Title: SHAP Plots for 'XGBoost'
Description: Aid in visual data investigations
using SHAP (SHapley Additive exPlanation) visualization plots for 'XGBoost' and 'LightGBM'.
It provides summary plot, dependence plot, interaction plot, and force plot and relies on
the SHAP implementation provided by 'XGBoost' and 'LightGBM'.
Author: Yang Liu [aut, cre] ,
Allan Just [aut, ctb] ,
Michael Mayer [ctb]
Maintainer: Yang Liu <lyhello@gmail.com>
Diff between SHAPforxgboost versions 0.1.3 dated 2023-05-29 and 0.2.0 dated 2025-12-13
DESCRIPTION | 21 ++-- LICENSE | 4 MD5 | 50 +++++------ NAMESPACE | 1 NEWS.md | 5 - R/SHAP_funcs.R | 151 ++++++++++++++++++----------------- R/example/example_categorical.R | 17 ++- R/example/example_dependence_plot.R | 42 +++++---- R/example/example_fit_summary.R | 34 ++++--- R/example/example_force_plot.R | 7 - R/example/example_interaction_plot.R | 28 +++--- README.md | 67 +++++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/basic_workflow.R | 2 inst/doc/basic_workflow.html | 109 ++++++++++++------------- man/shap.plot.dependence.Rd | 64 +++++++------- man/shap.plot.force_plot.Rd | 14 +-- man/shap.plot.force_plot_bygroup.Rd | 13 +-- man/shap.plot.summary.Rd | 55 ++++++------ man/shap.plot.summary.wrap1.Rd | 34 ++++--- man/shap.plot.summary.wrap2.Rd | 34 ++++--- man/shap.prep.Rd | 79 +++++++++--------- man/shap.prep.interaction.Rd | 34 ++++--- man/shap.prep.stack.data.Rd | 19 +++- man/shap.values.Rd | 46 ++++++---- 26 files changed, 502 insertions(+), 428 deletions(-)
More information about SHAPforxgboost at CRAN
Permanent link
Title: Cite 'R' Packages on the Fly in 'R Markdown' and 'Quarto'
Description: References and cites 'R' and 'R' packages on the fly in 'R
Markdown' and 'Quarto'. 'pakret' provides a minimalist API that
generates preformatted citations for 'R' and 'R' packages, and adds
their references to a '.bib' file directly from within your document.
Author: Arnaud Gallou [aut, cre, cph]
Maintainer: Arnaud Gallou <arangacas@gmail.com>
Diff between pakret versions 0.2.2 dated 2024-10-23 and 0.3.0 dated 2025-12-13
DESCRIPTION | 22 ++++++----- MD5 | 40 ++++++++++----------- NEWS.md | 33 +++++++++++++++-- R/aaa.R | 15 +++++++- R/checkers.R | 38 ++++++++++++++------ R/pakret.R | 76 +++++++++++++++++++---------------------- R/pkrt-list.R | 4 +- R/pkrt-set.R | 10 ++--- R/pkrt.R | 3 + R/utils-local.R | 2 - R/zzz.R | 23 ++++++++++-- README.md | 34 +++++++++--------- man/pakret-package.Rd | 2 - man/pkrt.Rd | 3 + man/pkrt_list.Rd | 4 +- man/pkrt_set.Rd | 4 +- tests/testthat/_snaps/pkrt.md | 23 +++++++++--- tests/testthat/helper.R | 2 - tests/testthat/test-onload.R | 1 tests/testthat/test-pkrt-set.R | 7 ++- tests/testthat/test-pkrt.R | 63 +++++++++++++++++++++++++++++---- 21 files changed, 267 insertions(+), 142 deletions(-)
Title: Variance Identification in Sparse Factor Analysis
Description: This is an implementation of the algorithm described in Section 3 of Hosszejni and Frühwirth-Schnatter (2026) <doi:10.1016/j.jmva.2025.105536>. The algorithm is used to verify that the counting rule CR(r,1) holds for the sparsity pattern of the transpose of a factor loading matrix. As detailed in Section 2 of the same paper, if CR(r,1) holds, then the idiosyncratic variances are generically identified. If CR(r,1) does not hold, then we do not know whether the idiosyncratic variances are identified or not.
Author: Darjus Hosszejni [aut, cre] ,
Sylvia Fruehwirth-Schnatter [ths]
Maintainer: Darjus Hosszejni <darjus.hosszejni@wu.ac.at>
Diff between sparvaride versions 0.1.0 dated 2023-03-13 and 1.0.0 dated 2025-12-13
DESCRIPTION | 17 +- MD5 | 28 ++-- R/RcppExports.R | 8 - README.md | 26 ++- build/vignette.rds |binary inst/CITATION | 11 + inst/doc/short_intro.R | 2 inst/doc/short_intro.Rmd | 4 inst/doc/short_intro.html | 289 ++++++++++++++++++++++++++------------------ man/counting_rule_holds.Rd | 8 - src/Makevars | 1 src/Makevars.win | 1 src/check_counting_rule.cpp | 8 - src/edmonds_karp.cpp | 23 --- vignettes/short_intro.Rmd | 4 15 files changed, 238 insertions(+), 192 deletions(-)
Title: Simulation of Diffusion Processes
Description: It provides users with a wide range of tools to simulate, estimate, analyze, and visualize the dynamics of stochastic differential systems in both forms Ito and Stratonovich. Statistical analysis with parallel Monte Carlo and moment equations methods of SDEs <doi:10.18637/jss.v096.i02>. Enabled many searchers in different domains to use these equations to modeling practical problems in financial and actuarial modeling and other areas of application, e.g., modeling and simulate of first passage time problem in shallow water using the attractive center (Boukhetala K, 1996) ISBN:1-56252-342-2.
Author: Arsalane Chouaib Guidoum [cre, aut] ,
Kamal Boukhetala [aut]
Maintainer: Arsalane Chouaib Guidoum <acguidoum@univ-tam.dz>
Diff between Sim.DiffProc versions 4.9 dated 2024-03-05 and 5.0 dated 2025-12-13
Sim.DiffProc-4.9/Sim.DiffProc/R/zzz.r |only Sim.DiffProc-4.9/Sim.DiffProc/src |only Sim.DiffProc-5.0/Sim.DiffProc/DESCRIPTION | 15 Sim.DiffProc-5.0/Sim.DiffProc/MD5 | 41 Sim.DiffProc-5.0/Sim.DiffProc/NAMESPACE | 6 Sim.DiffProc-5.0/Sim.DiffProc/build/vignette.rds |binary Sim.DiffProc-5.0/Sim.DiffProc/inst/CITATION | 1 Sim.DiffProc-5.0/Sim.DiffProc/inst/NEWS.Rd | 7 Sim.DiffProc-5.0/Sim.DiffProc/inst/doc/bridgesde.R | 50 - Sim.DiffProc-5.0/Sim.DiffProc/inst/doc/bridgesde.html | 452 +--------- Sim.DiffProc-5.0/Sim.DiffProc/inst/doc/fitsde.html | 572 ++----------- Sim.DiffProc-5.0/Sim.DiffProc/inst/doc/fptsde.R | 142 +-- Sim.DiffProc-5.0/Sim.DiffProc/inst/doc/fptsde.html | 588 ++----------- Sim.DiffProc-5.0/Sim.DiffProc/inst/doc/mcmsde.R | 24 Sim.DiffProc-5.0/Sim.DiffProc/inst/doc/mcmsde.html | 530 ++---------- Sim.DiffProc-5.0/Sim.DiffProc/inst/doc/sdetotex.html | 412 --------- Sim.DiffProc-5.0/Sim.DiffProc/inst/doc/snssde.R | 128 +- Sim.DiffProc-5.0/Sim.DiffProc/inst/doc/snssde.html | 612 +++----------- Sim.DiffProc-5.0/Sim.DiffProc/man/Sim.DiffProc-package.Rd | 4 Sim.DiffProc-5.0/Sim.DiffProc/tests/bridgesde.R | 4 Sim.DiffProc-5.0/Sim.DiffProc/tests/snssde.R | 4 21 files changed, 786 insertions(+), 2806 deletions(-)
Title: The n-vector Approach to Geographical Position Calculations
using an Ellipsoidal Model of Earth
Description: The n-vector framework uses the normal vector to
the Earth ellipsoid (called n-vector) as a non-singular position
representation that turns out to be very convenient for practical
position calculations. The n-vector is simple to use and gives exact
answers for all global positions, and all distances, for both
ellipsoidal and spherical Earth models. This package is a translation
of the 'Matlab' library from FFI, the Norwegian Defence Research
Establishment, as described in Gade (2010)
<doi:10.1017/S0373463309990415>.
Author: Enrico Spinielli [aut, cre] ,
EUROCONTROL [cph, fnd]
Maintainer: Enrico Spinielli <enrico.spinielli@eurocontrol.int>
Diff between nvctr versions 0.1.4 dated 2020-10-28 and 0.1.7 dated 2025-12-13
DESCRIPTION | 15 + MD5 | 25 +-- NEWS.md | 20 ++ R/cross_track_intersection.R | 6 R/xyz2R.R | 22 ++ README.md | 46 ++--- build/vignette.rds |binary inst/doc/position-calculations.Rmd | 6 inst/doc/position-calculations.html | 279 +++++++++++++++++------------------- man/cross_track_intersection.Rd | 2 man/nvctr.Rd | 3 man/xyz2R.Rd | 2 vignettes/ieee-with-url.csl |only vignettes/position-calculations.Rmd | 6 14 files changed, 231 insertions(+), 201 deletions(-)
Title: Fundamentos de estadística descriptiva e inferencial
Description: Este paquete pretende apoyar el proceso enseñanza-aprendizaje de estadística descriptiva e inferencial. Las funciones contenidas en el paquete 'estadistica' cubren los conceptos básicos estudiados en un curso introductorio. Muchos conceptos son ilustrados con gráficos dinámicos o web apps para facilitar su comprensión. This package aims to help the teaching-learning process of descriptive and inferential statistics. The functions contained in the package 'estadistica' cover the basic concepts studied in a statistics introductory course. Many concepts are illustrated with dynamic graphs or web apps to make the understanding easier. See: Esteban et al. (2005, ISBN: 9788497323741), Newbold et al.(2019, ISBN:9781292315034 ), Murgui et al. (2002, ISBN:9788484424673) .
Author: Vicente Coll-Serrano [aut, cre],
Rosario Martinez Verdu [aut]
Maintainer: Vicente Coll-Serrano <estadistic@uv.es>
Diff between estadistica versions 1.0 dated 2025-10-14 and 1.2 dated 2025-12-13
DESCRIPTION | 8 - MD5 | 157 +++++++++++------------ NAMESPACE | 3 R/coeficiente.variacion.R | 6 R/contraste.correlacion.R | 4 R/contraste.diferencia.medias.R | 2 R/contraste.diferencia.proporciones.R | 8 - R/contraste.media.R | 8 - R/contraste.proporcion.R | 4 R/contraste.razon.varianzas.R | 8 - R/contraste.varianza.R | 8 - R/contraste_bondad_cat.R | 2 R/correlacion.R | 6 R/covarianza.R | 8 - R/cuantiles.R | 50 +------ R/data.sets.R | 4 R/descriptivos.R | 95 +++++++++++--- R/desviacion.R | 8 - R/ic.correlacion.R | 4 R/ic.diferencia.medias.R | 16 +- R/ic.diferencia.proporciones.R | 4 R/ic.media.R | 10 - R/ic.proporcion.R | 8 - R/ic.razon.varianzas.R | 16 +- R/ic.varianza.R | 8 - R/leer.datos.R | 206 +++++++++++++++---------------- R/matriz.correlacion.R | 6 R/matriz.covarianzas.R | 8 - R/media.R | 8 - R/mediana.R | 4 R/medidas.forma.R | 14 +- R/moda.R | 182 ++++++++++++--------------- R/muestra.R | 12 - R/print.resumen.R | 3 R/regresion.simple.R | 16 +- R/series.temporales.R | 2 R/tabla.bidimensional.R | 2 R/tabla.frecuencias.R | 2 R/unir.vectores.R | 2 R/utils.R | 167 +++++++++++++++++++++++-- R/varianza.R | 8 - data/salarios2018.rdata |binary man/coeficiente.variacion.Rd | 6 man/contraste.correlacion.Rd | 4 man/contraste.diferencia.medias.Rd | 2 man/contraste.diferencia.proporciones.Rd | 8 - man/contraste.media.Rd | 8 - man/contraste.proporcion.Rd | 4 man/contraste.razon.varianzas.Rd | 8 - man/contraste.varianza.Rd | 8 - man/contraste_bondad_cat.Rd | 2 man/correlacion.Rd | 6 man/covarianza.Rd | 8 - man/cuantiles.Rd | 4 man/desviacion.Rd | 8 - man/ic.correlacion.Rd | 4 man/ic.diferencia.medias.Rd | 16 +- man/ic.diferencia.proporciones.Rd | 4 man/ic.media.Rd | 10 - man/ic.proporcion.Rd | 8 - man/ic.razon.varianzas.Rd | 16 +- man/ic.varianza.Rd | 8 - man/leer.datos.Rd | 4 man/matriz.correlacion.Rd | 6 man/matriz.covar.Rd | 8 - man/media.Rd | 8 - man/mediana.Rd | 4 man/medidas.forma.Rd | 14 +- man/moda.Rd | 2 man/muestra.Rd | 12 - man/print.resumen.Rd | 1 man/regresion.simple.Rd | 16 +- man/resumen.descriptivos.Rd | 2 man/resumir.Rd |only man/salarios2018.Rd | 4 man/series.temporales.Rd | 2 man/tabla.bidimensional.Rd | 2 man/tabla.frecuencias.Rd | 2 man/unir.vectores.Rd | 2 man/varianza.Rd | 8 - 80 files changed, 746 insertions(+), 590 deletions(-)
Title: R Toolkit for 'Databricks'
Description: Collection of utilities that improve using 'Databricks' from R.
Primarily functions that wrap specific 'Databricks' APIs
(<https://docs.databricks.com/api>), 'RStudio' connection pane support, quality
of life functions to make 'Databricks' simpler to use.
Author: Zac Davies [aut, cre],
Rafi Kurlansik [aut],
Databricks [cph, fnd]
Maintainer: Zac Davies <zac@databricks.com>
Diff between brickster versions 0.2.9 dated 2025-09-04 and 0.2.11 dated 2025-12-13
DESCRIPTION | 10 - MD5 | 57 +++++---- NAMESPACE | 4 NEWS.md | 23 +++ R/databricks-dbi.R | 159 +++++++++++++++------------ R/databricks-dbplyr.R | 4 R/jobs.R | 38 +++++- R/lakebase.R |only R/lib-management.R | 24 ++-- R/package-auth.R | 13 -- R/request-helpers.R | 16 +- R/sql-query-execution.R | 26 +++- R/volume-fs.R | 80 ++++++------- inst/doc/sql-backend.R | 12 +- inst/doc/sql-backend.Rmd | 15 ++ inst/doc/sql-backend.html | 12 +- man/dbConnect-DatabricksDriver-method.Rd | 8 + man/db_create_table_as_select_values.Rd | 4 man/db_escape_string_literal.Rd |only man/db_jobs_reset.Rd | 6 - man/db_jobs_update.Rd | 7 + man/db_lakebase_creds_generate.Rd |only man/db_lakebase_get.Rd |only man/db_lakebase_get_by_uid.Rd |only man/db_lakebase_list.Rd |only man/db_sql_fetch_results.Rd | 3 man/db_sql_query.Rd | 3 man/figures/logo.png |binary tests/testthat/test-databricks-dbi.R | 83 +++++++++++++- tests/testthat/test-databricks-env-helpers.R | 5 tests/testthat/test-jobs.R | 67 +++++++---- tests/testthat/test-lakebase.R |only vignettes/sql-backend.Rmd | 15 ++ 33 files changed, 465 insertions(+), 229 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-08 0.9-8
2021-01-20 0.9-7
2020-11-25 0.9-6
2020-02-19 0.9-5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-12-25 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-06-12 0.1.1
2021-10-14 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-04-13 0.1.0.7
2023-09-03 0.1.0.6
2022-03-25 0.1.0.5
2022-01-10 0.1.0.4
2020-10-04 0.1.0.3
2020-05-14 0.1.0.2
2020-03-20 0.1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-07 0.3.3
2022-12-09 0.3.2
2022-08-31 0.3.1
2022-03-11 0.3.0
2021-02-07 0.2.3
2021-02-01 0.2.2
2020-07-07 0.2.1
2020-01-10 0.2.0
2019-12-01 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-06-13 0.2.2
2023-04-09 0.2.1
2021-11-08 0.2.0
2020-06-11 0.1.5
2020-04-30 0.1.4
2019-07-09 0.1.3
2018-02-25 0.1.2
2017-07-14 0.1.1
2017-05-09 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-25 0.3.10
2024-01-23 0.3.9
2023-02-15 0.3.8
2022-11-07 0.3.7
2022-11-03 0.3.6
2021-10-15 0.3.2
2020-04-02 0.2.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-17 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-11 0.1.1
2022-04-21 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-31 0.1.10
2025-03-20 0.1.9
2023-07-04 0.1.7
2022-08-14 0.1.5
2021-10-30 0.1.4
2021-10-29 0.1.2
2021-10-08 0.1.1
Title: Recommended Learners for 'mlr3'
Description: Recommended Learners for 'mlr3'. Extends 'mlr3' with
interfaces to essential machine learning packages on CRAN. This
includes, but is not limited to: (penalized) linear and logistic
regression, linear and quadratic discriminant analysis, k-nearest
neighbors, naive Bayes, support vector machines, and gradient
boosting.
Author: Michel Lang [aut] ,
Quay Au [aut] ,
Stefan Coors [aut] ,
Patrick Schratz [aut] ,
Marc Becker [cre, aut] ,
John Zobolas [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3learners versions 0.13.0 dated 2025-10-02 and 0.14.0 dated 2025-12-13
DESCRIPTION | 12 - MD5 | 28 +-- NAMESPACE | 1 NEWS.md | 4 R/LearnerClassifXgboost.R | 223 ++++++++++++++---------- R/LearnerRegrXgboost.R | 137 ++++++++++---- R/bibentries.R | 4 R/zzz.R | 1 inst/paramtest/test_paramtest_classif.xgboost.R | 70 ++----- inst/paramtest/test_paramtest_regr.xgboost.R | 71 ++----- man/mlr_learners_classif.xgboost.Rd | 40 ++-- man/mlr_learners_regr.ranger.Rd | 9 man/mlr_learners_regr.xgboost.Rd | 44 +++- tests/testthat/test_classif_xgboost.R | 122 +++++-------- tests/testthat/test_regr_xgboost.R | 44 ++-- 15 files changed, 444 insertions(+), 366 deletions(-)
Title: Multi-Variate Measurement Error Adjustment
Description: A methodology to perform multivariate measurement error adjustment using external validation data. Allows users to remove the attenuating effect of measurement error by incorporating a distribution of external validation data, and allows for plotting of all resultant adjustments. Sensitivity analyses can also be run through this package to test how different ranges of validity coefficients can impact the effect of the measurement error adjustment. The methods implemented in this package are based on the work by Muoka, A., Agogo, G., Ngesa, O., Mwambi, H. (2020): <doi:10.12688/f1000research.27892.1>.
Author: Alexander Lee [aut, cre, cph]
Maintainer: Alexander Lee <westford14@gmail.com>
Diff between rACMEMEEV versions 1.0.0 dated 2025-12-12 and 1.0.1 dated 2025-12-13
DESCRIPTION | 6 - MD5 | 12 +-- NEWS.md | 10 +- R/sensitivity.R | 2 inst/doc/example_adjustment_workflow.html | 84 +++++++++++------------ inst/doc/jags-v-stan.html | 109 +++++++++++++----------------- man/sensitivity_analysis.Rd | 2 7 files changed, 110 insertions(+), 115 deletions(-)
Title: Circular / Ring Buffers
Description: Circular / ring buffers in R and C. There are a couple
of different buffers here with different implementations that
represent different trade-offs.
Author: Rich FitzJohn [aut, cre],
Imperial College of Science, Technology and Medicine [cph]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Diff between ring versions 1.0.6 dated 2024-09-06 and 1.0.8 dated 2025-12-13
DESCRIPTION | 8 MD5 | 18 README.md | 2 build/vignette.rds |binary inst/doc/ring.R | 12 inst/doc/ring.Rmd | 8 inst/doc/ring.html | 1806 ++++++++++++++++++++++------------------ inst/doc/ring_applications.html | 962 +++++++++++---------- src/convert.c | 32 vignettes/ring.Rmd | 8 10 files changed, 1538 insertions(+), 1318 deletions(-)
Title: Fit Text Inside a Box in 'ggplot2'
Description: A 'ggplot2' extension to fit text into a box by growing, shrinking or wrapping the text.
Author: David Wilkins [aut, cre],
Brady Johnston [ctb]
Maintainer: David Wilkins <david@wilkox.org>
Diff between ggfittext versions 0.10.2 dated 2024-01-31 and 0.10.3 dated 2025-12-13
DESCRIPTION | 6 MD5 | 89 +-- NEWS.md | 11 R/geom_bar_text.R | 31 - build/vignette.rds |binary inst/doc/introduction-to-ggfittext.html | 33 - tests/testthat/_snaps/geom_bar_text/contrasting-with-non-black-text.svg | 34 - tests/testthat/_snaps/geom_bar_text/geom-bar-text-with-width-to-match-geom-col-width.svg |only tests/testthat/_snaps/geom_fit_text/angled-text.svg | 12 tests/testthat/_snaps/geom_fit_text/blank-label.svg | 58 -- tests/testthat/_snaps/geom_fit_text/box-defined-with-x-and-ymin-ymax.svg | 132 ++-- tests/testthat/_snaps/geom_fit_text/box-defined-with-xmin-xmax-and-y.svg | 12 tests/testthat/_snaps/geom_fit_text/box-defined-with-xmin-xmax-and-ymin-ymax.svg | 62 -- tests/testthat/_snaps/geom_fit_text/complex-text-with-reflowing-and-growing.svg | 12 tests/testthat/_snaps/geom_fit_text/complex-text-with-reflowing-only.svg | 12 tests/testthat/_snaps/geom_fit_text/contrasting-text.svg | 34 - tests/testthat/_snaps/geom_fit_text/contrasting-with-non-black-text.svg | 34 - tests/testthat/_snaps/geom_fit_text/default-placement-middle.svg | 12 tests/testthat/_snaps/geom_fit_text/growing-with-placement-at-the-bottom.svg | 12 tests/testthat/_snaps/geom_fit_text/growing-with-reflowing.svg | 12 tests/testthat/_snaps/geom_fit_text/growing-without-reflowing.svg | 12 tests/testthat/_snaps/geom_fit_text/label-with-formatter-function.svg | 12 tests/testthat/_snaps/geom_fit_text/numeric-width-and-height.svg | 6 tests/testthat/_snaps/geom_fit_text/placing-at-the-bottom-right.svg | 12 tests/testthat/_snaps/geom_fit_text/placing-at-the-top.svg | 12 tests/testthat/_snaps/geom_fit_text/polar-geom-fit-text-plot.svg | 16 tests/testthat/_snaps/geom_fit_text/polar-plot-with-flip-and-shifted-start.svg | 16 tests/testthat/_snaps/geom_fit_text/polar-plot-with-flip-and-text-in-top-left.svg | 16 tests/testthat/_snaps/geom_fit_text/polar-plot-with-flip.svg | 16 tests/testthat/_snaps/geom_fit_text/polar-plot-with-growing-fullheight.svg | 16 tests/testthat/_snaps/geom_fit_text/polar-plot-with-growing-non-fullheight.svg | 16 tests/testthat/_snaps/geom_fit_text/polar-plot-with-height-of-20-mm.svg | 16 tests/testthat/_snaps/geom_fit_text/polar-plot-with-height-of-5-mm.svg | 16 tests/testthat/_snaps/geom_fit_text/polar-plot-with-text-placed-at-the-bottom.svg | 16 tests/testthat/_snaps/geom_fit_text/polar-plot-with-text-placed-at-the-top.svg | 16 tests/testthat/_snaps/geom_fit_text/polar-plot-with-width-of-100-mm.svg | 16 tests/testthat/_snaps/geom_fit_text/polar-plot-with-width-of-40-mm.svg | 16 tests/testthat/_snaps/geom_fit_text/reflowing-without-growing.svg | 12 tests/testthat/_snaps/richtext/basic-rich-text-with-grow-and-reflow.svg | 12 tests/testthat/_snaps/richtext/basic-rich-text-with-grow.svg | 12 tests/testthat/_snaps/richtext/basic-rich-text-with-reflow.svg | 12 tests/testthat/_snaps/richtext/basic-rich-text.svg | 12 tests/testthat/_snaps/richtext/complex-rich-text-with-grow-and-reflow.svg | 12 tests/testthat/_snaps/richtext/complex-rich-text-with-reflow-only.svg | 12 tests/testthat/test-geom_bar_text.R | 158 +++-- tests/testthat/test-geom_fit_text.R | 272 +++++----- 46 files changed, 726 insertions(+), 642 deletions(-)
Title: Visualization and Polytomous Modeling of Survival and Competing
Risks
Description: A publication-ready toolkit for modern survival and competing risks
analysis with a minimal, formula-based interface. Both nonparametric
estimation and direct polytomous regression of cumulative incidence
functions (CIFs) are supported. The main functions 'cifcurve()', 'cifplot()',
and 'cifpanel()' estimate survival and CIF curves and produce high-quality
graphics with risk tables, censoring and competing-risk marks, and
multi-panel or inset layouts built on 'ggplot2' and 'ggsurvfit'. The modeling
function 'polyreg()' performs direct polytomous regression for coherent joint
modeling of all cause-specific CIFs to estimate risk ratios, odds ratios, or
subdistribution hazard ratios at user-specified time points. All core
functions adopt a formula-and-data syntax and return tidy and extensible
outputs that integrate smoothly with 'modelsummary', 'broom', and the broader
'tidyverse' ecosystem. Key numerical routines are implemented in C++ via
'Rcpp'.
Author: Shiro Tanaka [aut, cre, cph] ,
Shigetaka Kobari [ctb],
Chisato Honda [ctb]
Maintainer: Shiro Tanaka <gestimation@gmail.com>
Diff between cifmodeling versions 0.9.4 dated 2025-12-04 and 0.9.6 dated 2025-12-13
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Title: Record Linkage Based on an Entropy-Maximizing Classifier
Description: The goal of 'automatedRecLin' is to perform record linkage (also known as entity resolution) in unsupervised or supervised settings. It compares pairs of records from two datasets using selected comparison functions to estimate the probability or density ratio between matched and non-matched records. Based on these estimates, it predicts a set of matches that maximizes entropy. For details see: Lee et al. (2022) <https://www150.statcan.gc.ca/n1/pub/12-001-x/2022001/article/00007-eng.htm>, Vo et al. (2023) <https://ideas.repec.org/a/eee/csdana/v179y2023ics0167947322002365.html>, Sugiyama et al. (2008) <doi:10.1007/s10463-008-0197-x>.
Author: Adam Struzik [aut, cre],
Maciej Beresewicz [aut, ctb]
Maintainer: Adam Struzik <adastr5@st.amu.edu.pl>
Diff between automatedRecLin versions 1.0.0 dated 2025-11-18 and 1.0.1 dated 2025-12-13
DESCRIPTION | 8 +++---- MD5 | 14 ++++++------- NEWS.md | 4 +++ R/supervised_learning.R | 12 +++-------- README.md | 33 +++++++++++++------------------ build/partial.rdb |binary inst/tinytest/test_supervised_learning.R | 24 +++++++++------------- man/custom_rec_lin_model.Rd | 12 +++-------- 8 files changed, 47 insertions(+), 60 deletions(-)
More information about automatedRecLin at CRAN
Permanent link
Title: Version, Share, Deploy, and Monitor Models
Description: The goal of 'vetiver' is to provide fluent tooling to
version, share, deploy, and monitor a trained model. Functions handle
both recording and checking the model's input data prototype, and
predicting from a remote API endpoint. The 'vetiver' package is
extensible, with generics that can support many kinds of models.
Author: Julia Silge [cre, aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Julia Silge <julia.silge@posit.co>
Diff between vetiver versions 0.2.6 dated 2025-10-28 and 0.2.7 dated 2025-12-13
DESCRIPTION | 22 LICENSE | 2 MD5 | 232 NAMESPACE | 1 NEWS.md | 4 R/api.R | 269 R/attach-pkgs.R | 35 R/caret.R | 30 R/dashboard.R | 181 R/endpoint.R | 58 R/gam.R | 14 R/glm.R | 10 R/handlers.R | 57 R/keras.R | 64 R/kproto.R | 33 R/lm.R | 30 R/luz.R | 56 R/meta.R | 15 R/mlr3.R | 37 R/monitor.R | 327 R/open-api-spec.R | 271 R/pin-read-write.R | 194 R/prepare.R | 8 R/probably.R | 128 R/prototype.R | 84 R/ranger.R | 37 R/recipe.R | 37 R/renv.R | 19 R/rsconnect.R | 95 R/sagemaker-utils.R | 371 R/sagemaker.R | 520 R/stacks.R | 46 R/tidymodels.R | 39 R/vetiver-model.R | 140 R/vetiver-package.R | 22 R/write-docker.R | 266 R/write-plumber.R | 201 R/xgboost.R | 60 R/zzz.R | 2 README.md | 12 build/vignette.rds |binary inst/biv_tidymodels.R | 28 inst/chicago_rpart.R | 62 inst/doc/vetiver.R | 28 inst/doc/vetiver.Rmd | 36 inst/doc/vetiver.html | 32 inst/mtcars_keras.R | 54 inst/mtcars_lm.R | 10 inst/mtcars_luz.R | 47 inst/mtcars_ranger.R | 14 inst/mtcars_xgb.R | 22 inst/netflix_tidymodels.R | 47 inst/pima_Learner.R | 4 inst/plumber/biv-svm/plumber.R | 2 inst/plumber/chicago-rpart/plumber.R | 2 inst/plumber/mtcars-lm/plumber.R | 2 inst/plumber/mtcars-ranger/plumber.R | 2 inst/plumber/mtcars-xgb/plumber.R | 2 inst/plumber/netflix-descriptions/plumber.R | 2 inst/rmarkdown/templates/vetiver_dashboard/skeleton/skeleton.Rmd | 12 inst/rmarkdown/templates/vetiver_model_card/skeleton/skeleton.Rmd | 12 inst/vendor/renv.R | 7397 +++++++--- man/api_spec.Rd | 2 man/vetiver-package.Rd | 2 man/vetiver_api.Rd | 4 man/vetiver_compute_metrics.Rd | 14 man/vetiver_pin_metrics.Rd | 14 man/vetiver_plot_metrics.Rd | 14 tests/testthat/_snaps/attach-pkgs.md | 31 tests/testthat/_snaps/caret.md | 2 tests/testthat/_snaps/dashboard.md | 2 tests/testthat/_snaps/gam.md | 2 tests/testthat/_snaps/glm.md | 2 tests/testthat/_snaps/keras.md | 2 tests/testthat/_snaps/kproto.md | 2 tests/testthat/_snaps/luz.md | 2 tests/testthat/_snaps/mlr3.md | 2 tests/testthat/_snaps/monitor.md | 6 tests/testthat/_snaps/probably.md | 8 tests/testthat/_snaps/ranger.md | 2 tests/testthat/_snaps/recipe.md | 2 tests/testthat/_snaps/rsconnect.md | 4 tests/testthat/_snaps/sagemaker.md | 2 tests/testthat/_snaps/stacks.md | 2 tests/testthat/_snaps/tidymodels.md | 2 tests/testthat/_snaps/write-docker.md | 2 tests/testthat/_snaps/write-plumber.md | 14 tests/testthat/_snaps/xgboost.md | 4 tests/testthat/helper.R | 25 tests/testthat/setup.R | 44 tests/testthat/test-api.R | 334 tests/testthat/test-attach-pkgs.R | 14 tests/testthat/test-caret.R | 93 tests/testthat/test-choose-version.R | 58 tests/testthat/test-create-ptype.R | 50 tests/testthat/test-dashboard.R | 80 tests/testthat/test-gam.R | 95 tests/testthat/test-glm.R | 106 tests/testthat/test-keras.R | 134 tests/testthat/test-kproto.R | 89 tests/testthat/test-luz.R | 116 tests/testthat/test-mlr3.R | 103 tests/testthat/test-monitor.R | 255 tests/testthat/test-pin-read-write.R | 287 tests/testthat/test-predict.R | 102 tests/testthat/test-probably.R | 393 tests/testthat/test-ranger.R | 89 tests/testthat/test-recipe.R | 93 tests/testthat/test-rsconnect.R | 44 tests/testthat/test-sagemaker.R | 411 tests/testthat/test-stacks.R | 98 tests/testthat/test-tidymodels.R | 102 tests/testthat/test-type-convert.R | 117 tests/testthat/test-write-docker.R | 180 tests/testthat/test-write-plumber.R | 209 tests/testthat/test-xgboost.R | 100 vignettes/vetiver.Rmd | 36 117 files changed, 10136 insertions(+), 5712 deletions(-)
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. It currently
supports lm(), glm(), randomForest(), ranger(), earth(),
xgb.Booster.complete(), cubist(), and ctree() models.
Author: Emil Hvitfeldt [aut, cre],
Edgar Ruiz [aut],
Max Kuhn [aut]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between tidypredict versions 1.0.0 dated 2025-11-29 and 1.0.1 dated 2025-12-13
DESCRIPTION | 10 ++++---- MD5 | 26 +++++++++++----------- NEWS.md | 6 +++++ R/model-xgboost.R | 39 +++++++++++++++++++++++++++++---- README.md | 2 - build/vignette.rds |binary inst/doc/glm.html | 6 ++--- inst/doc/lm.html | 8 +++--- inst/doc/mars.html | 36 +++++++++++++++--------------- inst/doc/save.html | 2 - inst/doc/sql.html | 12 +++++----- inst/doc/xgboost.html | 12 +++++----- tests/testthat/_snaps/model-xgboost.md | 30 ++++++++++--------------- tests/testthat/test-model-xgboost.R | 37 +++++++++++++++++++++---------- 14 files changed, 135 insertions(+), 91 deletions(-)
Title: Reproducible Data Embedding
Description: Allows caching of raw data directly in R code. This allows R
scripts and R Notebooks to be shared and re-run on a machine without access
to the original data. Cached data is encoded into an ASCII string that can
be pasted into R code. When the code is run, the data is automatically
loaded from the cached version if the original data file is unavailable.
Works best for small datasets (a few hundred observations).
Author: Stefan Kloppenborg [aut, cre]
Maintainer: Stefan Kloppenborg <stefan@kloppenborg.ca>
Diff between rde versions 0.1.0 dated 2018-07-02 and 0.1.1 dated 2025-12-13
DESCRIPTION | 9 MD5 | 22 - NEWS.md | 9 R/save.R | 7 README.md | 18 - build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/rde_tutorial.R | 20 - inst/doc/rde_tutorial.html | 577 +++++++++++++++++++++++++++++++++++++-------- man/copy_rde_var.Rd | 5 tests/testthat/test_lint.R | 34 ++ tests/testthat/test_load.R | 6 12 files changed, 566 insertions(+), 142 deletions(-)
Title: An API Generator for R
Description: Gives the ability to automatically generate and serve an HTTP
API from R functions using the annotations in the R documentation
around your functions.
Author: Barret Schloerke [cre, aut] ,
Jeff Allen [aut, ccp],
Bruno Tremblay [ctb],
Frans van Dunne [ctb],
Sebastiaan Vandewoude [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Barret Schloerke <barret@posit.co>
Diff between plumber versions 1.3.0 dated 2025-02-19 and 1.3.1 dated 2025-12-13
DESCRIPTION | 62 ++-- MD5 | 51 ++- NAMESPACE | 2 NEWS.md | 16 + R/parse-body.R | 12 R/plumb.R | 15 - R/plumber.R | 3 R/serializer.R | 16 + R/ui.R | 25 + README.md | 2 inst/WORDLIST | 1 man/parsers.Rd | 5 man/serializers.Rd | 5 tests/testthat/helper-cookies.R |only tests/testthat/test-cookies.R | 78 +++-- tests/testthat/test-options.R | 2 tests/testthat/test-parse-body.R | 20 + tests/testthat/test-parser.R | 35 +- tests/testthat/test-plumber-run.R | 40 +-- tests/testthat/test-serializer-arrow-ipc.R |only tests/testthat/test-serializer-device.R | 19 - tests/testthat/test-serializer-feather.R | 1 tests/testthat/test-serializer-htmlwidgets.R | 19 - tests/testthat/test-sessions.R | 45 ++- tests/testthat/test-tidy-plumber.R | 18 - tests/testthat/test-ui-apipath.R |only tests/testthat/test-zzz-openapi.R | 353 ++++++++++++++++----------- tests/testthat/test-zzzz-include.R | 8 28 files changed, 541 insertions(+), 312 deletions(-)
Title: MCMC, Particle Filtering, and Programmable Hierarchical Modeling
Description: A system for writing hierarchical statistical models largely
compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models
and do basic R-style math, and compiling both models and nimbleFunctions via
custom-generated C++. 'NIMBLE' includes default methods for MCMC, Laplace
Approximation, deterministic nested approximations, Monte Carlo Expectation
Maximization, and some other tools.
The nimbleFunction system makes it easy to do things like implement new MCMC
samplers from R, customize the assignment of samplers to different parts of
a model from R, and compile the new samplers automatically via C++ alongside
the samplers 'NIMBLE' provides. 'NIMBLE' extends the 'BUGS'/'JAGS' language
by making it extensible: New distributions and functions can be added,
including as calls to external compiled code. Although most people think
of MCMC as the main goal of the 'BUGS'/'JAGS' language for writing models,
one can use 'NIMBLE' for writing arbitrary other kinds of model-generic
al [...truncated...]
Author: Perry de Valpine [aut],
Christopher Paciorek [aut, cre],
Daniel Turek [aut],
Nick Michaud [aut],
Cliff Anderson-Bergman [aut],
Fritz Obermeyer [aut],
Claudia Wehrhahn Cortes [aut] ,
Abel Rodriguez [aut] ,
Duncan Temple Lang [aut] ,
Wei Zhang [aut] ,
[...truncated...]
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Diff between nimble versions 1.3.0 dated 2024-12-17 and 1.4.0 dated 2025-12-13
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Title: Treatment Effects with Multiple Periods and Groups
Description: The standard Difference-in-Differences (DID) setup involves two periods and two groups -- a treated group and untreated group. Many applications of DID methods involve more than two periods and have individuals that are treated at different points in time. This package contains tools for computing average treatment effect parameters in Difference in Differences setups with more than two periods and with variation in treatment timing using the methods developed in Callaway and Sant'Anna (2021) <doi:10.1016/j.jeconom.2020.12.001>. The main parameters are group-time average treatment effects which are the average treatment effect for a particular group at a a particular time. These can be aggregated into a fewer number of treatment effect parameters, and the package deals with the cases where there is selective treatment timing, dynamic treatment effects, calendar time effects, or combinations of these. There are also functions for testing the Difference in Differences assumpti [...truncated...]
Author: Brantly Callaway [aut, cre],
Pedro H. C. Sant'Anna [aut]
Maintainer: Brantly Callaway <brantly.callaway@uga.edu>
Diff between did versions 2.1.2 dated 2022-07-20 and 2.3.0 dated 2025-12-13
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Title: Tests for Geophysical Eigenvalues
Description: The eigenvalues of observed symmetric matrices are often of intense scientific interest. This package offers single sample tests for the eigenvalues of the population mean or the eigenvalue-multiplicity of the population mean. For k-samples, this package offers tests for equal eigenvalues between samples. Included is support for matrices with constraints common to geophysical tensors (constant trace, sum of squared eigenvalues, or both) and eigenvectors are usually considered nuisance parameters. Pivotal bootstrap methods enable these tests to have good performance for small samples (n=15 for 3x3 matrices). These methods were developed and studied by Hingee, Scealy and Wood (2026, "Nonparametric bootstrap inference for the eigenvalues of geophysical tensors", accepted by the Journal of American Statistical Association). Also available is a 2-sample test using a Gaussian orthogonal ensemble approximation and an eigenvalue-multiplicity test that assumes orthogonally-invariant covariance.
Author: Kassel Liam Hingee [aut, cre] ,
Art B. Owen [cph] ,
Board of Trustees Leland Stanford Junior University [cph]
Maintainer: Kassel Liam Hingee <kassel.hingee@anu.edu.au>
Diff between TFORGE versions 0.1.15 dated 2025-12-05 and 0.1.16 dated 2025-12-12
DESCRIPTION | 11 +++++++---- MD5 | 21 +++++++++++++++------ NEWS.md | 3 +++ R/Gonjo.R |only R/TFORGE-package.R | 8 ++++++-- README.md |only build/partial.rdb |binary build/vignette.rds |only data |only inst/REFERENCES.bib | 20 ++++++++++++++++++++ inst/doc |only man/Gonjo.Rd |only man/TFORGE-package.Rd | 7 +++++-- vignettes |only 14 files changed, 56 insertions(+), 14 deletions(-)
Title: Evaluation of Binary Classifiers
Description: Evaluates the performance of binary classifiers. Computes
confusion measures (TP, TN, FP, FN), derived measures (TPR, FDR,
accuracy, F1, DOR, ..), and area under the curve. Outputs are well
suited for nested dataframes.
Author: Antoine Bichat [aut, cre]
Maintainer: Antoine Bichat <antoine.bichat@proton.me>
Diff between evabic versions 0.1.1 dated 2022-08-17 and 0.1.4 dated 2025-12-12
DESCRIPTION | 11 +-- MD5 | 36 +++++------ NEWS.md | 14 ++++ R/area.R | 21 ++++-- R/confusion_measures.R | 29 +++++---- R/derived_measures.R | 42 +++++++------ R/helpers.R | 15 ++-- R/measures.R | 29 ++++++--- R/threshold.R | 22 ++++-- R/tidy.R | 84 +++++++++++++++++++------- README.md | 74 ++++++++++++++--------- man/ebc_allmeasures.Rd | 4 - tests/testthat/test-area.R | 67 +++++++++++++++------ tests/testthat/test-names.R | 1 tests/testthat/test-previous_outputs.R | 38 ++++++++--- tests/testthat/test-resultsCM.R | 5 - tests/testthat/test-resultsDM.R | 43 +++++++------ tests/testthat/test-threshold.R | 105 +++++++++++++++++++++------------ tests/testthat/test-tidy.R | 60 ++++++++++++------ 19 files changed, 460 insertions(+), 240 deletions(-)
Title: Convert Trained 'XGBoost' Model to SQL Query
Description: This tool enables in-database scoring of 'XGBoost' models built in R, by translating trained model objects into SQL query.
'XGBoost' <https://github.com/dmlc/xgboost> provides parallel tree boosting (also known as gradient boosting machine, or GBM) algorithms
in a highly efficient, flexible and portable way. GBM algorithm is introduced by Friedman (2001) <doi:10.1214/aos/1013203451>,
and more details on 'XGBoost' can be found in Chen & Guestrin (2016) <doi:10.1145/2939672.2939785>.
Author: Chengjun Hou [aut, cre],
Abhishek Bishoyi [aut]
Maintainer: Chengjun Hou <chengjun.hou@gmail.com>
Diff between xgb2sql versions 0.1.2 dated 2019-03-13 and 0.1.3 dated 2025-12-12
DESCRIPTION | 11 MD5 | 20 - NEWS.md |only R/booster2sql.R | 74 ++++-- R/onehot2sql.R | 40 ++- README.md |only build/vignette.rds |binary inst/doc/xgb2sql.R | 34 +-- inst/doc/xgb2sql.Rmd | 35 +-- inst/doc/xgb2sql.html | 554 ++++++++++++++++++++++++++++++-------------------- man/booster2sql.Rd | 22 - vignettes/xgb2sql.Rmd | 35 +-- 12 files changed, 489 insertions(+), 336 deletions(-)
Title: Classifications for Statistics Norway
Description: Functions to search, retrieve, apply and update classification
standards and code lists using Statistics Norway's API
<https://www.ssb.no/klass> from the system 'KLASS'. Retrieves classifications
by date with options to choose language, hierarchical level and formatting.
Author: Susie Jentoft [aut, cre],
Diana-Cristina Iancu [aut],
Lisa Li [aut],
Oeyvind I. Berntsen [aut],
Statistics Norway [cph]
Maintainer: Susie Jentoft <susie.jentoft@ssb.no>
This is a re-admission after prior archival of version 1.0.3 dated 2025-10-24
Diff between klassR versions 1.0.3 dated 2025-10-24 and 1.0.4 dated 2025-12-12
DESCRIPTION | 16 +-- MD5 | 18 +-- NEWS.md | 4 R/Klass_list.R | 3 R/UpdateKlass-graph-build.R | 172 ++++++++++++++++++++++---------------- R/UpdateKlass-graph-navigate.R | 9 - man/klass_node.Rd | 5 - man/update_klass_node.Rd | 4 tests/testthat/test-UpdateKlass.R | 57 +++++++----- tests/testthat/test_ApplyKlass.R | 1 10 files changed, 164 insertions(+), 125 deletions(-)
More information about bayestransmission at CRAN
Permanent link
Title: Parallel and Memory-Efficient Ecological Diversity Metrics
Description: Computes alpha and beta diversity metrics using concurrent 'C' threads.
Metrics include 'UniFrac', Faith's phylogenetic diversity, Bray-Curtis
dissimilarity, Shannon diversity index, and many others.
Also parses newick trees into 'phylo' objects and rarefies feature tables.
Author: Daniel P. Smith [aut, cre] ,
Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between ecodive versions 2.2.0 dated 2025-12-03 and 2.2.1 dated 2025-12-12
DESCRIPTION | 6 MD5 | 20 - NAMESPACE | 4 NEWS.md | 5 inst/doc/adiv.html | 505 +++++++++++------------------------- inst/doc/bdiv.html | 472 +++++++++------------------------- inst/doc/bdiv_guide.html | 405 +++-------------------------- inst/doc/ecodive.html | 628 ++++++++++++++-------------------------------- inst/doc/performance.html | 455 +++++++-------------------------- src/beta_div.c | 22 + src/unifrac.c | 23 + 11 files changed, 683 insertions(+), 1862 deletions(-)
Title: Biologically Informed Metabolomic Libraries from 'PubChem'
Description: All 'PubChem' compounds are downloaded to a local computer, but for each compound, only partial records are used. The data are organized into small files referenced by 'PubChem' CID. This package also contains functions to parse the biologically relevant compounds from all 'PubChem' compounds, using biological database sources, pathway presence, and taxonomic relationships. Taxonomy is used to generate a lowest common ancestor taxonomy ID (NCBI) for each biological metabolite, which then enables creation of taxonomically specific metabolome databases for any taxon.
Author: Corey Broeckling [aut, cre]
Maintainer: Corey Broeckling <cbroeckl@colostate.edu>
Diff between pubchem.bio versions 1.0.1 dated 2025-08-31 and 1.0.3 dated 2025-12-12
DESCRIPTION | 10 - MD5 | 40 ++-- NAMESPACE | 2 NEWS.md | 8 R/build.cid.lca.R | 4 R/build.element.count.R |only R/build.pubchem.bio.R | 25 ++ R/data.R | 7 R/export.CompoundDb.R |only R/get.pubchem.ftp.R | 43 ++-- R/globals.R |only README.md |only data/cid.inchi.rda |binary data/cid.synonym.rda |binary data/pubchem.bio.rda |binary inst/doc/pubchem.bio.vignette.R | 18 +- inst/doc/pubchem.bio.vignette.Rmd | 26 ++ inst/doc/pubchem.bio.vignette.html | 324 +++++++++++++++++++------------------ man/build.cid.lca.Rd | 2 man/build.element.count.Rd |only man/build.pubchem.bio.Rd | 6 man/cid.inchi.Rd | 6 man/export.ComboundDb.Rd |only vignettes/pubchem.bio.vignette.Rmd | 26 ++ 24 files changed, 328 insertions(+), 219 deletions(-)
Title: Download and Display Map Tiles
Description: To create maps from tiles, 'maptiles' downloads, composes and
displays tiles from a large number of providers (e.g. 'OpenStreetMap',
'Stadia', 'Esri', 'CARTO', or 'Thunderforest').
Author: Timothee Giraud [cre, aut] ,
Diego Hernangomez [ctb] ,
Robert J. Hijmans [ctb] ,
Hugh A. Graham [ctb],
Miles McBain [cph]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between maptiles versions 0.10.0 dated 2025-05-07 and 0.11.0 dated 2025-12-12
DESCRIPTION | 21 ++++++++++++++------- MD5 | 23 ++++++++++++----------- NEWS.md | 6 ++++++ R/create_provider.R | 8 ++++---- R/get_tiles.R | 2 +- R/slippymath.R |only R/utils.R | 8 ++++---- README.md | 6 +++--- inst/tinytest/test_maptiles.R | 6 +++--- man/create_provider.Rd | 8 ++++---- man/figures/README-example-1.png |binary man/figures/README-example2-1.png |binary man/maptiles.Rd | 1 + 13 files changed, 52 insertions(+), 37 deletions(-)
Title: Age-Depth Radiocarbon Modelling
Description: Enables quick calibration of radiocarbon dates under various calibration curves (including user generated ones); age-depth modelling as per the algorithm of Haslett and Parnell (2008) <DOI:10.1111/j.1467-9876.2008.00623.x>; Relative sea level rate estimation incorporating time uncertainty in polynomial regression models (Parnell and Gehrels 2015) <DOI:10.1002/9781118452547.ch32>; non-parametric phase modelling via Gaussian mixtures as a means to determine the activity of a site (and as an alternative to the 'Oxcal' function SUM(); currently unpublished), and reverse calibration of dates from calibrated into 14C years (also unpublished).
