION | 6 +- MD5 | 22 ++++---- NEWS | 47 ++++++++++++++++++ NEWS.md | 47 ++++++++++++++++++ R/metric_values_excel.R | 24 ++++++--- R/qc_taxa_phylo.R | 92 ++++++++++++++++++++++++++----------- README.md | 12 ++-- inst/doc/vignette_BioMonTools.html | 4 - inst/doc/vignette_MapTaxaObs.html | 4 - inst/doc/vignette_NewIndex.html | 4 - man/metvalgrpxl.Rd | 2 man/qc_taxa_phylo.Rd | 63 ++++++++++++++++--------- 12 files changed, 239 insertions(+), 88 deletions(-)
Title: Bayesian Logistic Regression for Oncology Dose-Escalation Trials
Description: Bayesian logistic regression model with optional
EXchangeability-NonEXchangeability parameter modelling for flexible
borrowing from historical or concurrent data-sources. The safety model
can guide dose-escalation decisions for adaptive oncology Phase I
dose-escalation trials which involve an arbitrary number of
drugs. Please refer to Neuenschwander et al. (2008)
<doi:10.1002/sim.3230> and Neuenschwander et al. (2016)
<doi:10.1080/19466315.2016.1174149> for details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Lukas A. Widmer [aut],
Andrew Bean [aut],
Trustees of Columbia University [cph]
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between OncoBayes2 versions 0.9-4 dated 2025-12-18 and 0.10-0 dated 2026-08-04
OncoBayes2-0.10-0/OncoBayes2/DESCRIPTION | 20 OncoBayes2-0.10-0/OncoBayes2/MD5 | 107 - OncoBayes2-0.10-0/OncoBayes2/NAMESPACE | 4 OncoBayes2-0.10-0/OncoBayes2/NEWS.md | 23 OncoBayes2-0.10-0/OncoBayes2/R/OncoBayes2-package.R | 3 OncoBayes2-0.10-0/OncoBayes2/R/blrm_exnex.R | 221 +-- OncoBayes2-0.10-0/OncoBayes2/R/blrm_trial.R | 2 OncoBayes2-0.10-0/OncoBayes2/R/diagnostics.R | 38 OncoBayes2-0.10-0/OncoBayes2/R/draws_backend.R |only OncoBayes2-0.10-0/OncoBayes2/R/nsamples.R | 8 OncoBayes2-0.10-0/OncoBayes2/R/plot_blrm.R | 116 - OncoBayes2-0.10-0/OncoBayes2/R/posterior.R | 75 - OncoBayes2-0.10-0/OncoBayes2/R/posterior_interval.R | 2 OncoBayes2-0.10-0/OncoBayes2/R/pp_data.R | 7 OncoBayes2-0.10-0/OncoBayes2/R/sysdata.rda |binary OncoBayes2-0.10-0/OncoBayes2/build/partial.rdb |binary OncoBayes2-0.10-0/OncoBayes2/build/vignette.rds |binary OncoBayes2-0.10-0/OncoBayes2/data/codata_combo2.rda |binary OncoBayes2-0.10-0/OncoBayes2/data/dose_info_combo2.rda |binary OncoBayes2-0.10-0/OncoBayes2/data/drug_info_combo2.rda |binary OncoBayes2-0.10-0/OncoBayes2/data/hist_SA.rda |binary OncoBayes2-0.10-0/OncoBayes2/data/hist_combo2.rda |binary OncoBayes2-0.10-0/OncoBayes2/data/hist_combo3.rda |binary OncoBayes2-0.10-0/OncoBayes2/inst/REFERENCES.bib |only OncoBayes2-0.10-0/OncoBayes2/inst/doc/OncoBayes2.pdf |binary OncoBayes2-0.10-0/OncoBayes2/inst/doc/introduction.Rmd | 53 OncoBayes2-0.10-0/OncoBayes2/inst/doc/introduction.html | 727 +++++----- OncoBayes2-0.10-0/OncoBayes2/inst/doc/map_approach.Rmd | 10 OncoBayes2-0.10-0/OncoBayes2/inst/doc/map_approach.html | 283 ++- OncoBayes2-0.10-0/OncoBayes2/inst/sbc/calibration.md5 | 6 OncoBayes2-0.10-0/OncoBayes2/inst/sbc/make_reference_rankhist.R | 282 ++- OncoBayes2-0.10-0/OncoBayes2/inst/sbc/sbc_report.html | 657 ++++----- OncoBayes2-0.10-0/OncoBayes2/inst/sbc/sbc_tools.R | 49 OncoBayes2-0.10-0/OncoBayes2/man/OncoBayes2.Rd | 25 OncoBayes2-0.10-0/OncoBayes2/man/blrm_exnex.Rd | 32 OncoBayes2-0.10-0/OncoBayes2/man/blrm_formula_saturating.Rd | 5 OncoBayes2-0.10-0/OncoBayes2/man/blrm_trial.Rd | 10 OncoBayes2-0.10-0/OncoBayes2/man/codata_combo2.Rd | 4 OncoBayes2-0.10-0/OncoBayes2/man/dose_info_combo2.Rd | 4 OncoBayes2-0.10-0/OncoBayes2/man/draws-OncoBayes2.Rd | 5 OncoBayes2-0.10-0/OncoBayes2/man/drug_info_combo2.Rd | 4 OncoBayes2-0.10-0/OncoBayes2/man/example-combo2.Rd | 4 OncoBayes2-0.10-0/OncoBayes2/man/example-combo2_trial.Rd | 4 OncoBayes2-0.10-0/OncoBayes2/man/example-combo3.Rd | 4 OncoBayes2-0.10-0/OncoBayes2/man/example-single-agent.Rd | 4 OncoBayes2-0.10-0/OncoBayes2/man/hist_SA.Rd | 4 OncoBayes2-0.10-0/OncoBayes2/man/hist_combo2.Rd | 4 OncoBayes2-0.10-0/OncoBayes2/man/plot_blrm.Rd | 10 OncoBayes2-0.10-0/OncoBayes2/src/stanExports_blrm_exnex.cc | 34 OncoBayes2-0.10-0/OncoBayes2/tests/testthat/helper-fixtures.R |only OncoBayes2-0.10-0/OncoBayes2/tests/testthat/helper-sampling.R | 135 - OncoBayes2-0.10-0/OncoBayes2/tests/testthat/test-blrm_exnex.R | 89 - OncoBayes2-0.10-0/OncoBayes2/tests/testthat/test-posterior.R | 12 OncoBayes2-0.10-0/OncoBayes2/vignettes/introduction.Rmd | 53 OncoBayes2-0.10-0/OncoBayes2/vignettes/map_approach.Rmd | 10 OncoBayes2-0.10-0/OncoBayes2/vignettes/references.bib |only OncoBayes2-0.9-4/OncoBayes2/man/dot-label_index.Rd |only 57 files changed, 1653 insertions(+), 1496 deletions(-)
Title: Minimal LLM Chat Interface
Description: A minimal-dependency client for Large Language Model chat APIs.
Supports 'OpenAI' <https://openai.com/>, 'Anthropic' 'Claude'
<https://claude.com/>, 'Moonshot' 'Kimi' <https://www.moonshot.ai/>,
'OpenAI' 'Codex' subscription endpoints, 'Ollama'
<https://ollama.com/>, and other 'OpenAI'-compatible endpoints.
Includes an agent loop with tool use and a 'Model Context
Protocol' client <https://modelcontextprotocol.io/>. API design is
derived from the 'ellmer' package, reimplemented with only base R,
'curl', 'jsonlite', and 'tinyoauth'.
Author: Troy Hernandez [aut, cre] ,
cornball.ai [cph],
ellmer team [cph]
Maintainer: Troy Hernandez <troy@cornball.ai>
Diff between llm.api versions 0.1.8 dated 2026-06-26 and 0.1.9 dated 2026-08-04
DESCRIPTION | 8 +-- MD5 | 47 +++++++++--------- NEWS.md | 24 +++++++++ R/agent.R | 33 +++++++++--- R/chat.R | 15 +++-- R/config.R | 53 +++++++++++++++++--- R/cost.R | 4 + R/providers.R | 52 +++++++++++++++++++- R/session.R | 5 + README.md | 79 ++++++++++++++++++++++++++++++- inst/tinytest/test_config.R | 44 ++++++++++++++--- inst/tinytest/test_moonshot_web_search.R | 2 inst/tinytest/test_openai_codex.R | 4 - inst/tinytest/test_openai_compatible.R |only inst/tinytest/test_openai_responses.R | 2 inst/tinytest/test_providers.R | 4 - man/agent.Rd | 13 +++-- man/anthropic_claude_credentials.Rd | 4 - man/chat.Rd | 7 +- man/chat_session.Rd | 6 +- man/create_agent.Rd | 5 + man/llm_base.Rd | 2 man/llm_key.Rd | 2 man/provider_default_model.Rd | 7 +- man/usage_cost.Rd | 4 + 25 files changed, 338 insertions(+), 88 deletions(-)
Title: Efficient Phylogenetics on Large Trees
Description: Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Author: Stilianos Louca [aut, cre, cph]
Maintainer: Stilianos Louca <louca.research@gmail.com>
Diff between castor versions 1.8.6 dated 2026-07-24 and 1.8.7 dated 2026-08-04
castor-1.8.6/castor/R/correlate_discrete_traits.R |only castor-1.8.6/castor/man/correlate_discrete_traits.Rd |only castor-1.8.7/castor/DESCRIPTION | 8 - castor-1.8.7/castor/MD5 | 24 +-- castor-1.8.7/castor/NAMESPACE | 2 castor-1.8.7/castor/R/auxiliary_routines.R | 97 ++++++++++++- castor-1.8.7/castor/R/correlate_categorical_traits.R |only castor-1.8.7/castor/R/fit_mk.R | 77 ++++++---- castor-1.8.7/castor/R/get_random_mk_transition_matrix.R | 2 castor-1.8.7/castor/R/simulate_mk_model.R | 8 - castor-1.8.7/castor/man/correlate_categorical_traits.Rd |only castor-1.8.7/castor/man/fit_mk.Rd | 2 castor-1.8.7/castor/man/get_random_mk_transition_matrix.Rd | 2 castor-1.8.7/castor/src/RcppExports.cpp | 4 castor-1.8.7/castor/src/phylogenetics_cpp_routines.cpp | 30 +++- 15 files changed, 193 insertions(+), 63 deletions(-)
Title: Runs Allelematch Regression Tests
Description: Automates regression testing of package 'allelematch'. Over
2500 tests cover all functions in 'allelematch', reproduce the
examples from the documentation, and include negative tests. The
implementation is based on 'testthat'.
Author: Department of Wildlife, Fish and Environmental Studies at Swedish
University of Agricultural Sciences [cph],
Goeran Spong [cph] ,
Paul Galpern [ctb] ,
Torvald Staxler [aut, cre]
Maintainer: Torvald Staxler <torvald.staxler@telia.com>
Diff between amregtest versions 1.2.0 dated 2026-07-13 and 1.3.2 dated 2026-08-04
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amregtest-1.3.2/amregtest/tests/testthat/test-allelematch_6-amUnique.R | 13 amregtest-1.3.2/amregtest/tests/testthat/test-allelematch_6-amUnique_negative.R | 16 amregtest-1.3.2/amregtest/tests/testthat/test-allelematch_6-amUnique_print.R | 18 amregtest-1.3.2/amregtest/tests/testthat/test-allelematch_7-amUniqueProfile.R | 12 amregtest-1.3.2/amregtest/tests/testthat/test-amExample1.R | 4 amregtest-1.3.2/amregtest/tests/testthat/test-amExample2.R | 8 amregtest-1.3.2/amregtest/tests/testthat/test-amExample3.R | 4 amregtest-1.3.2/amregtest/tests/testthat/test-amExample4.R | 9 amregtest-1.3.2/amregtest/tests/testthat/test-ggData.R | 1 85 files changed, 11795 insertions(+), 10472 deletions(-)
Title: Construct and Compare scGRN from Single-Cell Transcriptomic Data
Description: A workflow based on machine learning methods to construct and compare single-cell gene regulatory networks (scGRN) using single-cell RNA-seq (scRNA-seq) data collected from different conditions. Uses principal component regression, tensor decomposition, and manifold alignment, to accurately identify even subtly shifted gene expression programs. See <doi:10.1016/j.patter.2020.100139> for more details.
Author: Daniel Osorio [aut, cre] ,
Yan Zhong [aut, ctb],
Guanxun Li [aut, ctb],
Jianhua Huang [aut, ctb],
James Cai [aut, ctb, ths]
Maintainer: Daniel Osorio <dcosorioh@gmail.com>
Diff between scTenifoldNet versions 1.3 dated 2021-10-29 and 1.4 dated 2026-08-04
DESCRIPTION | 26 - MD5 | 65 ++-- NAMESPACE | 74 ++-- R/RcppExports.R |only R/asTensor.R | 53 +-- R/cpDecomposition.R | 412 +++++++++++++-------------- R/cpmNormalization.R | 130 ++++---- R/dModularity.R | 57 --- R/dRegulation.R | 274 +++++++++--------- R/makeNetworks.R | 218 ++++++++------ R/manifoldAlignment.R | 216 +++++++------- R/pcNet.R | 492 ++++++++++++++++++++++----------- R/scQC.R | 269 ++++++++++-------- R/scTenifoldNet.R | 479 ++++++++++++++++---------------- R/tensorDecomposition.R | 372 +++++++++++------------- README.md | 482 +++++++++++++------------------- inst/CITATION | 32 +- man/cpDecomposition.Rd | 85 +++-- man/cpmNormalization.Rd | 141 +++++---- man/dRegulation.Rd | 165 +++++------ man/makeNetworks.Rd | 213 +++++++------- man/manifoldAlignment.Rd | 181 ++++++------ man/pcNet.Rd | 160 +++++----- man/pcNetCoreRcpp.Rd |only man/scQC.Rd | 226 ++++++++------- man/scTenifoldNet.Rd | 422 ++++++++++++++-------------- man/tensorDecomposition.Rd | 185 ++++++------ src |only tests/testthat.R | 8 tests/testthat/test-cpmNormalization.R | 86 ++--- tests/testthat/test-makeNetworks.R | 56 +-- tests/testthat/test-pcNet.R | 120 ++++---- tests/testthat/test-pcNetRcpp.R |only tests/testthat/test-scQC.R | 98 +++--- 34 files changed, 3014 insertions(+), 2783 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Extra
Support Functions
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for
support functions like preconditioned fits
<doi:10.1208/s12248-016-9866-5>, boostrap and stepwise covariate
selection.
Author: Matthew Fidler [aut, cre] ,
Vipul Mann [aut],
Vishal Sarsani [aut] ,
Christian Bartels [ctb],
Bill Denney [aut] ,
Omar Elashkar [ctb]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2extra versions 5.1.0 dated 2026-06-07 and 5.2.0 dated 2026-08-04
DESCRIPTION | 10 MD5 | 28 +- NAMESPACE | 3 NEWS.md | 62 +++++ R/AICHelpers.R |only R/SCM.R | 12 - R/computingutil.R | 321 ++++++++++++++++++++---------- R/setCov.R | 8 R/theoFitOde.R | 42 +++ data/theoFitOde.rda |binary man/getMinAICFit.Rd |only man/isBoundaryFit.Rd |only man/listModelsTested.Rd |only man/theoFitOde.Rd | 8 tests/testthat/test-AICHelpers.R |only tests/testthat/test-SCM-covarSearchAuto.R |only tests/testthat/test-bootstrap.R | 264 ++++++++++++++++++++++++ tests/testthat/test-computing.R | 23 ++ 18 files changed, 650 insertions(+), 131 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation
Routines
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Wenping Wang [aut],
Audrey Lavenu [ctb],
Ben Goodrich [ctb],
David Ardia [cph],
Dirk Eddelbuettel [cph],
Elizabeth Eskow [ctb],
Emmanuelle Comets [ctb],
Hadley Wickham [ctb],
Hajar Besbassi [ctb],
Hidde van de Beek [ctb],
[...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 6.0.1 dated 2026-06-03 and 7.0.2 dated 2026-08-04
nlmixr2est-6.0.1/nlmixr2est/tests/testthat/fixtures/fit-one-compartment-fo.rds |only nlmixr2est-6.0.1/nlmixr2est/tests/testthat/fixtures/fit-one-compartment-foce.rds |only nlmixr2est-6.0.1/nlmixr2est/tests/testthat/fixtures/fit-one-compartment-focei-fast.rds |only nlmixr2est-6.0.1/nlmixr2est/tests/testthat/fixtures/fit-one-compartment-focei.rds |only nlmixr2est-6.0.1/nlmixr2est/tests/testthat/fixtures/fit-one-compartment-foi.rds |only nlmixr2est-6.0.1/nlmixr2est/tests/testthat/fixtures/fit-one-compartment-lag-focei.rds |only nlmixr2est-6.0.1/nlmixr2est/tests/testthat/fixtures/fit-one-compartment-lag-saem.rds |only nlmixr2est-6.0.1/nlmixr2est/tests/testthat/fixtures/fit-one-compartment-posthoc.rds |only nlmixr2est-6.0.1/nlmixr2est/tests/testthat/fixtures/fit-one-compartment-saem-cwres.rds |only nlmixr2est-6.0.1/nlmixr2est/tests/testthat/fixtures/fit-one-compartment-saem.rds |only nlmixr2est-7.0.2/nlmixr2est/DESCRIPTION | 24 nlmixr2est-7.0.2/nlmixr2est/MD5 | 712 nlmixr2est-7.0.2/nlmixr2est/NAMESPACE | 215 nlmixr2est-7.0.2/nlmixr2est/NEWS.md | 1854 + nlmixr2est-7.0.2/nlmixr2est/R/RcppExports.R | 451 nlmixr2est-7.0.2/nlmixr2est/R/addCwres.R | 1 nlmixr2est-7.0.2/nlmixr2est/R/augPred.R | 6 nlmixr2est-7.0.2/nlmixr2est/R/bobyqa.R | 155 nlmixr2est-7.0.2/nlmixr2est/R/cloneNlmixr.R | 13 nlmixr2est-7.0.2/nlmixr2est/R/compat.R | 83 nlmixr2est-7.0.2/nlmixr2est/R/complete.R | 2 nlmixr2est-7.0.2/nlmixr2est/R/cov.R | 297 nlmixr2est-7.0.2/nlmixr2est/R/covRecompute.R |only nlmixr2est-7.0.2/nlmixr2est/R/deparse.R | 10 nlmixr2est-7.0.2/nlmixr2est/R/emviControl.R |only nlmixr2est-7.0.2/nlmixr2est/R/fbvi.R |only nlmixr2est-7.0.2/nlmixr2est/R/fitSim.R | 4 nlmixr2est-7.0.2/nlmixr2est/R/fo.R | 7 nlmixr2est-7.0.2/nlmixr2est/R/focei.R | 1363 - nlmixr2est-7.0.2/nlmixr2est/R/foceiControl.R | 1182 nlmixr2est-7.0.2/nlmixr2est/R/foceiCov.R |only nlmixr2est-7.0.2/nlmixr2est/R/foceiCovAnalytic.R |only nlmixr2est-7.0.2/nlmixr2est/R/foceiCovFdFull.R |only nlmixr2est-7.0.2/nlmixr2est/R/foceiFast.R |only nlmixr2est-7.0.2/nlmixr2est/R/foceiGradAnalytic.R |only nlmixr2est-7.0.2/nlmixr2est/R/foceiLik.R |only nlmixr2est-7.0.2/nlmixr2est/R/focep.R |only nlmixr2est-7.0.2/nlmixr2est/R/foi.R | 7 nlmixr2est-7.0.2/nlmixr2est/R/hook.R | 117 nlmixr2est-7.0.2/nlmixr2est/R/iagq.R |only nlmixr2est-7.0.2/nlmixr2est/R/ifoce.R |only nlmixr2est-7.0.2/nlmixr2est/R/ifocei.R |only nlmixr2est-7.0.2/nlmixr2est/R/ifocep.R |only nlmixr2est-7.0.2/nlmixr2est/R/ilaplace.R |only nlmixr2est-7.0.2/nlmixr2est/R/imp.R |only nlmixr2est-7.0.2/nlmixr2est/R/impPsis.R |only nlmixr2est-7.0.2/nlmixr2est/R/impmap.R |only nlmixr2est-7.0.2/nlmixr2est/R/impmapThetaSens.R |only nlmixr2est-7.0.2/nlmixr2est/R/iov.R | 33 nlmixr2est-7.0.2/nlmixr2est/R/iterPrintControl.R |only nlmixr2est-7.0.2/nlmixr2est/R/lbfgsb3c.R | 161 nlmixr2est-7.0.2/nlmixr2est/R/magq.R |only nlmixr2est-7.0.2/nlmixr2est/R/mfoce.R |only nlmixr2est-7.0.2/nlmixr2est/R/mfocei.R |only nlmixr2est-7.0.2/nlmixr2est/R/mfocep.R |only nlmixr2est-7.0.2/nlmixr2est/R/mix.R | 453 nlmixr2est-7.0.2/nlmixr2est/R/mlaplace.R |only nlmixr2est-7.0.2/nlmixr2est/R/mu2.R | 62 nlmixr2est-7.0.2/nlmixr2est/R/muRefClassify.R |only nlmixr2est-7.0.2/nlmixr2est/R/muRefControl.R |only nlmixr2est-7.0.2/nlmixr2est/R/muRefLinear.R |only nlmixr2est-7.0.2/nlmixr2est/R/n1qn1.R | 120 nlmixr2est-7.0.2/nlmixr2est/R/newuoa.R | 115 nlmixr2est-7.0.2/nlmixr2est/R/nlm.R | 308 nlmixr2est-7.0.2/nlmixr2est/R/nlmShared.R | 311 nlmixr2est-7.0.2/nlmixr2est/R/nlme.R | 117 nlmixr2est-7.0.2/nlmixr2est/R/nlmeRxUiGet.R | 4 nlmixr2est-7.0.2/nlmixr2est/R/nlminb.R | 138 nlmixr2est-7.0.2/nlmixr2est/R/nlmixr2.R | 18 nlmixr2est-7.0.2/nlmixr2est/R/nlmixr2Est.R | 111 nlmixr2est-7.0.2/nlmixr2est/R/nlmixr2EstType.R |only nlmixr2est-7.0.2/nlmixr2est/R/nlmixr2_md5.R | 2 nlmixr2est-7.0.2/nlmixr2est/R/nlmixr2global.R | 1 nlmixr2est-7.0.2/nlmixr2est/R/nlmixr2output.R | 667 nlmixr2est-7.0.2/nlmixr2est/R/nlmixrGrad.R | 2 nlmixr2est-7.0.2/nlmixr2est/R/nls.R | 229 nlmixr2est-7.0.2/nlmixr2est/R/nmObjGet.R | 198 nlmixr2est-7.0.2/nlmixr2est/R/nmObjHandle.R | 8 nlmixr2est-7.0.2/nlmixr2est/R/npBox.R |only nlmixr2est-7.0.2/nlmixr2est/R/npCommon.R |only nlmixr2est-7.0.2/nlmixr2est/R/npInner.R |only nlmixr2est-7.0.2/nlmixr2est/R/npMuExpand.R |only nlmixr2est-7.0.2/nlmixr2est/R/npag.R |only nlmixr2est-7.0.2/nlmixr2est/R/npb.R |only nlmixr2est-7.0.2/nlmixr2est/R/odeSwapVerify.R |only nlmixr2est-7.0.2/nlmixr2est/R/ofv.R | 1 nlmixr2est-7.0.2/nlmixr2est/R/omegaBlock.R |only nlmixr2est-7.0.2/nlmixr2est/R/optim.R | 227 nlmixr2est-7.0.2/nlmixr2est/R/preProcessBoundedTransform.R | 160 nlmixr2est-7.0.2/nlmixr2est/R/preProcessCovariatesPresent.R | 11 nlmixr2est-7.0.2/nlmixr2est/R/preProcessLinCmtOde.R |only nlmixr2est-7.0.2/nlmixr2est/R/preProcessLiteralFix.R | 2 nlmixr2est-7.0.2/nlmixr2est/R/preProcessVaeNonMuTheta.R |only nlmixr2est-7.0.2/nlmixr2est/R/preProcessZeroOmega.R | 13 nlmixr2est-7.0.2/nlmixr2est/R/preProcessZeroTheta.R |only nlmixr2est-7.0.2/nlmixr2est/R/print.R | 10 nlmixr2est-7.0.2/nlmixr2est/R/qrpem.R |only nlmixr2est-7.0.2/nlmixr2est/R/resid.R | 249 nlmixr2est-7.0.2/nlmixr2est/R/rxNamedModel.R |only nlmixr2est-7.0.2/nlmixr2est/R/rxsolve.R | 41 nlmixr2est-7.0.2/nlmixr2est/R/saem.R | 576 nlmixr2est-7.0.2/nlmixr2est/R/saemControl.R | 273 nlmixr2est-7.0.2/nlmixr2est/R/saemRxUiGet.R | 177 nlmixr2est-7.0.2/nlmixr2est/R/saemRxUiGetModel.R | 150 nlmixr2est-7.0.2/nlmixr2est/R/saem_fit.R | 214 nlmixr2est-7.0.2/nlmixr2est/R/saem_fit_aux.R | 88 nlmixr2est-7.0.2/nlmixr2est/R/sharedControl.R | 88 nlmixr2est-7.0.2/nlmixr2est/R/timing.R | 15 nlmixr2est-7.0.2/nlmixr2est/R/uninformativeEtas.R | 108 nlmixr2est-7.0.2/nlmixr2est/R/uobyqa.R | 126 nlmixr2est-7.0.2/nlmixr2est/R/utils.R | 163 nlmixr2est-7.0.2/nlmixr2est/R/vae.R |only nlmixr2est-7.0.2/nlmixr2est/R/vaeCovSelectL0.R |only nlmixr2est-7.0.2/nlmixr2est/R/vaeCovShapes.R |only nlmixr2est-7.0.2/nlmixr2est/R/vaeData.R |only nlmixr2est-7.0.2/nlmixr2est/R/vaeDecoder.R |only nlmixr2est-7.0.2/nlmixr2est/R/vaeFit.R |only nlmixr2est-7.0.2/nlmixr2est/R/vaeGrad.R |only nlmixr2est-7.0.2/nlmixr2est/R/vaeInner.R |only nlmixr2est-7.0.2/nlmixr2est/R/vaeOutput.R |only nlmixr2est-7.0.2/nlmixr2est/R/vi.R |only nlmixr2est-7.0.2/nlmixr2est/R/viData.R |only nlmixr2est-7.0.2/nlmixr2est/R/vpc.R | 33 nlmixr2est-7.0.2/nlmixr2est/R/zzz.R | 64 nlmixr2est-7.0.2/nlmixr2est/configure | 1 nlmixr2est-7.0.2/nlmixr2est/configure.win | 2 nlmixr2est-7.0.2/nlmixr2est/inst/COPYRIGHT | 9 nlmixr2est-7.0.2/nlmixr2est/inst/tools/workaround.R | 21 nlmixr2est-7.0.2/nlmixr2est/man/agqControl.Rd | 41 nlmixr2est-7.0.2/nlmixr2est/man/bobyqaControl.Rd | 325 nlmixr2est-7.0.2/nlmixr2est/man/dot-absorbIterPrintControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/dot-collectWarn.Rd | 31 nlmixr2est-7.0.2/nlmixr2est/man/dot-deparseDifferent.Rd | 6 nlmixr2est-7.0.2/nlmixr2est/man/dot-deparseFinal.Rd | 4 nlmixr2est-7.0.2/nlmixr2est/man/dot-iniS3.Rd | 4 nlmixr2est-7.0.2/nlmixr2est/man/dot-loadSymengine.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/dot-nlmFamilyControlGeneric.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/dot-nlmFamilyFitGeneric.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/dot-nlmSetupEnv.Rd | 66 nlmixr2est-7.0.2/nlmixr2est/man/dot-nlmeGetNonMuRefNames.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/dot-nlmixr0preProcessNpMuExpand.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/dot-preProcessLinCmtOde.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/dot-preProcessVaeNonMuTheta.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/dot-preProcessZeroTheta.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/dot-saemDropMuRefFromModel.Rd | 4 nlmixr2est-7.0.2/nlmixr2est/man/dot-sensEtaOrTheta.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/emviControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/fbviControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/foControl.Rd | 27 nlmixr2est-7.0.2/nlmixr2est/man/foceControl.Rd | 27 nlmixr2est-7.0.2/nlmixr2est/man/foceiControl.Rd | 907 nlmixr2est-7.0.2/nlmixr2est/man/foceiGradPooledDirect_.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/foceiGradPooledSetupLoad_.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/foceiLikLoad.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/foceiLikRun.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/foceiLikUnload.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/focepControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/foiControl.Rd | 27 nlmixr2est-7.0.2/nlmixr2est/man/formatMinWidth.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/getBaseSimModelFit.Rd | 3 nlmixr2est-7.0.2/nlmixr2est/man/getValidNlmixrControl.Rd | 132 nlmixr2est-7.0.2/nlmixr2est/man/iagqControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/ifoceControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/ifoceiControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/ifocepControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/ilaplaceControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/impControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/impmapControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/iterPrintControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/iterPrintParams.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/laplaceControl.Rd | 39 nlmixr2est-7.0.2/nlmixr2est/man/lbfgsb3cControl.Rd | 325 nlmixr2est-7.0.2/nlmixr2est/man/magqControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/mfoceControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/mfoceiControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/mfocepControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/mlaplaceControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/n1qn1Control.Rd | 298 nlmixr2est-7.0.2/nlmixr2est/man/newuoaControl.Rd | 336 nlmixr2est-7.0.2/nlmixr2est/man/nlmControl.Rd | 336 nlmixr2est-7.0.2/nlmixr2est/man/nlmGetParHist.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/nlmerSolveGrad.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/nlminbControl.Rd | 331 nlmixr2est-7.0.2/nlmixr2est/man/nlmixr2.Rd | 12 nlmixr2est-7.0.2/nlmixr2est/man/nlmixr2AllEstType.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/nlmixr2Est.Rd | 134 nlmixr2est-7.0.2/nlmixr2est/man/nlmixr2Gill83.Rd | 10 nlmixr2est-7.0.2/nlmixr2est/man/nlmixr2GradFun.Rd | 23 nlmixr2est-7.0.2/nlmixr2est/man/nlmixr2NlmeControl.Rd | 123 nlmixr2est-7.0.2/nlmixr2est/man/nlmixr2Print.Rd | 8 nlmixr2est-7.0.2/nlmixr2est/man/nlmixr2fix.Rd | 32 nlmixr2est-7.0.2/nlmixr2est/man/nlmixrWithTiming.Rd | 7 nlmixr2est-7.0.2/nlmixr2est/man/nlsControl.Rd | 297 nlmixr2est-7.0.2/nlmixr2est/man/nmGetDistributionSaemLines.Rd | 6 nlmixr2est-7.0.2/nlmixr2est/man/nmNearPD.Rd | 9 nlmixr2est-7.0.2/nlmixr2est/man/nmObjGet.Rd | 15 nlmixr2est-7.0.2/nlmixr2est/man/nmObjGetControl.Rd | 78 nlmixr2est-7.0.2/nlmixr2est/man/nmObjGetFoceiControl.Rd | 66 nlmixr2est-7.0.2/nlmixr2est/man/nmObjHandleControlObject.Rd | 50 nlmixr2est-7.0.2/nlmixr2est/man/nmSuppressMsg.Rd | 14 nlmixr2est-7.0.2/nlmixr2est/man/npBuildPsi.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/npCondense_.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/npIpmBurke.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/npObjAtGamma_.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/npSobolGrid_.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/npagControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/npagCycle_.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/npbControl.Rd |only nlmixr2est-7.0.2/nlmixr2est/man/optimControl.Rd | 312 nlmixr2est-7.0.2/nlmixr2est/man/postFinalObjectHooks.Rd | 4 nlmixr2est-7.0.2/nlmixr2est/man/postFinalObjectHooksAdd.Rd | 12 nlmixr2est-7.0.2/nlmixr2est/man/postFinalObjectHooksRm.Rd | 5 nlmixr2est-7.0.2/nlmixr2est/man/posthocControl.Rd | 27 nlmixr2est-7.0.2/nlmixr2est/man/preFinalParTableHooks.Rd | 4 nlmixr2est-7.0.2/nlmixr2est/man/preFinalParTableHooksAdd.Rd | 23 nlmixr2est-7.0.2/nlmixr2est/man/preFinalParTableHooksRm.Rd | 5 nlmixr2est-7.0.2/nlmixr2est/man/preProcessHooks.Rd | 4 nlmixr2est-7.0.2/nlmixr2est/man/preProcessHooksAdd.Rd | 12 nlmixr2est-7.0.2/nlmixr2est/man/preProcessHooksRm.Rd | 5 nlmixr2est-7.0.2/nlmixr2est/man/predict.nlmixr2FitCore.Rd | 5 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nlmixr2est-7.0.2/nlmixr2est/src/inner.h | 9 nlmixr2est-7.0.2/nlmixr2est/src/nearPD.cpp | 2 nlmixr2est-7.0.2/nlmixr2est/src/nlm.cpp | 328 nlmixr2est-7.0.2/nlmixr2est/src/nmMcmcRng.h |only nlmixr2est-7.0.2/nlmixr2est/src/np.h |only nlmixr2est-7.0.2/nlmixr2est/src/npCommon.cpp |only nlmixr2est-7.0.2/nlmixr2est/src/npCommon.h |only nlmixr2est-7.0.2/nlmixr2est/src/npag.cpp |only nlmixr2est-7.0.2/nlmixr2est/src/npb.cpp |only nlmixr2est-7.0.2/nlmixr2est/src/npde.cpp | 99 nlmixr2est-7.0.2/nlmixr2est/src/odeSwap.cpp |only nlmixr2est-7.0.2/nlmixr2est/src/odeSwap.h |only nlmixr2est-7.0.2/nlmixr2est/src/rxProtect.h | 6 nlmixr2est-7.0.2/nlmixr2est/src/rxcmp.cpp | 12 nlmixr2est-7.0.2/nlmixr2est/src/rxomp.h | 9 nlmixr2est-7.0.2/nlmixr2est/src/saem.cpp | 2536 +- nlmixr2est-7.0.2/nlmixr2est/src/scale.h | 522 nlmixr2est-7.0.2/nlmixr2est/src/shi21.cpp | 25 nlmixr2est-7.0.2/nlmixr2est/src/shi21.h | 4 nlmixr2est-7.0.2/nlmixr2est/src/solveWarnHelper.h |only nlmixr2est-7.0.2/nlmixr2est/src/utilc.c | 48 nlmixr2est-7.0.2/nlmixr2est/src/utilc.h | 3 nlmixr2est-7.0.2/nlmixr2est/src/vaeEncoder.cpp |only nlmixr2est-7.0.2/nlmixr2est/src/vaeEncoder.h |only nlmixr2est-7.0.2/nlmixr2est/tests/testthat.R | 168 nlmixr2est-7.0.2/nlmixr2est/tests/testthat/baselines |only nlmixr2est-7.0.2/nlmixr2est/tests/testthat/fixtures/README.md | 7 nlmixr2est-7.0.2/nlmixr2est/tests/testthat/fixtures/npag |only nlmixr2est-7.0.2/nlmixr2est/tests/testthat/helper-gradref.R |only nlmixr2est-7.0.2/nlmixr2est/tests/testthat/helper-quiet.R | 24 nlmixr2est-7.0.2/nlmixr2est/tests/testthat/helper-vae-resid.R |only nlmixr2est-7.0.2/nlmixr2est/tests/testthat/helper-wang2007.R | 25 nlmixr2est-7.0.2/nlmixr2est/tests/testthat/helper-zzz-fits.R | 48 nlmixr2est-7.0.2/nlmixr2est/tests/testthat/test-agq-cov.R |only nlmixr2est-7.0.2/nlmixr2est/tests/testthat/test-agq-fast-grad.R |only nlmixr2est-7.0.2/nlmixr2est/tests/testthat/test-ar-est.R |only nlmixr2est-7.0.2/nlmixr2est/tests/testthat/test-augpred.R | 64 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nlmixr2est-7.0.2/nlmixr2est/tests/testthat/test-vpcSim.R | 50 nlmixr2est-7.0.2/nlmixr2est/tests/testthat/test-vpcSimExpand.R |only nlmixr2est-7.0.2/nlmixr2est/tests/testthat/test-warfarin.R | 20 nlmixr2est-7.0.2/nlmixr2est/tests/testthat/test-zero-omega-restore.R |only nlmixr2est-7.0.2/nlmixr2est/tests/testthat/testthat-problems.rds |only 466 files changed, 31074 insertions(+), 9146 deletions(-)
Title: Lagrangian Multiplier Smoothing Splines for Smooth Function
Estimation
Description: Implements Lagrangian multiplier smoothing splines for flexible
nonparametric regression and function estimation. Provides tools for fitting,
prediction, and inference using a constrained optimization approach to
enforce smoothness. Supports generalized linear models, Weibull accelerated
failure time (AFT) models, Cox proportional hazards models,
quadratic programming constraints, and customizable working-correlation
structures, with options for parallel fitting. The core spline construction
builds on Ezhov et al. (2018) <doi:10.1515/jag-2017-0029>.
Quadratic-programming and SQP details follow Goldfarb & Idnani (1983)
<doi:10.1007/BF02591962> and Nocedal & Wright (2006)
<doi:10.1007/978-0-387-40065-5>. For smoothing spline and penalized spline
background, see Wahba (1990) <doi:10.1137/1.9781611970128> and Wood (2017)
<doi:10.1201/9781315370279>. For variance-component and correlation-parameter
estimation, see Searle et al. (2006) <ISBN:978-04700 [...truncated...]
Author: Matthew Davis [aut, cre]
Maintainer: Matthew Davis <matthewlouisdavis@gmail.com>
Diff between lgspline versions 1.1.0 dated 2026-05-08 and 1.2.1 dated 2026-08-04
DESCRIPTION | 10 MD5 | 63 - NAMESPACE | 4 NEWS.md | 10 R/HelperFunctions.R | 71 + R/additive_lgspline.R |only R/blockfit_solve.R | 90 + R/cox_helpers.R | 1459 ++++++++++++++-------------- R/get_B.R | 105 -- R/integrate.R | 95 + R/leave_one_out.R | 168 ++- R/lgspline-details.R | 158 +-- R/lgspline.R | 168 ++- R/methods.R | 433 ++++++-- R/prior_loglik.R | 34 R/process_input.R | 159 ++- README.md | 41 inst/WORDLIST | 6 inst/simulations |only man/Details.Rd | 122 +- man/equation.Rd | 19 man/generate_posterior.Rd | 3 man/generate_posterior_correlation.Rd | 5 man/get_B.Rd | 11 man/integrate.lgspline.Rd | 4 man/leave_one_out.Rd | 45 man/lgspline.Rd | 43 man/lgspline.fit.Rd | 33 man/lgspline_cox.Rd | 1 man/logLik.lgspline.Rd | 9 man/print.additive_lgspline.Rd |only man/process_input.Rd | 19 man/summary.additive_lgspline.Rd |only tests/testthat/test-additive-splines.R |only tests/testthat/test_correlation_structure.R | 25 35 files changed, 2171 insertions(+), 1242 deletions(-)
Title: Analysis of Ecological Dynamic Regimes
Description: A toolbox for implementing the Ecological Dynamic Regime framework,
including functions to characterize and compare groups of ecological trajectories
(Sánchez-Pinillos et al., 2023 <doi:10.1002/ecm.1589>); assess the ecological
resilience of a disturbed system using a reference dynamic regime (Sánchez-Pinillos
et al., 2024 <doi:10.1016/j.biocon.2023.110409>); and forecast ecological
trajectories from a dynamic regime (Sánchez-Pinillos et al. 2026,
<doi:10.1111/2041-210x.70372>). Additional functions are also available for
visualizing ecological dynamic regimes, their representative trajectories,
as well as predicted trajectories in a multidimensional state space.
Author: Martina Sanchez-Pinillos [aut, cre, cph]
Maintainer: Martina Sanchez-Pinillos <martina.sanchez.pinillos@gmail.com>
Diff between ecoregime versions 0.3.1 dated 2026-06-07 and 0.4.1 dated 2026-08-04
ecoregime-0.3.1/ecoregime/R/deviation_metrics.R |only ecoregime-0.3.1/ecoregime/R/plot.R |only ecoregime-0.3.1/ecoregime/R/summary.R |only ecoregime-0.3.1/ecoregime/man/deviation_metrics.Rd |only ecoregime-0.3.1/ecoregime/tests/testthat/Rplots.pdf |only ecoregime-0.3.1/ecoregime/tests/testthat/test-deviation_metrics.R |only ecoregime-0.3.1/ecoregime/tests/testthat/test-plot.R |only ecoregime-0.3.1/ecoregime/tests/testthat/test-summary.R |only ecoregime-0.4.1/ecoregime/DESCRIPTION | 30 +- ecoregime-0.4.1/ecoregime/MD5 | 75 +++-- ecoregime-0.4.1/ecoregime/NAMESPACE | 5 ecoregime-0.4.1/ecoregime/NEWS.md | 28 + ecoregime-0.4.1/ecoregime/R/EDR_metrics.R | 2 ecoregime-0.4.1/ecoregime/R/MPD.R |only ecoregime-0.4.1/ecoregime/R/dist_edr.R | 29 -- ecoregime-0.4.1/ecoregime/R/ecoregime-package.R | 2 ecoregime-0.4.1/ecoregime/R/petra_edr.R |only ecoregime-0.4.1/ecoregime/R/plot_PETRA.R |only ecoregime-0.4.1/ecoregime/R/plot_RETRA.R |only ecoregime-0.4.1/ecoregime/R/plot_edr.R | 2 ecoregime-0.4.1/ecoregime/R/resilience_metrics.R |only ecoregime-0.4.1/ecoregime/R/summary_RETRA.R |only ecoregime-0.4.1/ecoregime/README.md | 80 +++++ ecoregime-0.4.1/ecoregime/build/vignette.rds |binary ecoregime-0.4.1/ecoregime/inst/CITATION | 15 + ecoregime-0.4.1/ecoregime/inst/doc/EDR_framework.Rmd | 43 ++- ecoregime-0.4.1/ecoregime/inst/doc/EDR_framework.html | 142 ++++++---- ecoregime-0.4.1/ecoregime/inst/doc/Predicting_trajectories.R |only ecoregime-0.4.1/ecoregime/inst/doc/Predicting_trajectories.Rmd |only ecoregime-0.4.1/ecoregime/inst/doc/Predicting_trajectories.html |only ecoregime-0.4.1/ecoregime/inst/doc/Resilience.Rmd | 8 ecoregime-0.4.1/ecoregime/inst/doc/Resilience.html | 57 ++-- ecoregime-0.4.1/ecoregime/man/EDR_metrics.Rd | 2 ecoregime-0.4.1/ecoregime/man/MPD.Rd |only ecoregime-0.4.1/ecoregime/man/dist_edr.Rd | 29 -- ecoregime-0.4.1/ecoregime/man/ecoregime-package.Rd | 2 ecoregime-0.4.1/ecoregime/man/figures/README-predict-1.png |only ecoregime-0.4.1/ecoregime/man/petra_edr.Rd |only ecoregime-0.4.1/ecoregime/man/plot.PETRA.Rd |only ecoregime-0.4.1/ecoregime/man/plot.RETRA.Rd | 5 ecoregime-0.4.1/ecoregime/man/plot_edr.Rd | 2 ecoregime-0.4.1/ecoregime/man/resilience_metrics.Rd |only ecoregime-0.4.1/ecoregime/man/summary.RETRA.Rd | 2 ecoregime-0.4.1/ecoregime/tests/testthat/test-MPD.R |only ecoregime-0.4.1/ecoregime/tests/testthat/test-dist_edr.R | 4 ecoregime-0.4.1/ecoregime/tests/testthat/test-petra_edr.R |only ecoregime-0.4.1/ecoregime/tests/testthat/test-plot_PETRA.R |only ecoregime-0.4.1/ecoregime/tests/testthat/test-plot_RETRA.R |only ecoregime-0.4.1/ecoregime/tests/testthat/test-resilience_metrics.R |only ecoregime-0.4.1/ecoregime/tests/testthat/test-summary_RETRA.R |only ecoregime-0.4.1/ecoregime/vignettes/EDR_framework.Rmd | 43 ++- ecoregime-0.4.1/ecoregime/vignettes/Predicting_trajectories.Rmd |only ecoregime-0.4.1/ecoregime/vignettes/Resilience.Rmd | 8 53 files changed, 406 insertions(+), 209 deletions(-)
Title: Bayesian Nonparametric Mixture Models
Description: Functions to perform Bayesian nonparametric univariate and multivariate density estimation and clustering, by means of Pitman-Yor mixtures, and dependent Dirichlet process mixtures for partially exchangeable data. See Corradin et al. (2021) <doi:10.18637/jss.v100.i15> for more details.
Author: Riccardo Corradin [aut, cre],
Antonio Canale [ctb],
Bernardo Nipoti [ctb]
Maintainer: Riccardo Corradin <riccardo.corradin@gmail.com>
Diff between BNPmix versions 1.2.1 dated 2026-03-06 and 1.2.3 dated 2026-08-04
DESCRIPTION | 8 ++-- MD5 | 6 +-- inst/doc/BNPmix.pdf |binary vignettes/BNPmix_ref.bib | 86 +++++++++++++++++++++++++---------------------- 4 files changed, 54 insertions(+), 46 deletions(-)
Title: Estimate Univariate Gaussian and Student's t Mixture
Autoregressive Models
Description: Maximum likelihood estimation of univariate Gaussian Mixture Autoregressive (GMAR),
Student's t Mixture Autoregressive (StMAR), and Gaussian and Student's t Mixture Autoregressive (G-StMAR) models,
quantile residual tests, graphical diagnostics, forecast and simulate from GMAR, StMAR and G-StMAR processes.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2015) <doi:10.1111/jtsa.12108>,
Mika Meitz, Daniel Preve, Pentti Saikkonen (2023) <doi:10.1080/03610926.2021.1916531>,
Savi Virolainen (2022) <doi:10.1515/snde-2020-0060>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@gmail.com>
Diff between uGMAR versions 3.6.0 dated 2025-06-19 and 3.6.1 dated 2026-08-04
DESCRIPTION | 12 ++++++------ MD5 | 28 ++++++++++++++-------------- NEWS.md | 5 +++++ build/vignette.rds |binary inst/doc/uGMARpaper.R | 2 -- inst/doc/uGMARpaper.Rnw | 1 + inst/doc/uGMARpaper.pdf |binary man/cond_moments.Rd | 10 +++++----- man/get_regime_autocovs.Rd | 10 +++++----- man/get_regime_means.Rd | 10 +++++----- man/get_regime_vars.Rd | 10 +++++----- man/uGMAR-package.Rd | 7 ++++++- man/uncond_moments.Rd | 10 +++++----- vignettes/refs.bib | 24 +++++++++++++----------- vignettes/uGMARpaper.Rnw | 1 + 15 files changed, 71 insertions(+), 59 deletions(-)
Title: In-Line Documentation for R
Description: Generate your Rd documentation, 'NAMESPACE' file, and
collation field using specially formatted comments. Writing
documentation in-line with code makes it easier to keep your
documentation up-to-date as your requirements change. 'roxygen2' is
inspired by the 'Doxygen' system for C++.
Author: Hadley Wickham [aut, cre, cph] ,
Peter Danenberg [aut, cph],
Gabor Csardi [aut],
Manuel Eugster [aut, cph],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between roxygen2 versions 8.0.0 dated 2026-05-01 and 8.1.0 dated 2026-08-04
roxygen2-8.0.0/roxygen2/man/markdown_pass1.Rd |only roxygen2-8.1.0/roxygen2/DESCRIPTION | 12 roxygen2-8.1.0/roxygen2/MD5 | 135 +++--- roxygen2-8.1.0/roxygen2/NAMESPACE | 34 - roxygen2-8.1.0/roxygen2/NEWS.md | 21 - roxygen2-8.1.0/roxygen2/R/markdown-code.R | 8 roxygen2-8.1.0/roxygen2/R/markdown-escaping.R | 9 roxygen2-8.1.0/roxygen2/R/markdown-link-resolve.R | 119 ----- roxygen2-8.1.0/roxygen2/R/markdown-link.R | 17 roxygen2-8.1.0/roxygen2/R/markdown.R | 201 ---------- roxygen2-8.1.0/roxygen2/R/namespace.R | 116 ++++- roxygen2-8.1.0/roxygen2/R/object-from-call.R | 14 roxygen2-8.1.0/roxygen2/R/options.R | 26 + roxygen2-8.1.0/roxygen2/R/rd-describe-in.R | 2 roxygen2-8.1.0/roxygen2/R/rd-examples.R | 2 roxygen2-8.1.0/roxygen2/R/rd-family.R | 2 roxygen2-8.1.0/roxygen2/R/rd-inherit.R | 49 +- roxygen2-8.1.0/roxygen2/R/rd-params.R | 2 roxygen2-8.1.0/roxygen2/R/rd-r6-external.R | 2 roxygen2-8.1.0/roxygen2/R/rd-raw.R | 2 roxygen2-8.1.0/roxygen2/R/rd-s4.R | 4 roxygen2-8.1.0/roxygen2/R/rd-s7.R | 2 roxygen2-8.1.0/roxygen2/R/rd-section.R | 27 + roxygen2-8.1.0/roxygen2/R/rd-template.R | 2 roxygen2-8.1.0/roxygen2/R/rd-usage.R | 25 + roxygen2-8.1.0/roxygen2/R/rd.R | 5 roxygen2-8.1.0/roxygen2/R/roxygenize-setup.R | 35 + roxygen2-8.1.0/roxygen2/R/roxygenize.R | 1 roxygen2-8.1.0/roxygen2/R/tag-parser.R | 95 +++- roxygen2-8.1.0/roxygen2/R/utils-rd.R | 20 roxygen2-8.1.0/roxygen2/build/vignette.rds |binary roxygen2-8.1.0/roxygen2/inst/doc/namespace.Rmd | 1 roxygen2-8.1.0/roxygen2/inst/doc/namespace.html | 5 roxygen2-8.1.0/roxygen2/inst/doc/rd-S3.Rmd | 2 roxygen2-8.1.0/roxygen2/inst/doc/rd-S3.html | 2 roxygen2-8.1.0/roxygen2/inst/doc/rd-S4.Rmd | 29 + roxygen2-8.1.0/roxygen2/inst/doc/rd-S4.html | 35 + roxygen2-8.1.0/roxygen2/inst/doc/roxygen2.R | 4 roxygen2-8.1.0/roxygen2/inst/doc/roxygen2.Rmd | 2 roxygen2-8.1.0/roxygen2/inst/doc/roxygen2.html | 2 roxygen2-8.1.0/roxygen2/inst/roxygen2-tags.yml | 4 roxygen2-8.1.0/roxygen2/man/markdown-internals.Rd | 10 roxygen2-8.1.0/roxygen2/man/tag_parsers.Rd | 25 - roxygen2-8.1.0/roxygen2/man/tags-namespace.Rd | 2 roxygen2-8.1.0/roxygen2/src/isComplete.cpp | 45 +- roxygen2-8.1.0/roxygen2/tests/testthat/_snaps/markdown.md | 9 roxygen2-8.1.0/roxygen2/tests/testthat/_snaps/namespace.md | 20 roxygen2-8.1.0/roxygen2/tests/testthat/_snaps/options.md |only roxygen2-8.1.0/roxygen2/tests/testthat/_snaps/rd-inherit.md | 4 roxygen2-8.1.0/roxygen2/tests/testthat/_snaps/roxygenize-setup.md | 14 roxygen2-8.1.0/roxygen2/tests/testthat/helper-test.R | 2 roxygen2-8.1.0/roxygen2/tests/testthat/test-markdown-link-resolve.R | 25 - roxygen2-8.1.0/roxygen2/tests/testthat/test-markdown.R | 9 roxygen2-8.1.0/roxygen2/tests/testthat/test-namespace.R | 157 +++++++ roxygen2-8.1.0/roxygen2/tests/testthat/test-object-from-call.R | 20 roxygen2-8.1.0/roxygen2/tests/testthat/test-options.R | 11 roxygen2-8.1.0/roxygen2/tests/testthat/test-rd-examples.R | 7 roxygen2-8.1.0/roxygen2/tests/testthat/test-rd-inherit.R | 66 +++ roxygen2-8.1.0/roxygen2/tests/testthat/test-rd-markdown-escaping.R | 11 roxygen2-8.1.0/roxygen2/tests/testthat/test-rd-section.R | 18 roxygen2-8.1.0/roxygen2/tests/testthat/test-rd-usage.R | 46 ++ roxygen2-8.1.0/roxygen2/tests/testthat/test-roxygenize-setup.R | 37 + roxygen2-8.1.0/roxygen2/tests/testthat/test-select-args.R | 5 roxygen2-8.1.0/roxygen2/tests/testthat/test-tag-parser.R | 9 roxygen2-8.1.0/roxygen2/tests/testthat/testImportFrom |only roxygen2-8.1.0/roxygen2/vignettes/namespace.Rmd | 1 roxygen2-8.1.0/roxygen2/vignettes/rd-S3.Rmd | 2 roxygen2-8.1.0/roxygen2/vignettes/rd-S4.Rmd | 29 + roxygen2-8.1.0/roxygen2/vignettes/roxygen2.Rmd | 2 69 files changed, 1057 insertions(+), 604 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible, and comprehensive framework for
quantitative text analysis in R. Provides functionality for corpus management,
creating and manipulating tokens and n-grams, exploring keywords in context,
forming and manipulating sparse matrices
of documents by features and feature co-occurrences, analyzing keywords, computing feature similarities and
distances, applying content dictionaries, applying supervised and unsupervised machine learning,
visually representing text and text analyses, and more.
Author: Kenneth Benoit [cre, aut, cph] ,
Kohei Watanabe [aut] ,
Haiyan Wang [aut] ,
Paul Nulty [aut] ,
Adam Obeng [aut] ,
Stefan Mueller [aut] ,
Akitaka Matsuo [aut] ,
William Lowe [aut] ,
Christian Mueller [ctb],
Olivier Delmarcelle [ctb] ,
European Research [...truncated...]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 4.4 dated 2026-04-06 and 4.5.0 dated 2026-08-04
quanteda-4.4/quanteda/man/dictionary_tokenize.Rd |only quanteda-4.4/quanteda/tests/testthat/testthat-problems.rds |only quanteda-4.5.0/quanteda/DESCRIPTION | 18 quanteda-4.5.0/quanteda/MD5 | 218 +++++----- quanteda-4.5.0/quanteda/NAMESPACE | 28 + quanteda-4.5.0/quanteda/NEWS.md | 41 + quanteda-4.5.0/quanteda/R/RcppExports.R | 36 + quanteda-4.5.0/quanteda/R/aaa.R | 2 quanteda-4.5.0/quanteda/R/casechange-functions.R | 50 +- quanteda-4.5.0/quanteda/R/corpus-methods.R | 24 - quanteda-4.5.0/quanteda/R/corpus_segment.R | 3 quanteda-4.5.0/quanteda/R/data-documentation.R | 79 +-- quanteda-4.5.0/quanteda/R/dfm-classes.R | 13 quanteda-4.5.0/quanteda/R/dfm-print.R | 27 - quanteda-4.5.0/quanteda/R/dfm.R | 25 - quanteda-4.5.0/quanteda/R/dfm_match.R | 34 - quanteda-4.5.0/quanteda/R/dfm_replace.R | 6 quanteda-4.5.0/quanteda/R/dfm_trim.R | 19 quanteda-4.5.0/quanteda/R/dictionaries.R | 69 +-- quanteda-4.5.0/quanteda/R/docvars.R | 19 quanteda-4.5.0/quanteda/R/fcm-classes.R | 9 quanteda-4.5.0/quanteda/R/fcm-print.R | 22 - quanteda-4.5.0/quanteda/R/fcm.R | 2 quanteda-4.5.0/quanteda/R/kwic.R | 13 quanteda-4.5.0/quanteda/R/message.R | 58 ++ quanteda-4.5.0/quanteda/R/meta.R | 18 quanteda-4.5.0/quanteda/R/object-builder.R | 23 - quanteda-4.5.0/quanteda/R/quanteda_options.R | 2 quanteda-4.5.0/quanteda/R/spacyr-methods.R | 11 quanteda-4.5.0/quanteda/R/tokenizers.R | 6 quanteda-4.5.0/quanteda/R/tokens-methods.R | 132 ++---- quanteda-4.5.0/quanteda/R/tokens.R | 101 ---- quanteda-4.5.0/quanteda/R/tokens_compound.R | 1 quanteda-4.5.0/quanteda/R/tokens_lookup.R | 2 quanteda-4.5.0/quanteda/R/tokens_match.R |only quanteda-4.5.0/quanteda/R/tokens_recompile.R |only quanteda-4.5.0/quanteda/R/tokens_replace.R | 5 quanteda-4.5.0/quanteda/R/tokens_segment.R | 1 quanteda-4.5.0/quanteda/R/tokens_trim.R | 14 quanteda-4.5.0/quanteda/R/tokens_xptr.R | 40 - quanteda-4.5.0/quanteda/R/validator.R | 22 - quanteda-4.5.0/quanteda/R/wordstem.R | 6 quanteda-4.5.0/quanteda/README.md | 2 quanteda-4.5.0/quanteda/build/partial.rdb |binary quanteda-4.5.0/quanteda/build/vignette.rds |binary quanteda-4.5.0/quanteda/inst/doc/quickstart.html | 32 - quanteda-4.5.0/quanteda/inst/include/lib.h | 5 quanteda-4.5.0/quanteda/inst/include/tokens.h | 79 ++- quanteda-4.5.0/quanteda/man/as.tokens.Rd | 18 quanteda-4.5.0/quanteda/man/check_integer.Rd | 22 - quanteda-4.5.0/quanteda/man/corpus.Rd | 4 quanteda-4.5.0/quanteda/man/data_char_sampletext.Rd | 7 quanteda-4.5.0/quanteda/man/data_char_ukimmig2010.Rd | 6 quanteda-4.5.0/quanteda/man/data_corpus_inaugural.Rd | 2 quanteda-4.5.0/quanteda/man/data_dfm_lbgexample.Rd | 2 quanteda-4.5.0/quanteda/man/data_dictionary_LSD2015.Rd | 8 quanteda-4.5.0/quanteda/man/dfm-class.Rd | 11 quanteda-4.5.0/quanteda/man/dfm.Rd | 8 quanteda-4.5.0/quanteda/man/dfm_match.Rd | 30 - quanteda-4.5.0/quanteda/man/dfm_trim.Rd | 5 quanteda-4.5.0/quanteda/man/fcm-class.Rd | 3 quanteda-4.5.0/quanteda/man/inflect.Rd |only quanteda-4.5.0/quanteda/man/make_meta.Rd | 2 quanteda-4.5.0/quanteda/man/msg.Rd | 6 quanteda-4.5.0/quanteda/man/print-methods.Rd | 3 quanteda-4.5.0/quanteda/man/quanteda-package.Rd | 8 quanteda-4.5.0/quanteda/man/reexports.Rd | 2 quanteda-4.5.0/quanteda/man/spacyr-methods.Rd | 9 quanteda-4.5.0/quanteda/man/split_values.Rd | 6 quanteda-4.5.0/quanteda/man/tokenize_dictionary.Rd |only quanteda-4.5.0/quanteda/man/tokens_match.Rd |only quanteda-4.5.0/quanteda/man/tokens_recompile.Rd | 55 -- quanteda-4.5.0/quanteda/man/tokens_tolower.Rd | 7 quanteda-4.5.0/quanteda/man/tokens_trim.Rd | 5 quanteda-4.5.0/quanteda/man/valuetype.Rd | 2 quanteda-4.5.0/quanteda/man/wrap.Rd |only quanteda-4.5.0/quanteda/src/RcppExports.cpp | 110 ++++- quanteda-4.5.0/quanteda/src/dfm.cpp |only quanteda-4.5.0/quanteda/src/fcm.cpp | 16 quanteda-4.5.0/quanteda/src/index.cpp | 11 quanteda-4.5.0/quanteda/src/kwic.cpp | 18 quanteda-4.5.0/quanteda/src/serialize.cpp | 12 quanteda-4.5.0/quanteda/src/tokens_chunk.cpp | 15 quanteda-4.5.0/quanteda/src/tokens_combine.cpp | 20 quanteda-4.5.0/quanteda/src/tokens_compound.cpp | 55 -- quanteda-4.5.0/quanteda/src/tokens_group.cpp | 10 quanteda-4.5.0/quanteda/src/tokens_lookup.cpp | 65 +- quanteda-4.5.0/quanteda/src/tokens_match.cpp |only quanteda-4.5.0/quanteda/src/tokens_ngrams.cpp | 29 - 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Title: Simulation of Chromosomal Regions Shared by Family Members
Description: Simulation of chromosomal segments shared
identical-by-descent (IBD) among pedigree members. Using sex-specific
recombination rates along the human genome (Halldorsson et al. (2019)
<doi:10.1126/science.aau1043>), phased chromosomes are simulated for
all pedigree members. Applications include calculation of realised
relatedness coefficients and IBD segment distributions. 'ibdsim2' is
part of the 'pedsuite' collection of packages for pedigree analysis.
A detailed presentation of the 'pedsuite', including a separate
chapter on 'ibdsim2', is available in the book 'Pedigree analysis in
R' (Vigeland, 2021, ISBN:9780128244302). A 'Shiny' app for visualising
and comparing IBD distributions is available at
<https://magnusdv.shinyapps.io/ibdsim2-shiny/>.
