Title: Bayesian Geostatistics Using Predictive Stacking
Description: Fits Bayesian hierarchical spatial and spatial-temporal process
models for point-referenced Gaussian, Poisson, binomial, and binary data
using stacking of predictive densities. It involves sampling from
analytically available posterior distributions conditional upon candidate
values of the spatial process parameters and, subsequently assimilate
inference from these individual posterior distributions using Bayesian
predictive stacking. Our algorithm is highly parallelizable and hence, much
faster than traditional Markov chain Monte Carlo algorithms while delivering
competitive predictive performance. See Zhang, Tang, and Banerjee (2025)
<doi:10.1080/01621459.2025.2566449>, and, Pan, Zhang, Bradley, and Banerjee
(2025) <doi:10.1214/25-BA1582> for details.
Author: Soumyakanti Pan [aut, cre] ,
Sudipto Banerjee [aut]
Maintainer: Soumyakanti Pan <span18@ucla.edu>
Diff between spStack versions 1.1.2 dated 2025-10-04 and 1.1.3 dated 2026-03-08
DESCRIPTION | 18 - MD5 | 86 ++++----- NAMESPACE | 9 NEWS.md | 6 R/predict.R | 2 R/spGLMexact.R | 2 R/spGLMstack.R | 38 +--- R/spLMstack.R | 28 +-- R/spStack-package.R | 2 R/stackedSampler.R | 3 R/stacking_weights.R | 213 +++++++++++++++++++++- R/stvcGLMexact.R | 2 R/stvcGLMstack.R | 25 +- R/utils.R | 2 README.md | 55 ++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/posterior-predictive.R | 10 - inst/doc/posterior-predictive.Rmd | 10 - inst/doc/posterior-predictive.html | 343 +++++++++++++++++++++---------------- inst/doc/spStack.R | 2 inst/doc/spStack.Rmd | 2 inst/doc/spStack.html | 128 ++++++++----- inst/doc/spatial-temporal.R | 21 +- inst/doc/spatial-temporal.Rmd | 25 +- inst/doc/spatial-temporal.html | 158 +++++++++-------- inst/doc/spatial.R | 36 ++- inst/doc/spatial.Rmd | 40 ++-- inst/doc/spatial.html | 227 ++++++++++++++---------- inst/doc/technical_overview.html | 5 man/get_stacking_weights.Rd | 12 - man/posteriorPredict.Rd | 2 man/spGLMexact.Rd | 2 man/spGLMstack.Rd | 12 - man/spLMstack.Rd | 10 - man/spStack-package.Rd | 2 man/stackedSampler.Rd | 3 man/stvcGLMexact.Rd | 2 man/stvcGLMstack.Rd | 8 vignettes/posterior-predictive.Rmd | 10 - vignettes/refs.bib | 14 - vignettes/spStack.Rmd | 2 vignettes/spatial-temporal.Rmd | 25 +- vignettes/spatial.Rmd | 40 ++-- 44 files changed, 1019 insertions(+), 623 deletions(-)
Title: Bessel Functions Rcpp Interface
Description: Exports an 'Rcpp' interface for the Bessel functions in the 'Bessel' package, which can then be called from the 'C++' code of other packages. For the original 'Fortran' implementation of these functions see Amos (1995) <doi:10.1145/212066.212078>.
Author: Alexios Galanos [aut, cre] ,
Martin Maechler [aut] ,
Donald E. Amos [aut]
Maintainer: Alexios Galanos <alexios@4dscape.com>
Diff between RcppBessel versions 1.0.0 dated 2024-08-27 and 1.0.1 dated 2026-03-08
RcppBessel-1.0.0/RcppBessel/README.md |only RcppBessel-1.0.1/RcppBessel/DESCRIPTION | 13 +-- RcppBessel-1.0.1/RcppBessel/MD5 | 12 +-- RcppBessel-1.0.1/RcppBessel/NEWS.md |only RcppBessel-1.0.1/RcppBessel/build/partial.rdb |binary RcppBessel-1.0.1/RcppBessel/inst/doc/RcppBessel.html | 67 +++++++++--------- RcppBessel-1.0.1/RcppBessel/man/RcppBessel-package.Rd | 2 RcppBessel-1.0.1/RcppBessel/src/RcppExports.cpp | 14 +-- 8 files changed, 55 insertions(+), 53 deletions(-)
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt' (<DOI:10.32614/CRAN.package.mlt>, <DOI:10.32614/CRAN.package.mlt.docreg>).
Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to
transformation models for clustered data is provided (Barbanti and Hothorn, 2022,
<DOI:10.1093/biostatistics/kxac048>) and a tutorial explains applications in survival analysis
(Siegfried et al., 2025, <DOI:10.48550/arXiv.2402.06428>). Multivariate conditional transformation models
(Klein et al, 2022, <DOI:10.1111/sjos.12501>) and shift-scale transformation models (Siegfried et al, 2023,
<DOI:10.108 [...truncated...]
