Title: A 'shiny' App for Test Analysis and Visualization
Description: This application provides exploratory and confirmatory factor analysis, classical test theory, unidimensional and multidimensional item response theory, and continuous item response model analysis, through the 'shiny' interactive interface. In addition, it offers rich functionalities for visualizing and downloading results. Users can download figures, tables, and analysis reports via the interactive interface.
Author: Youxiang Jiang [cre, aut, ths] ,
Qing Zeng [aut, ths],
Hongbo Wen [aut, ths]
Maintainer: Youxiang Jiang <jiangyouxiang34@163.com>
Diff between TestAnaAPP versions 1.1.1 dated 2024-09-10 and 1.1.2 dated 2024-11-08
DESCRIPTION | 8 +- MD5 | 30 +++++---- NAMESPACE | 2 R/CFA_module.R | 44 +++++++++---- R/CRM_module.R | 71 ++++++++++++++-------- R/CTT_module.R | 67 ++++++++++++++++----- R/DIF_module.R | 13 ---- R/EFA_module.R | 41 +++++++----- R/MIRT_module.R | 105 +++++++++++++++++++++------------ R/UIRT_module.R | 95 ++++++++++++++++++++--------- R/server.R | 83 ++++++++++++++++++-------- R/ui.R | 56 ++++++++++++----- inst/CITATION |only inst/rmd/Analysis_Report_template.docx |only inst/rmd/IRT_Analysis_Report.Rmd | 80 ++++++++++++++----------- inst/rmd/MIRT_Analysis_Report.Rmd | 60 +++++++++--------- tests/testthat/test-item_ana.R | 14 ---- 17 files changed, 485 insertions(+), 284 deletions(-)
Title: R-Object to R-Object Hash Maps
Description: Implementation of hash tables (hash sets and hash maps) in R,
featuring arbitrary R objects as keys,
arbitrary hash and key-comparison functions,
and customizable behaviour upon queries of missing keys.
Author: Valerio Gherardi [aut, cre]
Maintainer: Valerio Gherardi <vgherard840@gmail.com>
Diff between r2r versions 0.1.1 dated 2021-07-06 and 0.1.2 dated 2024-11-08
DESCRIPTION | 12 MD5 | 91 +- NAMESPACE | 102 +-- NEWS.md |only R/default_hash_fn.R | 110 +-- R/docs.R | 298 ++++----- R/generics.R | 450 ++++++------- R/hashmap.R | 456 ++++++------- R/hashset.R | 318 ++++----- R/new_hashtable.R | 26 R/r2r-package.R | 22 R/shared_methods.R | 78 +- R/utils.R | 86 +- README.md | 196 +++-- build/vignette.rds |binary inst/doc/benchmarks.R | 248 +++---- inst/doc/benchmarks.Rmd | 416 ++++++------ inst/doc/benchmarks.html | 984 ++++++++++++++++++------------ inst/doc/r2r.R | 138 ++-- inst/doc/r2r.Rmd | 286 ++++---- inst/doc/r2r.html | 790 +++++++++++++++--------- man/compare_fn.Rd | 56 - man/default.Rd | 82 +- man/default_hash_fn.Rd | 56 - man/delete.Rd | 68 +- man/has_key.Rd | 76 +- man/hash_fn.Rd | 56 - man/hashtable.Rd | 220 +++--- man/hashtable_methods.Rd | 92 +- man/insert.Rd | 80 +- man/keys.Rd | 56 - man/length.r2r_hashtable.Rd | 50 - man/on_missing_key.Rd | 84 +- man/query.Rd | 76 +- man/r2r-package.Rd | 52 - man/subsetting_hashtables.Rd | 132 ++-- man/values.Rd | 58 - tests/testthat.R | 8 tests/testthat/test-default_hash_fn.R | 46 - tests/testthat/test-hashmap_constructor.R | 230 +++---- tests/testthat/test-hashmap_functional.R | 198 +++--- tests/testthat/test-hashset_constructor.R | 200 +++--- tests/testthat/test-hashset_functional.R | 168 ++--- tests/testthat/test-new_hashtable.R | 68 +- tests/testthat/test-utils.R | 38 - vignettes/benchmarks.Rmd | 416 ++++++------ vignettes/r2r.Rmd | 286 ++++---- 47 files changed, 4284 insertions(+), 3775 deletions(-)
Title: Reading, Quality Control and Preprocessing of MBA (Multiplex
Bead Assay) Data
Description: Speeds up the process of loading raw data from MBA (Multiplex Bead Assay) examinations, performs quality control checks, and automatically normalises the data, preparing it for more advanced, downstream tasks. The main objective of the package is to create a simple environment for a user, who does not necessarily have experience with R language. The package is developed within the project of the same name - 'PvSTATEM', which is an international project aiming for malaria elimination.
Author: Tymoteusz Kwiecinski [aut, cre]
,
Jakub Grzywaczewski [aut],
Mateusz Nizwantowski [aut],
Przemyslaw Biecek [ths] ,
Nuno Sepulveda [ths]
Maintainer: Tymoteusz Kwiecinski <tymoteuszkwiecinski@gmail.com>
Diff between PvSTATEM versions 0.1.1 dated 2024-11-02 and 0.1.2 dated 2024-11-08
DESCRIPTION | 6 MD5 | 16 R/classes-plate_builder.R | 1040 +++++++++---------- R/generate_report.R | 1 R/process-plate.R | 328 +++--- inst/doc/example_script.html | 10 inst/extdata/CovidOISExPONTENT_CO_reduced.csv | 1420 +++++++++++++------------- inst/templates/plate_report_template.Rmd | 446 ++++---- tests/testthat/test-plots_plate.R | 15 9 files changed, 1649 insertions(+), 1633 deletions(-)
Title: Meta Clustering with Similarity Network Fusion
Description: Framework to facilitate patient subtyping with similarity network fusion and meta clustering. The similarity network fusion (SNF) algorithm was introduced by Wang et al. (2014) in <doi:10.1038/nmeth.2810>. SNF is a data integration approach that can transform high-dimensional and diverse data types into a single similarity network suitable for clustering with minimal loss of information from each initial data source. The meta clustering approach was introduced by Caruana et al. (2006) in <doi:10.1109/ICDM.2006.103>. Meta clustering involves generating a wide range of cluster solutions by adjusting clustering hyperparameters, then clustering the solutions themselves into a manageable number of qualitatively similar solutions, and finally characterizing representative solutions to find ones that are best for the user's specific context. This package provides a framework to easily transform multi-modal data into a wide range of similarity network fusion-derived cluster solutio [...truncated...]
Author: Prashanth S Velayudhan [aut, cre],
Xiaoqiao Xu [aut],
Prajkta Kallurkar [aut],
Ana Patricia Balbon [aut],
Maria T Secara [aut],
Adam Taback [aut],
Denise Sabac [aut],
Nicholas Chan [aut],
Shihao Ma [aut],
Bo Wang [aut],
Daniel Felsky [aut],
Stephanie [...truncated...]
Maintainer: Prashanth S Velayudhan <psvelayu@gmail.com>
Diff between metasnf versions 1.1.1 dated 2024-11-08 and 1.1.2 dated 2024-11-08
DESCRIPTION | 6 ++--- MD5 | 18 +++++++-------- NEWS.md | 4 +++ README.md | 21 ++++++++--------- inst/doc/clustering_algorithms.html | 4 +-- inst/doc/distance_metrics.html | 2 - inst/doc/settings_matrix.R | 6 ++--- inst/doc/settings_matrix.Rmd | 10 ++++---- inst/doc/settings_matrix.html | 43 +++++++++++++++++------------------- vignettes/settings_matrix.Rmd | 10 ++++---- 10 files changed, 63 insertions(+), 61 deletions(-)
Title: Interval Censored Multi-State Models
Description: Allows for the non-parametric estimation of transition intensities in interval-censored
multi-state models using the approach of Gomon and Putter (2024) <doi:10.48550/arXiv.2409.07176> or
Gu et al. (2023) <doi:10.1093/biomet/asad073>.
Author: Daniel Gomon [aut, cre] ,
Hein Putter [aut]
Maintainer: Daniel Gomon <dgstatsoft@gmail.com>
Diff between icmstate versions 0.1.0 dated 2024-10-28 and 0.1.1 dated 2024-11-08
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS.md | 5 +++++ R/sim_weibmsm.R | 3 ++- README.md | 2 ++ inst/doc/Overview.Rmd | 2 +- inst/doc/Overview.pdf |binary inst/doc/comparison-with-known-results.pdf |binary inst/doc/sim_msm.R | 12 ++++++++---- inst/doc/sim_msm.Rmd | 12 ++++++++---- inst/doc/sim_msm.pdf |binary vignettes/Overview.Rmd | 2 +- vignettes/sim_msm.Rmd | 12 ++++++++---- 13 files changed, 50 insertions(+), 30 deletions(-)
Title: Utilities for Interacting with the 'Posit Connect' Server API
Description: Provides a helpful 'R6' class and methods for interacting with
the 'Posit Connect' Server API along with some meaningful utility functions
for regular tasks. API documentation varies by 'Posit Connect' installation
and version, but the latest documentation is also hosted publicly at
<https://docs.posit.co/connect/api/>.
