Title: Taxa Waterbeheer Nederland voor R
Description: The TWN-list (Taxa Waterbeheer Nederland) is the Dutch standard for naming
taxons in Dutch Watermanagement. This package makes it easier to use the
TWN-list for ecological analyses. It consists of two parts. First it makes the
TWN-list itself available in R. Second, it has a few functions that make it
easy to perform some basic and often recurring tasks for checking and consulting
taxonomic data from the TWN-list.
Author: Johan van Tent [aut, cre]
Maintainer: Johan van Tent <tentvanjohan@hotmail.com>
Diff between twn versions 0.2.5 dated 2024-11-11 and 0.2.6 dated 2025-09-26
DESCRIPTION | 10 MD5 | 42 +-- NAMESPACE | 6 NEWS.md | 174 ++++++++------- R/ZZ_package_description.R | 3 R/sysdata.rda |binary R/twn_info.R | 49 +++- R/twn_lijst_doc.R | 8 README.md | 24 +- build/vignette.rds |binary data/twn_lijst.rda |binary data/twn_literatuur.rda |binary data/twn_statuscodes.rda |binary data/twn_taxonlevels.rda |binary inst/doc/krw_beoordeling.R | 450 ++++++++++++++++++++--------------------- inst/doc/krw_beoordeling.html | 62 ++--- man/twn.Rd | 13 + man/twn_info.Rd | 39 ++- man/twn_lijst.Rd | 4 man/twn_literatuur.Rd | 2 man/twn_statuscodes.Rd | 3 tests/testthat/test-twn_info.R | 10 22 files changed, 493 insertions(+), 406 deletions(-)
Title: Root Mean Square Curvature Calculation
Description: Calculates the RMS intrinsic and parameter-effects curvatures of a nonlinear regression model. The curvatures are global measures of assessing whether a model/data set combination is close-to-linear or not. See Bates and Watts (1980) <doi:10.1002/9780470316757> and Ratkowsky and Reddy (2017) <doi:10.1093/aesa/saw098> for details.
Author: Peijian Shi [aut, cre],
Peter M. Ridland [aut],
David A. Ratkowsky [aut],
Yang Li [aut]
Maintainer: Peijian Shi <pjshi@njfu.edu.cn>
Diff between IPEC versions 1.1.1 dated 2025-07-23 and 1.1.2 dated 2025-09-26
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/biasIPEC.R | 2 +- R/curvIPEC.R | 2 +- R/parinfo.R | 4 ++-- R/skewIPEC.R | 2 +- build/partial.rdb |binary man/biasIPEC.Rd | 2 +- man/curvIPEC.Rd | 2 +- man/parinfo.Rd | 4 +++- man/skewIPEC.Rd | 2 +- 11 files changed, 25 insertions(+), 23 deletions(-)
Title: Models of Decision Confidence and Measures of Metacognition
Description: Provides fitting functions and other tools for decision confidence
and metacognition researchers, including meta-d'/d', often considered to be
the gold standard to measure metacognitive efficiency, and information-theoretic measures of metacognition.
Also allows to fit and compare several static models of decision making and confidence.
Author: Manuel Rausch [aut, cre] ,
Sascha Meyen [aut] ,
Sebastian Hellmann [aut]
Maintainer: Manuel Rausch <manuel.rausch@ku.de>
Diff between statConfR versions 0.2.0 dated 2025-02-13 and 0.2.1 dated 2025-09-26
DESCRIPTION | 22 ++++--- MD5 | 23 ++++--- R/fitConf.R | 43 ++++++++++++-- R/fitConfModels.R | 40 +++++++++++-- R/int_fitCAS.R |only R/int_fitCEV.R | 5 + R/int_fitRCE.R |only R/int_llCASANDRE.R |only R/plotConfModelFit.R | 140 ++++++++++++++++++++++++++++++++++++++++++++++-- README.md | 25 ++++++-- inst/CITATION | 22 +++---- man/fitConf.Rd | 40 ++++++++++++- man/fitConfModels.Rd | 42 ++++++++++++-- man/plotConfModelFit.Rd | 2 14 files changed, 337 insertions(+), 67 deletions(-)
Title: Learning with Data on Riemannian Manifolds
Description: We provide a variety of algorithms for manifold-valued data, including Fréchet summaries, hypothesis testing, clustering, visualization, and other learning tasks. See Bhattacharya and Bhattacharya (2012) <doi:10.1017/CBO9781139094764> for general exposition to statistics on manifolds.
Author: Kisung You [aut, cre]
Maintainer: Kisung You <kisung.you@outlook.com>
Diff between Riemann versions 0.1.4 dated 2022-02-28 and 0.1.6 dated 2025-09-26
Riemann-0.1.4/Riemann/build/vignette.rds |only Riemann-0.1.4/Riemann/inst/doc |only Riemann-0.1.4/Riemann/src/functions_07_learning.cpp |only Riemann-0.1.4/Riemann/vignettes |only Riemann-0.1.6/Riemann/DESCRIPTION | 20 +-- Riemann-0.1.6/Riemann/MD5 | 66 +++++----- Riemann-0.1.6/Riemann/NEWS.md | 6 Riemann-0.1.6/Riemann/R/RcppExports.R | 16 ++ Riemann-0.1.6/Riemann/R/auxiliary_checkers.R | 4 Riemann-0.1.6/Riemann/R/dist_splaplace.R | 51 ++++++- Riemann-0.1.6/Riemann/R/future_spd_selection_unsupervised.R |only Riemann-0.1.6/Riemann/R/package-Riemann.R | 5 Riemann-0.1.6/Riemann/R/spatial_GlobalGeary.R |only Riemann-0.1.6/Riemann/R/spatial_GlobalMoran.R |only Riemann-0.1.6/Riemann/R/zzz.R | 2 Riemann-0.1.6/Riemann/README.md | 14 +- Riemann-0.1.6/Riemann/build/partial.rdb |binary Riemann-0.1.6/Riemann/inst/REFERENCES.bib | 6 Riemann-0.1.6/Riemann/src/Makevars | 1 Riemann-0.1.6/Riemann/src/Makevars.win | 1 Riemann-0.1.6/Riemann/src/RcppExports.cpp | 61 +++++++++ Riemann-0.1.6/Riemann/src/auxiliary.cpp | 1 Riemann-0.1.6/Riemann/src/distribution_sphere.cpp | 1 Riemann-0.1.6/Riemann/src/functions_01_basic.cpp | 1 Riemann-0.1.6/Riemann/src/functions_02_inference.cpp | 1 Riemann-0.1.6/Riemann/src/functions_03_clustering.cpp | 1 Riemann-0.1.6/Riemann/src/functions_03_clustering_criteria.cpp | 1 Riemann-0.1.6/Riemann/src/functions_06_curve.cpp | 1 Riemann-0.1.6/Riemann/src/functions_07_spatial.cpp |only Riemann-0.1.6/Riemann/src/functions_08_learning.cpp |only Riemann-0.1.6/Riemann/src/functions_special_others.cpp | 1 Riemann-0.1.6/Riemann/src/functions_special_spd.cpp | 31 ++++ Riemann-0.1.6/Riemann/src/riemann_general.cpp | 1 Riemann-0.1.6/Riemann/src/riemann_general.h | 1 Riemann-0.1.6/Riemann/src/riemann_manifolds.h | 11 - Riemann-0.1.6/Riemann/src/riemann_src.cpp | 2 Riemann-0.1.6/Riemann/src/riemann_src.h | 1 Riemann-0.1.6/Riemann/tests |only 38 files changed, 228 insertions(+), 80 deletions(-)
Title: Discrete Event Simulation in R and C++, with Tools for
Cost-Effectiveness Analysis
Description: Discrete event simulation using both R and C++ (Karlsson et al 2016; <doi:10.1109/eScience.2016.7870915>). The C++ code is adapted from the SSIM library <https://www.inf.usi.ch/carzaniga/ssim/>, allowing for event-oriented simulation. The code includes a SummaryReport class for reporting events and costs by age and other covariates. The C++ code is available as a static library for linking to other packages. A priority queue implementation is given in C++ together with an S3 closure and a reference class implementation. Finally, some tools are provided for cost-effectiveness analysis.