Author: Torsten Hothorn [aut, cre] ,
Luisa Barbanti [ctb] ,
Sandra Siegfried [aut] ,
Lucas Kook [aut] ,
Susanne Dandl [ctb] ,
Brian Ripley [ctb],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Nadja Klein [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 1.4-0 dated 2026-02-26 and 1.4-1 dated 2026-03-08
DESCRIPTION | 10 MD5 | 78 ++--- build/partial.rdb |binary demo/npn.R | 2 inst/NEWS.Rd | 7 inst/doc/NAMI.R | 10 inst/doc/NAMI.Rnw | 10 inst/doc/NAMI.pdf |binary inst/doc/mtram.R | 724 ----------------------------------------------- inst/doc/mtram.pdf |binary inst/doc/survtram.Rnw | 3 inst/doc/survtram.pdf |binary inst/doc/tram.Rnw | 1 inst/doc/tram.pdf |binary inst/npn_empeval/TDA.R | 8 inst/npn_empeval/fit.R | 2 inst/simulations/sim2d.R | 2 inst/simulations/sim5d.R | 2 man/Aareg.Rd | 4 man/BoxCox.Rd | 4 man/Colr.Rd | 4 man/Compris.Rd | 4 man/Coxph.Rd | 4 man/Lehmann.Rd | 4 man/Lm.Rd | 4 man/Polr.Rd | 4 man/Survreg.Rd | 4 man/mmlt.Rd | 4 man/mtram.Rd | 4 man/robust_score_test.Rd | 4 man/score_test.Rd | 4 man/tram-methods.Rd | 4 man/tram.Rd | 6 tests/mmlt-Ex.R | 8 tests/mmlt-Ex.Rout.save | 8 tests/mmlt-interface.R | 36 +- tests/mtram-Ex.Rout.save | 4 vignettes/NAMI.Rnw | 10 vignettes/survtram.Rnw | 3 vignettes/tram.Rnw | 1 40 files changed, 125 insertions(+), 866 deletions(-)
Title: Search Algorithms and Loss Functions for Bayesian Clustering
Description: The SALSO algorithm is an efficient randomized greedy search method to find a point estimate for a random partition based on a loss function and posterior Monte Carlo samples. The algorithm is implemented for many loss functions, including the Binder loss and a generalization of the variation of information loss, both of which allow for unequal weights on the two types of clustering mistakes. Efficient implementations are also provided for Monte Carlo estimation of the posterior expected loss of a given clustering estimate. See Dahl, Johnson, Müller (2022) <doi:10.1080/10618600.2022.2069779>.
Author: David B. Dahl [aut, cre] ,
Devin J. Johnson [aut] ,
Peter Mueller [aut],
Andres Felipe Barrientos [aut],
Garritt Page [aut],
David Dunson [aut],
Authors of the dependency Rust crates [ctb]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between salso versions 0.3.57 dated 2025-08-29 and 0.3.69 dated 2026-03-08
salso-0.3.57/salso/src/Makevars |only salso-0.3.57/salso/src/Makevars.win |only salso-0.3.57/salso/src/rust/vendor.tar.gz |only salso-0.3.57/salso/tools/build_rust_library.R |only salso-0.3.69/salso/DESCRIPTION | 54 +------- salso-0.3.69/salso/MD5 | 51 ++++---- salso-0.3.69/salso/NEWS | 17 ++ salso-0.3.69/salso/R/chips.R | 22 ++- salso-0.3.69/salso/R/roxido.R | 7 - salso-0.3.69/salso/R/synthetic-demo-data.R |only salso-0.3.69/salso/cleanup |only salso-0.3.69/salso/cleanup.win |only salso-0.3.69/salso/configure | 4 salso-0.3.69/salso/configure.win | 3 salso-0.3.69/salso/data/synthetic.rda |only salso-0.3.69/salso/demo |only salso-0.3.69/salso/inst |only salso-0.3.69/salso/man/chips.Rd | 27 ++-- salso-0.3.69/salso/man/salso-package.Rd | 16 -- salso-0.3.69/salso/man/synthetic.Rd |only salso-0.3.69/salso/src/Makevars.in |only salso-0.3.69/salso/src/Makevars.win.in |only salso-0.3.69/salso/src/abort_shim.c |only salso-0.3.69/salso/src/rust/Cargo.lock | 85 +++++-------- salso-0.3.69/salso/src/rust/Cargo.toml | 8 - salso-0.3.69/salso/src/rust/build.rs | 7 - salso-0.3.69/salso/src/rust/rbindings/src/lib.rs | 5 salso-0.3.69/salso/src/rust/roxido/Cargo.lock | 16 +- salso-0.3.69/salso/src/rust/roxido/src/lib.rs | 40 +++++- salso-0.3.69/salso/src/rust/roxido_macro/Cargo.lock | 16 +- salso-0.3.69/salso/src/rust/roxido_macro/src/lib.rs | 124 ++++++-------------- salso-0.3.69/salso/src/rust/src/lib.rs | 13 +- salso-0.3.69/salso/src/rust/vendor.tar.xz |only salso-0.3.69/salso/tools/configure.R |only 34 files changed, 237 insertions(+), 278 deletions(-)
Title: High Performance Tools for Combinatorics and Computational
Mathematics
Description: Provides optimized functions and flexible iterators implemented in
C++ for solving problems in combinatorics and computational mathematics.
