Title: Templated Word and PowerPoint Reporting of 'nlmixr2' Fitting
Results
Description: This allows you to generate reporting workflows around 'nlmixr2' analyses with outputs in Word and PowerPoint. You can specify figures, tables and report structure in a user-definable 'YAML' file. Also you can use the internal functions to access the figures and tables to allow their including in other outputs (e.g. R Markdown).
Author: John Harrold [aut, cre]
Maintainer: John Harrold <john.m.harrold@gmail.com>
Diff between nlmixr2rpt versions 0.2.2 dated 2025-10-11 and 0.2.3 dated 2026-09-25
DESCRIPTION | 16 ++++++------ MD5 | 15 +++++++----- NAMESPACE | 36 +++++++++++++++++++---------- NEWS.md | 2 - R/build_equations.R |only inst/doc/Accessing_Figures_and_Tables.html | 7 ++--- inst/doc/Reporting_nlmixr_Fit_Results.html | 29 +++++++++++++++++++---- inst/templates/report_fit.yaml | 20 ++++++++++++++++ man/gen_eqn_table.Rd |only tests/testthat/test-gen_eqn_table.R |only 10 files changed, 89 insertions(+), 36 deletions(-)
Title: Diagnostic Test Accuracy Meta-Analysis using Template Model
Builder
Description: Fits the hierarchical summary receiver operating characteristic (HSROC) model of
Rutter and Gatsonis (2001) <doi:10.1002/sim.942>, the bivariate binomial-normal model of
Reitsma et al. (2005) <doi:10.1016/j.jclinepi.2005.02.022>, the threshold-based bivariate
time-to-event model of Hoyer et al. (2018) <doi:10.1002/jrsm.1273>, and the latent class
extensions of Liu et al. (2015) <doi:10.1111/biom.12264> for diagnostic studies with an
imperfect reference standard. Provides subgroup analyses, HSROC meta-regression,
likelihood-ratio tests, summary ROC plots, and coupled forest plots.
Author: Claus Nowak [aut, cre]
Maintainer: Claus Nowak <claus.nowak@donau-uni.ac.at>
Diff between dtametaTMB versions 0.1.2 dated 2026-08-26 and 0.1.3 dated 2026-09-25
dtametaTMB-0.1.2/dtametaTMB/tests/testthat/test-firRutterGatsonis.R |only dtametaTMB-0.1.2/dtametaTMB/tests/testthat/test-firRutterGatsonisSubgroup.R |only dtametaTMB-0.1.3/dtametaTMB/DESCRIPTION | 6 dtametaTMB-0.1.3/dtametaTMB/MD5 | 164 +- dtametaTMB-0.1.3/dtametaTMB/NAMESPACE | 31 dtametaTMB-0.1.3/dtametaTMB/R/LogLik.R | 112 - dtametaTMB-0.1.3/dtametaTMB/R/coefvcov.R | 106 - dtametaTMB-0.1.3/dtametaTMB/R/dementia.R |only dtametaTMB-0.1.3/dtametaTMB/R/fitHoyerAFT.R | 8 dtametaTMB-0.1.3/dtametaTMB/R/fitReitsma.R | 4 dtametaTMB-0.1.3/dtametaTMB/R/fitReitsmaLCA.R | 15 dtametaTMB-0.1.3/dtametaTMB/R/fitReitsmaSubgroup.R | 5 dtametaTMB-0.1.3/dtametaTMB/R/fitReitsmaSubgroupLCA.R | 25 dtametaTMB-0.1.3/dtametaTMB/R/fitRutterGatsonis.R | 18 dtametaTMB-0.1.3/dtametaTMB/R/fitRutterGatsonisLCA.R | 17 dtametaTMB-0.1.3/dtametaTMB/R/fitRutterGatsonisReg.R | 25 dtametaTMB-0.1.3/dtametaTMB/R/fitRutterGatsonisSubgroup.R | 4 dtametaTMB-0.1.3/dtametaTMB/R/fitRutterGatsonisSubgroupLCA.R | 22 dtametaTMB-0.1.3/dtametaTMB/R/forest.R | 88 + dtametaTMB-0.1.3/dtametaTMB/R/forestHoyerAFT.R | 48 dtametaTMB-0.1.3/dtametaTMB/R/forestReitsma.R | 49 dtametaTMB-0.1.3/dtametaTMB/R/forestReitsmaLCA.R | 48 dtametaTMB-0.1.3/dtametaTMB/R/forestReitsmaSubgroup.R | 59 dtametaTMB-0.1.3/dtametaTMB/R/forestReitsmaSubgroupLCA.R | 61 dtametaTMB-0.1.3/dtametaTMB/R/forestRutterGatsonis.R | 60 dtametaTMB-0.1.3/dtametaTMB/R/forestRutterGatsonisLCA.R | 61 dtametaTMB-0.1.3/dtametaTMB/R/forestRutterGatsonisSubgroup.R | 63 dtametaTMB-0.1.3/dtametaTMB/R/forestRutterGatsonisSubgroupLCA.R | 67 dtametaTMB-0.1.3/dtametaTMB/R/getConfPredRegion.R | 8 dtametaTMB-0.1.3/dtametaTMB/R/getREIT.R | 6 dtametaTMB-0.1.3/dtametaTMB/R/plotHoyerAFT.R | 2 dtametaTMB-0.1.3/dtametaTMB/R/printRutterGatsonisSubgroup.R | 1 dtametaTMB-0.1.3/dtametaTMB/R/printsummary.R |only dtametaTMB-0.1.3/dtametaTMB/R/restructure_data.R | 33 dtametaTMB-0.1.3/dtametaTMB/R/summaryHoyerAFT.R | 8 dtametaTMB-0.1.3/dtametaTMB/R/summaryReitsma.R | 12 dtametaTMB-0.1.3/dtametaTMB/R/summaryReitsmaLCA.R | 14 dtametaTMB-0.1.3/dtametaTMB/R/summaryReitsmaSubgroup.R | 14 dtametaTMB-0.1.3/dtametaTMB/R/summaryReitsmaSubgroupLCA.R | 15 dtametaTMB-0.1.3/dtametaTMB/R/summaryRutterGatsonis.R | 12 dtametaTMB-0.1.3/dtametaTMB/R/summaryRutterGatsonisLCA.R | 21 dtametaTMB-0.1.3/dtametaTMB/R/summaryRutterGatsonisReg.R | 10 dtametaTMB-0.1.3/dtametaTMB/R/summaryRutterGatsonisSubgroup.R | 14 dtametaTMB-0.1.3/dtametaTMB/R/summaryRutterGatsonisSubgroupLCA.R | 17 dtametaTMB-0.1.3/dtametaTMB/data/dementia.rda |only dtametaTMB-0.1.3/dtametaTMB/inst/doc/LCA.pdf |binary dtametaTMB-0.1.3/dtametaTMB/inst/doc/LCA.qmd | 5 dtametaTMB-0.1.3/dtametaTMB/inst/doc/Meta-Regression.R | 7 dtametaTMB-0.1.3/dtametaTMB/inst/doc/Meta-Regression.pdf |binary dtametaTMB-0.1.3/dtametaTMB/inst/doc/Meta-Regression.qmd | 9 dtametaTMB-0.1.3/dtametaTMB/inst/doc/dtametaTMB.R | 4 dtametaTMB-0.1.3/dtametaTMB/inst/doc/dtametaTMB.pdf |binary dtametaTMB-0.1.3/dtametaTMB/inst/doc/dtametaTMB.qmd | 6 dtametaTMB-0.1.3/dtametaTMB/man/anova.dtametaTMB.Rd | 21 dtametaTMB-0.1.3/dtametaTMB/man/coef.dtametaTMB.Rd | 19 dtametaTMB-0.1.3/dtametaTMB/man/dementia.Rd |only dtametaTMB-0.1.3/dtametaTMB/man/fitReitsma.Rd | 2 dtametaTMB-0.1.3/dtametaTMB/man/fitReitsmaLCA.Rd | 8 dtametaTMB-0.1.3/dtametaTMB/man/fitReitsmaSubgroupLCA.Rd | 8 dtametaTMB-0.1.3/dtametaTMB/man/fitRutterGatsonisLCA.Rd | 3 dtametaTMB-0.1.3/dtametaTMB/man/fitRutterGatsonisSubgroupLCA.Rd | 3 dtametaTMB-0.1.3/dtametaTMB/man/forest.ReitsmaSubgroup.Rd | 14 dtametaTMB-0.1.3/dtametaTMB/man/forest.ReitsmaSubgroupLCA.Rd | 14 dtametaTMB-0.1.3/dtametaTMB/man/forest.RutterGatsonisSubgroup.Rd | 14 dtametaTMB-0.1.3/dtametaTMB/man/forest.RutterGatsonisSubgroupLCA.Rd | 14 dtametaTMB-0.1.3/dtametaTMB/man/logLik.dtametaTMB.Rd | 16 dtametaTMB-0.1.3/dtametaTMB/man/plot.HoyerAFT.Rd | 2 dtametaTMB-0.1.3/dtametaTMB/man/print.summary.DTAmodel.Rd |only dtametaTMB-0.1.3/dtametaTMB/man/summary.HoyerAFT.Rd | 2 dtametaTMB-0.1.3/dtametaTMB/man/summary.Reitsma.Rd | 2 dtametaTMB-0.1.3/dtametaTMB/man/summary.ReitsmaLCA.Rd | 3 dtametaTMB-0.1.3/dtametaTMB/man/summary.ReitsmaSubgroup.Rd | 2 dtametaTMB-0.1.3/dtametaTMB/man/summary.ReitsmaSubgroupLCA.Rd | 3 dtametaTMB-0.1.3/dtametaTMB/man/summary.RutterGatsonis.Rd | 2 dtametaTMB-0.1.3/dtametaTMB/man/summary.RutterGatsonisLCA.Rd | 10 dtametaTMB-0.1.3/dtametaTMB/man/summary.RutterGatsonisReg.Rd | 2 dtametaTMB-0.1.3/dtametaTMB/man/summary.RutterGatsonisSubgroup.Rd | 2 dtametaTMB-0.1.3/dtametaTMB/man/summary.RutterGatsonisSubgroupLCA.Rd | 5 dtametaTMB-0.1.3/dtametaTMB/man/vcov.dtametaTMB.Rd | 21 dtametaTMB-0.1.3/dtametaTMB/tests/testthat/test-S3Methods.R |only dtametaTMB-0.1.3/dtametaTMB/tests/testthat/test-fitRutterGatsonis.R |only dtametaTMB-0.1.3/dtametaTMB/tests/testthat/test-fitRutterGatsonisSubgroup.R |only dtametaTMB-0.1.3/dtametaTMB/vignettes/LCA.html | 534 +++--- dtametaTMB-0.1.3/dtametaTMB/vignettes/LCA.qmd | 5 dtametaTMB-0.1.3/dtametaTMB/vignettes/Meta-Regression.html | 793 +++++----- dtametaTMB-0.1.3/dtametaTMB/vignettes/Meta-Regression.qmd | 9 dtametaTMB-0.1.3/dtametaTMB/vignettes/dtametaTMB.html | 412 +++-- dtametaTMB-0.1.3/dtametaTMB/vignettes/dtametaTMB.qmd | 6 88 files changed, 1598 insertions(+), 1737 deletions(-)
Title: Embed 'SWI'-'Prolog'
Description: Interface to 'SWI'-'Prolog', <https://www.swi-prolog.org/>. This package is normally not loaded directly, please refer to package 'rolog' instead. The purpose of this package is to provide the 'Prolog' runtime on systems that do not have a software installation of 'SWI'-'Prolog'.
Author: Matthias Gondan [aut, com, cre] ,
Jan Wielemaker [ctb, cph] ,
European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
Diff between rswipl versions 10.1.15 dated 2026-09-17 and 10.1.16 dated 2026-09-25
rswipl-10.1.15/rswipl/src/swipl-devel/packages/xpce/src/bitmaps/ms_left_arrow.xpm |only rswipl-10.1.16/rswipl/DESCRIPTION | 8 rswipl-10.1.16/rswipl/MD5 | 317 +++--- rswipl-10.1.16/rswipl/NEWS.md | 6 rswipl-10.1.16/rswipl/src/install.libs.R | 2 rswipl-10.1.16/rswipl/src/swipl-devel/VERSION | 2 rswipl-10.1.16/rswipl/src/swipl-devel/boot/init.pl | 1 rswipl-10.1.16/rswipl/src/swipl-devel/boot/init.pl.new |only rswipl-10.1.16/rswipl/src/swipl-devel/boot/messages.pl | 2 rswipl-10.1.16/rswipl/src/swipl-devel/boot/syspred.pl | 3 rswipl-10.1.16/rswipl/src/swipl-devel/boot/toplevel.pl | 21 rswipl-10.1.16/rswipl/src/swipl-devel/demo/README.md | 62 - rswipl-10.1.16/rswipl/src/swipl-devel/demo/colours.pl | 3 rswipl-10.1.16/rswipl/src/swipl-devel/demo/likes.pl | 24 rswipl-10.1.16/rswipl/src/swipl-devel/demo/trace.pl |only rswipl-10.1.16/rswipl/src/swipl-devel/demo/unicode.pl | 18 rswipl-10.1.16/rswipl/src/swipl-devel/desktop/Info.plist.in | 2 rswipl-10.1.16/rswipl/src/swipl-devel/library/console_input.pl | 42 rswipl-10.1.16/rswipl/src/swipl-devel/library/dialect/swi/syspred_options.pl | 5 rswipl-10.1.16/rswipl/src/swipl-devel/library/edit.pl | 45 rswipl-10.1.16/rswipl/src/swipl-devel/library/listing.pl | 36 rswipl-10.1.16/rswipl/src/swipl-devel/library/prolog_colour.pl | 6 rswipl-10.1.16/rswipl/src/swipl-devel/library/prolog_source.pl | 31 rswipl-10.1.16/rswipl/src/swipl-devel/library/prolog_xref.pl | 4 rswipl-10.1.16/rswipl/src/swipl-devel/packages/clpqr/CMakeLists.txt | 2 rswipl-10.1.16/rswipl/src/swipl-devel/packages/clpqr/clpq.pl | 26 rswipl-10.1.16/rswipl/src/swipl-devel/packages/clpqr/clpq/bb_q.pl | 65 - rswipl-10.1.16/rswipl/src/swipl-devel/packages/clpqr/clpq/bv_q.pl | 154 --- rswipl-10.1.16/rswipl/src/swipl-devel/packages/clpqr/clpq/ineq_q.pl | 21 rswipl-10.1.16/rswipl/src/swipl-devel/packages/clpqr/clpq/nf_q.pl | 161 ++- rswipl-10.1.16/rswipl/src/swipl-devel/packages/clpqr/clpq/store_q.pl | 16 rswipl-10.1.16/rswipl/src/swipl-devel/packages/clpqr/clpqr/class.pl | 10 rswipl-10.1.16/rswipl/src/swipl-devel/packages/clpqr/clpqr/dump.pl | 141 +- rswipl-10.1.16/rswipl/src/swipl-devel/packages/clpqr/clpqr/geler.pl | 51 rswipl-10.1.16/rswipl/src/swipl-devel/packages/clpqr/clpqr/itf.pl | 4 rswipl-10.1.16/rswipl/src/swipl-devel/packages/clpqr/clpqr/ordering.pl | 130 ++ rswipl-10.1.16/rswipl/src/swipl-devel/packages/clpqr/clpqr/project.pl | 11 rswipl-10.1.16/rswipl/src/swipl-devel/packages/clpqr/clpqr/redund.pl | 10 rswipl-10.1.16/rswipl/src/swipl-devel/packages/clpqr/clpr.pl | 24 rswipl-10.1.16/rswipl/src/swipl-devel/packages/clpqr/clpr/bb_r.pl | 63 - rswipl-10.1.16/rswipl/src/swipl-devel/packages/clpqr/clpr/bv_r.pl | 161 --- rswipl-10.1.16/rswipl/src/swipl-devel/packages/clpqr/clpr/ineq_r.pl | 21 rswipl-10.1.16/rswipl/src/swipl-devel/packages/clpqr/clpr/nf_r.pl | 77 - rswipl-10.1.16/rswipl/src/swipl-devel/packages/clpqr/clpr/store_r.pl | 16 rswipl-10.1.16/rswipl/src/swipl-devel/packages/clpqr/doc |only rswipl-10.1.16/rswipl/src/swipl-devel/packages/clpqr/test_clpq.pl |only rswipl-10.1.16/rswipl/src/swipl-devel/packages/clpqr/test_clpr.pl |only rswipl-10.1.16/rswipl/src/swipl-devel/packages/json/json.c | 27 rswipl-10.1.16/rswipl/src/swipl-devel/packages/json/test_json.pl | 20 rswipl-10.1.16/rswipl/src/swipl-devel/packages/sgml/sgml_mode.pl | 4 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/Defaults.user | 6 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/man/course/ftp.pl | 12 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/man/refmanual/md/event.md | 10 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/man/refmanual/md/font.md | 18 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/man/refmanual/md/frame.md | 21 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/man/refmanual/md/menu.md | 9 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/man/refmanual/md/popup.md | 2 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/man/refmanual/md/popup_gesture.md | 8 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/man/refmanual/md/terminal_image.md | 5 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/man/userguide/online.plx | 8 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/prolog/boot/pce_keybinding.pl | 20 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/prolog/demo/ispell.pl | 33 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/prolog/lib/draw/attribute.pl | 2 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/prolog/lib/emacs/bookmark_store.pl | 19 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/prolog/lib/emacs/bookmarks.pl | 4 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/prolog/lib/emacs/fundamental_mode.pl | 6 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/prolog/lib/emacs/prolog_mode.pl | 62 - rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/prolog/lib/emacs/prompt.pl | 6 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/prolog/lib/emacs/sgml_mode.pl | 4 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/prolog/lib/emacs/window.pl | 2 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/prolog/lib/epilog.pl | 98 + rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/prolog/lib/man/classification.pl | 5 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/prolog/lib/man/v_inspector.pl | 5 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/prolog/lib/pane_frame.pl | 27 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/prolog/lib/pane_layouts.pl | 26 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/prolog/lib/pce_toc.pl | 53 - rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/prolog/lib/swi/thread_monitor.pl | 5 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/prolog/lib/tab_frame.pl | 511 ++++++++-- rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/prolog/lib/tabbed_window.pl | 43 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/evt/browserselgesture.c | 13 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/evt/event.c | 42 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/evt/popupgesture.c | 37 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/evt/proto.h | 1 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/gra/font.c | 136 +- rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/gra/graphical.c | 9 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/gra/image.c | 2 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/gra/listbrowser.c | 2 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/h/graphics.h | 1 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/h/kernel.h | 1 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/h/thread.h | 6 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/h/unix.h | 7 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/itf/srcsink.c | 24 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/ker/class.c | 33 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/ker/classvar.c | 49 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/ker/proto.h | 2 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/men/button.c | 6 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/men/menu.c | 53 - rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/men/popup.c | 13 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/men/proto.h | 1 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/namedb.txt | 2 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/sdl/sdldraw.c | 9 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/sdl/sdlevent.c | 44 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/sdl/sdlframe.c | 163 +++ rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/sdl/sdlframe.h | 1 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/sdl/sdlinput.c | 5 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/sdl/sdlstream.c | 18 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/txt/keybinding.c | 20 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/txt/terminal.c | 493 ++++++++- rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/txt/terminal.h | 5 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/unx/socket.c | 4 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/unx/stream.c | 338 ++++-- rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/win/frame.c | 51 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/win/proto.h | 1 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/src/win/window.c | 5 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/swipl/interface.c | 34 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/tests/CMakeLists.txt | 23 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/tests/test_barchart.pl | 2 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/tests/test_emacs_split.pl | 27 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/tests/test_epilog_tabs.pl | 61 + rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/tests/test_font_alias.pl |only rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/tests/test_no_display.pl | 2 rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/tests/test_popup_event.pl |only rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/tests/test_process_encoding.pl |only rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/tests/test_redraw_reentrance.pl |only rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/tests/test_tab_frame.pl | 351 ++++++ rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/tests/test_terminal.pl | 180 +++ rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/tests/test_terminal_bce.pl | 108 ++ rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/tests/test_terminal_client.pl |only rswipl-10.1.16/rswipl/src/swipl-devel/packages/xpce/tests/test_terminal_glyphs.pl | 6 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rswipl-10.1.16/rswipl/src/swipl-devel/src/pl-incl.h | 8 rswipl-10.1.16/rswipl/src/swipl-devel/src/pl-list.c | 30 rswipl-10.1.16/rswipl/src/swipl-devel/src/pl-modul.h | 2 rswipl-10.1.16/rswipl/src/swipl-devel/src/pl-prims.c | 338 ++++++ rswipl-10.1.16/rswipl/src/swipl-devel/src/pl-prims.h | 5 rswipl-10.1.16/rswipl/src/swipl-devel/src/pl-proc.c | 15 rswipl-10.1.16/rswipl/src/swipl-devel/src/pl-prof.c | 5 rswipl-10.1.16/rswipl/src/swipl-devel/src/pl-read.c | 153 ++ rswipl-10.1.16/rswipl/src/swipl-devel/src/pl-read.h | 3 rswipl-10.1.16/rswipl/src/swipl-devel/src/pl-setup.c | 12 rswipl-10.1.16/rswipl/src/swipl-devel/src/pl-srcfile.c | 20 rswipl-10.1.16/rswipl/src/swipl-devel/src/pl-tabling.c | 139 ++ rswipl-10.1.16/rswipl/src/swipl-devel/src/pl-thread.c | 2 rswipl-10.1.16/rswipl/src/swipl-devel/src/pl-trace.c | 10 rswipl-10.1.16/rswipl/src/swipl-devel/src/pl-vmi.c | 25 rswipl-10.1.16/rswipl/src/swipl-devel/src/pl-write.c | 131 +- rswipl-10.1.16/rswipl/src/swipl-devel/tests/compile/test_load_context.pl.new |only rswipl-10.1.16/rswipl/src/swipl-devel/tests/core_lang/test_compare_cyclic.pl |only rswipl-10.1.16/rswipl/src/swipl-devel/tests/core_lang/test_partial_compare.pl |only rswipl-10.1.16/rswipl/src/swipl-devel/tests/core_text/test_var_prefix.pl |only rswipl-10.1.16/rswipl/src/swipl-devel/tests/save/test_qlf.pl.new |only rswipl-10.1.16/rswipl/src/swipl-devel/tests/tabling/test_abolish_delay_deps.pl |only rswipl-10.1.16/rswipl/src/swipl-devel/tests/tabling/test_abolish_depending_table.pl |only rswipl-10.1.16/rswipl/src/swipl-devel/tests/tabling/test_delay_after_simplify.pl |only rswipl-10.1.16/rswipl/src/swipl-devel/tests/tabling/test_incr_retractall.pl |only rswipl-10.1.16/rswipl/src/swipl-devel/tests/tabling/test_reeval_wfs.pl |only rswipl-10.1.16/rswipl/src/swipl-devel/tests/tabling/test_simplify_completed.pl |only 171 files changed, 5314 insertions(+), 1483 deletions(-)
Title: Create Demographic Table
Description: To create demographic table with simple summary statistics, with optional comparison(s) over one or more groups.
Author: Tingting Zhan [aut, cre]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between DemographicTable versions 0.2.3 dated 2025-08-18 and 0.2.4 dated 2026-09-25
DemographicTable-0.2.3/DemographicTable/R/as_flextable.R |only DemographicTable-0.2.3/DemographicTable/R/c.R |only DemographicTable-0.2.3/DemographicTable/R/onLoad.R |only DemographicTable-0.2.3/DemographicTable/inst/extR |only DemographicTable-0.2.3/DemographicTable/man/as_flextable.DemographicTable.Rd |only DemographicTable-0.2.3/DemographicTable/man/c.DemographicTable.Rd |only DemographicTable-0.2.3/DemographicTable/man/msg_.Rd |only DemographicTable-0.2.3/DemographicTable/man/print.DemographicTable.Rd |only DemographicTable-0.2.3/DemographicTable/vignettes/DemographicTable.bib |only DemographicTable-0.2.4/DemographicTable/DESCRIPTION | 22 DemographicTable-0.2.4/DemographicTable/MD5 | 45 DemographicTable-0.2.4/DemographicTable/NAMESPACE | 45 DemographicTable-0.2.4/DemographicTable/NEWS.md | 2 DemographicTable-0.2.4/DemographicTable/R/0PACKAGE.R | 2 DemographicTable-0.2.4/DemographicTable/R/DemographicTable.R | 534 ++-------- DemographicTable-0.2.4/DemographicTable/R/border_hard.R |only DemographicTable-0.2.4/DemographicTable/R/msg.R | 42 DemographicTable-0.2.4/DemographicTable/R/pval_shapiro.R | 18 DemographicTable-0.2.4/DemographicTable/R/sumstat.R | 42 DemographicTable-0.2.4/DemographicTable/R/sumtab.R |only DemographicTable-0.2.4/DemographicTable/build/vignette.rds |binary DemographicTable-0.2.4/DemographicTable/inst/doc/intro.R | 88 - DemographicTable-0.2.4/DemographicTable/inst/doc/intro.html | 303 ++--- DemographicTable-0.2.4/DemographicTable/inst/doc/intro.qmd | 140 +- DemographicTable-0.2.4/DemographicTable/man/DemographicTable-package.Rd | 7 DemographicTable-0.2.4/DemographicTable/man/DemographicTable.Rd | 57 - DemographicTable-0.2.4/DemographicTable/man/pval_shapiro.Rd | 13 DemographicTable-0.2.4/DemographicTable/man/sumstat.Rd | 14 DemographicTable-0.2.4/DemographicTable/vignettes/intro.qmd | 140 +- 29 files changed, 599 insertions(+), 915 deletions(-)
More information about DemographicTable at CRAN
Permanent link
Title: Testing for Population Trends Using Low-Cost Ecological Count
Data
Description: A Bayesian tool to test for population trends and changes in trends under arbitrary designs, including before-after (BA), control-intervention (CI) and before-after-control-intervention (BACI) designs commonly used to assess conservation impact. It infers changes in trends jointly from data obtained with multiple survey methods, as well as from limited and noisy data not necessarily collected in standardized ecological surveys. Observed counts can be modeled as following either a Poisson or a negative binomial model, and both deterministic and stochastic trend models are available. For more details on the model see Singer et al. (2025) <doi:10.1101/2025.01.08.631844>, and the file 'AUTHORS' for a list of copyright holders and contributors.
