Title: Likelihood Estimation of Stochastic Volatility Models
Description: Parameter estimation for stochastic volatility models using maximum likelihood. The latent log-volatility is
integrated out of the likelihood using the Laplace approximation. The models are fitted via 'TMB' (Template Model
Builder) (Kristensen, Nielsen, Berg, Skaug, and Bell (2016) <doi:10.18637/jss.v070.i05>). The observation error can
be Gaussian, t, skew-Gaussian or skew t (Jones and Faddy (2003) <doi:10.1111/1467-9868.00378>), with or without
leverage. Exact one-step-ahead residuals, Value at Risk and Expected Shortfall are calculated with a filter on a
grid for the log-volatility, and the Value at Risk can be backtested with the tests of Kupiec (1995)
<doi:10.3905/jod.1995.407942> and Christoffersen (1998) <doi:10.2307/2527341>.
Author: Jens Wahl [aut, cre]
Maintainer: Jens Wahl <jens.c.wahl@gmail.com>
Diff between stochvolTMB versions 0.3.0 dated 2025-01-31 and 0.4.0 dated 2026-11-07
stochvolTMB-0.3.0/stochvolTMB/man/figures/README-unnamed-chunk-3-1.png |only stochvolTMB-0.3.0/stochvolTMB/man/figures/README-unnamed-chunk-3-2.png |only stochvolTMB-0.3.0/stochvolTMB/man/residuals.Rd |only stochvolTMB-0.4.0/stochvolTMB/DESCRIPTION | 21 stochvolTMB-0.4.0/stochvolTMB/MD5 | 93 stochvolTMB-0.4.0/stochvolTMB/NAMESPACE | 15 stochvolTMB-0.4.0/stochvolTMB/NEWS.md | 65 stochvolTMB-0.4.0/stochvolTMB/R/compare.R |only stochvolTMB-0.4.0/stochvolTMB/R/demo.R | 35 stochvolTMB-0.4.0/stochvolTMB/R/diagnostics.R |only stochvolTMB-0.4.0/stochvolTMB/R/optSV.R | 243 +- stochvolTMB-0.4.0/stochvolTMB/R/residuals.R | 241 ++ stochvolTMB-0.4.0/stochvolTMB/R/risk.R |only stochvolTMB-0.4.0/stochvolTMB/R/simSV.R | 76 stochvolTMB-0.4.0/stochvolTMB/R/skew_t.R |only stochvolTMB-0.4.0/stochvolTMB/R/stochvolTMB-package.R | 2 stochvolTMB-0.4.0/stochvolTMB/R/volplot.R | 24 stochvolTMB-0.4.0/stochvolTMB/R/zzz.R | 3 stochvolTMB-0.4.0/stochvolTMB/README.md | 245 +- stochvolTMB-0.4.0/stochvolTMB/build/partial.rdb |only stochvolTMB-0.4.0/stochvolTMB/build/vignette.rds |binary stochvolTMB-0.4.0/stochvolTMB/inst/REFERENCES.bib | 50 stochvolTMB-0.4.0/stochvolTMB/inst/doc/stochvolTMB_vignette.R | 63 stochvolTMB-0.4.0/stochvolTMB/inst/doc/stochvolTMB_vignette.Rmd | 312 ++- stochvolTMB-0.4.0/stochvolTMB/inst/doc/stochvolTMB_vignette.html | 946 +++++++--- stochvolTMB-0.4.0/stochvolTMB/inst/shiny-example/ui.R | 7 stochvolTMB-0.4.0/stochvolTMB/man/backtest_var.Rd |only stochvolTMB-0.4.0/stochvolTMB/man/coef.stochvolTMB.Rd |only stochvolTMB-0.4.0/stochvolTMB/man/compare_models.Rd |only stochvolTMB-0.4.0/stochvolTMB/man/demo.Rd | 15 stochvolTMB-0.4.0/stochvolTMB/man/estimate_parameters.Rd | 69 stochvolTMB-0.4.0/stochvolTMB/man/figures/README-example-1.png |binary stochvolTMB-0.4.0/stochvolTMB/man/figures/README-example-2.png |binary stochvolTMB-0.4.0/stochvolTMB/man/figures/README-unnamed-chunk-5-1.png |binary stochvolTMB-0.4.0/stochvolTMB/man/figures/README-unnamed-chunk-6-1.png |only stochvolTMB-0.4.0/stochvolTMB/man/figures/README-unnamed-chunk-7-1.png |only stochvolTMB-0.4.0/stochvolTMB/man/forecast_var_es.Rd |only stochvolTMB-0.4.0/stochvolTMB/man/grid_filter.Rd |only stochvolTMB-0.4.0/stochvolTMB/man/n_tmb_dlls.Rd |only stochvolTMB-0.4.0/stochvolTMB/man/osa_grid.Rd |only stochvolTMB-0.4.0/stochvolTMB/man/plot_diagnostics.Rd |only stochvolTMB-0.4.0/stochvolTMB/man/plot_returns.Rd |only stochvolTMB-0.4.0/stochvolTMB/man/plot_var.Rd |only stochvolTMB-0.4.0/stochvolTMB/man/residuals.stochvolTMB.Rd |only stochvolTMB-0.4.0/stochvolTMB/man/rsn_standard.Rd |only stochvolTMB-0.4.0/stochvolTMB/man/run_shiny_demo.Rd |only stochvolTMB-0.4.0/stochvolTMB/man/sim_sv.Rd | 12 stochvolTMB-0.4.0/stochvolTMB/man/skew_t.Rd |only stochvolTMB-0.4.0/stochvolTMB/man/skewness_to_alpha.Rd |only stochvolTMB-0.4.0/stochvolTMB/man/standard_error_distribution.Rd |only stochvolTMB-0.4.0/stochvolTMB/man/var_es.Rd |only stochvolTMB-0.4.0/stochvolTMB/src/stochvolTMB.cpp | 221 +- stochvolTMB-0.4.0/stochvolTMB/tests/testthat/test-optSV.R | 89 stochvolTMB-0.4.0/stochvolTMB/tests/testthat/test-risk.R |only stochvolTMB-0.4.0/stochvolTMB/tests/testthat/test-simSV.R | 23 stochvolTMB-0.4.0/stochvolTMB/tests/testthat/test-skew_t.R |only stochvolTMB-0.4.0/stochvolTMB/tests/testthat/test-volplot.R | 78 stochvolTMB-0.4.0/stochvolTMB/tests/testthat/test_objects/estimate_parameters.rds |binary stochvolTMB-0.4.0/stochvolTMB/tests/testthat/test_objects/generate_test_parameter_estimates.R | 23 stochvolTMB-0.4.0/stochvolTMB/tests/testthat/test_objects/test_parameter_estimates.rds |binary stochvolTMB-0.4.0/stochvolTMB/tests/testthat/test_objects/test_summary.rds |binary stochvolTMB-0.4.0/stochvolTMB/vignettes/stochvolTMB_vignette.Rmd | 312 ++- 62 files changed, 2712 insertions(+), 571 deletions(-)
Title: Genotype-by-Environment Interaction and Yield Stability Analysis
Description: Analyses multi-environment trials of plant breeding, laid out in
randomized complete blocks in every environment, to find genotypes that
are high-yielding and stable: analyses of variance in each
environment and combined; Eberhart and Russell's analysis (1966)
<doi:10.2135/cropsci1966.0011183X000600010011x> and Finlay and Wilkinson's
regression (1963) <doi:10.1071/AR9630742>; Wricke's ecovalence, Shukla's
stability variance (1972) <doi:10.1038/hdy.1972.87> and Kang and Pham's
yield-stability statistic (1991)
<doi:10.2134/agronj1991.00021962008300010037x>; Kang's rank-sum and Fox's
top-third ranking; Eskridge's safety-first indices (1990), Annicchiarico's
reliability index (1992), Lin and Binns' superiority measure (1988) and
Huehn's nonparametric statistics (1979) with tests; additive main effects and multiplicative interaction
(AMMI) analysis with biplots and AMMI stability values on any number of
axes; the GGE biplot with which-won-where, mean-stability and
di [...truncated...]
Author: Muhammad Yaseen [aut, cre, cph] ,
Kent Eskridge [aut, ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between stability versions 0.6.0 dated 2024-09-29 and 1.0.0 dated 2026-11-07
stability-0.6.0/stability/man/stability.Rd |only stability-1.0.0/stability/DESCRIPTION | 77 ++- stability-1.0.0/stability/MD5 | 203 ++++++-- stability-1.0.0/stability/NAMESPACE | 59 +- stability-1.0.0/stability/NEWS.md | 108 +++- stability-1.0.0/stability/R/add_anova.R | 169 ++++--- stability-1.0.0/stability/R/ammi.R | 265 +++++------ stability-1.0.0/stability/R/ammi_biplot.R | 177 +++---- stability-1.0.0/stability/R/common-notation.R |only stability-1.0.0/stability/R/common-objects.R |only stability-1.0.0/stability/R/common-plot.R |only stability-1.0.0/stability/R/common-reference.R |only stability-1.0.0/stability/R/common-validate.R |only stability-1.0.0/stability/R/core-ammi.R |only stability-1.0.0/stability/R/core-ge.R |only stability-1.0.0/stability/R/core-measures.R |only stability-1.0.0/stability/R/core-prep.R |only stability-1.0.0/stability/R/core-regression.R |only stability-1.0.0/stability/R/core-safety.R |only stability-1.0.0/stability/R/er_anova.R | 308 ++++++------- stability-1.0.0/stability/R/ge_data.R | 53 +- stability-1.0.0/stability/R/ge_effects.R | 157 +++--- stability-1.0.0/stability/R/ge_means.R | 190 ++++---- stability-1.0.0/stability/R/gge_biplot.R | 282 ++++++++---- stability-1.0.0/stability/R/indiv_anova.R | 197 +++++--- stability-1.0.0/stability/R/stab_asv.R | 188 +++----- stability-1.0.0/stability/R/stab_dist.R | 182 +++---- stability-1.0.0/stability/R/stab_eskridge.R |only stability-1.0.0/stability/R/stab_fox.R | 152 +++--- stability-1.0.0/stability/R/stab_huehn.R |only stability-1.0.0/stability/R/stab_interpret.R |only stability-1.0.0/stability/R/stab_kang.R | 193 +++----- stability-1.0.0/stability/R/stab_masv.R | 188 +++----- stability-1.0.0/stability/R/stab_measures.R | 250 ++++------ stability-1.0.0/stability/R/stab_par.R | 487 +++++++++------------ stability-1.0.0/stability/R/stab_reg.R | 220 ++++----- stability-1.0.0/stability/R/stab_reliability.R |only stability-1.0.0/stability/R/stab_superiority.R |only stability-1.0.0/stability/R/stability-package.R | 86 ++- stability-1.0.0/stability/README.md | 227 ++++++--- stability-1.0.0/stability/build |only stability-1.0.0/stability/inst/CITATION | 33 - stability-1.0.0/stability/inst/doc |only stability-1.0.0/stability/inst/extdata |only stability-1.0.0/stability/inst/notation |only stability-1.0.0/stability/man/add_anova.Rd | 111 +++- stability-1.0.0/stability/man/ammi.Rd | 113 +++- stability-1.0.0/stability/man/ammi_biplot.Rd | 98 +++- stability-1.0.0/stability/man/er_anova.Rd | 124 ++++- stability-1.0.0/stability/man/figures |only stability-1.0.0/stability/man/ge_data.Rd | 46 + stability-1.0.0/stability/man/ge_effects.Rd | 88 ++- stability-1.0.0/stability/man/ge_means.Rd | 99 ++-- stability-1.0.0/stability/man/gge_biplot.Rd | 131 ++++- stability-1.0.0/stability/man/indiv_anova.Rd | 107 +++- stability-1.0.0/stability/man/stab-methods.Rd |only stability-1.0.0/stability/man/stab_asv.Rd | 98 +++- stability-1.0.0/stability/man/stab_dist.Rd | 101 +++- stability-1.0.0/stability/man/stab_eskridge.Rd |only stability-1.0.0/stability/man/stab_fox.Rd | 95 ++-- stability-1.0.0/stability/man/stab_huehn.Rd |only stability-1.0.0/stability/man/stab_interpret.Rd |only stability-1.0.0/stability/man/stab_kang.Rd | 96 ++-- stability-1.0.0/stability/man/stab_masv.Rd | 101 +++- stability-1.0.0/stability/man/stab_measures.Rd | 99 +++- stability-1.0.0/stability/man/stab_notation.Rd |only stability-1.0.0/stability/man/stab_par.Rd | 135 ++++- stability-1.0.0/stability/man/stab_reference.Rd |only stability-1.0.0/stability/man/stab_reg.Rd | 116 +++-- stability-1.0.0/stability/man/stab_reliability.Rd |only stability-1.0.0/stability/man/stab_save.Rd |only stability-1.0.0/stability/man/stab_superiority.Rd |only stability-1.0.0/stability/man/stab_theme.Rd |only stability-1.0.0/stability/man/stability-package.Rd |only stability-1.0.0/stability/tests |only stability-1.0.0/stability/vignettes |only 76 files changed, 3633 insertions(+), 2576 deletions(-)
Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331>, Jiang, et al (2026) for more details.
Author: Andrew Butler [ctb] ,
Saket Choudhary [ctb] ,
David Collins [ctb] ,
Charlotte Darby [ctb] ,
Jeff Farrell [ctb],
Isabella Grabski [ctb] ,
Christoph Hafemeister [ctb] ,
Yuhan Hao [ctb] ,
Austin Hartman [ctb] ,
Paul Hoffman [ctb] ,
Jaison Jain [ctb] ,
L [...truncated...]
Maintainer: Rahul Satija <seurat@nygenome.org>
Diff between Seurat versions 5.6.0 dated 2026-10-03 and 6.0.0 dated 2026-11-07
Seurat-5.6.0/Seurat/man/Format10X_GeoJson_CellID.Rd |only Seurat-6.0.0/Seurat/DESCRIPTION | 45 Seurat-6.0.0/Seurat/MD5 | 131 Seurat-6.0.0/Seurat/NAMESPACE | 88 Seurat-6.0.0/Seurat/NEWS.md | 56 Seurat-6.0.0/Seurat/R/RcppExports.R | 8 Seurat-6.0.0/Seurat/R/clustering.R | 133 Seurat-6.0.0/Seurat/R/convenience.R | 142 Seurat-6.0.0/Seurat/R/differential_expression.R | 13 Seurat-6.0.0/Seurat/R/dimensional_reduction.R | 50 Seurat-6.0.0/Seurat/R/generics.R | 2 Seurat-6.0.0/Seurat/R/integration.R | 124 Seurat-6.0.0/Seurat/R/objects.R | 28 Seurat-6.0.0/Seurat/R/preprocessing.R | 2663 ++++++++-- Seurat-6.0.0/Seurat/R/preprocessing5.R | 5 Seurat-6.0.0/Seurat/R/scslide_de.R |only Seurat-6.0.0/Seurat/R/scslide_dimreduc.R |only Seurat-6.0.0/Seurat/R/scslide_sample_level.R |only Seurat-6.0.0/Seurat/R/sketching.R | 156 Seurat-6.0.0/Seurat/R/utilities.R | 6 Seurat-6.0.0/Seurat/R/visualization.R | 647 +- Seurat-6.0.0/Seurat/R/zzz.R | 2 Seurat-6.0.0/Seurat/README.md | 2 Seurat-6.0.0/Seurat/inst/CITATION | 17 Seurat-6.0.0/Seurat/man/CombinePlots.Rd | 2 Seurat-6.0.0/Seurat/man/FindNeighbors.Rd | 2 Seurat-6.0.0/Seurat/man/FindmmNN.Rd |only