Handles various combinatorial objects including combinations, permutations,
integer partitions and compositions, Cartesian products, unordered
Cartesian products, and partition of groups. Utilizes the RMatrix class
from 'RcppParallel' for thread safety. The combination and permutation
functions contain constraint parameters that allow for generation of all
results of a vector meeting specific criteria (e.g. finding all
combinations such that the sum is between two bounds). Capable of
ranking/unranking combinatorial objects efficiently (e.g. retrieve only the
nth lexicographical result) which sets up nicely for parallelization as
well as random sampling. Gmp support permits exploration where the total
number of results is large (e.g. comboSample(10000, 500, n = 4)).
Additionally, there are several high performance number theoretic
functions that are [...truncated...]
Author: Joseph Wood [aut, cre]
Maintainer: Joseph Wood <jwood000@gmail.com>
Diff between RcppAlgos versions 2.9.5 dated 2026-01-29 and 2.10.0 dated 2026-03-08
RcppAlgos-2.10.0/RcppAlgos/DESCRIPTION | 8 RcppAlgos-2.10.0/RcppAlgos/MD5 | 354 +- RcppAlgos-2.10.0/RcppAlgos/NEWS.md | 39 RcppAlgos-2.10.0/RcppAlgos/R/CheckLinkedVersion.R |only RcppAlgos-2.10.0/RcppAlgos/R/ComboPermuteUtility.R | 8 RcppAlgos-2.10.0/RcppAlgos/R/NumberTheory.R | 18 RcppAlgos-2.10.0/RcppAlgos/R/S4Classes.R | 2 RcppAlgos-2.10.0/RcppAlgos/R/Utility.R | 67 RcppAlgos-2.10.0/RcppAlgos/R/comboGroups.R | 6 RcppAlgos-2.10.0/RcppAlgos/R/comboRank.R | 6 RcppAlgos-2.10.0/RcppAlgos/R/compositionsCount.R | 8 RcppAlgos-2.10.0/RcppAlgos/R/compositionsDesign.R | 4 RcppAlgos-2.10.0/RcppAlgos/R/compositionsGeneral.R | 4 RcppAlgos-2.10.0/RcppAlgos/R/compositionsIter.R | 4 RcppAlgos-2.10.0/RcppAlgos/R/compositionsRank.R | 7 RcppAlgos-2.10.0/RcppAlgos/R/compositionsSample.R | 4 RcppAlgos-2.10.0/RcppAlgos/R/expandGrid.R | 4 RcppAlgos-2.10.0/RcppAlgos/R/partitionsCount.R | 8 RcppAlgos-2.10.0/RcppAlgos/R/partitionsDesign.R | 4 RcppAlgos-2.10.0/RcppAlgos/R/partitionsGeneral.R | 4 RcppAlgos-2.10.0/RcppAlgos/R/partitionsIter.R | 4 RcppAlgos-2.10.0/RcppAlgos/R/partitionsRank.R | 10 RcppAlgos-2.10.0/RcppAlgos/R/partitionsSample.R | 4 RcppAlgos-2.10.0/RcppAlgos/R/permuteCount.R | 34 RcppAlgos-2.10.0/RcppAlgos/R/permutePartsDesign.R |only RcppAlgos-2.10.0/RcppAlgos/R/permuteRank.R | 6 RcppAlgos-2.10.0/RcppAlgos/R/zzz.R | 10 RcppAlgos-2.10.0/RcppAlgos/README.md | 148 RcppAlgos-2.10.0/RcppAlgos/build/vignette.rds |binary RcppAlgos-2.10.0/RcppAlgos/inst/NEWS.Rd | 36 RcppAlgos-2.10.0/RcppAlgos/inst/doc/CombPermConstraints.Rmd | 494 --- RcppAlgos-2.10.0/RcppAlgos/inst/doc/CombPermConstraints.html | 832 ----- RcppAlgos-2.10.0/RcppAlgos/inst/doc/CombinatorialSampling.Rmd | 87 RcppAlgos-2.10.0/RcppAlgos/inst/doc/CombinatorialSampling.html | 629 +--- RcppAlgos-2.10.0/RcppAlgos/inst/doc/CombinatoricsIterators.Rmd | 285 + RcppAlgos-2.10.0/RcppAlgos/inst/doc/CombinatoricsIterators.html | 1485 ++++------ RcppAlgos-2.10.0/RcppAlgos/inst/doc/ComputationalMathematics.Rmd | 45 RcppAlgos-2.10.0/RcppAlgos/inst/doc/ComputationalMathematics.html | 276 - RcppAlgos-2.10.0/RcppAlgos/inst/doc/GeneralCombinatorics.Rmd | 43 