Title: Bayesian Hierarchical Analysis of Cognitive Models of Choice
Description: Fit Bayesian (hierarchical) cognitive models
using a linear modeling language interface using particle Metropolis Markov
chain Monte Carlo sampling with Gibbs steps. The diffusion decision model (DDM),
linear ballistic accumulator model (LBA), racing diffusion model (RDM), and the lognormal
race model (LNR) are supported. Additionally, users can specify their own likelihood
function and/or choose for non-hierarchical
estimation, as well as for a diagonal, blocked or full multivariate normal
group-level distribution to test individual differences. Prior specification
is facilitated through methods that visualize the (implied) prior.
A wide range of plotting functions assist in assessing model convergence and
posterior inference. Models can be easily evaluated using functions
that plot posterior predictions or using relative model comparison metrics
such as information criteria or Bayes factors.
References: Stevenson et al. (2024) <doi:10.31234/osf.io/2e4dq>.
Author: Niek Stevenson [aut, cre] ,
Michelle Donzallaz [aut],
Andrew Heathcote [aut],
Steven Miletic [ctb],
Raphael Hartmann [ctb],
Karl C. Klauer [ctb],
Steven G. Johnson [ctb],
Jean M. Linhart [ctb],
Brian Gough [ctb],
Gerard Jungman [ctb],
Rudolf Schuerer [...truncated...]
Maintainer: Niek Stevenson <niek.stevenson@gmail.com>
Diff between EMC2 versions 2.1.0 dated 2024-10-14 and 3.0.0 dated 2025-03-06
EMC2-2.1.0/EMC2/R/IS2.R |only EMC2-2.1.0/EMC2/R/variant_lm.R |only EMC2-2.1.0/EMC2/man/mapped_par.Rd |only EMC2-2.1.0/EMC2/man/plot_defective_density.Rd |only EMC2-2.1.0/EMC2/man/plot_fit.Rd |only EMC2-2.1.0/EMC2/man/plot_prior.Rd |only EMC2-2.1.0/EMC2/man/posterior_summary.Rd |only EMC2-2.1.0/EMC2/man/sampled_p_vector.Rd |only EMC2-2.1.0/EMC2/src/log_likelihood_race.cpp |only EMC2-2.1.0/EMC2/tests/testthat/_snaps/plot_defective_density |only EMC2-2.1.0/EMC2/tests/testthat/_snaps/plot_fit/cdfs-plot-fit.svg |only EMC2-2.1.0/EMC2/tests/testthat/test-plot_defective_density.R |only EMC2-3.0.0/EMC2/DESCRIPTION | 10 EMC2-3.0.0/EMC2/MD5 | 273 +- EMC2-3.0.0/EMC2/NAMESPACE | 49 EMC2-3.0.0/EMC2/NEWS.md | 27 EMC2-3.0.0/EMC2/R/EMC2-package.R | 6 EMC2-3.0.0/EMC2/R/MRI.R |only EMC2-3.0.0/EMC2/R/RcppExports.R | 52 EMC2-3.0.0/EMC2/R/SBC.R | 33 EMC2-3.0.0/EMC2/R/bridge_sampling.R | 28 EMC2-3.0.0/EMC2/R/data.R | 13 EMC2-3.0.0/EMC2/R/define_variants.R |only EMC2-3.0.0/EMC2/R/design.R | 860 +++++---- EMC2-3.0.0/EMC2/R/design_plot.R |only EMC2-3.0.0/EMC2/R/factor_analysis.R | 2 EMC2-3.0.0/EMC2/R/fitting.R | 591 +++--- EMC2-3.0.0/EMC2/R/get_type_objects.R | 58 EMC2-3.0.0/EMC2/R/joint.R | 7 EMC2-3.0.0/EMC2/R/likelihood.R | 36 EMC2-3.0.0/EMC2/R/make_data.R | 60 EMC2-3.0.0/EMC2/R/map.R | 438 +++- EMC2-3.0.0/EMC2/R/model_DDM.R | 75 EMC2-3.0.0/EMC2/R/model_LBA.R | 30 EMC2-3.0.0/EMC2/R/model_LNR.R | 18 EMC2-3.0.0/EMC2/R/model_RDM.R | 22 EMC2-3.0.0/EMC2/R/model_SDT.R | 4 EMC2-3.0.0/EMC2/R/objects.R | 91 EMC2-3.0.0/EMC2/R/plot_data.R |only EMC2-3.0.0/EMC2/R/plotting.R | 391 ---- EMC2-3.0.0/EMC2/R/priors.R | 330 +++ EMC2-3.0.0/EMC2/R/s3_funcs.R | 348 ++- EMC2-3.0.0/EMC2/R/sampling.R | 933 ++++------ EMC2-3.0.0/EMC2/R/statistics.R | 105 - EMC2-3.0.0/EMC2/R/variant_SEM.R | 22 EMC2-3.0.0/EMC2/R/variant_blocked.R | 14 EMC2-3.0.0/EMC2/R/variant_diag.R | 12 EMC2-3.0.0/EMC2/R/variant_diag_gamma.R | 22 EMC2-3.0.0/EMC2/R/variant_factor.R | 22 EMC2-3.0.0/EMC2/R/variant_infnt_factor.R | 21 EMC2-3.0.0/EMC2/R/variant_single.R | 13 EMC2-3.0.0/EMC2/R/variant_standard.R | 22 EMC2-3.0.0/EMC2/README.md | 4 EMC2-3.0.0/EMC2/build/partial.rdb |binary EMC2-3.0.0/EMC2/build/vignette.rds |binary EMC2-3.0.0/EMC2/data/samples_LNR.rda |binary EMC2-3.0.0/EMC2/inst/doc/Simulation-based-Calibration.R | 4 EMC2-3.0.0/EMC2/inst/doc/Simulation-based-Calibration.Rmd | 20 EMC2-3.0.0/EMC2/inst/doc/Simulation-based-Calibration.html | 24 EMC2-3.0.0/EMC2/man/DDM.Rd | 2 EMC2-3.0.0/EMC2/man/EMC2-package.Rd | 2 EMC2-3.0.0/EMC2/man/auto_thin.Rd |only EMC2-3.0.0/EMC2/man/chain_n.Rd | 2 EMC2-3.0.0/EMC2/man/check.Rd | 2 EMC2-3.0.0/EMC2/man/compare.Rd | 45 EMC2-3.0.0/EMC2/man/compare_subject.Rd | 28 EMC2-3.0.0/EMC2/man/contr.anova.Rd | 2 EMC2-3.0.0/EMC2/man/contr.bayes.Rd | 2 EMC2-3.0.0/EMC2/man/contr.decreasing.Rd | 2 EMC2-3.0.0/EMC2/man/contr.increasing.Rd | 2 EMC2-3.0.0/EMC2/man/credible.Rd | 34 EMC2-3.0.0/EMC2/man/credint.Rd |only EMC2-3.0.0/EMC2/man/design.Rd | 15 EMC2-3.0.0/EMC2/man/ess_summary.Rd | 2 EMC2-3.0.0/EMC2/man/fit.Rd | 18 EMC2-3.0.0/EMC2/man/forstmann.Rd | 2 EMC2-3.0.0/EMC2/man/gd_summary.Rd | 2 EMC2-3.0.0/EMC2/man/get_BayesFactor.Rd | 13 EMC2-3.0.0/EMC2/man/get_data.Rd | 2 EMC2-3.0.0/EMC2/man/get_design.Rd |only EMC2-3.0.0/EMC2/man/get_pars.Rd | 6 EMC2-3.0.0/EMC2/man/get_prior.Rd |only EMC2-3.0.0/EMC2/man/hypothesis.Rd | 6 EMC2-3.0.0/EMC2/man/init_chains.Rd | 13 EMC2-3.0.0/EMC2/man/make_data.Rd | 2 EMC2-3.0.0/EMC2/man/make_emc.Rd | 5 EMC2-3.0.0/EMC2/man/make_random_effects.Rd | 8 EMC2-3.0.0/EMC2/man/mapped_pars.Rd |only EMC2-3.0.0/EMC2/man/merge_chains.Rd | 2 EMC2-3.0.0/EMC2/man/pairs_posterior.Rd | 4 EMC2-3.0.0/EMC2/man/parameters.Rd | 47 EMC2-3.0.0/EMC2/man/plot.emc.Rd | 2 EMC2-3.0.0/EMC2/man/plot.emc.design.Rd |only EMC2-3.0.0/EMC2/man/plot.emc.prior.Rd |only EMC2-3.0.0/EMC2/man/plot_cdf.Rd |only EMC2-3.0.0/EMC2/man/plot_density.Rd |only EMC2-3.0.0/EMC2/man/plot_design.Rd |only EMC2-3.0.0/EMC2/man/plot_pars.Rd | 12 EMC2-3.0.0/EMC2/man/plot_relations.Rd | 2 EMC2-3.0.0/EMC2/man/plot_sbc_ecdf.Rd | 2 EMC2-3.0.0/EMC2/man/plot_sbc_hist.Rd | 2 EMC2-3.0.0/EMC2/man/plot_stat.Rd |only EMC2-3.0.0/EMC2/man/predict.emc.Rd | 29 EMC2-3.0.0/EMC2/man/prior.Rd | 10 EMC2-3.0.0/EMC2/man/prior_help.Rd |only EMC2-3.0.0/EMC2/man/profile_plot.Rd | 8 EMC2-3.0.0/EMC2/man/recovery.Rd | 2 EMC2-3.0.0/EMC2/man/run_bridge_sampling.Rd | 6 EMC2-3.0.0/EMC2/man/run_emc.Rd | 24 EMC2-3.0.0/EMC2/man/run_sbc.Rd | 2 EMC2-3.0.0/EMC2/man/sampled_pars.Rd |only EMC2-3.0.0/EMC2/man/samples_LNR.Rd | 11 EMC2-3.0.0/EMC2/man/subset.emc.Rd | 4 EMC2-3.0.0/EMC2/man/summary.emc.Rd | 2 EMC2-3.0.0/EMC2/man/summary.emc.design.Rd |only EMC2-3.0.0/EMC2/man/summary.emc.prior.Rd |only EMC2-3.0.0/EMC2/man/update2version.Rd |only EMC2-3.0.0/EMC2/src/Makevars | 3 EMC2-3.0.0/EMC2/src/Makevars.win | 3 EMC2-3.0.0/EMC2/src/RcppExports.cpp | 232 ++ EMC2-3.0.0/EMC2/src/hcubature.cpp | 169 - EMC2-3.0.0/EMC2/src/model_DDM.h | 35 EMC2-3.0.0/EMC2/src/model_LBA.h | 81 EMC2-3.0.0/EMC2/src/model_MRI.h |only EMC2-3.0.0/EMC2/src/model_RDM.h | 30 EMC2-3.0.0/EMC2/src/model_fMRI.h | 14 EMC2-3.0.0/EMC2/src/model_lnr.h | 31 EMC2-3.0.0/EMC2/src/mri.cpp |only EMC2-3.0.0/EMC2/src/particle_ll.cpp |only EMC2-3.0.0/EMC2/src/trend.h |only EMC2-3.0.0/EMC2/src/utility_functions.h | 428 ++++ EMC2-3.0.0/EMC2/tests/testthat/_snaps/Linux/fit.md | 22 EMC2-3.0.0/EMC2/tests/testthat/_snaps/Linux/variant_funs.md | 86 EMC2-3.0.0/EMC2/tests/testthat/_snaps/S3 |only EMC2-3.0.0/EMC2/tests/testthat/_snaps/S3.md |only EMC2-3.0.0/EMC2/tests/testthat/_snaps/compare.md | 8 EMC2-3.0.0/EMC2/tests/testthat/_snaps/customLL.md |only EMC2-3.0.0/EMC2/tests/testthat/_snaps/joint.md |only EMC2-3.0.0/EMC2/tests/testthat/_snaps/make_design.md | 6 EMC2-3.0.0/EMC2/tests/testthat/_snaps/make_emc.md | 39 EMC2-3.0.0/EMC2/tests/testthat/_snaps/model_functions.md | 280 +-- EMC2-3.0.0/EMC2/tests/testthat/_snaps/pairs_posterior/pairs-plot.svg | 851 ++++----- EMC2-3.0.0/EMC2/tests/testthat/_snaps/plot_chains/chain-plots.svg | 109 - 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Title: R Library for Spatial Data Analysis
Description: Provides spatial data analysis functionalities including Exploratory Spatial Data Analysis,
Spatial Cluster Detection and Clustering Analysis, Regionalization, etc. based on the C++ source code
of 'GeoDa', which is an open-source software tool that serves as an introduction to spatial data analysis.
The 'GeoDa' software and its documentation are available at <https://geodacenter.github.io>.
Author: Xun Li [aut, cre],
Luc Anselin [aut]
Maintainer: Xun Li <lixun910@gmail.com>
Diff between rgeoda versions 0.0.11-1 dated 2024-12-19 and 0.1.0 dated 2025-03-06
DESCRIPTION | 8 +-- MD5 | 29 ++++++------ NAMESPACE | 1 R/RcppExports.R | 4 + R/utils.R | 24 ++++++++++ man/eb_rates_standardization.Rd |only src/RcppExports.cpp | 13 +++++ src/libgeoda/clustering/redcap_wrapper.cpp | 17 ++++--- src/libgeoda/clustering/schc_wrapper.cpp | 27 +++++++---- src/libgeoda/gda_clustering.cpp | 22 +++++---- src/libgeoda/gda_clustering.h | 18 +++---- src/libgeoda/gda_data.cpp | 68 +++++++++++++++++++++++++++++ src/libgeoda/gda_data.h | 49 ++++++++++++-------- src/libgeoda/sa/BatchLISA.h | 7 ++ src/libgeoda/sa/LISA.h | 7 ++ src/rcpp_lisa.cpp | 21 ++++++++ 16 files changed, 243 insertions(+), 72 deletions(-)
Title: Create and Query a Local Copy of 'GenBank' in R
Description: Download large sections of
'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> and generate a local
SQL-based database. A user can then query this database using 'restez'
functions or through 'rentrez' <https://CRAN.R-project.org/package=rentrez>
wrappers.
Author: Joel H. Nitta [aut, cre] ,
Dom Bennett [aut]
Maintainer: Joel H. Nitta <joelnitta@gmail.com>
Diff between restez versions 2.1.4 dated 2023-10-25 and 2.1.5 dated 2025-03-06
DESCRIPTION | 8 - MD5 | 158 ++++++++++++++++----------------- NEWS.md | 15 ++- R/entrez-tools.R | 10 +- R/gb-get-tools.R | 5 + R/gb-setup-tools.R | 7 + README.md | 2 man/add_rcrd_log.Rd | 4 man/cat_line.Rd | 4 man/char.Rd | 4 man/check_connection.Rd | 4 man/cleanup.Rd | 4 man/connected.Rd | 4 man/connection_get.Rd | 4 man/db_download_intern.Rd | 4 man/db_sqlngths_get.Rd | 4 man/db_sqlngths_log.Rd | 4 man/dir_size.Rd | 4 man/dwnld_path_get.Rd | 4 man/dwnld_rcrd_log.Rd | 4 man/entrez_fasta_get.Rd | 4 man/entrez_gb_get.Rd | 4 man/extract_accession.Rd | 4 man/extract_by_patterns.Rd | 4 man/extract_clean_sequence.Rd | 4 man/extract_definition.Rd | 4 man/extract_features.Rd | 4 man/extract_inforecpart.Rd | 4 man/extract_keywords.Rd | 4 man/extract_locus.Rd | 4 man/extract_organism.Rd | 4 man/extract_seqrecpart.Rd | 4 man/extract_sequence.Rd | 4 man/extract_version.Rd | 4 man/file_download.Rd | 4 man/filename_log.Rd | 4 man/flatfile_read.Rd | 4 man/gb_build.Rd | 4 man/gb_df_create.Rd | 4 man/gb_df_generate.Rd | 4 man/gb_sql_add.Rd | 4 man/gb_sql_query.Rd | 4 man/gbrelease_check.Rd | 4 man/gbrelease_get.Rd | 4 man/gbrelease_log.Rd | 4 man/has_data.Rd | 4 man/identify_downloadable_files.Rd | 4 man/last_add_get.Rd | 4 man/last_dwnld_get.Rd | 4 man/last_entry_get.Rd | 4 man/latest_genbank_release.Rd | 2 man/latest_genbank_release_notes.Rd | 2 man/message_missing.Rd | 4 man/mock_def.Rd | 4 man/mock_gb_df_generate.Rd | 4 man/mock_org.Rd | 4 man/mock_rec.Rd | 4 man/mock_seq.Rd | 4 man/predict_datasizes.Rd | 4 man/readme_log.Rd | 4 man/restez.Rd | 2 man/restez_connect.Rd | 4 man/restez_disconnect.Rd | 4 man/restez_path_check.Rd | 4 man/restez_rl.Rd | 4 man/search_gz.Rd | 4 man/seshinfo_log.Rd | 4 man/setup.Rd | 4 man/slctn_get.Rd | 4 man/slctn_log.Rd | 4 man/sql_path_get.Rd | 4 man/stat.Rd | 2 man/status_class.Rd | 2 man/testdatadir_get.Rd | 6 - tests/testthat/test-biomartr-tools.R | 19 ++- tests/testthat/test-entrez-tools.R | 22 +--- tests/testthat/test-gb-setup-tools.R | 23 +--- tests/testthat/test-get-tools.R | 6 + tests/testthat/test-log-tools.R | 12 +- tests/testthat/test-rentrez-wrappers.R | 8 - 80 files changed, 290 insertions(+), 265 deletions(-)
Title: Risk Metrics to Evaluating R Packages
Description: Facilities for assessing R packages against a number of metrics to
help quantify their robustness.
Author: R Validation Hub [aut],
Doug Kelkhoff [aut],
Marly Gotti [aut],
Eli Miller [cre, aut],
Kevin K [aut],
Yilong Zhang [aut],
Eric Milliman [aut],
Juliane Manitz [aut],
Mark Padgham [ctb],
PSI special interest group Application and Implementation of
Meth [...truncated...]
Maintainer: Eli Miller <eli.miller@atorusresearch.com>
Diff between riskmetric versions 0.2.4 dated 2024-01-09 and 0.2.5 dated 2025-03-06
riskmetric-0.2.4/riskmetric/man/figures/hex-riskmetric-aspconfig.png |only riskmetric-0.2.4/riskmetric/tests/testthat/testPackage1 |only riskmetric-0.2.5/riskmetric/DESCRIPTION | 8 riskmetric-0.2.5/riskmetric/MD5 | 34 riskmetric-0.2.5/riskmetric/NEWS.md | 4 riskmetric-0.2.5/riskmetric/R/assess_dependencies.R | 4 riskmetric-0.2.5/riskmetric/R/assess_size_codebase.R | 9 riskmetric-0.2.5/riskmetric/R/pkg_ref_cache_news.R | 4 riskmetric-0.2.5/riskmetric/R/pkg_ref_class.R | 4 riskmetric-0.2.5/riskmetric/README.md | 8 riskmetric-0.2.5/riskmetric/build/vignette.rds |binary riskmetric-0.2.5/riskmetric/inst/doc/extending-riskmetric.R | 6 riskmetric-0.2.5/riskmetric/inst/doc/extending-riskmetric.html | 429 +++----- riskmetric-0.2.5/riskmetric/inst/doc/riskmetric.R | 16 riskmetric-0.2.5/riskmetric/inst/doc/riskmetric.html | 482 +++------- riskmetric-0.2.5/riskmetric/man/determine_pkg_source.Rd | 2 riskmetric-0.2.5/riskmetric/man/figures/logo.png |only riskmetric-0.2.5/riskmetric/man/metric_score.pkg_metric_size_codebase.Rd | 2 riskmetric-0.2.5/riskmetric/man/riskmetric.Rd | 2 19 files changed, 416 insertions(+), 598 deletions(-)
Title: Tools for R Package Developers
Description: R-hub v2 uses GitHub Actions to run 'R CMD check' and
similar package checks. The 'rhub' package helps you set up
R-hub v2 for your R package, and start running checks.
Author: Gabor Csardi [aut, cre],
Maelle Salmon [aut] ,
R Consortium [fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between rhub versions 2.0.0 dated 2024-04-11 and 2.0.1 dated 2025-03-06
DESCRIPTION | 8 +++---- MD5 | 36 +++++++++++++++++++------------- NEWS.md | 7 ++++++ R/aaa-async.R | 6 ++--- R/check.R | 2 - R/doctor.R | 2 - R/platforms.R | 13 +++++++---- man/figures/rhub-check-dark.svg |only man/figures/rhub-check.svg |only man/figures/rhub-doctor-dark.svg |only man/figures/rhub-doctor.svg |only man/figures/rhub-platforms-dark.svg |only man/figures/rhub-platforms.svg |only man/figures/rhub-setup-dark.svg |only man/figures/rhub-setup.svg |only man/rhub-package.Rd | 2 - man/rhub_check.Rd | 2 - man/rhubv2.Rd | 8 +++---- tests/testthat/_snaps/doctor.md | 2 - tests/testthat/_snaps/platforms.md | 12 +++++----- tests/testthat/fixtures/pkg/DESCRIPTION | 4 +-- tests/testthat/helpers.R | 3 +- tests/testthat/test-utils.R | 2 - 23 files changed, 64 insertions(+), 45 deletions(-)
Title: Wicked-Fast Streaming 'JSON' ('ndjson') Reader
Description: Streaming 'JSON' ('ndjson') has one 'JSON' record per-line
and many modern 'ndjson' files contain large numbers of records.
These constructs may not be columnar in nature, but it is often
useful to read in these files and "flatten" the structure out to
enable working with the data in an R 'data.frame'-like context.
Functions are provided that make it possible to read in plain
'ndjson' files or compressed ('gz') 'ndjson' files and either
validate the format of the records or create "flat" 'data.table'
structures from them.
Author: Bob Rudis [aut, cre] ,
Niels Lohmann [aut] ,
Deepak Bandyopadhyay [aut] ,
Lutz Kettner [aut] ,
Neal Fultz [ctb] ,
Maarten Demeyer [ctb]
Maintainer: Bob Rudis <bob@rud.is>
Diff between ndjson versions 0.9.0 dated 2022-10-17 and 0.9.1 dated 2025-03-06
DESCRIPTION | 10 MD5 | 18 R/ndjson-package.R | 3 R/ndjson.R | 4 inst/include/json.h |21477 ++++++++++++++++++++++++++++------------------------ man/ndjson.Rd | 9 man/stream_in.Rd | 2 man/validate.Rd | 2 src/Makevars | 1 src/Makevars.win | 1 10 files changed, 11605 insertions(+), 9922 deletions(-)
Title: Scalar-on-Function Regression with Measurement Error Correction
Description: Solve scalar-on-function linear models,
including generalized linear mixed effect model and quantile linear regression model,
and bias correction estimation methods due to measurement error.
Details about the measurement error bias correction methods, see
Luan et al. (2023) <doi:10.48550/arXiv.2305.12624>,
Tekwe et al. (2022) <doi:10.1093/biostatistics/kxac017>,
Zhang et al. (2023) <doi:10.5705/ss.202021.0246>,
Tekwe et al. (2019) <doi:10.1002/sim.8179>.
Author: Heyang Ji [aut, cre, ctb, dtc]
,
Ufuk Beyaztas [aut, ctb, rev] ,
Nicolas Escobar-Velasquez [com]
,
Yuanyuan Luan [aut, ctb],
Xiwei Chen [aut, ctb],
Mengli Zhang [aut, ctb],
Roger Zoh [aut, ths],
Lan Xue [aut, ths],
Carmen Tekwe [aut, ths]
Maintainer: Heyang Ji <jihx1015@outlook.com>
Diff between MECfda versions 0.1.0 dated 2024-10-21 and 0.2.0 dated 2025-03-06
DESCRIPTION | 43 - MD5 | 94 +- NAMESPACE | 17 NEWS.md |only R/FPC_basis_expansion.R |only R/FourierSeries2fun.R | 2 R/ME.fcLR_IV.R | 6 R/ME.fcQR_CLS.R | 8 R/ME.fcQR_IV.SIMEX.R | 27 R/ME.fcRegression_MEM.R | 8 R/MECfda_simDataGen_ME.R |only R/MECfda_simDataGen_fcReg.R |only R/MEM_X_hat.R |only R/basis2fun.R | 14 R/bsplineSeries2fun.R | 4 R/bspline_basis_expansion.R | 4 R/classDefintions.R | 90 ++ R/fcQR.R | 49 + R/fcRegression.R | 60 + R/fourier_basis_expansion.R | 8 R/functional_variable.R | 2 R/initialize.numeric_basis.R |only R/numericBasisSeries2fun.R |only R/numeric_basis_expansion.R |only R/plot.bspline_series.R | 4 R/plot.numeric_series.R |only R/predict.fcQR.R | 11 R/predict.fcRegression.R | 11 build/vignette.rds |binary inst/doc/MECfda.R | 168 ++-- inst/doc/MECfda.Rmd | 892 ++++++++++++------------ inst/doc/MECfda.html | 1188 ++++++++++++++++++++------------- man/FPC_basis_expansion.Rd |only man/FourierSeries2fun.Rd | 2 man/ME.fcLR_IV.Rd | 6 man/ME.fcQR_CLS.Rd | 8 man/ME.fcQR_IV.SIMEX.Rd | 4 man/ME.fcRegression_MEM.Rd | 8 man/MECfda_simDataGen_ME.Rd |only man/MECfda_simDataGen_fcReg.Rd |only man/MEM_X_hat.Rd |only man/basis2fun.Rd | 8 man/bsplineSeries2fun.Rd | 4 man/bspline_basis-class.Rd | 2 man/bspline_basis_expansion.Rd | 2 man/fcQR.Rd | 17 man/fcRegression.Rd | 23 man/fourier_basis_expansion.Rd | 2 man/functional_variable-class.Rd | 2 man/numericBasisSeries2fun.Rd |only man/numericBasis_series-class.Rd |only man/numeric_basis-class.Rd |only man/numeric_basis_expansion.Rd |only man/plot-bspline_series-method.Rd | 4 man/plot-numericBasis_series-method.Rd |only man/predict.fcRegression.Rd | 86 +- vignettes/MECfda.Rmd | 892 ++++++++++++------------ 57 files changed, 2175 insertions(+), 1605 deletions(-)
Title: Bindings to 'OpenCV' Computer Vision Library
Description: Exposes some of the available 'OpenCV' <https://opencv.org/> algorithms,
such as a QR code scanner, and edge, body or face detection. These can either be
applied to analyze static images, or to filter live video footage from a camera device.
Author: Jeroen Ooms [aut, cre] ,
Jan Wijffels [aut]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between opencv versions 0.4.1 dated 2024-10-04 and 0.5.0 dated 2025-03-06
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 3 +++ src/Makevars.win | 31 +++++++++++++++++++++++-------- 4 files changed, 32 insertions(+), 14 deletions(-)
Title: A Modular Platform for Reproducible Modeling of Species Niches
and Distributions
Description: The 'shiny' application Wallace is a modular platform for
reproducible modeling of species niches and distributions. Wallace
guides users through a complete analysis, from the acquisition of species
occurrence and environmental data to visualizing model predictions on an
interactive map, thus bundling complex workflows into a single,
streamlined interface. An extensive vignette, which guides users through
most package functionality can be found on the package's GitHub Pages
website: <https://wallaceecomod.github.io/wallace/articles/tutorial-v2.html>.
Author: Bethany A. Johnson [aut],
Daniel F. Lopez-Lozano [aut],
Jamie M. Kass [aut],
Gonzalo E. Pinilla-Buitrago [aut],
Andrea Paz [aut],
Valentina Grisales-Betancur [aut],
Dean Attali [aut],
Matthew E. Aiello-Lammens [aut],
Cory Merow [aut],
Mary E. Blair [ [...truncated...]
Maintainer: Mary E. Blair <mblair1@amnh.org>
Diff between wallace versions 2.1.3 dated 2024-07-18 and 2.2.0 dated 2025-03-06
DESCRIPTION | 16 +++-- MD5 | 84 +++++++++++++++--------------- NEWS.md | 6 ++ R/model_bioclim.R | 3 - R/model_maxent.R | 5 + R/part_partitionOccs.R | 18 +++--- R/vis_bioclimPlot.R | 1 R/xfer_area.R | 27 ++++++--- R/xfer_time.R | 20 +++---- R/xfer_userEnvs.R | 24 +++++--- README.md | 4 - inst/module_skeleton/skeleton.R | 2 inst/shiny/Rmd/text_about.Rmd | 2 inst/shiny/Rmd/text_intro_tab.Rmd | 2 inst/shiny/Rmd/userReport_intro.Rmd | 2 inst/shiny/modules/envs_userEnvs.md | 4 - inst/shiny/modules/model_bioclim.yml | 2 inst/shiny/modules/model_maxent.yml | 2 inst/shiny/modules/part_nonSpat.yml | 2 inst/shiny/modules/part_spat.yml | 2 inst/shiny/modules/vis_bioclimPlot.yml | 2 inst/shiny/modules/vis_mapPreds.R | 12 ++-- inst/shiny/modules/vis_mapPreds.Rmd | 18 +++--- inst/shiny/modules/vis_mapPreds.yml | 2 inst/shiny/modules/vis_maxentEvalPlot.yml | 2 inst/shiny/modules/vis_responsePlot.R | 2 inst/shiny/modules/vis_responsePlot.Rmd | 2 inst/shiny/modules/vis_responsePlot.yml | 2 inst/shiny/modules/xfer_area.R | 2 inst/shiny/modules/xfer_time.md | 2 inst/shiny/server.R | 2 man/model_bioclim.Rd | 2 man/model_maxent.Rd | 2 man/part_partitionOccs.Rd | 6 +- man/vis_bioclimPlot.Rd | 2 man/xfer_area.Rd | 19 +++++- man/xfer_time.Rd | 12 ++-- man/xfer_userEnvs.Rd | 16 ++++- tests/testthat/test_model_bioclim.R | 8 +- tests/testthat/test_model_maxent.R | 4 - tests/testthat/test_xfer_area.R | 17 ++++-- tests/testthat/test_xfer_time.R | 15 +++-- tests/testthat/test_xfer_userEnvs.R | 20 +++++-- 43 files changed, 249 insertions(+), 150 deletions(-)
Title: Mapping Data for 'usmap' Package
Description: Provides a container for data used by the 'usmap' package.
The data used by 'usmap' has been extracted into this package so that the
file size of the 'usmap' package can be reduced greatly. The data in this
package will be updated roughly once per year as new map data files are
provided by the US Census Bureau.
Author: Paolo Di Lorenzo [aut, cre]
Maintainer: Paolo Di Lorenzo <paolo@dilorenzo.org>
Diff between usmapdata versions 0.3.0 dated 2024-05-17 and 0.4.0 dated 2025-03-06
usmapdata-0.3.0/usmapdata/inst/extdata/us_counties.gpkg |only usmapdata-0.3.0/usmapdata/inst/extdata/us_counties_centroids.gpkg |only usmapdata-0.3.0/usmapdata/inst/extdata/us_states.gpkg |only usmapdata-0.3.0/usmapdata/inst/extdata/us_states_centroids.gpkg |only usmapdata-0.4.0/usmapdata/DESCRIPTION | 12 usmapdata-0.4.0/usmapdata/MD5 | 54 - usmapdata-0.4.0/usmapdata/NAMESPACE | 13 usmapdata-0.4.0/usmapdata/NEWS.md | 144 +- usmapdata-0.4.0/usmapdata/R/create-us-map.R | 525 +++++----- usmapdata-0.4.0/usmapdata/R/fips-data.R | 51 usmapdata-0.4.0/usmapdata/R/us-map.R | 232 ++-- usmapdata-0.4.0/usmapdata/R/usmapdata-package.R | 2 usmapdata-0.4.0/usmapdata/README.md | 196 +-- usmapdata-0.4.0/usmapdata/inst/WORDLIST | 24 usmapdata-0.4.0/usmapdata/inst/extdata/2021 |only usmapdata-0.4.0/usmapdata/inst/extdata/2022 |only usmapdata-0.4.0/usmapdata/inst/extdata/2023 |only usmapdata-0.4.0/usmapdata/man/available_map_years.Rd |only usmapdata-0.4.0/usmapdata/man/centroid_labels.Rd | 58 - usmapdata-0.4.0/usmapdata/man/create_us_map.Rd | 153 +- usmapdata-0.4.0/usmapdata/man/fips_data.Rd | 70 - usmapdata-0.4.0/usmapdata/man/select_map_year.Rd |only usmapdata-0.4.0/usmapdata/man/us_map.Rd | 109 +- usmapdata-0.4.0/usmapdata/man/usmapdata.Rd | 104 - usmapdata-0.4.0/usmapdata/tests/spelling.R | 2 usmapdata-0.4.0/usmapdata/tests/testthat.R | 24 usmapdata-0.4.0/usmapdata/tests/testthat/test-fips-data.R | 82 - usmapdata-0.4.0/usmapdata/tests/testthat/test-usmap.R | 175 +-- 28 files changed, 1095 insertions(+), 935 deletions(-)
Title: Mathematics PhD Genealogy Data and Plotting
Description: Query, extract, and plot genealogical data from The Mathematics
Genealogy Project <https://mathgenealogy.org/>. Data is gathered from the
'WebSocket' server run by the 'geneagrapher-core' project
<https://github.com/davidalber/geneagrapher-core>.
Author: Louis Aslett [aut, cre]
Maintainer: Louis Aslett <louis.aslett@durham.ac.uk>
Diff between maths.genealogy versions 0.1.1 dated 2025-03-03 and 0.1.2 dated 2025-03-06
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 5 +++++ R/get_genealogy.R | 4 ++++ R/plot_gg.R | 4 ++++ R/plot_gg_path.R | 4 ++++ R/plot_grviz.R | 4 ++++ R/search_id.R | 6 +++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/getting-started.html | 8 ++++---- man/get_genealogy.Rd | 4 ++++ man/maths.genealogy-package.Rd | 2 +- man/plot_gg.Rd | 4 ++++ man/plot_gg_path.Rd | 4 ++++ man/plot_grviz.Rd | 4 ++++ man/search_id.Rd | 4 ++++ 17 files changed, 71 insertions(+), 26 deletions(-)
More information about maths.genealogy at CRAN
Permanent link
Title: Dual Feature Reduction for SGL
Description: Implementation of the Dual Feature Reduction (DFR) approach for the Sparse Group Lasso (SGL) and the Adaptive Sparse Group Lasso (aSGL) (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.17094>). The DFR approach is a feature reduction approach that applies strong screening to reduce the feature space before optimisation, leading to speed-up improvements for fitting SGL (Simon et al. (2013) <doi:10.1080/10618600.2012.681250>) and aSGL (Mendez-Civieta et al. (2020) <doi:10.1007/s11634-020-00413-8> and Poignard (2020) <doi:10.1007/s10463-018-0692-7>) models. DFR is implemented using the Adaptive Three Operator Splitting (ATOS) (Pedregosa and Gidel (2018) <doi:10.48550/arXiv.1804.02339>) algorithm, with linear and logistic SGL models supported, both of which can be fit using k-fold cross-validation. Dense and sparse input matrices are supported.
Author: Fabio Feser [aut, cre]
Maintainer: Fabio Feser <ff120@ic.ac.uk>
Diff between dfr versions 0.1.4 dated 2025-02-06 and 0.1.5 dated 2025-03-06
DESCRIPTION | 8 ++-- MD5 | 22 ++++++------- R/dfr_adap_sgl.R | 31 ++++++++++++++++-- R/dfr_sgl.R | 25 +++++++++++++- R/fitting_code.R | 24 ++------------ R/global_wrapper_code.R | 81 +++++++++++++++++++++++++++++++++++------------- R/run_algorithm.R | 4 +- R/screen.R | 14 ++------ R/utils.R | 66 ++++++++++++++++++++++++++++++++------- build/partial.rdb |binary man/dfr_adap_sgl.Rd | 6 +-- man/dfr_sgl.Rd | 4 +- 12 files changed, 193 insertions(+), 92 deletions(-)
Title: Conditional Binary Quantile Models
Description: Estimates conditional binary quantile models developed by Lu (2020) <doi:10.1017/pan.2019.29>. The estimation procedure is implemented based on Markov chain Monte Carlo methods.
Author: Xiao Lu [aut, cre]
Maintainer: Xiao Lu <xiao.lu.research@gmail.com>
Diff between cbq versions 0.2.0.3 dated 2023-04-02 and 0.2.0.4 dated 2025-03-06
DESCRIPTION | 14 +++++++++----- MD5 | 14 +++++++------- inst/stan/cbqfixd.stan | 18 +++++++++--------- inst/stan/cbqfixdv.stan | 18 +++++++++--------- inst/stan/cbqpaneld.stan | 18 +++++++++--------- inst/stan/cbqpaneldv.stan | 18 +++++++++--------- inst/stan/cbqrandomd.stan | 18 +++++++++--------- inst/stan/cbqrandomdv.stan | 18 +++++++++--------- 8 files changed, 70 insertions(+), 66 deletions(-)
Title: Interface to the 'Zoltar' Forecast Repository API
Description: 'Zoltar' <https://www.zoltardata.com/> is a website that provides a repository of model forecast results
in a standardized format and a central location. It supports storing, retrieving, comparing, and analyzing time
series forecasts for prediction challenges of interest to the modeling community. This package provides functions
for working with the 'Zoltar' API, including connecting and authenticating, getting meta information (projects,
models, and forecasts, and truth), and uploading, downloading, and deleting forecast and truth data.
Author: Matthew Cornell [aut, cre],
Nicholas Reich [aut, cph]
Maintainer: Matthew Cornell <cornell@umass.edu>
Diff between zoltr versions 1.0.1 dated 2024-06-27 and 1.0.2 dated 2025-03-06
DESCRIPTION | 6 MD5 | 32 +-- NAMESPACE | 5 NEWS.md | 6 R/connection.R | 14 - R/model.R | 9 R/project.R | 14 - inst/doc/getting-started.html | 4 inst/doc/project-owners.html | 22 +- tests/testthat/test-cdc.R | 2 tests/testthat/test-connection.R | 134 +++++-------- tests/testthat/test-csv.R | 2 tests/testthat/test-forecast.R | 152 +++++++------- tests/testthat/test-job.R | 75 +++---- tests/testthat/test-model.R | 234 ++++++++++------------- tests/testthat/test-project.R | 396 ++++++++++++++++++--------------------- tests/testthat/test-quantile.R | 2 17 files changed, 523 insertions(+), 586 deletions(-)
Title: Generating Synthetic Versions of Sensitive Microdata for
Statistical Disclosure Control
Description: A tool for producing synthetic versions of microdata containing confidential information so that they are safe to be released to users for exploratory analysis. The key objective of generating synthetic data is to replace sensitive original values with synthetic ones causing minimal distortion of the statistical information contained in the data set. Variables, which can be categorical or continuous, are synthesised one-by-one using sequential modelling. Replacements are generated by drawing from conditional distributions fitted to the original data using parametric or classification and regression trees models. Data are synthesised via the function syn() which can be largely automated, if default settings are used, or with methods defined by the user. Optional parameters can be used to influence the disclosure risk and the analytical quality of the synthesised data. For a description of the implemented method see Nowok, Raab and Dibben (2016) <doi:10.18637/jss.v074.i11>. Functio [...truncated...]
Author: Beata Nowok [aut, cre],
Gillian M Raab [aut],
Chris Dibben [ctb],
Joshua Snoke [ctb],
Caspar van Lissa [ctb],
Lotte Pater [ctb]
Maintainer: Beata Nowok <beata.nowok@gmail.com>
Diff between synthpop versions 1.9-0 dated 2024-12-20 and 1.9-1 dated 2025-03-06
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 9 +++++++++ inst/doc/disclosure.pdf |binary inst/doc/inference.Rnw | 8 +++----- inst/doc/inference.pdf |binary inst/doc/synthpop.pdf |binary inst/doc/utility.pdf |binary man/synthpop-package.Rd | 4 ++-- vignettes/inference.Rnw | 8 +++----- 10 files changed, 30 insertions(+), 25 deletions(-)
Title: Perform Recursive Computations
Description: Mass rollup for a Bill of Materials is an example of a class of computations in which elements are arranged in a tree structure and some property of each element is a computed function of the corresponding values of its child elements. Leaf elements, i.e., those with no children, have values assigned. In many cases, the combining function is simple arithmetic sum; in other cases (e.g., mass properties), the combiner may involve other information such as the geometric relationship between parent and child, or statistical relations such as root-sum-of-squares (RSS). This package implements a general function for such problems. It is adapted to specific recursive computations by functional programming techniques; the caller passes a function as the update parameter to rollup() (or, at a lower level, passes functions as the get, set, combine, and override parameters to update_prop()) at runtime to specify the desired operations. The implementation relies on graph-theoretic algorithms from [...truncated...]
Author: James Steven Jenkins [aut, cre, cph]
Maintainer: James Steven Jenkins <sjenkins@studioj.us>
Diff between rollupTree versions 0.2.0 dated 2025-02-04 and 0.3.0 dated 2025-03-06
DESCRIPTION | 6 +- MD5 | 22 +++++---- NAMESPACE | 1 NEWS.md | 11 ++-- R/rollup.R | 20 +++++++- R/test_dag.R |only README.md | 4 + data/test_dag.rda |only inst/doc/rollupTree.Rmd | 2 inst/doc/rollupTree.html | 6 ++ man/default_validate_dag.Rd |only man/test_dag.Rd |only tests/testthat/test-rollup.R | 103 +++++++++++++++++++++++++++++++++++++++++++ vignettes/rollupTree.Rmd | 2 14 files changed, 159 insertions(+), 18 deletions(-)
Title: Shared, Joint (Generalized) Frailty Models; Surrogate Endpoints
Description: The following several classes of frailty models using a
penalized likelihood estimation on the hazard function but also a
parametric estimation can be fit using this R package: 1) A shared
frailty model (with gamma or log-normal frailty distribution) and Cox
proportional hazard model. Clustered and recurrent survival times can
be studied. 2) Additive frailty models for proportional hazard models
with two correlated random effects (intercept random effect with
random slope). 3) Nested frailty models for hierarchically clustered
data (with 2 levels of clustering) by including two iid gamma random
effects. 4) Joint frailty models in the context of the joint
modelling for recurrent events with terminal event for clustered data
or not. A joint frailty model for two semi-competing risks and
clustered data is also proposed. 5) Joint general frailty models in
the context of the joint modelling for recurrent events with terminal
event data with two independent frailty terms. 6) Joint Neste [...truncated...]
Author: Virginie Rondeau [aut, cre] ,
Juan R. Gonzalez [aut],
Yassin Mazroui [aut],
Audrey Mauguen [aut],
Amadou Diakite [aut],
Alexandre Laurent [aut],
Myriam Lopez [aut],
Agnieszka Krol [aut],
Casimir L. Sofeu [aut],
Julien Dumerc [aut],
Denis Rustand [aut [...truncated...]
Maintainer: Virginie Rondeau <virginie.rondeau@u-bordeaux.fr>
Diff between frailtypack versions 3.6.5 dated 2024-12-14 and 3.7.0 dated 2025-03-06
DESCRIPTION | 147 ++++++++++++++++++++++++++---------------- MD5 | 26 ++++--- NAMESPACE | 18 +++++ NEWS | 31 +++++--- R/frailtyDesign.R |only R/frailtypack-package.R | 20 ++++- R/print.frailtyDesign.R |only R/summary.frailtyDesign.R |only build/vignette.rds |binary inst/doc/Package_summary.Rmd | 30 ++++---- inst/doc/Package_summary.html | 123 ++++++++++++++++++++--------------- man/frailtyDesign.Rd |only man/frailtypack-package.Rd | 17 ++++ man/print.frailtyDesign.Rd |only man/print.prediction.Rd | 62 ++++++++--------- man/summary.frailtyDesign.Rd |only vignettes/Package_summary.Rmd | 30 ++++---- 17 files changed, 315 insertions(+), 189 deletions(-)
Title: Analyse Open-Ended Survey Responses in Finnish
Description: Annotates Finnish textual survey responses into CoNLL-U format using Finnish treebanks from <https://universaldependencies.org/format.html> using UDPipe as described in Straka and Straková (2017) <doi:10.18653/v1/K17-3009>. Formatted data is then analysed using single or comparison n-gram plots, wordclouds, summary tables and Concept Network plots. The Concept Network plots use the TextRank algorithm as outlined in Mihalcea, Rada & Tarau, Paul (2004) <https://aclanthology.org/W04-3252/>.
Author: Adeline Clarke [cre, aut],
Krista Lagus [aut],
Katja Laine [aut],
Maria Litova [aut],
Matti Nelimarkka [aut],
Joni Oksanen [aut],
Jaakko Peltonen [aut],
Tuukka Oikarinen [aut],
Jani-Matti Tirkkonen [aut],
Ida Toivanen [aut],
Maria Valaste [aut],
Shan [...truncated...]
Maintainer: Adeline Clarke <adelinepclarke@gmail.com>
Diff between finnsurveytext versions 2.1.0 dated 2024-11-08 and 2.1.1 dated 2025-03-06
DESCRIPTION | 6 MD5 | 56 ++++---- NEWS.md | 4 R/01_prepare.R | 30 ++-- R/01b_prepare_svydesign.R | 26 ++- R/02_data_exploration.R | 35 +++-- R/03_concept_network.R | 4 R/04_comparison_functions.R | 4 README.md | 16 +- inst/doc/Overview-PackageTutorial.R | 2 inst/doc/Overview-PackageTutorial.Rmd | 20 ++ inst/doc/Overview-PackageTutorial.html | 112 ++++++++++------ inst/doc/ReadMe.Rmd | 16 +- inst/doc/ReadMe.html | 27 +++ man/fst_find_stopwords.Rd | 2 man/fst_format.Rd | 9 - man/fst_format_svydesign.Rd | 10 - man/fst_freq_table.Rd | 2 man/fst_prepare.Rd | 13 + man/fst_prepare_svydesign.Rd | 16 +- man/fst_rm_stop_punct.Rd | 6 vignettes/Overview-PackageTutorial.Rmd | 20 ++ vignettes/ReadMe.Rmd | 16 +- vignettes/web_only/Extra-AnalysingOtherLanguages.Rmd | 109 +++++++++------ vignettes/web_only/Extra-UseWithSurveyPackage.Rmd | 3 vignettes/web_only/InDetail1-DataPreparation.Rmd | 15 +- vignettes/web_only/InDetail2-DataExploration.Rmd | 2 vignettes/web_only/InDetail3-ConceptNetworkOverview.Rmd | 6 vignettes/web_only/InDetail6-AnalysisExample2.Rmd | 1 29 files changed, 375 insertions(+), 213 deletions(-)
More information about finnsurveytext at CRAN
Permanent link
Title: Spectroscopy Related Utilities
Description: Utility functions for spectroscopy. 1. Functions to simulate
spectra for use in teaching or testing. 2. Functions to process files created by
'LoggerPro' and 'SpectraSuite' software.
Author: Bryan A. Hanson [aut, cre]
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between SpecHelpers versions 0.2.7 dated 2017-07-26 and 0.3.1 dated 2025-03-06
SpecHelpers-0.2.7/SpecHelpers/inst |only SpecHelpers-0.3.1/SpecHelpers/DESCRIPTION | 20 ++++--- SpecHelpers-0.3.1/SpecHelpers/MD5 | 42 +++++++-------- SpecHelpers-0.3.1/SpecHelpers/NAMESPACE | 1 SpecHelpers-0.3.1/SpecHelpers/NEWS | 5 + SpecHelpers-0.3.1/SpecHelpers/R/CIExyz.R | 5 + SpecHelpers-0.3.1/SpecHelpers/R/SpecHelpers-package.R | 3 - SpecHelpers-0.3.1/SpecHelpers/R/emSpectrum.R | 2 SpecHelpers-0.3.1/SpecHelpers/R/getGamutValues.R | 2 SpecHelpers-0.3.1/SpecHelpers/R/multiplet.R |only SpecHelpers-0.3.1/SpecHelpers/R/plotCIEchrom.R | 4 - SpecHelpers-0.3.1/SpecHelpers/R/prepCIEgradient.R | 2 SpecHelpers-0.3.1/SpecHelpers/R/sysdata.rda |binary SpecHelpers-0.3.1/SpecHelpers/build |only SpecHelpers-0.3.1/SpecHelpers/data/CIExyz.RData |binary SpecHelpers-0.3.1/SpecHelpers/man/CIExyz.Rd | 17 +++--- SpecHelpers-0.3.1/SpecHelpers/man/SpecHelpers-package.Rd | 8 ++ SpecHelpers-0.3.1/SpecHelpers/man/getGamutValues.Rd | 1 SpecHelpers-0.3.1/SpecHelpers/man/makeSpec.Rd | 12 +++- SpecHelpers-0.3.1/SpecHelpers/man/multiplet.Rd |only SpecHelpers-0.3.1/SpecHelpers/man/plot2DNMRspec.Rd | 12 +++- SpecHelpers-0.3.1/SpecHelpers/man/plotCIEchrom.Rd | 12 +++- SpecHelpers-0.3.1/SpecHelpers/man/plotNMRspec.Rd | 13 +++- SpecHelpers-0.3.1/SpecHelpers/man/qMS.Rd | 3 - 24 files changed, 109 insertions(+), 55 deletions(-)
Title: TK Rplot
Description: Simple mechanism for placing R graphics in a Tk widget.
Author: Luke Tierney <luke-tierney@uiowa.edu>
Maintainer: Luke Tierney <luke-tierney@uiowa.edu>
Diff between tkrplot versions 0.0-27 dated 2022-10-18 and 0.0-29 dated 2025-03-06
DESCRIPTION | 6 +++--- MD5 | 6 +++--- man/TkRplot.Rd | 7 +++++++ src/tcltkimg.c | 10 ++++++---- 4 files changed, 19 insertions(+), 10 deletions(-)
Title: Methods for Quantitative Magnetic Resonance Imaging ('qMRI')
Description: Implementation of methods for estimation of quantitative maps
from Multi-Parameter Mapping (MPM) acquisitions (Weiskopf et al. (2013)
<doi:10.3389/fnins.2013.00095>) and analysis of Inversion Recovery MRI data.
Usage of the package is described in
Polzehl and Tabelow (2023),
"Magnetic Resonance Brain Imaging", 2nd Edition, Chapter 6 and 7, Springer, Use R! Series.
<doi:10.1007/978-3-031-38949-8>.
J. Polzehl and K. Tabelow (2023), "Magnetic Resonance Brain Imaging - Modeling and Data Analysis Using R: Code and Data."
<doi:10.20347/WIAS.DATA.6> provides extensive example code and data.
Author: Joerg Polzehl [aut],
Karsten Tabelow [aut, cre],
WIAS Berlin [cph, fnd]
Maintainer: Karsten Tabelow <karsten.tabelow@wias-berlin.de>
Diff between qMRI versions 1.2.7.8 dated 2024-12-09 and 1.2.7.9 dated 2025-03-06
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- build/partial.rdb |binary inst/doc/IRMRI-Example.R | 2 +- inst/doc/IRMRI-Example.Rnw | 2 +- inst/doc/IRMRI-Example.pdf |binary inst/doc/qMRI-Example.pdf |binary man/estimateIR.Rd | 2 +- man/estimateIRfluid.Rd | 2 +- man/estimateIRsolid.Rd | 2 +- man/estimateIRsolidfixed.Rd | 2 +- man/readIRData.Rd | 2 +- man/smoothIRSolid.Rd | 2 +- vignettes/IRMRI-Example-2.pdf |binary vignettes/IRMRI-Example-9.pdf |binary vignettes/IRMRI-Example.Rnw | 2 +- vignettes/qMRI-Example-11.pdf |binary vignettes/qMRI-Example-8.pdf |binary 18 files changed, 30 insertions(+), 30 deletions(-)
Title: Simulation of Matrix Population Models with Defined Life History
Characteristics
Description: Allows users to simulate matrix population models with
particular characteristics based on aspects of life history such as
mortality trajectories and fertility trajectories. Also allows the
exploration of sampling error due to small sample size.
Author: Owen Jones [aut, cre]
Maintainer: Owen Jones <jones@biology.sdu.dk>
Diff between mpmsim versions 3.1.0 dated 2024-10-12 and 3.2.0 dated 2025-03-06
mpmsim-3.1.0/mpmsim/R/generate_mpm_set.R |only mpmsim-3.1.0/mpmsim/R/random_mpm.R |only mpmsim-3.1.0/mpmsim/man/generate_mpm_set.Rd |only mpmsim-3.1.0/mpmsim/man/random_mpm.Rd |only mpmsim-3.1.0/mpmsim/tests/testthat/test-generate_mpm_set.R |only mpmsim-3.1.0/mpmsim/tests/testthat/test-random_mpm.R |only mpmsim-3.2.0/mpmsim/DESCRIPTION | 10 - mpmsim-3.2.0/mpmsim/MD5 | 65 +++--- mpmsim-3.2.0/mpmsim/NAMESPACE | 2 mpmsim-3.2.0/mpmsim/NEWS.md | 5 mpmsim-3.2.0/mpmsim/R/make_leslie_mpm.R | 11 + mpmsim-3.2.0/mpmsim/R/plot_matrix.R | 6 mpmsim-3.2.0/mpmsim/R/rand_lefko_mpm.R | 13 + mpmsim-3.2.0/mpmsim/R/rand_lefko_set.R | 48 ++++- mpmsim-3.2.0/mpmsim/R/rand_leslie_set.R | 60 +++--- mpmsim-3.2.0/mpmsim/README.md | 55 +++-- mpmsim-3.2.0/mpmsim/build/partial.rdb |binary mpmsim-3.2.0/mpmsim/build/vignette.rds |binary mpmsim-3.2.0/mpmsim/inst/WORDLIST | 4 mpmsim-3.2.0/mpmsim/inst/doc/generating_lefkovitch_models.Rmd | 4 mpmsim-3.2.0/mpmsim/inst/doc/generating_lefkovitch_models.html | 4 mpmsim-3.2.0/mpmsim/inst/doc/generating_leslie_models.R | 9 mpmsim-3.2.0/mpmsim/inst/doc/generating_leslie_models.Rmd | 20 +- mpmsim-3.2.0/mpmsim/inst/doc/generating_leslie_models.html | 23 +- mpmsim-3.2.0/mpmsim/inst/doc/sampling_error_propagation.R | 30 +-- mpmsim-3.2.0/mpmsim/inst/doc/sampling_error_propagation.Rmd | 44 ++-- mpmsim-3.2.0/mpmsim/inst/doc/sampling_error_propagation.html | 94 +++++----- mpmsim-3.2.0/mpmsim/man/figures/logo_mpmsim.png |only mpmsim-3.2.0/mpmsim/man/make_leslie_mpm.Rd | 12 + mpmsim-3.2.0/mpmsim/man/model_fecundity.Rd | 8 mpmsim-3.2.0/mpmsim/man/rand_lefko_mpm.Rd | 15 + mpmsim-3.2.0/mpmsim/man/rand_lefko_set.Rd | 36 ++- mpmsim-3.2.0/mpmsim/man/rand_leslie_set.Rd | 21 +- mpmsim-3.2.0/mpmsim/tests/testthat/test-rand_lefko_set.R | 10 - mpmsim-3.2.0/mpmsim/vignettes/generating_lefkovitch_models.Rmd | 4 mpmsim-3.2.0/mpmsim/vignettes/generating_leslie_models.Rmd | 20 +- mpmsim-3.2.0/mpmsim/vignettes/sampling_error_propagation.Rmd | 44 ++-- 37 files changed, 389 insertions(+), 288 deletions(-)
Title: Miscellaneous Functions in C++
Description: Provides utility functions that are simply, frequently used,
but may require higher performance that what can be obtained from base R.
Incidentally provides support for 'reverse geocoding', such as matching a point
with its nearest neighbour in another array. Used as a complement to package
'hutils' by sacrificing compilation or installation time for higher running
speeds. The name is a portmanteau of the author and 'Rcpp'.
Author: Hugh Parsonage [aut, cre],
Simon Urbanek [ctb]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between hutilscpp versions 0.10.7 dated 2025-01-08 and 0.10.8 dated 2025-03-06
DESCRIPTION | 8 +++--- MD5 | 8 +++--- NEWS.md | 1 man/ModeC.Rd | 2 - src/fastmatch_fastmatch.c | 59 ++++++++++++++++++++++++---------------------- 5 files changed, 41 insertions(+), 37 deletions(-)
Title: Download Colombian Demographic, Climate and Geospatial Data
Description: Downloads wrangled Colombian socioeconomic, geospatial,population
and climate data from DANE <https://www.dane.gov.co/> (National
Administrative Department of Statistics) and IDEAM (Institute of Hydrology,
Meteorology and Environmental Studies). It solves the problem of Colombian
data being issued in different web pages and sources by using functions that
allow the user to select the desired database and download it without having
to do the exhausting acquisition process.
Author: Maria Camila Tavera-Cifuentes [aut, cre, cph]
,
Julian Otero [aut, cph] ,
Natalia Nino-Machado [ctb] ,
Catalina Gonzalez-Uribe [ctb] ,
Juan Manuel Cordovez [ctb] ,
Hugo Gruson [rev] ,
Chris Hartgerink [rev] ,
Karim Mane [rev] ,
Joshua W. Lambert [rev [...truncated...]
Maintainer: Maria Camila Tavera-Cifuentes <mc.tavera@uniandes.edu.co>
Diff between ColOpenData versions 0.3.1 dated 2024-10-30 and 1.0.0 dated 2025-03-06
DESCRIPTION | 16 MD5 | 56 NEWS.md | 34 R/download_climate.R | 640 +- R/download_demographic.R | 14 R/download_geospatial.R | 255 R/download_population_projections.R | 222 README.md | 56 build/vignette.rds |binary inst/WORDLIST | 247 inst/doc/climate_data.Rmd | 2 inst/doc/climate_data.html | 4 inst/doc/demographic_data.Rmd | 2 inst/doc/demographic_data.html | 4 inst/doc/design_principles.R |only inst/doc/design_principles.Rmd |only inst/doc/design_principles.html |only inst/doc/documentation_and_dictionaries.Rmd | 6 inst/doc/documentation_and_dictionaries.html | 21 inst/doc/geospatial_data.Rmd | 2 inst/doc/geospatial_data.html | 4 tests/testthat/_snaps/download_climate.md | 452 - tests/testthat/_snaps/download_demographic.md | 2484 ++++---- tests/testthat/_snaps/download_geospatial.md | 30 tests/testthat/_snaps/download_population_projections.md | 4400 +++++++-------- tests/testthat/_snaps/merge_geo_demographic.md | 108 vignettes/climate_data.Rmd | 2 vignettes/demographic_data.Rmd | 2 vignettes/design_principles.Rmd |only vignettes/documentation_and_dictionaries.Rmd | 6 vignettes/geospatial_data.Rmd | 2 31 files changed, 4598 insertions(+), 4473 deletions(-)
Title: Model Selection and Multimodel Inference Based on (Q)AIC(c)
Description: Functions to implement model selection and multimodel inference based on Akaike's information criterion (AIC) and the second-order AIC (AICc), as well as their quasi-likelihood counterparts (QAIC, QAICc) from various model object classes. The package implements classic model averaging for a given parameter of interest or predicted values, as well as a shrinkage version of model averaging parameter estimates or effect sizes. The package includes diagnostics and goodness-of-fit statistics for certain model types including those of 'unmarkedFit' classes estimating demographic parameters after accounting for imperfect detection probabilities. Some functions also allow the creation of model selection tables for Bayesian models of the 'bugs', 'rjags', and 'jagsUI' classes. Functions also implement model selection using BIC. Objects following model selection and multimodel inference can be formatted to LaTeX using 'xtable' methods included in the package.
Author: Marc J. Mazerolle [aut, cre]
Maintainer: Marc J. Mazerolle <marc.mazerolle@sbf.ulaval.ca>
Diff between AICcmodavg versions 2.3-3 dated 2023-11-16 and 2.3-4 dated 2025-03-06
DESCRIPTION | 15 MD5 | 70 +-- NAMESPACE | 36 + R/aictab.R | 132 ++++++ R/anovaOD.R | 237 +++++++++++ R/bictab.R | 102 ++++ R/detHist.R | 390 +++++++++++++++++-- R/extractCN.R | 3 R/extractX.R | 282 +++++++++++++ R/importance.R | 181 ++++++++ R/mb.gof.test.R | 4 R/modavg.R | 612 +++++++++++++++++++++++++++++ R/modavgEffect.R | 528 +++++++++++++++++++++++++ R/modavgPred.R | 780 ++++++++++++++++++++++++++++++++++++++ R/modavgShrink.R | 359 +++++++++++++++++ R/summaryOD.R | 121 +++++ build/vignette.rds |binary inst/NEWS | 8 inst/NEWS.Rd | 21 - inst/doc/AICcmodavg-unmarked.R | 16 inst/doc/AICcmodavg-unmarked.Rnw | 11 inst/doc/AICcmodavg-unmarked.pdf |binary inst/doc/AICcmodavg.pdf |binary man/AICcmodavg-package.Rd | 20 man/aictab.Rd | 8 man/anovaOD.Rd | 8 man/bictab.Rd | 10 man/detHist.Rd | 33 + man/extractX.Rd | 69 +-- man/importance.Rd | 22 - man/modavg.Rd | 42 +- man/modavgEffect.Rd | 134 +++++- man/modavgPred.Rd | 123 +++++ man/modavgShrink.Rd | 49 +- man/summaryOD.Rd | 14 vignettes/AICcmodavg-unmarked.Rnw | 11 36 files changed, 4221 insertions(+), 230 deletions(-)
Title: 'date' C++ Header Library for Date and Time Functionality
Description: A header-only C++ library is provided with support
for dates, time zones, ISO weeks, Julian dates, and Islamic dates.
'date' offers extensive date and time functionality for the C++11,
C++14 and C++17 standards and was written by Howard Hinnant and released
under the MIT license. A slightly modified version has been accepted
(along with 'tz.h') as part of C++20. This package regroups all
header files from the upstream repository by Howard Hinnant so that
other R packages can use them in their C++ code. At present, few of
the types have explicit 'Rcpp' wrappers though these may be added as
needed.
Author: Dirk Eddelbuettel [aut, cre] ,
Howard Hinnant [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppDate versions 0.0.4 dated 2024-10-14 and 0.0.5 dated 2025-03-06
ChangeLog | 21 +++++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- build/partial.rdb |binary inst/NEWS.Rd | 8 ++++++++ inst/include/date.h | 8 ++++---- inst/include/islamic.h | 8 ++++---- inst/include/iso_week.h | 4 ++-- inst/include/julian.h | 8 ++++---- inst/include/solar_hijri.h | 8 ++++---- inst/include/tz.h | 12 ++++++------ 11 files changed, 67 insertions(+), 38 deletions(-)
Title: Canonical Correlations and Tests of Independence
Description: A simple interface for multivariate correlation analysis that unifies various classical
statistical procedures including t-tests, tests in univariate and multivariate linear models,
parametric and nonparametric tests for correlation, Kruskal-Wallis tests, common approximate
versions of Wilcoxon rank-sum and signed rank tests, chi-squared tests of independence, score
tests of particular hypotheses in generalized linear models, canonical correlation analysis and
linear discriminant analysis.
Author: Robert Schlicht [aut, cre]
Maintainer: Robert Schlicht <robert.schlicht@tu-dresden.de>
Diff between cctest versions 1.2.0 dated 2025-01-07 and 1.2.1 dated 2025-03-06
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/cctest.R | 2 +- man/cctest.Rd | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Graphs and Tables for OMOP Results
Description: Provides methods to transform omop_result objects into
formatted tables and figures, facilitating the visualisation of study
results working with the Observational Medical Outcomes Partnership
(OMOP) Common Data Model.