Author: Andrew Parnell [cre, aut],
Nathan McJames [ctb],
Bruna Wundervald [ctb],
Keefe Murphy [ctb],
Mateus Maia [ctb],
Amin Shoari Nejad [ctb],
Yong Chen Goh [ctb]
Maintainer: Andrew Parnell <Andrew.Parnell1@ucd.ie>
Diff between Bchron versions 4.7.7 dated 2025-06-13 and 4.7.8 dated 2025-12-12
DESCRIPTION | 12 ++--- MD5 | 23 +++++----- NEWS.md | 6 ++ R/Bchronology.R | 31 ++++++-------- R/plot.BchronCalibratedDates.R | 3 - R/summary.BchronologyRun.R | 4 + build/vignette.rds |binary inst/doc/Bchron.R | 2 inst/doc/Bchron.Rmd | 6 +- inst/doc/Bchron.html | 89 ++++++++++++++++++++++------------------- man/summary.BchronologyRun.Rd | 3 + tests/testthat/test_order.R |only vignettes/Bchron.Rmd | 6 +- 13 files changed, 104 insertions(+), 81 deletions(-)
Title: Financial Time Series Objects (Rmetrics)
Description: 'S4' classes and various tools for financial time series:
Basic functions such as scaling and sorting, subsetting,
mathematical operations and statistical functions.
Author: Diethelm Wuertz [aut] ,
Tobias Setz [aut],
Yohan Chalabi [aut],
Martin Maechler [ctb] ,
Georgi N. Boshnakov [cre, aut]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between timeSeries versions 4041.111 dated 2024-09-22 and 4052.112 dated 2025-12-12
DESCRIPTION | 23 MD5 | 36 - NAMESPACE | 6 NEWS.md | 27 R/fin-turnpoints.R | 47 - R/methods-show.R | 2 R/statistics-rollMean.R | 107 +-- R/statistics-smoothLowess.R | 87 +- R/stats-na.omit.R | 190 ++--- build/vignette.rds |binary inst/doc/timeSeriesPlot.R | 1438 ++++++++++++++++++++--------------------- inst/doc/timeSeriesPlot.pdf |binary inst/doc/timeSeriesRefCard.pdf |binary inst/pkgdown.yml | 7 inst/unitTests/runit.NA.R | 251 +++---- man/00timeSeries-package.Rd | 6 man/stats-na.omit.Rd | 14 man/timeSeries-deprecated.Rd | 26 tests/doRUnit.R | 2 19 files changed, 1133 insertions(+), 1136 deletions(-)
Title: Data Structures for Single Cell Data
Description: Defines S4 classes for single-cell genomic data and associated
information, such as dimensionality reduction embeddings, nearest-neighbor
graphs, and spatially-resolved coordinates. Provides data access methods and
R-native hooks to ensure the Seurat object is familiar to other R users. 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>,
and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>,
Hao Y, Hao S, et al (2021) <doi:10.1016/j.cell.2021.04.048> and
Hao Y, et al (2023) <doi:10.1101/2022.02.24.481684> for
more details.
Author: Paul Hoffman [aut] ,
Rahul Satija [aut, cre] ,
David Collins [aut] ,
Yuhan Hao [aut] ,
Austin Hartman [aut] ,
Gesmira Molla [aut] ,
Andrew Butler [aut] ,
Tim Stuart [aut] ,
Madeline Kowalski [ctb] ,
Saket Choudhary [ctb] ,
Skylar Li [ctb],
Longda Jia [...truncated...]
Maintainer: Rahul Satija <seurat@nygenome.org>
Diff between SeuratObject versions 5.2.0 dated 2025-08-27 and 5.3.0 dated 2025-12-12
DESCRIPTION | 8 MD5 | 76 +++---- NAMESPACE | 1 NEWS.md | 13 + R/assay.R | 10 - R/assay5.R | 8 R/centroids.R | 22 ++ R/data.R | 2 R/default.R | 3 R/dimreduc.R | 2 R/fov.R | 35 ++- R/generics.R | 9 R/segmentation.R | 297 ++++++++++++++++++++---------- R/seurat.R | 70 ++++--- R/utils.R | 28 ++ R/zzz.R | 1 build/SeuratObject.pdf |binary build/partial.rdb |binary build/stage23.rdb |binary man/Centroids-methods.Rd | 4 man/CreateDimReducObject.Rd | 2 man/CreateSegmentation.Rd | 11 - man/FOV-class.Rd | 6 man/FOV-methods.Rd | 10 - man/FilterObjects.Rd | 4 man/GetTissueCoordinates.Rd | 21 +- man/PackageCheck.Rd | 4 man/SaveSeuratRds.Rd | 4 man/Segmentation-class.Rd | 5 man/Segmentation-methods.Rd | 13 - man/aggregate.Rd | 2 man/pbmc_small.Rd | 2 man/roxygen/templates/section-progressr.R | 2 man/split.Assay5.Rd | 2 man/split.Seurat.Rd | 2 man/split.StdAssay.Rd | 2 man/sub-LogMap-method.Rd | 2 tests/testthat/test_matrix.R | 2 tests/testthat/test_objects.R | 17 - 39 files changed, 449 insertions(+), 253 deletions(-)
Title: Interface to 'OxCal' Radiocarbon Calibration
Description: A set of tools that enables using 'OxCal' from within R. 'OxCal' (<https://c14.arch.ox.ac.uk/oxcal.html>) is a standard archaeological tool intended to provide 14C calibration and analysis of archaeological and environmental chronological information. 'OxcAAR' allows simple calibration with 'Oxcal' and plotting of the results as well as the execution of sophisticated ('OxCal') code and the import of the results of bulk analysis and complex Bayesian sequential calibration.
Author: Hinz Martin [aut, cre],
Clemens Schmid [aut],
Daniel Knitter [aut],
Carolin Tietze [aut]
Maintainer: Hinz Martin <martin.hinz@ufg.uni-kiel.de>
Diff between oxcAAR versions 1.1.1 dated 2021-07-05 and 1.1.2 dated 2025-12-12
DESCRIPTION | 14 MD5 | 64 +- NAMESPACE | 4 R/additional_plot_functions.R | 179 ++++-- R/executeOxcalScript.R | 13 R/globals.R |only R/oxcAARCalibratedDate.R | 662 +++++++++++++++---------- R/oxcAARCalibratedDatesList.R | 309 +++++++---- R/oxcalSumSim.R | 49 + R/parsing_functions.R | 667 +++++++++++-------------- README.md | 2 build/vignette.rds |binary inst/doc/basic-usage.R | 8 inst/doc/basic-usage.html | 852 ++++++++++++++++++++++++++++----- man/Boundary.Rd | 4 man/R_Date.Rd | 2 man/R_Simulate.Rd | 4 man/Sequence.Rd | 2 man/calcurve_plot.Rd | 22 man/executeOxcalScript.Rd | 6 man/format.oxcAARCalibratedDate.Rd |only man/is.oxcAARCalibratedDate.Rd | 5 man/is.oxcAARCalibratedDatesList.Rd | 5 man/oxcAARCalibratedDate.Rd | 28 - man/oxcAARCalibratedDatesList.Rd | 4 man/oxcal_Sum.Rd | 4 man/parseOxcalOutput.Rd | 2 man/plot.oxcAARCalibratedDate.Rd |only man/plot.oxcAARCalibratedDatesList.Rd |only man/print.oxcAARCalibratedDate.Rd |only man/print.oxcAARCalibratedDatesList.Rd |only man/wrap_in_boundaries.Rd | 6 tests/testthat/Rplots.pdf |binary tests/testthat/test_calibrate.R | 73 +- tests/testthat/test_oxcalsumsim.R | 79 ++- tests/testthat/test_simulate.R | 68 +- 36 files changed, 2025 insertions(+), 1112 deletions(-)
Title: Bhavcopy and Live Market Data from National Stock Exchange (NSE)
& Bombay Stock Exchange (BSE) India
Description: Download Current & Historical Bhavcopy. Get Live Market data from NSE India of Equities and Derivatives (F&O) segment. Data source <https://www.nseindia.com/>.
Author: Nandan Patil [cre, aut]
Maintainer: Nandan Patil <tryanother609@gmail.com>
This is a re-admission after prior archival of version 1.5.6 dated 2025-08-25
Diff between nser versions 1.5.6 dated 2025-08-25 and 1.5.7 dated 2025-12-12
DESCRIPTION | 10 +++++----- MD5 | 36 ++++++++++++++++++------------------ R/fobhav.R | 9 +++++++-- R/fobhav1.R | 5 ++++- build/vignette.rds |binary inst/doc/bhavfos.html | 5 +++-- inst/doc/bhavpr.html | 5 +++-- inst/doc/bhavs.html | 5 +++-- inst/doc/bhavtoday.html | 5 +++-- inst/doc/dailydata.html | 5 +++-- inst/doc/fobhav.html | 5 +++-- inst/doc/fobhav1.html | 5 +++-- inst/doc/fobhavtoday.html | 5 +++-- inst/doc/nselive.html | 5 +++-- inst/doc/nseopen.html | 5 +++-- inst/doc/nsetree.html | 5 +++-- inst/doc/optbanknifty.html | 5 +++-- inst/doc/optnifty.html | 5 +++-- man/fobhav.Rd | 2 +- 19 files changed, 74 insertions(+), 53 deletions(-)
Title: Orchestrate Geospatial (Meta)Data Management Workflows and
Manage FAIR Services
Description: An engine to facilitate the orchestration and execution of metadata-driven data management workflows, in compliance with 'FAIR'
(Findable, Accessible, Interoperable and Reusable) data management principles. By means of a pivot metadata model, relying on the 'DublinCore' standard (<https://dublincore.org/>),
a unique source of metadata can be used to operate multiple and inter-connected data management actions. Users can also customise their own workflows by creating specific actions
but the library comes with a set of native actions targeting common geographic information and data management, in particular actions oriented to the publication on the web of metadata
and data resources to provide standard discovery and access services. At first, default actions of the library were meant to focus on providing turn-key actions for geospatial (meta)data:
1) by creating manage geospatial (meta)data complying with 'ISO/TC211' (<https://committee.iso.org/home/tc211>) and 'OGC' (< [...truncated...]
Author: Emmanuel Blondel [aut, cre, cph] ,
Julien, Barde [aut] ,
Wilfried Heintz [aut] ,
Alexandre Bennici [ctb],
Sylvain Poulain [ctb],
Bastien Grasset [ctb],
Mathias Rouan [ctb],
Emilie Lerigoleur [ctb],
Yvan Le Bras [ctb],
Jeroen Ooms [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between geoflow versions 1.0.0 dated 2025-10-09 and 1.1.0 dated 2025-12-12
DESCRIPTION | 14 MD5 | 52 +-- NAMESPACE | 1 NEWS.md |only R/geoflow_data.R | 16 - R/geoflow_entity.R | 156 +++++++--- R/geoflow_relation.R | 10 R/geoflow_software.R | 4 R/geoflow_utils.R | 62 ++- R/geoflow_validator.R | 10 R/writeWorkflowJobDataResource.R | 7 README.md | 5 inst/actions/geometa_create_iso_19110.R | 2 inst/actions/geometa_create_iso_19115.R | 32 +- inst/actions/geonapi_publish_iso_19139.R | 22 - inst/actions/geonode4R_publish_ogc_services.R | 2 inst/actions/geosapi_publish_ogc_services.R | 15 inst/actions/geosapi_publish_ogc_services.yml | 4 inst/actions/metadataeditr_create_project.R | 2 inst/actions/ows4R_publish_iso_19139.R | 22 - inst/extdata/workflows/config_metadata_gsheets_iso19115_inspire.json | 12 inst/extdata/workflows/config_metadata_gsheets_iso19115_inspire_geonetwork.json | 11 inst/extdata/workflows/config_metadata_gsheets_iso19115_inspire_geonetwork_with_uuid.json | 11 inst/metadata/entity/entity_handler_ogc_csw.R | 42 +- man/geoflow.Rd | 2 man/geoflow_data.Rd | 20 + man/geoflow_relation.Rd | 21 + man/get_absolute_path.Rd |only 28 files changed, 374 insertions(+), 183 deletions(-)
Title: Download, Merge, and Process Redistricting Data
Description: Utility functions to download and process data produced by the ALARM Project,
including 2020 redistricting files Kenny and McCartan (2021)
<https://alarm-redist.org/posts/2021-08-10-census-2020/> and the 50-State
Redistricting Simulations of McCartan, Kenny, Simko, Garcia, Wang, Wu,
Kuriwaki, and Imai (2022) <doi:10.7910/DVN/SLCD3E>. The package extends
the data introduced in McCartan, Kenny, Simko, Garcia, Wang, Wu, Kuriwaki,
and Imai (2022) <doi:10.1038/s41597-022-01808-2> to also include states with
only a single district. The package also includes the Japanese 2022
redistricting files from the 47-Prefecture Redistricting Simulations of
Miyazaki, Yamada, Yatsuhashi, and Imai (2022) <doi:10.7910/DVN/Z9UKSH>.
Author: Cory McCartan [aut] ,
Christopher T. Kenny [aut, cre] ,
Tyler Simko [aut] ,
Michael Zhao [aut] ,
Sho Miyazaki [aut] ,
Kosuke Imai [aut]
Maintainer: Christopher T. Kenny <ctkenny@proton.me>
This is a re-admission after prior archival of version 0.2.1 dated 2024-02-28
Diff between alarmdata versions 0.2.1 dated 2024-02-28 and 0.2.4 dated 2025-12-12
DESCRIPTION | 34 +- LICENSE | 4 MD5 | 56 ++-- NAMESPACE | 44 +-- NEWS.md | 29 +- R/add_plan.R | 273 +++++++++++----------- R/alarmdata-package.R | 22 - R/cache.R | 108 ++++---- R/calc_plan_stats.R | 228 +++++++++--------- R/census_vest.R | 36 +- R/download.R | 26 +- R/epsg.R | 68 ++--- R/fiftystates.R | 469 ++++++++++++++++++-------------------- R/japan.R |only R/make_states.R | 148 +++++------ R/utils.R | 126 +++++----- README.md | 126 +++++----- build/partial.rdb |binary inst/WORDLIST | 30 +- man/alarm_50state.Rd | 160 ++++++------ man/alarm_add_plan.Rd | 128 +++++----- man/alarm_cache.Rd | 76 +++--- man/alarm_census_vest.Rd | 50 ++-- man/alarm_epsg.Rd | 42 +-- man/alarm_japan.Rd |only man/alarmdata-package.Rd | 69 ++--- tests/spelling.R | 6 tests/testthat.R | 24 - tests/testthat/test-add_plan.R | 51 ++-- tests/testthat/test-fiftystates.R | 30 +- 30 files changed, 1260 insertions(+), 1203 deletions(-)
Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation
models via the most likely transformation approach described in
Hothorn et al. (2018) <DOI:10.1111/sjos.12291> and Hothorn (2020)
<DOI:10.18637/jss.v092.i01>. Shift-scale (Siegfried et al, 2023, <DOI:10.1080/00031305.2023.2203177>)
and multivariate (Klein et al, 2022, <DOI:10.1111/sjos.12501>) transformation models
are part of this package. A package vignette is available from <DOI:10.32614/CRAN.package.mlt.docreg> and
more convenient user interfaces to many models from <DOI:10.32614/CRAN.package.tram>.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt versions 1.7-2 dated 2025-11-12 and 1.7-3 dated 2025-12-12
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/mlt.R | 2 +- R/mltoptim.R | 4 ++-- inst/NEWS.Rd | 9 +++++++++ 5 files changed, 20 insertions(+), 11 deletions(-)
Title: Multivariate Joint Grid Discretization
Description: Discretize multivariate continuous data using a grid
to capture the joint distribution that preserves clusters in
original data. It can handle both labeled or unlabeled data.
Both published methods (Wang et al 2020) <doi:10.1145/3388440.3412415>
and new methods are included. Joint grid discretization
can prepare data for model-free inference of association,
function, or causality.
Author: Jiandong Wang [aut],
Sajal Kumar [aut] ,
Joe Song [aut, cre]
Maintainer: Joe Song <joemsong@nmsu.edu>
Diff between GridOnClusters versions 0.1.0.2 dated 2025-05-27 and 0.3.2 dated 2025-12-12
GridOnClusters-0.1.0.2/GridOnClusters/src/wrapper.cpp |only GridOnClusters-0.3.2/GridOnClusters/DESCRIPTION | 29 GridOnClusters-0.3.2/GridOnClusters/MD5 | 85 - GridOnClusters-0.3.2/GridOnClusters/NAMESPACE | 5 GridOnClusters-0.3.2/GridOnClusters/NEWS.md | 595 ++++++-- GridOnClusters-0.3.2/GridOnClusters/R/RcppExports.R | 20 GridOnClusters-0.3.2/GridOnClusters/R/clustering.R |only GridOnClusters-0.3.2/GridOnClusters/R/discretize_jointly.R | 667 +++++----- GridOnClusters-0.3.2/GridOnClusters/R/plot_patterns.R | 184 +- GridOnClusters-0.3.2/GridOnClusters/R/tools.R |only GridOnClusters-0.3.2/GridOnClusters/README.md | 16 GridOnClusters-0.3.2/GridOnClusters/build/partial.rdb |binary GridOnClusters-0.3.2/GridOnClusters/build/vignette.rds |binary GridOnClusters-0.3.2/GridOnClusters/inst/doc/Examples.R | 225 +++ GridOnClusters-0.3.2/GridOnClusters/inst/doc/Examples.Rmd | 287 +++- GridOnClusters-0.3.2/GridOnClusters/inst/doc/Examples.html | 326 ++++ GridOnClusters-0.3.2/GridOnClusters/inst/extdata/TestforGridOnCluster.RData |only GridOnClusters-0.3.2/GridOnClusters/man/cluster.Rd | 7 GridOnClusters-0.3.2/GridOnClusters/man/discretize.jointly.Rd | 198 ++ GridOnClusters-0.3.2/GridOnClusters/man/gen_simdata.Rd |only GridOnClusters-0.3.2/GridOnClusters/man/plot.GridOnClusters.Rd | 21 GridOnClusters-0.3.2/GridOnClusters/man/plotGOCpatterns.Rd | 3 GridOnClusters-0.3.2/GridOnClusters/src/Clusters.cpp | 203 ++- GridOnClusters-0.3.2/GridOnClusters/src/Clusters.h | 83 + GridOnClusters-0.3.2/GridOnClusters/src/Cut_by_density.cpp |only GridOnClusters-0.3.2/GridOnClusters/src/Cut_by_density.h |only GridOnClusters-0.3.2/GridOnClusters/src/Cutting_Cluster_dp.cpp |only GridOnClusters-0.3.2/GridOnClusters/src/Cutting_Cluster_dp.h |only GridOnClusters-0.3.2/GridOnClusters/src/Cutting_Cluster_dp_compressed.cpp |only GridOnClusters-0.3.2/GridOnClusters/src/Cutting_Cluster_dp_compressed.h |only GridOnClusters-0.3.2/GridOnClusters/src/Dimension_reduction.cpp |only GridOnClusters-0.3.2/GridOnClusters/src/Dimension_reduction.h |only GridOnClusters-0.3.2/GridOnClusters/src/HCountTable.h |only GridOnClusters-0.3.2/GridOnClusters/src/HashTable.h |only GridOnClusters-0.3.2/GridOnClusters/src/HashedUpsilon.cpp |only GridOnClusters-0.3.2/GridOnClusters/src/HashedUpsilon.h |only GridOnClusters-0.3.2/GridOnClusters/src/Joint_Grid.cpp | 540 +++++--- GridOnClusters-0.3.2/GridOnClusters/src/Joint_Grid.h | 36 GridOnClusters-0.3.2/GridOnClusters/src/MyHash.h |only GridOnClusters-0.3.2/GridOnClusters/src/RcppExports.cpp | 67 - GridOnClusters-0.3.2/GridOnClusters/src/StatDistributions.cpp |only GridOnClusters-0.3.2/GridOnClusters/src/StatDistributions.h |only GridOnClusters-0.3.2/GridOnClusters/src/define.h |only GridOnClusters-0.3.2/GridOnClusters/src/discretization.cpp |only GridOnClusters-0.3.2/GridOnClusters/src/discretization.h |only GridOnClusters-0.3.2/GridOnClusters/src/evaluation.h |only GridOnClusters-0.3.2/GridOnClusters/src/evaluation_BIC.cpp |only GridOnClusters-0.3.2/GridOnClusters/src/evaluation_distance.cpp |only GridOnClusters-0.3.2/GridOnClusters/src/evaluation_purity.cpp |only GridOnClusters-0.3.2/GridOnClusters/src/rcpp_distance.cpp |only GridOnClusters-0.3.2/GridOnClusters/src/rcpp_findgrid.cpp |only GridOnClusters-0.3.2/GridOnClusters/src/rcpp_upsilon.cpp |only GridOnClusters-0.3.2/GridOnClusters/src/rcpp_utils.h |only GridOnClusters-0.3.2/GridOnClusters/src/telescope.cpp |only GridOnClusters-0.3.2/GridOnClusters/src/telescope.h |only GridOnClusters-0.3.2/GridOnClusters/src/upsilon.cpp |only GridOnClusters-0.3.2/GridOnClusters/src/upsilon.h |only GridOnClusters-0.3.2/GridOnClusters/src/utils.cpp |only GridOnClusters-0.3.2/GridOnClusters/src/utils.h |only GridOnClusters-0.3.2/GridOnClusters/tests/testthat/test-Ball-approx_likelihood.R |only GridOnClusters-0.3.2/GridOnClusters/tests/testthat/test-Ball-exact-likelihood.R |only GridOnClusters-0.3.2/GridOnClusters/tests/testthat/test-GridOnClusters.R | 206 +-- GridOnClusters-0.3.2/GridOnClusters/vignettes/Examples.Rmd | 287 +++- 63 files changed, 3015 insertions(+), 1075 deletions(-)
More information about GridOnClusters at CRAN
Permanent link
Title: Psychometric Functions from the Waller Lab
Description: Computes fungible coefficients and Monte Carlo data. Underlying theory for these functions is described in the following publications:
Waller, N. (2008). Fungible Weights in Multiple Regression. Psychometrika, 73(4), 691-703, <DOI:10.1007/s11336-008-9066-z>.
Waller, N. & Jones, J. (2009). Locating the Extrema of Fungible Regression Weights.
Psychometrika, 74(4), 589-602, <DOI:10.1007/s11336-008-9087-7>.
Waller, N. G. (2016). Fungible Correlation Matrices:
A Method for Generating Nonsingular, Singular, and Improper Correlation Matrices for
Monte Carlo Research. Multivariate Behavioral Research, 51(4), 554-568.
Jones, J. A. & Waller, N. G. (2015). The normal-theory and asymptotic distribution-free (ADF)
covariance matrix of standardized regression coefficients: theoretical extensions
and finite sample behavior. Psychometrika, 80, 365-378, <DOI:10.1007/s11336-013-9380-y>.
Waller, N. G. (2018). Direct Schmid-Leiman transformations and rank-deficient loadings mat [...truncated...]
Author: Niels Waller [aut, cre],
Justin Kracht [ctb],
Jeff Jones [ctb],
Casey Giordano [ctb],
Hoang V. Nguyen [ctb]
Maintainer: Niels Waller <nwaller@umn.edu>
Diff between fungible versions 2.4.4 dated 2024-03-09 and 2.4.4.1 dated 2025-12-12
DESCRIPTION | 8 MD5 | 44 - build/vignette.rds |binary data/ACL.rda |binary data/AmzBoxes.rda |binary data/BadRBY.rda |binary data/BadRJN.rda |binary data/BadRKtB.rda |binary data/BadRLG.rda |binary data/BadRRM.rda |binary data/Boruch70.rda |binary data/Box20.rda |binary data/Box26.rda |binary data/HS9Var.rda |binary data/HW.rda |binary data/Jackson67.rda |binary data/Malmi79.rda |binary data/Thurstone41.rda |binary data/ThurstoneBox20.rda |binary data/ThurstoneBox26.rda |binary inst/doc/simulate-model-error.R | 2 inst/doc/simulate-model-error.html | 1013 +++++++++++++++++++++++++------------ man/promaxQ.Rd | 2 23 files changed, 731 insertions(+), 338 deletions(-)
Title: Forest Many-Objective Robust Decision Making ('FoRDM')
Description: Forest Many-Objective Robust Decision Making ('FoRDM') is a R toolkit for supporting robust forest management under deep uncertainty.
It provides a forestry-focused application of Many-Objective Robust Decision Making ('MORDM') to forest simulation outputs,
enabling users to evaluate robustness using regret- and 'satisficing'-based measures. 'FoRDM' identifies robust solutions,
generates Pareto fronts, and offers interactive 2D, 3D, and parallel-coordinate visualizations.
Author: Marc Djahangard [aut, cre],
Rasoul Yousefpour [aut]
Maintainer: Marc Djahangard <marc.djahangard@ife.uni-freiburg.de>
Diff between FoRDM versions 1.0.0 dated 2025-12-03 and 1.0.1 dated 2025-12-12
DESCRIPTION | 6 +++--- MD5 | 5 +++-- NEWS |only R/FoRDM.R | 9 ++++++--- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Symbolic Central and Noncentral Moments of the Multivariate
Normal Distribution
Description: Symbolic central and non-central moments of the multivariate normal distribution. Computes a standard representation, LateX code, and values at specified mean and covariance matrices.
Author: Kem Phillips [aut, cre]
Maintainer: Kem Phillips <kemphillips@comcast.net>
Diff between symmoments versions 1.2.1 dated 2020-02-05 and 1.2.1.1 dated 2025-12-12
DESCRIPTION | 15 +- MD5 | 12 - build/vignette.rds |binary inst/doc/symmoments.R | 306 +++++++++++++++++++++++------------------------ inst/doc/symmoments.pdf |binary inst/doc/symmoments.rnw | 1 vignettes/symmoments.rnw | 1 7 files changed, 168 insertions(+), 167 deletions(-)
Title: qPCR Data Analysis
Description: Various methods are employed for statistical analysis and graphical presentation of real-time PCR (quantitative PCR or qPCR) data. 'rtpcr' handles amplification efficiency calculation, statistical analysis and graphical representation of real-time PCR data based on up to two reference genes. By accounting for amplification efficiency values, 'rtpcr' was developed using a general calculation method described by Ganger et al. (2017) <doi:10.1186/s12859-017-1949-5> and Taylor et al. (2019) <doi:10.1016/j.tibtech.2018.12.002>, covering both the Livak and Pfaffl methods. Based on the experimental conditions, the functions of the 'rtpcr' package use t-test (for experiments with a two-level factor), analysis of variance (ANOVA), analysis of covariance (ANCOVA) or analysis of repeated measure data to calculate the fold change (FC, Delta Delta Ct method) or relative expression (RE, Delta Ct method). The functions further provide standard errors and confidence intervals for means, a [...truncated...]
Author: Ghader Mirzaghaderi [aut, cre, cph]
Maintainer: Ghader Mirzaghaderi <gh.mirzaghaderi@uok.ac.ir>
Diff between rtpcr versions 2.0.4 dated 2025-12-04 and 2.0.5 dated 2025-12-12
rtpcr-2.0.4/rtpcr/R/oneFACTORplot.r |only rtpcr-2.0.4/rtpcr/R/qpcrANOVAFC.r |only rtpcr-2.0.4/rtpcr/R/qpcrANOVARE.r |only rtpcr-2.0.4/rtpcr/R/qpcrMeans.r |only rtpcr-2.0.4/rtpcr/R/qpcrREPEATED.r |only rtpcr-2.0.4/rtpcr/R/qpcrTTEST.r |only rtpcr-2.0.4/rtpcr/R/qpcrTTESTplot.r |only rtpcr-2.0.4/rtpcr/R/threeFACTORplot.r |only rtpcr-2.0.4/rtpcr/R/twoFACTORplot.r |only rtpcr-2.0.4/rtpcr/man/oneFACTORplot.Rd |only rtpcr-2.0.4/rtpcr/man/qpcrANOVAFC.Rd |only rtpcr-2.0.4/rtpcr/man/qpcrANOVARE.Rd |only rtpcr-2.0.4/rtpcr/man/qpcrMeans.Rd |only rtpcr-2.0.4/rtpcr/man/qpcrREPEATED.Rd |only rtpcr-2.0.4/rtpcr/man/qpcrTTEST.Rd |only rtpcr-2.0.4/rtpcr/man/qpcrTTESTplot.Rd |only rtpcr-2.0.4/rtpcr/man/threeFACTORplot.Rd |only rtpcr-2.0.4/rtpcr/man/twoFACTORplot.Rd |only rtpcr-2.0.4/rtpcr/vignettes/vignette_files |only rtpcr-2.0.5/rtpcr/DESCRIPTION | 8 rtpcr-2.0.5/rtpcr/MD5 | 69 - rtpcr-2.0.5/rtpcr/NAMESPACE | 17 rtpcr-2.0.5/rtpcr/R/ANOVA_DCt.r |only rtpcr-2.0.5/rtpcr/R/ANOVA_DDCt.r |only rtpcr-2.0.5/rtpcr/R/Means_DDCt.r |only rtpcr-2.0.5/rtpcr/R/REPEATED_DDCt.r |only rtpcr-2.0.5/rtpcr/R/TTEST_DDCt.r |only rtpcr-2.0.5/rtpcr/R/globalVariables.r |only rtpcr-2.0.5/rtpcr/R/multiplot.r | 32 rtpcr-2.0.5/rtpcr/R/plotOneFactor.r |only rtpcr-2.0.5/rtpcr/R/plotThreeFactor.r |only rtpcr-2.0.5/rtpcr/R/plotTwoFactor.r |only rtpcr-2.0.5/rtpcr/inst/doc/vignette.R | 399 +------ rtpcr-2.0.5/rtpcr/inst/doc/vignette.Rmd | 618 ++--------- rtpcr-2.0.5/rtpcr/inst/doc/vignette.html | 1516 +++++++---------------------- rtpcr-2.0.5/rtpcr/man/ANOVA_DCt.Rd |only rtpcr-2.0.5/rtpcr/man/ANOVA_DDCt.Rd |only rtpcr-2.0.5/rtpcr/man/Means_DDCt.Rd |only rtpcr-2.0.5/rtpcr/man/REPEATED_DDCt.Rd |only rtpcr-2.0.5/rtpcr/man/TTEST_DDCt.Rd |only rtpcr-2.0.5/rtpcr/man/globalVariables.Rd |only rtpcr-2.0.5/rtpcr/man/multiplot.Rd | 31 rtpcr-2.0.5/rtpcr/man/plotOneFactor.Rd |only rtpcr-2.0.5/rtpcr/man/plotThreeFactor.Rd |only rtpcr-2.0.5/rtpcr/man/plotTwoFactor.Rd |only rtpcr-2.0.5/rtpcr/vignettes/vignette.Rmd | 618 ++--------- 46 files changed, 747 insertions(+), 2561 deletions(-)
Title: Calculating Bilateral and Multilateral Price Indexes
Description: Preparing a scanner data set for price dynamics calculations (data selecting, data classification, data matching, data filtering). Computing bilateral and multilateral indexes. For details on these methods see: Diewert and Fox (2020)
<doi:10.1080/07350015.2020.1816176>, Białek (2019) <doi:10.2478/jos-2019-0014> or Białek (2020) <doi:10.2478/jos-2020-0037>.
Author: Jacek Bialek [aut, cre]
Maintainer: Jacek Bialek <jacek.bialek@uni.lodz.pl>
Diff between PriceIndices versions 0.2.5 dated 2025-10-12 and 0.2.6 dated 2025-12-12
PriceIndices-0.2.5/PriceIndices/R/f_Machine_Learning.R |only PriceIndices-0.2.5/PriceIndices/man/data_classifying.Rd |only PriceIndices-0.2.5/PriceIndices/man/figures/README-unnamed-chunk-19-1.png |only PriceIndices-0.2.5/PriceIndices/man/figures/README-unnamed-chunk-20-1.png |only PriceIndices-0.2.5/PriceIndices/man/figures/README-unnamed-chunk-38-1.png |only PriceIndices-0.2.5/PriceIndices/man/figures/README-unnamed-chunk-39-1.png |only PriceIndices-0.2.5/PriceIndices/man/figures/README-unnamed-chunk-45-1.png |only PriceIndices-0.2.5/PriceIndices/man/figures/README-unnamed-chunk-48-1.png |only PriceIndices-0.2.5/PriceIndices/man/figures/README-unnamed-chunk-50-1.png |only PriceIndices-0.2.5/PriceIndices/man/figures/README-unnamed-chunk-64-1.png |only PriceIndices-0.2.5/PriceIndices/man/figures/README-unnamed-chunk-66-1.png |only PriceIndices-0.2.5/PriceIndices/man/figures/README-unnamed-chunk-71-1.png |only PriceIndices-0.2.5/PriceIndices/man/figures/README-unnamed-chunk-72-1.png |only PriceIndices-0.2.5/PriceIndices/man/load_model.Rd |only PriceIndices-0.2.5/PriceIndices/man/model_classification.Rd |only PriceIndices-0.2.5/PriceIndices/man/save_model.Rd |only PriceIndices-0.2.6/PriceIndices/DESCRIPTION | 10 PriceIndices-0.2.6/PriceIndices/MD5 | 59 - PriceIndices-0.2.6/PriceIndices/NAMESPACE | 5 PriceIndices-0.2.6/PriceIndices/NEWS.md | 12 PriceIndices-0.2.6/PriceIndices/R/PriceIndices.R | 22 PriceIndices-0.2.6/PriceIndices/R/dataRSM.R |only PriceIndices-0.2.6/PriceIndices/R/f_bilateral_indices.R | 332 +++++++ PriceIndices-0.2.6/PriceIndices/README.md | 190 +--- PriceIndices-0.2.6/PriceIndices/data/dataRSM.rda |only PriceIndices-0.2.6/PriceIndices/inst/doc/PriceIndices.R | 34 PriceIndices-0.2.6/PriceIndices/inst/doc/PriceIndices.Rmd | 57 - PriceIndices-0.2.6/PriceIndices/inst/doc/PriceIndices.html | 430 ++++------ PriceIndices-0.2.6/PriceIndices/man/PriceIndices.Rd | 26 PriceIndices-0.2.6/PriceIndices/man/dataRSM.Rd |only PriceIndices-0.2.6/PriceIndices/man/figures/README-unnamed-chunk-31-1.png |only PriceIndices-0.2.6/PriceIndices/man/figures/README-unnamed-chunk-34-1.png |only PriceIndices-0.2.6/PriceIndices/man/figures/README-unnamed-chunk-35-1.png |binary PriceIndices-0.2.6/PriceIndices/man/figures/README-unnamed-chunk-40-1.png |only PriceIndices-0.2.6/PriceIndices/man/figures/README-unnamed-chunk-41-1.png |only PriceIndices-0.2.6/PriceIndices/man/figures/README-unnamed-chunk-42-1.png |only PriceIndices-0.2.6/PriceIndices/man/figures/README-unnamed-chunk-44-1.png |binary PriceIndices-0.2.6/PriceIndices/man/figures/README-unnamed-chunk-46-1.png |binary PriceIndices-0.2.6/PriceIndices/man/figures/README-unnamed-chunk-61-1.png |only PriceIndices-0.2.6/PriceIndices/man/figures/README-unnamed-chunk-63-1.png |only PriceIndices-0.2.6/PriceIndices/man/figures/README-unnamed-chunk-68-1.png |only PriceIndices-0.2.6/PriceIndices/man/figures/README-unnamed-chunk-69-1.png |only PriceIndices-0.2.6/PriceIndices/man/retro_index.Rd |only PriceIndices-0.2.6/PriceIndices/man/shrinkflation.Rd | 4 PriceIndices-0.2.6/PriceIndices/vignettes/PriceIndices.Rmd | 57 - 45 files changed, 707 insertions(+), 531 deletions(-)
Title: Functional Control Charts
Description: Provides functional control charts
for statistical process monitoring of functional data,
using the methods of Capezza et al. (2020) <doi:10.1002/asmb.2507>,
Centofanti et al. (2021) <doi:10.1080/00401706.2020.1753581>,
Capezza et al. (2024) <doi:10.1080/00224065.2024.2383674>,
Capezza et al. (2024) <doi:10.1080/00401706.2024.2327346>,
Centofanti et al. (2025) <doi:10.1080/00224065.2024.2430978>,
Capezza et al. (2025) <doi:10.48550/arXiv.2410.20138>.
The package is thoroughly illustrated in the paper of
Capezza et al (2023) <doi:10.1080/00224065.2023.2219012>.
Author: Christian Capezza [cre, aut],
Fabio Centofanti [aut],
Davide Forcina [aut],
Antonio Lepore [aut],
Biagio Palumbo [aut],
Alessandra Menafoglio [ctb],
Simone Vantini [ctb]
Maintainer: Christian Capezza <christian.capezza@unina.it>
Diff between funcharts versions 1.7.0 dated 2025-03-17 and 1.8.0 dated 2025-12-12
funcharts-1.7.0/funcharts/man/mean_mfd.Rd |only funcharts-1.8.0/funcharts/DESCRIPTION | 24 funcharts-1.8.0/funcharts/MD5 | 158 +- funcharts-1.8.0/funcharts/NAMESPACE | 27 funcharts-1.8.0/funcharts/NEWS.md | 29 funcharts-1.8.0/funcharts/R/00_mfd.R | 567 +++++++++- funcharts-1.8.0/funcharts/R/01_pca.mfd.R | 94 + funcharts-1.8.0/funcharts/R/02_fof_pc.R | 2 funcharts-1.8.0/funcharts/R/02_sof_pc.R | 7 funcharts-1.8.0/funcharts/R/03_phaseI_training.R | 12 funcharts-1.8.0/funcharts/R/04_phaseII.R | 8 funcharts-1.8.0/funcharts/R/AMFCC.R | 8 funcharts-1.8.0/funcharts/R/FRTM.R | 175 +-- funcharts-1.8.0/funcharts/R/FRTM_plot_functions.R | 6 funcharts-1.8.0/funcharts/R/FRTM_util.R | 72 - funcharts-1.8.0/funcharts/R/RcppExports.R | 12 funcharts-1.8.0/funcharts/R/amfewma.R | 61 - funcharts-1.8.0/funcharts/R/fmrcc.R |only funcharts-1.8.0/funcharts/R/funcharts-package.R | 9 funcharts-1.8.0/funcharts/R/real_time_01_pca.mfd.R | 1 funcharts-1.8.0/funcharts/R/real_time_02_fof_pc.R | 1 funcharts-1.8.0/funcharts/R/real_time_02_sof_pc.R | 1 funcharts-1.8.0/funcharts/R/real_time_04_phaseII.R | 2 funcharts-1.8.0/funcharts/R/rmfcc.R | 63 - funcharts-1.8.0/funcharts/R/simulate.R | 386 ++++++ funcharts-1.8.0/funcharts/build/partial.rdb |binary funcharts-1.8.0/funcharts/build/vignette.rds |binary funcharts-1.8.0/funcharts/inst/doc/capezza2020.html | 5 funcharts-1.8.0/funcharts/inst/doc/centofanti2021.html | 5 funcharts-1.8.0/funcharts/inst/doc/colosimo2010.html | 5 funcharts-1.8.0/funcharts/inst/doc/mfd.html | 5 funcharts-1.8.0/funcharts/man/AMFCC_PhaseI.Rd | 5 funcharts-1.8.0/funcharts/man/AMFCC_PhaseII.Rd | 3 funcharts-1.8.0/funcharts/man/AMFEWMA_PhaseI.Rd | 30 funcharts-1.8.0/funcharts/man/AMFEWMA_PhaseII.Rd | 31 funcharts-1.8.0/funcharts/man/FMRCC_PhaseI.Rd |only funcharts-1.8.0/funcharts/man/FMRCC_PhaseII.Rd |only funcharts-1.8.0/funcharts/man/FRTM_PhaseI.Rd | 9 funcharts-1.8.0/funcharts/man/FRTM_PhaseII.Rd | 9 funcharts-1.8.0/funcharts/man/OEBFDTW.Rd | 7 funcharts-1.8.0/funcharts/man/RoMFCC_PhaseI.Rd | 14 funcharts-1.8.0/funcharts/man/RoMFCC_PhaseII.Rd | 8 funcharts-1.8.0/funcharts/man/RoMFDI.Rd | 11 funcharts-1.8.0/funcharts/man/abline_mfd.Rd |only funcharts-1.8.0/funcharts/man/control_charts_sof_pc.Rd | 5 funcharts-1.8.0/funcharts/man/control_charts_sof_pc_real_time.Rd | 2 funcharts-1.8.0/funcharts/man/cor_mfd.Rd | 2 funcharts-1.8.0/funcharts/man/cov_mfd.Rd | 2 funcharts-1.8.0/funcharts/man/estimate_mixture.Rd |only funcharts-1.8.0/funcharts/man/fof_pc.Rd | 3 funcharts-1.8.0/funcharts/man/fof_pc_real_time.Rd | 3 funcharts-1.8.0/funcharts/man/funcharts-package.Rd | 11 funcharts-1.8.0/funcharts/man/functional_filter.Rd | 7 funcharts-1.8.0/funcharts/man/get_sof_pc_outliers.Rd | 2 funcharts-1.8.0/funcharts/man/lines.mfd.Rd |only funcharts-1.8.0/funcharts/man/mFPCA.Rd | 7 funcharts-1.8.0/funcharts/man/mean.mfd.Rd |only funcharts-1.8.0/funcharts/man/minus_mfd.Rd |only funcharts-1.8.0/funcharts/man/mixregfit_multivariate.Rd |only funcharts-1.8.0/funcharts/man/nbasis.Rd |only funcharts-1.8.0/funcharts/man/nobs.mfd.Rd |only funcharts-1.8.0/funcharts/man/nvar.Rd |only funcharts-1.8.0/funcharts/man/par.FDTW.Rd | 3 funcharts-1.8.0/funcharts/man/par.rtr.Rd | 3 funcharts-1.8.0/funcharts/man/pca_mfd_real_time.Rd | 3 funcharts-1.8.0/funcharts/man/plot.AMFCC_PhaseI.Rd | 2 funcharts-1.8.0/funcharts/man/plot.FRTM_PhaseI.Rd | 2 funcharts-1.8.0/funcharts/man/plot.mfd.Rd |only funcharts-1.8.0/funcharts/man/plot_bootstrap_sof_pc.Rd | 3 funcharts-1.8.0/funcharts/man/plus_mfd.Rd |only funcharts-1.8.0/funcharts/man/predict.pca_mfd.Rd |only funcharts-1.8.0/funcharts/man/predict_fof_pc.Rd | 3 funcharts-1.8.0/funcharts/man/predict_sof_pc.Rd | 3 funcharts-1.8.0/funcharts/man/regr_cc_fof.Rd | 3 funcharts-1.8.0/funcharts/man/regr_cc_sof.Rd | 3 funcharts-1.8.0/funcharts/man/rpca_mfd.Rd | 3 funcharts-1.8.0/funcharts/man/simulate_data_FRTM.Rd | 4 funcharts-1.8.0/funcharts/man/simulate_data_RoMFCC.Rd |only funcharts-1.8.0/funcharts/man/simulate_data_fmrcc.Rd |only funcharts-1.8.0/funcharts/man/sof_pc.Rd | 3 funcharts-1.8.0/funcharts/man/sof_pc_real_time.Rd | 3 funcharts-1.8.0/funcharts/man/times_mfd.Rd |only funcharts-1.8.0/funcharts/src/RcppExports.cpp | 50 funcharts-1.8.0/funcharts/src/src.cpp | 157 ++ funcharts-1.8.0/funcharts/tests/testthat/Rplots.pdf |binary funcharts-1.8.0/funcharts/tests/testthat/test_AMFCC.R | 2 funcharts-1.8.0/funcharts/tests/testthat/test_OEBFDTW.R | 19 funcharts-1.8.0/funcharts/tests/testthat/test_fmrcc.R |only funcharts-1.8.0/funcharts/tests/testthat/test_mFPCA.R | 16 funcharts-1.8.0/funcharts/tests/testthat/test_mfd.R | 2 90 files changed, 1727 insertions(+), 476 deletions(-)
Title: Stochastic Data Envelopment Analysis
Description: Set of functions for Stochastic Data Envelopment Analysis. Chance constrained versions of radial, directional and additive DEA models are implemented, as long as super-efficiency models. See: Cooper, W.W.; Deng, H.; Huang, Z.; Li, S.X. (2002). <doi:10.1057/palgrave.jors.2601433>, Bolós, V.J.; Benítez, R.; Coll-Serrano, V. (2024) <doi:10.1016/j.orp.2024.100307>.
Author: Vicente Bolos [aut, cre],
Vicente Coll-Serrano [aut],
Rafael Benitez Suarez [aut]
Maintainer: Vicente Bolos <vicente.bolos@uv.es>
Diff between SdeaR versions 1.0.1 dated 2025-10-16 and 1.0.2 dated 2025-12-12
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- R/efficiencies.dea_stoch.R | 3 ++- R/make_deadata_stoch.R | 27 +++++++++++++++++++-------- R/modelstoch_dir.R | 4 +++- R/modelstoch_dir_dd.R | 4 +++- R/modelstoch_radial.R | 37 +++++++++++++++++++++++++++++-------- R/modelstoch_radial_supereff.R | 26 -------------------------- man/efficiencies.dea_stoch.Rd | 3 ++- man/make_deadata_stoch.Rd | 27 +++++++++++++++++++-------- man/modelstoch_dir.Rd | 4 +++- man/modelstoch_dir_dd.Rd | 4 +++- man/modelstoch_radial.Rd | 36 ++++++++++++++++++++++++++++-------- man/modelstoch_radial_supereff.Rd | 27 --------------------------- 14 files changed, 127 insertions(+), 107 deletions(-)
Title: Wrapper for MUMPS Library
Description: Some basic features of 'MUMPS' (Multifrontal Massively Parallel
sparse direct Solver) are wrapped in a class whose methods can be used
for sequentially solving a sparse linear system (symmetric or not)
with one or many right hand sides (dense or sparse).
There is a possibility to do separately symbolic analysis,
LU (or LDL^t) factorization and system solving.
Third part ordering libraries are included and can be used: 'PORD', 'METIS', 'SCOTCH'.
'MUMPS' method was first described in Amestoy et al. (2001) <doi:10.1137/S0895479899358194>
and Amestoy et al. (2006) <doi:10.1016/j.parco.2005.07.004>.
Author: Serguei Sokol [aut, cre],
Emmanuel Agullo [ctb],
Patrick Amestoy [ctb, cph],
Maurice Bremond [ctb],
Alfredo Buttari [ctb],
Philippe Combes [ctb],
Marie Durand [ctb],
Aurelia Fevre [ctb],
Abdou Guermouche [ctb],
Guillaume Joslin [ctb],
Jacko Koster [c [...truncated...]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between rmumps versions 5.2.1-35 dated 2025-05-16 and 5.2.1-36 dated 2025-12-12
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 6 ++++++ src/lib/scotch_6.0.9/src/esmumps/symbol_fax_graph.c | 2 +- src/lib/scotch_6.0.9/src/libscotch/vgraph_separate_gg.c | 2 +- 5 files changed, 16 insertions(+), 10 deletions(-)
Title: Bootstrapping Estimates of Clustering Stability
Description: Implementation of the bootstrapping approach for the estimation of clustering stability and its application in estimating the number of clusters, as introduced by Yu et al (2016)<doi:10.1142/9789814749411_0007>. Implementation of the non-parametric bootstrap approach to assessing the stability of module detection in a graph, the extension for the selection of a parameter set that defines a graph from data in a way that optimizes stability and the corresponding visualization functions, as introduced by Tian et al (2021) <doi:10.1002/sam.11495>. Implemented out-of-bag stability estimation function and k-select Smin-based k-selection function as introduced by Liu et al (2022) <doi:10.1002/sam.11593>. Implemented ensemble clustering method based-on k-means clustering method, spectral clustering method and hierarchical clustering method.
Author: Han Yu [aut],
Mingmei Tian [aut],
Tianmou Liu [aut, cre]
Maintainer: Tianmou Liu <tianmouliu@outlook.com>
Diff between bootcluster versions 0.4.2 dated 2025-06-17 and 0.4.3 dated 2025-12-12
DESCRIPTION | 14 +++++++------- MD5 | 14 +++++++------- NAMESPACE | 1 - R/esmbl_stability.R | 2 +- R/kselect.R | 2 +- R/kselect_ref.R | 3 +-- R/stability.R | 2 +- R/stability_ob.R | 4 ++-- 8 files changed, 20 insertions(+), 22 deletions(-)
Title: Weighted Generalised Covariance Measure Conditional Independence
Test
Description: A conditional independence test that can be applied both to
univariate and multivariate random variables. The test is based on a
weighted form of the sample covariance of the residuals after a
nonlinear regression on the conditioning variables. Details are
described in Scheidegger, Hoerrmann and Buehlmann (2022) "The Weighted
Generalised Covariance Measure" <http://jmlr.org/papers/v23/21-1328.html>.
The test is a generalisation of the Generalised Covariance Measure (GCM)
implemented in the R package 'GeneralisedCovarianceMeasure' by Jonas Peters and
Rajen D. Shah based on Shah and Peters (2020) "The Hardness of
Conditional Independence Testing and the Generalised Covariance
Measure" <doi:10.1214/19-AOS1857>.
Author: Cyrill Scheidegger [aut, cre, cph],
Julia Hoerrmann [ths],
Peter Buehlmann [ths],
Jonas Peters [ctb, cph] ,
Rajen D. Shah [ctb, cph]
Maintainer: Cyrill Scheidegger <cyrill.scheidegger@stat.math.ethz.ch>
Diff between weightedGCM versions 0.1.0 dated 2021-11-29 and 0.1.1 dated 2025-12-12
weightedGCM-0.1.0/weightedGCM/R/trainFunctions.R |only weightedGCM-0.1.1/weightedGCM/DESCRIPTION | 42 - weightedGCM-0.1.1/weightedGCM/MD5 | 19 weightedGCM-0.1.1/weightedGCM/NEWS.md | 8 weightedGCM-0.1.1/weightedGCM/R/WGCM.R | 332 ++++---- weightedGCM-0.1.1/weightedGCM/R/utils.R | 462 +++++++----- weightedGCM-0.1.1/weightedGCM/README.md | 141 +-- weightedGCM-0.1.1/weightedGCM/man/wgcm.est.Rd | 8 weightedGCM-0.1.1/weightedGCM/man/wgcm.fix.Rd | 8 weightedGCM-0.1.1/weightedGCM/tests/testthat/test_wgcmest.R | 98 +- weightedGCM-0.1.1/weightedGCM/tests/testthat/test_wgcmfix.R | 159 ++-- 11 files changed, 696 insertions(+), 581 deletions(-)
Title: Neural Network Weights Transformation into Polynomial
Coefficients
Description: Implements a method that builds the coefficients of a polynomial
model that performs almost equivalently as a given neural network
(densely connected). This is achieved using Taylor expansion at the
activation functions. The obtained polynomial coefficients can be used
to explain features (and their interactions) importance in the neural network,
therefore working as a tool for interpretability or eXplainable Artificial
Intelligence (XAI). See Morala et al. 2021 <doi:10.1016/j.neunet.2021.04.036>,
and 2023 <doi:10.1109/TNNLS.2023.3330328>.
