Title: A Power Analysis Toolbox to Find Cost-Efficient Study Designs
Description: We implement a surrogate modeling algorithm to guide simulation-based
sample size planning. The method is described in detail in a recent preprint
(Zimmer & Debelak (2022) <doi:10.31234/osf.io/tnhb2>).
It supports multiple study design parameters and optimization with respect to a
cost function. It can find optimal designs that correspond to a desired
statistical power or that fulfill a cost constraint.
Author: Felix Zimmer [aut, cre] ,
Rudolf Debelak [aut]
Maintainer: Felix Zimmer <felix.zimmer@mail.de>
Diff between mlpwr versions 1.0.0 dated 2022-10-14 and 1.0.1 dated 2023-07-07
DESCRIPTION | 8 MD5 | 24 - NEWS.md | 6 R/find.design.R | 486 +++++++++++------------ R/fit.surrogate.R | 578 ++++++++++++++-------------- R/get.pred.R | 10 R/helper.R | 2 README.md | 14 build/vignette.rds |binary inst/doc/simulation_functions.Rmd | 760 ++++++++++++++++++------------------- inst/doc/simulation_functions.html | 477 +++++++++++------------ man/plot.designresult.Rd | 90 ++-- vignettes/simulation_functions.Rmd | 760 ++++++++++++++++++------------------- 13 files changed, 1617 insertions(+), 1598 deletions(-)
Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre] ,
Hadley Wickham [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Kevin Ushey <kevin@rstudio.com>
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Title: Methods to Create Hierarchical Age Length Keys for Age
Assignment
Description: Provides methods for implementing hierarchical age length keys
to estimate fish ages from lengths using data borrowing. Users can create
hierarchical age length keys and use them to assign ages given length.
Author: Paul Frater [aut, cre]
Maintainer: Paul Frater <paul.frater@wisconsin.gov>
Diff between halk versions 0.0.1 dated 2023-02-13 and 0.0.3 dated 2023-07-07
DESCRIPTION | 8 +-- MD5 | 25 +++++------ NAMESPACE | 4 + R/assess_age_models.R | 98 +++++++++++++++++++++++++++++++++++++++++++- R/fit_age_model.R | 4 - R/imports.R | 4 + R/predict_ages.R | 32 +++++++------- R/utils.R | 26 +++++++---- build/vignette.rds |binary inst/doc/halk.html | 92 ++++++++++++++++++++--------------------- man/integral_quotient.Rd |only man/make_alk.Rd | 5 -- man/min_samples.Rd | 5 -- tests/testthat/test-utils.R | 24 +++++++++- 14 files changed, 230 insertions(+), 97 deletions(-)
Title: Safely Access the RStudio API
Description: Access the RStudio API (if available) and provide informative error
messages when it's not.
Author: Kevin Ushey [aut, cre],
JJ Allaire [aut],
Hadley Wickham [aut],
Gary Ritchie [aut],
RStudio [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between rstudioapi versions 0.14 dated 2022-08-22 and 0.15.0 dated 2023-07-07
DESCRIPTION | 14 +++--- MD5 | 34 ++++++++-------- NAMESPACE | 1 NEWS.md | 6 ++ R/auth.R |only R/dictionaries.R | 6 -- R/launcher-functions.R | 2 build/vignette.rds |binary inst/doc/dialogs.html | 42 ++++++++++---------- inst/doc/document-manipulation.html | 62 +++++++++++++++--------------- inst/doc/projects.html | 16 +++---- inst/doc/r-session.html | 60 ++++++++++++++--------------- inst/doc/terminal.Rmd | 2 inst/doc/terminal.html | 74 ++++++++++++++++++------------------ inst/doc/visual-mode.html | 14 +++--- man/dictionaries.Rd | 6 -- man/getDelegatedAzureToken.Rd |only man/launcherSubmitJob.Rd | 2 vignettes/terminal.Rmd | 2 19 files changed, 171 insertions(+), 172 deletions(-)
Title: Support Compatibility Between 'Maelstrom' R Packages and 'Opal'
Environment
Description: The goal of this package is to provide functions to support
compatibility between 'Maelstrom' R packages and 'Opal' environment.
'Opal' is the 'OBiBa' core database application for biobanks. It is used
to build data repositories that integrates data collected from multiple
sources. 'Opal Maelstrom' is a specific implementation of this software.
This 'Opal' client is specifically designed to interact with
'Opal Maelstrom' distributions to perform operations on the R server side.
The user must have adequate credentials.
Please see <https://opaldoc.obiba.org/en/dev/> for complete documentation.
Author: Guillaume Fabre [aut, cre, cph]
,
Maelstrom-research group [cph, fnd],
OBiBa group [ctb]
Maintainer: Guillaume Fabre <guijoseph.fabre@gmail.com>
Diff between mlstrOpalr versions 1.0.0 dated 2023-06-23 and 1.0.1 dated 2023-07-07
DESCRIPTION | 6 +++--- MD5 | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)
Title: Bayes Screening and Model Discrimination
Description: Bayes screening and model discrimination follow-up designs.
Author: Ernesto Barrios based on Daniel Meyer's code.
Maintainer: Ernesto Barrios <ebarrios@itam.mx>
Diff between BsMD versions 2020.4.30 dated 2020-04-30 and 2023.707 dated 2023-07-07
BsMD-2020.4.30/BsMD/src/init.c |only BsMD-2023.707/BsMD/DESCRIPTION | 12 BsMD-2023.707/BsMD/MD5 | 54 +-- BsMD-2023.707/BsMD/NAMESPACE | 2 BsMD-2023.707/BsMD/R/BsProb.R | 166 +++++------ BsMD-2023.707/BsMD/R/DanielPlot.R | 212 +++++++------- BsMD-2023.707/BsMD/R/LenthPlot.R | 106 +++---- BsMD-2023.707/BsMD/R/MD.R | 154 +++++----- BsMD-2023.707/BsMD/R/plot.BsProb.R | 82 ++--- BsMD-2023.707/BsMD/R/print.BsProb.R | 152 +++++----- BsMD-2023.707/BsMD/R/print.MD.R | 108 +++---- BsMD-2023.707/BsMD/R/summary.BsProb.R | 112 +++---- BsMD-2023.707/BsMD/R/summary.MD.R | 60 ++-- BsMD-2023.707/BsMD/build/vignette.rds |binary BsMD-2023.707/BsMD/data/BM86.data.rda |binary BsMD-2023.707/BsMD/data/BM93.e1.data.rda |binary BsMD-2023.707/BsMD/data/BM93.e2.data.rda |binary BsMD-2023.707/BsMD/data/BM93.e3.data.rda |binary BsMD-2023.707/BsMD/data/PB12Des.rda |binary BsMD-2023.707/BsMD/data/Reactor.data.rda |binary BsMD-2023.707/BsMD/inst/doc/BsMD.R | 14 BsMD-2023.707/BsMD/inst/doc/BsMD.Rnw | 21 + BsMD-2023.707/BsMD/inst/doc/BsMD.pdf |binary BsMD-2023.707/BsMD/man/BsMD-package.Rd | 4 BsMD-2023.707/BsMD/man/BsProb.Rd | 3 BsMD-2023.707/BsMD/man/MD.Rd | 3 BsMD-2023.707/BsMD/src/BsMD_init.c |only BsMD-2023.707/BsMD/src/bsmd.f | 461 +++++++++++++++++++------------ BsMD-2023.707/BsMD/vignettes/BsMD.Rnw | 21 + 29 files changed, 938 insertions(+), 809 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 1.0.1 dated 2022-11-23 and 1.1.0 dated 2023-07-07
DESCRIPTION | 10 - MD5 | 37 ++-- NAMESPACE | 5 R/export.R | 2 R/extract.R | 2 R/paths.R | 2 R/plot.R | 370 ++++++++++++++++++++++++++++++++++++++------ R/prune.R | 3 R/vistla.R | 74 ++++++++ inst/NEWS | 5 man/branches.Rd | 2 man/flow.Rd |only man/mi_scores.Rd | 2 man/plot.vistla.Rd | 67 +++++++ man/vistla.Rd | 14 - man/write.dot.Rd | 2 src/heap.h | 46 +++++ src/vistla.h | 83 ++++++--- tests/testthat/test-algo.R | 15 + tests/testthat/test-tools.R | 28 +++ 20 files changed, 643 insertions(+), 126 deletions(-)
Title: Generate Code Lists for the OMOP Common Data Model
Description: Generate a candidate code list for the Observational Medical Outcomes Partnership (OMOP) common data model based on string matching. For a given search strategy, a candidate code list will be returned.
