Title: Multiscale Geographically Weighted Negative Binomial Regression
Description: Fits a geographically weighted regression model with different scales
for each covariate. Uses the negative binomial distribution as default,
but also accepts the normal, Poisson, or logistic distributions.
Can fit the global versions of each regression and also the geographically
weighted alternatives with only one scale, since they are all particular
cases of the multiscale approach.
Hanchen Yu (2024). "Exploring Multiscale Geographically Weighted Negative Binomial Regression", Annals of the American Association of Geographers <doi:10.1080/24694452.2023.2289986>.
Fotheringham AS, Yang W, Kang W (2017). "Multiscale Geographically Weighted Regression (MGWR)", Annals of the American Association of Geographers <doi:10.1080/24694452.2017.1352480>.
Da Silva AR, Rodrigues TCV (2014). "Geographically Weighted Negative Binomial Regression - incorporating overdispersion", Statistics and Computing <doi:10.1007/s11222-013-9401-9>.
Author: Juliana Rosa [aut, cre],
Jessica Vasconcelos [aut],
Alan da Silva [aut]
Maintainer: Juliana Rosa <julianamrosa00@gmail.com>
Diff between mgwnbr versions 0.2.0 dated 2024-03-26 and 0.3.0 dated 2025-10-01
mgwnbr-0.2.0/mgwnbr/R/globals.R |only mgwnbr-0.3.0/mgwnbr/DESCRIPTION | 8 mgwnbr-0.3.0/mgwnbr/MD5 | 19 mgwnbr-0.3.0/mgwnbr/NAMESPACE | 27 mgwnbr-0.3.0/mgwnbr/NEWS.md | 8 mgwnbr-0.3.0/mgwnbr/R/mgwnbr.R | 541 ++++++++++-------- mgwnbr-0.3.0/mgwnbr/R/print.R |only mgwnbr-0.3.0/mgwnbr/R/summary.R |only mgwnbr-0.3.0/mgwnbr/R/summary_print.R |only mgwnbr-0.3.0/mgwnbr/man/georgia.Rd | 62 +- mgwnbr-0.3.0/mgwnbr/man/mgwnbr.Rd | 213 +++---- mgwnbr-0.3.0/mgwnbr/man/print.mgwnbr_model.Rd |only mgwnbr-0.3.0/mgwnbr/man/print.summary.mgwnbr_model.Rd |only mgwnbr-0.3.0/mgwnbr/man/summary.mgwnbr_model.Rd |only 14 files changed, 496 insertions(+), 382 deletions(-)
Title: Topological Data Analysis: Mapper Algorithm
Description: The Mapper algorithm from Topological Data Analysis, the steps are as follows 1. Define a filter (lens) function on the data. 2. Perform clustering within each level set. 3. Generate a complex from the clustering results.
Author: ChiChien Wang [aut, cre, trl],
Paul Pearson [ctb],
Daniel Muellner [ctb],
Gurjeet Singh [ctb]
Maintainer: ChiChien Wang <kennywang2003@gmail.com>
Diff between MapperAlgo versions 1.0.4 dated 2025-08-22 and 1.0.5 dated 2025-10-01
DESCRIPTION | 14 - LICENSE | 2 MD5 | 51 ++-- NAMESPACE | 4 R/Cluster.R | 334 +++++++++++++++---------------- R/ConvertLevelsets.R | 66 +++--- R/Cover.R | 79 +++---- R/EdgeVertices.R | 98 ++++----- R/GridSearch.R |only R/MapperAlgo.R | 308 ++++++++++++++-------------- R/SimplicialComplex.R | 86 +++---- R/zzz.R | 2 README.md | 130 ++++-------- man/GridSearch.Rd |only man/MapperAlgo.Rd | 100 ++++----- man/MapperPlotter.Rd | 50 ++-- man/cluster_cutoff_at_first_empty_bin.Rd | 42 +-- man/cover_points.Rd | 74 +++--- man/find_best_k_for_kmeans.Rd | 42 +-- man/mapperEdges.Rd | 36 +-- man/mapperVertices.Rd | 40 +-- man/perform_clustering.Rd | 56 ++--- man/save_mapper_png.Rd |only man/simplcial_complex.Rd | 68 +++--- man/to_lsfi.Rd | 38 +-- man/to_lsmi.Rd | 38 +-- tests/testthat.R | 24 +- tests/testthat/test-MapperAlgo.R | 6 28 files changed, 887 insertions(+), 901 deletions(-)
Title: Utilities to Weave Hydrologic Fabrics
Description: A collection of utilities that support creation of network attributes for hydrologic networks. Methods and algorithms implemented are documented in Moore et al. (2019) <doi:10.3133/ofr20191096>), Cormen and Leiserson (2022) <ISBN:9780262046305> and Verdin and Verdin (1999) <doi:10.1016/S0022-1694(99)00011-6>.
Author: David Blodgett [aut, cre]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between hydroloom versions 1.1.0 dated 2024-08-26 and 1.1.1 dated 2025-10-01
DESCRIPTION | 13 +-- MD5 | 43 ++++++----- NAMESPACE | 2 NEWS.md | 7 + R/index_points_to_lines.R | 97 +++++++++++++++++++++++---- R/make_index_ids.R | 8 +- R/navigate_network_dfs.R | 19 ++--- R/navigation_network.R | 2 R/sort_network.R | 1 R/to_flownetwork.R | 4 - R/utils.R | 25 ++++++ build/vignette.rds |binary inst/doc/advanced_network.html | 7 + inst/doc/flow-table.html | 11 +-- inst/doc/hydroloom.html | 5 - inst/doc/network_navigation.html | 58 +++++++--------- inst/doc/non-dendritic.html | 5 - man/index_points_to_lines.Rd | 29 ++++++-- tests/testthat/data/sort_network_dups.rds |only tests/testthat/test_index.R | 31 +++++++- tests/testthat/test_navigate_hydro_network.R | 7 + tests/testthat/test_navigate_network_dfs.R | 7 + tests/testthat/test_sort_network.R | 14 +++ 23 files changed, 287 insertions(+), 108 deletions(-)
Title: Scalable Gaussian Process Regression with Hierarchical Shrinkage
Priors
Description: Efficient variational inference methods for fully Bayesian Gaussian
Process Regression (GPR) models with hierarchical shrinkage priors,
including the triple gamma prior for effective variable selection and
covariance shrinkage in high-dimensional settings. The package leverages normalizing
flows to approximate complex posterior distributions. For details on implementation,
see Knaus (2025) <doi:10.48550/arXiv.2501.13173>.
Author: Peter Knaus [aut, cre]
Maintainer: Peter Knaus <peter.knaus@wu.ac.at>
Diff between shrinkGPR versions 1.1 dated 2025-08-19 and 1.1.1 dated 2025-10-01
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 5 +++++ R/GPR_class.R | 6 +++--- R/TPR_class.R | 11 +++++++++-- R/pred_functions.R | 8 +++++--- R/shrinkGPR.R | 2 ++ R/shrinkGPR_package.R | 4 +++- R/shrinkTPR.R | 2 ++ tests/testthat/Rplots.pdf |binary tests/testthat/test_shrinkGPR.R | 10 +++++++++- tests/testthat/test_shrinkTPR.R | 10 +++++++++- 12 files changed, 61 insertions(+), 25 deletions(-)
Title: R Interface to ILOSTAT Open Data
Description: Provides tools to access, search, and manipulate ILO's ilostat database,
including bulk download of statistical data, dictionary lookups, and table of contents.
Author: David Bescond [aut, cre] ,
Mabelin Villarreal-Fuentes [ctb] ,
ILO Department of Statistics [cph, fnd]
Maintainer: David Bescond <bescond@ilo.org>
Diff between Rilostat versions 2.3.1 dated 2025-03-10 and 2.3.4 dated 2025-10-01
Rilostat-2.3.1/Rilostat/R/dataexplorer.R |only Rilostat-2.3.1/Rilostat/R/sysdata.rda |only Rilostat-2.3.1/Rilostat/man/dataexplorer.Rd |only Rilostat-2.3.4/Rilostat/DESCRIPTION | 53 ++- Rilostat-2.3.4/Rilostat/MD5 | 42 +- Rilostat-2.3.4/Rilostat/NAMESPACE | 13 Rilostat-2.3.4/Rilostat/NEWS.md | 156 +++++----- Rilostat-2.3.4/Rilostat/R/Rilostat.R | 284 +++++++++++--------- Rilostat-2.3.4/Rilostat/R/clean_ilostat_cache.R | 2 Rilostat-2.3.4/Rilostat/R/data-internal.R |only Rilostat-2.3.4/Rilostat/R/distribution_ilostat.r | 2 Rilostat-2.3.4/Rilostat/R/get_ilostat.R | 122 +++++--- Rilostat-2.3.4/Rilostat/R/get_ilostat_dic.R | 60 ++-- Rilostat-2.3.4/Rilostat/R/get_ilostat_toc.R | 68 ++-- Rilostat-2.3.4/Rilostat/R/label_ilostat.R | 3 Rilostat-2.3.4/Rilostat/R/runapp_ilostat.R |only Rilostat-2.3.4/Rilostat/README.md | 185 ++++++------- Rilostat-2.3.4/Rilostat/man/Rilostat.Rd | 29 +- Rilostat-2.3.4/Rilostat/man/clean_ilostat_cache.Rd | 2 Rilostat-2.3.4/Rilostat/man/distribution_ilostat.Rd | 2 Rilostat-2.3.4/Rilostat/man/get_ilostat.Rd | 7 Rilostat-2.3.4/Rilostat/man/get_ilostat_dic.Rd | 13 Rilostat-2.3.4/Rilostat/man/get_ilostat_toc.Rd | 16 - Rilostat-2.3.4/Rilostat/man/label_ilostat.Rd | 2 Rilostat-2.3.4/Rilostat/man/runapp_ilostat.Rd |only 25 files changed, 602 insertions(+), 459 deletions(-)
Title: A 'shiny' App for Reproducible QA/QC of Eddy Covariance Data
Description: An interactive 'shiny'-based tool for exploration and quality
assurance and quality control (QA/QC) of eddy covariance flux tower
data processing. It generates data-point removal code via
user-directed selection from a scatterplot, and can export a cleaned
.csv with removed points set to NA plus an R script for
reproducibility. Reference: Key (2025) <DOI:10.5281/zenodo.15597159>.
Author: Kesondra Key [aut, cre]
Maintainer: Kesondra Key <keyke@iu.edu>
Diff between fluxtools versions 0.7.0 dated 2025-09-18 and 0.7.1 dated 2025-10-01
DESCRIPTION | 6 MD5 | 26 R/prm.R | 1072 ++++++++++++++++++++-------------------- R/run_app.R | 70 +- R/zzz-deps.R | 14 R/zzz.R | 20 inst/CITATION | 32 - inst/app/app.R | 289 ++++++++-- inst/doc/introduction.html | 2 inst/extdata/test.R | 94 +-- man/apply_prm.Rd | 60 +- man/get_prm_rules.Rd | 28 - man/run_fluxtools.Rd | 40 - tests/testthat/test-apply_prm.R | 354 ++++++------- 14 files changed, 1141 insertions(+), 966 deletions(-)
Title: Simulation for Factorial Designs
Description: Create datasets with factorial structure through simulation by specifying variable parameters. Extended documentation at <https://scienceverse.github.io/faux/>. Described in DeBruine (2020) <doi:10.5281/zenodo.2669586>.
Author: Lisa DeBruine [aut, cre, cph] ,
Anna Krystalli [ctb] ,
Andrew Heiss [ctb]
Maintainer: Lisa DeBruine <debruine@gmail.com>
Diff between faux versions 1.2.2 dated 2025-01-15 and 1.2.3 dated 2025-10-01
DESCRIPTION | 24 +++++++++------- MD5 | 34 +++++++++++------------ NEWS.md | 13 ++++++++- R/distribution_convertors.R | 17 ----------- R/sim_design.R | 2 - R/zzz.R | 4 +- README.md | 18 +++++++----- build/vignette.rds |binary inst/CITATION | 2 - inst/doc/sim_design.html | 14 ++++----- man/faux.Rd | 6 ++-- man/norm2likert.Rd | 15 ---------- man/sim_design.Rd | 2 - tests/testthat/Rplots.pdf |binary tests/testthat/test-interactive_design.R | 2 - tests/testthat/test-norta.R | 2 - tests/testthat/test-plot_design.R | 44 +++++++++++++++++-------------- tests/testthat/test-zzz.R | 2 - 18 files changed, 96 insertions(+), 105 deletions(-)
Title: Estimating Remaining Useful Life with Linear Mixed Effects
Models
Description: Provides tools for estimating the Remaining Useful Life (RUL) of degrading systems using linear mixed-effects models and creating a health index. It supports both univariate and multivariate degradation signals. For multivariate inputs, the signals are merged into a univariate health index prior to modeling. Linear and exponential degradation trajectories are supported (the latter using a log transformation). Remaining Useful Life (RUL) distributions are estimated using Bayesian updating for new units, enabling on-site predictive maintenance. Based on the methodology of Liu and Huang (2016) <doi:10.1109/TASE.2014.2349733>.
