Title: Search Algorithms and Loss Functions for Bayesian Clustering
Description: The SALSO algorithm is an efficient randomized greedy search method to find a point estimate for a random partition based on a loss function and posterior Monte Carlo samples. The algorithm is implemented for many loss functions, including the Binder loss and a generalization of the variation of information loss, both of which allow for unequal weights on the two types of clustering mistakes. Efficient implementations are also provided for Monte Carlo estimation of the posterior expected loss of a given clustering estimate. See Dahl, Johnson, Müller (2022) <doi:10.1080/10618600.2022.2069779>.
Author: David B. Dahl [aut, cre] ,
Devin J. Johnson [aut] ,
Peter Mueller [aut],
Andres Felipe Barrientos [aut],
Garritt Page [aut],
David Dunson [aut],
Alex Crichton [ctb] ,
Brendan Zabarauskas [ctb] ,
David B. Dahl [ctb] ,
David Tolnay [ctb] ,
Jim Turner [c [...truncated...]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between salso versions 0.3.51 dated 2025-03-30 and 0.3.53 dated 2025-04-10
DESCRIPTION | 9 MD5 | 22 NEWS | 4 src/rust/Cargo.lock | 81 src/rust/Cargo.toml | 2 src/rust/rbindings/Cargo.lock | 2 src/rust/rbindings/src/lib.rs | 8363 --------------------------------------- src/rust/roxido/Cargo.lock | 23 src/rust/roxido/src/lib.rs | 10 src/rust/roxido_macro/Cargo.lock | 18 src/rust/vendor.tar.gz |binary tools/build_rust_library.R | 36 12 files changed, 104 insertions(+), 8466 deletions(-)
Title: Feature Allocation Neighborhood Greedy Search Algorithm
Description: A neighborhood-based, greedy search algorithm is performed to estimate a feature allocation by minimizing the expected loss based on posterior samples from the feature allocation distribution. The method is described in Dahl, Johnson, and Andros (2023) "Comparison and Bayesian Estimation of Feature Allocations" <doi:10.1080/10618600.2023.2204136>.
Author: David B. Dahl [aut, cre] ,
R. Jacob Andros [aut] ,
Devin J. Johnson [aut] ,
Alex Crichton [ctb] ,
Andrii Dmytrenko [ctb] ,
Brendan Zabarauskas [ctb] ,
David B. Dahl [ctb] ,
David Tolnay [ctb] ,
Jim Turner [ctb] ,
Josh Stone [ctb] ,
Niko Matsakis [ctb [...truncated...]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between fangs versions 0.2.18 dated 2025-03-29 and 0.2.21 dated 2025-04-10
DESCRIPTION | 11 MD5 | 43 NEWS | 5 R/compute_expected_loss.R | 2 R/compute_loss.R | 2 R/fangs.R | 2 man/compute_expected_loss.Rd | 2 man/compute_loss.Rd | 2 man/fangs-package.Rd | 2 man/fangs.Rd | 2 src/rust/Cargo.lock | 78 src/rust/Cargo.toml | 10 src/rust/lapjv-rust/Cargo.lock |only src/rust/lapjv-rust/Cargo.toml | 7 src/rust/lapjv-rust/src/lib.rs | 71 src/rust/rbindings/Cargo.lock | 2 src/rust/rbindings/src/lib.rs | 8363 --------------------------------------- src/rust/roxido/Cargo.lock | 2 src/rust/roxido/src/lib.rs | 10 src/rust/roxido_macro/Cargo.lock | 2 src/rust/src/lib.rs | 2 src/rust/vendor.tar.gz |binary tools/build_rust_library.R | 37 23 files changed, 187 insertions(+), 8470 deletions(-)
Title: Assessing Complex Heterogeneity in Surrogacy
Description: Provides functions to assess complex heterogeneity in the strength of a surrogate marker with respect to multiple baseline covariates, in either a randomized treatment setting or observational setting. For a randomized treatment setting, the functions assess and test for heterogeneity using both a parametric model and a semiparametric two-step model. More details for the randomized setting 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>. For an observational setting, functions in this package assess complex heterogeneity in the strength of a surrogate marker using meta-learners, with options for different base learners. More details for the observational setting will be available in the future in: Knowlton, R., Parast, L. (2025) "Assessing Surrogate Heterogeneity in Real World Data Using Meta-Learners." A tut [...truncated...]
Author: Rebecca Knowlton [aut],
Layla Parast [aut, cre]
Maintainer: Layla Parast <parast@austin.utexas.edu>
Diff between cohetsurr versions 1.1 dated 2025-03-05 and 2.0 dated 2025-04-10
DESCRIPTION | 12 ++++++------ MD5 | 24 +++++++++++++++++------- NAMESPACE | 6 ++++-- R/obs.boot.var.R |only R/obs.estimate.PTE.R |only R/obs.het.surr.R |only data/obs_exampledata_test.RData |only data/obs_exampledata_train.RData |only man/boot.var.Rd | 6 +++--- man/complex.heterogeneity.Rd | 26 ++++++-------------------- man/exampledata.Rd | 2 +- man/obs.boot.var.Rd |only man/obs.estimate.PTE.Rd |only man/obs.het.surr.Rd |only man/obs_exampledata_test.Rd |only man/obs_exampledata_train.Rd |only man/parametric.est.Rd | 6 +++--- man/two.step.est.Rd | 6 +++--- 18 files changed, 43 insertions(+), 45 deletions(-)
Title: Cytokine Profiling Analysis Tool
Description: Provides comprehensive cytokine profiling analysis through quality control using biologically meaningful cutoffs on raw cytokine measurements and by testing for distributional symmetry to recommend appropriate transformations. Offers exploratory data analysis with summary statistics, enhanced boxplots, and barplots, along with univariate and multivariate analytical capabilities for in-depth cytokine profiling such as Principal Component Analysis based on Andrzej Maćkiewicz and Waldemar Ratajczak (1993) <doi:10.1016/0098-3004(93)90090-R>, Sparse Partial Least Squares Discriminant Analysis based on Lê Cao K-A, Boitard S, and Besse P (2011) <doi:10.1186/1471-2105-12-253>, Random Forest based on Breiman, L. (2001) <doi:10.1023/A:1010933404324>, and Extreme Gradient Boosting based on Tianqi Chen and Carlos Guestrin (2016) <doi:10.1145/2939672.2939785>.
Author: Shubh Saraswat [cre, aut, cph]
,
Xiaohua Douglas Zhang [aut]
Maintainer: Shubh Saraswat <shubh.saraswat00@gmail.com>
Diff between CytoProfile versions 0.1.2 dated 2025-04-03 and 0.2.0 dated 2025-04-10
DESCRIPTION | 10 MD5 | 36 +- NEWS.md | 34 ++ R/cyt_bp.R | 8 R/cyt_bp2.R | 10 R/cyt_dualflashplot.R | 6 R/cyt_errbp.R | 448 +++++++++++++++++++----------------- R/cyt_pca.R | 2 R/cyt_skku.R | 18 + R/cyt_splsda.R | 387 +++++++++++++++++-------------- R/cyt_xgb.R | 22 - R/global_variables.R | 4 README.md | 515 ++++++++++-------------------------------- inst/WORDLIST | 5 inst/doc/getting_started.R | 142 +++-------- inst/doc/getting_started.Rmd | 144 +++-------- inst/doc/getting_started.html | 389 ++++++++++++++----------------- man/cyt_errbp.Rd | 141 +++++------ vignettes/getting_started.Rmd | 144 +++-------- 19 files changed, 1051 insertions(+), 1414 deletions(-)
Title: Estimate Functional and Stochastic Parameters of Linear Models
with Correlated Residuals and Missing Data
Description: Implements the Generalized Method of Wavelet Moments with Exogenous Inputs estimator (GMWMX) presented in Voirol, L., Xu, H., Zhang, Y., Insolia, L., Molinari, R. and Guerrier, S. (2024) <doi:10.48550/arXiv.2409.05160>.
The GMWMX estimator allows to estimate functional and stochastic parameters of linear models with correlated residuals in presence of missing data.
The 'gmwmx2' package provides functions to load and plot Global Navigation Satellite System (GNSS) data from the Nevada Geodetic Laboratory and functions to estimate linear model model with correlated residuals in presence of missing data.
Author: Lionel Voirol [aut, cre] ,
Haotian Xu [aut] ,
Yuming Zhang [aut] ,
Luca Insolia [aut] ,
Roberto Molinari [aut] ,
Stephane Guerrier [aut]
Maintainer: Lionel Voirol <lionelvoirol@hotmail.com>
Diff between gmwmx2 versions 0.0.1 dated 2025-03-10 and 0.0.2 dated 2025-04-10
DESCRIPTION | 6 +- MD5 | 26 ++++----- NAMESPACE | 1 NEWS.md | 6 +- R/ngl.R | 78 +++++++++++++++-------------- README.md | 27 ++++++++-- build/vignette.rds |binary inst/doc/estimate_small_network.R | 2 inst/doc/estimate_small_network.Rmd | 2 inst/doc/estimate_small_network.html | 94 ++++++++++++++++++++++++++++++----- inst/doc/fit_model.html | 6 +- inst/doc/load_plot_data_ngl.html | 16 ++--- vignettes/REFERENCES.bib | 2 vignettes/estimate_small_network.Rmd | 2 14 files changed, 181 insertions(+), 87 deletions(-)
Title: Dynamic Function-Oriented 'Make'-Like Declarative Pipelines
Description: Pipeline tools coordinate the pieces of computationally
demanding analysis projects.
The 'targets' package is a 'Make'-like pipeline tool for statistics and
data science in R. The package skips costly runtime for tasks
that are already up to date,
orchestrates the necessary computation with implicit parallel computing,
and abstracts files as R objects. If all the current output matches
the current upstream code and data, then the whole pipeline is up
to date, and the results are more trustworthy than otherwise.
The methodology in this package
borrows from GNU 'Make' (2015, ISBN:978-9881443519)
and 'drake' (2018, <doi:10.21105/joss.00550>).
Author: William Michael Landau [aut, cre]
,
Matthew T. Warkentin [ctb],
Mark Edmondson [ctb] ,
Samantha Oliver [rev] ,
Tristan Mahr [rev] ,
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between targets versions 1.10.1 dated 2025-01-31 and 1.11.1 dated 2025-04-10
targets-1.10.1/targets/R/class_forecast.R |only targets-1.10.1/targets/R/class_summary.R |only targets-1.10.1/targets/R/class_timestamp_positives.R |only targets-1.10.1/targets/R/class_verbose_positives.R |only targets-1.10.1/targets/R/utils_units.R |only targets-1.10.1/targets/tests/testthat/test-class_summary.R |only targets-1.10.1/targets/tests/testthat/test-class_timestamp_positives.R |only targets-1.10.1/targets/tests/testthat/test-class_verbose_positives.R |only targets-1.10.1/targets/tests/testthat/test-utils_units.R |only targets-1.11.1/targets/DESCRIPTION | 14 targets-1.11.1/targets/MD5 | 409 +++++----- targets-1.11.1/targets/NAMESPACE | 38 targets-1.11.1/targets/NEWS.md | 52 + targets-1.11.1/targets/R/class_active.R | 15 targets-1.11.1/targets/R/class_algorithm.R | 18 targets-1.11.1/targets/R/class_auto.R | 14 targets-1.11.1/targets/R/class_aws.R | 3 targets-1.11.1/targets/R/class_aws_file.R | 6 targets-1.11.1/targets/R/class_balanced.R |only targets-1.11.1/targets/R/class_branch.R | 3 targets-1.11.1/targets/R/class_bud.R | 5 targets-1.11.1/targets/R/class_build.R | 6 targets-1.11.1/targets/R/class_builder.R | 44 - targets-1.11.1/targets/R/class_cloud.R | 2 targets-1.11.1/targets/R/class_clustermq.R | 8 targets-1.11.1/targets/R/class_crew.R | 17 targets-1.11.1/targets/R/class_cue.R | 20 targets-1.11.1/targets/R/class_database.R | 33 targets-1.11.1/targets/R/class_database_aws.R | 75 + targets-1.11.1/targets/R/class_database_gcp.R | 59 + targets-1.11.1/targets/R/class_database_local.R | 12 targets-1.11.1/targets/R/class_file.R | 15 targets-1.11.1/targets/R/class_future.R | 6 targets-1.11.1/targets/R/class_gcp.R | 11 targets-1.11.1/targets/R/class_gcp_file.R | 6 targets-1.11.1/targets/R/class_group.R | 14 targets-1.11.1/targets/R/class_inspection.R | 14 targets-1.11.1/targets/R/class_junction.R | 21 targets-1.11.1/targets/R/class_local.R | 4 targets-1.11.1/targets/R/class_meta.R | 30 targets-1.11.1/targets/R/class_network.R | 4 targets-1.11.1/targets/R/class_options.R | 28 targets-1.11.1/targets/R/class_outdated.R | 16 targets-1.11.1/targets/R/class_parallel.R | 150 ++- targets-1.11.1/targets/R/class_passive.R | 10 targets-1.11.1/targets/R/class_pattern.R | 8 targets-1.11.1/targets/R/class_pipeline.R | 31 targets-1.11.1/targets/R/class_prelocal.R | 4 targets-1.11.1/targets/R/class_progress.R | 28 targets-1.11.1/targets/R/class_queue.R | 3 targets-1.11.1/targets/R/class_record.R | 3 targets-1.11.1/targets/R/class_reference.R | 11 targets-1.11.1/targets/R/class_reporter.R | 56 - targets-1.11.1/targets/R/class_runtime.R | 9 targets-1.11.1/targets/R/class_scheduler.R | 10 targets-1.11.1/targets/R/class_sequential.R | 85 +- targets-1.11.1/targets/R/class_settings.R | 24 targets-1.11.1/targets/R/class_silent.R | 7 targets-1.11.1/targets/R/class_sitrep.R | 18 targets-1.11.1/targets/R/class_stem.R | 7 targets-1.11.1/targets/R/class_store.R | 40 targets-1.11.1/targets/R/class_store_file.R | 2 targets-1.11.1/targets/R/class_store_repository_cas_file.R | 6 targets-1.11.1/targets/R/class_target.R | 33 targets-1.11.1/targets/R/class_terse.R |only targets-1.11.1/targets/R/class_timestamp.R | 100 +- targets-1.11.1/targets/R/class_url.R | 2 targets-1.11.1/targets/R/class_verbose.R | 83 +- targets-1.11.1/targets/R/class_visnetwork.R | 6 targets-1.11.1/targets/R/class_visual.R | 19 targets-1.11.1/targets/R/class_workspace.R | 15 targets-1.11.1/targets/R/rstudio_addin_tar_load.R | 2 targets-1.11.1/targets/R/rstudio_addin_tar_make_bg.R | 2 targets-1.11.1/targets/R/rstudio_addin_tar_read.R | 2 targets-1.11.1/targets/R/tar_active.R | 7 targets-1.11.1/targets/R/tar_config_get.R | 24 targets-1.11.1/targets/R/tar_config_set.R | 82 +- targets-1.11.1/targets/R/tar_cue.R | 2 targets-1.11.1/targets/R/tar_debug_instructions.R | 16 targets-1.11.1/targets/R/tar_destroy.R | 15 targets-1.11.1/targets/R/tar_glimpse.R | 2 targets-1.11.1/targets/R/tar_load.R | 2 targets-1.11.1/targets/R/tar_load_raw.R | 2 targets-1.11.1/targets/R/tar_make.R | 88 +- targets-1.11.1/targets/R/tar_make_clustermq.R | 9 targets-1.11.1/targets/R/tar_make_future.R | 9 targets-1.11.1/targets/R/tar_mermaid.R | 14 targets-1.11.1/targets/R/tar_meta.R | 2 targets-1.11.1/targets/R/tar_network.R | 14 targets-1.11.1/targets/R/tar_option_set.R | 21 targets-1.11.1/targets/R/tar_option_with.R |only targets-1.11.1/targets/R/tar_outdated.R | 63 + targets-1.11.1/targets/R/tar_package.R | 8 targets-1.11.1/targets/R/tar_poll.R | 4 targets-1.11.1/targets/R/tar_progress_summary.R | 6 targets-1.11.1/targets/R/tar_sitrep.R | 9 targets-1.11.1/targets/R/tar_target.R | 72 + targets-1.11.1/targets/R/tar_target_raw.R | 3 targets-1.11.1/targets/R/tar_visnetwork.R | 14 targets-1.11.1/targets/R/tar_watch_server.R | 4 targets-1.11.1/targets/R/tar_workspace.R | 10 targets-1.11.1/targets/R/tar_workspace_download.R |only targets-1.11.1/targets/R/tar_workspaces.R | 7 targets-1.11.1/targets/R/use_targets.R | 4 targets-1.11.1/targets/R/utils_assert.R | 2 targets-1.11.1/targets/R/utils_aws.R | 2 targets-1.11.1/targets/R/utils_callr.R | 79 - targets-1.11.1/targets/R/utils_cli.R | 244 +---- targets-1.11.1/targets/R/utils_condition.R | 14 targets-1.11.1/targets/R/utils_imports.R | 13 targets-1.11.1/targets/R/utils_packages.R | 30 targets-1.11.1/targets/R/utils_rstudio.R | 8 targets-1.11.1/targets/R/utils_time.R | 4 targets-1.11.1/targets/build/partial.rdb |binary targets-1.11.1/targets/build/vignette.rds |binary targets-1.11.1/targets/man/tar_config_get.Rd | 3 targets-1.11.1/targets/man/tar_config_projects.Rd | 3 targets-1.11.1/targets/man/tar_config_set.Rd | 26 targets-1.11.1/targets/man/tar_config_unset.Rd | 3 targets-1.11.1/targets/man/tar_config_yaml.Rd | 3 targets-1.11.1/targets/man/tar_cue.Rd | 2 targets-1.11.1/targets/man/tar_destroy.Rd | 10 targets-1.11.1/targets/man/tar_envvars.Rd | 3 targets-1.11.1/targets/man/tar_glimpse.Rd | 2 targets-1.11.1/targets/man/tar_load.Rd | 2 targets-1.11.1/targets/man/tar_load_globals.Rd | 1 targets-1.11.1/targets/man/tar_make.Rd | 51 - targets-1.11.1/targets/man/tar_make_clustermq.Rd | 51 - targets-1.11.1/targets/man/tar_make_future.Rd | 51 - targets-1.11.1/targets/man/tar_mermaid.Rd | 48 - targets-1.11.1/targets/man/tar_meta.Rd | 2 targets-1.11.1/targets/man/tar_network.Rd | 48 - targets-1.11.1/targets/man/tar_option_get.Rd | 3 targets-1.11.1/targets/man/tar_option_reset.Rd | 3 targets-1.11.1/targets/man/tar_option_set.Rd | 80 + targets-1.11.1/targets/man/tar_option_with.Rd |only targets-1.11.1/targets/man/tar_outdated.Rd | 51 - targets-1.11.1/targets/man/tar_sitrep.Rd | 48 - targets-1.11.1/targets/man/tar_target.Rd | 71 + targets-1.11.1/targets/man/tar_traceback.Rd | 1 targets-1.11.1/targets/man/tar_visnetwork.Rd | 50 - targets-1.11.1/targets/man/tar_watch.Rd | 2 targets-1.11.1/targets/man/tar_watch_app_ui.Rd | 2 targets-1.11.1/targets/man/tar_watch_ui.Rd | 2 targets-1.11.1/targets/man/tar_workspace.Rd | 11 targets-1.11.1/targets/man/tar_workspace_download.Rd |only targets-1.11.1/targets/man/tar_workspaces.Rd | 10 targets-1.11.1/targets/tests/aws/test-aws-workspaces.R |only targets-1.11.1/targets/tests/aws/test-aws_long.R | 3 targets-1.11.1/targets/tests/aws/test-aws_meta.R | 8 targets-1.11.1/targets/tests/aws/test-class_aws_file.R | 6 targets-1.11.1/targets/tests/gcp/test-class_gcp_file.R | 6 targets-1.11.1/targets/tests/gcp/test-gcp-workspaces.R |only targets-1.11.1/targets/tests/gcp/test-gcp_long.R | 3 targets-1.11.1/targets/tests/gcp/test-gcp_meta.R | 8 targets-1.11.1/targets/tests/hpc/test-crew_local.R | 10 targets-1.11.1/targets/tests/hpc/test-parallel.R | 42 - targets-1.11.1/targets/tests/interactive/test-crew_retries.R | 2 targets-1.11.1/targets/tests/interactive/test-reporter.R | 57 - targets-1.11.1/targets/tests/testthat/_targets |only targets-1.11.1/targets/tests/testthat/_targets.R |only targets-1.11.1/targets/tests/testthat/test-class_auto.R | 23 targets-1.11.1/targets/tests/testthat/test-class_bud.R | 2 targets-1.11.1/targets/tests/testthat/test-class_builder.R | 69 + targets-1.11.1/targets/tests/testthat/test-class_clustermq.R | 2 targets-1.11.1/targets/tests/testthat/test-class_cue.R | 4 targets-1.11.1/targets/tests/testthat/test-class_database.R | 56 + targets-1.11.1/targets/tests/testthat/test-class_database_aws.R | 1 targets-1.11.1/targets/tests/testthat/test-class_database_gcp.R | 1 targets-1.11.1/targets/tests/testthat/test-class_feather.R | 4 targets-1.11.1/targets/tests/testthat/test-class_inspection.R | 8 targets-1.11.1/targets/tests/testthat/test-class_junction.R | 7 targets-1.11.1/targets/tests/testthat/test-class_meta.R | 52 + targets-1.11.1/targets/tests/testthat/test-class_options.R | 48 - targets-1.11.1/targets/tests/testthat/test-class_outdated.R | 6 targets-1.11.1/targets/tests/testthat/test-class_parallel.R | 335 ++------ targets-1.11.1/targets/tests/testthat/test-class_parquet.R | 4 targets-1.11.1/targets/tests/testthat/test-class_pattern.R | 35 targets-1.11.1/targets/tests/testthat/test-class_pipeline.R | 34 targets-1.11.1/targets/tests/testthat/test-class_progress.R | 15 targets-1.11.1/targets/tests/testthat/test-class_record.R | 4 targets-1.11.1/targets/tests/testthat/test-class_reference.R | 18 targets-1.11.1/targets/tests/testthat/test-class_reporter.R | 3 targets-1.11.1/targets/tests/testthat/test-class_runtime.R | 12 targets-1.11.1/targets/tests/testthat/test-class_scheduler.R | 44 - targets-1.11.1/targets/tests/testthat/test-class_sequential.R | 188 +++- targets-1.11.1/targets/tests/testthat/test-class_stem.R | 49 - targets-1.11.1/targets/tests/testthat/test-class_store_file.R | 8 targets-1.11.1/targets/tests/testthat/test-class_target.R | 8 targets-1.11.1/targets/tests/testthat/test-class_terse.R |only targets-1.11.1/targets/tests/testthat/test-class_timestamp.R | 32 targets-1.11.1/targets/tests/testthat/test-class_torch.R | 1 targets-1.11.1/targets/tests/testthat/test-class_verbose.R | 20 targets-1.11.1/targets/tests/testthat/test-tar_config_set.R | 44 - targets-1.11.1/targets/tests/testthat/test-tar_delete.R | 2 targets-1.11.1/targets/tests/testthat/test-tar_make.R | 32 targets-1.11.1/targets/tests/testthat/test-tar_make_future.R | 2 targets-1.11.1/targets/tests/testthat/test-tar_meta.R | 2 targets-1.11.1/targets/tests/testthat/test-tar_option_set.R | 29 targets-1.11.1/targets/tests/testthat/test-tar_option_with.R |only targets-1.11.1/targets/tests/testthat/test-tar_outdated.R | 7 targets-1.11.1/targets/tests/testthat/test-tar_poll.R |only targets-1.11.1/targets/tests/testthat/test-tar_progress_summary.R | 2 targets-1.11.1/targets/tests/testthat/test-tar_prune.R | 2 targets-1.11.1/targets/tests/testthat/test-tar_read.R | 2 targets-1.11.1/targets/tests/testthat/test-tar_repository_cas_local.R | 22 targets-1.11.1/targets/tests/testthat/test-tar_target.R | 23 targets-1.11.1/targets/tests/testthat/test-tar_target_raw.R | 4 targets-1.11.1/targets/tests/testthat/test-tar_visnetwork.R | 6 targets-1.11.1/targets/tests/testthat/test-tar_workspace_download.R |only targets-1.11.1/targets/tests/testthat/test-utils_assert.R | 7 targets-1.11.1/targets/tests/testthat/test-utils_cli.R | 107 -- targets-1.11.1/targets/tests/testthat/test-utils_imports.R | 3 213 files changed, 2727 insertions(+), 2157 deletions(-)
Title: Automatically Runs 23 Individual and 17 Ensembles of Models
Description: Automatically runs 23 individual models and 17 ensembles on numeric data. The package automatically returns complete results on all 40 models,
25 charts, multiple tables. The user simply provides the data, and answers a few questions (for example, how many times would you like to resample the data).
