Title: Time Series for 'iNZight'
Description: Provides a collection of functions for working with time series data, including functions for drawing, decomposing, and forecasting. Includes capabilities to compare multiple series and fit both additive and multiplicative models. Used by 'iNZight', a graphical user interface providing easy exploration and visualisation of data for students of statistics, available in both desktop and online versions. Holt (1957) <doi:10.1016/j.ijforecast.2003.09.015>, Winters (1960) <doi:10.1287/mnsc.6.3.324>, Cleveland, Cleveland, & Terpenning (1990) "STL: A Seasonal-Trend Decomposition Procedure Based on Loess".
Author: Tom Elliott [aut, cre] ,
Zhaoming Su [aut],
Junjie Zeng [ctb],
Simon Potter [ctb],
David Banks [ctb],
Marco Kuper [ctb],
Dongning Zhang [ctb]
Maintainer: Tom Elliott <tom.elliott@auckland.ac.nz>
Diff between iNZightTS versions 2.0.0 dated 2024-01-17 and 2.0.2 dated 2025-07-02
DESCRIPTION | 15 +++++++++------ MD5 | 18 +++++++++--------- R/forecastplot.R | 5 +++-- R/rawplot.R | 2 +- man/figures/decomp-plot-1.png |binary man/figures/forecast-plot-1.png |binary man/figures/raw-plot-1.png |binary man/figures/season-plot-1.png |binary man/figures/subseries-plot-1.png |binary man/iNZightTS-package.Rd | 1 + 10 files changed, 23 insertions(+), 18 deletions(-)
Title: Spatial Statistical Modeling and Prediction
Description: Fit, summarize, and predict for a variety of spatial statistical models applied to point-referenced and areal (lattice) data. Parameters are estimated using various methods. Additional modeling features include anisotropy, non-spatial random effects, partition factors, big data approaches, and more. Model-fit statistics are used to summarize, visualize, and compare models. Predictions at unobserved locations are readily obtainable. For additional details, see Dumelle et al. (2023) <doi:10.1371/journal.pone.0282524>.
Author: Michael Dumelle [aut, cre] ,
Matt Higham [aut] ,
Ryan A. Hill [ctb] ,
Michael Mahon [ctb] ,
Jay M. Ver Hoef [aut]
Maintainer: Michael Dumelle <Dumelle.Michael@epa.gov>
Diff between spmodel versions 0.10.0 dated 2025-03-12 and 0.11.0 dated 2025-07-02
DESCRIPTION | 17 MD5 | 71 - NEWS.md | 15 R/anova.R | 462 +++++----- R/covmatrix.R | 460 +++++----- R/data.R | 20 R/dispersion_optim2orig.R | 37 R/dispersion_orig2optim.R | 33 R/esv.R | 434 ++++----- R/get_data_object.R | 1172 +++++++++++++------------- R/get_data_object_glm.R | 1282 ++++++++++++++-------------- R/get_esv.R | 146 +-- R/get_esv_dotlist.R | 122 +- R/get_local_list.R | 357 ++++---- R/get_model_stats.R | 712 ++++++++-------- R/glances.R | 308 +++--- R/glances_glm.R | 82 - R/laploglik_products.R | 1024 +++++++++++------------ R/plot.R | 676 +++++++-------- R/predict.R | 23 R/predict_block.R |only R/predict_glm.R | 2002 ++++++++++++++++++++++----------------------- R/sf_to_df.R | 54 - R/spautor.R | 592 ++++++------- R/spautorRF.R | 274 +++--- R/spgautor.R | 788 ++++++++--------- R/spglm.R | 996 +++++++++++----------- R/splm.R | 844 +++++++++--------- R/spmodel-package.R | 34 R/use_gloglik_iid.R | 4 build/partial.rdb |binary build/vignette.rds |binary data/fc_borders.rda |only inst/doc/introduction.html | 2 inst/references.bib | 1590 ++++++++++++++++++----------------- man/fc_borders.Rd |only man/predict.spmodel.Rd | 19 tests/testthat/test-splm.R | 924 ++++++++++---------- 38 files changed, 7873 insertions(+), 7703 deletions(-)
Title: A Collection of Functions for Directional Data Analysis
Description: A collection of functions for directional data (including massive data, with millions of observations) analysis.
Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included.
The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000).
Other references include:
a) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2018). "An elliptically symmetric angular Gaussian distribution". Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>.
b) Tsagris M. and Alenazi A. (2019). "Comparison of discriminant analysis methods on the sphere". Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>.
c) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2020). "Spherical regression models with general covariates and anisotropic errors". Statistics and Computing 30(1): 153--165. <doi:10.1007/s11222-019-09872 [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Christos Adam [aut],
Zehao Yu [aut],
Anamul Sajib [ctb],
Eli Amson [ctb],
Micah J. Waldstein [ctb],
Panagiotis Papastamoulis [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Directional versions 7.1 dated 2025-02-11 and 7.2 dated 2025-07-02
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/circbeta.mle.R | 4 ++-- R/circexp.mle.R | 2 +- R/mmvm.mle.R | 2 +- R/pmmvm.R | 15 +-------------- R/pvm.R | 2 +- R/vm.kde.R | 4 ++-- R/vmf.kde.R | 4 ++-- man/Directional-package.Rd | 6 ++++-- 10 files changed, 27 insertions(+), 38 deletions(-)
Title: Associated Kernel Estimations
Description: Continuous and discrete (count or categorical) estimation of density, probability mass function (p.m.f.) and regression functions are performed using associated kernels. The cross-validation technique and the local Bayesian procedure are also implemented for bandwidth selection.
Author: W. E. Wansouwe [aut, cre],
S. M. Some [aut],
C. C. Kokonendji [aut]
Maintainer: W. E. Wansouwe <ericwansouwe@gmail.com>
Diff between Ake versions 1.0.1 dated 2022-06-13 and 1.0.2 dated 2025-07-02
DESCRIPTION | 23 +++++++++++++++-------- MD5 | 4 ++-- man/plot.dke.fun.Rd | 2 +- 3 files changed, 18 insertions(+), 11 deletions(-)
Title: Miscellaneous Tools for Reproducible Research
Description: Tools to load 'R' packages
and automatically generate BibTeX files citing them as well as load and
cache plain-text and 'Excel' formatted data stored on 'GitHub', and
from other sources.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between repmis versions 0.5 dated 2016-02-07 and 0.5.1 dated 2025-07-02
DESCRIPTION | 17 +++++++++-------- MD5 | 28 ++++++++++++++-------------- NEWS | 4 ++-- R/LoadandCite.R | 6 ++++-- R/source_XlsxData.R | 10 +++++----- R/source_data.R | 4 ++-- README.md | 27 +++++++++++---------------- man/InstallOldPackages.Rd | 9 ++++++--- man/LoadandCite.Rd | 22 ++++++++++++++++------ man/git_stamp.Rd | 1 - man/scan_https.Rd | 1 - man/set_valid_wd.Rd | 1 - man/source_DropboxData.Rd | 1 - man/source_XlsxData.Rd | 13 +++++++++---- man/source_data.Rd | 20 ++++++++++++++------ 15 files changed, 92 insertions(+), 72 deletions(-)
Title: Toolbox for Regression Discontinuity Design ('RDD')
Description: Set of functions for Regression Discontinuity Design ('RDD'), for
data visualisation, estimation and testing.
Author: Matthieu Stigler [aut, cre] ,
Bastiaan Quast [aut]
Maintainer: Matthieu Stigler <Matthieu.Stigler@gmail.com>
Diff between rddtools versions 1.6.0 dated 2022-01-10 and 2.0.1 dated 2025-07-02
rddtools-1.6.0/rddtools/man/rddtools.Rd |only rddtools-2.0.1/rddtools/DESCRIPTION | 26 rddtools-2.0.1/rddtools/MD5 | 71 +- rddtools-2.0.1/rddtools/NAMESPACE | 6 rddtools-2.0.1/rddtools/NEWS.md | 16 rddtools-2.0.1/rddtools/R/as.npreg.R | 2 rddtools-2.0.1/rddtools/R/clusterInf.R | 7 rddtools-2.0.1/rddtools/R/dens_test.R | 4 rddtools-2.0.1/rddtools/R/get_methods.R | 19 rddtools-2.0.1/rddtools/R/model.matrix.rdd.R | 14 rddtools-2.0.1/rddtools/R/placebo.R | 28 rddtools-2.0.1/rddtools/R/rdd_data.R | 41 - rddtools-2.0.1/rddtools/R/rddtools.R | 8 rddtools-2.0.1/rddtools/R/reg_lm.R | 10 rddtools-2.0.1/rddtools/R/various_code.R | 6 rddtools-2.0.1/rddtools/R/waldci.R | 13 rddtools-2.0.1/rddtools/README.md | 1 rddtools-2.0.1/rddtools/build/vignette.rds |binary rddtools-2.0.1/rddtools/inst/CITATION | 2 rddtools-2.0.1/rddtools/inst/devtools_internal_tests.R | 7 rddtools-2.0.1/rddtools/inst/doc/morocco.R | 4 rddtools-2.0.1/rddtools/inst/doc/morocco.html | 467 ++++++++++--- rddtools-2.0.1/rddtools/inst/doc/rddtools.R | 2 rddtools-2.0.1/rddtools/inst/doc/rddtools.html | 479 ++++++++++---- rddtools-2.0.1/rddtools/man/STAR_MHE.Rd | 6 rddtools-2.0.1/rddtools/man/as.npregbw.Rd | 2 rddtools-2.0.1/rddtools/man/dens_test.Rd | 4 rddtools-2.0.1/rddtools/man/indh.Rd | 3 rddtools-2.0.1/rddtools/man/plotPlacebo.Rd | 21 rddtools-2.0.1/rddtools/man/rdd_data.Rd | 16 rddtools-2.0.1/rddtools/man/rdd_gen_reg.Rd | 4 rddtools-2.0.1/rddtools/man/rdd_reg_lm.Rd | 4 rddtools-2.0.1/rddtools/man/rddtools-package.Rd |only rddtools-2.0.1/rddtools/man/vcovCluster.Rd | 4 rddtools-2.0.1/rddtools/tests/testthat/test_plotPlacebo.R | 7 rddtools-2.0.1/rddtools/tests/testthat/test_plotSensi.R | 4 rddtools-2.0.1/rddtools/tests/testthat/test_rdd_reg_lm.R |only rddtools-2.0.1/rddtools/tests/testthat/test_rdddata.R | 21 38 files changed, 945 insertions(+), 384 deletions(-)
Title: Quality Control for Label-Free Proteomics Expression Data
Description: Label-free bottom-up proteomics expression data is often affected by data heterogeneity and missing values. Normalization and missing value imputation are commonly used techniques to address these issues and make the dataset suitable for further downstream analysis. This package provides an optimal combination of normalization and imputation methods for the dataset. The package utilizes three normalization methods and three imputation methods.The statistical evaluation measures named pooled co-efficient of variance, pooled estimate of variance and pooled median absolute deviation are used for selecting the best combination of normalization and imputation method for the given dataset. The user can also visualize the results by using various plots available in this package. The user can also perform the differential expression analysis between two sample groups with the function included in this package. The chosen three normalization methods, three imputation methods and three evaluati [...truncated...]
Author: Kabilan S [aut, cre],
Dr Shashi Bhushan Lal [aut, ths],
Dr Sudhir Srivastava [aut, ths],
Dr Krishna Kumar Chaturvedi [ths],
Dr Yasin Jeshima K [ths],
Dr Ramasubramanian V [ths],
Dr Girish Kumar Jha [ctb]
Maintainer: Kabilan S <kabilan151414@gmail.com>
Diff between lfproQC versions 1.4.0 dated 2024-10-10 and 1.4.1 dated 2025-07-02
DESCRIPTION | 10 +++--- MD5 | 25 ++++++++------- NEWS | 5 +++ R/Boxplot_data.R | 2 - R/Densityplot_data.R | 2 - R/QQplot_data.R | 48 ++++++++++++++---------------- R/best_combination.R | 3 + README.md | 6 ++- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/user_guide.html | 75 +++++++++++++++++++++++------------------------ man/best_combination.Rd | 3 + man/lfproQC-package.Rd | 4 +- 14 files changed, 97 insertions(+), 86 deletions(-)
Title: Extension to 'ggplot2' for Plotting Stats
Description: Provides new statistics, new geometries and new positions for
'ggplot2' and a suite of functions to facilitate the creation of
statistical plots.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between ggstats versions 0.9.0 dated 2025-03-10 and 0.10.0 dated 2025-07-02
DESCRIPTION | 9 ++++---- MD5 | 38 ++++++++++++++++++------------------- NAMESPACE | 2 + NEWS.md | 13 ++++++++++++ R/deprecated.R | 4 +-- R/ggcoef_model.R | 23 +++++++++++++++++----- R/gglikert.R | 6 +++-- R/ggstats-package.R | 2 - R/stat_weighted_mean.R | 23 +++++++++------------- build/vignette.rds |binary inst/doc/geom_diverging.html | 5 ++-- inst/doc/ggcoef_model.html | 24 +++++++++++++++++------ inst/doc/gglikert.html | 7 +++--- inst/doc/stat_cross.html | 5 ++-- inst/doc/stat_prop.html | 5 ++-- inst/doc/stat_weighted_mean.html | 5 ++-- man/ggcoef_model.Rd | 10 ++++++--- man/ggcoef_multicomponents.Rd | 4 +-- man/stat_weighted_mean.Rd | 24 +++++++++++------------ tests/testthat/test-ggcoef_model.R | 4 +-- 20 files changed, 131 insertions(+), 82 deletions(-)
Title: Summarise Patient-Level Drug Utilisation in Data Mapped to the
OMOP Common Data Model
Description: Summarise patient-level drug utilisation cohorts using data mapped
to the Observational Medical Outcomes Partnership (OMOP) common data model.
New users and prevalent users cohorts can be generated and their
characteristics, indication and drug use summarised.
Author: Marti Catala [aut, cre] ,
Mike Du [ctb] ,
Yuchen Guo [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Xintong Li [ctb] ,
Marta Alcalde-Herraiz [ctb] ,
Nuria Mercade-Besora [aut] ,
Xihang Chen [aut]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between DrugUtilisation versions 1.0.3 dated 2025-06-03 and 1.0.4 dated 2025-07-02
DESCRIPTION | 6 MD5 | 10 NEWS.md | 4 R/plots.R | 5 inst/doc/create_cohorts.html | 46 +- inst/doc/drug_utilisation.html | 741 ++++++++++++++++++++--------------------- 6 files changed, 410 insertions(+), 402 deletions(-)
More information about DrugUtilisation at CRAN
Permanent link
Title: A Basic Set of Functions for Compositional Data Analysis
Description: A minimum set of functions to perform compositional data analysis
using the log-ratio approach introduced by John Aitchison (1982). Main functions
have been implemented in c++ for better performance.
Author: Marc Comas-Cufi [aut, cre]
Maintainer: Marc Comas-Cufi <mcomas@imae.udg.edu>
Diff between coda.base versions 1.0.0 dated 2025-05-02 and 1.0.3 dated 2025-07-02
DESCRIPTION | 10 ++--- MD5 | 36 ++++++++++---------- R/RcppExports.R | 4 +- R/basis.R | 69 ++++++++++++++++++++++++++++----------- R/data.R | 24 +++++++++++++ R/pb_basis_constrained.R | 14 +++---- README.md | 6 +-- data/kilauea_iki.RData |only inst/doc/coordinates.Rmd | 2 - inst/doc/coordinates.html | 18 +++++----- inst/doc/features.html | 4 +- inst/doc/principal_balances.html | 4 +- man/kilauea_iki.Rd |only man/pb_basis.Rd | 11 +++++- src/Makevars | 1 src/Makevars.win | 1 src/RcppExports.cpp | 9 ++--- src/coda.cpp | 1 src/principal_balances.cpp | 10 ++--- vignettes/coordinates.Rmd | 2 - 20 files changed, 149 insertions(+), 77 deletions(-)
Title: Semi-Automated Marketing Mix Modeling (MMM) from Meta Marketing
Science
Description: Semi-Automated Marketing Mix Modeling (MMM) aiming to reduce human bias by means of ridge regression and evolutionary algorithms, enables actionable decision making providing a budget allocation and diminishing returns curves and allows ground-truth calibration to account for causation.
Author: Gufeng Zhou [aut],
Bernardo Lares [cre, aut],
Igor Skokan [aut],
Leonel Sentana [aut],
Meta Platforms, Inc. [cph, fnd]
Maintainer: Bernardo Lares <laresbernardo@gmail.com>
Diff between Robyn versions 3.11.1 dated 2024-06-27 and 3.12.1 dated 2025-07-02
Robyn-3.11.1/Robyn/man/fit_spend_exposure.Rd |only Robyn-3.11.1/Robyn/man/mic_men.Rd |only Robyn-3.12.1/Robyn/DESCRIPTION | 20 Robyn-3.12.1/Robyn/MD5 | 71 +- Robyn-3.12.1/Robyn/NAMESPACE | 8 Robyn-3.12.1/Robyn/R/allocator.R | 267 ++++------ Robyn-3.12.1/Robyn/R/auxiliary.R | 50 ++ Robyn-3.12.1/Robyn/R/calibration.R | 538 +++++++++++++++++++++- Robyn-3.12.1/Robyn/R/checks.R | 277 ++++------- Robyn-3.12.1/Robyn/R/clusters.R | 3 Robyn-3.12.1/Robyn/R/convergence.R | 2 Robyn-3.12.1/Robyn/R/data.R | 42 + Robyn-3.12.1/Robyn/R/imports.R | 5 Robyn-3.12.1/Robyn/R/inputs.R | 443 +++++++----------- Robyn-3.12.1/Robyn/R/json.R | 40 + Robyn-3.12.1/Robyn/R/model.R | 165 ++++-- Robyn-3.12.1/Robyn/R/outputs.R | 4 Robyn-3.12.1/Robyn/R/pareto.R | 538 ++++++++++------------ Robyn-3.12.1/Robyn/R/plots.R | 163 +++++- Robyn-3.12.1/Robyn/R/refresh.R | 9 Robyn-3.12.1/Robyn/R/response.R | 351 +++++++------- Robyn-3.12.1/Robyn/R/transformation.R | 150 +++--- Robyn-3.12.1/Robyn/data/df_curve_reach_freq.RData |only Robyn-3.12.1/Robyn/man/Robyn.Rd | 2 Robyn-3.12.1/Robyn/man/adstocks.Rd | 12 Robyn-3.12.1/Robyn/man/df_curve_reach_freq.Rd |only Robyn-3.12.1/Robyn/man/dt_prophet_holidays.Rd | 1 Robyn-3.12.1/Robyn/man/dt_simulated_weekly.Rd | 1 Robyn-3.12.1/Robyn/man/hyper_names.Rd | 51 -- Robyn-3.12.1/Robyn/man/prophet_decomp.Rd | 9 Robyn-3.12.1/Robyn/man/robyn_allocator.Rd | 6 Robyn-3.12.1/Robyn/man/robyn_calibrate.Rd |only Robyn-3.12.1/Robyn/man/robyn_mmm.Rd | 9 Robyn-3.12.1/Robyn/man/robyn_outputs.Rd | 24 Robyn-3.12.1/Robyn/man/robyn_response.Rd | 8 Robyn-3.12.1/Robyn/man/robyn_run.Rd | 4 Robyn-3.12.1/Robyn/man/robyn_train.Rd | 4 Robyn-3.12.1/Robyn/man/saturation_hill.Rd | 4 Robyn-3.12.1/Robyn/man/set_default_hyppar.Rd |only Robyn-3.12.1/Robyn/man/transformations.Rd |only 40 files changed, 1950 insertions(+), 1331 deletions(-)
Title: Missing Outcome Data in Health Economic Evaluation
Description: Contains a suite of functions for health economic evaluations with missing outcome data.
The package can fit different types of statistical models under a fully Bayesian approach using the software 'JAGS' (which should be installed locally and which is loaded in 'missingHE' via the 'R' package 'R2jags').
Three classes of models can be fitted under a variety of missing data assumptions: selection models, pattern mixture models and hurdle models.
In addition to model fitting, 'missingHE' provides a set of specialised functions to assess model convergence and fit, and to summarise the statistical and economic results using different types of measures and graphs.
The methods implemented are described in Mason (2018) <doi:10.1002/hec.3793>, Molenberghs (2000) <doi:10.1007/978-1-4419-0300-6_18> and Gabrio (2019) <doi:10.1002/sim.8045>.
Author: Andrea Gabrio [aut, cre]
Maintainer: Andrea Gabrio <a.gabrio@maastrichtuniversity.nl>
Diff between missingHE versions 1.5.0 dated 2023-03-21 and 1.5.1 dated 2025-07-02
missingHE-1.5.0/missingHE/R/data_read_selection_long.R |only missingHE-1.5.0/missingHE/R/menss-data.R |only missingHE-1.5.0/missingHE/R/pbs-data.R |only missingHE-1.5.0/missingHE/R/prior_selection_long.R |only missingHE-1.5.0/missingHE/R/run_selection_long.R |only missingHE-1.5.0/missingHE/R/selection_long.R |only missingHE-1.5.0/missingHE/R/write_selection_long.R |only missingHE-1.5.0/missingHE/data/PBS.RData |only missingHE-1.5.0/missingHE/inst/doc/Longitudinal_models_in_missingHE.R |only missingHE-1.5.0/missingHE/inst/doc/Longitudinal_models_in_missingHE.Rmd |only missingHE-1.5.0/missingHE/inst/doc/Longitudinal_models_in_missingHE.html |only missingHE-1.5.0/missingHE/man/PBS.Rd |only missingHE-1.5.0/missingHE/man/data_read_selection_long.Rd |only missingHE-1.5.0/missingHE/man/prior_selection_long.Rd |only missingHE-1.5.0/missingHE/man/run_selection_long.Rd |only missingHE-1.5.0/missingHE/man/selection_long.Rd |only missingHE-1.5.0/missingHE/man/write_selection_long.Rd |only missingHE-1.5.0/missingHE/vignettes/Longitudinal_models_in_missingHE.Rmd |only missingHE-1.5.1/missingHE/DESCRIPTION | 14 missingHE-1.5.1/missingHE/MD5 | 99 - missingHE-1.5.1/missingHE/NAMESPACE | 26 missingHE-1.5.1/missingHE/R/coef.missingHE.R | 712 -------- missingHE-1.5.1/missingHE/R/data.R |only missingHE-1.5.1/missingHE/R/diagnostic.R | 358 ---- missingHE-1.5.1/missingHE/R/hurdle.R | 12 missingHE-1.5.1/missingHE/R/pattern.R | 8 missingHE-1.5.1/missingHE/R/pic.R | 155 - missingHE-1.5.1/missingHE/R/plot.missingHE.R | 512 ------ missingHE-1.5.1/missingHE/R/ppc.R | 846 +--------- missingHE-1.5.1/missingHE/R/print.missingHE.R | 25 missingHE-1.5.1/missingHE/R/selection.R | 11 missingHE-1.5.1/missingHE/R/summary.missingHE.R | 27 missingHE-1.5.1/missingHE/R/write_hurdle.R | 8 missingHE-1.5.1/missingHE/R/write_pattern.R | 8 missingHE-1.5.1/missingHE/R/write_selection.R | 8 missingHE-1.5.1/missingHE/README.md | 2 missingHE-1.5.1/missingHE/build/vignette.rds |binary missingHE-1.5.1/missingHE/inst/doc/Fitting_MNAR_models_in_missingHE.R | 38 missingHE-1.5.1/missingHE/inst/doc/Fitting_MNAR_models_in_missingHE.Rmd | 2 missingHE-1.5.1/missingHE/inst/doc/Fitting_MNAR_models_in_missingHE.html | 44 missingHE-1.5.1/missingHE/inst/doc/Introduction_to_missingHE.R | 22 missingHE-1.5.1/missingHE/inst/doc/Introduction_to_missingHE.Rmd | 2 missingHE-1.5.1/missingHE/inst/doc/Introduction_to_missingHE.html | 152 - missingHE-1.5.1/missingHE/inst/doc/Model_customisation_in_missingHE.R | 28 missingHE-1.5.1/missingHE/inst/doc/Model_customisation_in_missingHE.Rmd | 6 missingHE-1.5.1/missingHE/inst/doc/Model_customisation_in_missingHE.html | 96 - missingHE-1.5.1/missingHE/man/MenSS.Rd | 94 - missingHE-1.5.1/missingHE/man/coef.missingHE.Rd | 12 missingHE-1.5.1/missingHE/man/diagnostic.Rd | 43 missingHE-1.5.1/missingHE/man/hurdle.Rd | 5 missingHE-1.5.1/missingHE/man/pattern.Rd | 1 missingHE-1.5.1/missingHE/man/pic.Rd | 22 missingHE-1.5.1/missingHE/man/plot.missingHE.Rd | 16 missingHE-1.5.1/missingHE/man/ppc.Rd | 22 missingHE-1.5.1/missingHE/man/print.missingHE.Rd | 4 missingHE-1.5.1/missingHE/man/selection.Rd | 3 missingHE-1.5.1/missingHE/man/summary.missingHE.Rd | 9 missingHE-1.5.1/missingHE/vignettes/Fitting_MNAR_models_in_missingHE.Rmd | 2 missingHE-1.5.1/missingHE/vignettes/Introduction_to_missingHE.Rmd | 2 missingHE-1.5.1/missingHE/vignettes/Model_customisation_in_missingHE.Rmd | 6 60 files changed, 587 insertions(+), 2875 deletions(-)
Title: Bayesian Sparse Estimation of a Covariance Matrix
Description: Bayesian estimations of a covariance matrix for multivariate
normal data. Assumes that the covariance matrix is sparse or band
matrix and positive-definite. Methods implemented include the beta-mixture
shrinkage prior (Lee et al. (2022) <doi:10.1016/j.jmva.2022.105067>),
screened beta-mixture prior (Lee et al. (2024) <doi:10.1214/24-BA1495>),
and post-processed posteriors for banded and sparse covariances
(Lee et al. (2023) <doi:10.1214/22-BA1333>; Lee and Lee (2023)
<doi:10.1016/j.jeconom.2023.105475>). This software has been developed using
funding supported by Basic Science Research Program through the National
Research Foundation of Korea ('NRF') funded by the Ministry of Education
('RS-2023-00211979', 'NRF-2022R1A5A7033499', 'NRF-2020R1A4A1018207'
and 'NRF-2020R1C1C1A01013338').