Author: Marti Catala [aut] ,
Nuria Mercade-Besora [aut, cre]
,
Yuchen Guo [ctb] ,
Elin Rowlands [ctb] ,
Marta Alcalde-Herraiz [ctb] ,
Edward Burn [ctb]
Maintainer: Nuria Mercade-Besora <nuria.mercadebesora@ndorms.ox.ac.uk>
Diff between visOmopResults versions 1.0.1 dated 2025-02-27 and 1.0.2 dated 2025-03-06
DESCRIPTION | 32 - MD5 | 37 - R/datatableInternal.R | 140 ++-- R/formatEstimateValue.R | 2 R/mockResults.R | 5 R/plot.R | 4 R/plottingThemes.R | 2 R/utilities.R | 550 +++++++++-------- R/visOmopTable.R | 536 ++++++++--------- R/visTable.R | 389 ++++++------ inst/doc/a01_tables.html | 925 +++++++++++++++--------------- inst/doc/a02_plots.R | 6 man/visOmopResults-package.Rd | 2 tests/testthat/_snaps |only tests/testthat/test-datatableInternal.R |only tests/testthat/test-formatEstimateName.R | 4 tests/testthat/test-formatEstimateValue.R | 4 tests/testthat/test-formatTable.R | 181 ++--- tests/testthat/test-visOmopTable.R | 732 ++++++++++++----------- tests/testthat/test-visTable.R | 297 ++++----- 20 files changed, 1974 insertions(+), 1874 deletions(-)
More information about visOmopResults at CRAN
Permanent link
Title: Calculate Earth’s Obliquity and Precession in the Past
Description: Easily calculate precession and obliquity from an orbital solution (defaults to ZB18a from Zeebe and Lourens (2019) <doi:10.1126/science.aax0612>) and assumed or reconstructed values for tidal dissipation (Td) and dynamical ellipticity (Ed). This is a translation and adaptation of the 'C'-code in the supplementary material to Zeebe and Lourens (2022) <doi:10.1029/2021PA004349>, with further details on the methodology described in Zeebe (2022) <doi:10.3847/1538-3881/ac80f8>. The name of the 'C'-routine is 'snvec', which refers to the key units of computation: spin vector s and orbit normal vector n.
Author: Ilja Kocken [aut, cre, trl, cph]
,
Richard Zeebe [aut]
Maintainer: Ilja Kocken <ikocken@hawaii.edu>
Diff between snvecR versions 3.10.0 dated 2025-03-01 and 3.10.1 dated 2025-03-06
snvecR-3.10.0/snvecR/man/PT-ZB18a.Rd |only snvecR-3.10.0/snvecR/man/ZB23.Rxx.Rd |only snvecR-3.10.1/snvecR/DESCRIPTION | 6 snvecR-3.10.1/snvecR/MD5 | 33 ++- snvecR-3.10.1/snvecR/NEWS.md | 38 +++- snvecR-3.10.1/snvecR/R/data.R | 7 snvecR-3.10.1/snvecR/R/get_solution.R | 34 ++- snvecR-3.10.1/snvecR/README.md | 102 ++++++++++- snvecR-3.10.1/snvecR/build/vignette.rds |binary snvecR-3.10.1/snvecR/inst/doc/analyze_grid_td-ed.html | 112 ++++++------- snvecR-3.10.1/snvecR/inst/doc/compare_with_c.R |only snvecR-3.10.1/snvecR/inst/doc/compare_with_c.Rmd |only snvecR-3.10.1/snvecR/inst/doc/compare_with_c.html |only snvecR-3.10.1/snvecR/man/PT_ZB18a.Rd |only snvecR-3.10.1/snvecR/man/ZB23.Rd |only snvecR-3.10.1/snvecR/man/get_solution.Rd | 8 snvecR-3.10.1/snvecR/tests/testthat/_snaps/get_solution.md | 73 ++++++++ snvecR-3.10.1/snvecR/tests/testthat/_snaps/snvec.md | 64 +++++++ snvecR-3.10.1/snvecR/tests/testthat/test-get_solution.R | 14 + snvecR-3.10.1/snvecR/tests/testthat/test-globals.R |only snvecR-3.10.1/snvecR/tests/testthat/test-snvec.R | 25 ++ snvecR-3.10.1/snvecR/vignettes/compare_with_c.Rmd |only 22 files changed, 387 insertions(+), 129 deletions(-)
Title: Distances on Directed Graphs
Description: Distances on dual-weighted directed graphs using
priority-queue shortest paths (Padgham (2019) <doi:10.32866/6945>).
Weighted directed graphs have weights from A to B which may differ
from those from B to A. Dual-weighted directed graphs have two sets
of such weights. A canonical example is a street network to be used
for routing in which routes are calculated by weighting distances
according to the type of way and mode of transport, yet lengths of
routes must be calculated from direct distances.
Author: Mark Padgham [aut, cre],
Andreas Petutschnig [aut],
David Cooley [aut],
Robin Lovelace [ctb],
Andrew Smith [ctb],
Malcolm Morgan [ctb],
Andrea Gilardi [ctb] ,
Shane Saunders [cph] ,
Stanislaw Adaszewski [cph]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between dodgr versions 0.4.1 dated 2024-07-07 and 0.4.2 dated 2025-03-06
DESCRIPTION | 12 +- MD5 | 118 ++++++++++---------- NEWS.md | 18 ++- R/centrality.R | 2 R/dists-nearest.R | 14 -- R/dists.R | 108 +++++++++++------- R/flows.R | 50 ++++++-- R/fund-cycles.R | 1 R/graph-contraction.R | 74 +++++++----- R/graph-conversion.R | 7 + R/graph-functions-misc.R | 35 ++++++ R/graph-functions.R | 11 + R/match-points.R | 7 - R/times.R | 10 - R/weight-streetnet.R | 186 +++++++++++++++++++++++--------- README.md | 47 +++++++- build/vignette.rds |binary inst/doc/dists-categorical.R | 2 inst/doc/dists-categorical.html | 18 +-- inst/doc/dodgr.R | 86 +++++++------- inst/doc/dodgr.html | 89 ++++++--------- inst/doc/flows.R | 72 ++++++------ inst/doc/flows.html | 8 - inst/doc/parallel.R | 2 inst/doc/parallel.html | 4 inst/doc/times.R | 28 ++-- inst/doc/times.html | 8 - man/dodgr.Rd | 1 man/dodgr_centrality.Rd | 2 man/dodgr_distances.Rd | 100 ++++++++++------- man/dodgr_dists.Rd | 100 ++++++++++------- man/dodgr_dists_categorical.Rd | 17 ++ man/dodgr_dists_nearest.Rd | 45 ++++++- man/dodgr_flows_aggregate.Rd | 34 ++++- man/dodgr_flows_disperse.Rd | 10 + man/dodgr_flows_si.Rd | 33 ++++- man/dodgr_times.Rd | 95 +++++++++------- man/dodgr_uncontract_graph.Rd | 13 ++ man/weight_streetnet.Rd | 140 ++++++++++++++++-------- src/deduplicate.cpp | 5 src/heaps/bheap.cpp | 1 src/heaps/fheap.cpp | 1 src/heaps/heap23.cpp | 1 src/heaps/triheap.cpp | 1 src/heaps/triheap_ext.cpp | 1 tests/testthat/test-cache.R | 45 ++++--- tests/testthat/test-centrality.R | 6 - tests/testthat/test-cycles.R | 2 tests/testthat/test-deduplicate.R | 4 tests/testthat/test-dists-categorical.R | 14 +- tests/testthat/test-dists-nearest.R | 6 - tests/testthat/test-dists.R | 82 +++++++++----- tests/testthat/test-flows.R | 6 - tests/testthat/test-graph-conversion.R | 6 - tests/testthat/test-graph-fns.R | 27 +++- tests/testthat/test-iso.R | 10 - tests/testthat/test-match-pts-fns.R | 7 - tests/testthat/test-save-load.R | 6 - tests/testthat/test-sc.R | 8 - tests/testthat/test-streetnet.R | 27 +++- 60 files changed, 1191 insertions(+), 682 deletions(-)
Title: Parallel Numerical Derivatives, Gradients, Jacobians, and
Hessians of Arbitrary Accuracy Order
Description: Numerical derivatives through finite-difference approximations
can be calculated using the 'pnd' package with parallel capabilities and
optimal step-size selection to improve accuracy. These functions facilitate
efficient computation of derivatives, gradients, Jacobians, and Hessians,
allowing for more evaluations to reduce the mathematical and machine errors.
Designed for compatibility with the 'numDeriv' package,
which has not received updates in several years, it introduces advanced features
such as computing derivatives of arbitrary order, improving
the accuracy of Hessian approximations by avoiding repeated differencing,
and parallelising slow functions on Windows, Mac, and Linux.
Author: Andrei Victorovitch Kostyrka [aut, cre]
Maintainer: Andrei Victorovitch Kostyrka <andrei.kostyrka@gmail.com>
Diff between pnd versions 0.0.7 dated 2025-03-01 and 0.0.8 dated 2025-03-06
DESCRIPTION | 6 +- MD5 | 36 ++++++++--------- NEWS.md | 7 +-- R/gradient.R | 15 +++---- R/helpers.R | 3 - R/zzz.R | 10 +++- build/partial.rdb |binary inst/CITATION | 16 +++---- inst/doc/compatibility-with-numDeriv.R | 13 +++--- inst/doc/compatibility-with-numDeriv.Rmd | 23 +++++++--- inst/doc/compatibility-with-numDeriv.html | 63 ++++++++++++++++++++---------- inst/doc/fast-and-accurate.html | 2 inst/doc/step-size-selection.html | 2 man/GenD.Rd | 2 man/Grad.Rd | 2 man/Jacobian.Rd | 2 man/checkDimensions.Rd | 2 tests/testthat/Rplots.pdf |binary vignettes/compatibility-with-numDeriv.Rmd | 23 +++++++--- 19 files changed, 136 insertions(+), 91 deletions(-)
Title: Latent Space Item Response Model
Description: Analysis of dichotomous and continuous response data using latent factor by both 1PL LSIRM and 2PL LSIRM as described in Jeon et al. (2021) <doi:10.1007/s11336-021-09762-5>. It includes original 1PL LSIRM and 2PL LSIRM provided for binary response data and its extension for continuous response data. Bayesian model selection with spike-and-slab prior and method for dealing data with missing value under missing at random, missing completely at random are also supported. Various diagnostic plots are available to inspect the latent space and summary of estimated parameters.
Author: Dongyoung Go [aut],
Gwanghee Kim [aut, cre],
Jina Park [aut],
Ickhoon Jin [ctb],
Minjeong Jeon [ctb]
Maintainer: Gwanghee Kim <musagh08@yonsei.ac.kr>
Diff between lsirm12pl versions 1.3.3 dated 2024-08-28 and 1.3.4 dated 2025-03-06
lsirm12pl-1.3.3/lsirm12pl/data/BFPT.csv |only lsirm12pl-1.3.3/lsirm12pl/data/TDRI.csv |only lsirm12pl-1.3.4/lsirm12pl/DESCRIPTION | 18 lsirm12pl-1.3.4/lsirm12pl/MD5 | 10 lsirm12pl-1.3.4/lsirm12pl/R/lsirm.R | 561 +++++++++++++---- lsirm12pl-1.3.4/lsirm12pl/R/lsirm1pl_fixed_gamma_mar.R | 300 ++++----- lsirm12pl-1.3.4/lsirm12pl/data/BFPT.csv.gz |only lsirm12pl-1.3.4/lsirm12pl/data/TDRI.csv.gz |only 8 files changed, 613 insertions(+), 276 deletions(-)
Title: Data Visualisation on 'Lifemap' Tree
Description: Allow to visualise data on the NCBI phylogenetic tree as presented in Lifemap <https://lifemap.cnrs.fr/>. It takes as input a dataframe with at least a "taxid" column containing NCBI format TaxIds and allows to draw multiple layers with different visualisation tools.
Author: Cassandra Bompard [aut],
Damien M. de Vienne [aut] ,
Julien Barnier [aut] ,
Aurelie Siberchicot [ctb, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between LifemapR versions 1.1.4 dated 2024-07-31 and 1.1.5 dated 2025-03-06
DESCRIPTION | 21 - MD5 | 38 +- R/build_Lifemap.R | 178 ++++----- R/create_matrix.R | 19 - R/data.R | 246 ++++++------- R/display_map.R | 50 +- R/draw_Lifemap.R | 850 +++++++++++++++++++++++----------------------- R/lifemap_obj.R | 16 R/lm_branches.R | 6 R/lm_piecharts.R | 1 R/make_newick.R | 6 README.md | 55 +- build/vignette.rds |binary inst/doc/runLifemapR.R | 116 +++--- inst/doc/runLifemapR.Rmd | 15 inst/doc/runLifemapR.html | 29 - man/build_Lifemap.Rd | 6 man/display_map.Rd | 10 man/draw_Lifemap.Rd | 4 vignettes/runLifemapR.Rmd | 15 20 files changed, 835 insertions(+), 846 deletions(-)
Title: Helpers for Model Coefficients Tibbles
Description: Provides suite of functions to work with regression model
'broom::tidy()' tibbles. The suite includes functions to group
regression model terms by variable, insert reference and header rows
for categorical variables, add variable labels, and more.
Author: Joseph Larmarange [aut, cre] ,
Daniel D. Sjoberg [aut]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between broom.helpers versions 1.19.0 dated 2025-01-29 and 1.20.0 dated 2025-03-06
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Title: Classes and Methods for Fast Memory-Efficient Boolean Selections
Description: Provided are classes for boolean and skewed boolean vectors,
fast boolean methods, fast unique and non-unique integer sorting,
fast set operations on sorted and unsorted sets of integers, and
foundations for ff (range index, compression, chunked processing).
Author: Michael Chirico [aut, cre],
Jens Oehlschlaegel [aut],
Brian Ripley [ctb]
Maintainer: Michael Chirico <MichaelChirico4@gmail.com>
Diff between bit versions 4.5.0.1 dated 2024-12-03 and 4.6.0 dated 2025-03-06
bit-4.5.0.1/bit/NEWS |only bit-4.5.0.1/bit/inst/doc/bit-demo.pdf |only bit-4.5.0.1/bit/inst/doc/bit-performance.pdf |only bit-4.5.0.1/bit/inst/doc/bit-usage.pdf |only bit-4.6.0/bit/DESCRIPTION | 32 bit-4.6.0/bit/MD5 | 201 - bit-4.6.0/bit/NEWS.md |only bit-4.6.0/bit/R/attrutil.R | 106 bit-4.6.0/bit/R/bit-package.R | 13 bit-4.6.0/bit/R/bit.R | 3100 +++++++++++------------- bit-4.6.0/bit/R/bitsort.R | 755 ++--- bit-4.6.0/bit/R/chunkutil.R | 519 +--- bit-4.6.0/bit/R/clone.R | 43 bit-4.6.0/bit/R/generics.R | 410 +-- bit-4.6.0/bit/R/integerutil.R | 116 bit-4.6.0/bit/R/merge.R | 300 +- bit-4.6.0/bit/R/rle.R | 196 - bit-4.6.0/bit/R/timeutil.R | 72 bit-4.6.0/bit/R/zzz.R | 41 bit-4.6.0/bit/build/vignette.rds |binary bit-4.6.0/bit/inst/doc/bit-demo.R | 28 bit-4.6.0/bit/inst/doc/bit-demo.Rmd | 39 bit-4.6.0/bit/inst/doc/bit-demo.html |only bit-4.6.0/bit/inst/doc/bit-performance.R | 543 ++-- bit-4.6.0/bit/inst/doc/bit-performance.Rmd | 556 ++-- bit-4.6.0/bit/inst/doc/bit-performance.html |only bit-4.6.0/bit/inst/doc/bit-usage.R | 276 +- bit-4.6.0/bit/inst/doc/bit-usage.Rmd | 335 +- bit-4.6.0/bit/inst/doc/bit-usage.html |only bit-4.6.0/bit/man/CoercionToStandard.Rd | 16 bit-4.6.0/bit/man/Extract.Rd | 28 bit-4.6.0/bit/man/Metadata.Rd | 13 bit-4.6.0/bit/man/PhysVirt.Rd | 11 bit-4.6.0/bit/man/Sorting.Rd | 68 bit-4.6.0/bit/man/Summaries.Rd | 43 bit-4.6.0/bit/man/as.bit.Rd | 36 bit-4.6.0/bit/man/as.bitwhich.Rd | 37 bit-4.6.0/bit/man/as.booltype.Rd | 5 bit-4.6.0/bit/man/as.character.bit.Rd | 2 bit-4.6.0/bit/man/as.character.bitwhich.Rd | 2 bit-4.6.0/bit/man/as.ri.Rd | 10 bit-4.6.0/bit/man/as.which.Rd | 32 bit-4.6.0/bit/man/bbatch.Rd | 14 bit-4.6.0/bit/man/bit-package.Rd | 9 bit-4.6.0/bit/man/bit.Rd | 8 bit-4.6.0/bit/man/bit_in.Rd | 10 bit-4.6.0/bit/man/bit_init.Rd | 6 bit-4.6.0/bit/man/bit_rangediff.Rd | 18 bit-4.6.0/bit/man/bit_setops.Rd | 14 bit-4.6.0/bit/man/bit_sort.Rd | 14 bit-4.6.0/bit/man/bit_sort_unique.Rd | 34 bit-4.6.0/bit/man/bit_unidup.Rd | 62 bit-4.6.0/bit/man/bitsort.Rd | 11 bit-4.6.0/bit/man/bitwhich.Rd | 36 bit-4.6.0/bit/man/bitwhich_representation.Rd | 6 bit-4.6.0/bit/man/booltype.Rd | 33 bit-4.6.0/bit/man/booltypes.Rd | 27 bit-4.6.0/bit/man/c.booltype.Rd | 8 bit-4.6.0/bit/man/chunk.Rd | 30 bit-4.6.0/bit/man/chunks.Rd | 28 bit-4.6.0/bit/man/clone.Rd | 20 bit-4.6.0/bit/man/copy_vector.Rd | 9 bit-4.6.0/bit/man/countsort.Rd | 8 bit-4.6.0/bit/man/firstNA.Rd | 4 bit-4.6.0/bit/man/get_length.Rd | 3 bit-4.6.0/bit/man/getsetattr.Rd | 28 bit-4.6.0/bit/man/in.bitwhich.Rd | 11 bit-4.6.0/bit/man/intrle.Rd | 40 bit-4.6.0/bit/man/is.booltype.Rd | 20 bit-4.6.0/bit/man/is.na.bit.Rd | 6 bit-4.6.0/bit/man/length.bit.Rd | 127 bit-4.6.0/bit/man/maxindex.Rd | 36 bit-4.6.0/bit/man/merge_rev.Rd | 168 - bit-4.6.0/bit/man/print.bitwhich.Rd | 2 bit-4.6.0/bit/man/quicksort2.Rd | 8 bit-4.6.0/bit/man/quicksort3.Rd | 8 bit-4.6.0/bit/man/range_na.Rd | 15 bit-4.6.0/bit/man/range_nanozero.Rd | 16 bit-4.6.0/bit/man/range_sortna.Rd | 30 bit-4.6.0/bit/man/rep.booltype.Rd | 12 bit-4.6.0/bit/man/repeat.time.Rd | 10 bit-4.6.0/bit/man/repfromto.Rd | 8 bit-4.6.0/bit/man/rev.booltype.Rd | 6 bit-4.6.0/bit/man/reverse_vector.Rd | 4 bit-4.6.0/bit/man/ri.Rd | 6 bit-4.6.0/bit/man/rlepack.Rd | 25 bit-4.6.0/bit/man/still.identical.Rd | 4 bit-4.6.0/bit/man/str.bit.Rd | 2 bit-4.6.0/bit/man/str.bitwhich.Rd | 2 bit-4.6.0/bit/man/symdiff.Rd | 12 bit-4.6.0/bit/man/unattr.Rd | 4 bit-4.6.0/bit/man/vecseq.Rd | 32 bit-4.6.0/bit/man/xor.Rd | 84 bit-4.6.0/bit/src/attrutil.c | 4 bit-4.6.0/bit/src/integerutil.c | 4 bit-4.6.0/bit/src/merge.h | 8 bit-4.6.0/bit/tests/ff_tests.R |only bit-4.6.0/bit/tests/testthat.R | 4 bit-4.6.0/bit/tests/testthat/test-bit.R | 611 ++-- bit-4.6.0/bit/tests/testthat/test-bitsort.R | 394 +-- bit-4.6.0/bit/tests/testthat/test-merge.R | 276 +- bit-4.6.0/bit/tests/testthat/test-old-regtest.R | 369 +- bit-4.6.0/bit/tests/testthat/test-rle.R | 98 bit-4.6.0/bit/vignettes/bit-demo.Rmd | 39 bit-4.6.0/bit/vignettes/bit-performance.Rmd | 556 ++-- bit-4.6.0/bit/vignettes/bit-usage.Rmd | 335 +- 106 files changed, 6141 insertions(+), 5679 deletions(-)
Title: Systematic Comparison of Trip Distribution Laws and Models
Description: The main purpose of this package is to propose a rigorous framework to fairly compare trip distribution laws and models as described in Lenormand et al. (2016) <doi:10.1016/j.jtrangeo.2015.12.008>.
Author: Maxime Lenormand [aut, cre]
Maintainer: Maxime Lenormand <maxime.lenormand@inrae.fr>
Diff between TDLM versions 1.1.0 dated 2025-01-07 and 1.1.1 dated 2025-03-06
DESCRIPTION | 6 - MD5 | 18 ++-- NEWS.md | 11 ++- R/extract_opportunities.R | 8 ++ R/run_law.R | 9 ++ R/run_law_model.R | 9 ++ R/run_model.R | 9 ++ README.md | 18 ++-- build/vignette.rds |binary inst/doc/TDLM.html | 168 +++++++++++++++++++++++----------------------- 10 files changed, 149 insertions(+), 107 deletions(-)
Title: CORe Multiple Sclerosis Outcomes Toolkit
Description: Enable operationalized evaluation of disease outcomes in
multiple sclerosis. ‘MSoutcomes’ requires longitudinally recorded
clinical data structured in long format. The package is based on the
research developed at Clinical Outcomes Research unit (CORe),
University of Melbourne and Neuroimmunology Centre, Royal Melbourne
Hospital. Kalincik et al. (2015) <doi:10.1093/brain/awv258>.
Lorscheider et al. (2016) <doi:10.1093/brain/aww173>. Sharmin et al.
(2022) <doi:10.1111/ene.15406>. Dzau et al. (2023)
<doi:10.1136/jnnp-2023-331748>.
Author: Sifat Sharmin [aut],
Johannes Lorscheider [aut],
Nathaniel Lizak [aut],
Sam Harding-Forrester [aut],
Winston Dzau [aut],
Jannis Mueller [aut],
Izanne Roos [aut],
Tomas Kalincik [aut, cre, cph]
Maintainer: Tomas Kalincik <tomas.kalincik@unimelb.edu.au>
Diff between MSoutcomes versions 0.2.0 dated 2024-02-29 and 0.2.1 dated 2025-03-05
DESCRIPTION | 14 +++++++++----- LICENSE | 2 +- MD5 | 16 ++++++++-------- NAMESPACE | 2 ++ NEWS.md | 11 +++++++++++ R/CDEseq.R | 59 ++++++++++++++++++++++++++++++++++++----------------------- R/CDI.R | 34 +++++++++++++++++++++------------- R/CDW.R | 34 +++++++++++++++++++++------------- R/PIRA.R | 34 +++++++++++++++++++++------------- 9 files changed, 130 insertions(+), 76 deletions(-)
Title: PD-Clustering and Related Methods
Description: Probabilistic distance clustering (PD-clustering) is an iterative, distribution-free, probabilistic clustering method. PD-clustering assigns units to a cluster according to their probability of membership under the constraint that the product of the probability and the distance of each point to any cluster center is a constant. PD-clustering is a flexible method that can be used with elliptical clusters, outliers, or noisy data. PDQ is an extension of the algorithm for clusters of different sizes. GPDC and TPDC use a dissimilarity measure based on densities. Factor PD-clustering (FPDC) is a factor clustering method that involves a linear transformation of variables and a cluster optimizing the PD-clustering criterion. It works on high-dimensional data sets.
Author: Cristina Tortora [aut, cre, cph],
Noe Vidales [aut],
Francesco Palumbo [aut],
Tina Kalra [aut],
Paul D. McNicholas [fnd]
Maintainer: Cristina Tortora <grikris1@gmail.com>
Diff between FPDclustering versions 2.3.4 dated 2025-02-13 and 2.3.5 dated 2025-03-05
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/PDQ.R | 5 ++--- 3 files changed, 8 insertions(+), 9 deletions(-)
Title: Free Knot-Bayesian Model Averaging
Description: Analysis of Bayesian adaptive enrichment clinical trial using Free-Knot Bayesian Model Averaging (FK-BMA) method of Maleyeff et al. (2024) for Gaussian data. Maleyeff, L., Golchi, S., Moodie, E. E. M., & Hudson, M. (2024) "An adaptive enrichment design using Bayesian model averaging for selection and threshold-identification of predictive variables" <doi:10.1093/biomtc/ujae141>.
Author: Lara Maleyeff [aut, cre],
Shirin Golchi [aut],
Erica E. M. Moodie [aut]
Maintainer: Lara Maleyeff <lara.maleyeff@mcgill.ca>
Diff between fkbma versions 0.1.0 dated 2025-01-31 and 0.2.0 dated 2025-03-05
fkbma-0.1.0/fkbma/man/fittedTrtEff.Rd |only fkbma-0.1.0/fkbma/man/predictTrtEff.Rd |only fkbma-0.2.0/fkbma/DESCRIPTION | 6 fkbma-0.2.0/fkbma/MD5 | 44 +- fkbma-0.2.0/fkbma/NAMESPACE | 5 fkbma-0.2.0/fkbma/R/data_generate.R | 4 fkbma-0.2.0/fkbma/R/rjMCMC.R | 81 ++-- fkbma-0.2.0/fkbma/R/s3-methods.R | 495 +++++++++++++------------ fkbma-0.2.0/fkbma/data/simulated_data.rda |binary fkbma-0.2.0/fkbma/man/coef.rjMCMC.Rd | 24 - fkbma-0.2.0/fkbma/man/credint.Rd | 7 fkbma-0.2.0/fkbma/man/fitted.rjMCMC.Rd | 24 - fkbma-0.2.0/fkbma/man/fittedExposureEff.Rd |only fkbma-0.2.0/fkbma/man/getEffectiveSubspace.Rd | 20 - fkbma-0.2.0/fkbma/man/pip.Rd | 25 - fkbma-0.2.0/fkbma/man/plot.rjMCMC.Rd | 24 - fkbma-0.2.0/fkbma/man/plotHistTrace.Rd | 8 fkbma-0.2.0/fkbma/man/predict.rjMCMC.Rd | 24 - fkbma-0.2.0/fkbma/man/predictExposureEff.Rd |only fkbma-0.2.0/fkbma/man/print.rjMCMC.Rd | 16 fkbma-0.2.0/fkbma/man/rhats.Rd | 33 - fkbma-0.2.0/fkbma/man/rjMCMC.Rd | 27 - fkbma-0.2.0/fkbma/man/simulated_data.Rd | 2 fkbma-0.2.0/fkbma/man/summary.rjMCMC.Rd | 26 - fkbma-0.2.0/fkbma/tests/testthat/test-rjMCMC.R | 18 25 files changed, 491 insertions(+), 422 deletions(-)
Title: An Extension of the Gap Statistic for Ordinal/Categorical Data
Description: The gap statistic approach is extended to estimate the number of clusters for categorical response format data. This approach and accompanying software is designed to be used with the output of any clustering algorithm and with distances specifically designed for categorical (i.e. multiple choice) or ordinal survey response data.
Author: Jeffrey Miecznikowski [aut],
Eduardo Cortes [aut, cre]
Maintainer: Eduardo Cortes <ecortesg@buffalo.edu>
Diff between DiscreteGapStatistic versions 1.0.0 dated 2024-12-09 and 1.1.2 dated 2025-03-05
DESCRIPTION | 6 - MD5 | 66 +++++------ R/AuxFuns.R | 11 + R/DiscreteClusGapFuns.R | 10 + R/DistanceFuns.R | 76 ++++++++---- R/SimDataFun.R | 3 R/VisualFuns.R | 35 ++++- R/data.R | 13 +- README.md | 185 +++++++++++++++++++------------ man/BhattacharyyaDist.Rd | 2 man/ChisqDist.Rd | 2 man/CramerV.Rd | 2 man/HellingerDist.Rd | 2 man/ResHeatmap.Rd | 21 ++- man/SimData.Rd | 3 man/clusGapDiscr.Rd | 4 man/clusGapDiscr0.Rd | 4 man/clusterFunSel.Rd | 5 man/concussion.Rd | 6 - man/cramersVmod.Rd | 8 - man/dissbhattacharyya.Rd | 8 - man/disschisquare.Rd | 8 - man/disscramerv.Rd | 8 - man/disshamming.Rd | 8 - man/disshellinger.Rd | 8 - man/distanceHeat.Rd | 15 +- man/distancematrix.Rd | 9 - man/figures/README-clusGapDiscrFit-1.png |binary man/figures/README-clusGapDiscrFit-2.png |binary man/figures/README-clusGapDiscrFit-3.png |binary man/findK.Rd | 2 man/kmodesD.Rd | 5 man/likert.heat.plot2.Rd | 8 - man/mass.Rd | 11 - 34 files changed, 320 insertions(+), 234 deletions(-)
More information about DiscreteGapStatistic at CRAN
Permanent link
Title: Tools and Metrics for 3D Surfaces and Objects
Description: A collection of functions for sampling and simulating 3D surfaces and objects
and estimating metrics like rugosity, fractal dimension, convexity, sphericity, circularity,
second moments of area and volume, and more.
Author: Joshua Madin [aut] ,
Nina Schiettekatte [aut, cre]
Maintainer: Nina Schiettekatte <nina.schiettekatte@gmail.com>
Diff between habtools versions 1.0.7 dated 2024-11-15 and 1.1.1 dated 2025-03-05
DESCRIPTION | 8 ++-- MD5 | 39 ++++++++++++---------- NAMESPACE | 4 ++ NEWS.md | 6 +++ R/entropy.R |only R/fd_boxes.R | 6 +-- R/fd_cubes.R | 13 ++++--- R/fd_diagnose.R | 36 +++++++++++--------- R/planar.R | 7 ---- R/rg.R | 2 - R/smv.R | 4 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/DEM_intro.html | 6 +-- inst/doc/fractal_intro.html | 76 ++++++++++++++++++++++---------------------- inst/doc/mesh_intro.html | 38 +++++++++++----------- man/entropy.Rd |only man/entropy_1d.Rd |only man/entropy_2d.Rd |only man/entropy_3d.Rd |only man/fd_cubes.Rd | 2 - man/fd_diagnose.Rd | 6 ++- man/smv.Rd | 4 +- 23 files changed, 138 insertions(+), 119 deletions(-)
Title: Miscellaneous Functions for Processing and Sample Selection of
Spectroscopic Data
Description: Functions to preprocess spectroscopic data
and conduct (representative) sample selection/calibration sampling.
Author: Antoine Stevens [aut] ,
Leonardo Ramirez-Lopez [aut, cre]
Maintainer: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Diff between prospectr versions 0.2.7 dated 2024-02-16 and 0.2.8 dated 2025-03-05
prospectr-0.2.7/prospectr/build/prospectr.pdf |only prospectr-0.2.8/prospectr/DESCRIPTION | 29 +++++++---- prospectr-0.2.8/prospectr/LICENSE | 2 prospectr-0.2.8/prospectr/MD5 | 30 +++++------ prospectr-0.2.8/prospectr/NEWS.md | 15 +++++ prospectr-0.2.8/prospectr/R/gapDer.R | 10 +-- prospectr-0.2.8/prospectr/R/kenstone.R | 5 + prospectr-0.2.8/prospectr/README.md | 14 ++--- prospectr-0.2.8/prospectr/build/stage23.rdb |only prospectr-0.2.8/prospectr/build/vignette.rds |binary prospectr-0.2.8/prospectr/inst/doc/prospectr.R | 46 ++++++++--------- prospectr-0.2.8/prospectr/inst/doc/prospectr.html | 54 ++++++++++----------- prospectr-0.2.8/prospectr/man/gapDer.Rd | 6 +- prospectr-0.2.8/prospectr/man/kenStone.Rd | 5 + prospectr-0.2.8/prospectr/man/prospectr-package.Rd | 2 prospectr-0.2.8/prospectr/src/Makevars | 1 prospectr-0.2.8/prospectr/src/Makevars.win | 1 17 files changed, 122 insertions(+), 98 deletions(-)
Title: Power Analysis for PLS Classification
Description: It estimates power and sample size for Partial Least Squares-based methods described in Andreella, et al., (2024), <doi:10.48550/arXiv.2403.10289>.
Author: Angela Andreella [aut, cre]
Maintainer: Angela Andreella <angela.andreella@unitn.it>
Diff between powerPLS versions 0.2.0 dated 2024-09-30 and 0.2.1 dated 2025-03-05
DESCRIPTION | 14 ++-- MD5 | 62 +++++++++++++-------- NAMESPACE | 10 +++ NEWS.md | 4 + R/AUCTest.R |only R/F1Test.R |only R/FMTest.R |only R/IDA.R | 25 ++++---- R/PLSc.R | 91 ++++++++++++++----------------- R/R2Test.R | 75 ++++++++++++++----------- R/computePower.R | 136 ++++++++++++++++++++++------------------------- R/computeSampleSize.R | 35 +++++------- R/computeWT.R | 55 ++++++++----------- R/dQ2Test.R |only R/global.R | 2 R/mccTest.R | 113 +++++++++++++++++++++------------------ R/ptPLSc.R | 64 +++++++++++----------- R/repeatedCV_test.R |only R/scoreTest.R | 109 ++++++++++++++++++++----------------- R/sensitivityTest.R |only R/sim_Tscore.R | 25 ++++---- R/sim_XY.R | 99 ++++++++++++++++------------------ R/simulatePilotData.R | 34 ++++++----- R/specificityTest.R |only R/utils.R | 128 ++++++++++++++++++++++++++++++++------------ README.md | 2 man/AUCTest.Rd |only man/F1Test.Rd |only man/FMTest.Rd |only man/PLSc.Rd | 8 +- man/R2Test.Rd | 16 ++++- man/computePower.Rd | 14 ++-- man/computeSampleSize.Rd | 8 +- man/dQ2Test.Rd |only man/mccTest.Rd | 18 ++++-- man/repeatedCV_test.Rd |only man/scoreTest.Rd | 16 ++++- man/sensitivityTest.Rd |only man/specificityTest.Rd |only 39 files changed, 645 insertions(+), 518 deletions(-)
Title: Download Official Data on Brazil's Federal Budget
Description: Allows users to download and analyze official data on Brazil's federal budget through the 'SPARQL' endpoint
provided by the Integrated Budget and Planning System ('SIOP'). This package enables access to detailed information on budget
allocations and expenditures of the federal government, making it easier to analyze and visualize these data. Technical
information on the Brazilian federal budget is available (Portuguese only) at <https://www1.siop.planejamento.gov.br/mto/>.
The 'SIOP' endpoint is available at <https://www1.siop.planejamento.gov.br/sparql/>.
Author: Daniel Gersten Reiss [aut, cre]
,
Bernardo Borba de Andrade [ctb]
,
Gustavo Jose de Guimaraes e Souza [ctb]
,
Ministerio do Planejamento e Orcamento [cph, fnd]
Maintainer: Daniel Gersten Reiss <daniel.reiss@planejamento.gov.br>
Diff between orcamentoBR versions 1.0.2 dated 2025-02-20 and 1.0.3 dated 2025-03-05
DESCRIPTION | 13 +++++++------ MD5 | 12 ++++++------ R/orcamentoBR.R | 8 +++++--- R/quaisDimensoes.R | 4 ++-- man/despesaDetalhada.Rd | 2 ++ man/quaisMembros.Rd | 2 +- man/whichMembers.Rd | 2 +- 7 files changed, 24 insertions(+), 19 deletions(-)
Title: Diagnostic Tools for a Multivariate Negative Binomial Regression
Model
Description: Diagnostic tools as residual analysis, global,
local and total-local influence for the multivariate model
from the random intercept Poisson generalized log gamma model
are available in this package. Including also, the estimation
process by maximum likelihood method, for details see
Fabio, L. C; Villegas, C. L.; Carrasco, J.M.F and de Castro, M. (2023)
<doi:10.1080/03610926.2021.1939380> and Fábio, L. C.; Villegas, C.;
Mamun, A. S. M. A. and Carrasco, J. M. F. (2025) <doi:10.28951/bjb.v43i1.728>.
Author: Jalmar Carrasco [aut, cre],
Cristian Lobos [aut],
Lizandra Fabio [aut]
Maintainer: Jalmar Carrasco <carrascojalmar@gmail.com>
Diff between MNB versions 1.1.0 dated 2022-04-22 and 1.2.0 dated 2025-03-05
DESCRIPTION | 18 - MD5 | 38 +-- R/Local.R | 650 ++++++++++++++++++++++++++-------------------------- R/MNB.R | 217 ++++++++--------- R/enveSim.R | 277 +++++++++++----------- R/estimate.R | 219 ++++++++--------- R/global.R | 180 +++++++------- R/qMNB.R | 215 ++++++++--------- R/rMNB.R | 96 +++---- R/residual.R | 393 +++++++++++++++---------------- man/MNB.Rd | 11 man/alzheimer.Rd | 7 man/envelope.MNB.Rd | 11 man/fit.MNB.Rd | 11 man/global.MNB.Rd | 8 man/local.MNB.Rd | 8 man/qMNB.Rd | 11 man/rMNB.Rd | 4 man/re.MNB.Rd | 11 man/seizures.Rd | 11 20 files changed, 1216 insertions(+), 1180 deletions(-)
Title: Assessing Complex Heterogeneity in Surrogacy
Description: Provides functions to assess and test for complex heterogeneity in the utility of a surrogate marker with respect to multiple baseline covariates, using both a parametric model and a semiparametric two-step model. More details are available in: Knowlton, R., Tian, L., & Parast, L. (2025). "A General Framework to Assess Complex Heterogeneity in the Strength of a Surrogate Marker," Statistics in Medicine, 44(5), e70001 <doi:10.1002/sim.70001>. A tutorial for this package can be found at <https://laylaparast.com/home/cohetsurr.html>.
Author: Rebecca Knowlton [aut],
Layla Parast [aut, cre]
Maintainer: Layla Parast <parast@austin.utexas.edu>
Diff between cohetsurr versions 1.0 dated 2024-11-21 and 1.1 dated 2025-03-05
DESCRIPTION | 17 ++-- MD5 | 4 - man/complex.heterogeneity.Rd | 158 +++++++++++++++++++++---------------------- 3 files changed, 90 insertions(+), 89 deletions(-)
Title: Calculate Mass Properties and Uncertainties of Tree Structures
Description: Recursively calculates mass properties (mass, center of mass, moments and products of inertia, and optionally, their uncertainties) for arbitrary decomposition trees. R. L. Zimmerman, J. H. Nakai. (2005) <https://www.sawe.org/product/paper-3360/>).
Author: James Steven Jenkins [aut, cre, cph]
Maintainer: James Steven Jenkins <sjenkins@studioj.us>
Diff between massProps versions 0.2.0 dated 2025-01-30 and 0.3.1 dated 2025-03-05
DESCRIPTION | 6 MD5 | 57 + NAMESPACE | 6 NEWS.md | 17 R/massprops.R | 42 - R/mp_table_small.R |only R/mp_tree_small.R |only R/radii.R |only R/test_unc_table.R |only README.md | 114 +++ data/mp_table_small.rda |only data/mp_tree.rda |binary data/mp_tree_small.rda |only data/test_tree.rda |binary data/test_unc_table.rda |only inst/doc/massProps.R | 142 +++- inst/doc/massProps.Rmd | 692 +++++++++++++++-------- inst/doc/massProps.html | 719 +++++++++++++++--------- man/add_radii_of_gyration.Rd |only man/get_mass_props_and_unc_and_radii.Rd |only man/get_mass_props_and_unc_and_radii_and_unc.Rd |only man/mp_table_small.Rd |only man/mp_tree_small.Rd |only man/rollup_mass_props.Rd | 2 man/rollup_mass_props_and_unc.Rd | 2 man/rollup_mass_props_and_unc_fast.Rd | 2 man/rollup_mass_props_unc.Rd | 4 man/rollup_radii_of_gyration_unc.Rd |only man/set_mass_props_unc.Rd | 2 man/set_radii_of_gyration.Rd |only man/set_radii_of_gyration_unc.Rd |only man/test_unc_table.Rd |only man/validate_mass_props_and_unc_table.Rd | 2 man/validate_mass_props_table.Rd | 2 tests/testthat/test-massProps.R | 1 tests/testthat/test-radii.R |only vignettes/massProps.Rmd | 692 +++++++++++++++-------- vignettes/references.bib | 8 38 files changed, 1709 insertions(+), 803 deletions(-)
Title: Retrieve Data from the Census APIs
Description: A wrapper for the U.S. Census Bureau APIs that returns data frames of
Census data and metadata. Available datasets include the
Decennial Census, American Community Survey, Small Area Health Insurance Estimates,
Small Area Income and Poverty Estimates, Population Estimates and Projections, and more.
Author: Hannah Recht [aut, cre]
Maintainer: Hannah Recht <censusapi.rstats@gmail.com>
Diff between censusapi versions 0.8.0 dated 2022-08-09 and 0.9.0 dated 2025-03-05
DESCRIPTION | 13 - MD5 | 36 ++-- NAMESPACE | 3 NEWS.md | 34 +++- R/api-key.R |only R/datasets.R | 2 R/getcensus_functions.R | 371 +++++++++++++++++++++++++++++++--------------- R/makevar_functions.R | 32 ++- R/metadata_functions.R | 250 ++++++++++++++++++++++-------- README.md | 146 +++++++++++++++++- build |only inst |only man/fips.Rd | 2 man/getCensus.Rd | 104 ++++++------ man/getFunction.Rd | 7 man/get_api_key.Rd |only man/has_api_key.Rd |only man/listCensusApis.Rd | 58 ++++++- man/listCensusMetadata.Rd | 128 +++++++++------ man/makeVarlist.Rd | 33 ++-- vignettes |only 21 files changed, 868 insertions(+), 351 deletions(-)
Title: Fast and Simple 'MongoDB' Client for R
Description: High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'.
Includes support for aggregation, indexing, map-reduce, streaming, encryption,
enterprise authentication, and GridFS. The online user manual provides an overview
of the available methods in the package: <https://jeroen.github.io/mongolite/>.
Author: Jeroen Ooms [aut, cre] ,
MongoDB, Inc [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between mongolite versions 3.1.0 dated 2025-02-25 and 3.1.1 dated 2025-03-05
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 3 +++ src/Makevars.in | 2 +- src/osx/Makevars | 2 +- 5 files changed, 12 insertions(+), 9 deletions(-)
Title: Interface to the National 'Phenology' Network 'API'
Description: Programmatic interface to the Web Service methods provided by
the National 'Phenology' Network (<https://usanpn.org/>), which
includes data on various life history events that occur at specific
times.
Author: Jeff Switzer [aut, cre],
Scott Chamberlain [aut],
Lee Marsh [aut],
Kevin Wong [aut],
Eric R Scott [aut] ,
David LeBauer [ctb]
Maintainer: Jeff Switzer <jeff@usanpn.org>
Diff between rnpn versions 1.2.9.0 dated 2024-08-19 and 1.3.0 dated 2025-03-05
rnpn-1.2.9.0/rnpn/man/check_geo_service.Rd |only rnpn-1.2.9.0/rnpn/man/check_service.Rd |only rnpn-1.2.9.0/rnpn/tests/test-all.R |only rnpn-1.3.0/rnpn/DESCRIPTION | 47 rnpn-1.3.0/rnpn/LICENSE | 4 rnpn-1.3.0/rnpn/MD5 | 194 - rnpn-1.3.0/rnpn/NAMESPACE | 8 rnpn-1.3.0/rnpn/NEWS.md | 78 rnpn-1.3.0/rnpn/R/base-reqs.R |only rnpn-1.3.0/rnpn/R/defunct.R | 12 rnpn-1.3.0/rnpn/R/lookup_names.R | 24 rnpn-1.3.0/rnpn/R/npn_data_download.R | 1460 ++++++------ rnpn-1.3.0/rnpn/R/npn_dataset.R | 21 rnpn-1.3.0/rnpn/R/npn_geoserver.R | 897 +++---- rnpn-1.3.0/rnpn/R/npn_get_species.R | 180 - rnpn-1.3.0/rnpn/R/npn_partner_groups.R | 47 rnpn-1.3.0/rnpn/R/npn_phenophases.R | 269 +- rnpn-1.3.0/rnpn/R/npn_stations.R | 121 rnpn-1.3.0/rnpn/R/release-reminders.R |only rnpn-1.3.0/rnpn/R/rnpn-package.R | 17 rnpn-1.3.0/rnpn/R/test-helpers.R |only rnpn-1.3.0/rnpn/R/utils.R |only rnpn-1.3.0/rnpn/R/zzz.R | 180 - rnpn-1.3.0/rnpn/README.md | 20 rnpn-1.3.0/rnpn/inst/CITATION |only rnpn-1.3.0/rnpn/inst/doc/III_individual_phenometrics.html | 2 rnpn-1.3.0/rnpn/inst/doc/II_status_intensity.html | 2 rnpn-1.3.0/rnpn/inst/doc/IV_site_phenometrics.html | 2 rnpn-1.3.0/rnpn/inst/doc/I_introduction.html | 2 rnpn-1.3.0/rnpn/inst/doc/VIII_data_cleaning.html | 2 rnpn-1.3.0/rnpn/inst/doc/VII_combine_raster_point.R | 49 rnpn-1.3.0/rnpn/inst/doc/VII_combine_raster_point.Rmd | 49 rnpn-1.3.0/rnpn/inst/doc/VII_combine_raster_point.html | 47 rnpn-1.3.0/rnpn/inst/doc/VI_geospatial.Rmd | 84 rnpn-1.3.0/rnpn/inst/doc/VI_geospatial.html | 40 rnpn-1.3.0/rnpn/inst/doc/V_magnitude_phenometrics.html | 2 rnpn-1.3.0/rnpn/inst/release-tasks.R |only rnpn-1.3.0/rnpn/man/get_additional_rasters.Rd | 13 rnpn-1.3.0/rnpn/man/npn_abundance_categories.Rd | 11 rnpn-1.3.0/rnpn/man/npn_check_point_cached.Rd | 8 rnpn-1.3.0/rnpn/man/npn_datasets.Rd | 9 rnpn-1.3.0/rnpn/man/npn_download_geospatial.Rd | 35 rnpn-1.3.0/rnpn/man/npn_download_individual_phenometrics.Rd | 183 - rnpn-1.3.0/rnpn/man/npn_download_magnitude_phenometrics.Rd | 155 - rnpn-1.3.0/rnpn/man/npn_download_site_phenometrics.Rd | 207 + rnpn-1.3.0/rnpn/man/npn_download_status_data.Rd | 169 - rnpn-1.3.0/rnpn/man/npn_get_agdd_point_data.Rd | 29 rnpn-1.3.0/rnpn/man/npn_get_common_query_vars.Rd | 5 rnpn-1.3.0/rnpn/man/npn_get_custom_agdd_raster.Rd | 42 rnpn-1.3.0/rnpn/man/npn_get_custom_agdd_time_series.Rd | 55 rnpn-1.3.0/rnpn/man/npn_get_data.Rd | 28 rnpn-1.3.0/rnpn/man/npn_get_data_by_year.Rd | 63 rnpn-1.3.0/rnpn/man/npn_get_download_url.Rd | 10 rnpn-1.3.0/rnpn/man/npn_get_layer_details.Rd | 19 rnpn-1.3.0/rnpn/man/npn_get_phenophases_for_taxon.Rd | 57 rnpn-1.3.0/rnpn/man/npn_get_point_data.Rd | 29 rnpn-1.3.0/rnpn/man/npn_groups.Rd | 20 rnpn-1.3.0/rnpn/man/npn_lookup_names.Rd | 17 rnpn-1.3.0/rnpn/man/npn_merge_geo_data.Rd | 8 rnpn-1.3.0/rnpn/man/npn_pheno_classes.Rd | 12 rnpn-1.3.0/rnpn/man/npn_phenophase_definitions.Rd | 10 rnpn-1.3.0/rnpn/man/npn_phenophase_details.Rd | 19 rnpn-1.3.0/rnpn/man/npn_phenophases.Rd | 9 rnpn-1.3.0/rnpn/man/npn_phenophases_by_species.Rd | 21 rnpn-1.3.0/rnpn/man/npn_species.Rd | 57 rnpn-1.3.0/rnpn/man/npn_species_types.Rd | 14 rnpn-1.3.0/rnpn/man/npn_stations.Rd | 6 rnpn-1.3.0/rnpn/man/npn_stations_by_location.Rd | 4 rnpn-1.3.0/rnpn/man/npn_stations_by_state.Rd | 4 rnpn-1.3.0/rnpn/man/npn_stations_with_spp.Rd | 8 rnpn-1.3.0/rnpn/man/resolve_six_raster.Rd | 31 rnpn-1.3.0/rnpn/man/rnpn-defunct.Rd | 12 rnpn-1.3.0/rnpn/man/rnpn-package.Rd | 29 rnpn-1.3.0/rnpn/tests/fixtures |only rnpn-1.3.0/rnpn/tests/testthat.R |only rnpn-1.3.0/rnpn/tests/testthat/test-npn-datasets.R | 13 rnpn-1.3.0/rnpn/tests/testthat/test-npn-defunct.R | 15 rnpn-1.3.0/rnpn/tests/testthat/test-npn-geoserver.R | 181 - rnpn-1.3.0/rnpn/tests/testthat/test-npn-get-species.R | 96 rnpn-1.3.0/rnpn/tests/testthat/test-npn-observations.R | 506 +--- rnpn-1.3.0/rnpn/tests/testthat/test-npn-partners.R | 20 rnpn-1.3.0/rnpn/tests/testthat/test-npn-phenophases.R | 154 - rnpn-1.3.0/rnpn/tests/testthat/test-npn-stations.R | 68 rnpn-1.3.0/rnpn/vignettes/VII_combine_raster_point.Rmd | 49 rnpn-1.3.0/rnpn/vignettes/VI_geospatial.Rmd | 84 rnpn-1.3.0/rnpn/vignettes/VI_geospatial.Rmd.orig | 44 86 files changed, 3478 insertions(+), 3020 deletions(-)
Title: Gaussian Parsimonious Clustering Models with Covariates and a
Noise Component
Description: Clustering via parsimonious Gaussian Mixtures of Experts using the MoEClust models introduced by Murphy and Murphy (2020) <doi:10.1007/s11634-019-00373-8>. This package fits finite Gaussian mixture models with a formula interface for supplying gating and/or expert network covariates using a range of parsimonious covariance parameterisations from the GPCM family via the EM/CEM algorithm. Visualisation of the results of such models using generalised pairs plots and the inclusion of an additional noise component is also facilitated. A greedy forward stepwise search algorithm is provided for identifying the optimal model in terms of the number of components, the GPCM covariance parameterisation, and the subsets of gating/expert network covariates.
Author: Keefe Murphy [aut, cre] ,
Thomas Brendan Murphy [ctb]
Maintainer: Keefe Murphy <keefe.murphy@mu.ie>
Diff between MoEClust versions 1.5.2 dated 2023-12-11 and 1.6.0 dated 2025-03-05
MoEClust-1.5.2/MoEClust/R/MoEClust.R |only MoEClust-1.6.0/MoEClust/DESCRIPTION | 14 MoEClust-1.6.0/MoEClust/MD5 | 66 +- MoEClust-1.6.0/MoEClust/NAMESPACE | 7 MoEClust-1.6.0/MoEClust/R/Functions.R | 452 +++++++++++-------- MoEClust-1.6.0/MoEClust/R/MoEClust-package.R |only MoEClust-1.6.0/MoEClust/R/Plotting_Functions.R | 553 ++++++++++++++---------- MoEClust-1.6.0/MoEClust/R/data.R | 4 MoEClust-1.6.0/MoEClust/README.md | 2 MoEClust-1.6.0/MoEClust/build/partial.rdb |binary MoEClust-1.6.0/MoEClust/build/vignette.rds |binary MoEClust-1.6.0/MoEClust/inst/NEWS.md | 81 +++ MoEClust-1.6.0/MoEClust/inst/doc/MoEClust.R | 87 +-- MoEClust-1.6.0/MoEClust/inst/doc/MoEClust.Rmd | 61 +- MoEClust-1.6.0/MoEClust/inst/doc/MoEClust.html | 75 +-- MoEClust-1.6.0/MoEClust/man/CO2data.Rd | 2 MoEClust-1.6.0/MoEClust/man/FARI.Rd | 2 MoEClust-1.6.0/MoEClust/man/MoEClust-package.Rd | 210 ++++----- MoEClust-1.6.0/MoEClust/man/MoE_Uncertainty.Rd | 130 +++-- MoEClust-1.6.0/MoEClust/man/MoE_clust.Rd | 26 - MoEClust-1.6.0/MoEClust/man/MoE_compare.Rd | 16 MoEClust-1.6.0/MoEClust/man/MoE_control.Rd | 396 ++++++++--------- MoEClust-1.6.0/MoEClust/man/MoE_crit.Rd | 2 MoEClust-1.6.0/MoEClust/man/MoE_cstep.Rd | 2 MoEClust-1.6.0/MoEClust/man/MoE_estep.Rd | 6 MoEClust-1.6.0/MoEClust/man/MoE_gpairs.Rd | 107 ++-- MoEClust-1.6.0/MoEClust/man/MoE_news.Rd | 4 MoEClust-1.6.0/MoEClust/man/MoE_plotCrit.Rd | 11 MoEClust-1.6.0/MoEClust/man/MoE_stepwise.Rd | 4 MoEClust-1.6.0/MoEClust/man/ais.Rd | 84 +-- MoEClust-1.6.0/MoEClust/man/as.Mclust.Rd | 51 +- MoEClust-1.6.0/MoEClust/man/expert_covar.Rd | 4 MoEClust-1.6.0/MoEClust/man/noise_vol.Rd | 2 MoEClust-1.6.0/MoEClust/man/plot.MoEClust.Rd | 8 MoEClust-1.6.0/MoEClust/vignettes/MoEClust.Rmd | 61 +- 35 files changed, 1423 insertions(+), 1107 deletions(-)
Title: Get Images Out of DICOM Format Quickly
Description: Provides tools to sort DICOM-format medical image files, and
convert them to NIfTI-1 format.
Author: Jon Clayden [aut, cre] ,
Chris Rorden [aut],
Martin J Fiedler [cph],
Cong Xu [cph],
Pascal Gloor [cph]
Maintainer: Jon Clayden <code@clayden.org>
Diff between divest versions 1.1.1 dated 2024-10-20 and 1.2.0 dated 2025-03-05
divest-1.1.1/divest/R/attribs.R |only divest-1.1.1/divest/build |only divest-1.1.1/divest/inst/tinytest/attributes.json |only divest-1.1.1/divest/man/bidsJson.Rd |only divest-1.1.1/divest/man/imageAttributes.Rd |only divest-1.2.0/divest/DESCRIPTION | 10 +++--- divest-1.2.0/divest/MD5 | 28 ++++++++----------- divest-1.2.0/divest/NAMESPACE | 4 ++ divest-1.2.0/divest/NEWS | 16 ++++++++++ divest-1.2.0/divest/R/read.R | 21 ++++++++------ divest-1.2.0/divest/R/zzz.R | 9 ++++++ divest-1.2.0/divest/configure | 20 ++++++------- divest-1.2.0/divest/configure.ac | 4 +- divest-1.2.0/divest/inst/tinytest/test-05-read.R | 7 ---- divest-1.2.0/divest/man/readDicom.Rd | 5 ++- divest-1.2.0/divest/man/reexports.Rd |only divest-1.2.0/divest/src/dcm2niix/nii_dicom_batch.cpp | 2 - divest-1.2.0/divest/src/main.cpp | 2 - 18 files changed, 76 insertions(+), 52 deletions(-)
Title: Data Quality in Epidemiological Research
Description: Data quality assessments guided by a
'data quality framework introduced by Schmidt and colleagues, 2021'
<doi:10.1186/s12874-021-01252-7> target the
data quality dimensions integrity, completeness, consistency, and
accuracy. The scope of applicable functions rests on the
availability of extensive metadata which can be provided in
spreadsheet tables. Either standardized (e.g. as 'html5' reports) or
individually tailored reports can be generated. For an introduction
into the specification of corresponding metadata, please refer to the
'package website'
<https://dataquality.qihs.uni-greifswald.de/VIN_Annotation_of_Metadata.html>.
Author: University Medicine Greifswald [cph],
Elisa Kasbohm [aut] ,
Elena Salogni [aut] ,
Joany Marino [aut] ,
Adrian Richter [aut] ,
Carsten Oliver Schmidt [aut] ,
Stephan Struckmann [aut, cre] ,
German Research Foundation [fnd],
National Research Data Inf [...truncated...]
Maintainer: Stephan Struckmann <stephan.struckmann@uni-greifswald.de>
Diff between dataquieR versions 2.5.0 dated 2025-02-20 and 2.5.1 dated 2025-03-05
DESCRIPTION | 18 MD5 | 280 +-- NEWS.md | 25 R/000_options.R | 24 R/acc_loess.R | 34 R/acc_margins.R | 8 R/acc_varcomp.R | 26 R/dq_report_by.R | 31 R/prep_check_for_dataquieR_updates.R | 1 R/summary.dataquieR_resultset2.R | 149 + R/util_acc_loess_bin.R | 64 R/util_acc_loess_continuous.R | 44 R/util_acc_varcomp.R | 16 R/util_compress_ggplots_in_res.R | 2 R/util_condition_constructor_factory.R | 9 R/util_eval_to_dataquieR_result.R | 3 R/util_evaluate_calls.R | 4 R/util_generate_pages_from_report.R | 2 R/util_generate_table_indicators_descriptors.R | 26 R/util_get_rule_sets.R | 13 R/util_interpret_limits.R | 2 R/util_margins_bin.R | 83 - R/util_margins_lm.R | 42 R/util_margins_nom.R | 19 R/util_margins_ord.R | 6 R/util_margins_poi.R | 39 R/util_view_file.R | 20 R/zzz_globs.R | 2 build/vignette.rds |binary inst/grading_rulesets.xlsx |binary inst/hovertext.rds |binary inst/menu/script.js | 3 inst/templates/default/grading_ruleset_text.html | 4 inst/templates/default/ruleset_formats_text.html | 4 man/acc_loess.Rd | 14 man/acc_varcomp.Rd | 3 man/dataquieR.CONDITIONS_LEVEL_TRHESHOLD.Rd | 2 man/dataquieR.CONDITIONS_WITH_STACKTRACE.Rd | 2 man/dataquieR.ELEMENT_MISSMATCH_CHECKTYPE.Rd | 2 man/dataquieR.ERRORS_WITH_CALLER.Rd | 2 man/dataquieR.GAM_for_LOESS.Rd | 2 man/dataquieR.MAX_LABEL_LEN.Rd | 2 man/dataquieR.MAX_VALUE_LABEL_LEN.Rd | 2 man/dataquieR.MESSAGES_WITH_CALLER.Rd | 2 man/dataquieR.MULTIVARIATE_OUTLIER_CHECK.Rd | 2 man/dataquieR.Rd | 6 man/dataquieR.VALUE_LABELS_htmlescaped.Rd | 2 man/dataquieR.WARNINGS_WITH_CALLER.Rd | 2 man/dataquieR.acc_loess.exclude_constant_subgroups.Rd | 2 man/dataquieR.acc_loess.mark_time_points.Rd | 2 man/dataquieR.acc_loess.min_bw.Rd |only man/dataquieR.acc_loess.min_proportion.Rd |only man/dataquieR.acc_loess.plot_format.Rd | 2 man/dataquieR.acc_loess.plot_observations.Rd | 2 man/dataquieR.acc_margins_num.Rd | 2 man/dataquieR.acc_margins_sort.Rd | 2 man/dataquieR.acc_multivariate_outlier.scale.Rd | 2 man/dataquieR.col_con_con_empirical.Rd | 2 man/dataquieR.col_con_con_logical.Rd | 2 man/dataquieR.debug.Rd | 2 man/dataquieR.des_summary_hard_lim_remove.Rd | 2 man/dataquieR.dontwrapresults.Rd | 2 man/dataquieR.fix_column_type_on_read.Rd | 2 man/dataquieR.flip_mode.Rd | 2 man/dataquieR.force_item_specific_missing_codes.Rd | 2 man/dataquieR.force_label_col.Rd | 2 man/dataquieR.grading_formats.Rd | 2 man/dataquieR.grading_rulesets.Rd | 2 man/dataquieR.guess_missing_codes.Rd | 2 man/dataquieR.lang.Rd | 2 man/dataquieR.max_group_var_levels_in_plot.Rd | 2 man/dataquieR.max_group_var_levels_with_violins.Rd | 2 man/dataquieR.min_obs_per_group_var_in_plot.Rd | 2 man/dataquieR.non_disclosure.Rd | 2 man/dataquieR.progress_fkt.Rd | 2 man/dataquieR.progress_msg_fkt.Rd | 2 man/dataquieR.scale_level_heuristics_control_binaryrecodelimit.Rd | 2 man/dataquieR.scale_level_heuristics_control_metriclevels.Rd | 2 man/dataquieR.testdebug.Rd | 2 man/util_acc_loess_bin.Rd | 14 man/util_acc_loess_continuous.Rd | 8 man/util_acc_varcomp.Rd | 4 man/util_generate_table_indicators_descriptors.Rd | 4 man/util_margins_bin.Rd | 8 tests/testthat/_snaps/R4.3/acc_loess/loess-combined-plot-for-crp-0-both-ok.svg | 47 tests/testthat/_snaps/R4.3/acc_loess/loess-combined-plot-for-crp-0-combined-ok.svg | 47 tests/testthat/_snaps/R4.3/acc_loess/loess-combined-plot-for-crp-0-ok.svg | 47 tests/testthat/_snaps/R4.3/acc_loess/loess-combined-plot-for-crp-0-with-covars-ok.svg | 39 tests/testthat/_snaps/R4.3/acc_loess/loess-facets-plot-for-crp-0-both-ok.svg | 175 +- tests/testthat/_snaps/R4.3/acc_loess/loess-facets-plot-for-crp-0-facets-ok.svg | 175 +- tests/testthat/_snaps/R4.3/acc_loess/loess-facets-plot-for-crp-0-ok.svg | 175 +- tests/testthat/_snaps/R4.3/acc_loess/loess-facets-plot-for-crp-0-with-covars-ok.svg | 139 - 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tests/testthat/_snaps/R4.5/acc_loess/loess-plot-for-crp-0-auto1-ok.svg | 47 tests/testthat/_snaps/R4.5/acc_loess/loess-plot-for-crp-0-auto2-ok.svg | 71 tests/testthat/_snaps/R4.5/plots/con-limit-deviations-all-quest-dt.svg | 4 tests/testthat/_snaps/R4.5/plots/con-limit-deviations-low-quest-dt.svg | 6 tests/testthat/_snaps/R4.5/plots/con-limit-deviations-upp-quest-dt.svg | 6 tests/testthat/_snaps/R4.5/plots/loess-def-dbp0.svg | 52 tests/testthat/_snaps/R4.5/plots/loess-def-edu0.svg | 90 - tests/testthat/_snaps/R4.5/plots/loess-fac-dbp0.svg | 322 ++-- tests/testthat/_snaps/R4.5/plots/loess-fac-edu0.svg | 761 +++++----- tests/testthat/_snaps/R4.5/plots/margins-dbp0.svg | 293 +-- tests/testthat/_snaps/R4.5/plots/margins-edu0.svg | 14 tests/testthat/test-acc_loess.R | 6 tests/testthat/test-acc_margins.R | 350 ++++ tests/testthat/test-acc_varcomp.R | 4 tests/testthat/test-dataquieR_resultset2.R | 2 tests/testthat/test-dq_report_by_m.R | 19 tests/testthat/test-prep_add_missing_codes.R | 1 tests/testthat/test-statichtmlWidget.R | 2 142 files changed, 4881 insertions(+), 4145 deletions(-)
Title: Extending Lasso Model Fitting to Big Data
Description: Extend lasso and elastic-net model fitting for large data sets that
cannot be loaded into memory. Designed to be more memory- and
computation-efficient than existing lasso-fitting packages like 'glmnet' and
'ncvreg', thus allowing the user to analyze big data with limited RAM
<doi:10.32614/RJ-2021-001>.