From there the package randomly splits the data into train, test and validation sets, builds models on the training data, makes predictions on the test and validation sets,
measures root mean squared error (RMSE), removes features above a user-set level of Variance Inflation Factor, and has several optional features including scaling
all numeric data, four different ways to handle strings in the data. Perhaps the most significant feature is the package's ability to make predictions
using the 40 pre trained models on totally new (untrained) data if the user selects that feature. This feature alone represents a very effective solution
to the issue of reproducibility of models in data science. [...truncated...]
Author: Russ Conte [aut, cre, cph]
Maintainer: Russ Conte <russconte@mac.com>
Diff between NumericEnsembles versions 0.5.0 dated 2025-04-01 and 0.7.0 dated 2025-04-10
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/NumericEnsembles.R | 7 ++++--- R/data.R | 4 ++-- data/Boston_housing.rda |binary data/New_Boston.rda |binary man/Boston_housing.Rd | 2 +- man/New_Boston.Rd | 2 +- 9 files changed, 23 insertions(+), 18 deletions(-)
More information about NumericEnsembles at CRAN
Permanent link
Title: Process ArcGIS Protocol Buffer FeatureCollections
Description: Fast processing of ArcGIS FeatureCollection protocol buffers in R.
It is designed to work seamlessly with 'httr2' and integrates with 'sf'.
Author: Josiah Parry [aut, cre]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between arcpbf versions 0.1.6 dated 2024-10-01 and 0.1.7 dated 2025-04-10
arcpbf-0.1.6/arcpbf/src/Makevars |only arcpbf-0.1.6/arcpbf/src/Makevars.win |only arcpbf-0.1.7/arcpbf/DESCRIPTION | 11 - arcpbf-0.1.7/arcpbf/MD5 | 36 ++- arcpbf-0.1.7/arcpbf/NAMESPACE | 1 arcpbf-0.1.7/arcpbf/NEWS.md | 6 arcpbf-0.1.7/arcpbf/R/extendr-wrappers.R | 41 ++-- arcpbf-0.1.7/arcpbf/R/post-process.R | 3 arcpbf-0.1.7/arcpbf/R/resp-body-pbf.R | 1 arcpbf-0.1.7/arcpbf/configure | 2 arcpbf-0.1.7/arcpbf/configure.win | 2 arcpbf-0.1.7/arcpbf/man/httr2.Rd | 5 arcpbf-0.1.7/arcpbf/man/process_pbf.Rd | 2 arcpbf-0.1.7/arcpbf/src/Makevars.in |only arcpbf-0.1.7/arcpbf/src/Makevars.win.in |only arcpbf-0.1.7/arcpbf/src/rust/Cargo.lock | 216 +++++++++++------------ arcpbf-0.1.7/arcpbf/src/rust/arcpbf/Cargo.toml | 3 arcpbf-0.1.7/arcpbf/src/rust/arcpbf/src/parse.rs | 30 ++- arcpbf-0.1.7/arcpbf/src/rust/src |only arcpbf-0.1.7/arcpbf/src/rust/vendor.tar.xz |binary arcpbf-0.1.7/arcpbf/tools/config.R |only arcpbf-0.1.7/arcpbf/tools/msrv.R | 4 22 files changed, 201 insertions(+), 162 deletions(-)
Title: Evapotranspiration R Recipes
Description: An R-based application for exploratory data analysis of global EvapoTranspiration (ET) datasets.
'evapoRe' enables users to download, validate, visualize, and analyze multi-source ET data across various spatio-temporal scales.
Also, the package offers calculation methods for estimating potential ET (PET), including temperature-based, combined type, and radiation-based approaches described in : Oudin et al., (2005) <doi:10.1016/j.jhydrol.2004.08.026>.
'evapoRe' supports hydrological modeling, climate studies, agricultural research, and other data-driven fields by facilitating access to ET data and offering powerful analysis capabilities.
Users can seamlessly integrate the package into their research applications and explore diverse ET data at different resolutions.
Author: Akbar Rahmati Ziveh [aut, cre]
,
Mijael Rodrigo Vargas Godoy [aut]
,
Vishal Thakur [ctb] ,
Yannis Markonis [aut, ths]
Maintainer: Akbar Rahmati Ziveh <rahmati_ziveh@fzp.czu.cz>
Diff between evapoRe versions 1.0.0 dated 2023-11-29 and 1.0.1 dated 2025-04-10
evapoRe-1.0.0/evapoRe/R/download_zheng.R |only evapoRe-1.0.0/evapoRe/R/muldpm.R |only evapoRe-1.0.0/evapoRe/man/download_zheng.Rd |only evapoRe-1.0.0/evapoRe/man/muldpm.Rd |only evapoRe-1.0.1/evapoRe/DESCRIPTION | 17 evapoRe-1.0.1/evapoRe/MD5 | 191 - evapoRe-1.0.1/evapoRe/NAMESPACE | 90 evapoRe-1.0.1/evapoRe/NEWS.md | 27 evapoRe-1.0.1/evapoRe/R/abtew.R |only evapoRe-1.0.1/evapoRe/R/baier_robertson.R |only evapoRe-1.0.1/evapoRe/R/blaney_criddle.R | 118 evapoRe-1.0.1/evapoRe/R/calc_rn.R |only evapoRe-1.0.1/evapoRe/R/calc_u2.R |only evapoRe-1.0.1/evapoRe/R/core_functions.R |only evapoRe-1.0.1/evapoRe/R/day_length.R | 84 evapoRe-1.0.1/evapoRe/R/detect_exeve.R |only evapoRe-1.0.1/evapoRe/R/download_all.R | 83 evapoRe-1.0.1/evapoRe/R/download_bess.R | 84 evapoRe-1.0.1/evapoRe/R/download_camele.R | 84 evapoRe-1.0.1/evapoRe/R/download_data.R | 185 - evapoRe-1.0.1/evapoRe/R/download_era5.R | 84 evapoRe-1.0.1/evapoRe/R/download_era5_land.R | 84 evapoRe-1.0.1/evapoRe/R/download_etmonitor.R |only evapoRe-1.0.1/evapoRe/R/download_etsynthesis.R |only evapoRe-1.0.1/evapoRe/R/download_fldas.R | 88 evapoRe-1.0.1/evapoRe/R/download_gldas_clsm.R | 106 evapoRe-1.0.1/evapoRe/R/download_gldas_noah.R | 102 evapoRe-1.0.1/evapoRe/R/download_gldas_vic.R | 106 evapoRe-1.0.1/evapoRe/R/download_gleam.R | 104 evapoRe-1.0.1/evapoRe/R/download_jra55.R | 87 evapoRe-1.0.1/evapoRe/R/download_merra2.R | 87 evapoRe-1.0.1/evapoRe/R/download_sith.R |only evapoRe-1.0.1/evapoRe/R/download_t_data.R | 228 - evapoRe-1.0.1/evapoRe/R/download_terraclimate.R | 91 evapoRe-1.0.1/evapoRe/R/esr.R | 102 evapoRe-1.0.1/evapoRe/R/esr_dates.R | 83 evapoRe-1.0.1/evapoRe/R/fetch_pet_requirements.R |only evapoRe-1.0.1/evapoRe/R/gldas_clsm_esp_ts.R | 20 evapoRe-1.0.1/evapoRe/R/gldas_clsm_global_ts.R | 20 evapoRe-1.0.1/evapoRe/R/gldas_clsm_subset_ts.R | 20 evapoRe-1.0.1/evapoRe/R/globals.R | 61 evapoRe-1.0.1/evapoRe/R/hamon.R | 121 evapoRe-1.0.1/evapoRe/R/hargreaves_samani.R |only evapoRe-1.0.1/evapoRe/R/heat_index.R | 106 evapoRe-1.0.1/evapoRe/R/jensen_haise.R | 124 evapoRe-1.0.1/evapoRe/R/mcguinness_bordne.R | 120 evapoRe-1.0.1/evapoRe/R/oudin.R | 123 evapoRe-1.0.1/evapoRe/R/penman_monteith_f56.R |only evapoRe-1.0.1/evapoRe/R/pet.R | 140 evapoRe-1.0.1/evapoRe/R/pet_oudin_esp_ts.R | 22 evapoRe-1.0.1/evapoRe/R/pet_oudin_global_ts.R | 22 evapoRe-1.0.1/evapoRe/R/pet_oudin_subset_ts.R | 22 evapoRe-1.0.1/evapoRe/R/pet_params.R |only evapoRe-1.0.1/evapoRe/R/priestly_taylor.R |only evapoRe-1.0.1/evapoRe/R/thornthwaite.R | 141 evapoRe-1.0.1/evapoRe/R/turc.R |only evapoRe-1.0.1/evapoRe/build/vignette.rds |binary evapoRe-1.0.1/evapoRe/inst/WORDLIST |only evapoRe-1.0.1/evapoRe/inst/WORDLIST.R | 130 evapoRe-1.0.1/evapoRe/inst/doc/evapoRe.R | 400 +- evapoRe-1.0.1/evapoRe/inst/doc/evapoRe.Rmd | 1492 ++++---- evapoRe-1.0.1/evapoRe/inst/doc/evapoRe.html | 3215 +++++++++---------- evapoRe-1.0.1/evapoRe/man/abtew.Rd |only evapoRe-1.0.1/evapoRe/man/baier_robertson.Rd |only evapoRe-1.0.1/evapoRe/man/blaney_criddle.Rd | 49 evapoRe-1.0.1/evapoRe/man/calc_rn.Rd |only evapoRe-1.0.1/evapoRe/man/calc_u2.Rd |only evapoRe-1.0.1/evapoRe/man/day_length.Rd | 36 evapoRe-1.0.1/evapoRe/man/detect_exeve.Rd |only evapoRe-1.0.1/evapoRe/man/download_all.Rd | 71 evapoRe-1.0.1/evapoRe/man/download_bess.Rd | 71 evapoRe-1.0.1/evapoRe/man/download_camele.Rd | 76 evapoRe-1.0.1/evapoRe/man/download_data.Rd | 128 evapoRe-1.0.1/evapoRe/man/download_era5.Rd | 71 evapoRe-1.0.1/evapoRe/man/download_era5_land.Rd | 76 evapoRe-1.0.1/evapoRe/man/download_etmonitor.Rd |only evapoRe-1.0.1/evapoRe/man/download_etsynthesis.Rd |only evapoRe-1.0.1/evapoRe/man/download_fldas.Rd | 71 evapoRe-1.0.1/evapoRe/man/download_gldas_clsm.Rd | 84 evapoRe-1.0.1/evapoRe/man/download_gldas_noah.Rd | 84 evapoRe-1.0.1/evapoRe/man/download_gldas_vic.Rd | 84 evapoRe-1.0.1/evapoRe/man/download_gleam.Rd | 84 evapoRe-1.0.1/evapoRe/man/download_jra55.Rd | 71 evapoRe-1.0.1/evapoRe/man/download_merra2.Rd | 76 evapoRe-1.0.1/evapoRe/man/download_sith.Rd |only evapoRe-1.0.1/evapoRe/man/download_t_data.Rd | 116 evapoRe-1.0.1/evapoRe/man/download_terraclimate.Rd | 76 evapoRe-1.0.1/evapoRe/man/esr.Rd | 46 evapoRe-1.0.1/evapoRe/man/esr_dates.Rd | 36 evapoRe-1.0.1/evapoRe/man/gldas_clsm_esp_ts.Rd | 46 evapoRe-1.0.1/evapoRe/man/gldas_clsm_global_ts.Rd | 46 evapoRe-1.0.1/evapoRe/man/gldas_clsm_subset_ts.Rd | 46 evapoRe-1.0.1/evapoRe/man/hamon.Rd | 49 evapoRe-1.0.1/evapoRe/man/hargreaves_samani.Rd |only evapoRe-1.0.1/evapoRe/man/heat_index.Rd | 36 evapoRe-1.0.1/evapoRe/man/jensen_haise.Rd | 49 evapoRe-1.0.1/evapoRe/man/mcguinness_bordne.Rd | 49 evapoRe-1.0.1/evapoRe/man/oudin.Rd | 49 evapoRe-1.0.1/evapoRe/man/penman_monteith_f56.Rd |only evapoRe-1.0.1/evapoRe/man/pet.Rd | 123 evapoRe-1.0.1/evapoRe/man/pet_method_requirements.Rd |only evapoRe-1.0.1/evapoRe/man/pet_oudin_esp_ts.Rd | 48 evapoRe-1.0.1/evapoRe/man/pet_oudin_global_ts.Rd | 48 evapoRe-1.0.1/evapoRe/man/pet_oudin_subset_ts.Rd | 48 evapoRe-1.0.1/evapoRe/man/pet_params_calc.Rd |only evapoRe-1.0.1/evapoRe/man/priestley_taylor.Rd |only evapoRe-1.0.1/evapoRe/man/reexports.Rd |only evapoRe-1.0.1/evapoRe/man/thornthwaite.Rd | 49 evapoRe-1.0.1/evapoRe/man/turc.Rd |only evapoRe-1.0.1/evapoRe/tests/spelling.R | 6 evapoRe-1.0.1/evapoRe/tests/testthat.R | 10 evapoRe-1.0.1/evapoRe/tests/testthat/test-evapoRe.R | 20 evapoRe-1.0.1/evapoRe/vignettes/evapoRe.Rmd | 1492 ++++---- evapoRe-1.0.1/evapoRe/vignettes/evapoRe.bib | 498 +- 114 files changed, 6846 insertions(+), 5886 deletions(-)
Title: Frequency Matrix Approach for Assessing Very Low Frequency
Variants in Sequence Records
Description: Using frequency matrices, very low frequency variants (VLFs) are assessed for amino acid and nucleotide sequences. The VLFs are then compared to see if they occur in only one member of a species, singleton VLFs, or if they occur in multiple members of a species, shared VLFs. The amino acid and nucleotide VLFs are then compared to see if they are concordant with one another. Amino acid VLFs are also assessed to determine if they lead to a change in amino acid residue type, and potential changes to protein structures. Based on Stoeckle and Kerr (2012) <doi:10.1371/journal.pone.0043992> and Phillips et al. (2023) <doi:10.3897/BDJ.11.e96480>.
Author: Taryn B. T. Athey [cre],
Paul D. McNicholas [aut],
Jarrett D. Phillips [ctb]
Maintainer: Taryn B. T. Athey <taryn.athey@gmail.com>
Diff between VLF versions 1.1 dated 2022-08-18 and 1.1-3 dated 2025-04-10
DESCRIPTION | 24 ++++++++++++---- MD5 | 11 ++++--- R/vlfFun.R | 75 ++++++++++++++++++++++++++++++++++++++++++++++++++++ README.md |only man/VLF-package.Rd | 9 ------ man/aminoAcidFun.Rd | 2 - man/vlfFun.Rd | 2 - 7 files changed, 102 insertions(+), 21 deletions(-)
Title: Archetypes for Targets
Description: Function-oriented Make-like declarative pipelines for
Statistics and data science are supported in the 'targets' R package.
As an extension to 'targets', the 'tarchetypes' package provides
convenient user-side functions to make 'targets' easier to use.
By establishing reusable archetypes for common kinds of
targets and pipelines, these functions help express complicated
reproducible pipelines concisely and compactly.
The methods in this package were influenced by the 'targets' R package.
by Will Landau (2018) <doi:10.21105/joss.00550>.
Author: William Michael Landau [aut, cre]
,
Rudolf Siegel [ctb] ,
Samantha Oliver [rev] ,
Tristan Mahr [rev] ,
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between tarchetypes versions 0.12.0 dated 2025-01-31 and 0.13.0 dated 2025-04-10
DESCRIPTION | 8 +-- MD5 | 48 +++++++++++----------- NAMESPACE | 2 NEWS.md | 8 +++ R/tar_map2.R | 2 R/tar_map2_count.R | 2 R/tar_map2_count_raw.R | 2 R/tar_map2_raw.R | 75 +++++++++++++++++++++++++++++++---- R/tar_map2_size.R | 2 R/tar_map2_size_raw.R | 2 R/tar_package.R | 6 +- R/tar_quarto.R | 6 +- R/tar_quarto_rep.R | 6 +- R/tar_quarto_rep_raw.R | 18 +++++--- R/tar_skip.R | 3 - R/utils_parallel.R | 10 ++++ man/tar_map2.Rd | 8 +++ man/tar_map2_count.Rd | 8 +++ man/tar_map2_size.Rd | 8 +++ man/tar_quarto.Rd | 6 +- man/tar_quarto_rep.Rd | 6 +- man/tar_skip.Rd | 13 ++++++ tests/testthat/test-tar_map2.R | 60 +++++++++++++++++++++++----- tests/testthat/test-tar_map2_count.R | 22 ++++++---- tests/testthat/test-tar_map2_size.R | 22 ++++++---- 25 files changed, 267 insertions(+), 86 deletions(-)
Title: Smooth Additive Quantile Regression Models
Description: Smooth additive quantile regression models, fitted using
the methods of Fasiolo et al. (2020) <doi:10.1080/01621459.2020.1725521>.
See Fasiolo at al. (2021) <doi:10.18637/jss.v100.i09> for an introduction to the package. Differently from
'quantreg', the smoothing parameters are estimated automatically by marginal
loss minimization, while the regression coefficients are estimated using either
PIRLS or Newton algorithm. The learning rate is determined so that the Bayesian
credible intervals of the estimated effects have approximately the correct
coverage. The main function is qgam() which is similar to gam() in 'mgcv', but
fits non-parametric quantile regression models.
