Title: Run Predictions Inside the Database
Description: It parses a fitted 'R' model object, and returns a formula in
'Tidy Eval' code that calculates the predictions. It works with
several databases back-ends because it leverages 'dplyr' and 'dbplyr'
for the final 'SQL' translation of the algorithm. Dozens of model
classes are supported; see the "Supported models" article at
<https://tidypredict.tidymodels.org/articles/models.html> for the
current list.
Author: Emil Hvitfeldt [aut, cre] ,
Edgar Ruiz [aut],
Max Kuhn [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between tidypredict versions 1.2.1 dated 2026-09-09 and 1.2.2 dated 2026-10-18
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ inst/doc/h2o.html | 10 +++++----- inst/doc/lm.R | 2 +- inst/doc/lm.Rmd | 2 +- inst/doc/lm.html | 2 +- vignettes/lm.Rmd | 2 +- 8 files changed, 23 insertions(+), 19 deletions(-)
Title: Spectral Majorization for Statistical Estimation
Description: Fits generalized linear, asymmetric and robust regression models
using spectral majorization and iterative quadratic subproblem solvers.
A shared C++ computational core supports dense and sparse designs, automatic
intercepts, optional Wald inference and detailed iteration diagnostics.
Native code is compiled automatically during package installation.
Author: Xun-Jian Li [aut, cre]
Maintainer: Xun-Jian Li <xunjianli@ucla.edu>
Diff between SpectralMM versions 0.1.0 dated 2026-10-15 and 0.2.0 dated 2026-10-18
SpectralMM-0.1.0/SpectralMM/tests/smoke.R |only SpectralMM-0.2.0/SpectralMM/DESCRIPTION | 8 SpectralMM-0.2.0/SpectralMM/MD5 | 28 +-- SpectralMM-0.2.0/SpectralMM/R/families.R | 4 SpectralMM-0.2.0/SpectralMM/R/model.R | 82 +++++++-- SpectralMM-0.2.0/SpectralMM/R/spectralmm.R | 41 ++-- SpectralMM-0.2.0/SpectralMM/README.md | 29 +-- SpectralMM-0.2.0/SpectralMM/man/spectralmm_fit.Rd | 2 SpectralMM-0.2.0/SpectralMM/man/spectralmm_methods.Rd | 4 SpectralMM-0.2.0/SpectralMM/src/native/c_api.cpp | 52 +++++ SpectralMM-0.2.0/SpectralMM/src/native/core.cpp | 88 +++++++++- SpectralMM-0.2.0/SpectralMM/src/native/include/spectralmm/c_api.h | 15 + SpectralMM-0.2.0/SpectralMM/src/native/include/spectralmm/core.hpp | 3 SpectralMM-0.2.0/SpectralMM/src/r_bridge.cpp | 11 - SpectralMM-0.2.0/SpectralMM/tests/model-api.R | 2 SpectralMM-0.2.0/SpectralMM/tests/output-prediction.R |only 16 files changed, 290 insertions(+), 79 deletions(-)
Title: Sampling Hi-C Contact Matrices for Aparametric Normalization
Description: Generate expected Hi-C (genome-wide chromosome conformation
capture) data maintaining marginal coverage, and the decay in contact probability
with increasing genomic distance. Expected Hi-C data is used for normalization
and graphical presentation of statistical significance of observed Hi-C contact
enrichments. The method is described in Mendelson Cohen et al. (2017)
<doi:10.1101/187203>.
Author: Amos Tanay [aut],
Netta Mendelson Cohen [aut],
Aviezer Lifshitz [aut, cre],
Weizmann Institute of Science [cph]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Diff between shaman versions 2.1.0 dated 2026-10-16 and 2.1.1 dated 2026-10-18
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ inst/doc/import.html | 4 ++-- src/ContactShuffler.cpp | 11 +++++++---- 5 files changed, 20 insertions(+), 13 deletions(-)
Title: Grammar of Graphics on 'base' Graphics
Description: Implements a grammar of graphics on top of the 'base' graphics
system. A 'bbplot' object is built incrementally with a '+' operator from
data, aesthetic mappings and layers, then rendered with base graphics, so
plotbb layers can be mixed with ordinary base plotting calls. The package
provides layers for points, lines, bars, histograms, densities, boxplots,
violins, ribbons, smooths, error bars and tiles, together with colour and
other aesthetic scales, automatic legends, faceting, themes, coordinate
flipping and significance annotations.