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between ibdsim2 versions 2.3.2 dated 2025-11-23 and 2.3.3 dated 2026-08-04
ibdsim2-2.3.2/ibdsim2/inst/shiny/R/rcode.R |only ibdsim2-2.3.2/ibdsim2/inst/shiny/www/scripts.js |only ibdsim2-2.3.3/ibdsim2/DESCRIPTION | 20 - ibdsim2-2.3.3/ibdsim2/MD5 | 100 ++++----- ibdsim2-2.3.3/ibdsim2/NAMESPACE | 1 ibdsim2-2.3.3/ibdsim2/NEWS.md | 24 +- ibdsim2-2.3.3/ibdsim2/R/estimateCoeffs.R | 26 +- ibdsim2-2.3.3/ibdsim2/R/findPattern.R | 44 +--- ibdsim2-2.3.3/ibdsim2/R/genedrop.R | 2 ibdsim2-2.3.3/ibdsim2/R/haploDraw.R | 16 - ibdsim2-2.3.3/ibdsim2/R/ibdsim.R | 70 ++++-- ibdsim2-2.3.3/ibdsim2/R/ibdsim2-package.R | 3 ibdsim2-2.3.3/ibdsim2/R/karyogram.R | 23 +- ibdsim2-2.3.3/ibdsim2/R/launchApp.R | 6 ibdsim2-2.3.3/ibdsim2/R/map_constructors.R | 71 +++--- ibdsim2-2.3.3/ibdsim2/R/map_utils.R | 73 ++++-- ibdsim2-2.3.3/ibdsim2/R/plotSegmentDistribution.R | 12 - ibdsim2-2.3.3/ibdsim2/R/profileSimIBD.R | 110 ++++++---- ibdsim2-2.3.3/ibdsim2/R/realisedCoeffs.R | 29 +- ibdsim2-2.3.3/ibdsim2/R/segment_utils.R | 102 ++++----- ibdsim2-2.3.3/ibdsim2/R/utils.R | 16 + ibdsim2-2.3.3/ibdsim2/R/zeroIBD.R | 37 +-- ibdsim2-2.3.3/ibdsim2/README.md | 29 +- ibdsim2-2.3.3/ibdsim2/build/partial.rdb |binary ibdsim2-2.3.3/ibdsim2/inst/shiny/R/builtin-peds.R | 21 + ibdsim2-2.3.3/ibdsim2/inst/shiny/R/plot-functions.R | 6 ibdsim2-2.3.3/ibdsim2/inst/shiny/R/saveData.R | 11 - ibdsim2-2.3.3/ibdsim2/inst/shiny/R/utils.R | 17 + ibdsim2-2.3.3/ibdsim2/inst/shiny/app.R | 49 ++-- ibdsim2-2.3.3/ibdsim2/inst/shiny/www/custom.css | 36 --- ibdsim2-2.3.3/ibdsim2/man/convertPos.Rd | 7 ibdsim2-2.3.3/ibdsim2/man/customMap.Rd | 2 ibdsim2-2.3.3/ibdsim2/man/estimateCoeffs.Rd | 10 ibdsim2-2.3.3/ibdsim2/man/figures/README-ibdsim2-example-distplot-1.png |binary ibdsim2-2.3.3/ibdsim2/man/findPattern.Rd | 2 ibdsim2-2.3.3/ibdsim2/man/haploDraw.Rd | 8 ibdsim2-2.3.3/ibdsim2/man/ibdsim.Rd | 17 + ibdsim2-2.3.3/ibdsim2/man/ibdsim2-package.Rd | 7 ibdsim2-2.3.3/ibdsim2/man/karyoHaploid.Rd | 5 ibdsim2-2.3.3/ibdsim2/man/launchApp.Rd | 5 ibdsim2-2.3.3/ibdsim2/man/loadMap.Rd | 8 ibdsim2-2.3.3/ibdsim2/man/plotSegmentDistribution.Rd | 10 ibdsim2-2.3.3/ibdsim2/man/profileSimIBD.Rd | 17 - ibdsim2-2.3.3/ibdsim2/man/realised.Rd | 7 ibdsim2-2.3.3/ibdsim2/man/zeroIBD.Rd | 4 ibdsim2-2.3.3/ibdsim2/src/ibdsim2.cpp | 29 +- ibdsim2-2.3.3/ibdsim2/tests/testthat/test-estimates.R |only ibdsim2-2.3.3/ibdsim2/tests/testthat/test-maps.R | 31 ++ ibdsim2-2.3.3/ibdsim2/tests/testthat/test-meisosis.R | 7 ibdsim2-2.3.3/ibdsim2/tests/testthat/test-patterns.R | 10 ibdsim2-2.3.3/ibdsim2/tests/testthat/test-profilesim-ibd.R |only ibdsim2-2.3.3/ibdsim2/tests/testthat/test-recombine.R | 1 ibdsim2-2.3.3/ibdsim2/tests/testthat/test-segments.R | 29 ++ 53 files changed, 693 insertions(+), 477 deletions(-)
Title: Base Class and Methods for 'gson' Format
Description: Provides a lightweight container and exchange format for gene set collections. It stores gene set membership, names, gene identifiers, species, versions, and source metadata, with utilities for reading, writing, validating, and converting gene set data for enrichment analysis and related workflows.
Author: Guangchuang Yu [aut, cre, cph]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between gson versions 0.2.0 dated 2026-07-01 and 0.2.1 dated 2026-08-04
DESCRIPTION | 9 ++++----- MD5 | 8 ++++---- NAMESPACE | 1 - NEWS.md | 4 ++++ R/GMT.R | 20 ++++++++++++-------- 5 files changed, 24 insertions(+), 18 deletions(-)
Title: Bayesian Generalized Linear Models (IID Samples)
Description: Provides Bayesian linear and generalized linear model fitting
with independent and identically distributed (iid) posterior samples. The
main functions mirror R's lm() and glm() interfaces while adding prior
family specifications for Gaussian, Poisson, binomial, and Gamma models
with log-concave likelihoods. Sampling for supported non-conjugate models
uses accept-reject methods based on likelihood subgradients as in Nygren
and Nygren (2006) <doi:10.1198/016214506000000357>. The package also
includes tools for prior setup, posterior summaries, prediction,
diagnostics, simulation, vignettes, and optional 'OpenCL' acceleration for
larger models.
Author: Kjell Nygren [aut, cre],
The R Core Team [ctb, cph] ,
The R Foundation [cph] ,
Ross Ihaka [ctb, cph] ,
Robert Gentleman [ctb, cph] ,
Simon Davies [ctb] ,
Morten Welinder [ctb, cph] ,
Martin Maechler [ctb]
Maintainer: Kjell Nygren <kjell.a.nygren@gmail.com>
This is a re-admission after prior archival of version 0.9.72 dated 2026-07-26
Diff between glmbayes versions 0.9.72 dated 2026-07-26 and 0.9.75 dated 2026-08-04
glmbayes-0.9.72/glmbayes/src/glmbayes_getRegisteredNamespace.cpp |only glmbayes-0.9.72/glmbayes/src/glmbayes_getRegisteredNamespace.h |only glmbayes-0.9.72/glmbayes/tools |only glmbayes-0.9.75/glmbayes/DESCRIPTION | 8 glmbayes-0.9.75/glmbayes/MD5 | 98 - glmbayes-0.9.75/glmbayes/NEWS.md | 675 ++++---- glmbayes-0.9.75/glmbayes/README.md | 794 +++++----- glmbayes-0.9.75/glmbayes/build/partial.rdb |binary glmbayes-0.9.75/glmbayes/configure | 92 - glmbayes-0.9.75/glmbayes/configure.win | 41 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-01.html | 12 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-02-S01.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-02-S02.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-02-S03.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-02-S04.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-02-S05.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-03.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-04.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-05.html | 166 +- glmbayes-0.9.75/glmbayes/inst/doc/Chapter-06.html | 162 +- glmbayes-0.9.75/glmbayes/inst/doc/Chapter-07.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-08.html | 50 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-09.html | 84 - glmbayes-0.9.75/glmbayes/inst/doc/Chapter-10.html | 84 - glmbayes-0.9.75/glmbayes/inst/doc/Chapter-11.html | 56 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-13.html | 8 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-14.html | 34 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-16.R | 9 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-16.Rmd | 6 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-17.html | 18 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-18.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A01.html | 26 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A02.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A03.html | 122 - glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A04.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A05.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A06.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A07.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A08.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A09.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A10.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A11.html | 4 glmbayes-0.9.75/glmbayes/inst/doc/Chapter-A12.html | 4 glmbayes-0.9.75/glmbayes/inst/examples/Ex_Boston_centered.R | 38 glmbayes-0.9.75/glmbayes/inst/examples/Ex_Cleveland.R | 8 glmbayes-0.9.75/glmbayes/inst/examples/Ex_load_kernel_source.R | 4 glmbayes-0.9.75/glmbayes/man/Boston_centered.Rd | 38 glmbayes-0.9.75/glmbayes/man/Cleveland.Rd | 8 glmbayes-0.9.75/glmbayes/man/gpu_diagnostics.Rd | 4 glmbayes-0.9.75/glmbayes/src/Makevars.win | 3 glmbayes-0.9.75/glmbayes/vignettes/Chapter-16.Rmd | 6 51 files changed, 1377 insertions(+), 1353 deletions(-)
Title: Heteroskedasticity-Consistent Inference for Linear Models
Description: Computes heteroskedasticity-consistent covariance matrix
estimators for ordinary least squares regression models. The published HC0
through HC5m estimators implemented in the package follow White (1980)
<doi:10.2307/1912934>, Hinkley (1977)
<doi:10.1080/00401706.1977.10489550>, MacKinnon and White (1985)
<doi:10.1016/0304-4076(85)90158-7>, Cribari-Neto (2004)
<doi:10.1016/S0167-9473(02)00366-3>, Cribari-Neto and da Silva
(2011) <doi:10.1007/s10182-010-0141-2>, Cribari-Neto et al. (2007)
<doi:10.1080/03610920601126589>, and Li et al. (2016)
<doi:10.1080/00949655.2016.1198906>. The package also includes HCbeta, a
new estimator proposed by the package authors. It provides normal Wald tests,
confidence intervals, diagnostics, and S3 output for applied inference.
Author: Pedro Rafael D. Marinho [aut, cre] ,
Francisco Cribari-Neto [aut] ,
Marina Oliveira Cunha [aut]
Maintainer: Pedro Rafael D. Marinho <pedro.rafael.marinho@gmail.com>
Diff between hcinfer versions 0.1.1 dated 2026-07-13 and 0.2.0 dated 2026-08-04
hcinfer-0.1.1/hcinfer/man/figures/README-unnamed-chunk-5-1.png |only hcinfer-0.1.1/hcinfer/man/figures/README-unnamed-chunk-6-1.png |only hcinfer-0.2.0/hcinfer/DESCRIPTION | 13 hcinfer-0.2.0/hcinfer/MD5 | 93 - hcinfer-0.2.0/hcinfer/NAMESPACE | 6 hcinfer-0.2.0/hcinfer/NEWS.md | 7 hcinfer-0.2.0/hcinfer/R/boot-pairs.R |only hcinfer-0.2.0/hcinfer/R/data.R | 75 + hcinfer-0.2.0/hcinfer/R/hc-weights.R | 68 - hcinfer-0.2.0/hcinfer/R/hcinfer.R | 14 hcinfer-0.2.0/hcinfer/R/methods.R | 2 hcinfer-0.2.0/hcinfer/R/model-info.R | 9 hcinfer-0.2.0/hcinfer/R/plot.R | 118 ++ hcinfer-0.2.0/hcinfer/R/tests.R | 5 hcinfer-0.2.0/hcinfer/R/utils-validation.R | 15 hcinfer-0.2.0/hcinfer/R/vcov-hc.R | 31 hcinfer-0.2.0/hcinfer/README.md | 77 - hcinfer-0.2.0/hcinfer/build/vignette.rds |binary hcinfer-0.2.0/hcinfer/data/Crime2009.rda |only hcinfer-0.2.0/hcinfer/data/Hprice.rda |only hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-bootstrap.R |only hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-bootstrap.Rmd |only hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-bootstrap.html |only hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-comparison.R | 27 hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-comparison.Rmd | 48 hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-comparison.html | 192 +-- hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-hcbeta-algorithm.R |only hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-hcbeta-algorithm.Rmd |only hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-hcbeta-algorithm.html |only hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-hcbeta.R | 113 -- hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-hcbeta.Rmd | 221 +-- hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-hcbeta.html | 561 ++++------ hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-methodology.R | 7 hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-methodology.Rmd | 120 -- hcinfer-0.2.0/hcinfer/inst/doc/hcinfer-methodology.html | 132 -- hcinfer-0.2.0/hcinfer/inst/doc/introduction.R | 21 hcinfer-0.2.0/hcinfer/inst/doc/introduction.Rmd | 59 - hcinfer-0.2.0/hcinfer/inst/doc/introduction.html | 95 - hcinfer-0.2.0/hcinfer/man/Crime2009.Rd |only hcinfer-0.2.0/hcinfer/man/Hprice.Rd |only hcinfer-0.2.0/hcinfer/man/boot_pairs.Rd |only hcinfer-0.2.0/hcinfer/man/figures/README-readme-ci-plot-1.png |only hcinfer-0.2.0/hcinfer/man/figures/README-readme-diagnostics-plot-1.png |only hcinfer-0.2.0/hcinfer/man/hcinfer.Rd | 14 hcinfer-0.2.0/hcinfer/man/hcinfer_boot-methods.Rd |only hcinfer-0.2.0/hcinfer/man/plot.hcinfer_boot.Rd |only hcinfer-0.2.0/hcinfer/man/tests.Rd | 5 hcinfer-0.2.0/hcinfer/man/vcov_hc.Rd | 31 hcinfer-0.2.0/hcinfer/tests/testthat/_snaps/boot-pairs.md |only hcinfer-0.2.0/hcinfer/tests/testthat/_snaps/hc-weights.md |only hcinfer-0.2.0/hcinfer/tests/testthat/test-boot-pairs.R |only hcinfer-0.2.0/hcinfer/tests/testthat/test-hc-methods.R | 2 hcinfer-0.2.0/hcinfer/tests/testthat/test-hc-weights.R | 228 ++++ hcinfer-0.2.0/hcinfer/vignettes/hcinfer-bootstrap.Rmd |only hcinfer-0.2.0/hcinfer/vignettes/hcinfer-comparison.Rmd | 48 hcinfer-0.2.0/hcinfer/vignettes/hcinfer-hcbeta-algorithm.Rmd |only hcinfer-0.2.0/hcinfer/vignettes/hcinfer-hcbeta.Rmd | 221 +-- hcinfer-0.2.0/hcinfer/vignettes/hcinfer-methodology.Rmd | 120 -- hcinfer-0.2.0/hcinfer/vignettes/introduction.Rmd | 59 - 59 files changed, 1372 insertions(+), 1485 deletions(-)
Title: 'C++' Implementations of Functional Enrichment Analysis
Description: Fast implementations of functional enrichment analysis methods using 'C++' via 'Rcpp'.
Currently provides Over-Representation Analysis (ORA), Gene Set Enrichment Analysis (GSEA),
Weighted Enrichment Analysis for ORA and GSEA, Network-based Set Enrichment Analysis (NSEA),
multi-layer network-based enrichment, and multi-omics integration workflows. Additional
features include early fusion at the feature level, late fusion at the pathway level,
multi-omics contribution tracing, topology-aware explanation helpers, Bayesian term
selection, and extremely fast Random Walk with Restart (RWR) using 'RcppEigen'. The
enrichment methods build on GSEA by Subramanian et al. (2005)
<doi:10.1073/pnas.0506580102>, the multilevel strategy derived from 'fgsea'
by Korotkevich et al. (2021) <doi:10.1101/060012>, and network-based
enrichment ideas described by Glaab et al. (2012)
<doi:10.1093/bioinformatics/bts389>.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between enrichit versions 0.2.0 dated 2026-07-01 and 0.2.1 dated 2026-08-04
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/gsea.R | 7 ++++++- R/utilities.R | 1 + build/partial.rdb |binary man/enrichit_params.Rd | 1 + 7 files changed, 21 insertions(+), 10 deletions(-)
Title: Cross-Platform 'zip' Compression
Description: Cross-Platform 'zip' Compression Library. A replacement for
the 'zip' function, that does not require any additional external
tools on any platform.
Author: Gabor Csardi [aut, cre],
Kuba Podgorski [ctb],
Rich Geldreich [ctb],
Arm Limited [ctb, cph] ),
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between zip versions 3.0.1 dated 2026-07-13 and 3.0.2 dated 2026-08-04
DESCRIPTION | 6 ++-- MD5 | 11 ++++---- NEWS.md | 5 +++ src/unixutils.c | 2 - src/zip.c | 41 +++++++++++++++++++++++--------- tests/testthat/fixtures/symlink-dir.zip |only tests/testthat/test-unzip.R | 18 ++++++++++++++ 7 files changed, 63 insertions(+), 20 deletions(-)
Title: Declarative API for Staged Survey Weights
Description: Builds survey weights from design base weights by chaining the
stages of a weighting workflow (unknown-eligibility redistribution,
nonresponse adjustment, calibration to known population totals, and weight
trimming) through a declarative, pipeable, 'tidymodels'-style API, with
nonresponse handled by weighting classes, by response-propensity
models fitted with logistic regression or machine-learning learners (trees,
random forests and gradient boosting), or by calibration. Calibration
follows Deville and Sarndal (1992) <doi:10.2307/2290268>, and a
range-restricted variant trims the weights into a fixed interval while
preserving the calibration totals, following the generalized exponential
method of Folsom and Singh (2000). Variances are obtained with a
recipe-aware bootstrap and jackknife that resample primary sampling units
and re-apply the whole cascade on each replicate, following the rescaling
bootstrap of Rao and Wu (1988) <doi:10.1080/01621459.1988.10478591>, so the
re [...truncated...]
Author: Juan Pablo Ferreira [aut, cre],
Andres Gutierrez [ctb]
Maintainer: Juan Pablo Ferreira <juanpablo.ferreira@fcea.edu.uy>
Diff between weightflow versions 0.2.0 dated 2026-07-22 and 1.0.0 dated 2026-08-04
DESCRIPTION | 46 - MD5 | 87 +- NAMESPACE | 2 NEWS.md | 149 ++++ R/adjustments.R | 406 +++++++++-- R/prep.R | 21 R/r-indicators.R | 5 R/report.R | 836 ++++++++++++++++++++++-- R/spec.R | 225 +++++- R/variance.R | 138 +++ build/vignette.rds |binary inst/CITATION |only inst/WORDLIST | 25 inst/doc/advanced-methods.R | 25 inst/doc/advanced-methods.Rmd | 51 + inst/doc/advanced-methods.html | 52 + inst/doc/model-calibration.html | 4 inst/doc/nonresponse-propensities.R | 31 inst/doc/nonresponse-propensities.Rmd | 70 +- inst/doc/nonresponse-propensities.html | 111 ++- inst/doc/quality-report.R |only inst/doc/quality-report.Rmd |only inst/doc/quality-report.html |only inst/doc/validation-against-survey.R | 15 inst/doc/validation-against-survey.Rmd | 28 inst/doc/validation-against-survey.html | 27 inst/doc/variance-estimation.Rmd | 13 inst/doc/variance-estimation.html | 29 man/bootstrap_weights.Rd | 18 man/jackknife_weights.Rd | 20 man/report_weighting.Rd | 39 + man/step_nonresponse.Rd | 71 +- man/step_trim_calibrated.Rd |only man/step_trim_weights.Rd | 17 man/weightflow-package.Rd | 5 tests/testthat/test-bootstrap.R | 33 tests/testthat/test-calibrate-reconcile.R |only tests/testthat/test-calibrate-totals.R | 19 tests/testthat/test-jackknife.R | 16 tests/testthat/test-nonresponse-calibration.R |only tests/testthat/test-nonresponse-weight-model.R |only tests/testthat/test-replication-card.R |only tests/testthat/test-report-diagnostics.R |only tests/testthat/test-report-scatter.R |only tests/testthat/test-report.R |only tests/testthat/test-trim-calibrated.R |only tests/testthat/test-trim-weights-redistribute.R |only vignettes/advanced-methods.Rmd | 51 + vignettes/nonresponse-propensities.Rmd | 70 +- vignettes/quality-report.Rmd |only vignettes/validation-against-survey.Rmd | 28 vignettes/variance-estimation.Rmd | 13 52 files changed, 2542 insertions(+), 254 deletions(-)
Title: Analyze and Visualize Data from 'Microsoft Viva Insights'
Description: Provides a versatile range of functions, including exploratory data analysis, time-series analysis, organizational network analysis, and data validation, whilst at the same time implements a set of best practices in analyzing and visualizing data specific to 'Microsoft Viva Insights'.
Author: Martin Chan [aut, cre],
Carlos Morales [aut]
Maintainer: Martin Chan <martin.chan@microsoft.com>
Diff between vivainsights versions 0.7.2 dated 2026-04-28 and 0.7.3 dated 2026-08-04
DESCRIPTION | 10 - MD5 | 251 +++++++++++++++--------------- NEWS.md | 226 +++++++++++++-------------- R/heat_colours.R | 5 R/network_p2p.R | 114 ++++++++++--- inst/discovery |only man/IV_report.Rd | 18 +- man/afterhours_dist.Rd | 134 ++++++++-------- man/afterhours_fizz.Rd | 134 ++++++++-------- man/afterhours_line.Rd | 134 ++++++++-------- man/afterhours_rank.Rd | 134 ++++++++-------- man/afterhours_summary.Rd | 134 ++++++++-------- man/afterhours_trend.Rd | 134 ++++++++-------- man/any_idate.Rd | 34 ++-- man/camel_clean.Rd | 34 ++-- man/check_inputs.Rd | 34 ++-- man/check_query.Rd | 40 ++-- man/collaboration_area.Rd | 134 ++++++++-------- man/collaboration_dist.Rd | 134 ++++++++-------- man/collaboration_fizz.Rd | 134 ++++++++-------- man/collaboration_line.Rd | 134 ++++++++-------- man/collaboration_rank.Rd | 134 ++++++++-------- man/collaboration_sum.Rd | 134 ++++++++-------- man/collaboration_trend.Rd | 134 ++++++++-------- man/copy_df.Rd | 10 - man/create_IV.Rd | 8 man/create_bar.Rd | 160 +++++++++---------- man/create_bar_asis.Rd | 160 +++++++++---------- man/create_boxplot.Rd | 160 +++++++++---------- man/create_bubble.Rd | 160 +++++++++---------- man/create_density.Rd | 40 ++-- man/create_dist.Rd | 160 +++++++++---------- man/create_dt.Rd | 10 - man/create_fizz.Rd | 160 +++++++++---------- man/create_hist.Rd | 40 ++-- man/create_inc.Rd | 160 +++++++++---------- man/create_line.Rd | 168 ++++++++++---------- man/create_line_asis.Rd | 168 ++++++++++---------- man/create_period_scatter.Rd | 168 ++++++++++---------- man/create_radar.Rd | 160 +++++++++---------- man/create_rank.Rd | 160 +++++++++---------- man/create_rogers.Rd | 120 +++++++------- man/create_sankey.Rd | 160 +++++++++---------- man/create_scatter.Rd | 160 +++++++++---------- man/create_stacked.Rd | 160 +++++++++---------- man/create_survival.Rd | 160 +++++++++---------- man/create_tracking.Rd | 160 +++++++++---------- man/create_trend.Rd | 168 ++++++++++---------- man/cut_hour.Rd | 34 ++-- man/email_dist.Rd | 132 +++++++-------- man/email_fizz.Rd | 132 +++++++-------- man/email_line.Rd | 132 +++++++-------- man/email_rank.Rd | 132 +++++++-------- man/email_summary.Rd | 132 +++++++-------- man/email_trend.Rd | 132 +++++++-------- man/export.Rd | 10 - man/external_dist.Rd | 128 +++++++-------- man/external_fizz.Rd | 128 +++++++-------- man/external_line.Rd | 128 +++++++-------- man/external_rank.Rd | 134 ++++++++-------- man/external_sum.Rd | 128 +++++++-------- man/extract_date_range.Rd | 34 ++-- man/extract_hr.Rd | 74 ++++---- man/flag_ch_ratio.Rd | 40 ++-- man/flag_em_ratio.Rd | 40 ++-- man/flag_extreme.Rd | 40 ++-- man/flag_outlooktime.Rd | 40 ++-- man/g2g_data.Rd | 14 - man/generate_report.Rd | 10 - man/heat_colours.Rd | 40 ++-- man/hr_trend.Rd | 160 +++++++++---------- man/hrvar_count.Rd | 160 +++++++++---------- man/hrvar_count_all.Rd | 40 ++-- man/hrvar_trend.Rd | 160 +++++++++---------- man/identify_churn.Rd | 40 ++-- man/identify_holidayweeks.Rd | 40 ++-- man/identify_inactiveweeks.Rd | 40 ++-- man/identify_nkw.Rd | 40 ++-- man/identify_outlier.Rd | 40 ++-- man/identify_privacythreshold.Rd | 40 ++-- man/identify_shifts.Rd | 40 ++-- man/identify_tenure.Rd | 40 ++-- man/import_query.Rd | 10 - man/is_date_format.Rd | 34 ++-- man/keymetrics_scan.Rd | 120 +++++++------- man/maxmin.Rd | 34 ++-- man/meeting_dist.Rd | 134 ++++++++-------- man/meeting_fizz.Rd | 134 ++++++++-------- man/meeting_line.Rd | 134 ++++++++-------- man/meeting_rank.Rd | 134 ++++++++-------- man/meeting_summary.Rd | 134 ++++++++-------- man/meeting_tm_report.Rd | 36 ++-- man/meeting_trend.Rd | 134 ++++++++-------- man/mt_data.Rd | 4 man/network_g2g.Rd | 8 man/network_p2p.Rd | 20 +- man/network_summary.Rd | 8 man/one2one_dist.Rd | 134 ++++++++-------- man/one2one_fizz.Rd | 134 ++++++++-------- man/one2one_freq.Rd | 134 ++++++++-------- man/one2one_line.Rd | 134 ++++++++-------- man/one2one_rank.Rd | 134 ++++++++-------- man/one2one_sum.Rd | 134 ++++++++-------- man/one2one_trend.Rd | 134 ++++++++-------- man/p2p_data.Rd | 14 - man/p2p_data_sim.Rd | 10 - man/pairwise_count.Rd | 46 ++--- man/pq_data.Rd | 4 man/prep_query.Rd | 10 - man/read_preamble.Rd | 44 ++--- man/rgb2hex.Rd | 34 ++-- man/theme_wpa.Rd | 4 man/theme_wpa_basic.Rd | 4 man/tm_clean.Rd | 12 - man/tm_cooc.Rd | 12 - man/tm_freq.Rd | 12 - man/tm_wordcloud.Rd | 12 - man/totals_bind.Rd | 34 ++-- man/totals_col.Rd | 34 ++-- man/track_HR_change.Rd | 40 ++-- man/tstamp.Rd | 34 ++-- man/us_to_space.Rd | 34 ++-- man/validation_report.Rd | 50 ++--- man/vivainsights-package.Rd | 1 man/wrap.Rd | 34 ++-- tests/testthat/test_discovery_catalogue.R |only tests/testthat/test_network_p2p.R | 113 +++++++++++++ 127 files changed, 5545 insertions(+), 5365 deletions(-)
Title: Compare and Verify File Contents
Description: Extendable 'R6' file comparison classes, including a 'shiny' app for combining the comparison functionality into a file comparison application. The package idea originates from pharma companies' drug development processes, where statisticians and statistical programmers need to review and compare different versions of the same outputs and datasets. The package implementation itself is not tied to any specific industry and can be used in any context for easy file comparisons between different file version sets.
Author: Juha Javanainen [aut, cre],
Tiina Kirsilae [ctb],
Anna Wiksten [ctb]
Maintainer: Juha Javanainen <ejuhjav@gmail.com>
Diff between verifyr2 versions 1.2.0 dated 2026-05-23 and 1.3.0 dated 2026-08-04
DESCRIPTION | 18 MD5 | 72 +-- NAMESPACE | 2 NEWS.md | 15 R/Config.R | 35 + R/FileComparatorFactory.R | 14 R/ImgFileComparator.R | 96 ++++ R/PdfFileComparator.R | 19 R/TxtFileComparator.R | 15 R/XlsxFileComparator.R |only README.md | 30 - inst/extdata/base_files/file12.xlsx |only inst/extdata/compare_files/file12.xlsx |only inst/shiny_examples/app/app.R | 85 --- inst/shiny_examples/app/image_diff_styles.css |only inst/shiny_examples/app/report_styles.css | 26 + inst/shiny_examples/app/report_template.Rmd | 384 ++++++++++-------- inst/shiny_examples/app/styles.css | 94 ---- man/ImgFileComparator.Rd | 22 + man/PdfFileComparator.Rd | 28 + man/RtfFileComparator.Rd | 1 man/TxtFileComparator.Rd | 25 + man/TxtWithImagesFileComparator.Rd | 1 man/XlsxFileComparator.Rd |only tests/testthat/_snaps/app-app/file_compare-001_.png |binary tests/testthat/_snaps/app-app/folder_compare-001.json | 3 tests/testthat/_snaps/app-app/folder_compare-001_.png |binary tests/testthat/_snaps/app-app/options_reset-001.json | 4 tests/testthat/test-details_comparison_bin.R | 26 - tests/testthat/test-details_comparison_img.R | 78 ++- tests/testthat/test-details_comparison_json.R | 32 - tests/testthat/test-details_comparison_pdf.R | 67 ++- tests/testthat/test-details_comparison_rtf.R | 75 ++- tests/testthat/test-details_comparison_txt.R | 66 +-- tests/testthat/test-details_comparison_xlsx.R |only tests/testthat/test-summary_comparison_img.R | 18 tests/testthat/test-summary_comparison_pdf.R | 6 tests/testthat/test-summary_comparison_xlsx.R |only tests/testthat/test-vrf_contents_xlsx.R |only tests/testthat/test_outputs/xlsx |only 40 files changed, 836 insertions(+), 521 deletions(-)
Title: Discover, Count, Categorise, Score, Translate and Relate 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, sentiment-scores and emotion-scores emoji, converts them to and
from text (for accessibility and NLP preprocessing), searches the emoji
catalogue, maps emoji co-occurrence and sequences (graph-ready edge lists
and n-grams), measures where and how densely emoji are used, and builds
document-by-emoji feature tables for machine learning, 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; the emotion
lexicon is from EmoTag12 [...truncated...]
Author: Youzhi Yu [aut, cre]
Maintainer: Youzhi Yu <yuyouzhi666@icloud.com>
Diff between tidyEmoji versions 0.2.0 dated 2026-06-17 and 0.3.0 dated 2026-08-04
tidyEmoji-0.2.0/tidyEmoji/vignettes/ata_tweets.rda |only tidyEmoji-0.3.0/tidyEmoji/DESCRIPTION | 31 tidyEmoji-0.3.0/tidyEmoji/MD5 | 97 - tidyEmoji-0.3.0/tidyEmoji/NAMESPACE | 18 tidyEmoji-0.3.0/tidyEmoji/NEWS.md | 154 ++ tidyEmoji-0.3.0/tidyEmoji/R/data.R | 43 tidyEmoji-0.3.0/tidyEmoji/R/emoji-categorize.R | 9 tidyEmoji-0.3.0/tidyEmoji/R/emoji-dfm.R |only tidyEmoji-0.3.0/tidyEmoji/R/emoji-emotion.R |only tidyEmoji-0.3.0/tidyEmoji/R/emoji-engine.R | 178 ++ tidyEmoji-0.3.0/tidyEmoji/R/emoji-extraction.R | 12 tidyEmoji-0.3.0/tidyEmoji/R/emoji-lexicon-api.R |only tidyEmoji-0.3.0/tidyEmoji/R/emoji-metrics.R |only tidyEmoji-0.3.0/tidyEmoji/R/emoji-relate.R |only tidyEmoji-0.3.0/tidyEmoji/R/emoji-search.R |only tidyEmoji-0.3.0/tidyEmoji/R/emoji-sentiment.R | 54 tidyEmoji-0.3.0/tidyEmoji/R/emoji-summary.R | 27 tidyEmoji-0.3.0/tidyEmoji/R/emoji-translate.R |only tidyEmoji-0.3.0/tidyEmoji/R/tidyEmoji.R | 28 tidyEmoji-0.3.0/tidyEmoji/R/top-n-emojis.R | 60 tidyEmoji-0.3.0/tidyEmoji/README.md | 175 ++ tidyEmoji-0.3.0/tidyEmoji/data/category_unicode_crosswalk.rda |binary tidyEmoji-0.3.0/tidyEmoji/data/emoji_emotion_lexicon.rda |only tidyEmoji-0.3.0/tidyEmoji/data/emoji_unicode_crosswalk.rda |binary tidyEmoji-0.3.0/tidyEmoji/inst/doc/introduction.R | 111 + tidyEmoji-0.3.0/tidyEmoji/inst/doc/introduction.Rmd | 264 +++- tidyEmoji-0.3.0/tidyEmoji/inst/doc/introduction.html | 655 +++++++--- tidyEmoji-0.3.0/tidyEmoji/man/as_emoji_name.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_cooccurrence.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_density.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_dfm.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_emotion.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_emotion_label.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_emotion_lexicon.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_extract_unnest.Rd | 4 tidyEmoji-0.3.0/tidyEmoji/man/emoji_filter.Rd | 4 tidyEmoji-0.3.0/tidyEmoji/man/emoji_frequency.Rd | 4 tidyEmoji-0.3.0/tidyEmoji/man/emoji_lexicons.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_ngrams.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_pairs.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_position.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_ratio.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_score.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_search.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_sentiment.Rd | 24 tidyEmoji-0.3.0/tidyEmoji/man/emoji_sentiment_lexicon.Rd | 20 tidyEmoji-0.3.0/tidyEmoji/man/emoji_summary.Rd | 4 tidyEmoji-0.3.0/tidyEmoji/man/emoji_to_text.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/emoji_unicode_crosswalk.Rd | 3 tidyEmoji-0.3.0/tidyEmoji/man/figures |only tidyEmoji-0.3.0/tidyEmoji/man/register_emoji_lexicon.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/text_to_emoji.Rd |only tidyEmoji-0.3.0/tidyEmoji/man/tidyEmoji-package.Rd | 20 tidyEmoji-0.3.0/tidyEmoji/tests/testthat/test-dfm.R |only tidyEmoji-0.3.0/tidyEmoji/tests/testthat/test-dimensions.R | 8 tidyEmoji-0.3.0/tidyEmoji/tests/testthat/test-edge-cases.R | 6 tidyEmoji-0.3.0/tidyEmoji/tests/testthat/test-emotion.R |only tidyEmoji-0.3.0/tidyEmoji/tests/testthat/test-extraction.R | 8 tidyEmoji-0.3.0/tidyEmoji/tests/testthat/test-frequency-categorize.R | 21 tidyEmoji-0.3.0/tidyEmoji/tests/testthat/test-metrics.R |only tidyEmoji-0.3.0/tidyEmoji/tests/testthat/test-regression-0.2.1.R |only tidyEmoji-0.3.0/tidyEmoji/tests/testthat/test-regression-0.3.0.R |only tidyEmoji-0.3.0/tidyEmoji/tests/testthat/test-relate.R |only tidyEmoji-0.3.0/tidyEmoji/tests/testthat/test-sentiment.R | 2 tidyEmoji-0.3.0/tidyEmoji/vignettes/ata_tweets.csv |only tidyEmoji-0.3.0/tidyEmoji/vignettes/introduction.Rmd | 264 +++- 66 files changed, 1940 insertions(+), 368 deletions(-)
Title: 'OpenCL' Tools for R Package Developers
Description: Runtime 'OpenCL' support for R package developers: probe hardware
and drivers, load and concatenate kernel sources, and manage
dependency-annotated '.cl' libraries, so packages like 'nmathopencl' and
other ported libraries can offer GPU acceleration without each re-implementing
and related helpers. Vignettes illustrate integration with suggested package
'nmathopencl' and with downstream applications such as 'glmbayes';
production kernels for those applications ship in those packages rather
than here.
Author: Kjell Nygren [aut, cre],
The R Core Team [ctb, cph] ,
The R Foundation [cph] ,
Ross Ihaka [ctb, cph] ,
Robert Gentleman [ctb, cph] ,
Simon Davies [ctb] ,
Morten Welinder [ctb, cph] ,
Martin Maechler [ctb]
Maintainer: Kjell Nygren <kjell.a.nygren@gmail.com>
Diff between opencltools versions 0.8.2 dated 2026-07-11 and 0.8.3 dated 2026-08-04
opencltools-0.8.2/opencltools/src/glmbayes_getRegisteredNamespace.cpp |only opencltools-0.8.2/opencltools/src/glmbayes_getRegisteredNamespace.h |only opencltools-0.8.2/opencltools/tools/patch_rcpp_function_h.R |only opencltools-0.8.2/opencltools/tools/rcpp_include.R |only opencltools-0.8.3/opencltools/DESCRIPTION | 18 opencltools-0.8.3/opencltools/MD5 | 18 opencltools-0.8.3/opencltools/NEWS.md | 353 +++++----- opencltools-0.8.3/opencltools/configure | 21 opencltools-0.8.3/opencltools/configure.win | 39 - opencltools-0.8.3/opencltools/src/Makevars | 4 opencltools-0.8.3/opencltools/src/Makevars.win | 3 opencltools-0.8.3/opencltools/tools/README.md | 30 12 files changed, 213 insertions(+), 273 deletions(-)
Title: Uniform Data Model and 'Zarr' Interchange for Single-Cell Omics
Description: A lightweight interchange layer for single-cell and spatial omics
data, built on the L-star model of labelled axes and typed fields over them,
serialized to the 'Zarr' format. Provides bidirectional converters
("profiles") for 'Seurat', 'SingleCellExperiment', 'Conos', and 'pagoda2'
objects, including collections of heterogeneous samples, via a shared C++
core ('libstar') so the same store is readable from R, 'Python', and C++.
Author: Peter Kharchenko [aut, cre]
Maintainer: Peter Kharchenko <pk.restricted@gmail.com>
Diff between lstar versions 0.2.1 dated 2026-07-22 and 0.2.2 dated 2026-08-04
DESCRIPTION | 8 ++--- MD5 | 10 +++--- NEWS.md | 29 ++++++++++++++++++ R/viewer.R | 42 ++++++++++++++++++++++++--- man/extend_for_viewer.Rd | 14 +++++++-- tests/testthat/test-viewer-export.R | 56 ++++++++++++++++++++++++++++++++++++ 6 files changed, 144 insertions(+), 15 deletions(-)
Title: Processing, Visualizing, and Labeling Americas Barometer Data
Description: Labeling, weighting, and plotting data following custom style guidelines for use in reports, presentations, and social media posts. The Center for Global Democracy (formerly the Latin American Public Opinion Project) at Vanderbilt University is a leader in public survey research, best known for the Americas Barometer project. The publicly available data can be downloaded from: <https://www.vanderbilt.edu/lapop/data-access.php>.
Author: Robert Vidigal [cre, aut] ,
Luke Plutowski [ctb, aut]
Maintainer: Robert Vidigal <robert.vidigal@vanderbilt.edu>
Diff between lapop versions 2.1.5 dated 2026-04-29 and 2.1.7 dated 2026-08-04
DESCRIPTION | 18 - LICENSE | 2 MD5 | 66 ++--- NAMESPACE | 2 NEWS.md | 8 R/globals.R | 7 R/lapop_cc.R | 268 +++++++++++++++------- R/lapop_ccm.R | 451 +++++++++++++++++++++---------------- R/lapop_coef.R | 167 +++++++++---- R/lapop_hist.R | 9 R/lapop_mover.R | 37 ++- R/lapop_save.R | 60 ++-- R/lapop_stack.R | 458 ++++++++++++++++++++++---------------- R/lpr_cc.R | 171 ++++++++++---- R/lpr_ccm.R | 214 +++++++++++------ R/lpr_dumb.R | 191 ++++++++++----- R/lpr_hist.R | 64 +++-- R/lpr_mline.R | 153 ++++++++---- R/lpr_mover.R | 137 ++++++----- R/lpr_na_attributes.R |only R/lpr_ts.R | 101 +++++--- README.md | 37 ++- build/vignette.rds |binary inst/cran_preflight.R | 2 inst/doc/lapop-visualization.R | 2 inst/doc/lapop-visualization.Rmd | 2 inst/doc/lapop-visualization.html | 10 man/lapop-deprecated.Rd | 1 man/lapop_cc.Rd | 35 ++ man/lapop_ccm.Rd | 14 - man/lapop_coef.Rd | 17 + man/lapop_stack.Rd | 24 + man/lpr_ccm.Rd | 29 +- man/lpr_na_attributes.Rd |only vignettes/lapop-visualization.Rmd | 2 35 files changed, 1779 insertions(+), 980 deletions(-)
Title: A Copy Number and Expression-Based Classifier for Breast Tumours
Description: Implementation of the classifier described in the paper Ali HR et al (2014) <doi:10.1186/s13059-014-0431-1>. It uses copy number and/or expression form breast cancer data, trains a Tibshirani's 'pamr' classifier with the features available and predicts the iC10 group.
Author: Oscar M Rueda [aut, cre]
Maintainer: Oscar M Rueda <Oscar.Rueda@mrc-bsu.cam.ac.uk>
Diff between iC10 versions 2.0.2 dated 2024-07-19 and 2.0.3 dated 2026-08-04
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- NEWS | 2 ++ R/compare.R | 10 +++++++++- build/partial.rdb |binary 5 files changed, 21 insertions(+), 10 deletions(-)
Title: Psychometric Analysis with Rasch Measurement Theory
Description: Streamlines reproducible Rasch measurement theory analyses
for ordinal item-response data, combining estimation routines from
'eRm', 'psychotools', 'mirt', 'iarm', and 'lavaan' with consistent
diagnostic, plotting, and reporting layers. Covers the four basic
psychometric criteria summarised by Christensen et al. (2021)
<doi:10.1111/sms.13908> -- unidimensionality, local independence,
ordered response category thresholds, and invariance across
subgroups -- together with item fit, targeting, reliability,
category functioning, and descriptive item-response plots. A
distinguishing feature is the use of simulation-based critical
values to replace rule-of-thumb cutoffs for conditional infit mean-square,
Yen's Q3 local-dependence statistic, the largest residual-PCA eigenvalue,
ordinal CFA fit indices, and partial-gamma DIF and local-dependence
coefficients, optionally augmented with multiplicity-corrected bootstrap
p-values. Outputs are knitr::kable() tables and
'ggplot2' figures suitab [...truncated...]
Author: Magnus Johansson [aut, cre] ,
Nicklas Korsell [ctb] ,
Mirka Henninger [ctb] ,
Jan Radek [ctb]
Maintainer: Magnus Johansson <pgmj@pm.me>
Diff between easyRasch2 versions 1.1.0 dated 2026-07-14 and 1.1.1 dated 2026-08-04
DESCRIPTION | 6 - MD5 | 28 ++--- NEWS.md | 29 ++++++ R/conditional_infit.R | 151 ++++++++++++++++++++++---------- R/infit_cutoff.R | 4 R/targeting_plot.R | 7 - README.md | 8 - inst/doc/easyRasch2.Rmd | 7 + inst/doc/easyRasch2.html | 10 +- man/RMitemInfit.Rd | 33 +++++- man/RMitemInfitCutoff.Rd | 4 man/RMtargeting.Rd | 2 tests/testthat/test-infit_pvalue.R | 61 ++++++++++++ vignettes/easyRasch2.Rmd | 7 + vignettes/figures/rasch-targeting-1.png |binary 15 files changed, 268 insertions(+), 89 deletions(-)
Title: Reading, Formatting, and Organizing the Panel Study of Income
Dynamics (PSID)
Description: Provides various functions for reading and preparing the Panel Study of Income Dynamics (PSID) for longitudinal analysis, including functions that read the PSID's fixed width format files directly into R, rename all of the PSID's longitudinal variables so that recurring variables have consistent names across years, simplify assembling longitudinal datasets from cross sections of the PSID Family Files, and export the resulting PSID files into file formats common among other statistical programming languages ('SAS', 'STATA', and 'SPSS').
Author: Brian Aronson [aut, cre]
Maintainer: Brian Aronson <bdaronson@gmail.com>
Diff between easyPSID versions 0.1.2 dated 2021-10-03 and 0.1.3 dated 2026-08-04
DESCRIPTION | 11 +-- LICENSE | 2 MD5 | 35 ++++++----- NAMESPACE | 3 NEWS.md | 25 +++++++- R/10find_desc.R | 8 -- R/2convert_to_rds.R | 152 +++++++++++++++++++++++++++++-------------------- R/3rename_fam_vars.R | 87 ++++++++++++++++------------ R/4rename_ind_vars.R | 51 ++++++++++------ R/8find_name.R | 35 +++-------- R/9find_years.R | 36 +++-------- R/reference_lookup.R |only R/sysdata.rda |binary README.md | 75 ++++++++++++++---------- man/convert_to_rds.Rd | 2 man/rename_ind_vars.Rd | 5 - tests |only 17 files changed, 302 insertions(+), 225 deletions(-)
Title: Das Gupta Standardisation and Decomposition
Description: Implementation of Das Gupta's standardisation and decomposition of population rates, as set out "Standardization and decomposition of rates: A user’s manual", Das Gupta (1993) <https://www2.census.gov/library/publications/1993/demographics/p23-186.pdf>. The goal of these methods is to calculate adjusted rates based on compositional 'factors' and quantify the contribution of each factor to the difference in crude rates between populations. The package offers functionality to handle various scenarios for any number of factors and populations, where said factors can be comprised of vectors across sub-populations (including cross-classified population breakdowns), and with the option to specify user-defined rate functions.
Author: Josiah King [aut, cre],
Ben Matthews [aut],
Prithwis Das Gupta [aut]
Maintainer: Josiah King <josiah.king@ed.ac.uk>
Diff between DasGuptR versions 2.1.0 dated 2025-04-07 and 2.2.0 dated 2026-08-04
DasGuptR-2.1.0/DasGuptR/R/uspop.R |only DasGuptR-2.1.0/DasGuptR/data/uspop.RData |only DasGuptR-2.1.0/DasGuptR/man/uspop.Rd |only DasGuptR-2.2.0/DasGuptR/DESCRIPTION | 18 DasGuptR-2.2.0/DasGuptR/MD5 | 94 + DasGuptR-2.2.0/DasGuptR/NAMESPACE | 30 DasGuptR-2.2.0/DasGuptR/NEWS.md | 12 DasGuptR-2.2.0/DasGuptR/R/dg2pop.R | 1 DasGuptR-2.2.0/DasGuptR/R/dg354.R | 6 DasGuptR-2.2.0/DasGuptR/R/dg611.R | 2 DasGuptR-2.2.0/DasGuptR/R/dg612.R | 57 - DasGuptR-2.2.0/DasGuptR/R/dg_check.R |only DasGuptR-2.2.0/DasGuptR/R/dg_plot.R | 16 DasGuptR-2.2.0/DasGuptR/R/dg_table.R | 3 DasGuptR-2.2.0/DasGuptR/R/dgeg2_1.R |only DasGuptR-2.2.0/DasGuptR/R/dgeg2_2.R |only DasGuptR-2.2.0/DasGuptR/R/dgeg2_3.R |only DasGuptR-2.2.0/DasGuptR/R/dgeg2_4.R |only DasGuptR-2.2.0/DasGuptR/R/dgeg3_1.R |only DasGuptR-2.2.0/DasGuptR/R/dgeg4_1.R |only DasGuptR-2.2.0/DasGuptR/R/dgeg4_3.R |only DasGuptR-2.2.0/DasGuptR/R/dgeg4_4.R |only DasGuptR-2.2.0/DasGuptR/R/dgeg5_1.R |only DasGuptR-2.2.0/DasGuptR/R/dgeg5_3.R |only DasGuptR-2.2.0/DasGuptR/R/dgeg6_5.R |only DasGuptR-2.2.0/DasGuptR/R/dgeg6_6.R |only DasGuptR-2.2.0/DasGuptR/R/dgnpop.R | 329 ++---- DasGuptR-2.2.0/DasGuptR/R/reconv.R | 31 DasGuptR-2.2.0/DasGuptR/R/split_popstr.R | 82 - DasGuptR-2.2.0/DasGuptR/README.md | 34 DasGuptR-2.2.0/DasGuptR/build/vignette.rds |binary DasGuptR-2.2.0/DasGuptR/data/dgeg2_1.RData |only DasGuptR-2.2.0/DasGuptR/data/dgeg2_2.RData |only DasGuptR-2.2.0/DasGuptR/data/dgeg2_3.RData |only DasGuptR-2.2.0/DasGuptR/data/dgeg2_4.RData |only DasGuptR-2.2.0/DasGuptR/data/dgeg3_1.RData |only DasGuptR-2.2.0/DasGuptR/data/dgeg4_1.RData |only DasGuptR-2.2.0/DasGuptR/data/dgeg4_3.RData |only DasGuptR-2.2.0/DasGuptR/data/dgeg4_4.RData |only DasGuptR-2.2.0/DasGuptR/data/dgeg5_1.RData |only DasGuptR-2.2.0/DasGuptR/data/dgeg5_3.RData |only DasGuptR-2.2.0/DasGuptR/data/dgeg6_5.RData |only DasGuptR-2.2.0/DasGuptR/data/dgeg6_6.RData |only DasGuptR-2.2.0/DasGuptR/inst/doc/category_effects.html | 524 ++++------ DasGuptR-2.2.0/DasGuptR/inst/doc/choosing_comparison_years.html |only DasGuptR-2.2.0/DasGuptR/inst/doc/choosing_comparison_years.html.asis |only DasGuptR-2.2.0/DasGuptR/man/dg611.Rd | 2 DasGuptR-2.2.0/DasGuptR/man/dg612.Rd | 6 DasGuptR-2.2.0/DasGuptR/man/dg_check.Rd |only DasGuptR-2.2.0/DasGuptR/man/dg_plot.Rd | 18 DasGuptR-2.2.0/DasGuptR/man/dg_table.Rd | 2 DasGuptR-2.2.0/DasGuptR/man/dgeg2_1.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgeg2_2.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgeg2_3.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgeg2_4.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgeg3_1.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgeg4_1.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgeg4_3.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgeg4_4.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgeg5_1.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgeg5_3.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgeg6_5.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgeg6_6.Rd |only DasGuptR-2.2.0/DasGuptR/man/dgnpop.Rd | 473 +++------ DasGuptR-2.2.0/DasGuptR/man/reconv.Rd | 30 DasGuptR-2.2.0/DasGuptR/tests |only DasGuptR-2.2.0/DasGuptR/vignettes/choosing_comparison_years.html.asis |only DasGuptR-2.2.0/DasGuptR/vignettes/qmd/bsamps_2004_2016.rds |only DasGuptR-2.2.0/DasGuptR/vignettes/qmd/bsamps_2015_2016.rds |only DasGuptR-2.2.0/DasGuptR/vignettes/qmd/category_effects.qmd | 28 DasGuptR-2.2.0/DasGuptR/vignettes/qmd/choosing_comparison_years.qmd |only 71 files changed, 870 insertions(+), 928 deletions(-)
Title: Fast and Portable Character String Processing Facilities
Description: A collection of character string/text/natural language
processing tools for pattern searching (e.g., with 'Java'-like regular
expressions or the 'Unicode' collation algorithm), random string generation,
case mapping, string transliteration, concatenation, sorting, padding,
wrapping, Unicode normalisation, date-time formatting and parsing,
and many more. They are fast, consistent, convenient, and -
thanks to 'ICU' (International Components for Unicode) -
portable across all locales and platforms. Documentation about 'stringi' is
provided via its website at <https://stringi.gagolewski.com/> and
the paper by Gagolewski (2022, <doi:10.18637/jss.v103.i02>).
Author: Marek Gagolewski [aut, cre, cph] ,
Bartek Tartanus [ctb],
Unicode, Inc. and others [ctb]
Maintainer: Marek Gagolewski <marek@gagolewski.com>
Diff between stringi versions 1.8.7 dated 2025-03-27 and 1.8.9 dated 2026-08-04
stringi-1.8.7/stringi/tools |only stringi-1.8.9/stringi/DESCRIPTION | 14 stringi-1.8.9/stringi/INSTALL | 9 stringi-1.8.9/stringi/LICENSE | 2 stringi-1.8.9/stringi/MD5 | 554 +-- stringi-1.8.9/stringi/NEWS | 7 stringi-1.8.9/stringi/R/ICU_settings.R | 2 stringi-1.8.9/stringi/R/compare.R | 2 stringi-1.8.9/stringi/R/encoding.R | 2 stringi-1.8.9/stringi/R/encoding_conversion.R | 2 stringi-1.8.9/stringi/R/encoding_detection.R | 2 stringi-1.8.9/stringi/R/encoding_management.R | 2 stringi-1.8.9/stringi/R/escape.R | 2 stringi-1.8.9/stringi/R/files.R | 2 stringi-1.8.9/stringi/R/install.R | 2 stringi-1.8.9/stringi/R/internal_prepare_arg.R | 2 stringi-1.8.9/stringi/R/internal_test.R | 2 stringi-1.8.9/stringi/R/join.R | 2 stringi-1.8.9/stringi/R/length.R | 2 stringi-1.8.9/stringi/R/locale.R | 2 stringi-1.8.9/stringi/R/locale_management.R | 2 stringi-1.8.9/stringi/R/opts.R | 2 stringi-1.8.9/stringi/R/pad.R | 2 stringi-1.8.9/stringi/R/random.R | 2 stringi-1.8.9/stringi/R/reverse.R | 2 stringi-1.8.9/stringi/R/search.R | 4 stringi-1.8.9/stringi/R/search_count_4.R | 2 stringi-1.8.9/stringi/R/search_count_bound.R | 2 stringi-1.8.9/stringi/R/search_detect_4.R | 2 stringi-1.8.9/stringi/R/search_extract_4.R | 2 stringi-1.8.9/stringi/R/search_extract_bound.R | 2 stringi-1.8.9/stringi/R/search_locate_4.R | 2 stringi-1.8.9/stringi/R/search_locate_bound.R | 2 stringi-1.8.9/stringi/R/search_match_4.R | 2 stringi-1.8.9/stringi/R/search_replace_4.R | 2 stringi-1.8.9/stringi/R/search_split_4.R | 2 stringi-1.8.9/stringi/R/search_split_bound.R | 2 stringi-1.8.9/stringi/R/search_startsendswith_4.R | 2 stringi-1.8.9/stringi/R/search_subset_4.R | 2 stringi-1.8.9/stringi/R/sort.R | 2 stringi-1.8.9/stringi/R/sprintf.R | 2 stringi-1.8.9/stringi/R/stats.R | 2 stringi-1.8.9/stringi/R/stringi_package.R | 2 stringi-1.8.9/stringi/R/sub.R | 2 stringi-1.8.9/stringi/R/time_calendar.R | 2 stringi-1.8.9/stringi/R/time_format.R | 8 stringi-1.8.9/stringi/R/time_symbols.R | 2 stringi-1.8.9/stringi/R/time_zone.R | 2 stringi-1.8.9/stringi/R/trans_casemap.R | 2 stringi-1.8.9/stringi/R/trans_normalization.R | 2 stringi-1.8.9/stringi/R/trans_other.R | 2 stringi-1.8.9/stringi/R/trans_transliterate.R | 2 stringi-1.8.9/stringi/R/trim.R | 2 stringi-1.8.9/stringi/R/utils.R | 2 stringi-1.8.9/stringi/R/wrap.R | 2 stringi-1.8.9/stringi/build/partial.rdb |binary stringi-1.8.9/stringi/configure | 1554 +++------- stringi-1.8.9/stringi/configure.ac | 203 - stringi-1.8.9/stringi/configure.win | 2 stringi-1.8.9/stringi/man/about_arguments.Rd | 2 stringi-1.8.9/stringi/man/about_encoding.Rd | 38 stringi-1.8.9/stringi/man/about_locale.Rd | 44 stringi-1.8.9/stringi/man/about_search.Rd | 94 stringi-1.8.9/stringi/man/about_search_boundaries.Rd | 54 stringi-1.8.9/stringi/man/about_search_charclass.Rd | 8 stringi-1.8.9/stringi/man/about_search_coll.Rd | 40 stringi-1.8.9/stringi/man/about_search_fixed.Rd | 6 stringi-1.8.9/stringi/man/about_search_regex.Rd | 6 stringi-1.8.9/stringi/man/operator_add.Rd | 10 stringi-1.8.9/stringi/man/operator_compare.Rd | 32 stringi-1.8.9/stringi/man/operator_dollar.Rd | 14 stringi-1.8.9/stringi/man/stri_compare.Rd | 32 stringi-1.8.9/stringi/man/stri_count.Rd | 4 stringi-1.8.9/stringi/man/stri_count_boundaries.Rd | 52 stringi-1.8.9/stringi/man/stri_datetime_add.Rd | 20 stringi-1.8.9/stringi/man/stri_datetime_create.Rd | 20 stringi-1.8.9/stringi/man/stri_datetime_fields.Rd | 20 stringi-1.8.9/stringi/man/stri_datetime_format.Rd | 26 stringi-1.8.9/stringi/man/stri_datetime_fstr.Rd | 20 stringi-1.8.9/stringi/man/stri_datetime_now.Rd | 20 stringi-1.8.9/stringi/man/stri_datetime_symbols.Rd | 20 stringi-1.8.9/stringi/man/stri_detect.Rd | 4 stringi-1.8.9/stringi/man/stri_dup.Rd | 10 stringi-1.8.9/stringi/man/stri_duplicated.Rd | 32 stringi-1.8.9/stringi/man/stri_enc_detect.Rd | 10 stringi-1.8.9/stringi/man/stri_enc_detect2.Rd | 42 stringi-1.8.9/stringi/man/stri_enc_fromutf32.Rd | 12 stringi-1.8.9/stringi/man/stri_enc_info.Rd | 8 stringi-1.8.9/stringi/man/stri_enc_isascii.Rd | 10 stringi-1.8.9/stringi/man/stri_enc_isutf16.Rd | 10 stringi-1.8.9/stringi/man/stri_enc_isutf8.Rd | 10 stringi-1.8.9/stringi/man/stri_enc_list.Rd | 8 stringi-1.8.9/stringi/man/stri_enc_mark.Rd | 8 stringi-1.8.9/stringi/man/stri_enc_set.Rd | 8 stringi-1.8.9/stringi/man/stri_enc_toascii.Rd | 12 stringi-1.8.9/stringi/man/stri_enc_tonative.Rd | 12 stringi-1.8.9/stringi/man/stri_enc_toutf32.Rd | 12 stringi-1.8.9/stringi/man/stri_enc_toutf8.Rd | 12 stringi-1.8.9/stringi/man/stri_encode.Rd | 12 stringi-1.8.9/stringi/man/stri_escape_unicode.Rd | 4 stringi-1.8.9/stringi/man/stri_extract.Rd | 6 stringi-1.8.9/stringi/man/stri_extract_boundaries.Rd | 54 stringi-1.8.9/stringi/man/stri_flatten.Rd | 10 stringi-1.8.9/stringi/man/stri_isempty.Rd | 14 stringi-1.8.9/stringi/man/stri_join.Rd | 10 stringi-1.8.9/stringi/man/stri_join_list.Rd | 10 stringi-1.8.9/stringi/man/stri_length.Rd | 14 stringi-1.8.9/stringi/man/stri_list2matrix.Rd | 8 stringi-1.8.9/stringi/man/stri_locale_info.Rd | 6 stringi-1.8.9/stringi/man/stri_locale_list.Rd | 6 stringi-1.8.9/stringi/man/stri_locale_set.Rd | 6 stringi-1.8.9/stringi/man/stri_locate.Rd | 12 stringi-1.8.9/stringi/man/stri_locate_boundaries.Rd | 60 stringi-1.8.9/stringi/man/stri_match.Rd | 6 stringi-1.8.9/stringi/man/stri_na2empty.Rd | 8 stringi-1.8.9/stringi/man/stri_numbytes.Rd | 14 stringi-1.8.9/stringi/man/stri_opts_brkiter.Rd | 16 stringi-1.8.9/stringi/man/stri_opts_collator.Rd | 34 stringi-1.8.9/stringi/man/stri_opts_fixed.Rd | 2 stringi-1.8.9/stringi/man/stri_opts_regex.Rd | 2 stringi-1.8.9/stringi/man/stri_order.Rd | 32 stringi-1.8.9/stringi/man/stri_pad.Rd | 14 stringi-1.8.9/stringi/man/stri_rand_lipsum.Rd | 6 stringi-1.8.9/stringi/man/stri_rand_shuffle.Rd | 6 stringi-1.8.9/stringi/man/stri_rand_strings.Rd | 6 stringi-1.8.9/stringi/man/stri_rank.Rd | 32 stringi-1.8.9/stringi/man/stri_read_lines.Rd | 6 stringi-1.8.9/stringi/man/stri_read_raw.Rd | 6 stringi-1.8.9/stringi/man/stri_remove_empty.Rd | 8 stringi-1.8.9/stringi/man/stri_replace.Rd | 6 stringi-1.8.9/stringi/man/stri_replace_na.Rd | 8 stringi-1.8.9/stringi/man/stri_replace_rstr.Rd | 6 stringi-1.8.9/stringi/man/stri_sort.Rd | 32 stringi-1.8.9/stringi/man/stri_sort_key.Rd | 32 stringi-1.8.9/stringi/man/stri_split.Rd | 6 stringi-1.8.9/stringi/man/stri_split_boundaries.Rd | 54 stringi-1.8.9/stringi/man/stri_split_lines.Rd | 22 stringi-1.8.9/stringi/man/stri_sprintf.Rd | 14 stringi-1.8.9/stringi/man/stri_startsendswith.Rd | 4 stringi-1.8.9/stringi/man/stri_stats_general.Rd | 4 stringi-1.8.9/stringi/man/stri_stats_latex.Rd | 4 stringi-1.8.9/stringi/man/stri_sub.Rd | 8 stringi-1.8.9/stringi/man/stri_sub_all.Rd | 8 stringi-1.8.9/stringi/man/stri_subset.Rd | 2 stringi-1.8.9/stringi/man/stri_timezone_info.Rd | 26 stringi-1.8.9/stringi/man/stri_timezone_list.Rd | 26 stringi-1.8.9/stringi/man/stri_timezone_set.Rd | 26 stringi-1.8.9/stringi/man/stri_trans_casemap.Rd | 58 stringi-1.8.9/stringi/man/stri_trans_char.Rd | 10 stringi-1.8.9/stringi/man/stri_trans_general.Rd | 10 stringi-1.8.9/stringi/man/stri_trans_list.Rd | 10 stringi-1.8.9/stringi/man/stri_trans_nf.Rd | 10 stringi-1.8.9/stringi/man/stri_trim.Rd | 8 stringi-1.8.9/stringi/man/stri_unescape_unicode.Rd | 4 stringi-1.8.9/stringi/man/stri_unique.Rd | 32 stringi-1.8.9/stringi/man/stri_width.Rd | 14 stringi-1.8.9/stringi/man/stri_wrap.Rd | 48 stringi-1.8.9/stringi/man/stri_write_lines.Rd | 6 stringi-1.8.9/stringi/man/stringi-package.Rd | 2 stringi-1.8.9/stringi/src/Makevars.in | 2 stringi-1.8.9/stringi/src/Makevars.win | 2 stringi-1.8.9/stringi/src/icu74/common/udata.cpp | 54 stringi-1.8.9/stringi/src/install.libs.R.in | 2 stringi-1.8.9/stringi/src/stri_ICU_settings.cpp | 2 stringi-1.8.9/stringi/src/stri_brkiter.cpp | 2 stringi-1.8.9/stringi/src/stri_brkiter.h | 2 stringi-1.8.9/stringi/src/stri_bytesearch_matcher.h | 2 stringi-1.8.9/stringi/src/stri_callables.cpp | 2 stringi-1.8.9/stringi/src/stri_callables.h | 2 stringi-1.8.9/stringi/src/stri_collator.cpp | 2 stringi-1.8.9/stringi/src/stri_common.cpp | 2 stringi-1.8.9/stringi/src/stri_compare.cpp | 2 stringi-1.8.9/stringi/src/stri_container_base.cpp | 4 stringi-1.8.9/stringi/src/stri_container_base.h | 5 stringi-1.8.9/stringi/src/stri_container_bytesearch.cpp | 2 stringi-1.8.9/stringi/src/stri_container_bytesearch.h | 2 stringi-1.8.9/stringi/src/stri_container_charclass.h | 2 stringi-1.8.9/stringi/src/stri_container_double.h | 2 stringi-1.8.9/stringi/src/stri_container_integer.h | 2 stringi-1.8.9/stringi/src/stri_container_listint.cpp | 2 stringi-1.8.9/stringi/src/stri_container_listint.h | 2 stringi-1.8.9/stringi/src/stri_container_listraw.cpp | 22 stringi-1.8.9/stringi/src/stri_container_listraw.h | 6 stringi-1.8.9/stringi/src/stri_container_listutf8.cpp | 2 stringi-1.8.9/stringi/src/stri_container_listutf8.h | 2 stringi-1.8.9/stringi/src/stri_container_logical.h | 2 stringi-1.8.9/stringi/src/stri_container_regex.cpp | 2 stringi-1.8.9/stringi/src/stri_container_regex.h | 2 stringi-1.8.9/stringi/src/stri_container_usearch.cpp | 2 stringi-1.8.9/stringi/src/stri_container_usearch.h | 2 stringi-1.8.9/stringi/src/stri_container_utf16.cpp | 2 stringi-1.8.9/stringi/src/stri_container_utf16.h | 2 stringi-1.8.9/stringi/src/stri_container_utf8.cpp | 16 stringi-1.8.9/stringi/src/stri_container_utf8.h | 6 stringi-1.8.9/stringi/src/stri_container_utf8_indexable.cpp | 4 stringi-1.8.9/stringi/src/stri_container_utf8_indexable.h | 2 stringi-1.8.9/stringi/src/stri_encoding_conversion.cpp | 2 stringi-1.8.9/stringi/src/stri_encoding_detection.cpp | 2 stringi-1.8.9/stringi/src/stri_encoding_management.cpp | 2 stringi-1.8.9/stringi/src/stri_escape.cpp | 2 stringi-1.8.9/stringi/src/stri_exception.cpp | 2 stringi-1.8.9/stringi/src/stri_exception.h | 2 stringi-1.8.9/stringi/src/stri_exports.h | 2 stringi-1.8.9/stringi/src/stri_external.h | 2 stringi-1.8.9/stringi/src/stri_interval.h | 2 stringi-1.8.9/stringi/src/stri_intvec.h | 2 stringi-1.8.9/stringi/src/stri_join.cpp | 2 stringi-1.8.9/stringi/src/stri_length.cpp | 2 stringi-1.8.9/stringi/src/stri_macros.h | 2 stringi-1.8.9/stringi/src/stri_messages.h | 2 stringi-1.8.9/stringi/src/stri_pad.cpp | 2 stringi-1.8.9/stringi/src/stri_prepare_arg.cpp | 2 stringi-1.8.9/stringi/src/stri_random.cpp | 2 stringi-1.8.9/stringi/src/stri_reverse.cpp | 2 stringi-1.8.9/stringi/src/stri_search_boundaries_count.cpp | 2 stringi-1.8.9/stringi/src/stri_search_boundaries_extract.cpp | 2 stringi-1.8.9/stringi/src/stri_search_boundaries_locate.cpp | 2 stringi-1.8.9/stringi/src/stri_search_boundaries_split.cpp | 2 stringi-1.8.9/stringi/src/stri_search_class_count.cpp | 2 stringi-1.8.9/stringi/src/stri_search_class_detect.cpp | 2 stringi-1.8.9/stringi/src/stri_search_class_extract.cpp | 2 stringi-1.8.9/stringi/src/stri_search_class_locate.cpp | 2 stringi-1.8.9/stringi/src/stri_search_class_replace.cpp | 2 stringi-1.8.9/stringi/src/stri_search_class_split.cpp | 2 stringi-1.8.9/stringi/src/stri_search_class_startsendswith.cpp | 2 stringi-1.8.9/stringi/src/stri_search_class_subset.cpp | 2 stringi-1.8.9/stringi/src/stri_search_class_trim.cpp | 2 stringi-1.8.9/stringi/src/stri_search_coll_count.cpp | 2 stringi-1.8.9/stringi/src/stri_search_coll_detect.cpp | 2 stringi-1.8.9/stringi/src/stri_search_coll_extract.cpp | 2 stringi-1.8.9/stringi/src/stri_search_coll_locate.cpp | 2 stringi-1.8.9/stringi/src/stri_search_coll_replace.cpp | 2 stringi-1.8.9/stringi/src/stri_search_coll_split.cpp | 2 stringi-1.8.9/stringi/src/stri_search_coll_startsendswith.cpp | 2 stringi-1.8.9/stringi/src/stri_search_coll_subset.cpp | 2 stringi-1.8.9/stringi/src/stri_search_common.cpp | 2 stringi-1.8.9/stringi/src/stri_search_fixed_count.cpp | 2 stringi-1.8.9/stringi/src/stri_search_fixed_detect.cpp | 2 stringi-1.8.9/stringi/src/stri_search_fixed_extract.cpp | 2 stringi-1.8.9/stringi/src/stri_search_fixed_locate.cpp | 2 stringi-1.8.9/stringi/src/stri_search_fixed_replace.cpp | 2 stringi-1.8.9/stringi/src/stri_search_fixed_split.cpp | 2 stringi-1.8.9/stringi/src/stri_search_fixed_startsendswith.cpp | 2 stringi-1.8.9/stringi/src/stri_search_fixed_subset.cpp | 2 stringi-1.8.9/stringi/src/stri_search_in.cpp | 2 stringi-1.8.9/stringi/src/stri_search_other_split.cpp | 2 stringi-1.8.9/stringi/src/stri_search_regex_count.cpp | 2 stringi-1.8.9/stringi/src/stri_search_regex_detect.cpp | 2 stringi-1.8.9/stringi/src/stri_search_regex_extract.cpp | 2 stringi-1.8.9/stringi/src/stri_search_regex_locate.cpp | 2 stringi-1.8.9/stringi/src/stri_search_regex_match.cpp | 2 stringi-1.8.9/stringi/src/stri_search_regex_replace.cpp | 2 stringi-1.8.9/stringi/src/stri_search_regex_split.cpp | 2 stringi-1.8.9/stringi/src/stri_search_regex_subset.cpp | 2 stringi-1.8.9/stringi/src/stri_sort.cpp | 2 stringi-1.8.9/stringi/src/stri_sprintf.cpp | 2 stringi-1.8.9/stringi/src/stri_stats.cpp | 2 stringi-1.8.9/stringi/src/stri_string8.cpp | 2 stringi-1.8.9/stringi/src/stri_string8.h | 2 stringi-1.8.9/stringi/src/stri_string8buf.h | 2 stringi-1.8.9/stringi/src/stri_stringi.cpp | 2 stringi-1.8.9/stringi/src/stri_stringi.h | 2 stringi-1.8.9/stringi/src/stri_sub.cpp | 2 stringi-1.8.9/stringi/src/stri_test.cpp | 2 stringi-1.8.9/stringi/src/stri_time_calendar.cpp | 11 stringi-1.8.9/stringi/src/stri_time_format.cpp | 12 stringi-1.8.9/stringi/src/stri_time_symbols.cpp | 2 stringi-1.8.9/stringi/src/stri_time_zone.cpp | 5 stringi-1.8.9/stringi/src/stri_trans_casemap.cpp | 2 stringi-1.8.9/stringi/src/stri_trans_normalization.cpp | 2 stringi-1.8.9/stringi/src/stri_trans_other.cpp | 2 stringi-1.8.9/stringi/src/stri_trans_transliterate.cpp | 2 stringi-1.8.9/stringi/src/stri_ucnv.cpp | 2 stringi-1.8.9/stringi/src/stri_ucnv.h | 2 stringi-1.8.9/stringi/src/stri_uloc.cpp | 2 stringi-1.8.9/stringi/src/stri_utils.cpp | 2 stringi-1.8.9/stringi/src/stri_wrap.cpp | 2 stringi-1.8.9/stringi/src/uconfig_local.h.in | 6 278 files changed, 1989 insertions(+), 2559 deletions(-)
Title: An Interface to the Nexus Class Library
Description: An interface to the Nexus Class Library which allows parsing
of NEXUS, Newick and other phylogenetic tree file formats. It provides
elements of the file that can be used to build phylogenetic objects
such as ape's 'phylo' or phylobase's 'phylo4(d)'. This functionality
is demonstrated with 'read_newick_phylo()' and 'read_nexus_phylo()'.