Seurat-6.0.0/Seurat/man/FindsmNN.Rd |only Seurat-6.0.0/Seurat/man/GenerateSampleObject.Rd |only Seurat-6.0.0/Seurat/man/ImageDimPlot.Rd | 11 Seurat-6.0.0/Seurat/man/ImageFeaturePlot.Rd | 12 Seurat-6.0.0/Seurat/man/InteractiveSpatialPlot.Rd | 4 Seurat-6.0.0/Seurat/man/LeverageScore.Rd | 2 Seurat-6.0.0/Seurat/man/LoadAteraCodewords.Rd |only Seurat-6.0.0/Seurat/man/LoadAteraMolecules.Rd |only Seurat-6.0.0/Seurat/man/LoadAteraSegmentations.Rd |only Seurat-6.0.0/Seurat/man/NormalizeChiSquared.Rd |only Seurat-6.0.0/Seurat/man/PlotAnnotatedHeatmap.Rd |only Seurat-6.0.0/Seurat/man/PrepSCTFindMarkers.Rd | 3 Seurat-6.0.0/Seurat/man/PrepareSampleObject.Rd |only Seurat-6.0.0/Seurat/man/QuickCorTest.Rd |only Seurat-6.0.0/Seurat/man/Read10X_Coordinates.Rd | 8 Seurat-6.0.0/Seurat/man/Read10X_HD_GeoJson.Rd | 4 Seurat-6.0.0/Seurat/man/Read10X_Image.Rd | 6 Seurat-6.0.0/Seurat/man/Read10X_Segmentations.Rd | 9 Seurat-6.0.0/Seurat/man/Read10X_h5.Rd | 5 Seurat-6.0.0/Seurat/man/ReadAtera.Rd |only Seurat-6.0.0/Seurat/man/ReadXenium.Rd | 81 Seurat-6.0.0/Seurat/man/RunDiffusionMap.Rd |only Seurat-6.0.0/Seurat/man/RunPLS.Rd |only Seurat-6.0.0/Seurat/man/Seurat-package.Rd | 4 Seurat-6.0.0/Seurat/man/SingleImagePlot.Rd | 15 Seurat-6.0.0/Seurat/man/SingleSpatialPlot.Rd | 6 Seurat-6.0.0/Seurat/man/SketchDataByGroup.Rd |only Seurat-6.0.0/Seurat/man/TrajDETest.Rd |only Seurat-6.0.0/Seurat/man/VizDimLoadings.Rd | 2 Seurat-6.0.0/Seurat/man/cppls_ondisk.IterableMatrix.Rd |only Seurat-6.0.0/Seurat/man/cppls_ondisk.Rd |only Seurat-6.0.0/Seurat/man/kernelpls.IterableMatrix.Rd |only Seurat-6.0.0/Seurat/man/kernelpls.Rd |only Seurat-6.0.0/Seurat/src/Makevars | 1 Seurat-6.0.0/Seurat/src/Makevars.win | 1 Seurat-6.0.0/Seurat/src/RcppExports.cpp | 37 Seurat-6.0.0/Seurat/src/pls.cpp |only Seurat-6.0.0/Seurat/src/pls.h |only Seurat-6.0.0/Seurat/src/pls_bpcells.h |only Seurat-6.0.0/Seurat/src/pls_bridge.cpp |only Seurat-6.0.0/Seurat/tests/testthat/test_differential_expression.R | 451 - Seurat-6.0.0/Seurat/tests/testthat/test_dimensional_reduction.R | 14 Seurat-6.0.0/Seurat/tests/testthat/test_find_clusters.R | 7 Seurat-6.0.0/Seurat/tests/testthat/test_integratedata.R | 2 Seurat-6.0.0/Seurat/tests/testthat/test_integration.R | 79 Seurat-6.0.0/Seurat/tests/testthat/test_integration5.R | 2 Seurat-6.0.0/Seurat/tests/testthat/test_load_10X.R | 126 Seurat-6.0.0/Seurat/tests/testthat/test_pls.R |only Seurat-6.0.0/Seurat/tests/testthat/test_preprocessing.R | 62 Seurat-6.0.0/Seurat/tests/testthat/test_scslide_nn.R |only Seurat-6.0.0/Seurat/tests/testthat/test_sketching.R | 201 Seurat-6.0.0/Seurat/tests/testthat/test_spatial.R | 690 ++ Seurat-6.0.0/Seurat/tests/testthat/test_tree.R | 1 Seurat-6.0.0/Seurat/tests/testthat/test_utilities.R | 2 81 files changed, 4883 insertions(+), 1287 deletions(-)
Title: Reproducible Data Capsules with Provenance and Fallback
Description: For analyzing published and unpublished tables, from open-data
portals and statistical agencies to a researcher's own data, so that a
result can be traced to the exact data behind it and checked again
afterwards. A 'capsule' records where each source came from, its Secure
Hash Algorithm 256 ('SHA-256') hash, the schema it should have and an
archived copy in the Internet Archive 'Wayback Machine'
('web.archive.org'); sources are found through the Comprehensive
Knowledge Archive Network ('CKAN', 'ckan.org'). Run again, a capsule
says whether each source still matches and, if it does not, how its
distribution moved (Kolmogorov-Smirnov, chi-square, population stability
index and 'Benford' first-digit screens), and when a source cannot be
reached it runs on schema-driven synthetic data that is marked as such.
Capsules can be signed with keyed hashes ('HMAC-SHA-256', RFC 2104) or
with the post-quantum signature standards 'ML-DSA' (FIPS 204), 'SLH-DSA'
(FIPS 205) and 'XMSS' (RFC 8391), implem [...truncated...]