Author: Guangchuang Yu [aut, cre, cph]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between plotbb versions 0.1.2 dated 2026-05-21 and 1.0.0 dated 2026-10-18
plotbb-0.1.2/plotbb/man/reexports.Rd |only plotbb-1.0.0/plotbb/DESCRIPTION | 36 plotbb-1.0.0/plotbb/MD5 | 121 plotbb-1.0.0/plotbb/NAMESPACE | 182 - plotbb-1.0.0/plotbb/NEWS.md | 215 + plotbb-1.0.0/plotbb/R/add-layer.R | 237 - plotbb-1.0.0/plotbb/R/aes.R | 32 plotbb-1.0.0/plotbb/R/auto-legend.R |only plotbb-1.0.0/plotbb/R/bb-bar-horizontal.R |only plotbb-1.0.0/plotbb/R/bb-bar.R | 129 plotbb-1.0.0/plotbb/R/bb-boxplot.R | 230 - plotbb-1.0.0/plotbb/R/bb-build.R |only plotbb-1.0.0/plotbb/R/bb-density.R | 145 plotbb-1.0.0/plotbb/R/bb-errorbar.R | 185 - plotbb-1.0.0/plotbb/R/bb-hist.R | 307 + plotbb-1.0.0/plotbb/R/bb-layer.R |only plotbb-1.0.0/plotbb/R/bb-line.R | 49 plotbb-1.0.0/plotbb/R/bb-lm.R | 392 +- plotbb-1.0.0/plotbb/R/bb-point.R | 114 plotbb-1.0.0/plotbb/R/bb-reference.R |only plotbb-1.0.0/plotbb/R/bb-ribbon.R |only plotbb-1.0.0/plotbb/R/bb-save.R |only plotbb-1.0.0/plotbb/R/bb-segment.R | 54 plotbb-1.0.0/plotbb/R/bb-signif.R | 90 plotbb-1.0.0/plotbb/R/bb-smooth.R |only plotbb-1.0.0/plotbb/R/bb-text.R | 80 plotbb-1.0.0/plotbb/R/bb-tile.R | 77 plotbb-1.0.0/plotbb/R/bb-violin.R |only plotbb-1.0.0/plotbb/R/bbplot.R | 36 plotbb-1.0.0/plotbb/R/coord-flip.R |only plotbb-1.0.0/plotbb/R/facet-grid.R |only plotbb-1.0.0/plotbb/R/grid.R | 88 plotbb-1.0.0/plotbb/R/labs.R | 120 plotbb-1.0.0/plotbb/R/position-scale.R |only plotbb-1.0.0/plotbb/R/print.R | 537 ++- plotbb-1.0.0/plotbb/R/scale.R | 1321 +++++--- plotbb-1.0.0/plotbb/R/state.R |only plotbb-1.0.0/plotbb/R/theme.R | 305 + plotbb-1.0.0/plotbb/R/utilities.R | 1348 +++++--- plotbb-1.0.0/plotbb/R/validate.R |only plotbb-1.0.0/plotbb/R/zzz.R | 20 plotbb-1.0.0/plotbb/build/vignette.rds |binary plotbb-1.0.0/plotbb/inst/WORDLIST |only plotbb-1.0.0/plotbb/inst/doc/plotbb.R | 772 +++- plotbb-1.0.0/plotbb/inst/doc/plotbb.html | 2169 +++++++++----- plotbb-1.0.0/plotbb/inst/doc/plotbb.qmd | 1467 +++++++-- plotbb-1.0.0/plotbb/man/bb-scale-aes.Rd | 21 plotbb-1.0.0/plotbb/man/bb-scale-fill.Rd |only plotbb-1.0.0/plotbb/man/bb-scale.Rd | 52 plotbb-1.0.0/plotbb/man/bb_build.Rd |only plotbb-1.0.0/plotbb/man/bb_coord_flip.Rd |only plotbb-1.0.0/plotbb/man/bb_facet_grid.Rd |only plotbb-1.0.0/plotbb/man/bb_facet_wrap.Rd | 31 plotbb-1.0.0/plotbb/man/bb_group_values.Rd |only plotbb-1.0.0/plotbb/man/bb_layer.Rd |only plotbb-1.0.0/plotbb/man/bb_legend.Rd | 22 plotbb-1.0.0/plotbb/man/bb_position.Rd |only plotbb-1.0.0/plotbb/man/bb_save.Rd |only plotbb-1.0.0/plotbb/man/bb_scale_x_continuous.Rd |only plotbb-1.0.0/plotbb/man/bbplot.Rd | 20 plotbb-1.0.0/plotbb/man/bbplot_add.Rd | 35 plotbb-1.0.0/plotbb/man/layer.Rd | 248 + plotbb-1.0.0/plotbb/man/set_bb_theme.Rd | 6 plotbb-1.0.0/plotbb/man/unset_bb_theme.Rd | 4 plotbb-1.0.0/plotbb/man/with_bb_theme.Rd |only plotbb-1.0.0/plotbb/tests/testthat.R | 8 plotbb-1.0.0/plotbb/tests/testthat/helper-device.R |only plotbb-1.0.0/plotbb/tests/testthat/test-auto-legend-0.9.R |only plotbb-1.0.0/plotbb/tests/testthat/test-build-save.R |only plotbb-1.0.0/plotbb/tests/testthat/test-coord-0.9.R |only plotbb-1.0.0/plotbb/tests/testthat/test-facets-0.6.R |only plotbb-1.0.0/plotbb/tests/testthat/test-grammar.R |only plotbb-1.0.0/plotbb/tests/testthat/test-inputs.R |only