Author: Edward Burn [aut, cre] ,
Marti Catala [ctb]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CodelistGenerator versions 1.5.0 dated 2023-06-13 and 1.6.0 dated 2023-07-07
DESCRIPTION | 24 MD5 | 75 - NAMESPACE | 1 NEWS.md | 4 R/checks.R |only R/codesFromConceptSet.R |only R/compareCodelists.R | 190 +-- R/drugCodes.R | 562 ++++++----- R/getICD10StandardCodes.R | 402 +++++--- R/mockVocabRef.R | 634 ++++++------- R/summariseCodeUse.R | 967 ++++++++++---------- R/vocabUtilities.R | 922 +++++++++---------- inst/concepts |only inst/concepts_for_mock |only inst/concepts_for_mock_with_exclude |only inst/concepts_for_mock_with_mapped |only inst/doc/a01_Introduction_to_CodelistGenerator.Rmd | 434 ++++---- inst/doc/a01_Introduction_to_CodelistGenerator.html | 228 ---- inst/doc/a02_Candidate_codes_OA.Rmd | 762 +++++++-------- inst/doc/a02_Candidate_codes_OA.html | 240 ---- inst/doc/a03_Options_for_CodelistGenerator.html | 20 inst/not_all_concept_sets |only man/CodelistGenerator-package.Rd | 5 man/codesFromConceptSet.Rd |only man/getATCCodes.Rd | 78 - man/getDrugIngredientCodes.Rd | 71 - man/getICD10StandardCodes.Rd | 73 - man/summariseCodeUse.Rd | 77 - tests/testthat/test-codesFromConceptSet.R |only tests/testthat/test-compareCodelists.R | 254 ++--- tests/testthat/test-drugCodes.R | 168 +-- tests/testthat/test-getCandidateCodes.R | 952 +++++++++---------- tests/testthat/test-getICD10StandardCodes.R | 103 +- tests/testthat/test-getMappings.R | 148 +-- tests/testthat/test-mockVocabRef.R | 26 tests/testthat/test-summariseCodeUse.R | 548 +++++------ tests/testthat/test-vocabUtilities.R | 180 +-- vignettes/a01_Introduction_to_CodelistGenerator.Rmd | 434 ++++---- vignettes/a02_Candidate_codes_OA.Rmd | 762 +++++++-------- 39 files changed, 4641 insertions(+), 4703 deletions(-)
More information about CodelistGenerator at CRAN
Permanent link
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to safely and efficiently organize and execute
Monte Carlo simulation experiments in R.
The package controls the structure and back-end of Monte Carlo simulation experiments
by utilizing a generate-analyse-summarise workflow. The workflow safeguards against
common simulation coding issues, such as automatically re-simulating non-convergent results,
prevents inadvertently overwriting simulation files, catches error and warning messages
during execution, and implicitly supports parallel processing.
For a pedagogical introduction to the package see
Sigal and Chalmers (2016) <doi:10.1080/10691898.2016.1246953>. For a more in-depth overview of
the package and its design philosophy see Chalmers and Adkins (2020) <doi:10.20982/tqmp.16.4.p248>.
Author: Phil Chalmers [aut, cre] ,
Matthew Sigal [ctb],
Ogreden Oguzhan [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 2.11 dated 2023-05-25 and 2.12 dated 2023-07-07
DESCRIPTION | 8 - MD5 | 68 +++++++------- NEWS.md | 31 ++++++ R/Design.R | 44 ++++++++- R/PBA.R | 25 +++-- R/SimExtract.R | 10 +- R/SimSolve.R | 77 ++++++++++----- R/aggregate_simulations.R | 22 ++++ R/analysis.R | 4 R/functions.R | 2 R/reSummarise.R | 61 ++++-------- R/runSimulation.R | 188 ++++++++++++++++++++++++++------------- R/util.R | 25 ++++- inst/doc/Catch_errors.html | 24 ++-- inst/doc/Fixed_obj_fun.html | 16 +-- inst/doc/MultipleAnalyses.R | 18 +++ inst/doc/MultipleAnalyses.Rmd | 25 ++++- inst/doc/MultipleAnalyses.html | 27 ++++- inst/doc/Parallel-computing.html | 4 inst/doc/Saving-results.R | 7 - inst/doc/Saving-results.Rmd | 22 ++-- inst/doc/Saving-results.html | 114 ++++++++++------------- inst/doc/SimDesign-intro.R | 2 inst/doc/SimDesign-intro.Rmd | 32 +++--- inst/doc/SimDesign-intro.html | 46 ++++----- man/SimExtract.Rd | 4 man/SimSolve.Rd | 45 +++++---- man/aggregate_simulations.Rd | 12 ++ man/createDesign.Rd | 36 +++++++ man/reSummarise.Rd | 45 +-------- man/runSimulation.Rd | 163 ++++++++++++++++++++------------- tests/tests/test-SimDesign.R | 39 +++++--- vignettes/MultipleAnalyses.Rmd | 25 ++++- vignettes/Saving-results.Rmd | 22 ++-- vignettes/SimDesign-intro.Rmd | 32 +++--- 35 files changed, 831 insertions(+), 494 deletions(-)
Title: Image Registration Using the 'NiftyReg' Library
Description: Provides an 'R' interface to the 'NiftyReg' image registration tools
<https://github.com/KCL-BMEIS/niftyreg>. Linear and nonlinear registration
are supported, in two and three dimensions.