Author: Vansh Singh Ruhela [aut, cre]
Maintainer: Vansh Singh Ruhela <vsruhela@proton.me>
Diff between rmoriebricklayer versions 1.0.4 dated 2026-10-31 and 1.1.0 dated 2026-11-07
DESCRIPTION | 12 +- MD5 | 88 +++++++++---------- NEWS.md | 14 +++ R/aaa_input_guards.R | 10 +- R/archive_rmorie.R | 140 ++++++++++++++++++++++++++----- R/areal.R | 4 R/box_readings.R | 2 R/categorical_guard.R | 15 +-- R/cli.R | 2 R/dashboard.R | 2 R/dashboard_cards.R | 6 - R/dashboard_modules.R | 2 R/falsify.R | 2 R/fetch_siu.R | 2 R/indigenous.R | 2 R/json_native.R | 95 +++++++++++++-------- R/justice.R | 2 R/lib_capsule.R | 2 R/mkbndl.R | 14 +-- R/mkbndlchk.R | 34 +++++-- R/policy_evaluation.R | 2 R/policy_plots.R | 2 R/print_methods.R | 4 R/rate.R | 2 R/survey.R | 2 R/trend.R | 2 R/wayback_save.R | 10 +- R/xmss_state.R | 10 +- R/yoy_labels.R | 2 README.md | 2 inst/WORDLIST | 1 inst/doc/applied-analyses.html | 18 +-- inst/doc/capsules-and-provenance.html | 30 +++--- inst/doc/describing-data-and-tables.html | 2 inst/doc/integrity-and-cryptography.html | 4 inst/smoke/smoke.R | 13 ++ src/rmbl_json.cpp | 12 +- tests/testthat/helper-noexists.R |only tests/testthat/test-archive_rmorie.R | 83 ++++++++++++++++++ tests/testthat/test-bndl-lib.R | 2 tests/testthat/test-c29-recheck.R | 18 +++ tests/testthat/test-conn-leak.R |only tests/testthat/test-download-branches.R | 5 - tests/testthat/test-json-branches.R | 9 + tests/testthat/test-json-edges.R | 86 +++++++++++++++++++ tests/testthat/test-round8.R | 10 +- 46 files changed, 587 insertions(+), 194 deletions(-)
More information about rmoriebricklayer at CRAN
Permanent link
Title: Quantity Calculus for R Vectors
Description: Integration of the 'units' and 'errors' packages for a complete
quantity calculus system for R vectors, matrices and arrays, with automatic
propagation, conversion, derivation and simplification of magnitudes and
uncertainties. Documentation about 'units' and 'errors' is provided in the
papers by Pebesma, Mailund & Hiebert (2016, <doi:10.32614/RJ-2016-061>) and
by Ucar, Pebesma & Azcorra (2018, <doi:10.32614/RJ-2018-075>), included in
those packages as vignettes; see 'citation("quantities")' for details.
Author: Inaki Ucar [aut, cph, cre]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>
Diff between quantities versions 0.2.3 dated 2025-01-18 and 0.2.4 dated 2026-11-07
DESCRIPTION | 11 +++--- MD5 | 28 +++++++-------- NEWS.md | 6 +++ R/misc.R | 11 +----- R/utils.R | 20 +++++++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/introduction.Rmd | 4 +- inst/doc/introduction.html | 80 +++++++++++++++++++++------------------------ inst/doc/parsing.html | 4 +- man/quantities.Rd | 6 +-- man/rep.quantities.Rd | 2 - man/units.Rd | 6 +-- tests/testthat/test-misc.R | 7 +++ vignettes/introduction.Rmd | 4 +- 15 files changed, 107 insertions(+), 82 deletions(-)
Title: Graphic Styles of Emile Cheysson for 'ggplot2'
Description: Implements for 'ggplot2' the stylistic elements (fonts, hatched patterns, color palettes) used by 'Emile
Cheysson' in the 'Albums de Statistique Graphique', sometimes called the pinnacle of the
Golden Age of Statistical Graphics.
Author: Michael Friendly [aut, cre] ,
RJ Andrews [ctb],
Tom Shanley [ctb],
Kenneth Fields [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between ggCheysson versions 1.1.0 dated 2026-10-01 and 1.2.0 dated 2026-11-07
ggCheysson-1.1.0/ggCheysson/R/globals.R |only ggCheysson-1.2.0/ggCheysson/DESCRIPTION | 16 ggCheysson-1.2.0/ggCheysson/MD5 | 68 +- ggCheysson-1.2.0/ggCheysson/NAMESPACE | 2 ggCheysson-1.2.0/ggCheysson/NEWS.md | 46 + ggCheysson-1.2.0/ggCheysson/R/cheysson_name.R | 6 ggCheysson-1.2.0/ggCheysson/R/migration.R | 94 +-- ggCheysson-1.2.0/ggCheysson/R/palettes.R | 10 ggCheysson-1.2.0/ggCheysson/R/patterns.R | 4 ggCheysson-1.2.0/ggCheysson/R/scale_cheysson.R | 122 ++-- ggCheysson-1.2.0/ggCheysson/R/scale_patterns.R | 4 ggCheysson-1.2.0/ggCheysson/R/scales.R | 8 ggCheysson-1.2.0/ggCheysson/R/show_swatches.R |only ggCheysson-1.2.0/ggCheysson/R/swatches.R |only ggCheysson-1.2.0/ggCheysson/R/utils.R |only ggCheysson-1.2.0/ggCheysson/README.md | 143 ++--- ggCheysson-1.2.0/ggCheysson/inst/doc/combining-colors-patterns.R | 49 - ggCheysson-1.2.0/ggCheysson/inst/doc/combining-colors-patterns.Rmd | 155 +++--- ggCheysson-1.2.0/ggCheysson/inst/doc/combining-colors-patterns.html | 255 +++++----- ggCheysson-1.2.0/ggCheysson/inst/doc/getting-started.R | 37 - ggCheysson-1.2.0/ggCheysson/inst/doc/getting-started.Rmd | 50 - ggCheysson-1.2.0/ggCheysson/inst/doc/getting-started.html | 121 ++-- ggCheysson-1.2.0/ggCheysson/inst/doc/guerry-maps.R | 73 -- ggCheysson-1.2.0/ggCheysson/inst/doc/guerry-maps.Rmd | 94 --- ggCheysson-1.2.0/ggCheysson/inst/doc/guerry-maps.html | 176 ++---- ggCheysson-1.2.0/ggCheysson/man/cheysson_swatches.Rd |only ggCheysson-1.2.0/ggCheysson/man/figures/README-complete-aesthetic-1.png |binary ggCheysson-1.2.0/ggCheysson/man/figures/README-pattern-bars-1.png |binary ggCheysson-1.2.0/ggCheysson/man/figures/README-pattern-swatches-1.png |binary ggCheysson-1.2.0/ggCheysson/man/figures/README-show-swatches-1.png |only ggCheysson-1.2.0/ggCheysson/man/figures/swatches.png |only ggCheysson-1.2.0/ggCheysson/man/scale_cheysson.Rd | 86 +-- ggCheysson-1.2.0/ggCheysson/man/scale_color_cheysson.Rd | 136 ++--- ggCheysson-1.2.0/ggCheysson/man/show_swatches.Rd |only ggCheysson-1.2.0/ggCheysson/tests |only ggCheysson-1.2.0/ggCheysson/vignettes/combining-colors-patterns.Rmd | 155 +++--- ggCheysson-1.2.0/ggCheysson/vignettes/getting-started.Rmd | 50 - ggCheysson-1.2.0/ggCheysson/vignettes/guerry-maps.Rmd | 94 --- 38 files changed, 949 insertions(+), 1105 deletions(-)
Title: Classify Aquatic Animal Behaviours from Vertical Movement Data
Description: Quantitatively analyse depth time-series data from pop-up satellite archival tags (PSATs) through the application of continuous wavelet transformation (CWT) combined with Principal Component Analysis (PCA), and k-means clustering.