Author: Madleina Caduff [aut],
Andreas Fueglistaler [aut, cre],
Daniel Wegmann [aut],
Liam Singer [aut],
Raphael Eckel [ctb],
Conrad Sanderson [cph] ,
Ryan Curtin [cph] ,
Daniel Lemire [cph] ,
Joao Paulo Magalhaes [cph] ,
Victor Zverovich [cph] ,
Rene Brun [c [...truncated...]
Maintainer: Andreas Fueglistaler <andreas.fueglistaler@unifr.ch>
This is a re-admission after prior archival of version 0.0.6 dated 2026-08-21
Diff between birp versions 0.0.6 dated 2026-08-21 and 0.9.0 dated 2026-09-25
DESCRIPTION | 51 +++++++++++------ MD5 | 17 +++-- NEWS.md | 8 ++ build/partial.rdb |binary inst/AUTHORS | 53 +++++++++++------- inst/COPYRIGHTS |only inst/doc/birp-introduction.html | 117 +++++++++++++++++++--------------------- src/Makevars.in | 106 +++++++++++++++++++++++------------- src/git_commit | 2 src/main.cpp | 4 - 10 files changed, 216 insertions(+), 142 deletions(-)
Title: More Flexible Form of Boolean Verbose
Description: R functions are not supposed to print text without giving
the user the option to turn the printing off or on using a Boolean
'verbose' in a construct like 'if(verbose) print(...)'. But this black/white
approach is rather rigid, and an approach with shades of gray might be more
appropriate in many circumstances. As of Version 1.4, also supports text
and background colors, as well as text styles.
Author: Barry Zeeberg [aut, cre]
Maintainer: Barry Zeeberg <barryz2013@gmail.com>
Diff between vprint versions 1.4 dated 2026-09-08 and 1.5 dated 2026-09-25
DESCRIPTION | 10 +- MD5 | 19 +++-- NAMESPACE | 5 + R/vprint.R | 179 +++++++++++++++++++++++++++++++++++++++++++++++++- inst/doc/vprint.Rmd | 11 +++ inst/doc/vprint.html | 10 ++ man/ncharz.Rd |only man/promptz.Rd |only man/splitNewline.Rd |only man/vprint.Rd | 33 ++++++++- man/vprint0.Rd |only vignettes/colors2.jpg |only vignettes/vprint.Rmd | 11 +++ 13 files changed, 261 insertions(+), 17 deletions(-)
Title: Survey Instrument Workflows
Description: Provides a design-first survey research workflow. An
instrument, an analysis plan declared before data collection, and a
measurement or structural model are held together in one typed,
integrity-checked object (the 'sframe'), so a study's confirmatory
tests are fixed before responses arrive rather than chosen
afterward. Includes
visual instrument design via a browser-based builder or 'Shiny'
studio, export to a self-contained static HTML survey, an embeddable
'Shiny' module, SHA-256 integrity-checked serialisation to the
'.sframe' format, multi-page survey rendering with branching logic,
response quality checking, scale scoring, psychometric diagnostics,
analysis-plan execution, model syntax generation for EFA, CFA,
CB-SEM, and PLS-SEM, an interactive response dashboard, codebook
generation, and reproducible HTML reporting. Also supports
multi-criteria decision analysis (AHP, ANP, DEMATEL, TOPSIS, VIKOR,
MOORA, SMART, WASPAS, PROMETHEE II, ELECTRE I), small-sample survey
helpers, and t [...truncated...]
Author: Mohammed Ali Sharafuddin [aut, cre]
Maintainer: Mohammed Ali Sharafuddin <mohammedali.page@gmail.com>
Diff between surveyframe versions 0.4.1 dated 2026-09-03 and 0.4.2 dated 2026-09-25
DESCRIPTION | 19 MD5 | 557 ++++++++----- NAMESPACE | 4 NEWS.md | 639 +++++++++++++++ R/accessors.R | 379 +++++++-- R/amendments.R | 211 ++++- R/analysis_plan.R | 352 ++++++-- R/analysis_syntax.R |only R/as_data_frame.R | 182 +++- R/bootstrap_ci.R | 123 ++- R/builder.R | 8 R/conjoint_design.R | 32 R/decision_data.R | 125 ++- R/decision_dematel.R | 61 + R/decision_methods.R | 163 +++- R/decision_preference.R | 70 + R/decision_ranking.R | 20 R/decision_sensitivity.R | 67 + R/demo_helpers.R | 26 R/demo_library.R | 143 ++- R/export_static_survey.R | 56 + R/git_link.R | 64 + R/google_sheets.R | 29 R/launch_studio.R | 49 + R/model_layer.R | 154 +++ R/plots.R | 373 ++++++++- R/psychometrics.R | 82 +- R/quality_report.R | 74 + R/read_responses.R | 187 +++- R/read_write_sframe.R | 142 ++- R/render_survey.R | 669 +++++++++++++--- R/reporting.R | 262 +++++- R/rstudio_addins.R | 91 ++ R/score_scales.R | 207 +++-- R/sf_branch.R | 6 R/sf_check.R | 14 R/sf_choices.R | 33 R/sf_instrument.R | 4 R/sf_item.R | 130 +++ R/sf_scale.R | 98 +- R/statistics_reports.R | 434 +++++++++- R/studio_builder.R | 173 +++- R/survey_module.R | 494 ++++++------ R/surveyframe-package.R | 49 + R/text_analysis.R | 135 ++- R/utils.R | 48 + R/validate_sframe.R | 342 +++++++- R/validation_result.R | 17 R/zzz.R |only README.md | 63 + inst/CITATION | 15 inst/builder/survey_builder.html | 727 ++++++++++++++---- inst/demos/analysis.qmd | 214 +++++ inst/demos/analysis_general.qmd | 156 +++ inst/doc/analysing-survey-responses.Rmd | 10 inst/doc/analysing-survey-responses.html | 69 - inst/doc/building-survey-instrument.R | 10 inst/doc/building-survey-instrument.Rmd | 15 inst/doc/building-survey-instrument.html | 51 - inst/doc/deploying-and-collecting.Rmd | 37 inst/doc/deploying-and-collecting.html | 35 inst/doc/efa-cfa-sem-pls-syntax.html | 12 inst/doc/learn-by-example.R | 5 inst/doc/learn-by-example.Rmd | 70 + inst/doc/learn-by-example.html | 309 ++++--- inst/doc/mcdm-analysis.R | 2 inst/doc/mcdm-analysis.Rmd | 68 + inst/doc/mcdm-analysis.html | 130 ++- inst/doc/scale-reliability-validity.R | 25 inst/doc/scale-reliability-validity.Rmd | 45 - inst/doc/scale-reliability-validity.html | 50 - inst/doc/small-sample.Rmd | 36 inst/doc/small-sample.html | 77 + inst/doc/surveybuilder-gui-overview.Rmd | 45 - inst/doc/surveybuilder-gui-overview.html | 111 ++ inst/doc/surveyframe.R | 4 inst/doc/surveyframe.Rmd | 141 +-- inst/doc/surveyframe.html | 226 ++--- inst/doc/text-analysis.Rmd | 47 - inst/doc/text-analysis.html | 97 +- inst/extdata/demos/categorical_results.csv | 4 inst/extdata/demos/correlation_regression_results.csv | 6 inst/extdata/demos/likert_scale.sframe | 4 inst/extdata/demos/likert_scale_results.csv | 14 inst/extdata/demos/matrix_likert_results.csv | 2 inst/extdata/demos/mcdm_choice_results.csv | 2 inst/extdata/demos/multi_group_results.csv | 40 inst/extdata/demos/open_text_results.csv | 178 ++-- inst/extdata/demos/paired_results.csv | 4 inst/extdata/demos/sem_pls_results.csv | 2 inst/extdata/demos/small_sample_results.csv | 2 inst/extdata/demos/two_group_results.csv | 4 inst/extdata/surveyframe_input_types_demo.sframe | 4 inst/rstudio/addins.dcf | 16 inst/schema/sframe_schema.json | 14 inst/shiny/app.R | 87 +- inst/static_survey/collector_template.gs | 123 ++- inst/static_survey/template.html | 473 ++++++++--- inst/templates/report.qmd | 87 +- man/add_model.Rd | 7 man/amend_sframe.Rd | 59 - man/analysis_syntax.Rd |only man/as.data.frame.sf_choices.Rd |only man/as.data.frame.sframe.Rd |only man/as.data.frame.sframe_analysis_results.Rd |only man/as.data.frame.sframe_assumption_report.Rd |only man/as.data.frame.sframe_codebook.Rd |only man/as.data.frame.sframe_descriptives_report.Rd |only man/as.data.frame.sframe_efa_report.Rd |only man/as.data.frame.sframe_efa_solution.Rd |only man/as.data.frame.sframe_item_report.Rd |only man/as.data.frame.sframe_missing_data_report.Rd |only man/as.data.frame.sframe_quality_report.Rd |only man/as.data.frame.sframe_reliability_report.Rd |only man/as.data.frame.sframe_sample_size_plan.Rd |only man/as.data.frame.sframe_sensitivity.Rd |only man/as.data.frame.sframe_validation.Rd |only man/as.data.frame.sframe_validity_report.Rd |only man/as_sframe.Rd | 6 man/assumption_report.Rd | 6 man/bootstrap_ci.Rd | 6 man/cfa_lavaan_syntax.Rd | 22 man/cfa_syntax.Rd | 12 man/clean_text_responses.Rd | 6 man/cohens_d_ci.Rd | 6 man/cramers_v_ci.Rd | 6 man/descriptives_report.Rd | 6 man/efa_report.Rd | 10 man/efa_solution.Rd | 10 man/efa_syntax.Rd | 4 man/eta_sq_ci.Rd | 6 man/export_google_sheet.Rd | 29 man/export_static_survey.Rd | 40 man/extract_quotes.Rd | 16 man/item_report.Rd | 29 man/launch_builder.Rd | 8 man/launch_builder_demo.Rd | 7 man/launch_dashboard_demo.Rd | 7 man/launch_studio.Rd | 21 man/launch_studio_demo.Rd | 7 man/link_git_commit.Rd | 27 man/missing_data_report.Rd | 5 man/model_json.Rd | 5 man/model_report_template.Rd | 5 man/ngram_frequency.Rd | 16 man/posthoc_report.Rd | 6 man/read_responses.Rd | 39 man/read_sframe.Rd | 13 man/reliability_report.Rd | 2 man/render_report.Rd | 9 man/run_analysis_plan.Rd | 13 man/sample_size_plan.Rd | 57 + man/sem_lavaan_syntax.Rd | 13 man/seminr_syntax.Rd | 11 man/sensitivity_analysis.Rd | 9 man/sf_accessors.Rd | 104 -- man/sf_apa.Rd |only man/sf_branches.Rd |only man/sf_checks.Rd |only man/sf_choice_sets.Rd |only man/sf_component_list.Rd | 14 man/sf_construct.Rd | 6 man/sf_covariance.Rd | 5 man/sf_flagged.Rd |only man/sf_id.Rd |only man/sf_identity.Rd | 49 - man/sf_indirect.Rd | 4 man/sf_instrument.Rd | 4 man/sf_is_valid.Rd |only man/sf_item.Rd | 7 man/sf_items.Rd |only man/sf_label.Rd |only man/sf_meta.Rd |only man/sf_missing_columns.Rd |only man/sf_model.Rd | 14 man/sf_models.Rd |only man/sf_object.Rd |only man/sf_path.Rd | 5 man/sf_plan-set.Rd | 3 man/sf_plan.Rd |only man/sf_problems.Rd |only man/sf_report_accessors.Rd | 60 - man/sf_scale.Rd | 30 man/sf_scales.Rd |only man/sf_validation_accessors.Rd | 24 man/sframe_analysis_qmd.Rd | 5 man/sframe_as_data_frame.Rd | 103 +- man/sframe_builder_empty_state.Rd | 5 man/sframe_builder_state_from_instrument.Rd | 6 man/sframe_builder_validate_draft.Rd | 24 man/sframe_codebook_items_display.Rd | 5 man/sframe_dematel_compute.Rd | 9 man/sframe_demo.Rd | 5 man/sframe_demo_data.Rd | 5 man/sframe_demo_qmd.Rd | 7 man/sframe_draw_likert_diverging.Rd | 5 man/sframe_draw_mosaic.Rd | 18 man/sframe_input_types_demo_data.Rd | 5 man/sframe_likert_scale_groups.Rd | 5 man/sframe_plot_cooccurrence.Rd | 9 man/sframe_plot_cooccurrence_network.Rd | 10 man/sframe_plot_correlation_matrix.Rd | 9 man/sframe_plot_decision_ranking.Rd | 9 man/sframe_plot_dematel_influence.Rd | 9 man/sframe_plot_descriptives.Rd | 9 man/sframe_plot_efa_loadings.Rd | 11 man/sframe_plot_efa_scree.Rd | 10 man/sframe_plot_group_comparison.Rd | 9 man/sframe_plot_item_chart.Rd | 17 man/sframe_plot_likert_matrix.Rd | 10 man/sframe_plot_likert_scale.Rd | 10 man/sframe_plot_missingness.Rd | 9 man/sframe_plot_ngram_frequency.Rd | 9 man/sframe_plot_paired_comparison.Rd | 9 man/sframe_plot_quality.Rd | 9 man/sframe_plot_regression_diagnostics.Rd | 10 man/sframe_plot_reliability.Rd | 10 man/sframe_plot_scale_chart.Rd | 9 man/sframe_plot_sentiment.Rd | 10 man/sframe_plot_term_frequency.Rd | 9 man/sframe_plot_topics.Rd | 11 man/sframe_plot_validity.Rd | 12 man/sframe_plot_variable_distribution.Rd | 9 man/sframe_plots.Rd |only man/sframe_rated_matrix.Rd | 16 man/sframe_reports.Rd |only man/sframe_result_supplement.Rd |only man/sframe_subset.Rd | 18 man/sframe_validation.Rd | 22 man/survey_module_server.Rd | 60 + man/survey_module_ui.Rd | 29 man/surveyframe-package.Rd | 46 - man/term_context.Rd | 5 man/term_frequency.Rd | 5 man/validate_model.Rd | 13 man/validate_sframe.Rd | 6 man/validity_report.Rd | 8 man/write_sframe.Rd | 33 tests/testthat/helper-apps-script.R |only tests/testthat/helper-source-tree.R |only tests/testthat/helper-v8-dom.R |only tests/testthat/setup-chrome-timeouts.R |only tests/testthat/test-accessors.R | 2 tests/testthat/test-amendment-write-boundary.R |only tests/testthat/test-analysis-syntax.R |only tests/testthat/test-apa-format.R |only tests/testthat/test-bootstrap-effects.R |only tests/testthat/test-branching-contract.R |only tests/testthat/test-branching-in-values.R | 16 tests/testthat/test-builder-autosave.R |only tests/testthat/test-builder-keyboard.R |only tests/testthat/test-builder-template-sync.R |only tests/testthat/test-chrome-detritus.R | 7 tests/testthat/test-citation.R |only tests/testthat/test-cochran-q.R |only tests/testthat/test-collector-formula-injection.R |only tests/testthat/test-collector-header-drift.R | 23 tests/testthat/test-collector-header-safety.R |only tests/testthat/test-collector-respondent-contract.R |only tests/testthat/test-core.R | 18 tests/testthat/test-decision-alignment.R |only tests/testthat/test-decision-data.R | 4 tests/testthat/test-decision-methods-math.R |only tests/testthat/test-decision-sensitivity-conjoint.R |only tests/testthat/test-demo-library.R | 29 tests/testthat/test-demo-results-parity.R |only tests/testthat/test-doc-contracts-2.R |only tests/testthat/test-doc-contracts-3.R |only tests/testthat/test-doc-contracts.R |only tests/testthat/test-figure-test-agreement.R |only tests/testthat/test-id-collision.R |only tests/testthat/test-instrument-core-contract-2.R |only tests/testthat/test-instrument-core-contract.R |only tests/testthat/test-item-report-scoring.R |only tests/testthat/test-known-vars-expansion.R | 6 tests/testthat/test-labelled-export-notebook.R |only tests/testthat/test-likert-geometry.R |only tests/testthat/test-mediation-moderation-output.R |only tests/testthat/test-model-syntax-structure.R |only tests/testthat/test-model-type-guards.R | 1 tests/testthat/test-pdf-attribution.R |only tests/testthat/test-plan-dispatch.R |only tests/testthat/test-preview-isolation.R |only tests/testthat/test-quality-coverage.R |only tests/testthat/test-quarto-params.R |only tests/testthat/test-read-responses-boundary.R |only tests/testthat/test-read-responses-name-repair.R | 6 tests/testthat/test-repeated-anova-strata.R | 45 - tests/testthat/test-report-distribution-coverage.R |only tests/testthat/test-report-multiselect.R |only tests/testthat/test-report-reproducibility.R | 10 tests/testthat/test-report-scoring-parity.R |only tests/testthat/test-response-append-schema.R |only tests/testthat/test-response-identifier.R |only tests/testthat/test-reverse-scope.R |only tests/testthat/test-review-pass-blockers.R |only tests/testthat/test-rstudio-addins.R | 194 ++++ tests/testthat/test-scale-parameters.R |only tests/testthat/test-schema-conformance.R |only tests/testthat/test-serialisation-fixed-point.R | 2 tests/testthat/test-sframe-schema.R | 6 tests/testthat/test-sheets-sharing-guidance.R |only tests/testthat/test-shiny-export-shape.R | 16 tests/testthat/test-shiny-respondent-browser.R |only tests/testthat/test-shiny-respondent-render.R |only tests/testthat/test-startup-message.R |only tests/testthat/test-static-template-a11y.R |only tests/testthat/test-static-template-delivery.R |only tests/testthat/test-static-template-js.R |only tests/testthat/test-static-template-pairwise-sync.R |only tests/testthat/test-static-template-progress.R |only tests/testthat/test-statistics-runners.R |only tests/testthat/test-studio-roundtrip-content.R |only tests/testthat/test-submission-retry.R |only tests/testthat/test-survey-module-items.R |only tests/testthat/test-text-tokeniser.R |only tests/testthat/test-ui-entry-points.R |only tests/testthat/test-v03-analysis-models.R | 3 tests/testthat/test-v034-effect-cis.R | 13 tests/testthat/test-v034-family-plots.R | 62 + vignettes/analysing-survey-responses.Rmd | 10 vignettes/building-survey-instrument.Rmd | 15 vignettes/deploying-and-collecting.Rmd | 37 vignettes/learn-by-example.Rmd | 70 + vignettes/mcdm-analysis.Rmd | 68 + vignettes/scale-reliability-validity.Rmd | 45 - vignettes/small-sample.Rmd | 36 vignettes/surveybuilder-gui-overview.Rmd | 45 - vignettes/surveyframe.Rmd | 141 +-- vignettes/text-analysis.Rmd | 47 - 330 files changed, 10834 insertions(+), 3309 deletions(-)
Title: R Interface to the 'OpenFHE' Fully Homomorphic Encryption
Library
Description: Provides an R interface to 'OpenFHE', the open-source C++
library for fully homomorphic encryption (Al Badawi and others, 2022)
<https://eprint.iacr.org/2022/915>, which allows computation directly
on encrypted data without access to the secret key. Supports the
Brakerski-Fan-Vercauteren (BFV, 2012) <https://eprint.iacr.org/2012/144>,
Brakerski-Gentry-Vaikuntanathan (BGV, 2014) <doi:10.1145/2633600>, and
Cheon-Kim-Kim-Song (CKKS, 2017) <https://eprint.iacr.org/2016/421>
schemes for arithmetic on encrypted numbers, together with the
Ducas-Micciancio (FHEW, 2015) <https://eprint.iacr.org/2014/816> and
Chillotti-Gama-Georgieva-Izabachene (TFHE, 2020)
<https://eprint.iacr.org/2018/421> schemes for evaluating arbitrary
functions on encrypted bits.
Author: Balasubramanian Narasimhan [aut, cre, cph] ,
New Jersey Institute of Technology [cph] ,
Duality Technologies, Inc. [ctb, cph] ,
Samuel Neves [ctb, cph] ,
Jean-Philippe Aumasson [ctb, cph] ,
Randolph Voorhies [ctb, cph] ,
Shane Grant [ctb, cph] ,
Juan [...truncated...]
Maintainer: Balasubramanian Narasimhan <naras@stanford.edu>
Diff between openfhe.R versions 1.5.1.1 dated 2026-08-23 and 1.5.1.2 dated 2026-09-25
DESCRIPTION | 10 MD5 | 128 ++--- NAMESPACE | 10 NEWS.md | 30 + R/binfhe.R | 19 R/cpp11.R | 6 R/methods-encrypt.R | 28 + R/openfhe-object.R | 27 + R/openfhe-package.R | 6 R/utils.R | 39 - R/zzz.R | 15 configure | 14 configure.win | 14 inst/doc/binfhe-boolean-circuits.R | 2 inst/doc/binfhe-boolean-circuits.Rmd | 2 inst/doc/binfhe-boolean-circuits.html | 4 inst/doc/ckks-bootstrapping.R | 2 inst/doc/ckks-bootstrapping.Rmd | 2 inst/doc/ckks-bootstrapping.html | 4 inst/doc/introduction.R | 2 inst/doc/introduction.Rmd | 2 inst/doc/introduction.html | 8 inst/openfhe/CMakeLists.txt | 14 inst/openfhe/src/core/include/lattice/dgsampling-impl.h | 4 inst/openfhe/src/core/include/math/matrix-impl.h | 12 inst/openfhe/src/core/include/math/matrix.h | 9 inst/openfhe/src/core/include/math/matrixstrassen-impl.h | 29 - inst/openfhe/src/core/include/math/matrixstrassen.h | 6 inst/openfhe/src/core/include/utils/parallel.h | 82 +-- inst/openfhe/src/core/lib/utils/get-call-stack.cpp | 10 inst/openfhe/src/pke/lib/scheme/ckksrns/ckksrns-schemeswitching.cpp | 3 inst/openfhe/src/pke/lib/schemebase/base-leveledshe.cpp | 2 inst/tinytest/test_decrypt_key_first.R |only inst/tinytest/test_pointer_tags.R |only man/BinFHEContext.Rd |only man/bin_fhe_context.Rd | 2 man/decrypt.Rd | 18 man/get_num_threads.Rd | 8 man/set_num_threads.Rd | 28 - src/binfhe_bindings.cpp | 72 +- src/cpp11.cpp | 13 src/init.cpp | 48 + src/openfhe_cpp11.h | 147 +++++- src/openfhe_helpers.h | 7 src/pke_bindings.cpp | 244 +++++----- src/pke_ccparams_getters.cpp | 198 ++++---- src/pke_ccparams_setters.cpp | 96 +-- src/pke_ciphertext_accessors.cpp | 28 - src/pke_ckks_complex.cpp | 22 src/pke_ckks_eval_poly.cpp | 16 src/pke_ckks_fast_rotation.cpp | 16 src/pke_ckks_interactive_boot.cpp | 60 +- src/pke_closers.cpp | 20 src/pke_cryptocontext_getters.cpp | 44 - src/pke_eval.cpp | 82 +-- src/pke_key_management_getters.cpp | 6 src/pke_key_management_insert.cpp | 4 src/pke_multi_eval_keys.cpp | 48 - src/pke_multiparty.cpp | 64 +- src/pke_plaintext_accessors.cpp | 52 +- src/pke_secret_sharing.cpp | 28 - src/pke_serialization.cpp | 16 src/xptr.cpp |only tests/tinytest.R | 10 vignettes/binfhe-boolean-circuits.Rmd | 2 vignettes/ckks-bootstrapping.Rmd | 2 vignettes/introduction.Rmd | 2 67 files changed, 1134 insertions(+), 814 deletions(-)
Title: An Implementation of Matrix Mathematics that Respects Row and
Column Names
Description: An implementation of matrix mathematics wherein operations are performed "by name."
Author: Matthew Heun [aut, cre]
Maintainer: Matthew Heun <matthew.heun@me.com>
Diff between matsbyname versions 0.6.14 dated 2026-01-30 and 0.6.15 dated 2026-09-25
DESCRIPTION | 10 MD5 | 32 - NAMESPACE | 7 NEWS.md | 18 R/efficient_vecs.R | 249 +++++++++ README.md | 3 build/vignette.rds |binary inst/CITATION | 4 inst/doc/aggregation-vignette.html | 4 inst/doc/applybyname-vignette.html | 4 inst/doc/matsbyname.html | 4 man/data.Rd | 2 man/mat_from_store_byname.Rd |only man/matsbyname-package.Rd | 5 man/rename_via_pattern_byname.Rd | 4 man/vec_from_store_byname.Rd | 2 tests/testthat/test-efficient_vecs.R | 946 ++++++++++++++++++++--------------- tests/testthat/test-profiles.R |only 18 files changed, 871 insertions(+), 423 deletions(-)
Title: Graphs and Covariance for Landscape Genetics
Description: Shared, dependency-light primitives for landscape-genetic network
methods: a lightweight deme/landscape graph (vertex coordinates and an undirected
edge list) with constructors from coordinates; genetic covariance and distance
from biallelic or multiallelic data (the Yang-style normalized-dosage covariance
and the Dyer-style multivariate covariance); and antisymmetric per-edge
directional covariate builders (the gradient of a scalar potential, and the
projection of a vector flow field). Used by 'terradish' (symmetric resistance).
