Title: Simple Definition Of Time Intervals
Description: Simple definition of time intervals for the current, previous, and next week, month, quarter and year.
Author: Alexey Seleznev [aut, cre]
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between timeperiodsR versions 0.7.7 dated 2026-05-12 and 0.7.9 dated 2026-10-16
DESCRIPTION | 9 ++- MD5 | 32 ++++++++----- NEWS.md | 15 +++++- R/check_dayoffs.R | 111 ++++++++++++++++++++++++------------------------ R/custom_period.R | 21 ++++++--- R/methods.R | 59 ++++++++++--------------- R/operators.R | 2 build/partial.rdb |binary inst/doc/tpr_intro.R | 8 +-- inst/doc/tpr_intro.Rmd | 4 - inst/doc/tpr_intro.html | 80 +++++++++++++++++----------------- man/check_dayoffs.Rd | 4 + tests |only vignettes/tpr_intro.Rmd | 4 - 14 files changed, 185 insertions(+), 164 deletions(-)
Title: Use Images in 'ggplot2'
Description: Supports image files and graphic objects to be visualized in
'ggplot2' graphic system. Images can be drawn at data points, used as the
background of a plot, or embedded as a sub-plot, and can be read from local
files or downloaded from remote services such as 'Pokemon', 'PhyloPic', and
emoji and icon collections. An interactive geom is provided for 'HTML'
output.
Author: Guangchuang Yu [aut, cre, cph] ,
Shuangbin Xu [ctb] ,
Yonghe Xia [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggimage versions 0.3.7 dated 2026-10-14 and 0.3.8 dated 2026-10-16
DESCRIPTION | 6 - MD5 | 25 ++--- NAMESPACE | 1 R/draw_key.R | 48 ++++++++-- R/geom_image.R | 143 +++++++++++++++++++++++++++---- R/ggpreview.R | 21 ++++ R/image_read2.R | 4 tests/testthat/helper-delegates.R |only tests/testthat/test-draw-key.R | 32 ++++++ tests/testthat/test-geom-image-cache.R | 62 +++++++++++++ tests/testthat/test-geom-subview-cache.R | 24 +++++ tests/testthat/test-ggpreview.R | 38 +++++++- tests/testthat/test-image-file-readers.R | 18 ++- tests/testthat/test-image-read2.R | 8 - 14 files changed, 377 insertions(+), 53 deletions(-)
Title: Ethnobotanical Analysis, Decision-Framing, and TEK Modeling
Description: Tools for quantifying Traditional Ecological Knowledge (TEK), modeling TEK in decision frameworks, and designing structured decision-framing exercises in conservation and development contexts. The package implements quantitative ethnobotany indices (Use Value, Relative Frequency of Citation, etc.) but positions them within a larger framework of Bayesian modeling and participatory decision analysis. Includes critical assessment of indices' limitations and case studies of participatory workshops.
Author: Cory Whitney [aut, cre]
Maintainer: Cory Whitney <whitney.cory@gmail.com>
Diff between ethnobotanyR versions 0.2.0 dated 2026-02-25 and 0.3.0 dated 2026-10-16
DESCRIPTION | 18 MD5 | 79 + NAMESPACE | 3 NEWS.md | 149 +-- R/ethno_bayes_consensus.R | 130 +- R/ethno_beta.R |only R/ethno_boot.R | 20 R/ethno_consensus.R |only R/ethno_saturation.R |only R/homegardens.R |only README.md | 48 - build/partial.rdb |binary build/vignette.rds |binary data/homegardens.rda |only data/homegardens_info.rda |only data/homegardens_species.rda |only inst/doc/TEK_modeling_vignette.R | 180 ++-- inst/doc/TEK_modeling_vignette.Rmd | 209 ++-- inst/doc/TEK_modeling_vignette.html | 805 +++++++++--------- inst/doc/benin_case_study.html | 4 inst/doc/decision_framing_guide.html | 4 inst/doc/ethnobotanyR_modeling_vignette.R | 200 ++-- inst/doc/ethnobotanyR_modeling_vignette.Rmd | 263 ++--- inst/doc/ethnobotanyR_modeling_vignette.html | 681 ++++++--------- inst/doc/ethnobotanyr_decision_framing_practical.html | 16 inst/doc/ethnobotanyr_vignette.R | 41 inst/doc/ethnobotanyr_vignette.Rmd | 41 inst/doc/ethnobotanyr_vignette.html | 98 +- inst/doc/honest_ethnobotany.R | 4 inst/doc/honest_ethnobotany.Rmd | 6 inst/doc/honest_ethnobotany.html | 14 man/ethno_bayes_consensus.Rd | 8 man/ethno_beta.Rd |only man/ethno_boot.Rd | 11 man/ethno_consensus.Rd |only man/ethno_saturation.Rd |only man/homegardens.Rd |only man/homegardens_info.Rd |only man/homegardens_species.Rd |only tests |only vignettes/TEK_modeling_vignette.Rmd | 209 ++-- vignettes/ethnobotanyR_modeling_vignette.Rmd | 263 ++--- vignettes/ethnobotanyr_vignette.Rmd | 41 vignettes/honest_ethnobotany.Rmd | 6 vignettes/references/ethnobotanyR.bib | 14 vignettes/references/model_packages.bib | 104 -- vignettes/references/packages.bib | 99 -- 47 files changed, 1827 insertions(+), 1941 deletions(-)
Title: Fitting Tails by the Empirical Residual Coefficient of Variation
Description: Provides a methodology simple and trustworthy for the analysis of extreme values and multiple threshold tests for a generalized Pareto distribution, together
with an automatic threshold selection algorithm. See del Castillo, J, Daoudi, J and Lockhart, R (2014) <doi:10.1111/sjos.12037>.
