Title: Weighted Mean SHAP and CI for Robust Feature Assessment in ML
Grid
Description: This R package introduces Weighted Mean SHapley Additive exPlanations
(WMSHAP), a framework for estimating and combining SHAP values across a
grid of fine-tuned machine learning models or the base learners of stacked
ensembles. Rather than relying on a single best-performing model, WMSHAP
combines SHAP values from multiple models, weighting their contributions
according to predictive performance. Model weights can be calculated using
R-squared for regression and classification models or, for binary
classifiers, the area under the precision-recall curve (AUCPR), the area
under the receiver operating characteristic curve (AUC), or the F2 score.
The package also provides weighted confidence intervals for mean SHAP
values, allowing feature importance to be evaluated across multiple models
while accounting for variability in their contributions. This approach
particularly improves accuracy if feature importance assessment at both local
(individual) and global (feature) levels and improves t [...truncated...]
Author: E. F. Haghish [aut, cre, cph]
Maintainer: E. F. Haghish <haghish@hotmail.com>
Diff between shapley versions 0.7.0 dated 2026-03-04 and 1.0.0 dated 2026-11-06
shapley-0.7.0/shapley/man/feature.selection.Rd |only shapley-1.0.0/shapley/DESCRIPTION | 47 shapley-1.0.0/shapley/MD5 | 50 shapley-1.0.0/shapley/NAMESPACE | 87 - shapley-1.0.0/shapley/R/feature.selection.R | 170 +-- shapley-1.0.0/shapley/R/shapley.R | 783 +++++++-------- shapley-1.0.0/shapley/R/shapley.aggregate.R |only shapley-1.0.0/shapley/R/shapley.bootstrap.R |only shapley-1.0.0/shapley/R/shapley.choose.class.R |only shapley-1.0.0/shapley/R/shapley.compute.R |only shapley-1.0.0/shapley/R/shapley.cores.R |only shapley-1.0.0/shapley/R/shapley.detect.R |only shapley-1.0.0/shapley/R/shapley.domain.R | 461 ++++---- shapley-1.0.0/shapley/R/shapley.domain.compare.test.R |only shapley-1.0.0/shapley/R/shapley.external.R |only shapley-1.0.0/shapley/R/shapley.external.one.R |only shapley-1.0.0/shapley/R/shapley.gpboost.R |only shapley-1.0.0/shapley/R/shapley.h2o.R |only shapley-1.0.0/shapley/R/shapley.h2o.one.R |only shapley-1.0.0/shapley/R/shapley.interval.R |only shapley-1.0.0/shapley/R/shapley.jitter.R |only shapley-1.0.0/shapley/R/shapley.models.R |only shapley-1.0.0/shapley/R/shapley.parallel.R |only shapley-1.0.0/shapley/R/shapley.performance.R |only shapley-1.0.0/shapley/R/shapley.plot.R | 381 +++---- shapley-1.0.0/shapley/R/shapley.predict.R |only shapley-1.0.0/shapley/R/shapley.row.plot.R | 275 +---- shapley-1.0.0/shapley/R/shapley.table.R | 124 +- shapley-1.0.0/shapley/R/shapley.weights.R |only shapley-1.0.0/shapley/R/threeDots.R |only shapley-1.0.0/shapley/README.md | 6 shapley-1.0.0/shapley/man/shapley.Rd | 417 +++++-- shapley-1.0.0/shapley/man/shapley.domain.Rd | 66 - shapley-1.0.0/shapley/man/shapley.domain.compare.test.Rd |only shapley-1.0.0/shapley/man/shapley.plot.Rd | 97 - shapley-1.0.0/shapley/man/shapley.row.plot.Rd | 119 -- shapley-1.0.0/shapley/man/shapley.table.Rd | 6 37 files changed, 1491 insertions(+), 1598 deletions(-)
Title: Protein Quantification in Mass Spectrometry-Based Proteomics
Description: An implementation of the MaxLFQ algorithm by
Cox et al. (2014) <doi:10.1074/mcp.M113.031591> using least-squares analysis in a comprehensive
pipeline for processing proteomics data in data-independent acquisition mode
(Pham et al. 2020 <doi:10.1093/bioinformatics/btz961>, and a new algorithm using the conjugate gradient method
Pham et al. 2026 <doi:10.1021/acs.jproteome.5c01038>).
