Title: Deploy Docs, Apps, and APIs to 'Posit Connect', 'shinyapps.io',
and 'RPubs'
Description: Programmatic deployment interface for 'RPubs',
'shinyapps.io', and 'Posit Connect'. Supported content types include R
Markdown documents, Shiny applications, Plumber APIs, plots, and
static web content.
Author: Aron Atkins [aut, cre],
Toph Allen [aut],
Hadley Wickham [aut],
Jonathan McPherson [aut],
JJ Allaire [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Aron Atkins <aron@posit.co>
Diff between rsconnect versions 1.1.1 dated 2023-10-04 and 1.2.0 dated 2023-12-14
DESCRIPTION | 6 MD5 | 48 - NEWS.md | 21 R/account-find.R | 3 R/accounts.R | 16 R/applications.R | 23 R/configureApp.R | 15 R/deployApp.R | 107 +-- R/deploymentTarget.R | 368 ++++++++--- R/deployments-find.R | 21 R/deployments.R | 27 R/rpubs.R | 11 man/deployApp.Rd | 9 man/deploySite.Rd | 5 man/showProperties.Rd | 2 tests/testthat/_snaps/deploymentTarget.md | 43 - tests/testthat/_snaps/deployments-find.md | 9 tests/testthat/helper.R | 2 tests/testthat/quarto-proj-r-shiny/quarto-proj-r-shiny.qmd | 8 tests/testthat/test-accounts.R | 46 + tests/testthat/test-client-cloud.R | 21 tests/testthat/test-deployApp.R | 2 tests/testthat/test-deploymentTarget.R | 410 ++++++++++--- tests/testthat/test-deployments-find.R | 31 tests/testthat/test-deployments.R | 13 25 files changed, 941 insertions(+), 326 deletions(-)
Title: Monochrome Bitmap Font Tools
Description: Provides functions for creating and modifying bitmaps with special emphasis on bitmap fonts and their glyphs. Provides native read/write support for the 'hex' and 'yaff' bitmap font formats and if 'Python' is installed can also read/write several more bitmap font formats using an embedded version of 'monobit'.
Author: Trevor L Davis [aut, cre] ,
Rob Hagemans [cph] ,
Frederic Cambus [cph]
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between bittermelon versions 1.1.1 dated 2023-02-12 and 1.1.2 dated 2023-12-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 9 +++++++++ R/utils-unicode.R | 7 ++++--- README.md | 2 +- 5 files changed, 22 insertions(+), 12 deletions(-)
Title: 'STK++' Core Library Integration to 'R' using 'Rcpp'
Description: 'STK++' <http://www.stkpp.org> is a collection of C++ classes
for statistics, clustering, linear algebra, arrays (with an 'Eigen'-like API),
regression, dimension reduction, etc. The integration of the library to 'R' is
using 'Rcpp'. The 'rtkore' package includes the header files from the 'STK++'
core library. All files contain only template classes and/or inline functions.
'STK++' is licensed under the GNU LGPL version 2 or later. 'rtkore' (the 'stkpp'
integration into 'R') is licensed under the GNU GPL version 2 or later. See file
LICENSE.note for details.
Author: Serge Iovleff [aut, cre],
Parmeet Bhatia [ctb]
Maintainer: Serge Iovleff <serge.iovleff@stkpp.org>
Diff between rtkore versions 1.6.7 dated 2022-10-25 and 1.6.10 dated 2023-12-14
rtkore-1.6.10/rtkore/DESCRIPTION | 8 +++---- rtkore-1.6.10/rtkore/MD5 | 19 ++++++++--------- rtkore-1.6.10/rtkore/build/vignette.rds |binary rtkore-1.6.10/rtkore/inst/NEWS.Rd | 6 +++++ rtkore-1.6.10/rtkore/inst/doc/rtkpp-Arrays.pdf |binary rtkore-1.6.10/rtkore/inst/doc/rtkpp-ArraysQuickRef.pdf |binary rtkore-1.6.10/rtkore/inst/doc/rtkpp-Introduction.pdf |binary rtkore-1.6.10/rtkore/inst/doc/rtkpp-Tips.pdf |binary rtkore-1.6.10/rtkore/inst/doc/rtkpp-Utilities.pdf |binary rtkore-1.6.10/rtkore/src/Makevars | 16 ++++---------- rtkore-1.6.10/rtkore/src/Makevars.win |only rtkore-1.6.7/rtkore/.Rinstignore |only 12 files changed, 25 insertions(+), 24 deletions(-)
Title: 'shiny' Widgets for 'teal' Applications
Description: Collection of 'shiny' widgets to support 'teal' applications.
Enables the manipulation of application layout and plot or table
settings.
