Title: 'Arrow' Database Connectivity ('ADBC') 'SQLite' Driver
Description: Provides a developer-facing interface to the 'Arrow' Database
Connectivity ('ADBC') 'SQLite' driver for the purposes of building high-level
database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is
an API standard for database access libraries that uses 'Arrow' for result
sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcsqlite versions 0.21.0 dated 2025-11-19 and 0.22.0 dated 2026-01-20
DESCRIPTION | 6 MD5 | 31 +-- R/adbcsqlite-package.R | 3 man/adbcsqlite.Rd | 3 src/arrow-adbc |only src/c/driver/postgresql/connection.cc | 35 +++ src/c/driver/postgresql/result_helper.cc | 10 - src/c/driver/sqlite/sqlite.cc | 8 src/c/driver/sqlite/statement_reader.c | 9 src/c/driver_manager/adbc_driver_manager.cc | 234 ++++++++++++++++++------- src/c/driver_manager/entrypoint.c |only src/c/validation/adbc_validation.cc | 11 - src/c/validation/adbc_validation_connection.cc | 2 src/c/validation/adbc_validation_statement.cc | 28 +- src/c/validation/adbc_validation_util.h | 17 + src/common |only tests/testthat/test-adbcsqlite-package.R | 18 + 17 files changed, 310 insertions(+), 105 deletions(-)
Title: Biologically Informed Metabolomic Libraries from 'PubChem'
Description: All 'PubChem' compounds are downloaded to a local computer, but for each compound, only partial records are used. The data are organized into small files referenced by 'PubChem' CID. This package also contains functions to parse the biologically relevant compounds from all 'PubChem' compounds, using biological database sources, pathway presence, and taxonomic relationships. Taxonomy is used to generate a lowest common ancestor taxonomy ID (NCBI) for each biological metabolite, which then enables creation of taxonomically specific metabolome databases for any taxon.
Author: Corey Broeckling [aut, cre]
Maintainer: Corey Broeckling <cbroeckl@colostate.edu>
Diff between pubchem.bio versions 1.0.3 dated 2025-12-12 and 1.0.5 dated 2026-01-20
DESCRIPTION | 9 - MD5 | 30 ++--- NAMESPACE | 2 NEWS.md | 11 +- R/build.pubchem.bio.R | 71 ++++++++++++- R/build.taxon.metabolome.R | 1 R/export.CompoundDb.R | 57 ++++++---- R/get.pubchem.ftp.R | 48 ++++++++ R/globals.R | 2 R/utils-pipe.R |only data/cid.lca.rda |binary inst/doc/pubchem.bio.vignette.R | 3 inst/doc/pubchem.bio.vignette.Rmd | 3 inst/doc/pubchem.bio.vignette.html | 199 ++++++++++++++++++------------------- man/build.pubchem.bio.Rd | 5 man/pipe.Rd |only vignettes/pubchem.bio.vignette.Rmd | 3 17 files changed, 293 insertions(+), 151 deletions(-)
Title: The FPCdpca Criterion on Distributed Principal Component
Analysis
Description: We consider optimal subset selection in the setting that one needs to use only one data subset to represent the whole data set with minimum information loss, and devise a novel intersection-based criterion on selecting optimal subset, called as the FPC criterion, to handle with the optimal sub-estimator in distributed principal component analysis; That is, the FPCdpca. The philosophy of the package is described in Guo G. (2025) <doi:10.1016/j.physa.2024.130308>.
Author: Guangbao Guo [aut, cre] ,
Jiarui Li [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between FPCdpca versions 0.3.0 dated 2025-05-08 and 0.4.0 dated 2026-01-20
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/FPC.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Fitting and Tuning Regularized Cause-Specific Cox Models with
Elastic-Net Penalty
Description: Flexible tools to fit, tune and obtain absolute risk predictions from regularized cause-specific cox models with elastic-net penalty.
Author: Shahin Roshani [aut, cre, cph]
Maintainer: Shahin Roshani <s.roshani@nki.nl>
Diff between CSCNet versions 0.1.3 dated 2026-01-08 and 0.1.4 dated 2026-01-20
DESCRIPTION | 10 - MD5 | 18 +- NAMESPACE | 3 NEWS.md | 8 R/tune_penCSC.R | 59 ++++-- inst/doc/CSCNet.R | 120 ++++++------- inst/doc/CSCNet.Rmd | 117 ++++++------- inst/doc/CSCNet.html | 439 +++++++++++++++++++++++++++++---------------------- man/tune_penCSC.Rd | 321 ++++++++++++++++++------------------- vignettes/CSCNet.Rmd | 117 ++++++------- 10 files changed, 631 insertions(+), 581 deletions(-)
Title: Interface to Download Data on Pests and Hosts from 'EPPO'
Description: Set of tools to automatize extraction of data on pests from 'EPPO
Data Services' and 'EPPO Global Database' and to put them into tables with
human readable format. Those function use 'EPPO database API', thus you
first need to register on <https://data.eppo.int> (free of charge).
Additional helpers allow to download, check and connect to
'SQLite EPPO database'.
Author: Michal Jan Czyz [aut, cre]
Maintainer: Michal Jan Czyz <m.czyz.j@gmail.com>
Diff between pestr versions 0.8.2 dated 2021-01-20 and 0.8.4 dated 2026-01-20
pestr-0.8.2/pestr/R/pestr.R |only pestr-0.8.4/pestr/DESCRIPTION | 14 pestr-0.8.4/pestr/LICENSE | 4 pestr-0.8.4/pestr/MD5 | 91 pestr-0.8.4/pestr/NAMESPACE | 38 pestr-0.8.4/pestr/NEWS.md | 439 +- pestr-0.8.4/pestr/R/eppo_api.R | 378 +- pestr-0.8.4/pestr/R/eppo_citation_helpers.R |only pestr-0.8.4/pestr/R/eppo_database_tools.R | 401 +- pestr-0.8.4/pestr/R/eppo_full_table.R | 86 pestr-0.8.4/pestr/R/eppo_tabletools.R | 1045 +++--- pestr-0.8.4/pestr/R/make_eppo_token.R | 155 pestr-0.8.4/pestr/R/message_helpers.R | 149 pestr-0.8.4/pestr/R/pestr-package.R |only pestr-0.8.4/pestr/README.md | 390 +- pestr-0.8.4/pestr/build/vignette.rds |binary pestr-0.8.4/pestr/inst/doc/pestr_example_n_of_taxon.R | 149 pestr-0.8.4/pestr/inst/doc/pestr_example_n_of_taxon.Rmd | 296 - pestr-0.8.4/pestr/inst/doc/pestr_example_n_of_taxon.html | 595 +-- pestr-0.8.4/pestr/inst/doc/pestr_workflow.R | 314 - pestr-0.8.4/pestr/inst/doc/pestr_workflow.Rmd | 577 +-- pestr-0.8.4/pestr/inst/doc/pestr_workflow.html | 2368 +++++++------- pestr-0.8.4/pestr/inst/doc/pra_tables.R |only pestr-0.8.4/pestr/inst/doc/pra_tables.Rmd |only pestr-0.8.4/pestr/inst/doc/pra_tables.html |only pestr-0.8.4/pestr/inst/figures/pestr-hex_center.png |binary pestr-0.8.4/pestr/man/check_eppo_token.Rd | 66 pestr-0.8.4/pestr/man/create_eppo_token.Rd | 64 pestr-0.8.4/pestr/man/eppo_citation.Rd |only pestr-0.8.4/pestr/man/eppo_database.Rd | 121 pestr-0.8.4/pestr/man/eppo_names_tables.Rd | 90 pestr-0.8.4/pestr/man/eppo_table_full.Rd | 60 pestr-0.8.4/pestr/man/eppo_tabletools.Rd | 266 - pestr-0.8.4/pestr/man/pestr.Rd | 38 pestr-0.8.4/pestr/tests/testthat.R | 8 pestr-0.8.4/pestr/tests/testthat/eppocodes.sqlite |binary pestr-0.8.4/pestr/tests/testthat/mocked_taxo.RDS |binary pestr-0.8.4/pestr/tests/testthat/test-citation.R |only pestr-0.8.4/pestr/tests/testthat/test-message_helpers.R | 16 pestr-0.8.4/pestr/tests/testthat/test-null_eppocodes.R | 18 pestr-0.8.4/pestr/tests/testthat/test-raw_eppocode_util.R | 38 pestr-0.8.4/pestr/tests/testthat/test-raw_eppocodes.R | 96 pestr-0.8.4/pestr/tests/testthat/test_api.R | 72 pestr-0.8.4/pestr/tests/testthat/test_database.R | 36 pestr-0.8.4/pestr/tests/testthat/test_dbnameextraction.R | 82 pestr-0.8.4/pestr/tests/testthat/test_tabletools.R | 873 ++--- pestr-0.8.4/pestr/tests/testthat/test_token.R | 34 pestr-0.8.4/pestr/vignettes/alert_style.css | 428 +- pestr-0.8.4/pestr/vignettes/pestr_example_n_of_taxon.Rmd | 296 - pestr-0.8.4/pestr/vignettes/pestr_workflow.Rmd | 577 +-- pestr-0.8.4/pestr/vignettes/pra_tables.Rmd |only 51 files changed, 5642 insertions(+), 5126 deletions(-)
Title: Prediction Explanation with Dependence-Aware Shapley Values
Description: Complex machine learning models are often hard to interpret. However, in
many situations it is crucial to understand and explain why a model made a specific
prediction. Shapley values is the only method for such prediction explanation framework
with a solid theoretical foundation. Previously known methods for estimating the Shapley
values do, however, assume feature independence. This package implements methods which accounts for any feature
dependence, and thereby produces more accurate estimates of the true Shapley values.
An accompanying 'Python' wrapper ('shaprpy') is available through PyPI.
Author: Martin Jullum [cre, aut] ,
Lars Henry Berge Olsen [aut] ,
Annabelle Redelmeier [aut],
Jon Lachmann [aut] ,
Nikolai Sellereite [aut] ,
Anders Loeland [ctb],
Jens Christian Wahl [ctb],
Camilla Lingjaerde [ctb],
Norsk Regnesentral [cph, fnd]
Maintainer: Martin Jullum <Martin.Jullum@nr.no>
Diff between shapr versions 1.0.7 dated 2025-12-22 and 1.0.8 dated 2026-01-20
DESCRIPTION | 6 MD5 | 236 NAMESPACE | 4 NEWS.md | 13 R/approach_empirical.R | 14 R/approach_gaussian.R | 4 R/approach_regression_separate.R | 4 R/explain.R | 16 R/model.R | 1 R/model_arima.R | 4 R/plot.R | 64 R/setup.R | 11 R/zzz.R | 3 README.md | 30 inst/REFERENCES.bib | 8 inst/doc/asymmetric_causal.Rmd | 538 inst/doc/asymmetric_causal.html | 2006 +- inst/doc/general_usage.Rmd | 403 inst/doc/general_usage.html | 2997 +-- inst/doc/regression.Rmd | 6749 +------ inst/doc/regression.html | 8997 ++-------- inst/doc/vaeac.Rmd | 235 inst/doc/vaeac.html | 971 - man/check_categorical_valid_MCsamp.Rd | 3 man/create_coalition_table.Rd | 5 man/create_marginal_data_cat.Rd | 3 man/explain.Rd | 38 man/explain_forecast.Rd | 34 man/figures/README-basic_example-1.png |binary man/get_extra_comp_args_default.Rd | 11 man/get_model_specs.Rd | 4 man/plot.shapr.Rd | 5 man/plot_MSEv_eval_crit.Rd | 15 man/predict_model.Rd | 5 man/regression.check_recipe_func.Rd | 2 man/regression.get_tune.Rd | 2 man/regression.train_model.Rd | 4 man/sample_coalition_table.Rd | 5 man/setup.Rd | 9 man/setup_approach.Rd | 22 tests/testthat/test-model-classes.R | 60 tests/testthat/test-plot.R | 6 vignettes/asymmetric_causal.Rmd | 538 vignettes/figure_asymmetric_causal/compare_plots-1.webp |binary vignettes/figure_asymmetric_causal/explanation_asym_cau_SV-1.webp |binary vignettes/figure_asymmetric_causal/explanation_asym_cau_beeswarm-1.webp |binary vignettes/figure_asymmetric_causal/explanation_asym_con_beeswarm-1.webp |binary vignettes/figure_asymmetric_causal/explanation_sym_cau_beeswarm-1.webp |binary vignettes/figure_asymmetric_causal/explanation_sym_con_SV-1.webp |binary vignettes/figure_asymmetric_causal/explanation_sym_con_beeswarm-1.webp |binary vignettes/figure_asymmetric_causal/explanation_sym_mar_beeswarm-1.webp |binary vignettes/figure_asymmetric_causal/group_cor-1.webp |binary vignettes/figure_asymmetric_causal/group_gaussian_plot_SV-1.webp |binary vignettes/figure_asymmetric_causal/group_gaussian_plot_beeswarm-1.webp |binary vignettes/figure_asymmetric_causal/n_coalitions_plot_SV-1.webp |binary vignettes/figure_asymmetric_causal/n_coalitions_plot_beeswarm-1.webp |binary vignettes/figure_asymmetric_causal/scatter_plots-1.webp |binary vignettes/figure_asymmetric_causal/setup_1-1.webp |binary vignettes/figure_asymmetric_causal/setup_2-1.webp |binary vignettes/figure_asymmetric_causal/setup_3-1.webp |binary vignettes/figure_asymmetric_causal/sym_and_asym_Shapley_values-1.webp |binary vignettes/figure_asymmetric_causal/two_dates_1-1.webp |binary vignettes/figure_asymmetric_causal/two_dates_2-1.webp |binary vignettes/figure_asymmetric_causal/two_dates_3-1.webp |binary vignettes/figure_general_usage/MSEv-plot-2-1.webp |binary vignettes/figure_general_usage/MSEv-plot-2-2.webp |binary vignettes/figure_general_usage/MSEv-plot-2-3.webp |only vignettes/figure_general_usage/MSEv-plot-3-1.webp |binary 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Title: Nonparametric Change Point Detection for Multivariate Time
Series
Description: Implements the nonparametric moving sum procedure for detecting
changes in the joint characteristic function (NP-MOJO) for multiple change
point detection in multivariate time series. See McGonigle, E. T., Cho, H.
(2025) <doi:10.1093/biomet/asaf024> for description of the NP-MOJO methodology.
Author: Euan T. McGonigle [aut, cre],
Haeran Cho [aut]
Maintainer: Euan T. McGonigle <e.t.mcgonigle@soton.ac.uk>
Diff between CptNonPar versions 0.3.1 dated 2025-11-25 and 0.3.2 dated 2026-01-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/multilag.cpts.merge.R | 6 +++--- 4 files changed, 13 insertions(+), 9 deletions(-)
Title: Datasets from "Modelling Survival Data in Medical Research" by
Collett
Description: Datasets for the book entitled "Modelling Survival Data in Medical Research" by Collett (2023) <doi:10.1201/9781003282525>. The datasets provide extensive examples of time-to-event data.