Author: Pablo Morala [aut, cre] ,
Inaki Ucar [aut] ,
Jose Ignacio Diez [ctr]
Maintainer: Pablo Morala <moralapablo@gmail.com>
Diff between nn2poly versions 0.1.2 dated 2024-11-11 and 0.1.3 dated 2025-12-12
nn2poly-0.1.2/nn2poly/src/Makevars |only nn2poly-0.1.3/nn2poly/DESCRIPTION | 15 nn2poly-0.1.3/nn2poly/LICENSE | 4 nn2poly-0.1.3/nn2poly/MD5 | 154 nn2poly-0.1.3/nn2poly/NAMESPACE | 34 nn2poly-0.1.3/nn2poly/NEWS.md | 7 nn2poly-0.1.3/nn2poly/R/RcppExports.R | 46 nn2poly-0.1.3/nn2poly/R/callback.R | 92 nn2poly-0.1.3/nn2poly/R/constraints.R | 170 nn2poly-0.1.3/nn2poly/R/constraints_torch.R | 74 nn2poly-0.1.3/nn2poly/R/eval_poly.R | 279 + nn2poly-0.1.3/nn2poly/R/helpers.R | 134 nn2poly-0.1.3/nn2poly/R/nn2poly_algorithm.R | 798 ++-- nn2poly-0.1.3/nn2poly/R/nn2poly_methods.R | 690 +-- nn2poly-0.1.3/nn2poly/R/parameters.R | 156 nn2poly-0.1.3/nn2poly/R/plot_diagonal.R | 82 nn2poly-0.1.3/nn2poly/R/plot_taylor_and_activation_potentials.R | 380 +- nn2poly-0.1.3/nn2poly/R/utils.R | 54 nn2poly-0.1.3/nn2poly/README.md | 83 nn2poly-0.1.3/nn2poly/build/vignette.rds |binary nn2poly-0.1.3/nn2poly/inst/CITATION | 52 nn2poly-0.1.3/nn2poly/inst/doc/nn2poly-01-introduction.Rmd | 977 ++--- nn2poly-0.1.3/nn2poly/inst/doc/nn2poly-01-introduction.html | 1803 +++++----- nn2poly-0.1.3/nn2poly/inst/doc/nn2poly-02-supported-DL-frameworks.Rmd | 956 ++--- nn2poly-0.1.3/nn2poly/inst/doc/nn2poly-02-supported-DL-frameworks.html | 1620 ++++---- nn2poly-0.1.3/nn2poly/inst/doc/nn2poly-03-classification-example.Rmd | 1000 ++--- nn2poly-0.1.3/nn2poly/inst/doc/nn2poly-03-classification-example.html | 1728 ++++----- nn2poly-0.1.3/nn2poly/inst/python/KerasCallback.py | 20 nn2poly-0.1.3/nn2poly/inst/python/KerasConstraint.py | 66 nn2poly-0.1.3/nn2poly/man/add_constraints.Rd | 154 nn2poly-0.1.3/nn2poly/man/eval_poly.Rd | 110 nn2poly-0.1.3/nn2poly/man/figures |only nn2poly-0.1.3/nn2poly/man/luz_model_sequential.Rd | 104 nn2poly-0.1.3/nn2poly/man/nn2poly.Rd | 266 - 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Title: Double Machine Learning with Instrumental Variables and
Heterogeneity
Description: Instrumental variable (IV) estimators for homogeneous and
heterogeneous treatment effects with efficient machine learning instruments.
The estimators are based on double/debiased machine learning allowing for
nonlinear and potentially high-dimensional control variables. Details can
be found in Scheidegger, Guo and Bühlmann (2025) "Inference for
heterogeneous treatment effects with efficient instruments and machine
learning" <doi:10.48550/arXiv.2503.03530>.
Author: Cyrill Scheidegger [aut, cre, cph]
Maintainer: Cyrill Scheidegger <cyrill.scheidegger@stat.math.ethz.ch>
Diff between IVDML versions 1.0.0 dated 2025-03-11 and 1.0.1 dated 2025-12-12
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/NuisanceML.R | 4 ++-- README.md | 4 ++-- build/partial.rdb |binary tests/testthat/test-fit_IVDML.R | 37 +++++++++++++++++++++++++++++++++++++ 7 files changed, 57 insertions(+), 16 deletions(-)
Title: Text Analysis for All
Description: An R 'shiny' app designed for diverse text analysis tasks, offering a wide range of methodologies tailored to Natural Language Processing (NLP) needs.
It is a versatile, general-purpose tool for analyzing textual data.
'tall' features a comprehensive workflow, including data cleaning, preprocessing, statistical analysis, and visualization, all integrated for effective text analysis.
Author: Massimo Aria [aut, cre, cph] ,
Maria Spano [aut] ,
Luca D'Aniello [aut] ,
Corrado Cuccurullo [ctb] ,
Michelangelo Misuraca [ctb]
Maintainer: Massimo Aria <aria@unina.it>
Diff between tall versions 0.5.0 dated 2025-12-06 and 0.5.1 dated 2025-12-12
DESCRIPTION | 6 MD5 | 23 +- NEWS.md | 7 build/partial.rdb |binary inst/tall/collocation.R |only inst/tall/libraries.R | 1 inst/tall/preprocessing.R | 2 inst/tall/server.R | 7 inst/tall/settings.R | 102 +++++----- inst/tall/tallAI.R | 28 +- inst/tall/tallFunctions.R | 33 +-- inst/tall/ui.R | 6 inst/tall/words.R | 450 +++++++++++++--------------------------------- 13 files changed, 244 insertions(+), 421 deletions(-)
Title: Accessing and Validating Marine Environmental Data from 'SHARK'
and Related Databases
Description: Provides functions to retrieve, process, analyze, and
quality-control marine physical, chemical, and biological data. The
main focus is on Swedish monitoring data available through the 'SHARK'
database <https://shark.smhi.se/en/>, with additional API support for 'Nordic
Microalgae' <https://nordicmicroalgae.org/>, 'Dyntaxa'
<https://artfakta.se/>, World Register of Marine Species ('WoRMS') <https://www.marinespecies.org>,
'AlgaeBase' <https://www.algaebase.org>, OBIS 'xylookup' web service
<https://iobis.github.io/xylookup/> and Intergovernmental Oceanographic Commission (IOC) -
UNESCO databases on harmful algae <https://www.marinespecies.org/hab/> and toxins
<https://toxins.hais.ioc-unesco.org/>.
Author: Markus Lindh [aut] ,
Anders Torstensson [aut, cre] ,
Mikael Hedblom [ctb] ,
Bengt Karlson [ctb] ,
SHARK [cph],
SBDI [fnd]
Maintainer: Anders Torstensson <anders.torstensson@smhi.se>
Diff between SHARK4R versions 1.0.1 dated 2025-12-09 and 1.0.2 dated 2025-12-12
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SHARK4R-1.0.2/SHARK4R/man/figures/lifecycle-archived.svg | 42 SHARK4R-1.0.2/SHARK4R/man/figures/lifecycle-defunct.svg | 42 SHARK4R-1.0.2/SHARK4R/man/figures/lifecycle-deprecated.svg | 42 SHARK4R-1.0.2/SHARK4R/man/figures/lifecycle-experimental.svg | 42 SHARK4R-1.0.2/SHARK4R/man/figures/lifecycle-maturing.svg | 42 SHARK4R-1.0.2/SHARK4R/man/figures/lifecycle-questioning.svg | 42 SHARK4R-1.0.2/SHARK4R/man/figures/lifecycle-soft-deprecated.svg | 42 SHARK4R-1.0.2/SHARK4R/man/figures/lifecycle-stable.svg | 58 SHARK4R-1.0.2/SHARK4R/man/figures/lifecycle-superseded.svg | 42 SHARK4R-1.0.2/SHARK4R/man/find_required_fields.Rd | 140 SHARK4R-1.0.2/SHARK4R/man/get_algaebase_genus.Rd | 168 SHARK4R-1.0.2/SHARK4R/man/get_algaebase_species.Rd | 184 SHARK4R-1.0.2/SHARK4R/man/get_delivery_template.Rd | 176 SHARK4R-1.0.2/SHARK4R/man/get_dyntaxa_dwca.Rd | 146 SHARK4R-1.0.2/SHARK4R/man/get_dyntaxa_parent_ids.Rd | 124 SHARK4R-1.0.2/SHARK4R/man/get_dyntaxa_records.Rd | 114 SHARK4R-1.0.2/SHARK4R/man/get_hab_list.Rd | 162 SHARK4R-1.0.2/SHARK4R/man/get_nomp_list.Rd | 116 SHARK4R-1.0.2/SHARK4R/man/get_nua_external_links.Rd | 92 SHARK4R-1.0.2/SHARK4R/man/get_nua_harmfulness.Rd | 90 SHARK4R-1.0.2/SHARK4R/man/get_nua_media_links.Rd | 78 SHARK4R-1.0.2/SHARK4R/man/get_nua_taxa.Rd | 70 SHARK4R-1.0.2/SHARK4R/man/get_peg_list.Rd | 102 SHARK4R-1.0.2/SHARK4R/man/get_shark_codes.Rd | 106 SHARK4R-1.0.2/SHARK4R/man/get_shark_data.Rd | 462 SHARK4R-1.0.2/SHARK4R/man/get_shark_datasets.Rd | 190 SHARK4R-1.0.2/SHARK4R/man/get_shark_options.Rd | 96 SHARK4R-1.0.2/SHARK4R/man/get_shark_statistics.Rd | 184 SHARK4R-1.0.2/SHARK4R/man/get_shark_table_counts.Rd | 292 SHARK4R-1.0.2/SHARK4R/man/get_toxin_list.Rd | 64 SHARK4R-1.0.2/SHARK4R/man/get_worms_classification.Rd | 164 SHARK4R-1.0.2/SHARK4R/man/get_worms_records.Rd | 106 SHARK4R-1.0.2/SHARK4R/man/get_worms_records_name.Rd | 122 SHARK4R-1.0.2/SHARK4R/man/get_worms_taxonomy_tree.Rd | 222 SHARK4R-1.0.2/SHARK4R/man/ifcb_is_near_land.Rd | 152 SHARK4R-1.0.2/SHARK4R/man/ifcb_which_basin.Rd | 104 SHARK4R-1.0.2/SHARK4R/man/is_in_dyntaxa.Rd | 154 SHARK4R-1.0.2/SHARK4R/man/load_shark4r_fields.Rd | 118 SHARK4R-1.0.2/SHARK4R/man/load_shark4r_stats.Rd | 94 SHARK4R-1.0.2/SHARK4R/man/load_station_bundle.Rd | 40 SHARK4R-1.0.2/SHARK4R/man/lookup_xy.Rd | 158 SHARK4R-1.0.2/SHARK4R/man/match_algaebase.Rd | 232 SHARK4R-1.0.2/SHARK4R/man/match_algaebase_genus.Rd | 158 SHARK4R-1.0.2/SHARK4R/man/match_algaebase_species.Rd | 174 SHARK4R-1.0.2/SHARK4R/man/match_algaebase_taxa.Rd | 228 SHARK4R-1.0.2/SHARK4R/man/match_dyntaxa.Rd | 80 SHARK4R-1.0.2/SHARK4R/man/match_dyntaxa_taxa.Rd | 160 SHARK4R-1.0.2/SHARK4R/man/match_station.Rd | 122 SHARK4R-1.0.2/SHARK4R/man/match_taxon_name.Rd | 170 SHARK4R-1.0.2/SHARK4R/man/match_worms_taxa.Rd | 162 SHARK4R-1.0.2/SHARK4R/man/match_wormstaxa.Rd | 54 SHARK4R-1.0.2/SHARK4R/man/nominal_station.Rd | 90 SHARK4R-1.0.2/SHARK4R/man/parse_scientific_names.Rd | 116 SHARK4R-1.0.2/SHARK4R/man/plot_map_leaflet.Rd | 106 SHARK4R-1.0.2/SHARK4R/man/plot_map_leaflet_deliv.Rd | 44 SHARK4R-1.0.2/SHARK4R/man/positions_are_near_land.Rd | 174 SHARK4R-1.0.2/SHARK4R/man/read_ptbx.Rd | 100 SHARK4R-1.0.2/SHARK4R/man/read_shark.Rd | 130 SHARK4R-1.0.2/SHARK4R/man/read_shark_deliv.Rd | 84 SHARK4R-1.0.2/SHARK4R/man/run_qc_app.Rd | 74 SHARK4R-1.0.2/SHARK4R/man/scatterplot.Rd | 166 SHARK4R-1.0.2/SHARK4R/man/shark_read.Rd | 78 SHARK4R-1.0.2/SHARK4R/man/shark_read_deliv.Rd | 50 SHARK4R-1.0.2/SHARK4R/man/shark_read_deliv_xls.Rd | 52 SHARK4R-1.0.2/SHARK4R/man/shark_read_zip.Rd | 76 SHARK4R-1.0.2/SHARK4R/man/translate_shark_datatype.Rd | 54 SHARK4R-1.0.2/SHARK4R/man/update_dyntaxa_taxonomy.Rd | 130 SHARK4R-1.0.2/SHARK4R/man/update_worms_taxonomy.Rd | 76 SHARK4R-1.0.2/SHARK4R/man/which_basin.Rd | 100 SHARK4R-1.0.2/SHARK4R/tests/spelling.R | 6 SHARK4R-1.0.2/SHARK4R/tests/testthat.R | 24 SHARK4R-1.0.2/SHARK4R/tests/testthat/helper.R | 316 SHARK4R-1.0.2/SHARK4R/tests/testthat/setup-cache.R |only SHARK4R-1.0.2/SHARK4R/tests/testthat/test-algaebase_api_functions.R | 102 SHARK4R-1.0.2/SHARK4R/tests/testthat/test-check_codes.R | 56 SHARK4R-1.0.2/SHARK4R/tests/testthat/test-check_depth.R | 240 SHARK4R-1.0.2/SHARK4R/tests/testthat/test-check_fields.R | 560 SHARK4R-1.0.2/SHARK4R/tests/testthat/test-check_logical.R | 1350 - SHARK4R-1.0.2/SHARK4R/tests/testthat/test-check_onland.R | 154 SHARK4R-1.0.2/SHARK4R/tests/testthat/test-check_outliers.R | 526 SHARK4R-1.0.2/SHARK4R/tests/testthat/test-check_stations.R | 802 - SHARK4R-1.0.2/SHARK4R/tests/testthat/test-defunct.R | 64 SHARK4R-1.0.2/SHARK4R/tests/testthat/test-dyntaxa_api_functions.R | 446 SHARK4R-1.0.2/SHARK4R/tests/testthat/test-hab_api_functions.R | 198 SHARK4R-1.0.2/SHARK4R/tests/testthat/test-iRfcb_functions.R | 275 SHARK4R-1.0.2/SHARK4R/tests/testthat/test-nua_api_functions.R | 92 SHARK4R-1.0.2/SHARK4R/tests/testthat/test-plankton_toolbox.R | 378 SHARK4R-1.0.2/SHARK4R/tests/testthat/test-plot_map_leaflet.R | 124 SHARK4R-1.0.2/SHARK4R/tests/testthat/test-read_delivery_template.R | 134 SHARK4R-1.0.2/SHARK4R/tests/testthat/test-run_qc_app.R | 32 SHARK4R-1.0.2/SHARK4R/tests/testthat/test-scatterplot.R | 246 SHARK4R-1.0.2/SHARK4R/tests/testthat/test-shark_api_functions.R | 514 SHARK4R-1.0.2/SHARK4R/tests/testthat/test-shark_read.R | 292 SHARK4R-1.0.2/SHARK4R/tests/testthat/test-util.R | 515 SHARK4R-1.0.2/SHARK4R/tests/testthat/test-worms_api_functions.R | 482 SHARK4R-1.0.2/SHARK4R/tests/testthat/test-xylookup.R | 246 SHARK4R-1.0.2/SHARK4R/vignettes/quality_control.Rmd | 548 SHARK4R-1.0.2/SHARK4R/vignettes/retrieve_hab_data.Rmd | 148 SHARK4R-1.0.2/SHARK4R/vignettes/retrieve_nordic_microalgae_data.Rmd | 258 SHARK4R-1.0.2/SHARK4R/vignettes/retrieve_shark_data.Rmd | 202 SHARK4R-1.0.2/SHARK4R/vignettes/retrieve_worms_data.Rmd | 468 256 files changed, 31176 insertions(+), 37423 deletions(-)
Title: The IsoSpec Algorithm
Description: IsoSpec is a fine structure calculator used for obtaining the most
probable masses of a chemical compound given the frequencies of the composing
isotopes and their masses. It finds the smallest set of isotopologues with
a given probability. The probability is assumed to be that of the product of
multinomial distributions, each corresponding to one particular element and
parametrized by the frequencies of finding these elements in nature. These
numbers are supplied by IUPAC - the International Union of Pure and Applied
Chemistry. See: Lacki, Valkenborg, Startek (2020) <DOI:10.1021/acs.analchem.0c00959>
and Lacki, Startek, Valkenborg, Gambin (2017) <DOI:10.1021/acs.analchem.6b01459>
for the description of the algorithms used.
Author: Mateusz Krzysztof Lacki [cre, aut] ,
Michal Piotr Startek [aut]
Maintainer: Mateusz Krzysztof Lacki <matteo.lacki@gmail.com>
Diff between IsoSpecR versions 2.1.3 dated 2020-10-30 and 2.3.3 dated 2025-12-12
DESCRIPTION | 28 ++ LICENCE | 2 MD5 | 58 +++--- R/IsoSpecR.R | 7 R/RcppExports.R | 4 inst/CITATION | 63 +++--- man/IsoSpecify.Rd | 14 + man/isotopicData.Rd | 6 src/IsoSpecR_init.c | 4 src/RcppExports.cpp | 7 src/Rinterface.cpp | 5 src/cwrapper.cpp | 60 ++++++ src/cwrapper.h | 158 +++++++++------- src/element_tables.cpp | 2 src/element_tables.h | 24 +- src/fasta.h | 22 ++ src/fixedEnvelopes.cpp | 464 ++++++++++++++++++++++++++++++++++++++++++++++++- src/fixedEnvelopes.h | 19 +- src/isoMath.cpp | 5 src/isoMath.h | 4 src/isoSpec++.cpp | 66 ++++-- src/isoSpec++.h | 123 +++++++++--- src/marginalTrek++.cpp | 109 ++++++++++- src/marginalTrek++.h | 171 ++++++++++++++++++ src/misc.cpp | 10 - src/misc.h | 27 +- src/mman.cpp | 15 + src/operators.h | 4 src/platform.h | 8 src/pod_vector.h | 74 +++++-- 30 files changed, 1271 insertions(+), 292 deletions(-)
Title: Rmetrics - Autoregressive Conditional Heteroskedastic Modelling
Description: Analyze and model heteroskedastic behavior in financial time series.
Author: Diethelm Wuertz [aut] ,
Yohan Chalabi [aut],
Tobias Setz [aut],
Martin Maechler [aut] ,
Chris Boudt [ctb],
Pierre Chausse [ctb],
Michal Miklovac [ctb],
Georgi N. Boshnakov [aut, cre]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between fGarch versions 4033.92 dated 2024-03-26 and 4052.93 dated 2025-12-12
fGarch-4033.92/fGarch/man/dist-gedSlider.Rd |only fGarch-4033.92/fGarch/man/dist-sgedSlider.Rd |only fGarch-4033.92/fGarch/man/dist-snormSlider.Rd |only fGarch-4033.92/fGarch/man/dist-sstdSlider.Rd |only fGarch-4033.92/fGarch/man/dist-stdSlider.Rd |only fGarch-4052.93/fGarch/DESCRIPTION | 22 - fGarch-4052.93/fGarch/MD5 | 76 +-- fGarch-4052.93/fGarch/NEWS.md | 492 ++++++++++++------------ fGarch-4052.93/fGarch/R/garch-Hessian.R | 2 fGarch-4052.93/fGarch/R/garch-Spec.R | 3 fGarch-4052.93/fGarch/R/methods-show.R | 184 +++++--- fGarch-4052.93/fGarch/R/methods-summary.R | 10 fGarch-4052.93/fGarch/README.md | 2 fGarch-4052.93/fGarch/build/partial.rdb |binary fGarch-4052.93/fGarch/inst/NEWS.Rd | 25 + fGarch-4052.93/fGarch/inst/_pkgdown.yml | 4 fGarch-4052.93/fGarch/inst/pkgdown.yml | 7 fGarch-4052.93/fGarch/man/00fGarch-package.Rd | 32 - fGarch-4052.93/fGarch/man/VaR.Rd | 3 fGarch-4052.93/fGarch/man/class-fGARCH.Rd | 122 +++-- fGarch-4052.93/fGarch/man/class-fGARCHSPEC.Rd | 5 fGarch-4052.93/fGarch/man/class-fUGARCHSPEC.Rd | 11 fGarch-4052.93/fGarch/man/dist-Slider.Rd |only fGarch-4052.93/fGarch/man/dist-absMoments.Rd | 11 fGarch-4052.93/fGarch/man/dist-ged.Rd | 4 fGarch-4052.93/fGarch/man/dist-gedFit.Rd | 18 fGarch-4052.93/fGarch/man/dist-sged.Rd | 58 +- fGarch-4052.93/fGarch/man/dist-sgedFit.Rd | 36 - fGarch-4052.93/fGarch/man/dist-snorm.Rd | 47 +- fGarch-4052.93/fGarch/man/dist-snormFit.Rd | 38 - fGarch-4052.93/fGarch/man/dist-sstd.Rd | 31 + fGarch-4052.93/fGarch/man/dist-sstdFit.Rd | 36 - fGarch-4052.93/fGarch/man/dist-std.Rd | 5 fGarch-4052.93/fGarch/man/dist-stdFit.Rd | 20 fGarch-4052.93/fGarch/man/garchFit.Rd | 313 +++++++-------- fGarch-4052.93/fGarch/man/garchFitControl.Rd | 5 fGarch-4052.93/fGarch/man/garchSim.Rd | 128 ++---- fGarch-4052.93/fGarch/man/garchSpec.Rd | 129 +++--- fGarch-4052.93/fGarch/man/methods-coef.Rd | 28 - fGarch-4052.93/fGarch/man/methods-formula.Rd | 67 +-- fGarch-4052.93/fGarch/man/methods-summary.Rd | 38 + fGarch-4052.93/fGarch/man/methods-volatility.Rd | 41 -- 42 files changed, 1061 insertions(+), 992 deletions(-)
Title: A Graphical User Interface for Dexter
Description: Classical Test and Item analysis,
Item Response analysis and data management for educational and psychological tests.
Author: Jesse Koops [aut, cre],
Eva de Schipper [aut],
Ivailo Partchev [aut, ctb],
Gunter Maris [aut, ctb],
Timo Bechger [aut, ctb],
Gareth Watts [cph] ,
Hakim El Hattab [cph]
Maintainer: Jesse Koops <jesse.koops@cito.nl>
Diff between dextergui versions 1.0.1 dated 2025-10-06 and 1.0.3 dated 2025-12-12
DESCRIPTION | 18 ++++++++-------- MD5 | 30 ++++++++++++++-------------- NAMESPACE | 3 +- NEWS.md | 6 ++++- R/abplot.R | 2 - R/busy.R | 21 ++++++++++--------- R/example.R | 8 ------- R/misc.R | 4 +-- R/serve.R | 18 ++++++++++------ R/tags.R | 22 ++++++++++---------- R/zzz.R | 2 - README.md | 2 - build/vignette.rds |binary inst/doc/dextergui.html | 4 +-- inst/www/shinydexter.css | 28 ++++++++++++++++++++++++++ inst/www/shinydexter.js | 50 ++++++++++++++++++++++++++++++++++++++++++++++- 16 files changed, 147 insertions(+), 71 deletions(-)
Title: Suite of GR Hydrological Models for Precipitation-Runoff
Modelling
Description: Hydrological modelling tools developed at INRAE-Antony (HYCAR Research Unit, France). The package includes several conceptual rainfall-runoff models (GR4H, GR5H, GR4J, GR5J, GR6J, GR2M, GR1A) that can be applied either on a lumped or semi-distributed way. A snow accumulation and melt model (CemaNeige) and the associated functions for the calibration and evaluation of models are also included. Use help(airGR) for package description and references.
Author: Laurent Coron [aut, trl] ,
Olivier Delaigue [aut, cre] ,
Guillaume Thirel [aut, ths] ,
David Dorchies [aut] ,
Charles Perrin [aut, ths] ,
Claude Michel [aut, ths],
Vazken Andreassian [ctb, ths] ,
Francois Bourgin [ctb] ,
Pierre Brigode [ctb] ,
Nicola [...truncated...]
Maintainer: Olivier Delaigue <airGR@inrae.fr>
Diff between airGR versions 1.7.6 dated 2023-10-26 and 1.7.8 dated 2025-12-12
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Title: Variable Importance Plots
Description: A general framework for constructing variable importance plots from
various types of machine learning models in R. Aside from some standard model-
specific variable importance measures, this package also provides model-
agnostic approaches that can be applied to any supervised learning algorithm.
These include 1) an efficient permutation-based variable importance measure,
2) variable importance based on Shapley values (Strumbelj and Kononenko,
2014) <doi:10.1007/s10115-013-0679-x>, and 3) the variance-based
approach described in Greenwell et al. (2018) <doi:10.48550/arXiv.1805.04755>. A
variance-based method for quantifying the relative strength of interaction
effects is also included (see the previous reference for details).
Author: Brandon M. Greenwell [aut, cre] ,
Brad Boehmke [aut]
Maintainer: Brandon M. Greenwell <greenwell.brandon@gmail.com>
This is a re-admission after prior archival of version 0.4.3 dated 2025-12-10
Diff between vip versions 0.4.3 dated 2025-12-10 and 0.4.5 dated 2025-12-12
DESCRIPTION | 6 +-- MD5 | 57 +++++++++++++++++----------------- NEWS.md | 20 +++++++++++ R/utils.R | 31 +++++++++++------- R/vi_model.R | 25 -------------- R/vi_permute.R | 16 --------- inst/tinytest/test_pkg_C50.R | 9 ++--- inst/tinytest/test_pkg_Cubist.R | 10 ++--- inst/tinytest/test_pkg_RSNNS.R | 9 +---- inst/tinytest/test_pkg_caret.R | 10 ++--- inst/tinytest/test_pkg_earth.R | 4 ++ inst/tinytest/test_pkg_gbm.R | 9 ++--- inst/tinytest/test_pkg_glmnet.R | 9 ++--- inst/tinytest/test_pkg_h2o.R | 6 +-- inst/tinytest/test_pkg_lightgbm.R | 8 +--- inst/tinytest/test_pkg_mixOmics.R | 8 +--- inst/tinytest/test_pkg_mlr.R | 12 +++---- inst/tinytest/test_pkg_mlr3.R | 10 +---- inst/tinytest/test_pkg_neuralnet.R | 10 ++--- inst/tinytest/test_pkg_nnet.R | 10 ++--- inst/tinytest/test_pkg_party.R | 4 ++ inst/tinytest/test_pkg_partykit.R | 4 ++ inst/tinytest/test_pkg_pls.R | 10 ++--- inst/tinytest/test_pkg_randomForest.R | 9 ++--- inst/tinytest/test_pkg_ranger.R | 9 ++--- inst/tinytest/test_pkg_rpart.R | 9 ++--- inst/tinytest/test_pkg_stats.R | 4 ++ inst/tinytest/test_pkg_tidymodels.R | 8 +--- inst/tinytest/test_pkg_xgboost.R | 9 ++--- man/skip_on_cran.Rd |only 30 files changed, 163 insertions(+), 182 deletions(-)
Title: Create Full Text Browsers from Annotated Token Lists
Description: Create browsers for reading full texts from a token list format.
Information obtained from text analyses (e.g., topic modeling, word scaling)
can be used to annotate the texts.
Author: Kasper Welbers [aut, cre],
Wouter van Atteveldt [aut]
Maintainer: Kasper Welbers <kasperwelbers@gmail.com>
Diff between tokenbrowser versions 0.1.5 dated 2020-10-16 and 0.1.6 dated 2025-12-12
tokenbrowser-0.1.5/tokenbrowser/R/RcppExports.R |only tokenbrowser-0.1.5/tokenbrowser/R/imports.r |only tokenbrowser-0.1.5/tokenbrowser/src |only tokenbrowser-0.1.6/tokenbrowser/DESCRIPTION | 28 +++++---- tokenbrowser-0.1.6/tokenbrowser/MD5 | 31 ++++------ tokenbrowser-0.1.6/tokenbrowser/NAMESPACE | 2 tokenbrowser-0.1.6/tokenbrowser/R/attributes.r | 13 ++-- tokenbrowser-0.1.6/tokenbrowser/R/html_misc.r | 7 +- tokenbrowser-0.1.6/tokenbrowser/R/tokenvis.r | 5 - tokenbrowser-0.1.6/tokenbrowser/R/wrap_documents.r | 18 ++--- tokenbrowser-0.1.6/tokenbrowser/README.md | 2 tokenbrowser-0.1.6/tokenbrowser/inst/template/browser.css | 6 + tokenbrowser-0.1.6/tokenbrowser/inst/template/browser.html | 1 tokenbrowser-0.1.6/tokenbrowser/man/create_browser.Rd | 5 + tokenbrowser-0.1.6/tokenbrowser/man/create_meta_tables.Rd | 4 - tokenbrowser-0.1.6/tokenbrowser/man/wrap_documents.Rd | 5 + tokenbrowser-0.1.6/tokenbrowser/tests/testthat/test_tokenvis.r | 8 ++ 17 files changed, 78 insertions(+), 57 deletions(-)
Title: Analyzing the Orientation of Maximum Horizontal Stress
Description: Models the direction of the maximum horizontal stress using
relative plate motion parameters. Statistical algorithms to evaluate
the modeling results compared with the observed data. Provides plots
to visualize the results. Methods described in Stephan et al. (2023)
<doi:10.1038/s41598-023-42433-2> and Wdowinski (1998)
<doi:10.1016/S0079-1946(98)00091-3>.
Author: Tobias Stephan [aut, cre]
Maintainer: Tobias Stephan <tobias.stephan1@yahoo.com>
Diff between tectonicr versions 0.4.7 dated 2025-05-22 and 0.4.8 dated 2025-12-12
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Title: Interactive Visual and Numerical Diagnostics and Posterior
Analysis for Bayesian Models
Description: A graphical user interface for interactive Markov chain Monte
Carlo (MCMC) diagnostics and plots and tables helpful for analyzing a
posterior sample. The interface is powered by the 'Shiny' web
application framework from 'RStudio' and works with the output of MCMC
programs written in any programming language (and has extended
functionality for 'Stan' models fit using the 'rstan' and 'rstanarm'
packages).
Author: Jonah Gabry [aut, cre],
Duco Veen [aut],
Stan Development Team [ctb],
Michael Andreae [ctb],
Michael Betancourt [ctb],
Bob Carpenter [ctb],
Yuanjun Gao [ctb],
Andrew Gelman [ctb],
Ben Goodrich [ctb],
Daniel Lee [ctb],
Dongying Song [ctb],
Rob Tranguc [...truncated...]
Maintainer: Jonah Gabry <jgabry@gmail.com>
Diff between shinystan versions 2.6.0 dated 2022-03-02 and 2.7.0 dated 2025-12-12
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Title: Enhancing the 'parallel' Package
Description: Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.
Author: Henrik Bengtsson [aut, cre, cph] ,
Mike Cheng [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between parallelly versions 1.45.1 dated 2025-07-24 and 1.46.0 dated 2025-12-12
DESCRIPTION | 8 MD5 | 162 ++++--- NAMESPACE | 1 NEWS.md | 28 + R/010.cli.R |only R/availableCores.R | 36 + R/availableWorkers.R | 2 R/cpuLoad.R | 2 R/freeCores.R | 2 R/makeClusterPSOCK.R | 16 R/makeClusterSequential.R | 1 R/makeNodePSOCK.R | 4 R/options.R | 2 R/ports.R | 55 ++ R/supportsMulticore.R | 4 R/utils,conditions.R | 4 R/utils.R | 9 R/zzz.R | 11 build/vignette.rds |binary inst/WORDLIST | 14 inst/doc/parallelly-01-intro.html | 4 inst/doc/parallelly-01-intro.md | 4 inst/doc/parallelly-10-local-workers.html | 4 inst/doc/parallelly-10-local-workers.md | 4 inst/doc/parallelly-12-remote-workers.html | 10 inst/doc/parallelly-12-remote-workers.md | 10 inst/doc/parallelly-17-hpc-workers.html | 12 inst/doc/parallelly-17-hpc-workers.md | 12 inst/doc/parallelly-25-sandbox-workers.html |only inst/doc/parallelly-25-sandbox-workers.md |only inst/testme/_epilogue/999.detritus.R | 4 inst/testme/_prologue/030.imports.R | 8 inst/testme/_prologue/090.context.R | 2 inst/testme/deploy.R | 2 inst/testme/run.R | 605 +++++++++++++++++----------- inst/testme/test-all.equal.connection.R | 4 inst/testme/test-as.cluster.R | 23 + inst/testme/test-autoStopCluster.R |only inst/testme/test-availableConnections.R |only inst/testme/test-cloneNode.R |only inst/testme/test-freePort.R | 30 + inst/testme/test-isConnectionValid.R | 110 ++--- inst/testme/test-isForkedNode.R |only inst/testme/test-isLocalhostNode.R |only inst/testme/test-isNodeAlive.R |only inst/testme/test-makeClusterPSOCK.R | 2 inst/testme/test-makeClusterSequential.R | 109 ++++- inst/testme/test-makeNodePSOCK.R |only inst/testme/test-registerClusterTypes.R |only inst/testme/test-serializedSize.R |only inst/testme/test-stealth_sample.R |only inst/testme/test-supportsMulticore.R |only inst/testme/test-utils,conditions.R |only inst/testme/test-utils,pid.R |only man/availableCores.Rd | 9 man/freePort.Rd | 57 ++ man/killNode.Rd | 2 man/makeClusterPSOCK.Rd | 13 man/makeClusterSequential.Rd | 2 man/zzz-parallelly.options.Rd | 2 tests/test-all.equal.connection.R | 1 tests/test-as.cluster.R | 1 tests/test-autoStopCluster.R |only tests/test-availableConnections.R |only tests/test-availableCores.R | 1 tests/test-availableWorkers.R | 1 tests/test-cgroups.R | 1 tests/test-cloneNode.R |only tests/test-cpuLoad.R | 1 tests/test-freeCores.R | 1 tests/test-freePort.R | 1 tests/test-isConnectionValid.R | 1 tests/test-isForkedChild.R | 1 tests/test-isForkedNode.R |only tests/test-isLocalhostNode.R |only tests/test-isNodeAlive.R |only tests/test-killNode.R | 1 tests/test-makeClusterMPI.R | 1 tests/test-makeClusterPSOCK.R | 1 tests/test-makeClusterSequential.R | 1 tests/test-makeNodePSOCK.R |only tests/test-options-and-envvars.R | 1 tests/test-r_bug18119.R | 1 tests/test-registerClusterTypes.R |only tests/test-serializedSize.R |only tests/test-startup.R | 1 tests/test-stealth_sample.R |only tests/test-supportsMulticore.R |only tests/test-utils,cluster.R | 1 tests/test-utils,conditions.R |only tests/test-utils,pid.R |only tests/test-utils.R | 1 vignettes/parallelly-01-intro.md | 4 vignettes/parallelly-10-local-workers.md | 4 vignettes/parallelly-12-remote-workers.md | 10 vignettes/parallelly-17-hpc-workers.md | 12 vignettes/parallelly-25-sandbox-workers.md |only 97 files changed, 1002 insertions(+), 452 deletions(-)
Title: Mine Metrics from Common Places on the Web
Description: Mine metrics on common places on the web through the power of their APIs (application programming interfaces).
It also helps make the data in a format that is easily used for a dashboard or other purposes.
There is an associated dashboard template and tutorials that are underdevelopment that help you
fully utilize 'metricminer'.
Author: Candace Savonen [aut, cre],
Kate Isaac [aut],
Howard Baek [aut]
Maintainer: Candace Savonen <cansav09@gmail.com>
This is a re-admission after prior archival of version 1.0.0 dated 2025-02-19
Diff between metricminer versions 1.0.0 dated 2025-02-19 and 1.0.1 dated 2025-12-12
metricminer-1.0.0/metricminer/inst/extdata/example_data/local_auth.R |only metricminer-1.0.0/metricminer/vignettes/cran-example.R |only metricminer-1.0.1/metricminer/DESCRIPTION | 13 +- metricminer-1.0.1/metricminer/MD5 | 62 ++++------ metricminer-1.0.1/metricminer/NAMESPACE | 3 metricminer-1.0.1/metricminer/NEWS.md | 5 metricminer-1.0.1/metricminer/R/auth.R | 6 metricminer-1.0.1/metricminer/R/citations.R | 14 ++ metricminer-1.0.1/metricminer/R/github.R | 39 +++--- metricminer-1.0.1/metricminer/R/google-analytics.R | 19 ++- metricminer-1.0.1/metricminer/R/slido.R | 36 ++--- metricminer-1.0.1/metricminer/README.md | 20 ++- metricminer-1.0.1/metricminer/build/vignette.rds |binary metricminer-1.0.1/metricminer/inst/doc/example-data.Rmd | 2 metricminer-1.0.1/metricminer/inst/doc/example-data.html | 38 +++--- metricminer-1.0.1/metricminer/inst/doc/getting-started.Rmd | 10 - metricminer-1.0.1/metricminer/inst/doc/getting-started.html | 44 +++---- metricminer-1.0.1/metricminer/inst/extdata/_config_automation.yml | 2 metricminer-1.0.1/metricminer/inst/extdata/example_data/example-data-setup.R | 2 metricminer-1.0.1/metricminer/man/clean_repo_metrics.Rd | 2 metricminer-1.0.1/metricminer/man/get_github_metrics.Rd | 10 - metricminer-1.0.1/metricminer/man/get_github_repo_summary.Rd | 6 metricminer-1.0.1/metricminer/man/get_github_repo_timecourse.Rd | 6 metricminer-1.0.1/metricminer/man/get_multiple_repos_metrics.Rd | 5 metricminer-1.0.1/metricminer/man/get_org_repo_list.Rd | 2 metricminer-1.0.1/metricminer/man/get_slido_files.Rd | 22 +-- metricminer-1.0.1/metricminer/man/get_user_repo_list.Rd | 2 metricminer-1.0.1/metricminer/man/gh_repo_wrapper.Rd | 4 metricminer-1.0.1/metricminer/tests/testthat/test-citation.R | 31 ++++- metricminer-1.0.1/metricminer/tests/testthat/test-github.R | 8 - metricminer-1.0.1/metricminer/tests/testthat/test-google-analytics.R | 30 ++++ metricminer-1.0.1/metricminer/vignettes/example-data.Rmd | 2 metricminer-1.0.1/metricminer/vignettes/getting-started.Rmd | 10 - 33 files changed, 267 insertions(+), 188 deletions(-)
Title: Landscape Meteorology Tools
Description: Functions to estimate weather variables at any position of a landscape [De Caceres et al. (2018) <doi:10.1016/j.envsoft.2018.08.003>].
Author: Miquel De Caceres [aut, cre] ,
Victor Granda [aut] ,
Nicolas Martin [aut] ,
Antoine Cabon [aut]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>
Diff between meteoland versions 2.2.3 dated 2025-01-28 and 2.2.5 dated 2025-12-12
DESCRIPTION | 19 +-- MD5 | 34 +++--- NEWS.md | 9 + R/tidy_interpolation.R | 13 ++ R/tidy_interpolator.R | 44 +++++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/reshaping-meteo.html | 69 ++++++------- inst/doc/tidy-meteoland.R | 8 - inst/doc/tidy-meteoland.Rmd | 8 - inst/doc/tidy-meteoland.html | 117 +++++++++++------------ man/interpolator_calibration.Rd | 2 man/write_interpolator.Rd | 12 ++ src/interpolationutils.cpp | 6 - src/temperature.cpp | 24 ++++ tests/testthat/test-04_interpolation_framework.R | 80 ++++++++++++++- tests/testthat/test-31_c_internals.R | 1 vignettes/tidy-meteoland.Rmd | 8 - 18 files changed, 302 insertions(+), 152 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre, dtc] ,
Christoph Burow [aut, trl, dtc] ,
Michael Dietze [aut] ,
Margret C. Fuchs [aut] ,
Christoph Schmidt [aut] ,
Manfred Fischer [aut, trl],
Johannes Friedrich [aut] ,
Norbert Mercier [aut] ,
Rachel K. Smedley [ct [...truncated...]