Author: Jon Clayden [cre, aut] ,
Marc Modat [aut],
Benoit Presles [aut],
Thanasis Anthopoulos [aut],
Pankaj Daga [aut]
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNiftyReg versions 2.7.1 dated 2022-11-18 and 2.8.0 dated 2023-07-07
RNiftyReg-2.7.1/RNiftyReg/tests/test-all.R |only RNiftyReg-2.7.1/RNiftyReg/tests/testthat |only RNiftyReg-2.8.0/RNiftyReg/DESCRIPTION | 12 +-- RNiftyReg-2.8.0/RNiftyReg/MD5 | 40 ++++++------ RNiftyReg-2.8.0/RNiftyReg/NAMESPACE | 4 + RNiftyReg-2.8.0/RNiftyReg/NEWS | 14 ++++ RNiftyReg-2.8.0/RNiftyReg/R/affine.R | 81 +++++++++++++++++-------- RNiftyReg-2.8.0/RNiftyReg/R/nifti.R | 18 +---- RNiftyReg-2.8.0/RNiftyReg/R/niftyreg.R | 26 ++------ RNiftyReg-2.8.0/RNiftyReg/R/transform.R | 63 +++++++++++++++---- RNiftyReg-2.8.0/RNiftyReg/README.md | 20 +++--- RNiftyReg-2.8.0/RNiftyReg/inst/tinytest |only RNiftyReg-2.8.0/RNiftyReg/man/affine.Rd | 34 ++++++++-- RNiftyReg-2.8.0/RNiftyReg/man/forward.Rd | 4 - RNiftyReg-2.8.0/RNiftyReg/man/readNifti.Rd | 8 +- RNiftyReg-2.8.0/RNiftyReg/man/reexports.Rd | 2 RNiftyReg-2.8.0/RNiftyReg/man/saveTransform.Rd | 15 +++- RNiftyReg-2.8.0/RNiftyReg/man/translate.Rd | 3 RNiftyReg-2.8.0/RNiftyReg/tests/tinytest.R |only 19 files changed, 223 insertions(+), 121 deletions(-)
Title: Mediation using MZIP Model
Description: We implement functions allowing for mediation analysis to be performed in cases where the mediator is a count variable with excess zeroes. First a function is provided allowing users to perform analysis for zero-inflated count variables using the marginalized zero-inflated Poisson (MZIP) model (Long et al. 2014 <DOI:10.1002/sim.6293>). Using the counterfactual approach to mediation and MZIP we can obtain natural direct and indirect effects for the overall population. Using delta method processes variance estimation can be performed instantaneously. Alternatively, bootstrap standard errors can be used. We also provide functions for cases with exposure-mediator interactions with four-way decomposition of total effect.
Author: Andrew Sims [aut, cre] ,
Dustin Long [aut],
Hemant Tiwari [aut],
Leann Long [aut]
Maintainer: Andrew Sims <ams329@uab.edu>
Diff between mzipmed versions 1.3.5 dated 2023-05-27 and 1.4.0 dated 2023-07-07
DESCRIPTION | 8 MD5 | 30 - R/mzipmed_package.R | 1197 +++++++++++++++++++++++++++-------------- inst/doc/mzipmed-vignette.R | 10 inst/doc/mzipmed-vignette.Rmd | 22 inst/doc/mzipmed-vignette.html | 67 +- man/binoutzimed.Rd | 17 man/binoutzimedint.Rd | 14 man/lmoutzimed.Rd | 7 man/lmoutzimedint.Rd | 11 man/mzip.Rd | 18 man/zioutbinmed.Rd | 12 man/zioutbinmedint.Rd | 8 man/zioutlmmed.Rd | 13 man/zioutlmmedint.Rd | 8 vignettes/mzipmed-vignette.Rmd | 22 16 files changed, 979 insertions(+), 485 deletions(-)
Title: R-Friendly Threading in C++
Description: Provides a C++11-style thread class and thread pool that can safely
be interrupted from R. See Nagler (2021) <doi:10.18637/jss.v097.c01>.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between RcppThread versions 2.1.4 dated 2023-07-06 and 2.1.5 dated 2023-07-07
DESCRIPTION | 8 ++--- MD5 | 16 +++++----- NEWS.md | 17 ++++++++++ R/LdFlags.R | 6 +++ R/inline.R | 1 inst/include/RcppThread/ThreadPool.hpp | 21 +++++++------ src/Makevars |only src/detectCores.cpp | 52 ++++++++++++++++++++------------- src/testGlobal.cpp |only tests/testthat/tests.R | 2 + 10 files changed, 83 insertions(+), 40 deletions(-)
Title: Create, Build and Maintain Packages
Description: Helper functions for package creation, building and
maintenance. Designed to work with a build system such as 'GNU make' or
package 'fakemake' to help you to conditionally work through the stages of
package development (such as spell checking, linting, testing, before
building and checking a package).
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between packager versions 1.15.0 dated 2023-06-18 and 1.15.1 dated 2023-07-07
DESCRIPTION | 6 +- MD5 | 10 ++-- NEWS.md | 4 + inst/NEWS.rd | 6 ++ inst/doc/An_Introduction_to_packager.html | 69 ++++++++++++++---------------- inst/runit_tests/test_main.R | 27 ++++------- 6 files changed, 62 insertions(+), 60 deletions(-)
Title: A 'dplyr' Back End for Databases
Description: A 'dplyr' back end for databases that allows you to work with
remote database tables as if they are in-memory data frames. Basic
features works with any database that has a 'DBI' back end; more
advanced features require 'SQL' translation to be provided by the
package author.
Author: Hadley Wickham [aut, cre],
Maximilian Girlich [aut],
Edgar Ruiz [aut],
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between dbplyr versions 2.3.2 dated 2023-03-21 and 2.3.3 dated 2023-07-07
DESCRIPTION | 6 MD5 | 56 ++++---- NEWS.md | 4 R/backend-hive.R | 1 R/backend-impala.R | 1 R/backend-mssql.R | 1 R/data-lahman.R | 2 build/dbplyr.pdf |binary build/vignette.rds |binary inst/doc/backend-2.html | 6 inst/doc/dbplyr.html | 250 ++++++++++++++++++------------------- inst/doc/new-backend.html | 36 ++--- inst/doc/reprex.html | 104 +++++++-------- inst/doc/sql.html | 86 ++++++------ inst/doc/translation-function.html | 214 +++++++++++++++---------------- inst/doc/translation-verb.html | 44 +++--- man/arrange.tbl_lazy.Rd | 5 man/backend-hive.Rd | 1 man/backend-impala.Rd | 1 man/backend-mssql.Rd | 1 man/count.tbl_lazy.Rd | 7 - man/distinct.tbl_lazy.Rd | 5 man/filter.tbl_lazy.Rd | 5 man/group_by.tbl_lazy.Rd | 5 man/lahman.Rd | 2 man/mutate.tbl_lazy.Rd | 5 man/pull.tbl_sql.Rd | 5 man/select.tbl_lazy.Rd | 5 man/summarise.tbl_lazy.Rd | 5 29 files changed, 438 insertions(+), 425 deletions(-)
Title: Restricted Statistical Estimation and Inference for Linear
Models
Description: Allow for easy-to-use testing or evaluating of linear equality and inequality restrictions about parameters and effects in (generalized) linear statistical models.