Author: Pedro Abraham Montoya Calzada [aut, cre, cph] ,
Rogelio Salinas Gutierrez [aut, cph] ,
Silvia Rodriguez-Narciso [aut, cph] ,
Netzahualcoyotl Castaneda-Leyva [aut, cph]
Maintainer: Pedro Abraham Montoya Calzada <pedroabraham.montoya@gmail.com>
Diff between degradr versions 1.0.0 dated 2025-08-25 and 1.0.1 dated 2025-10-01
degradr-1.0.0/degradr/README.md |only degradr-1.0.1/degradr/DESCRIPTION | 8 +++++--- degradr-1.0.1/degradr/MD5 | 25 ++++++++++++++++--------- degradr-1.0.1/degradr/NAMESPACE | 2 ++ degradr-1.0.1/degradr/R/RLD.R | 2 +- degradr-1.0.1/degradr/R/fit_healthindex.R | 2 +- degradr-1.0.1/degradr/R/g2.R | 1 + degradr-1.0.1/degradr/R/posterior.R | 6 +++++- degradr-1.0.1/degradr/R/predict_rul.R | 6 ------ degradr-1.0.1/degradr/R/prul.R |only degradr-1.0.1/degradr/R/qrul.R |only degradr-1.0.1/degradr/man/predict_rul.Rd | 2 +- degradr-1.0.1/degradr/man/prul.Rd |only degradr-1.0.1/degradr/man/qrul.Rd |only degradr-1.0.1/degradr/tests |only 15 files changed, 32 insertions(+), 22 deletions(-)
Title: ROC Analysis in Three-Class Classification Problems for
Clustered Data
Description: Statistical methods for ROC surface analysis in three-class classification problems for clustered data and in presence of covariates. In particular, the package allows to obtain covariate-specific point and interval estimation for:
(i) true class fractions (TCFs) at fixed pairs of thresholds;
(ii) the ROC surface;
(iii) the volume under ROC surface (VUS);
(iv) the optimal pairs of thresholds.
Methods considered in points (i), (ii) and (iv) are proposed and discussed in To et al. (2022) <doi:10.1177/09622802221089029>. Referring to point (iv), three different selection criteria are implemented: Generalized Youden Index (GYI), Closest to Perfection (CtP) and Maximum Volume (MV). Methods considered in point (iii) are proposed and discussed in Xiong et al. (2018) <doi:10.1177/0962280217742539>. Visualization tools are also provided. We refer readers to the articles cited above for all details.
Author: Duc-Khanh To [aut, cre] ,
Gianfranco Adimari [ctb],
Monica Chiogna [ctb]
Maintainer: Duc-Khanh To <tdkhanh@hcmus.edu.vn>
Diff between ClusROC versions 1.0.2 dated 2022-11-17 and 1.0.3 dated 2025-10-01
DESCRIPTION | 28 +++++++++++++++++++++------- MD5 | 12 ++++++------ R/clus_lme.R | 2 +- R/clus_opt_thresh_3class.R | 2 +- build/partial.rdb |binary man/plot.clus_lme.Rd | 2 +- man/plot.clus_opt_thres3.Rd | 2 +- 7 files changed, 31 insertions(+), 17 deletions(-)
Title: Client for Central Bank APIs
Description: A client for retrieving data and metadata from major central
bank APIs. It supports access to the 'Bundesbank SDMX Web Service API'
(<https://www.bundesbank.de/en/statistics/time-series-databases/help-for-sdmx-web-service/web-service-interface-data>),
the 'Swiss National Bank Data Portal' (<https://data.snb.ch/en>), the
'European Central Bank Data Portal API'
(<https://data.ecb.europa.eu/help/api/overview>), the 'Bank of England
Interactive Statistical Database'
(<https://www.bankofengland.co.uk/boeapps/database>), the 'Banco de
España API'
(<https://www.bde.es/webbe/en/estadisticas/recursos/api-estadisticas-bde.html>),
the 'Banque de France Web Service'
(<https://webstat.banque-france.fr/en/pages/guide-migration-api/>),
and 'Bank of Canada Valet API'
(<https://www.bankofcanada.ca/valet/docs>).
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between bbk versions 0.7.0 dated 2025-08-25 and 0.8.0 dated 2025-10-01
bbk-0.7.0/bbk/R/ecb-euro-rates.R |only bbk-0.7.0/bbk/man/ecb_euro_rates.Rd |only bbk-0.7.0/bbk/tests/testthat/test-ecb-euro-rates.R |only bbk-0.8.0/bbk/DESCRIPTION | 16 ++-- bbk-0.8.0/bbk/MD5 | 79 +++++++++++---------- bbk-0.8.0/bbk/NAMESPACE | 5 + bbk-0.8.0/bbk/NEWS.md | 6 + bbk-0.8.0/bbk/R/bbk.R | 52 +++++++------ bbk-0.8.0/bbk/R/bde.R | 2 bbk-0.8.0/bbk/R/bdf.R | 18 +++- bbk-0.8.0/bbk/R/boc.R |only bbk-0.8.0/bbk/R/ecb.R | 1 bbk-0.8.0/bbk/R/fx-rates.R |only bbk-0.8.0/bbk/R/onb.R | 20 +++-- bbk-0.8.0/bbk/R/snb.R | 1 bbk-0.8.0/bbk/README.md | 8 +- bbk-0.8.0/bbk/man/bbk-package.Rd | 2 bbk-0.8.0/bbk/man/bbk_data.Rd | 18 +++- bbk-0.8.0/bbk/man/bbk_metadata.Rd | 2 bbk-0.8.0/bbk/man/bbk_series.Rd | 3 bbk-0.8.0/bbk/man/bde_data.Rd | 3 bbk-0.8.0/bbk/man/bdf_codelist.Rd | 4 - bbk-0.8.0/bbk/man/bdf_data.Rd | 6 + bbk-0.8.0/bbk/man/bdf_dataset.Rd | 4 - bbk-0.8.0/bbk/man/boc_catalog.Rd |only bbk-0.8.0/bbk/man/boc_data.Rd |only bbk-0.8.0/bbk/man/boc_fx_rates.Rd |only bbk-0.8.0/bbk/man/boc_metadata.Rd |only bbk-0.8.0/bbk/man/boe_data.Rd | 3 bbk-0.8.0/bbk/man/ecb_data.Rd | 4 - bbk-0.8.0/bbk/man/ecb_fx_rates.Rd |only bbk-0.8.0/bbk/man/ecb_metadata.Rd | 2 bbk-0.8.0/bbk/man/figures/README-plotting-1.png |binary bbk-0.8.0/bbk/man/onb_data.Rd | 6 + bbk-0.8.0/bbk/man/onb_dimension.Rd | 2 bbk-0.8.0/bbk/man/onb_frequency.Rd | 2 bbk-0.8.0/bbk/man/onb_hierarchy.Rd | 2 bbk-0.8.0/bbk/man/onb_metadata.Rd | 2 bbk-0.8.0/bbk/man/onb_toc.Rd | 2 bbk-0.8.0/bbk/man/snb_data.Rd | 4 - bbk-0.8.0/bbk/tests/testthat/test-bbk.R | 8 -- bbk-0.8.0/bbk/tests/testthat/test-bde.R | 3 bbk-0.8.0/bbk/tests/testthat/test-boe.R | 3 bbk-0.8.0/bbk/tests/testthat/test-ecb.R | 6 - bbk-0.8.0/bbk/tests/testthat/test-exchange-rates.R |only bbk-0.8.0/bbk/tests/testthat/test-snb.R | 3 46 files changed, 188 insertions(+), 114 deletions(-)
Title: Sequential Trial Emulation
Description: Implementation of sequential trial emulation for the analysis of observational databases.
The 'SEQTaRget' software accommodates time-varying treatments and confounders, as well as binary
and failure time outcomes. 'SEQTaRget' allows to compare both static and dynamic strategies,
can be used to estimate observational analogs of intention-to-treat
and per-protocol effects, and can adjust for potential selection bias
induced by losses-to-follow-up. (Paper to come).
Author: Ryan O'Dea [aut, cre] ,
Alejandro Szmulewicz [aut] ,
Tom Palmer [aut] ,
Miguel Hernan [aut] ,
The President and Fellows of Harvard College [cph]
Maintainer: Ryan O'Dea <ryanodea@hsph.harvard.edu>
Diff between SEQTaRget versions 1.0.0 dated 2025-09-17 and 1.0.1 dated 2025-10-01
DESCRIPTION | 6 +- MD5 | 26 ++++---- R/SEQopts.R | 3 - R/SEQuential.R | 6 +- R/internal_plot.R | 2 README.md | 4 - inst/doc/SEQuential.Rmd | 7 ++ inst/doc/SEQuential.html | 17 +++++ inst/doc/doseresponse.R | 115 ++++++++++++++++++++++++++++++++++++++ inst/doc/doseresponse.Rmd | 134 ++++++++++++++++++++++++++++++++++++++++++++- inst/doc/doseresponse.html | 127 ++++++++++++++++++++++++++++++++++++++++++ man/SEQopts.Rd | 4 - vignettes/SEQuential.Rmd | 7 ++ vignettes/doseresponse.Rmd | 134 ++++++++++++++++++++++++++++++++++++++++++++- 14 files changed, 561 insertions(+), 31 deletions(-)
Title: Quantification of Asymmetric Dependence
Description: A copula-based measure for quantifying asymmetry in dependence and associations. Documentation and theory about 'qad' is provided
by the paper by Junker, Griessenberger & Trutschnig (2021, <doi:10.1016/j.csda.2020.107058>), and the paper by Trutschnig (2011, <doi:10.1016/j.jmaa.2011.06.013>).
Author: Thimo Kasper [aut],
Florian Griessenberger [aut],
Robert R. Junker [aut],
Valentin Petzel [aut],
Wolfgang Trutschnig [aut],
Lea Maislinger [cre]
Maintainer: Lea Maislinger <lea.maislinger@plus.ac.at>
Diff between qad versions 1.0.5 dated 2025-07-02 and 1.0.6 dated 2025-10-01
DESCRIPTION | 6 MD5 | 32 - inst/doc/qad-vignette.R | 3 inst/doc/qad-vignette.Rmd | 3 inst/doc/qad-vignette.html | 325 ++++++++++---------- tests/testthat/test-predict.R | 4 tests/testthat/test-qad.R | 5 tests/testthat/test-utilityfunctions.R | 24 - vignettes/man/figures/README-example2-1.png |binary vignettes/man/figures/README-plotforecast-1.png |binary vignettes/man/figures/README-plotforecast-2.png |binary vignettes/man/figures/README-unnamed-chunk-13-1.png |binary vignettes/man/figures/README-unnamed-chunk-6-1.png |binary vignettes/man/figures/README-unnamed-chunk-6-2.png |binary vignettes/man/figures/README-unnamed-chunk-7-1.png |binary vignettes/man/figures/README-unnamed-chunk-7-2.png |binary vignettes/qad-vignette.Rmd | 3 17 files changed, 208 insertions(+), 197 deletions(-)
Title: Analyzing and Visualizing Multidimensional Plant Traits
Description: Implements analytical methods for multidimensional plant traits, including Competitors-Stress tolerators-Ruderals strategy analysis using leaf traits, Leaf-Height-Seed strategy analysis, Niche Periodicity Table analysis, and Trait Network analysis. Provides functions for data analysis, visualization, and network metrics calculation. Methods are based on Grime (1974) <doi:10.1038/250026a0>, Pierce et al. (2017) <doi:10.1111/1365-2435.12882>, Westoby (1998) <doi:10.1023/A:1004327224729>, Winemiller et al. (2015) <doi:10.1111/ele.12462>, He et al. (2020) <doi:10.1016/j.tree.2020.06.003>.
