Fri, 08 Nov 2024

Package TestAnaAPP updated to version 1.1.2 with previous version 1.1.1 dated 2024-09-10

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(-)

More information about TestAnaAPP at CRAN
Permanent link

Package r2r updated to version 0.1.2 with previous version 0.1.1 dated 2021-07-06

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(-)

More information about r2r at CRAN
Permanent link

Package PvSTATEM updated to version 0.1.2 with previous version 0.1.1 dated 2024-11-02

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(-)

More information about PvSTATEM at CRAN
Permanent link

Package metasnf updated to version 1.1.2 with previous version 1.1.1 dated 2024-11-08

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(-)

More information about metasnf at CRAN
Permanent link

Package icmstate updated to version 0.1.1 with previous version 0.1.0 dated 2024-10-28

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(-)

More information about icmstate at CRAN
Permanent link

Package connectapi updated to version 0.4.0 with previous version 0.3.0 dated 2024-09-05

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(-)

More information about connectapi at CRAN
Permanent link

Package bigD updated to version 0.3.0 with previous version 0.2.0 dated 2022-09-05

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(-)

More information about bigD at CRAN
Permanent link

Package graphicalMCP updated to version 0.2.6 with previous version 0.2.5 dated 2024-07-13

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(-)

More information about graphicalMCP at CRAN
Permanent link

Package svydiags updated to version 0.7 with previous version 0.6 dated 2024-05-08

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(-)

More information about svydiags at CRAN
Permanent link

Package mlmc updated to version 2.1.0 with previous version 2.0.2 dated 2024-09-04

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(-)

More information about mlmc at CRAN
Permanent link

Package aebdata updated to version 0.1.2 with previous version 0.1.1 dated 2024-10-13

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(-)

More information about aebdata at CRAN
Permanent link

Package ravetools updated to version 0.1.9 with previous version 0.1.8 dated 2024-09-03

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(-)

More information about ravetools at CRAN
Permanent link

Package filearray updated to version 0.1.9 with previous version 0.1.8 dated 2024-09-03

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(-)

More information about filearray at CRAN
Permanent link

Package biogrowth updated to version 1.0.5 with previous version 1.0.4 dated 2024-04-29

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(-)

More information about biogrowth at CRAN
Permanent link

Package TestGenerator updated to version 0.3.3 with previous version 0.3.1 dated 2024-05-28

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(-)

More information about TestGenerator at CRAN
Permanent link

Package ALFAM2 updated to version 4.2 with previous version 4.1.3 dated 2024-06-17

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(-)

More information about ALFAM2 at CRAN
Permanent link

New package SimRDS with initial version 2.0.0
Package: SimRDS
Title: Simulation of Respondent Driven Samples
Version: 2.0.0
Maintainer: Ayesha Perera <gaayesha93@gmail.com>
Description: Simulate populations with desired properties and extract respondent driven samples. To better understand the usage of the package and the algorithm used, please refer to Perera, A., and Ramanayake, A. (2019) <https://www.aimr.tirdiconference.com/assets/images/portfolio/Conference-Proceeding-AIMR-19.pdf>.
License: GPL-2
Imports: RDS, e1071, stats
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
Suggests: knitr, rmarkdown
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-11-07 01:59:49 UTC; GPERERA
Author: Ayesha Perera [aut, cre]
Repository: CRAN
Date/Publication: 2024-11-08 15:10:09 UTC

More information about SimRDS at CRAN
Permanent link

Package mlr3tuning updated to version 1.2.0 with previous version 1.1.0 dated 2024-10-27

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(-)