Author: Toph Allen [aut, cre],
Neal Richardson [aut],
Sean Lopp [aut],
Cole Arendt [aut],
Posit, PBC [cph, fnd]
Maintainer: Toph Allen <toph@posit.co>
Diff between connectapi versions 0.3.0 dated 2024-09-05 and 0.4.0 dated 2024-11-08
connectapi-0.3.0/connectapi/build/stage23.rdb |only connectapi-0.3.0/connectapi/inst/doc/customize-http.R |only connectapi-0.3.0/connectapi/man/figures/lifecycle-archived.svg |only connectapi-0.3.0/connectapi/man/figures/lifecycle-defunct.svg |only connectapi-0.3.0/connectapi/man/figures/lifecycle-deprecated.svg |only connectapi-0.3.0/connectapi/man/figures/lifecycle-experimental.svg |only connectapi-0.3.0/connectapi/man/figures/lifecycle-maturing.svg |only connectapi-0.3.0/connectapi/man/figures/lifecycle-questioning.svg |only connectapi-0.3.0/connectapi/man/figures/lifecycle-retired.svg |only connectapi-0.3.0/connectapi/man/figures/lifecycle-soft-deprecated.svg |only connectapi-0.3.0/connectapi/man/figures/lifecycle-stable.svg |only connectapi-0.3.0/connectapi/tests/testthat/__api__ |only connectapi-0.4.0/connectapi/DESCRIPTION | 14 connectapi-0.4.0/connectapi/MD5 | 300 ++++++---- connectapi-0.4.0/connectapi/NAMESPACE | 8 connectapi-0.4.0/connectapi/NEWS.md | 36 + connectapi-0.4.0/connectapi/R/audits.R | 13 connectapi-0.4.0/connectapi/R/connect.R | 43 + connectapi-0.4.0/connectapi/R/connectapi-package.R |only connectapi-0.4.0/connectapi/R/content.R | 80 +- connectapi-0.4.0/connectapi/R/deploy.R | 192 ------ connectapi-0.4.0/connectapi/R/get.R | 112 ++- connectapi-0.4.0/connectapi/R/git.R | 24 connectapi-0.4.0/connectapi/R/lazy.R | 17 connectapi-0.4.0/connectapi/R/parse.R | 26 connectapi-0.4.0/connectapi/R/promote.R | 7 connectapi-0.4.0/connectapi/R/ptype.R | 6 connectapi-0.4.0/connectapi/R/remote.R | 59 + connectapi-0.4.0/connectapi/R/runtime-caches.R |only connectapi-0.4.0/connectapi/R/schedule.R | 235 ++++++- connectapi-0.4.0/connectapi/R/tags.R | 19 connectapi-0.4.0/connectapi/R/thumbnail.R |only connectapi-0.4.0/connectapi/R/utils-ci.R | 8 connectapi-0.4.0/connectapi/R/utils.R | 119 ++- connectapi-0.4.0/connectapi/R/variant.R | 7 connectapi-0.4.0/connectapi/README.md | 6 connectapi-0.4.0/connectapi/build/vignette.rds |binary connectapi-0.4.0/connectapi/inst/doc/customize-http.Rmd | 18 connectapi-0.4.0/connectapi/inst/doc/customize-http.html | 4 connectapi-0.4.0/connectapi/inst/doc/getting-started.Rmd | 2 connectapi-0.4.0/connectapi/inst/doc/getting-started.html | 6 connectapi-0.4.0/connectapi/man/PositConnect.Rd | 25 connectapi-0.4.0/connectapi/man/audit_access_open.Rd | 2 connectapi-0.4.0/connectapi/man/audit_r_versions.Rd | 2 connectapi-0.4.0/connectapi/man/audit_runas.Rd | 2 connectapi-0.4.0/connectapi/man/connectapi-package.Rd | 18 connectapi-0.4.0/connectapi/man/content_delete.Rd | 4 connectapi-0.4.0/connectapi/man/content_item.Rd | 4 connectapi-0.4.0/connectapi/man/content_list.Rd | 2 connectapi-0.4.0/connectapi/man/content_list_with_permissions.Rd | 2 connectapi-0.4.0/connectapi/man/content_title.Rd | 4 connectapi-0.4.0/connectapi/man/content_update.Rd | 4 connectapi-0.4.0/connectapi/man/create_random_name.Rd | 4 connectapi-0.4.0/connectapi/man/dashboard_url.Rd | 4 connectapi-0.4.0/connectapi/man/dashboard_url_chr.Rd | 4 connectapi-0.4.0/connectapi/man/delete_runtime_cache.Rd |only connectapi-0.4.0/connectapi/man/delete_thumbnail.Rd |only connectapi-0.4.0/connectapi/man/delete_vanity_url.Rd | 4 connectapi-0.4.0/connectapi/man/deploy.Rd | 3 connectapi-0.4.0/connectapi/man/deploy_repo.Rd | 9 connectapi-0.4.0/connectapi/man/environment.Rd | 4 connectapi-0.4.0/connectapi/man/get_audit_logs.Rd | 2 connectapi-0.4.0/connectapi/man/get_bundles.Rd | 8 connectapi-0.4.0/connectapi/man/get_content.Rd | 5 connectapi-0.4.0/connectapi/man/get_group_members.Rd | 4 connectapi-0.4.0/connectapi/man/get_groups.Rd | 11 connectapi-0.4.0/connectapi/man/get_image.Rd | 12 connectapi-0.4.0/connectapi/man/get_oauth_credentials.Rd | 2 connectapi-0.4.0/connectapi/man/get_procs.Rd | 2 connectapi-0.4.0/connectapi/man/get_runtime_caches.Rd |only connectapi-0.4.0/connectapi/man/get_runtimes.Rd |only connectapi-0.4.0/connectapi/man/get_thumbnail.Rd |only connectapi-0.4.0/connectapi/man/get_usage_shiny.Rd | 4 connectapi-0.4.0/connectapi/man/get_usage_static.Rd | 4 connectapi-0.4.0/connectapi/man/get_vanity_url.Rd | 4 connectapi-0.4.0/connectapi/man/get_variant_schedule.Rd | 2 connectapi-0.4.0/connectapi/man/git.Rd | 12 connectapi-0.4.0/connectapi/man/groups_create_remote.Rd | 15 connectapi-0.4.0/connectapi/man/has_thumbnail.Rd |only connectapi-0.4.0/connectapi/man/jobs.Rd | 6 connectapi-0.4.0/connectapi/man/permissions.Rd | 4 connectapi-0.4.0/connectapi/man/set_image.Rd | 14 connectapi-0.4.0/connectapi/man/set_run_as.Rd | 4 connectapi-0.4.0/connectapi/man/set_schedule.Rd | 2 connectapi-0.4.0/connectapi/man/set_thumbnail.Rd |only connectapi-0.4.0/connectapi/man/set_vanity_url.Rd | 4 connectapi-0.4.0/connectapi/man/swap_vanity_url.Rd | 4 connectapi-0.4.0/connectapi/man/tbl_connect.Rd | 2 connectapi-0.4.0/connectapi/man/users_create_remote.Rd | 10 connectapi-0.4.0/connectapi/man/vanity_is_available.Rd | 2 connectapi-0.4.0/connectapi/man/variant.Rd | 2 connectapi-0.4.0/connectapi/man/variant_render.Rd | 2 connectapi-0.4.0/connectapi/man/verify_content_name.Rd | 4 connectapi-0.4.0/connectapi/tests/integrated/test-connect.R | 6 connectapi-0.4.0/connectapi/tests/integrated/test-content.R | 14 connectapi-0.4.0/connectapi/tests/integrated/test-deploy.R | 91 ++- connectapi-0.4.0/connectapi/tests/integrated/test-get.R | 10 connectapi-0.4.0/connectapi/tests/integrated/test-git.R | 43 + connectapi-0.4.0/connectapi/tests/integrated/test-schedule.R | 74 +- connectapi-0.4.0/connectapi/tests/testthat/2024.08.0 |only connectapi-0.4.0/connectapi/tests/testthat/2024.09.0 |only connectapi-0.4.0/connectapi/tests/testthat/_snaps/utils.md | 6 connectapi-0.4.0/connectapi/tests/testthat/resources |only connectapi-0.4.0/connectapi/tests/testthat/setup.R | 96 +++ connectapi-0.4.0/connectapi/tests/testthat/test-connect.R | 19 connectapi-0.4.0/connectapi/tests/testthat/test-content.R | 19 connectapi-0.4.0/connectapi/tests/testthat/test-deploy.R | 6 connectapi-0.4.0/connectapi/tests/testthat/test-get.R |only connectapi-0.4.0/connectapi/tests/testthat/test-git.R | 10 connectapi-0.4.0/connectapi/tests/testthat/test-instrumentation.R | 40 - connectapi-0.4.0/connectapi/tests/testthat/test-oauth.R | 9 connectapi-0.4.0/connectapi/tests/testthat/test-print.R | 9 connectapi-0.4.0/connectapi/tests/testthat/test-remote.R |only connectapi-0.4.0/connectapi/tests/testthat/test-runtime-caches.R |only connectapi-0.4.0/connectapi/tests/testthat/test-schedule.R |only connectapi-0.4.0/connectapi/tests/testthat/test-thumbnail.R |only connectapi-0.4.0/connectapi/tests/testthat/test-utils.R | 31 - connectapi-0.4.0/connectapi/vignettes/articles/connectapi_tags.Rmd | 4 connectapi-0.4.0/connectapi/vignettes/articles/content_permissions.Rmd | 4 connectapi-0.4.0/connectapi/vignettes/customize-http.Rmd | 18 connectapi-0.4.0/connectapi/vignettes/getting-started.Rmd | 2 121 files changed, 1428 insertions(+), 692 deletions(-)
Title: Flexibly Format Dates and Times to a Given Locale
Description: Format dates and times flexibly and to whichever locales
make sense. Parses dates, times, and date-times in various formats
(including string-based ISO 8601 constructions). The formatting syntax gives
the user many options for formatting the date and time output in a precise
manner. Time zones in the input can be expressed in multiple ways and there
are many options for formatting time zones in the output as well. Several of
the provided helper functions allow for automatic generation of locale-aware
formatting patterns based on date/time skeleton formats and standardized
date/time formats with varying specificity.
Author: Richard Iannone [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Richard Iannone <rich@posit.co>
Diff between bigD versions 0.2.0 dated 2022-09-05 and 0.3.0 dated 2024-11-08
DESCRIPTION | 28 - LICENSE | 4 MD5 | 24 - NEWS.md | 8 R/days_months.R | 1 R/dt_formatters.R | 165 +++++++--- R/fdt.R | 622 +++++++++++++++++++++----------------- R/sysdata.rda |binary R/utils-date_time_parse.R | 41 +- R/utils.R | 2 man/fdt.Rd | 464 ++++++++++++++++++---------- tests/testthat/test-fdt_locales.R | 4 tests/testthat/test-time_zones.R | 46 +- 13 files changed, 866 insertions(+), 543 deletions(-)
Title: Graphical Multiple Comparison Procedures
Description: Multiple comparison procedures (MCPs) control the familywise error
rate in clinical trials. Graphical MCPs include many commonly used
procedures as special cases; see Bretz et al. (2011)
<doi:10.1002/bimj.201000239>, Lu (2016) <doi:10.1002/sim.6985>, and Xi et
al. (2017) <doi:10.1002/bimj.201600233>. This package is a low-dependency
implementation of graphical MCPs which allow mixed types of tests. It also
includes power simulations and visualization of graphical MCPs.
Author: Dong Xi [aut, cre],
Ethan Brockmann [aut],
Gilead Sciences, Inc. [cph, fnd]
Maintainer: Dong Xi <dong.xi1@gilead.com>
Diff between graphicalMCP versions 0.2.5 dated 2024-07-13 and 0.2.6 dated 2024-11-08
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NEWS.md | 5 +++++ R/graph_create.R | 4 ++-- README.md | 35 ++++++++++++++++++++++++++--------- build/partial.rdb |binary inst/CITATION | 4 ++-- inst/doc/closed-testing.html | 2 +- inst/doc/graph-examples.html | 2 +- inst/references.bib | 6 ++---- man/graph_create.Rd | 4 ++-- man/graphicalMCP-package.Rd | 4 ++-- 12 files changed, 59 insertions(+), 39 deletions(-)
Title: Regression Model Diagnostics for Survey Data
Description: Diagnostics for fixed effects linear and general linear regression models fitted with survey data. Extensions of standard diagnostics to complex survey data are included: standardized residuals, leverages, Cook's D, dfbetas, dffits, condition indexes, and variance inflation factors as found in Li and Valliant (Surv. Meth., 2009, 35(1), pp. 15-24; Jnl. of Off. Stat., 2011, 27(1), pp. 99-119; Jnl. of Off. Stat., 2015, 31(1), pp. 61-75); Liao and Valliant (Surv. Meth., 2012, 38(1), pp. 53-62; Surv. Meth., 2012, 38(2), pp. 189-202). Variance inflation factors and condition indexes are also computed for some general linear models as described in Liao (U. Maryland thesis, 2010).