Maintainer: Sebastian Kreutzer <maintainer_luminescence@r-luminescence.org>
Diff between Luminescence versions 1.1.1 dated 2025-09-11 and 1.1.2 dated 2025-12-12
Luminescence-1.1.1/Luminescence/man/BaseDataSet.ConversionFactors.Rd |only Luminescence-1.1.1/Luminescence/man/BaseDataSet.FractionalGammaDose.Rd |only Luminescence-1.1.1/Luminescence/man/BaseDataSet.GrainSizeAttenuation.Rd |only Luminescence-1.1.2/Luminescence/DESCRIPTION | 17 Luminescence-1.1.2/Luminescence/MD5 | 819 ++++---- Luminescence-1.1.2/Luminescence/NAMESPACE | 4 Luminescence-1.1.2/Luminescence/NEWS.md | 954 ++++------ Luminescence-1.1.2/Luminescence/R/Luminescence-generics.R | 40 Luminescence-1.1.2/Luminescence/R/Luminescence-package.R | 181 + Luminescence-1.1.2/Luminescence/R/RLum.Analysis-class.R | 48 Luminescence-1.1.2/Luminescence/R/RLum.Data-class.R | 8 Luminescence-1.1.2/Luminescence/R/RLum.Data.Curve-class.R | 106 - Luminescence-1.1.2/Luminescence/R/RLum.Data.Image-class.R | 26 Luminescence-1.1.2/Luminescence/R/RLum.Data.Spectrum-class.R | 54 Luminescence-1.1.2/Luminescence/R/RLum.Results-class.R | 86 Luminescence-1.1.2/Luminescence/R/Risoe.BINfileData-class.R | 30 Luminescence-1.1.2/Luminescence/R/Risoe.BINfileData2RLum.Analysis.R | 57 Luminescence-1.1.2/Luminescence/R/addins_RLum.R | 11 Luminescence-1.1.2/Luminescence/R/analyse_Al2O3C_CrossTalk.R | 75 Luminescence-1.1.2/Luminescence/R/analyse_Al2O3C_ITC.R | 32 Luminescence-1.1.2/Luminescence/R/analyse_Al2O3C_Measurement.R | 53 Luminescence-1.1.2/Luminescence/R/analyse_FadingMeasurement.R | 462 +--- Luminescence-1.1.2/Luminescence/R/analyse_IRSAR.RF.R | 345 +-- Luminescence-1.1.2/Luminescence/R/analyse_SAR.CWOSL.R | 458 ++-- Luminescence-1.1.2/Luminescence/R/analyse_SAR.TL.R | 70 Luminescence-1.1.2/Luminescence/R/analyse_ThermochronometryData.R | 70 Luminescence-1.1.2/Luminescence/R/analyse_baSAR.R | 352 +-- Luminescence-1.1.2/Luminescence/R/analyse_pIRIRSequence.R | 191 -- Luminescence-1.1.2/Luminescence/R/analyse_portableOSL.R | 42 Luminescence-1.1.2/Luminescence/R/apply_CosmicRayRemoval.R | 97 - Luminescence-1.1.2/Luminescence/R/apply_Crosstalk.R | 4 Luminescence-1.1.2/Luminescence/R/apply_EfficiencyCorrection.R | 17 Luminescence-1.1.2/Luminescence/R/calc_AliquotSize.R | 93 Luminescence-1.1.2/Luminescence/R/calc_AverageDose.R | 16 Luminescence-1.1.2/Luminescence/R/calc_CentralDose.R | 24 Luminescence-1.1.2/Luminescence/R/calc_CobbleDoseRate.R | 11 Luminescence-1.1.2/Luminescence/R/calc_CommonDose.R | 13 Luminescence-1.1.2/Luminescence/R/calc_CosmicDoseRate.R | 112 - Luminescence-1.1.2/Luminescence/R/calc_EED_Model.R | 55 Luminescence-1.1.2/Luminescence/R/calc_FadingCorr.R | 36 Luminescence-1.1.2/Luminescence/R/calc_FastRatio.R | 19 Luminescence-1.1.2/Luminescence/R/calc_FiniteMixture.R | 118 - Luminescence-1.1.2/Luminescence/R/calc_FuchsLang2001.R | 7 Luminescence-1.1.2/Luminescence/R/calc_HomogeneityTest.R | 9 Luminescence-1.1.2/Luminescence/R/calc_Huntley2006.R | 113 - Luminescence-1.1.2/Luminescence/R/calc_IEU.R | 4 Luminescence-1.1.2/Luminescence/R/calc_Lamothe2003.R | 13 Luminescence-1.1.2/Luminescence/R/calc_MaxDose.R | 11 Luminescence-1.1.2/Luminescence/R/calc_MinDose.R | 226 -- Luminescence-1.1.2/Luminescence/R/calc_MoransI.R | 7 Luminescence-1.1.2/Luminescence/R/calc_OSLLxTxDecomposed.R | 4 Luminescence-1.1.2/Luminescence/R/calc_OSLLxTxRatio.R | 32 Luminescence-1.1.2/Luminescence/R/calc_SourceDoseRate.R | 58 Luminescence-1.1.2/Luminescence/R/calc_Statistics.R | 7 Luminescence-1.1.2/Luminescence/R/calc_TLLxTxRatio.R | 14 Luminescence-1.1.2/Luminescence/R/calc_ThermalLifetime.R | 23 Luminescence-1.1.2/Luminescence/R/calc_WodaFuchs2008.R | 15 Luminescence-1.1.2/Luminescence/R/calc_gSGC.R | 16 Luminescence-1.1.2/Luminescence/R/calc_gSGC_feldspar.R | 32 Luminescence-1.1.2/Luminescence/R/combine_De_Dr.R | 112 - Luminescence-1.1.2/Luminescence/R/convert_Activity2Concentration.R | 4 Luminescence-1.1.2/Luminescence/R/convert_BIN2CSV.R | 4 Luminescence-1.1.2/Luminescence/R/convert_CW2pHMi.R | 14 Luminescence-1.1.2/Luminescence/R/convert_CW2pLM.R | 12 Luminescence-1.1.2/Luminescence/R/convert_CW2pLMi.R | 12 Luminescence-1.1.2/Luminescence/R/convert_CW2pPMi.R | 14 Luminescence-1.1.2/Luminescence/R/convert_Concentration2DoseRate.R | 30 Luminescence-1.1.2/Luminescence/R/convert_Daybreak2CSV.R | 9 Luminescence-1.1.2/Luminescence/R/convert_PSL2Risoe.BINfileData.R | 20 Luminescence-1.1.2/Luminescence/R/convert_RLum2Risoe.BINfileData.R | 9 Luminescence-1.1.2/Luminescence/R/convert_SG2MG.R | 5 Luminescence-1.1.2/Luminescence/R/convert_Second2Gray.R | 45 Luminescence-1.1.2/Luminescence/R/convert_Wavelength2Energy.R | 50 Luminescence-1.1.2/Luminescence/R/convert_XSYG2CSV.R | 3 Luminescence-1.1.2/Luminescence/R/correct_PMTLinearity.R | 4 Luminescence-1.1.2/Luminescence/R/extract_IrradiationTimes.R | 21 Luminescence-1.1.2/Luminescence/R/extract_ROI.R | 15 Luminescence-1.1.2/Luminescence/R/fit_CWCurve.R | 133 - Luminescence-1.1.2/Luminescence/R/fit_DoseResponseCurve.R | 17 Luminescence-1.1.2/Luminescence/R/fit_EmissionSpectra.R | 46 Luminescence-1.1.2/Luminescence/R/fit_IsothermalHolding.R | 143 - Luminescence-1.1.2/Luminescence/R/fit_LMCurve.R | 45 Luminescence-1.1.2/Luminescence/R/fit_OSLLifeTimes.R | 47 Luminescence-1.1.2/Luminescence/R/fit_SurfaceExposure.R | 17 Luminescence-1.1.2/Luminescence/R/fit_ThermalQuenching.R | 41 Luminescence-1.1.2/Luminescence/R/get_Layout.R | 35 Luminescence-1.1.2/Luminescence/R/get_Quote.R | 20 Luminescence-1.1.2/Luminescence/R/get_rightAnswer.R | 8 Luminescence-1.1.2/Luminescence/R/github.R | 37 Luminescence-1.1.2/Luminescence/R/import_Data.R | 4 Luminescence-1.1.2/Luminescence/R/install_DevelopmentVersion.R | 117 - Luminescence-1.1.2/Luminescence/R/internal_as.latex.table.R | 28 Luminescence-1.1.2/Luminescence/R/internals_RLum.R | 378 ++- Luminescence-1.1.2/Luminescence/R/internals_Thermochronometry.R | 10 Luminescence-1.1.2/Luminescence/R/merge_RLum.Data.Curve.R | 80 Luminescence-1.1.2/Luminescence/R/merge_RLum.Data.Spectrum.R | 103 - Luminescence-1.1.2/Luminescence/R/merge_RLum.R | 2 Luminescence-1.1.2/Luminescence/R/merge_Risoe.BINfileData.R | 2 Luminescence-1.1.2/Luminescence/R/methods_DRAC.R | 30 Luminescence-1.1.2/Luminescence/R/methods_RLum.R | 65 Luminescence-1.1.2/Luminescence/R/plot_AbanicoPlot.R | 274 +- Luminescence-1.1.2/Luminescence/R/plot_DRCSummary.R | 15 Luminescence-1.1.2/Luminescence/R/plot_DRTResults.R | 100 - Luminescence-1.1.2/Luminescence/R/plot_DetPlot.R | 16 Luminescence-1.1.2/Luminescence/R/plot_DoseResponseCurve.R | 89 Luminescence-1.1.2/Luminescence/R/plot_FilterCombinations.R | 8 Luminescence-1.1.2/Luminescence/R/plot_Histogram.R | 54 Luminescence-1.1.2/Luminescence/R/plot_KDE.R | 161 - Luminescence-1.1.2/Luminescence/R/plot_NRt.R | 4 Luminescence-1.1.2/Luminescence/R/plot_OSLAgeSummary.R | 15 Luminescence-1.1.2/Luminescence/R/plot_RLum.Analysis.R | 214 +- Luminescence-1.1.2/Luminescence/R/plot_RLum.Data.Curve.R | 133 - Luminescence-1.1.2/Luminescence/R/plot_RLum.Data.Image.R | 156 - 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Luminescence-1.1.2/Luminescence/R/report_RLum.R | 56 Luminescence-1.1.2/Luminescence/R/scale_GammaDose.R | 38 Luminescence-1.1.2/Luminescence/R/subset_SingleGrainData.R | 4 Luminescence-1.1.2/Luminescence/R/template_DRAC.R | 16 Luminescence-1.1.2/Luminescence/R/trim_RLum.Data.R | 16 Luminescence-1.1.2/Luminescence/R/tune_Data.R | 12 Luminescence-1.1.2/Luminescence/R/use_DRAC.R | 29 Luminescence-1.1.2/Luminescence/R/utils_DRAC.R | 2 Luminescence-1.1.2/Luminescence/R/verify_SingleGrainData.R | 18 Luminescence-1.1.2/Luminescence/R/write_R2BIN.R | 48 Luminescence-1.1.2/Luminescence/R/write_R2TIFF.R | 81 Luminescence-1.1.2/Luminescence/R/write_RLum2CSV.R | 67 Luminescence-1.1.2/Luminescence/R/zzz.R | 29 Luminescence-1.1.2/Luminescence/README.md | 2 Luminescence-1.1.2/Luminescence/build/partial.rdb |binary Luminescence-1.1.2/Luminescence/build/vignette.rds |binary Luminescence-1.1.2/Luminescence/data/ExampleData.portableOSL.rda |binary Luminescence-1.1.2/Luminescence/inst/doc/crosstalk.R | 1 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Luminescence-1.1.2/Luminescence/man/analyse_Al2O3C_Measurement.Rd | 2 Luminescence-1.1.2/Luminescence/man/analyse_FadingMeasurement.Rd | 78 Luminescence-1.1.2/Luminescence/man/analyse_IRSAR.RF.Rd | 183 - Luminescence-1.1.2/Luminescence/man/analyse_SAR.CWOSL.Rd | 12 Luminescence-1.1.2/Luminescence/man/analyse_SAR.TL.Rd | 9 Luminescence-1.1.2/Luminescence/man/analyse_baSAR.Rd | 70 Luminescence-1.1.2/Luminescence/man/analyse_pIRIRSequence.Rd | 18 Luminescence-1.1.2/Luminescence/man/analyse_portableOSL.Rd | 6 Luminescence-1.1.2/Luminescence/man/apply_CosmicRayRemoval.Rd | 2 Luminescence-1.1.2/Luminescence/man/apply_Crosstalk.Rd | 2 Luminescence-1.1.2/Luminescence/man/apply_EfficiencyCorrection.Rd | 2 Luminescence-1.1.2/Luminescence/man/as.Rd | 6 Luminescence-1.1.2/Luminescence/man/bin_RLum.Data.Rd | 2 Luminescence-1.1.2/Luminescence/man/calc_AliquotSize.Rd | 4 Luminescence-1.1.2/Luminescence/man/calc_AverageDose.Rd | 6 Luminescence-1.1.2/Luminescence/man/calc_CentralDose.Rd | 7 Luminescence-1.1.2/Luminescence/man/calc_CobbleDoseRate.Rd | 2 Luminescence-1.1.2/Luminescence/man/calc_CommonDose.Rd | 7 Luminescence-1.1.2/Luminescence/man/calc_CosmicDoseRate.Rd | 2 Luminescence-1.1.2/Luminescence/man/calc_EED_Model.Rd | 10 Luminescence-1.1.2/Luminescence/man/calc_FadingCorr.Rd | 2 Luminescence-1.1.2/Luminescence/man/calc_FastRatio.Rd | 2 Luminescence-1.1.2/Luminescence/man/calc_FiniteMixture.Rd | 12 Luminescence-1.1.2/Luminescence/man/calc_FuchsLang2001.Rd | 2 Luminescence-1.1.2/Luminescence/man/calc_HomogeneityTest.Rd | 2 Luminescence-1.1.2/Luminescence/man/calc_Huntley2006.Rd | 11 Luminescence-1.1.2/Luminescence/man/calc_IEU.Rd | 2 Luminescence-1.1.2/Luminescence/man/calc_Lamothe2003.Rd | 2 Luminescence-1.1.2/Luminescence/man/calc_MaxDose.Rd | 11 Luminescence-1.1.2/Luminescence/man/calc_MinDose.Rd | 72 Luminescence-1.1.2/Luminescence/man/calc_MoransI.Rd | 2 Luminescence-1.1.2/Luminescence/man/calc_OSLLxTxDecomposed.Rd | 2 Luminescence-1.1.2/Luminescence/man/calc_OSLLxTxRatio.Rd | 8 Luminescence-1.1.2/Luminescence/man/calc_SourceDoseRate.Rd | 31 Luminescence-1.1.2/Luminescence/man/calc_Statistics.Rd | 2 Luminescence-1.1.2/Luminescence/man/calc_TLLxTxRatio.Rd | 11 Luminescence-1.1.2/Luminescence/man/calc_ThermalLifetime.Rd | 2 Luminescence-1.1.2/Luminescence/man/calc_WodaFuchs2008.Rd | 2 Luminescence-1.1.2/Luminescence/man/calc_gSGC.Rd | 6 Luminescence-1.1.2/Luminescence/man/calc_gSGC_feldspar.Rd | 6 Luminescence-1.1.2/Luminescence/man/combine_De_Dr.Rd | 15 Luminescence-1.1.2/Luminescence/man/convert_Activity2Concentration.Rd | 2 Luminescence-1.1.2/Luminescence/man/convert_BIN2CSV.Rd | 2 Luminescence-1.1.2/Luminescence/man/convert_CW2pHMi.Rd | 5 Luminescence-1.1.2/Luminescence/man/convert_CW2pLM.Rd | 9 Luminescence-1.1.2/Luminescence/man/convert_CW2pLMi.Rd | 5 Luminescence-1.1.2/Luminescence/man/convert_CW2pPMi.Rd | 5 Luminescence-1.1.2/Luminescence/man/convert_Concentration2DoseRate.Rd | 14 Luminescence-1.1.2/Luminescence/man/convert_Daybreak2CSV.Rd | 2 Luminescence-1.1.2/Luminescence/man/convert_PSL2CSV.Rd | 2 Luminescence-1.1.2/Luminescence/man/convert_PSL2Risoe.BINfileData.Rd | 2 Luminescence-1.1.2/Luminescence/man/convert_RLum2Risoe.BINfileData.Rd | 2 Luminescence-1.1.2/Luminescence/man/convert_SG2MG.Rd | 2 Luminescence-1.1.2/Luminescence/man/convert_Second2Gray.Rd | 12 Luminescence-1.1.2/Luminescence/man/convert_Wavelength2Energy.Rd | 28 Luminescence-1.1.2/Luminescence/man/convert_XSYG2CSV.Rd | 2 Luminescence-1.1.2/Luminescence/man/correct_PMTLinearity.Rd | 6 Luminescence-1.1.2/Luminescence/man/dot-as.latex.table.Rd | 9 Luminescence-1.1.2/Luminescence/man/extract_IrradiationTimes.Rd | 2 Luminescence-1.1.2/Luminescence/man/extract_ROI.Rd | 2 Luminescence-1.1.2/Luminescence/man/fit_CWCurve.Rd | 6 Luminescence-1.1.2/Luminescence/man/fit_DoseResponseCurve.Rd | 2 Luminescence-1.1.2/Luminescence/man/fit_EmissionSpectra.Rd | 2 Luminescence-1.1.2/Luminescence/man/fit_LMCurve.Rd | 11 Luminescence-1.1.2/Luminescence/man/fit_OSLLifeTimes.Rd | 2 Luminescence-1.1.2/Luminescence/man/fit_SurfaceExposure.Rd | 2 Luminescence-1.1.2/Luminescence/man/fit_ThermalQuenching.Rd | 2 Luminescence-1.1.2/Luminescence/man/get_Layout.Rd | 2 Luminescence-1.1.2/Luminescence/man/get_RLum.Rd | 2 Luminescence-1.1.2/Luminescence/man/get_rightAnswer.Rd | 2 Luminescence-1.1.2/Luminescence/man/import_Data.Rd | 2 Luminescence-1.1.2/Luminescence/man/install_DevelopmentVersion.Rd | 23 Luminescence-1.1.2/Luminescence/man/length_RLum.Rd | 2 Luminescence-1.1.2/Luminescence/man/melt_RLum.Rd | 2 Luminescence-1.1.2/Luminescence/man/merge_RLum.Analysis.Rd | 2 Luminescence-1.1.2/Luminescence/man/merge_RLum.Data.Curve.Rd | 8 Luminescence-1.1.2/Luminescence/man/merge_RLum.Data.Spectrum.Rd | 8 Luminescence-1.1.2/Luminescence/man/merge_RLum.Rd | 2 Luminescence-1.1.2/Luminescence/man/merge_RLum.Results.Rd | 2 Luminescence-1.1.2/Luminescence/man/merge_Risoe.BINfileData.Rd | 2 Luminescence-1.1.2/Luminescence/man/metadata.Rd | 2 Luminescence-1.1.2/Luminescence/man/methods_RLum.Rd | 3 Luminescence-1.1.2/Luminescence/man/names_RLum.Rd | 2 Luminescence-1.1.2/Luminescence/man/plot_AbanicoPlot.Rd | 34 Luminescence-1.1.2/Luminescence/man/plot_DRCSummary.Rd | 2 Luminescence-1.1.2/Luminescence/man/plot_DRTResults.Rd | 8 Luminescence-1.1.2/Luminescence/man/plot_DetPlot.Rd | 2 Luminescence-1.1.2/Luminescence/man/plot_DoseResponseCurve.Rd | 4 Luminescence-1.1.2/Luminescence/man/plot_FilterCombinations.Rd | 6 Luminescence-1.1.2/Luminescence/man/plot_GrowthCurve.Rd | 2 Luminescence-1.1.2/Luminescence/man/plot_Histogram.Rd | 2 Luminescence-1.1.2/Luminescence/man/plot_KDE.Rd | 4 Luminescence-1.1.2/Luminescence/man/plot_MoranScatterplot.Rd | 2 Luminescence-1.1.2/Luminescence/man/plot_NRt.Rd | 2 Luminescence-1.1.2/Luminescence/man/plot_OSLAgeSummary.Rd | 2 Luminescence-1.1.2/Luminescence/man/plot_RLum.Analysis.Rd | 26 Luminescence-1.1.2/Luminescence/man/plot_RLum.Data.Curve.Rd | 2 Luminescence-1.1.2/Luminescence/man/plot_RLum.Data.Image.Rd | 11 Luminescence-1.1.2/Luminescence/man/plot_RLum.Data.Spectrum.Rd | 88 Luminescence-1.1.2/Luminescence/man/plot_RLum.Rd | 2 Luminescence-1.1.2/Luminescence/man/plot_RLum.Results.Rd | 2 Luminescence-1.1.2/Luminescence/man/plot_ROI.Rd | 4 Luminescence-1.1.2/Luminescence/man/plot_RadialPlot.Rd | 56 Luminescence-1.1.2/Luminescence/man/plot_Risoe.BINfileData.Rd | 4 Luminescence-1.1.2/Luminescence/man/plot_SingleGrainDisc.Rd | 2 Luminescence-1.1.2/Luminescence/man/plot_ViolinPlot.Rd | 2 Luminescence-1.1.2/Luminescence/man/read_BIN2R.Rd | 9 Luminescence-1.1.2/Luminescence/man/read_Daybreak2R.Rd | 2 Luminescence-1.1.2/Luminescence/man/read_HeliosOSL2R.Rd | 2 Luminescence-1.1.2/Luminescence/man/read_PSL2R.Rd | 26 Luminescence-1.1.2/Luminescence/man/read_RF2R.Rd | 2 Luminescence-1.1.2/Luminescence/man/read_SPE2R.Rd | 10 Luminescence-1.1.2/Luminescence/man/read_TIFF2R.Rd | 2 Luminescence-1.1.2/Luminescence/man/read_XSYG2R.Rd | 21 Luminescence-1.1.2/Luminescence/man/remove_RLum.Rd | 2 Luminescence-1.1.2/Luminescence/man/remove_SignalBackground.Rd | 2 Luminescence-1.1.2/Luminescence/man/replicate_RLum.Rd | 2 Luminescence-1.1.2/Luminescence/man/report_RLum.Rd | 2 Luminescence-1.1.2/Luminescence/man/sTeve.Rd | 4 Luminescence-1.1.2/Luminescence/man/scale_GammaDose.Rd | 8 Luminescence-1.1.2/Luminescence/man/set_RLum.Rd | 2 Luminescence-1.1.2/Luminescence/man/set_Risoe.BINfileData.Rd | 2 Luminescence-1.1.2/Luminescence/man/smooth_RLum.Rd | 2 Luminescence-1.1.2/Luminescence/man/sort_RLum.Rd | 2 Luminescence-1.1.2/Luminescence/man/structure_RLum.Rd | 2 Luminescence-1.1.2/Luminescence/man/subset_SingleGrainData.Rd | 2 Luminescence-1.1.2/Luminescence/man/template_DRAC.Rd | 2 Luminescence-1.1.2/Luminescence/man/trim_RLum.Data.Rd | 2 Luminescence-1.1.2/Luminescence/man/tune_Data.Rd | 2 Luminescence-1.1.2/Luminescence/man/use_DRAC.Rd | 15 Luminescence-1.1.2/Luminescence/man/verify_SingleGrainData.Rd | 4 Luminescence-1.1.2/Luminescence/man/view.Rd | 2 Luminescence-1.1.2/Luminescence/man/write_R2BIN.Rd | 2 Luminescence-1.1.2/Luminescence/man/write_R2TIFF.Rd | 25 Luminescence-1.1.2/Luminescence/man/write_RLum2CSV.Rd | 14 Luminescence-1.1.2/Luminescence/src/Makevars | 2 Luminescence-1.1.2/Luminescence/src/Makevars.win | 2 Luminescence-1.1.2/Luminescence/src/src_ThermoChronometry.cpp | 7 Luminescence-1.1.2/Luminescence/src/src_analyse_IRSARRF_SRS.cpp | 44 Luminescence-1.1.2/Luminescence/src/src_create_RLumDataCurve_matrix.cpp | 35 Luminescence-1.1.2/Luminescence/src/src_get_XSYG_curve_values.cpp | 20 Luminescence-1.1.2/Luminescence/tests/testthat/_data/KRG104_IRSL100.csv |only Luminescence-1.1.2/Luminescence/tests/testthat/_data/KRG104_IRSL150.csv |only Luminescence-1.1.2/Luminescence/tests/testthat/_data/KRG104_IRSL225.csv |only Luminescence-1.1.2/Luminescence/tests/testthat/_data/KRG104_IRSL50.csv |only Luminescence-1.1.2/Luminescence/tests/testthat/_data/xsyg-tests/XSYG_noSequence.xsyg |only Luminescence-1.1.2/Luminescence/tests/testthat/setup.R | 25 Luminescence-1.1.2/Luminescence/tests/testthat/test_RLum.Analysis-class.R | 2 Luminescence-1.1.2/Luminescence/tests/testthat/test_RLum.Data.Curve.R | 5 Luminescence-1.1.2/Luminescence/tests/testthat/test_RLum.Data.Image.R | 6 Luminescence-1.1.2/Luminescence/tests/testthat/test_RLum.Data.Spectrum.R | 4 Luminescence-1.1.2/Luminescence/tests/testthat/test_Risoe.BINfileData2RLum.Analysis.R | 11 Luminescence-1.1.2/Luminescence/tests/testthat/test_analyse_Al2O3C_CrossTalk.R | 17 Luminescence-1.1.2/Luminescence/tests/testthat/test_analyse_Al2O3C_ITC.R | 14 Luminescence-1.1.2/Luminescence/tests/testthat/test_analyse_Al2O3C_Measurement.R | 35 Luminescence-1.1.2/Luminescence/tests/testthat/test_analyse_FadingMeasurement.R | 174 + Luminescence-1.1.2/Luminescence/tests/testthat/test_analyse_IRSAR.RF.R | 77 Luminescence-1.1.2/Luminescence/tests/testthat/test_analyse_SAR.CWOSL.R | 25 Luminescence-1.1.2/Luminescence/tests/testthat/test_analyse_SAR.TL.R | 37 Luminescence-1.1.2/Luminescence/tests/testthat/test_analyse_ThermochronometryData.R | 10 Luminescence-1.1.2/Luminescence/tests/testthat/test_analyse_baSAR.R | 42 Luminescence-1.1.2/Luminescence/tests/testthat/test_analyse_pIRIRSequence.R | 6 Luminescence-1.1.2/Luminescence/tests/testthat/test_analyse_portableOSL.R | 57 Luminescence-1.1.2/Luminescence/tests/testthat/test_apply_CosmicRayRemoval.R | 102 - Luminescence-1.1.2/Luminescence/tests/testthat/test_apply_Crosstalk.R | 2 Luminescence-1.1.2/Luminescence/tests/testthat/test_calc_AliquotSize.R | 27 Luminescence-1.1.2/Luminescence/tests/testthat/test_calc_AverageDose.R | 6 Luminescence-1.1.2/Luminescence/tests/testthat/test_calc_CentralDose.R | 48 Luminescence-1.1.2/Luminescence/tests/testthat/test_calc_CosmicDoseRate.R | 31 Luminescence-1.1.2/Luminescence/tests/testthat/test_calc_EED_Model.R | 60 Luminescence-1.1.2/Luminescence/tests/testthat/test_calc_FadingCorr.R | 23 Luminescence-1.1.2/Luminescence/tests/testthat/test_calc_FastRatio.R | 31 Luminescence-1.1.2/Luminescence/tests/testthat/test_calc_FiniteMixture.R | 55 Luminescence-1.1.2/Luminescence/tests/testthat/test_calc_FuchsLang2001.R | 51 Luminescence-1.1.2/Luminescence/tests/testthat/test_calc_HomogeneityTest.R | 31 Luminescence-1.1.2/Luminescence/tests/testthat/test_calc_Huntley2006.R | 28 Luminescence-1.1.2/Luminescence/tests/testthat/test_calc_Lamothe2003.R | 2 Luminescence-1.1.2/Luminescence/tests/testthat/test_calc_MinDose.R | 26 Luminescence-1.1.2/Luminescence/tests/testthat/test_calc_MoransI.R | 2 Luminescence-1.1.2/Luminescence/tests/testthat/test_calc_OSLLxTxDecomposed.R | 2 Luminescence-1.1.2/Luminescence/tests/testthat/test_calc_OSLLxTxRatio.R | 4 Luminescence-1.1.2/Luminescence/tests/testthat/test_calc_SourceDoseRate.R | 4 Luminescence-1.1.2/Luminescence/tests/testthat/test_calc_Statistics.R | 7 Luminescence-1.1.2/Luminescence/tests/testthat/test_calc_TLLxTxRatio.R | 4 Luminescence-1.1.2/Luminescence/tests/testthat/test_calc_ThermalLifetime.R | 1 Luminescence-1.1.2/Luminescence/tests/testthat/test_calc_WodaFuchs2008.R | 22 Luminescence-1.1.2/Luminescence/tests/testthat/test_calc_gSGC.R | 1 Luminescence-1.1.2/Luminescence/tests/testthat/test_calc_gSGC_feldspar.R | 10 Luminescence-1.1.2/Luminescence/tests/testthat/test_combine_De_Dr.R | 63 Luminescence-1.1.2/Luminescence/tests/testthat/test_convert_CW2pX.R | 11 Luminescence-1.1.2/Luminescence/tests/testthat/test_convert_PSL2RisoeBINfiledata.R | 3 Luminescence-1.1.2/Luminescence/tests/testthat/test_convert_SG2MG.R | 2 Luminescence-1.1.2/Luminescence/tests/testthat/test_convert_Second2Gray.R | 2 Luminescence-1.1.2/Luminescence/tests/testthat/test_convert_Wavelength2Energy.R | 27 Luminescence-1.1.2/Luminescence/tests/testthat/test_convert_XSYG2CSV.R | 2 Luminescence-1.1.2/Luminescence/tests/testthat/test_correct_PMTLinearity.R | 2 Luminescence-1.1.2/Luminescence/tests/testthat/test_extract_IrradiationTimes.R | 40 Luminescence-1.1.2/Luminescence/tests/testthat/test_extract_ROI.R | 72 Luminescence-1.1.2/Luminescence/tests/testthat/test_fit_CWCurve.R | 88 Luminescence-1.1.2/Luminescence/tests/testthat/test_fit_DoseResponseCurve.R | 23 Luminescence-1.1.2/Luminescence/tests/testthat/test_fit_EmissionSpectra.R | 102 - Luminescence-1.1.2/Luminescence/tests/testthat/test_fit_IsothermalHolding.R | 20 Luminescence-1.1.2/Luminescence/tests/testthat/test_fit_LMCurve.R | 3 Luminescence-1.1.2/Luminescence/tests/testthat/test_fit_OSLLifeTimes.R | 55 Luminescence-1.1.2/Luminescence/tests/testthat/test_fit_SurfaceExposure.R | 51 Luminescence-1.1.2/Luminescence/tests/testthat/test_get_Layout.R | 3 Luminescence-1.1.2/Luminescence/tests/testthat/test_get_RLum.R | 12 Luminescence-1.1.2/Luminescence/tests/testthat/test_github.R | 91 Luminescence-1.1.2/Luminescence/tests/testthat/test_install_DevelopmentVersion.R |only Luminescence-1.1.2/Luminescence/tests/testthat/test_internals.R | 120 - Luminescence-1.1.2/Luminescence/tests/testthat/test_merge_RLum.Data.Curve.R | 4 Luminescence-1.1.2/Luminescence/tests/testthat/test_merge_RLum.Data.Spectrum.R | 5 Luminescence-1.1.2/Luminescence/tests/testthat/test_metadata.R | 12 Luminescence-1.1.2/Luminescence/tests/testthat/test_methods_S3.R | 59 Luminescence-1.1.2/Luminescence/tests/testthat/test_plot_AbanicoPlot.R | 48 Luminescence-1.1.2/Luminescence/tests/testthat/test_plot_DRCSummary.R | 1 Luminescence-1.1.2/Luminescence/tests/testthat/test_plot_DRTResults.R | 12 Luminescence-1.1.2/Luminescence/tests/testthat/test_plot_DetPlot.R | 3 Luminescence-1.1.2/Luminescence/tests/testthat/test_plot_DoseResponseCurve.R | 15 Luminescence-1.1.2/Luminescence/tests/testthat/test_plot_FilterCombinations.R | 1 Luminescence-1.1.2/Luminescence/tests/testthat/test_plot_Histogram.R | 24 Luminescence-1.1.2/Luminescence/tests/testthat/test_plot_KDE.R | 22 Luminescence-1.1.2/Luminescence/tests/testthat/test_plot_MoranScatterplot.R | 1 Luminescence-1.1.2/Luminescence/tests/testthat/test_plot_NRt.R | 1 Luminescence-1.1.2/Luminescence/tests/testthat/test_plot_OSLAgeSummary.R | 35 Luminescence-1.1.2/Luminescence/tests/testthat/test_plot_RLum.Analysis.R | 53 Luminescence-1.1.2/Luminescence/tests/testthat/test_plot_RLum.Data.Curve.R | 1 Luminescence-1.1.2/Luminescence/tests/testthat/test_plot_RLum.Data.Image.R | 54 Luminescence-1.1.2/Luminescence/tests/testthat/test_plot_RLum.Data.Spectrum.R | 278 -- Luminescence-1.1.2/Luminescence/tests/testthat/test_plot_RLum.R | 29 Luminescence-1.1.2/Luminescence/tests/testthat/test_plot_RLum.Results.R | 2 Luminescence-1.1.2/Luminescence/tests/testthat/test_plot_ROI.R | 1 Luminescence-1.1.2/Luminescence/tests/testthat/test_plot_RadialPlot.R | 72 Luminescence-1.1.2/Luminescence/tests/testthat/test_plot_Risoe.BINfileData.R | 3 Luminescence-1.1.2/Luminescence/tests/testthat/test_plot_SingleGrainDisc.R | 1 Luminescence-1.1.2/Luminescence/tests/testthat/test_plot_ViolinPlot.R | 6 Luminescence-1.1.2/Luminescence/tests/testthat/test_read_HeliosOSL2R.R | 2 Luminescence-1.1.2/Luminescence/tests/testthat/test_read_PSL2R.R | 4 Luminescence-1.1.2/Luminescence/tests/testthat/test_read_SPE2R.R | 18 Luminescence-1.1.2/Luminescence/tests/testthat/test_read_TIFF2R.R | 4 Luminescence-1.1.2/Luminescence/tests/testthat/test_read_XSYG2R.R | 11 Luminescence-1.1.2/Luminescence/tests/testthat/test_remove_SignalBackground.R | 2 Luminescence-1.1.2/Luminescence/tests/testthat/test_scale_GammaDose.R | 1 Luminescence-1.1.2/Luminescence/tests/testthat/test_set_RLum.R |only Luminescence-1.1.2/Luminescence/tests/testthat/test_structure_RLum.R | 17 Luminescence-1.1.2/Luminescence/tests/testthat/test_template_DRAC.R | 5 Luminescence-1.1.2/Luminescence/tests/testthat/test_use_DRAC.R | 21 Luminescence-1.1.2/Luminescence/tests/testthat/test_verify_SingleGrainData.R | 26 Luminescence-1.1.2/Luminescence/tests/testthat/test_write_R2BIN.R | 4 Luminescence-1.1.2/Luminescence/tests/testthat/test_write_R2TIFF.R | 6 Luminescence-1.1.2/Luminescence/tests/testthat/test_write_RLum2CSV.R | 11 Luminescence-1.1.2/Luminescence/tests/testthat/test_zzz.R | 8 Luminescence-1.1.2/Luminescence/vignettes/crosstalk.Rmd | 1 417 files changed, 7152 insertions(+), 7856 deletions(-)
Title: Triangle Meshes and Related Geometry Tools
Description: Generate planar and spherical triangle meshes,
compute finite element calculations for 1-, 2-, and 3-dimensional flat
and curved manifolds with associated basis function spaces, methods for
lines and polygons, and transparent handling of coordinate reference
systems and coordinate transformation, including 'sf' and 'sp' geometries.
The core 'fmesher' library code was originally part of the 'INLA' package,
and implements parts of "Triangulations and Applications" by
Hjelle and Daehlen (2006) <doi:10.1007/3-540-33261-8>.
Author: Finn Lindgren [aut, cre, cph] ,
Seaton Andy [ctb] ,
Suen Man Ho [ctb] ,
Fabian E. Bachl [ctb]
Maintainer: Finn Lindgren <finn.lindgren@gmail.com>
Diff between fmesher versions 0.5.0 dated 2025-07-07 and 0.6.1 dated 2025-12-12
fmesher-0.5.0/fmesher/man/fm_CRSargs.Rd |only fmesher-0.6.1/fmesher/DESCRIPTION | 12 fmesher-0.6.1/fmesher/MD5 | 135 +- fmesher-0.6.1/fmesher/NAMESPACE | 26 fmesher-0.6.1/fmesher/NEWS.md | 78 + fmesher-0.6.1/fmesher/R/RcppExports.R | 26 fmesher-0.6.1/fmesher/R/bary.R | 5 fmesher-0.6.1/fmesher/R/basis.R | 106 -- fmesher-0.6.1/fmesher/R/bbox.R | 2 fmesher-0.6.1/fmesher/R/components.R | 8 fmesher-0.6.1/fmesher/R/crs.R | 191 --- fmesher-0.6.1/fmesher/R/diameter.R | 2 fmesher-0.6.1/fmesher/R/evaluator.R | 8 fmesher-0.6.1/fmesher/R/fem.R | 7 fmesher-0.6.1/fmesher/R/ggplot.R | 41 fmesher-0.6.1/fmesher/R/integration.R | 683 ++++++++----- fmesher-0.6.1/fmesher/R/lattice_2d.R | 33 fmesher-0.6.1/fmesher/R/lattice_Nd.R | 30 fmesher-0.6.1/fmesher/R/list.R | 3 fmesher-0.6.1/fmesher/R/local.R | 12 fmesher-0.6.1/fmesher/R/manifold.R | 1 fmesher-0.6.1/fmesher/R/mapping.R | 3 fmesher-0.6.1/fmesher/R/matern.R | 3 fmesher-0.6.1/fmesher/R/mesh.R | 625 ++++++++++- fmesher-0.6.1/fmesher/R/mesh_1d.R | 5 fmesher-0.6.1/fmesher/R/mesh_2d.R | 66 - fmesher-0.6.1/fmesher/R/mesh_3d.R | 8 fmesher-0.6.1/fmesher/R/nonconvex_hull.R | 27 fmesher-0.6.1/fmesher/R/plot.R | 103 + fmesher-0.6.1/fmesher/R/print.R | 12 fmesher-0.6.1/fmesher/R/segm.R | 8 fmesher-0.6.1/fmesher/R/sf_mesh.R | 25 fmesher-0.6.1/fmesher/R/simplify.R | 4 fmesher-0.6.1/fmesher/R/sp_mesh.R | 22 fmesher-0.6.1/fmesher/R/utils.R | 10 fmesher-0.6.1/fmesher/build/partial.rdb |binary fmesher-0.6.1/fmesher/build/vignette.rds |binary fmesher-0.6.1/fmesher/inst/doc/basic_use.html | 5 fmesher-0.6.1/fmesher/inst/doc/custom_classes.html | 5 fmesher-0.6.1/fmesher/inst/doc/inla_conversion.R | 56 - fmesher-0.6.1/fmesher/inst/doc/inla_conversion.Rmd | 62 - fmesher-0.6.1/fmesher/inst/doc/inla_conversion.html | 89 + fmesher-0.6.1/fmesher/inst/doc/variable_mesh_quality.html | 5 fmesher-0.6.1/fmesher/man/as.triangles3d.fm_mesh_3d.Rd | 7 fmesher-0.6.1/fmesher/man/fm_components.Rd | 8 fmesher-0.6.1/fmesher/man/fm_int.Rd | 15 fmesher-0.6.1/fmesher/man/fm_int_multi_sampler.Rd | 6 fmesher-0.6.1/fmesher/man/fm_mesh_3d.Rd | 2 fmesher-0.6.1/fmesher/man/fm_mesh_intersection.Rd | 75 + fmesher-0.6.1/fmesher/man/fm_nonconvex_hull_inla.Rd | 10 fmesher-0.6.1/fmesher/man/fm_subdivide.Rd | 7 fmesher-0.6.1/fmesher/man/fm_subset.Rd |only fmesher-0.6.1/fmesher/man/fm_zm.Rd |only fmesher-0.6.1/fmesher/man/fmesher-deprecated.Rd | 43 fmesher-0.6.1/fmesher/man/fmesher_spherical_harmonics.Rd |only fmesher-0.6.1/fmesher/man/fmesher_subdivide.Rd | 5 fmesher-0.6.1/fmesher/man/geom_fm.Rd | 16 fmesher-0.6.1/fmesher/man/new_fm_int.Rd |only fmesher-0.6.1/fmesher/man/plot.fm_segm.Rd | 8 fmesher-0.6.1/fmesher/man/plot_rgl.Rd | 2 fmesher-0.6.1/fmesher/src/Makevars | 2 fmesher-0.6.1/fmesher/src/RcppExports.cpp | 14 fmesher-0.6.1/fmesher/src/Rcpp_interface.cc | 101 + fmesher-0.6.1/fmesher/src/basis.cc | 165 ++- fmesher-0.6.1/fmesher/src/basis.h | 2 fmesher-0.6.1/fmesher/src/locator.cc | 33 fmesher-0.6.1/fmesher/tests/testthat/test-01-integration.R | 13 fmesher-0.6.1/fmesher/tests/testthat/test-sf.R | 40 fmesher-0.6.1/fmesher/tests/testthat/test-subdivide.R | 40 fmesher-0.6.1/fmesher/tests/testthat/test-transform.R | 5 fmesher-0.6.1/fmesher/vignettes/inla_conversion.Rmd | 62 - 71 files changed, 2151 insertions(+), 1082 deletions(-)
Title: Scientific Content and Citation Analysis from PDF Documents
Description: Provides comprehensive tools for extracting and analyzing scientific
content from PDF documents, including citation extraction, reference matching,
text analysis, and bibliometric indicators. Supports multi-column PDF layouts,
'CrossRef' API <https://www.crossref.org/documentation/retrieve-metadata/rest-api/> integration, and advanced citation parsing.
Author: Massimo Aria [cre, aut, cph] ,
Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between contentanalysis versions 0.2.0 dated 2025-10-30 and 0.2.1 dated 2025-12-12
DESCRIPTION | 6 MD5 | 29 +- NEWS.md | 8 R/citation_analysis.R | 366 +++++++++++++++++++++++++++--- R/extract_metadata_from_pdf.R | 151 +++++++++--- R/pdf2txtAI.R | 10 R/pdf_import.R | 6 README.md | 312 ++++++++++--------------- inst/doc/introduction.html | 40 +-- inst/www |only man/extract_pdf_metadata.Rd | 4 man/figures/README-unnamed-chunk-10-1.png |binary man/gemini_content_ai.Rd | 6 man/pdf2txt_auto.Rd | 6 man/process_large_pdf.Rd | 4 tests/testthat/test-citation_matching.r | 32 +- 16 files changed, 661 insertions(+), 319 deletions(-)
More information about contentanalysis at CRAN
Permanent link
Title: Plotting for Bayesian Models
Description: Plotting functions for posterior analysis, MCMC diagnostics,
prior and posterior predictive checks, and other visualizations
to support the applied Bayesian workflow advocated in
Gabry, Simpson, Vehtari, Betancourt, and Gelman (2019) <doi:10.1111/rssa.12378>.
The package is designed not only to provide convenient functionality
for users, but also a common set of functions that can be easily used by
developers working on a variety of R packages for Bayesian modeling,
particularly (but not exclusively) packages interfacing with 'Stan'.
Author: Jonah Gabry [aut, cre],
Tristan Mahr [aut] ,
Paul-Christian Buerkner [ctb],
Martin Modrak [ctb],
Malcolm Barrett [ctb],
Frank Weber [ctb],
Eduardo Coronado Sroka [ctb],
Teemu Sailynoja [ctb],
Aki Vehtari [ctb],
Behram Ulukir [ctb],
Visruth Srimath Kan [...truncated...]
Maintainer: Jonah Gabry <jgabry@gmail.com>
Diff between bayesplot versions 1.14.0 dated 2025-08-31 and 1.15.0 dated 2025-12-12
bayesplot-1.14.0/bayesplot/man/figures/stanlogo.png |only bayesplot-1.15.0/bayesplot/DESCRIPTION | 23 - bayesplot-1.15.0/bayesplot/MD5 | 95 ++-- bayesplot-1.15.0/bayesplot/NEWS.md | 12 bayesplot-1.15.0/bayesplot/R/bayesplot-package.R | 9 bayesplot-1.15.0/bayesplot/R/helpers-ppc.R | 6 bayesplot-1.15.0/bayesplot/R/mcmc-scatterplots.R | 7 bayesplot-1.15.0/bayesplot/R/ppd-distributions.R | 2 bayesplot-1.15.0/bayesplot/R/zzz.R | 3 bayesplot-1.15.0/bayesplot/inst/doc/graphical-ppcs.R | 1 bayesplot-1.15.0/bayesplot/inst/doc/graphical-ppcs.Rmd | 1 bayesplot-1.15.0/bayesplot/inst/doc/graphical-ppcs.html | 30 - bayesplot-1.15.0/bayesplot/inst/doc/plotting-mcmc-draws.R | 1 bayesplot-1.15.0/bayesplot/inst/doc/plotting-mcmc-draws.Rmd | 1 bayesplot-1.15.0/bayesplot/inst/doc/plotting-mcmc-draws.html | 26 - bayesplot-1.15.0/bayesplot/inst/doc/visual-mcmc-diagnostics.html | 198 +++++----- bayesplot-1.15.0/bayesplot/man/MCMC-scatterplots.Rd | 3 bayesplot-1.15.0/bayesplot/man/bayesplot-package.Rd | 11 bayesplot-1.15.0/bayesplot/man/bayesplot_theme_get.Rd | 6 bayesplot-1.15.0/bayesplot/man/figures/logo.svg | 97 ---- bayesplot-1.15.0/bayesplot/tests/testthat/test-aesthetics.R | 36 + bayesplot-1.15.0/bayesplot/tests/testthat/test-available_ppc.R | 4 bayesplot-1.15.0/bayesplot/tests/testthat/test-bayesplot_grid.R | 3 bayesplot-1.15.0/bayesplot/tests/testthat/test-convenience-functions.R | 31 - bayesplot-1.15.0/bayesplot/tests/testthat/test-example-draws.R | 5 bayesplot-1.15.0/bayesplot/tests/testthat/test-extractors.R | 9 bayesplot-1.15.0/bayesplot/tests/testthat/test-helpers-mcmc.R | 17 bayesplot-1.15.0/bayesplot/tests/testthat/test-helpers-ppc.R | 3 bayesplot-1.15.0/bayesplot/tests/testthat/test-helpers-shared.R | 3 bayesplot-1.15.0/bayesplot/tests/testthat/test-mcmc-combo.R | 3 bayesplot-1.15.0/bayesplot/tests/testthat/test-mcmc-diagnostics.R | 3 bayesplot-1.15.0/bayesplot/tests/testthat/test-mcmc-distributions.R | 3 bayesplot-1.15.0/bayesplot/tests/testthat/test-mcmc-intervals.R | 12 bayesplot-1.15.0/bayesplot/tests/testthat/test-mcmc-nuts.R | 3 bayesplot-1.15.0/bayesplot/tests/testthat/test-mcmc-recover.R | 3 bayesplot-1.15.0/bayesplot/tests/testthat/test-mcmc-scatter-and-parcoord.R | 24 - bayesplot-1.15.0/bayesplot/tests/testthat/test-mcmc-traces.R | 3 bayesplot-1.15.0/bayesplot/tests/testthat/test-pp_check.R | 7 bayesplot-1.15.0/bayesplot/tests/testthat/test-ppc-censoring.R | 3 bayesplot-1.15.0/bayesplot/tests/testthat/test-ppc-discrete.R | 8 bayesplot-1.15.0/bayesplot/tests/testthat/test-ppc-distributions.R | 5 bayesplot-1.15.0/bayesplot/tests/testthat/test-ppc-errors.R | 3 bayesplot-1.15.0/bayesplot/tests/testthat/test-ppc-input-validation.R | 5 bayesplot-1.15.0/bayesplot/tests/testthat/test-ppc-intervals.R | 3 bayesplot-1.15.0/bayesplot/tests/testthat/test-ppc-loo.R | 7 bayesplot-1.15.0/bayesplot/tests/testthat/test-ppc-scatterplots.R | 3 bayesplot-1.15.0/bayesplot/tests/testthat/test-ppc-test-statistics.R | 3 bayesplot-1.15.0/bayesplot/vignettes/graphical-ppcs.Rmd | 1 bayesplot-1.15.0/bayesplot/vignettes/plotting-mcmc-draws.Rmd | 1 49 files changed, 312 insertions(+), 434 deletions(-)
Title: Pull Data from an 'ArcGIS REST' API
Description: Functions to efficiently query 'ArcGIS REST' APIs
<https://developers.arcgis.com/rest/>.
Both spatial and SQL queries can be used to retrieve data.
Simple Feature (sf) objects are utilized to perform spatial queries.
This package was neither produced nor is maintained by Esri.
Author: Paul Frater [aut, cre] ,
Zac Driscoll [aut]
Maintainer: Paul Frater <paul.frater@wisconsin.gov>
Diff between arcpullr versions 0.3.0 dated 2025-02-06 and 0.3.2 dated 2025-12-12
DESCRIPTION | 10 MD5 | 96 NAMESPACE | 99 R/arcpullr-package.R | 157 R/data.R | 270 - R/plot_layers.R | 808 +-- R/process_raster.R | 494 +- R/retrieve_layer_properties.R | 110 R/retrieve_layers.R | 1052 ++-- R/utilities.R | 1055 ++-- README.md | 96 build/vignette.rds |binary data/mke_county.rda |binary data/portage_county.rda |binary data/wis_counties.rda |binary data/wis_poly.rda |binary inst/doc/intro_to_arcpullr.R | 76 inst/doc/intro_to_arcpullr.Rmd | 287 - inst/doc/intro_to_arcpullr.html | 1194 ++--- inst/doc/raster_layers.R | 102 inst/doc/raster_layers.Rmd | 237 - inst/doc/raster_layers.html | 1136 +---- inst/doc/spatial_queries.R | 368 - inst/doc/spatial_queries.Rmd | 659 +- inst/doc/spatial_queries.html | 6352 +++++++++++++--------------- inst/wi_aerial_imagery.png.aux.xml | 74 inst/wi_landcover.png.aux.xml | 28 man/arcpullr-package.Rd | 151 man/get_image_layer.Rd | 136 man/get_layer_info.Rd | 50 man/get_layers_by_spatial.Rd | 122 man/get_map_layer.Rd | 144 man/get_raster_layer.Rd | 118 man/get_spatial_layer.Rd | 128 man/get_table_layer.Rd | 98 man/match_legend_colors.Rd | 82 man/plot_layer-SpatRaster-method.Rd | 80 man/raster_colors-SpatRaster-method.Rd | 52 man/sf_example_polys.Rd | 6 man/sp_rel_lookups.Rd | 100 man/sql_where.Rd | 62 tests/testthat.R | 8 tests/testthat/test_format_spatial_coords.R | 198 tests/testthat/test_layer_properties.R | 46 tests/testthat/test_process_terra_rasters.R | 122 tests/testthat/test_utilities.R | 186 vignettes/intro_to_arcpullr.Rmd | 287 - vignettes/raster_layers.Rmd | 237 - vignettes/spatial_queries.Rmd | 659 +- 49 files changed, 8546 insertions(+), 9286 deletions(-)
Title: Access and Analyse 'VALD' Data via Our External 'APIs'
Description: Provides helper functions and wrappers to simplify authentication,
data retrieval, and result processing from the 'VALD' 'APIs'.
Designed to streamline integration for analysts and researchers working
with 'VALD's external 'APIs'.
For further documentation on integrating with 'VALD' 'APIs', see:
<https://support.vald.com/hc/en-au/articles/23415335574553-How-to-integrate-with-VALD-APIs>.
For a step-by-step guide to using this package, see:
<https://support.vald.com/hc/en-au/articles/48730811824281-A-guide-to-using-the-valdr-R-package>.
Author: Kieran Harrison [aut, cre],
VALD Support [ctb],
VALD [cph]
Maintainer: Kieran Harrison <k.harrison@vald.com>
Diff between valdr versions 2.0.0 dated 2025-08-31 and 2.1.0 dated 2025-12-12
valdr-2.0.0/valdr/man/get_profiles.Rd |only valdr-2.1.0/valdr/DESCRIPTION | 10 valdr-2.1.0/valdr/MD5 | 68 - valdr-2.1.0/valdr/NAMESPACE | 3 valdr-2.1.0/valdr/R/config.R | 82 +- valdr-2.1.0/valdr/R/forcedecks_tests.R | 35 valdr-2.1.0/valdr/R/profiles.R | 391 +++++++++- valdr-2.1.0/valdr/R/session.R | 221 +++++ valdr-2.1.0/valdr/R/utils.R | 185 ++++ valdr-2.1.0/valdr/R/zzz.R | 3 valdr-2.1.0/valdr/man/dot-build_forceframe_df.Rd | 54 - valdr-2.1.0/valdr/man/dot-build_nordbord_df.Rd | 54 - valdr-2.1.0/valdr/man/dot-build_test_attributes_long.Rd |only valdr-2.1.0/valdr/man/dot-get_categories.Rd |only valdr-2.1.0/valdr/man/dot-get_groups.Rd |only valdr-2.1.0/valdr/man/dot-get_profile_group_ids.Rd |only valdr-2.1.0/valdr/man/dot-safe_extract.Rd | 44 - valdr-2.1.0/valdr/man/dot-safe_extract_first.Rd | 46 - valdr-2.1.0/valdr/man/dot-safe_value.Rd | 40 - valdr-2.1.0/valdr/man/dot-vald_default_endpoints.Rd |only valdr-2.1.0/valdr/man/dot-vald_default_export_dir.Rd |only valdr-2.1.0/valdr/man/dot-validate_single_guid.Rd | 44 - valdr-2.1.0/valdr/man/export_forcedecks_csv.Rd |only valdr-2.1.0/valdr/man/get_forcedecks_data.Rd | 18 valdr-2.1.0/valdr/man/get_forcedecks_tests.Rd | 17 valdr-2.1.0/valdr/man/get_forcedecks_tests_only.Rd | 23 valdr-2.1.0/valdr/man/get_forcedecks_tests_trials.Rd | 17 valdr-2.1.0/valdr/man/get_forceframe_data.Rd | 64 - valdr-2.1.0/valdr/man/get_forceframe_test_by_id.Rd | 50 - valdr-2.1.0/valdr/man/get_forceframe_tests.Rd | 46 - valdr-2.1.0/valdr/man/get_forceframe_tests_by_id.Rd | 38 valdr-2.1.0/valdr/man/get_forceframe_tests_only.Rd | 60 - valdr-2.1.0/valdr/man/get_nordbord_data.Rd | 64 - valdr-2.1.0/valdr/man/get_nordbord_test_by_id.Rd | 50 - valdr-2.1.0/valdr/man/get_nordbord_tests.Rd | 46 - valdr-2.1.0/valdr/man/get_nordbord_tests_by_id.Rd | 38 valdr-2.1.0/valdr/man/get_nordbord_tests_only.Rd | 60 - valdr-2.1.0/valdr/man/get_profiles_groups_categories.Rd |only valdr-2.1.0/valdr/man/get_profiles_groups_categories_mapping.Rd |only valdr-2.1.0/valdr/man/load_credentials.Rd | 6 40 files changed, 1356 insertions(+), 521 deletions(-)
Title: Biomarker Confirmation, Selection, Modelling, Prediction, and
Validation
Description: There are diverse purposes such as biomarker confirmation, novel biomarker discovery, constructing predictive models, model-based prediction, and validation.
It handles binary, continuous, and time-to-event outcomes at the sample or patient level.
- Biomarker confirmation utilizes established functions like glm() from 'stats', coxph() from 'survival', surv_fit(), and ggsurvplot() from 'survminer'.
- Biomarker discovery and variable selection are facilitated by three LASSO-related functions LASSO2(), LASSO_plus(), and LASSO2plus(), leveraging the 'glmnet' R package with additional steps.
- Eight versatile modeling functions are offered, each designed for predictive models across various outcomes and data types.
1) LASSO2(), LASSO_plus(), LASSO2plus(), and LASSO2_reg() perform variable selection using LASSO methods and construct predictive models based on selected variables.
2) XGBtraining() employs 'XGBoost' for model building and is the only function not involving variable selection.
3 [...truncated...]
Author: Aixiang Jiang [aut, cre, cph]
Maintainer: Aixiang Jiang <aijiang@bccrc.ca>
Diff between csmpv versions 1.0.3 dated 2024-03-01 and 1.0.5 dated 2025-12-11
DESCRIPTION | 20 LICENSE | 2 MD5 | 42 NAMESPACE | 4 R/XGBtraining.R | 253 - R/XGBtraining_predict.R | 135 R/XGpred.R | 419 +- R/XGpred_predict.R | 144 R/confirmVars.R | 10 R/coxTimeToEvent.R | 7 R/create_consistent_matrix.R |only R/create_model_matrix.R |only R/validation.R | 8 build/vignette.rds |binary inst/doc/csmpv_vignette.R | 997 ++--- inst/doc/csmpv_vignette.html | 7789 +++++++++++++++++++++---------------------- inst/doc/csmpv_vignette.rmd | 2321 ++++++------ man/XGBtraining_predict.Rd | 6 man/XGpred.Rd | 16 man/XGpred_predict.Rd | 2 man/confirmVars.Rd | 7 man/validation.Rd | 8 vignettes/csmpv_vignette.rmd | 2321 ++++++------ 23 files changed, 7352 insertions(+), 7159 deletions(-)
Title: Double Machine Learning for Static Panel Models with Fixed
Effects
Description: The 'xtdml' package implements partially linear panel regression (PLPR) models with high-dimensional confounding variables and an exogenous treatment variable within the double machine learning framework. The package is used to estimate the structural parameter (treatment effect) in static panel data models with fixed effects using the approaches established in Clarke and Polselli (2025) <doi:10.1093/ectj/utaf011>. 'xtdml' is built on the object-oriented package 'DoubleML' (Bach et al., 2024) <doi:10.18637/jss.v108.i03> using the 'mlr3' ecosystem.