Author: Mark Clements [aut, cre] ,
Enoch Yi-Tung Chen [ctb]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between collett versions 0.1.0 dated 2025-01-09 and 0.1.2 dated 2026-01-20
DESCRIPTION | 21 +++++++++---- MD5 | 23 +++++++++++---- NAMESPACE | 17 +++++++++++ R/data.R | 75 +++++++++++++++++++++++++++++++++++++++++++++++++ R/utilities.R |only build/partial.rdb |binary data/simdata.rda |only inst/doc |only man/Datasets.Rd | 5 +++ man/collett-package.Rd | 9 ++++- man/simdata.Rd |only man/utilities.Rd |only 12 files changed, 135 insertions(+), 15 deletions(-)
Title: Dynamic Relational Event Analysis and Modeling
Description: A set of tools for relational and event analysis, including two- and one-mode network brokerage and structural measures, and helper functions optimized for relational event analysis with large datasets, including creating relational risk sets, computing network statistics, estimating relational event models, and simulating relational event sequences. For more information on relational event models, see Butts (2008) <doi:10.1111/j.1467-9531.2008.00203.x>, Lerner and Lomi (2020) <doi:10.1017/nws.2019.57>, Bianchi et al. (2024) <doi:10.1146/annurev-statistics-040722-060248>, and Butts et al. (2023) <doi:10.1017/nws.2023.9>. In terms of the structural measures in this package, see Leal (2025) <doi:10.1177/00491241251322517>, Burchard and Cornwell (2018) <doi:10.1016/j.socnet.2018.04.001>, and Fujimoto et al. (2018) <doi:10.1017/nws.2018.11>. This package was developed with support from the National Science Foundation’s (NSF) Human Networks and Data [...truncated...]
Author: Kevin A. Carson [aut, cre] ,
Diego F. Leal [aut]
Maintainer: Kevin A. Carson <kacarson@arizona.edu>
Diff between dream versions 0.1.0 dated 2025-07-19 and 1.0.0 dated 2026-01-20
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dream-1.0.0/dream/R/twomode_homophilous4Cycles_deprecatedV100.R |only dream-1.0.0/dream/README.md |only dream-1.0.0/dream/build/partial.rdb |binary dream-1.0.0/dream/man/WikiEvent2018.first100k.Rd | 16 dream-1.0.0/dream/man/computeBCConstraint.Rd | 10 dream-1.0.0/dream/man/computeBCES.Rd | 8 dream-1.0.0/dream/man/computeBCRedund.Rd | 8 dream-1.0.0/dream/man/computeBurtsConstraint.Rd | 12 dream-1.0.0/dream/man/computeBurtsES.Rd | 10 dream-1.0.0/dream/man/computeFourCycles.Rd | 14 dream-1.0.0/dream/man/computeHomFourCycles.Rd | 6 dream-1.0.0/dream/man/computeISP.Rd | 12 dream-1.0.0/dream/man/computeITP.Rd | 12 dream-1.0.0/dream/man/computeLealBrokerage.Rd | 27 dream-1.0.0/dream/man/computeNPaths.Rd | 16 dream-1.0.0/dream/man/computeOSP.Rd | 12 dream-1.0.0/dream/man/computeOTP.Rd | 12 dream-1.0.0/dream/man/computePersistence.Rd | 8 dream-1.0.0/dream/man/computePrefAttach.Rd | 9 dream-1.0.0/dream/man/computeReceiverIndegree.Rd | 12 dream-1.0.0/dream/man/computeReceiverOutdegree.Rd | 12 dream-1.0.0/dream/man/computeRecency.Rd | 8 dream-1.0.0/dream/man/computeReciprocity.Rd | 12 dream-1.0.0/dream/man/computeRemDyadCut.Rd | 10 dream-1.0.0/dream/man/computeRepetition.Rd | 12 dream-1.0.0/dream/man/computeSenderIndegree.Rd | 12 dream-1.0.0/dream/man/computeSenderOutdegree.Rd | 12 dream-1.0.0/dream/man/computeTMDegree.Rd | 6 dream-1.0.0/dream/man/computeTMDens.Rd | 6 dream-1.0.0/dream/man/computeTMEgoDis.Rd | 6 dream-1.0.0/dream/man/computeTriads.Rd | 12 dream-1.0.0/dream/man/create_riskset.Rd |only dream-1.0.0/dream/man/dream-package.Rd |only dream-1.0.0/dream/man/dream.Rd | 55 dream-1.0.0/dream/man/estimateREM.Rd | 6 dream-1.0.0/dream/man/estimate_rem_logit.Rd |only dream-1.0.0/dream/man/figures/lifecycle-deprecated.svg |only dream-1.0.0/dream/man/figures/lifecycle-experimental.svg |only dream-1.0.0/dream/man/figures/lifecycle-stable.svg |only dream-1.0.0/dream/man/figures/lifecycle-superseded.svg |only dream-1.0.0/dream/man/netstats_om_constraint.Rd |only dream-1.0.0/dream/man/netstats_om_effective.Rd |only dream-1.0.0/dream/man/netstats_om_nwalks.Rd |only dream-1.0.0/dream/man/netstats_om_pib.Rd |only dream-1.0.0/dream/man/netstats_tm_constraint.Rd |only dream-1.0.0/dream/man/netstats_tm_degreecent.Rd |only dream-1.0.0/dream/man/netstats_tm_density.Rd |only dream-1.0.0/dream/man/netstats_tm_effective.Rd |only dream-1.0.0/dream/man/netstats_tm_egodistance.Rd |only dream-1.0.0/dream/man/netstats_tm_homfourcycles.Rd |only dream-1.0.0/dream/man/netstats_tm_redundancy.Rd |only dream-1.0.0/dream/man/processOMEventSeq.Rd | 6 dream-1.0.0/dream/man/processTMEventSeq.Rd | 6 dream-1.0.0/dream/man/remExpWeights.Rd | 6 dream-1.0.0/dream/man/remstats_degree.Rd |only dream-1.0.0/dream/man/remstats_dyadcut.Rd |only dream-1.0.0/dream/man/remstats_fourcycles.Rd |only dream-1.0.0/dream/man/remstats_persistence.Rd |only dream-1.0.0/dream/man/remstats_prefattachment.Rd |only dream-1.0.0/dream/man/remstats_recency.Rd |only 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dream-1.0.0/dream/src/prefattachincppwithtimespan.cpp |only dream-1.0.0/dream/src/processonemodeseq.cpp |only dream-1.0.0/dream/src/processtmeventseq.cpp |only dream-1.0.0/dream/src/recencyrankc.cpp |only dream-1.0.0/dream/src/remfourcycles.cpp |only dream-1.0.0/dream/src/tmdegreecentrailty.cpp |only dream-1.0.0/dream/src/twomodeegodisthomocpp.cpp |only 162 files changed, 1601 insertions(+), 3802 deletions(-)
Title: Real-Time Disease Surveillance
Description: Supports modelling real-time case data to facilitate the real-time
surveillance of infectious diseases and other point phenomena. The package provides automated computational grid generation over
an area of interest with methods to map covariates between geographies, model fitting including spatially aggregated case counts,
and predictions and visualisation. Both Bayesian and maximum likelihood methods are provided. Log-Gaussian Cox Processes are described by
Diggle et al. (2013) <doi:10.1214/13-STS441> and we provide both the low-rank approximation for Gaussian processes
described by Solin and Särkkä (2020) <doi:10.1007/s11222-019-09886-w> and Riutort-Mayol et al (2023) <doi:10.1007/s11222-022-10167-2> and the
nearest neighbour Gaussian process described by Datta et al (2016) <doi:10.1080/01621459.2015.1044091>.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <s.i.watson@bham.ac.uk>
Diff between rts2 versions 0.9.1 dated 2025-09-11 and 0.10.1 dated 2026-01-20
rts2-0.10.1/rts2/DESCRIPTION | 16 rts2-0.10.1/rts2/MD5 | 110 rts2-0.10.1/rts2/NAMESPACE | 5 rts2-0.10.1/rts2/R/RcppExports.R | 292 -- rts2-0.10.1/rts2/R/disaggregate.R |only rts2-0.10.1/rts2/R/griddata_class.R | 1576 +++++--------- rts2-0.10.1/rts2/R/print_mcmlrts.R | 63 rts2-0.10.1/rts2/R/stanmodels.R | 4 rts2-0.10.1/rts2/README.md |only rts2-0.10.1/rts2/build/partial.rdb |binary rts2-0.10.1/rts2/inst/stan/rtsbayes.stan | 33 rts2-0.10.1/rts2/man/birmingham_crime.Rd | 34 rts2-0.10.1/rts2/man/boundary.Rd | 32 rts2-0.10.1/rts2/man/coef.rtsFit.Rd | 38 rts2-0.10.1/rts2/man/confint.rtsFit.Rd | 38 rts2-0.10.1/rts2/man/covariance.parameters.Rd | 34 rts2-0.10.1/rts2/man/disaggregate_covariate.Rd |only rts2-0.10.1/rts2/man/disaggregate_positive.Rd |only rts2-0.10.1/rts2/man/example_points.Rd | 34 rts2-0.10.1/rts2/man/family.rtsFit.Rd | 38 rts2-0.10.1/rts2/man/fitted.rtsFit.Rd | 40 rts2-0.10.1/rts2/man/fixed.effects.Rd | 34 rts2-0.10.1/rts2/man/flat_disaggregate.Rd |only rts2-0.10.1/rts2/man/formula.grid.Rd | 42 rts2-0.10.1/rts2/man/formula.rtsFit.Rd | 42 rts2-0.10.1/rts2/man/grid.Rd | 324 +- rts2-0.10.1/rts2/man/logLik.rtsFit.Rd | 40 rts2-0.10.1/rts2/man/predict.grid.Rd | 138 - rts2-0.10.1/rts2/man/predict.rtsFit.Rd | 40 rts2-0.10.1/rts2/man/print.rtsFit.Rd | 50 rts2-0.10.1/rts2/man/print.rtsFitSummary.Rd | 44 rts2-0.10.1/rts2/man/random.effects.Rd | 34 rts2-0.10.1/rts2/man/residuals.grid.Rd | 44 rts2-0.10.1/rts2/man/residuals.rtsFit.Rd | 44 rts2-0.10.1/rts2/man/summary.grid.Rd | 38 rts2-0.10.1/rts2/man/summary.rtsFit.Rd | 48 rts2-0.10.1/rts2/man/vcov.grid.Rd | 40 rts2-0.10.1/rts2/man/vcov.rtsFit.Rd | 40 rts2-0.10.1/rts2/src/RcppExports.cpp | 1118 +-------- rts2-0.10.1/rts2/src/region_model.cpp |only rts2-0.10.1/rts2/src/region_model.h |only rts2-0.10.1/rts2/src/stanExports_rtsbayes.cc | 34 rts2-0.10.1/rts2/src/stanExports_rtsbayes.h | 1190 ++++------ rts2-0.10.1/rts2/src/stanExports_rtslgcp_region.cc | 34 rts2-0.9.1/rts2/inst/cmdstan |only rts2-0.9.1/rts2/inst/include |only rts2-0.9.1/rts2/inst/stan/rtsmcml_poisson.stan |only rts2-0.9.1/rts2/inst/stan/rtsmcml_poisson_region.stan |only rts2-0.9.1/rts2/src/model_module.cpp |only rts2-0.9.1/rts2/src/stanExports_rtsmcml_poisson.cc |only rts2-0.9.1/rts2/src/stanExports_rtsmcml_poisson.h |only rts2-0.9.1/rts2/src/stanExports_rtsmcml_poisson_region.cc |only rts2-0.9.1/rts2/src/stanExports_rtsmcml_poisson_region.h |only 53 files changed, 2062 insertions(+), 3743 deletions(-)
Title: User Friendly Data Visualization
Description: A comprehensive visualization toolkit built with coders of all
skill levels and color-vision impaired audiences in mind. It allows creation
of finely-tuned, publication-quality figures from single function calls.
Visualizations include scatter plots, compositional bar plots, violin, box,
and ridge plots, and more. Customization ranges from size and title
adjustments to discrete-group circling and labeling, hidden data overlay
upon cursor hovering via ggplotly() conversion, and many more, all with
simple, discrete inputs. Color blindness friendliness is powered by legend
adjustments (enlarged keys), and by allowing the use of shapes or
letter-overlay in addition to the carefully selected dittoColors().
Author: Daniel Bunis [aut, cre]
Maintainer: Daniel Bunis <daniel.bunis@ucsf.edu>
Diff between dittoViz versions 1.0.5 dated 2025-12-09 and 1.0.6 dated 2026-01-20
DESCRIPTION | 6 +- MD5 | 22 ++++----- NEWS.md | 9 +++ R/scatterHex.R | 99 ++++++++---------------------------------- R/scatterPlot.R | 19 ++++++-- R/utils_plot_mods.R | 25 ++++++++-- R/yPlot.R | 67 +++++++++++++--------------- man/scatterHex.Rd | 99 ++++++++---------------------------------- man/scatterPlot.Rd | 16 ++++-- tests/testthat/test-hover.R | 10 +++- tests/testthat/test-scatter.R | 26 +++++++++++ tests/testthat/test-y.R | 52 +++++++++++++++++++--- 12 files changed, 221 insertions(+), 229 deletions(-)
Title: Imputation of Missing Data in Sequence Analysis
Description: Multiple imputation of missing data in a dataset using MICT or
MICT-timing methods. The core idea of the algorithms is to fill gaps of
missing data, which is the typical form of missing data in a longitudinal
setting, recursively from their edges. Prediction is based on either a
multinomial or random forest regression model. Covariates and
time-dependent covariates can be included in the model.
Author: Kevin Emery [aut, cre],
Anthony Guinchard [aut],
Andre Berchtold [aut],
Kamyar Taher [aut]
Maintainer: Kevin Emery <kevin.emery@unige.ch>
Diff between seqimpute versions 2.2.0 dated 2025-01-15 and 2.2.1 dated 2026-01-20
seqimpute-2.2.0/seqimpute/R/plots.R |only seqimpute-2.2.1/seqimpute/DESCRIPTION | 6 seqimpute-2.2.1/seqimpute/MD5 | 42 +- seqimpute-2.2.1/seqimpute/NEWS.md | 15 seqimpute-2.2.1/seqimpute/R/checks.R | 49 +- seqimpute-2.2.1/seqimpute/R/final.transform.R | 27 - seqimpute-2.2.1/seqimpute/R/methods.seqimp.R | 5 seqimpute-2.2.1/seqimpute/R/mict.internal.R | 100 ++--- seqimpute-2.2.1/seqimpute/R/mict.timing.R | 230 ++++++------ seqimpute-2.2.1/seqimpute/R/seqQuickLook.R | 55 +- seqimpute-2.2.1/seqimpute/R/seqTrans.R | 79 +--- seqimpute-2.2.1/seqimpute/R/seqaddNA.R | 15 seqimpute-2.2.1/seqimpute/R/seqimpute.R | 173 ++++----- seqimpute-2.2.1/seqimpute/R/seqmissIplot.R |only seqimpute-2.2.1/seqimpute/R/seqmissfplot.R |only seqimpute-2.2.1/seqimpute/R/seqmissimplic.R |only seqimpute-2.2.1/seqimpute/build/vignette.rds |binary seqimpute-2.2.1/seqimpute/inst/doc/vignette.pdf |binary seqimpute-2.2.1/seqimpute/man/seqaddNA.Rd | 2 seqimpute-2.2.1/seqimpute/man/seqimpute.Rd | 446 ++++++++++++------------ seqimpute-2.2.1/seqimpute/man/seqmissIplot.Rd | 100 ++--- seqimpute-2.2.1/seqimpute/man/seqmissfplot.Rd | 122 +++--- seqimpute-2.2.1/seqimpute/man/seqmissimplic.Rd | 5 seqimpute-2.2.1/seqimpute/man/summary.seqimp.Rd | 38 +- 24 files changed, 759 insertions(+), 750 deletions(-)
Title: Perform a Relative Weights Analysis
Description: Perform a Relative Weights Analysis (RWA) (a.k.a. Key Drivers Analysis) as per the method described
in Tonidandel & LeBreton (2015) <DOI:10.1007/s10869-014-9351-z>, with its original roots in Johnson (2000) <DOI:10.1207/S15327906MBR3501_1>. In essence, RWA decomposes
the total variance predicted in a regression model into weights that accurately reflect the proportional
contribution of the predictor variables, which addresses the issue of multi-collinearity. In typical scenarios,
RWA returns similar results to Shapley regression, but with a significant advantage on computational performance.
