Title: Installing and Loading R Packages for Reproducible Workflows
Description: A single key function, 'Require' that makes rerun-tolerant
versions of 'install.packages' and `require` for CRAN packages, packages
no longer on CRAN (i.e., archived), specific versions of packages,
and GitHub packages. This approach is developed to create reproducible
workflows that are flexible and fast enough to use while in development stages,
while able to build snapshots once a stable package collection is found.
As with other functions in a reproducible workflow, this package
emphasizes functions that return the same result whether it is
the first or subsequent times running the function, with subsequent times being
sufficiently fast that they can be run every time without undue waiting burden on
the user or developer.
Author: Eliot J B McIntire [aut, cre] ,
Alex M Chubaty [ctb] ,
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between Require versions 0.2.6 dated 2023-01-05 and 0.3.0 dated 2023-03-14
Require-0.2.6/Require/man/Require-internals.Rd |only Require-0.3.0/Require/DESCRIPTION | 10 Require-0.3.0/Require/MD5 | 44 - Require-0.3.0/Require/NAMESPACE | 4 Require-0.3.0/Require/NEWS.md | 26 Require-0.3.0/Require/R/Require-helpers.R | 156 +--- Require-0.3.0/Require/R/Require2.R | 408 +++++++----- Require-0.3.0/Require/R/extract.R | 5 Require-0.3.0/Require/R/helpers.R | 21 Require-0.3.0/Require/R/pkgDep.R | 277 +++++--- Require-0.3.0/Require/R/setLibPaths.R | 7 Require-0.3.0/Require/R/setup.R | 42 - Require-0.3.0/Require/README.md | 48 - Require-0.3.0/Require/inst/WORDLIST | 10 Require-0.3.0/Require/man/dot-downloadFileMasterMainAuth.Rd |only Require-0.3.0/Require/man/messageVerbose.Rd | 13 Require-0.3.0/Require/man/setLinuxBinaryRepo.Rd | 2 Require-0.3.0/Require/man/setup.Rd | 7 Require-0.3.0/Require/tests/test-helpers.R | 2 Require-0.3.0/Require/tests/testit/test-2extract.R | 3 Require-0.3.0/Require/tests/testit/test-4other.R | 20 Require-0.3.0/Require/tests/testit/test-6pkgDep.R | 2 Require-0.3.0/Require/tests/testit/test-7pkgSnapshotLong.R | 9 Require-0.3.0/Require/tests/testit/test-8modules.R | 2 24 files changed, 681 insertions(+), 437 deletions(-)
Title: R Wrapper for OpenAI API
Description: An R wrapper of OpenAI API endpoints (see
<https://platform.openai.com/docs/introduction> for details). This package
covers Models, Completions, Chat, Edits, Images, Embeddings, Audio, Files,
Fine-tunes, Moderations, and legacy Engines endpoints.
Author: Iegor Rudnytskyi [aut, cre]
Maintainer: Iegor Rudnytskyi <iegor.rudnytskyi@gmail.com>
Diff between openai versions 0.4.0 dated 2023-03-07 and 0.4.1 dated 2023-03-14
DESCRIPTION | 8 ++--- MD5 | 40 ++++++++++++++--------------- NEWS.md | 4 ++ R/create_chat_completion.R | 8 ++--- R/create_embedding.R | 2 - R/create_fine_tune.R | 7 +---- R/create_moderation.R | 12 ++++---- R/create_transcription.R | 7 ++--- R/create_translation.R | 7 ++--- README.md | 3 +- man/create_chat_completion.Rd | 6 ++-- man/create_embedding.Rd | 2 - man/create_fine_tune.Rd | 5 +-- man/create_moderation.Rd | 10 ++++--- man/create_transcription.Rd | 6 ++-- man/create_translation.Rd | 6 ++-- tests/manual/test-create_chat_completion.R | 37 +++++++++++++------------- tests/manual/test-create_embedding.R | 2 - tests/manual/test-create_moderation.R | 5 ++- tests/manual/test-create_transcription.R | 2 - tests/manual/test-create_translation.R | 2 - 21 files changed, 92 insertions(+), 89 deletions(-)
Title: General Smoothing Splines
Description: A comprehensive package for structural multivariate
function estimation using smoothing splines.
Author: Chong Gu <chong@purdue.edu>
Maintainer: Chong Gu <chong@purdue.edu>
Diff between gss versions 2.2-3 dated 2021-08-05 and 2.2-4 dated 2023-03-14
ChangeLog | 11 +++++++++++ DESCRIPTION | 8 ++++---- MD5 | 36 ++++++++++++++++++------------------ R/dsscopu.R | 8 ++++---- R/dssden.R | 2 +- R/gssanova.R | 2 +- R/gssanova1.R | 2 +- R/predict.sscox.R | 2 +- R/predict.ssllrm.R | 2 +- R/ssanova.R | 2 +- R/sscox.R | 2 +- R/sshzd.R | 2 +- R/sshzd1.R | 2 +- R/sshzd2d.R | 10 +++++----- R/sshzd2d1.R | 10 +++++----- R/ssllrm.R | 2 +- R/summary.sscopu.R | 2 +- inst/CITATION | 4 ++-- src/smolyak.c | 8 ++++---- 19 files changed, 64 insertions(+), 53 deletions(-)
Title: Variable Table for Variable Documentation
Description: Automatically generates HTML variable documentation including variable names, labels, classes, value labels (if applicable), value ranges, and summary statistics. See the vignette "vtable" for a package overview.
Author: Nick Huntington-Klein [aut, cre]
Maintainer: Nick Huntington-Klein <nhuntington-klein@seattleu.edu>
Diff between vtable versions 1.4.1 dated 2022-11-02 and 1.4.2 dated 2023-03-14
vtable-1.4.1/vtable/vignettes/lifecycle_variabledocumentation.html |only vtable-1.4.2/vtable/DESCRIPTION | 10 vtable-1.4.2/vtable/MD5 | 56 vtable-1.4.2/vtable/NAMESPACE | 37 vtable-1.4.2/vtable/NEWS.md | 10 vtable-1.4.2/vtable/R/helpers.R | 138 + vtable-1.4.2/vtable/R/independencetest.R | 2 vtable-1.4.2/vtable/R/sumtable.R | 167 + vtable-1.4.2/vtable/R/vtable.R | 6 vtable-1.4.2/vtable/build/vignette.rds |binary vtable-1.4.2/vtable/inst/doc/dftotable.html | 115 - vtable-1.4.2/vtable/inst/doc/labeltable.R | 7 vtable-1.4.2/vtable/inst/doc/labeltable.Rmd | 12 vtable-1.4.2/vtable/inst/doc/labeltable.html | 276 ++ vtable-1.4.2/vtable/inst/doc/sumtable.R | 10 vtable-1.4.2/vtable/inst/doc/sumtable.Rmd | 35 vtable-1.4.2/vtable/inst/doc/sumtable.html | 992 ++++++---- vtable-1.4.2/vtable/inst/doc/vtable.html | 18 vtable-1.4.2/vtable/inst/doc/vtablefunction.Rmd | 4 vtable-1.4.2/vtable/inst/doc/vtablefunction.html | 124 - vtable-1.4.2/vtable/inst/doc/vtablehelpers.R | 5 vtable-1.4.2/vtable/inst/doc/vtablehelpers.Rmd | 20 vtable-1.4.2/vtable/inst/doc/vtablehelpers.html | 226 +- vtable-1.4.2/vtable/man/formatfunc.Rd |only vtable-1.4.2/vtable/man/notNA.Rd | 11 vtable-1.4.2/vtable/man/sumtable.Rd | 408 ++-- vtable-1.4.2/vtable/vignettes/labeltable.Rmd | 12 vtable-1.4.2/vtable/vignettes/sumtable.Rmd | 35 vtable-1.4.2/vtable/vignettes/vtablefunction.Rmd | 4 vtable-1.4.2/vtable/vignettes/vtablehelpers.Rmd | 20 30 files changed, 1773 insertions(+), 987 deletions(-)
Title: Partial Least Squares Regression for Generalized Linear Models
Description: Provides (weighted) Partial least squares Regression for generalized linear models and repeated k-fold cross-validation of such models using various criteria <arXiv:1810.01005>. It allows for missing data in the explanatory variables. Bootstrap confidence intervals constructions are also available.
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between plsRglm versions 1.5.0 dated 2022-05-02 and 1.5.1 dated 2023-03-14
DESCRIPTION | 10 ++-- MD5 | 92 +++++++++++++++++++++---------------------- R/PLS_glm_wvc.R | 2 R/PLS_lm_wvc.R | 2 R/cv.plsR.R | 13 ++---- R/cv.plsRglm.R | 14 +++--- R/cv.plsRglmmodel.default.R | 21 +++++++-- R/cv.plsRglmmodel.formula.R | 23 +++++++--- R/cv.plsRmodel.default.R | 18 ++++++-- R/cv.plsRmodel.formula.R | 21 +++++++-- R/kfolds2Chisq.R | 22 +++++----- R/kfolds2Chisqind.R | 22 +++++----- R/kfolds2Mclassed.R | 4 - R/kfolds2Mclassedind.R | 4 - R/kfolds2Press.R | 12 ++--- R/kfolds2Pressind.R | 12 ++--- R/kfolds2coeff.R | 2 R/plsR.R | 8 +-- R/plsRglm.R | 8 +-- R/plsRglmmodel.default.R | 18 ++++++-- R/plsRglmmodel.formula.R | 21 +++++++-- R/plsRmodel.default.R | 21 +++++++-- R/plsRmodel.formula.R | 24 +++++++---- R/predict.plsRglmmodel.R | 6 +- R/predict.plsRmodel.R | 6 +- R/print.cv.plsRglmmodel.R | 2 R/print.cv.plsRmodel.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 24 ++++++----- man/PLS_glm_wvc.Rd | 2 man/PLS_lm_wvc.Rd | 2 man/cv.plsR.Rd | 18 ++++---- man/cv.plsRglm.Rd | 24 +++++------ man/kfolds2Chisq.Rd | 22 +++++----- man/kfolds2Chisqind.Rd | 22 +++++----- man/kfolds2Mclassed.Rd | 4 - man/kfolds2Mclassedind.Rd | 4 - man/kfolds2Press.Rd | 12 ++--- man/kfolds2Pressind.Rd | 12 ++--- man/kfolds2coeff.Rd | 2 man/plsR.Rd | 12 ++--- man/plsRglm.Rd | 12 ++--- man/predict.plsRglmmodel.Rd | 6 +- man/predict.plsRmodel.Rd | 6 +- man/print.cv.plsRglmmodel.Rd | 2 man/print.cv.plsRmodel.Rd | 2 47 files changed, 333 insertions(+), 265 deletions(-)
Title: 3D Brain Visualization
Description: A fast, interactive cross-platform, and easy to share
'WebGL'-based 3D brain viewer that visualizes 'FreeSurfer' and/or
'AFNI/SUMA' surfaces. The viewer widget can be either standalone or
embedded into 'R-shiny' applications. The standalone version only require
a web browser with 'WebGL2' support (for example, 'Chrome', 'Firefox',
'Safari'), and can be inserted into any websites. The 'R-shiny'
support allows the 3D viewer to be dynamically generated from reactive user
inputs. This feature has been fully adopted by 'RAVE'
<https://openwetware.org/wiki/RAVE>, an interactive toolbox to
analyze 'iEEG' data. Documentation about 'threeBrain' is provided
by <https://dipterix.org/threeBrain/> and several vignettes included
in this package. To cite the package, please check our 'NeuroImage' paper
by Magnotti, Wang, and Beauchamp (2020, <doi:10.1016/j.neuroimage.2020.117341>),
or see 'citation("threeBrain")' for details.
