Title: Portfolio Analysis, Including Numerical Methods for Optimization
of Portfolios
Description: Portfolio optimization and analysis routines and graphics.
Author: Brian G. Peterson [cre, aut, cph],
Peter Carl [aut, cph],
Ross Bennett [ctb, cph],
Kris Boudt [ctb, cph],
Xinran Zhao [cph],
R. Douglas Martin [ctb],
Guy Yollin [ctb],
Hezky Varon [ctb],
Xiaokang Feng [ctb],
Yifu Kang [ctb]
Maintainer: Brian G. Peterson <brian@braverock.com>
Diff between PortfolioAnalytics versions 2.0.0 dated 2024-07-03 and 2.1.0 dated 2024-12-04
PortfolioAnalytics-2.0.0/PortfolioAnalytics/README |only PortfolioAnalytics-2.0.0/PortfolioAnalytics/man/meaneqs.efficient.frontier.Rd |only PortfolioAnalytics-2.0.0/PortfolioAnalytics/vignettes/todo_notes.Rmd |only PortfolioAnalytics-2.0.0/PortfolioAnalytics/vignettes/todo_notes.html |only PortfolioAnalytics-2.1.0/PortfolioAnalytics/DESCRIPTION | 12 PortfolioAnalytics-2.1.0/PortfolioAnalytics/MD5 | 88 PortfolioAnalytics-2.1.0/PortfolioAnalytics/NAMESPACE | 2 PortfolioAnalytics-2.1.0/PortfolioAnalytics/R/applyFUN.R | 8 PortfolioAnalytics-2.1.0/PortfolioAnalytics/R/backtest.plot.R | 49 PortfolioAnalytics-2.1.0/PortfolioAnalytics/R/charts.efficient.frontier.R | 12 PortfolioAnalytics-2.1.0/PortfolioAnalytics/R/constrained_objective.R | 2 PortfolioAnalytics-2.1.0/PortfolioAnalytics/R/extract.efficient.frontier.R | 40 PortfolioAnalytics-2.1.0/PortfolioAnalytics/R/extractrisk.R | 20 PortfolioAnalytics-2.1.0/PortfolioAnalytics/R/moment.functions.R | 6 PortfolioAnalytics-2.1.0/PortfolioAnalytics/R/optimize.portfolio.R | 72 PortfolioAnalytics-2.1.0/PortfolioAnalytics/R/plotFrontiers.R | 16 PortfolioAnalytics-2.1.0/PortfolioAnalytics/README.md |only PortfolioAnalytics-2.1.0/PortfolioAnalytics/build/vignette.rds |binary PortfolioAnalytics-2.1.0/PortfolioAnalytics/demo/00Index | 2 PortfolioAnalytics-2.1.0/PortfolioAnalytics/demo/demo_JPM2024MinDownsideRisk.R |only PortfolioAnalytics-2.1.0/PortfolioAnalytics/demo/demo_JPM2024MinDownsideRiskCVXR.R |only PortfolioAnalytics-2.1.0/PortfolioAnalytics/demo/demo_cvxrPortfolioAnalytics.R | 592 ++--- PortfolioAnalytics-2.1.0/PortfolioAnalytics/demo/demo_robustCovMatForPA.R | 723 +++--- PortfolioAnalytics-2.1.0/PortfolioAnalytics/inst/doc/ROI_vignette.R | 44 PortfolioAnalytics-2.1.0/PortfolioAnalytics/inst/doc/ROI_vignette.Rnw | 4 PortfolioAnalytics-2.1.0/PortfolioAnalytics/inst/doc/ROI_vignette.pdf |binary PortfolioAnalytics-2.1.0/PortfolioAnalytics/inst/doc/custom_moments_objectives.R | 28 PortfolioAnalytics-2.1.0/PortfolioAnalytics/inst/doc/custom_moments_objectives.Rnw | 2 PortfolioAnalytics-2.1.0/PortfolioAnalytics/inst/doc/custom_moments_objectives.pdf |binary PortfolioAnalytics-2.1.0/PortfolioAnalytics/inst/doc/cvxrPortfolioAnalytics.pdf |binary PortfolioAnalytics-2.1.0/PortfolioAnalytics/inst/doc/portfolio_vignette.R | 114 PortfolioAnalytics-2.1.0/PortfolioAnalytics/inst/doc/portfolio_vignette.Rnw | 5 PortfolioAnalytics-2.1.0/PortfolioAnalytics/inst/doc/portfolio_vignette.pdf |binary PortfolioAnalytics-2.1.0/PortfolioAnalytics/inst/doc/risk_budget_optimization.Rnw | 4 PortfolioAnalytics-2.1.0/PortfolioAnalytics/inst/doc/risk_budget_optimization.pdf |binary PortfolioAnalytics-2.1.0/PortfolioAnalytics/inst/doc/robustCovMatForPA.pdf |binary PortfolioAnalytics-2.1.0/PortfolioAnalytics/man/backtest.plot.Rd | 7 PortfolioAnalytics-2.1.0/PortfolioAnalytics/man/create.EfficientFrontier.Rd | 4 PortfolioAnalytics-2.1.0/PortfolioAnalytics/man/extract_risk.Rd | 4 PortfolioAnalytics-2.1.0/PortfolioAnalytics/man/meancsm.efficient.frontier.Rd |only PortfolioAnalytics-2.1.0/PortfolioAnalytics/man/meanrisk.efficient.frontier.Rd | 6 PortfolioAnalytics-2.1.0/PortfolioAnalytics/man/optimize.portfolio.Rd | 12 PortfolioAnalytics-2.1.0/PortfolioAnalytics/man/plotFrontiers.Rd | 10 PortfolioAnalytics-2.1.0/PortfolioAnalytics/vignettes/ROI_vignette.Rnw | 4 PortfolioAnalytics-2.1.0/PortfolioAnalytics/vignettes/custom_moments_objectives.Rnw | 2 PortfolioAnalytics-2.1.0/PortfolioAnalytics/vignettes/cvxrPortfolioAnalytics.Rmd | 721 +++--- PortfolioAnalytics-2.1.0/PortfolioAnalytics/vignettes/portfolio_vignette.Rnw | 5 PortfolioAnalytics-2.1.0/PortfolioAnalytics/vignettes/risk_budget_optimization.Rnw | 4 PortfolioAnalytics-2.1.0/PortfolioAnalytics/vignettes/robustCovMatForPA.Rmd | 1177 +++++----- 49 files changed, 2024 insertions(+), 1777 deletions(-)
More information about PortfolioAnalytics at CRAN
Permanent link
Title: Data for the 'Mastering Health Data Science Using R' Online
Textbook
Description: Contains ten datasets used in the chapters and exercises of Paul, Alice (2023) "Health Data Science in R" <https://alicepaul.github.io/health-data-science-using-r/>.
Author: Alice Paul [aut, cre],
Hannah Eglinton [aut],
Jialin Liu [ctb],
Joanna Walsh [aut],
Xinbei Yu [ctb]
Maintainer: Alice Paul <alice_paul@brown.edu>
Diff between HDSinRdata versions 0.1.2 dated 2024-06-10 and 0.1.3 dated 2024-12-04
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 5 ++--- data/covidcases.rda |binary data/lockdowndates.rda |binary data/mobility.rda |binary 6 files changed, 10 insertions(+), 11 deletions(-)
Title: Time Series Prediction Integrated Tuning
Description: Prediction is one of the most important activities while working with time series. There are many alternative ways to model the time series. Finding the right one is challenging to model them. Most data-driven models (either statistical or machine learning) demand tuning. Setting them right is mandatory for good predictions. It is even more complex since time series prediction also demands choosing a data pre-processing that complies with the chosen model. Many time series frameworks have features to build and tune models. The package differs as it provides a framework that seamlessly integrates tuning data pre-processing activities with the building of models. The package provides functions for defining and conducting time series prediction, including data pre(post)processing, decomposition, tuning, modeling, prediction, and accuracy assessment. More information is available at Izau et al. <doi:10.5753/sbbd.2022.224330>.