Author: Kwangmin Lee [aut],
Kyeongwon Lee [aut, cre],
Kyoungjae Lee [aut],
Seongil Jo [aut],
Jaeyong Lee [ctb]
Maintainer: Kyeongwon Lee <kwlee1718@gmail.com>
Diff between bspcov versions 1.0.1 dated 2024-11-13 and 1.0.2 dated 2025-07-02
bspcov-1.0.1/bspcov/R/data.SP500_idioerr.R |only bspcov-1.0.1/bspcov/data/SP500_idioerr.rda |only bspcov-1.0.1/bspcov/man/SP500_idioerr.Rd |only bspcov-1.0.2/bspcov/DESCRIPTION | 71 ++++++++++++++++------------- bspcov-1.0.2/bspcov/MD5 | 20 ++++---- bspcov-1.0.2/bspcov/NAMESPACE | 8 +++ bspcov-1.0.2/bspcov/R/data.SP500.R |only bspcov-1.0.2/bspcov/R/proc_SP500.R |only bspcov-1.0.2/bspcov/R/proc_colon.R |only bspcov-1.0.2/bspcov/README.md | 10 ++-- bspcov-1.0.2/bspcov/data/SP500.rda |only bspcov-1.0.2/bspcov/data/colon.rda |binary bspcov-1.0.2/bspcov/data/tissues.rda |binary bspcov-1.0.2/bspcov/man/SP500.Rd |only bspcov-1.0.2/bspcov/man/proc_SP500.Rd |only bspcov-1.0.2/bspcov/man/proc_colon.Rd |only 16 files changed, 66 insertions(+), 43 deletions(-)
Title: Tidy Plots for Scientific Papers
Description: The goal of 'tidyplots' is to streamline the creation of publication-ready plots for scientific papers. It allows to gradually add, remove and adjust plot components using a consistent and intuitive syntax.
Author: Jan Broder Engler [aut, cre, cph]
Maintainer: Jan Broder Engler <broder.engler@gmail.com>
Diff between tidyplots versions 0.2.2 dated 2025-03-07 and 0.3.1 dated 2025-07-02
tidyplots-0.2.2/tidyplots/R/labels.R |only tidyplots-0.2.2/tidyplots/man/format_number.Rd |only tidyplots-0.2.2/tidyplots/man/rename_x_axis_labels.Rd |only tidyplots-0.2.2/tidyplots/man/reorder_x_axis_labels.Rd |only tidyplots-0.2.2/tidyplots/man/reverse_x_axis_labels.Rd |only tidyplots-0.2.2/tidyplots/man/sort_x_axis_labels.Rd |only tidyplots-0.3.1/tidyplots/DESCRIPTION | 10 tidyplots-0.3.1/tidyplots/MD5 | 207 ++++++---- tidyplots-0.3.1/tidyplots/NAMESPACE | 15 tidyplots-0.3.1/tidyplots/NEWS.md | 26 + tidyplots-0.3.1/tidyplots/R/add-annotation.R | 39 + tidyplots-0.3.1/tidyplots/R/add-general.R | 11 tidyplots-0.3.1/tidyplots/R/add-misc.R | 36 + tidyplots-0.3.1/tidyplots/R/add-points.R | 85 ++-- tidyplots-0.3.1/tidyplots/R/add-proportional.R | 10 tidyplots-0.3.1/tidyplots/R/add-stats.R | 109 ++++- tidyplots-0.3.1/tidyplots/R/adjust.R | 44 +- tidyplots-0.3.1/tidyplots/R/data.R | 10 tidyplots-0.3.1/tidyplots/R/data_levels.R |only tidyplots-0.3.1/tidyplots/R/helpers.R | 26 - tidyplots-0.3.1/tidyplots/R/plot.R | 124 +++++ tidyplots-0.3.1/tidyplots/R/remove.R | 6 tidyplots-0.3.1/tidyplots/README.md | 8 tidyplots-0.3.1/tidyplots/build/vignette.rds |binary tidyplots-0.3.1/tidyplots/data/pca.rda |only tidyplots-0.3.1/tidyplots/inst/CITATION | 8 tidyplots-0.3.1/tidyplots/inst/doc/tidyplots.R | 1 tidyplots-0.3.1/tidyplots/inst/doc/tidyplots.Rmd | 1 tidyplots-0.3.1/tidyplots/inst/doc/tidyplots.html | 3 tidyplots-0.3.1/tidyplots/man/add_annotation_text.Rd | 13 tidyplots-0.3.1/tidyplots/man/add_barstack_absolute.Rd | 2 tidyplots-0.3.1/tidyplots/man/add_count_bar.Rd | 2 tidyplots-0.3.1/tidyplots/man/add_data_labels.Rd | 23 + tidyplots-0.3.1/tidyplots/man/add_ellipse.Rd |only tidyplots-0.3.1/tidyplots/man/add_mean_bar.Rd | 2 tidyplots-0.3.1/tidyplots/man/add_median_bar.Rd | 2 tidyplots-0.3.1/tidyplots/man/add_pie.Rd | 10 tidyplots-0.3.1/tidyplots/man/add_sem_errorbar.Rd | 2 tidyplots-0.3.1/tidyplots/man/add_sum_bar.Rd | 2 tidyplots-0.3.1/tidyplots/man/add_test_pvalue.Rd | 75 +++ tidyplots-0.3.1/tidyplots/man/adjust_font.Rd | 9 tidyplots-0.3.1/tidyplots/man/adjust_legend_title.Rd | 9 tidyplots-0.3.1/tidyplots/man/adjust_size.Rd | 15 tidyplots-0.3.1/tidyplots/man/adjust_title.Rd | 9 tidyplots-0.3.1/tidyplots/man/common_arguments.Rd | 12 tidyplots-0.3.1/tidyplots/man/figures/README-unnamed-chunk-10-1.png |binary tidyplots-0.3.1/tidyplots/man/figures/README-unnamed-chunk-11-1.png |binary tidyplots-0.3.1/tidyplots/man/figures/README-unnamed-chunk-4-1.png |binary tidyplots-0.3.1/tidyplots/man/format_p_value.Rd |only tidyplots-0.3.1/tidyplots/man/gene_expression.Rd | 2 tidyplots-0.3.1/tidyplots/man/pca.Rd |only tidyplots-0.3.1/tidyplots/man/rename_x_axis_levels.Rd |only tidyplots-0.3.1/tidyplots/man/reorder_x_axis_levels.Rd |only tidyplots-0.3.1/tidyplots/man/reverse_x_axis_levels.Rd |only tidyplots-0.3.1/tidyplots/man/save_plot.Rd | 2 tidyplots-0.3.1/tidyplots/man/sort_x_axis_levels.Rd |only tidyplots-0.3.1/tidyplots/man/split_plot.Rd | 21 - tidyplots-0.3.1/tidyplots/man/tidyplot.Rd | 37 + tidyplots-0.3.1/tidyplots/man/tidyplots_options.Rd |only tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-annotation/label-alignment.svg |only tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-annotation/label-repel-alignment.svg |only tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-misc/histogram-custom-color.svg |only tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-misc/histogram.svg |only tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-proportional/absolute-areastack-replace-na-x.svg | 10 tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-proportional/absolute-areastack-replace-na-xy.svg | 10 tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-proportional/absolute-areastack-replace-na-y.svg | 10 tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-proportional/absolute-areastack-replace-na-yx.svg | 10 tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-proportional/donut-count-1.svg | 10 tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-proportional/donut-count-2.svg | 10 tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-proportional/donut-count-3.svg | 10 tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-proportional/donut-count-4.svg | 10 tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-proportional/donut-sum.svg | 10 tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-proportional/pie-count-1.svg | 10 tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-proportional/pie-count-2.svg | 10 tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-proportional/pie-count-3.svg | 10 tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-proportional/pie-count-4.svg | 10 tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-proportional/pie-sum.svg | 10 tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-proportional/relative-areastack-replace-na-x.svg | 20 tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-proportional/relative-areastack-replace-na-xy.svg | 20 tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-proportional/relative-areastack-replace-na-y.svg | 20 tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-proportional/relative-areastack-replace-na-yx.svg | 20 tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-stats/add-grouped-stats-asterisks-bonferroni.svg | 187 ++++----- tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-stats/add-grouped-stats-pvalue-bonferroni.svg | 187 ++++----- tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-stats/add-grouped-stats-pvalue.svg | 187 ++++----- tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-stats/add-paired-stats-asterisks-control.svg |only tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-stats/add-paired-stats-asterisks.svg |only tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-stats/add-paired-stats-pvalue-control.svg |only tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-stats/add-paired-stats-pvalue.svg |only tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-stats/add-stats-asterisks-comparisons.svg |only tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-stats/add-stats-asterisks-ref-group-bonferroni.svg | 179 ++++---- tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-stats/add-stats-pvalue-comparisons.svg |only tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-stats/add-stats-pvalue-no-ref-group.svg |only tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-stats/add-stats-pvalue-ref-group-bonferroni.svg | 183 ++++---- tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/add-stats/add-stats-pvalue-ref-group.svg | 183 ++++---- tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/adjust/plot-area-size-height.svg |only tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/adjust/plot-area-size-nothing.svg |only tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/adjust/plot-area-size-tidyplot-height-adjust-width-inch.svg |only tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/adjust/plot-area-size-tidyplot-height-adjust-width.svg |only tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/adjust/plot-area-size-tidyplot-width-adjust-height.svg |only tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/adjust/plot-area-size-width-and-height-na-sequentially.svg |only tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/adjust/plot-area-size-width-and-height-sequentially.svg |only tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/adjust/plot-area-size-width-na-and-height-sequentially.svg |only tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/levels |only tidyplots-0.3.1/tidyplots/tests/testthat/_snaps/plot |only tidyplots-0.3.1/tidyplots/tests/testthat/test-add-annotation.R | 14 tidyplots-0.3.1/tidyplots/tests/testthat/test-add-misc.R | 13 tidyplots-0.3.1/tidyplots/tests/testthat/test-add-stats.R | 52 ++ tidyplots-0.3.1/tidyplots/tests/testthat/test-adjust.R | 51 ++ tidyplots-0.3.1/tidyplots/tests/testthat/test-levels.R |only tidyplots-0.3.1/tidyplots/tests/testthat/test-plot.R |only tidyplots-0.3.1/tidyplots/vignettes/tidyplots.Rmd | 1 111 files changed, 1623 insertions(+), 862 deletions(-)
Title: Datasets from the Book "Methods of Multivariate Analysis (3rd)"
Description: Provides the datasets in the book "Methods of Multivariate Analysis (3rd)", such as Table 6.27 Blood Pressure Data, for statistical analysis,especially MANOVA. The dataset names correspond to their numbering in the third edition of the book, such as table6.27. Based on the book by Rencher and Christensen (2012, ISBN:9780470178966).
Author: Atefeh Rashidi Pour [aut, cre],
Fatemeh Naderi [aut]
Maintainer: Atefeh Rashidi Pour <rashidiatefeh98@gmail.com>
Diff between rencher versions 0.1.3 dated 2025-05-26 and 0.1.4 dated 2025-07-02
rencher-0.1.3/rencher/man/figures/README-pressure-1.png |only rencher-0.1.4/rencher/DESCRIPTION | 8 - rencher-0.1.4/rencher/MD5 | 8 - rencher-0.1.4/rencher/NEWS.md |only rencher-0.1.4/rencher/README.md | 104 ++++------------ rencher-0.1.4/rencher/man/figures/hex_rencher.png |binary 6 files changed, 41 insertions(+), 79 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of
use. Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions. Various
matrix decompositions are provided through optional integration with
LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the
header files from the templated 'Armadillo' library. Thus users do
not need to install 'Armadillo' itself in order to use
'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed
under Apache License 2; previous releases were under licensed as MPL
2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed
under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
Doug Bates [aut] ,
Binxiang Ni [aut],
Conrad Sanderson [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 14.4.3-1 dated 2025-05-21 and 14.6.0-1 dated 2025-07-02
ChangeLog | 35 + DESCRIPTION | 8 MD5 | 152 ++--- build/partial.rdb |binary build/vignette.rds |binary configure | 18 configure.ac | 2 inst/NEWS.Rd | 20 inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/armadillo | 6 inst/include/armadillo_bits/BaseCube_meat.hpp | 4 inst/include/armadillo_bits/Base_meat.hpp | 8 inst/include/armadillo_bits/Cube_meat.hpp | 4 inst/include/armadillo_bits/MapMat_meat.hpp | 7 inst/include/armadillo_bits/Mat_meat.hpp | 4 inst/include/armadillo_bits/SpBase_meat.hpp | 4 inst/include/armadillo_bits/SpMat_meat.hpp | 7 inst/include/armadillo_bits/arma_cmath.hpp | 42 + inst/include/armadillo_bits/arma_forward.hpp | 2 inst/include/armadillo_bits/arma_ostream_meat.hpp | 4 inst/include/armadillo_bits/arma_version.hpp | 6 inst/include/armadillo_bits/arrayops_meat.hpp | 6 inst/include/armadillo_bits/auxlib_bones.hpp | 9 inst/include/armadillo_bits/auxlib_meat.hpp | 78 ++ inst/include/armadillo_bits/compiler_setup.hpp | 2 inst/include/armadillo_bits/def_lapack.hpp | 22 inst/include/armadillo_bits/diagview_meat.hpp | 12 inst/include/armadillo_bits/field_meat.hpp | 7 inst/include/armadillo_bits/fn_accu.hpp | 353 ++++++++++++ inst/include/armadillo_bits/fn_balance.hpp |only inst/include/armadillo_bits/fn_elem.hpp | 39 + inst/include/armadillo_bits/fn_find.hpp | 82 ++ inst/include/armadillo_bits/fn_misc.hpp | 2 inst/include/armadillo_bits/fn_omit.hpp |only inst/include/armadillo_bits/fn_powext.hpp | 4 inst/include/armadillo_bits/fn_randperm.hpp | 11 inst/include/armadillo_bits/fn_shift.hpp | 3 inst/include/armadillo_bits/fn_sort_index.hpp | 10 inst/include/armadillo_bits/fn_sylvester.hpp | 27 inst/include/armadillo_bits/glue_mvnrnd_meat.hpp | 4 inst/include/armadillo_bits/gmm_diag_meat.hpp | 6 inst/include/armadillo_bits/gmm_full_meat.hpp | 4 inst/include/armadillo_bits/mtSpOp_bones.hpp | 4 inst/include/armadillo_bits/mtSpOp_meat.hpp | 12 inst/include/armadillo_bits/op_expmat_meat.hpp | 2 inst/include/armadillo_bits/op_find_bones.hpp | 11 inst/include/armadillo_bits/op_find_meat.hpp | 52 + inst/include/armadillo_bits/op_hist_meat.hpp | 4 inst/include/armadillo_bits/op_mean_bones.hpp | 57 -- inst/include/armadillo_bits/op_mean_meat.hpp | 503 ++++-------------- inst/include/armadillo_bits/op_median_meat.hpp | 2 inst/include/armadillo_bits/op_misc_bones.hpp | 12 inst/include/armadillo_bits/op_misc_meat.hpp | 34 + inst/include/armadillo_bits/op_nonzeros_meat.hpp | 12 inst/include/armadillo_bits/op_norm2est_meat.hpp | 8 inst/include/armadillo_bits/op_omit_bones.hpp |only inst/include/armadillo_bits/op_omit_meat.hpp |only inst/include/armadillo_bits/op_shuffle_meat.hpp | 11 inst/include/armadillo_bits/op_sort_index_bones.hpp | 43 - inst/include/armadillo_bits/op_sort_index_meat.hpp | 121 ---- inst/include/armadillo_bits/op_sort_meat.hpp | 47 + inst/include/armadillo_bits/op_sp_nonzeros_meat.hpp | 33 - inst/include/armadillo_bits/op_stddev_bones.hpp | 10 inst/include/armadillo_bits/op_stddev_meat.hpp | 80 -- inst/include/armadillo_bits/op_var_bones.hpp | 12 inst/include/armadillo_bits/op_var_meat.hpp | 88 --- inst/include/armadillo_bits/podarray_meat.hpp | 12 inst/include/armadillo_bits/running_stat_meat.hpp | 8 inst/include/armadillo_bits/running_stat_vec_meat.hpp | 4 inst/include/armadillo_bits/spop_misc_bones.hpp | 11 inst/include/armadillo_bits/spop_misc_meat.hpp | 17 inst/include/armadillo_bits/spop_omit_bones.hpp |only inst/include/armadillo_bits/spop_omit_meat.hpp |only inst/include/armadillo_bits/subview_elem1_meat.hpp | 54 - inst/include/armadillo_bits/subview_elem2_bones.hpp | 2 inst/include/armadillo_bits/subview_elem2_meat.hpp | 234 ++++++++ inst/include/armadillo_bits/sym_helper.hpp | 16 inst/include/armadillo_bits/translate_lapack.hpp | 22 man/fastLm.Rd | 13 80 files changed, 1568 insertions(+), 997 deletions(-)
Title: Retrieve and Analyze Clinical Trials Data from Public Registers
Description: A system for querying, retrieving and analyzing
protocol- and results-related information on clinical trials from
four public registers, the 'European Union Clinical Trials Register'
('EUCTR', <https://www.clinicaltrialsregister.eu/>),
'ClinicalTrials.gov' (<https://clinicaltrials.gov/> and also
translating queries the retired classic interface), the
'ISRCTN' (<http://www.isrctn.com/>) and the
'European Union Clinical Trials Information System'
('CTIS', <https://euclinicaltrials.eu/>).
Trial information is downloaded, converted and stored in a database
('PostgreSQL', 'SQLite', 'DuckDB' or 'MongoDB'; via package 'nodbi').
Protocols, statistical analysis plans, informed consent sheets and other
documents in registers associated with trials can also be downloaded.
Other functions implement trial concepts canonically across registers,
identify deduplicated records, easily find and extract variables
(fields) of interest even from complex nested data as used by the
re [...truncated...]
Author: Ralf Herold [aut, cre] ,
Marek Kubica [cph] ,
Ivan Bozhanov [cph]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 1.22.3 dated 2025-06-08 and 1.23.0 dated 2025-07-02
DESCRIPTION | 15 MD5 | 140 +-- NAMESPACE | 33 NEWS.md | 13 R/ctrFindActiveSubstanceSynonyms.R | 44 - R/ctrGetQueryUrl.R | 11 R/ctrLoadQueryIntoDb.R | 20 R/ctrLoadQueryIntoDbCtgov2.R | 66 - R/ctrLoadQueryIntoDbCtis.R | 171 ++-- R/ctrLoadQueryIntoDbEuctr.R | 420 ++++++----- R/ctrLoadQueryIntoDbIsrctn.R | 151 ++-- R/ctrOpenSearchPagesInBrowser.R | 2 R/ctrRerunQuery.R | 185 ++--- R/ctrShowOneTrial.R | 2 R/ctrdata-package.R | 24 R/ctrdata-trial-concepts.R | 2 R/dbFindIdsUniqueTrials.R | 16 R/dbGetFieldsIntoDf.R | 12 R/dbQueryHistory.R | 3 R/dfName2Value.R | 6 R/f_likelyPlatformTrial.R | 6 R/f_numSites.R | 24 R/f_numTestArmsSubstances.R | 23 R/f_primaryEndpointDescription.R | 6 R/f_primaryEndpointResults.R | 2 R/f_sampleSize.R | 11 R/f_sponsorType.R | 84 +- R/f_statusRecruitment.R | 4 R/f_trialObjectives.R | 6 R/f_trialPhase.R | 2 R/f_trialPopulation.R | 1 R/f_trialTitle.R | 5 R/util_fields.R | 22 R/util_functions.R | 342 ++++++--- R/zzz.R | 11 README.md | 303 +++++--- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 5 inst/doc/ctrdata_install.Rmd | 4 inst/doc/ctrdata_install.html | 6 inst/doc/ctrdata_retrieve.R | 195 +++-- inst/doc/ctrdata_retrieve.Rmd | 216 +++-- inst/doc/ctrdata_retrieve.html | 470 ++++++------ inst/doc/ctrdata_summarise.R | 215 +++-- inst/doc/ctrdata_summarise.Rmd | 227 ++++-- inst/doc/ctrdata_summarise.html | 701 ++++++++++--------- inst/htmlwidgets/lib/jstree/LICENSE-MIT | 44 - inst/tinytest/ctrdata_ctis.R | 13 inst/tinytest/ctrdata_euctr.R | 1 inst/tinytest/ctrdata_isrctn.R | 30 inst/tinytest/test_ctrdata_function_params.R | 4 inst/tinytest/test_ctrdata_function_trial-concepts.R | 2 inst/tinytest/test_ctrdata_function_various.R | 8 man/ctrdata-trial-concepts.Rd | 2 man/ctrdata.Rd | 24 man/f.numTestArmsSubstances.Rd | 8 man/f.primaryEndpointDescription.Rd | 6 man/f.primaryEndpointResults.Rd | 2 man/f.sampleSize.Rd | 3 man/f.sponsorType.Rd | 11 man/f.trialTitle.Rd | 2 man/figures/README-ctrdata_across_registers.png |binary man/figures/README-ctrdata_results_neuroblastoma.png |binary vignettes/boxpep.png |binary vignettes/ctrdata_install.Rmd | 4 vignettes/ctrdata_retrieve.Rmd | 216 +++-- vignettes/ctrdata_summarise.Rmd | 227 ++++-- vignettes/nb1.png |binary vignettes/nbtrials.png |binary vignettes/samplesizechanges.png |binary 71 files changed, 2827 insertions(+), 2007 deletions(-)
Title: Streamline Population Genomic and Genetic Analyses
Description: Estimate commonly used population genomic statistics and generate publication quality figures. 'PopGenHelpR' uses vcf, 'geno' (012), and csv files to generate output.