Author: Matteo Fasiolo [aut, cre],
Ben Griffiths [aut],
Simon N. Wood [ctb],
Margaux Zaffran [ctb],
Yannig Goude [ctb],
Raphael Nedellec [ctb]
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>
Diff between qgam versions 1.3.4 dated 2021-11-22 and 2.0.0 dated 2025-04-10
qgam-1.3.4/qgam/R/I_gamlssFit.R |only qgam-1.3.4/qgam/R/I_getVp.R |only qgam-2.0.0/qgam/DESCRIPTION | 15 - qgam-2.0.0/qgam/MD5 | 84 +++--- qgam-2.0.0/qgam/NAMESPACE | 2 qgam-2.0.0/qgam/R/I_biasedCov.R | 29 -- qgam-2.0.0/qgam/R/I_brent.R | 6 qgam-2.0.0/qgam/R/I_getErrParam.R | 14 - qgam-2.0.0/qgam/R/I_init_gauss_fit.R |only qgam-2.0.0/qgam/R/I_invert_psdef_matrix.R |only qgam-2.0.0/qgam/R/I_llkGrads.R | 109 ++------ qgam-2.0.0/qgam/R/I_objFunLearnFast.R | 71 ++--- qgam-2.0.0/qgam/R/I_prepBootObj.R | 6 qgam-2.0.0/qgam/R/I_sandwichLoss.R | 94 +++---- qgam-2.0.0/qgam/R/I_should_we_use_discrete.R |only qgam-2.0.0/qgam/R/I_tuneLearnBootstrapping.R | 30 -- qgam-2.0.0/qgam/R/I_tuneLearnFullFits.R | 92 ++++--- qgam-2.0.0/qgam/R/check_learn.R | 2 qgam-2.0.0/qgam/R/check_learnFast.R | 2 qgam-2.0.0/qgam/R/check_qgam.R | 17 - qgam-2.0.0/qgam/R/elf.R | 118 +++++---- qgam-2.0.0/qgam/R/elflss.R | 2 qgam-2.0.0/qgam/R/mqgam.R | 42 +-- qgam-2.0.0/qgam/R/qgam.R | 61 ++-- qgam-2.0.0/qgam/R/tuneLearn.R | 41 +-- qgam-2.0.0/qgam/R/tuneLearnFast.R | 109 +++----- qgam-2.0.0/qgam/build/partial.rdb |binary qgam-2.0.0/qgam/build/vignette.rds |binary qgam-2.0.0/qgam/inst/doc/qgam.R | 7 qgam-2.0.0/qgam/inst/doc/qgam.Rmd | 18 + qgam-2.0.0/qgam/inst/doc/qgam.html | 170 +++++++------ qgam-2.0.0/qgam/man/check.learn.Rd | 2 qgam-2.0.0/qgam/man/check.learnFast.Rd | 2 qgam-2.0.0/qgam/man/check.qgam.Rd | 2 qgam-2.0.0/qgam/man/elf.Rd | 2 qgam-2.0.0/qgam/man/elflss.Rd | 2 qgam-2.0.0/qgam/man/mqgam.Rd | 5 qgam-2.0.0/qgam/man/qgam.Rd | 5 qgam-2.0.0/qgam/man/tuneLearn.Rd | 5 qgam-2.0.0/qgam/man/tuneLearnFast.Rd | 10 qgam-2.0.0/qgam/tests/testthat/test-calFastTuneLearn.R | 39 ++ qgam-2.0.0/qgam/tests/testthat/test-calFastTuneLearnFast.R | 30 +- qgam-2.0.0/qgam/tests/testthat/test-check_qgam.R | 26 - qgam-2.0.0/qgam/tests/testthat/test-qgam_discrete.R |only qgam-2.0.0/qgam/tests/testthat/test-tuneLearnFast.R | 24 - qgam-2.0.0/qgam/vignettes/qgam.Rmd | 18 + 46 files changed, 688 insertions(+), 625 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis (Balduzzi et al., 2023) <doi:10.18637/jss.v106.i02> and supporting Schwarzer et al. (2015) <doi:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis":
- frequentist network meta-analysis following Rücker (2012) <doi:10.1002/jrsm.1058>;
- additive network meta-analysis for combinations of treatments (Rücker et al., 2020) <doi:10.1002/bimj.201800167>;
- network meta-analysis of binary data using the Mantel-Haenszel or non-central hypergeometric distribution method (Efthimiou et al., 2019) <doi:10.1002/sim.8158>, or penalised logistic regression (Evrenoglou et al., 2022) <doi:10.1002/sim.9562>;
- rankograms and ranking of treatments by the Surface under the cumulative ranking curve (SUCRA) (Salanti et al., 2013) <doi:10.1016/j.jclinepi.2010.03.016>;
- ranking of treatments using P-scores (frequentist analogue of SUCRAs without resampling) according to [...truncated...]
Author: Gerta Ruecker [aut] ,
Ulrike Krahn [aut],
Jochem Koenig [aut] ,
Orestis Efthimiou [aut] ,
Annabel Davies [aut] ,
Theodoros Papakonstantinou [aut]
,
Theodoros Evrenoglou [ctb] ,
Krzysztof Ciomek [ctb] ,
Nana-Adjoa Kwarteng [ctb] ,
Guido Schwarzer [aut, [...truncated...]
Maintainer: Guido Schwarzer <guido.schwarzer@uniklinik-freiburg.de>
Diff between netmeta versions 3.1-1 dated 2025-02-06 and 3.2-0 dated 2025-04-10
DESCRIPTION | 15 +- MD5 | 247 +++++++++++++++++++++-------------------- NAMESPACE | 15 ++ NEWS.md | 42 ++++++ R/Baker2009.R | 23 --- R/Dogliotti2014.R | 15 -- R/Dong2013.R | 15 -- R/Franchini2012.R | 25 ---- R/Gurusamy2011.R | 15 -- R/Linde2015.R | 19 --- R/Linde2016.R | 11 - R/Senn2013.R | 26 ---- R/Stowe2010.R | 18 -- R/Woods2010.R | 22 --- R/as.data.frame.netmeta.R | 13 -- R/createC.R | 25 ---- R/crossnma2netmeta.R | 2 R/dietaryfat.R | 33 ----- R/discomb.R | 123 +++++++++++--------- R/forest.netbind.R | 33 ----- R/forest.netcomb.R | 33 ----- R/forest.netcomparison.R | 30 ---- R/forest.netcomplex.R | 2 R/forest.netmeta.R | 68 ----------- R/forest.netsplit.R | 26 ---- R/forest.subgroup.netmeta.R | 2 R/invmat.R | 9 - R/netbind.R | 7 + R/netcomb.R | 111 ++++++++++++------ R/netcomparison.R | 19 ++- R/netcontrib.R | 15 +- R/netgraph.R | 37 ------ R/netgraph.netimpact.R | 29 ---- R/netimpact.R | 16 ++ R/netleague.R | 10 - R/netmeasures.R | 30 ---- R/netmeta-package.R | 7 - R/netmeta.R | 161 ++++++++++++++++++++++++-- R/netmetabin.R | 47 +------ R/netmetareg-internal.R |only R/netmetareg.R |only R/netposet.R | 50 ++++---- R/netrank.R | 97 +++++++++++----- R/netsplit.R | 35 +++++ R/nma.additive.R | 33 +++-- R/nma.ruecker.R | 2 R/plot.netposet.R | 79 ------------- R/plot.netrank.R | 75 ------------ R/prepare.R | 52 -------- R/print.decomp.design.R | 16 -- R/print.netbind.R | 28 ---- R/print.netcomb.R | 96 ++++++--------- R/print.netimpact.R | 15 -- R/print.netmeta.R | 9 + R/print.rankogram.R | 18 +- R/print.summary.netcomb.R | 18 -- R/print.summary.netmeta.R | 49 -------- R/rankings.R | 21 ++- R/rankogram.R | 13 -- R/rankogram.default.R | 47 +++---- R/rankogram.netmeta.R | 30 ++++ R/ranksampling.R | 3 R/smokingcessation.R | 24 --- R/summary.netcomb.R | 34 ----- R/summary.netmeta.R | 27 ---- R/summary.netmetareg.R |only R/summary.rankogram.R |only R/treats.R | 34 +---- build/vignette.rds |binary inst/doc/netmeta.pdf |binary man/Baker2009.Rd | 22 --- man/Dogliotti2014.Rd | 15 -- man/Dong2013.Rd | 15 -- man/Franchini2012.Rd | 25 ---- man/Gurusamy2011.Rd | 15 -- man/Linde2015.Rd | 19 --- man/Linde2016.Rd | 11 - man/Senn2013.Rd | 26 ---- man/Stowe2010.Rd | 17 -- man/Woods2010.Rd | 22 --- man/as.data.frame.netmeta.Rd | 13 -- man/createC.Rd | 25 ---- man/crossnma2netmeta.Rd | 2 man/dietaryfat.Rd | 33 ----- man/discomb.Rd | 3 man/forest.netbind.Rd | 33 ----- man/forest.netcomb.Rd | 33 ----- man/forest.netcomparison.Rd | 30 ---- man/forest.netcomplex.Rd | 2 man/forest.netmeta.Rd | 68 ----------- man/forest.netsplit.Rd | 26 ---- man/forest.subgroup.netmeta.Rd | 2 man/invmat.Rd | 9 - man/netbind.Rd | 7 + man/netcomb.Rd | 17 ++ man/netcomparison.Rd | 19 ++- man/netcontrib.Rd | 9 - man/netgraph.Rd | 38 ------ man/netgraph.netimpact.Rd | 29 ---- man/netimpact.Rd | 14 ++ man/netleague.Rd | 10 - man/netmeasures.Rd | 30 ---- man/netmeta-package.Rd | 2 man/netmeta.Rd | 120 +++++++++++++++++++ man/netmetabin.Rd | 29 ---- man/netmetareg.Rd |only man/netposet.Rd | 48 +++---- man/netrank.Rd | 103 +++++++++++------ man/netsplit.Rd | 35 +++++ man/plot.netposet.Rd | 79 ------------- man/plot.netrank.Rd | 75 ------------ man/print.decomp.design.Rd | 16 -- man/print.netbind.Rd | 28 ---- man/print.netcomb.Rd | 34 ----- man/print.netimpact.Rd | 15 -- man/print.netmeta.Rd | 11 + man/print.rankogram.Rd | 16 +- man/print.summary.netcomb.Rd | 18 -- man/print.summary.netmeta.Rd | 49 -------- man/rankogram.Rd | 13 -- man/rankogram.default.Rd | 22 --- man/rankogram.netmeta.Rd | 3 man/smokingcessation.Rd | 23 --- man/summary.netcomb.Rd | 34 ----- man/summary.netmeta.Rd | 27 ---- man/summary.netmetareg.Rd |only man/summary.rankogram.Rd |only man/treats.Rd | 34 +---- 128 files changed, 1283 insertions(+), 2491 deletions(-)
Title: Estimation of Extreme Conditional Quantiles and Probabilities
Description: Extreme value theory, nonparametric kernel estimation, tail
conditional probabilities, extreme conditional quantile, adaptive estimation,
quantile regression, survival probabilities.
Author: Gilles Durrieu [aut],
Ion Grama [aut],
Kevin Jaunatre [aut, cre],
Quang-Khoai Pham [aut],
Jean-Marie Tricot [aut]
Maintainer: Kevin Jaunatre <kevin.jaunatre@hotmail.fr>
Diff between extremefit versions 1.0.2 dated 2019-05-04 and 1.0.3 dated 2025-04-10
DESCRIPTION | 33 ++++++++++++++++++++++++++------- MD5 | 37 +++++++++++++++++++------------------ NAMESPACE | 2 +- R/PackageOxygen.R | 12 +++--------- build/vignette.rds |binary inst/doc/extremefit.pdf |binary man/CriticalValue.Rd | 15 ++++++++++++--- man/Pareto-Distribution.Rd | 8 +------- man/Pareto-mix.Rd | 11 +++++++++-- man/bandwidth.CV.Rd | 14 +++++++++++--- man/bootCI.Rd | 19 +++++++++++++++---- man/bootCI.ts.Rd | 23 +++++++++++++++++++---- man/cox.adapt.Rd | 16 ++++++++++++---- man/hill.adapt.Rd | 12 ++++++++++-- man/hill.ts.Rd | 16 +++++++++++++--- man/predict.cox.adapt.Rd | 13 ++++++++++--- man/predict.hill.Rd | 11 +++++++++-- man/predict.hill.adapt.Rd | 3 +-- man/predict.hill.ts.Rd | 3 +-- vignettes/extremefit.Rmd |only 20 files changed, 172 insertions(+), 76 deletions(-)
Title: A Distributed Worker Launcher Framework
Description: In computationally demanding analysis projects,
statisticians and data scientists asynchronously
deploy long-running tasks to distributed systems,
ranging from traditional clusters to cloud services.
The 'NNG'-powered 'mirai' R package by Gao (2023)
<doi:10.5281/zenodo.7912722> is a sleek
and sophisticated scheduler that
efficiently processes these intense workloads.
The 'crew' package extends 'mirai' with a unifying
interface for third-party worker launchers.
Inspiration also comes from packages.
'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>,
'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>,
'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>),
and 'batchtools' by Lang, Bischel, and Surmann (2017)
<doi:10.21105/joss.00135>.
Author: William Michael Landau [aut, cre]
,
Daniel Woodie [ctb],
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between crew versions 1.0.0 dated 2025-02-03 and 1.1.0 dated 2025-04-10
DESCRIPTION | 6 - MD5 | 86 ++++++++++--------- NAMESPACE | 4 NEWS.md | 7 + R/crew_async.R | 2 R/crew_client.R | 69 ++++++++++----- R/crew_controller.R | 94 +++++++++++---------- R/crew_controller_local.R | 2 R/crew_controller_sequential.R |only R/crew_launcher.R | 6 - R/crew_launcher_local.R | 6 - R/crew_package.R | 6 - R/utils_mirai.R | 4 R/utils_names.R | 2 R/utils_packages.R | 30 +++--- R/utils_promises.R | 2 build/vignette.rds |binary inst/doc/introduction.Rmd | 8 - inst/doc/introduction.html | 18 ++-- inst/doc/plugins.Rmd | 2 inst/doc/plugins.html | 102 +++++++++++------------ inst/doc/risks.Rmd | 8 - inst/doc/risks.html | 25 ++--- inst/doc/shiny.Rmd | 4 inst/doc/shiny.html | 8 - man/crew-package.Rd | 4 man/crew_async.Rd | 2 man/crew_class_client.Rd | 44 ++++++--- man/crew_class_controller.Rd | 7 + man/crew_class_controller_sequential.Rd |only man/crew_class_launcher.Rd | 6 - man/crew_class_launcher_local.Rd | 6 - man/crew_client.Rd | 8 + man/crew_controller_local.Rd | 8 + man/crew_controller_sequential.Rd |only man/crew_launcher.Rd | 2 man/crew_launcher_local.Rd | 2 tests/local/test-launcher-system2.R | 2 tests/testthat/test-crew_client.R | 1 tests/testthat/test-crew_controller.R | 31 ++++++ tests/testthat/test-crew_controller_sequential.R |only tests/testthat/test-plugins.R | 10 ++ vignettes/introduction.Rmd | 8 - vignettes/plugins.Rmd | 2 vignettes/risks.Rmd | 8 - vignettes/shiny.Rmd | 4 46 files changed, 394 insertions(+), 262 deletions(-)
Title: Identify Relevant Clinical Codes and Evaluate Their Use
Description: Generate a candidate code list for the Observational Medical Outcomes Partnership (OMOP) common data model based on string matching. For a given search strategy, a candidate code list will be returned.
Author: Edward Burn [aut, cre] ,
Marti Catala [ctb] ,
Xihang Chen [aut] ,
Nuria Mercade-Besora [aut] ,
Mike Du [ctb] ,
Danielle Newby [ctb] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CodelistGenerator versions 3.4.1 dated 2025-03-26 and 3.5.0 dated 2025-04-10
CodelistGenerator-3.4.1/CodelistGenerator/R/data.R |only CodelistGenerator-3.4.1/CodelistGenerator/R/inputValidation.R |only CodelistGenerator-3.4.1/CodelistGenerator/data |only CodelistGenerator-3.4.1/CodelistGenerator/inst/cohorts |only CodelistGenerator-3.4.1/CodelistGenerator/inst/cohorts2 |only CodelistGenerator-3.4.1/CodelistGenerator/inst/concepts |only CodelistGenerator-3.4.1/CodelistGenerator/inst/concepts_for_mock/oa_desc.json |only CodelistGenerator-3.4.1/CodelistGenerator/inst/concepts_for_mock/oa_no_desc.json |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a01_Introduction_to_CodelistGenerator.R |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a01_Introduction_to_CodelistGenerator.Rmd |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a01_Introduction_to_CodelistGenerator.html |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a02_Candidate_codes_OA.R |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a02_Candidate_codes_OA.Rmd |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a02_Candidate_codes_OA.html |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a03_Options_for_CodelistGenerator.R |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a03_Options_for_CodelistGenerator.Rmd |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a03_Options_for_CodelistGenerator.html |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a04_Vocab_based_codelists.R |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a04_Vocab_based_codelists.Rmd |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a04_Vocab_based_codelists.html |only CodelistGenerator-3.4.1/CodelistGenerator/inst/introData01.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/introData02.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/introData03.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/introData04.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/introData05.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/introVocab.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/medData01.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/medData02a.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/medData02b.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/medData03.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/medDataConceptClass.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/medDataDoseForms.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/not_all_concept_sets |only CodelistGenerator-3.4.1/CodelistGenerator/inst/optionsData01.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/optionsData02.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/optionsData03.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/optionsData04.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/optionsData05.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/optionsData06.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/optionsData07.RData |only CodelistGenerator-3.4.1/CodelistGenerator/man/doseFormToRoute.Rd |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/a01_Introduction_to_CodelistGenerator.Rmd |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/a02_Candidate_codes_OA.Rmd |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/a03_Options_for_CodelistGenerator.Rmd |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/a04_Vocab_based_codelists.Rmd |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/mock_db_fig1.png |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/mock_db_fig2.png |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/mock_db_fig3.png |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/mock_db_fig4.png |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/mock_db_fig5.png |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/mock_db_fig6.png |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/mock_db_fig7.png |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/mock_db_fig8.png |only CodelistGenerator-3.5.0/CodelistGenerator/DESCRIPTION | 18 CodelistGenerator-3.5.0/CodelistGenerator/MD5 | 332 +- CodelistGenerator-3.5.0/CodelistGenerator/NAMESPACE | 17 CodelistGenerator-3.5.0/CodelistGenerator/R/CodelistFromCodelistWithDetails.R | 2 CodelistGenerator-3.5.0/CodelistGenerator/R/buildAchillesTables.R |only CodelistGenerator-3.5.0/CodelistGenerator/R/checks.R | 4 CodelistGenerator-3.5.0/CodelistGenerator/R/codesFromConceptSet.R | 46 CodelistGenerator-3.5.0/CodelistGenerator/R/codesInUse.R | 153 - CodelistGenerator-3.5.0/CodelistGenerator/R/compareCodelists.R | 99 CodelistGenerator-3.5.0/CodelistGenerator/R/documentation_helper.R |only CodelistGenerator-3.5.0/CodelistGenerator/R/drugCodes.R | 324 -- CodelistGenerator-3.5.0/CodelistGenerator/R/getCandidateCodes.R | 17 CodelistGenerator-3.5.0/CodelistGenerator/R/getDoseUnit.R | 21 CodelistGenerator-3.5.0/CodelistGenerator/R/getICD10StandardCodes.R | 228 + CodelistGenerator-3.5.0/CodelistGenerator/R/getMappings.R | 44 CodelistGenerator-3.5.0/CodelistGenerator/R/getRoutes.R | 17 CodelistGenerator-3.5.0/CodelistGenerator/R/helperFunctions.R | 97 CodelistGenerator-3.5.0/CodelistGenerator/R/mockVocabRef.R | 112 CodelistGenerator-3.5.0/CodelistGenerator/R/reexports.R |only CodelistGenerator-3.5.0/CodelistGenerator/R/runSearch.R | 6 CodelistGenerator-3.5.0/CodelistGenerator/R/stratifyByConcept.R | 30 CodelistGenerator-3.5.0/CodelistGenerator/R/stratifyByDoseUnit.R | 36 CodelistGenerator-3.5.0/CodelistGenerator/R/stratifyByRoute.R | 38 CodelistGenerator-3.5.0/CodelistGenerator/R/subsetOnDomain.R | 55 CodelistGenerator-3.5.0/CodelistGenerator/R/subsetOnDoseUnit.R | 45 CodelistGenerator-3.5.0/CodelistGenerator/R/subsetOnRouteCategory.R | 61 CodelistGenerator-3.5.0/CodelistGenerator/R/summariseAchillesCodeUse.R | 40 CodelistGenerator-3.5.0/CodelistGenerator/R/summariseCodeUse.R | 159 - CodelistGenerator-3.5.0/CodelistGenerator/R/summariseOrphanCodes.R | 22 CodelistGenerator-3.5.0/CodelistGenerator/R/summariseUnmappedCodes.R | 24 CodelistGenerator-3.5.0/CodelistGenerator/R/sysdata.rda |binary CodelistGenerator-3.5.0/CodelistGenerator/R/tableAchillesCodeUse.R | 71 CodelistGenerator-3.5.0/CodelistGenerator/R/tableCodeUse.R | 88 CodelistGenerator-3.5.0/CodelistGenerator/R/tableUnmappedCodes.R | 59 CodelistGenerator-3.5.0/CodelistGenerator/R/vocabUtilities.R | 194 - CodelistGenerator-3.5.0/CodelistGenerator/README.md | 91 CodelistGenerator-3.5.0/CodelistGenerator/build/vignette.rds |binary CodelistGenerator-3.5.0/CodelistGenerator/inst/cohorts_for_mock/oa_desc.json | 8 CodelistGenerator-3.5.0/CodelistGenerator/inst/concepts_for_mock/arthritis_desc.json |only CodelistGenerator-3.5.0/CodelistGenerator/inst/concepts_for_mock/arthritis_no_desc.json |only CodelistGenerator-3.5.0/CodelistGenerator/inst/concepts_for_mock/arthritis_with_excluded.json |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a01_GettingOmopCdmVocabularies.R |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a01_GettingOmopCdmVocabularies.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a01_GettingOmopCdmVocabularies.html |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a02_ExploreCDMvocabulary.R |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a02_ExploreCDMvocabulary.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a02_ExploreCDMvocabulary.html |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a03_GenerateCandidateCodelist.R |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a03_GenerateCandidateCodelist.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a03_GenerateCandidateCodelist.html |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a04_GenerateVocabularyBasedCodelist.R |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a04_GenerateVocabularyBasedCodelist.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a04_GenerateVocabularyBasedCodelist.html |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a04b_icd_codes.R |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a04b_icd_codes.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a04b_icd_codes.html |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a05_ExtractCodelistFromJSONfile.R |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a05_ExtractCodelistFromJSONfile.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a05_ExtractCodelistFromJSONfile.html |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a06_CreateSubsetsFromCodelist.R |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a06_CreateSubsetsFromCodelist.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a06_CreateSubsetsFromCodelist.html |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a07_RunCodelistDiagnostics.R |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a07_RunCodelistDiagnostics.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a07_RunCodelistDiagnostics.html |only CodelistGenerator-3.5.0/CodelistGenerator/man/ageGroupDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/availableATC.Rd | 12 CodelistGenerator-3.5.0/CodelistGenerator/man/availableICD10.Rd | 13 CodelistGenerator-3.5.0/CodelistGenerator/man/availableIngredients.Rd | 10 CodelistGenerator-3.5.0/CodelistGenerator/man/buildAchillesTables.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/byConceptDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/bySexDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/byYearDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/cdmDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/codesFromCohort.Rd | 25 CodelistGenerator-3.5.0/CodelistGenerator/man/codesFromConceptSet.Rd | 14 CodelistGenerator-3.5.0/CodelistGenerator/man/codesInUse.Rd | 10 CodelistGenerator-3.5.0/CodelistGenerator/man/compareCodelists.Rd | 10 CodelistGenerator-3.5.0/CodelistGenerator/man/countByDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/domainDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/doseFormDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/doseUnitDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/dot-optionsDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/figures/README-unnamed-chunk-8-1.png |only CodelistGenerator-3.5.0/CodelistGenerator/man/figures/logo.png |binary CodelistGenerator-3.5.0/CodelistGenerator/man/getATCCodes.Rd | 33 CodelistGenerator-3.5.0/CodelistGenerator/man/getCandidateCodes.Rd | 12 CodelistGenerator-3.5.0/CodelistGenerator/man/getConceptClassId.Rd | 13 CodelistGenerator-3.5.0/CodelistGenerator/man/getDescendants.Rd | 16 CodelistGenerator-3.5.0/CodelistGenerator/man/getDomains.Rd | 8 CodelistGenerator-3.5.0/CodelistGenerator/man/getDoseForm.Rd | 8 CodelistGenerator-3.5.0/CodelistGenerator/man/getDoseUnit.Rd | 18 CodelistGenerator-3.5.0/CodelistGenerator/man/getDrugIngredientCodes.Rd | 34 CodelistGenerator-3.5.0/CodelistGenerator/man/getICD10StandardCodes.Rd | 26 CodelistGenerator-3.5.0/CodelistGenerator/man/getMappings.Rd | 13 CodelistGenerator-3.5.0/CodelistGenerator/man/getRelationshipId.Rd | 8 CodelistGenerator-3.5.0/CodelistGenerator/man/getRouteCategories.Rd | 16 CodelistGenerator-3.5.0/CodelistGenerator/man/getVocabVersion.Rd | 8 CodelistGenerator-3.5.0/CodelistGenerator/man/getVocabularies.Rd | 8 CodelistGenerator-3.5.0/CodelistGenerator/man/groupColumnDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/groupColumnStrataDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/headerDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/headerStrataDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/hideDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/hideStrataDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/includeDescendantsDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/ingredientRangeDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/keepOriginalDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/levelATCDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/levelICD10Doc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/minimumCountDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/mockVocabRef.Rd | 5 CodelistGenerator-3.5.0/CodelistGenerator/man/nameStyleDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/reexports.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/routeCategoryDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/sourceCodesInUse.Rd | 8 CodelistGenerator-3.5.0/CodelistGenerator/man/standardConceptDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/stratifyByConcept.Rd | 22 CodelistGenerator-3.5.0/CodelistGenerator/man/stratifyByDoseUnit.Rd | 22 CodelistGenerator-3.5.0/CodelistGenerator/man/stratifyByRouteCategory.Rd | 22 CodelistGenerator-3.5.0/CodelistGenerator/man/subsetOnDomain.Rd | 35 CodelistGenerator-3.5.0/CodelistGenerator/man/subsetOnDoseUnit.Rd | 32 CodelistGenerator-3.5.0/CodelistGenerator/man/subsetOnRouteCategory.Rd | 28 CodelistGenerator-3.5.0/CodelistGenerator/man/subsetToCodesInUse.Rd | 14 CodelistGenerator-3.5.0/CodelistGenerator/man/summariseAchillesCodeUse.Rd | 12 CodelistGenerator-3.5.0/CodelistGenerator/man/summariseCodeUse.Rd | 21 CodelistGenerator-3.5.0/CodelistGenerator/man/summariseCohortCodeUse.Rd | 29 CodelistGenerator-3.5.0/CodelistGenerator/man/summariseOrphanCodes.Rd | 12 CodelistGenerator-3.5.0/CodelistGenerator/man/summariseUnmappedCodes.Rd | 27 CodelistGenerator-3.5.0/CodelistGenerator/man/tableAchillesCodeUse.Rd | 6 CodelistGenerator-3.5.0/CodelistGenerator/man/tableCodeUse.Rd | 4 CodelistGenerator-3.5.0/CodelistGenerator/man/tableCohortCodeUse.Rd | 16 CodelistGenerator-3.5.0/CodelistGenerator/man/tableDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/tableOrphanCodes.Rd | 8 CodelistGenerator-3.5.0/CodelistGenerator/man/tableUnmappedCodes.Rd | 42 CodelistGenerator-3.5.0/CodelistGenerator/man/typeBroadDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/typeNarrowDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/typeTableDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/xDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/setup.R |only CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-buildAchillesTables.R |only CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-codesFrom.R | 227 - CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-codesInUse.R | 15 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-compareCodelists.R | 24 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-dbms.R | 1218 +++---- CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-drugCodes.R | 1525 +++++----- CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-getDoseUnit.R | 8 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-getICD10StandardCodes.R | 188 - CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-getRouteCategories.R | 3 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-stratifyByConcept.R | 48 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-stratifyByDoseUnit.R | 44 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-subsetOnDomain.R | 18 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-subsetOnDoseUnit.R | 13 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-subsetOnRouteCategory.R | 83 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-summariseAchillesCodeUse.R | 7 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-summariseCodeUse.R | 302 - CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-summariseOrphanCodes.R | 2 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-tableCodeUse.R | 20 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-tableUnmappedCodes.R | 116 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-vocabUtilities.R | 2 CodelistGenerator-3.5.0/CodelistGenerator/vignettes/Figures |only CodelistGenerator-3.5.0/CodelistGenerator/vignettes/a01_GettingOmopCdmVocabularies.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/vignettes/a02_ExploreCDMvocabulary.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/vignettes/a03_GenerateCandidateCodelist.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/vignettes/a04_GenerateVocabularyBasedCodelist.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/vignettes/a04b_icd_codes.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/vignettes/a05_ExtractCodelistFromJSONfile.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/vignettes/a06_CreateSubsetsFromCodelist.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/vignettes/a07_RunCodelistDiagnostics.Rmd |only 222 files changed, 3712 insertions(+), 3389 deletions(-)
More information about CodelistGenerator at CRAN
Permanent link
Title: Bradley-Terry Models
Description: Specify and fit the Bradley-Terry model, including structured
versions in which the parameters are related to explanatory variables
through a linear predictor and versions with contest-specific effects,
such as a home advantage.