Author: Leonard Vanbrabant [aut, cre],
Rebecca Kuiper [aut],
Yves Rosseel [ctb],
Aleksandra Dacko [ctb]
Maintainer: Leonard Vanbrabant <info@restriktor.org>
Diff between restriktor versions 0.5-10 dated 2023-07-05 and 0.5-20 dated 2023-07-07
DESCRIPTION | 6 MD5 | 138 - R/Gaussian_Elimination.R | 114 - R/conGLM.R | 754 +++---- R/conGLM_fit.R | 490 ++-- R/conLM.R | 756 +++---- R/conMLM.R | 710 +++--- R/conRLM.R | 824 +++---- R/conRLM_fit.R | 404 +-- R/conRLM_tests_F_Wald_score.R | 302 +- R/conTestLavaan_plot.R | 362 +-- R/conTest_ceq_conGLM_F_Wald_score.R | 316 +- R/conTest_ceq_conLM_F_Wald_score.R | 374 +-- R/conTest_ceq_conRLM_F_Wald_score.R | 292 +- R/conTest_conGLM.R | 1504 +++++++------- R/conTest_conLM.R | 1824 ++++++++--------- R/conTest_conLavaan.R | 164 - R/conTest_conMLM.R | 512 ++-- R/conTest_conRLM.R | 1582 +++++++------- R/conTest_summary.R | 70 R/con_augmented_information.R | 200 - R/con_boot.R | 48 R/con_boot_data.R | 30 R/con_boot_fixed.R | 28 R/con_bootstrapD.R | 778 +++---- R/con_constraints.R | 598 ++--- R/con_constraints_nonlinear_idx.R | 18 R/con_goric.R | 2691 ++++++++++++------------- R/con_goric_penalty.R | 72 R/con_gorica_est.R | 544 ++--- R/con_gorica_est_summary.R | 106 R/con_iht.R | 18 R/con_incomplete.R | 1322 ++++++------ R/con_loglik.R | 84 R/con_pbar.R | 26 R/con_pvalue.R | 890 ++++---- R/con_sandwich.R | 446 ++-- R/con_weights.R | 246 +- R/evSyn.R | 1848 +++++++++-------- R/is_closed_convex_cone.R | 46 R/restriktor.R | 76 R/restriktor_print.R | 146 - R/restriktor_print_summary.R | 244 +- R/restriktor_summary.R | 474 ++-- R/utilities.R | 394 +-- R/zzz.R | 14 README.md | 112 - build/vignette.rds |binary inst/doc/Guidelines_GORIC_output.R | 1744 ++++++++-------- inst/doc/Guidelines_GORIC_output.Rmd | 2828 +++++++++++++------------- inst/doc/Guidelines_GORIC_output.html | 3621 ++++++++++++++++------------------ man/ConTestC.Rd | 230 +- man/ConTestLRT.Rd | 616 ++--- man/ConTestScore.Rd | 636 ++--- man/ConTestWald.Rd | 612 ++--- man/FacialBurns.Rd | 56 man/bootstrapD.Rd | 278 +- man/conTestF.Rd | 660 +++--- man/conTest_ceq.Rd | 330 +-- man/conTest_methods.Rd | 82 man/conTest_summary.Rd | 310 +- man/evSyn.Rd | 607 ++--- man/goric.Rd | 672 +++--- man/iht.Rd | 904 ++++---- man/myGORICs.Rd | 34 man/myLLs.Rd | 34 man/myPTs.Rd | 34 man/restriktor-package.rd | 312 +- man/restriktor_methods.Rd | 230 +- vignettes/Guidelines_GORIC_output.Rmd | 2828 +++++++++++++------------- 70 files changed, 20330 insertions(+), 20325 deletions(-)
Title: Interpreting High Resolution Mass Spectra
Description: High resolution mass spectrometry yields often large data
sets of spectra from compounds which are not present in available
libraries. These spectra need to be annotated and
interpreted.'InterpretMSSpectrum' provides a set of functions to
perform such tasks for Electrospray-Ionization and
Atmospheric-Pressure-Chemical-Ionization derived data in positive and
negative ionization mode.
Author: Jan Lisec [aut, cre] ,
Jaeger Carsten [aut]
Maintainer: Jan Lisec <jan.lisec@bam.de>
Diff between InterpretMSSpectrum versions 1.3.3 dated 2022-11-15 and 1.3.8 dated 2023-07-07
InterpretMSSpectrum-1.3.3/InterpretMSSpectrum/data/param.default.RData |only InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/DESCRIPTION | 51 +- InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/MD5 | 58 +-- InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/NAMESPACE | 19 InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/R/DetermineIsomainPeaks.R | 13 InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/R/GenerateMetaboliteSQLiteDB.R | 14 InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/R/GetIsotopeDistribution.R | 10 InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/R/InterpretMSSpectrum.R | 40 +- InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/R/PlausibleFormula.R | 3 InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/R/PlotSpec.R | 19 InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/R/RestrictByTypicalLosses.R | 3 InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/R/data.R | 2 InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/R/findMAIN.r | 192 +++++----- InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/R/findiso.R | 21 - InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/R/getRuleFromIonSymbol.R | 10 InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/R/get_exactmass.R |only InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/R/mScore.R | 3 InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/R/plot.findMAIN.R | 3 InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/R/print.findMAIN.R | 23 - InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/R/summary.findMAIN.R | 2 InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/R/writeMSF.r | 4 InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/data/param.default.rda |only InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/man/GenerateMetaboliteSQLiteDB.Rd | 5 InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/man/InterpretMSSpectrum.Rd | 5 InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/man/PlausibleFormula.Rd | 2 InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/man/PlotSpec.Rd | 2 InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/man/findMAIN.Rd | 51 ++ InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/man/get_exactmass.Rd |only InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/man/mScore.Rd | 3 InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/man/param.default.Rd | 2 InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/man/writeMSF.Rd | 4 InterpretMSSpectrum-1.3.8/InterpretMSSpectrum/tests/testthat/test-GenerateMetaboliteSQLiteDB.R | 12 32 files changed, 316 insertions(+), 260 deletions(-)
More information about InterpretMSSpectrum at CRAN
Permanent link
Title: Create Compact Hash Digests of R Objects
Description: Implementation of a function 'digest()' for the creation of hash
digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32',
'xxhash', 'murmurhash', 'spookyhash', 'blake3' and 'crc32c' algorithms) permitting
easy comparison of R language objects, as well as functions such as'hmac()' to
create hash-based message authentication code. Please note that this package
is not meant to be deployed for cryptographic purposes for which more
comprehensive (and widely tested) libraries such as 'OpenSSL' should be
used.
Author: Dirk Eddelbuettel <edd@debian.org> with contributions
by Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon Urbanek,
Mario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen,
Duncan Murdoch, Jim Hester, Wush Wu, Qiang Kou, Thierry Onkelinx,
[...truncated...]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between digest versions 0.6.32 dated 2023-06-26 and 0.6.33 dated 2023-07-07
ChangeLog | 18 ++++++++++++++++++ DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- README.md | 10 ++++++---- src/crc32c/crc32c_config.h | 12 +++++++++--- 5 files changed, 44 insertions(+), 18 deletions(-)
Title: Automated Model Sensitivity Analysis
Description: Methods and tools for creating a model set and estimating and evaluating the explanation or prediction power of its members.
'SUR' modelling (for parameter estimation), 'logit'/'probit' modelling (for binary classification), and 'VARMA' modelling (for time-series forecasting) are implemented.
Evaluations are both in-sample and out-of-sample. It tries to be both CPU and memory efficient.
This package can be applied to perform sensitivity analysis in studies involving regression analysis.
It can also be utilized for automatic model selection, multi-model inference, and model averaging within a frequentist framework (Claeskens and Hjort (2008, ISBN:1139471805, 9781139471800)),
calculating benchmarks, and extreme bound analysis (Leamer (1983) <https://www.jstor.org/stable/1803924>).