Author: Yan He [aut, cre],
Zhaogang Liu [aut],
Jiangshan Lai [aut],
Lingfeng Mao [aut]
Maintainer: Yan He <heyan@njfu.edu.cn>
Diff between MultiTraits versions 0.5.0 dated 2025-04-20 and 0.6.0 dated 2025-10-01
MultiTraits-0.5.0/MultiTraits/R/NPT.R |only MultiTraits-0.5.0/MultiTraits/R/TN.R |only MultiTraits-0.5.0/MultiTraits/R/data.R |only MultiTraits-0.5.0/MultiTraits/man/NPT.Rd |only MultiTraits-0.5.0/MultiTraits/man/NPT_plot.Rd |only MultiTraits-0.5.0/MultiTraits/man/Strate_CSR.Rd |only MultiTraits-0.5.0/MultiTraits/man/TN.Rd |only MultiTraits-0.5.0/MultiTraits/man/TN_corr.Rd |only MultiTraits-0.5.0/MultiTraits/man/TN_metrics.Rd |only MultiTraits-0.5.0/MultiTraits/man/TN_plot.Rd |only MultiTraits-0.5.0/MultiTraits/tests |only MultiTraits-0.6.0/MultiTraits/DESCRIPTION | 15 MultiTraits-0.6.0/MultiTraits/MD5 | 89 MultiTraits-0.6.0/MultiTraits/NAMESPACE | 66 MultiTraits-0.6.0/MultiTraits/NEWS.md | 63 MultiTraits-0.6.0/MultiTraits/R/CSR.R | 296 -- MultiTraits-0.6.0/MultiTraits/R/CSR_hodgson.R |only MultiTraits-0.6.0/MultiTraits/R/CSR_plot.R |only MultiTraits-0.6.0/MultiTraits/R/LHS.R | 244 -- MultiTraits-0.6.0/MultiTraits/R/LHS_plot.R |only MultiTraits-0.6.0/MultiTraits/R/LHS_strategy_scheme.R |only MultiTraits-0.6.0/MultiTraits/R/NPT_continuous.R |only MultiTraits-0.6.0/MultiTraits/R/NPT_continuous_plot.R |only MultiTraits-0.6.0/MultiTraits/R/NPT_discrete.R |only MultiTraits-0.6.0/MultiTraits/R/NPT_discrete_plot.R |only MultiTraits-0.6.0/MultiTraits/R/PFF.R |only MultiTraits-0.6.0/MultiTraits/R/PFF_tree.R |only MultiTraits-0.6.0/MultiTraits/R/PTN.R |only MultiTraits-0.6.0/MultiTraits/R/PTN_corr.R |only MultiTraits-0.6.0/MultiTraits/R/PTN_metrics.R |only MultiTraits-0.6.0/MultiTraits/R/PTN_plot.R |only MultiTraits-0.6.0/MultiTraits/R/phylo_correlation.R |only MultiTraits-0.6.0/MultiTraits/README.md | 199 - MultiTraits-0.6.0/MultiTraits/build/vignette.rds |binary MultiTraits-0.6.0/MultiTraits/data/PFF.rda |binary MultiTraits-0.6.0/MultiTraits/data/PFF_tree.rda |only MultiTraits-0.6.0/MultiTraits/inst/doc/MultiTraits_tutorial.R | 120 - MultiTraits-0.6.0/MultiTraits/inst/doc/MultiTraits_tutorial.Rmd | 196 - MultiTraits-0.6.0/MultiTraits/inst/doc/MultiTraits_tutorial.html | 1175 +++++----- MultiTraits-0.6.0/MultiTraits/man/CSR.Rd | 56 MultiTraits-0.6.0/MultiTraits/man/CSR_hodgson.Rd |only MultiTraits-0.6.0/MultiTraits/man/CSR_plot.Rd | 76 MultiTraits-0.6.0/MultiTraits/man/LHS.Rd | 59 MultiTraits-0.6.0/MultiTraits/man/LHS_plot.Rd | 92 MultiTraits-0.6.0/MultiTraits/man/LHS_strategy_scheme.Rd | 8 MultiTraits-0.6.0/MultiTraits/man/NPT_continuous.Rd |only MultiTraits-0.6.0/MultiTraits/man/NPT_continuous_plot.Rd |only MultiTraits-0.6.0/MultiTraits/man/NPT_discrete.Rd |only MultiTraits-0.6.0/MultiTraits/man/NPT_discrete_plot.Rd |only MultiTraits-0.6.0/MultiTraits/man/PFF.Rd | 15 MultiTraits-0.6.0/MultiTraits/man/PFF_tree.Rd |only MultiTraits-0.6.0/MultiTraits/man/PTN.Rd |only MultiTraits-0.6.0/MultiTraits/man/PTN_corr.Rd |only MultiTraits-0.6.0/MultiTraits/man/PTN_metrics.Rd |only MultiTraits-0.6.0/MultiTraits/man/PTN_plot.Rd |only MultiTraits-0.6.0/MultiTraits/man/figures/1.jpg |binary MultiTraits-0.6.0/MultiTraits/man/figures/2.jpg |binary MultiTraits-0.6.0/MultiTraits/man/figures/3.jpg |binary MultiTraits-0.6.0/MultiTraits/man/figures/4.jpg |binary MultiTraits-0.6.0/MultiTraits/man/figures/5.jpg |binary MultiTraits-0.6.0/MultiTraits/man/phylo_correlation.Rd |only MultiTraits-0.6.0/MultiTraits/vignettes/MultiTraits_tutorial.Rmd | 196 - 62 files changed, 1591 insertions(+), 1374 deletions(-)
Title: Scales, Geometries, and Extensions of 'ggplot2' for Election
Mapping
Description: Provides 'ggplot2' extensions for political map making. Implements
new geometries for groups of simple feature geometries. Adds palettes and scales
for red to blue color mapping and for discrete maps. Implements tools for easy
label generation and placement, automatic map coloring, and themes.
Author: Cory McCartan [aut],
Christopher T. Kenny [aut, cre]
Maintainer: Christopher T. Kenny <ctkenny@proton.me>
Diff between ggredist versions 0.0.3 dated 2025-08-29 and 0.0.4 dated 2025-10-01
DESCRIPTION | 14 +- MD5 | 16 +- NAMESPACE | 2 NEWS.md | 4 R/538.R | 99 ++++++++++-------- R/crop.R |only R/geom_place.R | 292 +++++++++++++++++++++++++++--------------------------- README.md | 10 - man/StatPlaces.Rd | 2 man/zoom.Rd |only 10 files changed, 226 insertions(+), 213 deletions(-)
Title: Archaeological Time Series
Description: A toolkit for archaeological time series and time intervals.
This package provides a system of classes and methods to represent and
work with archaeological time series and time intervals. Dates are
represented as "rata die" and can be converted to (virtually) any
calendar defined by Reingold and Dershowitz (2018)
<doi:10.1017/9781107415058>. This packages offers a simple API that
can be used by other specialized packages.
Author: Nicolas Frerebeau [aut, cre] ,
Joe Roe [aut] ,
Brice Lebrun [art] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between aion versions 1.5.0 dated 2025-04-29 and 1.6.0 dated 2025-10-01
DESCRIPTION | 39 - MD5 | 111 +-- NAMESPACE | 18 NEWS.md | 8 R/AllGenerics.R | 368 +++++++++- R/aion-package.R | 35 R/format.R | 14 R/graph.R |only R/mutators.R | 22 R/overlap.R | 4 R/relations.R |only README.md | 49 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/aion.Rmd | 6 inst/doc/aion.html | 10 inst/doc/extending.Rmd | 2 inst/doc/extending.html | 6 inst/doc/stratigraphy.R |only inst/doc/stratigraphy.Rmd |only inst/doc/stratigraphy.html |only inst/examples/ex-format.R | 1 inst/examples/ex-graph.R |only inst/examples/ex-relation.R |only inst/po/fr/LC_MESSAGES/R-aion.mo |binary inst/tinytest/_tinysnapshot/axis_Ma.svg | 34 inst/tinytest/_tinysnapshot/axis_default.svg | 30 inst/tinytest/_tinysnapshot/axis_ka.svg | 34 inst/tinytest/_tinysnapshot/plot_facet_BP.svg | 100 +- inst/tinytest/_tinysnapshot/plot_facet_CE.svg | 96 +- inst/tinytest/_tinysnapshot/plot_facet_b2k.svg | 84 +- inst/tinytest/_tinysnapshot/plot_facet_rd.svg | 100 +- inst/tinytest/_tinysnapshot/plot_image.svg | 666 +++++++++---------- inst/tinytest/_tinysnapshot/plot_interval_CE.svg | 42 - inst/tinytest/_tinysnapshot/plot_interval_Inf.svg | 18 inst/tinytest/_tinysnapshot/plot_interval_groups.svg | 42 - inst/tinytest/_tinysnapshot/plot_interval_rd.svg | 40 - inst/tinytest/_tinysnapshot/plot_single.svg | 24 inst/tinytest/_tinysnapshot/plot_zero_Julian.svg | 96 +- inst/tinytest/helpers.R |only inst/tinytest/test_graph.R |only inst/tinytest/test_intervals.R | 51 - inst/tinytest/test_plot.R | 154 ++-- inst/tinytest/test_relations.R |only inst/tinytest/test_show.R | 3 inst/tinytest/test_zero.R | 24 man/aion-package.Rd | 41 - man/as.data.frame.Rd | 1 man/format.Rd | 9 man/graph_create.Rd |only man/graph_prune.Rd |only man/labels.Rd | 1 man/length.Rd | 1 man/names.Rd |only man/overlap.Rd | 6 man/relations.Rd |only man/subset.Rd | 3 po/R-aion.pot | 32 po/R-fr.po | 40 - tests/tinytest.R | 6 vignettes/aion.Rmd | 6 vignettes/bibliography.bib | 68 + vignettes/extending.Rmd | 2 vignettes/stratigraphy.Rmd |only 64 files changed, 1521 insertions(+), 1026 deletions(-)
Title: Water Quality Analysis Tools for the Brazilian Context
Description: Tools to import, clean, validate, and analyze freshwater quality data in Brazil.
Implements water quality indices including the Water Quality Index (WQI/IQA),
the Trophic State Index (TSI/IET) after Carlson (1977) <doi:10.4319/lo.1977.22.2.0361>
and Lamparelli (2004) <https://www.teses.usp.br/teses/disponiveis/41/41134/tde-20032006-075813/publico/TeseLamparelli2004.pdf>,
and the National Sanitation Foundation Water Quality Index (NSF WQI)
<doi:10.1007/s11157-023-09650-7>. The package also checks
compliance with Brazilian standard CONAMA Resolution 357/2005
<https://conama.mma.gov.br/?id=450&option=com_sisconama&task=arquivo.download>
and generates reproducible reports for routine monitoring workflows.