Author: Eduardo Ogasawara [aut, ths, cre]
,
Carla Pacheco [aut],
Cristiane Gea [aut],
Diogo Santos [aut],
Rebecca Salles [aut],
Vitoria Birindiba [aut],
Eduardo Bezerra [aut],
Esther Pacitti [aut],
Fabio Porto [aut],
Federal Center for Technological Educatio [...truncated...]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between tspredit versions 1.0.777 dated 2024-07-29 and 1.0.787 dated 2024-12-04
DESCRIPTION | 20 +- LICENSE | 6 MD5 | 122 +++++++------- NAMESPACE | 202 ++++++++++++------------ R/data.R | 36 ++-- R/globals.R | 4 R/recursive_filter.R | 70 ++++---- R/ts_aug_awareness.R | 142 ++++++++--------- R/ts_aug_awaresmooth.R | 210 ++++++++++++------------- R/ts_aug_flip.R | 96 +++++------ R/ts_aug_jitter.R | 120 +++++++------- R/ts_aug_none.R | 68 ++++---- R/ts_aug_shrink.R | 104 ++++++------ R/ts_aug_stretch.R | 104 ++++++------ R/ts_aug_wormhole.R | 118 +++++++------- R/ts_fil_ema.R | 98 +++++------ R/ts_fil_emd.R | 98 +++++------ R/ts_fil_fft.R | 122 +++++++------- R/ts_fil_hp.R | 100 +++++------ R/ts_fil_kalman.R | 84 +++++----- R/ts_fil_lowess.R | 68 ++++---- R/ts_fil_ma.R | 74 ++++---- R/ts_fil_none.R | 66 +++---- R/ts_fil_qes.R | 78 ++++----- R/ts_fil_remd.R | 144 ++++++++--------- R/ts_fil_seas_adj.R | 84 +++++----- R/ts_fil_ses.R | 76 ++++----- R/ts_fil_smooth.R | 114 ++++++------- R/ts_fil_spline.R | 76 ++++----- R/ts_fil_wavelet.R | 140 ++++++++-------- R/ts_fil_winsor.R | 6 R/ts_maintune.R | 384 +++++++++++++++++++++++----------------------- R/ts_norm_none.R | 68 ++++---- README.md | 112 ++++++------- man/fertilizers.Rd | 62 +++---- man/ts_aug_awareness.Rd | 62 +++---- man/ts_aug_awaresmooth.Rd | 62 +++---- man/ts_aug_flip.Rd | 56 +++--- man/ts_aug_jitter.Rd | 56 +++--- man/ts_aug_none.Rd | 54 +++--- man/ts_aug_shrink.Rd | 62 +++---- man/ts_aug_stretch.Rd | 62 +++---- man/ts_aug_wormhole.Rd | 56 +++--- man/ts_fil_ema.Rd | 66 +++---- man/ts_fil_emd.Rd | 66 +++---- man/ts_fil_fft.Rd | 56 +++--- man/ts_fil_hp.Rd | 84 +++++----- man/ts_fil_kalman.Rd | 68 ++++---- man/ts_fil_lowess.Rd | 64 +++---- man/ts_fil_ma.Rd | 62 +++---- man/ts_fil_none.Rd | 56 +++--- man/ts_fil_qes.Rd | 66 +++---- man/ts_fil_recursive.Rd | 62 +++---- man/ts_fil_remd.Rd | 66 +++---- man/ts_fil_seas_adj.Rd | 64 +++---- man/ts_fil_ses.Rd | 66 +++---- man/ts_fil_smooth.Rd | 56 +++--- man/ts_fil_spline.Rd | 62 +++---- man/ts_fil_wavelet.Rd | 62 +++---- man/ts_fil_winsor.Rd | 63 +++---- man/ts_maintune.Rd | 106 ++++++------ man/ts_norm_none.Rd | 54 +++--- 62 files changed, 2595 insertions(+), 2600 deletions(-)
Title: Interface to the 'Pharmpy' 'Pharmacometrics' Library
Description: Interface to the 'Pharmpy' 'pharmacometrics' library. The 'Reticulate' package is used to interface Python from R.
Author: Rikard Nordgren [aut, cre, cph],
Stella Belin [aut, cph],
Mats O. Karlsson [sad],
Andrew C. Hooker [sad],
Xiaomei Chen [sad],
Sebastian Ueckert [sad] ,
Simon Buatois [rev],
Joao A. Abrantes [rev],
Emilie Schindler [rev],
F. Hoffmann-La Roche Ltd. [fn [...truncated...]
Maintainer: Rikard Nordgren <rikard.nordgren@farmaci.uu.se>
Diff between pharmr versions 1.0.1 dated 2024-06-17 and 1.4.0 dated 2024-12-04
DESCRIPTION | 12 MD5 | 83 +- NAMESPACE | 9 R/functions_wrapper.R | 1097 +++++++++++++++++++++++++++++++---- R/install.R | 12 R/internals.R | 5 R/overloads.R |only man/calculate_parameters_from_ucp.Rd | 2 man/cleanup_model.Rd | 4 man/create_context.Rd |only man/fix_or_unfix_parameters.Rd | 4 man/fix_parameters.Rd | 4 man/fix_parameters_to.Rd | 6 man/get_model_code.Rd | 4 man/get_mu_connected_to_parameter.Rd |only man/has_mu_reference.Rd |only man/has_zero_order_absorption.Rd | 2 man/install_pharmpy_devel.Rd | 2 man/plot_abs_cwres_vs_ipred.Rd | 2 man/plot_cwres_vs_idv.Rd | 2 man/plot_dv_vs_ipred.Rd | 2 man/plot_dv_vs_pred.Rd | 2 man/print_log.Rd |only man/print_model_code.Rd | 2 man/read_model.Rd | 5 man/remove_loq_data.Rd | 2 man/remove_predictions.Rd | 6 man/remove_residuals.Rd | 6 man/replace_fixed_thetas.Rd |only man/retrieve_model.Rd |only man/retrieve_modelfit_results.Rd |only man/run_amd.Rd | 16 man/run_covsearch.Rd | 19 man/run_iivsearch.Rd | 4 man/run_iovsearch.Rd | 2 man/run_linearize.Rd | 16 man/run_modelsearch.Rd | 4 man/run_structsearch.Rd | 18 man/set_description.Rd |only man/set_evaluation_step.Rd | 5 man/set_initial_estimates.Rd | 11 man/set_lower_bounds.Rd | 4 man/set_reference_values.Rd | 2 man/set_upper_bounds.Rd | 4 man/unconstrain_parameters.Rd | 4 man/unfix_parameters.Rd | 4 man/unfix_parameters_to.Rd | 6 47 files changed, 1167 insertions(+), 227 deletions(-)
Title: 'Matrix-Based Flexible Project Planning'
Description: Matrix-Based Flexible Project Planning. This package models, plans, and schedules flexible, such as agile, extreme, and hybrid project plans. The package contains project planning, scheduling, and risk assessment functions. Kosztyan (2022) <doi:10.1016/j.softx.2022.100973>.
Author: Zsolt T. Kosztyan [aut, cre],
Aamir Sagir [aut]
Maintainer: Zsolt T. Kosztyan <kosztyan.zsolt@gtk.uni-pannon.hu>
Diff between mfpp versions 0.0.7 dated 2024-06-05 and 0.0.8 dated 2024-12-04
DESCRIPTION | 6 MD5 | 6 R/plot.mfpp.R | 837 +++++++++++++++++++++++++++++----------------------------- inst/NEWS | 72 ++-- 4 files changed, 465 insertions(+), 456 deletions(-)
Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates graphics with
details from statistical tests included in the plots themselves. It
provides an easier syntax to generate information-rich plots for
statistical analysis of continuous (violin plots, scatterplots,
histograms, dot plots, dot-and-whisker plots) or categorical (pie and
bar charts) data. Currently, it supports the most common types of
statistical approaches and tests: parametric, nonparametric, robust,
and Bayesian versions of t-test/ANOVA, correlation analyses,
contingency table analysis, meta-analysis, and regression analyses.
References: Patil (2021) <doi:10.21105/joss.03236>.