Author: Ramin Mojab [aut, cre],
Stephen Becker [cph] by Ciyou Zhu . L-BFGS-B Version 3.0 is an
algorithmic update from 2011, with coding changes by J. L. Morales)
Maintainer: Ramin Mojab <rmojab63@gmail.com>
Diff between ldt versions 0.3.0.0 dated 2023-07-04 and 0.3.1.0 dated 2023-07-07
ldt-0.3.0.0/ldt/man/s.combine.by.moments4.Rd |only ldt-0.3.0.0/ldt/src/weighted4.cpp |only ldt-0.3.0.0/ldt/src/weighted_mean.cpp |only ldt-0.3.0.0/ldt/src/weighted_variance.cpp |only ldt-0.3.1.0/ldt/DESCRIPTION | 13 ldt-0.3.1.0/ldt/MD5 | 59 +-- ldt-0.3.1.0/ldt/NAMESPACE | 2 ldt-0.3.1.0/ldt/NEWS.md | 8 ldt-0.3.1.0/ldt/R/RcppExports.R | 4 ldt-0.3.1.0/ldt/R/helpers.R | 8 ldt-0.3.1.0/ldt/R/options.R | 2 ldt-0.3.1.0/ldt/R/statistics.R | 37 +- ldt-0.3.1.0/ldt/inst/COPYRIGHTS/README.md | 1 ldt-0.3.1.0/ldt/inst/doc/bin.html | 10 ldt-0.3.1.0/ldt/inst/doc/sur.html | 20 - ldt-0.3.1.0/ldt/inst/doc/varma.html | 6 ldt-0.3.1.0/ldt/man/get.options.metric.Rd | 2 ldt-0.3.1.0/ldt/man/s.combine.stats4.Rd |only ldt-0.3.1.0/ldt/src/RcppExports.cpp | 14 ldt-0.3.1.0/ldt/src/array.cpp | 6 ldt-0.3.1.0/ldt/src/array.h | 326 +++++++++++++++----- ldt-0.3.1.0/ldt/src/mixture.cpp | 24 - ldt-0.3.1.0/ldt/src/modelset.cpp | 6 ldt-0.3.1.0/ldt/src/nelder_mead.cpp | 2 ldt-0.3.1.0/ldt/src/r_ldt.cpp | 22 - ldt-0.3.1.0/ldt/src/r_statistics.cpp | 32 -- ldt-0.3.1.0/ldt/src/running.h | 363 ++++++++++++----------- ldt-0.3.1.0/ldt/src/searchers.h | 12 ldt-0.3.1.0/ldt/src/summary.cpp | 16 - ldt-0.3.1.0/ldt/tests/testthat/test-bin.R | 4 ldt-0.3.1.0/ldt/tests/testthat/test-statistics.R | 8 ldt-0.3.1.0/ldt/tests/testthat/test-sur.R | 8 ldt-0.3.1.0/ldt/tests/testthat/test-varma.R | 6 33 files changed, 601 insertions(+), 420 deletions(-)
Title: 'SCS' Plug-in for the 'R' Optimization Infrastructure
Description: Enhances the 'R' Optimization Infrastructure ('ROI') package
with the 'SCS' solver for solving convex cone problems.
Author: Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between ROI.plugin.scs versions 1.1-1 dated 2021-11-09 and 1.1-2 dated 2023-07-07
DESCRIPTION | 17 +++++++++-------- MD5 | 10 +++++----- R/plugin.R | 4 ---- man/Example_01.Rd | 1 + man/Example_02.Rd | 1 + man/Example_03.Rd | 1 + 6 files changed, 17 insertions(+), 17 deletions(-)
More information about ROI.plugin.scs at CRAN
Permanent link
Title: 'qpOASES' Plugin for the 'R' Optimization Infrastructure
Description: Enhances the 'R' Optimization Infrastructure ('ROI') package
with the quadratic solver 'qpOASES'. More information about
'qpOASES' can be found at <https://github.com/coin-or/qpOASES>.
Author: Florian Schwendinger [aut, cre],
Hans Joachim Ferreau [cph],
Andreas Potschka [cph],
Christian Kirches [cph],
Dennis Janka [cph],
Andreas Waechter [cph]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between ROI.plugin.qpoases versions 1.0-2 dated 2022-10-16 and 1.0-3 dated 2023-07-07
DESCRIPTION | 12 ++++++------ MD5 | 7 ++++--- man/Example_01.Rd | 1 + src/qpoases/include/qpOASES/QProblem.hpp | 1 + src/qpoases/src/Makefile |only 5 files changed, 12 insertions(+), 9 deletions(-)
More information about ROI.plugin.qpoases at CRAN
Permanent link
Title: 'Multi-Solution' Binary Linear Problem Plug-in for the 'R'
Optimization Interface
Description: Enhances the 'R' Optimization Infrastructure ('ROI') package
with the possibility to obtain multiple solutions for linear
problems with binary variables. The main function is copied
(with small modifications) from the relations package.
Author: Kurt Hornik [aut],
David Meyer [aut],
Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between ROI.plugin.msbinlp versions 1.0-0 dated 2020-08-29 and 1.0-1 dated 2023-07-07
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- man/Example_01.Rd | 1 + man/Example_02.Rd | 1 + 4 files changed, 11 insertions(+), 9 deletions(-)
More information about ROI.plugin.msbinlp at CRAN
Permanent link
Title: 'alabama' Plug-in for the 'R' Optimization Infrastructure
Description: Enhances the R Optimization Infrastructure ('ROI') package
with the 'alabama' solver for solving nonlinear optimization problems.
Author: Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between ROI.plugin.alabama versions 1.0-0 dated 2020-08-29 and 1.0-2 dated 2023-07-07
ROI.plugin.alabama-1.0-0/ROI.plugin.alabama/man/ROI.plugin.alabama-package.Rd |only ROI.plugin.alabama-1.0-2/ROI.plugin.alabama/DESCRIPTION | 17 +++++----- ROI.plugin.alabama-1.0-2/ROI.plugin.alabama/MD5 | 9 ++--- ROI.plugin.alabama-1.0-2/ROI.plugin.alabama/man/Example_01.Rd | 1 ROI.plugin.alabama-1.0-2/ROI.plugin.alabama/man/Example_02.Rd | 1 ROI.plugin.alabama-1.0-2/ROI.plugin.alabama/man/Example_03.Rd | 1 6 files changed, 16 insertions(+), 13 deletions(-)
More information about ROI.plugin.alabama at CRAN
Permanent link
Title: Solvers for Boundary Value Problems of Differential Equations
Description: Functions that solve boundary value problems ('BVP') of systems of ordinary
differential equations ('ODE') and differential algebraic equations ('DAE').
The functions provide an interface to the FORTRAN functions
'twpbvpC', 'colnew/colsys', and an R-implementation of the shooting method.
Mazzia, F., J.R. Cash and K. Soetaert, 2014.