Author: Francois Michonneau [aut, cre] ,
Ben Bolker [aut] ,
Mark Holder [aut] ,
Paul Lewis [aut] ,
Brian O'Meara [aut]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between rncl versions 0.8.9 dated 2026-01-21 and 0.8.10 dated 2026-08-04
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 8 ++++++++ README.md | 2 +- build/partial.rdb |binary src/ncl/nxscxxdiscretematrix.h | 6 +++--- src/ncl/nxsstring.h | 9 +++------ 7 files changed, 24 insertions(+), 19 deletions(-)
Title: R Bayesian Evidence Synthesis Tools
Description: Tool-set to support Bayesian evidence synthesis. This
includes meta-analysis, (robust) prior derivation from historical
data, operating characteristics and analysis (1 and 2 sample
cases). Please refer to Weber et al. (2021) <doi:10.18637/jss.v100.i19>
for details on applying this package while Neuenschwander et al. (2010)
<doi:10.1177/1740774509356002> and Schmidli et al. (2014)
<doi:10.1111/biom.12242> explain details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Beat Neuenschwander [ctb],
Heinz Schmidli [ctb],
Baldur Magnusson [ctb],
Yue Li [ctb],
Satrajit Roychoudhury [ctb],
Lukas A. Widmer [ctb] ,
Daniel Sabanes Bove [ctb] ,
Trustees of Columbia Univers [...truncated...]
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between RBesT versions 1.10-0 dated 2026-07-02 and 1.11-0 dated 2026-08-04
DESCRIPTION | 9 MD5 | 105 ++--- NAMESPACE | 1 NEWS.md | 51 ++ R/AS.R | 2 R/BinaryExactCI.R | 3 R/RBesT-package.R | 4 R/asthma.R | 2 R/automixfit.R | 4 R/colitis.R | 4 R/crohn.R | 2 R/decision1S.R | 4 R/decision2S.R | 4 R/decision2S_boundary.R | 596 +++++++++++++++++++++++------- R/gMAP.R | 14 R/mixess.R | 9 R/mixfit.R | 4 R/oc2S.R | 6 R/pos2S.R | 2 R/postmix.R | 4 R/robustify.R | 5 R/sysdata.rda |binary R/transplant.R | 4 R/uniroot_int.R | 48 +- build/partial.rdb |only inst/REFERENCES.bib |only inst/doc/RBesT.pdf |binary inst/doc/introduction.Rmd | 22 - inst/doc/introduction.html | 169 +++++--- inst/sbc/calibration.md5 | 6 inst/sbc/sbc_report.html | 590 ++++++++++++++--------------- inst/sbc/sbc_tools.R | 38 + man/AS.Rd | 2 man/BinaryExactCI.Rd | 3 man/RBesT-package.Rd | 3 man/asthma.Rd | 2 man/automixfit.Rd | 4 man/colitis.Rd | 4 man/crohn.Rd | 2 man/decision1S.Rd | 4 man/decision2S.Rd | 4 man/decision2S_boundary.Rd | 2 man/ess.Rd | 9 man/gMAP.Rd | 13 man/mixfit.Rd | 4 man/oc2S.Rd | 6 man/pos2S.Rd | 2 man/postmix.Rd | 4 man/robustify.Rd | 5 man/transplant.Rd | 4 man/uniroot_int.Rd | 10 tests/testthat/test-decision2S.R | 6 tests/testthat/test-decision2S_boundary.R | 160 +++++++- vignettes/REFERENCES.bib |only vignettes/introduction.Rmd | 22 - 55 files changed, 1282 insertions(+), 705 deletions(-)
Title: Optimize PTSD Diagnostic Criteria
Description: Provides tools for analyzing and optimizing PTSD (Post-Traumatic
Stress Disorder) diagnostic criteria using PCL-5 (PTSD Checklist for DSM-5)
and CAPS-5 (Clinician-Administered PTSD Scale for DSM-5) data. Functions
identify optimal subsets of PCL-5 items that maintain diagnostic accuracy
while reducing assessment burden. Includes tools for both hierarchical
(cluster-based) and non-hierarchical symptom combinations, calculation of
diagnostic metrics, and comparison with standard DSM-5 criteria. Redundancy
analysis quantifies how many item subsets perform equivalently, through
plateau sizes and bootstrap stability, and reports item selection against
the chance baseline of the searched candidate space. A transport layer
allows a site to evaluate subsets derived elsewhere and return only
aggregate summaries, supporting multi-site validation without sharing
individual-level data. Model validation is conducted using holdout and
cross-validation methods to assess robustness and generalizabilit [...truncated...]
Author: Laura Weidmann [aut] ,
Tobias R. Spiller [aut, cre] ,
Flavio A. Schueepp [aut]
Maintainer: Tobias R. Spiller <tobias.spiller@access.uzh.ch>
Diff between PTSDdiag versions 0.4.1 dated 2026-07-13 and 0.5.0 dated 2026-08-04
DESCRIPTION | 36 ++++--- MD5 | 73 +++++++++++--- NAMESPACE | 31 ++++++ NEWS.md | 148 ++++++++++++++++++++++++++++++ R/bootstrap_stability.R |only R/compare_rule_forms.R |only R/diagnostic_metrics.R |only R/evaluate_sets.R |only R/internals.R | 14 ++ R/internals_stability.R |only R/plateau.R |only R/plot_symptom_selection.R |only R/scenario_plots.R | 56 +++++++++-- R/scenario_tables.R | 61 ++++++++++-- R/symptom_selection.R |only R/transport.R |only inst/doc/multi-site-validation.html | 2 inst/doc/validation.R | 19 +++ inst/doc/validation.Rmd | 34 ++++++ inst/doc/validation.html | 83 ++++++++++++++++ man/as_set_matrix.Rd |only man/ba_ci.Rd |only man/bootstrap_stability.Rd |only man/chance_baseline.Rd |only man/compare_rule_forms.Rd |only man/compute_plateau.Rd |only man/diagnostic_metrics.Rd |only man/diagnostic_metrics_family.Rd |only man/evaluate_sets.Rd |only man/exact_ci.Rd |only man/five_number.Rd |only man/fmt_est_ci.Rd |only man/fmt_ratio_ci.Rd |only man/icd11_items.Rd |only man/icd11_performance.Rd |only man/kappa_ci.Rd |only man/lr_ci.Rd |only man/n_candidates.Rd |only man/pcl5_item_labels.Rd |only man/plot_symptom_frequency.Rd | 22 +++- man/plot_symptom_selection.Rd |only man/print.ptsdiag_plateau.Rd |only man/print.ptsdiag_rule_forms.Rd |only man/print.ptsdiag_stability.Rd |only man/print.ptsdiag_transport.Rd |only man/read_transport.Rd |only man/set_id_to_items.Rd |only man/symptom_frequency.Rd | 21 +++- man/symptom_selection.Rd |only man/transport_plateau.Rd |only man/wilson_ci.Rd |only man/write_transport.Rd |only tests/testthat/test-analysis.R | 53 ++++++++++ tests/testthat/test-bootstrap_stability.R |only tests/testthat/test-diagnostic_metrics.R |only tests/testthat/test-evaluate_sets.R |only tests/testthat/test-plateau.R |only tests/testthat/test-symptom_selection.R |only tests/testthat/test-transport.R |only vignettes/validation.Rmd | 34 ++++++ 60 files changed, 630 insertions(+), 57 deletions(-)
Title: Libraries, Data Dictionaries, and a Data Step for R
Description: Contains a set of functions to create data libraries,
generate data dictionaries, and simulate a data step.
The libname() function will load a directory of data into
a library in one line of code. The dictionary() function
will generate data dictionaries for individual
data frames or an entire library. And the datestep() function
will perform row-by-row data processing.
Author: David Bosak [aut, cre],
Brian Varney [ctb],
Archytas Clinical Solutions [cph]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between libr versions 1.4.1 dated 2026-04-04 and 1.4.2 dated 2026-08-04
DESCRIPTION | 8 MD5 | 89 +-- NEWS.md | 5 R/datastep.R | 2 R/utilities.R | 19 build/vignette.rds |binary inst/doc/libr-basics.R | 162 ++--- inst/doc/libr-datastep.R | 1130 ++++++++++++++++++++--------------------- inst/doc/libr-example1.R | 236 ++++---- inst/doc/libr-example2.R | 354 ++++++------ inst/doc/libr-faq.R | 114 ++-- inst/doc/libr-management.R | 254 ++++----- inst/doc/libr.R | 216 +++---- man/datastep.Rd | 14 man/delete.Rd | 14 man/dsarray.Rd | 14 man/dsattr.Rd | 14 man/import_spec.Rd | 10 man/is.lib.Rd | 32 - man/length.dsarray.Rd | 14 man/lib_add.Rd | 32 - man/lib_copy.Rd | 32 - man/lib_delete.Rd | 32 - man/lib_export.Rd | 32 - man/lib_info.Rd | 32 - man/lib_load.Rd | 32 - man/lib_path.Rd | 32 - man/lib_remove.Rd | 32 - man/lib_replace.Rd | 32 - man/lib_size.Rd | 32 - man/lib_sync.Rd | 32 - man/lib_unload.Rd | 32 - man/lib_write.Rd | 32 - man/libname.Rd | 32 - man/libr.Rd | 5 man/output.Rd | 14 man/print.lib.Rd | 32 - man/print.specs.Rd | 10 man/read.specs.Rd | 10 man/specs.Rd | 10 man/sub-.dsarray.Rd | 14 man/write.specs.Rd | 10 tests/testthat/data/types |only tests/testthat/test-datastep.R | 1 tests/testthat/test-libname.R | 15 tests/testthat/test-specs.R | 14 46 files changed, 1663 insertions(+), 1621 deletions(-)
Title: Visually Exploring Random Forests
Description: Graphic elements for exploring Random Forests using the
'randomForest' or 'randomForestSRC' package for survival, regression
and classification forests and 'ggplot2' package plotting. Implements
visualizations of the methods described in Breiman (2001)
<doi:10.1023/A:1010933404324> and Ishwaran, Kogalur, Blackstone, and
Lauer (2008) <doi:10.1214/08-AOAS169>.
Author: John Ehrlinger [aut, cre]
Maintainer: John Ehrlinger <john.ehrlinger@gmail.com>
Diff between ggRandomForests versions 3.4.0 dated 2026-07-02 and 3.5.0 dated 2026-08-04
DESCRIPTION | 22 LICENSE | 4 MD5 | 240 NAMESPACE | 16 NEWS.md | 205 R/autoplot_methods.R | 13 R/calc_roc.R | 4 R/gg_beta_varpro.R | 17 R/gg_brier.R | 17 R/gg_error.R | 64 R/gg_isopro.R | 25 R/gg_ivarpro.R | 6 R/gg_partial.R | 39 R/gg_partial_rfsrc.R | 11 R/gg_partial_varpro.R | 161 R/gg_rfsrc.R | 7 R/gg_roc.R | 4 R/gg_shap.R |only R/gg_variable.R | 9 R/gg_varpro.R | 12 R/gg_vimp.R | 269 R/help.R | 123 R/plot.gg_beta_uvarpro.R | 2 R/plot.gg_beta_varpro.R | 6 R/plot.gg_error.R | 40 R/plot.gg_isopro.R | 10 R/plot.gg_ivarpro.R | 2 R/plot.gg_partial.R | 23 R/plot.gg_partial_varpro.R | 4 R/plot.gg_rfsrc.R | 12 R/plot.gg_roc.R | 10 R/plot.gg_sdependent.R | 6 R/plot.gg_shap.R |only R/plot.gg_udependent.R | 8 R/plot.gg_variable.R | 16 R/plot.gg_varpro.R | 13 R/plot.gg_vimp.R | 8 R/print_methods.R | 10 R/quantile_pts.R | 20 R/ribbon_style.R | 2 R/summary_methods.R | 31 build/vignette.rds |binary inst/doc/ggRandomForests-classification.R |only inst/doc/ggRandomForests-classification.html |only inst/doc/ggRandomForests-classification.qmd |only inst/doc/ggRandomForests-regression.R | 25 inst/doc/ggRandomForests-regression.html | 216 inst/doc/ggRandomForests-regression.qmd | 82 inst/doc/ggRandomForests-survival.R | 7 inst/doc/ggRandomForests-survival.html | 56 inst/doc/ggRandomForests-survival.qmd | 9 inst/doc/ggRandomForests.R | 3 inst/doc/ggRandomForests.html | 10 inst/doc/ggRandomForests.qmd | 3 inst/doc/uvarpro.R | 3 inst/doc/uvarpro.html | 12 inst/doc/uvarpro.qmd | 5 inst/doc/varpro.R | 32 inst/doc/varpro.html | 7010 ---------- inst/doc/varpro.qmd | 117 man/autoplot.gg.Rd | 10 man/dot-varpro_imp_stats.Rd | 4 man/ggRandomForests-package.Rd | 129 man/gg_beta_varpro.Rd | 15 man/gg_brier.Rd | 8 man/gg_error.Rd | 52 man/gg_isopro.Rd | 25 man/gg_ivarpro.Rd | 4 man/gg_partial.Rd | 34 man/gg_partial_rfsrc.Rd | 12 man/gg_partial_varpro.Rd | 72 man/gg_roc.rfsrc.Rd | 2 man/gg_shap.Rd |only man/gg_varpro.Rd | 8 man/gg_vimp.Rd | 66 man/plot.gg_beta_uvarpro.Rd | 2 man/plot.gg_beta_varpro.Rd | 6 man/plot.gg_error.Rd | 30 man/plot.gg_isopro.Rd | 2 man/plot.gg_ivarpro.Rd | 2 man/plot.gg_partial.Rd | 2 man/plot.gg_partial_rfsrc.Rd | 4 man/plot.gg_partial_varpro.Rd | 4 man/plot.gg_rfsrc.Rd | 6 man/plot.gg_roc.Rd | 4 man/plot.gg_sdependent.Rd | 6 man/plot.gg_shap.Rd |only man/plot.gg_udependent.Rd | 8 man/plot.gg_variable.Rd | 2 man/plot.gg_varpro.Rd | 6 man/plot.gg_vimp.Rd | 6 man/print.gg.Rd | 3 man/quantile_pts.Rd | 18 man/shap_beeswarm.Rd |only man/shap_dependence.Rd |only man/shap_importance.Rd |only man/summary.gg.Rd | 3 tests/testthat/_snaps/snapshots/gg-isopro-default.svg |only tests/testthat/_snaps/snapshots/gg-isopro-predict-overlay.svg |only tests/testthat/_snaps/snapshots/gg-isopro-threshold.svg |only tests/testthat/_snaps/snapshots/gg-roc-multiclass-facet.svg |only tests/testthat/_snaps/snapshots/gg-roc-multiclass-overlay.svg |only tests/testthat/_snaps/snapshots/gg-shap-beeswarm.svg |only tests/testthat/_snaps/snapshots/gg-shap-dependence.svg |only tests/testthat/_snaps/snapshots/gg-shap-importance.svg |only tests/testthat/_snaps/snapshots/gg-udependent-default.svg |only tests/testthat/_snaps/snapshots/gg-udependent-undirected.svg |only tests/testthat/_snaps/snapshots/gg-variable-rf-classification-default.svg |only tests/testthat/_snaps/snapshots/gg-variable-rf-classification-smooth.svg |only tests/testthat/_snaps/snapshots/gg-vimp-classification-rf.svg | 184 tests/testthat/_snaps/snapshots/gg-vimp-regression-rf.svg | 48 tests/testthat/test_default_dispatch.R |only tests/testthat/test_gg_error.R | 2 tests/testthat/test_gg_isopro.R | 6 tests/testthat/test_gg_partial.R | 53 tests/testthat/test_gg_partial_rfsrc.R | 2 tests/testthat/test_gg_partial_varpro.R | 179 tests/testthat/test_gg_shap.R |only tests/testthat/test_gg_varpro.R | 35 tests/testthat/test_gg_vimp.R | 210 tests/testthat/test_plot_layer_data.R | 10 tests/testthat/test_print_summary.R | 96 tests/testthat/test_snapshots.R | 26 tests/testthat/test_surv_partial.R | 2 vignettes/_fig_optim.R |only vignettes/ggRandomForests-classification.qmd |only vignettes/ggRandomForests-regression.qmd | 82 vignettes/ggRandomForests-survival.qmd | 9 vignettes/ggRandomForests.bib | 19 vignettes/ggRandomForests.qmd | 3 vignettes/precompute_varpro.R | 23 vignettes/uvarpro.qmd | 5 vignettes/varpro.qmd | 117 vignettes/varpro_precomputed.rds |binary 134 files changed, 2992 insertions(+), 7755 deletions(-)
More information about ggRandomForests at CRAN
Permanent link
Title: Enhanced Office Open XML Charting for 'openxlsx2'
Description: Provides a high-level 'R6' interface for creating complex
Office Open XML (OOXML) charts. Allows users to build
multi-series combo charts with secondary axes and granular styling
options, designed to integrate seamlessly with 'openxlsx2'.
Author: Jan Marvin Garbuszus [aut, cre]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between encharter versions 0.9.1 dated 2026-06-27 and 0.10 dated 2026-08-04
DESCRIPTION | 6 +++--- MD5 | 17 +++++++++-------- NEWS.md |only R/encharter.R | 22 ++++++++++++---------- R/encharter_chart.R | 18 +++++++++++------- inst/AUTHORS | 1 + man/EncharterBase.Rd | 4 ++++ man/encharter.Rd | 4 ++++ src/pugixml.cpp | 4 ++-- tests/testthat/test-axis_logic.R | 39 +++++++++++++++++++++++++++++++++++++++ 10 files changed, 85 insertions(+), 30 deletions(-)
Title: Bayesian Parameter Estimation and Forecasting for
Epidemiological Models
Description: Methods for Bayesian parameter estimation and forecasting in epidemiological models.
Functions enable model fitting using Bayesian methods and generate forecasts with uncertainty quantification.
Implements approaches described in <doi:10.48550/arXiv.2411.05371> and <doi:10.1002/sim.9164>.
Author: Hamed Karami [aut],
Amanda Bleichrodt [aut],
Ruiyan Luo [aut],
Gerardo Chowell [aut, cre]
Maintainer: Gerardo Chowell <gchowell@gsu.edu>
Diff between BayesianFitForecast versions 1.1.0 dated 2025-08-19 and 1.1.1 dated 2026-08-04
DESCRIPTION | 11 +++--- MD5 | 14 +++++--- NEWS.md |only R/Imports.R |only R/Run_analyzeResults.R | 1 inst/doc/BayesianFitForecast.html | 5 +-- inst/extdata/ode_model.stan | 60 ++++++++++++++++++++------------------ inst/scripts/run_analyzeResults.R | 14 +++----- inst/scripts/stancreator.R | 2 - 9 files changed, 55 insertions(+), 52 deletions(-)
More information about BayesianFitForecast at CRAN
Permanent link
Title: Inference for Functions of Multinomial Parameters
Description: We consider the problem where we observe k vectors (possibly of different lengths), each representing an independent multinomial random vector. For a given function that takes in the concatenated vector of multinomial probabilities and outputs a real number, this is a Monte Carlo estimation procedure of an exact p-value and confidence interval. The resulting inference is valid even in small samples, when the parameter is on the boundary, and when the function is not differentiable at the parameter value, all situations where asymptotic methods and the bootstrap would fail. For more details see Sachs, Fay, and Gabriel (2025) <doi:10.48550/arXiv.2406.19141>.
Author: Michael C Sachs [aut, cre],
Michael P Fay [aut],
Erin E Gabriel [aut],
David B Dahl [ctb] )
Maintainer: Michael C Sachs <sachsmc@gmail.com>
Diff between xactonomial versions 1.2.1 dated 2026-07-30 and 1.2.2 dated 2026-08-04
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ src/Makevars.in | 1 - 4 files changed, 11 insertions(+), 8 deletions(-)
Title: Dynamic Multi-Species Size Spectrum Modelling
Description: A set of classes and methods to set up and run multi-species, trait
based and community size spectrum ecological models, focused on the marine
environment.
Author: Gustav Delius [cre, aut, cph] ,
Finlay Scott [aut, cph],
Julia Blanchard [aut, cph] ,
Ken Andersen [aut, cph] ,
Richard Southwell [ctb, cph]
Maintainer: Gustav Delius <gustav.delius@york.ac.uk>
Diff between mizer versions 3.2.0 dated 2026-07-19 and 3.2.1 dated 2026-08-04
mizer-3.2.0/mizer/tests/testthat/Rplots.pdf |only mizer-3.2.1/mizer/DESCRIPTION | 6 mizer-3.2.1/mizer/MD5 | 31 mizer-3.2.1/mizer/NAMESPACE | 8 mizer-3.2.1/mizer/NEWS.md | 105 +++ mizer-3.2.1/mizer/R/helpers.R | 14 mizer-3.2.1/mizer/R/matchGrowth.R | 13 mizer-3.2.1/mizer/R/setFishing.R | 21 mizer-3.2.1/mizer/R/species_params.R | 420 ++++++++++-- mizer-3.2.1/mizer/R/zzz.R | 27 mizer-3.2.1/mizer/man/print.mizer_plot.Rd |only mizer-3.2.1/mizer/man/record_given_species_params.Rd |only mizer-3.2.1/mizer/man/species_params.Rd | 53 + mizer-3.2.1/mizer/tests/testthat/test-matchGrowth.R | 18 mizer-3.2.1/mizer/tests/testthat/test-setFishing.R | 14 mizer-3.2.1/mizer/tests/testthat/test-species_params.R | 439 ++++++++++++- mizer-3.2.1/mizer/tests/testthat/test-validSpeciesParams.R | 9 mizer-3.2.1/mizer/tests/testthat/test-zzz.R | 24 18 files changed, 1046 insertions(+), 156 deletions(-)
Title: Bayesian Longitudinal Regularized Quantile Mixed Model
Description: With high-dimensional omics features, repeated measure ANOVA leads to longitudinal gene-environment interaction studies that have intra-cluster correlations, outlying observations and structured sparsity arising from the ANOVA design. In this package, we have developed robust sparse Bayesian mixed effect models tailored for the above studies (Fan et al. (2025) <doi:10.1093/jrsssc/qlaf027>). An efficient Gibbs sampler has been developed to facilitate fast computation. The Markov chain Monte Carlo algorithms of the proposed and alternative methods are efficiently implemented in 'C++'. The development of this software package and the associated statistical methods have been partially supported by an Innovative Research Award from Johnson Cancer Research Center, Kansas State University.
Author: Kun Fan [aut, cre],
Shejuty Devnath [aut],
Cen Wu [aut]
Maintainer: Kun Fan <fzt0428@gmail.com>
Diff between mixedBayes versions 0.2.5 dated 2026-04-23 and 0.2.6 dated 2026-08-04
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/mixedBayes-package.R | 6 ++++++ build/partial.rdb |binary man/mixedBayes-package.Rd | 6 ++++++ 6 files changed, 26 insertions(+), 10 deletions(-)
Title: Collection of Utility Functions for Data Analysis and Computing
Description: Provides utility functions for data analysis and computing. Includes functions for logging, parallel processing, and other computational tasks to streamline workflows.
Author: Meng Xu [aut, cre] ,
Haoliang Zhu [aut]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between thisutils versions 0.4.7 dated 2026-05-24 and 0.4.9 dated 2026-08-04
thisutils-0.4.7/thisutils/tests/testthat/test-package-startup.R |only thisutils-0.4.9/thisutils/DESCRIPTION | 16 thisutils-0.4.9/thisutils/MD5 | 52 thisutils-0.4.9/thisutils/NAMESPACE | 6 thisutils-0.4.9/thisutils/NEWS.md | 24 thisutils-0.4.9/thisutils/R/BiocNeighborsKNN.R |only thisutils-0.4.9/thisutils/R/ClassificationMetrics.R |only thisutils-0.4.9/thisutils/R/MatrixTopK.R |only thisutils-0.4.9/thisutils/R/RcppExports.R | 12 thisutils-0.4.9/thisutils/R/log_message.R | 10 thisutils-0.4.9/thisutils/R/package_management.R | 406 +++- thisutils-0.4.9/thisutils/R/parallelize_fun.R | 860 +++++++--- thisutils-0.4.9/thisutils/R/row_variance.R |only thisutils-0.4.9/thisutils/README.md | 2 thisutils-0.4.9/thisutils/inst/include |only thisutils-0.4.9/thisutils/inst/python |only thisutils-0.4.9/thisutils/man/check_r.Rd | 33 thisutils-0.4.9/thisutils/man/classification_metrics_compute.Rd |only thisutils-0.4.9/thisutils/man/fast_row_vars.Rd |only thisutils-0.4.9/thisutils/man/filter_nonzero_variance_features.Rd |only thisutils-0.4.9/thisutils/man/log_message.Rd | 2 thisutils-0.4.9/thisutils/man/parallelize_fun.Rd | 27 thisutils-0.4.9/thisutils/man/run_biocneighbors_knn.Rd |only thisutils-0.4.9/thisutils/man/run_dense_topk_by_column.Rd |only thisutils-0.4.9/thisutils/man/run_sparse_topk_by_column.Rd |only thisutils-0.4.9/thisutils/src/ClassificationMetrics.cpp |only thisutils-0.4.9/thisutils/src/MatrixTopK.cpp |only thisutils-0.4.9/thisutils/src/RcppExports.cpp | 43 thisutils-0.4.9/thisutils/tests/testthat/test-biocneighbors-knn.R |only thisutils-0.4.9/thisutils/tests/testthat/test-classification-metrics.R |only thisutils-0.4.9/thisutils/tests/testthat/test-matrix-topk.R |only thisutils-0.4.9/thisutils/tests/testthat/test-package-management.R |only thisutils-0.4.9/thisutils/tests/testthat/test-parallelize_fun.R | 819 +++++++++ thisutils-0.4.9/thisutils/tests/testthat/test-row-variance.R |only 34 files changed, 2007 insertions(+), 305 deletions(-)
Title: Spectral Preprocessing and Chemometric Calibration of NIR
Sensors
Description: Provides tools to build quantitative chemometric models and
applications for near-infrared (NIR) sensors. Chemometric regression
models are based on partial least squares regression as described by
Wold (1975) <doi:10.1016/B978-0-12-103950-9.50017-4> and modified
partial least squares regression as described by Shenk and Westerhaus
(1991) <doi:10.2135/cropsci1991.0011183X003100020049x>, with further
discussion by Westerhaus (2014) <doi:10.1255/nirn.1492>.
Author: Leonardo Ramirez-Lopez [aut, cre] ,
Claudio Orellano [aut] ,
Nicolae Cudlenco [aut] ,
Mai Said [aut] ,
Mohamed Abushosha [aut],
Marcal Plans [aut]
Maintainer: Leonardo Ramirez-Lopez <ramirez-lopez.l@buchi.com>
Diff between proximetricsR versions 0.6.5 dated 2026-07-17 and 0.7.0 dated 2026-08-04
DESCRIPTION | 17 LICENSE | 2 MD5 | 81 NAMESPACE | 1 NEWS | 10 R/AAA.R | 11 R/calibrate_models.R | 8 R/plot.spectral_model.R | 71 R/proximate_read_data.R | 57 R/proxiscout_read_data.R | 188 - R/proxiscout_write_model_info.R |only R/write_rtf.R | 60 README.md | 8 build/stage23.rdb |binary inst/CITATION | 2 inst/doc/aa-intro.html | 4 inst/doc/ab-pre-processing-recipes.html | 4 inst/doc/ac-mathematical-overview-of-regression-algorithms.html | 4 inst/doc/ad-proximate-building-applications.R | 21 inst/doc/ad-proximate-building-applications.html | 27 inst/doc/ad-proximate-building-applications.qmd | 21 inst/doc/ae-proxiscout-building-applications.html | 4 inst/doc/af-proximate-structure-of-the-applications.html | 6 inst/doc/ag-proxiscout-structure-of-the-applications.html | 4 inst/doc/ah-read-and-recalibrate-applications.html | 4 inst/figure_xls.qmd |only inst/logo.R | 99 inst/model_plot_template.qmd | 1484 ++++++---- inst/zebra_handdrawn-wb.png |only man/figures/logo.png |binary man/plot.spectral_model.Rd | 35 man/proximate_read_data.Rd | 6 man/proximetricsR-package.Rd | 7 man/proxiscout_read_data.Rd | 46 man/proxiscout_write_model_info.Rd |only tests/testthat/_snaps/write_nax/test_nax.CBD.rtf | 34 tests/testthat/_snaps/write_nax/test_nax.CBDA.rtf | 22 tests/testthat/_snaps/write_nax/test_nax1.THC.rtf | 36 tests/testthat/_snaps/write_rtf/test_rtf1.THC.rtf | 140 tests/testthat/test-plot.spectral_model.R | 1 tests/testthat/test-proxiscout_read_data.R | 152 + tests/testthat/test-proxiscout_write_model_info.R |only tests/testthat/test-write_rtf.R | 2 vignettes/ad-proximate-building-applications.qmd | 21 44 files changed, 1878 insertions(+), 822 deletions(-)
Title: Lightweight Toolkit for Messaging, Concurrency and the Web
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ.
A toolkit for messaging, concurrency and the web. High-performance
socket messaging over in-process, IPC, TCP, WebSocket and secure TLS
transports implements 'Scalability Protocols', a standard for common
communications patterns including publish/subscribe, request/reply and
survey. A threaded concurrency framework with intuitive 'aio' objects
that resolve automatically upon completion of asynchronous operations,
and synchronisation primitives that allow R to wait on events
signalled by concurrent threads. A unified HTTP server hosting REST
endpoints, WebSocket connections and streaming on a single port, with
a built-in HTTP client.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd] ,
Hibiki AI Limited [cph],
Staysail Systems, Inc. [cph] ,
Capitar IT Group BV [cph] ,
The Mbed TLS Contributors [cph] ,
Pierre L'Ecuyer [cph] ,
sakura authors [cph] ,
R Consortium [fnd]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between nanonext versions 1.10.1 dated 2026-07-09 and 1.10.2 dated 2026-08-04
DESCRIPTION | 8 MD5 | 44 - NEWS.md | 10 R/dispatcher.R | 6 R/ncurl.R | 14 build/vignette.rds |binary inst/doc/nanonext.html | 20 inst/doc/v01-messaging.html | 20 inst/doc/v02-protocols.html | 20 inst/doc/v03-configuration.html | 20 inst/doc/v04-web.html | 20 man/dot-dispatcher_start.Rd | 4 man/ncurl.Rd | 14 src/aio.c | 58 - src/dispatcher.c | 1077 ++++++++++++++++++------------ src/init.c | 2 src/nanonext.h | 3 src/nng/src/core/msgqueue.c | 2 src/nng/src/supplemental/tls/tls_common.c | 3 src/server.c | 12 src/sync.c | 4 tests/tests.R | 70 + tools/patch_nng.sh | 42 + 23 files changed, 933 insertions(+), 540 deletions(-)
Title: MRI Tissue Classification
Description: Implements various methods for tissue classification in magnetic
resonance (MR) images of the brain, including normal mixture models
and hidden Markov normal mixture models, as outlined in Feng &
Tierney (2011) <doi:10.18637/jss.v044.i07>. These methods allow a
structural MR image to be classified into gray matter, white matter
and cerebrospinal fluid tissue types.
Author: Dai Feng [aut],
Luke Tierney [aut],
Jon Clayden [cre, aut]
Maintainer: Jon Clayden <code@clayden.org>
Diff between mritc versions 0.6.0 dated 2026-07-24 and 0.6.1 dated 2026-08-04
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 5 +++++ src/registerDynamicSymbol.c | 4 ++++ src/updateDistanceUnit_omp.c | 4 ++-- 5 files changed, 19 insertions(+), 10 deletions(-)
Title: Inference on Granger-Causality in the Frequency Domain
Description: Implements unconditional and conditional Granger-causality spectra in the frequency domain, bootstrap inference for both spectra and their difference, and the Breitung-Candelon parametric tests. The bootstrap procedures follow Farnè and Montanari (2022) <doi:10.1007/s10614-021-10112-x>.
Author: Matteo Farne [aut, cre],
Angela Montanari [aut]
Maintainer: Matteo Farne <matteo.farne@unibo.it>
Diff between grangers versions 0.1.0 dated 2019-06-03 and 0.1.1 dated 2026-08-04
DESCRIPTION | 26 ++++++++++++++++------- MD5 | 37 +++++++++++++++++---------------- R/Granger_conditional.R | 6 ++--- R/Granger_inference_conditional.R | 12 +++++----- R/Granger_inference_difference.R | 18 ++++++++-------- R/Granger_inference_unconditional.R | 12 +++++----- R/Granger_unconditional.R | 6 ++--- R/bc_test_cond.R | 6 ++--- R/bc_test_uncond.R | 6 ++--- R/euro_area_indicators.R | 6 ++--- README.md |only build |only inst |only man/Granger.conditional.Rd | 19 ++++++++++++---- man/Granger.inference.conditional.Rd | 29 +++++++++++++++++-------- man/Granger.inference.difference.Rd | 36 +++++++++++++++++++++----------- man/Granger.inference.unconditional.Rd | 26 ++++++++++++++++------- man/Granger.unconditional.Rd | 17 ++++++++++----- man/bc_test_cond.Rd | 19 ++++++++++++---- man/bc_test_uncond.Rd | 18 +++++++++++----- man/euro_area_indicators.Rd | 10 +++++--- 21 files changed, 195 insertions(+), 114 deletions(-)
Title: Parse and Manipulate R Code
Description: Parsing R code is key to build tools such as linters and stylers.
This package provides a binding to the 'Rust' crate 'ast-grep' so that one
can parse and explore R code.
Author: Etienne Bacher [aut, cre, cph]
Maintainer: Etienne Bacher <etienne.bacher@protonmail.com>
Diff between astgrepr versions 0.1.1 dated 2025-06-07 and 0.1.2 dated 2026-08-04
DESCRIPTION | 10 ++--- MD5 | 32 +++++++++--------- NEWS.md | 4 ++ R/rule.R | 2 - README.md | 24 +++++++++----- build/vignette.rds |binary inst/doc/astgrepr.R | 8 ++-- inst/doc/astgrepr.Rmd | 40 +++++++++++------------ inst/doc/astgrepr.html | 13 ++++--- man/pattern_rule.Rd | 2 - src/Makevars.win.in | 2 - src/rust/Cargo.lock | 21 +++--------- src/rust/Cargo.toml | 2 - src/rust/src/language.rs | 80 +++++++++++++++++++++++------------------------ src/rust/vendor.tar.xz |binary tools/config.R | 12 +++++++ vignettes/astgrepr.Rmd | 40 +++++++++++------------ 17 files changed, 155 insertions(+), 137 deletions(-)
Title: Creating Composite Plots using 'aplot'
Description: Many complex plots are actually composite plots, such as 'oncoplot', 'funkyheatmap', 'upsetplot', etc. We can produce subplots using 'ggplot2' and combine them to create composite plots using 'aplot'. In this way, it is easy to customize these complex plots, by adding, deleting or modifying subplots in the final plot. This package provides a set of utilities to help users to create subplots and complex plots.
Author: Guangchuang Yu [aut, cre] ,
Shuangbin Xu [ctb] ,
Chun-Hui Gao [ctb] ,
Shensuo Li [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between aplotExtra versions 0.0.5 dated 2026-07-13 and 0.0.6 dated 2026-08-04
DESCRIPTION | 6 +-- MD5 | 9 +++-- NAMESPACE | 1 NEWS.md | 5 +++ R/oncoplot.r | 75 ++++++++++++++++++++++++++++++++------------- man/oncoplot_components.Rd |only 6 files changed, 68 insertions(+), 28 deletions(-)
Title: Toolkit for Reduced Form and Structural Smooth Transition Vector
Autoregressive Models
Description: Penalized and non-penalized maximum likelihood estimation of smooth
transition vector autoregressive models with various types of transition weight
functions, conditional distributions, and identification methods. Constrained
estimation with various types of constraints is available. Residual based
model diagnostics, forecasting, simulations, counterfactual analysis, and
computation of impulse response functions, generalized impulse response functions,
generalized forecast error variance decompositions, as well as historical
decompositions. See
Heather Anderson, Farshid Vahid (1998) <doi:10.1016/S0304-4076(97)00076-6>,
Helmut Lütkepohl, Aleksei Netšunajev (2017) <doi:10.1016/j.jedc.2017.09.001>,
Markku Lanne, Savi Virolainen (2025) <doi:10.1016/j.jedc.2025.105162>,
Savi Virolainen (2026) <doi:10.1080/07474938.2026.2673986>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@gmail.com>
Diff between sstvars versions 1.2.4 dated 2026-05-29 and 1.2.5 dated 2026-08-04
DESCRIPTION | 12 ++--- MD5 | 88 ++++++++++++++++++++--------------------- NEWS.md | 5 ++ R/LSest.R | 4 - R/MAINest.R | 4 - R/STVARconstruction.R | 4 - R/argumentChecks.R | 4 - R/data.R | 4 - R/distributionFuns.R | 4 - R/jointSpectralRadius.R | 4 - R/loglikelihood.R | 4 - R/moreEst.R | 4 - README.md | 6 +- inst/doc/sstvars-vignette.pdf |binary man/STVAR.Rd | 4 - man/alt_stvar.Rd | 4 - man/bound_JSR.Rd | 4 - man/bound_jsr_G.Rd | 4 - man/change_regime.Rd | 4 - man/check_params.Rd | 4 - man/diagnostic_plot.Rd | 4 - man/estim_NLS.Rd | 4 - man/fitSSTVAR.Rd | 4 - man/fitSTVAR.Rd | 4 - man/fitbsSSTVAR.Rd | 4 - man/get_alpha_mt.Rd | 4 - man/get_residuals.Rd | 4 - man/in_paramspace.Rd | 4 - man/iterate_more.Rd | 4 - man/loglikelihood.Rd | 4 - man/n_params.Rd | 4 - man/plot_struct_shocks.Rd | 4 - man/predict.stvar.Rd | 4 - man/profile_logliks.Rd | 4 - man/reform_constrained_pars.Rd | 4 - man/regime_distance.Rd | 4 - man/simulate.stvar.Rd | 4 - man/simulate_from_regime.Rd | 4 - man/simulate_stvar_int.Rd | 4 - man/sstvars-package.Rd | 4 - man/stand_t_dens.Rd | 4 - man/standard_errors.Rd | 4 - man/swap_parametrization.Rd | 4 - man/usacpu.Rd | 4 - vignettes/refs.bib | 6 ++ 45 files changed, 141 insertions(+), 132 deletions(-)
Title: Robust Estimation for Multi-Study High-Dimensional Elliptical
Factor Analytics
Description: We introduce a multi-study high-dimensional factor analysis toolbox 'MultiEFM' based on the elliptical factor model framework, which learns latent heterogeneous features and accounts for cross-study variation among sources. It provides robust estimation algorithms for heterogeneous datasets, particularly tailored for multi-study RNA sequencing arrays and complex spatial multi-omics layers. The package implements highly efficient initialization strategies, identifiability constraints alignment, and computationally scalable parameter estimation paradigms.
Author: Ruihan Zhang [aut, cre],
Wei Liu [aut]
Maintainer: Ruihan Zhang <ruihanzhang6166@gmail.com>
Diff between MultiEFM versions 0.1.3 dated 2026-07-28 and 0.1.4 dated 2026-08-04
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/main.R | 10 +++++----- inst/doc/simu_high_dim.html | 10 +++++----- inst/doc/simu_low_dim.html | 10 +++++----- 5 files changed, 23 insertions(+), 23 deletions(-)
Title: Multi-Armed Qini
Description: Fits generalized Qini curves for evaluating treatment allocation
policies with one or more mutually exclusive treatment arms. Given
estimated conditional treatment effects and treatment costs, 'maq'
computes the optimal treatment allocation over a range of budget levels
and estimates the resulting policy value using doubly robust or
inverse-propensity weighted scores. The underlying optimization exploits
the linear multiple-choice knapsack structure of the allocation problem
to compute the full solution path efficiently.
For details see Sverdrup, Wu, Athey, and Wager (2025) <doi:10.1080/10618600.2024.2418820>.
Author: Erik Sverdrup [aut, cre],
Han Wu [aut],
Susan Athey [aut],
Stefan Wager [aut]
Maintainer: Erik Sverdrup <erik.sverdrup@gmail.com>
Diff between maq versions 0.6.0 dated 2025-04-14 and 0.6.1 dated 2026-08-04
DESCRIPTION | 24 +++++++++++++++--------- MD5 | 14 +++++++------- R/get_aipw_scores.R | 2 +- R/maq.R | 25 ++++++++++++++----------- R/plot.R | 15 +++++++++------ man/get_aipw_scores.Rd | 2 +- man/maq.Rd | 25 ++++++++++++++----------- man/plot.maq.Rd | 15 +++++++++------ 8 files changed, 70 insertions(+), 52 deletions(-)
Title: Kernel Smoothing
Description: Kernel smoothers for univariate and multivariate data, with comprehensive visualisation and bandwidth selection capabilities, including for densities, density derivatives, cumulative distributions, clustering, classification, density ridges, significant modal regions, and two-sample hypothesis tests. Chacon & Duong (2018) <doi:10.1201/9780429485572>.
Author: Tarn Duong [aut, cre] ,
Matt Wand [ctb] ,
Jose Chacon [ctb] ,
Artur Gramacki [ctb]
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between ks versions 1.15.2 dated 2026-05-09 and 1.15.3 dated 2026-08-04
CHANGELOG | 4 ++ DESCRIPTION | 15 +++---- MD5 | 94 +++++++++++++++++++++++++------------------------- R/kcopula.R | 2 - R/kdde.R | 4 +- R/kde-boundary.R | 2 - R/kde.R | 3 - R/kfs.R | 2 - README.md | 24 +++++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/ks.Rmd | 4 +- inst/doc/ks.html | 6 +-- inst/pkgdown.yml | 2 - man/Hbcv.Rd | 10 ++--- man/Hlscv.Rd | 4 +- man/Hnm.Rd | 6 +-- man/Hns.Rd | 4 +- man/Hpi.Rd | 10 ++--- man/Hscv.Rd | 6 +-- man/as.kde.Rd | 4 +- man/binning.Rd | 2 - man/hsct.Rd | 2 - man/ise.mixt.Rd | 2 - man/kcde.Rd | 2 - man/kcopula.Rd | 2 - man/kdcde.Rd | 7 +-- man/kdde.Rd | 2 - man/kde.boundary.Rd | 8 ++-- man/kde.local.test.Rd | 8 ++-- man/kde.test.Rd | 2 - man/kdr.Rd | 8 ++-- man/kfe.Rd | 4 +- man/kfs.Rd | 12 +++--- man/kms.Rd | 10 ++--- man/kroc.Rd | 4 +- man/ks-package.Rd | 15 ++++--- man/ksupp.Rd | 4 +- man/plot.kcde.Rd | 4 +- man/plot.kda.Rd | 4 +- man/plot.kdde.Rd | 4 +- man/plot.kde.Rd | 6 +-- man/plotmixt.Rd | 4 +- man/quake.Rd | 2 - man/tempb.Rd | 5 -- man/unicef.Rd | 2 - man/vkde.Rd | 8 ++-- vignettes/ks.Rmd | 4 +- 48 files changed, 173 insertions(+), 170 deletions(-)
Title: Induced Priors in Bayesian Mixture Models
Description: Computes implicitly induced quantities from prior/hyperparameter
specifications of three Mixtures of Finite Mixtures models: Dirichlet
Process Mixtures (DPMs; Escobar and West (1995)
<doi:10.1080/01621459.1995.10476550>), Static Mixtures of Finite Mixtures
(Static MFMs; Miller and Harrison (2018)
<doi:10.1080/01621459.2016.1255636>), and Dynamic Mixtures of Finite
Mixtures (Dynamic MFMs; Frühwirth-Schnatter, Malsiner-Walli and Grün (2021)
<doi:10.1214/21-ba1294>). For methodological details, please refer to
Greve, Grün, Malsiner-Walli and Frühwirth-Schnatter (2022)
<doi:10.1111/anzs.12350>) as well as the package vignette.
Author: Jan Greve [aut, cre],
Bettina Gruen [ctb] ,
Gertraud Malsiner-Walli [ctb] ,
Sylvia Fruehwirth-Schnatter [ctb]
Maintainer: Jan Greve <jangre@uio.no>
This is a re-admission after prior archival of version 1.0.0 dated 2021-02-11
Diff between fipp versions 1.0.0 dated 2021-02-11 and 1.0.1 dated 2026-08-04
fipp-1.0.0/fipp/man/figures |only fipp-1.0.1/fipp/DESCRIPTION | 34 - fipp-1.0.1/fipp/MD5 | 28 - fipp-1.0.1/fipp/NEWS.md | 7 fipp-1.0.1/fipp/R/fipp.R | 38 - fipp-1.0.1/fipp/R/utils.R | 7 fipp-1.0.1/fipp/build/partial.rdb |only fipp-1.0.1/fipp/build/vignette.rds |binary fipp-1.0.1/fipp/inst/doc/fippCrashCourse.R | 18 fipp-1.0.1/fipp/inst/doc/fippCrashCourse.html | 718 +++++++++++++++++--------- fipp-1.0.1/fipp/man/dbnb.Rd | 7 fipp-1.0.1/fipp/man/fipp.Rd | 19 fipp-1.0.1/fipp/man/nClusters.Rd | 19 fipp-1.0.1/fipp/src/Makevars | 1 fipp-1.0.1/fipp/src/Makevars.win | 1 fipp-1.0.1/fipp/src/RcppExports.cpp | 5 16 files changed, 583 insertions(+), 319 deletions(-)
Title: Financial Instrument Modeling Infrastructure
Description: Provides infrastructure for defining, storing, and managing
financial instrument metadata independently of market data sources.
Models instrument identities, contract specifications, identifiers, and
relationships among financial instruments, including currencies,
equities, funds, bonds, futures, options, spreads, exchange rates, and
synthetic instruments. Supports reusable instrument definitions for
research, portfolio management, trading, and quantitative finance
applications.
Author: Peter Carl [aut],
Brian G. Peterson [aut],
Garrett See [aut],
Ross Bennett [aut],
Justin M. Shea [cre, ctb]
Maintainer: Justin M. Shea <jshea01@uic.edu>
This is a re-admission after prior archival of version 1.3.1 dated 2018-01-10
Diff between FinancialInstrument versions 1.3.1 dated 2018-01-10 and 1.4.1 dated 2026-08-04
FinancialInstrument-1.3.1/FinancialInstrument/data/currencies.csv.gz |only FinancialInstrument-1.3.1/FinancialInstrument/data/future_series.csv.gz |only FinancialInstrument-1.3.1/FinancialInstrument/data/root_contracts.csv.gz |only FinancialInstrument-1.3.1/FinancialInstrument/inst/tests |only FinancialInstrument-1.3.1/FinancialInstrument/tests/test-all.R |only FinancialInstrument-1.4.1/FinancialInstrument/DESCRIPTION | 73 FinancialInstrument-1.4.1/FinancialInstrument/MD5 | 181 +- FinancialInstrument-1.4.1/FinancialInstrument/NAMESPACE | 3 FinancialInstrument-1.4.1/FinancialInstrument/NEWS | 122 + FinancialInstrument-1.4.1/FinancialInstrument/R/CompareInstrumentFiles.R | 84 FinancialInstrument-1.4.1/FinancialInstrument/R/FinancialInstrument-package.R | 373 ---- FinancialInstrument-1.4.1/FinancialInstrument/R/FindCommonInstrumentAttributes.R | 15 FinancialInstrument-1.4.1/FinancialInstrument/R/Tick2Sec.R | 178 +- FinancialInstrument-1.4.1/FinancialInstrument/R/all.equal.instrument.R | 49 FinancialInstrument-1.4.1/FinancialInstrument/R/build_symbols.R | 33 FinancialInstrument-1.4.1/FinancialInstrument/R/expires.R | 133 - FinancialInstrument-1.4.1/FinancialInstrument/R/find.instrument.R | 68 FinancialInstrument-1.4.1/FinancialInstrument/R/instrument.R | 849 +++++----- FinancialInstrument-1.4.1/FinancialInstrument/R/load.instruments.R | 328 ++- FinancialInstrument-1.4.1/FinancialInstrument/R/ls_by_currency.R | 250 +- FinancialInstrument-1.4.1/FinancialInstrument/R/ls_instruments.R | 177 -- FinancialInstrument-1.4.1/FinancialInstrument/R/parse_id.R | 162 - FinancialInstrument-1.4.1/FinancialInstrument/R/redenominate.R | 103 - FinancialInstrument-1.4.1/FinancialInstrument/R/saveInstruments.R | 174 +- FinancialInstrument-1.4.1/FinancialInstrument/R/saveSymbols.R | 75 FinancialInstrument-1.4.1/FinancialInstrument/R/splice.R |only FinancialInstrument-1.4.1/FinancialInstrument/R/splooth.R |only FinancialInstrument-1.4.1/FinancialInstrument/R/update_instruments.iShares.R | 40 FinancialInstrument-1.4.1/FinancialInstrument/R/update_instruments.morningstar.R | 24 FinancialInstrument-1.4.1/FinancialInstrument/R/update_instruments.yahoo.R | 179 +- FinancialInstrument-1.4.1/FinancialInstrument/R/utils_quantmod.R |only FinancialInstrument-1.4.1/FinancialInstrument/R/volep.R | 7 FinancialInstrument-1.4.1/FinancialInstrument/README.md |only FinancialInstrument-1.4.1/FinancialInstrument/data/currencies.csv |only FinancialInstrument-1.4.1/FinancialInstrument/data/future_series.csv |only FinancialInstrument-1.4.1/FinancialInstrument/data/root_contracts.csv |only FinancialInstrument-1.4.1/FinancialInstrument/inst/tinytest |only FinancialInstrument-1.4.1/FinancialInstrument/man/C2M.Rd | 1 FinancialInstrument-1.4.1/FinancialInstrument/man/CompareInstrumentFiles.Rd | 80 FinancialInstrument-1.4.1/FinancialInstrument/man/FinancialInstrument-package.Rd | 294 +-- FinancialInstrument-1.4.1/FinancialInstrument/man/FindCommonInstrumentAttributes.Rd | 16 FinancialInstrument-1.4.1/FinancialInstrument/man/Tick2Sec.Rd | 56 FinancialInstrument-1.4.1/FinancialInstrument/man/add.defined.by.Rd | 14 FinancialInstrument-1.4.1/FinancialInstrument/man/add.identifier.Rd | 4 FinancialInstrument-1.4.1/FinancialInstrument/man/all.equal.instrument.Rd | 22 FinancialInstrument-1.4.1/FinancialInstrument/man/buildRatio.Rd | 6 FinancialInstrument-1.4.1/FinancialInstrument/man/buildSpread.Rd | 20 FinancialInstrument-1.4.1/FinancialInstrument/man/build_series_symbols.Rd | 7 FinancialInstrument-1.4.1/FinancialInstrument/man/build_spread_symbols.Rd | 26 FinancialInstrument-1.4.1/FinancialInstrument/man/exchange_rate.Rd | 47 FinancialInstrument-1.4.1/FinancialInstrument/man/expires.Rd | 29 FinancialInstrument-1.4.1/FinancialInstrument/man/expires.character.Rd | 24 FinancialInstrument-1.4.1/FinancialInstrument/man/expires.instrument.Rd | 16 FinancialInstrument-1.4.1/FinancialInstrument/man/expires.spread.Rd | 21 FinancialInstrument-1.4.1/FinancialInstrument/man/expires.xts.Rd | 18 FinancialInstrument-1.4.1/FinancialInstrument/man/find.instrument.Rd | 71 FinancialInstrument-1.4.1/FinancialInstrument/man/fn_SpreadBuilder.Rd | 20 FinancialInstrument-1.4.1/FinancialInstrument/man/getInstrument.Rd | 29 FinancialInstrument-1.4.1/FinancialInstrument/man/getSymbols.FI.Rd | 111 - FinancialInstrument-1.4.1/FinancialInstrument/man/get_rate.Rd | 10 FinancialInstrument-1.4.1/FinancialInstrument/man/instrument.Rd | 171 +- FinancialInstrument-1.4.1/FinancialInstrument/man/instrument.auto.Rd | 72 FinancialInstrument-1.4.1/FinancialInstrument/man/instrument_attr.Rd | 24 FinancialInstrument-1.4.1/FinancialInstrument/man/is.currency.Rd | 4 FinancialInstrument-1.4.1/FinancialInstrument/man/is.currency.name.Rd | 8 FinancialInstrument-1.4.1/FinancialInstrument/man/is.instrument.Rd | 4 FinancialInstrument-1.4.1/FinancialInstrument/man/is.instrument.name.Rd | 4 FinancialInstrument-1.4.1/FinancialInstrument/man/load.instruments.Rd | 65 FinancialInstrument-1.4.1/FinancialInstrument/man/ls_by_currency.Rd | 102 - FinancialInstrument-1.4.1/FinancialInstrument/man/ls_by_expiry.Rd | 1 FinancialInstrument-1.4.1/FinancialInstrument/man/ls_expiries.Rd | 17 FinancialInstrument-1.4.1/FinancialInstrument/man/ls_instruments.Rd | 53 FinancialInstrument-1.4.1/FinancialInstrument/man/ls_instruments_by.Rd | 3 FinancialInstrument-1.4.1/FinancialInstrument/man/next.future_id.Rd | 8 FinancialInstrument-1.4.1/FinancialInstrument/man/option_series.yahoo.Rd | 33 FinancialInstrument-1.4.1/FinancialInstrument/man/parse_id.Rd | 14 FinancialInstrument-1.4.1/FinancialInstrument/man/parse_suffix.Rd | 7 FinancialInstrument-1.4.1/FinancialInstrument/man/print.id.list.Rd | 3 FinancialInstrument-1.4.1/FinancialInstrument/man/print.instrument.Rd | 3 FinancialInstrument-1.4.1/FinancialInstrument/man/print.suffix.list.Rd | 3 FinancialInstrument-1.4.1/FinancialInstrument/man/redenominate.Rd | 16 FinancialInstrument-1.4.1/FinancialInstrument/man/saveInstruments.Rd | 63 FinancialInstrument-1.4.1/FinancialInstrument/man/saveSymbols.days.Rd | 57 FinancialInstrument-1.4.1/FinancialInstrument/man/series_instrument.Rd | 83 FinancialInstrument-1.4.1/FinancialInstrument/man/setSymbolLookup.FI.Rd | 40 FinancialInstrument-1.4.1/FinancialInstrument/man/sort.instrument.Rd | 4 FinancialInstrument-1.4.1/FinancialInstrument/man/synthetic.instrument.Rd | 101 - FinancialInstrument-1.4.1/FinancialInstrument/man/update_instruments.iShares.Rd | 18 FinancialInstrument-1.4.1/FinancialInstrument/man/update_instruments.instrument.Rd | 35 FinancialInstrument-1.4.1/FinancialInstrument/man/update_instruments.masterDATA.Rd | 32 FinancialInstrument-1.4.1/FinancialInstrument/man/update_instruments.morningstar.Rd | 15 FinancialInstrument-1.4.1/FinancialInstrument/man/update_instruments.yahoo.Rd | 16 FinancialInstrument-1.4.1/FinancialInstrument/man/volep.Rd | 5 FinancialInstrument-1.4.1/FinancialInstrument/tests/tinytest.R |only 94 files changed, 3084 insertions(+), 2622 deletions(-)
More information about FinancialInstrument at CRAN
Permanent link
Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Description: NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D
biological image data, especially traced neurons. Reads and writes 3D images
in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf
format. Traced neurons can be imported from and written to SWC and 'Amira'
LineSet and SkeletonGraph formats. These data can then be visualised in 3D
via 'rgl', manipulated including applying calculated registrations, e.g.
using the 'CMTK' registration suite, and analysed. There is also a simple
representation for neurons that have been subjected to 3D skeletonisation
but not formally traced; this allows morphological comparison between
neurons including searches and clustering (via the 'nat.nblast' extension
package).