No compiled code.
Author: Bill Peterman [aut, cre, cph],
Nathaniel S. Pope [aut, cph]
Maintainer: Bill Peterman <peterman.73@osu.edu>
Diff between landgraph versions 0.0.1 dated 2026-07-06 and 0.0.3 dated 2026-09-25
DESCRIPTION | 12 MD5 | 36 - NEWS.md | 45 + R/deme_graph.R | 184 +++---- R/edge_covariates.R | 10 R/genetic_covariance.R | 51 +- R/landgraph-package.R | 2 inst/WORDLIST |only inst/doc/getting-started.R | 41 + inst/doc/getting-started.Rmd | 18 inst/doc/getting-started.html | 200 +++----- man/cov_from_biallelic.Rd | 205 ++++---- man/cov_from_genetic_data.Rd | 364 ++++++++------- man/deme_graph.Rd | 6 man/edge_flow.Rd | 10 man/fst_from_biallelic.Rd | 109 ++-- man/landgraph-package.Rd | 2 tests/testthat/test-covariance-metadata.R |only tests/testthat/test-genetic-covariance.R | 691 +++++++++++++++--------------- vignettes/getting-started.Rmd | 18 20 files changed, 1027 insertions(+), 977 deletions(-)
Title: Differential Evolution Optimization in Pure R
Description: Differential Evolution (DE) stochastic heuristic algorithms for
global optimization of problems with and without general constraints.
The aim is to curate a collection of its variants that
(1) do not sacrifice simplicity of design,
(2) are essentially tuning-free, and
(3) can be efficiently implemented directly in the R language.
Currently, it provides implementations of the algorithms 'jDE' by
Brest et al. (2006) <doi:10.1109/TEVC.2006.872133> for single-objective
optimization and 'NCDE' by Qu et al. (2012) <doi:10.1109/TEVC.2011.2161873>
for multimodal optimization (single-objective problems with
multiple solutions).
Author: Eduardo L. T. Conceicao [aut, cre],
Martin Maechler [ctb]
Maintainer: Eduardo L. T. Conceicao <mail@eduardoconceicao.org>
Diff between DEoptimR versions 1.2-1 dated 2026-08-20 and 1.2-2 dated 2026-09-25
DESCRIPTION | 12 +++++----- MD5 | 10 ++++---- R/JDEoptim.R | 44 ++++++++++++++++++++----------------- R/NCDEoptim.R | 54 ++++++++++++++++++++++++--------------------- R/SPJDEoptim.R | 66 +++++++++++++++++++++++++++++++------------------------- man/JDEoptim.Rd | 6 ++--- 6 files changed, 104 insertions(+), 88 deletions(-)
Title: Cognitive Models for Subjective Scales and Decision Making Tasks
Description: Implements cognitive models for data from subjective (Likert or
analog) scales and from decision making tasks with reaction times and
choice data. Provides random generation, density functions, and custom
response distributions for Bayesian estimation with 'brms', covering
discrete beta, ordered beta and choice-confidence models for subjective
ratings; reaction time distributions such as the ex-Gaussian and the
shifted log-normal, Wald, gamma and Weibull; and sequential sampling
models of choice and reaction time, including the drift diffusion model
(DDM), the racing diffusion model (RDM), the lognormal race model (LNR)
and the linear ballistic accumulator (LBA). The website provides
examples and tutorials for using and interpreting the models.
Methods are described in Ratcliff and McKoon (2008) <doi:10.1162/neco.2008.12-06-420>,
Brown and Heathcote (2008) <doi:10.1016/j.cogpsych.2007.12.002>, Rouder et al. (2015)
<doi:10.1007/s11336-013-9396-3>, Tillman et al. (2020) [...truncated...]
Author: Dominique Makowski [aut, cre]
Maintainer: Dominique Makowski <D.Makowski@sussex.ac.uk>
Diff between cogmod versions 0.3.0 dated 2026-09-12 and 0.3.3 dated 2026-09-25
DESCRIPTION | 20 LICENSE | 4 MD5 | 172 - NAMESPACE | 14 NEWS.md | 1902 ++++-------- R/cogmod_checkdata.R |only R/cogmod_inits.R | 1430 +++++---- R/cogmod_priors.R | 1681 ++++++---- R/cogmod_stanvars.R | 199 - R/cogmod_warmstart.R |only R/core_choice.R | 1672 +++++----- R/core_shifted.R | 4988 +++++++++++++++++++------------- R/draft.R |only R/internals.R | 570 +-- R/model_betadiscrete.R | 1126 +++---- R/model_betagate.R | 1010 +++--- R/model_bisa.R | 468 +-- R/model_conf_sdt.R | 862 ++--- R/model_ddm.R | 2793 ++++++++++------- R/model_exgaussian.R | 848 +++-- R/model_exwald.R | 380 +- R/model_gamma.R | 350 +- R/model_geg.R | 970 +++--- R/model_invgamma.R | 284 - R/model_invgaussian.R | 687 ++-- R/model_invweibull.R | 284 - R/model_lba1.R | 490 +-- R/model_lba2.R | 940 +++--- R/model_lnr.R | 741 ++-- R/model_loggamma.R | 901 ++--- R/model_lognormal.R | 708 ++-- R/model_logstudent.R | 420 +- R/model_logweibull.R | 286 - R/model_rdm.R | 2907 +++++++++--------- R/model_weibull.R | 464 +- inst/doc/overview.Rmd | 152 inst/doc/overview.html | 4 man/badlm.Rd | 118 man/cogmod_inits.Rd | 308 + man/cogmod_priors.Rd | 798 +++-- man/cogmod_stanvars.Rd | 132 man/cogmod_warmstart.Rd |only man/p_outlier.Rd | 114 man/rcogmod_betadiscrete.Rd | 446 +- man/rcogmod_betagate.Rd | 324 +- man/rcogmod_bisa.Rd | 448 +- man/rcogmod_choco.Rd | 390 +- man/rcogmod_ddm.Rd | 855 ++--- man/rcogmod_exgaussian.Rd | 320 +- man/rcogmod_exwald.Rd | 372 +- man/rcogmod_gamma.Rd | 352 +- man/rcogmod_geg.Rd | 358 +- man/rcogmod_invgamma.Rd | 272 - man/rcogmod_invgaussian.Rd | 666 ++-- man/rcogmod_invweibull.Rd | 286 - man/rcogmod_lba1.Rd | 474 +-- man/rcogmod_lba2.Rd | 689 ++-- man/rcogmod_lnr.Rd | 634 ++-- man/rcogmod_loggamma.Rd | 581 +-- man/rcogmod_lognormal.Rd | 654 ++-- man/rcogmod_logstudent.Rd | 404 +- man/rcogmod_logweibull.Rd | 288 - man/rcogmod_rdm.Rd | 847 ++--- man/rcogmod_weibull.Rd | 454 +- man/with_outliers.Rd | 168 - tests/testthat.R | 8 tests/testthat/helper-grid.R | 90 tests/testthat/helper-slow.R | 68 tests/testthat/helper-stan.R | 241 - tests/testthat/test-censoring.R |only tests/testthat/test-cogmod_generics.R | 1765 +++++++---- tests/testthat/test-cogmod_warmstart.R |only tests/testthat/test-model_betagate.R | 718 ++-- tests/testthat/test-model_bisa.R | 446 +- tests/testthat/test-model_choco.R | 792 ++--- tests/testthat/test-model_conf_sdt.R | 452 +- tests/testthat/test-model_ddm.R | 1780 ++++++----- tests/testthat/test-model_exgaussian.R | 236 - tests/testthat/test-model_exwald.R | 470 +-- tests/testthat/test-model_geg.R | 432 +- tests/testthat/test-model_invgaussian.R | 1346 +++++--- tests/testthat/test-model_lba1.R | 852 ++--- tests/testthat/test-model_lba2.R | 1689 +++++----- tests/testthat/test-model_lnr.R | 1420 +++++---- tests/testthat/test-model_loggamma.R | 1196 +++---- tests/testthat/test-model_lognormal.R | 1410 +++++---- tests/testthat/test-model_logstudent.R | 502 +-- tests/testthat/test-model_ordbeta.R | 240 - tests/testthat/test-model_rdm.R | 2454 ++++++++------- vignettes/overview.Rmd | 152 90 files changed, 33201 insertions(+), 28037 deletions(-)
Title: Analysis of Basketball Data
Description: Collection of tools to work with European basketball data. Functions available are related to friendly
web scraping, data management and visualization. Data were obtained from <https://www.euroleaguebasketball.net/euroleague/>,
<https://www.euroleaguebasketball.net/eurocup/> and <https://acb.com/>, following the instructions
of their respectives robots.txt files, when available. Box score data are available for the three leagues.
Play-by-play and spatial shooting data are also available for the Spanish league. Methods for analysis include a
population pyramid, 2D plots, circular plots of players' percentiles, plots of players' monthly/yearly stats,
team heatmaps, team shooting plots, team four factors plots, cross-tables with the results of regular season games,
maps of nationalities, combinations of lineups, possessions-related variables, timeouts,
performance by periods, personal fouls, offensive rebounds and different types of shooting charts.
Please see Vinue (202 [...truncated...]
Author: Guillermo Vinue [aut, cre]
Maintainer: Guillermo Vinue <guillermo.vinue@uv.es>
Diff between BAwiR versions 1.5.4 dated 2026-09-07 and 1.5.5 dated 2026-09-25
DESCRIPTION | 13 ++++----- MD5 | 56 +++++++++++++++++++-------------------- NEWS | 4 ++ R/do_scrape_days_acb.R | 2 - R/scraping_games_acb_old.R | 4 +- R/scraping_rosters_acb.R | 4 +- inst/doc/BAwiR.html | 4 +- inst/doc/BAwiR_pbp.html | 4 +- inst/doc/BAwiR_sc.Rmd | 2 - inst/doc/BAwiR_sc.html | 6 ++-- man/acb_age_profile_data_2526.Rd | 2 - man/acb_combs.Rd | 2 - man/acb_games_1718.Rd | 2 - man/acb_games_2223_coach.Rd | 2 - man/acb_games_2223_info.Rd | 2 - man/acb_players_1718.Rd | 2 - man/acb_players_2425.Rd | 2 - man/acb_shields.Rd | 2 - man/acb_shooting_data_2425.Rd | 2 - man/acb_sticker_data_2526.Rd | 2 - man/acb_usage_act_data_2526.Rd | 2 - man/acb_usage_data_2526.Rd | 2 - man/acb_vbc_cz_pbp_2223.Rd | 2 - man/acb_vbc_cz_sl_2223.Rd | 2 - man/do_scrape_days_acb.Rd | 2 - man/metrics_player_zone.Rd | 2 - man/scraping_games_acb_old.Rd | 4 +- man/scraping_rosters_acb.Rd | 4 +- vignettes/BAwiR_sc.Rmd | 2 - 29 files changed, 73 insertions(+), 68 deletions(-)
Title: Combines Changepoint Analysis with 'ggplot2'
Description: A unified, tidy, 'ggplot2'-native interface to changepoint
detection in R. Provides the 'ggcpt' S3 result class with
'broom'-style tidy/glance/augment methods, 'autoplot()' (with
confidence intervals, significance regions, detector statistics,
solution paths, scale space, and multivariate facets), composable
geoms ('geom_changepoint()', 'geom_cpt_segment()', 'geom_cpt_ci()',
'geom_cpt_region()', 'geom_cpt_label()', 'geom_cpt_event()',
'stat_changepoint()'), and a 'cpt_detect()' dispatcher covering
fifty methods with introspection via 'cpt_methods()':
penalised/optimal partitioning, multiscale and search methods,
nonparametric and kernel methods, Bayesian methods, high-dimensional,
functional, covariance and network methods, regression breaks,
seasonal-trend decomposition, the classical single-change tests, and
robust detection under drift and autocorrelation. Adds inference
(Narrowest Significance Pursuit regions, a unified 'cpt_confint()',
post-detection tests), selection of the numbe [...truncated...]
Author: Youzhi Yu [aut, cre]
Maintainer: Youzhi Yu <yuyouzhi666@icloud.com>
Diff between ggchangepoint versions 0.4.0 dated 2026-08-24 and 0.5.0 dated 2026-09-25
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Title: Cryptographic Hash Functions and Data Encoding
Description: Fast and memory-efficient streaming hash functions,
binary/text encoding and serialization. Hashes strings and raw vectors
directly. Stream hashes files which can be larger than memory, as
well as in-memory objects through R's serialization mechanism.
Implements the SHA-256, SHA-3 and 'Keccak' cryptographic hash
functions, SHAKE256 extendable-output function (XOF), 'SipHash'
pseudo-random function, base64 (including the URL-safe variant) and
base58 encoding, 'CBOR' and 'JSON' serialization.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd] ,
Hibiki AI Limited [cph],
The Mbed TLS Contributors [cph] ,
Red Hat, Inc. [cph] ,
Luke Dashjr [cph]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between secretbase versions 1.3.0 dated 2026-06-12 and 1.3.1 dated 2026-09-25
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ build/partial.rdb |binary src/base64.c | 2 +- src/sha3.c | 2 +- 6 files changed, 15 insertions(+), 11 deletions(-)
Title: Forest Plots and Subgroup Effects from Fitted Regression Models
Description: Draws forest plots of exposure effects from fitted regression
models. Name an exposure and 'foresty' plots its effect. Name an effect
modifier as well and it refits the model with the interaction term,
estimates the exposure effect within each level of the modifier as a
linear combination of the coefficients, and reports the joint interaction
test beside those estimates. It takes one exposure and one modifier at a
time, so the interaction is always a two-way one. Rows of the plot and of
the table beside it share one scale, in a layout that can follow a
journal's house style. The same results go to a self-contained HTML page
holding the subgroup estimates, the joint test and the coefficient table.
The 'car' package computes the linear combinations and their tests.
Models fitted by stats::glm(), stats::lm(), the 'survival' package, the
'lme4' package, the 'geepack' package and the 'survey' package are
supported, as is any fit supplying coef() and vcov(). Ordinal outcomes are supported th [...truncated...]
Author: Akihiro Shiroshita [aut, cre, cph],
Yuki Kataoka [aut]
Maintainer: Akihiro Shiroshita <akihirokun8@gmail.com>
Diff between foresty versions 0.1.0 dated 2026-09-12 and 0.2.0 dated 2026-09-25
DESCRIPTION | 15 MD5 | 64 NEWS.md | 10 R/app.R | 8187 ++++++++++++++++++------------------ R/colors.R | 348 - R/combine.R | 22 R/foresty_data.R | 1139 ++--- R/foresty_interaction.R | 98 R/foresty_main.R | 14 R/layout.R | 3 R/lincom.R | 544 +- R/methods.R | 1224 ++--- R/model_info.R | 2213 +++++---- R/plot.R | 6 R/report.R | 1007 ++-- README.md | 28 inst/CITATION | 48 inst/doc/forest.R | 9 inst/doc/forest.Rmd | 28 inst/doc/forest.html | 55 man/foresty-package.Rd | 64 man/foresty_data.Rd | 494 +- man/foresty_interaction.Rd | 12 man/foresty_layout.Rd | 5 man/foresty_main.Rd | 13 tests/testthat/helper-fits.R | 398 - tests/testthat/test-app.R | 40 tests/testthat/test-combine.R | 734 +-- tests/testthat/test-data.R | 539 +- tests/testthat/test-lincom.R | 516 +- tests/testthat/test-model-classes.R | 1868 ++++---- tests/testthat/test-robust.R | 328 - vignettes/forest.Rmd | 28 33 files changed, 10545 insertions(+), 9556 deletions(-)
Title: Logging for 'data.table' Operations
Description: Provides feedback about 'data.table' operations. 'dtlog' redefines
the subsetting method for data tables as well as several functions exported
by 'data.table' so that each operation prints a short message describing
what it did: how many rows were removed, which columns were added, updated
or dropped, how many groups an aggregation produced, and so on. The
operations themselves are left untouched, including modification by
reference. It also provides dttable(), which describes the variables a
single data table holds and passes every other call on to base::table()
unchanged. Inspired by the 'tidylog' package.
Author: Akihiro Shiroshita [aut, cre, cph]
Maintainer: Akihiro Shiroshita <akihirokun8@gmail.com>
Diff between dtlog versions 0.1.0 dated 2026-09-15 and 0.2.0 dated 2026-09-25
DESCRIPTION | 8 MD5 | 43 + NAMESPACE | 16 NEWS.md | 106 +++- R/group.R |only R/merge.R | 53 ++ R/rows.R | 51 ++ R/set_functions.R | 94 ++++ R/wrap.R | 55 ++ README.md | 725 +++++++++++++++++---------------- inst/CITATION |only inst/WORDLIST | 2 inst/doc/dtlog.html | 12 man/copy.Rd |only man/foverlaps.Rd |only man/grouping_sets.Rd |only man/rows.Rd | 3 man/set_functions.Rd | 6 man/split.data.table.Rd |only tests/testthat/helper-dtlog.R | 255 ++++++----- tests/testthat/test-dots.R |only tests/testthat/test-functions-parity.R | 21 tests/testthat/test-log-fallbacks.R |only tests/testthat/test-messages.R | 129 +++++ tests/testthat/test-no-side-effects.R | 4 tests/testthat/test-reshape.R |only tests/testthat/test-utils.R | 128 ++++- 27 files changed, 1162 insertions(+), 549 deletions(-)
Title: Fast Access to Brazilian Public Health Data from 'DATASUS'
Description: Provides fast, in-memory reading of 'DATASUS' 'DBC' files using
native 'C' code, along with a catalog of public health data sources,
'FTP' file discovery, caching downloads, and a high-level datasus_fetch()
function that lists, downloads, and reads files in a single call. Bundles
the 'blast' decompressor from 'zlib' contrib/blast to decode 'PKWare DCL'
compressed 'DBC' files and parses 'DBF' records directly for efficient
import into tibbles. See the 'DATASUS' file transfer site
<https://datasus.saude.gov.br> and Adler (2003)
<https://github.com/madler/zlib/tree/master/contrib/blast> for details on
the underlying data and compression format.
Author: Andre Leite [aut, cre] ,
Marcos Wasiliew [aut] ,
Hugo Vasconcelos [aut] ,
Carlos Amorim [aut] ,
Diogo Bezerra [aut] ,
Mark Adler [ctb, cph]
Maintainer: Andre Leite <leite@castlab.org>
Diff between datasusr versions 0.1.0 dated 2026-05-04 and 0.1.1 dated 2026-09-25
DESCRIPTION | 35 +-- MD5 | 39 +-- NEWS.md | 100 ++++++++ R/datasus_catalog.R | 434 +++++++++++++++++++++++++++++++------- R/read_datasus_dbc.R | 54 ++++ R/utils.R | 4 build/vignette.rds |binary inst/doc/cache-and-downloads.R | 2 inst/doc/cache-and-downloads.Rmd | 32 ++ inst/doc/cache-and-downloads.html | 62 ++++- man/datasus_download.Rd | 41 ++- man/datasus_fetch.Rd | 32 ++ man/datasus_list_files.Rd | 13 - man/datasusr-package.Rd | 13 - man/figures/datasusr_rpkg.svg |only man/read_datasus_dbc.Rd | 16 - src/dbc_reader.c | 285 ++++++++++++++++-------- src/dbf_parser.c | 246 +++++++++++---------- tests |only vignettes/cache-and-downloads.Rmd | 32 ++ 20 files changed, 1078 insertions(+), 362 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 0.2.0 dated 2026-08-04 and 0.2.1 dated 2026-09-25
DESCRIPTION | 11 MD5 | 23 NEWS.md | 148 +++++ R/save.R | 1150 +++++++++++++++++++++++++++++++++------ R/zzz.R |only build/vignette.rds |binary inst/doc/models-directory.R |only inst/doc/models-directory.Rmd |only inst/doc/models-directory.html |only man/colon-equals.Rd | 15 man/loadFit.Rd | 6 man/saveFit.Rd | 6 tests/testthat/helper-fitfiles.R |only tests/testthat/test-datatable.R |only tests/testthat/test-save.R | 950 ++++++++++++++++++++++++++++++++ vignettes/models-directory.Rmd |only 16 files changed, 2127 insertions(+), 182 deletions(-)
Title: Fast and Functional Data Structures
Description: Provides fast, side-effect free data structures, including
catenable named lists, priority queues, double-ended queues, ordered
sequences, and interval indices. Implementation is based on the
finger-tree data structure of Hinze and Paterson (2006)
<doi:10.1017/S0956796805005769>.