Author: Annalivia Polselli [aut, cre]
Maintainer: Annalivia Polselli <apolselli.econ@gmail.com>
Diff between xtdml versions 0.1.10 dated 2025-12-10 and 0.1.11 dated 2025-12-11
DESCRIPTION | 12 MD5 | 10 R/helper.R | 888 +++++++++++++++++++++++++++---------------------------- R/xtdml_plr.R | 2 R/zzz.R | 39 +- man/xtdml_plr.Rd | 2 6 files changed, 476 insertions(+), 477 deletions(-)
Title: Transcription Elongation Profiling
Description: The general principle relies on calculating the cumulative signal of nascent
RNA sequencing over the gene body of any given gene or transcription unit.
'tepr' can identify transcription attenuation sites by comparing profile to
a null model which assumes uniform read density over the entirety of the
transcription unit. It can also identify increased or diminished
transcription attenuation by comparing two conditions. Besides rigorous
statistical testing and high sensitivity, a major feature of 'tepr' is its
ability to provide the elongation pattern of each individual gene, including
the position of the main attenuation point when such a phenomenon occurs.
Using 'tepr', users can visualize and refine genome-wide aggregated analyses
of elongation patterns to robustly identify effects specific to subsets of
genes. These metrics are suitable for internal comparisons (between genes in
each condition) and for studying elongation of the same gene in different
conditions or comparing it to a p [...truncated...]
Author: Nicolas Descostes [cre],
Victor Billon [aut],
Gael Cristofari [aut]
Maintainer: Nicolas Descostes <nicolas.descostes@gmail.com>
Diff between tepr versions 1.1.12 dated 2025-11-04 and 1.1.13 dated 2025-12-11
DESCRIPTION | 6 MD5 | 102 +- NEWS | 13 R/allauc.R | 16 R/attenuation.R | 10 R/averageandfilterexprs.R | 12 R/countna.R | 7 R/genesECDF.R | 19 R/kneeid.R | 8 R/meandifference.R | 26 R/plotauc.R | 16 R/plotecdf.R | 21 R/plothistoknee.R | 7 R/plotmetagenes.R | 21 R/plotmulti.R | 56 - R/preprocessing-blacklisthighmap-utils.R | 27 R/preprocessing-blacklisthighmap.R | 28 R/preprocessing-createtablescores.R | 10 R/preprocessing-makewindows.R | 7 R/preprocessing.R | 18 R/tepr.R | 101 +- R/universegroup.R | 2 R/utils.R | 67 - build/vignette.rds |binary inst/doc/tepr.R | 2 inst/doc/tepr.Rmd | 28 inst/doc/tepr.html | 652 +++++++++--------- man/allauc.Rd | 2 man/attenuation.Rd | 2 man/genesECDF.Rd | 7 man/kneeid.Rd | 2 man/meandifference.Rd | 2 man/plotauc.Rd | 2 man/plotecdf.Rd | 2 man/plothistoknee.Rd | 2 man/plotmetagenes.Rd | 2 man/teprmulti.Rd | 14 man/universegroup.Rd | 2 tests/testthat/test-allauc.R | 6 tests/testthat/test-attenuation.R | 8 tests/testthat/test-averageandfilterexprs.R | 16 tests/testthat/test-checkexptab.R | 12 tests/testthat/test-countna.R | 9 tests/testthat/test-genesECDF.R | 9 tests/testthat/test-kneeid.R | 2 tests/testthat/test-meandifference.R | 10 tests/testthat/test-preprocessing-blacklisthighmap.R | 15 tests/testthat/test-preprocessing-createtablescores.R | 7 tests/testthat/test-preprocessing.R | 11 tests/testthat/test-tepr.R | 11 tests/testthat/test-universegroup.R | 2 vignettes/tepr.Rmd | 28 52 files changed, 778 insertions(+), 689 deletions(-)
Title: Geographic Tools for Studying Gerrymandering
Description: A compilation of tools to complete common tasks for studying gerrymandering.
This focuses on the geographic tool side of common problems, such as linking
different levels of spatial units or estimating how to break up units. Functions
exist for creating redistricting-focused data for the US.
Author: Christopher T. Kenny [aut, cre] ,
Cory McCartan [ctb]
Maintainer: Christopher T. Kenny <ctkenny@proton.me>
This is a re-admission after prior archival of version 2.5.0 dated 2025-09-01
Diff between geomander versions 2.5.0 dated 2025-09-01 and 2.5.2 dated 2025-12-11
DESCRIPTION | 8 MD5 | 32 NEWS.md | 9 R/RcppExports.R | 12 R/alarm.R | 2 R/datatables.R | 4 R/lewis.R | 1898 +++++++++++++-------------- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 6 inst/doc/Merging_Election_Data.html | 2 inst/doc/Redistricting_School_Districts.html | 22 man/block2prec.Rd | 2 man/get_heda.Rd | 2 man/get_lewis.Rd | 9 src/RcppExports.cpp | 39 src/contiguity.cpp | 137 + 17 files changed, 1161 insertions(+), 1023 deletions(-)
Title: Building and Managing Local Databases from 'Google Earth Engine'
Description: Simplifies the creation, management, and updating of local databases using data extracted from 'Google Earth Engine' ('GEE'). It integrates with 'GEE' to store, aggregate, and process spatio-temporal data, leveraging 'SQLite' for efficient, serverless storage. The 'geeLite' package provides utilities for data transformation and supports real-time monitoring and analysis of geospatial features, making it suitable for researchers and practitioners in geospatial science. For details, see Kurbucz and Andrée (2025) "Building and Managing Local Databases from Google Earth Engine with the geeLite R Package" <https://hdl.handle.net/10986/43165>.
Author: Marcell T. Kurbucz [aut, cre],
Bo Pieter Johannes Andree [aut]
Maintainer: Marcell T. Kurbucz <m.kurbucz@ucl.ac.uk>
Diff between geeLite versions 1.0.5 dated 2025-12-09 and 1.0.6 dated 2025-12-11
DESCRIPTION | 6 - MD5 | 22 ++-- NAMESPACE | 2 R/access_db.R | 241 +++++++++++++++++++++++++++++++++++++------------ R/run_geelite.R | 4 R/utils.R | 17 ++- man/aggr_by_freq.Rd | 29 +++++ man/fetch_vars.Rd | 3 man/init_postp.Rd | 13 +- man/read_db.Rd | 44 +++++--- man/read_variables.Rd | 35 ++++++- man/validate_params.Rd | 2 12 files changed, 301 insertions(+), 117 deletions(-)
Title: Double/Debiased Machine Learning
Description: Estimate common causal parameters using double/debiased machine
learning as proposed by Chernozhukov et al. (2018) <doi:10.1111/ectj.12097>.
'ddml' simplifies estimation based on (short-)stacking as discussed in
Ahrens et al. (2024) <doi:10.1002/jae.3103>, which leverages multiple base
learners to increase robustness to the underlying data generating process.
Author: Achim Ahrens [aut],
Christian B Hansen [aut],
Mark E Schaffer [aut],
Thomas Wiemann [aut, cre]
Maintainer: Thomas Wiemann <thomas.wiemann@chicagobooth.edu>
Diff between ddml versions 0.3.0 dated 2024-10-02 and 0.3.1 dated 2025-12-11
ddml-0.3.0/ddml/man/ddml.Rd |only ddml-0.3.1/ddml/DESCRIPTION | 18 ddml-0.3.1/ddml/MD5 | 119 - ddml-0.3.1/ddml/NAMESPACE | 62 ddml-0.3.1/ddml/NEWS.md | 65 ddml-0.3.1/ddml/R/AE98.R | 60 ddml-0.3.1/ddml/R/crosspred.R | 594 ++++---- ddml-0.3.1/ddml/R/crossval.R | 276 +-- ddml-0.3.1/ddml/R/ddml.R | 31 ddml-0.3.1/ddml/R/ddml_ate.R | 613 ++++---- ddml-0.3.1/ddml/R/ddml_att.R | 290 +-- ddml-0.3.1/ddml/R/ddml_fpliv.R | 702 ++++----- ddml-0.3.1/ddml/R/ddml_late.R | 704 ++++----- ddml-0.3.1/ddml/R/ddml_pliv.R | 574 +++---- ddml-0.3.1/ddml/R/ddml_plm.R | 730 +++++----- ddml-0.3.1/ddml/R/ensemble.R | 355 ++-- ddml-0.3.1/ddml/R/get_CEF.R | 150 +- ddml-0.3.1/ddml/R/help_functions.R | 100 - ddml-0.3.1/ddml/R/inference_functions.R | 206 +- ddml-0.3.1/ddml/R/ml_wrappers.R | 436 ++--- ddml-0.3.1/ddml/R/ols.R | 130 - ddml-0.3.1/ddml/R/shortstacking.R | 336 ++-- ddml-0.3.1/ddml/R/subsample_functions.R | 416 ++--- ddml-0.3.1/ddml/README.md | 310 ++-- ddml-0.3.1/ddml/build/partial.rdb |only ddml-0.3.1/ddml/build/vignette.rds |binary ddml-0.3.1/ddml/inst/doc/ddml.Rmd | 318 ++-- ddml-0.3.1/ddml/inst/doc/ddml.html | 1020 ++++++-------- ddml-0.3.1/ddml/man/AE98.Rd | 82 - ddml-0.3.1/ddml/man/crosspred.Rd | 334 ++-- ddml-0.3.1/ddml/man/crossval.Rd | 178 +- ddml-0.3.1/ddml/man/ddml-package.Rd |only ddml-0.3.1/ddml/man/ddml_ate.Rd | 455 +++--- ddml-0.3.1/ddml/man/ddml_fpliv.Rd | 372 ++--- ddml-0.3.1/ddml/man/ddml_late.Rd | 444 +++--- ddml-0.3.1/ddml/man/ddml_pliv.Rd | 370 ++--- ddml-0.3.1/ddml/man/ddml_plm.Rd | 370 ++--- ddml-0.3.1/ddml/man/mdl_glmnet.Rd | 100 - ddml-0.3.1/ddml/man/mdl_ranger.Rd | 2 ddml-0.3.1/ddml/man/mdl_xgboost.Rd | 103 - ddml-0.3.1/ddml/man/ols.Rd | 86 - ddml-0.3.1/ddml/man/print.summary.ddml_ate.Rd | 88 - ddml-0.3.1/ddml/man/print.summary.ddml_plm.Rd | 88 - ddml-0.3.1/ddml/man/shortstacking.Rd | 316 ++-- ddml-0.3.1/ddml/man/summary.ddml_ate.Rd | 88 - ddml-0.3.1/ddml/man/summary.ddml_plm.Rd | 122 - ddml-0.3.1/ddml/tests/testthat.R | 8 ddml-0.3.1/ddml/tests/testthat/test-crosspred.R | 262 +-- ddml-0.3.1/ddml/tests/testthat/test-crossval.R | 168 +- ddml-0.3.1/ddml/tests/testthat/test-ddml_ate.R | 390 ++--- ddml-0.3.1/ddml/tests/testthat/test-ddml_att.R | 396 ++--- ddml-0.3.1/ddml/tests/testthat/test-ddml_fpliv.R | 754 +++++----- ddml-0.3.1/ddml/tests/testthat/test-ddml_late.R | 476 +++--- ddml-0.3.1/ddml/tests/testthat/test-ddml_pliv.R | 492 +++--- ddml-0.3.1/ddml/tests/testthat/test-ddml_plm.R | 590 ++++---- ddml-0.3.1/ddml/tests/testthat/test-ensemble.R | 241 +-- ddml-0.3.1/ddml/tests/testthat/test-help_functions.R | 18 ddml-0.3.1/ddml/tests/testthat/test-ml_wrappers.R | 151 +- ddml-0.3.1/ddml/tests/testthat/test-ols.R | 58 ddml-0.3.1/ddml/tests/testthat/test-shortstacking.R | 48 ddml-0.3.1/ddml/tests/testthat/test-subsample_functions.R | 216 +- ddml-0.3.1/ddml/vignettes/ddml.Rmd | 318 ++-- 62 files changed, 8423 insertions(+), 8376 deletions(-)
Title: "Nested Partially Latent Class Models"
Description: Provides functions to specify, fit and visualize
nested partially-latent class models (
Wu, Deloria-Knoll, Hammitt, and Zeger (2016) <doi:10.1111/rssc.12101>;
Wu, Deloria-Knoll, and Zeger (2017) <doi:10.1093/biostatistics/kxw037>;
Wu and Chen (2021) <doi:10.1002/sim.8804>) for
inference of population disease etiology and individual diagnosis. In the motivating
Pneumonia Etiology Research for Child Health (PERCH) study, because both quantities
of interest sum to one hundred percent, the PERCH scientists frequently refer to
them as population etiology pie and individual etiology pie, hence the name of the package.
Author: Zhenke Wu [cre, aut, cph] ,
Scott Zeger [aut] ,
John Muschelli [ctb] ,
Irena Chen [ctb]
Maintainer: Zhenke Wu <zhenkewu@gmail.com>
This is a re-admission after prior archival of version 1.0.3 dated 2024-01-30
Diff between baker versions 1.0.3 dated 2024-01-30 and 1.0.4 dated 2025-12-11
baker-1.0.3/baker/man/baker.Rd |only baker-1.0.4/baker/DESCRIPTION | 19 - baker-1.0.4/baker/LICENSE | 2 baker-1.0.4/baker/MD5 | 102 ++++---- baker-1.0.4/baker/NEWS.md | 2 baker-1.0.4/baker/R/baker.R | 5 baker-1.0.4/baker/R/nplcm-read-folder.R | 22 + baker-1.0.4/baker/R/nplcm.R | 34 ++ baker-1.0.4/baker/R/plot-model-check.R | 32 +- baker-1.0.4/baker/R/utils.R | 13 - baker-1.0.4/baker/README.md | 89 ++++--- baker-1.0.4/baker/build/vignette.rds |binary baker-1.0.4/baker/inst/CITATION | 4 baker-1.0.4/baker/inst/WORDLIST | 116 ++++----- baker-1.0.4/baker/inst/doc/baker_demo.R | 120 +++++----- baker-1.0.4/baker/inst/doc/baker_demo.html | 9 baker-1.0.4/baker/man/add_meas_BrS_case_Nest_Slice.Rd | 12 - baker-1.0.4/baker/man/add_meas_BrS_case_Nest_Slice_jags.Rd | 12 - baker-1.0.4/baker/man/add_meas_BrS_case_NoNest_Slice.Rd | 12 - baker-1.0.4/baker/man/add_meas_BrS_case_NoNest_Slice_jags.Rd | 12 - baker-1.0.4/baker/man/add_meas_BrS_case_NoNest_reg_Slice_jags.Rd | 16 - baker-1.0.4/baker/man/add_meas_BrS_case_NoNest_reg_discrete_predictor_Slice_jags.Rd | 16 - baker-1.0.4/baker/man/add_meas_BrS_ctrl_Nest_Slice.Rd | 16 - baker-1.0.4/baker/man/add_meas_BrS_ctrl_NoNest_Slice.Rd | 16 - baker-1.0.4/baker/man/add_meas_BrS_ctrl_NoNest_reg_Slice_jags.Rd | 16 - baker-1.0.4/baker/man/add_meas_BrS_ctrl_NoNest_reg_discrete_predictor_Slice_jags.Rd | 16 - baker-1.0.4/baker/man/add_meas_BrS_param_Nest_Slice.Rd | 12 - baker-1.0.4/baker/man/add_meas_BrS_param_Nest_Slice_jags.Rd | 12 - baker-1.0.4/baker/man/add_meas_BrS_param_Nest_reg_Slice_jags.Rd | 16 - baker-1.0.4/baker/man/add_meas_BrS_param_NoNest_Slice.Rd | 12 - baker-1.0.4/baker/man/add_meas_BrS_param_NoNest_Slice_jags.Rd | 12 - baker-1.0.4/baker/man/add_meas_BrS_param_NoNest_reg_Slice_jags.Rd | 16 - baker-1.0.4/baker/man/add_meas_BrS_param_NoNest_reg_discrete_predictor_Slice_jags.Rd | 16 - baker-1.0.4/baker/man/add_meas_BrS_subclass_Nest_Slice.Rd | 16 - baker-1.0.4/baker/man/add_meas_SS_case.Rd | 16 - baker-1.0.4/baker/man/add_meas_SS_param.Rd | 16 - baker-1.0.4/baker/man/baker-package.Rd |only baker-1.0.4/baker/man/beta_parms_from_quantiles.Rd | 3 baker-1.0.4/baker/man/check_dir_create.Rd | 10 baker-1.0.4/baker/man/get_individual_prediction.Rd | 11 baker-1.0.4/baker/man/jags2_baker.Rd | 2 baker-1.0.4/baker/man/make_list.Rd | 2 baker-1.0.4/baker/man/nplcm.Rd | 15 - baker-1.0.4/baker/man/nplcm_read_folder.Rd | 11 baker-1.0.4/baker/man/plot_check_common_pattern.Rd | 10 baker-1.0.4/baker/man/plot_check_pairwise_SLORD.Rd | 12 - baker-1.0.4/baker/man/print.nplcm.Rd | 4 baker-1.0.4/baker/man/print.summary.nplcm.no_reg.Rd | 4 baker-1.0.4/baker/man/print.summary.nplcm.reg_nest.Rd | 2 baker-1.0.4/baker/man/print.summary.nplcm.reg_nest_strat.Rd | 2 baker-1.0.4/baker/man/print.summary.nplcm.reg_nonest.Rd | 2 baker-1.0.4/baker/man/print.summary.nplcm.reg_nonest_strat.Rd | 2 baker-1.0.4/baker/man/summary.nplcm.Rd | 6 53 files changed, 523 insertions(+), 432 deletions(-)
Title: Estimating Infection Rates from Serological Data
Description: Translates antibody levels measured in cross-sectional
population samples into estimates of the frequency with which
seroconversions (infections) occur in the sampled populations.
Replaces the previous `seroincidence` package.
Author: Kristina Lai [aut, cre],
Chris Orwa [aut],
Kwan Ho Lee [ctb],
Peter Teunis [aut, cph] ,
Kristen Aiemjoy [aut],
Douglas Ezra Morrison [aut]
Maintainer: Kristina Lai <kwlai@ucdavis.edu>
Diff between serocalculator versions 1.3.0 dated 2025-01-25 and 1.4.0 dated 2025-12-11
serocalculator-1.3.0/serocalculator/R/as_curve_params.R |only serocalculator-1.3.0/serocalculator/R/est.incidence.R |only serocalculator-1.3.0/serocalculator/R/est.incidence.by.R |only serocalculator-1.3.0/serocalculator/R/graph.decay.curves.R |only serocalculator-1.3.0/serocalculator/R/load_curve_params.R |only serocalculator-1.3.0/serocalculator/R/rho-funcs.R |only serocalculator-1.3.0/serocalculator/R/sim.cs.R |only serocalculator-1.3.0/serocalculator/R/sim.cs.multi.R |only serocalculator-1.3.0/serocalculator/R/strata.seroincidence.ests.R |only serocalculator-1.3.0/serocalculator/R/tau-funcs.R |only serocalculator-1.3.0/serocalculator/man/mkbaseline.Rd |only serocalculator-1.3.0/serocalculator/man/row_longitudinal_parameter.Rd |only serocalculator-1.3.0/serocalculator/man/serocalculator.Rd |only serocalculator-1.3.0/serocalculator/man/strata.seroincidence.by.Rd |only serocalculator-1.3.0/serocalculator/man/warn.missing.strata.Rd |only serocalculator-1.3.0/serocalculator/tests/testthat/_snaps/as_curve_params |only serocalculator-1.3.0/serocalculator/tests/testthat/_snaps/as_curve_params.md |only serocalculator-1.3.0/serocalculator/tests/testthat/_snaps/class_attributes.md |only serocalculator-1.3.0/serocalculator/tests/testthat/_snaps/est.incidence.by.md |only serocalculator-1.3.0/serocalculator/tests/testthat/_snaps/est.incidence.md |only serocalculator-1.3.0/serocalculator/tests/testthat/test-as_curve_params.R |only serocalculator-1.3.0/serocalculator/tests/testthat/test-est.incidence.R |only serocalculator-1.3.0/serocalculator/tests/testthat/test-est.incidence.by.R |only serocalculator-1.4.0/serocalculator/DESCRIPTION | 39 serocalculator-1.4.0/serocalculator/MD5 | 338 ++-- serocalculator-1.4.0/serocalculator/NAMESPACE | 32 serocalculator-1.4.0/serocalculator/NEWS.md | 91 + serocalculator-1.4.0/serocalculator/R/ab.R | 46 serocalculator-1.4.0/serocalculator/R/ab1.R |only serocalculator-1.4.0/serocalculator/R/age_scatter.R |only serocalculator-1.4.0/serocalculator/R/analyze_sims.R |only serocalculator-1.4.0/serocalculator/R/as_pop_data.R | 16 serocalculator-1.4.0/serocalculator/R/as_sr_params.R |only serocalculator-1.4.0/serocalculator/R/autoplot.curve_params.R | 70 serocalculator-1.4.0/serocalculator/R/autoplot.pop_data.R | 133 - serocalculator-1.4.0/serocalculator/R/autoplot.seroincidence.R | 19 serocalculator-1.4.0/serocalculator/R/autoplot.seroincidence.by.R | 17 serocalculator-1.4.0/serocalculator/R/autoplot.sim_results.R |only serocalculator-1.4.0/serocalculator/R/autoplot.summary.seroincidence.by.R | 82 - serocalculator-1.4.0/serocalculator/R/baseline.R |only serocalculator-1.4.0/serocalculator/R/check_parallel_cores.R | 17 serocalculator-1.4.0/serocalculator/R/check_pop_data.R | 16 serocalculator-1.4.0/serocalculator/R/check_strata.R | 45 serocalculator-1.4.0/serocalculator/R/class_attributes.R | 131 - serocalculator-1.4.0/serocalculator/R/count_strata.R | 48 serocalculator-1.4.0/serocalculator/R/density_plot.R |only serocalculator-1.4.0/serocalculator/R/df_to_array.R | 4 serocalculator-1.4.0/serocalculator/R/est_seroincidence.R |only serocalculator-1.4.0/serocalculator/R/est_seroincidence_by.R |only serocalculator-1.4.0/serocalculator/R/example_noise_params_pk.R | 31 serocalculator-1.4.0/serocalculator/R/example_typhoid_curves_nostrat.R | 2 serocalculator-1.4.0/serocalculator/R/expect_snapshot_data.R |only serocalculator-1.4.0/serocalculator/R/f_dev.r | 109 - serocalculator-1.4.0/serocalculator/R/get_biomarker_names.R |only serocalculator-1.4.0/serocalculator/R/get_biomarker_names_var.R |only serocalculator-1.4.0/serocalculator/R/get_ids.R |only serocalculator-1.4.0/serocalculator/R/graph.curve.params.R | 320 ++-- serocalculator-1.4.0/serocalculator/R/graph_seroresponse_model_1.R |only serocalculator-1.4.0/serocalculator/R/ldpar.R |only serocalculator-1.4.0/serocalculator/R/load_sr_params.R |only serocalculator-1.4.0/serocalculator/R/nlm_exit_codes.R | 17 serocalculator-1.4.0/serocalculator/R/plot_curve_params_one_ab.R |only serocalculator-1.4.0/serocalculator/R/print.seroincidence.R | 44 serocalculator-1.4.0/serocalculator/R/print.seroincidence.by.R | 57 serocalculator-1.4.0/serocalculator/R/print.summary.seroincidence.by.R | 53 serocalculator-1.4.0/serocalculator/R/sees_pop_data_pakistan_100.R | 24 serocalculator-1.4.0/serocalculator/R/sees_typhoid_ests_strat.R |only serocalculator-1.4.0/serocalculator/R/serocalculator-package.R | 135 - serocalculator-1.4.0/serocalculator/R/set_id.R |only serocalculator-1.4.0/serocalculator/R/sim.cs-utils.r | 100 - serocalculator-1.4.0/serocalculator/R/sim_pop_data.R |only serocalculator-1.4.0/serocalculator/R/sim_pop_data_multi.R |only serocalculator-1.4.0/serocalculator/R/simcs.tinf.R | 93 - serocalculator-1.4.0/serocalculator/R/simpar.R | 5 serocalculator-1.4.0/serocalculator/R/simresp.tinf.R | 192 +- serocalculator-1.4.0/serocalculator/R/strat_ests_barplot.R |only serocalculator-1.4.0/serocalculator/R/strat_ests_scatterplot.R |only serocalculator-1.4.0/serocalculator/R/strata.R |only serocalculator-1.4.0/serocalculator/R/stratify_data.R | 139 - serocalculator-1.4.0/serocalculator/R/subset.seroincidence.ests.R | 1 serocalculator-1.4.0/serocalculator/R/summary.pop_data.R | 36 serocalculator-1.4.0/serocalculator/R/summary.seroincidence.R | 84 - serocalculator-1.4.0/serocalculator/R/summary.seroincidence.by.R | 79 - serocalculator-1.4.0/serocalculator/R/utils.R | 42 serocalculator-1.4.0/serocalculator/R/warn_missing_strata.R | 83 - serocalculator-1.4.0/serocalculator/README.md | 139 - serocalculator-1.4.0/serocalculator/data/example_noise_params_pk.rda |binary serocalculator-1.4.0/serocalculator/data/example_noise_params_sees.rda |only serocalculator-1.4.0/serocalculator/data/sees_pop_data_100.rda |only serocalculator-1.4.0/serocalculator/data/sees_pop_data_pk_100.rda |binary serocalculator-1.4.0/serocalculator/data/sees_pop_data_pk_100_old_names.rda |binary serocalculator-1.4.0/serocalculator/data/sees_typhoid_ests_strat.rda |only serocalculator-1.4.0/serocalculator/inst/WORDLIST | 87 - serocalculator-1.4.0/serocalculator/inst/examples |only serocalculator-1.4.0/serocalculator/man/ab.Rd | 45 serocalculator-1.4.0/serocalculator/man/analyze_sims.Rd |only serocalculator-1.4.0/serocalculator/man/as_curve_params.Rd | 27 serocalculator-1.4.0/serocalculator/man/as_pop_data.Rd | 4 serocalculator-1.4.0/serocalculator/man/as_sr_params.Rd |only serocalculator-1.4.0/serocalculator/man/autoplot.curve_params.Rd | 63 serocalculator-1.4.0/serocalculator/man/autoplot.pop_data.Rd | 8 serocalculator-1.4.0/serocalculator/man/autoplot.seroincidence.Rd | 9 serocalculator-1.4.0/serocalculator/man/autoplot.seroincidence.by.Rd | 13 serocalculator-1.4.0/serocalculator/man/autoplot.sim_results.Rd |only serocalculator-1.4.0/serocalculator/man/autoplot.summary.seroincidence.by.Rd | 67 serocalculator-1.4.0/serocalculator/man/baseline.Rd |only serocalculator-1.4.0/serocalculator/man/check_pop_data.Rd | 4 serocalculator-1.4.0/serocalculator/man/count_strata.Rd |only serocalculator-1.4.0/serocalculator/man/df_to_array.Rd |only serocalculator-1.4.0/serocalculator/man/est.incidence.Rd | 119 - serocalculator-1.4.0/serocalculator/man/est.incidence.by.Rd | 155 - serocalculator-1.4.0/serocalculator/man/est_seroincidence.Rd |only serocalculator-1.4.0/serocalculator/man/est_seroincidence_by.Rd |only serocalculator-1.4.0/serocalculator/man/example_noise_params_pk.Rd | 4 serocalculator-1.4.0/serocalculator/man/example_noise_params_sees.Rd |only serocalculator-1.4.0/serocalculator/man/expect_snapshot_data.Rd |only serocalculator-1.4.0/serocalculator/man/f_dev.Rd | 13 serocalculator-1.4.0/serocalculator/man/f_dev0.Rd | 12 serocalculator-1.4.0/serocalculator/man/get_biomarker_levels.Rd |only serocalculator-1.4.0/serocalculator/man/get_biomarker_names.Rd |only serocalculator-1.4.0/serocalculator/man/get_biomarker_names_var.Rd |only serocalculator-1.4.0/serocalculator/man/get_values.Rd |only serocalculator-1.4.0/serocalculator/man/get_values_var.Rd |only serocalculator-1.4.0/serocalculator/man/graph.curve.params.Rd | 91 + serocalculator-1.4.0/serocalculator/man/graph_seroresponse_model_1.Rd |only serocalculator-1.4.0/serocalculator/man/ids.Rd |only serocalculator-1.4.0/serocalculator/man/ids_varname.Rd |only serocalculator-1.4.0/serocalculator/man/ldpar.Rd | 9 serocalculator-1.4.0/serocalculator/man/load_curve_params.Rd | 22 serocalculator-1.4.0/serocalculator/man/load_sr_params.Rd |only serocalculator-1.4.0/serocalculator/man/log_likelihood.Rd | 3 serocalculator-1.4.0/serocalculator/man/mk_baseline.Rd | 5 serocalculator-1.4.0/serocalculator/man/plot_curve_params_one_ab.Rd | 27 serocalculator-1.4.0/serocalculator/man/print.seroincidence.Rd | 32 serocalculator-1.4.0/serocalculator/man/print.seroincidence.by.Rd | 36 serocalculator-1.4.0/serocalculator/man/print.summary.seroincidence.by.Rd | 39 serocalculator-1.4.0/serocalculator/man/sees_pop_data_100.Rd |only serocalculator-1.4.0/serocalculator/man/sees_pop_data_pk_100.Rd | 3 serocalculator-1.4.0/serocalculator/man/sees_pop_data_pk_100_old_names.Rd | 5 serocalculator-1.4.0/serocalculator/man/sees_typhoid_ests_strat.Rd |only serocalculator-1.4.0/serocalculator/man/serocalculator-package.Rd |only serocalculator-1.4.0/serocalculator/man/set_id_var.Rd |only serocalculator-1.4.0/serocalculator/man/sim.cs.Rd | 123 - serocalculator-1.4.0/serocalculator/man/sim.cs.multi.Rd | 76 serocalculator-1.4.0/serocalculator/man/sim_pop_data.Rd |only serocalculator-1.4.0/serocalculator/man/sim_pop_data_multi.Rd |only serocalculator-1.4.0/serocalculator/man/simcs.tinf.Rd | 53 serocalculator-1.4.0/serocalculator/man/simresp.tinf.Rd | 43 serocalculator-1.4.0/serocalculator/man/strat_ests_barplot.Rd |only serocalculator-1.4.0/serocalculator/man/strat_ests_scatterplot.Rd |only serocalculator-1.4.0/serocalculator/man/strata.Rd | 9 serocalculator-1.4.0/serocalculator/man/strata.default.Rd |only serocalculator-1.4.0/serocalculator/man/stratify_data.Rd | 48 serocalculator-1.4.0/serocalculator/man/sub-.seroincidence.by.Rd | 1 serocalculator-1.4.0/serocalculator/man/summary.pop_data.Rd | 7 serocalculator-1.4.0/serocalculator/man/summary.seroincidence.Rd | 40 serocalculator-1.4.0/serocalculator/man/summary.seroincidence.by.Rd | 52 serocalculator-1.4.0/serocalculator/man/typhoid_curves_nostrat_100.Rd | 2 serocalculator-1.4.0/serocalculator/man/warn_missing_strata.Rd |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/ab |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/ab1.md |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/analyze_sims |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/as_noise_params.md | 60 serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/as_pop_data.md |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/as_sr_params |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/as_sr_params.md |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/autoplot.curve_params |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/autoplot.pop_data/age-scatter-no-strat.svg | 536 +++--- serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/autoplot.pop_data/age-scatter-strat-country.svg | 561 +++---- serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/autoplot.pop_data/density-log.svg |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/autoplot.pop_data/density.svg | 4 serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/autoplot.seroincidence.by |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/autoplot.sim_results |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/autoplot.summary.seroincidence.by |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/autoplot.summary.seroincidence.by.md |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/est_seroincidence.md |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/est_seroincidence_by.md |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/f_dev.md | 34 serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/get_biomarker_names.md |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/get_ids.md |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/graph.curve.params |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/print.seroincidence.by.md |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/print.seroincidence.md |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/print.summary.seroincidence.by.md |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/set_id.md |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/sim_pop_data |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/sim_pop_data_multi |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/strata |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/stratify_data.md | 785 ++++++++-- serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/summary.pop_data.md | 102 - serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/summary.seroincidence.by.md |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/warn_missing_strata.md |only serocalculator-1.4.0/serocalculator/tests/testthat/fixtures |only serocalculator-1.4.0/serocalculator/tests/testthat/helper-noise_ymax.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-ab.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-ab0.R | 6 serocalculator-1.4.0/serocalculator/tests/testthat/test-ab1.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-analyze_sims.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-as_pop_data.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-as_sr_params.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-autoplot.curve_params.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-autoplot.pop_data.R | 22 serocalculator-1.4.0/serocalculator/tests/testthat/test-autoplot.seroincidence.by.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-autoplot.sim_results.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-autoplot.summary.seroincidence.by.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-check_parallel_cores.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-check_strata.R | 27 serocalculator-1.4.0/serocalculator/tests/testthat/test-class_attributes.R | 24 serocalculator-1.4.0/serocalculator/tests/testthat/test-count_strata.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-df_to_array.R | 12 serocalculator-1.4.0/serocalculator/tests/testthat/test-est_seroincidence.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-est_seroincidence_by.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-f_dev.R | 126 + serocalculator-1.4.0/serocalculator/tests/testthat/test-get_biomarker_names.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-get_biomarker_names_var.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-get_ids.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-graph.curve.params.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-load_sr_params.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-plot_curve_params_one_ab.R | 3 serocalculator-1.4.0/serocalculator/tests/testthat/test-print.seroincidence.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-print.seroincidence.by.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-print.summary.seroincidence.by.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-serocalculator_example.R | 4 serocalculator-1.4.0/serocalculator/tests/testthat/test-set_id.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-sim_pop_data.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-sim_pop_data_multi.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-strata.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-stratify_data.R | 112 - serocalculator-1.4.0/serocalculator/tests/testthat/test-summary.seroincidence.by.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-warn_missing_strata.R | 33 230 files changed, 3727 insertions(+), 3009 deletions(-)
More information about serocalculator at CRAN
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Title: Predictors of Resilience to a Stressor in a Single-Arm Study
Description: Studies of resilience in older adults employ a single-arm design where everyone experiences the stressor. The simplistic approach of regressing change versus baseline yields biased estimates due to regression-to-the-mean. This package provides a method to correct the bias. It also allows covariates to be included. The method implemented in the package is described in Varadhan, R., Zhu, J., and Bandeen-Roche, K (2024), Biostatistics 25(4): 1094-1111.
Author: Ravi Varadhan [aut, cre],
Jiafeng Zhu [ctb]
Maintainer: Ravi Varadhan <ravi.varadhan@jhu.edu>
Diff between resilience versions 2024.1.2 dated 2024-08-22 and 2025.1.0 dated 2025-12-11
resilience-2024.1.2/resilience/data/tkr.RData |only resilience-2024.1.2/resilience/man/resilience-package.Rd |only resilience-2025.1.0/resilience/DESCRIPTION | 16 resilience-2025.1.0/resilience/MD5 | 19 resilience-2025.1.0/resilience/NAMESPACE | 38 + resilience-2025.1.0/resilience/R/pre-post-regression.R | 124 +++++ resilience-2025.1.0/resilience/R/prepost_mi_list.R |only resilience-2025.1.0/resilience/R/tkr-dat.R |only resilience-2025.1.0/resilience/data/tkr.dat.rda |only resilience-2025.1.0/resilience/man/plot.prepost_resilience_mi_list.Rd |only resilience-2025.1.0/resilience/man/prepost.Rd | 214 +++++----- resilience-2025.1.0/resilience/man/prepost_resilience_mi_list.Rd |only resilience-2025.1.0/resilience/man/print.prepost_resilience_mi_list.Rd |only resilience-2025.1.0/resilience/man/summary.prepost_resilience_mi_list.Rd |only resilience-2025.1.0/resilience/man/tkr.dat.Rd | 51 +- 15 files changed, 332 insertions(+), 130 deletions(-)
Title: Stochastic Tree Ensembles (XBART and BART) for Supervised
Learning and Causal Inference
Description: Flexible stochastic tree ensemble software.
Robust implementations of Bayesian Additive Regression Trees (BART)
Chipman, George, McCulloch (2010) <doi:10.1214/09-AOAS285>
for supervised learning and Bayesian Causal Forests (BCF)
Hahn, Murray, Carvalho (2020) <doi:10.1214/19-BA1195>
for causal inference. Enables model serialization and parallel sampling
and provides a low-level interface for custom stochastic forest samplers.
Author: Drew Herren [aut, cre] ,
Richard Hahn [aut],
Jared Murray [aut],
Carlos Carvalho [aut],
Jingyu He [aut],
Pedro Lima [ctb],
stochtree contributors [cph],
Eigen contributors [cph] ,
xgboost contributors [cph] ,
treelite contributors [cph] ,
Microsoft C [...truncated...]
Maintainer: Drew Herren <drewherrenopensource@gmail.com>
Diff between stochtree versions 0.2.0 dated 2025-11-22 and 0.2.1 dated 2025-12-11
DESCRIPTION | 6 MD5 | 17 +- NEWS.md | 10 + R/bart.R | 17 ++ R/bcf.R | 68 +++++---- R/posterior_transformation.R | 108 +++++++++----- configure | 18 +- configure.ac | 2 tests/testthat/test-api-combinations.R |only tests/testthat/test-predict.R | 238 +++++++++++++++++++++++++++++++++ 10 files changed, 392 insertions(+), 92 deletions(-)
Title: Tree Guided Machine Learning for Personalized Predictions and
Precision Diagnostics
Description: Generalization of the classification and regression tree (CART) model that partitions subjects into terminal nodes and tailors machine learning model to each terminal node.
Author: Yunro Chung [aut, cre]
Maintainer: Yunro Chung <yunro.chung@asu.edu>
Diff between tgml versions 0.2.0 dated 2025-09-24 and 0.3.0 dated 2025-12-11
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/05b.combML_mse.R | 22 ++++++++++++++-------- R/05c.combML_bs.R | 26 ++++++++++++++++---------- R/tgml.R | 2 ++ 5 files changed, 41 insertions(+), 27 deletions(-)
Title: Genomic Mediation Analysis with Adaptive Confounding Adjustment
Description: Performs genomic mediation
analysis with adaptive confounding adjustment (GMAC) proposed by Yang et al. (2017) <doi:10.1101/gr.216754.116>. It implements large scale
mediation analysis and adaptively selects potential confounding variables to
adjust for each mediation test from a pool of candidate confounders. The package
is tailored for but not limited to genomic mediation analysis (e.g., cis-gene
mediating trans-gene regulation pattern where an eQTL, its cis-linking gene
transcript, and its trans-gene transcript play the roles as treatment, mediator
and the outcome, respectively), restricting to scenarios with the presence of
cis-association (i.e., treatment-mediator association) and random eQTL (i.e.,
treatment).
Author: Fan Yang [aut],
Jiebiao Wang [aut, cre],
Lin Chen [aut]
Maintainer: Jiebiao Wang <randel.wang@gmail.com>
Diff between GMAC versions 3.1 dated 2022-03-17 and 3.2 dated 2025-12-11
DESCRIPTION | 26 +++++++++++++++++++------- MD5 | 9 +++++---- R/GMAC.R | 2 +- build/partial.rdb |binary man/figures/Thumbs.db |only man/gmac.Rd | 2 +- 6 files changed, 26 insertions(+), 13 deletions(-)
Title: Perpendicular Line Transects for Geosciences
Description: Toolset to create perpendicular profile graphs and swath
profiles. Method are based on coordinate rotation algorithm by
Schaeben et al. (2024) <doi:10.1002/mma.9823>.
Author: Tobias Stephan [aut, cre]
Maintainer: Tobias Stephan <tobias.stephan1@yahoo.com>
Diff between geoprofiler versions 0.0.2 dated 2025-04-10 and 0.0.3 dated 2025-12-11
DESCRIPTION | 11 MD5 | 31 +- NAMESPACE | 17 - NEWS.md |only R/swath.R | 588 ++++++++++++++++++++++++++++------------------ README.md | 18 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/A_Distances.R | 4 inst/doc/A_Distances.Rmd | 6 inst/doc/A_Distances.html | 12 inst/doc/B_Swath.R | 2 inst/doc/B_Swath.Rmd | 292 +++++++++++----------- inst/doc/B_Swath.html | 12 man/swath_stats.Rd | 4 vignettes/A_Distances.Rmd | 6 vignettes/B_Swath.Rmd | 292 +++++++++++----------- 17 files changed, 733 insertions(+), 562 deletions(-)
Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM
or Gibbs sampling, single step (<doi:10.1534/g3.119.400728>),
univariate and multivariate (<doi:10.1186/s12711-022-00730-w>, <doi:10.1093/genetics/iyae179>),
with optional kernel term and sampling techniques (<doi:10.1186/s12859-017-1582-3>).
Author: Alencar Xavier [aut, cre] ,
William Muir [aut],
David Habier [aut],
Kyle Kocak [aut],
Shizhong Xu [aut],
Katy Rainey [aut]
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between bWGR versions 2.2.15 dated 2025-11-05 and 2.2.17 dated 2025-12-11
bWGR-2.2.15/bWGR/src/RcppEigenX20251103.cpp |only bWGR-2.2.17/bWGR/DESCRIPTION | 8 - bWGR-2.2.17/bWGR/MD5 | 16 +- bWGR-2.2.17/bWGR/R/RcppExports.R | 24 +++- bWGR-2.2.17/bWGR/demo/multivariates.R | 3 bWGR-2.2.17/bWGR/man/bWGR.Rd | 4 bWGR-2.2.17/bWGR/man/mvr.Rd | 11 + bWGR-2.2.17/bWGR/src/RcppEigen20230423.cpp | 155 ---------------------------- bWGR-2.2.17/bWGR/src/RcppEigenX20251203.cpp |only bWGR-2.2.17/bWGR/src/RcppExports.cpp | 104 ++++++++++++++---- 10 files changed, 128 insertions(+), 197 deletions(-)
Title: Workflows for Health Technology Assessments in R using Discrete
EveNts
Description: Toolkit to support and perform discrete event simulations with and without
resource constraints in the context of health technology assessments (HTA).
The package focuses on cost-effectiveness modelling and aims to be submission-ready
to relevant HTA bodies in alignment with 'NICE TSD 15'
<https://sheffield.ac.uk/nice-dsu/tsds/patient-level-simulation>.
More details an examples can be found in the package website <https://jsanchezalv.github.io/WARDEN/>.
Author: Javier Sanchez Alvarez [aut, cre],
Gabriel Lemyre [ctb],
Valerie Aponte Ribero [ctb]
Maintainer: Javier Sanchez Alvarez <javiersanchezeco@gmail.com>
Diff between WARDEN versions 2.0.0 dated 2025-10-13 and 2.0.1 dated 2025-12-11
DESCRIPTION | 6 MD5 | 22 +-- NEWS.md | 17 +- R/engine_helper_f.R | 1 R/input_f.R | 24 ++- build/vignette.rds |binary inst/doc/example_ssd.html | 292 ++++++++++++++++++++---------------------- man/adj_val.Rd | 18 ++ man/ast_as_list.Rd | 126 +++++++++--------- man/qgamma_mse.Rd | 54 +++---- man/with_write_flags_lang.Rd | 122 ++++++++--------- tests/testthat/test-input_f.R | 1 12 files changed, 352 insertions(+), 331 deletions(-)
Title: Structural Equation Modeling with Deep Neural Network and
Machine Learning Algorithms
Description: Training and validation of a custom (or data-driven) Structural
Equation Models using Deep Neural Networks or Machine Learning algorithms, which
extend the fitting procedures of the 'SEMgraph' R package <doi:10.32614/CRAN.package.SEMgraph>.
Author: Mario Grassi [aut],
Barbara Tarantino [cre]
Maintainer: Barbara Tarantino <barbara.tarantino01@universitadipavia.it>
Diff between SEMdeep versions 1.1.0 dated 2025-11-10 and 1.1.1 dated 2025-12-11
DESCRIPTION | 13 +-- MD5 | 31 ++++---- NAMESPACE | 3 NEWS.md | 8 ++ R/SEMdnn.R | 20 ++--- R/SEMhelp.R | 160 +++++++++++++++++++++++++++++++++++++++++-- R/SEMml.R | 54 +++++++------- man/SEMdnn.Rd | 6 - man/SEMml.Rd | 5 - man/crossValidation.Rd | 13 +-- man/getConnectionWeight.Rd | 2 man/getGradientWeight.Rd | 2 man/getSignificanceTest.Rd | 2 man/getVariableImportance.Rd | 4 - man/predict.DNN.Rd | 4 - man/predict.ML.Rd | 5 - man/trainingReport.Rd |only 17 files changed, 248 insertions(+), 84 deletions(-)
Title: Geometric Single Cell Deconvolution
Description: Deconvolution of bulk RNA-Sequencing data into proportions of cells based on a reference single-cell RNA-Sequencing dataset using high-dimensional geometric methodology.
Author: Myles Lewis [aut, cre] ,
Rachel Lau [ctb]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between cellGeometry versions 0.5.4 dated 2025-09-15 and 0.5.7 dated 2025-12-11
cellGeometry-0.5.4/cellGeometry/R/subMarkers.R |only cellGeometry-0.5.7/cellGeometry/DESCRIPTION | 7 - cellGeometry-0.5.7/cellGeometry/MD5 | 35 ++++---- cellGeometry-0.5.7/cellGeometry/NAMESPACE | 3 cellGeometry-0.5.7/cellGeometry/NEWS.md | 13 +++ cellGeometry-0.5.7/cellGeometry/R/cellMarkers.R | 5 - cellGeometry-0.5.7/cellGeometry/R/deconvolute.R | 37 +++++--- cellGeometry-0.5.7/cellGeometry/R/mergeMarkers.R | 67 +++++++++++++--- cellGeometry-0.5.7/cellGeometry/R/rstudent.R | 40 +++++++++ cellGeometry-0.5.7/cellGeometry/R/scedasticity.R | 1 cellGeometry-0.5.7/cellGeometry/R/specificity_plot.R | 6 - cellGeometry-0.5.7/cellGeometry/R/stack_plot.R | 3 cellGeometry-0.5.7/cellGeometry/README.md | 2 cellGeometry-0.5.7/cellGeometry/inst/doc/intro.Rmd | 7 + cellGeometry-0.5.7/cellGeometry/inst/doc/intro.html | 7 + cellGeometry-0.5.7/cellGeometry/man/cellMarkers.Rd | 5 - cellGeometry-0.5.7/cellGeometry/man/deconvolute.Rd | 17 ++-- cellGeometry-0.5.7/cellGeometry/man/fix_group.Rd |only cellGeometry-0.5.7/cellGeometry/man/residuals.deconv.Rd |only cellGeometry-0.5.7/cellGeometry/vignettes/intro.Rmd | 7 + 20 files changed, 205 insertions(+), 57 deletions(-)
Title: Tabular Data Suppression using Gaussian Elimination
Description: A statistical disclosure control tool to protect tables by suppression
using the Gaussian elimination secondary suppression algorithm
(Langsrud, 2024) <doi:10.1007/978-3-031-69651-0_6>. A suggestion is
to start by working with functions SuppressSmallCounts() and
SuppressDominantCells(). These functions use primary suppression functions for
the minimum frequency rule and the dominance rule, respectively. Novel
functionality for suppression of disclosive cells is also included. General
primary suppression functions can be supplied as input to the general working
horse function, GaussSuppressionFromData(). Suppressed frequencies can be
replaced by synthetic decimal numbers as described in
Langsrud (2019) <doi:10.1007/s11222-018-9848-9>.
Author: Oeyvind Langsrud [aut, cre] ,
Daniel Lupp [aut] ,
Hege Boevelstad [ctb] ,
Vidar Norstein Klungre [rev] ,
Jonas Lindblad [ctb],
Statistics Norway [cph]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between GaussSuppression versions 1.2.0 dated 2025-09-25 and 1.2.3 dated 2025-12-11
DESCRIPTION | 10 - MD5 | 34 ++-- NAMESPACE | 2 NEWS.md | 48 ++++++ R/GaussSuppressionFromData.R | 126 ++++++++++++++- R/MagnitudeRule.R | 142 +++++++++++++----- R/Singleton.R | 11 + R/SuppressDominantCells.R | 34 ++++ inst/doc/Linked_table_suppression.html | 5 inst/doc/Magnitude_table_suppression.html | 17 +- inst/doc/Small_count_frequency_table_suppression.html | 5 inst/doc/define_tables.html | 5 man/GaussSuppressionFromData.Rd | 32 +++- man/MagnitudeRule.Rd | 21 ++ man/SingletonUniqueContributor.Rd | 3 man/SuppressDominantCells.Rd | 34 ++++ man/figures/logo.png |binary tests/testthat/test-Wrappers.R | 41 +++++ 18 files changed, 482 insertions(+), 88 deletions(-)
More information about GaussSuppression at CRAN
Permanent link
Title: Access the Felt API
Description: Upload, download, and edit internet maps with the Felt API
(<https://developers.felt.com/rest-api/getting-started>).
Allows users to create new maps, edit existing maps, and extract data.
Provides tools for working with layers, which represent geographic data, and elements,
which are interactive annotations. Spatial data accessed from the API is
transformed to work with 'sf'.