More information about mlr3tuning at CRAN
Permanent link

New package lofifonts with initial version 0.1.3
Package: lofifonts
Title: Text Rendering with Bitmap and Vector Fonts
Version: 0.1.3
Maintainer: Mike Cheng <mikefc@coolbutuseless.com>
Description: Alternate font rendering is useful when rendering text to novel graphics outputs where modern font rendering is not available or where bespoke text positioning is required. Bitmap and vector fonts allow for custom layout and rendering using pixel coordinates and line drawing. Formatted text is created as a data.frame of pixel coordinates (for bitmap fonts) or stroke coordinates (for vector fonts). All text can be easily previewed as a matrix or raster image. A selection of fonts is included with this package.
License: MIT + file LICENSE
Encoding: UTF-8
Copyright: The included 'spleen' font is BSD licensed and Copyright (c) 2018-2024, Frederic Cambus. The included 'Tamzen' font is free to distribute and Copyright 2011 Suraj N. Kurapati (it is based upon the 'Tamsyn' font which is also free to distribute Copyright 2010 Scott Fial) The included 'unifont' font is SIL Open Font Licensed, and is Copyright the GNU unifont authors. The included 'gridfont' is MIT licensed is Copyright (c) 2019 Anders Hoff. See 'COPYRIGHTS' file for more details.
URL: https://github.com/coolbutuseless/lofifonts
BugReports: https://github.com/coolbutuseless/lofifonts/issues
Depends: R (>= 2.10)
Suggests: knitr, rmarkdown, bittermelon, ggplot2, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-07 09:48:56 UTC; mike
Author: Mike Cheng [aut, cre, cph], June Choe [ctb] , Frederic Cambus [cph, tyd] , GNU Unifont authors [cph, tyd] , Suraj Kurapati [cph, tyd] , Scott Fial [cph, tyd] , Anders Hoff [cph, tyd]
Repository: CRAN
Date/Publication: 2024-11-08 15:20:02 UTC

More information about lofifonts at CRAN
Permanent link

New package FGRepo with initial version 1.3.2.0
Package: FGRepo
Title: Functional Genomics Repository for POST-GWAS Analysis
Version: 1.3.2.0
Date: 2024-11-07
Author: Alireza Ani [aut, cre], Ahmad Vaez [aut]
Maintainer: Alireza Ani <a.ani@umcg.nl>
Depends: R (>= 3.5)
Description: A collection of datasets essential for functional genomic analysis. Gene names, gene positions, cytoband information, sourced from Ensembl and phenotypes association graph prepared from GWAScatalog are included. Data is available in both GRCh37 and 38 builds. These datasets facilitate a wide range of genomic studies, including the identification of genetic variants, exploration of genomic features, and post-GWAS functional analysis.
License: GPL-3
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
NeedsCompilation: no
Packaged: 2024-11-07 06:27:56 UTC; Alireza
Repository: CRAN
Date/Publication: 2024-11-08 15:10:12 UTC

More information about FGRepo at CRAN
Permanent link

New package AIscreenR with initial version 0.1.0
Package: AIscreenR
Title: AI Screening Tools in R for Systematic Reviewing
Version: 0.1.0
Description: Provides functions to conduct title and abstract screening in systematic reviews using large language models, such as the Generative Pre-trained Transformer (GPT) models from 'OpenAI' <https://platform.openai.com/>. These functions can enhance the quality of title and abstract screenings while reducing the total screening time significantly. In addition, the package includes tools for quality assessment of title and abstract screenings, as described in Vembye, Christensen, Mølgaard, and Schytt (2024) <DOI:10.31219/osf.io/yrhzm>.
Depends: R (>= 4.1.0)
License: GPL (>= 3)
Encoding: UTF-8
Imports: dplyr, tibble, httr2, stringr, furrr, tidyr, tictoc, askpass, curl, purrr, lifecycle, jsonlite
Suggests: future, knitr, rmarkdown, usethis, testthat (>= 3.0.0)
URL: https://mikkelvembye.github.io/AIscreenR/, https://github.com/MikkelVembye/AIscreenR
BugReports: https://github.com/MikkelVembye/AIscreenR/issues
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-07 09:01:08 UTC; B199526
Author: Mikkel H. Vembye [aut, cre, cph]
Maintainer: Mikkel H. Vembye <mikkel.vembye@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-08 15:10:15 UTC