Author: Shawn T. O'Neil [aut, cre]
Maintainer: Shawn T. O'Neil <shawn@tislab.org>
Diff between Immutables versions 1.1.0 dated 2026-08-21 and 1.2.0 dated 2026-09-25
Immutables-1.1.0/Immutables/inst/extdata/benchmarks.rds |only Immutables-1.1.0/Immutables/man/peek_all_overlaps.Rd |only Immutables-1.1.0/Immutables/man/peek_overlaps.Rd |only Immutables-1.1.0/Immutables/man/pop_all_overlaps.Rd |only Immutables-1.1.0/Immutables/man/pop_overlaps.Rd |only Immutables-1.1.0/Immutables/vignettes/inst |only Immutables-1.2.0/Immutables/DESCRIPTION | 6 Immutables-1.2.0/Immutables/MD5 | 184 ++--- Immutables-1.2.0/Immutables/NAMESPACE | 6 Immutables-1.2.0/Immutables/NEWS.md | 44 + Immutables-1.2.0/Immutables/R/00-core-ref-add-left.R | 20 Immutables-1.2.0/Immutables/R/00-core-ref-add-right.R | 13 Immutables-1.2.0/Immutables/R/00-core-ref-concat.R | 2 Immutables-1.2.0/Immutables/R/00-core-ref-helpers.R | 74 ++ Immutables-1.2.0/Immutables/R/00-core-ref-locate-impl.R | 6 Immutables-1.2.0/Immutables/R/00-core-ref-measured.R | 14 Immutables-1.2.0/Immutables/R/00-core-ref-split-tree-impl.R | 8 Immutables-1.2.0/Immutables/R/00-core-ref-view.R | 97 +- Immutables-1.2.0/Immutables/R/20-api-generics.R | 2 Immutables-1.2.0/Immutables/R/20-backend-cpp.R | 20 Immutables-1.2.0/Immutables/R/30-api-flexseq-core.R | 2 Immutables-1.2.0/Immutables/R/30-api-flexseq-ends.R | 40 - Immutables-1.2.0/Immutables/R/30-api-flexseq-indexing.R | 6 Immutables-1.2.0/Immutables/R/30-api-flexseq-iter.R | 2 Immutables-1.2.0/Immutables/R/30-api-flexseq-print.R | 4 Immutables-1.2.0/Immutables/R/30-api-flexseq-validate.R | 4 Immutables-1.2.0/Immutables/R/50-ordered_sequence-ops.R | 147 ++++ Immutables-1.2.0/Immutables/R/60-interval_index-internals.R | 2 Immutables-1.2.0/Immutables/R/60-interval_index-query-api.R | 24 Immutables-1.2.0/Immutables/R/60-interval_index-query-engine.R | 2 Immutables-1.2.0/Immutables/R/60-interval_index-query-specs.R | 2 Immutables-1.2.0/Immutables/R/70-plotting.R | 5 Immutables-1.2.0/Immutables/R/99-deprecated.R |only Immutables-1.2.0/Immutables/README.md | 4 Immutables-1.2.0/Immutables/build/vignette.rds |binary Immutables-1.2.0/Immutables/inst/doc/benchmarks.R | 55 - Immutables-1.2.0/Immutables/inst/doc/benchmarks.Rmd | 63 - Immutables-1.2.0/Immutables/inst/doc/benchmarks.html | 45 - Immutables-1.2.0/Immutables/inst/doc/developer-api.Rmd | 4 Immutables-1.2.0/Immutables/inst/doc/developer-api.html | 5 Immutables-1.2.0/Immutables/inst/doc/flexseq.R | 39 + Immutables-1.2.0/Immutables/inst/doc/flexseq.Rmd | 52 + Immutables-1.2.0/Immutables/inst/doc/flexseq.html | 65 + Immutables-1.2.0/Immutables/inst/doc/index.R | 2 Immutables-1.2.0/Immutables/inst/doc/index.Rmd | 6 Immutables-1.2.0/Immutables/inst/doc/index.html | 7 Immutables-1.2.0/Immutables/inst/doc/interval-indices.R | 61 + Immutables-1.2.0/Immutables/inst/doc/interval-indices.Rmd | 77 ++ Immutables-1.2.0/Immutables/inst/doc/interval-indices.html | 94 ++ Immutables-1.2.0/Immutables/inst/doc/ordered-sequences.R | 70 + Immutables-1.2.0/Immutables/inst/doc/ordered-sequences.Rmd | 90 ++ Immutables-1.2.0/Immutables/inst/doc/ordered-sequences.html | 310 ++++++-- Immutables-1.2.0/Immutables/inst/doc/priority-queues.R | 59 + Immutables-1.2.0/Immutables/inst/doc/priority-queues.Rmd | 76 ++ Immutables-1.2.0/Immutables/inst/doc/priority-queues.html | 96 ++ Immutables-1.2.0/Immutables/inst/extdata/benchmarks-ivx.rds |binary Immutables-1.2.0/Immutables/inst/extdata/benchmarks-ordered.rds |binary Immutables-1.2.0/Immutables/inst/extdata/benchmarks-pq.rds |binary Immutables-1.2.0/Immutables/inst/extdata/benchmarks-sequence.rds |binary Immutables-1.2.0/Immutables/man/Immutables-deprecated.Rd |only Immutables-1.2.0/Immutables/man/fapply.Rd | 2 Immutables-1.2.0/Immutables/man/get_graph_df.Rd | 4 Immutables-1.2.0/Immutables/man/key_at.Rd |only Immutables-1.2.0/Immutables/man/loop.Rd | 2 Immutables-1.2.0/Immutables/man/max_key.Rd | 5 Immutables-1.2.0/Immutables/man/min_key.Rd | 5 Immutables-1.2.0/Immutables/man/nearest_key.Rd |only Immutables-1.2.0/Immutables/man/peek_all_overlapping.Rd |only Immutables-1.2.0/Immutables/man/peek_overlapping.Rd |only Immutables-1.2.0/Immutables/man/pop_all_overlapping.Rd |only Immutables-1.2.0/Immutables/man/pop_at.Rd | 3 Immutables-1.2.0/Immutables/man/pop_back.Rd | 3 Immutables-1.2.0/Immutables/man/pop_front.Rd | 3 Immutables-1.2.0/Immutables/man/pop_overlapping.Rd |only Immutables-1.2.0/Immutables/man/print.FingerTree.Rd | 4 Immutables-1.2.0/Immutables/man/print.flexseq.Rd | 4 Immutables-1.2.0/Immutables/man/validate_name_state.Rd | 2 Immutables-1.2.0/Immutables/man/validate_tree.Rd | 2 Immutables-1.2.0/Immutables/src/ft_cpp.cpp | 353 ++++++++-- Immutables-1.2.0/Immutables/src/init.c | 6 Immutables-1.2.0/Immutables/tests/testthat/test-cpp-gc-safety.R | 16 Immutables-1.2.0/Immutables/tests/testthat/test-cpp-parity.R | 88 ++ Immutables-1.2.0/Immutables/tests/testthat/test-interval-index-as-list.R | 8 Immutables-1.2.0/Immutables/tests/testthat/test-interval-index-deprecated.R |only Immutables-1.2.0/Immutables/tests/testthat/test-interval-index-end-measure-fastpath.R | 10 Immutables-1.2.0/Immutables/tests/testthat/test-interval-index-native-peek.R | 8 Immutables-1.2.0/Immutables/tests/testthat/test-interval-index-native-pop.R | 56 - Immutables-1.2.0/Immutables/tests/testthat/test-interval-index-nonnumeric-native.R | 4 Immutables-1.2.0/Immutables/tests/testthat/test-interval-index.R | 26 Immutables-1.2.0/Immutables/tests/testthat/test-invariants.R | 4 Immutables-1.2.0/Immutables/tests/testthat/test-lazy-middle.R |only Immutables-1.2.0/Immutables/tests/testthat/test-ordered-sequence.R | 125 +++ Immutables-1.2.0/Immutables/tests/testthat/test-tree-from-ordered-bulk.R | 27 Immutables-1.2.0/Immutables/vignettes/benchmarks.Rmd | 63 - Immutables-1.2.0/Immutables/vignettes/developer-api.Rmd | 4 Immutables-1.2.0/Immutables/vignettes/flexseq.Rmd | 52 + Immutables-1.2.0/Immutables/vignettes/index.Rmd | 6 Immutables-1.2.0/Immutables/vignettes/interval-indices.Rmd | 77 ++ Immutables-1.2.0/Immutables/vignettes/ordered-sequences.Rmd | 90 ++ Immutables-1.2.0/Immutables/vignettes/priority-queues.Rmd | 76 ++ 100 files changed, 2592 insertions(+), 562 deletions(-)
Title: Recovering Structure of Long Molecules from Structural Variation
Data
Description: Implements a method to combine multiple levels of multiple
sequence alignment to uncover the structure of complex DNA rearrangements.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between SVAlignR versions 0.9.2 dated 2025-09-24 and 0.10.5 dated 2026-09-25
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++++------- NAMESPACE | 9 ++++++--- R/03-svalign.R | 4 ++-- R/08-evidence.R |only build/vignette.rds |binary data/GUMC395-bp.rda |only data/GUMC395-lr.rda |only data/breakpoints.rda |binary data/longreads.rda |binary man/03-align.Rd | 6 ++++-- man/09-evidence.Rd |only 12 files changed, 28 insertions(+), 19 deletions(-)
Title: Sparse Projected Averaged Regression
Description: A flexible framework combining variable screening and random projection techniques for fitting ensembles of
predictive generalized linear models to high-dimensional data. Designed for extensibility, the package implements
key techniques as S3 classes with user-friendly constructors, enabling easy integration and development of new procedures for
high-dimensional applications.
Author: Laura Vana-Guer [aut, cre] ,
Roman Parzer [aut] ,
Peter Filzmoser [aut]
Maintainer: Laura Vana-Guer <laura.vana.guer@tuwien.ac.at>
Diff between spareg versions 1.1.1 dated 2025-08-19 and 1.2.0 dated 2026-09-25
DESCRIPTION | 21 MD5 | 119 + NAMESPACE | 54 NEWS.md | 18 R/getmethods.R |only R/rp_classes.R | 347 +++-- R/screening_classes.R | 329 +++-- R/simulate.R | 13 R/spareg.R | 856 ++++++------- R/sparegcv.R | 914 ++++++++------ R/sparmodel_classes.R | 237 ++- R/utilities.R | 12 build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 33 inst/doc/spareg.R | 535 ++------ inst/doc/spareg.Rnw | 2266 +++++++++++++++++------------------- inst/doc/spareg.pdf |binary man/coef.spar.Rd | 28 man/coef.spar.cv.Rd | 40 man/constructor_randomprojection.Rd | 89 - man/constructor_screencoef.Rd | 45 man/constructor_sparmodel.Rd | 44 man/generate_cw.Rd | 12 man/generate_gaussian.Rd | 14 man/generate_scrcoef_cor.Rd | 6 man/generate_scrcoef_glmnet.Rd | 6 man/generate_scrcoef_marglik.Rd | 6 man/generate_sparse.Rd | 14 man/get_coef.Rd | 2 man/get_intercept.Rd | 2 man/get_measure.Rd | 2 man/get_model.Rd | 33 man/get_model.spar.Rd |only man/get_model.spar.cv.Rd |only man/plot.spar.Rd | 52 man/plot.spar.cv.Rd | 25 man/predict.spar.Rd | 2 man/predict.spar.cv.Rd | 13 man/print.coefspar.Rd | 11 man/print.randomprojection.Rd | 14 man/print.spar.Rd | 15 man/print.spar.cv.Rd | 6 man/randomprojection-class.Rd |only man/rp_cw.Rd | 13 man/rp_gaussian.Rd | 4 man/rp_sparse.Rd | 2 man/screen_cor.Rd | 22 man/screen_glmnet.Rd | 22 man/screen_marglik.Rd | 24 man/screencoef-class.Rd |only man/simulate_spareg_data.Rd | 12 man/spar.Rd | 165 +- man/spar.cv.Rd | 52 man/spar_glm.Rd | 23 man/spar_glmnet.Rd | 28 man/sparmodel-class.Rd |only man/summary.coefspar.Rd | 9 man/update_rp_default.Rd |only man/update_rpm_identity.Rd |only man/update_screen_glmnet.Rd |only tests/testthat/test-spareg.R | 51 tests/testthat/test-sparegcv.R | 187 ++ vignettes/spareg.Rnw | 2266 +++++++++++++++++------------------- vignettes/spareg.bib | 24 65 files changed, 4767 insertions(+), 4372 deletions(-)
Title: Affine Invariant Tests of Multivariate Normality
Description: Various affine invariant multivariate normality tests are provided. It is designed to accompany the survey article Ebner, B. and Henze, N. (2020) <doi:10.1007/s11749-020-00740-0> titled "Tests for multivariate normality -- a critical review with emphasis on weighted L^2-statistics". We implement new and time honoured L^2-type tests of multivariate normality, such as the Baringhaus-Henze-Epps-Pulley (BHEP) test, the Henze-Zirkler test, the test of Henze-Jiménes-Gamero, the test of Henze-Jiménes-Gamero-Meintanis, the test of Henze-Visage, the Dörr-Ebner-Henze test based on harmonic oscillator and the Dörr-Ebner-Henze test based on a double estimation in a PDE. Secondly, we include the measures of multivariate skewness and kurtosis by Mardia, Koziol, Malkovich and Afifi and Móri, Rohatgi and Székely, as well as the associated tests. Thirdly, we include the tests of multivariate normality by Cox and Small, the 'energy' test of Székely and Rizzo, the tests based on spherical harmonics [...truncated...]
Author: Lucas Butsch [aut],
Bruno Ebner [aut, cre],
Jaco Visagie [ctb],
Johann Siemens [ctb]
Maintainer: Bruno Ebner <bruno.ebner@kit.edu>
Diff between mnt versions 1.3 dated 2020-07-31 and 1.4 dated 2026-09-25
DESCRIPTION | 12 - MD5 | 97 +++++----- NAMESPACE | 2 NEWS.md |only R/mnt-package.R | 28 ++ R/multNormTest.R | 492 +++++++++++++++++++++++++++++++++++++++++++++++----- R/teststatistics.R | 24 +- build |only man/BHEP.Rd | 66 +++--- man/CS.Rd | 68 +++---- man/DEHT.Rd | 62 +++--- man/DEHU.Rd | 54 ++--- man/EHS.Rd | 60 +++--- man/HJG.Rd | 62 +++--- man/HJM.Rd | 62 +++--- man/HV.Rd | 68 +++---- man/HZ.Rd | 60 +++--- man/KKurt.Rd | 60 +++--- man/MAKurt.Rd | 68 +++---- man/MASkew.Rd | 68 +++---- man/MQ1.Rd | 48 ++--- man/MQ2.Rd | 48 ++--- man/MRSSkew.Rd | 56 ++--- man/MSkew.Rd | 64 +++--- man/PU.Rd | 58 +++--- man/Quantile09.Rd | 54 ++--- man/Quantile095.Rd | 54 ++--- man/Quantile099.Rd | 54 ++--- man/SR.Rd | 60 +++--- man/cv.quan.Rd | 76 ++++---- man/mnt-package.Rd |only man/standard.Rd | 32 +-- man/test.BHEP.Rd | 159 ++++++++++++---- man/test.CS.Rd | 92 ++++----- man/test.DEHT.Rd | 90 ++++----- man/test.DEHU.Rd | 90 ++++----- man/test.EHS.Rd | 90 ++++----- man/test.HJG.Rd | 88 ++++----- man/test.HJM.Rd | 90 ++++----- man/test.HV.Rd | 96 +++++----- man/test.HZ.Rd | 80 ++++---- man/test.KKurt.Rd | 84 ++++---- man/test.MAKurt.Rd | 96 +++++----- man/test.MASkew.Rd | 96 +++++----- man/test.MKurt.Rd | 88 ++++----- man/test.MQ1.Rd | 74 +++---- man/test.MQ2.Rd | 72 +++---- man/test.MRSSkew.Rd | 88 ++++----- man/test.MSkew.Rd | 88 ++++----- man/test.PU.Rd | 86 ++++----- man/test.SR.Rd | 76 ++++---- 51 files changed, 2128 insertions(+), 1612 deletions(-)
Title: Computing Graph Structures on WikiPathways
Description: Converts pathways from 'WikiPathways' GPML format or
'KEGG' KGML format into 'igraph' objects. Includes tools to find all
cycles in the resulting graphs and determine which ones involve
negative feedback (inhibition). See <doi:10.1093/nargab/lqag051>.
Author: Kevin R. Coombes [aut, cre],
Polina Bombina [aut]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between WayFindR versions 0.7.0 dated 2026-01-08 and 0.7.1 dated 2026-09-25
DESCRIPTION | 12 - MD5 | 50 +++--- R/01-edges.R | 150 +++++++++--------- R/02-nodes.R | 96 +++++------ R/03-groups.R | 226 +++++++++++++-------------- R/04-anchors.R | 130 +++++++-------- R/05-toIgraph.R | 314 +++++++++++++++++++------------------- R/06-cycles.R | 218 +++++++++++++------------- R/11-graphNEL.R | 68 ++++---- R/sysdata.rda |binary build/vignette.rds |binary data/edgeColors.rda |binary data/edgeTypes.rda |binary data/nodeColors.rda |binary data/nodeShapes.rda |binary inst/doc/WayFindR_getStarted.html | 4 inst/doc/WayFindR_metrics.html | 11 - inst/doc/WayFindR_plots.html | 4 inst/profile/10-profilenno.R | 74 ++++---- tests/01-testEdge.R | 34 ++-- tests/02-testNode.R | 34 ++-- tests/03-testGroup.R | 12 - tests/04-testAnchor.R | 12 - tests/05-testIgraph.R | 28 +-- tests/06-testCycle.R | 26 +-- tests/10-testKeggUtil.R | 34 ++-- 26 files changed, 768 insertions(+), 769 deletions(-)
Title: Statistical Process Control with Tidyverse-Native Workflows
Description: A comprehensive toolkit for Statistical Process Control (SPC)
that combines the rigor of classical Shewhart methodology with modern
tidyverse-native interfaces. Provides classical control charts for
variables (I-MR, Xbar-R, Xbar-S) and attributes (p, np, c, u), as
well as regression-based control charts for processes with trend.
Includes Nelson runs tests, Average Run Length (ARL) simulation,
process capability indices with bootstrap confidence intervals,
Box-Cox transformation guidance, and a clean Phase I / Phase II
workflow. All chart objects integrate with broom via 'tidy',
'glance' and 'augment' methods. References: Shewhart (1931,
ISBN:0-87389-076-0); Montgomery (2019, ISBN:978-1-119-39930-8);
Nelson (1984) <doi:10.1080/00224065.1984.11978921>; Woodall (2000)
<doi:10.1080/00224065.2000.11980013>; Box & Cox (1964)
<doi:10.1111/j.2517-6161.1964.tb00553.x>.
Author: Andre Leite [aut, cre],
Hugo Vasconcelos [aut],
Raydonal Ospina [aut],
Cristiano Ferraz [aut],
Castlab [cph, fnd]
Maintainer: Andre Leite <leite@castlab.org>
Diff between shewhartr versions 1.3.0 dated 2026-05-13 and 1.4.0 dated 2026-09-25
DESCRIPTION | 11 MD5 | 203 +++++----- NEWS.md | 211 +++++++++++ R/as_plotly.R | 27 + R/autoplot.R | 184 ++++++++- R/broom.R | 57 ++- R/calibrate.R | 267 +++++++++++--- R/capability.R | 159 +++++++- R/chart-c.R | 11 R/chart-cusum.R | 13 R/chart-ewma.R | 48 +- R/chart-hotelling.R | 14 R/chart-mcusum.R | 42 +- R/chart-mewma.R | 76 +++- R/chart-p.R | 16 R/chart-regression.R | 610 +++++++++++++++++++++++++++++---- R/chart-u.R | 10 R/chart-xbar-r.R | 12 R/chart-xbar-s.R | 11 R/data.R | 57 +++ R/models-growth.R | 13 R/runs-tests.R | 133 +++++-- R/transforms.R | 6 R/utils-locale.R | 42 ++ README.md | 51 ++ build/partial.rdb |binary build/vignette.rds |binary data/cvd_brazil.rda |only inst/doc/arl-simulation.Rmd | 8 inst/doc/arl-simulation.html | 13 inst/doc/article-charts.R |only inst/doc/article-charts.Rmd |only inst/doc/article-charts.html |only inst/doc/attributes-charts.R | 6 inst/doc/attributes-charts.Rmd | 2 inst/doc/attributes-charts.html | 35 + inst/doc/box-cox.R | 4 inst/doc/box-cox.Rmd | 18 inst/doc/box-cox.html | 20 - inst/doc/covid-recife.R | 3 inst/doc/covid-recife.Rmd | 44 +- inst/doc/covid-recife.html | 66 ++- inst/doc/diagnostics.R | 14 inst/doc/diagnostics.Rmd | 4 inst/doc/diagnostics.html | 15 inst/doc/getting-started.R | 4 inst/doc/getting-started.Rmd | 2 inst/doc/getting-started.html | 7 inst/doc/memory-based-charts.R | 4 inst/doc/memory-based-charts.Rmd | 27 + inst/doc/memory-based-charts.html | 46 +- inst/doc/phase1-phase2.R | 4 inst/doc/phase1-phase2.Rmd | 4 inst/doc/phase1-phase2.html | 3 inst/doc/prospective-replay.R |only inst/doc/prospective-replay.Rmd |only inst/doc/prospective-replay.html |only inst/doc/regression-charts.Rmd | 26 - inst/doc/regression-charts.html | 55 +- inst/doc/variables-charts.R | 10 inst/doc/variables-charts.Rmd | 4 inst/doc/variables-charts.html | 7 inst/extdata/cvd_states_raw.rds |only man/Gompertz.Rd | 11 man/as_plotly.Rd | 17 man/autoplot.shewhart_regression.Rd |only man/cvd_brazil.Rd |only man/figures/README-regression-cvd.png |binary man/glance.shewhart_chart.Rd | 4 man/inv_box_cox.Rd | 6 man/print.shewhart_chart.Rd | 4 man/shewhart_capability.Rd | 21 - man/shewhart_cusum.Rd | 4 man/shewhart_ewma.Rd | 22 - man/shewhart_hotelling.Rd | 3 man/shewhart_mcusum.Rd | 7 man/shewhart_mewma.Rd | 17 man/shewhart_regression.Rd | 117 +++++- man/shewhart_xbar_r.Rd | 4 man/shewhart_xbar_s.Rd | 4 man/shewhartr-package.Rd | 1 man/tidy.shewhart_chart.Rd | 5 tests/testthat/test-article-features.R |only tests/testthat/test-as-plotly.R | 36 + tests/testthat/test-attributes.R | 80 ++++ tests/testthat/test-autoplot.R |only tests/testthat/test-broom.R |only tests/testthat/test-capability.R | 87 ++++ tests/testthat/test-cusum.R | 9 tests/testthat/test-ewma.R | 63 +++ tests/testthat/test-growth.R | 13 tests/testthat/test-hotelling.R | 30 + tests/testthat/test-mcusum.R | 44 ++ tests/testthat/test-mewma.R | 65 +++ tests/testthat/test-monitor.R | 106 +++++ tests/testthat/test-phases.R | 31 + tests/testthat/test-regression.R | 85 ++++ tests/testthat/test-runs.R | 65 +++ vignettes/arl-simulation.Rmd | 8 vignettes/article-charts.Rmd |only vignettes/attributes-charts.Rmd | 2 vignettes/box-cox.Rmd | 18 vignettes/covid-recife.Rmd | 44 +- vignettes/diagnostics.Rmd | 4 vignettes/getting-started.Rmd | 2 vignettes/memory-based-charts.Rmd | 27 + vignettes/phase1-phase2.Rmd | 4 vignettes/prospective-replay.Rmd |only vignettes/regression-charts.Rmd | 26 - vignettes/variables-charts.Rmd | 4 110 files changed, 3194 insertions(+), 645 deletions(-)
Title: Visualizing Topological Loops and Voids
Description: Visualizations to explain the results of a topological
data analysis. The goal of topological data analysis is to identify
persistent topological structures, such as loops (topological circles)
and voids (topological spheres), in data sets. The output of an
analysis using the 'TDA' package is a Rips diagram (named after the
mathematician Eliyahu Rips). The goal of 'RPointCloud' is to fill in
these holes in the data by providing tools to visualize the features
that help explain the structures found in the Rips diagram. See McGee
and colleagues (2024) <doi:10.1101/2024.05.16.593927> and (2026)
<doi: 10.3390/biotech15030063>.
Author: Kevin R. Coombes [aut, cre],
Jake Reed [aut],
RB McGee [aut]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between RPointCloud versions 0.9.1 dated 2026-02-17 and 0.9.2 dated 2026-09-25
DESCRIPTION | 13 +- MD5 | 22 ++-- R/01-disentangle.R | 78 ++++++++--------- R/04-angles.R | 146 ++++++++++++++++----------------- build/vignette.rds |binary data/CLL.rda |binary data/cytof.rda |binary data/treg.rda |binary inst/doc/clinical.html | 86 ++++++++++--------- inst/doc/cytof.html | 2 inst/doc/treg.html | 2 man/m08-LoopCircos-Class.Rd | 194 ++++++++++++++++++++++---------------------- 12 files changed, 274 insertions(+), 269 deletions(-)
Title: Seeking and Finding Clones in Copy Number and Sequencing Data
Description: Defines the classes and functions used to simulate and
to analyze data sets describing copy number variants and,
optionally, sequencing mutations in order to detect clonal subsets.
See Zucker et al. (2019) <doi:10.1093/bioinformatics/btz057>.
Author: Mark Zucker [aut],
Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between CloneSeeker versions 1.0.16 dated 2026-02-10 and 1.0.17 dated 2026-09-25
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/sysdata.rda |binary build/vignette.rds |binary inst/doc/CloneSeeker.R | 2 -- inst/doc/CloneSeeker.pdf |binary 6 files changed, 10 insertions(+), 12 deletions(-)
Title: Graphs and Tables for OMOP Results
Description: Provides methods to transform omop_result objects into
formatted tables and figures, facilitating the visualisation of study
results working with the Observational Medical Outcomes Partnership
(OMOP) Common Data Model.
Author: Marti Catala [aut] ,
Nuria Mercade-Besora [aut, cre] ,
Yuchen Guo [ctb] ,
Elin Rowlands [ctb] ,
Marta Alcalde-Herraiz [ctb] ,
Edward Burn [ctb]
Maintainer: Nuria Mercade-Besora <nuria.mercadebesora@ndorms.ox.ac.uk>
Diff between visOmopResults versions 1.5.0 dated 2026-05-18 and 1.5.1 dated 2026-09-25
visOmopResults-1.5.0/visOmopResults/inst/app.R |only visOmopResults-1.5.0/visOmopResults/inst/createMockReportData.R |only visOmopResults-1.5.0/visOmopResults/inst/darwinReportExample.docx |only visOmopResults-1.5.0/visOmopResults/inst/darwinReportExample.qmd |only visOmopResults-1.5.0/visOmopResults/inst/darwinReportRef.docx |only visOmopResults-1.5.0/visOmopResults/inst/mockReportData.RData |only visOmopResults-1.5.1/visOmopResults/DESCRIPTION | 6 visOmopResults-1.5.1/visOmopResults/MD5 | 60 - visOmopResults-1.5.1/visOmopResults/NEWS.md | 8 visOmopResults-1.5.1/visOmopResults/R/plot.R | 27 visOmopResults-1.5.1/visOmopResults/R/plottingThemes.R | 41 - visOmopResults-1.5.1/visOmopResults/R/styles.R | 87 ++ visOmopResults-1.5.1/visOmopResults/R/utilities.R | 86 +- visOmopResults-1.5.1/visOmopResults/R/visOmopTable.R | 17 visOmopResults-1.5.1/visOmopResults/R/visTable.R | 12 visOmopResults-1.5.1/visOmopResults/inst/brand/darwin.yml | 2 visOmopResults-1.5.1/visOmopResults/inst/doc/a01_tables.Rmd | 2 visOmopResults-1.5.1/visOmopResults/inst/doc/a01_tables.html | 354 +++++----- visOmopResults-1.5.1/visOmopResults/inst/doc/a02_plots.html | 24 visOmopResults-1.5.1/visOmopResults/inst/doc/a03_quarto_reports.R | 3 visOmopResults-1.5.1/visOmopResults/inst/doc/a03_quarto_reports.Rmd | 16 visOmopResults-1.5.1/visOmopResults/inst/doc/a03_quarto_reports.html | 41 - visOmopResults-1.5.1/visOmopResults/inst/doc/a04_shiny_apps.R | 15 visOmopResults-1.5.1/visOmopResults/inst/doc/a04_shiny_apps.Rmd | 55 + visOmopResults-1.5.1/visOmopResults/inst/doc/a04_shiny_apps.html | 63 + visOmopResults-1.5.1/visOmopResults/inst/doc/a05_style.html | 235 +++--- visOmopResults-1.5.1/visOmopResults/inst/mockData |only visOmopResults-1.5.1/visOmopResults/inst/quarto |only visOmopResults-1.5.1/visOmopResults/inst/shinyApp |only visOmopResults-1.5.1/visOmopResults/tests/testthat/test-plot.R | 49 + visOmopResults-1.5.1/visOmopResults/tests/testthat/test-visOmopTable.R | 55 + visOmopResults-1.5.1/visOmopResults/vignettes/a01_tables.Rmd | 2 visOmopResults-1.5.1/visOmopResults/vignettes/a03_quarto_reports.Rmd | 16 visOmopResults-1.5.1/visOmopResults/vignettes/a04_shiny_apps.Rmd | 55 + 34 files changed, 841 insertions(+), 490 deletions(-)
More information about visOmopResults at CRAN
Permanent link
Title: Silly Putty Clustering
Description: Implements a simple, novel clustering algorithm based on
optimizing the silhouette width. See <doi:10.1101/2023.11.07.566055>
for details.