Author: Yaohui Zeng [aut],
Chuyi Wang [aut],
Tabitha Peter [aut],
Patrick Breheny [aut, cre]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between biglasso versions 1.6.0 dated 2024-04-21 and 1.6.1 dated 2025-03-05
DESCRIPTION | 37 +++++++++--------- MD5 | 39 +++++++++++-------- NAMESPACE | 3 - NEWS.md | 9 ++++ R/biglasso-package.R | 34 ++++++++++++----- R/biglasso.R | 18 ++++++--- R/cv-biglasso.R | 7 --- R/predict.R | 7 ++- R/setupX.R | 2 - README.md |only build/partial.rdb |only build/vignette.rds |binary inst/doc/biglasso.html | 24 ++++++------ inst/tinytest |only man/biglasso-package.Rd | 32 +++++++++++----- man/biglasso.Rd | 6 +++ man/setupX.Rd | 2 - src/binomial.cpp | 9 ---- src/init.c | 6 ++- src/utilities.cpp | 95 +++++++++++++----------------------------------- tests |only 21 files changed, 168 insertions(+), 162 deletions(-)
Title: Species Distribution Models with Tidymodels
Description: Fit species distribution models (SDMs) using the 'tidymodels' framework,
which provides a standardised interface to define models and process their
outputs. 'tidysdm' expands 'tidymodels' by providing methods for spatial objects,
models and metrics specific to SDMs,
as well as a number of specialised functions to process occurrences
for contemporary and palaeo datasets. The full
functionalities of the package are described
in Leonardi et al. (2023) <doi:10.1101/2023.07.24.550358>.
Author: Michela Leonardi [aut],
Margherita Colucci [aut],
Andrea Vittorio Pozzi [aut],
Eleanor M.L. Scerri [aut],
Ben Tupper [ctb],
Andrea Manica [aut, cre]
Maintainer: Andrea Manica <am315@cam.ac.uk>
Diff between tidysdm versions 0.9.5 dated 2024-06-23 and 1.0.0 dated 2025-03-05
tidysdm-0.9.5/tidysdm/inst/extdata/lacerta_climate_future_10m.nc |only tidysdm-0.9.5/tidysdm/inst/extdata/lacerta_climate_present_10m.nc |only tidysdm-0.9.5/tidysdm/inst/extdata/lacerta_climate_sf.RDS |only tidysdm-0.9.5/tidysdm/inst/extdata/lacerta_land_mask.nc |only tidysdm-0.9.5/tidysdm/inst/notes |only tidysdm-1.0.0/tidysdm/DESCRIPTION | 34 tidysdm-1.0.0/tidysdm/MD5 | 349 - tidysdm-1.0.0/tidysdm/NAMESPACE | 6 tidysdm-1.0.0/tidysdm/NEWS.md | 20 tidysdm-1.0.0/tidysdm/R/add_member.R | 37 tidysdm-1.0.0/tidysdm/R/add_repeat.R | 18 tidysdm-1.0.0/tidysdm/R/autoplot_simple_ensemble.R | 11 tidysdm-1.0.0/tidysdm/R/autoplot_spatial_initial_split.R | 5 tidysdm-1.0.0/tidysdm/R/blockcv2rsample.R | 42 tidysdm-1.0.0/tidysdm/R/boyce_cont.R | 103 tidysdm-1.0.0/tidysdm/R/calib_class_thresh.R | 63 tidysdm-1.0.0/tidysdm/R/check_coords_names.R | 5 tidysdm-1.0.0/tidysdm/R/check_sdm_presence.R | 15 tidysdm-1.0.0/tidysdm/R/check_split_balance.R | 77 tidysdm-1.0.0/tidysdm/R/clamp_predictors.R | 88 tidysdm-1.0.0/tidysdm/R/collect_metrics.R | 10 tidysdm-1.0.0/tidysdm/R/confusion_matrix_df.R | 3 tidysdm-1.0.0/tidysdm/R/datasets_docs.R | 5 tidysdm-1.0.0/tidysdm/R/dist_pres_vs_bg.R | 20 tidysdm-1.0.0/tidysdm/R/explain_tidysdm.R | 74 tidysdm-1.0.0/tidysdm/R/extrapol_mess.R | 301 - tidysdm-1.0.0/tidysdm/R/filter_caret.R | 83 tidysdm-1.0.0/tidysdm/R/filter_collinear.R | 273 - tidysdm-1.0.0/tidysdm/R/filter_high_cor.R | 61 tidysdm-1.0.0/tidysdm/R/filter_vif.R | 82 tidysdm-1.0.0/tidysdm/R/gam_formula.R | 10 tidysdm-1.0.0/tidysdm/R/geom_split_violin.R | 46 tidysdm-1.0.0/tidysdm/R/grid_cellsize.R | 22 tidysdm-1.0.0/tidysdm/R/grid_offset.R | 15 tidysdm-1.0.0/tidysdm/R/kap_max.R | 86 tidysdm-1.0.0/tidysdm/R/make_mask_from_presence.R |only tidysdm-1.0.0/tidysdm/R/make_maxent.R | 17 tidysdm-1.0.0/tidysdm/R/maxent.R | 28 tidysdm-1.0.0/tidysdm/R/maxent_params.R | 15 tidysdm-1.0.0/tidysdm/R/maxnet_fit.R | 28 tidysdm-1.0.0/tidysdm/R/niche_overlap.R | 60 tidysdm-1.0.0/tidysdm/R/optim_thresh.R | 54 tidysdm-1.0.0/tidysdm/R/out_of_range_warning.R | 50 tidysdm-1.0.0/tidysdm/R/pairs.R |only tidysdm-1.0.0/tidysdm/R/plot_pres_vs_bg.R | 18 tidysdm-1.0.0/tidysdm/R/predict_raster.R | 42 tidysdm-1.0.0/tidysdm/R/predict_repeat_ensemble.R | 37 tidysdm-1.0.0/tidysdm/R/predict_simple_ensemble.R | 151 tidysdm-1.0.0/tidysdm/R/prob_metrics.R | 24 tidysdm-1.0.0/tidysdm/R/recipe_sf.R | 46 tidysdm-1.0.0/tidysdm/R/recipes_sf_methods.R | 54 tidysdm-1.0.0/tidysdm/R/repeat_ensemble.R | 8 tidysdm-1.0.0/tidysdm/R/sample_background.R | 92 tidysdm-1.0.0/tidysdm/R/sample_background_time.R | 180 tidysdm-1.0.0/tidysdm/R/sample_pseudoabs.R | 107 tidysdm-1.0.0/tidysdm/R/sample_pseudoabs_time.R | 147 tidysdm-1.0.0/tidysdm/R/sdm_spec_boost_tree.R | 52 tidysdm-1.0.0/tidysdm/R/sdm_spec_gam.R | 26 tidysdm-1.0.0/tidysdm/R/sdm_spec_glm.R | 15 tidysdm-1.0.0/tidysdm/R/sdm_spec_maxent.R | 24 tidysdm-1.0.0/tidysdm/R/sdm_spec_rand_forest.R | 13 tidysdm-1.0.0/tidysdm/R/simple_ensemble.R | 16 tidysdm-1.0.0/tidysdm/R/spatial_initial_split.R | 29 tidysdm-1.0.0/tidysdm/R/thin_by_cell.R | 68 tidysdm-1.0.0/tidysdm/R/thin_by_cell_time.R | 75 tidysdm-1.0.0/tidysdm/R/thin_by_dist.R | 51 tidysdm-1.0.0/tidysdm/R/thin_by_dist_time.R | 68 tidysdm-1.0.0/tidysdm/R/tidysdm-package.R | 3 tidysdm-1.0.0/tidysdm/R/tss.R | 50 tidysdm-1.0.0/tidysdm/R/tss_max.R | 63 tidysdm-1.0.0/tidysdm/R/zzz.R | 10 tidysdm-1.0.0/tidysdm/README.md | 62 tidysdm-1.0.0/tidysdm/build/partial.rdb |binary tidysdm-1.0.0/tidysdm/build/vignette.rds |binary tidysdm-1.0.0/tidysdm/data/horses.rda |binary tidysdm-1.0.0/tidysdm/data/lacerta.rda |binary tidysdm-1.0.0/tidysdm/data/lacerta_ensemble.rda |binary tidysdm-1.0.0/tidysdm/data/lacerta_rep_ens.rda |binary tidysdm-1.0.0/tidysdm/data/lacertidae_background.rda |binary tidysdm-1.0.0/tidysdm/inst/WORDLIST | 10 tidysdm-1.0.0/tidysdm/inst/doc/a0_tidysdm_overview.R | 402 + tidysdm-1.0.0/tidysdm/inst/doc/a0_tidysdm_overview.Rmd | 450 + tidysdm-1.0.0/tidysdm/inst/doc/a0_tidysdm_overview.html | 2337 ++-------- tidysdm-1.0.0/tidysdm/inst/doc/a1_palaeodata_application.R | 5 tidysdm-1.0.0/tidysdm/inst/doc/a1_palaeodata_application.Rmd | 5 tidysdm-1.0.0/tidysdm/inst/doc/a1_palaeodata_application.html | 26 tidysdm-1.0.0/tidysdm/inst/doc/a2_tidymodels_additions.R | 136 tidysdm-1.0.0/tidysdm/inst/doc/a2_tidymodels_additions.Rmd | 154 tidysdm-1.0.0/tidysdm/inst/doc/a2_tidymodels_additions.html | 649 +- tidysdm-1.0.0/tidysdm/inst/doc/a3_troubleshooting.R | 19 tidysdm-1.0.0/tidysdm/inst/doc/a3_troubleshooting.Rmd | 15 tidysdm-1.0.0/tidysdm/inst/doc/a3_troubleshooting.html | 149 tidysdm-1.0.0/tidysdm/inst/extdata/lacerta_climate_future_10m.rds |only tidysdm-1.0.0/tidysdm/inst/extdata/lacerta_climate_present_10m.rds |only tidysdm-1.0.0/tidysdm/inst/extdata/lacerta_land_mask.rds |only tidysdm-1.0.0/tidysdm/inst/extdata/lacerta_thin.rds |only tidysdm-1.0.0/tidysdm/inst/extdata/lacerta_thin_all_vars.rds |only tidysdm-1.0.0/tidysdm/man/autoplot.simple_ensemble.Rd | 2 tidysdm-1.0.0/tidysdm/man/blockcv2rsample.Rd | 8 tidysdm-1.0.0/tidysdm/man/boyce_cont.Rd | 67 tidysdm-1.0.0/tidysdm/man/calib_class_thresh.Rd | 19 tidysdm-1.0.0/tidysdm/man/check_sdm_presence.Rd | 7 tidysdm-1.0.0/tidysdm/man/check_splits_balance.Rd | 12 tidysdm-1.0.0/tidysdm/man/clamp_predictors.Rd | 25 tidysdm-1.0.0/tidysdm/man/collect_metrics.simple_ensemble.Rd | 9 tidysdm-1.0.0/tidysdm/man/conf_matrix_df.Rd | 3 tidysdm-1.0.0/tidysdm/man/dist_pres_vs_bg.Rd | 13 tidysdm-1.0.0/tidysdm/man/explain_tidysdm.Rd | 16 tidysdm-1.0.0/tidysdm/man/extrapol_mess.Rd | 30 tidysdm-1.0.0/tidysdm/man/filter_collinear.Rd | 87 tidysdm-1.0.0/tidysdm/man/filter_high_cor.Rd | 44 tidysdm-1.0.0/tidysdm/man/form_resp.Rd | 3 tidysdm-1.0.0/tidysdm/man/geom_split_violin.Rd | 31 tidysdm-1.0.0/tidysdm/man/grid_cellsize.Rd | 15 tidysdm-1.0.0/tidysdm/man/grid_offset.Rd | 15 tidysdm-1.0.0/tidysdm/man/kap_max.Rd | 73 tidysdm-1.0.0/tidysdm/man/lacertidae_background.Rd | 5 tidysdm-1.0.0/tidysdm/man/make_mask_from_presence.Rd |only tidysdm-1.0.0/tidysdm/man/maxent.Rd | 24 tidysdm-1.0.0/tidysdm/man/maxent_params.Rd | 11 tidysdm-1.0.0/tidysdm/man/maxnet_fit.Rd | 20 tidysdm-1.0.0/tidysdm/man/niche_overlap.Rd | 16 tidysdm-1.0.0/tidysdm/man/optim_thresh.Rd | 16 tidysdm-1.0.0/tidysdm/man/optim_thresh_kap_max.Rd | 4 tidysdm-1.0.0/tidysdm/man/optim_thresh_sens.Rd | 4 tidysdm-1.0.0/tidysdm/man/optim_thresh_tss_max.Rd | 4 tidysdm-1.0.0/tidysdm/man/pairs-stars.Rd |only tidysdm-1.0.0/tidysdm/man/plot_pres_vs_bg.Rd | 7 tidysdm-1.0.0/tidysdm/man/predict.repeat_ensemble.Rd | 37 tidysdm-1.0.0/tidysdm/man/predict.simple_ensemble.Rd | 41 tidysdm-1.0.0/tidysdm/man/predict_raster.Rd | 14 tidysdm-1.0.0/tidysdm/man/prob_metrics_sf.Rd | 22 tidysdm-1.0.0/tidysdm/man/recipe.sf.Rd | 34 tidysdm-1.0.0/tidysdm/man/repeat_ensemble.Rd | 4 tidysdm-1.0.0/tidysdm/man/sample_background.Rd | 43 tidysdm-1.0.0/tidysdm/man/sample_background_time.Rd | 86 tidysdm-1.0.0/tidysdm/man/sample_pseudoabs.Rd | 47 tidysdm-1.0.0/tidysdm/man/sample_pseudoabs_time.Rd | 79 tidysdm-1.0.0/tidysdm/man/sdm_spec_boost_tree.Rd | 18 tidysdm-1.0.0/tidysdm/man/sdm_spec_gam.Rd | 27 tidysdm-1.0.0/tidysdm/man/sdm_spec_glm.Rd | 13 tidysdm-1.0.0/tidysdm/man/sdm_spec_maxent.Rd | 14 tidysdm-1.0.0/tidysdm/man/simple_ensemble.Rd | 10 tidysdm-1.0.0/tidysdm/man/spatial_initial_split.Rd | 15 tidysdm-1.0.0/tidysdm/man/thin_by_cell.Rd | 38 tidysdm-1.0.0/tidysdm/man/thin_by_cell_time.Rd | 61 tidysdm-1.0.0/tidysdm/man/thin_by_dist.Rd | 35 tidysdm-1.0.0/tidysdm/man/thin_by_dist_time.Rd | 47 tidysdm-1.0.0/tidysdm/man/tidysdm-package.Rd | 8 tidysdm-1.0.0/tidysdm/man/tss.Rd | 58 tidysdm-1.0.0/tidysdm/man/tss_max.Rd | 63 tidysdm-1.0.0/tidysdm/tests/spelling.R | 9 tidysdm-1.0.0/tidysdm/tests/testthat/Rplots.pdf |only tidysdm-1.0.0/tidysdm/tests/testthat/test_blockcv2rsample.R | 104 tidysdm-1.0.0/tidysdm/tests/testthat/test_check_sdm_presence.R | 6 tidysdm-1.0.0/tidysdm/tests/testthat/test_check_split_balance.R | 39 tidysdm-1.0.0/tidysdm/tests/testthat/test_clamp_predictors.R | 181 tidysdm-1.0.0/tidysdm/tests/testthat/test_dist_pres_vs_bg.R |only tidysdm-1.0.0/tidysdm/tests/testthat/test_explain_tidysdm.R | 105 tidysdm-1.0.0/tidysdm/tests/testthat/test_extrapol_mess.R | 117 tidysdm-1.0.0/tidysdm/tests/testthat/test_filter_collinear.R | 109 tidysdm-1.0.0/tidysdm/tests/testthat/test_initial_spatial_split.R | 56 tidysdm-1.0.0/tidysdm/tests/testthat/test_make_mask_from_presence.R |only tidysdm-1.0.0/tidysdm/tests/testthat/test_maxnet_fit.R | 21 tidysdm-1.0.0/tidysdm/tests/testthat/test_out_of_range_warning.R | 26 tidysdm-1.0.0/tidysdm/tests/testthat/test_overlap_niche.R | 33 tidysdm-1.0.0/tidysdm/tests/testthat/test_predict_repeat_ensemble.R | 49 tidysdm-1.0.0/tidysdm/tests/testthat/test_predict_simple_ensemble.R | 83 tidysdm-1.0.0/tidysdm/tests/testthat/test_prob_metrics_sf.R | 28 tidysdm-1.0.0/tidysdm/tests/testthat/test_recipe_sf.R | 48 tidysdm-1.0.0/tidysdm/tests/testthat/test_repeat_ensemble.R | 16 tidysdm-1.0.0/tidysdm/tests/testthat/test_sample_background.R | 82 tidysdm-1.0.0/tidysdm/tests/testthat/test_sample_background_time.R | 239 - tidysdm-1.0.0/tidysdm/tests/testthat/test_sample_pseudoabs.R | 85 tidysdm-1.0.0/tidysdm/tests/testthat/test_sample_pseudoabs_time.R | 245 - tidysdm-1.0.0/tidysdm/tests/testthat/test_simple_ensemble.R | 37 tidysdm-1.0.0/tidysdm/tests/testthat/test_thin_by_cell.R |only tidysdm-1.0.0/tidysdm/tests/testthat/test_thin_by_cell_time.R | 21 tidysdm-1.0.0/tidysdm/tests/testthat/test_thin_by_dist.R | 35 tidysdm-1.0.0/tidysdm/tests/testthat/test_thin_by_dist_time.R | 48 tidysdm-1.0.0/tidysdm/vignettes/a0_tidysdm_overview.Rmd | 450 + tidysdm-1.0.0/tidysdm/vignettes/a1_palaeodata_application.Rmd | 5 tidysdm-1.0.0/tidysdm/vignettes/a2_tidymodels_additions.Rmd | 154 tidysdm-1.0.0/tidysdm/vignettes/a3_troubleshooting.Rmd | 15 184 files changed, 6935 insertions(+), 5019 deletions(-)
Title: Interlinear Glossed Linguistic Examples and Abbreviation Lists
Generation
Description: Helps to render interlinear glossed linguistic examples in html
'rmarkdown' documents and then semi-automatically compiles the list of
glosses at the end of the document. It also provides a database of linguistic
glosses.
Author: George Moroz [aut, cre]
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between lingglosses versions 0.0.8 dated 2024-09-06 and 0.0.9 dated 2025-03-05
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NAMESPACE | 7 +++++++ NEWS.md | 7 +++++-- R/gloss_example.R | 44 ++++++++++++++++++++++++++++++++++++++++++-- data/glosses_df.RData |binary man/gloss_example.Rd | 1 + 7 files changed, 66 insertions(+), 15 deletions(-)
Title: Multivariate Markov Chains
Description: Provides routines to estimate the Mixture Transition Distribution Model based on Raftery (1985) <http://www.jstor.org/stable/2345788> and Nicolau (2014) <doi:10.1111/sjos.12087> specifications, for multivariate data. Additionally, provides a function for the estimation of a new model for multivariate non-homogeneous Markov chains. This new specification, Generalized Multivariate Markov Chains (GMMC) was proposed by Carolina Vasconcelos and Bruno Damasio and considers (continuous or discrete) covariates exogenous to the Markov chain.
Author: Carolina Vasconcelos [aut, cre],
Bruno Damasio [aut]
Maintainer: Carolina Vasconcelos <cvasconcelos@novaims.unl.pt>
Diff between GenMarkov versions 0.2.0 dated 2023-12-19 and 0.2.1 dated 2025-03-05
DESCRIPTION | 6 ++-- MD5 | 10 ++++---- R/CalculateInitialValues.R | 12 ++++++++- R/ProbValuesXDependent.R | 55 ++++++++++++++++++++++++++++++++++++++------- R/multi.mtd.R | 7 ++++- build/partial.rdb |binary 6 files changed, 71 insertions(+), 19 deletions(-)
Title: Cox MultiBlock Survival
Description: This software package provides Cox survival analysis for high-dimensional and multiblock datasets.
It encompasses a suite of functions dedicated from the classical Cox regression to newest analysis,
including Cox proportional hazards model, Stepwise Cox regression, and Elastic-Net Cox regression,
Sparse Partial Least Squares Cox regression (sPLS-COX) incorporating three distinct strategies,
and two Multiblock-PLS Cox regression (MB-sPLS-COX) methods. This tool is designed to adeptly handle
high-dimensional data, and provides tools for cross-validation, plot generation, and additional resources
for interpreting results. While references are available within the corresponding functions,
key literature is mentioned below.
Terry M Therneau (2024) <https://CRAN.R-project.org/package=survival>,
Noah Simon et al. (2011) <doi:10.18637/jss.v039.i05>,
Philippe Bastien et al. (2005) <doi:10.1016/j.csda.2004.02.005>,
Philippe Bastien (2008) <doi:10.1016/j.chemolab.2007.09.009& [...truncated...]
Author: Pedro Salguero Garcia [aut, cre, rev]
,
Sonia Tarazona Campos [ths],
Ana Conesa Cegarra [ths],
Kassu Mehari Beyene [ctb],
Luis Meira Machado [ctb],
Marta Sestelo [ctb],
Artur Araujo [ctb]
Maintainer: Pedro Salguero Garcia <pedrosalguerog@gmail.com>
Diff between Coxmos versions 1.1.1 dated 2025-02-06 and 1.1.2 dated 2025-03-05
Coxmos-1.1.1/Coxmos/man/plot_LP.multipleObservations.Rd |only Coxmos-1.1.1/Coxmos/man/plot_LP.multipleObservations.list.Rd |only Coxmos-1.1.1/Coxmos/man/plot_pseudobeta_newObservation.Rd |only Coxmos-1.1.1/Coxmos/man/plot_pseudobeta_newObservation.list.Rd |only Coxmos-1.1.2/Coxmos/DESCRIPTION | 15 Coxmos-1.1.2/Coxmos/MD5 | 144 Coxmos-1.1.2/Coxmos/NAMESPACE | 233 Coxmos-1.1.2/Coxmos/R/Coxmos_common_functions.R | 249 Coxmos-1.1.2/Coxmos/R/Coxmos_coxEN.R | 44 Coxmos-1.1.2/Coxmos/R/Coxmos_evaluation_functions.R | 28 Coxmos-1.1.2/Coxmos/R/Coxmos_isb_splsdacox_dynamic.R | 1206 ++-- Coxmos-1.1.2/Coxmos/R/Coxmos_isb_splsdrcox.R | 1218 ++-- Coxmos-1.1.2/Coxmos/R/Coxmos_isb_splsdrcox_dynamic.R | 1284 ++-- Coxmos-1.1.2/Coxmos/R/Coxmos_isb_splsicox.R | 1220 ++-- Coxmos-1.1.2/Coxmos/R/Coxmos_mb_splsdacox_dynamic.R | 48 Coxmos-1.1.2/Coxmos/R/Coxmos_mb_splsdrcox_dynamic.R | 48 Coxmos-1.1.2/Coxmos/R/Coxmos_multiblock_functions.R | 1878 +++--- Coxmos-1.1.2/Coxmos/R/Coxmos_plot_functions.R | 1276 +++- Coxmos-1.1.2/Coxmos/R/Coxmos_plot_functions_others.R | 16 Coxmos-1.1.2/Coxmos/R/Coxmos_sb_splsdacox_dynamic.R | 48 Coxmos-1.1.2/Coxmos/R/Coxmos_sb_splsdrcox.R | 1620 ++--- Coxmos-1.1.2/Coxmos/R/Coxmos_sb_splsdrcox_dynamic.R | 48 Coxmos-1.1.2/Coxmos/R/Coxmos_sb_splsicox.R | 50 Coxmos-1.1.2/Coxmos/R/Coxmos_splsdacox_dynamic.R | 52 Coxmos-1.1.2/Coxmos/R/Coxmos_splsdrcox.R | 48 Coxmos-1.1.2/Coxmos/R/Coxmos_splsdrcox_dynamic.R | 2127 +++---- Coxmos-1.1.2/Coxmos/R/Coxmos_splsdrcox_median.R | 2777 +++++----- Coxmos-1.1.2/Coxmos/R/Coxmos_splsicox.R | 64 Coxmos-1.1.2/Coxmos/README.md | 6 Coxmos-1.1.2/Coxmos/build/partial.rdb |binary Coxmos-1.1.2/Coxmos/inst/doc/Coxmos-MO-pipeline.R | 72 Coxmos-1.1.2/Coxmos/inst/doc/Coxmos-MO-pipeline.Rmd | 87 Coxmos-1.1.2/Coxmos/inst/doc/Coxmos-MO-pipeline.html | 427 - Coxmos-1.1.2/Coxmos/inst/doc/Coxmos-pipeline.R | 20 Coxmos-1.1.2/Coxmos/inst/doc/Coxmos-pipeline.Rmd | 30 Coxmos-1.1.2/Coxmos/inst/doc/Coxmos-pipeline.html | 253 Coxmos-1.1.2/Coxmos/man/cv.coxEN.Rd | 18 Coxmos-1.1.2/Coxmos/man/cv.isb.splsdacox.Rd | 356 - Coxmos-1.1.2/Coxmos/man/cv.isb.splsdrcox.Rd | 426 - Coxmos-1.1.2/Coxmos/man/cv.isb.splsdrcox_penalty.Rd | 390 - Coxmos-1.1.2/Coxmos/man/cv.isb.splsicox.Rd | 12 Coxmos-1.1.2/Coxmos/man/cv.mb.splsdacox.Rd | 14 Coxmos-1.1.2/Coxmos/man/cv.mb.splsdrcox.Rd | 14 Coxmos-1.1.2/Coxmos/man/cv.sb.splsdacox.Rd | 496 - Coxmos-1.1.2/Coxmos/man/cv.sb.splsdrcox.Rd | 496 - Coxmos-1.1.2/Coxmos/man/cv.sb.splsdrcox_penalty.Rd | 454 - Coxmos-1.1.2/Coxmos/man/cv.sb.splsicox.Rd | 16 Coxmos-1.1.2/Coxmos/man/cv.splsdacox.Rd | 448 - Coxmos-1.1.2/Coxmos/man/cv.splsdrcox.Rd | 466 - Coxmos-1.1.2/Coxmos/man/cv.splsdrcox_penalty.Rd | 636 +- Coxmos-1.1.2/Coxmos/man/cv.splsicox.Rd | 30 Coxmos-1.1.2/Coxmos/man/getAutoKM.Rd | 3 Coxmos-1.1.2/Coxmos/man/getAutoKM.list.Rd | 6 Coxmos-1.1.2/Coxmos/man/getTestKM.Rd | 5 Coxmos-1.1.2/Coxmos/man/getTestKM.list.Rd | 3 Coxmos-1.1.2/Coxmos/man/loadingplot.Coxmos.Rd | 10 Coxmos-1.1.2/Coxmos/man/loadingplot.fromVector.Coxmos.Rd | 5 Coxmos-1.1.2/Coxmos/man/mb.splsdacox.Rd | 4 Coxmos-1.1.2/Coxmos/man/mb.splsdrcox.Rd | 4 Coxmos-1.1.2/Coxmos/man/plot_evaluation.Rd | 19 Coxmos-1.1.2/Coxmos/man/plot_evaluation.list.Rd | 18 Coxmos-1.1.2/Coxmos/man/plot_events.Rd | 25 Coxmos-1.1.2/Coxmos/man/plot_multipleObservations.LP.Rd |only Coxmos-1.1.2/Coxmos/man/plot_multipleObservations.LP.list.Rd |only Coxmos-1.1.2/Coxmos/man/plot_observation.pseudobeta.Rd |only Coxmos-1.1.2/Coxmos/man/plot_observation.pseudobeta.list.Rd |only Coxmos-1.1.2/Coxmos/man/plot_pseudobeta.Rd | 31 Coxmos-1.1.2/Coxmos/man/plot_pseudobeta.list.Rd | 36 Coxmos-1.1.2/Coxmos/man/plot_time.list.Rd | 6 Coxmos-1.1.2/Coxmos/man/sb.splsdacox.Rd | 426 - Coxmos-1.1.2/Coxmos/man/sb.splsdrcox.Rd | 420 - Coxmos-1.1.2/Coxmos/man/splsdacox.Rd | 406 - Coxmos-1.1.2/Coxmos/man/splsdrcox.Rd | 428 - Coxmos-1.1.2/Coxmos/man/splsdrcox_penalty.Rd | 4 Coxmos-1.1.2/Coxmos/man/w.starplot.Coxmos.Rd | 10 Coxmos-1.1.2/Coxmos/vignettes/Coxmos-MO-pipeline.Rmd | 87 Coxmos-1.1.2/Coxmos/vignettes/Coxmos-pipeline.Rmd | 30 77 files changed, 11996 insertions(+), 10898 deletions(-)
Title: Local Regression, Likelihood and Density Estimation
Description: Local regression, likelihood and density estimation methods as described in the 1999 book by Loader.
Author: Catherine Loader [aut],
Jiayang Sun [ctb],
Lucent Technologies [cph],
Andy Liaw [cre]
Maintainer: Andy Liaw <andy_liaw@merck.com>
Diff between locfit versions 1.5-9.11 dated 2025-02-03 and 1.5-9.12 dated 2025-03-05
DESCRIPTION | 8 - MD5 | 54 ++++---- src/S_enter.c | 14 ++ src/band.c | 10 - src/cversion.h | 30 ++++ src/dbinom.c | 15 ++ src/dens_int.c | 1 src/density.c | 5 src/design.h | 2 src/ev_kdtre.c | 1 src/ev_trian.c | 14 ++ src/frend.c | 4 src/lf_nbhd.c | 1 src/lffuns.h | 346 +++++++++++++++++++++++++++++++++++++++++++++----------- src/m_eigen.c | 2 src/m_icirc.c | 4 src/m_imont.c | 2 src/m_isimp.c | 7 + src/m_isphr.c | 8 + src/m_jacob.c | 2 src/math.c | 2 src/mutil.h | 22 ++- src/prob.c | 5 src/scb.c | 1 src/scb_iface.c | 2 src/smisc.c | 4 src/tube.h | 33 ++++- src/weight.c | 1 28 files changed, 465 insertions(+), 135 deletions(-)
Title: REDCap Metadata Casting and Castellated Data Handling
Description: Casting metadata for REDCap database creation and handling of
castellated data using repeated instruments and longitudinal projects in
'REDCap'. Keeps a focused data export approach, by allowing to only export
required data from the database. Also for casting new REDCap databases based
on datasets from other sources.
Originally forked from the R part of 'REDCapRITS' by Paul Egeler.
See <https://github.com/pegeler/REDCapRITS>.
'REDCap' (Research Electronic Data Capture) is a secure, web-based software
platform designed to support data capture for research studies, providing
1) an intuitive interface for validated data capture; 2) audit trails for
tracking data manipulation and export procedures; 3) automated export
procedures for seamless data downloads to common statistical packages; and
4) procedures for data integration and interoperability with external
sources (Harris et al (2009) <doi:10.1016/j.jbi.2008.08.010>;
Harris et al (2019) <doi:10.1016/j.jbi.2019.103208> [...truncated...]
Author: Andreas Gammelgaard Damsbo [aut, cre]
,
Paul Egeler [aut]
Maintainer: Andreas Gammelgaard Damsbo <agdamsbo@clin.au.dk>
Diff between REDCapCAST versions 25.1.1 dated 2025-01-29 and 25.3.1 dated 2025-03-05
DESCRIPTION | 17 +- MD5 | 40 ++-- NAMESPACE | 3 NEWS.md | 10 + R/REDCap_split.r | 5 R/as_factor.R | 21 ++ R/as_logical.R |only R/ds2dd_detailed.R | 49 +++-- R/easy_redcap.R | 39 ++++ R/read_redcap_tables.R | 69 ++++---- README.md | 3 inst/WORDLIST | 2 inst/doc/Database-creation.html | 5 inst/doc/REDCapCAST.html | 335 ++++++++++++++++++++-------------------- inst/doc/Shiny-app.html | 5 man/as_factor.Rd | 11 + man/as_logical.Rd |only man/ds2dd.Rd | 2 man/ds2dd_detailed.Rd | 7 man/easy_redcap.Rd | 16 + man/format_redcap_factor.Rd | 2 man/read_redcap_tables.Rd | 4 22 files changed, 376 insertions(+), 269 deletions(-)
Title: R6-Based ML Learners for 'mlexperiments'
Description: Enhances 'mlexperiments'
<https://CRAN.R-project.org/package=mlexperiments> with additional
machine learning ('ML') learners. The package provides R6-based
learners for the following algorithms: 'glmnet'
<https://CRAN.R-project.org/package=glmnet>, 'ranger'
<https://CRAN.R-project.org/package=ranger>, 'xgboost'
<https://CRAN.R-project.org/package=xgboost>, and 'lightgbm'
<https://CRAN.R-project.org/package=lightgbm>. These can be used
directly with the 'mlexperiments' R package.
Author: Lorenz A. Kapsner [cre, aut, cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between mllrnrs versions 0.0.4 dated 2024-07-05 and 0.0.5 dated 2025-03-05
DESCRIPTION | 10 MD5 | 118 +++++----- NAMESPACE | 18 - R/learner_glmnet.R | 24 +- R/learner_xgboost.R | 14 - R/zzz.R | 58 ++--- build/vignette.rds |binary inst/doc/mllrnrs_glmnet_binary.html | 5 inst/doc/mllrnrs_glmnet_binary.qmd | 1 inst/doc/mllrnrs_glmnet_multiclass.R | 29 +- inst/doc/mllrnrs_glmnet_multiclass.html | 68 ++--- inst/doc/mllrnrs_glmnet_multiclass.qmd | 30 +- inst/doc/mllrnrs_glmnet_regression.html | 5 inst/doc/mllrnrs_glmnet_regression.qmd | 1 inst/doc/mllrnrs_lightgbm_binary.html | 5 inst/doc/mllrnrs_lightgbm_binary.qmd | 1 inst/doc/mllrnrs_lightgbm_multiclass.R | 39 +-- inst/doc/mllrnrs_lightgbm_multiclass.html | 78 +++--- inst/doc/mllrnrs_lightgbm_multiclass.qmd | 40 +-- inst/doc/mllrnrs_lightgbm_regression.html | 5 inst/doc/mllrnrs_lightgbm_regression.qmd | 1 inst/doc/mllrnrs_ranger_binary.html | 5 inst/doc/mllrnrs_ranger_binary.qmd | 1 inst/doc/mllrnrs_ranger_multiclass.R | 25 +- inst/doc/mllrnrs_ranger_multiclass.html | 68 ++--- inst/doc/mllrnrs_ranger_multiclass.qmd | 26 +- inst/doc/mllrnrs_ranger_regression.html | 5 inst/doc/mllrnrs_ranger_regression.qmd | 1 inst/doc/mllrnrs_xgboost_binary.html | 5 inst/doc/mllrnrs_xgboost_binary.qmd | 1 inst/doc/mllrnrs_xgboost_multiclass.R | 34 +- inst/doc/mllrnrs_xgboost_multiclass.html | 73 ++---- inst/doc/mllrnrs_xgboost_multiclass.qmd | 35 +-- inst/doc/mllrnrs_xgboost_regression.html | 5 inst/doc/mllrnrs_xgboost_regression.qmd | 1 man/LearnerGlmnet.Rd | 296 ++++++++++++------------- man/LearnerLightgbm.Rd | 342 +++++++++++++++--------------- man/LearnerRanger.Rd | 298 +++++++++++++------------- man/LearnerXgboost.Rd | 342 +++++++++++++++--------------- tests/testthat.R | 27 +- tests/testthat/test-glmnet_binary.R | 288 ++++++++++++------------- tests/testthat/test-glmnet_regression.R | 300 +++++++++++++------------- tests/testthat/test-lightgbm_regression.R | 314 +++++++++++++-------------- tests/testthat/test-lints.R | 26 +- tests/testthat/test-ranger_regression.R | 284 ++++++++++++------------ tests/testthat/test-xgboost_binary.R | 211 ++++++++---------- tests/testthat/test-xgboost_multiclass.R | 15 - tests/testthat/test-xgboost_regression.R | 295 ++++++++++++------------- vignettes/mllrnrs_glmnet_binary.qmd | 1 vignettes/mllrnrs_glmnet_multiclass.qmd | 30 +- vignettes/mllrnrs_glmnet_regression.qmd | 1 vignettes/mllrnrs_lightgbm_binary.qmd | 1 vignettes/mllrnrs_lightgbm_multiclass.qmd | 40 +-- vignettes/mllrnrs_lightgbm_regression.qmd | 1 vignettes/mllrnrs_ranger_binary.qmd | 1 vignettes/mllrnrs_ranger_multiclass.qmd | 26 +- vignettes/mllrnrs_ranger_regression.qmd | 1 vignettes/mllrnrs_xgboost_binary.qmd | 1 vignettes/mllrnrs_xgboost_multiclass.qmd | 35 +-- vignettes/mllrnrs_xgboost_regression.qmd | 1 60 files changed, 1955 insertions(+), 2057 deletions(-)
Title: Helper Functions for Creating Tutorials
Description: Helper functions for creating, editing, and testing tutorials
created with the 'learnr' package. Provides a simple method for allowing
students to download their answers to tutorial questions. For examples
of its use, see the 'r4ds.tutorials' package.
Author: David Kane [aut, cre, cph]
Maintainer: David Kane <dave.kane@gmail.com>
Diff between tutorial.helpers versions 0.3.1 dated 2024-12-07 and 0.4.2 dated 2025-03-05
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More information about tutorial.helpers at CRAN
Permanent link
Title: Expression Data Analysis and Visualization
Description: The Gene Expression Omnibus (<https://www.ncbi.nlm.nih.gov/geo/>) and The Cancer Genome Atlas (<https://portal.gdc.cancer.gov/>) are widely used medical public databases. Our platform integrates routine analysis and visualization tools for expression data to provide concise and intuitive data analysis and presentation.
Author: Xiaojie Sun [aut, cre]
Maintainer: Xiaojie Sun <18763899370@163.com>
Diff between tinyarray versions 2.4.2 dated 2024-06-13 and 2.4.3 dated 2025-03-05
DESCRIPTION | 8 ++-- MD5 | 17 +++++---- NAMESPACE | 2 + NEWS.md | 6 +++ R/2_geo_id.R | 83 +++++++++++++++++++++++++++++++++++++++++++--- R/7_quick_double_enrich.R | 7 ++- R/get_anno.R |only R/start_massage.R | 2 - R/tmp.R |only man/double_enrich.Rd | 4 +- man/geo_parser.Rd |only 11 files changed, 109 insertions(+), 20 deletions(-)
Title: Simple Framework for Simple Automation
Description: Build a project framework for users with
access to only the most basic of automation tools.
Author: Alexander Senetcky [aut, cre, cph]
Maintainer: Alexander Senetcky <asenetcky@gmail.com>
Diff between strata versions 1.4.0 dated 2025-02-03 and 1.4.3 dated 2025-03-05
DESCRIPTION | 6 LICENSE | 4 MD5 | 102 - NAMESPACE | 44 NEWS.md | 8 R/adhoc-core.R | 405 +++---- R/adhoc-utils.R | 154 +- R/build-core.R | 414 +++---- R/build-quick.R | 454 ++++---- R/log-core.R | 172 +-- R/main-core.R | 104 - R/main-utils.R | 502 ++++---- R/strata-package.R | 18 R/survey-core.R | 372 +++--- R/survey-utils.R | 236 ++-- R/toml-core.R | 272 ++-- R/toml-io.R | 274 ++-- R/toml-utils.R | 300 ++--- README.md | 1852 ++++++++++++++++----------------- man/adhoc.Rd | 86 - man/adhoc_lamina.Rd | 72 - man/adhoc_stratum.Rd | 72 - man/build_lamina.Rd | 60 - man/build_outlined_strata_project.Rd | 116 +- man/build_quick_strata_project.Rd | 66 - man/build_stratum.Rd | 54 man/edit_toml.Rd | 146 +- man/figures/lifecycle-deprecated.svg | 42 man/figures/lifecycle-experimental.svg | 42 man/figures/lifecycle-stable.svg | 58 - man/figures/lifecycle-superseded.svg | 42 man/log_error.Rd | 58 - man/log_message.Rd | 74 - man/log_total_time.Rd | 64 - man/main.Rd | 114 +- man/strata-package.Rd | 48 man/survey_log.Rd | 82 - man/survey_strata.Rd | 82 - man/survey_tomls.Rd | 58 - man/view_toml.Rd | 48 tests/testthat.R | 24 tests/testthat/test-adhoc-core.R | 440 +++---- tests/testthat/test-adhoc-utils.R | 154 +- tests/testthat/test-build-core.R | 250 ++-- tests/testthat/test-build-quick.R | 718 ++++++------ tests/testthat/test-log-core.R | 72 - tests/testthat/test-main-core.R | 148 +- tests/testthat/test-main-utils.R | 107 + tests/testthat/test-survey-core.R | 264 ++-- tests/testthat/test-survey-utils.R | 104 - tests/testthat/test-toml-core.R | 368 +++--- tests/testthat/test-toml-utils.R | 200 +-- 52 files changed, 5022 insertions(+), 5004 deletions(-)
Title: A Package for Analyzing Skew Factor Models
Description: Generates Skew Factor Models data and applies Sparse Online Principal Component (SOPC), Incremental Principal Component (IPC), Projected Principal Component (PPC), Perturbation Principal Component (PPC), Stochastic Approximation Principal Component (SAPC), Sparse Principal Component (SPC) and other PC methods to estimate model parameters. It includes capabilities for calculating mean squared error, relative error, and sparsity of the loading matrix.The philosophy of the package is described in Guo G. (2023) <doi:10.1007/s00180-022-01270-z>.
Author: Guangbao Guo [aut, cre],
Yu Jin [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between SFM versions 0.1.0 dated 2024-11-12 and 0.2.0 dated 2025-03-05
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Title: Identify Characteristics of Patients in the OMOP Common Data
Model
Description: Identify the characteristics of patients in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Mike Du [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [aut] ,
Xintong Li [ctb] ,
Xihang Chen [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between PatientProfiles versions 1.3.0 dated 2025-02-26 and 1.3.1 dated 2025-03-05
DESCRIPTION | 6 MD5 | 26 +-- NEWS.md | 6 R/addCategories.R | 305 +++++++++++++++++++----------------- R/checks.R | 62 ------- R/filterCohortId.R | 1 R/summariseResult.R | 4 inst/doc/cohort-intersect.html | 64 +++---- inst/doc/concept-intersect.html | 94 +++++------ inst/doc/demographics.html | 220 ++++++++++++------------- inst/doc/summarise.html | 196 +++++++++++------------ inst/doc/table-intersect.html | 86 +++++----- man/addCategories.Rd | 6 tests/testthat/test-addCategories.R | 6 14 files changed, 529 insertions(+), 553 deletions(-)
More information about PatientProfiles at CRAN
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Title: Extra Functionality for 'leaflet' Package
Description: Several 'leaflet' plugins are integrated, which are available as extension to the 'leaflet' package.
Author: Gatscha Sebastian [aut, cre],
Ricardo Rodrigo Basa [ctb],
Jeffrey O Hanson [ctb]
Maintainer: Gatscha Sebastian <sebastian_gatscha@gmx.at>
Diff between leaflet.extras2 versions 1.3.0 dated 2025-01-12 and 1.3.1 dated 2025-03-05
DESCRIPTION | 6 - MD5 | 10 +-- NEWS.md | 115 ++++++++++++++++++------------------ R/clusterCharts.R | 3 inst/examples/sidebar_app.R | 10 ++- tests/testthat/test-clustercharts.R | 2 6 files changed, 78 insertions(+), 68 deletions(-)
More information about leaflet.extras2 at CRAN
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Title: Easily Create and Style Tables for LaTeX, HTML and Other Formats
Description: Creates styled tables for data presentation. Export to HTML, LaTeX,
RTF, 'Word', 'Excel', and 'PowerPoint'. Simple, modern interface to manipulate
borders, size, position, captions, colours, text styles and number formatting.
Table cells can span multiple rows and/or columns.
Includes a 'huxreg' function for creation of regression tables, and 'quick_*'
one-liners to print data to a new document.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between huxtable versions 5.5.7 dated 2024-10-01 and 5.6.0 dated 2025-03-05
huxtable-5.5.7/huxtable/tests/testthat/404.html |only huxtable-5.5.7/huxtable/tests/testthat/quarto-test.aux |only huxtable-5.5.7/huxtable/tests/testthat/quarto-test.log |only huxtable-5.6.0/huxtable/DESCRIPTION | 6 huxtable-5.6.0/huxtable/MD5 | 54 huxtable-5.6.0/huxtable/NEWS.md | 15 huxtable-5.6.0/huxtable/R/Workbook.R | 5 huxtable-5.6.0/huxtable/R/dplyr.R | 60 - huxtable-5.6.0/huxtable/R/latex-dependencies.R | 11 huxtable-5.6.0/huxtable/R/zzz.R | 10 huxtable-5.6.0/huxtable/README.md | 68 - huxtable-5.6.0/huxtable/build/vignette.rds |binary huxtable-5.6.0/huxtable/inst/doc/design-principles-html.html | 10 huxtable-5.6.0/huxtable/inst/doc/design-principles-pdf.pdf |binary huxtable-5.6.0/huxtable/inst/doc/huxreg-html.html | 19 huxtable-5.6.0/huxtable/inst/doc/huxreg-pdf.pdf |binary huxtable-5.6.0/huxtable/inst/doc/huxtable-html.html | 46 huxtable-5.6.0/huxtable/inst/doc/huxtable-pdf.pdf |binary huxtable-5.6.0/huxtable/inst/doc/themes-html.html | 6 huxtable-5.6.0/huxtable/man/as_Workbook.Rd | 3 huxtable-5.6.0/huxtable/man/huxtable-news.Rd | 21 huxtable-5.6.0/huxtable/tests/testthat/filecec5332acc3.log |only huxtable-5.6.0/huxtable/tests/testthat/filecec53854bfe2.log |only huxtable-5.6.0/huxtable/tests/testthat/filecec567db13c6.log |only huxtable-5.6.0/huxtable/tests/testthat/multirow.rds |binary huxtable-5.6.0/huxtable/tests/testthat/quarto-test-tex-labels-out.pdf |binary huxtable-5.6.0/huxtable/tests/testthat/table-tester-2.log | 550 +++++----- huxtable-5.6.0/huxtable/tests/testthat/test-dplyr.R | 11 huxtable-5.6.0/huxtable/tests/testthat/test-latex-dependencies.R | 42 huxtable-5.6.0/huxtable/tests/testthat/test-openxlsx.R | 8 huxtable-5.6.0/huxtable/tests/testthat/test-print.R | 11 31 files changed, 488 insertions(+), 468 deletions(-)
Title: Bootstrap p-Values
Description: Computation of bootstrap p-values through inversion of confidence intervals, including convenience functions for regression models and tests of location.
Author: Mans Thulin [aut, cre]
Maintainer: Mans Thulin <mans@statistikkonsult.com>
Diff between boot.pval versions 0.6 dated 2025-01-14 and 0.7.0 dated 2025-03-05
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Title: Create Tests According to QTI 2.1 Standard
Description: Create tests and tasks compliant with the Question & Test Interoperability (QTI) information model version 2.1. Input sources are Rmd/md description files or S4-class objects. Output formats include standalone zip or xml files. Supports the generation of basic task types (single and multiple choice, order, pair association, matching tables, filling gaps and essay) and provides a comprehensive set of attributes for customizing tests.
Author: Andrey Shevandrin [aut, cre, cph]
,
Petr Bondarenko [ctb] ,
Ivonne Ojeda [ctb],
Johannes Titz [aut, cph] ,
Brian Mottershead [cph] ,
Stiftung fuer Innovation in der Hochschullehre [fnd]
Maintainer: Andrey Shevandrin <shevandrin@gmail.com>
Diff between rqti versions 0.3.0 dated 2024-07-19 and 1.0.0 dated 2025-03-05
rqti-0.3.0/rqti/R/api_opal.R |only rqti-0.3.0/rqti/man/auth_opal.Rd |only rqti-0.3.0/rqti/man/get_course_elements.Rd |only rqti-0.3.0/rqti/man/get_course_results.Rd |only rqti-0.3.0/rqti/man/get_resource_url.Rd |only rqti-0.3.0/rqti/man/get_resources.Rd |only rqti-0.3.0/rqti/man/publish_course.Rd |only rqti-0.3.0/rqti/man/update_course_test.Rd |only rqti-0.3.0/rqti/tests/testthat/test-api_opal.R |only rqti-1.0.0/rqti/DESCRIPTION | 24 rqti-1.0.0/rqti/MD5 | 259 rqti-1.0.0/rqti/NAMESPACE | 253 rqti-1.0.0/rqti/NEWS.md | 86 rqti-1.0.0/rqti/R/AssessmentItem.R | 21 rqti-1.0.0/rqti/R/AssessmentSection.R | 49 rqti-1.0.0/rqti/R/AssessmentTest.R | 87 rqti-1.0.0/rqti/R/AssessmentTestOpal.R | 93 rqti-1.0.0/rqti/R/CorrectFeedback.R | 7 rqti-1.0.0/rqti/R/DirectedPair.R | 274 rqti-1.0.0/rqti/R/Entry.R | 7 rqti-1.0.0/rqti/R/Essay.R | 327 rqti-1.0.0/rqti/R/LMS.R |only rqti-1.0.0/rqti/R/ModalFeedback.R | 7 rqti-1.0.0/rqti/R/MultipleChoice.R | 7 rqti-1.0.0/rqti/R/MultipleChoiceTable.R | 345 rqti-1.0.0/rqti/R/OneInColTable.R | 247 rqti-1.0.0/rqti/R/OneInRowTable.R | 247 rqti-1.0.0/rqti/R/Opal.R |only rqti-1.0.0/rqti/R/Ordering.R | 345 rqti-1.0.0/rqti/R/QtiMetadata.R | 70 rqti-1.0.0/rqti/R/SingleChoice.R | 291 rqti-1.0.0/rqti/R/WrongFeedback.R | 7 rqti-1.0.0/rqti/R/character.R | 39 rqti-1.0.0/rqti/R/extract_results.R | 31 rqti-1.0.0/rqti/R/knit_functions.R | 8 rqti-1.0.0/rqti/R/object_builder.R | 25 rqti-1.0.0/rqti/R/qti_task.R | 44 rqti-1.0.0/rqti/R/qti_test.R | 479 rqti-1.0.0/rqti/R/response_processing.R | 20 rqti-1.0.0/rqti/R/rqti_project.R | 3 rqti-1.0.0/rqti/R/section_builder.R | 741 rqti-1.0.0/rqti/inst/QTIJS/index.xml | 315 rqti-1.0.0/rqti/inst/QTIJS/qti.js | 32 rqti-1.0.0/rqti/inst/QTIJS/rqti.js | 2 rqti-1.0.0/rqti/inst/QTIJS/themecc/style.css | 12 rqti-1.0.0/rqti/inst/exercises/metadata_template.Rmd | 38 rqti-1.0.0/rqti/inst/imsqti_v2p1p2.xsd |20968 +++++----- rqti-1.0.0/rqti/inst/qti_v2p1p2_extension.xsd |only 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rqti-1.0.0/rqti/inst/rmarkdown/templates/gap-complex/skeleton/skeleton.Rmd | 26 rqti-1.0.0/rqti/inst/rmarkdown/templates/gap-complex/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/gap-simple/skeleton/skeleton.Rmd | 4 rqti-1.0.0/rqti/inst/rmarkdown/templates/gap-simple/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/multiplechoice-complex/skeleton/skeleton.Rmd | 3 rqti-1.0.0/rqti/inst/rmarkdown/templates/multiplechoice-complex/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/multiplechoice-simple/skeleton/skeleton.Rmd | 4 rqti-1.0.0/rqti/inst/rmarkdown/templates/multiplechoice-simple/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/order-complex/skeleton/skeleton.Rmd | 9 rqti-1.0.0/rqti/inst/rmarkdown/templates/order-complex/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/order-simple/skeleton/skeleton.Rmd | 6 rqti-1.0.0/rqti/inst/rmarkdown/templates/order-simple/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/singlechoice-complex/skeleton/skeleton.Rmd | 61 rqti-1.0.0/rqti/inst/rmarkdown/templates/singlechoice-complex/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/singlechoice-simple/skeleton/skeleton.Rmd | 14 rqti-1.0.0/rqti/inst/rmarkdown/templates/singlechoice-simple/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/table-complex/skeleton/skeleton.Rmd | 14 rqti-1.0.0/rqti/inst/rmarkdown/templates/table-complex/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/table-simple/skeleton/skeleton.Rmd | 15 rqti-1.0.0/rqti/inst/rmarkdown/templates/table-simple/template.yaml | 2 rqti-1.0.0/rqti/inst/test_results.zip |binary rqti-1.0.0/rqti/man/AssessmentItem-class.Rd | 2 rqti-1.0.0/rqti/man/AssessmentTest-class.Rd | 8 rqti-1.0.0/rqti/man/AssessmentTestOpal-class.Rd | 8 rqti-1.0.0/rqti/man/DirectedPair-class.Rd | 2 rqti-1.0.0/rqti/man/Entry-class.Rd | 2 rqti-1.0.0/rqti/man/Essay-class.Rd | 2 rqti-1.0.0/rqti/man/LMS-class.Rd |only rqti-1.0.0/rqti/man/MatchTable-class.Rd | 2 rqti-1.0.0/rqti/man/MultipleChoice-class.Rd | 2 rqti-1.0.0/rqti/man/MultipleChoiceTable-class.Rd | 2 rqti-1.0.0/rqti/man/OneInColTable-class.Rd | 2 rqti-1.0.0/rqti/man/OneInRowTable-class.Rd | 2 rqti-1.0.0/rqti/man/Opal-class.Rd |only rqti-1.0.0/rqti/man/Ordering-class.Rd | 2 rqti-1.0.0/rqti/man/QtiContributor-class.Rd | 2 rqti-1.0.0/rqti/man/SingleChoice-class.Rd | 2 rqti-1.0.0/rqti/man/assessmentSection.Rd |only rqti-1.0.0/rqti/man/assessmentTest.Rd |only rqti-1.0.0/rqti/man/assessmentTestOpal.Rd |only rqti-1.0.0/rqti/man/authLMS-methods.Rd |only rqti-1.0.0/rqti/man/correctFeedback.Rd | 6 rqti-1.0.0/rqti/man/createQtiTask-methods.Rd | 6 rqti-1.0.0/rqti/man/create_qti_task.Rd | 5 rqti-1.0.0/rqti/man/create_question_object.Rd |only rqti-1.0.0/rqti/man/directedPair.Rd | 11 rqti-1.0.0/rqti/man/essay.Rd | 29 rqti-1.0.0/rqti/man/extract_results.Rd | 11 rqti-1.0.0/rqti/man/getCourseElements-methods.Rd |only rqti-1.0.0/rqti/man/getCourseResult-methods.Rd |only rqti-1.0.0/rqti/man/getLMSResourceURL-methods.Rd |only rqti-1.0.0/rqti/man/getLMSResources-methods.Rd |only rqti-1.0.0/rqti/man/getLMSResourcesByName-methods.Rd |only rqti-1.0.0/rqti/man/isUserLoggedIn-methods.Rd |only rqti-1.0.0/rqti/man/modalFeedback.Rd | 6 rqti-1.0.0/rqti/man/multipleChoice.Rd | 6 rqti-1.0.0/rqti/man/multipleChoiceTable.Rd | 8 rqti-1.0.0/rqti/man/oneInColTable.Rd | 8 rqti-1.0.0/rqti/man/oneInRowTable.Rd | 8 rqti-1.0.0/rqti/man/opal.Rd |only rqti-1.0.0/rqti/man/ordering.Rd | 6 rqti-1.0.0/rqti/man/publishCourse-Opal-method.Rd |only rqti-1.0.0/rqti/man/publishCourse-missing-method.Rd |only rqti-1.0.0/rqti/man/publishCourse.Rd |only rqti-1.0.0/rqti/man/qtiContributor.Rd |only rqti-1.0.0/rqti/man/qtiMetadata.Rd |only rqti-1.0.0/rqti/man/qti_contributor.Rd | 6 rqti-1.0.0/rqti/man/qti_metadata.Rd | 2 rqti-1.0.0/rqti/man/singleChoice.Rd | 6 rqti-1.0.0/rqti/man/test.Rd | 12 rqti-1.0.0/rqti/man/test4opal.Rd | 12 rqti-1.0.0/rqti/man/updateCourseElementResource-Opal-method.Rd |only rqti-1.0.0/rqti/man/updateCourseElementResource-missing-method.Rd |only rqti-1.0.0/rqti/man/updateCourseElementResource.Rd |only rqti-1.0.0/rqti/man/upload2LMS-methods.Rd |only rqti-1.0.0/rqti/man/upload2opal.Rd | 18 rqti-1.0.0/rqti/man/verify_qti.Rd |only rqti-1.0.0/rqti/man/wrongFeedback.Rd | 6 rqti-1.0.0/rqti/tests/testthat/file/xml/InlineChoice.xml | 8 rqti-1.0.0/rqti/tests/testthat/file/xml/InlineChoice_sign_more_less.xml | 8 rqti-1.0.0/rqti/tests/testthat/file/xml/NumericGap.xml | 8 rqti-1.0.0/rqti/tests/testthat/file/xml/TextGapOpal.xml | 8 rqti-1.0.0/rqti/tests/testthat/test-api_lms.R |only rqti-1.0.0/rqti/tests/testthat/test-assessment_test.R | 98 rqti-1.0.0/rqti/tests/testthat/test-extract_results.R | 18 rqti-1.0.0/rqti/tests/testthat/test-qti_metadata.R | 8 rqti-1.0.0/rqti/tests/testthat/test-qti_task.R | 2 rqti-1.0.0/rqti/tests/testthat/test-text_gap.R | 835 rqti-1.0.0/rqti/tests/testthat/test-text_inline_choice.R | 524 149 files changed, 14224 insertions(+), 13549 deletions(-)
Title: One-Dimensional Probability Distribution Support for the
'spatstat' Family
Description: Estimation of one-dimensional probability distributions
including kernel density estimation, weighted empirical cumulative
distribution functions, Kaplan-Meier and reduced-sample estimators
for right-censored data, heat kernels, kernel properties,
quantiles and integration.
Author: Adrian Baddeley [aut, cre, cph]
,
Tilman M. Davies [aut, ctb, cph]
,
Martin L. Hazelton [aut, ctb, cph]
,
Ege Rubak [aut, cph] ,
Rolf Turner [aut, cph] ,
Greg McSwiggan [ctb, cph]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.univar versions 3.1-1 dated 2024-11-04 and 3.1-2 dated 2025-03-05
DESCRIPTION | 10 +- MD5 | 14 +-- NEWS | 8 + R/adaptive.R | 6 + inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/densityBC.Rd | 181 +++++++++++++++++++++++++++++++++++++-------- man/macros/newdefns.Rd | 4 8 files changed, 179 insertions(+), 46 deletions(-)
More information about spatstat.univar at CRAN
Permanent link
Title: Hierarchical Bayesian Aldrich-McKelvey Scaling via 'Stan'
Description: Perform hierarchical Bayesian Aldrich-McKelvey scaling using Hamiltonian Monte
Carlo via 'Stan'. Aldrich-McKelvey ('AM') scaling is a method for estimating the ideological
positions of survey respondents and political actors on a common scale using positional survey
data. The hierarchical versions of the Bayesian 'AM' model included in this package outperform
other versions both in terms of yielding meaningful posterior distributions for respondent
positions and in terms of recovering true respondent positions in simulations. The package
contains functions for preparing data, fitting models, extracting estimates, plotting key
results, and comparing models using cross-validation. The original version of the default
model is described in Bølstad (2024) <doi:10.1017/pan.2023.18>.
Author: Joergen Boelstad [aut, cre]
Maintainer: Joergen Boelstad <jorgen.bolstad@stv.uio.no>
Diff between hbamr versions 2.4.1 dated 2025-02-13 and 2.4.2 dated 2025-03-05
DESCRIPTION | 6 MD5 | 24 - NEWS.md | 10 R/hbam.R | 8 R/inits.R | 2 R/prep_data.R | 6 inst/doc/hbamr.R | 3 inst/doc/hbamr.Rmd | 12 inst/doc/hbamr.html | 91 ++--- inst/stan/omni.stan | 27 - man/hbam.Rd | 5 src/stanExports_omni.h | 835 ++++++++++++++++++++++++------------------------- vignettes/hbamr.Rmd | 12 13 files changed, 521 insertions(+), 520 deletions(-)
Title: Two Highly Customizable 'rmarkdown' Themes for Scientific
Reports
Description: Offers 'markdown' output formats designed with various styles, allowing users to generate HTML reports tailored for scientific or machine learning showcase. The output has a contemporary appearance with vibrant visuals, providing numerous styles for effective highlighting. Created using the 'tufte' <https://rstudio.github.io/tufte/> package code as a starting point.
Author: Obinna Obianom [aut, cre]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between scientific versions 2025.0 dated 2025-02-02 and 2025.1 dated 2025-03-05
DESCRIPTION | 6 +-- MD5 | 20 ++++++----- NEWS.md | 13 +++++-- R/base_func.R | 4 -- R/markdown.R | 11 +++++- README.md | 2 + inst/doc/Introduction.html | 6 +-- inst/rmarkdown/templates/html/layout/template1.tpl2 |only inst/rmarkdown/templates/html/layout/template2.tpl | 36 +------------------- inst/rmarkdown/templates/html/layout/template2.tpl2 |only inst/rmarkdown/templates/html/skeleton/skeleton.Rmd | 2 - inst/rmarkdown/templates/html/template.yaml | 2 - 12 files changed, 43 insertions(+), 59 deletions(-)
Title: Signal and Image Processing Toolbox for Analyzing Intracranial
Electroencephalography Data
Description: Implemented fast and memory-efficient Notch-filter,
Welch-periodogram, discrete wavelet spectrogram for minutes of
high-resolution signals, fast 3D convolution, image registration,
3D mesh manipulation; providing fundamental toolbox for intracranial
Electroencephalography (iEEG) pipelines.
Documentation and examples about 'RAVE' project are provided at
<https://rave.wiki>, and the paper by John F. Magnotti,
Zhengjia Wang, Michael S. Beauchamp (2020)
<doi:10.1016/j.neuroimage.2020.117341>; see 'citation("ravetools")' for
details.
Author: Zhengjia Wang [aut, cre],
John Magnotti [aut],
Michael Beauchamp [aut],
Trustees of the University of Pennsylvania [cph] ,
Karim Rahim [cph, ctb] ,
Thomas Possidente [cph, ctb] ,
Michael Prerau [cph, ctb] ,
Marcus Geelnard [ctb, cph] ,
Stefan Schlage [...truncated...]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ravetools versions 0.2.1 dated 2025-01-24 and 0.2.2 dated 2025-03-05
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 4 R/dijkstras-path.R | 1 src/vcglib/vcg/complex/algorithms/parametrization/voronoi_atlas.h | 6 src/vcglib/vcg/complex/algorithms/voronoi_processing.h | 20 +- src/vcglib/vcg/complex/allocate.h | 72 +++++----- src/vcglib/wrap/callback.h | 37 ++--- 8 files changed, 83 insertions(+), 77 deletions(-)
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Yoonkyoung Jeon [aut],
Jaehun Shon [aut],
Hyojong Myung [aut],
Hyungwoo Jo [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 1.3.8 dated 2024-12-11 and 1.3.9 dated 2025-03-05
DESCRIPTION | 8 +- MD5 | 21 ++++-- NEWS.md | 3 R/cox2.R | 8 +- build/vignette.rds |binary inst/doc/jstable.html | 88 +++++++++++++------------- inst/doc/jstable_competing_risk_analysis.R |only inst/doc/jstable_competing_risk_analysis.Rmd |only inst/doc/jstable_competing_risk_analysis.html |only inst/doc/jstable_options.R |only inst/doc/jstable_options.Rmd |only inst/doc/jstable_options.html |only tests/testthat/test-forestcox.R | 1 vignettes/jstable_competing_risk_analysis.Rmd |only vignettes/jstable_options.Rmd |only vignettes/vignette-styles.css |only 16 files changed, 73 insertions(+), 56 deletions(-)
Title: Design and Analysis of Hierarchical Composite Endpoints
Description: Simulate and analyze hierarchical composite endpoints. Win odds is the main analysis method, but other win statistics (win ratio, net benefit) are also implemented, provided there is no censoring. See Gasparyan SB et al (2023) "Hierarchical Composite Endpoints in COVID-19: The DARE-19 Trial." Case Studies in Innovative Clinical Trials, 95-148. Chapman; Hall/CRC. <doi:10.1201/9781003288640-7>.