Author: Martin Chan [aut, cre]
Maintainer: Martin Chan <martinchan53@gmail.com>
Diff between rwa versions 0.1.0 dated 2025-07-16 and 0.1.1 dated 2026-01-20
rwa-0.1.0/rwa/man/extract_ci.Rd |only rwa-0.1.0/rwa/man/run_rwa_bootstrap.Rd |only rwa-0.1.1/rwa/DESCRIPTION | 6 rwa-0.1.1/rwa/MD5 | 38 rwa-0.1.1/rwa/NAMESPACE | 1 rwa-0.1.1/rwa/NEWS.md | 18 rwa-0.1.1/rwa/R/bootstrap_rwa.R | 232 +- rwa-0.1.1/rwa/R/rwa.R | 67 rwa-0.1.1/rwa/README.md | 7 rwa-0.1.1/rwa/build/vignette.rds |binary rwa-0.1.1/rwa/inst/WORDLIST | 4 rwa-0.1.1/rwa/inst/doc/bootstrap-confidence-intervals.html | 129 - rwa-0.1.1/rwa/inst/doc/evaluating-rwa-method-reference.Rmd | 122 - rwa-0.1.1/rwa/inst/doc/evaluating-rwa-method-reference.html | 1063 +++++------- rwa-0.1.1/rwa/inst/doc/introduction-to-rwa.Rmd | 74 rwa-0.1.1/rwa/inst/doc/introduction-to-rwa.html | 105 - rwa-0.1.1/rwa/tests/testthat/test-bootstrap.R | 8 rwa-0.1.1/rwa/tests/testthat/test-rwa.R | 331 ++- rwa-0.1.1/rwa/vignettes/README.md | 1 rwa-0.1.1/rwa/vignettes/evaluating-rwa-method-reference.Rmd | 122 - rwa-0.1.1/rwa/vignettes/introduction-to-rwa.Rmd | 74 21 files changed, 1313 insertions(+), 1089 deletions(-)
Title: Regression by Composition
Description: Flexible statistical modelling using a modular framework for
regression, in which groups of transformations are composed together
and act on probability distributions.
Author: Daniel Farewell [aut, cre, cph] ,
Simon Schoenbuchner [ctb]
Maintainer: Daniel Farewell <farewelld@cardiff.ac.uk>
Diff between rbc versions 0.1.0 dated 2024-11-06 and 0.1.1 dated 2026-01-20
rbc-0.1.0/rbc/man/AIC.RegressionByComposition.Rd |only rbc-0.1.1/rbc/DESCRIPTION | 13 ++-- rbc-0.1.1/rbc/MD5 | 26 +++++--- rbc-0.1.1/rbc/NAMESPACE | 4 + rbc-0.1.1/rbc/NEWS.md | 6 ++ rbc-0.1.1/rbc/R/DataFeatures.R | 27 ++++++--- rbc-0.1.1/rbc/R/S3methods.R | 16 +---- rbc-0.1.1/rbc/R/append_flow.R | 2 rbc-0.1.1/rbc/R/flows.R | 68 +++++++++++++++++++++++ rbc-0.1.1/rbc/R/rbc.R | 4 - rbc-0.1.1/rbc/data/starr.rda |binary rbc-0.1.1/rbc/man/BinomialGLM.Rd |only rbc-0.1.1/rbc/man/Cinch.Rd |only rbc-0.1.1/rbc/man/PowerOdds.Rd |only rbc-0.1.1/rbc/man/rbc.Rd | 4 - rbc-0.1.1/rbc/tests/testthat/test-DataFeatures.R |only rbc-0.1.1/rbc/tests/testthat/test-S3methods.R |only 17 files changed, 128 insertions(+), 42 deletions(-)
Title: Beyond the Border - Kernel Density Estimation for Urban
Geography
Description: The kernelSmoothing() function allows you to square and smooth geolocated data. It calculates a classical kernel smoothing (conservative) or a geographically weighted median. There are four major call modes of the function.
The first call mode is kernelSmoothing(obs, epsg, cellsize, bandwidth) for a classical kernel smoothing and automatic grid.
The second call mode is kernelSmoothing(obs, epsg, cellsize, bandwidth, quantiles) for a geographically weighted median and automatic grid.
The third call mode is kernelSmoothing(obs, epsg, cellsize, bandwidth, centroids) for a classical kernel smoothing and user grid.
The fourth call mode is kernelSmoothing(obs, epsg, cellsize, bandwidth, quantiles, centroids) for a geographically weighted median and user grid.
Geographically weighted summary statistics : a framework for localised exploratory data analysis, C.Brunsdon & al., in Computers, Environment and Urban Systems C.Brunsdon & al. (2002) <doi:10.1016/S0198-9715(01)00009-6>,
S [...truncated...]
Author: Arlindo Dos Santos [aut],
Francois Semecurbe [aut],
Julien Pramil [aut],
Solene Colin [cre, ctb],
Kim Antunez [ctb],
Auriane Renaud [ctb],
Farida Marouchi [ctb],
Joachim Timoteo [ctb],
Institut national de la statistique et des etudes economiques [cp [...truncated...]
Maintainer: Solene Colin <solene.colin@insee.fr>
Diff between btb versions 0.2.1 dated 2025-03-17 and 0.2.2 dated 2026-01-20
DESCRIPTION | 8 +++---- MD5 | 16 +++++++-------- NEWS.md | 10 +++++++++ build/vignette.rds |binary inst/doc/btb.html | 20 +++++++++---------- inst/doc/logo.R | 2 - inst/doc/logo.Rmd | 2 - inst/doc/logo.html | 54 +++++++++++++++++++++++++++-------------------------- vignettes/logo.Rmd | 2 - 9 files changed, 63 insertions(+), 51 deletions(-)
Title: Spatial Logistic Gaussian Process for Field Density Estimation
Description: Provides tools for conditional and spatially dependent
density estimation using Spatial Logistic Gaussian Processes (SLGPs).
The approach represents probability densities through finite-rank
Gaussian process priors transformed via a spatial logistic density
transformation, enabling flexible non-parametric modeling of
heterogeneous data. Functionality includes density prediction,
quantile and moment estimation, sampling methods, and preprocessing
routines for basis functions. Applications arise in spatial statistics,
machine learning, and uncertainty quantification.
The methodology builds on the framework of Leonard (1978)
<doi:10.1111/j.2517-6161.1978.tb01655.x>, Lenk (1988) <doi:10.1080/01621459.1988.10478625>,
Tokdar (2007) <doi:10.1198/106186007X210206>, Tokdar (2010) <doi:10.1214/10-BA605>,
and is further aligned with recent developments
in Bayesian non-parametric modelling: see Gautier (2023) <https://boristheses.unibe.ch/4377/>,
and Gautier (2025) &l [...truncated...]
Author: Athenais Gautier [aut, cre]
Maintainer: Athenais Gautier <athenais.gautier@onera.fr>
Diff between SLGP versions 1.0.0 dated 2025-09-05 and 1.0.1 dated 2026-01-20
DESCRIPTION | 6 - MD5 | 40 +++--- R/PredictAndSimulate.R | 151 +++++++++++++++++++++---- R/SLGPclass.R | 2 R/datamanagement.R | 52 +++++++- R/slgp.R | 112 +++++++++++++++---- inst/doc/IntroductionSLGP.html | 73 ++++++------ inst/doc/SLGPdiscrete.html | 2 inst/extdata/composed_model.rds |binary inst/extdata/simple_model.rds |binary inst/stan/likelihoodComposed.stan | 128 +++++++++++---------- inst/stan/likelihoodSimple.stan | 106 +++++++++--------- man/SLGP-class.Rd | 2 man/pre_comput_NN.Rd | 2 man/pre_comput_WNN.Rd | 3 man/pre_comput_nothing.Rd | 2 man/predictSLGP_newNode.Rd | 5 man/retrainSLGP.Rd | 7 - man/slgp.Rd | 7 - src/stanExports_likelihoodComposed.h | 206 ++++++++++++++++++++--------------- src/stanExports_likelihoodSimple.h | 165 +++++++++++++++++----------- 21 files changed, 693 insertions(+), 378 deletions(-)
Title: Draw Samples with the Desired Properties from a Data Set
Description: A tool to sample data with the desired properties.Samples can be
drawn by purposive sampling with determining distributional
conditions, such as deviation from normality (skewness and kurtosis),
and sample size in quantitative research studies.
For purposive sampling, a researcher has something in mind and participants that
fit the purpose of the study are included (Etikan,Musa, & Alkassim, 2015)
<doi:10.11648/j.ajtas.20160501.11>.Purposive sampling can be useful for answering
many research questions (Klar & Leeper, 2019)
<doi:10.1002/9781119083771.ch21>.
Author: Kubra Atalay Kabasakal [aut, cre] ,
Huseyin Yildiz [ctb]
Maintainer: Kubra Atalay Kabasakal <katalay@hacettepe.edu.tr>
Diff between drawsample versions 1.0.1 dated 2022-09-05 and 1.0.2 dated 2026-01-20
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- R/globals.R | 3 ++- build/partial.rdb |binary inst/CITATION | 29 +++++++++++++---------------- 5 files changed, 25 insertions(+), 27 deletions(-)
Title: A C++11 Interface for R's C Interface
Description: Provides a header only, C++11 interface to R's C
interface. Compared to other approaches 'cpp11' strives to be safe
against long jumps from the C API as well as C++ exceptions, conform
to normal R function semantics and supports interaction with 'ALTREP'
vectors.
Author: Davis Vaughan [aut, cre] ,
Jim Hester [aut] ,
Romain Francois [aut] ,
Benjamin Kietzman [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Davis Vaughan <davis@posit.co>
Diff between cpp11 versions 0.5.2-2 dated 2026-01-06 and 0.5.3 dated 2026-01-20
DESCRIPTION | 6 MD5 | 52 - NEWS.md | 12 README.md | 2 build/vignette.rds |binary inst/doc/FAQ.Rmd | 2 inst/doc/FAQ.html | 15 inst/doc/converting.html | 5 inst/doc/cpp11.R | 344 +++++----- inst/doc/cpp11.Rmd | 14 inst/doc/cpp11.html | 108 ++- inst/doc/internals.Rmd | 2 inst/doc/internals.html | 7 inst/doc/motivations.R | 58 - inst/doc/motivations.Rmd | 12 inst/doc/motivations.html | 1193 +++++++++++--------------------------- inst/include/cpp11/data_frame.hpp | 40 - inst/include/cpp11/function.hpp | 3 inst/include/cpp11/list.hpp | 7 inst/include/cpp11/named_arg.hpp | 2 inst/include/cpp11/r_vector.hpp | 10 inst/include/cpp11/sexp.hpp | 5 tests/testthat/_snaps/register.md | 8 vignettes/FAQ.Rmd | 2 vignettes/cpp11.Rmd | 14 vignettes/internals.Rmd | 2 vignettes/motivations.Rmd | 12 27 files changed, 772 insertions(+), 1165 deletions(-)
Title: Trait Matching and Abundance for Predicting Bipartite Networks
Description: Functions to produce, fit and predict from bipartite networks with abundance, trait and phylogenetic information. Its methods are described in detail in Benadi, G., Dormann, C.F., Fruend, J., Stephan, R. & Vazquez, D.P. (2021) Quantitative prediction of interactions in bipartite networks based on traits, abundances, and phylogeny. The American Naturalist, in press.
Author: Carsten Dormann [aut, cre],
Gita Benadi [aut],
Boris Tinoco [dtc],
Ruth Stephan [ctb],
Jochen Fruend [ctb]
Maintainer: Carsten Dormann <carsten.dormann@biom.uni-freiburg.de>
Diff between tapnet versions 0.3 dated 2021-01-28 and 0.6 dated 2026-01-20
DESCRIPTION | 10 +- MD5 | 38 +++++----- NAMESPACE | 2 R/fit_tapnet.R | 54 +++++++++----- R/gof_tapnet.R | 9 +- R/helper_tapnet.R | 175 ++++++++++++++++++++++++++++++++++++++--------- R/make_tapnet.R | 107 +++++++++++++++++++--------- R/predict_tapnet.R | 16 +--- R/simnetfromtap.R | 69 +++++++++++------- R/tapnet-package.R | 31 ++++++-- R/tapnet2df.R | 24 ++++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/CaseStudy.pdf |binary man/fit_tapnet.Rd | 11 +- man/gof_tapnet.Rd | 2 man/internalFunctions.Rd | 31 ++++++-- man/make_tapnet.Rd | 5 + man/simnetfromtap.Rd | 2 man/tapnet-package.Rd | 29 ++++++- 20 files changed, 436 insertions(+), 179 deletions(-)
Title: An Interface to the 'AutoNavi Maps' API Geocoding Services
Description: Getting and parsing data of location geocode/reverse-geocode and administrative regions from 'AutoNavi Maps'<https://lbs.amap.com/api/webservice/summary> API.
Author: Han Chen [aut, cre],
Wanyanhan Jiang [ctb]
Maintainer: Han Chen <chenhan28@gmail.com>
Diff between amapGeocode versions 0.9.0 dated 2026-01-19 and 1.0.0 dated 2026-01-20
DESCRIPTION | 10 MD5 | 55 - NAMESPACE | 1 NEWS.md | 15 R/amap_gui.R |only R/amap_http.R | 770 ++++++++++++--------- R/convertCoord.R | 442 ++++++------ R/getAdmin.R | 646 +++++++++--------- R/getCoord.R | 884 +++++++++++++----------- R/getLocation.R | 1064 ++++++++++++++++-------------- R/helpers.R | 17 README.md | 55 + build/vignette.rds |binary inst/doc/Introduction_to_Shiny_App.R |only inst/doc/Introduction_to_Shiny_App.Rmd |only inst/doc/Introduction_to_Shiny_App.html |only inst/doc/Introduction_to_amapGeocode.Rmd | 21 inst/doc/Introduction_to_amapGeocode.html | 21 inst/shiny |only man/amap_config.Rd | 23 man/amap_gui.Rd |only man/getAdmin.Rd | 6 man/getCoord.Rd | 6 man/getLocation.Rd | 9 tests/spelling.R | 9 tests/testthat/test_convertCoord.R | 140 +++ tests/testthat/test_getAdmin.R | 175 +++- tests/testthat/test_getCoord.R | 263 +++++-- tests/testthat/test_getLocation.R | 204 ++++- tests/testthat/test_signature.R | 176 ++++ vignettes/Introduction_to_Shiny_App.Rmd |only vignettes/Introduction_to_amapGeocode.Rmd | 21 32 files changed, 3033 insertions(+), 2000 deletions(-)
Title: Visualise and Report 'VALD ForceDecks' Test Results
Description: Provides a 'shiny' dashboard and plotting utilities to explore and
report 'VALD ForceDecks' testing data. Includes interactive modules for
metric exploration, radar charts, longitudinal comparisons, quadrant plots,
and athlete reports.