Author: Vinicius Saraiva Santos [aut, cre]
Maintainer: Vinicius Saraiva Santos <vinisaraiva@gmail.com>
Diff between tikatuwq versions 0.4.6 dated 2025-09-22 and 0.5.1 dated 2025-10-01
tikatuwq-0.4.6/tikatuwq/man/iqa_curve_table.Rd |only tikatuwq-0.4.6/tikatuwq/man/qi_interp.Rd |only tikatuwq-0.5.1/tikatuwq/DESCRIPTION | 10 tikatuwq-0.5.1/tikatuwq/MD5 | 95 ++-- tikatuwq-0.5.1/tikatuwq/NAMESPACE | 6 tikatuwq-0.5.1/tikatuwq/NEWS.md | 24 - tikatuwq-0.5.1/tikatuwq/R/analysis_text.R | 82 ++- tikatuwq-0.5.1/tikatuwq/R/conama.R | 294 ++++++------ tikatuwq-0.5.1/tikatuwq/R/data_wq_demo.R | 34 + tikatuwq-0.5.1/tikatuwq/R/iet.R | 73 ++- tikatuwq-0.5.1/tikatuwq/R/iet_lamparelli.R | 82 ++- tikatuwq-0.5.1/tikatuwq/R/io_clean.R | 108 +++- tikatuwq-0.5.1/tikatuwq/R/iqa.R | 131 ++++- tikatuwq-0.5.1/tikatuwq/R/iqa_curves.R | 111 +++- tikatuwq-0.5.1/tikatuwq/R/iqa_equations.R | 333 ++++++++------ tikatuwq-0.5.1/tikatuwq/R/nsfwqi.R | 160 +++++- tikatuwq-0.5.1/tikatuwq/R/plot_map.R |only tikatuwq-0.5.1/tikatuwq/R/report.R | 96 +++- tikatuwq-0.5.1/tikatuwq/R/summaries.R | 74 ++- tikatuwq-0.5.1/tikatuwq/R/tikatuwq-package.R | 58 ++ tikatuwq-0.5.1/tikatuwq/R/viz.R | 151 +++++- tikatuwq-0.5.1/tikatuwq/README.md | 21 tikatuwq-0.5.1/tikatuwq/inst/CITATION | 20 tikatuwq-0.5.1/tikatuwq/inst/WORDLIST | 392 ++++++++--------- tikatuwq-0.5.1/tikatuwq/inst/doc/tikatuwq.R | 114 ++++ tikatuwq-0.5.1/tikatuwq/inst/doc/tikatuwq.Rmd | 120 ++++- tikatuwq-0.5.1/tikatuwq/inst/doc/tikatuwq.html | 246 +++++++--- tikatuwq-0.5.1/tikatuwq/man/clean_units.Rd | 19 tikatuwq-0.5.1/tikatuwq/man/conama_check.Rd | 37 - tikatuwq-0.5.1/tikatuwq/man/conama_limits.Rd | 14 tikatuwq-0.5.1/tikatuwq/man/conama_report.Rd | 43 - tikatuwq-0.5.1/tikatuwq/man/conama_summary.Rd | 22 tikatuwq-0.5.1/tikatuwq/man/conama_text.Rd | 22 tikatuwq-0.5.1/tikatuwq/man/generate_analysis.Rd | 45 + tikatuwq-0.5.1/tikatuwq/man/iet_carlson.Rd | 52 +- tikatuwq-0.5.1/tikatuwq/man/iet_lamparelli.Rd | 60 ++ tikatuwq-0.5.1/tikatuwq/man/iqa.Rd | 69 ++ tikatuwq-0.5.1/tikatuwq/man/nsfwqi.Rd | 51 +- tikatuwq-0.5.1/tikatuwq/man/plot_box.Rd | 18 tikatuwq-0.5.1/tikatuwq/man/plot_heatmap.Rd | 21 tikatuwq-0.5.1/tikatuwq/man/plot_iqa.Rd | 15 tikatuwq-0.5.1/tikatuwq/man/plot_map.Rd |only tikatuwq-0.5.1/tikatuwq/man/plot_series.Rd | 24 - tikatuwq-0.5.1/tikatuwq/man/read_wq.Rd | 50 +- tikatuwq-0.5.1/tikatuwq/man/render_report.Rd | 53 +- tikatuwq-0.5.1/tikatuwq/man/resume_wq.Rd | 38 + tikatuwq-0.5.1/tikatuwq/man/tikatuwq-package.Rd | 52 +- tikatuwq-0.5.1/tikatuwq/man/validate_wq.Rd | 23 tikatuwq-0.5.1/tikatuwq/man/wq_demo.Rd | 31 - tikatuwq-0.5.1/tikatuwq/tests/testthat/test-plot_map.R |only tikatuwq-0.5.1/tikatuwq/vignettes/tikatuwq.Rmd | 120 ++++- 51 files changed, 2676 insertions(+), 1038 deletions(-)
Title: Embedding and Clustering with Alignment for Spatial Omics
Datasets
Description: An efficient data integration method is provided for multiple spatial transcriptomics data with non-cluster-relevant effects such as the complex batch effects. It unifies spatial factor analysis simultaneously with spatial clustering and embedding alignment, requiring only partially shared cell/domain clusters across datasets. More details can be referred to Wei Liu, et al. (2023) <doi:10.1038/s41467-023-35947-w>.
Author: Wei Liu [aut, cre],
Yi Yang [aut],
Jin Liu [aut]
Maintainer: Wei Liu <liuweideng@gmail.com>
Diff between PRECAST versions 1.6.6 dated 2025-03-27 and 1.7 dated 2025-10-01
DESCRIPTION | 17 MD5 | 62 +-- NAMESPACE | 11 R/SetClass.R | 334 ++++++++--------- R/main.R | 570 +++++++++++++++++++----------- README.md | 5 build/vignette.rds |binary inst/doc/PRECAST.BreastCancer.R | 8 inst/doc/PRECAST.BreastCancer.Rmd | 6 inst/doc/PRECAST.BreastCancer.html | 581 +++++++++++++++++------------- inst/doc/PRECAST.DLPFC.R | 6 inst/doc/PRECAST.DLPFC.Rmd | 6 inst/doc/PRECAST.DLPFC.html | 358 ++++++++++-------- inst/doc/PRECAST.DLPFC4.R | 9 inst/doc/PRECAST.DLPFC4.Rmd | 7 inst/doc/PRECAST.DLPFC4.html | 502 ++++++++++++++------------ inst/doc/PRECAST.R | 2 inst/doc/PRECAST.Simu.R | 4 inst/doc/PRECAST.Simu.Rmd | 2 inst/doc/PRECAST.Simu.html | 703 ++++++++++++++++++++----------------- inst/doc/PRECAST.html | 174 ++++----- man/chooseColors.Rd | 58 +-- man/getAdj_fixedNumber.Rd | 2 man/getAdj_reg.Rd | 2 man/idrsc.Rd | 16 man/model_set.Rd | 8 src/idrsc2.cpp | 311 +++++++++------- src/utilMultIntcluster.cpp | 51 ++ vignettes/PRECAST.BreastCancer.Rmd | 6 vignettes/PRECAST.DLPFC.Rmd | 6 vignettes/PRECAST.DLPFC4.Rmd | 7 vignettes/PRECAST.Simu.Rmd | 2 32 files changed, 2222 insertions(+), 1614 deletions(-)
Title: Access to Spanish Meteorological Stations Services
Description: Access to different Spanish meteorological stations data services and APIs (AEMET, SMC, MG,
Meteoclimatic...).
Author: Victor Granda [aut, cre] ,
Miquel de Caceres [ctb] ,
Aitor Ameztegui [ctb] ,
Luis Franco [ctb],
Ruben Fernandez-Casal [ctb]
Maintainer: Victor Granda <victorgrandagarcia@gmail.com>
Diff between meteospain versions 0.2.1 dated 2025-07-01 and 0.2.2 dated 2025-10-01
DESCRIPTION | 6 - MD5 | 30 ++++----- NEWS.md | 9 ++ R/aemet_helpers.R | 57 +++++++++-------- R/meteogalicia_helpers.R | 2 R/utils.R | 13 ++++ inst/doc/aemet.html | 88 ++++++++++++--------------- inst/doc/api_limits.Rmd | 2 inst/doc/api_limits.html | 108 +++++++++++++++------------------ inst/doc/compatibility.html | 142 +++++++++++++++++++++++--------------------- inst/doc/meteocat.html | 12 +-- inst/doc/meteoclimatic.html | 56 ++++++++--------- inst/doc/meteogalicia.html | 28 ++++---- inst/doc/ria.html | 12 +-- tests/testthat/test-aemet.R | 2 vignettes/api_limits.Rmd | 2 16 files changed, 294 insertions(+), 275 deletions(-)
Title: Interface to Download Meteorological (and Hydrological) Datasets
Description: Automatize downloading of meteorological and hydrological data from publicly available repositories:
OGIMET (<http://ogimet.com/index.phtml.en>),
University of Wyoming - atmospheric vertical profiling data (<http://weather.uwyo.edu/upperair/>),
Polish Institute of Meteorology and Water Management - National Research Institute (<https://danepubliczne.imgw.pl>),
and National Oceanic & Atmospheric Administration (NOAA).
This package also allows for searching geographical coordinates for each observation and calculate distances to the nearest stations.
Author: Bartosz Czernecki [aut, cre] ,
Arkadiusz Glogowski [aut] ,
Jakub Nowosad [aut] ,
IMGW-PIB [ctb]
Maintainer: Bartosz Czernecki <nwp@amu.edu.pl>
Diff between climate versions 1.2.3 dated 2025-04-23 and 1.2.4 dated 2025-10-01
DESCRIPTION | 21 ++++++++++------- MD5 | 38 +++++++++++++++++--------------- NAMESPACE | 3 ++ NEWS.md | 14 +++++++---- R/get_coord_from_string.R | 22 +++++++++++------- R/hydro_imgw_daily.R | 2 + R/hydro_imgw_datastore.R |only R/meteo_imgw_datastore.R | 17 +++++++++----- R/nearest_stations_imgw.R | 20 +++++++++-------- R/nearest_stations_ogimet.R | 36 +++++++++++++++++------------- R/ogimet_daily.R | 25 ++++++++++++++------- R/ogimet_hourly.R | 35 ++++++++++++++++++----------- R/stations_hydro_imgw_telemetry.R |only R/stations_meteo_imgw_telemetry.R | 6 ++--- R/stations_ogimet.R | 19 +++++++++++----- README.md | 8 ++++-- inst/doc/getstarted.html | 41 ++++++++++++++++------------------- man/hydro_imgw_datastore.Rd |only man/meteo_imgw_datastore.Rd | 2 - man/nearest_stations_ogimet.Rd | 5 +--- man/stations_hydro_imgw_telemetry.Rd |only man/stations_meteo_imgw_telemetry.Rd | 6 ++--- 22 files changed, 189 insertions(+), 131 deletions(-)
Title: System Native Font Finding
Description: Provides system native access to the font catalogue. As font
handling varies between systems it is difficult to correctly locate
installed fonts across different operating systems. The 'systemfonts'
package provides bindings to the native libraries on Windows, macOS
and Linux for finding font files that can then be used further by e.g.
graphic devices. The main use is intended to be from compiled code but
'systemfonts' also provides access from R.
Author: Thomas Lin Pedersen [aut, cre] ,
Jeroen Ooms [aut] ,
Devon Govett [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between systemfonts versions 1.3.0 dated 2025-09-30 and 1.3.1 dated 2025-10-01
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- NEWS.md | 6 ++++++ R/font_variation.R | 18 +++++++++++++++++- R/register_font.R | 15 ++++++--------- inst/doc/systemfonts.R | 9 ++++++++- inst/doc/systemfonts.Rmd | 15 +++++++++++++-- inst/doc/systemfonts.html | 2 +- man/register_font.Rd | 16 +++++++--------- src/font_metrics.cpp | 2 +- src/ft_cache.cpp | 4 ++-- src/ft_cache.h | 4 ++-- src/utils.h | 9 ++++++--- vignettes/systemfonts.Rmd | 15 +++++++++++++-- 14 files changed, 98 insertions(+), 49 deletions(-)
Title: Simulation Methods for Legislative Redistricting
Description: Enables researchers to sample redistricting plans from a pre-specified
target distribution using Sequential Monte Carlo and Markov Chain Monte Carlo
algorithms. The package allows for the implementation of various constraints in
the redistricting process such as geographic compactness and population parity
requirements. Tools for analysis such as computation of various summary statistics
and plotting functionality are also included. The package implements the SMC
algorithm of McCartan and Imai (2023) <doi:10.1214/23-AOAS1763>, the enumeration
algorithm of Fifield, Imai, Kawahara, and Kenny (2020) <doi:10.1080/2330443X.2020.1791773>,
the Flip MCMC algorithm of Fifield, Higgins, Imai and Tarr (2020) <doi:10.1080/10618600.2020.1739532>,
the Merge-split/Recombination algorithms of Carter et al. (2019) <doi:10.48550/arXiv.1911.01503>
and DeFord et al. (2021) <doi:10.1162/99608f92.eb30390f>, and the Short-burst
optimization algorithm of Cannon et al. (2020) < [...truncated...]