Author: Samvel B. Gasparyan [aut, cre]
Maintainer: Samvel B. Gasparyan <gasparyan.co@gmail.com>
Diff between hce versions 0.6.7 dated 2025-01-07 and 0.7.0 dated 2025-03-05
DESCRIPTION | 6 MD5 | 76 ++++---- NAMESPACE | 2 NEWS.md | 11 + R/IWP.R |only R/as_hce.data.frame.R | 13 - R/as_hce.default.R |only R/calcWINS_data_frame.R | 121 ++++++++---- R/calcWINS_formula.R | 24 +- R/calcWINS_hce.R | 22 +- R/data.R | 2 R/plot_hce.R | 37 +++ R/simHCE.R | 126 +++++++++---- README.md | 2 inst/doc/Introduction.R | 6 inst/doc/Introduction.Rmd | 18 + inst/doc/Introduction.html | 106 +++++++++-- inst/doc/Wins.R | 2 inst/doc/Wins.Rmd | 2 inst/doc/Wins.html | 6 inst/doc/hce.R | 24 +- inst/doc/hce.Rmd | 117 ++++++++++-- inst/doc/hce.html | 391 +++++++++++++++++++----------------------- inst/doc/maraca.R | 2 inst/doc/maraca.Rmd | 2 inst/doc/maraca.html | 6 man/ADLB.Rd | 2 man/IWP.Rd |only man/as_hce.data.frame.Rd | 3 man/as_hce.default.Rd |only man/calcWINS.data.frame.Rd | 57 +++++- man/calcWINS.formula.Rd | 20 +- man/calcWINS.hce.Rd | 20 +- man/plot.hce.Rd | 16 + man/simHCE.Rd | 8 tests/testthat/test-test-WO.R | 51 +++++ vignettes/Introduction.Rmd | 18 + vignettes/REFERENCES.bib | 93 +++++++++ vignettes/Wins.Rmd | 2 vignettes/hce.Rmd | 117 ++++++++++-- vignettes/maraca.Rmd | 2 41 files changed, 1045 insertions(+), 488 deletions(-)
Title: Permutation Test for Weighted Quantile Sum Regression
Description: Implements a permutation test method for the weighted quantile sum (WQS) regression, building off the 'gWQS' package (Renzetti et al. <https://CRAN.R-project.org/package=gWQS>). Weighted quantile sum regression is a statistical technique to evaluate the effect of complex exposure mixtures on an outcome (Carrico et al. 2015 <doi:10.1007/s13253-014-0180-3>). The model features a statistical power and Type I error (i.e., false positive) rate trade-off, as there is a machine learning step to determine the weights that optimize the linear model fit. This package provides an alternative method based on a permutation test that should reliably allow for both high power and low false positive rate when utilizing WQS regression (Day et al. 2022 <doi:10.1289/EHP10570>).
Author: Drew Day [aut, cre],
James Peng [aut],
Adam Szpiro [aut]
Maintainer: Drew Day <dday612@gmail.com>
Diff between wqspt versions 1.0.1 dated 2023-03-06 and 1.0.2 dated 2025-03-05
DESCRIPTION | 17 - MD5 | 36 ++- NAMESPACE | 43 ++-- NEWS.md |only R/utils.R |only R/wqs_full_perm.R | 123 ++++++++----- R/wqs_pt.R | 182 +++++++++++-------- R/wqs_sim.R | 29 +-- R/wqspt_plot.R | 90 ++++++--- README.md | 109 +++++------ build/vignette.rds |binary inst/WORDLIST | 14 - inst/doc/introduction.R | 215 +++++++++++----------- inst/doc/introduction.Rmd | 201 ++++++++++++++------- inst/doc/introduction.html | 425 +++++++++++++++++++++++++-------------------- man/wqs_full_perm.Rd | 271 ++++++++++++++++------------ man/wqs_pt.Rd | 287 ++++++++++++++++-------------- man/wqs_sim.Rd | 275 ++++++++++++++--------------- man/wqspt_plot.Rd | 185 ++++++++++++------- vignettes/introduction.Rmd | 201 ++++++++++++++------- 20 files changed, 1571 insertions(+), 1132 deletions(-)
Title: Indices and Graphics for Assess Seed Germination Process
Description: A collection of different indices and visualization techniques for evaluate the seed germination process in ecophysiological studies (Lozano-Isla et al. 2019) <doi:10.1111/1440-1703.1275>.
Author: Flavio Lozano-Isla [aut, cre] ,
Omar Benites Alfaro [aut] ,
Marcelo F. Pompelli [aut, ths]
,
Denise Garcia de Santana [aut],
Marli A. Ranal [aut],
Federal University of Pernambuco [cph] ,
Federal Rural University of Pernambuco [cph] ,
Inkaverse [ctb]
Maintainer: Flavio Lozano-Isla <flozanoisla@gmail.com>
Diff between GerminaR versions 2.1.4 dated 2022-05-18 and 2.1.5 dated 2025-03-05
DESCRIPTION | 14 MD5 | 36 NEWS.md | 11 R/utils.R | 7 build/vignette.rds |binary inst/CITATION | 39 inst/GerminaQuant/rsconnect/shinyapps.io/flavjack/germinaquant.dcf | 10 inst/GerminaQuant/ui.R | 49 inst/doc/GerminaQuant.R | 2 inst/doc/GerminaQuant.Rmd | 2 inst/doc/GerminaQuant.html | 75 - inst/doc/GerminaR.R | 14 inst/doc/GerminaR.html | 611 +++++----- inst/doc/introduction.html | 63 - inst/rstudio/addins.dcf | 4 man/figures/logo.png |binary man/gquant_analysis.Rd | 122 - vignettes/GerminaQuant.Rmd | 2 vignettes/files/pkgs.bib | 332 ----- 19 files changed, 598 insertions(+), 795 deletions(-)
Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services
<https://aws.amazon.com>. The functions handle building, signing, and
sending requests, and receiving responses. They are designed to help build
higher-level interfaces to individual services, such as Simple Storage
Service (S3).
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.common versions 0.8.1 dated 2025-02-08 and 0.8.2 dated 2025-03-04
DESCRIPTION | 6 MD5 | 155 +- NAMESPACE | 3 NEWS.md | 7 R/RcppExports.R | 12 R/cache.R | 6 R/client.R | 168 +- R/config.R | 64 - R/convert.R | 6 R/credential_providers.R | 213 +-- R/credential_sso.R | 36 R/credential_sts.R | 72 - R/custom_rds.R | 18 R/custom_s3.R | 162 -- R/dateutil.R | 5 R/error.R | 4 R/handlers.R | 10 R/handlers_ec2query.R | 9 R/handlers_jsonrpc.R | 8 R/handlers_query.R | 14 R/handlers_rest.R | 36 R/handlers_restxml.R | 3 R/handlers_stream.R | 30 R/head_bucket.R | 61 R/iniutil.R | 10 R/jsonutil.R | 12 R/logging.R | 28 R/mock_bindings.R | 4 R/net.R | 30 R/onLoad.R | 2 R/paginate.R | 83 - R/populate.R | 11 R/queryutil.R | 3 R/request.R | 22 R/retry.R | 5 R/service.R | 41 R/signer_v1.R | 40 R/signer_v4.R | 75 - R/tags.R | 7 R/url.R | 9 R/util.R | 18 R/xmlutil.R | 97 + src/RcppExports.cpp | 19 src/ini_utils.cpp | 18 src/resolve_endpoint.cpp | 30 src/set_partition_name.cpp |only tests/testthat/helper.R | 5 tests/testthat/test_aws_error.R | 10 tests/testthat/test_cache.R | 6 tests/testthat/test_client.R | 106 + tests/testthat/test_config.R | 328 ++--- tests/testthat/test_convert.R | 13 tests/testthat/test_credential_providers.R | 37 tests/testthat/test_credentials.R | 69 - tests/testthat/test_custom_s3.R | 138 +- tests/testthat/test_dateutil.R | 20 tests/testthat/test_endpoint_vendor.R | 72 - tests/testthat/test_escape.R | 24 tests/testthat/test_handlers_core.R | 5 tests/testthat/test_handlers_ec2query.R | 196 +-- tests/testthat/test_handlers_jsonrpc.R | 285 +--- tests/testthat/test_handlers_query.R | 388 +++--- tests/testthat/test_handlers_rest.R | 41 tests/testthat/test_handlers_restjson.R | 401 +++--- tests/testthat/test_handlers_restxml.R | 414 +++--- tests/testthat/test_handlers_sse.R | 45 tests/testthat/test_handlers_stream.R | 1776 ++++++++++++++++++++++++++--- tests/testthat/test_iniutil.R | 13 tests/testthat/test_logging.R | 44 tests/testthat/test_net.R | 36 tests/testthat/test_paginate.R | 279 ++-- tests/testthat/test_populateutil.R | 6 tests/testthat/test_request.R | 5 tests/testthat/test_retry.R | 51 tests/testthat/test_service.R | 41 tests/testthat/test_signer_query.R | 521 ++++---- tests/testthat/test_signer_v4.R | 92 - tests/testthat/test_util.R | 5 tests/testthat/test_xmlutil.R | 42 79 files changed, 4197 insertions(+), 2989 deletions(-)
Title: Statistical Functions for the Design of Studies with Composite
Endpoints
Description: It has been designed to calculate the required sample size in randomized clinical trials with composite endpoints. It also calculates the expected effect and the probability of observing the composite endpoint, among others. The methodology can be found in Bofill & Gómez (2019) <doi:10.1002/sim.8092> and Gómez & Lagakos (2013) <doi:10.1002/sim.5547>.
Author: Marta Bofill Roig [aut, cre],
Jordi Cortes Martinez [aut],
Guadalupe Gomez Melis [ctb]
Maintainer: Marta Bofill Roig <marta.bofill.roig@upc.edu>
Diff between CompAREdesign versions 2.3.1 dated 2024-02-15 and 2.4.0 dated 2025-03-04
DESCRIPTION | 27 +++++-- MD5 | 54 +++++++++------ R/ARE_tte.R | 57 ++++++---------- R/MarginalsSelection.R | 47 +++++++------ R/effectsize_tte.R | 111 ++++++++++++++++--------------- R/get_prob1.R | 6 - R/plot_tte.R | 126 +++++++++++++++++++++++------------ R/sample_size_tte.R | 64 +++++++++--------- R/simula_cbe.R | 24 +++--- R/simula_tte.R | 17 +++- R/surv_tte.R | 152 ++++++++++++++++++++++--------------------- build |only inst |only man/ARE_tte.Rd | 16 ++-- man/CompAREdesign-package.Rd | 25 ++++++- man/MarginalsSelection.Rd | 5 + man/effectsize_tte.Rd | 20 +++-- man/figures |only man/get_prob1.Rd | 12 +++ man/plot_tte.Rd | 26 +++++-- man/samplesize_tte.Rd | 26 +++++-- man/simula_tte.Rd | 11 ++- man/surv_tte.Rd | 27 +++++-- vignettes |only 24 files changed, 520 insertions(+), 333 deletions(-)
Title: Make PX-Files in R
Description: Create PX-files from scratch or read and modify existing ones.
Includes a function for every PX keyword, making metadata manipulation
simple and human-readable.
Author: Johan Ejstrud [cre, aut],
Lars Pedersen [aut],
Statistics Greenland [cph]
Maintainer: Johan Ejstrud <johan@ejstrud.com>
Diff between pxmake versions 0.15.1 dated 2025-02-17 and 0.16.0 dated 2025-03-04
DESCRIPTION | 12 +++--- MD5 | 26 ++++++------- NEWS.md | 15 +++++++ R/data_df.R | 28 ++++++++------ R/px.R | 21 +++++++--- R/px_file.R | 3 - README.md | 19 ++------- inst/doc/first-px-file.html | 42 ++++++++++----------- inst/doc/micro-files.html | 26 ++++++------- man/px.Rd | 21 +++++++--- tests/testthat/test-50-px.R | 2 + tests/testthat/test-52-px-ordering.R | 64 ++++++++++++++++++++++++++++++--- tests/testthat/test-55-modify-cells1.R | 2 - tests/testthat/test-91-micromake.R | 3 - 14 files changed, 180 insertions(+), 104 deletions(-)
Title: Extended Legends and Axes for 'ggplot2'
Description: A 'ggplot2' extension that focusses on expanding the
plotter's arsenal of guides. Guides in 'ggplot2' include axes and
legends. 'legendry' offers new axes and annotation options, as well as
new legends and colour displays.
Author: Teun van den Brand [aut, cre, cph]
Maintainer: Teun van den Brand <tahvdbrand@gmail.com>
Diff between legendry versions 0.2.0 dated 2024-12-14 and 0.2.1 dated 2025-03-04
DESCRIPTION | 6 MD5 | 100 - NEWS.md | 19 R/aaa.R | 2 R/compose-.R | 2 R/compose-crux.R | 486 +++--- R/compose-sandwich.R | 228 +- R/compose-stack.R | 15 R/gizmo-density.R | 6 R/gizmo-histogram.R | 45 R/guide-circles.R | 790 +++++----- R/guide-colring.R | 5 R/guide-legend-base.R | 4 R/guide-legend-cross.R | 4 R/guide-legend-group.R | 4 R/key-.R | 744 ++++----- R/key-group.R | 4 R/key-range.R | 6 R/key-segment.R | 44 R/primitive-bracket.R | 614 +++---- R/primitive-labels.R | 5 R/primitive-line.R | 389 ++-- R/primitive-segments.R | 28 R/themes.R | 3 R/utils-checks.R | 33 R/utils-ggplot2.R | 531 +++--- R/utils.R | 10 man/figures/README-composition-1.svg | 1 man/figures/README-full_guides-1.svg | 1 man/gizmo_density.Rd | 5 man/gizmo_histogram.Rd | 15 man/key_group.Rd | 4 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/compose-sandwich/horizontal-sandwich-flipped.svg | 1 tests/testthat/_snaps/compose-sandwich/horizontal-sandwich.svg | 1 tests/testthat/_snaps/compose-sandwich/vertical-sandwich-flipped.svg | 1 tests/testthat/_snaps/compose-sandwich/vertical-sandwich.svg | 1 tests/testthat/_snaps/compose-stack/compose-stack-cartesian.svg | 16 tests/testthat/_snaps/guide-circles.md |only tests/testthat/_snaps/guide-colbar/bottom-position.svg | 4 tests/testthat/_snaps/guide-colbar/left-position.svg | 4 tests/testthat/_snaps/guide-colbar/right-position.svg | 4 tests/testthat/_snaps/guide-colbar/top-position.svg | 4 tests/testthat/_snaps/guide-colsteps/bottom-position.svg | 4 tests/testthat/_snaps/guide-colsteps/left-position.svg | 4 tests/testthat/_snaps/guide-colsteps/right-position.svg | 4 tests/testthat/_snaps/guide-colsteps/top-position.svg | 4 tests/testthat/test-aaa.R | 3 tests/testthat/test-guide-circles.R | 142 - tests/testthat/test-key-range.R | 14 tests/testthat/test-key-segment.R | 14 tests/testthat/test-themes.R |only 52 files changed, 2293 insertions(+), 2085 deletions(-)
Title: Scientific Analysis of Trial Errors (SATE)
Description: Bundles functions used to analyze the harmfulness of trial errors in criminal trials.
Functions in the Scientific Analysis of Trial Errors ('SATE') package help users estimate the
probability that a jury will find a defendant guilty given jurors' preferences for a guilty
verdict and the uncertainty of that estimate. Users can also compare actual and hypothetical
trial conditions to conduct harmful error analysis. The relationship between individual jurors'
verdict preferences and the probability that a jury returns a guilty verdict has been studied
by Davis (1973) <doi:10.1037/h0033951>; MacCoun & Kerr (1988) <doi:10.1037/0022-3514.54.1.21>,
and Devine et el. (2001) <doi:10.1037/1076-8971.7.3.622>, among others.
Author: Barry Edwards [aut, cre]
Maintainer: Barry Edwards <bce@uga.edu>
Diff between sate versions 2.3.0 dated 2025-02-06 and 2.4.0 dated 2025-03-04
DESCRIPTION | 6 +++--- MD5 | 8 +++++--- NEWS.md | 14 ++++++++++++-- R/data.R | 26 ++++++++++++++++++++++++++ data/observed.deliberations.rda |only man/observed.deliberations.Rd |only 6 files changed, 46 insertions(+), 8 deletions(-)
Title: Sparse-Group SLOPE: Adaptive Bi-Level Selection with FDR Control
Description: Implementation of Sparse-group SLOPE (SGS) (Feser and Evangelou (2023) <doi:10.48550/arXiv.2305.09467>) models. Linear and logistic regression models are supported, both of which can be fit using k-fold cross-validation. Dense and sparse input matrices are supported. In addition, a general Adaptive Three Operator Splitting (ATOS) (Pedregosa and Gidel (2018) <doi:10.48550/arXiv.1804.02339>) implementation is provided. Group SLOPE (gSLOPE) (Brzyski et al. (2019) <doi:10.1080/01621459.2017.1411269>) and group-based OSCAR models (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.15357>) are also implemented. All models are available with strong screening rules (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.15357>) for computational speed-up.
Author: Fabio Feser [aut, cre]
Maintainer: Fabio Feser <ff120@ic.ac.uk>
Diff between sgs versions 0.3.4 dated 2025-02-06 and 0.3.5 dated 2025-03-04
DESCRIPTION | 8 ++-- MD5 | 28 +++++++------- R/fit_goscar.R | 26 +++++++++++-- R/fit_gslope.R | 24 +++++++++++- R/fit_sgo.R | 24 +++++++++++- R/fit_sgs.R | 23 +++++++++++- R/fitting_code.R | 22 +---------- R/global_wrapper_code.R | 41 ++++++++++++++------- R/screen.R | 2 - R/utils.R | 70 +++++++++++++++++++++++++++++-------- inst/doc/reproducible_example.html | 12 +++--- man/fit_goscar.Rd | 2 - man/fit_gslope.Rd | 2 - man/fit_sgo.Rd | 2 - man/fit_sgs.Rd | 2 - 15 files changed, 201 insertions(+), 87 deletions(-)
Title: A Spotlight 'React' Widget for 'shiny' Apps
Description: Creates a contextual menu that can be triggered with keyboard shortcuts or programmatically.
This can replace traditional sidebars or navigation bars, thereby enhancing the
user experience with lighter user interfaces.
Author: David Granjon [aut, cre],
Adenekan Wonderful [cph]
Maintainer: David Granjon <dgranjon@ymail.com>
Diff between scoutbaR versions 0.0.1 dated 2024-11-21 and 0.1.0 dated 2025-03-04
scoutbaR-0.0.1/scoutbaR/tests/testthat/_snaps/scoutbar/simple-002_.new.png |only scoutbaR-0.1.0/scoutbaR/DESCRIPTION | 6 scoutbaR-0.1.0/scoutbaR/MD5 | 22 scoutbaR-0.1.0/scoutbaR/NEWS.md | 7 scoutbaR-0.1.0/scoutbaR/R/scoutbar.R | 2 scoutbaR-0.1.0/scoutbaR/inst/examples/simple/app.R | 2 scoutbaR-0.1.0/scoutbaR/inst/www/scoutbar/scoutbar.js | 2659 ---------- scoutbaR-0.1.0/scoutbaR/inst/www/scoutbar/scoutbar.js.LICENSE.txt |only scoutbaR-0.1.0/scoutbaR/inst/www/scoutbar/scoutbar.js.map | 2 scoutbaR-0.1.0/scoutbaR/tests/testthat/_snaps/scoutbar/simple-001.json | 3 scoutbaR-0.1.0/scoutbaR/tests/testthat/_snaps/scoutbar/simple-002.json | 1 scoutbaR-0.1.0/scoutbaR/tests/testthat/_snaps/scoutbar/simple-002_.png |binary scoutbaR-0.1.0/scoutbaR/tests/testthat/_snaps/scoutbar/simple-003.json | 1 13 files changed, 30 insertions(+), 2675 deletions(-)
Title: Ternary Plots
Description: Ternary plots made simple. This package allows to create
ternary plots using 'graphics'. It provides functions to display the
data in the ternary space, to add or tune graphical elements and to
display statistical summaries. It also includes common ternary
diagrams which are useful for the archaeologist (e.g. soil texture
charts, ceramic phase diagram).
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [art] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between isopleuros versions 1.3.0 dated 2024-11-22 and 1.4.0 dated 2025-03-04
DESCRIPTION | 30 ++- MD5 | 40 ++-- NAMESPACE | 3 NEWS.md | 7 R/AllGenerics.R | 49 +++++- R/coordinates.R | 2 R/isopleuros-internal.R | 38 ++++ R/isopleuros-package.R | 2 R/ternary_contour.R | 5 R/ternary_image.R | 245 ++++++++++++++++++++---------- R/ternary_window.R | 2 README.md | 38 +++- build/partial.rdb |binary inst/CITATION | 2 inst/examples/ex-tile.R |only inst/po |only inst/tinytest/_tinysnapshot/image_bin.svg |only inst/tinytest/test_tiles.R | 13 + man/isopleuros-package.Rd | 6 man/ternary_contour.Rd | 2 man/ternary_image.Rd | 3 man/ternary_tile.Rd |only po |only 23 files changed, 354 insertions(+), 133 deletions(-)
Title: Cryptographic Hash, Extendable-Output and Base64 Functions
Description: Fast and memory-efficient streaming hash functions and base64
encoding / decoding. Hashes strings and raw vectors directly. Stream hashes
files which can be larger than memory, as well as in-memory objects through
R's serialization mechanism. Implementations include the SHA-256, SHA-3 and
'Keccak' cryptographic hash functions, SHAKE256 extendable-output function
(XOF), and 'SipHash' pseudo-random function.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between secretbase versions 1.0.4 dated 2025-01-16 and 1.0.5 dated 2025-03-04
DESCRIPTION | 8 +++---- LICENSE |only MD5 | 25 +++++++++++----------- NEWS.md | 4 +++ R/base.R | 16 -------------- R/secret.R | 16 -------------- README.md | 28 ++++++++---------------- build/partial.rdb |binary src/base.c | 35 +++++++++--------------------- src/init.c | 16 -------------- src/secret.c | 16 -------------- src/secret.h | 18 --------------- src/secret2.c | 16 -------------- src/secret3.c | 61 ++++++++++++++++++++++-------------------------------- 14 files changed, 67 insertions(+), 192 deletions(-)
Title: Search and Retrieve Spatial Data from 'GUGiK'
Description: Automatic open data acquisition from resources of Polish Head Office
of Geodesy and Cartography ('Główny Urząd Geodezji i Kartografii')
(<https://www.gov.pl/web/gugik>).
Available datasets include various types of numeric, raster and vector data,
such as orthophotomaps, digital elevation models (digital terrain models,
digital surface model, point clouds), state register of borders, spatial
databases, geometries of cadastral parcels, 3D models of buildings, and more.
It is also possible to geocode addresses or objects using the geocodePL_get()
function.
Author: Krzysztof Dyba [aut, cre] ,
Jakub Nowosad [aut] ,
Maciej Beresewicz [ctb] ,
Grzegorz Sapijaszko [ctb],
GUGiK [ctb]
Maintainer: Krzysztof Dyba <adres7@gmail.com>
Diff between rgugik versions 0.4.1 dated 2024-05-11 and 0.4.2 dated 2025-03-04
DESCRIPTION | 15 ++++++--- MD5 | 57 ++++++++++++++++++++---------------- NAMESPACE | 1 NEWS.md | 13 ++++++++ R/DEM_request.R | 10 ++++-- R/borders_download.R | 6 +-- R/commune_names.R | 2 - R/egib_download.R |only R/egib_layers.R |only R/geodb_download.R | 2 - R/geonames_download.R | 2 - R/minmaxDTM_get.R | 3 + R/topodb_download.R | 2 - README.md | 33 +++++++++++--------- build/vignette.rds |binary data/commune_names.rda |binary data/egib_layers.rda |only inst/doc/DEM.html | 4 +- inst/doc/orthophotomap.html | 2 - inst/doc/topodb.html | 2 - man/borders_download.Rd | 2 - man/commune_names.Rd | 4 +- man/egib_download.Rd |only man/egib_layers.Rd |only man/figures/README-f1-1.png |binary man/figures/README-f2-1.png |binary man/geonames_download.Rd | 2 - man/rgugik-package.Rd | 1 tests/test-tile_download.R |only tests/testthat/test-DEM_request.R | 2 - tests/testthat/test-egib_download.R |only tests/testthat/test-geocodePL_get.R | 6 +-- tests/testthat/test-tile_download.R | 8 +---- 33 files changed, 106 insertions(+), 73 deletions(-)
Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various
statistical models. Beyond computing p values, CIs, and other indices
for a wide variety of models (see list of supported models using the
function 'insight::supported_models()'), this package implements
features like bootstrapping or simulating of parameters and models,
feature reduction (feature extraction and variable selection) as well
as functions to describe data and variable characteristics (e.g.
skewness, kurtosis, smoothness or distribution).
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Soeren Hoejsgaard [aut],
Brenton M. Wiernik [aut] ,
Zen J. Lau [ctb],
Vincent Arel-Bundock [ctb] ,
Jeffrey Girard [ctb] ,
Christina Maimone [re [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between parameters versions 0.24.1 dated 2025-01-14 and 0.24.2 dated 2025-03-04
DESCRIPTION | 30 +++--- MD5 | 116 +++++++++++++-------------- NAMESPACE | 2 NEWS.md | 15 +++ R/1_model_parameters.R | 15 --- R/dof_kenward.R | 8 - R/extract_random_variances.R | 2 R/format.R | 5 + R/group_level_total.R |only R/methods_aod.R | 7 - R/methods_aov.R | 12 ++ R/methods_averaging.R | 7 - R/methods_betareg.R | 7 - R/methods_bfsl.R | 7 - R/methods_brglm2.R | 14 --- R/methods_brms.R | 20 ++-- R/methods_cplm.R | 7 - R/methods_fixest.R | 14 --- R/methods_glmmTMB.R | 24 +++-- R/methods_hglm.R | 7 - R/methods_lme4.R | 20 ++-- R/methods_marginaleffects.R | 37 +++++++- R/methods_mclogit.R | 7 - R/methods_mmrm.R | 7 - R/methods_mvord.R | 7 - R/methods_nestedLogit.R | 7 - R/methods_ordinal.R | 7 - R/methods_panelr.R | 1 R/methods_rstanarm.R | 8 + R/methods_selection.R | 7 - R/methods_survey.R | 7 - R/methods_svy2lme.R | 4 R/methods_systemfit.R | 7 - R/print.parameters_model.R | 7 + R/print_html.R | 1 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 1 man/compare_parameters.Rd | 12 +- man/display.parameters_model.Rd | 5 - man/equivalence_test.lm.Rd | 7 - man/model_parameters.BFBayesFactor.Rd | 10 +- man/model_parameters.befa.Rd | 10 +- man/model_parameters.brmsfit.Rd | 24 ++--- man/model_parameters.default.Rd | 3 man/model_parameters.glimML.Rd | 3 man/model_parameters.glmmTMB.Rd | 10 -- man/model_parameters.zcpglm.Rd | 3 man/p_function.Rd | 7 - man/pool_parameters.Rd | 7 - man/print.compare_parameters.Rd | 5 - man/print.parameters_model.Rd | 5 - man/simulate_parameters.Rd | 10 +- tests/testthat/_snaps/marginaleffects.md | 2 tests/testthat/_snaps/weightit.md | 2 tests/testthat/test-group_level_total.R |only tests/testthat/test-marginaleffects.R | 19 ++++ tests/testthat/test-model_parameters.aov.R | 48 +++++++++++ tests/testthat/test-model_parameters.mixed.R | 8 + 60 files changed, 324 insertions(+), 332 deletions(-)
Title: Generalized Pairwise Comparisons
Description: Implementation of the Generalized Pairwise Comparisons (GPC) as defined in Buyse (2010) <doi:10.1002/sim.3923> for complete observations, and extended in Peron (2018) <doi:10.1177/0962280216658320> to deal with right-censoring. GPC compare two groups of observations (intervention vs. control group) regarding several prioritized endpoints to estimate the probability that a random observation drawn from one group performs better/worse/equivalently than a random observation drawn from the other group. Summary statistics such as the net treatment benefit, win ratio, or win odds are then deduced from these probabilities. Confidence intervals and p-values are obtained based on asymptotic results (Ozenne 2021 <doi:10.1177/09622802211037067>), non-parametric bootstrap, or permutations. The software enables the use of thresholds of minimal importance difference, stratification, non-prioritized endpoints (O Brien test), and can handle right-censoring and competing-risks.
Author: Brice Ozenne [aut, cre] ,
Eva Cantagallo [aut],
William Anderson [aut],
Julien Peron [ctb],
Johan Verbeeck [ctb]
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>
Diff between BuyseTest versions 3.0.5 dated 2024-10-13 and 3.1.0 dated 2025-03-04
BuyseTest-3.0.5/BuyseTest/man/S4BuyseTest-getCount.Rd |only BuyseTest-3.0.5/BuyseTest/man/S4BuyseTest-getIid.Rd |only BuyseTest-3.0.5/BuyseTest/man/S4BuyseTest-getPairScore.Rd |only BuyseTest-3.0.5/BuyseTest/man/S4BuyseTest-getPseudovalue.Rd |only BuyseTest-3.0.5/BuyseTest/man/S4BuyseTest-getSurvival.Rd |only BuyseTest-3.0.5/BuyseTest/man/S4BuyseTest-sensitivity.Rd |only BuyseTest-3.1.0/BuyseTest/DESCRIPTION | 16 BuyseTest-3.1.0/BuyseTest/MD5 | 304 - BuyseTest-3.1.0/BuyseTest/NAMESPACE | 193 BuyseTest-3.1.0/BuyseTest/NEWS | 540 +- BuyseTest-3.1.0/BuyseTest/R/0-onLoad.R | 22 BuyseTest-3.1.0/BuyseTest/R/1-setGeneric.R | 118 BuyseTest-3.1.0/BuyseTest/R/BuyseMultComp.R | 996 ++-- BuyseTest-3.1.0/BuyseTest/R/BuyseTTEM.R | 1403 +++-- BuyseTest-3.1.0/BuyseTest/R/BuyseTest-Peron.R | 714 +- BuyseTest-3.1.0/BuyseTest/R/BuyseTest-check.R | 1139 ++-- BuyseTest-3.1.0/BuyseTest/R/BuyseTest-inference.R | 1028 ++-- BuyseTest-3.1.0/BuyseTest/R/BuyseTest-initialization.R | 1738 +++---- BuyseTest-3.1.0/BuyseTest/R/BuyseTest-package.R | 142 BuyseTest-3.1.0/BuyseTest/R/BuyseTest-print.R | 357 - BuyseTest-3.1.0/BuyseTest/R/BuyseTest.R | 1557 +++--- BuyseTest-3.1.0/BuyseTest/R/BuyseTest.options.R | 222 BuyseTest-3.1.0/BuyseTest/R/CasinoTest.R | 666 +- BuyseTest-3.1.0/BuyseTest/R/PairScore.R | 108 BuyseTest-3.1.0/BuyseTest/R/RcppExports.R | 462 - BuyseTest-3.1.0/BuyseTest/R/S4-BuysePower-model.tables.R | 338 - BuyseTest-3.1.0/BuyseTest/R/S4-BuysePower-nobs.R | 96 BuyseTest-3.1.0/BuyseTest/R/S4-BuysePower-print.R | 66 BuyseTest-3.1.0/BuyseTest/R/S4-BuysePower-show.R | 64 BuyseTest-3.1.0/BuyseTest/R/S4-BuysePower-summary.R | 350 - BuyseTest-3.1.0/BuyseTest/R/S4-BuysePower.R | 166 BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest-coef.R | 678 +- BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest-confint.R | 2166 ++++---- BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest-get.R | 1706 +++---- BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest-model.tables.R | 564 +- BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest-nobs.R | 204 BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest-plot.R | 178 BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest-print.R | 70 BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest-sensitivity.R | 730 +-- BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest-show.R | 98 BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest-summary.R | 947 +-- BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest.R | 612 +- BuyseTest-3.1.0/BuyseTest/R/S4-BuyseTest.options.R | 464 - BuyseTest-3.1.0/BuyseTest/R/as.data.table.performance.R | 282 - BuyseTest-3.1.0/BuyseTest/R/auc.R | 792 +-- BuyseTest-3.1.0/BuyseTest/R/autoplot.S4BuyseTest.R | 342 - BuyseTest-3.1.0/BuyseTest/R/brier.R | 604 +- BuyseTest-3.1.0/BuyseTest/R/constStrata.R | 178 BuyseTest-3.1.0/BuyseTest/R/discreteRoot.R | 580 +- BuyseTest-3.1.0/BuyseTest/R/doc-data.R |only BuyseTest-3.1.0/BuyseTest/R/efronlim.R |only BuyseTest-3.1.0/BuyseTest/R/iid.S3sensitivity.R | 50 BuyseTest-3.1.0/BuyseTest/R/iid.prodlim.R | 404 - BuyseTest-3.1.0/BuyseTest/R/normexp.R | 424 - BuyseTest-3.1.0/BuyseTest/R/performance.R | 2424 +++++----- BuyseTest-3.1.0/BuyseTest/R/performanceResample.R | 572 +- BuyseTest-3.1.0/BuyseTest/R/plot.S3sensitivity.R | 358 - BuyseTest-3.1.0/BuyseTest/R/powerBuyseTest.R | 1621 +++--- BuyseTest-3.1.0/BuyseTest/R/predict.logit.R | 564 +- BuyseTest-3.1.0/BuyseTest/R/rbind.performanceResample.R | 226 BuyseTest-3.1.0/BuyseTest/R/sim.simBuyseTest.R | 66 BuyseTest-3.1.0/BuyseTest/R/simBuyseTest.R | 1470 +++--- BuyseTest-3.1.0/BuyseTest/R/simCompetingRisks.R | 284 - BuyseTest-3.1.0/BuyseTest/R/summary.performance.R | 228 BuyseTest-3.1.0/BuyseTest/R/valid.R | 960 +-- BuyseTest-3.1.0/BuyseTest/build/vignette.rds |binary BuyseTest-3.1.0/BuyseTest/data |only BuyseTest-3.1.0/BuyseTest/inst/CITATION | 116 BuyseTest-3.1.0/BuyseTest/inst/doc/overview.pdf |binary BuyseTest-3.1.0/BuyseTest/inst/doc/overview.pdf.asis | 1118 ++-- BuyseTest-3.1.0/BuyseTest/inst/doc/wilcoxonTest.pdf.asis | 210 BuyseTest-3.1.0/BuyseTest/inst/source |only BuyseTest-3.1.0/BuyseTest/man/BuyseMultComp.Rd | 230 BuyseTest-3.1.0/BuyseTest/man/BuyseTTEM.Rd | 157 BuyseTest-3.1.0/BuyseTest/man/BuyseTest-package.Rd | 166 BuyseTest-3.1.0/BuyseTest/man/BuyseTest.Rd | 635 +- BuyseTest-3.1.0/BuyseTest/man/BuyseTest.options-class.Rd | 32 BuyseTest-3.1.0/BuyseTest/man/BuyseTest.options-methods.Rd | 44 BuyseTest-3.1.0/BuyseTest/man/BuyseTest.options.Rd | 66 BuyseTest-3.1.0/BuyseTest/man/CasinoTest.Rd | 224 BuyseTest-3.1.0/BuyseTest/man/GPC_cpp.Rd | 380 - BuyseTest-3.1.0/BuyseTest/man/S4BuysePower-class.Rd | 34 BuyseTest-3.1.0/BuyseTest/man/S4BuysePower-nobs.Rd | 50 BuyseTest-3.1.0/BuyseTest/man/S4BuysePower-summary.Rd | 118 BuyseTest-3.1.0/BuyseTest/man/S4BuyseTest-class.Rd | 34 BuyseTest-3.1.0/BuyseTest/man/S4BuyseTest-coef.Rd | 132 BuyseTest-3.1.0/BuyseTest/man/S4BuyseTest-confint.Rd | 254 - BuyseTest-3.1.0/BuyseTest/man/S4BuyseTest-nobs.Rd | 62 BuyseTest-3.1.0/BuyseTest/man/S4BuyseTest-plot.Rd | 136 BuyseTest-3.1.0/BuyseTest/man/S4BuyseTest-print.Rd | 52 BuyseTest-3.1.0/BuyseTest/man/S4BuyseTest-show.Rd | 72 BuyseTest-3.1.0/BuyseTest/man/S4BuyseTest-summary.Rd | 284 - BuyseTest-3.1.0/BuyseTest/man/as.data.table.performance.Rd | 66 BuyseTest-3.1.0/BuyseTest/man/auc.Rd | 166 BuyseTest-3.1.0/BuyseTest/man/autoplot-S4BuyseTest.Rd | 82 BuyseTest-3.1.0/BuyseTest/man/calcIntegralSurv2_cpp.Rd | 94 BuyseTest-3.1.0/BuyseTest/man/coef.BuyseTestAuc.Rd | 38 BuyseTest-3.1.0/BuyseTest/man/coef.BuyseTestBrier.Rd | 40 BuyseTest-3.1.0/BuyseTest/man/confint.BuyseTestAuc.Rd | 38 BuyseTest-3.1.0/BuyseTest/man/confint.BuyseTestBrier.Rd | 40 BuyseTest-3.1.0/BuyseTest/man/constStrata.Rd | 122 BuyseTest-3.1.0/BuyseTest/man/data-CHARM.Rd |only BuyseTest-3.1.0/BuyseTest/man/data-EB.Rd |only BuyseTest-3.1.0/BuyseTest/man/data-prodige.Rd |only BuyseTest-3.1.0/BuyseTest/man/dot-calcIntegralCif_cpp.Rd | 98 BuyseTest-3.1.0/BuyseTest/man/dot-calcIntegralSurv_cpp.Rd | 84 BuyseTest-3.1.0/BuyseTest/man/dot-colCenter_cpp.Rd | 40 BuyseTest-3.1.0/BuyseTest/man/dot-colCumSum_cpp.Rd | 36 BuyseTest-3.1.0/BuyseTest/man/dot-colMultiply_cpp.Rd | 40 BuyseTest-3.1.0/BuyseTest/man/dot-colScale_cpp.Rd | 40 BuyseTest-3.1.0/BuyseTest/man/dot-rowCenter_cpp.Rd | 40 BuyseTest-3.1.0/BuyseTest/man/dot-rowCumProd_cpp.Rd | 36 BuyseTest-3.1.0/BuyseTest/man/dot-rowCumSum_cpp.Rd | 36 BuyseTest-3.1.0/BuyseTest/man/dot-rowMultiply_cpp.Rd | 40 BuyseTest-3.1.0/BuyseTest/man/dot-rowScale_cpp.Rd | 40 BuyseTest-3.1.0/BuyseTest/man/efronlim.Rd |only BuyseTest-3.1.0/BuyseTest/man/getCount.Rd |only BuyseTest-3.1.0/BuyseTest/man/getIid.Rd |only BuyseTest-3.1.0/BuyseTest/man/getPairScore.Rd |only BuyseTest-3.1.0/BuyseTest/man/getPseudovalue.Rd |only BuyseTest-3.1.0/BuyseTest/man/getSurvival.Rd |only BuyseTest-3.1.0/BuyseTest/man/iid.BuyseTestAuc.Rd | 38 BuyseTest-3.1.0/BuyseTest/man/iid.BuyseTestBrier.Rd | 40 BuyseTest-3.1.0/BuyseTest/man/iid.prodlim.Rd | 110 BuyseTest-3.1.0/BuyseTest/man/performance.Rd | 212 BuyseTest-3.1.0/BuyseTest/man/performanceResample.Rd | 114 BuyseTest-3.1.0/BuyseTest/man/powerBuyseTest.Rd | 314 - BuyseTest-3.1.0/BuyseTest/man/predict.BuyseTTEM.Rd | 62 BuyseTest-3.1.0/BuyseTest/man/rbind.performance.Rd | 122 BuyseTest-3.1.0/BuyseTest/man/sensitivity.Rd |only BuyseTest-3.1.0/BuyseTest/man/simBuyseTest.Rd | 422 - BuyseTest-3.1.0/BuyseTest/man/simCompetingRisks.Rd | 212 BuyseTest-3.1.0/BuyseTest/man/summary.performance.Rd | 46 BuyseTest-3.1.0/BuyseTest/man/validFCTs.Rd | 312 - BuyseTest-3.1.0/BuyseTest/tests/testthat.R | 84 BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuysePower.R | 400 - BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTTEM.R | 568 +- BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-CR.R | 468 - BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-PairScore.R | 240 BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-Pairs.R | 1204 ++-- BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-checkValues.R | 1148 ++-- BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-correctionTTE.R | 450 - BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-engine.R | 214 BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-iid.R | 1601 +++--- BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-multcomp.R | 178 BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-neutralAsUnif.R | 206 BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-operator.R | 202 BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-previousBug.R | 1556 +++--- BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-resampling.R | 1198 ++-- BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-restricted.R | 188 BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-strata.R | 864 +-- BuyseTest-3.1.0/BuyseTest/tests/testthat/test-BuyseTest-weightObs.R | 130 BuyseTest-3.1.0/BuyseTest/tests/testthat/test-auc.R | 268 - BuyseTest-3.1.0/BuyseTest/tests/testthat/test-initSurvival.R | 438 - BuyseTest-3.1.0/BuyseTest/tests/testthat/test-initThreshold.R | 168 BuyseTest-3.1.0/BuyseTest/tests/testthat/test-otherPackages.R | 394 - BuyseTest-3.1.0/BuyseTest/tests/testthat/testthat-problems.rds |only BuyseTest-3.1.0/BuyseTest/vignettes/overview.pdf.asis | 1118 ++-- BuyseTest-3.1.0/BuyseTest/vignettes/vignette_CR.Rmd | 146 BuyseTest-3.1.0/BuyseTest/vignettes/wilcoxonTest.pdf.asis | 210 160 files changed, 27637 insertions(+), 27481 deletions(-)
Title: Maximum Likelihood Estimation for Univariate Densities
Description: User-friendly maximum likelihood estimation (Fisher (1921)
<doi:10.1098/rsta.1922.0009>) of univariate densities.
Author: Jonas Moss [aut, cre] ,
Thomas Nagler [ctb],
Chitu Okoli [ctb]
Maintainer: Jonas Moss <jonas.gjertsen@gmail.com>
Diff between univariateML versions 1.1.1 dated 2022-01-25 and 1.5.0 dated 2025-03-04
univariateML-1.1.1/univariateML/R/imports.R |only univariateML-1.1.1/univariateML/man/ml_input_checker.Rd |only univariateML-1.5.0/univariateML/DESCRIPTION | 16 univariateML-1.5.0/univariateML/LICENSE | 4 univariateML-1.5.0/univariateML/MD5 | 339 ++- univariateML-1.5.0/univariateML/NAMESPACE | 118 - univariateML-1.5.0/univariateML/R/aaa.R |only univariateML-1.5.0/univariateML/R/bootstrap.R | 189 +- univariateML-1.5.0/univariateML/R/data-abalone.R | 62 univariateML-1.5.0/univariateML/R/data-corbet.R |only univariateML-1.5.0/univariateML/R/data-egypt.R | 58 univariateML-1.5.0/univariateML/R/densities.R | 4 univariateML-1.5.0/univariateML/R/functions.R | 168 - univariateML-1.5.0/univariateML/R/generics.R | 372 ++-- univariateML-1.5.0/univariateML/R/helpers.R | 291 +-- univariateML-1.5.0/univariateML/R/mlbeta.R | 177 -- univariateML-1.5.0/univariateML/R/mlbetapr.R | 101 - univariateML-1.5.0/univariateML/R/mlbinom.R |only univariateML-1.5.0/univariateML/R/mlburr.R |only univariateML-1.5.0/univariateML/R/mlcauchy.R | 111 - univariateML-1.5.0/univariateML/R/mldunif.R |only univariateML-1.5.0/univariateML/R/mlexp.R | 84 univariateML-1.5.0/univariateML/R/mlfatigue.R |only univariateML-1.5.0/univariateML/R/mlgamma.R | 151 - univariateML-1.5.0/univariateML/R/mlged.R | 86 - univariateML-1.5.0/univariateML/R/mlgeom.R |only univariateML-1.5.0/univariateML/R/mlgompertz.R |only univariateML-1.5.0/univariateML/R/mlgumbel.R | 163 - univariateML-1.5.0/univariateML/R/mlinvburr.R |only univariateML-1.5.0/univariateML/R/mlinvgamma.R | 99 - univariateML-1.5.0/univariateML/R/mlinvgauss.R | 101 - univariateML-1.5.0/univariateML/R/mlinvweibull.R | 117 - univariateML-1.5.0/univariateML/R/mlkumar.R | 178 -- univariateML-1.5.0/univariateML/R/mllaplace.R | 91 - univariateML-1.5.0/univariateML/R/mllgamma.R | 105 - univariateML-1.5.0/univariateML/R/mllgser.R |only univariateML-1.5.0/univariateML/R/mlllogis.R | 109 - univariateML-1.5.0/univariateML/R/mllnorm.R | 96 - univariateML-1.5.0/univariateML/R/mllogis.R | 104 - univariateML-1.5.0/univariateML/R/mllogitnorm.R | 106 - univariateML-1.5.0/univariateML/R/mllomax.R | 196 -- univariateML-1.5.0/univariateML/R/mlnaka.R | 121 - univariateML-1.5.0/univariateML/R/mlnbinom.R |only univariateML-1.5.0/univariateML/R/mlnorm.R | 93 - univariateML-1.5.0/univariateML/R/mlparalogis.R |only univariateML-1.5.0/univariateML/R/mlpareto.R | 94 - univariateML-1.5.0/univariateML/R/mlpois.R |only univariateML-1.5.0/univariateML/R/mlpower.R | 131 - univariateML-1.5.0/univariateML/R/mlrayleigh.R | 85 univariateML-1.5.0/univariateML/R/mlsged.R | 86 - univariateML-1.5.0/univariateML/R/mlsnorm.R | 80 univariateML-1.5.0/univariateML/R/mlsstd.R | 81 univariateML-1.5.0/univariateML/R/mlstd.R | 80 univariateML-1.5.0/univariateML/R/mlunif.R | 84 univariateML-1.5.0/univariateML/R/mlweibull.R | 140 - univariateML-1.5.0/univariateML/R/mlzip.R |only univariateML-1.5.0/univariateML/R/mlzipf.R |only univariateML-1.5.0/univariateML/R/model_select.R | 205 +- univariateML-1.5.0/univariateML/R/probability_plots.R | 308 ++- univariateML-1.5.0/univariateML/R/univariateML-package.R | 44 univariateML-1.5.0/univariateML/R/utility.R | 173 +- univariateML-1.5.0/univariateML/R/zzz.R |only univariateML-1.5.0/univariateML/README.md | 290 +-- univariateML-1.5.0/univariateML/build/vignette.rds |binary univariateML-1.5.0/univariateML/data/corbet.rda |only univariateML-1.5.0/univariateML/inst/CITATION | 33 univariateML-1.5.0/univariateML/inst/doc/copula.R | 86 - univariateML-1.5.0/univariateML/inst/doc/copula.Rmd | 218 +- univariateML-1.5.0/univariateML/inst/doc/copula.html | 770 +++++--- univariateML-1.5.0/univariateML/inst/doc/distributions.R | 25 univariateML-1.5.0/univariateML/inst/doc/distributions.Rmd | 124 - univariateML-1.5.0/univariateML/inst/doc/distributions.html | 659 ++----- univariateML-1.5.0/univariateML/inst/doc/overview.R | 185 +- univariateML-1.5.0/univariateML/inst/doc/overview.Rmd | 411 ++-- univariateML-1.5.0/univariateML/inst/doc/overview.html | 859 ++++------ univariateML-1.5.0/univariateML/man/MaximumLikelihoodDistribution.Rd | 138 - univariateML-1.5.0/univariateML/man/ProbabilityPlots.Rd | 189 +- univariateML-1.5.0/univariateML/man/abalone.Rd | 88 - univariateML-1.5.0/univariateML/man/bootstrapml.Rd | 184 +- univariateML-1.5.0/univariateML/man/confint.univariateML.Rd | 98 - univariateML-1.5.0/univariateML/man/corbet.Rd |only univariateML-1.5.0/univariateML/man/decorator.Rd |only univariateML-1.5.0/univariateML/man/egypt.Rd | 84 univariateML-1.5.0/univariateML/man/figures/README-weibull_plot-1.png |binary univariateML-1.5.0/univariateML/man/get_start.Rd |only univariateML-1.5.0/univariateML/man/inverse_digamma.Rd |only univariateML-1.5.0/univariateML/man/listmerge.Rd | 50 univariateML-1.5.0/univariateML/man/mlbeta.Rd | 95 - univariateML-1.5.0/univariateML/man/mlbetapr.Rd | 98 - univariateML-1.5.0/univariateML/man/mlbinom.Rd |only univariateML-1.5.0/univariateML/man/mlburr.Rd |only univariateML-1.5.0/univariateML/man/mlcauchy.Rd | 94 - univariateML-1.5.0/univariateML/man/mldunif.Rd |only univariateML-1.5.0/univariateML/man/mlexp.Rd | 89 - univariateML-1.5.0/univariateML/man/mlfatigue.Rd |only univariateML-1.5.0/univariateML/man/mlgamma.Rd | 100 - univariateML-1.5.0/univariateML/man/mlged.Rd | 92 - univariateML-1.5.0/univariateML/man/mlgeom.Rd |only univariateML-1.5.0/univariateML/man/mlgompertz.Rd |only univariateML-1.5.0/univariateML/man/mlgumbel.Rd | 93 - univariateML-1.5.0/univariateML/man/mlinvburr.Rd |only univariateML-1.5.0/univariateML/man/mlinvgamma.Rd | 88 - univariateML-1.5.0/univariateML/man/mlinvgauss.Rd | 92 - univariateML-1.5.0/univariateML/man/mlinvweibull.Rd | 102 - univariateML-1.5.0/univariateML/man/mlkumar.Rd | 106 - univariateML-1.5.0/univariateML/man/mllaplace.Rd | 90 - univariateML-1.5.0/univariateML/man/mllgamma.Rd | 92 - univariateML-1.5.0/univariateML/man/mllgser.Rd |only univariateML-1.5.0/univariateML/man/mlllogis.Rd | 102 - univariateML-1.5.0/univariateML/man/mllnorm.Rd | 92 - univariateML-1.5.0/univariateML/man/mllogis.Rd | 90 - univariateML-1.5.0/univariateML/man/mllogitnorm.Rd | 92 - univariateML-1.5.0/univariateML/man/mllomax.Rd | 113 - univariateML-1.5.0/univariateML/man/mlnaka.Rd | 103 - univariateML-1.5.0/univariateML/man/mlnbinom.Rd |only univariateML-1.5.0/univariateML/man/mlnorm.Rd | 90 - univariateML-1.5.0/univariateML/man/mlparalogis.Rd |only univariateML-1.5.0/univariateML/man/mlpareto.Rd | 90 - univariateML-1.5.0/univariateML/man/mlpois.Rd |only univariateML-1.5.0/univariateML/man/mlpower.Rd | 106 - univariateML-1.5.0/univariateML/man/mlrayleigh.Rd | 88 - univariateML-1.5.0/univariateML/man/mlsged.Rd | 92 - univariateML-1.5.0/univariateML/man/mlsnorm.Rd | 86 - univariateML-1.5.0/univariateML/man/mlsstd.Rd | 86 - univariateML-1.5.0/univariateML/man/mlstd.Rd | 86 - univariateML-1.5.0/univariateML/man/mlunif.Rd | 86 - univariateML-1.5.0/univariateML/man/mlweibull.Rd | 94 - univariateML-1.5.0/univariateML/man/mlzip.Rd |only univariateML-1.5.0/univariateML/man/mlzipf.Rd |only univariateML-1.5.0/univariateML/man/model_select.Rd | 126 - univariateML-1.5.0/univariateML/man/newton_raphson_1d.Rd |only univariateML-1.5.0/univariateML/man/plot.univariateML.Rd | 68 univariateML-1.5.0/univariateML/man/plot_wrangler.Rd | 38 univariateML-1.5.0/univariateML/man/ppqq_wrangler.Rd | 42 univariateML-1.5.0/univariateML/man/simulate_default.Rd |only univariateML-1.5.0/univariateML/man/to_univariateML.Rd | 34 univariateML-1.5.0/univariateML/man/univariateML-package.Rd | 93 - univariateML-1.5.0/univariateML/man/univariateML_construct.Rd |only univariateML-1.5.0/univariateML/man/univariateML_metadata.Rd |only univariateML-1.5.0/univariateML/man/univariateML_models.Rd | 38 univariateML-1.5.0/univariateML/man/univariateML_to_function.Rd | 44 univariateML-1.5.0/univariateML/man/univariateML_to_string.Rd | 44 univariateML-1.5.0/univariateML/tests/testthat.R | 8 univariateML-1.5.0/univariateML/tests/testthat/Rplots.pdf |binary univariateML-1.5.0/univariateML/tests/testthat/test_bootstrap.R | 99 - univariateML-1.5.0/univariateML/tests/testthat/test_confint.R | 28 univariateML-1.5.0/univariateML/tests/testthat/test_functions.R | 95 - univariateML-1.5.0/univariateML/tests/testthat/test_generics.R | 80 univariateML-1.5.0/univariateML/tests/testthat/test_helpers.R | 77 univariateML-1.5.0/univariateML/tests/testthat/test_input_checks.R | 33 univariateML-1.5.0/univariateML/tests/testthat/test_mlbeta.R | 83 univariateML-1.5.0/univariateML/tests/testthat/test_mlbetapr.R | 135 - univariateML-1.5.0/univariateML/tests/testthat/test_mlbinom.R |only univariateML-1.5.0/univariateML/tests/testthat/test_mlcauchy.R | 146 - univariateML-1.5.0/univariateML/tests/testthat/test_mlexp.R | 58 univariateML-1.5.0/univariateML/tests/testthat/test_mlgamma.R | 90 - univariateML-1.5.0/univariateML/tests/testthat/test_mlged.R | 103 - univariateML-1.5.0/univariateML/tests/testthat/test_mlgumbel.R | 118 - univariateML-1.5.0/univariateML/tests/testthat/test_mlinvgamma.R | 86 - univariateML-1.5.0/univariateML/tests/testthat/test_mlinvgauss.R | 138 - univariateML-1.5.0/univariateML/tests/testthat/test_mlinvweibull.R | 72 univariateML-1.5.0/univariateML/tests/testthat/test_mlkumar.R | 122 - univariateML-1.5.0/univariateML/tests/testthat/test_mllaplace.R | 56 univariateML-1.5.0/univariateML/tests/testthat/test_mllgamma.R | 82 univariateML-1.5.0/univariateML/tests/testthat/test_mllgser.R |only univariateML-1.5.0/univariateML/tests/testthat/test_mlllogis.R | 89 - univariateML-1.5.0/univariateML/tests/testthat/test_mllnorm.R | 60 univariateML-1.5.0/univariateML/tests/testthat/test_mllogis.R | 184 +- univariateML-1.5.0/univariateML/tests/testthat/test_mllogitnorm.R | 64 univariateML-1.5.0/univariateML/tests/testthat/test_mllomax.R | 112 - univariateML-1.5.0/univariateML/tests/testthat/test_mlnaka.R | 90 - univariateML-1.5.0/univariateML/tests/testthat/test_mlnbinom.R |only univariateML-1.5.0/univariateML/tests/testthat/test_mlnorm.R | 56 univariateML-1.5.0/univariateML/tests/testthat/test_mlpareto.R | 122 - univariateML-1.5.0/univariateML/tests/testthat/test_mlpower.R | 128 - univariateML-1.5.0/univariateML/tests/testthat/test_mlrayleigh.R | 58 univariateML-1.5.0/univariateML/tests/testthat/test_mlsged.R | 102 - univariateML-1.5.0/univariateML/tests/testthat/test_mlsnorm.R | 103 - univariateML-1.5.0/univariateML/tests/testthat/test_mlsstd.R | 102 - univariateML-1.5.0/univariateML/tests/testthat/test_mlstd.R | 102 - univariateML-1.5.0/univariateML/tests/testthat/test_mlunif.R | 111 - univariateML-1.5.0/univariateML/tests/testthat/test_mlweibull.R | 92 - univariateML-1.5.0/univariateML/tests/testthat/test_mlzip.R |only univariateML-1.5.0/univariateML/tests/testthat/test_mlzipf.R |only univariateML-1.5.0/univariateML/tests/testthat/test_model_select.R | 97 - univariateML-1.5.0/univariateML/tests/testthat/test_probability_plots.R | 172 +- univariateML-1.5.0/univariateML/tests/testthat/test_utility.R | 45 univariateML-1.5.0/univariateML/vignettes/copula.Rmd | 218 +- univariateML-1.5.0/univariateML/vignettes/copula.bib | 12 univariateML-1.5.0/univariateML/vignettes/copula.md | 234 +- univariateML-1.5.0/univariateML/vignettes/copula_files/figure-html/make_data-1.png |binary univariateML-1.5.0/univariateML/vignettes/distributions.Rmd | 124 - univariateML-1.5.0/univariateML/vignettes/overview.Rmd | 411 ++-- 193 files changed, 9068 insertions(+), 8875 deletions(-)
Title: Routines for Common fMRI Processing Tasks
Description: Supports fMRI (functional magnetic resonance imaging)
analysis tasks including reading in 'CIFTI', 'GIFTI' and
'NIFTI' data, temporal filtering, nuisance regression, and
aCompCor (anatomical Components Correction) (Muschelli et al.
(2014) <doi:10.1016/j.neuroimage.2014.03.028>).
Author: Amanda Mejia [aut, cre],
Damon Pham [aut] ,
Mark Fiecas [ctb]
Maintainer: Amanda Mejia <mandy.mejia@gmail.com>
Diff between fMRItools versions 0.4.7 dated 2024-05-30 and 0.5.3 dated 2025-03-04
fMRItools-0.4.7/fMRItools/man/detrend.Rd |only fMRItools-0.4.7/fMRItools/man/image.scale.Rd |only fMRItools-0.5.3/fMRItools/DESCRIPTION | 8 fMRItools-0.5.3/fMRItools/MD5 | 34 ++- fMRItools-0.5.3/fMRItools/NAMESPACE | 3 fMRItools-0.5.3/fMRItools/R/DCT_FFT_detrending.R | 199 +++++++++++++++++------ fMRItools-0.5.3/fMRItools/R/UT.R | 20 +- fMRItools-0.5.3/fMRItools/R/carpetplot.R | 1 fMRItools-0.5.3/fMRItools/R/dual_reg.R | 36 ++-- fMRItools-0.5.3/fMRItools/R/expand_RPs.R |only fMRItools-0.5.3/fMRItools/R/fsl_bptf.R | 131 ++++++++++----- fMRItools-0.5.3/fMRItools/R/norm_BOLD.R | 85 ++++++--- fMRItools-0.5.3/fMRItools/R/plot_FC.R | 15 + fMRItools-0.5.3/fMRItools/man/UT2mat.Rd | 13 - fMRItools-0.5.3/fMRItools/man/dct_bases.Rd | 2 fMRItools-0.5.3/fMRItools/man/dual_reg.Rd | 15 + fMRItools-0.5.3/fMRItools/man/expand_RPs.Rd |only fMRItools-0.5.3/fMRItools/man/fsl_bptf.Rd | 13 + fMRItools-0.5.3/fMRItools/man/image_scale.Rd |only fMRItools-0.5.3/fMRItools/man/norm_BOLD.Rd | 24 +- fMRItools-0.5.3/fMRItools/man/temporal_filter.Rd |only 21 files changed, 411 insertions(+), 188 deletions(-)
Title: Kernel Density Estimation with Parametric Starts and Asymmetric
Kernels
Description: Handles univariate non-parametric density estimation with
parametric starts and asymmetric kernels in a simple and flexible way.
Kernel density estimation with parametric starts involves fitting a
parametric density to the data before making a correction with kernel
density estimation, see Hjort & Glad (1995) <doi:10.1214/aos/1176324627>.
Asymmetric kernels make kernel density estimation more efficient on bounded
intervals such as (0, 1) and the positive half-line. Supported asymmetric
kernels are the gamma kernel of Chen (2000) <doi:10.1023/A:1004165218295>,
the beta kernel of Chen (1999) <doi:10.1016/S0167-9473(99)00010-9>, and the
copula kernel of Jones & Henderson (2007) <doi:10.1093/biomet/asm068>.
User-supplied kernels, parametric starts, and bandwidths are supported.
Author: Jonas Moss [aut, cre] ,
Martin Tveten [ctb]
Maintainer: Jonas Moss <jonas.gjertsen@gmail.com>
Diff between kdensity versions 1.1.0 dated 2020-09-30 and 1.1.1 dated 2025-03-04
DESCRIPTION | 19 LICENSE | 2 MD5 | 103 +-- NAMESPACE | 30 NEWS.md | 28 R/builtin_bandwidths.R | 396 ++++++------ R/builtin_bandwidths_get_bw.R | 136 ++-- R/builtin_bandwidths_ucv_helpers.R | 47 - R/builtin_kernels.R | 427 ++++++------- R/builtin_kernels_get_kernel.R | 85 +- R/builtin_starts_get_start.R | 89 +- R/builtin_starts_list.R | 229 +++---- R/cran.r |only R/generics.R | 532 ++++++++-------- R/kdensity.R | 611 +++++++++--------- R/kdensity_helpers.R | 241 +++---- R/utility_functions.R | 239 +++---- README.md | 403 ++++++------ build/vignette.rds |binary inst/doc/tutorial.R | 171 ++--- inst/doc/tutorial.Rmd | 317 ++++----- inst/doc/tutorial.html | 1000 ++++++++++++++++--------------- man/add_bw.Rd | 40 - man/add_kernel.Rd | 40 - man/add_start.Rd | 40 - man/bandwidths.Rd | 138 ++-- man/get_bw.Rd | 36 - man/get_kernel.Rd | 38 - man/get_kernel_start_support.Rd | 60 - man/get_range.Rd | 36 - man/get_standard_bw.Rd | 44 - man/get_start.Rd | 36 - man/kdensity.Rd | 274 ++++---- man/kernels.Rd | 174 ++--- man/listmerge.Rd | 50 - man/parametric_starts.Rd | 106 +-- man/plot.kdensity.Rd | 90 +- man/plot_helper.Rd | 72 +- man/recycle.Rd | 46 - man/support_compatible.Rd | 38 - tests/testthat.R | 8 tests/testthat/Rplots.pdf |binary tests/testthat/test_assignments.R | 32 tests/testthat/test_bandwidth.r | 48 - tests/testthat/test_generics.r | 23 tests/testthat/test_generics_invisible.R | 16 tests/testthat/test_kdensity.R | 108 +-- tests/testthat/test_kdensity_helpers.R | 16 tests/testthat/test_kernels.r | 42 - tests/testthat/test_starts.r | 60 - tests/testthat/test_univariateML.R | 83 +- tests/testthat/test_utility_functions.R | 60 - vignettes/tutorial.Rmd | 317 ++++----- 53 files changed, 3727 insertions(+), 3549 deletions(-)
Title: Tidy Structural Equation Modeling
Description: A tidy workflow for generating, estimating, reporting,
and plotting structural equation models using 'lavaan', 'OpenMx', or
'Mplus'. Throughout this workflow, elements of syntax, results, and graphs
are represented as 'tidy' data, making them easy to customize.
Includes functionality to estimate latent class analyses.