plotbb-1.0.0/plotbb/tests/testthat/test-layers-0.4.R |only plotbb-1.0.0/plotbb/tests/testthat/test-layers-0.7.R |only plotbb-1.0.0/plotbb/tests/testthat/test-legends-0.8.R |only plotbb-1.0.0/plotbb/tests/testthat/test-orientation-0.9.R |only plotbb-1.0.0/plotbb/tests/testthat/test-position-0.9.R |only plotbb-1.0.0/plotbb/tests/testthat/test-registry-0.9.R |only plotbb-1.0.0/plotbb/tests/testthat/test-scales.R |only plotbb-1.0.0/plotbb/tests/testthat/test-state.R |only plotbb-1.0.0/plotbb/vignettes/plotbb.qmd | 1467 +++++++-- 82 files changed, 9160 insertions(+), 3612 deletions(-)
Title: Assessment of Regression Models Performance
Description: Utilities for computing measures to assess model quality,
which are not directly provided by R's 'base' or 'stats' packages.
These include e.g. measures like r-squared, intraclass correlation
coefficient (Nakagawa, Johnson & Schielzeth (2017)
<doi:10.1098/rsif.2017.0213>), root mean squared error or functions to
check models for overdispersion, singularity or zero-inflation and
more. Functions apply to a large variety of regression models,
including generalized linear models, mixed effects models and Bayesian
models. References: Lüdecke et al. (2021) <doi:10.21105/joss.03139>.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Remi Theriault [aut, ctb] ,
Vincent Arel-Bundock [ctb] ,
Martin J [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between performance versions 0.18.2 dated 2026-09-10 and 0.19.0 dated 2026-10-18
DESCRIPTION | 40 MD5 | 91 +- NAMESPACE | 5 NEWS.md | 256 +++++ R/check_collinearity.R | 668 +++++++++++++-- R/check_model.R | 430 +++++++++ R/check_model_diagnostics.R | 288 ++++++ R/check_outliers.R | 808 +++++++++++++++++- R/check_overdispersion.R | 158 +++ R/check_predictions.R | 76 + R/check_singularity.R | 9 R/compare_performance.R | 13 R/format.R | 21 R/helpers.R | 46 + R/icc.R | 5 R/model_performance.lavaan.R | 192 ++-- R/r2_efron.R | 8 R/r2_mckelvey.R | 8 R/r2_nakagawa.R | 7 R/r2_somers.R | 7 R/r2_tjur.R | 8 R/test_performance.R | 102 ++ R/test_vuong.R | 8 R/test_wald.R | 8 inst/WORDLIST | 3 man/check_collinearity.Rd | 41 man/check_model.Rd | 36 man/check_outliers.Rd | 50 + man/check_overdispersion.Rd | 15 man/check_predictions.Rd | 6 man/icc.Rd | 5 man/model_performance.lavaan.Rd | 26 man/r2_nakagawa.Rd | 7 tests/testthat/test-check_collinearity.R | 1104 ++++++++++++++++++++++++- tests/testthat/test-check_group_variation.R | 5 tests/testthat/test-check_model.R | 372 ++++++++ tests/testthat/test-check_model_glmmTMB.R |only tests/testthat/test-check_outliers.R | 55 + tests/testthat/test-check_outliers_cook.R |only tests/testthat/test-check_outliers_glmmTMB.R |only tests/testthat/test-check_outliers_group.R |only tests/testthat/test-check_overdispersion.R | 460 ++++++++++ tests/testthat/test-check_predictions.R | 173 +++ tests/testthat/test-check_singularity.R | 20 tests/testthat/test-compare_performance.R | 36 tests/testthat/test-model_performance.lavaan.R | 252 +++++ tests/testthat/test-r2_binomial_aggregated.R |only tests/testthat/test-r2_nakagawa.R | 42 tests/testthat/test-test_performance.R | 64 + 49 files changed, 5670 insertions(+), 364 deletions(-)
Title: Exponential Multivariate Hawkes Model
Description: Simulate and fit multivariate Hawkes models with exponential
kernels, introduced by Hawkes (1971) <doi:10.2307/2334319>.