It offers additional options for protein quantification using
the N most intense fragment ions, using all fragment ions,
the median polish algorithm by Tukey (1977, ISBN:0201076160),
a robust linear model, and fragment weighting. A new iq format enables the processing of large-scale datasets.
In general, the tool can be used to integrate
multiple proportional observations into a single quantitative value.
Author: Thang V. Pham [aut, cre, cph] ,
Alex A. Henneman [ctb]
Maintainer: Thang V. Pham <t.pham@amsterdamumc.nl>
Diff between iq versions 2.1.0 dated 2026-10-27 and 2.2.0 dated 2026-11-06
iq-2.1.0/iq/vignettes/iq1-1.png |only iq-2.1.0/iq/vignettes/iq2-1.png |only iq-2.1.0/iq/vignettes/iq3-1.png |only iq-2.1.0/iq/vignettes/iq4-1.png |only iq-2.1.0/iq/vignettes/iq5-1.png |only iq-2.1.0/iq/vignettes/iq6-1.png |only iq-2.1.0/iq/vignettes/iq7-1.png |only iq-2.2.0/iq/DESCRIPTION | 30 iq-2.2.0/iq/MD5 | 107 - iq-2.2.0/iq/NAMESPACE | 32 iq-2.2.0/iq/R/iq-fast.R | 540 +++++--- iq-2.2.0/iq/R/iq-format.R | 1622 ++++++++++++++++++++++----- iq-2.2.0/iq/R/iq.R | 1326 +++++++++++----------- iq-2.2.0/iq/R/utils.R |only iq-2.2.0/iq/build/vignette.rds |binary iq-2.2.0/iq/inst/CITATION | 16 iq-2.2.0/iq/inst/doc/iq-fast.Rmd | 1040 ++++++++--------- iq-2.2.0/iq/inst/doc/iq-fast.html | 194 +-- iq-2.2.0/iq/inst/doc/iq-v2.Rmd |only iq-2.2.0/iq/inst/doc/iq-v2.html |only iq-2.2.0/iq/inst/doc/iq.Rmd | 862 +++++++------- iq-2.2.0/iq/inst/doc/iq.html | 147 +- iq-2.2.0/iq/man/connected_component.Rd | 4 iq-2.2.0/iq/man/create_protein_list.Rd | 2 iq-2.2.0/iq/man/create_protein_table.Rd | 3 iq-2.2.0/iq/man/extract_annotation.Rd | 2 iq-2.2.0/iq/man/fast_MaxLFQ.Rd | 13 iq-2.2.0/iq/man/fast_preprocess.Rd | 11 iq-2.2.0/iq/man/fast_read.Rd | 29 iq-2.2.0/iq/man/fast_read_data_frame.Rd |only iq-2.2.0/iq/man/fast_read_parquet.Rd |only iq-2.2.0/iq/man/huber_weight.Rd | 4 iq-2.2.0/iq/man/iq_format_to_protein_list.Rd |only iq-2.2.0/iq/man/long_format_to_iq_format.Rd | 46 iq-2.2.0/iq/man/maxLFQ.Rd | 4 iq-2.2.0/iq/man/meanInt.Rd | 2 iq-2.2.0/iq/man/median_polish.Rd | 2 iq-2.2.0/iq/man/plot_protein.Rd | 2 iq-2.2.0/iq/man/preprocess.Rd | 10 iq-2.2.0/iq/man/process.Rd |only