Author: Dwayne Tally [aut],
Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between SillyPutty versions 0.4.3 dated 2026-09-25 and 0.4.4 dated 2026-09-25
DESCRIPTION | 6 MD5 | 8 inst/doc/SillyPuttyVignette.Rmd | 1 inst/doc/SillyPuttyVignette.html | 436 ++++++++++++++++++++++++--------------- vignettes/SillyPuttyVignette.Rmd | 1 5 files changed, 281 insertions(+), 171 deletions(-)
Title: Undo and Redo for 'Shiny' Applications
Description: Adds a user-facing undo and redo history to 'Shiny'
applications. Application state, comprising registered inputs and
optionally server-side reactive values, is captured as the user
interacts with the application. Users may then step backwards and
forwards through that history with the keyboard, with buttons, or by
scrubbing a visual history rail. Rapid successive changes, such as
dragging a slider, are coalesced into a single history entry, and
related changes may be grouped explicitly into semantic steps.
Author: Tanmay Chanda [aut, cre, cph]
Maintainer: Tanmay Chanda <tanmaychanda96@gmail.com>
Diff between rewind versions 0.2.0 dated 2026-08-21 and 0.3.0 dated 2026-09-25
DESCRIPTION | 6 +- MD5 | 45 ++++++++------- NAMESPACE | 1 NEWS.md | 73 ++++++++++++++++++++++++ R/api.R | 68 +++++++++++++++++----- R/controller.R | 29 ++++++++- R/diff.R |only R/history.R | 14 ++++ R/ui.R | 87 ++++++++++++++++++++++++++--- R/utils.R | 28 +++++++++ README.md | 28 +++++++++ inst/WORDLIST | 3 - inst/examples/demo/app.R | 2 inst/www/rewind.css | 7 ++ inst/www/rewind.js | 40 ++++++++++++- man/figures |only man/rewind_buttons.Rd | 31 +++++++++- man/rewind_diff.Rd |only man/rewind_enable.Rd | 28 ++++++++- tests/testthat/helper-shiny-smoke.R | 9 +++ tests/testthat/test-api.R | 105 +++++++++++++++++++++++++++++++++++ tests/testthat/test-app-smoke.R | 36 +++++++++++- tests/testthat/test-diff.R |only tests/testthat/test-module-browser.R |only tests/testthat/test-rail-scroll.R |only tests/testthat/test-rail-time.R |only tests/testthat/test-state.R | 22 +++++++ 27 files changed, 596 insertions(+), 66 deletions(-)
Title: Noncompartmental Analysis for Pharmacokinetic Report
Description: Conduct a noncompartmental analysis with industrial strength.
Some features are
1) CDISC SDTM terms
2) Automatic or manual slope selection
3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method
4) Interval(partial) AUCs with 'linear' or 'log' interpolation method
5) Steady-state analysis over the dosing interval (AUCTAU, CAVG, CL and Vz from AUCTAU)
6) Produce pdf, rtf, text report files.
7) Produce Installation and Operational Qualification (IQ/OQ) reports in pdf.
After installation, qualify the package in your own environment:
run pdfIQ() for Installation Qualification and pdfOQ() for Operational
Qualification. Run writeMD5() once after installation so the IQ
file-integrity check passes. To approve a report, sign it digitally in
Adobe Acrobat Reader (generate with sigField=TRUE, or run addSigField(),
to add click-to-sign fields), instead of printing and scanning; or use
signPDF()/verifyPDF() for a scriptable signature.
* Reference: Gabrielsson J, Weiner D. Pharmac [...truncated...]
Author: Kyun-Seop Bae [aut, cre],
Michael E. Schaffer [ctb, cph]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between ncar versions 0.7.1 dated 2026-08-27 and 0.7.2 dated 2026-09-25
DESCRIPTION | 15 ++-- MD5 | 31 +++++---- R/Res2Txt.R | 7 +- R/pdfNCA.R | 57 +++++++++++------ R/pdfOQ.R | 36 ++++++++++ R/rtfNCA.R | 45 +++++++++---- R/sysdata.rda |binary R/txtNCA.R | 6 - inst/NEWS.Rd | 9 ++ inst/OQ/Reference_Analytic_SS_Extravascular_Linear.csv |only man/Res2Txt.Rd | 7 +- man/RptCfg.Rd | 2 man/pdfNCA.Rd | 18 +++-- man/pdfOQ.Rd | 13 ++- man/rtfNCA.Rd | 17 +++-- man/txtNCA.Rd | 12 ++- tests/Rplots.pdf |only tests/Test-SS.R |only 18 files changed, 193 insertions(+), 82 deletions(-)
Title: Dynamic Stochastic General Equilibrium Models
Description: Specify, solve, and estimate dynamic stochastic general
equilibrium (DSGE) models by maximum likelihood and Bayesian methods.
Supports both linear models via an equation-based formula interface
and nonlinear models via string-based equations with perturbation up to
third order (Schmitt-Grohe and Uribe, 2004
<doi:10.1016/S0165-1889(03)00043-5>).
Solution uses the method of undetermined coefficients (Klein, 2000
<doi:10.1016/S0165-1889(99)00045-7>). Likelihood evaluated via the
Kalman filter or a bootstrap particle filter (Gordon et al., 1993).
Bayesian estimation uses adaptive Random-Walk Metropolis-Hastings or
Particle Marginal Metropolis-Hastings (Andrieu et al., 2010
<doi:10.1111/j.1467-9868.2009.00736.x>) with parallel chain support.
Additional tools include Bayes factor model comparison with
Kass-Raftery evidence scales, Ramsey optimal policy via linear-quadratic
regulator, nonlinear perfect foresight via stacked-time Newton
(Juillard et al., 1998), Kalman smoothi [...truncated...]
Author: Mustapha Wasseja Mohammed [aut, cre]
Maintainer: Mustapha Wasseja Mohammed <muswaseja@gmail.com>
Diff between dsge versions 1.0.0 dated 2026-04-02 and 1.2.0 dated 2026-09-25
DESCRIPTION | 27 MD5 | 222 ++ NAMESPACE | 358 ++-- NEWS.md | 452 +++++ R/bayes-diagnostics.R | 245 +++ R/bayes-estimate.R | 266 +++ R/bayes-methods.R | 123 - R/bayes-smc.R |only R/calibrated-smoother.R |only R/conditional-forecast.R |only R/discretionary-policy.R |only R/dsge-var-forecast.R |only R/dsge-var-mh.R |only R/dsge-var.R |only R/dsgenl-model.R | 12 R/dynare-macro.R |only R/dynare-matlab.R |only R/dynare-occbin.R |only R/dynare-perfect-foresight.R |only R/dynare-policy.R |only R/endogenous-prior.R |only R/estimate.R | 31 R/extended-path.R |only R/forecast.R | 66 R/global-sensitivity.R |only R/identification.R | 632 ++++---- R/irf-match.R |only R/kalman-filter.R | 161 +- R/kalman-skewed.R |only R/linearize.R | 16 R/markov-switching.R |only R/model-latex.R |only R/model-specification.R | 65 R/moment-estimation.R |only R/occbin.R | 1048 ++++++------- R/osr.R |only R/pac-equations.R |only R/particle-filter.R |only R/perfect-foresight-expecterr.R |only R/perfect-foresight.R | 1488 +++++++++++++------ R/perturbation.R |only R/plot-methods.R | 135 + R/plot-theme.R |only R/predetermined.R |only R/prior-posterior.R | 535 +++--- R/prior.R | 58 R/ramsey-policy.R |only R/read-dynare.R |only R/second-order.R | 958 ++++-------- R/sensitivity.R | 830 +++++----- R/smoother.R | 1404 +++++++++--------- R/solve-klein.R | 826 ++++++---- R/symbolic-derivs.R |only R/third-order.R |only R/variance-decomposition.R |only README.md | 566 ++++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/introduction.R | 338 ++-- inst/doc/introduction.Rmd | 1 inst/doc/introduction.html | 1712 +++++++++++----------- inst/examples/rbc.mod |only man/bayes_dsge.Rd | 41 man/bayes_dsge_var.Rd |only man/bayes_dsge_var_mh.Rd |only man/bayes_factor.Rd |only man/bayes_particle.Rd |only man/bayes_smc.Rd |only man/calibrated_smoother.Rd |only man/check_identification.Rd | 160 +- man/conditional_forecast.Rd |only man/conditional_forecast.dsge_dsgevar.Rd |only man/discretionary_policy.Rd |only man/dot-compute_equation_hessians.Rd | 24 man/dsge-package.Rd | 2 man/dsge_model.Rd | 11 man/dsgenl_model.Rd | 5 man/endogenous_prior.Rd |only man/estimate.Rd | 11 man/extended_path.Rd |only man/forecast.dsge_dsgevar.Rd |only man/forecast.dsge_fit.Rd | 13 man/global_sensitivity.Rd |only man/gmm_estimate.Rd |only man/irf_2nd_order.Rd | 56 man/irf_match.Rd |only man/kalman_filter_skewed.Rd |only man/model_latex.Rd |only man/ms_filter.Rd |only man/osr.Rd |only man/pac_simulate.Rd |only man/pac_target_loading.Rd |only man/pac_weights.Rd |only man/parameter_sensitivity.Rd | 160 +- man/particle_filter.Rd |only man/particle_filter_loglik.Rd |only man/perfect_foresight.Rd | 226 +- man/perfect_foresight_expect_err.Rd |only man/perfect_foresight_nonlinear.Rd |only man/plot.dsge_decomposition.Rd | 50 man/plot.dsge_perfect_foresight.Rd | 68 man/plot.dsge_smoothed.Rd | 52 man/plot.dsge_variance_decomposition.Rd |only man/predetermined.Rd |only man/prior.Rd | 9 man/prior_posterior_update.Rd | 130 - man/ramsey_policy.Rd |only man/read_dynare.Rd |only man/shock_decomposition.Rd | 131 - man/simulate_2nd_order.Rd | 50 man/simulate_3rd_order.Rd |only man/simulate_occbin.Rd | 10 man/simulate_perfect_foresight.Rd |only man/smm_estimate.Rd |only man/smooth_shocks.Rd | 81 - man/smooth_states.Rd | 132 - man/solve_2nd_order.Rd | 72 man/solve_3rd_order.Rd |only man/solve_dsge.Rd | 115 - man/summary.dsge_perfect_foresight.Rd | 42 man/variance_decomposition.Rd |only man/welfare_loss.Rd |only tests/testthat/Rplots.pdf |binary tests/testthat/test-bayes-factor.R |only tests/testthat/test-bayes-smc.R |only tests/testthat/test-calibrated-smoother.R |only tests/testthat/test-conditional-forecast.R |only tests/testthat/test-discretionary-policy.R |only tests/testthat/test-dsge-var-forecast.R |only tests/testthat/test-dsge-var-mh.R |only tests/testthat/test-dsge-var.R |only tests/testthat/test-endogenous-prior.R |only tests/testthat/test-extended-path.R |only tests/testthat/test-global-sensitivity.R |only tests/testthat/test-identification.R | 508 +++--- tests/testthat/test-irf-match.R |only tests/testthat/test-kalman-skewed.R |only tests/testthat/test-markov-switching.R |only tests/testthat/test-model-latex.R |only tests/testthat/test-moment-estimation.R |only tests/testthat/test-news-shocks.R |only tests/testthat/test-occbin.R | 604 +++---- tests/testthat/test-osr.R |only tests/testthat/test-pac-equations.R |only tests/testthat/test-parallel-chains.R |only tests/testthat/test-particle-filter.R |only tests/testthat/test-perfect-foresight-nonlinear.R |only tests/testthat/test-perfect-foresight.R | 528 +++--- tests/testthat/test-pf-expecterr.R |only tests/testthat/test-predetermined.R |only tests/testthat/test-prediction-tools.R | 10 tests/testthat/test-ramsey-policy.R |only tests/testthat/test-read-dynare-matlab.R |only tests/testthat/test-read-dynare-pf.R |only tests/testthat/test-read-dynare-policy.R |only tests/testthat/test-read-dynare.R |only tests/testthat/test-robust-vcov.R | 10 tests/testthat/test-second-order.R | 418 ++--- tests/testthat/test-smoother.R | 404 ++--- tests/testthat/test-third-order.R |only tests/testthat/test-variance-decomposition.R |only vignettes/introduction.Rmd | 1 162 files changed, 9552 insertions(+), 7157 deletions(-)
Title: Create Elegant Table 1 in HTML/'LaTeX' for Bio-Statistics
Description: Creates the "table one" of bio-medical papers. Fill it with your
data and the name of the variable which you'll make the group(s) out of and
it will make univariate and bivariate analysis, and parse the result into an
HTML or 'LaTeX' table ready to paste into a paper.
Author: Edouard Baudouin [aut, cre]
Maintainer: Edouard Baudouin <edouardpierre.baudouin@aphp.fr>
Diff between doudpackage versions 2.1.0 dated 2023-06-29 and 2.2.0 dated 2026-09-25
DESCRIPTION | 27 + MD5 | 41 +- NEWS.md | 85 ++++- R/Classes.R | 11 R/bivariate.R | 155 ++++------ R/descTab.R | 141 +++++++-- R/makeTable.R | 14 R/parse.R | 163 ++++++---- R/tools.R | 152 +++++++--- R/univariate.R | 30 + README.md | 453 ++++++------------------------ inst/WORDLIST | 5 man/anaBiv-data.frame-character-method.Rd | 30 + man/anaBiv-listVar-character-method.Rd | 4 man/anaBiv.Rd | 4 man/descTab.Rd | 89 ++++- man/parseClassFun-parseClass-method.Rd | 54 ++- man/parseClassFun.Rd | 54 ++- tests |only 19 files changed, 822 insertions(+), 690 deletions(-)
Title: Watch the File System for Changes
Description: R binding for 'libfswatch', a file system monitoring library.
Watch files, or directories recursively, for changes in the
background. Log activity, or call an R function, upon every change
event.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd] ,
Enrico M. Crisostomo [cph] ,
Alan Dipert [cph]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between watcher versions 0.2.0 dated 2026-06-22 and 0.2.1 dated 2026-09-25
DESCRIPTION | 6 MD5 | 42 ++--- NEWS.md | 5 README.md | 2 configure | 11 - src/fswatch/README.md | 59 ++++++- src/fswatch/libfswatch/src/libfswatch/c++/fanotify_monitor.cpp | 10 - src/fswatch/libfswatch/src/libfswatch/c++/fanotify_monitor.hpp | 2 src/fswatch/libfswatch/src/libfswatch/c++/fen_monitor.cpp | 3 src/fswatch/libfswatch/src/libfswatch/c++/inotify_monitor.cpp | 27 ++- src/fswatch/libfswatch/src/libfswatch/c++/inotify_monitor.hpp | 2 src/fswatch/libfswatch/src/libfswatch/c++/kqueue_monitor.cpp | 11 - src/fswatch/libfswatch/src/libfswatch/c++/kqueue_monitor.hpp | 2 src/fswatch/libfswatch/src/libfswatch/c++/monitor.cpp | 79 ++++++++++ src/fswatch/libfswatch/src/libfswatch/c++/monitor.hpp | 56 +++++++ src/fswatch/libfswatch/src/libfswatch/c++/poll_monitor.cpp | 16 +- src/fswatch/libfswatch/src/libfswatch/c++/poll_monitor.hpp | 4 src/fswatch/libfswatch/src/libfswatch/c/cfilter.h | 16 +- src/fswatch/libfswatch/src/libfswatch/c/libfswatch.cpp | 62 +++++++ src/fswatch/libfswatch/src/libfswatch/c/libfswatch.h | 22 ++ tests/testthat/test-watch.R | 35 ++++ tools/update_libfswatch.sh | 1 22 files changed, 401 insertions(+), 72 deletions(-)
Title: Threshing and Reaping for Principal Components
Description: Defines the classes used to identify
outliers (threshing) and compute the number of significant principal
components and number of clusters (reaping) in a joint application
of PCA and hierarchical clustering. See Wang et al., 2018,
<doi:10.1186/s12859-017-1998-9>.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Thresher versions 1.1.5 dated 2025-04-07 and 1.1.6 dated 2026-09-25
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- build/vignette.rds |binary data/savedSims.rda |binary inst/doc/Thresher.R | 2 -- inst/doc/Thresher.pdf |binary 6 files changed, 10 insertions(+), 12 deletions(-)
Title: Silly Putty Clustering
Description: Implements a simple, novel clustering algorithm based on
optimizing the silhouette width. See <doi:10.1101/2023.11.07.566055>
for details.
Author: Dwayne Tally [aut],
Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between SillyPutty versions 0.4.2 dated 2025-04-08 and 0.4.3 dated 2026-09-25
DESCRIPTION | 10 - MD5 | 8 build/vignette.rds |binary data/eucdist.rda |binary inst/doc/SillyPuttyVignette.html | 321 +++++++++++++-------------------------- 5 files changed, 119 insertions(+), 220 deletions(-)
Title: Using Cytogenetics Data in R
Description: Defines classes and methods to process text-based
cytogenetics using the CytoGPS web site, then import the results
into R for further analysis and graphing.
Author: Kevin R. Coombes [aut, cre],
Dwayne Tally [aut]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between RCytoGPS versions 1.2.13 dated 2026-07-06 and 1.2.14 dated 2026-09-25
DESCRIPTION | 10 MD5 | 16 - R/sysdata.rda |binary build/vignette.rds |binary data/cytoData.rda |binary data/cytobandLocations.rda |binary inst/PreClean/badStrings.txt | 36 +-- inst/doc/Gallery.html | 427 +++++++++++++++++++---------------------- inst/doc/IntroRCytoGPS.html | 441 +++++++++++++++++++------------------------ 9 files changed, 427 insertions(+), 503 deletions(-)
Title: Finding the Number of Significant Principal Components
Description: Implements methods to automate the Auer-Gervini graphical
Bayesian approach for determining the number of significant
principal components. Automation uses clustering, change points, or
simple statistical models to distinguish "long" from "short" steps
in a graph showing the posterior number of components as a function
of a prior parameter. See <doi:10.1101/237883>.
Author: Min Wang [aut],
Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between PCDimension versions 1.1.14 dated 2025-04-07 and 1.1.15 dated 2026-09-25
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- build/vignette.rds |binary data/spca.rda |binary inst/doc/PCDimension.R | 2 -- inst/doc/PCDimension.pdf |binary 6 files changed, 10 insertions(+), 12 deletions(-)
Title: Clustering and Visualizing Distance Matrices
Description: Defines the classes used to explore, cluster and
visualize distance matrices, especially those arising from binary
data. See Abrams and colleagues, 2021, <doi:10.1093/bioinformatics/btab037>.
Author: Kevin R. Coombes [aut, cre],
Caitlin E. Coombes [aut]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Mercator versions 1.1.7 dated 2025-05-27 and 1.1.8 dated 2026-09-25
DESCRIPTION | 10 +++---- MD5 | 20 +++++++-------- build/vignette.rds |binary data/CML1000.rda |binary data/CML500.rda |binary data/fakedata.rda |binary data/lgfFeatures.rda |binary inst/doc/mercVis.html | 61 +++++++++++++++++++++++---------------------- inst/doc/mercator.html | 6 ++-- inst/doc/umap-som.html | 65 ++++++++++++++++++++++++------------------------- man/datasets.Rd | 4 +-- 11 files changed, 84 insertions(+), 82 deletions(-)
Title: Miscellaneous Functions for the Analysis of Educational
Assessments
Description: Miscellaneous functions for data cleaning and data analysis of educational assessments. Includes functions for descriptive
analyses, character vector manipulations and weighted statistics. Mainly a lightweight dependency for the packages 'eatRep',
'eatGADS', 'eatPrep' and 'eatModel' (which will be subsequently submitted to 'CRAN').
The function for defining (weighted) contrasts in weighted effect coding refers to
te Grotenhuis et al. (2017) <doi:10.1007/s00038-016-0901-1>.
Functions for weighted statistics refer to
Wolter (2007) <doi:10.1007/978-0-387-35099-8>.
Author: Sebastian Weirich [aut, cre],
Martin Hecht [aut],
Karoline Sachse [aut],
Benjamin Becker [aut],
Nicole Mahler [aut],
Edna Grewers [ctb]
Maintainer: Sebastian Weirich <sebastian.weirich@iqb.hu-berlin.de>
Diff between eatTools versions 0.7.9 dated 2025-09-12 and 0.7.10 dated 2026-09-25
DESCRIPTION | 8 MD5 | 126 ++++---- NEWS.md | 5 R/addLeadingZeros.R | 52 +-- R/asNumericIfPossible.R | 198 ++++++------- R/catch_asNumericIfPossible.R | 38 +- R/cleanifyString.r | 98 +++--- R/existsBackgroundVariables.r | 2 R/facToChar.r | 2 R/insert.col.r | 32 +- R/mergeAttr.r | 4 R/readMultisep.R | 34 +- R/remove_funs.R | 136 ++++----- R/seq2.R | 22 - R/whereAre.r | 44 +-- README.md | 54 +-- inst/WORDLIST | 56 +-- man/addLeadingZeros.Rd | 54 +-- man/asNumericIfPossible.Rd | 112 +++---- man/catch_asNumericIfPossible.Rd | 84 ++--- man/checkBackgroundVariables.Rd | 126 ++++---- man/cleanifyString.Rd | 88 +++--- man/contr.wec.weighted.Rd | 72 ++--- man/crop.Rd | 60 ++-- man/data.timss1.rd | 72 ++--- man/eatTools-package.Rd | 54 +-- man/existsBackgroundVariables.Rd | 66 ++-- man/facToChar.Rd | 84 ++--- man/figures/logo.png |binary man/gsubAll.rd | 66 ++-- man/halveString.rd | 74 ++--- man/insert.col.rd | 38 +- man/makeDataFrame.rd | 72 ++--- man/makeTria.rd | 64 ++-- man/mergeAttr.rd | 276 ++++++++++--------- man/multiseq.Rd | 52 +-- man/na_omit_selection.rd | 58 ++-- man/num.to.cat.rd | 68 ++-- man/operator.Rd | 64 ++-- man/print_and_capture.rd | 58 ++-- man/pwc.rd | 48 +-- man/rbind_common.rd | 70 ++-- man/rbind_fill_vector.rd | 38 +- man/removeNonNumeric.Rd | 60 ++-- man/removeNumeric.Rd | 60 ++-- man/removePattern.Rd | 44 +-- man/seq2.Rd | 48 +-- man/tableUnlist.rd | 46 +-- man/whereAre.rd | 72 ++--- tests/testthat.R | 8 tests/testthat/test_addLeadingZeros.R | 48 +-- tests/testthat/test_asNumericIfPossible.R | 344 ++++++++++++------------ tests/testthat/test_catch_asNumericIfPossible.R | 30 +- tests/testthat/test_checkBackgroundVariables.R | 66 ++-- tests/testthat/test_cleanifyString.R | 88 +++--- tests/testthat/test_makeDataFrame.R | 58 ++-- tests/testthat/test_makeTria.R | 16 - tests/testthat/test_mergeAttr.R | 77 ++--- tests/testthat/test_print_and_capture.R | 34 +- tests/testthat/test_pwc.R | 34 +- tests/testthat/test_rbindCommon.R | 54 +-- tests/testthat/test_readMultisep.R | 44 +-- tests/testthat/test_remove_funs.R | 146 +++++----- tests/testthat/test_seq2.R | 60 ++-- 64 files changed, 2153 insertions(+), 2113 deletions(-)
Title: The Tail-Rank Statistic
Description: Implements the tail-rank statistic for selecting biomarkers
from a microarray data set, an efficient nonparametric test focused
on the distributional tails. See
<https://gitlab.com/krcoombes/coombeslab/-/blob/master/doc/papers/tolstoy-new.pdf>.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between TailRank versions 3.2.4 dated 2025-04-07 and 3.2.6 dated 2026-09-25
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ build/vignette.rds |binary inst/doc/betabinomial.R | 2 -- inst/doc/betabinomial.pdf |binary inst/doc/tailrank.R | 2 -- inst/doc/tailrank.pdf |binary 7 files changed, 11 insertions(+), 15 deletions(-)
Title: Digitally Sign and Verify PDF Documents
Description: Digitally sign PDF documents with a 'PKCS#12' keystore and verify
their signatures. Signing produces a detached 'PKCS#7' / 'CMS' signature
('adbe.pkcs7.detached') over the document and is applied as an incremental
update, so existing signatures remain valid. The cryptography and PDF
manipulation are performed by a bundled, pure-'Rust' backend (the
'pdf_signer' crate); no Java runtime, 'OpenSSL', or external command-line
tools are required. Visible signature appearances with custom text are
supported.
Author: Andre Leite [aut, cre],
Hugo Vasconcelos [aut],
Diogo Bezerra [aut],
Authors of the vendored Rust crates [ctb, cph]
Maintainer: Andre Leite <leite@castlab.org>
This is a re-admission after prior archival of version 0.2.5 dated 2026-07-02
Diff between pdfsigner versions 0.2.5 dated 2026-07-02 and 0.3.0 dated 2026-09-25
DESCRIPTION | 8 MD5 | 17 NEWS.md |only R/sign.R | 35 + man/verify_pdf_signature.Rd | 35 + src/rust/Cargo.lock | 762 ++++++++++++++++--------------------------- src/rust/Cargo.toml | 4 src/rust/src/lib.rs | 23 + src/rust/vendor.tar.xz |binary tests/testthat/test-verify.R | 24 + 10 files changed, 393 insertions(+), 515 deletions(-)
Title: Turnkey Visualisations for Exploratory Data Analysis
Description: Provides interactive visualisations for exploratory data analysis of high-dimensional datasets.
Includes parallel coordinate plots for exploring large datasets with mostly quantitative features,
but also stacked one-dimensional visualisations that more effectively show missingness and complex categorical relationships in smaller datasets.