Author: Mark Clements [aut, cre, cph],
Alexandra Jauhiainen [aut],
Andreas Karlsson [aut],
Antonio Carzaniga [cph],
University of Colorado [cph],
Pierre L'Ecuyer [cph]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between microsimulation versions 1.4.4 dated 2024-08-19 and 1.4.5 dated 2025-09-26
DESCRIPTION | 7 +- MD5 | 6 +- inst/include/microsimulation.h | 116 ++++++++++++++++++++++++++++++++++++++--- src/pqueue.cpp | 2 4 files changed, 117 insertions(+), 14 deletions(-)
More information about microsimulation at CRAN
Permanent link
Title: D-Score for Child Development
Description: The D-score summarizes the child's performance on a set of
milestones into a single number. The package implements four Rasch model
keys to convert milestone scores into a D-score. It provides tools to
calculate the D-score and its precision from the child's milestone scores,
to convert the D-score into the Development-for-Age Z-score (DAZ)
using age-conditional references, and to map milestone names into a
generic 9-position item naming convention.
Author: Stef van Buuren [cre, aut],
Iris Eekhout [aut],
Arjan Huizing [aut],
Jonathan Seiden [aut]
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>
Diff between dscore versions 1.10.0 dated 2025-06-05 and 1.11.0 dated 2025-09-26
DESCRIPTION | 11 MD5 | 91 +++--- NAMESPACE | 2 NEWS.md | 42 ++ R/builtin_itemtable.R | 2 R/builtin_keys.R | 2 R/builtin_translate.R |only R/daz.R | 24 + R/decompose_itemnames.R | 4 R/dscore.R | 264 ++++++++++-------- R/get_age_equivalent.R | 26 + R/get_itemnames.R | 42 ++ R/get_itemtable.R | 7 R/get_labels.R | 8 R/get_mu.R | 25 + R/get_reference.R | 36 +- R/get_tau.R | 10 R/gsample.R | 12 R/import.R | 2 R/initialize.R | 4 R/internal.R | 67 +++- R/rename_gcdg_gsed.R | 93 +++++- R/rename_vector.R |only R/set_default.R | 15 - README.md | 9 data/builtin_itembank.rda |binary data/builtin_itemtable.rda |binary data/builtin_keys.rda |binary data/builtin_references.rda |binary data/builtin_translate.rda |only data/gsample.rda |binary data/sample_hf.rda |binary data/sample_lf.rda |binary data/sample_sf.rda |binary inst/doc/custom_priors.html | 5 inst/doc/getting_started.R | 94 ++++-- inst/doc/getting_started.Rmd | 246 +++++++++------- inst/doc/getting_started.html | 613 +++++++++++++++++++++++++++++++++--------- inst/doc/scoring_GSED.html | 317 ++++++++++----------- inst/doc/using_DAZ.html | 5 man/builtin_itemtable.Rd | 2 man/builtin_translate.Rd |only man/gsample.Rd | 5 man/rename_vector.Rd |only man/sample_sf.Rd | 5 src/dscore.cpp | 2 tests/testthat/test-dscore.R | 218 +++++++++++--- tests/testthat/test-prior.R | 2 vignettes/getting_started.Rmd | 246 +++++++++------- 49 files changed, 1719 insertions(+), 839 deletions(-)
Title: Spatial Extreme Value Analysis with the Hierarchical Model of
Reich and Shaby (2012)
Description: Several procedures for the hierarchical kernel extreme value process of Reich and Shaby (2012) <DOI:10.1214/12-AOAS591>, including simulation, estimation and spatial extrapolation. The spatial latent variable model <DOI:10.1214/11-STS376> is also included.
Author: Quentin Sebille [aut],
Leo Belzile [cre]
Maintainer: Leo Belzile <belzilel@gmail.com>
Diff between hkevp versions 1.1.5 dated 2023-04-18 and 1.1.6 dated 2025-09-26
DESCRIPTION | 21 ++++++++++---- MD5 | 8 ++--- R/hkevp.R | 85 +++++++++++++++++++++------------------------------------- man/hkevp.Rd | 8 +++++ src/hkevp.cpp | 46 +++++++++++++++---------------- 5 files changed, 81 insertions(+), 87 deletions(-)
Title: Inference and Prediction of Toxicokinetic Models
Description: Provides bioaccumulation factors from a toxicokinetic model
fitted to accumulation-depuration data. It is designed to fulfil the requirements
of regulators when examining applications for market authorization of active
substances.
Author: Virgile Baudrot [aut, cre],
Sandrine Charles [aut],
Ophelia Gestin [ctb],
Milena Kaag [aut],
Christelle Lopes [ctb],
Gauthier Multari [ctb],
Alain Pave [ctb],
Aude Ratier [aut],
Aurelie Siberchicot [aut]
Maintainer: Virgile Baudrot <virgile.baudrot@qonfluens.com>
This is a re-admission after prior archival of version 1.2.1 dated 2024-02-26
Diff between rbioacc versions 1.2.1 dated 2024-02-26 and 1.3.1 dated 2025-09-26
rbioacc-1.2.1/rbioacc/README.md |only rbioacc-1.3.1/rbioacc/DESCRIPTION | 17 rbioacc-1.3.1/rbioacc/MD5 | 59 - rbioacc-1.3.1/rbioacc/NAMESPACE | 1 rbioacc-1.3.1/rbioacc/R/bioacc_metric.R | 4 rbioacc-1.3.1/rbioacc/R/plot_PP.R | 8 rbioacc-1.3.1/rbioacc/R/plot_exposure.R | 2 rbioacc-1.3.1/rbioacc/R/plot_fit.R | 6 rbioacc-1.3.1/rbioacc/R/plot_predict.R | 10 rbioacc-1.3.1/rbioacc/R/ppc_fit.R | 16 rbioacc-1.3.1/rbioacc/R/zzz_internals.R | 15 rbioacc-1.3.1/rbioacc/build/vignette.rds |binary rbioacc-1.3.1/rbioacc/inst/WORDLIST |only rbioacc-1.3.1/rbioacc/inst/doc/MWE.R | 20 rbioacc-1.3.1/rbioacc/inst/doc/MWE.html | 1 rbioacc-1.3.1/rbioacc/inst/doc/Tutorial.R | 144 +-- rbioacc-1.3.1/rbioacc/inst/doc/Tutorial.html | 11 rbioacc-1.3.1/rbioacc/man/rmMessWarn.Rd |only rbioacc-1.3.1/rbioacc/src/stanExports_TK.h | 480 +++++----- rbioacc-1.3.1/rbioacc/src/stanExports_odeTK.h | 442 ++++----- rbioacc-1.3.1/rbioacc/tests/testthat/test-PP.R | 22 rbioacc-1.3.1/rbioacc/tests/testthat/test-correlation.R | 49 - rbioacc-1.3.1/rbioacc/tests/testthat/test-elim.R | 52 - rbioacc-1.3.1/rbioacc/tests/testthat/test-mcmcTraces.R | 12 rbioacc-1.3.1/rbioacc/tests/testthat/test-metric.R | 12 rbioacc-1.3.1/rbioacc/tests/testthat/test-ppc.R | 12 rbioacc-1.3.1/rbioacc/tests/testthat/test-predict.R | 159 ++- rbioacc-1.3.1/rbioacc/tests/testthat/test-predict_manual.R | 48 - rbioacc-1.3.1/rbioacc/tests/testthat/test-psrf.R | 8 rbioacc-1.3.1/rbioacc/tests/testthat/test-waic.R | 12 rbioacc-1.3.1/rbioacc/vignettes/Tutorial_files/figure-html/plotMGS-1.png |binary rbioacc-1.3.1/rbioacc/vignettes/Tutorial_files/figure-html/ppcMGS-1.png |binary 32 files changed, 858 insertions(+), 764 deletions(-)
Title: Optimization Frameworks for Tie-Oriented and Actor-Oriented
Relational Event Models
Description: A comprehensive set of tools designed for optimizing likelihood within a tie-oriented (Butts, C., 2008, <doi:10.1111/j.1467-9531.2008.00203.x>) or an actor-oriented modelling framework (Stadtfeld, C., & Block, P., 2017, <doi:10.15195/v4.a14>) in relational event networks. The package accommodates both frequentist and Bayesian approaches. The frequentist approaches that the package incorporates are the Maximum Likelihood Optimization (MLE) and the Gradient-based Optimization (GDADAMAX). The Bayesian methodologies included in the package are the Bayesian Sampling Importance Resampling (BSIR) and the Hamiltonian Monte Carlo (HMC). The flexibility of choosing between frequentist and Bayesian optimization approaches allows researchers to select the estimation approach which aligns the most with their analytical preferences.