Author: Heather Turner [aut, cre],
David Firth [aut]
Maintainer: Heather Turner <ht@heatherturner.net>
Diff between BradleyTerry2 versions 1.1-2 dated 2020-02-03 and 1.1.3 dated 2025-04-10
BradleyTerry2-1.1-2/BradleyTerry2/data/CEMS.rda |only BradleyTerry2-1.1-2/BradleyTerry2/data/chameleons.rda |only BradleyTerry2-1.1-2/BradleyTerry2/data/citations.rda |only BradleyTerry2-1.1-2/BradleyTerry2/data/icehockey.rda |only BradleyTerry2-1.1-2/BradleyTerry2/data/seeds.rda |only BradleyTerry2-1.1-2/BradleyTerry2/data/sound.fields.rda |only BradleyTerry2-1.1-2/BradleyTerry2/data/springall.rda |only BradleyTerry2-1.1-2/BradleyTerry2/inst/doc/BradleyTerry.Rnw |only BradleyTerry2-1.1-2/BradleyTerry2/inst/doc/BradleyTerry.pdf |only BradleyTerry2-1.1-2/BradleyTerry2/vignettes/BradleyTerry-concordance.tex |only BradleyTerry2-1.1-2/BradleyTerry2/vignettes/BradleyTerry.Rnw |only BradleyTerry2-1.1-2/BradleyTerry2/vignettes/baseball-qvplot.pdf |only BradleyTerry2-1.1-2/BradleyTerry2/vignettes/residuals.pdf |only BradleyTerry2-1.1.3/BradleyTerry2/DESCRIPTION | 27 - BradleyTerry2-1.1.3/BradleyTerry2/MD5 | 70 ++-- BradleyTerry2-1.1.3/BradleyTerry2/NEWS.md | 12 BradleyTerry2-1.1.3/BradleyTerry2/R/flatlizards.R | 2 BradleyTerry2-1.1.3/BradleyTerry2/R/predict.BTm.R | 2 BradleyTerry2-1.1.3/BradleyTerry2/R/qvcalc.BTabilities.R | 4 BradleyTerry2-1.1.3/BradleyTerry2/README.md | 6 BradleyTerry2-1.1.3/BradleyTerry2/build/partial.rdb |only BradleyTerry2-1.1.3/BradleyTerry2/build/vignette.rds |binary BradleyTerry2-1.1.3/BradleyTerry2/data/CEMS.R |only BradleyTerry2-1.1.3/BradleyTerry2/data/chameleons.R |only BradleyTerry2-1.1.3/BradleyTerry2/data/citations.R |only BradleyTerry2-1.1.3/BradleyTerry2/data/icehockey.R |only BradleyTerry2-1.1.3/BradleyTerry2/data/seeds.R |only BradleyTerry2-1.1.3/BradleyTerry2/data/sound.fields.R |only BradleyTerry2-1.1.3/BradleyTerry2/data/springall.R |only BradleyTerry2-1.1.3/BradleyTerry2/inst/CITATION | 31 - BradleyTerry2-1.1.3/BradleyTerry2/inst/doc/BradleyTerry.R | 170 ++-------- BradleyTerry2-1.1.3/BradleyTerry2/inst/doc/BradleyTerry.Rmd |only BradleyTerry2-1.1.3/BradleyTerry2/inst/doc/BradleyTerry.html |only BradleyTerry2-1.1.3/BradleyTerry2/man/CEMS.Rd | 6 BradleyTerry2-1.1.3/BradleyTerry2/man/baseball.Rd | 6 BradleyTerry2-1.1.3/BradleyTerry2/man/chameleons.Rd | 6 BradleyTerry2-1.1.3/BradleyTerry2/man/citations.Rd | 6 BradleyTerry2-1.1.3/BradleyTerry2/man/flatlizards.Rd | 8 BradleyTerry2-1.1.3/BradleyTerry2/man/football.Rd | 6 BradleyTerry2-1.1.3/BradleyTerry2/man/icehockey.Rd | 6 BradleyTerry2-1.1.3/BradleyTerry2/man/predict.BTm.Rd | 2 BradleyTerry2-1.1.3/BradleyTerry2/man/qvcalc.BTabilities.Rd | 4 BradleyTerry2-1.1.3/BradleyTerry2/man/seeds.Rd | 6 BradleyTerry2-1.1.3/BradleyTerry2/man/sound.fields.Rd | 6 BradleyTerry2-1.1.3/BradleyTerry2/man/springall.Rd | 6 BradleyTerry2-1.1.3/BradleyTerry2/vignettes/BradleyTerry.Rmd |only BradleyTerry2-1.1.3/BradleyTerry2/vignettes/BradleyTerry.bib | 46 +- BradleyTerry2-1.1.3/BradleyTerry2/vignettes/baseball-qvplot.png |only BradleyTerry2-1.1.3/BradleyTerry2/vignettes/residuals.png |only 49 files changed, 188 insertions(+), 250 deletions(-)
Title: ArcGIS Utility Functions
Description: Developer oriented utility functions designed to be used as
the building blocks of R packages that work with ArcGIS Location
Services. It provides functionality for authorization, Esri JSON
construction and parsing, as well as other utilities pertaining to
geometry and Esri type conversions. To support 'ArcGIS Pro' users,
authorization can be done via 'arcgisbinding'. Installation
instructions for 'arcgisbinding' can be found at
<https://developers.arcgis.com/r-bridge/installation/>.
Author: Josiah Parry [aut, cre] ,
Kenneth Vernon [ctb] ,
Martha Bass [ctb]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between arcgisutils versions 0.3.1 dated 2024-09-26 and 0.3.3 dated 2025-04-10
arcgisutils-0.3.1/arcgisutils/src/Makevars |only arcgisutils-0.3.1/arcgisutils/src/Makevars.win |only arcgisutils-0.3.3/arcgisutils/DESCRIPTION | 15 arcgisutils-0.3.3/arcgisutils/MD5 | 31 - arcgisutils-0.3.3/arcgisutils/NEWS.md | 7 arcgisutils-0.3.3/arcgisutils/R/arc-base-req.R | 16 arcgisutils-0.3.3/arcgisutils/R/feature-collection.R | 80 +-- arcgisutils-0.3.3/arcgisutils/R/rbind-results.R | 9 arcgisutils-0.3.3/arcgisutils/configure | 2 arcgisutils-0.3.3/arcgisutils/configure.win | 2 arcgisutils-0.3.3/arcgisutils/man/layer_json.Rd | 8 arcgisutils-0.3.3/arcgisutils/src/Makevars.in |only arcgisutils-0.3.3/arcgisutils/src/Makevars.win.in |only arcgisutils-0.3.3/arcgisutils/src/rust/Cargo.lock | 288 ++++++------ arcgisutils-0.3.3/arcgisutils/src/rust/Cargo.toml | 3 arcgisutils-0.3.3/arcgisutils/src/rust/src/to/attributes.rs | 38 - arcgisutils-0.3.3/arcgisutils/src/rust/vendor.tar.xz |binary arcgisutils-0.3.3/arcgisutils/tools/config.R |only arcgisutils-0.3.3/arcgisutils/tools/msrv.R | 4 19 files changed, 255 insertions(+), 248 deletions(-)
Title: Merge and Download International Large-Scale Assessments (ILSA)
Data
Description: Merges and downloads 'SPSS' data from different International Large-Scale Assessments (ILSA), including: Trends in International Mathematics and Science Study (TIMSS), Progress in International Reading Literacy Study (PIRLS), and others.
Author: Andres Christiansen [aut, cre]
,
Andres Strello [ctb]
Maintainer: Andres Christiansen <andres.christiansen@iea-hamburg.de>
Diff between ILSAmerge versions 1.3.6 dated 2025-02-12 and 1.3.8 dated 2025-04-10
DESCRIPTION | 6 - MD5 | 34 +++---- NEWS.md | 13 ++ R/ILSAready.R | 10 +- R/addSchools.R | 2 R/mistoNAs.R | 6 + R/sysdata.rda |binary R/untibble.R | 19 ++- build/vignette.rds |binary inst/doc/Download.R | 14 +- inst/doc/Download.html | 50 +++++----- inst/doc/IdentifyILSAfiles.html | 16 +-- inst/doc/Load.html | 102 ++++++++++----------- inst/doc/Merge.R | 6 - inst/doc/Merge.html | 174 ++++++++++++++++++------------------ inst/doc/Onestep.html | 124 ++++++++++++------------- inst/doc/Rename.html | 28 ++--- inst/extdata/ilsainfo/ILSAlinks.csv | 2 18 files changed, 319 insertions(+), 287 deletions(-)
Title: Density and Abundance from Distance-Sampling Surveys
Description: Distance-sampling (<doi:10.1007/978-3-319-19219-2>)
estimates density and abundance of survey targets (e.g., animals) when
detection probability declines with distance.
Distance-sampling is popular in ecology,
especially when survey targets are observed from aerial platforms (e.g.,
airplane or drone), surface vessels (e.g., boat or truck), or along
walking transects.
Distance-sampling includes line-transect studies that measure observation
distances as the closest approach of the sample route (transect) to the target
(i.e., perpendicular off-transect distance), and point-transect studies that
measure observation distances from stationary observers to
the target (i.e., radial distance).
The routines included here fit smooth (parametric) curves to
histograms of observation distances
and use those functions to compute effective sampling distances, density of
targets in the surveyed area, and abundance
of targets in a surrounding study area. Curve shapes include the
half-normal, haza [...truncated...]
Author: Trent McDonald [cre, aut],
Jason Carlisle [aut],
Aidan McDonald [aut] ,
Ryan Nielson [ctb] ,
Ben Augustine [ctb] ,
James Griswald [ctb] ,
Patrick McKann [ctb] ,
Lacey Jeroue [ctb] ,
Hoffman Abigail [ctb] ,
Kleinsausser Michael [ctb] ,
Joel Reynolds [ [...truncated...]
Maintainer: Trent McDonald <trent@mcdonalddatasciences.com>
Diff between Rdistance versions 4.0.3 dated 2025-03-29 and 4.0.5 dated 2025-04-10
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 24 ++++++++++++++++++++---- R/RdistDf.R | 35 ++++++++++++++++++++++++++++------- R/predDensity.R | 6 +++++- man/RdistDf.Rd | 8 ++++---- 6 files changed, 66 insertions(+), 25 deletions(-)
Title: Search for POIs using ArcGIS 'Places Service'
Description: The ArcGIS 'Places service' is a ready-to-use location
service that can search for businesses and geographic locations around
the world. It allows you to find, locate, and discover detailed
information about each place. Query for places near a point, within a
bounding box, filter based on categories, or provide search text.
'arcgisplaces' integrates with 'sf' for out of the box compatibility
with other spatial libraries. Learn more in the 'Places service' API reference <https://developers.arcgis.com/rest/places/>.
Author: Josiah Parry [aut, cre]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between arcgisplaces versions 0.1.1 dated 2025-01-15 and 0.1.2 dated 2025-04-10
DESCRIPTION | 8 MD5 | 19 - configure | 15 - configure.win | 15 - src/Makevars.in | 18 - src/Makevars.win.in | 25 - src/rust/Cargo.lock | 627 +++++++++++++++++++++++++++++++------------------ src/rust/Cargo.toml | 13 - src/rust/vendor.tar.xz |binary tools/config.R |only tools/msrv.R | 4 11 files changed, 440 insertions(+), 304 deletions(-)
Title: Execute 'SQL' Scripts in 'R' Containing Multiple Queries
Description: The nature of working with structured query language ('SQL') scripts
efficiently often requires the creation of temporary tables and there
are few clean and simple 'R' 'SQL' execution approaches that allow
you to complete this kind of work with the 'R' environment. This
package seeks to give 'SQL' implementations in 'R' a little love
by deploying functions that allow you to deploy complex 'SQL'
scripts within a typical 'R' workflow.
Author: Kerns Sam [aut, cre]
Maintainer: Kerns Sam <samwkerns@gmail.com>
Diff between SQLove versions 0.0.4 dated 2023-11-13 and 1.0.1 dated 2025-04-10
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/dbGetMultiQuery.R | 23 ++++++++++++++++++++--- R/dbSendMultiUpdate.R | 3 +++ inst/doc/SQLove.html | 4 ++-- 6 files changed, 37 insertions(+), 13 deletions(-)
Title: Truncated Exponential Family
Description: Handles truncated members from the exponential family of
probability distributions. Contains functions such as rtruncnorm() and
dtruncpois(), which are truncated versions of rnorm() and dpois() from the
stats package that also offer richer output containing, for example, the
distribution parameters. It also provides functions to retrieve the original
distribution parameters from a truncated sample by maximum-likelihood
estimation.
Author: Rene Holst [aut],
Waldir Leoncio [cre, aut]
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>
Diff between TruncExpFam versions 1.2.0 dated 2024-09-26 and 1.2.1 dated 2025-04-10
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/Sampling_and_ML_estimation.R | 2 +- inst/doc/Sampling_and_ML_estimation.html | 2 +- tests/testthat/test-qtrunc-truncated-a.R | 2 +- 7 files changed, 18 insertions(+), 13 deletions(-)
Title: Pre- And Post-Processing in Bayesian Evolutionary Analyses
Description: Functions are provided for prior specification in divergence time
estimation using fossils as well as other kinds of data. It
provides tools for interacting with the input and output of Bayesian
platforms in evolutionary biology such as 'BEAST2', 'MrBayes', 'RevBayes',
or 'MCMCTree'.
It Implements a simple measure similarity between probability
density functions for comparing prior and
posterior Bayesian densities, as well as code for calculating the
combination of distributions using conflation of Hill (2008). Functions for estimating the
origination time in collections of distributions using the x-intercept (e.g., Draper and Smith, 1998) and
stratigraphic intervals (Marshall 2010) are also available.
Hill, T. 2008. "Conflations of probability distributions". Transactions of the American Mathematical Society, 363:3351-3372. <doi:10.48550/arXiv.0808.1808>,
Draper, N. R. and Smith, H. 1998. "Applied Regression Analysis". 1--706. Wiley Interscience, New York. <DOI:10.1002/978111 [...truncated...]
Author: Gustavo A. Ballen [aut, cre],
Sandra Reinales [aut]
Maintainer: Gustavo A. Ballen <gustavo.a.ballen@gmail.com>
Diff between tbea versions 1.5.0 dated 2024-07-01 and 1.6.1 dated 2025-04-10
DESCRIPTION | 6 +-- MD5 | 19 +++++----- NAMESPACE | 2 + R/conflate.R | 82 ++++++++++++++++++++++++++++++++++++++++++++- README.md | 1 build/partial.rdb |binary build/vignette.rds |binary inst/doc/intro.html | 13 +++---- inst/doc/whyInitVals.html | 25 +++++++------ man/conflate.Rd | 2 - man/quantile_conflation.Rd |only 11 files changed, 118 insertions(+), 32 deletions(-)
Title: Sample Size Calculation in Reversible Catalytic Models
Description: Sample size and confidence interval calculations in reversible catalytic models, with applications in malaria research. Further details can be found in the paper by Sepúlveda and Drakeley (2015, <doi:10.1186/s12936-015-0661-z>).
Author: Marcia Graca [aut, cre],
Fernanda Diamantino [aut, ths],
Nuno Sepulveda [aut, ctb, ths]
Maintainer: Marcia Graca <marcia_da_graca@hotmail.com>
Diff between RCMsize versions 1.0.0 dated 2024-12-02 and 1.0.1 dated 2025-04-10
DESCRIPTION | 17 ++++++++++------- MD5 | 12 ++++++------ NEWS.md | 16 +++++++++++----- inst/doc/Using_RCMsize_for_Malaria_Research.Rmd | 4 ---- inst/doc/Using_RCMsize_for_Malaria_Research.html | 5 ----- man/RCMsize-package.Rd | 11 ++++++++--- vignettes/Using_RCMsize_for_Malaria_Research.Rmd | 4 ---- 7 files changed, 35 insertions(+), 34 deletions(-)
Title: Personalised Synthetic Controls
Description: Allows the comparison of data cohorts (DC) against a Counter Factual Model (CFM) and measures the difference in terms of an efficacy parameter. Allows the application of Personalised Synthetic Controls.
Author: Richard Jackson [cre, aut, cph]
Maintainer: Richard Jackson <richJ23@liverpool.ac.uk>
Diff between psc versions 1.1.0 dated 2024-12-12 and 1.2.0 dated 2025-04-10
DESCRIPTION | 14 MD5 | 34 - R/dataComb.flexsurvreg.R | 49 +- R/dataComb.glm.R | 53 +- R/plot.psc.flexsurvreg.R | 2 R/pscEst.R | 3 R/pscEst.flexsurvreg.R | 13 R/pscEst.glm.R | 11 R/pscfit.R | 8 README.md | 6 build/vignette.rds |binary inst/doc/psc-vignette.R | 2 inst/doc/psc-vignette.html | 792 ++------------------------------------ man/figures/README-pressure-1.png |binary man/psc-package.Rd | 2 man/pscEst.Rd | 4 man/pscEst.flexsurvreg.Rd | 4 man/pscEst.glm.Rd | 4 18 files changed, 173 insertions(+), 828 deletions(-)
Title: Prior Diagnostics and Sensitivity Analysis
Description: Provides functions for prior and likelihood sensitivity analysis in Bayesian models. Currently it implements methods to determine the sensitivity of the posterior to power-scaling perturbations of the prior and likelihood.