Author: Sam El-Kamand [aut, cre] ,
Children's Cancer Institute Australia [cph]
Maintainer: Sam El-Kamand <sam.elkamand@gmail.com>
Diff between ggEDA versions 0.2.0 dated 2025-09-09 and 0.3.0 dated 2026-09-25
DESCRIPTION | 12 +-- MD5 | 30 ++++--- NEWS.md | 25 ++++++ R/ggparallel.R | 1 R/ggparallel_options.R | 6 + R/ggstack.R | 112 +++++++++++++++++++++-------- R/ggstack_options.R | 30 +++++++ README.md | 6 + man/figures/README-customise_colours-1.png |binary man/figures/README-example-1.png |binary man/figures/README-minibeans_noclass-1.png |binary man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/ggparallel_options.Rd | 3 man/ggstack_options.Rd | 19 ++++ tests/testthat/_snaps/bugfixes.md |only tests/testthat/test-bugfixes.R |only 17 files changed, 189 insertions(+), 55 deletions(-)
Title: 'DBI' Compliant Database Access Using 'ADBC'
Description: In order to make Arrow Database Connectivity ('ADBC' <https://arrow.apache.org/adbc/>) accessible from R, an interface compliant with the 'DBI' package is provided, using driver back-ends that are implemented in the 'adbcdrivermanager' framework. This enables interacting with database systems using the Arrow data format, thereby offering an efficient alternative to 'ODBC' for analytical applications.
Author: Nicolas Bennett [aut, cre, cph],
Voltron Data [fnd]
Maintainer: Nicolas Bennett <nicolas@cynkra.com>
This is a re-admission after prior archival of version 0.1.2 dated 2025-09-03
Diff between adbi versions 0.1.2 dated 2025-09-03 and 0.1.3 dated 2026-09-25
DESCRIPTION | 18 +-- MD5 | 106 +++++++++--------- NAMESPACE | 6 - NEWS.md | 11 + R/AdbiConnection.R | 37 ++++-- R/AdbiDriver.R | 15 -- R/AdbiResult.R | 73 ++++++++---- R/AdbiResultArrow.R | 17 ++ R/dbAppendTable_AdbiConnection_character_data.frame.R | 10 + R/dbBegin_AdbiConnection.R | 1 R/dbBind_AdbiResult.R | 11 - R/dbClearResult_AdbiResult.R | 4 R/dbColumnInfo_AdbiResult.R | 1 R/dbCommit_AdbiConnection.R | 7 - R/dbConnect_AdbiDriver.R | 2 R/dbDisconnect_AdbiConnection.R | 33 ++--- R/dbExistsTable_AdbiConnection_Id.R | 5 R/dbFetchArrowChunk_AdbiResultArrow.R | 15 -- R/dbFetchArrow_AdbiResultArrow.R | 22 --- R/dbFetch_AdbiResult.R | 55 +-------- R/dbGetInfo_AdbiConnection.R | 1 R/dbGetRowCount_AdbiResult.R | 1 R/dbGetRowsAffected_AdbiResult.R | 5 R/dbGetStatement_AdbiResult.R | 1 R/dbHasCompleted_AdbiResult.R | 3 R/dbListFields_AdbiConnection_Id.R | 5 R/dbListTables_AdbiConnection.R | 18 +-- R/dbRemoveTable_AdbiConnection_character.R | 10 + R/dbRollback_AdbiConnection.R | 7 - R/dbSendQueryArrow_AdbiConnection.R | 11 + R/dbSendQuery_AdbiConnection_character.R | 11 + R/dbSendStatement_AdbiConnection_character.R | 11 + R/dbWriteTable_AdbiConnection_Id_data.frame.R | 27 +++- R/dbWriteTable_AdbiConnection_character_data.frame.R | 7 + R/export.R | 8 - R/show_AdbiConnection.R | 4 R/show_AdbiDriver.R | 1 R/show_AdbiResult.R | 4 R/show_AdbiResultArrow.R | 4 R/utils.R | 36 ++++-- README.md | 14 ++ inst |only man/AdbiConnection-class.Rd | 11 + man/AdbiDriver-class.Rd | 5 man/AdbiResult-class.Rd | 8 + man/AdbiResultArrow-class.Rd | 5 man/adbi-package.Rd | 7 + man/dbConnect.Rd | 6 - man/reexports.Rd | 2 tests/testthat/helper-DBItest.R | 64 ++++++---- tests/testthat/test-DBItest.R | 40 +++++- tests/testthat/test-connection.R |only tests/testthat/test-fetch.R | 1 tests/testthat/test-show.R | 1 tests/testthat/test-utils.R | 1 55 files changed, 438 insertions(+), 351 deletions(-)
Title: Interactive Feature-Based Analysis of AIRR-Seq Data
Description: An interactive framework for the exploration and analysis of
adaptive immune receptor repertoire sequencing (AIRR-seq) data. It
enables large-scale computation and integrated analysis of
sequence-derived features, including physicochemical properties, amino
acid descriptor sets, sequence motifs, compositional patterns, and
somatic hypermutation metrics. The application supports multiscale
analysis across sequences, clones, and repertoires, with interactive
visualizations and statistical feature selection. 'AbSolution' also
facilitates reproducible research by enabling structured export of
data, code, parameters, and computational environments. See
<https://github.com/EDS-Bioinformatics-Laboratory/AbSolution> for more
details.
Author: Rodrigo Garcia-Valiente [cre, aut] ,
Charisios Triantafyllou [aut] ,
Antoine van Kampen [aut, ths]
Maintainer: Rodrigo Garcia-Valiente <r.garciavaliente@amsterdamumc.nl>
Diff between AbSolution versions 1.0.1 dated 2026-04-27 and 1.0.2 dated 2026-09-25
DESCRIPTION | 20 ++--- MD5 | 10 +- NEWS.md | 16 ++++ R/app_server.R | 48 ++++--------- R/fct_2_Feature_determination.R | 146 +++++++++++++++++++++++++++++----------- R/globals.R | 4 - 6 files changed, 160 insertions(+), 84 deletions(-)
Title: Performs the Transformed-Stationary Extreme Values Analysis
Description: Adaptation of the 'Matlab' 'tsEVA' toolbox developed by Lorenzo Mentaschi
available here:
<https://github.com/menta78/tsEva>. It contains an implementation of the
Transformed-Stationary (TS) methodology for non-stationary extreme
value Analysis (EVA) as described in Mentaschi et al. (2016) <doi:10.5194/hess-20-3527-2016>.
In synthesis this approach consists in:
(i) transforming a non-stationary time series into a
stationary one to which the stationary extreme value theory can be applied; and
(ii) reverse-transforming the result into a non-stationary extreme
value distribution.
'RtsEva' offers several options for trend estimation (mean, extremes, seasonal)
and contains multiple plotting functions displaying different aspects
of the non-stationarity of extremes.
Author: Alois Tilloy [aut, cre]
Maintainer: Alois Tilloy <alois.tilloy@ec.europa.eu>
Diff between RtsEva versions 1.1.0 dated 2025-06-10 and 1.2.0 dated 2026-09-25
DESCRIPTION | 7 MD5 | 30 +- NEWS.md | 51 ++++ R/eva_functions.R | 282 +++++++++++------------- R/mainTSEVA.R | 47 ++-- R/plot_functions.R | 16 - R/trend_functions.R | 265 ++++++++++------------ inst/doc/general-demo.html | 37 +-- man/TsEvaNs.Rd | 12 - man/tsEVstatistics.Rd | 154 ++++++------- man/tsEvaPlotReturnLevelsGEVFromAnalysisObj.Rd | 4 man/tsEvaPlotReturnLevelsGPDFromAnalysisObj.Rd | 4 man/tsEvaPlotSeriesTrendStdDevFromAnalyisObj.Rd | 4 man/tsEvaPlotTransfToStatFromAnalysisObj.Rd | 4 man/tsEvaSampleData.Rd | 6 man/tsGetPOT.Rd | 7 16 files changed, 495 insertions(+), 435 deletions(-)
Title: Primary Event Censored Distributions
Description: Provides functions for working with primary
event censored distributions and 'Stan' implementations for use in Bayesian
modeling. Primary event censored distributions are useful for modeling
delayed reporting scenarios in epidemiology and other fields (Charniga et
al. (2024) <doi:10.48550/arXiv.2405.08841>). It also provides support for
arbitrary delay distributions, a range of common primary distributions, and
allows for truncation and secondary event censoring to be accounted for
(Park et al. (2024) <doi:10.1101/2024.01.12.24301247>). A subset of
common distributions also have analytical solutions implemented, allowing
for faster computation. In addition, it provides multiple methods for
fitting primary event censored distributions to data via optional
dependencies.
Author: Sam Abbott [aut, cre, cph] ,
Sam Brand [aut] ,
Adam Howes [ctb] ,
James Mba Azam [aut] ,
Carl Pearson [aut] ,
Sebastian Funk [aut] ,
Kelly Charniga [aut]
Maintainer: Sam Abbott <contact@samabbott.co.uk>
Diff between primarycensored versions 1.5.2 dated 2026-09-10 and 1.6.0 dated 2026-09-25
primarycensored-1.5.2/primarycensored/tests/testthat/Rplots.pdf |only primarycensored-1.6.0/primarycensored/DESCRIPTION | 6 primarycensored-1.6.0/primarycensored/MD5 | 125 +- primarycensored-1.6.0/primarycensored/NAMESPACE | 4 primarycensored-1.6.0/primarycensored/NEWS.md | 65 + primarycensored-1.6.0/primarycensored/R/check.R | 8 primarycensored-1.6.0/primarycensored/R/dprimarycensored.R | 189 ---- primarycensored-1.6.0/primarycensored/R/fitdistdoublecens.R | 230 +++-- primarycensored-1.6.0/primarycensored/R/nonparametric_helpers.R | 20 primarycensored-1.6.0/primarycensored/R/pcens.R | 199 ++++ primarycensored-1.6.0/primarycensored/R/pcens_cdf.R | 36 primarycensored-1.6.0/primarycensored/R/pcens_pmf.R |only primarycensored-1.6.0/primarycensored/R/pprimarycensored.R | 46 - primarycensored-1.6.0/primarycensored/R/qprimarycensored.R | 20 primarycensored-1.6.0/primarycensored/R/utils.R | 189 +++- primarycensored-1.6.0/primarycensored/build/partial.rdb |binary primarycensored-1.6.0/primarycensored/build/vignette.rds |binary primarycensored-1.6.0/primarycensored/inst/doc/analytic-solutions.html | 159 +-- primarycensored-1.6.0/primarycensored/inst/doc/primarycensored.html | 149 +-- primarycensored-1.6.0/primarycensored/inst/doc/why-it-works.html | 151 +-- primarycensored-1.6.0/primarycensored/inst/stan/functions/primarycensored.stan | 62 + primarycensored-1.6.0/primarycensored/inst/stan/functions/primarycensored_analytical_cdf.stan | 445 ++++++---- primarycensored-1.6.0/primarycensored/man/check_dprimary.Rd | 6 primarycensored-1.6.0/primarycensored/man/dot-build_pcens.Rd |only primarycensored-1.6.0/primarycensored/man/dot-build_pcens_closures.Rd | 9 primarycensored-1.6.0/primarycensored/man/dot-canonical_name.Rd |only primarycensored-1.6.0/primarycensored/man/dot-check_named_list.Rd |only primarycensored-1.6.0/primarycensored/man/dot-check_primary_names.Rd |only primarycensored-1.6.0/primarycensored/man/dot-delay_cdf.Rd |only primarycensored-1.6.0/primarycensored/man/dot-dist_name.Rd |only primarycensored-1.6.0/primarycensored/man/dot-dpcens.Rd | 7 primarycensored-1.6.0/primarycensored/man/dot-fit_pcens_state.Rd |only primarycensored-1.6.0/primarycensored/man/dot-format_class.Rd | 16 primarycensored-1.6.0/primarycensored/man/dot-is_exact_window.Rd |only primarycensored-1.6.0/primarycensored/man/dot-lookup_ddist.Rd |only primarycensored-1.6.0/primarycensored/man/dot-lookup_pprimary.Rd | 4 primarycensored-1.6.0/primarycensored/man/dot-new_pcens.Rd |only primarycensored-1.6.0/primarycensored/man/dot-param_groups.Rd |only primarycensored-1.6.0/primarycensored/man/dot-pcens_cdf_at.Rd |only primarycensored-1.6.0/primarycensored/man/dot-pcens_cdf_gengamma_unif.Rd | 3 primarycensored-1.6.0/primarycensored/man/dot-pcens_density.Rd |only primarycensored-1.6.0/primarycensored/man/dot-ppcens.Rd | 11 primarycensored-1.6.0/primarycensored/man/dot-recycle_params.Rd |only primarycensored-1.6.0/primarycensored/man/dot-registry_name.Rd |only primarycensored-1.6.0/primarycensored/man/dot-resolve_pprimary.Rd | 4 primarycensored-1.6.0/primarycensored/man/dot-same_primary.Rd |only primarycensored-1.6.0/primarycensored/man/dprimarycensored.Rd | 41 primarycensored-1.6.0/primarycensored/man/fitdistdoublecens.Rd | 26 primarycensored-1.6.0/primarycensored/man/new_pcens.Rd | 25 primarycensored-1.6.0/primarycensored/man/pcens_cdf.Rd | 14 primarycensored-1.6.0/primarycensored/man/pcens_cdf.default.Rd | 8 primarycensored-1.6.0/primarycensored/man/pcens_cdf.pcens_pdiscretehazard.Rd | 8 primarycensored-1.6.0/primarycensored/man/pcens_cdf.pcens_pdiscretestep.Rd | 8 primarycensored-1.6.0/primarycensored/man/pcens_cdf.pcens_pgamma_dunif.Rd | 8 primarycensored-1.6.0/primarycensored/man/pcens_cdf.pcens_pgengamma.orig_dunif.Rd | 8 primarycensored-1.6.0/primarycensored/man/pcens_cdf.pcens_pgengamma_dunif.Rd | 8 primarycensored-1.6.0/primarycensored/man/pcens_cdf.pcens_plnorm_dunif.Rd | 8 primarycensored-1.6.0/primarycensored/man/pcens_cdf.pcens_pweibull_dunif.Rd | 8 primarycensored-1.6.0/primarycensored/man/pcens_pmf.Rd |only primarycensored-1.6.0/primarycensored/man/pcens_pmf.default.Rd |only primarycensored-1.6.0/primarycensored/man/pcens_quantile.Rd | 8 primarycensored-1.6.0/primarycensored/man/pcens_quantile.default.Rd | 8 primarycensored-1.6.0/primarycensored/man/pprimarycensored.Rd | 3 primarycensored-1.6.0/primarycensored/man/qprimarycensored.Rd | 3 primarycensored-1.6.0/primarycensored/man/rprimarycensored.Rd | 3 primarycensored-1.6.0/primarycensored/man/update.pcens.Rd |only primarycensored-1.6.0/primarycensored/tests/testthat/helper-stan-gradient.R |only primarycensored-1.6.0/primarycensored/tests/testthat/test-fitdistdoublecens.R | 82 + primarycensored-1.6.0/primarycensored/tests/testthat/test-pcens-equivalence.R |only 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More information about primarycensored at CRAN
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Title: Model Evaluation and Analysis
Description: Analyses species distribution models and evaluates their performance. It includes functions for variation partitioning, extracting variable importance, computing several metrics of model discrimination and calibration performance, optimizing prediction thresholds based on a number of criteria, performing multivariate environmental similarity surface (MESS) analysis, and displaying various analytical plots. Initially described in Barbosa et al. (2013) <doi:10.1111/ddi.12100>.
Author: A. Marcia Barbosa [aut, cre],
Jennifer A. Brown [aut],
Alberto Jimenez-Valverde [aut],
Raimundo Real [aut],
Oswald van Ginkel [ctb],
Jurica Levatic [ctb],
Victoria Formoso-Freire [ctb],
Andres Baselga [ctb],
Carola Gomez-Rodriguez [ctb],
Carlos C. Ra [...truncated...]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between modEvA versions 3.46 dated 2026-08-28 and 3.47 dated 2026-09-25
DESCRIPTION | 8 ++-- MD5 | 16 ++++----- NEWS.md | 12 ++++++ R/predDensity.R | 12 +++--- R/predPlot.R | 6 +-- R/varImp.R | 86 +++++++++++++++++++++++++++++++++----------------- man/Miller.Rd | 6 +-- man/modEvA-package.Rd | 4 +- man/varImp.Rd | 15 ++++---- 9 files changed, 103 insertions(+), 62 deletions(-)
Title: Create and Investigate Magic Squares
Description: A collection of functions for the manipulation and
analysis of arbitrarily dimensioned arrays. The original motivation
for the package was the development of efficient, vectorized
algorithms for the creation and investigation of magic squares and
high-dimensional magic hypercubes.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between magic versions 1.6-1 dated 2022-11-15 and 1.6-1-1 dated 2026-09-25
DESCRIPTION | 14 +++++----- MD5 | 64 +++++++++++++++++++++++------------------------ NEWS.md | 7 ++++- R/magic.R | 30 ++++++++++++---------- build/partial.rdb |binary build/vignette.rds |binary data/Frankenstein.rda |binary data/Ollerenshaw.rda |binary data/cube2.rda |binary data/hendricks.rda |binary data/magiccubes.rda |binary data/perfectcube5.rda |binary data/perfectcube6.rda |binary inst/CITATION | 41 +++++++++++------------------- inst/doc/magic.R | 14 ++++------ inst/doc/magic.Rnw | 9 ++---- inst/doc/magic.pdf |binary man/adiag.Rd | 17 +++++++++--- man/aplus.Rd | 6 ++-- man/as.standard.Rd | 4 +- man/circulant.Rd | 5 +++ man/is.magichypercube.Rd | 2 - man/is.ok.Rd | 2 - man/latin.Rd | 13 +++++++-- man/magic.2np1.Rd | 4 +- man/magic.4np2.Rd | 2 - man/magic.8.Rd | 2 - man/magicplot.Rd | 15 +++++------ man/panmagic.4.Rd | 2 - man/panmagic.6npm1.Rd | 4 +- man/sam.Rd | 12 ++++---- man/subsums.Rd | 14 +++++----- vignettes/magic.Rnw | 9 ++---- 33 files changed, 153 insertions(+), 139 deletions(-)
Title: Fuzzy Similarity in Species Distributions
Description: Functions to compute fuzzy versions of species occurrence patterns based on presence-absence data (including inverse distance interpolation, trend surface analysis, and prevalence-independent favourability obtained from probability of presence), as well as pair-wise fuzzy similarity (based on fuzzy logic versions of commonly used similarity indices) among those occurrence patterns. Includes also functions for model consensus and comparison (overlap and fuzzy similarity, fuzzy loss, fuzzy gain), and for data preparation, such as obtaining unique abbreviations of species names, defining the background region, cleaning and gridding (thinning) point occurrence data onto raster maps, selecting among (pseudo)absences to address survey bias, converting species lists (long format) to presence-absence tables (wide format), transposing part of a data frame, selecting relevant variables for models, assessing the false discovery rate, or analysing and dealing with multicollinearity. Initially desc [...truncated...]
Author: A. Marcia Barbosa [aut],
Alba Estrada [ctb],
Paul Melloy [ctb],
Jose Carlos Guerrero [fnd],
A. Marcia Barbosa [cre]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between fuzzySim versions 4.59 dated 2026-08-28 and 4.60 dated 2026-09-25
DESCRIPTION | 8 ++-- MD5 | 26 +++++++------- NAMESPACE | 2 + NEWS.md | 24 +++++++++++++ R/cleanCoords.R | 8 +++- R/fuzzyOverlay.R | 7 ++- R/selectAbsences.R | 87 +++++++++++++++++++++++++++++------------------- man/biasLayer.Rd | 8 ++-- man/clampVars.Rd | 4 +- man/cleanCoords.Rd | 7 ++- man/fuzSim.Rd | 4 +- man/fuzzyRangeChange.Rd | 75 ++++++++++++++++++++++++++++++----------- man/fuzzySim-package.Rd | 4 +- man/selectAbsences.Rd | 20 ++++++----- 14 files changed, 191 insertions(+), 93 deletions(-)
Title: Teaching Hydrological Modelling with the GR Rainfall-Runoff
Models ('Shiny' Interface Included)
Description: Add-on package to the 'airGR' package that simplifies its use and is aimed at being used for teaching hydrology. The package provides 1) three functions that allow to complete very simply a hydrological modelling exercise 2) plotting functions to help students to explore observed data and to interpret the results of calibration and simulation of the GR ('Génie rural') models 3) a 'Shiny' graphical interface that allows for displaying the impact of model parameters on hydrographs and models internal variables.
Author: Olivier Delaigue [aut, cre] ,
Laurent Coron [aut] ,
Pierre Brigode [aut] ,
Guillaume Thirel [aut]
Maintainer: Olivier Delaigue <airGR@inrae.fr>
Diff between airGRteaching versions 0.3.7 dated 2026-07-09 and 0.3.8 dated 2026-09-25
DESCRIPTION | 8 MD5 | 18 NEWS.md | 10 build/partial.rdb |binary inst/ShinyGR/server.R | 6 inst/doc/v00_teaching_hydrology.html | 646 ++++++++++++++----------------- inst/doc/v01_EN_flow_reconstruction.html | 121 ++--- inst/doc/v01_FR_flow_reconstruction.html | 121 ++--- inst/doc/v02_EN_flow_forecasting.html | 188 ++++----- inst/doc/v02_FR_flow_forecasting.html | 188 ++++----- 10 files changed, 606 insertions(+), 700 deletions(-)
Title: Design and Analysis of Pilot Trials Assessing Recruitment
Feasibility
Description: Find optimal decisions rules for guiding progression decisions
following a pilot trial, assuming a hierarchical recruitment model. Estimate
the time until the main trial recruits to target, given the recruitment data
observed in the pilot.
Author: Duncan Wilson [aut, cre, cph]
Maintainer: Duncan Wilson <d.t.wilson@leeds.ac.uk>
Diff between fahb versions 1.0.0 dated 2026-04-29 and 1.0.1 dated 2026-09-25
DESCRIPTION | 12 +-- LICENSE | 4 - MD5 | 40 +++++------ NEWS.md | 8 +- R/forecast.R | 15 +++- R/simulate_data.R | 16 +++- README.md | 42 ++++++------ build/vignette.rds |binary inst/doc/fahb.html | 5 - man/check_priors.Rd | 48 +++++++------- man/fahb-package.Rd | 55 ++++++++-------- man/fahb_analysis.Rd | 104 +++++++++++++++---------------- man/fahb_design.Rd | 54 ++++++++-------- man/fahb_problem.Rd | 102 +++++++++++++++--------------- man/figures/README-unnamed-chunk-2-1.png |binary man/forecast.Rd | 57 ++++++++-------- man/plot.fahb_analysis.Rd | 42 ++++++------ man/plot.fahb_design.Rd | 42 ++++++------ man/print.fahb_analysis.Rd | 38 +++++------ man/print.fahb_design.Rd | 44 ++++++------- tests/testthat.R | 24 +++---- 21 files changed, 392 insertions(+), 360 deletions(-)
Title: S3 Infrastructure for Regular and Irregular Time Series (Z's
Ordered Observations)
Description: An S3 class with methods for working with regular and irregular time series.
The class stores data as numeric vectors/matrices (or factors) along with a time index of arbitrary class
(including numeric, Date, POSIXct, chron, yearmon, yearqtr, etc.). Functions and methods
are consistent with the ts class and base R and also extend standard generics. Tools include:
Data import/export, coercion, visualization (with base R, 'ggplot2', 'lattice', 'tinyplot'), alignment and merging,
aggregation, lags and subsets, rolling analytics, and time-based interpolation/filling.
The design is introduced in Zeileis and Grothendieck (2005) <doi:10.18637/jss.v014.i06>.
Author: Achim Zeileis [aut, cre] ,
Gabor Grothendieck [aut],
Jeffrey A. Ryan [aut],
Joshua M. Ulrich [ctb],
Felix Andrews [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between zoo versions 1.9-0 dated 2026-07-31 and 1.9-1 dated 2026-09-25
DESCRIPTION | 8 MD5 | 49 +-- NEWS.md | 12 inst/doc/zoo-faq.html | 2 inst/doc/zoo.pdf |binary man/MATCH.Rd | 3 man/aggregate.zoo.Rd | 5 man/as.Date.Rd |only man/as.zoo.Rd | 20 + man/coredata.Rd | 1 man/ggplot2.zoo.Rd | 13 man/index.Rd | 8 man/lattice-deprecated.Rd |only man/merge.zoo.Rd | 6 man/na.trim.Rd | 1 man/read.zoo.Rd | 3 man/rollmean.Rd | 9 man/tinyplot.zoo.Rd | 8 man/xblocks.Rd | 4 man/xyplot.zoo.Rd | 54 +-- man/yearmon.Rd | 23 + man/yearqtr.Rd | 10 man/zoo-methods.Rd |only man/zoo.Rd | 18 - man/zooreg.Rd | 7 src/lag.c | 34 -- tests/Examples/zoo-Ex.Rout.save | 579 +++++++++++++++++++++++----------------- 27 files changed, 506 insertions(+), 371 deletions(-)
Title: Makefile Generator for R Analytical Projects
Description: Creates and maintains a build process for complex analytic tasks in R.
Package allows to easily generate Makefile for the (GNU) 'make' tool, which drives the build process
by (in parallel) executing build commands in order to update results accordingly to given dependencies
on changed data or updated source files.