Author: Christopher T. Kenny [aut, cre]
Maintainer: Christopher T. Kenny <ctkenny@proton.me>
Diff between feltr versions 0.0.4 dated 2023-11-05 and 0.1.0 dated 2025-12-11
feltr-0.0.4/feltr/R/finish_upload.R |only feltr-0.0.4/feltr/man/felt_finish_upload.Rd |only feltr-0.0.4/feltr/man/felt_get_style.Rd |only feltr-0.0.4/feltr/tests/testthat/t/create/felt.com |only feltr-0.0.4/feltr/tests/testthat/t/get_elements/felt.com |only feltr-0.0.4/feltr/tests/testthat/t/user/felt.com |only feltr-0.1.0/feltr/DESCRIPTION | 23 feltr-0.1.0/feltr/MD5 | 83 +- feltr-0.1.0/feltr/NAMESPACE | 19 feltr-0.1.0/feltr/NEWS.md | 15 feltr-0.1.0/feltr/R/add.R | 283 ++++++---- feltr-0.1.0/feltr/R/api_url.R | 2 feltr-0.1.0/feltr/R/comments.R | 15 feltr-0.1.0/feltr/R/create.R | 26 feltr-0.1.0/feltr/R/delete.R | 138 +++- feltr-0.1.0/feltr/R/details.R |only feltr-0.1.0/feltr/R/felt_key.R | 209 +++---- feltr-0.1.0/feltr/R/feltr-package.R |only feltr-0.1.0/feltr/R/library.R |only feltr-0.1.0/feltr/R/map.R | 186 ++++-- feltr-0.1.0/feltr/R/map_elements.R | 75 ++ feltr-0.1.0/feltr/R/proc.R | 92 +-- feltr-0.1.0/feltr/R/refresh.R |only feltr-0.1.0/feltr/R/roxygen.R |only feltr-0.1.0/feltr/R/style.R | 61 -- feltr-0.1.0/feltr/R/user.R | 56 + feltr-0.1.0/feltr/R/utils.R |only feltr-0.1.0/feltr/inst/bbox.geojson |only feltr-0.1.0/feltr/inst/httptest2/redact.R | 3 feltr-0.1.0/feltr/man/felt_add_library_layer.Rd |only feltr-0.1.0/feltr/man/felt_add_library_layer_group.Rd |only feltr-0.1.0/feltr/man/felt_add_map_elements.Rd |only feltr-0.1.0/feltr/man/felt_add_map_layers.Rd | 28 feltr-0.1.0/feltr/man/felt_add_map_layers_url.Rd | 16 feltr-0.1.0/feltr/man/felt_create_map.Rd | 19 feltr-0.1.0/feltr/man/felt_delete_map.Rd | 4 feltr-0.1.0/feltr/man/felt_delete_map_elements.Rd |only feltr-0.1.0/feltr/man/felt_delete_map_layer.Rd | 26 feltr-0.1.0/feltr/man/felt_get_comments.Rd | 8 feltr-0.1.0/feltr/man/felt_get_library.Rd |only feltr-0.1.0/feltr/man/felt_get_map.Rd | 17 feltr-0.1.0/feltr/man/felt_get_map_elements.Rd | 18 feltr-0.1.0/feltr/man/felt_get_map_layer_group.Rd |only feltr-0.1.0/feltr/man/felt_get_user.Rd | 7 feltr-0.1.0/feltr/man/felt_patch_style.Rd | 25 feltr-0.1.0/feltr/man/felt_refresh_layer.Rd |only feltr-0.1.0/feltr/man/felt_update_layer_details.Rd |only feltr-0.1.0/feltr/man/felt_update_layer_group_details.Rd |only feltr-0.1.0/feltr/man/felt_update_map_details.Rd |only feltr-0.1.0/feltr/man/feltr-package.Rd |only feltr-0.1.0/feltr/man/key.Rd | 6 feltr-0.1.0/feltr/man/set_felt_key.Rd | 3 feltr-0.1.0/feltr/tests/testthat/t/create/maps-b1286e-POST.json |only feltr-0.1.0/feltr/tests/testthat/t/get_elements/maps |only feltr-0.1.0/feltr/tests/testthat/t/user/user.json |only feltr-0.1.0/feltr/tests/testthat/test-comments.R | 14 56 files changed, 929 insertions(+), 548 deletions(-)
Title: Exponential-Family Models for Signed Networks
Description: Extends the 'ergm.multi' packages from the Statnet suite to fit (temporal) exponential-family random graph models for signed networks. The framework models positive and negative ties as interdependent, which allows estimation and testing of structural balance theory. The package also includes options for descriptive summaries, visualization, and simulation of signed networks. See Krivitsky, Koehly, and Marcum (2020) <doi:10.1007/s11336-020-09720-7> and Fritz, C., Mehrl, M., Thurner, P. W., & Kauermann, G. (2025) <doi:10.1017/pan.2024.21>.
Author: Marc Schalberger [cre],
Cornelius Fritz [aut],
Pavel Krivitsky [ctb]
Maintainer: Marc Schalberger <m.schalberger@fu-berlin.de>
Diff between ergm.sign versions 0.1.0 dated 2025-11-21 and 0.1.1 dated 2025-12-11
ergm.sign-0.1.0/ergm.sign/man/InitErgmTerm.delese.Rd |only ergm.sign-0.1.0/ergm.sign/man/InitErgmTerm.delesf.Rd |only ergm.sign-0.1.0/ergm.sign/man/InitErgmTerm.gwdelese.Rd |only ergm.sign-0.1.0/ergm.sign/man/InitErgmTerm.gwdelesf.Rd |only ergm.sign-0.1.1/ergm.sign/DESCRIPTION | 6 ergm.sign-0.1.1/ergm.sign/MD5 | 42 - ergm.sign-0.1.1/ergm.sign/NAMESPACE | 2 ergm.sign-0.1.1/ergm.sign/R/InitErgmTerm.sign.R | 596 +++++---------- ergm.sign-0.1.1/ergm.sign/R/UnLayer.R | 10 ergm.sign-0.1.1/ergm.sign/R/ergm.sign-package.R | 2 ergm.sign-0.1.1/ergm.sign/R/mple_sign.R | 6 ergm.sign-0.1.1/ergm.sign/R/network.sign.R | 40 - ergm.sign-0.1.1/ergm.sign/R/networks.sign.R | 1 ergm.sign-0.1.1/ergm.sign/R/path_sampler.R |only ergm.sign-0.1.1/ergm.sign/build/partial.rdb |binary ergm.sign-0.1.1/ergm.sign/build/stage23.rdb |binary ergm.sign-0.1.1/ergm.sign/data/sponsor.rda |binary ergm.sign-0.1.1/ergm.sign/inst/doc/tribes.html | 24 ergm.sign-0.1.1/ergm.sign/man/ese-ergmTerm-8531b67b.Rd | 2 ergm.sign-0.1.1/ergm.sign/man/esf-ergmTerm-c450f580.Rd | 2 ergm.sign-0.1.1/ergm.sign/man/eval_loglik.Rd |only ergm.sign-0.1.1/ergm.sign/man/gwese-ergmTerm-0e3a2475.Rd | 2 ergm.sign-0.1.1/ergm.sign/man/gwesf-ergmTerm-81ee6379.Rd | 2 ergm.sign-0.1.1/ergm.sign/man/mple_sign.Rd | 10 ergm.sign-0.1.1/ergm.sign/tests/testthat/test-delayed.R | 16 25 files changed, 322 insertions(+), 441 deletions(-)
Title: Genome Polarization via Diagnostic Index Expectation
Maximization
Description: Implements a likelihood-based method for genome polarization, identifying
which alleles of SNV markers belong to either side of a barrier to gene flow. The
approach co-estimates individual assignment, barrier strength, and divergence between
sides, with direct application to studies of hybridization. Includes VCF-to-diem
conversion and input checks, support for mixed ploidy and parallelization, and tools
for visualization and diagnostic outputs. Based on diagnostic index expectation
maximization as described in Baird et al. (2023) <doi:10.1111/2041-210X.14010>.
Author: Natalia Martinkova [aut, cre] ,
Stuart Baird [aut]
Maintainer: Natalia Martinkova <martinkova@ivb.cz>
Diff between diemr versions 1.5.1 dated 2025-10-09 and 1.5.2 dated 2025-12-11
DESCRIPTION | 6 MD5 | 56 ++-- NAMESPACE | 1 NEWS.md | 12 + R/CheckDiemFormat.r | 14 - R/hybridIndex.r | 114 +++++++--- R/importPolarized.r | 47 ++-- R/internal.r | 41 +-- R/rank2map.r | 54 ++-- R/readIncludedSites.r |only R/smoothPolarizedGenotypes.r | 85 +++---- R/vcf2diem.r | 86 +++++-- README.md | 23 +- build/vignette.rds |binary inst/doc/Importing-data-for-genome-polarisation.html | 4 inst/doc/Understanding-genome-polarisation-output-files.html | 4 inst/doc/diemr-diagnostic-index-expecation-maximisation-in-r.html | 4 inst/extdata/myotis.vcf |binary man/CheckDiemFormat.Rd | 4 man/hybridIndex.Rd | 89 +++++-- man/importPolarized.Rd | 12 - man/rank2map.Rd | 12 - man/readIncludedSites.Rd | 14 - man/resolveChosenInds.Rd |only man/smoothPolarizedGenotypes.Rd | 26 +- man/variantSites.Rd | 2 man/vcf2diem.Rd | 34 ++ tests/testthat/test_hybridIndex.r | 105 +++++++++ tests/testthat/test_importPolarized.r | 34 ++ tests/testthat/test_internal.r | 43 +++ 30 files changed, 666 insertions(+), 260 deletions(-)
Title: Transformation-Free Linear Regression for Compositional Outcomes
and Predictors
Description: Implements the expectation-maximization (EM) algorithm as described in Fiksel et al. (2022) <doi:10.1111/biom.13465>
for transformation-free linear regression for compositional outcomes and predictors.
Author: Jacob Fiksel [aut] ,
Abhirup Datta [ctb],
Sandipan Pramanik [cre, ctb]
Maintainer: Sandipan Pramanik <sandy.pramanik@gmail.com>
Diff between codalm versions 0.1.2 dated 2021-07-26 and 0.1.3 dated 2025-12-11
codalm-0.1.2/codalm/R/data.R |only codalm-0.1.2/codalm/data |only codalm-0.1.2/codalm/man/educFM.Rd |only codalm-0.1.2/codalm/man/predict_codalm.Rd |only codalm-0.1.3/codalm/DESCRIPTION | 46 - codalm-0.1.3/codalm/MD5 | 39 - codalm-0.1.3/codalm/NAMESPACE | 1 codalm-0.1.3/codalm/NEWS.md | 4 codalm-0.1.3/codalm/R/codalm_em.R | 56 - codalm-0.1.3/codalm/R/independence_test.R | 17 codalm-0.1.3/codalm/README.md | 5 codalm-0.1.3/codalm/build/partial.rdb |only codalm-0.1.3/codalm/build/vignette.rds |binary codalm-0.1.3/codalm/inst/doc/codalm_quickstart.R | 30 codalm-0.1.3/codalm/inst/doc/codalm_quickstart.Rmd | 39 - codalm-0.1.3/codalm/inst/doc/codalm_quickstart.html | 462 ++++++++---- codalm-0.1.3/codalm/man/codalm.Rd | 17 codalm-0.1.3/codalm/man/codalm_ci.Rd | 13 codalm-0.1.3/codalm/man/codalm_indep_test.Rd | 15 codalm-0.1.3/codalm/tests/testthat/test-codalm.R | 2 codalm-0.1.3/codalm/tests/testthat/test-codalm_ci.R | 12 codalm-0.1.3/codalm/tests/testthat/test-independence_test.R | 4 codalm-0.1.3/codalm/vignettes/codalm_quickstart.Rmd | 39 - 23 files changed, 514 insertions(+), 287 deletions(-)
Title: Comprehensive Science Mapping Analysis
Description: Tool for quantitative research in scientometrics and bibliometrics.
It implements the comprehensive workflow for science mapping analysis proposed in Aria M. and
Cuccurullo C. (2017) <doi:10.1016/j.joi.2017.08.007>.
'bibliometrix' provides various routines for importing bibliographic data from 'SCOPUS',
'Clarivate Analytics Web of Science' (<https://www.webofknowledge.com/>), 'Digital Science Dimensions'
(<https://www.dimensions.ai/>), 'OpenAlex' (<https://openalex.org/>), 'Cochrane Library' (<https://www.cochranelibrary.com/>), 'Lens' (<https://lens.org>),
and 'PubMed' (<https://pubmed.ncbi.nlm.nih.gov/>) databases, performing bibliometric analysis
and building networks for co-citation, coupling, scientific collaboration and co-word analysis.
Author: Massimo Aria [cre, aut, cph] ,
Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between bibliometrix versions 5.2.0 dated 2025-11-08 and 5.2.1 dated 2025-12-11
bibliometrix-5.2.0/bibliometrix/inst/biblioshiny/utils_old.R |only bibliometrix-5.2.1/bibliometrix/DESCRIPTION | 6 bibliometrix-5.2.1/bibliometrix/MD5 | 21 bibliometrix-5.2.1/bibliometrix/NEWS | 8 bibliometrix-5.2.1/bibliometrix/build/partial.rdb |binary bibliometrix-5.2.1/bibliometrix/inst/biblioshiny/biblioAI.R | 8 bibliometrix-5.2.1/bibliometrix/inst/biblioshiny/biblioShot.R | 192 ++++---- bibliometrix-5.2.1/bibliometrix/inst/biblioshiny/helpContent.R | 198 ++++++++ bibliometrix-5.2.1/bibliometrix/inst/biblioshiny/libraries.R | 103 +++- bibliometrix-5.2.1/bibliometrix/inst/biblioshiny/server.R | 165 +++---- bibliometrix-5.2.1/bibliometrix/inst/biblioshiny/ui.R | 63 ++ bibliometrix-5.2.1/bibliometrix/inst/biblioshiny/utils.R | 227 +++++++++- 12 files changed, 763 insertions(+), 228 deletions(-)
Title: Bayesian Analysis of Non-Stationary Gaussian Process Models
Description: Enables off-the-shelf functionality for fully Bayesian, nonstationary Gaussian process modeling. The approach to nonstationary modeling involves a closed-form, convolution-based covariance function with spatially-varying parameters; these parameter processes can be specified either deterministically (using covariates or basis functions) or stochastically (using approximate Gaussian processes). Stationary Gaussian processes are a special case of our methodology, and we furthermore implement approximate Gaussian process inference to account for very large spatial data sets (Finley, et al (2017) <doi:10.48550/arXiv.1702.00434>). Bayesian inference is carried out using Markov chain Monte Carlo methods via the "nimble" package, and posterior prediction for the Gaussian process at unobserved locations is provided as a post-processing step.
Author: Daniel Turek [aut, cre],
Mark Risser [aut]
Maintainer: Daniel Turek <danielturek@gmail.com>
Diff between BayesNSGP versions 0.1.2 dated 2022-01-08 and 0.2.0 dated 2025-12-11
DESCRIPTION | 17 MD5 | 43 - NAMESPACE | 12 R/SGV.R | 32 - R/core.R | 1178 +++++++++++++++++++++++++++--------------- R/gp2Scale.R |only man/Cy_sm.Rd |only man/R_sparse_cholesky.Rd |only man/R_sparse_solveMat.Rd |only man/crossCy_sm.Rd |only man/determineNeighbors.Rd | 8 man/dmnorm_gp2Scale.Rd |only man/inverseEigen.Rd | 6 man/matern_corr.Rd | 12 man/nimble_sparse_cholesky.Rd |only man/nimble_sparse_solveMat.Rd |only man/nsCorr.Rd | 18 man/nsCrosscorr.Rd | 26 man/nsCrossdist.Rd | 4 man/nsCrossdist3d.Rd | 2 man/nsDist.Rd | 2 man/nsDist3d.Rd | 2 man/nsgpModel.Rd | 36 - man/nsgpPredict.Rd | 28 man/orderCoordinatesMMD.Rd | 8 man/rmnorm_gp2Scale.Rd |only man/sgvSetup.Rd | 5 27 files changed, 929 insertions(+), 510 deletions(-)
Title: Causal Inference using Bayesian Additive Regression Trees
Description: Contains a variety of methods to generate typical causal inference estimates using Bayesian Additive Regression Trees (BART) as the underlying regression model (Hill (2012) <doi:10.1198/jcgs.2010.08162>).
Author: Vincent Dorie [aut, cre] ,
Jennifer Hill [aut]
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between bartCause versions 1.0-9 dated 2024-09-16 and 1.0-10 dated 2025-12-11
DESCRIPTION | 13 ++++++------ MD5 | 20 +++++++++---------- R/generics.R | 8 +++++-- R/responseFit.R | 5 +++- R/utility.R | 37 +++++++++++++++++++++++++++++++++++- build/partial.rdb |binary inst/NEWS.Rd | 9 ++++++++ tests/testthat/test-04-bartc.R | 22 +++++++++++++++------ tests/testthat/test-05-generics.R | 7 ++++++ tests/testthat/test-06-regression.R | 4 ++- tests/testthat/test-11-stan4bart.R | 6 ++--- 11 files changed, 101 insertions(+), 30 deletions(-)
Title: Distance and Similarity Measures
Description: Provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.
Author: David Meyer [aut, cre] ,
Christian Buchta [aut]
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between proxy versions 0.4-27 dated 2022-06-09 and 0.4-28 dated 2025-12-11
DESCRIPTION | 14 +++++++------ MD5 | 28 +++++++++++++-------------- NAMESPACE | 5 ++-- R/registry.R | 8 +++---- R/util.R | 16 +++++++++++++-- build/vignette.rds |binary inst/NEWS.Rd | 13 ++++++++++++ inst/doc/overview.pdf |binary man/dist.Rd | 2 - src/apply.c | 36 ++++++++++++++++++++--------------- src/arrayIndex.c | 35 ++++++++++++++++++++++++++++++++-- src/distance.c | 20 ++++++++++--------- src/util.c | 38 +++++++++++++++++++++---------------- tests/util.R | 6 +++-- tests/util.Rout.save | 51 +++++++++++++++++++++++++++++++++----------------- 15 files changed, 182 insertions(+), 90 deletions(-)
Title: Local Interpretable Model-Agnostic Explanations
Description: When building complex models, it is often difficult to
explain why the model should be trusted. While global measures such as
accuracy are useful, they cannot be used for explaining why a model
made a specific prediction. 'lime' (a port of the 'lime' 'Python'
package) is a method for explaining the outcome of black box models by
fitting a local model around the point in question an perturbations of
this point. The approach is described in more detail in the article by
Ribeiro et al. (2016) <doi:10.48550/arXiv.1602.04938>.
Author: Emil Hvitfeldt [aut, cre] ,
Thomas Lin Pedersen [aut] ,
Michael Benesty [aut]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between lime versions 0.5.3 dated 2022-08-19 and 0.5.4 dated 2025-12-11
lime-0.5.3/lime/demo |only lime-0.5.4/lime/DESCRIPTION | 79 +- lime-0.5.4/lime/LICENSE | 4 lime-0.5.4/lime/MD5 | 68 - lime-0.5.4/lime/NAMESPACE | 6 lime-0.5.4/lime/NEWS.md | 4 lime-0.5.4/lime/R/a_dataframe.R | 316 +++++--- lime-0.5.4/lime/R/character.R | 109 ++ lime-0.5.4/lime/R/explain.R | 21 lime-0.5.4/lime/R/image.R | 188 +++-- lime-0.5.4/lime/R/import-standalone-purrr.R |only lime-0.5.4/lime/R/lime-package.r | 36 lime-0.5.4/lime/R/lime.R | 132 +++ lime-0.5.4/lime/R/models.R | 84 +- lime-0.5.4/lime/R/permute_cases.R | 177 +++- lime-0.5.4/lime/R/plot.R | 81 +- lime-0.5.4/lime/R/plot_image.R | 202 +++-- lime-0.5.4/lime/R/plot_text.R | 43 - lime-0.5.4/lime/R/shiny.R | 126 ++- lime-0.5.4/lime/README.md | 48 - lime-0.5.4/lime/build/partial.rdb |only lime-0.5.4/lime/build/vignette.rds |binary lime-0.5.4/lime/inst/doc/Understanding_lime.R | 88 +- lime-0.5.4/lime/inst/doc/Understanding_lime.Rmd | 94 +- lime-0.5.4/lime/inst/doc/Understanding_lime.html | 548 ++++++++------- lime-0.5.4/lime/man/figures/README-unnamed-chunk-2-1.png |binary lime-0.5.4/lime/man/figures/README-unnamed-chunk-3-1.png |binary lime-0.5.4/lime/man/figures/lifecycle-deprecated.svg |only lime-0.5.4/lime/man/figures/lifecycle-experimental.svg |only lime-0.5.4/lime/man/figures/lifecycle-stable.svg |only lime-0.5.4/lime/man/figures/lifecycle-superseded.svg |only lime-0.5.4/lime/man/lime-package.Rd | 11 lime-0.5.4/lime/tests/testthat.R | 8 lime-0.5.4/lime/tests/testthat/test-data.frame.R | 9 lime-0.5.4/lime/tests/testthat/test-h2o.R | 182 ++-- lime-0.5.4/lime/tests/testthat/test-permutations.R | 32 lime-0.5.4/lime/tests/testthat/test-text.R | 46 - lime-0.5.4/lime/vignettes/Understanding_lime.Rmd | 94 +- 38 files changed, 1922 insertions(+), 914 deletions(-)
Title: Less Code with More Comprehensive Results
Description: Each function replaces multiple standard R functions. For example,
two function calls, Read() and CountAll(), generate summary statistics for
all variables in the data frame, plus histograms and bar charts. Other
functions provide data aggregation via pivot tables; comprehensive
regression, ANOVA, and t-test; visualizations including integrated
Violin/Box/Scatter plot for a numerical variable, bar chart, histogram,
box plot, density curves, calibrated power curve; reading multiple data
formats with the same call; variable labels; time series with aggregation
and forecasting; color themes; and Trellis (facet) graphics. Also includes
a confirmatory factor analysis of multiple-indicator measurement models,
pedagogical routines for data simulation (e.g., Central Limit Theorem),
generation and rendering of regression instructions for interpretative output,
and both interactive construction of visualizations and interactive
visualizations with plotly.
Author: David W. Gerbing [aut, cre]
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 4.4.5 dated 2025-08-22 and 4.5 dated 2025-12-11
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Title: Accelerated Oblique Random Forests
Description: Fit, interpret, and compute predictions with oblique random
forests. Includes support for partial dependence, variable importance,
passing customized functions for variable importance and identification
of linear combinations of features. Methods for the oblique random
survival forest are described in Jaeger et al., (2023)
<DOI:10.1080/10618600.2023.2231048>.
Author: Byron Jaeger [aut, cre] ,
Nicholas Pajewski [ctb],
Sawyer Welden [ctb],
Christopher Jackson [rev],
Marvin Wright [rev],
Lukas Burk [rev]
Maintainer: Byron Jaeger <byron.jaeger@gmail.com>
Diff between aorsf versions 0.1.5 dated 2024-05-29 and 0.1.6 dated 2025-12-11
DESCRIPTION | 15 LICENSE | 4 MD5 | 124 +-- NEWS.md | 274 ++++--- R/bibentries.R | 252 +++---- R/check.R | 47 + R/coerce_nans.R | 4 R/collapse_misc.R | 124 +-- R/data-pbc_orsf.R | 86 +- R/fctr.R | 348 +++++----- R/orsf.R | 1000 ++++++++++++++-------------- R/orsf_R6.R | 105 ++- R/orsf_control.R | 1113 +++++++++++++++----------------- R/orsf_data_prep.R | 111 +-- R/orsf_print.R | 86 +- R/orsf_vi.R | 2 R/orsf_vs.R | 20 R/prep_x.R | 4 R/ref_code.R | 270 +++---- R/roxy.R | 374 +++++----- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 150 ++-- inst/doc/aorsf.R | 26 inst/doc/aorsf.Rmd | 316 ++++----- inst/doc/aorsf.html | 33 inst/doc/fast.html | 11 inst/doc/oobag.html | 57 + inst/doc/pd.R | 14 inst/doc/pd.Rmd | 1108 +++++++++++++++---------------- inst/doc/pd.html | 11 man/orsf.Rd | 50 - man/orsf_control.Rd | 28 man/orsf_control_cph.Rd | 4 man/orsf_control_custom.Rd | 4 man/orsf_control_fast.Rd | 4 man/orsf_control_net.Rd | 4 man/orsf_ice_oob.Rd | 56 - man/orsf_pd_oob.Rd | 107 ++- man/orsf_scale_cph.Rd | 112 +-- man/orsf_vs.Rd | 9 man/predict.ObliqueForest.Rd | 10 man/roxygen/meta.R | 8 src/TreeClassification.cpp | 3 tests/testthat/_snaps/verbosity.md | 66 - tests/testthat/test-compute-gini.R | 8 tests/testthat/test-fctr.R | 26 tests/testthat/test-find_cutpoints.R | 190 ++--- tests/testthat/test-find_rows_inbag.R | 56 - tests/testthat/test-impute_meanmode.R | 374 +++++----- tests/testthat/test-is_col_splittable.R | 124 +-- tests/testthat/test-orsf.R | 8 tests/testthat/test-orsf_pd.R | 632 +++++++++--------- tests/testthat/test-orsf_print.R | 16 tests/testthat/test-orsf_scale_x.R | 116 +-- tests/testthat/test-orsf_train.R | 74 +- tests/testthat/test-orsf_vi.R | 1021 ++++++++++++++--------------- tests/testthat/test-orsf_vs.R | 28 tests/testthat/test-orsf_weights.R | 130 +-- tests/testthat/test-ref_code.R | 32 tests/testthat/test-sprout_node.R | 90 +- vignettes/aorsf.Rmd | 316 ++++----- vignettes/pd.Rmd | 1108 +++++++++++++++---------------- 63 files changed, 5583 insertions(+), 5320 deletions(-)
More information about impermanentlosscalc at CRAN
Permanent link
Title: Cox Models by Likelihood Based Boosting for a Single Survival
Endpoint or Competing Risks
Description: Provides routines for fitting Cox models by likelihood based
boosting for single event survival data with right censoring or in the
presence of competing risks. The methodology is described in Binder
and Schumacher (2008) <doi:10.1186/1471-2105-9-14> and Binder et al.
(2009) <doi:10.1093/bioinformatics/btp088>.
Author: John Zobolas [cre, aut] ,
Harald Binder [aut]
Maintainer: John Zobolas <bblodfon@gmail.com>
This is a re-admission after prior archival of version 1.4 dated 2013-05-10
Diff between CoxBoost versions 1.4 dated 2013-05-10 and 1.5.1 dated 2025-12-11
CoxBoost-1.4/CoxBoost/R/optimStepSizeFactor.R |only CoxBoost-1.4/CoxBoost/changeLog |only CoxBoost-1.4/CoxBoost/man/optimStepSizeFactor.Rd |only CoxBoost-1.5.1/CoxBoost/DESCRIPTION | 39 CoxBoost-1.5.1/CoxBoost/LICENSE |only CoxBoost-1.5.1/CoxBoost/MD5 | 50 CoxBoost-1.5.1/CoxBoost/NAMESPACE | 39 CoxBoost-1.5.1/CoxBoost/NEWS.md |only CoxBoost-1.5.1/CoxBoost/R/CoxBoost.R | 2144 +++++++++++++++----- CoxBoost-1.5.1/CoxBoost/R/estimPVal.R | 105 CoxBoost-1.5.1/CoxBoost/R/iCoxBoost.R | 379 +++ CoxBoost-1.5.1/CoxBoost/R/resample.CoxBoost.R |only CoxBoost-1.5.1/CoxBoost/R/zzz.R |only CoxBoost-1.5.1/CoxBoost/README.md |only CoxBoost-1.5.1/CoxBoost/build |only CoxBoost-1.5.1/CoxBoost/inst |only CoxBoost-1.5.1/CoxBoost/man/CoxBoost-package.Rd |only CoxBoost-1.5.1/CoxBoost/man/CoxBoost.Rd | 285 ++ CoxBoost-1.5.1/CoxBoost/man/coef.CoxBoost.Rd | 26 CoxBoost-1.5.1/CoxBoost/man/cv.CoxBoost.Rd | 150 + CoxBoost-1.5.1/CoxBoost/man/cvcb.control.Rd | 70 CoxBoost-1.5.1/CoxBoost/man/estimPVal.Rd | 101 CoxBoost-1.5.1/CoxBoost/man/figures |only CoxBoost-1.5.1/CoxBoost/man/iCoxBoost.Rd | 233 +- CoxBoost-1.5.1/CoxBoost/man/optimCoxBoostPenalty.Rd | 102 CoxBoost-1.5.1/CoxBoost/man/plot.CoxBoost.Rd | 32 CoxBoost-1.5.1/CoxBoost/man/predict.CoxBoost.Rd | 86 CoxBoost-1.5.1/CoxBoost/man/predict.iCoxBoost.Rd | 67 CoxBoost-1.5.1/CoxBoost/man/print.CoxBoost.Rd |only CoxBoost-1.5.1/CoxBoost/man/resample.CoxBoost.Rd |only CoxBoost-1.5.1/CoxBoost/man/stabtrajec.Rd |only CoxBoost-1.5.1/CoxBoost/man/summary.CoxBoost.Rd |only CoxBoost-1.5.1/CoxBoost/src/find_best.c | 229 -- CoxBoost-1.5.1/CoxBoost/src/init.c |only 34 files changed, 3137 insertions(+), 1000 deletions(-)
Title: Download and Process Oklahoma Mesonet Data
Description: A collection of functions to download and process weather data from
the Oklahoma Mesonet <https://mesonet.org>. Functions are available for downloading station metadata,
downloading Mesonet time series (MTS) files, importing MTS files into R, and
converting soil temperature change measurements into soil matric potential and
volumetric soil moisture.
Author: Phillip D. Alderman [aut, cre]
Maintainer: Phillip D. Alderman <phillip.alderman@okstate.edu>
Diff between mesonet versions 0.0.1 dated 2025-07-28 and 0.0.2 dated 2025-12-11
DESCRIPTION | 8 ++-- MD5 | 32 ++++++++-------- NEWS.md | 8 ++++ R/mnet_concatenate.R | 3 + R/mnet_download_mts.R | 12 +++++- R/mnet_requisition_list.R | 4 +- R/mnet_retrieve.R | 4 +- R/mnet_site_info.R | 7 ++- R/mnet_summarize.R | 11 ++++- R/mnet_test_cache.R | 56 ++++++++++++++-------------- inst/tinytest/test_01_mnet_site_info.R | 2 - inst/tinytest/test_05_mnet_concatenate.R | 61 +++++++++++++++---------------- man/mnet_concatenate.Rd | 3 + man/mnet_download_mts.Rd | 6 ++- man/mnet_requisition_list.Rd | 2 - man/mnet_retrieve.Rd | 4 +- man/mnet_summarize.Rd | 4 +- 17 files changed, 133 insertions(+), 94 deletions(-)
Title: Custom Visualizations & Functions for Streamlined Analyses of
Single Cell Sequencing
Description: Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430> RRID:SCR_024675.
Author: Samuel Marsh [aut, cre] ,
Ming Tang [ctb],
Velina Kozareva [ctb],
Lucas Graybuck [ctb],
Zoe Clarke [ctb]
Maintainer: Samuel Marsh <sccustomize@gmail.com>
Diff between scCustomize versions 3.2.3 dated 2025-12-09 and 3.2.4 dated 2025-12-11
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 2 +- R/Utilities.R | 15 ++++++++------- 4 files changed, 16 insertions(+), 15 deletions(-)
Title: Fit and Compare Species-Area Relationship Models Using
Multimodel Inference
Description: Implements the basic elements of the multi-model
inference paradigm for up to twenty species-area relationship models (SAR), using simple
R list-objects and functions, as in Triantis et al. 2012 <DOI:10.1111/j.1365-2699.2011.02652.x>.
The package is scalable and users can easily create their own model and data objects. Additional
SAR related functions are provided.
Author: Thomas J. Matthews [aut, cre] ,
Francois Guilhaumon [aut] ,
Kevin Cazelles [rev]
Maintainer: Thomas J. Matthews <txm676@gmail.com>
Diff between sars versions 2.0.0 dated 2025-03-03 and 2.1.0 dated 2025-12-11
sars-2.0.0/sars/inst/_pkgdown.yml |only sars-2.0.0/sars/tests/testthat/Rplots.pdf |only sars-2.1.0/sars/DESCRIPTION | 22 sars-2.1.0/sars/MD5 | 97 +-- sars-2.1.0/sars/NEWS.md | 7 sars-2.1.0/sars/R/class_plot.R | 233 +++++++-- sars-2.1.0/sars/R/coleman.R | 2 sars-2.1.0/sars/R/gdm.R | 2 sars-2.1.0/sars/R/mod_linear_power.R | 2 sars-2.1.0/sars/R/sar_asymp.R | 2 sars-2.1.0/sars/R/sar_average.R | 13 sars-2.1.0/sars/R/sar_betap.R | 2 sars-2.1.0/sars/R/sar_chapman.R | 2 sars-2.1.0/sars/R/sar_countryside.R | 7 sars-2.1.0/sars/R/sar_epm1.R | 2 sars-2.1.0/sars/R/sar_epm2.R | 2 sars-2.1.0/sars/R/sar_gompertz.R | 2 sars-2.1.0/sars/R/sar_habitat.R | 4 sars-2.1.0/sars/R/sar_heleg.R | 2 sars-2.1.0/sars/R/sar_koba.R | 2 sars-2.1.0/sars/R/sar_loga.R | 2 sars-2.1.0/sars/R/sar_logistic.R | 2 sars-2.1.0/sars/R/sar_mmf.R | 2 sars-2.1.0/sars/R/sar_monod.R | 2 sars-2.1.0/sars/R/sar_negexpo.R | 2 sars-2.1.0/sars/R/sar_p1.R | 2 sars-2.1.0/sars/R/sar_p2.R | 2 sars-2.1.0/sars/R/sar_power.R | 2 sars-2.1.0/sars/R/sar_powerR.R | 2 sars-2.1.0/sars/R/sar_ratio.R | 2 sars-2.1.0/sars/R/sar_threshold.R | 2 sars-2.1.0/sars/R/sar_weibull3.R | 2 sars-2.1.0/sars/R/sar_weibull4.R | 2 sars-2.1.0/sars/README.md | 58 +- sars-2.1.0/sars/inst/REFERENCES.bib | 36 + sars-2.1.0/sars/inst/doc/sars-r-package.R | 68 ++ sars-2.1.0/sars/inst/doc/sars-r-package.Rmd | 127 ++++ sars-2.1.0/sars/inst/doc/sars-r-package.html | 385 +++++++++++++-- sars-2.1.0/sars/inst/model_factory.R | 5 sars-2.1.0/sars/man/countryside_extrap.Rd | 2 sars-2.1.0/sars/man/figures/README-unnamed-chunk-5-1.png |binary sars-2.1.0/sars/man/figures/README-unnamed-chunk-7-1.png |only sars-2.1.0/sars/man/figures/README-unnamed-chunk-7-2.png |only sars-2.1.0/sars/man/figures/README-unnamed-chunk-7-3.png |only sars-2.1.0/sars/man/plot.habitat.Rd | 73 ++ sars-2.1.0/sars/man/sar_countryside.Rd | 3 sars-2.1.0/sars/man/sar_habitat.Rd | 2 sars-2.1.0/sars/tests/testthat/test_countryside.R | 29 + sars-2.1.0/sars/tests/testthat/test_multi.R | 7 sars-2.1.0/sars/tests/testthat/test_power.R | 3 sars-2.1.0/sars/vignettes/REFERENCES.bib | 47 + sars-2.1.0/sars/vignettes/sars-r-package.Rmd | 127 ++++ 52 files changed, 1194 insertions(+), 209 deletions(-)
Title: High-Level Plotting Built Upon 'ggplot2' and Other Plotting
Packages
Description: Provides high-level API and a wide range of options to create stunning, publication-quality plots effortlessly.
It is built upon 'ggplot2' and other plotting packages, and is designed to be easy to use and to work seamlessly with 'ggplot2' objects.
It is particularly useful for creating complex plots with multiple layers, facets, and annotations.
It also provides a set of functions to create plots for specific types of data, such as Venn diagrams, alluvial diagrams, and phylogenetic trees.
The package is designed to be flexible and customizable, and to work well with the 'ggplot2' ecosystem.
The API can be found at <https://pwwang.github.io/plotthis/reference/index.html>.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>
Diff between plotthis versions 0.8.2 dated 2025-11-10 and 0.9.0 dated 2025-12-11
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- R/boxviolinplot.R | 12 +++++++++--- R/densityplot.R | 2 +- R/dimplot.R | 18 +++++++++--------- R/heatmap.R | 8 +++++++- R/network.R | 5 +++-- R/roccurve.R | 3 ++- R/theming.R | 9 +++++---- R/velocityplot.R | 4 ++-- man/Heatmap.Rd | 3 ++- man/HeatmapAtomic.Rd | 3 ++- man/ROCCurve.Rd | 3 ++- man/theme_this.Rd | 3 ++- 14 files changed, 62 insertions(+), 43 deletions(-)
Title: Extract Event Statistics in Hydrologic Time Series
Description: Events from individual hydrologic time series are extracted, and events
are matched across multiple time series. The package has been applied in studies
such as Wasko and Guo (2022) <doi:10.1002/hyp.14563> and Mohammadpour Khoie,
Guo and Wasko (2025) <doi:10.1016/j.envsoft.2025.106521>.
Author: Conrad Wasko [aut, cre],
Danlu Guo [aut],
Mohammad Masoud Mohammadpour Khoie [ctb]
Maintainer: Conrad Wasko <conrad.wasko@gmail.com>
Diff between hydroEvents versions 0.12.0 dated 2025-02-12 and 0.13.0 dated 2025-12-11
DESCRIPTION | 24 +- MD5 | 26 +- NAMESPACE | 39 +-- NEWS.md | 16 - R/calcREIC.R |only R/eventRVEIM.R |only R/plotEvents.R | 13 - R/postCorrection.R |only README.md | 534 ++++++++++++++++++++++++++++---------------------- data/hourlyQ.rda |only man/calcREIC.Rd |only man/eventBaseflow.Rd | 95 ++++---- man/eventMaxima.Rd | 121 +++++------ man/eventMinima.Rd | 121 +++++------ man/eventPOT.Rd | 109 +++++----- man/eventRVEIM.Rd |only man/hourlyQ.Rd |only man/postCorrection.Rd |only 18 files changed, 595 insertions(+), 503 deletions(-)
Title: Calculate Model-Based Metrics of Proportionality on Count-Based
Compositional Data
Description: Calculates metrics of proportionality using the logit-normal multinomial model. It can also provide empirical and plugin estimates of these metrics.
Author: Kevin McGregor [aut, cre, cph],
Nneka Okaeme [aut]
Maintainer: Kevin McGregor <kevin.mcgregor@umanitoba.ca>
Diff between countprop versions 1.0.1 dated 2023-08-18 and 1.1.1 dated 2025-12-11
DESCRIPTION | 12 +-- MD5 | 33 ++++----- NAMESPACE | 2 NEWS.md | 17 ++++ R/mle.R | 79 ++++++++++++++++------ R/proportionality.R | 155 ++++++++++++++++++++++++++------------------ README.md | 12 +++ build/vignette.rds |binary inst/doc/countprop.R | 2 inst/doc/countprop.pdf |binary man/convertSigma.Rd |only man/ebicPlot.Rd | 2 man/logLik.Rd | 6 + man/logitNormalVariation.Rd | 9 +- man/mleLR.Rd | 6 + man/mlePath.Rd | 5 + man/naiveVariation.Rd | 6 + man/pluginVariation.Rd | 2 18 files changed, 232 insertions(+), 116 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-10 1.6.7
2024-05-19 1.6.6
2023-09-23 1.6.1
2023-09-11 1.6.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-21 1.6.6
2023-12-17 1.6.1
2023-09-11 1.6.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-12 0.4.2
2023-11-22 0.4
2023-10-05 0.3.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-10-01 1.6.8
2024-10-11 1.6.7
2024-05-15 1.6.6
2023-10-16 1.6.3
2023-09-10 1.6.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-10-27 0.1.1
2024-06-18 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-12-10 0.4.3
2025-12-02 0.4.2
2023-08-21 0.4.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-16 0.1.3
2023-10-09 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-01 2.5.0
2024-02-15 2.3.0
2023-04-16 2.2.1
2022-06-23 2.1.0
2022-03-06 2.0.3
2021-12-08 2.0.2
2021-06-16 1.0.8
2021-06-14 1.0.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-28 0.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-06 1.0.1
Title: Read the Swiss Register of Plant Protection Products
Description: Generate data objects from XML versions of the Swiss
Register of Plant Protection Products. An online version of the
register can be accessed at <https://www.psm.admin.ch/de/produkte>. There is no
guarantee of correspondence of the data read in using this package with that
online version, or with the original registration documents. Also, the
Federal Food Safety and Veterinary Office, coordinating the authorisation of
plant protection products in Switzerland, does not answer requests regarding
this package.
Author: Daniel Baumgartner [ctb] ,
Marcel Mathis [rev, ctb],
Romualdus Kasteel [rev] ,
Elisabeth Lutz [ctb],
Johannes Ranke [aut, cre] ,
Agroscope [cph]
Maintainer: Johannes Ranke <johannes.ranke@agroscope.admin.ch>
Diff between srppp versions 1.1.0 dated 2025-07-17 and 2.0.0 dated 2025-12-11
DESCRIPTION | 12 MD5 | 37 NAMESPACE | 1 NEWS.md | 9 R/resolve_cultures.R | 8 R/srppp-package.R | 1 R/srppp-xml.R | 129 README.md | 3 build/vignette.rds |binary inst/doc/srppp.html | 3314 +++++----- inst/doc/srppp_products_with_MO.html | 755 +- inst/testdata/Daten_Pflanzenschutzmittelverzeichnis_2024-12-16.zip |binary inst/testdata/PublicationData_2025_12_01.xml.xz |only man/resolve_cultures.Rd | 2 man/srppp_xml_get.Rd | 2 tests/testthat/setup.R | 13 tests/testthat/test-alternative_products.R | 23 tests/testthat/test-resolve_cultures.R | 74 tests/testthat/test-srppp_xml.R | 33 tests/testthat/test-use_rates.R | 56 20 files changed, 2354 insertions(+), 2118 deletions(-)
Title: Visualization Tool for Numerical Data on Human/Mouse Organs and
Organelles
Description: A tool for visualizing numerical data (e.g., gene expression, protein abundance) on predefined anatomical maps of human/mouse organs and subcellular organelles. It supports customization of color schemes, filtering by organ systems (for organisms) or organelle types, and generation of optional bar charts for quantitative comparison. The package integrates coordinate data for organs and organelles to plot anatomical/subcellular contours, mapping data values to specific structures for intuitive visualization of biological data distribution.The underlying method was described in the preprint by Zhou et al. (2022) <doi:10.1101/2022.09.07.506938>.
Author: Qirui Shen [aut, cre]
Maintainer: Qirui Shen <shenqr@i.smu.edu.cn>
Diff between OrgHeatmap versions 0.3.1 dated 2025-11-26 and 0.3.2 dated 2025-12-11
DESCRIPTION | 14 ++--- MD5 | 14 ++--- NAMESPACE | 106 ++++++++++++++++++++++----------------------- NEWS.md | 7 +- R/OrgHeatmap.R | 6 +- README.md | 2 data/mouse_organ_coord.rda |binary man/OrgHeatmap.Rd | 4 - 8 files changed, 78 insertions(+), 75 deletions(-)
Title: Curated Datasets and Tools for Epidemiological Data Analysis
Description: Curated datasets and intuitive data management functions to streamline epidemiological data workflows. It is designed to support researchers in quickly accessing clean, structured data and applying essential cleaning, summarizing, visualization, and export operations with minimal effort. Whether you're preparing a cohort for analysis or creating reports, 'DIVINE' makes the process more efficient, transparent, and reproducible.
Author: Natalia Pallares [aut, cre],
Joao Carmezim [aut],
Pau Satorra [aut],
Lucia Blanc [aut],
Cristian Tebe [aut]
Maintainer: Natalia Pallares <npallares@igtp.cat>
Diff between DIVINE versions 0.1.0 dated 2025-11-11 and 0.1.1 dated 2025-12-11
DESCRIPTION | 6 MD5 | 56 +- NEWS.md | 6 R/end_followup.R | 4 R/export_data.R | 8 R/icu.R | 4 R/multi_plot.R | 773 ++++++++++++++++++++------------------- build/vignette.rds |binary data/analytics.rda |binary data/comorbidities.rda |binary data/complications.rda |binary data/concomitant_medication.rda |binary data/demographic.rda |binary data/end_followup.rda |binary data/icu.rda |binary data/inhosp_antibiotics.rda |binary data/inhosp_antivirals.rda |binary data/inhosp_other_treatments.rda |binary data/scores.rda |binary data/symptoms.rda |binary data/vaccine.rda |binary data/vital_signs.rda |binary inst/doc/DIVINE.R | 16 inst/doc/DIVINE.Rmd | 668 ++++++++++++++++----------------- inst/doc/DIVINE.html | 30 - man/end_followup.Rd | 4 man/icu.Rd | 4 man/multi_plot.Rd | 63 +-- vignettes/DIVINE.Rmd | 668 ++++++++++++++++----------------- 29 files changed, 1166 insertions(+), 1144 deletions(-)
Title: 'vcd' Extensions and Additions
Description: Provides additional data sets, methods and documentation to complement the 'vcd' package for Visualizing Categorical Data
and the 'gnm' package for Generalized Nonlinear Models.
In particular, 'vcdExtra' extends mosaic, assoc and sieve plots from 'vcd' to handle 'glm()' and 'gnm()' models and
adds a 3D version in 'mosaic3d'. Additionally, methods are provided for comparing and visualizing lists of
'glm' and 'loglm' objects. This package is now a support package for the book, "Discrete Data Analysis with R" by
Michael Friendly and David Meyer.