Author: Karline Soetaert [aut, cre] ,
Jeff Cash [aut],
Francesca Mazzia [aut],
Uri M. Ascher [ctb] ,
G. Bader [ctb] ,
J. Christiansen [ctb] ,
Robert R. Russell [ctb]
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between bvpSolve versions 1.4.3 dated 2021-10-06 and 1.4.4 dated 2023-07-07
bvpSolve-1.4.3/bvpSolve/inst/doc/dynload |only bvpSolve-1.4.3/bvpSolve/inst/doc/examples |only bvpSolve-1.4.3/bvpSolve/inst/doc/inline |only bvpSolve-1.4.3/bvpSolve/inst/doc/opuscula_math_3424.pdf |only bvpSolve-1.4.4/bvpSolve/DESCRIPTION | 6 - bvpSolve-1.4.4/bvpSolve/MD5 | 63 +++------------- bvpSolve-1.4.4/bvpSolve/build |only bvpSolve-1.4.4/bvpSolve/inst/CITATION | 35 ++++---- bvpSolve-1.4.4/bvpSolve/inst/doc/bvpSolve.R |only bvpSolve-1.4.4/bvpSolve/inst/doc/bvpSolve.Rnw |only bvpSolve-1.4.4/bvpSolve/inst/doc/bvpSolve.pdf |binary bvpSolve-1.4.4/bvpSolve/inst/doc/bvpTests.R |only bvpSolve-1.4.4/bvpSolve/inst/doc/bvpTests.Rnw |only bvpSolve-1.4.4/bvpSolve/inst/doc/bvpTests.pdf |binary bvpSolve-1.4.4/bvpSolve/src/colmodR.f | 34 ++++---- bvpSolve-1.4.4/bvpSolve/src/colnewR.f | 38 ++++----- bvpSolve-1.4.4/bvpSolve/src/colsysR.f | 32 ++++---- 17 files changed, 85 insertions(+), 123 deletions(-)
Title: 'lp_solve' Plugin for the 'R' Optimization Infrastructure
Description: Enhances the 'R' Optimization Infrastructure ('ROI') package
with the 'lp_solve' solver.
Author: Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between ROI.plugin.lpsolve versions 1.0-1 dated 2021-06-15 and 1.0-2 dated 2023-07-07
DESCRIPTION | 15 ++++++++------- MD5 | 14 +++++++------- R/plugin.R | 40 +++++++++++++++++++++++----------------- R/zzz.R | 2 +- README.md | 4 ++-- man/Example_01.Rd | 1 + man/read.lp.Rd | 2 +- man/write.lp.Rd | 2 +- 8 files changed, 44 insertions(+), 36 deletions(-)
More information about ROI.plugin.lpsolve at CRAN
Permanent link
Title: Probabilistic Knowledge Structures
Description: Fitting and testing probabilistic knowledge structures,
especially the basic local independence model (BLIM, Doignon & Flamagne,
1999) and the simple learning model (SLM), using the minimum discrepancy
maximum likelihood (MDML) method (Heller & Wickelmaier, 2013
<doi:10.1016/j.endm.2013.05.145>).
Author: Florian Wickelmaier [aut, cre],
Juergen Heller [aut],
Julian Mollenhauer [aut],
Pasquale Anselmi [ctb],
Debora de Chiusole [ctb],
Andrea Brancaccio [ctb],
Luca Stefanutti [ctb]
Maintainer: Florian Wickelmaier <wickelmaier@web.de>
Diff between pks versions 0.5-0 dated 2022-04-14 and 0.6-0 dated 2023-07-07
pks-0.5-0/pks/R/fwd_bck_graded.R |only pks-0.5-0/pks/man/fwd_bck_graded.Rd |only pks-0.6-0/pks/ChangeLog | 21 ++++++++++ pks-0.6-0/pks/DESCRIPTION | 24 ++++++++---- pks-0.6-0/pks/MD5 | 47 +++++++++++++++--------- pks-0.6-0/pks/NAMESPACE | 12 +++++- pks-0.6-0/pks/R/blim.R | 24 ++++++------ pks-0.6-0/pks/R/blimit.R |only pks-0.6-0/pks/R/conversion.R | 62 +++++++++++++++++++------------- pks-0.6-0/pks/R/gradedness.R |only pks-0.6-0/pks/R/ita.R | 30 ++++++++++----- pks-0.6-0/pks/R/slm.R |only pks-0.6-0/pks/build/partial.rdb |binary pks-0.6-0/pks/build/vignette.rds |only pks-0.6-0/pks/data/DoignonFalmagne7.rda |binary pks-0.6-0/pks/data/Taagepera.rda |binary pks-0.6-0/pks/data/endm.rda |binary pks-0.6-0/pks/data/schoolarithm.rda |only pks-0.6-0/pks/inst/CITATION | 21 +++------- pks-0.6-0/pks/inst/doc |only pks-0.6-0/pks/man/blimit.Rd |only pks-0.6-0/pks/man/chess.Rd | 2 - pks-0.6-0/pks/man/conversion.Rd | 41 ++++++++++++++++----- pks-0.6-0/pks/man/getKFringe.Rd |only pks-0.6-0/pks/man/gradedness.Rd |only pks-0.6-0/pks/man/ita.Rd | 20 +++++++--- pks-0.6-0/pks/man/schoolarithm.Rd |only pks-0.6-0/pks/man/simulate.blim.Rd | 27 ++++++++++--- pks-0.6-0/pks/man/slm.Rd |only pks-0.6-0/pks/vignettes |only 30 files changed, 222 insertions(+), 109 deletions(-)
Title: Preparation, Checking and Post-Processing Data for PK/PD
Modeling
Description: Efficient tools for preparation, checking and post-processing of data in PK/PD (pharmacokinetics/pharmacodynamics) modeling, with focus on use of Nonmem. Attention is paid to ensure consistency, traceability, and Nonmem compatibility of Data. Rigorously checks final Nonmem datasets. Implemented in 'data.table', but easily integrated with 'base' and 'tidyverse'.