Author: Keaka Farleigh [aut, cph, cre] ,
Mason Murphy [aut, cph, ctb] ,
Christopher Blair [aut, cph, ctb] ,
Tereza Jezkova [aut, cph, ctb]
Maintainer: Keaka Farleigh <keakafarleigh@gmail.com>
Diff between PopGenHelpR versions 1.3.2 dated 2024-08-02 and 1.4.0 dated 2025-07-02
PopGenHelpR-1.3.2/PopGenHelpR/R/Pairwise_heatmap.R |only PopGenHelpR-1.3.2/PopGenHelpR/vignettes/articles |only PopGenHelpR-1.4.0/PopGenHelpR/DESCRIPTION | 26 PopGenHelpR-1.4.0/PopGenHelpR/MD5 | 136 - PopGenHelpR-1.4.0/PopGenHelpR/NEWS.md | 28 PopGenHelpR-1.4.0/PopGenHelpR/R/Ancestry_barchart.R | 339 +-- PopGenHelpR-1.4.0/PopGenHelpR/R/Differentiation.R | 1072 +++++----- PopGenHelpR-1.4.0/PopGenHelpR/R/Heterozygosity.R | 1049 +++++---- PopGenHelpR-1.4.0/PopGenHelpR/R/Network_map.R | 806 +++++-- PopGenHelpR-1.4.0/PopGenHelpR/R/Pariwise_heatmap.R |only PopGenHelpR-1.4.0/PopGenHelpR/R/Piechart_map.R | 890 +++++--- PopGenHelpR-1.4.0/PopGenHelpR/R/Plot_coordinates.R | 582 ++++- PopGenHelpR-1.4.0/PopGenHelpR/R/Point_map.R | 620 ++++- PopGenHelpR-1.4.0/PopGenHelpR/R/data.R | 236 +- PopGenHelpR-1.4.0/PopGenHelpR/README.md | 2 PopGenHelpR-1.4.0/PopGenHelpR/build/partial.rdb |binary PopGenHelpR-1.4.0/PopGenHelpR/build/vignette.rds |binary PopGenHelpR-1.4.0/PopGenHelpR/inst/doc/PopGenHelpR_vignette.R | 93 PopGenHelpR-1.4.0/PopGenHelpR/inst/doc/PopGenHelpR_vignette.Rmd | 495 ++-- PopGenHelpR-1.4.0/PopGenHelpR/inst/doc/PopGenHelpR_vignette.html | 134 - PopGenHelpR-1.4.0/PopGenHelpR/inst/extdata |only PopGenHelpR-1.4.0/PopGenHelpR/man/Ancestry_barchart.Rd | 9 PopGenHelpR-1.4.0/PopGenHelpR/man/Differentiation.Rd | 2 PopGenHelpR-1.4.0/PopGenHelpR/man/Heterozygosity.Rd | 2 PopGenHelpR-1.4.0/PopGenHelpR/man/Network_map.Rd | 55 PopGenHelpR-1.4.0/PopGenHelpR/man/Pairwise_heatmap.Rd | 11 PopGenHelpR-1.4.0/PopGenHelpR/man/Piechart_map.Rd | 35 PopGenHelpR-1.4.0/PopGenHelpR/man/Plot_coordinates.Rd | 63 PopGenHelpR-1.4.0/PopGenHelpR/man/Point_map.Rd | 53 PopGenHelpR-1.4.0/PopGenHelpR/vignettes/PopGenHelpR_vignette.Rmd | 495 ++-- PopGenHelpR-1.4.0/PopGenHelpR/vignettes/img/MapLayer_Arguments.jpg |only 31 files changed, 4695 insertions(+), 2538 deletions(-)
Title: Simulate Fractal Trees and Forests
Description: Create and visualize fractal trees and fractal forests, based on the Lindenmayer system (L-system). For more details see Lindenmayer (1968a) <doi:10.1016/0022-5193(68)90079-9> and Lindenmayer (1968b) <doi:10.1016/0022-5193(68)90080-5>.
Author: Sergio Costa [aut, cre, cph] ,
Gilmara Machado [aut, cph]
Maintainer: Sergio Costa <sergio.vscf@gmail.com>
Diff between fractalforest versions 1.0.0 dated 2025-06-19 and 1.0.1 dated 2025-07-02
DESCRIPTION | 8 MD5 | 16 - NEWS.md | 9 - inst/WORDLIST | 4 inst/doc/customizing-fractal-trees.R | 200 ++++++++++++++++++++++ inst/doc/customizing-fractal-trees.Rmd | 283 +++++++++++++++++++++++++++++++- inst/doc/customizing-fractal-trees.html | 257 ++++++++++++++++++++++++++++- inst/doc/intro-to-fractal-forest.html | 6 vignettes/customizing-fractal-trees.Rmd | 283 +++++++++++++++++++++++++++++++- 9 files changed, 1046 insertions(+), 20 deletions(-)
Title: Package Required POI Jars for the xlsx Package
Description: The xlsxjars package collects all the external jars
required for the xlxs package. This release corresponds to POI
3.13.
Author: Cole Arendt [aut, cre],
Adrian A. Dragulescu [aut],
The Apache Software Foundation [ctb, cph]
Maintainer: Cole Arendt <cole.arendt@outlook.com>
Diff between xlsxjars versions 0.6.1 dated 2014-08-22 and 0.9.0 dated 2025-07-02
xlsxjars-0.6.1/xlsxjars/NEWS |only xlsxjars-0.6.1/xlsxjars/inst/java/commons-codec-1.6.jar |only xlsxjars-0.6.1/xlsxjars/inst/java/dom4j-1.6.1.jar |only xlsxjars-0.6.1/xlsxjars/inst/java/poi-3.10.1-20140818.jar |only xlsxjars-0.6.1/xlsxjars/inst/java/poi-ooxml-3.10.1-20140818.jar |only xlsxjars-0.6.1/xlsxjars/inst/java/poi-ooxml-schemas-3.10.1-20140818.jar |only xlsxjars-0.9.0/xlsxjars/DESCRIPTION | 35 +++++----- xlsxjars-0.9.0/xlsxjars/MD5 | 20 +++-- xlsxjars-0.9.0/xlsxjars/NEWS.md |only xlsxjars-0.9.0/xlsxjars/inst/COPYRIGHTS | 9 -- xlsxjars-0.9.0/xlsxjars/inst/java/commons-codec-1.9.jar |only xlsxjars-0.9.0/xlsxjars/inst/java/poi-3.13-20150929.jar |only xlsxjars-0.9.0/xlsxjars/inst/java/poi-ooxml-3.13-20150929.jar |only xlsxjars-0.9.0/xlsxjars/inst/java/poi-ooxml-schemas-3.13-20150929.jar |only xlsxjars-0.9.0/xlsxjars/man/xlsxjars-package.Rd | 15 +--- xlsxjars-0.9.0/xlsxjars/tests |only 16 files changed, 36 insertions(+), 43 deletions(-)
Title: Identifying Important Areas from Animal Tracking Data
Description: Functions for preparing and analyzing animal tracking data,
with the intention of identifying areas which are potentially important at
the population level and therefore of conservation interest. Areas identified
using this package may be checked against global or regionally-defined criteria,
such as those set by the Key Biodiversity Area program. The method
published herein is described in full in Beal et al. 2021 <doi:10.1111/2041-210X.13713>.
Author: Martin Beal [aut, cre] ,
Steffen Oppel [aut] ,
Maria Dias [aut] ,
Mark Miller [ctb],
Phillip Taylor [ctb],
Virginia Morera-Pujol [ctb] ,
Elizabeth Pearmain [ctb] ,
Jonathan Handley [ctb] ,
Ben Lascelles [ctb]
Maintainer: Martin Beal <martinbeal88@gmail.com>
Diff between track2KBA versions 1.1.2 dated 2024-07-01 and 1.1.3 dated 2025-07-02
DESCRIPTION | 22 ++-- MD5 | 12 +- R/mapKDE.R | 166 +++++++++++++++--------------- R/mapSite.R | 214 +++++++++++++++++++-------------------- build/vignette.rds |binary inst/doc/track2kba_workflow.R | 186 ++++++++++++++++----------------- inst/doc/track2kba_workflow.html | 12 +- 7 files changed, 307 insertions(+), 305 deletions(-)
Title: Super Learner for Survival Prediction from Censored Data
Description: Several functions and S3 methods to construct a super learner in the presence of censored times-to-event and to evaluate its prognostic capacities.
Author: Yohann Foucher [aut, cre] ,
Camille Sabathe [aut]
Maintainer: Yohann Foucher <yohann.foucher@univ-poitiers.fr>
Diff between survivalSL versions 0.97.1 dated 2025-02-17 and 0.98 dated 2025-07-02
survivalSL-0.97.1/survivalSL/R/LIB_SNN.R |only survivalSL-0.97.1/survivalSL/R/plot.rocrisca.R |only survivalSL-0.97.1/survivalSL/R/roc.R |only survivalSL-0.97.1/survivalSL/R/tuneCOXaic.R |only survivalSL-0.97.1/survivalSL/R/tuneSNN.R |only survivalSL-0.97.1/survivalSL/man/LIB_SNN.Rd |only survivalSL-0.97.1/survivalSL/man/plot.rocrisca.Rd |only survivalSL-0.97.1/survivalSL/man/roc.Rd |only survivalSL-0.97.1/survivalSL/man/tuneCOXaic.Rd |only survivalSL-0.97.1/survivalSL/man/tuneSNN.Rd |only survivalSL-0.98/survivalSL/DESCRIPTION | 15 survivalSL-0.98/survivalSL/MD5 | 134 - survivalSL-0.98/survivalSL/NAMESPACE | 32 survivalSL-0.98/survivalSL/R/LIB_AFTgamma.R | 96 - survivalSL-0.98/survivalSL/R/LIB_AFTggamma.R | 99 - survivalSL-0.98/survivalSL/R/LIB_AFTllogis.R | 94 - survivalSL-0.98/survivalSL/R/LIB_AFTweibull.R | 95 - survivalSL-0.98/survivalSL/R/LIB_COXaic.R | 93 + survivalSL-0.98/survivalSL/R/LIB_COXall.R | 96 - survivalSL-0.98/survivalSL/R/LIB_COXen.R | 176 +- survivalSL-0.98/survivalSL/R/LIB_COXlasso.R | 179 +- survivalSL-0.98/survivalSL/R/LIB_COXridge.R | 166 -- survivalSL-0.98/survivalSL/R/LIB_PHexponential.R | 93 - survivalSL-0.98/survivalSL/R/LIB_PHgompertz.R | 96 - survivalSL-0.98/survivalSL/R/LIB_PHspline.R | 101 - survivalSL-0.98/survivalSL/R/LIB_PLANN.R | 126 + survivalSL-0.98/survivalSL/R/LIB_RSF.R | 118 + survivalSL-0.98/survivalSL/R/metrics.R | 549 ++++++- survivalSL-0.98/survivalSL/R/plot.libsl.R | 109 - survivalSL-0.98/survivalSL/R/plot.sltime.R | 136 + survivalSL-0.98/survivalSL/R/predict.libsl.R | 389 +++-- survivalSL-0.98/survivalSL/R/predict.sltime.R | 36 survivalSL-0.98/survivalSL/R/print.sltime.R | 5 survivalSL-0.98/survivalSL/R/summary.libsl.R | 198 ++ survivalSL-0.98/survivalSL/R/summary.sltime.R | 213 ++- survivalSL-0.98/survivalSL/R/survivalSL.R | 1376 +++++--------------- survivalSL-0.98/survivalSL/R/tuneCOXen.R | 157 +- survivalSL-0.98/survivalSL/R/tuneCOXlasso.R | 152 +- survivalSL-0.98/survivalSL/R/tuneCOXridge.R | 152 +- survivalSL-0.98/survivalSL/R/tunePHspline.R | 258 ++- survivalSL-0.98/survivalSL/R/tunePLANN.R | 344 +++-- survivalSL-0.98/survivalSL/R/tuneRSF.R | 95 - survivalSL-0.98/survivalSL/README.md | 30 survivalSL-0.98/survivalSL/man/LIB_AFTgamma.Rd | 27 survivalSL-0.98/survivalSL/man/LIB_AFTggamma.Rd | 29 survivalSL-0.98/survivalSL/man/LIB_AFTllogis.Rd | 32 survivalSL-0.98/survivalSL/man/LIB_AFTweibull.Rd | 31 survivalSL-0.98/survivalSL/man/LIB_COXaic.Rd | 40 survivalSL-0.98/survivalSL/man/LIB_COXall.Rd | 30 survivalSL-0.98/survivalSL/man/LIB_COXen.Rd | 33 survivalSL-0.98/survivalSL/man/LIB_COXlasso.Rd | 35 survivalSL-0.98/survivalSL/man/LIB_COXridge.Rd | 40 survivalSL-0.98/survivalSL/man/LIB_PHexponential.Rd | 30 survivalSL-0.98/survivalSL/man/LIB_PHgompertz.Rd | 29 survivalSL-0.98/survivalSL/man/LIB_PHspline.Rd | 36 survivalSL-0.98/survivalSL/man/LIB_PLANN.Rd | 31 survivalSL-0.98/survivalSL/man/LIB_RSF.Rd | 29 survivalSL-0.98/survivalSL/man/metrics.Rd | 42 survivalSL-0.98/survivalSL/man/plot.libsl.Rd | 18 survivalSL-0.98/survivalSL/man/plot.sltime.Rd | 26 survivalSL-0.98/survivalSL/man/predict.libsl.Rd | 14 survivalSL-0.98/survivalSL/man/predict.sltime.Rd | 31 survivalSL-0.98/survivalSL/man/print.libsl.Rd | 13 survivalSL-0.98/survivalSL/man/print.sltime.Rd | 11 survivalSL-0.98/survivalSL/man/summary.libsl.Rd | 46 survivalSL-0.98/survivalSL/man/summary.sltime.Rd | 38 survivalSL-0.98/survivalSL/man/survivalSL.Rd | 65 survivalSL-0.98/survivalSL/man/tuneCOXen.Rd | 32 survivalSL-0.98/survivalSL/man/tuneCOXlasso.Rd | 38 survivalSL-0.98/survivalSL/man/tuneCOXridge.Rd | 33 survivalSL-0.98/survivalSL/man/tunePHspline.Rd | 37 survivalSL-0.98/survivalSL/man/tunePLANN.Rd | 49 survivalSL-0.98/survivalSL/man/tuneRSF.Rd | 23 73 files changed, 3670 insertions(+), 3306 deletions(-)
Title: High Throughput Phenotyping (HTP) Data Analysis
Description: Phenotypic analysis of data coming from high throughput
phenotyping (HTP) platforms, including different types of outlier detection,
spatial analysis, and parameter estimation. The package is being developed
within the EPPN2020 project (<https://cordis.europa.eu/project/id/731013>).
Some functions have been created to be used in conjunction with the R
package 'asreml' for the 'ASReml' software, which can be obtained upon
purchase from 'VSN' international (<https://vsni.co.uk/software/asreml-r/>).
Author: Emilie J Millet [aut] ,
Maria Xose Rodriguez Alvarez [aut] ,
Diana Marcela Perez Valencia [aut] ,
Isabelle Sanchez [aut],
Nadine Hilgert [aut],
Bart-Jan van Rossum [aut, cre] ,
Fred van Eeuwijk [aut] ,
Martin Boer [aut]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenHTP versions 1.0.8 dated 2025-04-29 and 1.0.9 dated 2025-07-02
DESCRIPTION | 33 +++++------- MD5 | 32 +++++------ NEWS.md | 2 R/createFitMod.R | 47 ++++++++++------- R/createTimePoints.R | 31 ++++++----- R/detectSerieOut.R | 105 ++++++++++++++++++++++++++++----------- R/utils.R | 28 ++++------ README.md | 4 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/Overview_HTP.Rmd | 2 inst/doc/Overview_HTP.html | 32 +++++++---- inst/tinytest/serieOut |binary inst/tinytest/test_fitModPlots.R | 29 +++++----- inst/tinytest/test_utils.R | 14 ++--- man/statgenHTP-package.Rd | 2 vignettes/Overview_HTP.Rmd | 2 17 files changed, 214 insertions(+), 149 deletions(-)
Title: Species Distribution Modelling for Rare Species
Description: Performs species distribution modeling for rare species with unprecedented accuracy (Mondanaro et al., 2023 <doi:10.1111/2041-210X.14066>) and finds the area of origin of species and past contact between them taking climatic variability in full consideration (Mondanaro et al., 2025 <doi:10.1111/2041-210X.14478>).
Author: Alessandro Mondanaro [aut],
Mirko Di Febbraro [aut],
Silvia Castiglione [aut, cre],
Carmela Serio [aut],
Marina Melchionna [aut],
Giorgia Girardi [aut],
Pasquale Raia [aut]
Maintainer: Silvia Castiglione <silvia.castiglione@unina.it>
Diff between RRgeo versions 0.0.3 dated 2025-04-01 and 0.0.5 dated 2025-07-02
DESCRIPTION | 6 MD5 | 30 - NAMESPACE | 5 R/IMPUTED_CALIBRATION.R | 2 R/RRgeo_internals.R | 5 R/RRphylogeography.R | 637 +++++++++++++++----------------- R/cal14C.R | 2 R/sf.kde.R | 92 ++-- build/vignette.rds |binary inst/doc/ENphylo.html | 7 inst/doc/Preparing-Data.html | 13 inst/doc/RRgeo_vignette.html | 5 inst/doc/RRphylogeo.html | 5 inst/exdata/U.maritimus_suitability.tif |binary man/RRphylogeography.Rd | 25 - man/cal14C.Rd | 2 16 files changed, 420 insertions(+), 416 deletions(-)
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <https://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, <doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013,
<doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Balamuta (2018,
<doi:10.1080/00031305.2017.1375990>); see 'citation("Rcpp")' for details.
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
JJ Allaire [aut] ,
Kevin Ushey [aut] ,
Qiang Kou [aut] ,
Nathan Russell [aut],
Inaki Ucar [aut] ,
Doug Bates [aut] ,
John Chambers [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 1.0.14 dated 2025-01-12 and 1.1.0 dated 2025-07-02
Rcpp-1.0.14/Rcpp/inst/include/Rcpp/exceptions |only Rcpp-1.0.14/Rcpp/inst/include/Rcpp/generated |only Rcpp-1.0.14/Rcpp/inst/include/Rcpp/module/Module_generated_Constructor.h |only Rcpp-1.0.14/Rcpp/inst/include/Rcpp/module/Module_generated_CppFunction.h |only Rcpp-1.0.14/Rcpp/inst/include/Rcpp/module/Module_generated_CppMethod.h |only Rcpp-1.0.14/Rcpp/inst/include/Rcpp/module/Module_generated_Factory.h |only Rcpp-1.0.14/Rcpp/inst/include/Rcpp/module/Module_generated_Pointer_CppMethod.h |only Rcpp-1.0.14/Rcpp/inst/include/Rcpp/module/Module_generated_Pointer_method.h |only Rcpp-1.0.14/Rcpp/inst/include/Rcpp/module/Module_generated_class_constructor.h |only Rcpp-1.0.14/Rcpp/inst/include/Rcpp/module/Module_generated_class_factory.h |only Rcpp-1.0.14/Rcpp/inst/include/Rcpp/module/Module_generated_class_signature.h |only Rcpp-1.0.14/Rcpp/inst/include/Rcpp/module/Module_generated_ctor_signature.h |only Rcpp-1.0.14/Rcpp/inst/include/Rcpp/module/Module_generated_function.h |only Rcpp-1.0.14/Rcpp/inst/include/Rcpp/module/Module_generated_get_signature.h |only Rcpp-1.0.14/Rcpp/inst/include/Rcpp/module/Module_generated_method.h |only Rcpp-1.1.0/Rcpp/ChangeLog | 271 ++++++++++ Rcpp-1.1.0/Rcpp/DESCRIPTION | 23 Rcpp-1.1.0/Rcpp/MD5 | 205 +++---- Rcpp-1.1.0/Rcpp/R/Attributes.R | 7 Rcpp-1.1.0/Rcpp/R/Rcpp.package.skeleton.R | 25 Rcpp-1.1.0/Rcpp/README.md | 14 Rcpp-1.1.0/Rcpp/build/partial.rdb |binary Rcpp-1.1.0/Rcpp/build/vignette.rds |binary Rcpp-1.1.0/Rcpp/inst/NEWS.Rd | 60 ++ Rcpp-1.1.0/Rcpp/inst/bib/Rcpp.bib | 248 +++++---- Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-FAQ.pdf |binary Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-attributes.pdf |binary Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-extending.pdf |binary Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-introduction.pdf |binary Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-jss-2011.pdf |binary Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-libraries.pdf |binary Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-modules.pdf |binary Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-package.pdf |binary Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-quickref.pdf |binary Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-sugar.pdf |binary Rcpp-1.1.0/Rcpp/inst/include/Rcpp.h | 1 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/DataFrame.h | 14 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/DottedPair.h | 14 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/Environment.h | 2 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/Function.h | 16 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/InternalFunction.h | 6 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/InternalFunctionWithStdFunction.h | 10 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/Language.h | 30 - Rcpp-1.1.0/Rcpp/inst/include/Rcpp/Module.h | 33 - Rcpp-1.1.0/Rcpp/inst/include/Rcpp/Pairlist.h | 15 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/String.h | 24 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/StringTransformer.h | 6 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/Symbol.h | 4 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/algorithm.h | 49 - Rcpp-1.1.0/Rcpp/inst/include/Rcpp/config.h | 9 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/date_datetime/newDateVector.h | 6 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/date_datetime/newDatetimeVector.h | 6 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/exceptions.h | 36 - Rcpp-1.1.0/Rcpp/inst/include/Rcpp/grow.h | 23 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/internal/call.h | 5 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/internal/wrap.h | 26 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/lgrow.h |only Rcpp-1.1.0/Rcpp/inst/include/Rcpp/longlong.h | 27 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/macros/dispatch.h | 36 - Rcpp-1.1.0/Rcpp/inst/include/Rcpp/module/class.h | 104 +-- Rcpp-1.1.0/Rcpp/inst/include/Rcpp/platform/compiler.h | 176 ------ Rcpp-1.1.0/Rcpp/inst/include/Rcpp/sugar/functions/lapply.h | 5 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/sugar/functions/mapply/mapply_2.h | 15 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/sugar/functions/mapply/mapply_3.h | 7 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/sugar/functions/sapply.h | 42 - Rcpp-1.1.0/Rcpp/inst/include/Rcpp/sugar/functions/self_match.h | 5 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/sugar/functions/setdiff.h | 11 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/sugar/functions/table.h | 40 - Rcpp-1.1.0/Rcpp/inst/include/Rcpp/sugar/matrix/outer.h | 7 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/sugar/sets.h | 46 - Rcpp-1.1.0/Rcpp/inst/include/Rcpp/traits/index_sequence.h | 5 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/traits/is_arithmetic.h | 8 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/traits/longlong.h | 5 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/traits/named_object.h | 21 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/traits/r_type_traits.h | 3 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/traits/result_of.h | 29 - Rcpp-1.1.0/Rcpp/inst/include/Rcpp/traits/wrap_type_traits.h | 3 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/unwindProtect.h | 10 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/utils/tinyformat.h | 9 Rcpp-1.1.0/Rcpp/inst/include/Rcpp/vector/Vector.h | 102 +-- Rcpp-1.1.0/Rcpp/inst/include/RcppCommon.h | 3 Rcpp-1.1.0/Rcpp/inst/tinytest/cpp/dates.cpp | 13 Rcpp-1.1.0/Rcpp/inst/tinytest/cpp/language.cpp | 7 Rcpp-1.1.0/Rcpp/inst/tinytest/cpp/sugar.cpp | 69 ++ Rcpp-1.1.0/Rcpp/inst/tinytest/cpp/wrap.cpp | 30 - Rcpp-1.1.0/Rcpp/inst/tinytest/test_attribute_package.R | 6 Rcpp-1.1.0/Rcpp/inst/tinytest/test_date.R | 14 Rcpp-1.1.0/Rcpp/inst/tinytest/test_expose_class.R | 2 Rcpp-1.1.0/Rcpp/inst/tinytest/test_language.R | 2 Rcpp-1.1.0/Rcpp/inst/tinytest/test_rcpp_package_skeleton.R | 6 Rcpp-1.1.0/Rcpp/inst/tinytest/test_sugar.R | 78 ++ Rcpp-1.1.0/Rcpp/inst/tinytest/test_wrap.R | 3 Rcpp-1.1.0/Rcpp/man/Rcpp.package.skeleton.Rd | 58 +- Rcpp-1.1.0/Rcpp/man/evalCpp.Rd | 23 Rcpp-1.1.0/Rcpp/src/api.cpp | 77 -- Rcpp-1.1.0/Rcpp/src/attributes.cpp | 10 Rcpp-1.1.0/Rcpp/src/barrier.cpp | 6 Rcpp-1.1.0/Rcpp/vignettes/pdf/Rcpp-FAQ.pdf |binary Rcpp-1.1.0/Rcpp/vignettes/pdf/Rcpp-attributes.pdf |binary Rcpp-1.1.0/Rcpp/vignettes/pdf/Rcpp-extending.pdf |binary Rcpp-1.1.0/Rcpp/vignettes/pdf/Rcpp-introduction.pdf |binary Rcpp-1.1.0/Rcpp/vignettes/pdf/Rcpp-jss-2011.pdf |binary Rcpp-1.1.0/Rcpp/vignettes/pdf/Rcpp-libraries.pdf |binary Rcpp-1.1.0/Rcpp/vignettes/pdf/Rcpp-modules.pdf |binary Rcpp-1.1.0/Rcpp/vignettes/pdf/Rcpp-package.pdf |binary Rcpp-1.1.0/Rcpp/vignettes/pdf/Rcpp-quickref.pdf |binary Rcpp-1.1.0/Rcpp/vignettes/pdf/Rcpp-sugar.pdf |binary 107 files changed, 1186 insertions(+), 1125 deletions(-)
Title: Deciphering Biological Networks with Patterned Heterogeneous
Measurements
Description: A modeling tool dedicated to biological network modeling (Bertrand and others 2020, <doi:10.1093/bioinformatics/btaa855>). It allows for single or joint modeling of, for instance, genes and proteins. It starts with the selection of the actors that will be the used in the reverse engineering upcoming step. An actor can be included in that selection based on its differential measurement (for instance gene expression or protein abundance) or on its time course profile. Wrappers for actors clustering functions and cluster analysis are provided. It also allows reverse engineering of biological networks taking into account the observed time course patterns of the actors. Many inference functions are provided and dedicated to get specific features for the inferred network such as sparsity, robust links, high confidence links or stable through resampling links. Some simulation and prediction tools are also available for cascade networks (Jung and others 2014, <doi:10.1093/bioinformati [...truncated...]