Author: Joan del Castillo [aut],
David Morina Soler [aut],
Isabel Serra [aut],
Sergi Vilardell [cre]
Maintainer: Sergi Vilardell <sergi.vilardell13@gmail.com>
Diff between ercv versions 1.0.1 dated 2019-10-15 and 1.0.2 dated 2026-10-16
DESCRIPTION | 23 ++++- MD5 | 26 +++--- R/ccdfplot.R | 2 R/confint.fitpot.R | 2 R/cvplot.R | 2 R/egpd.R | 4 - R/fitpot.R | 2 R/print.fitpot.R | 2 R/thrselect.R | 2 man/Tm.Rd | 176 ++++++++++++++++++++++---------------------- man/cvplot.Rd | 179 ++++++++++++++++++++++---------------------- man/fitpot.Rd | 154 +++++++++++++++++++------------------- man/tdata.Rd | 120 +++++++++++++++--------------- man/thrselect.Rd | 211 ++++++++++++++++++++++++++--------------------------- 14 files changed, 460 insertions(+), 445 deletions(-)
Title: Embedded Conic Solver in R
Description: R interface to the Embedded COnic Solver (ECOS), an efficient
and robust C library for convex problems. Conic and equality
constraints can be specified in addition to integer and
boolean variable constraints for mixed-integer problems. This
R interface is inspired by the python interface and has
similar calling conventions.
Author: Anqi Fu [aut],
Balasubramanian Narasimhan [aut, cre],
Florian Schwendinger [ctb],
Martin Maechler [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>
Diff between ECOSolveR versions 0.6 dated 2026-02-18 and 0.6.2 dated 2026-10-16
DESCRIPTION | 10 ++++----- MD5 | 28 ++++++++++++------------- NAMESPACE | 2 + NEWS.md | 14 +++++++++--- R/ecos.R | 2 + README.md | 41 ++++++++++++++++++------------------- build/vignette.rds |binary inst/doc/examples.Rmd | 24 ++++++++++++++------- inst/doc/examples.html | 33 ++++++++++++++++++----------- man/ECOSolveR-package.Rd | 1 src/ecos/ecos_bb/ecos_bb.c | 4 +-- src/ecos/ecos_bb/ecos_bb_preproc.c | 4 +-- src/ecos/include/ecos_bb.h | 6 ++--- src/ecosolve.c | 13 +++++++---- vignettes/examples.Rmd | 24 ++++++++++++++------- 15 files changed, 122 insertions(+), 84 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-03-30 0.1.1
2026-01-27 0.1.0
Title: Visualize Probability Distributions
Description: Visualize and compute percentiles/probabilities of normal, t, f, chi square
and binomial distributions.
Author: Aravind Hebbali [aut, cre]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Diff between vistributions versions 0.2.0 dated 2024-11-07 and 0.2.1 dated 2026-10-16
vistributions-0.2.0/vistributions/man/figures/README-binom-1.png |only vistributions-0.2.0/vistributions/man/figures/README-normal-1.png |only vistributions-0.2.0/vistributions/man/figures/README-normal-2.png |only vistributions-0.2.0/vistributions/man/figures/README-normal-3.png |only vistributions-0.2.0/vistributions/man/vdist_t.Rd |only vistributions-0.2.0/vistributions/tests/figs |only vistributions-0.2.1/vistributions/DESCRIPTION | 13 vistributions-0.2.1/vistributions/MD5 | 155 -- vistributions-0.2.1/vistributions/NAMESPACE | 5 vistributions-0.2.1/vistributions/NEWS.md | 44 vistributions-0.2.1/vistributions/R/vdist-app.R | 7 vistributions-0.2.1/vistributions/R/vdist-binomial.R | 14 vistributions-0.2.1/vistributions/R/vdist-chisquare.R | 12 vistributions-0.2.1/vistributions/R/vdist-data-prep.R | 84 - vistributions-0.2.1/vistributions/R/vdist-f.R | 15 vistributions-0.2.1/vistributions/R/vdist-normal.R | 6 vistributions-0.2.1/vistributions/R/vdist-plots.R | 30 vistributions-0.2.1/vistributions/R/vdist-t.R | 16 vistributions-0.2.1/vistributions/R/vdist-utils.R | 14 vistributions-0.2.1/vistributions/R/zzz.R | 29 vistributions-0.2.1/vistributions/README.md | 171 ++ vistributions-0.2.1/vistributions/build/vignette.rds |binary vistributions-0.2.1/vistributions/inst/doc/introduction-to-vistributions.R | 72 vistributions-0.2.1/vistributions/inst/doc/introduction-to-vistributions.Rmd | 744 +++++----- vistributions-0.2.1/vistributions/inst/doc/introduction-to-vistributions.html | 93 - vistributions-0.2.1/vistributions/man/figures/README-binom-plot-1.png |only vistributions-0.2.1/vistributions/man/figures/README-binom-plot-2.png |only vistributions-0.2.1/vistributions/man/figures/README-binom-plot-3.png |only vistributions-0.2.1/vistributions/man/figures/README-chisquare-plot-1.png |only vistributions-0.2.1/vistributions/man/figures/README-chisquare-plot-2.png |only vistributions-0.2.1/vistributions/man/figures/README-chisquare-plot-3.png |only vistributions-0.2.1/vistributions/man/figures/README-composable-1.png |only vistributions-0.2.1/vistributions/man/figures/README-f-plot-1.png |only vistributions-0.2.1/vistributions/man/figures/README-f-plot-2.png |only vistributions-0.2.1/vistributions/man/figures/README-f-plot-3.png |only vistributions-0.2.1/vistributions/man/figures/README-normal-plot-1.png |only vistributions-0.2.1/vistributions/man/figures/README-normal-plot-2.png |only vistributions-0.2.1/vistributions/man/figures/README-normal-plot-3.png |only vistributions-0.2.1/vistributions/man/figures/README-t-plot-1.png |only vistributions-0.2.1/vistributions/man/figures/README-t-plot-2.png |only vistributions-0.2.1/vistributions/man/figures/README-t-plot-3.png |only vistributions-0.2.1/vistributions/man/figures/logo.png |only vistributions-0.2.1/vistributions/man/vdist_binom_plot.Rd | 10 vistributions-0.2.1/vistributions/man/vdist_chisquare_plot.Rd | 4 vistributions-0.2.1/vistributions/man/vdist_f_plot.Rd | 8 vistributions-0.2.1/vistributions/man/vdist_launch_app.Rd | 4 vistributions-0.2.1/vistributions/man/vdist_normal_plot.Rd | 4 vistributions-0.2.1/vistributions/man/vdist_t_plot.Rd |only vistributions-0.2.1/vistributions/tests/testthat/_snaps/visual/binomial-perc-upper.svg | 2 vistributions-0.2.1/vistributions/tests/testthat/_snaps/visual/binomial-prob-upper.svg | 4 vistributions-0.2.1/vistributions/tests/testthat/_snaps/visual/chisquare-plot-1a.svg | 2 vistributions-0.2.1/vistributions/tests/testthat/_snaps/visual/f-plot-2.svg | 42 vistributions-0.2.1/vistributions/tests/testthat/_snaps/visual/normal-perc-both.svg | 8 vistributions-0.2.1/vistributions/tests/testthat/_snaps/visual/normal-perc-lower.svg | 6 vistributions-0.2.1/vistributions/tests/testthat/_snaps/visual/normal-perc-upper.svg | 6 vistributions-0.2.1/vistributions/tests/testthat/_snaps/visual/normal-plot-1.svg | 38 vistributions-0.2.1/vistributions/tests/testthat/_snaps/visual/normal-plot-2.svg | 40 vistributions-0.2.1/vistributions/tests/testthat/_snaps/visual/normal-prob-both.svg | 8 vistributions-0.2.1/vistributions/tests/testthat/_snaps/visual/normal-prob-lower.svg | 6 vistributions-0.2.1/vistributions/tests/testthat/_snaps/visual/normal-prob-upper.svg | 6 vistributions-0.2.1/vistributions/tests/testthat/_snaps/visual/t-prob-both.svg | 26 vistributions-0.2.1/vistributions/tests/testthat/_snaps/visual/t-prob-interval.svg | 26 vistributions-0.2.1/vistributions/tests/testthat/_snaps/visual/t-prob-upper.svg | 4 vistributions-0.2.1/vistributions/tests/testthat/test-binomial.R | 6 vistributions-0.2.1/vistributions/tests/testthat/test-bug-regressions.R |only vistributions-0.2.1/vistributions/tests/testthat/test-chisquare.R | 2 vistributions-0.2.1/vistributions/tests/testthat/test-f.R | 2 vistributions-0.2.1/vistributions/tests/testthat/test-normal.R | 2 vistributions-0.2.1/vistributions/tests/testthat/test-plot-assembly.R |only vistributions-0.2.1/vistributions/tests/testthat/test-t.R | 2 vistributions-0.2.1/vistributions/tests/testthat/test-visual.R | 84 - vistributions-0.2.1/vistributions/vignettes/introduction-to-vistributions.Rmd | 744 +++++----- 72 files changed, 1402 insertions(+), 1218 deletions(-)
Title: Simplified Vertex-Wise Analyses of Whole-Brain and Subcortical
Surface
Description: Provides functions to run statistical analyses on
surface-based neuroimaging data, computing measures including cortical
thickness and surface area of the whole-brain and of the hippocampi.
It can make use of 'FreeSurfer', 'fMRIprep', 'XCP-D', 'HCP' and 'CAT12'
preprocessed datasets, 'HippUnfold' hippocampal outputs and
'SubCortexMesh' subcortical outputs for a given sample by
restructuring the data values into a single file. The single file can
then be used by the package for analyses independently from its base
dataset and without need for its access.