Author: Giuseppe Arena [aut, cre] ,
Rumana Lakdawala [aut],
Fabio Generoso Vieira [aut],
Marlyne Meijerink-Bosman [ctb],
Diana Karimova [ctb],
Mahdi Shafiee Kamalabad [ctb],
Roger Leenders [ctb],
Joris Mulder [ctb]
Maintainer: Giuseppe Arena <g.arena@uva.nl>
Diff between remstimate versions 2.3.13 dated 2025-01-29 and 2.3.14 dated 2025-09-26
DESCRIPTION | 11 +++++---- MD5 | 16 +++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/remstimate.R | 8 +++---- inst/doc/remstimate.Rmd | 10 ++++---- inst/doc/remstimate.html | 53 +++++++++++++++++++++-------------------------- src/remstimate.cpp | 4 +-- vignettes/remstimate.Rmd | 10 ++++---- 9 files changed, 54 insertions(+), 58 deletions(-)
Title: Monte Carlo for Classical Ising Model
Description: Classical Ising Model is a land mark system in statistical physics.The model explains the physics of spin glasses and magnetic materials, and cooperative phenomenon in general, for example phase transitions and neural networks.This package provides utilities to simulate one dimensional Ising Model with Metropolis and Glauber Monte Carlo with single flip dynamics in periodic boundary conditions. Utility functions for exact solutions are provided. Such as transfer matrix for 1D. Utility functions for exact solutions are provided. Example use cases are as follows: Measuring effective ergodicity and power-laws in so called functional-diffusion.
Author: Mehmet Suzen [aut, cre]
Maintainer: Mehmet Suzen <mehmet.suzen@physics.org>
Diff between isingLenzMC versions 0.2.7 dated 2025-09-18 and 0.2.8 dated 2025-09-26
isingLenzMC-0.2.7/isingLenzMC/inst/examples/effectiveErgodicity/README |only isingLenzMC-0.2.8/isingLenzMC/DESCRIPTION | 10 +++--- isingLenzMC-0.2.8/isingLenzMC/MD5 | 16 +++++----- isingLenzMC-0.2.8/isingLenzMC/NEWS | 15 ++++++++- isingLenzMC-0.2.8/isingLenzMC/README.md | 15 +++++++-- isingLenzMC-0.2.8/isingLenzMC/inst/doc/isingLenzMC.Rnw | 6 +-- isingLenzMC-0.2.8/isingLenzMC/inst/doc/isingLenzMC.pdf |binary isingLenzMC-0.2.8/isingLenzMC/inst/examples/effectiveErgodicity/README.md |only isingLenzMC-0.2.8/isingLenzMC/inst/examples/powerLawErgodicity/README.md | 2 - isingLenzMC-0.2.8/isingLenzMC/vignettes/isingLenzMC.Rnw | 6 +-- 10 files changed, 46 insertions(+), 24 deletions(-)
Title: Self-Validated Ensemble Models with Lasso and Relaxed Elastic
Net Regression
Description: Implements Self-Validated Ensemble Models (SVEM; Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) using elastic net regression via 'glmnet' (Friedman et al. (2010) <doi:10.18637/jss.v033.i01>). SVEM averages predictions from multiple models fitted to fractionally weighted bootstraps of the data, tuned with anti-correlated validation weights. Also implements the randomized permutation whole-model test for SVEM (Karl (2024) <doi:10.1016/j.chemolab.2024.105122>).