Import, crop, and plot depth time-depth records (TDRs). Using CWT to detect important signals within the non-stationary data, we create daily wavelet statistics to summarise vertical movements on different wavelet periods and combine with daily and diel depth statistics.
Classify depth time-series with unsupervised k-means clustering into 24-hour periods of vertical movement behaviour with distinct patterns of vertical movement. Plot example days from each behaviour cluster, and plot the TDR coloured by cluster.
Based on principles of combining CWT with k-means first developed by Sakamoto et al. (2009) <doi:10.1371/journal.pone.0005379> and redeveloped by Beale et al. (2026) <doi:10.1186/s40462-025-00622-w>.
Author: Calvin Beale [aut, cre, cph]
Maintainer: Calvin Beale <calvin.beale.8@gmail.com>
Diff between FishDiveR versions 1.1.0 dated 2026-01-26 and 1.3.0 dated 2026-11-07
DESCRIPTION | 18 MD5 | 106 + NAMESPACE | 101 - NEWS.md | 41 R/10_plot_clusters.R | 1307 ++++++++---------- R/1_import_tag_data.R | 985 +++++++------ R/2_create_wavelet.R | 1099 +++++++-------- R/3_create_wavelet_stats.R | 356 ++--- R/4_create_depth_stats.R | 930 ++++++------- R/5_pca_data.R | 426 +++--- R/6_pca_results.R | 1910 +++++++++++++-------------- R/7_select_k.R | 566 ++++---- R/8_k_clustering.R | 929 ++++++------- R/9_plot_cluster_TDR.R | 609 ++++---- R/FishDiveR-package.R | 40 R/app_helpers.R |only R/app_mod_cluster.R |only R/app_mod_import.R |only R/app_mod_pca.R |only R/app_mod_project.R |only R/app_mod_results.R |only R/app_mod_stats.R |only R/app_mod_wavelet.R |only R/app_ui.R |only R/app_utils.R |only R/globals.R | 101 - R/plot_time_at.R |only R/run_app.R |only R/sampling_report.R |only R/thin_archive.R |only R/utils.R | 33 R/zzz.R | 16 README.md | 1061 +++++++------- build |only inst/CITATION | 28 inst/doc |only man/FishDiveR-package.Rd | 9 man/create_wavelet.Rd | 5 man/figures/logo.png |binary man/import_tag_data.Rd | 10 man/plot_TDR.Rd | 18 man/plot_cluster_TDR.Rd | 9 man/plot_time_at.Rd |only man/run_app.Rd |only man/sampling_report.Rd |only man/thin_archive.Rd |only tests/testthat/test-10_plot_clusters.R | 112 - tests/testthat/test-1_import_tag_data.R | 213 +-- tests/testthat/test-2_create_wavelet.R | 142 -- tests/testthat/test-3_create_wavelet_stats.R | 40 tests/testthat/test-4_create_depth_stats.R | 128 - tests/testthat/test-5_pca_data.R | 88 - tests/testthat/test-6_pca_results.R | 196 +- tests/testthat/test-7_select_k.R | 82 - tests/testthat/test-8_k_clustering.R | 86 - tests/testthat/test-9_plot_cluster_TDR.R | 96 - tests/testthat/test-app.R |only tests/testthat/test-plot_time_at.R |only tests/testthat/test-sampling_report.R |only tests/testthat/test-thin_archive.R |only vignettes |only 61 files changed, 6130 insertions(+), 5766 deletions(-)
Title: Dynamic Modeling and Machine Learning Environment
Description: Estimates, predict and forecast dynamic models as well as Machine Learning metrics which assists in model selection for further analysis. The package also have capabilities to provide tools and metrics that are useful in machine learning and modeling. For example, there is quick summary, percent sign, Mallow's Cp tools and others. The ecosystem of this package is analysis of economic data for national development. The package is so far stable and has high reliability and efficiency as well as time-saving. The package is a variety but the following references are important guide to the major themes in the package (Hyndman & Athanasopoulos (2014 ISBN 978-0-9875071-0-5), Alkire & Santos (2014, doi.org/10.1016/j.worlddev.2014.01.026)).
