Title: Evolutionary Algorithm
Description: Runs an evolutionary algorithm using the 'AlphaSimR' machinery <doi:10.1093/g3journal/jkaa017> .
Author: Giovanny Covarrubias-Pazaran [aut, cre]
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between evola versions 1.0.4 dated 2025-01-18 and 1.0.5 dated 2025-04-25
evola-1.0.4/evola/man/fitnessf.Rd |only evola-1.0.4/evola/man/varM.Rd |only evola-1.0.5/evola/ChangeLog | 15 evola-1.0.5/evola/DESCRIPTION | 10 evola-1.0.5/evola/MD5 | 50 +- evola-1.0.5/evola/NAMESPACE | 12 evola-1.0.5/evola/R/AllClass.R |only evola-1.0.5/evola/R/evolafit.R | 493 +++++++++++++++++---------- evola-1.0.5/evola/R/methods.R |only evola-1.0.5/evola/R/plotting_funs.R | 57 +-- evola-1.0.5/evola/R/utlis.R | 214 +++++++++--- evola-1.0.5/evola/inst/doc/evola_intro.R | 339 +++++++++++++------ evola-1.0.5/evola/inst/doc/evola_intro.Rmd | 368 +++++++++++++++----- evola-1.0.5/evola/inst/doc/evola_intro.html | 499 +++++++++++++++++++--------- evola-1.0.5/evola/man/DT_cpdata.Rd | 22 - evola-1.0.5/evola/man/DT_technow.Rd | 22 - evola-1.0.5/evola/man/DT_wheat.Rd | 15 evola-1.0.5/evola/man/addZeros.Rd |only evola-1.0.5/evola/man/bestSol.Rd | 11 evola-1.0.5/evola/man/evolaPop-class.Rd |only evola-1.0.5/evola/man/evolafit.Rd | 171 ++++++--- evola-1.0.5/evola/man/importHaploSparse.Rd |only evola-1.0.5/evola/man/inbFun.Rd |only evola-1.0.5/evola/man/logspace.Rd |only evola-1.0.5/evola/man/nQtl.Rd |only evola-1.0.5/evola/man/ocsFun.Rd |only evola-1.0.5/evola/man/plot.monitor.Rd | 13 evola-1.0.5/evola/man/plot.pareto.Rd | 2 evola-1.0.5/evola/man/regFun.Rd |only evola-1.0.5/evola/man/stan.Rd | 10 evola-1.0.5/evola/man/update.method.Rd |only evola-1.0.5/evola/man/varQ.Rd |only evola-1.0.5/evola/vignettes/evola_intro.Rmd | 368 +++++++++++++++----- 33 files changed, 1911 insertions(+), 780 deletions(-)
Title: Model-Based Geostatistics
Description: Modern model-based geostatistics for point-referenced data. This package provides a
simple interface to run spatial machine learning models and geostatistical models
that estimate a continuous (raster) surface from point-referenced outcomes and,
optionally, a set of raster covariates. The package also includes functions to
summarize raster outcomes by (polygon) region while preserving uncertainty.
Author: Nathaniel Henry [aut, cre] ,
Benjamin Mayala [aut]
Maintainer: Nathaniel Henry <nat@henryspatialanalysis.com>
Diff between mbg versions 1.0.0 dated 2025-04-02 and 1.1.0 dated 2025-04-25
DESCRIPTION | 6 ++--- MD5 | 9 ++++---- R/generate_cell_draws_and_summarize.R | 2 - R/prepare_inla_data_stack.R | 4 ++- README.md | 38 +++++++++++++++++++--------------- man/figures |only 6 files changed, 34 insertions(+), 25 deletions(-)
Title: Communicate with 'Ollama' to Run Large Language Models Locally
Description: Wraps the 'Ollama' <https://ollama.com> API, which can be used to
communicate with generative large language models locally.
Author: Johannes B. Gruber [aut, cre] ,
Maximilian Weber [aut, ctb]
Maintainer: Johannes B. Gruber <JohannesB.Gruber@gmail.com>
Diff between rollama versions 0.2.1 dated 2025-04-24 and 0.2.2 dated 2025-04-25
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 2 ++ R/lib.R | 6 ++---- R/models.r | 8 +++++++- 5 files changed, 18 insertions(+), 12 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 14.4.1-1 dated 2025-03-28 and 14.4.2-1 dated 2025-04-25
ChangeLog | 26 +++++ DESCRIPTION | 8 - MD5 | 40 ++++----- build/partial.rdb |binary build/vignette.rds |binary configure | 18 ++-- configure.ac | 2 inst/NEWS.Rd | 9 ++ inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/armadillo_bits/arma_version.hpp | 2 inst/include/armadillo_bits/config.hpp | 12 ++ inst/include/armadillo_bits/def_superlu.hpp | 24 ++--- inst/include/armadillo_bits/glue_times_meat.hpp | 34 +++++++ inst/include/armadillo_bits/include_superlu.hpp | 97 +++++++++++----------- inst/include/armadillo_bits/op_expmat_meat.hpp | 25 ++++- inst/include/armadillo_bits/op_sp_sum_bones.hpp | 8 - inst/include/armadillo_bits/op_sp_sum_meat.hpp | 12 +- inst/include/armadillo_bits/sp_auxlib_meat.hpp | 30 +++--- inst/include/armadillo_bits/translate_superlu.hpp | 12 +- inst/tinytest/test_sparse.R | 5 - 21 files changed, 236 insertions(+), 128 deletions(-)
Title: Oblique Decision Random Forest for Classification and Regression
Description: The oblique decision tree (ODT) uses linear combinations of predictors as partitioning variables in a decision tree. Oblique Decision Random Forest (ODRF) is an ensemble of multiple ODTs generated by feature bagging. Oblique Decision Boosting Tree (ODBT) applies feature bagging during the training process of ODT-based boosting trees to ensemble multiple boosting trees. All three methods can be used for classification and regression, and ODT and ODRF serve as supplements to the classical CART of Breiman (1984) <DOI:10.1201/9781315139470> and Random Forest of Breiman (2001) <DOI:10.1023/A:1010933404324> respectively.
Author: Yu Liu [aut, cre, cph],
Yingcun Xia [aut]
Maintainer: Yu Liu <liuyuchina123@gmail.com>
Diff between ODRF versions 0.0.4 dated 2023-05-28 and 0.0.5 dated 2025-04-25
DESCRIPTION | 18 - MD5 | 114 +++++------ NAMESPACE | 11 + NEWS.md | 9 R/Accuracy.R | 14 - R/ODBT.R |only R/ODRF.R | 49 ++-- R/ODT.R | 268 ++++++++++++++++++--------- R/PPO.R | 6 R/RcppExports.R | 4 R/RotMat.R | 8 R/VarImp.R | 144 +++++++------- R/as_party_ODT.R | 10 - R/best_cut_node.R | 67 +++++- R/body_fat.R | 4 R/defaults.R | 2 R/linear_split.R |only R/online_ODRF.R | 38 +-- R/online_ODT.R | 39 +-- R/plot_Accuracy.R | 22 +- R/plot_ODT.R | 16 - R/plot_ODT_depth.R | 22 +- R/plot_VarImp.R | 28 +- R/plot_prune_ODT.R | 22 +- R/predictTree.R | 21 +- R/predict_ODRF.R | 48 ++-- R/predict_ODT.R | 101 ++++++++-- R/print_ODRF.R | 2 R/print_ODT.R | 26 +- R/prune_ODRF.R | 32 +-- R/prune_ODT.R | 17 - README.md | 106 ++++++---- inst/CITATION | 7 inst/WORDLIST | 8 inst/doc/Oblique-Decision-Random-Forest.R | 37 ++- inst/doc/Oblique-Decision-Random-Forest.Rmd | 37 ++- inst/doc/Oblique-Decision-Random-Forest.html | 265 +++++++++++++------------- man/Accuracy.Rd | 6 man/ODBT.Rd |only man/ODRF.Rd | 4 man/ODT.Rd | 60 +++++- man/PPO.Rd | 4 man/RotMatMake.Rd | 2 man/VarImp.Rd | 16 - man/as.party.ODT.Rd | 2 man/best.cut.node.Rd | 41 +++- man/figures/README-plot-1.png |binary man/plot.Accuracy.Rd | 6 man/plot.ODT.Rd | 2 man/plot.VarImp.Rd | 6 man/predict.ODRF.Rd | 8 man/predict.ODT.Rd | 54 ++++- man/prune.ODRF.Rd | 2 src/BODT.cpp |only src/RcppExports.cpp | 23 ++ tests/spelling.R | 9 tests/testthat/test-ODRF.R | 28 +- tests/testthat/test-ODT.R | 14 - tests/testthat/test-predict_ODT.R | 4 vignettes/Oblique-Decision-Random-Forest.Rmd | 37 ++- 60 files changed, 1204 insertions(+), 746 deletions(-)
Title: Exporting 'flextable' to 'xlsx' Files
Description: Exports 'flextable' objects to 'xlsx' files,
utilizing functionalities provided by 'flextable' and 'openxlsx2'.
Author: Tobias Heidler [aut, cre, cph]
Maintainer: Tobias Heidler <flexlsx@heidler.ovh>
Diff between flexlsx versions 0.3.4 dated 2025-02-26 and 0.3.5 dated 2025-04-25
flexlsx-0.3.4/flexlsx/tests/testthat/test-RcppExports.R |only flexlsx-0.3.5/flexlsx/DESCRIPTION | 10 +++++----- flexlsx-0.3.5/flexlsx/MD5 | 7 +++---- flexlsx-0.3.5/flexlsx/NEWS.md | 5 +++++ flexlsx-0.3.5/flexlsx/R/wb_apply_cell_styles.R | 4 ++-- 5 files changed, 15 insertions(+), 11 deletions(-)
Title: R Interface for the GPlates Web Service and Desktop Application
Description: Query functions to the GPlates <https://www.gplates.org/> Desktop Application and the GPlates Web Service <https://gws.gplates.org/> allow users to reconstruct past positions of geographic entities based on user-selected rotation models without leaving the R running environment. The online method (GPlates Web Service) makes the rotation of static plates, coastlines, and a low number of geographic coordinates available using nothing but an internet connection. The offline method requires an external installation of the GPlates Desktop Application, but allows the efficient batch rotation of thousands of coordinates, Simple Features (sf) and Spatial (sp) objects with custom reconstruction trees and partitioning polygons. Examples of such plate tectonic models are accessible via the chronosphere <https://cran.r-project.org/package=chronosphere>. This R extension is developed under the umbrella of the DFG (Deutsche Forschungsgemeinschaft) Research Unit TERSANE2 (For 2332, [...truncated...]
Author: Adam T. Kocsis [cre, aut] ,
Nussaibah B. Raja [ctb] ,
Simon Williams [ctb] ,
Elizabeth M. Dowding [ctb] ,
Deutsche Forschungsgemeinschaft [fnd],
FAU GeoZentrum Nordbayern [fnd]
Maintainer: Adam T. Kocsis <adam.t.kocsis@gmail.com>
Diff between rgplates versions 0.5.0 dated 2024-09-06 and 0.6.0 dated 2025-04-25
DESCRIPTION | 8 - MD5 | 29 ++++-- NAMESPACE | 6 + NEWS.md | 27 ++++++ R/data.R | 2 R/front_end.R | 4 R/offline.R | 155 +++++++++++++++++++++++++++++++++++-- R/online.R | 46 +++++++++- R/platemodel.R | 15 +++ R/plot_utils.R |only R/plots.R |only R/zzz.R | 7 + data/gws.RData |binary man/figures/subduction_example.png |only man/gws.Rd | 2 man/sawteeth.Rd |only man/subductionlines.Rd |only man/velocities.Rd | 4 18 files changed, 268 insertions(+), 37 deletions(-)
Title: Performs Quality Control, Data Normalization, and Batch Effect
Correction for 'NanoString nCounter' Data
Description: Provides quality control (QC), normalization, and batch
effect correction operations for 'NanoString nCounter' data, Talhouk
et al. (2016) <doi:10.1371/journal.pone.0153844>. Various metrics are
used to determine which samples passed or failed QC. Gene expression
should first be normalized to housekeeping genes, before a
reference-based approach is used to adjust for batch effects. Raw
NanoString data can be imported in the form of Reporter Code Count
(RCC) files.
Author: Derek Chiu [aut, cre] ,
Aline Talhouk [aut] ,
Samuel Leung [aut]
Maintainer: Derek Chiu <dchiu@bccrc.ca>
Diff between nanostringr versions 0.5.0 dated 2025-02-05 and 0.6.0 dated 2025-04-25
DESCRIPTION | 10 +++---- MD5 | 24 ++++++++-------- NAMESPACE | 1 NEWS.md | 5 +++ R/HKnorm.R | 2 - R/NanoStringQC.R | 46 ++++++++++++++------------------ R/nanostringr-package.R | 1 R/normalize_pools.R | 27 +++++++++---------- R/normalize_random.R | 12 ++++---- R/read_rcc.R | 68 +++++++++++++++++++++++++++++------------------- R/utils.R | 29 +++++++++----------- inst/doc/Overview.html | 8 ++--- man/rcc.Rd | 1 13 files changed, 124 insertions(+), 110 deletions(-)
Title: Analysis of Geostatistical Data
Description: Geostatistical analysis including variogram-based, likelihood-based and Bayesian methods. Software companion for Diggle and Ribeiro (2007) <doi:10.1007/978-0-387-48536-2>.
Author: Paulo Justiniano Ribeiro Jr [aut, cre],
Peter Diggle [aut],
Ole Christensen [ctb],
Martin Schlather [ctb],
Roger Bivand [ctb],
Brian Ripley [ctb]
Maintainer: Paulo Justiniano Ribeiro Jr <paulojus@ufpr.br>
Diff between geoR versions 1.9-4 dated 2024-02-15 and 1.9-5 dated 2025-04-25
DESCRIPTION | 42 +++++++++++++++++++++++++++++++----------- MD5 | 4 ++-- man/SIC.Rd | 3 ++- 3 files changed, 35 insertions(+), 14 deletions(-)
Title: Causal Inference Modeling for Estimation of Causal Effects
Description: Provides an array of statistical models common in causal inference such as
standardization, IP weighting, propensity matching, outcome regression, and doubly-robust
estimators. Estimates of the average treatment effects from each model are given with the
standard error and a 95% Wald confidence interval (Hernan, Robins (2020) <https://miguelhernan.org/whatifbook/>).