More information about AIscreenR at CRAN
Permanent link

New package tidyplots with initial version 0.1.2
Package: tidyplots
Title: Tidy Plots for Scientific Papers
Version: 0.1.2
Description: The goal of 'tidyplots' is to streamline the creation of publication-ready plots for scientific papers. It allows to gradually add, remove and adjust plot components using a consistent and intuitive syntax.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: cli, dplyr, forcats, ggbeeswarm, ggplot2, ggpubr, ggrastr, ggrepel, glue, Hmisc, htmltools, lifecycle, patchwork, purrr, rlang, scales, stringr, tidyr, tidyselect
Depends: R (>= 2.10)
LazyData: true
URL: https://github.com/jbengler/tidyplots, https://jbengler.github.io/tidyplots/
BugReports: https://github.com/jbengler/tidyplots/issues
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), vdiffr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-06 23:27:30 UTC; janbroderengler
Author: Jan Broder Engler [aut, cre, cph]
Maintainer: Jan Broder Engler <broder.engler@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-08 15:00:02 UTC

More information about tidyplots at CRAN
Permanent link

New package redcas with initial version 0.1.1
Package: redcas
Depends: R (>= 3.5.0), methods
Title: An Interface to the Computer Algebra System 'REDUCE'
Version: 0.1.1
Date: 2024-11-05
Author: Martin Gregory [aut, cre]
Maintainer: Martin Gregory <mairtin.macghreagoir@gmail.com>
Description: 'REDUCE' is a portable general-purpose computer algebra system supporting scalar, vector, matrix and tensor algebra, symbolic differential and integral calculus, arbitrary precision numerical calculations and output in 'LaTeX' format. 'REDUCE' is based on 'Lisp' and is available on the two dialects 'Portable Standard Lisp' ('PSL') and 'Codemist Standard Lisp' ('CSL'). The 'redcas' package provides an interface for executing arbitrary 'REDUCE' code interactively from 'R', returning output as character vectors. 'R' code and 'REDUCE' code can be interspersed. It also provides a specialized function for calling the 'REDUCE' feature for solving systems of equations, returning the output as an 'R' object designed for the purpose. A further specialized function uses 'REDUCE' features to generate 'LaTeX' output and post-processes this for direct use in 'LaTeX' documents, e.g. using 'Sweave'.
License: GPL-3
SystemRequirements: 'REDUCE' <http://www.reduce-algebra.com>. At least one of the 'CSL' or 'PSL' dialects must be installed in order to use the package. Tested with 'REDUCE' releases 6860 and 6558 for both 'CSL' and 'PSL' on Linux, and 6558 and 6339 for 'CSL' on MacOS
NeedsCompilation: no
OS_type: unix
Packaged: 2024-11-05 16:30:11 UTC; mg
Repository: CRAN
Date/Publication: 2024-11-08 14:50:02 UTC

More information about redcas at CRAN
Permanent link

New package metasnf with initial version 1.1.1
Package: metasnf
Title: Meta Clustering with Similarity Network Fusion
Version: 1.1.1
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...]
License: GPL (>= 3)
Encoding: UTF-8
Imports: cluster, digest, dplyr, ggplot2, grDevices, MASS, mclust, methods, progressr, purrr, rlang, SNFtool, stats, tidyr, utils
Suggests: circlize, ComplexHeatmap, InteractiveComplexHeatmap, clv, future, future.apply, knitr, rmarkdown, testthat (>= 3.0.0), ggalluvial, dbscan
Depends: R (>= 4.1.0)
LazyData: true
VignetteBuilder: knitr
URL: https://branchlab.github.io/metasnf/, https://github.com/BRANCHlab/metasnf/
BugReports: https://github.com/BRANCHlab/metasnf/issues
NeedsCompilation: no
Packaged: 2024-11-06 18:40:32 UTC; prashanth
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>
Repository: CRAN
Date/Publication: 2024-11-08 15:00:08 UTC