RcppAlgos-2.10.0/RcppAlgos/inst/doc/GeneralCombinatorics.html | 274 - RcppAlgos-2.10.0/RcppAlgos/inst/doc/HighPerformanceBenchmarks.Rmd | 198 - RcppAlgos-2.10.0/RcppAlgos/inst/doc/HighPerformanceBenchmarks.html | 609 +--- RcppAlgos-2.10.0/RcppAlgos/inst/doc/IntegerCompositions.Rmd |only RcppAlgos-2.10.0/RcppAlgos/inst/doc/IntegerCompositions.html |only RcppAlgos-2.10.0/RcppAlgos/inst/doc/IntegerPartitions.Rmd |only RcppAlgos-2.10.0/RcppAlgos/inst/doc/IntegerPartitions.html |only RcppAlgos-2.10.0/RcppAlgos/inst/doc/OtherCombinatorics.Rmd | 33 RcppAlgos-2.10.0/RcppAlgos/inst/doc/OtherCombinatorics.html | 264 - RcppAlgos-2.10.0/RcppAlgos/inst/doc/SubsetSum.Rmd | 47 RcppAlgos-2.10.0/RcppAlgos/inst/doc/SubsetSum.html | 284 - RcppAlgos-2.10.0/RcppAlgos/inst/include/ClassUtils/ComboClass.h | 2 RcppAlgos-2.10.0/RcppAlgos/inst/include/ClassUtils/ComboResClass.h | 2 RcppAlgos-2.10.0/RcppAlgos/inst/include/Constraints/ConstraintsTypes.h | 2 RcppAlgos-2.10.0/RcppAlgos/inst/include/Constraints/ConstraintsUtils.h | 10 RcppAlgos-2.10.0/RcppAlgos/inst/include/Partitions/BigPartsCountDistinct.h | 75 RcppAlgos-2.10.0/RcppAlgos/inst/include/Partitions/BigPartsCountRep.h | 40 RcppAlgos-2.10.0/RcppAlgos/inst/include/Partitions/BigPartsCountSection.h | 2 RcppAlgos-2.10.0/RcppAlgos/inst/include/Partitions/CompositionsDistinct.h |only RcppAlgos-2.10.0/RcppAlgos/inst/include/Partitions/CompositionsRep.h | 27 RcppAlgos-2.10.0/RcppAlgos/inst/include/Partitions/CompositionsUtils.h |only RcppAlgos-2.10.0/RcppAlgos/inst/include/Partitions/NextComposition.h | 9 RcppAlgos-2.10.0/RcppAlgos/inst/include/Partitions/NextPartition.h | 4 RcppAlgos-2.10.0/RcppAlgos/inst/include/Partitions/NthPartition.h | 4 RcppAlgos-2.10.0/RcppAlgos/inst/include/Partitions/PartitionsClass.h | 20 RcppAlgos-2.10.0/RcppAlgos/inst/include/Partitions/PartitionsCount.h | 295 + RcppAlgos-2.10.0/RcppAlgos/inst/include/Partitions/PartitionsCountDistinct.h | 64 RcppAlgos-2.10.0/RcppAlgos/inst/include/Partitions/PartitionsCountMultiset.h | 6 RcppAlgos-2.10.0/RcppAlgos/inst/include/Partitions/PartitionsCountRep.h | 36 RcppAlgos-2.10.0/RcppAlgos/inst/include/Partitions/PartitionsCountSection.h | 2 RcppAlgos-2.10.0/RcppAlgos/inst/include/Partitions/PartitionsDistinct.h | 50 RcppAlgos-2.10.0/RcppAlgos/inst/include/Partitions/PartitionsManager.h | 33 RcppAlgos-2.10.0/RcppAlgos/inst/include/Partitions/PartitionsMultiset.h | 6 RcppAlgos-2.10.0/RcppAlgos/inst/include/Partitions/PartitionsRep.h | 46 RcppAlgos-2.10.0/RcppAlgos/inst/include/Partitions/PartitionsTypes.h | 474 ++- RcppAlgos-2.10.0/RcppAlgos/inst/include/Partitions/PartitionsUtils.h | 3 RcppAlgos-2.10.0/RcppAlgos/inst/include/Partitions/RankPartition.h | 2 RcppAlgos-2.10.0/RcppAlgos/inst/include/Partitions/ThreadSafeParts.h | 23 RcppAlgos-2.10.0/RcppAlgos/inst/include/Permutations/PermuteCount.h | 4 RcppAlgos-2.10.0/RcppAlgos/inst/include/PopulateUtils.h |only RcppAlgos-2.10.0/RcppAlgos/inst/include/RankUtils.h | 29 RcppAlgos-2.10.0/RcppAlgos/inst/include/SetUpUtils.h | 2 RcppAlgos-2.10.0/RcppAlgos/man/combinatoricsRank.Rd | 5 RcppAlgos-2.10.0/RcppAlgos/man/partitionsRank.Rd | 6 RcppAlgos-2.10.0/RcppAlgos/src/BigComboCount.cpp | 24 RcppAlgos-2.10.0/RcppAlgos/src/BigPartsCountDistinct.cpp | 252 + RcppAlgos-2.10.0/RcppAlgos/src/BigPartsCountRep.cpp | 191 - RcppAlgos-2.10.0/RcppAlgos/src/BigPartsCountSection.cpp | 7 RcppAlgos-2.10.0/RcppAlgos/src/CartesianClass.cpp | 16 RcppAlgos-2.10.0/RcppAlgos/src/CartesianUtils.cpp | 12 RcppAlgos-2.10.0/RcppAlgos/src/ClassUtils.cpp | 10 RcppAlgos-2.10.0/RcppAlgos/src/CombinatoricsCount.cpp | 26 RcppAlgos-2.10.0/RcppAlgos/src/ComboClass.cpp | 5 RcppAlgos-2.10.0/RcppAlgos/src/ComboCount.cpp | 24 RcppAlgos-2.10.0/RcppAlgos/src/ComboGridContainer.cpp | 18 RcppAlgos-2.10.0/RcppAlgos/src/ComboGroups.cpp | 2 RcppAlgos-2.10.0/RcppAlgos/src/ComboResClass.cpp | 2 RcppAlgos-2.10.0/RcppAlgos/src/ComboResMain.cpp | 4 RcppAlgos-2.10.0/RcppAlgos/src/CompositionsDistinct.cpp |only RcppAlgos-2.10.0/RcppAlgos/src/CompositionsRep.cpp | 146 RcppAlgos-2.10.0/RcppAlgos/src/CompositionsUtils.cpp |only RcppAlgos-2.10.0/RcppAlgos/src/ConstraintsClass.cpp | 13 RcppAlgos-2.10.0/RcppAlgos/src/ConstraintsGeneral.cpp | 16 RcppAlgos-2.10.0/RcppAlgos/src/ConstraintsMain.cpp | 43 RcppAlgos-2.10.0/RcppAlgos/src/ConstraintsSpecial.cpp | 4 RcppAlgos-2.10.0/RcppAlgos/src/ConstraintsUtils.cpp | 43 RcppAlgos-2.10.0/RcppAlgos/src/ConvertUtils.cpp | 9 RcppAlgos-2.10.0/RcppAlgos/src/DivNumSieve.cpp | 8 RcppAlgos-2.10.0/RcppAlgos/src/Eratosthenes.cpp | 4 RcppAlgos-2.10.0/RcppAlgos/src/ExposeClass.cpp | 97 RcppAlgos-2.10.0/RcppAlgos/src/GetCombPerm.cpp | 10 RcppAlgos-2.10.0/RcppAlgos/src/GetCombPermApply.cpp | 34 RcppAlgos-2.10.0/RcppAlgos/src/GetComboGroups.cpp | 12 RcppAlgos-2.10.0/RcppAlgos/src/GetConstraints.cpp | 26 RcppAlgos-2.10.0/RcppAlgos/src/GetPrevCombPerm.cpp | 10 RcppAlgos-2.10.0/RcppAlgos/src/GetPrevCombPermApply.cpp | 34 RcppAlgos-2.10.0/RcppAlgos/src/GetProduct.cpp | 24 RcppAlgos-2.10.0/RcppAlgos/src/GmpConvert.cpp | 15 RcppAlgos-2.10.0/RcppAlgos/src/MotleyPrimes.cpp | 8 RcppAlgos-2.10.0/RcppAlgos/src/NextCombinatorics.cpp | 4 RcppAlgos-2.10.0/RcppAlgos/src/NextComposition.cpp | 288 + RcppAlgos-2.10.0/RcppAlgos/src/NextPartition.cpp | 277 + RcppAlgos-2.10.0/RcppAlgos/src/NthCombination.cpp | 5 RcppAlgos-2.10.0/RcppAlgos/src/NthPartition.cpp | 1008 +++++- RcppAlgos-2.10.0/RcppAlgos/src/NthPermutation.cpp | 11 RcppAlgos-2.10.0/RcppAlgos/src/NthResult.cpp | 8 RcppAlgos-2.10.0/RcppAlgos/src/PartitionsClass.cpp | 78 RcppAlgos-2.10.0/RcppAlgos/src/PartitionsCount.cpp | 737 +++- RcppAlgos-2.10.0/RcppAlgos/src/PartitionsCountDistinct.cpp | 431 +- RcppAlgos-2.10.0/RcppAlgos/src/PartitionsCountMultiset.cpp | 40 RcppAlgos-2.10.0/RcppAlgos/src/PartitionsCountRep.cpp | 252 + RcppAlgos-2.10.0/RcppAlgos/src/PartitionsCountSection.cpp | 27 RcppAlgos-2.10.0/RcppAlgos/src/PartitionsDesign.cpp | 60 RcppAlgos-2.10.0/RcppAlgos/src/PartitionsDistinct.cpp | 154 - 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Title: Extended Structural Equation Modelling
Description: Create structural equation models that can be manipulated programmatically.
Models may be specified with matrices or paths (LISREL or RAM)
Example models include confirmatory factor, multiple group, mixture
distribution, categorical threshold, modern test theory, differential
Fit functions include full information maximum likelihood, maximum likelihood, and weighted least squares.