Author: Richard Valliant [aut, cre]
Maintainer: Richard Valliant <valliant@umich.edu>
Diff between svydiags versions 0.6 dated 2024-05-08 and 0.7 dated 2024-11-08
DESCRIPTION | 10 ++-- MD5 | 16 +++---- NAMESPACE | 23 +++++----- NEWS.md | 9 ++++ R/svycollinear.R | 112 +++++++++++++++++++++++++++++++--------------------- R/svyvif.R | 27 ++++++++++-- man/svycollinear.Rd | 61 ++++++++++++---------------- man/svystdres.Rd | 2 man/svyvif.Rd | 15 ++---- 9 files changed, 157 insertions(+), 118 deletions(-)
Title: Multi-Level Monte Carlo
Description: An implementation of MLMC (Multi-Level Monte Carlo), Giles (2008)
<doi:10.1287/opre.1070.0496>, Heinrich (1998) <doi:10.1006/jcom.1998.0471>,
for R. This package builds on the original 'Matlab' and 'C++' implementations
by Mike Giles to provide a full MLMC driver and example level samplers.
Multi-core parallel sampling of levels is provided built-in.
Author: Louis Aslett [cre, aut, trl] ,
Mike Giles [ctb] ,
Tigran Nagapetyan [ctb] ,
Sebastian Vollmer [ctb]
Maintainer: Louis Aslett <louis.aslett@durham.ac.uk>
Diff between mlmc versions 2.0.2 dated 2024-09-04 and 2.1.0 dated 2024-11-08
DESCRIPTION | 6 +-- MD5 | 10 ++--- NEWS.md | 9 ++++ R/mlmc.test.R | 99 +++++++++++++++++++++++++++++++++++++++++++++--------- build/partial.rdb |binary man/mlmc.test.Rd | 27 +++++++++++--- 6 files changed, 120 insertions(+), 31 deletions(-)
Title: Access Data from the Atlas do Estado Brasileiro
Description: Facilitates access to the data from the Atlas do Estado Brasileiro
(<https://www.ipea.gov.br/atlasestado/>), maintained by the Instituto de
Pesquisa Econômica Aplicada (Ipea). It allows users to search for specific
series, list series or themes, and download data when available.
Author: Hugo Macedo [aut, cre, cph]
Maintainer: Hugo Macedo <aebdata@hhmace.do>
Diff between aebdata versions 0.1.1 dated 2024-10-13 and 0.1.2 dated 2024-11-08
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 2 ++ tests/testthat/_data/list.rds |binary tests/testthat/_data/search.rds |binary tests/testthat/test-search.R | 2 +- 6 files changed, 11 insertions(+), 9 deletions(-)
Title: Signal and Image Processing Toolbox for Analyzing Intracranial
Electroencephalography Data
Description: Implemented fast and memory-efficient Notch-filter,
Welch-periodogram, discrete wavelet spectrogram for minutes of
high-resolution signals, fast 3D convolution, image registration,
3D mesh manipulation; providing fundamental toolbox for intracranial
Electroencephalography (iEEG) pipelines.
Documentation and examples about 'RAVE' project are provided at
<https://rave.wiki>, and the paper by John F. Magnotti,
Zhengjia Wang, Michael S. Beauchamp (2020)
<doi:10.1016/j.neuroimage.2020.117341>; see 'citation("ravetools")' for
details.
Author: Zhengjia Wang [aut, cre],
John Magnotti [aut],
Michael Beauchamp [aut],
Trustees of the University of Pennsylvania [cph] ,
Karim Rahim [cph, ctb] ,
Thomas Possidente [cph, ctb] ,
Michael Prerau [cph, ctb] ,
Marcus Geelnard [ctb, cph] ,
Stefan Schlage [...truncated...]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ravetools versions 0.1.8 dated 2024-09-03 and 0.1.9 dated 2024-11-08
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- NEWS.md | 4 ++++ 3 files changed, 12 insertions(+), 8 deletions(-)
Title: File-Backed Array for Out-of-Memory Computation
Description: Stores large arrays in files to avoid occupying large
memories. Implemented with super fast gigabyte-level multi-threaded
reading/writing via 'OpenMP'. Supports multiple non-character data
types (double, float, complex, integer, logical, and raw).
Author: Zhengjia Wang [aut, cre, cph]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between filearray versions 0.1.8 dated 2024-09-03 and 0.1.9 dated 2024-11-08
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ inst/doc/performance.html | 8 ++++---- tests/testthat/test-cpp.R | 5 ++++- 5 files changed, 20 insertions(+), 13 deletions(-)
Title: Modelling of Population Growth
Description: Modelling of population growth under static and dynamic environmental conditions.
Includes functions for model fitting and making prediction under isothermal and
dynamic conditions. The methods (algorithms & models) are based on
predictive microbiology (See Perez-Rodriguez and Valero (2012, ISBN:978-1-4614-5519-6)).
Author: Alberto Garre [aut, cre] ,
Jeroen Koomen [aut],
Heidy den Besten [aut],
Marcel Zwietering [aut]
Maintainer: Alberto Garre <garre.alberto@gmail.com>
Diff between biogrowth versions 1.0.4 dated 2024-04-29 and 1.0.5 dated 2024-11-08
DESCRIPTION | 6 MD5 | 132 +-- NEWS.md | 7 R/DynamicGrowth_class.R | 342 ++++----- R/FitDynamicGrowthMCMC_class.R | 670 ++++++++--------- R/FitDynamicGrowth_class.R | 650 ++++++++--------- R/FitIsoGrowth_class.R | 564 +++++++-------- R/FitSecondaryGrowth_class.R | 704 +++++++++--------- R/GrowthFit_class.R | 946 ++++++++++++------------- R/GrowthPrediction_class.R | 592 +++++++-------- R/GrowthUncertainty_class.R | 10 R/IsothermalGrowth_class.R | 240 +++--- R/StochasticGrowth_class.R | 196 ++--- R/TimeDistribution_class.R | 154 ++-- R/baranyi_model.R | 120 +-- R/fit_dynamic_growth.R | 804 ++++++++++----------- R/fit_iso_growth.R | 376 +++++----- R/fit_multi_dynamic.R | 6 R/fit_secondary_models.R | 497 ++++++------- R/gamma_models.R | 297 ++++--- R/initial_guesses.R | 1069 ++++++++++++++-------------- R/meatinfo_primary.R | 325 ++++---- R/metainfo_secondary.R | 358 +++++---- R/predict_dynamic_growth.R | 378 +++++----- R/predict_isothermal_growth.R | 321 +++++--- R/top_fit.R | 1314 +++++++++++++++++------------------ R/top_predict.R | 744 +++++++++---------- build/vignette.rds |binary inst/doc/v01_growth_predictions.html | 8 inst/doc/v02_growth_fitting.html | 11 inst/doc/v03_growth_uncertainty.html | 12 inst/doc/v05_custom_stochastic.Rmd | 182 ++-- inst/doc/v21_math_models.Rmd | 859 ++++++++++++---------- inst/doc/v21_math_models.html | 116 +++ man/Aryani_model.Rd |only man/DynamicGrowth.Rd | 6 man/FitDynamicGrowth.Rd | 12 man/FitDynamicGrowthMCMC.Rd | 12 man/FitIsoGrowth.Rd | 14 man/FitMultipleDynamicGrowth.Rd | 6 man/FitMultipleGrowthMCMC.Rd | 6 man/FitSecondaryGrowth.Rd | 2 man/GlobalGrowthFit.Rd | 6 man/GrowthFit.Rd | 12 man/GrowthPrediction.Rd | 6 man/GrowthUncertainty.Rd | 10 man/IsothermalGrowth.Rd | 6 man/Rossoaw_model.Rd |only man/StochasticGrowth.Rd | 10 man/TimeDistribution.Rd | 2 man/bilinear_lag.Rd |only man/bilinear_stationary.Rd |only man/check_growth_guess.Rd | 2 man/dBaranyi.Rd | 4 man/fit_growth.Rd | 8 man/fit_isothermal_growth.Rd | 2 man/fit_multiple_growth.Rd | 2 man/fit_multiple_growth_MCMC.Rd | 2 man/fit_secondary_growth.Rd | 2 man/get_dyna_residuals.Rd | 4 man/get_multi_dyna_residuals.Rd | 2 man/inhibitory_model.Rd |only man/iso_Baranyi_noLag.Rd |only man/iso_Baranyi_noStat.Rd |only man/loglinear_model.Rd |only man/predict_dynamic_growth.Rd | 2 man/predict_growth.Rd | 2 man/show_guess_dynamic.Rd | 2 man/show_guess_primary.Rd | 2 vignettes/v05_custom_stochastic.Rmd | 182 ++-- vignettes/v21_math_models.Rmd | 859 ++++++++++++---------- 71 files changed, 7383 insertions(+), 6814 deletions(-)
Title: Integration Unit Tests for Pharmacoepidemiological Studies
Description: Push a sample population for unit testing on data mapped to the Observational Medical Outcomes Partnership (OMOP) Common Data Model.
Author: Cesar Barboza [cre, aut] ,
Ioanna Nika [aut],
Ger Inberg [aut] ,
Adam Black [aut]
Maintainer: Cesar Barboza <c.barboza@darwin-eu.org>
Diff between TestGenerator versions 0.3.1 dated 2024-05-28 and 0.3.3 dated 2024-11-08
DESCRIPTION | 13 MD5 | 158 NAMESPACE | 72 NEWS.md | 92 R/download.R | 114 R/generateTestTable.R |only R/globals.R | 46 R/patients.R | 782 R/utilsCdm.R | 66 R/visualisations.R | 134 README.md | 389 inst/cdmTableSpecifications |only inst/extdata/mimic_sample/condition_occurrence.csv | 202 inst/extdata/mimic_sample/drug_exposure.csv | 202 inst/extdata/mimic_sample/measurement.csv | 202 inst/extdata/mimic_sample/observation_period.csv | 202 inst/extdata/mimic_sample/person.csv | 202 inst/extdata/mimic_sample/visit_detail.csv | 202 inst/extdata/mimic_sample/visit_occurrence.csv | 202 inst/extdata/test_cohorts/diazepam.json |49408 +++++++++---------- inst/extdata/test_cohorts/hospitalisation.json | 174 inst/extdata/test_cohorts/icu_visit.json | 138 man/downloadTestData.Rd | 72 man/figures/README-unnamed-chunk-8-1.png |binary man/generateTestTables.Rd |only man/graphCohort.Rd | 78 man/patientsCDM.Rd | 65 man/readPatients.Rd | 66 man/readPatients.csv.Rd | 72 man/readPatients.xl.Rd | 66 tests/testthat.R | 24 tests/testthat/mimic_sample/condition_occurrence.csv | 202 tests/testthat/mimic_sample/drug_exposure.csv | 202 tests/testthat/mimic_sample/measurement.csv | 202 tests/testthat/mimic_sample/observation_period.csv | 202 tests/testthat/mimic_sample/person.csv | 202 tests/testthat/mimic_sample/visit_detail.csv | 202 tests/testthat/mimic_sample/visit_occurrence.csv | 202 tests/testthat/test-generateTestTable.R |only tests/testthat/test-patients.R | 244 tests/testthat/test-utilsCdm.R | 20 tests/testthat/test-visualisations.R | 154 tests/testthat/testCases/mimic_sample.json |19370 +++---- tests/testthat/testCases/test.json | 1925 tests/testthat/test_cdm_data.xlsx |only 45 files changed, 38258 insertions(+), 38312 deletions(-)
Title: Dynamic Model of Ammonia Emission from Field-Applied Manure
Description: An implementation of the ALFAM2 dynamic emission model for ammonia volatilization from field-applied animal slurry (manure with dry matter below about 15%). The model can be used to predict cumulative emission and emission rate of ammonia following field application of slurry. Predictions may be useful for emission inventory calculations, fertilizer management, assessment of mitigation strategies, or research aimed at understanding ammonia emission. Default parameter sets include effects of application method, slurry composition, and weather. The model structure is based on a simplified representation of the physical-chemical slurry-soil-atmosphere system. See Hafner et al. (2018) <doi:10.1016/j.atmosenv.2018.11.034> for information on the model and Hafner et al. (2019) <doi:10.1016/j.agrformet.2017.11.027> for more on the measurement data used for parameter development.