Includes marked, state-dependent, and multi-kernel specifications.
Parameter estimation uses maximum likelihood, following Ozaki (1979)
<doi:10.1007/BF02480272>, through the optional 'maxLik' package or
the optimization functions supplied with R.
Author: Kyungsub Lee [aut, cre]
Maintainer: Kyungsub Lee <kyungsub@gmail.com>
Diff between emhawkes versions 1.0.0 dated 2026-10-17 and 1.0.1 dated 2026-10-18
DESCRIPTION | 6 +- MD5 | 60 +++++++++++++++-------------- NAMESPACE | 1 NEWS.md | 26 ++++++++++++ R/harrival.R | 78 +++++++++++++++++++++++++++++++------- R/hengine.R | 1 R/hfitted.R | 8 +++ R/hgfit.R | 6 +- R/himpact.R | 6 +- R/hinterface.R | 4 + R/hllf.R | 12 +++++ R/hmoment.R | 18 +++++++- R/hoptimizer.R | 26 ++++++++++++ R/tzexp.R | 23 ++++++++--- R/zzz.R | 2 inst/doc/example.html | 4 - man/fitted_hspec.Rd | 8 +++ man/logLik.Rd | 4 + src/hawkes_simulate.cpp | 7 --- src/hawkes_simulate_callbacks.cpp | 7 --- src/hawkes_simulate_equal.cpp | 7 --- src/simulation_state.h | 15 +++++++ tests/callback-history-context.R |only tests/computation-regressions.R | 8 +++ tests/expected-wait.R | 26 ++++++++++++ tests/fit-rds-session.R | 32 ++++++++++----- tests/s4-minimal-session.R | 26 ++++++++---- tests/simulation-subnormal.R |only tests/state-replay.R | 4 - tests/stats-isolated-session.R | 39 ++++++++++++------- tests/tzexp-distribution.R | 8 +++ tests/volatility.R | 10 ++++ 32 files changed, 370 insertions(+), 112 deletions(-)
Title: Census of India Data, 1901-2011, with Boundaries and Projections
Description: Tables from every decennial Census of India from 1901 to 2011:
population time series, Primary Census Abstracts at state, district and
sub-district level, mother tongue tables, Scheduled Caste and
Scheduled Tribe populations, and the 1931 caste tables by religion,
together with Ministry of Health and Family Welfare population
projections to 2036. Historical series are drawn
from Jolad and Singh (2026) <doi:10.7910/DVN/ON8CP8>. Census variables
can be returned with state or district boundaries of the matching
census year attached for mapping. Boundary files and the largest
village-level tables are downloaded on first use and cached locally.
Author: Saket Choudhary [aut, cre, cph]
Maintainer: Saket Choudhary <saketc@iitb.ac.in>
Diff between censusindia versions 0.2.0 dated 2026-10-15 and 0.2.1 dated 2026-10-18
DESCRIPTION | 18 ++-- MD5 | 65 +++++++++------- NAMESPACE | 2 NEWS.md | 43 ++++++---- R/data.R | 108 +++++++++++++++++++++++---- R/download.R | 13 +-- R/geometry.R | 6 - R/get_census.R | 45 ++++++++--- R/population.R | 54 +++++++++++-- R/serve.R |only R/variables.R | 2 README.md | 1 data/census_1931_castes.rda |only data/census_1931_exterior_castes.rda |only data/census_1971.rda |binary data/census_1981.rda |binary data/census_subdistricts_2011.rda |binary data/population_projections_district_lgd.rda |binary data/population_projections_state.rda |binary inst/COPYRIGHTS | 6 + inst/manifest.csv | 4 - inst/plumber |only man/census_1931_castes.Rd |only man/census_1931_exterior_castes.Rd |only man/census_subdistricts_2011.Rd | 9 ++ man/censusindia-package.Rd | 4 - man/figures/logo.png |binary man/get_census.Rd | 3 man/get_population.Rd | 26 +++++- man/population_projections_district_age.Rd | 9 +- man/population_projections_district_lgd.Rd | 6 - man/population_projections_state.Rd | 39 +++++++-- man/serve.Rd |only tests/testthat/test-castes-1931.R |only tests/testthat/test-get-census.R | 19 ++-- tests/testthat/test-na-fixes.R |only tests/testthat/test-population-estimate.R | 36 +++++++++ tests/testthat/test-reconciliation.R |only tests/testthat/test-serve.R |only 39 files changed, 384 insertions(+), 134 deletions(-)
Title: Prospective Trial Planning for Average Hazard Estimands
Description: Provides a simulation-based prospective planning workflow for
average hazard estimands in two-arm time-to-event trials. Supports
calibration and freezing of design-specific information-support rules,
assessment of clinically preferred truncation horizons, conditional
selection of clinically acceptable alternative horizons, and reverse
design over sample size and additional follow-up. Separates information
support from statistical power and supports auditable planning reports.