Author: Kieran Harrison [aut, cre],
VALD Support [ctb],
VALD [cph]
Maintainer: Kieran Harrison <k.harrison@vald.com>
Diff between valdrViz versions 1.0.0 dated 2026-01-17 and 1.0.1 dated 2026-01-20
DESCRIPTION | 6 +-- MD5 | 14 +++---- R/app_core.R | 6 ++- R/app_server.R | 59 ++++++++++++++++++++++++++------ R/utils.R | 15 +++++--- man/fd_read_folder.Rd | 4 +- man/forcedecks_performance_dashboard.Rd | 2 - man/read_fd.Rd | 4 +- 8 files changed, 81 insertions(+), 29 deletions(-)
Title: Adaptive Machine Learning-Powered, Context-Matching Tool for
Single-Cell and Spatial Transcriptomics Annotation
Description: Annotates single-cell and spatial-transcriptomic (ST) data using marker datasets. Supports unified markers list ('Markers_list') creation from built-in databases (e.g., 'Cellmarker2', 'PanglaoDB', 'scIBD', 'TCellSI', 'PCTIT', 'PCTAM'), Seurat objects, or user-supplied Excel files. SlimR can predict calculation parameters by adaptive machine learning algorithms, and based on Markers_list, calculate gene expression of different cell types and predict annotation information, and calculate corresponding AUC and annotate it, then verify it. At the same time, it can calculate gene expression corresponding to the cell type to generate a reference map for manual annotation (e.g., 'Heat Map', 'Feature Plots', 'Combined Plots'). For more details, see Kabacoff (2020, ISBN:9787115420572).
Author: Zhaoqing Wang [aut, cre]
Maintainer: Zhaoqing Wang <zhaoqingwang@mail.sdu.edu.cn>
Diff between SlimR versions 1.0.9 dated 2025-12-17 and 1.1.0 dated 2026-01-20
SlimR-1.0.9/SlimR/man/generate_training_data.Rd |only SlimR-1.0.9/SlimR/man/postprocess_parameters.Rd |only SlimR-1.0.9/SlimR/man/predict_optimal_parameters.Rd |only SlimR-1.0.9/SlimR/man/train_parameter_model.Rd |only SlimR-1.1.0/SlimR/DESCRIPTION | 20 SlimR-1.1.0/SlimR/MD5 | 35 SlimR-1.1.0/SlimR/NAMESPACE | 6 SlimR-1.1.0/SlimR/NEWS.md | 8 SlimR-1.1.0/SlimR/R/Celltype_Calculate.R | 155 +++- SlimR-1.1.0/SlimR/R/Probability_parameter.R | 655 ++++++++--------- SlimR-1.1.0/SlimR/R/onattach.R | 12 SlimR-1.1.0/SlimR/README.md | 53 - SlimR-1.1.0/SlimR/man/Celltype_Calculate.Rd | 7 SlimR-1.1.0/SlimR/man/Parameter_Calculate.Rd | 43 - SlimR-1.1.0/SlimR/man/calculate_cluster_variability.Rd | 7 SlimR-1.1.0/SlimR/man/calculate_expression.Rd | 7 SlimR-1.1.0/SlimR/man/calculate_expression_skewness.Rd | 7 SlimR-1.1.0/SlimR/man/calculate_probability.Rd | 7 SlimR-1.1.0/SlimR/man/compute_adaptive_parameters.Rd |only SlimR-1.1.0/SlimR/man/estimate_batch_effect.Rd | 7 SlimR-1.1.0/SlimR/man/extract_dataset_features.Rd | 9 21 files changed, 535 insertions(+), 503 deletions(-)
Title: Retrieval, Analysis and Visualization of Air Traffic Data
Description: Provides functionalities and data structures to retrieve, analyze and visualize aviation
data. It includes a client interface to the 'OpenSky' API <https://opensky-network.org>. It allows
retrieval of flight information, as well as aircraft state vectors.
Author: Rafael Ayala [aut, cre] ,
Daniel Ayala [aut] ,
David Ruiz [aut] ,
Aleix Selles [aut],
Pablo Hernandez [aut] ,
Lara Selles Vidal [aut]
Maintainer: Rafael Ayala <rafaelayalahernandez@gmail.com>
Diff between openSkies versions 1.2.2 dated 2025-08-21 and 1.3.0 dated 2026-01-20
DESCRIPTION | 10 +- MD5 | 44 +++++------ NEWS | 6 + R/openSkies_getFlightsFunctions.R | 48 ++++++++---- R/openSkies_getStateVectorsFunctions.R | 47 ++++++++---- R/openSkies_otherSupportFunctions.R | 123 ++++++++++++++++++++++++--------- R/openSkies_plottingFunctions.R | 6 - inst/doc/openSkies.R | 12 +++ inst/doc/openSkies.Rmd | 27 +++++++ inst/doc/openSkies.html | 38 +++++++--- man/clusterRoutes.Rd | 4 - man/getAircraftFlights.Rd | 24 ++++-- man/getAircraftStateVectorsSeries.Rd | 21 ++++- man/getAirportArrivals.Rd | 24 ++++-- man/getAirportDepartures.Rd | 24 ++++-- man/getIntervalFlights.Rd | 24 ++++-- man/getIntervalStateVectors.Rd | 21 ++++- man/getSingleTimeStateVectors.Rd | 17 +++- man/plotPlanes.Rd | 6 + man/plotRoute.Rd | 6 + man/plotRoutes.Rd | 8 +- tests/runTests.R | 10 +- vignettes/openSkies.Rmd | 27 +++++++ 23 files changed, 431 insertions(+), 146 deletions(-)
Title: Bayesian Additive Regression Trees
Description: An advanced implementation of Bayesian Additive Regression Trees with expanded features for data analysis and visualization.
Author: Adam Kapelner [aut, cre] ,
Justin Bleich [aut]
Maintainer: Adam Kapelner <kapelner@qc.cuny.edu>
Diff between bartMachine versions 1.4.1 dated 2026-01-19 and 1.4.1.1 dated 2026-01-20
CHANGELOG | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/bartMachine.pdf |binary inst/java/bart_java.jar |binary 5 files changed, 11 insertions(+), 8 deletions(-)
Title: Parametric Mixture Models for Uncertainty Estimation of
Fatalities in UCDP Conflict Data
Description: Provides functions for estimating uncertainty in the number of fatalities in the Uppsala Conflict Data Program (UCDP) data. The package implements a parametric reported-value Gumbel mixture distribution that accounts for the uncertainty in the number of fatalities in the UCDP data. The model is based on information from a survey on UCDP coders and how they view the uncertainty of the number of fatalities from UCDP events. The package provides functions for making random draws of fatalities from the mixture distribution, as well as to estimate percentiles, quantiles, means, and other statistics of the distribution. Full details on the survey and estimation procedure can be found in Vesco et al (2024).
Author: David Randahl [cre, aut]
Maintainer: David Randahl <david.randahl@pcr.uu.se>
Diff between uncertainUCDP versions 0.6.1 dated 2025-08-19 and 0.7.0 dated 2026-01-20
uncertainUCDP-0.6.1/uncertainUCDP/LICENSE |only uncertainUCDP-0.7.0/uncertainUCDP/DESCRIPTION | 10 uncertainUCDP-0.7.0/uncertainUCDP/MD5 | 13 uncertainUCDP-0.7.0/uncertainUCDP/NAMESPACE | 2 uncertainUCDP-0.7.0/uncertainUCDP/R/globals.R |only uncertainUCDP-0.7.0/uncertainUCDP/R/rubin_rules.R |only uncertainUCDP-0.7.0/uncertainUCDP/R/uncertainUCDP-package.R | 1 uncertainUCDP-0.7.0/uncertainUCDP/R/uncertainUCDP.R | 191 +++++------- uncertainUCDP-0.7.0/uncertainUCDP/man/models_rubin_rules.Rd |only uncertainUCDP-0.7.0/uncertainUCDP/man/rubin_b_and_ses.Rd |only 10 files changed, 105 insertions(+), 112 deletions(-)
Title: Report Templates and Helper Functions for Applied Epidemiology
Description: A meta-package that loads the complete sitrep ecosystem for
applied epidemiology analysis. This package provides report templates
and automatically loads companion packages, including 'epitabulate' (for
epidemiological tables), 'epidict' (for data dictionaries), 'epikit' (for
epidemiological utilities), and 'apyramid' (for age-sex pyramids).
Simply load 'sitrep' to access all functions from the ecosystem.
Author: Alexander Spina [aut, cre] ,
Zhian N. Kamvar [aut] ,
Dirk Schumacher [aut],
Kate Doyle [aut],
Chris Jarvis [aut],
Lukas Richter [aut],
Paula Blomquist [aut],
Annick Lenglet [ctb],
Neale Batra [ctb],
Applied Epi Incorporated [cph],
Medecins Sans Front [...truncated...]
Maintainer: Alexander Spina <aspina@appliedepi.org>
Diff between sitrep versions 0.3.0 dated 2026-01-11 and 0.4.0 dated 2026-01-20
DESCRIPTION | 6 MD5 | 8 NEWS.md | 3 inst/rmarkdown/templates/ajs_intersectional_outbreak/skeleton/skeleton.Rmd | 40 +-- inst/rmarkdown/templates/cholera_intersectional_outbreak/skeleton/skeleton.Rmd | 106 +++++----- 5 files changed, 83 insertions(+), 80 deletions(-)
Title: Robust Methods for High-Dimensional Data
Description: Robust methods for high-dimensional data, in particular linear
model selection techniques based on least angle regression and sparse
regression. Specifically, the package implements robust least angle
regression (Khan, Van Aelst & Zamar, 2007; <doi:10.1198/016214507000000950>),
(robust) groupwise least angle regression (Alfons, Croux & Gelper, 2016;
<doi:10.1016/j.csda.2015.02.007>), and sparse least trimmed squares
regression (Alfons, Croux & Gelper, 2013; <doi:10.1214/12-AOAS575>).
Author: Andreas Alfons [aut, cre] ,
Dirk Eddelbuettel [ctb]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between robustHD versions 0.8.3 dated 2025-12-09 and 0.8.4 dated 2026-01-20
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 8 ++++++++ build/partial.rdb |binary data/TopGear.RData |binary data/nci60.RData |binary src/Makevars | 4 +--- src/Makevars.win | 5 +---- src/fastLars.cpp | 4 ++-- src/fastRlars.cpp | 2 +- 10 files changed, 26 insertions(+), 23 deletions(-)
Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model
(Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>;
Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>;
Sorensen et al., R Journal, 2020 <doi:10.32614/RJ-2020-026>;
Stein, PhD Thesis, 2023 <https://eprints.lancs.ac.uk/id/eprint/195759>). Both Metropolis-Hastings
and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule,
Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be
analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well
as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the
posterior distributions of parameters are provided. The package also provides functions for estimating
the partition function (normalizing constant) of the Mallows rank mo [...truncated...]
Author: Oystein Sorensen [aut, cre] ,
Waldir Leoncio [aut],
Valeria Vitelli [aut] ,
Marta Crispino [aut],
Qinghua Liu [aut],
Cristina Mollica [aut],
Luca Tardella [aut],
Anja Stein [aut]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between BayesMallows versions 2.2.6 dated 2025-11-25 and 2.2.7 dated 2026-01-20
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 6 ++++++ R/acceptance_ratio.R | 9 +++++++-- build/partial.rdb |binary build/vignette.rds |binary man/get_acceptance_ratios.Rd | 11 +++++++++-- src/run_mcmc.cpp | 8 +++++--- tests/testthat/test-acceptance_ratio.R | 18 ++++++++++++++++++ 9 files changed, 56 insertions(+), 18 deletions(-)
Title: Treatment of Zeros, Left-Censored and Missing Values in
Compositional Data Sets
Description: Principled methods for the imputation of zeros, left-censored and missing data in
compositional data sets (Palarea-Albaladejo and Martin-Fernandez (2015) <doi:10.1016/j.chemolab.2015.02.019>).
Author: Javier Palarea-Albaladejo [cre, aut] ,
Josep Antoni Martin-Fernandez [aut]
Maintainer: Javier Palarea-Albaladejo <javier.palarea@udg.edu>
Diff between zCompositions versions 1.5.0-5 dated 2025-06-30 and 1.6.0 dated 2026-01-20
DESCRIPTION | 10 +++++----- MD5 | 14 ++++++++------ NAMESPACE | 2 ++ NEWS | 7 +++++++ R/perLog.R |only man/lrEM.Rd | 2 +- man/lrSVD.Rd | 2 +- man/perLog.Rd |only man/zCompositions-package.Rd | 4 ++-- 9 files changed, 26 insertions(+), 15 deletions(-)
Title: Easy and Powerful Web Servers
Description: Automatically create a web server from annotated 'R' files or by
building it up programmatically. Provides automatic 'OpenAPI' documentation,
input handling, asynchronous evaluation, and plugin support.
Author: Thomas Lin Pedersen [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between plumber2 versions 0.1.1 dated 2025-12-18 and 0.2.0 dated 2026-01-20
DESCRIPTION | 24 - MD5 | 156 +++++++----- NAMESPACE | 13 + NEWS.md | 25 + R/Plumber2.R | 465 +++++++++++++++++++++++++++++++++++-- R/api.R | 2 R/api_assets.R | 18 + R/api_auth.R |only R/api_docs.R | 10 R/api_handlers.R | 253 ++++++++++++++++++-- R/api_logger.R | 4 R/api_run.R | 4 R/api_storage.R | 13 - R/async.R | 2 R/create_request_handler.R | 38 +-- R/create_server_yml.R | 2 R/extension_tags.R | 73 +++-- R/open_api.R | 2 R/options.R | 22 + R/parse_plumber_file.R | 191 ++++++++++++--- R/parsers.R | 2 R/roxygen_tags.R | 20 + R/serializers.R | 23 + R/spec_constructor.R | 4 build/vignette.rds |binary inst/doc/annotations.R | 24 + inst/doc/annotations.html | 201 ++++++++++++--- inst/doc/annotations.qmd | 77 +++++- inst/doc/execution-model.html | 2 inst/doc/execution-model.qmd | 2 inst/doc/extending.R |only inst/doc/extending.html |only inst/doc/extending.qmd |only inst/doc/hosting.R |only inst/doc/hosting.html |only inst/doc/hosting.qmd |only inst/doc/otel.R |only inst/doc/otel.html |only inst/doc/otel.qmd |only inst/doc/plumber.R | 4 inst/doc/plumber.html | 35 +- inst/doc/plumber.qmd | 8 inst/doc/rendering-output.R | 5 inst/doc/rendering-output.html | 201 +++++++-------- inst/doc/rendering-output.qmd | 5 inst/doc/routing-and-input.R | 4 inst/doc/routing-and-input.html | 142 +++++------ inst/doc/routing-and-input.qmd | 4 inst/doc/security.R | 17 + inst/doc/security.html | 92 ++++--- inst/doc/security.qmd | 45 +++ inst/doc/server_yml.R |only inst/doc/server_yml.html |only inst/doc/server_yml.qmd |only man/Plumber2.Rd | 169 +++++++++++++ man/add_plumber2_tag.Rd | 38 +-- man/api_assets.Rd | 7 man/api_auth.Rd |only man/api_auth_guard.Rd |only man/api_datastore.Rd | 11 man/api_docs.Rd | 10 man/api_forward.Rd | 7 man/api_logger.Rd | 7 man/api_message.Rd | 4 man/api_redirect.Rd | 6 man/api_report.Rd |only man/api_request_handlers.Rd | 123 +++++++-- man/api_request_header_handlers.Rd | 44 +-- man/api_run.Rd | 4 man/api_shiny.Rd | 7 man/apply_plumber2_block.Rd | 3 man/create_server_yml.Rd | 2 man/device_formatter.Rd | 3 man/get_opts.Rd | 23 + man/parse_plumber_file.Rd | 4 man/plumber2-package.Rd | 4 man/register_async.Rd | 3 man/register_parser.Rd | 3 man/register_serializer.Rd | 3 vignettes/annotations.qmd | 77 +++++- vignettes/execution-model.qmd | 2 vignettes/extending.qmd |only vignettes/hosting.qmd |only vignettes/otel.qmd |only vignettes/plumber.qmd | 8 vignettes/rendering-output.qmd | 5 vignettes/routing-and-input.qmd | 4 vignettes/security.qmd | 45 +++ vignettes/server_yml.qmd |only 89 files changed, 2230 insertions(+), 630 deletions(-)
Title: Quantify Rhythmicity and Differential Rhythmicity in Genomic
Data
Description: Fit linear models based on periodic splines, moderate model
coefficients using multivariate adaptive shrinkage, then compute properties of
the moderated curves.