Author: Job Nmadu [aut, cre]
Maintainer: Job Nmadu <job.nmadu@gmail.com>
Diff between Dyn4cast versions 11.11.26 dated 2026-07-23 and 11.11.28 dated 2026-11-07
Dyn4cast |only 1 file changed
Title: Backward Joint Model for the Dynamic Prediction of Both
Time-to-Event and Longitudinal Outcomes
Description: Provides tools to fit joint models of multivariate longitudinal data and time-to-event data for dynamic prediction. It allows the joint prediction of both future time-to-event outcomes and future longitudinal outcomes conditional on survival. The models accommodate irregularly measured longitudinal data and competing risks outcomes. The use of the backward joint model enables fast and efficient computation, especially for applications with large sample sizes and many longitudinal variables. Methods without competing risks are described in Shen and Li (2021) <doi:10.1002/sim.9037>, and their extension to competing risks is described in Li et al. (2026) <doi:10.1007/s10985-026-09725-x>.
Author: Wenhao Li [aut, cre],
Liang Li [aut]
Maintainer: Wenhao Li <wenhaoli.jlu@gmail.com>
Diff between BJM versions 0.3.0 dated 2026-10-31 and 0.3.1 dated 2026-11-07
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 10 ++++++++++ tests/testthat/test-longitudinalSubCopula.R | 20 +++++++++++++++++--- tests/testthat/test-survivalSubInterval.R | 2 +- 5 files changed, 35 insertions(+), 11 deletions(-)
Title: Read and Process 'FPOD' and 'CPOD' Data
Description: Read 'FPOD' and 'CPOD' data into 'R' directly from the
'FPOD' data files (i.e. .CP1, .CP3, .FP1 and .FP3 files). The 'FPOD' data
files contain binary data, so they can't trivially be read into 'R' using the
usual approach, e.g. fread() or read.csv(). This package decodes the binary
data and imports all the data in one go (i.e. header/metadata, clicks,
'KERNO' classifications, environmental data and pseudo-WAV data). It is then
trivial to aggregate data as you please, e.g. detection-positive-minutes per
time block. The advantage of handling data processing in 'R' is a long topic,
but suffice it to say that it 1) simplifies things (many fewer steps, as
different vars have to be exported in multiple goes in the official 'FPOD'
app), and more importantly, 2) makes data processing transparent and
reproducible.
References: Pirotta et al. 2014 <doi:10.1111/1365-2435.12146>.
Author: Andre Moan [aut, cre, cph]
Maintainer: Andre Moan <andre.moan@hi.no>
Diff between fpod versions 1.0.2 dated 2026-09-14 and 1.1.0 dated 2026-11-07
DESCRIPTION | 8 - MD5 | 18 +-- NEWS.md | 14 ++ R/fp_find_buzzes.R | 178 +++++++++++++++++++++++++++++------ R/misc.R | 5 inst/doc/advanced-usage.html | 60 +++++------ inst/doc/fpod.html | 14 +- man/fp_find_buzzes.Rd | 82 +++++++++++++--- tests/testthat/test-fp_find_buzzes.R | 13 +- tests/testthat/test-fp_summarize.R | 2 10 files changed, 299 insertions(+), 95 deletions(-)
Title: Residual Diagnostics for Hierarchical (Multi-Level / Mixed)
Regression Models
Description: Uses a simulation-based approach to create readily
interpretable scaled (quantile) residuals for fitted generalized linear (mixed)
models. Currently supported are linear and generalized linear (mixed) models from
'lme4' (classes 'lmerMod', 'glmerMod'), 'glmmTMB', 'GLMMadaptive', 'spaMM', and 'brms'
(simple models); phylogenetic linear models from 'phylolm' (classes 'phylolm' and 'phyloglm');
generalized additive models ('gam' from 'mgcv'); 'glm' (including 'negbin' from 'MASS', but excluding
quasi-distributions) and 'lm' model classes. Moreover, externally created simulations,
e.g. posterior predictive simulations from Bayesian software such as 'JAGS', 'STAN',
or 'BUGS' can be processed as well. The resulting residuals are standardized to
values between 0 and 1 and can be interpreted as intuitively as residuals from a
linear regression. The package also provides a number of plot and test functions
for typical model misspecification problems, such as over/underdispersion, zero-inflation [...truncated...]