Author: Xinyue Zhao [aut, cre],
Haitao Pan [aut]
Maintainer: Xinyue Zhao <xinyuezhao27@gwu.edu>
Diff between AHTauDesign versions 0.1.0 dated 2026-09-10 and 1.0 dated 2026-10-18
AHTauDesign-0.1.0/AHTauDesign/R/assess_tau.R |only AHTauDesign-0.1.0/AHTauDesign/R/optimize_tau.R |only AHTauDesign-0.1.0/AHTauDesign/R/twostage_tau.R |only AHTauDesign-0.1.0/AHTauDesign/inst/doc/AHTauDesign.R |only AHTauDesign-0.1.0/AHTauDesign/inst/doc/AHTauDesign.Rmd |only AHTauDesign-0.1.0/AHTauDesign/inst/doc/AHTauDesign.html |only AHTauDesign-0.1.0/AHTauDesign/man/assess_tau.Rd |only AHTauDesign-0.1.0/AHTauDesign/man/default_fail_thresholds.Rd |only AHTauDesign-0.1.0/AHTauDesign/man/default_feasibility_thresholds.Rd |only AHTauDesign-0.1.0/AHTauDesign/man/optimize_tau.Rd |only AHTauDesign-0.1.0/AHTauDesign/man/twostage_tau.Rd |only AHTauDesign-0.1.0/AHTauDesign/vignettes/AHTauDesign.Rmd |only AHTauDesign-0.1.0/AHTauDesign/vignettes/precomputed_results.rds |only AHTauDesign-1.0/AHTauDesign/DESCRIPTION | 41 +++---- AHTauDesign-1.0/AHTauDesign/MD5 | 58 +++++++--- AHTauDesign-1.0/AHTauDesign/NAMESPACE | 21 +-- AHTauDesign-1.0/AHTauDesign/NEWS.md |only AHTauDesign-1.0/AHTauDesign/R/calib_reliability_functions.R |only AHTauDesign-1.0/AHTauDesign/R/calibration.R |only AHTauDesign-1.0/AHTauDesign/R/calibration_simulation.R |only AHTauDesign-1.0/AHTauDesign/R/part2_design.R |only AHTauDesign-1.0/AHTauDesign/R/planning_report.R |only AHTauDesign-1.0/AHTauDesign/R/simulate_design.R |only AHTauDesign-1.0/AHTauDesign/R/stage1_audit.R |only AHTauDesign-1.0/AHTauDesign/R/stage2_select.R |only AHTauDesign-1.0/AHTauDesign/R/support_rule.R |only AHTauDesign-1.0/AHTauDesign/README.md |only AHTauDesign-1.0/AHTauDesign/build/vignette.rds |binary AHTauDesign-1.0/AHTauDesign/inst/doc/getting-started.R |only AHTauDesign-1.0/AHTauDesign/inst/doc/getting-started.Rmd |only AHTauDesign-1.0/AHTauDesign/inst/doc/getting-started.html |only AHTauDesign-1.0/AHTauDesign/inst/extdata |only AHTauDesign-1.0/AHTauDesign/man/classify_calib_reliability.Rd |only AHTauDesign-1.0/AHTauDesign/man/count_calib_reliability.Rd |only AHTauDesign-1.0/AHTauDesign/man/evaluate_calib_rules.Rd |only AHTauDesign-1.0/AHTauDesign/man/find_n_req.Rd |only AHTauDesign-1.0/AHTauDesign/man/freeze_support_rule.Rd |only AHTauDesign-1.0/AHTauDesign/man/planning_report.Rd |only AHTauDesign-1.0/AHTauDesign/man/print.ahtau_planning_report.Rd |only AHTauDesign-1.0/AHTauDesign/man/simulate_calibration_null.Rd |only AHTauDesign-1.0/AHTauDesign/man/simulate_design.Rd |only AHTauDesign-1.0/AHTauDesign/man/stage1_audit.Rd |only AHTauDesign-1.0/AHTauDesign/man/stage2_evaluate.Rd |only AHTauDesign-1.0/AHTauDesign/man/stage2_select.Rd |only AHTauDesign-1.0/AHTauDesign/man/summarize_calibration_support.Rd |only AHTauDesign-1.0/AHTauDesign/tests |only AHTauDesign-1.0/AHTauDesign/vignettes/getting-started.Rmd |only 47 files changed, 71 insertions(+), 49 deletions(-)