Author: Jake Hughey [aut, cre],
Dora Obodo [aut],
Elliot Outland [aut]
Maintainer: Jake Hughey <jakejhughey@gmail.com>
Diff between limorhyde2 versions 0.1.0 dated 2023-01-26 and 0.1.1 dated 2026-01-20
limorhyde2-0.1.0/limorhyde2/tests/testthat/data/diff_rhy_stats_post_2.qs |only limorhyde2-0.1.0/limorhyde2/tests/testthat/data/diff_rhy_stats_samps12_2.qs |only limorhyde2-0.1.0/limorhyde2/tests/testthat/data/diff_rhy_stats_samps32_2.qs |only limorhyde2-0.1.0/limorhyde2/tests/testthat/data/expected_meas_2.qs |only limorhyde2-0.1.0/limorhyde2/tests/testthat/data/expected_meas_3.qs |only limorhyde2-0.1.0/limorhyde2/tests/testthat/data/meas_ints_2.qs |only limorhyde2-0.1.0/limorhyde2/tests/testthat/data/model_fit_1.qs |only limorhyde2-0.1.0/limorhyde2/tests/testthat/data/model_fit_2.qs |only limorhyde2-0.1.0/limorhyde2/tests/testthat/data/model_fit_3.qs |only limorhyde2-0.1.0/limorhyde2/tests/testthat/data/model_fit_4.qs |only limorhyde2-0.1.0/limorhyde2/tests/testthat/data/posterior_fit_2.qs |only limorhyde2-0.1.0/limorhyde2/tests/testthat/data/posterior_samples_2.qs |only limorhyde2-0.1.0/limorhyde2/tests/testthat/data/rhy_stats_post_2.qs |only limorhyde2-0.1.0/limorhyde2/tests/testthat/data/rhy_stats_raw_1.qs |only limorhyde2-0.1.0/limorhyde2/tests/testthat/data/rhy_stats_samps_2.qs |only limorhyde2-0.1.0/limorhyde2/tests/testthat/data/stats_ints_diff_2.qs |only limorhyde2-0.1.0/limorhyde2/tests/testthat/data/stats_ints_rhy_2.qs |only limorhyde2-0.1.1/limorhyde2/DESCRIPTION | 11 limorhyde2-0.1.1/limorhyde2/MD5 | 72 - limorhyde2-0.1.1/limorhyde2/NEWS.md | 3 limorhyde2-0.1.1/limorhyde2/build/vignette.rds |binary limorhyde2-0.1.1/limorhyde2/inst/doc/differential-rhythmicity.R | 3 limorhyde2-0.1.1/limorhyde2/inst/doc/differential-rhythmicity.Rmd | 1 limorhyde2-0.1.1/limorhyde2/inst/doc/differential-rhythmicity.html | 373 ++++----- limorhyde2-0.1.1/limorhyde2/inst/doc/rhythmicity.R | 3 limorhyde2-0.1.1/limorhyde2/inst/doc/rhythmicity.Rmd | 1 limorhyde2-0.1.1/limorhyde2/inst/doc/rhythmicity.html | 257 +++--- limorhyde2-0.1.1/limorhyde2/inst/doc/rnaseq.R | 38 limorhyde2-0.1.1/limorhyde2/inst/doc/rnaseq.html | 37 limorhyde2-0.1.1/limorhyde2/inst/doc/uncertainty.R | 3 limorhyde2-0.1.1/limorhyde2/inst/doc/uncertainty.Rmd | 1 limorhyde2-0.1.1/limorhyde2/inst/doc/uncertainty.html | 393 +++++----- limorhyde2-0.1.1/limorhyde2/tests/testthat/data/diff_rhy_stats_post_2.rds |only limorhyde2-0.1.1/limorhyde2/tests/testthat/data/diff_rhy_stats_samps12_2.rds |only limorhyde2-0.1.1/limorhyde2/tests/testthat/data/diff_rhy_stats_samps32_2.rds |only limorhyde2-0.1.1/limorhyde2/tests/testthat/data/expected_meas_2.rds |only limorhyde2-0.1.1/limorhyde2/tests/testthat/data/expected_meas_3.rds |only limorhyde2-0.1.1/limorhyde2/tests/testthat/data/meas_ints_2.rds |only limorhyde2-0.1.1/limorhyde2/tests/testthat/data/model_fit_1.rds |only limorhyde2-0.1.1/limorhyde2/tests/testthat/data/model_fit_2.rds |only limorhyde2-0.1.1/limorhyde2/tests/testthat/data/model_fit_3.rds |only limorhyde2-0.1.1/limorhyde2/tests/testthat/data/model_fit_4.rds |only limorhyde2-0.1.1/limorhyde2/tests/testthat/data/posterior_fit_2.rds |only limorhyde2-0.1.1/limorhyde2/tests/testthat/data/posterior_samples_2.rds |only limorhyde2-0.1.1/limorhyde2/tests/testthat/data/rhy_stats_post_2.rds |only limorhyde2-0.1.1/limorhyde2/tests/testthat/data/rhy_stats_raw_1.rds |only limorhyde2-0.1.1/limorhyde2/tests/testthat/data/rhy_stats_samps_2.rds |only limorhyde2-0.1.1/limorhyde2/tests/testthat/data/stats_ints_diff_2.rds |only limorhyde2-0.1.1/limorhyde2/tests/testthat/data/stats_ints_rhy_2.rds |only limorhyde2-0.1.1/limorhyde2/tests/testthat/setup.R | 6 limorhyde2-0.1.1/limorhyde2/tests/testthat/test_exported.R | 76 - limorhyde2-0.1.1/limorhyde2/vignettes/differential-rhythmicity.Rmd | 1 limorhyde2-0.1.1/limorhyde2/vignettes/rhythmicity.Rmd | 1 limorhyde2-0.1.1/limorhyde2/vignettes/uncertainty.Rmd | 1 54 files changed, 640 insertions(+), 641 deletions(-)
Title: Differential Analysis of Rhythmic Transcriptome Data
Description: A flexible approach, inspired by cosinor regression, for
differential analysis of rhythmic transcriptome data. See Singer and Hughey
(2018) <doi:10.1177/0748730418813785>.
Author: Jake Hughey [aut, cre],
Jordan Singer [ctb]
Maintainer: Jake Hughey <jakejhughey@gmail.com>
Diff between limorhyde versions 1.0.1 dated 2022-02-18 and 1.0.3 dated 2026-01-20
limorhyde-1.0.1/limorhyde/inst/extdata/GSE34018_expression_data.qs |only limorhyde-1.0.1/limorhyde/inst/extdata/GSE34018_metadata.qs |only limorhyde-1.0.1/limorhyde/tests |only limorhyde-1.0.3/limorhyde/DESCRIPTION | 14 limorhyde-1.0.3/limorhyde/MD5 | 20 limorhyde-1.0.3/limorhyde/NEWS.md | 6 limorhyde-1.0.3/limorhyde/build/vignette.rds |binary limorhyde-1.0.3/limorhyde/inst/doc/introduction.R | 13 limorhyde-1.0.3/limorhyde/inst/doc/introduction.Rmd | 7 limorhyde-1.0.3/limorhyde/inst/doc/introduction.html | 511 +++++----- limorhyde-1.0.3/limorhyde/inst/extdata/GSE34018_expression_data.rds |only limorhyde-1.0.3/limorhyde/inst/extdata/GSE34018_metadata.rds |only limorhyde-1.0.3/limorhyde/vignettes/introduction.Rmd | 7 13 files changed, 306 insertions(+), 272 deletions(-)
Title: Epidemiology Data Dictionaries and Random Data Generators
Description: The 'R4EPIs' project <https://r4epi.github.io/sitrep/> seeks
to provide a set of standardized tools for analysis of outbreak and
survey data in humanitarian aid settings. This package currently
provides standardized data dictionaries from Medecins Sans Frontieres
Operational Centre Amsterdam for outbreak scenarios (Acute Jaundice
Syndrome, Cholera, Diphtheria, Measles, Meningitis) and surveys
(Retrospective mortality and access to care, Malnutrition, Vaccination
coverage and Event Based Surveillance) - as described in the following
<https://scienceportal.msf.org/assets/standardised-mortality-surveys?utm_source=chatgpt.com>.
In addition, a data generator from these dictionaries is provided. It
is also possible to read in any Open Data Kit format data dictionary.
Author: Alexander Spina [aut, cre] ,
Zhian N. Kamvar [aut] ,
Lukas Richter [aut],
Patrick Keating [aut],
Annick Lenglet [ctb],
Applied Epi Incorporated [cph],
Medecins Sans Frontieres Operational Centre Amsterdam [fnd]
Maintainer: Alexander Spina <aspina@appliedepi.org>
Diff between epidict versions 0.2.0 dated 2026-01-11 and 0.3.0 dated 2026-01-20
DESCRIPTION | 6 MD5 | 76 NAMESPACE | 62 NEWS.md | 59 R/dict_rename_helper.R | 182 R/epidict-package.R | 26 R/gen_data.R | 160 R/gen_msf_data.R | 2126 +-- R/msf_dict.R | 195 R/msf_dict_rename_helper.R | 132 R/read_dict.R | 423 R/template_data_frame.R | 182 R/utils-generators.R | 1032 - R/utils.R | 286 README.md | 530 build/vignette.rds |binary inst/doc/Outbreaks.R | 194 inst/doc/Outbreaks.Rmd | 482 inst/doc/Outbreaks.html | 5962 +++++------ inst/doc/Surveys.R | 94 inst/doc/Surveys.Rmd | 238 inst/doc/Surveys.html | 5732 +++++----- inst/doc/intro.R | 86 inst/doc/intro.Rmd | 38 inst/doc/intro.html | 1153 +- inst/extdata/MSF-outbreak-intersectional-dict.xlsx |binary inst/extdata/coords.csv |11378 ++++++++++----------- man/dict_rename_helper.Rd | 76 man/epidict-package.Rd | 74 man/gen_data.Rd | 126 man/msf_dict.Rd | 153 man/read_dict.Rd | 89 man/rmdhunks/introduction.Rmd | 230 tests/testthat.R | 8 tests/testthat/test-gen_data.R | 312 tests/testthat/test-rename_helper.R | 936 - vignettes/Outbreaks.Rmd | 482 vignettes/Surveys.Rmd | 238 vignettes/intro.Rmd | 38 39 files changed, 16815 insertions(+), 16781 deletions(-)
Title: Visualisations for Model Ensembles
Description: Displays for model fits of multiple models and their ensembles. For classification models, the plots are heatmaps, for regression, scatterplots.
Author: Katarina Domijan [aut, cre]
Maintainer: Katarina Domijan <domijank@tcd.ie>
This is a re-admission after prior archival of version 0.1.0 dated 2022-07-21
Diff between ensModelVis versions 0.1.0 dated 2022-07-21 and 0.2.0 dated 2026-01-20
DESCRIPTION | 14 MD5 | 34 - NAMESPACE | 1 R/plot_ensemble.R | 117 +++--- README.md | 8 build/vignette.rds |binary inst/doc/ClassificationEg.R | 147 ++++---- inst/doc/ClassificationEg.Rmd | 159 ++++---- inst/doc/ClassificationEg.html | 709 ++++++++++++++++++++------------------- inst/doc/RegressionEg.R | 49 +- inst/doc/RegressionEg.Rmd | 45 +- inst/doc/RegressionEg.html | 348 +++++++++---------- man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/figures/README-example-3.png |binary man/plot_ensemble.Rd | 2 vignettes/ClassificationEg.Rmd | 159 ++++---- vignettes/RegressionEg.Rmd | 45 +- 18 files changed, 946 insertions(+), 891 deletions(-)
Title: Dependency Coefficients
Description: Functions to compute coefficients measuring the dependence of two or more than two variables. The functions can be deployed to gain information about functional dependencies of the variables with emphasis on monotone functions. The statistics describe how well one response variable can be approximated by a monotone function of other variables. In regression analysis the variable selection is an important issue. In this framework the functions could be useful tools in modeling the regression function. Detailed explanations on the subject can be found in papers Liebscher (2014) <doi:10.2478/demo-2014-0004>; Liebscher (2017) <doi:10.1515/demo-2017-0012>; Liebscher (2021): <https://arfjournals.com/image/catalog/Journals%20Papers/AJSS/No%202%20(2021)/4-AJSS_123-150.pdf>; Liebscher (2021): Kendall regression coefficient. Computational Statistics and Data Analysis 157. 107140.
Author: Eckhard Liebscher [aut, cre]
Maintainer: Eckhard Liebscher <eckhard.liebscher@hs-merseburg.de>
This is a re-admission after prior archival of version 0.0.1 dated 2020-01-23
Diff between depcoeff versions 0.0.1 dated 2020-01-23 and 0.1.1 dated 2026-01-20
depcoeff-0.0.1/depcoeff/src/Makevars |only depcoeff-0.0.1/depcoeff/src/Makevars.win |only depcoeff-0.1.1/depcoeff/DESCRIPTION | 23 ++++++++----- depcoeff-0.1.1/depcoeff/MD5 | 23 +++++++------ depcoeff-0.1.1/depcoeff/R/RcppExports.R | 48 ++++++++++++++-------------- depcoeff-0.1.1/depcoeff/R/packdepcoeff.R | 32 +++++++----------- depcoeff-0.1.1/depcoeff/inst |only depcoeff-0.1.1/depcoeff/man/kendr.Rd | 2 - depcoeff-0.1.1/depcoeff/man/kendrs.Rd | 2 - depcoeff-0.1.1/depcoeff/man/spearr.Rd | 2 - depcoeff-0.1.1/depcoeff/man/spearrs.Rd | 2 - depcoeff-0.1.1/depcoeff/src/RcppExports.cpp | 5 ++ depcoeff-0.1.1/depcoeff/src/coeffpm.cpp | 36 ++++++++++----------- depcoeff-0.1.1/depcoeff/tests |only 14 files changed, 89 insertions(+), 86 deletions(-)
Title: Convert 'R Markdown' and 'Quarto' Documents to Ecological
Metadata Language
Description: Ecological Metadata Language or 'EML' is a long-established format
for describing ecological datasets to facilitate sharing and re-use. Because
'EML' is effectively a modified 'xml' schema, however, it is challenging to
write and manipulate for non-expert users. 'delma' supports users to write
metadata statements in 'R Markdown' or 'Quarto markdown' format, and parse
them to 'EML' and (optionally) back again.