Author: Philip Delff [aut, cre]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMdata versions 0.0.17 dated 2023-05-02 and 0.1.0 dated 2023-07-07
NMdata-0.0.17/NMdata/tests/testthat/testOutput/stampedData_8.csv |only NMdata-0.0.17/NMdata/tests/testthat/testOutput/stampedData_8_meta.txt |only NMdata-0.0.17/NMdata/tests/testthat/testOutput/stampedData_9.csv |only NMdata-0.0.17/NMdata/tests/testthat/testOutput/stampedData_9_meta.txt |only NMdata-0.0.17/NMdata/tests/testthat/testReference/NMdataConf1.rds |only NMdata-0.0.17/NMdata/tests/testthat/testReference/NMscanInput4.rds |only NMdata-0.0.17/NMdata/tests/testthat/testReference/NMscanInput5.rds |only NMdata-0.0.17/NMdata/tests/testthat/testReference/NMscanInput6.rds |only NMdata-0.0.17/NMdata/tests/testthat/testReference/NMscanInput_1.rds |only NMdata-0.0.17/NMdata/tests/testthat/testReference/NMscanInput_2.rds |only NMdata-0.1.0/NMdata/DESCRIPTION | 11 NMdata-0.1.0/NMdata/MD5 | 296 - NMdata-0.1.0/NMdata/NAMESPACE | 5 NMdata-0.1.0/NMdata/NEWS.md | 39 NMdata-0.1.0/NMdata/R/NMapplyFilters.R | 2 NMdata-0.1.0/NMdata/R/NMcheckColnames.R | 2 NMdata-0.1.0/NMdata/R/NMcheckData.R | 77 NMdata-0.1.0/NMdata/R/NMdataConf.R | 113 NMdata-0.1.0/NMdata/R/NMextractDataFile.R | 20 NMdata-0.1.0/NMdata/R/NMextractText.R | 56 NMdata-0.1.0/NMdata/R/NMreadCsv.R | 47 NMdata-0.1.0/NMdata/R/NMreadSection.R | 63 NMdata-0.1.0/NMdata/R/NMreplaceDataFile.R |only NMdata-0.1.0/NMdata/R/NMscanData.R | 97 NMdata-0.1.0/NMdata/R/NMscanInput.R | 90 NMdata-0.1.0/NMdata/R/NMscanMultiple.R | 22 NMdata-0.1.0/NMdata/R/NMscanTables.R | 46 NMdata-0.1.0/NMdata/R/NMtransInp.R | 4 NMdata-0.1.0/NMdata/R/NMwriteData.R | 175 NMdata-0.1.0/NMdata/R/NMwriteSection.R | 137 NMdata-0.1.0/NMdata/R/NMwriteSectionOne.R |only NMdata-0.1.0/NMdata/R/addTAPD.R | 14 NMdata-0.1.0/NMdata/R/compareCols.R | 29 NMdata-0.1.0/NMdata/R/deprecatedArg.R |only NMdata-0.1.0/NMdata/R/dims.R | 23 NMdata-0.1.0/NMdata/R/editCharCols.R |only NMdata-0.1.0/NMdata/R/filePathSimple.R | 3 NMdata-0.1.0/NMdata/R/findCovs.R | 9 NMdata-0.1.0/NMdata/R/findVars.R | 10 NMdata-0.1.0/NMdata/R/flagsAssign.R | 2 NMdata-0.1.0/NMdata/R/flagsCount.R | 2 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NMdata-0.1.0/NMdata/tests/testthat/test_fnAppend.R | 8 NMdata-0.1.0/NMdata/tests/testthat/test_fnExtension.R | 14 NMdata-0.1.0/NMdata/tests/testthat/test_getArgs.R |only NMdata-0.1.0/NMdata/tests/testthat/test_renameByContents.R | 8 183 files changed, 2376 insertions(+), 1585 deletions(-)
Title: Hamiltonian Monte Carlo and Other Gradient-Based MCMC Sampling
Algorithms for 'nimble'
Description: Provides gradient-based MCMC sampling algorithms for use with the MCMC engine provided by the 'nimble' package. This includes Hamiltonian Monte Carlo (HMC) and (under development) Langevin samplers. The HMC sampler dynamically determines step size and number of leapfrog steps using the No-U-Turn (NUTS) algorithm as described in Hoffman and Gelman (2014) <arXiv:1111.4246>. In addition, convenience functions are provided for generating and modifying MCMC configuration objects which employ HMC sampling.
Author: Daniel Turek [aut, cre],
Perry de Valpine [aut],
Christopher Paciorek [aut]
Maintainer: Daniel Turek <danielturek@gmail.com>
Diff between nimbleHMC versions 0.1.0 dated 2023-05-31 and 0.1.1 dated 2023-07-07
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/configuration.R | 21 +++++++++++---------- inst/NEWS.md | 4 ++++ man/addHMC.Rd | 2 +- tests/testthat/test-HMC.R | 23 ++++++++++++++++++++++- 6 files changed, 47 insertions(+), 21 deletions(-)
Title: Runs Monte Carlo Markov Chain - With Either 'JAGS', 'nimble' or
'greta' - While Adjusting Burn-in and Thinning Parameters
Description: The function runMCMC_btadjust() returns a mcmc.list object which is the output of a
Markov Chain Monte Carlo obtained - from either 'JAGS', 'nimble' or 'greta' - after adjusting burn-in and thinning parameters to meet
pre-specified criteria in terms of convergence & effective sample size.
Author: Frederic Gosselin [cre, aut] ,
Institut national de recherche pour l'agriculture, l'alimentation et
l'environnement [cph]
Maintainer: Frederic Gosselin <frederic.gosselin@inrae.fr>
Diff between runMCMCbtadjust versions 1.0.1 dated 2023-06-29 and 1.0.2 dated 2023-07-07
DESCRIPTION | 6 MD5 | 10 NEWS.md | 7 R/runMCMC_btadjust.r | 6 inst/doc/runMCMCbtadjust_Presentation.html | 491 ++++++++++++++--------------- man/runMCMC_btadjust.Rd | 4 6 files changed, 261 insertions(+), 263 deletions(-)
More information about runMCMCbtadjust at CRAN
Permanent link
More information about fastLogisticRegressionWrap at CRAN
Permanent link
Title: Clustering of Weighted Data
Description: Clusters state sequences and weighted data. It provides an optimized weighted PAM algorithm as well as functions for aggregating replicated cases, computing cluster quality measures for a range of clustering solutions and plotting (fuzzy) clusters of state sequences. Parametric bootstraps methods to validate typology of sequences are also provided.
Author: Matthias Studer [aut, cre]
Maintainer: Matthias Studer <matthias.studer@unige.ch>
Diff between WeightedCluster versions 1.6-2 dated 2023-05-17 and 1.6-4 dated 2023-07-07
DESCRIPTION | 11 ++++++----- MD5 | 20 +++++++++++--------- NAMESPACE | 6 +++++- NEWS | 11 ++++++++++- R/clustassoc.R |only inst/doc/WeightedCluster.pdf |binary inst/doc/WeightedClusterFR.pdf |binary inst/doc/WeightedClusterPreview.pdf |binary man/as.clustrange.Rd | 2 +- man/clustassoc.Rd |only src/cluster.h | 2 +- src/clusterquality.cpp | 3 ++- 12 files changed, 36 insertions(+), 19 deletions(-)
More information about WeightedCluster at CRAN
Permanent link
Title: Import Professional Baseball Data from 'Retrosheet'
Description: A collection of tools to import and structure the (currently) single-season
event, game-log, roster, and schedule data available from <https://www.retrosheet.org>.
In particular, the event (a.k.a. play-by-play) files can be especially difficult to parse.
This package does the parsing on those files, returning the requested data in the most
practical R structure to use for sabermetric or other analyses.
Author: Colin Douglas [aut, cre, cph],
Richard Scriven [aut, cph]
Maintainer: Colin Douglas <colin@douglas.science>
Diff between retrosheet versions 1.1.4 dated 2021-09-16 and 1.1.5 dated 2023-07-07
DESCRIPTION | 10 +-- MD5 | 20 +++---- NEWS.md | 5 + README.md | 75 +++++++++++++-------------- tests/testthat/test-getFileNames.R | 18 +++++- tests/testthat/test-getParkIDs.R | 87 ++++++++++++++++---------------- tests/testthat/test-getPartialGamelog.R | 26 ++++++--- tests/testthat/test-getRetrosheet.R | 14 ++++- tests/testthat/test-getTeamIDs.R | 43 +++++++++------ tests/testthat/test-get_retrosheet.R | 52 ++++++++++++++++--- tests/testthat/test-rmarkdown.R | 2 11 files changed, 219 insertions(+), 133 deletions(-)
More information about optDesignSlopeInt at CRAN
Permanent link
Title: Efficient Algorithm for High-Dimensional Frailty Model
Description: The penalized and non-penalized Minorize-Maximization (MM) method for frailty models to fit the clustered data, multi-event data and recurrent data. Least absolute shrinkage and selection operator (LASSO), minimax concave penalty (MCP) and smoothly clipped absolute deviation (SCAD) penalized functions are implemented. All the methods are computationally efficient. These general methods are proposed based on the following papers,
Huang, Xu and Zhou (2022) <doi:10.3390/math10040538>,
Huang, Xu and Zhou (2023) <doi:10.1177/09622802221133554>.