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between SVEMnet versions 2.1.3 dated 2025-09-09 and 2.2.4 dated 2025-09-26
SVEMnet-2.1.3/SVEMnet/R/svem_random_table.R |only SVEMnet-2.1.3/SVEMnet/man/plot_svem_significance_tests.Rd |only SVEMnet-2.1.3/SVEMnet/man/svem_random_table_from_model.Rd |only SVEMnet-2.2.4/SVEMnet/DESCRIPTION | 24 SVEMnet-2.2.4/SVEMnet/MD5 | 79 ++- SVEMnet-2.2.4/SVEMnet/NAMESPACE | 18 SVEMnet-2.2.4/SVEMnet/NEWS | 3 SVEMnet-2.2.4/SVEMnet/R/SVEMnet-package.R | 42 - SVEMnet-2.2.4/SVEMnet/R/SVEMnet.R | 268 ++++++---- SVEMnet-2.2.4/SVEMnet/R/bigexp.R |only SVEMnet-2.2.4/SVEMnet/R/coef.R | 107 ++-- SVEMnet-2.2.4/SVEMnet/R/glmnet_with_cv.R | 4 SVEMnet-2.2.4/SVEMnet/R/globals.R | 1 SVEMnet-2.2.4/SVEMnet/R/lipid_screen.R |only SVEMnet-2.2.4/SVEMnet/R/plot.svemtest.R | 2 SVEMnet-2.2.4/SVEMnet/R/predict.svem_lasso.R | 171 ++++-- SVEMnet-2.2.4/SVEMnet/R/predict_with_ci.R |only SVEMnet-2.2.4/SVEMnet/R/svem_optimize_random.R |only SVEMnet-2.2.4/SVEMnet/R/svem_random_table_multi.R |only SVEMnet-2.2.4/SVEMnet/R/svem_significance_test.R | 225 ++++++--- SVEMnet-2.2.4/SVEMnet/R/svem_significance_test_parallel.R | 235 ++++++--- SVEMnet-2.2.4/SVEMnet/build/partial.rdb |binary SVEMnet-2.2.4/SVEMnet/build/vignette.rds |binary SVEMnet-2.2.4/SVEMnet/data |only SVEMnet-2.2.4/SVEMnet/inst/doc/SVEMnet_vignette.R | 140 +++++ SVEMnet-2.2.4/SVEMnet/inst/doc/SVEMnet_vignette.Rmd | 206 ++++++++ SVEMnet-2.2.4/SVEMnet/inst/doc/SVEMnet_vignette.html | 275 +++++++++-- SVEMnet-2.2.4/SVEMnet/man/SVEMnet-package.Rd | 33 + SVEMnet-2.2.4/SVEMnet/man/SVEMnet.Rd | 217 +++++--- SVEMnet-2.2.4/SVEMnet/man/bigexp_formula.Rd |only SVEMnet-2.2.4/SVEMnet/man/bigexp_model_matrix.Rd |only SVEMnet-2.2.4/SVEMnet/man/bigexp_prepare.Rd |only SVEMnet-2.2.4/SVEMnet/man/bigexp_terms.Rd |only SVEMnet-2.2.4/SVEMnet/man/bigexp_train.Rd |only SVEMnet-2.2.4/SVEMnet/man/coef.svem_model.Rd | 9 SVEMnet-2.2.4/SVEMnet/man/lipid_screen.Rd |only SVEMnet-2.2.4/SVEMnet/man/plot.svem_significance_test.Rd |only SVEMnet-2.2.4/SVEMnet/man/predict.svem_model.Rd | 54 +- SVEMnet-2.2.4/SVEMnet/man/predict_with_ci.Rd |only SVEMnet-2.2.4/SVEMnet/man/svem_optimize_random.Rd |only SVEMnet-2.2.4/SVEMnet/man/svem_random_table_multi.Rd |only SVEMnet-2.2.4/SVEMnet/man/svem_significance_test.Rd | 69 ++ SVEMnet-2.2.4/SVEMnet/man/svem_significance_test_parallel.Rd | 56 +- SVEMnet-2.2.4/SVEMnet/man/with_bigexp_contrasts.Rd |only SVEMnet-2.2.4/SVEMnet/tests |only SVEMnet-2.2.4/SVEMnet/vignettes/SVEMnet_vignette.Rmd | 206 ++++++++ 46 files changed, 1862 insertions(+), 582 deletions(-)
Title: Partial Least Squares (PLS) Data Analysis Methods
Description: Different methods for PLS analysis of one or two data tables such as Tucker's Inter-Battery, NIPALS, SIMPLS, SIMPLS-CA, PLS Regression, and PLS Canonical Analysis. The main reference for this software is the awesome book (in French) 'La Regression PLS: Theorie et Pratique' by Michel Tenenhaus.
Author: Frederic Bertrand [cre] ,
Gaston Sanchez [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between plsdepot versions 0.2.0 dated 2023-03-13 and 0.3.0 dated 2025-09-26
plsdepot-0.2.0/plsdepot/NEWS |only plsdepot-0.3.0/plsdepot/DESCRIPTION | 36 ++++++++-------- plsdepot-0.3.0/plsdepot/MD5 | 43 +++++++++++-------- plsdepot-0.3.0/plsdepot/NAMESPACE | 54 +++++++++++++++--------- plsdepot-0.3.0/plsdepot/R/plot.interbat.R | 3 - plsdepot-0.3.0/plsdepot/R/plot.nipals.R | 3 - plsdepot-0.3.0/plsdepot/R/plot.plsca.R | 3 - plsdepot-0.3.0/plsdepot/R/plot.plsreg1.R | 3 - plsdepot-0.3.0/plsdepot/R/plot.plsreg2.R | 3 - plsdepot-0.3.0/plsdepot/R/plot.simpls.R | 3 - plsdepot-0.3.0/plsdepot/R/plot.simplsca.R | 3 - plsdepot-0.3.0/plsdepot/R/plsdepot-package.R |only plsdepot-0.3.0/plsdepot/R/print.interbat.R | 3 - plsdepot-0.3.0/plsdepot/R/print.nipals.R | 3 - plsdepot-0.3.0/plsdepot/R/print.plsca.R | 3 - plsdepot-0.3.0/plsdepot/R/print.plsreg1.R | 3 - plsdepot-0.3.0/plsdepot/R/print.plsreg2.R | 3 - plsdepot-0.3.0/plsdepot/R/print.simpls.R | 3 - plsdepot-0.3.0/plsdepot/R/print.simplsca.R | 3 - plsdepot-0.3.0/plsdepot/inst |only plsdepot-0.3.0/plsdepot/man/plsdepot-package.Rd |only plsdepot-0.3.0/plsdepot/tests |only 22 files changed, 92 insertions(+), 83 deletions(-)
Title: Inferring Causal Network from Mixed Observational Data Using a
Directed Acyclic Graph
Description: Learning a mixed directed acyclic graph based on both continuous and categorical data.
Author: Wujuan Zhong [aut, cre],
Li Dong [aut],
Quefeng Li [aut],
Xiaojing Zheng [aut]
Maintainer: Wujuan Zhong <zhongwujuan@gmail.com>
Diff between mDAG versions 1.2.2 dated 2019-08-20 and 1.2.3 dated 2025-09-26
DESCRIPTION | 28 ++++++++++++++++++++++------ MD5 | 10 +++++----- man/mDAG.Rd | 15 ++++++++++++--- src/Makevars | 1 - src/Makevars.win | 1 - src/RcppExports.cpp | 5 +++++ 6 files changed, 44 insertions(+), 16 deletions(-)
Title: Fast Algorithm for Penalized Quantile Regression
Description: Implements an efficient algorithm for fitting the entire regularization path of quantile regression models with elastic-net penalties using a generalized coordinate descent scheme. The framework also supports SCAD and MCP penalties. It is designed for high-dimensional datasets and emphasizes numerical accuracy and computational efficiency. This package implements the algorithms proposed in Tang, Q., Zhang, Y., & Wang, B. (2022) <https://openreview.net/pdf?id=RvwMTDYTOb>.
Author: Qian Tang [aut, cre],
Yikai Zhang [aut],
Boxiang Wang [aut]
Maintainer: Qian Tang <qian-tang@uiowa.edu>
Diff between hdqr versions 1.0.1 dated 2025-02-12 and 1.0.2 dated 2025-09-26
DESCRIPTION | 10 +++++----- MD5 | 41 +++++++++++++++++++++-------------------- R/cv.nc.hdqr-methods.R | 36 ++++++++++++++++++------------------ R/cv.nc.hdqr.R | 2 +- R/nc.hdqr-methods.R | 36 ++++++++++++++++++------------------ R/nc.hdqr.R | 2 +- R/qr-methods.R | 36 ++++++++++++++++++------------------ R/qr.R | 12 ++++++------ inst/CITATION |only inst/doc/hdqr-vignette.Rmd | 8 ++++++-- inst/doc/hdqr-vignette.html | 10 +++++++--- man/coef.cv.nc.hdqr.Rd | 18 +++++++++--------- man/coef.hdqr.Rd | 22 +++++++++++----------- man/coef.nc.hdqr.Rd | 22 +++++++++++----------- man/cv.nc.hdqr.Rd | 2 +- man/hdqr.Rd | 14 +++++++------- man/nc.hdqr.Rd | 2 +- man/predict.cv.nc.hdqr.Rd | 18 +++++++++--------- man/predict.hdqr.Rd | 14 +++++++------- man/predict.nc.hdqr.Rd | 14 +++++++------- src/lqr_hd.f90 | 7 +++---- vignettes/hdqr-vignette.Rmd | 8 ++++++-- 22 files changed, 173 insertions(+), 161 deletions(-)
Title: Generalized Promotion Time Cure Model with Bayesian Shrinkage
Priors
Description: Generalized promotion time cure model (GPTCM) via Bayesian hierarchical modeling for multiscale data integration (Zhao et al. (2025) <doi:10.48550/arXiv.2509.01001>). The Bayesian GPTCMs are applicable for both low- and high-dimensional data.