Author: Sasha D. Hafner [aut, cre] ,
Christoph Haeni [aut] ,
Roland Fuss [aut] ,
Frederik Dalby [aut] ,
Johanna Pedersen [ctb] ,
Valdemar Petersen [ctb]
Maintainer: Sasha D. Hafner <sasha.hafner@bce.au.dk>
Diff between ALFAM2 versions 4.1.3 dated 2024-06-17 and 4.2 dated 2024-11-08
DESCRIPTION | 32 MD5 | 31 NEWS.md |only R/alfam2.R | 31 build/partial.rdb |binary build/vignette.rds |binary data/alfam2pars01.rda |binary data/alfam2pars02.rda |binary data/alfam2pars03.rda |binary data/alfam2pars03var.rda |binary inst/CITATION |only inst/doc/ALFAM2-start.R | 51 - inst/doc/ALFAM2-start.Rmd | 41 inst/doc/ALFAM2-start.html | 1827 +++++++++++++++++++++++++++----------------- inst/tinytest/test_alfam2.R | 11 man/alfam2.Rd | 24 man/alfam2pars.Rd |only vignettes/ALFAM2-start.Rmd | 41 18 files changed, 1320 insertions(+), 769 deletions(-)
Title: Hyperparameter Optimization for 'mlr3'
Description: Hyperparameter optimization package of the 'mlr3' ecosystem.
It features highly configurable search spaces via the 'paradox'
package and finds optimal hyperparameter configurations for any 'mlr3'
learner. 'mlr3tuning' works with several optimization algorithms e.g.
Random Search, Iterated Racing, Bayesian Optimization (in 'mlr3mbo')
and Hyperband (in 'mlr3hyperband'). Moreover, it can automatically
optimize learners and estimate the performance of optimized models
with nested resampling.
Author: Marc Becker [cre, aut] ,
Michel Lang [aut] ,
Jakob Richter [aut] ,
Bernd Bischl [aut] ,
Daniel Schalk [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3tuning versions 1.1.0 dated 2024-10-27 and 1.2.0 dated 2024-11-08
DESCRIPTION | 8 - MD5 | 115 ++++++++-------- NAMESPACE | 5 NEWS.md | 8 + R/AutoTuner.R | 19 +- R/CallbackAsyncTuning.R | 139 +++++++++++++++----- R/CallbackBatchTuning.R | 138 +++++++++++++++---- R/ContextAsyncTuning.R | 22 ++- R/ContextBatchTuning.R | 26 ++- R/Tuner.R | 11 - R/TuningInstanceAsyncMulticrit.R | 53 ++++--- R/TuningInstanceAsyncSingleCrit.R | 60 +++++--- R/TuningInstanceBatchMulticrit.R | 62 +++++--- R/TuningInstanceBatchSingleCrit.R | 78 +++++++---- R/auto_tuner.R | 12 + R/bibentries.R | 11 + R/mlr_callbacks.R | 133 +++++++++++++++++++ R/tune.R | 14 -- R/zzz.R | 3 README.md | 96 ++++++------- inst/testthat/helper_misc.R | 2 inst/testthat/helper_tuner.R | 2 man/AutoTuner.Rd | 42 ++++-- man/CallbackAsyncTuning.Rd | 10 + man/CallbackBatchTuning.Rd | 10 + man/ContextAsyncTuning.Rd | 3 man/ContextBatchTuning.Rd | 3 man/Tuner.Rd | 29 ++-- man/TunerAsync.Rd | 13 + man/TunerBatch.Rd | 13 + man/TuningInstanceAsyncMultiCrit.Rd | 16 ++ man/TuningInstanceAsyncSingleCrit.Rd | 15 +- man/TuningInstanceBatchMultiCrit.Rd | 15 ++ man/TuningInstanceBatchSingleCrit.Rd | 14 +- man/assert_async_tuning_callback.Rd |only man/assert_batch_tuning_callback.Rd |only man/auto_tuner.Rd | 26 +++ man/callback_async_tuning.Rd | 58 ++++++-- man/callback_batch_tuning.Rd | 60 ++++++-- man/mlr3tuning.one_se_rule.Rd |only man/mlr_tuners_cmaes.Rd | 13 + man/mlr_tuners_design_points.Rd | 13 + man/mlr_tuners_gensa.Rd | 13 + man/mlr_tuners_grid_search.Rd | 13 + man/mlr_tuners_internal.Rd | 13 + man/mlr_tuners_irace.Rd | 13 + man/mlr_tuners_nloptr.Rd | 13 + man/mlr_tuners_random_search.Rd | 13 + man/ti.Rd | 14 +- man/ti_async.Rd | 14 +- man/tune.Rd | 42 +++--- tests/testthat/test_ArchiveAsyncTuning.R | 30 ++++ tests/testthat/test_AutoTuner.R | 43 +++++- tests/testthat/test_CallbackAsyncTuning.R |only tests/testthat/test_CallbackBatchTuning.R |only tests/testthat/test_Tuner.R | 45 ++++++ tests/testthat/test_TuningInstanceBatchMultiCrit.R | 4 tests/testthat/test_TuningInstanceBatchSingleCrit.R | 4 tests/testthat/test_extract_inner_tuning_archives.R | 12 - tests/testthat/test_extract_inner_tuning_results.R | 30 +++- tests/testthat/test_mlr_callbacks.R | 38 +++++ 61 files changed, 1291 insertions(+), 433 deletions(-)
Title: Automated Multicollinearity Management
Description: Effortless multicollinearity management in data frames with both numeric and categorical variables for statistical and machine learning applications. The package simplifies multicollinearity analysis by combining four robust methods: 1) target encoding for categorical variables (Micci-Barreca, D. 2001 <doi:10.1145/507533.507538>); 2) automated feature prioritization to prevent key variable loss during filtering; 3) pairwise correlation for all variable combinations (numeric-numeric, numeric-categorical, categorical-categorical); and 4) fast computation of variance inflation factors.
Author: Blas M. Benito [aut, cre, cph]
Maintainer: Blas M. Benito <blasbenito@gmail.com>
Diff between collinear versions 1.1.1 dated 2023-12-08 and 2.0.0 dated 2024-11-08
collinear-1.1.1/collinear/R/cramer_v.R |only collinear-1.1.1/collinear/build |only collinear-1.1.1/collinear/man/auc_score.Rd |only collinear-1.1.1/collinear/man/cramer_v.Rd |only collinear-1.1.1/collinear/man/f_gam_auc_balanced.Rd |only collinear-1.1.1/collinear/man/f_gam_auc_unbalanced.Rd |only collinear-1.1.1/collinear/man/f_gam_deviance.Rd |only collinear-1.1.1/collinear/man/f_logistic_auc_balanced.Rd |only collinear-1.1.1/collinear/man/f_logistic_auc_unbalanced.Rd |only collinear-1.1.1/collinear/man/f_rf_auc_balanced.Rd |only collinear-1.1.1/collinear/man/f_rf_auc_unbalanced.Rd |only collinear-1.1.1/collinear/man/f_rf_rsquared.Rd |only collinear-1.1.1/collinear/man/f_rsquared.Rd |only collinear-1.1.1/collinear/man/identify_non_numeric_predictors.Rd |only collinear-1.1.1/collinear/man/identify_numeric_predictors.Rd |only collinear-1.1.1/collinear/man/identify_zero_variance_predictors.Rd |only collinear-1.1.1/collinear/man/internal.Rd |only collinear-1.1.1/collinear/tests/testthat/test-auc_score.R |only collinear-2.0.0/collinear/DESCRIPTION | 27 collinear-2.0.0/collinear/MD5 | 164 - collinear-2.0.0/collinear/NAMESPACE | 72 collinear-2.0.0/collinear/NEWS.md | 90 collinear-2.0.0/collinear/R/case_weights.R |only collinear-2.0.0/collinear/R/collinear.R | 449 ++-- collinear-2.0.0/collinear/R/cor_clusters.R |only collinear-2.0.0/collinear/R/cor_cramer_v.R |only collinear-2.0.0/collinear/R/cor_df.R | 518 ++-- collinear-2.0.0/collinear/R/cor_matrix.R | 119 - collinear-2.0.0/collinear/R/cor_select.R | 318 +- collinear-2.0.0/collinear/R/data.R | 59 collinear-2.0.0/collinear/R/drop_geometry_column.R | 22 collinear-2.0.0/collinear/R/globals.R | 16 collinear-2.0.0/collinear/R/identify.R | 500 ++++ collinear-2.0.0/collinear/R/imports.R | 1 collinear-2.0.0/collinear/R/model_formula.R |only collinear-2.0.0/collinear/R/performance_score_auc.R |only collinear-2.0.0/collinear/R/performance_score_r2.R |only collinear-2.0.0/collinear/R/performance_score_v.R |only collinear-2.0.0/collinear/R/preference_order.R | 976 ++------ collinear-2.0.0/collinear/R/preference_order_collinear.R |only collinear-2.0.0/collinear/R/preference_order_methods.R |only collinear-2.0.0/collinear/R/target_encoding_lab.R | 356 +-- collinear-2.0.0/collinear/R/target_encoding_methods.R | 588 +---- collinear-2.0.0/collinear/R/validate.R | 1048 +++++++-- collinear-2.0.0/collinear/R/vif_df.R | 236 +- collinear-2.0.0/collinear/R/vif_select.R | 415 ++- collinear-2.0.0/collinear/README.md | 1102 +--------- collinear-2.0.0/collinear/data/vi.rda |binary collinear-2.0.0/collinear/data/vi_predictors_categorical.rda |only collinear-2.0.0/collinear/data/vi_predictors_numeric.rda |only collinear-2.0.0/collinear/inst/WORDLIST | 48 collinear-2.0.0/collinear/man/add_white_noise.Rd |only collinear-2.0.0/collinear/man/case_weights.Rd |only collinear-2.0.0/collinear/man/collinear-package.Rd | 2 collinear-2.0.0/collinear/man/collinear.Rd | 256 +- collinear-2.0.0/collinear/man/cor_clusters.Rd |only collinear-2.0.0/collinear/man/cor_cramer_v.Rd |only collinear-2.0.0/collinear/man/cor_df.Rd | 107 collinear-2.0.0/collinear/man/cor_matrix.Rd | 92 collinear-2.0.0/collinear/man/cor_select.Rd | 181 - collinear-2.0.0/collinear/man/drop_geometry_column.Rd | 14 collinear-2.0.0/collinear/man/encoded_predictor_name.Rd |only collinear-2.0.0/collinear/man/f_auc.Rd |only collinear-2.0.0/collinear/man/f_auto.Rd |only collinear-2.0.0/collinear/man/f_auto_rules.Rd |only collinear-2.0.0/collinear/man/f_functions.Rd |only collinear-2.0.0/collinear/man/f_r2.Rd |only collinear-2.0.0/collinear/man/f_r2_counts.Rd |only collinear-2.0.0/collinear/man/f_v.Rd |only collinear-2.0.0/collinear/man/f_v_rf_categorical.Rd |only collinear-2.0.0/collinear/man/identify_predictors.Rd |only collinear-2.0.0/collinear/man/identify_predictors_categorical.Rd |only collinear-2.0.0/collinear/man/identify_predictors_numeric.Rd |only collinear-2.0.0/collinear/man/identify_predictors_type.Rd |only collinear-2.0.0/collinear/man/identify_predictors_zero_variance.Rd |only collinear-2.0.0/collinear/man/identify_response_type.Rd |only collinear-2.0.0/collinear/man/model_formula.Rd |only collinear-2.0.0/collinear/man/performance_score_auc.Rd |only collinear-2.0.0/collinear/man/performance_score_r2.Rd |only collinear-2.0.0/collinear/man/performance_score_v.Rd |only collinear-2.0.0/collinear/man/preference_order.Rd | 202 + collinear-2.0.0/collinear/man/preference_order_collinear.Rd |only collinear-2.0.0/collinear/man/target_encoding_lab.Rd | 81 collinear-2.0.0/collinear/man/target_encoding_methods.Rd | 189 - collinear-2.0.0/collinear/man/toy.Rd | 28 collinear-2.0.0/collinear/man/validate_data_cor.Rd |only collinear-2.0.0/collinear/man/validate_data_vif.Rd |only collinear-2.0.0/collinear/man/validate_df.Rd | 27 collinear-2.0.0/collinear/man/validate_encoding_arguments.Rd |only collinear-2.0.0/collinear/man/validate_predictors.Rd | 34 collinear-2.0.0/collinear/man/validate_preference_order.Rd |only collinear-2.0.0/collinear/man/validate_response.Rd | 27 collinear-2.0.0/collinear/man/vi.Rd | 20 collinear-2.0.0/collinear/man/vi_predictors.Rd | 11 collinear-2.0.0/collinear/man/vi_predictors_categorical.Rd |only collinear-2.0.0/collinear/man/vi_predictors_numeric.Rd |only collinear-2.0.0/collinear/man/vif_df.Rd | 78 collinear-2.0.0/collinear/man/vif_select.Rd | 232 +- collinear-2.0.0/collinear/tests/testthat/test-auc.R |only collinear-2.0.0/collinear/tests/testthat/test-case_weights.R | 35 collinear-2.0.0/collinear/tests/testthat/test-collinear.R | 403 ++- collinear-2.0.0/collinear/tests/testthat/test-cor_clusters.R |only collinear-2.0.0/collinear/tests/testthat/test-cor_df.R | 115 - collinear-2.0.0/collinear/tests/testthat/test-cor_matrix.R | 36 collinear-2.0.0/collinear/tests/testthat/test-cor_select.R | 203 + collinear-2.0.0/collinear/tests/testthat/test-cramer_v.R | 6 collinear-2.0.0/collinear/tests/testthat/test-identify.R | 31 collinear-2.0.0/collinear/tests/testthat/test-preference_order.R | 282 +- collinear-2.0.0/collinear/tests/testthat/test-preference_order_methods.R |only collinear-2.0.0/collinear/tests/testthat/test-target_encoding_lab.R | 28 collinear-2.0.0/collinear/tests/testthat/test-target_encoding_methods.R | 85 collinear-2.0.0/collinear/tests/testthat/test-validate.R | 35 collinear-2.0.0/collinear/tests/testthat/test-vif_df.R | 144 - collinear-2.0.0/collinear/tests/testthat/test-vif_select.R | 215 + 114 files changed, 5496 insertions(+), 4827 deletions(-)
Title: Analyse Open-Ended Survey Responses in Finnish
Description: Annotates Finnish textual survey responses into CoNLL-U format using Finnish treebanks from <https://universaldependencies.org/format.html> using UDPipe as described in Straka and Straková (2017) <doi:10.18653/v1/K17-3009>. Formatted data is then analysed using single or comparison n-gram plots, wordclouds, summary tables and Concept Network plots. The Concept Network plots use the TextRank algorithm as outlined in Mihalcea, Rada & Tarau, Paul (2004) <https://aclanthology.org/W04-3252/>.
Author: Adeline Clarke [cre, aut],
Krista Lagus [aut],
Katja Laine [aut],
Maria Litova [aut],
Matti Nelimarkka [aut],
Joni Oksanen [aut],
Jaakko Peltonen [aut],
Tuukka Oikarinen [aut],
Jani-Matti Tirkkonen [aut],
Ida Toivanen [aut],
Maria Valaste [aut],
Shan [...truncated...]
Maintainer: Adeline Clarke <adelinepclarke@gmail.com>
Diff between finnsurveytext versions 2.0.0 dated 2024-08-27 and 2.1.0 dated 2024-11-08
DESCRIPTION | 6 LICENSE | 4 MD5 | 163 NAMESPACE | 87 NEWS.md | 115 R/01_prepare.R | 584 +- R/01b_prepare_svydesign.R | 368 - R/02_data_exploration.R | 1631 +++---- R/03_concept_network.R | 612 +- R/04_comparison_functions.R | 1424 +++--- R/05_comparison_concept_network.R | 566 +- R/data.R | 355 - R/globals.R | 68 R/runDemo.R | 34 R/utils-pipe.R | 28 README.md | 172 build/vignette.rds |binary data/english_sample_survey.rda |only inst/doc/Overview-PackageTutorial.R | 540 +- inst/doc/Overview-PackageTutorial.Rmd | 1014 ++-- inst/doc/Overview-PackageTutorial.html | 3344 ++++++++-------- inst/doc/ReadMe.R | 18 inst/doc/ReadMe.Rmd | 208 inst/doc/ReadMe.html | 1044 ++-- inst/shiny-examples/app/app.R | 1572 +++---- inst/shiny-examples/app/instructionspage.html | 68 man/child.Rd | 66 man/dev_coop.Rd | 70 man/english_sample_survey.Rd |only man/fst_child.Rd | 88 man/fst_child_2.Rd | 78 man/fst_cn_compare_plot.Rd | 150 man/fst_cn_edges.Rd | 96 man/fst_cn_get_unique.Rd | 58 man/fst_cn_get_unique_separate.Rd | 60 man/fst_cn_nodes.Rd | 70 man/fst_cn_plot.Rd | 70 man/fst_cn_search.Rd | 66 man/fst_comparison_cloud.Rd | 158 man/fst_concept_network.Rd | 106 man/fst_concept_network_compare.Rd | 160 man/fst_dev_coop.Rd | 86 man/fst_dev_coop_2.Rd | 76 man/fst_find_stopwords.Rd | 44 man/fst_format.Rd | 108 man/fst_format_svydesign.Rd | 122 man/fst_freq.Rd | 134 man/fst_freq_compare.Rd | 180 man/fst_freq_plot.Rd | 54 man/fst_freq_table.Rd | 138 man/fst_get_unique_ngrams.Rd | 54 man/fst_get_unique_ngrams_separate.Rd | 56 man/fst_join_unique.Rd | 58 man/fst_length_compare.Rd | 80 man/fst_length_summary.Rd | 56 man/fst_ngrams.Rd | 142 man/fst_ngrams_compare.Rd | 186 man/fst_ngrams_compare_plot.Rd | 96 man/fst_ngrams_plot.Rd | 56 man/fst_ngrams_table.Rd | 146 man/fst_ngrams_table2.Rd | 138 man/fst_pos.Rd | 48 man/fst_pos_compare.Rd | 62 man/fst_prepare.Rd | 160 man/fst_prepare_svydesign.Rd | 150 man/fst_print_available_models.Rd |only man/fst_rm_stop_punct.Rd | 102 man/fst_summarise.Rd | 56 man/fst_summarise_compare.Rd | 72 man/fst_summarise_short.Rd | 46 man/fst_use_svydesign.Rd | 80 man/fst_wordcloud.Rd | 114 man/pipe.Rd | 40 man/runDemo.Rd | 38 vignettes/Overview-PackageTutorial.Rmd | 1014 ++-- vignettes/ReadMe.Rmd | 208 vignettes/web_only/Extra-AnalysingOtherLanguages.Rmd | 263 - vignettes/web_only/Extra-UseWithSurveyPackage.Rmd | 322 - vignettes/web_only/InDetail1-DataPreparation.Rmd | 422 +- vignettes/web_only/InDetail2-DataExploration.Rmd | 634 +-- vignettes/web_only/InDetail3-ConceptNetworkOverview.Rmd | 444 +- vignettes/web_only/InDetail4-ComparisonFunctions.Rmd | 510 +- vignettes/web_only/InDetail5-AnalysisExample1.Rmd | 1008 ++-- vignettes/web_only/InDetail6-AnalysisExample2.Rmd | 614 +- 84 files changed, 11911 insertions(+), 11827 deletions(-)
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Title: Estimation of Cell Infiltration Based on Cell Crosstalk
Description: A systematic biology tool was developed to identify cell infiltration via an Individualized Cell crosstalk network. 'CITMIC' first constructed a weighted cell crosstalk network by integrating Cell-target interaction information, biological process data from the Gene Ontology (GO) database, and gene transcriptomic data in a specific sample, and then, it used a network propagation algorithm on the network to identify cell infiltration for the sample. Ultimately, cell infiltration in the patient dataset was obtained by normalizing the centrality scores of the cells.
Author: Junwei Han [aut, cre, cph],
Xilong Zhao [aut]
Maintainer: Junwei Han <hanjunwei1981@163.com>
Diff between CITMIC versions 0.1.1 dated 2024-09-17 and 0.1.2 dated 2024-11-08
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- R/CITMIC.R | 6 +++++- build/vignette.rds |binary inst/doc/CITMIC.html | 19 +++++++++---------- man/figures |only 6 files changed, 23 insertions(+), 19 deletions(-)
Title: Stratified and Personalised Models Based on Model-Based Trees
and Forests
Description: Model-based trees for subgroup analyses in clinical trials and
model-based forests for the estimation and prediction of personalised
treatment effects (personalised models). Currently partitioning of linear
models, lm(), generalised linear models, glm(), and Weibull models,
survreg(), is supported. Advanced plotting functionality is supported for
the trees and a test for parameter heterogeneity is provided for the
personalised models. For details on model-based trees for subgroup analyses
see Seibold, Zeileis and Hothorn (2016) <doi:10.1515/ijb-2015-0032>; for
details on model-based forests for estimation of individual treatment effects
see Seibold, Zeileis and Hothorn (2017) <doi:10.1177/0962280217693034>.
Author: Heidi Seibold [aut, cre],
Achim Zeileis [aut],
Torsten Hothorn [aut]
Maintainer: Heidi Seibold <heidi@seibold.co>
Diff between model4you versions 0.9-7 dated 2021-01-20 and 0.9-8 dated 2024-11-08
DESCRIPTION | 13 ++- MD5 | 6 - inst/reproducing_papers/2017_individual_treatment_effect_als_smmr.Rmd | 2 tests/test-pmtree.Rout.save | 34 +++++----- 4 files changed, 29 insertions(+), 26 deletions(-)
Title: Filter Based Feature Selection for 'mlr3'
Description: Extends 'mlr3' with filter methods for feature selection.
Besides standalone filter methods built-in methods of any
machine-learning algorithm are supported. Partial scoring of
multivariate filter methods is supported.