Title: Health Geography Toolbox for Model-Based Analysis of Infections
Panel Data
Description: Within epidemic outbreaks, infections grow and decline differently between regions, and the velocity of spatial spread differs between countries. The swash library offers a set of model-based analyses for these topics. Spread velocity may be analysed with the Swash-Backwash Model for the Single Epidemic Wave by Cliff and Haggett (2006) <doi:10.1007/s10109-006-0027-8> and corresponding functions for bootstrap confidence intervals, country comparison, and visualization of results. Differences in epidemic growth between regions may be analysed using logistic growth models, exponential growth models, Hawkes processes and breakpoint analyses. Cluster and hotspot analyses can be conducted using neighborhood matrices. See Wieland (2020) <doi:10.18335/region.v7i2.324> for an application of some of the mentioned analysis methods. All functionalities are accessed by the class "infpan" for infections panel data defined in this package, which is built from a data.frame provided by the [...truncated...]
Author: Thomas Wieland [aut, cre]
Maintainer: Thomas Wieland <geowieland@googlemail.com>
Diff between swash versions 3.0.1 dated 2026-10-11 and 3.0.2 dated 2026-10-18
DESCRIPTION | 8 +- MD5 | 66 ++++++++++---------- NEWS.md |only R/config.R | 6 - R/growthmodels.R | 47 ++++++++++---- R/helper.R | 119 +++++++++++++++++++++++++++++++++++-- R/infpan.R | 43 +++++++++++-- R/stathelp.R | 53 +++++++++++----- R/swash.R | 84 ++++++++++++++++++-------- inst |only man/C19dNUTSdata.Rd | 4 - man/COVID19Cases_geoRegion.Rd | 2 man/K4kant20260101gf_ch2007Poly.Rd | 6 - man/RKI_Corona_counties.Rd | 4 - man/add_geodata.Rd | 2 man/as_balanced.Rd | 11 ++- man/binary_metrics.Rd | 4 - man/binary_metrics_glm.Rd | 4 - man/breaks_growth.Rd | 7 +- man/calculate_incidence-method.Rd | 2 man/calculate_incidence.Rd | 2 man/countries-class.Rd | 6 - man/growth-methods.Rd | 2 man/growth_hawkes.Rd | 2 man/growth_initial.Rd | 2 man/growthmodels-class.Rd | 7 +- man/hawkes_growth.Rd | 6 - man/infpan-class.Rd | 6 - man/is_balanced.Rd | 18 ++++- man/nbstat.Rd | 2 man/plot-methods.Rd | 2 man/plot_map.Rd | 2 man/sbm-class.Rd | 2 man/sbm_ci-class.Rd | 2 man/swash-package.Rd | 8 +- 35 files changed, 386 insertions(+), 155 deletions(-)
Title: List Things to Do
Description: Manage a 'GitHub' problem using R: wrangle issues, labels and
milestones. It includes functions for storing, prioritizing (sorting),
displaying, adding, deleting, and selecting (filtering) issues based
on qualitative and quantitative information. Issues (labels and
milestones) are written in lists and categorized into the S3 class to
be easily manipulated as datasets in R.