equations, state space, and many others.
Support and advanced package binaries available at <https://openmx.ssri.psu.edu>.
The software is described in Neale, Hunter, Pritikin, Zahery, Brick,
Kirkpatrick, Estabrook, Bates, Maes, & Boker (2016) <doi:10.1007/s11336-014-9435-8>.
Author: Steven M. Boker [aut],
Michael C. Neale [aut],
Hermine H. Maes [aut],
Michael J. Wilde [ctb],
Michael Spiegel [aut],
Timothy R. Brick [aut],
Ryne Estabrook [aut],
Timothy C. Bates [aut],
Paras Mehta [ctb],
Timo von Oertzen [ctb],
Ross J. Gore [aut],
[...truncated...]
Maintainer: Robert M. Kirkpatrick <rkirkpatrick2@vcu.edu>
Diff between OpenMx versions 2.22.10 dated 2025-11-07 and 2.22.11 dated 2026-03-08
DESCRIPTION | 12 +++++------ MD5 | 32 +++++++++++++++---------------- R/MxVersion.R | 2 - R/sysdata.rda |binary build/stage23.rdb |binary build/vignette.rds |binary data/LongitudinalOverdispersedCounts.rda |binary data/jointdata.rda |binary data/nhanesDemo.rda |binary data/ordinalTwinData.rda |binary data/twinData.rda |binary inst/doc/deriv.html | 18 ++++++++--------- inst/doc/factor_analysis.html | 22 ++++++++++----------- inst/doc/mr.html | 8 +++---- inst/doc/reg_mimic.html | 10 ++++----- inst/doc/regularization.html | 10 ++++----- src/glue.cpp | 2 - 17 files changed, 58 insertions(+), 58 deletions(-)
Title: Lightweight Toolkit for Messaging, Concurrency and the Web
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ.
A toolkit for messaging, concurrency and the web. High-performance
socket messaging over in-process, IPC, TCP, WebSocket and secure TLS
transports implements 'Scalability Protocols', a standard for common
communications patterns including publish/subscribe, request/reply and
survey. A threaded concurrency framework with intuitive 'aio' objects
that resolve automatically upon completion of asynchronous operations,
and synchronisation primitives that allow R to wait on events
signalled by concurrent threads. A unified HTTP server hosting REST
endpoints, WebSocket connections and streaming on a single port, with
a built-in HTTP client.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd] ,
Hibiki AI Limited [cph],
R Consortium [fnd]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between nanonext versions 1.8.0 dated 2026-02-09 and 1.8.1 dated 2026-03-08
DESCRIPTION | 11 ++++---- MD5 | 32 ++++++++++++------------- NEWS.md | 7 +++++ R/server.R | 6 +++- R/stream.R | 10 ++++++- README.md | 3 ++ inst/doc/v04-web.Rmd | 33 +++++++++++++------------ inst/doc/v04-web.html | 33 +++++++++++++------------ man/handler_ws.Rd | 6 +++- man/nanonext-package.Rd | 2 - man/stream.Rd | 14 ++++++++++- src/init.c | 2 - src/nanonext.h | 2 - src/proto.c | 19 ++++++++++++-- src/server.c | 61 +++++++++++++++++++++++++++++++++++++++++++++--- tests/tests.R | 28 ++++++++++++++++++---- vignettes/v04-web.Rmd | 33 +++++++++++++------------ 17 files changed, 212 insertions(+), 90 deletions(-)
Title: Bayesian Latent Gaussian Modelling using INLA and Extensions
Description: Facilitates spatial and general latent Gaussian modeling using
integrated nested Laplace approximation via the INLA package (<https://www.r-inla.org>).