Author: Dawid Kaledkowski [aut, cre],
Pawel Rucki [aut],
Mahmoud Hallal [aut],
Nikolas Burkoff [aut],
Maciej Nasinski [aut],
Konrad Pagacz [aut],
Junlue Zhao [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.widgets versions 0.4.1 dated 2023-10-10 and 0.4.2 dated 2023-12-14
DESCRIPTION | 14 +- MD5 | 52 +++++----- NAMESPACE | 1 NEWS.md | 7 + R/get_dt_rows.R | 2 R/nested_closeable_modal.R |only R/optionalInput.R | 2 R/plot_with_settings.R | 39 ++++--- R/table_with_settings.R | 4 R/utils.R | 13 ++ README.md | 6 - build/vignette.rds |binary inst/WORDLIST | 2 inst/doc/custom-basic-table-arguments.R | 2 inst/doc/custom-basic-table-arguments.Rmd | 2 inst/doc/custom-basic-table-arguments.html | 2 inst/doc/custom-ggplot2-arguments.R | 2 inst/doc/custom-ggplot2-arguments.Rmd | 2 inst/doc/custom-ggplot2-arguments.html | 2 man/get_dt_rows.Rd | 2 man/nested_closeable_modal.Rd |only man/optionalSelectInput.Rd | 2 man/plot_suppress.Rd |only man/plot_with_settings.Rd | 19 ++- man/table_with_settings.Rd | 2 tests/testthat/Rplots.pdf |only tests/testthat/_snaps/app_tws_ui/table_with_settings_ui/tws-final_values.json | 4 vignettes/custom-basic-table-arguments.Rmd | 2 vignettes/custom-ggplot2-arguments.Rmd | 2 29 files changed, 111 insertions(+), 76 deletions(-)
Title: Robust Linear Mixed Effects Models
Description: Implements the Robust Scoring Equations estimator to fit linear
mixed effects models robustly.
Robustness is achieved by modification of the scoring equations
combined with the Design Adaptive Scale approach.
Author: Manuel Koller
Maintainer: Manuel Koller <kollerma@proton.me>
Diff between robustlmm versions 3.2-5 dated 2023-11-14 and 3.3-1 dated 2023-12-14
DESCRIPTION | 8 - MD5 | 20 +-- R/AllClass.R | 1 R/accessors.R | 215 +++++++++++++++++++++++---------- R/fromLme4.R | 30 ++++ R/plot.R | 36 ++++- inst/doc/rlmer.pdf |binary inst/doc/simulationStudies.pdf |binary man/getME.Rd | 260 ++++++++++++++++++++++++----------------- man/plot.rlmerMod.Rd | 8 + tests/getME.Rout.save | 125 +++++++++++++++++-- 11 files changed, 487 insertions(+), 216 deletions(-)
Title: Projection Predictive Feature Selection
Description: Performs projection predictive feature selection for generalized linear
models (Piironen, Paasiniemi, and Vehtari, 2020, <doi:10.1214/20-EJS1711>)
with or without multilevel or additive terms (Catalina, Bürkner, and
Vehtari, 2022, <https://proceedings.mlr.press/v151/catalina22a.html>), for
some ordinal and nominal regression models (Weber, Glass, and Vehtari, 2023,
<arXiv:2301.01660>), and for many other regression models (using the latent
projection by Catalina, Bürkner, and Vehtari, 2021, <arXiv:2109.04702>,
which can also be applied to most of the former models). The package is
compatible with the 'rstanarm' and 'brms' packages, but other reference
models can also be used. See the vignettes and the documentation for more
information and examples.
Author: Juho Piironen [aut],
Markus Paasiniemi [aut],
Alejandro Catalina [aut],
Frank Weber [cre, aut],
Aki Vehtari [aut],
Jonah Gabry [ctb],
Marco Colombo [ctb],
Paul-Christian Buerkner [ctb],
Hamada S. Badr [ctb],
Brian Sullivan [ctb],
Soelvi Roegnvaldsson [c [...truncated...]
Maintainer: Frank Weber <fweber144@protonmail.com>
Diff between projpred versions 2.7.0 dated 2023-09-30 and 2.8.0 dated 2023-12-14
DESCRIPTION | 14 MD5 | 133 +- NAMESPACE | 6 NEWS.md | 42 R/augdat.R | 97 - R/cv_varsel.R | 611 ++++++++---- R/divergence_minimizers.R | 514 ++++++---- R/formula.R | 2 R/glmfun.R | 4 R/latent.R | 12 R/methods.R | 805 ++++++++++------ R/misc.R | 82 + R/project.R | 197 ++- R/projfun.R | 86 - R/projpred-package.R | 102 +- R/refmodel.R | 312 +++--- R/search.R | 90 + R/summary_funs.R | 152 +-- R/varsel.R | 206 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/latent.Rmd | 2 inst/doc/latent.html | 195 ++- inst/doc/projpred.R | 41 inst/doc/projpred.Rmd | 132 +- inst/doc/projpred.html | 786 +++++++++------ man/as.matrix.projection.Rd | 12 man/as_draws_matrix.projection.Rd | 4 man/augdat-internals.Rd | 18 man/cl_agg.Rd | 6 man/cv_varsel.Rd | 142 +- man/do_call.Rd | 