Author: Tanguy Barthelemy [aut, cre, art, cph]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between IssueTrackeR versions 1.5.0 dated 2026-08-21 and 2.0.0 dated 2026-10-18
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Title: Fill in Missing Species Traits Using a Phylogenetic Tree
Description: Imputes missing species trait data for comparative analyses
by combining three sources of information: phylogenetic similarity
(closely related species share similar traits), cross-trait
correlations (observed traits inform missing ones), and optional
environmental covariates (climate, habitat, geography). Handles
continuous measurements, counts, binary variables, ordered categories,
unordered categories, bounded proportions, zero-inflated counts, and
compositional multi-proportion data in a single call. The default
method is a phylogenetic baseline calibrated on held-out data; an
optional graph neural network correction, which is needed to use
covariates, is blended in through a per-trait gate that retains a
baseline fallback. Provides conformal
prediction intervals for continuous, count, ordinal, and proportion
traits and an experimental analysis-aware multiple-imputation workflow
for one missing continuous covariate in Gaussian linear, binomial-logit,
and Gaussian random-intercept m [...truncated...]
Author: Shinichi Nakagawa [aut, cre, cph]
Maintainer: Shinichi Nakagawa <itchyshin@gmail.com>
Diff between pigauto versions 0.10.0 dated 2026-07-30 and 0.11.0 dated 2026-10-18
DESCRIPTION | 31 MD5 | 271 +- NAMESPACE | 6 NEWS.md | 1003 ++++++++- R/active_impute.R | 20 R/bm_internal.R | 104 R/build_phylo_graph.R | 10 R/check_pigauto.R |only R/cross_validate.R | 10 R/data.R | 75 R/draws_conditional.R |only R/evaluate.R | 57 R/exact_conditional.R |only R/fit_baseline.R | 1210 ++++++++++ R/fit_helpers.R | 886 ++++++-- R/fit_pigauto.R | 1321 +++++++++--- R/henderson_s_inv.R | 49 R/impute.R | 386 +++ R/joint_mvn_baseline.R | 85 R/joint_mvn_solver.R | 850 +++++++ R/joint_threshold_baseline.R | 175 + R/mask_missing.R | 12 R/mi_posterior.R |only R/multi_impute.R | 617 +++++ R/multi_impute_analysis.R | 5 R/multi_impute_trees.R | 278 +- R/ovr_categorical.R | 78 R/pagel_lambda.R | 197 + R/phylo_signal.R | 37 R/plot.R | 53 R/plot_pigauto.R | 14 R/pool_mi.R | 211 + R/predict_pigauto.R | 809 +++++-- R/preprocess_traits.R | 241 ++ R/read_traits.R | 13 R/read_tree.R | 34 R/report.R | 183 + R/result_accessors.R |only R/save_load.R | 8 R/simulate_benchmark.R | 9 R/utils.R | 36 R/utils_torch.R | 11 R/with_imputations.R | 132 - README.md | 405 +-- build/partial.rdb |only build/vignette.rds |binary inst/NOTICE | 30 inst/doc/common-pitfalls.R | 6 inst/doc/common-pitfalls.Rmd | 81 inst/doc/common-pitfalls.html | 117 - inst/doc/getting-started.R | 79 inst/doc/getting-started.Rmd | 328 +- inst/doc/getting-started.html | 647 +++-- inst/doc/gnn-architecture.Rmd | 138 - inst/doc/gnn-architecture.html | 184 - inst/doc/mixed-types.R | 3 inst/doc/mixed-types.Rmd | 27 inst/doc/mixed-types.html | 202 - inst/doc/multiple-imputation.R |only inst/doc/multiple-imputation.Rmd |only inst/doc/multiple-imputation.html |only inst/doc/tree-uncertainty.R | 10 inst/doc/tree-uncertainty.Rmd | 56 inst/doc/tree-uncertainty.html | 95 inst/examples |only inst/extdata/novice_traits.csv |only inst/extdata/novice_tree.nwk |only man/build_phylo_graph.Rd | 7 man/calibration_df.Rd | 5 man/check_pigauto.Rd |only man/compare_methods.Rd | 26 man/completed_data.Rd |only man/cross_validate.Rd | 12 man/evaluate.Rd | 2 man/fit_baseline.Rd | 265 ++ man/fit_pigauto.Rd | 320 ++ man/impute.Rd | 254 +- man/multi_impute.Rd | 315 ++ man/multi_impute_analysis.Rd | 4 man/multi_impute_trees.Rd | 110 man/pigauto_report.Rd | 29 man/plot.pigauto_fit.Rd | 13 man/plot.pigauto_result.Rd |only man/plot_comparison.Rd | 13 man/plot_uncertainty.Rd | 3 man/pool_mi.Rd | 43 man/predict.pigauto_fit.Rd | 76 man/preprocess_traits.Rd | 14 man/print.pigauto_check.Rd |only man/print.summary_pigauto_result.Rd |only man/read_traits.Rd | 13 man/read_tree.Rd | 39 man/save_pigauto.Rd | 3 man/simulate_benchmark.Rd | 8 man/suggest_next_observation.Rd | 16 man/summary.pigauto_result.Rd |only man/tree300.Rd | 27 man/tree_full.Rd | 26 man/trees300.Rd | 32 man/with_imputations.Rd | 49 tests/testthat/fixtures/cran-audit-exported-formals.tsv |only tests/testthat/fixtures/lambda_fixed1_reference_ab02e31.rds |only tests/testthat/test-bm-internal.R | 29 tests/testthat/test-calibration-df.R |only tests/testthat/test-check-pigauto.R |only tests/testthat/test-clamp-outliers.R | 24 tests/testthat/test-community-surface.R |only tests/testthat/test-covariate-alignment.R |only tests/testthat/test-cran-audit-defaults.R |only tests/testthat/test-discrete-lambda.R |only tests/testthat/test-docs-phytools-warning.R |only tests/testthat/test-draws-auto.R |only tests/testthat/test-draws-conditional.R |only tests/testthat/test-evaluate-null.R |only tests/testthat/test-exact-centring.R |only tests/testthat/test-exact-conditional.R |only tests/testthat/test-exact-default.R |only tests/testthat/test-fit-predict.R | 36 tests/testthat/test-gbif-centroids.R | 2 tests/testthat/test-gnn-off.R |only tests/testthat/test-gnn-train-cal-symmetry.R |only tests/testthat/test-honesty-warnings.R |only tests/testthat/test-input-checks-206-207.R |only tests/testthat/test-input-checks-210-214.R |only tests/testthat/test-joint-baseline.R | 82 tests/testthat/test-joint-lambda.R |only tests/testthat/test-joint-refine-iter.R |only tests/testthat/test-joint-solver.R |only tests/testthat/test-joint-threshold-baseline.R | 75 tests/testthat/test-lambda-covariates.R |only tests/testthat/test-lambda-default.R |only tests/testthat/test-lambda-dispatch.R |only tests/testthat/test-lambda-per-type.R |only tests/testthat/test-mi-posterior.R |only tests/testthat/test-mi-provenance.R |only tests/testthat/test-mondrian-conformal.R |only tests/testthat/test-mondrian-mi-draws.R |only tests/testthat/test-monomorphic-discrete.R |only tests/testthat/test-multi-impute-posterior.R |only tests/testthat/test-multi-impute-trees.R |only tests/testthat/test-multi-impute.R | 352 --- tests/testthat/test-new-features.R | 22 tests/testthat/test-pagel-eigendecomp.R | 11 tests/testthat/test-pagel-lambda.R | 77 tests/testthat/test-phase9-integration.R | 4 tests/testthat/test-phylo-signal-gate.R | 13 tests/testthat/test-phylo-signal-multiobs.R |only tests/testthat/test-plot-comparison-methods.R |only tests/testthat/test-pmm.R | 14 tests/testthat/test-pool-mi-adapter-fixtures.R |only tests/testthat/test-pool-mi-backends.R |only tests/testthat/test-read-tree-multiphlo.R |only tests/testthat/test-report-213.R |only tests/testthat/test-result-contract.R |only tests/testthat/test-result-save-209.R |only tests/testthat/test-route-choice.R |only tests/testthat/test-safety-floor.R | 105 tests/testthat/test-shipping-coverage.R | 17 tests/testthat/test-sigma-fisher-ml.R |only tests/testthat/test-small-tree-k-eigen.R |only tests/testthat/test-species-mismatch-205.R |only tests/testthat/test-type-detection.R |only tests/testthat/test-zi-count-conformal-intervals.R |only tests/testthat/test-zi-count-conformal-mi.R |only tests/testthat/test-zi-count-splits.R |only vignettes/common-pitfalls.Rmd | 81 vignettes/getting-started.Rmd | 328 +- vignettes/gnn-architecture.Rmd | 138 - vignettes/mixed-types.Rmd | 27 vignettes/multiple-imputation.Rmd |only vignettes/tree-uncertainty.Rmd | 56 171 files changed, 11621 insertions(+), 3531 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-02-09 0.7.0
2025-12-10 0.6.0
2025-11-16 0.5.0
2025-07-08 0.4.0
2025-04-15 0.3.0
2024-11-27 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-09-23 1.2.6
2026-07-08 1.2.5
2026-04-23 1.2.4
2026-04-10 1.2.3
2026-03-30 1.2.2
2026-03-18 1.2.1
2026-03-15 1.2
2025-11-28 1.1
2025-11-25 1.0