Author: Martin Westgate [aut, cre],
Shandiya Balasubramaniam [aut],
Dax Kellie [aut]
Maintainer: Martin Westgate <martin.westgate@csiro.au>
This is a re-admission after prior archival of version 0.1.1 dated 2025-05-14
Diff between delma versions 0.1.1 dated 2025-05-14 and 0.1.2 dated 2026-01-20
DESCRIPTION | 8 +- MD5 | 32 ++++----- NEWS.md | 4 + R/check_metadata.R | 22 +++++- R/parse_lp_to_tibble.R | 76 ++++++++++++++++++++++- R/parse_tibble_to_list.R | 101 ++++++++++++++++++++++++------- build/vignette.rds |binary inst/doc/quick_start_guide.Rmd | 2 inst/doc/quick_start_guide.html | 7 +- inst/extdata/metadata_example.Rmd | 67 ++++++++++++-------- man/figures/logo.png |binary tests/testthat/test-as_eml_list.R | 46 +++++++++++--- tests/testthat/test-as_eml_xml.R | 19 +++-- tests/testthat/test-as_lp_tbl.R | 26 +++++++ tests/testthat/test-metadata-functions.R | 28 +++++--- tests/testthat/test-xml_roundtripping.R | 2 vignettes/quick_start_guide.Rmd | 2 17 files changed, 340 insertions(+), 102 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-03-15 1.0
Title: Geometrical Functionality of the 'spatstat' Family
Description: Defines spatial data types and supports geometrical operations
on them. Data types include point patterns, windows (domains),
pixel images, line segment patterns, tessellations and hyperframes.
Capabilities include creation and manipulation of data
(using command line or graphical interaction),
plotting, geometrical operations (rotation, shift, rescale,
affine transformation), convex hull, discretisation and
pixellation, Dirichlet tessellation, Delaunay triangulation,
pairwise distances, nearest-neighbour distances,
distance transform, morphological operations
(erosion, dilation, closing, opening), quadrat counting,
geometrical measurement, geometrical covariance,
colour maps, calculus on spatial domains,
Gaussian blur, level sets of images, transects of images,
intersections between objects, minimum distance matching.
(Excludes spatial data on a network, which are supported by
the package 'spatstat.linnet'.)
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Warick Brown [ctb],
Tilman Davies [ctb],
Ute Hahn [ctb],
Martin Hazelton [ctb],
Abdollah Jalilian [ctb],
Greg McSwiggan [ctb, cph],
Sebastian Meyer [ctb, cph],
Jens Oeh [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.geom versions 3.6-1 dated 2025-11-20 and 3.7-0 dated 2026-01-20
DESCRIPTION | 20 +- MD5 | 111 ++++++++-------- NAMESPACE | 16 ++ NEWS | 123 +++++++++++++++++ R/classes.R | 18 +- R/colourtables.R | 86 +++++++++++- R/connected.R | 94 +++++++++---- R/distfun.R | 178 +++++++++++++++++++++++++ R/distmap.R | 13 + R/dummy.R | 4 R/funxy.R | 30 ++-- R/is.subset.owin.R | 5 R/levelset.R | 29 ++-- R/morphology.R | 8 - R/options.R | 14 -- R/persp.im.R | 59 +++++++- R/persp.ppp.R | 50 +++++-- R/plot.anylist.R | 290 +++++++++++++++++++++++++++++------------- R/plot.im.R | 17 ++ R/plot.ppp.R | 44 +++++- R/plot.psp.R | 45 +----- R/pointweights.R | 40 ++++- R/quadclass.R | 4 R/randomseg.R | 2 R/symbolmap.R | 21 ++- R/tess.R | 94 +++++++++---- R/tessfun.R | 29 ++++ R/unique.ppp.R | 27 ++- R/weights.R | 6 R/xypolycomponents.R | 6 inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/connected.Rd | 15 +- man/default.colourmap.Rd |only man/default.symbolmap.ppp.Rd | 72 ++++++++-- man/distfun.Rd | 9 + man/distmap.owin.Rd | 26 ++- man/levelset.Rd | 8 + man/levelset.distfun.Rd |only man/methods.funxy.Rd | 5 man/persp.im.Rd | 38 ++++- man/persp.ppp.Rd | 44 +++++- man/plot.anylist.Rd | 4 man/plot.colourmap.Rd | 10 + man/plot.im.Rd | 16 +- man/plot.listof.Rd | 4 man/plot.ppp.Rd | 27 +++ man/plot.psp.Rd | 26 +++ man/plot.solist.Rd | 4 man/plot.symbolmap.Rd | 11 + man/spatstat.geom-internal.Rd | 16 +- man/spatstat.geom-package.Rd | 2 man/tile.centroids.Rd |only man/tileindex.Rd | 29 +++- tests/testsGtoJ.R | 9 + tests/testsQ.R | 4 tests/testsS.R | 61 ++++++++ tests/testsT.R | 9 + 58 files changed, 1501 insertions(+), 433 deletions(-)
Title: Low-Level R to Java Interface
Description: Low-level interface to Java VM very much like .C/.Call and friends. Allows creation of objects, calling methods and accessing fields.
Author: Simon Urbanek [aut, cre, cph]
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between rJava versions 1.0-11 dated 2024-01-26 and 1.0-14 dated 2026-01-20
DESCRIPTION | 12 ++++--- MD5 | 20 ++++++------ NEWS | 20 ++++++++++++ R/jfirst.R | 4 -- R/jinit.R | 17 ++++++++++ inst/jri/JRIEngine.jar |binary inst/jri/REngine.jar |binary man/jinit.Rd | 17 ++++++---- src/Rglue.c | 78 ++++++++++++++++++++----------------------------- src/rJava.c | 25 ++++++++------- src/rJava.h | 39 +++++++++++++++++++++++- 11 files changed, 148 insertions(+), 84 deletions(-)
Title: Contour-Enhanced Forest Plots for Meta-Analysis
Description: Provides functions to create contour-enhanced forest plots for meta-analysis,
supporting binary outcomes (e.g., odds ratios, risk ratios), continuous outcomes (e.g., correlations),
and prevalence estimates. Includes options for prediction intervals, customized colors, study labeling,
and contour shading to highlight regions of statistical significance. Based on 'metafor' and 'ggplot2'.
Author: Umar Hussain [aut, cre],
Muhammad Abdullah Kamran [aut],
Fayez Hussain Niazi [aut]
Maintainer: Umar Hussain <drumarhussain@gmail.com>
Diff between contourforest versions 0.1.0 dated 2025-12-22 and 0.2.0 dated 2026-01-20
DESCRIPTION | 24 ++++++++++++++++-------- LICENSE | 4 ++-- MD5 | 12 ++++++++---- NAMESPACE | 3 +++ R/correlation.R |only R/prevalence.R |only R/zzz.R | 6 +++++- man/forest_corr.Rd |only man/forest_prev.Rd |only 9 files changed, 34 insertions(+), 15 deletions(-)
Title: Tools for Causal Discovery on Observational Data
Description: Various tools for inferring causal models from observational data. The package
includes an implementation of the temporal Peter-Clark (TPC) algorithm. Petersen, Osler
and Ekstrøm (2021) <doi:10.1093/aje/kwab087>. It also includes general tools
for evaluating differences in adjacency matrices, which can be used for evaluating
performance of causal discovery procedures.
Author: Anne Helby Petersen [aut],
Tobias Ellegaard Larsen [ctb],
Claus Thorn Ekstroem [ctb],
Bjarke Hautop Kristensen [ctb, cre]
Maintainer: Bjarke Hautop Kristensen <bjarke.kristensen@sund.ku.dk>
Diff between causalDisco versions 0.9.1 dated 2022-05-12 and 0.9.5 dated 2026-01-20
DESCRIPTION | 58 ++- MD5 | 145 ++++---- NAMESPACE | 156 +++++---- NEWS.md | 32 + R/amat.R |only R/causalDisco-package.R | 40 +- R/compare.R | 126 +++---- R/confusion.R | 408 +++++++++++++++-------- R/corTest.R | 38 +- R/edges.R | 82 ++-- R/evaluate.R | 246 +++++++------- R/fci.R |only R/gausCorScore.R | 122 +++---- R/maketikz.R | 496 ++++++++++++++++------------ R/metrics.R | 376 ++++++++++----------- R/misc.R | 313 ++++++++++-------- R/nDAGs.R | 40 +- R/pc.R |only R/plot.R | 187 ++++++++-- R/plotTempoMech.R | 510 ++++++++++++++++------------- R/probmat2amat.R | 272 +++++++-------- R/regTest.R | 239 +++++++------ R/simDAG.R | 88 ++--- R/simGausFromDAG.R | 124 +++---- R/tamat.R | 65 ++- R/tfci.R |only R/tges.R |only R/tpc.R | 724 ++++++++++++++++++++++-------------------- R/tplot.R |only man/F1.Rd | 38 +- man/FDR.Rd | 38 +- man/FOR.Rd | 38 +- man/G1.Rd | 48 +- man/NPV.Rd | 38 +- man/TemporalBDeu-class.Rd |only man/TemporalBIC-class.Rd |only man/adj_confusion.Rd | 111 ++++-- man/amat.Rd |only man/as.graphNEL.Rd | 34 - man/average_degree.Rd | 36 +- man/compare.Rd | 54 +-- man/confusion.Rd | 117 ++++-- man/corTest.Rd | 50 +- man/dir_confusion.Rd | 111 ++++-- man/dir_confusion_original.Rd |only man/edges.Rd | 36 +- man/essgraph2amat.Rd | 40 +- man/evaluate.Rd | 104 +++--- man/evaluate.array.Rd | 104 +++--- man/evaluate.matrix.Rd | 110 +++--- man/evaluate.tamat.Rd | 104 +++--- man/fci.Rd |only man/gausCorScore.Rd | 83 ++-- man/getvar.character.Rd |only man/getvar.data.frame.Rd |only man/graph2amat.Rd | 52 ++- man/is_cpdag.Rd | 42 +- man/is_pdag.Rd | 42 +- man/maketikz.Rd | 172 +++++---- man/maxnedges.Rd | 36 +- man/nDAGs.Rd | 36 +- man/nedges.Rd | 34 - man/pc.Rd |only man/plot.pag.Rd |only man/plot.tamat.Rd | 40 +- man/plot.tpag.Rd |only man/plot.tpdag.Rd | 40 +- man/plot.tskeleton.Rd | 40 +- man/plotTempoMech.Rd | 80 ++-- man/precision.Rd | 40 +- man/probmat2amat.Rd | 142 ++++---- man/recall.Rd | 38 +- man/regTest.Rd | 74 ++-- man/shd.Rd | 50 +- man/simDAG.Rd | 68 +-- man/simGausFromDAG.Rd | 107 +++--- man/specificity.Rd | 38 +- man/tamat.Rd | 60 ++- man/tfci.Rd |only man/tges.Rd |only man/tpc.Rd | 230 +++++++------ man/tpcExample.Rd | 66 +-- man/tplot.Rd |only 83 files changed, 4285 insertions(+), 3423 deletions(-)
Title: Build a Docker Image from a Directory or Project
Description: Simple utilities to generate a Dockerfile from a directory or
project, build the corresponding Docker image, push the image to
DockerHub, and publicly share the project via Binder.
Author: Daniel Molitor [aut, cph, cre]
Maintainer: Daniel Molitor <molitdj97@gmail.com>
Diff between tugboat versions 0.1.5 dated 2025-11-10 and 0.1.6 dated 2026-01-20
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 10 ++++++++++ R/binderize.R | 10 ++++++---- README.md | 24 ++++++++++++------------ man/binderize.Rd | 5 ++++- 6 files changed, 40 insertions(+), 25 deletions(-)
Title: Code Storage and Execution Class for 'teal' Applications
Description: Introduction of 'qenv' S4 class, that facilitates code
execution and reproducibility in 'teal' applications.
Author: Dawid Kaledkowski [aut, cre],
Aleksander Chlebowski [aut],
Marcin Kosinski [aut],
Pawel Rucki [aut],
Nikolas Burkoff [aut],
Mahmoud Hallal [aut],
Maciej Nasinski [aut],
Konrad Pagacz [aut],
Junlue Zhao [aut],
Chendi Liao [rev],
Dony Unardi [rev],
F. [...truncated...]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.code versions 0.7.0 dated 2025-08-18 and 0.7.1 dated 2026-01-20
DESCRIPTION | 10 MD5 | 143 - NAMESPACE | 56 NEWS.md | 6 R/qenv-c.R | 212 +- R/qenv-class.R | 130 - R/qenv-concat.R | 98 - R/qenv-constructor.R | 78 R/qenv-errors.R | 20 R/qenv-eval_code.R | 226 +- R/qenv-extract.R | 106 - R/qenv-get_code.R | 274 +-- R/qenv-get_env.R | 54 R/qenv-get_messages.r | 80 R/qenv-get_outputs.R | 62 R/qenv-get_var.R | 80 R/qenv-get_warnings.R | 80 R/qenv-join.R | 26 R/qenv-length.R | 10 R/qenv-show.R | 102 - R/qenv-within.R | 138 - R/teal.code-package.R | 22 R/utils-get_code_dependency.R | 1192 +++++++------- R/utils.R | 200 +- README.md | 230 +- build/vignette.rds |binary inst/WORDLIST | 9 inst/doc/qenv.R | 254 +-- inst/doc/qenv.Rmd | 410 ++--- inst/doc/qenv.html | 1242 +++++++-------- inst/doc/teal-code.Rmd | 40 inst/doc/teal-code.html | 558 +++--- inst/pkgdown/_pkgdown.yml | 20 inst/pkgdown/templates/footer.html | 6 man/concat.Rd | 74 man/dev_suppress.Rd | 56 man/dot-check_joinable.Rd | 42 man/eval_code.Rd | 82 - man/get_code.Rd | 226 +- man/get_code_dependency.Rd | 74 man/get_env.Rd | 56 man/get_messages.Rd | 60 man/get_outputs.Rd | 66 man/get_var.Rd | 46 man/get_warn_message_util.Rd | 40 man/get_warnings.Rd | 60 man/join.Rd | 66 man/lang2calls.Rd | 56 man/qenv-class.Rd | 66 man/qenv.Rd | 86 - man/show-qenv-method.Rd | 48 man/subset-qenv.Rd | 54 man/teal.code-package.Rd | 90 - man/within.qenv.Rd | 129 - tests/testthat.R | 6 tests/testthat/Rplots.pdf |only tests/testthat/setup-options.R | 40 tests/testthat/test-get_outputs.R | 228 +- tests/testthat/test-qenv-class.R | 40 tests/testthat/test-qenv_concat.R | 186 +- tests/testthat/test-qenv_constructor.R | 134 - tests/testthat/test-qenv_eval_code.R | 358 ++-- tests/testthat/test-qenv_extract.R | 186 +- tests/testthat/test-qenv_get_code.R | 1951 ++++++++++++------------ tests/testthat/test-qenv_get_messages.R | 152 - tests/testthat/test-qenv_get_var.R | 96 - tests/testthat/test-qenv_get_warnings.R | 152 - tests/testthat/test-qenv_join.R | 346 ++-- tests/testthat/test-qenv_within.R | 312 +-- tests/testthat/test-utils-get_code_dependency.R | 335 +++- tests/testthat/test-utils.R | 122 - vignettes/qenv.Rmd | 410 ++--- vignettes/teal-code.Rmd | 40 73 files changed, 6536 insertions(+), 6209 deletions(-)
Title: Sample Selection Models
Description: Two-step
and maximum likelihood estimation
of Heckman-type sample selection models:
standard sample selection models (Tobit-2),
endogenous switching regression models (Tobit-5),
sample selection models with binary dependent outcome variable,
interval regression with sample selection (only ML estimation),
and endogenous treatment effects models.
These methods are described in the three vignettes
that are included in this package
and in econometric textbooks such as
Greene (2011, Econometric Analysis, 7th edition, Pearson).