Author: Christopher T. Kenny [aut, cre] ,
Cory McCartan [aut] ,
Ben Fifield [aut] ,
Kosuke Imai [aut] ,
Jun Kawahara [ctb],
Alexander Tarr [ctb],
Michael Higgins [ctb]
Maintainer: Christopher T. Kenny <ctkenny@proton.me>
Diff between redist versions 4.3.0 dated 2025-07-08 and 4.3.1 dated 2025-10-01
DESCRIPTION | 12 ++-- MD5 | 86 +++++++++++++++---------------- R/adjacency.R | 24 ++++---- R/classify_compare.R | 6 +- R/confint.R | 6 +- R/cores.R | 2 R/counties.R | 4 - R/deprecations.R | 52 +++++++++--------- R/diagnostics.R | 24 ++++---- R/distances.R | 8 +- R/enumpart.R | 4 - R/flip_helpers.R | 8 +- R/freeze.R | 14 ++--- R/map_helpers.R | 8 +- R/numbering.R | 14 ++--- R/parity.R | 8 +- R/plans_helpers.R | 26 ++++----- R/plot_cores.R | 4 - R/plot_diagnostics.R | 8 +- R/plot_map.R | 14 ++--- R/plot_plans.R | 22 +++---- R/plot_weighted_adj.R | 2 R/proj.R | 8 +- R/redist_constr.R | 122 ++++++++++++++++++++++---------------------- R/redist_findparams.R | 16 ++--- R/redist_map.R | 66 +++++++++++------------ R/redist_ms.R | 28 +++++----- R/redist_ms_parallel.R | 28 +++++----- R/redist_plans.R | 68 ++++++++++++------------ R/redist_shortburst.R | 28 +++++----- R/redist_smc.R | 32 +++++------ R/reindex.R | 2 R/tidy_deprecations.R | 4 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/common_args.html | 9 +-- inst/doc/flip.html | 20 +++---- inst/doc/map-preproc.Rmd | 2 inst/doc/map-preproc.html | 9 +-- inst/doc/redist.Rmd | 2 inst/doc/redist.html | 7 +- tests/testthat/test_burst.R | 5 + vignettes/map-preproc.Rmd | 2 vignettes/redist.Rmd | 2 44 files changed, 412 insertions(+), 404 deletions(-)
Title: Identify Characteristics of Patients in the OMOP Common Data
Model
Description: Identify the characteristics of patients in data mapped to the
Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Mike Du [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [aut] ,
Xintong Li [ctb] ,
Xihang Chen [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between PatientProfiles versions 1.4.2 dated 2025-07-09 and 1.4.3 dated 2025-10-01
DESCRIPTION | 22 +- MD5 | 218 ++++++++++---------- NAMESPACE | 1 R/PatientProfiles-package.R | 1 R/addCategories.R | 10 R/addCohortIntersect.R | 37 ++- R/addConceptIntersect.R | 120 ++++++++--- R/addDeath.R | 15 - R/addDemographics.R | 34 +-- R/addDemographicsQuery.R | 83 ++++--- R/addIntersect.R | 56 +++-- R/addObservationPeriodId.R | 16 - R/addTableIntersect.R | 54 +++-- R/checks.R | 108 ---------- R/filterInObservation.R | 12 - R/formats.R | 7 R/mockPatientProfiles.R | 103 +++++---- R/summariseResult.R | 22 +- R/utilities.R | 13 - README.md | 253 +++++++++++------------ inst/doc/cohort-intersect.R | 11 - inst/doc/cohort-intersect.Rmd | 11 - inst/doc/cohort-intersect.html | 111 +++++----- inst/doc/concept-intersect.R | 56 ++--- inst/doc/concept-intersect.Rmd | 56 ++--- inst/doc/concept-intersect.html | 169 ++++++++-------- inst/doc/demographics.R | 2 inst/doc/demographics.html | 240 +++++++++++----------- inst/doc/demographics.rmd | 2 inst/doc/summarise.R | 21 - inst/doc/summarise.Rmd | 21 - inst/doc/summarise.html | 202 ++++++++++--------- inst/doc/table-intersect.R | 19 - inst/doc/table-intersect.Rmd | 19 - inst/doc/table-intersect.html | 120 +++++------ man/PatientProfiles-package.Rd | 2 man/addAge.Rd | 6 man/addAgeQuery.Rd | 5 man/addCategories.Rd | 6 man/addCdmName.Rd | 3 man/addCohortIntersectCount.Rd | 5 man/addCohortIntersectDate.Rd | 5 man/addCohortIntersectDays.Rd | 5 man/addCohortIntersectFlag.Rd | 6 man/addCohortName.Rd | 2 man/addConceptIntersectCount.Rd | 13 - man/addConceptIntersectDate.Rd | 13 - man/addConceptIntersectDays.Rd | 13 - man/addConceptIntersectField.Rd | 18 + man/addConceptIntersectFlag.Rd | 13 - man/addConceptName.Rd | 8 man/addDateOfBirth.Rd | 4 man/addDateOfBirthQuery.Rd | 4 man/addDeathDate.Rd | 5 man/addDeathDays.Rd | 5 man/addDeathFlag.Rd | 5 man/addDemographics.Rd | 4 man/addDemographicsQuery.Rd | 4 man/addFutureObservation.Rd | 5 man/addFutureObservationQuery.Rd | 5 man/addInObservation.Rd | 5 man/addInObservationQuery.Rd | 5 man/addObservationPeriodId.Rd | 5 man/addObservationPeriodIdQuery.Rd | 5 man/addPriorObservation.Rd | 5 man/addPriorObservationQuery.Rd | 5 man/addSex.Rd | 5 man/addSexQuery.Rd | 5 man/addTableIntersectCount.Rd | 5 man/addTableIntersectDate.Rd | 5 man/addTableIntersectDays.Rd | 5 man/addTableIntersectField.Rd | 12 - man/addTableIntersectFlag.Rd | 5 man/endDateColumn.Rd | 1 man/filterInObservation.Rd | 12 - man/mockDisconnect.Rd | 4 man/mockPatientProfiles.Rd | 22 +- man/sourceConceptIdColumn.Rd | 1 man/standardConceptIdColumn.Rd | 1 man/startDateColumn.Rd | 1 man/summariseResult.Rd | 12 - man/variableTypes.Rd | 5 tests/testthat/setup.R | 89 ++++---- tests/testthat/test-addAttributes.R | 12 - tests/testthat/test-addCategories.R | 45 ++-- tests/testthat/test-addCohortIntersect.R | 175 +++++++--------- tests/testthat/test-addConceptIntersect.R | 174 ++++++++-------- tests/testthat/test-addDeath.R | 56 ++--- tests/testthat/test-addDemographics.R | 264 ++++++++++++++----------- tests/testthat/test-addFutureObservation.R | 73 +++--- tests/testthat/test-addInObservation.R | 37 +-- tests/testthat/test-addIntersect.R | 148 +++++++------- tests/testthat/test-addObservationPeriodId.R | 39 +-- tests/testthat/test-addPriorObservation.R | 62 +++-- tests/testthat/test-addSex.R | 44 ++-- tests/testthat/test-addTableIntersect.R | 82 ++++--- tests/testthat/test-benchmarkPatientProfiles.R | 8 tests/testthat/test-checks.R | 59 +---- tests/testthat/test-class.R | 10 tests/testthat/test-filterCohortId.R | 25 +- tests/testthat/test-filterInObservation.R | 7 tests/testthat/test-mockPatientProfiles.R | 5 tests/testthat/test-name.R | 23 +- tests/testthat/test-summariseResult.R | 244 +++++++++++++++-------- tests/testthat/test-utilities.R | 6 vignettes/cohort-intersect.Rmd | 11 - vignettes/concept-intersect.Rmd | 56 ++--- vignettes/demographics.rmd | 2 vignettes/summarise.Rmd | 21 - vignettes/table-intersect.Rmd | 19 - 110 files changed, 2279 insertions(+), 2057 deletions(-)
More information about PatientProfiles at CRAN
Permanent link
Title: Local Projections Impulse Response Functions
Description: Provides functions to estimate and visualize linear as well as nonlinear impulse
responses based on local projections by Jordà (2005) <doi:10.1257/0002828053828518>.
The methods and the package are explained in detail in Adämmer (2019) <doi:10.32614/RJ-2019-052>.
Author: Philipp Adaemmer [aut, cre] ,
James P. LeSage [ctb],
Mehmet Balcilar [ctb],
Jon Danielsson [ctb]
Maintainer: Philipp Adaemmer <philipp.adaemmer@uni-greifswald.de>
Diff between lpirfs versions 0.2.4 dated 2025-03-18 and 0.2.5 dated 2025-10-01
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/get_std_err_tsls.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/lpirfs_vignette.html | 6 +++--- 7 files changed, 20 insertions(+), 14 deletions(-)
Title: CRISPR Pooled Screen Analysis using Beta-Binomial Test
Description: Provides functions for hit gene identification and quantification of sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis.
Details are in Jeong et al. (2019) <doi:10.1101/gr.245571.118> and Baggerly et al. (2003) <doi:10.1093/bioinformatics/btg173>.
Author: Hyun-Hwan Jeong [aut, cre]
Maintainer: Hyun-Hwan Jeong <hyunhwanjeong@icloud.com>
Diff between CB2 versions 1.3.4 dated 2020-07-24 and 1.3.6 dated 2025-10-01
DESCRIPTION | 18 MD5 | 36 - NAMESPACE | 1 R/data.R | 4 R/helpers.R | 4 R/utils.R | 10 README.md | 31 - build/vignette.rds |binary inst/doc/cb2-input-handling.html | 689 ++++++++++++++++++---------- inst/doc/cb2-tutorial.html | 959 ++++++++++++++++++++++----------------- inst/extdata/toydata/sg2seq.tsv |only man/Evers_CRISPRn_RT112.Rd | 2 man/Sanson_CRISPRn_A375.Rd | 2 man/rep_row.Rd |only src/AdaptiveHash.h | 2 src/CB2.cpp | 9 src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 5 tests/testthat/test.toydata.R | 12 20 files changed, 1100 insertions(+), 688 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-16 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-21 0.3.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-25 0.1.5
2025-09-15 0.1.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-18 2.1.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-15 0.1.1
2025-09-01 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-17 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-09 1.0.0
Title: Estimates and Plots Single-Level and Multilevel Latent Class
Models
Description: Efficiently estimates single- and multilevel latent class models with covariates, allowing for output visualization in all specifications. For more technical details, see Lyrvall et al. (2025) <doi:10.1080/00273171.2025.2473935>.
Author: Roberto Di Mari [aut, cre],
Johan Lyrvall [aut],
Zsuzsa Bakk [ctb],
Jennifer Oser [ctb],
Jouni Kuha [ctb]
Maintainer: Roberto Di Mari <roberto.dimari@unict.it>
Diff between multilevLCA versions 2.1.0 dated 2025-09-22 and 2.1.1 dated 2025-10-01
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- build/partial.rdb |binary 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Gene Cluster Visualizations
Description: Provides tools for plotting gene clusters and transcripts by
importing data from GenBank, FASTA, and GFF files. It performs BLASTP and
MUMmer alignments [Altschul et al. (1990) <doi:10.1016/S0022-2836(05)80360-2>;
Delcher et al. (1999) <doi:10.1093/nar/27.11.2369>] and displays results on
gene arrow maps. Extensive customization options are available, including
legends, labels, annotations, scales, colors, tooltips, and more.
Author: Niels van der Velden [aut, cre]
Maintainer: Niels van der Velden <n.s.j.vandervelden@gmail.com>
Diff between geneviewer versions 0.1.10 dated 2025-01-10 and 0.1.11 dated 2025-10-01
geneviewer-0.1.10/geneviewer/inst/htmlwidgets/lib/geneviewer-0.1.10 |only geneviewer-0.1.11/geneviewer/DESCRIPTION | 6 +-- geneviewer-0.1.11/geneviewer/MD5 | 18 ++++----- geneviewer-0.1.11/geneviewer/NEWS.md | 9 ++++ geneviewer-0.1.11/geneviewer/R/geneviewer.R | 19 ++++++---- geneviewer-0.1.11/geneviewer/R/read_genbank.R | 10 +++-- geneviewer-0.1.11/geneviewer/README.md | 18 ++++++++- geneviewer-0.1.11/geneviewer/inst/htmlwidgets/geneviewer.yaml | 10 ++--- geneviewer-0.1.11/geneviewer/inst/htmlwidgets/lib/geneviewer-0.1.11 |only geneviewer-0.1.11/geneviewer/man/GC_legend.Rd | 1 10 files changed, 61 insertions(+), 30 deletions(-)
Title: Circular-Linear Copulas with Angular Symmetry for Movement Data
Description: Classes (S4) of circular-linear, symmetric copulas with corresponding
methods, extending the 'copula' package. These copulas are especially useful
for modeling correlation in discrete-time movement data. Methods for density,
(conditional) distribution, random number generation, bivariate dependence
measures and fitting parameters using maximum likelihood and other
approaches. The package also contains methods for visualizing movement data
and copulas.