iq-2.2.0/iq/man/process_iq_format.Rd | 30 iq-2.2.0/iq/man/process_long_format.Rd | 18 iq-2.2.0/iq/man/process_matrix.Rd | 44 iq-2.2.0/iq/man/process_wide_format.Rd | 6 iq-2.2.0/iq/man/read_fasta_file.Rd |only iq-2.2.0/iq/man/rescale.Rd | 13 iq-2.2.0/iq/man/spikeins.Rd | 58 iq-2.2.0/iq/man/topN.Rd | 2 iq-2.2.0/iq/src/Makevars | 10 iq-2.2.0/iq/src/coordinate_descent.h | 8 iq-2.2.0/iq/src/iq.cpp | 1266 +++++++++++++++------ iq-2.2.0/iq/src/iq_writer.h |only iq-2.2.0/iq/src/maxlfq.h | 7 iq-2.2.0/iq/src/maxlfq_bit.h | 103 + iq-2.2.0/iq/src/stream.cpp |only iq-2.2.0/iq/src/utils.h | 162 ++ iq-2.2.0/iq/src/writer.cpp |only iq-2.2.0/iq/vignettes/iq-fast.Rmd | 1040 ++++++++--------- iq-2.2.0/iq/vignettes/iq-v2.Rmd |only iq-2.2.0/iq/vignettes/iq.Rmd | 862 +++++++------- iq-2.2.0/iq/vignettes/iq1-1.svg |only iq-2.2.0/iq/vignettes/iq2-1.svg |only iq-2.2.0/iq/vignettes/iq3-1.svg |only iq-2.2.0/iq/vignettes/iq4-1.svg |only iq-2.2.0/iq/vignettes/iq5-1.svg |only iq-2.2.0/iq/vignettes/iq6-1.svg |only iq-2.2.0/iq/vignettes/iq7-1.svg |only iq-2.2.0/iq/vignettes/iqv2-1.svg |only 68 files changed, 6003 insertions(+), 3676 deletions(-)
Title: Functional Machine Learning Framework
Description: A compact and explicit machine learning framework for
supervised learning, resampling-based evaluation, hyperparameter
tuning, learner comparison, interpretation, and plug-in
g-computation. The package uses standard formulas for model
specification and provides stable S3 interfaces for fitting,
evaluation, tuning, interpretation, and causal estimation across a
learner registry with multiple backend engines. Implemented
interpretation methods build on established approaches such as
permutation-based variable importance, partial dependence,
individual conditional expectation, accumulated local effects, SHAP,
and LIME; see Friedman (2001) <doi:10.1214/aos/1013203451>,
Goldstein et al. (2015) <doi:10.1080/10618600.2014.907095>, Apley
and Zhu (2020) <doi:10.1111/rssb.12377>, Lundberg and Lee (2017)
<doi:10.48550/arXiv.1705.07874>, and Ribeiro et al. (2016)
<doi:10.48550/arXiv.1602.04938>. The framework is intentionally
opinionated: preprocessing is expected to [...truncated...]