Author: Junhong Yu [aut] ,
Charly Billaud [aut, cre]
Maintainer: Charly Billaud <charly.billaud@ntu.edu.sg>
Diff between VertexWiseR versions 1.5.4 dated 2026-09-16 and 1.5.5 dated 2026-10-16
VertexWiseR-1.5.4/VertexWiseR/vignettes/allaseg_plotsurf3d.jpg |only VertexWiseR-1.5.5/VertexWiseR/DESCRIPTION | 10 VertexWiseR-1.5.5/VertexWiseR/MD5 | 40 +- VertexWiseR-1.5.5/VertexWiseR/NAMESPACE | 1 VertexWiseR-1.5.5/VertexWiseR/NEWS.md | 14 VertexWiseR-1.5.5/VertexWiseR/R/CAT12vextract.R | 3 VertexWiseR-1.5.5/VertexWiseR/R/DTSERIESvextract.R | 3 VertexWiseR-1.5.5/VertexWiseR/R/FSLRvextract.R | 1 VertexWiseR-1.5.5/VertexWiseR/R/HIPvextract.R | 10 VertexWiseR-1.5.5/VertexWiseR/R/SCMvextract.R | 78 ++-- VertexWiseR-1.5.5/VertexWiseR/R/SURFvextract.R | 1 VertexWiseR-1.5.5/VertexWiseR/R/VWRfirstrun.R | 14 VertexWiseR-1.5.5/VertexWiseR/R/decode_surf_data.R | 173 +++++++++- VertexWiseR-1.5.5/VertexWiseR/README.md | 2 VertexWiseR-1.5.5/VertexWiseR/inst/doc/VertexWiseR_Example_3.html | 14 VertexWiseR-1.5.5/VertexWiseR/inst/doc/VertexWiseR_surface_extraction.html | 118 +++--- VertexWiseR-1.5.5/VertexWiseR/man/HIPvextract.Rd | 12 VertexWiseR-1.5.5/VertexWiseR/man/SCMvextract.Rd | 7 VertexWiseR-1.5.5/VertexWiseR/man/decode_surf_data.Rd | 2 VertexWiseR-1.5.5/VertexWiseR/vignettes/VertexWiseR_Example_3.Rmd | 2 VertexWiseR-1.5.5/VertexWiseR/vignettes/VertexWiseR_surface_extraction.Rmd | 2 VertexWiseR-1.5.5/VertexWiseR/vignettes/allaseg_plotsurf3d.png |only 22 files changed, 350 insertions(+), 157 deletions(-)
Title: Recency, Frequency and Monetary Value Analysis
Description: Tools for RFM (recency, frequency and monetary value) analysis.
Generate RFM score from both transaction and customer level data. Visualize the
relationship between recency, frequency and monetary value using heatmap,
histograms, bar charts and scatter plots. Includes a 'shiny' app for
interactive segmentation. References:
i. Blattberg R.C., Kim BD., Neslin S.A (2008) <doi:10.1007/978-0-387-72579-6_12>.
Author: Aravind Hebbali [aut, cre]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Diff between rfm versions 0.4.0 dated 2026-04-30 and 0.5.0 dated 2026-10-16
rfm-0.4.0/rfm/tests/figs |only rfm-0.4.0/rfm/tests/testthat/Rplots.pdf |only rfm-0.5.0/rfm/DESCRIPTION | 15 rfm-0.5.0/rfm/MD5 | 64 rfm-0.5.0/rfm/NAMESPACE | 7 rfm-0.5.0/rfm/NEWS.md | 18 rfm-0.5.0/rfm/R/rfm-ggplot.R | 7 rfm-0.5.0/rfm/R/rfm-plots.R | 13 rfm-0.5.0/rfm/R/rfm-report.R | 108 rfm-0.5.0/rfm/R/rfm-segment.R | 46 rfm-0.5.0/rfm/R/rfm-shiny-app.R | 33 rfm-0.5.0/rfm/R/utils.R | 30 rfm-0.5.0/rfm/R/zzz.R | 40 rfm-0.5.0/rfm/README.md | 6 rfm-0.5.0/rfm/inst/doc/rfm-introduction.html | 42 rfm-0.5.0/rfm/man/rfm_create_report.Rd | 134 rfm-0.5.0/rfm/man/rfm_plot_bar_chart.Rd | 118 rfm-0.5.0/rfm/man/rfm_plot_heatmap.Rd | 160 rfm-0.5.0/rfm/man/rfm_plot_histogram.Rd | 166 rfm-0.5.0/rfm/man/rfm_plot_order_dist.Rd | 172 rfm-0.5.0/rfm/man/rfm_plot_revenue_dist.Rd | 196 rfm-0.5.0/rfm/man/rfm_plot_segment.Rd | 146 rfm-0.5.0/rfm/man/rfm_plot_segment_scatter.Rd | 166 rfm-0.5.0/rfm/man/rfm_plot_segment_summary.Rd | 240 - rfm-0.5.0/rfm/man/rfm_segment_summary.Rd | 88 rfm-0.5.0/rfm/tests/testthat.R | 24 rfm-0.5.0/rfm/tests/testthat/_snaps/rfm-plotly.md | 4670 +++++++++++----------- rfm-0.5.0/rfm/tests/testthat/test-guards.R |only rfm-0.5.0/rfm/tests/testthat/test-rfm-report.R |only rfm-0.5.0/rfm/tests/testthat/test-rfm-shiny.R |only rfm-0.5.0/rfm/tests/testthat/test-zzz.R |only 31 files changed, 3346 insertions(+), 3363 deletions(-)
Title: Population Fisher Information Matrix
Description: Evaluate or optimize designs for nonlinear mixed effects models
using the Fisher Information matrix; see <doi:10.1093/biomet/84.2.429> and
<doi:10.1016/S0169-2607(00)00117-6>. Supports population, individual, and
Bayesian 'FIMs', covariates, inter-occasion variability, and D-optimal search
('Fedorov-Wynn', multiplicative, simplex, 'PSO', 'PGBO').