Author: Florian Hartig [aut, cre] ,
Lukas Lohse [ctb],
Melina de Souza Leite [ctb] ,
Cosmina Werneke [ctb]
Maintainer: Florian Hartig <florian.hartig@biologie.uni-regensburg.de>
Diff between DHARMa versions 0.5.0 dated 2026-06-01 and 0.5.1 dated 2026-11-07
DHARMa-0.5.0/DHARMa/tests/manualTests |only DHARMa-0.5.1/DHARMa/DESCRIPTION | 16 DHARMa-0.5.1/DHARMa/MD5 | 152 - DHARMa-0.5.1/DHARMa/NAMESPACE | 13 DHARMa-0.5.1/DHARMa/NEWS.md | 85 + DHARMa-0.5.1/DHARMa/R/DHARMa.R | 16 DHARMa-0.5.1/DHARMa/R/compatibility.R | 300 ++- DHARMa-0.5.1/DHARMa/R/data.R | 2 DHARMa-0.5.1/DHARMa/R/helper.R | 59 DHARMa-0.5.1/DHARMa/R/plots.R | 110 - DHARMa-0.5.1/DHARMa/R/runBenchmarks.R | 32 DHARMa-0.5.1/DHARMa/R/simulateLRT.R | 8 DHARMa-0.5.1/DHARMa/R/simulateResiduals.R | 37 DHARMa-0.5.1/DHARMa/R/startup.R | 2 DHARMa-0.5.1/DHARMa/R/tests.R | 128 + DHARMa-0.5.1/DHARMa/R/transformQuantiles.R | 2 DHARMa-0.5.1/DHARMa/build/vignette.rds |binary DHARMa-0.5.1/DHARMa/inst/doc/DHARMa.R | 38 DHARMa-0.5.1/DHARMa/inst/doc/DHARMa.Rmd | 139 + DHARMa-0.5.1/DHARMa/inst/doc/DHARMa.html | 764 +++++----- DHARMa-0.5.1/DHARMa/inst/doc/DHARMaForBayesians.Rmd | 2 DHARMa-0.5.1/DHARMa/inst/doc/DHARMaForBayesians.html | 13 DHARMa-0.5.1/DHARMa/inst/examples/createDataHelp.R | 6 DHARMa-0.5.1/DHARMa/inst/examples/hurricanes.R | 2 DHARMa-0.5.1/DHARMa/inst/examples/plotResidualsHelp.R | 12 DHARMa-0.5.1/DHARMa/inst/examples/testDispersionHelp.R | 2 DHARMa-0.5.1/DHARMa/inst/examples/testTemporalAutocorrelationHelp.R | 7 DHARMa-0.5.1/DHARMa/inst/examples/testsHelp.R | 2 DHARMa-0.5.1/DHARMa/inst/examples/wrappersHelp.R | 4 DHARMa-0.5.1/DHARMa/man/DHARMa-package.Rd | 11 DHARMa-0.5.1/DHARMa/man/checkBinomialMatrixWeights.Rd |only DHARMa-0.5.1/DHARMa/man/createDHARMa.Rd | 5 DHARMa-0.5.1/DHARMa/man/createData.Rd | 6 DHARMa-0.5.1/DHARMa/man/getFitted.Rd | 4 DHARMa-0.5.1/DHARMa/man/getFittedResponse.Rd |only DHARMa-0.5.1/DHARMa/man/getFixedEffects.Rd | 4 DHARMa-0.5.1/DHARMa/man/getObservedResponse.Rd | 4 DHARMa-0.5.1/DHARMa/man/getPearsonResiduals.Rd | 10 DHARMa-0.5.1/DHARMa/man/getPredictorNames.Rd | 3 DHARMa-0.5.1/DHARMa/man/getRefit.Rd | 7 DHARMa-0.5.1/DHARMa/man/getRefitData.Rd |only DHARMa-0.5.1/DHARMa/man/getResiduals.Rd | 4 DHARMa-0.5.1/DHARMa/man/getSimulations.Rd | 8 DHARMa-0.5.1/DHARMa/man/hasWeights.Rd |only DHARMa-0.5.1/DHARMa/man/hurricanes.Rd | 4 DHARMa-0.5.1/DHARMa/man/outliers.Rd | 2 DHARMa-0.5.1/DHARMa/man/plot.DHARMa.Rd | 4 DHARMa-0.5.1/DHARMa/man/plotResiduals.Rd | 18 DHARMa-0.5.1/DHARMa/man/plotResidualsAll.Rd | 26 DHARMa-0.5.1/DHARMa/man/plotSimulatedResiduals.Rd | 2 DHARMa-0.5.1/DHARMa/man/recalculateResiduals.Rd | 4 DHARMa-0.5.1/DHARMa/man/residuals.DHARMa.Rd | 2 DHARMa-0.5.1/DHARMa/man/simulateLRT.Rd | 8 DHARMa-0.5.1/DHARMa/man/simulateResiduals.Rd | 10 DHARMa-0.5.1/DHARMa/man/testCategorical.Rd | 2 DHARMa-0.5.1/DHARMa/man/testDispersion.Rd | 6 DHARMa-0.5.1/DHARMa/man/testGeneric.Rd | 2 DHARMa-0.5.1/DHARMa/man/testOutliers.Rd | 10 DHARMa-0.5.1/DHARMa/man/testPhylogeneticAutocorrelation.Rd | 2 DHARMa-0.5.1/DHARMa/man/testQuantiles.Rd | 4 DHARMa-0.5.1/DHARMa/man/testResiduals.Rd | 2 DHARMa-0.5.1/DHARMa/man/testSpatialAutocorrelation.Rd | 2 DHARMa-0.5.1/DHARMa/man/testTemporalAutocorrelation.Rd | 11 DHARMa-0.5.1/DHARMa/man/testUniformity.Rd | 2 DHARMa-0.5.1/DHARMa/man/testZeroInflation.Rd | 2 DHARMa-0.5.1/DHARMa/man/transformQuantiles.Rd | 2 DHARMa-0.5.1/DHARMa/tests/testthat/_snaps/testNumericReproducibility.md |only DHARMa-0.5.1/DHARMa/tests/testthat/_snaps/testTests.md | 524 ------ DHARMa-0.5.1/DHARMa/tests/testthat/testCompatibility.R | 111 + DHARMa-0.5.1/DHARMa/tests/testthat/testDharmaClass.R | 27 DHARMa-0.5.1/DHARMa/tests/testthat/testHelper.R | 56 DHARMa-0.5.1/DHARMa/tests/testthat/testModelTypes.R | 17 DHARMa-0.5.1/DHARMa/tests/testthat/testNumericReproducibility.R | 6 DHARMa-0.5.1/DHARMa/tests/testthat/testPlots.R | 24 DHARMa-0.5.1/DHARMa/tests/testthat/testSimulateResiduals.R | 31 DHARMa-0.5.1/DHARMa/tests/testthat/testTests.R | 151 + DHARMa-0.5.1/DHARMa/vignettes/DHARMa.Rmd | 139 + DHARMa-0.5.1/DHARMa/vignettes/DHARMaForBayesians.Rmd | 2 78 files changed, 1789 insertions(+), 1445 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-04-10 0.0.1