Author: Michael Friendly [aut, cre] ,
Heather Turner [ctb],
David Meyer [ctb],
Achim Zeileis [ctb] ,
Duncan Murdoch [ctb],
David Firth [ctb],
Matt Kumar [ctb],
Shuguang Sun [ctb],
Daniel Sabanes Bove [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between vcdExtra versions 0.8-6 dated 2025-07-24 and 0.8.7 dated 2025-12-11
vcdExtra-0.8-6/vcdExtra/R/vcdExtra-deprecated.R |only vcdExtra-0.8-6/vcdExtra/build/partial.rdb |only vcdExtra-0.8-6/vcdExtra/man/figures |only vcdExtra-0.8-6/vcdExtra/man/vcdExtra-deprecated.Rd |only vcdExtra-0.8.7/vcdExtra/DESCRIPTION | 27 vcdExtra-0.8.7/vcdExtra/MD5 | 241 +++--- vcdExtra-0.8.7/vcdExtra/NAMESPACE | 246 ++---- vcdExtra-0.8.7/vcdExtra/NEWS.md | 13 vcdExtra-0.8.7/vcdExtra/R/CMHtest.R | 708 ++++++++++++------ vcdExtra-0.8.7/vcdExtra/R/CrabSatellites.R |only vcdExtra-0.8.7/vcdExtra/R/Crossings.R | 76 + vcdExtra-0.8.7/vcdExtra/R/GKgamma.R | 80 +- vcdExtra-0.8.7/vcdExtra/R/HLtest.R | 90 ++ vcdExtra-0.8.7/vcdExtra/R/Kway.R | 93 ++ vcdExtra-0.8.7/vcdExtra/R/LRstats.R | 88 +- vcdExtra-0.8.7/vcdExtra/R/Summarise.R | 89 +- vcdExtra-0.8.7/vcdExtra/R/blogits.R | 54 + vcdExtra-0.8.7/vcdExtra/R/collapse.table.R | 94 ++ vcdExtra-0.8.7/vcdExtra/R/cutfac.R | 73 + vcdExtra-0.8.7/vcdExtra/R/data.R |only vcdExtra-0.8.7/vcdExtra/R/datasets.R | 48 + vcdExtra-0.8.7/vcdExtra/R/expand.dft.R | 48 + vcdExtra-0.8.7/vcdExtra/R/glmlist.R | 98 ++ vcdExtra-0.8.7/vcdExtra/R/logLik.loglm.R | 63 + vcdExtra-0.8.7/vcdExtra/R/loglin-utilities.R | 102 ++ vcdExtra-0.8.7/vcdExtra/R/logseries.R | 185 +++- vcdExtra-0.8.7/vcdExtra/R/mcaplot.R | 96 +- vcdExtra-0.8.7/vcdExtra/R/modFit.R | 41 + vcdExtra-0.8.7/vcdExtra/R/mosaic.glm.R | 219 +++++ vcdExtra-0.8.7/vcdExtra/R/mosaic.glmlist.R | 149 +++ vcdExtra-0.8.7/vcdExtra/R/mosaic3d.R | 184 +++- vcdExtra-0.8.7/vcdExtra/R/print.Kappa.R | 36 vcdExtra-0.8.7/vcdExtra/R/seq_loglm.R | 88 +- vcdExtra-0.8.7/vcdExtra/R/seq_mosaic.R | 80 +- vcdExtra-0.8.7/vcdExtra/R/split3d.R | 78 + vcdExtra-0.8.7/vcdExtra/R/update.xtabs.R | 39 vcdExtra-0.8.7/vcdExtra/R/vcdExtra-package.R |only vcdExtra-0.8.7/vcdExtra/R/zero.test.R | 64 + vcdExtra-0.8.7/vcdExtra/data/CrabSatellites.rda |only vcdExtra-0.8.7/vcdExtra/inst/doc/a1-creating.html | 4 vcdExtra-0.8.7/vcdExtra/inst/doc/a2-tests.html | 10 vcdExtra-0.8.7/vcdExtra/inst/doc/a3-loglinear.html | 4 vcdExtra-0.8.7/vcdExtra/inst/doc/a4-mosaics.html | 4 vcdExtra-0.8.7/vcdExtra/inst/doc/a5-demo-housing.html | 4 vcdExtra-0.8.7/vcdExtra/inst/doc/a6-mobility.html | 4 vcdExtra-0.8.7/vcdExtra/inst/doc/a7-continuous.Rmd | 1 vcdExtra-0.8.7/vcdExtra/inst/doc/a7-continuous.html | 4 vcdExtra-0.8.7/vcdExtra/inst/doc/datasets.html | 6 vcdExtra-0.8.7/vcdExtra/inst/doc/tidyCats.html | 4 vcdExtra-0.8.7/vcdExtra/man/Abortion.Rd | 78 - vcdExtra-0.8.7/vcdExtra/man/Accident.Rd | 99 +- vcdExtra-0.8.7/vcdExtra/man/AirCrash.Rd | 52 - vcdExtra-0.8.7/vcdExtra/man/Alligator.Rd | 61 - vcdExtra-0.8.7/vcdExtra/man/Asbestos.Rd | 79 -- vcdExtra-0.8.7/vcdExtra/man/Bartlett.Rd | 69 - vcdExtra-0.8.7/vcdExtra/man/Burt.Rd | 69 - vcdExtra-0.8.7/vcdExtra/man/CMHtest.Rd | 309 +++---- vcdExtra-0.8.7/vcdExtra/man/Caesar.Rd | 82 -- vcdExtra-0.8.7/vcdExtra/man/Cancer.Rd | 58 - vcdExtra-0.8.7/vcdExtra/man/Cormorants.Rd | 91 +- vcdExtra-0.8.7/vcdExtra/man/CrabSatellites.Rd |only vcdExtra-0.8.7/vcdExtra/man/Crossings.Rd | 79 -- vcdExtra-0.8.7/vcdExtra/man/CyclingDeaths.Rd | 54 - vcdExtra-0.8.7/vcdExtra/man/DaytonSurvey.Rd | 97 +- vcdExtra-0.8.7/vcdExtra/man/Depends.Rd | 44 - vcdExtra-0.8.7/vcdExtra/man/Detergent.Rd | 68 - vcdExtra-0.8.7/vcdExtra/man/Donner.Rd | 146 +-- vcdExtra-0.8.7/vcdExtra/man/Draft1970.Rd | 83 +- vcdExtra-0.8.7/vcdExtra/man/Draft1970table.Rd | 81 -- vcdExtra-0.8.7/vcdExtra/man/Dyke.Rd | 76 - vcdExtra-0.8.7/vcdExtra/man/Fungicide.Rd | 71 - vcdExtra-0.8.7/vcdExtra/man/GKgamma.Rd | 100 +- vcdExtra-0.8.7/vcdExtra/man/GSS.Rd | 46 - vcdExtra-0.8.7/vcdExtra/man/Geissler.Rd | 85 +- vcdExtra-0.8.7/vcdExtra/man/Gilby.Rd | 70 - vcdExtra-0.8.7/vcdExtra/man/Glass.Rd | 95 +- vcdExtra-0.8.7/vcdExtra/man/HLtest.Rd | 123 +-- vcdExtra-0.8.7/vcdExtra/man/HairEyePlace.Rd | 65 - vcdExtra-0.8.7/vcdExtra/man/Hauser79.Rd | 117 +- vcdExtra-0.8.7/vcdExtra/man/Heart.Rd | 43 - vcdExtra-0.8.7/vcdExtra/man/Heckman.Rd | 90 +- vcdExtra-0.8.7/vcdExtra/man/HospVisits.Rd | 62 - vcdExtra-0.8.7/vcdExtra/man/HouseTasks.Rd | 52 - vcdExtra-0.8.7/vcdExtra/man/Hoyt.Rd | 104 +- vcdExtra-0.8.7/vcdExtra/man/ICU.Rd | 127 +-- vcdExtra-0.8.7/vcdExtra/man/JobSat.Rd | 44 - vcdExtra-0.8.7/vcdExtra/man/Kway.Rd | 148 +-- vcdExtra-0.8.7/vcdExtra/man/LRstats.Rd | 114 +- vcdExtra-0.8.7/vcdExtra/man/Mammograms.Rd | 43 - vcdExtra-0.8.7/vcdExtra/man/Mental.Rd | 59 - vcdExtra-0.8.7/vcdExtra/man/Mice.Rd | 62 - vcdExtra-0.8.7/vcdExtra/man/Mobility.Rd | 59 - vcdExtra-0.8.7/vcdExtra/man/PhdPubs.Rd | 69 - vcdExtra-0.8.7/vcdExtra/man/ShakeWords.Rd | 68 - vcdExtra-0.8.7/vcdExtra/man/Summarise.Rd | 105 +- vcdExtra-0.8.7/vcdExtra/man/TV.Rd | 88 +- vcdExtra-0.8.7/vcdExtra/man/Titanicp.Rd | 76 - vcdExtra-0.8.7/vcdExtra/man/Toxaemia.Rd | 76 - vcdExtra-0.8.7/vcdExtra/man/Vietnam.Rd | 70 - vcdExtra-0.8.7/vcdExtra/man/Vote1980.Rd | 75 - vcdExtra-0.8.7/vcdExtra/man/WorkerSat.Rd | 45 - vcdExtra-0.8.7/vcdExtra/man/Yamaguchi87.Rd | 125 +-- vcdExtra-0.8.7/vcdExtra/man/blogits.Rd | 102 +- vcdExtra-0.8.7/vcdExtra/man/collapse.table.Rd | 64 - vcdExtra-0.8.7/vcdExtra/man/cutfac.Rd | 120 +-- vcdExtra-0.8.7/vcdExtra/man/datasets.Rd | 100 +- vcdExtra-0.8.7/vcdExtra/man/expand.dft.Rd | 82 +- vcdExtra-0.8.7/vcdExtra/man/glmlist.Rd | 113 +- vcdExtra-0.8.7/vcdExtra/man/logLik.loglm.Rd | 96 +- vcdExtra-0.8.7/vcdExtra/man/loglin-utilities.Rd | 296 ++----- vcdExtra-0.8.7/vcdExtra/man/logseries.Rd | 127 +-- vcdExtra-0.8.7/vcdExtra/man/mcaplot.Rd | 125 +-- vcdExtra-0.8.7/vcdExtra/man/modFit.Rd | 64 - vcdExtra-0.8.7/vcdExtra/man/mosaic.glm.Rd | 276 +++---- vcdExtra-0.8.7/vcdExtra/man/mosaic.glmlist.Rd | 214 ++--- vcdExtra-0.8.7/vcdExtra/man/mosaic3d.Rd | 281 +++---- vcdExtra-0.8.7/vcdExtra/man/print.Kappa.Rd | 65 - vcdExtra-0.8.7/vcdExtra/man/seq_loglm.Rd | 156 +-- vcdExtra-0.8.7/vcdExtra/man/seq_mosaic.Rd | 122 +-- vcdExtra-0.8.7/vcdExtra/man/split3d.Rd | 115 +- vcdExtra-0.8.7/vcdExtra/man/update.xtabs.Rd | 66 - vcdExtra-0.8.7/vcdExtra/man/vcdExtra-package.Rd | 189 ++-- vcdExtra-0.8.7/vcdExtra/man/zero.test.Rd | 98 +- vcdExtra-0.8.7/vcdExtra/tests |only vcdExtra-0.8.7/vcdExtra/vignettes/a7-continuous.Rmd | 1 125 files changed, 6175 insertions(+), 4683 deletions(-)
Title: Powerful Classes for HTTP Requests and Responses
Description: In order to facilitate parsing of http requests and creating
appropriate responses this package provides two classes to handle a lot of
the housekeeping involved in working with http exchanges. The infrastructure
builds upon the 'rook' specification and is thus well suited to be combined
with 'httpuv' based web servers.
Author: Thomas Lin Pedersen [cre, aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between reqres versions 1.1.0 dated 2025-11-06 and 1.2.0 dated 2025-12-11
DESCRIPTION | 12 ++- MD5 | 19 +++-- NAMESPACE | 5 + NEWS.md | 6 + R/aaa.R | 7 + R/mock_request.R |only R/request.R | 105 ++++++++++++++++++----------- R/response.R | 51 +++++++------- man/maybe_request.Rd |only man/mock_request.Rd |only man/random_key.Rd | 2 tests/testthat/_snaps/request_unclassed.md |only tests/testthat/test-request_unclassed.R |only 13 files changed, 133 insertions(+), 74 deletions(-)
Title: Efficient Implementation of Kendall's Correlation Coefficient
Computation
Description: The computational complexity of the implemented algorithm for
Kendall's correlation is O(n log(n)), which is faster than the base R
implementation with a computational complexity of O(n^2). For small vectors
(i.e., less than 100 observations), the time difference is negligible.
However, for larger vectors, the speed difference can be substantial and the
numerical difference is minimal. The references are
Knight (1966) <doi:10.2307/2282833>,
Abrevaya (1999) <doi:10.1016/S0165-1765(98)00255-9>,
Christensen (2005) <doi:10.1007/BF02736122> and
Emara (2024) <https://learningcpp.org/>.
This implementation is described in
Vargas Sepulveda (2025) <doi:10.1371/journal.pone.0326090>.
Author: Mauricio Vargas Sepulveda [aut, cre] ,
Loader Catherine [ctb] ),
Ross Ihaka [ctb] )
Maintainer: Mauricio Vargas Sepulveda <m.vargas.sepulveda@gmail.com>
Diff between kendallknight versions 1.0.0 dated 2025-08-31 and 1.0.1 dated 2025-12-11
kendallknight-1.0.0/kendallknight/R/cpp11.R |only kendallknight-1.0.0/kendallknight/build/vignette.rds |only kendallknight-1.0.0/kendallknight/data |only kendallknight-1.0.0/kendallknight/inst/doc |only kendallknight-1.0.0/kendallknight/man/arcade.Rd |only kendallknight-1.0.0/kendallknight/src/cpp11.cpp |only kendallknight-1.0.0/kendallknight/vignettes |only kendallknight-1.0.1/kendallknight/DESCRIPTION | 12 - kendallknight-1.0.1/kendallknight/MD5 | 30 +-- kendallknight-1.0.1/kendallknight/NEWS.md | 4 kendallknight-1.0.1/kendallknight/R/cpp4r.R |only kendallknight-1.0.1/kendallknight/R/kendallknight-package.R | 20 -- kendallknight-1.0.1/kendallknight/README.md | 30 ++- kendallknight-1.0.1/kendallknight/build/partial.rdb |binary kendallknight-1.0.1/kendallknight/inst/CITATION |only kendallknight-1.0.1/kendallknight/inst/WORDLIST | 2 kendallknight-1.0.1/kendallknight/man/figures/logo.svg | 81 ++-------- kendallknight-1.0.1/kendallknight/man/kendallknight-package.Rd | 2 kendallknight-1.0.1/kendallknight/src/cpp4r.cpp |only kendallknight-1.0.1/kendallknight/src/kendall_correlation.cpp | 8 20 files changed, 70 insertions(+), 119 deletions(-)
Title: Datastore for 'fiery' Web Servers
Description: Provides a persistent datastore for 'fiery' apps. The datastore is
build on top of the 'storr' package and can thus be based on a variety of
backends. The datastore contains both a global and session-scoped section.
Author: Thomas Lin Pedersen [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between firesale versions 0.1.0 dated 2025-08-27 and 0.1.1 dated 2025-12-11
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/FireSale.R | 4 ++++ man/FireSale.Rd | 4 +++- man/firesale-package.Rd | 2 +- 6 files changed, 21 insertions(+), 11 deletions(-)
Title: Simplifies Exploratory Data Analysis
Description: Interactive data exploration with one line of code, automated
reporting or use an easy to remember set of tidy functions for low
code exploratory data analysis.
Author: Roland Krasser [aut, cre]
Maintainer: Roland Krasser <roland.krasser@gmail.com>
Diff between explore versions 1.3.6 dated 2025-10-02 and 1.4.0 dated 2025-12-11
DESCRIPTION | 8 +- MD5 | 82 ++++++++++++------------- NEWS.md | 6 + R/explain-xgboost.R | 130 ++++++++++++++++++++++++++++++++--------- R/explain.R | 25 ++++++- build/vignette.rds |binary inst/doc/abtest.html | 24 +++---- inst/doc/clean-drop.html | 6 - inst/doc/data.html | 6 - inst/doc/describe.html | 6 - inst/doc/explain.html | 52 ++++++++-------- inst/doc/explore-mtcars.html | 34 +++++----- inst/doc/explore-penguins.html | 14 ++-- inst/doc/explore-titanic.html | 24 +++---- inst/doc/explore.html | 58 +++++++++--------- inst/doc/predict.html | 10 +-- inst/doc/report-target.html | 12 +-- inst/doc/report-targetpct.html | 12 +-- inst/doc/report.html | 10 +-- inst/doc/tips-tricks.html | 16 ++--- man/check_vec_low_variance.Rd | 50 +++++++-------- man/create_data_abtest.Rd | 90 ++++++++++++++-------------- man/create_data_esoteric.Rd | 72 +++++++++++----------- man/create_notebook_explore.Rd | 2 man/cut_vec_num_avg.Rd | 38 +++++------ man/drop_obs_if.Rd | 46 +++++++------- man/drop_obs_with_na.Rd | 44 ++++++------- man/drop_var_by_names.Rd | 46 +++++++------- man/drop_var_low_variance.Rd | 46 +++++++------- man/drop_var_no_variance.Rd | 42 ++++++------- man/drop_var_not_numeric.Rd | 42 ++++++------- man/drop_var_with_na.Rd | 42 ++++++------- man/explain_forest.Rd | 2 man/explain_logreg.Rd | 2 man/explain_tree.Rd | 4 - man/explore_col.Rd | 106 ++++++++++++++++----------------- man/get_color.Rd | 72 +++++++++++----------- man/interact.Rd | 54 ++++++++--------- man/log_info_if.Rd | 38 +++++------ man/predict_target.Rd | 2 man/show_color.Rd | 42 ++++++------- man/use_data_wordle.Rd | 42 ++++++------- 42 files changed, 778 insertions(+), 681 deletions(-)
Title: Read bigWig and bigBed Files
Description: Read bigWig and bigBed files using "libBigWig"
<https://github.com/dpryan79/libBigWig>. Provides lightweight access
to the binary bigWig and bigBed formats developed by the UCSC Genome
Browser group.
Author: Jay Hesselberth [aut, cre],
RNA Bioscience Initiative [fnd, cph],
Devon Ryan [cph]
Maintainer: Jay Hesselberth <jay.hesselberth@gmail.com>
Diff between cpp11bigwig versions 0.1.2 dated 2025-08-18 and 0.1.3 dated 2025-12-11
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 4 R/read.r | 49 +----- README.md | 8 - man/read_bigbed.Rd | 10 - src/cpp11bigwig.cpp | 333 ++++++++++++++++++++++++++++++--------------- tests/testthat/test-read.R | 33 ++++ 8 files changed, 293 insertions(+), 164 deletions(-)
Title: Statistical Methods for Phenology Analysis in Temperate Fruit
Trees
Description: The phenology of plants (i.e. the timing of their annual life
phases) depends on climatic cues. For temperate trees and many other plants,
spring phases, such as leaf emergence and flowering, have been found to result
from the effects of both cool (chilling) conditions and heat. Fruit tree
scientists (pomologists) have developed some metrics to quantify chilling
and heat (e.g. see Luedeling (2012) <doi:10.1016/j.scienta.2012.07.011>).
'chillR' contains functions for processing temperature records into
chilling (Chilling Hours, Utah Chill Units and Chill Portions) and heat units
(Growing Degree Hours). Regarding chilling metrics, Chill Portions are often
considered the most promising, but they are difficult to calculate. This package
makes it easy. 'chillR' also contains procedures for conducting a PLS analysis
relating phenological dates (e.g. bloom dates) to either mean temperatures or
mean chill and heat accumulation rates, based on long-term weather and phenology
records (Lued [...truncated...]
Author: Eike Luedeling [aut, cre] ,
Lars Caspersen [aut] ,
Eduardo Fernandez [aut]
Maintainer: Eike Luedeling <eike@eikeluedeling.com>
Diff between chillR versions 0.76 dated 2024-11-14 and 0.77 dated 2025-12-11
DESCRIPTION | 28 +- MD5 | 40 ++- NAMESPACE | 4 R/Kendall.R |only R/chillR-package.R | 10 R/download_baseline_cmip6_ecmwfr.R | 101 +++++++-- R/download_cmip6_ecmwfr.R | 150 +++++++------- R/extract_cmip6_data.R | 69 ++++-- R/plot_phenology_trends.R | 8 R/plot_scenarios.R | 8 R/print.Kendall.R |only R/summary.Kendall.R |only build/partial.rdb |only build/vignette.rds |binary inst/doc/PhenoFlex.html | 208 +++++++++---------- inst/doc/hourly_temperatures.html | 9 man/chillR-package.Rd | 32 ++- man/download_baseline_cmip6_ecmwfr.Rd | 214 ++++++++++---------- man/download_cmip6_ecmwfr.Rd | 360 +++++++++++++++++----------------- man/plot_phenology_trends.Rd | 8 man/plot_scenarios.Rd | 8 src/Kendall.f |only src/RcppExports.cpp | 10 src/init.c |only 24 files changed, 684 insertions(+), 583 deletions(-)
Title: Bioinformatics Modeling with Recursion and Autoencoder-Based
Ensemble
Description: Tools for bioinformatics modeling using recursive transformer-inspired
architectures, autoencoders, random forests, XGBoost, and stacked ensemble models.
Includes utilities for cross-validation, calibration, benchmarking, and threshold
optimization in predictive modeling workflows. The methodology builds on ensemble
learning (Breiman 2001 <doi:10.1023/A:1010933404324>), gradient boosting (Chen and
Guestrin 2016 <doi:10.1145/2939672.2939785>), autoencoders (Hinton and Salakhutdinov
2006 <doi:10.1126/science.1127647>), and recursive transformer efficiency approaches
such as Mixture-of-Recursions (Bae et al. 2025 <doi:10.48550/arXiv.2507.10524>).
Author: MD. Arshad [aut, cre]
Maintainer: MD. Arshad <arshad10867c@gmail.com>
Diff between BioMoR versions 0.1.0 dated 2025-10-03 and 0.1.1 dated 2025-12-10
DESCRIPTION | 10 MD5 | 37 +- R/autoencoder.R | 4 R/train_biomor.R | 4 build/vignette.rds |binary inst/doc/biomor-autoencoder.R | 11 inst/doc/biomor-autoencoder.Rmd | 30 + inst/doc/biomor-autoencoder.html | 608 ++++++++++++++++------------------- inst/doc/biomor-benchmarking.R | 15 inst/doc/biomor-benchmarking.Rmd | 35 +- inst/doc/biomor-benchmarking.html | 654 +++++++++++++++++++------------------- inst/doc/biomor-intro.R | 14 inst/doc/biomor-intro.Rmd | 53 +-- inst/doc/biomor-intro.html | 59 +-- tests/testthat/test_benchmark.R | 4 tests/testthat/test_models.R | 11 tests/testthat/test_utils.R |only vignettes/biomor-autoencoder.Rmd | 30 + vignettes/biomor-benchmarking.Rmd | 35 +- vignettes/biomor-intro.Rmd | 53 +-- 20 files changed, 849 insertions(+), 818 deletions(-)
Title: Analysis of Moderation, Statistical Power, and Optimal Design
for Studies Detecting Difference and Equivalence
Description: Analysis of moderation (ANOMO) method conceptualizes
the difference and equivalence tests as a moderation problem to
test the difference and equivalence of
two estimates (e.g., two means or two effects).
Author: Zuchao Shen [aut, cre]
Maintainer: Zuchao Shen <zuchao.shen@gmail.com>
Diff between anomo versions 1.0.0 dated 2025-02-23 and 1.2.2 dated 2025-12-10
anomo-1.0.0/anomo/R/od.eq.2group.R |only anomo-1.0.0/anomo/R/power.eq.2group.R |only anomo-1.0.0/anomo/man/od.eq.2group.Rd |only anomo-1.0.0/anomo/man/power.eq.2group.Rd |only anomo-1.2.2/anomo/DESCRIPTION | 16 - anomo-1.2.2/anomo/MD5 | 32 +-- anomo-1.2.2/anomo/NAMESPACE | 5 anomo-1.2.2/anomo/R/mcci.R | 294 +++++++++++++++++++------------ anomo-1.2.2/anomo/R/od.1.eq.R |only anomo-1.2.2/anomo/R/plot.power.eq.R |only anomo-1.2.2/anomo/R/power.1.eq.R |only anomo-1.2.2/anomo/R/re.R | 8 anomo-1.2.2/anomo/build/vignette.rds |binary anomo-1.2.2/anomo/inst/doc/anomo.R | 46 +--- anomo-1.2.2/anomo/inst/doc/anomo.Rmd | 100 ++++------ anomo-1.2.2/anomo/inst/doc/anomo.html | 167 ++++++++--------- anomo-1.2.2/anomo/man/mcci.Rd | 80 +++++--- anomo-1.2.2/anomo/man/od.1.eq.Rd |only anomo-1.2.2/anomo/man/plot.power.eq.Rd |only anomo-1.2.2/anomo/man/power.1.eq.Rd |only anomo-1.2.2/anomo/man/re.Rd | 8 anomo-1.2.2/anomo/vignettes/anomo.Rmd | 100 ++++------ 22 files changed, 462 insertions(+), 394 deletions(-)
Title: Pull Spatial Layers from 'WDNR ArcGIS REST API'
Description: Functions for finding and pulling data from the
'Wisconsin Department of Natural Resources ArcGIS REST APIs'
<https://dnrmaps.wi.gov/arcgis/rest/services> and
<https://dnrmaps.wi.gov/arcgis2/rest/services>.
Author: Paul Frater [aut, cre] ,
Zac Driscoll [aut]
Maintainer: Paul Frater <paul.frater@wisconsin.gov>
Diff between wdnr.gis versions 0.1.6 dated 2025-10-13 and 0.1.7 dated 2025-12-10
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/wdnr.gis-package.R | 2 +- man/wdnr.gis-package.Rd | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-)
More information about spatialAtomizeR at CRAN
Permanent link
Title: Machine Coded Genetic Algorithms for Real-Valued Optimization
Problems
Description: Machine coded genetic algorithm (MCGA) is a fast tool for
real-valued optimization problems. It uses the byte
representation of variables rather than real-values. It
performs the classical crossover operations (uniform) on these
byte representations. Mutation operator is also similar to
classical mutation operator, which is to say, it changes a
randomly selected byte value of a chromosome by +1 or -1 with
probability 1/2. In MCGAs there is no need for
encoding-decoding process and the classical operators are
directly applicable on real-values. It is fast and can handle a
wide range of a search space with high precision. Using a
256-unary alphabet is the main disadvantage of this algorithm
but a moderate size population is convenient for many problems.
Package also includes multi_mcga function for multi objective
optimization problems. This function sorts the chromosomes
using their ranks calculated from the non-dominated sorting
algorithm.
Author: Mehmet Hakan Satman [aut, cre]
Maintainer: Mehmet Hakan Satman <mhsatman@istanbul.edu.tr>
Diff between mcga versions 3.0.7 dated 2023-11-27 and 3.0.9 dated 2025-12-10
DESCRIPTION | 14 +++++++++----- MD5 | 6 +++--- src/mcga.h | 2 +- src/multi_mcga.h | 2 +- 4 files changed, 14 insertions(+), 10 deletions(-)
Title: Parse Farm Credit Administration Call Report Data into Tidy Data
Frames
Description: Parses financial condition and performance data (Call Reports) for
institutions in the United States Farm Credit System. Contains functions for
downloading files from the Farm Credit Administration (FCA) Call Report
archive website and reading the files into tidy data frame format.
The archive website can be found at
<https://www.fca.gov/bank-oversight/call-report-data-for-download>.
Author: Michael Thomas [aut, cre],
Ivan Millanes [aut],
Ketchbrook Analytics [cph, fnd]
Maintainer: Michael Thomas <mthomas@ketchbrookanalytics.com>
Diff between fcall versions 0.1.5 dated 2025-11-19 and 0.1.6 dated 2025-12-10
DESCRIPTION | 6 +- MD5 | 10 +-- NEWS.md | 8 ++ R/download_data.R | 15 +++-- README.md | 152 ++++++++++++++++++++++++++------------------------- man/download_data.Rd | 7 +- 6 files changed, 111 insertions(+), 87 deletions(-)
Title: Network Scale-Up Models for Aggregated Relational Data
Description: Provides a variety of Network Scale-up Models for researchers to
analyze Aggregated Relational Data, through the use of Stan and 'glmmTMB'.
Also provides tools for model checking
In this version, the package implements models from
Laga, I., Bao, L., and Niu, X (2023) <doi:10.1080/01621459.2023.2165929>,
Zheng, T., Salganik, M. J., and Gelman, A. (2006) <doi:10.1198/016214505000001168>,
Killworth, P. D., Johnsen, E. C., McCarty, C., Shelley, G. A.,
and Bernard, H. R. (1998) <doi:10.1016/S0378-8733(96)00305-X>, and
Killworth, P. D., McCarty, C., Bernard, H. R., Shelley, G. A., and
Johnsen, E. C. (1998) <doi:10.1177/0193841X9802200205>.
Author: Ian Laga [aut, cre] ,
Owen G. Ward [aut],
Anna L. Smith [aut],
Benjamin Vogel [aut],
Jieyun Wang [aut],
Le Bao [aut],
Xiaoyue Niu [aut]
Maintainer: Ian Laga <ilaga25@gmail.com>
Diff between networkscaleup versions 0.1-2 dated 2024-02-25 and 0.2-1 dated 2025-12-10
networkscaleup-0.1-2/networkscaleup/man/networkscaleup-package.Rd |only networkscaleup-0.2-1/networkscaleup/DESCRIPTION | 41 networkscaleup-0.2-1/networkscaleup/MD5 | 192 ++- networkscaleup-0.2-1/networkscaleup/NAMESPACE | 14 networkscaleup-0.2-1/networkscaleup/R/aux_functions.R |only networkscaleup-0.2-1/networkscaleup/R/corr_perms.R |only networkscaleup-0.2-1/networkscaleup/R/correlatedStan.R | 255 ++--- networkscaleup-0.2-1/networkscaleup/R/cov_plots.R |only networkscaleup-0.2-1/networkscaleup/R/fit_ard.R |only networkscaleup-0.2-1/networkscaleup/R/killworth.R | 78 - networkscaleup-0.2-1/networkscaleup/R/make_ard.R |only networkscaleup-0.2-1/networkscaleup/R/networkscaleup-package.R | 3 networkscaleup-0.2-1/networkscaleup/R/overdispersed.R | 267 ++--- networkscaleup-0.2-1/networkscaleup/R/overdispersedStan.R | 135 +- networkscaleup-0.2-1/networkscaleup/R/plot_fitted.R |only networkscaleup-0.2-1/networkscaleup/R/rootogram.R |only networkscaleup-0.2-1/networkscaleup/R/scaling.R | 98 - networkscaleup-0.2-1/networkscaleup/R/surrogate.R |only networkscaleup-0.2-1/networkscaleup/README.md |only networkscaleup-0.2-1/networkscaleup/build/vignette.rds |binary networkscaleup-0.2-1/networkscaleup/inst/doc/ARD-Diagnostics.R |only networkscaleup-0.2-1/networkscaleup/inst/doc/ARD-Diagnostics.Rmd |only networkscaleup-0.2-1/networkscaleup/inst/doc/ARD-Diagnostics.html |only networkscaleup-0.2-1/networkscaleup/inst/doc/FittingNetworkScaleup.R | 91 - networkscaleup-0.2-1/networkscaleup/inst/doc/FittingNetworkScaleup.Rmd | 108 +- networkscaleup-0.2-1/networkscaleup/inst/doc/FittingNetworkScaleup.html | 505 +++++----- networkscaleup-0.2-1/networkscaleup/inst/inst |only networkscaleup-0.2-1/networkscaleup/inst/stan/Correlated_basic.stan | 100 - networkscaleup-0.2-1/networkscaleup/inst/stan/Correlated_x.stan | 106 +- networkscaleup-0.2-1/networkscaleup/inst/stan/Correlated_x_zglobal.stan | 114 +- networkscaleup-0.2-1/networkscaleup/inst/stan/Correlated_x_zsubpop.stan | 114 +- networkscaleup-0.2-1/networkscaleup/inst/stan/Correlated_x_zsubpop_zglobal.stan | 122 +- networkscaleup-0.2-1/networkscaleup/inst/stan/Correlated_zglobal.stan | 108 +- networkscaleup-0.2-1/networkscaleup/inst/stan/Correlated_zsubpop.stan | 108 +- networkscaleup-0.2-1/networkscaleup/inst/stan/Correlated_zsubpop_zglobal.stan | 116 +- networkscaleup-0.2-1/networkscaleup/inst/stan/Overdispersed_Stan.stan | 86 - networkscaleup-0.2-1/networkscaleup/inst/stan/Uncorrelated_basic.stan | 88 - networkscaleup-0.2-1/networkscaleup/inst/stan/Uncorrelated_x.stan | 96 - networkscaleup-0.2-1/networkscaleup/inst/stan/Uncorrelated_x_zglobal.stan | 104 +- networkscaleup-0.2-1/networkscaleup/inst/stan/Uncorrelated_x_zsubpop.stan | 106 +- networkscaleup-0.2-1/networkscaleup/inst/stan/Uncorrelated_x_zsubpop_zglobal.stan | 110 +- networkscaleup-0.2-1/networkscaleup/inst/stan/Uncorrelated_zglobal.stan | 98 - networkscaleup-0.2-1/networkscaleup/inst/stan/Uncorrelated_zsubpop.stan | 96 - networkscaleup-0.2-1/networkscaleup/inst/stan/Uncorrelated_zsubpop_zglobal.stan | 102 +- networkscaleup-0.2-1/networkscaleup/man/construct_pearson.Rd |only networkscaleup-0.2-1/networkscaleup/man/construct_rqr.Rd |only networkscaleup-0.2-1/networkscaleup/man/correlatedStan.Rd | 95 - networkscaleup-0.2-1/networkscaleup/man/cov_plots.Rd |only networkscaleup-0.2-1/networkscaleup/man/dispersion_metric.Rd |only networkscaleup-0.2-1/networkscaleup/man/figures |only networkscaleup-0.2-1/networkscaleup/man/fit_mle.Rd |only networkscaleup-0.2-1/networkscaleup/man/get_surrogate.Rd |only networkscaleup-0.2-1/networkscaleup/man/hang_rootogram_ard.Rd |only networkscaleup-0.2-1/networkscaleup/man/killworth.Rd | 32 networkscaleup-0.2-1/networkscaleup/man/log_mix_uniform.Rd |only networkscaleup-0.2-1/networkscaleup/man/make_ard.Rd |only networkscaleup-0.2-1/networkscaleup/man/make_ard_tidy.Rd |only networkscaleup-0.2-1/networkscaleup/man/networkscaleup.Rd |only networkscaleup-0.2-1/networkscaleup/man/overdispersed.Rd | 33 networkscaleup-0.2-1/networkscaleup/man/overdispersedStan.Rd | 37 networkscaleup-0.2-1/networkscaleup/man/plot_fitted.Rd |only networkscaleup-0.2-1/networkscaleup/man/residual_correlation.Rd |only networkscaleup-0.2-1/networkscaleup/man/residual_heatmap.Rd |only networkscaleup-0.2-1/networkscaleup/man/rqr_nbinom_logs.Rd |only networkscaleup-0.2-1/networkscaleup/man/rqr_pois_logs.Rd |only networkscaleup-0.2-1/networkscaleup/man/tw_group_corr_test.Rd |only networkscaleup-0.2-1/networkscaleup/src/Makevars.win | 5 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_basic.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_basic.h | 36 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_x.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_x.h | 40 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_x_zglobal.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_x_zglobal.h | 42 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_x_zsubpop.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_x_zsubpop.h | 42 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_x_zsubpop_zglobal.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_x_zsubpop_zglobal.h | 44 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_zglobal.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_zglobal.h | 40 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_zsubpop.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_zsubpop.h | 40 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_zsubpop_zglobal.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_zsubpop_zglobal.h | 42 networkscaleup-0.2-1/networkscaleup/src/stanExports_Overdispersed_Stan.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Overdispersed_Stan.h | 32 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_basic.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_basic.h | 30 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_x.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_x.h | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_x_zglobal.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_x_zglobal.h | 36 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_x_zsubpop.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_x_zsubpop.h | 36 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_x_zsubpop_zglobal.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_x_zsubpop_zglobal.h | 38 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_zglobal.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_zglobal.h | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_zsubpop.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_zsubpop.h | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_zsubpop_zglobal.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Uncorrelated_zsubpop_zglobal.h | 36 networkscaleup-0.2-1/networkscaleup/vignettes/ARD-Diagnostics.Rmd |only networkscaleup-0.2-1/networkscaleup/vignettes/FittingNetworkScaleup.Rmd | 108 +- 103 files changed, 2607 insertions(+), 2478 deletions(-)
More information about networkscaleup at CRAN
Permanent link
Title: Likelihood Based Inference for ARIMA Modeling
Description: Estimating and analyzing auto regressive integrated moving average
(ARIMA) models. The primary function in this package is arima(), which fits
an ARIMA model to univariate time series data using a random restart
algorithm. This approach frequently leads to models that have model
likelihood greater than or equal to that of the likelihood obtained by
fitting the same model using the arima() function from the 'stats' package.
This package enables proper optimization of model likelihoods, which is a
necessary condition for performing likelihood ratio tests. This package
relies heavily on the source code of the arima() function of the 'stats'
package. For more information, please see Jesse Wheeler and Edward L.
Ionides (2025) <doi:10.1371/journal.pone.0333993>.
Author: Jesse Wheeler [aut, cre, cph],
Noel McAllister [aut],
Dhajanae Sylvertooth [aut],
Edward Ionides [ctb],
Brian Ripley [ctb] ,
R Core Team [cph]
Maintainer: Jesse Wheeler <jessewheeler@isu.edu>
Diff between arima2 versions 3.4.2 dated 2025-10-31 and 3.4.3 dated 2025-12-10
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 5 +++++ README.md | 4 ++-- man/figures/README-PlotARMAresults-1.png |binary man/figures/README-PlotARMAresults-2.png |binary 6 files changed, 17 insertions(+), 12 deletions(-)
Title: Data Validation Infrastructure
Description: Declare data validation rules and data quality indicators;
confront data with them and analyze or visualize the results.
The package supports rules that are per-field, in-record,
cross-record or cross-dataset. Rules can be automatically
analyzed for rule type and connectivity. Supports checks implied
by an SDMX DSD file as well. See also Van der Loo
and De Jonge (2018) <doi:10.1002/9781118897126>, Chapter 6
and the JSS paper (2021) <doi:10.18637/jss.v097.i10>.
Author: Mark van der Loo [cre, aut] ,
Edwin de Jonge [aut] ,
Paul Hsieh [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between validate versions 1.1.6 dated 2025-11-14 and 1.1.7 dated 2025-12-10
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS | 7 +++++++ R/compare.R | 4 ++-- inst/doc/JSS_3483.pdf |binary inst/doc/cookbook.Rmd | 4 +--- inst/doc/cookbook.html | 38 ++++++++++++++++++-------------------- inst/tinytest/test_validator.R | 6 +++--- man/cells.Rd | 2 +- man/compare.Rd | 2 +- vignettes/cookbook.Rmd | 4 +--- 11 files changed, 47 insertions(+), 46 deletions(-)
Title: Methods and Classes for the OMOP Common Data Model
Description: Provides definitions of core classes and methods used by analytic
pipelines that query the OMOP (Observational Medical Outcomes Partnership)
common data model.
Author: Marti Catala [aut, cre] ,
Edward Burn [aut] ,
Mike Du [ctb] ,
Yuchen Guo [ctb] ,
Adam Black [ctb] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between omopgenerics versions 1.3.4 dated 2025-12-01 and 1.3.5 dated 2025-12-10
DESCRIPTION | 6 MD5 | 24 NEWS.md | 6 R/classCdmTable.R | 14 R/classCodelist.R | 83 ++- R/classCodelistWithDetails.R | 39 - R/classConceptSetExpression.R | 42 - R/compute.R | 114 ---- R/logger.R | 124 +++++ inst/doc/logging.html | 44 - inst/doc/summarised_result.html | 886 ++++++++++++++++++------------------ tests/testthat/test-classCodelist.R | 3 tests/testthat/test-logger.R | 3 13 files changed, 729 insertions(+), 659 deletions(-)
Title: Double Machine Learning for Static Panel Models with Fixed
Effects
Description: The 'xtdml' package implements partially linear panel regression (PLPR) models with high-dimensional confounding variables and an exogenous treatment variable within the double machine learning framework. The package is used to estimate the structural parameter (treatment effect) in static panel data models with fixed effects using the approaches established in Clarke and Polselli (2025) <doi:10.1093/ectj/utaf011>. 'xtdml' is built on the object-oriented package 'DoubleML' (Bach et al., 2024) <doi:10.18637/jss.v108.i03> using the 'mlr3' ecosystem.
Author: Annalivia Polselli [aut, cre]
Maintainer: Annalivia Polselli <apolselli.econ@gmail.com>
Diff between xtdml versions 0.1.9 dated 2025-11-12 and 0.1.10 dated 2025-12-10
DESCRIPTION | 10 +- MD5 | 26 ++--- NAMESPACE | 3 R/dataset.R | 5 - R/helper.R | 2 R/xtdml_data.R | 36 ++++--- R/xtdml_main.R | 183 +++++++++++++++++++++----------------- R/xtdml_plr.R | 20 +--- R/zzz.R | 39 ++++---- man/make_plpr_data.Rd | 4 man/xtdml.Rd | 82 ++++++++--------- man/xtdml_data.Rd | 32 ++++-- man/xtdml_data_from_data_frame.Rd | 8 - man/xtdml_plr.Rd | 21 ++-- 14 files changed, 249 insertions(+), 222 deletions(-)
Title: Integrative Analysis of Several Related Data Matrices
Description: A generalization of principal component analysis for integrative
analysis. The method finds principal components that describe single matrices
or that are common to several matrices. The solutions are sparse. Rank of
solutions is automatically selected using cross validation. The method is
described in Kallus et al. (2019) <doi:10.48550/arXiv.1911.04927>.
Author: Jonatan Kallus [aut],
Felix Held [ctb, cre]
Maintainer: Felix Held <felix.held@gmail.com>
Diff between mmpca versions 2.0.3 dated 2022-11-15 and 2.0.4 dated 2025-12-10
DESCRIPTION | 17 ++++++++--------- MD5 | 15 ++++++++------- NEWS.md | 6 +++++- README.md | 2 +- src/Makevars.in | 2 -- src/compile_commands.json |only src/fdf.cpp | 6 +++--- src/fdf.h | 8 ++++++++ src/optim.cpp | 1 + 9 files changed, 34 insertions(+), 23 deletions(-)
Title: Multilevel Latent Time Series Models with 'R' and 'Stan'
Description: Fit multilevel manifest or latent time-series models, including popular Dynamic Structural Equation Models (DSEM).
The models can be set up and modified with user-friendly functions and are fit to the data using 'Stan' for Bayesian inference.
Path models and formulas for user-defined models can be easily created with functions using 'knitr'.
Asparouhov, Hamaker, & Muthen (2018) <doi:10.1080/10705511.2017.1406803>.
Author: Kenneth Koslowski [aut, cre, cph] ,
Fabian Muench [aut] ,
Tobias Koch [aut] ,
Jana Holtmann [aut]
Maintainer: Kenneth Koslowski <kenneth.koslowski@uni-leipzig.de>
Diff between mlts versions 2.0.0 dated 2025-12-08 and 2.0.1 dated 2025-12-10
DESCRIPTION | 6 MD5 | 12 NEWS.md | 7 R/mlts_paths.R | 1630 +++++++++++++++++++++++----------------------- R/mlts_sim.R | 978 +++++++++++++-------------- R/mlts_standardized_btw.R | 685 +++++++++---------- R/prepare_data.R | 466 ++++++------- 7 files changed, 1911 insertions(+), 1873 deletions(-)
Title: Easily Convert GDP Data
Description: Convert GDP time series data from one unit to
another. All common GDP units are included, i.e. current and constant
local currency units, US$ via market exchange rates and international
dollars via purchasing power parities.
Author: Johannes Koch [aut, cre]
Maintainer: Johannes Koch <jokoch@pik-potsdam.de>
Diff between GDPuc versions 1.6.0 dated 2025-11-19 and 1.6.1 dated 2025-12-10
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ R/transform_user_input.R | 2 +- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Vectors Representing Random Variables
Description: Random vectors, called rvecs. An rvec holds
multiple draws, but tries to behave like a standard
R vector, including working well in data frames.
Rvecs are useful for analysing
output from a simulation or a Bayesian analysis.
Author: John Bryant [aut, cre],
Bayesian Demography Limited [cph]
Maintainer: John Bryant <john@bayesiandemography.com>
Diff between rvec versions 0.0.8 dated 2025-07-12 and 1.0.0 dated 2025-12-10
rvec-0.0.8/rvec/man/new_rvec.Rd |only rvec-0.0.8/rvec/tests/testthat/_snaps/plot |only rvec-1.0.0/rvec/DESCRIPTION | 15 rvec-1.0.0/rvec/MD5 | 142 +++--- rvec-1.0.0/rvec/NAMESPACE | 19 rvec-1.0.0/rvec/NEWS.md | 25 + rvec-1.0.0/rvec/R/aaa-rvec-classes.R |only rvec-1.0.0/rvec/R/as_list_col.R | 25 - rvec-1.0.0/rvec/R/atomic_to_rvec.R | 26 - rvec-1.0.0/rvec/R/check-functions.R | 75 +++ rvec-1.0.0/rvec/R/collapse_to_rvec.R | 25 - rvec-1.0.0/rvec/R/compare.R | 2 rvec-1.0.0/rvec/R/constructors.R | 145 +++++- rvec-1.0.0/rvec/R/distributions.R | 312 ++++--------- rvec-1.0.0/rvec/R/draws.R | 419 +++++++++++------ rvec-1.0.0/rvec/R/format.R | 48 +- rvec-1.0.0/rvec/R/if_else_rvec.R | 4 rvec-1.0.0/rvec/R/map_rvec.R | 4 rvec-1.0.0/rvec/R/matrixOps.R | 109 +--- rvec-1.0.0/rvec/R/missing.R | 30 - rvec-1.0.0/rvec/R/pool_draws.R |only rvec-1.0.0/rvec/R/rvec-package.R | 34 - rvec-1.0.0/rvec/R/rvec_to_rvec.R | 20 rvec-1.0.0/rvec/R/util.R | 8 rvec-1.0.0/rvec/R/vec_math.R | 6 rvec-1.0.0/rvec/README.md | 11 rvec-1.0.0/rvec/build/vignette.rds |binary rvec-1.0.0/rvec/inst/doc/vig1_overview.R | 21 rvec-1.0.0/rvec/inst/doc/vig1_overview.Rmd | 78 ++- rvec-1.0.0/rvec/inst/doc/vig1_overview.html | 104 ++-- rvec-1.0.0/rvec/man/as_list_col.Rd | 13 rvec-1.0.0/rvec/man/collapse_to_rvec.Rd | 25 - rvec-1.0.0/rvec/man/dbeta_rvec.Rd | 14 rvec-1.0.0/rvec/man/dbinom_rvec.Rd | 26 - rvec-1.0.0/rvec/man/dcauchy_rvec.Rd | 17 rvec-1.0.0/rvec/man/dchisq_rvec.Rd | 14 rvec-1.0.0/rvec/man/dexp_rvec.Rd | 14 rvec-1.0.0/rvec/man/df_rvec.Rd | 11 rvec-1.0.0/rvec/man/dgamma_rvec.Rd | 16 rvec-1.0.0/rvec/man/dgeom_rvec.Rd | 23 rvec-1.0.0/rvec/man/dhyper_rvec.Rd | 22 rvec-1.0.0/rvec/man/dlnorm_rvec.Rd | 16 rvec-1.0.0/rvec/man/dmultinom_rvec.Rd | 23 rvec-1.0.0/rvec/man/dnbinom_rvec.Rd | 28 - rvec-1.0.0/rvec/man/dnorm_rvec.Rd | 16 rvec-1.0.0/rvec/man/dpois_rvec.Rd | 24 - rvec-1.0.0/rvec/man/draws_all.Rd | 9 rvec-1.0.0/rvec/man/draws_ci.Rd | 11 rvec-1.0.0/rvec/man/draws_fun.Rd | 7 rvec-1.0.0/rvec/man/draws_median.Rd | 14 rvec-1.0.0/rvec/man/draws_min.Rd | 9 rvec-1.0.0/rvec/man/draws_quantile.Rd | 13 rvec-1.0.0/rvec/man/draws_sd.Rd |only rvec-1.0.0/rvec/man/dt_rvec.Rd | 14 rvec-1.0.0/rvec/man/dunif_rvec.Rd | 14 rvec-1.0.0/rvec/man/dweibull_rvec.Rd | 14 rvec-1.0.0/rvec/man/figures |only rvec-1.0.0/rvec/man/if_else_rvec.Rd | 4 rvec-1.0.0/rvec/man/map_rvec.Rd | 4 rvec-1.0.0/rvec/man/missing.Rd | 30 - rvec-1.0.0/rvec/man/new_rvec_blank.Rd |only rvec-1.0.0/rvec/man/new_rvec_deprecated.Rd |only rvec-1.0.0/rvec/man/pool_draws.Rd |only rvec-1.0.0/rvec/man/rvec-matrix-mult.Rd |only rvec-1.0.0/rvec/man/rvec-package.Rd | 25 - rvec-1.0.0/rvec/tests/testthat/test-check-functions.R | 48 ++ rvec-1.0.0/rvec/tests/testthat/test-constructors.R | 423 ++++++++++-------- rvec-1.0.0/rvec/tests/testthat/test-draws.R | 145 ++++++ rvec-1.0.0/rvec/tests/testthat/test-format.R | 2 rvec-1.0.0/rvec/tests/testthat/test-matrixOps.R | 130 +++++ rvec-1.0.0/rvec/tests/testthat/test-pool_draws.R |only rvec-1.0.0/rvec/tests/testthat/test-util.R | 8 rvec-1.0.0/rvec/vignettes/vig1_overview.Rmd | 78 ++- 73 files changed, 1824 insertions(+), 1187 deletions(-)
Title: J&J Innovative Medicine ADaM Test Data
Description: A set of Analysis Data Model (ADaM) datasets constructed by
modifying the ADaM datasets in the 'pharmaverseadam' package to meet J&J Innovative Medicine's
standard data structure for Clinical and Statistical Programming.
Author: David Munoz Tord [aut, cre],
Nicholas Masel [aut],
Joe Kovach [aut],
Mahesh Divakaran [ctb],
J&J Innovative Medicine [cph, fnd]
Maintainer: David Munoz Tord <david.munoztord@mailbox.org>
Diff between pharmaverseadamjnj versions 0.0.1 dated 2025-07-15 and 0.0.2 dated 2025-12-10
pharmaverseadamjnj-0.0.1/pharmaverseadamjnj/R/adaefmq.R |only pharmaverseadamjnj-0.0.1/pharmaverseadamjnj/data/adaefmq.rda |only pharmaverseadamjnj-0.0.1/pharmaverseadamjnj/man/adaefmq.Rd |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/DESCRIPTION | 10 - pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/MD5 | 73 +++++----- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/NEWS.md | 31 +--- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adae.R | 19 +- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adaeocmq.R |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adagocmq.R |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adcm.R | 7 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adeg.R | 7 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adex.R | 16 +- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adexsum.R | 4 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adlb.R | 19 +- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adpc.R |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adsl.R | 18 +- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adttesaf.R | 4 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/advs.R | 4 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/README.md | 28 +++ pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adae.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adaeocmq.rda |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adagocmq.rda |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adcm.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adeg.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adex.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adexsum.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adlb.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adpc.rda |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adsl.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adttesaf.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/advs.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/inst |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adae.Rd | 17 +- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adaeocmq.Rd |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adagocmq.Rd |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adcm.Rd | 5 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adeg.Rd | 5 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adex.Rd | 14 - pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adexsum.Rd | 2 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adlb.Rd | 17 +- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adpc.Rd |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adsl.Rd | 16 +- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adttesaf.Rd | 2 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/advs.Rd | 2 44 files changed, 179 insertions(+), 141 deletions(-)
More information about pharmaverseadamjnj at CRAN
Permanent link
Title: Download Radar Data for Biological Research
Description: Load polar volume and vertical profile data for
aeroecological research directly into R. With 'getRad' you can access
data from several sources in Europe and the US and standardize it to
facilitate further exploration in tools such as 'bioRad'.
Author: Bart Kranstauber [aut, cre] ,
Pieter Huybrechts [aut] ),
Peter Desmet [aut] ),
Cecilia Nilsson [ctb] ,
Alexander Tedeschi [ctb] ,
Hidde Leijnse [ctb] ,
Bart Hoekstra [ctb] ,
University of Amsterdam [cph] ,
Biodiversa+ [fnd]
Maintainer: Bart Kranstauber <b.kranstauber@uva.nl>
Diff between getRad versions 0.2.3 dated 2025-10-14 and 0.2.4 dated 2025-12-10
DESCRIPTION | 6 +- MD5 | 70 +++++++++++++++--------------- NEWS.md | 8 +++ R/get_pvol.R | 21 ++++----- R/get_pvol_de.R | 9 ++- R/get_pvol_dk.R | 3 - R/get_pvol_ee.R | 8 +-- R/get_pvol_nl.R | 71 +++++++++++++++++++++---------- R/get_pvol_se.R | 7 +-- R/get_pvol_us.R | 8 +-- R/get_vpts.R | 32 +++++-------- R/get_vpts_aloft.R | 11 ++-- R/get_vpts_coverage.R | 2 R/get_vpts_coverage_rmi.R | 8 +-- R/get_weather_radars.R | 33 ++++++++------ R/secrets.R | 16 ++---- R/utils.R | 43 +++++++++++------- R/utils_pvol.R | 2 README.md | 1 inst/doc/supported_sources.R | 2 inst/doc/supported_sources.Rmd | 2 inst/doc/supported_sources.html | 4 - man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/figures/README-example-3.png |binary man/figures/README-example-4.png |binary man/figures/README-vpts-1.png |binary man/get_weather_radars.Rd | 4 - tests/testthat/test-get_pvol.R | 6 +- tests/testthat/test-get_pvol_dk.R | 5 -- tests/testthat/test-get_pvol_nl.R | 57 +++++++++++++++++++----- tests/testthat/test-get_pvol_ro.R | 7 +-- tests/testthat/test-get_vpts_aloft.R | 29 +++++------- tests/testthat/test-get_weather_radars.R | 4 - tests/testthat/test-secrets.R | 8 +-- vignettes/supported_sources.Rmd | 2 36 files changed, 276 insertions(+), 213 deletions(-)
Title: Fit Multivariate Diversity-Interactions Models with Repeated
Measures
Description: An add-on package to 'DImodels' for the fitting of biodiversity and ecosystem function relationship study data with multiple ecosystem function responses and/or time points. This package uses the multivariate and repeated measures Diversity-Interactions (DI) methods developed by Kirwan et al. (2009) <doi:10.1890/08-1684.1>, Finn et al. (2013) <doi:10.1111/1365-2664.12041>, and Dooley et al. (2015) <doi:10.1111/ele.12504>.