Author: Joshua Anderson [aut, cre, cph],
Cyril Rakovski [rev],
Yesha Patel [rev],
Erin Lee [rev]
Maintainer: Joshua Anderson <jwanderson198@gmail.com>
Diff between CausalModels versions 0.2.0 dated 2022-11-23 and 0.2.1 dated 2025-04-25
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 6 ++++++ R/outcome_regression.R | 19 ++++++++++++++----- README.md | 46 +++++++++++++++++++++++++++------------------- 5 files changed, 55 insertions(+), 32 deletions(-)
Title: Working with United States ZIP Code and ZIP Code Tabulation Area
Data
Description: Provides a set of functions for working with American postal codes,
which are known as ZIP Codes. These include accessing ZIP Code to ZIP Code
Tabulation Area (ZCTA) crosswalks, retrieving demographic data for ZCTAs, and
tabulating demographic data for three-digit ZCTAs.
Author: Christopher Prener [aut, cre] ,
Timothy Wiemken [aut] ,
Angela Cook [aut]
Maintainer: Christopher Prener <Christopher.Prener@pfizer.com>
Diff between zippeR versions 0.1.1 dated 2025-02-25 and 0.1.2 dated 2025-04-25
DESCRIPTION | 6 - MD5 | 22 ++--- NEWS.md | 4 R/zi_aggregate.R | 182 ++++++++++++++++++++++-------------------- R/zi_crosswalk.R | 4 R/zi_get_demographics.R | 33 ++++--- R/zi_get_geometry.R | 18 ---- R/zi_utils.R | 64 ++++++++++++++ build/vignette.rds |binary inst/doc/converting-zips.Rmd | 2 inst/doc/converting-zips.html | 2 vignettes/converting-zips.Rmd | 2 12 files changed, 204 insertions(+), 135 deletions(-)
Title: Interpreted String Literals
Description: An implementation of interpreted string literals. Based on the
'glue' package by Hester & Bryan (2024) <doi:10.32614/CRAN.package.glue> but
with a focus on efficiency and simplicity at a cost of flexibility.
Author: Tim Taylor [aut, cre] ,
Jim Hester [aut] ,
Jennifer Bryan [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between super versions 0.1.0 dated 2025-03-11 and 0.1.1 dated 2025-04-25
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/glue.R | 2 -- README.md | 2 +- inst/doc/super.Rmd | 2 +- inst/doc/super.html | 34 +++++++++++++++++----------------- src/glue.c | 20 +------------------- src/init.c | 2 -- vignettes/super.Rmd | 2 +- 10 files changed, 37 insertions(+), 55 deletions(-)
Title: Functions for Working with 'Eprime' Text Files
Description: 'Eprime' is a set of programs for administering
psychological experiments by computer. This package provides functions
for loading, parsing, filtering and exporting data in the text files
produced by 'Eprime' experiments.
Author: Tristan Mahr [aut, cre]
Maintainer: Tristan Mahr <tristan.mahr@wisc.edu>
Diff between rprime versions 0.1.2 dated 2020-09-24 and 0.1.3 dated 2025-04-25
DESCRIPTION | 11 MD5 | 28 - NEWS.md | 4 R/to_data_frame.R | 7 build/vignette.rds |binary inst/doc/multiple-files.R | 2 inst/doc/multiple-files.html | 323 +++++++++------- inst/doc/parsing-summary.R | 2 inst/doc/parsing-summary.Rmd | 9 inst/doc/parsing-summary.html | 447 ++++++++++++++-------- inst/doc/quick-start-demo.R | 6 inst/doc/quick-start-demo.html | 810 ++++++++++++++++++++++------------------- man/rprime.Rd | 7 man/to_data_frame.Rd | 8 vignettes/parsing-summary.Rmd | 9 15 files changed, 949 insertions(+), 724 deletions(-)
Title: Synthetic Control Methods with Micro- And Meso-Level Data
Description: A generalization of the 'Synth' package that is
designed for data at a more granular level (e.g., micro-level).
Provides functions to construct weights (including propensity
score-type weights) and run analyses for synthetic control methods
with micro- and meso-level data; see Robbins, Saunders, and Kilmer
(2017) <doi:10.1080/01621459.2016.1213634> and Robbins and Davenport
(2021) <doi:10.18637/jss.v097.i02>.
Author: Michael Robbins [aut, cre],
Steven Davenport [aut]
Maintainer: Michael Robbins <mrobbins@rand.org>
Diff between microsynth versions 2.0.44 dated 2023-06-30 and 2.0.51 dated 2025-04-25
DESCRIPTION | 44 MD5 | 36 NEWS.md | 28 R/microsynth-class.R | 263 -- R/microsynth.R | 2968 +++++++++++++------------- R/miscellaneous.R | 27 R/plot_microsynth.R | 56 R/results.r | 1588 +++++++------ R/weights.r | 2293 ++++++++++---------- build/vignette.rds |binary data/seattledmi.rda |binary inst/doc/aggregating_variables_over_time.html | 642 ++--- inst/doc/ensuring_model_feasibility.html | 718 +++--- inst/doc/introduction.R | 366 +-- inst/doc/introduction.html | 2871 ++++++++++++------------- man/microsynth.Rd | 35 man/plot_microsynth.Rd | 9 man/print.microsynth.Rd | 28 man/summary.microsynth.Rd | 30 19 files changed, 6057 insertions(+), 5945 deletions(-)
Title: Discontinuous Hamiltonian Monte Carlo with Varying Trajectory
Length
Description: Hamiltonian Monte Carlo for both continuous and discontinuous
posterior distributions with customisable trajectory length
termination criterion. See Nishimura et al. (2020) <doi:10.1093/biomet/asz083> for
the original Discontinuous Hamiltonian Monte Carlo,
Hoffman et al. (2014) <doi:10.48550/arXiv.1111.4246> and Betancourt (2016)
<doi:10.48550/arXiv.1601.00225> for the definition of possible Hamiltonian
Monte Carlo termination criteria.
Author: Paolo Manildo [aut, cre]
Maintainer: Paolo Manildo <paolo.manildo@phd.unipd.it>
Diff between XDNUTS versions 1.5.6 dated 2025-01-28 and 1.6 dated 2025-04-25
DESCRIPTION | 8 MD5 | 17 R/RcppExports.R | 35 R/interface.R | 39 build/partial.rdb |binary inst/doc/Tutorial_for_main_functions.R | 4 man/print.XDNUTS.Rd | 2 man/trajectories.Rd |only src/RcppExports.cpp | 20 src/dnuts.cpp | 1458 +++++++++++++++++++++++++++++++++ 10 files changed, 1565 insertions(+), 18 deletions(-)
Title: Design of Experiments Suite: Generate and Evaluate Optimal
Designs
Description: Generates and evaluates D, I, A, Alias, E, T, and G optimal designs. Supports generation and evaluation of blocked and split/split-split/.../N-split plot designs. Includes parametric and Monte Carlo power evaluation functions, and supports calculating power for censored responses. Provides a framework to evaluate power using functions provided in other packages or written by the user. Includes a Shiny graphical user interface that displays the underlying code used to create and evaluate the design to improve ease-of-use and make analyses more reproducible. For details, see Morgan-Wall et al. (2021) <doi:10.18637/jss.v099.i01>.
Author: Tyler Morgan-Wall [aut, cre],
George Khoury [aut]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between skpr versions 1.7.1 dated 2024-03-25 and 1.8.2 dated 2025-04-25
skpr-1.7.1/skpr/R/gen_momentsmatrix.R |only skpr-1.7.1/skpr/R/parallel_search_progress.R |only skpr-1.7.1/skpr/R/shiny_server_code.R |only skpr-1.7.1/skpr/R/shiny_ui_code.R |only skpr-1.7.1/skpr/man/gen_momentsmatrix.Rd |only skpr-1.8.2/skpr/DESCRIPTION | 14 skpr-1.8.2/skpr/MD5 | 144 skpr-1.8.2/skpr/R/add_ci_bounds_mc_power.R | 10 skpr-1.8.2/skpr/R/anticoef_from_delta.R | 43 skpr-1.8.2/skpr/R/anticoef_from_delta_surv.R | 33 skpr-1.8.2/skpr/R/calc_conservative_anticoef.R | 4 skpr-1.8.2/skpr/R/calc_interaction_degrees.R | 99 skpr-1.8.2/skpr/R/calcnoncentralparam.R | 17 skpr-1.8.2/skpr/R/calculate_block_nesting.R | 14 skpr-1.8.2/skpr/R/calculate_convex_hull_moment_matrix.R |only skpr-1.8.2/skpr/R/calculate_degrees_of_freedom.R | 177 skpr-1.8.2/skpr/R/calculate_gefficiency.R | 88 skpr-1.8.2/skpr/R/calculate_level_vector.R | 21 skpr-1.8.2/skpr/R/calculate_power_curves.R | 631 +- skpr-1.8.2/skpr/R/calculate_split_columns.R | 27 skpr-1.8.2/skpr/R/calculate_v_from_blocks.R | 25 skpr-1.8.2/skpr/R/calculatepower.R | 11 skpr-1.8.2/skpr/R/check_for_suggest_packages.R | 18 skpr-1.8.2/skpr/R/constructRunMatrix.R | 2 skpr-1.8.2/skpr/R/contr.simplex.R | 8 skpr-1.8.2/skpr/R/convert_blockcolumn_rownames.R | 142 skpr-1.8.2/skpr/R/convert_model_dots.R | 98 skpr-1.8.2/skpr/R/convert_rownames_to_covariance.R | 48 skpr-1.8.2/skpr/R/disallowed_combinations.R | 26 skpr-1.8.2/skpr/R/effectpower.R | 45 skpr-1.8.2/skpr/R/effectpowermc.R | 136 skpr-1.8.2/skpr/R/eval_design.R | 835 +- skpr-1.8.2/skpr/R/eval_design_custom_mc.R | 287 skpr-1.8.2/skpr/R/eval_design_mc.R | 1330 ++-- skpr-1.8.2/skpr/R/eval_design_survival_mc.R | 358 - skpr-1.8.2/skpr/R/extractPvalues.R | 6 skpr-1.8.2/skpr/R/gen_anticoef.R | 7 skpr-1.8.2/skpr/R/gen_binomial_anticoef.R | 4 skpr-1.8.2/skpr/R/gen_design.R | 1642 +++-- skpr-1.8.2/skpr/R/gen_exponential_anticoef.R | 8 skpr-1.8.2/skpr/R/gen_momentsmatrix_ideal.R |only skpr-1.8.2/skpr/R/gen_poisson_anticoef.R | 6 skpr-1.8.2/skpr/R/generate_noise_block.R | 11 skpr-1.8.2/skpr/R/genparammatrix.R | 4 skpr-1.8.2/skpr/R/get_attribute.R | 54 skpr-1.8.2/skpr/R/get_block_groups.R | 4 skpr-1.8.2/skpr/R/get_moment_matrix.R |only skpr-1.8.2/skpr/R/get_optimality.R | 89 skpr-1.8.2/skpr/R/input_validation.R | 9 skpr-1.8.2/skpr/R/is_intralayer_interaction.R | 51 skpr-1.8.2/skpr/R/methods.R | 364 - skpr-1.8.2/skpr/R/normalize_design.R | 24 skpr-1.8.2/skpr/R/normalize_numeric_runmatrix.R | 13 skpr-1.8.2/skpr/R/parameterpower.R | 48 skpr-1.8.2/skpr/R/permutation_functions.R | 22 skpr-1.8.2/skpr/R/plot_correlations.R | 124 skpr-1.8.2/skpr/R/plot_fds.R | 114 skpr-1.8.2/skpr/R/quad.R | 19 skpr-1.8.2/skpr/R/rearrange_formula_by_order.R | 24 skpr-1.8.2/skpr/R/reduceRunMatrix.R | 29 skpr-1.8.2/skpr/R/remove_skpr_blockcols.R | 2 skpr-1.8.2/skpr/R/set_up_progressr_handler.R | 34 skpr-1.8.2/skpr/R/skprGUI.R | 4973 +++++++++------- skpr-1.8.2/skpr/R/skprGUI_dynamic_ui_elements.R | 293 skpr-1.8.2/skpr/R/startupmessage.R | 4 skpr-1.8.2/skpr/R/zzz.R | 17 skpr-1.8.2/skpr/man/convhull_halfspace.Rd |only skpr-1.8.2/skpr/man/detect_disallowed_combinations.Rd |only skpr-1.8.2/skpr/man/eval_design.Rd | 13 skpr-1.8.2/skpr/man/eval_design_mc.Rd | 14 skpr-1.8.2/skpr/man/gen_design.Rd | 11 skpr-1.8.2/skpr/man/gen_exponential_anticoef.Rd | 2 skpr-1.8.2/skpr/man/gen_momentsmatrix_constrained.Rd |only skpr-1.8.2/skpr/man/gen_momentsmatrix_ideal.Rd |only skpr-1.8.2/skpr/man/get_moment_matrix.Rd |only skpr-1.8.2/skpr/man/interpolate_convex_hull.Rd |only skpr-1.8.2/skpr/src/RcppExports.cpp | 2 skpr-1.8.2/skpr/src/genOptimalDesign.cpp | 20 skpr-1.8.2/skpr/src/genSplitPlotOptimalDesign.cpp | 4 skpr-1.8.2/skpr/src/getBlockedOptimalDesign.cpp | 6 80 files changed, 8421 insertions(+), 4341 deletions(-)
Title: R Bayesian Evidence Synthesis Tools
Description: Tool-set to support Bayesian evidence synthesis. This
includes meta-analysis, (robust) prior derivation from historical
data, operating characteristics and analysis (1 and 2 sample
cases). Please refer to Weber et al. (2021) <doi:10.18637/jss.v100.i19>
for details on applying this package while Neuenschwander et al. (2010)
<doi:10.1177/1740774509356002> and Schmidli et al. (2014)
<doi:10.1111/biom.12242> explain details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Beat Neuenschwander [ctb],
Heinz Schmidli [ctb],
Baldur Magnusson [ctb],
Yue Li [ctb],
Satrajit Roychoudhury [ctb],
Lukas A. Widmer [ctb] ,
Trustees of Columbia University [cph]
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between RBesT versions 1.8-1 dated 2025-01-21 and 1.8-2 dated 2025-04-25
DESCRIPTION | 12 MD5 | 233 +++++---- NAMESPACE | 6 NEWS.md | 13 R/AS.R | 2 R/BinaryExactCI.R | 7 R/EM_bmm_ab.R | 101 +++- R/EM_bmm_mun.R | 81 ++- R/EM_gmm.R | 79 ++- R/EM_mnmm.R | 128 ++++- R/EM_msmm.R | 70 ++ R/EM_plot.R | 112 +++- R/KLdivmix.R | 12 R/RBesT-package.R | 58 +- R/SimSum.R | 10 R/automixfit.R | 39 + R/colVars.R | 10 R/colitis.R | 2 R/crohn.R | 2 R/dBetaBinomial.R | 11 R/decision1S.R | 18 R/decision1S_boundary.R | 41 + R/decision2S.R | 57 +- R/decision2S_boundary.R | 131 ++++- R/dlink.R | 38 + R/forest_plot.R | 84 ++- R/gMAP.R | 506 ++++++++++++++------- R/get_color.R | 10 R/integrate_logit_log.R | 104 +++- R/knn.R | 24 - R/likelihood.R | 4 R/lodds.R | 12 R/mix.R | 183 +++++-- R/mixbeta.R | 17 R/mixcombine.R | 12 R/mixdiff.R | 72 ++- R/mixess.R | 123 +++-- R/mixfit.R | 68 +- R/mixgamma.R | 32 - R/mixjson.R |only R/mixmode.R | 7 R/mixmvnorm.R | 208 +++++++- R/mixnorm.R | 23 R/mixplot.R | 68 ++ R/mixstanvar.R | 164 ++++-- R/oc1S.R | 12 R/oc2S.R | 85 ++- R/plot_gMAP.R | 131 ++++- R/pos1S.R | 10 R/pos2S.R | 79 ++- R/postmix.R | 57 +- R/preddist.R | 11 R/predict_gMAP.R | 64 ++ R/robustify.R | 61 +- R/support.R | 3 R/sysdata.rda |binary R/transplant.R | 2 R/uniroot_int.R | 19 R/zzz.R | 10 data/AS.rda |binary data/colitis.rda |binary data/crohn.rda |binary data/transplant.rda |binary inst/doc/RBesT.pdf |binary inst/doc/introduction.R | 2 inst/doc/introduction.html | 98 ++-- inst/doc/settings-knitr.txt | 2 inst/sbc/sbc_report.html | 927 ++++++++++++++++----------------------- man/AS.Rd | 8 man/BinaryExactCI.Rd | 4 man/RBesT-package.Rd | 20 man/SimSum.Rd | 2 man/automixfit.Rd | 2 man/colitis.Rd | 6 man/crohn.Rd | 6 man/decision1S.Rd | 4 man/decision1S_boundary.Rd | 2 man/ess.Rd | 20 man/figures |only man/forest_plot.Rd | 8 man/gMAP.Rd | 15 man/likelihood.Rd | 4 man/lodds.Rd | 12 man/mix.Rd | 13 man/mixbeta.Rd | 1 man/mixcombine.Rd | 3 man/mixdiff.Rd | 4 man/mixfit.Rd | 8 man/mixgamma.Rd | 1 man/mixjson.Rd |only man/mixmvnorm.Rd | 65 +- man/mixnorm.Rd | 1 man/mixplot.Rd | 7 man/mixstanvar.Rd | 54 +- man/oc1S.Rd | 4 man/oc2S.Rd | 4 man/plot.EM.Rd | 6 man/plot.gMAP.Rd | 8 man/pos2S.Rd | 4 man/postmix.Rd | 6 man/preddist.Rd | 4 man/predict.gMAP.Rd | 4 man/robustify.Rd | 4 man/transplant.Rd | 6 src/stanExports_gMAP.cc | 34 - tests/testthat/helper-utils.R | 24 - tests/testthat/test-EM.R | 102 ++-- tests/testthat/test-gMAP.R | 302 ++++++++---- tests/testthat/test-mixdiff.R | 49 +- tests/testthat/test-mixdist.R | 419 +++++++++++++++++ tests/testthat/test-mixjson.R |only tests/testthat/test-mixstanvar.R | 240 ++++++++-- tests/testthat/test-oc1S.R | 22 tests/testthat/test-oc2S.R | 328 +++++++++++-- tests/testthat/test-pos2S.R | 84 ++- tests/testthat/test-preddist.R | 18 tests/testthat/test-utils.R | 359 ++++++++++++--- vignettes/settings-knitr.txt | 2 118 files changed, 4842 insertions(+), 2028 deletions(-)
Title: Adaptive, Sine-Multitaper Power Spectral Density and Cross
Spectrum Estimation
Description: Produces power spectral density estimates through iterative
refinement of the optimal number of sine-tapers at each frequency. This
optimization procedure is based on the method of Riedel and Sidorenko
(1995), which minimizes the Mean Square Error (sum of variance and bias)
at each frequency, but modified for computational stability. The same
procedure can now be used to calculate the cross spectrum (multivariate
analyses).