Author: Zhengjia Wang [aut, cre, cph],
John Magnotti [aut, res],
Xiang Zhang [ctb, res],
Brian Metzger [res],
Elizabeth Nesbitt [res],
Meng Li [ths],
Michael Beauchamp [ths, dtc]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between threeBrain versions 0.2.7 dated 2022-10-15 and 0.2.9 dated 2023-03-14
threeBrain-0.2.7/threeBrain/inst/htmlwidgets/lib/dipterixThreeBrain-1.0.1 |only threeBrain-0.2.7/threeBrain/inst/htmlwidgets/lib/threejs-0.101.1 |only threeBrain-0.2.7/threeBrain/man/three_scatter.Rd |only threeBrain-0.2.9/threeBrain/DESCRIPTION | 26 threeBrain-0.2.9/threeBrain/LICENSE | 34 threeBrain-0.2.9/threeBrain/MD5 | 101 +- threeBrain-0.2.9/threeBrain/NAMESPACE | 35 threeBrain-0.2.9/threeBrain/NEWS.md | 44 + threeBrain-0.2.9/threeBrain/R/aaa.R | 74 + threeBrain-0.2.9/threeBrain/R/class_brain.R | 389 ++++++++-- threeBrain-0.2.9/threeBrain/R/class_brainatlas.R | 59 + threeBrain-0.2.9/threeBrain/R/class_brainelectrodes.R | 45 + threeBrain-0.2.9/threeBrain/R/class_brainvolume.R | 2 threeBrain-0.2.9/threeBrain/R/class_multibrain.R | 36 threeBrain-0.2.9/threeBrain/R/fs_brain.R | 2 threeBrain-0.2.9/threeBrain/R/fs_brain2.R | 257 ++++-- threeBrain-0.2.9/threeBrain/R/fs_import-t1.R | 1 threeBrain-0.2.9/threeBrain/R/fs_import-xform.R | 2 threeBrain-0.2.9/threeBrain/R/func_scatter.R | 278 +++---- threeBrain-0.2.9/threeBrain/R/geom_abstract.R | 20 threeBrain-0.2.9/threeBrain/R/geom_datacube.R | 212 +++-- threeBrain-0.2.9/threeBrain/R/geom_datacube2.R | 75 + threeBrain-0.2.9/threeBrain/R/geom_electrode.R | 3 threeBrain-0.2.9/threeBrain/R/loaders.R | 14 threeBrain-0.2.9/threeBrain/R/print.R |only threeBrain-0.2.9/threeBrain/R/s3_geom.R | 10 threeBrain-0.2.9/threeBrain/R/shiny-localization.R | 18 threeBrain-0.2.9/threeBrain/R/simple_server.R |only threeBrain-0.2.9/threeBrain/R/threeBrain.R |only threeBrain-0.2.9/threeBrain/R/threejs_brain.R | 24 threeBrain-0.2.9/threeBrain/R/utils_outer_smooth.R |only threeBrain-0.2.9/threeBrain/R/utils_palette_voxel.R | 25 threeBrain-0.2.9/threeBrain/R/zzz.R | 26 threeBrain-0.2.9/threeBrain/build/vignette.rds |binary threeBrain-0.2.9/threeBrain/inst/CITATION | 28 threeBrain-0.2.9/threeBrain/inst/WORDLIST | 6 threeBrain-0.2.9/threeBrain/inst/doc/A-getting-started.html | 111 +- threeBrain-0.2.9/threeBrain/inst/doc/B-electrode-localization.html | 111 +- threeBrain-0.2.9/threeBrain/inst/doc/C-data-visualization.html | 111 +- threeBrain-0.2.9/threeBrain/inst/favicon.ico |only threeBrain-0.2.9/threeBrain/inst/htmlwidgets/threejs_brain.js | 40 - threeBrain-0.2.9/threeBrain/inst/htmlwidgets/threejs_brain.yaml | 16 threeBrain-0.2.9/threeBrain/inst/palettes/datacube2/FreeSurferColorLUT.json | 2 threeBrain-0.2.9/threeBrain/inst/threeBrainJS |only threeBrain-0.2.9/threeBrain/man/create_group.Rd | 6 threeBrain-0.2.9/threeBrain/man/freesurfer_brain.Rd | 2 threeBrain-0.2.9/threeBrain/man/generate_smooth_envelope.Rd |only threeBrain-0.2.9/threeBrain/man/geom_freemesh.Rd | 2 threeBrain-0.2.9/threeBrain/man/geom_sphere.Rd | 2 threeBrain-0.2.9/threeBrain/man/localization_module.Rd | 9 threeBrain-0.2.9/threeBrain/man/reexports.Rd |only threeBrain-0.2.9/threeBrain/man/threeBrain.Rd |only threeBrain-0.2.9/threeBrain/man/threejs_brain.Rd | 9 threeBrain-0.2.9/threeBrain/man/voxel_colormap.Rd | 4 threeBrain-0.2.9/threeBrain/man/voxel_cube.Rd | 26 55 files changed, 1559 insertions(+), 738 deletions(-)
Title: Tools for Voice Analysis, Speaker Recognition and Mood Inference
Description: Tools for voice analysis, speaker recognition and mood inference.
Gathers 'R' and 'Python' tools to solve problems concerning voice and audio
in general.
Author: Zabala Filipe J. [cre, aut]
Maintainer: Zabala Filipe J. <filipezabala@gmail.com>
Diff between voice versions 0.4.14 dated 2022-09-02 and 0.4.17 dated 2023-03-14
voice-0.4.14/voice/R/poetry.R |only voice-0.4.14/voice/data/id_path.rda |only voice-0.4.14/voice/man/id_path.Rd |only voice-0.4.14/voice/man/poetry.Rd |only voice-0.4.17/voice/DESCRIPTION | 20 voice-0.4.17/voice/MD5 | 46 + voice-0.4.17/voice/NAMESPACE | 2 voice-0.4.17/voice/NEWS.md | 48 + voice-0.4.17/voice/R/conv_df.R | 9 voice-0.4.17/voice/R/diarize.R |only voice-0.4.17/voice/R/extract_features.R | 2 voice-0.4.17/voice/R/feat_summary.R | 4 voice-0.4.17/voice/R/tag.R | 4 voice-0.4.17/voice/README.md | 17 voice-0.4.17/voice/data/mozilla_id_path.rda |only voice-0.4.17/voice/inst/doc/voicegnette_R.R | 35 - voice-0.4.17/voice/inst/doc/voicegnette_R.Rmd | 51 + voice-0.4.17/voice/inst/doc/voicegnette_R.html | 539 +++++++++++++++------ voice-0.4.17/voice/man/diarize.Rd |only voice-0.4.17/voice/man/extract_features.Rd | 2 voice-0.4.17/voice/man/feat_summary.Rd | 4 voice-0.4.17/voice/man/mozilla_id_path.Rd |only voice-0.4.17/voice/man/tag.Rd | 4 voice-0.4.17/voice/tests/extract_f0.py |only voice-0.4.17/voice/tests/extract_formants.py |only voice-0.4.17/voice/tests/libs.py |only voice-0.4.17/voice/vignettes/index.html | 443 +++++++++-------- voice-0.4.17/voice/vignettes/index_2021-11-08.html |only voice-0.4.17/voice/vignettes/index_2022-09-07.html |only voice-0.4.17/voice/vignettes/index_2022-09-14.html |only voice-0.4.17/voice/vignettes/voicegnette_R.Rmd | 51 + 31 files changed, 817 insertions(+), 464 deletions(-)
Title: Functions to Find an Acceptable Python Binary
Description: Package designed to find an acceptable python binary.
Author: Trevor L Davis [aut, cre] ,
Paul Gilbert [aut]
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between findpython versions 1.0.7 dated 2021-01-27 and 1.0.8 dated 2023-03-14
DESCRIPTION | 15 +++++++++------ MD5 | 8 ++++---- NEWS.md | 7 ++++++- R/find_python_cmd.r | 2 +- README.md | 8 ++------ 5 files changed, 22 insertions(+), 18 deletions(-)
Title: Unified Multiple Testing Procedures
Description: Designed to ease the application and comparison of multiple
hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods are
standardized and usable by the accompanying 'mutossGUI'.
Author: MuToss Coding Team , Gilles Blanchard, Thorsten Dickhaus,
Niklas Hack, Frank Konietschke, Kornelius Rohmeyer,
Jonathan Rosenblatt, Marsel Scheer, Wiebke Werft
Maintainer: Kornelius Rohmeyer <rohmeyer@small-projects.de>
Diff between mutoss versions 0.1-12 dated 2017-12-04 and 0.1-13 dated 2023-03-14
DESCRIPTION | 7 ++++--- MD5 | 16 ++++++++-------- NEWS | 7 ++++++- R/Rank_Truncated.R | 4 ++++ build/vignette.rds |binary inst/doc/quickstart.pdf |binary inst/doc/simToolManual.pdf |binary man/adaptiveBH.Rd | 4 +++- man/ranktruncated.Rd | 4 +++- 9 files changed, 28 insertions(+), 14 deletions(-)
Title: Fitting the Multinomial Probit Model
Description: Fits the Bayesian multinomial probit model via Markov chain
Monte Carlo. The multinomial probit model is often used to analyze
the discrete choices made by individuals recorded in survey data.
Examples where the multinomial probit model may be useful include the
analysis of product choice by consumers in market research and the
analysis of candidate or party choice by voters in electoral studies.
The MNP package can also fit the model with different choice sets for
each individual, and complete or partial individual choice orderings
of the available alternatives from the choice set. The estimation is
based on the efficient marginal data augmentation algorithm that is
developed by Imai and van Dyk (2005). "A Bayesian Analysis of the
Multinomial Probit Model Using the Data Augmentation." Journal of
Econometrics, Vol. 124, No. 2 (February), pp. 311-334.
<doi:10.1016/j.jeconom.2004.02.002> Detailed examples are given in
Imai and van Dyk (2005). "MNP: R Package for Fitting the Multi [...truncated...]
Author: Kosuke Imai [aut, cre],
David van Dyk [aut],
Hubert Jin [ctb]
Maintainer: Kosuke Imai <imai@harvard.edu>
Diff between MNP versions 3.1-3 dated 2022-04-07 and 3.1-4 dated 2023-03-14
MNP-3.1-3/MNP/R/cov.mnp.R |only MNP-3.1-3/MNP/man/cov.mnp.Rd |only MNP-3.1-4/MNP/ChangeLog | 9 + MNP-3.1-4/MNP/DESCRIPTION | 12 +- MNP-3.1-4/MNP/MD5 | 52 +++++------ MNP-3.1-4/MNP/NAMESPACE | 20 +--- MNP-3.1-4/MNP/R/coef.mnp.R | 17 +-- MNP-3.1-4/MNP/R/mnp.R | 109 +++++++++++------------ MNP-3.1-4/MNP/R/onAttach.R | 6 - MNP-3.1-4/MNP/R/predict.mnp.R | 39 ++++---- MNP-3.1-4/MNP/R/print.mnp.R | 1 MNP-3.1-4/MNP/R/print.summary.mnp.R | 19 +--- MNP-3.1-4/MNP/R/summary.mnp.R | 23 ++-- MNP-3.1-4/MNP/R/vcov.mnp.R |only MNP-3.1-4/MNP/R/xmatrix.mnp.R | 2 MNP-3.1-4/MNP/R/ymatrix.mnp.R | 10 +- MNP-3.1-4/MNP/build/vignette.rds |binary MNP-3.1-4/MNP/inst/doc/MNP.Rnw | 150 ++++++++++++++++---------------- MNP-3.1-4/MNP/inst/doc/MNP.pdf |binary MNP-3.1-4/MNP/man/coef.mnp.Rd | 5 - MNP-3.1-4/MNP/man/detergent.Rd | 6 - MNP-3.1-4/MNP/man/japan.Rd | 6 - MNP-3.1-4/MNP/man/mnp.Rd | 52 +++++++---- MNP-3.1-4/MNP/man/predict.mnp.Rd | 28 +++--- MNP-3.1-4/MNP/man/summary.mnp.Rd | 4 MNP-3.1-4/MNP/man/vcov.mnp.Rd |only MNP-3.1-4/MNP/src/MNP.c | 168 ++++++++++++++++++------------------ MNP-3.1-4/MNP/src/init.c | 6 - MNP-3.1-4/MNP/vignettes/MNP.Rnw | 150 ++++++++++++++++---------------- 29 files changed, 457 insertions(+), 437 deletions(-)
Title: Latent Variable Analysis
Description: Fit a variety of latent variable models, including confirmatory
factor analysis, structural equation modeling and latent growth curve models.
Author: Yves Rosseel [aut, cre] ,
Terrence D. Jorgensen [aut] ,
Nicholas Rockwood [aut] ,
Daniel Oberski [ctb],
Jarrett Byrnes [ctb],
Leonard Vanbrabant [ctb],
Victoria Savalei [ctb],
Ed Merkle [ctb],
Michael Hallquist [ctb],
Mijke Rhemtulla [ctb],
Myrsini K [...truncated...]
Maintainer: Yves Rosseel <Yves.Rosseel@UGent.be>
Diff between lavaan versions 0.6-14 dated 2023-02-09 and 0.6-15 dated 2023-03-14
DESCRIPTION | 6 +-- MD5 | 25 ++++++++-------- NAMESPACE | 2 - R/lav_bootstrap.R | 2 - R/lav_cfa_jamesstein.R |only R/lav_cfa_utils.R | 74 ++++++++++++++++++++++++++++++++++++++++++++++++ R/lav_cor.R | 21 +++++++++++-- R/lav_fit_measures.R | 2 - R/lav_matrix.R | 54 ++++++++++++++++++++++++++++++++++- R/lav_optim_noniter.R | 11 ++++++- R/lav_options.R | 23 ++++++++++---- R/lav_partable_vnames.R | 3 + R/lav_print.R | 31 ++++++++++++++++++++ man/lavCor.Rd | 5 ++- 14 files changed, 226 insertions(+), 33 deletions(-)
Title: Spatial Visualization with ggplot2
Description: A collection of functions to visualize spatial data and models
on top of static maps from various online sources (e.g Google Maps and Stamen
Maps). It includes tools common to those tasks, including functions for
geolocation and routing.
Author: David Kahle [aut, cre] ,
Hadley Wickham [aut] ,
Scott Jackson [aut],
Mikko Korpela [ctb]
Maintainer: David Kahle <david@kahle.io>
Diff between ggmap versions 3.0.1 dated 2022-11-03 and 3.0.2 dated 2023-03-14
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 6 ++++++ R/attach.R | 20 ++++++++++++++++++-- README.md | 21 ++++++++++++++------- inst/CITATION | 5 ++--- tools/README-faceting-1.png |binary tools/README-google_maps-1.png |binary tools/README-maptypes-1.png |binary tools/README-qmplot-1.png |binary tools/README-route_trek-1.png |binary tools/README-styling-1.png |binary 12 files changed, 54 insertions(+), 26 deletions(-)
Title: Animated Interactive Grammar of Graphics
Description: Functions are provided for defining animated,
interactive data visualizations in R code, and rendering
on a web page. The 2018 Journal of Computational and
Graphical Statistics paper,
<doi:10.1080/10618600.2018.1513367>
describes the concepts implemented.