Author: Laura Byrne [aut, cre] ,
Rishabh Vishwakarma [aut],
Rafael de Andrade Moral [aut],
Caroline Brophy [aut]
Maintainer: Laura Byrne <Laura.Byrne.Work@outlook.com>
Diff between DImodelsMulti versions 1.2.0 dated 2025-08-21 and 1.2.1 dated 2025-12-10
DESCRIPTION | 15 +- MD5 | 39 +++-- NAMESPACE | 1 R/DImodelsMulti_HelpFile.R | 6 R/DImulti_fit.R | 20 ++ R/DImulti_predict.R | 28 +++- R/DImulti_runApp.R |only README.md | 52 +++---- build/vignette.rds |binary inst/doc/DImulti_commonErrors.html | 5 inst/doc/DImulti_onTheta.html | 5 inst/doc/DImulti_prediction.html | 5 inst/doc/DImulti_workflow.Rmd | 3 inst/doc/DImulti_workflow.html | 12 + inst/shiny |only man/Belgium.Rd | 164 ++++++++++++------------ man/Belgium_MV.Rd | 252 ++++++++++++++++++------------------- man/Belgium_RM.Rd | 232 +++++++++++++++++----------------- man/DImodelsMulti.Rd | 6 man/DImulti.Rd | 6 man/DImultiApp.Rd |only vignettes/DImulti_workflow.Rmd | 3 22 files changed, 454 insertions(+), 400 deletions(-)
Title: Covariate-Based Covariance Functions for Nonstationary Spatial
Modeling
Description: Estimation, prediction, and simulation of nonstationary Gaussian process with modular covariate-based covariance functions.
Sources of nonstationarity, such as spatial mean, variance, geometric anisotropy, smoothness, and nugget, can be considered based on spatial characteristics.
An induced compact-supported nonstationary covariance function is provided, enabling fast and memory-efficient computations when handling densely sampled domains.
Author: Federico Blasi [aut, cre] ,
Reinhard Furrer [ctb]
Maintainer: Federico Blasi <federicoblasi@gmail.com>
Diff between cocons versions 0.1.4 dated 2024-12-12 and 0.1.5 dated 2025-12-10
DESCRIPTION | 15 - MD5 | 45 ++--- NEWS.md | 7 R/RcppExports.R | 10 + R/checkFunctions.R | 143 ++++++++++++++++- R/cocons.R | 21 ++ R/getFunctions.R | 103 ++++++++++-- R/methods.R | 62 +++++++ R/neg2loglikelihood.R | 10 - R/optim.R | 262 +++++++++++++++++++++++++++++--- R/profile.R | 5 inst/doc/cocons.pdf |binary man/GetNeg2loglikelihood.Rd | 2 man/GetNeg2loglikelihoodProfile.Rd | 2 man/GetNeg2loglikelihoodREML.Rd | 2 man/GetNeg2loglikelihoodTaper.Rd | 2 man/GetNeg2loglikelihoodTaperProfile.Rd | 2 man/coco.Rd | 5 man/cocoOptim.Rd | 15 - man/getBoundariesV4.Rd |only man/show-methods.Rd |only man/sumsmoothlone.Rd |only src/RcppExports.cpp | 14 + src/cocons_full.cpp | 96 +++++++++-- src/cocons_taper.cpp | 34 +++- 25 files changed, 743 insertions(+), 114 deletions(-)
Title: Text Mining Package
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut] ,
Kurt Hornik [aut, cre] ,
Artifex Software, Inc. [ctb, cph]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between tm versions 0.7-16 dated 2025-02-19 and 0.7-17 dated 2025-12-10
DESCRIPTION | 12 +++++------ MD5 | 50 +++++++++++++++++++++++------------------------ build/partial.rdb |binary build/vignette.rds |binary data/acq.rda |binary data/crude.rda |binary inst/doc/extensions.pdf |binary inst/doc/tm.pdf |binary man/Corpus.Rd | 2 - man/PCorpus.Rd | 4 +-- man/PlainTextDocument.Rd | 4 +-- man/SimpleCorpus.Rd | 2 - man/TextDocument.Rd | 2 - man/XMLSource.Rd | 2 - man/XMLTextDocument.Rd | 4 +-- man/foreign.Rd | 2 - man/matrix.Rd | 6 ++--- man/meta.Rd | 2 - man/plot.Rd | 3 +- man/readDOC.Rd | 2 - man/readPDF.Rd | 4 +-- man/readXML.Rd | 2 - man/removeWords.Rd | 2 - man/stemDocument.Rd | 1 man/termFreq.Rd | 2 - man/tokenizer.Rd | 8 +++---- 26 files changed, 59 insertions(+), 57 deletions(-)
Title: Store and Retrieve Data.frames in a Git Repository
Description: The git2rdata package is an R package for writing and reading
dataframes as plain text files. A metadata file stores important
information. 1) Storing metadata allows to maintain the classes of
variables. By default, git2rdata optimizes the data for file storage.
The optimization is most effective on data containing factors. The
optimization makes the data less human readable. The user can turn
this off when they prefer a human readable format over smaller files.
Details on the implementation are available in vignette("plain_text",
package = "git2rdata"). 2) Storing metadata also allows smaller row
based diffs between two consecutive commits. This is a useful feature
when storing data as plain text files under version control. Details
on this part of the implementation are available in
vignette("version_control", package = "git2rdata"). Although we
envisioned git2rdata with a git workflow in mind, you can use it in
combination with other version control systems like subversion [...truncated...]
Author: Thierry Onkelinx [aut, cre] ),
Floris Vanderhaeghe [ctb] ),
Peter Desmet [ctb] ),
Els Lommelen [ctb] ),
Research Institute for Nature and Forest [cph, fnd]
Maintainer: Thierry Onkelinx <thierry.onkelinx@inbo.be>
Diff between git2rdata versions 0.5.0 dated 2025-01-24 and 0.5.1 dated 2025-12-10
DESCRIPTION | 32 - MD5 | 133 +++---- NAMESPACE | 5 NEWS.md | 7 R/clean_data_path.R | 3 R/data_package.R | 47 +- R/datahash.R | 54 ++ R/is_git2rdata.R | 52 ++ R/is_git2rmeta.R | 57 ++- R/list_data.R | 46 +- R/meta.R | 350 ++++++++++++------ R/prune.R | 141 +++++-- R/read_vc.R | 146 +++---- R/recent_commit.R | 60 +-- R/reinstate.R |only R/relabel.R | 17 R/rename_variable.R | 24 - R/update_metadata.R | 54 ++ R/upgrade_data.R | 77 +++- R/verify_vc.R | 5 R/write_vc.R | 188 +++++++--- README.md | 62 ++- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 6 inst/Dockerfile |only inst/Rprofile.site |only inst/doc/efficiency.R | 25 - inst/doc/efficiency.Rmd | 25 - inst/doc/efficiency.html | 83 ++-- inst/doc/metadata.R | 9 inst/doc/metadata.Rmd | 9 inst/doc/metadata.html | 59 +-- inst/doc/plain_text.html | 75 ++-- inst/doc/split_by.html | 9 inst/doc/version_control.html | 85 ++-- inst/doc/workflow.R | 36 - inst/doc/workflow.Rmd | 42 +- inst/doc/workflow.html | 186 +++++---- man/git2rdata-package.Rd | 2 man/is_git2rdata.Rd | 4 man/is_git2rmeta.Rd | 4 man/list_data.Rd | 9 man/prune_meta.Rd | 9 man/read_vc.Rd | 13 man/recent_commit.Rd | 14 man/rm_data.Rd | 9 man/write_vc.Rd | 13 tests/testthat/setup_test_data.R | 27 + tests/testthat/test_a_basics.R | 372 +++++++++++++++++-- tests/testthat/test_b_is_git2rmeta.R | 157 +++++--- tests/testthat/test_b_prune.R | 56 ++ tests/testthat/test_b_special.R | 66 ++- tests/testthat/test_b_update.R | 18 tests/testthat/test_b_verify_vc.R | 9 tests/testthat/test_c_git.R | 561 +++++++++++++++++------------- tests/testthat/test_d_description.R | 52 +- tests/testthat/test_d_recent_commit.R | 167 ++++---- tests/testthat/test_d_relabel.R | 48 +- tests/testthat/test_e_data_package.R | 56 ++ tests/testthat/test_e_empty_label.R | 5 tests/testthat/test_e_non_ascii.R | 21 - tests/testthat/test_e_upgrade.R | 21 - tests/testthat/test_e_validate_metadata.R | 30 + tests/testthat/test_f_split_by.R | 55 ++ tests/testthat/test_g_rename_variable.R | 52 ++ vignettes/efficiency.Rmd | 25 - vignettes/metadata.Rmd | 9 vignettes/workflow.Rmd | 42 +- 69 files changed, 2673 insertions(+), 1462 deletions(-)
Title: Parse 'Tableau' Workbooks into Functional Data
Description: High-performance parsing of 'Tableau' workbook files into
tidy data frames and dependency graphs for other visualization tools
like R 'Shiny' or 'Power BI' replication.
Author: George Arthur [aut, cre]
Maintainer: George Arthur <prigasgenthian48@gmail.com>
Diff between twbparser versions 0.2.3 dated 2025-09-30 and 0.3.1 dated 2025-12-10
twbparser-0.2.3/twbparser/inst/extdata/test-for_zip.twbx |only twbparser-0.3.1/twbparser/DESCRIPTION | 6 twbparser-0.3.1/twbparser/MD5 | 52 - twbparser-0.3.1/twbparser/NAMESPACE | 14 twbparser-0.3.1/twbparser/NEWS.md | 70 - twbparser-0.3.1/twbparser/R/active-bindings.R |only twbparser-0.3.1/twbparser/R/calculated_fields.R | 35 twbparser-0.3.1/twbparser/R/datasources.R | 76 - twbparser-0.3.1/twbparser/R/insights.R |only twbparser-0.3.1/twbparser/R/published.R | 68 - twbparser-0.3.1/twbparser/R/twb_parser.R | 493 +++++----- twbparser-0.3.1/twbparser/R/utils.R | 20 twbparser-0.3.1/twbparser/README.md | 107 +- twbparser-0.3.1/twbparser/inst/doc/twbparser-intro.R | 87 - twbparser-0.3.1/twbparser/inst/doc/twbparser-intro.Rmd | 111 +- twbparser-0.3.1/twbparser/inst/doc/twbparser-intro.html | 222 ++-- twbparser-0.3.1/twbparser/inst/extdata/test_for_zip.twbx |only twbparser-0.3.1/twbparser/man/TwbParser.Rd | 2 twbparser-0.3.1/twbparser/man/extract_calculated_fields.Rd | 15 twbparser-0.3.1/twbparser/man/extract_datasource_details.Rd | 29 twbparser-0.3.1/twbparser/man/extract_named_connections.Rd | 14 twbparser-0.3.1/twbparser/man/twb_charts.Rd |only twbparser-0.3.1/twbparser/man/twb_colors.Rd |only twbparser-0.3.1/twbparser/man/twb_dashboard_filters.Rd |only twbparser-0.3.1/twbparser/man/twb_dashboard_summary.Rd |only twbparser-0.3.1/twbparser/man/twb_dashboards.Rd |only twbparser-0.3.1/twbparser/man/twb_page_composition.Rd |only twbparser-0.3.1/twbparser/man/twb_pages.Rd |only twbparser-0.3.1/twbparser/man/twb_pages_summary.Rd |only twbparser-0.3.1/twbparser/tests/testthat/test-active-bindings.R |only twbparser-0.3.1/twbparser/tests/testthat/test-calculated-fields.R |only twbparser-0.3.1/twbparser/tests/testthat/test-insights.R |only twbparser-0.3.1/twbparser/tests/testthat/test-overview.R |only twbparser-0.3.1/twbparser/tests/testthat/test-utils-extract_named_connections.R | 12 twbparser-0.3.1/twbparser/vignettes/twbparser-intro.Rmd | 111 +- 35 files changed, 863 insertions(+), 681 deletions(-)
Title: Tropical Cyclone (Hurricane, Typhoon) Spatial Hazard Modelling
Description: Methods for generating modelled parametric Tropical Cyclone (TC) spatial hazard fields and time series output at point locations from TC tracks. R's compatibility to simply use fast 'cpp' code via the 'Rcpp' package and the wide range spatial analysis tools via the 'terra' package makes it an attractive open source environment to study 'TCs'. This package estimates TC vortex wind and pressure fields using parametric equations originally coded up in 'python' by 'TCRM' <https://github.com/GeoscienceAustralia/tcrm> and then coded up in 'Cuda' 'cpp' by 'TCwindgen' <https://github.com/CyprienBosserelle/TCwindgen>.
Author: Julian O'Grady [aut, cre]
Maintainer: Julian O'Grady <julian.ogrady@csiro.au>
Diff between TCHazaRds versions 1.1.4 dated 2025-08-24 and 1.1.5 dated 2025-12-10
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/WindHazaRds.R | 32 ++++++++++++++++++++++++++------ README.md | 10 ++++++---- inst/doc/Introduction_to_TCHazaRds.R | 3 ++- inst/doc/Introduction_to_TCHazaRds.Rmd | 5 +++-- inst/doc/Introduction_to_TCHazaRds.html | 32 +++++++++++++++++++------------- man/update_Track.Rd | 3 ++- src/TCHazaRds.cpp | 16 ++++++++-------- vignettes/Introduction_to_TCHazaRds.Rmd | 5 +++-- 10 files changed, 82 insertions(+), 50 deletions(-)
Title: Posetic Data Analysis
Description: Build and manipulate partially ordered sets (posets), to perform some data analysis
on them and to implement multi-criteria decision making procedures. Several efficient ways for generating linear extensions are implemented, together with functions for building mutual ranking probabilities, incomparability, dominance and separation scores (Fattore, M., De Capitani, L., Avellone, A., Suardi, A. (2024). A fuzzy posetic toolbox for multi-criteria evaluation on ordinal data systems. ANNALS OF OPERATIONS RESEARCH <doi:10.1007/s10479-024-06352-3>).
Author: Alessandro Avellone [aut, cre],
Lucio De Capitani [aut],
Marco Fattore [aut]
Maintainer: Alessandro Avellone <alessandro.avellone@unimib.it>
Diff between poseticDataAnalysis versions 0.1.1 dated 2025-10-29 and 1.0.0 dated 2025-12-10
DESCRIPTION | 6 MD5 | 8 - src/lexicographicProductPOSet.cpp | 175 ++++++++++++++-------------- src/posetWrapper.cpp | 41 +++--- src/rwrapper.cpp | 234 +++++++++++++++++++------------------- 5 files changed, 232 insertions(+), 232 deletions(-)
More information about poseticDataAnalysis at CRAN
Permanent link
Title: Toolkit for Analysis of Genomic Data
Description: A toolkit for analysis of genomic data. The 'misha' package
implements an efficient data structure for storing genomic data, and
provides a set of functions for data extraction, manipulation and
analysis. Some of the 2D genome algorithms were described in Yaffe and Tanay
(2011) <doi:10.1038/ng.947>.
Author: Misha Hoichman [aut],
Aviezer Lifshitz [aut, cre],
Eitan Yaffe [aut],
Amos Tanay [aut],
Weizmann Institute of Science [cph]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Diff between misha versions 4.3.12 dated 2025-08-31 and 5.3.1 dated 2025-12-10
misha-4.3.12/misha/R/compute.R |only misha-4.3.12/misha/R/db.R |only misha-4.3.12/misha/R/intervals.R |only misha-4.3.12/misha/R/track.R |only misha-4.3.12/misha/tests/testthat/test-gextract.R |only misha-4.3.12/misha/tests/testthat/test-gintervals.R |only misha-4.3.12/misha/tests/testthat/test-gtrack.import.R |only misha-5.3.1/misha/DESCRIPTION | 13 misha-5.3.1/misha/MD5 | 559 ++- misha-5.3.1/misha/NAMESPACE | 25 misha-5.3.1/misha/NEWS.md | 111 misha-5.3.1/misha/R/compute-analysis.R |only misha-5.3.1/misha/R/compute-bins.R |only misha-5.3.1/misha/R/compute-core.R |only misha-5.3.1/misha/R/compute-distribution.R |only misha-5.3.1/misha/R/compute-partition.R |only misha-5.3.1/misha/R/compute-sequence.R |only misha-5.3.1/misha/R/compute-utils.R |only misha-5.3.1/misha/R/db-attrs.R |only misha-5.3.1/misha/R/db-cache.R |only misha-5.3.1/misha/R/db-core.R |only misha-5.3.1/misha/R/db-create.R |only misha-5.3.1/misha/R/db-dir.R |only misha-5.3.1/misha/R/db-index.R |only misha-5.3.1/misha/R/db-management.R |only misha-5.3.1/misha/R/db-root.R |only misha-5.3.1/misha/R/intervals-annotation.R |only misha-5.3.1/misha/R/intervals-bigset.R |only misha-5.3.1/misha/R/intervals-core.R |only misha-5.3.1/misha/R/intervals-iterator.R |only misha-5.3.1/misha/R/intervals-liftover.R |only misha-5.3.1/misha/R/intervals-load-save.R |only misha-5.3.1/misha/R/intervals-management.R |only misha-5.3.1/misha/R/intervals-operations.R |only misha-5.3.1/misha/R/intervals-tracks.R |only misha-5.3.1/misha/R/intervals-utils.R |only misha-5.3.1/misha/R/misha-package.R | 34 misha-5.3.1/misha/R/neighbors.R |only misha-5.3.1/misha/R/pssm_utils.R |only misha-5.3.1/misha/R/sequence.R | 486 +++ misha-5.3.1/misha/R/track-2d.R | 20 misha-5.3.1/misha/R/track-array.R | 17 misha-5.3.1/misha/R/track-attr.R | 5 misha-5.3.1/misha/R/track-convert.R |only misha-5.3.1/misha/R/track-core.R |only misha-5.3.1/misha/R/track-create.R |only misha-5.3.1/misha/R/track-import.R |only misha-5.3.1/misha/R/track-liftover.R |only misha-5.3.1/misha/R/track-management.R |only misha-5.3.1/misha/R/track-modify.R |only misha-5.3.1/misha/R/track-var.R | 14 misha-5.3.1/misha/R/utils-memory.R |only misha-5.3.1/misha/R/utils.R | 21 misha-5.3.1/misha/R/vtrack.R | 749 ++++- misha-5.3.1/misha/R/zzz.R | 25 misha-5.3.1/misha/build/vignette.rds |binary misha-5.3.1/misha/inst/WORDLIST | 43 misha-5.3.1/misha/inst/doc/Database-Formats.R |only misha-5.3.1/misha/inst/doc/Database-Formats.Rmd |only misha-5.3.1/misha/inst/doc/Database-Formats.html |only misha-5.3.1/misha/inst/doc/Manual.R | 31 misha-5.3.1/misha/inst/doc/Manual.Rmd | 245 + misha-5.3.1/misha/inst/doc/Manual.html | 356 ++ misha-5.3.1/misha/man/directional-neighbors.Rd |only misha-5.3.1/misha/man/dot-misha.Rd | 2 misha-5.3.1/misha/man/gbins.quantiles.Rd | 2 misha-5.3.1/misha/man/gbins.summary.Rd | 2 misha-5.3.1/misha/man/gcis_decay.Rd | 2 misha-5.3.1/misha/man/gcompute_strands_autocorr.Rd | 2 misha-5.3.1/misha/man/gdb.convert_to_indexed.Rd |only misha-5.3.1/misha/man/gdb.create.Rd | 63 misha-5.3.1/misha/man/gdb.create_genome.Rd | 2 misha-5.3.1/misha/man/gdb.get_readonly_attrs.Rd | 2 misha-5.3.1/misha/man/gdb.info.Rd |only misha-5.3.1/misha/man/gdb.init.Rd | 13 misha-5.3.1/misha/man/gdb.mark_cache_dirty.Rd |only misha-5.3.1/misha/man/gdb.reload.Rd | 2 misha-5.3.1/misha/man/gdb.set_readonly_attrs.Rd | 2 misha-5.3.1/misha/man/gdir.cd.Rd | 2 misha-5.3.1/misha/man/gdir.create.Rd | 2 misha-5.3.1/misha/man/gdir.cwd.Rd | 2 misha-5.3.1/misha/man/gdir.rm.Rd | 2 misha-5.3.1/misha/man/gdist.Rd | 2 misha-5.3.1/misha/man/gextract.Rd | 2 misha-5.3.1/misha/man/gintervals.2d.Rd | 2 misha-5.3.1/misha/man/gintervals.2d.all.Rd | 2 misha-5.3.1/misha/man/gintervals.2d.band_intersect.Rd | 2 misha-5.3.1/misha/man/gintervals.2d.convert_to_indexed.Rd |only misha-5.3.1/misha/man/gintervals.Rd | 2 misha-5.3.1/misha/man/gintervals.all.Rd | 2 misha-5.3.1/misha/man/gintervals.annotate.Rd | 6 misha-5.3.1/misha/man/gintervals.as_chain.Rd |only misha-5.3.1/misha/man/gintervals.canonic.Rd | 2 misha-5.3.1/misha/man/gintervals.chrom_sizes.Rd | 2 misha-5.3.1/misha/man/gintervals.convert_to_indexed.Rd |only misha-5.3.1/misha/man/gintervals.coverage_fraction.Rd |only misha-5.3.1/misha/man/gintervals.covered_bp.Rd |only misha-5.3.1/misha/man/gintervals.diff.Rd | 2 misha-5.3.1/misha/man/gintervals.exists.Rd | 2 misha-5.3.1/misha/man/gintervals.force_range.Rd | 2 misha-5.3.1/misha/man/gintervals.import_genes.Rd | 2 misha-5.3.1/misha/man/gintervals.intersect.Rd | 2 misha-5.3.1/misha/man/gintervals.is.bigset.Rd | 2 misha-5.3.1/misha/man/gintervals.liftover.Rd | 62 misha-5.3.1/misha/man/gintervals.load.Rd | 2 misha-5.3.1/misha/man/gintervals.load_chain.Rd | 55 misha-5.3.1/misha/man/gintervals.ls.Rd | 2 misha-5.3.1/misha/man/gintervals.mapply.Rd | 2 misha-5.3.1/misha/man/gintervals.mark_overlaps.Rd |only misha-5.3.1/misha/man/gintervals.neighbors.Rd | 97 misha-5.3.1/misha/man/gintervals.normalize.Rd | 2 misha-5.3.1/misha/man/gintervals.path.Rd |only misha-5.3.1/misha/man/gintervals.quantiles.Rd | 2 misha-5.3.1/misha/man/gintervals.random.Rd |only misha-5.3.1/misha/man/gintervals.rbind.Rd | 2 misha-5.3.1/misha/man/gintervals.rm.Rd | 2 misha-5.3.1/misha/man/gintervals.save.Rd | 2 misha-5.3.1/misha/man/gintervals.summary.Rd | 2 misha-5.3.1/misha/man/gintervals.union.Rd | 2 misha-5.3.1/misha/man/gintervals.update.Rd | 2 misha-5.3.1/misha/man/giterator.cartesian_grid.Rd | 2 misha-5.3.1/misha/man/giterator.intervals.Rd | 2 misha-5.3.1/misha/man/glookup.Rd | 2 misha-5.3.1/misha/man/gpartition.Rd | 2 misha-5.3.1/misha/man/gquantiles.Rd | 2 misha-5.3.1/misha/man/gsample.Rd | 2 misha-5.3.1/misha/man/gscreen.Rd | 2 misha-5.3.1/misha/man/gsegment.Rd | 2 misha-5.3.1/misha/man/gseq.comp.Rd |only misha-5.3.1/misha/man/gseq.extract.Rd | 2 misha-5.3.1/misha/man/gseq.kmer.Rd |only misha-5.3.1/misha/man/gseq.pwm.Rd |only misha-5.3.1/misha/man/gseq.rev.Rd |only misha-5.3.1/misha/man/gseq.revcomp.Rd |only misha-5.3.1/misha/man/gsummary.Rd | 2 misha-5.3.1/misha/man/gtrack.convert.Rd | 2 misha-5.3.1/misha/man/gtrack.convert_to_indexed.Rd |only misha-5.3.1/misha/man/gtrack.create.Rd | 2 misha-5.3.1/misha/man/gtrack.create_dense.Rd | 2 misha-5.3.1/misha/man/gtrack.create_dirs.Rd | 2 misha-5.3.1/misha/man/gtrack.create_pwm_energy.Rd | 2 misha-5.3.1/misha/man/gtrack.create_sparse.Rd | 2 misha-5.3.1/misha/man/gtrack.exists.Rd | 2 misha-5.3.1/misha/man/gtrack.import.Rd | 2 misha-5.3.1/misha/man/gtrack.import_mappedseq.Rd | 2 misha-5.3.1/misha/man/gtrack.import_set.Rd | 2 misha-5.3.1/misha/man/gtrack.info.Rd | 6 misha-5.3.1/misha/man/gtrack.liftover.Rd | 53 misha-5.3.1/misha/man/gtrack.lookup.Rd | 2 misha-5.3.1/misha/man/gtrack.ls.Rd | 2 misha-5.3.1/misha/man/gtrack.modify.Rd | 2 misha-5.3.1/misha/man/gtrack.path.Rd |only misha-5.3.1/misha/man/gtrack.rm.Rd | 2 misha-5.3.1/misha/man/gtrack.smooth.Rd | 2 misha-5.3.1/misha/man/gvtrack.create.Rd | 399 +- misha-5.3.1/misha/man/gvtrack.filter.Rd |only misha-5.3.1/misha/man/gwilcox.Rd | 2 misha-5.3.1/misha/man/misha-package.Rd | 32 misha-5.3.1/misha/src/AggregationHelpers.h |only misha-5.3.1/misha/src/BinsManager.h | 11 misha-5.3.1/misha/src/BufferedFile.h | 113 misha-5.3.1/misha/src/CRC64.h |only misha-5.3.1/misha/src/Chain2Interval.cpp | 137 misha-5.3.1/misha/src/ChainIntervalConverter.cpp |only misha-5.3.1/misha/src/ChainIntervalConverter.h |only misha-5.3.1/misha/src/ConfigurationManager.cpp |only misha-5.3.1/misha/src/ConfigurationManager.h |only misha-5.3.1/misha/src/DataFrameUtils.cpp |only misha-5.3.1/misha/src/DataFrameUtils.h |only misha-5.3.1/misha/src/DnaPSSM.cpp | 190 + misha-5.3.1/misha/src/DnaPSSM.h | 8 misha-5.3.1/misha/src/Filter.cpp |only misha-5.3.1/misha/src/Filter.h |only misha-5.3.1/misha/src/FilterInterface.cpp |only misha-5.3.1/misha/src/FilterRegistry.cpp |only misha-5.3.1/misha/src/FilterRegistry.h |only misha-5.3.1/misha/src/GInterval.cpp | 49 misha-5.3.1/misha/src/GInterval.h | 6 misha-5.3.1/misha/src/GIntervalsBigSet1D.cpp | 105 misha-5.3.1/misha/src/GIntervalsBigSet1D.h | 34 misha-5.3.1/misha/src/GIntervalsBigSet2D.cpp | 101 misha-5.3.1/misha/src/GIntervalsBigSet2D.h | 34 misha-5.3.1/misha/src/GTrack2DImportContacts.cpp | 11 misha-5.3.1/misha/src/GTrackIntervalsFetcher.cpp | 3 misha-5.3.1/misha/src/GTrackIntervalsFetcher1D.h | 5 misha-5.3.1/misha/src/GTrackLiftover.cpp | 495 ++- misha-5.3.1/misha/src/GenomeChromKey.h | 47 misha-5.3.1/misha/src/GenomeIndex.cpp |only misha-5.3.1/misha/src/GenomeIndex.h |only misha-5.3.1/misha/src/GenomeIntervalUtils.cpp | 213 + misha-5.3.1/misha/src/GenomeSeqFetch.cpp | 179 + misha-5.3.1/misha/src/GenomeSeqFetch.h | 19 misha-5.3.1/misha/src/GenomeSeqMultiImport.cpp |only misha-5.3.1/misha/src/GenomeSeqRead.cpp | 39 misha-5.3.1/misha/src/GenomeSeqScorer.cpp | 50 misha-5.3.1/misha/src/GenomeSeqScorer.h | 7 misha-5.3.1/misha/src/GenomeTrack.cpp | 154 - misha-5.3.1/misha/src/GenomeTrack.h | 17 misha-5.3.1/misha/src/GenomeTrack1D.h | 35 misha-5.3.1/misha/src/GenomeTrackApply.cpp | 1 misha-5.3.1/misha/src/GenomeTrackArrayImport.cpp | 7 misha-5.3.1/misha/src/GenomeTrackArrays.cpp | 81 misha-5.3.1/misha/src/GenomeTrackArrays.h | 37 misha-5.3.1/misha/src/GenomeTrackCreateDense.cpp | 94 misha-5.3.1/misha/src/GenomeTrackCreateSparse.cpp | 16 misha-5.3.1/misha/src/GenomeTrackExtract.cpp | 191 + misha-5.3.1/misha/src/GenomeTrackFindNeighbors.cpp | 113 misha-5.3.1/misha/src/GenomeTrackFixedBin.cpp | 295 +- misha-5.3.1/misha/src/GenomeTrackFixedBin.h | 24 misha-5.3.1/misha/src/GenomeTrackImportWig.cpp | 96 misha-5.3.1/misha/src/GenomeTrackInMemory.cpp |only misha-5.3.1/misha/src/GenomeTrackInMemory.h |only misha-5.3.1/misha/src/GenomeTrackIndexedFormat.cpp |only misha-5.3.1/misha/src/GenomeTrackInfo.cpp | 55 misha-5.3.1/misha/src/GenomeTrackModify.cpp | 3 misha-5.3.1/misha/src/GenomeTrackScreener.cpp | 51 misha-5.3.1/misha/src/GenomeTrackSparse.cpp | 122 misha-5.3.1/misha/src/GenomeTrackSparse.h | 84 misha-5.3.1/misha/src/GenomeUtils.cpp | 20 misha-5.3.1/misha/src/GenomeUtils.h | 2 misha-5.3.1/misha/src/GenomeUtilsR.cpp | 346 ++ misha-5.3.1/misha/src/GseqString.cpp |only misha-5.3.1/misha/src/IntervVarProcessor.cpp |only misha-5.3.1/misha/src/IntervVarProcessor.h |only misha-5.3.1/misha/src/IntervalConverter.cpp |only misha-5.3.1/misha/src/IntervalConverter.h |only misha-5.3.1/misha/src/IntervalValidator.cpp |only misha-5.3.1/misha/src/IntervalValidator.h |only misha-5.3.1/misha/src/IntervalsIndex1D.cpp |only misha-5.3.1/misha/src/IntervalsIndex1D.h |only misha-5.3.1/misha/src/IntervalsIndex2D.cpp |only misha-5.3.1/misha/src/IntervalsIndex2D.h |only misha-5.3.1/misha/src/IntervalsIndexedFormat.cpp |only misha-5.3.1/misha/src/IntervalsLiftover.cpp | 591 ++++ misha-5.3.1/misha/src/KmerCounter.cpp | 91 misha-5.3.1/misha/src/KmerCounter.h | 20 misha-5.3.1/misha/src/MaskedBpCounter.cpp |only misha-5.3.1/misha/src/MaskedBpCounter.h |only misha-5.3.1/misha/src/PWMScorer.cpp | 1424 +++++++++ misha-5.3.1/misha/src/PWMScorer.h | 164 + misha-5.3.1/misha/src/PwmCoreParams.cpp |only misha-5.3.1/misha/src/PwmCoreParams.h |only misha-5.3.1/misha/src/Segment.h | 6 misha-5.3.1/misha/src/SequenceVarProcessor.cpp |only misha-5.3.1/misha/src/SequenceVarProcessor.h |only misha-5.3.1/misha/src/TrackExpressionParams.h |only misha-5.3.1/misha/src/TrackExpressionScanner.cpp | 54 misha-5.3.1/misha/src/TrackExpressionSparseIterator.cpp | 5 misha-5.3.1/misha/src/TrackExpressionTrackRectsIterator.cpp | 2 misha-5.3.1/misha/src/TrackExpressionVars.cpp | 1043 ++++--- misha-5.3.1/misha/src/TrackExpressionVars.h | 129 misha-5.3.1/misha/src/TrackIndex.cpp |only misha-5.3.1/misha/src/TrackIndex.h |only misha-5.3.1/misha/src/TrackVarProcessor.cpp |only misha-5.3.1/misha/src/TrackVarProcessor.h |only misha-5.3.1/misha/src/ValueVarProcessor.cpp |only misha-5.3.1/misha/src/ValueVarProcessor.h |only misha-5.3.1/misha/src/misha-init.cpp | 42 misha-5.3.1/misha/src/rdbinterval.cpp | 1455 +++------- misha-5.3.1/misha/src/rdbinterval.h | 245 + misha-5.3.1/misha/src/rdbutils.cpp | 104 misha-5.3.1/misha/src/rdbutils.h | 24 misha-5.3.1/misha/src/utils |only misha-5.3.1/misha/tests/testthat/helper-hic-data.R |only misha-5.3.1/misha/tests/testthat/helper-liftover.R |only misha-5.3.1/misha/tests/testthat/helper-pwm.R | 1 misha-5.3.1/misha/tests/testthat/helper-regression.R | 44 misha-5.3.1/misha/tests/testthat/helper-test_db.R |only misha-5.3.1/misha/tests/testthat/helper-track.R |only misha-5.3.1/misha/tests/testthat/setup-hic-test-data.R |only misha-5.3.1/misha/tests/testthat/setup.R | 16 misha-5.3.1/misha/tests/testthat/test-2d-hic-analysis.R |only misha-5.3.1/misha/tests/testthat/test-2d-parity.R |only misha-5.3.1/misha/tests/testthat/test-auto-config-stress.R |only misha-5.3.1/misha/tests/testthat/test-auto-config.R |only misha-5.3.1/misha/tests/testthat/test-chromid-ordering.R |only misha-5.3.1/misha/tests/testthat/test-db-cache-updates.R |only misha-5.3.1/misha/tests/testthat/test-db-format-conversion.R |only misha-5.3.1/misha/tests/testthat/test-db.R | 231 + misha-5.3.1/misha/tests/testthat/test-directional-neighbors.R |only misha-5.3.1/misha/tests/testthat/test-gbins.R | 2 misha-5.3.1/misha/tests/testthat/test-gcis_decay.R | 4 misha-5.3.1/misha/tests/testthat/test-gcluster.run.R | 2 misha-5.3.1/misha/tests/testthat/test-gdist.R | 2 misha-5.3.1/misha/tests/testthat/test-gextract1.R |only misha-5.3.1/misha/tests/testthat/test-gextract2.R |only misha-5.3.1/misha/tests/testthat/test-gextract3.R |only misha-5.3.1/misha/tests/testthat/test-gintervals-2d-indexed.R |only misha-5.3.1/misha/tests/testthat/test-gintervals-format-conversion.R |only misha-5.3.1/misha/tests/testthat/test-gintervals-multicontig-extended.R |only misha-5.3.1/misha/tests/testthat/test-gintervals.annotate.R | 11 misha-5.3.1/misha/tests/testthat/test-gintervals.canonic.R | 18 misha-5.3.1/misha/tests/testthat/test-gintervals.coverage.R |only misha-5.3.1/misha/tests/testthat/test-gintervals.intersect.R | 11 misha-5.3.1/misha/tests/testthat/test-gintervals.liftover-agg.R |only misha-5.3.1/misha/tests/testthat/test-gintervals.liftover-bin.R |only misha-5.3.1/misha/tests/testthat/test-gintervals.liftover-canonic.R |only misha-5.3.1/misha/tests/testthat/test-gintervals.mapply.R | 20 misha-5.3.1/misha/tests/testthat/test-gintervals.neighbors.R | 510 +++ misha-5.3.1/misha/tests/testthat/test-gintervals.normalize.R | 11 misha-5.3.1/misha/tests/testthat/test-gintervals.quantiles.R | 20 misha-5.3.1/misha/tests/testthat/test-gintervals.summary.R | 20 misha-5.3.1/misha/tests/testthat/test-gintervals1.R |only misha-5.3.1/misha/tests/testthat/test-gintervals2.R |only misha-5.3.1/misha/tests/testthat/test-giterator.cartesian_grid.R | 2 misha-5.3.1/misha/tests/testthat/test-giterator.intervals.R | 2 misha-5.3.1/misha/tests/testthat/test-glookup.R | 2 misha-5.3.1/misha/tests/testthat/test-gpartition.R | 20 misha-5.3.1/misha/tests/testthat/test-gquantiles.R | 2 misha-5.3.1/misha/tests/testthat/test-gsample.R | 2 misha-5.3.1/misha/tests/testthat/test-gscreen.R | 2 misha-5.3.1/misha/tests/testthat/test-gsegment.R | 11 misha-5.3.1/misha/tests/testthat/test-gseq.extract.R | 2 misha-5.3.1/misha/tests/testthat/test-gseq_pwm-parallel.R |only misha-5.3.1/misha/tests/testthat/test-gsummary.R | 2 misha-5.3.1/misha/tests/testthat/test-gtrack-format-conversion.R |only misha-5.3.1/misha/tests/testthat/test-gtrack-multicontig.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.array.R | 11 misha-5.3.1/misha/tests/testthat/test-gtrack.create.R | 89 misha-5.3.1/misha/tests/testthat/test-gtrack.create_dense.R | 53 misha-5.3.1/misha/tests/testthat/test-gtrack.import1.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.import2.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.import3.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.import4.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.import5.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.info.R | 29 misha-5.3.1/misha/tests/testthat/test-gtrack.liftover-agg.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.liftover-bin.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.liftover.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.lookup.R | 29 misha-5.3.1/misha/tests/testthat/test-gtrack.smooth.R | 41 misha-5.3.1/misha/tests/testthat/test-gtrack.var.R | 34 misha-5.3.1/misha/tests/testthat/test-gvtrack.filter.R |only misha-5.3.1/misha/tests/testthat/test-gwilcox.R | 11 misha-5.3.1/misha/tests/testthat/test-indexed-integration.R |only misha-5.3.1/misha/tests/testthat/test-kmer.R | 2 misha-5.3.1/misha/tests/testthat/test-liftover-autoscore-kent.R |only misha-5.3.1/misha/tests/testthat/test-liftover-best_source_cluster.R |only misha-5.3.1/misha/tests/testthat/test-liftover-hg19-hg38.R |only misha-5.3.1/misha/tests/testthat/test-liftover.R |only misha-5.3.1/misha/tests/testthat/test-masked.R |only misha-5.3.1/misha/tests/testthat/test-motifs.R | 11 misha-5.3.1/misha/tests/testthat/test-multicontig-edge-cases-errors.R |only misha-5.3.1/misha/tests/testthat/test-multifasta-import.R |only misha-5.3.1/misha/tests/testthat/test-path-functions.R |only misha-5.3.1/misha/tests/testthat/test-pwm-count-spatial-bidirect.R |only misha-5.3.1/misha/tests/testthat/test-pwm-count.R |only misha-5.3.1/misha/tests/testthat/test-pwm-indexed-gtrack-create.R |only misha-5.3.1/misha/tests/testthat/test-pwm-prego-regression.R |only misha-5.3.1/misha/tests/testthat/test-pwm-sliding-window.R |only misha-5.3.1/misha/tests/testthat/test-pwm-spatial.R |only misha-5.3.1/misha/tests/testthat/test-pwm.R | 277 + misha-5.3.1/misha/tests/testthat/test-random-genome.R |only misha-5.3.1/misha/tests/testthat/test-sequence.R | 1427 +++++++++ misha-5.3.1/misha/tests/testthat/test-track.attrs.R | 275 + misha-5.3.1/misha/tests/testthat/test-vtrack-coverage.R | 2 misha-5.3.1/misha/tests/testthat/test-vtrack-distance-edge.R |only misha-5.3.1/misha/tests/testthat/test-vtrack-max-pos.R |only misha-5.3.1/misha/tests/testthat/test-vtrack-neighbor-count.R |only misha-5.3.1/misha/tests/testthat/test-vtrack-new-funcs.R |only misha-5.3.1/misha/tests/testthat/test-vtrack-values-equivalence.R |only misha-5.3.1/misha/tests/testthat/test-vtrack-values.R |only misha-5.3.1/misha/tests/testthat/test-vtrack.R | 81 misha-5.3.1/misha/vignettes/Database-Formats.Rmd |only misha-5.3.1/misha/vignettes/Manual.Rmd | 245 + 365 files changed, 13370 insertions(+), 2986 deletions(-)
Title: Tools for Quantitative Risk Management
Description: Functions and data sets for reproducing selected results from
the book "Quantitative Risk Management: Concepts, Techniques and Tools".
Furthermore, new developments and auxiliary functions for Quantitative
Risk Management practice.
Author: Marius Hofert [aut, cre],
Kurt Hornik [aut],
Alexander J. McNeil [aut]
Maintainer: Marius Hofert <mhofert@hku.hk>
Diff between qrmtools versions 0.0-18 dated 2025-09-10 and 0.0-19 dated 2025-12-10
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- R/get_data.R | 23 +++++++++++++---------- inst/NEWS.Rd | 9 +++++++++ inst/doc/ARMA_GARCH_VaR.html | 4 ++-- inst/doc/VaR_bounds.html | 6 +++--- inst/doc/geometric_risk_measures.html | 4 ++-- man/get_data.Rd | 7 +++---- 9 files changed, 46 insertions(+), 35 deletions(-)
Title: Miscellaneous Statistical Functions Used in 'guide-R'
Description: Companion package for the manual
'guide-R : Guide pour l’analyse de données d’enquêtes avec R' available at
<https://larmarange.github.io/guide-R/>. 'guideR' implements miscellaneous
functions introduced in 'guide-R' to facilitate statistical analysis and
manipulation of survey data.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between guideR versions 0.7.0 dated 2025-11-26 and 0.8.0 dated 2025-12-10
DESCRIPTION | 12 MD5 | 59 +- NAMESPACE | 17 NEWS.md | 34 + R/gtsummary_tests.R | 41 ++ R/gtsummary_themes.R | 58 ++ R/mean_sd.R |only R/median_iqr.R |only R/plot_categorical.R |only R/plot_continuous.R |only R/plot_means.R |only R/plot_multiple_answers.R | 9 R/plot_proportions.R | 522 +++++++++++++++++--------- R/proportion.R | 29 - R/safe_pal.R |only R/svyoneway.R |only R/vdiffr-helper.R |only inst/WORDLIST | 6 man/gtsummary_test.Rd | 17 man/gtsummary_themes.Rd | 27 + man/mean_sd.Rd |only man/median_iqr.Rd |only man/plot_categorical.Rd |only man/plot_continuous.Rd |only man/plot_means.Rd |only man/plot_multiple_answers.Rd | 5 man/plot_proportions.Rd | 26 - man/safe_pal.Rd |only man/svyoneway.Rd |only tests/testthat/test-gtsummary-themes.R | 18 tests/testthat/test-mean_sd.R |only tests/testthat/test-median_iqr.R |only tests/testthat/test-observed_vs_theoretical.R | 6 tests/testthat/test-plot_categorical.R |only tests/testthat/test-plot_continuous.R |only tests/testthat/test-plot_inertia_from_tree.R | 5 tests/testthat/test-plot_means.R |only tests/testthat/test-plot_multiple_answers.R | 66 ++- tests/testthat/test-plot_proportions.R | 66 ++- tests/testthat/test-plot_trajectories.R | 29 + tests/testthat/test-svyoneway.R |only 41 files changed, 783 insertions(+), 269 deletions(-)
Title: Functions to Estimate Tree Volume and Phytomass in the Italian
Forest Inventory 2005
Description: Tabacchi et al. (2011) published a very detailed study producing a uniform system of functions to estimate tree volume and
phytomass components (stem, branches, stool). The estimates of the 2005 Italian forest inventory (<https://www.inventarioforestale.org/it/>)
are based on these functions. The study documents the domain of applicability of each function and the equations to quantify estimates
accuracies for individual estimates as well as for aggregated estimates. This package makes the functions available in the R environment.
Version 2 exposes two distinct functions for individual and summary estimates. To facilitate access to the functions, tree species
identification is now based on EPPO species codes (<https://data.eppo.int/>).
Author: Nicola Puletti [aut, cre] ,
Mirko Grotti [aut],
Roberto Scotti [aut]
Maintainer: Nicola Puletti <nicola.puletti@gmail.com>
Diff between ForIT versions 2.5.1 dated 2025-09-22 and 2.5.2 dated 2025-12-10
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 8 +++++++- R/ForIT_DataBase.R | 2 +- R/INFCtabulate.R | 2 +- R/INFCvpe.R | 5 ++--- R/INFCvpeSUM.R | 2 +- R/examples/INFCvpeSUM_e.R | 2 +- man/ForIT_DataBase.Rd | 2 +- man/INFCvpe.Rd | 2 +- man/INFCvpeSUM.Rd | 4 ++-- 11 files changed, 30 insertions(+), 25 deletions(-)
Title: Serialize Model Objects with a Consistent Interface
Description: Typically, models in 'R' exist in memory and can be saved via
regular 'R' serialization. However, some models store information in
locations that cannot be saved using 'R' serialization alone. The goal
of 'bundle' is to provide a common interface to capture this
information, situate it within a portable object, and restore it for
use in new settings.
Author: Julia Silge [aut, cre] ,
Simon Couch [aut],
Qiushi Yan [aut],
Max Kuhn [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Julia Silge <julia.silge@posit.co>
Diff between bundle versions 0.1.2 dated 2024-11-12 and 0.1.3 dated 2025-12-10
bundle-0.1.2/bundle/R/package.R |only bundle-0.1.2/bundle/man/bundle_description.Rd |only bundle-0.1.3/bundle/DESCRIPTION | 30 ++-- bundle-0.1.3/bundle/LICENSE | 2 bundle-0.1.3/bundle/MD5 | 86 ++++++----- bundle-0.1.3/bundle/NAMESPACE | 2 bundle-0.1.3/bundle/NEWS.md | 4 bundle-0.1.3/bundle/R/bundle-package.R |only bundle-0.1.3/bundle/R/bundle_bart.R | 6 bundle-0.1.3/bundle/R/bundle_embed.R | 6 bundle-0.1.3/bundle/R/bundle_keras.R | 19 +- bundle-0.1.3/bundle/R/bundle_parsnip.R | 6 bundle-0.1.3/bundle/R/bundle_stacks.R | 8 - bundle-0.1.3/bundle/R/bundle_torch.R | 19 +- bundle-0.1.3/bundle/R/bundle_workflows.R | 12 - bundle-0.1.3/bundle/R/bundle_xgboost.R | 38 +++-- bundle-0.1.3/bundle/R/utils.R | 12 - bundle-0.1.3/bundle/README.md | 64 +++----- bundle-0.1.3/bundle/build/vignette.rds |binary bundle-0.1.3/bundle/inst/doc/bundle.R | 48 +++--- bundle-0.1.3/bundle/inst/doc/bundle.Rmd | 94 +++++++++---- bundle-0.1.3/bundle/inst/doc/bundle.html | 83 ++++++----- bundle-0.1.3/bundle/man/bundle-package.Rd |only bundle-0.1.3/bundle/man/bundle_bart.Rd | 6 bundle-0.1.3/bundle/man/bundle_caret.Rd | 6 bundle-0.1.3/bundle/man/bundle_embed.Rd | 12 - bundle-0.1.3/bundle/man/bundle_h2o.Rd | 2 bundle-0.1.3/bundle/man/bundle_keras.Rd | 16 +- bundle-0.1.3/bundle/man/bundle_parsnip.Rd | 12 - bundle-0.1.3/bundle/man/bundle_stacks.Rd | 10 - bundle-0.1.3/bundle/man/bundle_torch.Rd | 12 - bundle-0.1.3/bundle/man/bundle_workflows.Rd | 18 +- bundle-0.1.3/bundle/man/bundle_xgboost.Rd | 20 +- bundle-0.1.3/bundle/man/figures/lifecycle-deprecated.svg |only bundle-0.1.3/bundle/man/figures/lifecycle-experimental.svg |only bundle-0.1.3/bundle/man/figures/lifecycle-stable.svg |only bundle-0.1.3/bundle/man/figures/lifecycle-superseded.svg |only bundle-0.1.3/bundle/tests/testthat.R | 4 bundle-0.1.3/bundle/tests/testthat/test_bundle_embed.R | 9 - bundle-0.1.3/bundle/tests/testthat/test_bundle_h2o.R | 25 ++- bundle-0.1.3/bundle/tests/testthat/test_bundle_keras.R | 24 ++- bundle-0.1.3/bundle/tests/testthat/test_bundle_parsnip.R | 6 bundle-0.1.3/bundle/tests/testthat/test_bundle_stacks.R | 8 - bundle-0.1.3/bundle/tests/testthat/test_bundle_torch.R | 24 +-- bundle-0.1.3/bundle/tests/testthat/test_bundle_workflows.R | 24 +-- bundle-0.1.3/bundle/tests/testthat/test_bundle_xgboost.R | 29 +++- bundle-0.1.3/bundle/tests/testthat/test_utils.R | 11 - bundle-0.1.3/bundle/vignettes/bundle.Rmd | 94 +++++++++---- 48 files changed, 536 insertions(+), 375 deletions(-)