Author: Imad El Badisy [aut, cre]
Maintainer: Imad El Badisy <elbadisyimad@gmail.com>
Diff between funcml versions 0.9.0 dated 2026-08-22 and 0.9.6 dated 2026-11-06
funcml-0.9.0/funcml/R/funcml-package.R |only funcml-0.9.0/funcml/R/mlp_internal.R |only funcml-0.9.0/funcml/build/partial.rdb |only funcml-0.9.0/funcml/man/funcml-package.Rd |only funcml-0.9.6/funcml/DESCRIPTION | 10 funcml-0.9.6/funcml/MD5 | 63 - funcml-0.9.6/funcml/NAMESPACE | 2 funcml-0.9.6/funcml/NEWS.md | 121 +++ funcml-0.9.6/funcml/R/compare.R | 81 +- funcml-0.9.6/funcml/R/densemlp_learner.R | 92 ++ funcml-0.9.6/funcml/R/dt-utils.R | 6 funcml-0.9.6/funcml/R/estimate.R | 107 ++ funcml-0.9.6/funcml/R/fastgbm_learner.R |only funcml-0.9.6/funcml/R/fit.R | 10 funcml-0.9.6/funcml/R/globals.R | 4 funcml-0.9.6/funcml/R/interpret.R | 369 +++++++++- funcml-0.9.6/funcml/R/registry.R | 150 +++- funcml-0.9.6/funcml/R/tune-grids.R |only funcml-0.9.6/funcml/R/tune.R | 11 funcml-0.9.6/funcml/R/utils.R | 8 funcml-0.9.6/funcml/README.md | 109 ++ funcml-0.9.6/funcml/inst/doc/funcml.pdf |binary funcml-0.9.6/funcml/man/compare.Rd | 4 funcml-0.9.6/funcml/man/default_tune_grid.Rd |only funcml-0.9.6/funcml/man/estimate.Rd | 5 funcml-0.9.6/funcml/man/figures/README-interpret-ceteris-paribus-1.png |only funcml-0.9.6/funcml/man/figures/README-interpret-lime-1.png |only funcml-0.9.6/funcml/man/fit.Rd | 2 funcml-0.9.6/funcml/man/interpret-ceteris-paribus-methods.Rd |only funcml-0.9.6/funcml/man/interpret-ice-methods.Rd | 6 funcml-0.9.6/funcml/man/interpret.Rd | 31 funcml-0.9.6/funcml/man/learners.Rd | 2 funcml-0.9.6/funcml/man/tune.Rd | 5 funcml-0.9.6/funcml/tests/testthat/test-estimate.R | 21 funcml-0.9.6/funcml/tests/testthat/test-interpret.R | 152 +++- funcml-0.9.6/funcml/tests/testthat/test-learner-audit-contract.R | 2 funcml-0.9.6/funcml/tests/testthat/test-learner-fixes.R |only funcml-0.9.6/funcml/tests/testthat/test-plots.R | 40 + 38 files changed, 1163 insertions(+), 250 deletions(-)
Title: Kriging Modeling
Description: An 'Eigen'-based computationally efficient 'C++' implementation for fitting various kriging models to data. This research is supported by U.S. National Science Foundation grant DMS-2310637.
Author: Chaofan Huang [aut],
Difan Song [aut, cre],
V. Roshan Joseph [aut]
Maintainer: Difan Song <dfsong96@gmail.com>
Diff between rkriging versions 1.0.2 dated 2025-03-28 and 1.1.0 dated 2026-11-06
DESCRIPTION | 19 MD5 | 81 + NAMESPACE | 49 - R/kernel.R | 1628 +++++++++++++++++++----------------- R/kriging.R | 319 ++++--- R/sequential.R |only build |only man/ALM.Sequential.Rd |only man/Add.Next.Design.Rd |only man/EI.Sequential.Rd |only man/Evaluate.Kernel.Rd | 2 man/Fit.Kriging.Rd | 22 man/Gaussian.Kernel.Rd | 2 man/Generalized.Rational.Kriging.Rd | 9 man/Get.Best.Design.Rd |only man/Get.Data.Rd |only man/Get.Kernel.Rd | 16 man/Get.Kriging.Parameters.Rd | 19 man/Get.Next.Design.Rd |only man/Get.Sequential.Rd |only man/IM.Kernel.Rd |only man/Limit.Kriging.Rd | 5 man/Matern.Kernel.Rd | 2 man/Matern12.Kernel.Rd | 2 