More information about metasnf at CRAN
Permanent link

New package ineAtlas with initial version 0.1.2
Package: ineAtlas
Title: Access to Spanish Household Income Distribution Atlas Data
Version: 0.1.2
Description: Provides access to granular socioeconomic indicators from the Spanish Statistical Office (INE) Household Income Distribution Atlas. The package downloads and processes data from a companion 'GitHub' repository (<https://github.com/pablogguz/ineAtlas.data/>) which contains processed versions of the official INE Atlas data. Functions are provided to fetch data at multiple geographic levels (municipalities, districts, and census tracts), including income indicators, demographic characteristics, and inequality metrics. The data repository is updated every year when new releases are published by INE.
License: MIT + file LICENSE
URL: https://github.com/pablogguz/ineAtlas, https://pablogguz.github.io/ineAtlas/
BugReports: https://github.com/pablogguz/ineAtlas/issues
Imports: dplyr, httr, readr, sf, stringr, utils, zip
Suggests: data.table, extrafont, ggplot2, ggtext, knitr, mapSpain, mockery, rmarkdown, spelling, testthat (>= 3.0.0), tidyr
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2024-11-06 19:31:47 UTC; pablo
Author: Pablo Garcia Guzman [aut, cre, cph]
Maintainer: Pablo Garcia Guzman <garciagp@ebrd.com>
Repository: CRAN
Date/Publication: 2024-11-08 15:00:17 UTC

More information about ineAtlas at CRAN
Permanent link

New package ILSAmerge with initial version 1.0.0
Package: ILSAmerge
Title: Merge and Download International Large-Scale Assessments (ILSA) Data
Version: 1.0.0
Maintainer: Andres Christiansen <andres.christiansen@iea-hamburg.de>
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), Programme for International Student Assessment (PISA), and others.
License: GPL (>= 3.0)
URL: https://github.com/dopatendo/ILSAmerge
Imports: haven
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-11-06 17:24:19 UTC; andreschristiansen
Author: Andres Christiansen [aut, cre]
Repository: CRAN
Date/Publication: 2024-11-08 14:50:06 UTC

More information about ILSAmerge at CRAN
Permanent link

New package ife with initial version 0.1.0
Package: ife
Title: Influence Function Based Estimate Objects
Version: 0.1.0
Maintainer: Nicholas Williams <ntwilliams.personal@gmail.com>
Description: Implements an S7 class for estimates based on influence functions. Standard arithmetic operations are defined for the class.
License: GPL (>= 3)
Encoding: UTF-8
Imports: cli, generics, S7
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-11-06 19:03:21 UTC; nicholaswilliams
Author: Nicholas Williams [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-11-08 15:00:20 UTC

More information about ife at CRAN
Permanent link

New package epicmodel with initial version 0.1.1
Package: epicmodel
Title: Causal Modeling in Epidemiology
Version: 0.1.1
Description: Create causal models for use in epidemiological studies, including sufficient-component cause models as introduced by Rothman (1976) <doi:10.1093/oxfordjournals.aje.a112335>.
License: GPL (>= 3)
Encoding: UTF-8
Imports: checkmate, cli, dagitty, DiagrammeR, dplyr, DT, ggplot2, gtools, magrittr, methods, prompter, purrr, rlang, shiny, shinyalert, shinyjs, shinythemes, spsUtil, stringr, tibble, tidyr
Suggests: ggdag, ggforce, ggraph, knitr, rmarkdown, testthat (>= 3.0.0)
Depends: R (>= 3.5.0)
LazyData: true
VignetteBuilder: knitr
URL: https://forsterepi.github.io/epicmodel/, https://github.com/forsterepi/epicmodel
BugReports: https://github.com/forsterepi/epicmodel/issues
NeedsCompilation: no
Packaged: 2024-11-06 10:44:37 UTC; ffors
Author: Felix Forster [aut, cre, cph]
Maintainer: Felix Forster <felix.forster@med.uni-muenchen.de>
Repository: CRAN
Date/Publication: 2024-11-08 14:30:01 UTC