Author: Florian Hodel [aut, cre]
Maintainer: Florian Hodel <florian.hodel@yahoo.com>
Diff between cylcop versions 0.2.0 dated 2022-10-29 and 0.2.1 dated 2025-10-01
cylcop-0.2.0/cylcop/man/Cramer_vonMises.Rd |only cylcop-0.2.1/cylcop/DESCRIPTION | 15 +- cylcop-0.2.1/cylcop/MD5 | 86 +++++------ cylcop-0.2.1/cylcop/NEWS.md | 14 + cylcop-0.2.1/cylcop/R/Ccond.R | 4 cylcop-0.2.1/cylcop/R/cyl_cop_class.R | 14 - cylcop-0.2.1/cylcop/R/cyl_rect_combine.R | 14 - cylcop-0.2.1/cylcop/R/cyl_rot_combine.R | 8 - cylcop-0.2.1/cylcop/R/fit_cop_mle.R | 4 cylcop-0.2.1/cylcop/R/gof.R | 8 - cylcop-0.2.1/cylcop/R/joint_distr.R | 14 - cylcop-0.2.1/cylcop/R/mixed_linear.R | 64 ++++---- cylcop-0.2.1/cylcop/R/mixedvonmises.R | 16 +- cylcop-0.2.1/cylcop/R/plotting_functions.R | 60 ++++---- cylcop-0.2.1/cylcop/R/utils.R | 4 cylcop-0.2.1/cylcop/R/wrappedcauchy.R | 16 +- cylcop-0.2.1/cylcop/build/partial.rdb |binary cylcop-0.2.1/cylcop/man/Cylcop.Rd | 8 - cylcop-0.2.1/cylcop/man/ccylcop.Rd | 4 cylcop-0.2.1/cylcop/man/cramer_vonmises.Rd |only cylcop-0.2.1/cylcop/man/cyl_copula-class.Rd | 110 +++++++-------- cylcop-0.2.1/cylcop/man/cyl_rect_combine-class.Rd | 10 - cylcop-0.2.1/cylcop/man/cyl_rect_combine.Rd | 4 cylcop-0.2.1/cylcop/man/cyl_rot_combine-class.Rd | 108 +++++++------- cylcop-0.2.1/cylcop/man/cyl_rot_combine.Rd | 2 cylcop-0.2.1/cylcop/man/cylcop-package.Rd | 4 cylcop-0.2.1/cylcop/man/cylcop_get_option.Rd | 50 +++--- cylcop-0.2.1/cylcop/man/cylcop_set_option.Rd | 50 +++--- cylcop-0.2.1/cylcop/man/fit_cylcop_ml.Rd | 4 cylcop-0.2.1/cylcop/man/full2half_circ.Rd | 2 cylcop-0.2.1/cylcop/man/gammamix.Rd | 16 +- cylcop-0.2.1/cylcop/man/half2full_circ.Rd | 2 cylcop-0.2.1/cylcop/man/joint.Rd | 14 - cylcop-0.2.1/cylcop/man/lnormmix.Rd | 16 +- cylcop-0.2.1/cylcop/man/normmix.Rd | 16 +- cylcop-0.2.1/cylcop/man/numerical_conditional_cop.Rd | 2 cylcop-0.2.1/cylcop/man/numerical_inv_conditional_cop.Rd | 82 +++++------ cylcop-0.2.1/cylcop/man/plot_cop_surf.Rd | 2 cylcop-0.2.1/cylcop/man/plot_joint_box.Rd | 2 cylcop-0.2.1/cylcop/man/prob-cyl_copula-method.Rd | 70 ++++----- cylcop-0.2.1/cylcop/man/show-cyl_copula-method.Rd | 50 +++--- cylcop-0.2.1/cylcop/man/vonmisesmix.Rd | 16 +- cylcop-0.2.1/cylcop/man/wasserstein.Rd | 4 cylcop-0.2.1/cylcop/man/weibullmix.Rd | 16 +- cylcop-0.2.1/cylcop/man/wrappedcauchy.Rd | 16 +- 45 files changed, 519 insertions(+), 502 deletions(-)
Title: Analyzing and Interactive Visualization of Archival Tagging Data
Description: A set of functions to generate, access and analyze standard data products from archival tagging data.
Author: Robert K. Bauer [aut, cre]
Maintainer: Robert K. Bauer <marine.biologging@gmail.com>
This is a re-admission after prior archival of version 0.1.9 dated 2023-11-10
Diff between RchivalTag versions 0.1.9 dated 2023-11-10 and 0.2.2 dated 2025-10-01
ChangeLog | 10 ++ DESCRIPTION | 22 +++- MD5 | 38 ++++---- NAMESPACE | 1 R/get_thermalstrat.r | 35 ++++--- R/ggboxplot_DepthTS_by_hour.r | 2 R/ggplot_geopos.r | 17 ++- R/ggplotly_geopos.r | 15 +-- R/hidden_functions.r | 20 ++++ build/partial.rdb |binary inst/doc/RchivalTag.pdf |binary man/classify_DayTime.Rd | 36 ++------ man/dy_DepthTS.Rd | 103 +++++++---------------- man/get_DayTimeLimits.Rd | 29 ++---- man/ggplot_geopos.Rd | 183 +++++++++-------------------------------- man/ggplotly_geopos.Rd | 6 - man/image_TempDepthProfiles.Rd | 4 man/leaflet_geopos.Rd | 4 man/plot_DepthTempTS.Rd | 2 man/plot_data_coverage.Rd | 2 20 files changed, 209 insertions(+), 320 deletions(-)
Title: Static Analysis of R-Code Dependencies
Description: A minimal R-package to approximately detect global and imported functions or variables from R-source code or R-packages by static code analysis.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>
Diff between checkglobals versions 0.1.3 dated 2025-02-06 and 0.1.4 dated 2025-10-01
DESCRIPTION | 10 MD5 | 29 +- NAMESPACE | 2 NEWS.md | 5 R/as.R | 368 ++++++++++++++++++++++++++++++ R/check_internal.R | 5 R/check_pkg.R | 364 +++++++++++++++-------------- R/check_source.R | 244 ++++++++++--------- R/print.R | 2 inst/extdata |only inst/unit_tests/unit_tests_checkglobals.R | 13 + man/as_sarif_json.Rd |only man/as_sarif_json.checkglobals.Rd |only src/checkglobals.h | 5 src/handlers.c | 9 src/init.c | 4 src/walk_expr.c | 8 17 files changed, 741 insertions(+), 327 deletions(-)
Title: Model Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Model menu includes interfaces for linear and logistic
regression, naive Bayes, neural networks, classification and regression trees,
model evaluation, collaborative filtering, decision analysis, and simulation.
The application extends the functionality in 'radiant.data'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.model versions 1.6.7 dated 2024-10-11 and 1.6.8 dated 2025-10-01
radiant.model-1.6.7/radiant.model/inst/app/tools/help/figures/place_holder.txt |only radiant.model-1.6.8/radiant.model/DESCRIPTION | 10 radiant.model-1.6.8/radiant.model/MD5 | 82 +- radiant.model-1.6.8/radiant.model/NEWS.md | 403 +++++----- radiant.model-1.6.8/radiant.model/R/logistic.R | 2 radiant.model-1.6.8/radiant.model/README.md | 32 radiant.model-1.6.8/radiant.model/inst/app/tools/help/crs.md | 2 radiant.model-1.6.8/radiant.model/inst/app/tools/help/dtree.Rmd | 8 radiant.model-1.6.8/radiant.model/inst/app/tools/help/dtree.md | 8 radiant.model-1.6.8/radiant.model/inst/app/tools/help/evalbin.md | 8 radiant.model-1.6.8/radiant.model/inst/app/tools/help/evalreg.md | 6 radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/cf_summary.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/dtree_model.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/dtree_plot_final.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/dtree_plot_initial.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/dtree_sensitivity.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/evalbin_confusion.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/evalbin_lift_gains.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/evalbin_logistic.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/evalreg_nn.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/evalreg_summary_plot.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/logistic_dvd-full.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/logistic_dvd.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/logistic_plot.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/logistic_predict.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/logistic_predict_data.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/logistic_summary.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/mnl_choice_shares.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/mnl_plot.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/mnl_predict.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/mnl_summary.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/regress_catalog_F_critical.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/regress_catalog_F_test.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/regress_catalog_prob_calc.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/regress_catalog_summary.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/regress_diamonds_corr.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/regress_diamonds_dashboard.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/regress_diamonds_hist.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/regress_diamonds_res_vs_pred.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/regress_diamonds_scatter.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/regress_ideal_corr.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/regress_ideal_dashboard.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/regress_ideal_hist.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/regress_ideal_res_vs_pred.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/regress_ideal_scatter.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/regress_ideal_summary.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/regress_log_diamonds_corr.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/regress_log_diamonds_dashboard.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/regress_log_diamonds_hist.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/regress_log_diamonds_res_vs_pred.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/regress_log_diamonds_scatter.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/regress_log_diamonds_summary.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/regress_log_diamonds_viz_scatter.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/simulater_repeat.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/simulater_repeat_plot.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/simulater_sim.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/simulater_sim_plot.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/figures/simulater_view.png |only radiant.model-1.6.8/radiant.model/inst/app/tools/help/logistic.Rmd | 18 radiant.model-1.6.8/radiant.model/inst/app/tools/help/logistic.md | 18 radiant.model-1.6.8/radiant.model/inst/app/tools/help/mnl.Rmd | 24 radiant.model-1.6.8/radiant.model/inst/app/tools/help/mnl.md | 24 radiant.model-1.6.8/radiant.model/inst/app/tools/help/regress.Rmd | 70 - radiant.model-1.6.8/radiant.model/inst/app/tools/help/regress.md | 70 - radiant.model-1.6.8/radiant.model/inst/app/tools/help/simulater.Rmd | 10 radiant.model-1.6.8/radiant.model/inst/app/tools/help/simulater.md | 12 66 files changed, 418 insertions(+), 389 deletions(-)
Title: Pattern Causality Algorithm
Description: Pattern causality is a novel approach for detecting the hidden causality in the complex system.
Author: Stavros Stavroglou [aut, cre] ,
Athanasios Pantelous [aut] ,
Hui Wang [aut]
Maintainer: Stavros Stavroglou <stavros.k.stavroglou@gmail.com>
Diff between patterncausality versions 0.2.2 dated 2025-09-04 and 0.2.3 dated 2025-10-01
patterncausality-0.2.2/patterncausality/R/convertSignatureToValue.R |only patterncausality-0.2.2/patterncausality/man/validate_custom_fn_output.Rd |only patterncausality-0.2.3/patterncausality/DESCRIPTION | 8 patterncausality-0.2.3/patterncausality/MD5 | 163 ++-- patterncausality-0.2.3/patterncausality/NAMESPACE | 11 patterncausality-0.2.3/patterncausality/R/PC.Mk.II.Full.Details.R | 32 patterncausality-0.2.3/patterncausality/R/PC.Mk.II.Lightweight.R | 38 - patterncausality-0.2.3/patterncausality/R/classes.R | 336 ++++++---- patterncausality-0.2.3/patterncausality/R/data.R | 10 patterncausality-0.2.3/patterncausality/R/dataBank.R | 16 patterncausality-0.2.3/patterncausality/R/distanceMatrix.R | 24 patterncausality-0.2.3/patterncausality/R/fillPCMatrix.R | 28 patterncausality-0.2.3/patterncausality/R/firstCausalityPoint.R | 26 patterncausality-0.2.3/patterncausality/R/firstCausalityPointCHECK.R | 22 patterncausality-0.2.3/patterncausality/R/geom-rtile.R | 10 patterncausality-0.2.3/patterncausality/R/interfaces.R | 83 +- patterncausality-0.2.3/patterncausality/R/natureOfCausality.R | 59 - 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More information about patterncausality at CRAN
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Title: Compute and Visualize Wildfire Exposure
Description: Methods for computing and visualizing wildfire ignition exposure
and directional vulnerability that are published in a series of scientific
publications are automated by the functions in this package. See Beverly
et al. (2010) <doi:10.1071/WF09071>, Beverly et al. (2021)
<doi:10.1007/s10980-020-01173-8>, and Beverly and Forbes (2023)
<doi:10.1007/s11069-023-05885-3> for background and methodology.