Author: Indrajeet Patil [cre, aut, cph]
,
Chuck Powell [ctb]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between ggstatsplot versions 0.12.5 dated 2024-11-01 and 0.13.0 dated 2024-12-04
DESCRIPTION | 14 ++--- MD5 | 48 +++++++++--------- NEWS.md | 8 ++- R/combine-plots.R | 11 ++-- R/extract-stats.R | 1 R/ggbarstats.R | 72 ++++++++++++++------------- R/ggbetweenstats-helpers.R | 80 +++++++++++++++--------------- R/ggbetweenstats.R | 100 +++++++++++++++++++------------------- R/ggcoefstats.R | 93 ++++++++++++++++++++++------------- R/ggcorrmat.R | 58 +++++++++++----------- R/ggdotplotstats.R | 60 +++++++++++----------- R/gghistostats.R | 62 ++++++++++++----------- R/ggpiestats-ggbarstats-helpers.R | 13 ++-- R/ggpiestats.R | 68 +++++++++++++------------ R/ggscatterstats.R | 68 +++++++++++++------------ R/ggwithinstats.R | 84 ++++++++++++++++--------------- README.md | 44 +++------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/additional.Rmd | 2 inst/doc/additional.html | 2 inst/doc/ggstatsplot.R | 2 man/ggcoefstats.Rd | 22 ++++++++ vignettes/additional.Rmd | 2 vignettes/web_only/faq.Rmd | 1 25 files changed, 481 insertions(+), 434 deletions(-)
Title: Statistical Methods for Survival Data with Dependent Censoring
Description: Several statistical methods for analyzing survival data under various forms of dependent
censoring are implemented in the package. In addition to accounting for dependent censoring, it
offers tools to adjust for unmeasured confounding factors. The implemented approaches allow
users to estimate the dependency between survival time and dependent censoring time, based
solely on observed survival data. For more details on the methods, refer to Deresa and Van
Keilegom (2021) <doi:10.1093/biomet/asaa095>, Czado and Van Keilegom (2023)
<doi:10.1093/biomet/asac067>, Crommen et al. (2024) <doi:10.1007/s11749-023-00903-9>,
Deresa and Van Keilegom (2024) <doi:10.1080/01621459.2022.2161387>
and Willems et al. (2024+) <doi:10.48550/arXiv.2403.11860>.
Author: Ilias Willems [aut] ,
Gilles Crommen [aut] ,
Negera Wakgari Deresa [aut, cre]
,
Claudia Czado [aut] ,
Ingrid Van Keilegom [aut]
Maintainer: Negera Wakgari Deresa <negera.deresa@gmail.com>
Diff between depCensoring versions 0.1.3 dated 2024-10-17 and 0.1.4 dated 2024-12-04
DESCRIPTION | 19 +++++++------- MD5 | 27 ++++++++++++++++----- NAMESPACE | 13 +++++++++- NEWS.md | 32 +++++++++++++------------ R/CopulaBasedCoxPH_pseudoLikelihoodFunctions.R |only R/CopulaCoxPHmodel_BootstrapMethods.R |only R/FitCopulaBasedCoxPHmodels.R |only R/NonparametricTransformation.R | 8 +++--- man/CompC.Rd |only man/Distance.Rd | 7 ++++- man/LikCopInd.Rd |only man/LongNPT.Rd |only man/Longfun.Rd | 12 +++++---- man/PseudoL.Rd |only man/SolveL.Rd |only man/SolveLI.Rd |only man/boot.fun.Rd |only man/boot.funI.Rd |only man/fitDepCens.Rd |only man/fitIndepCens.Rd |only man/summary.depFit.Rd |only man/summary.indepFit.Rd |only 22 files changed, 77 insertions(+), 41 deletions(-)
Title: Data Pre-Processing Extensions
Description: An important aspect of data analytics is related to data management support for artificial intelligence. It is related to preparing data correctly. This package provides extensions to support data preparation in terms of both data sampling and data engineering. Overall, the package provides researchers with a comprehensive set of functionalities for data science based on experiment lines, promoting ease of use, extensibility, and integration with various tools and libraries. Information on Experiment Line is based on Ogasawara et al. (2009) <doi:10.1007/978-3-642-02279-1_20>.
Author: Eduardo Ogasawara [aut, ths, cre]
,
Federal Center for Technological Education of Rio de Janeiro
[cph]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between daltoolboxdp versions 1.0.767 dated 2024-03-27 and 1.0.777 dated 2024-12-04
DESCRIPTION | 8 +++---- LICENSE | 2 - MD5 | 6 ++--- README.md | 62 ++++++++++++++---------------------------------------------- 4 files changed, 23 insertions(+), 55 deletions(-)
Title: A C++11 Interface for R's C Interface
Description: Provides a header only, C++11 interface to R's C
interface. Compared to other approaches 'cpp11' strives to be safe
against long jumps from the C API as well as C++ exceptions, conform
to normal R function semantics and supports interaction with 'ALTREP'
vectors.
Author: Davis Vaughan [aut, cre] ,
Jim Hester [aut] ,
Romain Francois [aut] ,
Benjamin Kietzman [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Davis Vaughan <davis@posit.co>
Diff between cpp11 versions 0.5.0 dated 2024-08-27 and 0.5.1 dated 2024-12-04
DESCRIPTION | 10 MD5 | 34 - NEWS.md | 24 inst/doc/FAQ.html | 11 inst/doc/cpp11.html | 22 inst/doc/motivations.html | 1056 ++++++++++++++++++++++-------------- inst/include/cpp11/R.hpp | 7 inst/include/cpp11/altrep.hpp | 42 - inst/include/cpp11/declarations.hpp | 11 inst/include/cpp11/doubles.hpp | 2 inst/include/cpp11/environment.hpp | 14 inst/include/cpp11/integers.hpp | 2 inst/include/cpp11/list.hpp | 2 inst/include/cpp11/logicals.hpp | 2 inst/include/cpp11/protect.hpp | 17 inst/include/cpp11/r_vector.hpp | 9 inst/include/cpp11/raws.hpp | 2 inst/include/cpp11/strings.hpp | 2 18 files changed, 761 insertions(+), 508 deletions(-)
Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included. We further include functions for percentages (or proportions).
The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include:
a) Tsagris M.T., Preston S. and Wood A.T.A. (2011). "A data-based power transformation for compositional data". Fourth International International Workshop on Compositional Data Analysis. <doi:10.48550/arXiv.1106.1451>
b) Tsagris M. (2014). "The k-NN algorithm for compositional data: a revised approach with and without zero values present". Journal of Data Science, 12(3): 519--534. <doi:10.6339/JDS.201407_12(3).0008>.
c) Tsagris M. (2015). "A novel, divergence based, regression for compositional data". Proceedings of the 28th Panhellenic Statistics Conference, 15-18 April 2015, Athens, Greece, 430--444. <doi:10.48550/arXiv.151 [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Abdulaziz Alenazi [ctb],
Christos Adam [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Compositional versions 7.1 dated 2024-10-09 and 7.2 dated 2024-12-04
DESCRIPTION | 20 +++++++-------- MD5 | 55 ++++++++++++++++++++++++++++--------------- NAMESPACE | 4 --- R/alfa.rda.R | 2 - R/alfa.reg.R | 11 ++++++-- R/alfa.reg3.R | 5 +++ R/alfarda.tune.R | 2 - R/ascls.R | 6 ++-- R/comp.test.R | 14 +++++----- R/diri.reg.R | 34 +++++++++++++------------- R/diri.reg2.R | 30 +++++++++++------------ R/diri.reg3.R | 6 ++-- R/eel.test2.R |only R/el.test2.R |only R/hellinger.compreg.R |only R/hotel2T2.R |only R/james.R |only R/maov.R |only R/maovjames.R |only R/ols.compreg.R | 41 +++++++++++++++++--------------- R/rda.R |only R/rda.tune.R |only R/scls.R | 10 +++---- R/scls.betest.R | 9 +++---- R/scls.indeptest.R | 9 +++---- man/Compositional-package.Rd | 4 +-- man/eel.test2.Rd |only man/el.test2.Rd |only man/hotel2T2.Rd |only man/james.Rd |only man/kl.compreg.Rd | 16 +++++++----- man/lasso.klcompreg.Rd | 4 +-- man/maov.Rd |only man/maovjames.Rd |only man/rda.Rd |only man/rda.tune.Rd |only man/tflr.indeptest.Rd | 2 - 37 files changed, 156 insertions(+), 128 deletions(-)
Title: Infer Geographic Origin from Isotopic Data
Description: Routines for re-scaling isotope maps using known-origin tissue isotope data, assigning origin of unknown samples, and summarizing and assessing assignment results. Methods are adapted from Wunder (2010, in ISBN:9789048133536) and Vander Zanden, H. B. et al. (2014) <doi:10.1111/2041-210X.12229> as described in Ma, C. et al. (2020) <doi:10.1111/2041-210X.13426>.