Author: Romain Leroux [aut] ,
France Mentre [cre] ,
Lucie Fayette [ctb] ,
Antoine Croxo [ctb] ,
Jeremy Seurat [ctb]
Maintainer: France Mentre <pfim@inserm.fr>
Diff between PFIM versions 8.0 dated 2026-09-28 and 8.0.1 dated 2026-10-16
PFIM-8.0.1/PFIM/DESCRIPTION | 32 - PFIM-8.0.1/PFIM/MD5 | 242 +++++----- PFIM-8.0.1/PFIM/NAMESPACE | 4 PFIM-8.0.1/PFIM/NEWS.md | 218 ++++----- PFIM-8.0.1/PFIM/R/Administration.R | 8 PFIM-8.0.1/PFIM/R/AdministrationConstraints.R | 4 PFIM-8.0.1/PFIM/R/Arm.R | 22 PFIM-8.0.1/PFIM/R/BayesianFim.R | 10 PFIM-8.0.1/PFIM/R/CovariateModelEquation.R | 12 PFIM-8.0.1/PFIM/R/CovariateTest.R | 2 PFIM-8.0.1/PFIM/R/Design.R | 8 PFIM-8.0.1/PFIM/R/Distribution.R | 5 PFIM-8.0.1/PFIM/R/Evaluation.R | 2 PFIM-8.0.1/PFIM/R/FedorovWynnAlgorithm.R | 10 PFIM-8.0.1/PFIM/R/Fim.R | 13 PFIM-8.0.1/PFIM/R/IndividualFim.R | 26 - PFIM-8.0.1/PFIM/R/LibraryOfModels.R | 2 PFIM-8.0.1/PFIM/R/Model.R | 52 +- PFIM-8.0.1/PFIM/R/ModelAnalytic.R | 8 PFIM-8.0.1/PFIM/R/ModelAnalyticInfusion.R | 8 PFIM-8.0.1/PFIM/R/ModelAnalyticInfusionSteadyState.R | 8 PFIM-8.0.1/PFIM/R/ModelAnalyticSteadyState.R | 8 PFIM-8.0.1/PFIM/R/ModelODEInfusionDoseInEquation.R | 4 PFIM-8.0.1/PFIM/R/ModelParameter.R | 6 PFIM-8.0.1/PFIM/R/MultiplicativeAlgorithm.R | 6 PFIM-8.0.1/PFIM/R/Optimization.R | 82 +++ PFIM-8.0.1/PFIM/R/PFIM-package.R | 234 ++++----- PFIM-8.0.1/PFIM/R/PFIMProject.R | 40 - PFIM-8.0.1/PFIM/R/PGBOAlgorithm.R | 6 PFIM-8.0.1/PFIM/R/PSOAlgorithm.R | 6 PFIM-8.0.1/PFIM/R/PopulationFim.R | 5 PFIM-8.0.1/PFIM/R/SamplingTimeConstraints.R | 12 PFIM-8.0.1/PFIM/R/SamplingTimes.R | 4 PFIM-8.0.1/PFIM/R/SimplexAlgorithm.R | 6 PFIM-8.0.1/PFIM/R/model-ode-bolus.R | 10 PFIM-8.0.1/PFIM/R/pfim-constraints-helpers.R | 2 PFIM-8.0.1/PFIM/R/pfim-fim-labels.R | 79 ++- PFIM-8.0.1/PFIM/R/pfim-fim-report-render.R | 20 PFIM-8.0.1/PFIM/R/pfim-rd-examples.R | 10 PFIM-8.0.1/PFIM/R/zzz.R | 9 PFIM-8.0.1/PFIM/build/vignette.rds |binary PFIM-8.0.1/PFIM/inst/CITATION | 38 - PFIM-8.0.1/PFIM/inst/WORDLIST |only PFIM-8.0.1/PFIM/inst/doc/LibraryOfModels.R | 1 PFIM-8.0.1/PFIM/inst/doc/LibraryOfModels.Rmd | 3 PFIM-8.0.1/PFIM/inst/doc/LibraryOfModels.html | 2 PFIM-8.0.1/PFIM/inst/doc/Vignette_01_discrete_design.R |only PFIM-8.0.1/PFIM/inst/doc/Vignette_01_discrete_design.Rmd |only PFIM-8.0.1/PFIM/inst/doc/Vignette_01_discrete_design.html |only PFIM-8.0.1/PFIM/inst/doc/Vignette_02_continuous_design.R |only PFIM-8.0.1/PFIM/inst/doc/Vignette_02_continuous_design.Rmd |only PFIM-8.0.1/PFIM/inst/doc/Vignette_02_continuous_design.html |only PFIM-8.0.1/PFIM/inst/doc/Vignette_03_covariates_analytical_pk.R |only PFIM-8.0.1/PFIM/inst/doc/Vignette_03_covariates_analytical_pk.Rmd |only PFIM-8.0.1/PFIM/inst/doc/Vignette_03_covariates_analytical_pk.html |only PFIM-8.0.1/PFIM/inst/doc/Vignette_04_tim_waterhouse_pediatric.R |only PFIM-8.0.1/PFIM/inst/doc/Vignette_04_tim_waterhouse_pediatric.Rmd |only PFIM-8.0.1/PFIM/inst/doc/Vignette_04_tim_waterhouse_pediatric.html |only PFIM-8.0.1/PFIM/inst/doc/Vignette_05_gcse_pkpd.R |only PFIM-8.0.1/PFIM/inst/doc/Vignette_05_gcse_pkpd.Rmd |only PFIM-8.0.1/PFIM/inst/doc/Vignette_05_gcse_pkpd.html |only PFIM-8.0.1/PFIM/inst/examples/gcsf-poped-evaluation.R | 8 PFIM-8.0.1/PFIM/inst/fixtures/gold-fim.R | 13 PFIM-8.0.1/PFIM/inst/include/pfim/pfim-linalg.hpp | 4 PFIM-8.0.1/PFIM/inst/vignette-scripts/pfim-vignette-utils.R | 26 - 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Title: Client for the 'enviPath' 'RESTful' API
Description: The environmental pathway database ('enviPath') is a key resource for the
functional annotation and pathway prediction of microbial communities,
providing knowledge on biotransformation pathways along with the chemical
reactions and produced compounds. This package enables the programmatic
access to 'enviPath' by porting the database 'RESTful' API from R. This
includes methods to both retrieve entries and predict pathways for custom
compounds.