Author: Andrew J. Barbour [aut, cre] ,
Jonathan Kennel [aut] ,
Robert L. Parker [aut]
Maintainer: Andrew J. Barbour <andy.barbour@gmail.com>
Diff between psd versions 2.1.1 dated 2022-01-31 and 2.1.2 dated 2025-04-25
DESCRIPTION | 15 ++-- MD5 | 41 ++++++----- R/func_riedsid.R | 2 R/func_tapers.R | 2 R/psd-package.R | 5 - README.md | 12 ++- build/partial.rdb |only build/vignette.rds |binary inst/NEWS.Rd | 18 ++--- inst/doc/fftw.R | 152 ++++++++++++++++++++++---------------------- inst/doc/fftw.pdf |binary inst/doc/multivariate.pdf |binary inst/doc/normalization.Rnw | 2 inst/doc/normalization.pdf |binary inst/doc/psd_overview.R | 2 inst/doc/psd_overview.pdf |binary man/psd-package.Rd | 17 ++++ man/riedsid.Rd | 2 man/wipp30.Rd | 3 src/resample_fft.cpp | 5 - tests/testthat/Rplots.pdf |binary vignettes/normalization.Rnw | 2 22 files changed, 151 insertions(+), 129 deletions(-)
Title: Designing and Weighting Survey Samples
Description: Functions and datasets to support Valliant, Dever, and Kreuter (2018), <doi:10.1007/978-3-319-93632-1>, "Practical Tools for Designing and Weighting Survey Samples". Contains functions for sample size calculation for survey samples using stratified or clustered one-, two-, and three-stage sample designs, and single-stage audit sample designs. Functions are included that will group geographic units accounting for distances apart and measures of size. Other functions compute variance components for multistage designs and sample sizes in two-phase designs. A number of example data sets are included.
Author: Richard Valliant [aut, cre],
Jill A. Dever [ctb],
Frauke Kreuter [ctb],
George Zipf [aut]
Maintainer: Richard Valliant <valliant@umich.edu>
Diff between PracTools versions 1.5 dated 2024-06-24 and 1.6 dated 2025-04-25
DESCRIPTION | 10 +++--- MD5 | 52 ++++++++++++++++++------------------ NAMESPACE | 3 ++ NEWS.md | 6 +++- R/SampStop.R |only build/vignette.rds |binary data/Domainy1y2.RData |binary data/MDarea.popA.RData |binary data/TPV.RData |binary data/Test_Data_US.RData |binary data/ThirdGrade.RData |binary data/hospital.RData |binary data/labor.RData |binary data/mibrfss.RData |binary data/nhis.RData |binary data/nhis.large.RData |binary data/nhispart.RData |binary data/smho.N874.RData |binary data/smho98.RData |binary inst/doc/Design-effects.html | 8 ++--- inst/doc/Distance-and-MOS-PSUs.html | 14 ++++----- inst/doc/Select-samsize-fcns.html | 2 - inst/doc/Singlestage-samsize.html | 8 ++--- inst/doc/Varcomps-multistage.html | 6 ++-- man/BW2stageSRS.Rd | 4 +- man/SampStop.Rd |only man/nAuditAttr.Rd | 4 +- man/smho.N874.Rd | 2 - 28 files changed, 64 insertions(+), 55 deletions(-)
Title: Bayesian Logistic Regression for Oncology Dose-Escalation Trials
Description: Bayesian logistic regression model with optional
EXchangeability-NonEXchangeability parameter modelling for flexible
borrowing from historical or concurrent data-sources. The safety model
can guide dose-escalation decisions for adaptive oncology Phase I
dose-escalation trials which involve an arbitrary number of
drugs. Please refer to Neuenschwander et al. (2008)
<doi:10.1002/sim.3230> and Neuenschwander et al. (2016)
<doi:10.1080/19466315.2016.1174149> for details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Lukas A. Widmer [aut],
Andrew Bean [aut],
Trustees of Columbia University [cph]
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between OncoBayes2 versions 0.9-2 dated 2025-04-07 and 0.9-3 dated 2025-04-25
DESCRIPTION | 8 MD5 | 78 NEWS.md | 9 R/blrm_exnex.R | 847 ++- R/blrm_formula_linear.R | 80 R/blrm_formula_saturating.R | 108 R/blrm_trial.R | 611 ++ R/critical_quantile.R | 148 R/diagnostics.R | 5 R/example_model.R | 5 R/lodds.R | 8 R/nsamples.R | 5 R/plot_blrm.R | 618 +- R/posterior.R | 272 - R/posterior_linpred.R | 32 R/posterior_predict.R | 24 R/pp_data.R | 56 R/predictive_interval.R | 22 R/prior_summary.R | 188 R/summary.R | 182 R/sysdata.rda |binary R/update.R | 31 R/zzz.R | 10 inst/doc/OncoBayes2.pdf |binary inst/doc/introduction.html | 12 inst/doc/map_approach.html | 12 man/blrm_exnex.Rd | 2 man/lodds.Rd | 8 tests/testthat/helper-load_gold.R | 10 tests/testthat/helper-sampling.R | 120 tests/testthat/helper-trial_examples.R | 5 tests/testthat/test-blrm_exnex.R | 3938 ++++++++++++------ tests/testthat/test-blrm_trial.R | 1068 +++- tests/testthat/test-critical_quantile.R | 104 tests/testthat/test-examples.R | 46 tests/testthat/test-plot_toxicity_curve.R | 379 - tests/testthat/test-plot_toxicity_intervals.R | 217 tests/testthat/test-plot_toxicity_intervals_stacked.R | 473 +- tests/testthat/test-posterior.R | 195 tests/testthat/test-sbc.R | 32 40 files changed, 6923 insertions(+), 3045 deletions(-)
Title: Faster Raster and Spatial Vector Processing Using 'GRASS GIS'
Description: Processing of large-in-memory/large-on disk rasters and spatial
vectors using 'GRASS GIS' <https://grass.osgeo.org/>. Most functions in
the 'terra' package are recreated. Processing of medium-sized and smaller
spatial objects will nearly always be faster using 'terra' or 'sf', but
for large-in-memory/large-on-disk objects, 'fasterRaster' may be faster.
To use most of the functions, you must have the stand-alone version (not
the 'OSGeoW4' installer version) of 'GRASS GIS' 8.0 or higher.
Author: Adam B. Smith [cre, aut]
Maintainer: Adam B. Smith <adam.smith@mobot.org>
Diff between fasterRaster versions 8.4.0.5 dated 2025-02-25 and 8.4.0.7 dated 2025-04-25
DESCRIPTION | 12 +++++----- MD5 | 44 +++++++++++++++++++------------------- NAMESPACE | 1 NEWS.md | 10 +++++++- R/03_options.r | 1 R/dim.r | 11 +++++++++ R/extract.r | 2 - R/fast.r | 11 +++++---- R/mow.r | 8 +++--- R/plot.r | 9 +++---- R/plotRGB.r | 7 +++--- R/subset_single_bracket.r | 3 +- README.md | 4 +-- inst/doc/GRasters.html | 4 +-- inst/doc/addons.html | 4 +-- inst/doc/fasterRaster.html | 23 ++++++++++--------- inst/doc/faster_fasterRaster.html | 4 +-- inst/doc/hidden_functions.html | 4 +-- inst/doc/projects_mapsets.html | 4 +-- inst/doc/regions.html | 4 +-- inst/doc/three_d_objects.html | 4 +-- inst/pkgdown.yml | 4 +-- man/mow.Rd | 7 +++--- 23 files changed, 104 insertions(+), 81 deletions(-)
Title: Small Area Estimation for Key Health and Demographic Indicators
from Household Surveys
Description: Enables small area estimation (SAE) of health and demographic indicators in low- and middle-income countries (LMICs). It powers an R 'shiny' application that helps public health analysts, policymakers, and researchers generate subnational estimates and prevalence maps for 150+ binary indicators from Demographic and Health Surveys (DHS). Basing its core SAE analysis workflow on the 'surveyPrev' package, the app ensures methodological rigor through guided model selection, automated fitting, and interactive visualization. For more details, visit <https://sae4health.stat.uw.edu/>.
Author: Yunhan Wu [cre, aut],
Qianyu Dong [aut],
Zehang R Li [aut],
Jon Wakefield [aut]
Maintainer: Yunhan Wu <wu-thomas@outlook.com>
Diff between sae4health versions 1.2.1 dated 2025-04-01 and 1.2.2 dated 2025-04-25
DESCRIPTION | 6 MD5 | 26 +- R/app_server.R | 182 ++++++++-------- R/fct_analysis_helpers.R | 12 - R/fct_dat_input_helpers.R | 6 R/fct_helpers.R | 7 R/mod_landing_page.R | 196 ++++++++++++++--- R/mod_model_selection.R | 300 +++++++++++++++++++++++++- R/mod_survey_dat_input.R | 498 ++++++++++++++++++++++++++++++++------------ R/prepare_preload_dat.R | 41 +-- data/DHS_api_est.rda |binary data/indicator_list_all.rda |binary data/indicator_list_new.rda |binary data/match_all_result.rda |binary 14 files changed, 969 insertions(+), 305 deletions(-)
Title: Risk Calculator for Cardiovascular Disease in Japan
Description: A calculation tool to obtain the 10-year risk of cardiovascular disease from various risk models (Hisayama, Suita, EPOCH Japan).
Author: Hiroshi Okumiyama [aut, cre],
Ryosuke Fujii [aut]
Maintainer: Hiroshi Okumiyama <xzxz2019@iCloud.com>
Diff between Jcvrisk versions 0.1.1 dated 2025-04-18 and 0.1.2 dated 2025-04-25
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 6 ++++++ R/02_suita_wECG.R | 2 +- R/03_suita_woECG.R | 2 +- 5 files changed, 15 insertions(+), 9 deletions(-)
Title: Meta Clustering with Similarity Network Fusion
Description: Framework to facilitate patient subtyping with similarity network fusion and meta clustering. The similarity network fusion (SNF) algorithm was introduced by Wang et al. (2014) in <doi:10.1038/nmeth.2810>. SNF is a data integration approach that can transform high-dimensional and diverse data types into a single similarity network suitable for clustering with minimal loss of information from each initial data source. The meta clustering approach was introduced by Caruana et al. (2006) in <doi:10.1109/ICDM.2006.103>. Meta clustering involves generating a wide range of cluster solutions by adjusting clustering hyperparameters, then clustering the solutions themselves into a manageable number of qualitatively similar solutions, and finally characterizing representative solutions to find ones that are best for the user's specific context. This package provides a framework to easily transform multi-modal data into a wide range of similarity network fusion-derived cluster solutio [...truncated...]
Author: Prashanth S Velayudhan [aut, cre],
Xiaoqiao Xu [aut],
Prajkta Kallurkar [aut],
Ana Patricia Balbon [aut],
Maria T Secara [aut],
Adam Taback [aut],
Denise Sabac [aut],
Nicholas Chan [aut],
Shihao Ma [aut],
Bo Wang [aut],
Daniel Felsky [aut],
Stephanie [...truncated...]