6 man/force_search_terms.Rd | 2 man/performances.Rd |only man/plot.cv_proportions.Rd | 2 man/plot.vsel.Rd | 83 + man/pred-projection.Rd | 12 man/predictor_terms.Rd | 4 man/print.projection.Rd |only man/print.refmodel.Rd |only man/print.vsel.Rd | 7 man/print.vselsummary.Rd | 22 man/project.Rd | 42 man/projpred-package.Rd | 105 +- man/refmodel-init-get.Rd | 99 - man/run_cvfun.Rd | 44 man/suggest_size.Rd | 82 + man/summary.vsel.Rd | 62 - man/varsel.Rd | 68 - tests/testthat/helpers/args.R | 58 - tests/testthat/helpers/formul_handlers.R | 4 tests/testthat/helpers/getters.R | 9 tests/testthat/helpers/testers.R | 645 ++++++++---- tests/testthat/setup.R | 351 ++++-- tests/testthat/test_as_matrix.R | 42 tests/testthat/test_augdat.R | 260 ++--- tests/testthat/test_datafit.R | 109 +- tests/testthat/test_div_minimizer.R | 21 tests/testthat/test_glm_elnet.R | 2 tests/testthat/test_latent.R | 12 tests/testthat/test_methods_vsel.R | 120 +- tests/testthat/test_parallel.R | 11 tests/testthat/test_proj_pred.R | 593 ++++++----- tests/testthat/test_proj_predfun.R | 11 tests/testthat/test_project.R | 161 +-- tests/testthat/test_refmodel.R | 55 - tests/testthat/test_varsel.R | 1555 ++++++++++++++++++++++++++----- vignettes/latent.Rmd | 2 vignettes/projpred.Rmd | 132 +- 69 files changed, 6349 insertions(+), 3249 deletions(-)
Title: Get or Set UNIX Niceness
Description: Get or set UNIX priority (niceness) of running R process.
Author: Charles J. Geyer <geyer@umn.edu>.
Maintainer: Charles J. Geyer <geyer@umn.edu>
Diff between nice versions 0.4-1 dated 2016-11-28 and 0.4-2 dated 2023-12-14
CHANGES | 3 +++ DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- src/get_my_priority.c | 4 ++-- 4 files changed, 14 insertions(+), 11 deletions(-)
Title: Implementation of the Vegetation Model ModVege
Description: Run grass growth simulations using a grass growth model based
on ModVege (Jouven, M., P. Carrère, and R. Baumont "Model Predicting
Dynamics of Biomass, Structure and Digestibility of Herbage in Managed
Permanent Pastures. 1. Model Description." (2006)
<doi:10.1111/j.1365-2494.2006.00515.x>). The implementation in
this package contains a few additions to the above cited version of ModVege,
such as simulations of management decisions, and influences of snow cover.
As such, the model is fit to simulate grass growth in mountainous
regions, such as the Swiss Alps. The package also contains routines for
calibrating the model and helpful tools for analysing model outputs and
performance.
Author: Kevin Kramer [aut, cre, cph]
Maintainer: Kevin Kramer <kevin.pasqual.kramer@protonmail.ch>
Diff between growR versions 1.1.0 dated 2023-11-22 and 1.2.0 dated 2023-12-14
DESCRIPTION | 6 MD5 | 26 NEWS.md | 20 R/modvegesite.R | 51 R/setup.R | 3 R/support_functions.R | 15 R/weather.R | 16 build/partial.rdb |binary inst/REFERENCES.bib | 28 inst/doc/calibration.html | 33 inst/doc/growR.html | 59 man/WeatherData.Rd | 12 man/fCO2_transpiration_mod.Rd | 13 tests/testthat/_snaps/modvegesite/modvege_reference_output.dat | 592 +++++----- 14 files changed, 495 insertions(+), 379 deletions(-)
Title: Easily Install Pharmacometric Packages and Shiny Applications
Developed by Certara
Description: A convenient set of wrapper functions to install
pharmacometric packages and Shiny applications developed by Certara
PMX and Integrated Drug Development (iDD). The functions ensure the
successful installation of packages from non-standard repositories.
Author: James Craig [aut, cre],
Certara USA, Inc. [cph, fnd]
Maintainer: James Craig <james.craig@certara.com>
Diff between Certara.R versions 1.0.0 dated 2022-02-11 and 1.1.0 dated 2023-12-14
DESCRIPTION | 8 ++-- MD5 | 6 +-- R/install.R | 6 +-- README.md | 100 ++++++++++++++++++++++++++++++++++++++++++++++++++---------- 4 files changed, 94 insertions(+), 26 deletions(-)
Title: Analysing Convergent Evolution using the Wheatsheaf Index
Description: Analysing convergent evolution using the Wheatsheaf index, described in Arbuckle et al. (2014) <doi: 10.1111/2041-210X.12195>, and some other unrelated but perhaps useful functions.