Author: Marc Becker [cre, aut] ,
Patrick Schratz [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Martin Binder [aut],
John Zobolas [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3filters versions 0.8.0 dated 2024-04-10 and 0.8.1 dated 2024-11-08
DESCRIPTION | 19 ++++++---- MD5 | 34 +++++++++---------- NEWS.md | 67 ++++++++++++++++++++------------------ R/Filter.R | 6 ++- R/FilterBoruta.R | 11 +++++- R/FilterCorrelation.R | 2 - R/bibentries.R | 2 - R/mlr_filters.R | 6 +-- build/partial.rdb |binary man/Filter.Rd | 2 - man/flt.Rd | 5 +- man/mlr3filters-package.Rd | 3 + man/mlr_filters.Rd | 6 +-- man/mlr_filters_boruta.Rd | 12 ++++++ man/mlr_filters_carsurvscore.Rd | 2 - man/mlr_filters_correlation.Rd | 2 - tests/testthat/test_filter_regr.R | 4 +- tests/testthat/test_filter_surv.R | 2 + 18 files changed, 110 insertions(+), 75 deletions(-)
Title: Minimal Type Guesser
Description: Port the type guesser from 'readr' (so-called 'readr' first edition parsing engine, now superseded by 'vroom').
Author: Chung-hong Chan [aut, cre] ,
Hadley Wickham [aut] ,
Jim Hester [aut] ,
Romain Francois [ctb] ,
Jennifer Bryan [aut] ,
Shelby Bearrows [ctb] ,
Posit Software, PBC [cph] ,
David Olson [aut]
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between minty versions 0.0.1 dated 2024-05-22 and 0.0.4 dated 2024-11-08
DESCRIPTION | 10 ++-- MD5 | 30 ++++++------ R/cpp11.R | 4 - R/parser.R | 20 +++++--- R/type_convert.R | 6 +- README.md | 81 ++++++++++++++++++++++++++++++++-- man/parse_guess.Rd | 3 + man/type_convert.Rd | 3 + src/Collector.h | 10 ---- src/CollectorGuess.cpp | 31 +++++++------ src/QiParsers.h | 23 +++++++-- src/cpp11.cpp | 8 +-- src/utils.h | 7 ++ tests/testthat/test-parsing-numeric.R | 22 +++++++++ tests/testthat/test-parsing.R | 23 +++++++++ tests/testthat/test-type-convert.R | 9 +++ 16 files changed, 224 insertions(+), 66 deletions(-)
Title: Tidy Flowchart Generator
Description: Creates participant flow diagrams directly from a dataframe. Representing the flow of participants through each stage of a study, especially in clinical trials, is essential to assess the generalisability and validity of the results. This package provides a set of functions that can be combined with a pipe operator to create all kinds of flowcharts from a data frame in an easy way.
Author: Pau Satorra [aut, cre] ,
Joao Carmezim [aut] ,
Natalia Pallares [aut] ,
Cristian Tebe [aut] ,
Kenneth Taylor [ctb]
Maintainer: Pau Satorra <psatorra@igtp.cat>
Diff between flowchart versions 0.5.1 dated 2024-09-27 and 0.6.0 dated 2024-11-08
DESCRIPTION | 15 +- MD5 | 34 ++--- NAMESPACE | 6 + NEWS.md | 13 ++ R/fc_draw.R | 25 +++- R/fc_export.R | 165 ++++++++++++++++++++++++----- R/fc_filter.R | 11 + R/fc_modify.R | 8 + R/fc_split.R | 128 +++++++++++++++------- R/fc_view.R | 9 + inst/doc/flowchart.R | 29 ++++- inst/doc/flowchart.Rmd | 56 ++++++++- inst/doc/flowchart.html | 273 ++++++++++++++++++++++++++++-------------------- man/fc_draw.Rd | 3 man/fc_export.Rd | 42 +++++-- man/fc_modify.Rd | 1 man/fc_split.Rd | 2 vignettes/flowchart.Rmd | 56 ++++++++- 18 files changed, 634 insertions(+), 242 deletions(-)
Title: Multi-Format Archive and Compression Support
Description: Bindings to 'libarchive' <http://www.libarchive.org> the
Multi-format archive and compression library. Offers R connections and
direct extraction for many archive formats including 'tar', 'ZIP',
'7-zip', 'RAR', 'CAB' and compression formats including 'gzip',
'bzip2', 'compress', 'lzma' and 'xz'.
Author: Jim Hester [aut] ,
Gabor Csardi [aut, cre],
Ondrej Holy [cph] ,
RStudio [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between archive versions 1.1.9 dated 2024-09-12 and 1.1.10 dated 2024-11-08
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ src/Makevars.ucrt | 8 ++++++-- src/cpp11/include/cpp11/list.hpp | 3 ++- src/cpp11/include/cpp11/r_vector.hpp | 8 ++++++-- 6 files changed, 26 insertions(+), 13 deletions(-)
Title: Package Admix for Admixture (aka Contamination) Models
Description: Implements techniques to estimate the unknown quantities
related to two-component admixture models, where the two components
can belong to any distribution (note that in the case of multinomial
mixtures, the two components must belong to the same family).
Estimation methods depend on the assumptions made on the unknown
component density; see Bordes and Vandekerkhove (2010)
<doi:10.3103/S1066530710010023>, Patra and Sen (2016)
<doi:10.1111/rssb.12148>, and Milhaud, Pommeret, Salhi, Vandekerkhove
(2024) <doi:10.3150/23-BEJ1593>. In practice, one can estimate both
the mixture weight and the unknown component density in a wide variety
of frameworks. On top of that, hypothesis tests can be performed in
one and two-sample contexts to test the unknown component density (see
Milhaud, Pommeret, Salhi and Vandekerkhove (2022)
<doi:10.1016/j.jspi.2021.05.010>, and Milhaud, Pommeret, Salhi,
Vandekerkhove (2024) <doi:10.3150/23-BEJ1593>). Finally, clustering of
unknown [...truncated...]
Author: Xavier Milhaud [aut, cre],
Pierre Vandekerkhove [ctb],
Denys Pommeret [ctb],
Yahia Salhi [ctb]
Maintainer: Xavier Milhaud <xavier.milhaud.research@gmail.com>
Diff between admix versions 2.3.2 dated 2024-11-05 and 2.3.3 dated 2024-11-08
DESCRIPTION | 6 MD5 | 62 +++--- R/IBM_k_samples_test.R | 53 +++-- R/admix_cluster.R | 279 ++++++++++-------------------- R/admix_estim.R | 6 R/admix_model.R | 8 R/admix_test.R | 11 - R/estim_BVdk.R | 4 R/estim_IBM.R | 4 R/estim_PS.R | 13 - R/gaussianity_test.R | 7 R/orthobasis_test.R | 4 R/twoComp_mixt.R | 13 - build/partial.rdb |binary inst/doc/admixture-clustering.R | 6 inst/doc/admixture-clustering.Rmd | 6 inst/doc/admixture-clustering.html | 10 - inst/doc/admixture-weight-estimation.html | 19 -- inst/doc/test-hypothesis.html | 6 man/IBM_k_samples_test.Rd | 25 +- man/IBM_tabul_stochasticInteg.Rd | 17 - man/admix_cluster.Rd | 33 +-- man/admix_estim.Rd | 4 man/admix_model.Rd | 2 man/admix_test.Rd | 11 - man/estim_BVdk.Rd | 4 man/estim_IBM.Rd | 4 man/estim_PS.Rd | 10 - man/gaussianity_test.Rd | 4 man/orthobasis_test.Rd | 4 man/twoComp_mixt.Rd | 2 vignettes/admixture-clustering.Rmd | 6 32 files changed, 290 insertions(+), 353 deletions(-)
Title: Visualizing the Decision Rules Underlying Binary Classification
Description: Visualization of decision rules for binary classification and Receiver Operating Characteristic (ROC) curve estimation under different generalizations proposed in the literature:
- making the classification subsets flexible to cover those scenarios where both extremes of the
marker are associated with a higher risk of being positive, considering two thresholds
(gROC() function);
- transforming the marker by a proper function trying to improve the classification performance
(hROC() function);
- when dealing with multivariate markers, considering a proper transformation to univariate space
trying to maximize the resulting AUC of the TPR for each FPR (multiROC() function).
The classification regions behind each point of the ROC curve are displayed in both static
graphics (plot_buildROC(), plot_regions() or plot_funregions() function) or
videos (movieROC() function).
Author: Sonia Perez-Fernandez [aut, cre]
Maintainer: Sonia Perez-Fernandez <perezsonia@uniovi.es>
Diff between movieROC versions 0.1.1 dated 2024-06-28 and 0.1.2 dated 2024-11-08
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/doc/movieROC_vignette.pdf |binary 3 files changed, 5 insertions(+), 5 deletions(-)
Title: Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs
Description: Lp_solve is freely available (under LGPL 2) software for
solving linear, integer and mixed integer programs. In this
implementation we supply a "wrapper" function in C and some R
functions that solve general linear/integer problems,
assignment problems, and transportation problems. This version
calls lp_solve version 5.5.
Author: Gabor Csardi [cre],
Michel Berkelaar [aut]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between lpSolve versions 5.6.21 dated 2024-09-12 and 5.6.22 dated 2024-11-08
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ src/lusol.c | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)
Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R
using Literate Programming techniques.