Maintainer: Prashanth S Velayudhan <psvelayu@gmail.com>
Diff between metasnf versions 2.0.6 dated 2025-03-25 and 2.1.1 dated 2025-04-25
metasnf-2.0.6/metasnf/R/arrange.R |only metasnf-2.0.6/metasnf/man/arrange.Rd |only metasnf-2.0.6/metasnf/man/config_heatmap.Rd |only metasnf-2.0.6/metasnf/man/meta_cluster_heatmap.Rd |only metasnf-2.1.1/metasnf/DESCRIPTION | 6 metasnf-2.1.1/metasnf/MD5 | 379 +- metasnf-2.1.1/metasnf/NAMESPACE | 95 metasnf-2.1.1/metasnf/NEWS.md | 31 metasnf-2.1.1/metasnf/R/alluvial_plot.R | 11 metasnf-2.1.1/metasnf/R/as_data_frame.R | 94 metasnf-2.1.1/metasnf/R/as_list.R | 38 metasnf-2.1.1/metasnf/R/as_matrix.R | 12 metasnf-2.1.1/metasnf/R/assignment.R | 118 metasnf-2.1.1/metasnf/R/batch_snf.R | 26 metasnf-2.1.1/metasnf/R/c.R | 71 metasnf-2.1.1/metasnf/R/clust_fns_list.R | 16 metasnf-2.1.1/metasnf/R/coclustering.R | 444 +-- metasnf-2.1.1/metasnf/R/data.R | 199 + metasnf-2.1.1/metasnf/R/data_list.R | 69 metasnf-2.1.1/metasnf/R/deprecated.R | 355 +- metasnf-2.1.1/metasnf/R/dist_fns_list.R | 15 metasnf-2.1.1/metasnf/R/ext_solutions_df.R | 28 metasnf-2.1.1/metasnf/R/extraction.R | 36 metasnf-2.1.1/metasnf/R/feature_plots.R | 28 metasnf-2.1.1/metasnf/R/features.R | 4 metasnf-2.1.1/metasnf/R/get_representative_solutions.R | 2 metasnf-2.1.1/metasnf/R/heatmaps.R | 1350 +++------- metasnf-2.1.1/metasnf/R/label_propagation.R | 6 metasnf-2.1.1/metasnf/R/manhattan_plot.R | 4 metasnf-2.1.1/metasnf/R/merge.R | 237 + metasnf-2.1.1/metasnf/R/n_features.R | 2 metasnf-2.1.1/metasnf/R/n_observations.R | 2 metasnf-2.1.1/metasnf/R/nclust_estimation.R | 5 metasnf-2.1.1/metasnf/R/nmi.R | 174 - metasnf-2.1.1/metasnf/R/plot.R |only metasnf-2.1.1/metasnf/R/print.R | 658 ++-- metasnf-2.1.1/metasnf/R/quality_measures.R | 40 metasnf-2.1.1/metasnf/R/rbind.R | 68 metasnf-2.1.1/metasnf/R/settings_df.R | 27 metasnf-2.1.1/metasnf/R/signal.R | 8 metasnf-2.1.1/metasnf/R/snf_config.R | 2 metasnf-2.1.1/metasnf/R/solutions_df.R | 2 metasnf-2.1.1/metasnf/R/str.R |only metasnf-2.1.1/metasnf/R/summary.R | 260 + metasnf-2.1.1/metasnf/R/summary_features.R | 2 metasnf-2.1.1/metasnf/R/t.R | 138 - metasnf-2.1.1/metasnf/R/uids.R | 41 metasnf-2.1.1/metasnf/R/utils.R | 381 +- metasnf-2.1.1/metasnf/README.md | 2 metasnf-2.1.1/metasnf/build/partial.rdb |binary metasnf-2.1.1/metasnf/build/vignette.rds |binary metasnf-2.1.1/metasnf/data/cache_a_complete_example_ext_sol_df.rda |only metasnf-2.1.1/metasnf/data/cache_a_complete_example_lp_ext_sol_df.rda |only metasnf-2.1.1/metasnf/data/cache_a_complete_example_sol_df.rda |only metasnf-2.1.1/metasnf/data/mock_ari_matrix.rda |only metasnf-2.1.1/metasnf/data/mock_clust_fns_list.rda |only metasnf-2.1.1/metasnf/data/mock_data_list.rda |only metasnf-2.1.1/metasnf/data/mock_dist_fns_list.rda |only metasnf-2.1.1/metasnf/data/mock_ext_solutions_df.rda |only metasnf-2.1.1/metasnf/data/mock_mc_solutions_df.rda |only metasnf-2.1.1/metasnf/data/mock_rep_solutions_df.rda |only metasnf-2.1.1/metasnf/data/mock_settings_df.rda |only metasnf-2.1.1/metasnf/data/mock_snf_config.rda |only metasnf-2.1.1/metasnf/data/mock_solutions_df.rda |only metasnf-2.1.1/metasnf/data/mock_t_solutions_df.rda |only metasnf-2.1.1/metasnf/data/mock_weights_matrix.rda |only metasnf-2.1.1/metasnf/inst/doc/a_complete_example.R | 94 metasnf-2.1.1/metasnf/inst/doc/a_complete_example.Rmd | 43 metasnf-2.1.1/metasnf/inst/doc/a_complete_example.html | 1001 +++---- metasnf-2.1.1/metasnf/inst/doc/a_simple_example.html | 4 metasnf-2.1.1/metasnf/inst/doc/alluvial_plots.html | 4 metasnf-2.1.1/metasnf/inst/doc/clustering_algorithms.R | 35 metasnf-2.1.1/metasnf/inst/doc/clustering_algorithms.Rmd | 13 metasnf-2.1.1/metasnf/inst/doc/clustering_algorithms.html | 65 metasnf-2.1.1/metasnf/inst/doc/confounders.html | 42 metasnf-2.1.1/metasnf/inst/doc/distance_metrics.html | 2 metasnf-2.1.1/metasnf/inst/doc/feature_plots.html | 8 metasnf-2.1.1/metasnf/inst/doc/label_propagation.R | 110 metasnf-2.1.1/metasnf/inst/doc/label_propagation.Rmd | 121 metasnf-2.1.1/metasnf/inst/doc/label_propagation.html | 254 - metasnf-2.1.1/metasnf/inst/doc/nmi_scores.R | 4 metasnf-2.1.1/metasnf/inst/doc/nmi_scores.Rmd | 4 metasnf-2.1.1/metasnf/inst/doc/nmi_scores.html | 10 metasnf-2.1.1/metasnf/inst/doc/snf_config.html | 4 metasnf-2.1.1/metasnf/man/abcd_anxiety.Rd | 2 metasnf-2.1.1/metasnf/man/abcd_colour.Rd | 2 metasnf-2.1.1/metasnf/man/abcd_cort_sa.Rd | 2 metasnf-2.1.1/metasnf/man/abcd_cort_t.Rd | 2 metasnf-2.1.1/metasnf/man/abcd_depress.Rd | 2 metasnf-2.1.1/metasnf/man/abcd_h_income.Rd | 2 metasnf-2.1.1/metasnf/man/abcd_income.Rd | 2 metasnf-2.1.1/metasnf/man/abcd_pubertal.Rd | 2 metasnf-2.1.1/metasnf/man/abcd_subc_v.Rd | 2 metasnf-2.1.1/metasnf/man/add_settings_df_rows.Rd | 2 metasnf-2.1.1/metasnf/man/adjusted_rand_index_heatmap.Rd | 1 metasnf-2.1.1/metasnf/man/alluvial_cluster_plot.Rd | 11 metasnf-2.1.1/metasnf/man/anxiety.Rd | 2 metasnf-2.1.1/metasnf/man/arrange_dll.Rd | 7 metasnf-2.1.1/metasnf/man/as.data.frame.settings_df.Rd |only metasnf-2.1.1/metasnf/man/as.data.frame.snf_config.Rd |only metasnf-2.1.1/metasnf/man/as.data.frame.t_ext_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/as.data.frame.t_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/as.data.frame.weights_matrix.Rd |only metasnf-2.1.1/metasnf/man/as.list.sim_mats_list.Rd |only metasnf-2.1.1/metasnf/man/as.list.snf_config.Rd |only metasnf-2.1.1/metasnf/man/as.matrix.ari_matrix.Rd |only metasnf-2.1.1/metasnf/man/assoc_pval_heatmap.Rd | 5 metasnf-2.1.1/metasnf/man/batch_snf.Rd | 6 metasnf-2.1.1/metasnf/man/batch_snf_subsamples.Rd | 50 metasnf-2.1.1/metasnf/man/cache_a_complete_example_ext_sol_df.Rd |only metasnf-2.1.1/metasnf/man/cache_a_complete_example_lp_ext_sol_df.Rd |only metasnf-2.1.1/metasnf/man/cache_a_complete_example_sol_df.Rd |only metasnf-2.1.1/metasnf/man/calc_nmis.Rd | 15 metasnf-2.1.1/metasnf/man/calculate_coclustering.Rd | 61 metasnf-2.1.1/metasnf/man/cell_significance_fn.Rd | 2 metasnf-2.1.1/metasnf/man/check_dfll_subitems_are_fns.Rd | 6 metasnf-2.1.1/metasnf/man/check_dll_empty_input.Rd | 4 metasnf-2.1.1/metasnf/man/check_dll_subitem_names.Rd | 2 metasnf-2.1.1/metasnf/man/clust_fns_list.Rd | 2 metasnf-2.1.1/metasnf/man/cocluster_density.Rd | 69 metasnf-2.1.1/metasnf/man/cocluster_heatmap.Rd | 107 metasnf-2.1.1/metasnf/man/coclustering_coverage_check.Rd | 6 metasnf-2.1.1/metasnf/man/collapse_dl.Rd | 1 metasnf-2.1.1/metasnf/man/convert_uids.Rd | 2 metasnf-2.1.1/metasnf/man/cort_sa.Rd | 2 metasnf-2.1.1/metasnf/man/cort_t.Rd | 2 metasnf-2.1.1/metasnf/man/depress.Rd | 2 metasnf-2.1.1/metasnf/man/discretisation_evec_data.Rd | 2 metasnf-2.1.1/metasnf/man/dl_variable_summary.Rd | 1 metasnf-2.1.1/metasnf/man/dlapply.Rd | 2 metasnf-2.1.1/metasnf/man/domains.Rd | 2 metasnf-2.1.1/metasnf/man/ensure_dll_df.Rd | 6 metasnf-2.1.1/metasnf/man/ext_solutions_df.Rd | 2 metasnf-2.1.1/metasnf/man/extend_solutions.Rd | 26 metasnf-2.1.1/metasnf/man/fav_colour.Rd | 2 metasnf-2.1.1/metasnf/man/features.Rd | 1 metasnf-2.1.1/metasnf/man/generate_clust_algs_list.Rd | 1 metasnf-2.1.1/metasnf/man/generate_distance_metrics_list.Rd | 1 metasnf-2.1.1/metasnf/man/generate_settings_matrix.Rd | 1 metasnf-2.1.1/metasnf/man/get_cluster_df.Rd | 1 metasnf-2.1.1/metasnf/man/get_cluster_solutions.Rd | 8 metasnf-2.1.1/metasnf/man/get_clusters.Rd | 1 metasnf-2.1.1/metasnf/man/get_dl_uids.Rd | 1 metasnf-2.1.1/metasnf/man/get_matrix_order.Rd | 2 metasnf-2.1.1/metasnf/man/gselect.Rd | 4 metasnf-2.1.1/metasnf/man/income.Rd | 4 metasnf-2.1.1/metasnf/man/label_propagate.Rd | 6 metasnf-2.1.1/metasnf/man/mc_manhattan_plot.Rd | 2 metasnf-2.1.1/metasnf/man/merge.clust_fns_list.Rd |only metasnf-2.1.1/metasnf/man/merge.dist_fns_list.Rd |only metasnf-2.1.1/metasnf/man/merge.ext_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/merge.settings_df.Rd |only metasnf-2.1.1/metasnf/man/merge.sim_mats_list.Rd |only metasnf-2.1.1/metasnf/man/merge.solutions_df.Rd |only metasnf-2.1.1/metasnf/man/merge.t_ext_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/merge.t_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/merge.weights_matrix.Rd |only metasnf-2.1.1/metasnf/man/metasnf_defunct.Rd | 4 metasnf-2.1.1/metasnf/man/metasnf_deprecated.Rd | 4 metasnf-2.1.1/metasnf/man/metasnf_error.Rd | 4 metasnf-2.1.1/metasnf/man/metasnf_warning.Rd | 4 metasnf-2.1.1/metasnf/man/mock_ari_matrix.Rd |only metasnf-2.1.1/metasnf/man/mock_clust_fns_list.Rd |only metasnf-2.1.1/metasnf/man/mock_data_list.Rd |only metasnf-2.1.1/metasnf/man/mock_dist_fns_list.Rd |only metasnf-2.1.1/metasnf/man/mock_ext_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/mock_mc_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/mock_rep_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/mock_settings_df.Rd |only metasnf-2.1.1/metasnf/man/mock_snf_config.Rd |only metasnf-2.1.1/metasnf/man/mock_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/mock_t_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/mock_weights_matrix.Rd |only metasnf-2.1.1/metasnf/man/n_features.Rd | 1 metasnf-2.1.1/metasnf/man/n_observations.Rd | 1 metasnf-2.1.1/metasnf/man/not_shown_message.Rd | 4 metasnf-2.1.1/metasnf/man/ord_reg_pval.Rd | 2 metasnf-2.1.1/metasnf/man/pl.Rd |only metasnf-2.1.1/metasnf/man/plot.ari_matrix.Rd |only metasnf-2.1.1/metasnf/man/plot.data_list.Rd |only metasnf-2.1.1/metasnf/man/plot.ext_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/plot.snf_config.Rd |only metasnf-2.1.1/metasnf/man/plot.solutions_df.Rd |only metasnf-2.1.1/metasnf/man/prefix_dll_uid.Rd | 2 metasnf-2.1.1/metasnf/man/print.sim_mats_list.Rd |only metasnf-2.1.1/metasnf/man/pubertal.Rd | 2 metasnf-2.1.1/metasnf/man/quality_measures.Rd | 2 metasnf-2.1.1/metasnf/man/random_removal.Rd | 3 metasnf-2.1.1/metasnf/man/rbind.ext_solutions_df.Rd | 4 metasnf-2.1.1/metasnf/man/rbind.solutions_df.Rd | 4 metasnf-2.1.1/metasnf/man/rbind.t_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/rbind.weights_matrix.Rd |only metasnf-2.1.1/metasnf/man/remove_dll_incomplete.Rd | 3 metasnf-2.1.1/metasnf/man/rename_dl.Rd | 2 metasnf-2.1.1/metasnf/man/resample.Rd | 2 metasnf-2.1.1/metasnf/man/settings_df.Rd | 4 metasnf-2.1.1/metasnf/man/snf_config.Rd | 4 metasnf-2.1.1/metasnf/man/snf_scheme.Rd | 2 metasnf-2.1.1/metasnf/man/str.ari_matrix.Rd |only metasnf-2.1.1/metasnf/man/str.clust_fns_list.Rd |only metasnf-2.1.1/metasnf/man/str.data_list.Rd |only metasnf-2.1.1/metasnf/man/str.dist_fns_list.Rd |only metasnf-2.1.1/metasnf/man/str.ext_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/str.settings_df.Rd |only metasnf-2.1.1/metasnf/man/str.sim_mats_list.Rd |only metasnf-2.1.1/metasnf/man/str.snf_config.Rd |only metasnf-2.1.1/metasnf/man/str.solutions_df.Rd |only metasnf-2.1.1/metasnf/man/str.t_ext_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/str.t_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/str.weights_matrix.Rd |only metasnf-2.1.1/metasnf/man/subc_v.Rd | 2 metasnf-2.1.1/metasnf/man/subsample_dl.Rd | 24 metasnf-2.1.1/metasnf/man/subsample_pairwise_aris.Rd | 75 metasnf-2.1.1/metasnf/man/summarize_clust_fns_list.Rd | 5 metasnf-2.1.1/metasnf/man/summarize_dfl.Rd | 11 metasnf-2.1.1/metasnf/man/summarize_dl.Rd | 1 metasnf-2.1.1/metasnf/man/summary.ari_matrix.Rd |only metasnf-2.1.1/metasnf/man/summary.clust_fns_list.Rd |only metasnf-2.1.1/metasnf/man/summary.dist_fns_list.Rd |only metasnf-2.1.1/metasnf/man/summary.ext_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/summary.settings_df.Rd |only metasnf-2.1.1/metasnf/man/summary.sim_mats_list.Rd |only metasnf-2.1.1/metasnf/man/summary.snf_config.Rd |only metasnf-2.1.1/metasnf/man/summary.solutions_df.Rd |only metasnf-2.1.1/metasnf/man/summary.t_ext_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/summary.t_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/summary.weights_matrix.Rd |only metasnf-2.1.1/metasnf/man/summary_features.Rd | 1 metasnf-2.1.1/metasnf/tests/testthat/test-batch_snf.R | 5 metasnf-2.1.1/metasnf/vignettes/a_complete_example.Rmd | 43 metasnf-2.1.1/metasnf/vignettes/clustering_algorithms.Rmd | 13 metasnf-2.1.1/metasnf/vignettes/label_propagation.Rmd | 121 metasnf-2.1.1/metasnf/vignettes/nmi_scores.Rmd | 4 233 files changed, 4212 insertions(+), 3916 deletions(-)
Title: Standardized Git Repository Data
Description: Obtain standardized data from multiple 'Git' services, including 'GitHub' and 'GitLab'.