Author: Chao Ma [aut],
Gabe Bowen [aut, cre]
Maintainer: Gabe Bowen <gabe.bowen@utah.edu>
Diff between assignR versions 2.4.1 dated 2024-05-30 and 2.4.3 dated 2024-12-04
DESCRIPTION | 20 +++++++++++++----- MD5 | 14 ++++++------- NAMESPACE | 2 - NEWS.md | 4 +++ R/calRaster.R | 3 ++ R/summarize.R | 2 - inst/doc/assignR.html | 42 +++++++++++++++++++-------------------- tests/testthat/test_processing.R | 2 + 8 files changed, 53 insertions(+), 36 deletions(-)
Title: Estimate Univariate Gaussian and Student's t Mixture
Autoregressive Models
Description: Maximum likelihood estimation of univariate Gaussian Mixture Autoregressive (GMAR),
Student's t Mixture Autoregressive (StMAR), and Gaussian and Student's t Mixture Autoregressive (G-StMAR) models,
quantile residual tests, graphical diagnostics, forecast and simulate from GMAR, StMAR and G-StMAR processes.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2015) <doi:10.1111/jtsa.12108>,
Mika Meitz, Daniel Preve, Pentti Saikkonen (2023) <doi:10.1080/03610926.2021.1916531>,
Savi Virolainen (2022) <doi:10.1515/snde-2020-0060>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between uGMAR versions 3.5.0 dated 2024-07-04 and 3.5.1 dated 2024-12-04
DESCRIPTION | 15 ++-- MD5 | 16 ++-- NEWS.md | 4 + build/vignette.rds |binary inst/doc/uGMARpaper.Rnw | 153 ++++++++++++++++++++++++++++++++++------------- inst/doc/uGMARpaper.pdf |binary man/uGMAR-package.Rd | 2 vignettes/refs.bib | 34 +++++----- vignettes/uGMARpaper.Rnw | 153 ++++++++++++++++++++++++++++++++++------------- 9 files changed, 260 insertions(+), 117 deletions(-)
Title: Statistics Norway's Miscellaneous Tools
Description: Functions used by other packages from Statistics Norway are gathered. General data manipulation functions, algorithms for statistical disclosure control (Langsrud, 2024) <doi:10.1007/978-3-031-69651-0_6> and functions for hierarchical computations by sparse model matrices are included (Langsrud, 2023) <doi:10.32614/RJ-2023-088>.
Author: Oeyvind Langsrud [aut, cre] ,
Daniel Lupp [aut] ,
Bjoern-Helge Mevik [ctb],
Vidar Norstein Klungre [rev] ,
Statistics Norway [cph]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between SSBtools versions 1.5.5 dated 2024-10-21 and 1.6.0 dated 2024-12-04
SSBtools-1.5.5/SSBtools/man/formula_include_hierarchies.Rd |only SSBtools-1.6.0/SSBtools/DESCRIPTION | 8 SSBtools-1.6.0/SSBtools/MD5 | 36 ++-- SSBtools-1.6.0/SSBtools/NAMESPACE | 11 + SSBtools-1.6.0/SSBtools/NEWS.md | 51 +++++ SSBtools-1.6.0/SSBtools/R/AutoHierarchies.R | 106 +++++++++++- SSBtools-1.6.0/SSBtools/R/Extend0.R | 8 SSBtools-1.6.0/SSBtools/R/FormulaSelection.R | 2 SSBtools-1.6.0/SSBtools/R/FormulaSums.R | 2 SSBtools-1.6.0/SSBtools/R/formula_utils.R | 48 +++-- SSBtools-1.6.0/SSBtools/R/hierarchies_as_vars.R |only SSBtools-1.6.0/SSBtools/R/map_hierarchies_to_data.R |only SSBtools-1.6.0/SSBtools/R/max_contribution.R |only SSBtools-1.6.0/SSBtools/R/table_all_integers.R |only SSBtools-1.6.0/SSBtools/R/total_collapse.R |only SSBtools-1.6.0/SSBtools/man/AutoHierarchies.Rd | 16 + SSBtools-1.6.0/SSBtools/man/formula_utils.Rd | 2 SSBtools-1.6.0/SSBtools/man/hierarchies_as_vars.Rd |only SSBtools-1.6.0/SSBtools/man/map_hierarchies_to_data.Rd |only SSBtools-1.6.0/SSBtools/man/max_contribution.Rd |only SSBtools-1.6.0/SSBtools/man/substitute_formula_vars.Rd |only SSBtools-1.6.0/SSBtools/man/table_all_integers.Rd |only SSBtools-1.6.0/SSBtools/man/total_collapse.Rd |only SSBtools-1.6.0/SSBtools/man/vars_to_hierarchies.Rd |only SSBtools-1.6.0/SSBtools/tests/testthat/test-ModelMatrix.R | 9 - SSBtools-1.6.0/SSBtools/tests/testthat/test-formula_utils.R |only 26 files changed, 245 insertions(+), 54 deletions(-)
Title: Estimate Gaussian and Student's t Mixture Vector Autoregressive
Models
Description: Unconstrained and constrained maximum likelihood estimation of structural and reduced form
Gaussian mixture vector autoregressive, Student's t mixture vector autoregressive, and Gaussian and Student's t
mixture vector autoregressive models, quantile residual tests, graphical diagnostics,
simulations, forecasting, and estimation of generalized impulse response function and generalized
forecast error variance decomposition.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2016) <doi:10.1016/j.jeconom.2016.02.012>,
Savi Virolainen (forthcoming) <doi:10.1080/07350015.2024.2322090>,
Savi Virolainen (2022) <doi:10.48550/arXiv.2109.13648>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between gmvarkit versions 2.1.2 dated 2024-02-29 and 2.1.3 dated 2024-12-04
DESCRIPTION | 17 ++- MD5 | 24 ++--- NEWS.md | 5 + R/generateParams.R | 2 R/parameterReforms.R | 2 build/vignette.rds |binary inst/doc/gmvarkit-vignette.Rnw | 144 +++++++++++++++++++++++++++------ inst/doc/gmvarkit-vignette.pdf |binary man/gmvarkit-package.Rd | 2 tests/testthat/test_linearIRF.R | 4 tests/testthat/test_parameterReforms.R | 2 vignettes/gmvarkit-vignette.Rnw | 144 +++++++++++++++++++++++++++------ vignettes/refs.bib | 4 13 files changed, 279 insertions(+), 71 deletions(-)
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 1.40.0 dated 2024-12-02 and 1.40.1 dated 2024-12-04
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 15 ++++++++++++--- R/vignette_engine.R | 3 --- 4 files changed, 18 insertions(+), 12 deletions(-)
Title: Reading and Writing Open Data Format Files
Description: The Open Data Format (ODF) is a new, non-proprietary, multilingual, metadata enriched, and zip-compressed data format with metadata structured in the Data Documentation Initiative (DDI) Codebook standard. This package allows reading and writing of data files in the Open Data Format (ODF) in R, and displaying metadata in different languages. For further information on the Open Data Format, see <https://opendataformat.github.io/>.
Author: Tom Hartl [aut, cre] ,
Claudia Saalbach [ctb]
Maintainer: Tom Hartl <thartl@diw.de>
Diff between opendataformat versions 2.1.0 dated 2024-12-03 and 2.1.1 dated 2024-12-04
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/docu_odf.R | 26 +++++++++++++++++++------- R/merge.R | 22 ++++++++++------------ inst/doc/opendataformat.html | 2 +- man/merge.odf.Rd | 4 ++-- tests/testthat/test_merge.R | 8 ++++---- 7 files changed, 45 insertions(+), 35 deletions(-)
More information about opendataformat at CRAN
Permanent link
Title: Protein Quantification in Mass Spectrometry-Based Proteomics
Description: An implementation of the MaxLFQ algorithm by
Cox et al. (2014) <doi:10.1074/mcp.M113.031591> in a comprehensive
pipeline for processing proteomics data in data-independent acquisition mode
(Pham et al. 2020 <doi:10.1093/bioinformatics/btz961>).
It offers additional options for protein quantification using
the N most intense fragment ions, using all fragment ions, and
a wrapper for the median polish algorithm by Tukey (1977, ISBN:0201076160).
In general, the tool can be used to integrate multiple
proportional observations into a single quantitative value.