Author: Caspar J. van Lissa [aut, cre]
,
Mauricio Garnier-Villarreal [ctb]
,
Frank C Gootjes [ctb]
Maintainer: Caspar J. van Lissa <c.j.vanlissa@tilburguniversity.edu>
Diff between tidySEM versions 0.2.7 dated 2024-06-04 and 0.2.8 dated 2025-03-04
DESCRIPTION | 16 MD5 | 157 +- NAMESPACE | 19 R/blrt.R | 15 R/dagitty.R | 100 + R/lr_vml.R | 16 R/mixture-3step.R | 24 R/mixture-pseudo_class.R | 976 ++++++++-------- R/mixture_gradient.R | 10 R/mixture_predict.R | 2 R/mx_dummies.R | 6 R/mx_mixture.R | 117 + R/mx_simple_thresholds.R | 230 +-- R/mx_switch_labels.R | 2 R/mx_temp_start.R | 30 R/openmx_functions.R | 28 R/plot-bivariate.R | 21 R/plot-plot_sem.R | 29 R/results-table_fit.R | 2 R/results-table_results_mx_model.R | 21 R/syntax-add_paths.R | 26 R/syntax-run.R | 27 R/syntax_data_dictionary.R | 4 R/syntax_factor.R | 1 R/utilities.R | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Generating_syntax.R | 72 - inst/doc/Generating_syntax.Rmd | 2 inst/doc/Generating_syntax.html | 10 inst/doc/Plotting_graphs.R | 218 +-- inst/doc/Plotting_graphs.html | 34 inst/doc/SMART_LCA_checklist.Rmd | 256 ++-- inst/doc/SMART_LCA_checklist.html | 4 inst/doc/Tabulating_results.R | 70 - inst/doc/Tabulating_results.Rmd | 2 inst/doc/Tabulating_results.html | 2 inst/doc/lca_confirmatory.R | 252 ++-- inst/doc/lca_confirmatory.html | 2 inst/doc/lca_exploratory.R | 230 +-- inst/doc/lca_exploratory.html | 2 inst/doc/lca_lcga.R | 412 +++--- inst/doc/lca_lcga.html | 2 inst/doc/lca_ordinal.R | 156 +- inst/doc/lca_ordinal.html | 2 inst/doc/sem_graph.R | 58 inst/doc/sem_graph.html | 20 man/BCH.Rd | 2 man/add_paths.Rd | 16 man/append_class_draws.Rd | 2 man/lr_lmr.Rd | 2 man/lr_test.Rd | 2 man/mixture_starts.Rd | 12 man/mx_dummies.Rd | 2 man/mx_growth_mixture.Rd | 4 man/mx_lca.Rd | 4 man/mx_mixture.Rd | 2 man/mx_profiles.Rd | 2 man/plot_bivariate.Rd | 2 man/pseudo_class.Rd | 2 man/tidy_sem.Rd | 4 tests/testthat.R | 2 tests/testthat/test-BLRT_lr_lmr.R | 35 tests/testthat/test-dagitty_nodes_edges.R |only tests/testthat/test-lr_test_negative_df.R | 28 tests/testthat/test-lrt_bch.R | 69 - tests/testthat/test-lrt_multigroup.R | 21 tests/testthat/test-multigroup_mx.R | 89 - tests/testthat/test-namespace_checks_dominique.R | 34 tests/testthat/test-openmx_binary.R | 243 ++- tests/testthat/test-openmx_ordinal.R | 133 +- tests/testthat/test-openmx_ordinal_and_cont.R | 134 +- tests/testthat/test-openmx_ordinal_methods.R | 346 ++--- tests/testthat/test-openmx_ordinal_thresh_constraints.R | 101 - tests/testthat/test-plot_plot_prob.R | 1 tests/testthat/test-plot_profiles_varyingcov.R | 1 tests/testthat/test-pseudo_class_technique.R | 2 vignettes/Generating_syntax.Rmd | 2 vignettes/SMART_LCA_checklist.Rmd | 256 ++-- vignettes/Tabulating_results.Rmd | 2 80 files changed, 2681 insertions(+), 2565 deletions(-)
Title: Estimating (Time-Dependent) Drift Diffusion Models
Description: Fit and explore Drift Diffusion Models (DDMs),
a common tool in psychology for describing decision processes in simple
tasks. It can handle both time-independent and time-dependent DDMs. You
either choose prebuilt models or create your own, and the package takes
care of model predictions and parameter estimation. Model predictions
are derived via the numerical solutions provided by Richter, Ulrich, and
Janczyk (2023, <doi:10.1016/j.jmp.2023.102756>).
Author: Valentin Koob [cre, aut, cph],
Thomas Richter [aut, cph],
Markus Janczyk [aut]
Maintainer: Valentin Koob <v.koob@web.de>
Diff between dRiftDM versions 0.2.1 dated 2025-01-08 and 0.2.2 dated 2025-03-04
dRiftDM-0.2.1/dRiftDM/R/formatting_dm_fits_ids.R |only dRiftDM-0.2.1/dRiftDM/R/formatting_rest.R |only dRiftDM-0.2.1/dRiftDM/inst/doc/use_ddm_models.R |only dRiftDM-0.2.1/dRiftDM/inst/doc/use_ddm_models.Rmd |only dRiftDM-0.2.1/dRiftDM/inst/doc/use_ddm_models.html |only dRiftDM-0.2.1/dRiftDM/man/plot.list_stats_dm.Rd |only dRiftDM-0.2.1/dRiftDM/tests/testthat/_snaps/formatting_rest.md |only dRiftDM-0.2.1/dRiftDM/tests/testthat/fixtures/dm_fits_ids |only dRiftDM-0.2.1/dRiftDM/tests/testthat/fixtures/dm_fits_ids.R |only dRiftDM-0.2.1/dRiftDM/tests/testthat/test-formatting_rest.R |only dRiftDM-0.2.1/dRiftDM/vignettes/use_ddm_models.Rmd |only dRiftDM-0.2.2/dRiftDM/DESCRIPTION | 14 dRiftDM-0.2.2/dRiftDM/MD5 | 168 +-- dRiftDM-0.2.2/dRiftDM/NAMESPACE | 45 dRiftDM-0.2.2/dRiftDM/NEWS.md | 29 dRiftDM-0.2.2/dRiftDM/R/core_dm.R | 552 ++++++++-- dRiftDM-0.2.2/dRiftDM/R/core_estimate.R | 2 dRiftDM-0.2.2/dRiftDM/R/core_estimate_wrapper.R | 14 dRiftDM-0.2.2/dRiftDM/R/core_flex_prms.R | 23 dRiftDM-0.2.2/dRiftDM/R/core_stats.R | 91 + dRiftDM-0.2.2/dRiftDM/R/dRiftDM-package.R | 19 dRiftDM-0.2.2/dRiftDM/R/extended_s3_methods.R | 51 dRiftDM-0.2.2/dRiftDM/R/formatting_coefs_dm.R |only dRiftDM-0.2.2/dRiftDM/R/formatting_drift_dm.R | 39 dRiftDM-0.2.2/dRiftDM/R/formatting_fits_ids_dm.R |only dRiftDM-0.2.2/dRiftDM/R/formatting_flex_prms.R | 6 dRiftDM-0.2.2/dRiftDM/R/formatting_stats_dm.R |only dRiftDM-0.2.2/dRiftDM/R/formatting_traces_dm.R |only dRiftDM-0.2.2/dRiftDM/R/models.R | 16 dRiftDM-0.2.2/dRiftDM/R/plotting.R | 46 dRiftDM-0.2.2/dRiftDM/R/utils.R | 4 dRiftDM-0.2.2/dRiftDM/README.md | 75 - 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Title: Clean and Standardize Epidemiological Data
Description: Cleaning and standardizing tabular data package, tailored
specifically for curating epidemiological data. It streamlines various
data cleaning tasks that are typically expected when working with
datasets in epidemiology. It returns the processed data in the same
format, and generates a comprehensive report detailing the outcomes of
each cleaning task.
Author: Karim Mane [aut, cre] ,
Thibaut Jombart [ctb] .),
Abdoelnaser Degoot [aut] ,
Bankole Ahadzie [aut],
Nuredin Mohammed [aut],
Bubacarr Bah [aut] ,
Hugo Gruson [ctb, rev] ,
Pratik R. Gupte [rev] ,
James M. Azam [rev] ,
Joshua W. Lambert [rev] ,
Chris Ha [...truncated...]
Maintainer: Karim Mane <karim.mane@lshtm.ac.uk>
Diff between cleanepi versions 1.0.2 dated 2024-06-17 and 1.1.0 dated 2025-03-04
cleanepi-1.0.2/cleanepi/man/date_check_column_existence.Rd |only cleanepi-1.0.2/cleanepi/man/date_convert_and_update.Rd |only cleanepi-1.0.2/cleanepi/man/date_i_extract_string.Rd |only cleanepi-1.0.2/cleanepi/man/date_i_find_format.Rd |only cleanepi-1.0.2/cleanepi/man/default_cleanepi_settings.Rd |only cleanepi-1.0.2/cleanepi/man/get_sum.Rd |only cleanepi-1.0.2/cleanepi/man/make_readcap_dictionary.Rd |only cleanepi-1.0.2/cleanepi/man/scan_columns.Rd |only cleanepi-1.1.0/cleanepi/DESCRIPTION | 62 cleanepi-1.1.0/cleanepi/LICENSE | 2 cleanepi-1.1.0/cleanepi/MD5 | 224 cleanepi-1.1.0/cleanepi/NAMESPACE | 2 cleanepi-1.1.0/cleanepi/NEWS.md |only cleanepi-1.1.0/cleanepi/R/check_date_sequence.R | 105 cleanepi-1.1.0/cleanepi/R/clean_data.R | 241 - cleanepi-1.1.0/cleanepi/R/clean_data_helpers.R | 246 - cleanepi-1.1.0/cleanepi/R/cleanepi-package.R | 1 cleanepi-1.1.0/cleanepi/R/column_name_standardization.R | 213 cleanepi-1.1.0/cleanepi/R/convert_numeric_to_date.R | 29 cleanepi-1.1.0/cleanepi/R/convert_to_numeric.R | 121 cleanepi-1.1.0/cleanepi/R/date_standardization_helpers.R | 525 +- cleanepi-1.1.0/cleanepi/R/default_cleanepi_settings.R | 56 cleanepi-1.1.0/cleanepi/R/dictionary_based_cleaning.R | 271 - cleanepi-1.1.0/cleanepi/R/find_and_remove_duplicates.R | 116 cleanepi-1.1.0/cleanepi/R/guess_dates.R | 391 - cleanepi-1.1.0/cleanepi/R/print_report.R | 172 cleanepi-1.1.0/cleanepi/R/remove_constants.R | 195 cleanepi-1.1.0/cleanepi/R/replace_missing_values.R | 78 cleanepi-1.1.0/cleanepi/R/span.R | 107 cleanepi-1.1.0/cleanepi/R/standardize_date.R | 160 cleanepi-1.1.0/cleanepi/R/standardize_subject_ids.R | 197 cleanepi-1.1.0/cleanepi/R/utils-pipe.R |only cleanepi-1.1.0/cleanepi/R/utils-potools.R |only cleanepi-1.1.0/cleanepi/R/utils.R | 201 cleanepi-1.1.0/cleanepi/README.md | 494 +- cleanepi-1.1.0/cleanepi/build/vignette.rds |binary cleanepi-1.1.0/cleanepi/inst/WORDLIST | 17 cleanepi-1.1.0/cleanepi/inst/doc/cleanepi.R | 518 +- 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cleanepi-1.1.0/cleanepi/tests/testthat/test-clean_data.R | 156 cleanepi-1.1.0/cleanepi/tests/testthat/test-clean_data_helpers.R | 64 cleanepi-1.1.0/cleanepi/tests/testthat/test-column_name_standardization.R | 50 cleanepi-1.1.0/cleanepi/tests/testthat/test-convert_numeric_to_date.R | 44 cleanepi-1.1.0/cleanepi/tests/testthat/test-convert_to_numeric.R | 37 cleanepi-1.1.0/cleanepi/tests/testthat/test-dictionary_based_cleaning.R | 91 cleanepi-1.1.0/cleanepi/tests/testthat/test-find_and_remove_duplicates.R | 23 cleanepi-1.1.0/cleanepi/tests/testthat/test-print_report.R | 90 cleanepi-1.1.0/cleanepi/tests/testthat/test-remove_constants.R | 126 cleanepi-1.1.0/cleanepi/tests/testthat/test-replace_missing_values.R | 25 cleanepi-1.1.0/cleanepi/tests/testthat/test-span.R | 151 cleanepi-1.1.0/cleanepi/tests/testthat/test-standardize_date.R | 232 cleanepi-1.1.0/cleanepi/tests/testthat/test-standardize_subject_ids.R | 215 cleanepi-1.1.0/cleanepi/tests/testthat/test-utils.R | 84 cleanepi-1.1.0/cleanepi/vignettes/cleanepi.Rmd | 617 +- cleanepi-1.1.0/cleanepi/vignettes/design_principle.Rmd | 403 - 124 files changed, 6750 insertions(+), 5895 deletions(-)
Title: Flexible Bayesian Optimization
Description: A modern and flexible approach to Bayesian Optimization / Model
Based Optimization building on the 'bbotk' package. 'mlr3mbo' is a toolbox
providing both ready-to-use optimization algorithms as well as their fundamental
building blocks allowing for straightforward implementation of custom
algorithms. Single- and multi-objective optimization is supported as well as
mixed continuous, categorical and conditional search spaces. Moreover, using
'mlr3mbo' for hyperparameter optimization of machine learning models within the
'mlr3' ecosystem is straightforward via 'mlr3tuning'. Examples of ready-to-use
optimization algorithms include Efficient Global Optimization by Jones et al.
(1998) <doi:10.1023/A:1008306431147>, ParEGO by Knowles (2006)
<doi:10.1109/TEVC.2005.851274> and SMS-EGO by Ponweiser et al. (2008)
<doi:10.1007/978-3-540-87700-4_78>.
Author: Lennart Schneider [cre, aut] ,
Jakob Richter [aut] ,
Marc Becker [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Florian Pfisterer [aut] ,
Martin Binder [aut],
Sebastian Fischer [aut] ,
Michael H. Buselli [cph],
Wessel Dankers [cph],
Carlos Fonseca [...truncated...]
Maintainer: Lennart Schneider <lennart.sch@web.de>
Diff between mlr3mbo versions 0.2.8 dated 2024-11-21 and 0.2.9 dated 2025-03-04
DESCRIPTION | 8 ++--- MD5 | 36 +++++++++++------------ NEWS.md | 24 +++++++++------ R/AcqFunction.R | 12 +++---- R/AcqOptimizer.R | 4 +- R/ResultAssignerSurrogate.R | 10 +++--- man/AcqFunction.Rd | 12 +++---- man/AcqOptimizer.Rd | 4 +- tests/testthat.R | 1 tests/testthat/helper.R | 16 ++++++++-- tests/testthat/setup.R | 19 ++++++++++-- tests/testthat/teardown.R | 5 +-- tests/testthat/test_AcqFunctionMulti.R | 2 - tests/testthat/test_ResultAssignerArchive.R | 16 +++++----- tests/testthat/test_ResultAssignerSurrogate.R | 16 +++++----- tests/testthat/test_SurrogateLearnerCollection.R | 8 ++--- tests/testthat/test_TunerADBO.R | 2 - tests/testthat/test_TunerAsyncMbo.R | 2 - tests/testthat/test_TunerMbo.R | 2 - 19 files changed, 117 insertions(+), 82 deletions(-)
Title: Generalized Linear Mixed Models using Adaptive Gaussian
Quadrature
Description: Fits generalized linear mixed models for a single grouping factor under
maximum likelihood approximating the integrals over the random effects with an
adaptive Gaussian quadrature rule; Jose C. Pinheiro and Douglas M. Bates (1995)
<doi:10.1080/10618600.1995.10474663>.
Author: Dimitris Rizopoulos [aut, cre]
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between GLMMadaptive versions 0.9-1 dated 2023-10-17 and 0.9-7 dated 2025-03-04
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 2 +- R/Functions.R | 12 +++++++----- R/methods.R | 18 ++++++++++-------- R/mixed_fit.R | 2 +- R/mixed_model.R | 4 ++-- build/vignette.rds |binary inst/doc/GLMMadaptive.R | 6 +++--- inst/doc/GLMMadaptive.html | 10 +++++----- man/GLMMadaptive.Rd | 4 ++-- 11 files changed, 45 insertions(+), 41 deletions(-)
Title: Characterise Tables of an OMOP Common Data Model Instance
Description: Summarises key information in data mapped to the Observational
Medical Outcomes Partnership (OMOP) common data model. Assess suitability to
perform specific epidemiological studies and explore the different domains
to obtain feasibility counts and trends.
Author: Marta Alcalde-Herraiz [aut] ,
Kim Lopez-Guell [aut] ,
Elin Rowlands [aut] ,
Cecilia Campanile [aut, cre] ,
Edward Burn [aut] ,
Marti Catala [aut]
Maintainer: Cecilia Campanile <cecilia.campanile@ndorms.ox.ac.uk>
Diff between OmopSketch versions 0.2.2 dated 2025-01-28 and 0.3.0 dated 2025-03-04
OmopSketch-0.2.2/OmopSketch/inst/doc/A-summarise_clinical_tables_records.R |only OmopSketch-0.2.2/OmopSketch/inst/doc/A-summarise_clinical_tables_records.Rmd |only OmopSketch-0.2.2/OmopSketch/inst/doc/A-summarise_clinical_tables_records.html |only OmopSketch-0.2.2/OmopSketch/inst/doc/B-summarise_concept_set_counts.R |only OmopSketch-0.2.2/OmopSketch/inst/doc/B-summarise_concept_set_counts.Rmd |only OmopSketch-0.2.2/OmopSketch/inst/doc/B-summarise_concept_set_counts.html |only OmopSketch-0.2.2/OmopSketch/inst/doc/C-summarise_observation_period.R |only OmopSketch-0.2.2/OmopSketch/inst/doc/C-summarise_observation_period.Rmd |only OmopSketch-0.2.2/OmopSketch/inst/doc/C-summarise_observation_period.html |only OmopSketch-0.2.2/OmopSketch/vignettes/A-summarise_clinical_tables_records.Rmd |only OmopSketch-0.2.2/OmopSketch/vignettes/B-summarise_concept_set_counts.Rmd |only OmopSketch-0.2.2/OmopSketch/vignettes/C-summarise_observation_period.Rmd |only OmopSketch-0.3.0/OmopSketch/DESCRIPTION | 14 OmopSketch-0.3.0/OmopSketch/MD5 | 74 ++-- OmopSketch-0.3.0/OmopSketch/NEWS.md |only OmopSketch-0.3.0/OmopSketch/R/documentationHelper.R | 9 OmopSketch-0.3.0/OmopSketch/R/summariseClinicalRecords.R | 3 OmopSketch-0.3.0/OmopSketch/R/summariseConceptCounts.R | 2 OmopSketch-0.3.0/OmopSketch/R/summariseConceptIdCounts.R | 57 ++- OmopSketch-0.3.0/OmopSketch/R/summariseConceptSetCounts.R | 15 OmopSketch-0.3.0/OmopSketch/R/summariseInObservation.R | 14 OmopSketch-0.3.0/OmopSketch/R/summariseMissingData.R | 167 ++++++---- OmopSketch-0.3.0/OmopSketch/R/summariseRecordCount.R | 4 OmopSketch-0.3.0/OmopSketch/R/tableClinicalRecords.R | 10 OmopSketch-0.3.0/OmopSketch/R/tableConceptIdCounts.R | 10 OmopSketch-0.3.0/OmopSketch/R/tableMissingData.R | 10 OmopSketch-0.3.0/OmopSketch/R/tableObservationPeriod.R | 9 OmopSketch-0.3.0/OmopSketch/R/tableOmopSnapshot.R | 14 OmopSketch-0.3.0/OmopSketch/build/vignette.rds |binary OmopSketch-0.3.0/OmopSketch/inst/doc/characterisation.R |only OmopSketch-0.3.0/OmopSketch/inst/doc/characterisation.Rmd |only OmopSketch-0.3.0/OmopSketch/inst/doc/characterisation.html |only OmopSketch-0.3.0/OmopSketch/inst/doc/summarise_clinical_tables_records.R |only OmopSketch-0.3.0/OmopSketch/inst/doc/summarise_clinical_tables_records.Rmd |only OmopSketch-0.3.0/OmopSketch/inst/doc/summarise_clinical_tables_records.html |only OmopSketch-0.3.0/OmopSketch/inst/doc/summarise_concept_set_counts.R |only OmopSketch-0.3.0/OmopSketch/inst/doc/summarise_concept_set_counts.Rmd |only OmopSketch-0.3.0/OmopSketch/inst/doc/summarise_concept_set_counts.html |only OmopSketch-0.3.0/OmopSketch/inst/doc/summarise_observation_period.R |only OmopSketch-0.3.0/OmopSketch/inst/doc/summarise_observation_period.Rmd |only OmopSketch-0.3.0/OmopSketch/inst/doc/summarise_observation_period.html |only OmopSketch-0.3.0/OmopSketch/man/interval.Rd |only OmopSketch-0.3.0/OmopSketch/man/summariseConceptIdCounts.Rd | 11 OmopSketch-0.3.0/OmopSketch/man/summariseMissingData.Rd | 7 OmopSketch-0.3.0/OmopSketch/tests/testthat/test-summariseClinicalRecords.R | 2 OmopSketch-0.3.0/OmopSketch/tests/testthat/test-summariseConceptIdCounts.R | 120 ++++++- OmopSketch-0.3.0/OmopSketch/tests/testthat/test-summariseInObservation.R | 1 OmopSketch-0.3.0/OmopSketch/tests/testthat/test-summariseMissingData.R | 108 ++++++ OmopSketch-0.3.0/OmopSketch/tests/testthat/test-summariseObservationPeriod.R | 3 OmopSketch-0.3.0/OmopSketch/vignettes/characterisation.Rmd |only OmopSketch-0.3.0/OmopSketch/vignettes/summarise_clinical_tables_records.Rmd |only OmopSketch-0.3.0/OmopSketch/vignettes/summarise_concept_set_counts.Rmd |only OmopSketch-0.3.0/OmopSketch/vignettes/summarise_observation_period.Rmd |only 53 files changed, 506 insertions(+), 158 deletions(-)
Title: Format BibTeX Entries and Files
Description: Format BibTeX entries and files in an opinionated way.
Author: Wenjie Wang [aut, cre]
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between formatBibtex versions 0.1.0 dated 2023-02-03 and 0.1.1 dated 2025-03-03
formatBibtex-0.1.0/formatBibtex/R/zzz.R |only formatBibtex-0.1.1/formatBibtex/DESCRIPTION | 11 +- formatBibtex-0.1.1/formatBibtex/MD5 | 26 +++--- formatBibtex-0.1.1/formatBibtex/NAMESPACE | 2 formatBibtex-0.1.1/formatBibtex/NEWS.md |only formatBibtex-0.1.1/formatBibtex/R/bibtex.R | 12 +-- formatBibtex-0.1.1/formatBibtex/R/default_options.R |only formatBibtex-0.1.1/formatBibtex/R/format_string.R | 39 +++++++--- formatBibtex-0.1.1/formatBibtex/R/misc.R | 5 + formatBibtex-0.1.1/formatBibtex/README.md | 6 - formatBibtex-0.1.1/formatBibtex/inst/CITATION | 4 - formatBibtex-0.1.1/formatBibtex/inst/examples/ex-bibtex.R | 24 ++---- formatBibtex-0.1.1/formatBibtex/inst/examples/ex-format_string.R | 12 +-- formatBibtex-0.1.1/formatBibtex/man/format_bibtex_entry.Rd | 28 +++---- formatBibtex-0.1.1/formatBibtex/man/format_options.Rd |only formatBibtex-0.1.1/formatBibtex/man/format_string.Rd | 27 +++--- 16 files changed, 108 insertions(+), 88 deletions(-)
Title: Analysing 'SNP' and 'Silicodart' Data - Basic Functions
Description: Facilitates the import and analysis of 'SNP' (single nucleotide 'polymorphism')
and 'silicodart' (presence/absence) data. The main focus is on data generated by 'DarT'
(Diversity Arrays Technology), however, data from other sequencing platforms can be used
once 'SNP' or related fragment presence/absence data from any source is imported. Genetic
datasets are stored in a derived 'genlight' format (package 'adegenet'), that allows for
a very compact storage of data and metadata. Functions are available for
importing and exporting of 'SNP' and 'silicodart' data, for reporting on and
filtering on various criteria (e.g. 'callrate', 'heterozygosity', 'reproducibility',
maximum allele frequency). Additional functions are available for visualization
(e.g. Principle Coordinate Analysis) and creating a spatial representation
using maps. 'dartR.base' is the 'base' package of the 'dartRverse' suits of packages.
To install the other packages, we recommend to install the 'dartRverse' package, that
su [...truncated...]
Author: Bernd Gruber [aut, cre],
Arthur Georges [aut],
Jose L. Mijangos [aut],
Carlo Pacioni [aut],
Diana Robledo-Ruiz [aut],
Peter J. Unmack [ctb],
Oliver Berry [ctb],
Lindsay V. Clark [ctb],
Floriaan Devloo-Delva [ctb],
Eric Archer [ctb],
Ching Ching Lau [ [...truncated...]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Diff between dartR.base versions 0.98 dated 2024-09-19 and 1.0.5 dated 2025-03-03
dartR.base-0.98/dartR.base/R/gl.prop.shared.r |only dartR.base-0.98/dartR.base/R/gl2svdquartets.r |only dartR.base-0.98/dartR.base/man/gl2svdquartets.Rd |only dartR.base-1.0.5/dartR.base/DESCRIPTION | 16 dartR.base-1.0.5/dartR.base/MD5 | 230 +-- dartR.base-1.0.5/dartR.base/NAMESPACE | 18 dartR.base-1.0.5/dartR.base/R/gl.compliance.check.r | 12 dartR.base-1.0.5/dartR.base/R/gl.diagnostics.hwe.r | 10 dartR.base-1.0.5/dartR.base/R/gl.dist.phylo.r | 20 dartR.base-1.0.5/dartR.base/R/gl.dist.pop.r | 71 - dartR.base-1.0.5/dartR.base/R/gl.drop.ind.r | 24 dartR.base-1.0.5/dartR.base/R/gl.drop.pop.r | 61 dartR.base-1.0.5/dartR.base/R/gl.filter.excess.het.r |only dartR.base-1.0.5/dartR.base/R/gl.filter.hwe.r | 5 dartR.base-1.0.5/dartR.base/R/gl.filter.monomorphs.r | 3 dartR.base-1.0.5/dartR.base/R/gl.filter.rdepth.r | 20 dartR.base-1.0.5/dartR.base/R/gl.filter.reproducibility.r | 28 dartR.base-1.0.5/dartR.base/R/gl.filter.secondaries.r | 21 dartR.base-1.0.5/dartR.base/R/gl.join.r | 346 +++-- dartR.base-1.0.5/dartR.base/R/gl.keep.ind.r | 32 dartR.base-1.0.5/dartR.base/R/gl.keep.pop.r | 51 dartR.base-1.0.5/dartR.base/R/gl.load.r | 26 dartR.base-1.0.5/dartR.base/R/gl.map.interactive.r | 75 - dartR.base-1.0.5/dartR.base/R/gl.pcoa.r | 186 ++ dartR.base-1.0.5/dartR.base/R/gl.propShared.r |only dartR.base-1.0.5/dartR.base/R/gl.read.PLINK.r | 1 dartR.base-1.0.5/dartR.base/R/gl.read.csv.r | 17 dartR.base-1.0.5/dartR.base/R/gl.read.dart.r | 3 dartR.base-1.0.5/dartR.base/R/gl.read.vcf.r | 15 dartR.base-1.0.5/dartR.base/R/gl.report.allelerich.r |only dartR.base-1.0.5/dartR.base/R/gl.report.allna.r | 8 dartR.base-1.0.5/dartR.base/R/gl.report.bases.r | 2 dartR.base-1.0.5/dartR.base/R/gl.report.callrate.r | 50 dartR.base-1.0.5/dartR.base/R/gl.report.diversity.r | 98 - dartR.base-1.0.5/dartR.base/R/gl.report.excess.het.r |only dartR.base-1.0.5/dartR.base/R/gl.report.heterozygosity.r | 18 dartR.base-1.0.5/dartR.base/R/gl.report.hwe.r | 5 dartR.base-1.0.5/dartR.base/R/gl.report.ld.map.r | 11 dartR.base-1.0.5/dartR.base/R/gl.report.maf.r | 6 dartR.base-1.0.5/dartR.base/R/gl.report.pa.r | 135 + dartR.base-1.0.5/dartR.base/R/gl.report.polyploid_heterozygosity.r | 24 dartR.base-1.0.5/dartR.base/R/gl.report.reproducibility.r | 31 dartR.base-1.0.5/dartR.base/R/gl.report.shannon.r |only dartR.base-1.0.5/dartR.base/R/gl.save.r | 5 dartR.base-1.0.5/dartR.base/R/gl.sort.r | 78 - dartR.base-1.0.5/dartR.base/R/gl.subsample.ind.r | 145 +- dartR.base-1.0.5/dartR.base/R/gl.subsample.loc.r | 84 - dartR.base-1.0.5/dartR.base/R/gl.tree.fitch.r | 7 dartR.base-1.0.5/dartR.base/R/gl.tree.nj.r | 37 dartR.base-1.0.5/dartR.base/R/gl2bpp.r | 101 + dartR.base-1.0.5/dartR.base/R/gl2fasta.r | 21 dartR.base-1.0.5/dartR.base/R/gl2genepop.r | 4 dartR.base-1.0.5/dartR.base/R/gl2paup.parsimony.r |only dartR.base-1.0.5/dartR.base/R/gl2paup.svdquartets.r |only dartR.base-1.0.5/dartR.base/R/utils.check.datatype.R | 4 dartR.base-1.0.5/dartR.base/R/utils.collapse.matrix.r |only dartR.base-1.0.5/dartR.base/R/utils.dart2genlight.r | 56 dartR.base-1.0.5/dartR.base/R/utils.het.report.r | 16 dartR.base-1.0.5/dartR.base/R/utils.read.dart.r | 14 dartR.base-1.0.5/dartR.base/R/utils.read.ped.r | 15 dartR.base-1.0.5/dartR.base/man/gl.alf.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.allele.freq.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.dist.phylo.Rd | 2 dartR.base-1.0.5/dartR.base/man/gl.dist.pop.Rd | 10 dartR.base-1.0.5/dartR.base/man/gl.filter.excess.het.Rd |only dartR.base-1.0.5/dartR.base/man/gl.filter.hwe.Rd | 5 dartR.base-1.0.5/dartR.base/man/gl.join.Rd | 21 dartR.base-1.0.5/dartR.base/man/gl.load.Rd | 13 dartR.base-1.0.5/dartR.base/man/gl.map.interactive.Rd | 31 dartR.base-1.0.5/dartR.base/man/gl.prop.shared.Rd | 2 dartR.base-1.0.5/dartR.base/man/gl.read.csv.Rd | 6 dartR.base-1.0.5/dartR.base/man/gl.read.vcf.Rd | 14 dartR.base-1.0.5/dartR.base/man/gl.report.allelerich.Rd |only dartR.base-1.0.5/dartR.base/man/gl.report.allna.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.bases.Rd | 2 dartR.base-1.0.5/dartR.base/man/gl.report.basics.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.callrate.Rd | 7 dartR.base-1.0.5/dartR.base/man/gl.report.diversity.Rd | 26 dartR.base-1.0.5/dartR.base/man/gl.report.excess.het.Rd |only dartR.base-1.0.5/dartR.base/man/gl.report.hamming.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.heterozygosity.Rd | 7 dartR.base-1.0.5/dartR.base/man/gl.report.hwe.Rd | 5 dartR.base-1.0.5/dartR.base/man/gl.report.ld.map.Rd | 4 dartR.base-1.0.5/dartR.base/man/gl.report.locmetric.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.maf.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.overshoot.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.pa.Rd | 39 dartR.base-1.0.5/dartR.base/man/gl.report.polyploid_heterozygosity.Rd | 684 ++++------ dartR.base-1.0.5/dartR.base/man/gl.report.rdepth.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.reproducibility.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.secondaries.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.report.shannon.Rd |only dartR.base-1.0.5/dartR.base/man/gl.report.taglength.Rd | 1 dartR.base-1.0.5/dartR.base/man/gl.sort.Rd | 42 dartR.base-1.0.5/dartR.base/man/gl.subsample.ind.Rd | 7 dartR.base-1.0.5/dartR.base/man/gl.subsample.loc.Rd | 8 dartR.base-1.0.5/dartR.base/man/gl.tree.fitch.Rd | 5 dartR.base-1.0.5/dartR.base/man/gl.tree.nj.Rd | 7 dartR.base-1.0.5/dartR.base/man/gl2bpp.Rd | 4 dartR.base-1.0.5/dartR.base/man/gl2genepop.Rd | 4 dartR.base-1.0.5/dartR.base/man/gl2paup.parsimony.Rd |only dartR.base-1.0.5/dartR.base/man/gl2paup.svdquartets.Rd |only dartR.base-1.0.5/dartR.base/man/utils.check.datatype.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.collapse.matrix.Rd |only dartR.base-1.0.5/dartR.base/man/utils.dart2genlight.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.dist.binary.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.flag.start.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.hamming.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.het.pop.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.impute.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.is.fixed.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.jackknife.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.n.var.invariant.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.plot.save.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.read.fasta.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.read.ped.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.recalc.avgpic.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.recalc.callrate.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.recalc.freqhets.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.recalc.freqhomref.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.recalc.freqhomsnp.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.recalc.maf.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.reset.flags.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.transpose.Rd | 1 dartR.base-1.0.5/dartR.base/man/utils.vcfr2genlight.polyploid.Rd | 1 125 files changed, 2112 insertions(+), 1143 deletions(-)
Title: Load and Process Passive Acoustic Data
Description: Tools for loading and processing passive acoustic data. Read in data
that has been processed in 'Pamguard' (<https://www.pamguard.org/>), apply a suite
processing functions, and export data for reports or external modeling tools. Parameter
calculations implement methods by Oswald et al (2007) <doi:10.1121/1.2743157>,
Griffiths et al (2020) <doi:10.1121/10.0001229> and Baumann-Pickering et al (2010)
<doi:10.1121/1.3479549>.
Author: Taiki Sakai [aut, cre],
Jay Barlow [ctb],
Emily Griffiths [ctb],
Michael Oswald [ctb],
Simone Baumann-Pickering [ctb],
Julie Oswald [ctb]
Maintainer: Taiki Sakai <taiki.sakai@noaa.gov>
Diff between PAMpal versions 1.2.1 dated 2024-07-11 and 1.4.4 dated 2025-03-03
DESCRIPTION | 8 - MD5 | 58 ++++----- NAMESPACE | 10 + NEWS.md | 41 ++++++ R/PAMpalSettings.R | 7 - R/addFunction.R | 16 ++ R/addRecordings.R | 41 ++++-- R/calculateAverageSpectra.R | 5 R/calculateEchoDepth.R | 242 ++++++++++++++++++++++++++++++++------- R/calculateICI.R | 38 +++--- R/calculateModuleData.R | 51 -------- R/getClipData.R | 2 R/getDetectorData.R | 4 R/plotGram.R | 15 +- R/processPgDetections.R | 170 +++++++++++++++++++-------- R/runDepthReview.R | 124 +++++++++++++++---- R/runIciReview.R |only R/setSpecies.R | 7 - R/standardClickCalcs.R | 6 R/updateFiles.R | 22 +++ R/utils.R | 4 R/wavUtils.R | 2 man/PAMpalSettings.Rd | 3 man/addFunction.Rd | 4 man/addRecordings.Rd | 7 + man/calculateEchoDepth.Rd | 10 + man/calculateICI.Rd | 6 man/getDetectorData.Rd | 4 man/processPgDetections.Rd | 14 +- man/runIciReview.Rd |only tests/testthat/test-processPps.R | 28 +++- 31 files changed, 681 insertions(+), 268 deletions(-)
Title: Influential Cases in Structural Equation Modeling
Description: Sensitivity analysis in structural equation modeling using
influence measures and diagnostic plots. Support leave-one-out casewise
sensitivity analysis presented by Pek and MacCallum (2011)
<doi:10.1080/00273171.2011.561068> and approximate casewise influence
using scores and casewise likelihood.
Author: Shu Fai Cheung [aut, cre] ,
Mark Hok Chio Lai [aut]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between semfindr versions 0.1.8 dated 2024-04-08 and 0.1.9 dated 2025-03-03
DESCRIPTION | 11 - MD5 | 63 +++++---- NEWS.md | 50 +++++++ R/approx_check.R | 11 - R/est_change_plot.R | 4 R/est_change_raw_user.R | 46 +++++-- R/generic_index_plot.R | 6 R/influence_plot.R | 4 R/lavaan_rerun.R | 60 +++++++-- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/casewise_scores.html | 14 +- inst/doc/selecting_cases.html | 8 - inst/doc/semfindr.R | 40 +++--- inst/doc/semfindr.Rmd | 2 inst/doc/semfindr.html | 38 ++--- inst/doc/user_id.R | 2 inst/doc/user_id.html | 8 - man/approx_check.Rd | 8 - man/est_change_plot.Rd | 4 man/index_plot.Rd | 2 man/influence_plot.Rd | 4 man/lavaan_rerun.Rd | 17 ++ man/pars_id_to_lorg.Rd | 6 man/semfindr-package.Rd | 2 man/user_change_raw.Rd | 22 ++- tests/testthat/test-approx_check.R | 2 tests/testthat/test-est_change_raw_loo_single_user_function.R | 64 ++++++++++ tests/testthat/test-lavaan_rerun_parallel.R |only vignettes/articles/user_fun-1.png |only vignettes/articles/user_fun2-1.png |only vignettes/articles/user_function.Rmd |only vignettes/articles/user_function.Rmd.original |only vignettes/semfindr.Rmd | 2 35 files changed, 354 insertions(+), 148 deletions(-)
Title: Convert Among Citation Formats
Description: Converts among many citation formats, including 'BibTeX',
'Citeproc', 'Codemeta', 'RDF XML', 'RIS', 'Schema.org', and
'Citation File Format'. A low level 'R6' class is provided, as well
as stand-alone functions for each citation format for both read
and write.
Author: Scott Chamberlain [aut] ,
Brenton M. Wiernik [aut, cre] ,
Thierry Onkelinx [ctb]
Maintainer: Brenton M. Wiernik <brenton@wiernik.org>
Diff between handlr versions 0.3.0 dated 2020-10-15 and 0.3.1 dated 2025-03-03
DESCRIPTION | 27 ++++--- MD5 | 66 ++++++++--------- NEWS.md | 9 ++ R/a_types.R | 2 R/cff_reader.R | 76 +++++++++++++------- R/cff_writer.R | 64 +++++++++++----- R/codemeta_reader.R | 12 +-- R/codemeta_writer.R | 16 ++-- R/doi_utils.R | 17 ++-- R/handlr-package.r | 20 ++--- R/schema_org_writer.R | 34 ++++---- R/translations.R | 12 +-- README.md | 75 ++++++++----------- inst/extdata/bib-many.bib | 4 - inst/extdata/citation_1.2.0.cff |only inst/extdata/citation_1.2.0_project.cff |only inst/extdata/citeproc-many.json | 2 inst/extdata/citeproc2.json | 2 inst/extdata/codemeta-many.json | 36 ++++----- inst/extdata/codemeta.json | 18 ++-- inst/extdata/crosscite.json | 4 - inst/extdata/crossref.bib | 4 - inst/extdata/crossref.ris | 2 inst/extdata/elsevier.ris | 2 man/HandlrClient.Rd | 36 ++++----- man/cff_reader.Rd | 14 ++- man/cff_reference_types.Rd | 2 man/cff_writer.Rd | 20 ++++- man/codemeta_writer.Rd | 2 man/handl.Rd | 6 + man/handlr-package.Rd | 12 ++- man/schema_org_writer.Rd | 2 tests/testthat/test-cff_reader.R | 121 +++++++++++++++++++++++++++++--- tests/testthat/test-cff_writer.R | 70 +++++++++++++++++- tests/testthat/test-client.R | 3 35 files changed, 528 insertions(+), 264 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 0.5.1 dated 2024-12-04 and 0.5.2 dated 2025-03-03
DESCRIPTION | 6 - MD5 | 24 +++--- NEWS.md | 4 + inst/doc/FAQ.R | 6 + inst/doc/FAQ.html | 6 - inst/doc/cpp11.Rmd | 2 inst/doc/cpp11.html | 25 +++--- inst/doc/motivations.R | 148 +++++++++++++++++++-------------------- inst/doc/motivations.html | 99 ++++++++++++++++---------- inst/include/cpp11/R.hpp | 2 inst/include/cpp11/named_arg.hpp | 2 inst/include/fmt/format.h | 4 - vignettes/cpp11.Rmd | 2 13 files changed, 180 insertions(+), 150 deletions(-)
Title: Output Space-Filling Design
Description: Methods to generate a design in the input space that sequentially fills the output space of a black-box function. The output space-filling designs are helpful in inverse design or feature-based modeling problems.
See Wang, Shangkun, Adam P. Generale, Surya R. Kalidindi, and V. Roshan Joseph. (2024), Sequential designs for filling output spaces, Technometrics, 66, 65–76. for details. This work is supported by U.S. National Foundation grant CMMI-1921646.
Author: Shangkun Wang [aut, cre],
Roshan Joseph [aut]
Maintainer: Shangkun Wang <sk_wang@gatech.edu>
Diff between OSFD versions 3.0 dated 2025-01-15 and 3.1 dated 2025-03-03
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/OSFD.cpp | 11 ++++++++--- 3 files changed, 14 insertions(+), 9 deletions(-)
Title: Machine Learning Experiments
Description: Provides 'R6' objects to perform parallelized hyperparameter
optimization and cross-validation. Hyperparameter optimization can be
performed with Bayesian optimization (via 'ParBayesianOptimization'
<https://cran.r-project.org/package=ParBayesianOptimization>) and grid
search. The optimized hyperparameters can be validated using k-fold
cross-validation. Alternatively, hyperparameter optimization and
validation can be performed with nested cross-validation. While
'mlexperiments' focuses on core wrappers for machine learning
experiments, additional learner algorithms can be supplemented by
inheriting from the provided learner base class.
Author: Lorenz A. Kapsner [cre, aut, cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between mlexperiments versions 0.0.4 dated 2024-07-05 and 0.0.5 dated 2025-03-03
DESCRIPTION | 10 MD5 | 108 +-- NAMESPACE | 38 - R/MLTuneParameters.R | 410 ++++++------ R/cv_helper_base.R | 14 R/cv_performance.R | 390 ++++++------ R/cv_predictions.R | 282 ++++---- R/learner_lm.R | 4 R/optimizer_class_base.R | 84 +- R/optimizer_class_bayesian.R | 70 +- R/optimizer_helper_base.R | 102 +-- R/utils_handle_cat_vars.R | 66 +- R/utils_method_params_refactor.R | 22 R/utils_metrics.R | 472 +++++++------- R/utils_validate_fold_equality.R | 260 ++++---- R/zzz.R | 40 - build/vignette.rds |binary inst/doc/mlexperiments_knn_binary.html | 5 inst/doc/mlexperiments_knn_multiclass.html | 5 inst/doc/mlexperiments_knn_multiclass.qmd | 1 inst/doc/mlexperiments_rpart_binary.html | 7 inst/doc/mlexperiments_rpart_multiclass.html | 5 inst/doc/mlexperiments_rpart_multiclass.qmd | 1 inst/doc/mlexperiments_rpart_regression.R | 6 inst/doc/mlexperiments_rpart_regression.html | 23 inst/doc/mlexperiments_rpart_regression.qmd | 6 inst/doc/mlexperiments_starter.R | 262 ++++---- inst/doc/mlexperiments_starter.html | 7 inst/doc/mlexperiments_starter.qmd | 1 man/LearnerGlm.Rd | 210 +++--- man/LearnerKnn.Rd | 242 +++---- man/LearnerLm.Rd | 210 +++--- man/LearnerRpart.Rd | 272 ++++---- man/MLBase.Rd | 132 ++-- man/MLCrossValidation.Rd | 716 +++++++++++----------- man/MLExperimentsBase.Rd | 208 +++--- man/MLLearnerBase.Rd | 792 ++++++++++++------------- man/MLNestedCV.Rd | 852 +++++++++++++-------------- man/MLTuneParameters.Rd | 584 +++++++++--------- man/handle_cat_vars.Rd | 66 +- man/metric_types_helper.Rd | 94 +- man/performance.Rd | 216 +++--- man/predictions.Rd | 168 ++--- man/validate_fold_equality.Rd | 186 ++--- tests/testthat.R | 3 tests/testthat/test-fold_equality.R | 194 +++--- tests/testthat/test-glm_predictions.R | 438 ++++++------- tests/testthat/test-knn.R | 602 +++++++++---------- tests/testthat/test-lints.R | 26 tests/testthat/test-lm.R | 73 ++ tests/testthat/test-rpart_regression.R | 502 +++++++-------- vignettes/mlexperiments_knn_multiclass.qmd | 1 vignettes/mlexperiments_rpart_multiclass.qmd | 1 vignettes/mlexperiments_rpart_regression.qmd | 6 vignettes/mlexperiments_starter.qmd | 1 55 files changed, 4787 insertions(+), 4709 deletions(-)
Title: A Simple and Robust JSON Parser and Generator for R
Description: A reasonably fast JSON parser and generator, optimized for statistical
data and the web. Offers simple, flexible tools for working with JSON in R, and
is particularly powerful for building pipelines and interacting with a web API.
The implementation is based on the mapping described in the vignette (Ooms, 2014).
In addition to converting JSON data from/to R objects, 'jsonlite' contains
functions to stream, validate, and prettify JSON data. The unit tests included
with the package verify that all edge cases are encoded and decoded consistently
for use with dynamic data in systems and applications.
Author: Jeroen Ooms [aut, cre] ,
Duncan Temple Lang [ctb],
Lloyd Hilaiel [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between jsonlite versions 1.9.0 dated 2025-02-19 and 1.9.1 dated 2025-03-03
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS | 3 +++ build/vignette.rds |binary inst/doc/json-aaquickstart.html | 2 +- inst/doc/json-mapping.pdf |binary tests/testthat/test-fromJSON-datasets.R | 6 +++--- 7 files changed, 16 insertions(+), 13 deletions(-)
Title: Toolkit for HLA Immunogenomics
Description: A toolkit for the analysis and management of data for genes in the so-called "Human Leukocyte Antigen" (HLA) region. Functions extract reference data from the Anthony Nolan HLA Informatics Group/ImmunoGeneTics HLA 'GitHub' repository (ANHIG/IMGTHLA) <https://github.com/ANHIG/IMGTHLA>, validate Genotype List (GL) Strings, convert between UNIFORMAT and GL String Code (GLSC) formats, translate HLA alleles and GLSCs across ImmunoPolymorphism Database (IPD) IMGT/HLA Database release versions, identify differences between pairs of alleles at a locus, generate customized, multi-position sequence alignments, trim and convert allele-names across nomenclature epochs, and extend existing data-analysis methods.
Author: Livia Tran [aut],
Ryan Nickens [aut],
Leamon Crooms IV [aut],
Derek Pappas [aut],
Vinh Luu [ctb],
Josh Bredeweg [ctb],
Steven Mack [aut, cre]
Maintainer: Steven Mack <Steven.Mack@ucsf.edu>
Diff between HLAtools versions 1.3.0 dated 2024-11-14 and 1.4.0 dated 2025-03-03
DESCRIPTION | 8 MD5 | 115 ++++---- NAMESPACE | 3 NEWS.md | 19 + R/AlleleTrim.R | 16 - R/BDtoPyPop.R | 4 R/GIANT.R | 29 +- R/GLStoUNI.R | 4 R/GLupdater.R | 590 ++++++++++++++++++++---------------------- R/SearchandBuildAlignments.R | 26 + R/ThirdPartyFunctions.R | 3 R/VersionValidation.R | 8 R/accessoryFunctions.R | 51 ++- R/atlasMaker.R | 2 R/buildGazeteer.R | 2 R/compareSequences.R | 2 R/data.R | 4 R/locusValidator.R | 2 R/relRisk.R | 2 README.md | 40 +- build/vignette.rds |binary data/HLAatlas.rda |binary data/HLAgazeteer.rda |binary data/alleleListHistory.rda |binary data/fragmentFeatureNames.rda |binary inst/doc/HLAtools.Rmd | 22 + inst/doc/HLAtools.html | 43 ++- man/GIANT.Rd | 4 man/GLSC.ex.Rd | 2 man/GLV.Rd | 4 man/GLV2.Rd | 4 man/GLVhelper.Rd | 4 man/GLupdate.Rd | 34 -- man/GLvalidate.Rd | 6 man/HLAatlas.Rd | 2 man/alignmentSearch.Rd | 12 man/atlasMaker.Rd | 2 man/compareSequences.Rd | 2 man/convertAny.Rd | 6 man/countSpaces.Rd | 3 man/customAlign.Rd | 10 man/formatHead.Rd | 6 man/getAlignmentNames.Rd | 2 man/getField.Rd | 2 man/multiAlign.Rd | 2 man/multiTranslateGLstring.Rd |only man/multiUpdateGL.Rd | 23 - man/parseAlignmentHead.Rd | 2 man/redec.Rd | 2 man/relRisk.Rd | 2 man/repoVersion.Rd | 4 man/squashVersion.Rd | 4 man/translateAllele.Rd |only man/translateGLstring.Rd |only man/uniAlign.Rd | 2 man/updateGL.Rd | 29 -- man/validateAllele.Rd | 4 man/validateLocus.Rd | 2 man/verifyAllele.Rd | 16 - vignettes/HLAtools.Rmd | 22 + 60 files changed, 660 insertions(+), 554 deletions(-)
Title: Group Sequential Design
Description: Derives group sequential clinical trial designs and describes
their properties. Particular focus on time-to-event, binary, and
continuous outcomes. Largely based on methods described in
Jennison, Christopher and Turnbull, Bruce W., 2000,
"Group Sequential Methods with Applications to Clinical Trials"
ISBN: 0-8493-0316-8.
Author: Keaven Anderson [aut, cre],
Merck & Co., Inc., Rahway, NJ, USA and its affiliates [cph]
Maintainer: Keaven Anderson <keaven_anderson@merck.com>
Diff between gsDesign versions 3.6.6 dated 2025-02-10 and 3.6.7 dated 2025-03-03
DESCRIPTION | 8 MD5 | 93 - NEWS.md | 11 inst/doc/ConditionalErrorSpending.R | 4 inst/doc/ConditionalErrorSpending.Rmd | 4 inst/doc/ConditionalErrorSpending.html | 1367 +++++++++++++++-- inst/doc/ConditionalPowerPlot.R | 4 inst/doc/ConditionalPowerPlot.Rmd | 4 inst/doc/ConditionalPowerPlot.html | 607 +++++++ inst/doc/GentleIntroductionToGSD.R | 4 inst/doc/GentleIntroductionToGSD.Rmd | 4 inst/doc/GentleIntroductionToGSD.html | 2 inst/doc/PoissonMixtureModel.R | 4 inst/doc/PoissonMixtureModel.Rmd | 4 inst/doc/PoissonMixtureModel.html | 1818 ++++++++++++++++++++++- inst/doc/SpendingFunctionOverview.R | 4 inst/doc/SpendingFunctionOverview.Rmd | 4 inst/doc/SurvivalOverview.R | 4 inst/doc/SurvivalOverview.Rmd | 4 inst/doc/SurvivalOverview.html | 651 ++++++++ inst/doc/VaccineEfficacy.R | 4 inst/doc/VaccineEfficacy.Rmd | 4 inst/doc/VaccineEfficacy.html | 442 ++--- inst/doc/binomialSPRTExample.R | 4 inst/doc/binomialSPRTExample.Rmd | 4 inst/doc/binomialSPRTExample.html | 1763 ++++++++++++++++++++-- inst/doc/gsDesignPackageOverview.R | 4 inst/doc/gsDesignPackageOverview.Rmd | 4 inst/doc/gsDesignPackageOverview.html | 512 ++++++ inst/doc/gsSurvBasicExamples.R | 4 inst/doc/gsSurvBasicExamples.Rmd | 4 inst/doc/gsSurvBasicExamples.html | 1224 +++++++++++++-- inst/doc/nNormal.R | 4 inst/doc/nNormal.Rmd | 4 inst/doc/nNormal.html | 328 ++++ inst/doc/toInteger.html | 2 tests/testthat/test-independent-test-toInteger.R |only vignettes/ConditionalErrorSpending.Rmd | 4 vignettes/ConditionalPowerPlot.Rmd | 4 vignettes/GentleIntroductionToGSD.Rmd | 4 vignettes/PoissonMixtureModel.Rmd | 4 vignettes/SpendingFunctionOverview.Rmd | 4 vignettes/SurvivalOverview.Rmd | 4 vignettes/VaccineEfficacy.Rmd | 4 vignettes/binomialSPRTExample.Rmd | 4 vignettes/gsDesignPackageOverview.Rmd | 4 vignettes/gsSurvBasicExamples.Rmd | 4 vignettes/nNormal.Rmd | 4 48 files changed, 8066 insertions(+), 894 deletions(-)
Title: Fractional Weighted Bootstrap
Description: An implementation of the fractional weighted bootstrap to be used as a drop-in for functions in
the 'boot' package. The fractional weighted bootstrap (also known as the Bayesian bootstrap) involves drawing
weights randomly that are applied to the data rather than resampling units from the data. See Xu et al. (2020)
<doi:10.1080/00031305.2020.1731599> for details.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between fwb versions 0.2.0 dated 2023-12-06 and 0.3.0 dated 2025-03-03
fwb-0.2.0/fwb/build/fwb.pdf |only fwb-0.3.0/fwb/DESCRIPTION | 16 fwb-0.3.0/fwb/MD5 | 53 +- fwb-0.3.0/fwb/NAMESPACE | 1 fwb-0.3.0/fwb/NEWS.md | 26 + fwb-0.3.0/fwb/R/fwb.R | 323 ++++++++++++---- fwb-0.3.0/fwb/R/fwb.ci.R | 130 ++++-- fwb-0.3.0/fwb/R/plot.fwb.R | 12 fwb-0.3.0/fwb/R/set_fwb_wtype.R | 8 fwb-0.3.0/fwb/R/summary.fwb.R | 83 ++-- fwb-0.3.0/fwb/R/utils.R | 287 ++++++++------ fwb-0.3.0/fwb/R/vcovFWB.R | 145 +++++-- fwb-0.3.0/fwb/README.md | 61 +-- fwb-0.3.0/fwb/build/stage23.rdb |binary fwb-0.3.0/fwb/build/vignette.rds |only fwb-0.3.0/fwb/inst |only fwb-0.3.0/fwb/man/figures/README-unnamed-chunk-10-1.png |binary fwb-0.3.0/fwb/man/figures/README-unnamed-chunk-5-1.png |binary fwb-0.3.0/fwb/man/figures/README-unnamed-chunk-9-1.png |binary fwb-0.3.0/fwb/man/fwb-package.Rd | 1 fwb-0.3.0/fwb/man/fwb.Rd | 36 + fwb-0.3.0/fwb/man/fwb.ci.Rd | 5 fwb-0.3.0/fwb/man/get_ci.Rd | 2 fwb-0.3.0/fwb/man/set_fwb_wtype.Rd | 8 fwb-0.3.0/fwb/man/summary.fwb.Rd | 17 fwb-0.3.0/fwb/man/vcovFWB.Rd | 40 + fwb-0.3.0/fwb/tests |only fwb-0.3.0/fwb/vignettes |only 28 files changed, 871 insertions(+), 383 deletions(-)
Title: Using CF-Compliant Calendars with Climate Projection Data
Description: Support for all calendars as specified in the Climate and Forecast
(CF) Metadata Conventions for climate and forecasting data. The CF Metadata
Conventions is widely used for distributing files with climate observations
or projections, including the Coupled Model Intercomparison Project (CMIP)
data used by climate change scientists and the Intergovernmental Panel on
Climate Change (IPCC). This package specifically allows the user to work
with any of the CF-compliant calendars (many of which are not compliant with
POSIXt). The CF time coordinate is formally defined in the CF Metadata
Conventions document available at <https://cfconventions.org/Data/cf-conventions/cf-conventions-1.12/cf-conventions.html#time-coordinate>.
Author: Patrick Van Laake [aut, cre, cph]
Maintainer: Patrick Van Laake <patrick@vanlaake.net>
Diff between CFtime versions 1.5.0 dated 2025-01-15 and 1.5.1 dated 2025-03-03
DESCRIPTION | 9 MD5 | 50 ++-- NEWS.md | 7 R/CFCalendar.R | 9 R/CFCalendarProleptic.R | 2 R/CFCalendarStandard.R | 4 R/CFCalendarUTC.R | 22 +- R/CFtime.R | 113 +++++----- R/api.R | 16 - R/deprecated.R | 4 README.md | 133 +++++------- TODO | 5 inst/doc/CFtime.R | 63 +++--- inst/doc/CFtime.Rmd | 79 +++---- inst/doc/CFtime.html | 263 ++++++++++++++++++------- inst/doc/Processing.R | 74 +++---- inst/doc/Processing.Rmd | 116 +++++------ inst/doc/Processing.html | 376 +++++++++++++++++++++++------------- man/CFCalendar.Rd | 2 man/CFTime.Rd | 30 +- tests/testthat/test-CFformat.R | 17 + tests/testthat/test-CFtime.R | 31 +- tests/testthat/test-functions.R | 16 + tests/testthat/test-parse_deparse.R | 44 ++++ vignettes/CFtime.Rmd | 79 +++---- vignettes/Processing.Rmd | 116 +++++------ 26 files changed, 1005 insertions(+), 675 deletions(-)
Title: R6-Based ML Survival Learners for 'mlexperiments'
Description: Enhances 'mlexperiments'
<https://CRAN.R-project.org/package=mlexperiments> with additional
machine learning ('ML') learners for survival analysis. The package
provides R6-based survival learners for the following algorithms:
'glmnet' <https://CRAN.R-project.org/package=glmnet>, 'ranger'
<https://CRAN.R-project.org/package=ranger>, 'xgboost'
<https://CRAN.R-project.org/package=xgboost>, and 'rpart'
<https://CRAN.R-project.org/package=rpart>. These can be used directly
with the 'mlexperiments' R package.
Author: Lorenz A. Kapsner [cre, aut, cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between mlsurvlrnrs versions 0.0.4 dated 2024-07-05 and 0.0.5 dated 2025-03-03
DESCRIPTION | 10 MD5 | 52 +-- NAMESPACE | 24 - R/learner_surv_coxph_cox.R | 316 +++++++++++----------- R/surv_c_index.R | 54 +-- R/zzz.R | 50 +-- build/vignette.rds |binary inst/doc/mlsurvlrnrs_glmnet_survival.html | 5 inst/doc/mlsurvlrnrs_ranger_survival.html | 5 inst/doc/mlsurvlrnrs_rpart_survival.html | 5 inst/doc/mlsurvlrnrs_xgboost_survival_aft.html | 5 inst/doc/mlsurvlrnrs_xgboost_survival_cox.html | 5 man/LearnerSurvCoxPHCox.Rd | 284 +++++++++---------- man/LearnerSurvGlmnetCox.Rd | 308 ++++++++++----------- man/LearnerSurvRangerCox.Rd | 314 +++++++++++----------- man/LearnerSurvRpartCox.Rd | 342 ++++++++++++------------ man/LearnerSurvXgboostAft.Rd | 356 ++++++++++++------------- man/LearnerSurvXgboostCox.Rd | 348 ++++++++++++------------ man/c_index.Rd | 66 ++-- tests/testthat.R | 27 + tests/testthat/test-lints.R | 26 - tests/testthat/test-surv_coxph_cox.R | 128 ++++---- tests/testthat/test-surv_glmnet_cox.R | 214 +++++++-------- tests/testthat/test-surv_ranger_cox.R | 236 ++++++++-------- tests/testthat/test-surv_rpart_cox.R | 230 ++++++++-------- tests/testthat/test-surv_xgboost_aft.R | 248 ++++++++--------- tests/testthat/test-surv_xgboost_cox.R | 246 ++++++++--------- 27 files changed, 1951 insertions(+), 1953 deletions(-)
Title: (Kernel) Isotope Niche Estimation
Description: Applies methods used to estimate animal homerange, but
instead of geospatial coordinates, we use isotopic coordinates. The estimation
methods include: 1) 2-dimensional bivariate normal kernel utilization density
estimator, 2) bivariate normal ellipse estimator, and 3) minimum convex polygon
estimator, all applied to stable isotope data. Additionally, functions to
determine niche area, polygon overlap between groups and levels (confidence
contours) and plotting capabilities.
Author: Shannon E Albeke [aut, cre]
Maintainer: Shannon E Albeke <salbeke@uwyo.edu>
Diff between rKIN versions 1.0.3 dated 2025-02-14 and 1.0.4 dated 2025-03-03
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/getColors.R | 17 ++++++----------- 3 files changed, 12 insertions(+), 17 deletions(-)
Title: Color-Based Image Segmentation
Description: Automatic, semi-automatic, and manual functions for
generating color maps from images. The idea is to simplify
the colors of an image according to a metric that is useful for
the user, using deterministic methods whenever possible.
Many images will be clustered well using the out-of-the-box
functions, but the package also includes a toolbox of functions
for making manual adjustments (layer merging/isolation, blurring,
fitting to provided color clusters or those from another image, etc).
Also includes export methods for other color/pattern analysis packages
(pavo, patternize, colordistance).
Author: Hannah Weller [aut, cre]
Maintainer: Hannah Weller <hannahiweller@gmail.com>
Diff between recolorize versions 0.1.0 dated 2021-12-07 and 0.2.0 dated 2025-03-03
DESCRIPTION | 15 MD5 | 200 ++--- NAMESPACE | 3 NEWS.md | 9 R/absorbLayer.R | 60 + R/apply_imager_operation.R | 10 R/assignPixels.R | 4 R/backgroundCondition.R | 2 R/backgroundIndex.R | 14 R/blurImage.R | 16 R/brick_to_array.R | 11 R/cimgConversions.R | 2 R/colorClusters.R | 70 + R/colorResiduals.R | 6 R/editLayers.R | 28 R/imDist.R | 20 R/imposeColors.R | 5 R/medianColors.R |only R/mergeLayers.R | 31 R/pixelAssignMatrix.R | 4 R/plotColorPalette.R | 4 R/plotImageArray.R | 4 R/plot_recolorize.R | 6 R/raster_array_conversions.R | 4 R/readImage.R | 17 R/recluster.R | 22 R/recolorImage.R | 4 R/recolorize-package.R |only R/recolorize.R | 27 R/recolorize2.R | 8 R/recolorizeVector.R | 19 R/recolorize_adjacency.R | 1 R/reorder_colors.R |only R/rerun_recolorize.R | 2 R/splitByColor.R | 19 R/thresholdRecolor.R | 6 R/wernerColor.R | 16 README.md | 113 ++ build/vignette.rds |binary inst/doc/Introduction.R | 223 ++--- inst/doc/Introduction.Rmd | 11 inst/doc/Introduction.html | 1166 ++++++++++++++++-------------- inst/doc/step00_prep.R | 79 +- inst/doc/step00_prep.Rmd | 1 inst/doc/step00_prep.html | 715 ++++++++++-------- inst/doc/step01_loading.R | 83 +- inst/doc/step01_loading.Rmd | 1 inst/doc/step01_loading.html | 835 +++++++++++---------- inst/doc/step02_initial_cluster.R | 253 +++--- inst/doc/step02_initial_cluster.Rmd | 1 inst/doc/step02_initial_cluster.html | 1095 ++++++++++++++++------------ inst/doc/step03_refinement.R | 79 +- inst/doc/step03_refinement.Rmd | 1 inst/doc/step03_refinement.html | 848 +++++++++++---------- inst/doc/step04_manual_tweak.R | 82 +- inst/doc/step04_manual_tweak.Rmd | 6 inst/doc/step04_manual_tweak.html | 858 +++++++++++----------- inst/doc/step05_visualization_export.R | 139 +-- inst/doc/step05_visualization_export.Rmd | 1 inst/doc/step05_visualization_export.html | 965 +++++++++++++----------- inst/extdata/msc/corbetti_vector.rds |binary man/absorbLayer.Rd | 9 man/apply_imager_operation.Rd | 10 man/array_to_RasterStack.Rd | 2 man/array_to_cimg.Rd | 2 man/assignPixels.Rd | 4 man/backgroundCondition.Rd | 2 man/backgroundIndex.Rd | 6 man/blurImage.Rd | 14 man/col2col.Rd | 7 man/colorClusters.Rd | 14 man/colorClustersHist.Rd | 12 man/colorClustersKMeans.Rd | 6 man/colorResiduals.Rd | 6 man/editLayer.Rd | 12 man/editLayers.Rd | 12 man/figures |only man/imDist.Rd | 10 man/imHeatmap.Rd | 6 man/imposeColors.Rd | 5 man/match_colors.Rd |only man/medianColors.Rd |only man/mergeLayers.Rd | 12 man/pixelAssignMatrix.Rd | 4 man/plot.recolorize.Rd | 6 man/plotColorPalette.Rd | 4 man/plotImageArray.Rd | 4 man/readImage.Rd | 2 man/recluster.Rd | 20 man/recoloredImage.Rd | 2 man/recolorize-package.Rd |only man/recolorize.Rd | 14 man/recolorize2.Rd | 8 man/reorder_colors.Rd |only man/splitByColor.Rd | 14 man/thresholdRecolor.Rd | 2 man/wernerColor.Rd | 10 vignettes/Introduction.Rmd | 11 vignettes/step00_prep.Rmd | 1 vignettes/step01_loading.Rmd | 1 vignettes/step02_initial_cluster.Rmd | 1 vignettes/step03_refinement.Rmd | 1 vignettes/step04_manual_tweak.Rmd | 6 vignettes/step05_visualization_export.Rmd | 1 104 files changed, 4692 insertions(+), 3795 deletions(-)
Title: Reference Based Multiple Imputation
Description: Implements standard and reference based multiple imputation methods for continuous
longitudinal endpoints (Gower-Page et al. (2022) <doi:10.21105/joss.04251>). In particular,
this package supports deterministic conditional mean imputation and jackknifing as described
in Wolbers et al. (2022) <doi:10.1002/pst.2234>, Bayesian multiple imputation as described
in Carpenter et al. (2013) <doi:10.1080/10543406.2013.834911>, and bootstrapped maximum
likelihood imputation as described in von Hippel and Bartlett (2021) <doi: 10.1214/20-STS793>.