Designed to be 'Git' service-agnostic, this package assists teams with activities spread across various
'Git' platforms by providing a unified way to access repository data.
Author: Maciej Banas [aut, cre],
Kamil Koziej [aut],
Karolina Marcinkowska [aut],
Matt Secrest [aut]
Maintainer: Maciej Banas <banasmaciek@gmail.com>
Diff between GitStats versions 2.3.0 dated 2025-04-03 and 2.3.1 dated 2025-04-25
DESCRIPTION | 6 MD5 | 78 ++--- NEWS.md | 8 R/EngineGraphQLGitHub.R | 52 ++- R/EngineGraphQLGitLab.R | 136 +++++---- R/EngineRestGitLab.R | 264 +++++++++++------- R/GQLQueryGitLab.R | 5 R/GitHost.R | 184 ++++++++---- R/GitHostGitHub.R | 5 R/GitHostGitLab.R | 85 +++++ R/GitStats.R | 120 ++++---- R/error_handlers.R |only inst/get_orgs_workflow.R | 6 inst/roche/roche_get_issues.R |only inst/roche/roche_get_orgs.R | 3 inst/roche/roche_get_repos_with_R_package.R | 25 + inst/roche/roche_get_repos_workflow.R | 11 tests/testthat/_snaps/00-get_orgs-GitLab.md | 66 ++++ tests/testthat/_snaps/01-get_repos-GitLab.md | 30 ++ tests/testthat/_snaps/01-get_repos-GitStats.md | 8 tests/testthat/_snaps/02-get_commits-GitStats.md | 9 tests/testthat/_snaps/04-get_files_content-GitLab.md | 2 tests/testthat/_snaps/06-get_issues-GitStats.md | 9 tests/testthat/_snaps/get_release-GitStats.md | 9 tests/testthat/_snaps/get_repos_with_R_packages.md | 12 tests/testthat/helper-fixtures.R | 71 ++++ tests/testthat/test-00-get_orgs-GitLab.R | 262 ++++++++++++++++++ tests/testthat/test-01-get_repos-GitHub.R | 11 tests/testthat/test-01-get_repos-GitLab.R | 274 +++++++++++++++++-- tests/testthat/test-01-get_repos-GitStats.R | 15 + tests/testthat/test-02-get_commits-GitLab.R | 7 tests/testthat/test-02-get_commits-GitStats.R | 17 + tests/testthat/test-03-get_files_structure-GitHub.R | 5 tests/testthat/test-03-get_files_structure-GitLab.R | 4 tests/testthat/test-04-get_files_content-GitHub.R | 1 tests/testthat/test-04-get_files_content-GitLab.R | 8 tests/testthat/test-06-get_issues-GitStats.R | 29 +- tests/testthat/test-get_release-GitStats.R | 17 + tests/testthat/test-get_repos_with_R_packages.R | 34 -- tests/testthat/test-get_urls_repos-GitLab.R | 6 tests/testthat/test-helpers.R | 4 41 files changed, 1458 insertions(+), 440 deletions(-)
Title: Procedures for Gaussian and Non Gaussian Geostatistical (Large)
Data Analysis
Description: Functions for Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data analysis are provided for a) (fast) simulation of random fields, b) inference for random fields using standard likelihood and a likelihood approximation method called weighted composite likelihood based on pairs and b) prediction using (local) best linear unbiased prediction. Weighted composite likelihood can be very efficient for estimating massive datasets. Both regression and spatial (temporal) dependence analysis can be jointly performed. Flexible covariance models for spatial and spatial-temporal data on Euclidean domains and spheres are provided. There are also many useful functions for plotting and performing diagnostic analysis. Different non Gaussian random fields can be considered in the analysis. Among them, random fields with marginal distributions such as Skew-Gaussian, Student-t, Tukey-h, Sin-Arcsin, Two-piece, Weibull, Gamma, Log-Gaussian, Binomial, Negative Binomial and Poisson. Se [...truncated...]
Author: Moreno Bevilacqua [aut, cre, cph],
Victor Morales-Onate [ctb],
Francisco Cuevas-Pacheco [ctb],
Christian Caamano-Carrillo [ctb]
Maintainer: Moreno Bevilacqua <moreno.bevilacqua89@gmail.com>
Diff between GeoModels versions 2.1.1 dated 2025-04-13 and 2.1.2 dated 2025-04-25
DESCRIPTION | 8 MD5 | 74 - R/GeoCV.R | 442 +++++--- R/GeoCovariogram.r | 2 R/GeoCovmatrix.r | 4 R/GeoDoScores.R | 2 R/GeoFit.r | 51 R/GeoFit2.R | 8 R/GeoKrig.r | 24 R/GeoKrigloc.R | 146 +- R/GeoLik.r | 322 +++--- R/GeoNA.R | 171 ++- R/GeoNeighIndex.R | 359 +++--- R/GeoNeighbSelect.R | 32 R/GeoNeighborhood.R | 218 +++- R/GeoResiduals.r | 23 R/GeoScatterplot.R | 28 R/GeoSim.r | 3 R/GeoSimapprox.r | 1 R/GeoWls.r | 2 R/Geovarestbootstrap.R | 360 +++--- R/Utility.r | 76 + data/Jamaicatemp.RData |binary data/anomalies.rda |binary data/austemp.rda |binary data/madagascartemp.rda |binary data/spanish_wind.rda |binary data/winds.coords.rda |binary data/winds.rda |binary man/GeoNeighborhood.Rd | 6 man/GeoResiduals.Rd | 2 src/CompositeLikelihood2.c | 2136 +++++++++++++++++++++++++++-------------- src/CompositeLikelihoodCond2.c | 2087 ++++++++++++++++++++++++---------------- src/Distributions.c | 1914 ++++++++++++++++++++---------------- src/GeoModels_init.c | 15 src/Utility.c | 8 src/header.h | 2 src/weightedleastsquare.c | 6 38 files changed, 5224 insertions(+), 3308 deletions(-)
Title: NCA Calculations and Population Model Diagnosis
Description: A flexible tool that can perform
(i) traditional non-compartmental analysis (NCA) and
(ii) Simulation-based posterior predictive checks for population
pharmacokinetic (PK) and/or pharmacodynamic (PKPD) models using
NCA metrics. The methods are described in Acharya et al. (2016)
<doi:10.1016/j.cmpb.2016.01.013>.
Author: Chayan Acharya [aut],
Gulbeyaz Y. Turkyilmaz [aut],
Siv Jonsson [aut],
Mats O. Karlsson [aut],
Andrew C. Hooker [aut, cre]
Maintainer: Andrew C. Hooker <andrew.hooker@uu.se>
Diff between ncappc versions 0.3.0 dated 2018-08-24 and 1.0.0 dated 2025-04-25
DESCRIPTION | 41 - MD5 | 68 +- NAMESPACE | 3 NEWS.md | 17 R/est.nca.R | 4 R/estimate_nca_tidy.R | 32 + R/hist_mean_var.R | 39 + R/hist_mean_var_plot.R | 43 + R/nca.check.obs.R | 4 R/nca_ind_data.R | 2 R/ncappc.R | 4 R/read_nm_table.R | 55 +- R/zzz.R | 7 README.md | 86 ++- build/vignette.rds |binary inst/CITATION | 28 - inst/doc/ncappc-vignette.R | 12 inst/doc/ncappc-vignette.html | 896 +++++++++++++++++++++++++++-------- inst/misc/ncappcReport-NCA-NOPPC.Rnw | 4 inst/misc/ncappcReport-NCA-PPC.Rnw | 4 inst/misc/ncappcReport-NCA.Rnw | 4 man/dv.plot.Rd | 32 - man/est.nca.Rd | 30 - man/histobs.plot.Rd | 11 man/histpop.plot.Rd | 12 man/nca.check.obs.Rd | 42 + man/nca.check.sim.Rd | 28 - man/nca.deviation.plot.Rd | 11 man/nca.ind.data.Rd | 18 man/nca.npde.plot.Rd | 10 man/nca.pde.deviation.outlier.Rd | 18 man/nca_ind_data.Rd | 17 man/ncappc.Rd | 83 ++- man/read_nm_table.Rd | 13 tests/testthat/test-ncappc.R | 46 - 35 files changed, 1310 insertions(+), 414 deletions(-)
Title: Automatic Replication Tools for Meta-Analysis
Description: Provides a unified and straightforward interface for performing a variety of meta-analysis methods directly from user data. Users can input a data frame, specify key parameters, and effortlessly execute and compare multiple common meta-analytic models. Designed for immediate usability, the package facilitates transparent, reproducible research without manual implementation of each analytical method. Ideal for researchers aiming for efficiency and reproducibility, it streamlines workflows from data preparation to results interpretation.
Author: Petr Čala [aut, cre]
Maintainer: Petr Čala <61505008@fsv.cuni.cz>
Diff between artma versions 0.1.19 dated 2025-04-12 and 0.2.1 dated 2025-04-25
artma-0.1.19/artma/R/setup.R |only artma-0.1.19/artma/inst/artma/data/clean.R |only artma-0.1.19/artma/inst/artma/libs/logs |only artma-0.1.19/artma/inst/artma/testing/test_const.R |only artma-0.1.19/artma/inst/artma/testing/test_utils.R |only artma-0.1.19/artma/man/artma.setup.Rd |only artma-0.1.19/artma/man/ensure_valid_boxpath.Rd |only artma-0.1.19/artma/man/static_setup.Rd |only artma-0.1.19/artma/tests/E2E/test_installation.R |only artma-0.2.1/artma/DESCRIPTION | 14 artma-0.2.1/artma/MD5 | 123 ++-- artma-0.2.1/artma/NAMESPACE | 3 artma-0.2.1/artma/NEWS.md |only artma-0.2.1/artma/R/aaa.R | 50 - artma-0.2.1/artma/R/data_config.R |only artma-0.2.1/artma/R/dummy_functions.R | 10 artma-0.2.1/artma/R/globals.R | 30 - artma-0.2.1/artma/R/main.R | 16 artma-0.2.1/artma/R/methods.R | 6 artma-0.2.1/artma/R/options.R | 167 +++-- artma-0.2.1/artma/R/run.R | 29 - artma-0.2.1/artma/R/zzz.R |only artma-0.2.1/artma/build/vignette.rds |binary artma-0.2.1/artma/inst/artma/calc/dof.R | 3 artma-0.2.1/artma/inst/artma/calc/index.R |only artma-0.2.1/artma/inst/artma/calc/meta.R |only artma-0.2.1/artma/inst/artma/calc/pcc.R | 21 artma-0.2.1/artma/inst/artma/const.R | 50 + artma-0.2.1/artma/inst/artma/data/compute.R |only artma-0.2.1/artma/inst/artma/data/fill.R | 65 -- artma-0.2.1/artma/inst/artma/data/index.R | 21 artma-0.2.1/artma/inst/artma/data/preprocess.R | 244 +++++--- artma-0.2.1/artma/inst/artma/data/read.R | 36 - artma-0.2.1/artma/inst/artma/data/utils.R | 122 +++- artma-0.2.1/artma/inst/artma/data_config |only artma-0.2.1/artma/inst/artma/libs/ask.R |only artma-0.2.1/artma/inst/artma/libs/file_utils.R | 10 artma-0.2.1/artma/inst/artma/libs/modules.R | 17 artma-0.2.1/artma/inst/artma/libs/number_utils.R | 23 artma-0.2.1/artma/inst/artma/libs/path.R | 9 artma-0.2.1/artma/inst/artma/libs/string.R | 53 + artma-0.2.1/artma/inst/artma/libs/utils.R | 26 artma-0.2.1/artma/inst/artma/libs/validation.R | 45 + artma-0.2.1/artma/inst/artma/methods/variable_summary_stats.R | 2 artma-0.2.1/artma/inst/artma/options/ask.R | 5 artma-0.2.1/artma/inst/artma/options/prompts.R |only artma-0.2.1/artma/inst/artma/options/template.R | 289 ++++++---- artma-0.2.1/artma/inst/artma/options/templates/options_template.yaml | 211 ++++--- artma-0.2.1/artma/inst/artma/options/utils.R | 71 +- artma-0.2.1/artma/inst/artma/paths.R | 38 - artma-0.2.1/artma/inst/artma/testing/fixtures |only artma-0.2.1/artma/inst/artma/testing/load_test_modules.R |only artma-0.2.1/artma/inst/artma/testing/mocks/index.R |only artma-0.2.1/artma/inst/artma/testing/mocks/mock_df.R | 86 ++ artma-0.2.1/artma/inst/artma/testing/mocks/mock_options.R |only artma-0.2.1/artma/inst/artma/testing/mocks/mock_utils.R | 2 artma-0.2.1/artma/man/config.fix.Rd |only artma-0.2.1/artma/man/dot-onLoad.Rd |only artma-0.2.1/artma/man/dot-onUnload.Rd |only artma-0.2.1/artma/man/get_valid_boxpath.Rd |only artma-0.2.1/artma/man/is_devtools_load.Rd |only artma-0.2.1/artma/man/main.Rd | 8 artma-0.2.1/artma/man/methods.list.Rd | 2 artma-0.2.1/artma/man/options.copy.Rd | 5 artma-0.2.1/artma/man/options.create.Rd | 2 artma-0.2.1/artma/man/options.help.Rd | 2 artma-0.2.1/artma/man/options.load.Rd | 6 artma-0.2.1/artma/man/options.modify.Rd | 2 artma-0.2.1/artma/man/options.open.Rd |only artma-0.2.1/artma/man/run.Rd | 4 artma-0.2.1/artma/man/runtime_setup.Rd | 2 artma-0.2.1/artma/tests/E2E/test-installation.R |only artma-0.2.1/artma/tests/testthat/helper.R |only artma-0.2.1/artma/tests/testthat/setup.R |only artma-0.2.1/artma/tests/testthat/test-data-utils.R |only artma-0.2.1/artma/tests/testthat/test-dir_create_linter.R | 2 76 files changed, 1236 insertions(+), 696 deletions(-)
Title: Extracting Signals from Wavelet Spectra
Description: The continuous wavelet transform enables the observation of transient/non-stationary cyclicity in time-series. The goal of cyclostratigraphic studies is to define frequency/period in the depth/time domain. By conducting the continuous wavelet transform on cyclostratigraphic data series one can observe and extract cyclic signals/signatures from signals. These results can then be visualized and interpreted enabling one to identify/interpret cyclicity in the geological record, which can be used to construct astrochronological age-models and identify and interpret cyclicity in past and present climate systems. The 'WaverideR' R package builds upon existing literature and existing codebase. The list of articles which are relevant can be grouped in four subjects; cyclostratigraphic data analysis,example data sets,the (continuous) wavelet transform and astronomical solutions. References for the cyclostratigraphic data analysis articles are: Stephen Meyers (2019) <doi:10.1016/j.earscirev.20 [...truncated...]