More information about epicmodel at CRAN
Permanent link

New package DTSR with initial version 0.1.0
Package: DTSR
Version: 0.1.0
Date: 2024-10-22
Title: Distributed Trimmed Scores Regression for Handling Missing Data
Author: Guangbao Guo [aut, cre, cph] , Ruiling Niu [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Description: Provides functions for handling missing data using Distributed Trimmed Scores Regression and other imputation methods. It includes facilities for data imputation, evaluation metrics, and clustering analysis. It is designed to work in distributed computing environments to handle large datasets efficiently. The philosophy of the package is described in Guo G. (2024) <doi:10.1080/03610918.2022.2091779>.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.5.0)
Repository: CRAN
Imports: stats, mvdalab, DMwR2, cluster, MASS
NeedsCompilation: no
Packaged: 2024-11-06 08:37:30 UTC; ASUS
Date/Publication: 2024-11-08 14:30:06 UTC

More information about DTSR at CRAN
Permanent link

Package collinear updated to version 2.0.0 with previous version 1.1.1 dated 2023-12-08

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(-)

More information about collinear at CRAN
Permanent link

Package finnsurveytext updated to version 2.1.0 with previous version 2.0.0 dated 2024-08-27

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(-)

More information about finnsurveytext at CRAN
Permanent link

Package CITMIC updated to version 0.1.2 with previous version 0.1.1 dated 2024-09-17

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(-)

More information about CITMIC at CRAN
Permanent link

Package model4you updated to version 0.9-8 with previous version 0.9-7 dated 2021-01-20

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(-)

More information about model4you at CRAN
Permanent link

Package mlr3filters updated to version 0.8.1 with previous version 0.8.0 dated 2024-04-10

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(-)

More information about mlr3filters at CRAN
Permanent link

Package minty updated to version 0.0.4 with previous version 0.0.1 dated 2024-05-22

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(-)

More information about minty at CRAN
Permanent link

Package flowchart updated to version 0.6.0 with previous version 0.5.1 dated 2024-09-27

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(-)

More information about flowchart at CRAN
Permanent link

Package archive updated to version 1.1.10 with previous version 1.1.9 dated 2024-09-12

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(-)

More information about archive at CRAN
Permanent link

Package admix updated to version 2.3.3 with previous version 2.3.2 dated 2024-11-05

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(-)

More information about admix at CRAN
Permanent link

Package movieROC updated to version 0.1.2 with previous version 0.1.1 dated 2024-06-28

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(-)

More information about movieROC at CRAN
Permanent link

Package lpSolve updated to version 5.6.22 with previous version 5.6.21 dated 2024-09-12

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(-)

More information about lpSolve at CRAN
Permanent link

Package knitr updated to version 1.49 with previous version 1.48 dated 2024-07-07

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(-)

More information about knitr at CRAN
Permanent link

Package dimensio updated to version 0.10.0 with previous version 0.9.0 dated 2024-08-26

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(-)

More information about dimensio at CRAN
Permanent link

Package DescTools updated to version 0.99.58 with previous version 0.99.57 dated 2024-09-25

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(-)

More information about DescTools at CRAN
Permanent link

Package descriptr updated to version 0.6.0 with previous version 0.5.2 dated 2020-12-09

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(-)

More information about descriptr at CRAN
Permanent link

Package CTxCC updated to version 0.2.0 with previous version 0.1.0 dated 2024-10-25

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(-)

More information about CTxCC at CRAN
Permanent link

Package BiplotGUI updated to version 0.0-12 with previous version 0.0-7 dated 2013-03-19

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(-)

More information about BiplotGUI at CRAN
Permanent link

Package bayesTFR updated to version 7.4-4 with previous version 7.4-2 dated 2023-10-18

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(-)

More information about bayesTFR at CRAN
Permanent link

Package ranger updated to version 0.17.0 with previous version 0.16.0 dated 2023-11-12

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(-)

More information about ranger at CRAN
Permanent link

Package rTwig updated to version 1.2.0 with previous version 1.1.0 dated 2024-08-20

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(-)

More information about rTwig at CRAN
Permanent link


Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.