man/Matern32.Kernel.Rd | 2 man/Matern52.Kernel.Rd | 2 man/MultiplicativeIM.Kernel.Rd |only man/MultiplicativeMatern.Kernel.Rd | 2 man/MultiplicativeRQ.Kernel.Rd | 6 man/MultiplicativeUDF.Kernel.Rd | 2 man/Ordinary.Kriging.Rd | 9 man/PI.Sequential.Rd |only man/Predict.Kriging.Rd | 15 man/Predict.Sequential.Rd |only man/RQ.Kernel.Rd | 2 man/Rational.Kriging.Rd | 9 man/UCB.Sequential.Rd |only man/UDF.Kernel.Rd | 2 man/UDF.Sequential.Rd |only man/Universal.Kriging.Rd | 9 src/RcppExports.cpp | 2 src/export.cpp | 161 ++- src/kernel.cpp | 130 +- src/kernel.h | 124 +- src/kriging.cpp | 907 +++++++++++++------- src/kriging.h | 223 +++- src/sequential.cpp |only src/sequential.h |only src/utils.cpp | 100 +- src/utils.h | 2 50 files changed, 2334 insertions(+), 1550 deletions(-)
Title: A 'C++20' API for R
Description: A header-only 'C++20' API for manipulating R data structures
from 'C++'. Provides 'C++20' concepts specific to R, custom scalar and
vector classes with built-in NA handling, automatic object protection,
'SIMD' (single-instruction-multiple-data), parallelisation, and a
streamlined system for registering 'C++' functions, including
templates, to R. Full API reference and documentation are available at
<https://nicchr.github.io/cppally/>.
Author: Nick Christofides [aut, cre, cph] ,
Martin Leitner-Ankerl [cph] ,
Malte Skarupke [cph] ,
Ryo Suzuki [cph] ,
Posit Software, PBC [cph]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between cppally versions 1.2.0 dated 2026-11-05 and 1.2.1 dated 2026-11-06
DESCRIPTION | 8 +++---- MD5 | 20 +++++++++---------- NEWS.md | 5 ++++ inst/doc/cppally.html | 6 ++--- inst/doc/functionals.R | 7 ++++++ inst/doc/functionals.Rmd | 7 ++++++ inst/doc/functionals.html | 47 ++++++++++++++++++++++++--------------------- inst/doc/protection.html | 22 ++++++++++----------- inst/doc/random.html | 28 ++++++++++++-------------- inst/doc/vector_names.html | 28 +++++++++++++------------- vignettes/functionals.Rmd | 7 ++++++ 11 files changed, 107 insertions(+), 78 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-08 1.0.3
2017-04-18 0.9.5
2016-11-30 0.9.3
2016-04-24 0.9.2
2015-12-24 0.9.0
2014-03-09 0.8.2
2014-01-22 0.8.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-10-16 0.4.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-12 1.5.2
2023-11-24 1.5.1
2023-11-15 1.4.5
2023-11-08 1.4.4
2022-02-10 1.3.1
2021-12-14 1.2.1
2021-09-07 1.1.6
Title: Read xlsx Files with a Native Parser
Description: Reads tabular data from xlsx files with a specialized C parser.
Worksheet XML is scanned in a single pass into compact per-column
buffers, with no intermediate document model, and the R vectors are
built from those. Bundles the 'miniz' and 'libdeflate' decompressors to
read the underlying archive.
Author: Vincent Shields [aut, cre, cph],
Rich Geldreich [ctb, cph] ,
Tenacious Software LLC [cph] ,
RAD Game Tools and Valve Software [cph] ,
Martin Raiber [ctb, cph] ,
Alex Evans [ctb] ,
Alistair Moffat [ctb] ,
Jyrki Katajainen [ctb] ,
Eric Biggers [ctb, cp [...truncated...]