Author: Noa Kallioinen [aut, cre, cph],
Topi Paananen [aut],
Paul-Christian Buerkner [aut],
Aki Vehtari [aut],
Frank Weber [ctb]
Maintainer: Noa Kallioinen <noa.kallioinen@aalto.fi>
Diff between priorsense versions 1.0.4 dated 2024-11-01 and 1.1.0 dated 2025-04-10
priorsense-1.0.4/priorsense/inst/doc/powerscaling.Rmd |only priorsense-1.0.4/priorsense/man/figures/README-dens_plot-1.png |only priorsense-1.0.4/priorsense/man/figures/README-ecdf_plot-1.png |only priorsense-1.0.4/priorsense/man/figures/README-quants_plot-1.png |only priorsense-1.0.4/priorsense/man/measure_divergence.Rd |only priorsense-1.0.4/priorsense/man/scaled_log_ratio.Rd |only priorsense-1.0.4/priorsense/man/weighted_quantities.Rd |only priorsense-1.0.4/priorsense/man/weighted_summary_measures.Rd |only priorsense-1.0.4/priorsense/vignettes/powerscaling.Rmd |only priorsense-1.1.0/priorsense/DESCRIPTION | 26 priorsense-1.1.0/priorsense/MD5 | 111 +- priorsense-1.1.0/priorsense/NAMESPACE | 6 priorsense-1.1.0/priorsense/NEWS.md | 9 priorsense-1.1.0/priorsense/R/additional_divergence_measures.R | 122 +- priorsense-1.1.0/priorsense/R/cjs.R | 48 priorsense-1.1.0/priorsense/R/create_priorsense_data.R | 66 + priorsense-1.1.0/priorsense/R/cumulative_plot.R | 38 priorsense-1.1.0/priorsense/R/example_powerscale_model.R | 1 priorsense-1.1.0/priorsense/R/find_alpha_threshold.R | 28 priorsense-1.1.0/priorsense/R/ggplot_theme.R | 4 priorsense-1.1.0/priorsense/R/helpers.R | 74 - priorsense-1.1.0/priorsense/R/log_prior_draws.R | 14 priorsense-1.1.0/priorsense/R/measure_divergence.R | 1 priorsense-1.1.0/priorsense/R/plots.R | 409 +++++-- priorsense-1.1.0/priorsense/R/powerscale.R | 91 + priorsense-1.1.0/priorsense/R/powerscale_derivative.R | 4 priorsense-1.1.0/priorsense/R/powerscale_gradients.R | 31 priorsense-1.1.0/priorsense/R/powerscale_sensitivity.R | 19 priorsense-1.1.0/priorsense/R/powerscale_sequence.R | 43 priorsense-1.1.0/priorsense/R/print.R | 27 priorsense-1.1.0/priorsense/R/priorsense-package.R | 27 priorsense-1.1.0/priorsense/R/scale_draws.R | 7 priorsense-1.1.0/priorsense/R/scaled_log_ratio.R | 11 priorsense-1.1.0/priorsense/R/srr-stats-standards.R |only priorsense-1.1.0/priorsense/R/summarise_draws.R | 1 priorsense-1.1.0/priorsense/R/weighted_quantities.R | 78 + priorsense-1.1.0/priorsense/R/whiten_draws.R | 6 priorsense-1.1.0/priorsense/README.md | 41 priorsense-1.1.0/priorsense/build/vignette.rds |binary priorsense-1.1.0/priorsense/inst/doc/powerscaling.R | 64 - priorsense-1.1.0/priorsense/inst/doc/powerscaling.html | 546 +++------- priorsense-1.1.0/priorsense/inst/doc/powerscaling.qmd |only priorsense-1.1.0/priorsense/inst/doc/priorsense_with_jags.R |only priorsense-1.1.0/priorsense/inst/doc/priorsense_with_jags.html |only priorsense-1.1.0/priorsense/inst/doc/priorsense_with_jags.qmd |only priorsense-1.1.0/priorsense/inst/logo/logo.R | 19 priorsense-1.1.0/priorsense/man/cjs_dist.Rd | 15 priorsense-1.1.0/priorsense/man/create-priorsense-data.Rd | 19 priorsense-1.1.0/priorsense/man/figures/powerscale-plot_dens-1.png |only priorsense-1.1.0/priorsense/man/figures/powerscale_plot_ecdf-1.png |only priorsense-1.1.0/priorsense/man/figures/powerscale_plot_quantities-1.png |only priorsense-1.1.0/priorsense/man/powerscale-gradients.Rd | 16 priorsense-1.1.0/priorsense/man/powerscale-overview.Rd | 32 priorsense-1.1.0/priorsense/man/powerscale-sensitivity.Rd | 23 priorsense-1.1.0/priorsense/man/powerscale_derivative.Rd | 4 priorsense-1.1.0/priorsense/man/powerscale_plots.Rd | 15 priorsense-1.1.0/priorsense/man/priorsense-package.Rd | 13 priorsense-1.1.0/priorsense/tests/testthat/test_cjs.R | 11 priorsense-1.1.0/priorsense/tests/testthat/test_deriv.R | 2 priorsense-1.1.0/priorsense/tests/testthat/test_div_measures.R |only priorsense-1.1.0/priorsense/tests/testthat/test_plots.R | 25 priorsense-1.1.0/priorsense/tests/testthat/test_powerscale.R | 73 + priorsense-1.1.0/priorsense/tests/testthat/test_print.R |only priorsense-1.1.0/priorsense/tests/testthat/test_rstan.R | 5 priorsense-1.1.0/priorsense/tests/testthat/test_scale_draws.R |only priorsense-1.1.0/priorsense/tests/testthat/test_whiten_draws.R |only priorsense-1.1.0/priorsense/vignettes/powerscaling.qmd |only priorsense-1.1.0/priorsense/vignettes/priorsense_with_jags.qmd |only 68 files changed, 1376 insertions(+), 849 deletions(-)
Title: Interface for 'Google Gemini' API
Description: Provides a comprehensive interface for Google Gemini API,
enabling users to access and utilize Gemini Large Language Model (LLM) functionalities directly from R.
This package facilitates seamless integration with Google Gemini, allowing for advanced language processing,
text generation, and other AI-driven capabilities within the R environment.
For more information, please visit <https://ai.google.dev/docs/gemini_api_overview>.
Author: Jinhwan Kim [aut, cre, cph] ,
Maciej Nasinski [ctb]
Maintainer: Jinhwan Kim <hwanistic@gmail.com>
Diff between gemini.R versions 0.11.0 dated 2025-03-29 and 0.12.0 dated 2025-04-10
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++++-------- NAMESPACE | 4 ++++ NEWS.md | 6 +++++- R/countTokens.R | 4 ++-- R/gemini.R | 6 +++--- R/gemini_search.R |only R/gemini_searchR.R |only R/gen_image.R | 24 +++++++++++++----------- R/setEnv.R | 24 ++++++++++++------------ man/countTokens.Rd | 4 ++-- man/gemini_search.Rd |only man/gemini_searchR.Rd |only 13 files changed, 56 insertions(+), 42 deletions(-)
Title: Plotting for Bayesian Models
Description: Plotting functions for posterior analysis, MCMC diagnostics,
prior and posterior predictive checks, and other visualizations
to support the applied Bayesian workflow advocated in
Gabry, Simpson, Vehtari, Betancourt, and Gelman (2019) <doi:10.1111/rssa.12378>.
The package is designed not only to provide convenient functionality
for users, but also a common set of functions that can be easily used by
developers working on a variety of R packages for Bayesian modeling,
particularly (but not exclusively) packages interfacing with 'Stan'.
Author: Jonah Gabry [aut, cre],
Tristan Mahr [aut],
Paul-Christian Buerkner [ctb],
Martin Modrak [ctb],
Malcolm Barrett [ctb],
Frank Weber [ctb],
Eduardo Coronado Sroka [ctb],
Teemu Sailynoja [ctb],
Aki Vehtari [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between bayesplot versions 1.11.1 dated 2024-02-15 and 1.12.0 dated 2025-04-10
DESCRIPTION | 12 - MD5 | 107 +++++------ NEWS.md | 14 + R/available-module-functions.R | 3 R/mcmc-diagnostics.R | 9 R/mcmc-distributions.R | 2 R/mcmc-overview.R | 2 R/mcmc-scatterplots.R | 2 R/mcmc-traces.R | 17 + R/ppc-discrete.R | 1 R/ppc-distributions.R | 4 R/ppc-errors.R | 2 R/ppc-test-statistics.R | 36 ++- R/ppd-distributions.R | 2 build/vignette.rds |binary inst/doc/graphical-ppcs.R | 6 inst/doc/graphical-ppcs.html | 35 +-- inst/doc/plotting-mcmc-draws.R | 38 ++-- inst/doc/plotting-mcmc-draws.Rmd | 36 +-- inst/doc/plotting-mcmc-draws.html | 60 +++--- inst/doc/visual-mcmc-diagnostics.R | 32 +-- inst/doc/visual-mcmc-diagnostics.Rmd | 38 ++-- inst/doc/visual-mcmc-diagnostics.html | 222 +++++++++++------------- man/MCMC-combos.Rd | 2 man/MCMC-diagnostics.Rd | 2 man/MCMC-distributions.Rd | 2 man/MCMC-intervals.Rd | 2 man/MCMC-overview.Rd | 2 man/MCMC-parcoord.Rd | 2 man/MCMC-recover.Rd | 2 man/MCMC-scatterplots.Rd | 4 man/MCMC-traces.Rd | 2 man/PPC-test-statistics.Rd | 17 + tests/testthat/data-for-mcmc-tests.R | 7 tests/testthat/helper.R |only tests/testthat/test-aesthetics.R | 1 tests/testthat/test-available_ppc.R | 1 tests/testthat/test-mcmc-combo.R | 3 tests/testthat/test-mcmc-diagnostics.R | 17 + tests/testthat/test-mcmc-distributions.R | 6 tests/testthat/test-mcmc-intervals.R | 3 tests/testthat/test-mcmc-nuts.R | 5 tests/testthat/test-mcmc-recover.R | 3 tests/testthat/test-mcmc-scatter-and-parcoord.R | 4 tests/testthat/test-mcmc-traces.R | 18 + tests/testthat/test-ppc-censoring.R | 2 tests/testthat/test-ppc-discrete.R | 11 - tests/testthat/test-ppc-distributions.R | 13 + tests/testthat/test-ppc-errors.R | 19 ++ tests/testthat/test-ppc-intervals.R | 4 tests/testthat/test-ppc-loo.R | 4 tests/testthat/test-ppc-scatterplots.R | 3 tests/testthat/test-ppc-test-statistics.R | 35 +++ vignettes/plotting-mcmc-draws.Rmd | 36 +-- vignettes/visual-mcmc-diagnostics.Rmd | 38 ++-- 55 files changed, 577 insertions(+), 373 deletions(-)
Title: Wrapper for 'SUNDIALS' Solving ODE and Sensitivity Problem
Description: Wrapper for widely used 'SUNDIALS' software (SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers) and more precisely to its 'CVODES' solver. It is aiming to solve ordinary differential equations (ODE) and optionally pending forward sensitivity problem. The wrapper is made 'R' friendly by allowing to pass custom parameters to user's callback functions. Such functions can be both written in 'R' and in 'C++' ('RcppArmadillo' flavor). In case of 'C++', performance is greatly improved so this option is highly advisable when performance matters. If provided, Jacobian matrix can be calculated either in dense or sparse format. In the latter case 'rmumps' package is used to solve corresponding linear systems. Root finding and pending event management are optional and can be specified as 'R' or 'C++' functions too. This makes them a very flexible tool for controlling the ODE system during the time course simulation. 'SUNDIALS' library was published in Hindmarsh et al. (2005) <doi:1 [...truncated...]
Author: Serguei Sokol [cre, aut],
Carol S. Woodward [ctb],
Daniel R. Reynolds [ctb],
Alan C. Hindmarsh [ctb],
David J. Gardner [ctb],
Cody J. Balos [ctb],
Radu Serban [ctb],
Scott D. Cohen [ctb],
Peter N. Brown [ctb],
George Byrne [ctb],
Allan G. Taylor [ctb [...truncated...]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between r2sundials versions 6.5.0-5 dated 2024-07-22 and 7.2.1-3 dated 2025-04-10
r2sundials-6.5.0-5/r2sundials/inst/cvodes.txt.in |only r2sundials-6.5.0-5/r2sundials/inst/include/cvodes/cvodes_direct.h |only r2sundials-6.5.0-5/r2sundials/inst/include/cvodes/cvodes_spils.h |only r2sundials-6.5.0-5/r2sundials/inst/include/sundials/sundials_context_impl.h |only r2sundials-6.5.0-5/r2sundials/inst/include/sundials/sundials_cuda.h |only r2sundials-6.5.0-5/r2sundials/inst/include/sundials/sundials_debug.h |only r2sundials-6.5.0-5/r2sundials/inst/include/sundials/sundials_fconfig.in |only r2sundials-6.5.0-5/r2sundials/inst/include/sundials/sundials_fnvector.h |only r2sundials-6.5.0-5/r2sundials/inst/include/sundials/sundials_hashmap.h |only r2sundials-6.5.0-5/r2sundials/inst/include/sundials/sundials_hip.h |only r2sundials-6.5.0-5/r2sundials/inst/include/sundials/sundials_iterative_impl.h |only r2sundials-6.5.0-5/r2sundials/inst/include/sundials/sundials_lapack.h |only r2sundials-6.5.0-5/r2sundials/inst/include/sundials/sundials_lapack_defs.h |only r2sundials-6.5.0-5/r2sundials/inst/include/sundials/sundials_logger_impl.h |only r2sundials-6.5.0-5/r2sundials/inst/include/sundials/sundials_sycl.h |only r2sundials-6.5.0-5/r2sundials/inst/include/sundials/sundials_utils.h |only r2sundials-6.5.0-5/r2sundials/src/lib-5.0.0 |only r2sundials-6.5.0-5/r2sundials/src/lib/cvodes/cvodes_direct.c |only r2sundials-6.5.0-5/r2sundials/src/lib/cvodes/cvodes_spils.c |only r2sundials-6.5.0-5/r2sundials/src/lib/sundials/sundials_context_impl.h |only r2sundials-6.5.0-5/r2sundials/src/lib/sundials/sundials_hashmap.h |only r2sundials-7.2.1-3/r2sundials/DESCRIPTION | 12 r2sundials-7.2.1-3/r2sundials/MD5 | 471 r2sundials-7.2.1-3/r2sundials/NEWS | 7 r2sundials-7.2.1-3/r2sundials/R/RcppExports.R | 8 r2sundials-7.2.1-3/r2sundials/R/translate.R |only r2sundials-7.2.1-3/r2sundials/build/partial.rdb |binary r2sundials-7.2.1-3/r2sundials/inst/COPYRIGHTS | 2 r2sundials-7.2.1-3/r2sundials/inst/include/cvodes/cvodes.h | 787 - r2sundials-7.2.1-3/r2sundials/inst/include/cvodes/cvodes_bandpre.h | 25 r2sundials-7.2.1-3/r2sundials/inst/include/cvodes/cvodes_bbdpre.h | 57 r2sundials-7.2.1-3/r2sundials/inst/include/cvodes/cvodes_diag.h | 31 r2sundials-7.2.1-3/r2sundials/inst/include/cvodes/cvodes_ls.h | 265 r2sundials-7.2.1-3/r2sundials/inst/include/cvodes/cvodes_proj.h | 25 r2sundials-7.2.1-3/r2sundials/inst/include/nvector/nvector_cuda.h | 200 r2sundials-7.2.1-3/r2sundials/inst/include/nvector/nvector_hip.h | 204 r2sundials-7.2.1-3/r2sundials/inst/include/nvector/nvector_kokkos.hpp | 95 r2sundials-7.2.1-3/r2sundials/inst/include/nvector/nvector_manyvector.h | 291 r2sundials-7.2.1-3/r2sundials/inst/include/nvector/nvector_mpimanyvector.h | 340 r2sundials-7.2.1-3/r2sundials/inst/include/nvector/nvector_mpiplusx.h | 37 r2sundials-7.2.1-3/r2sundials/inst/include/nvector/nvector_openmp.h | 296 r2sundials-7.2.1-3/r2sundials/inst/include/nvector/nvector_openmpdev.h | 199 r2sundials-7.2.1-3/r2sundials/inst/include/nvector/nvector_parallel.h | 384 r2sundials-7.2.1-3/r2sundials/inst/include/nvector/nvector_parhyp.h | 233 r2sundials-7.2.1-3/r2sundials/inst/include/nvector/nvector_petsc.h | 211 r2sundials-7.2.1-3/r2sundials/inst/include/nvector/nvector_pthreads.h | 357 r2sundials-7.2.1-3/r2sundials/inst/include/nvector/nvector_raja.h | 171 r2sundials-7.2.1-3/r2sundials/inst/include/nvector/nvector_serial.h | 285 r2sundials-7.2.1-3/r2sundials/inst/include/nvector/nvector_sycl.h | 227 r2sundials-7.2.1-3/r2sundials/inst/include/nvector/nvector_trilinos.h | 77 r2sundials-7.2.1-3/r2sundials/inst/include/nvector/trilinos/SundialsTpetraVectorInterface.hpp | 45 r2sundials-7.2.1-3/r2sundials/inst/include/nvector/trilinos/SundialsTpetraVectorKernels.hpp | 1368 + r2sundials-7.2.1-3/r2sundials/inst/include/r2sundials.h | 19 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/priv |only r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_adaptcontroller.h |only r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_band.h | 80 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_base.hpp | 52 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_config.h | 251 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_config.in | 233 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_context.h | 49 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_context.hpp | 33 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_convertibleto.hpp | 4 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_core.h |only r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_core.hpp |only r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_cuda_policies.hpp | 45 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_dense.h | 108 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_direct.h | 126 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_errors.h |only r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_export.h | 2 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_futils.h | 12 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_hip_policies.hpp | 49 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_iterative.h | 124 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_linearsolver.h | 114 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_linearsolver.hpp | 8 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_logger.h | 63 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_math.h | 124 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_matrix.h | 86 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_matrix.hpp | 5 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_memory.h | 114 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_memory.hpp |only r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_mpi_errors.h |only r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_mpi_types.h | 21 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_nonlinearsolver.h | 109 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_nonlinearsolver.hpp | 11 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_nvector.h | 238 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_nvector.hpp | 5 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_nvector_senswrapper.h | 64 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_profiler.h | 85 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_profiler.hpp |only r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_stepper.h |only r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_sycl_policies.hpp | 34 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_types.h | 129 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_types_deprecated.h |only r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_version.h | 13 r2sundials-7.2.1-3/r2sundials/inst/include/sundials/sundials_xbraid.h | 74 r2sundials-7.2.1-3/r2sundials/inst/include/sunlinsol/sunlinsol_band.h | 56 r2sundials-7.2.1-3/r2sundials/inst/include/sunlinsol/sunlinsol_cusolversp_batchqr.h | 59 r2sundials-7.2.1-3/r2sundials/inst/include/sunlinsol/sunlinsol_dense.h | 57 r2sundials-7.2.1-3/r2sundials/inst/include/sunlinsol/sunlinsol_ginkgo.hpp | 184 r2sundials-7.2.1-3/r2sundials/inst/include/sunlinsol/sunlinsol_klu.h | 60 r2sundials-7.2.1-3/r2sundials/inst/include/sunlinsol/sunlinsol_kokkosdense.hpp | 14 r2sundials-7.2.1-3/r2sundials/inst/include/sunlinsol/sunlinsol_lapackband.h | 28 r2sundials-7.2.1-3/r2sundials/inst/include/sunlinsol/sunlinsol_lapackdense.h | 28 r2sundials-7.2.1-3/r2sundials/inst/include/sunlinsol/sunlinsol_magmadense.h | 47 r2sundials-7.2.1-3/r2sundials/inst/include/sunlinsol/sunlinsol_onemkldense.h | 51 r2sundials-7.2.1-3/r2sundials/inst/include/sunlinsol/sunlinsol_pcg.h | 117 r2sundials-7.2.1-3/r2sundials/inst/include/sunlinsol/sunlinsol_spbcgs.h | 77 r2sundials-7.2.1-3/r2sundials/inst/include/sunlinsol/sunlinsol_spfgmr.h | 98 r2sundials-7.2.1-3/r2sundials/inst/include/sunlinsol/sunlinsol_spgmr.h | 98 r2sundials-7.2.1-3/r2sundials/inst/include/sunlinsol/sunlinsol_sptfqmr.h | 79 r2sundials-7.2.1-3/r2sundials/inst/include/sunlinsol/sunlinsol_superludist.h | 85 r2sundials-7.2.1-3/r2sundials/inst/include/sunlinsol/sunlinsol_superlumt.h | 76 r2sundials-7.2.1-3/r2sundials/inst/include/sunlinsol_rmumps.h | 6 r2sundials-7.2.1-3/r2sundials/inst/include/sunmatrix/sunmatrix_band.h | 72 r2sundials-7.2.1-3/r2sundials/inst/include/sunmatrix/sunmatrix_cusparse.h | 83 r2sundials-7.2.1-3/r2sundials/inst/include/sunmatrix/sunmatrix_dense.h | 58 r2sundials-7.2.1-3/r2sundials/inst/include/sunmatrix/sunmatrix_ginkgo.hpp | 116 r2sundials-7.2.1-3/r2sundials/inst/include/sunmatrix/sunmatrix_kokkosdense.hpp | 28 r2sundials-7.2.1-3/r2sundials/inst/include/sunmatrix/sunmatrix_magmadense.h | 106 r2sundials-7.2.1-3/r2sundials/inst/include/sunmatrix/sunmatrix_onemkldense.h | 104 r2sundials-7.2.1-3/r2sundials/inst/include/sunmatrix/sunmatrix_slunrloc.h | 52 r2sundials-7.2.1-3/r2sundials/inst/include/sunmatrix/sunmatrix_sparse.h | 166 r2sundials-7.2.1-3/r2sundials/inst/include/sunnonlinsol/sunnonlinsol_fixedpoint.h | 132 r2sundials-7.2.1-3/r2sundials/inst/include/sunnonlinsol/sunnonlinsol_newton.h | 113 r2sundials-7.2.1-3/r2sundials/inst/include/sunnonlinsol/sunnonlinsol_petscsnes.h | 79 r2sundials-7.2.1-3/r2sundials/man/r2cvodes.Rd | 9 r2sundials-7.2.1-3/r2sundials/src/Makevars | 14 r2sundials-7.2.1-3/r2sundials/src/lib/cvodes/LICENSE | 2 r2sundials-7.2.1-3/r2sundials/src/lib/cvodes/README.md | 21 r2sundials-7.2.1-3/r2sundials/src/lib/cvodes/cvodea.c | 2506 ++- r2sundials-7.2.1-3/r2sundials/src/lib/cvodes/cvodea_io.c | 645 r2sundials-7.2.1-3/r2sundials/src/lib/cvodes/cvodes.c | 6864 +++++----- r2sundials-7.2.1-3/r2sundials/src/lib/cvodes/cvodes_bandpre.c | 527 r2sundials-7.2.1-3/r2sundials/src/lib/cvodes/cvodes_bandpre_impl.h | 41 r2sundials-7.2.1-3/r2sundials/src/lib/cvodes/cvodes_bbdpre.c | 791 - r2sundials-7.2.1-3/r2sundials/src/lib/cvodes/cvodes_bbdpre_impl.h | 50 r2sundials-7.2.1-3/r2sundials/src/lib/cvodes/cvodes_diag.c | 380 r2sundials-7.2.1-3/r2sundials/src/lib/cvodes/cvodes_diag_impl.h | 29 r2sundials-7.2.1-3/r2sundials/src/lib/cvodes/cvodes_impl.h | 1166 - r2sundials-7.2.1-3/r2sundials/src/lib/cvodes/cvodes_io.c | 2153 +-- r2sundials-7.2.1-3/r2sundials/src/lib/cvodes/cvodes_ls.c | 2594 +-- r2sundials-7.2.1-3/r2sundials/src/lib/cvodes/cvodes_ls_impl.h | 208 r2sundials-7.2.1-3/r2sundials/src/lib/cvodes/cvodes_nls.c | 283 r2sundials-7.2.1-3/r2sundials/src/lib/cvodes/cvodes_nls_sim.c | 449 r2sundials-7.2.1-3/r2sundials/src/lib/cvodes/cvodes_nls_stg.c | 363 r2sundials-7.2.1-3/r2sundials/src/lib/cvodes/cvodes_nls_stg1.c | 280 r2sundials-7.2.1-3/r2sundials/src/lib/cvodes/cvodes_proj.c | 252 r2sundials-7.2.1-3/r2sundials/src/lib/cvodes/cvodes_proj_impl.h | 36 r2sundials-7.2.1-3/r2sundials/src/lib/nvector/hip/VectorArrayKernels.hip.hpp | 124 r2sundials-7.2.1-3/r2sundials/src/lib/nvector/hip/VectorKernels.hip.hpp | 233 r2sundials-7.2.1-3/r2sundials/src/lib/nvector/hip/nvector_hip.hip.cpp | 1891 +- r2sundials-7.2.1-3/r2sundials/src/lib/nvector/serial/nvector_serial.E |only r2sundials-7.2.1-3/r2sundials/src/lib/nvector/serial/nvector_serial.c | 1562 +- r2sundials-7.2.1-3/r2sundials/src/lib/readme.txt | 16 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_adaptcontroller.c |only r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_adiak_metadata.h |only r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_band.c | 257 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_context.c | 262 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_cuda.h | 71 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_cuda_kernels.cuh | 245 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_cusolver.h |only r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_cusparse.h |only r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_debug.h | 12 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_dense.c | 383 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_direct.c | 373 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_errors.c |only r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_futils.c | 29 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_hashmap.c |only r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_hashmap_impl.h |only r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_hip.h | 33 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_hip_kernels.hip.hpp | 253 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_iterative.c | 730 - r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_iterative_impl.h | 15 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_lapack_defs.h | 136 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_lapack_defs.h.in |only r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_linearsolver.c | 191 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_logger.c | 459 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_logger_impl.h | 149 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_macros.h |only r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_math.c | 128 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_matrix.c | 125 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_memory.c | 260 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_nonlinearsolver.c | 172 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_nvector.c | 809 - r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_nvector_senswrapper.c | 344 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_profiler.c | 463 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_reductions.hpp | 33 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_stepper.c |only r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_stepper_impl.h |only r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_sycl.h | 80 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_utils.h | 78 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_version.c | 35 r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/band/sunlinsol_band.c | 172 r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/cusolversp/sunlinsol_cusolversp_batchqr.cu | 168 r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/dense/sunlinsol_dense.c | 148 r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/lapackband/sunlinsol_lapackband.c | 181 r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/lapackdense/sunlinsol_lapackdense.c | 165 r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/magmadense/sunlinsol_magmadense.cpp | 283 r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/onemkldense/sunlinsol_onemkldense.cpp | 366 r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/pcg/sunlinsol_pcg.c | 601 r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/spbcgs/sunlinsol_spbcgs.c | 824 - r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/spfgmr/sunlinsol_spfgmr.c | 751 - r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/spgmr/sunlinsol_spgmr.c | 855 - r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/sptfqmr/sunlinsol_sptfqmr.c | 1147 - r2sundials-7.2.1-3/r2sundials/src/lib/sunmatrix/band/sunmatrix_band.c | 447 r2sundials-7.2.1-3/r2sundials/src/lib/sunmatrix/cusparse/cusparse_kernels.cuh | 225 r2sundials-7.2.1-3/r2sundials/src/lib/sunmatrix/cusparse/sunmatrix_cusparse.cu | 904 - r2sundials-7.2.1-3/r2sundials/src/lib/sunmatrix/dense/sunmatrix_dense.c | 244 r2sundials-7.2.1-3/r2sundials/src/lib/sunmatrix/magmadense/dense_cuda_kernels.cuh | 127 r2sundials-7.2.1-3/r2sundials/src/lib/sunmatrix/magmadense/dense_hip_kernels.hip.hpp | 129 r2sundials-7.2.1-3/r2sundials/src/lib/sunmatrix/magmadense/sunmatrix_magmadense.cpp | 547 r2sundials-7.2.1-3/r2sundials/src/lib/sunmatrix/onemkldense/sunmatrix_onemkldense.cpp | 450 r2sundials-7.2.1-3/r2sundials/src/lib/sunmatrix/sparse/sunmatrix_sparse.c | 1152 - r2sundials-7.2.1-3/r2sundials/src/lib/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.c | 698 - r2sundials-7.2.1-3/r2sundials/src/lib/sunnonlinsol/newton/sunnonlinsol_newton.c | 391 r2sundials-7.2.1-3/r2sundials/src/r2sundials.cpp | 33 r2sundials-7.2.1-3/r2sundials/src/sunlinsol_rmumps.cpp | 23 r2sundials-7.2.1-3/r2sundials/tests/RUnit.R | 1 218 files changed, 27008 insertions(+), 25161 deletions(-)
Title: 'WebSocket' Client Library
Description: Provides a 'WebSocket' client interface for R.
'WebSocket' is a protocol for low-overhead real-time communication:
<https://en.wikipedia.org/wiki/WebSocket>.
Author: Winston Chang [aut, cre],
Joe Cheng [aut],
Alan Dipert [aut],
Barbara Borges [aut],
Posit, PBC [cph],
Peter Thorson [ctb, cph] ,
Rene Nyffenegger [ctb, cph] ,
Micael Hildenborg [ctb, cph] ,
Aladdin Enterprises [cph] ,
Bjoern Hoehrmann [ctb, cph]
Maintainer: Winston Chang <winston@posit.co>
Diff between websocket versions 1.4.2 dated 2024-07-22 and 1.4.4 dated 2025-04-10
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 10 +++++++++- build/vignette.rds |binary cleanup | 1 - inst/doc/overview.R | 50 +++++++++++++++++++++++++------------------------- src/Makevars.in | 2 +- src/Makevars.ucrt | 9 +++++++-- 8 files changed, 52 insertions(+), 40 deletions(-)
Title: Get Executing Script's Path
Description: Determine the path of the executing script. Compatible
with several popular GUIs: 'Rgui', 'RStudio', 'Positron',
'VSCode', 'Jupyter', 'Emacs', and 'Rscript' (shell). Compatible
with several functions and packages: 'source()',
'sys.source()', 'debugSource()' in 'RStudio',
'compiler::loadcmp()', 'utils::Sweave()', 'box::use()',
'knitr::knit()', 'plumber::plumb()', 'shiny::runApp()',
'package:targets', and 'testthat::source_file()'.
Author: Iris Simmons [aut, cre]
Maintainer: Iris Simmons <ikwsimmo@gmail.com>
Diff between this.path versions 2.6.0 dated 2024-12-18 and 2.7.0 dated 2025-04-10
DESCRIPTION | 8 LICENSE | 2 MD5 | 70 ++--- NAMESPACE | 45 +-- NEWS | 23 + R/defunct.R | 10 R/files.R | 30 +- R/make_fix_funs.R | 75 ++++-- R/setsyspath.R | 12 - R/zzz.R | 40 +-- README.md | 16 + build/stage23.rdb |binary build/this.path.pdf |binary inst/NEWS.in.Rd | 26 ++ inst/doc/NEWS.1 | 2 man/basename2.Rd | 10 man/ext.Rd | 18 - man/make_fix_funs.Rd | 14 - man/set.sys.path.Rd | 7 man/this.path-defunct.Rd | 10 src/0.c | 2 src/backports.c | 2 src/backports.h | 44 +++ src/basename2.c | 54 ++-- src/ext.c | 101 ++++---- src/files.c | 44 ++- src/files.h | 14 - src/ns-hooks.c | 14 + src/ns-hooks.h | 3 src/pathjoin.c | 563 ++++++++++++++++++++++++++++++----------------- src/pathsplit.c | 106 +++++--- src/promises.c | 14 - src/setsyspath.c | 11 src/startup.c | 6 src/thispathdefn.h | 93 ++++++- tests/ext-tests.R | 8 36 files changed, 972 insertions(+), 525 deletions(-)
Title: Testing for Shiny Applications
Description: Automated unit testing of Shiny applications through a headless 'Chromium' browser.
Author: Barret Schloerke [cre, aut] ,
Posit Software, PBC [cph, fnd],
Winston Chang [ctb] ,
Gabor Csardi [ctb] ,
Hadley Wickham [ctb] ,
Mango Solutions [cph, ccp]
Maintainer: Barret Schloerke <barret@posit.co>
Diff between shinytest2 versions 0.3.2 dated 2024-04-28 and 0.4.0 dated 2025-04-10
DESCRIPTION | 14 - MD5 | 81 +++--- NAMESPACE | 15 - NEWS.md | 21 + R/app-driver-expect-download.R | 37 +- R/app-driver-expect-js.R | 65 +++-- R/app-driver-expect-screenshot.R | 106 +++++--- R/app-driver-expect-values.R | 145 +++++++---- R/app-driver-initialize.R | 131 +++++++--- R/app-driver-start.R | 11 R/app-driver.R | 310 ++++++++++++++++-------- R/compare-screenshot-threshold.R | 55 ++-- R/expect-snapshot.R | 38 +- R/shinytest2-logs.R | 8 build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/in-depth.R | 210 ++++++++-------- inst/doc/in-depth.html | 8 inst/doc/robust.Rmd | 4 inst/doc/robust.html | 10 inst/doc/shinytest2.R | 54 ++-- inst/doc/shinytest2.html | 12 inst/doc/use-application-audit.html | 8 inst/doc/use-ci.html | 4 inst/doc/use-package.R | 78 +++--- inst/doc/use-package.Rmd | 19 + inst/doc/use-package.html | 32 +- inst/doc/using-monkey-testing.html | 16 - inst/doc/z-migration.html | 4 inst/doc/zzz-faq.R | 58 ++-- inst/doc/zzz-faq.html | 4 inst/internal/js/shiny-tracer.js | 8 man/AppDriver.Rd | 120 +++++---- man/compare_screenshot_threshold.Rd | 43 ++- man/figures/logo.svg | 167 ++++-------- tests/testthat/_snaps |only tests/testthat/test-app-expect-file-transform.R |only tests/testthat/test-image-diff.R | 49 +++ tests/testthat/test-migration-transformation.R | 4 vignettes/robust.Rmd | 4 vignettes/use-package.Rmd | 19 + 41 files changed, 1199 insertions(+), 774 deletions(-)
Title: Graphic Devices Based on AGG
Description: Anti-Grain Geometry (AGG) is a high-quality and
high-performance 2D drawing library. The 'ragg' package provides a set
of graphic devices based on AGG to use as alternative to the raster
devices provided through the 'grDevices' package.
Author: Thomas Lin Pedersen [cre, aut]
,
Maxim Shemanarev [aut, cph] ,
Tony Juricic [ctb, cph] ,
Milan Marusinec [ctb, cph] ,
Spencer Garrett [ctb] ,
Posit, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between ragg versions 1.3.3 dated 2024-09-11 and 1.4.0 dated 2025-04-10
DESCRIPTION | 9 MD5 | 39 +-- NAMESPACE | 1 NEWS.md | 8 R/aaa.R | 8 R/agg_dev.R | 280 ++++++++++++++---------- R/ragg-package.R | 6 README.md | 1 configure | 2 man/agg_record.Rd |only src/AggDevice.h | 435 +++++++++++++++++++------------------- src/AggDeviceRecord.h |only src/AggDeviceTiff.h | 75 ++++-- src/Makevars.win | 31 +- src/agg/include/agg_dda_line.h | 14 - src/agg/include/agg_pixfmt_rgba.h | 30 ++ src/init.cpp | 3 src/init_device.h | 203 ++++++++++------- src/ragg.h | 22 + src/record_dev.cpp |only src/tiff_dev.cpp | 4 tests/testthat/test-tiff.R | 19 + 22 files changed, 681 insertions(+), 509 deletions(-)
Title: Detect Heatwaves and Cold-Spells
Description: The different methods for defining, detecting, and categorising the extreme events
known as heatwaves or cold-spells, as first proposed in Hobday et al. (2016) <doi: 10.1016/j.pocean.2015.12.014>
and Hobday et al. (2018) <https://www.jstor.org/stable/26542662>. The functions in this package work on both air
and water temperature data. These detection algorithms may be used on non-temperature data as well.
Author: Robert W. Schlegel [aut, cre, ctb]
,
Albertus J. Smit [aut, ctb]
Maintainer: Robert W. Schlegel <robwschlegel@gmail.com>
Diff between heatwaveR versions 0.4.6 dated 2021-10-27 and 0.5.4 dated 2025-04-10
heatwaveR-0.4.6/heatwaveR/R/make_whole.R |only heatwaveR-0.4.6/heatwaveR/man/make_whole.Rd |only heatwaveR-0.4.6/heatwaveR/src/Makevars.win |only heatwaveR-0.4.6/heatwaveR/tests/testthat/test-make_whole.R |only heatwaveR-0.5.4/heatwaveR/DESCRIPTION | 18 heatwaveR-0.5.4/heatwaveR/MD5 | 188 +- heatwaveR-0.5.4/heatwaveR/NAMESPACE | 11 heatwaveR-0.5.4/heatwaveR/NEWS.md | 174 + heatwaveR-0.5.4/heatwaveR/R/block_average.R | 117 - heatwaveR-0.5.4/heatwaveR/R/category.R | 273 +- heatwaveR-0.5.4/heatwaveR/R/clim_calc.R | 32 heatwaveR-0.5.4/heatwaveR/R/clim_spread.R | 40 heatwaveR-0.5.4/heatwaveR/R/detect_event.R | 363 ++- heatwaveR-0.5.4/heatwaveR/R/detect_event3.R |only heatwaveR-0.5.4/heatwaveR/R/exceedance.R | 322 +-- heatwaveR-0.5.4/heatwaveR/R/geoms.R | 22 heatwaveR-0.5.4/heatwaveR/R/graph_functions.R | 235 +- heatwaveR-0.5.4/heatwaveR/R/make_whole_fast.R | 82 heatwaveR-0.5.4/heatwaveR/R/na_interp.R | 8 heatwaveR-0.5.4/heatwaveR/R/proto_event.R | 58 heatwaveR-0.5.4/heatwaveR/R/proto_event3.R |only heatwaveR-0.5.4/heatwaveR/R/smooth_percentile.R | 44 heatwaveR-0.5.4/heatwaveR/R/sst_med.R | 5 heatwaveR-0.5.4/heatwaveR/R/sst_nw_atl.R | 5 heatwaveR-0.5.4/heatwaveR/R/sst_wa.R | 5 heatwaveR-0.5.4/heatwaveR/R/ts2clm.R | 262 +- heatwaveR-0.5.4/heatwaveR/R/ts2clm3.R |only heatwaveR-0.5.4/heatwaveR/README.md | 72 heatwaveR-0.5.4/heatwaveR/build/partial.rdb |only heatwaveR-0.5.4/heatwaveR/build/vignette.rds |binary heatwaveR-0.5.4/heatwaveR/data/sst_Med.rda |binary heatwaveR-0.5.4/heatwaveR/data/sst_NW_Atl.rda |binary heatwaveR-0.5.4/heatwaveR/data/sst_WA.rda |binary heatwaveR-0.5.4/heatwaveR/inst/CITATION | 2 heatwaveR-0.5.4/heatwaveR/inst/doc/Download_SST_v2.R |only heatwaveR-0.5.4/heatwaveR/inst/doc/Download_SST_v2.Rmd |only heatwaveR-0.5.4/heatwaveR/inst/doc/Download_SST_v2.html |only heatwaveR-0.5.4/heatwaveR/inst/doc/MHW_metric_trends.R |only heatwaveR-0.5.4/heatwaveR/inst/doc/MHW_metric_trends.Rmd |only heatwaveR-0.5.4/heatwaveR/inst/doc/MHW_metric_trends.html |only heatwaveR-0.5.4/heatwaveR/inst/doc/MHW_to_nc.R | 272 +- heatwaveR-0.5.4/heatwaveR/inst/doc/MHW_to_nc.html | 639 ++++-- heatwaveR-0.5.4/heatwaveR/inst/doc/OISST_preparation.R | 266 +- heatwaveR-0.5.4/heatwaveR/inst/doc/OISST_preparation.Rmd | 130 - heatwaveR-0.5.4/heatwaveR/inst/doc/OISST_preparation.html | 800 ++++++-- heatwaveR-0.5.4/heatwaveR/inst/doc/complex_clims.R | 12 heatwaveR-0.5.4/heatwaveR/inst/doc/complex_clims.Rmd | 12 heatwaveR-0.5.4/heatwaveR/inst/doc/complex_clims.html | 869 ++++++--- heatwaveR-0.5.4/heatwaveR/inst/doc/detection_and_visualisation.R | 222 +- heatwaveR-0.5.4/heatwaveR/inst/doc/detection_and_visualisation.Rmd | 8 heatwaveR-0.5.4/heatwaveR/inst/doc/detection_and_visualisation.html | 937 ++++++---- heatwaveR-0.5.4/heatwaveR/inst/doc/event_categories.R | 29 heatwaveR-0.5.4/heatwaveR/inst/doc/event_categories.Rmd | 35 heatwaveR-0.5.4/heatwaveR/inst/doc/event_categories.html | 818 +++++--- heatwaveR-0.5.4/heatwaveR/inst/doc/exceedance.html | 508 +++-- heatwaveR-0.5.4/heatwaveR/inst/doc/gridded_event_detection.R | 220 +- heatwaveR-0.5.4/heatwaveR/inst/doc/gridded_event_detection.Rmd | 2 heatwaveR-0.5.4/heatwaveR/inst/doc/gridded_event_detection.html | 691 +++++-- heatwaveR-0.5.4/heatwaveR/inst/doc/internal_workflow.R |only heatwaveR-0.5.4/heatwaveR/inst/doc/internal_workflow.Rmd |only heatwaveR-0.5.4/heatwaveR/inst/doc/internal_workflow.html |only heatwaveR-0.5.4/heatwaveR/man/block_average.Rd | 9 heatwaveR-0.5.4/heatwaveR/man/category.Rd | 61 heatwaveR-0.5.4/heatwaveR/man/clim_calc.Rd | 3 heatwaveR-0.5.4/heatwaveR/man/clim_spread.Rd | 5 heatwaveR-0.5.4/heatwaveR/man/detect_event.Rd | 40 heatwaveR-0.5.4/heatwaveR/man/detect_event3.Rd |only heatwaveR-0.5.4/heatwaveR/man/event_line.Rd | 40 heatwaveR-0.5.4/heatwaveR/man/exceedance.Rd | 35 heatwaveR-0.5.4/heatwaveR/man/geom_flame.Rd | 12 heatwaveR-0.5.4/heatwaveR/man/geom_lolli.Rd | 2 heatwaveR-0.5.4/heatwaveR/man/heatwaveR-package.Rd | 2 heatwaveR-0.5.4/heatwaveR/man/lolli_plot.Rd | 21 heatwaveR-0.5.4/heatwaveR/man/make_whole_fast.Rd | 25 heatwaveR-0.5.4/heatwaveR/man/na_interp.Rd | 7 heatwaveR-0.5.4/heatwaveR/man/proto_event.Rd | 1 heatwaveR-0.5.4/heatwaveR/man/proto_event3.Rd |only heatwaveR-0.5.4/heatwaveR/man/smooth_percentile.Rd | 3 heatwaveR-0.5.4/heatwaveR/man/sst_Med.Rd | 7 heatwaveR-0.5.4/heatwaveR/man/sst_NW_Atl.Rd | 7 heatwaveR-0.5.4/heatwaveR/man/sst_WA.Rd | 7 heatwaveR-0.5.4/heatwaveR/man/ts2clm.Rd | 64 heatwaveR-0.5.4/heatwaveR/man/ts2clm3.Rd |only heatwaveR-0.5.4/heatwaveR/src/Makevars | 2 heatwaveR-0.5.4/heatwaveR/tests/testthat/test-block_average.R | 20 heatwaveR-0.5.4/heatwaveR/tests/testthat/test-category.R | 90 heatwaveR-0.5.4/heatwaveR/tests/testthat/test-clim_calc.R | 3 heatwaveR-0.5.4/heatwaveR/tests/testthat/test-clim_spread.R | 4 heatwaveR-0.5.4/heatwaveR/tests/testthat/test-detect_event.R | 110 - heatwaveR-0.5.4/heatwaveR/tests/testthat/test-detect_event3.R |only heatwaveR-0.5.4/heatwaveR/tests/testthat/test-exceedance.R | 78 heatwaveR-0.5.4/heatwaveR/tests/testthat/test-graph_functions.R | 99 - heatwaveR-0.5.4/heatwaveR/tests/testthat/test-make_whole_fast.R | 4 heatwaveR-0.5.4/heatwaveR/tests/testthat/test-na_interp.R | 8 heatwaveR-0.5.4/heatwaveR/tests/testthat/test-proto_event.R | 20 heatwaveR-0.5.4/heatwaveR/tests/testthat/test-proto_event3.R |only heatwaveR-0.5.4/heatwaveR/tests/testthat/test-smooth_percentile.R | 2 heatwaveR-0.5.4/heatwaveR/tests/testthat/test-ts2clm.R | 86 heatwaveR-0.5.4/heatwaveR/tests/testthat/test-ts2clm3.R |only heatwaveR-0.5.4/heatwaveR/vignettes/Download_SST_v2.Rmd |only heatwaveR-0.5.4/heatwaveR/vignettes/MHW_metric_trends.Rmd |only heatwaveR-0.5.4/heatwaveR/vignettes/OISST_preparation.Rmd | 130 - heatwaveR-0.5.4/heatwaveR/vignettes/bibliography.bib | 106 + heatwaveR-0.5.4/heatwaveR/vignettes/complex_clims.Rmd | 12 heatwaveR-0.5.4/heatwaveR/vignettes/detection_and_visualisation.Rmd | 8 heatwaveR-0.5.4/heatwaveR/vignettes/event_categories.Rmd | 35 heatwaveR-0.5.4/heatwaveR/vignettes/gridded_event_detection.Rmd | 2 heatwaveR-0.5.4/heatwaveR/vignettes/internal_workflow.Rmd |only 108 files changed, 6517 insertions(+), 3461 deletions(-)
Title: Unified Parallel and Distributed Processing in R for Everyone
Description: The purpose of this package is to provide a lightweight and
unified Future API for sequential and parallel processing of R
expression via futures. The simplest way to evaluate an expression
in parallel is to use `x %<-% { expression }` with `plan(multisession)`.