Author: Zhi Zhao [aut, cre]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Diff between GPTCM versions 1.1.1 dated 2025-09-16 and 1.1.2 dated 2025-09-26
GPTCM-1.1.1/GPTCM/man/mcmc.Rd |only GPTCM-1.1.2/GPTCM/DESCRIPTION | 6 - GPTCM-1.1.2/GPTCM/MD5 | 60 ++++++------- GPTCM-1.1.2/GPTCM/NEWS.md | 24 ++++- GPTCM-1.1.2/GPTCM/R/GPTCM.R | 5 - GPTCM-1.1.2/GPTCM/R/RcppExports.R | 54 ++++++------ GPTCM-1.1.2/GPTCM/R/plotBrier.R | 25 +++-- GPTCM-1.1.2/GPTCM/R/plotCoeff.R | 5 - GPTCM-1.1.2/GPTCM/R/plotMCMC.R | 3 GPTCM-1.1.2/GPTCM/R/predict.GPTCM.R | 2 GPTCM-1.1.2/GPTCM/R/simData.R | 61 ++++++++----- GPTCM-1.1.2/GPTCM/README.md | 17 +-- GPTCM-1.1.2/GPTCM/configure | 18 ++-- GPTCM-1.1.2/GPTCM/configure.ac | 12 +- GPTCM-1.1.2/GPTCM/inst/CITATION | 5 - GPTCM-1.1.2/GPTCM/inst/doc/GPTCM.R | 31 +++++++ GPTCM-1.1.2/GPTCM/inst/doc/GPTCM.Rmd | 33 +++++++ GPTCM-1.1.2/GPTCM/inst/doc/GPTCM.html | 18 ++-- GPTCM-1.1.2/GPTCM/man/GPTCM.Rd | 6 + GPTCM-1.1.2/GPTCM/man/figures/cran_betas.png |binary GPTCM-1.1.2/GPTCM/man/figures/cran_brier.png |binary GPTCM-1.1.2/GPTCM/man/figures/cran_etas.png |binary GPTCM-1.1.2/GPTCM/man/figures/cran_gammas.png |binary GPTCM-1.1.2/GPTCM/man/figures/cran_km.png |binary GPTCM-1.1.2/GPTCM/man/figures/cran_zetas.png |binary GPTCM-1.1.2/GPTCM/man/run_mcmc.Rd |only GPTCM-1.1.2/GPTCM/src/BVS.cpp | 114 ++++++++++++++------------ GPTCM-1.1.2/GPTCM/src/BVS.h | 13 ++ GPTCM-1.1.2/GPTCM/src/drive.cpp | 62 +++++++------- GPTCM-1.1.2/GPTCM/src/eval_func.cpp | 4 GPTCM-1.1.2/GPTCM/src/eval_func.h | 4 GPTCM-1.1.2/GPTCM/vignettes/GPTCM.Rmd | 33 +++++++ 32 files changed, 382 insertions(+), 233 deletions(-)
Title: Shrinkage for Effect Estimation
Description: Computes shrinkage estimators for regression problems. Selects penalty parameter by minimizing bias and variance in the effect estimate, where bias and variance are estimated from the posterior predictive distribution. See Keller and Rice (2017) <doi:10.1093/aje/kwx225> for more details.
Author: Kayleigh Keller [aut, cre]
Maintainer: Kayleigh Keller <kayleigh.keller@colostate.edu>
Diff between eshrink versions 0.1.2 dated 2020-09-09 and 0.2.0 dated 2025-09-26
DESCRIPTION | 18 +++++++++--------- MD5 | 28 ++++++++++++++-------------- R/eshrink.R | 1 - R/functions_bayes.R | 2 +- R/functions_ci.R | 4 ++-- R/functions_lasso.R | 2 +- R/functions_ridge.R | 12 ++++++------ man/check_CIbound.Rd | 2 +- man/eshrink-package.Rd | 1 - man/estRidge.Rd | 2 +- man/festRidge.Rd | 2 +- man/mseRidge.Rd | 2 +- man/samplePosterior.Rd | 2 +- man/simLASSO.Rd | 2 +- man/vcovfestRidge.Rd | 2 +- 15 files changed, 40 insertions(+), 42 deletions(-)
Title: Spatial and Network Based Individual Level Models for Epidemics
Description: Provides tools for simulating from discrete-time individual level models for infectious disease data analysis. This epidemic model class contains spatial and contact-network based models with two disease types: Susceptible-Infectious (SI) and Susceptible-Infectious-Removed (SIR).
Author: Vineetha Warriyar K. V. [aut],
Waleed Almutiry [aut, cre],
Rob Deardon [aut, ths]
Maintainer: Waleed Almutiry <wkmtierie@qu.edu.sa>
This is a re-admission after prior archival of version 1.5.2 dated 2020-09-30
Diff between EpiILM versions 1.5.2 dated 2020-09-30 and 1.5.3 dated 2025-09-26
EpiILM-1.5.2/EpiILM/tests/EpiILM.network.Rout.save |only EpiILM-1.5.2/EpiILM/tests/EpiILM.spatial.Rout.save |only EpiILM-1.5.3/EpiILM/DESCRIPTION | 24 - EpiILM-1.5.3/EpiILM/MD5 | 38 - EpiILM-1.5.3/EpiILM/build/partial.rdb |binary EpiILM-1.5.3/EpiILM/build/vignette.rds |binary EpiILM-1.5.3/EpiILM/inst/doc/Predict.R | 320 +++++++------- EpiILM-1.5.3/EpiILM/inst/doc/Predict.Rnw | 460 ++++++++++----------- EpiILM-1.5.3/EpiILM/inst/doc/Predict.pdf |binary EpiILM-1.5.3/EpiILM/man/EpiILM-package.Rd | 95 ++-- EpiILM-1.5.3/EpiILM/man/as.epidata.Rd | 38 - EpiILM-1.5.3/EpiILM/man/epiBR0.Rd | 201 ++++----- EpiILM-1.5.3/EpiILM/man/epidata.Rd | 366 ++++++++-------- EpiILM-1.5.3/EpiILM/man/epidic.Rd | 138 +++--- EpiILM-1.5.3/EpiILM/man/epilike.Rd | 188 ++++---- EpiILM-1.5.3/EpiILM/man/epimcmc.Rd | 370 ++++++++-------- EpiILM-1.5.3/EpiILM/man/plot.epimcmc.Rd | 100 ++-- EpiILM-1.5.3/EpiILM/man/pred.epi.Rd | 248 +++++------ EpiILM-1.5.3/EpiILM/tests/EpiILM.network.R | 115 ++--- EpiILM-1.5.3/EpiILM/tests/EpiILM.spatial.R | 101 ++-- EpiILM-1.5.3/EpiILM/vignettes/Predict.Rnw | 460 ++++++++++----------- 21 files changed, 1679 insertions(+), 1583 deletions(-)
Title: Parallel and Memory-Efficient Ecological Diversity Metrics
Description: Computes alpha and beta diversity metrics using concurrent 'C' threads.