Author: Giulio Benedetti [aut, cre, cph]
Maintainer: Giulio Benedetti <giulio.benedetti@utu.fi>
Diff between enviPathR versions 1.0.0 dated 2026-10-14 and 1.0.1 dated 2026-10-16
DESCRIPTION | 6 - MD5 | 26 ++--- README.md | 1 inst/doc/enviPathR.R | 6 - inst/doc/enviPathR.html | 26 +++-- tests/httptest/get/package_reaction/wrong.R | 10 +- tests/httptest/link/package_compound/wrong.R | 10 +- tests/httptest/list/package.json | 120 +++++++++++++-------------- tests/httptest/list/package/wrong/reaction.R | 10 +- tests/httptest/login/NA-2f7c1a-POST.R | 12 +- tests/httptest/model/util-e1f28b-POST.R | 6 - tests/testthat/setup.R | 2 tests/testthat/test-get.R | 8 - tests/testthat/test-link.R | 6 - 14 files changed, 127 insertions(+), 122 deletions(-)
Title: Easy and Accessible Bayesian Measurement Models Using 'brms'
Description: Fit computational and measurement models using full Bayesian
inference. The package provides a simple and accessible interface by
translating complex domain-specific models into 'brms' syntax, a
powerful and flexible framework for fitting Bayesian regression models
using 'Stan'. The package is designed so that users can easily apply
state-of-the-art models in various research fields, and so that
researchers can use it as a new model development framework.
References: Frischkorn and Popov (2025) <doi:10.3758/s13428-025-02643-0>.
Author: Vencislav Popov [aut, cph] ,
Gidon T. Frischkorn [aut, cre, cph] ,
Chenyu Li [ctb],
Paul-Christian Buerkner [cph]
Maintainer: Gidon T. Frischkorn <gfrischkorn@icloud.com>
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|only bmm-1.4.1/bmm/man/roc_sdt.Rd |only bmm-1.4.1/bmm/man/sdm.Rd | 10 bmm-1.4.1/bmm/man/sdt_cdp.Rd |only bmm-1.4.1/bmm/man/sdt_cdp_dist.Rd |only bmm-1.4.1/bmm/man/sdt_cdp_logmu.Rd |only bmm-1.4.1/bmm/man/sdt_dpsdt_dist.Rd |only bmm-1.4.1/bmm/man/sdt_mafc.Rd |only bmm-1.4.1/bmm/man/sdt_mafc_dist.Rd |only bmm-1.4.1/bmm/man/sdt_metad_dist.Rd |only bmm-1.4.1/bmm/man/sdt_ranking.Rd |only bmm-1.4.1/bmm/man/sdt_ranking_dist.Rd |only bmm-1.4.1/bmm/man/sdt_ranking_logmu.Rd |only bmm-1.4.1/bmm/man/sdt_rating.Rd |only bmm-1.4.1/bmm/man/sdt_rating_dist.Rd |only bmm-1.4.1/bmm/man/sdt_rating_logmu.Rd |only bmm-1.4.1/bmm/man/sdt_sensitivity.Rd |only bmm-1.4.1/bmm/man/sdt_thresholds.Rd |only bmm-1.4.1/bmm/man/sdt_yn.Rd |only bmm-1.4.1/bmm/man/sdt_yn_dist.Rd |only bmm-1.4.1/bmm/man/stancode.bmmformula.Rd | 6 bmm-1.4.1/bmm/man/standata.bmmformula.Rd | 6 bmm-1.4.1/bmm/man/summary.bmmfit.Rd | 2 bmm-1.4.1/bmm/man/supported_models.Rd | 27 bmm-1.4.1/bmm/man/update.bmmfit.Rd | 32 bmm-1.4.1/bmm/man/use_model_template.Rd | 2 bmm-1.4.1/bmm/tests/testthat/helper-epred.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-cases.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-cswald.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-data.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-ddm.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-ezdm.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-imm.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-m3.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-mixture2p.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-mixture3p.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-mpt.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-sdm.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-sdt_cdp.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-sdt_mafc.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-sdt_ranking.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-sdt_rating.