Author: Xifen Huang [aut],
Yunpeng Zhou [aut, cre],
Jinfeng Xu [ctb]
Maintainer: Yunpeng Zhou <u3514104@connect.hku.hk>
Diff between frailtyMMpen versions 1.1.1 dated 2023-07-06 and 1.1.2 dated 2023-07-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 2 ++ src/Makevars | 2 +- 4 files changed, 9 insertions(+), 7 deletions(-)
Title: Discrete Matrix/Tensor Decomposition
Description: Semi-Binary and Semi-Ternary Matrix Decomposition are performed based on Non-negative Matrix Factorization (NMF) and Singular Value Decomposition (SVD). For the details of the methods, see the reference section of GitHub README.md <https://github.com/rikenbit/dcTensor>.
Author: Koki Tsuyuzaki [aut, cre]
Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>
Diff between dcTensor versions 1.1.0 dated 2023-06-23 and 1.2.0 dated 2023-07-07
DESCRIPTION | 6 +-- MD5 | 52 ++++++++++++++++----------------- R/dNMF.R | 43 ---------------------------- R/dNTD.R | 27 ----------------- R/dNTF.R | 27 ----------------- R/dPLS.R | 17 +---------- R/dSVD.R | 15 +-------- R/djNMF.R | 72 ----------------------------------------------- R/dsiNMF.R | 47 ------------------------------ build/partial.rdb |binary inst/NEWS | 4 ++ inst/doc/dcTensor-1.html | 38 ++++-------------------- inst/doc/dcTensor-2.html | 14 +++------ inst/doc/dcTensor-3.html | 28 +++--------------- inst/doc/dcTensor-4.html | 22 +++----------- inst/doc/dcTensor-5.html | 12 +++---- inst/doc/dcTensor-6.html | 20 +++---------- inst/doc/dcTensor-7.html | 28 ++++++------------ man/dNMF.Rd | 4 -- man/dNTD.Rd | 2 - man/dNTF.Rd | 2 - man/dPLS.Rd | 3 - man/dSVD.Rd | 1 man/djNMF.Rd | 6 --- man/dsiNMF.Rd | 4 -- man/toyModel.Rd | 2 - tests/testthat.R | 10 +++--- 27 files changed, 94 insertions(+), 412 deletions(-)
Title: Storing, Manipulating and Analysis Spectroscopy and Associated
Data
Description: Stores and eases the manipulation of spectra and associated data,
with dedicated classes for spatial and soil-related data.
Author: Pierre Roudier [aut, cre],
Max Kuhn [ctb],
Kristian Hovde Liland [ctb],
Bjorn-Helge Mevik [ctb],
Hadley Wickham [ctb],
Raphael Viscarra Rossel [dtc]
Maintainer: Pierre Roudier <roudierp@landcareresearch.co.nz>
Diff between spectacles versions 0.5-3 dated 2021-01-11 and 0.5-4 dated 2023-07-07
spectacles-0.5-3/spectacles/data/datalist |only spectacles-0.5-4/spectacles/DESCRIPTION | 10 spectacles-0.5-4/spectacles/MD5 | 43 spectacles-0.5-4/spectacles/R/Spectra-methods.R | 2526 +++++----- spectacles-0.5-4/spectacles/R/SpectraDataFrame-methods.R | 1011 ++-- spectacles-0.5-4/spectacles/R/aggregate_spectra.R | 278 - spectacles-0.5-4/spectacles/R/kenstone.R | 228 spectacles-0.5-4/spectacles/R/performance.R | 169 spectacles-0.5-4/spectacles/R/plot-methods.R | 754 +- spectacles-0.5-4/spectacles/R/preprocessing.R | 560 +- spectacles-0.5-4/spectacles/R/setters.R | 893 +-- spectacles-0.5-4/spectacles/R/splice.R | 268 - spectacles-0.5-4/spectacles/README.md | 161 spectacles-0.5-4/spectacles/build/vignette.rds |binary spectacles-0.5-4/spectacles/inst/CITATION | 27 spectacles-0.5-4/spectacles/inst/doc/interfacing-with-caret.R | 220 spectacles-0.5-4/spectacles/inst/doc/interfacing-with-caret.html | 1245 ++-- spectacles-0.5-4/spectacles/inst/doc/quickstart.R | 130 spectacles-0.5-4/spectacles/inst/doc/quickstart.html | 1016 +--- spectacles-0.5-4/spectacles/man/Spectra-class.Rd | 2 spectacles-0.5-4/spectacles/man/features.Rd | 8 spectacles-0.5-4/spectacles/man/rbind.Rd | 2 spectacles-0.5-4/spectacles/man/spectra-methods.Rd | 4 23 files changed, 4785 insertions(+), 4770 deletions(-)
Title: In-Text Expandable and Resizable Containers, Images, Tables and
Data Tables in 'Shiny', 'Rmarkdown' and 'Quarto' Documents
Description: Automatic resizing toolbar for containers, images and tables. Most suitable to include resize functionality in 'Markdown', 'Rmarkdown' and 'Quarto' documents.
Author: Obinna Obianom [aut, cre]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between r2resize versions 1.6 dated 2023-04-07 and 1.7 dated 2023-07-07
DESCRIPTION | 6 +-- MD5 | 26 +++++++-------- NEWS.md | 7 ++++ R/markdownResizer.R | 9 ++++- README.md | 5 +- inst/doc/example_frequently_asked_r2resize.html | 4 +- inst/doc/introduction_r2resize.R | 3 + inst/doc/introduction_r2resize.Rmd | 3 + inst/doc/introduction_r2resize.html | 11 +++--- inst/doc/resizable_containers_split_screen_r2resize.html | 4 +- inst/themes/default_bottom.js | 2 - inst/themes/default_top.js | 2 - man/add.resizer.Rd | 8 +++- vignettes/introduction_r2resize.Rmd | 3 + 14 files changed, 57 insertions(+), 36 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-12 0.2.2
2019-05-03 0.2.1
2019-04-05 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-14 0.7.1
2020-12-16 0.7.0
2020-10-10 0.6.9
2020-08-25 0.6.8
2020-06-13 0.6.7
2020-04-01 0.6.4.1
2020-02-03 0.6.4
2019-11-11 0.6.3
2019-09-07 0.6.2
2019-06-03 0.6.1
2019-01-07 0.6.0
2018-12-04 0.5.9
2018-09-29 0.5.7
2018-07-19 0.5.5
2018-05-16 0.5.3
2018-03-06 0.5.0
2018-01-04 0.4.5
2017-11-05 0.4.0
2017-08-17 0.3.5
2017-06-14 0.3.3
2017-05-29 0.3.2
2017-03-31 0.3.0
2017-01-19 0.2.0
2016-12-06 0.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-09-15 0.1.1
2021-09-14 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-30 1.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-28 0.6.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-10 1.8.0
2020-06-24 1.7.9
2020-05-02 1.7.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-12 2.1.4
2022-10-06 2.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-03-22 0.5.17
2022-11-30 0.5.14
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-12-16 0.6.2
2022-08-30 0.6.1
2022-05-10 0.6.0
2020-05-11 0.5.2
2020-04-01 0.5.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-06-19 0.11.0
2023-01-05 0.10.0
2022-09-19 0.9.2
2022-04-07 0.9.0
2022-02-15 0.8.0
2022-02-08 0.7.0
2021-10-26 0.5.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-07-18 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-05-30 1.0.4
2016-02-21 1.0.3
2016-02-20 1.0.2
2015-05-22 1.0.1
2015-05-20 1.0.0