Author: Toby Hocking [aut, cre] ,
Hadley Wickham [aut] ,
Winston Chang [aut] ,
RStudio [cph] ,
Nicholas Lewin-Koh [aut] ,
Martin Maechler [aut] ,
Randall Prium [aut] ,
Susan VanderPlas [aut] ,
Carson Sievert [aut] ,
Kevin Ferris [aut] ,
Jun Cai [aut] ,
Faiza [...truncated...]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between animint2 versions 2022.9.14 dated 2022-09-15 and 2023.3.14 dated 2023-03-14
DESCRIPTION | 18 +++++--- MD5 | 44 +++++++++++---------- NAMESPACE | 1 NEWS | 10 ++++ R/facet-.r | 2 R/grob-dotstack.r | 3 - R/guides-.r | 8 +-- R/stat-ellipse.R | 3 - R/theme-defaults.r | 3 - R/uu_zzz.r | 8 +-- R/z_animint.R | 25 ++++++++---- R/z_animintHelpers.R | 9 ---- R/z_print.R | 2 build/partial.rdb |binary inst/htmljs/animint.js | 21 +++++----- man/animint.Rd | 2 man/graphical-units.Rd |only man/scale_brewer.Rd | 7 +-- man/stat_ellipse.Rd | 3 - tests/testthat/helper-functions.R | 12 +++++ tests/testthat/pids.txt | 2 tests/testthat/test-renderer1-facets-strips.R | 4 - tests/testthat/test-renderer1-theme-text-size.R | 49 +++++++++++++++++++++++- tests/testthat/testthat-problems.rds |only 24 files changed, 155 insertions(+), 81 deletions(-)
Title: ADaM in R Asset Library
Description: A toolbox for programming Clinical Data Interchange Standards Consortium
(CDISC) compliant Analysis Data Model (ADaM) datasets in R. ADaM datasets are a
mandatory part of any New Drug or Biologics License Application submitted to the
United States Food and Drug Administration (FDA). Analysis derivations are
implemented in accordance with the "Analysis Data Model Implementation Guide"
(CDISC Analysis Data Model Team, 2021, <https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package>).
Author: Thomas Neitmann [aut, cre],
Stefan Bundfuss [aut],
Ben Straub [aut],
Samia Kabi [aut],
Gordon Miller [aut],
Teckla Akinyi [aut],
Andrew Smith [aut],
Konstantina Koukourikou [aut],
Ross Farrugia [aut],
Eric Simms [aut],
Annie Yang [aut],
Robin Koeger [...truncated...]
Maintainer: Thomas Neitmann <thomas.neitmann@roche.com>
Diff between admiral versions 0.10.0 dated 2023-03-08 and 0.10.1 dated 2023-03-14
DESCRIPTION | 12 MD5 | 40 - NEWS.md | 5 R/derive_date_vars.R | 24 - build/vignette.rds |binary inst/doc/adsl.html | 690 ++++++------------------------ inst/doc/bds_exposure.html | 523 ++++------------------- inst/doc/bds_finding.html | 736 ++++++--------------------------- inst/doc/bds_tte.html | 578 +++++-------------------- inst/doc/generic.html | 505 ++++------------------ inst/doc/higher_order.html | 424 +++---------------- inst/doc/hys_law.html | 433 +++---------------- inst/doc/imputation.html | 493 ++++------------------ inst/doc/lab_grading.html | 590 +++++--------------------- inst/doc/occds.html | 498 ++++------------------ inst/doc/pk_adnca.html | 673 ++++-------------------------- inst/doc/queries_dataset.html | 392 ++--------------- inst/doc/questionnaires.html | 479 +++------------------ inst/doc/visits_periods.html | 407 +++--------------- man/admiral-package.Rd | 3 tests/testthat/test-derive_date_vars.R | 112 +++-- 21 files changed, 1529 insertions(+), 6088 deletions(-)
Title: Power Simulation for Sequential Analyses and Multiple Hypotheses
Description: Calculates, via simulation, power and appropriate stopping
alpha boundaries (and/or futility bounds) for sequential analyses (i.e.,
group sequential design) as well as for multiple hypotheses (multiple tests
included in an analysis), given any specified global error rate. This enables
the sequential use of practically any significance test, as long as the
underlying data can be simulated in advance to a reasonable approximation.
Lukács (2022) <doi:10.21105/joss.04643>.
Author: Gaspar Lukacs [aut, cre]
Maintainer: Gaspar Lukacs <lkcsgaspar@gmail.com>
Diff between POSSA versions 0.6.1 dated 2022-08-29 and 0.6.3 dated 2023-03-14
POSSA-0.6.1/POSSA/build |only POSSA-0.6.1/POSSA/inst |only POSSA-0.6.1/POSSA/vignettes |only POSSA-0.6.3/POSSA/DESCRIPTION | 14 POSSA-0.6.3/POSSA/MD5 | 39 -- POSSA-0.6.3/POSSA/R/pow.R | 10 POSSA-0.6.3/POSSA/R/sim.R | 18 - POSSA-0.6.3/POSSA/README.md | 4 POSSA-0.6.3/POSSA/man/get_p.Rd | 6 POSSA-0.6.3/POSSA/man/pow.Rd | 4 POSSA-0.6.3/POSSA/man/sim.Rd | 7 POSSA-0.6.3/POSSA/tests/testthat/test_1_ttests.R | 158 +++++------ POSSA-0.6.3/POSSA/tests/testthat/test_2_factors.R | 182 ++++++------ POSSA-0.6.3/POSSA/tests/testthat/test_5_aov.R | 316 +++++++++++----------- POSSA-0.6.3/POSSA/tests/testthat/test_get_p.R | 275 +++++++++---------- 15 files changed, 522 insertions(+), 511 deletions(-)
Title: Package to Patch '.dvi' or '.synctex' Files
Description: Functions to patch specials in '.dvi' files,
or entries in '.synctex' files. Works with concordance=TRUE
in Sweave, knitr or R Markdown to link sources to previews.
Author: Duncan Murdoch
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between patchDVI versions 1.10.1 dated 2020-05-08 and 1.11.0 dated 2023-03-14
patchDVI-1.10.1/patchDVI/inst/NEWS |only patchDVI-1.10.1/patchDVI/inst/doc/patchDVI.Rnw |only patchDVI-1.10.1/patchDVI/inst/doc/patchDVI.pdf |only patchDVI-1.10.1/patchDVI/vignettes/patchDVI.Rnw |only patchDVI-1.10.1/patchDVI/vignettes/sample.Rnw.txt |only patchDVI-1.11.0/patchDVI/DESCRIPTION | 19 patchDVI-1.11.0/patchDVI/MD5 | 66 + patchDVI-1.11.0/patchDVI/NAMESPACE | 20 patchDVI-1.11.0/patchDVI/NEWS.md |only patchDVI-1.11.0/patchDVI/R/SweaveAll.R | 130 +-- patchDVI-1.11.0/patchDVI/R/knitr.R | 22 patchDVI-1.11.0/patchDVI/R/needsPackages.R | 8 patchDVI-1.11.0/patchDVI/R/patchDVI.R | 440 +++++------ patchDVI-1.11.0/patchDVI/R/patchLog.R | 385 ++++----- patchDVI-1.11.0/patchDVI/R/patchPDF.R | 848 ++++++++++------------ patchDVI-1.11.0/patchDVI/R/patchmark.R |only patchDVI-1.11.0/patchDVI/R/rstudio.R | 42 - patchDVI-1.11.0/patchDVI/R/texi2dvi.R | 212 ++--- patchDVI-1.11.0/patchDVI/R/zzz.R | 10 patchDVI-1.11.0/patchDVI/README.md |only patchDVI-1.11.0/patchDVI/build/vignette.rds |binary patchDVI-1.11.0/patchDVI/inst/doc/Japanese.Rnw | 58 - patchDVI-1.11.0/patchDVI/inst/doc/Japanese.pdf |binary patchDVI-1.11.0/patchDVI/inst/doc/patchDVI.R | 51 - patchDVI-1.11.0/patchDVI/inst/doc/patchDVI.Rmd |only patchDVI-1.11.0/patchDVI/inst/doc/patchDVI.html |only patchDVI-1.11.0/patchDVI/inst/sample |only patchDVI-1.11.0/patchDVI/man/SweaveAll.Rd | 26 patchDVI-1.11.0/patchDVI/man/SweaveMiktex.Rd | 81 +- patchDVI-1.11.0/patchDVI/man/knitPDF.Rd | 97 -- patchDVI-1.11.0/patchDVI/man/patchDVI.Rd | 218 ++--- patchDVI-1.11.0/patchDVI/man/pdf_documentC.Rd |only patchDVI-1.11.0/patchDVI/man/pdf_with_patches.Rd |only patchDVI-1.11.0/patchDVI/man/renderPDF.Rd |only patchDVI-1.11.0/patchDVI/src/patchDVI.c | 308 +++---- patchDVI-1.11.0/patchDVI/vignettes/Japanese.Rnw | 58 - patchDVI-1.11.0/patchDVI/vignettes/patchDVI.Rmd |only patchDVI-1.11.0/patchDVI/vignettes/patchDVI.bib | 30 38 files changed, 1534 insertions(+), 1595 deletions(-)
Title: Standardized Folder Names
Description: Supports the use of standardized folder names.
Author: Brian High [aut, cre],
University of Washington [cph, fnd]
Maintainer: Brian High <bhigh@live.com>
Diff between folders versions 0.0.6 dated 2023-03-14 and 0.0.8 dated 2023-03-14
DESCRIPTION | 6 +- MD5 | 22 +++---- R/cleanup_folders.R | 20 ++++--- R/create_folders.R | 6 +- R/get_folders.R | 19 ++++-- README.md | 95 ++++++++++++++++++---------------- man/cleanup_folders.Rd | 8 +- man/create_folders.Rd | 6 +- man/get_folders.Rd | 10 +-- tests/testthat/test-cleanup_folders.R | 75 ++++++++++++++++++++------ tests/testthat/test-create_folders.R | 9 +-- tests/testthat/test-get_folders.R | 29 ++++++++-- 12 files changed, 193 insertions(+), 112 deletions(-)
Title: Deterministic Categorization of Items Based on External Code
Data
Description: Fast categorization of items based on external code data identified by
regular expressions. A typical use case considers patient with medically coded
data, such as codes from the International Classification of Diseases ('ICD') or
the Anatomic Therapeutic Chemical ('ATC') classification system.
Functions of the package relies on a triad of objects: (1) case data with unit
id:s and possible dates of interest; (2) external code data for corresponding
units in (1) and with optional dates of interest and; (3) a classification
scheme ('classcodes' object) with regular expressions to identify and
categorize relevant codes from (2).
It is easy to introduce new classification schemes ('classcodes' objects) or
to use default schemes included in the package. Use cases includes patient
categorization based on 'comorbidity indices' such as 'Charlson', 'Elixhauser',
'RxRisk V', or the 'comorbidity-polypharmacy' score (CPS), as well as adverse
events after hip and knee replacement surgery.
Author: Erik Bulow [aut, cre] ,
Emely C Zabore [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/381>),
David Robinson [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/381>)
Maintainer: Erik Bulow <eriklgb@gmail.com>
Diff between coder versions 0.13.8 dated 2022-08-29 and 0.13.10 dated 2023-03-14
coder-0.13.10/coder/DESCRIPTION | 8 coder-0.13.10/coder/MD5 | 61 +-- coder-0.13.10/coder/NEWS.md | 4 coder-0.13.10/coder/R/as.keyvalue.R | 3 coder-0.13.10/coder/R/manual_for_datasets.R | 16 coder-0.13.10/coder/README.md | 81 +--- coder-0.13.10/coder/build/vignette.rds |binary coder-0.13.10/coder/data/charlson.rda |binary coder-0.13.10/coder/data/cps.rda |binary coder-0.13.10/coder/data/elixhauser.rda |binary coder-0.13.10/coder/data/ex_atc.rda |binary coder-0.13.10/coder/data/ex_icd10.rda |binary coder-0.13.10/coder/data/ex_people.rda |binary coder-0.13.10/coder/data/hip_ae.rda |binary coder-0.13.10/coder/data/hip_ae_hailer.rda |binary coder-0.13.10/coder/data/knee_ae.rda |binary coder-0.13.10/coder/data/rxriskv.rda |binary coder-0.13.10/coder/inst/doc/Interpret_regular_expressions.html | 133 +++---- coder-0.13.10/coder/inst/doc/classcodes.html | 149 ++++---- coder-0.13.10/coder/inst/doc/coder.html | 173 ++++------ coder-0.13.10/coder/inst/doc/ex_data.html | 171 ++++----- coder-0.13.10/coder/man/ae.Rd | 6 coder-0.13.10/coder/man/as.keyvalue.classcodes.Rd | 4 coder-0.13.10/coder/man/categorize.Rd | 7 coder-0.13.10/coder/man/charlson.Rd | 5 coder-0.13.10/coder/man/codebook.Rd | 4 coder-0.13.10/coder/man/cps.Rd | 1 coder-0.13.10/coder/man/elixhauser.Rd | 3 coder-0.13.10/coder/man/examples/categorize.R | 7 coder-0.13.10/coder/man/examples/codebook.R | 4 coder-0.13.10/coder/man/rxriskv.Rd | 1 coder-0.13.8/coder/build/partial.rdb |only 32 files changed, 402 insertions(+), 439 deletions(-)
Title: Fetch Zonal Statistics of Weather Indicators for Brazilian
Municipalities
Description: Fetches zonal statistics from weather indicators that were calculated for each municipality in Brazil using data from the BR-DWGD and TerraClimate projects.
Zonal statistics such as mean, maximum, minimum, standard deviation, and sum were computed by taking into account the data cells that intersect the boundaries of each municipality and stored in Parquet files. This procedure was carried out for all Brazilian municipalities, and for all available dates, for every indicator available in the weather products (BR-DWGD and TerraClimate projects). This package queries on-line the already calculated statistics on the Parquet files and returns easy-to-use data.frames.
Author: Raphael Saldanha [aut, cre] ,
Reza Akbarinia [aut],
Patrick Valduriez [aut],
Marcel Pedroso [aut],
Victor Ribeiro [aut],
Carlos Cardoso [aut],
Eduardo Pena [aut],
Fabio Porto [aut]
Maintainer: Raphael Saldanha <raphael.de-freitas-saldanha@inria.fr>
Diff between brclimr versions 0.1.1 dated 2023-03-12 and 0.1.2 dated 2023-03-14
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/fetch_data.R | 4 ++-- README.md | 8 ++++++-- data/brdwgd_data.rda |binary data/terraclimate_data.rda |binary man/fetch_data.Rd | 4 ++-- man/figures/README-unnamed-chunk-8-1.png |binary 9 files changed, 26 insertions(+), 17 deletions(-)
Title: Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets
Description: Several implementations of a novel Bayesian hierarchical statistical model of nucleotide
recoding RNA-seq experiments (NR-seq; TimeLapse-seq, SLAM-seq, TUC-seq, etc.)
for analyzing and comparing NR-seq datasets (see 'Vock and Simon' (2022) <doi:10.1101/2022.09.02.505697>).