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-sdt_yn.R |only bmm-1.4.1/bmm/tests/testthat/helper-mpt.R |only bmm-1.4.1/bmm/tests/testthat/helper-sdt-analysis.R |only bmm-1.4.1/bmm/tests/testthat/helper-tiers.R |only bmm-1.4.1/bmm/tests/testthat/helper-warnings.R |only bmm-1.4.1/bmm/tests/testthat/setup.R |only bmm-1.4.1/bmm/tests/testthat/test-bmm.R | 144 bmm-1.4.1/bmm/tests/testthat/test-bmm_setup.R |only bmm-1.4.1/bmm/tests/testthat/test-conditional_effects.R | 1692 ++++++ bmm-1.4.1/bmm/tests/testthat/test-conventions.R |only bmm-1.4.1/bmm/tests/testthat/test-data_check.R |only bmm-1.4.1/bmm/tests/testthat/test-default-priors.R | 357 + bmm-1.4.1/bmm/tests/testthat/test-distributions.R | 759 ++- bmm-1.4.1/bmm/tests/testthat/test-emmeans.R | 44 bmm-1.4.1/bmm/tests/testthat/test-helpers-analysis.R |only bmm-1.4.1/bmm/tests/testthat/test-helpers-data-coercion.R |only bmm-1.4.1/bmm/tests/testthat/test-helpers-data.R | 508 +- bmm-1.4.1/bmm/tests/testthat/test-helpers-formula.R | 28 bmm-1.4.1/bmm/tests/testthat/test-helpers-init.R | 691 ++ bmm-1.4.1/bmm/tests/testthat/test-helpers-model.R | 445 + bmm-1.4.1/bmm/tests/testthat/test-helpers-parameters.R | 757 ++ bmm-1.4.1/bmm/tests/testthat/test-helpers-postprocess.R | 56 bmm-1.4.1/bmm/tests/testthat/test-helpers-prior.R | 577 ++ bmm-1.4.1/bmm/tests/testthat/test-links.R |only bmm-1.4.1/bmm/tests/testthat/test-model_cswald.R | 428 + bmm-1.4.1/bmm/tests/testthat/test-model_ddm.R | 177 bmm-1.4.1/bmm/tests/testthat/test-model_ezdm.R | 826 +++ bmm-1.4.1/bmm/tests/testthat/test-model_imm.R | 38 bmm-1.4.1/bmm/tests/testthat/test-model_m3.R | 436 + bmm-1.4.1/bmm/tests/testthat/test-model_mixture3p.R | 4 bmm-1.4.1/bmm/tests/testthat/test-model_mpt-stancode.R |only bmm-1.4.1/bmm/tests/testthat/test-model_mpt.R |only bmm-1.4.1/bmm/tests/testthat/test-model_mpt_data.R |only bmm-1.4.1/bmm/tests/testthat/test-model_mpt_expressions.R |only bmm-1.4.1/bmm/tests/testthat/test-model_mpt_import.R |only bmm-1.4.1/bmm/tests/testthat/test-model_mpt_plot.R |only 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|only bmm-1.4.1/bmm/tests/testthat/test-summary.R | 58 bmm-1.4.1/bmm/tests/testthat/test-update.R | 760 ++- bmm-1.4.1/bmm/tests/testthat/test-utils.R | 292 + 237 files changed, 18873 insertions(+), 2544 deletions(-)
Title: Understand and Describe Bayesian Models and Posterior
Distributions
Description: Provides utilities to describe posterior
distributions and Bayesian models. It includes point-estimates such as
Maximum A Posteriori (MAP), measures of dispersion (Highest Density
Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and
indices used for null-hypothesis testing (such as ROPE percentage, pd
and Bayes factors). References: Makowski et al. (2021) <doi:10.21105/joss.01541>.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Micah K. Wilson [aut] ,
Brenton M. Wiernik [aut] ,
Paul-Christian Buerkner [rev],
Tristan Mahr [rev] ,
Henrik Singmann [ctb] ,
Quentin F. Gron [...truncated...]
Maintainer: Dominique Makowski <officialeasystats@gmail.com>
Diff between bayestestR versions 0.19.0 dated 2026-09-09 and 0.20.0 dated 2026-10-16
bayestestR-0.19.0/bayestestR/R/p_rope.R |only bayestestR-0.19.0/bayestestR/man/p_rope.Rd |only bayestestR-0.19.0/bayestestR/tests/testthat/test-p_rope.R |only bayestestR-0.20.0/bayestestR/DESCRIPTION | 8 bayestestR-0.20.0/bayestestR/MD5 | 86 ++- bayestestR-0.20.0/bayestestR/NAMESPACE | 32 - bayestestR-0.20.0/bayestestR/NEWS.md | 51 ++ bayestestR-0.20.0/bayestestR/R/check_prior.R | 9 bayestestR-0.20.0/bayestestR/R/convert_bayesian_to_frequentist.R | 100 ++++ bayestestR-0.20.0/bayestestR/R/describe_posterior.R | 25 + bayestestR-0.20.0/bayestestR/R/display.R | 2 bayestestR-0.20.0/bayestestR/R/equivalence_test.R | 93 +++- bayestestR-0.20.0/bayestestR/R/format.R | 3 bayestestR-0.20.0/bayestestR/R/mediation.R | 69 ++- bayestestR-0.20.0/bayestestR/R/print.R | 25 - bayestestR-0.20.0/bayestestR/R/print.equivalence_test.R | 22 bayestestR-0.20.0/bayestestR/R/print_html.R | 19 bayestestR-0.20.0/bayestestR/R/print_md.R | 19 bayestestR-0.20.0/bayestestR/R/rope.R | 80 ++- bayestestR-0.20.0/bayestestR/R/rope_range.R | 65 ++ bayestestR-0.20.0/bayestestR/R/sensitivity_to_prior.R | 230 +++++++++- bayestestR-0.20.0/bayestestR/R/simulate_priors.R | 33 + bayestestR-0.20.0/bayestestR/man/convert_bayesian_as_frequentist.Rd | 14 bayestestR-0.20.0/bayestestR/man/dot-brms_cauchy_priors.Rd |only bayestestR-0.20.0/bayestestR/man/dot-brms_check_refit_priors.Rd |only bayestestR-0.20.0/bayestestR/man/dot-brms_priors.Rd |only bayestestR-0.20.0/bayestestR/man/dot-brms_slope_info.Rd |only bayestestR-0.20.0/bayestestR/man/dot-refit_brms.Rd |only bayestestR-0.20.0/bayestestR/man/equivalence_test.Rd | 