Author: Kevin Arbuckle and Amanda Minter
Maintainer: Kevin Arbuckle <kevin.arbuckle@swansea.ac.uk>
Diff between windex versions 2.0.6 dated 2023-10-11 and 2.0.7 dated 2023-12-14
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NAMESPACE | 2 +- R/nodeDist.R | 5 ++++- R/test.windex.R | 7 ++++++- R/windex.sim.test.R | 9 +++++++-- man/nodeDist.Rd | 15 +++++++++++---- man/test.windex.Rd | 2 +- man/windex.Rd | 2 +- man/windex.sim.test.Rd | 2 +- 10 files changed, 45 insertions(+), 25 deletions(-)
More information about randomMachines at CRAN
Permanent link
Title: Probabilistic Suffix Trees and Variable Length Markov Chains
Description: Provides a framework for analysing state sequences with probabilistic suffix trees (PST), the construction that stores variable length Markov chains (VLMC). Besides functions for learning and optimizing VLMC models, the PST library includes many additional tools to analyse sequence data with these models: visualization tools, functions for sequence prediction and artificial sequences generation, as well as for context and pattern mining. The package is specifically adapted to the field of social sciences by allowing to learn VLMC models from sets of individual sequences possibly containing missing values, and by accounting for case weights. The library also allows to compute probabilistic divergence between two models, and to fit segmented VLMC, where sub-models fitted to distinct strata of the learning sample are stored in a single PST. This software results from research work executed within the framework of the Swiss National Centre of Competence in Research LIVES, which is finance [...truncated...]
Author: Alexis Gabadinho [aut, cre, cph]
Maintainer: Alexis Gabadinho <alexis.gabadinho@wanadoo.fr>
Diff between PST versions 0.94 dated 2017-02-03 and 0.94.1 dated 2023-12-14
DESCRIPTION | 9 ++++----- MD5 | 8 ++++---- data/SRH.RData |binary data/s1.rda |binary man/SRH-data.Rd | 2 +- 5 files changed, 9 insertions(+), 10 deletions(-)
Title: Nonparametric Monotone Regression
Description: Estimates monotone regression and variance functions in a nonparametric model, based on Dette, Holger, Neumeyer, and Pilz (2006) <doi:10.3150/bj/1151525131>.
Author: This version Kay Pilz and Steffanie Titoff. Earlier
developements by Holger Dette and Kay Pilz.
Maintainer: Scott Kostyshak <scott.kostyshak@gmail.com>
Diff between monreg versions 0.1.4 dated 2020-04-26 and 0.1.4.1 dated 2023-12-14
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/monreg.r | 10 +++++----- R/monvardiff.r | 10 +++++----- R/monvarresid.r | 10 +++++----- man/monreg.rd | 2 +- 6 files changed, 26 insertions(+), 26 deletions(-)
Title: GUI to Analyse qPCR Results after PMA Treatment or not
Description: Graphical User Interface allowing to determine the concentration in the sample in CFU per mL or in number of copies per mL provided to qPCR results after with or without PMA treatment. This package is simply to use because no knowledge in R commands is necessary. A graphic represents the standard curve, and a table containing the result for each sample is created.
Author: Olivier LE GOFF [aut, cre]
Maintainer: Olivier LE GOFF <olivierlegoff1@gmail.com>
Diff between InterfaceqPCR versions 1.0 dated 2017-04-01 and 1.0.1 dated 2023-12-14
DESCRIPTION | 9 ++++----- MD5 | 16 ++++++++-------- R/Interface_Chargement_Fichiers.R | 18 +++++++++--------- R/Start.R | 4 ++-- R/Start_Langue.R | 4 ++-- R/Start_select_qPCR_PMA_qPCR.R | 14 +++++++------- inst/doc/InterfaceqPCR-manual.pdf |binary man/InterfaceqPCR-package.Rd | 2 +- man/Start_qPCR.Rd | 2 +- 9 files changed, 34 insertions(+), 35 deletions(-)
Title: Classic Gamma Regression: Joint Modeling of Mean and Shape
Parameters
Description: Performs Gamma regression, where both mean and shape parameters follows lineal regression structures.
Author: Martha Corrales and Edilberto Cepeda-Cuervo, with the colaboration of Margarita Marin, Maria Fernanda Zarate, Ricardo Duplat and Campo Elias Pardo.
Maintainer: Martha Corrales <martha.corrales@usa.edu.co>
Diff between Gammareg versions 3.0 dated 2020-06-19 and 3.0.1 dated 2023-12-14
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- man/Gammareg.Rd | 4 ++-- man/gammahetero1.Rd | 4 ++-- man/gammahetero2.Rd | 4 ++-- man/print.Gammareg.Rd | 4 ++-- man/print.summary.Gammareg.Rd | 4 ++-- man/summaryGammareg.Rd | 4 ++-- 8 files changed, 23 insertions(+), 23 deletions(-)
Title: Partial Frontier Efficiency Analysis
Description: It calculates the alpha-quantile proposed by Daouia and Simar (2007) <doi:10.1016/j.jeconom.2006.07.002> and order-m efficiency score in multi-dimension proposed by Daouia and Gijbels (2011) <doi:10.1016/j.jeconom.2010.12.002> and computes several summaries and representation of the associated frontiers in 2d and 3d.