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between Patterns versions 1.5 dated 2024-05-06 and 1.6 dated 2025-07-02
DESCRIPTION | 18 MD5 | 36 - NAMESPACE | 1 NEWS.md | 4 R/Patterns-package.R | 1 R/datasets.R | 5 README.md | 3 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/doc/ExampleCLL.R | 186 ------ inst/doc/ExampleCLL.Rmd | 4 inst/doc/ExampleCLL.html | 346 +---------- inst/doc/IntroPatterns.R | 313 ---------- inst/doc/IntroPatterns.Rmd | 2 inst/doc/IntroPatterns.html | 1279 +++++--------------------------------------- man/CLL.Rd | 5 vignettes/ExampleCLL.Rmd | 4 vignettes/IntroPatterns.Rmd | 2 19 files changed, 276 insertions(+), 1935 deletions(-)
Title: Interpolation and Extrapolation for Three Dimensions of
Biodiversity
Description: Biodiversity is a multifaceted concept covering different levels of organization from
genes to ecosystems. 'iNEXT.3D' extends 'iNEXT' to include three dimensions (3D)
of biodiversity, i.e., taxonomic diversity (TD), phylogenetic diversity (PD) and functional
diversity (FD). This package provides functions to compute standardized 3D diversity estimates
with a common sample size or sample coverage. A unified framework based on Hill numbers
and their generalizations (Hill-Chao numbers) are used to quantify 3D. All 3D estimates
are in the same units of species/lineage equivalents and can be meaningfully compared.
The package features size- and coverage-based rarefaction and extrapolation sampling
curves to facilitate rigorous comparison of 3D diversity across individual assemblages.
Asymptotic 3D diversity estimates are also provided. See Chao et al. (2021)
<doi:10.1111/2041-210X.13682> for more details.
Author: Anne Chao [aut, cre],
KaiHsiang Hu [ctb],
PoYen Chuang [ctb]
Maintainer: Anne Chao <chao@stat.nthu.edu.tw>
Diff between iNEXT.3D versions 1.0.9 dated 2025-07-01 and 1.0.10 dated 2025-07-02
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 4 ++++ inst/doc/Introduction.pdf |binary vignettes/mypaper.pdf |binary 5 files changed, 11 insertions(+), 7 deletions(-)
Title: The Generalized DINA Model Framework
Description: A set of psychometric tools for cognitive diagnosis modeling based on the generalized deterministic inputs, noisy and gate (G-DINA) model by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7> and its extensions, including the sequential G-DINA model by Ma and de la Torre (2016) <DOI:10.1111/bmsp.12070> for polytomous responses, and the polytomous G-DINA model by Chen and de la Torre <DOI:10.1177/0146621613479818> for polytomous attributes. Joint attribute distribution can be independent, saturated, higher-order, loglinear smoothed or structured. Q-matrix validation, item and model fit statistics, model comparison at test and item level and differential item functioning can also be conducted. A graphical user interface is also provided. For tutorials, please check Ma and de la Torre (2020) <DOI:10.18637/jss.v093.i14>, Ma and de la Torre (2019) <DOI:10.1111/emip.12262>, Ma (2019) <DOI:10.1007/978-3-030-05584-4_29> and de la Torre and Akbay (2019).
Author: Wenchao Ma [aut, cre, cph],
Jimmy de la Torre [aut, cph],
Miguel Sorrel [ctb],
Zhehan Jiang [ctb],
Pablo Najera [ctb]
Maintainer: Wenchao Ma <wma@umn.edu>
Diff between GDINA versions 2.9.9 dated 2025-05-01 and 2.9.12 dated 2025-07-02
GDINA-2.9.12/GDINA/DESCRIPTION | 37 GDINA-2.9.12/GDINA/MD5 | 61 - GDINA-2.9.12/GDINA/NAMESPACE | 4 GDINA-2.9.12/GDINA/NEWS.md | 8 GDINA-2.9.12/GDINA/R/CA.R | 2 GDINA-2.9.12/GDINA/R/DTM.R | 38 - GDINA-2.9.12/GDINA/R/GDI.R | 7 GDINA-2.9.12/GDINA/R/MultipleGroup_Estimation.R | 4 GDINA-2.9.12/GDINA/R/SingleGroup_Estimation.R | 4 GDINA-2.9.12/GDINA/R/anova.GDINA.R | 96 +- GDINA-2.9.12/GDINA/R/bootSE.R | 46 + GDINA-2.9.12/GDINA/R/extract.R | 829 +++++++++++----------- GDINA-2.9.12/GDINA/R/itemfitPD.R |only GDINA-2.9.12/GDINA/R/print.GDINA.R | 652 ++++++++--------- GDINA-2.9.12/GDINA/R/realdata_ECPE.R |only GDINA-2.9.12/GDINA/R/realdata_Tatsuoka1990.R |only GDINA-2.9.12/GDINA/R/summary.GDINA.R | 228 +++--- GDINA-2.9.12/GDINA/data/realdata_ECPE.rda |only GDINA-2.9.12/GDINA/data/realdata_Tatsuoka1990.rda |only GDINA-2.9.12/GDINA/inst/doc/GDINA.Rmd | 7 GDINA-2.9.12/GDINA/inst/doc/GDINA.html | 14 GDINA-2.9.12/GDINA/man/CA.Rd | 2 GDINA-2.9.12/GDINA/man/DTM.Rd | 33 GDINA-2.9.12/GDINA/man/bootSE.Rd | 14 GDINA-2.9.12/GDINA/man/itemfitPD.Rd |only GDINA-2.9.12/GDINA/man/realdata_ECPE.Rd |only GDINA-2.9.12/GDINA/man/realdata_Tatsuoka1990.Rd |only GDINA-2.9.12/GDINA/vignettes/GDINA.Rmd | 7 GDINA-2.9.9/GDINA/R/ecpe.R |only GDINA-2.9.9/GDINA/R/frac20.R |only GDINA-2.9.9/GDINA/R/tan2023.R |only GDINA-2.9.9/GDINA/R/tan2023p25.R |only GDINA-2.9.9/GDINA/R/tan2023p50.R |only GDINA-2.9.9/GDINA/data/ecpe.rda |only GDINA-2.9.9/GDINA/data/frac20.rda |only GDINA-2.9.9/GDINA/data/tan2023.rda |only GDINA-2.9.9/GDINA/data/tan2023p25.rda |only GDINA-2.9.9/GDINA/data/tan2023p50.rda |only GDINA-2.9.9/GDINA/man/ecpe.Rd |only GDINA-2.9.9/GDINA/man/frac20.Rd |only GDINA-2.9.9/GDINA/man/tan2023.Rd |only GDINA-2.9.9/GDINA/man/tan2023p25.Rd |only GDINA-2.9.9/GDINA/man/tan2023p50.Rd |only 43 files changed, 1114 insertions(+), 979 deletions(-)
Title: Fused Extended Two-Way Fixed Effects
Description: Calculates the fused extended two-way fixed effects (FETWFE) estimator for unbiased and efficient estimation of difference-in-differences in panel data with staggered treatment adoption. This estimator eliminates bias inherent in conventional two-way fixed effects estimators, while also employing a novel bridge regression regularization approach to improve efficiency and yield valid standard errors. Also implements extended TWFE (etwfe) and bridge-penalized ETWFE (betwfe). Provides S3 classes for streamlined workflow and supports flexible tuning (ridge and rank-condition guarantees), automatic covariate centering/scaling, and detailed overall and cohort-specific effect estimates with valid standard errors. Includes simulation and formatting utilities, extensive diagnostic tools, vignettes, and examples. See Faletto (2025) (<doi:10.48550/arXiv.2312.05985>).
Author: Gregory Faletto [aut, cre]
Maintainer: Gregory Faletto <gfaletto@gmail.com>
Diff between fetwfe versions 1.0.0 dated 2025-05-15 and 1.5.0 dated 2025-07-02
fetwfe-1.0.0/fetwfe/R/did_funcs.R |only fetwfe-1.5.0/fetwfe/DESCRIPTION | 13 fetwfe-1.5.0/fetwfe/MD5 | 75 fetwfe-1.5.0/fetwfe/NAMESPACE | 18 fetwfe-1.5.0/fetwfe/NEWS.md | 40 fetwfe-1.5.0/fetwfe/R/betwfe_core.R |only fetwfe-1.5.0/fetwfe/R/convert_dfs.R |only fetwfe-1.5.0/fetwfe/R/core_funcs.R |only fetwfe-1.5.0/fetwfe/R/etwfe_class.R |only fetwfe-1.5.0/fetwfe/R/etwfe_core.R |only fetwfe-1.5.0/fetwfe/R/fetwfe.R | 1499 +++----------- fetwfe-1.5.0/fetwfe/R/fetwfe_class.R |only fetwfe-1.5.0/fetwfe/R/fetwfe_core.R |only fetwfe-1.5.0/fetwfe/R/gen_funcs.R | 1066 +++++++++ fetwfe-1.5.0/fetwfe/R/ols_calcs.R |only fetwfe-1.5.0/fetwfe/R/twfeCovs.R |only fetwfe-1.5.0/fetwfe/R/utility.R |only fetwfe-1.5.0/fetwfe/README.md | 90 fetwfe-1.5.0/fetwfe/build/partial.rdb |only fetwfe-1.5.0/fetwfe/inst/CITATION | 4 fetwfe-1.5.0/fetwfe/inst/doc/simulation_vignette.R | 23 fetwfe-1.5.0/fetwfe/inst/doc/simulation_vignette.Rmd | 29 fetwfe-1.5.0/fetwfe/inst/doc/simulation_vignette.html | 87 fetwfe-1.5.0/fetwfe/inst/doc/vignette.R | 6 fetwfe-1.5.0/fetwfe/inst/doc/vignette.Rmd | 8 fetwfe-1.5.0/fetwfe/inst/doc/vignette.html | 127 - fetwfe-1.5.0/fetwfe/man/attgtToFetwfeDf.Rd |only fetwfe-1.5.0/fetwfe/man/betwfe.Rd |only fetwfe-1.5.0/fetwfe/man/betwfeWithSimulatedData.Rd |only fetwfe-1.5.0/fetwfe/man/etwfe-class.Rd |only fetwfe-1.5.0/fetwfe/man/etwfe.Rd |only fetwfe-1.5.0/fetwfe/man/etwfeToFetwfeDf.Rd |only fetwfe-1.5.0/fetwfe/man/etwfeWithSimulatedData.Rd |only fetwfe-1.5.0/fetwfe/man/fetwfe-class.Rd |only fetwfe-1.5.0/fetwfe/man/fetwfe.Rd | 112 - fetwfe-1.5.0/fetwfe/man/fetwfeWithSimulatedData.Rd | 94 fetwfe-1.5.0/fetwfe/man/genCoefs.Rd | 6 fetwfe-1.5.0/fetwfe/man/genCoefsCore.Rd | 7 fetwfe-1.5.0/fetwfe/man/getTes.Rd | 2 fetwfe-1.5.0/fetwfe/man/simulateData.Rd | 18 fetwfe-1.5.0/fetwfe/man/simulateDataCore.Rd | 10 fetwfe-1.5.0/fetwfe/man/twfeCovs.Rd |only fetwfe-1.5.0/fetwfe/man/twfeCovsWithSimulatedData.Rd |only fetwfe-1.5.0/fetwfe/tests/testthat/test-attgtToFetwfeDf.R |only fetwfe-1.5.0/fetwfe/tests/testthat/test-betwfe.R |only fetwfe-1.5.0/fetwfe/tests/testthat/test-etwfe.R |only fetwfe-1.5.0/fetwfe/tests/testthat/test-etwfeToFetwfeDf.R |only fetwfe-1.5.0/fetwfe/tests/testthat/test-fetwfe.R | 20 fetwfe-1.5.0/fetwfe/tests/testthat/test-simulateData.R | 12 fetwfe-1.5.0/fetwfe/tests/testthat/test-twfeCovs.R |only fetwfe-1.5.0/fetwfe/vignettes/simulation_vignette.Rmd | 29 fetwfe-1.5.0/fetwfe/vignettes/vignette.Rmd | 8 52 files changed, 1820 insertions(+), 1583 deletions(-)
Title: Relational Data Models
Description: Provides tools for working with multiple related
tables, stored as data frames or in a relational database. Multiple
tables (data and metadata) are stored in a compound object, which can
then be manipulated with a pipe-friendly syntax.
Author: Tobias Schieferdecker [aut],
Kirill Mueller [aut, cre] ,
Antoine Fabri [ctb],
Darko Bergant [aut],
Katharina Brunner [ctb],
James Wondrasek [ctb],
Indrajeet Patil [ctb] ,
Maelle Salmon [ctb] ,
energie360 AG [fnd],
cynkra GmbH [fnd, cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between dm versions 1.0.11 dated 2024-11-25 and 1.0.12 dated 2025-07-02
dm-1.0.11/dm/tests/testthat/helper-print.R |only dm-1.0.12/dm/DESCRIPTION | 25 +++--- dm-1.0.12/dm/MD5 | 87 ++++++++++------------ dm-1.0.12/dm/NEWS.md | 43 ++++++++++ dm-1.0.12/dm/R/db-interface.R | 21 ++--- dm-1.0.12/dm/R/dm_from_con.R | 11 +- dm-1.0.12/dm/R/dm_sql.R | 36 +++++---- dm-1.0.12/dm/R/error-helpers.R | 1 dm-1.0.12/dm/R/gui-gui_global.R | 2 dm-1.0.12/dm/R/gui-gui_ui.R | 6 - dm-1.0.12/dm/R/learn.R | 3 dm-1.0.12/dm/R/postgres.R | 2 dm-1.0.12/dm/build/vignette.rds |binary dm-1.0.12/dm/demo/basel.R | 72 +++++++----------- dm-1.0.12/dm/demo/hamburg.R | 60 +++++++-------- dm-1.0.12/dm/demo/milano.R | 2 dm-1.0.12/dm/demo/neuchatel.R | 2 dm-1.0.12/dm/demo/nyc.R | 63 ++++++--------- dm-1.0.12/dm/demo/seattle.R | 53 ++++++------- dm-1.0.12/dm/inst/doc/dm.html | 9 +- dm-1.0.12/dm/inst/doc/howto-dm-copy.html | 9 +- dm-1.0.12/dm/inst/doc/howto-dm-db.html | 9 +- dm-1.0.12/dm/inst/doc/howto-dm-df.html | 9 +- dm-1.0.12/dm/inst/doc/howto-dm-rows.html | 9 +- dm-1.0.12/dm/inst/doc/howto-dm-theory.Rmd | 2 dm-1.0.12/dm/inst/doc/howto-dm-theory.html | 15 ++- dm-1.0.12/dm/inst/doc/tech-dm-cdm.html | 9 +- dm-1.0.12/dm/inst/doc/tech-dm-class.html | 9 +- dm-1.0.12/dm/inst/doc/tech-dm-draw.html | 9 +- dm-1.0.12/dm/inst/doc/tech-dm-filter.Rmd | 2 dm-1.0.12/dm/inst/doc/tech-dm-filter.html | 11 +- dm-1.0.12/dm/inst/doc/tech-dm-join.html | 9 +- dm-1.0.12/dm/inst/doc/tech-dm-keyed.html | 5 - dm-1.0.12/dm/inst/doc/tech-dm-low-level.html | 9 +- dm-1.0.12/dm/inst/doc/tech-dm-zoom.html | 5 - dm-1.0.12/dm/man/dm-package.Rd | 2 dm-1.0.12/dm/tests/testthat/_snaps/deconstruct.md | 32 ++++---- dm-1.0.12/dm/tests/testthat/_snaps/learn.md | 8 -- dm-1.0.12/dm/tests/testthat/_snaps/zoom.md | 8 +- dm-1.0.12/dm/tests/testthat/setup.R | 9 ++ dm-1.0.12/dm/tests/testthat/test-deconstruct.R | 1 dm-1.0.12/dm/tests/testthat/test-learn.R | 15 +++ dm-1.0.12/dm/vignettes/howto-dm-theory.Rmd | 2 dm-1.0.12/dm/vignettes/setup/setup.R | 10 ++ dm-1.0.12/dm/vignettes/tech-dm-filter.Rmd | 2 45 files changed, 374 insertions(+), 334 deletions(-)
Title: Create TLGs using the 'tidyverse'
Description: Generate tables, listings, and graphs (TLG) using 'tidyverse.'
Tables can be created functionally, using a standard TLG process, or by
specifying table and column metadata to create generic analysis summaries.
The 'envsetup' package can also be leveraged to create environments for table
creation.
Author: Nicholas Masel [aut],
Steven Haesendonckx [aut],
Pelagia Alexandra Papadopoulou [aut],
Sheng-Wei Wang [aut],
Eli Miller [aut] ,
Nathan Kosiba [aut] ,
Aidan Ceney [aut] ,
Janssen R&D [cph, fnd],
David Hugh-Jones [cph] ,
Konrad Pagacz [aut, cre]
Maintainer: Konrad Pagacz <kpagacz@its.jnj.com>
Diff between tidytlg versions 0.1.6 dated 2025-05-02 and 0.10.0 dated 2025-07-02
DESCRIPTION | 8 MD5 | 163 +++--- NEWS.md | 36 - R/add_format.R | 47 + R/add_indent.R | 48 + R/add_newrows.R | 105 ++-- R/bind_table.R | 163 ++++-- R/check_args.R | 97 ++- R/freq.R | 541 ++++++++++++---------- R/generate_results.R | 204 ++++---- R/gentlg.R | 37 + R/gentlg_single.R | 11 R/getFileName.R | 38 - R/nested_freq.R | 416 ++++++++--------- R/print.R | 53 +- R/roundSAS.R | 9 R/statlist.R | 9 R/tidytlg-package.R | 26 - R/tlgsetup.R | 123 ++--- R/univar.R | 502 +++++++++++--------- R/utility.R | 85 +-- data/cdisc_adae.rda |binary data/cdisc_adsl.rda |binary inst/doc/freq.R | 151 +++--- inst/doc/freq.Rmd | 151 +++--- inst/doc/freq.html | 235 +++++---- inst/doc/symbols.R | 43 - inst/doc/symbols.Rmd | 43 - inst/doc/symbols.html | 92 +-- inst/doc/tbl_manipulation.R | 152 +++--- inst/doc/tbl_manipulation.Rmd | 152 +++--- inst/doc/tbl_manipulation.html | 444 +++++++++--------- inst/doc/tidytlg.R | 217 +++++--- inst/doc/tidytlg.Rmd | 217 +++++--- inst/doc/tidytlg.html | 384 ++++++++------- inst/doc/tlgsetup.R | 9 inst/doc/tlgsetup.Rmd | 9 inst/doc/tlgsetup.html | 31 - inst/doc/univar.R | 70 +- inst/doc/univar.Rmd | 70 +- inst/doc/univar.html | 96 ++- man/gentlg.Rd | 21 tests/testthat.R | 2 tests/testthat/_snaps/png/png1.rtf |only tests/testthat/_snaps/png/png2.rtf |only tests/testthat/freq_rowtext_row_header.R | 103 ++-- tests/testthat/test-bind_table.R | 106 ++-- tests/testthat/test-check_args.R | 732 +++++++++++++++++------------- tests/testthat/test-colheader.R | 14 tests/testthat/test-freq.R | 652 +++++++++++++------------- tests/testthat/test-freq_cutoff.R | 57 +- tests/testthat/test-freq_descending_by.R | 34 - tests/testthat/test-freq_ord.R | 152 +++--- tests/testthat/test-freq_pad.R | 44 - tests/testthat/test-freq_sparse.R | 75 +-- tests/testthat/test-freq_subset.R | 22 tests/testthat/test-gentlg.R |only tests/testthat/test-getFileName.R | 2 tests/testthat/test-metadata.R | 35 - tests/testthat/test-nested.R | 404 ++++++++-------- tests/testthat/test-nested_cutoff.R | 174 +++---- tests/testthat/test-nested_freq.R | 57 -- tests/testthat/test-nested_ord.R | 55 +- tests/testthat/test-remove_zero_padding.R | 2 tests/testthat/test-roundSAS.R | 48 + tests/testthat/test-spanning_headers.R | 19 tests/testthat/test-titles.R | 12 tests/testthat/test-univar.R | 290 ++++++----- tests/testthat/test-univar_keep.R | 40 - tests/testthat/test-univar_ord.R | 47 - tests/testthat/test-univar_precision.R | 43 - tests/testthat/test-univar_rowbyvar.R | 134 ++--- tests/testthat/test-univar_rowtext.R | 83 +-- tests/testthat/test-utility.R | 55 +- tests/testthat/test_outputs/png1.png |binary tests/testthat/test_outputs/png1.rtf | 2 tests/testthat/test_outputs/png2.png |binary tests/testthat/test_outputs/png2.rtf | 2 vignettes/freq.Rmd | 151 +++--- vignettes/symbols.Rmd | 43 - vignettes/tbl_manipulation.Rmd | 152 +++--- vignettes/tidytlg.Rmd | 217 +++++--- vignettes/tlgsetup.Rmd | 9 vignettes/univar.Rmd | 70 +- 84 files changed, 5113 insertions(+), 4334 deletions(-)
Title: ATLAS Formatting Functions and Templates
Description: Provides templates, formatting tools, and 'ggplot2' themes
tailored for the Accessible Teaching, Learning, and Assessment Systems (ATLAS)
organization. These templates facilitate the creation of topic guides and
technical reports, while the formatting functions enable users to customize
numbers and tables to meet specific requirements. Additionally, the themes
ensure a uniform visual style across graphics.