26 - bayestestR-0.20.0/bayestestR/man/mediation.Rd | 5 bayestestR-0.20.0/bayestestR/man/rope.Rd | 22 bayestestR-0.20.0/bayestestR/man/sensitivity_to_prior.Rd | 35 + bayestestR-0.20.0/bayestestR/tests/testthat/helper.R | 14 bayestestR-0.20.0/bayestestR/tests/testthat/test-bayesfactor_models.R | 4 bayestestR-0.20.0/bayestestR/tests/testthat/test-bayesian_as_frequentist.R | 65 ++ bayestestR-0.20.0/bayestestR/tests/testthat/test-bayesian_as_frequentist_BayesFactor.R |only bayestestR-0.20.0/bayestestR/tests/testthat/test-blavaan.R | 3 bayestestR-0.20.0/bayestestR/tests/testthat/test-check_prior.R | 86 ++- bayestestR-0.20.0/bayestestR/tests/testthat/test-describe_posterior.R | 38 + bayestestR-0.20.0/bayestestR/tests/testthat/test-emmGrid.R | 37 - bayestestR-0.20.0/bayestestR/tests/testthat/test-equivalence_test.R | 14 bayestestR-0.20.0/bayestestR/tests/testthat/test-format.R | 20 bayestestR-0.20.0/bayestestR/tests/testthat/test-marginaleffects.R | 52 +- bayestestR-0.20.0/bayestestR/tests/testthat/test-mediation.R |only bayestestR-0.20.0/bayestestR/tests/testthat/test-rope.R | 63 ++ bayestestR-0.20.0/bayestestR/tests/testthat/test-rope_range.R | 83 +++ bayestestR-0.20.0/bayestestR/tests/testthat/test-sensitivity_to_prior.R |only bayestestR-0.20.0/bayestestR/tests/testthat/test-si.R | 7 bayestestR-0.20.0/bayestestR/tests/testthat/test-simulate_prior.R |only bayestestR-0.20.0/bayestestR/tests/testthat/test-weighted_posteriors.R | 44 + 50 files changed, 1257 insertions(+), 346 deletions(-)
Title: 'ggplot2'-Based Tools for Visualising DNA Sequences and
Modifications
Description: Uses 'ggplot2' to visualise either (a) a single DNA/RNA sequence split across multiple lines, (b) multiple DNA/RNA sequences, each occupying a whole line, or (c) base modifications such as DNA methylation called by modified bases models in Dorado or Guppy. Functions starting with visualise_<>() are the main plotting functions, and functions starting with extract_and_sort_<>() are key helper functions for reading files and reformatting data. Source code is available at <https://github.com/ejade42/ggDNAvis>, a full non-expert user guide is available at <https://ejade42.github.io/ggDNAvis/>, and an interactive web-app version of the software is available at <https://ejade42.github.io/ggDNAvis/articles/interactive_app.html>.
Author: Evelyn Jade [aut, cre, cph]
Maintainer: Evelyn Jade <evelynjade42@gmail.com>
Diff between ggDNAvis versions 1.0.1 dated 2026-06-22 and 1.1.0 dated 2026-10-16
DESCRIPTION | 6 MD5 | 62 +++--- NAMESPACE | 3 NEWS.md | 32 +++ R/alias_maps.R | 6 R/dna_tools.R | 40 ++++ R/merge_with_metadata.R | 92 +++++++++- R/visualise_many_sequences.R | 46 ++++- R/visualise_methylation.R | 35 ++- R/visualise_single_sequence.R | 14 - build/partial.rdb |binary build/vignette.rds |binary inst/shinyapp/mod_visualise_many_sequences.R | 2 inst/shinyapp/mod_visualise_methylation.R | 2 inst/shinyapp/mod_visualise_single_sequence.R | 2 man/extract_and_sort_methylation.Rd | 13 - man/invert_direction_vector.Rd |only man/merge_fastq_with_metadata.Rd | 7 man/merge_methylation_with_metadata.Rd | 9 man/sanitise_sequences_vector.Rd |only man/visualise_many_sequences.Rd | 29 +++ man/visualise_methylation.Rd | 7 man/visualise_single_sequence.Rd | 3 tests/testthat/reference_images/sone_2019_f1_1_expanded_test_33.png |binary tests/testthat/reference_images/sone_2019_f1_1_expanded_test_40.png |only tests/testthat/reference_images/visualise_many_sequences_test_29.png |only tests/testthat/reference_images/visualise_methylation_test_25.png |only tests/testthat/test-dna_tools.R | 22 ++ tests/testthat/test-merge_with_metadata.R | 36 +++ tests/testthat/test-visualise_many_sequences.R | 14 + tests/testthat/test-visualise_methylation.R | 28 +++ tests/testthat/test-visualise_single_sequence.R | 13 + tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_33.png |binary tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_40.png |only tests/testthat/test_plot_images/visualise_many_sequences_test_29.png |only tests/testthat/test_plot_images/visualise_methylation_test_25.png |only 36 files changed, 450 insertions(+), 73 deletions(-)