Author: Thibault Laurent [aut, cre, cph],
Abdelaati Daouia [aut]
Maintainer: Thibault Laurent <thibault.laurent@univ-tlse1.fr>
Diff between frontiles versions 1.3 dated 2023-04-02 and 1.3.1 dated 2023-12-14
DESCRIPTION | 7 +++---- MD5 | 10 +++++----- build/vignette.rds |binary data/burposte.rda |binary data/spain.rda |binary inst/doc/frontiles1.pdf |binary 6 files changed, 8 insertions(+), 9 deletions(-)
Title: Bayesian t Regression for Modeling Mean and Scale Parameters
Description: Performs Bayesian t Regression where mean and scale parameters are modeling by lineal regression structures, and the degrees of freedom parameters are estimated.
Author: Margarita Marin and Edilberto Cepeda-Cuervo.
Maintainer: Margarita Marin <mmarinj@unal.edu.co>
Diff between Bayesiantreg versions 1.0 dated 2022-01-18 and 1.0.1 dated 2023-12-14
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/BayesiantregEst.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Rmetrics - Chronological and Calendar Objects
Description: The 'timeDate' class fulfils the conventions of the ISO 8601
standard as well as of the ANSI C and POSIX standards. Beyond
these standards it provides the "Financial Center" concept
which allows to handle data records collected in different time
zones and mix them up to have always the proper time stamps with
respect to your personal financial center, or alternatively to the GMT
reference time. It can thus also handle time stamps from historical
data records from the same time zone, even if the financial
centers changed day light saving times at different calendar
dates.
Author: Diethelm Wuertz [aut] ,
Tobias Setz [aut],
Yohan Chalabi [aut],
Martin Maechler [ctb] ,
Joe W. Byers [ctb],
Georgi N. Boshnakov [cre, aut]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between timeDate versions 4022.108 dated 2023-01-07 and 4032.109 dated 2023-12-14
timeDate-4022.108/timeDate/R/namespace-tags.R |only timeDate-4032.109/timeDate/DESCRIPTION | 11 timeDate-4032.109/timeDate/MD5 | 62 timeDate-4032.109/timeDate/NAMESPACE | 1307 ++++---- timeDate-4032.109/timeDate/NEWS.md | 95 timeDate-4032.109/timeDate/R/base-summary.R | 47 timeDate-4032.109/timeDate/R/base-weekdays.R | 105 timeDate-4032.109/timeDate/R/calendar-Easter.R | 115 timeDate-4032.109/timeDate/R/holiday-Dates.R | 1500 ++++------ timeDate-4032.109/timeDate/R/holiday-LONDON.R | 217 - timeDate-4032.109/timeDate/R/holiday-Listing.R | 14 timeDate-4032.109/timeDate/R/holiday-NYSE.R | 52 timeDate-4032.109/timeDate/R/methods-plot.R | 35 timeDate-4032.109/timeDate/R/stats-window.R | 2 timeDate-4032.109/timeDate/R/sysdata.rda |binary timeDate-4032.109/timeDate/R/timeDate-midnightStandard.R | 45 timeDate-4032.109/timeDate/R/timeDate-whichFormat.R | 32 timeDate-4032.109/timeDate/R/timeDate.R | 215 - timeDate-4032.109/timeDate/inst/pkgdown.yml | 2 timeDate-4032.109/timeDate/inst/unitTests/holidayLONDON_1834_to_2024_corrected.rds |only timeDate-4032.109/timeDate/inst/unitTests/runit.Class.R | 4 timeDate-4032.109/timeDate/inst/unitTests/runit.HolidayCalendars.R | 6 timeDate-4032.109/timeDate/inst/unitTests/runit.HolidayDates.R | 13 timeDate-4032.109/timeDate/man/00timeDate-package.Rd | 35 timeDate-4032.109/timeDate/man/base-rev.Rd | 9 timeDate-4032.109/timeDate/man/base-summary.Rd | 44 timeDate-4032.109/timeDate/man/earlyCloseNYSE.Rd |only timeDate-4032.109/timeDate/man/graphics-plot.Rd | 2 timeDate-4032.109/timeDate/man/holiday-Dates.Rd | 556 ++- timeDate-4032.109/timeDate/man/holiday-LONDON.Rd | 23 timeDate-4032.109/timeDate/man/holiday-NYSE.Rd | 4 timeDate-4032.109/timeDate/man/holiday.Rd | 2 timeDate-4032.109/timeDate/man/methods-mathOps.Rd | 60 timeDate-4032.109/timeDate/man/specialHolidayGB.Rd |only 34 files changed, 2391 insertions(+), 2223 deletions(-)
Title: Packages and Functions for 'CourseKata' Courses
Description: Easily install and load all packages and functions used in
'CourseKata' courses. Aid teaching with helper functions and augment
generic functions to provide cohesion between the network of packages.
Learn more about 'CourseKata' at <https://coursekata.org>.