Author: Michiel Arts [aut, cre]
Maintainer: Michiel Arts <michiel.arts@stratigraphy.eu>
Diff between WaverideR versions 0.3.2 dated 2023-09-06 and 0.4.0 dated 2025-04-25
DESCRIPTION | 18 MD5 | 132 +-- NAMESPACE | 17 NEWS.md | 10 R/Hilbert_transform.R | 4 R/WaverideR.R | 3 R/WaverideR_Datasets.R | 18 R/add_wavelet.R | 35 R/add_wavelet_avg.R | 7 R/analyze_wavelet.R | 513 ++++++++++++- R/anchor2time.R | 54 + R/astro_anchor.R | 3 R/curve2time_unc_anchor.R | 1214 +++++++++++++++++++++++-------- R/curve2tune.R | 8 R/dur_gaps.R | 77 + R/dynamic_extraction.R |only R/extract_amplitude.R | 6 R/extract_power.R | 3 R/extract_power_stable.R | 3 R/extract_signal.R | 2 R/extract_signal_stable.R | 3 R/extract_signal_stable_V2.R | 3 R/extract_signal_standard_deviation.R | 8 R/flmw.R | 4 R/lag_1.R |only R/loess_auto.R | 4 R/model_red_noise_wt.R | 13 R/plot_wavelet.R | 665 +++++++++++++--- R/plot_win_timeOpt.R |only R/retrack_wt_MC.R | 62 + R/sum_power_sedrate.R | 8 R/track_period_wavelet.R | 743 ++++++++++++------ R/wavelet_uncertainty.R | 17 R/win_fft.R | 37 R/win_timeOpt.R |only build/partial.rdb |binary man/Hilbert_transform.Rd | 2 man/WaverideR.Rd | 3 man/WaverideR_Datasets.Rd | 16 man/add_wavelet.Rd | 7 man/add_wavelet_avg.Rd | 7 man/analyze_wavelet.Rd | 284 ++++--- man/anchor2time.Rd | 2 man/anchor_points_grey.Rd | 2 man/astro_anchor.Rd | 2 man/completed_series.Rd | 200 ++--- man/curve2sedrate.Rd | 130 +-- man/curve2time.Rd | 174 ++-- man/curve2time_unc_anchor.Rd | 385 ++++++--- man/curve2tune.Rd | 196 ++--- man/dur_gaps.Rd | 4 man/dynamic_extraction.Rd |only man/extract_amplitude.Rd | 5 man/extract_power.Rd | 244 +++--- man/extract_power_stable.Rd | 2 man/extract_signal.Rd | 238 +++--- man/extract_signal_stable.Rd | 2 man/extract_signal_stable_V2.Rd | 2 man/extract_signal_standard_deviation.Rd | 383 ++++----- man/lag_1.Rd |only man/loess_auto.Rd | 164 ++-- man/model_red_noise_wt.Rd | 7 man/percentile_from_red_noise.Rd | 108 +- man/plot_avg_wavelet.Rd | 172 ++-- man/plot_wavelet.Rd | 593 +++++++-------- man/plot_win_timeOpt.Rd |only man/retrack_wt_MC.Rd | 17 man/track_period_wavelet.Rd | 59 + man/wavelet_uncertainty.Rd | 379 ++++----- man/win_fft.Rd | 6 man/win_timeOpt.Rd |only 71 files changed, 4773 insertions(+), 2716 deletions(-)
Title: Computes Proximity in Large Sparse Matrices
Description: Computes proximity between rows or columns of large matrices efficiently in C++.
Functions are optimised for large sparse matrices using the Armadillo and Intel TBB libraries.
Among various built-in similarity/distance measures, computation of correlation,
cosine similarity, Dice coefficient and Euclidean distance is particularly fast.
Author: Kohei Watanabe [cre, aut, cph]
,
Robrecht Cannoodt [aut]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between proxyC versions 0.5.1 dated 2025-04-24 and 0.5.2 dated 2025-04-25
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 6 ++++++ build/vignette.rds |binary inst/doc/measures.html | 4 ++-- tests/testthat/test-crossprod.R | 4 ++-- 6 files changed, 18 insertions(+), 12 deletions(-)
Title: Processing of Accelerometry Data with 'GGIR' in mMARCH
Description: Mobile Motor Activity Research Consortium for Health (mMARCH) is a collaborative network of studies of clinical and community samples that employ common clinical, biological, and digital mobile measures across involved studies. One of the main scientific goals of mMARCH sites is developing a better understanding of the inter-relationships between accelerometry-measured physical activity (PA), sleep (SL), and circadian rhythmicity (CR) and mental and physical health in children, adolescents, and adults. Currently, there is no consensus on a standard procedure for a data processing pipeline of raw accelerometry data, and few open-source tools to facilitate their development. The R package 'GGIR' is the most prominent open-source software package that offers great functionality and tremendous user flexibility to process raw accelerometry data. However, even with 'GGIR', processing done in a harmonized and reproducible fashion requires a non-trivial amount of expertise combined with a care [...truncated...]
Author: Wei Guo [aut, cre],
Andrew Leroux [aut],
Vadim Zipunnikov [aut],
Kathleen Merikangas [aut]
Maintainer: Wei Guo <wei.guo3@nih.gov>
Diff between mMARCH.AC versions 3.2.0.0 dated 2025-04-23 and 3.2.0.1 dated 2025-04-25
DESCRIPTION | 6 +- MD5 | 12 ++-- inst/doc/features.dictionary.xlsx |binary inst/doc/mMARCH.AC.html | 4 - inst/template/features.dictionary.xlsx |binary inst/template/module7a_calculate_newfeatures.Rmd | 4 - inst/template/module7b_merge_GGIRfeatures.Rmd | 62 +++++++++++++++++------ 7 files changed, 61 insertions(+), 27 deletions(-)
Title: Functions for Calculating Fit-Robustness of CNA-Solutions
Description: Functions for automatically performing
a reanalysis series
on a data set using CNA, and for calculating the fit-robustness
of the resulting models, as described in
Parkkinen and Baumgartner (2021) <doi:10.1177/0049124120986200>.
Author: Veli-Pekka Parkkinen [aut, cre, cph],
Michael Baumgartner [aut, cph],
Mathias Ambuehl [aut, cph]
Maintainer: Veli-Pekka Parkkinen <parkkinenv@gmail.com>
Diff between frscore versions 0.5.0 dated 2025-04-24 and 0.5.1 dated 2025-04-25
DESCRIPTION | 6 +++--- MD5 | 4 ++-- NEWS.md | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Bayesian Treed Distributed Lag Models
Description: Estimation of distributed lag models (DLMs) based on a Bayesian additive regression trees framework. Includes several extensions of DLMs: treed DLMs and distributed lag mixture models (Mork and Wilson, 2023) <doi:10.1111/biom.13568>; treed distributed lag nonlinear models (Mork and Wilson, 2022) <doi:10.1093/biostatistics/kxaa051>; heterogeneous DLMs (Mork, et. al., 2024) <doi:10.1080/01621459.2023.2258595>; monotone DLMs (Mork and Wilson, 2024) <doi:10.1214/23-BA1412>. The package also includes visualization tools and a 'shiny' interface to check model convergence and to help interpret results.
Author: Daniel Mork [aut, cre, cph] ,
Seongwon Im [aut] ,
Ander Wilson [aut]
Maintainer: Daniel Mork <dmork@hsph.harvard.edu>
Diff between dlmtree versions 1.0.0 dated 2024-05-31 and 1.1.0 dated 2025-04-25
dlmtree-1.0.0/dlmtree/R/tdlmm.R |only dlmtree-1.0.0/dlmtree/R/tdlnm.R |only dlmtree-1.0.0/dlmtree/man/predict.hdlm.Rd |only dlmtree-1.0.0/dlmtree/man/predict.hdlmm.Rd |only dlmtree-1.0.0/dlmtree/man/print.hdlm.Rd |only dlmtree-1.0.0/dlmtree/man/print.hdlmm.Rd |only dlmtree-1.0.0/dlmtree/man/print.monotone.Rd |only dlmtree-1.0.0/dlmtree/man/print.summary.hdlm.Rd |only dlmtree-1.0.0/dlmtree/man/print.summary.hdlmm.Rd |only dlmtree-1.0.0/dlmtree/man/print.summary.monotone.Rd |only dlmtree-1.0.0/dlmtree/man/print.summary.tdlm.Rd |only dlmtree-1.0.0/dlmtree/man/print.summary.tdlmm.Rd |only dlmtree-1.0.0/dlmtree/man/print.summary.tdlnm.Rd |only dlmtree-1.0.0/dlmtree/man/print.tdlm.Rd |only dlmtree-1.0.0/dlmtree/man/print.tdlmm.Rd |only dlmtree-1.0.0/dlmtree/man/print.tdlnm.Rd |only dlmtree-1.0.0/dlmtree/man/shiny.hdlm.Rd |only dlmtree-1.0.0/dlmtree/man/shiny.hdlmm.Rd |only dlmtree-1.0.0/dlmtree/man/summary.hdlm.Rd |only dlmtree-1.0.0/dlmtree/man/summary.hdlmm.Rd |only dlmtree-1.0.0/dlmtree/man/summary.monotone.Rd |only dlmtree-1.0.0/dlmtree/man/summary.tdlm.Rd |only dlmtree-1.0.0/dlmtree/man/summary.tdlmm.Rd |only dlmtree-1.0.0/dlmtree/man/summary.tdlnm.Rd |only dlmtree-1.0.0/dlmtree/man/tdlmm.Rd |only dlmtree-1.0.0/dlmtree/man/tdlnm.Rd |only dlmtree-1.1.0/dlmtree/DESCRIPTION | 12 dlmtree-1.1.0/dlmtree/MD5 | 145 +++---- dlmtree-1.1.0/dlmtree/NAMESPACE | 23 - dlmtree-1.1.0/dlmtree/NEWS.md | 51 ++ dlmtree-1.1.0/dlmtree/R/adj_coexposure.R | 27 - dlmtree-1.1.0/dlmtree/R/combine.models.R | 22 - dlmtree-1.1.0/dlmtree/R/control.R |only dlmtree-1.1.0/dlmtree/R/diagnose.summary.hdlm.R |only dlmtree-1.1.0/dlmtree/R/diagnose.summary.hdlmm.R |only dlmtree-1.1.0/dlmtree/R/diagnose.summary.monotone.R |only dlmtree-1.1.0/dlmtree/R/diagnose.summary.tdlm.R |only dlmtree-1.1.0/dlmtree/R/diagnose.summary.tdlmm.R |only dlmtree-1.1.0/dlmtree/R/diagnose.summary.tdlnm.R |only dlmtree-1.1.0/dlmtree/R/dlmtree.R | 245 ++++-------- dlmtree-1.1.0/dlmtree/R/drawTree.R | 3 dlmtree-1.1.0/dlmtree/R/estDLM.R | 92 +--- dlmtree-1.1.0/dlmtree/R/generic.R | 118 +++++ dlmtree-1.1.0/dlmtree/R/get_sbd_dlmtree.R | 10 dlmtree-1.1.0/dlmtree/R/pip.R | 5 dlmtree-1.1.0/dlmtree/R/plot.summary.monotone.R | 10 dlmtree-1.1.0/dlmtree/R/plot.summary.tdlm.R | 47 -- dlmtree-1.1.0/dlmtree/R/plot.summary.tdlmm.R | 29 - dlmtree-1.1.0/dlmtree/R/plot.summary.tdlnm.R | 19 dlmtree-1.1.0/dlmtree/R/predict.hdlm.R | 109 +---- dlmtree-1.1.0/dlmtree/R/predict.hdlmm.R | 146 ++----- dlmtree-1.1.0/dlmtree/R/print.dlmtree.R | 57 -- dlmtree-1.1.0/dlmtree/R/print.summary.hdlm.R | 92 ---- dlmtree-1.1.0/dlmtree/R/print.summary.hdlmm.R | 101 ----- dlmtree-1.1.0/dlmtree/R/print.summary.monotone.R | 73 --- dlmtree-1.1.0/dlmtree/R/print.summary.tdlm.R | 19 dlmtree-1.1.0/dlmtree/R/print.summary.tdlmm.R | 63 +-- dlmtree-1.1.0/dlmtree/R/print.summary.tdlnm.R | 28 - dlmtree-1.1.0/dlmtree/R/shiny.hdlm.R | 54 +- dlmtree-1.1.0/dlmtree/R/shiny.hdlmm.R | 48 -- dlmtree-1.1.0/dlmtree/R/splitpoints.R | 2 dlmtree-1.1.0/dlmtree/R/summary.hdlm.R | 90 +++- dlmtree-1.1.0/dlmtree/R/summary.hdlmm.R | 110 +++-- dlmtree-1.1.0/dlmtree/R/summary.monotone.R | 133 +++--- dlmtree-1.1.0/dlmtree/R/summary.tdlm.R | 135 ++++-- dlmtree-1.1.0/dlmtree/R/summary.tdlmm.R | 362 ++++++++---------- dlmtree-1.1.0/dlmtree/R/summary.tdlnm.R | 135 +++--- dlmtree-1.1.0/dlmtree/README.md | 12 dlmtree-1.1.0/dlmtree/inst/examples/dlmtree_example.R | 8 dlmtree-1.1.0/dlmtree/man/adj_coexposure.Rd | 13 dlmtree-1.1.0/dlmtree/man/diagnose.Rd |only dlmtree-1.1.0/dlmtree/man/dlmtree-package.Rd | 2 dlmtree-1.1.0/dlmtree/man/dlmtree.Rd | 139 +----- dlmtree-1.1.0/dlmtree/man/dlmtree.control.diagnose.Rd |only dlmtree-1.1.0/dlmtree/man/dlmtree.control.family.Rd |only dlmtree-1.1.0/dlmtree/man/dlmtree.control.het.Rd |only dlmtree-1.1.0/dlmtree/man/dlmtree.control.hyper.Rd |only dlmtree-1.1.0/dlmtree/man/dlmtree.control.mcmc.Rd |only dlmtree-1.1.0/dlmtree/man/dlmtree.control.mix.Rd |only dlmtree-1.1.0/dlmtree/man/dlmtree.control.monotone.Rd |only dlmtree-1.1.0/dlmtree/man/dlmtree.control.tdlnm.Rd |only dlmtree-1.1.0/dlmtree/man/drawTree.Rd | 2 dlmtree-1.1.0/dlmtree/man/estDLM.Rd | 21 - dlmtree-1.1.0/dlmtree/man/get_sbd_dlmtree.Rd | 10 dlmtree-1.1.0/dlmtree/man/pip.Rd | 5 dlmtree-1.1.0/dlmtree/man/plot.summary.tdlm.Rd | 4 dlmtree-1.1.0/dlmtree/man/plot.summary.tdlnm.Rd | 9 dlmtree-1.1.0/dlmtree/man/predict.Rd |only dlmtree-1.1.0/dlmtree/man/print.Rd |only dlmtree-1.1.0/dlmtree/man/shiny.Rd | 14 dlmtree-1.1.0/dlmtree/man/splitpoints.Rd | 2 dlmtree-1.1.0/dlmtree/man/summary.Rd |only dlmtree-1.1.0/dlmtree/src/dlmtreeHDLMGaussian.cpp | 21 - dlmtree-1.1.0/dlmtree/src/dlmtreeHDLMMGaussian.cpp | 38 + dlmtree-1.1.0/dlmtree/src/tdlmm_Cpp.cpp | 27 - dlmtree-1.1.0/dlmtree/src/tdlnm_Cpp.cpp | 9 96 files changed, 1314 insertions(+), 1637 deletions(-)
More information about branchingprocess at CRAN
Permanent link
Title: Import 'Stata' Data Files
Description: Function to read and write the 'Stata' file format.