Author: Air Forbes [aut, cre] ,
Jennifer Beverly [ths]
Maintainer: Air Forbes <heyairf@gmail.com>
This is a re-admission after prior archival of version 1.1.0 dated 2025-05-27
Diff between fireexposuR versions 1.1.0 dated 2025-05-27 and 1.2.0 dated 2025-10-01
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Title: Analysing 'SNP' and 'Silicodart' Data - Basic Functions
Description: Facilitates the import and analysis of 'SNP' (single nucleotide 'polymorphism')
and 'silicodart' (presence/absence) data. The main focus is on data generated by 'DarT'
(Diversity Arrays Technology), however, data from other sequencing platforms can be used
once 'SNP' or related fragment presence/absence data from any source is imported. Genetic
datasets are stored in a derived 'genlight' format (package 'adegenet'), that allows for
a very compact storage of data and metadata. Functions are available for
importing and exporting of 'SNP' and 'silicodart' data, for reporting on and
filtering on various criteria (e.g. 'callrate', 'heterozygosity', 'reproducibility',
maximum allele frequency). Additional functions are available for visualization
(e.g. Principle Coordinate Analysis) and creating a spatial representation
using maps. 'dartR.base' is the 'base' package of the 'dartRverse' suits of packages.
To install the other packages, we recommend to install the 'dartRverse' package, that
su [...truncated...]
Author: Bernd Gruber [aut, cre],
Arthur Georges [aut],
Jose L. Mijangos [aut],
Carlo Pacioni [aut],
Diana Robledo-Ruiz [aut],
Peter J. Unmack [ctb],
Oliver Berry [ctb],
Lindsay V. Clark [ctb],
Floriaan Devloo-Delva [ctb],
Eric Archer [ctb],
Ching Ching Lau [ [...truncated...]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Diff between dartR.base versions 1.0.5 dated 2025-03-03 and 1.0.7 dated 2025-10-01
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/gl.diagnostics.hwe.r | 11 +++++++++++ R/gl2related.r | 3 +-- man/gl2related.Rd | 3 +-- 5 files changed, 21 insertions(+), 12 deletions(-)
Title: Frequentist Confidence Analysis for Clinical Trials
Description: Frequentist confidence analysis answers the question: How
confident are we in a particular treatment effect? This package calculates
the frequentist confidence in a treatment effect of interest given observed data,
and returns the family of
confidence curves associated with that data.
Author: Freda Werdiger [aut, cre]
Maintainer: Freda Werdiger <freda.werdiger@unimelb.edu.au>
Diff between confidenceCurves versions 0.1.0 dated 2025-08-19 and 0.2.0 dated 2025-10-01
DESCRIPTION | 6 ++-- LICENSE | 4 +-- MD5 | 10 +++---- NAMESPACE | 10 +++---- R/confidenceCurves.R | 64 +++++++++++++++++++++++++++++++++++---------------- tests/testthat.R | 24 +++++++++---------- 6 files changed, 71 insertions(+), 47 deletions(-)
More information about confidenceCurves at CRAN
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Title: Bayesian Estimation and Forecasting of Age-Specific Rates
Description: Fast Bayesian estimation and forecasting of age-specific
rates, probabilities, and means, based on 'Template Model Builder'.
Author: John Bryant [aut, cre],
Junni Zhang [aut],
Bayesian Demography Limited [cph]
Maintainer: John Bryant <john@bayesiandemography.com>
Diff between bage versions 0.9.4 dated 2025-07-20 and 0.9.6 dated 2025-10-01
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bage-0.9.6/bage/vignettes/vig09_covariates.Rmd |only bage-0.9.6/bage/vignettes/vig10_datamod.Rmd |only 174 files changed, 14858 insertions(+), 2458 deletions(-)
Title: Simplified Vertex-Wise Analyses of Whole-Brain and Hippocampal
Surface
Description: Provides functions to run statistical analyses on
surface-based neuroimaging data, computing measures including cortical
thickness and surface area of the whole-brain and of the hippocampi.
It can make use of 'FreeSurfer', 'fMRIprep', 'XCP-D', 'HCP' and 'CAT12' preprocessed
datasets and 'HippUnfold' hippocampal segmentation outputs for a given
sample by restructuring the data values into a single file. The single
file can then be used by the package for analyses independently from
its base dataset and without need for its access.
Author: Junhong Yu [aut] ,
Charly Billaud [aut, cre]
Maintainer: Charly Billaud <charly.billaud@ntu.edu.sg>
Diff between VertexWiseR versions 1.4.1 dated 2025-08-19 and 1.4.2 dated 2025-10-01
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- NEWS.md | 6 ++++++ R/VWRfirstrun.R | 17 +---------------- 4 files changed, 16 insertions(+), 24 deletions(-)
Title: Calculate Step and Cadence Metrics from Wearable Data
Description: Provides functions to calculate step- and cadence-based metrics from
timestamped accelerometer and wearable device data. Supports CSV and AGD files from
'ActiGraph' devices, CSV files from 'Fitbit' devices, and step counts derived
with R package 'GGIR' <https://github.com/wadpac/GGIR>, with automatic handling
of epoch lengths from 1 to 60 seconds. Metrics include total steps, cadence
peaks, minutes and steps in predefined cadence bands, and time and steps in
moderate-to-vigorous physical activity (MVPA). Methods and thresholds are
informed by the literature, e.g.,
Tudor-Locke and Rowe (2012) <doi:10.2165/11599170-000000000-00000>,
Barreira et al. (2012) <doi:10.1249/MSS.0b013e318254f2a3>,
and Tudor-Locke et al. (2018) <doi:10.1136/bjsports-2017-097628>.
The package record is also available on Zenodo (2023) <doi:10.5281/zenodo.7858094>.
Author: Jairo H Migueles [aut, cre],
Elroy J Aguiar [fnd] ,
University of Alabama [fnd]
Maintainer: Jairo H Migueles <jairo@jhmigueles.com>
Diff between stepmetrics versions 1.0.1 dated 2025-09-16 and 1.0.3 dated 2025-10-01
DESCRIPTION | 8 +- MD5 | 21 +++-- NEWS.md | 16 ++++ R/define_day_indices.R | 2 R/get_cadence_bands.R | 2 R/readFile.R | 113 +++++++++++++++++-------------- inst/WORDLIST | 2 man/define_day_indices.Rd | 2 man/get_cadence_bands.Rd | 2 man/readFile.Rd | 86 +++++++++++++---------- tests/testthat/test-readFile.R | 47 +++++++++--- tests/testthat/test-timezone_preserved.R |only 12 files changed, 184 insertions(+), 117 deletions(-)
Title: Empirical Bayes Methods for Pharmacovigilance
Description: A suite of empirical Bayes methods to use in pharmacovigilance. Contains various model fitting and post-processing functions. For more details see Tan et al. (2025) <doi:10.48550/arXiv.2502.09816>, Koenker and Mizera (2014) <doi:10.1080/01621459.2013.869224> and Efron (2016) <doi:10.1093/biomet/asv068>.
Author: Yihao Tan [aut, cre] ,
Marianthi Markatou [aut] ,
Saptarshi Chakraborty [aut] ,
Raktim Mukhopadhyay [aut]
Maintainer: Yihao Tan <yihaotan@buffalo.edu>
Diff between pvEBayes versions 0.1.1 dated 2025-07-10 and 0.1.2 dated 2025-10-01
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- R/pvEBayes_main_function.R | 4 ++-- R/pvEBayes_object_S3_methods.R | 14 ++++++-------- README.md |only tests/testthat/test-pvEBayes_main_function.R | 2 +- tests/testthat/test-pvEBayes_object_S3_methods.R | 12 ++++++------ 7 files changed, 24 insertions(+), 25 deletions(-)
Title: NNG (Nanomsg Next Gen) Lightweight Messaging Library
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ.
NNG is a socket library for reliable, high-performance messaging over
in-process, IPC, TCP, WebSocket and secure TLS transports. Implements
'Scalability Protocols', a standard for common communications patterns
including publish/subscribe, request/reply and service discovery. As
its own threaded concurrency framework, provides a toolkit for
asynchronous programming and distributed computing. Intuitive 'aio'
objects resolve automatically when asynchronous operations complete,
and synchronisation primitives allow R to wait upon events signalled
by concurrent threads.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd] ,
Hibiki AI Limited [cph],
R Consortium [fnd]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between nanonext versions 1.7.0 dated 2025-09-01 and 1.7.1 dated 2025-10-01
nanonext-1.7.0/nanonext/man/dot-interrupt.Rd |only nanonext-1.7.1/nanonext/DESCRIPTION | 8 - nanonext-1.7.1/nanonext/MD5 | 31 ++--- nanonext-1.7.1/nanonext/NAMESPACE | 1 nanonext-1.7.1/nanonext/NEWS.md | 7 + nanonext-1.7.1/nanonext/R/context.R | 3 nanonext-1.7.1/nanonext/R/utils.R | 13 -- nanonext-1.7.1/nanonext/README.md | 22 +-- nanonext-1.7.1/nanonext/inst/doc/nanonext.Rmd | 146 ++++++++++++------------ nanonext-1.7.1/nanonext/inst/doc/nanonext.html | 96 +++++++-------- nanonext-1.7.1/nanonext/man/nanonext-package.Rd | 2 nanonext-1.7.1/nanonext/man/request.Rd | 3 nanonext-1.7.1/nanonext/src/aio.c | 17 +- nanonext-1.7.1/nanonext/src/nanonext.h | 4 nanonext-1.7.1/nanonext/src/sync.c | 15 +- nanonext-1.7.1/nanonext/tests/tests.R | 4 nanonext-1.7.1/nanonext/vignettes/nanonext.Rmd | 146 ++++++++++++------------ 17 files changed, 254 insertions(+), 264 deletions(-)
Title: 'ggplot2'-Based Tools for Visualising DNA Sequences and
Modifications
Description: Uses 'ggplot2' to visualise either (a) a single DNA/RNA sequence split across multiple lines, (b) multiple DNA/RNA sequences, each occupying a whole line, or (c) base modifications such as DNA methylation called by modified bases models in Dorado or Guppy. Functions starting with visualise_<something>() are the main plotting functions, and functions starting with extract_<something>() are key helper functions for reading files and reformatting data. Source code is available at <https://github.com/ejade42/ggDNAvis> and a full non-expert user guide is available at <https://ejade42.github.io/ggDNAvis/>.
Author: Evelyn Jade [aut, cre, cph]
Maintainer: Evelyn Jade <evelynjade42@gmail.com>
Diff between ggDNAvis versions 0.2.1 dated 2025-09-21 and 0.3.0 dated 2025-10-01
DESCRIPTION | 9 MD5 | 51 ++--- NAMESPACE | 1 NEWS.md | 26 ++ R/dna_tools.R | 83 +++++++- R/ggDNAvis-package.R | 17 - R/visualise_methylation.R | 2 R/visualise_single_sequence.R | 102 +++++----- man/convert_base_to_number.Rd | 2 man/convert_input_seq_to_sequence_list.Rd | 22 +- man/convert_sequence_to_numbers.Rd | 2 man/rasterise_matrix.Rd |only tests/testthat/reference_images/sone_2019_f1_1_expanded_test_14.PNG |binary tests/testthat/reference_images/sone_2019_f1_1_expanded_test_18.png |binary tests/testthat/reference_images/sone_2019_f1_1_expanded_test_29.png |only tests/testthat/test-dna_tools.R | 27 ++ tests/testthat/test-visualise_single_sequence.R | 52 ++++- tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_04.png |binary tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_08.png |binary tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_10.jpg |binary tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_12.PNG |binary tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_14.PNG |binary tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_18.png |binary tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_29.png |only tests/testthat/test_plot_images/visualise_methylation_scalebar_test_03.png |binary tests/testthat/test_plot_images/visualise_methylation_scalebar_test_04.png |binary tests/testthat/test_plot_images/visualise_methylation_scalebar_test_05.png |binary tests/testthat/test_plot_images/visualise_methylation_test_03.png |binary 28 files changed, 287 insertions(+), 109 deletions(-)
Title: Misspecified Models for Gene-Environment Interaction
Description: The first major functionality is to compute the bias in regression coefficients of misspecified linear gene-environment interaction models. The most generalized function for this objective is GE_bias(). However GE_bias() requires specification of many higher order moments of covariates in the model. If users are unsure about how to calculate/estimate these higher order moments, it may be easier to use GE_bias_normal_squaredmis(). This function places many more assumptions on the covariates (most notably that they are all jointly generated from a multivariate normal distribution) and is thus able to automatically calculate many of the higher order moments automatically, necessitating only that the user specify some covariances. There are also functions to solve for the bias through simulation and non-linear equation solvers; these can be used to check your work. Second major functionality is to implement the Bootstrap Inference with Correct Sandwich (BICS) testing procedure, which we ha [...truncated...]