Author: W. Jake Thompson [aut, cre] ,
Noelle Pablo [aut],
Jeffrey Hoover [aut] ,
University of Kansas [cph, fnd]
Maintainer: W. Jake Thompson <wjakethompson@gmail.com>
Diff between ratlas versions 0.1.0 dated 2024-11-06 and 0.1.1 dated 2025-07-02
DESCRIPTION | 29 MD5 | 417 - NAMESPACE | 142 NEWS.md |only R/aliases.R | 54 R/atlas-color-scales.R | 154 R/auto-set-format.R | 18 R/data-checks.R | 240 R/data.R | 24 R/format-text.R | 122 R/formatting.R | 528 - R/hook-plot-rat.R | 430 - R/kbl-defaults.R | 94 R/lcrost-color-scales.R | 156 R/misc-manipulation.R | 148 R/okabeito-color-scales.R | 154 R/palettes.R | 82 R/proj.R | 6 R/rat-cap-words.R | 120 R/ratlas.R | 36 R/reexport-hrbrthemes.R | 24 R/render.R | 716 - R/save-plot.R | 120 R/set-theme.R | 136 R/skeleton.R | 326 R/stat-bin.R | 574 - R/table-format.R | 640 - R/theme-atlas.R | 335 R/utils-hook.R | 174 R/utils-pipe.R | 24 R/utils.R | 68 R/zzz.R | 60 README.md | 52 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 18 inst/WORDLIST | 149 inst/doc/plotting.R | 437 - inst/doc/plotting.Rmd | 625 - inst/doc/plotting.html | 1396 +-- inst/doc/report-writing.R | 264 inst/doc/report-writing.Rmd | 692 - inst/doc/report-writing.html | 2177 ++--- inst/rmarkdown/templates/atlas-presentation/skeleton/assets/css/atlas-fonts.css | 4 inst/rmarkdown/templates/atlas-presentation/skeleton/assets/css/atlas.css | 326 inst/rmarkdown/templates/atlas-presentation/skeleton/assets/header.html | 2 inst/rmarkdown/templates/atlas-presentation/skeleton/skeleton.Rmd | 210 inst/rmarkdown/templates/atlas-presentation/skeleton/skeleton.html | 542 - inst/rmarkdown/templates/atlas-presentation/skeleton/skeleton_files/figure-html/cars-1.svg | 374 inst/rmarkdown/templates/atlas-presentation/template.yaml | 6 inst/rmarkdown/templates/measr_pdf/resources/template.tex | 744 - inst/rmarkdown/templates/techreport/resources/apa6-template.tex | 704 - inst/rmarkdown/templates/techreport/resources/template.tex | 978 +- inst/rmarkdown/templates/topicguide_pdf/resources/template.tex | 824 +- inst/rstudio/templates/project/measr_pdf.dcf | 8 inst/rstudio/templates/project/measr_pdf_resources/bib/refs.bib | 144 inst/rstudio/templates/project/measr_pdf_resources/csl/apa.csl | 3832 +++++----- inst/rstudio/templates/project/measr_pdf_resources/index.Rmd | 105 inst/rstudio/templates/project/techreport_html.dcf | 8 inst/rstudio/templates/project/techreport_html_resources/_bookdown.yml | 4 inst/rstudio/templates/project/techreport_html_resources/assets/footnote.lua | 90 inst/rstudio/templates/project/techreport_html_resources/assets/style.css | 272 inst/rstudio/templates/project/techreport_html_resources/assets/style.html | 10 inst/rstudio/templates/project/techreport_html_resources/bib/refs.bib | 144 inst/rstudio/templates/project/techreport_html_resources/csl/apa.csl | 3832 +++++----- inst/rstudio/templates/project/techreport_html_resources/front-matter/preface-html.Rmd | 10 inst/rstudio/templates/project/techreport_html_resources/front-matter/preface-latex.Rmd | 24 inst/rstudio/templates/project/techreport_html_resources/index.Rmd | 278 inst/rstudio/templates/project/techreport_pdf.dcf | 8 inst/rstudio/templates/project/techreport_pdf_resources/_bookdown.yml | 4 inst/rstudio/templates/project/techreport_pdf_resources/bib/packages.bib |only inst/rstudio/templates/project/techreport_pdf_resources/bib/refs.bib | 144 inst/rstudio/templates/project/techreport_pdf_resources/csl/apa.csl | 3832 +++++----- inst/rstudio/templates/project/techreport_pdf_resources/front-matter/preface.Rmd | 24 inst/rstudio/templates/project/techreport_pdf_resources/index.Rmd | 120 inst/rstudio/templates/project/topicguide_docx.dcf | 8 inst/rstudio/templates/project/topicguide_docx_resources/_bookdown.yml | 10 inst/rstudio/templates/project/topicguide_docx_resources/bib/refs.bib | 144 inst/rstudio/templates/project/topicguide_docx_resources/csl/apa.csl | 3832 +++++----- inst/rstudio/templates/project/topicguide_docx_resources/index.Rmd | 82 inst/rstudio/templates/project/topicguide_pdf.dcf | 8 inst/rstudio/templates/project/topicguide_pdf_resources/_bookdown.yml | 4 inst/rstudio/templates/project/topicguide_pdf_resources/bib/refs.bib | 144 inst/rstudio/templates/project/topicguide_pdf_resources/csl/apa.csl | 3832 +++++----- inst/rstudio/templates/project/topicguide_pdf_resources/index.Rmd | 100 man/ArialNarrow.Rd | 32 man/apa_words.Rd | 52 man/append_summary.Rd | 70 man/combine_n_pct.Rd | 74 man/dlm_ll_info.Rd | 48 man/dlmalias.Rd | 70 man/figures/logo.svg | 846 +- man/fmt_italic.Rd | 52 man/fmt_kbl.Rd | 146 man/fmt_kbl_header.Rd | 86 man/fmt_table.Rd | 124 man/formatting.Rd | 270 man/ggsave2.Rd | 143 man/inc.Rd | 48 man/measr_pdf.Rd | 46 man/only_if.Rd | 52 man/padding.Rd | 162 man/palette_atlas.Rd | 44 man/palette_lcrost.Rd | 42 man/palette_okabeito.Rd | 46 man/pipe.Rd | 30 man/rat_cap_words.Rd | 54 man/ratlas-ggproto.Rd | 30 man/ratlas-package.Rd | 82 man/reexports.Rd | 38 man/scale_atlas.Rd | 76 man/scale_lcrost.Rd | 78 man/scale_okabeito.Rd | 76 man/set_theme.Rd | 78 man/slides_html.Rd | 46 man/techreport_gitbook.Rd | 46 man/techreport_pdf.Rd | 50 man/theme_atlas.Rd | 169 man/topicguide_docx.Rd | 46 man/topicguide_pdf.Rd | 46 man/topicguide_rdocx.Rd | 46 man/update_geom_font_defaults.Rd | 54 tests/figs/deps.txt | 6 tests/figs/test-atlas-color-scales/atlas-alpha.svg | 136 tests/figs/test-atlas-color-scales/atlas-color.svg | 150 tests/figs/test-atlas-color-scales/atlas-darken.svg | 136 tests/figs/test-atlas-color-scales/atlas-fill.svg | 136 tests/figs/test-atlas-color-scales/atlas-lighten.svg | 136 tests/figs/test-lcrost-color-scales/lcrost-alpha.svg | 136 tests/figs/test-lcrost-color-scales/lcrost-color.svg | 150 tests/figs/test-lcrost-color-scales/lcrost-darken.svg | 136 tests/figs/test-lcrost-color-scales/lcrost-fill.svg | 136 tests/figs/test-lcrost-color-scales/lcrost-lighten.svg | 136 tests/figs/test-okabeito-color-scales/okabeito-alpha.svg | 136 tests/figs/test-okabeito-color-scales/okabeito-color.svg | 150 tests/figs/test-okabeito-color-scales/okabeito-darken.svg | 136 tests/figs/test-okabeito-color-scales/okabeito-fill.svg | 136 tests/figs/test-okabeito-color-scales/okabeito-lighten.svg | 136 tests/figs/test-set-theme/an-cividis.svg | 136 tests/figs/test-set-theme/an-ggplot2-c.svg | 136 tests/figs/test-set-theme/an-ggplot2.svg | 164 tests/figs/test-set-theme/an-viridis.svg | 136 tests/figs/test-set-theme/ms-atlas.svg | 164 tests/figs/test-set-theme/ms-inferno.svg | 136 tests/figs/test-set-theme/ms-magma.svg | 136 tests/figs/test-set-theme/ms-okabeito.svg | 164 tests/figs/test-set-theme/ms-plasma.svg | 136 tests/figs/test-stat-bin/bins30-bound0.svg | 412 - tests/figs/test-stat-bin/no-color-hist.svg | 474 - tests/figs/test-stat-bin/one-bin.svg | 322 tests/figs/test-stat-bin/trimmed-hist-bound0.svg | 442 - tests/figs/test-stat-bin/trimmed-hist-center0.svg | 474 - tests/figs/test-themes/theme-atlas.svg | 150 tests/spelling.R | 8 tests/testthat.R | 8 tests/testthat/_snaps/atlas-color-scales.md |only tests/testthat/_snaps/atlas-color-scales/atlas-alpha.svg | 147 tests/testthat/_snaps/atlas-color-scales/atlas-color.svg | 161 tests/testthat/_snaps/atlas-color-scales/atlas-darken.svg | 147 tests/testthat/_snaps/atlas-color-scales/atlas-fill.svg | 147 tests/testthat/_snaps/atlas-color-scales/atlas-lighten.svg | 147 tests/testthat/_snaps/format-text.md | 642 - tests/testthat/_snaps/lcrost-color-scales.md |only tests/testthat/_snaps/lcrost-color-scales/lcrost-alpha.svg | 147 tests/testthat/_snaps/lcrost-color-scales/lcrost-color.svg | 161 tests/testthat/_snaps/lcrost-color-scales/lcrost-darken.svg | 147 tests/testthat/_snaps/lcrost-color-scales/lcrost-fill.svg | 147 tests/testthat/_snaps/lcrost-color-scales/lcrost-lighten.svg | 147 tests/testthat/_snaps/okabeito-color-scales.md |only tests/testthat/_snaps/okabeito-color-scales/okabeito-alpha.svg | 147 tests/testthat/_snaps/okabeito-color-scales/okabeito-color.svg | 161 tests/testthat/_snaps/okabeito-color-scales/okabeito-darken.svg | 147 tests/testthat/_snaps/okabeito-color-scales/okabeito-fill.svg | 147 tests/testthat/_snaps/okabeito-color-scales/okabeito-lighten.svg | 147 tests/testthat/_snaps/set-theme/an-atlas.svg | 177 tests/testthat/_snaps/set-theme/an-cividis.svg | 149 tests/testthat/_snaps/set-theme/an-ggplot2-c.svg | 149 tests/testthat/_snaps/set-theme/an-ggplot2.svg | 177 tests/testthat/_snaps/set-theme/an-inferno.svg | 149 tests/testthat/_snaps/set-theme/an-magma.svg | 149 tests/testthat/_snaps/set-theme/an-okabeito.svg | 177 tests/testthat/_snaps/set-theme/an-plasma.svg | 149 tests/testthat/_snaps/set-theme/an-viridis.svg | 149 tests/testthat/_snaps/stat-bin/bins30-bound0.svg | 415 - tests/testthat/_snaps/stat-bin/no-color-hist.svg | 477 - tests/testthat/_snaps/stat-bin/one-bin.svg | 325 tests/testthat/_snaps/stat-bin/trimmed-hist-bound0.svg | 445 - tests/testthat/_snaps/stat-bin/trimmed-hist-center0.svg | 477 - tests/testthat/_snaps/themes/theme-atlas.svg | 161 tests/testthat/helper.R | 120 tests/testthat/test-atlas-color-scales.R | 73 tests/testthat/test-data-checks.R | 276 tests/testthat/test-format-text.R | 138 tests/testthat/test-formatting.R | 342 tests/testthat/test-hook-plot-rat.R | 94 tests/testthat/test-lcrost-color-scales.R | 73 tests/testthat/test-misc-manipulation.R | 100 tests/testthat/test-okabeito-color-scales.R | 73 tests/testthat/test-rat-cap-words.R | 42 tests/testthat/test-render.R | 146 tests/testthat/test-save-plot.R | 60 tests/testthat/test-set-theme.R | 367 tests/testthat/test-skeleton.R | 161 tests/testthat/test-stat-bin.R | 152 tests/testthat/test-theme-atlas.R | 101 tests/testthat/test-themes.R | 26 vignettes/bib/apa.csl | 3428 ++++---- vignettes/bib/example-bib.bib | 36 vignettes/bib/packages.bib | 414 - vignettes/children/chunk-options.txt | 50 vignettes/plotting.Rmd | 625 - vignettes/report-writing.Rmd | 692 - 212 files changed, 30331 insertions(+), 30788 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-14 2.6.1
2023-06-30 2.6.0
2022-07-19 2.5.0
2022-01-25 2.4.0
2021-11-17 2.3.0
2021-09-02 2.2.0
2021-08-16 2.1.2
2021-08-05 2.1.1
2020-11-16 2.0.3
2020-11-09 2.0.2
2020-11-06 2.0.1
2020-11-05 2.0.0
2020-10-16 1.0.0
2020-09-29 0.1.0
Title: Rapid Manipulation of the Variant Call Format (VCF)
Description: The 'vcfpp.h' (<https://github.com/Zilong-Li/vcfpp>) provides an easy-to-use 'C++' 'API' of 'htslib', offering full functionality for manipulating Variant Call Format (VCF) files. The 'vcfppR' package serves as the R bindings of the 'vcfpp.h' library, enabling rapid processing of both compressed and uncompressed VCF files. Explore a range of powerful features for efficient VCF data manipulation.
Author: Zilong Li [aut, cre] ,
Bonfield, James K and Marshall, John and Danecek, Petr and Li, Heng and
Ohan, Valeriu and Whitwham, Andrew and Keane, Thomas and Davies,
Robert M [cph]
Maintainer: Zilong Li <zilong.dk@gmail.com>
Diff between vcfppR versions 0.7.6 dated 2025-03-31 and 0.8.0 dated 2025-07-02
vcfppR-0.7.6/vcfppR/src/Makevars.win |only vcfppR-0.7.6/vcfppR/src/htslib-1.21/config.log |only vcfppR-0.8.0/vcfppR/DESCRIPTION | 8 vcfppR-0.8.0/vcfppR/MD5 | 51 - vcfppR-0.8.0/vcfppR/NAMESPACE | 1 vcfppR-0.8.0/vcfppR/NEWS.md | 3 vcfppR-0.8.0/vcfppR/R/RcppExports.R | 4 vcfppR-0.8.0/vcfppR/R/vcf-compare.R | 3 vcfppR-0.8.0/vcfppR/R/vcf-info.R |only vcfppR-0.8.0/vcfppR/R/vcf-tables.R | 19 vcfppR-0.8.0/vcfppR/README.md | 4 vcfppR-0.8.0/vcfppR/build/vignette.rds |binary vcfppR-0.8.0/vcfppR/cleanup.win | 2 vcfppR-0.8.0/vcfppR/configure | 45 - vcfppR-0.8.0/vcfppR/configure.win | 47 + vcfppR-0.8.0/vcfppR/inst/doc/concordance-of-two-vcf-files.Rmd | 19 vcfppR-0.8.0/vcfppR/inst/doc/concordance-of-two-vcf-files.html | 25 vcfppR-0.8.0/vcfppR/inst/include/vcfpp.h | 387 +++++----- vcfppR-0.8.0/vcfppR/man/vcfcomp.Rd | 3 vcfppR-0.8.0/vcfppR/man/vcfinfo.Rd |only vcfppR-0.8.0/vcfppR/man/vcftable.Rd | 7 vcfppR-0.8.0/vcfppR/src/Makevars.in |only vcfppR-0.8.0/vcfppR/src/Makevars.win.in |only vcfppR-0.8.0/vcfppR/src/RcppExports.cpp | 22 vcfppR-0.8.0/vcfppR/src/htslib-1.21/config.mk | 2 vcfppR-0.8.0/vcfppR/src/htslib-1.21/config.status | 8 vcfppR-0.8.0/vcfppR/src/vcf-reader.cpp | 9 vcfppR-0.8.0/vcfppR/src/vcf-table.cpp | 72 + vcfppR-0.8.0/vcfppR/tests/testthat/test-vcf-info.R |only vcfppR-0.8.0/vcfppR/vignettes/concordance-of-two-vcf-files.Rmd | 19 30 files changed, 496 insertions(+), 264 deletions(-)
Title: Justifying Alpha Levels for Hypothesis Tests
Description: Functions to justify alpha levels for statistical hypothesis tests by avoiding Lindley's paradox, or by minimizing or balancing error rates. For more information about the package please read the following: Maier & Lakens (2021) <doi:10.31234/osf.io/ts4r6>).
Author: Maximilian Maier [aut, cre],
Daniel Lakens [aut]
Maintainer: Maximilian Maier <maximilianmaier0401@gmail.com>
Diff between JustifyAlpha versions 0.1.1 dated 2021-09-15 and 0.1.2 dated 2025-07-02
DESCRIPTION | 15 MD5 | 22 R/minimize_balance_alpha.R | 6 R/optimal_sample.R | 5 build/vignette.rds |binary inst/CITATION | 5 inst/doc/Introduction_to_JustifyAlpha.R | 38 - inst/doc/Introduction_to_JustifyAlpha.Rmd | 2 inst/doc/Introduction_to_JustifyAlpha.html | 878 +++++++++++++++++++++-------- inst/shiny-examples/shiny.R | 18 man/optimal_alpha.Rd | 2 vignettes/Introduction_to_JustifyAlpha.Rmd | 2 12 files changed, 733 insertions(+), 260 deletions(-)
Title: Population Fisher Information Matrix
Description: Evaluate or optimize designs for nonlinear mixed effects models using the Fisher Information matrix. Methods used in the package refer to
Mentré F, Mallet A, Baccar D (1997) <doi:10.1093/biomet/84.2.429>,
Retout S, Comets E, Samson A, Mentré F (2007) <doi:10.1002/sim.2910>,
Bazzoli C, Retout S, Mentré F (2009) <doi:10.1002/sim.3573>,
Le Nagard H, Chao L, Tenaillon O (2011) <doi:10.1186/1471-2148-11-326>,
Combes FP, Retout S, Frey N, Mentré F (2013) <doi:10.1007/s11095-013-1079-3> and
Seurat J, Tang Y, Mentré F, Nguyen TT (2021) <doi:10.1016/j.cmpb.2021.106126>.
Author: Romain Leroux [aut, cre] ,
France Mentre [aut] ,
Jeremy Seurat [ctb]
Maintainer: Romain Leroux <romainlerouxPFIM@gmail.com>
Diff between PFIM versions 6.1 dated 2024-10-23 and 7.0 dated 2025-07-02
PFIM-6.1/PFIM/R/GenericMethods.R |only PFIM-6.1/PFIM/R/LibraryOfPKPDModels.R |only PFIM-6.1/PFIM/R/ModelAnalyticBolus.R |only PFIM-6.1/PFIM/R/ModelAnalyticBolusSteadyState.R |only PFIM-6.1/PFIM/R/ModelBolus.R |only PFIM-6.1/PFIM/R/ModelODEInfusionDoseInEquations.R |only PFIM-6.1/PFIM/R/OptimizationAlgorithm.R |only PFIM-6.1/PFIM/R/PlotEvaluation.R |only PFIM-6.1/PFIM/inst/report |only PFIM-6.1/PFIM/inst/rmarkdown/templates/skeleton/templateEvaluationBayesianFim.Rmd |only PFIM-6.1/PFIM/inst/rmarkdown/templates/skeleton/templateEvaluationIndividualFim.Rmd |only PFIM-6.1/PFIM/inst/rmarkdown/templates/skeleton/templateEvaluationPopulationFim.Rmd |only PFIM-6.1/PFIM/inst/rmarkdown/templates/skeleton/template_FedorovAlgorithm.Rmd |only PFIM-6.1/PFIM/inst/rmarkdown/templates/skeleton/template_PGBOAlgorithm.Rmd |only PFIM-6.1/PFIM/inst/rmarkdown/templates/skeleton/template_PSOAlgorithm.Rmd |only PFIM-6.1/PFIM/inst/rmarkdown/templates/skeleton/template_SimplexAlgorithm.Rmd |only PFIM-6.1/PFIM/inst/rmarkdown/templates/skeleton/template_evaluation.Rmd |only PFIM-6.1/PFIM/inst/rmarkdown/templates/skeleton/template_multiplicativeAlgorithm.Rmd |only PFIM-6.1/PFIM/inst/rmarkdown/templates/template.yaml |only PFIM-6.1/PFIM/man/Administration-class.Rd |only PFIM-6.1/PFIM/man/AdministrationConstraints-class.Rd |only PFIM-6.1/PFIM/man/Arm-class.Rd |only PFIM-6.1/PFIM/man/BayesianFim-class.Rd |only PFIM-6.1/PFIM/man/Combined1-class.Rd |only PFIM-6.1/PFIM/man/Constant-class.Rd |only PFIM-6.1/PFIM/man/Design-class.Rd |only PFIM-6.1/PFIM/man/Distribution-class.Rd |only PFIM-6.1/PFIM/man/EvaluateArm.Rd |only PFIM-6.1/PFIM/man/EvaluateDesign.Rd |only PFIM-6.1/PFIM/man/EvaluateErrorModelDerivatives.Rd |only PFIM-6.1/PFIM/man/EvaluateFisherMatrix.Rd |only PFIM-6.1/PFIM/man/EvaluateModel.Rd |only PFIM-6.1/PFIM/man/EvaluateModelGradient.Rd |only PFIM-6.1/PFIM/man/EvaluateVarianceFIM.Rd |only PFIM-6.1/PFIM/man/EvaluateVarianceModel.Rd |only PFIM-6.1/PFIM/man/Evaluation-class.Rd |only PFIM-6.1/PFIM/man/FedorovWynnAlgorithm-class.Rd |only PFIM-6.1/PFIM/man/Fim-class.Rd |only PFIM-6.1/PFIM/man/IndividualFim-class.Rd |only PFIM-6.1/PFIM/man/LibraryOfModels-class.Rd |only PFIM-6.1/PFIM/man/LibraryOfPKPDModels-class.Rd |only PFIM-6.1/PFIM/man/LogNormal-class.Rd |only PFIM-6.1/PFIM/man/Model-class.Rd |only PFIM-6.1/PFIM/man/ModelAnalytic-class.Rd |only PFIM-6.1/PFIM/man/ModelAnalyticBolus-class.Rd |only PFIM-6.1/PFIM/man/ModelAnalyticBolusSteadyState-class.Rd |only PFIM-6.1/PFIM/man/ModelAnalyticInfusion-class.Rd |only PFIM-6.1/PFIM/man/ModelAnalyticInfusionSteadyState-class.Rd |only PFIM-6.1/PFIM/man/ModelAnalyticSteadyState-class.Rd |only PFIM-6.1/PFIM/man/ModelBolus-class.Rd |only PFIM-6.1/PFIM/man/ModelError-class.Rd |only PFIM-6.1/PFIM/man/ModelInfusion-class.Rd |only PFIM-6.1/PFIM/man/ModelODE-class.Rd |only PFIM-6.1/PFIM/man/ModelODEDoseInEquations-class.Rd |only PFIM-6.1/PFIM/man/ModelODEDoseNotInEquations-class.Rd |only PFIM-6.1/PFIM/man/ModelODEInfusion-class.Rd |only PFIM-6.1/PFIM/man/ModelODEInfusionDoseInEquations-class.Rd |only PFIM-6.1/PFIM/man/ModelParameter-class.Rd |only PFIM-6.1/PFIM/man/MultiplicativeAlgorithm-class.Rd |only PFIM-6.1/PFIM/man/Normal-class.Rd |only PFIM-6.1/PFIM/man/Optimization-class.Rd |only PFIM-6.1/PFIM/man/OptimizationAlgorithm-class.Rd |only PFIM-6.1/PFIM/man/PFIMProject-class.Rd |only PFIM-6.1/PFIM/man/PGBOAlgorithm-class.Rd |only PFIM-6.1/PFIM/man/PSOAlgorithm-class.Rd |only PFIM-6.1/PFIM/man/PlotEvaluation-class.Rd |only PFIM-6.1/PFIM/man/PopulationFim-class.Rd |only PFIM-6.1/PFIM/man/Proportional-class.Rd |only PFIM-6.1/PFIM/man/SamplingTimeConstraints-class.Rd |only PFIM-6.1/PFIM/man/SamplingTimes-class.Rd |only PFIM-6.1/PFIM/man/SimplexAlgorithm-class.Rd |only PFIM-6.1/PFIM/man/addModel.Rd |only PFIM-6.1/PFIM/man/addModels.Rd |only PFIM-6.1/PFIM/man/checkSamplingTimeConstraintsForContinuousOptimization.Rd |only PFIM-6.1/PFIM/man/dataForArmEvaluation.Rd |only PFIM-6.1/PFIM/man/defineModel.Rd |only PFIM-6.1/PFIM/man/defineModelEquationsFromStringToFunction.Rd |only PFIM-6.1/PFIM/man/defineModelFromLibraryOfModels.Rd |only PFIM-6.1/PFIM/man/defineModelUserDefined.Rd |only PFIM-6.1/PFIM/man/fisher.simplex.Rd |only PFIM-6.1/PFIM/man/generateTables.Rd |only PFIM-6.1/PFIM/man/getAdjustedGradient.Rd |only PFIM-6.1/PFIM/man/getAdministration.Rd |only PFIM-6.1/PFIM/man/getAdministrationConstraint.Rd |only PFIM-6.1/PFIM/man/getAdministrations.Rd |only PFIM-6.1/PFIM/man/getAdministrationsConstraints.Rd |only PFIM-6.1/PFIM/man/getArms.Rd |only PFIM-6.1/PFIM/man/getColumnAndParametersNamesFIM.Rd |only PFIM-6.1/PFIM/man/getColumnAndParametersNamesFIMInLatex.Rd |only PFIM-6.1/PFIM/man/getConditionNumberFixedEffects.Rd |only PFIM-6.1/PFIM/man/getConditionNumberVarianceEffects.Rd |only PFIM-6.1/PFIM/man/getContent.Rd |only PFIM-6.1/PFIM/man/getDataForArmEvaluation.Rd |only PFIM-6.1/PFIM/man/getDataFrameResults.Rd |only PFIM-6.1/PFIM/man/getDelta.Rd |only PFIM-6.1/PFIM/man/getDerivatives.Rd |only PFIM-6.1/PFIM/man/getDescription.Rd |only PFIM-6.1/PFIM/man/getDesigns.Rd |only PFIM-6.1/PFIM/man/getDistribution.Rd |only PFIM-6.1/PFIM/man/getDose.Rd |only PFIM-6.1/PFIM/man/getEigenValues.Rd |only PFIM-6.1/PFIM/man/getElementaryProtocols.Rd |only PFIM-6.1/PFIM/man/getEquation.Rd |only PFIM-6.1/PFIM/man/getEquations.Rd |only PFIM-6.1/PFIM/man/getEquationsAfterInfusion.Rd |only PFIM-6.1/PFIM/man/getEquationsDuringInfusion.Rd |only PFIM-6.1/PFIM/man/getEvaluationFIMResults.Rd |only PFIM-6.1/PFIM/man/getEvaluationInitialDesignResults.Rd |only PFIM-6.1/PFIM/man/getFixedEffects.Rd |only PFIM-6.1/PFIM/man/getFixedMu.Rd |only PFIM-6.1/PFIM/man/getFixedOmega.Rd |only PFIM-6.1/PFIM/man/getFixedParameters.Rd |only PFIM-6.1/PFIM/man/getFixedTimes.Rd |only PFIM-6.1/PFIM/man/getInitialConditions.Rd |only PFIM-6.1/PFIM/man/getIterationAndCriteria.Rd |only PFIM-6.1/PFIM/man/getLambda.Rd |only PFIM-6.1/PFIM/man/getLibraryPDModels.Rd |only PFIM-6.1/PFIM/man/getLibraryPKModels.Rd |only PFIM-6.1/PFIM/man/getMinSampling.Rd |only PFIM-6.1/PFIM/man/getModel.Rd |only PFIM-6.1/PFIM/man/getModelEquations.Rd |only PFIM-6.1/PFIM/man/getModelError.Rd |only PFIM-6.1/PFIM/man/getModelErrorParametersValues.Rd |only PFIM-6.1/PFIM/man/getModelFromLibrary.Rd |only PFIM-6.1/PFIM/man/getModelParameters.Rd |only PFIM-6.1/PFIM/man/getModelParametersValues.Rd |only PFIM-6.1/PFIM/man/getMu.Rd |only PFIM-6.1/PFIM/man/getName.Rd |only PFIM-6.1/PFIM/man/getNames.Rd |only PFIM-6.1/PFIM/man/getNumberOfArms.Rd |only PFIM-6.1/PFIM/man/getNumberOfIterations.Rd |only PFIM-6.1/PFIM/man/getNumberOfParameters.Rd |only PFIM-6.1/PFIM/man/getNumberOfTimesByWindows.Rd |only PFIM-6.1/PFIM/man/getNumberOfsamplingsOptimisable.Rd |only PFIM-6.1/PFIM/man/getOdeSolverParameters.Rd |only PFIM-6.1/PFIM/man/getOmega.Rd |only PFIM-6.1/PFIM/man/getOptimalDesign.Rd |only PFIM-6.1/PFIM/man/getOptimalFrequencies.Rd |only PFIM-6.1/PFIM/man/getOptimalWeights.Rd |only PFIM-6.1/PFIM/man/getOptimizationResults.Rd |only PFIM-6.1/PFIM/man/getOptimizer.Rd |only PFIM-6.1/PFIM/man/getOptimizerParameters.Rd |only PFIM-6.1/PFIM/man/getOutcome.Rd |only PFIM-6.1/PFIM/man/getOutcomes.Rd |only PFIM-6.1/PFIM/man/getOutcomesEvaluation.Rd |only PFIM-6.1/PFIM/man/getOutcomesForEvaluation.Rd |only PFIM-6.1/PFIM/man/getOutcomesGradient.Rd |only PFIM-6.1/PFIM/man/getPDModel.Rd |only PFIM-6.1/PFIM/man/getPKModel.Rd |only PFIM-6.1/PFIM/man/getPKPDModel.Rd |only PFIM-6.1/PFIM/man/getParameters.Rd |only PFIM-6.1/PFIM/man/getPlotOptions.Rd |only PFIM-6.1/PFIM/man/getProportionsOfSubjects.Rd |only PFIM-6.1/PFIM/man/getSamplingTime.Rd |only PFIM-6.1/PFIM/man/getSamplingTimeConstraint.Rd |only PFIM-6.1/PFIM/man/getSamplingTimes.Rd |only PFIM-6.1/PFIM/man/getSamplingTimesConstraints.Rd |only PFIM-6.1/PFIM/man/getSamplings.Rd |only PFIM-6.1/PFIM/man/getSamplingsWindows.Rd |only PFIM-6.1/PFIM/man/getSigmaInter.Rd |only PFIM-6.1/PFIM/man/getSigmaSlope.Rd |only PFIM-6.1/PFIM/man/getSize.Rd |only PFIM-6.1/PFIM/man/getTau.Rd |only PFIM-6.1/PFIM/man/getTimeDose.Rd |only PFIM-6.1/PFIM/man/getTinf.Rd |only PFIM-6.1/PFIM/man/getVariables.Rd |only PFIM-6.1/PFIM/man/getVarianceEffects.Rd |only PFIM-6.1/PFIM/man/getWeightThreshold.Rd |only PFIM-6.1/PFIM/man/getcError.Rd |only PFIM-6.1/PFIM/man/initialize-Administration-method.Rd |only PFIM-6.1/PFIM/man/initialize-AdministrationConstraints-method.Rd |only PFIM-6.1/PFIM/man/initialize-Arm-method.Rd |only PFIM-6.1/PFIM/man/initialize-Combined1-method.Rd |only PFIM-6.1/PFIM/man/initialize-Constant-method.Rd |only PFIM-6.1/PFIM/man/initialize-Design-method.Rd |only PFIM-6.1/PFIM/man/initialize-Distribution-method.Rd |only PFIM-6.1/PFIM/man/initialize-Evaluation-method.Rd |only PFIM-6.1/PFIM/man/initialize-FedorovWynnAlgorithm-method.Rd |only PFIM-6.1/PFIM/man/initialize-Fim-method.Rd |only PFIM-6.1/PFIM/man/initialize-LibraryOfModels-method.Rd |only PFIM-6.1/PFIM/man/initialize-LibraryOfPKPDModels-method.Rd |only PFIM-6.1/PFIM/man/initialize-LogNormal-method.Rd |only PFIM-6.1/PFIM/man/initialize-Model-method.Rd |only PFIM-6.1/PFIM/man/initialize-ModelAnalytic-method.Rd |only PFIM-6.1/PFIM/man/initialize-ModelAnalyticBolus-method.Rd |only PFIM-6.1/PFIM/man/initialize-ModelAnalyticBolusSteadyState-method.Rd |only PFIM-6.1/PFIM/man/initialize-ModelAnalyticInfusion-method.Rd |only PFIM-6.1/PFIM/man/initialize-ModelAnalyticInfusionSteadyState-method.Rd |only PFIM-6.1/PFIM/man/initialize-ModelAnalyticSteadyState-method.Rd |only PFIM-6.1/PFIM/man/initialize-ModelBolus-method.Rd |only PFIM-6.1/PFIM/man/initialize-ModelError-method.Rd |only PFIM-6.1/PFIM/man/initialize-ModelInfusion-method.Rd |only PFIM-6.1/PFIM/man/initialize-ModelParameter-method.Rd |only PFIM-6.1/PFIM/man/initialize-MultiplicativeAlgorithm-method.Rd |only PFIM-6.1/PFIM/man/initialize-Normal-method.Rd |only PFIM-6.1/PFIM/man/initialize-Optimization-method.Rd |only PFIM-6.1/PFIM/man/initialize-OptimizationAlgorithm-method.Rd |only PFIM-6.1/PFIM/man/initialize-PFIMProject-method.Rd |only PFIM-6.1/PFIM/man/initialize-PGBOAlgorithm-method.Rd |only PFIM-6.1/PFIM/man/initialize-PSOAlgorithm-method.Rd |only PFIM-6.1/PFIM/man/initialize-Proportional-method.Rd |only PFIM-6.1/PFIM/man/initialize-SamplingTimeConstraints-method.Rd |only PFIM-6.1/PFIM/man/initialize-SamplingTimes-method.Rd |only PFIM-6.1/PFIM/man/initialize-SimplexAlgorithm-method.Rd |only PFIM-6.1/PFIM/man/isDoseInEquations.Rd |only PFIM-6.1/PFIM/man/isModelAnalytic.Rd |only PFIM-6.1/PFIM/man/isModelBolus.Rd |only PFIM-6.1/PFIM/man/isModelInfusion.Rd |only PFIM-6.1/PFIM/man/isModelODE.Rd |only PFIM-6.1/PFIM/man/isModelSteadyState.Rd |only PFIM-6.1/PFIM/man/optimize.Rd |only PFIM-6.1/PFIM/man/parametersForComputingGradient.Rd |only PFIM-6.1/PFIM/man/plotOutcomesEvaluation.Rd |only PFIM-6.1/PFIM/man/plotOutcomesGradient.Rd |only PFIM-6.1/PFIM/man/plotSensitivityIndice.Rd |only PFIM-6.1/PFIM/man/reportTablesAdministration.Rd |only PFIM-6.1/PFIM/man/reportTablesDesign.Rd |only PFIM-6.1/PFIM/man/reportTablesFIM.Rd |only PFIM-6.1/PFIM/man/reportTablesModelError.Rd |only PFIM-6.1/PFIM/man/reportTablesModelParameters.Rd |only PFIM-6.1/PFIM/man/reportTablesPlot.Rd |only PFIM-6.1/PFIM/man/reportTablesSamplingConstraints.Rd |only PFIM-6.1/PFIM/man/resizeFisherMatrix.Rd |only PFIM-6.1/PFIM/man/setAdministrations.Rd |only PFIM-6.1/PFIM/man/setArm.Rd |only PFIM-6.1/PFIM/man/setArms.Rd |only PFIM-6.1/PFIM/man/setContent.Rd |only PFIM-6.1/PFIM/man/setDataForArmEvaluation.Rd |only PFIM-6.1/PFIM/man/setDataForModelEvaluation.Rd |only PFIM-6.1/PFIM/man/setDerivatives.Rd |only PFIM-6.1/PFIM/man/setDescription.Rd |only PFIM-6.1/PFIM/man/setDesigns.Rd |only PFIM-6.1/PFIM/man/setDistribution.Rd |only PFIM-6.1/PFIM/man/setDose.Rd |only PFIM-6.1/PFIM/man/setEquation.Rd |only PFIM-6.1/PFIM/man/setEquations.Rd |only PFIM-6.1/PFIM/man/setEquationsAfterInfusion.Rd |only PFIM-6.1/PFIM/man/setEquationsDuringInfusion.Rd |only PFIM-6.1/PFIM/man/setEvaluationFIMResults.Rd |only PFIM-6.1/PFIM/man/setEvaluationInitialDesignResults.Rd |only PFIM-6.1/PFIM/man/setFim.Rd |only PFIM-6.1/PFIM/man/setFimTypeToString.Rd |only PFIM-6.1/PFIM/man/setFisherMatrix.Rd |only PFIM-6.1/PFIM/man/setFixedEffects.Rd |only PFIM-6.1/PFIM/man/setFixedMu.Rd |only PFIM-6.1/PFIM/man/setFixedOmega.Rd |only PFIM-6.1/PFIM/man/setInitialConditions.Rd |only PFIM-6.1/PFIM/man/setIterationAndCriteria.Rd |only PFIM-6.1/PFIM/man/setModel.Rd |only PFIM-6.1/PFIM/man/setModelError.Rd |only PFIM-6.1/PFIM/man/setModelFromLibrary.Rd |only PFIM-6.1/PFIM/man/setMu.Rd |only PFIM-6.1/PFIM/man/setName.Rd |only PFIM-6.1/PFIM/man/setNumberOfArms.Rd |only PFIM-6.1/PFIM/man/setOdeSolverParameters.Rd |only PFIM-6.1/PFIM/man/setOmega.Rd |only PFIM-6.1/PFIM/man/setOptimalDesign.Rd |only PFIM-6.1/PFIM/man/setOptimalWeights.Rd |only PFIM-6.1/PFIM/man/setOptimizationResults.Rd |only PFIM-6.1/PFIM/man/setOutcome.Rd |only PFIM-6.1/PFIM/man/setOutcomes.Rd |only PFIM-6.1/PFIM/man/setOutcomesEvaluation.Rd |only PFIM-6.1/PFIM/man/setOutcomesForEvaluation.Rd |only PFIM-6.1/PFIM/man/setOutcomesGradient.Rd |only PFIM-6.1/PFIM/man/setParameters.Rd |only PFIM-6.1/PFIM/man/setSamplingTime.Rd |only PFIM-6.1/PFIM/man/setSamplingTimes.Rd |only PFIM-6.1/PFIM/man/setSamplingTimesConstraints.Rd |only PFIM-6.1/PFIM/man/setSamplings.Rd |only PFIM-6.1/PFIM/man/setShrinkage.Rd |only PFIM-6.1/PFIM/man/setSigmaInter.Rd |only PFIM-6.1/PFIM/man/setSigmaSlope.Rd |only PFIM-6.1/PFIM/man/setSize.Rd |only PFIM-6.1/PFIM/man/setTau.Rd |only PFIM-6.1/PFIM/man/setTimeDose.Rd |only PFIM-6.1/PFIM/man/setTinf.Rd |only PFIM-6.1/PFIM/man/setVarianceEffects.Rd |only PFIM-6.1/PFIM/man/setcError.Rd |only PFIM-6.1/PFIM/tests/testthat/test_PKModels-PFIM.R |only PFIM-6.1/PFIM/tests/testthat/test_PKPDModels-PFIM.R |only PFIM-7.0/PFIM/DESCRIPTION | 85 PFIM-7.0/PFIM/MD5 | 582 +-- PFIM-7.0/PFIM/NAMESPACE | 340 - PFIM-7.0/PFIM/NEWS.md |only PFIM-7.0/PFIM/R/Administration.R | 322 - PFIM-7.0/PFIM/R/AdministrationConstraints.R | 95 PFIM-7.0/PFIM/R/Arm.R | 1178 +++--- PFIM-7.0/PFIM/R/BayesianFim.R | 925 ++--- PFIM-7.0/PFIM/R/Combined1.R | 133 PFIM-7.0/PFIM/R/Constant.R | 138 PFIM-7.0/PFIM/R/Design.R | 1497 +------- PFIM-7.0/PFIM/R/Distribution.R | 180 - PFIM-7.0/PFIM/R/Evaluation.R | 1028 ++---- PFIM-7.0/PFIM/R/FedorovWynnAlgorithm.R | 677 +-- PFIM-7.0/PFIM/R/Fim.R | 594 --- PFIM-7.0/PFIM/R/IndividualFim.R | 1017 +++-- PFIM-7.0/PFIM/R/LibraryOfModels.R | 236 - PFIM-7.0/PFIM/R/LibraryOfPDModels.R | 219 - PFIM-7.0/PFIM/R/LibraryOfPKModels.R | 895 +---- PFIM-7.0/PFIM/R/LogNormal.R | 67 PFIM-7.0/PFIM/R/Model.R | 1705 +--------- PFIM-7.0/PFIM/R/ModelAnalytic.R | 1156 +----- PFIM-7.0/PFIM/R/ModelAnalyticInfusion.R | 1687 ++------- PFIM-7.0/PFIM/R/ModelAnalyticInfusionSteadyState.R | 905 ++--- PFIM-7.0/PFIM/R/ModelAnalyticSteadyState.R | 1120 +----- PFIM-7.0/PFIM/R/ModelError.R | 517 --- PFIM-7.0/PFIM/R/ModelInfusion.R | 194 - PFIM-7.0/PFIM/R/ModelODE.R | 59 PFIM-7.0/PFIM/R/ModelODEBolus.R | 748 +--- PFIM-7.0/PFIM/R/ModelODEDoseInEquations.R | 837 +--- PFIM-7.0/PFIM/R/ModelODEDoseNotInEquations.R | 701 +--- PFIM-7.0/PFIM/R/ModelODEInfusion.R | 60 PFIM-7.0/PFIM/R/ModelODEInfusionDoseInEquation.R |only PFIM-7.0/PFIM/R/ModelParameter.R | 354 -- PFIM-7.0/PFIM/R/MultiplicativeAlgorithm.R | 696 +--- PFIM-7.0/PFIM/R/Normal.R | 61 PFIM-7.0/PFIM/R/Optimization.R | 1551 +++------ PFIM-7.0/PFIM/R/PFIM-package.R | 667 --- PFIM-7.0/PFIM/R/PFIMProject.R | 524 +-- PFIM-7.0/PFIM/R/PGBOAlgorithm.R | 933 +---- PFIM-7.0/PFIM/R/PSOAlgorithm.R | 1066 ++---- PFIM-7.0/PFIM/R/PopulationFim.R | 1226 +++---- PFIM-7.0/PFIM/R/Proportional.R | 138 PFIM-7.0/PFIM/R/SamplingTimeConstraints.R | 551 --- PFIM-7.0/PFIM/R/SamplingTimes.R | 140 PFIM-7.0/PFIM/R/SimplexAlgorithm.R | 707 +--- PFIM-7.0/PFIM/R/zzz.R |only PFIM-7.0/PFIM/build/partial.rdb |binary PFIM-7.0/PFIM/build/vignette.rds |binary PFIM-7.0/PFIM/inst/CITATION |only PFIM-7.0/PFIM/inst/doc/Example01.R | 718 ++-- PFIM-7.0/PFIM/inst/doc/Example01.Rmd | 185 - PFIM-7.0/PFIM/inst/doc/Example01.html | 533 +-- PFIM-7.0/PFIM/inst/doc/Example02.R | 537 +-- PFIM-7.0/PFIM/inst/doc/Example02.Rmd | 209 - PFIM-7.0/PFIM/inst/doc/Example02.html | 441 +- PFIM-7.0/PFIM/inst/doc/LibraryOfModels.R | 143 PFIM-7.0/PFIM/inst/doc/LibraryOfModels.Rmd | 211 + PFIM-7.0/PFIM/inst/doc/LibraryOfModels.html | 316 + PFIM-7.0/PFIM/inst/rmarkdown/templates/skeleton/EvaluationBayesianFIM.Rmd |only PFIM-7.0/PFIM/inst/rmarkdown/templates/skeleton/EvaluationIndividualFIM.Rmd |only PFIM-7.0/PFIM/inst/rmarkdown/templates/skeleton/EvaluationPopulationFIM.Rmd |only PFIM-7.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationFedorovWynnAlgorithmBayesianFIM.Rmd |only PFIM-7.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationFedorovWynnAlgorithmIndividualFIM.Rmd |only PFIM-7.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationFedorovWynnAlgorithmPopulationFIM.Rmd |only PFIM-7.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationMultiplicativeAlgorithmBayesianFIM.Rmd |only PFIM-7.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationMultiplicativeAlgorithmIndividualFIM.Rmd |only PFIM-7.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationMultiplicativeAlgorithmPopulationFIM.Rmd |only PFIM-7.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationPGBOAlgorithmBayesianFIM.Rmd |only PFIM-7.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationPGBOAlgorithmIndividualFIM.Rmd |only PFIM-7.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationPGBOAlgorithmPopulationFIM.Rmd |only PFIM-7.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationPSOAlgorithmBayesianFIM.Rmd |only PFIM-7.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationPSOAlgorithmIndividualFIM.Rmd |only PFIM-7.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationPSOAlgorithmPopulationFIM.Rmd |only PFIM-7.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationSimplexAlgorithmBayesianFIM.Rmd |only PFIM-7.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationSimplexAlgorithmIndividualFIM.Rmd |only PFIM-7.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationSimplexAlgorithmPopulationFIM.Rmd |only PFIM-7.0/PFIM/man/Administration.Rd |only PFIM-7.0/PFIM/man/AdministrationConstraints.Rd |only PFIM-7.0/PFIM/man/Arm.Rd |only PFIM-7.0/PFIM/man/BayesianFim.Rd |only PFIM-7.0/PFIM/man/Combined1.Rd |only PFIM-7.0/PFIM/man/Constant.Rd |only PFIM-7.0/PFIM/man/Dcriterion.Rd |only PFIM-7.0/PFIM/man/Design.Rd |only PFIM-7.0/PFIM/man/Distribution.Rd |only PFIM-7.0/PFIM/man/Evaluation.Rd |only PFIM-7.0/PFIM/man/FedorovWynnAlgorithm.Rd |only PFIM-7.0/PFIM/man/FedorovWynnAlgorithm_Rcpp.Rd | 98 PFIM-7.0/PFIM/man/Fim.Rd |only PFIM-7.0/PFIM/man/IndividualFim.Rd |only PFIM-7.0/PFIM/man/LibraryOfModels.Rd |only PFIM-7.0/PFIM/man/LibraryOfPDModels.Rd | 27 PFIM-7.0/PFIM/man/LibraryOfPKModels.Rd | 27 PFIM-7.0/PFIM/man/Linear2BolusSingleDose_ClQV1V2.Rd |only PFIM-7.0/PFIM/man/Linear2BolusSingleDose_kk12k21V.Rd |only PFIM-7.0/PFIM/man/Linear2BolusSteadyState_ClQV1V2tau.Rd |only PFIM-7.0/PFIM/man/Linear2BolusSteadyState_kk12k21Vtau.Rd |only PFIM-7.0/PFIM/man/Linear2FirstOrderSingleDose_kaClQV1V2.Rd |only PFIM-7.0/PFIM/man/Linear2FirstOrderSingleDose_kakk12k21V.Rd |only PFIM-7.0/PFIM/man/Linear2FirstOrderSteadyState_kaClQV1V2tau.Rd |only PFIM-7.0/PFIM/man/Linear2FirstOrderSteadyState_kakk12k21Vtau.Rd |only PFIM-7.0/PFIM/man/Linear2InfusionSingleDose_ClQV1V2.Rd |only PFIM-7.0/PFIM/man/Linear2InfusionSingleDose_kk12k21V.Rd |only PFIM-7.0/PFIM/man/Linear2InfusionSteadyState_ClQV1V2tau.Rd |only PFIM-7.0/PFIM/man/Linear2InfusionSteadyState_kk12k21Vtau.Rd |only PFIM-7.0/PFIM/man/LogNormal.Rd |only PFIM-7.0/PFIM/man/Model.Rd |only PFIM-7.0/PFIM/man/ModelAnalytic.Rd |only PFIM-7.0/PFIM/man/ModelAnalyticInfusion.Rd |only PFIM-7.0/PFIM/man/ModelAnalyticInfusionSteadyState.Rd |only PFIM-7.0/PFIM/man/ModelAnalyticSteadyState.Rd |only PFIM-7.0/PFIM/man/ModelError.Rd |only PFIM-7.0/PFIM/man/ModelInfusion.Rd |only PFIM-7.0/PFIM/man/ModelODE.Rd |only PFIM-7.0/PFIM/man/ModelODEBolus.Rd |only PFIM-7.0/PFIM/man/ModelODEDoseInEquations.Rd |only PFIM-7.0/PFIM/man/ModelODEDoseNotInEquations.Rd |only PFIM-7.0/PFIM/man/ModelODEInfusion.Rd |only PFIM-7.0/PFIM/man/ModelODEInfusionDoseInEquation.Rd |only PFIM-7.0/PFIM/man/ModelParameter.Rd |only PFIM-7.0/PFIM/man/MultiplicativeAlgorithm.Rd |only PFIM-7.0/PFIM/man/MultiplicativeAlgorithm_Rcpp.Rd | 77 PFIM-7.0/PFIM/man/Normal.Rd |only PFIM-7.0/PFIM/man/Optimization.Rd |only PFIM-7.0/PFIM/man/PFIM-package.Rd | 659 --- PFIM-7.0/PFIM/man/PFIMProject.Rd |only PFIM-7.0/PFIM/man/PGBOAlgorithm.Rd |only PFIM-7.0/PFIM/man/PSOAlgorithm.Rd |only PFIM-7.0/PFIM/man/PopulationFim.Rd |only PFIM-7.0/PFIM/man/Proportional.Rd |only PFIM-7.0/PFIM/man/Report.Rd | 55 PFIM-7.0/PFIM/man/SamplingTimeConstraints.Rd |only PFIM-7.0/PFIM/man/SamplingTimes.Rd |only PFIM-7.0/PFIM/man/SimplexAlgorithm.Rd |only PFIM-7.0/PFIM/man/adjustGradient.Rd |only PFIM-7.0/PFIM/man/armAdministration.Rd |only PFIM-7.0/PFIM/man/checkSamplingTimeConstraintsForMetaheuristic.Rd |only PFIM-7.0/PFIM/man/checkValiditySamplingConstraint.Rd | 34 PFIM-7.0/PFIM/man/computeVMat.Rd | 42 PFIM-7.0/PFIM/man/constraintsTableForReport.Rd |only PFIM-7.0/PFIM/man/convertPKModelAnalyticToPKModelODE.Rd | 43 PFIM-7.0/PFIM/man/defineFim.Rd |only PFIM-7.0/PFIM/man/defineModelAdministration.Rd |only PFIM-7.0/PFIM/man/defineModelEquationsFromLibraryOfModel.Rd |only PFIM-7.0/PFIM/man/defineModelType.Rd | 36 PFIM-7.0/PFIM/man/defineModelWrapper.Rd |only PFIM-7.0/PFIM/man/defineOptimizationAlgorithm.Rd |only PFIM-7.0/PFIM/man/definePKModel.Rd | 70 PFIM-7.0/PFIM/man/definePKPDModel.Rd | 86 PFIM-7.0/PFIM/man/evaluateArm.Rd |only PFIM-7.0/PFIM/man/evaluateDesign.Rd |only PFIM-7.0/PFIM/man/evaluateErrorModelDerivatives.Rd |only PFIM-7.0/PFIM/man/evaluateFim.Rd |only PFIM-7.0/PFIM/man/evaluateInitialConditions.Rd |only PFIM-7.0/PFIM/man/evaluateModel.Rd |only PFIM-7.0/PFIM/man/evaluateModelGradient.Rd |only PFIM-7.0/PFIM/man/evaluateModelVariance.Rd |only PFIM-7.0/PFIM/man/evaluateVarianceFIM.Rd |only PFIM-7.0/PFIM/man/finiteDifferenceHessian.Rd |only PFIM-7.0/PFIM/man/fisherSimplex.Rd |only PFIM-7.0/PFIM/man/fun.amoeba.Rd | 63 PFIM-7.0/PFIM/man/generateDosesCombination.Rd |only PFIM-7.0/PFIM/man/generateFimsFromConstraints.Rd | 36 PFIM-7.0/PFIM/man/generateReportEvaluation.Rd | 84 PFIM-7.0/PFIM/man/generateReportOptimization.Rd | 141 PFIM-7.0/PFIM/man/generateSamplingTimesCombination.Rd |only PFIM-7.0/PFIM/man/generateSamplingsFromSamplingConstraints.Rd | 34 PFIM-7.0/PFIM/man/getArmConstraints.Rd |only PFIM-7.0/PFIM/man/getArmData.Rd |only PFIM-7.0/PFIM/man/getCorrelationMatrix.Rd | 45 PFIM-7.0/PFIM/man/getDcriterion.Rd | 45 PFIM-7.0/PFIM/man/getDeterminant.Rd | 45 PFIM-7.0/PFIM/man/getFim.Rd | 41 PFIM-7.0/PFIM/man/getFisherMatrix.Rd | 45 PFIM-7.0/PFIM/man/getListLastName.Rd |only PFIM-7.0/PFIM/man/getModelErrorData.Rd |only PFIM-7.0/PFIM/man/getModelParametersData.Rd |only PFIM-7.0/PFIM/man/getRSE.Rd | 53 PFIM-7.0/PFIM/man/getSE.Rd | 45 PFIM-7.0/PFIM/man/getSamplingData.Rd |only PFIM-7.0/PFIM/man/getShrinkage.Rd | 51 PFIM-7.0/PFIM/man/optimizeDesign.Rd |only PFIM-7.0/PFIM/man/plotEvaluation.Rd | 38 PFIM-7.0/PFIM/man/plotEvaluationResults.Rd |only PFIM-7.0/PFIM/man/plotEvaluationSI.Rd |only PFIM-7.0/PFIM/man/plotFrequencies.Rd | 38 PFIM-7.0/PFIM/man/plotFrequenciesFedorovWynnAlgorithm.Rd |only PFIM-7.0/PFIM/man/plotRSE.Rd | 42 PFIM-7.0/PFIM/man/plotRSEFIM.Rd |only PFIM-7.0/PFIM/man/plotSE.Rd | 42 PFIM-7.0/PFIM/man/plotSEFIM.Rd |only PFIM-7.0/PFIM/man/plotSensitivityIndices.Rd |only PFIM-7.0/PFIM/man/plotShrinkage.Rd | 38 PFIM-7.0/PFIM/man/plotWeights.Rd | 38 PFIM-7.0/PFIM/man/plotWeightsMultiplicativeAlgorithm.Rd |only PFIM-7.0/PFIM/man/processArmEvaluationResults.Rd |only PFIM-7.0/PFIM/man/processArmEvaluationSI.Rd |only PFIM-7.0/PFIM/man/replaceVariablesLibraryOfModels.Rd |only PFIM-7.0/PFIM/man/run.Rd | 43 PFIM-7.0/PFIM/man/setEvaluationFim.Rd |only PFIM-7.0/PFIM/man/setOptimalArms.Rd |only PFIM-7.0/PFIM/man/setSamplingConstraintForOptimization.Rd | 34 PFIM-7.0/PFIM/man/show.Rd | 71 PFIM-7.0/PFIM/man/showFIM.Rd |only PFIM-7.0/PFIM/man/tablesForReport.Rd |only PFIM-7.0/PFIM/man/updateSamplingTimes.Rd |only PFIM-7.0/PFIM/tests/testthat.R |only PFIM-7.0/PFIM/tests/testthat/test-example.R |only PFIM-7.0/PFIM/vignettes/Example01.Rmd | 185 - PFIM-7.0/PFIM/vignettes/Example02.Rmd | 209 - PFIM-7.0/PFIM/vignettes/LibraryOfModels.Rmd | 211 + 492 files changed, 11469 insertions(+), 23306 deletions(-)
Title: Unbiased Distances for Mixed-Type Data
Description: A comprehensive framework for calculating unbiased distances in datasets
containing mixed-type variables (numerical and categorical). The package implements
a general formulation that ensures multivariate additivity and commensurability,
meaning that variables contribute equally to the overall distance regardless of
their type, scale, or distribution. Supports multiple distance measures including
Gower's distance, Euclidean distance, Manhattan distance, and various categorical
variable distances such as simple matching, Eskin, occurrence frequency, and
association-based distances. Provides tools for variable scaling (standard
deviation, range, robust range, and principal component scaling), and handles
both independent and association-based category dissimilarities. Implements
methods to correct for biases that typically arise from different variable types,
distributions, and number of categories. Particularly useful for cluster analysis,
data visualization, and other distance-based me [...truncated...]