NR-seq is a powerful extension of RNA-seq that provides information about the kinetics
of RNA metabolism (e.g., RNA degradation rate constants), which is notably lacking
in standard RNA-seq data. The statistical model makes maximal use of these high-throughput
datasets by sharing information across transcripts to significantly improve
uncertainty quantification and increase statistical power. 'bakR' includes a maximally
efficient implementation of this model for conservative initial investigations of datasets. 'bakR'
also provides more highly powered implementations using the probabilistic programming language
'Stan' to sample from the full posterior distribution. 'bakR' performs multiple-test
adjusted statisti [...truncated...]
Author: Isaac Vock [aut, cre]
Maintainer: Isaac Vock <isaac.vock@gmail.com>
Diff between bakR versions 0.2.4 dated 2022-10-10 and 0.4.0 dated 2023-03-14
DESCRIPTION | 10 MD5 | 67 NAMESPACE | 2 NEWS.md | 90 - R/Fast_analysis.R | 2099 +++++++++++++------------ R/Fitting_Models.R | 932 +++++------ R/NSSHeat.R | 628 +++++-- R/QC.R |only R/Simulations.R | 1610 ++++++++++--------- R/TL_stan.R | 622 +++---- R/Visualizations.R | 846 +++++----- R/bakRData.R | 432 ++--- R/cBprocessing.R | 1191 +++++++------- README.md | 8 build/vignette.rds |binary configure |only configure.win |only inst/doc/Further-Analyses.R | 9 inst/doc/Further-Analyses.Rmd | 9 inst/doc/Further-Analyses.html | 165 +- inst/doc/Getting-Started.Rmd | 622 +++---- inst/doc/Getting-Started.html | 152 - man/FnPCA.Rd | 2 man/NSSHeat2.Rd |only man/QC_checks.Rd |only man/Simulate_bakRData.Rd | 11 man/bakRFit.Rd | 6 man/fast_analysis.Rd | 2 src/Makevars | 4 src/Makevars.win | 4 src/stanExports_Hybrid2.h | 2505 ++++++++++++++++-------------- src/stanExports_Hybrid_NSS2.h | 2527 ++++++++++++++++-------------- src/stanExports_MCMC.h | 3325 +++++++++++++++++++++------------------- src/stanExports_MCMC_NSS2.h | 3347 +++++++++++++++++++++-------------------- src/stanExports_Mutrate_est2.h | 1814 ++++++++++++---------- vignettes/Further-Analyses.Rmd | 9 vignettes/Getting-Started.Rmd | 622 +++---- 37 files changed, 12613 insertions(+), 11059 deletions(-)
Title: Oncology Extension Package for ADaM in 'R' Asset Library
Description: Programming oncology specific Clinical Data Interchange Standards Consortium
(CDISC) compliant Analysis Data Model (ADaM) datasets in 'R'. ADaM datasets are a
mandatory part of any New Drug or Biologics License Application submitted to the
United States Food and Drug Administration (FDA). Analysis derivations are
implemented in accordance with the "Analysis Data Model Implementation Guide"
(CDISC Analysis Data Model Team (2021), <https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package>).
The package is an extension package of the 'admiral' package.
Author: Stefan Bundfuss [aut, cre],
Ross Farrugia [aut],
Amit Jain [aut],
Andrew Smith [aut],
Teckla Akinyi [aut],
Samia Kabi [aut],
Stephen Gormley [aut],
Hinal Patel [aut],
Karl Kennedy [ctb],
Matt Marino [ctb],
Gopi Vegesna [ctb],
Thomas Neitmann [ctb],
A [...truncated...]
Maintainer: Stefan Bundfuss <stefan.bundfuss@roche.com>
Diff between admiralonco versions 0.2.0 dated 2022-12-07 and 0.3.0 dated 2023-03-14
DESCRIPTION | 12 MD5 | 103 +++--- NAMESPACE | 10 NEWS.md | 17 + R/admiralonco-package.R | 8 R/check_crpr.R | 18 - R/derive_param_bor.R | 32 -- R/derive_param_clinbenefit.R | 30 - R/derive_param_confirmed_bor.R | 54 +-- R/derive_param_confirmed_resp.R | 42 +- R/derive_param_lasta.R | 12 R/derive_param_response.R | 21 - R/filter_pd.R | 10 R/tte_sources.R | 12 R/utils.R | 2 README.md | 14 build/vignette.rds |binary data/admiral_adrs.rda |binary inst/WORDLIST | 9 inst/doc/admiralonco.R | 2 inst/doc/admiralonco.Rmd | 2 inst/doc/admiralonco.html | 5 inst/doc/adrs.R | 88 ++--- inst/doc/adrs.Rmd | 88 ++--- inst/doc/adrs.html | 336 ++++++++++------------ inst/doc/adtr.R |only inst/doc/adtr.Rmd |only inst/doc/adtr.html |only inst/doc/adtte.R | 45 +- inst/doc/adtte.Rmd | 49 +-- inst/doc/adtte.html | 193 ++++++------ inst/templates/ad_adrs.R | 46 +-- inst/templates/ad_adtr.R |only inst/templates/ad_adtte.R | 34 -- man/admiral_adrs.Rd | 2 man/derive_param_bor.Rd | 14 man/derive_param_clinbenefit.Rd | 12 man/derive_param_confirmed_bor.Rd | 14 man/derive_param_confirmed_resp.Rd | 10 man/derive_param_lasta.Rd | 12 man/derive_param_response.Rd | 8 man/filter_pd.Rd | 2 man/get_crpr_dataset.Rd | 3 man/signal_crpr.Rd | 7 tests/testthat/test-check_crpr.R | 52 +-- tests/testthat/test-deprecation.R | 2 tests/testthat/test-derive_param_bor.R | 17 - tests/testthat/test-derive_param_clinbenefit.R | 8 tests/testthat/test-derive_param_confirmed_bor.R | 32 +- tests/testthat/test-derive_param_confirmed_resp.R | 9 tests/testthat/test-derive_param_response.R | 5 vignettes/admiralonco.Rmd | 2 vignettes/adrs.Rmd | 88 ++--- vignettes/adtr.Rmd |only vignettes/adtte.Rmd | 49 +-- 55 files changed, 811 insertions(+), 831 deletions(-)
Title: Plots of the Empirical Attainment Function
Description: Computation and visualization of the empirical attainment function (EAF) for the analysis of random sets in multi-criterion optimization. M. López-Ibáñez, L. Paquete, and T. Stützle (2010) <doi:10.1007/978-3-642-02538-9_9>.
Author: Manuel Lopez-Ibanez [aut, cre]
,
Marco Chiarandini [aut],
Carlos Fonseca [aut],
Luis Paquete [aut],
Thomas Stuetzle [aut],
Mickael Binois [ctb]
Maintainer: Manuel Lopez-Ibanez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between eaf versions 2.4 dated 2023-01-12 and 2.4.1 dated 2023-03-14
DESCRIPTION | 8 MD5 | 42 - NEWS.md | 4 R/eaf-package.R | 23 R/eaf.R | 6 build/partial.rdb |binary configure | 1585 ++++++++++-------------------------------- configure.ac | 30 inst/CITATION | 44 - inst/REFERENCES.bib | 26 man/eaf-package.Rd | 27 man/eafs.Rd | 5 man/figures/eafdiff-color.png |binary src/eaf/cvector.h | 3 src/eaf/eaf.c | 8 src/eaf/eaf3d.c | 4 src/eaf/gcc_attribs.h | 18 src/eaf/io.c | 2 src/eaf/svn_version | 2 src/mo-tools/gcc_attribs.h | 18 src/mo-tools/io.c | 2 src/mo-tools/svn_version | 2 22 files changed, 552 insertions(+), 1307 deletions(-)
Title: Bayesian Regression Models using 'Stan'
Description: Fit Bayesian generalized (non-)linear multivariate multilevel models
using 'Stan' for full Bayesian inference. A wide range of distributions
and link functions are supported, allowing users to fit -- among others --
linear, robust linear, count data, survival, response times, ordinal,
zero-inflated, hurdle, and even self-defined mixture models all in a
multilevel context. Further modeling options include both theory-driven and
data-driven non-linear terms, auto-correlation structures, censoring and
truncation, meta-analytic standard errors, and quite a few more.
In addition, all parameters of the response distribution can be predicted
in order to perform distributional regression. Prior specifications are
flexible and explicitly encourage users to apply prior distributions that
actually reflect their prior knowledge. Models can easily be evaluated and
compared using several methods assessing posterior or prior predictions.
References: Bürkner (2017) <doi:10.18637/jss.v080.i01>;
B [...truncated...]
Author: Paul-Christian Buerkner [aut, cre],
Jonah Gabry [ctb],
Sebastian Weber [ctb],
Andrew Johnson [ctb],
Martin Modrak [ctb],
Hamada S. Badr [ctb],
Frank Weber [ctb],
Mattan S. Ben-Shachar [ctb],
Hayden Rabel [ctb],
Simon C. Mills [ctb],
Stephen Wild [ctb]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between brms versions 2.18.0 dated 2022-09-19 and 2.19.0 dated 2023-03-14
DESCRIPTION | 22 +- MD5 | 191 +++++++++-------- NAMESPACE | 6 NEWS.md | 24 ++ R/autocor.R | 12 - R/bridgesampling.R | 18 + R/brmsfit-helpers.R | 26 +- R/brmsfit-methods.R | 10 R/brmsformula.R | 2 R/brmsterms.R | 9 R/conditional_effects.R | 79 ++++--- R/data-predictor.R | 32 ++ R/data-response.R | 40 ++- R/diagnostics.R | 27 +- R/distributions.R | 67 +++--- R/emmeans.R | 2 R/exclude_pars.R | 8 R/families.R | 37 ++- R/family-lists.R | 19 + R/formula-ac.R | 100 ++++++--- R/formula-ad.R | 32 +- R/formula-gp.R | 6 R/formula-re.R | 15 - R/formula-sm.R | 16 + R/formula-sp.R | 18 - R/kfold.R | 15 - R/log_lik.R | 55 ++++- R/loo.R | 8 R/loo_moment_match.R | 15 + R/lsp.R | 2 R/make_standata.R | 5 R/misc.R | 21 + R/posterior_epred.R | 32 ++ R/posterior_predict.R | 108 +++++---- R/predictor.R | 26 +- R/prepare_predictions.R | 26 ++ R/priors.R | 44 ++-- R/projpred.R | 161 +++++++++++--- R/reloo.R | 9 R/rename_pars.R | 20 + R/stan-helpers.R | 193 +++++++++++++---- R/stan-likelihood.R | 75 +++++- R/stan-predictor.R | 195 +++++++++++------ R/stan-prior.R | 5 R/stan-response.R | 121 +++++++++++ R/stanvars.R | 2 R/summary.R | 120 ++++++----- README.md | 77 +++---- build/vignette.rds |binary inst/chunks/fun_cauchit.stan | 22 +- inst/chunks/fun_cloglog.stan | 11 - inst/chunks/fun_is_equal.stan |only inst/chunks/fun_logm1.stan | 22 +- inst/chunks/fun_normal_time.stan | 142 +++++++++---- inst/chunks/fun_normal_time_se.stan |only inst/chunks/fun_scale_time_err.stan | 48 ++++ inst/chunks/fun_softit.stan | 22 +- inst/chunks/fun_softplus.stan | 11 - inst/chunks/fun_squareplus.stan | 22 +- inst/chunks/fun_stack_vectors.stan |only inst/chunks/fun_student_t_time.stan | 102 ++++++--- inst/chunks/fun_student_t_time_se.stan |only inst/chunks/fun_tan_half.stan | 23 +- inst/doc/brms_customfamilies.html | 183 ++++++++-------- inst/doc/brms_distreg.html | 209 +++++++++---------- inst/doc/brms_families.html | 42 ++- inst/doc/brms_missings.html | 169 +++++++-------- inst/doc/brms_monotonic.html | 250 +++++++++++----------- inst/doc/brms_multilevel.pdf |binary inst/doc/brms_multivariate.html | 294 +++++++++++++-------------- inst/doc/brms_nonlinear.html | 226 ++++++++++---------- inst/doc/brms_overview.pdf |binary inst/doc/brms_phylogenetics.html | 229 ++++++++++----------- inst/doc/brms_threading.html | 266 ++++++++++++------------ man/GenExtremeValue.Rd | 12 + man/StudentT.Rd | 2 man/autocor-terms.Rd | 14 - man/bridge_sampler.brmsfit.Rd | 7 man/brmsfamily.Rd | 26 +- man/conditional_effects.brmsfit.Rd | 32 +- man/diagnostic-quantities.Rd | 4 man/figures/README-conditional_effects-1.png |binary man/figures/README-plot-1.png |binary man/figures/brms.png |binary man/get_refmodel.brmsfit.Rd | 14 + man/horseshoe.Rd | 12 - man/kfold.brmsfit.Rd | 5 man/loo_moment_match.brmsfit.Rd | 6 man/prepare_predictions.Rd | 5 man/reloo.brmsfit.Rd | 5 man/s.Rd | 16 + man/unstr.Rd |only tests/testthat/tests.brmsfit-methods.R | 14 - tests/testthat/tests.distributions.R | 5 tests/testthat/tests.families.R | 9 tests/testthat/tests.log_lik.R | 12 - tests/testthat/tests.make_stancode.R | 136 ++++++++++-- tests/testthat/tests.make_standata.R | 11 + tests/testthat/tests.posterior_predict.R | 11 - 99 files changed, 3035 insertions(+), 1769 deletions(-)
Title: 3D Scatter Plot
Description: Plots a three dimensional (3D) point cloud.