Maintainer: Vincent Shields <vince.shields913@gmail.com>
Diff between rcxl versions 0.1.1 dated 2026-10-05 and 0.1.2 dated 2026-11-06
DESCRIPTION | 13 +-- MD5 | 16 ++-- NEWS.md | 18 ++++ R/rcxl-package.R | 12 +-- README.md | 89 ++++++++++++++++++++-- inst/extdata/na.xlsx |binary man/rcxl-package.Rd | 24 +++--- src/read_xlsx.c | 202 +++++++++++++++++++++++++++++++++++++++------------ tests/golden.R | 87 +++++++++++++++++++++ 9 files changed, 377 insertions(+), 84 deletions(-)
Title: Meta-Population Compartmental Model for Respiratory Virus
Diseases
Description: Simulates respiratory virus epidemics using meta-population compartmental models following Fadikar et. al. (2025) <doi:10.1109/WSC68292.2025.11338996>. 'MetaRVM' implements a stochastic
SEIRD (Susceptible-Exposed-Infected-Recovered-Dead) framework with demographic
stratification by user provided attributes. It supports complex
epidemiological scenarios including asymptomatic and presymptomatic transmission,
hospitalization dynamics, vaccination schedules, and time-varying contact patterns
via mixing matrices.
Author: Arindam Fadikar [aut, cre, cph] ,
Charles Macal [ctb],
Martinez Moyano Ignacio Javier [ctb],
Ozik Jonathan [ctb]
Maintainer: Arindam Fadikar <afadikar@anl.gov>
Diff between MetaRVM versions 2.1.0 dated 2026-03-26 and 2.2.0 dated 2026-11-06
DESCRIPTION | 9 MD5 | 104 + NAMESPACE | 3 NEWS.md | 26 R/build_config.R |only R/classes.R | 376 +++++- R/disease_registry.R |only R/format_output.R | 87 - R/globals.R | 2 R/metaODIN.R | 40 R/metaODIN_measles.R |only R/metaRVM.R | 306 ++++- R/metaRVM_measles.R |only R/parse_config.R | 1174 +++++++++++++------- R/parse_config_measles.R |only R/utils.R |only README.md | 152 -- inst/doc/checkpointing.Rmd | 34 inst/doc/checkpointing.html | 36 inst/doc/getting-started.Rmd | 7 inst/doc/getting-started.html | 91 - inst/doc/running-a-simulation.R | 32 inst/doc/running-a-simulation.Rmd | 78 + inst/doc/running-a-simulation.html | 492 ++++---- inst/doc/yaml-configuration.R | 15 inst/doc/yaml-configuration.Rmd | 218 ++- inst/doc/yaml-configuration.html | 614 ++++++---- inst/extdata/example_config.yaml | 3 inst/extdata/example_config_checkpoint.yaml | 5 inst/extdata/example_config_dist.yaml | 5 inst/extdata/example_config_measles_checkpoint.yaml |only inst/extdata/example_config_measles_min.yaml |only inst/extdata/example_config_stochastic.yaml | 3 inst/extdata/example_config_subgroup_dist.yaml | 5 inst/extdata/m_weekday_day_measles_min.csv |only inst/extdata/m_weekday_night_measles_min.csv |only inst/extdata/m_weekend_day_measles_min.csv |only inst/extdata/m_weekend_night_measles_min.csv |only inst/extdata/population_init_measles_min.csv |only man/MetaRVMCheck.Rd | 40 man/MetaRVMConfig.Rd | 147 ++ man/MetaRVMResults.Rd | 44 man/build_config.Rd |only man/copy_config.Rd |only man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/format_metarvm_output.Rd | 51 man/metaRVM.Rd | 28 man/metaRVM_measles.Rd |only man/meta_measles_sim.Rd |only man/meta_sim.Rd | 13 man/parse_config.Rd | 79 - man/parse_config_measles.Rd |only tests/testthat/test-build_config.R |only tests/testthat/test-measles.R |only tests/testthat/test-metaRVM.R | 41 tests/testthat/test-meta_sim.R | 6 tests/testthat/test-parse_config.R | 203 +++ tests/testthat/testdata/sample_config.yaml | 2 vignettes/checkpointing.Rmd | 34 vignettes/getting-started.Rmd | 7 vignettes/running-a-simulation.Rmd | 78 + vignettes/yaml-configuration.Rmd | 218 ++- 63 files changed, 3493 insertions(+), 1415 deletions(-)