Author: Adam Blake [cre, aut] ,
Ji Son [aut] ,
Jim Stigler [aut]
Maintainer: Adam Blake <adam@coursekata.org>
Diff between coursekata versions 0.14.1 dated 2023-10-27 and 0.15.0 dated 2023-12-14
coursekata-0.14.1/coursekata/data/Fingers.messy.rda |only coursekata-0.14.1/coursekata/man/Fingers.messy.Rd |only coursekata-0.15.0/coursekata/DESCRIPTION | 16 ++++---- coursekata-0.15.0/coursekata/MD5 | 20 +++++----- coursekata-0.15.0/coursekata/NEWS.md | 4 ++ coursekata-0.15.0/coursekata/R/data.R | 2 - coursekata-0.15.0/coursekata/README.md | 10 ++--- coursekata-0.15.0/coursekata/build/partial.rdb |binary coursekata-0.15.0/coursekata/data/FingersMessy.rda |only coursekata-0.15.0/coursekata/man/FingersMessy.Rd |only coursekata-0.15.0/coursekata/man/coursekata-package.Rd | 6 +-- coursekata-0.15.0/coursekata/man/figures/README-samp_dist_of_b1-1.png |binary coursekata-0.15.0/coursekata/man/figures/README-samp_dist_of_hp-1.png |binary 13 files changed, 31 insertions(+), 27 deletions(-)
Title: Aster Models
Description: Aster models (Geyer, Wagenius, and Shaw, 2007,
<doi:10.1093/biomet/asm030>; Shaw, Geyer, Wagenius, Hangelbroek, and
Etterson, 2008, <doi:10.1086/588063>; Geyer, Ridley, Latta, Etterson,
and Shaw, 2013, <doi:10.1214/13-AOAS653>) are exponential family
regression models for life
history analysis. They are like generalized linear models except that
elements of the response vector can have different families (e. g.,
some Bernoulli, some Poisson, some zero-truncated Poisson, some normal)
and can be dependent, the dependence indicated by a graphical structure.
Discrete time survival analysis, life table analysis,
zero-inflated Poisson regression, and
generalized linear models that are exponential family (e. g., logistic
regression and Poisson regression with log link) are special cases.
Main use is for data in which there is survival over discrete time periods
and there is additional data about what happens conditional on survival
(e. g., number of offspring). Uses the ex [...truncated...]
Author: Charles J. Geyer <geyer@umn.edu>
Maintainer: Charles J. Geyer <geyer@umn.edu>
Diff between aster versions 1.1-2 dated 2021-06-13 and 1.1-3 dated 2023-12-14
CHANGES | 2 ++ DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/linkingTo.pdf |binary inst/doc/re.pdf |binary inst/doc/trunc.pdf |binary inst/doc/tutor.pdf |binary src/raster.c | 2 +- 10 files changed, 18 insertions(+), 16 deletions(-)
Title: Detecting Influence Paths with Information Theory
Description: Traces information spread through interactions between features, utilising information theory measures and a higher-order generalisation of the concept of widest paths in graphs.
In particular, 'vistla' can be used to better understand the results of high-throughput biomedical experiments, by organising the effects of the investigated intervention in a tree-like hierarchy from direct to indirect ones, following the plausible information relay circuits.
Due to its higher-order nature, 'vistla' can handle multi-modality and assign multiple roles to a single feature.
Author: Miron B. Kursa [aut, cre]
Maintainer: Miron B. Kursa <m@mbq.me>
Diff between vistla versions 2.0.0 dated 2023-10-04 and 2.0.1 dated 2023-12-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- inst/NEWS | 6 ++++++ src/heap.h | 4 ++-- src/vistla.h | 4 +++- 5 files changed, 18 insertions(+), 10 deletions(-)
Title: Multivariate Normal Mixture Models and Mixtures of Generalized
Linear Mixed Models Including Model Based Clustering
Description: Contains a mixture of statistical methods including the MCMC methods to analyze normal mixtures. Additionally, model based clustering methods are implemented to perform classification based on (multivariate) longitudinal (or otherwise correlated) data. The basis for such clustering is a mixture of multivariate generalized linear mixed models.
Author: Arnost Komarek [aut, cre]
Maintainer: Arnost Komarek <arnost.komarek@mff.cuni.cz>
Diff between mixAK versions 5.6 dated 2023-09-25 and 5.7 dated 2023-12-14
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NEWS | 3 +++ build/partial.rdb |binary data/Acidity.rda |binary data/Enzyme.rda |binary data/Galaxy.rda |binary src/AK_Basic.h | 12 +++++++++--- src/GLMM_MCMC.cpp | 3 ++- src/GLMM_NMixRelabel.cpp | 3 ++- src/GLMM_dY_meanY.cpp | 3 ++- src/NMix_NMixRelabel.cpp | 3 ++- 12 files changed, 36 insertions(+), 23 deletions(-)
Title: 'REDCap' Data Management
Description: Access and manage 'REDCap' data. 'REDCap' (Research Electronic Data CAPture; <https://projectredcap.org>) is a web application for building and managing online surveys and databases developed at Vanderbilt University. The API allows users to programmatic access data and project meta data (such as the data dictionary) from the web. This package allows us to read 'REDCap' data, exported or using an API connection, identify missing or extreme values, identify missing 'REDCap' events in each observation, do a follow-up of the queries initially identified and it also facilitates the process of data management.