Metrics include 'UniFrac', Faith's phylogenetic diversity, Bray-Curtis
dissimilarity, Shannon diversity index, and many others.
Also parses newick trees into 'phylo' objects and rarefies feature tables.
Author: Daniel P. Smith [aut, cre] ,
Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between ecodive versions 2.0.0 dated 2025-09-21 and 2.1.0 dated 2025-09-26
DESCRIPTION | 8 ++-- MD5 | 48 ++++++++++++++-------------- NEWS.md | 16 +++++++++ R/alpha_div.r | 55 ++++++++++++++++++++++----------- R/beta_div.r | 68 +++++++++++++++++++++++------------------ R/documentation.r | 10 ++++-- R/utils.r | 3 + R/validate.r | 23 ++++++------- README.md | 13 ++++++- inst/doc/bdiv.Rmd | 4 +- inst/doc/bdiv.html | 6 +-- inst/doc/benchmark.Rmd | 14 ++++---- inst/doc/benchmark.html | 14 ++++---- man/adiv_functions.Rd | 18 +++++++--- man/alpha_div.Rd | 66 ++++++++++++++++++++++++++++++++------- man/bdiv_functions.Rd | 58 +++++++++++++++++++--------------- man/beta_div.Rd | 46 +++++++++++++++++++++++++-- man/documentation.Rd | 10 ++++-- src/beta_div.c | 7 ++++ src/unifrac.c | 45 +++++++++++++++------------ tests/testthat/test-beta_div.r | 24 ++++++++++++++ tests/testthat/test-methods.r | 2 - tests/testthat/test-validate.r | 25 ++++++++++++--- vignettes/bdiv.Rmd | 4 +- vignettes/benchmark.Rmd | 14 ++++---- 25 files changed, 405 insertions(+), 196 deletions(-)
Title: Causal Effect Random Forest of Interaction Trees
Description: Fits a Causal Effect Random Forest of Interaction Tress (CERFIT) which is a modification of the Random Forest algorithm where each split is chosen to maximize subgroup treatment heterogeneity. Doing this allows it to estimate the individualized treatment effect for each observation in either randomized controlled trial (RCT) or observational data. For more information see L. Li, R. A. Levine, and J. Fan (2022) <doi:10.1002/sta4.457>.
Author: Justin Thorp [aut, cre],
Luo Li [aut],
Juanjuan Fan [aut]
Maintainer: Justin Thorp <jjtthorp@gmail.com>
Diff between CERFIT versions 0.1.0 dated 2022-06-01 and 0.1.1 dated 2025-09-26
DESCRIPTION | 12 ++--- MD5 | 20 ++++---- NAMESPACE | 42 +++++++++--------- R/CERFIT.R | 8 ++- R/RcppExports.R | 14 +++--- R/growTree.R | 20 ++++---- R/ordinalize.R | 50 ++++++++++----------- README.md | 128 +++++++++++++++++++++++++++---------------------------- man/CERFIT.Rd | 3 + src/Makevars | 1 src/Makevars.win | 1 11 files changed, 152 insertions(+), 147 deletions(-)
Title: Bayesian Marginal Effects for 'brms' Models
Description: Calculate Bayesian marginal effects, average marginal effects, and marginal coefficients (also called population averaged coefficients) for models fit using the 'brms' package including fixed effects, mixed effects, and location scale models. These are based on marginal predictions that integrate out random effects if necessary (see for example <doi:10.1186/s12874-015-0046-6> and <doi:10.1111/biom.12707>).
Author: Joshua F. Wiley [aut, cre] ,
Donald Hedeker [aut]
Maintainer: Joshua F. Wiley <jwiley.psych@gmail.com>
Diff between brmsmargins versions 0.2.0 dated 2022-05-18 and 0.2.1 dated 2025-09-26
DESCRIPTION | 13 MD5 | 124 NEWS.md | 67 R/RcppExports.R | 236 R/assert.R | 314 R/averageposterior.R | 74 R/builders.R | 209 R/imp-brms.R | 60 R/marginalcoef.R | 195 R/margins.R | 145 R/prediction.R | 430 - R/rimplementation.R | 110 R/utils.R | 703 - README.md | 364 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/fixed-effects-marginaleffects.Rmd | 1122 +-- inst/doc/fixed-effects-marginaleffects.html | 4874 ++++++------- inst/doc/location-scale-marginaleffects.Rmd | 854 +- inst/doc/location-scale-marginaleffects.html | 4439 ++++++------ inst/doc/mixed-effects-marginaleffects.Rmd | 306 inst/doc/mixed-effects-marginaleffects.html | 6745 +++++++++---------- man/assertall.Rd | 18 man/brmsmargins.Rd | 31 man/bsummary.Rd | 30 man/builders.Rd | 23 man/dot-averagePosterior.Rd | 2 man/dot-extractlink.Rd | 6 man/dot-links.Rd | 15 man/dot-percent.Rd | 2 man/integratemvn.Rd | 4 man/integratere.Rd | 4 man/is.random.Rd | 4 man/marginalcoef.Rd | 24 man/prediction.Rd | 29 man/tab2mat.Rd | 4 src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 6 src/integratemvn.cpp | 17 src/integratemvn.h | 2 src/integratere.cpp | 30 src/lmcpp.cpp | 15 tests/testthat.R | 12 tests/testthat/test-bsummary.R | 118 tests/testthat/test-builders.R | 32 tests/testthat/test-dot-checktab.R | 22 tests/testthat/test-dot-links.R | 144 tests/testthat/test-dot-percent.R | 98 tests/testthat/test-fixedeffects-bernoulli-margins.R | 120 tests/testthat/test-fixedeffects-beta-margins.R | 140 tests/testthat/test-fixedeffects-gamma-margins.R | 154 tests/testthat/test-integratemvn.R | 90 tests/testthat/test-marginalcoef-mixedlogit.R | 130 tests/testthat/test-marginalcoef-mixedpoisson.R | 126 tests/testthat/test-predict-mixedlogit.R | 342 tests/testthat/test-predict-mixedlogtrans.R | 230 tests/testthat/test-predict-mixedpoisson.R | 222 tests/testthat/test-rowbootmeans.R | 16 tests/testthat/test-tab2mat.R | 10 vignettes/fixed-effects-marginaleffects.Rmd | 1122 +-- vignettes/location-scale-marginaleffects.Rmd | 854 +- vignettes/mixed-effects-marginaleffects.Rmd | 306 63 files changed, 13045 insertions(+), 12897 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-04-03 3.0.3
2018-01-25 3.0.2
2016-01-09 3.0.1
2015-07-27 3.0.0
Title: Clinical Trial Simulator
Description: Simulate phase II and/or phase III clinical trials. It supports various types of endpoints and adaptive strategies. Tools for carrying out graphical testing procedure and combination test under group sequential design are also provided.