This package implements sequential, multicore, multisession, and
cluster futures. With these, R expressions can be evaluated on the
local machine, in parallel a set of local machines, or distributed
on a mix of local and remote machines.
Extensions to this package implement additional backends for
processing futures via compute cluster schedulers, etc.
Because of its unified API, there is no need to modify any code in order
switch from sequential on the local machine to, say, distributed
processing on a remote compute cluster.
Another strength of this package is that global variables and functions
are automatically identified and exported as needed, making it
straightforward to tweak existing code to make use of futures.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 1.34.0 dated 2024-07-29 and 1.40.0 dated 2025-04-10
future-1.34.0/future/R/ClusterFuture-class.R |only future-1.34.0/future/R/ClusterRegistry.R |only future-1.34.0/future/R/ConstantFuture-class.R |only future-1.34.0/future/R/Future-class.R |only future-1.34.0/future/R/FutureCondition-class.R |only future-1.34.0/future/R/FutureGlobals-class.R |only future-1.34.0/future/R/FutureRegistry.R |only future-1.34.0/future/R/FutureResult-class.R |only future-1.34.0/future/R/MulticoreFuture-class.R |only future-1.34.0/future/R/MultiprocessFuture-class.R |only future-1.34.0/future/R/MultisessionFuture-class.R |only future-1.34.0/future/R/UniprocessFuture-class.R |only future-1.34.0/future/R/backtrace.R |only future-1.34.0/future/R/capture_journals.R |only future-1.34.0/future/R/cluster.R |only future-1.34.0/future/R/conditions_OP.R |only future-1.34.0/future/R/connections.R |only future-1.34.0/future/R/constant.R |only future-1.34.0/future/R/expressions.R |only future-1.34.0/future/R/future.R |only future-1.34.0/future/R/futureAssign.R |only future-1.34.0/future/R/futureAssign_OP.R |only future-1.34.0/future/R/futureCall.R |only future-1.34.0/future/R/futureOf.R |only future-1.34.0/future/R/futureSessionInfo.R |only future-1.34.0/future/R/futures.R |only future-1.34.0/future/R/globals.R |only future-1.34.0/future/R/globals_OP.R |only future-1.34.0/future/R/journal.R |only future-1.34.0/future/R/label_OP.R |only future-1.34.0/future/R/lazy_OP.R |only future-1.34.0/future/R/makeClusterPSOCK_args.R |only future-1.34.0/future/R/mandelbrot.R |only future-1.34.0/future/R/multicore.R |only future-1.34.0/future/R/multisession.R |only future-1.34.0/future/R/nbrOfWorkers.R |only future-1.34.0/future/R/options.R |only future-1.34.0/future/R/plan_OP.R |only future-1.34.0/future/R/resolve.R |only future-1.34.0/future/R/resolved.R |only future-1.34.0/future/R/rng_utils.R |only future-1.34.0/future/R/seed_OP.R |only future-1.34.0/future/R/sequential.R |only future-1.34.0/future/R/sessionDetails.R |only future-1.34.0/future/R/signalConditions.R |only future-1.34.0/future/R/signalEarly.R |only future-1.34.0/future/R/stdout_OP.R |only future-1.34.0/future/R/stealth_sample.R |only future-1.34.0/future/R/sticky_globals.R |only future-1.34.0/future/R/tweak.R |only future-1.34.0/future/R/tweakExpression.R |only future-1.34.0/future/R/tweak_OP.R |only future-1.34.0/future/R/utils,conditions.R |only future-1.34.0/future/R/utils.R |only future-1.34.0/future/R/uuid.R |only future-1.34.0/future/R/value.R |only future-1.34.0/future/R/whichIndex.R |only future-1.34.0/future/R/zzz.plan.R |only future-1.34.0/future/man/ClusterFuture-class.Rd |only future-1.34.0/future/man/ConstantFuture-class.Rd |only future-1.34.0/future/man/future.options.Rd |only future-1.34.0/future/man/grapes-conditions-grapes.Rd |only future-1.34.0/future/man/grapes-globals-grapes.Rd |only future-1.34.0/future/man/grapes-label-grapes.Rd |only future-1.34.0/future/man/grapes-lazy-grapes.Rd |only future-1.34.0/future/man/grapes-plan-grapes.Rd |only future-1.34.0/future/man/grapes-seed-grapes.Rd |only future-1.34.0/future/man/grapes-stdout-grapes.Rd |only future-1.34.0/future/man/grapes-tweak-grapes.Rd |only future-1.34.0/future/man/tweak.Rd |only future-1.34.0/future/tests/000.sessionDetails.R |only future-1.34.0/future/tests/ClusterRegistry.R |only future-1.34.0/future/tests/Future-class.R |only future-1.34.0/future/tests/FutureError.R |only future-1.34.0/future/tests/FutureGlobals.R |only future-1.34.0/future/tests/FutureRegistry.R |only future-1.34.0/future/tests/adhoc_native_to_utf8.R |only future-1.34.0/future/tests/backtrace.R |only future-1.34.0/future/tests/bquote.R |only future-1.34.0/future/tests/capture_journals.R |only future-1.34.0/future/tests/cluster,worker-termination.R |only future-1.34.0/future/tests/cluster-missing-future-pkg.R |only future-1.34.0/future/tests/cluster.R |only future-1.34.0/future/tests/constant.R |only future-1.34.0/future/tests/demo.R |only future-1.34.0/future/tests/dotdotdot.R |only future-1.34.0/future/tests/early-signaling.R |only future-1.34.0/future/tests/future,labels.R |only future-1.34.0/future/tests/future,optsenvvars.R |only future-1.34.0/future/tests/future.R |only future-1.34.0/future/tests/futureAssign.R |only future-1.34.0/future/tests/futureAssign_OP.R |only future-1.34.0/future/tests/futureAssign_OP_with_environment.R |only future-1.34.0/future/tests/futureAssign_OP_with_listenv.R |only future-1.34.0/future/tests/futureCall.R |only future-1.34.0/future/tests/futureOf.R |only future-1.34.0/future/tests/futureOf_with_environment.R |only future-1.34.0/future/tests/futureOf_with_listenv.R |only future-1.34.0/future/tests/futureSessionInfo.R |only future-1.34.0/future/tests/futures.R |only future-1.34.0/future/tests/globals,NSE.R |only future-1.34.0/future/tests/globals,S4methods.R |only future-1.34.0/future/tests/globals,formulas.R |only future-1.34.0/future/tests/globals,locals.R |only future-1.34.0/future/tests/globals,manual.R |only future-1.34.0/future/tests/globals,resolve.R |only future-1.34.0/future/tests/globals,subassignment.R |only future-1.34.0/future/tests/globals,toolarge.R |only future-1.34.0/future/tests/globals,tricky.R |only future-1.34.0/future/tests/globals,tricky_recursive.R |only future-1.34.0/future/tests/globalsOf,tweaks.R |only future-1.34.0/future/tests/immediateCondition.R |only future-1.34.0/future/tests/incl |only future-1.34.0/future/tests/invalid-owner.R |only future-1.34.0/future/tests/mandelbrot.R |only future-1.34.0/future/tests/mpi.R |only future-1.34.0/future/tests/multicore,multithreading.R |only future-1.34.0/future/tests/multicore,worker-termination.R |only future-1.34.0/future/tests/multicore.R |only future-1.34.0/future/tests/multisession.R |only future-1.34.0/future/tests/nbrOfWorkers.R |only future-1.34.0/future/tests/nested_futures,mc.cores.R |only future-1.34.0/future/tests/nested_futures.R |only future-1.34.0/future/tests/non-exportable,connections.R |only future-1.34.0/future/tests/objectSize.R |only future-1.34.0/future/tests/plan.R |only future-1.34.0/future/tests/relaying,muffle.R |only future-1.34.0/future/tests/relaying,split.R |only future-1.34.0/future/tests/relaying.R |only future-1.34.0/future/tests/requestCore.R |only future-1.34.0/future/tests/requestNode.R |only future-1.34.0/future/tests/reserved-keyword-functions.R |only future-1.34.0/future/tests/resolve.R |only future-1.34.0/future/tests/resolved-non-blocking-test.R |only future-1.34.0/future/tests/rng.R |only future-1.34.0/future/tests/rng_utils.R |only future-1.34.0/future/tests/sequential.R |only future-1.34.0/future/tests/sessionDetails.R |only future-1.34.0/future/tests/startup.R |only future-1.34.0/future/tests/stdout.R |only future-1.34.0/future/tests/tweak.R |only future-1.34.0/future/tests/utils.R |only future-1.34.0/future/tests/uuid.R |only future-1.34.0/future/tests/whichIndex.R |only future-1.40.0/future/DESCRIPTION | 13 future-1.40.0/future/MD5 | 528 +++++----- future-1.40.0/future/NAMESPACE | 102 + future-1.40.0/future/NEWS.md | 160 +++ future-1.40.0/future/R/000.bquote.R | 4 future-1.40.0/future/R/000.import.R | 15 future-1.40.0/future/R/000.re-exports.R | 50 future-1.40.0/future/R/010.tweakable.R |only future-1.40.0/future/R/010.utils-parallelly.R |only future-1.40.0/future/R/backend_api-01-FutureBackend-class.R |only future-1.40.0/future/R/backend_api-03.MultiprocessFutureBackend-class.R |only future-1.40.0/future/R/backend_api-11.ClusterFutureBackend-class.R |only future-1.40.0/future/R/backend_api-11.MulticoreFutureBackend-class.R |only future-1.40.0/future/R/backend_api-11.SequentialFutureBackend-class.R |only future-1.40.0/future/R/backend_api-13.MultisessionFutureBackend-class.R |only future-1.40.0/future/R/backend_api-ConstantFuture-class.R |only future-1.40.0/future/R/backend_api-Future-class.R |only future-1.40.0/future/R/backend_api-FutureRegistry.R |only future-1.40.0/future/R/backend_api-UniprocessFuture-class.R |only future-1.40.0/future/R/backend_api-evalFuture.R |only future-1.40.0/future/R/core_api-future.R |only future-1.40.0/future/R/core_api-interrupt.R |only future-1.40.0/future/R/core_api-reset.R |only future-1.40.0/future/R/core_api-resolved.R |only future-1.40.0/future/R/core_api-value.R |only future-1.40.0/future/R/delayed_api-futureAssign.R |only future-1.40.0/future/R/delayed_api-futureOf.R |only future-1.40.0/future/R/demo_api-mandelbrot.R |only future-1.40.0/future/R/infix_api-01-futureAssign_OP.R |only future-1.40.0/future/R/infix_api-02-globals_OP.R |only future-1.40.0/future/R/infix_api-03-seed_OP.R |only future-1.40.0/future/R/infix_api-04-stdout_OP.R |only future-1.40.0/future/R/infix_api-05-conditions_OP.R |only future-1.40.0/future/R/infix_api-06-lazy_OP.R |only future-1.40.0/future/R/infix_api-07-label_OP.R |only future-1.40.0/future/R/infix_api-08-plan_OP.R |only future-1.40.0/future/R/infix_api-09-tweak_OP.R |only future-1.40.0/future/R/protected_api-FutureCondition-class.R |only future-1.40.0/future/R/protected_api-FutureGlobals-class.R |only future-1.40.0/future/R/protected_api-FutureResult-class.R |only future-1.40.0/future/R/protected_api-futures.R |only future-1.40.0/future/R/protected_api-globals.R |only future-1.40.0/future/R/protected_api-journal.R |only future-1.40.0/future/R/protected_api-resolve.R |only future-1.40.0/future/R/protected_api-signalConditions.R |only future-1.40.0/future/R/testme.R |only future-1.40.0/future/R/utils-basic.R |only future-1.40.0/future/R/utils-conditions.R |only future-1.40.0/future/R/utils-connections.R |only future-1.40.0/future/R/utils-debug.R |only future-1.40.0/future/R/utils-immediateCondition.R | 66 - future-1.40.0/future/R/utils-objectSize.R | 11 future-1.40.0/future/R/utils-options.R |only future-1.40.0/future/R/utils-prune_pkg_code.R |only future-1.40.0/future/R/utils-rng_utils.R |only future-1.40.0/future/R/utils-signalEarly.R |only future-1.40.0/future/R/utils-stealth_sample.R |only future-1.40.0/future/R/utils-sticky_globals.R |only future-1.40.0/future/R/utils-tweakExpression.R |only future-1.40.0/future/R/utils-uuid.R |only future-1.40.0/future/R/utils-whichIndex.R |only future-1.40.0/future/R/utils_api-backtrace.R |only future-1.40.0/future/R/utils_api-capture_journals.R |only future-1.40.0/future/R/utils_api-futureCall.R |only future-1.40.0/future/R/utils_api-futureSessionInfo.R |only future-1.40.0/future/R/utils_api-minifuture.R |only future-1.40.0/future/R/utils_api-nbrOfWorkers.R |only future-1.40.0/future/R/utils_api-plan-with.R |only future-1.40.0/future/R/utils_api-plan.R |only future-1.40.0/future/R/utils_api-sessionDetails.R |only future-1.40.0/future/R/utils_api-tweak.R |only future-1.40.0/future/R/zzz.R | 31 future-1.40.0/future/build/vignette.rds |binary future-1.40.0/future/demo/fibonacci.R | 4 future-1.40.0/future/demo/mandelbrot.R | 4 future-1.40.0/future/inst/WORDLIST | 20 future-1.40.0/future/inst/doc/future-1-overview.html | 418 ++++--- future-1.40.0/future/inst/doc/future-1-overview.md.rsp | 134 +- future-1.40.0/future/inst/doc/future-2-output.html | 202 +-- future-1.40.0/future/inst/doc/future-3-topologies.html | 223 +--- future-1.40.0/future/inst/doc/future-3-topologies.md.rsp | 21 future-1.40.0/future/inst/doc/future-4-issues.html | 295 +++-- future-1.40.0/future/inst/doc/future-4-issues.md.rsp | 99 + future-1.40.0/future/inst/doc/future-4-non-exportable-objects.html | 256 ++-- future-1.40.0/future/inst/doc/future-4-non-exportable-objects.md.rsp | 2 future-1.40.0/future/inst/doc/future-5-startup.html | 200 +-- future-1.40.0/future/inst/doc/future-6-future-api-backend-specification.html | 142 +- future-1.40.0/future/inst/doc/future-6-future-api-backend-specification.md.rsp | 2 future-1.40.0/future/inst/doc/future-7-for-package-developers.html | 215 +--- future-1.40.0/future/inst/doc/future-7-for-package-developers.md.rsp | 9 future-1.40.0/future/inst/doc/future-8-how-future-is-validated.html | 124 +- future-1.40.0/future/inst/testme |only future-1.40.0/future/inst/vignettes-static/future-1-overview.md.rsp.rsp | 48 future-1.40.0/future/man/Future-class.Rd | 12 future-1.40.0/future/man/FutureBackend.Rd |only future-1.40.0/future/man/FutureCondition.Rd | 67 - future-1.40.0/future/man/FutureGlobals.Rd | 4 future-1.40.0/future/man/FutureResult.Rd | 6 future-1.40.0/future/man/MulticoreFuture-class.Rd | 17 future-1.40.0/future/man/MultiprocessFuture-class.Rd | 5 future-1.40.0/future/man/UniprocessFuture-class.Rd | 30 future-1.40.0/future/man/backtrace.Rd | 4 future-1.40.0/future/man/cluster.Rd | 30 future-1.40.0/future/man/clusterExportSticky.Rd | 4 future-1.40.0/future/man/future.Rd | 118 -- future-1.40.0/future/man/futureAssign.Rd |only future-1.40.0/future/man/futureOf.Rd | 2 future-1.40.0/future/man/futureSessionInfo.Rd | 2 future-1.40.0/future/man/futures.Rd | 4 future-1.40.0/future/man/getExpression.Rd | 6 future-1.40.0/future/man/getGlobalsAndPackages.Rd | 7 future-1.40.0/future/man/interrupt.Rd |only future-1.40.0/future/man/mandelbrot.Rd | 2 future-1.40.0/future/man/multicore.Rd | 20 future-1.40.0/future/man/multisession.Rd | 21 future-1.40.0/future/man/nbrOfWorkers.Rd | 4 future-1.40.0/future/man/nullcon.Rd | 2 future-1.40.0/future/man/plan.Rd | 176 ++- future-1.40.0/future/man/private_length.Rd | 2 future-1.40.0/future/man/re-exports.Rd | 18 future-1.40.0/future/man/requestCore.Rd | 10 future-1.40.0/future/man/reset.Rd |only future-1.40.0/future/man/resetWorkers.Rd | 2 future-1.40.0/future/man/resolve.Rd | 4 future-1.40.0/future/man/resolved.Rd | 4 future-1.40.0/future/man/result.Rd | 4 future-1.40.0/future/man/run.Rd | 4 future-1.40.0/future/man/save_rds.Rd | 2 future-1.40.0/future/man/sequential.Rd | 18 future-1.40.0/future/man/sessionDetails.Rd | 2 future-1.40.0/future/man/signalConditions.Rd | 4 future-1.40.0/future/man/sticky_globals.Rd | 2 future-1.40.0/future/man/usedCores.Rd | 2 future-1.40.0/future/man/value.Rd | 119 ++ future-1.40.0/future/man/zzz-future.options.Rd |only future-1.40.0/future/tests/test-FutureError.R |only future-1.40.0/future/tests/test-FutureGlobals.R |only future-1.40.0/future/tests/test-FutureRegistry.R |only future-1.40.0/future/tests/test-adhoc_native_to_utf8.R |only future-1.40.0/future/tests/test-backtrace.R |only future-1.40.0/future/tests/test-bquote.R |only future-1.40.0/future/tests/test-capture_journals.R |only future-1.40.0/future/tests/test-cluster,worker-termination.R |only future-1.40.0/future/tests/test-cluster-connection-clashes.R |only future-1.40.0/future/tests/test-cluster-missing-future-pkg.R |only future-1.40.0/future/tests/test-demo-fibonacci.R |only future-1.40.0/future/tests/test-demo-mandelbrot.R |only future-1.40.0/future/tests/test-dotdotdot.R |only future-1.40.0/future/tests/test-early-signaling.R |only future-1.40.0/future/tests/test-future,labels.R |only future-1.40.0/future/tests/test-future,optsenvvars.R |only future-1.40.0/future/tests/test-future.R |only future-1.40.0/future/tests/test-futureAssign.R |only future-1.40.0/future/tests/test-futureAssign_OP.R |only future-1.40.0/future/tests/test-futureAssign_OP_with_environment.R |only future-1.40.0/future/tests/test-futureAssign_OP_with_listenv.R |only future-1.40.0/future/tests/test-futureCall.R |only future-1.40.0/future/tests/test-futureOf.R |only future-1.40.0/future/tests/test-futureOf_with_environment.R |only future-1.40.0/future/tests/test-futureOf_with_listenv.R |only future-1.40.0/future/tests/test-futureSessionInfo.R |only future-1.40.0/future/tests/test-futures.R |only future-1.40.0/future/tests/test-globals,NSE.R |only future-1.40.0/future/tests/test-globals,S4methods.R |only future-1.40.0/future/tests/test-globals,formulas.R |only future-1.40.0/future/tests/test-globals,locals.R |only future-1.40.0/future/tests/test-globals,manual.R |only future-1.40.0/future/tests/test-globals,resolve.R |only future-1.40.0/future/tests/test-globals,subassignment.R |only future-1.40.0/future/tests/test-globals,toolarge.R |only future-1.40.0/future/tests/test-globals,tricky.R |only future-1.40.0/future/tests/test-globals,tricky_recursive.R |only future-1.40.0/future/tests/test-globalsOf,tweaks.R |only future-1.40.0/future/tests/test-immediateCondition.R |only future-1.40.0/future/tests/test-interrupt-sets.R |only future-1.40.0/future/tests/test-interrupt.R |only future-1.40.0/future/tests/test-interrupts-from-worker-itself.R |only future-1.40.0/future/tests/test-invalid-owner.R |only future-1.40.0/future/tests/test-mandelbrot.R |only future-1.40.0/future/tests/test-misuse-connections.R |only future-1.40.0/future/tests/test-mpi.R |only future-1.40.0/future/tests/test-multicore,multithreading.R |only future-1.40.0/future/tests/test-multicore,worker-termination.R |only future-1.40.0/future/tests/test-nbrOfWorkers.R |only future-1.40.0/future/tests/test-nested_futures,mc.cores.R |only future-1.40.0/future/tests/test-nested_futures.R |only future-1.40.0/future/tests/test-non-exportable,connections.R |only future-1.40.0/future/tests/test-objectSize.R |only future-1.40.0/future/tests/test-plan.R |only future-1.40.0/future/tests/test-relaying,muffle.R |only future-1.40.0/future/tests/test-relaying,split.R |only future-1.40.0/future/tests/test-relaying.R |only future-1.40.0/future/tests/test-requestCore.R |only future-1.40.0/future/tests/test-requestNode.R |only future-1.40.0/future/tests/test-reserved-keyword-functions.R |only future-1.40.0/future/tests/test-reset.R |only future-1.40.0/future/tests/test-resolve.R |only future-1.40.0/future/tests/test-resolved-non-blocking-test.R |only future-1.40.0/future/tests/test-rng.R |only future-1.40.0/future/tests/test-rng_utils.R |only future-1.40.0/future/tests/test-sequential.R |only future-1.40.0/future/tests/test-sessionDetails.R |only future-1.40.0/future/tests/test-startup-onAttach.R |only future-1.40.0/future/tests/test-startup-onLoad.R |only future-1.40.0/future/tests/test-startup-parseCmdArgs.R |only future-1.40.0/future/tests/test-stdout.R |only future-1.40.0/future/tests/test-timeouts.R |only future-1.40.0/future/tests/test-tweak.R |only future-1.40.0/future/tests/test-utils.R |only future-1.40.0/future/tests/test-uuid.R |only future-1.40.0/future/tests/test-value.R |only future-1.40.0/future/tests/test-whichIndex.R |only future-1.40.0/future/vignettes/future-1-overview.md.rsp | 134 +- future-1.40.0/future/vignettes/future-3-topologies.md.rsp | 21 future-1.40.0/future/vignettes/future-4-issues.md.rsp | 99 + future-1.40.0/future/vignettes/future-4-non-exportable-objects.md.rsp | 2 future-1.40.0/future/vignettes/future-6-future-api-backend-specification.md.rsp | 2 future-1.40.0/future/vignettes/future-7-for-package-developers.md.rsp | 9 362 files changed, 2612 insertions(+), 1793 deletions(-)
Title: A 'ggplot2' Extension for Consistent Axis Alignment
Description: A 'ggplot2' extension offers various tools the creation of complex,
multi-plot visualizations. Built on the familiar grammar of graphics, it
provides intuitive tools to align and organize plots, making it ideal for
complex visualizations. It excels in multi-omics research—such as genomics
and microbiomes—by simplifying the visualization of intricate relationships
between datasets, for example, linking genes to pathways. Whether you need
to stack plots, arrange them around a central figure, or create a circular
layout, 'ggalign' delivers flexibility and accuracy with minimal effort.