Author: Isaac Gravestock [aut, cre],
Craig Gower-Page [aut],
Alessandro Noci [aut],
Marcel Wolbers [ctb],
Daniel Sabanes Bove [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Isaac Gravestock <isaac.gravestock@roche.com>
Diff between rbmi versions 1.4.0 dated 2025-02-07 and 1.4.1 dated 2025-03-03
DESCRIPTION | 16 +++++----- MD5 | 24 ++++++++-------- NEWS.md | 5 +++ R/utilities.R | 26 ++++++++++------- build/vignette.rds |binary inst/doc/advanced.html | 2 - inst/doc/quickstart.html | 50 +++++++++++++++++----------------- inst/stan/MMRM.stan | 2 - man/rbmi-package.Rd | 4 +- man/rbmi-settings.Rd | 10 ++++++ tests/testthat.R | 5 +++ tests/testthat/test-reproducibility.R | 5 +++ tests/testthat/test-utilities.R | 10 +++--- 13 files changed, 95 insertions(+), 64 deletions(-)
Title: Fit and Compare Species-Area Relationship Models Using
Multimodel Inference
Description: Implements the basic elements of the multi-model
inference paradigm for up to twenty species-area relationship models (SAR), using simple
R list-objects and functions, as in Triantis et al. 2012 <DOI:10.1111/j.1365-2699.2011.02652.x>.
The package is scalable and users can easily create their own model and data objects. Additional
SAR related functions are provided.
Author: Thomas J. Matthews [aut, cre] ,
Francois Guilhaumon [aut] ,
Kevin Cazelles [rev]
Maintainer: Thomas J. Matthews <txm676@gmail.com>
Diff between sars versions 1.3.7 dated 2024-10-03 and 2.0.0 dated 2025-03-03
DESCRIPTION | 8 MD5 | 81 +++--- NAMESPACE | 6 NEWS.md | 12 R/class_plot.R | 407 +++++++++++++++++++++++++++++-- R/class_print.R | 20 + R/class_summary.R | 11 R/data_countryside.R |only R/obs_shape.R | 9 R/sar_countryside.R |only R/sar_habitat.R | 67 ++--- README.md | 102 +++---- build/vignette.rds |binary data/countryside.rda |only inst/doc/sars-r-package.Rmd | 23 + inst/doc/sars-r-package.html | 155 ++--------- man/coleman.Rd | 108 ++++---- man/countryside.Rd |only man/countryside_extrap.Rd |only man/display_sars_models.Rd | 56 ++-- man/figures/README-unnamed-chunk-5-1.png |binary man/gdm.Rd | 356 +++++++++++++-------------- man/lin_pow.Rd | 144 +++++----- man/plot.habitat.Rd | 213 ++++++++++++++-- man/sar_countryside.Rd |only man/sar_habitat.Rd | 335 ++++++++++++------------- man/sar_linear.Rd | 148 +++++------ man/sar_logistic.Rd | 194 +++++++------- man/sar_multi.Rd | 142 +++++----- tests/testthat.R | 10 tests/testthat/Rplots.pdf |only tests/testthat/test_coleman.R | 2 tests/testthat/test_countryside.R |only tests/testthat/test_fit_collection.R | 6 tests/testthat/test_gdm.R | 12 tests/testthat/test_habitat.R |only tests/testthat/test_lin_pow.R | 14 - tests/testthat/test_loga.R | 4 tests/testthat/test_monod.R | 1 tests/testthat/test_multi.R | 52 +++ tests/testthat/test_power.R | 13 tests/testthat/test_pred.R | 2 tests/testthat/test_sar_linear.R | 6 tests/testthat/test_thresholds.R | 32 ++ tests/testthat/test_weibull3.R | 22 + vignettes/sars-r-package.Rmd | 23 + 46 files changed, 1734 insertions(+), 1062 deletions(-)
Title: Rating and Evaluating Texts Using Large Language Models
Description: Generates ratings and psycholinguistic metrics for textual stimuli using large language models.
It enables users to evaluate idioms and other language materials by combining context, prompts, and stimulus inputs.
It supports multiple LLM APIs (such as 'OpenAI', 'DeepSeek', 'Anthropic', 'Cohere', 'Google PaLM', and 'Ollama')
by allowing users to switch models with a single parameter. In addition to generating numeric ratings,
'chatRater' provides functions for obtaining detailed psycholinguistic metrics including word frequency (with optional corpus input),
lexical coverage (with customizable vocabulary size and test basis), Zipf metric, Levenshtein distance, and semantic transparency.
Author: Shiyang Zheng [aut, cre]
Maintainer: Shiyang Zheng <Shiyang.Zheng@nottingham.ac.uk>
Diff between chatRater versions 1.0.0 dated 2025-02-17 and 1.1.0 dated 2025-03-03
DESCRIPTION | 20 - MD5 | 19 NAMESPACE | 9 R/chatRater.R | 762 +++++++++++++++++++++++++++++++-------- README.md | 70 +++ man/chatRater-package.Rd |only man/generate_ratings.Rd | 51 +- man/generate_ratings_for_all.Rd | 47 +- man/get_levenshtein_d.Rd |only man/get_lexical_coverage.Rd |only man/get_semantic_transparency.Rd |only man/get_word_frequency.Rd |only man/get_zipf_metric.Rd |only man/llm_api_call.Rd |only 14 files changed, 763 insertions(+), 215 deletions(-)
Title: Structural Bayesian Vector Autoregression Models
Description: Provides a function for estimating the parameters of Structural Bayesian Vector Autoregression models with the method developed by Baumeister and Hamilton (2015) <doi:10.3982/ECTA12356>, Baumeister and Hamilton (2017) <doi:10.3386/w24167>, and Baumeister and Hamilton (2018) <doi:10.1016/j.jmoneco.2018.06.005>. Functions for plotting impulse responses, historical decompositions, and posterior distributions of model parameters are also provided.
Author: Paul Richardson [aut, cre]
Maintainer: Paul Richardson <p.richardson.54391@gmail.com>
Diff between BHSBVAR versions 3.1.1 dated 2022-11-05 and 3.1.2 dated 2025-03-03
DESCRIPTION | 17 - MD5 | 42 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/BHSBVAR.Rnw | 1 inst/doc/BHSBVAR.pdf |binary man/BHSBVAR-package.Rd | 50 ++--- man/BH_SBVAR.Rd | 372 ++++++++++++++++++++--------------------- man/Dist_Plots.Rd | 268 ++++++++++++++--------------- man/FEVD_Plots.Rd | 292 ++++++++++++++++---------------- man/HD_Plots.Rd | 308 ++++++++++++++++----------------- man/IRF_Plots.Rd | 274 +++++++++++++++--------------- man/USLMData.Rd | 54 ++--- src/BHSBVAR.cpp | 2 src/Makevars | 12 - src/Makevars.win | 12 - vignettes/BHSBVAR.Rnw | 1 vignettes/fig/Dist_plots-1.pdf |binary vignettes/fig/FEVD_plots-1.pdf |binary vignettes/fig/HD_plots-1.pdf |binary vignettes/fig/IRF_plots-1.pdf |binary vignettes/fig/Model-1.pdf |binary 22 files changed, 842 insertions(+), 863 deletions(-)
Title: Utilities for Scoring and Assessing Predictions
Description: Facilitate the evaluation of forecasts in a convenient
framework based on data.table. It allows user to to check their forecasts
and diagnose issues, to visualise forecasts and missing data, to transform
data before scoring, to handle missing forecasts, to aggregate scores, and
to visualise the results of the evaluation. The package mostly focuses on
the evaluation of probabilistic forecasts and allows evaluating several
different forecast types and input formats. Find more information about the
package in the Vignettes as well as in the accompanying paper,
<doi:10.48550/arXiv.2205.07090>.
Author: Nikos Bosse [aut, cre] ,
Sam Abbott [aut] ,
Hugo Gruson [aut] ,
Johannes Bracher [ctb] ,
Toshiaki Asakura [ctb] ,
James Mba Azam [ctb] ,
Sebastian Funk [aut],
Michael Chirico [ctb]
Maintainer: Nikos Bosse <nikosbosse@gmail.com>
Diff between scoringutils versions 2.0.0 dated 2024-10-31 and 2.1.0 dated 2025-03-03
scoringutils-2.0.0/scoringutils/R/z-packageStartupMessage.R |only scoringutils-2.1.0/scoringutils/DESCRIPTION | 34 scoringutils-2.1.0/scoringutils/MD5 | 148 +-- scoringutils-2.1.0/scoringutils/NAMESPACE | 13 scoringutils-2.1.0/scoringutils/NEWS.md | 78 - scoringutils-2.1.0/scoringutils/R/class-forecast-binary.R | 29 scoringutils-2.1.0/scoringutils/R/class-forecast-nominal.R | 50 - scoringutils-2.1.0/scoringutils/R/class-forecast-ordinal.R |only scoringutils-2.1.0/scoringutils/R/class-forecast-point.R | 11 scoringutils-2.1.0/scoringutils/R/class-forecast-quantile.R | 18 scoringutils-2.1.0/scoringutils/R/class-forecast-sample.R | 42 scoringutils-2.1.0/scoringutils/R/class-forecast.R | 30 scoringutils-2.1.0/scoringutils/R/documentation-templates.R | 15 scoringutils-2.1.0/scoringutils/R/get-forecast-type.R | 9 scoringutils-2.1.0/scoringutils/R/get-pit-histogram.R | 6 scoringutils-2.1.0/scoringutils/R/helper-quantile-interval-range.R | 3 scoringutils-2.1.0/scoringutils/R/metrics-nominal.R | 76 + scoringutils-2.1.0/scoringutils/R/metrics-ordinal.R |only scoringutils-2.1.0/scoringutils/R/metrics-quantile.R | 11 scoringutils-2.1.0/scoringutils/R/metrics-sample.R | 24 scoringutils-2.1.0/scoringutils/R/score.R | 2 scoringutils-2.1.0/scoringutils/README.md | 7 scoringutils-2.1.0/scoringutils/build/partial.rdb |binary scoringutils-2.1.0/scoringutils/build/vignette.rds |binary scoringutils-2.1.0/scoringutils/data/example_ordinal.rda |only scoringutils-2.1.0/scoringutils/inst/create-example-data.R | 14 scoringutils-2.1.0/scoringutils/inst/doc/Deprecated-functions.html | 5 scoringutils-2.1.0/scoringutils/inst/doc/Deprecated-visualisations.R | 478 +++++----- scoringutils-2.1.0/scoringutils/inst/doc/Deprecated-visualisations.Rmd | 10 scoringutils-2.1.0/scoringutils/inst/doc/Deprecated-visualisations.html | 9 scoringutils-2.1.0/scoringutils/inst/doc/scoring-rules.Rmd | 6 scoringutils-2.1.0/scoringutils/inst/doc/scoring-rules.html | 15 scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript.Rmd | 23 scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript.aux | 70 - scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript.log | 228 ++-- scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript.tex | 85 + scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/calibration-plots-1.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/correlation-plot-1.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/coverage-1.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/pairwise-plot-1.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/pit-plots-1.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/plot-forecast-counts-1.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/score-heatmap-1.pdf |binary scoringutils-2.1.0/scoringutils/inst/manuscript/manuscript_files/figure-latex/wis-components-1.pdf |binary scoringutils-2.1.0/scoringutils/man/as_forecast_binary.Rd | 12 scoringutils-2.1.0/scoringutils/man/as_forecast_generic.Rd | 15 scoringutils-2.1.0/scoringutils/man/as_forecast_nominal.Rd | 15 scoringutils-2.1.0/scoringutils/man/as_forecast_ordinal.Rd |only scoringutils-2.1.0/scoringutils/man/as_forecast_point.Rd | 4 scoringutils-2.1.0/scoringutils/man/as_forecast_quantile.Rd | 4 scoringutils-2.1.0/scoringutils/man/as_forecast_sample.Rd | 15 scoringutils-2.1.0/scoringutils/man/assert_input_categorical.Rd |only scoringutils-2.1.0/scoringutils/man/assert_input_nominal.Rd | 26 scoringutils-2.1.0/scoringutils/man/assert_input_ordinal.Rd |only scoringutils-2.1.0/scoringutils/man/example_ordinal.Rd |only scoringutils-2.1.0/scoringutils/man/figures/metrics-ordinal.png |only scoringutils-2.1.0/scoringutils/man/figures/workflow.png |binary scoringutils-2.1.0/scoringutils/man/get_metrics.Rd | 1 scoringutils-2.1.0/scoringutils/man/get_metrics.forecast_binary.Rd | 1 scoringutils-2.1.0/scoringutils/man/get_metrics.forecast_nominal.Rd | 3 scoringutils-2.1.0/scoringutils/man/get_metrics.forecast_ordinal.Rd |only scoringutils-2.1.0/scoringutils/man/get_metrics.forecast_point.Rd | 1 scoringutils-2.1.0/scoringutils/man/get_metrics.forecast_quantile.Rd | 1 scoringutils-2.1.0/scoringutils/man/get_metrics.forecast_sample.Rd | 1 scoringutils-2.1.0/scoringutils/man/get_metrics.scores.Rd | 1 scoringutils-2.1.0/scoringutils/man/get_pit_histogram.Rd | 6 scoringutils-2.1.0/scoringutils/man/illustration-input-metric-ordinal.Rd |only scoringutils-2.1.0/scoringutils/man/is_forecast.Rd | 8 scoringutils-2.1.0/scoringutils/man/logs_sample.Rd | 2 scoringutils-2.1.0/scoringutils/man/rps_ordinal.Rd |only scoringutils-2.1.0/scoringutils/man/score.Rd | 8 scoringutils-2.1.0/scoringutils/man/scoring-functions-binary.Rd | 2 scoringutils-2.1.0/scoringutils/man/scoring-functions-nominal.Rd | 31 scoringutils-2.1.0/scoringutils/tests/testthat/setup.R | 2 scoringutils-2.1.0/scoringutils/tests/testthat/test-class-forecast-ordinal.R |only scoringutils-2.1.0/scoringutils/tests/testthat/test-class-forecast-quantile.R | 19 scoringutils-2.1.0/scoringutils/tests/testthat/test-metrics-nominal.R | 14 scoringutils-2.1.0/scoringutils/tests/testthat/test-metrics-ordinal.R |only scoringutils-2.1.0/scoringutils/tests/testthat/test-metrics-sample.R | 10 scoringutils-2.1.0/scoringutils/vignettes/Deprecated-visualisations.Rmd | 10 scoringutils-2.1.0/scoringutils/vignettes/scoring-rules.Rmd | 6 82 files changed, 1004 insertions(+), 763 deletions(-)
Title: Penalized Linear Mixed Models for Correlated Data
Description: Fits penalized linear mixed models that correct for
unobserved confounding factors. 'plmmr' infers and corrects for the
presence of unobserved confounding effects such as population
stratification and environmental heterogeneity. It then fits a linear
model via penalized maximum likelihood. Originally designed for the
multivariate analysis of single nucleotide polymorphisms (SNPs)
measured in a genome-wide association study (GWAS), 'plmmr' eliminates
the need for subpopulation-specific analyses and post-analysis p-value
adjustments. Functions for the appropriate processing of 'PLINK'
files are also supplied. For examples, see the package homepage.
<https://pbreheny.github.io/plmmr/>.
Author: Tabitha K. Peter [aut] ,
Anna C. Reisetter [aut] ,
Patrick J. Breheny [aut, cre] ,
Yujing Lu [aut]
Maintainer: Patrick J. Breheny <patrick-breheny@uiowa.edu>
Diff between plmmr versions 4.2.0 dated 2025-02-18 and 4.2.1 dated 2025-03-03
plmmr-4.2.0/plmmr/tests/tinytest.R |only plmmr-4.2.1/plmmr/DESCRIPTION | 8 ++++---- plmmr-4.2.1/plmmr/MD5 | 14 +++++++------- plmmr-4.2.1/plmmr/NEWS.md | 4 ++++ plmmr-4.2.1/plmmr/build/partial.rdb |binary plmmr-4.2.1/plmmr/build/vignette.rds |binary plmmr-4.2.1/plmmr/inst/doc/getting-started.html | 10 +++++----- plmmr-4.2.1/plmmr/src/plmm_init.c | 9 ++++++--- plmmr-4.2.1/plmmr/tests/test.R |only 9 files changed, 26 insertions(+), 19 deletions(-)
Title: Generates Expectations for 'testthat' Unit Testing
Description: Helps systematize and ease the process of
building unit tests with the 'testthat' package by providing
tools for generating expectations.
Author: Ludvig Renbo Olsen [aut, cre] ,
R. Mark Sharp [ctb]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between xpectr versions 0.4.3 dated 2022-11-18 and 0.4.4 dated 2025-03-03
xpectr-0.4.3/xpectr/build/xpectr.pdf |only xpectr-0.4.3/xpectr/man/xpectr.Rd |only xpectr-0.4.4/xpectr/DESCRIPTION | 13 xpectr-0.4.4/xpectr/MD5 | 38 xpectr-0.4.4/xpectr/NEWS.md | 8 xpectr-0.4.4/xpectr/R/create_expectations.R | 2 xpectr-0.4.4/xpectr/R/do_if.R | 9 xpectr-0.4.4/xpectr/R/element_descriptors.R | 20 xpectr-0.4.4/xpectr/R/package_info.R | 4 xpectr-0.4.4/xpectr/R/strip.R | 1 xpectr-0.4.4/xpectr/R/strip_side_effect_messages.R | 10 xpectr-0.4.4/xpectr/README.md | 135 - xpectr-0.4.4/xpectr/build/stage23.rdb |only xpectr-0.4.4/xpectr/build/vignette.rds |binary xpectr-0.4.4/xpectr/inst/doc/readme.R | 986 ++++---- xpectr-0.4.4/xpectr/inst/doc/readme.Rmd | 2 xpectr-0.4.4/xpectr/inst/doc/readme.html | 1204 +++++----- xpectr-0.4.4/xpectr/man/stop_if.Rd | 9 xpectr-0.4.4/xpectr/man/strip_msg.Rd | 10 xpectr-0.4.4/xpectr/man/xpectr-package.Rd |only xpectr-0.4.4/xpectr/tests/testthat/test_capture_side_effects.R | 3 xpectr-0.4.4/xpectr/vignettes/readme.Rmd | 2 22 files changed, 1247 insertions(+), 1209 deletions(-)
Title: Survival Analysis in Health Economic Evaluation
Description: Contains a suite of functions for survival analysis in health economics.
These can be used to run survival models under a frequentist (based on maximum likelihood)
or a Bayesian approach (both based on Integrated Nested Laplace Approximation or Hamiltonian
Monte Carlo). To run the Bayesian models, the user needs to install additional modules
(packages), i.e. 'survHEinla' and 'survHEhmc'. These can be installed using
'remotes::install_github' from their GitHub repositories:
(<https://github.com/giabaio/survHEhmc> and <https://github.com/giabaio/survHEinla/>
respectively). 'survHEinla' is based on the package INLA, which is available for download at
<https://inla.r-inla-download.org/R/stable/>. The user can specify a set of parametric models
using a common notation and select the preferred mode of inference. The results can also be
post-processed to produce probabilistic sensitivity analysis and can be used to export the
output to an Excel file (e.g. for a Markov model, [...truncated...]
Author: Gianluca Baio [aut, cre],
Andrea Berardi [ctb],
Philip Cooney [ctb],
Andrew Jones [ctb],
Nathan Green [ctb]
Maintainer: Gianluca Baio <g.baio@ucl.ac.uk>
Diff between survHE versions 2.0.2 dated 2024-10-04 and 2.0.3 dated 2025-03-03
survHE-2.0.2/survHE/inst |only survHE-2.0.3/survHE/DESCRIPTION | 12 ++-- survHE-2.0.3/survHE/MD5 | 17 +++--- survHE-2.0.3/survHE/NEWS.md | 64 ++++++++++++++++++++++++-- survHE-2.0.3/survHE/R/make.transition.probs.R | 2 survHE-2.0.3/survHE/R/psa.plot.R | 6 +- survHE-2.0.3/survHE/R/utils_plot_survHE.R | 6 +- survHE-2.0.3/survHE/R/write.surv.R | 2 survHE-2.0.3/survHE/README.md | 4 + survHE-2.0.3/survHE/build/partial.rdb |binary 10 files changed, 86 insertions(+), 27 deletions(-)
Title: High Performance Algorithms for Vine Copula Modeling
Description: Provides an interface to 'vinecopulib', a C++ library for vine
copula modeling. The 'rvinecopulib' package implements the core features of the
popular 'VineCopula' package, in particular inference algorithms for both vine
copula and bivariate copula models. Advantages over 'VineCopula' are a sleeker
and more modern API, improved performances, especially in high dimensions,
nonparametric and multi-parameter families, and the ability to model discrete
variables. The 'rvinecopulib' package includes 'vinecopulib' as header-only
C++ library (currently version 0.7.1). Thus users do not need to install
'vinecopulib' itself in order to use 'rvinecopulib'. Since their initial
releases, 'vinecopulib' is licensed under the MIT License, and 'rvinecopulib'
is licensed under the GNU GPL version 3.
Author: Thomas Nagler [aut, cre],
Thibault Vatter [aut]
Maintainer: Thomas Nagler <info@vinecopulib.org>
Diff between rvinecopulib versions 0.7.1.1.1 dated 2025-02-10 and 0.7.1.1.2 dated 2025-03-03
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 6 ++++++ inst/include/vinecopulib/misc/nlohmann_json.hpp | 4 ++-- 4 files changed, 14 insertions(+), 8 deletions(-)
Title: Realistic Quantitative Structure Models
Description: Real Twig is a method to correct branch overestimation in quantitative structure models. Overestimated cylinders are correctly tapered using measured twig diameters of corresponding tree species. Supported quantitative structure modeling software includes 'TreeQSM', 'SimpleForest', 'Treegraph', and 'aRchi'. Also included is a novel database of twig diameters and tools for fractal analysis of point clouds.
Author: Aidan Morales [aut, cre, cph] ,
David W. MacFarlane [aut, cph]
Maintainer: Aidan Morales <moral169@msu.edu>
Diff between rTwig versions 1.3.0 dated 2024-11-21 and 1.4.0 dated 2025-03-03
rTwig-1.3.0/rTwig/R/import_qsm.R |only rTwig-1.3.0/rTwig/R/qsm_summary.R |only rTwig-1.3.0/rTwig/R/standardize_qsm.R |only rTwig-1.3.0/rTwig/man/standardize_qsm.Rd |only rTwig-1.4.0/rTwig/DESCRIPTION | 6 rTwig-1.4.0/rTwig/MD5 | 115 +-- rTwig-1.4.0/rTwig/NAMESPACE | 5 rTwig-1.4.0/rTwig/NEWS.md | 424 ++++++------ rTwig-1.4.0/rTwig/R/RcppExports.R | 73 ++ rTwig-1.4.0/rTwig/R/box_dimension.R | 12 rTwig-1.4.0/rTwig/R/cluster_cloud.R | 18 rTwig-1.4.0/rTwig/R/correct_radii.R | 5 rTwig-1.4.0/rTwig/R/export_mat.R | 4 rTwig-1.4.0/rTwig/R/export_mesh.R | 353 +++++++--- rTwig-1.4.0/rTwig/R/import_leaves.R |only rTwig-1.4.0/rTwig/R/import_treeqsm.R |only rTwig-1.4.0/rTwig/R/plot_qsm.R | 466 ++++++++++--- rTwig-1.4.0/rTwig/R/prune_qsm.R | 37 - rTwig-1.4.0/rTwig/R/run_rtwig.R | 73 +- rTwig-1.4.0/rTwig/R/smooth_qsm.R | 5 rTwig-1.4.0/rTwig/R/standardise_qsm.R |only rTwig-1.4.0/rTwig/R/summarise_qsm.R |only rTwig-1.4.0/rTwig/R/tools.R | 13 rTwig-1.4.0/rTwig/R/tree_metrics.R | 298 ++++++-- rTwig-1.4.0/rTwig/R/twigs.R | 21 rTwig-1.4.0/rTwig/R/update_cylinders.R | 7 rTwig-1.4.0/rTwig/README.md | 15 rTwig-1.4.0/rTwig/build/partial.rdb |binary rTwig-1.4.0/rTwig/data/twigs_index.rda |only rTwig-1.4.0/rTwig/inst/REFERENCES.bib | 50 + rTwig-1.4.0/rTwig/inst/doc/Dictionary.Rmd | 272 +++++++ rTwig-1.4.0/rTwig/inst/doc/Dictionary.html | 328 +++++++++ rTwig-1.4.0/rTwig/inst/doc/Metrics.html | 6 rTwig-1.4.0/rTwig/inst/doc/Overview.R | 10 rTwig-1.4.0/rTwig/inst/doc/Overview.Rmd | 16 rTwig-1.4.0/rTwig/inst/doc/Overview.html | 39 - rTwig-1.4.0/rTwig/inst/doc/Twigs.R | 49 + rTwig-1.4.0/rTwig/inst/doc/Twigs.Rmd | 73 ++ rTwig-1.4.0/rTwig/inst/doc/Twigs.html | 97 ++ rTwig-1.4.0/rTwig/inst/doc/Validation.html | 770 +++++++++++----------- rTwig-1.4.0/rTwig/inst/include/helper_functions.h | 1 rTwig-1.4.0/rTwig/man/box_dimension.Rd | 9 rTwig-1.4.0/rTwig/man/cluster_cloud.Rd | 6 rTwig-1.4.0/rTwig/man/correct_radii.Rd | 5 rTwig-1.4.0/rTwig/man/export_mat.Rd | 4 rTwig-1.4.0/rTwig/man/export_mesh.Rd | 93 ++ rTwig-1.4.0/rTwig/man/import_leaves.Rd |only rTwig-1.4.0/rTwig/man/import_qsm.Rd | 26 rTwig-1.4.0/rTwig/man/import_treeqsm.Rd |only rTwig-1.4.0/rTwig/man/plot_qsm.Rd | 113 ++- rTwig-1.4.0/rTwig/man/prune_qsm.Rd | 24 rTwig-1.4.0/rTwig/man/qsm_summary.Rd | 28 rTwig-1.4.0/rTwig/man/run_rtwig.Rd | 24 rTwig-1.4.0/rTwig/man/smooth_qsm.Rd | 5 rTwig-1.4.0/rTwig/man/standardise_qsm.Rd |only rTwig-1.4.0/rTwig/man/summarise_qsm.Rd |only rTwig-1.4.0/rTwig/man/tree_metrics.Rd | 15 rTwig-1.4.0/rTwig/man/twigs.Rd | 4 rTwig-1.4.0/rTwig/man/twigs_index.Rd |only rTwig-1.4.0/rTwig/man/update_cylinders.Rd | 7 rTwig-1.4.0/rTwig/src/RcppExports.cpp | 65 + rTwig-1.4.0/rTwig/src/helper_functions.cpp | 67 + rTwig-1.4.0/rTwig/src/io.cpp |only rTwig-1.4.0/rTwig/vignettes/Dictionary.Rmd | 272 +++++++ rTwig-1.4.0/rTwig/vignettes/Overview.Rmd | 16 rTwig-1.4.0/rTwig/vignettes/Twigs.Rmd | 73 ++ 66 files changed, 3363 insertions(+), 1154 deletions(-)
Title: Rearranging Data
Description: Arrange data by a set of methods. Use rearrangers to reorder
data points and mutators to change their values. From basic utilities,
to centering the greatest value, to swirling in 3-dimensional space,
'rearrr' enables creativity when plotting and experimenting with data.
Author: Ludvig Renbo Olsen [aut, cre]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between rearrr versions 0.3.4 dated 2024-02-07 and 0.3.5 dated 2025-03-03
rearrr-0.3.4/rearrr/build/rearrr.pdf |only rearrr-0.3.5/rearrr/DESCRIPTION | 13 - rearrr-0.3.5/rearrr/MD5 | 37 +-- rearrr-0.3.5/rearrr/NEWS.md | 6 rearrr-0.3.5/rearrr/R/transfer_centroids.R | 2 rearrr-0.3.5/rearrr/README.md | 111 +++++----- rearrr-0.3.5/rearrr/build/stage23.rdb |only rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-11-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-14-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-16-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-19-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-21-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-27-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-29-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-31-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-33-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-35-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-6-1.png |binary rearrr-0.3.5/rearrr/man/figures/README-unnamed-chunk-9-1.png |binary rearrr-0.3.5/rearrr/man/figures/rearrr_square_logo_242x225_259dpi.png |only rearrr-0.3.5/rearrr/tests/testthat/test_n_fn.R | 24 -- 21 files changed, 92 insertions(+), 101 deletions(-)
Title: DIF and DDF Detection by Non-Linear Regression Models
Description: Detection of differential item functioning (DIF) among dichotomously scored items and differential distractor functioning (DDF) among unscored items with non-linear regression procedures based on generalized logistic regression models (Hladka & Martinkova, 2020, <doi:10.32614/RJ-2020-014>).
Author: Adela Hladka [aut, cre],
Patricia Martinkova [aut],
Karel Zvara [ctb]
Maintainer: Adela Hladka <hladka@cs.cas.cz>
Diff between difNLR versions 1.5.0 dated 2024-12-19 and 1.5.1-1 dated 2025-03-03
DESCRIPTION | 11 MD5 | 72 +++-- NEWS.md | 43 +++ R/GMAT.R | 2 R/GMAT2test.R | 2 R/GMATtest.R | 4 R/NLR.R | 612 +++++++++++++++++++------------------------------- R/ORD.R | 2 R/difNLR-package.R | 31 +- R/difNLR.R | 77 +++--- R/difORD.R | 5 R/estimNLR.R | 4 R/formulaNLR.R | 10 R/genNLR.R | 2 R/private.R | 2 README.md | 48 ++- build/partial.rdb |binary man/GMAT.Rd | 2 man/GMAT2test.Rd | 2 man/GMATtest.Rd | 4 man/NLR.Rd | 6 man/ORD.Rd | 2 man/coef.difNLR.Rd | 5 man/difNLR-package.Rd | 31 +- man/difNLR.Rd | 2 man/difORD.Rd | 5 man/estimNLR.Rd | 2 man/genNLR.Rd | 2 tests |only 29 files changed, 478 insertions(+), 512 deletions(-)
Title: Methods for Correlation Analysis
Description: Lightweight package for computing different kinds
of correlations, such as partial correlations, Bayesian correlations,
multilevel correlations, polychoric correlations, biweight
correlations, distance correlations and more. Part of the 'easystats'
ecosystem. References: Makowski et al. (2020) <doi:10.21105/joss.02306>.
Author: Dominique Makowski [aut, inv] ,
Brenton M. Wiernik [aut, cre] ,
Indrajeet Patil [aut] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Remi Theriault [aut] ,
Mark White [rev],
Maximilian M. Rabe [rev]
Maintainer: Brenton M. Wiernik <brenton@wiernik.org>
Diff between correlation versions 0.8.6 dated 2024-10-26 and 0.8.7 dated 2025-03-03
correlation-0.8.6/correlation/tests/testthat/_snaps/as.list.md |only correlation-0.8.6/correlation/tests/testthat/test-as.list.R |only correlation-0.8.7/correlation/DESCRIPTION | 12 correlation-0.8.7/correlation/MD5 | 56 +-- correlation-0.8.7/correlation/NEWS.md | 10 correlation-0.8.7/correlation/R/cor_sort.R | 90 ++++- correlation-0.8.7/correlation/R/cormatrix_to_excel.R | 22 - correlation-0.8.7/correlation/R/correlation.R | 82 ++-- correlation-0.8.7/correlation/R/display.R | 3 correlation-0.8.7/correlation/R/methods_format.R | 25 + correlation-0.8.7/correlation/R/methods_print.R | 10 correlation-0.8.7/correlation/README.md | 49 +- correlation-0.8.7/correlation/inst/doc/multilevel.R | 42 +- correlation-0.8.7/correlation/inst/doc/multilevel.html | 64 ++- correlation-0.8.7/correlation/inst/doc/types.R | 154 ++++---- correlation-0.8.7/correlation/inst/doc/types.html | 175 +++++----- correlation-0.8.7/correlation/man/correlation-package.Rd | 12 correlation-0.8.7/correlation/man/correlation.Rd | 21 - correlation-0.8.7/correlation/man/display.easycormatrix.Rd | 3 correlation-0.8.7/correlation/man/figures/README-12-1.png |binary correlation-0.8.7/correlation/man/figures/README-7-1.png |binary correlation-0.8.7/correlation/man/figures/README-corr-1.png |binary correlation-0.8.7/correlation/tests/testthat/_snaps/as_list.md |only correlation-0.8.7/correlation/tests/testthat/_snaps/display_print_dataframe.md | 54 --- correlation-0.8.7/correlation/tests/testthat/_snaps/display_print_matrix.md | 27 - correlation-0.8.7/correlation/tests/testthat/_snaps/methods.md | 14 correlation-0.8.7/correlation/tests/testthat/_snaps/windows |only correlation-0.8.7/correlation/tests/testthat/test-as_list.R |only correlation-0.8.7/correlation/tests/testthat/test-cor_sort.R |only correlation-0.8.7/correlation/tests/testthat/test-correlation.R | 13 correlation-0.8.7/correlation/tests/testthat/test-display_print_dataframe.R | 12 correlation-0.8.7/correlation/tests/testthat/test-display_print_matrix.R | 21 - 32 files changed, 543 insertions(+), 428 deletions(-)
Title: Topic Inference to Identify Tissue Architecture in Multiplexed
Images
Description: A novel spatial topic model to integrate both cell type and spatial information to identify the complex spatial tissue architecture on multiplexed tissue images without human intervention. The Package implements a collapsed Gibbs sampling algorithm for inference. 'SpaTopic' is scalable to large-scale image datasets without extracting neighborhood information for every single cell. For more details on the methodology, see <https://xiyupeng.github.io/SpaTopic/>.
Author: Xiyu Peng [aut, cre]
Maintainer: Xiyu Peng <pansypeng124@gmail.com>
Diff between SpaTopic versions 1.1.0 dated 2024-04-22 and 1.2.0 dated 2025-03-03
SpaTopic-1.1.0/SpaTopic/man/gibbs.res-class.Rd |only SpaTopic-1.2.0/SpaTopic/DESCRIPTION | 10 SpaTopic-1.2.0/SpaTopic/MD5 | 38 SpaTopic-1.2.0/SpaTopic/NAMESPACE | 3 SpaTopic-1.2.0/SpaTopic/NEWS.md | 5 SpaTopic-1.2.0/SpaTopic/R/Gibbs_sampler.R | 981 ++++++++++--------- SpaTopic-1.2.0/SpaTopic/R/RcppExports.R | 46 SpaTopic-1.2.0/SpaTopic/R/SpaTopic-package.R | 27 SpaTopic-1.2.0/SpaTopic/R/class.R | 10 SpaTopic-1.2.0/SpaTopic/R/prepare_SpaTopic_input.R | 28 SpaTopic-1.2.0/SpaTopic/README.md | 209 +--- SpaTopic-1.2.0/SpaTopic/build/vignette.rds |binary SpaTopic-1.2.0/SpaTopic/inst/doc/Intro_SpaTopic.R | 41 SpaTopic-1.2.0/SpaTopic/inst/doc/Intro_SpaTopic.Rmd | 145 +- SpaTopic-1.2.0/SpaTopic/inst/doc/Intro_SpaTopic.html | 672 ++++++++----- SpaTopic-1.2.0/SpaTopic/man/SpaTopic-Package.Rd | 34 SpaTopic-1.2.0/SpaTopic/man/SpaTopic-class.Rd |only SpaTopic-1.2.0/SpaTopic/man/SpaTopic_inference.Rd | 4 SpaTopic-1.2.0/SpaTopic/man/print.SpaTopic.Rd |only SpaTopic-1.2.0/SpaTopic/man/spatopic_message.Rd |only SpaTopic-1.2.0/SpaTopic/src/Makevars | 4 SpaTopic-1.2.0/SpaTopic/vignettes/Intro_SpaTopic.Rmd | 145 +- 22 files changed, 1388 insertions(+), 1014 deletions(-)
Title: A Collection of Loss Functions for Assessing Point Forecasts
Description: Implements multiple consistent scoring functions
(Gneiting T (2011) <doi:10.1198/jasa.2011.r10138>) for assessing point
forecasts and point predictions. Detailed documentation of scoring
functions' properties is included for facilitating interpretation of
results.
Author: Hristos Tyralis [aut, cre] ,
Georgia Papacharalampous [aut]
Maintainer: Hristos Tyralis <montchrister@gmail.com>
Diff between scoringfunctions versions 1.0 dated 2024-12-01 and 1.1 dated 2025-03-03
DESCRIPTION | 10 +++++----- MD5 | 20 +++++++++++++++----- NAMESPACE | 5 +++++ R/meanlog_if.R |only R/serrexp_sf.R |only R/serrlog_sf.R |only R/serrpower_sf.R |only R/serrsq_sf.R |only build/partial.rdb |binary man/mean_if.Rd | 4 ++-- man/meanlog_if.Rd |only man/scoringfunctions-package.Rd | 14 ++++++++++++-- man/serrexp_sf.Rd |only man/serrlog_sf.Rd |only man/serrpower_sf.Rd |only man/serrsq_sf.Rd |only 16 files changed, 39 insertions(+), 14 deletions(-)
More information about scoringfunctions at CRAN
Permanent link
Title: Calculate Bark Beetle Phenology Using Different Models
Description: Calculate the bark beetle phenology based on raster data or
point-related data. There are multiple models implemented for two bark
beetle species. The models can be customized and their submodels (onset of
infestation, beetle development, diapause initiation, mortality) can be
combined. The following models are available in the package:
PHENIPS-Clim (first-time release in this package),
PHENIPS (Baier et al. 2007) <doi:10.1016/j.foreco.2007.05.020>,
RITY (Ogris et al. 2019) <doi:10.1016/j.ecolmodel.2019.108775>,
CHAPY (Ogris et al. 2020) <doi:10.1016/j.ecolmodel.2020.109137>,
BSO (Jakoby et al. 2019) <doi:10.1111/gcb.14766>,
Lange et al. (2008) <doi:10.1007/978-3-540-85081-6_32>,
Jönsson et al. (2011) <doi:10.1007/s10584-011-0038-4>.
The package may be expanded by models for other bark beetle species in the
future.
Author: Jakob Jentschke [aut, cre],
FVA BW, Abt. Waldschutz [cph, fnd]
Maintainer: Jakob Jentschke <jakob.jentschke@forst.bwl.de>
Diff between barrks versions 1.0.1 dated 2024-11-04 and 1.1.0 dated 2025-03-03
DESCRIPTION | 6 MD5 | 68 ++--- NEWS.md | 32 ++ R/model-joensson.R | 10 R/model-lange.R | 6 R/model-phenips-clim.R | 73 ++++- R/model-phenips.R | 21 + R/phenology-results.R | 12 R/phenology.R | 5 R/plot-development-diagram.R | 69 ++++- R/utils-log.R | 86 +++--- R/utils-model-functions.R | 272 ++++++++++++---------- build/partial.rdb |binary inst/doc/bso.html | 10 inst/doc/model-comparison.html | 33 +- inst/doc/model-customization.html | 12 inst/doc/stations.html | 4 inst/doc/storage.html | 4 inst/tinytest/data/test-data-phenips-clim.rda |binary inst/tinytest/data/test-data-spring-mortality.rda |binary inst/tinytest/storage-test.R | 72 ++--- inst/tinytest/test-model-phenips-clim.R | 25 +- inst/tinytest/test-models-min.R | 46 +-- inst/tinytest/test-spring-mortality.R | 5 inst/tinytest/test-storage-chapy.R | 36 +- inst/tinytest/test-storage-combine.R | 48 +-- inst/tinytest/test-storage-joensson.R | 36 +- inst/tinytest/test-storage-lange.R | 36 +- inst/tinytest/test-storage-phenips-clim.R | 36 +- inst/tinytest/test-storage-phenips.R | 36 +- inst/tinytest/test-storage-rity.R | 36 +- man/get_generations.Rd | 10 man/model.joensson.customize.Rd | 4 man/model.phenips_clim.customize.Rd | 12 tests/tinytest.R | 12 35 files changed, 671 insertions(+), 502 deletions(-)
Title: Ergonomic Methods for Assessing Spatial Models
Description: Assessing predictive models of spatial data can be
challenging, both because these models are typically built for
extrapolating outside the original region represented by training data
and due to potential spatially structured errors, with "hot spots" of
higher than expected error clustered geographically due to spatial
structure in the underlying data. Methods are provided for assessing
models fit to spatial data, including approaches for measuring the
spatial structure of model errors, assessing model predictions at
multiple spatial scales, and evaluating where predictions can be made
safely. Methods are particularly useful for models fit using the
'tidymodels' framework. Methods include Moran's I ('Moran' (1950)
<doi:10.2307/2332142>), Geary's C ('Geary' (1954)
<doi:10.2307/2986645>), Getis-Ord's G ('Ord' and 'Getis' (1995)
<doi:10.1111/j.1538-4632.1995.tb00912.x>), agreement coefficients from
'Ji' and Gallo (2006) (<doi: 10.14358/PERS.72.7.823>), agreement
m [...truncated...]
Author: Michael Mahoney [aut, cre] ,
Lucas Johnson [ctb] ,
Virgilio Gomez-Rubio [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/571>),
Jakub Nowosad [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/571 [...truncated...]
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>
Diff between waywiser versions 0.6.1 dated 2025-02-16 and 0.6.2 dated 2025-03-03
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ inst/doc/multi-scale-assessment.R | 6 +++++- inst/doc/multi-scale-assessment.Rmd | 6 +++++- inst/doc/multi-scale-assessment.html | 8 ++++++-- vignettes/multi-scale-assessment.Rmd | 6 +++++- 7 files changed, 34 insertions(+), 14 deletions(-)
Title: Generate Analysis Results Programmes Using ARS Metadata
Description: Analysis Results Standard (ARS), a foundational standard by CDISC
(Clinical Data Interchange Standards Consortium), provides a logical
data model for metadata describing all components to calculate Analysis Results.
<https://www.cdisc.org/standards/foundational/analysis-results-standard>
Using 'siera' package, ARS metadata is ingested (JSON or Excel format),
producing programmes to generate Analysis Results Datasets (ARDs).
Author: Malan Bosman [aut, cre],
Clymb Clinical [cph, fnd]
Maintainer: Malan Bosman <malanbos@gmail.com>
Diff between siera versions 0.1.0 dated 2025-02-10 and 0.3.0 dated 2025-03-03
DESCRIPTION | 6 MD5 | 16 NEWS.md | 4 R/globals.R | 2 R/readARS.R | 49 - README.md | 36 inst/extdata/ADAE.csv | 2384 +++++++++++++++++++++++++------------------------- man/ARS_example.Rd | 44 man/readARS.Rd | 3 9 files changed, 1275 insertions(+), 1269 deletions(-)
Title: A Mini-Dictionary for 'R', 'shiny' and 'rmarkdown' Documents
Description: Despite the predominant use of R for data manipulation and various robust statistical calculations, in recent years, more people from various disciplines are beginning to use R for other purposes. In doing this seemlessly, further tools are needed users to easily and freely write in R for all kinds of purposes. The r2dictionary introduces a means for users to directly search for definitions of terms within the R environment.
Author: Obinna Obianom [aut, cre]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between r2dictionary versions 0.2 dated 2023-07-16 and 0.3 dated 2025-03-03
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- NEWS.md | 4 ++++ inst/complete.dic |binary inst/doc/simple_samples.html | 4 ++-- man/defineSelected.Rd | 2 +- 6 files changed, 19 insertions(+), 15 deletions(-)
Title: Text Extraction, Rendering and Converting of PDF Documents
Description: Utilities based on 'libpoppler' <https://poppler.freedesktop.org> for extracting
text, fonts, attachments and metadata from a PDF file. Also supports high quality rendering
of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for further
processing in R.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between pdftools versions 3.4.1 dated 2024-09-20 and 3.5.0 dated 2025-03-03
DESCRIPTION | 18 +++++++++--------- MD5 | 6 +++--- NEWS | 3 +++ src/Makevars.win | 42 ++++++++++++++++++++++++------------------ 4 files changed, 39 insertions(+), 30 deletions(-)
Title: Exact Matching and Matching-Adjusted Indirect Comparison (MAIC)
Description: The second version (0.2.0) contains implementation for exact matching which is an alternative to propensity score matching (see Glimm & Yau (2025)). The initial version (0.1.2) contains a collection of easy-to-implement tools for checking whether a MAIC can be conducted, as well as an alternative way of calculating weights (see Glimm & Yau (2021) <doi:10.1002/pst.2210>.)
Author: Lillian Yau [aut, cre],
Ekkehard Glimm [aut],
Xinlei Deng [aut]
Maintainer: Lillian Yau <maicChecks@gmail.com>
Diff between maicChecks versions 0.1.2 dated 2022-01-04 and 0.2.0 dated 2025-03-03
DESCRIPTION | 28 ++++-- MD5 | 51 +++++++----- NAMESPACE | 19 ++-- R/eAD.R | 40 +++++---- R/eIPD.R | 40 +++++---- R/exmLP.2ipd.R |only R/exmWt.2ipd.R |only R/maicChecks-package.R |only R/maicLP.R | 73 ++++++++++++------ R/maicMD.R | 184 +++++++++++++++++++++++++-------------------- R/maicPCA.R | 186 ++++++++++++++++++++++++++-------------------- R/maicT2Test.R | 82 +++++++++++--------- R/maicWt.R | 102 +++++++++++++++---------- R/maxessWt.R | 92 +++++++++++++--------- R/sim110.R |only README.md |only build |only data/eAD.txt | 8 - data/eIPD.txt | 86 ++++++++++----------- data/sim110.rda |only man/eAD.Rd | 47 ++++++----- man/eIPD.Rd | 45 ++++++----- man/exmLP.2ipd.Rd |only man/exmWt.2ipd.Rd |only man/maicChecks-package.Rd |only man/maicLP.Rd | 60 +++++++------- man/maicMD.Rd | 66 +++++++++------- man/maicPCA.Rd | 78 +++++++++---------- man/maicT2Test.Rd | 66 ++++++++-------- man/maicWt.Rd | 67 ++++++++-------- man/maxessWt.Rd | 57 +++++++------- man/sim110.Rd |only 32 files changed, 832 insertions(+), 645 deletions(-)
Title: Generate Simulated Sawn Timber Strength Grading Data
Description: Tools for generating simulated sawn timber
strength grading data with a main focus on statistical simulation based on
covariance matrices. Simulation data
for Norway spruce sawn timber from Austria and reference values of means and
standard deviations of grade determining properties from literature
for a number of European countries are provided, as well.
Author: Andreas Weidenhiller [cre, aut]
,
Anton Wegscheider [aut]
Maintainer: Andreas Weidenhiller <a.weidenhiller@holzforschung.at>
Diff between WoodSimulatR versions 0.6.1 dated 2023-12-04 and 0.6.2 dated 2025-03-03
DESCRIPTION | 10 MD5 | 42 NEWS.md | 113 +- R/data.r | 4 R/stat_sim_dataset.r | 945 ++++++++++----------- R/statistical_simulation.r | 1296 ++++++++++++++--------------- R/subsample_data.r | 436 ++++----- README.md | 7 build/vignette.rds |binary inst/doc/woodsimulatr_basics.Rmd | 1072 +++++++++++------------ inst/doc/woodsimulatr_basics.html | 11 man/gdp_data.Rd | 2 man/get_subsample_definitions.Rd | 6 man/get_transform_names.Rd | 6 man/simbase.Rd | 2 man/simbase_covar.Rd | 12 man/simbase_labeler.Rd | 2 man/simbase_list.Rd | 12 man/simulate_conditionally.Rd | 2 man/simulate_conditionally.simbase_list.Rd | 6 man/simulate_dataset.Rd | 28 vignettes/woodsimulatr_basics.Rmd | 1072 +++++++++++------------ 22 files changed, 2546 insertions(+), 2540 deletions(-)
Title: Gene Locus Plot with Gene Annotations
Description: Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots <doi:10.1093/bioadv/vbaf006>.
Author: Myles Lewis [aut, cre]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between locuszoomr versions 0.3.7 dated 2025-02-10 and 0.3.8 dated 2025-03-03
DESCRIPTION | 6 +- MD5 | 18 +++---- NEWS.md | 4 + R/gg_scatter.R | 2 R/locus.R | 7 ++ inst/doc/locuszoomr.R | 104 ++++++++++++++++++++++++++++++++++--------- inst/doc/locuszoomr.Rmd | 113 ++++++++++++++++++++++++++++++++++++++--------- inst/doc/locuszoomr.html | 53 +++++++--------------- man/locus.Rd | 5 +- vignettes/locuszoomr.Rmd | 113 ++++++++++++++++++++++++++++++++++++++--------- 10 files changed, 311 insertions(+), 114 deletions(-)
Title: 'ade4' Tcl/Tk Graphical User Interface
Description: A Tcl/Tk GUI for some basic functions in the 'ade4' package.
Author: Jean Thioulouse [aut] ,
Stephane Dray [aut] ,
Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between ade4TkGUI versions 0.3-1 dated 2020-12-03 and 0.3.3 dated 2025-03-03
DESCRIPTION | 27 +++++++++++++++++++-------- MD5 | 10 +++++----- NAMESPACE | 30 +++++++++++++++++++++++++++++- R/choose.R | 10 +++++----- R/ordiClust.R | 14 +++++++------- inst/CITATION | 41 +++++++++++++++++------------------------ 6 files changed, 82 insertions(+), 50 deletions(-)
Title: Simulation of Chromosomal Regions Shared by Family Members
Description: Simulation of segments shared identical-by-descent (IBD) by
pedigree members. Using sex specific recombination rates along the
human genome (Halldorsson et al. (2019)
<doi:10.1126/science.aau1043>), phased chromosomes are simulated for
all pedigree members. Applications include calculation of realised
relatedness coefficients and IBD segment distributions. 'ibdsim2' is
part of the 'pedsuite' collection of packages for pedigree analysis.
A detailed presentation of the 'pedsuite', including a separate
chapter on 'ibdsim2', is available in the book 'Pedigree analysis in
R' (Vigeland, 2021, ISBN:9780128244302). A 'Shiny' app for visualising
and comparing IBD distributions is available at
<https://magnusdv.shinyapps.io/ibdsim2-shiny/>.
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between ibdsim2 versions 2.1.1 dated 2024-09-08 and 2.2.0 dated 2025-03-03
DESCRIPTION | 14 +++--- MD5 | 27 ++++++------ NEWS.md | 15 ++++++ R/launchApp.R | 2 R/realisedCoeffs.R | 49 ++++++++++++---------- README.md | 17 +++---- build/partial.rdb |binary inst/shiny/R/plot-functions.R | 2 inst/shiny/R/saveData.R | 8 +-- inst/shiny/app.R | 28 +++++++----- inst/shiny/www/custom.css | 2 inst/shiny/www/scripts.js |only man/figures/README-ibdsim2-example-distplot-1.png |binary man/ibdsim2-package.Rd | 2 man/realised.Rd | 11 +++- 15 files changed, 103 insertions(+), 74 deletions(-)
Title: The Echelon Analysis and the Detection of Spatial Clusters using
Echelon Scan Method
Description: Functions for the echelon analysis proposed by Myers et al. (1997) <doi:10.1023/A:1018518327329>, and the detection of spatial clusters using echelon scan method proposed by Kurihara (2003) <doi:10.20551/jscswabun.15.2_171>.
Author: Fumio Ishioka [aut, cre]
Maintainer: Fumio Ishioka <fishioka@okayama-u.ac.jp>
Diff between echelon versions 0.2.0 dated 2024-02-08 and 0.3.0 dated 2025-03-03
echelon-0.2.0/echelon/R/e.monte.bin.r |only echelon-0.2.0/echelon/R/e.monte.poi.r |only echelon-0.2.0/echelon/R/e.scan.pop.r |only echelon-0.2.0/echelon/man/e.cluster.decision.Rd |only echelon-0.2.0/echelon/man/e.cluster.dendrogram.Rd |only echelon-0.2.0/echelon/man/e.cluster.map.Rd |only echelon-0.2.0/echelon/man/e.dendrogram.Rd |only echelon-0.2.0/echelon/man/e.dendrogram.axis.Rd |only echelon-0.2.0/echelon/man/e.main.Rd |only echelon-0.2.0/echelon/man/e.monte.bin.Rd |only echelon-0.2.0/echelon/man/e.monte.poi.Rd |only echelon-0.2.0/echelon/man/e.profile.Rd |only echelon-0.2.0/echelon/man/e.scan.Rd |only echelon-0.2.0/echelon/man/e.scan.pop.Rd |only echelon-0.2.0/echelon/man/nlimb.Rd |only echelon-0.3.0/echelon/DESCRIPTION | 23 - echelon-0.3.0/echelon/MD5 | 53 -- echelon-0.3.0/echelon/NAMESPACE | 4 echelon-0.3.0/echelon/NEWS.md | 4 echelon-0.3.0/echelon/R/RcppExports.R |only echelon-0.3.0/echelon/R/e.cluster.decision.r | 49 +- echelon-0.3.0/echelon/R/e.cluster.dendrogram.r | 154 +++--- echelon-0.3.0/echelon/R/e.cluster.map.r | 81 +-- echelon-0.3.0/echelon/R/e.dendrogram.axis.r | 74 +-- echelon-0.3.0/echelon/R/e.dendrogram.r | 163 +++---- echelon-0.3.0/echelon/R/e.echebin.r | 480 ++++++++++----------- echelon-0.3.0/echelon/R/e.echelon.r | 357 +++++++-------- echelon-0.3.0/echelon/R/e.echepoi.r | 502 +++++++++++----------- echelon-0.3.0/echelon/R/e.profile.r | 226 ++++----- echelon-0.3.0/echelon/R/e.scan.r | 335 +++++++++----- echelon-0.3.0/echelon/R/e_main.monte.r |only echelon-0.3.0/echelon/R/e_main.r | 342 +++++++------- echelon-0.3.0/echelon/man/echebin.Rd | 34 - echelon-0.3.0/echelon/man/echelon.Rd | 56 +- echelon-0.3.0/echelon/man/echepoi.Rd | 34 - echelon-0.3.0/echelon/src |only 36 files changed, 1543 insertions(+), 1428 deletions(-)
Title: Data on Base and Recommended Packages for Current and Previous
Versions of R
Description: Provides a dataset of functions in all base and recommended packages of R versions 0.50 onwards.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between rcheology versions 4.4.2.0 dated 2024-11-11 and 4.4.3.0 dated 2025-03-03
DESCRIPTION | 8 ++--- MD5 | 14 ++++----- NEWS.md | 5 +++ README.md | 48 ++++++++++++++++--------------- data/Rversions.rda |binary data/rcheology.rda |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary 8 files changed, 41 insertions(+), 34 deletions(-)
Title: Multivariate Bidirectional Mendelian Randomization Networks
Description: Addressing a central challenge encountered in Mendelian randomization (MR) studies, where MR primarily focuses on discerning the effects of individual exposures on specific outcomes and establishes causal links between them. Using a network-based methodology, the intricacy involving interdependent outcomes due to numerous factors has been tackled through this routine. Based on Ni et al. (2018) <doi:10.1214/17-BA1087>, 'MR.RGM' extends to a broader exploration of the causal landscape by leveraging on network structures and involves the construction of causal graphs that capture interactions between response variables and consequently between responses and instrument variables. The resulting Graph visually represents these causal connections, showing directed edges with effect sizes labeled. 'MR.RGM' facilitates the navigation of various data availability scenarios effectively by accommodating three input formats, i.e., individual-level data and two types of summary-level data. In [...truncated...]
Author: Bitan Sarkar [aut, cre],
Yang Ni [aut]
Maintainer: Bitan Sarkar <bitan@tamu.edu>
Diff between MR.RGM versions 0.0.3 dated 2024-09-18 and 0.0.4 dated 2025-03-03
DESCRIPTION | 12 ++++---- MD5 | 13 +++++---- R/CausalNetwork.R |only R/RGM.R | 42 ++++++++++++++++++++---------- README.md | 7 +---- man/RGM.Rd | 38 +++++++++++++++++---------- man/figures/README-unnamed-chunk-13-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary 8 files changed, 69 insertions(+), 43 deletions(-)
Title: Latent Space-Based Transfer Learning
Description: Implements transfer learning methods for low-rank matrix
estimation. These methods leverage similarity in the latent row and column
spaces between the source and target populations to improve estimation in
the target population. The methods include the LatEnt spAce-based tRaNsfer
lEaRning (LEARNER) method and the direct projection LEARNER (D-LEARNER)
method described by McGrath et al. (2024) <doi:10.48550/arXiv.2412.20605>.
Author: Sean McGrath [aut, cre] ,
Ryan ODea [aut],
Cenhao Zhu [aut],
Rui Duan [aut]
Maintainer: Sean McGrath <sean.mcgrath514@gmail.com>
Diff between learner versions 0.1.0 dated 2025-01-08 and 1.0.0 dated 2025-03-03
learner-0.1.0/learner/R/cv_learner.R |only learner-1.0.0/learner/DESCRIPTION | 14 + learner-1.0.0/learner/MD5 | 26 +- learner-1.0.0/learner/NAMESPACE | 5 learner-1.0.0/learner/NEWS.md | 11 + learner-1.0.0/learner/R/RcppExports.R |only learner-1.0.0/learner/R/dlearner.R | 5 learner-1.0.0/learner/R/globals.R | 11 + learner-1.0.0/learner/R/learner-package.R |only learner-1.0.0/learner/R/learner.R | 205 ++++++++++------------- learner-1.0.0/learner/README.md | 11 + learner-1.0.0/learner/man/cv.learner.Rd | 5 learner-1.0.0/learner/src |only learner-1.0.0/learner/tests/testthat/test-main.R | 85 +++++++++ 14 files changed, 240 insertions(+), 138 deletions(-)
Title: R Interface to 'Keras'
Description: Interface to 'Keras' <https://keras.io>, a high-level neural
networks API. 'Keras' was developed with a focus on enabling fast experimentation,
supports both convolution based networks and recurrent networks (as well as
combinations of the two), and runs seamlessly on both CPU and GPU devices.