Author: Jan Marvin Garbuszus [aut],
Sebastian Jeworutzki [aut, cre]
,
R Core Team [cph],
Magnus Thor Torfason [ctb],
Luke M. Olson [ctb],
Giovanni Righi [ctb],
Kevin Jin [ctb]
Maintainer: Sebastian Jeworutzki <Sebastian.Jeworutzki@ruhr-uni-bochum.de>
Diff between readstata13 versions 0.10.1 dated 2023-02-21 and 0.11.0 dated 2025-04-25
readstata13-0.10.1/readstata13/src/Makevars.win |only readstata13-0.11.0/readstata13/DESCRIPTION | 11 readstata13-0.11.0/readstata13/MD5 | 72 ++- readstata13-0.11.0/readstata13/NAMESPACE | 3 readstata13-0.11.0/readstata13/NEWS | 200 +++++------ readstata13-0.11.0/readstata13/NEWS.md |only readstata13-0.11.0/readstata13/R/RcppExports.R | 4 readstata13-0.11.0/readstata13/R/convert.R | 12 readstata13-0.11.0/readstata13/R/dbcal.R | 2 readstata13-0.11.0/readstata13/R/read.R | 37 +- readstata13-0.11.0/readstata13/R/readstata13.R | 4 readstata13-0.11.0/readstata13/R/save.R | 17 readstata13-0.11.0/readstata13/R/tools.R | 92 +++++ readstata13-0.11.0/readstata13/README.md | 154 +++----- readstata13-0.11.0/readstata13/build |only readstata13-0.11.0/readstata13/inst/doc |only readstata13-0.11.0/readstata13/inst/extdata/myproject2.dtas |only readstata13-0.11.0/readstata13/inst/include/read_dta.h | 3 readstata13-0.11.0/readstata13/inst/include/read_pre13_dta.h | 3 readstata13-0.11.0/readstata13/inst/include/readstata.h | 21 - readstata13-0.11.0/readstata13/inst/include/statadefines.h | 3 readstata13-0.11.0/readstata13/man/get.frames.Rd |only readstata13-0.11.0/readstata13/man/read.dta13.Rd | 16 readstata13-0.11.0/readstata13/man/read.dtas.Rd |only readstata13-0.11.0/readstata13/man/readstata13.Rd | 1 readstata13-0.11.0/readstata13/man/save.dta13.Rd | 8 readstata13-0.11.0/readstata13/src/Makevars | 3 readstata13-0.11.0/readstata13/src/RcppExports.cpp | 11 readstata13-0.11.0/readstata13/src/read.cpp | 11 readstata13-0.11.0/readstata13/src/read_data.cpp | 15 readstata13-0.11.0/readstata13/src/read_dta.cpp | 67 ++- readstata13-0.11.0/readstata13/src/read_pre13_dta.cpp | 27 + readstata13-0.11.0/readstata13/src/save_dta.cpp | 22 - readstata13-0.11.0/readstata13/src/save_pre13_dta.cpp | 2 readstata13-0.11.0/readstata13/tests/testthat/data |only readstata13-0.11.0/readstata13/tests/testthat/test_read.R | 127 ++++++ readstata13-0.11.0/readstata13/tests/testthat/test_save.R | 182 +++++++++- readstata13-0.11.0/readstata13/vignettes |only 38 files changed, 785 insertions(+), 345 deletions(-)
Title: Age-Depth Modelling using Bayesian Statistics
Description: An approach to age-depth modelling that uses Bayesian statistics to reconstruct accumulation histories for deposits, through combining radiocarbon and other dates with prior information on accumulation rates and their variability. See Blaauw & Christen (2011).
Author: Maarten Blaauw [aut, cre] ,
J. Andres Christen [aut, ctb, cph]
,
Marco A. Aquino Lopez [aut] ,
Judith Esquivel Vazquez [ctb],
Oscar M. Gonzalez V. [ctb],
Ted Belding [cph],
James Theiler [cph],
Brian Gough [cph],
Charles Karney [cph]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rbacon versions 3.3.1 dated 2024-09-28 and 3.4.1 dated 2025-04-25
DESCRIPTION | 10 +- MD5 | 68 ++++++++--------- NAMESPACE | 9 ++ NEWS.md | 16 +++- R/MCMC.R | 4 - R/accrate.R | 54 ++++++++------ R/agedepth.R | 68 ++++++++++++----- R/calc.R | 21 ++--- R/calibrate.R | 46 +++++++----- R/forplum.R | 14 +-- R/internal_plots.R | 69 ++++++++++++++++-- R/plots.R | 29 ++++--- R/rbacon-package.R | 8 +- R/rbacon.R | 60 +++++++++++---- R/read_write.R | 24 +++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/rbacon.R | 92 ++++++++++++------------ inst/doc/rbacon.Rmd | 31 ++++---- inst/doc/rbacon.html | 193 +++++++++++++++++++++++++-------------------------- man/Bacon.Rd | 8 +- man/Bacon.hist.Rd | 2 man/accrate.depth.Rd | 10 ++ man/add.dates.Rd | 6 - man/agedepth.Rd | 10 ++ man/agemodel.it.Rd | 2 man/calib.plot.Rd | 3 man/scissors.Rd | 2 man/thinner.Rd | 7 + src/bacon.cpp | 95 +------------------------ src/bacon.h | 11 ++ src/input.cpp | 2 src/ranfun.cpp | 8 +- src/ranfun.h | 2 vignettes/rbacon.Rmd | 31 ++++---- 35 files changed, 572 insertions(+), 443 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors as described in Migueles and colleagues (JMPB 2019), and van Hees and colleagues (JApplPhysiol 2014; PLoSONE 2015). The package has been developed and tested for binary data from 'GENEActiv' <https://activinsights.com/>, binary (.gt3x) and .csv-export data from 'Actigraph' <https://theactigraph.com> devices, and binary (.cwa) and .csv-export data from 'Axivity' <https://axivity.com>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format. Also the package allows for external function embedding.
Author: Vincent T van Hees [aut, cre],
Jairo H Migueles [aut] ,
Severine Sabia [ctb],
Matthew R Patterson [ctb],
Zhou Fang [ctb],
Joe Heywood [ctb],
Joan Capdevila Pujol [ctb],
Lena Kushleyeva [ctb],
Mathilde Chen [ctb],
Manasa Yerramalla [ctb],
Patrick Bos [...truncated...]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
Diff between GGIR versions 3.2-0 dated 2025-02-20 and 3.2-6 dated 2025-04-25
DESCRIPTION | 8 MD5 | 177 ++-- NAMESPACE | 4 NEWS.md | 93 ++ R/CalcSleepRegularityIndex.R | 32 R/GGIR.R | 134 ++- R/HASIB.R | 75 + R/HASPT.R | 286 +++++++ R/addSplitNames.R |only R/appendRecords.R | 16 R/check_params.R | 142 +-- R/convertEpochData.R | 909 ++++++++++++++--------- R/extract_params.R | 16 R/g.analyse.R | 16 R/g.analyse.avday.R | 25 R/g.analyse.perday.R | 126 ++- R/g.analyse.perfile.R | 36 R/g.calibrate.R | 4 R/g.dotorcomma.R | 2 R/g.fragmentation.R | 2 R/g.getM5L5.R | 18 R/g.getmeta.R | 1 R/g.impute.R | 24 R/g.inspectfile.R | 25 R/g.loadlog.R | 7 R/g.part1.R | 2 R/g.part2.R | 4 R/g.part3.R | 4 R/g.part4.R | 38 - R/g.part5.R | 27 R/g.part5.addfirstwake.R | 17 R/g.part5.analyseRest.R | 10 R/g.part5.definedays.R | 12 R/g.part5.savetimeseries.R | 21 R/g.part5_analyseSegment.R | 18 R/g.part5_initialise_ts.R | 6 R/g.part6.R | 34 R/g.readaccfile.R | 18 R/g.report.part2.R | 13 R/g.report.part4.R | 103 +- R/g.report.part5.R | 13 R/g.report.part6.R | 23 R/g.sib.det.R | 84 +- R/g.sibreport.R | 17 R/g.weardec.R | 3 R/getPart1BasicInfo.R |only R/getSplitNames.R |only R/get_nw_clip_block_params.R | 1 R/inspect_binFile_brand.R |only R/isfilelist.R | 3 R/load_params.R | 18 R/markerButtonForRest.R |only R/monitor_types.R | 2 R/splitRecords.R |only R/visualReport.R | 35 README.md | 3 build/vignette.rds |binary inst/doc/CutPoints.Rmd | 106 +- inst/doc/CutPoints.html | 911 ++++++++++-------------- inst/doc/GGIR.R | 44 - inst/doc/GGIR.Rmd | 215 ----- inst/doc/GGIR.html | 261 ------ inst/doc/GGIRParameters.Rmd | 20 inst/doc/GGIRParameters.html | 458 ++++++++---- inst/doc/GGIRoutput.Rmd | 11 inst/doc/GGIRoutput.html | 98 +- man/CalcSleepRegularityIndex.Rd | 12 man/GGIR-package.Rd | 4 man/GGIR.Rd | 437 +++++++---- man/HASIB.Rd | 12 man/HASPT.Rd | 17 man/addSplitNames.Rd |only man/convertEpochData.Rd | 9 man/g.analyse.perday.Rd | 14 man/g.getM5L5.Rd | 5 man/g.part5.analyseRest.Rd | 1 man/g.weardec.Rd | 6 man/getPart1BasicInfo.Rd |only man/getSplitNames.Rd |only man/inspect_binFile_brand.Rd |only man/markerButtonForRest.Rd |only man/splitRecords.Rd |only tests/testthat/test_HASIB.R | 7 tests/testthat/test_HASPT.R |only tests/testthat/test_convertExtEpochData.R | 75 + tests/testthat/test_greadaccfile.R | 24 tests/testthat/test_gweardec.R | 24 tests/testthat/test_lightPart5.R | 4 tests/testthat/test_load_check_params.R | 56 - tests/testthat/test_part5_fixmissingnight.R | 2 tests/testthat/test_part5_markerButtonForRest.R |only tests/testthat/test_part6.R | 9 tests/testthat/test_splitRecords.R |only vignettes/CutPoints.Rmd | 106 +- vignettes/GGIR.Rmd | 215 ----- vignettes/GGIRParameters.Rmd | 20 vignettes/GGIRoutput.Rmd | 11 97 files changed, 3251 insertions(+), 2650 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-07 0.4.5
2014-08-06 0.4.2
2012-11-06 0.4.1
2012-07-10 0.4.0
2011-11-29 0.3.3
2011-10-20 0.3.2
2011-09-19 0.3.1
2011-07-06 0.3.0
2011-02-08 0.2.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-05-15 0.11.3
2019-04-25 0.11.2
2019-03-14 0.11.1
2018-05-23 0.11.0
2018-02-05 0.10.1
2017-11-27 0.10.0
2017-06-30 0.9.0
Title: Treatment Switching
Description: Implements rank-preserving structural failure time model (RPSFTM), iterative parameter estimation (IPE), inverse probability of censoring weights (IPCW), and two-stage estimation (TSE) methods for treatment switching in randomized clinical trials.