Author: Arne Henningsen [aut, cre],
Ott Toomet [aut],
Sebastian Petersen [ctb]
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>
Diff between sampleSelection versions 1.2-12 dated 2020-12-15 and 1.2-14 dated 2026-01-20
DESCRIPTION | 10 ++--- MD5 | 66 ++++++++++++++++----------------- NEWS | 11 +++++ R/heckit2fit.R | 6 +-- R/heckit5fit.R | 2 - R/heckitTfit.R | 2 - R/summary.selection.R | 2 - build/vignette.rds |binary inst/CITATION | 7 ++- inst/doc/intReg.pdf |binary inst/doc/selection.Rnw | 10 ++--- inst/doc/selection.bib | 18 ++++----- inst/doc/selection.pdf |binary inst/doc/treatReg.pdf |binary man/RandHIE.Rd | 2 - man/binaryChoice.Rd | 12 +++--- man/nlswork.Rd | 2 - tests/Mroz87SelectionTest.R | 2 - tests/Mroz87SelectionTest.Rout.save | 18 ++------- tests/binarySelectionOutcome.R | 2 - tests/binarySelectionOutcome.Rout.save | 10 ++--- tests/fail.Rout.save | 8 ++-- tests/heckitIvTest.R | 2 - tests/heckitIvTest.Rout.save | 10 ++--- tests/intervalTest.R | 2 - tests/intervalTest.Rout.save | 10 ++--- tests/invMillsRatioTest.R | 4 +- tests/invMillsRatioTest.Rout.save | 23 +++-------- tests/probit.R | 2 - tests/probit.Rout.save | 18 ++------- tests/selection.R | 4 +- tests/selection.Rout.save | 20 +++------- vignettes/selection.Rnw | 10 ++--- vignettes/selection.bib | 18 ++++----- 34 files changed, 145 insertions(+), 168 deletions(-)
More information about sampleSelection at CRAN
Permanent link
Title: A Library for using 'Pathling'
Description: R API for 'Pathling', a tool for querying and transforming electronic health record data that is represented using the 'Fast Healthcare Interoperability Resources' (FHIR) standard - see <https://pathling.csiro.au/docs>.
Author: Australian e-Health Research Centre, CSIRO [cph, cre],
Piotr Szul [aut],
John Grimes [aut]
Maintainer: "Australian e-Health Research Centre, CSIRO" <pathling@csiro.au>
Diff between pathling versions 9.0.0 dated 2025-10-28 and 9.2.0 dated 2026-01-20
DESCRIPTION | 10 - MD5 | 82 ++++---- R/context.R | 212 +++++++++++---------- R/data.R | 1 R/datasource.R | 387 ++++++++++++++++++++++----------------- R/dependencies.R | 8 R/encoding.R | 40 ++-- R/etc.R | 83 ++++---- R/fhir.R | 8 R/functions.R | 109 +++++----- R/udfs.R | 245 +++++++++++++----------- R/view.R | 70 +++---- man/ds_read.Rd | 10 - man/ds_view.Rd | 62 +++--- man/ds_write_delta.Rd | 9 man/ds_write_ndjson.Rd | 11 - man/ds_write_parquet.Rd | 7 man/ds_write_tables.Rd | 7 man/pathling_connect.Rd | 13 + man/pathling_encode.Rd | 9 man/pathling_encode_bundle.Rd | 13 - man/pathling_example_resource.Rd | 4 man/pathling_examples.Rd | 2 man/pathling_install_spark.Rd | 2 man/pathling_read_bulk.Rd | 8 man/pathling_read_bundles.Rd | 10 - man/pathling_read_datasets.Rd | 8 man/pathling_read_delta.Rd | 6 man/pathling_read_ndjson.Rd | 10 - man/pathling_read_parquet.Rd | 8 man/pathling_read_tables.Rd | 6 man/tx_designation.Rd | 20 +- man/tx_display.Rd | 12 - man/tx_member_of.Rd | 2 man/tx_property_of.Rd | 15 - man/tx_subsumed_by.Rd | 18 + man/tx_subsumes.Rd | 16 + man/tx_to_coding.Rd | 8 man/tx_to_ecl_value_set.Rd | 4 man/tx_to_loinc_coding.Rd | 8 man/tx_to_snomed_coding.Rd | 8 man/tx_translate.Rd | 16 + 42 files changed, 875 insertions(+), 712 deletions(-)
Title: Maxwell Boltzmann Bose Einstein Fermi Dirac Distribution and
Destruction Rate Modelling
Description: Distributions that are typically used for exposure rating in
general insurance, in particular to price reinsurance contracts.
The vignette shows code snippets to fit the distribution to
empirical data. See, e.g., Bernegger (1997) <doi:10.2143/AST.27.1.563208>
freely available on-line.
Author: Christophe Dutang [aut, cre] ,
Giorgio Spedicato [aut] ,
Markus Gesmann [ctb]
Maintainer: Christophe Dutang <dutangc@gmail.com>
Diff between mbbefd versions 0.8.13 dated 2024-12-18 and 0.8.14 dated 2026-01-20
mbbefd-0.8.13/mbbefd/inst/NEWS.Rd |only mbbefd-0.8.13/mbbefd/inst/doc/Introduction_to_mbbefd.R |only mbbefd-0.8.13/mbbefd/inst/doc/Introduction_to_mbbefd.Rmd |only mbbefd-0.8.13/mbbefd/inst/doc/Introduction_to_mbbefd.pdf |only mbbefd-0.8.13/mbbefd/tests/test-fit-mbbefd.R |only mbbefd-0.8.13/mbbefd/vignettes/Introduction_to_mbbefd.Rmd |only mbbefd-0.8.14/mbbefd/DESCRIPTION | 14 mbbefd-0.8.14/mbbefd/MD5 | 42 - mbbefd-0.8.14/mbbefd/NAMESPACE | 2 mbbefd-0.8.14/mbbefd/R/distr-mbbefdCpp.R | 38 - mbbefd-0.8.14/mbbefd/R/distr-mbbefdR-1stparam.R | 458 +++++++----- mbbefd-0.8.14/mbbefd/R/distr-mbbefdR-2ndparam.R | 441 ++++++++--- mbbefd-0.8.14/mbbefd/R/util-gendilogintegral.R | 42 - mbbefd-0.8.14/mbbefd/README.md | 2 mbbefd-0.8.14/mbbefd/build/partial.rdb |binary mbbefd-0.8.14/mbbefd/build/vignette.rds |binary mbbefd-0.8.14/mbbefd/inst/CITATION | 4 mbbefd-0.8.14/mbbefd/inst/NEWS.md |only mbbefd-0.8.14/mbbefd/inst/doc/Introduction.R |only mbbefd-0.8.14/mbbefd/inst/doc/Introduction.Rmd |only mbbefd-0.8.14/mbbefd/inst/doc/Introduction.pdf |only mbbefd-0.8.14/mbbefd/man/mbbefd-package.Rd | 3 mbbefd-0.8.14/mbbefd/src/mbbefdRcppCode.cpp | 39 - mbbefd-0.8.14/mbbefd/tests/test-fit-MBBEFDgb.R | 6 mbbefd-0.8.14/mbbefd/tests/test-fit-mbbefdab.R |only mbbefd-0.8.14/mbbefd/tests/testthat/testsDistr.R | 4 mbbefd-0.8.14/mbbefd/vignettes/Introduction.Rmd |only mbbefd-0.8.14/mbbefd/vignettes/mbbefd.bib | 529 +++++++------- 28 files changed, 1007 insertions(+), 617 deletions(-)
Title: Meteorological Data Processing
Description: Set of tools aimed at processing meteorological data, converting hourly recorded data to daily, monthly and annual data.
Author: Wagner Martins dos Santos [aut, cre] ,
Hoi Leong Lee [aut],
Edimir Xavier Leal Ferraz [aut] ,
Abelardo Antonio de Assuncao Montenegro [aut],
Lady Daiane Costa de Sousa Martins [aut] ,
Alan Cezar Bezerra [aut],
Ênio Farias de Franca e Silva [aut],
Thi [...truncated...]
Maintainer: Wagner Martins dos Santos <wagnnerms97@gmail.com>
This is a re-admission after prior archival of version 1.0.7 dated 2025-10-30
Diff between DataMetProcess versions 1.0.7 dated 2025-10-30 and 1.0.8 dated 2026-01-20
DESCRIPTION | 6 MD5 | 18 - R/calculateETrefPM.R | 329 +++++++++++++--------------------- R/list_inmet.R | 20 +- inst/doc/DataMetProcess-vignette.html | 54 ++--- man/DMPshiny.Rd | 78 ++++---- man/adjustDate.Rd | 104 +++++----- man/calculateDMY.Rd | 176 +++++++++--------- man/calculateETrefPM.Rd | 175 ++++++------------ man/list_inmet.Rd | 74 +++---- 10 files changed, 464 insertions(+), 570 deletions(-)
More information about DataMetProcess at CRAN
Permanent link
Title: Datasets and Supplemental Functions from Bayes Rules! Book
Description: Provides datasets and functions used for analysis
and visualizations in the Bayes Rules! book (<https://www.bayesrulesbook.com>).
The package contains a set of functions that summarize and plot Bayesian models from some conjugate families
and another set of functions for evaluation of some Bayesian models.
Author: Mine Dogucu [aut, cre] ,
Alicia Johnson [aut],
Miles Ott [aut]
Maintainer: Mine Dogucu <mdogucu@gmail.com>
Diff between bayesrules versions 0.0.2 dated 2021-09-25 and 0.0.3 dated 2026-01-20
DESCRIPTION | 12 MD5 | 28 - NEWS.md | 14 R/data_cherry_blossom_sample.R | 2 R/data_pulse_of_the_nation.R | 2 README.md | 1 build/vignette.rds |binary inst/doc/conjugate-families.R | 2 inst/doc/conjugate-families.html | 426 ++++++++++++++++++++++------- inst/doc/model-evaluation.R | 8 inst/doc/model-evaluation.Rmd | 6 inst/doc/model-evaluation.html | 561 +++++++++++++++++++++++++++------------ man/cherry_blossom_sample.Rd | 2 man/pulse_of_the_nation.Rd | 2 vignettes/model-evaluation.Rmd | 6 15 files changed, 778 insertions(+), 294 deletions(-)
Title: Efficient Serialization of R Objects
Description: Streamlines and accelerates the process of saving and loading R objects, improving speed and compression compared to other methods. The package provides two compression formats: the 'qs2' format, which uses R serialization via the C API while optimizing compression and disk I/O, and the 'qdata' format, featuring custom serialization for slightly faster performance and better compression. Additionally, the 'qs2' format can be directly converted to the standard 'RDS' format, ensuring long-term compatibility with future versions of R.
Author: Travers Ching [aut, cre, cph],
Yann Collet [ctb, cph] ,
Facebook, Inc. [cph] ,
Reichardt Tino [ctb, cph] ,
Skibinski Przemyslaw [ctb, cph] ,
Mori Yuta [ctb, cph] ,
Francesc Alted [ctb, cph]
Maintainer: Travers Ching <traversc@gmail.com>
Diff between qs2 versions 0.1.6 dated 2025-11-21 and 0.1.7 dated 2026-01-20
qs2-0.1.6/qs2/man/zstd_compress_file.Rd |only qs2-0.1.6/qs2/man/zstd_decompress_file.Rd |only qs2-0.1.7/qs2/ChangeLog | 6 qs2-0.1.7/qs2/DESCRIPTION | 10 qs2-0.1.7/qs2/MD5 | 32 qs2-0.1.7/qs2/NAMESPACE | 3 qs2-0.1.7/qs2/R/zstd_file_functions.R | 115 +- qs2-0.1.7/qs2/README.md | 137 +- qs2-0.1.7/qs2/configure | 1646 +++++++++++++++++++----------- qs2-0.1.7/qs2/configure.ac | 66 - qs2-0.1.7/qs2/inst/doc/vignette.R | 30 qs2-0.1.7/qs2/inst/doc/vignette.html | 140 +- qs2-0.1.7/qs2/inst/doc/vignette.rmd | 60 - qs2-0.1.7/qs2/man/zstd_file_functions.Rd |only qs2-0.1.7/qs2/man/zstd_in_out.Rd |only qs2-0.1.7/qs2/src/Makevars.in | 6 qs2-0.1.7/qs2/src/qd_deserializer.h | 73 + qs2-0.1.7/qs2/src/qd_serializer.h | 34 qs2-0.1.7/qs2/vignettes/vignette.rmd | 60 - 19 files changed, 1669 insertions(+), 749 deletions(-)
Title: Maximum Likelihood Estimates of Gaussian Processes
Description: Maximum likelihood Gaussian process modeling for
univariate and multi-dimensional outputs with diagnostic plots
following Santner et al (2003) <doi:10.1007/978-1-4757-3799-8>.
Contact the maintainer for a package version that includes
sensitivity analysis.
Author: Garrett M. Dancik [aut, cre]
Maintainer: Garrett M. Dancik <dancikg@easternct.edu>
Diff between mlegp versions 3.1.9 dated 2022-03-10 and 3.1.10 dated 2026-01-20
CHANGES | 3 +++ DESCRIPTION | 16 ++++++++++------ MD5 | 15 ++++++++------- build |only inst/CITATION | 2 +- inst/doc/mlegp.Rnw | 8 ++++---- inst/doc/mlegp.pdf |binary man/gp.list.Rd | 2 +- vignettes/mlegp.Rnw | 8 ++++---- 9 files changed, 31 insertions(+), 23 deletions(-)
Title: Miscellaneous Tools and Utilities
Description: Miscellaneous small tools and utilities.
Many of them facilitate the work with matrices,
e.g. inserting rows or columns, creating symmetric matrices,
or checking for semidefiniteness.
Other tools facilitate the work with regression models,
e.g. extracting the standard errors,
obtaining the number of (estimated) parameters,
or calculating R-squared values.
Author: Arne Henningsen [aut, cre],
Ott Toomet [aut]
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>
Diff between miscTools versions 0.6-28 dated 2023-05-03 and 0.6-30 dated 2026-01-20
DESCRIPTION | 15 ++++++++++----- MD5 | 6 +++--- NEWS | 5 +++++ man/sumKeepAttr.Rd | 4 ++-- 4 files changed, 20 insertions(+), 10 deletions(-)
Title: Estimation and Testing for a Lognormal-Pareto Mixture
Description: Estimates a lognormal-Pareto mixture by means of the Expectation-Conditional-Maximization-Either algorithm and by maximizing the profile likelihood function. A likelihood ratio test for discriminating between lognormal and Pareto tail is also implemented. See Bee, M. (2022) <doi:10.1007/s11634-022-00497-4>.
Author: Marco Bee [aut, cre]
Maintainer: Marco Bee <marco.bee@unitn.it>
Diff between LNPar versions 1.1.2 dated 2025-08-26 and 1.1.3 dated 2026-01-20
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/LPfitEM.R | 7 +------ R/LPfitProf.R | 9 +-------- R/ParallelTest.R | 7 +------ R/ParallelTestEM.R | 7 +------ R/ProfBoot.R | 4 ++-- build/partial.rdb |binary man/ProfBoot.Rd | 4 ++-- 9 files changed, 20 insertions(+), 42 deletions(-)
Title: Estimation of Dynamic Mixtures
Description: Estimation of a dynamic lognormal - Generalized Pareto mixture via the Approximate Maximum Likelihood and the Cross-Entropy methods. See Bee, M. (2023) <doi:10.1016/j.csda.2023.107764>.