Author: Gregory Jefferis [aut, cre] ,
James Manton [aut] ,
Dominik Krzeminski [ctb]
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Diff between nat versions 1.8.25 dated 2025-08-18 and 1.8.26 dated 2026-08-04
DESCRIPTION | 6 - MD5 | 42 ++++---- NEWS | 5 + R/neuron-io-neuroml.R | 2 R/neuron-io.R | 4 R/neuronlistfh.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Installation.html | 9 + inst/doc/neurons-intro.R | 38 +++---- inst/doc/neurons-intro.html | 168 ++++++++++++++++++----------------- tests/testthat/test-cmtk.R | 14 +- tests/testthat/test-cmtk_io.R | 2 tests/testthat/test-dotprops.R | 2 tests/testthat/test-hxsurf.R | 4 tests/testthat/test-im3d.R | 6 - tests/testthat/test-landmarks-io.R | 2 tests/testthat/test-neuron-fiji-io.R | 4 tests/testthat/test-neuron-io.R | 20 ++-- tests/testthat/test-neuron.R | 2 tests/testthat/test-ngraph.R | 4 tests/testthat/test-xformimage.R | 16 +-- 22 files changed, 183 insertions(+), 169 deletions(-)
Title: Testing, Monitoring, and Dating Structural Changes
Description: Testing, monitoring and dating structural changes in (linear)
regression models. strucchange features tests/methods from
the generalized fluctuation test framework as well as from
the F test (Chow test) framework. This includes methods to
fit, plot and test fluctuation processes (e.g., CUSUM, MOSUM,
recursive/moving estimates) and F statistics, respectively.
It is possible to monitor incoming data online using
fluctuation processes.
Finally, the breakpoints in regression models with structural
changes can be estimated together with confidence intervals.
Emphasis is always given to methods for visualizing the data.
Author: Achim Zeileis [aut, cre] ,
Friedrich Leisch [aut] ,
Kurt Hornik [aut] ,
Christian Kleiber [aut] ,
Bruce E. Hansen [ctb],
Edgar C. Merkle [ctb] ,
Nikolaus Umlauf [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between strucchange versions 1.5-4 dated 2024-09-02 and 1.6-0 dated 2026-08-04
strucchange-1.5-4/strucchange/NEWS |only strucchange-1.6-0/strucchange/DESCRIPTION | 45 +++--- strucchange-1.6-0/strucchange/MD5 | 51 +++---- strucchange-1.6-0/strucchange/NEWS.md |only strucchange-1.6-0/strucchange/R/critvals-monitoring.R | 6 strucchange-1.6-0/strucchange/R/critvals.R | 10 - strucchange-1.6-0/strucchange/R/gefp.R | 37 +++-- strucchange-1.6-0/strucchange/R/monitoring.R | 18 +- strucchange-1.6-0/strucchange/R/pvalue.Fstats.R | 8 - strucchange-1.6-0/strucchange/README.md |only strucchange-1.6-0/strucchange/build/partial.rdb |binary strucchange-1.6-0/strucchange/build/vignette.rds |binary strucchange-1.6-0/strucchange/inst/doc/strucchange-intro.R | 2 strucchange-1.6-0/strucchange/inst/doc/strucchange-intro.Rnw | 57 ++++--- strucchange-1.6-0/strucchange/inst/doc/strucchange-intro.pdf |binary strucchange-1.6-0/strucchange/inst/doc/strucchange-seatbelt.R |only strucchange-1.6-0/strucchange/inst/doc/strucchange-seatbelt.Rmd |only strucchange-1.6-0/strucchange/inst/doc/strucchange-seatbelt.html |only strucchange-1.6-0/strucchange/man/GermanM1.Rd | 10 - strucchange-1.6-0/strucchange/man/Grossarl.Rd | 6 strucchange-1.6-0/strucchange/man/USIncExp.Rd | 2 strucchange-1.6-0/strucchange/man/breakpoints.Rd | 4 strucchange-1.6-0/strucchange/man/efp.Rd | 13 - strucchange-1.6-0/strucchange/man/gefp.Rd | 1 strucchange-1.6-0/strucchange/man/plot.efp.Rd | 6 strucchange-1.6-0/strucchange/man/sctest.efp.Rd | 6 strucchange-1.6-0/strucchange/tests/Examples/strucchange-Ex.Rout.save | 2 strucchange-1.6-0/strucchange/vignettes/strucchange-intro.Rnw | 57 ++++--- strucchange-1.6-0/strucchange/vignettes/strucchange-seatbelt.Rmd |only strucchange-1.6-0/strucchange/vignettes/strucchange.bib | 72 ++++++++-- 30 files changed, 243 insertions(+), 170 deletions(-)
Title: Character String Operations and Interpolation, Magic Edition
Description: Performs complex string operations compactly and efficiently. Supports string interpolation jointly with over 50 string operations. Also enhances regular string functions (like grep() and co). See an introduction at <https://lrberge.github.io/stringmagic/>.
Author: Laurent R Berge [aut, cre] ,
Morgan Jacob [ctb]
Maintainer: Laurent R Berge <laurent.berge@u-bordeaux.fr>
Diff between stringmagic versions 1.2.0 dated 2025-04-18 and 1.3.0 dated 2026-08-04
DESCRIPTION | 9 + MD5 | 50 +++++----- NEWS.md | 18 +++ R/AUTO_help.R | 4 R/check.R | 39 +++++--- R/string_magic_doc.R | 15 ++- R/string_magic_main.R | 56 +++++++---- R/string_tools.R | 18 ++- R/to_index.R | 5 - build/vignette.rds |binary inst/doc/guide_customization.R | 4 inst/doc/guide_customization.html | 34 +++---- inst/doc/guide_string_magic.html | 25 ++--- inst/doc/guide_string_tools.html | 5 - inst/doc/ref_operations.R | 10 +- inst/doc/ref_operations.html | 58 +++++++++--- inst/doc/ref_operations.rmd | 22 ++++ inst/doc/ref_regex_flags.html | 5 - inst/doc/ref_regex_logic.html | 5 - inst/doc/ref_string_magic_special_operations.html | 27 ++--- man/cat_magic.Rd | 10 +- man/string_magic.Rd | 15 ++- man/string_magic_alias.Rd | 2 man/string_vec.Rd | 8 + src/to_index.cpp | 104 +++++++++++++--------- vignettes/ref_operations.rmd | 22 ++++ 26 files changed, 377 insertions(+), 193 deletions(-)
Title: Alt String Implementation
Description: Provides an extendable, performant and multithreaded 'alt-string' implementation backed by 'C++' vectors and strings.
Author: Travers Ching [aut, cre, cph],
Phillip Hazel [ctb] ,
Zoltan Herczeg [ctb, cph] ,
University of Cambridge [cph] ,
Tilera Corporation [cph] ,
Yann Collet [ctb, cph] ,
Martin Leitner-Ankerl [ctb, cph]
Maintainer: Travers Ching <traversc@gmail.com>
Diff between stringfish versions 0.19.0 dated 2026-04-21 and 0.19.2 dated 2026-08-04
ChangeLog | 5 ++ DESCRIPTION | 22 +++++--- MD5 | 56 ++++++++++++---------- R/zz_help_files.R | 2 build/vignette.rds |binary inst/doc/vignette.html | 7 +- inst/include/ankerl |only inst/include/rstring_indexer.h | 28 ++--------- inst/include/sf_internal/slice_store.h | 56 +++++++++++----------- inst/include/sf_internal/string_types.h | 80 ++++++++++++++++++++++++-------- inst/include/simple_array |only man/sf_vector.Rd | 2 src/exported_functions/c_sf_paste.h | 4 - src/exported_functions/sf_collapse.h | 6 +- src/exported_functions/sf_compare.h | 2 src/exported_functions/sf_grepl.h | 2 src/exported_functions/sf_gsub.h | 4 - src/exported_functions/sf_iconv.h | 4 - src/exported_functions/sf_match.h | 56 ++++++++++++++++------ src/exported_functions/sf_nchar.h | 2 src/exported_functions/sf_split.h | 2 src/exported_functions/sf_substr.h | 4 - src/sf_altrep/common.h | 5 +- src/sf_altrep/slice_st_altrep.h | 4 - src/sf_encoding_helpers.h | 8 +-- src/sf_functions.cpp | 3 - src/sf_utility.h | 7 ++ vignettes/bench_v3.png |binary 28 files changed, 223 insertions(+), 148 deletions(-)
Title: Species Sensitivity Distribution Data
Description: Reference data sets of species sensitivities to compare the
results of fitting species sensitivity distributions using software
such as 'ssdtools' and 'Burrlioz'. It consists of curated data sets
for individual chemicals from Australian, New Zealand and Canadian
organizations, several data sets from anonymous sources, and larger
uncurated compilations drawn from the ANZTOX, WQBench and EnviroTox
databases. It also includes a data set of the results of fitting
various distributions using different software.
Author: Rebecca Fisher [aut, cre],
Joe Thorley [aut] ,
Ayla Pearson [aut] ,
Carl Schwarz [ctb],
David Fox [ctb]
Maintainer: Rebecca Fisher <R.Fisher@aims.gov.au>
Diff between ssddata versions 1.0.0 dated 2021-11-05 and 2.0.0 dated 2026-08-04
DESCRIPTION | 37 - MD5 | 323 ++++++-- NAMESPACE | 21 NEWS.md | 131 +++ R/aims_aluminium_marine.R | 68 - R/aims_data.R | 83 +- R/aims_gallium_marine.R | 68 - R/aims_molybdenum_marine.R | 68 - R/anon_a.R | 55 - R/anon_b.R | 55 - R/anon_c.R | 55 - R/anon_d.R | 55 - R/anon_data.R | 52 - R/anon_e.R | 55 - R/anzg_alpha_cypermethrin_fresh.R |only R/anzg_aluminium_marine.R |only R/anzg_ametryn_fresh.R |only R/anzg_ammonia_fresh.R |only R/anzg_bisphenol_a_fresh.R |only R/anzg_bisphenol_a_marine.R |only R/anzg_boron_fresh.R |only R/anzg_chlorine_marine.R |only R/anzg_chromium_III_fresh.R |only R/anzg_copper_marine.R |only R/anzg_data.R | 138 ++- R/anzg_dioxins_fresh.R |only R/anzg_diuron_fresh.R |only R/anzg_diuron_marine.R |only R/anzg_fipronil_fresh.R |only R/anzg_fluoride_fresh.R |only R/anzg_glyphosate_fresh.R |only R/anzg_iron_fresh.R |only R/anzg_iron_marine.R |only R/anzg_mancozeb_fresh.R |only R/anzg_manganese_marine.R |only R/anzg_mcpa_fresh.R |only R/anzg_metolachlor_fresh.R | 92 +- R/anzg_metsulfuron_methyl_fresh.R |only R/anzg_nickel_marine.R |only R/anzg_nitrate_hard_fresh.R |only R/anzg_nitrate_moderate_fresh.R |only R/anzg_nitrate_soft_fresh.R |only R/anzg_paraquat_fresh.R |only R/anzg_perfluorooctane_sulfonate_pfos_fresh.R |only R/anzg_picloram_fresh.R |only R/anzg_simazine_fresh.R |only R/anzg_simazine_marine.R |only R/anzg_sulfometuron_methyl_fresh.R |only R/anzg_zinc_marine.R |only R/anztox_data.R |only R/ccme_boron.R | 59 - R/ccme_cadmium.R | 59 - R/ccme_chloride.R | 59 - R/ccme_data.R | 79 +- R/ccme_endosulfan.R | 59 - R/ccme_glyphosate.R | 59 - R/ccme_silver.R | 59 - R/ccme_uranium.R | 59 - R/csiro_chlorine_marine.R | 76 +- R/csiro_cobalt_marine.R | 80 +- R/csiro_data.R | 101 +- R/csiro_lead_marine.R | 80 +- R/csiro_nickel_fresh.R | 78 +- R/envirotox_acute.R |only R/envirotox_chemical.R |only R/envirotox_chronic.R |only R/envirotox_data.R |only R/get_ssddata.R | 777 +++++++++++++++++---- R/namespace.R | 8 R/ssd-fits.R | 86 +- R/ssddata-package.R | 12 R/wqbench_data.R |only README.md | 49 - build/partial.rdb |binary build/vignette.rds |only data/aims_aluminium_marine.rda |binary data/aims_data.rda |binary data/aims_gallium_marine.rda |binary data/aims_molybdenum_marine.rda |binary data/anon_a.rda |binary data/anon_b.rda |binary data/anon_c.rda |binary data/anon_d.rda |binary data/anon_data.rda |binary data/anon_e.rda |binary data/anzg_alpha_cypermethrin_fresh.rda |only data/anzg_aluminium_marine.rda |only data/anzg_ametryn_fresh.rda |only data/anzg_ammonia_fresh.rda |only data/anzg_bisphenol_a_fresh.rda |only data/anzg_bisphenol_a_marine.rda |only data/anzg_boron_fresh.rda |only data/anzg_chlorine_marine.rda |only data/anzg_chromium_III_fresh.rda |only data/anzg_copper_marine.rda |only data/anzg_data.rda |binary data/anzg_dioxins_fresh.rda |only data/anzg_diuron_fresh.rda |only data/anzg_diuron_marine.rda |only data/anzg_fipronil_fresh.rda |only data/anzg_fluoride_fresh.rda |only data/anzg_glyphosate_fresh.rda |only data/anzg_iron_fresh.rda |only data/anzg_iron_marine.rda |only data/anzg_mancozeb_fresh.rda |only data/anzg_manganese_marine.rda |only data/anzg_mcpa_fresh.rda |only data/anzg_metolachlor_fresh.rda |binary data/anzg_metsulfuron_methyl_fresh.rda |only data/anzg_nickel_marine.rda |only data/anzg_nitrate_hard_fresh.rda |only data/anzg_nitrate_moderate_fresh.rda |only data/anzg_nitrate_soft_fresh.rda |only data/anzg_paraquat_fresh.rda |only data/anzg_perfluorooctane_sulfonate_pfos_fresh.rda |only data/anzg_picloram_fresh.rda |only data/anzg_simazine_fresh.rda |only data/anzg_simazine_marine.rda |only data/anzg_sulfometuron_methyl_fresh.rda |only data/anzg_zinc_marine.rda |only data/anztox_data.rda |only data/ccme_boron.rda |binary data/ccme_cadmium.rda |binary data/ccme_chloride.rda |binary data/ccme_data.rda |binary data/ccme_endosulfan.rda |binary data/ccme_glyphosate.rda |binary data/ccme_silver.rda |binary data/ccme_uranium.rda |binary data/csiro_chlorine_marine.rda |binary data/csiro_cobalt_marine.rda |binary data/csiro_data.rda |binary data/csiro_lead_marine.rda |binary data/csiro_nickel_fresh.rda |binary data/envirotox_acute.rda |only data/envirotox_chemical.rda |only data/envirotox_chronic.rda |only data/envirotox_data.rda |only data/ssd_fits.rda |binary data/wqbench_data.rda |only inst/REFERENCES.bib | 712 +++++++++++++++---- inst/doc |only man/aims_aluminium_marine.Rd | 81 +- man/aims_data.Rd | 101 +- man/aims_gallium_marine.Rd | 81 +- man/aims_molybdenum_marine.Rd | 81 +- man/anon_a.Rd | 66 - man/anon_b.Rd | 66 - man/anon_c.Rd | 66 - man/anon_d.Rd | 66 - man/anon_data.Rd | 70 - man/anon_e.Rd | 66 - man/anzg_alpha_cypermethrin_fresh.Rd |only man/anzg_aluminium_marine.Rd |only man/anzg_ametryn_fresh.Rd |only man/anzg_ammonia_fresh.Rd |only man/anzg_bisphenol_a_fresh.Rd |only man/anzg_bisphenol_a_marine.Rd |only man/anzg_boron_fresh.Rd |only man/anzg_chlorine_marine.Rd |only man/anzg_chromium_III_fresh.Rd |only man/anzg_copper_marine.Rd |only man/anzg_data.Rd | 154 ++-- man/anzg_dioxins_fresh.Rd |only man/anzg_diuron_fresh.Rd |only man/anzg_diuron_marine.Rd |only man/anzg_fipronil_fresh.Rd |only man/anzg_fluoride_fresh.Rd |only man/anzg_glyphosate_fresh.Rd |only man/anzg_iron_fresh.Rd |only man/anzg_iron_marine.Rd |only man/anzg_mancozeb_fresh.Rd |only man/anzg_manganese_marine.Rd |only man/anzg_mcpa_fresh.Rd |only man/anzg_metolachlor_fresh.Rd | 103 +- man/anzg_metsulfuron_methyl_fresh.Rd |only man/anzg_nickel_marine.Rd |only man/anzg_nitrate_hard_fresh.Rd |only man/anzg_nitrate_moderate_fresh.Rd |only man/anzg_nitrate_soft_fresh.Rd |only man/anzg_paraquat_fresh.Rd |only man/anzg_perfluorooctane_sulfonate_pfos_fresh.Rd |only man/anzg_picloram_fresh.Rd |only man/anzg_simazine_fresh.Rd |only man/anzg_simazine_marine.Rd |only man/anzg_sulfometuron_methyl_fresh.Rd |only man/anzg_zinc_marine.Rd |only man/anztox_data.Rd |only man/ccme_boron.Rd | 72 - man/ccme_cadmium.Rd | 72 - man/ccme_chloride.Rd | 72 - man/ccme_data.Rd | 97 +- man/ccme_endosulfan.Rd | 72 - man/ccme_glyphosate.Rd | 72 - man/ccme_silver.Rd | 72 - man/ccme_uranium.Rd | 72 - man/csiro_chlorine_marine.Rd | 87 +- man/csiro_cobalt_marine.Rd | 91 +- man/csiro_data.Rd | 117 +-- man/csiro_lead_marine.Rd | 91 +- man/csiro_nickel_fresh.Rd | 89 +- man/envirotox_acute.Rd |only man/envirotox_chemical.Rd |only man/envirotox_chronic.Rd |only man/envirotox_data.Rd |only man/envirotox_data_sets.Rd |only man/get_ssddata.Rd | 80 +- man/getdata.Rd | 36 man/gm_mean.Rd | 48 - man/list_datasets.Rd |only man/ssd_data_sets.Rd |only man/ssd_fits.Rd | 78 +- man/ssddata-package.Rd | 68 - man/wqbench_data.Rd |only tests/testthat/helper-datasets.R |only tests/testthat/test-data-aggregates.R |only tests/testthat/test-data-integrity.R |only tests/testthat/test-envirotox.R |only tests/testthat/test-get_ssddata-args.R |only tests/testthat/test-get_ssddata.R | 147 ++- tests/testthat/test-getdata.R | 4 tests/testthat/test-ssd-data-sets.R |only tests/testthat/test-ssd_fits.R |only tests/testthat/test-units-consistency.R |only vignettes |only 225 files changed, 3943 insertions(+), 2502 deletions(-)
Title: Interface to 'NetCDF' Datasets
Description: An interface to the 'NetCDF' file formats designed by Unidata
for efficient storage of array-oriented scientific data and descriptions.
Most capabilities of 'NetCDF' version 4 are supported. Optional conversions
of time units are enabled by 'UDUNITS' version 2, also from Unidata.
Author: Pavel Michna [aut],
Milton Woods [aut, cre]
Maintainer: Milton Woods <miltonjwoods@gmail.com>
Diff between RNetCDF versions 2.11-1 dated 2025-04-30 and 2.11-2 dated 2026-08-04
DESCRIPTION | 12 ++--- INSTALL | 4 - LICENSE | 2 MD5 | 108 +++++++++++++++++++++++++-------------------------- NEWS | 3 + R/RNetCDF.R | 2 R/config.R.in | 2 configure | 18 ++++---- configure.ac | 2 man/00RNetCDF.Rd | 4 - man/att.copy.nc.Rd | 2 man/att.delete.nc.Rd | 2 man/att.get.nc.Rd | 2 man/att.inq.nc.Rd | 2 man/att.put.nc.Rd | 2 man/att.rename.nc.Rd | 2 man/close.nc.Rd | 2 man/create.nc.Rd | 2 man/dim.def.nc.Rd | 2 man/dim.inq.nc.Rd | 2 man/dim.rename.nc.Rd | 2 man/file.inq.nc.Rd | 2 man/grp.def.nc.Rd | 2 man/grp.inq.nc.Rd | 2 man/grp.rename.nc.Rd | 2 man/open.nc.Rd | 2 man/print.nc.Rd | 2 man/read.nc.Rd | 2 man/sync.nc.Rd | 2 man/type.def.nc.Rd | 2 man/type.inq.nc.Rd | 2 man/utcal.nc.Rd | 6 +- man/utinit.nc.Rd | 2 man/utinvcal.nc.Rd | 2 man/var.def.nc.Rd | 2 man/var.get.nc.Rd | 2 man/var.inq.nc.Rd | 2 man/var.par.nc.Rd | 2 man/var.put.nc.Rd | 2 man/var.rename.nc.Rd | 2 src/RNetCDF.h | 4 - src/attribute.c | 4 - src/common.c | 6 +- src/common.h | 4 - src/convert.c | 4 - src/convert.h | 4 - src/dataset.c | 4 - src/dimension.c | 4 - src/group.c | 4 - src/init.c | 4 - src/type.c | 4 - src/udunits.c | 4 - src/variable.c | 4 - tests/RNetCDF-test.R | 4 - tools/convert.m4 | 4 - 55 files changed, 143 insertions(+), 140 deletions(-)
Title: Policy Learning via Doubly Robust Empirical Welfare Maximization
over Trees
Description: Learn optimal policies via doubly robust empirical welfare
maximization over trees. Given reward estimates, the algorithm finds a
rule-based treatment allocation, where the policy takes the form of a
shallow decision tree that is globally optimal (or nearly so). Methods are
described in Sverdrup, Kanodia, Zhou, Athey, and Wager (2020)
<doi:10.21105/joss.02232>, Athey and Wager (2021)
<doi:10.3982/ECTA15732>, and Zhou, Athey, and Wager (2023)
<doi:10.1287/opre.2022.2271>.
Author: Erik Sverdrup [aut, cre],
Ayush Kanodia [aut],
Zhengyuan Zhou [aut],
Susan Athey [aut],
Stefan Wager [aut]
Maintainer: Erik Sverdrup <erik.sverdrup@gmail.com>
Diff between policytree versions 1.2.4 dated 2026-02-18 and 1.2.5 dated 2026-08-04
DESCRIPTION | 24 ++++++++++++++---------- MD5 | 10 +++++----- R/hybrid_policy_tree.R | 2 +- R/policy_tree.R | 6 +++--- man/policy_tree.Rd | 2 +- man/policytree-package.Rd | 2 +- 6 files changed, 25 insertions(+), 21 deletions(-)
Title: Various Methods for the Two Sample Problem in D>1 Dimensions
Description: The routine twosample_test() in this package runs the
two-sample test using various test statistic for multivariate data.
The user can also run several tests and then find a p value adjusted for simultaneous inference.
The p values are found via permutation or via the parametric bootstrap.
The routine twosample_power() allows the estimation of the power of the tests.
The routine run.studies() allows a user to quickly study the power of a new method and
how it compares to those included in the package.
For details of the methods and references see the included vignettes.
Author: Wolfgang Rolke [aut, cre]
Maintainer: Wolfgang Rolke <wolfgang.rolke@upr.edu>
Diff between MD2sample versions 1.2.2 dated 2026-06-25 and 1.3.0 dated 2026-08-04
MD2sample-1.2.2/MD2sample/R/signif.digits.R |only MD2sample-1.2.2/MD2sample/man/signif.digits.Rd |only MD2sample-1.3.0/MD2sample/DESCRIPTION | 9 - MD2sample-1.3.0/MD2sample/MD5 | 36 +++-- MD2sample-1.3.0/MD2sample/NAMESPACE | 1 MD2sample-1.3.0/MD2sample/NEWS.md | 7 + MD2sample-1.3.0/MD2sample/R/MD2sample-package.R | 22 +-- MD2sample-1.3.0/MD2sample/R/case.studies.R | 2 MD2sample-1.3.0/MD2sample/R/change.marginals.R | 2 MD2sample-1.3.0/MD2sample/R/rDalitz.R | 2 MD2sample-1.3.0/MD2sample/R/run.studies.R | 2 MD2sample-1.3.0/MD2sample/R/signif_digits.R |only MD2sample-1.3.0/MD2sample/R/twosample_power.R | 2 MD2sample-1.3.0/MD2sample/R/twosample_test.R | 4 MD2sample-1.3.0/MD2sample/R/twosample_test_adjusted_pvalue.R | 2 MD2sample-1.3.0/MD2sample/inst/doc/CaseStudies.html | 68 +++++------ MD2sample-1.3.0/MD2sample/inst/legacy-tests |only MD2sample-1.3.0/MD2sample/man/MD2sample-package.Rd | 5 MD2sample-1.3.0/MD2sample/man/signif_digits.Rd |only MD2sample-1.3.0/MD2sample/tests |only 20 files changed, 92 insertions(+), 72 deletions(-)
Title: High-Dimensional Undirected Graph Estimation
Description: Provides a general framework for
high-dimensional undirected graph estimation. It integrates
data preprocessing, neighborhood screening, graph estimation,
and model selection techniques into a pipeline. In
preprocessing stage, the nonparanormal(npn) transformation is
applied to help relax the normality assumption. In the graph
estimation stage, the graph structure is estimated by
Meinshausen-Buhlmann graph estimation, the graphical lasso,
or the TIGER (tuning-insensitive graph estimation and
regression) method, and the first two can be further
accelerated by the lossy screening rule preselecting the
neighborhood of each variable by correlation thresholding. We
target on high-dimensional data analysis usually d >> n, and
the computation is memory-optimized using the sparse matrix
output. We also provide a computationally efficient approach,
correlation thresholding graph estimation. Three
regularization/thresholding parameter selection methods are
included in this package: (1)stab [...truncated...]
Author: Haoming Jiang [aut],
Xinyu Fei [aut],
Han Liu [aut],
Kathryn Roeder [aut],
John Lafferty [aut],
Larry Wasserman [aut],
Xingguo Li [aut],
Tuo Zhao [aut, cre]
Maintainer: Tuo Zhao <tourzhao@gatech.edu>
Diff between huge versions 2.0.0 dated 2026-07-26 and 2.0.1 dated 2026-08-04
DESCRIPTION | 6 +- MD5 | 16 ++--- NEWS.md | 17 ++++++ R/huge.select.R | 17 ++++-- configure | 18 +++--- configure.ac | 2 inst/doc/huge.pdf |binary src/huge_core.cpp | 33 +++++++++++ tests/testthat/test-regressions.R | 105 ++++++++++++++++++++++++++++++++++++++ 9 files changed, 187 insertions(+), 27 deletions(-)
Title: Graphical Markov Models with Mixed Graphs
Description: Provides functions for defining
mixed graphs containing three types of edges, directed,
undirected and bi-directed, with possibly multiple edges.
These graphs are useful because they capture fundamental
independence structures in multivariate distributions
and in the induced distributions after marginalization
and conditioning.
The package is especially concerned with Gaussian graphical
models for
(i) ML estimation for directed acyclic graphs, undirected and
bi-directed graphs and ancestral graph models
(ii) testing several conditional independencies
(iii) checking global identification of DAG Gaussian models
with one latent variable
(iv) testing Markov equivalences and generating Markov
equivalent graphs of specific types.
Author: Giovanni M. Marchetti [aut, cre] ,
Mathias Drton [aut] ,
Kayvan Sadeghi [aut]
Maintainer: Giovanni M. Marchetti <giovanni.marchetti@unifi.it>
Diff between ggm versions 2.5.2 dated 2025-07-25 and 2.5.4 dated 2026-08-04
DESCRIPTION | 9 +++++---- MD5 | 14 +++++++------- NEWS | 7 +++++++ man/drawGraph.Rd | 8 +++++--- man/fitAncestralGraph.Rd | 4 ++-- man/fitDag.Rd | 4 ++-- man/ggm.Rd | 3 ++- man/plotGraph.Rd | 20 +++++++++++++++++++- 8 files changed, 49 insertions(+), 20 deletions(-)
Title: GDP - Workflow Management
Description: Tools, methods and processes for the management
of analysis workflows. These lightweight solutions facilitate
structuring R&D activities. These solutions were developed to comply
with Good Documentation Practice (GDP),
with ALCOA+ principles as proposed by the U.S. FDA, and
with FAIR principles as discussed by Jacobsen et al. (2017) <doi:10.1162/dint_r_00024>.
Author: Gregoire Thomas [aut, cre, cph] ,
Metabolomic Diagnostics Ltd. [fnd]
Maintainer: Gregoire Thomas <gregoire.thomas@SQU4RE.com>
Diff between D4TAlink.light versions 2.1.22 dated 2026-07-21 and 2.1.23 dated 2026-08-04
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 5 +++++ R/taskFiles.R | 20 +++++++++++++++++++- inst/doc/D4TAlink_basics.html | 4 ++-- inst/doc/D4TAlink_quickstart.html | 4 ++-- man/saveReportXls.Rd | 10 ++++++++-- 7 files changed, 46 insertions(+), 17 deletions(-)
More information about D4TAlink.light at CRAN
Permanent link
Title: Brazilian Maps from Different Geographic Levels
Description: Provides simplified Brazilian territorial meshes derived from
official data published by the Brazilian Institute of Geography and
Statistics (IBGE) <https://www.ibge.gov.br/> as local spatial objects,
with no download required at use time. Municipal meshes cover selected
official editions from 2000 onwards whenever the number of municipalities
changes, and current meshes are available for states, regions and other
geographic levels. Convenience functions support filtering, joining and
plotting the maps, as well as consulting Brazilian territorial codes.
Author: Renato Prado Siqueira [aut, cre]
Maintainer: Renato Prado Siqueira <rpradosiqueira@gmail.com>
This is a re-admission after prior archival of version 0.1.0 dated 2017-09-21
Diff between brazilmaps versions 0.1.0 dated 2017-09-21 and 1.0.0 dated 2026-08-04
brazilmaps-0.1.0/brazilmaps/inst/maps/Brazil.rds |only brazilmaps-0.1.0/brazilmaps/inst/maps/City.rds |only brazilmaps-0.1.0/brazilmaps/inst/maps/MesoRegion.rds |only brazilmaps-0.1.0/brazilmaps/inst/maps/MicroRegion.rds |only brazilmaps-0.1.0/brazilmaps/inst/maps/Region.rds |only brazilmaps-0.1.0/brazilmaps/inst/maps/State.rds |only brazilmaps-0.1.0/brazilmaps/man/join_data.Rd |only brazilmaps-0.1.0/brazilmaps/man/theme_map.Rd |only brazilmaps-1.0.0/brazilmaps/DESCRIPTION | 40 - brazilmaps-1.0.0/brazilmaps/MD5 | 87 ++- brazilmaps-1.0.0/brazilmaps/NAMESPACE | 12 brazilmaps-1.0.0/brazilmaps/NEWS.md | 61 ++ brazilmaps-1.0.0/brazilmaps/R/brmap_years.R |only brazilmaps-1.0.0/brazilmaps/R/datasets.R | 114 +--- brazilmaps-1.0.0/brazilmaps/R/get_brmap.R | 226 ++++---- brazilmaps-1.0.0/brazilmaps/R/get_dtb_info.R |only brazilmaps-1.0.0/brazilmaps/R/get_dtb_lvl.R |only brazilmaps-1.0.0/brazilmaps/R/join_data.R | 89 +-- brazilmaps-1.0.0/brazilmaps/R/plot_brmap.R | 273 +++++----- brazilmaps-1.0.0/brazilmaps/R/utils.R |only brazilmaps-1.0.0/brazilmaps/R/zzz.R |only brazilmaps-1.0.0/brazilmaps/README.md | 162 +++++ brazilmaps-1.0.0/brazilmaps/build |only brazilmaps-1.0.0/brazilmaps/data/deaths.rda |binary brazilmaps-1.0.0/brazilmaps/data/gini2015.rda |binary brazilmaps-1.0.0/brazilmaps/data/pop2017.rda |binary brazilmaps-1.0.0/brazilmaps/inst/COPYRIGHTS |only brazilmaps-1.0.0/brazilmaps/inst/doc |only brazilmaps-1.0.0/brazilmaps/inst/dtb |only brazilmaps-1.0.0/brazilmaps/inst/maps/Brazil.topojson.gz |only brazilmaps-1.0.0/brazilmaps/inst/maps/Imediate.topojson.gz |only brazilmaps-1.0.0/brazilmaps/inst/maps/Intermediary.topojson.gz |only brazilmaps-1.0.0/brazilmaps/inst/maps/MesoRegion.topojson.gz |only brazilmaps-1.0.0/brazilmaps/inst/maps/MicroRegion.topojson.gz |only brazilmaps-1.0.0/brazilmaps/inst/maps/Region.topojson.gz |only brazilmaps-1.0.0/brazilmaps/inst/maps/State.topojson.gz |only brazilmaps-1.0.0/brazilmaps/inst/maps/StateHex.topojson.gz |only brazilmaps-1.0.0/brazilmaps/inst/maps/StateReg.topojson.gz |only brazilmaps-1.0.0/brazilmaps/inst/maps/municipality |only brazilmaps-1.0.0/brazilmaps/man/brmap_editions.Rd |only brazilmaps-1.0.0/brazilmaps/man/deaths.Rd | 51 - brazilmaps-1.0.0/brazilmaps/man/get_brmap.Rd | 118 ++-- brazilmaps-1.0.0/brazilmaps/man/get_dtb.Rd |only brazilmaps-1.0.0/brazilmaps/man/get_dtb_info.Rd |only brazilmaps-1.0.0/brazilmaps/man/get_dtb_levels.Rd |only brazilmaps-1.0.0/brazilmaps/man/get_dtb_lvl.Rd |only brazilmaps-1.0.0/brazilmaps/man/gini2015.Rd | 52 - brazilmaps-1.0.0/brazilmaps/man/join_brmap.Rd |only brazilmaps-1.0.0/brazilmaps/man/plot_brmap.Rd | 123 ++-- brazilmaps-1.0.0/brazilmaps/man/pop2017.Rd | 53 - brazilmaps-1.0.0/brazilmaps/man/theme_brmap.Rd |only brazilmaps-1.0.0/brazilmaps/tests |only brazilmaps-1.0.0/brazilmaps/vignettes |only 53 files changed, 842 insertions(+), 619 deletions(-)
Title: Regime-Switching Dynamic Correlation Models
Description: Estimation, forecasting, simulation, and portfolio construction for
regime-switching models with exogenous variables as in
Pelletier (2006) <doi:10.1016/j.jeconom.2005.01.013>.
Author: David Ardia [aut, cre, cph, fnd] ,
Benjamin Seguin [aut],
Roosevelt Ymele Nguemo [aut]
Maintainer: David Ardia <david.ardia.ch@gmail.com>
Diff between RSDC versions 1.1-2 dated 2025-09-03 and 1.7-0 dated 2026-08-04
RSDC-1.1-2/RSDC/inst/extdata/green-brown-ptf.xlsx |only RSDC-1.7-0/RSDC/DESCRIPTION | 36 RSDC-1.7-0/RSDC/MD5 | 113 +- RSDC-1.7-0/RSDC/NAMESPACE | 54 + RSDC-1.7-0/RSDC/NEWS.md | 215 +++++ RSDC-1.7-0/RSDC/R/RcppExports.R |only RSDC-1.7-0/RSDC/R/bands.R |only RSDC-1.7-0/RSDC/R/bootstrap.R |only RSDC-1.7-0/RSDC/R/broom.R |only RSDC-1.7-0/RSDC/R/ff5ind.R |only RSDC-1.7-0/RSDC/R/forecast_ahead.R |only RSDC-1.7-0/RSDC/R/global_search.R |only RSDC-1.7-0/RSDC/R/greenbrown.R | 5 RSDC-1.7-0/RSDC/R/inference.R |only RSDC-1.7-0/RSDC/R/mccc.R |only RSDC-1.7-0/RSDC/R/methods.R |only RSDC-1.7-0/RSDC/R/model_estimate.R | 716 +++++++++++++---- RSDC-1.7-0/RSDC/R/model_fit.R | 276 ++++-- RSDC-1.7-0/RSDC/R/parallel.R |only RSDC-1.7-0/RSDC/R/partial_corr.R |only RSDC-1.7-0/RSDC/R/pf_optimize.R | 175 ++-- RSDC-1.7-0/RSDC/R/predict_corr.R | 139 ++- RSDC-1.7-0/RSDC/R/rsdc.R | 37 RSDC-1.7-0/RSDC/R/simulate_data.R | 99 +- RSDC-1.7-0/RSDC/R/starts.R |only RSDC-1.7-0/RSDC/R/unpack.R |only RSDC-1.7-0/RSDC/R/viterbi.R |only RSDC-1.7-0/RSDC/build/partial.rdb |binary RSDC-1.7-0/RSDC/build/vignette.rds |only RSDC-1.7-0/RSDC/data/ff5ind.rda |only RSDC-1.7-0/RSDC/data/mccc.rda |only RSDC-1.7-0/RSDC/inst/CITATION | 7 RSDC-1.7-0/RSDC/inst/REFERENCES.bib | 35 RSDC-1.7-0/RSDC/inst/WORDLIST |only RSDC-1.7-0/RSDC/inst/doc |only RSDC-1.7-0/RSDC/inst/extdata/mccc-monthly.csv |only RSDC-1.7-0/RSDC/inst/simulation |only RSDC-1.7-0/RSDC/man/RSDC.Rd | 34 RSDC-1.7-0/RSDC/man/augment.rsdc_fit.Rd |only RSDC-1.7-0/RSDC/man/autoplot.rsdc_fit.Rd |only RSDC-1.7-0/RSDC/man/ff5ind.Rd |only RSDC-1.7-0/RSDC/man/glance.rsdc_fit.Rd |only RSDC-1.7-0/RSDC/man/greenbrown.Rd | 5 RSDC-1.7-0/RSDC/man/mccc.Rd |only RSDC-1.7-0/RSDC/man/rsdc_bootstrap.Rd |only RSDC-1.7-0/RSDC/man/rsdc_corr_bands.Rd |only RSDC-1.7-0/RSDC/man/rsdc_estimate.Rd | 102 ++ RSDC-1.7-0/RSDC/man/rsdc_fit-methods.Rd |only RSDC-1.7-0/RSDC/man/rsdc_forecast.Rd | 26 RSDC-1.7-0/RSDC/man/rsdc_forecast_ahead.Rd |only RSDC-1.7-0/RSDC/man/rsdc_hamilton.Rd | 49 - RSDC-1.7-0/RSDC/man/rsdc_likelihood.Rd | 19 RSDC-1.7-0/RSDC/man/rsdc_maxdiv.Rd | 15 RSDC-1.7-0/RSDC/man/rsdc_minvar.Rd | 63 - RSDC-1.7-0/RSDC/man/rsdc_simulate.Rd | 46 - RSDC-1.7-0/RSDC/man/rsdc_starts.Rd |only RSDC-1.7-0/RSDC/man/rsdc_viterbi.Rd |only RSDC-1.7-0/RSDC/man/tidy.rsdc_fit.Rd |only RSDC-1.7-0/RSDC/src |only RSDC-1.7-0/RSDC/tests/testthat/test-additions.R |only RSDC-1.7-0/RSDC/tests/testthat/test-bootstrap.R |only RSDC-1.7-0/RSDC/tests/testthat/test-controls-forward.R |only RSDC-1.7-0/RSDC/tests/testthat/test-correctness.R |only RSDC-1.7-0/RSDC/tests/testthat/test-cpp-equivalence.R |only RSDC-1.7-0/RSDC/tests/testthat/test-forecast.R | 72 + RSDC-1.7-0/RSDC/tests/testthat/test-global-search.R |only RSDC-1.7-0/RSDC/tests/testthat/test-guards.R |only RSDC-1.7-0/RSDC/tests/testthat/test-hamilton.R | 19 RSDC-1.7-0/RSDC/tests/testthat/test-inference.R |only RSDC-1.7-0/RSDC/tests/testthat/test-likelihood.R | 21 RSDC-1.7-0/RSDC/tests/testthat/test-methods.R |only RSDC-1.7-0/RSDC/tests/testthat/test-minvar-maxdiv.R | 26 RSDC-1.7-0/RSDC/tests/testthat/test-parallel.R |only RSDC-1.7-0/RSDC/tests/testthat/test-partial-corr.R |only RSDC-1.7-0/RSDC/tests/testthat/test-rsdc-estimate.R | 54 + RSDC-1.7-0/RSDC/tests/testthat/test-simulate.R | 7 RSDC-1.7-0/RSDC/tests/testthat/test-starts.R |only RSDC-1.7-0/RSDC/vignettes |only 78 files changed, 2001 insertions(+), 464 deletions(-)
Title: Structural Equation Modeling and Confirmatory Network Analysis
Description: Multi-group (dynamical) structural equation models in combination with confirmatory network models from cross-sectional, time-series and panel data <doi:10.31234/osf.io/8ha93>. Allows for confirmatory testing and fit as well as exploratory model search.
Author: Sacha Epskamp [aut, cre]
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between psychonetrics versions 0.16.9 dated 2026-07-16 and 0.17.8 dated 2026-08-04
DESCRIPTION | 6 MD5 | 75 ++--- NAMESPACE | 5 NEWS | 226 ++++++++++++++++ R/03_modelformation_matrixSetup_mu.R | 90 +++++- R/18_dlvm1_derivatives.R | 47 ++- R/18_dlvm1_implied.R | 23 + R/25_panelvar_derivatives.R | 23 + R/25_panelvar_implied.R | 12 R/a_models_dlvm1.R | 103 ++++++- R/a_models_name_aliases.R | 14 + R/a_models_panelvar.R | 71 ++++- R/a_models_ri_clpm.R | 43 +++ R/e_modelmodifications_ri_clpm_stationarity.R | 360 ++++++++++++++++++++++---- R/f_convenience_CIplot.R | 95 ++++++ R/f_convenience_getmatrix.R | 83 +++++ R/f_convenience_plot.R |only R/f_convenience_ri_clpm_blocks.R |only build/partial.rdb |binary inst/tinytest/_helpers.R |only inst/tinytest/test_dlvm1_beta_epsilon.R | 12 inst/tinytest/test_free_means.R |only inst/tinytest/test_meta.R | 22 - inst/tinytest/test_ml_lvm_2L.R | 8 inst/tinytest/test_ml_var1.R | 10 inst/tinytest/test_ml_varcov.R | 8 inst/tinytest/test_pdc_temporal.R | 20 - inst/tinytest/test_plot.R |only inst/tinytest/test_ri_clpm.R |only inst/tinytest/test_robust_ml.R | 5 inst/tinytest/test_var_panel.R | 32 +- man/CIplot.Rd | 12 man/dlvm1_family.Rd | 23 + man/getmatrix.Rd | 22 + man/panelvar_family.Rd | 31 +- man/plot.psychonetrics.Rd |only man/psychonetrics-package.Rd | 2 man/ri_clpm.Rd | 100 +++++-- src/18_dlvm1_derivatives_cpp.cpp | 60 ++-- src/18_dlvm1_implied_cpp.cpp | 24 + src/25_panelvar_derivatives_cpp.cpp | 24 + src/25_panelvar_implied_cpp.cpp | 22 + 42 files changed, 1429 insertions(+), 284 deletions(-)
Title: Expected Value of Information Based Sample Size Calculation
Description: Computes sample sizes for trial-based cost-effectiveness analyses using the expected value of information. The implementation follows the method described by Bader et al. (2018) <doi:10.1186/s12874-018-0571-1>.
Author: Audrey Cordon [aut, cre],
Clement Bader [ctb],
Morgane Donadel [ctb],
Aline Maillard [ctb],
Sebastien Cossin [ctb],
Mohamedou Sow [ctb],
Antoine Benard [ctb]
Maintainer: Audrey Cordon <audrey.cordon@chu-bordeaux.fr>
This is a re-admission after prior archival of version 0.1 dated 2016-10-02
Diff between EBASS versions 0.1 dated 2016-10-02 and 0.1.1 dated 2026-08-04
EBASS-0.1.1/EBASS/DESCRIPTION | 34 - EBASS-0.1.1/EBASS/MD5 | 76 +- EBASS-0.1.1/EBASS/NAMESPACE | 26 EBASS-0.1.1/EBASS/NEWS.md |only EBASS-0.1.1/EBASS/R/EVPI.R | 462 ++++++++--------- EBASS-0.1.1/EBASS/R/INMB.R | 232 ++++---- EBASS-0.1.1/EBASS/R/INMB_DIRECT.R | 116 ++-- EBASS-0.1.1/EBASS/R/Lambda.R | 102 +-- EBASS-0.1.1/EBASS/R/POP.R | 268 ++++----- EBASS-0.1.1/EBASS/R/VAR_INMB.R | 280 +++++----- EBASS-0.1.1/EBASS/R/VAR_INMB_DIFF.R | 369 ++++++------- EBASS-0.1.1/EBASS/R/VAR_INMB_DIRECT.R | 146 ++--- EBASS-0.1.1/EBASS/R/fonctions_sujets.R | 448 +++++++++------- EBASS-0.1.1/EBASS/R/internal.R | 200 +++---- EBASS-0.1.1/EBASS/README.md |only EBASS-0.1.1/EBASS/build/vignette.rds |binary EBASS-0.1.1/EBASS/inst/doc/my-vignette.R | 197 +++---- EBASS-0.1.1/EBASS/inst/doc/my-vignette.Rmd | 384 +++++++------- EBASS-0.1.1/EBASS/inst/doc/my-vignette.html |only EBASS-0.1.1/EBASS/man/EBASS-internal.Rd | 26 EBASS-0.1.1/EBASS/man/EVPI_DECREASE.Rd | 76 +- EBASS-0.1.1/EBASS/man/INMB.Rd | 94 +-- EBASS-0.1.1/EBASS/man/INMB_DIRECT.Rd | 56 +- EBASS-0.1.1/EBASS/man/Lambda.Rd | 50 - EBASS-0.1.1/EBASS/man/POP.Rd | 72 +- EBASS-0.1.1/EBASS/man/VAR_INMB.Rd | 96 +-- EBASS-0.1.1/EBASS/man/VAR_INMB_DIFF.Rd | 97 +-- EBASS-0.1.1/EBASS/man/VAR_INMB_DIRECT.Rd | 70 +- EBASS-0.1.1/EBASS/man/create_object_evpi_decrease.Rd | 86 +-- EBASS-0.1.1/EBASS/man/create_object_inmb.Rd | 75 +- EBASS-0.1.1/EBASS/man/create_object_inmb_direct.Rd | 49 - EBASS-0.1.1/EBASS/man/create_object_lambda.Rd | 49 - EBASS-0.1.1/EBASS/man/create_object_pop.Rd | 65 +- EBASS-0.1.1/EBASS/man/create_object_var_inmb.Rd | 81 +- EBASS-0.1.1/EBASS/man/create_object_var_inmb_diff.Rd | 87 +-- EBASS-0.1.1/EBASS/man/create_object_var_inmb_direct.Rd | 57 +- EBASS-0.1.1/EBASS/man/gamma_risk.Rd | 36 - EBASS-0.1.1/EBASS/man/graph_gain_n.Rd | 38 - EBASS-0.1.1/EBASS/man/sample_size.Rd | 45 - EBASS-0.1.1/EBASS/vignettes/my-vignette.Rmd | 384 +++++++------- EBASS-0.1/EBASS/inst/doc/my-vignette.pdf |only 41 files changed, 2575 insertions(+), 2454 deletions(-)
Title: Twin Support Vector Machines
Description: Provides twin support vector machine classifiers and visualization
tools for small to moderate classification problems. Includes one-vs-one
multi-class classification and a standard support vector machine baseline
for comparison.
Author: Shamika Tissera [aut, cre]
Maintainer: Shamika Tissera <nimeshshamika@gmail.com>
This is a re-admission after prior archival of version 0.0.2 dated 2026-06-09
Diff between twinsvm versions 0.0.2 dated 2026-06-09 and 0.0.4 dated 2026-08-04
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++++------ NAMESPACE | 4 ++++ NEWS.md | 25 +++++++++++++++++++++++++ R/resample.R |only man/plot.resample_accuracy.Rd |only man/resample_accuracy.Rd |only tests/testthat/test-baselines.R | 16 ++++++++++++++-- tests/testthat/test-multiclass.R | 18 ++++++++++++------ tests/testthat/test-phase0.R | 1 + tests/testthat/test-resample.R |only 11 files changed, 69 insertions(+), 17 deletions(-)
Title: Coarse-to-Fine Spatial and Spatio-Temporal Modeling
Description: Provides functions for coarse-to-fine spatial and spatio-temporal modeling, enabling fast prediction, regression, and uncertainty quantification for moderate to large datasets. For methodological details, see Murakami et al. (2026) <doi:10.1111/gean.70034> and related work on generalized linear, downscaling, and dynamic spatio-temporal extensions.
Author: Daisuke Murakami [aut, cre],
Alexis Comber [aut],
Takahiro Yoshida [aut],
Narumasa Tsutsumida [aut],
Chris Brunsdon [aut],
Tomoki Nakaya [aut],
Jose Luis Blanco-Claraco [ctb, cph] ),
Marius Muja [cph] ,
David G. Lowe [cph]
Maintainer: Daisuke Murakami <dmuraka@ism.ac.jp>
Diff between spCF versions 0.1.2 dated 2026-06-29 and 0.2.0 dated 2026-08-04
DESCRIPTION | 37 +++- MD5 | 100 ++++++++---- NAMESPACE | 8 - R/RcppExports.R | 8 + R/cf_dglm.R |only R/cf_dglm_hv.R |only R/cf_downscale.R | 13 - R/cf_downscale_hv.R | 28 ++- R/cf_glm.R | 76 ++++++++- R/cf_glm_hv.R | 49 ++++-- R/cf_lm.R | 81 ++++++++-- R/cf_lm_hv.R | 33 ++-- R/internal_prediction_se.R |only R/internal_utils_dglm.R |only R/internal_utils_glm.R | 198 ++++++++++++++++++------- R/internal_utils_lm.R | 111 ++++++-------- R/internal_validate.R |only R/spCFmap.R |only R/sp_map_core.R |only R/sp_scalewise.R | 131 +++++++++++++--- build/vignette.rds |binary inst/COPYRIGHTS |only inst/doc/spCF_dglm.R |only inst/doc/spCF_dglm.Rmd |only inst/doc/spCF_dglm.html |only inst/doc/spCF_downscale.Rmd | 2 inst/doc/spCF_downscale.html | 145 +++++++++--------- inst/doc/spCF_glm.R | 6 inst/doc/spCF_glm.Rmd | 18 ++ inst/doc/spCF_glm.html | 335 ++++++++++++++++++------------------------- inst/doc/spCF_lm.R | 6 inst/doc/spCF_lm.Rmd | 18 ++ inst/doc/spCF_lm.html | 182 +++++++++++------------ inst/shiny |only man/cf_dglm.Rd |only man/cf_dglm_hv.Rd |only man/cf_downscale.Rd | 2 man/cf_glm.Rd | 28 +++ man/cf_lm.Rd | 30 +++ man/cf_lm_hv.Rd | 3 man/spCF.Rd | 16 ++ man/spCFmap.Rd |only man/sp_scalewise.Rd | 45 +++-- src/RcppExports.cpp | 48 ++++++ src/dglm_chunk.cpp |only src/lwr_chunk_glm_fused.cpp |only src/nanoflann.h |only tests |only vignettes/spCF_dglm.Rmd |only vignettes/spCF_downscale.Rmd | 2 vignettes/spCF_glm.Rmd | 18 ++ vignettes/spCF_lm.Rmd | 18 ++ 52 files changed, 1158 insertions(+), 637 deletions(-)
Title: Individual-Based Forest Growth Simulator 'TROLL'
Description: 'TROLL' is coded in C++ and it typically simulates hundreds of
thousands of individuals over hundreds of years. The 'rcontroll' R package
is a wrapper of 'TROLL'. 'rcontroll' includes functions that generate inputs
for simulations and run simulations. Finally, it is possible to analyse
the 'TROLL' outputs through tables, figures, and maps taking advantage of
other R visualisation packages. 'rcontroll' also offers the possibility to
generate a virtual LiDAR point cloud that corresponds to a snapshot of
the simulated forest.
Author: Sylvain Schmitt [aut, cre] ,
Guillaume Salzet [aut] ,
Fabian Fischer [aut] ,
Isabelle Marechaux [aut] ,
Jerome Chave [aut]
Maintainer: Sylvain Schmitt <sylvain.m.schmitt@gmail.com>
This is a re-admission after prior archival of version 0.1.2 dated 2024-09-30
Diff between rcontroll versions 0.1.2 dated 2024-09-30 and 0.1.3 dated 2026-08-04
rcontroll-0.1.2/rcontroll/man/rcontroll.Rd |only rcontroll-0.1.3/rcontroll/DESCRIPTION | 25 rcontroll-0.1.3/rcontroll/MD5 | 60 +- rcontroll-0.1.3/rcontroll/NAMESPACE | 5 rcontroll-0.1.3/rcontroll/NEWS.md | 11 rcontroll-0.1.3/rcontroll/R/generate_climate.R | 23 rcontroll-0.1.3/rcontroll/R/get_chm.trollsim.R | 13 rcontroll-0.1.3/rcontroll/R/load_output.R | 9 rcontroll-0.1.3/rcontroll/R/rcontroll.R | 6 rcontroll-0.1.3/rcontroll/R/trollsim.R | 5 rcontroll-0.1.3/rcontroll/R/trollstack.R | 3 rcontroll-0.1.3/rcontroll/R/zzz.R | 12 rcontroll-0.1.3/rcontroll/build/vignette.rds |binary rcontroll-0.1.3/rcontroll/inst/doc/climate.R | 205 +++---- rcontroll-0.1.3/rcontroll/inst/doc/climate.Rmd | 24 rcontroll-0.1.3/rcontroll/inst/doc/climate.html | 86 +-- rcontroll-0.1.3/rcontroll/inst/doc/lidar.R | 8 rcontroll-0.1.3/rcontroll/inst/doc/lidar.Rmd | 10 rcontroll-0.1.3/rcontroll/inst/doc/lidar.html | 285 +++++----- rcontroll-0.1.3/rcontroll/inst/doc/troll.html | 16 rcontroll-0.1.3/rcontroll/inst/doc/workflow.R | 34 - rcontroll-0.1.3/rcontroll/inst/doc/workflow.html | 29 - rcontroll-0.1.3/rcontroll/inst/extdata/ERA5land_hr_Nouragues_2022.nc |binary rcontroll-0.1.3/rcontroll/inst/extdata/ERA5land_mth_Nouragues_2021_2022.nc |binary rcontroll-0.1.3/rcontroll/man/option.rcontroll.Rd | 17 rcontroll-0.1.3/rcontroll/man/rcontroll-package.Rd |only rcontroll-0.1.3/rcontroll/man/trollCpp.Rd | 16 rcontroll-0.1.3/rcontroll/man/trollsim-class.Rd | 2 rcontroll-0.1.3/rcontroll/man/trollsim.Rd | 2 rcontroll-0.1.3/rcontroll/man/trollstack.Rd | 2 rcontroll-0.1.3/rcontroll/vignettes/climate.Rmd | 24 rcontroll-0.1.3/rcontroll/vignettes/lidar.Rmd | 10 32 files changed, 484 insertions(+), 458 deletions(-)
Title: Nonparametric Multiple Change Point Detection Using Wild Binary
Segmentation
Description: Implements nonparametric multiple change-point detection for
univariate sequences using Wild Binary Segmentation, as described in
Ross (2026) "Nonparametric Detection of Multiple Location-Scale Change
Points via Wild Binary Segmentation"
<doi:10.48550/arXiv.2107.01742>. The package provides Mann--Whitney,
Mood, Lepage, Cramér--von Mises, modified Baumgartner, and standardised
Zhang Z_C rank-based statistics, together with method-specific thresholds for controlling
the probability of incorrectly detecting a change point in a homogeneous
sequence.
Author: Gordon J. Ross [aut, cre]
Maintainer: Gordon J. Ross <gordon.ross@ed.ac.uk>
Diff between npwbs versions 0.4.0 dated 2026-07-28 and 0.5.0 dated 2026-08-04
DESCRIPTION | 14 ++-- MD5 | 20 +++--- NAMESPACE | 1 R/RcppExports.R | 4 + R/package-functions.R | 34 ++++++++-- R/sysdata.rda |binary R/zhang.R |only inst/extdata |only man/detectChanges.Rd | 6 + man/download_zhang_moments.Rd |only src/RcppExports.cpp | 17 +++++ src/zhang.cpp |only tests/test-package.R | 140 ++++++++++++++++++++++++++++++++++++++++-- 13 files changed, 210 insertions(+), 26 deletions(-)
Title: Kernel Independent Component Analysis
Description: The kernel independent component analysis (kernel ICA) method introduced by Bach and Jordan (2002) <doi:10.1162/153244303768966085>. A separate function for the incomplete Cholesky decomposition used in kernel ICA is also provided.
Author: Christoph L. Koesner [aut] ,
Juho Eagling [aut] ,
Klaus Nordhausen [aut, cre]
Maintainer: Klaus Nordhausen <klausnordhausenR@gmail.com>
This is a re-admission after prior archival of version 0.1.0 dated 2021-03-01
Diff between KernelICA versions 0.1.0 dated 2021-03-01 and 2.0.0 dated 2026-08-04
DESCRIPTION | 37 +++++++++++++++++----------- MD5 | 53 ++++++++++++++++++++--------------------- NAMESPACE | 1 NEWS.md |only R/MD_distant_matrices.R | 13 +++++----- R/RcppExports.R | 38 ++++++++++++++--------------- R/incomplete_cholesky.R | 15 ++++++----- R/kernel_ica.R | 25 ++++++++----------- R/kernel_matrix.R | 16 ++++-------- R/load_modules.R | 2 - R/package.R | 18 +++++-------- build/partial.rdb |binary man/KernelICA-package.Rd | 15 +++++++++-- man/MD_distant_matrices.Rd | 5 --- man/incomplete_cholesky.Rd | 13 +++------- man/kernel_ica.Rd | 24 +++++++----------- man/kernel_matrix.Rd | 7 +---- src/Debugging.h | 2 - src/IncompleteCholesky.cpp | 2 - src/KernelGauss.cpp | 1 src/KernelHermite.cpp | 4 ++- src/KernelHermite.h | 2 - src/KernelICAProblem.cpp | 23 +++++++++-------- src/Makevars | 14 +--------- src/Makevars.win | 16 ++---------- src/RcppExports.cpp | 5 +++ src/RcppIncompleteCholesky.cpp | 21 +++------------- src/RcppKernelMatrices.cpp | 7 ++--- 28 files changed, 176 insertions(+), 203 deletions(-)
Title: Spectral Density Estimation and Comparison for Functional Time
Series
Description: Functions for estimating spectral density operator of functional
time series (FTS) and comparing the spectral density operator of two
functional time series, in a way that allows detection of differences of
the spectral density operator in frequencies and along the curve length.
A description of the implemented tests can be found in the paper
Tavakoli & Panaretos (2016) <doi:10.1080/01621459.2016.1147355>.
Author: Shahin Tavakoli [aut, cre]
Maintainer: Shahin Tavakoli <shahin.tavakoli@unige.ch>
This is a re-admission after prior archival of version 1.0.0 dated 2015-09-08
Diff between ftsspec versions 1.0.0 dated 2015-09-08 and 1.0.1 dated 2026-08-04
DESCRIPTION | 17 ++++++---- MD5 | 43 +++++++++++++------------- NAMESPACE | 2 - R/functional-spectral-density.R | 12 +++---- README.md |only man/Epanechnikov_kernel.Rd | 3 - man/Generate_filterMA.Rd | 16 ++++++--- man/Get_noise_sd.Rd | 3 - man/Marginal_basis_pval.Rd | 7 +--- man/PvalAdjust.Rd | 3 - man/Simulate_new_MA.Rd | 8 ++-- man/Spec.Rd | 20 ++++++++---- man/SpecMA.Rd | 3 - man/Spec_compare_fixed_freq.Rd | 20 ++++++++---- man/Spec_compare_localize_freq.Rd | 29 ++++++++++++----- man/Spec_compare_localize_freq_curvelength.Rd | 25 +++++++++------ man/ftsspec.Rd | 14 ++++++-- man/lines.SampleSpecDiffFreq.Rd | 6 +-- man/plot.SampleSpec.Rd | 3 - man/plot.SampleSpecDiffFreq.Rd | 3 - man/plot.SampleSpecDiffFreqCurvelength.Rd | 3 - man/plot.SpecMA.Rd | 3 - man/print.SampleSpecDiffFreqCurvelength.Rd | 3 - 23 files changed, 141 insertions(+), 105 deletions(-)
Title: Bioinformatic Distances
Description: A collection of high-performance methods for computing distance
measures for bioinformatics data. The weighted Euclidean distance can be
computed using 'OpenCL' on a GPU or a parallelized implementation on a CPU.
Other important distance measures for bioinformatics data are provided by
the R package 'parallelDist'. A specialized distance measure for the Gene
Ontology is also available.
Author: Quirin Stier [aut, rev, ctb] ,
Michael Thrun [aut, cre] ,
Luca Brinkmann [ctb]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between BIDistances versions 0.1.3 dated 2025-05-10 and 0.1.5 dated 2026-08-04
BIDistances-0.1.3/BIDistances/inst/NEWS.md |only BIDistances-0.1.5/BIDistances/DESCRIPTION | 50 BIDistances-0.1.5/BIDistances/MD5 | 77 - BIDistances-0.1.5/BIDistances/NAMESPACE | 18 BIDistances-0.1.5/BIDistances/R/Dist2All.R | 150 +- BIDistances-0.1.5/BIDistances/R/DistanceDistributions.R | 1 BIDistances-0.1.5/BIDistances/R/DistanceMatrix.R | 516 +++++++--- BIDistances-0.1.5/BIDistances/R/EuclideanDistances_GPU.R |only BIDistances-0.1.5/BIDistances/R/Hellinger4ConditionalPDF.R |only BIDistances-0.1.5/BIDistances/R/Kullback_Leibler_div.R |only BIDistances-0.1.5/BIDistances/R/TransformSimilarity2MetricDistance.R | 16 BIDistances-0.1.5/BIDistances/R/calculateMemoryDemandGPU.R |only BIDistances-0.1.5/BIDistances/R/fastPdist.R | 1 BIDistances-0.1.5/BIDistances/R/knneighborDistances.R |only BIDistances-0.1.5/BIDistances/R/nearest.R | 21 BIDistances-0.1.5/BIDistances/R/ocl4BID.R |only BIDistances-0.1.5/BIDistances/R/pdistToroid.R |only BIDistances-0.1.5/BIDistances/build/partial.rdb |binary BIDistances-0.1.5/BIDistances/build/vignette.rds |binary BIDistances-0.1.5/BIDistances/inst/WeightedEuclideanBatchOCL.cl |only BIDistances-0.1.5/BIDistances/inst/WeightedEuclideanBlockOCL.cl |only BIDistances-0.1.5/BIDistances/inst/WeightedEuclideanOCL.cl |only BIDistances-0.1.5/BIDistances/inst/doc/BIDistances.html | 9 BIDistances-0.1.5/BIDistances/man/CosinusDistance.Rd | 23 BIDistances-0.1.5/BIDistances/man/Dist2All.Rd | 87 - BIDistances-0.1.5/BIDistances/man/DistanceDistributions.Rd | 8 BIDistances-0.1.5/BIDistances/man/DistanceMatrix.Rd | 497 +++++++-- BIDistances-0.1.5/BIDistances/man/EuclideanDistances_GPU.Rd |only BIDistances-0.1.5/BIDistances/man/GiniDist.Rd | 32 BIDistances-0.1.5/BIDistances/man/Hellinger4ConditionalPDF.Rd |only BIDistances-0.1.5/BIDistances/man/Kullback_Leibler_div.Rd |only BIDistances-0.1.5/BIDistances/man/Mahalanobis.Rd | 8 BIDistances-0.1.5/BIDistances/man/Tfidf_dist.Rd | 5 BIDistances-0.1.5/BIDistances/man/ToroidDist2All.Rd | 125 ++ BIDistances-0.1.5/BIDistances/man/TransformSimilarity2MetricDistance.Rd | 9 BIDistances-0.1.5/BIDistances/man/VariablePrecision.Rd | 2 BIDistances-0.1.5/BIDistances/man/calculateMemoryDemandGPU.Rd |only BIDistances-0.1.5/BIDistances/man/fastPdist.Rd | 6 BIDistances-0.1.5/BIDistances/man/fastPdistC.Rd | 4 BIDistances-0.1.5/BIDistances/man/jaccard.Rd | 5 BIDistances-0.1.5/BIDistances/man/knneighborDistances.Rd |only BIDistances-0.1.5/BIDistances/man/msmd.Rd | 4 BIDistances-0.1.5/BIDistances/man/nearest.Rd | 5 BIDistances-0.1.5/BIDistances/man/pdistToroid.Rd |only BIDistances-0.1.5/BIDistances/man/twed.Rd | 4 BIDistances-0.1.5/BIDistances/src/InnerVariableDifferencesRcpp.cpp | 4 BIDistances-0.1.5/BIDistances/src/SND.cpp | 2 BIDistances-0.1.5/BIDistances/src/fastPdistC.cpp | 74 + 48 files changed, 1236 insertions(+), 527 deletions(-)
Title: Helper Functions for Package 'secr'
Description: Functions are provided for internal use by the spatial
capture-recapture package 'secr' (from version 5.4.0). The idea is to speed up
the installation of 'secr', and possibly reduce its size. Initially the functions
are those for area and transect search that use numerical integration code from
'RcppNumerical' and 'RcppEigen'. The functions are not intended to be user-friendly
and require considerable preprocessing of data.