Author: Yun Peng [aut, cre] ,
Shixiang Wang [aut] ,
Guangchuang Yu [ths]
Maintainer: Yun Peng <yunyunp96@163.com>
Diff between ggalign versions 1.0.0 dated 2025-03-15 and 1.0.1 dated 2025-04-10
ggalign-1.0.0/ggalign/R/geom-draw.R |only ggalign-1.0.0/ggalign/R/geom-gshape.R |only ggalign-1.0.0/ggalign/R/geom-pie.R |only ggalign-1.0.0/ggalign/R/geom-subrect.R |only ggalign-1.0.0/ggalign/R/geom-tile3d.R |only ggalign-1.0.0/ggalign/R/utils-grid.R |only ggalign-1.0.1/ggalign/DESCRIPTION | 29 - ggalign-1.0.1/ggalign/MD5 | 103 ++--- ggalign-1.0.1/ggalign/NAMESPACE | 7 ggalign-1.0.1/ggalign/NEWS.md | 8 ggalign-1.0.1/ggalign/R/align-.R | 4 ggalign-1.0.1/ggalign/R/alignpatch-.R | 42 +- ggalign-1.0.1/ggalign/R/alignpatch-align_plots.R | 12 ggalign-1.0.1/ggalign/R/alignpatch-alignpatches.R | 199 +++++++--- ggalign-1.0.1/ggalign/R/alignpatch-free-guide.R | 20 - ggalign-1.0.1/ggalign/R/alignpatch-guides.R | 35 + ggalign-1.0.1/ggalign/R/alignpatch-patch.R | 4 ggalign-1.0.1/ggalign/R/fortify-matrix-matrix.R | 3 ggalign-1.0.1/ggalign/R/ggfree.R | 2 ggalign-1.0.1/ggalign/R/ggmark.R | 2 ggalign-1.0.1/ggalign/R/ggplot-coord-circle.R | 46 +- ggalign-1.0.1/ggalign/R/ggplot-facet-sector.R | 24 - ggalign-1.0.1/ggalign/R/ggplot-geom-draw.R |only ggalign-1.0.1/ggalign/R/ggplot-geom-gshape.R |only ggalign-1.0.1/ggalign/R/ggplot-geom-pie.R |only ggalign-1.0.1/ggalign/R/ggplot-geom-subrect.R |only ggalign-1.0.1/ggalign/R/ggplot-geom-tile3d.R |only ggalign-1.0.1/ggalign/R/ggplot-helper.R | 44 +- ggalign-1.0.1/ggalign/R/ggplot-theme.R | 4 ggalign-1.0.1/ggalign/R/ggplot-utils.R | 23 - ggalign-1.0.1/ggalign/R/grid-grob-channel.R |only ggalign-1.0.1/ggalign/R/grid-utils.R |only ggalign-1.0.1/ggalign/R/import-standalone-pkg.R | 92 ++-- ggalign-1.0.1/ggalign/R/layout-align.R | 30 - ggalign-1.0.1/ggalign/R/layout-chain-circle-build.R | 23 - ggalign-1.0.1/ggalign/R/mark.R | 2 ggalign-1.0.1/ggalign/R/raster-magick.R | 39 + ggalign-1.0.1/ggalign/R/scheme-align.R | 6 ggalign-1.0.1/ggalign/R/utils-assert.R | 18 ggalign-1.0.1/ggalign/man/align_plots.Rd | 4 ggalign-1.0.1/ggalign/man/channelGrob.Rd |only ggalign-1.0.1/ggalign/man/coord_circle.Rd | 6 ggalign-1.0.1/ggalign/man/draw_key_gshape.Rd | 2 ggalign-1.0.1/ggalign/man/free.Rd | 6 ggalign-1.0.1/ggalign/man/geom_draw.Rd | 2 ggalign-1.0.1/ggalign/man/geom_gshape.Rd | 2 ggalign-1.0.1/ggalign/man/geom_pie.Rd | 2 ggalign-1.0.1/ggalign/man/geom_rect3d.Rd | 2 ggalign-1.0.1/ggalign/man/geom_subrect.Rd | 2 ggalign-1.0.1/ggalign/man/ggalign-package.Rd | 2 ggalign-1.0.1/ggalign/man/layout_design.Rd | 4 ggalign-1.0.1/ggalign/man/raster_magick.Rd | 35 - ggalign-1.0.1/ggalign/man/reexports.Rd | 2 ggalign-1.0.1/ggalign/man/scale_gshape_manual.Rd | 2 ggalign-1.0.1/ggalign/man/scheme_align.Rd | 4 ggalign-1.0.1/ggalign/tests/testthat/_snaps/alignpatch/collect-inside-guides.svg |only ggalign-1.0.1/ggalign/tests/testthat/_snaps/grid |only ggalign-1.0.1/ggalign/tests/testthat/_snaps/layout-heatmap/heatmap-hmanno-align-action-guides.svg | 4 ggalign-1.0.1/ggalign/tests/testthat/helper-setup.R | 23 - ggalign-1.0.1/ggalign/tests/testthat/test-alignpatch.R | 29 + ggalign-1.0.1/ggalign/tests/testthat/test-grid.R |only 61 files changed, 617 insertions(+), 337 deletions(-)
Title: Tools for Functional Response Analysis
Description: Tools to support sensible statistics for functional response analysis.
Author: Daniel Pritchard [aut, cre],
Daniel Barrios-O'Neill [ctb],
Helene Bovy [ctb],
Rachel Paterson [ctb]
Maintainer: Daniel Pritchard <daniel@pritchard.co>
Diff between frair versions 0.5.100 dated 2017-03-26 and 0.5.203 dated 2025-04-10
DESCRIPTION | 11 ++++++----- MD5 | 38 +++++++++++++++++++------------------- NAMESPACE | 1 + NEWS.md | 28 ++++++++++++++++++++++++---- man/fr_emdII.Rd | 4 ++-- man/fr_flexp.Rd | 7 +++---- man/fr_flexpnr.Rd | 6 +++--- man/fr_hassIII.Rd | 2 +- man/fr_hassIIInr.Rd | 4 ++-- man/fr_hollingsII.Rd | 2 +- man/fr_rogersII.Rd | 4 ++-- man/fr_typeI.Rd | 2 +- man/frair_boot.Rd | 1 + man/frair_boot_methods.Rd | 4 ++-- man/frair_compare.Rd | 3 ++- man/frair_fit.Rd | 2 +- man/frair_fit_methods.Rd | 1 + tests/testthat/test_flexpnr.R | 1 + tests/testthat/test_frair_fit.R | 1 + tests/testthat/test_typeI.R | 11 ++++++----- 20 files changed, 80 insertions(+), 53 deletions(-)
Title: S3 Infrastructure for Regular and Irregular Time Series (Z's
Ordered Observations)
Description: An S3 class with methods for totally ordered indexed
observations. It is particularly aimed at irregular time series
of numeric vectors/matrices and factors. zoo's key design goals
are independence of a particular index/date/time class and
consistency with ts and base R by providing methods to extend
standard generics.
Author: Achim Zeileis [aut, cre] ,
Gabor Grothendieck [aut],
Jeffrey A. Ryan [aut],
Joshua M. Ulrich [ctb],
Felix Andrews [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between zoo versions 1.8-13 dated 2025-02-22 and 1.8-14 dated 2025-04-10
DESCRIPTION | 10 MD5 | 38 +- NEWS | 610 +++++++++++++++++++++++---------------------- R/ggplot2.zoo.R | 8 build/vignette.rds |binary inst/doc/msft2004.rda |only inst/doc/zoo-design.pdf |binary inst/doc/zoo-faq.pdf |binary inst/doc/zoo-quickref.R | 63 +--- inst/doc/zoo-quickref.Rnw | 72 +---- inst/doc/zoo-quickref.pdf |binary inst/doc/zoo-read.R | 59 ++-- inst/doc/zoo-read.Rnw | 16 + inst/doc/zoo-read.pdf |binary inst/doc/zoo.Rnw | 4 inst/doc/zoo.pdf |binary src/lag.c | 4 vignettes/.install_extras | 1 vignettes/msft2004.rda |only vignettes/zoo-quickref.Rnw | 72 +---- vignettes/zoo-read.Rnw | 16 + vignettes/zoo.Rnw | 4 22 files changed, 496 insertions(+), 481 deletions(-)
Title: Network Analysis for Omics Data
Description: Comprehensive network analysis package.
Calculate correlation network fastly, accelerate lots of analysis by parallel computing.
Support for multi-omics data, search sub-nets fluently.
Handle bigger data, more than 10,000 nodes in each omics.
Offer various layout method for multi-omics network and some interfaces to other software ('Gephi', 'Cytoscape', 'ggplot2'), easy to visualize.
Provide comprehensive topology indexes calculation, including ecological network stability.
Author: Chen Peng [aut, cre]
Maintainer: Chen Peng <pengchen2001@zju.edu.cn>
Diff between MetaNet versions 0.1.2 dated 2024-03-25 and 0.2.5 dated 2025-04-10
MetaNet-0.1.2/MetaNet/R/build.R |only MetaNet-0.1.2/MetaNet/R/calculate.R |only MetaNet-0.1.2/MetaNet/R/modules.R |only MetaNet-0.1.2/MetaNet/R/plot.R |only MetaNet-0.1.2/MetaNet/R/stability.R |only MetaNet-0.1.2/MetaNet/R/topological.R |only MetaNet-0.1.2/MetaNet/man/extract_sub_net.Rd |only MetaNet-0.1.2/MetaNet/man/input_corr.Rd |only MetaNet-0.2.5/MetaNet/DESCRIPTION | 13 - MetaNet-0.2.5/MetaNet/MD5 | 183 +++++++++--------- MetaNet-0.2.5/MetaNet/NAMESPACE | 24 ++ MetaNet-0.2.5/MetaNet/NEWS.md | 41 ++++ MetaNet-0.2.5/MetaNet/R/1.calculate.R |only MetaNet-0.2.5/MetaNet/R/2-1.build.R |only MetaNet-0.2.5/MetaNet/R/2-2.manipulate.R |only MetaNet-0.2.5/MetaNet/R/2-3.RMT.R |only MetaNet-0.2.5/MetaNet/R/3-1.layout.R |only MetaNet-0.2.5/MetaNet/R/3-2.shapes.R |only MetaNet-0.2.5/MetaNet/R/3-3.plot.R |only MetaNet-0.2.5/MetaNet/R/3-4.other_plot.R |only MetaNet-0.2.5/MetaNet/R/5.topological.R |only MetaNet-0.2.5/MetaNet/R/6.modules.R |only MetaNet-0.2.5/MetaNet/R/7.stability.R |only MetaNet-0.2.5/MetaNet/R/MetaNet-package.R | 11 - MetaNet-0.2.5/MetaNet/R/print.R | 59 +++++ MetaNet-0.2.5/MetaNet/R/utils-pipe.R | 34 +++ MetaNet-0.2.5/MetaNet/README.md | 10 MetaNet-0.2.5/MetaNet/data/c_net.rda |binary MetaNet-0.2.5/MetaNet/inst/doc/MetaNet.html | 7 MetaNet-0.2.5/MetaNet/man/Cohesion.Rd | 2 MetaNet-0.2.5/MetaNet/man/RMT_threshold.Rd | 2 MetaNet-0.2.5/MetaNet/man/anno_edge.Rd | 3 MetaNet-0.2.5/MetaNet/man/anno_vertex.Rd | 3 MetaNet-0.2.5/MetaNet/man/as.ggig.Rd | 3 MetaNet-0.2.5/MetaNet/man/as_arc.Rd | 6 MetaNet-0.2.5/MetaNet/man/as_circle_tree.Rd | 4 MetaNet-0.2.5/MetaNet/man/as_coors.Rd |only MetaNet-0.2.5/MetaNet/man/as_line.Rd | 4 MetaNet-0.2.5/MetaNet/man/as_multi_layer.Rd |only MetaNet-0.2.5/MetaNet/man/as_poly_sector.Rd |only MetaNet-0.2.5/MetaNet/man/as_polyarc.Rd | 4 MetaNet-0.2.5/MetaNet/man/as_polycircle.Rd | 6 MetaNet-0.2.5/MetaNet/man/as_polygon.Rd | 4 MetaNet-0.2.5/MetaNet/man/c_net_annotate.Rd | 3 MetaNet-0.2.5/MetaNet/man/c_net_build.Rd | 4 MetaNet-0.2.5/MetaNet/man/c_net_calculate.Rd | 6 MetaNet-0.2.5/MetaNet/man/c_net_filter.Rd | 3 MetaNet-0.2.5/MetaNet/man/c_net_from_edgelist.Rd | 8 MetaNet-0.2.5/MetaNet/man/c_net_layout.Rd | 7 MetaNet-0.2.5/MetaNet/man/c_net_load.Rd |only MetaNet-0.2.5/MetaNet/man/c_net_plot.Rd | 47 +++- MetaNet-0.2.5/MetaNet/man/c_net_save.Rd | 3 MetaNet-0.2.5/MetaNet/man/c_net_set.Rd | 7 MetaNet-0.2.5/MetaNet/man/c_net_stability.Rd | 2 MetaNet-0.2.5/MetaNet/man/c_net_union.Rd | 3 MetaNet-0.2.5/MetaNet/man/c_net_update.Rd | 17 + MetaNet-0.2.5/MetaNet/man/cal_sim.Rd | 12 - MetaNet-0.2.5/MetaNet/man/check_tabs.Rd | 2 MetaNet-0.2.5/MetaNet/man/clean_igraph.Rd | 2 MetaNet-0.2.5/MetaNet/man/clean_multi_edge_metanet.Rd |only MetaNet-0.2.5/MetaNet/man/compare_rand.Rd | 8 MetaNet-0.2.5/MetaNet/man/df2net_tree.Rd | 2 MetaNet-0.2.5/MetaNet/man/extract_sample_net.Rd |only MetaNet-0.2.5/MetaNet/man/fast_cor.Rd | 6 MetaNet-0.2.5/MetaNet/man/filter_n_module.Rd | 2 MetaNet-0.2.5/MetaNet/man/fit_power.Rd | 4 MetaNet-0.2.5/MetaNet/man/g_layout.Rd | 24 -- MetaNet-0.2.5/MetaNet/man/g_layout_nice.Rd |only MetaNet-0.2.5/MetaNet/man/g_layout_poly_sector.Rd |only MetaNet-0.2.5/MetaNet/man/g_layout_polygon.Rd | 23 ++ MetaNet-0.2.5/MetaNet/man/get_community.Rd | 2 MetaNet-0.2.5/MetaNet/man/get_e.Rd | 7 MetaNet-0.2.5/MetaNet/man/get_group_skeleton.Rd | 8 MetaNet-0.2.5/MetaNet/man/get_module.Rd | 2 MetaNet-0.2.5/MetaNet/man/get_module_eigen.Rd | 2 MetaNet-0.2.5/MetaNet/man/get_n.Rd | 7 MetaNet-0.2.5/MetaNet/man/get_v.Rd | 7 MetaNet-0.2.5/MetaNet/man/input_cytoscape.Rd |only MetaNet-0.2.5/MetaNet/man/input_gephi.Rd | 3 MetaNet-0.2.5/MetaNet/man/is_metanet.Rd | 3 MetaNet-0.2.5/MetaNet/man/links_stat.Rd | 35 +-- MetaNet-0.2.5/MetaNet/man/module_detect.Rd | 2 MetaNet-0.2.5/MetaNet/man/module_expression.Rd | 2 MetaNet-0.2.5/MetaNet/man/module_net.Rd | 2 MetaNet-0.2.5/MetaNet/man/multi_net_build.Rd | 2 MetaNet-0.2.5/MetaNet/man/nc.Rd | 4 MetaNet-0.2.5/MetaNet/man/netD3plot.Rd | 3 MetaNet-0.2.5/MetaNet/man/net_par.Rd | 13 - MetaNet-0.2.5/MetaNet/man/olympic_rings_net.Rd | 3 MetaNet-0.2.5/MetaNet/man/p.adjust.table.Rd | 4 MetaNet-0.2.5/MetaNet/man/plot.ggig.Rd | 20 + MetaNet-0.2.5/MetaNet/man/plot.metanet.Rd | 2 MetaNet-0.2.5/MetaNet/man/plot.rmt_res.Rd | 2 MetaNet-0.2.5/MetaNet/man/rand_net.Rd | 8 MetaNet-0.2.5/MetaNet/man/read_corr.Rd |only MetaNet-0.2.5/MetaNet/man/robust_test.Rd | 4 MetaNet-0.2.5/MetaNet/man/robustness.Rd | 2 MetaNet-0.2.5/MetaNet/man/save_corr.Rd |only MetaNet-0.2.5/MetaNet/man/smallworldness.Rd | 4 MetaNet-0.2.5/MetaNet/man/spatstat_layout.Rd |only MetaNet-0.2.5/MetaNet/man/summ_2col.Rd | 2 MetaNet-0.2.5/MetaNet/man/summary.corr.Rd |only MetaNet-0.2.5/MetaNet/man/summary_module.Rd | 2 MetaNet-0.2.5/MetaNet/man/to_module_net.Rd | 6 MetaNet-0.2.5/MetaNet/man/transform_coors.Rd |only MetaNet-0.2.5/MetaNet/man/twocol_edgelist.Rd | 3 MetaNet-0.2.5/MetaNet/man/venn_net.Rd | 3 MetaNet-0.2.5/MetaNet/man/vulnerability.Rd | 2 MetaNet-0.2.5/MetaNet/man/zp_analyse.Rd | 9 109 files changed, 533 insertions(+), 265 deletions(-)
Title: Expanded Replacement and Extension of the 'optim' Function
Description: Provides a replacement and extension of the optim()
function to call to several function minimization codes in R in a single
statement. These methods handle smooth, possibly box constrained functions
of several or many parameters. Note that function 'optimr()' was prepared to
simplify the incorporation of minimization codes going forward. Also implements some
utility codes and some extra solvers, including safeguarded Newton methods.
Many methods previously separate are now included here.
This is the version for CRAN.
Author: John C Nash [aut, cre],
Ravi Varadhan [aut],
Hans W Borchers [ctb],
Gabor Grothendieck [ctb]
Maintainer: John C Nash <profjcnash@gmail.com>
Diff between optimx versions 2024-12.2 dated 2024-12-10 and 2025-4.9 dated 2025-04-10
DESCRIPTION | 8 +- MD5 | 43 ++++++------ NAMESPACE | 2 NEWS | 19 +++++ R/ctrldefault.R | 1 R/kktchk.R | 67 ++++++++++--------- R/opm.R | 8 +- R/optimr.R | 20 ++++- R/optimr2opm.R | 124 +++++++++++++++++++----------------- R/pd_check.R |only build/vignette.rds |binary inst/doc/AddPracmaNM2optimx.pdf |binary inst/doc/ExplainGradMinR.pdf |binary inst/doc/Extend-optimx.pdf |binary inst/doc/Intro-to-optimx.pdf |binary inst/doc/Rvmmin.pdf |binary inst/doc/SNewton.pdf |binary inst/doc/vignette-source/Rvmmin.Rmd | 2 man/kktchk.Rd | 4 - man/opm.Rd | 4 + man/opm2optimr.Rd | 2 man/optimr.Rd | 17 ++++ man/optimr2opm.Rd |only man/pd_check.Rd |only 24 files changed, 192 insertions(+), 129 deletions(-)
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre],
Javier Luraschi [aut],
Kevin Kuo [aut] ,
RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>
Diff between mlflow versions 2.21.2 dated 2025-04-02 and 2.21.3 dated 2025-04-10
DESCRIPTION | 6 +++--- MD5 | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)