Author: Uwe Ligges <ligges@statistik.tu-dortmund.de>, Martin Maechler, Sarah Schnackenberg
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between scatterplot3d versions 0.3-42 dated 2022-09-08 and 0.3-43 dated 2023-03-14
CHANGES | 5 ++++- DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/scatterplot3d.R | 12 ++++++------ inst/CITATION | 6 +++--- inst/doc/s3d.pdf |binary man/scatterplot3d.Rd | 17 ++++++++++------- 7 files changed, 33 insertions(+), 27 deletions(-)
Title: MultiDimensional Feature Selection
Description: Functions for MultiDimensional Feature Selection (MDFS):
calculating multidimensional information gains, scoring variables,
finding important variables, plotting selection results.
This package includes an optional CUDA implementation that speeds up
information gain calculation using NVIDIA GPGPUs.
R. Piliszek et al. (2019) <doi:10.32614/RJ-2019-019>.
Author: Radoslaw Piliszek [aut, cre],
Krzysztof Mnich [aut],
Pawel Tabaszewski [aut],
Szymon Migacz [aut],
Andrzej Sulecki [aut],
Witold Remigiusz Rudnicki [aut]
Maintainer: Radoslaw Piliszek <r.piliszek@uwb.edu.pl>
Diff between MDFS versions 1.4.0 dated 2023-01-31 and 1.5.0 dated 2023-03-14
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 12 ++++++++++++ R/information_gain.R | 5 +---- R/tuples.R | 7 +------ R/utils.R | 4 ++-- man/GetRange.Rd | 4 ++-- 7 files changed, 28 insertions(+), 24 deletions(-)
Title: Creating and Representing Functional Trait Spaces
Description: Estimation of functional spaces based on traits of organisms.
The package includes functions to impute missing trait values (with or
without considering phylogenetic information), and to create,
represent and analyse two dimensional functional spaces based on
principal components analysis, other ordination methods, or raw
traits. It also allows for mapping a third variable onto the
functional space. See 'Carmona et al. (2021)'
<doi:10.1038/s41586-021-03871-y>, 'Puglielli et al. (2021)'
<doi:10.1111/nph.16952>, 'Carmona et al. (2021)'
<doi:10.1126/sciadv.abf2675>, 'Carmona et al. (2019)'
<doi:10.1002/ecy.2876> for more information.
Author: Carlos P. Carmona [cre] ,
Nicola Pavanetto [aut] ,
Giacomo Puglielli [aut]
Maintainer: Carlos P. Carmona <perezcarmonacarlos@gmail.com>
Diff between funspace versions 0.1.0 dated 2023-03-08 and 0.1.1 dated 2023-03-14
funspace-0.1.0/funspace/data/datalist |only funspace-0.1.1/funspace/DESCRIPTION | 6 funspace-0.1.1/funspace/MD5 | 11 funspace-0.1.1/funspace/NEWS.md | 4 funspace-0.1.1/funspace/R/00_Utils.R | 11 funspace-0.1.1/funspace/R/plot.funspace.R | 1023 +++++++++++++-------------- funspace-0.1.1/funspace/man/plot.funspace.Rd | 4 7 files changed, 529 insertions(+), 530 deletions(-)
Title: Including Known Interactions in Species Distribution Models
Description: A collection of tools to fit and work with trophic Species Distribution Models. Trophic Species Distribution Models combine knowledge of trophic interactions with Bayesian structural equation models that model each species as a function of its prey (or predators) and environmental conditions. It exploits the topological ordering of the known trophic interaction network to predict species distribution in space and/or time, where the prey (or predator) distribution is unavailable. The method implemented by the package is described in Poggiato, Andréoletti, Pollock and Thuiller (2022) <doi:10.22541/au.166853394.45823739/v1>.
Author: Giovanni Poggiato [aut, cre, cph]
,
Jeremy Andreoletti [aut]
Maintainer: Giovanni Poggiato <giov.poggiato@gmail.com>
Diff between webSDM versions 1.1-1 dated 2022-11-25 and 1.1-3 dated 2023-03-14
webSDM-1.1-1/webSDM/R/compute_TL_laplacian.R |only webSDM-1.1-1/webSDM/man/compute_TL_laplacian.Rd |only webSDM-1.1-3/webSDM/DESCRIPTION | 8 - webSDM-1.1-3/webSDM/MD5 | 26 ++--- webSDM-1.1-3/webSDM/NAMESPACE | 10 -- webSDM-1.1-3/webSDM/NEWS.md | 9 + webSDM-1.1-3/webSDM/R/SDMfit.R | 86 +++++++++--------- webSDM-1.1-3/webSDM/R/loo.trophicSDMfit.R | 21 ++-- webSDM-1.1-3/webSDM/R/plot.SDMfit.R | 7 - webSDM-1.1-3/webSDM/R/predict.trophicSDMfit.R | 13 +- webSDM-1.1-3/webSDM/R/trophicSDM.R | 9 + webSDM-1.1-3/webSDM/man/figures/unnamed-chunk-4-1.png |binary webSDM-1.1-3/webSDM/man/figures/varImpo-1.png |binary webSDM-1.1-3/webSDM/man/loo.trophicSDMfit.Rd | 8 + webSDM-1.1-3/webSDM/man/plot.SDMfit.Rd | 2 15 files changed, 107 insertions(+), 92 deletions(-)
Title: Procedures for Gaussian and Non Gaussian Geostatistical (Large)
Data Analysis
Description: Functions for Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data analysis are provided for a) simulation and inference for random fields using standard likelihood and a likelihood approximation method called weighted composite likelihood based on pairs and b) prediction using (local) best linear unbiased prediction. Weighted composite likelihood can be very efficient for estimating massive datasets. Both regression and spatial (temporal) dependence analysis can be jointly performed. Covariance functions for spatial and spatial-temporal data on Euclidean domains and spheres are provided. There are also many useful functions for plotting and performing diagnostic analysis. Different non Gaussian random fields can be considered in the analysis. Among them, random fields with marginal distributions such as Skew-Gaussian, Student-t, Tukey-h, Sin-Arcsin, Two-piece, Weibull, Gamma, Log-Gaussian, Binomial, Negative Binomial and Poisson. See the URL for the papers associ [...truncated...]
Author: Moreno Bevilacqua [aut, cre] ,
Victor Morales-Onate [aut] ,
Christian Caamano-Carrillo [aut]
Maintainer: Moreno Bevilacqua <moreno.bevilacqua89@gmail.com>
Diff between GeoModels versions 1.0.6 dated 2023-01-07 and 1.0.7 dated 2023-03-14
DESCRIPTION | 8 +-- MD5 | 23 +++++------ R/GeoCV.R | 95 +++++++++++++++++++++++++++++++--------------- R/GeoCompositeLik2.R | 14 +++--- R/GeoSimapprox.r | 8 ++- R/Utility.r | 5 +- man/GeoCorrFct.Rd | 24 +++++++---- man/GeoCovmatrix.Rd | 93 +++++++++++++++++++++++++++------------------ src/CorrelationFunction.c | 27 ++++++++++++- src/Distributions.c | 47 ++++++++++++++++------ src/GeoModels_init.c | 3 + src/header.h | 10 ++++ src/specfun.f |only 13 files changed, 243 insertions(+), 114 deletions(-)
Title: Analysis of Music and Speech
Description: Analyze music and speech, extract features like MFCCs, handle wave files and their representation in various ways, read mp3, read midi, perform steps of a transcription, ...
Also contains functions ported from the 'rastamat' 'Matlab' package.
Author: Uwe Ligges [aut, cre, cph] ,
Sebastian Krey [aut, cph],
Olaf Mersmann [aut, cph],
Sarah Schnackenberg [aut, cph],
Guillaume Guenard [aut, cph] ,
Daniel P. W. Ellis [aut, cph] ,
Underbit Technologies [aut, cph] ,
Andrea Preusser [ctb],
Anita Thieler [ [...truncated...]
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between tuneR versions 1.4.2 dated 2023-01-17 and 1.4.3 dated 2023-03-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/periodogram.R | 4 ++-- inst/CITATION | 3 ++- man/periodogram.Rd | 11 +++++++++++ 5 files changed, 23 insertions(+), 11 deletions(-)
Title: Rendering Parameterized SQL and Translation to Dialects
Description: A rendering tool for parameterized SQL that also translates into
different SQL dialects. These dialects include 'Microsoft SQL Server', 'Oracle',
'PostgreSql', 'Amazon RedShift', 'Apache Impala', 'IBM Netezza', 'Google BigQuery', 'Microsoft PDW', 'Snowflake',
'Azure Synapse Analytics Dedicated', 'Apache Spark', and 'SQLite'.
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between SqlRender versions 1.12.1 dated 2023-02-21 and 1.13.0 dated 2023-03-14
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 14 ++++++++++++++ inst/csv/replacementPatterns.csv | 30 ++++++++++++++++-------------- inst/doc/UsingSqlRender.pdf |binary tests/testthat/test-translate-duckdb.R | 14 +++++++++++--- tests/testthat/test-translate-sqlite.R | 2 +- 7 files changed, 52 insertions(+), 28 deletions(-)
Title: Import Origin(R) Project Files
Description: Read the data from Origin(R) project files ('*.opj')
<https://www.originlab.com/doc/User-Guide/Origin-File-Types>.
No write support is planned.
Author: Miquel Garriga [aut, cph],
Stefan Gerlach [aut, cph],
Ion Vasilief [aut, cph],
Alex Kargovsky [aut, cph],
Knut Franke [ctb, cph],
Alexander Semke [ctb, cph],
Tilman Benkert [ctb, cph],
Kasper Peeters [ctb, cph],
Russell Standish [ctb, cph],
Ivan Kryl [...truncated...]
Maintainer: Ivan Krylov <krylov.r00t@gmail.com>
Diff between Ropj versions 0.3-3 dated 2023-01-08 and 0.3-4 dated 2023-03-14
Ropj-0.3-3/Ropj/src/Makevars |only Ropj-0.3-4/Ropj/DESCRIPTION | 7 ++++--- Ropj-0.3-4/Ropj/MD5 | 14 +++++++++----- Ropj-0.3-4/Ropj/build/partial.rdb |binary Ropj-0.3-4/Ropj/cleanup |only Ropj-0.3-4/Ropj/cleanup.win |only Ropj-0.3-4/Ropj/configure |only Ropj-0.3-4/Ropj/configure.win |only Ropj-0.3-4/Ropj/inst/NEWS.Rd | 5 +++++ Ropj-0.3-4/Ropj/src/RcppExports.cpp | 5 +++++ Ropj-0.3-4/Ropj/tools |only 11 files changed, 23 insertions(+), 8 deletions(-)
Title: A Wrapper of the JavaScript Library 'jsTree'
Description: Creates interactive trees that can be included in 'Shiny'
apps and R markdown documents. A tree allows to represent hierarchical
data (e.g. the contents of a directory). Similar to the 'shinyTree'
package but offers more features and options, such as the grid
extension, restricting the drag-and-drop behavior, and settings for
the search functionality. It is possible to attach some data to the
nodes of a tree and then to get these data in 'Shiny' when a node is
selected. Also provides a 'Shiny' gadget allowing to manipulate one or
more folders, and a 'Shiny' module allowing to navigate in the server
side file system.
Author: Stephane Laurent [aut, cre],
jQuery contributors [ctb, cph] ,
Ivan Bozhanov [ctb, cph] ,
Vedran Opacic [ctb, cph] ,
Avi Deitcher [ctb, cph] ,
Philip Hutchison [ctb, cph] ,
Terence Eden [ctb, cph]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between jsTreeR versions 2.3.0 dated 2023-02-10 and 2.3.1 dated 2023-03-14
DESCRIPTION | 6 +++--- MD5 | 7 +++++-- NEWS.md | 5 +++++ inst/examples/contextMenu2 |only 4 files changed, 13 insertions(+), 5 deletions(-)
Title: Aggregated Survey Data from the World Risk Poll
Description: Provides users with programmatic access to aggregated survey
data from the World Risk Poll, conveniently packaged for consumption by R
users. It first downloads and formats the Lloyd's Register Foundation World
Risk Poll individual survey responses. It then processes this
data and provides weighting functions for users to select questions
of interest and aggregate to national levels, by gender, age, income,
education urban/rural and household composition. The method of aggregation
can be found at <https://www.gallup.com/178667/gallup-world-poll-work.aspx/>.
More information about the World Risk Poll Survey can be found here
<https://wrp.lrfoundation.org.uk/>.