Author: Tomasz Kalinowski [aut, cph, cre],
Daniel Falbel [ctb, cph],
JJ Allaire [aut, cph],
Francois Chollet [aut, cph],
Posit Software, PBC [cph, fnd],
Google [cph, fnd],
Yuan Tang [ctb, cph] ,
Wouter Van Der Bijl [ctb, cph],
Martin Studer [ctb, cph],
Sigri [...truncated...]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between keras3 versions 1.2.0 dated 2024-09-05 and 1.3.0 dated 2025-03-03
DESCRIPTION | 10 MD5 | 1203 ++++++------- NAMESPACE | 72 NEWS.md | 165 + R/Layer.R | 11 R/Loss.R | 9 R/activations.R | 282 +++ R/applications.R | 8 R/callbacks.R | 26 R/config.R | 75 R/image-utils.R | 2 R/initializers.R | 53 R/install.R | 238 ++ R/layers-attention.R | 25 R/layers-backend-wrappers.R | 2 R/layers-convolutional.R | 2 R/layers-core.R | 4 R/layers-normalization.R | 2 R/layers-preprocessing.R | 1092 +++++++++++ R/layers-rnn.R | 29 R/losses.R | 272 ++ R/metrics.R | 217 ++ R/model-creation.R | 122 + R/model-persistence.R | 211 ++ R/model-training.R | 136 - R/module-tethers.R | 20 R/ops-linalg.R | 4 R/ops-nn.R | 440 ++++ R/ops-numpy.R | 460 ++++ R/ops.R | 59 R/optimizers.R | 6 R/package.R | 28 R/r-utils.R | 16 R/random.R | 214 +- R/reexports.R | 5 R/s3-methods.R | 30 R/utils.R | 18 build/vignette.rds |binary inst/doc/custom_train_step_in_tensorflow.Rmd | 29 inst/doc/custom_train_step_in_tensorflow.html | 29 inst/doc/distribution.Rmd | 20 inst/doc/distribution.html | 20 inst/doc/functional_api.Rmd | 10 inst/doc/functional_api.html | 10 inst/doc/getting_started.Rmd | 2 inst/doc/getting_started.html | 2 inst/doc/intro_to_keras_for_engineers.Rmd | 26 inst/doc/intro_to_keras_for_engineers.html | 26 inst/doc/making_new_layers_and_models_via_subclassing.Rmd | 13 inst/doc/making_new_layers_and_models_via_subclassing.html | 13 inst/doc/sequential_model.Rmd | 7 inst/doc/sequential_model.html | 7 inst/doc/training_with_built_in_methods.Rmd | 78 inst/doc/training_with_built_in_methods.html | 78 inst/doc/transfer_learning.Rmd | 10 inst/doc/transfer_learning.html | 12 inst/doc/writing_a_custom_training_loop_in_tensorflow.Rmd | 42 inst/doc/writing_a_custom_training_loop_in_tensorflow.html | 42 man/Layer.Rd | 26 man/LearningRateSchedule.Rd | 2 man/Loss.Rd | 10 man/Metric.Rd | 2 man/activation_celu.Rd |only man/activation_elu.Rd | 11 man/activation_exponential.Rd | 11 man/activation_gelu.Rd | 11 man/activation_glu.Rd |only man/activation_hard_shrink.Rd |only man/activation_hard_sigmoid.Rd | 11 man/activation_hard_tanh.Rd |only man/activation_leaky_relu.Rd | 11 man/activation_linear.Rd | 11 man/activation_log_sigmoid.Rd |only man/activation_log_softmax.Rd | 11 man/activation_mish.Rd | 11 man/activation_relu.Rd | 11 man/activation_relu6.Rd | 11 man/activation_selu.Rd | 11 man/activation_sigmoid.Rd | 11 man/activation_silu.Rd | 11 man/activation_soft_shrink.Rd |only man/activation_softmax.Rd | 11 man/activation_softplus.Rd | 11 man/activation_softsign.Rd | 11 man/activation_sparse_plus.Rd |only man/activation_sparsemax.Rd |only man/activation_squareplus.Rd |only man/activation_tanh.Rd | 11 man/activation_tanh_shrink.Rd |only man/activation_threshold.Rd |only man/application_densenet121.Rd | 2 man/application_densenet169.Rd | 2 man/application_densenet201.Rd | 2 man/application_resnet50.Rd | 2 man/callback_backup_and_restore.Rd | 8 man/callback_model_checkpoint.Rd | 11 man/callback_tensorboard.Rd | 7 man/config_backend.Rd | 4 man/config_disable_flash_attention.Rd |only man/config_disable_interactive_logging.Rd | 4 man/config_disable_traceback_filtering.Rd | 4 man/config_dtype_policy.Rd | 22 man/config_enable_flash_attention.Rd |only man/config_enable_interactive_logging.Rd | 4 man/config_enable_traceback_filtering.Rd | 4 man/config_enable_unsafe_deserialization.Rd | 4 man/config_epsilon.Rd | 4 man/config_floatx.Rd | 4 man/config_image_data_format.Rd | 4 man/config_is_flash_attention_enabled.Rd |only man/config_is_interactive_logging_enabled.Rd | 4 man/config_is_traceback_filtering_enabled.Rd | 4 man/config_set_backend.Rd | 4 man/config_set_dtype_policy.Rd | 22 man/config_set_epsilon.Rd | 4 man/config_set_floatx.Rd | 4 man/config_set_image_data_format.Rd | 4 man/custom_metric.Rd | 2 man/deserialize_keras_object.Rd | 4 man/evaluate.keras.src.models.model.Model.Rd | 29 man/export_savedmodel.keras.src.models.model.Model.Rd | 54 man/fit.keras.src.models.model.Model.Rd | 87 man/get_config.Rd | 2 man/get_file.Rd | 13 man/get_layer.Rd | 2 man/get_state_tree.Rd |only man/image_from_array.Rd | 2 man/image_load.Rd | 2 man/image_to_array.Rd | 2 man/initializer_constant.Rd | 2 man/initializer_glorot_normal.Rd | 1 man/initializer_glorot_uniform.Rd | 1 man/initializer_he_normal.Rd | 1 man/initializer_he_uniform.Rd | 1 man/initializer_identity.Rd | 2 man/initializer_lecun_normal.Rd | 1 man/initializer_lecun_uniform.Rd | 1 man/initializer_ones.Rd | 2 man/initializer_orthogonal.Rd | 1 man/initializer_random_normal.Rd | 1 man/initializer_random_uniform.Rd | 1 man/initializer_stft.Rd |only man/initializer_truncated_normal.Rd | 1 man/initializer_variance_scaling.Rd | 1 man/initializer_zeros.Rd | 2 man/keras3-package.Rd | 2 man/keras_model.Rd | 2 man/keras_model_sequential.Rd | 2 man/layer_activation.Rd | 15 man/layer_activation_elu.Rd | 15 man/layer_activation_leaky_relu.Rd | 15 man/layer_activation_parametric_relu.Rd | 15 man/layer_activation_relu.Rd | 15 man/layer_activation_softmax.Rd | 15 man/layer_activity_regularization.Rd | 15 man/layer_add.Rd | 15 man/layer_additive_attention.Rd | 15 man/layer_alpha_dropout.Rd | 15 man/layer_attention.Rd | 17 man/layer_auto_contrast.Rd |only man/layer_average.Rd | 15 man/layer_average_pooling_1d.Rd | 15 man/layer_average_pooling_2d.Rd | 15 man/layer_average_pooling_3d.Rd | 15 man/layer_batch_normalization.Rd | 15 man/layer_bidirectional.Rd | 15 man/layer_category_encoding.Rd | 30 man/layer_center_crop.Rd | 44 man/layer_concatenate.Rd | 15 man/layer_conv_1d.Rd | 15 man/layer_conv_1d_transpose.Rd | 15 man/layer_conv_2d.Rd | 15 man/layer_conv_2d_transpose.Rd | 15 man/layer_conv_3d.Rd | 15 man/layer_conv_3d_transpose.Rd | 15 man/layer_conv_lstm_1d.Rd | 15 man/layer_conv_lstm_2d.Rd | 15 man/layer_conv_lstm_3d.Rd | 15 man/layer_cropping_1d.Rd | 15 man/layer_cropping_2d.Rd | 15 man/layer_cropping_3d.Rd | 15 man/layer_dense.Rd | 15 man/layer_depthwise_conv_1d.Rd | 15 man/layer_depthwise_conv_2d.Rd | 19 man/layer_discretization.Rd | 30 man/layer_dot.Rd | 15 man/layer_dropout.Rd | 15 man/layer_einsum_dense.Rd | 15 man/layer_embedding.Rd | 19 man/layer_equalization.Rd |only man/layer_feature_space.Rd | 30 man/layer_flatten.Rd | 15 man/layer_flax_module_wrapper.Rd | 15 man/layer_gaussian_dropout.Rd | 15 man/layer_gaussian_noise.Rd | 15 man/layer_global_average_pooling_1d.Rd | 15 man/layer_global_average_pooling_2d.Rd | 15 man/layer_global_average_pooling_3d.Rd | 15 man/layer_global_max_pooling_1d.Rd | 15 man/layer_global_max_pooling_2d.Rd | 15 man/layer_global_max_pooling_3d.Rd | 15 man/layer_group_normalization.Rd | 15 man/layer_group_query_attention.Rd | 25 man/layer_gru.Rd | 15 man/layer_hashed_crossing.Rd | 30 man/layer_hashing.Rd | 30 man/layer_identity.Rd | 15 man/layer_integer_lookup.Rd | 32 man/layer_jax_model_wrapper.Rd | 17 man/layer_lambda.Rd | 15 man/layer_layer_normalization.Rd | 15 man/layer_lstm.Rd | 15 man/layer_masking.Rd | 15 man/layer_max_num_bounding_boxes.Rd |only man/layer_max_pooling_1d.Rd | 15 man/layer_max_pooling_2d.Rd | 15 man/layer_max_pooling_3d.Rd | 15 man/layer_maximum.Rd | 15 man/layer_mel_spectrogram.Rd | 33 man/layer_minimum.Rd | 15 man/layer_mix_up.Rd |only man/layer_multi_head_attention.Rd | 22 man/layer_multiply.Rd | 15 man/layer_normalization.Rd | 30 man/layer_permute.Rd | 15 man/layer_pipeline.Rd |only man/layer_rand_augment.Rd |only man/layer_random_brightness.Rd | 38 man/layer_random_color_degeneration.Rd |only man/layer_random_color_jitter.Rd |only man/layer_random_contrast.Rd | 43 man/layer_random_crop.Rd | 39 man/layer_random_flip.Rd | 47 man/layer_random_grayscale.Rd |only man/layer_random_hue.Rd |only man/layer_random_posterization.Rd |only man/layer_random_rotation.Rd | 48 man/layer_random_saturation.Rd |only man/layer_random_sharpness.Rd |only man/layer_random_shear.Rd |only man/layer_random_translation.Rd | 30 man/layer_random_zoom.Rd | 30 man/layer_repeat_vector.Rd | 15 man/layer_rescaling.Rd | 44 man/layer_reshape.Rd | 15 man/layer_resizing.Rd | 44 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| 10 man/set_state_tree.Rd |only man/summary.keras.src.models.model.Model.Rd | 2 man/use_backend.Rd | 21 tests/testthat/helper-utils.R | 9 tests/testthat/test-activations.R | 13 tests/testthat/test-layer-text_vectorization.R | 6 tests/testthat/test-layers-preprocessing.R | 1 vignettes/custom_train_step_in_tensorflow.Rmd | 29 vignettes/distribution.Rmd | 20 vignettes/functional_api.Rmd | 10 vignettes/getting_started.Rmd | 2 vignettes/intro_to_keras_for_engineers.Rmd | 26 vignettes/making_new_layers_and_models_via_subclassing.Rmd | 13 vignettes/sequential_model.Rmd | 7 vignettes/training_with_built_in_methods.Rmd | 78 vignettes/transfer_learning.Rmd | 10 vignettes/transfer_learning/unnamed-chunk-17-1.png |binary vignettes/writing_a_custom_training_loop_in_tensorflow.Rmd | 42 635 files changed, 17475 insertions(+), 1546 deletions(-)
Title: Regression Models for Event History Outcomes
Description: A user friendly, easy to understand way of doing event
history regression for marginal estimands of interest,
including the cumulative incidence and the restricted mean
survival, using the pseudo observation framework for
estimation. For a review of the methodology, see Andersen and
Pohar Perme (2010) <doi:10.1177/0962280209105020> or Sachs
and Gabriel (2022) <doi:10.18637/jss.v102.i09>. The
interface uses the well known formulation of a generalized
linear model and allows for features including plotting of
residuals, the use of sampling weights, and corrected
variance estimation.
Author: Michael C Sachs [aut, cre],
Erin E Gabriel [aut],
Morten Overgaard [ctb] ,
Thomas A Gerds [ctb] ,
Terry Therneau [ctb]
Maintainer: Michael C Sachs <sachsmc@gmail.com>
Diff between eventglm versions 1.2.2 dated 2022-04-26 and 1.4.5 dated 2025-03-03
DESCRIPTION | 10 MD5 | 51 NAMESPACE | 1 NEWS.md | 125 +- R/event-model-fit.R | 1121 ++++++++++---------- R/eventglm-package.R | 37 R/pseudo-modules.R | 127 ++ R/pseudoglm-methods.R | 2 R/utils.R | 526 ++++----- README.md | 84 - build/vignette.rds |binary inst/doc/example-analysis.R | 513 ++++----- inst/doc/example-analysis.Rmd | 784 +++++++------- inst/doc/example-analysis.html | 2044 +++++++++++++++++++++---------------- inst/doc/extenstions.R | 188 +-- inst/doc/extenstions.Rmd | 6 inst/doc/extenstions.html | 933 ++++++++++------ inst/doc/stata-sas-comparason.R | 26 inst/doc/stata-sas-comparason.html | 1162 ++++++++++++--------- man/cumincglm.Rd | 11 man/eventglm.Rd | 25 man/pseudo_infjack.Rd |only man/rmeanglm.Rd | 13 src/loo.c | 67 + tests/testthat/test-model-fit.R | 556 ++++++---- vignettes/example-analysis.Rmd | 784 +++++++------- vignettes/extenstions.Rmd | 6 27 files changed, 5242 insertions(+), 3960 deletions(-)
Title: Computes Statistics from Discrimination Experimental Data
Description: In discrimination experiments candidates are sent on the same test (e.g. job, house rental) and one examines whether they receive the same outcome. The number of non negative answers are first examined in details looking for outcome differences. Then various statistics are computed. This package can also be used for analyzing the results from random experiments.
Author: Emmanuel Duguet [aut, cre] ,
David Gray [ctb] ,
Loic du Parquet [dtc],
Yannick L'Horty [ctb] ,
Remi Le Gall [dtc] ,
Noam Leandri [dtc],
Pascale Petit [ctb] ,
Florent Sari [ctb]
Maintainer: Emmanuel Duguet <emmanuel.duguet@u-pec.fr>
Diff between callback versions 0.1.1 dated 2024-07-13 and 0.1.3 dated 2025-03-03
callback-0.1.1/callback/R/callback_graph.R |only callback-0.1.1/callback/inst/doc/getting-started.R |only callback-0.1.1/callback/inst/doc/getting-started.Rmd |only callback-0.1.1/callback/inst/doc/getting-started.html |only callback-0.1.1/callback/man/g_prop.Rd |only callback-0.1.1/callback/man/graph.Rd |only callback-0.1.1/callback/man/graph.stat_ecs.Rd |only callback-0.1.1/callback/man/graph.stat_glob.Rd |only callback-0.1.1/callback/man/graph.stat_mcr.Rd |only callback-0.1.1/callback/man/graph.stat_tcs.Rd |only callback-0.1.1/callback/man/print.stat_count.Rd |only callback-0.1.1/callback/man/print.stat_ecs.Rd |only callback-0.1.1/callback/man/print.stat_glob.Rd |only callback-0.1.1/callback/man/print.stat_prop.Rd |only callback-0.1.1/callback/man/stat_count.Rd |only callback-0.1.1/callback/man/stat_glob.Rd |only callback-0.1.1/callback/vignettes/getting-started.Rmd |only callback-0.1.3/callback/DESCRIPTION | 51 callback-0.1.3/callback/MD5 | 101 callback-0.1.3/callback/NAMESPACE | 30 callback-0.1.3/callback/R/callback.R | 421 - callback-0.1.3/callback/R/callback_comp.R |only callback-0.1.3/callback/R/callback_data.R | 964 ++-- callback-0.1.3/callback/R/callback_misc.R | 2 callback-0.1.3/callback/R/callback_plot.R |only callback-0.1.3/callback/R/callback_print.R | 471 - callback-0.1.3/callback/R/callback_reg.R |only callback-0.1.3/callback/R/callback_stat.R | 2409 +++++----- callback-0.1.3/callback/R/callback_summary.R |only callback-0.1.3/callback/build/vignette.rds |binary callback-0.1.3/callback/data/train1.RData |only callback-0.1.3/callback/data/train2.RData |only callback-0.1.3/callback/inst/doc/callback-components-models.R |only callback-0.1.3/callback/inst/doc/callback-components-models.Rmd |only callback-0.1.3/callback/inst/doc/callback-components-models.html |only callback-0.1.3/callback/inst/doc/callback-presentation.R |only callback-0.1.3/callback/inst/doc/callback-presentation.Rmd |only callback-0.1.3/callback/inst/doc/callback-presentation.html |only callback-0.1.3/callback/man/address1.Rd | 26 callback-0.1.3/callback/man/callback.Rd | 42 callback-0.1.3/callback/man/callback_comp.Rd |only callback-0.1.3/callback/man/g_difp.Rd | 20 callback-0.1.3/callback/man/g_ecs.Rd | 20 callback-0.1.3/callback/man/g_mcr.Rd |only callback-0.1.3/callback/man/g_raw.Rd |only callback-0.1.3/callback/man/g_tcs.Rd | 10 callback-0.1.3/callback/man/gender1.Rd | 42 callback-0.1.3/callback/man/gender2.Rd | 34 callback-0.1.3/callback/man/gender3.Rd | 34 callback-0.1.3/callback/man/gender4.Rd | 34 callback-0.1.3/callback/man/inter1.Rd | 36 callback-0.1.3/callback/man/labour1.Rd | 18 callback-0.1.3/callback/man/labour2.Rd | 18 callback-0.1.3/callback/man/mobility1.Rd | 35 callback-0.1.3/callback/man/origin1.Rd | 52 callback-0.1.3/callback/man/origin2.Rd | 56 callback-0.1.3/callback/man/plot.callback_stat.Rd |only callback-0.1.3/callback/man/print.callback.Rd | 2 callback-0.1.3/callback/man/print.callback_comp.Rd |only callback-0.1.3/callback/man/print.callback_reg.Rd |only callback-0.1.3/callback/man/print.callback_stat.Rd |only callback-0.1.3/callback/man/print.stat_paired.Rd |only callback-0.1.3/callback/man/reg.Rd |only callback-0.1.3/callback/man/reg.callback_comp.Rd |only callback-0.1.3/callback/man/reg_als.Rd |only callback-0.1.3/callback/man/stat_ecs.Rd | 119 callback-0.1.3/callback/man/stat_mcr.Rd | 111 callback-0.1.3/callback/man/stat_paired.Rd |only callback-0.1.3/callback/man/stat_raw.Rd |only callback-0.1.3/callback/man/stat_tcs.Rd | 129 callback-0.1.3/callback/man/summary.callback_reg.Rd |only callback-0.1.3/callback/man/train1.Rd |only callback-0.1.3/callback/man/train2.Rd |only callback-0.1.3/callback/vignettes/callback-components-models.Rmd |only callback-0.1.3/callback/vignettes/callback-presentation.Rmd |only 75 files changed, 2692 insertions(+), 2595 deletions(-)
Title: CAESAR: a Cross-Technology and Cross-Resolution Framework for
Spatial Omics Annotation
Description: Biotechnology in spatial omics has advanced rapidly over the past few years, enhancing both throughput and resolution. However, existing annotation pipelines in spatial omics predominantly rely on clustering methods, lacking the flexibility to integrate extensive annotated information from single-cell RNA sequencing (scRNA-seq) due to discrepancies in spatial resolutions, species, or modalities. Here we introduce the CAESAR suite, an open-source software package that provides image-based spatial co-embedding of locations and genomic features. It uniquely transfers labels from scRNA-seq reference, enabling the annotation of spatial omics datasets across different technologies, resolutions, species, and modalities, based on the conserved relationship between signature genes and cells/locations at an appropriate level of granularity. Notably, CAESAR enriches location-level pathways, allowing for the detection of gradual biological pathway activation within spatially defined domain types. [...truncated...]
Author: Xiao Zhang [aut, cre],
Wei Liu [aut],
Jin Liu [aut]
Maintainer: Xiao Zhang <zhangxiao1994@cuhk.edu.cn>
Diff between CAESAR.Suite versions 0.1.0 dated 2024-09-16 and 0.2.0 dated 2025-03-03
DESCRIPTION | 6 MD5 | 16 - R/CAESAR_enrich_pathway.R | 22 +- R/caesar_annotation.R | 20 + R/caesar_enrichscore.R | 20 + README.md | 1 build/vignette.rds |binary inst/doc/STMOB.html | 374 ++++++++++++++++++----------------- inst/doc/XeniumBC.html | 479 +++++++++++++++++++++++----------------------- 9 files changed, 499 insertions(+), 439 deletions(-)
Title: Streamlines the Process of Fitting Areal Spatial Models
Description: Helpers for addressing the issue of disconnected spatial units.
It allows for convenient adding and removal of neighbourhood connectivity between areal units prior to modelling, with the visual aid of maps.
Post-modelling, it reduces the human workload for extracting, tidying and mapping predictions from areal models.
Author: Kevin Horan [aut, cre, cph] ,
Katarina Domijan [aut, ths] ,
Chris Brunsdon [aut, ths]
Maintainer: Kevin Horan <kevin.horan.2021@mumail.ie>
Diff between sfislands versions 1.1.0 dated 2025-03-01 and 1.1.2 dated 2025-03-03
DESCRIPTION | 6 +++--- MD5 | 4 ++-- NEWS.md | 5 +++++ 3 files changed, 10 insertions(+), 5 deletions(-)
Title: Matching Methods for Causal Inference with Time-Series
Cross-Sectional Data
Description: Implements a set of methodological tools
that enable researchers to apply matching methods to
time-series cross-sectional data. Imai, Kim, and Wang
(2023) <http://web.mit.edu/insong/www/pdf/tscs.pdf>
proposes a nonparametric generalization of the
difference-in-differences estimator, which does not rely
on the linearity assumption as often done in
practice. Researchers first select a method of matching
each treated observation for a given unit in a
particular time period with control observations from
other units in the same time period that have a similar
treatment and covariate history. These methods include
standard matching methods based on propensity score and
Mahalanobis distance, as well as weighting methods. Once
matching and refinement is done,
treatment effects can be estimated with
standard errors. The package also offers diagnostics for researchers to assess the quality
of their results.
Author: In Song Kim [aut, cre],
Adam Rauh [aut],
Erik Wang [aut],
Kosuke Imai [aut]
Maintainer: In Song Kim <insong@mit.edu>
Diff between PanelMatch versions 2.2.0 dated 2024-06-04 and 3.0.0 dated 2025-03-03
PanelMatch-2.2.0/PanelMatch/R/balance_scatter.R |only PanelMatch-2.2.0/PanelMatch/inst/doc/matched_set_objects.R |only PanelMatch-2.2.0/PanelMatch/inst/doc/matched_set_objects.Rmd |only PanelMatch-2.2.0/PanelMatch/inst/doc/matched_set_objects.html |only PanelMatch-2.2.0/PanelMatch/inst/doc/using_panelmatch.R |only PanelMatch-2.2.0/PanelMatch/inst/doc/using_panelmatch.Rmd |only PanelMatch-2.2.0/PanelMatch/inst/doc/using_panelmatch.pdf |only PanelMatch-2.2.0/PanelMatch/man/balance_scatter.Rd |only PanelMatch-2.2.0/PanelMatch/vignettes/matched_set_objects.Rmd |only PanelMatch-2.2.0/PanelMatch/vignettes/using_panelmatch.Rmd |only PanelMatch-3.0.0/PanelMatch/DESCRIPTION | 8 PanelMatch-3.0.0/PanelMatch/MD5 | 144 + PanelMatch-3.0.0/PanelMatch/NAMESPACE | 21 PanelMatch-3.0.0/PanelMatch/R/DisplayTreatment.R | 82 PanelMatch-3.0.0/PanelMatch/R/PanelBalance.R |only PanelMatch-3.0.0/PanelMatch/R/PanelData.R |only PanelMatch-3.0.0/PanelMatch/R/PanelEstimate.R | 93 - PanelMatch-3.0.0/PanelMatch/R/PanelEstimateObject.R | 139 + PanelMatch-3.0.0/PanelMatch/R/PanelMatch-package.R | 7 PanelMatch-3.0.0/PanelMatch/R/PanelMatch.R | 174 -- PanelMatch-3.0.0/PanelMatch/R/PanelMatchObject.R |only PanelMatch-3.0.0/PanelMatch/R/bootstrap_placebo.R | 5 PanelMatch-3.0.0/PanelMatch/R/calculate_estimates.R | 10 PanelMatch-3.0.0/PanelMatch/R/calculate_placebo_estimates.R | 7 PanelMatch-3.0.0/PanelMatch/R/data.R | 2 PanelMatch-3.0.0/PanelMatch/R/data_preprocessing.R | 17 PanelMatch-3.0.0/PanelMatch/R/do_exact_matching.R | 2 PanelMatch-3.0.0/PanelMatch/R/enforce_lead_restrictions.R | 1 PanelMatch-3.0.0/PanelMatch/R/estimation_components.R | 6 PanelMatch-3.0.0/PanelMatch/R/get_covariate_balance.R | 225 +- PanelMatch-3.0.0/PanelMatch/R/get_set_treatment_effects.R | 31 PanelMatch-3.0.0/PanelMatch/R/handle_moderating_variable.R | 3 PanelMatch-3.0.0/PanelMatch/R/listwise_delete.R | 74 PanelMatch-3.0.0/PanelMatch/R/matched_set_helpers.r | 10 PanelMatch-3.0.0/PanelMatch/R/matched_set_obj.R | 330 ++- PanelMatch-3.0.0/PanelMatch/R/perform_refinement.R | 55 PanelMatch-3.0.0/PanelMatch/R/placebo_test.R | 97 - PanelMatch-3.0.0/PanelMatch/R/point_estimates.R | 2 PanelMatch-3.0.0/PanelMatch/R/prepare_data.R | 2 PanelMatch-3.0.0/PanelMatch/R/standard_errors.R | 23 PanelMatch-3.0.0/PanelMatch/R/weighting_refinement.R | 40 PanelMatch-3.0.0/PanelMatch/build/vignette.rds |binary PanelMatch-3.0.0/PanelMatch/inst/doc/panelmatch-overview.R |only PanelMatch-3.0.0/PanelMatch/inst/doc/panelmatch-overview.Rmd |only PanelMatch-3.0.0/PanelMatch/inst/doc/panelmatch-overview.pdf |only PanelMatch-3.0.0/PanelMatch/man/DisplayTreatment.Rd | 41 PanelMatch-3.0.0/PanelMatch/man/PanelData.Rd |only PanelMatch-3.0.0/PanelMatch/man/PanelEstimate.Rd | 37 PanelMatch-3.0.0/PanelMatch/man/PanelMatch-package.Rd | 7 PanelMatch-3.0.0/PanelMatch/man/PanelMatch.Rd | 69 PanelMatch-3.0.0/PanelMatch/man/dem.Rd | 2 PanelMatch-3.0.0/PanelMatch/man/distances.Rd |only PanelMatch-3.0.0/PanelMatch/man/distances.matched.set.Rd |only PanelMatch-3.0.0/PanelMatch/man/enforce_lead_restrictions.Rd | 1 PanelMatch-3.0.0/PanelMatch/man/extract.PanelMatch.Rd |only PanelMatch-3.0.0/PanelMatch/man/extract.Rd |only PanelMatch-3.0.0/PanelMatch/man/get_covariate_balance.Rd | 55 PanelMatch-3.0.0/PanelMatch/man/get_set_treatment_effects.Rd | 27 PanelMatch-3.0.0/PanelMatch/man/get_unrefined_balance.PanelBalance.Rd |only PanelMatch-3.0.0/PanelMatch/man/get_unrefined_balance.Rd |only PanelMatch-3.0.0/PanelMatch/man/handle_moderating_variable.Rd | 5 PanelMatch-3.0.0/PanelMatch/man/matched_set.Rd | 7 PanelMatch-3.0.0/PanelMatch/man/perunitSum.Rd | 1 PanelMatch-3.0.0/PanelMatch/man/perunitSum_Dit.Rd | 1 PanelMatch-3.0.0/PanelMatch/man/placebo_test.Rd | 38 PanelMatch-3.0.0/PanelMatch/man/plot.PanelBalance.Rd |only PanelMatch-3.0.0/PanelMatch/man/plot.PanelData.Rd |only PanelMatch-3.0.0/PanelMatch/man/plot.PanelEstimate.Rd | 17 PanelMatch-3.0.0/PanelMatch/man/plot.PanelMatch.Rd |only PanelMatch-3.0.0/PanelMatch/man/plot.matched.set.Rd | 67 PanelMatch-3.0.0/PanelMatch/man/plot_matched_set.Rd |only PanelMatch-3.0.0/PanelMatch/man/print.PanelBalance.Rd |only PanelMatch-3.0.0/PanelMatch/man/print.PanelData.Rd |only PanelMatch-3.0.0/PanelMatch/man/print.PanelEstimate.Rd |only PanelMatch-3.0.0/PanelMatch/man/print.PanelMatch.Rd |only PanelMatch-3.0.0/PanelMatch/man/print.matched.set.Rd | 24 PanelMatch-3.0.0/PanelMatch/man/sub-.PanelBalance.Rd |only PanelMatch-3.0.0/PanelMatch/man/sub-.matched.set.Rd |only PanelMatch-3.0.0/PanelMatch/man/summary.PanelBalance.Rd |only PanelMatch-3.0.0/PanelMatch/man/summary.PanelData.Rd |only PanelMatch-3.0.0/PanelMatch/man/summary.PanelEstimate.Rd | 33 PanelMatch-3.0.0/PanelMatch/man/summary.PanelMatch.Rd |only PanelMatch-3.0.0/PanelMatch/man/summary.matched.set.Rd | 20 PanelMatch-3.0.0/PanelMatch/man/weights.Rd |only PanelMatch-3.0.0/PanelMatch/man/weights.matched.set.Rd |only PanelMatch-3.0.0/PanelMatch/tests/manual_tests/test-MSM_methods.R |only PanelMatch-3.0.0/PanelMatch/tests/manual_tests/test-PanelData.R |only PanelMatch-3.0.0/PanelMatch/tests/manual_tests/test-PanelEstimate.R |only PanelMatch-3.0.0/PanelMatch/tests/manual_tests/test-PanelEstimateObject.R |only PanelMatch-3.0.0/PanelMatch/tests/manual_tests/test-PanelMatch.R | 853 ++-------- PanelMatch-3.0.0/PanelMatch/tests/manual_tests/test-PanelMatchObject.R |only PanelMatch-3.0.0/PanelMatch/tests/manual_tests/test-get_covariate_balance.R |only PanelMatch-3.0.0/PanelMatch/tests/manual_tests/test-machedsetobject.R |only PanelMatch-3.0.0/PanelMatch/tests/manual_tests/test-placebo_test.R |only PanelMatch-3.0.0/PanelMatch/tests/manual_tests/test-summary_PanelEstimate.R |only PanelMatch-3.0.0/PanelMatch/tests/testthat/test-PanelMatch.R | 52 PanelMatch-3.0.0/PanelMatch/vignettes/panelmatch-overview.Rmd |only 97 files changed, 1340 insertions(+), 1627 deletions(-)
Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre] ,
Hadley Wickham [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 1.1.1 dated 2025-02-07 and 1.1.2 dated 2025-03-02
renv-1.1.1/renv/inst/repos/src/contrib/renv_1.1.1.tar.gz |only renv-1.1.2/renv/DESCRIPTION | 6 renv-1.1.2/renv/MD5 | 110 +++++++-------- renv-1.1.2/renv/NAMESPACE | 1 renv-1.1.2/renv/NEWS.md | 26 +++ renv-1.1.2/renv/R/abi.R | 4 renv-1.1.2/renv/R/aliases.R | 8 - renv-1.1.2/renv/R/available-packages.R | 2 renv-1.1.2/renv/R/bioconductor.R | 75 +++++----- renv-1.1.2/renv/R/cache.R | 12 - renv-1.1.2/renv/R/caution.R | 14 - renv-1.1.2/renv/R/clean.R | 12 - renv-1.1.2/renv/R/config-defaults.R | 9 + renv-1.1.2/renv/R/dependencies.R | 2 renv-1.1.2/renv/R/diagnostics.R | 16 ++ renv-1.1.2/renv/R/download.R | 3 renv-1.1.2/renv/R/equip-macos.R | 4 renv-1.1.2/renv/R/extsoft.R | 4 renv-1.1.2/renv/R/hydrate.R | 4 renv-1.1.2/renv/R/install.R | 15 +- renv-1.1.2/renv/R/library.R | 2 renv-1.1.2/renv/R/load.R | 26 --- renv-1.1.2/renv/R/lockfile-read.R | 2 renv-1.1.2/renv/R/mask.R | 7 renv-1.1.2/renv/R/migrate.R | 2 renv-1.1.2/renv/R/platform.R | 27 +++ renv-1.1.2/renv/R/properties.R | 6 renv-1.1.2/renv/R/purge.R | 4 renv-1.1.2/renv/R/python-virtualenv.R | 4 renv-1.1.2/renv/R/rehash.R | 2 renv-1.1.2/renv/R/repair.R | 2 renv-1.1.2/renv/R/restore.R | 7 renv-1.1.2/renv/R/retrieve.R | 4 renv-1.1.2/renv/R/snapshot.R | 32 ++-- renv-1.1.2/renv/R/status.R | 2 renv-1.1.2/renv/R/sysreqs.R |only renv-1.1.2/renv/R/tests.R | 12 - renv-1.1.2/renv/R/update.R | 4 renv-1.1.2/renv/R/upgrade.R | 14 + renv-1.1.2/renv/R/zzz.R | 12 - renv-1.1.2/renv/inst/config.yml | 8 + renv-1.1.2/renv/inst/repos/src/contrib/PACKAGES | 4 renv-1.1.2/renv/inst/repos/src/contrib/PACKAGES.gz |binary renv-1.1.2/renv/inst/repos/src/contrib/PACKAGES.rds |binary renv-1.1.2/renv/inst/repos/src/contrib/renv_1.1.2.tar.gz |only renv-1.1.2/renv/inst/sysreqs |only renv-1.1.2/renv/man/config.Rd | 2 renv-1.1.2/renv/man/sysreqs.Rd |only renv-1.1.2/renv/man/upgrade.Rd | 12 + renv-1.1.2/renv/tests/testthat/_snaps/caution.md | 6 renv-1.1.2/renv/tests/testthat/helper-setup.R | 24 ++- renv-1.1.2/renv/tests/testthat/test-caution.R | 12 - renv-1.1.2/renv/tests/testthat/test-init.R | 5 renv-1.1.2/renv/tests/testthat/test-internal.R | 2 renv-1.1.2/renv/tests/testthat/test-lockfile.R | 24 +++ renv-1.1.2/renv/tests/testthat/test-reload.R | 3 renv-1.1.2/renv/tests/testthat/test-remotes.R | 1 renv-1.1.2/renv/tests/testthat/test-snapshot.R | 14 + renv-1.1.2/renv/tests/testthat/test-sysreqs.R |only 59 files changed, 400 insertions(+), 215 deletions(-)
Title: Election Vote Counting
Description: Counting election votes and determining election results by different methods, including
the single transferable vote or ranked choice, approval, score, plurality, condorcet and two-round
runoff methods (Raftery et al., 2021 <doi:10.32614/RJ-2021-086>).
Author: Hana Sevcikova [aut, cre],
Bernard Silverman [aut],
Adrian Raftery [aut]
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between vote versions 2.4-3 dated 2023-12-10 and 2.4-4 dated 2025-03-02
ChangeLog | 4 ++++ DESCRIPTION | 27 ++++++++++++++++++++------- MD5 | 16 ++++++++-------- R/stv.R | 6 ++++-- build/partial.rdb |binary data/ims_approval.rda |binary data/ims_plurality.rda |binary data/ims_score.rda |binary data/ims_stv.rda |binary 9 files changed, 36 insertions(+), 17 deletions(-)
Title: Forest Yield Tables for Northwest Germany and their Application
Description: The new yield tables developed by the Northwest German Forest
Research Institute (NW-FVA) provide a forest management tool for the five
main commercial tree species oak, beech, spruce, Douglas-fir and pine for
northwestern Germany. The new method applied for deriving yield tables
combines measurements of growth and yield trials with growth simulations
using a state-of-the-art single-tree growth simulator. By doing so, the new
yield tables reflect the current increment level and the recommended
graduated thinning from above is the underlying management concept. The yield
tables are provided along with methods for deriving the site index and for
interpolating between age and site indices and extrapolating beyond age and
site index ranges. The inter-/extrapolations are performed traditionally by
the rule of proportion or with a functional approach.
Author: Robert Nuske [aut, cre] ,
Kai Staupendahl [aut] ,
Matthias Albert [aut] ,
Nordwestdeutsche Forstliche Versuchsanstalt [cph, fnd]
Maintainer: Robert Nuske <robert.nuske@mailbox.org>
Diff between et.nwfva versions 0.1.1 dated 2022-11-22 and 0.2.0 dated 2025-03-02
DESCRIPTION | 10 +- LICENSE |only MD5 | 40 ++++++----- NEWS.md | 7 ++ R/bonitieren.R | 29 +++++--- R/bontrans.R | 7 +- R/hoehen.R | 55 ++++++++++------ R/klassisches.R | 8 ++ R/tafel.R | 21 ++++-- README.md | 13 +++ build/vignette.rds |binary inst/doc/beispiele.R | 2 inst/doc/beispiele.html | 132 +++++++++++++++++++++++---------------- inst/doc/nutzerhinweise.html | 29 ++++++++ inst/doc/vergleich_methoden.R | 2 inst/doc/vergleich_methoden.html | 32 +++++++++ inst/tinytest/test_issues.R |only inst/tinytest/test_tafel.R | 8 ++ man/et_bonitaet.Rd | 8 +- man/et_bontrans.Rd | 7 +- man/et_hoehe.Rd | 32 +++++---- man/et_tafel.Rd | 9 +- 22 files changed, 310 insertions(+), 141 deletions(-)
Title: Random Fields on Metric Graphs
Description: Facilitates creation and manipulation of metric graphs, such as street or river networks. Further facilitates operations and visualizations of data on metric graphs, and the creation of a large class of random fields and stochastic partial differential equations on such spaces. These random fields can be used for simulation, prediction and inference. In particular, linear mixed effects models including random field components can be fitted to data based on computationally efficient sparse matrix representations. Interfaces to the R packages 'INLA' and 'inlabru' are also provided, which facilitate working with Bayesian statistical models on metric graphs. The main references for the methods are Bolin, Simas and Wallin (2024) <doi:10.3150/23-BEJ1647>, Bolin, Kovacs, Kumar and Simas (2023) <doi:10.1090/mcom/3929> and Bolin, Simas and Wallin (2023) <doi:10.48550/arXiv.2304.03190> and <doi:10.48550/arXiv.2304.10372>.
Author: David Bolin [cre, aut],
Alexandre Simas [aut],
Jonas Wallin [aut]
Maintainer: David Bolin <davidbolin@gmail.com>
Diff between MetricGraph versions 1.4.0 dated 2024-12-13 and 1.4.1 dated 2025-03-02
DESCRIPTION | 8 MD5 | 25 +- NAMESPACE | 4 NEWS.md | 5 R/RcppExports.R | 4 R/metric_graph.R | 465 +++++++++++++++++++++++++----------------- R/psp_to_metricgraph.R |only R/selected_inv.R |only R/util.R | 239 ++++++++------------- inst/CITATION | 7 inst/doc/MetricGraph_pkg.html | 4 man/linnet.to.graph.Rd |only man/psp.to.graph.Rd |only man/selected_inv.Rd |only man/stlpp.to.graph.Rd |only src/RcppExports.cpp | 12 + src/selected_inv.cpp |only 17 files changed, 432 insertions(+), 341 deletions(-)
Title: An Extension of 'Tidymodels' Supporting Offset Terms
Description: Extend the 'tidymodels' ecosystem <https://www.tidymodels.org/> to
enable the creation of predictive models with offset terms. Models with
offsets are most useful when working with count data or when fitting an
adjustment model on top of an existing model with a prior expectation.
The former situation is common in insurance where data is often weighted by
exposures. The latter is common in life insurance where industry mortality
tables are often used as a starting point for setting assumptions.
Author: Matt Heaphy [aut, cre, cph]
Maintainer: Matt Heaphy <mattrmattrs@gmail.com>
Diff between offsetreg versions 1.1.0 dated 2024-04-11 and 1.1.1 dated 2025-03-02
DESCRIPTION | 10 MD5 | 36 +-- NEWS.md | 4 R/boost_tree_offset.R | 2 R/glm.R | 174 ++++++++------- R/glmnet.R | 140 ++++++------ R/poisson_reg_offset.R | 2 R/rpart.R | 162 +++++++------- R/us_deaths.R | 2 R/xgboost.R | 528 ++++++++++++++++++++++++------------------------ build/vignette.rds |binary inst/doc/usage.R | 4 inst/doc/usage.html | 56 ++--- man/glm_offset.Rd | 8 man/glmnet_offset.Rd | 8 man/rpart_exposure.Rd | 6 man/us_deaths.Rd | 2 man/xgb_train_offset.Rd | 16 - tests/testthat.R | 1 19 files changed, 590 insertions(+), 571 deletions(-)
Title: Comparing and Visualizing Differences Between Surveys
Description: Easily analyze and visualize differences between samples (e.g., benchmark comparisons, nonresponse comparisons in surveys) on three levels. The comparisons can be univariate, bivariate or multivariate. On univariate level the variables of interest of a survey and a comparison survey (i.e. benchmark) are compared, by calculating one of several difference measures (e.g., relative difference in mean), and an average difference between the surveys. On bivariate level a function can calculate significant differences in correlations for the surveys. And on multivariate levels a function can calculate significant differences in model coefficients between the surveys of comparison. All of those differences can be easily plotted and outputted as a table. For more detailed information on the methods and example use see Rohr, B., Silber, H., & Felderer, B. (2024). Comparing the Accuracy of Univariate, Bivariate, and Multivariate Estimates across Probability and Nonprobability Surveys with Po [...truncated...]
Author: Bjoern Rohr [aut, cre, cph],
Barbara Felderer [aut]
Maintainer: Bjoern Rohr <bjoern.rohr@gesis.org>
Diff between sampcompR versions 0.2.6 dated 2024-12-08 and 0.3.0 dated 2025-03-02
DESCRIPTION | 10 MD5 | 25 NAMESPACE | 4 NEWS.md | 14 R/Bivdiff.R | 42 - R/Bivdiff_Plot.R | 1685 +++++++++---------------------------------- R/Multidiff.R | 11 R/Multidiff_Plot.R | 4 R/Output_Tables.R | 427 +++++++++- R/Unidiff.R | 21 R/Unidiff_Plot.R | 2 man/biv_bias_per_variable.Rd |only man/heatmap_biv_compare.Rd |only man/missing_table.Rd |only man/plot_biv_compare.Rd | 2 15 files changed, 823 insertions(+), 1424 deletions(-)
Title: A Fast, User-Friendly Implementation of Self-Organizing Maps
(SOMs)
Description: Methods for building self-organizing maps (SOMs) with a number of distinguishing features such automatic centroid detection and cluster visualization using starbursts. For more details see the paper "Improved Interpretability of the Unified Distance Matrix with Connected Components" by Hamel and Brown (2011) in <ISBN:1-60132-168-6>. The package provides user-friendly access to two models we construct: (a) a SOM model and (b) a centroid based clustering model. The package also exposes a number of quality metrics for the quantitative evaluation of the map, Hamel (2016) <doi:10.1007/978-3-319-28518-4_4>. Finally, we reintroduced our fast, vectorized training algorithm for SOM with substantial improvements. It is about an order of magnitude faster than the canonical, stochastic C implementation <doi:10.1007/978-3-030-01057-7_60>.
Author: Lutz Hamel [aut, cre],
Benjamin Ott [aut],
Gregory Breard [aut],
Robert Tatoian [aut],
Michael Eiger [aut],
Vishakh Gopu [aut]
Maintainer: Lutz Hamel <lutzhamel@uri.edu>
Diff between popsom7 versions 7.0.0 dated 2025-02-19 and 7.1.0 dated 2025-03-02
popsom7-7.0.0/popsom7/tests/testthat/Rplots.pdf |only popsom7-7.1.0/popsom7/DESCRIPTION | 16 +-- popsom7-7.1.0/popsom7/MD5 | 18 ++- popsom7-7.1.0/popsom7/NAMESPACE | 2 popsom7-7.1.0/popsom7/NEWS.md | 6 + popsom7-7.1.0/popsom7/R/maputils.R | 100 ++++++++++++++++---- popsom7-7.1.0/popsom7/man/map.significance.Rd | 9 - popsom7-7.1.0/popsom7/src |only popsom7-7.1.0/popsom7/tests/testthat/test-build.R | 2 popsom7-7.1.0/popsom7/tests/testthat/test-summary.R | 2 10 files changed, 108 insertions(+), 47 deletions(-)
Title: Sensitivities of Prices of Financial Options and Implied
Volatilities
Description: Methods to calculate sensitivities of financial option prices for
European, geometric and arithmetic Asian, and American options, with various
payoff functions in the Black Scholes model, and in more general jump diffusion
models. A shiny app to interactively plot the results is included. Furthermore,
methods to compute implied volatilities are provided for a wide range of option
types and custom payoff functions. Classical formulas are implemented for
European options in the Black Scholes Model, as is presented in Hull, J. C.
(2017), Options, Futures, and Other Derivatives.
In the case of Asian options, Malliavin Monte Carlo Greeks are implemented, see
Hudde, A. & Rüschendorf, L. (2023). European and Asian Greeks for exponential
Lévy processes. <doi:10.1007/s11009-023-10014-5>. For American
options, the Binomial Tree Method is implemented, as is presented in Hull,
J. C. (2017).
Author: Anselm Hudde [aut, cre]
Maintainer: Anselm Hudde <anselmhudde@gmx.de>
Diff between greeks versions 1.4.3 dated 2024-09-17 and 1.4.4 dated 2025-03-02
DESCRIPTION | 6 +-- MD5 | 8 ++--- R/Greeks_UI.R | 4 +- R/Malliavin_Geometric_Asian_Greeks.R | 26 +++++++++-------- tests/testthat/test-Malliavin_Geometric_Asian_Greeks.R | 2 - 5 files changed, 24 insertions(+), 22 deletions(-)
Title: Quick and Essential 'R' Tricks for Better Scripts
Description: The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to improve your scripts. Improve the quality and reproducibility of 'R' scripts.
Author: Obinna Obianom [aut, cre],
Brice Richard [aut]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between quickcode versions 1.0.5 dated 2025-02-03 and 1.0.6 dated 2025-03-02
DESCRIPTION | 6 +- MD5 | 53 ++++++++++++------- NAMESPACE | 30 +++++++++++ NEWS.md | 6 ++ R/aaa.R | 10 +-- R/aided_chatgpt.R |only R/date.R | 2 R/detect_outlier.R |only R/github.R | 4 + R/pkg_by.R | 4 - R/track.R | 17 +++++- R/trim_file.R |only README.md | 28 ++++++++-- inst/doc/add_today_date_to_filenames_quickcode.html | 54 ++++++++++---------- inst/doc/nullish_coalescing_operator_r.html | 4 - inst/doc/quickcode_r_introduction.html | 4 - inst/doc/track_function_usage_r.html | 4 - inst/rstudio/addins.dcf | 5 + man/cols.rep.Rd |only man/date_tweaks.Rd | 4 + man/detect_outlier2.Rd |only man/find_packages.Rd | 4 - man/from_tensor_slices.Rd |only man/github-tweaks.Rd | 4 + man/learn_rate_scheduler.Rd |only man/mode.calc.Rd |only man/multihead_att.Rd |only man/na.cumsum.Rd |only man/normalize.vector.Rd |only man/outlierdetect1.Rd |only man/rows.rep.Rd |only man/simplechaining.Rd | 4 - man/sub.range.Rd |only man/track_func.Rd | 18 +++++- man/trim.file.Rd |only 35 files changed, 187 insertions(+), 78 deletions(-)
Title: Processing METAR Weather Reports
Description: Allows to download current and historical METAR weather reports
extract and parse basic parameters and present main weather information.
Current reports are downloaded from Aviation Weather Center
<https://aviationweather.gov/data/metar/> and historical reports from
Iowa Environmental Mesonet web page of Iowa State University
ASOS-AWOS-METAR <http://mesonet.agron.iastate.edu/AWOS/>.
Author: Pawel Cwiek [aut, cre],
David Megginson [ctb] ,
Greg Thompson [ctb]
Maintainer: Pawel Cwiek <prc.altodato@gmail.com>
Diff between pmetar versions 0.5.0 dated 2023-10-25 and 0.5.1 dated 2025-03-02
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/metar_decode.R | 4 +++- R/pmetar-package.R | 2 +- README.md | 3 ++- build/vignette.rds |binary data/ourairports.rda |binary inst/doc/pmetar.R | 8 ++++---- inst/doc/pmetar.html | 28 ++++++++++++++-------------- man/mst.Rd | 2 +- tests/testthat/test_metar_location.R | 2 +- 11 files changed, 40 insertions(+), 37 deletions(-)
Title: Likelihood-Free Parameter Estimation using Neural Networks
Description: An 'R' interface to the 'Julia' package 'NeuralEstimators.jl'. The package facilitates the user-friendly development of neural Bayes estimators, which are neural networks that map data to a point summary of the posterior distribution (Sainsbury-Dale et al., 2024, <doi:10.1080/00031305.2023.2249522>). These estimators are likelihood-free and amortised, in the sense that, once the neural networks are trained on simulated data, inference from observed data can be made in a fraction of the time required by conventional approaches. The package also supports amortised Bayesian or frequentist inference using neural networks that approximate the posterior or likelihood-to-evidence ratio (Zammit-Mangion et al., 2025, Sec. 3.2, 5.2, <doi:10.48550/arXiv.2404.12484>). The package accommodates any model for which simulation is feasible by allowing users to define models implicitly through simulated data.
Author: Matthew Sainsbury-Dale [aut, cre]
Maintainer: Matthew Sainsbury-Dale <msainsburydale@gmail.com>
Diff between NeuralEstimators versions 0.1.3 dated 2025-01-14 and 0.2.0 dated 2025-03-02
NeuralEstimators-0.1.3/NeuralEstimators/man/initialise_estimator.Rd |only NeuralEstimators-0.1.3/NeuralEstimators/man/loadweights.Rd |only NeuralEstimators-0.1.3/NeuralEstimators/man/mapestimate.Rd |only NeuralEstimators-0.1.3/NeuralEstimators/man/mlestimate.Rd |only NeuralEstimators-0.1.3/NeuralEstimators/man/spatialgraphlist.Rd |only NeuralEstimators-0.2.0/NeuralEstimators/DESCRIPTION | 12 NeuralEstimators-0.2.0/NeuralEstimators/MD5 | 54 NeuralEstimators-0.2.0/NeuralEstimators/NAMESPACE | 6 NeuralEstimators-0.2.0/NeuralEstimators/R/NeuralEstimators.R | 4 NeuralEstimators-0.2.0/NeuralEstimators/R/core.R | 403 -- NeuralEstimators-0.2.0/NeuralEstimators/R/missingdata.R | 172 - NeuralEstimators-0.2.0/NeuralEstimators/README.md | 15 NeuralEstimators-0.2.0/NeuralEstimators/inst/doc/NeuralEstimators.html | 1416 +++++----- NeuralEstimators-0.2.0/NeuralEstimators/man/NeuralEstimators-package.Rd | 11 NeuralEstimators-0.2.0/NeuralEstimators/man/assess.Rd | 12 NeuralEstimators-0.2.0/NeuralEstimators/man/bias.Rd | 4 NeuralEstimators-0.2.0/NeuralEstimators/man/bootstrap.Rd | 31 NeuralEstimators-0.2.0/NeuralEstimators/man/encodedata.Rd | 9 NeuralEstimators-0.2.0/NeuralEstimators/man/estimate.Rd | 32 NeuralEstimators-0.2.0/NeuralEstimators/man/loadstate.Rd | 6 NeuralEstimators-0.2.0/NeuralEstimators/man/posteriormode.Rd |only NeuralEstimators-0.2.0/NeuralEstimators/man/risk.Rd | 2 NeuralEstimators-0.2.0/NeuralEstimators/man/rmse.Rd | 4 NeuralEstimators-0.2.0/NeuralEstimators/man/sampleposterior.Rd | 29 NeuralEstimators-0.2.0/NeuralEstimators/man/spatialgraph.Rd | 55 NeuralEstimators-0.2.0/NeuralEstimators/man/tanhloss.Rd | 2 NeuralEstimators-0.2.0/NeuralEstimators/man/train.Rd | 28 NeuralEstimators-0.2.0/NeuralEstimators/tests/testthat.R | 10 NeuralEstimators-0.2.0/NeuralEstimators/tests/testthat/test-core.R | 41 NeuralEstimators-0.2.0/NeuralEstimators/tests/testthat/test-missingdata.R | 115 NeuralEstimators-0.2.0/NeuralEstimators/tests/testthat/test-plotting.R | 35 31 files changed, 1192 insertions(+), 1316 deletions(-)
More information about NeuralEstimators at CRAN
Permanent link
Title: Tools for Outbreak Investigation/Infectious Disease Surveillance
Description: Create epicurves or epigantt charts in 'ggplot2'. Prepare
data for visualisation or other reporting for infectious disease
surveillance and outbreak investigation. Includes tidy functions to solve
date based transformations for common reporting tasks, like
(A) seasonal date alignment for respiratory disease surveillance,
(B) date-based case binning based on specified time intervals like
isoweek, epiweek, month and more, (C) automated detection and marking
of the new year based on the date/datetime axis of the 'ggplot2'.
An introduction on how to use epicurves can be found on the US CDC website
(2012, <https://www.cdc.gov/training/quicklearns/epimode/index.html>).
Author: Alexander Bartel [aut, cre]
Maintainer: Alexander Bartel <alexander.bartel@fu-berlin.de>
Diff between ggsurveillance versions 0.1.2 dated 2025-02-11 and 0.2.0 dated 2025-03-02
DESCRIPTION | 6 - MD5 | 56 +++++++----- NAMESPACE | 2 NEWS.md | 9 +- R/create_agegroups.R | 6 - R/data.R | 54 ++++++++++++ R/geom_epicurve.R | 8 - R/geom_epigantt.R | 86 ++++++++++++++++++- R/geometric_mean.R | 10 +- R/scale_discrete_reverse.R |only README.md | 42 +++++++-- data/linelist_hospital_outbreak.rda |only inst/WORDLIST | 8 + inst/doc/Epigantt_with_ggsurveillance.R | 52 +++++++++++ inst/doc/Epigantt_with_ggsurveillance.Rmd | 63 +++++++++++++- inst/doc/Epigantt_with_ggsurveillance.html | 120 +++++++++++++++++++++------ inst/doc/align_dates_seasonal.R | 2 inst/doc/align_dates_seasonal.Rmd | 2 inst/doc/align_dates_seasonal.html | 2 man/create_agegroups.Rd | 6 - man/figures/ggepicurve_plot_readme.png |only man/figures/seasonal_plot_readme.png |binary man/geom_epicurve.Rd | 8 - man/geom_epigantt.Rd | 113 +++++++++++++------------ man/geometric_mean.Rd | 5 - man/linelist_hospital_outbreak.Rd |only man/scale_y_discrete_reverse.Rd |only tests/testthat/test-geom_epicurve.R | 15 ++- tests/testthat/test-geom_epigantt.R |only tests/testthat/test-geom_vline_year.R |only tests/testthat/test-scale_discrete_reverse.R |only vignettes/Epigantt_with_ggsurveillance.Rmd | 63 +++++++++++++- vignettes/align_dates_seasonal.Rmd | 2 33 files changed, 576 insertions(+), 164 deletions(-)
More information about ggsurveillance at CRAN
Permanent link
Title: Radix Tree and Trie-Based String Distances
Description: A collection of Radix Tree and Trie algorithms for finding similar sequences and calculating sequence distances (Levenshtein and other distance metrics). This work was inspired by a trie implementation in Python: "Fast and Easy Levenshtein distance using a Trie." Hanov (2011) <https://stevehanov.ca/blog/index.php?id=114>.
Author: Travers Ching [aut, cre, cph],
Martin Moene [ctb, cph] ,
Steve Hanov [ctb] ,
Martin Leitner-Ankerl [ctb]
Maintainer: Travers Ching <traversc@gmail.com>
Diff between seqtrie versions 0.2.8 dated 2024-05-04 and 0.2.9 dated 2025-03-02
ChangeLog | 4 DESCRIPTION | 12 +- MD5 | 28 +++--- README.md | 17 +--- build/vignette.rds |binary inst/doc/vignette.R | 25 ++---- inst/doc/vignette.html | 189 ++++++++++++++++++++++++++-------------------- inst/doc/vignette.rmd | 5 - src/CharCounter.cpp | 6 - src/RadixForest.cpp | 8 - src/RadixTree.cpp | 8 - src/seqtrie_types.h | 7 + tests/test_pairwise.R | 36 ++++++-- vignettes/simple_tree.png |binary vignettes/vignette.rmd | 5 - 15 files changed, 199 insertions(+), 151 deletions(-)
Title: Tools to Analyze Repertory Grid Data
Description: Analyze repertory grids, a qualitative-quantitative
data collection technique devised by George A. Kelly in the 1950s. Today, grids are used across
various domains ranging from clinical psychology to marketing. The package contains functions
to quantitatively analyze and visualize repertory grid data (e.g. 'Fransella', 'Bell', & 'Bannister',
2004, ISBN: 978-0-470-09080-0). The package is part of the The package is part of the
<https://openrepgrid.org/> project.
Author: Mark Heckmann [aut, cre, cph] ,
Alejandro Garcia Gutierrez [ctb],
Diego Vitali [ctb]
Maintainer: Mark Heckmann <heckmann.mark@gmail.com>
Diff between OpenRepGrid versions 0.1.16 dated 2024-12-02 and 0.1.17 dated 2025-03-02
DESCRIPTION | 8 +- MD5 | 40 ++++++------ NAMESPACE | 3 NEWS.md | 11 +++ R/bertin.r | 36 ++++++++--- R/calc.r | 7 +- R/repgrid-basicops.r | 131 +++++++++++++++++++++++++++++++++-------- R/repgrid-elements.r | 13 ++-- R/repgrid-plots.r | 50 ++++++++++----- inst/CITATION | 20 +++--- inst/figures |only man/bertin.Rd | 12 +++ man/biplot2d.Rd | 5 + man/cbind.repgrid.Rd |only man/cluster.Rd | 2 man/clusterBoot.Rd | 4 + man/extract-methods.Rd | 9 +- man/figures/logo.png |binary man/ops-methods.Rd | 8 +- man/prepareBiplotData.Rd | 5 + tests/testthat/test-basicops.R | 38 +++++++++++ tests/testthat/test-elements.R |only 22 files changed, 305 insertions(+), 97 deletions(-)
Title: Propensity Score Weighting for Causal Inference with
Observational Studies and Randomized Trials
Description: Supports propensity score weighting analysis of observational studies and randomized trials. Enables the estimation and inference of average causal effects with binary and multiple treatments using overlap weights (ATO), inverse probability of treatment weights (ATE), average treatment effect among the treated weights (ATT), matching weights (ATM) and entropy weights (ATEN), with and without propensity score trimming. These weights are members of the family of balancing weights introduced in Li, Morgan and Zaslavsky (2018) <doi:10.1080/01621459.2016.1260466> and Li and Li (2019) <doi:10.1214/19-AOAS1282>.
Author: Tianhui Zhou [aut],
Guangyu Tong [aut],
Fan Li [aut],
Laine Thomas [aut],
Fan Li [aut],
Yukang Zeng [cre]
Maintainer: Yukang Zeng <yukang.zeng@yale.edu>
Diff between PSweight versions 2.1.0 dated 2025-02-12 and 2.1.1 dated 2025-03-02
DESCRIPTION | 8 ++-- MD5 | 20 +++++------ NEWS.md | 4 +- R/OUTmethod_SW.R | 27 ++++++++++++--- R/PSmethod_SW.R | 29 ++++++++++++++-- R/PStrim_SW.R | 26 ++++++++++---- README.md | 80 +++++++++++++++++++++++++++++++++++++++++++++- inst/doc/Software_vig.pdf |binary man/OUTmethod_SW.Rd | 25 +++++++++++--- man/PSmethod_SW.Rd | 29 ++++++++++++++-- man/PStrim_SW.Rd | 22 +++++++++--- 11 files changed, 221 insertions(+), 49 deletions(-)
Title: Download and Tidy Time Series Data from the Australian Bureau of
Statistics
Description: Downloads, imports, and tidies time series data from the
Australian Bureau of Statistics <https://www.abs.gov.au/>.
Author: Matt Cowgill [aut, cre] ,
Zoe Meers [aut],
Jaron Lee [aut],
David Diviny [aut],
Hugh Parsonage [ctb],
Kinto Behr [ctb],
Angus Moore [ctb],
Francis Markham [ctb]
Maintainer: Matt Cowgill <mattcowgill@gmail.com>
Diff between readabs versions 0.4.16 dated 2024-05-27 and 0.4.18 dated 2025-03-01
DESCRIPTION | 17 +++++-- MD5 | 43 ++++++++++--------- NAMESPACE | 5 ++ NEWS.md | 9 ++++ R/check_abs_connection.R | 3 - R/download_data_cube.r | 67 ++++++++++++++++++++++++------- R/read_abs.R | 8 ++- R/read_api.R | 46 ++++++++++----------- R/read_erp.R |only R/read_job_mobility.R | 3 - R/read_payrolls.R | 41 +++++++----------- R/sysdata.rda |binary README.md | 22 +++++----- build/vignette.rds |binary inst/doc/readabs_vignette.R | 26 ++++++------ inst/doc/readabs_vignette.html | 10 ++-- man/abs_api.Rd | 6 +- man/read_abs.Rd | 8 ++- man/read_erp.Rd |only man/read_payrolls.Rd | 22 +++++----- tests/testthat/test-abs_api.R | 2 tests/testthat/test-download_data_cube.R | 7 +++ tests/testthat/test-read_erp.R |only tests/testthat/test-read_payrolls.R | 3 - 24 files changed, 210 insertions(+), 138 deletions(-)
Title: Interface to the 'Microsoft 365' Suite of Cloud Services
Description: An interface to the 'Microsoft 365' (formerly known as 'Office 365') suite of cloud services, building on the framework supplied by the 'AzureGraph' package. Enables access from R to data stored in 'Teams', 'SharePoint Online' and 'OneDrive', including the ability to list drive folder contents, upload and download files, send messages, and retrieve data lists. Also provides a full-featured 'Outlook' email client, with the ability to send emails and manage emails and mail folders.
Author: Hong Ooi [aut, cre],
Roman Zenka [ctb],
Robert Ashton [ctb],
Philip Zheng [ctb],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi73@gmail.com>
Diff between Microsoft365R versions 2.4.0 dated 2023-05-30 and 2.4.1 dated 2025-03-01
DESCRIPTION | 9 ++++--- MD5 | 61 ++++++++++++++++++++++++------------------------- NEWS.md | 22 +++++++++++++++++ R/Microsoft365R.R | 3 +- R/add_methods.R | 2 - R/client.R | 4 +-- R/ms_channel.R | 4 +-- R/ms_chat.R | 4 +-- R/ms_chat_message.R | 11 ++------ R/ms_drive.R | 18 ++++++++++---- R/ms_drive_item.R | 38 ++++++++++++++++++++++++++---- R/ms_list_item.R | 2 - R/ms_outlook.R | 2 - R/ms_plan.R | 4 +-- R/ms_site.R | 4 +-- R/ms_team.R | 19 ++++++++++----- R/ms_team_member.R | 2 - R/ms_teams_object.R |only inst/doc/auth.Rmd | 15 ++---------- inst/doc/auth.html | 54 ++++++++++++++++--------------------------- man/add_methods.Rd | 2 - man/ms_channel.Rd | 2 - man/ms_chat.Rd | 2 - man/ms_chat_message.Rd | 4 +-- man/ms_drive.Rd | 2 - man/ms_drive_item.Rd | 8 +++--- man/ms_list_item.Rd | 2 - man/ms_outlook.Rd | 2 - man/ms_plan.Rd | 2 - man/ms_site.Rd | 4 +-- man/ms_team.Rd | 6 ++-- vignettes/auth.Rmd | 15 ++---------- 32 files changed, 180 insertions(+), 149 deletions(-)
Title: Comprehensive TIFF I/O with Full Support for 'ImageJ' TIFF Files
Description: General purpose TIFF file I/O for R users. Currently the
only such package with read and write support for TIFF files with
floating point (real-numbered) pixels, and the only package that can
correctly import TIFF files that were saved from 'ImageJ' and write
TIFF files than can be correctly read by 'ImageJ'
<https://imagej.net/ij/>. Also supports text image I/O.
Author: Rory Nolan [aut, cre] ,
Kent Johnson [aut],
Simon Urbanek [ctb],
Sergi Padilla-Parra [ths] ,
Jeroen Ooms [rev, ctb] ,
Jon Clayden [rev]
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between ijtiff versions 2.3.5 dated 2025-01-29 and 3.0.0 dated 2025-03-01
ijtiff-2.3.5/ijtiff/tests/testthat/_snaps/graphics |only ijtiff-3.0.0/ijtiff/DESCRIPTION | 11 ijtiff-3.0.0/ijtiff/MD5 | 94 - ijtiff-3.0.0/ijtiff/NAMESPACE | 1 ijtiff-3.0.0/ijtiff/NEWS.md | 100 - ijtiff-3.0.0/ijtiff/R/argument-checking.R | 98 + ijtiff-3.0.0/ijtiff/R/class_constructors.R | 2 ijtiff-3.0.0/ijtiff/R/print.R | 20 ijtiff-3.0.0/ijtiff/R/read.R | 162 + ijtiff-3.0.0/ijtiff/R/tags.R |only ijtiff-3.0.0/ijtiff/R/utils.R | 100 - ijtiff-3.0.0/ijtiff/R/write.R | 139 + ijtiff-3.0.0/ijtiff/README.md | 6 ijtiff-3.0.0/ijtiff/inst/WORDLIST | 25 ijtiff-3.0.0/ijtiff/inst/doc/reading-and-writing-images.R | 21 ijtiff-3.0.0/ijtiff/inst/doc/reading-and-writing-images.Rmd | 21 ijtiff-3.0.0/ijtiff/inst/doc/reading-and-writing-images.html | 84 ijtiff-3.0.0/ijtiff/inst/doc/text-images.html | 4 ijtiff-3.0.0/ijtiff/inst/doc/the-imagej-problem.R | 2 ijtiff-3.0.0/ijtiff/inst/doc/the-imagej-problem.Rmd | 2 ijtiff-3.0.0/ijtiff/inst/doc/the-imagej-problem.html | 32 ijtiff-3.0.0/ijtiff/inst/extdata/tiff-tag-conversions.json |only ijtiff-3.0.0/ijtiff/man/get_supported_tags.Rd |only ijtiff-3.0.0/ijtiff/man/read_tags.Rd | 14 ijtiff-3.0.0/ijtiff/man/read_tif.Rd | 6 ijtiff-3.0.0/ijtiff/man/write_tif.Rd | 62 ijtiff-3.0.0/ijtiff/src/common.c | 53 ijtiff-3.0.0/ijtiff/src/common.h | 7 ijtiff-3.0.0/ijtiff/src/init.c | 13 ijtiff-3.0.0/ijtiff/src/read.c | 902 +++------- ijtiff-3.0.0/ijtiff/src/tags.c |only ijtiff-3.0.0/ijtiff/src/tags.h |only ijtiff-3.0.0/ijtiff/src/write.c | 279 +-- ijtiff-3.0.0/ijtiff/tests/testthat/_snaps/io.md | 4 ijtiff-3.0.0/ijtiff/tests/testthat/_snaps/print.md | 22 ijtiff-3.0.0/ijtiff/tests/testthat/helper-tag-tests.R |only ijtiff-3.0.0/ijtiff/tests/testthat/test-as_EBImage-examples.R | 2 ijtiff-3.0.0/ijtiff/tests/testthat/test-io.R | 122 - ijtiff-3.0.0/ijtiff/tests/testthat/test-read_tags-examples.R | 104 - ijtiff-3.0.0/ijtiff/tests/testthat/test-tag-artist.R |only ijtiff-3.0.0/ijtiff/tests/testthat/test-tag-copyright.R |only ijtiff-3.0.0/ijtiff/tests/testthat/test-tag-datetime.R |only ijtiff-3.0.0/ijtiff/tests/testthat/test-tag-documentname.R |only ijtiff-3.0.0/ijtiff/tests/testthat/test-tag-handling.R |only ijtiff-3.0.0/ijtiff/tests/testthat/test-tag-orientation.R |only ijtiff-3.0.0/ijtiff/tests/testthat/test-tag-resolutionunit.R |only ijtiff-3.0.0/ijtiff/tests/testthat/test-tag-xposition.R |only ijtiff-3.0.0/ijtiff/tests/testthat/test-tag-xresolution.R |only ijtiff-3.0.0/ijtiff/tests/testthat/test-tag-yposition.R |only ijtiff-3.0.0/ijtiff/tests/testthat/test-tag-yresolution.R |only ijtiff-3.0.0/ijtiff/tests/testthat/test-tags.R |only ijtiff-3.0.0/ijtiff/tests/testthat/test-utils.R | 49 ijtiff-3.0.0/ijtiff/tests/testthat/test_class_constructors.R | 4 ijtiff-3.0.0/ijtiff/vignettes/reading-and-writing-images.Rmd | 21 ijtiff-3.0.0/ijtiff/vignettes/the-imagej-problem.Rmd | 2 55 files changed, 1363 insertions(+), 1227 deletions(-)
Title: Animation of Multiple Trajectories with Uncertainty
Description: Animation of observed trajectories using spline-based interpolation (see for example, Buderman, F. E., Hooten, M. B., Ivan, J. S. and Shenk, T. M. (2016), <doi:10.1111/2041-210X.12465> "A functional model for characterizing long-distance movement behaviour". Methods Ecol Evol). Intended to be used exploratory data analysis, and perhaps for preparation of presentations.