Author: Yihui Xie [aut, cre] ,
Abhraneel Sarma [ctb],
Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Amar Al-Zubaidi [ctb],
Andre Simon [ctb] ,
Aron Atkins [ctb],
Aaron Wolen [ctb],
Ashley Manton [ctb],
Atsushi Yasumoto [ctb] ,
Ben Baumer [ctb], [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between knitr versions 1.48 dated 2024-07-07 and 1.49 dated 2024-11-08
knitr-1.48/knitr/inst/doc/knitr-refcard.pdf |only knitr-1.48/knitr/vignettes/assets |only knitr-1.49/knitr/.Rinstignore | 1 knitr-1.49/knitr/DESCRIPTION | 21 knitr-1.49/knitr/MD5 | 102 - knitr-1.49/knitr/NAMESPACE | 1 knitr-1.49/knitr/R/block.R | 20 knitr-1.49/knitr/R/cache.R | 4 knitr-1.49/knitr/R/highlight.R | 2 knitr-1.49/knitr/R/hooks-asciidoc.R | 4 knitr-1.49/knitr/R/hooks-extra.R | 6 knitr-1.49/knitr/R/hooks-html.R | 5 knitr-1.49/knitr/R/hooks-latex.R | 7 knitr-1.49/knitr/R/hooks-md.R | 10 knitr-1.49/knitr/R/hooks-rst.R | 4 knitr-1.49/knitr/R/hooks-textile.R | 1 knitr-1.49/knitr/R/output.R | 12 knitr-1.49/knitr/R/package.R | 2 knitr-1.49/knitr/R/parser.R | 17 knitr-1.49/knitr/R/plot.R | 32 knitr-1.49/knitr/R/table.R | 4 knitr-1.49/knitr/R/utils.R | 40 knitr-1.49/knitr/R/zzz.R | 2 knitr-1.49/knitr/build/vignette.rds |binary knitr-1.49/knitr/inst/CITATION | 2 knitr-1.49/knitr/inst/doc/datatables.R |only knitr-1.49/knitr/inst/doc/datatables.Rmd | 21 knitr-1.49/knitr/inst/doc/datatables.html | 1222 ++++++++++++----------- knitr-1.49/knitr/inst/doc/docco-classic.html | 6 knitr-1.49/knitr/inst/doc/docco-linear.html | 2 knitr-1.49/knitr/inst/doc/knit_expand.R |only knitr-1.49/knitr/inst/doc/knit_expand.Rmd | 20 knitr-1.49/knitr/inst/doc/knit_expand.html | 203 +-- knitr-1.49/knitr/inst/doc/knit_print.Rmd | 4 knitr-1.49/knitr/inst/doc/knit_print.html | 180 ++- knitr-1.49/knitr/inst/doc/knitr-html.html | 28 knitr-1.49/knitr/inst/doc/knitr-intro.R |only knitr-1.49/knitr/inst/doc/knitr-intro.Rmd | 21 knitr-1.49/knitr/inst/doc/knitr-intro.html | 47 knitr-1.49/knitr/inst/doc/knitr-markdown.R |only knitr-1.49/knitr/inst/doc/knitr-markdown.Rmd | 12 knitr-1.49/knitr/inst/doc/knitr-markdown.html | 185 --- knitr-1.49/knitr/inst/doc/knitr-refcard.Rmd | 169 ++- knitr-1.49/knitr/inst/doc/knitr-refcard.html |only knitr-1.49/knitr/man/knit_global.Rd | 19 knitr-1.49/knitr/tests/testit/test-cache.R | 79 + knitr-1.49/knitr/tests/testit/test-hooks-latex.R |only knitr-1.49/knitr/tests/testit/test-parser.R | 5 knitr-1.49/knitr/tests/testit/test-plot.R | 2 knitr-1.49/knitr/tests/testit/test-table.R | 2 knitr-1.49/knitr/tests/testit/test-utils.R | 4 knitr-1.49/knitr/vignettes/datatables.Rmd | 21 knitr-1.49/knitr/vignettes/knit_expand.Rmd | 20 knitr-1.49/knitr/vignettes/knit_print.Rmd | 4 knitr-1.49/knitr/vignettes/knitr-intro.Rmd | 21 knitr-1.49/knitr/vignettes/knitr-markdown.Rmd | 12 knitr-1.49/knitr/vignettes/knitr-refcard.Rmd | 169 ++- 57 files changed, 1482 insertions(+), 1295 deletions(-)
Title: Multivariate Data Analysis
Description: Simple Principal Components Analysis (PCA) and (Multiple)
Correspondence Analysis (CA) based on the Singular Value Decomposition
(SVD). This package provides S4 classes and methods to compute,
extract, summarize and visualize results of multivariate data
analysis. It also includes methods for partial bootstrap validation
described in Greenacre (1984, ISBN: 978-0-12-299050-2) and Lebart et
al. (2006, ISBN: 978-2-10-049616-7).
Author: Nicolas Frerebeau [aut, cre] ,
Jean-Baptiste Fourvel [ctb] ,
Brice Lebrun [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between dimensio versions 0.9.0 dated 2024-08-26 and 0.10.0 dated 2024-11-08
DESCRIPTION | 22 ++--- MD5 | 100 ++++++++++++++------------- NAMESPACE | 1 NEWS.md | 9 ++ R/AllClasses.R | 3 R/AllGenerics.R | 24 ++++++ R/annotations.R | 9 +- R/augment.R | 4 - R/biplot.R | 20 ----- R/bootstrap.R | 4 + R/ca.R | 19 ++--- R/dimensio-internal.R | 6 - R/dimensio-package.R | 2 R/export.R |only R/get_contributions.R | 3 R/get_coordinates.R | 5 + R/get_correlations.R | 2 R/get_cos2.R | 3 R/get_distances.R | 2 R/get_inertia.R | 2 R/mca.R | 2 R/pca.R | 11 +- R/pcoa.R | 3 R/plot.R | 4 + R/viz_coordinates.R | 23 +++++- R/viz_ellipse.R | 55 +++++++++----- R/viz_hull.R | 36 +++++---- R/wrap_ellipses.R | 10 ++ R/wrap_hull.R | 5 + README.md | 4 - inst/doc/pca.R | 4 - inst/doc/pca.Rmd | 4 - inst/doc/pca.html | 16 ++-- inst/examples/ex-envelopes.R | 4 - inst/examples/ex-export.R |only inst/po |only inst/tinytest/_tinysnapshot/CA_boot_col.svg | 8 +- inst/tinytest/_tinysnapshot/CA_boot_row.svg | 8 +- inst/tinytest/_tinysnapshot/PCA_boot_col.svg | 16 ++-- inst/tinytest/test_pca.R | 2 man/PCOA-class.Rd | 3 man/dimensio-package.Rd | 2 man/export.Rd |only man/figures/README-biplot-1.png |binary man/figures/README-plot-var-1.png |binary man/get_contributions.Rd | 1 man/get_coordinates.Rd | 1 man/get_data.Rd | 1 man/get_eigenvalues.Rd | 1 man/viz_labels.Rd | 3 man/viz_wrap.Rd | 90 ++++++++++++++++++++---- po |only vignettes/pca.Rmd | 4 - 53 files changed, 371 insertions(+), 190 deletions(-)
Title: Tools for Descriptive Statistics
Description: A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in ab [...truncated...]
Author: Andri Signorell [aut, cre] ,
Ken Aho [ctb],
Andreas Alfons [ctb],
Nanina Anderegg [ctb],
Tomas Aragon [ctb],
Chandima Arachchige [ctb],
Antti Arppe [ctb],
Adrian Baddeley [ctb],
Kamil Barton [ctb],
Ben Bolker [ctb],
Hans W. Borchers [ctb],
Frederico [...truncated...]
Maintainer: Andri Signorell <andri@signorell.net>
Diff between DescTools versions 0.99.57 dated 2024-09-25 and 0.99.58 dated 2024-11-08
DESCRIPTION | 17 +++--- MD5 | 12 ++-- NAMESPACE | 6 +- NEWS | 18 ++++++ R/DescTools.r | 140 +++++++++++++++++++++++++++----------------------- R/Mod_BrierScore.R | 9 ++- man/AppendRowNames.Rd |only man/ReadSPSS.Rd |only 8 files changed, 122 insertions(+), 80 deletions(-)
Title: Generate Descriptive Statistics
Description: Generate descriptive statistics such as measures of location,
dispersion, frequency tables, cross tables, group summaries and multiple
one/two way tables.
Author: Aravind Hebbali [aut, cre]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Diff between descriptr versions 0.5.2 dated 2020-12-09 and 0.6.0 dated 2024-11-08
DESCRIPTION | 15 MD5 | 195 ++-- NAMESPACE | 7 NEWS.md | 19 R/ds-auto-summary.R | 22 R/ds-cross-table.R | 126 +- R/ds-describe.R | 700 ++++++++++----- R/ds-descriptr.R | 14 R/ds-freq-factor.R | 37 R/ds-freq-mult.R | 20 R/ds-freq-numeric.R | 71 - R/ds-freq-table.R | 30 R/ds-group-summary-interact.R | 18 R/ds-group-summary.R | 58 - R/ds-mult-table.R | 33 R/ds-multistats.R | 16 R/ds-output.R | 79 - R/ds-plots.R | 161 +-- R/ds-screener.R | 14 R/ds-summary-stats.R | 147 +-- R/ds-utils.R | 93 +- R/zzz.R | 12 README.md | 49 - build/vignette.rds |binary inst/doc/categorical-data.R | 2 inst/doc/categorical-data.html | 709 +++++++--------- inst/doc/continuous-data.R | 2 inst/doc/continuous-data.html | 1191 +++++++++++++-------------- inst/doc/visualization.R | 2 inst/doc/visualization.html | 270 ++---- man/descriptr.Rd | 16 man/ds_auto_freq_table.Rd | 11 man/ds_auto_group_summary.Rd | 1 man/ds_auto_summary_stats.Rd | 3 man/ds_cross_table.Rd | 19 man/ds_css.Rd | 14 man/ds_cvar.Rd | 14 man/ds_extreme_obs.Rd | 15 man/ds_freq_table.Rd | 4 man/ds_gmean.Rd | 16 man/ds_group_summary.Rd | 6 man/ds_group_summary_interact.Rd | 4 man/ds_hmean.Rd | 16 man/ds_kurtosis.Rd | 14 man/ds_mdev.Rd | 14 man/ds_measures_location.Rd | 28 man/ds_measures_symmetry.Rd | 21 man/ds_measures_variation.Rd | 21 man/ds_mode.Rd | 12 man/ds_percentiles.Rd | 21 man/ds_plot_bar.Rd | 7 man/ds_plot_bar_grouped.Rd | 7 man/ds_plot_bar_stacked.Rd | 7 man/ds_plot_box_group.Rd | 7 man/ds_plot_box_single.Rd | 7 man/ds_plot_density.Rd | 7 man/ds_plot_histogram.Rd | 7 man/ds_plot_scatter.Rd | 5 man/ds_range.Rd | 14 man/ds_rindex.Rd | 4 man/ds_skewness.Rd | 14 man/ds_summary_stats.Rd | 12 man/ds_tailobs.Rd | 17 man/ds_tidy_stats.Rd | 3 tests/testthat.R | 16 tests/testthat/_snaps |only tests/testthat/test-auto-summary.R | 147 --- tests/testthat/test-cross-table.R | 65 - tests/testthat/test-describe.R | 120 +- tests/testthat/test-freq-table.R | 62 - tests/testthat/test-group-summary-interact.R | 2 tests/testthat/test-group-summary.R | 14 tests/testthat/test-multistats.R | 24 tests/testthat/test-output.R | 290 ------ tests/testthat/test-plots.R | 85 + tests/testthat/test-screen.R | 16 tests/testthat/test-summary-stats.R | 18 tests/testthat/test-utils.R | 38 78 files changed, 2814 insertions(+), 2583 deletions(-)
Title: Multivariate Normal Mean Monitoring Through Critical-to-X
Control Chart
Description: A comprehensive set of functions designed for multivariate mean monitoring using the Critical-to-X Control Chart. These functions enable the determination of optimal control limits based on a specified in-control Average Run Length (ARL), the calculation of out-of-control ARL for a given control limit, and post-signal analysis to identify the specific variable responsible for a detected shift in the mean. This suite of tools provides robust support for precise and effective process monitoring and analysis.
Author: Dr. Burcu Aytacoglu [aut] ,
Dr. Diana Barraza-Barraza [aut, cre] ,
Dr. Victor G. Tercero-Gomez [aut] ,
Dr. A. Eduardo Cordero-Franco [aut]
Maintainer: Dr. Diana Barraza-Barraza <diana.barraza@ujed.mx>
Diff between CTxCC versions 0.1.0 dated 2024-10-25 and 0.2.0 dated 2024-11-08
DESCRIPTION | 8 +++++--- MD5 | 4 ++-- R/Functions.R | 6 ------ 3 files changed, 7 insertions(+), 11 deletions(-)
Title: Interactive Biplots in R
Description: Provides a GUI with which users can construct and interact
with biplots.