Author: Thang Pham [aut, cre, cph, ctb]
,
Alex Henneman [ctb]
Maintainer: Thang Pham <t.pham@amsterdamumc.nl>
Diff between iq versions 1.10 dated 2024-12-03 and 1.10.1 dated 2024-12-04
DESCRIPTION | 6 +++--- MD5 | 15 +++++++++++---- inst/doc/iq.Rmd | 16 ++++++++-------- inst/doc/iq.html | 4 ++-- vignettes/iq.Rmd | 16 ++++++++-------- vignettes/iq1-1.png |only vignettes/iq2-1.png |only vignettes/iq3-1.png |only vignettes/iq4-1.png |only vignettes/iq5-1.png |only vignettes/iq6-1.png |only vignettes/iq7-1.png |only 12 files changed, 32 insertions(+), 25 deletions(-)
Title: Genotyping Triploids (or Diploids) from Luminescence Data
Description: Genotyping of triploid individuals from luminescence data (marker probeset A and B). Works also for diploids.
Two main functions: Run_Clustering() that regroups individuals with a same genotype based on proximity and
Run_Genotyping() that assigns a genotype to each cluster. For Shiny interface use: launch_GenoShiny().
Author: Julien Roche [aut, cre],
Florence Phocas [aut],
Mathieu Besson [aut],
Pierre Patrice [aut],
Marc Vandeputte [aut],
Francois Allal [aut],
Pierrick Haffray [aut]
Maintainer: Julien Roche <julien.roche@inrae.fr>
Diff between GenoTriplo versions 1.1.0 dated 2024-07-31 and 1.1.2 dated 2024-12-04
DESCRIPTION | 10 - MD5 | 12 - R/function_GenoTot_pop_dif.R | 197 ++++++++++---------- R/function_GenoTot_pop_same.R | 400 +++++++++++++++++++++--------------------- R/function_create_dataset.R | 2 R/function_run_genotyping.R | 4 R/zzz.R | 20 +- 7 files changed, 333 insertions(+), 312 deletions(-)
Title: Dynamic Function-Oriented 'Make'-Like Declarative Pipelines
Description: Pipeline tools coordinate the pieces of computationally
demanding analysis projects.
The 'targets' package is a 'Make'-like pipeline tool for statistics and
data science in R. The package skips costly runtime for tasks
that are already up to date,
orchestrates the necessary computation with implicit parallel computing,
and abstracts files as R objects. If all the current output matches
the current upstream code and data, then the whole pipeline is up
to date, and the results are more trustworthy than otherwise.
The methodology in this package
borrows from GNU 'Make' (2015, ISBN:978-9881443519)
and 'drake' (2018, <doi:10.21105/joss.00550>).
Author: William Michael Landau [aut, cre]
,
Matthew T. Warkentin [ctb],
Mark Edmondson [ctb] ,
Samantha Oliver [rev] ,
Tristan Mahr [rev] ,
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between targets versions 1.9.0 dated 2024-11-20 and 1.9.1 dated 2024-12-04
DESCRIPTION | 6 ++-- MD5 | 45 +++++++++++++++++----------------- NAMESPACE | 2 + NEWS.md | 13 +++++++++ R/class_branch.R | 2 - R/class_bud.R | 2 - R/class_database.R | 2 - R/class_future.R | 2 - R/class_meta.R | 3 ++ R/class_pipeline.R | 6 ++-- R/class_reference.R | 39 +++++++++++++++-------------- R/class_runtime.R | 14 +++++++++- R/class_store_repository_cas.R | 5 +++ R/class_store_repository_cas_file.R | 3 ++ R/class_summary.R | 2 - R/tar_config_set.R | 2 - R/utils_files.R | 8 +++--- R/utils_igraph.R | 25 +++++++++++++++++- tests/aws/test-branching.R |only tests/aws/test-class_aws_qs.R | 12 ++++----- tests/testthat/test-class_builder.R | 1 tests/testthat/test-class_imports.R | 14 ++++++++++ tests/testthat/test-class_pipeline.R | 12 ++++----- tests/testthat/test-class_reference.R | 28 ++++++++++----------- 24 files changed, 163 insertions(+), 85 deletions(-)
Title: Visualizing of Distributions of Covariance Matrices
Description: Visualizing of distributions of covariance matrices.
The package implements the methodology described in Tokuda, T., Goodrich, B., Van Mechelen, I., Gelman, A., & Tuerlinckx, F. (2012) <https://stat.columbia.edu/~gelman/research/unpublished/Visualization.pdf>.
Author: Tomoki Tokuda [aut],
Ben Goodrich [ctb],
Iven Van Mechelen [ctb],
Andrew Gelman [ctb],
Francis Tuerlinckx [ctb],
Kristof Meers [cre]
Maintainer: Kristof Meers <kristof.meers+cran@kuleuven.be>
Diff between VisCov versions 1.4.0 dated 2024-10-24 and 1.5.0 dated 2024-12-04
DESCRIPTION | 11 +- MD5 | 13 +- NAMESPACE | 6 - R/VisCov.R | 216 +++++++++++++++++++++++++++++++++++++++++---- man/VisCov.Rd | 177 ++++++++++++++++++++++-------------- man/panelSelect.Rd | 33 +++--- man/panelSelectCorr.Rd |only man/panelSelectMultiple.Rd | 49 +++++----- 8 files changed, 368 insertions(+), 137 deletions(-)
Title: Multiple Imputation of Covariates by Substantive Model
Compatible Fully Conditional Specification
Description: Implements multiple imputation of missing covariates by
Substantive Model Compatible Fully Conditional Specification.
This is a modification of the popular FCS/chained equations
multiple imputation approach, and allows imputation of missing
covariate values from models which are compatible with the user
specified substantive model.
Author: Jonathan Bartlett [aut, cre],
Ruth Keogh [aut],
Edouard F. Bonneville [aut],
Claus Thorn Ekstroem [ctb]
Maintainer: Jonathan Bartlett <jonathan.bartlett1@lshtm.ac.uk>
Diff between smcfcs versions 1.9.0 dated 2024-11-07 and 1.9.1 dated 2024-12-04
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/smcfcs.r | 4 ++-- inst/doc/smcfcs-vignette.html | 4 ++-- inst/doc/smcfcs_coverror-vignette.html | 4 ++-- 5 files changed, 13 insertions(+), 13 deletions(-)
Title: Lattice Plot for Panel Data
Description: It creates a lattice plot to visualize panel or longitudinal data. The observed values are plotted as dots and the fitted values as lines, both against time. The plot is customizable and easy to edit, even if you do not know how to construct a lattice plot from scratch.
Author: Michail Tsagris [aut, cre],
Christos Adam [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between plattice versions 1.0 dated 2022-10-03 and 1.1 dated 2024-12-04
DESCRIPTION | 9 +++++---- MD5 | 4 ++-- man/plattice-package.Rd | 4 ++-- 3 files changed, 9 insertions(+), 8 deletions(-)
Title: A Pipeline Toolkit for Reproducible Computation at Scale
Description: A general-purpose computational engine for data
analysis, drake rebuilds intermediate data objects when their
dependencies change, and it skips work when the results are already up
to date. Not every execution starts from scratch, there is native
support for parallel and distributed computing, and completed projects
have tangible evidence that they are reproducible. Extensive
documentation, from beginner-friendly tutorials to practical examples
and more, is available at the reference website
<https://docs.ropensci.org/drake/> and the online manual
<https://books.ropensci.org/drake/>.
Author: William Michael Landau [aut, cre]
,
Alex Axthelm [ctb],
Jasper Clarkberg [ctb],
Kirill Mueller [ctb],
Ben Bond-Lamberty [ctb] ,
Tristan Mahr [ctb] ,
Miles McBain [ctb] ,
Noam Ross [ctb] ,
Ellis Hughes [ctb],
Matthew Mark Strasiotto [ctb],
Ben Marwick [...truncated...]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between drake versions 7.13.10 dated 2024-05-15 and 7.13.11 dated 2024-12-04
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/cache.R | 2 +- R/deprecated.R | 2 +- R/igraph.R | 23 ++++++++++++++++++++++- man/new_cache.Rd | 2 +- man/recover_cache.Rd | 2 +- 8 files changed, 41 insertions(+), 16 deletions(-)
Title: Cycle Routing and Data for Cycling Advocacy
Description: An interface to the cycle routing/data services provided by
'CycleStreets', a not-for-profit social enterprise and advocacy
organisation. The application programming interfaces (APIs) provided
by 'CycleStreets' are documented at
(<https://www.cyclestreets.net/api/>). The focus of this package is
the journey planning API, which aims to emulate the routes taken by a
knowledgeable cyclist. An innovative feature of the routing service
of its provision of fastest, quietest and balanced profiles. These
represent routes taken to minimise time, avoid traffic and compromise
between the two, respectively.