Author: Murray Efford [aut, cre] ,
Philipp Jund [ctb] )
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secrfunc versions 1.0.0 dated 2025-12-01 and 1.1.4 dated 2026-08-04
DESCRIPTION | 8 - MD5 | 23 ++- NAMESPACE | 19 +-- NEWS | 28 +++- R/RcppExports.R | 21 --- man/hdotpolycpp.Rd | 154 ++++++++++++------------- man/polygonhistoriescpp.Rd | 250 ++++++++++++++++++++++-------------------- man/secrfunc-package.Rd | 131 +++++++++++----------- src/RcppExports.cpp | 37 ++++++ src/hdot.cpp | 2 src/prwipolygon2.cpp |only src/prwipolygonfxi.cpp | 31 +++-- tests/testthat/test-initial.R | 182 ++++++++++++++++++------------ 13 files changed, 498 insertions(+), 388 deletions(-)
Title: Rapid Manipulation of the Variant Call Format (VCF)
Description: The 'vcfpp.h' (<https://github.com/Zilong-Li/vcfpp>) provides an easy-to-use 'C++' 'API' of 'htslib', offering full functionality for manipulating Variant Call Format (VCF) files. The 'vcfppR' package serves as the R bindings of the 'vcfpp.h' library, enabling rapid processing of both compressed and uncompressed VCF files. Explore a range of powerful features for efficient VCF data manipulation.
Author: Zilong Li [aut, cre] ,
Bonfield, James K and Marshall, John and Danecek, Petr and Li, Heng and
Ohan, Valeriu and Whitwham, Andrew and Keane, Thomas and Davies,
Robert M [cph]
Maintainer: Zilong Li <zilong.dk@gmail.com>
Diff between vcfppR versions 0.8.3 dated 2026-03-31 and 0.8.4 dated 2026-08-04
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- src/htslib-1.21/config.status | 10 +++++----- src/htslib-1.21/cram/cram_decode.c | 2 +- src/htslib-1.21/cram/cram_io.c | 4 ++-- src/htslib-1.21/faidx.c | 2 +- src/htslib-1.21/hts.c | 17 ++++++++++------- src/htslib-1.21/sam.c | 3 ++- 8 files changed, 31 insertions(+), 27 deletions(-)
Title: Simple Unified Wrappers for Hosted Foundation Model Inference
APIs
Description: Provides lightweight R wrappers for querying and listing models
from several hosted foundation model inference platforms, currently
including 'OpenAI' <https://developers.openai.com/api/docs/>,
'Google Gemini' <https://ai.google.dev/gemini-api/docs>,
'Groq' <https://console.groq.com/docs/>,
'OpenRouter' <https://openrouter.ai/docs/>,
'Cerebras' <https://inference-docs.cerebras.ai/>, and
'Ollama Cloud' <https://docs.ollama.com/cloud>.
The package is designed for simple inference workflows and quick
experimentation, with minimal abstraction and a consistent interface
across providers. It includes helper functions for model discovery, text
generation, embeddings, image generation, and multimodal inputs, while
leaving room for future support of provider-specific parameters and
advanced options.
Author: Oliver Zhou [aut, cre]
Maintainer: Oliver Zhou <oliver.yxzhou@gmail.com>
Diff between inferencer versions 0.1.4.5 dated 2026-07-10 and 0.2.0 dated 2026-08-04
DESCRIPTION | 13 MD5 | 37 +- NAMESPACE | 3 NEWS.md | 26 + R/inferencer-package.R | 13 R/llm_cerebras.R | 31 -- R/llm_groq.R | 37 +- R/llm_helpers.R | 354 +++++++++++++++++++++++++ R/llm_multimodal.R | 59 ++-- R/llm_openai.R |only R/llm_openrouter.R | 68 ++++ README.md | 85 ++++++ man/inferencer-package.Rd | 13 man/list_openai_models.Rd |only man/list_openrouter_benchmarks.Rd |only man/query_cerebras.Rd | 3 man/query_groq.Rd | 9 man/query_openai.Rd |only man/query_openrouter.Rd | 8 man/query_openrouter_content.Rd | 8 tests/testthat/test-api-wrappers.R | 479 ++++++++++++++++++++++++++++++++++- tests/testthat/test-live-providers.R |only 22 files changed, 1149 insertions(+), 97 deletions(-)
Title: Statistical Analysis in Epidemiology
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data. In
particular representation, manipulation, rate estimation and
simulation for multistate data - the Lexis suite of functions, which
includes interfaces to 'mstate', 'etm' and 'cmprsk' packages.
Contains functions for Age-Period-Cohort and Lee-Carter modeling and
a function for interval censored data. Has functions for extracting
and manipulating parameter estimates and predicted values (ci.lin
and its cousins), as well as a number of epidemiological data sets.
Author: Bendix Carstensen [aut, cre],
Martyn Plummer [aut],
Esa Laara [ctb],
Michael Hills [ctb]
Maintainer: Bendix Carstensen <b@bxc.dk>
Diff between Epi versions 2.65 dated 2026-04-15 and 2.66 dated 2026-08-03
Epi-2.65/Epi/inst/CITATION |only Epi-2.65/Epi/inst/doc/00Index.html |only Epi-2.65/Epi/inst/doc/01flup.R |only Epi-2.65/Epi/inst/doc/01flup.pdf |only Epi-2.65/Epi/inst/doc/02addLexis.R |only Epi-2.65/Epi/inst/doc/02addLexis.pdf |only Epi-2.65/Epi/inst/doc/03crisk.R |only Epi-2.65/Epi/inst/doc/03crisk.pdf |only Epi-2.65/Epi/inst/doc/04simLexis.R |only Epi-2.65/Epi/inst/doc/04simLexis.pdf |only Epi-2.65/Epi/inst/doc/05yll.R |only Epi-2.65/Epi/inst/doc/05yll.pdf |only Epi-2.65/Epi/vignettes/01flup.rnw |only Epi-2.65/Epi/vignettes/01flup.tex |only Epi-2.65/Epi/vignettes/02addLexis.rnw |only Epi-2.65/Epi/vignettes/02addLexis.tex |only Epi-2.65/Epi/vignettes/03crisk.rnw |only Epi-2.65/Epi/vignettes/03crisk.tex |only Epi-2.65/Epi/vignettes/04simLexis.rnw |only Epi-2.65/Epi/vignettes/04simLexis.tex |only Epi-2.65/Epi/vignettes/05yll.rnw |only Epi-2.65/Epi/vignettes/05yll.tex |only Epi-2.66/Epi/CHANGES | 91 +++++++++++++++++--------------- Epi-2.66/Epi/DESCRIPTION | 8 +- Epi-2.66/Epi/MD5 | 76 +++++++++++++------------- Epi-2.66/Epi/R/lexis.R | 1 Epi-2.66/Epi/R/mod.Lexis.R | 26 ++++----- Epi-2.66/Epi/R/paths.Lexis.R | 4 - Epi-2.66/Epi/build |only Epi-2.66/Epi/inst/doc/n01-flup.R |only Epi-2.66/Epi/inst/doc/n01-flup.pdf |only Epi-2.66/Epi/inst/doc/n01-flup.rnw |only Epi-2.66/Epi/inst/doc/n02-addLexis.R |only Epi-2.66/Epi/inst/doc/n02-addLexis.pdf |only Epi-2.66/Epi/inst/doc/n02-addLexis.rnw |only Epi-2.66/Epi/inst/doc/n03-crisk.R |only Epi-2.66/Epi/inst/doc/n03-crisk.pdf |only Epi-2.66/Epi/inst/doc/n03-crisk.rnw |only Epi-2.66/Epi/inst/doc/n04-simLexis.R |only Epi-2.66/Epi/inst/doc/n04-simLexis.pdf |only Epi-2.66/Epi/inst/doc/n04-simLexis.rnw |only Epi-2.66/Epi/inst/doc/n05-yll.R |only Epi-2.66/Epi/inst/doc/n05-yll.pdf |only Epi-2.66/Epi/inst/doc/n05-yll.rnw |only Epi-2.66/Epi/man/Lexis.Rd | 8 +- Epi-2.66/Epi/man/addCov.Lexis.Rd | 14 ++-- Epi-2.66/Epi/man/paths.Lexis.Rd | 10 ++- Epi-2.66/Epi/man/plot.Lexis.Rd | 6 +- Epi-2.66/Epi/man/rbind.Lexis.Rd | 4 - Epi-2.66/Epi/man/splitLexis.Rd | 2 Epi-2.66/Epi/man/unLexis.Rd | 2 Epi-2.66/Epi/vignettes/fixall.bat | 78 +++++++++++++-------------- Epi-2.66/Epi/vignettes/mvall.bat |only Epi-2.66/Epi/vignettes/n01-flup.rnw |only Epi-2.66/Epi/vignettes/n02-addLexis.rnw |only Epi-2.66/Epi/vignettes/n03-crisk.rnw |only Epi-2.66/Epi/vignettes/n04-simLexis.rnw |only Epi-2.66/Epi/vignettes/n05-yll.rnw |only Epi-2.66/Epi/vignettes/rtall.bat | 10 +-- Epi-2.66/Epi/vignettes/rwall.bat | 10 +-- Epi-2.66/Epi/vignettes/simLexis.pdf |only Epi-2.66/Epi/vignettes/yll.pdf |only 62 files changed, 184 insertions(+), 166 deletions(-)
Title: Bayesian Analysis of Graphical Models
Description: Bayesian estimation and edge selection for graphical models of
mixed binary, ordinal, and continuous variables. The variable types determine
the model: an ordinal Markov random field for discrete data, a Gaussian
graphical model for continuous data, or a mixed Markov random field combining
both. Edge inclusion is determined through spike-and-slab priors, yielding
posterior inclusion probabilities for each edge. Supports multi-group
comparison via 'bgmCompare()', simulation, prediction, and missing data
imputation.
Author: Maarten Marsman [aut, cre] ,
Don van den Bergh [aut] ,
Nikola Sekulovski [ctb] ,
Giuseppe Arena [ctb] ,
Laura Groot [ctb],
Gali Geller [ctb]
Maintainer: Maarten Marsman <m.marsman@uva.nl>
Diff between bgms versions 0.1.6.3 dated 2026-02-14 and 0.2.0.0 dated 2026-08-03
bgms-0.1.6.3/bgms/R/bgmcompare-methods.r |only bgms-0.1.6.3/bgms/R/bgms-methods.R |only bgms-0.1.6.3/bgms/R/data_utils.R |only bgms-0.1.6.3/bgms/R/function_input_utils.R |only bgms-0.1.6.3/bgms/R/nuts_diagnostics.R |only bgms-0.1.6.3/bgms/R/output_utils.R |only bgms-0.1.6.3/bgms/man/extractor_functions.Rd |only bgms-0.1.6.3/bgms/src/RcppExports-9e54f986.o.tmp |only bgms-0.1.6.3/bgms/src/bgm |only bgms-0.1.6.3/bgms/src/bgmCompare |only bgms-0.1.6.3/bgms/src/bgm_interface.cpp |only bgms-0.1.6.3/bgms/src/math/custom_exp.cpp |only bgms-0.1.6.3/bgms/src/math/e_arma_exp.h |only bgms-0.1.6.3/bgms/src/math/e_exp.cpp |only bgms-0.1.6.3/bgms/src/math/e_exp.h |only bgms-0.1.6.3/bgms/src/math/explog_switch.h |only bgms-0.1.6.3/bgms/src/mcmc/mcmc_adaptation.h |only bgms-0.1.6.3/bgms/src/mcmc/mcmc_hmc.cpp |only bgms-0.1.6.3/bgms/src/mcmc/mcmc_hmc.h |only bgms-0.1.6.3/bgms/src/mcmc/mcmc_leapfrog.cpp |only bgms-0.1.6.3/bgms/src/mcmc/mcmc_leapfrog.h |only bgms-0.1.6.3/bgms/src/mcmc/mcmc_memoization.h |only bgms-0.1.6.3/bgms/src/mcmc/mcmc_nuts.cpp |only bgms-0.1.6.3/bgms/src/mcmc/mcmc_nuts.h |only bgms-0.1.6.3/bgms/src/mcmc/mcmc_rwm.cpp |only bgms-0.1.6.3/bgms/src/mcmc/mcmc_rwm.h |only bgms-0.1.6.3/bgms/src/mcmc/mcmc_utils.cpp |only bgms-0.1.6.3/bgms/src/mcmc/mcmc_utils.h |only bgms-0.1.6.3/bgms/src/utils/print_mutex.h |only bgms-0.2.0.0/bgms/DESCRIPTION | 32 bgms-0.2.0.0/bgms/MD5 | 446 ++ bgms-0.2.0.0/bgms/NAMESPACE | 80 bgms-0.2.0.0/bgms/NEWS.md | 991 ++++++ bgms-0.2.0.0/bgms/R/RcppExports.R | 176 + bgms-0.2.0.0/bgms/R/anchor_curve.R |only bgms-0.2.0.0/bgms/R/bgm.R | 1144 +++---- bgms-0.2.0.0/bgms/R/bgmCompare.R | 776 ++--- bgms-0.2.0.0/bgms/R/bgm_spec.R |only bgms-0.2.0.0/bgms/R/bgms-package.R | 28 bgms-0.2.0.0/bgms/R/build_arguments.R |only bgms-0.2.0.0/bgms/R/build_output.R |only bgms-0.2.0.0/bgms/R/build_output_bgm.R |only bgms-0.2.0.0/bgms/R/build_output_compare.R |only bgms-0.2.0.0/bgms/R/build_output_mixed_mrf.R |only bgms-0.2.0.0/bgms/R/build_spec.R |only bgms-0.2.0.0/bgms/R/calibration_check.R |only bgms-0.2.0.0/bgms/R/centrality.R |only bgms-0.2.0.0/bgms/R/class_s7.R |only bgms-0.2.0.0/bgms/R/compute_utils.R |only bgms-0.2.0.0/bgms/R/correction_tables.R |only bgms-0.2.0.0/bgms/R/datasets.R | 10 bgms-0.2.0.0/bgms/R/diagnostics_am.R |only bgms-0.2.0.0/bgms/R/diagnostics_nuts.R |only bgms-0.2.0.0/bgms/R/extract_prior_inclusion_probabilities.R |only bgms-0.2.0.0/bgms/R/extractor_functions.R | 1469 ++++++++- bgms-0.2.0.0/bgms/R/fit_accessors.R |only bgms-0.2.0.0/bgms/R/mcmc_summary.R | 1071 +++---- bgms-0.2.0.0/bgms/R/mcmc_summary_sbm.R |only bgms-0.2.0.0/bgms/R/methods_bgmcompare.R |only bgms-0.2.0.0/bgms/R/methods_bgms.R |only bgms-0.2.0.0/bgms/R/plot_bgms.R |only bgms-0.2.0.0/bgms/R/plot_style.R |only bgms-0.2.0.0/bgms/R/predict_simulate_ggm.R |only bgms-0.2.0.0/bgms/R/predict_simulate_mixed.R |only bgms-0.2.0.0/bgms/R/prior_sensitivity.R |only bgms-0.2.0.0/bgms/R/priors.R |only bgms-0.2.0.0/bgms/R/refit_engine.R |only 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Title: Phylogenetic Estimation of Shifts in the Tempo of Origination
Description: Implements diversification analyses using the phylogenetic birth-death-shift model. It leverages belief propagation techniques to calculate branch-specific diversification rates, see Kopperud & Hoehna (2025) <doi:10.1093/sysbio/syaf041>.
Author: Bjoern Tore Kopperud [aut, cre],
Sebastian Hoehna [aut]
Maintainer: Bjoern Tore Kopperud <kopperud@protonmail.com>
Diff between RPesto versions 0.1.4 dated 2025-11-26 and 0.1.5 dated 2026-08-03
DESCRIPTION | 8 - MD5 | 26 +-- NEWS.md | 3 R/extendr-wrappers.R | 14 - R/fit.R | 126 ++++++++--------- build/partial.rdb |binary man/fit_bds.Rd | 8 - src/rust/Cargo.lock | 65 +++++--- src/rust/src/bayes_factor.rs | 126 +++++++++-------- src/rust/src/categories.rs | 32 ++-- src/rust/src/lib.rs | 314 +++++++++++++++++++++++++++++-------------- src/rust/src/models.rs | 28 ++- src/rust/src/writenewick.rs | 43 +++-- src/rust/vendor.tar.xz |binary 14 files changed, 481 insertions(+), 312 deletions(-)
Title: Various Methods for the Goodness-of-Fit Problem in D>1
Dimensions
Description: The routine gof_test() in this package runs the
goodness-of-fit test using various test statistic for multivariate data.
Models under the null hypothesis can either be simple or allow for parameter estimation.
p values are found via the parametric bootstrap (simulation).
The routine gof_test_adjusted_pvalues() runs several tests and then finds a
p value adjusted for simultaneous inference.
The routine gof_power() allows the estimation of the power of the tests.
hybrid_test() and hybrid_power() do the same by first generating a Monte Carlo data set under
the null hypothesis and then running a number of two-sample methods.
The routine run.studies() allows a user to quickly study the power of a new method and
how it compares to those included in the package via a large number of case studies.
For details of the methods and references see the included vignettes.
Author: Wolfgang Rolke [aut, cre]
Maintainer: Wolfgang Rolke <wolfgang.rolke@upr.edu>
Diff between MDgof versions 1.0.2 dated 2026-06-25 and 1.1.0 dated 2026-08-03
MDgof-1.0.2/MDgof/R/signif.digits.R |only MDgof-1.0.2/MDgof/man/signif.digits.Rd |only MDgof-1.1.0/MDgof/DESCRIPTION | 11 +-- MDgof-1.1.0/MDgof/MD5 | 68 ++++++++++++--------- MDgof-1.1.0/MDgof/NAMESPACE | 1 MDgof-1.1.0/MDgof/NEWS.md | 5 + MDgof-1.1.0/MDgof/R/check.functions.R | 12 ++- MDgof-1.1.0/MDgof/R/chisq2D_test.R | 18 ++--- MDgof-1.1.0/MDgof/R/gof_power.R | 2 MDgof-1.1.0/MDgof/R/gof_test.R | 3 MDgof-1.1.0/MDgof/R/gof_test_adjusted_pvalue.R | 1 MDgof-1.1.0/MDgof/R/hybrid_power.R | 2 MDgof-1.1.0/MDgof/R/hybrid_test.R | 2 MDgof-1.1.0/MDgof/R/run.studies.R | 2 MDgof-1.1.0/MDgof/R/signif_digits.R |only MDgof-1.1.0/MDgof/inst/doc/MDgof-Case-Studies.html | 54 ++++++++-------- MDgof-1.1.0/MDgof/inst/legacy-tests |only MDgof-1.1.0/MDgof/man/signif_digits.Rd |only MDgof-1.1.0/MDgof/src/RcppExports.cpp | 36 +++++------ MDgof-1.1.0/MDgof/src/TS_cont.cpp | 9 +- MDgof-1.1.0/MDgof/src/TS_disc.cpp | 2 MDgof-1.1.0/MDgof/src/bakshaev.cpp | 8 +- MDgof-1.1.0/MDgof/src/bakshaev.h | 8 +- MDgof-1.1.0/MDgof/src/calcTS.cpp | 2 MDgof-1.1.0/MDgof/src/ksd.cpp | 2 MDgof-1.1.0/MDgof/src/ksd.h | 2 MDgof-1.1.0/MDgof/src/p2dC.cpp | 2 MDgof-1.1.0/MDgof/src/p2dC.h | 2 MDgof-1.1.0/MDgof/src/powerC.cpp | 3 MDgof-1.1.0/MDgof/src/rosenblattC.cpp | 5 - MDgof-1.1.0/MDgof/src/rosenblattC.h | 2 MDgof-1.1.0/MDgof/src/testC.cpp | 4 - MDgof-1.1.0/MDgof/tests |only 33 files changed, 147 insertions(+), 121 deletions(-)
Title: Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown'
Description: Simplifies custom 'CSS' styling of both 'shiny' and
'rmarkdown' via 'Bootstrap' 'Sass'. Supports 'Bootstrap' 3, 4 and 5 as
well as their various 'Bootswatch' themes. An interactive widget is
also provided for previewing themes in real time.
Author: Carson Sievert [aut, cre] ,
Joe Cheng [aut],
Garrick Aden-Buie [aut] ,
Posit Software, PBC [cph, fnd],
Bootstrap contributors [ctb] ,
Twitter, Inc [cph] ,
Javi Aguilar [ctb, cph] ,
Thomas Park [ctb, cph] ,
PayPal [ctb, cph]
Maintainer: Carson Sievert <carson@posit.co>
Diff between bslib versions 0.11.0 dated 2026-05-16 and 0.12.0 dated 2026-08-03
bslib-0.11.0/bslib/inst/fonts/07d40e985ad7c747025dabb9f22142c4.woff2 |only bslib-0.11.0/bslib/inst/fonts/1f5e011d6aae0d98fc0518e1a303e99a.woff2 |only bslib-0.11.0/bslib/inst/fonts/626330658504e338ee86aec8e957426b.woff2 |only bslib-0.11.0/bslib/inst/fonts/c2f002b3a87d3f9bfeebb23d32cfd9f8.woff2 |only bslib-0.11.0/bslib/inst/fonts/ee91700cdbf7ce16c054c2bb8946c736.woff2 |only bslib-0.12.0/bslib/DESCRIPTION | 16 - bslib-0.12.0/bslib/MD5 | 93 +++++----- bslib-0.12.0/bslib/NAMESPACE | 6 bslib-0.12.0/bslib/NEWS.md | 20 ++ bslib-0.12.0/bslib/R/buttons.R | 2 bslib-0.12.0/bslib/R/layout.R | 14 + bslib-0.12.0/bslib/R/offcanvas.R |only bslib-0.12.0/bslib/R/page.R | 2 bslib-0.12.0/bslib/R/sysdata.rda |binary bslib-0.12.0/bslib/R/value-box.R | 34 +++ bslib-0.12.0/bslib/inst/bs3compat/_shiny_input.scss | 4 bslib-0.12.0/bslib/inst/components/dist/code-editor.js | 2 bslib-0.12.0/bslib/inst/components/dist/code-editor.min.js | 2 bslib-0.12.0/bslib/inst/components/dist/components.css | 2 bslib-0.12.0/bslib/inst/components/dist/components.js | 48 ++++- bslib-0.12.0/bslib/inst/components/dist/components.js.map | 6 bslib-0.12.0/bslib/inst/components/dist/components.min.js | 10 - bslib-0.12.0/bslib/inst/components/dist/components.min.js.map | 8 bslib-0.12.0/bslib/inst/components/dist/web-components.js | 77 ++++++++ bslib-0.12.0/bslib/inst/components/dist/web-components.js.map | 8 bslib-0.12.0/bslib/inst/components/dist/web-components.min.js | 32 ++- bslib-0.12.0/bslib/inst/components/dist/web-components.min.js.map | 8 bslib-0.12.0/bslib/inst/components/scss/card.scss | 8 bslib-0.12.0/bslib/inst/components/scss/offcanvas.scss |only bslib-0.12.0/bslib/inst/components/scss/sidebar.scss | 12 + bslib-0.12.0/bslib/inst/components/scss/toolbar.scss | 6 bslib-0.12.0/bslib/inst/components/scss/tooltip-popover.scss |only bslib-0.12.0/bslib/inst/css-precompiled/5/bootstrap.min.css | 2 bslib-0.12.0/bslib/inst/fonts/109cfdfecabbfbf5e2364aaceece5d12.woff2 |only bslib-0.12.0/bslib/inst/fonts/5cd426f27cf61d86c207d97f8db6cf8a.woff2 |only bslib-0.12.0/bslib/inst/fonts/a8e2cb7ac3da2c4d38cd7c8c06ca5e46.woff2 |only bslib-0.12.0/bslib/inst/fonts/c0540813382b64c1dde636c1fa0b592a.woff2 |only bslib-0.12.0/bslib/inst/fonts/e0243c1a22ed284bb57c07b3ac886694.woff2 |only bslib-0.12.0/bslib/inst/lib/bsw4/dist/lux/font.css | 20 +- bslib-0.12.0/bslib/inst/lib/bsw5/dist/lux/font.css | 60 +++--- bslib-0.12.0/bslib/inst/themer-demo/app.R | 2 bslib-0.12.0/bslib/man/accordion.Rd | 1 bslib-0.12.0/bslib/man/card.Rd | 1 bslib-0.12.0/bslib/man/fragments/value-box-showcase.Rmd | 1 bslib-0.12.0/bslib/man/input_task_button.Rd | 2 bslib-0.12.0/bslib/man/layout_column_wrap.Rd | 12 - bslib-0.12.0/bslib/man/layout_columns.Rd | 11 - bslib-0.12.0/bslib/man/navbar_options.Rd | 2 bslib-0.12.0/bslib/man/offcanvas.Rd |only bslib-0.12.0/bslib/man/page.Rd | 2 bslib-0.12.0/bslib/man/popover.Rd | 1 bslib-0.12.0/bslib/man/show_offcanvas.Rd |only bslib-0.12.0/bslib/man/showcase.Rd |only bslib-0.12.0/bslib/man/tooltip.Rd | 1 bslib-0.12.0/bslib/man/value_box.Rd | 52 ----- bslib-0.12.0/bslib/tests/testthat/test-offcanvas.R |only 56 files changed, 387 insertions(+), 203 deletions(-)
Title: (Bayesian) Additive Voronoi Tessellations
Description: Implements the Bayesian Additive Voronoi Tessellation
model for non-parametric regression and machine learning as introduced
in Stone and Gosling (2025) <doi:10.1080/10618600.2024.2414104>.
This package provides a flexible alternative to BART (Bayesian Additive
Regression Trees) using Voronoi tessellations instead of trees. Users can
fit Bayesian regression models (estimating the associated posterior
distributions and make predictions. It is particularly useful for spatial
data analysis, machine learning regression, complex function approximation
and Bayesian modeling where the underlying structure is unknown. The method
is well-suited to capturing spatial patterns and non-linear relationships.
Author: Adam Stone [aut] ,
John Paul Gosling [aut, cre] ,
Andrew Iskauskas [aut]
Maintainer: John Paul Gosling <john-paul.gosling@durham.ac.uk>
Diff between AddiVortes versions 0.6.8 dated 2026-07-30 and 0.6.9 dated 2026-08-03
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 13 +++++++++++++ inst/doc/categorical.html | 4 ++-- inst/doc/introduction.html | 4 ++-- inst/doc/prediction.html | 4 ++-- inst/doc/spherical.html | 4 ++-- src/addi_vortes_code.cpp | 5 +---- 8 files changed, 32 insertions(+), 22 deletions(-)
Title: Apply-Style Dispatch for High-Performance Computing
Description: Provides apply-style functions using the Message Passing Interface ('MPI')
to improve the High-Performance Computing ('HPC') environment in R.
The package supports long vectors and efficient handling of large datasets for
MPI-based parallel computations.
Author: Ei-ji Nakama [aut, cre],
Junji NAKANO [aut]
Maintainer: Ei-ji Nakama <nakama@ki.rim.or.jp>
Diff between Rhpc versions 0.26.4 dated 2026-07-21 and 0.26.5 dated 2026-08-03
ChangeLog | 2 ++ DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/RhpcRNG.R | 1 - inst/doc/Rhpc_intro.Rnw | 2 +- inst/doc/Rhpc_intro.pdf |binary inst/doc/Rhpc_intro_ja.Rnw | 2 +- inst/doc/Rhpc_intro_ja.pdf |binary vignettes/Rhpc_intro.Rnw | 2 +- vignettes/Rhpc_intro_ja.Rnw | 2 +- 10 files changed, 19 insertions(+), 18 deletions(-)
Title: Access to the 'RESOURCECODE' Hindcast Database
Description: Utility functions to download data from the 'RESOURCECODE'
hindcast database of sea-states, time series of sea-state parameters
and time series of 1D and 2D wave spectra. See
<https://resourcecode.ifremer.fr> for more details about the available
data. Also provides facilities to plot and analyse downloaded data,
such as computing the sea-state parameters from both the 1D and 2D
surface elevation variance spectral density.
Author: Nicolas Raillard [aut, cre]
Maintainer: Nicolas Raillard <nicolas.raillard@ifremer.fr>
Diff between resourcecode versions 0.5.4 dated 2026-05-07 and 0.5.5 dated 2026-08-03
DESCRIPTION | 6 ++-- MD5 | 35 ++++++++++++------------ NEWS.md | 5 +++ build/vignette.rds |binary man/figures/README-data_fetcher-1.png |binary man/resourcecode-package.Rd | 1 src/Makevars | 2 - src/Makevars.win | 2 - tests/testthat/Rplots.pdf |binary tests/testthat/_vcr/Date_dates.yml |only tests/testthat/_vcr/boundary_dates.yml | 16 ++++------ tests/testthat/_vcr/character_dates.yml | 16 ++++------ tests/testthat/_vcr/get_multiple_parameters.yml | 32 ++++++++------------- tests/testthat/_vcr/get_single_parameter.yml | 16 ++++------ tests/testthat/_vcr/numeric_dates.yml | 16 ++++------ tests/testthat/_vcr/tp_conversion.yml | 16 ++++------ tests/testthat/_vcr/week_of_data.yml | 33 ++++++++-------------- tests/testthat/test-spectral_data_download.R | 23 +++++++++++++-- tests/testthat/tests_download_parameters.R | 2 - 19 files changed, 103 insertions(+), 118 deletions(-)
Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre] ,
Hadley Wickham [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 1.2.3 dated 2026-05-16 and 1.2.4 dated 2026-08-03
renv-1.2.3/renv/inst/repos/src/contrib/renv_1.2.3.tar.gz |only renv-1.2.3/renv/man/lockfile-api.Rd |only renv-1.2.3/renv/man/renv_lockfile_from_manifest.Rd |only renv-1.2.4/renv/DESCRIPTION | 8 renv-1.2.4/renv/MD5 | 168 ++--- renv-1.2.4/renv/NAMESPACE | 1 renv-1.2.4/renv/NEWS.md | 428 ++++++++++----- renv-1.2.4/renv/R/bioconductor.R | 114 +++ renv-1.2.4/renv/R/cache.R | 70 ++ renv-1.2.4/renv/R/check.R | 15 renv-1.2.4/renv/R/config-defaults.R | 9 renv-1.2.4/renv/R/dcf.R | 13 renv-1.2.4/renv/R/dependencies.R | 179 ++++++ renv-1.2.4/renv/R/description.R | 6 renv-1.2.4/renv/R/download.R | 50 + renv-1.2.4/renv/R/graph.R | 192 +++++- renv-1.2.4/renv/R/install.R | 10 renv-1.2.4/renv/R/load.R | 53 + renv-1.2.4/renv/R/lock.R | 65 ++ renv-1.2.4/renv/R/lockfile-api.R | 106 ++- renv-1.2.4/renv/R/lockfile.R | 5 renv-1.2.4/renv/R/manifest-convert.R | 37 - renv-1.2.4/renv/R/package.R | 29 + renv-1.2.4/renv/R/pak.R | 94 ++- renv-1.2.4/renv/R/platform.R | 4 renv-1.2.4/renv/R/project.R | 6 renv-1.2.4/renv/R/properties.R | 15 renv-1.2.4/renv/R/record.R | 6 renv-1.2.4/renv/R/records.R | 46 + renv-1.2.4/renv/R/rehash.R | 16 renv-1.2.4/renv/R/remove.R | 11 renv-1.2.4/renv/R/report.R | 10 renv-1.2.4/renv/R/restore.R | 26 renv-1.2.4/renv/R/retrieve.R | 85 ++ renv-1.2.4/renv/R/settings.R | 22 renv-1.2.4/renv/R/snapshot.R | 142 +++- renv-1.2.4/renv/R/utils.R | 27 renv-1.2.4/renv/README.md | 2 renv-1.2.4/renv/build/vignette.rds |binary renv-1.2.4/renv/inst/config.yml | 11 renv-1.2.4/renv/inst/doc/package-sources.R | 2 renv-1.2.4/renv/inst/doc/package-sources.Rmd | 58 +- renv-1.2.4/renv/inst/doc/package-sources.html | 66 ++ renv-1.2.4/renv/inst/doc/renv.html | 2 renv-1.2.4/renv/inst/repos/src/contrib/PACKAGES | 4 renv-1.2.4/renv/inst/repos/src/contrib/PACKAGES.gz |binary renv-1.2.4/renv/inst/repos/src/contrib/PACKAGES.rds |binary renv-1.2.4/renv/inst/repos/src/contrib/renv_1.2.4.tar.gz |only renv-1.2.4/renv/man/config.Rd | 4 renv-1.2.4/renv/man/dependencies.Rd | 11 renv-1.2.4/renv/man/lockfile.Rd |only renv-1.2.4/renv/man/lockfiles.Rd | 6 renv-1.2.4/renv/man/paths.Rd | 2 renv-1.2.4/renv/man/record.Rd | 9 renv-1.2.4/renv/man/rehash.Rd | 10 renv-1.2.4/renv/man/remove.Rd | 11 renv-1.2.4/renv/man/renv-package.Rd | 1 renv-1.2.4/renv/man/restore.Rd | 14 renv-1.2.4/renv/man/sandbox.Rd | 2 renv-1.2.4/renv/man/settings.Rd | 16 renv-1.2.4/renv/man/snapshot.Rd | 38 + renv-1.2.4/renv/tests/testthat/_snaps/init.md | 2 renv-1.2.4/renv/tests/testthat/_snaps/install.md | 7 renv-1.2.4/renv/tests/testthat/_snaps/preflight.md | 3 renv-1.2.4/renv/tests/testthat/_snaps/snapshot.md | 6 renv-1.2.4/renv/tests/testthat/helper-skip.R | 8 renv-1.2.4/renv/tests/testthat/test-bioconductor.R | 37 - renv-1.2.4/renv/tests/testthat/test-cache.R | 55 + renv-1.2.4/renv/tests/testthat/test-cellar.R | 43 + renv-1.2.4/renv/tests/testthat/test-dcf.R | 12 renv-1.2.4/renv/tests/testthat/test-dependencies.R | 169 +++++ renv-1.2.4/renv/tests/testthat/test-description.R | 13 renv-1.2.4/renv/tests/testthat/test-graph.R | 94 +++ renv-1.2.4/renv/tests/testthat/test-install.R | 57 + renv-1.2.4/renv/tests/testthat/test-load.R | 53 + renv-1.2.4/renv/tests/testthat/test-lock.R | 74 ++ renv-1.2.4/renv/tests/testthat/test-lockfile.R | 35 + renv-1.2.4/renv/tests/testthat/test-pak.R | 205 +++++++ renv-1.2.4/renv/tests/testthat/test-ppm.R | 5 renv-1.2.4/renv/tests/testthat/test-r.R | 5 renv-1.2.4/renv/tests/testthat/test-records.R | 39 + renv-1.2.4/renv/tests/testthat/test-rehash.R | 25 renv-1.2.4/renv/tests/testthat/test-remove.R |only renv-1.2.4/renv/tests/testthat/test-restore.R | 56 + renv-1.2.4/renv/tests/testthat/test-retrieve.R | 129 ++++ renv-1.2.4/renv/tests/testthat/test-snapshot.R | 298 ++++++++++ renv-1.2.4/renv/tests/testthat/test-utils.R | 6 renv-1.2.4/renv/vignettes/package-sources.Rmd | 58 +- 88 files changed, 3327 insertions(+), 504 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: NNS (Nonlinear Nonparametric Statistics) leverages partial moments – the fundamental elements of variance that asymptotically approximate the area under f(x) – to provide a robust foundation for nonlinear analysis while maintaining linear equivalences. Designed for real-world data that violates symmetry, linearity, or distributional assumptions, NNS delivers a comprehensive suite of advanced statistical techniques, including: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic superiority / dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995, Second edition: <https://ovvo-financial.github.io/NNS/book/>).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb],
Rasheed Khoshnaw [ctb]
Maintainer: Fred Viole <ovvo.open.source@gmail.com>
Diff between NNS versions 13.1 dated 2026-07-16 and 13.2 dated 2026-08-03
DESCRIPTION | 10 MD5 | 39 - R/Boost.R | 599 +++++++++++----------- R/Regression.R | 61 +- R/Stack.R | 38 - R/dy_d_wrt.R | 469 ++++++----------- README.md | 4 inst/doc/NNSvignette_08_Classification.R | 21 inst/doc/NNSvignette_08_Classification.Rmd | 21 inst/doc/NNSvignette_08_Classification.html | 27 man/NNS.boost.Rd | 20 man/NNS.reg.Rd | 2 man/NNS.stack.Rd | 2 man/dy.d_.Rd | 2 src/NNS_mreg_predict.cpp | 188 ++++++ tests/testthat/Rplots.pdf |binary tests/testthat/test-boost-iris-integration.R |only tests/testthat/test-boost-plots.R |only tests/testthat/test-boost-threshold.R |only tests/testthat/test-mreg-1d-fast-path-ranges.R |only tests/testthat/test-mreg-partial-selection.R |only tests/testthat/test-native-nns-distance-default.R | 6 vignettes/NNSvignette_08_Classification.Rmd | 21 23 files changed, 839 insertions(+), 691 deletions(-)
Title: Bayesian Context Trees for Discrete Time Series
Description: An implementation of a collection of tools for exact Bayesian inference with discrete times series. This package contains functions that can be used for prediction, model selection, estimation, segmentation/change-point detection and other statistical tasks. Specifically, the functions provided can be used for the exact computation of the prior predictive likelihood of the data, for the identification of the a posteriori most likely (MAP) variable-memory Markov models, for calculating the exact posterior probabilities and the AIC and BIC scores of these models, for prediction with respect to log-loss and 0-1 loss and segmentation/change-point detection. Example data sets from finance, genetics, animal communication and meteorology are also provided. Detailed descriptions of the underlying theory and algorithms can be found in [Kontoyiannis et al. 'Bayesian Context Trees: Modelling and exact inference for discrete time series.' Journal of the Royal Statistical Society: Series B (Statist [...truncated...]
Author: Ioannis Papageorgiou [aut],
Valentinian Mihai Lungu [aut, cre],
Ioannis Kontoyiannis [aut]
Maintainer: Valentinian Mihai Lungu <valentinian.mihai@gmail.com>
This is a re-admission after prior archival of version 1.2 dated 2022-05-12
Diff between BCT versions 1.2 dated 2022-05-12 and 1.3 dated 2026-08-03
DESCRIPTION | 29 ++++++++++++------ MD5 | 31 ++++++++++--------- R/RcppExports.R | 2 - R/SARS-CoV-2.R | 2 - R/el_nino.R | 2 - R/gene_s.R | 8 ++--- R/pewee.R | 4 -- R/sp500.R | 2 - build |only man/SP500.Rd | 2 - man/compute_counts.Rd | 2 - man/el_nino.Rd | 2 - man/gene_s.Rd | 8 ++--- man/pewee.Rd | 2 - man/sars_cov_2.Rd | 2 - src/bct_rcpp.cpp | 2 - src/utils.h | 78 +++++++++++++++++++++++++------------------------- 17 files changed, 94 insertions(+), 84 deletions(-)
Title: Group Based Modeling Trajectory
Description: Estimation of group-based trajectory models, including finite mixture models for longitudinal data,
supporting censored normal, zero-inflated Poisson, logit, and beta distributions,
using expectation-maximization and quasi-Newton methods, with tools for model selection,
diagnostics, and visualization of latent trajectory groups,
<doi:10.4159/9780674041318>, Nagin, D. (2005). Group-Based Modeling of Development. Cambridge, MA: Harvard University Press.
and Noel (2022), <https://orbilu.uni.lu/>, thesis.
Author: Cedric Noel [aut, cre],
Jang Schiltz [aut]
Maintainer: Cedric Noel <cedric.noel@univ-lorraine.fr>
Diff between trajeR versions 0.11.1 dated 2025-05-21 and 1.0 dated 2026-08-03
trajeR-0.11.1/trajeR/NEWS.md |only trajeR-0.11.1/trajeR/inst/WORDLIST |only trajeR-0.11.1/trajeR/inst/extdata/BETA2grTCOV.csv |only trajeR-0.11.1/trajeR/inst/extdata/BETA2grTCOV2.csv |only trajeR-0.11.1/trajeR/inst/extdata/BETA2grTCOV3.csv |only trajeR-0.11.1/trajeR/inst/extdata/BETA2grTCOV4 |only trajeR-0.11.1/trajeR/inst/extdata/BETA2grTCOV4.csv |only trajeR-0.11.1/trajeR/inst/extdata/BETA2grTCOV5.csv |only trajeR-0.11.1/trajeR/inst/extdata/CNORM2grwithNA.csv |only trajeR-0.11.1/trajeR/inst/figures |only trajeR-0.11.1/trajeR/inst/logo |only trajeR-0.11.1/trajeR/inst/tools |only trajeR-0.11.1/trajeR/tests |only trajeR-1.0/trajeR/DESCRIPTION | 22 trajeR-1.0/trajeR/MD5 | 169 trajeR-1.0/trajeR/NAMESPACE | 17 trajeR-1.0/trajeR/R/CommonFunction.R | 391 + trajeR-1.0/trajeR/R/GroupProfiles.R | 26 trajeR-1.0/trajeR/R/InternalTrajeR.R | 1611 +++++-- trajeR-1.0/trajeR/R/NonLinear.R | 2904 ++++++++++--- trajeR-1.0/trajeR/R/PlotTrajeR.R | 1150 ++++- trajeR-1.0/trajeR/R/PrintTrajeR.R | 981 +++- trajeR-1.0/trajeR/R/RcppExports.R | 292 + trajeR-1.0/trajeR/R/data.R | 93 trajeR-1.0/trajeR/R/main.R | 537 +- trajeR-1.0/trajeR/R/mapping_ucminf.R | 254 - trajeR-1.0/trajeR/R/model_adequacy.R | 126 trajeR-1.0/trajeR/R/multiple_model.R |only trajeR-1.0/trajeR/R/trajeR-package.R | 4 trajeR-1.0/trajeR/R/trajeRmodelSelection.R | 62 trajeR-1.0/trajeR/R/utils.R |only trajeR-1.0/trajeR/README.md | 25 trajeR-1.0/trajeR/build |only trajeR-1.0/trajeR/data/data_CNORM.rda |only trajeR-1.0/trajeR/data/data_CNORM_Censored.rda |only trajeR-1.0/trajeR/data/data_LOGIT.rda |only trajeR-1.0/trajeR/data/data_ZIP.rda |only trajeR-1.0/trajeR/inst/doc |only trajeR-1.0/trajeR/inst/include/logotrajeR.png |only trajeR-1.0/trajeR/inst/include/trajeR_RcppExports.h | 952 ++++ trajeR-1.0/trajeR/inst/include/trajeRdev.h |only trajeR-1.0/trajeR/inst/include/trajeRdev_RcppExports.h |only trajeR-1.0/trajeR/inst/include/trajeRprod.h |only trajeR-1.0/trajeR/inst/include/trajeRprod_RcppExports.h |only trajeR-1.0/trajeR/man/AvePP.Rd | 22 trajeR-1.0/trajeR/man/ConfIntT.Rd | 22 trajeR-1.0/trajeR/man/GroupProb.Rd | 12 trajeR-1.0/trajeR/man/GroupProfiles.Rd | 26 trajeR-1.0/trajeR/man/OCC.Rd | 21 trajeR-1.0/trajeR/man/adequacy.Rd | 14 trajeR-1.0/trajeR/man/confidenceInt.Rd |only trajeR-1.0/trajeR/man/data_CNORM.Rd |only trajeR-1.0/trajeR/man/data_CNORM_Censored.Rd |only trajeR-1.0/trajeR/man/data_LOGIT.Rd |only trajeR-1.0/trajeR/man/data_ZIP.Rd |only trajeR-1.0/trajeR/man/figures |only trajeR-1.0/trajeR/man/get_group_probabilities.Rd |only trajeR-1.0/trajeR/man/plot_trajectory_mult.Rd |only trajeR-1.0/trajeR/man/plotrajeR.Rd | 15 trajeR-1.0/trajeR/man/plotrajeR.Trajectory.BETA.Rd | 27 trajeR-1.0/trajeR/man/plotrajeR.Trajectory.CNORM.Rd | 24 trajeR-1.0/trajeR/man/plotrajeR.Trajectory.LOGIT.Rd | 26 trajeR-1.0/trajeR/man/plotrajeR.Trajectory.NL.Rd | 27 trajeR-1.0/trajeR/man/plotrajeR.Trajectory.POIS.Rd | 29 trajeR-1.0/trajeR/man/plotrajeR.Trajectory.ZIP.Rd | 29 trajeR-1.0/trajeR/man/print.Trajectory.CNORM.Rd | 10 trajeR-1.0/trajeR/man/print.Trajectory.LOGIT.Rd | 10 trajeR-1.0/trajeR/man/print.Trajectory.NL.Rd | 10 trajeR-1.0/trajeR/man/print.Trajectory.POIS.Rd | 10 trajeR-1.0/trajeR/man/print.trajectory.mult.Rd |only trajeR-1.0/trajeR/man/propAssign.Rd | 13 trajeR-1.0/trajeR/man/trajeR.BETA.Rd | 99 trajeR-1.0/trajeR/man/trajeR.CNORM.Rd | 104 trajeR-1.0/trajeR/man/trajeR.LOGIT.Rd | 90 trajeR-1.0/trajeR/man/trajeR.NL.Rd | 101 trajeR-1.0/trajeR/man/trajeR.POIS.Rd | 94 trajeR-1.0/trajeR/man/trajeR.Rd | 147 trajeR-1.0/trajeR/man/trajeR.ZIP.Rd | 98 trajeR-1.0/trajeR/man/trajeRAIC.Rd | 8 trajeR-1.0/trajeR/man/trajeRBIC.Rd | 8 trajeR-1.0/trajeR/man/trajeRSH.Rd | 25 trajeR-1.0/trajeR/man/trajeR_mult.Rd |only trajeR-1.0/trajeR/src/Beta.cpp | 554 +- trajeR-1.0/trajeR/src/CensoredNormal.cpp | 2742 ++++++------ trajeR-1.0/trajeR/src/CensoredNormalMatrixEM.cpp | 1 trajeR-1.0/trajeR/src/CommonFunction.cpp | 141 trajeR-1.0/trajeR/src/LOGITMatrixEM.cpp | 5 trajeR-1.0/trajeR/src/Logit.cpp | 1623 ++++--- trajeR-1.0/trajeR/src/Makevars | 32 trajeR-1.0/trajeR/src/Makevars.win | 14 trajeR-1.0/trajeR/src/Pois.cpp | 375 - trajeR-1.0/trajeR/src/Pois.h |only trajeR-1.0/trajeR/src/RcppExports.cpp | 2322 ++++++++++ trajeR-1.0/trajeR/src/ZIP.cpp | 2519 +++++------ trajeR-1.0/trajeR/src/ZIPMatrixEM.cpp | 50 trajeR-1.0/trajeR/src/multi.cpp | 3464 +++++++--------- trajeR-1.0/trajeR/vignettes |only 97 files changed, 15883 insertions(+), 8696 deletions(-)
Title: Pedigree-based Relatedness Coefficients
Description: Recursive algorithms for computing various relatedness
coefficients, including pairwise kinship, kappa and identity
coefficients. Both autosomal and X-linked coefficients are computed.
Founders are allowed to be inbred, which enables construction of any
given kappa coefficients, as described in Vigeland (2020)
<doi:10.1007/s00285-020-01505-x>. In addition to the standard
coefficients, 'ribd' also computes a range of lesser-known
coefficients, including generalised kinship coefficients, multi-person
coefficients and two-locus coefficients (Vigeland, 2023,
<doi:10.1093/g3journal/jkac326>). Many features of 'ribd' are
available through the online app 'QuickPed' at
<https://magnusdv.shinyapps.io/quickped>; see Vigeland (2022)
<doi:10.1186/s12859-022-04759-y>.
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between ribd versions 1.7.1 dated 2025-02-08 and 1.7.2 dated 2026-08-03
DESCRIPTION | 14 ++-- MD5 | 80 ++++++++++++------------- NEWS.md | 21 ++++++ R/ancestralKinship.R |only R/coeffTable.R | 20 +++++- R/condensedIdentity.R | 2 R/constructPedigree.R | 2 R/external_relatedness.R | 4 - R/gKinship.R | 98 ++++++++++++++++++++++++------- R/gip.R | 10 ++- R/ibdDraw.R | 8 +- R/ibdTriangle.R | 80 ++++++++++++++++--------- R/identityCoefs.R | 66 +++++++++++++------- R/identity_GC.R | 5 + R/identity_Karigl.R | 3 R/identity_LS.R | 5 + R/identity_WL.R | 4 - R/kappaIbd.R | 34 +++++++--- R/kinship.R | 27 +++----- R/twoLocusGeneralisedKinship_boundary.R | 2 R/twoLocusIBD.R | 4 - R/twoLocusIdentity.R | 17 +---- R/twoLocusInbreeding.R | 1 R/twoLocusKinship.R | 2 R/twoLocusPlot.R | 2 R/utils.R | 27 ++++++-- README.md | 18 ++--- build/partial.rdb |binary inst/WORDLIST | 9 ++ man/constructPedigree.Rd | 2 man/figures/README-coef-construct-1.png |binary man/figures/README-halfsibstack-1.png |binary man/figures/README-triangle-S-1.png |binary man/gKinship.Rd | 24 +++---- man/ibdTriangle.Rd | 11 +-- man/ribd-package.Rd | 5 + tests/testthat/test-coeffTable.R |only tests/testthat/test-generalisedKinship.R | 4 - tests/testthat/test-identity.R | 6 + tests/testthat/test-kappa.R | 13 ++++ tests/testthat/test-two-locus-identity.R | 22 ++++++ tests/testthat/test-two-locus-kinship.R | 11 +++ 42 files changed, 443 insertions(+), 220 deletions(-)
Title: The Equiplot Graph and Complex Inequality Measures
Description: Generates the equiplot, an iconic dot-plot graph for visualizing inequalities, as well as three complex inequality measures: the slope index of inequality, the concentration index and the mean absolute difference to the mean. For more details see World Health Organization (2013) <https://www.who.int/docs/default-source/gho-documents/health-equity/handbook-on-health-inequality-monitoring/handbook-on-health-inequality-monitoring.pdf>.
Author: Leonardo Ferreira [aut, cre],
Luisa Arroyave [aut]
Maintainer: Leonardo Ferreira <lferreira@equidade.org>
Diff between ICEHmeasures versions 1.1.0 dated 2026-04-16 and 2.0.0 dated 2026-08-03
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ NAMESPACE | 1 + NEWS.md |only R/cixr.R | 8 ++++---- R/equiplot.R | 35 ++++++++++++++++++++++++++++++----- R/siilogit.R | 1 + man/equiplot.Rd | 18 ++++++++++++++---- 8 files changed, 61 insertions(+), 23 deletions(-)
Title: Utilities to Weave Hydrologic Fabrics
Description: A collection of utilities that support creation of network attributes for hydrologic networks. Methods and algorithms implemented are documented in Moore et al. (2019) <doi:10.3133/ofr20191096>, Cormen and Leiserson (2022) <ISBN:9780262046305> and Verdin and Verdin (1999) <doi:10.1016/S0022-1694(99)00011-6>.
Author: David Blodgett [aut, cre] ,
Andrew Psoras [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between hydroloom versions 1.2.0 dated 2026-05-23 and 1.2.1 dated 2026-08-03
hydroloom-1.2.0/hydroloom/inst/doc/accumulate_downstream.R |only hydroloom-1.2.0/hydroloom/inst/doc/accumulate_downstream.Rmd |only hydroloom-1.2.0/hydroloom/inst/doc/accumulate_downstream.html |only hydroloom-1.2.0/hydroloom/inst/doc/advanced_network.R |only hydroloom-1.2.0/hydroloom/inst/doc/advanced_network.Rmd |only hydroloom-1.2.0/hydroloom/inst/doc/advanced_network.html |only hydroloom-1.2.0/hydroloom/inst/doc/flow-table.R |only hydroloom-1.2.0/hydroloom/inst/doc/flow-table.Rmd |only hydroloom-1.2.0/hydroloom/inst/doc/flow-table.html |only hydroloom-1.2.0/hydroloom/inst/doc/network_navigation.R |only hydroloom-1.2.0/hydroloom/inst/doc/network_navigation.Rmd |only hydroloom-1.2.0/hydroloom/inst/doc/network_navigation.html |only hydroloom-1.2.0/hydroloom/inst/doc/non-dendritic.R |only hydroloom-1.2.0/hydroloom/inst/doc/non-dendritic.Rmd |only hydroloom-1.2.0/hydroloom/inst/doc/non-dendritic.html |only hydroloom-1.2.0/hydroloom/vignettes/accumulate_downstream.Rmd |only hydroloom-1.2.0/hydroloom/vignettes/advanced_network.Rmd |only hydroloom-1.2.0/hydroloom/vignettes/flow-table-fig.jpeg |only hydroloom-1.2.0/hydroloom/vignettes/flow-table.Rmd |only hydroloom-1.2.0/hydroloom/vignettes/network_navigation.Rmd |only hydroloom-1.2.0/hydroloom/vignettes/non-dendritic.Rmd |only hydroloom-1.2.1/hydroloom/DESCRIPTION | 12 hydroloom-1.2.1/hydroloom/MD5 | 242 - hydroloom-1.2.1/hydroloom/NEWS.md | 17 hydroloom-1.2.1/hydroloom/R/00_hydroloom.R | 462 +- hydroloom-1.2.1/hydroloom/R/accumulate_downstream.R | 638 +-- hydroloom-1.2.1/hydroloom/R/add_divergence.R | 986 +++--- hydroloom-1.2.1/hydroloom/R/add_levelpaths.R | 664 ++-- hydroloom-1.2.1/hydroloom/R/add_measures.R | 238 - hydroloom-1.2.1/hydroloom/R/add_pathlength.R | 154 hydroloom-1.2.1/hydroloom/R/add_pfafstetter.R | 492 +-- hydroloom-1.2.1/hydroloom/R/add_streamorder-level.R | 610 +-- hydroloom-1.2.1/hydroloom/R/add_toids.R | 310 - hydroloom-1.2.1/hydroloom/R/align_names.R | 278 - hydroloom-1.2.1/hydroloom/R/check_hy_graph.R | 456 +- hydroloom-1.2.1/hydroloom/R/check_valid.R | 518 +-- hydroloom-1.2.1/hydroloom/R/disambiguate.R | 234 - hydroloom-1.2.1/hydroloom/R/dissolve_polygons.R | 712 ++-- hydroloom-1.2.1/hydroloom/R/get_bridges.R | 444 +- hydroloom-1.2.1/hydroloom/R/get_hydro_location.R | 156 hydroloom-1.2.1/hydroloom/R/hy.R | 366 +- hydroloom-1.2.1/hydroloom/R/hy_classes.R | 1614 +++++----- hydroloom-1.2.1/hydroloom/R/index_points_to_lines.R | 1012 +++--- hydroloom-1.2.1/hydroloom/R/make_attribute_topology.R | 208 - hydroloom-1.2.1/hydroloom/R/make_index_ids.R | 974 +++--- hydroloom-1.2.1/hydroloom/R/make_node_topology.R | 538 +-- hydroloom-1.2.1/hydroloom/R/navigate_connected_paths.R | 404 +- hydroloom-1.2.1/hydroloom/R/navigate_network_dfs.R | 530 +-- hydroloom-1.2.1/hydroloom/R/navigation_network.R | 788 ++-- hydroloom-1.2.1/hydroloom/R/sort_network.R | 660 ++-- hydroloom-1.2.1/hydroloom/R/subset_network.R | 254 - hydroloom-1.2.1/hydroloom/R/to_flownetwork.R | 270 - hydroloom-1.2.1/hydroloom/R/utils.R | 682 ++-- hydroloom-1.2.1/hydroloom/README.md | 61 hydroloom-1.2.1/hydroloom/build/vignette.rds |binary hydroloom-1.2.1/hydroloom/inst/CITATION | 24 hydroloom-1.2.1/hydroloom/inst/doc/hydroloom.R | 352 +- hydroloom-1.2.1/hydroloom/inst/doc/hydroloom.Rmd | 695 ++-- hydroloom-1.2.1/hydroloom/inst/doc/hydroloom.html | 1555 ++++----- hydroloom-1.2.1/hydroloom/man/accumulate_downstream.Rd | 236 - hydroloom-1.2.1/hydroloom/man/add_divergence.Rd | 262 - hydroloom-1.2.1/hydroloom/man/add_levelpaths.Rd | 234 - hydroloom-1.2.1/hydroloom/man/add_measures.Rd | 100 hydroloom-1.2.1/hydroloom/man/add_pathlength.Rd | 84 hydroloom-1.2.1/hydroloom/man/add_pfafstetter.Rd | 200 - hydroloom-1.2.1/hydroloom/man/add_return_divergence.Rd | 142 hydroloom-1.2.1/hydroloom/man/add_streamlevel.Rd | 136 hydroloom-1.2.1/hydroloom/man/add_streamorder.Rd | 114 hydroloom-1.2.1/hydroloom/man/add_toids.Rd | 110 hydroloom-1.2.1/hydroloom/man/add_topo_sort.Rd | 78 hydroloom-1.2.1/hydroloom/man/check_hy_graph.Rd | 70 hydroloom-1.2.1/hydroloom/man/check_valid.Rd | 82 hydroloom-1.2.1/hydroloom/man/disambiguate_indexes.Rd | 130 hydroloom-1.2.1/hydroloom/man/dissolve_polygons.Rd | 288 - hydroloom-1.2.1/hydroloom/man/figures/github-social.png |only hydroloom-1.2.1/hydroloom/man/format_index_ids.Rd | 46 hydroloom-1.2.1/hydroloom/man/get_bridge_flowlines.Rd | 114 hydroloom-1.2.1/hydroloom/man/get_hydro_location.Rd | 68 hydroloom-1.2.1/hydroloom/man/get_node.Rd | 72 hydroloom-1.2.1/hydroloom/man/get_partial_length.Rd | 78 hydroloom-1.2.1/hydroloom/man/hy.Rd | 84 hydroloom-1.2.1/hydroloom/man/hy_capabilities.Rd | 62 hydroloom-1.2.1/hydroloom/man/hy_flownetwork.Rd | 188 - hydroloom-1.2.1/hydroloom/man/hy_network_type.Rd | 62 hydroloom-1.2.1/hydroloom/man/index_points_to_lines.Rd | 260 - hydroloom-1.2.1/hydroloom/man/index_points_to_waterbodies.Rd | 112 hydroloom-1.2.1/hydroloom/man/is_dendritic.Rd | 60 hydroloom-1.2.1/hydroloom/man/make_attribute_topology.Rd | 100 hydroloom-1.2.1/hydroloom/man/make_fromids.Rd | 52 hydroloom-1.2.1/hydroloom/man/make_index_ids.Rd | 156 hydroloom-1.2.1/hydroloom/man/make_node_topology.Rd | 132 hydroloom-1.2.1/hydroloom/man/navigate_connected_paths.Rd | 86 hydroloom-1.2.1/hydroloom/man/navigate_hydro_network.Rd | 176 - hydroloom-1.2.1/hydroloom/man/navigate_network_dfs.Rd | 130 hydroloom-1.2.1/hydroloom/man/rename_geometry.Rd | 52 hydroloom-1.2.1/hydroloom/man/rescale_measures.Rd | 70 hydroloom-1.2.1/hydroloom/man/sort_network.Rd | 156 hydroloom-1.2.1/hydroloom/man/subset_network.Rd | 128 hydroloom-1.2.1/hydroloom/man/to_flownetwork.Rd | 122 hydroloom-1.2.1/hydroloom/tests/testthat.R | 24 hydroloom-1.2.1/hydroloom/tests/testthat/data/diversions.csv | 120 hydroloom-1.2.1/hydroloom/tests/testthat/data/diversions.geojson | 132 hydroloom-1.2.1/hydroloom/tests/testthat/data/simple_diversions.geojson | 78 hydroloom-1.2.1/hydroloom/tests/testthat/test_accumulate.R | 484 +- hydroloom-1.2.1/hydroloom/tests/testthat/test_add_divergence.R | 580 +-- hydroloom-1.2.1/hydroloom/tests/testthat/test_add_levelpaths.R | 358 +- hydroloom-1.2.1/hydroloom/tests/testthat/test_add_measures.R | 98 hydroloom-1.2.1/hydroloom/tests/testthat/test_add_pathlength.R | 22 hydroloom-1.2.1/hydroloom/tests/testthat/test_add_pfafstetter.R | 112 hydroloom-1.2.1/hydroloom/tests/testthat/test_add_toids.R | 92 hydroloom-1.2.1/hydroloom/tests/testthat/test_check_hy_graph.R | 228 - hydroloom-1.2.1/hydroloom/tests/testthat/test_check_valid.R | 219 + hydroloom-1.2.1/hydroloom/tests/testthat/test_dissolve_polygons.R | 490 +-- hydroloom-1.2.1/hydroloom/tests/testthat/test_get_bridges.R | 594 +-- hydroloom-1.2.1/hydroloom/tests/testthat/test_get_hydro_location.R | 64 hydroloom-1.2.1/hydroloom/tests/testthat/test_get_partial_length.R | 90 hydroloom-1.2.1/hydroloom/tests/testthat/test_hy_classes.R | 752 ++-- hydroloom-1.2.1/hydroloom/tests/testthat/test_hydroloom.R | 114 hydroloom-1.2.1/hydroloom/tests/testthat/test_index.R | 684 ++-- hydroloom-1.2.1/hydroloom/tests/testthat/test_is_outlet.R | 78 hydroloom-1.2.1/hydroloom/tests/testthat/test_make_attribute_topology.R | 76 hydroloom-1.2.1/hydroloom/tests/testthat/test_make_index_ids.R | 408 +- hydroloom-1.2.1/hydroloom/tests/testthat/test_make_node_topology.R | 280 - hydroloom-1.2.1/hydroloom/tests/testthat/test_navigate_connected_paths.R | 144 hydroloom-1.2.1/hydroloom/tests/testthat/test_navigate_hydro_network.R | 354 +- hydroloom-1.2.1/hydroloom/tests/testthat/test_navigate_network_dfs.R | 314 - hydroloom-1.2.1/hydroloom/tests/testthat/test_outlet_conventions.R | 306 - hydroloom-1.2.1/hydroloom/tests/testthat/test_sort_network.R | 520 +-- hydroloom-1.2.1/hydroloom/tests/testthat/test_streamorder-level.R | 204 - hydroloom-1.2.1/hydroloom/tests/testthat/test_subset_network.R | 170 - hydroloom-1.2.1/hydroloom/tests/testthat/test_to_flownetwork.R | 108 hydroloom-1.2.1/hydroloom/tests/testthat/test_utils.R | 258 - hydroloom-1.2.1/hydroloom/vignettes/hydroloom.Rmd | 695 ++-- 133 files changed, 16405 insertions(+), 16287 deletions(-)
Title: Automatic Database Normalisation for Data Frames
Description: Automatic normalisation of a data frame to third normal form, with
the intention of easing the process of data cleaning. (Usage to design your
actual database for you is not advised.)