Author: Alfonso Iodice D'Enza [aut],
Angelos Markos [aut, cre],
Michel van de Velden [aut],
Carlo Cavicchia [aut]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between manydist versions 0.4.4 dated 2025-06-23 and 0.4.5 dated 2025-07-02
DESCRIPTION | 6 - MD5 | 8 +- NAMESPACE | 2 R/gower_recipe.R | 38 +++------- R/indicator_based.R | 191 ++++++++++++++++++++++++++-------------------------- 5 files changed, 116 insertions(+), 129 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-06-29 1.24-4
2025-06-27 1.24-3
2025-06-24 1.24-2
Title: Comparing and Visualizing Differences Between Surveys
Description: Easily analyze and visualize differences between samples (e.g., benchmark comparisons, nonresponse comparisons in surveys) on three levels. The comparisons can be univariate, bivariate or multivariate. On univariate level the variables of interest of a survey and a comparison survey (i.e. benchmark) are compared, by calculating one of several difference measures (e.g., relative difference in mean), and an average difference between the surveys. On bivariate level a function can calculate significant differences in correlations for the surveys. And on multivariate levels a function can calculate significant differences in model coefficients between the surveys of comparison. All of those differences can be easily plotted and outputted as a table. For more detailed information on the methods and example use see Rohr, B., Silber, H., & Felderer, B. (2024). Comparing the Accuracy of Univariate, Bivariate, and Multivariate Estimates across Probability and Nonprobability Surveys with Po [...truncated...]
Author: Bjoern Rohr [aut, cre, cph],
Barbara Felderer [aut]
Maintainer: Bjoern Rohr <bjoern.rohr@gesis.org>
Diff between sampcompR versions 0.3.0 dated 2025-03-02 and 0.3.1.1 dated 2025-07-02
DESCRIPTION | 8 +-- MD5 | 12 ++-- NEWS.md | 9 +++ R/Bivdiff.R | 4 + R/Unidiff.R | 33 +++++++----- R/Unidiff_Plot.R | 124 ++++++++++++++++++++++++++---------------------- man/plot_uni_compare.Rd | 14 ++++- 7 files changed, 122 insertions(+), 82 deletions(-)
Title: Ecological Restoration Planning
Description: Flexible framework for ecological restoration planning. It aims to identify priority areas for restoration efforts using optimization algorithms (based on Justeau-Allaire et al. 2021 <doi:10.1111/1365-2664.13803>). Priority areas can be identified by maximizing landscape indices, such as the effective mesh size (Jaeger 2000 <doi:10.1023/A:1008129329289>), or the integral index of connectivity (Pascual-Hortal & Saura 2006 <doi:10.1007/s10980-006-0013-z>). Additionally, constraints can be used to ensure that priority areas exhibit particular characteristics (e.g., ensure that particular places are not selected for restoration, ensure that priority areas form a single contiguous network). Furthermore, multiple near-optimal solutions can be generated to explore multiple options in restoration planning. The package leverages the 'Choco-solver' software to perform optimization using constraint programming (CP) techniques (<https://choco-solver.org/>).
Author: Dimitri Justeau-Allaire [aut, cre] ,
Jeffrey O Hanson [aut] ,
Ghislain Vieilledent [aut] ,
Guillaume Lannuzel [aut],
Philippe Vismara [aut],
Xavier Lorca [aut],
Philippe Birnbaum [aut]
Maintainer: Dimitri Justeau-Allaire <dimitri.justeau@gmail.com>
Diff between restoptr versions 1.1.0 dated 2025-07-01 and 1.1.1 dated 2025-07-02
DESCRIPTION | 10 ++++-- MD5 | 16 ++++----- NEWS.md | 4 ++ README.md | 2 - inst/CITATION | 22 +++++++++++++ inst/doc/case_study.html | 2 - inst/doc/restoptr.html | 72 ++++++++++++++++++++++---------------------- man/restoptr.Rd | 1 tests/testthat/test_solve.R | 4 +- 9 files changed, 82 insertions(+), 51 deletions(-)
Title: Split, Combine and Compress PDF Files
Description: Content-preserving transformations transformations of PDF files such
as split, combine, and compress. This package interfaces directly to the 'qpdf'
C++ library <https://qpdf.sourceforge.io/> and does not require any command
line utilities. Note that 'qpdf' does not read actual content from PDF files:
to extract text and data you need the 'pdftools' package.
Author: Jeroen Ooms [aut, cre] ,
Ben Raymond [ctb],
Jay Berkenbilt [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between qpdf versions 1.4.0 dated 2025-06-29 and 1.4.1 dated 2025-07-02
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 3 +++ src/Makevars | 2 +- 4 files changed, 10 insertions(+), 7 deletions(-)
Title: Prediction Model Validation and Updating
Description: Evaluate the predictive performance of an existing (i.e. previously
developed) prediction/ prognostic model given relevant information about the
existing prediction model (e.g. coefficients) and a new dataset. Provides a
range of model updating methods that help tailor the existing model to the
new dataset; see Su et al. (2018) <doi:10.1177/0962280215626466>. Techniques
to aggregate multiple existing prediction models on the new data are also
provided; see Debray et al. (2014) <doi:10.1002/sim.6080> and Martin et al.
(2018) <doi:10.1002/sim.7586>).
Author: Glen P. Martin [aut, cre, cph] ,
David Jenkins [aut, cph],
Matthew Sperrin [aut, cph]
Maintainer: Glen P. Martin <glen.martin31@gmail.com>
Diff between predRupdate versions 0.2.0 dated 2024-08-23 and 0.2.1 dated 2025-07-02
DESCRIPTION | 10 - MD5 | 16 - NEWS.md | 6 build/partial.rdb |binary build/vignette.rds |binary inst/doc/predRupdate.R | 92 ++++----- inst/doc/predRupdate.html | 10 - inst/doc/predRupdate_splineIllustration.html | 6 tests/testthat/test-flex_calplot.R | 265 +++++++++++++-------------- 9 files changed, 204 insertions(+), 201 deletions(-)
Title: Tools for Outbreak Investigation/Infectious Disease Surveillance
Description: Create epicurves, epigantt charts, and diverging bar charts
using 'ggplot2'. Prepare data for visualisation or other reporting for
infectious disease surveillance and outbreak investigation (time
series data). Includes tidy functions to solve date based
transformations for common reporting tasks, like (A) seasonal date
alignment for respiratory disease surveillance, (B) date-based case
binning based on specified time intervals like isoweek, epiweek, month
and more, (C) automated detection and marking of the new year based on
the date/datetime axis of the 'ggplot2', (D) labelling of the last
value of a time-series. An introduction on how to use epicurves can
be found on the US CDC website (2012,
<https://www.cdc.gov/training/quicklearns/epimode/index.html>).
Author: Alexander Bartel [aut, cre]
Maintainer: Alexander Bartel <alexander.bartel@fu-berlin.de>
Diff between ggsurveillance versions 0.5.0 dated 2025-07-01 and 0.5.1 dated 2025-07-02
DESCRIPTION | 6 MD5 | 30 ++-- NEWS.md | 4 R/bin_by_date.R | 49 ++++--- R/geom_epicurve.R | 2 R/label.R | 2 R/reexport.R | 2 R/stat_last_value.R | 4 man/bin_by_date.Rd | 238 +++++++++++++++++++------------------- man/geom_epicurve.Rd | 2 man/geom_vline_year.Rd | 198 +++++++++++++++---------------- man/guide_axis_nested_date.Rd | 222 +++++++++++++++++------------------ man/label_power10.Rd | 186 ++++++++++++++--------------- man/stat_last_value.Rd | 4 man/uncount.Rd | 2 tests/testthat/test-bin_by_date.R | 51 +++++--- 16 files changed, 513 insertions(+), 489 deletions(-)
More information about ggsurveillance at CRAN
Permanent link
Title: Constrained B-Splines (Sparse Matrix Based)
Description: Qualitatively Constrained (Regression) Smoothing Splines via
Linear Programming and Sparse Matrices.
Author: Pin T. Ng [aut],
Martin Maechler [aut, cre]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between cobs versions 1.3-9 dated 2024-12-19 and 1.3-9-1 dated 2025-07-02
ChangeLog | 9 +++++ DESCRIPTION | 14 ++++---- MD5 | 20 ++++++------ build/partial.rdb |binary inst/util.R | 10 ++++++ src/nrutil.h | 42 ++----------------------- tests/ex3.Rout.save | 12 +++---- tests/multi-constr.R | 6 +-- tests/multi-constr.Rout.save | 71 ++++++------------------------------------- tests/small-ex.Rout.save | 10 ++---- tests/temp.Rout.save | 32 ++++--------------- 11 files changed, 71 insertions(+), 155 deletions(-)
Title: Neural Networks to Predict Survival
Description: Several functions and S3 methods to predict survival by using neural networks. We implemented Partial Logistic Artificial Neural Networks (PLANN) as proposed by Biganzoli et al. (1998) <https://pubmed.ncbi.nlm.nih.gov/9618776>.
Author: Yohann Foucher [aut, cre] ,
Thomas Ollard [aut]
Maintainer: Yohann Foucher <yohann.foucher@univ-poitiers.fr>
Diff between survivalPLANN versions 0.1 dated 2024-08-20 and 0.4 dated 2025-07-02
survivalPLANN-0.1/survivalPLANN/R/predict.survivalPLANN.R |only survivalPLANN-0.1/survivalPLANN/R/print.survivalPLANN.R |only survivalPLANN-0.1/survivalPLANN/R/survivalPLANN.R |only survivalPLANN-0.1/survivalPLANN/man/predict.survivalPLANN.Rd |only survivalPLANN-0.1/survivalPLANN/man/print.survivalPLANN.Rd |only survivalPLANN-0.1/survivalPLANN/man/survivalPLANN.Rd |only survivalPLANN-0.4/survivalPLANN/DESCRIPTION | 13 - survivalPLANN-0.4/survivalPLANN/MD5 | 28 +- survivalPLANN-0.4/survivalPLANN/NAMESPACE | 23 + survivalPLANN-0.4/survivalPLANN/R/cvPLANN.R |only survivalPLANN-0.4/survivalPLANN/R/metrics.R |only survivalPLANN-0.4/survivalPLANN/R/plot.sPLANN.R |only survivalPLANN-0.4/survivalPLANN/R/predict.sPLANN.R |only survivalPLANN-0.4/survivalPLANN/R/print.sPLANN.R |only survivalPLANN-0.4/survivalPLANN/R/sPLANN.R |only survivalPLANN-0.4/survivalPLANN/README.md | 141 +++++++++-- survivalPLANN-0.4/survivalPLANN/data/dataK.RData |binary survivalPLANN-0.4/survivalPLANN/data/fr.ratetable.RData |only survivalPLANN-0.4/survivalPLANN/man/cvPLANN.Rd |only survivalPLANN-0.4/survivalPLANN/man/fr.ratetable.Rd |only survivalPLANN-0.4/survivalPLANN/man/metrics.Rd |only survivalPLANN-0.4/survivalPLANN/man/plot.sPLANN.Rd |only survivalPLANN-0.4/survivalPLANN/man/predict.sPLANN.Rd |only survivalPLANN-0.4/survivalPLANN/man/print.sPLANN.Rd |only survivalPLANN-0.4/survivalPLANN/man/sPLANN.Rd |only 25 files changed, 170 insertions(+), 35 deletions(-)
Title: Sorted L1 Penalized Estimation
Description: Efficient implementations for Sorted L-One Penalized Estimation
(SLOPE): generalized linear models regularized with the sorted L1-norm
(Bogdan et al. 2015). Supported models include
ordinary least-squares regression, binomial regression, multinomial
regression, and Poisson regression. Both dense and sparse predictor
matrices are supported. In addition, the package features predictor
screening rules that enable fast and efficient solutions to high-dimensional
problems.
Author: Johan Larsson [aut, cre] ,
Jonas Wallin [aut] ,
Malgorzata Bogdan [aut] ,
Ewout van den Berg [aut],
Chiara Sabatti [aut],
Emmanuel Candes [aut],
Evan Patterson [aut],
Weijie Su [aut],
Jakub Kala [aut],
Krystyna Grzesiak [aut],
Mathurin Massias [aut], [...truncated...]
Maintainer: Johan Larsson <johanlarsson@outlook.com>
Diff between SLOPE versions 1.0.0 dated 2025-06-30 and 1.0.1 dated 2025-07-02
DESCRIPTION | 6 ++--- MD5 | 10 ++++---- NEWS.md | 6 +++++ inst/doc/introduction.html | 4 +-- inst/doc/solvers.html | 8 +++---- tests/testthat/test-deviance.R | 46 +++++++++++++++++++++++------------------ 6 files changed, 46 insertions(+), 34 deletions(-)
Title: Automated Reproducibility Checks for R Markdown Documents
Description: Provide reproducible R chunks in R Markdown document that automatically check computational results for reproducibility. This is achieved by creating json files storing metadata about computational results. A comprehensive tutorial to the package is available as preprint by Brandmaier & Peikert (2024, <doi:10.31234/osf.io/3zjvf>).
Author: Andreas M. Brandmaier [aut, cre],
Aaron Peikert [ctb]
Maintainer: Andreas M. Brandmaier <andreas.brandmaier@medicalschool-berlin.de>
Diff between reproducibleRchunks versions 1.0.3 dated 2025-02-26 and 1.1.0 dated 2025-07-02
DESCRIPTION | 11 +++-- MD5 | 45 +++++++++++++++-------- NEWS.md | 14 +++++-- R/reproducibleR.R | 44 +++++++++------------- README.md | 29 ++++++++++++++ build |only inst/WORDLIST | 42 ++++++++++----------- inst/doc |only inst/examples/plot |only tests/testthat/test-mix_hash_and_raw.R | 13 +++++- tests/testthat/test-problematic_variable_names.R | 11 ++++- tests/testthat/test-rmd_compiles.R | 13 +++++- tests/testthat/testdata/test2.pdf | 6 +-- tests/testthat/testdata/test3.html | 3 - tests/testthat/testdata/test_empty.Rmd |only tests/testthat/testdata/test_empty.html |only tests/testthat/testdata/test_json.Rmd | 13 ++++++ tests/testthat/testdata/test_json.html | 41 ++++++++++++++++++++ tests/testthat/testdata/test_plot.Rmd |only tests/testthat/testdata/test_plot.html |only tests/testthat/testdata/test_simulation.Rmd |only tests/testthat/testdata/test_simulation.html |only tests/testthat/testdata/test_suite.Rmd | 15 +++++++ tests/testthat/testdata/test_suite.html | 34 ++++++++++++----- vignettes |only 25 files changed, 240 insertions(+), 94 deletions(-)
More information about reproducibleRchunks at CRAN
Permanent link
Title: Quantification of Multivariate Dependence
Description: A multivariate copula-based dependence measure. For more information, see Griessenberger, Junker, Trutschnig (2022), On a multivariate copula-based dependence measure and its estimation, Electronic Journal of Statistics, 16, 2206-2251.
Author: Lea Maislinger [aut, cre],
Florian Griessenberger [aut],
Robert R. Junker [aut],
Valentin Petztel [aut],
Wolfgang Trutschnig [aut]
Maintainer: Lea Maislinger <lea.maislinger@plus.ac.at>
Diff between qmd versions 1.1.2 dated 2022-08-22 and 1.1.3 dated 2025-07-02
DESCRIPTION | 16 ++++++++-------- MD5 | 2 +- 2 files changed, 9 insertions(+), 9 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 1.0.4 dated 2022-12-14 and 1.0.5 dated 2025-07-02
qad-1.0.4/qad/inst/CITATION |only qad-1.0.5/qad/DESCRIPTION | 27 qad-1.0.5/qad/MD5 | 29 qad-1.0.5/qad/R/ECBC.R | 19 qad-1.0.5/qad/R/emp_c_copula.R | 19 qad-1.0.5/qad/README.md | 2 qad-1.0.5/qad/build/partial.rdb |binary qad-1.0.5/qad/build/vignette.rds |binary qad-1.0.5/qad/inst/doc/qad-vignette.R | 62 - qad-1.0.5/qad/inst/doc/qad-vignette.Rmd | 22 qad-1.0.5/qad/inst/doc/qad-vignette.html | 471 +++++----- qad-1.0.5/qad/man/ECBC.Rd | 19 qad-1.0.5/qad/man/emp_c_copula.Rd | 131 +- qad-1.0.5/qad/vignettes/man/figures/README-unnamed-chunk-7-1.png |binary qad-1.0.5/qad/vignettes/man/figures/README-unnamed-chunk-7-2.png |binary qad-1.0.5/qad/vignettes/qad-vignette.Rmd | 22 16 files changed, 418 insertions(+), 405 deletions(-)
Title: Fast and Light-Weight Partial Distance Correlation
Description: Fast and memory-less computation of the partial distance correlation for vectors and matrices. Permutation-based and asymptotic hypothesis testing for zero partial distance correlation are also performed. References include: Szekely G. J. and Rizzo M. L. (2014). "Partial distance correlation with methods for dissimilarities". The Annals Statistics, 42(6): 2382--2412. <doi:10.1214/14-AOS1255>. Shen C., Panda S. and Vogelstein J. T. (2022). "The Chi-Square Test of Distance Correlation". Journal of Computational and Graphical Statistics, 31(1): 254--262. <doi:10.1080/10618600.2021.1938585>. Szekely G. J. and Rizzo M. L. (2023). "The Energy of Data and Distance Correlation". Chapman and Hall/CRC. <ISBN:9781482242744>. Kontemeniotis N., Vargiakakis R. and Tsagris M. (2025). On independence testing using the (partial) distance correlation. <doi:10.48550/arXiv.2506.15659>.
Author: Michail Tsagris [aut, cre],
Nikolaos Kontemeniotis [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between pdcor versions 1.0 dated 2025-02-25 and 1.2 dated 2025-07-02
DESCRIPTION | 10 ++++---- MD5 | 16 ++++++++------ R/mpdcor.R |only R/mpdcor.test.R |only R/pdcor.R | 2 - R/pdcor.test.R | 58 ++++++++++++++++++++++++++++----------------------- man/mpdcor.Rd |only man/mpdcor.test.Rd |only man/pdcor-package.Rd | 4 +-- man/pdcor.Rd | 4 ++- man/pdcor.test.Rd | 18 ++++++++------- 11 files changed, 63 insertions(+), 49 deletions(-)
Title: A 'tidyverse' Extension for Ordinations and Biplots
Description: Ordination comprises several multivariate exploratory and
explanatory techniques with theoretical foundations in geometric data
analysis; see Podani (2000, ISBN:90-5782-067-6) for techniques and
applications and Le Roux & Rouanet (2005) <doi:10.1007/1-4020-2236-0> for
foundations.
Greenacre (2010, ISBN:978-84-923846) shows how the most established of
these, including principal components analysis, correspondence analysis,
multidimensional scaling, factor analysis, and discriminant analysis,
rely on eigen-decompositions or singular value decompositions of
pre-processed numeric matrix data.
These decompositions give rise to a set of shared coordinates along which
the row and column elements can be measured. The overlay of their
scatterplots on these axes, introduced by Gabriel (1971)
<doi:10.1093/biomet/58.3.453>, is called a biplot.
'ordr' provides inspection, extraction, manipulation, and visualization
tools for several popular ordination classes supported by a set of r [...truncated...]