Author: Michal Burda [aut, cre]
Maintainer: Michal Burda <michal.burda@osu.cz>
Diff between rmake versions 1.2.2 dated 2026-01-08 and 1.2.3 dated 2026-09-25
DESCRIPTION | 10 +++++----- MD5 | 26 ++++++++++++++------------ NAMESPACE | 15 ++++++++++----- NEWS.md | 7 +++++++ R/markdownRule.R | 4 ++-- R/pythonRule.R |only build/vignette.rds |binary inst/doc/build-rules.html | 4 ++-- inst/doc/getting-started.html | 4 ++-- inst/doc/project-management.html | 4 ++-- inst/doc/tasks-and-templates.html | 4 ++-- man/defaultVars.Rd | 5 ----- man/pythonRule.Rd |only man/rmake-package.Rd | 5 +++++ tests/testthat/test-markdownRule.R | 4 ++-- 15 files changed, 53 insertions(+), 39 deletions(-)
Title: Lexical Optimisation and Hardware-Timed Experiment Generation
Description: A cross-platform toolkit that unifies many-language lexical-corpus
access, parallel multidimensional stimulus matching, deterministic pseudoword
generation, counterbalancing and the automated generation of experiments from a
declarative trial-event model, for 'PsychoPy', 'OpenSesame' and the browser
('jsPsych'). The laboratory targets bind electroencephalography onset triggers
to the stimulus flip. It is the R member of a dual-language pair; a structurally
identical 'Python' package is also provided. Several paradigms (factorial word
contrasts, lexical decision, priming, self-paced reading and cued
categorisation) are supported, and
each design is accompanied by a machine- and human-readable materials datasheet
for reproducibility.
Author: Pablo Bernabeu [aut, cre]
Maintainer: Pablo Bernabeu <pcbernabeu@gmail.com>
Diff between lexsync versions 0.1.0 dated 2026-09-22 and 0.1.1 dated 2026-09-25
DESCRIPTION | 8 MD5 | 110 NAMESPACE | 1 NEWS.md | 746 ++- R/corpora.R | 149 R/datasheet.R | 2 R/paradigms.R | 296 - R/run_pipeline.R | 9 R/scripting.R | 64 R/validation.R | 40 README.md | 275 - inst/CITATION | 20 inst/WORDLIST | 9 inst/doc/about.R | 3 inst/doc/about.Rmd | 33 inst/doc/about.html | 41 inst/doc/experiments-and-triggers.R | 4 inst/doc/experiments-and-triggers.Rmd | 1061 ++--- inst/doc/experiments-and-triggers.html | 139 inst/doc/lexsync.R | 3 inst/doc/lexsync.Rmd | 484 +- inst/doc/lexsync.html | 141 inst/doc/matching-and-designs.Rmd | 1609 ++++---- inst/doc/matching-and-designs.html | 47 inst/doc/references.Rmd | 310 - inst/doc/references.html | 4 inst/doc/reproducibility-and-parity.Rmd | 1016 ++--- inst/doc/reproducibility-and-parity.html | 18 inst/doc/the-app.Rmd | 380 - inst/extdata/en_example.csv | 6002 +++++++++++++++---------------- inst/extdata/es_example.csv | 6002 +++++++++++++++---------------- man/assign_triggers.Rd | 28 man/cohens_d_ci.Rd | 25 man/export_experiments.Rd | 21 man/fetch_corpus.Rd | 17 man/figures/logo.svg | 64 man/lexsync_cache_clear.Rd |only man/lexsync_cache_dir.Rd | 30 man/match_report.Rd | 7 tests/testthat/helper-repo.R |only tests/testthat/test-apps.R | 12 tests/testthat/test-blocks.R | 9 tests/testthat/test-categorisation.R | 8 tests/testthat/test-config.R | 2 tests/testthat/test-corpora.R | 206 + tests/testthat/test-metadata.R | 2 tests/testthat/test-querying.R | 4 tests/testthat/test-scripting.R | 47 tests/testthat/test-templates.R | 15 tests/testthat/test-validation.R | 18 vignettes/about.Rmd | 33 vignettes/experiments-and-triggers.Rmd | 1061 ++--- vignettes/lexsync.Rmd | 484 +- vignettes/matching-and-designs.Rmd | 1609 ++++---- vignettes/references.Rmd | 310 - vignettes/reproducibility-and-parity.Rmd | 1016 ++--- vignettes/the-app.Rmd | 380 - 57 files changed, 12599 insertions(+), 11835 deletions(-)
Title: Preliminary Visualisation of Data
Description: Create preliminary exploratory data visualisations of an entire
dataset to identify problems or unexpected features using 'ggplot2'.
Author: Nicholas Tierney [aut, cre] ,
Sean Hughes [rev] ,
Mara Averick [rev] ,
Stuart Lee [ctb],
Earo Wang [ctb],
Nic Crane [ctb],
Christophe Regouby [ctb],
Jordi Rosell [ctb]
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>
Diff between visdat versions 0.6.0 dated 2023-02-01 and 0.6.1 dated 2026-09-25
visdat-0.6.0/visdat/R/data-typical-data.r |only visdat-0.6.0/visdat/R/utils-pipe.R |only visdat-0.6.0/visdat/man/pipe.Rd |only visdat-0.6.1/visdat/DESCRIPTION | 91 ++- visdat-0.6.1/visdat/MD5 | 235 ++++---- visdat-0.6.1/visdat/NAMESPACE | 3 visdat-0.6.1/visdat/NEWS.md | 20 visdat-0.6.1/visdat/R/abbreviate.R | 9 visdat-0.6.1/visdat/R/data-typical-data-large.R | 9 visdat-0.6.1/visdat/R/data-typical-data.R |only visdat-0.6.1/visdat/R/data-vis-cor.R | 32 - visdat-0.6.1/visdat/R/data-vis-dat.R | 20 visdat-0.6.1/visdat/R/data-vis-miss.R | 35 - visdat-0.6.1/visdat/R/internals.R | 267 ++++------ visdat-0.6.1/visdat/R/vis-binary.R | 38 - visdat-0.6.1/visdat/R/vis-compare.R | 107 +--- visdat-0.6.1/visdat/R/vis-cor.R | 67 +- visdat-0.6.1/visdat/R/vis-dat.R | 48 - visdat-0.6.1/visdat/R/vis-expect.R | 96 +-- visdat-0.6.1/visdat/R/vis-guess.R | 36 - visdat-0.6.1/visdat/R/vis-histogram.R |only visdat-0.6.1/visdat/R/vis-miss.R | 37 - visdat-0.6.1/visdat/R/vis-value.R | 19 visdat-0.6.1/visdat/R/visdat-package.r | 29 - visdat-0.6.1/visdat/README.md | 22 visdat-0.6.1/visdat/build/vignette.rds |binary visdat-0.6.1/visdat/inst/WORDLIST | 49 - visdat-0.6.1/visdat/inst/doc/customising-colour-palettes.R | 2 visdat-0.6.1/visdat/inst/doc/customising-colour-palettes.html | 73 +- visdat-0.6.1/visdat/inst/doc/using_visdat.R | 38 - visdat-0.6.1/visdat/inst/doc/using_visdat.Rmd | 16 visdat-0.6.1/visdat/inst/doc/using_visdat.html | 225 ++++---- visdat-0.6.1/visdat/inst/scratch |only visdat-0.6.1/visdat/man/abbreviate_vars.Rd | 2 visdat-0.6.1/visdat/man/data-vis-cor.Rd | 4 visdat-0.6.1/visdat/man/data-vis-dat.Rd | 4 visdat-0.6.1/visdat/man/data-vis-miss.Rd | 4 visdat-0.6.1/visdat/man/figures/README-iris-error-fix-1.png |binary visdat-0.6.1/visdat/man/figures/README-vis-bin-1.png |binary visdat-0.6.1/visdat/man/figures/README-vis-compare-iris-1.png |binary visdat-0.6.1/visdat/man/figures/README-vis-cor-1.png |binary visdat-0.6.1/visdat/man/figures/README-vis-dat-aq-1.png |binary visdat-0.6.1/visdat/man/figures/README-vis-dat-month-1.png |binary visdat-0.6.1/visdat/man/figures/README-vis-expect-1.png |binary visdat-0.6.1/visdat/man/figures/README-vis-guess-messy-df-1.png |binary visdat-0.6.1/visdat/man/figures/README-vis-guess-messy-df-2.png |binary visdat-0.6.1/visdat/man/figures/README-vis-histogram-1.png |only visdat-0.6.1/visdat/man/figures/README-vis-miss-aq-1.png |binary visdat-0.6.1/visdat/man/figures/README-vis-miss-aq-cluster-1.png |binary visdat-0.6.1/visdat/man/figures/README-vis-miss-aq-sort-miss-1.png |binary visdat-0.6.1/visdat/man/figures/README-vis-miss-mtcars-1.png |binary visdat-0.6.1/visdat/man/figures/README-vis-miss-test-1.png |binary visdat-0.6.1/visdat/man/figures/README-vis-value-1.png |binary visdat-0.6.1/visdat/man/typical_data.Rd | 2 visdat-0.6.1/visdat/man/typical_data_large.Rd | 9 visdat-0.6.1/visdat/man/vis_cor.Rd | 2 visdat-0.6.1/visdat/man/vis_dat.Rd | 8 visdat-0.6.1/visdat/man/vis_expect.Rd | 18 visdat-0.6.1/visdat/man/vis_histogram.Rd |only visdat-0.6.1/visdat/man/vis_miss.Rd | 8 visdat-0.6.1/visdat/man/vis_value.Rd | 4 visdat-0.6.1/visdat/man/visdat.Rd | 10 visdat-0.6.1/visdat/tests/spelling.R | 10 visdat-0.6.1/visdat/tests/testthat/_snaps/gather_funs.md | 4 visdat-0.6.1/visdat/tests/testthat/_snaps/test-vis-miss-one-col/vis-miss-with-one-col-cluster.svg | 5 visdat-0.6.1/visdat/tests/testthat/_snaps/test-vis-miss-one-col/vis-miss-with-one-col-no-show-pct-in-columns.svg | 5 visdat-0.6.1/visdat/tests/testthat/_snaps/test-vis-miss-one-col/vis-miss-with-one-col-show-pct-in-columns.svg | 5 visdat-0.6.1/visdat/tests/testthat/_snaps/test-vis-miss-one-col/vis-miss-with-one-col-show-pct.svg | 5 visdat-0.6.1/visdat/tests/testthat/_snaps/test-vis-miss-one-col/vis-miss-with-one-col-sort-rows.svg | 5 visdat-0.6.1/visdat/tests/testthat/_snaps/test-vis-miss-one-col/vis-miss-with-one-col-vanilla.svg | 5 visdat-0.6.1/visdat/tests/testthat/_snaps/vis-binary.md | 5 visdat-0.6.1/visdat/tests/testthat/_snaps/vis-binary/vis-binary-vanilla.svg | 7 visdat-0.6.1/visdat/tests/testthat/_snaps/vis-compare.md | 20 visdat-0.6.1/visdat/tests/testthat/_snaps/vis-compare/vis-compare-vanilla.svg | 15 visdat-0.6.1/visdat/tests/testthat/_snaps/vis-cor.md | 14 visdat-0.6.1/visdat/tests/testthat/_snaps/vis-cor/vis-cor-facet.svg | 29 - 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visdat-0.6.1/visdat/tests/testthat/test-test-vis-miss-one-col.R | 38 - visdat-0.6.1/visdat/tests/testthat/test-vis-binary.R | 10 visdat-0.6.1/visdat/tests/testthat/test-vis-compare.R | 14 visdat-0.6.1/visdat/tests/testthat/test-vis-cor.R | 17 visdat-0.6.1/visdat/tests/testthat/test-vis-dat.R | 32 - visdat-0.6.1/visdat/tests/testthat/test-vis-expect.R | 37 - visdat-0.6.1/visdat/tests/testthat/test-vis-guess.R | 10 visdat-0.6.1/visdat/tests/testthat/test-vis-histogram.R |only visdat-0.6.1/visdat/tests/testthat/test-vis-large.R | 14 visdat-0.6.1/visdat/tests/testthat/test-vis-miss.R | 45 + visdat-0.6.1/visdat/tests/testthat/test-vis-value.R | 15 visdat-0.6.1/visdat/tests/testthat/test-visdat-internals.R | 63 -- visdat-0.6.1/visdat/tests/testthat/test-vismiss-legend.R | 52 + visdat-0.6.1/visdat/tests/testthat/test_variable_spaces.R | 10 visdat-0.6.1/visdat/vignettes/using_visdat.Rmd | 16 124 files changed, 1346 insertions(+), 1316 deletions(-)
Title: Fully Customizable Chain Event Graphs over Spatial Areas
Description: Enables the creation of Chain Event Graphs over spatial areas, with an optional 'Shiny' user interface. Allows users to fully customise both the structure and underlying model of the Chain Event Graph, offering a high degree of flexibility for tailored analyses. For more details on Chain Event Graphs, see Freeman, G., & Smith, J. Q. (2011) <doi:10.1016/j.jmva.2011.03.008>, Collazo R. A., Görgen C. and Smith J. Q. (2018, ISBN:9781498729604) and Barclay, L. M., Hutton, J. L., & Smith, J. Q. (2014) <doi:10.1214/13-BA843>.
Author: Hollie Calley [aut, cre] ,
Daniel Williamson [ctb]
Maintainer: Hollie Calley <hc629@exeter.ac.uk>
Diff between stCEG versions 0.1.0 dated 2025-07-07 and 1.1.0 dated 2026-09-25
stCEG-0.1.0/stCEG/R/summary_functions.R |only stCEG-0.1.0/stCEG/man/create_ceg.Rd |only stCEG-0.1.0/stCEG/man/create_reduced_CEG.Rd |only stCEG-0.1.0/stCEG/man/delete_nodes.Rd |only stCEG-0.1.0/stCEG/man/staged_tree_prior.Rd |only stCEG-0.1.0/stCEG/man/summary.chain_event_graph.Rd |only stCEG-1.1.0/stCEG/DESCRIPTION | 17 stCEG-1.1.0/stCEG/MD5 | 86 stCEG-1.1.0/stCEG/NAMESPACE | 295 - stCEG-1.1.0/stCEG/NEWS.md | 17 stCEG-1.1.0/stCEG/R/ahc_colouring.R | 386 + stCEG-1.1.0/stCEG/R/create_ceg.R | 1175 ++++-- stCEG-1.1.0/stCEG/R/create_event_tree.R | 461 +- stCEG-1.1.0/stCEG/R/create_reduced_CEG.R | 417 +- stCEG-1.1.0/stCEG/R/create_staged_tree.R |only stCEG-1.1.0/stCEG/R/delete_nodes.R | 349 - stCEG-1.1.0/stCEG/R/globals.R |only stCEG-1.1.0/stCEG/R/map_plotting.R | 745 ++- stCEG-1.1.0/stCEG/R/package.R |only stCEG-1.1.0/stCEG/R/run_stceg.R | 3484 +++++++----------- stCEG-1.1.0/stCEG/R/specify_priors.R | 481 +- stCEG-1.1.0/stCEG/R/staged_tree_prior.R | 519 +- stCEG-1.1.0/stCEG/R/update_node_colours.R | 277 - stCEG-1.1.0/stCEG/man/ahc_colouring.Rd | 74 stCEG-1.1.0/stCEG/man/calculate_area_probabilities.Rd | 60 stCEG-1.1.0/stCEG/man/calculate_conditional_prob.Rd | 65 stCEG-1.1.0/stCEG/man/calculate_path_products.Rd | 54 stCEG-1.1.0/stCEG/man/compare_ceg_models.Rd | 111 stCEG-1.1.0/stCEG/man/compute_ceg.Rd |only stCEG-1.1.0/stCEG/man/compute_deleted_nodes.Rd |only stCEG-1.1.0/stCEG/man/compute_reduced_ceg.Rd |only stCEG-1.1.0/stCEG/man/compute_staged_tree_priors.Rd |only stCEG-1.1.0/stCEG/man/create_event_tree.Rd | 64 stCEG-1.1.0/stCEG/man/create_staged_tree.Rd |only stCEG-1.1.0/stCEG/man/edit_priors.Rd |only stCEG-1.1.0/stCEG/man/generate_CEG_map.Rd | 80 stCEG-1.1.0/stCEG/man/plot.ceg.Rd |only stCEG-1.1.0/stCEG/man/plot.ceg_map.Rd |only stCEG-1.1.0/stCEG/man/plot.event_tree.Rd |only stCEG-1.1.0/stCEG/man/plot.reduced_ceg.Rd |only stCEG-1.1.0/stCEG/man/plot.staged_tree.Rd |only stCEG-1.1.0/stCEG/man/plot.staged_tree_priors.Rd |only stCEG-1.1.0/stCEG/man/print.ceg.Rd |only stCEG-1.1.0/stCEG/man/print.ceg_map.Rd |only stCEG-1.1.0/stCEG/man/print.event_tree.Rd |only stCEG-1.1.0/stCEG/man/print.prior_table.Rd |only stCEG-1.1.0/stCEG/man/print.reduced_ceg.Rd |only stCEG-1.1.0/stCEG/man/print.staged_tree.Rd |only stCEG-1.1.0/stCEG/man/print.staged_tree_priors.Rd |only stCEG-1.1.0/stCEG/man/print.summary_ceg_map.Rd |only stCEG-1.1.0/stCEG/man/run_stceg.Rd | 67 stCEG-1.1.0/stCEG/man/specify_priors.Rd | 73 stCEG-1.1.0/stCEG/man/stCEG-package.Rd |only stCEG-1.1.0/stCEG/man/summary.ceg.Rd |only stCEG-1.1.0/stCEG/man/summary.ceg_map.Rd |only stCEG-1.1.0/stCEG/man/summary.compare_ceg_models.Rd |only stCEG-1.1.0/stCEG/man/summary.event_tree.Rd | 28 stCEG-1.1.0/stCEG/man/summary.prior_table.Rd |only stCEG-1.1.0/stCEG/man/summary.reduced_ceg.Rd |only stCEG-1.1.0/stCEG/man/summary.staged_tree.Rd | 49 stCEG-1.1.0/stCEG/man/summary.staged_tree_priors.Rd |only stCEG-1.1.0/stCEG/man/update_node_colours.Rd | 87 62 files changed, 5283 insertions(+), 4238 deletions(-)
Title: Estimation Methods for Causal Inference Based on Inverse
Probability Weighting and Doubly Robust Estimation
Description: Various estimators of causal effects based on inverse probability weighting, doubly robust estimation, and double machine learning. Specifically, the package includes methods for estimating average treatment effects, direct and indirect effects in causal mediation analysis, and dynamic treatment effects based on different identification strategies (unconfoundedness, instruments, difference-in-differences, regression discontinuity designs).
Author: Hugo Bodory [aut, cre] ,
Martin Huber [aut] ,
Jannis Kueck [aut]
Maintainer: Hugo Bodory <hugo.bodory@unisg.ch>
Diff between causalweight versions 1.1.5 dated 2026-06-08 and 1.1.6 dated 2026-09-25
DESCRIPTION | 12 MD5 | 52 - NAMESPACE | 66 + R/ATETDML.R | 1 R/c401k.R |only R/catehetDML.R |only R/detectIV.R |only R/didDML.R | 1 R/didcontDML.R | 13 R/didcontDMLpanel.R | 13 R/didmedDML.R |only R/didmedDMLpanel.R |only R/dyntreatDML.R | 13 R/functions.R | 1667 ++++++++++++++++++++++++++++++++--------- R/identificationDML.R | 265 +++--- R/medDML.R | 10 R/medqteDML.R |only R/paneltestDML.R | 203 ++-- R/testmedident.R | 1 R/treatDML.R | 3 R/treatcontDML.R |only R/treatselDML.R | 3 data/c401k.RData |only man/c401k.Rd |only man/catehetDML.Rd |only man/detectIV.Rd |only man/didcontDML.Rd | 4 man/didcontDMLpanel.Rd | 4 man/didmedDML.Rd |only man/didmedDMLpanel.Rd |only man/dyntreatDML.Rd | 9 man/medDML.Rd | 7 man/medqteDML.Rd |only man/predict.cw_superlearner.Rd |only man/treatcontDML.Rd |only 35 files changed, 1704 insertions(+), 643 deletions(-)
Title: Null Hypothesis Bayesian Response-Adaptive Randomization
Description: Implements Bayesian response-adaptive randomization methods based on Bayesian hypothesis testing for multi-arm settings (Pawel and Held, 2025, <doi:10.48550/arXiv.2510.01734>).
Author: Samuel Pawel [aut, cre]
Maintainer: Samuel Pawel <samuel.pawel@uzh.ch>
Diff between brar versions 0.1 dated 2026-03-06 and 0.1.1 dated 2026-09-25
DESCRIPTION | 14 +++++------ MD5 | 12 ++++----- NEWS.md | 6 ++++ R/brar_binomial.R | 40 +++++++++++++++++--------------- R/brar_normal.R | 38 +++++++++++++++++------------- man/brar_binomial.Rd | 63 +++++++++++++++++++++++++++++---------------------- man/brar_normal.Rd | 38 +++++++++++++++++------------- 7 files changed, 121 insertions(+), 90 deletions(-)
Title: Vasicek-Type Distributions and Regression Models
Description: Provides density, cumulative distribution, quantile, and
random generation functions for Vasicek-type distributions with standard
normal, standard logistic, and standard hyperbolic-secant kernels. The
normal-kernel distribution is parameterized by either its mean or a fixed
quantile, whereas the logistic- and hyperbolic-secant-kernel distributions
use fixed-quantile parameterizations. Zero-augmented, one-augmented, and
zero-and-one-augmented extensions of the normal-kernel mean
parameterization are also provided for responses that include boundary
values. The corresponding 'NVASIM', 'NVASIQ', 'LVASIQ', 'HVASIQ',
'ZANVASIM', 'OANVASIM', and 'ZOANVASIM' families are available for fitting
Generalized Additive Models for Location, Scale and Shape (GAMLSS),
as introduced by Rigby and Stasinopoulos (2005,
<doi:10.1111/j.1467-9876.2005.00510.x>). Two-part random-intercept
regression models for zero-augmented longitudinal responses are included
with either a beta or a normal-kernel Vasic [...truncated...]
Author: Josmar Mazucheli [aut, cre],
Bruna Alves [ctb]
Maintainer: Josmar Mazucheli <jmazucheli@gmail.com>
Diff between vasicekreg versions 1.1.0 dated 2026-08-20 and 1.3.0 dated 2026-09-25
vasicekreg-1.1.0/vasicekreg/tests/testthat/helper-global-tau.R |only vasicekreg-1.3.0/vasicekreg/DESCRIPTION | 43 - vasicekreg-1.3.0/vasicekreg/LICENSE | 4 vasicekreg-1.3.0/vasicekreg/MD5 | 101 +- vasicekreg-1.3.0/vasicekreg/NAMESPACE | 29 vasicekreg-1.3.0/vasicekreg/NEWS.md | 171 ++++ vasicekreg-1.3.0/vasicekreg/R/RcppExports.R | 44 - vasicekreg-1.3.0/vasicekreg/R/aep.R |only vasicekreg-1.3.0/vasicekreg/R/bodyfat.R | 43 - vasicekreg-1.3.0/vasicekreg/R/dpqr-01NvasicekM.R | 32 vasicekreg-1.3.0/vasicekreg/R/dpqr-0NvasicekM.R | 9 vasicekreg-1.3.0/vasicekreg/R/dpqr-1NvasicekM.R | 9 vasicekreg-1.3.0/vasicekreg/R/dpqr-HvasicekQ.R |only vasicekreg-1.3.0/vasicekreg/R/dpqr-LvasicekQ.R | 186 ++-- vasicekreg-1.3.0/vasicekreg/R/dpqr-NvasicekM.R | 17 vasicekreg-1.3.0/vasicekreg/R/dpqr-NvasicekQ.R | 182 ++-- vasicekreg-1.3.0/vasicekreg/R/please_microbiome.R |only vasicekreg-1.3.0/vasicekreg/R/transport.R |only vasicekreg-1.3.0/vasicekreg/R/trees.R |only vasicekreg-1.3.0/vasicekreg/R/utils.R | 14 vasicekreg-1.3.0/vasicekreg/R/vasicek-envelope.R |only vasicekreg-1.3.0/vasicekreg/R/vasicekreg-package.R | 205 +++-- vasicekreg-1.3.0/vasicekreg/R/zabr.R |only vasicekreg-1.3.0/vasicekreg/R/zabv_common.R |only vasicekreg-1.3.0/vasicekreg/R/zavr.R |only vasicekreg-1.3.0/vasicekreg/README.md | 380 ++++++++-- vasicekreg-1.3.0/vasicekreg/build/partial.rdb |binary vasicekreg-1.3.0/vasicekreg/build/vignette.rds |only vasicekreg-1.3.0/vasicekreg/data/aep.rda |only vasicekreg-1.3.0/vasicekreg/data/bodyfat.rda |binary vasicekreg-1.3.0/vasicekreg/data/please_microbiome.rda |only vasicekreg-1.3.0/vasicekreg/data/transport.rda |only vasicekreg-1.3.0/vasicekreg/data/trees.rda |only vasicekreg-1.3.0/vasicekreg/inst |only vasicekreg-1.3.0/vasicekreg/man/HVASIQ.Rd |only vasicekreg-1.3.0/vasicekreg/man/LVASIQ.Rd | 61 - vasicekreg-1.3.0/vasicekreg/man/NVASIM.Rd | 15 vasicekreg-1.3.0/vasicekreg/man/NVASIQ.Rd | 79 +- vasicekreg-1.3.0/vasicekreg/man/OANVASIM.Rd | 6 vasicekreg-1.3.0/vasicekreg/man/ZANVASIM.Rd | 6 vasicekreg-1.3.0/vasicekreg/man/ZOANVASIM.Rd | 27 vasicekreg-1.3.0/vasicekreg/man/aep.Rd |only vasicekreg-1.3.0/vasicekreg/man/bodyfat.Rd | 43 - vasicekreg-1.3.0/vasicekreg/man/please_microbiome.Rd |only vasicekreg-1.3.0/vasicekreg/man/transport.Rd |only vasicekreg-1.3.0/vasicekreg/man/trees.Rd |only vasicekreg-1.3.0/vasicekreg/man/vasicek_envelope.Rd |only vasicekreg-1.3.0/vasicekreg/man/vasicekreg-package.Rd | 202 +++-- vasicekreg-1.3.0/vasicekreg/man/zabr.Rd |only vasicekreg-1.3.0/vasicekreg/man/zavr.Rd |only vasicekreg-1.3.0/vasicekreg/src/HvasicekQ.cpp |only vasicekreg-1.3.0/vasicekreg/src/LvasicekQ.cpp | 38 - vasicekreg-1.3.0/vasicekreg/src/NvasicekQ.cpp | 42 - vasicekreg-1.3.0/vasicekreg/src/RcppExports.cpp | 121 ++- vasicekreg-1.3.0/vasicekreg/tests/testthat.R | 8 vasicekreg-1.3.0/vasicekreg/tests/testthat/test-augmented-dpqr.R |only vasicekreg-1.3.0/vasicekreg/tests/testthat/test-data-augmented.R |only vasicekreg-1.3.0/vasicekreg/tests/testthat/test-derivatives.R | 126 +-- vasicekreg-1.3.0/vasicekreg/tests/testthat/test-dpqr.R | 60 + vasicekreg-1.3.0/vasicekreg/tests/testthat/test-families.R | 174 +--- vasicekreg-1.3.0/vasicekreg/tests/testthat/test-fixed-quantile.R |only vasicekreg-1.3.0/vasicekreg/tests/testthat/test-hvasicek.R |only vasicekreg-1.3.0/vasicekreg/tests/testthat/test-moments.R |only vasicekreg-1.3.0/vasicekreg/tests/testthat/test-quantile-derivative-grid.R |only vasicekreg-1.3.0/vasicekreg/tests/testthat/test-vasicek-envelope.R |only vasicekreg-1.3.0/vasicekreg/tests/testthat/test-zabr-zavr-integration.R |only vasicekreg-1.3.0/vasicekreg/vignettes |only 67 files changed, 1623 insertions(+), 854 deletions(-)
Title: Wrapper for Interactive and Static Data Visualization
Description: Provides a fast and consistent general-purpose wrapper for arranging
microdata and generating interactive and static visualizations. Offers a
library of graphical functions with a highly configurable and simple syntax.