Additionally, extends the GAM-like model class to more general nonlinear predictor
expressions, and implements a log Gaussian Cox process likelihood for
modeling univariate and spatial point processes based on ecological survey data.
Model components are specified with general inputs and mapping methods to the
latent variables, and the predictors are specified via general R expressions,
with separate expressions for each observation likelihood model in
multi-likelihood models. A prediction method based on fast Monte Carlo sampling
allows posterior prediction of general expressions of the latent variables.
Ecology-focused introduction in Bachl, Lindgren, Borchers, and Illian (2019)
<doi:10.1111/2041-210X.13168>.
Author: Finn Lindgren [aut, cre, cph] ,
Fabian E. Bachl [aut, cph] ,
David L. Borchers [ctb, dtc, cph] ,
Daniel Simpson [ctb, cph] ,
Lindesay Scott-Howard [ctb, dtc, cph] ,
Seaton Andy [ctb] ,
Suen Man Ho [ctb, cph] ,
Roudier Pierre [ctb, cph] ,
Meehan Tim [ [...truncated...]
Maintainer: Finn Lindgren <finn.lindgren@gmail.com>
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inlabru-2.14.0/inlabru/tests/testthat/test-latent_rw2.R | 2 inlabru-2.14.0/inlabru/tests/testthat/test-lgcp_1d.R | 6 inlabru-2.14.0/inlabru/tests/testthat/test-lgcp_1d_nonlinear.R | 10 inlabru-2.14.0/inlabru/tests/testthat/test-lgcp_2d_covars.R | 18 inlabru-2.14.0/inlabru/tests/testthat/test-lgcp_2d_plotsample.R | 4 inlabru-2.14.0/inlabru/tests/testthat/test-linearisation.R | 16 inlabru-2.14.0/inlabru/tests/testthat/test-mapper.R | 94 inlabru-2.14.0/inlabru/tests/testthat/test-mdata.R | 3 inlabru-2.14.0/inlabru/tests/testthat/test-response_size.R | 2 inlabru-2.14.0/inlabru/tests/testthat/test-utils.R | 3 inlabru-2.14.0/inlabru/vignettes/articles.Rmd | 25 inlabru-2.14.0/inlabru/vignettes/bru_mapper.Rmd | 69 inlabru-2.14.0/inlabru/vignettes/classes.Rmd |only inlabru-2.14.0/inlabru/vignettes/method.Rmd | 1 inlabru-2.14.0/inlabru/vignettes/prediction_scores.Rmd | 17 235 files changed, 7769 insertions(+), 6213 deletions(-)
Title: Geometry-Adaptive Lyapunov-Assured Hybrid Optimizer with
Softplus Reparameterization and Trust-Region Control
Description: Implements the GALAHAD algorithm (Geometry-Adaptive
Lyapunov-Assured Hybrid Optimizer), updated in version 2 to replace the
hard-clamp positivity constraint of v1 with a numerically smooth softplus
reparameterization, add rho-based trust-region adaptation (actual vs.
predicted objective reduction), extend convergence detection to include
both absolute and relative function-stall criteria, and enrich the
per-iteration history with Armijo backtrack counts and trust-region
quality ratios. Parameters constrained to be positive (rates,
concentrations, scale parameters) are handled in a transformed z-space
via the softplus map so that gradients remain well-defined at the
constraint boundary. A two-partition API (positive / euclidean) replaces
the three-way T/P/E partition of v1; the legacy form is still accepted
for backwards compatibility. Designed for biological modeling problems
(germination, dose-response, prion RT-QuIC, survival) where rates,
concentrations, and unconstrained coefficien [...truncated...]