Author: David Hammond [aut, cre]
Maintainer: David Hammond <dhammond@economicsandpeace.org>
Diff between worldriskpollr versions 0.7.0 dated 2023-02-23 and 0.7.2 dated 2023-03-14
worldriskpollr-0.7.0/worldriskpollr/man/dot-get_question_column.Rd |only worldriskpollr-0.7.0/worldriskpollr/man/dot-get_regional_column.Rd |only worldriskpollr-0.7.0/worldriskpollr/man/dot-get_weight_column.Rd |only worldriskpollr-0.7.0/worldriskpollr/man/dot-print_one_year_summary.Rd |only worldriskpollr-0.7.0/worldriskpollr/man/dot-print_question_summary.Rd |only worldriskpollr-0.7.0/worldriskpollr/man/dot-print_two_year_summary.Rd |only worldriskpollr-0.7.0/worldriskpollr/man/wrp_aggregate.Rd |only worldriskpollr-0.7.0/worldriskpollr/man/wrp_clean.Rd |only worldriskpollr-0.7.2/worldriskpollr/DESCRIPTION | 8 worldriskpollr-0.7.2/worldriskpollr/MD5 | 44 +--- worldriskpollr-0.7.2/worldriskpollr/NEWS.md | 10 worldriskpollr-0.7.2/worldriskpollr/R/02-get_regional_column.R | 6 worldriskpollr-0.7.2/worldriskpollr/R/03-get_question_column.R | 1 worldriskpollr-0.7.2/worldriskpollr/R/04-get_weight_column.R | 1 worldriskpollr-0.7.2/worldriskpollr/R/05-wrp_aggregate.R | 4 worldriskpollr-0.7.2/worldriskpollr/R/06-wrp_clean.R | 3 worldriskpollr-0.7.2/worldriskpollr/R/07-print_question_summary.R | 2 worldriskpollr-0.7.2/worldriskpollr/R/08-print_two_year_summary.R | 5 worldriskpollr-0.7.2/worldriskpollr/R/09-print_one_year_summary.R | 6 worldriskpollr-0.7.2/worldriskpollr/R/11-wrp_get.R | 15 + worldriskpollr-0.7.2/worldriskpollr/README.md | 8 worldriskpollr-0.7.2/worldriskpollr/inst/doc/wrp_vignette.R | 3 worldriskpollr-0.7.2/worldriskpollr/inst/doc/wrp_vignette.Rmd | 16 + worldriskpollr-0.7.2/worldriskpollr/inst/doc/wrp_vignette.html | 104 +++++----- worldriskpollr-0.7.2/worldriskpollr/man/wrp_get.Rd | 2 worldriskpollr-0.7.2/worldriskpollr/tests/testthat/test-02-wrp_get.R | 16 + worldriskpollr-0.7.2/worldriskpollr/vignettes/wrp_vignette.Rmd | 16 + 27 files changed, 176 insertions(+), 94 deletions(-)
More information about worldriskpollr at CRAN
Permanent link
Title: Tools for Working with Posterior Distributions
Description: Provides useful tools for both users and developers of packages
for fitting Bayesian models or working with output from Bayesian models.
The primary goals of the package are to:
(a) Efficiently convert between many different useful formats of
draws (samples) from posterior or prior distributions.
(b) Provide consistent methods for operations commonly performed on draws,
for example, subsetting, binding, or mutating draws.
(c) Provide various summaries of draws in convenient formats.
(d) Provide lightweight implementations of state of the art posterior
inference diagnostics. References: Vehtari et al. (2021)
<doi:10.1214/20-BA1221>.
Author: Paul-Christian Buerkner [aut, cre],
Jonah Gabry [aut],
Matthew Kay [aut],
Aki Vehtari [aut],
Mans Magnusson [ctb],
Rok Česnovar [ctb],
Ben Lambert [ctb],
Ozan Adiguezel [ctb],
Jacob Socolar [ctb]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between posterior versions 1.4.0 dated 2023-02-22 and 1.4.1 dated 2023-03-14
DESCRIPTION | 8 +- MD5 | 17 +++-- NAMESPACE | 3 - NEWS.md | 9 +++ R/rvar-.R | 7 +- R/summarise_draws.R | 41 ++++++++++++- inst/doc/posterior.html | 100 +++++++++++++++++----------------- inst/doc/rvar.html | 4 - man/print.draws_summary.Rd |only tests/testthat/test-summarise_draws.R | 23 +++++++ 10 files changed, 136 insertions(+), 76 deletions(-)
Title: Multivariate Outlier Detection and Imputation for Incomplete
Survey Data
Description: Algorithms for multivariate outlier detection when missing values
occur. Algorithms are based on Mahalanobis distance or data depth.
Imputation is based on the multivariate normal model or uses nearest
neighbour donors. The algorithms take sample designs, in particular
weighting, into account. The methods are described in Bill and Hulliger
(2016) <doi:10.17713/ajs.v45i1.86>.
Author: Beat Hulliger [aut, cre],
Martin Sterchi [ctb],
Tobias Schoch [ctb]
Maintainer: Beat Hulliger <beat.hulliger@fhnw.ch>
Diff between modi versions 0.1.1 dated 2023-03-03 and 0.1.2 dated 2023-03-14
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/data.R | 4 ++-- inst/doc/modi_vignette.Rmd | 5 +++-- inst/doc/modi_vignette.html | 30 ++++++++++++++++-------------- man/lival.Rd | 4 ++-- vignettes/modi_vignette.Rmd | 5 +++-- 7 files changed, 35 insertions(+), 31 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-01-11 1.7.2
2020-11-12 1.6.2
2020-09-11 1.6.1
2020-04-23 1.5.4
2020-03-27 1.5.3
2020-02-03 1.5.1
2019-06-25 1.5
2016-07-04 1.4-3
2015-01-06 1.3
2013-04-09 1.2
2012-03-14 1.1
2010-05-19 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-08 0.1.2
2022-04-10 0.1.1
2022-01-24 0.1.0
Title: A Modular Platform for Reproducible Modeling of Species Niches
and Distributions
Description: The 'shiny' application Wallace is a modular platform for
reproducible modeling of species niches and distributions. Wallace
guides users through a complete analysis, from the acquisition of species
occurrence and environmental data to visualizing model predictions on an
interactive map, thus bundling complex workflows into a single,
streamlined interface. An extensive vignette, which guides users through
most package functionality can be found on the package's GitHub Pages
website: <https://wallaceecomod.github.io/wallace/articles/tutorial-v2.html>.
Author: Jamie M. Kass [aut],
Gonzalo E. Pinilla-Buitrago [aut, cre],
Andrea Paz [aut],
Bethany A. Johnson [aut],
Valentina Grisales-Betancur [aut],
Dean Attali [aut],
Matthew E. Aiello-Lammens [aut],
Cory Merow [aut],
Mary E. Blair [aut],
Robert P. Anderson [...truncated...]
Maintainer: Gonzalo E. Pinilla-Buitrago <gpinillabuitrago@gradcenter.cuny.edu>
Diff between wallace versions 2.0.3 dated 2023-01-16 and 2.0.4 dated 2023-03-14
DESCRIPTION | 8 ++--- MD5 | 22 +++++++-------- NEWS.md | 6 ++++ README.md | 6 ++-- inst/CITATION | 48 +++++++++++++++++----------------- inst/shiny/Rmd/text_about.Rmd | 2 - inst/shiny/Rmd/text_intro_tab.Rmd | 2 - inst/shiny/Rmd/userReport_intro.Rmd | 2 - tests/testthat/test_envs_ecoClimate.R | 4 ++ tests/testthat/test_envs_worldclim.R | 2 + tests/testthat/test_occs_paleoDb.R | 10 ++++--- tests/testthat/test_occs_queryDb.R | 6 ++-- 12 files changed, 67 insertions(+), 51 deletions(-)
Title: Handling Vegetation Data Sets
Description: Import and handling data from vegetation-plot databases, especially
data stored in 'Turboveg 2' (<https://www.synbiosys.alterra.nl/turboveg/>).
Also import/export routines for exchange of data with 'Juice'
(<https://www.sci.muni.cz/botany/juice/>) are implemented.
Author: Miguel Alvarez [aut, cre]
Maintainer: Miguel Alvarez <kamapu78@gmail.com>
Diff between vegtable versions 0.1.7 dated 2021-10-13 and 0.1.8 dated 2023-03-14
vegtable-0.1.7/vegtable/R/aggregate.R |only vegtable-0.1.7/vegtable/R/as.list.R |only vegtable-0.1.7/vegtable/R/aspect_con-data.R |only vegtable-0.1.7/vegtable/R/match_names.R |only vegtable-0.1.7/vegtable/R/merge_taxa.R |only vegtable-0.1.7/vegtable/R/transform.R |only vegtable-0.1.7/vegtable/R/vegtable-deprecated.R |only vegtable-0.1.7/vegtable/R/vegtable2kml.R |only vegtable-0.1.7/vegtable/man/aggregate.Rd |only vegtable-0.1.7/vegtable/man/as.list.Rd |only vegtable-0.1.7/vegtable/man/match_names.Rd |only vegtable-0.1.7/vegtable/man/merge_taxa.Rd |only vegtable-0.1.7/vegtable/man/transform.Rd |only vegtable-0.1.7/vegtable/man/vegtable-deprecated.Rd |only vegtable-0.1.7/vegtable/man/vegtable2kml.Rd |only vegtable-0.1.7/vegtable/tests/testthat/test-add_releves.R |only vegtable-0.1.8/vegtable/DESCRIPTION | 38 vegtable-0.1.8/vegtable/MD5 | 175 + vegtable-0.1.8/vegtable/NAMESPACE | 36 vegtable-0.1.8/vegtable/NEWS.md | 33 vegtable-0.1.8/vegtable/R/Extract.R | 226 +- vegtable-0.1.8/vegtable/R/Kenya_veg-data.R | 24 vegtable-0.1.8/vegtable/R/Wetlands-data.R | 17 vegtable-0.1.8/vegtable/R/add_releves.R | 525 +++-- vegtable-0.1.8/vegtable/R/aspect_conv-data.R |only vegtable-0.1.8/vegtable/R/braun_blanquet-data.R | 13 vegtable-0.1.8/vegtable/R/clean.R | 172 - vegtable-0.1.8/vegtable/R/coerce-methods.R |only vegtable-0.1.8/vegtable/R/count_taxa.R | 332 +-- vegtable-0.1.8/vegtable/R/cover_trans.R | 297 +-- vegtable-0.1.8/vegtable/R/coverconvert-class.R | 137 - vegtable-0.1.8/vegtable/R/crosstable.R | 493 ++--- vegtable-0.1.8/vegtable/R/df2coverconvert.R |only vegtable-0.1.8/vegtable/R/df2vegtable.R | 145 - vegtable-0.1.8/vegtable/R/dune_veg-data.R | 13 vegtable-0.1.8/vegtable/R/header.R | 121 - vegtable-0.1.8/vegtable/R/imports.R | 4 vegtable-0.1.8/vegtable/R/layers2samples.R | 132 - vegtable-0.1.8/vegtable/R/make_cocktail.R | 949 +++++----- vegtable-0.1.8/vegtable/R/names.R | 138 - vegtable-0.1.8/vegtable/R/new_relation.R |only vegtable-0.1.8/vegtable/R/relation2header.R |only vegtable-0.1.8/vegtable/R/shaker-class.R | 148 - vegtable-0.1.8/vegtable/R/subset.R | 211 +- vegtable-0.1.8/vegtable/R/summary.R | 584 +++--- vegtable-0.1.8/vegtable/R/taxa2samples.R |only vegtable-0.1.8/vegtable/R/trait_stats.R | 691 +++---- vegtable-0.1.8/vegtable/R/tv2vegtable.R | 358 ++- vegtable-0.1.8/vegtable/R/update_det.R | 88 vegtable-0.1.8/vegtable/R/used_synonyms.R | 241 +- vegtable-0.1.8/vegtable/R/veg_aggregate.R |only vegtable-0.1.8/vegtable/R/veg_diversity.R |only vegtable-0.1.8/vegtable/R/veg_relation.R | 238 +- vegtable-0.1.8/vegtable/R/vegtable-class.R | 261 +- vegtable-0.1.8/vegtable/R/vegtable_stat.R | 293 +-- vegtable-0.1.8/vegtable/R/write_juice.R | 396 ++-- vegtable-0.1.8/vegtable/data/Kenya_veg.rda |binary vegtable-0.1.8/vegtable/data/Wetlands.rda |binary vegtable-0.1.8/vegtable/data/aspect_conv.rda |binary vegtable-0.1.8/vegtable/data/braun_blanquet.rda |binary vegtable-0.1.8/vegtable/data/dune_veg.rda |binary vegtable-0.1.8/vegtable/man/Extract.Rd | 13 vegtable-0.1.8/vegtable/man/Wetlands-data.Rd | 1 vegtable-0.1.8/vegtable/man/aspect_conv-data.Rd | 2 vegtable-0.1.8/vegtable/man/braun_blanquet-data.Rd | 12 vegtable-0.1.8/vegtable/man/check_args.Rd |only vegtable-0.1.8/vegtable/man/clean.Rd | 9 vegtable-0.1.8/vegtable/man/coerce-methods.Rd |only vegtable-0.1.8/vegtable/man/count_taxa.Rd | 8 vegtable-0.1.8/vegtable/man/cover_trans.Rd | 34 vegtable-0.1.8/vegtable/man/coverconvert.Rd | 11 vegtable-0.1.8/vegtable/man/crosstable.Rd | 36 vegtable-0.1.8/vegtable/man/df2coverconvert.Rd |only vegtable-0.1.8/vegtable/man/df2vegtable.Rd | 9 vegtable-0.1.8/vegtable/man/dune_veg-data.Rd | 7 vegtable-0.1.8/vegtable/man/header.Rd | 1 vegtable-0.1.8/vegtable/man/make_cocktail.Rd | 38 vegtable-0.1.8/vegtable/man/names.Rd | 7 vegtable-0.1.8/vegtable/man/new_relation.Rd |only vegtable-0.1.8/vegtable/man/relation2heder.Rd |only vegtable-0.1.8/vegtable/man/shaker-class.Rd | 1 vegtable-0.1.8/vegtable/man/subset.Rd | 36 vegtable-0.1.8/vegtable/man/summary.Rd | 3 vegtable-0.1.8/vegtable/man/taxa2samples.Rd |only vegtable-0.1.8/vegtable/man/trait_stats.Rd | 72 vegtable-0.1.8/vegtable/man/tv2vegtable.Rd | 12 vegtable-0.1.8/vegtable/man/used_synonyms.Rd | 38 vegtable-0.1.8/vegtable/man/veg_aggregate.Rd |only vegtable-0.1.8/vegtable/man/veg_diversity.Rd |only vegtable-0.1.8/vegtable/man/veg_relation.Rd | 25 vegtable-0.1.8/vegtable/man/vegtable-class.Rd | 1 vegtable-0.1.8/vegtable/man/vegtable_stat.Rd | 8 vegtable-0.1.8/vegtable/man/write_juice.Rd | 13 vegtable-0.1.8/vegtable/tests/testthat/test-Extract.R |only vegtable-0.1.8/vegtable/tests/testthat/test-as.R |only vegtable-0.1.8/vegtable/tests/testthat/test-clean.R |only vegtable-0.1.8/vegtable/tests/testthat/test-count_taxa.R | 35 vegtable-0.1.8/vegtable/tests/testthat/test-cover_trans.R |only vegtable-0.1.8/vegtable/tests/testthat/test-crosstable.R |only vegtable-0.1.8/vegtable/tests/testthat/test-df2coverconvert.R |only vegtable-0.1.8/vegtable/tests/testthat/test-df2vegtable.R |only vegtable-0.1.8/vegtable/tests/testthat/test-header.R |only vegtable-0.1.8/vegtable/tests/testthat/test-make_cocktail.R |only vegtable-0.1.8/vegtable/tests/testthat/test-names.R |only vegtable-0.1.8/vegtable/tests/testthat/test-new_relation.R |only vegtable-0.1.8/vegtable/tests/testthat/test-relation2header.R |only vegtable-0.1.8/vegtable/tests/testthat/test-subset.R |only vegtable-0.1.8/vegtable/tests/testthat/test-summary.R |only vegtable-0.1.8/vegtable/tests/testthat/test-taxa2samples.R |only vegtable-0.1.8/vegtable/tests/testthat/test-trait_stats.R |only vegtable-0.1.8/vegtable/tests/testthat/test-used_synonyms.R |only vegtable-0.1.8/vegtable/tests/testthat/test-veg_aggregate.R |only vegtable-0.1.8/vegtable/tests/testthat/test-veg_diversity.R |only vegtable-0.1.8/vegtable/tests/testthat/test-veg_relation.R |only vegtable-0.1.8/vegtable/tests/testthat/test-vegtable_stat.R |only 115 files changed, 4345 insertions(+), 3616 deletions(-)
Title: Implementations of Semi-Supervised Learning Approaches for
Classification
Description: A collection of implementations of semi-supervised classifiers
and methods to evaluate their performance. The package includes implementations
of, among others, Implicitly Constrained Learning, Moment Constrained Learning,
the Transductive SVM, Manifold regularization, Maximum Contrastive Pessimistic
Likelihood estimation, S4VM and WellSVM.