Author: Anthony la Grange [aut],
Niel le Roux [cre]
Maintainer: Niel le Roux <njlr@sun.ac.za>
Diff between BiplotGUI versions 0.0-7 dated 2013-03-19 and 0.0-12 dated 2024-11-08
BiplotGUI-0.0-12/BiplotGUI/DESCRIPTION | 30 - BiplotGUI-0.0-12/BiplotGUI/LICENSE |only BiplotGUI-0.0-12/BiplotGUI/MD5 | 15 BiplotGUI-0.0-12/BiplotGUI/NAMESPACE | 53 + BiplotGUI-0.0-12/BiplotGUI/R/Biplots.R | 48 + BiplotGUI-0.0-12/BiplotGUI/inst/CITATION | 32 - BiplotGUI-0.0-12/BiplotGUI/man/FighterAircraft.Rd | 78 +- BiplotGUI-0.0-12/BiplotGUI/src/abagplot.f | 429 ++++++++-------- BiplotGUI-0.0-12/BiplotGUI/src/registerDynamicSymbols.c |only BiplotGUI-0.0-7/BiplotGUI/inst/doc |only 10 files changed, 378 insertions(+), 307 deletions(-)
Title: Bayesian Fertility Projection
Description: Making probabilistic projections of total fertility rate for all countries of the world, using a Bayesian hierarchical model <doi:10.1007/s13524-011-0040-5> <doi:10.18637/jss.v106.i08>. Subnational probabilistic projections are also supported <doi:10.4054/DemRes.2018.38.60>.
Author: Hana Sevcikova [cre, aut],
Leontine Alkema [aut],
Peiran Liu [aut],
Adrian Raftery [aut],
Bailey Fosdick [aut],
Patrick Gerland [aut]
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between bayesTFR versions 7.4-2 dated 2023-10-18 and 7.4-4 dated 2024-11-08
ChangeLog | 20 ++++++ DESCRIPTION | 40 +++++++++++-- MD5 | 47 ++++++++------- NAMESPACE | 2 R/get_outputs.R | 27 +++++++-- R/mcmc_ini.R | 6 +- R/plot_functions.R | 119 ++++++++++++++++++++++++++++++---------- R/predict_tfr.R | 79 +++++++++++++++----------- R/predict_tfr_subnat.R | 4 - R/tfr_median_set_new.R | 52 +++++++++-------- data/UN_variants.rda |binary data/include_2024.rda |only man/bayesTFR-internal.Rd | 1 man/convert.trajectories.Rd | 3 - man/get.tfr.estimation.Rd | 6 +- man/get.tfr.prediction.Rd | 21 +++++-- man/include.Rd | 2 man/plot-trajectories.Rd | 3 + man/predict-tfr.Rd | 6 +- man/tfr.median.set.Rd | 16 +++-- man/tfr.median.set.all.Rd | 3 - man/tfr.predict.extra.Rd | 3 - man/tfr.predict.subnat.Rd | 7 +- man/write.projection.summary.Rd | 10 ++- tests/run_tests.R | 4 - 25 files changed, 328 insertions(+), 153 deletions(-)
Title: A Fast Implementation of Random Forests
Description: A fast implementation of Random Forests, particularly suited for high
dimensional data. Ensembles of classification, regression, survival and
probability prediction trees are supported. Data from genome-wide association
studies can be analyzed efficiently. In addition to data frames, datasets of
class 'gwaa.data' (R package 'GenABEL') and 'dgCMatrix' (R package 'Matrix')
can be directly analyzed.
Author: Marvin N. Wright [aut, cre],
Stefan Wager [ctb],
Philipp Probst [ctb]
Maintainer: Marvin N. Wright <cran@wrig.de>
Diff between ranger versions 0.16.0 dated 2023-11-12 and 0.17.0 dated 2024-11-08
DESCRIPTION | 22 + MD5 | 98 +++---- NAMESPACE | 3 NEWS | 8 R/RcppExports.R | 16 + R/hshrink.R |only R/onAttach.R |only R/predict.R | 31 +- R/print.R | 2 R/ranger.R | 158 +++++++++-- R/treeInfo.R | 2 build/partial.rdb |binary man/hshrink.Rd |only man/predict.ranger.Rd | 5 man/predict.ranger.forest.Rd | 5 man/ranger.Rd | 27 + src/Data.cpp | 39 ++ src/Data.h | 7 src/DataRcpp.h | 3 src/DataSparse.cpp | 3 src/DataSparse.h | 2 src/Forest.cpp | 38 +- src/Forest.h | 26 + src/ForestClassification.cpp | 8 src/ForestProbability.cpp | 8 src/ForestRegression.cpp | 23 + src/ForestSurvival.cpp | 8 src/RcppExports.cpp | 65 ++++ src/Tree.cpp | 83 ++++- src/Tree.h | 14 - src/TreeClassification.cpp | 487 ++++++++++++++++++++++++++++++++-- src/TreeClassification.h | 11 src/TreeProbability.cpp | 488 ++++++++++++++++++++++++++++++++--- src/TreeProbability.h | 11 src/TreeRegression.cpp | 467 ++++++++++++++++++++++++++++++--- src/TreeRegression.h | 24 + src/TreeSurvival.cpp | 20 - src/globals.h | 5 src/rangerCpp.cpp | 14 - src/utility.cpp | 20 + src/utility.h | 41 ++ src/utilityRcpp.cpp | 63 ++++ tests/testthat/test_classification.R | 4 tests/testthat/test_classweights.R | 4 tests/testthat/test_hshrink.R |only tests/testthat/test_missings.R |only tests/testthat/test_poissonsplit.R |only tests/testthat/test_predict.R | 9 tests/testthat/test_print.R | 2 tests/testthat/test_ranger.R | 122 +++++++- tests/testthat/test_regression.R | 4 tests/testthat/test_regularization.R | 2 tests/testthat/test_survival.R | 4 53 files changed, 2134 insertions(+), 372 deletions(-)
Title: Realistic Quantitative Structure Models
Description: Real Twig is a method to correct branch overestimation in quantitative structure models. Overestimated cylinders are correctly tapered using measured twig diameters of corresponding tree species. Supported quantitative structure modeling software includes 'TreeQSM', 'SimpleForest', 'Treegraph', and 'aRchi'. Also included is a novel database of twig diameters and tools for fractal analysis of point clouds.
Author: Aidan Morales [aut, cre, cph] ,
David W. MacFarlane [aut, cph]
Maintainer: Aidan Morales <moral169@msu.edu>
Diff between rTwig versions 1.1.0 dated 2024-08-20 and 1.2.0 dated 2024-11-08
rTwig-1.1.0/rTwig/src/helper_functions.h |only rTwig-1.2.0/rTwig/DESCRIPTION | 15 rTwig-1.2.0/rTwig/MD5 | 121 +- rTwig-1.2.0/rTwig/NAMESPACE | 12 rTwig-1.2.0/rTwig/NEWS.md | 63 + rTwig-1.2.0/rTwig/R/RcppExports.R | 171 +++ rTwig-1.2.0/rTwig/R/box_dimension.R | 292 +++-- rTwig-1.2.0/rTwig/R/cluster_cloud.R |only rTwig-1.2.0/rTwig/R/correct_radii.R | 1277 ++++++-------------------- rTwig-1.2.0/rTwig/R/export_mat.R | 93 + rTwig-1.2.0/rTwig/R/export_mesh.R | 126 ++ rTwig-1.2.0/rTwig/R/import_qsm.R | 74 + rTwig-1.2.0/rTwig/R/import_treegraph.R | 43 rTwig-1.2.0/rTwig/R/plot_qsm.R | 740 +++++++++++---- rTwig-1.2.0/rTwig/R/prune_qsm.R |only rTwig-1.2.0/rTwig/R/qsm_summary.R | 551 ++++------- rTwig-1.2.0/rTwig/R/rTwig-package.R | 10 rTwig-1.2.0/rTwig/R/run_rtwig.R | 104 +- rTwig-1.2.0/rTwig/R/smooth_qsm.R | 35 rTwig-1.2.0/rTwig/R/standardize_qsm.R | 171 ++- rTwig-1.2.0/rTwig/R/tools.R |only rTwig-1.2.0/rTwig/R/tree_metrics.R | 181 ++- rTwig-1.2.0/rTwig/R/update_cylinders.R | 512 +++++----- rTwig-1.2.0/rTwig/README.md | 182 ++- rTwig-1.2.0/rTwig/build/partial.rdb |binary rTwig-1.2.0/rTwig/data/twigs.rda |binary rTwig-1.2.0/rTwig/inst/CITATION |only rTwig-1.2.0/rTwig/inst/REFERENCES.bib | 233 ++-- rTwig-1.2.0/rTwig/inst/doc/Box-Dimension.html | 4 rTwig-1.2.0/rTwig/inst/doc/Dictionary.Rmd | 10 rTwig-1.2.0/rTwig/inst/doc/Dictionary.html | 20 rTwig-1.2.0/rTwig/inst/doc/Metrics.R | 22 rTwig-1.2.0/rTwig/inst/doc/Metrics.Rmd | 24 rTwig-1.2.0/rTwig/inst/doc/Metrics.html | 898 +++++++++--------- rTwig-1.2.0/rTwig/inst/doc/Overview.R | 10 rTwig-1.2.0/rTwig/inst/doc/Overview.Rmd | 17 rTwig-1.2.0/rTwig/inst/doc/Overview.html | 88 - rTwig-1.2.0/rTwig/inst/doc/Twigs.html | 101 +- rTwig-1.2.0/rTwig/inst/doc/Validation.R | 22 rTwig-1.2.0/rTwig/inst/doc/Validation.Rmd | 23 rTwig-1.2.0/rTwig/inst/doc/Validation.html | 732 +++++++------- rTwig-1.2.0/rTwig/inst/extdata/QSM2.csv |only rTwig-1.2.0/rTwig/inst/include |only rTwig-1.2.0/rTwig/man/cluster_cloud.Rd |only rTwig-1.2.0/rTwig/man/correct_radii.Rd | 6 rTwig-1.2.0/rTwig/man/export_mat.Rd | 6 rTwig-1.2.0/rTwig/man/export_mesh.Rd | 27 rTwig-1.2.0/rTwig/man/import_qsm.Rd | 4 rTwig-1.2.0/rTwig/man/import_treegraph.Rd | 4 rTwig-1.2.0/rTwig/man/plot_qsm.Rd | 82 - rTwig-1.2.0/rTwig/man/prune_qsm.Rd |only rTwig-1.2.0/rTwig/man/qsm_summary.Rd | 26 rTwig-1.2.0/rTwig/man/rTwig-package.Rd | 2 rTwig-1.2.0/rTwig/man/run_rtwig.Rd | 19 rTwig-1.2.0/rTwig/man/standardize_qsm.Rd | 6 rTwig-1.2.0/rTwig/man/update_cylinders.Rd | 17 rTwig-1.2.0/rTwig/src/Makevars |only rTwig-1.2.0/rTwig/src/Makevars.win |only rTwig-1.2.0/rTwig/src/RcppExports.cpp | 174 +++ rTwig-1.2.0/rTwig/src/cluster_cloud.cpp |only rTwig-1.2.0/rTwig/src/correct_radii.cpp |only rTwig-1.2.0/rTwig/src/generate_cloud.cpp | 179 ++- rTwig-1.2.0/rTwig/src/helper_functions.cpp | 29 rTwig-1.2.0/rTwig/src/pan_plot.cpp |only rTwig-1.2.0/rTwig/vignettes/Dictionary.Rmd | 10 rTwig-1.2.0/rTwig/vignettes/Metrics.Rmd | 24 rTwig-1.2.0/rTwig/vignettes/Overview.Rmd | 17 rTwig-1.2.0/rTwig/vignettes/Validation.Rmd | 23 68 files changed, 4202 insertions(+), 3430 deletions(-)