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between trtswitch versions 0.1.5 dated 2025-04-23 and 0.1.6 dated 2025-04-25
DESCRIPTION | 8 +++---- MD5 | 6 ++--- NEWS.md | 4 +++ src/survival_analysis.cpp | 48 ++++++++++++++++++++++++++-------------------- 4 files changed, 39 insertions(+), 27 deletions(-)
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Yoonkyoung Jeon [aut],
Jaehun Shon [aut],
Hyojong Myung [aut],
Hyungwoo Jo [aut],
Sungho Choi [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 1.3.11 dated 2025-04-04 and 1.3.12 dated 2025-04-25
DESCRIPTION | 10 MD5 | 31 NAMESPACE | 6 NEWS.md | 6 R/CreateTableOneJS.R | 11 R/forestcox.R | 737 ++++++--------- R/forestglm.R | 1237 +++++++++++++++----------- R/utils.R |only inst/doc/jstable.html | 28 inst/doc/jstable_competing_risk_analysis.html | 4 inst/doc/jstable_options.html | 12 man/TableSubgroupGLM.Rd | 8 man/TableSubgroupMultiGLM.Rd | 8 man/collapse_counts.Rd |only man/count_event_by.Rd | 2 man/count_event_by_glm.Rd |only tests/testthat/test-CreateTableOneJS.R | 1 tests/testthat/test-forestglm.R | 24 18 files changed, 1152 insertions(+), 973 deletions(-)
Title: Classes and Methods for Seismic Data Analysis
Description: Provides classes and methods for seismic data analysis. The
base classes and methods are inspired by the python code found in
the 'ObsPy' python toolbox <https://github.com/obspy/obspy>. Additional classes and
methods support data returned by web services provided by the 'IRIS DMC'
<http://service.iris.edu/>.
Author: Jonathan Callahan [aut],
Rob Casey [aut],
Gillian Sharer [aut, cre],
Mary Templeton [aut],
Chad Trabant [ctb]
Maintainer: Gillian Sharer <gillian.sharer@earthscope.org>
Diff between IRISSeismic versions 1.6.7 dated 2024-12-10 and 1.7.0 dated 2025-04-25
DESCRIPTION | 12 MD5 | 57 +- R/Class-IrisClient.R | 865 ++++++++++++++++++++++++++-------------- R/Class-Stream.R | 2 R/Class-Trace.R | 2 R/spectralUtils.R | 9 R/zzz.R |only build/vignette.rds |binary inst/doc/IRISSeismic-intro.Rmd | 23 - inst/doc/IRISSeismic-intro.html | 20 man/IRISSeismic-package.Rd | 53 +- man/IrisClient-class.Rd | 13 man/Stream-class.Rd | 2 man/butterworth.Rd | 2 man/getDataAvailability.Rd | 2 man/getDataselect.Rd | 7 man/getEvent.Rd | 4 man/getSNCL.Rd | 2 man/getTimeseries.Rd | 10 man/getUnavailability.Rd | 2 src/Makevars | 2 src/Makevars.win | 2 src/libmseed/fileutils.c | 50 +- src/libmseed/genutils.c | 47 -- src/libmseed/libmseed.def | 6 src/libmseed/libmseed.h | 11 src/libmseed/logging.c | 9 src/libmseed/parseutils.c | 2 src/libmseed/unpack.c | 4 vignettes/IRISSeismic-intro.Rmd | 23 - 30 files changed, 751 insertions(+), 492 deletions(-)
Title: Apply Functions to All Combinations of List Elements
Description: Provides an extension to the 'purrr' family of mapping
functions to apply a function to each combination of elements in a
list of inputs. Also includes functions for automatically detecting
output type in mapping functions, finding every combination of
elements of lists or rows of data frames, and applying multiple models
to multiple subsets of a dataset.
Author: Alexander Rossell Hayes [aut, cre, cph]
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>
Diff between crossmap versions 0.4.1 dated 2025-04-21 and 0.4.2 dated 2025-04-25
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ tests/testthat/test-errors.R | 2 ++ tests/testthat/test-future_xmap.R | 34 ++++------------------------------ 5 files changed, 17 insertions(+), 37 deletions(-)
Title: Alternating Optimization
Description: An iterative process that optimizes a function by alternately
performing restricted optimization over parameter subsets. Instead of joint
optimization, it breaks the optimization problem down into simpler
sub-problems. This approach can make optimization feasible when joint
optimization is too difficult.
Author: Lennart Oelschlaeger [aut, cre]
,
Siddhartha Chib [ctb]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between ao versions 1.1.0 dated 2024-07-13 and 1.2.0 dated 2025-04-25
ao-1.1.0/ao/R/procedure.R |only ao-1.1.0/ao/man/Procedure.Rd |only ao-1.1.0/ao/man/ao_input_check.Rd |only ao-1.1.0/ao/tests/testthat/test-procedure.R |only ao-1.2.0/ao/DESCRIPTION | 24 ao-1.2.0/ao/MD5 | 40 ao-1.2.0/ao/NAMESPACE | 44 ao-1.2.0/ao/NEWS.md | 276 +- ao-1.2.0/ao/R/ao-package.R | 85 ao-1.2.0/ao/R/ao.R | 1104 ++++----- ao-1.2.0/ao/R/process.R |only ao-1.2.0/ao/README.md | 277 +- ao-1.2.0/ao/build/vignette.rds |binary ao-1.2.0/ao/inst/doc/ao.R | 328 +- ao-1.2.0/ao/inst/doc/ao.Rmd | 779 +++--- ao-1.2.0/ao/inst/doc/ao.html | 1905 ++++++++-------- ao-1.2.0/ao/man/Process.Rd |only ao-1.2.0/ao/man/ao-package.Rd | 60 ao-1.2.0/ao/man/ao.Rd | 585 ++-- ao-1.2.0/ao/man/figures/README-rosenbrock_ao_path-1.png |binary ao-1.2.0/ao/tests/testthat.R | 8 ao-1.2.0/ao/tests/testthat/test-ao.R | 146 - ao-1.2.0/ao/vignettes/ao.Rmd | 779 +++--- ao-1.2.0/ao/vignettes/ref.bib | 108 24 files changed, 3324 insertions(+), 3224 deletions(-)
Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by
providing a high level interface to writing, styling and editing
worksheets.
Author: Jordan Mark Barbone [aut] ,
Jan Marvin Garbuszus [aut, cre],
Olivier Roy [ctb],
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 1.14 dated 2025-03-20 and 1.15 dated 2025-04-25
DESCRIPTION | 6 MD5 | 155 +++++++++--------- NEWS.md | 33 ++++ R/RcppExports.R | 25 ++- R/class-comment.R | 23 -- R/class-style_mgr.R | 66 ++++---- R/class-workbook-wrappers.R | 19 +- R/class-workbook.R | 153 +++++++++--------- R/class-worksheet.R | 33 +--- R/dates.R | 96 ++++------- R/deprecate.R | 20 ++ R/helper-functions.R | 77 +++++++-- R/openxlsx2-package.R | 20 ++ R/read.R | 187 ++++++++++++++++------ R/utils.R | 38 ---- R/wb_functions.R | 50 +----- R/wb_load.R | 7 R/wb_styles.R | 11 - R/write.R | 34 ++-- R/write_xlsx.R | 10 + README.md | 44 ++--- build/vignette.rds |binary inst/WORDLIST | 10 - inst/doc/Update-from-openxlsx.html | 22 +- inst/doc/conditional-formatting.html | 109 +++++-------- inst/doc/openxlsx2_charts_manual.html | 6 inst/doc/openxlsx2_read_to_df.html | 132 ++++++++-------- inst/doc/openxlsx2_style_manual.R | 6 inst/doc/openxlsx2_style_manual.Rmd | 6 inst/doc/openxlsx2_style_manual.html | 14 - man/create_cell_style.Rd | 6 man/create_comment.Rd | 2 man/create_numfmt.Rd | 2 man/openxlsx2-package.Rd | 21 ++ man/wb_add_data.Rd | 13 + man/wb_add_data_table.Rd | 13 + man/wb_cell_style.Rd | 2 man/wb_to_df.Rd | 13 + man/write_datatable.Rd | 13 + src/RcppExports.cpp | 61 +++++-- src/date.cpp |only src/helper_functions.cpp | 207 ++++++++++++++++++++++--- src/load_workbook.cpp | 45 ++--- src/openxlsx2.h | 58 +++---- src/strings_xml.cpp | 58 +------ src/styles_xml.cpp | 51 ++---- src/write_file.cpp | 2 src/xlsb.cpp | 4 tests/testthat/test-base_font.R | 2 tests/testthat/test-class-color.R | 12 - tests/testthat/test-class-comment.R | 83 +++++++--- tests/testthat/test-class-hyperlink.R | 14 - tests/testthat/test-class-workbook-wrappers.R | 22 +- tests/testthat/test-class-workbook.R | 22 +- tests/testthat/test-class-worksheet.R | 6 tests/testthat/test-clean_sheet.R | 2 tests/testthat/test-cloneWorksheet.R | 6 tests/testthat/test-conditional_formatting.R | 214 ++++++++++---------------- tests/testthat/test-date_time_conversion.R | 143 ++++++++++++++++- tests/testthat/test-fill_merged_cells.R | 52 +++--- tests/testthat/test-form_control.R | 12 - tests/testthat/test-formulas.R | 90 ++++++++++ tests/testthat/test-freeze_pane.R | 28 +-- tests/testthat/test-helper-functions.R | 17 ++ tests/testthat/test-loading_workbook.R | 20 +- tests/testthat/test-named_regions.R | 2 tests/testthat/test-outlines.R | 19 +- tests/testthat/test-protect-workbook.R | 4 tests/testthat/test-read_from_created_wb.R | 2 tests/testthat/test-read_sources.R | 8 tests/testthat/test-read_write_logicals.R | 2 tests/testthat/test-save.R | 111 ++++++++----- tests/testthat/test-strings_xml.R | 14 - tests/testthat/test-utils.R | 27 +++ tests/testthat/test-wb_functions.R | 16 - tests/testthat/test-wb_styles.R | 116 ++++++-------- tests/testthat/test-write.R | 42 ++++- tests/testthat/test-writing_posixct.R | 4 vignettes/openxlsx2_style_manual.Rmd | 6 79 files changed, 1867 insertions(+), 1234 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 1.6.4 dated 2025-03-10 and 1.6.8 dated 2025-04-25
DESCRIPTION | 20 ++-- MD5 | 49 ++++++---- NAMESPACE | 5 + NEWS.md | 18 +++ R/coxph.R | 59 ++++--------- R/gee.R | 121 +++++++++++++++++++------- R/jsBasicGadget.R | 12 +- R/jsPropensityGadget.R | 68 +++++++++------ R/jsRepeatedGadget.R | 35 +++++-- R/jsSurveyGadget.R | 38 +++++--- R/kaplan.R | 12 +- R/regress.R | 149 ++++++++++++++++++++++++++++----- R/roc.R | 18 ++- R/templateGenerator.R |only R/theme.R |only build/vignette.rds |binary inst/assets |only inst/doc/jsmodule.html | 4 inst/doc/jsmodule_subgroup_cmprsk.html | 4 inst/rstudio/addins.dcf | 7 + inst/www/style_basic.css |only inst/www/style_ps.css |only inst/www/style_repeated.css |only inst/www/style_survey.css |only man/GEEModuleLinear.Rd | 5 - man/GEEModuleLogistic.Rd | 5 - man/logisticModule2.Rd | 5 - man/regressModule2.Rd | 5 - man/templateGenerator.Rd |only man/use_jsmodule_style.Rd |only 30 files changed, 437 insertions(+), 202 deletions(-)
Title: Functions to Estimate Tree Volume and Phytomass in the Italian
Forest Inventory 2005
Description: Tabacchi et al. (2011) published a very detailed study producing a uniform system of functions to estimate tree volume and
phytomass components (stem, branches, stool). The estimates of the 2005 Italian forest inventory (<https://www.inventarioforestale.org/it/>)
are based on these functions. The study documents the domain of applicability of each function and the equations to quantify estimates
accuracies for individual estimates as well as for aggregated estimates. This package makes the functions available in the R environment.
Version 2 exposes two distinct functions for individual and summary estimates. To facilitate access to the functions, tree species
identification is now based on EPPO species codes (<https://data.eppo.int/>).
Author: Nicola Puletti [aut, cre] ,
Mirko Grotti [aut],
Roberto Scotti [aut]
Maintainer: Nicola Puletti <nicola.puletti@gmail.com>
Diff between ForIT versions 2.4.0 dated 2023-09-26 and 2.5.0 dated 2025-04-25
ForIT-2.4.0/ForIT/man/ForIT.Rd |only ForIT-2.5.0/ForIT/DESCRIPTION | 16 ++++++++-------- ForIT-2.5.0/ForIT/MD5 | 16 ++++++++-------- ForIT-2.5.0/ForIT/NAMESPACE | 1 + ForIT-2.5.0/ForIT/NEWS.md | 6 ++---- ForIT-2.5.0/ForIT/R/ForIT.R | 6 ++---- ForIT-2.5.0/ForIT/R/INFCaccuracyPlot.R | 4 ++-- ForIT-2.5.0/ForIT/R/INFCvpeSUM.R | 8 +++++--- ForIT-2.5.0/ForIT/man/ForIT-package.Rd |only ForIT-2.5.0/ForIT/man/PlottingINFCaccuracy.Rd | 4 ++-- 10 files changed, 30 insertions(+), 31 deletions(-)
Title: Fast Change Point Detection via Sequential Gradient Descent
Description: Implements fast change point detection algorithm based on the
paper "Sequential Gradient Descent and Quasi-Newton's Method for
Change-Point Analysis" by Xianyang Zhang, Trisha Dawn
<https://proceedings.mlr.press/v206/zhang23b.html>. The algorithm is
based on dynamic programming with pruning and sequential gradient
descent. It is able to detect change points a magnitude faster than
the vanilla Pruned Exact Linear Time(PELT). The package includes
examples of linear regression, logistic regression, Poisson
regression, penalized linear regression data, and whole lot more
examples with custom cost function in case the user wants to use their
own cost function.
Author: Xingchi Li [aut, cre, cph] ,
Xianyang Zhang [aut, cph]
Maintainer: Xingchi Li <anthony.li.stat.tamu.edu@lixingchi.com>
Diff between fastcpd versions 0.16.1 dated 2025-03-20 and 0.16.2 dated 2025-04-25
DESCRIPTION | 6 - MD5 | 18 +-- NEWS.md | 6 + R/fastcpd.R | 4 build/vignette.rds |binary man/fastcpd.Rd | 2 src/fastcpd_classes.cc | 59 +++++----- src/ref_r_family.c | 5 tests/testthat/test-vignettes-comparison-pelt-logistic-regression.R | 2 tests/testthat/test-vignettes-comparison-pelt-poisson-regression.R | 2 10 files changed, 58 insertions(+), 46 deletions(-)