Author: Robin Lovelace [aut, cre] ,
Martin Lucas-Smith [aut],
Eric Krueger [ctb],
Joey Talbot [aut] ,
Malcolm Morgan [ctb] ,
Zhao Wang [ctb]
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between cyclestreets versions 1.0.2 dated 2024-09-02 and 1.0.3 dated 2024-12-04
DESCRIPTION | 13 ++++++++----- MD5 | 6 +++--- NEWS.md | 6 ++++++ R/batch.R | 56 +++++++++++++++++++++++++++++++++++++++++++++++++------- 4 files changed, 66 insertions(+), 15 deletions(-)
Title: Tools to Match Corporate Lending Portfolios with Climate Data
Description: These tools implement in R a fundamental part of the software
'PACTA' (Paris Agreement Capital Transition Assessment), which is a
free tool that calculates the alignment between financial portfolios
and climate scenarios (<https://www.transitionmonitor.com/>). Financial
institutions use 'PACTA' to study how their capital allocation
decisions align with climate change mitigation goals. This package
matches data from corporate lending portfolios to asset level data
from market-intelligence databases (e.g. power plant capacities,
emission factors, etc.). This is the first step to assess if a
financial portfolio aligns with climate goals.
Author: Alex Axthelm [aut, cre] ,
Jackson Hoffart [aut, ctr] ,
Mauro Lepore [aut, ctr] ,
Klaus Hagedorn [aut],
Florence Palandri [aut],
Evgeny Petrovsky [aut],
Jacob Kastl [ctr] ,
RMI [cph, fnd]
Maintainer: Alex Axthelm <aaxthelm@rmi.org>
Diff between r2dii.match versions 0.2.1 dated 2024-06-19 and 0.3.0 dated 2024-12-04
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- NEWS.md | 6 ++++++ R/add_sector_and_borderline.R | 19 +++++-------------- R/match_name.R | 38 ++++++++++++++++++-------------------- R/restructure_abcd.R | 8 ++++---- man/match_name.Rd | 35 +++++++++++++++-------------------- man/r2dii.match-package.Rd | 2 +- tests/testthat/test-match_name.R | 12 ++++++------ 9 files changed, 69 insertions(+), 79 deletions(-)
Title: Superefficient Estimation of Future Conditional Hazards Based on
Marker Information
Description: Provides a nonparametric smoothed kernel density estimator for the future conditional hazard when time-dependent covariates are present. It also provides pointwise and uniform confidence bands and a bandwidth selection.
Author: Dimitrios Bagkavos [aut, cre],
Alex Isakson [ctb],
Enno Mammen [ctb],
Jens Nielsen [ctb],
Cecile Proust-Lima [ctb]
Maintainer: Dimitrios Bagkavos <dimitrios.bagkavos@gmail.com>
Diff between HQM versions 0.1.1 dated 2024-09-24 and 0.1.2 dated 2024-12-04
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++++---- NAMESPACE | 9 ++++++--- R/auc.hqm.R |only R/bs.hqm.R |only man/auc.hqm.Rd |only man/bs.hqm.Rd |only man/get_h_xll.Rd | 49 +++++++++++++++++++++++++++++++++++++++++++++++-- man/h_xt_vec.Rd | 39 +++++++++++++++++++++++++++++++++++++++ 9 files changed, 104 insertions(+), 13 deletions(-)
Title: Qualitative Comparative Analysis
Description: An extensive set of functions to perform Qualitative Comparative Analysis:
crisp sets ('csQCA'), temporal ('tQCA'), multi-value ('mvQCA')
and fuzzy sets ('fsQCA'), using a GUI - graphical user interface.
'QCA' is a methodology that bridges the qualitative and quantitative
divide in social science research. It uses a Boolean minimization
algorithm, resulting in a minimal causal configuration associated
with a given phenomenon.
Author: Adrian Dusa [aut, cre, cph] ,
Ciprian Paduraru [ctb] ,
jQuery Foundation [cph] ,
jQuery contributors [ctb, cph] ,
Vasil Dinkov [ctb, cph] ,
Dmitry Baranovskiy [ctb, cph] ,
Emmanuel Quentin [ctb, cph] ,
Jimmy Breck-McKye [ctb, cph] ,
Alrik Thiem [aut] [...truncated...]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between QCA versions 3.22 dated 2024-03-15 and 3.23 dated 2024-12-04
DESCRIPTION | 10 MD5 | 112 ++++---- R/findRows.R | 1 R/findmin.R | 73 ++++- R/fuzzyand.R | 3 R/fuzzyor.R | 3 R/minimize.R | 20 + R/pof.R | 33 ++ R/print.R | 363 ++++++++++++++++++++++---- R/superSubset.R | 30 +- R/truthTable.R | 21 + build/partial.rdb |binary data/HarKem.rda |binary data/LC.rda |binary data/LF.rda |binary data/LM.rda |binary data/d.HK.rda |binary data/d.partybans.rda |binary inst/ChangeLog | 16 + inst/gui/www/js/maincode.js | 2 inst/staticdocs/CV.html | 4 inst/staticdocs/LegacyDatasets.html | 4 inst/staticdocs/Lipset.html | 4 inst/staticdocs/QCA_package.html | 8 inst/staticdocs/RS.html | 4 inst/staticdocs/SOPexpressions.html | 4 inst/staticdocs/XYplot.html | 4 inst/staticdocs/Xplot.html | 4 inst/staticdocs/calibrate.html | 4 inst/staticdocs/causalChain.html | 4 inst/staticdocs/chartFunctions.html | 4 inst/staticdocs/export.html | 4 inst/staticdocs/factorize.html | 4 inst/staticdocs/findRows.html | 4 inst/staticdocs/findTh.html | 4 inst/staticdocs/fuzzyops.html | 4 inst/staticdocs/generate.html | 4 inst/staticdocs/implicantMatrixFunctions.html | 4 inst/staticdocs/index.html | 4 inst/staticdocs/intersection.html | 4 inst/staticdocs/minimize.html | 4 inst/staticdocs/modelFit.html | 4 inst/staticdocs/negate.html | 4 inst/staticdocs/pof.html | 4 inst/staticdocs/retention.html | 4 inst/staticdocs/runGUI.html | 4 inst/staticdocs/subsetsAndSupersets.html | 4 inst/staticdocs/truthTable.html | 4 man/QCA_package.Rd | 4 man/minimize.Rd | 2 man/modelFit.Rd | 2 src/CCubes.c | 154 +++++++---- src/CCubes.h | 21 - src/QCA.c | 38 +- src/find_models.c | 20 - src/utils.c | 62 ++-- src/utils.h | 10 57 files changed, 785 insertions(+), 331 deletions(-)
Title: R Interface to Geochemical Modeling Software
Description: A geochemical modeling program developed by the US Geological
Survey that is designed to perform a wide variety of aqueous geochemical
calculations, including speciation, batch-reaction, one-dimensional
reactive-transport, and inverse geochemical calculations.