Originally inspired by the 'AutoNormalize' library for 'Python' by 'Alteryx'
(<https://github.com/alteryx/autonormalize>), with various changes and
improvements. Automatic discovery of functional or approximate dependencies,
normalisation based on those, and plotting of the resulting "database" via
'Graphviz', with options to exclude some attributes at discovery time, or
remove discovered dependencies at normalisation time.
Author: Mark Webster [aut, cre]
Maintainer: Mark Webster <markwebster204@yahoo.co.uk>
Diff between autodb versions 3.2.4 dated 2025-11-17 and 3.3.0 dated 2026-08-03
DESCRIPTION | 8 MD5 | 128 +- NAMESPACE | 24 NEWS.md | 448 +++++---- R/DFD.r | 369 -------- R/FDHits.r | 78 + R/autodb.r | 3 R/autokey.r |only R/compatibility.r | 218 ++++ R/database.r | 103 ++ R/database_schema.r | 22 R/decompose.r | 32 R/discover.r | 429 +++++++++ R/discover_keys.r |only R/functional_dependency.r | 67 - R/join.r | 110 ++ R/partition_handler.r | 8 R/plot.r | 555 +++++++++--- R/print_utilities.r | 4 R/rejoin.r | 5 R/relation.r | 83 + R/relation_schema.r | 38 R/shared_class_functions.r | 45 + R/synthesise.r | 37 build/vignette.rds |binary inst/WORDLIST | 6 inst/doc/autodb.html | 64 - inst/doc/limits.html | 42 inst/doc/nest.R |only inst/doc/nest.Rmd |only inst/doc/nest.html |only inst/doc/nudge.html | 52 - inst/doc/null.html | 16 inst/doc/plans.html | 46 - man/add_lookup.Rd |only man/autokey.Rd |only man/d2.Rd | 39 man/d2.data.frame.Rd | 6 man/d2.database.Rd | 12 man/d2.relation.Rd | 6 man/df_duplicated.Rd | 7 man/discover.Rd | 2 man/discover_keys.Rd |only man/functional_dependency.Rd | 1 man/gv.Rd | 30 man/gv.data.frame.Rd | 6 man/gv.database.Rd | 6 man/gv.relation.Rd | 6 man/remove_extraneous.Rd |only tests/testthat/helper.r | 677 ++++++++++----- tests/testthat/test-FDHits.r | 19 tests/testthat/test-autodb.r | 48 - tests/testthat/test-autokey.r |only tests/testthat/test-autoref.r | 6 tests/testthat/test-compatibility.r | 127 ++ tests/testthat/test-database.r | 46 - tests/testthat/test-database_schema.r | 44 tests/testthat/test-decompose.r | 229 ++--- tests/testthat/test-discover.r | 1211 ++++++++++----------------- tests/testthat/test-discover_keys.r |only tests/testthat/test-functional_dependency.r | 79 + tests/testthat/test-helper.r | 501 +++++------ tests/testthat/test-join.r | 80 + tests/testthat/test-normalise.r | 4 tests/testthat/test-plot.r | 653 +++++++++++++- tests/testthat/test-rejoin.r | 6 tests/testthat/test-relation.r | 45 - tests/testthat/test-relation_schema.r | 45 - tests/testthat/test-shared_class_functions.r | 517 ++++++++++- tests/testthat/test-synthesise.r | 50 + vignettes/nest.Rmd |only 71 files changed, 5088 insertions(+), 2460 deletions(-)
Title: Native R 'torch' Implementation of 'OpenAI' 'Whisper'
Description: Speech-to-text transcription using a native R 'torch' implementation
of 'OpenAI' 'Whisper' model <https://github.com/openai/whisper>. Supports
multiple model sizes from tiny (39M parameters) to large-v3 (1.5B parameters)
with integrated download from 'HuggingFace' <https://huggingface.co/> via the
'hfhub' package. Provides automatic speech recognition with optional language
detection and translation to English. Audio preprocessing, mel spectrogram
computation, and transformer-based encoder-decoder inference are all
implemented in R using the 'torch' package.
Author: Troy Hernandez [aut, cre] ,
cornball.ai [cph],
OpenAI [cph] )
Maintainer: Troy Hernandez <troy@cornball.ai>
Diff between whisper versions 0.4.0 dated 2026-06-19 and 0.5.1 dated 2026-08-03
DESCRIPTION | 9 ++- MD5 | 29 +++++++++--- NAMESPACE | 8 +++ NEWS.md | 68 ++++++++++++++++++++++++++++++ R/audio.R | 15 ++++-- R/devices.R | 95 ++++++++++++++++++++++++++++++++++-------- R/interop.R |only R/resident.R |only R/transcribe.R | 2 inst/tinytest/test_interop.R |only inst/tinytest/test_resident.R |only inst/tinytest/test_tune_gc.R |only man/audio_to_mel.Rd | 15 ++++-- man/print.whisper_resident.Rd |only man/print.whisper_result.Rd |only man/resident_activate.Rd |only man/resident_deactivate.Rd |only man/resident_load.Rd |only man/resident_status.Rd |only man/resident_transcribe.Rd |only man/resident_unload.Rd |only man/whisper_tune_gc.Rd | 8 +++ 22 files changed, 212 insertions(+), 37 deletions(-)
Title: Weighting for Covariate Balance in Observational Studies
Description: Generates balancing weights for causal effect estimation in observational studies with
binary, multi-category, or continuous point or longitudinal treatments by easing and
extending the functionality of several R packages and providing in-house estimation methods.
Available methods include those that rely on parametric modeling, optimization, and machine learning. Also
allows for assessment of weights and checking of covariate balance by interfacing directly
with the 'cobalt' package. Methods for estimating weighted regression models that take into account
uncertainty in the estimation of the weights via M-estimation or bootstrapping are available. See the vignette "Installing Supporting Packages" for instructions on how
to install any optional package 'WeightIt' uses, including those that may not be on CRAN.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between WeightIt versions 1.7.0 dated 2026-04-22 and 2.0.0 dated 2026-08-03
DESCRIPTION | 24 MD5 | 192 +++--- NAMESPACE | 2 NEWS.md | 127 ++++ R/anova.glm_weightit.R | 2 R/cens.R |only R/coxph_weightit.R | 173 ++++- R/functions_for_processing.R | 747 +++++++++++++++++++++---- R/get_w_from_ps.R | 43 + R/glm_weightit-methods.R | 48 + R/glm_weightit.R | 29 R/glm_weightit_helpers.R | 190 +++++- R/multinom_weightit.R | 189 +++++- R/ordinal_weightit.R | 392 ++++++++++++- R/sbps.R | 5 R/summary.weightit.R | 10 R/treat.R | 4 R/utils.R | 230 +++++++ R/weightit.R | 211 +++++-- R/weightit.fit.R | 120 +++- R/weightit2bart.R | 315 +++++++--- R/weightit2cbps.R | 613 ++++++++++++++++++-- R/weightit2cfd.R | 175 +++++ R/weightit2ebal.R | 223 +++++++ R/weightit2energy.R | 190 ++++++ R/weightit2gbm.R | 342 +++++++---- R/weightit2glm.R | 594 +++++++++++++------ R/weightit2ipt.R | 145 ++++ R/weightit2npcbps.R | 8 R/weightit2null.R | 6 R/weightit2optweight.R | 71 ++ R/weightit2ps.R | 50 + R/weightit2super.R | 268 ++++++-- R/weightit2user.R | 2 R/weightitMSM.R | 384 ++++++++++-- R/weightit_methods.R | 34 - README.md | 93 +-- build/stage23.rdb |binary build/vignette.rds |binary inst/doc/WeightIt.Rmd | 53 + inst/doc/WeightIt.html | 97 ++- inst/doc/estimating-effects.Rmd | 20 inst/doc/estimating-effects.html | 87 +- inst/doc/installing-packages.Rmd | 76 +- inst/doc/installing-packages.html | 91 ++- man/WeightIt-package.Rd | 5 man/anova.glm_weightit.Rd | 2 man/coxph_weightit.Rd | 3 man/dot-cens.Rd |only man/dot-weightit_methods.Rd | 8 man/get_w_from_ps.Rd | 9 man/glm_weightit.Rd | 5 man/method_bart.Rd | 65 +- man/method_cbps.Rd | 34 - man/method_cfd.Rd | 23 man/method_ebal.Rd | 7 man/method_energy.Rd | 11 man/method_gbm.Rd | 41 - man/method_glm.Rd | 93 ++- man/method_ipt.Rd | 9 man/method_npcbps.Rd | 5 man/method_optweight.Rd | 7 man/method_super.Rd | 44 - man/method_user.Rd | 2 man/multinom_weightit.Rd | 53 + man/ordinal_weightit.Rd | 66 ++ man/sbps.Rd | 4 man/weightit.Rd | 116 +++ man/weightit.fit.Rd | 27 man/weightitMSM.Rd | 124 +++- tests/testthat/fixtures/make_test_data.R | 41 + tests/testthat/fixtures/test_data.rds |binary tests/testthat/helpers.R | 48 + tests/testthat/test-anova.R |only tests/testthat/test-by_mest.R |only tests/testthat/test-calibrate.R |only tests/testthat/test-censoring.R |only tests/testthat/test-coxph_weightit.R |only tests/testthat/test-empty_formula.R |only tests/testthat/test-glm_weightit.R | 230 +++++++ tests/testthat/test-method_bart.R |only tests/testthat/test-method_bart_re.R |only tests/testthat/test-method_cbps.R | 331 ++++++----- tests/testthat/test-method_cfd.R |only tests/testthat/test-method_ebal.R | 287 ++++----- tests/testthat/test-method_energy.R |only tests/testthat/test-method_gbm.R |only tests/testthat/test-method_glm.R | 254 ++++++++ tests/testthat/test-method_glm_re.R |only tests/testthat/test-method_ipt.R | 188 ++---- tests/testthat/test-method_npcbps.R |only tests/testthat/test-method_optweight.R |only tests/testthat/test-method_super.R |only tests/testthat/test-missing.R |only tests/testthat/test-moments.R | 263 +++++--- tests/testthat/test-multinom_weightit.R | 405 +++++++++++++ tests/testthat/test-ordinal_weightit.R | 443 ++++++++++++++ tests/testthat/test-predict.R |only tests/testthat/test-ps_arg.R |only tests/testthat/test-sbps.R |only tests/testthat/test-summary_plot_as_weightit.R |only tests/testthat/test-trim_ESS_full_rank.R |only tests/testthat/test-update.R | 5 tests/testthat/test-vcov_arg.R | 306 ++++++++-- tests/testthat/test-weightitMSM.R |only vignettes/WeightIt.Rmd | 53 + vignettes/estimating-effects.Rmd | 20 vignettes/installing-packages.Rmd | 76 +- vignettes/references.bib | 182 ++++++ 109 files changed, 8524 insertions(+), 2046 deletions(-)
Title: 'vcd' Extensions and Additions
Description: Provides additional data sets, methods and documentation to complement the 'vcd' package for Visualizing Categorical Data
and the 'gnm' package for Generalized Nonlinear Models.
In particular, 'vcdExtra' extends mosaic, assoc and sieve plots from 'vcd' to handle 'glm()' and 'gnm()' models and
adds a 3D version in 'mosaic3d'. Additionally, methods are provided for comparing and visualizing lists of
'glm' and 'loglm' objects. This package is now a support package for the book, "Discrete Data Analysis with R" by
Michael Friendly and David Meyer.
Author: Michael Friendly [aut, cre] ,
David Meyer [ctb],
Achim Zeileis [ctb] ,
Duncan Murdoch [ctb],
Heather Turner [ctb] ,
David Firth [ctb],
Daniel Sabanes Bove [ctb],
Matt Kumar [ctb],
Shuguang Sun [ctb],
Gavin Klorfine [aut]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between vcdExtra versions 0.9.6 dated 2026-06-07 and 0.9.7 dated 2026-08-03
vcdExtra-0.9.6/vcdExtra/R/summarise-old.R |only vcdExtra-0.9.7/vcdExtra/DESCRIPTION | 15 - vcdExtra-0.9.7/vcdExtra/MD5 | 59 ++-- vcdExtra-0.9.7/vcdExtra/NAMESPACE | 4 vcdExtra-0.9.7/vcdExtra/NEWS.md | 21 + vcdExtra-0.9.7/vcdExtra/R/CMHtest.R | 228 +++++++++++++++--- vcdExtra-0.9.7/vcdExtra/R/breslow_day_test.R |only vcdExtra-0.9.7/vcdExtra/R/color_table.R | 92 ++++++- vcdExtra-0.9.7/vcdExtra/R/data.R | 21 + vcdExtra-0.9.7/vcdExtra/build/partial.rdb |binary vcdExtra-0.9.7/vcdExtra/build/vignette.rds |binary vcdExtra-0.9.7/vcdExtra/inst/doc/a1-creating.html | 4 vcdExtra-0.9.7/vcdExtra/inst/doc/a2-tests.html | 25 + vcdExtra-0.9.7/vcdExtra/inst/doc/a3-loglinear.html | 4 vcdExtra-0.9.7/vcdExtra/inst/doc/a4-mosaics.html | 8 vcdExtra-0.9.7/vcdExtra/inst/doc/a5-demo-housing.html | 4 vcdExtra-0.9.7/vcdExtra/inst/doc/a6-mobility.html | 10 vcdExtra-0.9.7/vcdExtra/inst/doc/a7-continuous.html | 6 vcdExtra-0.9.7/vcdExtra/inst/doc/datasets.html | 4 vcdExtra-0.9.7/vcdExtra/inst/doc/tidyCats.Rmd | 7 vcdExtra-0.9.7/vcdExtra/inst/doc/tidyCats.html | 13 - vcdExtra-0.9.7/vcdExtra/man/CMHtest.Rd | 94 +++++-- vcdExtra-0.9.7/vcdExtra/man/GKgamma.Rd | 1 vcdExtra-0.9.7/vcdExtra/man/HLtest.Rd | 1 vcdExtra-0.9.7/vcdExtra/man/Mental.Rd | 21 + vcdExtra-0.9.7/vcdExtra/man/assoc_graph.Rd | 2 vcdExtra-0.9.7/vcdExtra/man/breslow_day_test.Rd |only vcdExtra-0.9.7/vcdExtra/man/color_table.Rd | 33 ++ vcdExtra-0.9.7/vcdExtra/man/figures/logo.png |binary vcdExtra-0.9.7/vcdExtra/man/woolf_test.Rd | 1 vcdExtra-0.9.7/vcdExtra/man/zero.test.Rd | 1 vcdExtra-0.9.7/vcdExtra/vignettes/tidyCats.Rmd | 7 32 files changed, 533 insertions(+), 153 deletions(-)
Title: Observational Health Data Sciences and Informatics Report
Generator
Description: Extract results into R from the Observational Health Data Sciences and Informatics result database (see <https://ohdsi.github.io/Strategus/results-schema/index.html>) and generate reports/presentations via 'quarto' that summarize results in HTML format. Learn more about 'OhdsiReportGenerator' at <https://ohdsi.github.io/OhdsiReportGenerator/>.
Author: Jenna Reps [aut, cre],
Anthony Sena [aut]
Maintainer: Jenna Reps <jreps@its.jnj.com>
Diff between OhdsiReportGenerator versions 2.2.0 dated 2026-05-16 and 2.3.1 dated 2026-08-03
OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/inst/sql/sql_server/characterization/getCaseBinaryFeaturesV0.sql |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/inst/sql/sql_server/characterization/getCaseContinuousFeaturesV0.sql |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/inst/sql/sql_server/characterization/getCaseTargetBinaryFeaturesV0.sql |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/inst/sql/sql_server/characterization/getCaseTargetCountsV0.sql |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/inst/sql/sql_server/characterization/getCaseTargetCountsV3_0_0.sql |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/inst/sql/sql_server/characterization/getCharacterizationCohortBinaryV0.sql |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/inst/sql/sql_server/characterization/getCharacterizationCohortBinaryV3_0_0.sql |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/inst/sql/sql_server/characterization/getCharacterizationCohortCountsV0.sql |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/inst/sql/sql_server/characterization/getCharacterizationCohortCountsV3_0_0.sql |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/inst/sql/sql_server/characterization/getDechallengeRechallenge.sql |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/inst/sql/sql_server/characterization/getTargetBinaryFeaturesV0.sql |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/inst/sql/sql_server/characterization/getTargetBinaryFeaturesV3_0_0.sql |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/inst/sql/sql_server/characterization/getTargetContinuousFeaturesV0.sql |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/inst/sql/sql_server/characterization/getTargetContinuousFeaturesV3_0_0.sql |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/inst/sql/sql_server/characterization/getTimeToEvent.sql |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/man/getCaseTargetCounts.Rd |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/man/getCharacterizationCohortBinary.Rd |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/man/getCharacterizationCohortContinuous.Rd |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/man/getCharacterizationOutcomes.Rd |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/man/getCharacterizationTargets.Rd |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/man/getIncidenceOutcomes.Rd |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/man/getIncidenceTargets.Rd |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/man/getTargetBinaryFeatures.Rd |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/man/getTargetContinuousFeatures.Rd |only OhdsiReportGenerator-2.2.0/OhdsiReportGenerator/tests/testthat/Rplots.pdf |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/DESCRIPTION | 10 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/MD5 | 303 - OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/NAMESPACE | 21 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/R/CharacterizationPlots.R | 173 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/R/CharacterzationQueries.R | 2896 ++++------ OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/R/Generate.R | 27 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/R/Indexes.R | 29 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/R/SummaryReports.R | 23 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/R/TargetOutcomeInfo.R | 8 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/build/vignette.rds |binary OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/doc/ExampleCode.R | 34 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/doc/ExampleCode.Rmd | 36 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/doc/ExampleCode.html | 846 -- OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/exampledata/results.sqlite.zip |binary OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getBinaryCaseSeriesV0.sql | 40 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getBinaryCaseSeriesV3_0_0.sql | 42 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getBinaryCaseSeriesV4_0_0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getBinaryRiskFactorsV0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getBinaryRiskFactorsV3_0_0.sql | 57 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getBinaryRiskFactorsV4_0_0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getBinaryTargetBaselineV0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getBinaryTargetBaselineV3_0_0.sql | 21 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getBinaryTargetBaselineV4_0_0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getCaseCountsV0.sql | 20 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getCaseCountsV3_0_0.sql | 47 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getCaseCountsV4_0_0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getCaseSettingsV0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getCaseSettingsV3_0_0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getCaseSettingsV4_0_0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getCharacterizationOutcomesV4_0_0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getContinuousCaseSeriesV0.sql | 46 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getContinuousCaseSeriesV3_0_0.sql | 38 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getContinuousCaseSeriesV4_0_0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getContinuousRiskFactorsV0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getContinuousRiskFactorsV3_0_0.sql | 16 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getContinuousRiskFactorsV4_0_0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getContinuousTargetBaselineV0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getContinuousTargetBaselineV3_0_0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getContinuousTargetBaselineV4_0_0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getDechallengeRechallengeFails.sql | 2 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getDechallengeRechallengeV3_0_0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getDechallengeRechallengeV4_0_0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getIncidenceOutcomesV0.sql | 15 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getIncidenceRatesV0.sql | 1 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getIncidenceTargetSettings.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getNonCaseCountsV0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getNonCaseCountsV3_0_0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getNonCaseCountsV4_0_0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getTargetCountsV0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getTargetCountsV3_0_0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getTargetCountsV4_0_0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getTargetIds.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getTargetSettingsV0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getTargetSettingsV3_0_0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getTargetSettingsV4_0_0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getTimeToEventV3_0_0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/getTimeToEventV4_0_0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/characterization/indexesCharacterizationV4_0_0.sql |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/estimation/getCmDiagnosticsDataV5.sql | 2 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/sql/sql_server/estimation/getCmMetaEstimationV5.sql | 12 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/templates/full-report/causal_inference.qmd | 11 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/templates/full-report/characterization.qmd | 35 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/templates/full-report/characterization/demographics.qmd | 136 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/templates/full-report/characterization/index_breakdown.qmd | 125 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/inst/templates/full-report/characterization/risk_factors.qmd | 116 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/OhdsiReportGenerator.Rd | 1 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/addTarColumn.Rd | 14 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/characterizationCompareBinary.Rd |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/characterizationCompareContinuous.Rd |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/createCharacterizationIndexes.Rd | 8 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/createCohortIndexes.Rd | 8 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/createIncidenceIndexes.Rd | 8 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/createPredictionReport.Rd | 6 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/createSccsIndexes.Rd | 8 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/dot-getCmVersion.Rd | 42 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/dot-getSccsVersion.Rd | 42 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/formatBinaryCovariateName.Rd | 14 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/generateFullReport.Rd | 6 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/generateSummaryPredictionReport.Rd | 6 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getAnalysisCohorts.Rd | 6 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getBinaryCaseSeries.Rd | 63 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getBinaryRiskFactors.Rd | 61 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getBinaryTargetBaseline.Rd | 67 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getCMEstimation.Rd | 42 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getCaseCounts.Rd | 65 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getCharacterizationCaseSettings.Rd |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getCharacterizationDemographics.Rd | 53 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getCharacterizationTargetSettings.Rd |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getCmDiagnosticsData.Rd | 42 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getCmMetaEstimation.Rd | 42 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getCmNegativeControlEstimates.Rd | 42 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getCmOutcomes.Rd | 42 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getCmPropensityModel.Rd | 42 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getCmTable.Rd | 42 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getCmTargets.Rd | 42 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getCohortAttrition.Rd | 26 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getCohortCounts.Rd | 26 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getCohortDefinitions.Rd | 26 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getCohortInclusionRules.Rd | 26 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getCohortInclusionStats.Rd | 26 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getCohortInclusionSummary.Rd | 26 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getCohortMeta.Rd | 26 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getCohortSubsetAttrition.Rd | 26 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getCohortSubsetDefinitions.Rd | 26 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getContinuousCaseSeries.Rd | 63 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getContinuousRiskFactors.Rd | 61 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getContinuousTargetBaseline.Rd |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getDechallengeRechallenge.Rd | 53 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getDechallengeRechallengeFails.Rd | 55 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getEventDuration.Rd | 6 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getExampleConnectionDetails.Rd | 14 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getFullPredictionPerformances.Rd | 30 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getIncidenceRates.Rd | 52 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getIncidenceTargetSettings.Rd |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getNonCaseCounts.Rd |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getOutcomeTable.Rd | 14 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getOutcomesUsedInCharacterization.Rd |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getOutcomesUsedInIncidence.Rd |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getPredictionAggregateTopPredictors.Rd | 30 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getPredictionCohorts.Rd | 30 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getPredictionCovariates.Rd | 30 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getPredictionDiagnosticTable.Rd | 30 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getPredictionDiagnostics.Rd | 30 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getPredictionHyperParamSearch.Rd | 30 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getPredictionIntercept.Rd | 30 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getPredictionLift.Rd | 30 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getPredictionModelDesigns.Rd | 30 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getPredictionOutcomes.Rd | 30 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getPredictionPerformanceTable.Rd | 30 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getPredictionPerformances.Rd | 30 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getPredictionTargets.Rd | 30 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getPredictionTopPredictors.Rd | 30 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getSccsDiagnosticsData.Rd | 42 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getSccsEstimation.Rd | 42 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getSccsMetaEstimation.Rd | 42 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getSccsModel.Rd | 42 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getSccsNegativeControlEstimates.Rd | 42 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getSccsOutcomes.Rd | 42 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getSccsTable.Rd | 42 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getSccsTargets.Rd | 42 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getSccsTimeToEvent.Rd | 42 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getSubsetText.Rd | 26 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getTargetCounts.Rd |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getTargetTable.Rd | 14 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getTargetsUsedInCharacterization.Rd |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getTargetsUsedInIncidence.Rd |only OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getTimeToEvent.Rd | 62 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/getTreatmentPathways.Rd | 6 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/kableDark.Rd | 14 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/plotAgeDistributions.Rd | 72 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/plotCmEstimates.Rd | 42 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/plotSccsEstimates.Rd | 42 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/plotSexDistributions.Rd | 71 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/processCohortDefinitionsForQuarto.Rd | 26 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/processCohorts.Rd | 26 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/removeSpaces.Rd | 14 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/restrictCohortDefinitionsForQuarto.Rd | 26 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/man/viewIncidenceRate.Rd | 49 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/tests/testthat/test-CharacterizationPlots.R | 39 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/tests/testthat/test-CharacterizationQueries.R | 1098 ++- OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/tests/testthat/test-Indexes.R | 2 OhdsiReportGenerator-2.3.1/OhdsiReportGenerator/vignettes/ExampleCode.Rmd | 36 187 files changed, 4581 insertions(+), 4466 deletions(-)
More information about OhdsiReportGenerator at CRAN
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Title: A Unified Tidy Interface to R's Machine Learning Ecosystem
Description: Provides a unified tidyverse-compatible interface to R's machine
learning ecosystem - from data ingestion to model publishing. The tl_read()
family reads data from files ('CSV', 'Excel', 'Parquet', 'JSON'), databases
('SQLite', 'PostgreSQL', 'MySQL', 'BigQuery'), and cloud sources ('S3',
'GitHub', 'Kaggle'). The tl_model() function wraps established
implementations from 'glmnet', 'randomForest', 'xgboost', 'e1071', 'rpart',
'gbm', 'nnet', 'cluster', 'dbscan', and others with consistent function
signatures and tidy tibble output. Results flow into unified 'ggplot2'-based
visualization and optional formatted 'gt' tables via the tl_table() family.
The underlying algorithms are unchanged; 'tidylearn' simply makes them
easier to use together. Access raw model objects via the $fit slot for
package-specific functionality.
Methods include random forests Breiman (2001) <doi:10.1023/A:1010933404324>,
LASSO regression Tibshirani (1996) <doi:10.1111/j.2517-6161.1996.tb02080.x>,
elastic [...truncated...]
Author: Cesaire Tobias [aut, cre]
Maintainer: Cesaire Tobias <cesaire@sheetsolved.com>
Diff between tidylearn versions 0.3.1 dated 2026-05-19 and 0.4.0 dated 2026-08-03
tidylearn-0.3.1/tidylearn/man/tl_predict_elastic_net.Rd |only tidylearn-0.3.1/tidylearn/man/tl_predict_lasso.Rd |only tidylearn-0.3.1/tidylearn/man/tl_predict_linear.Rd |only tidylearn-0.3.1/tidylearn/man/tl_predict_polynomial.Rd |only tidylearn-0.3.1/tidylearn/man/tl_predict_regularized.Rd |only tidylearn-0.3.1/tidylearn/man/tl_predict_ridge.Rd |only tidylearn-0.3.1/tidylearn/tests/testthat/Rplots.pdf |only tidylearn-0.4.0/tidylearn/DESCRIPTION | 21 tidylearn-0.4.0/tidylearn/MD5 | 136 +- tidylearn-0.4.0/tidylearn/NAMESPACE | 7 tidylearn-0.4.0/tidylearn/NEWS.md | 338 +++++ tidylearn-0.4.0/tidylearn/R/compute-advisor.R |only tidylearn-0.4.0/tidylearn/R/compute-detection.R |only tidylearn-0.4.0/tidylearn/R/compute-routing.R |only tidylearn-0.4.0/tidylearn/R/core.R | 185 ++- tidylearn-0.4.0/tidylearn/R/metrics.R | 170 ++ tidylearn-0.4.0/tidylearn/R/pipeline.R | 169 +- tidylearn-0.4.0/tidylearn/R/supervised-deep-learning.R | 10 tidylearn-0.4.0/tidylearn/R/supervised-regression.R | 81 - tidylearn-0.4.0/tidylearn/R/supervised-regularization.R | 317 +---- tidylearn-0.4.0/tidylearn/R/supervised-trees.R | 12 tidylearn-0.4.0/tidylearn/R/supervised-xgboost.R | 15 tidylearn-0.4.0/tidylearn/R/tidylearn-package.R |only tidylearn-0.4.0/tidylearn/R/tuning.R | 69 - tidylearn-0.4.0/tidylearn/R/workflows.R | 204 ++- tidylearn-0.4.0/tidylearn/README.md | 61 - tidylearn-0.4.0/tidylearn/build/partial.rdb |only tidylearn-0.4.0/tidylearn/inst/WORDLIST | 116 + tidylearn-0.4.0/tidylearn/inst/doc/automl.R | 19 tidylearn-0.4.0/tidylearn/inst/doc/automl.Rmd | 59 tidylearn-0.4.0/tidylearn/inst/doc/automl.html | 170 +- tidylearn-0.4.0/tidylearn/inst/doc/data-ingestion.R | 27 tidylearn-0.4.0/tidylearn/inst/doc/data-ingestion.Rmd | 27 tidylearn-0.4.0/tidylearn/inst/doc/data-ingestion.html | 34 tidylearn-0.4.0/tidylearn/inst/doc/getting-started.R | 38 tidylearn-0.4.0/tidylearn/inst/doc/getting-started.Rmd | 53 tidylearn-0.4.0/tidylearn/inst/doc/getting-started.html | 366 +++--- tidylearn-0.4.0/tidylearn/inst/doc/integration-workflows.R | 68 - tidylearn-0.4.0/tidylearn/inst/doc/integration-workflows.Rmd | 68 - tidylearn-0.4.0/tidylearn/inst/doc/integration-workflows.html | 233 +-- tidylearn-0.4.0/tidylearn/inst/doc/reporting.R | 19 tidylearn-0.4.0/tidylearn/inst/doc/reporting.Rmd | 20 tidylearn-0.4.0/tidylearn/inst/doc/reporting.html | 346 ++--- tidylearn-0.4.0/tidylearn/inst/doc/supervised-learning.R | 94 - tidylearn-0.4.0/tidylearn/inst/doc/supervised-learning.Rmd | 57 tidylearn-0.4.0/tidylearn/inst/doc/supervised-learning.html | 605 +++++----- tidylearn-0.4.0/tidylearn/inst/doc/unsupervised-learning.R | 67 - tidylearn-0.4.0/tidylearn/inst/doc/unsupervised-learning.Rmd | 14 tidylearn-0.4.0/tidylearn/inst/doc/unsupervised-learning.html | 410 +++--- tidylearn-0.4.0/tidylearn/inst/security |only tidylearn-0.4.0/tidylearn/man/figures/logo.png |binary tidylearn-0.4.0/tidylearn/man/predict.tidylearn_model.Rd | 26 tidylearn-0.4.0/tidylearn/man/print.tidylearn_compute_advice.Rd |only tidylearn-0.4.0/tidylearn/man/print.tidylearn_gpu_check.Rd |only tidylearn-0.4.0/tidylearn/man/tidylearn-package.Rd |only tidylearn-0.4.0/tidylearn/man/tl_auto_ml.Rd | 8 tidylearn-0.4.0/tidylearn/man/tl_check_gpu.Rd |only tidylearn-0.4.0/tidylearn/man/tl_compute_advisor.Rd |only tidylearn-0.4.0/tidylearn/man/tl_cv.Rd | 8 tidylearn-0.4.0/tidylearn/man/tl_evaluate.Rd | 18 tidylearn-0.4.0/tidylearn/man/tl_fit_deep.Rd | 11 tidylearn-0.4.0/tidylearn/man/tl_fit_xgboost.Rd | 8 tidylearn-0.4.0/tidylearn/man/tl_model.Rd | 11 tidylearn-0.4.0/tidylearn/man/tl_run_pipeline.Rd | 7 tidylearn-0.4.0/tidylearn/man/tl_tune_grid.Rd | 112 - tidylearn-0.4.0/tidylearn/tests/testthat/setup.R |only tidylearn-0.4.0/tidylearn/tests/testthat/test-compute-advisor.R |only tidylearn-0.4.0/tidylearn/tests/testthat/test-compute-detection.R |only tidylearn-0.4.0/tidylearn/tests/testthat/test-compute-routing.R |only tidylearn-0.4.0/tidylearn/tests/testthat/test-metrics.R |only tidylearn-0.4.0/tidylearn/tests/testthat/test-pipeline.R |only tidylearn-0.4.0/tidylearn/tests/testthat/test-supervised-predict.R |only tidylearn-0.4.0/tidylearn/tests/testthat/test-tuning.R | 556 ++++++--- tidylearn-0.4.0/tidylearn/tests/testthat/test-unsupervised-predict.R |only tidylearn-0.4.0/tidylearn/tests/testthat/test-workflows.R | 84 + tidylearn-0.4.0/tidylearn/vignettes/automl.Rmd | 59 tidylearn-0.4.0/tidylearn/vignettes/data-ingestion.Rmd | 27 tidylearn-0.4.0/tidylearn/vignettes/getting-started.Rmd | 53 tidylearn-0.4.0/tidylearn/vignettes/integration-workflows.Rmd | 68 - tidylearn-0.4.0/tidylearn/vignettes/reporting.Rmd | 20 tidylearn-0.4.0/tidylearn/vignettes/supervised-learning.Rmd | 57 tidylearn-0.4.0/tidylearn/vignettes/unsupervised-learning.Rmd | 14 82 files changed, 3567 insertions(+), 2285 deletions(-)
Title: Patterned Sensitivity Analysis for IV with Fixed Effects
Description: Patterned sensitivity analysis for instrumental-variables designs
with fixed effects or other residualization steps. The package provides
uniform Conley-style sensitivity as a baseline, researcher-specified
direct-effect patterns, sensitivity paths and tipping points, and optional
confirmatory Beyond Plausibly Exogenous diagnostics.
Author: Ore Koren [aut, cre]
Maintainer: Ore Koren <okoren@iu.edu>
Diff between spliv versions 0.1.1 dated 2026-07-29 and 0.2.1 dated 2026-08-03
spliv-0.1.1/spliv/R/plausexog.R |only spliv-0.1.1/spliv/man/bpe_find_subset.Rd |only spliv-0.1.1/spliv/man/demean_fixest.Rd |only spliv-0.1.1/spliv/man/demean_lfe.Rd |only spliv-0.1.1/spliv/man/embed_prior_into_full_Z.Rd |only spliv-0.1.1/spliv/man/estimate_gamma_zero_first_stage.Rd |only spliv-0.1.1/spliv/man/iv_inst_names.Rd |only spliv-0.1.1/spliv/tests/testthat/test-deprecated-wrapper.R |only spliv-0.2.1/spliv/DESCRIPTION | 6 spliv-0.2.1/spliv/MD5 | 78 - spliv-0.2.1/spliv/NAMESPACE | 17 spliv-0.2.1/spliv/NEWS.md | 41 spliv-0.2.1/spliv/R/bpe.R | 251 ---- spliv-0.2.1/spliv/R/bpe_design.R | 229 +++- spliv-0.2.1/spliv/R/core_mats.R | 181 ++- spliv-0.2.1/spliv/R/fe_demean.R | 37 spliv-0.2.1/spliv/R/iv_parse.R | 16 spliv-0.2.1/spliv/R/plotting.R | 258 ++-- spliv-0.2.1/spliv/R/spliv-package.R | 2 spliv-0.2.1/spliv/R/spliv.R | 519 +++++----- spliv-0.2.1/spliv/README.md | 152 ++ spliv-0.2.1/spliv/inst/doc/getting-started.R | 23 spliv-0.2.1/spliv/inst/doc/getting-started.Rmd | 39 spliv-0.2.1/spliv/inst/doc/getting-started.html | 130 +- spliv-0.2.1/spliv/man/bpe_design.Rd | 9 spliv-0.2.1/spliv/man/bpe_explore_subsets.Rd | 4 spliv-0.2.1/spliv/man/bpe_validate_design.Rd | 20 spliv-0.2.1/spliv/man/plot_sp_sensitivity.Rd | 18 spliv-0.2.1/spliv/man/sp_ltz.Rd | 13 spliv-0.2.1/spliv/man/sp_prior_ltz.Rd | 13 spliv-0.2.1/spliv/man/sp_sensitivity_ltz_normal.Rd | 23 spliv-0.2.1/spliv/man/sp_sensitivity_ltz_uniform01_as_normal.Rd | 21 spliv-0.2.1/spliv/man/sp_sensitivity_uci_support.Rd | 24 spliv-0.2.1/spliv/man/sp_uci.Rd | 13 spliv-0.2.1/spliv/man/spliv-package.Rd | 3 spliv-0.2.1/spliv/man/spliv.Rd | 117 -- spliv-0.2.1/spliv/man/spliv_sensitivity_path.Rd | 2 spliv-0.2.1/spliv/tests/testthat/helper-sensitivity-path-reference.R |only spliv-0.2.1/spliv/tests/testthat/test-core-api.R | 140 -- spliv-0.2.1/spliv/tests/testthat/test-final-hardening.R |only spliv-0.2.1/spliv/tests/testthat/test-ltz-bias-correction.R | 4 spliv-0.2.1/spliv/tests/testthat/test-public-api.R |only spliv-0.2.1/spliv/tests/testthat/test-public-workflows.R | 5 spliv-0.2.1/spliv/tests/testthat/test-rjournal-hardening.R |only spliv-0.2.1/spliv/tests/testthat/test-sensitivity-path-optimization.R |only spliv-0.2.1/spliv/tests/testthat/test-spliv-fit-class.R |only spliv-0.2.1/spliv/vignettes/getting-started.Rmd | 39 47 files changed, 1139 insertions(+), 1308 deletions(-)
Title: Kinship Analysis with Linked Markers
Description: A 'shiny' application for forensic kinship testing, based on
the 'pedsuite' R packages. 'KLINK' is closely aligned with the (non-R)
software 'Familias' and 'FamLink', but offers several unique features,
including visualisations and automated report generation. The
calculation of likelihood ratios supports pairs of linked markers, and
all common mutation models. The program is described in Vigeland and
Gilfillan (2026) <doi:10.1016/j.fsigen.2026.103578>.
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between KLINK versions 1.2.0 dated 2026-04-21 and 1.2.2 dated 2026-08-03
KLINK-1.2.0/KLINK/R/writeMasked.R |only KLINK-1.2.2/KLINK/DESCRIPTION | 22 +++++---- KLINK-1.2.2/KLINK/MD5 | 43 +++++++++--------- KLINK-1.2.2/KLINK/NEWS.md | 20 +++++++- KLINK-1.2.2/KLINK/R/getLinkedPairs.R | 2 KLINK-1.2.2/KLINK/R/karyo.R | 13 ++++- KLINK-1.2.2/KLINK/R/linkedLR.R | 7 ++ KLINK-1.2.2/KLINK/R/loadFamFile.R | 6 ++ KLINK-1.2.2/KLINK/R/loadMap.R | 47 +++++++++++++++---- KLINK-1.2.2/KLINK/R/prettyTable.R | 5 +- KLINK-1.2.2/KLINK/R/writeResult.R | 32 ++++++------- KLINK-1.2.2/KLINK/README.md | 15 ++++-- KLINK-1.2.2/KLINK/build |only KLINK-1.2.2/KLINK/inst/CITATION |only KLINK-1.2.2/KLINK/inst/shiny/R/utils.R | 9 +++ KLINK-1.2.2/KLINK/inst/shiny/app.R | 62 +++++++++++++------------- KLINK-1.2.2/KLINK/inst/shiny/help/input.md | 2 KLINK-1.2.2/KLINK/inst/shiny/help/settings.md | 2 KLINK-1.2.2/KLINK/inst/shiny/www/GA.html | 28 ++++++----- KLINK-1.2.2/KLINK/man/KLINK-package.Rd | 8 ++- KLINK-1.2.2/KLINK/man/linkedLR.Rd | 4 - KLINK-1.2.2/KLINK/man/loadFamFile.Rd | 6 ++ KLINK-1.2.2/KLINK/man/loadMap.Rd | 15 ++++-- KLINK-1.2.2/KLINK/man/map50.Rd | 5 -- 24 files changed, 224 insertions(+), 129 deletions(-)
Title: Miscellaneous Statistical Functions Used in 'guide-R'
Description: Companion package for the manual
'guide-R : Guide pour l’analyse de données d’enquêtes avec R' available at
<https://larmarange.github.io/guide-R/>. 'guideR' implements miscellaneous
functions introduced in 'guide-R' to facilitate statistical analysis and
manipulation of survey data.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between guideR versions 0.10.0 dated 2026-07-27 and 0.11.0 dated 2026-08-03
DESCRIPTION | 21 +- MD5 | 26 ++- NAMESPACE | 15 ++ NEWS.md | 13 + R/contributions.R | 257 +++++++++++++++++++++++++++++------- R/gtsummary_utilities.R | 18 ++ R/tbl_maihda.R |only R/titanic.R | 1 build |only inst/WORDLIST | 6 man/contributions.Rd | 20 ++ man/gtsummary_utilities.Rd | 5 man/tbl_maihda.Rd |only tests/testthat/test-contributions.R | 20 ++ tests/testthat/test-maihda.R |only tests/testthat/test-proportion.R | 2 16 files changed, 327 insertions(+), 77 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson [aut, cre] ,
Evan Sergeant [aut],
Cord Heuer [ctb],
Ian Kopacka [ctb],
Klemens Fuchs [ctb],
Telmo Nunes [ctb],
Cord Heuer [ctb],
Jonathon Marshall [ctb],
Javier Sanchez [ctb],
Ron Thornton [ctb],
Jeno Reiczigel [ctb],
Jim Robison-Cox [ [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.95 dated 2026-07-17 and 2.0.96 dated 2026-08-03
DESCRIPTION | 15 MD5 | 18 - NEWS | 7 R/epi.prev.R | 624 +++++++++++++++++++++++------------ inst/doc/epiR_descriptive_epi.html | 18 - inst/doc/epiR_diagnostic_tests.html | 23 - inst/doc/epiR_measures_of_assoc.html | 12 inst/doc/epiR_sample_size.html | 4 inst/doc/epiR_surveillance.html | 14 man/epi.prev.Rd | 35 + 10 files changed, 515 insertions(+), 255 deletions(-)
Title: Exploratory Graphics for Pharmacometrics
Description: Supports a structured approach
for exploring PKPD data <https://opensource.nibr.com/xgx/>. It also
contains helper functions for enabling the modeler to follow best R
practices (by appending the program name, figure name location, and
draft status to each plot). In addition, it enables the modeler to
follow best graphical practices (by providing a theme that
reduces chart ink, and by providing time-scale, log-scale, and
reverse-log-transform-scale functions for more readable axes).
Finally, it provides some data checking and summarizing functions for
rapidly exploring pharmacokinetics and pharmacodynamics (PKPD) datasets.
Author: Andrew Stein [aut, cre],
Alison Margolskee [aut],
Fariba Khanshan [aut],
Konstantin Krismer [aut] ,
Matthew Fidler [ctb] ,
Novartis Pharma AG [cph, fnd]
Maintainer: Andrew Stein <andy.stein@gmail.com>
Diff between xgxr versions 1.1.2 dated 2023-03-22 and 1.1.6 dated 2026-08-03
xgxr-1.1.2/xgxr/inst/doc/sad_pkpd.R |only xgxr-1.1.2/xgxr/inst/doc/sad_pkpd.Rmd |only xgxr-1.1.2/xgxr/inst/doc/sad_pkpd.html |only xgxr-1.1.2/xgxr/inst/doc/theoph.R |only xgxr-1.1.2/xgxr/inst/doc/theoph.Rmd |only xgxr-1.1.2/xgxr/inst/doc/theoph.html |only xgxr-1.1.2/xgxr/vignettes/sad_pkpd.Rmd |only xgxr-1.1.2/xgxr/vignettes/theoph.Rmd |only xgxr-1.1.6/xgxr/DESCRIPTION | 21 xgxr-1.1.6/xgxr/MD5 | 77 - xgxr-1.1.6/xgxr/NAMESPACE | 5 xgxr-1.1.6/xgxr/NEWS | 46 xgxr-1.1.6/xgxr/R/predict.nls.R | 127 - xgxr-1.1.6/xgxr/R/xgx_annotate_status.R | 24 xgxr-1.1.6/xgxr/R/xgx_breaks_log10.R | 43 xgxr-1.1.6/xgxr/R/xgx_breaks_time.R | 43 xgxr-1.1.6/xgxr/R/xgx_check_data.R | 3 xgxr-1.1.6/xgxr/R/xgx_scale_x_log10.R | 13 xgxr-1.1.6/xgxr/R/xgx_scale_x_time_units.R | 51 xgxr-1.1.6/xgxr/R/xgx_scale_y_log10.R | 12 xgxr-1.1.6/xgxr/R/xgx_scale_y_percentchangelog10.R | 18 xgxr-1.1.6/xgxr/R/xgx_stat_ci.R | 106 + xgxr-1.1.6/xgxr/R/xgx_stat_smooth.R | 431 ++--- xgxr-1.1.6/xgxr/R/zzz.R |only xgxr-1.1.6/xgxr/README.md | 6 xgxr-1.1.6/xgxr/build/vignette.rds |binary xgxr-1.1.6/xgxr/inst/doc/xgxr_overview.R | 58 xgxr-1.1.6/xgxr/inst/doc/xgxr_overview.Rmd | 1025 ++++++------- xgxr-1.1.6/xgxr/inst/doc/xgxr_overview.html | 1377 ++++++------------ xgxr-1.1.6/xgxr/man/StatSmoothOrdinal.Rd | 5 xgxr-1.1.6/xgxr/man/StatSummaryBinQuant.Rd | 5 xgxr-1.1.6/xgxr/man/StatSummaryOrdinal.Rd | 5 xgxr-1.1.6/xgxr/man/predict.nls.Rd | 38 xgxr-1.1.6/xgxr/man/predictdf.nls.Rd | 16 xgxr-1.1.6/xgxr/man/predictdf.polr.Rd | 2 xgxr-1.1.6/xgxr/man/reexports.Rd | 4 xgxr-1.1.6/xgxr/man/xgx_annotate_status.Rd | 21 xgxr-1.1.6/xgxr/man/xgx_breaks_time.Rd | 24 xgxr-1.1.6/xgxr/man/xgx_check_data.Rd | 3 xgxr-1.1.6/xgxr/man/xgx_conf_int.Rd | 10 xgxr-1.1.6/xgxr/man/xgx_scale_x_time_units.Rd | 8 xgxr-1.1.6/xgxr/man/xgx_stat_smooth.Rd | 90 - xgxr-1.1.6/xgxr/tests/testthat/test-xgx_breaks_time.R |only xgxr-1.1.6/xgxr/tests/testthat/test-xgx_stat_ci.R |only xgxr-1.1.6/xgxr/vignettes/xgxr_overview.Rmd | 1025 ++++++------- 45 files changed, 2167 insertions(+), 2575 deletions(-)
Title: Classification and Regression Trees
Description: Classification and regression trees.
Author: Brian Ripley [aut, cre]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between tree versions 1.0-46 dated 2026-07-20 and 1.0-47 dated 2026-08-03
ChangeLog | 4 - DESCRIPTION | 8 +-- MD5 | 18 +++--- man/plot.tree.sequence.Rd | 6 +- man/predict.tree.Rd | 10 +-- man/prune.tree.Rd | 6 +- man/tile.tree.Rd | 8 +-- man/tree.Rd | 9 +-- man/tree.screens.Rd | 10 +-- tests/Examples/tree-Ex.Rout.save | 102 +++++++++++++++++++-------------------- 10 files changed, 91 insertions(+), 90 deletions(-)
Title: Quick and Essential 'R' Tricks for Better Scripts
Description: The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to improve your scripts. Improve the quality and reproducibility of 'R' scripts.
Author: Obinna Obianom [aut, cre],
Brice Richard [aut]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between quickcode versions 1.0.9 dated 2026-04-04 and 1.1.0 dated 2026-08-03
DESCRIPTION | 6 MD5 | 30 - NEWS.md | 220 ++----- R/pairDist.R | 85 +- README.md | 582 ++++++++------------ build/vignette.rds |binary inst/doc/add_today_date_to_filenames_quickcode.html | 59 +- inst/doc/not_functions_data_validation_r.R |only inst/doc/not_functions_data_validation_r.Rmd |only inst/doc/not_functions_data_validation_r.html |only inst/doc/nullish_coalescing_operator_r.html | 4 inst/doc/quickcode_r_introduction.html | 4 inst/doc/super_variables_newSuperVar_r.R |only inst/doc/super_variables_newSuperVar_r.Rmd |only inst/doc/super_variables_newSuperVar_r.html |only inst/doc/track_function_usage_r.html | 4 inst/logo.png |binary man/machine_learning.Rd | 41 - vignettes/not_functions_data_validation_r.Rmd |only vignettes/super_variables_newSuperVar_r.Rmd |only 20 files changed, 453 insertions(+), 582 deletions(-)
Title: Spatiotemporal Resampling Methods for 'mlr3'
Description: Extends the mlr3 machine learning framework with
spatio-temporal resampling methods to account for the presence of
spatiotemporal autocorrelation (STAC) in predictor variables. STAC may
cause highly biased performance estimates in cross-validation if
ignored. A JSS article is available at <doi:10.18637/jss.v111.i07>.
Author: Patrick Schratz [aut, cre] ,
Marc Becker [aut] ,
Jannes Muenchow [ctb] ,
Michel Lang [ctb]
Maintainer: Patrick Schratz <patrick.schratz@gmail.com>
Diff between mlr3spatiotempcv versions 2.3.4 dated 2025-09-12 and 2.3.5 dated 2026-08-03
DESCRIPTION | 7 +- MD5 | 56 +++++++++++----------- NEWS.md | 16 ++++++ R/ResamplingRepeatedSpCVBlock.R | 2 R/ResamplingRepeatedSpCVCoords.R | 2 R/ResamplingRepeatedSpCVEnv.R | 2 R/ResamplingRepeatedSpCVknndm.R | 5 + R/ResamplingRepeatedSptCVCstf.R | 2 R/ResamplingSpCVBlock.R | 2 R/ResamplingSpCVCoords.R | 2 R/ResamplingSpCVDisc.R | 4 - R/ResamplingSpCVEnv.R | 2 R/ResamplingSpCVKnndm.R | 5 + R/ResamplingSpCVTiles.R | 4 - R/ResamplingSptCVCstf.R | 2 R/Task_classif_diplodia.R | 2 R/Task_classif_ecuador.R | 2 R/Task_regr_cookfarm_profiles.R | 2 README.md | 4 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/mlr3spatiotempcv.html | 38 +++++++------- inst/doc/spatiotemp-viz.html | 4 - man/TaskClassifST.Rd | 1 man/TaskRegrST.Rd | 1 tests/testthat/test-2-autoplot.R | 3 - tests/testthat/test-ResamplingRepeatedSpCVBlock.R | 18 +------ tests/testthat/test-ResamplingSpCVBlock.R | 22 -------- tests/testthat/test-mlr_sptcv_generic.R | 28 +++++++++++ 29 files changed, 127 insertions(+), 111 deletions(-)
More information about mlr3spatiotempcv at CRAN
Permanent link
Title: Generalized Estimation Equation Solver
Description: Generalized Estimation Equation solver.
Author: Vincent J Carey [aut],
Thomas S Lumley [trl] ,
Cleve Moler [ctb] ,
Brian Ripley [trl, cre, ctb]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between gee versions 4.13-29 dated 2024-12-11 and 4.13-30 dated 2026-08-03
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/gee.Rd | 4 +--- tests/Examples/gee-Ex.Rout.save | 15 +++++++-------- 4 files changed, 15 insertions(+), 18 deletions(-)
Title: Utilities from 'Seminar fuer Statistik' ETH Zurich
Description: Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich,
some of which were ported from S-plus in the 1990s.
For graphics, have pretty (Log-scale) axes eaxis(), an enhanced Tukey-Anscombe
plot, combining histogram and boxplot, 2d-residual plots, a 'tachoPlot()',
pretty arrows, etc.
For robustness, have a robust F test and robust range().
For system support, notably on Linux, provides 'Sys.*()' functions with
more access to system and CPU information.
Finally, miscellaneous utilities such as simple efficient prime numbers,
integer codes, Duplicated(), toLatex.numeric() and is.whole().
Author: Martin Maechler [aut, cre] ,
Werner Stahel [ctb] , f.robftest, last,
p.scales, p.dnorm),
Andreas Ruckstuhl [ctb] , p.profileTraces,
p.res.2x),
Christian Keller [ctb] , p.tachoPlot),
Kjetil Halvorsen [ctb] , ecdf.ksCI),
Alain Hauser [ctb] , is.whole,
[...truncated...]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between sfsmisc versions 1.1-24 dated 2026-05-15 and 1.1-25 dated 2026-08-03
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- R/sessionInfo-ext.R | 3 ++- build/partial.rdb |binary inst/NEWS.Rd | 15 +++++++++++++++ man/shortRversion.Rd | 8 +++++++- tests/dDA.R | 4 +++- tests/dDA.Rout.save | 7 +++---- 8 files changed, 43 insertions(+), 20 deletions(-)
Title: Easy Manipulation of Out of Memory Data Sets
Description: Hard drive data: Class of data allowing the easy importation/manipulation of out of memory data sets. The data sets are located on disk but look like in-memory, the syntax for manipulation is similar to 'data.table'. Operations are performed "chunk-wise" behind the scene. See <https://lrberge.github.io/hdd/> for more information.
Author: Laurent Berge [aut, cre]
Maintainer: Laurent Berge <laurent.berge@u-bordeaux.fr>
Diff between hdd versions 0.1.1 dated 2023-08-25 and 0.1.2 dated 2026-08-03
DESCRIPTION | 14 MD5 | 50 +-- NAMESPACE | 4 NEWS.md | 24 + R/core.R | 641 +++++++++++++++++++++++++----------------- R/misc.R | 51 +++ R/onLoad.R | 2 R/test_fun.R |only build/vignette.rds |binary inst/doc/hdd_walkthrough.R | 192 ++++++------ inst/doc/hdd_walkthrough.html | 18 - man/dim.hdd.Rd | 2 man/guess_col_types.Rd | 10 man/guess_delim.Rd | 10 man/hdd-package.Rd | 1 man/hdd.Rd | 2 man/hdd_merge.Rd | 27 + man/hdd_setkey.Rd | 26 + man/hdd_slice.Rd | 31 +- man/names.hdd.Rd | 2 man/peek.Rd | 24 + man/print.hdd.Rd | 2 man/sub-.hdd.Rd | 63 +++- man/summary.hdd.Rd | 2 man/txt2hdd.Rd | 52 ++- man/write_hdd.Rd | 29 + tests |only 27 files changed, 782 insertions(+), 497 deletions(-)
Title: Indicators for the Analysis of Dispersion of Datasets with
Batched and Ordered Samples
Description: Provides methods for analyzing the dispersion of tabular datasets
with batched and ordered samples. Based on convex hull or integrated covariance
Mahalanobis, several indicators are implemented for inter and intra batch dispersion
analysis. It is designed to facilitate robust statistical assessment of data
variability, supporting applications in exploratory data analysis and quality
control, for such datasets as the one found in metabololomics studies.
For more details see Salanon (2024) <doi:10.1016/j.chemolab.2024.105148> and
Salanon (2025) <doi:10.1101/2025.08.01.668073>.
Author: Brice Mulot [aut],
Elfried Salanon [ctb],
Etienne Jules [aut, cre],
INRAE [cph]
Maintainer: Etienne Jules <etienne.jules@inrae.fr>
Diff between dispersionIndicators versions 0.1.5 dated 2025-11-18 and 0.1.6 dated 2026-08-03
DESCRIPTION | 8 +- MD5 | 13 ++-- NAMESPACE | 3 NEWS.md | 6 + R/convex_function.R | 104 ++++++++++++++++++++++++++++++++ README.md | 107 ++++++++++++++++++++++++++------- man/shared_single_plot_convex_hulls.Rd |only tests/testthat/test-convex_function.R | 56 ++++++++++++++--- 8 files changed, 256 insertions(+), 41 deletions(-)
More information about dispersionIndicators at CRAN
Permanent link
Title: Robust Covariance Matrix Estimators
Description: Object-oriented software for model-robust covariance matrix estimators. Starting out from the basic
robust Eicker-Huber-White sandwich covariance methods include: heteroscedasticity-consistent (HC)
covariances for cross-section data; heteroscedasticity- and autocorrelation-consistent (HAC)
covariances for time series data (such as Andrews' kernel HAC, Newey-West, and WEAVE estimators);
clustered covariances (one-way and multi-way); panel and panel-corrected covariances;
outer-product-of-gradients covariances; and (clustered) bootstrap covariances. All methods are
applicable to (generalized) linear model objects fitted by lm() and glm() but can also be adapted
to other classes through S3 methods. Details can be found in Zeileis et al. (2020) <doi:10.18637/jss.v095.i01>,
Zeileis (2004) <doi:10.18637/jss.v011.i10> and Zeileis (2006) <doi:10.18637/jss.v016.i09>.
Author: Achim Zeileis [aut, cre] ,
Thomas Lumley [aut] ,
Nathaniel Graham [ctb] ,
Susanne Koell [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between sandwich versions 3.1-2 dated 2026-07-12 and 3.1-3 dated 2026-08-03
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NEWS.md | 9 +++++++++ inst/doc/sandwich-CL.pdf |binary inst/doc/sandwich-OOP.pdf |binary inst/doc/sandwich.pdf |binary man/vcovBS.Rd | 2 +- 7 files changed, 22 insertions(+), 13 deletions(-)
Title: Generalized Additive Mixed Models using 'mgcv' and 'lme4'
Description: Estimate generalized additive mixed models via a version of
function gamm() from 'mgcv', using 'lme4' for estimation.
Author: Simon Wood [aut, cre],
Fabian Scheipl [aut],
Arno Schneuwly [aut]
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between gamm4 versions 0.2-7 dated 2025-04-22 and 0.3-0 dated 2026-08-03
gamm4-0.2-7/gamm4/README.md |only gamm4-0.3-0/gamm4/ChangeLog | 21 +- gamm4-0.3-0/gamm4/DESCRIPTION | 13 - gamm4-0.3-0/gamm4/MD5 | 11 - gamm4-0.3-0/gamm4/NAMESPACE | 3 gamm4-0.3-0/gamm4/R/gamm4.r | 393 ++++++++++++++++++++++++++++++----------- gamm4-0.3-0/gamm4/man/gamm4.Rd | 14 - 7 files changed, 335 insertions(+), 120 deletions(-)
Title: Fishing Effort Standardization
Description: Marine fisheries governance and management rely heavily on reliable
indicators of stock abundance and fishing pressure to ensure the sustainable
utilization of marine resources. Catch Per Unit Effort (CPUE) is widely used
as an index of relative abundance, but direct comparison of catch rates is
often affected by differences in fishing effort, vessel characteristics,
gear efficiency, and operational practices. The FESta package provides
methods for fishing effort and CPUE standardization, including vessel-based,
gear-based, relative effort, derived effort, generalized linear models,
generalized additive models, generalized linear mixed models, ordered
quantile transformation models, and multi-gear standardization techniques
for fisheries stock assessment and monitoring.
To cite our package run this command, citation("FESta").
Author: Eldho Varghese [aut, cre],
Jayasankar J [aut],
Ashutosh Dalal [aut, ctb],
Sathianandan T V [aut],
Sreepriya V [aut, ctb],
Reshma Gills [ctb],
Grinson George [ctb]
Maintainer: Eldho Varghese <eldhoiasri@gmail.com>
Diff between FESta versions 1.0.0 dated 2020-05-11 and 1.0.1 dated 2026-08-03
FESta-1.0.0/FESta/R/RCode.R |only FESta-1.0.0/FESta/data/Example.RData |only FESta-1.0.0/FESta/data/data.R |only FESta-1.0.0/FESta/man/Example.Rd |only FESta-1.0.1/FESta/DESCRIPTION | 64 ++++++++-- FESta-1.0.1/FESta/MD5 | 56 ++++++++- FESta-1.0.1/FESta/NAMESPACE | 71 +++++++++++ FESta-1.0.1/FESta/R/DEstd.R |only FESta-1.0.1/FESta/R/DEstd_dataset.R |only FESta-1.0.1/FESta/R/GAMstd.R |only FESta-1.0.1/FESta/R/GAMstd_dataset.R |only FESta-1.0.1/FESta/R/GLMMstd.R |only FESta-1.0.1/FESta/R/GLMMstd_dataset.R |only FESta-1.0.1/FESta/R/GLMstd.R |only FESta-1.0.1/FESta/R/GLMstd_dataset.R |only FESta-1.0.1/FESta/R/MGMSstd.R |only FESta-1.0.1/FESta/R/MGMSstd_dataset.R |only FESta-1.0.1/FESta/R/ORQGLMstd.R |only FESta-1.0.1/FESta/R/ORQGLMstd_dataset.R |only FESta-1.0.1/FESta/R/REstd.R |only FESta-1.0.1/FESta/R/REstd_dataset.R |only FESta-1.0.1/FESta/R/SVstd.R |only FESta-1.0.1/FESta/R/SVstd_dataset.R |only FESta-1.0.1/FESta/R/StdEffort.R |only FESta-1.0.1/FESta/R/StdEffort_dataset.R |only FESta-1.0.1/FESta/R/calculate_and_plot_cpue.R |only FESta-1.0.1/FESta/data/DEstd_dataset.rda |only FESta-1.0.1/FESta/data/GAMstd_dataset.rda |only FESta-1.0.1/FESta/data/GLMMstd_dataset.rda |only FESta-1.0.1/FESta/data/GLMstd_dataset.rda |only FESta-1.0.1/FESta/data/MGMSstd_dataset.rda |only FESta-1.0.1/FESta/data/ORQGLMstd_dataset.rda |only FESta-1.0.1/FESta/data/REstd_dataset.rda |only FESta-1.0.1/FESta/data/SVstd_dataset.rda |only FESta-1.0.1/FESta/data/StdEffort_dataset.rda |only FESta-1.0.1/FESta/inst |only FESta-1.0.1/FESta/man/DEstd.Rd |only FESta-1.0.1/FESta/man/DEstd_dataset.Rd |only FESta-1.0.1/FESta/man/GAMstd.Rd |only FESta-1.0.1/FESta/man/GAMstd_dataset.Rd |only FESta-1.0.1/FESta/man/GLMMstd.Rd |only FESta-1.0.1/FESta/man/GLMMstd_dataset.Rd |only FESta-1.0.1/FESta/man/GLMstd.Rd |only FESta-1.0.1/FESta/man/GLMstd_dataset.Rd |only FESta-1.0.1/FESta/man/MGMSstd.Rd |only FESta-1.0.1/FESta/man/MGMSstd_dataset.Rd |only FESta-1.0.1/FESta/man/ORQGLMstd.Rd |only FESta-1.0.1/FESta/man/ORQGLMstd_dataset.Rd |only FESta-1.0.1/FESta/man/REstd.Rd |only FESta-1.0.1/FESta/man/REstd_dataset.Rd |only FESta-1.0.1/FESta/man/SVstd.Rd |only FESta-1.0.1/FESta/man/SVstd_dataset.Rd |only FESta-1.0.1/FESta/man/StdEffort.Rd | 156 +++++++++++++++++--------- FESta-1.0.1/FESta/man/StdEffort_dataset.Rd |only 54 files changed, 270 insertions(+), 77 deletions(-)
Title: Functions for Kriging and Point Pattern Analysis
Description: Functions for kriging and point pattern analysis.