Author: Jason Cory Brunson [aut, cre] ,
Emily Paul [ctb]
Maintainer: Jason Cory Brunson <cornelioid@gmail.com>
Diff between ordr versions 0.1.1 dated 2022-10-20 and 0.1.2 dated 2025-07-02
DESCRIPTION | 17 +- MD5 | 108 ++++++++--------- NAMESPACE | 1 NEWS.md | 4 R/biplot.r | 42 ++---- R/data.r | 36 ++--- R/fun-lda.r | 2 R/fun-lra.r | 16 +- R/geom-axis.r | 1 R/geom-intervals.r | 2 R/geom-origin.r | 1 R/geom-unit-circle.r | 1 R/geom-vector.r | 1 R/ord-plot.r | 5 R/ord-supplementation.r | 4 R/ord-tbl.r | 2 R/ordinate.r | 6 R/ordr.r | 3 R/stat-center.r | 2 R/stat-chull.r | 1 R/stat-cone.r | 1 R/stat-scale.r | 1 R/stat-spantree.r | 1 README.md | 19 ++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/cmds-variables.R | 14 +- inst/doc/cmds-variables.html | 205 ++++++++++++++++----------------- inst/doc/cmds-variables.rmd | 6 inst/doc/ordr.R | 2 inst/doc/ordr.html | 260 +++++++++++++++++++++---------------------- man/biplot-geoms.Rd | 38 ++++-- man/biplot-stats.Rd | 31 +++-- man/geom_axis.Rd | 32 +++-- man/geom_isoline.Rd | 32 +++-- man/geom_lineranges.Rd | 32 +++-- man/geom_origin.Rd | 32 +++-- man/geom_text_radiate.Rd | 62 ++++++++-- man/geom_unit_circle.Rd | 32 +++-- man/geom_vector.Rd | 32 +++-- man/glass.Rd | 10 - man/lda-ord.Rd | 5 man/lra-ord.Rd | 12 - man/ordinate.Rd | 6 man/ordr.Rd | 19 ++- man/qswur_usa.Rd | 26 ++-- man/stat_center.Rd | 31 +++-- man/stat_chull.Rd | 31 +++-- man/stat_cone.Rd | 31 +++-- man/stat_rows.Rd | 31 +++-- man/stat_scale.Rd | 31 +++-- man/stat_spantree.Rd | 31 +++-- man/supplementation.Rd | 4 man/tbl_ord.Rd | 2 vignettes/cmds-variables.rmd | 6 55 files changed, 836 insertions(+), 527 deletions(-)
Title: Construct and Visualize TDA Mapper Graphs
Description: Topological data analysis (TDA) is a method of data analysis that
uses techniques from topology to analyze high-dimensional data. Here we
implement Mapper, an algorithm from this area developed by Singh, Mémoli and
Carlsson (2007) which generalizes the concept of a
Reeb graph <https://en.wikipedia.org/wiki/Reeb_graph>.
Author: George Clare Kennedy [aut, cre]
Maintainer: George Clare Kennedy <george-clarekennedy@uiowa.edu>
Diff between mappeR versions 2.2.0 dated 2025-06-28 and 2.2.1 dated 2025-07-02
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ README.md | 4 ++-- tests/testthat/test-covering.R | 16 ++++++++-------- 5 files changed, 21 insertions(+), 17 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Hyunki Lee [aut],
Changwoo Lim [aut],
Jinhwan Kim [aut] ,
Yoonkyoung Jeon [aut],
Jaewoong Heo [aut],
Youngsun Park [aut] ,
Hyungwoo Jo [aut],
Jeongmin Seo [aut],
Hojun LEE [aut],
Sungho Choi [aut],
Yeji Ka [...truncated...]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 1.6.9 dated 2025-05-27 and 1.6.11 dated 2025-07-02
DESCRIPTION | 10 MD5 | 48 +- NAMESPACE | 4 NEWS.md | 8 R/DataManager.R |only R/FilePsInput.R | 709 ++++++++------------------------- R/FileRepeatedInput.R | 456 ++------------------- R/FileSurveyInput.R | 597 +++++---------------------- R/coxph.R | 10 R/csvFileInput.R | 503 ++--------------------- R/kaplan.R | 4 R/roc.R | 12 R/timeroc.R | 13 build/vignette.rds |binary inst/doc/jsmodule.html | 20 inst/doc/jsmodule_subgroup_cmprsk.html | 4 man/DataManager.Rd |only man/FilePs.Rd | 58 -- man/FilePsInput.Rd | 68 +-- man/FileRepeated.Rd | 51 -- man/FileRepeatedInput.Rd | 61 +- man/FileSurvey.Rd | 51 -- man/FileSurveyInput.Rd | 70 +-- man/csvFile.Rd | 52 -- man/csvFileInput.Rd | 64 +- man/timerocModule.Rd | 137 ++++++ 26 files changed, 774 insertions(+), 2236 deletions(-)
Title: Experimental Statistics and Graphics for Agricultural Sciences
Description: Performs the analysis of completely randomized experimental designs (CRD), randomized blocks (RBD) and Latin square (LSD), experiments in double and triple factorial scheme (in CRD and RBD), experiments in subdivided plot scheme (in CRD and RBD), subdivided and joint analysis of experiments in CRD and RBD, linear regression analysis, test for two samples. The package performs analysis of variance, ANOVA assumptions and multiple comparison test of means or regression, according to Pimentel-Gomes (2009, ISBN: 978-85-7133-055-9), nonparametric test (Conover, 1999, ISBN: 0471160687), test for two samples, joint analysis of experiments according to Ferreira (2018, ISBN: 978-85-7269-566-4) and generalized linear model (glm) for binomial and Poisson family in CRD and RBD (Carvalho, FJ (2019), <doi:10.14393/ufu.te.2019.1244>). It can also be used to obtain descriptive measures and graphics, in addition to correlations and creative graphics used in agricultural sciences (Agronomy, Zootech [...truncated...]
Author: Gabriel Danilo Shimizu [aut, cre] ,
Rodrigo Yudi Palhaci Marubayashi [aut, ctb] ,
Leandro Simoes Azeredo Goncalves [aut, ctb]
Maintainer: Gabriel Danilo Shimizu <gabrield.shimizu@gmail.com>
Diff between AgroR versions 1.3.6 dated 2024-04-23 and 1.3.7 dated 2025-07-02
AgroR-1.3.6/AgroR/R/radargraph_function.R |only AgroR-1.3.6/AgroR/man/radargraph.Rd |only AgroR-1.3.7/AgroR/DESCRIPTION | 26 AgroR-1.3.7/AgroR/MD5 | 298 ++++---- AgroR-1.3.7/AgroR/NAMESPACE | 1 AgroR-1.3.7/AgroR/NEWS.md | 8 AgroR-1.3.7/AgroR/R/DBCglm_function.R | 23 AgroR-1.3.7/AgroR/R/DICglm_function.R | 19 AgroR-1.3.7/AgroR/R/FAT2DBC_function.R | 293 ++++---- AgroR-1.3.7/AgroR/R/FAT2DBCad_function.R | 199 +++-- AgroR-1.3.7/AgroR/R/FAT2DIC_function.R | 268 ++++--- AgroR-1.3.7/AgroR/R/FAT2DICad_function.R | 215 +++-- AgroR-1.3.7/AgroR/R/FAT3DBC_function.R | 95 +- AgroR-1.3.7/AgroR/R/FAT3DBCad_function.R | 90 +- AgroR-1.3.7/AgroR/R/FAT3DIC_function.R | 110 +-- AgroR-1.3.7/AgroR/R/FAT3DICad_function.R | 94 +- AgroR-1.3.7/AgroR/R/PSUBDBC_function.R | 283 ++++--- AgroR-1.3.7/AgroR/R/PSUBDIC_function.R | 277 ++++--- AgroR-1.3.7/AgroR/R/PSUBFAT2DBC_function.R | 2 AgroR-1.3.7/AgroR/R/PSUBSUB_function.R | 2 AgroR-1.3.7/AgroR/R/aac_function.R | 2 AgroR-1.3.7/AgroR/R/auxiliar_function.R | 48 + AgroR-1.3.7/AgroR/R/bar_dunnett.R | 39 - AgroR-1.3.7/AgroR/R/barfacets_function.R | 65 - AgroR-1.3.7/AgroR/R/bargraph2_function.R | 34 AgroR-1.3.7/AgroR/R/bargraph_function.R | 44 - AgroR-1.3.7/AgroR/R/bargraph_onefactor.R | 17 AgroR-1.3.7/AgroR/R/bargraph_twofactor.R | 11 AgroR-1.3.7/AgroR/R/barplot_positive_function.R | 81 +- AgroR-1.3.7/AgroR/R/conjdbc_function.R | 46 - AgroR-1.3.7/AgroR/R/conjdic_function.R | 50 - AgroR-1.3.7/AgroR/R/conjfatdbc_function.R | 2 AgroR-1.3.7/AgroR/R/coric_function.R | 4 AgroR-1.3.7/AgroR/R/correlation_function.R | 6 AgroR-1.3.7/AgroR/R/croqui_function.R | 2 AgroR-1.3.7/AgroR/R/dbc_ad.R | 17 AgroR-1.3.7/AgroR/R/dbc_function.R | 107 ++ AgroR-1.3.7/AgroR/R/dbct_function.R | 25 AgroR-1.3.7/AgroR/R/desc2fat_function.R | 36 AgroR-1.3.7/AgroR/R/desc3fat_function.R | 16 AgroR-1.3.7/AgroR/R/desc_function.R | 14 AgroR-1.3.7/AgroR/R/desd_fat2_quant_ad.R | 50 - AgroR-1.3.7/AgroR/R/dic_ad.R | 17 AgroR-1.3.7/AgroR/R/dic_function.R | 131 ++- AgroR-1.3.7/AgroR/R/dict_function.R | 20 AgroR-1.3.7/AgroR/R/dispvar_function.R | 2 AgroR-1.3.7/AgroR/R/dql_function.R | 85 +- AgroR-1.3.7/AgroR/R/dqlt_function.R | 20 AgroR-1.3.7/AgroR/R/dunn_function.R | 2 AgroR-1.3.7/AgroR/R/dunnet_function.R | 20 AgroR-1.3.7/AgroR/R/fat2_table.R | 2 AgroR-1.3.7/AgroR/R/grid_onefactor.R | 94 +- AgroR-1.3.7/AgroR/R/ibarplot_double.R | 19 AgroR-1.3.7/AgroR/R/jointcluster.R | 10 AgroR-1.3.7/AgroR/R/logistic_function.R | 2 AgroR-1.3.7/AgroR/R/pca_function.R | 12 AgroR-1.3.7/AgroR/R/plot_TH1_function.R | 4 AgroR-1.3.7/AgroR/R/plot_TH_function.R | 5 AgroR-1.3.7/AgroR/R/plot_interaction_function.R | 19 AgroR-1.3.7/AgroR/R/plot_tonetest.R | 2 AgroR-1.3.7/AgroR/R/plotcor_function.R | 7 AgroR-1.3.7/AgroR/R/plotjitter_function.R | 70 - AgroR-1.3.7/AgroR/R/polynomial2_function.R | 48 - AgroR-1.3.7/AgroR/R/polynomial2color_function.R | 47 - AgroR-1.3.7/AgroR/R/polynomial_function.R | 52 - AgroR-1.3.7/AgroR/R/quantfat2desd_function.R | 2 AgroR-1.3.7/AgroR/R/seggraph2_function.R | 30 AgroR-1.3.7/AgroR/R/seggraph_function.R | 40 - AgroR-1.3.7/AgroR/R/sk_graph_function.R | 41 - AgroR-1.3.7/AgroR/R/spider_graph_function.R | 17 AgroR-1.3.7/AgroR/R/stripplot_function.R | 2 AgroR-1.3.7/AgroR/R/summarise_conj.R | 24 AgroR-1.3.7/AgroR/R/summarise_dunnett.R | 14 AgroR-1.3.7/AgroR/R/summarise_function.R | 876 ++++++++++++------------ AgroR-1.3.7/AgroR/R/tabledesc_function.R | 2 AgroR-1.3.7/AgroR/R/tbarplotreverse_function.R | 25 AgroR-1.3.7/AgroR/R/test_two_function.R | 13 AgroR-1.3.7/AgroR/R/time_plot_function.R | 17 AgroR-1.3.7/AgroR/R/tonetest_function.R | 2 AgroR-1.3.7/AgroR/R/transf_function.R | 2 AgroR-1.3.7/AgroR/build/partial.rdb |binary AgroR-1.3.7/AgroR/man/AgroR-package.Rd | 2 AgroR-1.3.7/AgroR/man/DBC.Rd | 19 AgroR-1.3.7/AgroR/man/DBC.glm.Rd | 6 AgroR-1.3.7/AgroR/man/DBCT.Rd | 6 AgroR-1.3.7/AgroR/man/DIC.Rd | 32 AgroR-1.3.7/AgroR/man/DIC.glm.Rd | 6 AgroR-1.3.7/AgroR/man/DICT.Rd | 6 AgroR-1.3.7/AgroR/man/DQL.Rd | 12 AgroR-1.3.7/AgroR/man/DQLT.Rd | 6 AgroR-1.3.7/AgroR/man/FAT2DBC.Rd | 32 AgroR-1.3.7/AgroR/man/FAT2DBC.ad.Rd | 25 AgroR-1.3.7/AgroR/man/FAT2DIC.Rd | 26 AgroR-1.3.7/AgroR/man/FAT2DIC.ad.Rd | 25 AgroR-1.3.7/AgroR/man/FAT3DBC.Rd | 12 AgroR-1.3.7/AgroR/man/FAT3DBC.ad.Rd | 12 AgroR-1.3.7/AgroR/man/FAT3DIC.Rd | 12 AgroR-1.3.7/AgroR/man/FAT3DIC.ad.Rd | 12 AgroR-1.3.7/AgroR/man/PCA_function.Rd | 6 AgroR-1.3.7/AgroR/man/PSUBDBC.Rd | 23 AgroR-1.3.7/AgroR/man/PSUBDIC.Rd | 24 AgroR-1.3.7/AgroR/man/PSUBSUBDBC.Rd | 2 AgroR-1.3.7/AgroR/man/STRIPLOT.Rd | 2 AgroR-1.3.7/AgroR/man/TBARPLOT.reverse.Rd | 2 AgroR-1.3.7/AgroR/man/aacp.Rd | 2 AgroR-1.3.7/AgroR/man/bar_dunnett.Rd | 11 AgroR-1.3.7/AgroR/man/bar_graph.Rd | 14 AgroR-1.3.7/AgroR/man/bar_graph2.Rd | 7 AgroR-1.3.7/AgroR/man/barfacet.Rd | 5 AgroR-1.3.7/AgroR/man/bargraph_onefactor.Rd | 3 AgroR-1.3.7/AgroR/man/barplot_positive.Rd | 6 AgroR-1.3.7/AgroR/man/conjdbc.Rd | 6 AgroR-1.3.7/AgroR/man/conjdic.Rd | 6 AgroR-1.3.7/AgroR/man/conjfat2dbc.Rd | 2 AgroR-1.3.7/AgroR/man/cor_ic.Rd | 2 AgroR-1.3.7/AgroR/man/corgraph.Rd | 2 AgroR-1.3.7/AgroR/man/dbc.ad.Rd | 6 AgroR-1.3.7/AgroR/man/desc.Rd | 6 AgroR-1.3.7/AgroR/man/desc2fat.Rd | 17 AgroR-1.3.7/AgroR/man/desc3fat.Rd | 8 AgroR-1.3.7/AgroR/man/desd_fat2_quant_ad.Rd | 4 AgroR-1.3.7/AgroR/man/dic.ad.Rd | 6 AgroR-1.3.7/AgroR/man/dispvar.Rd | 2 AgroR-1.3.7/AgroR/man/dunn.Rd | 2 AgroR-1.3.7/AgroR/man/dunnett.Rd | 7 AgroR-1.3.7/AgroR/man/fat2_table.Rd | 2 AgroR-1.3.7/AgroR/man/grid.onefactor.Rd | 12 AgroR-1.3.7/AgroR/man/jointcluster.Rd | 2 AgroR-1.3.7/AgroR/man/line_plot.Rd | 8 AgroR-1.3.7/AgroR/man/logistic.Rd | 2 AgroR-1.3.7/AgroR/man/plot_TH.Rd | 4 AgroR-1.3.7/AgroR/man/plot_TH1.Rd | 4 AgroR-1.3.7/AgroR/man/plot_cor.Rd | 2 AgroR-1.3.7/AgroR/man/plot_interaction.Rd | 7 AgroR-1.3.7/AgroR/man/plot_jitter.Rd | 2 AgroR-1.3.7/AgroR/man/plot_tonetest.Rd | 2 AgroR-1.3.7/AgroR/man/polynomial.Rd | 14 AgroR-1.3.7/AgroR/man/polynomial2.Rd | 16 AgroR-1.3.7/AgroR/man/polynomial2_color.Rd | 16 AgroR-1.3.7/AgroR/man/quant.fat2.desd.Rd | 2 AgroR-1.3.7/AgroR/man/seg_graph.Rd | 4 AgroR-1.3.7/AgroR/man/seg_graph2.Rd | 4 AgroR-1.3.7/AgroR/man/sk_graph.Rd | 4 AgroR-1.3.7/AgroR/man/sketch.Rd | 2 AgroR-1.3.7/AgroR/man/spider_graph.Rd | 8 AgroR-1.3.7/AgroR/man/summarise_anova.Rd | 12 AgroR-1.3.7/AgroR/man/summarise_conj.Rd | 2 AgroR-1.3.7/AgroR/man/tabledesc.Rd | 2 AgroR-1.3.7/AgroR/man/test_two.Rd | 6 AgroR-1.3.7/AgroR/man/tonetest.Rd | 2 AgroR-1.3.7/AgroR/man/transf.Rd | 2 151 files changed, 2999 insertions(+), 2394 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-11-19 1.0.1
2018-09-11 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-17 1.0.4
2019-05-15 1.0.3
2019-02-16 1.0.2
2018-11-16 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-29 0.4.3
2025-05-19 0.4.2
2021-12-20 0.4.1
2021-02-16 0.4.0
2020-10-13 0.3.0
2020-10-07 0.2.0
2020-03-29 0.1.4
2020-03-19 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-04-06 1.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-04-01 0.8.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-19 0.7.2
2024-10-08 0.7.1
2024-09-06 0.7.0
2024-04-18 0.6.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-04-09 0.5.0
2025-03-10 0.3.1
2024-02-13 0.3.0
2023-10-19 0.2.0
2023-08-29 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-19 1.1.0
2024-10-22 1.0.0
2024-09-18 0.5.0
2024-04-23 0.4.1
2023-12-04 0.4.0
2023-06-29 0.3.0
2022-11-27 0.2.1
2022-05-05 0.2.0
2022-03-18 0.1.2
2022-03-06 0.1.1
2022-02-08 0.1.0
2022-01-21 0.0.1
Title: The R WINS Package
Description: Calculate the win statistics (win ratio, net benefit and win odds) for prioritized multiple endpoints, plot the win statistics and win proportions over study time if at least one time-to-event endpoint is analyzed, and simulate datasets with dependent endpoints. The package can handle any type of outcomes (continuous, ordinal, binary, time-to-event) and allow users to perform stratified analysis, inverse probability of censoring weighting (IPCW) and inverse probability of treatment weighting (IPTW) analysis.
Author: Ying Cui [aut, cre],
Bo Huang [aut]
Maintainer: Ying Cui <cuiyingbeicheng@gmail.com>
Diff between WINS versions 1.5 dated 2025-05-05 and 1.5.1 dated 2025-07-02
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/win.strategy.default.R | 4 ++-- inst/doc/vignette.pdf |binary 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Stepwise Clustered Ensemble
Description: Implementation of Stepwise Clustered Ensemble (SCE) and Stepwise Cluster Analysis (SCA) for multivariate data analysis. The package provides comprehensive tools for feature selection, model training, prediction, and evaluation in hydrological and environmental modeling applications. Key functionalities include recursive feature elimination (RFE), Wilks feature importance analysis, model validation through out-of-bag (OOB) validation, and ensemble prediction capabilities. The package supports both single and multivariate response variables, making it suitable for complex environmental modeling scenarios. For more details see Li et al. (2021) <doi:10.5194/hess-25-4947-2021>.
Author: Kailong Li [aut, cre]
Maintainer: Kailong Li <lkl98509509@gmail.com>
Diff between SCE versions 1.0.0 dated 2025-06-23 and 1.1.0 dated 2025-07-02
SCE-1.0.0/SCE/R/SCE-package.R |only SCE-1.0.0/SCE/man/Air_quality_testing.Rd |only SCE-1.0.0/SCE/man/Air_quality_training.Rd |only SCE-1.0.0/SCE/man/Model_evaluation.Rd |only SCE-1.0.0/SCE/man/Model_simulation.Rd |only SCE-1.0.0/SCE/man/OOB_validation.Rd |only SCE-1.0.0/SCE/man/SCA.Rd |only SCE-1.0.0/SCE/man/SCA_importance.Rd |only SCE-1.0.0/SCE/man/SCA_tree_predict.Rd |only SCE-1.0.0/SCE/man/SCE_Prediction.Rd |only SCE-1.0.0/SCE/man/Streamflow_testing_10var.Rd |only SCE-1.0.0/SCE/man/Streamflow_testing_22var.Rd |only SCE-1.0.0/SCE/man/Streamflow_training_10var.Rd |only SCE-1.0.0/SCE/man/Streamflow_training_22var.Rd |only SCE-1.0.0/SCE/man/Wilks_importance.Rd |only SCE-1.1.0/SCE/DESCRIPTION | 6 SCE-1.1.0/SCE/MD5 | 42 +--- SCE-1.1.0/SCE/NAMESPACE | 18 +- SCE-1.1.0/SCE/NEWS.md |only SCE-1.1.0/SCE/R/Model_simulation.R | 40 ++-- SCE-1.1.0/SCE/R/RFE_SCE.R | 104 +++++++++++ SCE-1.1.0/SCE/R/SCA.R | 169 +++++++++++++++++- SCE-1.1.0/SCE/R/SCE.R | 225 ++++++++++++++++++++++++- SCE-1.1.0/SCE/R/Wilks_importance.R | 68 ++++--- SCE-1.1.0/SCE/README.md | 219 ++++++++++++++++-------- SCE-1.1.0/SCE/man/Air_quality.Rd |only SCE-1.1.0/SCE/man/RFE_SCE.Rd | 92 +++++++++- SCE-1.1.0/SCE/man/SCE.Rd | 215 +++++++++++++---------- SCE-1.1.0/SCE/man/Streamflow.Rd |only SCE-1.1.0/SCE/man/evaluate.Rd |only SCE-1.1.0/SCE/man/importance.Rd |only SCE-1.1.0/SCE/man/predict.Rd |only SCE-1.1.0/SCE/man/print.Rd |only 33 files changed, 938 insertions(+), 260 deletions(-)
Title: The Inverse Gamma Distribution
Description: Light weight implementation of the standard distribution
functions for the inverse gamma distribution, wrapping those for the gamma
distribution in the stats package.
Author: David Kahle [aut, cre, cph],
James Stamey [aut, cph]
Maintainer: David Kahle <david.kahle@gmail.com>
Diff between invgamma versions 1.1 dated 2017-05-07 and 1.2 dated 2025-07-02
DESCRIPTION | 15 - LICENSE |only MD5 | 34 ++- NEWS.md |only R/attach.R |only R/invchisq.R | 39 ++-- R/invexp.R | 35 ++- R/invgamma.R | 104 +++++++---- README.md | 338 ++++++++++++++++++++++++++++++++---- man/invchisq.Rd | 28 +- man/invexp.Rd | 28 +- man/invgamma.Rd | 72 ++++--- tests |only tools/README-unnamed-chunk-10-1.png |only tools/README-unnamed-chunk-14-1.png |only tools/README-unnamed-chunk-15-1.png |only tools/README-unnamed-chunk-16-1.png |only tools/README-unnamed-chunk-17-1.png |only tools/README-unnamed-chunk-18-1.png |only tools/README-unnamed-chunk-19-1.png |only tools/README-unnamed-chunk-4-1.png |binary tools/README-unnamed-chunk-9-1.png |binary 22 files changed, 528 insertions(+), 165 deletions(-)
Title: Set Axis Break for 'ggplot2'
Description: An implementation of scale functions for setting axis breaks of a 'gg' plot (S Xu (2021) <doi:10.3389/fgene.2021.774846>).
Author: Guangchuang Yu [aut, cre, cph] ,
Shuangbin Xu [aut]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggbreak versions 0.1.4 dated 2025-02-04 and 0.1.5 dated 2025-07-02
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/method-ggplot-add.R | 16 ++++++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/ggbreak.html | 43 ++++++++++++++++++++++--------------------- 7 files changed, 46 insertions(+), 41 deletions(-)
Title: Decorate a 'ggplot' with Associated Information
Description: For many times, we are not just aligning plots as what 'cowplot' and 'patchwork' did. Users would like to align associated information that requires axes to be exactly matched in subplots, e.g. hierarchical clustering with a heatmap. Inspired by the 'Method 2' in 'ggtree' (G Yu (2018) <doi:10.1093/molbev/msy194>), 'aplot' provides utilities to aligns associated subplots to a main plot at different sides (left, right, top and bottom) with axes exactly matched.
Author: Guangchuang Yu [aut, cre] ,
Shuangbin Xu [ctb] ,
Thomas Hackl [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between aplot versions 0.2.7 dated 2025-06-21 and 0.2.8 dated 2025-07-02
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- NAMESPACE | 4 +++- NEWS.md | 4 ++++ R/plot-list.R | 7 +++---- R/zzz.R |only 6 files changed, 19 insertions(+), 13 deletions(-)