Author: Joao Carmezim [aut, cre],
Pau Satorra [aut],
Judith Penafiel [aut],
Esther Garcia [aut],
Natalia Pallares [aut],
Cristian Tebe [aut]
Maintainer: Joao Carmezim <jcarmezim@igtp.cat>
Diff between REDCapDM versions 0.8.5 dated 2023-12-05 and 0.9.0 dated 2023-12-14
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 11 +++++++++++ R/rd_transform.R | 9 +++++++-- R/redcap_data.R | 21 ++++++++++++++++++--- man/redcap_data.Rd | 5 ++++- 6 files changed, 48 insertions(+), 14 deletions(-)
Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation
models via the most likely transformation approach described in
Hothorn et al. (2018) <DOI:10.1111/sjos.12291> and Hothorn (2020)
<DOI:10.18637/jss.v092.i01>.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt versions 1.4-9 dated 2023-08-21 and 1.5-0 dated 2023-12-14
DESCRIPTION | 8 ++-- MD5 | 10 ++--- R/R.R | 6 ++- R/mlt.R | 106 ++++++++++++++++++++++++++++++++++++++++++++++++++---- build/partial.rdb |binary inst/NEWS.Rd | 16 ++++++++ 6 files changed, 130 insertions(+), 16 deletions(-)
Title: Dereplicate and Cherry-Pick Mass Spectrometry Spectra
Description: Convenient wrapper functions for the analysis of
matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF)
spectra data in order to select only representative spectra (also
called cherry-pick). The package covers the preprocessing and
dereplication steps (based on Strejcek, Smrhova, Junkova and Uhlik
(2018) <doi:10.3389/fmicb.2018.01294>) needed to cluster MALDI-TOF
spectra before the final cherry-picking step. It enables the easy
exclusion of spectra and/or clusters to accommodate complex
cherry-picking strategies. Alternatively, cherry-picking using
taxonomic identification MALDI-TOF data is made easy with functions to
import inconsistently formatted reports.
Author: Charlie Pauvert [aut, cre, cph]
,
David Wylensek [ctb] ,
Selina Nuechtern [ctb],
Thomas Clavel [ctb, fnd, cph]
Maintainer: Charlie Pauvert <cpauvert@ukaachen.de>
Diff between maldipickr versions 1.2.0 dated 2023-10-25 and 1.3.0 dated 2023-12-14
DESCRIPTION | 10 ++-- MD5 | 39 +++++++++++-------- NAMESPACE | 3 + NEWS.md | 19 +++++++++ R/check_spectra.R | 12 +---- R/get_spectra_names.R |only R/maldipickr-package.R | 1 R/merge_processed_spectra.R | 7 ++- R/process_spectra.R | 38 +++++++++--------- R/remove_spectra.R |only R/remove_spectra_logical.R |only inst/doc/dereplicate-bruker-maldi-biotyper-spectra.R | 2 inst/doc/import-data-from-bruker-maldi-biotyper.R | 2 inst/doc/import-data-from-bruker-maldi-biotyper.html | 12 ++--- man/figures/lifecycle-deprecated.svg |only man/get_spectra_names.Rd |only man/merge_processed_spectra.Rd | 2 man/process_spectra.Rd | 10 +++- man/remove_spectra.Rd |only tests/testthat/test-check_spectra.R | 10 ++-- tests/testthat/test-get_spectra_names.R |only tests/testthat/test-merge_processed_spectra.R | 14 +++--- tests/testthat/test-process_spectra.R | 24 ++++++++++- tests/testthat/test-remove_spectra.R |only tests/testthat/test-remove_spectra_logical.R |only 25 files changed, 131 insertions(+), 74 deletions(-)
Title: Computation of Tree (Im)Balance Indices
Description: The aim of the 'R' package 'treebalance' is to provide functions for the computation of
a large variety of (im)balance indices for rooted trees. The package accompanies the book
''Tree balance indices: a comprehensive survey'' by M. Fischer, L. Herbst, S. Kersting,
L. Kuehn and K. Wicke (2023) <ISBN: 978-3-031-39799-8>, <doi:10.1007/978-3-031-39800-1>, which gives a precise definition for the terms 'balance index' and 'imbalance index' (Chapter 4)
and provides an overview of the terminology in this manual (Chapter 2). For further information
on (im)balance indices, see also Fischer et al. (2021) <https://treebalance.wordpress.com>.
Considering both established and new (im)balance indices, 'treebalance' provides (among
others) functions for calculating the following 18 established indices and index families: the
average leaf depth, the B1 and B2 index, the Colijn-Plazzotta rank, the normal, corrected,
quadratic and equal weights Colless index, the family of Colless-lik [...truncated...]