Features include HTML tables, time series, bar and pie charts, and maps
supported by various JavaScript libraries. Allows seamless transitions
between interactive and static graphics without changing the core syntax.
Originally developed to standardize the publication of official statistics
at the National University of Colombia <https://unal.edu.co>. Spanish:
Proporciona una herramienta de propósito general rápida y consistente para
organizar microdatos y generar visualizaciones interactivas y estáticas.
Ofrece una biblioteca de funciones gráficas con una sintaxis simple y
altamente configurable. Permite transiciones fluidas entre gráficos
interactivos y estáticos sin cambiar la sintaxis base. Desarrollado
originalmente para estandarizar la publicación de estadíst [...truncated...]
Author: Jeison Alarcon [aut, cre, ctr] ,
Alberto Rodriguez [aut, rev],
Direccion Nacional de Planeacion y Estadistica Universidad Nacional de
Colombia [cph, fnd]
Maintainer: Jeison Alarcon <jmalarconbe@unal.edu.co>
This is a re-admission after prior archival of version 1.0.1 dated 2025-09-18
Diff between UnalR versions 1.0.1 dated 2025-09-18 and 1.0.2 dated 2026-09-25
DESCRIPTION | 56 +- MD5 | 39 - NAMESPACE | 252 +++++---- NEWS.md | 16 R/Agregar.R | 4 R/Plot_Boxplot.R | 2 R/Plot_Mapa.R | 33 - R/Plot_Mundo.R | 13 R/Plot_Series.R | 9 R/Tabla.R | 1294 ++++++++++++++++++++++++------------------------- R/Tabla_General.R | 480 +++++++++--------- R/leaflet_plugins.R |only inst/COPYRIGHTS |only inst/htmlwidgets |only man/Plot.Histograma.Rd | 2 man/Plot.Mapa.Rd | 13 man/Plot.Mundo.Rd | 9 man/Plot.Series.Rd | 8 man/Tabla.General.Rd | 2 man/Tabla.Rd | 2 20 files changed, 1144 insertions(+), 1090 deletions(-)
Title: Prior-Data Fitted Network Foundational Model for Tabular Data
Description: Provides a consistent API for classification and regression models
based on the 'TabPFN' model of Hollmann et al. (2025), "Accurate predictions
on small data with a tabular foundation model," Nature, 637(8045)
<doi:10.1038/s41586-024-08328-6>. The calculations are served via 'Python'
to train and predict the model.
Author: Max Kuhn [aut, cre] ,
Edgar Ruiz [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between tabpfn versions 0.3.0 dated 2026-09-01 and 0.4.0 dated 2026-09-25
DESCRIPTION | 10 - MD5 | 44 +++--- NEWS.md | 18 ++ R/TabPFN-fit.R | 213 ++++++++++++++++++++++---------- R/TabPFN-predict.R | 20 +-- R/control.R | 10 - R/install.R | 44 ++++++ R/misc.R | 134 +++++++++++++------- R/zzz.R | 16 ++ README.md | 42 ++---- build/partial.rdb |binary inst/WORDLIST | 4 man/control_tab_pfn.Rd | 10 - man/figures/README-boundaries-1.png |binary man/install_tabpfn.Rd | 42 ++++++ man/tab_pfn.Rd | 101 ++++++++++----- man/tabpfn-package.Rd | 1 tests/testthat/_snaps/classification.md | 8 - tests/testthat/_snaps/regression.md | 8 - tests/testthat/setup.R | 13 + tests/testthat/teardown.R | 13 + tests/testthat/test-TabPFN-fit.R | 210 +++++++++++++++++++++++++------ tests/testthat/test-misc.R | 31 ++++ 23 files changed, 730 insertions(+), 262 deletions(-)
Title: Miscellaneous Functions for Southwest Fisheries Science Center
Description: Collection of conversion, analytical, geodesic, mapping, and
plotting functions. Used to support packages and code written by
researchers at the Southwest Fisheries Science Center of the National
Oceanic and Atmospheric Administration.
Author: Eric Archer [aut, cre]
Maintainer: Eric Archer <eric.ivan.archer@gmail.com>
Diff between swfscMisc versions 1.7 dated 2025-06-04 and 1.7.6 dated 2026-09-25
DESCRIPTION | 10 +-- MD5 | 22 ++++---- NAMESPACE | 44 +++++++++------- R/destination.R | 2 R/distSmry.R | 8 +-- R/ggBiplot.R | 135 ++++++++++++++++++++++++++++++++++------------------ R/plotAssignments.R | 6 +- README.md | 6 ++ man/destination.Rd | 2 man/distSmry.Rd | 4 - man/ggBiplot.Rd | 30 ++++++++--- man/swfscMisc.Rd | 5 + 12 files changed, 175 insertions(+), 99 deletions(-)
Title: Kriging Models using the 'libKriging' Library
Description: Interface to 'libKriging' 'C++' library <https://github.com/libKriging> that should
provide most standard Kriging / Gaussian process regression features
(like in 'DiceKriging', 'kergp' or 'RobustGaSP' packages).
'libKriging' relies on Armadillo linear algebra library (Apache 2 license) by Conrad Sanderson,
'lbfgsb_cpp' is a 'C++' port around by Pascal Have of 'lbfgsb' library (BSD-3 license) by
Ciyou Zhu, Richard Byrd, Jorge Nocedal and Jose Luis Morales used for hyperparameters optimization.
Author: Yann Richet [aut, cre] ,
Pascal Have [aut],
Yves Deville [aut],
Conrad Sanderson [ctb],
Ciyou Zhu [ctb],
Richard Byrd [ctb],
Jorge Nocedal [ctb],
Jose Luis Morales [ctb],
Mike Smith [ctb]
Maintainer: Yann Richet <yann.richet@asnr.fr>
Diff between rlibkriging versions 1.2-2 dated 2026-09-23 and 1.2-3 dated 2026-09-25
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NEWS.md | 11 +++++++++++ cleanup | 10 ++++++---- cleanup.win | 10 ++++++---- src/Makevars | 7 ++++++- src/libK/CHANGELOG.md | 6 ++++++ src/libK/cmake/update_version.sh | 2 +- src/libK/tools/common/before_script.sh | 2 +- src/libK/tools/linux-macos/install.sh | 2 +- src/libK/tools/linux-macos/loadenv.sh | 6 +++--- src/libK/tools/linux-macos/test.sh | 2 +- tools/gitmodules-shas | 2 +- tools/setup.sh | 7 +++++++ 14 files changed, 67 insertions(+), 34 deletions(-)
Title: R Commander
Description: A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut],
Milan Bouchet-Valat [aut],
Manuel Munoz-Marquez [aut, cre],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Vilmantas Gegzna [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ct [...truncated...]
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Diff between Rcmdr versions 2.14.1 dated 2026-09-16 and 2.15.0 dated 2026-09-25
DESCRIPTION | 12 MD5 | 43 - NAMESPACE | 3 NEWS | 10 R/Commander-es.R |only R/Rcmdr-package.R | 4 R/commander.R | 357 ++++++++++++ R/sigma-test.R |only build/partial.rdb |only inst/doc/Commander-ru.pdf |binary inst/doc/Empezando-con-Rcmdr-es.pdf |binary inst/doc/Getting-Started-with-the-Rcmdr-ja.pdf |binary inst/doc/Getting-Started-with-the-Rcmdr-ko.pdf |binary inst/doc/Getting-Started-with-the-Rcmdr.pdf |binary inst/etc/Rcmdr-menus.txt | 6 inst/po/es/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/sl/LC_MESSAGES/R-Rcmdr.mo |binary man/Commander-es.Rd | 287 +++++----- man/Commander.Rd | 693 ++++++++++--------------- man/Rcmdr-package.Rd | 4 man/sigma.test.Rd |only man/sigmaTestMenu.Rd |only po/R-Rcmdr.pot | 18 po/R-es.po | 319 +++++++---- po/R-sl.po | 20 25 files changed, 1092 insertions(+), 684 deletions(-)
Title: Parametric Modal ARIMA and Seasonal ARIMA Models using the SKD
Family
Description: Implements parametric modal Autoregressive Integrated Moving Average (ARIMA) and seasonal ARIMA (SARIMA) models utilizing the Skewed Distribution (SKD) family, in which the conditional mode, rather than the conditional mean, follows the (seasonal) ARIMA recursion. Current distributions supported are the Skew-Normal, Skewed Student-t, and Skewed Laplace. The parameters are estimated by maximum likelihood using analytical gradients. Includes residual diagnostics, simulation envelopes, automatic order selection, joint and marginal modal forecasts, exact and parametric bootstrap prediction intervals, and classical asymptotic inference via the Fisher Information matrix. Methods are described in Galarza, C.E., Lachos, V.H., Cabral, C.R.B., & Castro, L.M. (2017) <doi:10.1002/sta4.140>.
Author: Christian Galarza [aut, cre],
Sergio Luis Mercado Londono [ctb],
Victor Hugo Lachos [ctb]
Maintainer: Christian Galarza <chedgala@espol.edu.ec>
Diff between ModalForecast versions 0.1.0 dated 2026-05-12 and 0.2.0 dated 2026-09-25
ModalForecast-0.1.0/ModalForecast/inst |only ModalForecast-0.2.0/ModalForecast/DESCRIPTION | 25 ModalForecast-0.2.0/ModalForecast/MD5 | 44 ModalForecast-0.2.0/ModalForecast/NAMESPACE | 9 ModalForecast-0.2.0/ModalForecast/NEWS.md | 74 + ModalForecast-0.2.0/ModalForecast/R/ModalForecast-package.R |only ModalForecast-0.2.0/ModalForecast/R/auto_modal_arima.R | 194 +-- ModalForecast-0.2.0/ModalForecast/R/core.R |only ModalForecast-0.2.0/ModalForecast/R/diagnostics.R | 418 +++--- ModalForecast-0.2.0/ModalForecast/R/methods.R | 226 +-- ModalForecast-0.2.0/ModalForecast/R/modal_arima.R | 631 +++------- ModalForecast-0.2.0/ModalForecast/R/predict.R | 441 +++--- ModalForecast-0.2.0/ModalForecast/R/skd.R |only ModalForecast-0.2.0/ModalForecast/README.md | 56 ModalForecast-0.2.0/ModalForecast/build |only ModalForecast-0.2.0/ModalForecast/man/ModalForecast-package.Rd |only ModalForecast-0.2.0/ModalForecast/man/auto.modal.arima.Rd | 169 +- ModalForecast-0.2.0/ModalForecast/man/diagnostics.Rd | 91 - ModalForecast-0.2.0/ModalForecast/man/envelope.Rd | 76 - ModalForecast-0.2.0/ModalForecast/man/figures/air_forecast.png |only ModalForecast-0.2.0/ModalForecast/man/fit_modal_arima.Rd | 183 +- ModalForecast-0.2.0/ModalForecast/man/forecast.modal_arima.Rd | 139 +- ModalForecast-0.2.0/ModalForecast/man/predict.modal_arima.Rd |only ModalForecast-0.2.0/ModalForecast/tests/testthat/helper-sim.R |only ModalForecast-0.2.0/ModalForecast/tests/testthat/test-distributions.R |only ModalForecast-0.2.0/ModalForecast/tests/testthat/test-fit.R |only ModalForecast-0.2.0/ModalForecast/tests/testthat/test-forecast.R |only ModalForecast-0.2.0/ModalForecast/tests/testthat/test-gradient.R |only ModalForecast-0.2.0/ModalForecast/tests/testthat/test-main.R | 32 ModalForecast-0.2.0/ModalForecast/tests/testthat/test-methods.R |only 30 files changed, 1362 insertions(+), 1446 deletions(-)
Title: Fast Stratified Descriptive Figures with a Point-and-Click GUI
Description: A point-and-click 'shiny' interface for the descriptive analysis
that comes before any model is chosen. Pass a data frame, pick the
variable to describe, and add the layers you want to see it within: a
second variable becomes the panels of a 'ggplot2' facet_wrap(), and
further variables become separate figures, one file each, taken either one
variable at a time or crossed. Every stratum is reported with the number
of observations behind it, on the figure and on each of its panels; strata
that contain none are listed rather than dropped, and rows with a missing
value in a layer variable are excluded and counted. A continuous variable
can be categorized into quantile groups, equal-width bins or user-supplied
cut points, a variable of any type can be turned into whether it is
missing or observed, so that the rows a layer would exclude become a
stratum of their own, and a date or date-time variable can be read at a
chosen resolution, either as a calendar period or as a position in the
year [...truncated...]
Author: Akihiro Shiroshita [aut, cre, cph],
Yuki Kataoka [aut]
Maintainer: Akihiro Shiroshita <akihirokun8@gmail.com>
Diff between ggstratify versions 0.0.1 dated 2026-09-02 and 0.2.0 dated 2026-09-25
DESCRIPTION | 34 MD5 | 54 - NAMESPACE | 1 NEWS.md | 210 +++++ R/app_launch.R | 395 +++++----- R/app_server.R | 1319 +++++++++++++++++++---------------- R/app_ui.R | 200 ++++- R/categorize.R | 545 +++++++++----- R/codegen.R | 789 ++++++++++++++++++++- R/data.R | 128 ++- R/data_utils.R | 1431 +++++++++++++++++++++++---------------- R/globals.R | 48 - R/spec.R | 519 +++++++++++++- README.md | 244 ++++-- data/epi_cohort.rda |binary inst/CITATION |only inst/doc/ggstratify.R | 81 ++ inst/doc/ggstratify.Rmd | 672 +++++++++++++----- inst/doc/ggstratify.html | 312 +++++++- man/epi_cohort.Rd | 152 ++-- man/ggstratify-package.Rd | 62 - man/ggstratify.Rd | 303 ++++---- tests/testthat/test-app.R | 498 +++++++++++++ tests/testthat/test-categorize.R | 680 +++++++++++++----- tests/testthat/test-codegen.R | 591 ++++++++++++++++ tests/testthat/test-data_utils.R | 940 ++++++++++++++----------- tests/testthat/test-spec.R | 172 +++- tests/testthat/test-weights.R |only vignettes/ggstratify.Rmd | 672 +++++++++++++----- 29 files changed, 7932 insertions(+), 3120 deletions(-)
Title: Neighbour Balanced Block Designs (NBBDesigns)
Description: Neighbour-balanced designs ensure that no treatment is disadvantaged unfairly by its surroundings. The treatment allocation in these designs is such that every treatment appears equally often as a neighbour with every other treatment. Neighbour Balanced Designs are employed when there is a possibility of neighbour effects from treatments used in adjacent experimental units. In the literature, a vast number of such designs have been developed. This package generates some efficient neighbour balanced block designs which are balanced and partially variance balanced for estimating the contrast pertaining to direct and neighbour effects, as well as provides a function for analysing the data obtained from such trials (Azais, J.M., Bailey, R.A. and Monod, H. (1993). "A catalogue of efficient neighbour designs with border plots". Biometrics, 49, 1252-1261 ; Tomar, J. S., Jaggi, Seema and Varghese, Cini (2005)<DOI: 10.1080/0266476042000305177>. "On totally balanced block designs for compe [...truncated...]
Author: Eldho Varghese [aut, ctb],
Ashutosh Dalal [aut, cre],
Seema Jaggi [aut, ctb],
Arpan Bhowmik [aut],
Cini Varghese [aut]
Maintainer: Ashutosh Dalal <ashutosh.dalal97@gmail.com>
Diff between NBBDesigns versions 1.1.0 dated 2023-12-16 and 1.2.0 dated 2026-09-25
DESCRIPTION | 8 +++--- MD5 | 10 ++++---- NAMESPACE | 3 ++ R/NBBDesigns.R | 65 ++++++++++++++++++++++++++++++++++++----------------- man/anlys.Rd | 30 +++++++++++++++++------- man/sample_data.Rd | 5 ---- 6 files changed, 80 insertions(+), 41 deletions(-)
Title: Fit Two-Component Normal and Lognormal Mixture Models
Description: Fits, bootstraps, and evaluates two-component normal and lognormal
mixture models. Parameters are searched within data-derived bounds by
differential-evolution global optimization, as implemented in the 'DEoptim'
package (Mullen, Ardia, Gil, Windover and Cline, 2011)
<doi:10.18637/jss.v040.i06>, followed by a local 'L-BFGS-B' refinement step
via optim(). Also provides preliminary diagnostic plots, diagnostic plots
for fitted mixtures, automatic normal-versus-lognormal model selection by
the Bayesian or Akaike information criterion, 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 0.2.0 dated 2026-08-02 and 0.3.0 dated 2026-09-25
DESCRIPTION | 31 +- MD5 | 67 +++-- NAMESPACE | 61 +++-- NEWS.md | 77 ++++++ R/bootstrap.R | 152 ++++++++++--- R/core_fit.R | 208 +++++++++++++----- R/demulti.R | 48 +++- R/evaluate_init.R | 50 ++-- R/fit.R | 44 +++ R/imports.R | 2 R/loglikelihoods.R | 58 +++-- R/methods.R | 78 ++++++ R/plot.R | 36 ++- R/selection.R | 68 ++++-- R/utils.R | 215 +++++++++++++++++-- build/vignette.rds |binary inst/doc/introduction.R | 13 - inst/doc/introduction.Rmd | 174 ++++++++++++--- inst/doc/introduction.html | 407 ++++++++++++++++++++++++------------ man/bootstrap_mix2.Rd | 61 ++++- man/dot-fit_mix2_core.Rd | 52 +++- man/evaluate_init.Rd | 15 - man/fit_lognorm2.Rd | 26 +- man/fit_norm2.Rd | 24 +- man/mix2_bounds.Rd |only man/plot.demixr_fit.Rd | 17 + man/prelim_plots.Rd | 9 man/select_best_mixture.Rd | 36 ++- tests/testthat/test-bootstrap.R | 84 ++++++- tests/testthat/test-evaluate-init.R | 8 tests/testthat/test-fit.R | 107 ++++++++- tests/testthat/test-likelihood.R |only tests/testthat/test-plot.R | 18 + tests/testthat/test-selection.R | 26 ++ tests/testthat/test-validation.R |only vignettes/introduction.Rmd | 174 ++++++++++++--- 36 files changed, 1928 insertions(+), 518 deletions(-)
Title: Linear Networks Functionality of the 'spatstat' Family
Description: Defines types of spatial data on a linear network
and provides functionality for geometrical operations,
data analysis and modelling of data on a linear network,
in the 'spatstat' family of packages.
Contains definitions and support for linear networks, including creation of networks, geometrical measurements, topological connectivity, geometrical operations such as inserting and deleting vertices, intersecting a network with another object, and interactive editing of networks.
Data types defined on a network include point patterns, pixel images, functions, and tessellations.
Exploratory methods include kernel estimation of intensity on a network, K-functions and pair correlation functions on a network, simulation envelopes, nearest neighbour distance and empty space distance, relative risk estimation with cross-validated bandwidth selection. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Mont [...truncated...]
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Greg McSwiggan [aut, cph],
Tilman Davies [ctb, cph],
Mehdi Moradi [ctb, cph],
Suman Rakshit [ctb, cph],
Ottmar Cronie [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.linnet versions 3.5-3 dated 2026-07-30 and 3.5-4 dated 2026-09-25
DESCRIPTION | 16 +- MD5 | 20 +-- NAMESPACE | 5 NEWS | 26 ++++ R/relrisk.lpp.R | 221 +++++++++++++++++++++++++++++++++------- R/transectlinim.R |only inst/doc/packagesizes.txt | 2 inst/info/packagesizes.txt | 2 man/relrisk.lpp.Rd | 29 ++++- man/spatstat.linnet-internal.Rd | 4 man/transect.linim.Rd |only tests/testsL.R | 23 +++- 12 files changed, 287 insertions(+), 61 deletions(-)
More information about spatstat.linnet at CRAN
Permanent link
Title: Cluster Analysis via Random Partition Distributions
Description: Cluster analysis is performed using pairwise distance information and a random partition distribution. The method is
implemented for two random partition distributions. It draws samples and then obtains and plots clustering estimates.
An implementation of a selection algorithm is provided for the mass parameter of the partition distribution. Since
pairwise distances are the principal input to this procedure, it is most comparable to the hierarchical and k-medoids
clustering methods. The method is Dahl, Andros, Carter (2022+) <doi:10.1002/sam.11602>.
Author: David B. Dahl [aut, cre] ,
R. Jacob Andros [aut] ,
J. Brandon Carter [aut] ,
Authors of the dependency Rust crates [ctb]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between caviarpd versions 0.3.22 dated 2026-03-07 and 0.3.25 dated 2026-09-25
caviarpd-0.3.22/caviarpd/src/abort_shim.c |only caviarpd-0.3.22/caviarpd/src/shim.c |only caviarpd-0.3.25/caviarpd/DESCRIPTION | 12 caviarpd-0.3.25/caviarpd/LICENSE | 2 caviarpd-0.3.25/caviarpd/MD5 | 52 +-- caviarpd-0.3.25/caviarpd/NEWS | 13 caviarpd-0.3.25/caviarpd/build/partial.rdb |binary caviarpd-0.3.25/caviarpd/src/Makevars.win.in | 12 caviarpd-0.3.25/caviarpd/src/r_init_shim.c |only caviarpd-0.3.25/caviarpd/src/rust/Cargo.lock | 190 ++++------- caviarpd-0.3.25/caviarpd/src/rust/Cargo.toml | 12 caviarpd-0.3.25/caviarpd/src/rust/build.rs | 12 caviarpd-0.3.25/caviarpd/src/rust/epa/Cargo.lock | 137 ++------ caviarpd-0.3.25/caviarpd/src/rust/epa/Cargo.toml | 5 caviarpd-0.3.25/caviarpd/src/rust/epa/src/clust.rs | 20 - caviarpd-0.3.25/caviarpd/src/rust/epa/src/epa.rs | 4 caviarpd-0.3.25/caviarpd/src/rust/rbindings/Cargo.lock | 2 caviarpd-0.3.25/caviarpd/src/rust/rbindings/Cargo.toml | 5 caviarpd-0.3.25/caviarpd/src/rust/rbindings/src/lib.rs | 225 ++++++-------- caviarpd-0.3.25/caviarpd/src/rust/roxido/Cargo.lock | 6 caviarpd-0.3.25/caviarpd/src/rust/roxido/Cargo.toml | 5 caviarpd-0.3.25/caviarpd/src/rust/roxido/src/lib.rs | 130 ++++---- caviarpd-0.3.25/caviarpd/src/rust/roxido_macro/Cargo.lock | 2 caviarpd-0.3.25/caviarpd/src/rust/roxido_macro/Cargo.toml | 5 caviarpd-0.3.25/caviarpd/src/rust/roxido_macro/src/lib.rs | 4 caviarpd-0.3.25/caviarpd/src/rust/src/lib.rs | 13 caviarpd-0.3.25/caviarpd/src/rust/vendor.tar.xz |binary caviarpd-0.3.25/caviarpd/src/shims.c |only caviarpd-0.3.25/caviarpd/tools/configure.R | 195 +++++++++--- 29 files changed, 537 insertions(+), 526 deletions(-)