Author: Richard A. Feiss [aut, cre]
Maintainer: Richard A. Feiss <feiss026@umn.edu>
Diff between GALAHAD versions 1.0.0 dated 2025-11-07 and 2.0.0 dated 2026-03-08
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Title: Fast and Exact Computation of Gaussian Stochastic Process
Description: Implements fast and exact computation of Gaussian stochastic process with the Matern kernel using forward filtering and backward smoothing algorithm. It includes efficient implementations of the inverse Kalman filter, with applications such as estimating particle interaction functions. These tools support models with or without noise. Additionally, the package offers algorithms for fast parameter estimation in latent factor models, where the factor loading matrix is orthogonal, and latent processes are modeled by Gaussian processes. See the references: 1) Mengyang Gu and Yanxun Xu (2020), Journal of Computational and Graphical Statistics; 2) Xinyi Fang and Mengyang Gu (2024), <doi:10.48550/arXiv.2407.10089>; 3) Mengyang Gu and Weining Shen (2020), Journal of Machine Learning Research; 4) Yizi Lin, Xubo Liu, Paul Segall and Mengyang Gu (2025), <doi:10.48550/arXiv.2501.01324>.
Author: Mengyang Gu [aut, cre],
Xinyi Fang [aut],
Yizi Lin [aut]
Maintainer: Mengyang Gu <mengyang@pstat.ucsb.edu>
Diff between FastGaSP versions 0.6.2 dated 2025-08-27 and 0.6.3 dated 2026-03-08
CHANGELOG | 6 + DESCRIPTION | 8 +- MD5 | 22 +++---- NAMESPACE | 2 R/functions.R | 127 +++++++++++++++++++++++++++++------------- R/structure.R | 19 ++++-- build/partial.rdb |binary inst/extdata/example.r | 18 ++--- man/Sample_KF.Rd | 2 man/fgasp-class.Rd | 2 man/predict.fgasp.Rd | 20 +++--- man/predictobj.fgasp-class.Rd | 5 + 12 files changed, 154 insertions(+), 77 deletions(-)
Title: Automate Data Exploration and Treatment
Description: Automated data exploration process for analytic tasks and predictive modeling, so
that users could focus on understanding data and extracting insights. The package scans and
analyzes each variable, and visualizes them with typical graphical techniques. Common
data processing methods are also available to treat and format data.
Author: Boxuan Cui [aut, cre]
Maintainer: Boxuan Cui <boxuancui@gmail.com>
Diff between DataExplorer versions 0.8.4 dated 2025-07-24 and 0.9.0 dated 2026-03-08
DESCRIPTION | 12 LICENSE | 2 MD5 | 113 ++--- NAMESPACE | 1 NEWS.md | 12 R/create_report.R | 27 + R/plot.R | 75 +++ R/plot_bar.R | 11 R/plot_boxplot.R | 4 R/plot_correlation.R | 7 R/plot_density.R | 48 +- R/plot_histogram.R | 48 +- R/plot_intro.R | 14 R/plot_missing.R | 17 R/plot_prcomp.R | 32 + R/plot_qq.R | 10 R/plot_scatterplot.R | 6 README.md | 29 + inst/doc/dataexplorer-intro.R | 21 + inst/doc/dataexplorer-intro.Rmd | 68 +++ inst/doc/dataexplorer-intro.html | 552 ++++++++++++++++----------- inst/rmd_template/report.rmd | 64 ++- man/create_report.Rd | 10 man/figures/README-plot-bar-by-1.png |binary man/figures/README-plot-density-1.png |binary man/figures/README-plot-histogram-1.png |binary man/figures/README-plot-histogram-by-1.png |only man/figures/README-plot-intro-1.png |binary man/figures/README-plot-missing-1.png |binary man/figures/README-plot-qq-1.png |binary man/figures/README-plot-qq-cut-1.png |binary man/figures/README-plot_prcomp-1.png |binary man/figures/logo.png |binary man/plotDataExplorer.Rd | 4 man/plotDataExplorer.grid.Rd | 3 man/plotDataExplorer.multiple.Rd | 3 man/plotDataExplorer.single.Rd | 4 man/plot_bar.Rd | 10 man/plot_boxplot.Rd | 5 man/plot_correlation.Rd | 5 man/plot_density.Rd | 11 man/plot_histogram.Rd | 11 man/plot_intro.Rd | 5 man/plot_missing.Rd | 5 man/plot_prcomp.Rd | 5 man/plot_qq.Rd | 5 man/plot_scatterplot.Rd | 5 tests/testthat/Rplots.pdf |binary tests/testthat/helper-ggplot.R |only tests/testthat/test-create-report.R | 20 tests/testthat/test-plot-bar.R | 4 tests/testthat/test-plot-boxplot.R | 4 tests/testthat/test-plot-correlation.R | 2 tests/testthat/test-plot-histogram-density.R | 15 tests/testthat/test-plot-intro.R | 2 tests/testthat/test-plot-missing.R | 2 tests/testthat/test-plot-scatterplot.R | 4 tests/testthat/test-plotly.R |only vignettes/dataexplorer-intro.Rmd | 68 +++ 59 files changed, 994 insertions(+), 391 deletions(-)