Author: Mareike Fischer [aut],
Lina Herbst [aut],
Sophie Kersting [aut],
Luise Kuehn [aut, cre],
Kristina Wicke [aut]
Maintainer: Luise Kuehn <treebalanceindices@gmail.com>
Diff between treebalance versions 1.1.0 dated 2021-10-17 and 1.2.0 dated 2023-12-14
DESCRIPTION | 50 - MD5 | 124 ++-- NAMESPACE | 6 NEWS.md | 21 R/B1I.R | 100 +-- R/B2I.R | 137 ++-- R/IbasedI.R | 296 ++++----- R/areaPerPairI.R | 82 +- R/auxFuncs.R | 1567 +++++++++++++++++++++++++-------------------------- R/avgLeafDepI.R | 83 +- R/avgVertDep.R |only R/cherryI.R | 94 +-- R/colPlaLab.R | 159 ++--- R/colPlaLab_inv.R | 90 +- R/collessI.R | 164 ++--- R/collesslikeI.R | 234 +++---- R/ewCollessI.R | 96 +-- R/furnasI.R | 87 +- R/furnasI_inv.R | 140 ++-- R/mCherryI.R |only R/mWovermD.R |only R/maxDelW.R | 93 +-- R/maxDepth.R | 84 +- R/maxWidth.R | 74 +- R/rQuartetI.R | 200 +++--- R/rogersI.R | 110 +-- R/sShapeI.R | 78 +- R/sackinI.R | 72 +- R/stairs1.R | 78 +- R/stairs2.R | 106 +-- R/symNodesI.R | 126 ++-- R/totCophI.R | 82 +- R/totIntPathLen.R |only R/totPathLen.R |only R/varLeafDepI.R | 86 +- R/weighL1dist.R | 100 +-- man/B1I.Rd | 4 man/B2I.Rd | 15 man/IbasedI.Rd | 24 man/areaPerPairI.Rd | 6 man/auxFuncs.Rd | 2 man/avgLeafDepI.Rd | 3 man/avgVertDep.Rd |only man/cherryI.Rd | 4 man/colPlaLab.Rd | 32 - man/colPlaLab_inv.Rd | 8 man/collessI.Rd | 12 man/collesslikeI.Rd | 6 man/ewCollessI.Rd | 4 man/furnasI.Rd | 11 man/furnasI_inv.Rd | 6 man/mCherryI.Rd |only man/mWovermD.Rd |only man/maxDelW.Rd | 30 man/maxDepth.Rd | 12 man/maxWidth.Rd | 12 man/rQuartetI.Rd | 38 - man/rogersI.Rd | 4 man/sShapeI.Rd | 4 man/sackinI.Rd | 6 man/stairs1.Rd | 6 man/stairs2.Rd | 6 man/symNodesI.Rd | 6 man/totCophI.Rd | 8 man/totIntPathLen.Rd |only man/totPathLen.Rd |only man/varLeafDepI.Rd | 6 man/weighL1dist.Rd | 6 68 files changed, 2608 insertions(+), 2492 deletions(-)
More information about SweepDiscovery at CRAN
Permanent link
Title: Estimating the Sample Mean and Standard Deviation from Commonly
Reported Quantiles in Meta-Analysis
Description: Implements the methods of McGrath et al. (2020)
<doi:10.1177/0962280219889080> and Cai et al. (2021)
<doi:10.1177/09622802211047348> for estimating the sample mean and standard
deviation from commonly reported quantiles in meta-analysis. These methods
can be applied to studies that report the sample median, sample size, and
one or both of (i) the sample minimum and maximum values and (ii) the first
and third quartiles. The corresponding standard error estimators described
by McGrath et al. (2023) <doi:10.1177/09622802221139233> are also included.
Author: Sean McGrath [aut, cre] ,
XiaoFei Zhao [aut],
Russell Steele [aut],
Andrea Benedetti [aut]
Maintainer: Sean McGrath <sean.mcgrath@mail.mcgill.ca>
Diff between estmeansd versions 1.0.0 dated 2022-06-18 and 1.0.1 dated 2023-12-14
DESCRIPTION | 11 +++---- MD5 | 20 ++++++------ NEWS.md | 5 +++ R/bc.helper.functions.R | 10 +++--- R/boot.R | 8 ++--- R/mln.mean.sd.R | 2 - README.md | 72 +++++++++++++++++++++++++++++++++++----------- man/get_SE.Rd | 2 - man/get_SE.bc.mean.sd.Rd | 2 - man/get_SE.mln.mean.sd.Rd | 2 - man/get_SE.qe.mean.sd.Rd | 2 - 11 files changed, 90 insertions(+), 46 deletions(-)
Title: Dynamic Survey Sampling Solutions
Description: A robust solution employing both systematic and PPS
(Probability Proportional to Size) sampling methods, ensuring a
methodical and representative selection of data. Seamlessly allocate
predetermined allocations to smaller levels. Kish, L. (1965)
<https://books.google.co.id/books?id=xiZmAAAAIAAJ>.
Author: Choerul Afifanto [aut, cre, cph]
Maintainer: Choerul Afifanto <choerulafifanto@gmail.com>
Diff between samplingin versions 1.0.1 dated 2023-12-04 and 1.0.3 dated 2023-12-14
DESCRIPTION | 18 ++++++++++-------- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/samplingin.R | 25 ++++++++++++++++++++----- man/doSampling.Rd | 2 +- 5 files changed, 39 insertions(+), 18 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-01-05 0.8.0
2022-12-03 0.7.0
2022-08-24 0.6.0
2022-07-05 0.5.0
2022-01-22 0.4.0
2021-12-11 0.3.0
2021-09-06 0.2.0
2021-08-10 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-29 1.0.1
2023-11-28 1.0.0