Author: Han Zhang [cre, aut]
Maintainer: Han Zhang <zhangh.ustc@gmail.com>
Diff between TrialSimulator versions 1.0.0 dated 2025-09-03 and 1.3.0 dated 2025-09-26
TrialSimulator-1.0.0/TrialSimulator/R/Arm.R |only TrialSimulator-1.0.0/TrialSimulator/R/Controller.R |only TrialSimulator-1.0.0/TrialSimulator/R/Endpoint.R |only TrialSimulator-1.0.0/TrialSimulator/R/Listener.R |only TrialSimulator-1.0.0/TrialSimulator/R/Trial.R |only TrialSimulator-1.0.0/TrialSimulator/man/default_action.Rd |only TrialSimulator-1.3.0/TrialSimulator/DESCRIPTION | 6 TrialSimulator-1.3.0/TrialSimulator/MD5 | 209 ++++------ TrialSimulator-1.3.0/TrialSimulator/NEWS.md | 26 + TrialSimulator-1.3.0/TrialSimulator/R/Arms.R | 55 +- TrialSimulator-1.3.0/TrialSimulator/R/Controllers.R | 54 +- TrialSimulator-1.3.0/TrialSimulator/R/CorrelatedPfsAndOs3.R | 34 + TrialSimulator-1.3.0/TrialSimulator/R/CorrelatedPfsAndOs4.R | 43 +- TrialSimulator-1.3.0/TrialSimulator/R/DynamicRNGFunction.R | 41 + TrialSimulator-1.3.0/TrialSimulator/R/Endpoints.R | 115 ++++- TrialSimulator-1.3.0/TrialSimulator/R/EnrollmentCountCondition.R | 15 TrialSimulator-1.3.0/TrialSimulator/R/Listeners.R | 28 + TrialSimulator-1.3.0/TrialSimulator/R/Milestones.R | 69 ++- TrialSimulator-1.3.0/TrialSimulator/R/PiecewiseConstantExponentialRNG.R | 34 + TrialSimulator-1.3.0/TrialSimulator/R/StaggeredRecruiter.R | 25 - TrialSimulator-1.3.0/TrialSimulator/R/Trials.R | 206 +++++++-- TrialSimulator-1.3.0/TrialSimulator/R/arm.R |only TrialSimulator-1.3.0/TrialSimulator/R/calendarTime.R | 17 TrialSimulator-1.3.0/TrialSimulator/R/controller.R |only TrialSimulator-1.3.0/TrialSimulator/R/default_action.R | 12 TrialSimulator-1.3.0/TrialSimulator/R/doNothing.R | 31 + TrialSimulator-1.3.0/TrialSimulator/R/endpoint.R |only TrialSimulator-1.3.0/TrialSimulator/R/enrollment.R | 43 +- TrialSimulator-1.3.0/TrialSimulator/R/eventNumber.R | 24 - TrialSimulator-1.3.0/TrialSimulator/R/fitCoxph.R | 24 - TrialSimulator-1.3.0/TrialSimulator/R/fitFarringtonManning.R | 8 TrialSimulator-1.3.0/TrialSimulator/R/fitLinear.R | 8 TrialSimulator-1.3.0/TrialSimulator/R/fitLogistic.R | 6 TrialSimulator-1.3.0/TrialSimulator/R/fitLogrank.R | 14 TrialSimulator-1.3.0/TrialSimulator/R/listener.R |only TrialSimulator-1.3.0/TrialSimulator/R/milestone.R | 33 + TrialSimulator-1.3.0/TrialSimulator/R/rconst.R | 12 TrialSimulator-1.3.0/TrialSimulator/R/solveMixtureExponentialDistribution.R | 13 TrialSimulator-1.3.0/TrialSimulator/R/solveThreeStateModel.R | 13 TrialSimulator-1.3.0/TrialSimulator/R/summarizeMilestoneTime.R | 16 TrialSimulator-1.3.0/TrialSimulator/R/summarizeTable.R | 9 TrialSimulator-1.3.0/TrialSimulator/R/trial.R |only TrialSimulator-1.3.0/TrialSimulator/R/weibullDropout.R | 11 TrialSimulator-1.3.0/TrialSimulator/README.md | 15 TrialSimulator-1.3.0/TrialSimulator/build/vignette.rds |binary TrialSimulator-1.3.0/TrialSimulator/inst/doc/actionFunctions.Rmd | 60 +- TrialSimulator-1.3.0/TrialSimulator/inst/doc/actionFunctions.html | 113 ++--- TrialSimulator-1.3.0/TrialSimulator/inst/doc/adaptiveDesign.R | 18 TrialSimulator-1.3.0/TrialSimulator/inst/doc/adaptiveDesign.Rmd | 22 - TrialSimulator-1.3.0/TrialSimulator/inst/doc/adaptiveDesign.html | 42 -- TrialSimulator-1.3.0/TrialSimulator/inst/doc/conditionSystem.R | 3 TrialSimulator-1.3.0/TrialSimulator/inst/doc/conditionSystem.Rmd | 12 TrialSimulator-1.3.0/TrialSimulator/inst/doc/conditionSystem.html | 92 ++-- TrialSimulator-1.3.0/TrialSimulator/inst/doc/defineArms.html | 5 TrialSimulator-1.3.0/TrialSimulator/inst/doc/defineLongitudinalEndpoints.Rmd | 4 TrialSimulator-1.3.0/TrialSimulator/inst/doc/defineLongitudinalEndpoints.html | 10 TrialSimulator-1.3.0/TrialSimulator/inst/doc/defineNonTimeToEventEndpoints.Rmd | 4 TrialSimulator-1.3.0/TrialSimulator/inst/doc/defineNonTimeToEventEndpoints.html | 10 TrialSimulator-1.3.0/TrialSimulator/inst/doc/defineTimeToEventEndpoints.Rmd | 4 TrialSimulator-1.3.0/TrialSimulator/inst/doc/defineTimeToEventEndpoints.html | 10 TrialSimulator-1.3.0/TrialSimulator/inst/doc/fixedDesign.R | 6 TrialSimulator-1.3.0/TrialSimulator/inst/doc/fixedDesign.Rmd | 6 TrialSimulator-1.3.0/TrialSimulator/inst/doc/fixedDesign.html | 13 TrialSimulator-1.3.0/TrialSimulator/inst/doc/responseAdaptive.R | 20 TrialSimulator-1.3.0/TrialSimulator/inst/doc/responseAdaptive.Rmd | 22 - TrialSimulator-1.3.0/TrialSimulator/inst/doc/responseAdaptive.html | 23 - TrialSimulator-1.3.0/TrialSimulator/inst/doc/simulatePfsAndOs.Rmd | 4 TrialSimulator-1.3.0/TrialSimulator/inst/doc/simulatePfsAndOs.html | 9 TrialSimulator-1.3.0/TrialSimulator/inst/doc/wrappers.html | 5 TrialSimulator-1.3.0/TrialSimulator/man/Arms.Rd | 78 +++ TrialSimulator-1.3.0/TrialSimulator/man/Controllers.Rd | 51 +- TrialSimulator-1.3.0/TrialSimulator/man/CorrelatedPfsAndOs3.Rd | 32 + TrialSimulator-1.3.0/TrialSimulator/man/CorrelatedPfsAndOs4.Rd | 41 + TrialSimulator-1.3.0/TrialSimulator/man/DynamicRNGFunction.Rd | 39 + TrialSimulator-1.3.0/TrialSimulator/man/Endpoints.Rd | 137 +++++- TrialSimulator-1.3.0/TrialSimulator/man/Listeners.Rd | 47 ++ TrialSimulator-1.3.0/TrialSimulator/man/Milestones.Rd | 22 - TrialSimulator-1.3.0/TrialSimulator/man/PiecewiseConstantExponentialRNG.Rd | 33 + TrialSimulator-1.3.0/TrialSimulator/man/StaggeredRecruiter.Rd | 27 - TrialSimulator-1.3.0/TrialSimulator/man/Trials.Rd | 177 ++++++-- TrialSimulator-1.3.0/TrialSimulator/man/arm.Rd | 21 - TrialSimulator-1.3.0/TrialSimulator/man/calendarTime.Rd | 18 TrialSimulator-1.3.0/TrialSimulator/man/controller.Rd | 27 - TrialSimulator-1.3.0/TrialSimulator/man/doNothing.Rd | 22 - TrialSimulator-1.3.0/TrialSimulator/man/endpoint.Rd | 94 ++-- TrialSimulator-1.3.0/TrialSimulator/man/enrollment.Rd | 37 + TrialSimulator-1.3.0/TrialSimulator/man/eventNumber.Rd | 24 - TrialSimulator-1.3.0/TrialSimulator/man/fitCoxph.Rd | 24 - TrialSimulator-1.3.0/TrialSimulator/man/fitFarringtonManning.Rd | 8 TrialSimulator-1.3.0/TrialSimulator/man/fitLinear.Rd | 8 TrialSimulator-1.3.0/TrialSimulator/man/fitLogistic.Rd | 6 TrialSimulator-1.3.0/TrialSimulator/man/fitLogrank.Rd | 13 TrialSimulator-1.3.0/TrialSimulator/man/listener.Rd | 10 TrialSimulator-1.3.0/TrialSimulator/man/milestone.Rd | 32 + TrialSimulator-1.3.0/TrialSimulator/man/rconst.Rd | 11 TrialSimulator-1.3.0/TrialSimulator/man/solveMixtureExponentialDistribution.Rd | 13 TrialSimulator-1.3.0/TrialSimulator/man/solveThreeStateModel.Rd | 11 TrialSimulator-1.3.0/TrialSimulator/man/summarizeDataFrame.Rd | 9 TrialSimulator-1.3.0/TrialSimulator/man/summarizeMilestoneTime.Rd | 16 TrialSimulator-1.3.0/TrialSimulator/man/trial.Rd | 54 +- TrialSimulator-1.3.0/TrialSimulator/man/weibullDropout.Rd | 12 TrialSimulator-1.3.0/TrialSimulator/tests/testthat/test-trial.R | 116 +++-- TrialSimulator-1.3.0/TrialSimulator/vignettes/actionFunctions.Rmd | 60 +- TrialSimulator-1.3.0/TrialSimulator/vignettes/adaptiveDesign.Rmd | 22 - TrialSimulator-1.3.0/TrialSimulator/vignettes/conditionSystem.Rmd | 12 TrialSimulator-1.3.0/TrialSimulator/vignettes/defineLongitudinalEndpoints.Rmd | 4 TrialSimulator-1.3.0/TrialSimulator/vignettes/defineNonTimeToEventEndpoints.Rmd | 4 TrialSimulator-1.3.0/TrialSimulator/vignettes/defineTimeToEventEndpoints.Rmd | 4 TrialSimulator-1.3.0/TrialSimulator/vignettes/fixedDesign.Rmd | 6 TrialSimulator-1.3.0/TrialSimulator/vignettes/responseAdaptive.Rmd | 22 - TrialSimulator-1.3.0/TrialSimulator/vignettes/simulatePfsAndOs.Rmd | 4 111 files changed, 2112 insertions(+), 1082 deletions(-)
More information about TrialSimulator at CRAN
Permanent link
Title: Precision Agriculture Computational Utilities
Description: Support for a variety of commonly used precision agriculture operations. Includes functions to download and process raw satellite images from Sentinel-2 <https://documentation.dataspace.copernicus.eu/APIs/OData.html>. Includes functions that download vegetation index statistics for a given period of time, without the need to download the raw images <https://documentation.dataspace.copernicus.eu/APIs/SentinelHub/Statistical.html>. There are also functions to download and visualize weather data in a historical context. Lastly, the package also contains functions to process yield monitor data. These functions can build polygons around recorded data points, evaluate the overlap between polygons, clean yield data, and smooth yield maps.
Author: dos Santos Caio [aut, cre],
Miguez Fernando [aut]
Maintainer: dos Santos Caio <clsantos@iastate.edu>
Diff between pacu versions 0.1.63 dated 2025-05-29 and 0.1.72 dated 2025-09-26
DESCRIPTION | 6 MD5 | 45 - NAMESPACE | 4 R/get_rgb.R | 35 R/merge.R |only R/pacu_internal.R | 18 R/plot.R | 82 +- R/print.R | 39 R/trial.R | 279 ++++--- R/yield.R | 16 build/vignette.rds |binary inst/doc/pacu.html | 730 +++++++++--------- inst/doc/pacu_faq.R | 44 - inst/doc/pacu_faq.html | 816 ++++++++++---------- inst/doc/pacu_sat.R | 226 ++--- inst/doc/pacu_sat.html | 1204 +++++++++++++++--------------- inst/doc/pacu_weather.R | 68 - inst/doc/pacu_weather.html | 898 +++++++++++----------- inst/doc/pacu_ym.R | 314 +++---- inst/doc/pacu_ym.html | 1784 ++++++++++++++++++++++----------------------- man/pa_get_rgb.Rd | 12 man/pa_merge.Rd |only man/pa_print.Rd | 3 man/pa_trial.Rd |only man/pa_yield.Rd | 2 25 files changed, 3398 insertions(+), 3227 deletions(-)
Title: Meta-Analytic Effect Size Calculation for Pre-Post Designs with
Correlation Imputation
Description: Tools for the calculation of effect sizes (standardised mean difference) and mean difference in pre-post controlled studies, including robust imputation of missing variances (standard deviation of changes) and correlations (Pearson correlation coefficient). The main function 'metacor_dual()' implements several methods for imputing missing standard deviation of changes or Pearson correlation coefficient, and generates transparent imputation reports. Designed for meta-analyses with incomplete summary statistics. For details on the methods, see Higgins et al. (2023) and Fu et al. (2013).
Author: Iker J. Bautista [aut, cre],
Saul M. Rodriguez [ctb]
Maintainer: Iker J. Bautista <ikerugr@gmail.com>
Diff between metacor versions 1.1.2 dated 2025-07-28 and 1.2.0 dated 2025-09-26
DESCRIPTION | 24 - MD5 | 6 R/metacor_dual.R | 1025 ++++++++++++++++++++++----------------------- inst/doc/introduccion.html | 40 + 4 files changed, 549 insertions(+), 546 deletions(-)
Title: Irish Grid Reference Utilities
Description: Convert between Irish grid references and Irish Grid coordinates. Irish grid
references can also be converted to or from an 'sf' object in any coordinate reference
system. Precisions from 1 m to 100 km including 2 km (tetrads) are supported, as are
datasets with mixed precision. Conversion to 'sf' polygons is precision-aware.
Author: John Kennedy [aut, cre, cph] ,
Digital Nature [fnd]
Maintainer: John Kennedy <john@digitalnature.ie>
Diff between igr versions 1.0.0 dated 2025-01-07 and 1.0.1 dated 2025-09-26
DESCRIPTION | 15 +++-- MD5 | 28 +++++------ NEWS.md | 5 + R/st_irishgridrefs.R | 7 +- R/utils.R | 6 +- README.md | 4 + build/vignette.rds |binary inst/doc/igr.R | 55 ++++++--------------- inst/doc/igr.Rmd | 57 +++++++--------------- inst/doc/igr.html | 66 +++++++++----------------- man/figures/README-example-igr-points-1.png |binary man/figures/README-example-igr-polygons-1.png |binary man/st_irishgridrefs.Rd | 2 tests/testthat/test-st_irishgridrefs.R | 8 +++ vignettes/igr.Rmd | 57 +++++++--------------- 15 files changed, 124 insertions(+), 186 deletions(-)