Author: Marco Bee [aut, cre]
Maintainer: Marco Bee <marco.bee@unitn.it>
Diff between FitDynMix versions 1.0.1 dated 2025-05-20 and 1.0.2 dated 2026-01-20
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/AMLEfit.R | 7 +------ R/CENoisyFit.R | 4 ++-- R/CENoisyFitBoot.R | 9 ++------- R/MLEfit.R | 7 +------ build/partial.rdb |binary man/CENoisyFit.Rd | 4 ++-- man/CENoisyFitBoot.Rd | 2 +- 9 files changed, 21 insertions(+), 36 deletions(-)
Title: Discrete Global Grids
Description: Spatial analyses involving binning require that every bin have the same area, but this is impossible using a rectangular grid laid over the Earth or over any projection of the Earth. Discrete global grids use hexagons, triangles, and diamonds to overcome this issue, overlaying the Earth with equally-sized bins. This package provides utilities for working with discrete global grids, along with utilities to aid in plotting such data.
Author: Richard Barnes [aut],
Kevin Sahr [aut, cph],
Gerald Evenden [cph],
Angus Johnson [cph],
Frank Warmerdam [cph],
Even Rouault [cph],
Lian Song [ctb],
Edzer Pebesma [ctb],
Sebastian Krantz [ctb, cre]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between dggridR versions 3.1.0 dated 2024-07-26 and 3.1.1 dated 2026-01-20
DESCRIPTION | 34 +++++++++++++++++--------------- MD5 | 18 ++++++++--------- NEWS | 4 +++ R/dggridR.R | 36 ++++++++++++++++++---------------- README.md | 11 +++++++--- build/vignette.rds |binary inst/doc/dggridR.R | 24 +++++++++++------------ inst/doc/dggridR.Rmd | 10 +++++---- inst/doc/dggridR.html | 52 ++++++++++++++++++++++---------------------------- vignettes/dggridR.Rmd | 10 +++++---- 10 files changed, 105 insertions(+), 94 deletions(-)
Title: Continuous Time Structural Equation Modelling
Description: Hierarchical continuous (and discrete) time state space modelling, for linear
and nonlinear systems measured by continuous variables, with limited support for
binary data. The subject specific dynamic system is modelled as a stochastic
differential equation (SDE) or difference equation, measurement models are typically multivariate normal factor models.
Linear mixed effects SDE's estimated via maximum likelihood and optimization are the default.
Nonlinearities, (state dependent parameters) and random effects on all parameters
are possible, using either max likelihood / max a posteriori optimization
(with optional importance sampling) or Stan's Hamiltonian Monte Carlo sampling.
See <https://github.com/cdriveraus/ctsem/raw/master/vignettes/hierarchicalmanual.pdf>
for details. See <https://osf.io/preprints/psyarxiv/4q9ex_v2> for a detailed tutorial.
Priors may be used. For the conceptual overview of the hierarchical Bayesian
linear SDE approach,
see <https://www.research [...truncated...]
Author: Charles Driver [aut, cre, cph],
Manuel Voelkle [aut, cph],
Han Oud [aut, cph],
Trustees of Columbia University [cph]
Maintainer: Charles Driver <charles.driver2@uzh.ch>
Diff between ctsem versions 3.10.4 dated 2025-06-30 and 3.10.5 dated 2026-01-20
ctsem-3.10.4/ctsem/R/ctExtractComplexMatrix.R |only ctsem-3.10.4/ctsem/R/ctIndplot.R |only ctsem-3.10.4/ctsem/R/databasedTIpreds.R |only ctsem-3.10.4/ctsem/man/ctIndplot.Rd |only ctsem-3.10.4/ctsem/man/plot.ctFitCovCheck.Rd |only ctsem-3.10.5/ctsem/DESCRIPTION | 15 ctsem-3.10.5/ctsem/MD5 | 58 ctsem-3.10.5/ctsem/NAMESPACE | 3 ctsem-3.10.5/ctsem/R/ctCheckFit.R | 19 ctsem-3.10.5/ctsem/R/ctCoverageCheck.R |only ctsem-3.10.5/ctsem/R/ctModel.R | 7 ctsem-3.10.5/ctsem/R/ctModelLatex.R | 75 ctsem-3.10.5/ctsem/R/ctStanFit.R | 6 ctsem-3.10.5/ctsem/R/ctStanPostPredict.R | 237 + ctsem-3.10.5/ctsem/R/ctsem-package.R | 42 ctsem-3.10.5/ctsem/R/ctsemUtils.R | 12 ctsem-3.10.5/ctsem/R/priorcheck.R | 48 ctsem-3.10.5/ctsem/R/sdpcor2cov.R | 154 - ctsem-3.10.5/ctsem/R/stanoptimis.R | 1369 +++++----- ctsem-3.10.5/ctsem/R/summary.ctStanFit.R | 2 ctsem-3.10.5/ctsem/README.md | 13 ctsem-3.10.5/ctsem/build/partial.rdb |binary ctsem-3.10.5/ctsem/build/vignette.rds |binary ctsem-3.10.5/ctsem/inst/doc/hierarchicalmanual.pdf |binary ctsem-3.10.5/ctsem/inst/stan/ctsmgen.stan | 1 ctsem-3.10.5/ctsem/man/ctDocs.Rd | 34 ctsem-3.10.5/ctsem/man/ctFitCovCheck.Rd | 4 ctsem-3.10.5/ctsem/man/ctFitCovCheckPlot.Rd |only ctsem-3.10.5/ctsem/man/ctModelCoverage_check.Rd |only ctsem-3.10.5/ctsem/man/ctModelLatex.Rd | 5 ctsem-3.10.5/ctsem/man/ctPostPredPlots.Rd | 8 ctsem-3.10.5/ctsem/man/ctStanFit.Rd | 766 ++--- ctsem-3.10.5/ctsem/tests/testthat/test-bootstrapScoreHessian.R | 143 - ctsem-3.10.5/ctsem/tests/testthat/test-ctLOO.R | 27 34 files changed, 1731 insertions(+), 1317 deletions(-)
Title: Bayesian Latent Variable Analysis
Description: Fit a variety of Bayesian latent variable models, including confirmatory
factor analysis, structural equation models, and latent growth curve models. References: Merkle & Rosseel (2018) <doi:10.18637/jss.v085.i04>; Merkle et al. (2021) <doi:10.18637/jss.v100.i06>.
Author: Edgar Merkle [aut, cre] ,
Yves Rosseel [aut],
Ben Goodrich [aut],
Mauricio Garnier-Villarreal [ctb] ,
Terrence D. Jorgensen [ctb] ,
Huub Hoofs [ctb] ,
Rens van de Schoot [ctb] ,
Andrew Johnson [ctb] ,
Matthew Emery [ctb] ,
Michael S. Truong [ctb] )
Maintainer: Edgar Merkle <merklee@missouri.edu>
Diff between blavaan versions 0.5-9 dated 2025-10-10 and 0.5-10 dated 2026-01-20
DESCRIPTION | 19 ++++++++------- MD5 | 36 ++++++++++++++--------------- NEWS.md | 10 ++++++++ R/blav_object_inspect.R | 42 +++++++++++++++++++++++++++------ R/blav_predict.R | 6 ++++ R/blavaan.R | 12 ++++++--- R/lav_export_stanmarg.R | 35 ++++++++++++++++------------ R/lvgqs.R | 11 ++++++-- R/stanmarg_data.R | 15 ++++++++---- R/zzz.R | 1 README.md | 2 - inst/stan/stanmarg.stan | 52 ++++++++++++++++++++++-------------------- inst/testdata/sysdata.rda |binary inst/tinytest/tests.blavaan.R | 17 +++++++++---- man/bcfa.Rd | 6 ++-- man/bgrowth.Rd | 2 - man/blavaan.Rd | 4 +-- man/bsem.Rd | 6 ++-- src/stanExports_stanmarg.cc | 34 +++++++++++++-------------- 19 files changed, 192 insertions(+), 118 deletions(-)
Title: Bayesian Analysis of Networks of Binary and/or Ordinal Variables
Description: Bayesian variable selection methods for analyzing the structure of a Markov random field model for a network of binary and/or ordinal variables.
Author: Maarten Marsman [aut, cre] ,
Giuseppe Arena [ctb] ,
Karoline Huth [ctb] ,
Nikola Sekulovski [ctb] ,
Don van den Bergh [ctb]
Maintainer: Maarten Marsman <m.marsman@uva.nl>
Diff between bgms versions 0.1.6.1 dated 2025-10-04 and 0.1.6.2 dated 2026-01-20
bgms-0.1.6.1/bgms/inst/bgms_sticker.svg |only bgms-0.1.6.1/bgms/src/bgmCompare_helper.cpp |only bgms-0.1.6.1/bgms/src/bgmCompare_helper.h |only bgms-0.1.6.1/bgms/src/bgmCompare_logp_and_grad.cpp |only bgms-0.1.6.1/bgms/src/bgmCompare_logp_and_grad.h |only bgms-0.1.6.1/bgms/src/bgmCompare_parallel.cpp |only bgms-0.1.6.1/bgms/src/bgmCompare_sampler.cpp |only bgms-0.1.6.1/bgms/src/bgmCompare_sampler.h |only bgms-0.1.6.1/bgms/src/bgm_helper.cpp |only bgms-0.1.6.1/bgms/src/bgm_helper.h |only bgms-0.1.6.1/bgms/src/bgm_logp_and_grad.cpp |only bgms-0.1.6.1/bgms/src/bgm_logp_and_grad.h |only bgms-0.1.6.1/bgms/src/bgm_parallel.cpp |only bgms-0.1.6.1/bgms/src/bgm_sampler.cpp |only bgms-0.1.6.1/bgms/src/bgm_sampler.h |only bgms-0.1.6.1/bgms/src/chainResults.h |only bgms-0.1.6.1/bgms/src/common_helpers.h |only bgms-0.1.6.1/bgms/src/custom_exp.cpp |only bgms-0.1.6.1/bgms/src/e_arma_exp.h |only bgms-0.1.6.1/bgms/src/e_exp.cpp |only bgms-0.1.6.1/bgms/src/e_exp.h |only bgms-0.1.6.1/bgms/src/explog_switch.h |only bgms-0.1.6.1/bgms/src/mcmc_adaptation.h |only bgms-0.1.6.1/bgms/src/mcmc_hmc.cpp |only bgms-0.1.6.1/bgms/src/mcmc_hmc.h |only bgms-0.1.6.1/bgms/src/mcmc_leapfrog.cpp |only bgms-0.1.6.1/bgms/src/mcmc_leapfrog.h |only bgms-0.1.6.1/bgms/src/mcmc_memoization.h |only bgms-0.1.6.1/bgms/src/mcmc_nuts.cpp |only bgms-0.1.6.1/bgms/src/mcmc_nuts.h |only bgms-0.1.6.1/bgms/src/mcmc_rwm.cpp |only bgms-0.1.6.1/bgms/src/mcmc_rwm.h |only bgms-0.1.6.1/bgms/src/mcmc_utils.cpp |only bgms-0.1.6.1/bgms/src/mcmc_utils.h |only bgms-0.1.6.1/bgms/src/print_mutex.h |only bgms-0.1.6.1/bgms/src/progress_manager.cpp |only bgms-0.1.6.1/bgms/src/progress_manager.h |only bgms-0.1.6.1/bgms/src/rng_utils.h |only bgms-0.1.6.1/bgms/src/sampler_output.h |only bgms-0.1.6.1/bgms/src/sbm_edge_prior.cpp |only bgms-0.1.6.1/bgms/src/sbm_edge_prior.h |only bgms-0.1.6.2/bgms/DESCRIPTION | 11 bgms-0.1.6.2/bgms/MD5 | 170 +++--- bgms-0.1.6.2/bgms/NEWS.md | 24 bgms-0.1.6.2/bgms/R/RcppExports.R | 20 bgms-0.1.6.2/bgms/R/bgm.R | 260 +++++---- bgms-0.1.6.2/bgms/R/bgmCompare.R | 259 +++++---- bgms-0.1.6.2/bgms/R/bgmcompare-methods.r | 143 ++--- bgms-0.1.6.2/bgms/R/bgms-methods.R | 63 +- bgms-0.1.6.2/bgms/R/bgms-package.R | 1 bgms-0.1.6.2/bgms/R/data_utils.R | 449 ++++++++++------ bgms-0.1.6.2/bgms/R/extractor_functions.R | 246 +++++---- bgms-0.1.6.2/bgms/R/function_input_utils.R | 561 +++++++++++++-------- bgms-0.1.6.2/bgms/R/mcmc_summary.R | 358 +++++++------ bgms-0.1.6.2/bgms/R/nuts_diagnostics.R | 17 bgms-0.1.6.2/bgms/R/output_utils.R | 158 ++--- bgms-0.1.6.2/bgms/R/sampleMRF.R | 262 +++++---- bgms-0.1.6.2/bgms/README.md | 30 - bgms-0.1.6.2/bgms/build/partial.rdb |binary bgms-0.1.6.2/bgms/cleanup | 1 bgms-0.1.6.2/bgms/configure | 5 bgms-0.1.6.2/bgms/configure.win | 4 bgms-0.1.6.2/bgms/inst/CITATION | 2 bgms-0.1.6.2/bgms/inst/REFERENCES.bib | 5 bgms-0.1.6.2/bgms/inst/doc/comparison.R | 15 bgms-0.1.6.2/bgms/inst/doc/comparison.Rmd | 17 bgms-0.1.6.2/bgms/inst/doc/comparison.html | 13 bgms-0.1.6.2/bgms/inst/doc/diagnostics.R | 6 bgms-0.1.6.2/bgms/inst/doc/diagnostics.Rmd | 6 bgms-0.1.6.2/bgms/inst/doc/diagnostics.html | 6 bgms-0.1.6.2/bgms/inst/doc/intro.R | 15 bgms-0.1.6.2/bgms/inst/doc/intro.Rmd | 17 bgms-0.1.6.2/bgms/inst/doc/intro.html | 15 bgms-0.1.6.2/bgms/inst/generate_makevars_sources.R |only bgms-0.1.6.2/bgms/man/bgm.Rd | 18 bgms-0.1.6.2/bgms/man/bgmCompare.Rd | 2 bgms-0.1.6.2/bgms/man/bgms-package.Rd | 1 bgms-0.1.6.2/bgms/man/figures |only bgms-0.1.6.2/bgms/man/mrfSampler.Rd | 40 - bgms-0.1.6.2/bgms/src/Makevars.in | 6 bgms-0.1.6.2/bgms/src/RcppExports.cpp | 53 - bgms-0.1.6.2/bgms/src/bgm |only bgms-0.1.6.2/bgms/src/bgmCompare |only bgms-0.1.6.2/bgms/src/bgmCompare_interface.cpp |only bgms-0.1.6.2/bgms/src/bgm_interface.cpp |only bgms-0.1.6.2/bgms/src/data_simulation.cpp | 23 bgms-0.1.6.2/bgms/src/math |only bgms-0.1.6.2/bgms/src/mcmc |only bgms-0.1.6.2/bgms/src/priors |only bgms-0.1.6.2/bgms/src/rng |only bgms-0.1.6.2/bgms/src/sbm_edge_prior_interface.cpp |only bgms-0.1.6.2/bgms/src/sbm_edge_prior_interface.h |only bgms-0.1.6.2/bgms/src/utils |only bgms-0.1.6.2/bgms/tests/testthat/test-bgm.R | 14 bgms-0.1.6.2/bgms/vignettes/comparison.Rmd | 17 bgms-0.1.6.2/bgms/vignettes/diagnostics.Rmd | 6 bgms-0.1.6.2/bgms/vignettes/intro.Rmd | 17 97 files changed, 1901 insertions(+), 1455 deletions(-)