Author: Brian Ripley [aut, cre, cph],
Roger Bivand [ctb],
William Venables [cph]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between spatial versions 7.3-18 dated 2025-01-01 and 7.3-19 dated 2026-08-03
DESCRIPTION | 11 ++++---- MD5 | 32 +++++++++++++------------ data |only inst/CITATION | 10 ++++---- inst/NEWS | 4 ++- man/anova.trls.Rd | 3 -- man/correlogram.Rd | 3 -- man/expcov.Rd | 3 -- man/predict.trls.Rd | 4 ++- man/prmat.Rd | 3 -- man/semat.Rd | 3 -- man/surf.gls.Rd | 8 ++---- man/surf.ls.Rd | 8 ++---- man/topo.Rd |only man/trls.influence.Rd | 6 +--- man/trmat.Rd | 3 -- man/variogram.Rd | 3 -- tests/Examples/spatial-Ex.Rout.save | 45 +++++++++--------------------------- 18 files changed, 61 insertions(+), 88 deletions(-)
Title: Feed-Forward Neural Networks and Multinomial Log-Linear Models
Description: Software for feed-forward neural networks with a single
hidden layer, and for multinomial log-linear models.
Author: Brian Ripley [aut, cre, cph],
William Venables [cph]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between nnet versions 7.3-20 dated 2025-01-01 and 7.3-21 dated 2026-08-03
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/vcovmultinom.R | 2 +- inst/CITATION | 8 +++++--- inst/NEWS | 2 ++ man/multinom.Rd | 4 +++- 6 files changed, 20 insertions(+), 14 deletions(-)
Title: Functions for Classification
Description: Various functions for classification, including k-nearest
neighbour, Learning Vector Quantization and Self-Organizing Maps.
Author: Brian Ripley [aut, cre, cph],
William Venables [cph]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between class versions 7.3-23 dated 2025-01-01 and 7.3-24 dated 2026-08-03
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/SOM.R | 13 ++++++------- inst/CITATION | 10 ++++++---- man/SOM.Rd | 8 ++++---- man/batchSOM.Rd | 9 +++++---- 6 files changed, 31 insertions(+), 29 deletions(-)
Title: Gradient Projection Factor Rotation
Description: Gradient projection algorithms for orthogonal and oblique rotation
of factor loadings matrices in factor analysis. Implements a comprehensive
set of rotation criteria including quartimax, quartimin, oblimin, geomin,
simplimax, the Crawford-Ferguson family, and target rotation, among others.
Supports multiple random starts. For details see Bernaards and Jennrich (2005)
<doi:10.1177/0013164404272507>.
Author: Coen Bernaards [aut, cre],
Paul Gilbert [aut],
Robert Jennrich [aut]
Maintainer: Coen Bernaards <cab.gparotation@gmail.com>
Diff between GPArotation versions 2026.7-1 dated 2026-07-28 and 2026.8-1 dated 2026-08-03
DESCRIPTION | 6 MD5 | 47 +++--- NEWS | 8 + R/NormalizingWeight.R | 123 +++++++++++----- R/rotations.R | 13 - inst/doc/GPA1guide.R | 67 ++++++++ inst/doc/GPA1guide.Rnw | 144 ++++++++++++++++++- inst/doc/GPA1guide.pdf |binary inst/doc/GPA2local.pdf |binary inst/doc/GPA3bifactor.pdf |binary inst/doc/GPA4fitstats.pdf |binary man/rotations.Rd | 2 man/vgQ.Rd | 2 tests/Harman.R | 8 - tests/MASSoblimin.R | 4 tests/Thurstone.R | 32 ++-- tests/WansbeekMeijer.R | 12 - tests/cm_browne.R |only tests/legacyVsBB.R | 50 ++---- tests/legacyVsBB_extra.R | 348 +++++++++++++++++++++++++--------------------- tests/lp.R | 283 ++++++++++++++++--------------------- tests/rotations.R | 10 - tests/rotationsRS.R | 62 ++++---- tests/varimaxVarimax.R | 2 vignettes/GPA1guide.Rnw | 144 ++++++++++++++++++- 25 files changed, 895 insertions(+), 472 deletions(-)
Title: Probabilistic Reconciliation via Conditioning
Description: Provides methods for probabilistic reconciliation of hierarchical forecasts of time series.
The available methods include analytical Gaussian reconciliation (Corani et al., 2021)
<doi:10.1007/978-3-030-67664-3_13>,
MCMC reconciliation of count time series (Corani et al., 2024)
<doi:10.1016/j.ijforecast.2023.04.003>,
Bottom-Up Importance Sampling (Zambon et al., 2024)
<doi:10.1007/s11222-023-10343-y>,
methods for the reconciliation of mixed hierarchies (Mix-Cond and TD-cond) (Zambon et al., 2024)
<https://proceedings.mlr.press/v244/zambon24a.html>,
analytical reconciliation with Bayesian treatment of the covariance matrix (Carrara et al., 2025)
<doi: 10.48550/arXiv.2506.19554>.
Author: Dario Azzimonti [aut, cre] ,
Lorenzo Zambon [aut] ,
Stefano Damato [aut] ,
Nicolo Rubattu [aut] ,
Giorgio Corani [aut]
Maintainer: Dario Azzimonti <dario.azzimonti@gmail.com>
Diff between bayesRecon versions 1.0.1 dated 2026-04-16 and 1.0.2 dated 2026-08-03
bayesRecon-1.0.1/bayesRecon/vignettes/bayesRecon_cache/html/hier-fore_f8fe5b9ba34df8ac093d0218efa5e362.RData |only bayesRecon-1.0.1/bayesRecon/vignettes/bayesRecon_cache/html/hier-fore_f8fe5b9ba34df8ac093d0218efa5e362.rdb |only bayesRecon-1.0.1/bayesRecon/vignettes/bayesRecon_cache/html/hier-fore_f8fe5b9ba34df8ac093d0218efa5e362.rdx |only bayesRecon-1.0.2/bayesRecon/DESCRIPTION | 10 bayesRecon-1.0.2/bayesRecon/MD5 | 44 - bayesRecon-1.0.2/bayesRecon/NEWS.md | 8 bayesRecon-1.0.2/bayesRecon/README.md | 25 bayesRecon-1.0.2/bayesRecon/build/partial.rdb |binary bayesRecon-1.0.2/bayesRecon/build/vignette.rds |binary bayesRecon-1.0.2/bayesRecon/inst/doc/bayesRecon.html | 27 bayesRecon-1.0.2/bayesRecon/inst/doc/mixed_reconciliation.html | 37 bayesRecon-1.0.2/bayesRecon/inst/doc/reconciliation_properties.html | 21 bayesRecon-1.0.2/bayesRecon/inst/doc/t_reconciliation.R | 97 +- bayesRecon-1.0.2/bayesRecon/inst/doc/t_reconciliation.Rmd | 156 +-- bayesRecon-1.0.2/bayesRecon/inst/doc/t_reconciliation.html | 399 ++++------ bayesRecon-1.0.2/bayesRecon/man/bayesRecon-package.Rd | 1 bayesRecon-1.0.2/bayesRecon/man/figures/README-unnamed-chunk-11-1.png |binary bayesRecon-1.0.2/bayesRecon/man/figures/README-unnamed-chunk-14-1.png |binary bayesRecon-1.0.2/bayesRecon/man/figures/README-unnamed-chunk-19-1.png |binary bayesRecon-1.0.2/bayesRecon/man/figures/README-unnamed-chunk-7-1.png |binary bayesRecon-1.0.2/bayesRecon/vignettes/bayesRecon_cache/html/hier-fore_2508237f724d9a8e5df6a1b2ca20c49a.RData |only bayesRecon-1.0.2/bayesRecon/vignettes/bayesRecon_cache/html/hier-fore_2508237f724d9a8e5df6a1b2ca20c49a.rdb |only bayesRecon-1.0.2/bayesRecon/vignettes/bayesRecon_cache/html/hier-fore_2508237f724d9a8e5df6a1b2ca20c49a.rdx |only bayesRecon-1.0.2/bayesRecon/vignettes/bayesRecon_cache/latex |only bayesRecon-1.0.2/bayesRecon/vignettes/t_reconciliation.Rmd | 156 +-- 25 files changed, 481 insertions(+), 500 deletions(-)
Title: Consensus Value Constructor
Description: An implementation of the generalized consensus estimators used to assign the reference value in a key comparison exercise. This can also be applied to any interlaboratory study. Given a set of different sources, primary laboratories or measurement methods this package provides an evaluation of the variance components according to the selected statistical method for consensus building. It also implements the comparison among different consensus builders and evaluates the participating method or sources against the consensus reference value. Based on a diverse set of references, DerSimonian-Laird (1986) <doi:10.1016/0197-2456(86)90046-2>, for a complete list of references look at the reference section in the package documentation.
Author: Hugo Gasca-Aragon [aut, cre]
Maintainer: Hugo Gasca-Aragon <hugo_gasca_aragon@hotmail.com>
Diff between gconsensus versions 0.3.2 dated 2022-11-04 and 0.3.2.1 dated 2026-08-03
DESCRIPTION | 14 ++++--- MD5 | 18 ++++----- R/gconsensus-internal.R | 83 +++++++++++++++++++++++++--------------------- R/gconsensus.R | 42 +++++++++++++++-------- build/partial.rdb |binary man/doe.gconsensus.Rd | 8 ++-- man/gconsensus-package.Rd | 57 ++++++++++++++++++++++++------- man/gconsensus.Rd | 21 ++++++----- man/plot.doe.Rd | 6 +-- man/print.doe.Rd | 4 +- 10 files changed, 157 insertions(+), 96 deletions(-)
Title: Recursive Partitioning Based on Psychometric Models
Description: Recursive partitioning based on psychometric models,
employing the general MOB algorithm (from package partykit) to obtain
Bradley-Terry trees, Rasch trees, rating scale and partial credit trees, and
MPT trees, trees for 1PL, 2PL, 3PL and 4PL models and generalized partial
credit models.
Author: Achim Zeileis [aut, cre] ,
Carolin Strobl [aut] ,
Florian Wickelmaier [aut],
Basil Komboz [aut],
Julia Kopf [aut],
Lennart Schneider [aut] ,
David Dreifuss [aut],
Rudolf Debelak [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between psychotree versions 0.16-2 dated 2025-07-25 and 0.16-3 dated 2026-08-03
psychotree-0.16-2/psychotree/inst/doc/raschtree.Rnw |only psychotree-0.16-2/psychotree/inst/doc/raschtree.pdf |only psychotree-0.16-2/psychotree/vignettes/raschtree.Rnw |only psychotree-0.16-3/psychotree/DESCRIPTION | 14 - psychotree-0.16-3/psychotree/MD5 | 29 +- psychotree-0.16-3/psychotree/NEWS.md | 11 psychotree-0.16-3/psychotree/README.md |only psychotree-0.16-3/psychotree/build/partial.rdb |binary psychotree-0.16-3/psychotree/build/vignette.rds |binary psychotree-0.16-3/psychotree/inst/doc/raschtree.R | 147 +++---------- psychotree-0.16-3/psychotree/inst/doc/raschtree.Rmd |only psychotree-0.16-3/psychotree/inst/doc/raschtree.html |only psychotree-0.16-3/psychotree/man/CEMSChoice.Rd | 8 psychotree-0.16-3/psychotree/man/SPISA.Rd | 4 psychotree-0.16-3/psychotree/man/Topmodel2007.Rd | 4 psychotree-0.16-3/psychotree/man/mpttree.Rd | 2 psychotree-0.16-3/psychotree/vignettes/psychotree.bib | 60 ++--- psychotree-0.16-3/psychotree/vignettes/raschtree.Rmd |only psychotree-0.16-3/psychotree/vignettes/raschtree.Rout.save | 23 -- 19 files changed, 116 insertions(+), 186 deletions(-)
Title: Less Code with More Comprehensive Results
Description: Each function replaces multiple standard R functions. For example,
two function calls, Read() and CountAll(), generate summary statistics for
all variables in the data frame, plus histograms and bar charts. Other
functions provide data aggregation via pivot tables; comprehensive
regression, ANOVA, and t-test; visualizations including integrated
Violin/Box/Scatter plot for a numerical variable, bar chart, histogram,
box plot, density curves, calibrated power curve; reading multiple data
formats with the same call; variable labels; time series with aggregation
and forecasting; color themes; and Trellis (facet) graphics. Also includes
a confirmatory factor analysis of multiple-indicator measurement models,
pedagogical routines for data simulation (e.g., Central Limit Theorem),
generation and rendering of regression instructions for interpretative output,
and both interactive construction of visualizations and interactive
visualizations with plotly.
Author: David W. Gerbing [aut, cre]
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 4.5.5 dated 2026-06-21 and 4.5.6 dated 2026-08-03
lessR-4.5.5/lessR/R/ViolinPlot.R |only lessR-4.5.6/lessR/DESCRIPTION | 8 lessR-4.5.6/lessR/MD5 | 97 - lessR-4.5.6/lessR/NAMESPACE | 2 lessR-4.5.6/lessR/NEWS.md | 35 lessR-4.5.6/lessR/R/ANOVA.R | 34 lessR-4.5.6/lessR/R/Chart.R | 290 ++- lessR-4.5.6/lessR/R/Correlation.R | 83 lessR-4.5.6/lessR/R/Logit.R | 16 lessR-4.5.6/lessR/R/Model.R | 183 +- lessR-4.5.6/lessR/R/Regression.R | 30 lessR-4.5.6/lessR/R/X.R | 241 ++ lessR-4.5.6/lessR/R/XY.R | 606 +++--- lessR-4.5.6/lessR/R/Xsub.R | 10 lessR-4.5.6/lessR/R/aliases.R | 58 lessR-4.5.6/lessR/R/bc.main.R | 55 lessR-4.5.6/lessR/R/bc.plotly.R | 188 +- lessR-4.5.6/lessR/R/bubble.plotly.R | 514 +++-- lessR-4.5.6/lessR/R/dn.plotly.R | 6 lessR-4.5.6/lessR/R/hier.plotly.R | 9 lessR-4.5.6/lessR/R/hst.stats.R | 4 lessR-4.5.6/lessR/R/logit.3Residual.R | 11 lessR-4.5.6/lessR/R/param.old.R | 15 lessR-4.5.6/lessR/R/piechart.plotly.R | 13 lessR-4.5.6/lessR/R/plt.contour.R | 2 lessR-4.5.6/lessR/R/plt.contourFacet.R |only lessR-4.5.6/lessR/R/plt.distFacet.R |only lessR-4.5.6/lessR/R/plt.facetSeries.R |only lessR-4.5.6/lessR/R/plt.funnel.R | 13 lessR-4.5.6/lessR/R/plt.hexbinFacet.R |only lessR-4.5.6/lessR/R/plt.main.R | 57 lessR-4.5.6/lessR/R/plt.txt.R | 4 lessR-4.5.6/lessR/R/reg.1ancova.R | 15 lessR-4.5.6/lessR/R/reg.Kfold.R | 4 lessR-4.5.6/lessR/R/ttest.R | 55 lessR-4.5.6/lessR/R/zzz.R | 133 + lessR-4.5.6/lessR/R/zzz_on.R | 9 lessR-4.5.6/lessR/build/vignette.rds |binary lessR-4.5.6/lessR/inst/doc/intro.R | 11 lessR-4.5.6/lessR/inst/doc/intro.Rmd | 17 lessR-4.5.6/lessR/inst/doc/intro.html | 766 ++++---- lessR-4.5.6/lessR/man/ANOVA.Rd | 11 lessR-4.5.6/lessR/man/Chart.Rd | 193 +- lessR-4.5.6/lessR/man/Correlation.Rd | 13 lessR-4.5.6/lessR/man/Logit.Rd | 21 lessR-4.5.6/lessR/man/Model.Rd | 112 - lessR-4.5.6/lessR/man/Regression.Rd | 16 lessR-4.5.6/lessR/man/X.Rd | 167 + lessR-4.5.6/lessR/man/XY.Rd | 2971 ++++++++++++++++----------------- lessR-4.5.6/lessR/man/style.Rd | 2 lessR-4.5.6/lessR/man/ttest.Rd | 14 lessR-4.5.6/lessR/vignettes/intro.Rmd | 17 52 files changed, 4196 insertions(+), 2935 deletions(-)
Title: Extended Model Formulas
Description: Infrastructure for extended formulas with multiple parts on the
right-hand side and/or multiple responses on the left-hand side
(see <doi:10.18637/jss.v034.i01>).
Author: Achim Zeileis [aut, cre] ,
Yves Croissant [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between Formula versions 1.2-5 dated 2023-02-24 and 1.2-6 dated 2026-08-03
Formula-1.2-5/Formula/inst/doc/Formula.Rnw |only Formula-1.2-5/Formula/inst/doc/Formula.pdf |only Formula-1.2-5/Formula/vignettes/Formula.Rnw |only Formula-1.2-6/Formula/DESCRIPTION | 22 ++- Formula-1.2-6/Formula/MD5 | 25 ++-- Formula-1.2-6/Formula/NAMESPACE | 6 Formula-1.2-6/Formula/NEWS.md | 14 ++ Formula-1.2-6/Formula/R/Formula.R | 2 Formula-1.2-6/Formula/README.md |only Formula-1.2-6/Formula/build/partial.rdb |binary Formula-1.2-6/Formula/build/vignette.rds |binary Formula-1.2-6/Formula/inst/doc/Formula.R | 134 +++++----------------- Formula-1.2-6/Formula/inst/doc/Formula.Rmd |only Formula-1.2-6/Formula/inst/doc/Formula.html |only Formula-1.2-6/Formula/vignettes/Formula.Rmd |only Formula-1.2-6/Formula/vignettes/Formula.Rout.save | 12 + Formula-1.2-6/Formula/vignettes/Formula.bib | 61 ++++------ 17 files changed, 116 insertions(+), 160 deletions(-)
Title: Use Foreach to Parallelize via the Future Framework
Description: The 'future' package provides a unifying parallelization framework for R that supports many parallel and distributed backends <doi:10.32614/RJ-2021-048>. The 'foreach' package provides a powerful API for iterating over an R expression in parallel. The 'doFuture' package brings the best of the two together. There are three ways to use this package. The recommended approach is to use 'y <- foreach(...) %do% { ... } |> futurize()' via the 'futurize' package (<doi:10.48550/arXiv.2601.17578>). The second alternative, which was formerly recommended, is to use 'y <- foreach(...) %dofuture% { ... }', which does not require using 'registerDoFuture()' and has many advantages over '%dopar%'. The third alternative is the traditional 'foreach' approach by registering the 'foreach' adapter 'registerDoFuture()' and so that 'y <- foreach(...) %dopar% { ... }' parallelizes with the 'future' framework.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between doFuture versions 1.2.2 dated 2026-05-22 and 1.3.0 dated 2026-08-03
DESCRIPTION | 10 - MD5 | 42 ++++--- NEWS.md | 33 +++-- R/doFuture.R | 128 ++++++++++----------- R/doFuture2.R | 185 +++++++++++++++---------------- build/vignette.rds |binary inst/CITATION | 28 ++++ inst/doc/doFuture-1-overview.html | 18 +-- inst/doc/doFuture-2-dopar.html | 18 +-- inst/doc/doFuture-3-dofuture.html | 18 +-- inst/testme/test-condition-handlers.R |only inst/testme/test-debug,dofuture.R |only inst/testme/test-debug,dopar.R |only inst/testme/test-foreach_dopar,globals.R | 2 inst/testme/test-imports.R |only inst/testme/test-internals.R | 42 ++++++- inst/testme/test-labels.R |only inst/testme/test-registerDoFuture.R | 94 +++++++++++++++ inst/testme/test-reserved-globals.R |only inst/testme/test-rng-misuse.R | 75 ++++++++++++ inst/testme/test-verbose.R | 37 ++++++ inst/testme/test-with.DoPar.R | 42 ++++++- tests/test-condition-handlers.R |only tests/test-debug,dofuture.R |only tests/test-debug,dopar.R |only tests/test-imports.R |only tests/test-labels.R |only tests/test-reserved-globals.R |only 28 files changed, 561 insertions(+), 211 deletions(-)
Title: R Client for the YouTube Analytics and Reporting API
Description: Provides access to YouTube Analytics API v2 for retrieving
YouTube Analytics data including views, engagement metrics, demographics, and
revenue data. Supports OAuth 2.0 authentication and channel group management.
See <https://developers.google.com/youtube/analytics/> for API documentation.
Author: Gaurav Sood [aut, cre]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between tubern versions 0.5.0 dated 2026-04-12 and 0.5.1 dated 2026-08-02
DESCRIPTION | 9 +- MD5 | 62 +++++++++------- NEWS.md | 28 +++++++ R/data_transformation.R | 98 +++++++++++++------------- R/date_helpers.R | 110 +++++++++++++++++++----------- R/error_handling.R | 33 +++++++-- R/get_report.R | 20 ++++- R/report_helpers.R | 90 ++++++++++++------------ R/validation_helpers.R | 64 +++++++++++++++-- R/yt_oauth.R | 11 ++- README.md | 4 - build/vignette.rds |binary inst/doc/basic_tubern.R | 2 inst/doc/basic_tubern.Rmd | 2 inst/doc/basic_tubern.html | 6 - inst/doc/tubern_examples.Rmd | 24 +++--- inst/doc/tubern_examples.html | 16 ++-- man/get_report.Rd | 4 - tests/testthat/test-api-conformance.R |only tests/testthat/test-audit-correctness.R |only tests/testthat/test-client.R | 2 tests/testthat/test-data-transformation.R | 2 tests/testthat/test-date-range-typos.R |only tests/testthat/test-error-handling.R | 9 +- tests/testthat/test-get-report.R | 22 +++++- tests/testthat/test-group-items.R | 4 - tests/testthat/test-groups-live.R |only tests/testthat/test-groups.R | 4 - tests/testthat/test-pkg-style.R | 9 +- tests/testthat/test-record-fixtures.R | 4 - tests/testthat/test-reports.R | 4 - tests/testthat/test-validation.R | 26 ++++++- vignettes/basic_tubern.Rmd | 2 vignettes/tubern_examples.Rmd | 24 +++--- 34 files changed, 443 insertions(+), 252 deletions(-)
Title: AI Copilot for R Analysis Workflows in 'RStudio'
Description: An AI copilot for R users in 'RStudio' and Posit workflows with
active-editor, workspace, object, console, plot, and git-aware context.
Provides statistical helpers for interpreting lm() and glm()
models, stages code and file actions before execution, drafts
reproducible 'Quarto' content, and connects to official provider
APIs or CLIs for 'OpenAI', 'GitHub Copilot', 'Gemini', and 'Anthropic'.
Author: Markuss Saule [aut, cre, cph]
Maintainer: Markuss Saule <markusstomas@gmail.com>
Diff between ravel versions 0.1.2 dated 2026-06-28 and 0.1.4 dated 2026-08-02
DESCRIPTION | 8 - MD5 | 48 +++---- NEWS.md | 22 +++ R/approvals.R | 3 R/auth.R | 63 +++++++-- R/execution.R | 35 +++++ R/mcp.R | 198 +++++++++++++++++++++++++++++-- R/provider_interface.R | 52 +++++++- R/providers_anthropic.R | 10 - R/providers_copilot.R | 43 +++++- R/providers_gemini.R | 112 ++++++++++++----- R/providers_openai.R | 106 ++++++++++++++-- R/setup.R | 5 R/ui_gadget.R | 136 +++++++++++++++++++-- build/vignette.rds |binary inst/WORDLIST |only inst/doc/ravel-mvp.Rmd | 3 inst/doc/ravel-mvp.html | 24 +-- inst/doc/ravel-showcase.html | 7 - man/ravel-package.Rd | 5 man/ravel_mcp_tool.Rd | 11 + man/ravel_set_bearer_token.Rd | 8 - tests/testthat/teardown.R | 6 tests/testthat/test-auth.R | 9 + tests/testthat/test-provider-hardening.R |only vignettes/ravel-mvp.Rmd | 3 26 files changed, 770 insertions(+), 147 deletions(-)
Title: Adjust Estimates of Learning for Guessing
Description: Provides tools to adjust estimates of learning for guessing-related
bias in educational and survey research. Implements standard guessing
correction methods and latent class models that leverage informative
pre-post test transitions to account for guessing behavior.
The package helps researchers obtain more accurate estimates of actual
learning when respondents may guess on closed-ended knowledge items.
For theoretical background and empirical validation, see Cor and Sood (2016)
<https://gsood.com/research/papers/guess.pdf>.
Author: Gaurav Sood [aut, cre],
Ken Cor [aut]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between guess versions 0.3.0 dated 2026-03-31 and 0.7.0 dated 2026-08-02
guess-0.3.0/guess/R/fit_dk.R |only guess-0.3.0/guess/R/fit_nodk.R |only guess-0.7.0/guess/DESCRIPTION | 25 guess-0.7.0/guess/MD5 | 179 +++-- guess-0.7.0/guess/NAMESPACE | 31 guess-0.7.0/guess/NEWS.md | 227 +++++++ guess-0.7.0/guess/R/fit_unified.R | 149 +++- guess-0.7.0/guess/R/group_adj.R | 104 +-- guess-0.7.0/guess/R/guess.R | 2 guess-0.7.0/guess/R/internal-helpers.R | 223 +++++-- guess-0.7.0/guess/R/lca_cor.R | 245 ++++++- guess-0.7.0/guess/R/lca_se.R | 154 ++-- guess-0.7.0/guess/R/lca_subset.R | 85 +- guess-0.7.0/guess/R/model-criticism.R |only guess-0.7.0/guess/R/multi_transmat.R | 47 + guess-0.7.0/guess/R/nona.R | 34 - guess-0.7.0/guess/R/person_lca.R |only guess-0.7.0/guess/R/s3-methods.R |only guess-0.7.0/guess/R/simulate.R |only guess-0.7.0/guess/R/stnd_cor.R | 113 ++- guess-0.7.0/guess/R/transmat.R | 63 + guess-0.7.0/guess/R/utils-constants.R | 28 guess-0.7.0/guess/R/utils-matrix.R | 62 + guess-0.7.0/guess/R/utils-validation.R | 112 +++ guess-0.7.0/guess/README.md | 274 ++++++-- guess-0.7.0/guess/build/vignette.rds |binary guess-0.7.0/guess/inst/doc/model_validation.R |only guess-0.7.0/guess/inst/doc/model_validation.Rmd |only guess-0.7.0/guess/inst/doc/model_validation.html |only guess-0.7.0/guess/inst/doc/using_guess.R | 216 ++++++ guess-0.7.0/guess/inst/doc/using_guess.Rmd | 317 +++++++++- guess-0.7.0/guess/inst/doc/using_guess.html | 317 +++++++++- guess-0.7.0/guess/man/cell_probs.Rd |only guess-0.7.0/guess/man/class_conditional_item.Rd |only guess-0.7.0/guess/man/coef.guess_fit.Rd |only guess-0.7.0/guess/man/cross_sectional_learning.Rd |only guess-0.7.0/guess/man/cross_sectional_learning_score.Rd |only guess-0.7.0/guess/man/cv_individuals.Rd |only guess-0.7.0/guess/man/cv_items.Rd |only guess-0.7.0/guess/man/difficulty_to_gamma.Rd |only guess-0.7.0/guess/man/dk_cell_probs.Rd |only guess-0.7.0/guess/man/eq1dk.Rd | 2 guess-0.7.0/guess/man/eqn1.Rd | 4 guess-0.7.0/guess/man/estimate_logit_score.Rd |only guess-0.7.0/guess/man/extract_params.Rd |only guess-0.7.0/guess/man/fit_model.Rd | 59 + guess-0.7.0/guess/man/gamma_to_difficulty.Rd |only guess-0.7.0/guess/man/group_adj.Rd | 32 - guess-0.7.0/guess/man/guess-package.Rd | 1 guess-0.7.0/guess/man/guess_lik.Rd | 2 guess-0.7.0/guess/man/guessdk_lik.Rd | 2 guess-0.7.0/guess/man/individual_likelihood_details.Rd |only guess-0.7.0/guess/man/item_lca_fit.Rd |only guess-0.7.0/guess/man/lca_adj.Rd | 20 guess-0.7.0/guess/man/lca_cor.Rd | 10 guess-0.7.0/guess/man/lca_difficulty.Rd |only guess-0.7.0/guess/man/lca_se.Rd | 37 - guess-0.7.0/guess/man/log_likelihood.Rd |only guess-0.7.0/guess/man/make_guess_lik_difficulty.Rd |only guess-0.7.0/guess/man/make_guessdk_lik_difficulty.Rd |only guess-0.7.0/guess/man/multi_transmat.Rd | 34 - guess-0.7.0/guess/man/multinomial_nll.Rd |only guess-0.7.0/guess/man/new_guess_cv.Rd |only guess-0.7.0/guess/man/new_guess_fit.Rd |only guess-0.7.0/guess/man/nodk_cell_probs.Rd |only guess-0.7.0/guess/man/nona.Rd | 25 guess-0.7.0/guess/man/normalize_missing_action.Rd |only guess-0.7.0/guess/man/normalize_na_as.Rd |only guess-0.7.0/guess/man/normalize_responses.Rd |only guess-0.7.0/guess/man/perplexity_individuals.Rd |only guess-0.7.0/guess/man/perplexity_items.Rd |only guess-0.7.0/guess/man/person_item_expectation.Rd |only guess-0.7.0/guess/man/person_item_lca_fit.Rd |only guess-0.7.0/guess/man/person_item_maximization.Rd |only guess-0.7.0/guess/man/person_item_response_probs.Rd |only guess-0.7.0/guess/man/posterior_class_probs.Rd |only guess-0.7.0/guess/man/posterior_learned.Rd |only guess-0.7.0/guess/man/prepare_response_data.Rd |only guess-0.7.0/guess/man/print.guess_cv.Rd |only guess-0.7.0/guess/man/print.guess_fit.Rd |only guess-0.7.0/guess/man/response_to_cell.Rd |only guess-0.7.0/guess/man/simulate_lca.Rd |only guess-0.7.0/guess/man/simulate_lca_dk.Rd |only guess-0.7.0/guess/man/stnd_cor.Rd | 51 + guess-0.7.0/guess/man/summary.guess_cv.Rd |only guess-0.7.0/guess/man/summary.guess_fit.Rd |only guess-0.7.0/guess/man/transmat.Rd | 39 - guess-0.7.0/guess/man/validate_recovery.Rd |only guess-0.7.0/guess/tests/testthat/helper-simulation.R | 53 - guess-0.7.0/guess/tests/testthat/test-audit-regressions.R |only guess-0.7.0/guess/tests/testthat/test-comprehensive-battery.R | 244 ++++--- guess-0.7.0/guess/tests/testthat/test-comprehensive-validation.R | 152 ++-- guess-0.7.0/guess/tests/testthat/test-dk-model-spec.R |only guess-0.7.0/guess/tests/testthat/test-econometric-identification.R | 20 guess-0.7.0/guess/tests/testthat/test-econometric-likelihood.R | 93 +- guess-0.7.0/guess/tests/testthat/test-econometric-parameter-recovery.R | 64 +- guess-0.7.0/guess/tests/testthat/test-econometric-se-validation.R | 38 - guess-0.7.0/guess/tests/testthat/test-end-to-end-model-criticism.R |only guess-0.7.0/guess/tests/testthat/test-end-to-end-workflows.R |only guess-0.7.0/guess/tests/testthat/test-fit-unified.R | 121 ++- guess-0.7.0/guess/tests/testthat/test-group-validation.R |only guess-0.7.0/guess/tests/testthat/test-individual-validation.R |only guess-0.7.0/guess/tests/testthat/test-integration.R | 144 ++-- guess-0.7.0/guess/tests/testthat/test-interleave.R | 14 guess-0.7.0/guess/tests/testthat/test-lca-adj.R | 26 guess-0.7.0/guess/tests/testthat/test-lca-cor.R | 127 ++-- guess-0.7.0/guess/tests/testthat/test-lca-difficulty.R |only guess-0.7.0/guess/tests/testthat/test-missing-response-contract.R |only guess-0.7.0/guess/tests/testthat/test-model-criticism.R |only guess-0.7.0/guess/tests/testthat/test-model-levels.R |only guess-0.7.0/guess/tests/testthat/test-multi-transmat.R | 137 ++-- guess-0.7.0/guess/tests/testthat/test-nona.R | 11 guess-0.7.0/guess/tests/testthat/test-param-recovery.R |only guess-0.7.0/guess/tests/testthat/test-pkg-style.R | 3 guess-0.7.0/guess/tests/testthat/test-posterior-recovery.R |only guess-0.7.0/guess/tests/testthat/test-release-review-0-7-0.R |only guess-0.7.0/guess/tests/testthat/test-simulate.R |only guess-0.7.0/guess/tests/testthat/test-stnd-adj.R | 20 guess-0.7.0/guess/tests/testthat/test-stnd-cor.R | 6 guess-0.7.0/guess/tests/testthat/test-tidy-compatibility.R |only guess-0.7.0/guess/tests/testthat/test-transmat.R | 22 guess-0.7.0/guess/tests/testthat/test-utils.R | 120 ++- guess-0.7.0/guess/vignettes/model_validation.Rmd |only guess-0.7.0/guess/vignettes/using_guess.Rmd | 317 +++++++++- 124 files changed, 3679 insertions(+), 1378 deletions(-)
Title: Client for the YouTube API
Description: Get comments posted on YouTube videos, information on how
many times a video has been liked, search for videos with particular
content, and much more. You can also scrape captions from a few
videos. To learn more about the YouTube API, see
<https://developers.google.com/youtube/v3/>.
Author: Gaurav Sood [aut, cre],
Kate Lyons [ctb],
John Muschelli [ctb]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between tuber versions 1.4.0 dated 2026-03-24 and 1.4.1 dated 2026-08-02
tuber-1.4.0/tuber/tests/testthat/token_file.rds.enc |only tuber-1.4.1/tuber/DESCRIPTION | 13 + tuber-1.4.1/tuber/MD5 | 67 +++++----- tuber-1.4.1/tuber/NEWS.md | 47 +++++++ tuber-1.4.1/tuber/R/extended_endpoints.R | 50 +++++-- tuber-1.4.1/tuber/R/get_all_channel_video_stats.R | 2 tuber-1.4.1/tuber/R/get_comments.R | 20 ++ tuber-1.4.1/tuber/R/list_abuse_report_reasons.R | 2 tuber-1.4.1/tuber/R/list_guidecats.R | 16 +- tuber-1.4.1/tuber/R/list_regions.R | 2 tuber-1.4.1/tuber/R/list_videocats.R | 20 ++ tuber-1.4.1/tuber/R/upload_caption.R | 2 tuber-1.4.1/tuber/build/vignette.rds |binary tuber-1.4.1/tuber/inst/doc/batch-processing-quota.html | 4 tuber-1.4.1/tuber/inst/doc/tuber-ex.html | 4 tuber-1.4.1/tuber/man/EMOJI_PATTERN.Rd | 4 tuber-1.4.1/tuber/man/get_live_streams.Rd | 8 - tuber-1.4.1/tuber/man/tuber-package.Rd | 5 tuber-1.4.1/tuber/man/upload_caption.Rd | 2 tuber-1.4.1/tuber/tests/testthat/_problems |only tuber-1.4.1/tuber/tests/testthat/test-auth.R | 2 tuber-1.4.1/tuber/tests/testthat/test-basic-functionality.R | 3 tuber-1.4.1/tuber/tests/testthat/test-captions.R | 4 tuber-1.4.1/tuber/tests/testthat/test-comment-threads.R | 2 tuber-1.4.1/tuber/tests/testthat/test-comments.R | 3 tuber-1.4.1/tuber/tests/testthat/test-get-related-videos.R | 4 tuber-1.4.1/tuber/tests/testthat/test-integration-ready.R | 4 tuber-1.4.1/tuber/tests/testthat/test-list-channel-activities.R | 4 tuber-1.4.1/tuber/tests/testthat/test-list-channel-sections.R | 6 tuber-1.4.1/tuber/tests/testthat/test-pagination-mocks.R | 3 tuber-1.4.1/tuber/tests/testthat/test-playlist-items.R | 2 tuber-1.4.1/tuber/tests/testthat/test-playlists.R | 2 tuber-1.4.1/tuber/tests/testthat/test-request-assembly.R |only tuber-1.4.1/tuber/tests/testthat/test-search.R | 2 tuber-1.4.1/tuber/tests/testthat/test-videos.R | 5 tuber-1.4.1/tuber/tests/testthat/test-write-operations.R | 3 36 files changed, 192 insertions(+), 125 deletions(-)
Title: Liquid Glass Design Themes for 'shiny' Applications
Description: Drop-in Liquid Glass themes for 'shiny'. Call
glass_theme() and pass the result to fluidPage(),
navbarPage(), or any 'bslib'-aware page function to get
translucent surfaces, backdrop blur, and system typography on
'Bootstrap' components. Light and dark presets are included, with
options for accent color, blur, and corner radius.
Author: Eric Anderson [aut, cre]
Maintainer: Eric Anderson <eric.ray.anderson@gmail.com>
Diff between shinyglass versions 0.1.0 dated 2026-07-28 and 0.1.1 dated 2026-08-02
DESCRIPTION | 6 MD5 | 10 NEWS.md | 13 + README.md | 30 ++ inst/scss/glass.scss | 456 ++++++++++++++++++++++++++++++++++---- tests/testthat/test-glass-theme.R | 30 ++ 6 files changed, 499 insertions(+), 46 deletions(-)
Title: Luck-Corrected Peer Performance Analysis in R
Description: Provides functions to perform the peer performance analysis of
funds' returns as described in Ardia and Boudt (2018)
<doi:10.1016/j.jbankfin.2017.10.014>. For each fund, the package estimates
the proportion of peers it outperforms, is equalled by, and is outperformed
by, correcting for luck with the false discovery approach of Storey (2002)
<doi:10.1111/1467-9868.00346>. Screenings can be based on factor-model
alphas, Sharpe ratios, or modified Sharpe ratios, the latter using the
equality test of Ardia and Boudt (2015) <doi:10.1016/j.frl.2015.02.008>.
Funds can be screened within a universe or against a separate peer group,
over rolling windows, and results come with bootstrap confidence intervals,
summary, plot, and tidy data frame methods.
Author: David Ardia [aut, cre, cph, fnd] ,
Nabil Bouamara [ctb],
Kris Boudt [aut] ,
Sebastien Legros [ctb],
Murilo Andre Peres Pereira [ctb] ,
Benjamin Seguin [ctb]
Maintainer: David Ardia <david.ardia.ch@gmail.com>
Diff between PeerPerformance versions 2.3.2 dated 2025-08-18 and 2.4.0 dated 2026-08-02
DESCRIPTION | 44 +++++--- MD5 | 73 ++++++++----- NAMESPACE | 28 +++++ NEWS.md | 98 ++++++++++++++++++ R/PeerPerformance.R | 4 R/alphaScreening.R | 204 ++++++++++++++++++++++++-------------- R/alphaTesting.R | 52 +++++++-- R/computePi.R | 83 +++++++++++++-- R/functions.R | 99 +++++++++++++++++- R/methods.R |only R/msharpeBlockSize.R | 2 R/msharpeScreening.R | 109 ++++++++++++++++---- R/msharpeTesting.R | 4 R/rollScreening.R |only R/screeningXY.R |only R/sharpeBlockSize.R | 2 R/sharpeScreening.R | 111 ++++++++++++++++---- R/sharpeTesting.R | 17 +-- R/targetPeerPerformance.R |only build/partial.rdb |binary build/vignette.rds |only inst/CITATION | 15 ++ inst/doc |only inst/scripts |only man/PeerPerformance.Rd | 2 man/alphaScreening.Rd | 67 ++++++++++-- man/alphaTesting.Rd | 26 ++-- man/as.data.frame.SCREENING.Rd |only man/confint.SCREENING.Rd |only man/exposureHeterogeneity.Rd |only man/msharpeScreening.Rd | 46 +++++++- man/msharpeTesting.Rd | 2 man/plot.SCREENING.Rd |only man/plot.exposureHeterogeneity.Rd |only man/plot.rollScreening.Rd |only man/print.SCREENING.Rd |only man/print.TESTING.Rd |only man/print.summary.SCREENING.Rd |only man/rollScreening.Rd |only man/sharpe.Rd | 2 man/sharpeScreening.Rd | 49 +++++++-- man/sharpeTesting.Rd | 6 - man/summary.SCREENING.Rd |only man/targetPeerPerformance.Rd |only tests/testthat.R | 2 tests/testthat/test_numerical.R |only vignettes |only 47 files changed, 909 insertions(+), 238 deletions(-)
More information about PeerPerformance at CRAN
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Title: Simple Component Analysis
Description: Simple Component Analysis (SCA) often provides much more
interpretable components than Principal Components (PCA) while still
representing much of the variability in the data.
Author: Valentin Rousson [aut],
Martin Maechler [aut, cre]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between sca versions 0.9-2 dated 2024-02-02 and 0.9-3 dated 2026-08-02
ChangeLog | 4 ++++ DESCRIPTION | 18 ++++++++++++------ MD5 | 6 +++--- build/partial.rdb |binary 4 files changed, 19 insertions(+), 9 deletions(-)
Title: Automated Machine Learning and AI Agent Tools for Clinical
Prediction Modelling
Description: Provides a streamlined workflow for building, validating, and reporting clinical prediction models. Combines standard machine learning tools with an optional AI agent that recommends appropriate statistical methods, runs sensitivity analyses, and flags common pitfalls. Includes automated generation of reports aligned with TRIPOD+AI reporting guidance (Collins et al. (2024 <doi:10.1136/bmj-2023-078378>)) for reproducible, guideline-aligned research.
Author: Uwakmfon Paul [aut, cre, cph]
Maintainer: Uwakmfon Paul <uwakmfon31@gmail.com>
Diff between triageR versions 0.1.0 dated 2026-07-29 and 0.1.1 dated 2026-08-02
DESCRIPTION | 10 - MD5 | 25 +- NEWS.md | 4 README.md | 68 +----- inst/doc/triageR-breast-cancer.R | 6 inst/doc/triageR-breast-cancer.Rmd | 6 inst/doc/triageR-breast-cancer.html | 8 inst/doc/triageR-intro.R | 29 +- inst/doc/triageR-intro.Rmd | 29 +- inst/doc/triageR-intro.html | 321 ++++++++++++++++----------------- man/figures/README-example-model-1.png |binary man/figures/README-setup-1.png |only vignettes/triageR-breast-cancer.Rmd | 6 vignettes/triageR-intro.Rmd | 29 +- 14 files changed, 250 insertions(+), 291 deletions(-)
Title: Access 'Office for Budget Responsibility' Data
Description: Provides clean, tidy access to data published by the 'Office for
Budget Responsibility' ('OBR'), the UK's independent fiscal watchdog. Covers
the Public Finances Databank (outturn for PSNB, PSND, receipts, and
expenditure since 1946), the Historical Official Forecasts Database (every
'OBR' forecast since 2010), the Economic and Fiscal Outlook detailed forecast
tables (five-year projections from the latest Budget), the monthly
profiles for the public finances (the 'OBR' forecast apportioned across
the months of the fiscal year), the Welfare Trends Report (incapacity
benefit spending and caseloads), and the Fiscal Risks and
Sustainability Report (50-year state pension projections). All returned
objects carry provenance metadata recording the source URL, publication
vintage, retrieval time, and file fingerprint, so analyses can be audited
and reproduced. Data is downloaded from the 'OBR' on first use and cached
locally for subsequent calls. Data is sourced from the 'OBR' website
<https [...truncated...]
Author: Charles Coverdale [aut, cre]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between obr versions 0.5.1 dated 2026-07-27 and 0.6.0 dated 2026-08-02
DESCRIPTION | 12 ++++--- MD5 | 50 +++++++++++++++++-------------- NAMESPACE | 2 + NEWS.md | 46 ++++++++++++++++++++++++++++ R/compare.R | 53 ++++++++++++++++++++++++--------- R/fiscal_rules.R | 4 +- R/headroom.R |only R/monthly_profiles.R |only R/policy_measures.R | 2 - R/tbl.R | 1 R/utils.R | 27 ++++++++++++++-- R/vintages.R | 46 +++++++++++++++++++++++----- README.md | 7 +++- man/get_efo_economy.Rd | 1 man/get_efo_fiscal.Rd | 1 man/get_efo_table.Rd | 1 man/get_monthly_profiles.Rd |only man/list_efo_economy_measures.Rd | 1 man/obr-package.Rd | 2 - man/obr_compare_vintages.Rd | 19 ++++++----- man/obr_efo_catalogue.Rd | 1 man/obr_fiscal_rules.Rd | 8 +++- man/obr_headroom.Rd |only man/obr_pin.Rd | 6 +++ tests/testthat/test-compare.R | 12 ++++++- tests/testthat/test-headroom.R |only tests/testthat/test-monthly-profiles.R |only tests/testthat/test-utils.R | 13 ++++++++ tests/testthat/test-vintages.R | 24 ++++++++++++++ 29 files changed, 269 insertions(+), 70 deletions(-)
Title: Corrected Sandwich Inference for Inverse Probability Weighted
Cox Models
Description: An implementation of the corrected sandwich variance (CSV) method for inverse probability weighted (IPW) Cox models described in Shu et al (2021) <doi:10.1111/biom.13332>. The method accounts for the uncertainty in estimating propensity score weights to improve variance and confidence interval estimation for adjusted marginal hazard ratios (HRs) in observational and randomized studies. The package supports estimation of the average treatment effect (ATE) using conventional and stabilized ATE weights, and the average treatment effect in the treated (ATT) using ATT weights, for both independent and clustered data. Propensity scores are estimated using logistic regression.
Author: Di Shu [aut, cre],
Rui Wang [aut]
Maintainer: Di Shu <shudi1991@gmail.com>
Diff between ipwCoxCSV versions 1.0 dated 2019-10-09 and 1.1 dated 2026-08-02
DESCRIPTION | 28 +- MD5 | 13 - NEWS.md |only R/ipwCoxCluster.R | 551 +++++++++++++++++++++++++++----------------- R/ipwCoxInd.R | 588 +++++++++++++++++++++++++++++------------------ man/ipwCoxCSV-package.Rd | 8 man/ipwCoxCluster.Rd | 37 +- man/ipwCoxInd.Rd | 34 +- 8 files changed, 779 insertions(+), 480 deletions(-)
Title: Aggregated Functional Data Calibration using Splines and
Wavelets
Description: Implements methods for calibrating an aggregated functional data model using
wavelets or splines. Each aggregated curve is modeled as a linear combination of
component functions and known weights. The component functions are estimated using
wavelets or splines. The package is based on dos Santos Sousa (2024) <doi:10.1515/mcma-2023-2016>,
Saraiva and Dias (2009) <doi:10.47749/T/UNICAMP.2009.471073> and Johnstone and Silverman (1997) <doi:10.1111/1467-9868.00071>.
Author: Vitor Perrone [aut, cre] ,
Alex Sousa [aut]
Maintainer: Vitor Perrone <vitor.perrone10@gmail.com>
Diff between FunctionalCalibration versions 1.0.0 dated 2025-06-19 and 2.0.0 dated 2026-08-02
FunctionalCalibration-1.0.0/FunctionalCalibration/data/simulated_data.rda |only FunctionalCalibration-1.0.0/FunctionalCalibration/man/simulated_data.Rd |only FunctionalCalibration-2.0.0/FunctionalCalibration/DESCRIPTION | 10 FunctionalCalibration-2.0.0/FunctionalCalibration/MD5 | 31 +-- FunctionalCalibration-2.0.0/FunctionalCalibration/R/data.R | 79 ++++++- FunctionalCalibration-2.0.0/FunctionalCalibration/R/functional_calibration_splines.R | 6 FunctionalCalibration-2.0.0/FunctionalCalibration/R/functional_calibration_wavelets.R | 103 ++++++++-- FunctionalCalibration-2.0.0/FunctionalCalibration/R/plot_aggregated_curve.R | 6 FunctionalCalibration-2.0.0/FunctionalCalibration/R/weight_aggregated_data_estimation.R | 17 - FunctionalCalibration-2.0.0/FunctionalCalibration/data/simulated_data_cor.rda |only FunctionalCalibration-2.0.0/FunctionalCalibration/data/simulated_data_spl.rda |only FunctionalCalibration-2.0.0/FunctionalCalibration/data/simulated_data_wav.rda |only FunctionalCalibration-2.0.0/FunctionalCalibration/man/Bayesian_Shrinkage.Rd | 2 FunctionalCalibration-2.0.0/FunctionalCalibration/man/Universal_Shrinkage.Rd |only FunctionalCalibration-2.0.0/FunctionalCalibration/man/functional_calibration_splines.Rd | 6 FunctionalCalibration-2.0.0/FunctionalCalibration/man/functional_calibration_wavelets.Rd | 18 + FunctionalCalibration-2.0.0/FunctionalCalibration/man/plot_aggregated_curve.Rd | 6 FunctionalCalibration-2.0.0/FunctionalCalibration/man/simulated_data_cor.Rd |only FunctionalCalibration-2.0.0/FunctionalCalibration/man/simulated_data_spl.Rd |only FunctionalCalibration-2.0.0/FunctionalCalibration/man/simulated_data_wav.Rd |only FunctionalCalibration-2.0.0/FunctionalCalibration/man/weight_estimation.Rd | 2 21 files changed, 212 insertions(+), 74 deletions(-)
More information about FunctionalCalibration at CRAN
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Title: Fit Two-Component Normal and Lognormal Mixture Models
Description: Fits, bootstraps, and evaluates two-component normal and lognormal
mixture models. Parameters are estimated by combining differential-evolution
global optimization, as implemented in the 'DEoptim' package (Mullen, Ardia,
Gil, Windover and Cline, 2011) <doi:10.18637/jss.v040.i06>, with a local
'L-BFGS-B' refinement step via optim(). Also provides preliminary diagnostic
plots, automatic normal-versus-lognormal model selection by information
criteria, and parametric or nonparametric bootstrap confidence intervals for
the fitted parameters.
Author: Farrokh Habibzadeh [aut, cre]
Maintainer: Farrokh Habibzadeh <farrokh.habibzadeh@gmail.com>
Diff between DEmixR versions 0.1.1 dated 2025-09-27 and 0.2.0 dated 2026-08-02
DEmixR-0.1.1/DEmixR/man/default_bounds_lognorm2.Rd |only DEmixR-0.1.1/DEmixR/man/default_bounds_norm2.Rd |only DEmixR-0.1.1/DEmixR/man/dot-run_demulti.Rd |only DEmixR-0.1.1/DEmixR/man/loglik_lognorm.Rd |only DEmixR-0.1.1/DEmixR/man/loglik_norm.Rd |only DEmixR-0.1.1/DEmixR/man/order_components.Rd |only DEmixR-0.2.0/DEmixR/DESCRIPTION | 32 - DEmixR-0.2.0/DEmixR/MD5 | 66 +- DEmixR-0.2.0/DEmixR/NAMESPACE | 9 DEmixR-0.2.0/DEmixR/NEWS.md |only DEmixR-0.2.0/DEmixR/R/bootstrap.R | 22 DEmixR-0.2.0/DEmixR/R/core_fit.R | 37 + DEmixR-0.2.0/DEmixR/R/demulti.R | 4 DEmixR-0.2.0/DEmixR/R/evaluate_init.R | 5 DEmixR-0.2.0/DEmixR/R/fit.R | 26 DEmixR-0.2.0/DEmixR/R/imports.R | 9 DEmixR-0.2.0/DEmixR/R/loglikelihoods.R | 8 DEmixR-0.2.0/DEmixR/R/methods.R |only DEmixR-0.2.0/DEmixR/R/plot.R | 22 DEmixR-0.2.0/DEmixR/R/selection.R | 17 DEmixR-0.2.0/DEmixR/R/utils.R | 10 DEmixR-0.2.0/DEmixR/inst/doc/introduction.R | 103 +-- DEmixR-0.2.0/DEmixR/inst/doc/introduction.Rmd | 332 +++++------- DEmixR-0.2.0/DEmixR/inst/doc/introduction.html | 531 +++++++++----------- DEmixR-0.2.0/DEmixR/man/bootstrap_mix2.Rd | 14 DEmixR-0.2.0/DEmixR/man/dot-fit_mix2_core.Rd | 49 + DEmixR-0.2.0/DEmixR/man/evaluate_init.Rd | 6 DEmixR-0.2.0/DEmixR/man/fit_lognorm2.Rd | 14 DEmixR-0.2.0/DEmixR/man/fit_norm2.Rd | 14 DEmixR-0.2.0/DEmixR/man/plot.demixr_fit.Rd |only DEmixR-0.2.0/DEmixR/man/prelim_plots.Rd | 17 DEmixR-0.2.0/DEmixR/man/print.demixr_boot.Rd |only DEmixR-0.2.0/DEmixR/man/print.demixr_fit.Rd |only DEmixR-0.2.0/DEmixR/man/print.demixr_select.Rd |only DEmixR-0.2.0/DEmixR/man/print.summary.demixr_fit.Rd |only DEmixR-0.2.0/DEmixR/man/select_best_mixture.Rd | 13 DEmixR-0.2.0/DEmixR/man/summary.demixr_fit.Rd |only DEmixR-0.2.0/DEmixR/tests |only DEmixR-0.2.0/DEmixR/vignettes/introduction.Rmd | 332 +++++------- 39 files changed, 873 insertions(+), 819 deletions(-)
Title: 'Binance' REST API Client
Description: Client for the 'Binance' <https://www.binance.com/> Spot,
USD-M Futures, and Options REST APIs. Provides helper functions for signed
and unsigned requests, market data retrieval, account access, and order
management with 'data.table' output by default. COIN-M Futures, Portfolio
Margin, WebSocket, SBE, and FIX APIs are not included.
Author: Oliver Zhou [aut, cre],
Lily Li [aut]
Maintainer: Oliver Zhou <oliver.yxzhou@gmail.com>
Diff between binxr versions 0.1.1 dated 2026-05-18 and 0.1.2 dated 2026-08-02
DESCRIPTION | 11 - MD5 | 43 ++-- NAMESPACE | 15 + NEWS.md | 18 + R/binxr-package.R | 4 R/endpoints-futures-market.R | 106 +++++++++ R/endpoints-futures-trade.R | 267 +++++++++++++++++++++++-- R/endpoints-spot-market.R | 33 +++ README.md | 5 man/binxr-package.Rd | 5 man/futures_cancel_algo_order.Rd |only man/futures_cancel_all_algo_orders.Rd |only man/futures_get_algo_order.Rd |only man/futures_get_algo_orders.Rd |only man/futures_get_historical_trades.Rd |only man/futures_get_index_constituents.Rd |only man/futures_get_insurance_balance.Rd |only man/futures_get_open_algo_orders.Rd |only man/futures_get_order_amendments.Rd |only man/futures_get_rpi_depth.Rd |only man/futures_get_symbol_adl_risk.Rd |only man/futures_get_trading_schedule.Rd |only man/futures_modify_order.Rd |only man/futures_place_algo_order.Rd |only man/spot_get_historical_block_trades.Rd |only tests/testthat/test-endpoints-futures-market.R | 39 +++ tests/testthat/test-endpoints-futures-trade.R | 75 +++++++ tests/testthat/test-endpoints-spot-account.R | 9 tests/testthat/test-endpoints-spot-general.R | 14 + tests/testthat/test-endpoints-spot-market.R | 39 +++ 30 files changed, 645 insertions(+), 38 deletions(-)
Title: Discrete Time Survival and Longitudinal Data Analysis
Description: Various functions for discrete time survival analysis and longitudinal analysis. SIMEX method for correcting for bias for errors-in-variables
in a mixed effects model. Asymptotic mean and variance of different proportional hazards test statistics using different ties methods given two
survival curves and censoring distributions. Score test and Wald test for regression analysis of grouped survival data. Calculation of survival
curves for events defined by the response variable in a mixed effects model crossing a threshold with or without confirmation.
Author: John Lawrence [aut, cre],
Jianjin Xu [ctb],
Sue Jane Wang [ctb],
Jim Hung [ctb]
Maintainer: John Lawrence <john.lawrence@fda.hhs.gov>
Diff between SurvDisc versions 0.1.1 dated 2018-05-06 and 0.1.2 dated 2026-08-02
SurvDisc-0.1.1/SurvDisc/data/datalist |only SurvDisc-0.1.2/SurvDisc/DESCRIPTION | 6 +++--- SurvDisc-0.1.2/SurvDisc/MD5 | 9 ++++----- SurvDisc-0.1.2/SurvDisc/man/AsympDiscSurv.Rd | 2 +- SurvDisc-0.1.2/SurvDisc/man/LongToSurv.Rd | 2 +- SurvDisc-0.1.2/SurvDisc/man/SampleSizeDiscSurv.Rd | 2 +- 6 files changed, 10 insertions(+), 11 deletions(-)
Title: Factor Analysis for All
Description: Provides a comprehensive Shiny-based graphical user interface
for conducting a wide range of factor analysis procedures. 'FAfA'
(Factor Analysis for All) guides users through data uploading,
assumption checking (descriptives, collinearity, multivariate
normality, outliers), data wrangling (variable exclusion, data
splitting), factor retention analysis (e.g., Parallel Analysis, Hull
method, EGA), Exploratory Factor Analysis (EFA) with various rotation
and extraction methods, Confirmatory Factor Analysis (CFA) for model
testing, Reliability Analysis (e.g., Cronbach's Alpha, McDonald's
Omega), Measurement Invariance testing across groups, and item
weighting techniques. The application leverages established R packages
such as 'lavaan' and 'psych' to perform these analyses, offering an
accessible platform for researchers and students. Results are
presented in user-friendly tables and plots, with options for
downloading outputs. Analysis projects can be saved and restored, and
reproducible R [...truncated...]
Author: Abdullah Faruk KILIC [aut, cre, cph],
Ahmet Caliskan [aut, cph],
Melissa G. Wolf [ctb, cph] ,
Daniel McNeish [ctb, cph]
Maintainer: Abdullah Faruk KILIC <afarukkilic@trakya.edu.tr>
Diff between FAfA versions 1.1 dated 2026-05-03 and 1.2 dated 2026-08-02
FAfA-1.1/FAfA/LICENSE |only FAfA-1.1/FAfA/R/itemrest_internal.R |only FAfA-1.1/FAfA/R/mod_replicability_server.r |only FAfA-1.1/FAfA/R/mod_replicability_ui.r |only FAfA-1.1/FAfA/man/print.itemrest_result.Rd |only FAfA-1.2/FAfA/DESCRIPTION | 47 FAfA-1.2/FAfA/MD5 | 128 - FAfA-1.2/FAfA/NAMESPACE | 124 - FAfA-1.2/FAfA/NEWS.md | 44 FAfA-1.2/FAfA/R/app_config.R | 117 - FAfA-1.2/FAfA/R/app_server.R | 237 +- FAfA-1.2/FAfA/R/app_ui.R | 116 - FAfA-1.2/FAfA/R/dynamic_fit_utils.R |only FAfA-1.2/FAfA/R/ega_bootstrap_utils.R |only FAfA-1.2/FAfA/R/globals.r | 3 FAfA-1.2/FAfA/R/i18n.R |only FAfA-1.2/FAfA/R/invariance_utils.R |only FAfA-1.2/FAfA/R/mod_about_server.r | 113 - FAfA-1.2/FAfA/R/mod_about_ui.r | 20 FAfA-1.2/FAfA/R/mod_assumptions_server.r | 100 - FAfA-1.2/FAfA/R/mod_assumptions_ui.R | 10 FAfA-1.2/FAfA/R/mod_cfa_server.r | 712 ++++--- FAfA-1.2/FAfA/R/mod_cfa_ui.r | 484 ++-- FAfA-1.2/FAfA/R/mod_data_selection_server.r | 169 - FAfA-1.2/FAfA/R/mod_data_selection_ui.r | 103 - FAfA-1.2/FAfA/R/mod_efa_server.r | 669 ++++-- FAfA-1.2/FAfA/R/mod_efa_ui.r | 251 +- FAfA-1.2/FAfA/R/mod_ega_server.r | 487 ++++ FAfA-1.2/FAfA/R/mod_ega_ui.r | 154 + FAfA-1.2/FAfA/R/mod_inv_server.r | 371 ++- FAfA-1.2/FAfA/R/mod_inv_ui.R | 49 FAfA-1.2/FAfA/R/mod_item_weighting_server.r | 18 FAfA-1.2/FAfA/R/mod_item_weighting_ui.r | 20 FAfA-1.2/FAfA/R/mod_itemrest_server.r | 378 +-- FAfA-1.2/FAfA/R/mod_itemrest_ui.r | 149 - FAfA-1.2/FAfA/R/mod_missing_server.r | 206 +- FAfA-1.2/FAfA/R/mod_missing_ui.r | 27 FAfA-1.2/FAfA/R/mod_project_server.R |only FAfA-1.2/FAfA/R/mod_project_ui.R |only FAfA-1.2/FAfA/R/mod_reliability_server.r | 300 +-- FAfA-1.2/FAfA/R/mod_reliability_ui.r | 80 FAfA-1.2/FAfA/R/mod_wrangling_server.r | 332 ++- FAfA-1.2/FAfA/R/mod_wrangling_ui.r | 68 FAfA-1.2/FAfA/R/project_utils.R |only FAfA-1.2/FAfA/R/report_utils.R |only FAfA-1.2/FAfA/R/utils.r | 1085 ++++++++--- FAfA-1.2/FAfA/README.md | 37 FAfA-1.2/FAfA/inst/COPYRIGHTS |only FAfA-1.2/FAfA/inst/WORDLIST | 45 FAfA-1.2/FAfA/inst/app/app.R |only FAfA-1.2/FAfA/inst/app/www/fafa-project.js |only FAfA-1.2/FAfA/inst/app/www/fonts |only FAfA-1.2/FAfA/inst/extdata |only FAfA-1.2/FAfA/man/about_server.Rd |only FAfA-1.2/FAfA/man/assumptions_server.Rd |only FAfA-1.2/FAfA/man/cfa_server.Rd |only FAfA-1.2/FAfA/man/cfa_ui.Rd |only FAfA-1.2/FAfA/man/data_selection_server.Rd |only FAfA-1.2/FAfA/man/efa_server_analysis.Rd |only FAfA-1.2/FAfA/man/efa_server_fac_ret.Rd |only FAfA-1.2/FAfA/man/efa_server_report.Rd |only FAfA-1.2/FAfA/man/inv_server.Rd |only FAfA-1.2/FAfA/man/item_weighting_server.Rd |only FAfA-1.2/FAfA/man/mod_itemrest_server.Rd |only FAfA-1.2/FAfA/man/mod_itemrest_ui.Rd |only FAfA-1.2/FAfA/man/mod_missing_server.Rd |only FAfA-1.2/FAfA/man/mod_missing_ui.Rd |only FAfA-1.2/FAfA/man/op_null_or.Rd |only FAfA-1.2/FAfA/man/reliability_server.Rd |only FAfA-1.2/FAfA/man/wrangling_server_ex_var.Rd |only FAfA-1.2/FAfA/man/write_apa7_report.Rd |only FAfA-1.2/FAfA/tests/spelling.Rout.save |only FAfA-1.2/FAfA/tests/testthat/Rplots.pdf |only FAfA-1.2/FAfA/tests/testthat/_problems |only FAfA-1.2/FAfA/tests/testthat/test-about.R |only FAfA-1.2/FAfA/tests/testthat/test-bootstrap-ega.R |only FAfA-1.2/FAfA/tests/testthat/test-data-processing.R |only FAfA-1.2/FAfA/tests/testthat/test-invariance.R |only FAfA-1.2/FAfA/tests/testthat/test-project-reports.R |only FAfA-1.2/FAfA/tests/testthat/test-shinytest2-critical-flow.R |only FAfA-1.2/FAfA/tests/testthat/testthat-problems.rds |only 81 files changed, 4881 insertions(+), 2372 deletions(-)
Title: Access the Open Experience Sampling Method Database
Description: Provides programmatic access to the Open Experience Sampling Method ('openESM') database (<https://openesmdata.org>),
a collection of harmonized experience sampling datasets. The package enables researchers to discover, download,
and work with the datasets while ensuring proper citation and license compliance.