Author: S.R. Charlton [aut, cre],
D.L. Parkhurst [aut],
C.A.J. Appelo [aut],
with contributions from D. Gillespie for Chipmunk BASIC [aut],
S.D. Cohen [aut],
A.C. Hindmarsh [aut],
R. Serban [aut],
D. Shumaker [aut],
A.G. Taylor for CVODE/SUNDIALS [aut]
Maintainer: S.R. Charlton <charlton@usgs.gov>
Diff between phreeqc versions 3.8.0 dated 2024-07-18 and 3.8.5 dated 2024-12-04
DESCRIPTION | 47 +++- MD5 | 167 +++++++-------- R/phreeqc.R | 91 +++++--- build/partial.rdb |binary data/databases.rda |binary data/examples.rda |binary man/Amm.dat.Rd | 3 man/ColdChem.dat.Rd | 3 man/Kinec.v2.dat.Rd | 3 man/Kinec_v3.dat.Rd |only man/PHREEQC_ThermoddemV1.10_15Dec2020.dat.Rd | 3 man/Tipping_Hurley.dat.Rd | 1 man/core10.dat.Rd | 1 man/ex1.Rd | 2 man/ex10.Rd | 2 man/ex11.Rd | 2 man/ex12.Rd | 2 man/ex13.Rd | 2 man/ex14.Rd | 2 man/ex15.Rd | 2 man/ex15.dat.Rd | 3 man/ex16.Rd | 2 man/ex17.Rd | 2 man/ex18.Rd | 2 man/ex19.Rd | 2 man/ex2.Rd | 2 man/ex20.Rd | 2 man/ex21.Rd | 2 man/ex22.Rd | 2 man/ex3.Rd | 2 man/ex4.Rd | 2 man/ex5.Rd | 2 man/ex6.Rd | 2 man/ex7.Rd | 2 man/ex8.Rd | 2 man/ex9.Rd | 2 man/frezchem.dat.Rd | 1 man/iso.dat.Rd | 3 man/llnl.dat.Rd | 1 man/minteq.dat.Rd | 3 man/minteq.v4.dat.Rd | 3 man/phrGetLogStringsOn.Rd | 2 man/phreeqc-package.Rd | 2 man/phreeqc.dat.Rd | 3 man/phreeqc_rates.dat.Rd | 3 man/pitzer.dat.Rd | 3 man/sit.dat.Rd | 3 man/wateq4f.dat.Rd | 3 src/IPhreeqc.cpp | 2 src/IPhreeqc.h | 8 src/IPhreeqcLib.cpp | 2 src/IPhreeqchpp.h | 2 src/Version.h | 8 src/phreeqcpp/Keywords.cpp | 4 src/phreeqcpp/Keywords.h | 1 src/phreeqcpp/PBasic.cpp | 20 + src/phreeqcpp/Parser.h | 2 src/phreeqcpp/Phreeqc.cpp | 3 src/phreeqcpp/Phreeqc.h | 9 src/phreeqcpp/Solution.cpp | 21 + src/phreeqcpp/Solution.h | 3 src/phreeqcpp/Utils.cpp | 2 src/phreeqcpp/basicsubs.cpp | 59 ++++- src/phreeqcpp/cl1.cpp | 2 src/phreeqcpp/cvode.cpp | 8 src/phreeqcpp/gases.cpp | 115 +++++++--- src/phreeqcpp/global_structures.h | 239 +++++++++++----------- src/phreeqcpp/input.cpp | 2 src/phreeqcpp/inverse.cpp | 2 src/phreeqcpp/kinetics.cpp | 17 - src/phreeqcpp/mainsubs.cpp | 7 src/phreeqcpp/model.cpp | 2 src/phreeqcpp/nvector_serial.cpp | 2 src/phreeqcpp/nvector_serial.h | 2 src/phreeqcpp/pitzer.cpp | 26 +- src/phreeqcpp/prep.cpp | 68 +++--- src/phreeqcpp/print.cpp | 36 ++- src/phreeqcpp/read.cpp | 101 +++++++++ src/phreeqcpp/sit.cpp | 2 src/phreeqcpp/step.cpp | 79 +++++++ src/phreeqcpp/structures.cpp | 4 src/phreeqcpp/tally.cpp | 6 src/phreeqcpp/tidy.cpp | 2 src/phreeqcpp/transport.cpp | 288 ++++++++++++++------------- src/phreeqcpp/utilities.cpp | 2 85 files changed, 995 insertions(+), 559 deletions(-)
Title: Structural Handling of Finnish Personal Identity Codes
Description: Structural handling of Finnish identity codes (natural persons and
organizations); extract information, check ID validity and diagnostics.
Author: Pyry Kantanen [aut, cre] ,
Mans Magnusson [aut],
Jussi Paananen [aut],
Juho Kopra [ctb],
Oskari Luomala [ctb],
Tuomo Nieminen [ctb],
Leo Lahti [aut]
Maintainer: Pyry Kantanen <pyry.kantanen@gmail.com>
Diff between hetu versions 1.0.7 dated 2022-05-23 and 1.1.0 dated 2024-12-04
DESCRIPTION | 12 - MD5 | 50 ++-- NAMESPACE | 9 NEWS.md | 7 R/hetu.R | 173 ++++++++++++---- R/hetu_control_char.R | 13 - R/hetu_diagnostic.R | 230 ++++++++++++++++++++++ R/pin_age.R | 6 R/pin_ctrl.R | 2 R/pin_sex.R | 2 R/rpin.R | 103 ++++++---- README.md | 26 +- build/vignette.rds |binary inst/CITATION | 21 +- inst/doc/hetu.R | 13 - inst/doc/hetu.Rmd | 24 +- inst/doc/hetu.html | 458 +++++++++++++++++++++++---------------------- man/hetu.Rd | 94 ++++++++- man/hetu_diagnostic.Rd | 8 man/is.diagnostic.Rd |only man/pin_age.Rd | 2 man/pin_sex.Rd | 2 man/plot.diagnostic.Rd |only man/rpin.Rd | 48 +++- man/satu_control_char.Rd | 4 tests/testthat/test_hetu.R | 32 ++- vignettes/hetu.Rmd | 24 +- 27 files changed, 930 insertions(+), 433 deletions(-)
Title: Embed 'SWI'-'Prolog'
Description: Interface to 'SWI'-'Prolog', <https://www.swi-prolog.org/>. This package is normally not loaded directly, please refer to package 'rolog' instead. The purpose of this package is to provide the 'Prolog' runtime on systems that do not have a software installation of 'SWI'-'Prolog'.
Author: Matthias Gondan [aut, com, cre] ,
Jan Wielemaker [ctb, cph] ,
European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
Diff between rswipl versions 9.3.12 dated 2024-09-29 and 9.3.16 dated 2024-12-04
rswipl-9.3.12/rswipl/src/swipl-devel/packages/cpp/pl2cpp2.doc |only rswipl-9.3.16/rswipl/DESCRIPTION | 14 rswipl-9.3.16/rswipl/MD5 | 254 rswipl-9.3.16/rswipl/NEWS.md | 14 rswipl-9.3.16/rswipl/R/rswipl.R | 1 rswipl-9.3.16/rswipl/inst/include/linkingto.txt | 2 rswipl-9.3.16/rswipl/src/Makevars | 6 rswipl-9.3.16/rswipl/src/install.libs.R | 2 rswipl-9.3.16/rswipl/src/swipl-devel/VERSION | 2 rswipl-9.3.16/rswipl/src/swipl-devel/bench/port/sicstus.pl | 10 rswipl-9.3.16/rswipl/src/swipl-devel/bench/port/swi.pl | 169 rswipl-9.3.16/rswipl/src/swipl-devel/bench/port/yap.pl | 10 rswipl-9.3.16/rswipl/src/swipl-devel/bench/run.pl | 154 rswipl-9.3.16/rswipl/src/swipl-devel/boot/autoload.pl | 24 rswipl-9.3.16/rswipl/src/swipl-devel/boot/dcg.pl | 33 rswipl-9.3.16/rswipl/src/swipl-devel/boot/expand.pl | 16 rswipl-9.3.16/rswipl/src/swipl-devel/boot/history.pl | 9 rswipl-9.3.16/rswipl/src/swipl-devel/boot/init.pl | 10 rswipl-9.3.16/rswipl/src/swipl-devel/boot/load.pl | 5 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| 3 rswipl-9.3.16/rswipl/src/swipl-devel/library/nb_set.pl | 180 rswipl-9.3.16/rswipl/src/swipl-devel/library/option.pl | 172 rswipl-9.3.16/rswipl/src/swipl-devel/library/pprint.pl | 5 rswipl-9.3.16/rswipl/src/swipl-devel/library/prolog_clause.pl | 18 rswipl-9.3.16/rswipl/src/swipl-devel/library/prolog_colour.pl | 22 rswipl-9.3.16/rswipl/src/swipl-devel/library/prolog_deps.pl | 22 rswipl-9.3.16/rswipl/src/swipl-devel/library/prolog_locale.pl |only rswipl-9.3.16/rswipl/src/swipl-devel/library/prolog_pack.pl | 25 rswipl-9.3.16/rswipl/src/swipl-devel/library/shlib.pl | 93 rswipl-9.3.16/rswipl/src/swipl-devel/library/solution_sequences.pl | 80 rswipl-9.3.16/rswipl/src/swipl-devel/library/theme/dark.pl | 4 rswipl-9.3.16/rswipl/src/swipl-devel/library/ugraphs.pl | 26 rswipl-9.3.16/rswipl/src/swipl-devel/library/wasm.pl | 4 rswipl-9.3.16/rswipl/src/swipl-devel/packages/clib/udp_broadcast.pl | 4 rswipl-9.3.16/rswipl/src/swipl-devel/packages/cpp/CMakeLists.txt | 2 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rswipl-9.3.16/rswipl/src/swipl-devel/src/os/pl-fmt.c | 220 rswipl-9.3.16/rswipl/src/swipl-devel/src/os/pl-fmt.h |only rswipl-9.3.16/rswipl/src/swipl-devel/src/os/pl-option.c | 51 rswipl-9.3.16/rswipl/src/swipl-devel/src/os/pl-prologflag.c | 