Author: Jesse Krijthe [aut, cre]
Maintainer: Jesse Krijthe <jkrijthe@gmail.com>
Diff between RSSL versions 0.9.5 dated 2022-01-17 and 0.9.6 dated 2023-03-14
DESCRIPTION | 10 +++++----- MD5 | 28 ++++++++++++++-------------- R/CrossValidation.R | 4 ++-- R/GRFClassifier.R | 8 ++++---- R/HelperFunctions.R | 4 ++-- R/LearningCurve.R | 12 ++++++------ R/Plotting.R | 2 +- README.md | 26 +++++++++++--------------- inst/CITATION | 10 ++++------ man/EMNearestMeanClassifier.Rd | 3 ++- man/GRFClassifier.Rd | 4 ++-- man/NearestMeanClassifier.Rd | 3 ++- man/evaluation-measures.Rd | 10 +++++----- src/ssl.cpp | 4 ++-- tools/example-1.png |binary 15 files changed, 62 insertions(+), 66 deletions(-)
Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features
like the condition system, and core 'Tidyverse' features like tidy
evaluation.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
mikefc [cph] ,
Yann Collet [cph] ,
Posit, PBC [cph, fnd]
Maintainer: Lionel Henry <lionel@posit.co>
Diff between rlang versions 1.0.6 dated 2022-09-24 and 1.1.0 dated 2023-03-14
rlang-1.0.6/rlang/R/compat-cli.R |only rlang-1.0.6/rlang/R/compat-defer.R |only rlang-1.0.6/rlang/R/compat-downstream-deps.R |only rlang-1.0.6/rlang/R/compat-lazyeval.R |only rlang-1.0.6/rlang/R/compat-lifecycle.R |only rlang-1.0.6/rlang/R/compat-linked-version.R |only rlang-1.0.6/rlang/R/compat-obj-type.R |only rlang-1.0.6/rlang/R/compat-oldrel.R |only rlang-1.0.6/rlang/R/compat-purrr.R |only rlang-1.0.6/rlang/R/compat-rlang.R |only rlang-1.0.6/rlang/R/compat-s3-register.R |only rlang-1.0.6/rlang/R/compat-sizes.R |only rlang-1.0.6/rlang/R/compat-types-check.R |only rlang-1.0.6/rlang/R/compat-vctrs.R |only rlang-1.0.6/rlang/R/compat-zeallot.R |only rlang-1.0.6/rlang/R/vec-squash.R |only rlang-1.0.6/rlang/man/vector-old-ctors.Rd |only rlang-1.0.6/rlang/src/rlang-rcc.cpp |only rlang-1.0.6/rlang/tests/testthat/_snaps/compat-cli.md |only rlang-1.0.6/rlang/tests/testthat/_snaps/compat-downstream-deps.md |only rlang-1.0.6/rlang/tests/testthat/_snaps/compat-rlang.md |only rlang-1.0.6/rlang/tests/testthat/_snaps/compat-s3-register.md |only rlang-1.0.6/rlang/tests/testthat/_snaps/compat-types-check.md |only rlang-1.0.6/rlang/tests/testthat/_snaps/compat-vctrs.md |only rlang-1.0.6/rlang/tests/testthat/test-compat-cli.R |only rlang-1.0.6/rlang/tests/testthat/test-compat-downstream-deps.R |only rlang-1.0.6/rlang/tests/testthat/test-compat-obj-type.R |only rlang-1.0.6/rlang/tests/testthat/test-compat-purrr.R |only rlang-1.0.6/rlang/tests/testthat/test-compat-rlang.R |only rlang-1.0.6/rlang/tests/testthat/test-compat-s3-register.R |only rlang-1.0.6/rlang/tests/testthat/test-compat-types-check.R |only rlang-1.0.6/rlang/tests/testthat/test-compat-vctrs.R |only rlang-1.0.6/rlang/tests/testthat/test-compat-zeallot.R |only rlang-1.0.6/rlang/tests/testthat/test-compat.R |only rlang-1.0.6/rlang/tests/testthat/test-vec-squash.R |only rlang-1.1.0/rlang/DESCRIPTION | 21 rlang-1.1.0/rlang/MD5 | 427 ++- rlang-1.1.0/rlang/NAMESPACE | 6 rlang-1.1.0/rlang/NEWS.md | 141 + rlang-1.1.0/rlang/R/aaa.R | 7 rlang-1.1.0/rlang/R/arg.R | 47 rlang-1.1.0/rlang/R/attr.R | 36 rlang-1.1.0/rlang/R/c-lib.R | 20 rlang-1.1.0/rlang/R/cnd-abort.R | 60 rlang-1.1.0/rlang/R/cnd-entrace.R | 65 rlang-1.1.0/rlang/R/cnd-handlers.R | 48 rlang-1.1.0/rlang/R/cnd-last.R | 117 - 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Title: Representative and Adequate Prioritization Toolkit in R
Description: Biodiversity is in crisis. The overarching aim of conservation
is to preserve biodiversity patterns and processes. To this end, protected
areas are established to buffer species and preserve biodiversity processes.
But resources are limited and so protected areas must be cost-effective.
This package contains tools to generate plans for protected areas
(prioritizations), using spatially explicit targets for biodiversity
patterns and processes. To obtain solutions in a feasible amount of time,
this package uses the commercial 'Gurobi' software (obtained from
<https://www.gurobi.com/>). For more information on using
this package, see Hanson et al. (2018) <doi:10.1111/2041-210X.12862>.
Author: Jeffrey O Hanson [aut, cre],
Jonathan R Rhodes [aut],
Hugh P Possingham [aut],
Richard A Fuller [aut]
Maintainer: Jeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>
Diff between raptr versions 0.2.1 dated 2022-07-25 and 1.0.0 dated 2023-03-14
raptr-0.2.1/raptr/R/SpatialPolygons2PolySet.R |only raptr-0.2.1/raptr/R/dependencies.R |only raptr-0.2.1/raptr/R/raptr.R |only raptr-0.2.1/raptr/data/cs_pus.rda |only raptr-0.2.1/raptr/data/cs_space.rda |only raptr-0.2.1/raptr/data/cs_spp.rda |only raptr-0.2.1/raptr/man/SpatialPolygons2PolySet.Rd |only raptr-1.0.0/raptr/DESCRIPTION | 34 raptr-1.0.0/raptr/MD5 | 237 +- raptr-1.0.0/raptr/NAMESPACE | 19 raptr-1.0.0/raptr/NEWS.md | 28 raptr-1.0.0/raptr/R/AttributeSpace.R | 69 raptr-1.0.0/raptr/R/AttributeSpaces.R | 45 raptr-1.0.0/raptr/R/DemandPoints.R | 127 - raptr-1.0.0/raptr/R/GurobiOpts.R | 74 raptr-1.0.0/raptr/R/ManualOpts.R | 11 raptr-1.0.0/raptr/R/PlanningUnitPoints.R | 39 raptr-1.0.0/raptr/R/RapData.R | 862 ++++++---- raptr-1.0.0/raptr/R/RapReliableOpts.R | 3 raptr-1.0.0/raptr/R/RapSolved.R | 2 raptr-1.0.0/raptr/R/RapUnreliableOpts.R | 3 raptr-1.0.0/raptr/R/RapUnsolved.R | 7 raptr-1.0.0/raptr/R/calcBoundaryData.R | 70 raptr-1.0.0/raptr/R/calcSpeciesAverageInPus.R | 109 - raptr-1.0.0/raptr/R/convert2PolySet.R |only raptr-1.0.0/raptr/R/data.R | 28 raptr-1.0.0/raptr/R/deprecated.R |only raptr-1.0.0/raptr/R/generics.R | 254 -- raptr-1.0.0/raptr/R/misc.R | 192 +- raptr-1.0.0/raptr/R/package.R |only raptr-1.0.0/raptr/R/rap.R | 66 raptr-1.0.0/raptr/R/raptr-internal.R | 529 +++--- raptr-1.0.0/raptr/R/rrap.proportion.held.R | 3 raptr-1.0.0/raptr/R/sim.pus.R | 54 raptr-1.0.0/raptr/R/sim.space.R | 80 raptr-1.0.0/raptr/R/sim.species.R | 105 + raptr-1.0.0/raptr/R/urap.proportion.held.R | 3 raptr-1.0.0/raptr/R/zzz.R | 17 raptr-1.0.0/raptr/README.md | 16 raptr-1.0.0/raptr/build/vignette.rds |binary raptr-1.0.0/raptr/data/sim_rs.rda |binary raptr-1.0.0/raptr/data/sim_ru.rda |binary raptr-1.0.0/raptr/inst/CITATION | 6 raptr-1.0.0/raptr/inst/WORDLIST | 1 raptr-1.0.0/raptr/inst/doc/raptr.Rmd | 287 ++- raptr-1.0.0/raptr/inst/doc/raptr.html | 801 +++++---- raptr-1.0.0/raptr/inst/extdata |only raptr-1.0.0/raptr/inst/scripts |only raptr-1.0.0/raptr/man/AttributeSpace-class.Rd | 2 raptr-1.0.0/raptr/man/AttributeSpace.Rd | 22 raptr-1.0.0/raptr/man/AttributeSpaces.Rd | 24 raptr-1.0.0/raptr/man/DemandPoints.Rd | 14 raptr-1.0.0/raptr/man/GurobiOpts-class.Rd | 4 raptr-1.0.0/raptr/man/GurobiOpts.Rd | 12 raptr-1.0.0/raptr/man/ManualOpts.Rd | 5 raptr-1.0.0/raptr/man/PlanningUnitPoints.Rd | 6 raptr-1.0.0/raptr/man/RapData.Rd | 70 raptr-1.0.0/raptr/man/RapReliableOpts.Rd | 3 raptr-1.0.0/raptr/man/RapUnreliableOpts.Rd | 3 raptr-1.0.0/raptr/man/RapUnsolved.Rd | 7 raptr-1.0.0/raptr/man/amount.held.Rd | 3 raptr-1.0.0/raptr/man/amount.target.Rd | 3 raptr-1.0.0/raptr/man/as.list.Rd | 2 raptr-1.0.0/raptr/man/blank.raster.Rd | 13 raptr-1.0.0/raptr/man/calcBoundaryData.Rd | 19 raptr-1.0.0/raptr/man/calcSpeciesAverageInPus.Rd | 50 raptr-1.0.0/raptr/man/casestudy_data.Rd | 26 raptr-1.0.0/raptr/man/convert2PolySet.Rd |only raptr-1.0.0/raptr/man/dp.subset.Rd | 3 raptr-1.0.0/raptr/man/is.GurobiInstalled.Rd | 1 raptr-1.0.0/raptr/man/logging.file.Rd | 3 raptr-1.0.0/raptr/man/make.DemandPoints.Rd | 23 raptr-1.0.0/raptr/man/make.RapData.Rd | 28 raptr-1.0.0/raptr/man/maximum.targets.Rd | 3 raptr-1.0.0/raptr/man/names.Rd | 2 raptr-1.0.0/raptr/man/plot.Rd | 2 raptr-1.0.0/raptr/man/print.Rd | 2 raptr-1.0.0/raptr/man/prob.subset.Rd | 3 raptr-1.0.0/raptr/man/pu.subset.Rd | 3 raptr-1.0.0/raptr/man/randomPoints.Rd | 10 raptr-1.0.0/raptr/man/rap.Rd | 10 raptr-1.0.0/raptr/man/raptr-deprecated.Rd |only raptr-1.0.0/raptr/man/raptr.Rd | 2 raptr-1.0.0/raptr/man/rrap.proportion.held.Rd | 3 raptr-1.0.0/raptr/man/score.Rd | 3 raptr-1.0.0/raptr/man/selections.Rd | 3 raptr-1.0.0/raptr/man/show.Rd | 2 raptr-1.0.0/raptr/man/sim.pus.Rd | 9 raptr-1.0.0/raptr/man/sim.space.Rd | 27 raptr-1.0.0/raptr/man/sim.species.Rd | 25 raptr-1.0.0/raptr/man/simulated_data.Rd | 2 raptr-1.0.0/raptr/man/solve.Rd | 3 raptr-1.0.0/raptr/man/space.held.Rd | 3 raptr-1.0.0/raptr/man/space.plot.Rd | 6 raptr-1.0.0/raptr/man/space.target.Rd | 17 raptr-1.0.0/raptr/man/spp.plot.Rd | 3 raptr-1.0.0/raptr/man/spp.subset.Rd | 3 raptr-1.0.0/raptr/man/summary.Rd | 2 raptr-1.0.0/raptr/man/update.Rd | 7 raptr-1.0.0/raptr/man/urap.proportion.held.Rd | 3 raptr-1.0.0/raptr/src/dump_object.cpp | 2 raptr-1.0.0/raptr/src/rcpp_Polygons2PolySet.cpp | 2 raptr-1.0.0/raptr/src/rcpp_append_model_object.cpp | 2 raptr-1.0.0/raptr/src/rcpp_calcBoundaryDF.cpp | 2 raptr-1.0.0/raptr/src/rcpp_extract_model_object.cpp | 2 raptr-1.0.0/raptr/src/rcpp_generate_model_object.cpp | 2 raptr-1.0.0/raptr/src/rcpp_groupcombine.cpp | 2 raptr-1.0.0/raptr/src/rcpp_proportion_held.cpp | 2 raptr-1.0.0/raptr/src/rcpp_rrap_proportion_held.cpp | 2 raptr-1.0.0/raptr/src/rcpp_rrap_squared_distance.cpp | 2 raptr-1.0.0/raptr/src/rcpp_squared_distance.cpp | 2 raptr-1.0.0/raptr/src/rcpp_sum_duplicates.cpp | 2 raptr-1.0.0/raptr/tests/testthat.R | 35 raptr-1.0.0/raptr/tests/testthat/setup.R |only raptr-1.0.0/raptr/tests/testthat/test-01-rapr-internal-test.R | 156 - raptr-1.0.0/raptr/tests/testthat/test-02-misc.R | 14 raptr-1.0.0/raptr/tests/testthat/test-03-SolverOpts.R | 8 raptr-1.0.0/raptr/tests/testthat/test-05-simulate-data.R | 40 raptr-1.0.0/raptr/tests/testthat/test-07-DemandPoints.R | 39 raptr-1.0.0/raptr/tests/testthat/test-08-AttributeSpace.R | 15 raptr-1.0.0/raptr/tests/testthat/test-09-AttributeSpaces.R | 28 raptr-1.0.0/raptr/tests/testthat/test-10-RapData.R | 231 +- raptr-1.0.0/raptr/tests/testthat/test-11-RapUnsolved.R | 271 +-- raptr-1.0.0/raptr/tests/testthat/test-12-RapSolved.R | 96 - raptr-1.0.0/raptr/tests/testthat/test-13-rap.R | 140 - raptr-1.0.0/raptr/vignettes/raptr.Rmd | 287 ++- 126 files changed, 3596 insertions(+), 2473 deletions(-)
Title: Connector Between 'mlr3' and 'OpenML'
Description: Provides an interface to 'OpenML.org' to list and download
machine learning data, tasks and experiments. The 'OpenML' objects can
be automatically converted to 'mlr3' objects. For a more
sophisticated interface which also allows uploading to 'OpenML', see
the 'OpenML' package.