Author: Ryan Sun [aut, cre],
Richard Barfield [ctb]
Maintainer: Ryan Sun <ryansun.work@gmail.com>
This is a re-admission after prior archival of version 1.0 dated 2022-05-18
Diff between GEint versions 1.0 dated 2022-05-18 and 1.1 dated 2025-10-01
GEint-1.0/GEint/R/GE_BICS_old.R |only GEint-1.0/GEint/R/GE_bias_normal_squaredmis_old.R |only GEint-1.0/GEint/R/GE_bias_old.R |only GEint-1.0/GEint/R/GE_enumerate_inputs.R |only GEint-1.0/GEint/R/GE_enumerate_inputs_old.R |only GEint-1.0/GEint/R/GE_nleqslv_old.R |only GEint-1.0/GEint/R/GE_scoreeq_sim_old.R |only GEint-1.0/GEint/R/GE_test_moment_calcs_old.R |only GEint-1.0/GEint/R/GE_translate_inputs_old.R |only GEint-1.0/GEint/man/GE_BICS_old.Rd |only GEint-1.0/GEint/man/GE_bias_normal_squaredmis_old.Rd |only GEint-1.0/GEint/man/GE_bias_old.Rd |only GEint-1.0/GEint/man/GE_enumerate_inputs.Rd |only GEint-1.0/GEint/man/GE_enumerate_inputs_old.Rd |only GEint-1.0/GEint/man/GE_nleqslv_old.Rd |only GEint-1.0/GEint/man/GE_scoreeq_sim_old.Rd |only GEint-1.0/GEint/man/GE_test_moment_calcs_old.Rd |only GEint-1.0/GEint/man/GE_translate_inputs_old.Rd |only GEint-1.0/GEint/tests/testthat/test_legacy_code.R |only GEint-1.0/GEint/tests/testthat/test_methods_match.R |only GEint-1.1/GEint/DESCRIPTION | 10 GEint-1.1/GEint/MD5 | 40 -- GEint-1.1/GEint/NAMESPACE | 9 GEint-1.1/GEint/R/GE_bias.R | 18 - GEint-1.1/GEint/R/GE_scoreeq_sim.R | 2 GEint-1.1/GEint/R/GE_test_moment_calcs.R | 4 GEint-1.1/GEint/R/GE_translate_inputs.R | 8 GEint-1.1/GEint/build/vignette.rds |binary GEint-1.1/GEint/inst/doc/GEint_example.html | 339 ++++++++++++------- GEint-1.1/GEint/man/GE_translate_inputs.Rd | 8 GEint-1.1/GEint/tests/testthat/test_BICS.R | 43 -- 31 files changed, 259 insertions(+), 222 deletions(-)
Title: Fit Growth Curves to Fish Data
Description: Fit growth models to otoliths and/or tagging data, using the 'RTMB'
package and maximum likelihood. The otoliths (or similar measurements of age)
provide direct observed coordinates of age and length. The tagging data
provide information about the observed length at release and length at
recapture at a later time, where the age at release is unknown and estimated
as a vector of parameters. The growth models provided by this package can be
fitted to otoliths only, tagging data only, or a combination of the two.
Growth variability can be modelled as constant or increasing with length.
Author: Arni Magnusson [aut, cre],
Mark Maunder [aut]
Maintainer: Arni Magnusson <thisisarni@gmail.com>
Diff between fishgrowth versions 1.0.2 dated 2025-04-08 and 1.0.3 dated 2025-10-01
DESCRIPTION | 10 ++++----- MD5 | 42 +++++++++++++++++++-------------------- NEWS.md | 7 ++++++ R/gcm.R | 58 ++++++++++++++++++++++++++++++------------------------ R/gompertz.R | 52 +++++++++++++++++++++++++++--------------------- R/gompertzo.R | 52 +++++++++++++++++++++++++++--------------------- R/pred_band.R | 3 -- R/richards.R | 52 +++++++++++++++++++++++++++--------------------- R/richardso.R | 52 +++++++++++++++++++++++++++--------------------- R/schnute3.R | 52 +++++++++++++++++++++++++++--------------------- R/vonbert.R | 52 +++++++++++++++++++++++++++--------------------- R/vonberto.R | 52 +++++++++++++++++++++++++++--------------------- build/partial.rdb |binary man/gcm.Rd | 58 ++++++++++++++++++++++++++++++------------------------ man/gompertz.Rd | 52 +++++++++++++++++++++++++++--------------------- man/gompertzo.Rd | 52 +++++++++++++++++++++++++++--------------------- man/pred_band.Rd | 3 -- man/richards.Rd | 52 +++++++++++++++++++++++++++--------------------- man/richardso.Rd | 52 +++++++++++++++++++++++++++--------------------- man/schnute3.Rd | 52 +++++++++++++++++++++++++++--------------------- man/vonbert.Rd | 52 +++++++++++++++++++++++++++--------------------- man/vonberto.Rd | 52 +++++++++++++++++++++++++++--------------------- 22 files changed, 521 insertions(+), 388 deletions(-)
More information about ExtendedABSurvTDC at CRAN
Permanent link
Title: Using CF-Compliant Calendars with Climate Projection Data
Description: Support for all calendars as specified in the Climate and Forecast
(CF) Metadata Conventions for climate and forecasting data. The CF Metadata
Conventions is widely used for distributing files with climate observations
or projections, including the Coupled Model Intercomparison Project (CMIP)
data used by climate change scientists and the Intergovernmental Panel on
Climate Change (IPCC). This package specifically allows the user to work
with any of the CF-compliant calendars (many of which are not compliant with
POSIXt). The CF time coordinate is formally defined in the CF Metadata
Conventions document available at <https://cfconventions.org/Data/cf-conventions/cf-conventions-1.12/cf-conventions.html#time-coordinate>.
Author: Patrick Van Laake [aut, cre, cph]
Maintainer: Patrick Van Laake <patrick@vanlaake.net>
Diff between CFtime versions 1.7.0 dated 2025-08-23 and 1.7.1 dated 2025-10-01
CFtime-1.7.0/CFtime/build |only CFtime-1.7.0/CFtime/inst/doc |only CFtime-1.7.0/CFtime/vignettes |only CFtime-1.7.1/CFtime/DESCRIPTION | 13 -- CFtime-1.7.1/CFtime/MD5 | 32 +---- CFtime-1.7.1/CFtime/NEWS.md | 8 + CFtime-1.7.1/CFtime/R/CFtime.R | 108 ++++++++--------- CFtime-1.7.1/CFtime/R/api.R | 38 +++++- CFtime-1.7.1/CFtime/README.md | 123 -------------------- CFtime-1.7.1/CFtime/TODO | 2 CFtime-1.7.1/CFtime/man/CFTime.Rd | 75 ++++++------ CFtime-1.7.1/CFtime/man/as.character.CFTime.Rd | 4 CFtime-1.7.1/CFtime/man/format.CFTime.Rd |only CFtime-1.7.1/CFtime/tests/testthat/test-functions.R | 2 14 files changed, 165 insertions(+), 240 deletions(-)
Title: Draw Three Dimensional Predict Plot Using Package 'rgl'
Description: Draw 2 dimensional and three dimensional plot for multiple regression models using package 'ggplot2' and 'rgl'.
Supports linear models (lm), generalized linear models (glm) and local polynomial regression fittings (loess).
Author: Keon-Woong Moon [aut, cre]
Maintainer: Keon-Woong Moon <cardiomoon@gmail.com>
Diff between predict3d versions 0.1.5 dated 2024-04-04 and 0.1.6 dated 2025-10-01
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NAMESPACE | 4 +++- NEWS.md | 7 +++++++ R/add_lines.R | 4 ++-- R/ggPredict.R | 30 +++++++++++++++++------------- build/vignette.rds |binary inst/doc/predict3d.R | 26 +++++++++++++------------- inst/doc/predict3d.html | 27 ++++++++++++++------------- man/fit2newdata.Rd | 2 +- man/getAspectRatio.Rd | 4 ++++ 11 files changed, 76 insertions(+), 58 deletions(-)
More information about BlockwiseRankTest at CRAN
Permanent link
Title: Robust Pathway Enrichment for DNA Methylation Studies Using
Ensemble Voting
Description: Performs pathway enrichment analysis using a voting-based framework that integrates CpG–gene regulatory information from expression quantitative trait methylation (eQTM) data. For a grid of top-ranked CpGs and filtering thresholds, gene sets are generated and refined using an entropy-based pruning strategy that balances information richness, stability, and probe bias correction. In particular, gene lists dominated by genes with disproportionately high numbers of CpG mappings are penalized to mitigate active probe bias—a common artifact in methylation data analysis. Enrichment results across parameter combinations are then aggregated using a voting scheme, prioritizing pathways that are consistently recovered under diverse settings and robust to parameter perturbations.
Author: Yinan Zheng [aut, cre]
Maintainer: Yinan Zheng <y-zheng@northwestern.edu>
Diff between PathwayVote versions 0.1.1 dated 2025-06-25 and 0.1.2 dated 2025-10-01
DESCRIPTION | 10 - MD5 | 10 - NAMESPACE | 5 R/pathway-vote.R | 278 ++++++++++++++++++++++++++++++++++---------------- R/utils.R | 287 ++++++++++++++++++++++++++++++---------------------- man/pathway_vote.Rd | 50 +++++---- 6 files changed, 404 insertions(+), 236 deletions(-)
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Yoonkyoung Jeon [aut],
Jaehun Shon [aut],
Hyojong Myung [aut],
Hyungwoo Jo [aut],
Sungho Choi [aut],
Jaewoong Heo [aut],
Mingu Jee [aut],
Yujeong Yoon [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 1.3.17 dated 2025-09-03 and 1.3.18 dated 2025-10-01
DESCRIPTION | 20 ++++++------ MD5 | 16 ++++----- NAMESPACE | 1 NEWS.md | 4 ++ R/cox2.R | 43 ++++++++++++++++++++++++-- R/forestcox.R | 4 +- inst/doc/jstable.html | 28 ++++++++-------- inst/doc/jstable_competing_risk_analysis.html | 4 +- inst/doc/jstable_options.html | 4 +- 9 files changed, 86 insertions(+), 38 deletions(-)
Title: Kaplan-Meier Plot with 'ggplot2'
Description: The function 'jskm()' creates publication quality Kaplan-Meier plot with at risk tables below. 'svyjskm()' provides plot for weighted Kaplan-Meier estimator.
Author: Jinseob Kim [aut, cre] ,
yoonkyoung Chun [aut],
Zarathu [cph, fnd],
sungho Choi [aut],
Mingu Jee [aut],
Wonbin Hahn [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jskm versions 0.5.16 dated 2025-08-19 and 0.5.20 dated 2025-10-01
DESCRIPTION | 14 +++++----- MD5 | 14 +++++----- NEWS.md | 3 ++ R/jskm.R | 73 +++++++++++++++++++++++++++++++++++++++++++---------- R/svyjskm.R | 73 ++++++++++++++++++++++++++++++++++++++++++----------- inst/doc/jskm.html | 32 +++++++++++------------ man/jskm.Rd | 3 ++ man/svyjskm.Rd | 3 ++ 8 files changed, 158 insertions(+), 57 deletions(-)