55 rswipl-9.3.16/rswipl/src/swipl-devel/src/os/pl-prologflag.h | 9 rswipl-9.3.16/rswipl/src/swipl-devel/src/os/pl-stream.c | 14 rswipl-9.3.16/rswipl/src/swipl-devel/src/os/pl-string.c | 12 rswipl-9.3.16/rswipl/src/swipl-devel/src/os/pl-string.h | 29 rswipl-9.3.16/rswipl/src/swipl-devel/src/os/pl-tai.c | 64 rswipl-9.3.16/rswipl/src/swipl-devel/src/os/pl-text.c | 48 rswipl-9.3.16/rswipl/src/swipl-devel/src/os/pl-text.h | 19 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-alloc.c | 2 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-arith.c | 6 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-arith.h | 20 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-attvar.c | 12 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-attvar.h | 8 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-debug.c | 2 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-debug.h | 2 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-dict.c | 433 - rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-error.c | 61 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-error.h | 23 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-ext.c | 236 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-ext.h | 2 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-fli.c | 160 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-gc.h | 21 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-global.h | 2 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-gmp.c | 14 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-gmp.h | 8 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-incl.h | 18 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-init.c | 374 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-op.c | 1 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-prims.c | 13 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-prims.h | 1 rswipl-9.3.16/rswipl/src/swipl-devel/src/pl-pro.c 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rswipl-9.3.16/rswipl/src/swipl-devel/src/wasm/server.pl | 25 131 files changed, 7428 insertions(+), 2388 deletions(-)
Title: Analyzing Gastric Emptying from MRI or Scintigraphy
Description: Fits gastric emptying time series from MRI or 'scintigraphic' measurements
using nonlinear mixed-model population fits with 'nlme' and Bayesian methods with
Stan; computes derived parameters such as t50 and AUC.
Author: Dieter Menne [aut, cre]
Maintainer: Dieter Menne <dieter.menne@menne-biomed.de>
Diff between gastempt versions 0.6.1 dated 2024-09-27 and 0.6.2 dated 2024-12-04
gastempt-0.6.1/gastempt/tests/testthat/_snaps |only gastempt-0.6.2/gastempt/DESCRIPTION | 6 gastempt-0.6.2/gastempt/MD5 | 36 +- gastempt-0.6.2/gastempt/README.md | 2 gastempt-0.6.2/gastempt/build/vignette.rds |binary gastempt-0.6.2/gastempt/inst/doc/gastempt.Rmd | 4 gastempt-0.6.2/gastempt/inst/doc/gastempt.html | 9 gastempt-0.6.2/gastempt/man/coef.nlme_gastempt.Rd | 38 +- gastempt-0.6.2/gastempt/man/coef.stan_gastempt.Rd | 38 +- gastempt-0.6.2/gastempt/man/gastemptfunc.Rd | 184 +++++------ gastempt-0.6.2/gastempt/man/nlme_gastempt.Rd | 184 +++++------ gastempt-0.6.2/gastempt/man/plot.nlme_gastempt.Rd | 38 +- gastempt-0.6.2/gastempt/man/plot.stan_gastempt.Rd | 40 +- gastempt-0.6.2/gastempt/man/run_shiny.Rd | 28 - gastempt-0.6.2/gastempt/man/simulate_gastempt.Rd | 182 +++++----- gastempt-0.6.2/gastempt/man/stan_gastempt.Rd | 158 ++++----- gastempt-0.6.2/gastempt/man/stan_model_names.Rd | 46 +- gastempt-0.6.2/gastempt/man/t50.Rd | 40 +- gastempt-0.6.2/gastempt/tests/testthat/testthat-problems.rds |only gastempt-0.6.2/gastempt/vignettes/gastempt.Rmd | 4 20 files changed, 518 insertions(+), 519 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-16 1.0.0
2015-07-07 0.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-07-04 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-06-02 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-08-16 0.0.2-1
2017-12-11 0.0.1-5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-10-06 1.1
2017-08-25 0.1.0
Title: Metabolomics Data Analysis Functions
Description: A collection of functions for processing and analyzing metabolite data.
The namesake function mrbin() converts 1D
or 2D Nuclear Magnetic Resonance data into a matrix of values suitable for further data analysis and
performs basic processing steps in a reproducible way. Negative values, a
common issue in such data, can be replaced by positive values (<doi:10.1021/acs.jproteome.0c00684>). All used
parameters are stored in a readable text file and can be restored from that
file to enable exact reproduction of the data at a later time. The function fia() ranks features according
to their impact on classifier models, especially artificial neural network models.
Author: Matthias Klein [aut, cre]
Maintainer: Matthias Klein <matthias.s.klein@gmx.net>
Diff between mrbin versions 1.7.5 dated 2024-06-12 and 1.8.0 dated 2024-12-04
DESCRIPTION | 6 MD5 | 76 - NEWS.md | 13 R/mrbin.R | 2266 ++++++++++++++++++++++++++------------- inst/doc/mrbin.R | 94 - inst/doc/mrbin.Rnw | 64 - inst/doc/mrbin.pdf |binary inst/extdata/1/10/pdata/10/title | 3 inst/extdata/1/12/pdata/10/title | 3 inst/extdata/2/10/pdata/10/title | 3 inst/extdata/2/12/pdata/10/title | 3 inst/extdata/3/10/pdata/10/title | 3 inst/extdata/3/12/pdata/10/title | 3 man/PQNScaling.Rd | 4 man/addToPlot.Rd | 5 man/annotatemrbin.Rd | 8 man/atnv.Rd | 6 man/cropNMR.Rd | 2 man/dilutionCorrection.Rd | 4 man/editmetabolitesmrbin.Rd | 6 man/logTrafo.Rd | 4 man/metadatamrbin.Rd | 8 man/mrbin.Rd | 14 man/mrbinrun.Rd | 17 man/mrplot.Rd | 29 man/plotMultiNMR.Rd | 34 man/plotNMR.Rd | 33 man/plotPCA.Rd | 4 man/plotResults.Rd | 4 man/recreatemrbin.Rd | 4 man/removeNoise.Rd | 4 man/removeSpectrum.Rd | 9 man/setCurrentSpectrum.Rd | 4 man/setDilutionFactors.Rd | 9 man/setNoiseLevels.Rd | 9 man/trimZeros.Rd | 4 man/unitVarianceScaling.Rd | 4 man/zoom.Rd | 13 vignettes/mrbin.Rnw | 64 - 39 files changed, 1950 insertions(+), 893 deletions(-)
Title: Structured Learning in Time-Dependent Cox Models
Description: Efficient procedures for fitting and cross-validating the structurally-regularized time-dependent Cox models.
Author: Yi Lian [aut, cre],
Guanbo Wang [aut],
Archer Y. Yang [aut],
Mireille E. Schnitzer [aut],
Robert W. Platt [aut],
Rui Wang [aut],
Marc Dorais [aut],
Sylvie Perreault [aut],
Julien Mairal [ctb],
Yuansi Chen [ctb]
Maintainer: Yi Lian <yi.lian@mail.mcgill.ca>
Diff between sox versions 1.2 dated 2024-07-15 and 1.2.1 dated 2024-12-04
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 2 +- R/auxiliary_functions.R | 2 +- tests/testthat/Rplots.pdf |binary 5 files changed, 10 insertions(+), 10 deletions(-)