Author: Henry Scharf [aut, cre],
Kristine Dinh [aut],
Rosales Hugo [aut],
Rivera Angelica [aut]
Maintainer: Henry Scharf <hscharf@arizona.edu>
Diff between anipaths versions 0.10.4 dated 2025-01-13 and 0.10.5 dated 2025-03-01
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 5 +++++ R/animate_paths.R | 15 +++++++++++---- R/animation_expression.R | 26 ++++++++++++++------------ build/vignette.rds |binary inst/doc/anipaths.html | 4 ++-- inst/doc/anipaths_crawl.html | 4 ++-- man/animate_paths.Rd | 2 +- 9 files changed, 47 insertions(+), 33 deletions(-)
Title: Parallel Numerical Derivatives, Gradients, Jacobians, and
Hessians of Arbitrary Accuracy Order
Description: Numerical derivatives through finite-difference approximations
can be calculated using the 'pnd' package with parallel capabilities and
optimal step-size selection to improve accuracy. These functions facilitate
efficient computation of derivatives, gradients, Jacobians, and Hessians,
allowing for more evaluations to reduce the mathematical and machine errors.
Designed for compatibility with the 'numDeriv' package,
which has not received updates in several years, it introduces advanced features
such as computing derivatives of arbitrary order, improving
the accuracy of Hessian approximations by avoiding repeated differencing,
and parallelising slow functions on Windows, Mac, and Linux.
Author: Andrei Victorovitch Kostyrka [aut, cre]
Maintainer: Andrei Victorovitch Kostyrka <andrei.kostyrka@gmail.com>
Diff between pnd versions 0.0.6 dated 2025-02-25 and 0.0.7 dated 2025-03-01
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- NEWS.md | 7 +++++-- R/zzz.R | 8 +++++--- build/partial.rdb |binary inst/CITATION | 16 ++++++++-------- inst/doc/compatibility-with-numDeriv.html | 8 ++++---- inst/doc/fast-and-accurate.html | 2 +- inst/doc/step-size-selection.html | 2 +- 9 files changed, 38 insertions(+), 33 deletions(-)
Title: Bayesian Logistic Regression for Oncology Dose-Escalation Trials
Description: Bayesian logistic regression model with optional
EXchangeability-NonEXchangeability parameter modelling for flexible
borrowing from historical or concurrent data-sources. The safety model
can guide dose-escalation decisions for adaptive oncology Phase I
dose-escalation trials which involve an arbitrary number of
drugs. Please refer to Neuenschwander et al. (2008)
<doi:10.1002/sim.3230> and Neuenschwander et al. (2016)
<doi:10.1080/19466315.2016.1174149> for details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Lukas A. Widmer [aut],
Andrew Bean [aut],
Trustees of Columbia University [cph]
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between OncoBayes2 versions 0.8-9 dated 2023-07-20 and 0.9-0 dated 2025-03-01
OncoBayes2-0.8-9/OncoBayes2/inst/stan/include/common_functions.stan |only OncoBayes2-0.9-0/OncoBayes2/DESCRIPTION | 32 OncoBayes2-0.9-0/OncoBayes2/MD5 | 208 OncoBayes2-0.9-0/OncoBayes2/NAMESPACE | 23 OncoBayes2-0.9-0/OncoBayes2/NEWS.md | 41 OncoBayes2-0.9-0/OncoBayes2/R/OncoBayes2-package.R | 8 OncoBayes2-0.9-0/OncoBayes2/R/bind_rows_0.R | 14 OncoBayes2-0.9-0/OncoBayes2/R/blrm_exnex.R | 1769 - OncoBayes2-0.9-0/OncoBayes2/R/blrm_formula_linear.R | 88 OncoBayes2-0.9-0/OncoBayes2/R/blrm_formula_saturating.R | 74 OncoBayes2-0.9-0/OncoBayes2/R/blrm_trial.R | 541 OncoBayes2-0.9-0/OncoBayes2/R/critical_quantile.R | 224 OncoBayes2-0.9-0/OncoBayes2/R/diagnostics.R | 4 OncoBayes2-0.9-0/OncoBayes2/R/example_model.R | 32 OncoBayes2-0.9-0/OncoBayes2/R/lodds.R | 14 OncoBayes2-0.9-0/OncoBayes2/R/log_sum_exp.R | 2 OncoBayes2-0.9-0/OncoBayes2/R/nsamples.R | 8 OncoBayes2-0.9-0/OncoBayes2/R/plot_blrm.R | 828 OncoBayes2-0.9-0/OncoBayes2/R/posterior.R |only OncoBayes2-0.9-0/OncoBayes2/R/posterior_interval.R | 21 OncoBayes2-0.9-0/OncoBayes2/R/posterior_linpred.R | 46 OncoBayes2-0.9-0/OncoBayes2/R/posterior_predict.R | 40 OncoBayes2-0.9-0/OncoBayes2/R/pp_data.R | 293 OncoBayes2-0.9-0/OncoBayes2/R/predictive_interval.R | 30 OncoBayes2-0.9-0/OncoBayes2/R/prior_summary.R | 332 OncoBayes2-0.9-0/OncoBayes2/R/summary.R | 331 OncoBayes2-0.9-0/OncoBayes2/R/sysdata.rda |binary OncoBayes2-0.9-0/OncoBayes2/R/update.R | 109 OncoBayes2-0.9-0/OncoBayes2/R/utils.R | 8 OncoBayes2-0.9-0/OncoBayes2/R/zzz.R | 10 OncoBayes2-0.9-0/OncoBayes2/build/partial.rdb |binary OncoBayes2-0.9-0/OncoBayes2/build/vignette.rds |binary OncoBayes2-0.9-0/OncoBayes2/data/codata_combo2.rda |binary OncoBayes2-0.9-0/OncoBayes2/data/dose_info_combo2.rda |binary OncoBayes2-0.9-0/OncoBayes2/data/drug_info_combo2.rda |binary OncoBayes2-0.9-0/OncoBayes2/data/hist_SA.rda |binary OncoBayes2-0.9-0/OncoBayes2/data/hist_combo2.rda |binary OncoBayes2-0.9-0/OncoBayes2/data/hist_combo3.rda |binary OncoBayes2-0.9-0/OncoBayes2/inst/doc/OncoBayes2.pdf |binary OncoBayes2-0.9-0/OncoBayes2/inst/doc/introduction.R | 172 OncoBayes2-0.9-0/OncoBayes2/inst/doc/introduction.Rmd | 146 OncoBayes2-0.9-0/OncoBayes2/inst/doc/introduction.html | 965 OncoBayes2-0.9-0/OncoBayes2/inst/extra/run-oq.R | 9 OncoBayes2-0.9-0/OncoBayes2/inst/sbc/calibration.md5 | 6 OncoBayes2-0.9-0/OncoBayes2/inst/sbc/lkj.R | 74 OncoBayes2-0.9-0/OncoBayes2/inst/sbc/make_reference_rankhist.R | 299 OncoBayes2-0.9-0/OncoBayes2/inst/sbc/sbc_example_models.R | 296 OncoBayes2-0.9-0/OncoBayes2/inst/sbc/sbc_job_startup.R |only OncoBayes2-0.9-0/OncoBayes2/inst/sbc/sbc_report.R | 179 OncoBayes2-0.9-0/OncoBayes2/inst/sbc/sbc_report.html | 1228 - 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OncoBayes2-0.9-0/OncoBayes2/tests/testthat/test-critical_quantile.R | 236 OncoBayes2-0.9-0/OncoBayes2/tests/testthat/test-examples.R | 18 OncoBayes2-0.9-0/OncoBayes2/tests/testthat/test-numeric_utils.R | 19 OncoBayes2-0.9-0/OncoBayes2/tests/testthat/test-plot_toxicity_curve.R | 215 OncoBayes2-0.9-0/OncoBayes2/tests/testthat/test-plot_toxicity_intervals.R | 102 OncoBayes2-0.9-0/OncoBayes2/tests/testthat/test-plot_toxicity_intervals_stacked.R | 263 OncoBayes2-0.9-0/OncoBayes2/tests/testthat/test-posterior.R | 180 OncoBayes2-0.9-0/OncoBayes2/tests/testthat/test-sbc.R | 88 OncoBayes2-0.9-0/OncoBayes2/vignettes/introduction.Rmd | 146 OncoBayes2-0.9-0/OncoBayes2/vignettes/settings-knitr.txt |only OncoBayes2-0.9-0/OncoBayes2/vignettes/settings-sampling.txt |only 107 files changed, 16479 insertions(+), 12190 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb]
,
Brenton M. Wiernik [aut, ctb] ,
Vincent Arel-Bundock [aut, ctb]
,
Etienne Bacher [aut, ctb] ,
Ale [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between insight versions 1.0.2 dated 2025-02-06 and 1.1.0 dated 2025-03-01
DESCRIPTION | 8 MD5 | 69 +++-- NAMESPACE | 4 NEWS.md | 34 ++ R/export_table.R | 8 R/find_formula.R | 18 + R/find_response.R | 20 + R/find_transformation.R | 19 + R/format_table.R | 78 ++++++ R/format_table_glue.R |only R/get_datagrid.R | 110 ++++++--- R/get_predicted.R | 89 +++++++ R/get_predicted_gam.R | 2 R/get_predicted_mixed.R | 6 R/get_sigma.R | 5 R/get_transformation.R | 6 R/standardize_column_order.R | 299 +++++++++++++++++-------- R/validate_argument.R | 8 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 2 inst/doc/display.html | 220 +++++++++--------- man/easystats_columns.Rd |only man/find_transformation.Rd | 6 man/format_table.Rd | 55 ++++ man/get_datagrid.Rd | 28 +- man/get_sigma.Rd | 4 man/standardize_column_order.Rd | 2 tests/testthat/test-bias_correction.R |only tests/testthat/test-export_table.R | 6 tests/testthat/test-find_transformation.R | 5 tests/testthat/test-format_table.R | 72 +++++- tests/testthat/test-get_datagrid.R | 65 ++++- tests/testthat/test-get_transformation.R | 12 + tests/testthat/test-mgcv.R | 41 +++ tests/testthat/test-standardize_column_order.R | 19 + 37 files changed, 999 insertions(+), 323 deletions(-)
Title: Explore and Import 'Metopio' Health Atlas Data and Spatial
Layers
Description: Allows for painless use of the 'Metopio' health atlas APIs
<https://metopio.com/how-it-works/atlas/> to explore and import data.
'Metopio' health atlases store open public health data. See what topics
(or indicators) are available among specific populations, periods, and
geographic layers. Download relevant data along with geographic
boundaries or point datasets. Spatial datasets are returned as 'sf'
objects.
Author: Ryan Zomorrodi [aut, cre, cph]
Maintainer: Ryan Zomorrodi <rzomor2@uic.edu>
Diff between healthatlas versions 0.1.1 dated 2024-12-17 and 0.2.0 dated 2025-03-01
healthatlas-0.1.1/healthatlas/inst/doc/typical_usage.R |only healthatlas-0.1.1/healthatlas/inst/doc/typical_usage.Rmd |only healthatlas-0.1.1/healthatlas/inst/doc/typical_usage.html |only healthatlas-0.1.1/healthatlas/vignettes/typical_usage.Rmd |only healthatlas-0.2.0/healthatlas/DESCRIPTION | 7 healthatlas-0.2.0/healthatlas/MD5 | 26 +-- healthatlas-0.2.0/healthatlas/NEWS.md | 6 healthatlas-0.2.0/healthatlas/R/ha_api_req.R | 11 - healthatlas-0.2.0/healthatlas/R/ha_topics.R | 71 ++++++++- healthatlas-0.2.0/healthatlas/R/helpers.R | 5 healthatlas-0.2.0/healthatlas/README.md | 72 +++++----- healthatlas-0.2.0/healthatlas/build/vignette.rds |binary healthatlas-0.2.0/healthatlas/inst/doc/healthatlas.R |only healthatlas-0.2.0/healthatlas/inst/doc/healthatlas.Rmd |only healthatlas-0.2.0/healthatlas/inst/doc/healthatlas.html |only healthatlas-0.2.0/healthatlas/tests/testthat/helpers.R | 59 +++++++- healthatlas-0.2.0/healthatlas/tests/testthat/test-ha_topics.R | 5 healthatlas-0.2.0/healthatlas/vignettes/healthatlas.Rmd |only 18 files changed, 186 insertions(+), 76 deletions(-)
Title: Rhythmic Patterns Modeling by FMM Models
Description: Provides a collection of functions to fit and explore single, multi-component and restricted Frequency Modulated Moebius (FMM) models. 'FMM' is a nonlinear parametric regression model capable of fitting non-sinusoidal shapes in rhythmic patterns. Details about the mathematical formulation of 'FMM' models can be found in Rueda et al. (2019) <doi:10.1038/s41598-019-54569-1>.
Author: Itziar Fernandez [aut, cre],
Yolanda Larriba [aut],
Christian Canedo [aut],
Alejandro Rodriguez-Collado [aut],
Adrian Lamela [aut],
Cristina Rueda [aut]
Maintainer: Itziar Fernandez <itziar.fernandez@uva.es>
Diff between FMM versions 0.3.1 dated 2021-12-17 and 0.4.0 dated 2025-03-01
DESCRIPTION | 40 MD5 | 42 NEWS.md | 83 + R/FMM_internal.R | 465 ++++----- R/FMM_internal_restr.R | 869 ++++++++++-------- R/ecgData-data.R | 60 - R/fitFMM.R | 124 +- R/fitFMM_back.R | 36 R/fitFMM_restr.R | 498 +++++----- R/fitFMM_unit.R | 194 +--- R/generateFMM.R | 192 +-- R/plotFMM.R | 87 - README.md | 4 build/vignette.rds |binary inst/doc/FMMVignette.R | 16 inst/doc/FMMVignette.Rmd | 33 inst/doc/FMMVignette.html | 2114 ++++++++++++++++++++++++++++++++++++++------ man/ecgData.Rd | 2 man/fitFMM.Rd | 247 ++--- man/plotFMM.Rd | 167 +-- vignettes/FMMVignette.Rmd | 33 vignettes/ReferencesFMM.bib | 80 + 22 files changed, 3581 insertions(+), 1805 deletions(-)
Title: Sequence Symmetry Analysis Using the Observational Medical
Outcomes Partnership Common Data Model
Description: Calculating crude sequence ratio, adjusted sequence ratio and
confidence intervals using data mapped to the Observational Medical
Outcomes Partnership Common Data Model.
Author: Xihang Chen [aut, cre] ,
Tyman Stanford [aut] ,
Berta Raventos [aut] ,
Nicole Pratt [aut] ,
Ed Burn [aut] ,
Marti Catala [aut] ,
Danielle Newby [aut] ,
Nuria Mercade-Besora [aut] ,
Mike Du [aut] ,
Yuchen Guo [aut] ,
Kim Lopez [aut] ,
Marta Alcalde-He [...truncated...]
Maintainer: Xihang Chen <xihang.chen@ndorms.ox.ac.uk>
Diff between CohortSymmetry versions 0.2.2 dated 2025-02-28 and 0.2.3 dated 2025-03-01
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/generateSequenceCohortSet.R | 3 ++- inst/doc/a01_Introduction.html | 14 +++++++------- inst/doc/a02_Generate_a_sequence_cohort.html | 4 ++-- inst/doc/a03_Summarise_sequence_ratios.html | 2 +- inst/doc/a04_Visualise_sequence_ratios.html | 6 +++--- inst/doc/a05_Summarise_temporal_symmetry.html | 10 +++++----- 8 files changed, 30 insertions(+), 29 deletions(-)
More information about CohortSymmetry at CRAN
Permanent link
Title: Streamlines the Process of Fitting Areal Spatial Models
Description: Helpers for addressing the issue of disconnected spatial units.
It allows for convenient adding and removal of neighbourhood connectivity between areal units prior to modelling, with the visual aid of maps.
Post-modelling, it reduces the human workload for extracting, tidying and mapping predictions from areal models.
Author: Kevin Horan [aut, cre, cph] ,
Katarina Domijan [aut, ths] ,
Chris Brunsdon [aut, ths]
Maintainer: Kevin Horan <kevin.horan.2021@mumail.ie>
Diff between sfislands versions 1.0.0 dated 2024-03-21 and 1.1.0 dated 2025-03-01
DESCRIPTION | 12 +- MD5 | 30 +++--- NAMESPACE | 2 NEWS.md | 24 ++++ R/st_bridges.R | 40 ++++++-- R/st_check_islands.R | 9 + R/st_force_cut_nb.R |only R/st_force_join_nb.R |only R/st_manual_cut_nb.R | 2 R/st_manual_join_nb.R | 2 R/st_quickmap_nb.R | 161 +++++++++++---------------------- R/st_quickmap_preds.R | 3 README.md | 42 ++++---- man/st_bridges.Rd | 12 +- man/st_force_cut_nb.Rd |only man/st_force_join_nb.Rd |only tests/testthat/test-st_bridges.R | 20 +--- tests/testthat/test-st_check_islands.R | 2 18 files changed, 190 insertions(+), 171 deletions(-)
Title: Reproducible Data Science Environments with 'Nix'
Description: Simplifies the creation of reproducible data science environments
using the 'Nix' package manager, as described in
Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()`
function generates a complete description of the environment as a
`default.nix` file, which can then be built using 'Nix'. This results in
project specific software environments with pinned versions of R, packages,
linked system dependencies, and other tools. Additional helpers make it easy
to run R code in 'Nix' software environments for testing and production.
Author: Bruno Rodrigues [aut, cre] ,
Philipp Baumann [aut] ,
David Watkins [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/625>),
Jacob Wujiciak-Jens [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/62 [...truncated...]
Maintainer: Bruno Rodrigues <bruno@brodrigues.co>
Diff between rix versions 0.15.2 dated 2025-02-15 and 0.15.5 dated 2025-03-01
rix-0.15.2/rix/tests/testthat/_snaps/rix/dups-entries_default.nix |only rix-0.15.2/rix/tests/testthat/_snaps/rix/skip-dups-entries_default.nix |only rix-0.15.5/rix/DESCRIPTION | 8 rix-0.15.5/rix/MD5 | 126 +-- rix-0.15.5/rix/NAMESPACE | 1 rix-0.15.5/rix/NEWS.md | 19 rix-0.15.5/rix/R/available_r.R | 9 rix-0.15.5/rix/R/fetchers.R | 353 +++++----- rix-0.15.5/rix/R/ga_cachix.R | 15 rix-0.15.5/rix/R/get_latest.R | 49 - rix-0.15.5/rix/R/make_launcher.R | 9 rix-0.15.5/rix/R/make_nixpkgs_url.R | 10 rix-0.15.5/rix/R/nix_build.R | 34 rix-0.15.5/rix/R/nix_build_helpers.R | 33 rix-0.15.5/rix/R/nix_hash.R | 165 ---- rix-0.15.5/rix/R/renv_helpers.R | 57 + rix-0.15.5/rix/R/rix.R | 243 +++--- rix-0.15.5/rix/R/rix_helpers.R | 70 + rix-0.15.5/rix/R/rix_init.R | 130 ++- rix-0.15.5/rix/R/setup_cachix.R | 6 rix-0.15.5/rix/R/tar_nix_ga.R | 3 rix-0.15.5/rix/R/with_nix.R | 55 + rix-0.15.5/rix/R/with_nix_helpers.R | 107 ++- rix-0.15.5/rix/R/zzz.R | 25 rix-0.15.5/rix/build/vignette.rds |binary rix-0.15.5/rix/inst/doc/b2-setting-up-and-using-rix-on-macos.Rmd | 26 rix-0.15.5/rix/inst/doc/b2-setting-up-and-using-rix-on-macos.html | 34 rix-0.15.5/rix/inst/doc/e-configuring-ide.R | 2 rix-0.15.5/rix/inst/doc/e-configuring-ide.Rmd | 38 - rix-0.15.5/rix/inst/doc/e-configuring-ide.html | 45 - rix-0.15.5/rix/inst/doc/z-advanced-topic-handling-packages-with-remote-dependencies.Rmd | 64 + rix-0.15.5/rix/inst/doc/z-advanced-topic-handling-packages-with-remote-dependencies.html | 46 + rix-0.15.5/rix/inst/doc/z-advanced-topic-using-nix-inside-docker.Rmd | 2 rix-0.15.5/rix/inst/doc/z-advanced-topic-walkthrough-project.R |only rix-0.15.5/rix/inst/doc/z-advanced-topic-walkthrough-project.Rmd |only rix-0.15.5/rix/inst/doc/z-advanced-topic-walkthrough-project.html |only rix-0.15.5/rix/inst/extdata/available_df.csv | 13 rix-0.15.5/rix/inst/extdata/default.nix | 14 rix-0.15.5/rix/inst/extdata/run-pipeline.yaml | 17 rix-0.15.5/rix/man/rix.Rd | 49 - rix-0.15.5/rix/tests/testthat/_snaps/renv_helpers/default_datathin.nix | 32 rix-0.15.5/rix/tests/testthat/_snaps/renv_helpers/default_v0-15-5.nix | 1 rix-0.15.5/rix/tests/testthat/_snaps/rix/bleeding-edge_default.nix | 1 rix-0.15.5/rix/tests/testthat/_snaps/rix/code_default.nix | 1 rix-0.15.5/rix/tests/testthat/_snaps/rix/codium_default.nix | 1 rix-0.15.5/rix/tests/testthat/_snaps/rix/date_default.nix | 1 rix-0.15.5/rix/tests/testthat/_snaps/rix/frozen-edge_default.nix | 1 rix-0.15.5/rix/tests/testthat/_snaps/rix/other_default.nix | 1 rix-0.15.5/rix/tests/testthat/_snaps/rix/positron_default.nix | 1 rix-0.15.5/rix/tests/testthat/_snaps/rix/rstudio_default.nix | 1 rix-0.15.5/rix/tests/testthat/_snaps/tar_nix_ga/run-pipeline.yaml | 17 rix-0.15.5/rix/tests/testthat/test-available_r.R | 42 - rix-0.15.5/rix/tests/testthat/test-fetchers.R | 63 + rix-0.15.5/rix/tests/testthat/test-ga_cachix.R | 2 rix-0.15.5/rix/tests/testthat/test-get_sri_hash_deps.R | 17 rix-0.15.5/rix/tests/testthat/test-renv_helpers.R | 57 + rix-0.15.5/rix/tests/testthat/test-rix.R | 175 ++-- rix-0.15.5/rix/tests/testthat/test-rix_init.R | 5 rix-0.15.5/rix/tests/testthat/test-setup_cachix.R | 10 rix-0.15.5/rix/tests/testthat/test-tar_nix_ga.R | 2 rix-0.15.5/rix/tests/testthat/test-with_nix.R | 2 rix-0.15.5/rix/tests/testthat/testdata/remote-pkgs/mlr3_default.nix |only rix-0.15.5/rix/tests/testthat/testdata/remote-pkgs/mlr3_dups_default.nix |only rix-0.15.5/rix/vignettes/b2-setting-up-and-using-rix-on-macos.Rmd | 26 rix-0.15.5/rix/vignettes/e-configuring-ide.Rmd | 38 - rix-0.15.5/rix/vignettes/z-advanced-topic-handling-packages-with-remote-dependencies.Rmd | 64 + rix-0.15.5/rix/vignettes/z-advanced-topic-using-nix-inside-docker.Rmd | 2 rix-0.15.5/rix/vignettes/z-advanced-topic-walkthrough-project.Rmd |only 68 files changed, 1405 insertions(+), 1035 deletions(-)
Title: Transition Network Analysis (TNA)
Description: Provides tools for performing Transition Network Analysis (TNA) to
study relational dynamics, including functions for building and plotting TNA
models, calculating centrality measures, and identifying dominant events and
patterns. TNA statistical techniques (e.g., bootstrapping and permutation
tests) ensure the reliability of observed insights and confirm that
identified dynamics are meaningful. See (Saqr et al., 2025)
<doi:10.1145/3706468.3706513> for more details on TNA.
Author: Mohammed Saqr [aut],
Santtu Tikka [aut],
Sonsoles Lopez-Pernas [aut, cre]
Maintainer: Sonsoles Lopez-Pernas <sonsoles.lopez@uef.fi>
Diff between tna versions 0.3.0 dated 2024-12-11 and 0.4.0 dated 2025-03-01
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Title: Tools to Support the Sheffield Elicitation Framework
Description: Implements various methods for eliciting a probability
distribution for a single parameter from an expert or a group of
experts. The expert provides a small number of probability judgements,
corresponding to points on his or her cumulative distribution
function. A range of parametric distributions can then be fitted and
displayed, with feedback provided in the form of fitted probabilities
and percentiles. For multiple experts, a weighted linear pool can be
calculated. Also includes functions for eliciting beliefs about
population distributions; eliciting multivariate distributions using a
Gaussian copula; eliciting a Dirichlet distribution; eliciting
distributions for variance parameters in a random effects
meta-analysis model; survival extrapolation. R Shiny apps for most of the methods are
included.
Author: Jeremy Oakley [aut, cre]
Maintainer: Jeremy Oakley <j.oakley@sheffield.ac.uk>
Diff between SHELF versions 1.11.0 dated 2024-09-06 and 1.12.0 dated 2025-03-01
DESCRIPTION | 8 MD5 | 32 NAMESPACE | 2 R/elicitSurvivalExtrapolation.R | 649 +++------- R/makeSurvivalTable.R |only R/survivalExtrapolatePlot.R |only R/survivalModelExtrapolations.R | 20 R/survivalScenario.R | 53 inst/NEWS.md | 10 inst/doc/Dirichlet-elicitation.html | 6 inst/doc/SHELF-overview.html | 6 inst/shinyAppFiles/elicitationShinySummarySurvivalExtrapolation.Rmd | 306 +--- man/makeSurvivalTable.Rd |only man/survivalExtrapolatePlot.Rd |only man/survivalModelExtrapolations.Rd | 3 man/survivalScenario.Rd | 15 tests/testthat/_snaps/plots/multiple-expert-plot.new.svg |only tests/testthat/_snaps/plots/survival-extrapolations-plot.svg |only tests/testthat/_snaps/plots/survival-scenario-plot.svg |only tests/testthat/test-plots.R | 30 tests/testthat/test-survival-extrapolation.R |only 21 files changed, 422 insertions(+), 718 deletions(-)
Title: Counting Codes in a Text and Preparing Data for Analysis
Description: Data analysis often requires coding, especially when data are collected through interviews, observations, or questionnaires. As a result, code counting and data preparation are essential steps in the analysis process. Analysts may need to count the codes in a text (Tokenization, counting of pre-established codes, computing the co-occurrence matrix by line) and prepare the data (e.g., min-max normalization, Z-score, robust scaling, Box-Cox transformation, and non-parametric bootstrap). For the Box-Cox transformation (Box & Cox, 1964, <https://www.jstor.org/stable/2984418>), the optimal Lambda is determined using the log-likelihood method. Non-parametric bootstrap involves randomly sampling data with replacement. Two random number generators are also integrated: a Lehmer congruential generator for uniform distribution and a Box-Muller generator for normal distribution. Package for educational purposes.
Author: Philippe Cohard [aut, cre]
Maintainer: Philippe Cohard <p.cohard@laposte.net>
Diff between codecountR versions 0.0.4.7 dated 2025-01-22 and 0.0.4.8 dated 2025-03-01
DESCRIPTION | 6 +++--- MD5 | 6 ++++-- NAMESPACE | 1 + R/verify.R |only man/verify.Rd |only 5 files changed, 8 insertions(+), 5 deletions(-)
Title: Describe Pedigree Relationships in Words
Description: Describe in words the genealogical relationship between two
members of a given pedigree, using the algorithm in Vigeland (2022)
<doi:10.1186/s12859-022-04759-y>. 'verbalisr' is part of the
'pedsuite' collection of packages for pedigree analysis. For a
demonstration of 'verbalisr', see the online app 'QuickPed' at
<https://magnusdv.shinyapps.io/quickped>.
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between verbalisr versions 0.7.1 dated 2024-09-02 and 0.7.2 dated 2025-03-01
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 7 +++++++ R/verbalise.R | 4 +++- README.md | 2 +- build/partial.rdb |binary man/figures/README-habsburg-1.png |binary tests/testthat/test-verbalise.R | 9 ++------- 8 files changed, 24 insertions(+), 20 deletions(-)
Title: Access Formula 1 Data
Description: Obtain Formula 1 data via the 'Jolpica API' <https://jolpi.ca> and the unofficial API <https://www.formula1.com/en/timing/f1-live> via the 'fastf1' 'Python' library <https://docs.fastf1.dev/>.
Author: Santiago Casanova [aut, cre, cph],
Philip Bulsink [aut]
Maintainer: Santiago Casanova <santiago.casanova@yahoo.com>
Diff between f1dataR versions 1.6.0 dated 2024-08-27 and 2.0.0 dated 2025-03-01
f1dataR-1.6.0/f1dataR/inst/doc/ergast-data-analysis.Rmd |only f1dataR-1.6.0/f1dataR/inst/doc/ergast-data-analysis.html |only f1dataR-1.6.0/f1dataR/vignettes/ergast-data-analysis-driver_laptime_scatterplot-1.png |only f1dataR-1.6.0/f1dataR/vignettes/ergast-data-analysis-drivers_laptimes-1.png |only f1dataR-1.6.0/f1dataR/vignettes/ergast-data-analysis-grid_to_finish_one-1.png |only f1dataR-1.6.0/f1dataR/vignettes/ergast-data-analysis-grid_to_finish_season-1.png |only f1dataR-1.6.0/f1dataR/vignettes/ergast-data-analysis-quali_compare-1.png |only f1dataR-1.6.0/f1dataR/vignettes/ergast-data-analysis-remade_rounds_points-1.png |only f1dataR-1.6.0/f1dataR/vignettes/ergast-data-analysis-round_position-1.png |only f1dataR-1.6.0/f1dataR/vignettes/ergast-data-analysis-rounds_points-1.png |only f1dataR-1.6.0/f1dataR/vignettes/ergast-data-analysis.Rmd |only f1dataR-2.0.0/f1dataR/DESCRIPTION | 8 f1dataR-2.0.0/f1dataR/MD5 | 96 +++++----- f1dataR-2.0.0/f1dataR/NEWS.md | 10 - f1dataR-2.0.0/f1dataR/R/clear_f1_cache.R | 2 f1dataR-2.0.0/f1dataR/R/load_circuits.R | 2 f1dataR-2.0.0/f1dataR/R/load_constructors.R | 28 ++ f1dataR-2.0.0/f1dataR/R/load_drivers.R | 4 f1dataR-2.0.0/f1dataR/R/load_laps.R | 30 +-- f1dataR-2.0.0/f1dataR/R/load_pitstops.R | 4 f1dataR-2.0.0/f1dataR/R/load_quali.R | 2 f1dataR-2.0.0/f1dataR/R/load_results.R | 5 f1dataR-2.0.0/f1dataR/R/load_schedule.R | 2 f1dataR-2.0.0/f1dataR/R/load_sprint.R | 2 f1dataR-2.0.0/f1dataR/R/load_standings.R | 2 f1dataR-2.0.0/f1dataR/R/plot_fastest.R | 9 f1dataR-2.0.0/f1dataR/R/utils.R | 90 +++++++++ f1dataR-2.0.0/f1dataR/README.md | 37 --- f1dataR-2.0.0/f1dataR/build/vignette.rds |binary f1dataR-2.0.0/f1dataR/inst/doc/alonso-penalty-2024.html | 7 f1dataR-2.0.0/f1dataR/inst/doc/introduction.html | 15 - f1dataR-2.0.0/f1dataR/inst/doc/jolpica-data-analysis.Rmd |only f1dataR-2.0.0/f1dataR/inst/doc/jolpica-data-analysis.html |only f1dataR-2.0.0/f1dataR/inst/doc/plotting-turn-info.html | 9 f1dataR-2.0.0/f1dataR/inst/doc/setup_fastf1.html | 1 f1dataR-2.0.0/f1dataR/man/clear_cache.Rd | 2 f1dataR-2.0.0/f1dataR/man/get_jolpica_content.Rd |only f1dataR-2.0.0/f1dataR/tests/testthat/Rplots.pdf |only f1dataR-2.0.0/f1dataR/tests/testthat/setup.R | 10 - f1dataR-2.0.0/f1dataR/tests/testthat/test-clear_f1_cache.R | 8 f1dataR-2.0.0/f1dataR/tests/testthat/test-load_circuits.R | 4 f1dataR-2.0.0/f1dataR/tests/testthat/test-load_constructors.R | 5 f1dataR-2.0.0/f1dataR/tests/testthat/test-load_drivers.R | 4 f1dataR-2.0.0/f1dataR/tests/testthat/test-load_laps.R | 10 - f1dataR-2.0.0/f1dataR/tests/testthat/test-load_pitstops.R | 4 f1dataR-2.0.0/f1dataR/tests/testthat/test-load_quali.R | 4 f1dataR-2.0.0/f1dataR/tests/testthat/test-load_results.R | 6 f1dataR-2.0.0/f1dataR/tests/testthat/test-load_schedule.R | 4 f1dataR-2.0.0/f1dataR/tests/testthat/test-load_sprint.R | 4 f1dataR-2.0.0/f1dataR/tests/testthat/test-load_standings.R | 4 f1dataR-2.0.0/f1dataR/tests/testthat/test-utils.R | 6 f1dataR-2.0.0/f1dataR/vignettes/jolpica-data-analysis-driver_laptime_scatterplot-1.png |only f1dataR-2.0.0/f1dataR/vignettes/jolpica-data-analysis-drivers_laptimes-1.png |only f1dataR-2.0.0/f1dataR/vignettes/jolpica-data-analysis-grid_to_finish_one-1.png |only f1dataR-2.0.0/f1dataR/vignettes/jolpica-data-analysis-grid_to_finish_season-1.png |only f1dataR-2.0.0/f1dataR/vignettes/jolpica-data-analysis-quali_compare-1.png |only f1dataR-2.0.0/f1dataR/vignettes/jolpica-data-analysis-remade_rounds_points-1.png |only f1dataR-2.0.0/f1dataR/vignettes/jolpica-data-analysis-round_position-1.png |only f1dataR-2.0.0/f1dataR/vignettes/jolpica-data-analysis-rounds_points-1.png |only f1dataR-2.0.0/f1dataR/vignettes/jolpica-data-analysis.Rmd |only f1dataR-2.0.0/f1dataR/vignettes/precompile.R | 5 61 files changed, 279 insertions(+), 166 deletions(-)
Title: Plot Function for Single-Case Data Frames
Description: Add-on for the 'scan' package that creates plots
from single-case data frames ('scdf'). It includes functions for styling
single-case plots, adding phase-based lines to indicate various statistical
parameters, and predefined themes for presentations and publications. More
information and in depth examples can be found in the online book
"Analyzing Single-Case Data with R and 'scan"
Jürgen Wilbert (2025) <https://jazznbass.github.io/scan-Book/>.
Author: Juergen Wilbert [aut, cre]
Maintainer: Juergen Wilbert <juergen.wilbert@uni-muenster.de>
Diff between scplot versions 0.5.0 dated 2025-02-05 and 0.5.1 dated 2025-03-01
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ R/scplot.sc_rand.R | 2 +- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Single-Case Data Analyses for Single and Multiple Baseline
Designs
Description: A collection of procedures for analysing, visualising,
and managing single-case data. These include piecewise linear regression
models, multilevel models, overlap indices ('PND', 'PEM', 'PAND', 'PET', 'tau-u',
'baseline corrected tau', 'CDC'), and randomization tests. Data preparation functions
support outlier detection, handling missing values, scaling, and custom transformations.
An export function helps to generate
html, word, and latex tables in a publication friendly style. More details can be
found in the online book 'Analyzing single-case data with R and scan', Juergen Wilbert (2025)
<https://jazznbass.github.io/scan-Book/>.
Author: Juergen Wilbert [cre, aut] ,
Timo Lueke [aut]
Maintainer: Juergen Wilbert <juergen.wilbert@uni-muenster.de>
Diff between scan versions 0.62.0 dated 2025-02-05 and 0.63.0 dated 2025-03-01
DESCRIPTION | 12 - MD5 | 75 +++++---- NAMESPACE | 7 NEWS.md | 20 ++ R/anova.R |only R/between_smd.R | 133 +++++++++++++--- R/bplm.R |only R/coefficents.sc_plm.R | 5 R/export.R | 1 R/export.sc_hplm.R | 76 +++------ R/export.scdf.R | 34 +++- R/hplm.R | 44 +++-- R/mplm.R | 34 ++-- R/plm.R | 20 +- R/plm_contrasts.R | 136 +++++++++++------ R/print-export-bplm.R |only R/print-export-plm.R | 296 ++++++++++++++++++++----------------- R/print.sc_bcsmd.R | 5 R/print.sc_hplm.R | 116 ++++++++++---- R/print.sc_mplm.R | 28 --- R/privat-rename_phase_duplicates.R | 9 + R/private-regression.R | 114 ++++++++------ R/private_options.R | 2 R/private_options_mc.R | 8 - R/scan-package.R | 1 R/scan.R | 1 inst/shiny/resources.R | 1 inst/shiny/server.R | 2 inst/shiny/ui.R | 6 man/add_dummy_variables.Rd |only man/anova.sc_plm.Rd |only man/autocorr.Rd | 1 man/between_smd.Rd | 42 ++++- man/bplm.Rd |only man/corrected_tau.Rd | 1 man/export.Rd | 7 man/hplm.Rd | 9 - man/mplm.Rd | 1 man/plm.Rd | 1 man/print.sc.Rd | 7 man/trend.Rd | 1 tests/testthat/test-plm.R |only 42 files changed, 799 insertions(+), 457 deletions(-)
Title: Utilities for Importing and Manipulating Biomedical Data Files
Description: Tools to read various file types into one list of data structures, usually, but not limited to, data frames.
Excel files are read sheet-wise, i.e., all or a selection of sheets can be read. Field delimiters and decimal
separators are determined automatically.
Author: Vidal Fey [aut, cre]
Maintainer: Vidal Fey <vidal.fey@gmail.com>
Diff between readmoRe versions 0.2-12 dated 2021-08-19 and 0.2-15 dated 2025-03-01
DESCRIPTION | 13 +++++++------ MD5 | 16 ++++++++-------- R/get.skip.R | 2 +- R/read.to.list.R | 12 ++++++------ R/rm.empty.cols.R | 6 +++--- man/get.skip.Rd | 2 +- man/read.to.list.Rd | 10 +++++----- man/readmoRe.Rd | 2 +- man/rm.empty.cols.Rd | 6 +++--- 9 files changed, 35 insertions(+), 34 deletions(-)
Title: Analysis Results Data
Description: Construct CDISC (Clinical Data Interchange Standards
Consortium) compliant Analysis Results Data objects. These objects are
used and re-used to construct summary tables, visualizations, and
written reports. The package also exports utilities for working with
these objects and creating new Analysis Results Data objects.
Author: Daniel D. Sjoberg [aut, cre] ,
Becca Krouse [aut],
Emily de la Rua [aut],
F. Hoffmann-La Roche AG [cph, fnd],
GlaxoSmithKline Research & Development Limited [cph]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between cards versions 0.5.0 dated 2025-02-17 and 0.5.1 dated 2025-03-01
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/apply_fmt_fn.R | 2 +- tests/testthat/test-apply_fmt_fn.R | 11 +++++++++++ 5 files changed, 23 insertions(+), 8 deletions(-)
Title: Calculate Earth’s Obliquity and Precession in the Past
Description: Easily calculate precession and obliquity from an orbital solution (defaults to ZB18a from Zeebe and Lourens (2019) <doi:10.1126/science.aax0612>) and assumed or reconstructed values for tidal dissipation (Td) and dynamical ellipticity (Ed). This is a translation and adaptation of the 'C'-code in the supplementary material to Zeebe and Lourens (2022) <doi:10.1029/2021PA004349>, with further details on the methodology described in Zeebe (2022) <doi:10.3847/1538-3881/ac80f8>. The name of the 'C'-routine is 'snvec', which refers to the key units of computation: spin vector s and orbit normal vector n.
Author: Ilja Kocken [aut, cre, trl, cph]
,
Richard Zeebe [aut]
Maintainer: Ilja Kocken <ikocken@hawaii.edu>
Diff between snvecR versions 3.9.4 dated 2024-05-29 and 3.10.0 dated 2025-03-01
DESCRIPTION | 12 MD5 | 42 +-- NEWS.md | 6 R/data.R | 48 +++ R/euler.R | 60 ++++ R/get_solution.R | 341 ++++++++++++++++------------ R/prepare_solution.R | 1 R/snvec.R | 68 +++-- R/unwrap.R | 1 README.md | 14 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/analyze_grid_td-ed.R | 2 inst/doc/analyze_grid_td-ed.html | 409 ++++++++++++++++------------------ man/PT-ZB18a.Rd |only man/ZB23.Rxx.Rd |only man/get_solution.Rd | 1 man/snvec.Rd | 1 tests/testthat/_snaps/get_solution.md | 98 +++++++- tests/testthat/_snaps/snvec.md | 111 ++++----- tests/testthat/test-euler.R | 12 tests/testthat/test-get_solution.R | 48 +++ tests/testthat/test-snvec.R | 136 ++++++++--- 23 files changed, 890 insertions(+), 521 deletions(-)
Title: Create Pharmacometric Models
Description: Provides a user interface to create or modify pharmacometric
models for various modeling and simulation software platforms.
Author: Sebastien Bihorel [cre, aut]
Maintainer: Sebastien Bihorel <sb.pmlab@gmail.com>
Diff between pmxcode versions 0.1.4 dated 2024-10-19 and 0.2.0 dated 2025-02-28
pmxcode-0.1.4/pmxcode/man/get_mrg_individual_parm_code.Rd |only pmxcode-0.2.0/pmxcode/DESCRIPTION | 6 pmxcode-0.2.0/pmxcode/LICENSE | 2 pmxcode-0.2.0/pmxcode/MD5 | 36 pmxcode-0.2.0/pmxcode/NEWS.md | 7 pmxcode-0.2.0/pmxcode/R/golem_utils_ui.R | 30 pmxcode-0.2.0/pmxcode/R/new_model_server.R | 394 ++++++++-- pmxcode-0.2.0/pmxcode/R/new_model_ui.R | 9 pmxcode-0.2.0/pmxcode/R/utils_common.R | 28 pmxcode-0.2.0/pmxcode/R/utils_mrgsolve.R | 237 ++++-- pmxcode-0.2.0/pmxcode/R/utils_nonmem.R | 203 +++-- pmxcode-0.2.0/pmxcode/R/zzz.R | 3 pmxcode-0.2.0/pmxcode/inst/resources/labelunit_lib.json | 20 pmxcode-0.2.0/pmxcode/inst/resources/logit_variability_derivation.Rmd |only pmxcode-0.2.0/pmxcode/inst/resources/parm_lib.json | 4 pmxcode-0.2.0/pmxcode/inst/resources/rv_lib.json | 8 pmxcode-0.2.0/pmxcode/man/get_mrg_parms_code.Rd | 4 pmxcode-0.2.0/pmxcode/man/get_mrg_parms_code_minion.Rd |only pmxcode-0.2.0/pmxcode/man/replace_mrg_omega.Rd | 4 pmxcode-0.2.0/pmxcode/man/replace_mrg_param.Rd | 4 pmxcode-0.2.0/pmxcode/man/scale_value.Rd |only 21 files changed, 738 insertions(+), 261 deletions(-)
Title: Analyzing the Orientation of Maximum Horizontal Stress
Description: Models the direction of the maximum horizontal stress using
relative plate motion parameters. Statistical algorithms to evaluate
the modeling results compared with the observed data. Provides plots
to visualize the results. Methods described in Stephan et al. (2023)
<doi:10.1038/s41598-023-42433-2> and Wdowinski (1998)
<doi:10.1016/S0079-1946(98)00091-3>.
Author: Tobias Stephan [aut, cre]
Maintainer: Tobias Stephan <tobias.stephan1@yahoo.com>
Diff between tectonicr versions 0.4.5 dated 2025-02-26 and 0.4.6 dated 2025-02-28
tectonicr-0.4.5/tectonicr/tests/testthat/Rplots.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots1.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots10.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots11.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots12.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots13.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots14.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots15.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots16.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots17.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots18.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots19.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots2.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots20.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots21.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots22.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots23.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots24.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots25.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots26.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots27.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots3.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots4.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots5.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots6.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots7.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots8.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/Rplots9.pdf |only tectonicr-0.4.5/tectonicr/tests/testthat/test-coordinates.R |only tectonicr-0.4.5/tectonicr/tests/testthat/test-draw_eulerpole.R |only tectonicr-0.4.5/tectonicr/tests/testthat/test-misfit_shmax.R |only tectonicr-0.4.5/tectonicr/tests/testthat/test-model_shmax.R |only tectonicr-0.4.5/tectonicr/tests/testthat/test-nuvel1.R |only tectonicr-0.4.5/tectonicr/tests/testthat/test-rotation.R |only tectonicr-0.4.5/tectonicr/tests/testthat/test-various.R |only tectonicr-0.4.6/tectonicr/DESCRIPTION | 6 tectonicr-0.4.6/tectonicr/MD5 | 79 tectonicr-0.4.6/tectonicr/NEWS.md | 4 tectonicr-0.4.6/tectonicr/R/draw_eulerpole.R | 557 +- tectonicr-0.4.6/tectonicr/R/interpolation.R | 2039 ++++--- tectonicr-0.4.6/tectonicr/R/model_shmax.R | 1081 ++- tectonicr-0.4.6/tectonicr/R/pb_distance.R | 443 - tectonicr-0.4.6/tectonicr/R/plotting.R | 2719 +++++----- tectonicr-0.4.6/tectonicr/R/statistics.R | 2393 ++++---- tectonicr-0.4.6/tectonicr/R/various.R | 691 +- tectonicr-0.4.6/tectonicr/inst/doc/A_tectonicr.html | 4 tectonicr-0.4.6/tectonicr/inst/doc/B_datasets.html | 4 tectonicr-0.4.6/tectonicr/inst/doc/C_stress_trajectories.html | 4 tectonicr-0.4.6/tectonicr/inst/doc/D_statistics.html | 10 tectonicr-0.4.6/tectonicr/inst/doc/E_interpolation.html | 4 tectonicr-0.4.6/tectonicr/inst/doc/F_spatial.html | 8 tectonicr-0.4.6/tectonicr/man/PoR2Geo_azimuth.Rd | 4 tectonicr-0.4.6/tectonicr/man/PoR_azi.Rd | 4 tectonicr-0.4.6/tectonicr/man/PoR_map.Rd | 5 tectonicr-0.4.6/tectonicr/man/axes.Rd | 2 tectonicr-0.4.6/tectonicr/man/line_azimuth.Rd | 7 tectonicr-0.4.6/tectonicr/tests/testthat.R | 24 tectonicr-0.4.6/tectonicr/tests/testthat/test_that.R | 50 58 files changed, 5157 insertions(+), 4985 deletions(-)
Title: An R 'Pandoc' Writer
Description: Contains some functions catching all messages, 'stdout' and other
useful information while evaluating R code and other helpers to return user
specified text elements (like: header, paragraph, table, image, lists etc.)
in 'pandoc' markdown or several type of R objects similarly automatically
transformed to markdown format. Also capable of exporting/converting (the
resulting) complex 'pandoc' documents to e.g. HTML, 'PDF', 'docx' or 'odt'. This
latter reporting feature is supported in brew syntax or with a custom reference
class with a smarty caching 'backend'.
Author: Gergely Daroczi [aut, cre] ,
Roman Tsegelskyi [aut]
Maintainer: Gergely Daroczi <daroczig@rapporter.net>
Diff between pander versions 0.6.5 dated 2022-03-18 and 0.6.6 dated 2025-02-28
pander-0.6.5/pander/NEWS |only pander-0.6.6/pander/DESCRIPTION | 10 pander-0.6.6/pander/MD5 | 36 +- pander-0.6.6/pander/NAMESPACE | 1 pander-0.6.6/pander/NEWS.md |only pander-0.6.6/pander/R/S3.R | 3 pander-0.6.6/pander/R/convert.R | 2 pander-0.6.6/pander/R/helpers.R | 4 pander-0.6.6/pander/README.md | 4 pander-0.6.6/pander/build/vignette.rds |binary pander-0.6.6/pander/inst/README.brew | 4 pander-0.6.6/pander/inst/doc/evals.html | 425 ++++--------------------- pander-0.6.6/pander/inst/doc/knitr.html | 291 +---------------- pander-0.6.6/pander/inst/doc/pander.html | 374 +++------------------- pander-0.6.6/pander/inst/doc/pandoc_table.Rmd | 2 pander-0.6.6/pander/inst/doc/pandoc_table.html | 338 +------------------ pander-0.6.6/pander/man/Pandoc.convert.Rd | 2 pander-0.6.6/pander/man/splitLine.Rd | 4 pander-0.6.6/pander/src/RcppExports.cpp | 5 pander-0.6.6/pander/vignettes/pandoc_table.Rmd | 2 20 files changed, 231 insertions(+), 1276 deletions(-)
Title: Transfer Learning under Regularized Generalized Linear Models
Description: We provide an efficient implementation for two-step multi-source transfer learning algorithms in high-dimensional generalized linear models (GLMs). The elastic-net penalized GLM with three popular families, including linear, logistic and Poisson regression models, can be fitted. To avoid negative transfer, a transferable source detection algorithm is proposed. We also provides visualization for the transferable source detection results. The details of methods can be found in "Tian, Y., & Feng, Y. (2023). Transfer learning under high-dimensional generalized linear models. Journal of the American Statistical Association, 118(544), 2684-2697.".
Author: Ye Tian [aut, cre],
Yang Feng [aut]
Maintainer: Ye Tian <ye.t@columbia.edu>
Diff between glmtrans versions 2.0.0 dated 2022-02-08 and 2.1.0 dated 2025-02-28
DESCRIPTION | 11 +++---- MD5 | 32 ++++++++++---------- R/glmtrans.R | 49 +++++++++++++++++-------------- R/glmtrans_inf.R | 14 +++++---- R/models.R | 8 ++--- R/plot.glmtrans.R | 2 - R/predict.glmtrans.R | 10 +++--- R/source_detection.R | 69 +++++++++++++++++++++++++++++++-------------- build/vignette.rds |binary inst/doc/glmtrans-demo.R | 16 +++++----- inst/doc/glmtrans-demo.pdf |binary man/glmtrans.Rd | 35 ++++++++++++---------- man/glmtrans_inf.Rd | 6 +-- man/models.Rd | 12 +++---- man/plot.glmtrans.Rd | 2 - man/predict.glmtrans.Rd | 10 +++--- man/source_detection.Rd | 22 ++++++++------ 17 files changed, 170 insertions(+), 128 deletions(-)
Title: Sequence Symmetry Analysis Using the Observational Medical
Outcomes Partnership Common Data Model
Description: Calculating crude sequence ratio, adjusted sequence ratio and
confidence intervals using data mapped to the Observational Medical
Outcomes Partnership Common Data Model.
Author: Xihang Chen [aut, cre] ,
Tyman Stanford [aut] ,
Berta Raventos [aut] ,
Nicole Pratt [aut] ,
Ed Burn [aut] ,
Marti Catala [aut] ,
Danielle Newby [aut] ,
Nuria Mercade-Besora [aut] ,
Mike Du [aut] ,
Yuchen Guo [aut] ,
Kim Lopez [aut] ,
Marta Alcalde-He [...truncated...]
Maintainer: Xihang Chen <xihang.chen@ndorms.ox.ac.uk>
Diff between CohortSymmetry versions 0.2.1 dated 2025-02-12 and 0.2.2 dated 2025-02-28
DESCRIPTION | 22 +- MD5 | 18 - R/mockCohortSymmetry.R | 5 inst/doc/a01_Introduction.Rmd | 260 +++++++++++++------------- inst/doc/a01_Introduction.html | 14 - inst/doc/a02_Generate_a_sequence_cohort.html | 4 inst/doc/a03_Summarise_sequence_ratios.html | 2 inst/doc/a04_Visualise_sequence_ratios.html | 6 inst/doc/a05_Summarise_temporal_symmetry.html | 12 - vignettes/a01_Introduction.Rmd | 260 +++++++++++++------------- 10 files changed, 301 insertions(+), 302 deletions(-)
More information about CohortSymmetry at CRAN
Permanent link
Title: Miscellaneous (Stats) Helper Functions with Sane Defaults for
Reporting
Description: Helper functions that act as wrappers to more advanced statistical
methods with the advantage of having sane defaults for quick reporting.
Author: Gergely Daroczi [aut, cre] ,
Aleksandar Blagotic [aut]
Maintainer: Gergely Daroczi <daroczig@rapporter.net>
Diff between rapportools versions 1.1 dated 2022-03-21 and 1.2 dated 2025-02-28
rapportools-1.1/rapportools/inst/CITATION |only rapportools-1.2/rapportools/DESCRIPTION | 19 +++++++++++-------- rapportools-1.2/rapportools/MD5 | 13 ++++++------- rapportools-1.2/rapportools/NEWS | 26 +++++++++++++++----------- rapportools-1.2/rapportools/R/univar.R | 4 ++-- rapportools-1.2/rapportools/R/utils.R | 2 +- rapportools-1.2/rapportools/man/max.Rd | 2 +- rapportools-1.2/rapportools/man/min.Rd | 2 +- 8 files changed, 37 insertions(+), 31 deletions(-)
Title: Insurance Reserve Calculations
Description: Calculates insurance reserves and equivalence premiums using advanced numerical methods, including the Runge-Kutta algorithm and product integrals for transition probabilities. This package is useful for actuarial analyses and life insurance modeling, facilitating accurate financial projections.
Author: Oskar Allerslev [aut, cre]
Maintainer: Oskar Allerslev <Oskar.m1660@gmail.com>
Diff between lifepack versions 0.0.8 dated 2025-01-29 and 0.1.0 dated 2025-02-28
DESCRIPTION | 10 +- MD5 | 33 +++++--- NAMESPACE | 2 R/RcppExports.R |only R/equiv_premium.R | 66 ++++++++--------- R/lifepack-package.R |only R/prodint.R | 40 +++------- R/reserve.R | 56 +++++++------- R/sreserve.R | 62 ++++++++-------- build/vignette.rds |binary inst/doc/lifepack-overview.Rmd | 136 ++++++++++++++++++------------------ man/prodint.Rd | 21 ++--- man/sreserve.Rd | 72 +++++++++---------- src |only tests/testthat/test-equiv_premium.R | 56 +++++++------- tests/testthat/test-reserve.R | 56 +++++++------- tests/testthat/test-sreserve.R | 56 +++++++------- vignettes/lifepack-overview.Rmd | 136 ++++++++++++++++++------------------ 18 files changed, 397 insertions(+), 405 deletions(-)
Title: Adapted Pair Correlation Function
Description: The adapted pair correlation function transfers the concept of the
pair correlation function from point patterns to patterns of objects of
finite size and irregular shape (e.g. lakes within a country). The pair
correlation function describes the spatial distribution of objects, e.g.
random, aggregated or regularly spaced. This is a reimplementation of the
method suggested by Nuske et al. (2009) <doi:10.1016/j.foreco.2009.09.050>
using the library 'GEOS'.
Author: Robert Nuske [aut, cre]
Maintainer: Robert Nuske <robert.nuske@mailbox.org>
Diff between apcf versions 0.3.1 dated 2024-06-13 and 0.3.2 dated 2025-02-28
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 3 +++ build/vignette.rds |binary configure | 18 +----------------- configure.ac | 18 +----------------- inst/doc/intro.html | 14 +++++++------- 7 files changed, 21 insertions(+), 50 deletions(-)
Title: Generalized Additive Extreme Value Models for Location, Scale
and Shape
Description: Fits generalized additive models for the location, scale and shape
parameters of a generalized extreme value response distribution. The
methodology is based on Rigby, R.A. and Stasinopoulos, D.M. (2005),
<doi:10.1111/j.1467-9876.2005.00510.x> and implemented using functions from
the 'gamlss' package <doi:10.32614/CRAN.package.gamlss>.
Author: Paul J. Northrop [aut, cre, cph],
Jennifer Ji [aut]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Diff between gamlssx versions 1.0.1 dated 2024-06-26 and 1.0.2 dated 2025-02-28
DESCRIPTION | 12 +++++------ MD5 | 33 ++++++++++++++++++------------- NAMESPACE | 1 NEWS.md |only R/GEVfamily.R | 10 ++++----- R/fitGEV.R | 10 +++++---- R/gamlssx-package.R | 1 R/gevExpInfo.R | 2 - README.md | 26 ++++++++++++------------ build/partial.rdb |binary man/GEV.Rd | 6 ++--- man/figures/README-unnamed-chunk-2-4.png |binary man/figures/README-unnamed-chunk-2-5.png |binary man/figures/README-unnamed-chunk-3-1.png |only man/figures/README-unnamed-chunk-4-1.png |only man/figures/README-unnamed-chunk-6-1.png |only man/figures/README-unnamed-chunk-7-1.png |only man/figures/README-unnamed-chunk-8-1.png |only man/fitGEV.Rd | 8 ++++--- man/gevExpInfo.Rd | 2 - tools |only 21 files changed, 62 insertions(+), 49 deletions(-)
Title: Fast Estimators for Design-Based Inference
Description: Fast procedures for small set of commonly-used, design-appropriate estimators with robust standard errors and confidence intervals. Includes estimators for linear regression, instrumental variables regression, difference-in-means, Horvitz-Thompson estimation, and regression improving precision of experimental estimates by interacting treatment with centered pre-treatment covariates introduced by Lin (2013) <doi:10.1214/12-AOAS583>.
Author: Graeme Blair [aut, cre],
Jasper Cooper [aut],
Alexander Coppock [aut],
Macartan Humphreys [aut],
Luke Sonnet [aut],
Neal Fultz [ctb],
Lily Medina [ctb],
Russell Lenth [ctb],
Molly Offer-Westort [ctb]
Maintainer: Graeme Blair <graeme.blair@gmail.com>
Diff between estimatr versions 1.0.4 dated 2024-03-31 and 1.0.6 dated 2025-02-28
DESCRIPTION | 14 ++-- MD5 | 32 +++++----- NEWS.md | 12 +++ R/S3_predict.R | 100 ++++++++++++++++++++++++-------- R/estimatr_lh_robust.R | 37 +++++++++-- R/estimatr_lm_lin.R | 47 +++++++++------ build/partial.rdb |binary man/estimatr.Rd | 1 man/lh_robust.Rd | 6 + man/lm_lin.Rd | 21 +++++- man/predict.lm_robust.Rd | 21 ++++++ tests/testthat/helper-se-types.R | 1 tests/testthat/test-lh-robust.R | 64 +++++++++++++++++++- tests/testthat/test-lm-cluster.R | 1 tests/testthat/test-lm-lin.R | 11 +++ tests/testthat/test-lm-robust_margins.R | 10 +-- tests/testthat/test-s3-methods.R | 64 ++++++++++++++++++-- 17 files changed, 353 insertions(+), 89 deletions(-)
Title: Methods to Analyse Seasonal Radial Tree Growth Data
Description: Methods for comparing different regression algorithms for
describing the temporal dynamics of secondary tree growth (xylem and
phloem). Users can compare the accuracy of the most common fitting methods
usually used to analyse xylem and phloem data, i.e., Gompertz function,
Double Gompertz function, General Additive Models (GAMs); and an algorithm
newly introduced to the field, i.e., Bayesian Regularised Neural Networks
(brnn). The core function of the package is XPSgrowth(), while the results
can be interpreted using implemented generic S3 methods, such as plot() and
summary().
Author: Jernej Jevsenak [aut, cre]
Maintainer: Jernej Jevsenak <jernej.jevsenak@gmail.com>
Diff between rTG versions 1.0.3 dated 2024-07-25 and 1.0.4 dated 2025-02-28
DESCRIPTION | 12 - MD5 | 18 +- NAMESPACE | 2 NEWS.md | 4 R/XPSgrowth.R | 162 ++++++++++++++---- man/XPSgrowth.Rd | 410 ++++++++++++++++++++++------------------------- man/data_dendrometers.Rd | 56 +++--- man/data_trees.Rd | 80 ++++----- man/double_gompertz.Rd | 60 +++--- man/parameters.Rd | 58 +++--- 10 files changed, 473 insertions(+), 389 deletions(-)
Title: Run Interruptible Code Asynchronously
Description: Takes an R expression and returns a Job object with a $stop() method
which can be called to terminate the background job. Also provides timeouts
and other mechanisms for automatically terminating a background job. The
result of the expression is available synchronously via $result or
asynchronously with callbacks or through the 'promises' package framework.
Author: Daniel P. Smith [aut, cre] ,
Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between jobqueue versions 1.4.1 dated 2025-02-21 and 1.5.1 dated 2025-02-28
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 5 +++++ R/process.r | 12 +++++++----- R/queue.r | 21 +++++++++++++-------- R/utils.r | 11 +++++++++++ R/validate.r | 5 +++-- R/worker.r | 31 ++++++++++++++++++------------- man/Queue.Rd | 8 ++++++-- man/Worker.Rd | 8 ++++++-- tests/testthat/test-process.r | 2 +- tests/testthat/test-queue.r | 4 ++++ 12 files changed, 89 insertions(+), 48 deletions(-)
Title: My Toolbox for Assisting Document Editing and Data Presenting
Description: The purpose of this package is to share a collection of functions the author wrote during weekends for managing
kitchen and garden tasks, e.g. making plant growth charts or Thanksgiving kitchen schedule charts, etc.
Functions might include but not limited to:
(1) aiding summarizing time related data;
(2) generating axis transformation from data; and
(3) aiding Markdown (with html output) and Shiny file editing.
Author: Y Hsu [aut, cre]
Maintainer: Y Hsu <yh202109@gmail.com>
Diff between mtb versions 0.1.8 dated 2022-10-20 and 0.1.9 dated 2025-02-28
DESCRIPTION | 14 MD5 | 42 - NEWS.md | 117 ++-- R/helper_timerelated.R | 148 ++--- R/helper_timerelated2.R | 246 ++++---- README.md | 180 +++--- build/vignette.rds |binary inst/doc/mtb_axis.R | 78 +- inst/doc/mtb_axis.html | 887 +++++++++++++++---------------- inst/doc/mtb_bill_summary.R | 66 +- inst/doc/mtb_bill_summary.html | 870 +++++++++++++++--------------- inst/doc/mtb_color.R | 58 +- inst/doc/mtb_color.html | 815 ++++++++++++++-------------- inst/doc/mtb_md.R | 48 - inst/doc/mtb_md.html | 787 +++++++++++++-------------- inst/doc/mtb_timerelated.R | 56 - inst/doc/mtb_timerelated.html | 837 ++++++++++++++--------------- man/figures/README-example_color_2-1.png |binary man/figures/README-example_color_2-2.png |binary man/time_plot_event.Rd | 6 man/time_plot_interval.Rd | 4 tests/testthat/test-helper_timerelated.R | 2 22 files changed, 2635 insertions(+), 2626 deletions(-)