Author: Bjoern S. Siepe [aut, cre, cph] ,
Matthias Kloft [aut]
Maintainer: Bjoern S. Siepe <bjoernsiepe@gmail.com>
Diff between openesm versions 0.2.0 dated 2026-05-06 and 0.2.1 dated 2026-08-02
DESCRIPTION | 8 ++-- MD5 | 32 ++++++++-------- R/S3_methods.R | 25 +++++++++++-- R/generics.R | 22 +++++++++-- R/get_dataset.R | 30 +++++---------- R/list_datasets.R | 30 ++++++--------- R/utils.R | 44 ++++++++++++++++------ man/cache_info.Rd | 8 ++++ man/cite.Rd | 11 ++++- man/clear_cache.Rd | 12 +++++- man/get_dataset.Rd | 31 +++++----------- man/list_datasets.Rd | 21 ++++------ man/notes.Rd | 11 ++++- man/openesm-package.Rd | 1 man/print.openesm_dataset.Rd | 17 ++++++++ man/print.openesm_dataset_list.Rd | 8 +++- tests/testthat/test-utils.R | 73 +++++++++++++++++++++++++++----------- 17 files changed, 247 insertions(+), 137 deletions(-)
Title: Access the 'Anthropic Economic Index' Dataset
Description: Provides clean, tidy access to the 'Anthropic Economic Index'
(AEI) dataset hosted on 'Hugging Face'
<https://huggingface.co/datasets/Anthropic/EconomicIndex>. The AEI
is a recurring release from 'Anthropic' that maps usage of the
'Claude' family of large language models to occupations and tasks
using the 'O*NET' taxonomy and the 'Standard Occupational
Classification' system, following the methodology of Handa et al.
(2025) <doi:10.48550/arXiv.2503.04761> and the privacy-preserving system 'Clio'
of Tamkin et al. (2024) <doi:10.48550/arXiv.2412.13678>. Functions list available
releases, fetch raw and enriched usage tables, retrieve task
statements, request hierarchies, country-level breakdowns, and the
standalone labor market impacts tables (job exposure and task
penetration), compare two releases, join the index to user-supplied
data on a shared key, and compute usage-concentration metrics
(Herfindahl-Hirschman Index, top-N concentration ratios, Shannon
entropy). Data [...truncated...]
Author: Charles Coverdale [aut, cre]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between aieconindex versions 0.1.1 dated 2026-06-01 and 0.2.0 dated 2026-08-02
DESCRIPTION | 13 ++-- MD5 | 59 ++++++++++--------- NAMESPACE | 1 NEWS.md | 51 ++++++++++++++++ R/compare.R | 70 ++++++++++++++++++---- R/concentration.R | 34 +++++++---- R/geography.R | 111 ++++++++++++++++++++++++------------ R/index.R | 51 ++++++++++++---- R/labor_market.R |only R/releases.R | 2 R/utilities.R | 100 ++++++++++++++++++++++++++++---- README.md | 43 ++++++++----- inst/WORDLIST | 9 ++ inst/doc/aieconindex.R | 12 +++ inst/doc/aieconindex.Rmd | 23 +++++++ inst/doc/aieconindex.html | 31 ++++++++-- man/aei_clusters.Rd | 1 man/aei_compare.Rd | 34 ++++++----- man/aei_concentration.Rd | 32 +++++++--- man/aei_download.Rd | 1 man/aei_geography.Rd | 57 +++++++++++------- man/aei_index.Rd | 32 +++++++--- man/aei_labor_market.Rd |only man/aei_releases.Rd | 2 man/aei_tasks.Rd | 3 tests/testthat/test-compare.R | 33 ++++++++++ tests/testthat/test-concentration.R | 13 ++++ tests/testthat/test-geography.R | 40 ++++++++++++ tests/testthat/test-labor-market.R |only tests/testthat/test-releases.R | 10 +++ tests/testthat/test-utilities.R | 43 +++++++++++++ vignettes/aieconindex.Rmd | 23 +++++++ 32 files changed, 731 insertions(+), 203 deletions(-)
Title: Download Data from the 'Bank of England' Statistical Database
Description: Provides functions to download and tidy statistical data
published by the 'Bank of England' <https://www.bankofengland.co.uk>.
Covers Bank Rate, 'SONIA', gilt yields, exchange rates, mortgage rates,
mortgage approvals, consumer credit, and money supply. Series are
fetched from the 'Bank of England Interactive Statistical Database'
using its CSV endpoint. Data is cached locally between sessions.
Author: Charles Coverdale [aut, cre]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between boe versions 0.3.0 dated 2026-05-30 and 0.4.0 dated 2026-08-02
DESCRIPTION | 6 MD5 | 26 +- NEWS.md | 55 ++++ R/boe_consumer_credit.R | 34 ++ R/boe_mpr_forecasts.R | 375 +++++++++++++++++++++++------- R/utils.R | 17 + README.md | 70 +++-- data/boe_series.rda |binary inst/doc/yield-curves.html | 4 man/boe_consumer_credit.Rd | 18 + man/boe_mpr_forecasts.Rd | 72 +++-- tests/testthat/test-boe_consumer_credit.R | 33 ++ tests/testthat/test-boe_get.R | 30 ++ tests/testthat/test-boe_mpr_forecasts.R | 182 +++++++++++++- 14 files changed, 738 insertions(+), 184 deletions(-)
Title: Get the Category of Content Hosted by a Domain
Description: Get the category of content hosted by a domain. Use Shallalist (service discontinued),
'VirusTotal' (which provides access to lots of services) <https://www.virustotal.com/>,
'DMOZ' <https://archive.org/details/dmoz-rdf-20150327>, University Domain list
<https://github.com/Hipo/university-domains-list>, 'OpenAI' 'GPT' models, 'Anthropic' 'Claude' models,
or validated machine learning classifiers based on 'Shallalist' data to learn about the kind
of content hosted by a domain.
Author: Gaurav Sood [aut, cre]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between rdomains versions 0.4.0 dated 2026-05-13 and 0.5.0 dated 2026-08-02
DESCRIPTION | 21 ++++++----- MD5 | 57 ++++++++++++++++++++----------- NAMESPACE | 33 ++++++++++++++++++ NEWS.md | 61 +++++++++++++++++++++++++++++++++ R/collect_content.R |only R/dmoz_cat.R | 14 ++++++- R/extract_text.R |only R/get_dmoz_data.R | 7 ++- R/outcomes.R |only R/page_signals.R |only R/rdomains.R | 14 ++++--- R/robots.R |only R/shalla_cat.R | 14 ++++++- R/source_vintage.R |only R/stevenblack_cat.R | 62 ++++++++++++++++++++++++---------- build/vignette.rds |binary inst/doc/rdomains.html | 4 +- man/collect_content.Rd |only man/dmoz_cat.Rd | 12 ++++++ man/fetch_error_codes.Rd |only man/fetch_report.Rd |only man/html_text_content.Rd |only man/page_signals.Rd |only man/shalla_cat.Rd | 12 ++++++ man/source_vintage.Rd |only man/stevenblack_cat.Rd | 13 ++++++- tests/testthat/test-claude-cat.R | 8 +--- tests/testthat/test-collect-content.R |only tests/testthat/test-dmoz-cat.R | 37 +++++++++++++++----- tests/testthat/test-extract-text.R |only tests/testthat/test-ml-cat.R | 4 -- tests/testthat/test-openai-cat.R | 8 +--- tests/testthat/test-outcomes.R |only tests/testthat/test-page-signals.R |only tests/testthat/test-shalla-cat.R | 14 +++++-- tests/testthat/test-source-vintage.R |only tests/testthat/test-stevenblack-cat.R | 12 +++--- tests/testthat/test-utils.R | 2 - 38 files changed, 311 insertions(+), 98 deletions(-)
Title: Access Australian Electoral Commission Data
Description: Provides clean, tidy access to Australian Electoral Commission
(AEC) federal election data. Includes results for the House of
Representatives and Senate from 2007 onwards, at both division and polling
place level, plus by-elections from 2008 onwards, the 2023 referendum,
and the full distribution of preferences. Data is downloaded directly from the AEC
<https://results.aec.gov.au> on first use and cached locally for
subsequent calls.
Author: Charles Coverdale [aut, cre]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between readaec versions 0.1.2 dated 2026-03-16 and 0.2.0 dated 2026-08-02
DESCRIPTION | 12 ++- MD5 | 63 +++++++++++------- NAMESPACE | 11 +++ NEWS.md | 43 ++++++++++++ R/by_elections.R |only R/candidates.R | 24 ++++-- R/globals.R | 7 +- R/house.R | 129 ++++++++++++++++++++++++++----------- R/referendum.R |only R/senate.R | 37 +++++++++- R/swing.R | 35 ++++++++-- R/utils.R | 49 +++++++++++--- README.md | 61 ++++++++++++++++- inst/doc/richmond-example.html | 6 - man/aec_download.Rd |only man/get_by_election_candidates.Rd |only man/get_by_election_fp.Rd |only man/get_by_election_tcp.Rd |only man/get_by_election_tpp.Rd |only man/get_candidates.Rd | 5 + man/get_dop.Rd |only man/get_enrolment.Rd | 5 + man/get_fp.Rd | 5 + man/get_fp_by_booth.Rd | 5 + man/get_members_elected.Rd | 5 + man/get_polling_places.Rd | 5 + man/get_referendum_by_booth.Rd |only man/get_referendum_turnout.Rd |only man/get_senate.Rd | 5 + man/get_senators_elected.Rd |only man/get_swing.Rd | 15 +++- man/get_tcp.Rd | 5 + man/get_tcp_by_booth.Rd |only man/get_tpp.Rd | 5 + man/get_tpp_by_booth.Rd | 5 + man/get_turnout.Rd | 5 + man/list_by_elections.Rd |only man/list_referendums.Rd |only tests/testthat/test-by-elections.R |only tests/testthat/test-new-house.R |only tests/testthat/test-referendum.R |only 41 files changed, 431 insertions(+), 116 deletions(-)
Title: Draw Beautiful Symbol Nomenclature for Glycans
Description: A 'ggplot2'-native plotting engine for drawing reproducible beautiful
Symbol Nomenclature for Glycans (SNFG) glycan cartoons from glycan structure
objects or text notations, with support for batch export, structural
highlighting, and deep appearance customization. It follows the SNFG
specification described at <https://www.ncbi.nlm.nih.gov/glycans/snfg.html>.
Author: Bin Fu [aut, cre, cph] ,
Xisong Feng [aut]
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>
Diff between glydraw versions 0.7.0 dated 2026-07-25 and 0.8.0 dated 2026-08-02
glydraw-0.7.0/glydraw/R/glydraw-style.R |only glydraw-0.7.0/glydraw/man/glydraw_style.Rd |only glydraw-0.8.0/glydraw/DESCRIPTION | 13 glydraw-0.8.0/glydraw/MD5 | 209 +- glydraw-0.8.0/glydraw/NAMESPACE | 10 glydraw-0.8.0/glydraw/NEWS.md | 31 glydraw-0.8.0/glydraw/R/anno-glycan.R |only glydraw-0.8.0/glydraw/R/draw-cartoon-sketch.R |only glydraw-0.8.0/glydraw/R/draw-cartoon.R | 82 glydraw-0.8.0/glydraw/R/export-cartoons.R | 118 - glydraw-0.8.0/glydraw/R/geom-glycan.R | 187 +- glydraw-0.8.0/glydraw/R/geom-node-glycan.R | 4 glydraw-0.8.0/glydraw/R/glycan-grob.R | 161 - glydraw-0.8.0/glydraw/R/guide-glycan.R | 86 glydraw-0.8.0/glydraw/R/internal-annotations.R | 772 +++++++- glydraw-0.8.0/glydraw/R/internal-cartoon.R | 483 ++++- glydraw-0.8.0/glydraw/R/internal-data.R | 13 glydraw-0.8.0/glydraw/R/internal-grid.R |only glydraw-0.8.0/glydraw/R/internal-sketch.R |only glydraw-0.8.0/glydraw/R/save-cartoon.R | 31 glydraw-0.8.0/glydraw/R/scale-glycan.R | 501 ++++- 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Title: Expression Data Analysis and Visualization
Description: A toolkit for microarray and RNA-seq data analysis, including annotation conversion, differential expression, enrichment, survival analysis, and visualization.
Author: Xiaojie Sun [aut, cre]
Maintainer: Xiaojie Sun <18763899370@163.com>
Diff between tinyarray versions 2.4.3 dated 2025-03-05 and 3.0.0 dated 2026-08-02
tinyarray-2.4.3/tinyarray/NEWS.md |only tinyarray-2.4.3/tinyarray/R/tmp.R |only tinyarray-2.4.3/tinyarray/data/lnc_annov23.rda |only tinyarray-2.4.3/tinyarray/data/mRNA_annov23.rda |only tinyarray-2.4.3/tinyarray/man/lnc_annov23.Rd |only tinyarray-2.4.3/tinyarray/man/mRNA_annov23.Rd |only tinyarray-3.0.0/tinyarray/DESCRIPTION | 21 tinyarray-3.0.0/tinyarray/MD5 | 161 +- tinyarray-3.0.0/tinyarray/NAMESPACE | 23 tinyarray-3.0.0/tinyarray/R/00_internal_helpers.R |only tinyarray-3.0.0/tinyarray/R/10_survival_cut_cox_km.R | 20 tinyarray-3.0.0/tinyarray/R/11_surv_box_plot.R | 93 - tinyarray-3.0.0/tinyarray/R/12_cor_and_hyper.R | 12 tinyarray-3.0.0/tinyarray/R/13_network_edge_node.R | 16 tinyarray-3.0.0/tinyarray/R/14_dumd_all.R | 25 tinyarray-3.0.0/tinyarray/R/15_auto_geo_group.R |only tinyarray-3.0.0/tinyarray/R/1_plots.R | 446 +++--- tinyarray-3.0.0/tinyarray/R/2_geo_id.R | 786 +++++++++-- tinyarray-3.0.0/tinyarray/R/3_get_deg.R | 88 - tinyarray-3.0.0/tinyarray/R/4_multi_deg.R | 148 -- tinyarray-3.0.0/tinyarray/R/5_get_deg_all.R | 26 tinyarray-3.0.0/tinyarray/R/6_multi_deg_all.R | 126 + tinyarray-3.0.0/tinyarray/R/7_quick_double_enrich.R | 289 ++-- tinyarray-3.0.0/tinyarray/R/8_tcga_group_trans_exp.R | 549 ++++--- tinyarray-3.0.0/tinyarray/R/9_cor_t_choose.R | 20 tinyarray-3.0.0/tinyarray/R/data.R | 44 tinyarray-3.0.0/tinyarray/R/start_massage.R | 6 tinyarray-3.0.0/tinyarray/README.md | 1278 ++++++++++++++++-- tinyarray-3.0.0/tinyarray/data/lnc_anno.rda |binary tinyarray-3.0.0/tinyarray/data/mRNA_anno.rda |binary tinyarray-3.0.0/tinyarray/inst |only tinyarray-3.0.0/tinyarray/man/auto_geo_group.Rd |only tinyarray-3.0.0/tinyarray/man/box_surv.Rd | 23 tinyarray-3.0.0/tinyarray/man/cod.Rd | 2 tinyarray-3.0.0/tinyarray/man/cor.full.Rd | 2 tinyarray-3.0.0/tinyarray/man/cor.one.Rd | 4 tinyarray-3.0.0/tinyarray/man/corheatmap.Rd | 2 tinyarray-3.0.0/tinyarray/man/corscatterplot.Rd | 9 tinyarray-3.0.0/tinyarray/man/deg.Rd | 2 tinyarray-3.0.0/tinyarray/man/deseq_data.Rd | 2 tinyarray-3.0.0/tinyarray/man/double_enrich.Rd | 20 tinyarray-3.0.0/tinyarray/man/draw_KM.Rd | 9 tinyarray-3.0.0/tinyarray/man/draw_boxplot.Rd | 39 tinyarray-3.0.0/tinyarray/man/draw_heatmap.Rd | 34 tinyarray-3.0.0/tinyarray/man/draw_heatmap2.Rd | 9 tinyarray-3.0.0/tinyarray/man/draw_pca.Rd | 49 tinyarray-3.0.0/tinyarray/man/draw_tsne.Rd | 11 tinyarray-3.0.0/tinyarray/man/draw_venn.Rd | 28 tinyarray-3.0.0/tinyarray/man/draw_volcano.Rd | 21 tinyarray-3.0.0/tinyarray/man/draw_volcano2.Rd | 14 tinyarray-3.0.0/tinyarray/man/exists_anno_list.Rd | 2 tinyarray-3.0.0/tinyarray/man/exp_boxplot.Rd | 22 tinyarray-3.0.0/tinyarray/man/exp_hub1.Rd | 2 tinyarray-3.0.0/tinyarray/man/exp_surv.Rd | 5 tinyarray-3.0.0/tinyarray/man/exprSet_hub1.Rd | 2 tinyarray-3.0.0/tinyarray/man/find_anno.Rd | 15 tinyarray-3.0.0/tinyarray/man/genes.Rd | 2 tinyarray-3.0.0/tinyarray/man/geo_download.Rd | 43 tinyarray-3.0.0/tinyarray/man/geo_parser.Rd | 33 tinyarray-3.0.0/tinyarray/man/get_count_txt.Rd | 8 tinyarray-3.0.0/tinyarray/man/get_deg.Rd | 24 tinyarray-3.0.0/tinyarray/man/get_deg_all.Rd | 36 tinyarray-3.0.0/tinyarray/man/get_gpl_txt.Rd | 5 tinyarray-3.0.0/tinyarray/man/get_ids.Rd |only tinyarray-3.0.0/tinyarray/man/ggheat.Rd | 14 tinyarray-3.0.0/tinyarray/man/interaction_to_edges.Rd | 4 tinyarray-3.0.0/tinyarray/man/lnc_anno.Rd | 8 tinyarray-3.0.0/tinyarray/man/mRNA_anno.Rd | 8 tinyarray-3.0.0/tinyarray/man/make_tcga_group.Rd | 9 tinyarray-3.0.0/tinyarray/man/match_exp_cl.Rd | 6 tinyarray-3.0.0/tinyarray/man/meta1.Rd | 2 tinyarray-3.0.0/tinyarray/man/multi_deg.Rd | 24 tinyarray-3.0.0/tinyarray/man/multi_deg_all.Rd | 32 tinyarray-3.0.0/tinyarray/man/pkg_all.Rd | 2 tinyarray-3.0.0/tinyarray/man/plot_deg.Rd | 23 tinyarray-3.0.0/tinyarray/man/point_cut.Rd | 2 tinyarray-3.0.0/tinyarray/man/print.geo_auto_group.Rd |only tinyarray-3.0.0/tinyarray/man/quick_enrich.Rd | 35 tinyarray-3.0.0/tinyarray/man/risk_plot.Rd | 8 tinyarray-3.0.0/tinyarray/man/sam_filter.Rd | 15 tinyarray-3.0.0/tinyarray/man/surv_KM.Rd | 9 tinyarray-3.0.0/tinyarray/man/surv_cox.Rd | 9 tinyarray-3.0.0/tinyarray/man/t_choose.Rd | 6 tinyarray-3.0.0/tinyarray/man/trans_array.Rd | 10 tinyarray-3.0.0/tinyarray/man/trans_ensembl_exp.Rd |only tinyarray-3.0.0/tinyarray/man/trans_entrezexp.Rd | 22 tinyarray-3.0.0/tinyarray/man/trans_exp.Rd | 11 tinyarray-3.0.0/tinyarray/man/trans_exp_new.Rd | 41 88 files changed, 3420 insertions(+), 1536 deletions(-)
Title: Extra Recipes Steps for Dealing with Unbalanced Data
Description: A dataset with an uneven number of cases in each class is
said to be unbalanced. Many models produce a subpar performance on
unbalanced datasets. A dataset can be balanced by increasing the
number of minority cases using SMOTE 2011
<doi:10.48550/arXiv.1106.1813>, BorderlineSMOTE 2005
<doi:10.1007/11538059_91> and ADASYN 2008. Or by decreasing the number
of majority cases using NearMiss 2003
<https://www.site.uottawa.ca/~nat/Workshop2003/jzhang.pdf> or Tomek
link removal 1976.
Author: Emil Hvitfeldt [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between themis versions 1.0.3 dated 2025-01-22 and 1.1.0 dated 2026-08-02
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themis-1.1.0/themis/man/bsmote.Rd | 107 + themis-1.1.0/themis/man/circle_example.Rd | 5 themis-1.1.0/themis/man/cluster_centroids.Rd |only themis-1.1.0/themis/man/cnn.Rd |only themis-1.1.0/themis/man/enn.Rd |only themis-1.1.0/themis/man/figures/README-unnamed-chunk-2-1.png |binary themis-1.1.0/themis/man/figures/README-unnamed-chunk-3-1.png |binary themis-1.1.0/themis/man/figures/README-unnamed-chunk-4-1.png |binary themis-1.1.0/themis/man/figures/README-unnamed-chunk-5-1.png |binary themis-1.1.0/themis/man/figures/README-unnamed-chunk-6-1.png |binary themis-1.1.0/themis/man/instance_hardness.Rd |only themis-1.1.0/themis/man/kmeans_smote.Rd |only themis-1.1.0/themis/man/ncl.Rd |only themis-1.1.0/themis/man/nearmiss.Rd | 117 + themis-1.1.0/themis/man/oss.Rd |only themis-1.1.0/themis/man/reexports.Rd | 2 themis-1.1.0/themis/man/required_pkgs.step.Rd | 36 themis-1.1.0/themis/man/rmd/tunable-args.Rmd | 16 themis-1.1.0/themis/man/rose.Rd |only themis-1.1.0/themis/man/smogn.Rd |only themis-1.1.0/themis/man/smote.Rd | 78 - themis-1.1.0/themis/man/smoten.Rd |only themis-1.1.0/themis/man/smotenc.Rd | 50 themis-1.1.0/themis/man/step_adasyn.Rd | 130 + themis-1.1.0/themis/man/step_bsmote.Rd | 163 +- themis-1.1.0/themis/man/step_cluster_centroids.Rd |only themis-1.1.0/themis/man/step_cnn.Rd |only themis-1.1.0/themis/man/step_downsample.Rd | 97 - themis-1.1.0/themis/man/step_enn.Rd |only themis-1.1.0/themis/man/step_instance_hardness.Rd |only themis-1.1.0/themis/man/step_kmeans_smote.Rd |only themis-1.1.0/themis/man/step_ncl.Rd |only themis-1.1.0/themis/man/step_nearmiss.Rd | 159 +- themis-1.1.0/themis/man/step_oss.Rd |only themis-1.1.0/themis/man/step_rose.Rd | 120 - themis-1.1.0/themis/man/step_smogn.Rd |only themis-1.1.0/themis/man/step_smote.Rd | 151 +- themis-1.1.0/themis/man/step_smoten.Rd |only themis-1.1.0/themis/man/step_smotenc.Rd | 106 - themis-1.1.0/themis/man/step_svmsmote.Rd |only themis-1.1.0/themis/man/step_tomek.Rd | 118 + themis-1.1.0/themis/man/step_upsample.Rd | 94 - themis-1.1.0/themis/man/svmsmote.Rd |only themis-1.1.0/themis/man/themis-package.Rd | 9 themis-1.1.0/themis/man/tomek.Rd | 68 themis-1.1.0/themis/man/tunable_themis.Rd | 30 themis-1.1.0/themis/tests/testthat/_snaps/adasyn.md | 87 + themis-1.1.0/themis/tests/testthat/_snaps/adasyn_impl.md | 16 themis-1.1.0/themis/tests/testthat/_snaps/bsmote.md | 86 + themis-1.1.0/themis/tests/testthat/_snaps/bsmote_impl.md | 34 themis-1.1.0/themis/tests/testthat/_snaps/cluster_centroids.md |only themis-1.1.0/themis/tests/testthat/_snaps/cluster_centroids_impl.md |only themis-1.1.0/themis/tests/testthat/_snaps/cnn.md |only themis-1.1.0/themis/tests/testthat/_snaps/cnn_impl.md |only themis-1.1.0/themis/tests/testthat/_snaps/downsample.md | 62 themis-1.1.0/themis/tests/testthat/_snaps/enn.md |only themis-1.1.0/themis/tests/testthat/_snaps/enn_impl.md |only themis-1.1.0/themis/tests/testthat/_snaps/instance_hardness.md |only themis-1.1.0/themis/tests/testthat/_snaps/instance_hardness_impl.md |only themis-1.1.0/themis/tests/testthat/_snaps/kmeans_smote.md |only themis-1.1.0/themis/tests/testthat/_snaps/kmeans_smote_impl.md |only themis-1.1.0/themis/tests/testthat/_snaps/misc.md |only themis-1.1.0/themis/tests/testthat/_snaps/ncl.md |only themis-1.1.0/themis/tests/testthat/_snaps/ncl_impl.md |only themis-1.1.0/themis/tests/testthat/_snaps/nearmiss.md | 120 + themis-1.1.0/themis/tests/testthat/_snaps/nearmiss_impl.md | 59 themis-1.1.0/themis/tests/testthat/_snaps/oss.md |only themis-1.1.0/themis/tests/testthat/_snaps/oss_impl.md |only themis-1.1.0/themis/tests/testthat/_snaps/rose.md | 159 ++ themis-1.1.0/themis/tests/testthat/_snaps/smogn.md |only themis-1.1.0/themis/tests/testthat/_snaps/smogn_impl.md |only themis-1.1.0/themis/tests/testthat/_snaps/smote.md | 119 + themis-1.1.0/themis/tests/testthat/_snaps/smote_impl.md | 25 themis-1.1.0/themis/tests/testthat/_snaps/smoten.md |only themis-1.1.0/themis/tests/testthat/_snaps/smoten_impl.md |only themis-1.1.0/themis/tests/testthat/_snaps/smotenc.md | 80 + themis-1.1.0/themis/tests/testthat/_snaps/svmsmote.md |only themis-1.1.0/themis/tests/testthat/_snaps/svmsmote_impl.md |only themis-1.1.0/themis/tests/testthat/_snaps/tomek.md | 44 themis-1.1.0/themis/tests/testthat/_snaps/tomek_impl.md | 16 themis-1.1.0/themis/tests/testthat/_snaps/upsample.md | 86 + themis-1.1.0/themis/tests/testthat/test-S3-methods.R | 39 themis-1.1.0/themis/tests/testthat/test-adasyn.R | 380 ++++- themis-1.1.0/themis/tests/testthat/test-adasyn_impl.R | 136 + themis-1.1.0/themis/tests/testthat/test-bsmote.R | 524 +++++-- themis-1.1.0/themis/tests/testthat/test-bsmote_impl.R | 190 ++ themis-1.1.0/themis/tests/testthat/test-cluster_centroids.R |only themis-1.1.0/themis/tests/testthat/test-cluster_centroids_impl.R |only themis-1.1.0/themis/tests/testthat/test-cnn.R |only themis-1.1.0/themis/tests/testthat/test-cnn_impl.R |only themis-1.1.0/themis/tests/testthat/test-downsample.R | 405 ++++- themis-1.1.0/themis/tests/testthat/test-enn.R |only themis-1.1.0/themis/tests/testthat/test-enn_impl.R |only themis-1.1.0/themis/tests/testthat/test-instance_hardness.R |only themis-1.1.0/themis/tests/testthat/test-instance_hardness_impl.R |only themis-1.1.0/themis/tests/testthat/test-kmeans_smote.R |only themis-1.1.0/themis/tests/testthat/test-kmeans_smote_impl.R |only themis-1.1.0/themis/tests/testthat/test-misc.R |only themis-1.1.0/themis/tests/testthat/test-ncl.R |only themis-1.1.0/themis/tests/testthat/test-ncl_impl.R |only themis-1.1.0/themis/tests/testthat/test-nearmiss.R | 422 +++++- themis-1.1.0/themis/tests/testthat/test-nearmiss_impl.R | 194 ++ themis-1.1.0/themis/tests/testthat/test-oss.R |only themis-1.1.0/themis/tests/testthat/test-oss_impl.R |only themis-1.1.0/themis/tests/testthat/test-rose.R | 322 +++- themis-1.1.0/themis/tests/testthat/test-smogn.R |only themis-1.1.0/themis/tests/testthat/test-smogn_impl.R |only themis-1.1.0/themis/tests/testthat/test-smote.R | 471 +++++- themis-1.1.0/themis/tests/testthat/test-smote_impl.R | 150 ++ themis-1.1.0/themis/tests/testthat/test-smoten.R |only themis-1.1.0/themis/tests/testthat/test-smoten_impl.R |only themis-1.1.0/themis/tests/testthat/test-smotenc.R | 371 ++++- themis-1.1.0/themis/tests/testthat/test-smotenc_impl.R | 52 themis-1.1.0/themis/tests/testthat/test-svmsmote.R |only themis-1.1.0/themis/tests/testthat/test-svmsmote_impl.R |only themis-1.1.0/themis/tests/testthat/test-tomek.R | 204 ++ themis-1.1.0/themis/tests/testthat/test-tomek_impl.R | 48 themis-1.1.0/themis/tests/testthat/test-tunable.R |only themis-1.1.0/themis/tests/testthat/test-upsample.R | 445 +++++- 168 files changed, 8534 insertions(+), 1867 deletions(-)
Title: Miscellaneous Functions 'T. Yanagida'
Description: Miscellaneous functions for (1) data handling (e.g., grand-mean and group-mean centering, coding variables and reverse coding items, scale and cluster scores, reading and writing Excel and SPSS files), (2) descriptive statistics (e.g., frequency table, cross tabulation, effect size measures), (3) missing data (e.g., descriptive statistics for missing data, missing data pattern, Little's test of Missing Completely at Random, and auxiliary variable analysis), (4) multilevel data (e.g., multilevel descriptive statistics, within-group and between-group correlation matrix, multilevel confirmatory factor analysis, level-specific fit indices, cross-level measurement equivalence evaluation, multilevel composite reliability, and multilevel R-squared measures), (5) item analysis (e.g., confirmatory factor analysis, coefficient alpha and omega, between-group and longitudinal measurement equivalence evaluation), (6) statistical analysis (e.g., bootstrap confidence intervals, collinearity and resid [...truncated...]
Author: Takuya Yanagida [aut, cre]
Maintainer: Takuya Yanagida <takuya.yanagida@univie.ac.at>
Diff between misty versions 0.8.2 dated 2026-05-16 and 0.8.3 dated 2026-08-02
DESCRIPTION | 15 MD5 | 321 +- NAMESPACE | 19 NEWS.md | 64 R/aov.b.R | 14 R/aov.w.R | 28 R/blimp.R | 92 R/blimp.bayes.R | 50 R/blimp.plot.R | 80 R/blimp.print.R | 11 R/blimp.run.R | 12 R/blimp.update.R | 92 R/boot.bs.R | 38 R/center.R | 70 R/check.collin.R | 19 R/check.outlier.R | 10 R/check.resid.R | 67 R/chr.color.R | 37 R/chr.grep.R | 19 R/chr.omit.R | 17 R/chr.trunc.R | 4 R/ci.cor.R | 44 R/ci.mean.R | 84 R/ci.mean.diff.R | 97 R/ci.mean.w.R | 38 R/ci.prop.R | 48 R/ci.prop.diff.R | 112 R/ci.var.R | 90 R/cluster.rwg.R | 26 R/cluster.scores.R | 44 R/coding.R | 44 R/coeff.robust.R | 20 R/coeff.std.R | 65 R/cohens.d.R | 158 - R/cor.matrix.R | 451 +-- R/crosstab.R | 59 R/data.R |only R/descript.R | 38 R/df.check.R | 16 R/df.duplicated.R | 38 R/df.head.R | 44 R/df.long.R | 52 R/df.merge.R | 2 R/df.move.R | 8 R/df.rename.R | 12 R/df.subset.R | 67 R/difftest.chibarsq.R | 50 R/dominance.R | 34 R/dominance.manual.R | 32 R/effsize.R | 38 R/freq.R | 40 R/indirect.R | 54 R/item.alpha.R | 504 ++-- R/item.cfa.R | 1362 +++++++---- R/item.dfi.R | 69 R/item.distract.R |only R/item.invar.R | 1258 +++++++--- R/item.noninvar.R | 74 R/item.omega.R | 297 +- R/item.reverse.R | 92 R/item.scores.R | 131 - R/item.stats.R |only R/lagged.R | 48 R/libraries.R | 84 R/modcomp.R | 43 R/mplus.R | 76 R/mplus.bayes.R | 68 R/mplus.lca.R | 102 R/mplus.lca.summa.R | 112 R/mplus.plot.R | 132 - R/mplus.print.R | 244 +- R/mplus.update.R | 106 R/multilevel.alpha.R |only R/multilevel.cfa.R | 1954 ++++++++++------ R/multilevel.cor.R | 499 ++-- R/multilevel.descript.R | 181 - R/multilevel.fit.R | 965 ++------ R/multilevel.icc.R | 71 R/multilevel.indirect.R | 16 R/multilevel.invar.R | 1064 +++++---- R/multilevel.omega.R | 669 +++-- R/multilevel.r2.R | 78 R/multilevel.r2.manual.R | 407 --- R/na.as.R | 23 R/na.auxiliary.R | 60 R/na.coverage.R | 12 R/na.descript.R | 67 R/na.indicator.R | 16 R/na.pattern.R | 14 R/na.prop.R | 6 R/na.satcor.R | 16 R/na.test.R | 28 R/plot.misty.object.R | 70 R/print.misty.object.R | 5126 +++++++++++++++++++++++++++----------------- R/read.data.R | 18 R/read.dta.R | 23 R/read.mplus.R | 54 R/read.sav.R | 23 R/read.xlsx.R | 6 R/rec.R | 80 R/robust.lmer.R | 27 R/script.copy.R | 12 R/script.open.R | 8 R/sim.lavaan.R | 2 R/size.mean.R | 58 R/skewness.R | 58 R/summa.R | 119 - R/test.t.R | 26 R/test.welch.R | 28 R/test.z.R | 24 R/uniq.R | 8 R/utils.R | 2897 +++++++++++++----------- R/write.data.R | 6 R/write.mplus.R | 8 R/write.result.R | 1488 ++++++++---- R/write.sav.R | 22 R/write.xlsx.R | 2 data |only man/boot.bs.Rd | 6 man/center.Rd | 36 man/chr.color.Rd | 12 man/chr.omit.Rd | 4 man/ci.cor.Rd | 6 man/ci.mean.Rd | 8 man/ci.mean.diff.Rd | 6 man/ci.prop.Rd | 6 man/ci.var.Rd | 8 man/coeff.std.Rd | 8 man/cohens.d.Rd | 6 man/cor.matrix.Rd | 142 - man/data.items.Rd |only man/df.duplicated.Rd | 30 man/df.long.Rd | 4 man/df.subset.Rd | 24 man/difftest.chibarsq.Rd | 22 man/dominance.Rd | 4 man/dominance.manual.Rd | 8 man/item.alpha.Rd | 170 - man/item.cfa.Rd | 374 ++- man/item.dfi.Rd | 23 man/item.distract.Rd |only man/item.invar.Rd | 326 +- man/item.noninvar.Rd | 42 man/item.omega.Rd | 111 man/item.reverse.Rd | 37 man/item.scores.Rd | 21 man/item.stats.Rd |only man/modcomp.Rd | 13 man/mplus.lca.Rd | 4 man/mplus.plot.Rd | 44 man/multilevel.alpha.Rd |only man/multilevel.cfa.Rd | 407 ++- man/multilevel.cor.Rd | 195 - man/multilevel.descript.Rd | 41 man/multilevel.fit.Rd | 61 man/multilevel.icc.Rd | 38 man/multilevel.invar.Rd | 127 - man/multilevel.omega.Rd | 185 + man/multilevel.r2.Rd | 30 man/multilevel.r2.manual.Rd | 10 man/na.as.Rd | 9 man/print.misty.object.Rd | 86 man/size.mean.Rd | 6 man/summa.Rd | 4 man/write.mplus.Rd | 2 man/write.result.Rd | 38 166 files changed, 15552 insertions(+), 11317 deletions(-)
Title: Fit the Vector Autoregressive Model for Multiple Individuals
Description: Fit the vector autoregressive model for multiple individuals
using the 'OpenMx' package (Hunter, 2017 <doi:10.1080/10705511.2017.1369354>).
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between fitVARMxID versions 1.0.3 dated 2026-03-31 and 1.0.5 dated 2026-08-02
DESCRIPTION | 8 MD5 | 49 +- NAMESPACE | 9 NEWS.md | 7 R/fitVARMxID-fit-dt-var-mx-id-dot.R | 3 R/fitVARMxID-fit-dt-var-mx-id-save.R |only R/fitVARMxID-fit-dt-var-mx-id.R | 4 R/fitVARMxID-methods-var-mx-id.R | 204 ++++++++++ R/fitVARMxID-plot-coef-forest-dot.R |only R/wald-ci-wald-dot.R |only R/wald-probs-of-alpha-dot.R |only build/partial.rdb |binary man/FitVARMxID.Rd | 5 man/FitVARMxIDSave.Rd |only man/LDL.Rd | 1 man/Softplus.Rd | 1 man/confint.varmxid.Rd |only man/plot.varmxid.Rd |only man/vcov.varmxid.Rd | 5 tests/testthat/test-fitVARMxID-fitvarmxid-center-false-alpha-fixed-ct.R | 33 + tests/testthat/test-fitVARMxID-fitvarmxid-center-false-alpha-fixed.R | 31 + tests/testthat/test-fitVARMxID-fitvarmxid-center-false-ct.R | 31 + tests/testthat/test-fitVARMxID-fitvarmxid-center-false.R | 29 + tests/testthat/test-fitVARMxID-fitvarmxid-center-true-ct.R | 31 + tests/testthat/test-fitVARMxID-fitvarmxid-center-true-mu-fixed-ct.R | 33 + tests/testthat/test-fitVARMxID-fitvarmxid-center-true-mu-fixed.R | 31 + tests/testthat/test-fitVARMxID-fitvarmxid-center-true.R | 29 + tests/testthat/test-fitVARMxID-fitvarmxid-nu-theta-mu0.R | 40 + tests/testthat/test-fitVARMxID-fitvarmxid-trigger-ensure-good-hessian.R | 24 + 29 files changed, 525 insertions(+), 83 deletions(-)
Title: Multivariate Meta-Analysis of Dynamic Model Estimates
Description: Fits fixed-, random-, or mixed-effects multivariate meta-analysis models
using dynamic model estimates from each individual
building on and extending Lee and Gates (2023) <doi:10.1080/00273171.2023.2229310>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between metaDyn versions 1.0.1 dated 2026-03-24 and 1.0.3 dated 2026-08-01
metaDyn-1.0.1/metaDyn/R/metaDyn-average-within-multivariate-dot.R |only metaDyn-1.0.1/metaDyn/R/metaDyn-meta-v-hat-multivariate-dot.R |only metaDyn-1.0.3/metaDyn/DESCRIPTION | 8 metaDyn-1.0.3/metaDyn/MD5 | 109 +-- metaDyn-1.0.3/metaDyn/NAMESPACE | 6 metaDyn-1.0.3/metaDyn/NEWS.md | 10 metaDyn-1.0.3/metaDyn/R/metaDyn-ci-mc-meta-dot.R |only metaDyn-1.0.3/metaDyn/R/metaDyn-ci-wald-meta-dot.R | 56 + metaDyn-1.0.3/metaDyn/R/metaDyn-drop-id-dot.R |only metaDyn-1.0.3/metaDyn/R/metaDyn-meta-alpha-dot.R | 3 metaDyn-1.0.3/metaDyn/R/metaDyn-meta-check-free.R | 45 + metaDyn-1.0.3/metaDyn/R/metaDyn-meta-expected-covariances-cond-y-dot.R |only metaDyn-1.0.3/metaDyn/R/metaDyn-meta-expected-covariances-cond-z-dot.R |only metaDyn-1.0.3/metaDyn/R/metaDyn-meta-expected-covariances-dot.R | 97 -- metaDyn-1.0.3/metaDyn/R/metaDyn-meta-expected-covariances-joint-x-y-dot.R |only metaDyn-1.0.3/metaDyn/R/metaDyn-meta-expected-covariances-joint-x-z-dot.R |only metaDyn-1.0.3/metaDyn/R/metaDyn-meta-expected-means-dot.R | 171 +++- metaDyn-1.0.3/metaDyn/R/metaDyn-meta-extract-dot.R | 23 metaDyn-1.0.3/metaDyn/R/metaDyn-meta-fit-dot.R | 28 metaDyn-1.0.3/metaDyn/R/metaDyn-meta-gamma-dot.R | 3 metaDyn-1.0.3/metaDyn/R/metaDyn-meta-i-sqr-dot.R | 41 - metaDyn-1.0.3/metaDyn/R/metaDyn-meta-indirect-dot.R | 26 metaDyn-1.0.3/metaDyn/R/metaDyn-meta-kappa-dot.R | 3 metaDyn-1.0.3/metaDyn/R/metaDyn-meta-model-dot.R | 52 + metaDyn-1.0.3/metaDyn/R/metaDyn-meta-mu-x-dot.R |only metaDyn-1.0.3/metaDyn/R/metaDyn-meta-mx-matrices-parameters-dot.R | 73 +- metaDyn-1.0.3/metaDyn/R/metaDyn-meta-mx-matrices-variables-dot.R | 42 - metaDyn-1.0.3/metaDyn/R/metaDyn-meta-omega-dot.R | 3 metaDyn-1.0.3/metaDyn/R/metaDyn-meta-phi-dot.R | 3 metaDyn-1.0.3/metaDyn/R/metaDyn-meta-psi-diag-dot.R | 3 metaDyn-1.0.3/metaDyn/R/metaDyn-meta-psi-dot.R | 9 metaDyn-1.0.3/metaDyn/R/metaDyn-meta-psi-sym-dot.R | 3 metaDyn-1.0.3/metaDyn/R/metaDyn-meta-sigma-x-dot.R |only metaDyn-1.0.3/metaDyn/R/metaDyn-meta-starts-dot.R | 355 +++++----- metaDyn-1.0.3/metaDyn/R/metaDyn-meta-tau-sqr-diag-dot.R | 3 metaDyn-1.0.3/metaDyn/R/metaDyn-meta-tau-sqr-dot.R | 9 metaDyn-1.0.3/metaDyn/R/metaDyn-meta-tau-sqr-sym-dot.R | 3 metaDyn-1.0.3/metaDyn/R/metaDyn-meta-v-hat-dot.R | 22 metaDyn-1.0.3/metaDyn/R/metaDyn-meta-var-mx.R | 36 - metaDyn-1.0.3/metaDyn/R/metaDyn-meta.R | 107 ++- metaDyn-1.0.3/metaDyn/R/metaDyn-methods-metadynmeta.R | 124 ++- metaDyn-1.0.3/metaDyn/build/partial.rdb |binary metaDyn-1.0.3/metaDyn/man/Meta.Rd | 70 + metaDyn-1.0.3/metaDyn/man/MetaVARMx.Rd | 73 +- metaDyn-1.0.3/metaDyn/man/confint.metadynmeta.Rd | 23 metaDyn-1.0.3/metaDyn/man/print.metadynmeta.Rd | 19 metaDyn-1.0.3/metaDyn/man/summary.metadynmeta.Rd | 23 metaDyn-1.0.3/metaDyn/tests/testthat.R | 5 metaDyn-1.0.3/metaDyn/tests/testthat/test-metaDyn-distal-mixed-effects-null-cov-diag.R | 39 - metaDyn-1.0.3/metaDyn/tests/testthat/test-metaDyn-distal-mixed-effects-null-error.R | 96 ++ metaDyn-1.0.3/metaDyn/tests/testthat/test-metaDyn-distal-mixed-effects-null.R | 39 - metaDyn-1.0.3/metaDyn/tests/testthat/test-metaDyn-distal-mixed-effects-stochastic-x.R |only metaDyn-1.0.3/metaDyn/tests/testthat/test-metaDyn-distal-mixed-effects-values.R | 39 - metaDyn-1.0.3/metaDyn/tests/testthat/test-metaDyn-distal-random-effects-null.R | 37 - metaDyn-1.0.3/metaDyn/tests/testthat/test-metaDyn-distal-random-effects-values.R | 37 - metaDyn-1.0.3/metaDyn/tests/testthat/test-metaDyn-fixed-effect-null.R | 140 ++- metaDyn-1.0.3/metaDyn/tests/testthat/test-metaDyn-fixed-effect-values.R | 159 ++-- metaDyn-1.0.3/metaDyn/tests/testthat/test-metaDyn-mixed-effects-null.R | 175 ++-- metaDyn-1.0.3/metaDyn/tests/testthat/test-metaDyn-mixed-effects-values.R | 227 +++--- metaDyn-1.0.3/metaDyn/tests/testthat/test-metaDyn-random-effects-null.R | 185 ++--- metaDyn-1.0.3/metaDyn/tests/testthat/test-metaDyn-random-effects-values.R | 231 +++--- 61 files changed, 1991 insertions(+), 1102 deletions(-)
Title: Classification with Parallel Factor Analysis
Description: Classification using Richard A. Harshman's Parallel Factor
Analysis-1 (Parafac) model or Parallel Factor Analysis-2 (Parafac2) model fit to
a three-way or four-way data array. See Harshman and Lundy (1994):
<doi:10.1016/0167-9473(94)90132-5>. Classification using principal component
analysis (PCA) fit to a two-way data matrix is also supported. Uses component
weights from one mode of a Parafac, Parafac2, or PCA model as features to tune
parameters for one or more classification methods via a k-fold cross-validation
procedure. Allows for constraints on different tensor modes. Allows for
inclusion of additional features alongside features generated by the component
model. Supports penalized logistic regression, support vector machine, random
forest, feed-forward neural network, regularized discriminant analysis, and
gradient boosting machine. Supports binary and multiclass classification.
Predicts class labels or class probabilities and calculates multiple
classification performanc [...truncated...]
Author: Matthew A. Asisgress [aut, cre]
Maintainer: Matthew A. Asisgress <mattgress@protonmail.ch>
Diff between cpfa versions 1.3.1 dated 2026-07-13 and 1.3.2 dated 2026-08-01
ChangeLog | 20 ++++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/cpfa.R | 18 +++++++++++++++--- R/kcv.nn.R | 11 +++++++---- R/kcv.plr.R | 4 ++-- R/simcpfa.R | 5 ++++- R/tunecpfa.R | 39 ++++++++++++++++++++++++++++++++++----- inst/doc/cpfa.pdf |binary man/cpfa.Rd | 23 +++++++++++++++-------- man/tunecpfa.Rd | 4 ++-- 11 files changed, 113 insertions(+), 39 deletions(-)
Title: General Modules for 'teal' Applications
Description: Prebuilt 'shiny' modules containing tools for viewing data,
visualizing data, understanding missing and outlier values within your
data and performing simple data analysis. This extends 'teal'
framework that supports reproducible research and analysis.
Author: Dony Unardi [aut, cre],
Dawid Kaledkowski [aut],
Pawel Rucki [aut],
Mahmoud Hallal [aut],
Ondrej Slama [ctb],
Maciej Nasinski [aut],
Konrad Pagacz [aut],
Nikolas Burkoff [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dony Unardi <unardid@gene.com>
Diff between teal.modules.general versions 0.7.0 dated 2026-07-01 and 0.8.0 dated 2026-08-01
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More information about teal.modules.general at CRAN
Permanent link
Title: Clinical Table Styling Tools and Utilities
Description: The primary motivation of this package is to take the things that are great about the R packages 'flextable' <https://davidgohel.github.io/flextable/> and 'officer' <https://davidgohel.github.io/officer/>, take the standard and complex pieces of formatting clinical tables for regulatory use, and simplify the tedious pieces.
Author: Mike Stackhouse [aut, cre] ,
Ross Didenko [aut],
Yevhenii Boiko [aut],
Marat Zakirov [ctb],
Roman Rogoza [ctb],
Atorus Research, Inc. [cph],
Incyte Corporation [cph]
Maintainer: Mike Stackhouse <mike.stackhouse@atorusresearch.com>
Diff between clinify versions 0.3.1 dated 2026-06-02 and 0.4.0 dated 2026-08-01
DESCRIPTION | 6 MD5 | 86 +++-- NAMESPACE | 4 R/add_titles_footnotes.R | 372 ++++++++++++++++++++++- R/clindoc.R | 15 R/clintable.R | 157 +++++++++ R/col_width.R | 45 ++ R/column_headers.R | 361 ++++++++++++++++++++-- R/header_pad.R |only R/pagination.R | 4 R/print.R | 27 + R/row_height.R |only R/slice_clintable.R | 130 +++----- R/spanner_rule.R |only R/styles.R | 39 +- R/write.R | 6 inst/defaults_template.R | 33 +- inst/doc/clinify.R | 28 + inst/doc/clinify.Rmd | 50 +++ inst/doc/clinify.html | 251 ++++++++++----- inst/doc/defaults.R | 24 - inst/doc/defaults.Rmd | 24 - inst/doc/defaults.html | 24 - inst/doc/end_to_end.html | 2 inst/doc/pagination.html | 26 - inst/doc/titles_footnotes.R | 18 + inst/doc/titles_footnotes.Rmd | 29 + inst/doc/titles_footnotes.html | 113 +++++-- man/add_titles_footnotes.Rd | 71 ++++ man/as_clintable.Rd | 15 man/clin_column_headers.Rd | 59 +++ man/clin_header_pad.Rd |only man/clin_row_height.Rd |only man/clin_spanner_rule.Rd |only man/clin_table_align.Rd |only man/clintable.Rd | 74 ++++ man/new_title_footnote.Rd | 10 tests/testthat/test-add_titles_footnotes.R | 261 ++++++++++++++++ tests/testthat/test-clintable.R | 341 +++++++++++++++++++++ tests/testthat/test-col_width.R | 39 ++ tests/testthat/test-column_headers.R | 459 +++++++++++++++++++++++++++++ tests/testthat/test-header_pad.R |only tests/testthat/test-row_height.R |only tests/testthat/test-slice_clintable.R | 359 ++++++++++++++++++++-- tests/testthat/test-spanner_rule.R |only tests/testthat/test-styles.R | 64 ++++ vignettes/clinify.Rmd | 50 +++ vignettes/defaults.Rmd | 24 - vignettes/titles_footnotes.Rmd | 29 + 49 files changed, 3281 insertions(+), 448 deletions(-)
Title: Grammar of Graphics for Linear Model Diagnostic Plots
Description: Allows for easy creation of diagnostic plots for a variety of model objects using the Grammar of Graphics.
Provides functionality for both individual diagnostic plots and an array of four standard diagnostic plots.
Author: Grayson White [aut, cre]
Maintainer: Grayson White <graysonwhite13@gmail.com>
Diff between gglm versions 1.0.5 dated 2026-02-21 and 1.1.0 dated 2026-08-01
gglm-1.0.5/gglm/man/figures/unnamed-chunk-3-1.png |only gglm-1.1.0/gglm/DESCRIPTION | 11 ++-- gglm-1.1.0/gglm/MD5 | 59 +++++++++++----------- gglm-1.1.0/gglm/NAMESPACE | 1 gglm-1.1.0/gglm/R/aaa.R | 17 ++++++ gglm-1.1.0/gglm/R/gglm.R | 54 +++++++++++++------- gglm-1.1.0/gglm/R/launch.R |only gglm-1.1.0/gglm/R/launch_css.R |only gglm-1.1.0/gglm/R/list_model_classes.R | 13 ++-- gglm-1.1.0/gglm/R/stat_cooks_leverage.R | 30 +++++++---- gglm-1.1.0/gglm/R/stat_cooks_obs.R | 20 +++++-- gglm-1.1.0/gglm/R/stat_fitted_resid.R | 22 +++++--- gglm-1.1.0/gglm/R/stat_normal_qq.R | 22 ++++++-- gglm-1.1.0/gglm/R/stat_resid_hist.R | 20 +++++-- gglm-1.1.0/gglm/R/stat_resid_leverage.R | 28 +++++++--- gglm-1.1.0/gglm/R/stat_scale_location.R | 30 +++++++---- gglm-1.1.0/gglm/R/utils.R | 29 ++++++++++ gglm-1.1.0/gglm/README.md | 18 ++++-- gglm-1.1.0/gglm/inst |only gglm-1.1.0/gglm/man/figures/unnamed-chunk-4-1.png |binary gglm-1.1.0/gglm/man/figures/unnamed-chunk-5-1.png |binary gglm-1.1.0/gglm/man/figures/unnamed-chunk-5-2.png |only gglm-1.1.0/gglm/man/figures/unnamed-chunk-6-1.png |binary gglm-1.1.0/gglm/man/figures/unnamed-chunk-7-1.png |only gglm-1.1.0/gglm/man/gglm.Rd | 16 +++-- gglm-1.1.0/gglm/man/launch.Rd |only gglm-1.1.0/gglm/man/list_model_classes.Rd | 12 ++-- gglm-1.1.0/gglm/man/stat_cooks_leverage.Rd | 14 +++-- gglm-1.1.0/gglm/man/stat_cooks_obs.Rd | 13 +++- gglm-1.1.0/gglm/man/stat_fitted_resid.Rd | 13 +++- gglm-1.1.0/gglm/man/stat_normal_qq.Rd | 11 ++-- gglm-1.1.0/gglm/man/stat_resid_hist.Rd | 11 ++-- gglm-1.1.0/gglm/man/stat_resid_leverage.Rd | 14 +++-- gglm-1.1.0/gglm/man/stat_scale_location.Rd | 14 +++-- 34 files changed, 340 insertions(+), 152 deletions(-)
Title: Rapid Gene Characterization Using Public Genomic Databases
Description: A user-friendly interface for characterizing gene function by
disease type and tissue site, integrating curated data from publicly
available genomic and proteomic databases to support candidate gene
prioritization in experimental workflows.
Author: Cydnie Martin [aut, cre]
Maintainer: Cydnie Martin <martincydenise@gmail.com>
Diff between genefindr versions 1.0.0 dated 2026-06-08 and 1.1.0 dated 2026-08-01
DESCRIPTION | 12 ++- MD5 | 17 +++-- NAMESPACE | 6 + R/findr.R | 156 ++++------------------------------------------ R/integrations.R |only R/plots.R |only README.md | 2 man/findr_from_deseq.Rd |only man/findr_plot_genes.Rd |only man/findr_plot_heatmap.Rd |only man/findr_plot_sites.Rd |only man/findr_sites_table.Rd |only tests/testthat |only tests/testthat.R |only 14 files changed, 42 insertions(+), 151 deletions(-)
Title: Time Series Forecasting Functions
Description: Fundamental time series forecasting models such as autoregressive integrated moving average (ARIMA), exponential smoothing, and simple moving average are included. For ARIMA models, the output follows the traditional parameterisation by Box and Jenkins (1970, ISBN: 0816210942, 9780816210947). Furthermore, there are functions for detailed time series exploration and decomposition, respectively. All data and result visualisations are generated by 'ggplot2' instead of conventional R graphical output. For more details regarding the theoretical background of the models see Hyndman, R.J. and Athanasopoulos, G. (2021) <https://otexts.com/fpp3/>.
Author: Ka Yui Karl Wu [aut, cre]
Maintainer: Ka Yui Karl Wu <karlwuky@suss.edu.sg>
Diff between tsforecast versions 1.3.0 dated 2026-01-21 and 1.3.1 dated 2026-08-01
tsforecast-1.3.0/tsforecast/R/tsforecast_1.3.0.R |only tsforecast-1.3.1/tsforecast/DESCRIPTION | 10 ++-- tsforecast-1.3.1/tsforecast/MD5 | 50 +++++++++++------------ tsforecast-1.3.1/tsforecast/R/tsforecast_1.3.1.R |only tsforecast-1.3.1/tsforecast/build/partial.rdb |binary tsforecast-1.3.1/tsforecast/man/airport.Rd | 2 tsforecast-1.3.1/tsforecast/man/is.outlier.Rd | 2 tsforecast-1.3.1/tsforecast/man/predict.Rd | 2 tsforecast-1.3.1/tsforecast/man/ts-functions.Rd | 2 tsforecast-1.3.1/tsforecast/man/tsacf.Rd | 2 tsforecast-1.3.1/tsforecast/man/tsarima.Rd | 6 +- tsforecast-1.3.1/tsforecast/man/tsboxplot.Rd | 2 tsforecast-1.3.1/tsforecast/man/tsconvert.Rd | 2 tsforecast-1.3.1/tsforecast/man/tsdecomp.Rd | 2 tsforecast-1.3.1/tsforecast/man/tsdiff.Rd | 2 tsforecast-1.3.1/tsforecast/man/tsesm.Rd | 2 tsforecast-1.3.1/tsforecast/man/tsexplore.Rd | 2 tsforecast-1.3.1/tsforecast/man/tsforecast.Rd | 2 tsforecast-1.3.1/tsforecast/man/tshistogram.Rd | 2 tsforecast-1.3.1/tsforecast/man/tslag.Rd | 2 tsforecast-1.3.1/tsforecast/man/tslineplot.Rd | 2 tsforecast-1.3.1/tsforecast/man/tslm.Rd | 2 tsforecast-1.3.1/tsforecast/man/tsmltest.Rd | 2 tsforecast-1.3.1/tsforecast/man/tsmodeleval.Rd | 2 tsforecast-1.3.1/tsforecast/man/tsmovav.Rd | 2 tsforecast-1.3.1/tsforecast/man/tsqqplot.Rd | 2 tsforecast-1.3.1/tsforecast/man/tsscatterplot.Rd | 2 27 files changed, 54 insertions(+), 54 deletions(-)
Title: Estimating Propensity Scores (PS), PS-Based Weights, and Effects
Description: Toolbox that provides a streamlined, end-to-end workflow for propensity
score analysis in generating real-world evidence from real-world data.
The package covers the full analytic pipeline - from estimating propensity scores
via logistic regression, to calculating weights or creating a matched cohort,
to generating publication-ready Table 1s with standardized mean
differences and weighted balance diagnostics. It also estimates incidence rates,
hazard ratios, risk ratios, and risk differences with support for stratified and
direct-standardized analyses. All core functions produce formatted 'Excel' reports
with embedded 'README' documentation, making results immediately shareable with
collaborators and stakeholders. Methods are based on Rosenbaum and Rubin (1983)
<doi:10.1093/biomet/70.1.41>, Austin (2011) <doi:10.1080/00273171.2011.568786>,
and Desai et al. (2017) <doi:10.1097/EDE.0000000000000595>.
Author: Hanseul Cho [aut, cre],
Georg Hahn [aut],
Janinne Ortega-Montiel [aut],
Julie Paik [aut],
Elisabetta Patorno [aut]
Maintainer: Hanseul Cho <hanseul0618@gmail.com>
Diff between rwetools versions 0.2.0 dated 2026-06-21 and 0.4.0 dated 2026-08-01
rwetools-0.2.0/rwetools/man/create_ps_weights.Rd |only rwetools-0.4.0/rwetools/DESCRIPTION | 7 rwetools-0.4.0/rwetools/MD5 | 60 rwetools-0.4.0/rwetools/NAMESPACE | 20 rwetools-0.4.0/rwetools/NEWS.md | 136 rwetools-0.4.0/rwetools/R/build_table1.R | 3 rwetools-0.4.0/rwetools/R/create_psweights.R | 621 ++- rwetools-0.4.0/rwetools/R/effect_measures.R | 1983 ++++------ rwetools-0.4.0/rwetools/R/estimate_ps.R | 184 rwetools-0.4.0/rwetools/R/helpers_effect_engines.R |only rwetools-0.4.0/rwetools/R/helpers_effect_measures.R | 570 ++ rwetools-0.4.0/rwetools/R/helpers_ps_psweights.R | 169 rwetools-0.4.0/rwetools/man/build_table1.Rd | 319 - rwetools-0.4.0/rwetools/man/check_ps_assumptions_internal.Rd | 54 rwetools-0.4.0/rwetools/man/create_iptw.Rd |only rwetools-0.4.0/rwetools/man/create_love_plot.Rd | 116 rwetools-0.4.0/rwetools/man/create_matching_weights.Rd |only rwetools-0.4.0/rwetools/man/create_overlap_weights.Rd |only rwetools-0.4.0/rwetools/man/create_ps_matched_cohort.Rd | 291 - rwetools-0.4.0/rwetools/man/dot-is_balanced.Rd |only rwetools-0.4.0/rwetools/man/dot-plot_ps_distribution_set.Rd | 149 rwetools-0.4.0/rwetools/man/dot-trim_ps.Rd |only rwetools-0.4.0/rwetools/man/dot-truncate_ps_weights.Rd |only rwetools-0.4.0/rwetools/man/estimate_hr_ir.Rd | 383 - rwetools-0.4.0/rwetools/man/estimate_ps.Rd | 225 - rwetools-0.4.0/rwetools/man/estimate_rr_rd.Rd | 421 -- rwetools-0.4.0/rwetools/tests/testthat/fixtures |only rwetools-0.4.0/rwetools/tests/testthat/test-build_table1.R | 3 rwetools-0.4.0/rwetools/tests/testthat/test-create_ps_matched_cohort.R | 29 rwetools-0.4.0/rwetools/tests/testthat/test-create_psweights.R | 121 rwetools-0.4.0/rwetools/tests/testthat/test-estimate_hr_ir.R | 334 + rwetools-0.4.0/rwetools/tests/testthat/test-estimate_ps.R | 125 rwetools-0.4.0/rwetools/tests/testthat/test-estimate_rr_rd.R | 238 - rwetools-0.4.0/rwetools/tests/testthat/test-finegray.R |only rwetools-0.4.0/rwetools/tests/testthat/test-helpers-engines.R |only rwetools-0.4.0/rwetools/tests/testthat/test-irr.R |only rwetools-0.4.0/rwetools/tests/testthat/test-ps_weight_features.R |only 37 files changed, 4037 insertions(+), 2524 deletions(-)