Author: Michel Lang [aut] ,
Sebastian Fischer [cre, aut]
Maintainer: Sebastian Fischer <sebf.fischer@gmail.com>
Diff between mlr3oml versions 0.7.0 dated 2022-12-12 and 0.7.1 dated 2023-03-14
DESCRIPTION | 31 ++++++++++++++++--------------- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/OMLRun.R | 4 ++-- R/read_arff.R | 9 ++++++++- README.md | 3 ++- tests/testthat/test_read_arff.R | 11 +++++++++++ 7 files changed, 49 insertions(+), 25 deletions(-)
Title: Inferential Statistics
Description: Computation of various confidence intervals (Altman et al. (2000), ISBN:978-0-727-91375-3; Hedderich and Sachs (2018), ISBN:978-3-662-56657-2) including bootstrapped versions (Davison and Hinkley (1997), ISBN:978-0-511-80284-3) as well as Hsu (Hedderich and Sachs (2018), ISBN:978-3-662-56657-2), permutation (Janssen (1997), <doi:10.1016/S0167-7152(97)00043-6>), bootstrap (Davison and Hinkley (1997), ISBN:978-0-511-80284-3) and multiple imputation (Barnard and Rubin (1999), <doi:10.1093/biomet/86.4.948>) t-test. Graphical visualization by volcano and Bland-Altman plots (Bland and Altman (1986), <doi:10.1016/S0140-6736(86)90837-8>; Shieh (2018), <doi:10.1186/s12874-018-0505-y>).
Author: Matthias Kohl [aut, cre]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between MKinfer versions 0.9 dated 2022-11-16 and 1.0 dated 2023-03-14
DESCRIPTION | 13 MD5 | 38 + NAMESPACE | 5 NEWS | 19 R/baplot.R |only R/boot.t.test.R | 4 R/hsu.t.test.R | 2 R/perm.t.test.R | 4 R/quantileCI.R | 70 ++- R/rm.oneway.test.R | 7 build/vignette.rds |binary data |only inst/doc/MKinfer.R | 24 + inst/doc/MKinfer.Rmd | 37 + inst/doc/MKinfer.html | 997 +++++++++++++++++++++++++++--------------------- man/0MKinfer-package.Rd | 10 man/baplot.Rd |only man/fingsys.Rd |only man/quantileCI.Rd | 13 man/volcano.Rd | 8 vignettes/MKinfer.Rmd | 37 + vignettes/MKinfer.bib | 22 + 22 files changed, 816 insertions(+), 494 deletions(-)
Title: Linear Mixed-Effects Models using 'Eigen' and S4
Description: Fit linear and generalized linear mixed-effects models.
The models and their components are represented using S4 classes and
methods. The core computational algorithms are implemented using the
'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Douglas Bates [aut] ,
Martin Maechler [aut] ,
Ben Bolker [aut, cre] ,
Steven Walker [aut] ,
Rune Haubo Bojesen Christensen [ctb]
,
Henrik Singmann [ctb] ,
Bin Dai [ctb],
Fabian Scheipl [ctb] ,
Gabor Grothendieck [ctb],
Peter Green [ctb] ,
John Fox [c [...truncated...]
Maintainer: Ben Bolker <bbolker+lme4@gmail.com>
Diff between lme4 versions 1.1-31 dated 2022-10-31 and 1.1-32 dated 2023-03-14
DESCRIPTION | 6 +- MD5 | 53 +++++++++++----------- R/lmer.R | 66 ++++++++++++++++------------ R/plot.R | 23 ++++++++- R/utilities.R | 4 + build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 30 +++++++++++- inst/doc/PLSvGLS.pdf |binary inst/doc/Theory.pdf |binary inst/doc/lmer.pdf |binary inst/doc/lmerperf.R | 2 inst/doc/lmerperf.Rmd | 2 inst/doc/lmerperf.html | 3 - inst/testdata/confint_ex.rda |binary inst/tinytest |only man/InstEval.Rd | 2 man/VarCorr.Rd | 18 +++++-- man/confint.merMod.Rd | 17 +++---- man/lmerControl.Rd | 4 + man/merMod-class.Rd | 15 +++++- man/plot.merMod.Rd | 3 - man/profile-methods.Rd | 99 ++++++++++++++++++++---------------------- man/utilities.Rd | 27 ++++++++--- tests/lmer-1.Rout.save | 2 tests/testthat/test-methods.R | 18 ++++++- tests/vcov-etc.R | 32 +++++++++---- vignettes/lmerperf.Rmd | 2 28 files changed, 268 insertions(+), 160 deletions(-)
Title: Local Approximate Gaussian Process Regression
Description: Performs approximate GP regression for large computer experiments and spatial datasets. The approximation is based on finding small local designs for prediction (independently) at particular inputs. OpenMP and SNOW parallelization are supported for prediction over a vast out-of-sample testing set; GPU acceleration is also supported for an important subroutine. OpenMP and GPU features may require special compilation. An interface to lower-level (full) GP inference and prediction is provided. Wrapper routines for blackbox optimization under mixed equality and inequality constraints via an augmented Lagrangian scheme, and for large scale computer model calibration, are also provided. For details and tutorial, see Gramacy (2016 <doi:10.18637/jss.v072.i01>.
Author: Robert B. Gramacy <rbg@vt.edu>, Furong Sun <furongs@vt.edu>
Maintainer: Robert B. Gramacy <rbg@vt.edu>
Diff between laGP versions 1.5-8 dated 2022-10-23 and 1.5-9 dated 2023-03-14
ChangeLog | 6 ++++++ DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/laGP.pdf |binary man/newGP.Rd | 2 +- src/gp_sep.c | 4 ++-- 8 files changed, 20 insertions(+), 14 deletions(-)
Title: Post-Process 'ggplot2' Plots with 'TikZ' Code Using Plot
Coordinates
Description: Annotation of 'ggplot2' plots with arbitrary 'TikZ' code, using absolute data or relative plot coordinates.
Author: Oliver Thomas [aut, cre]
Maintainer: Oliver Thomas <oliver.thomas@sgbm.uni-freiburg.de>
Diff between ggtikz versions 0.1.1 dated 2022-07-20 and 0.1.2 dated 2023-03-14
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/generics.R | 28 ++++++++++++++-------------- R/ggtikzAnnotation.R | 2 +- R/ggtikzCanvas.R | 27 ++++++++++++++------------- build/vignette.rds |binary inst/doc/examples.R | 4 ++-- inst/doc/examples.Rnw | 4 ++-- inst/doc/examples.pdf |binary man/gg_to_npc.ggtikzCanvas.Rd | 4 +++- tests/testthat/test-ggtikzUninfinite.R | 4 ++-- tests/testthat/test-padding.R | 22 +++++++++++----------- vignettes/examples.Rnw | 4 ++-- 13 files changed, 67 insertions(+), 64 deletions(-)
Title: Bayesian Quantile Regression for Ordinal Models
Description: Package provides functions for estimation and inference in Bayesian quantile regression with ordinal outcomes. An ordinal model with 3 or more outcomes (labeled OR1 model) is estimated by a combination of Gibbs sampling and Metropolis-Hastings (MH) algorithm. Whereas an ordinal model with exactly 3 outcomes (labeled OR2 model) is estimated using a Gibbs sampling algorithm. The summary output presents the posterior mean, posterior standard deviation, 95% credible intervals, and the inefficiency factors along with the two model comparison measures – logarithm of marginal likelihood and the deviance information criterion (DIC). The package also provides functions for computing the covariate effects and other functions that aids either the estimation or inference in quantile ordinal models.
Rahman, M. A. (2016).“Bayesian Quantile Regression for Ordinal Models.” Bayesian Analysis, 11(1): 1-24 <doi: 10.1214/15-BA939>.
Yu, K., and Moyeed, R. A. (2001). “Bayesian Quantile Regression.” St [...truncated...]
Author: Mohammad Arshad Rahman Developer [aut],
Prajual Maheshwari [cre]
Maintainer: Prajual Maheshwari <prajual1391@gmail.com>
Diff between bqror versions 1.4.0 dated 2022-07-06 and 1.5.0 dated 2023-03-14
bqror-1.4.0/bqror/man/devianceOR1.Rd |only bqror-1.4.0/bqror/man/devianceOR2.Rd |only bqror-1.4.0/bqror/man/infactorOR1.Rd |only bqror-1.4.0/bqror/man/infactorOR2.Rd |only bqror-1.4.0/bqror/man/logLik.bqrorOR1.Rd |only bqror-1.5.0/bqror/DESCRIPTION | 31 - bqror-1.5.0/bqror/MD5 | 85 +-- bqror-1.5.0/bqror/NAMESPACE | 11 bqror-1.5.0/bqror/R/ORI.R | 525 ++++++++---------------- bqror-1.5.0/bqror/R/ORII.R | 423 ++++++++++--------- bqror-1.5.0/bqror/R/bqror.R | 35 - bqror-1.5.0/bqror/R/data.R | 58 +- bqror-1.5.0/bqror/data/Policy_Opinion.RData |binary bqror-1.5.0/bqror/man/Educational_Attainment.Rd | 4 bqror-1.5.0/bqror/man/Policy_Opinion.Rd | 6 bqror-1.5.0/bqror/man/alcdf.Rd | 4 bqror-1.5.0/bqror/man/bqror.Rd | 35 - bqror-1.5.0/bqror/man/covEffectOR1.Rd | 20 bqror-1.5.0/bqror/man/covEffectOR2.Rd | 18 bqror-1.5.0/bqror/man/data25j3.Rd | 10 bqror-1.5.0/bqror/man/data25j4.Rd | 10 bqror-1.5.0/bqror/man/data50j3.Rd | 10 bqror-1.5.0/bqror/man/data50j4.Rd | 10 bqror-1.5.0/bqror/man/data75j3.Rd | 10 bqror-1.5.0/bqror/man/data75j4.Rd | 10 bqror-1.5.0/bqror/man/dicOR1.Rd |only bqror-1.5.0/bqror/man/dicOR2.Rd |only bqror-1.5.0/bqror/man/drawbetaOR1.Rd | 20 bqror-1.5.0/bqror/man/drawbetaOR2.Rd | 19 bqror-1.5.0/bqror/man/drawdeltaOR1.Rd | 17 bqror-1.5.0/bqror/man/drawlatentOR1.Rd | 18 bqror-1.5.0/bqror/man/drawlatentOR2.Rd | 26 - bqror-1.5.0/bqror/man/drawnuOR2.Rd | 10 bqror-1.5.0/bqror/man/drawsigmaOR2.Rd | 25 - bqror-1.5.0/bqror/man/drawwOR1.Rd | 23 - bqror-1.5.0/bqror/man/ineffactorOR1.Rd |only bqror-1.5.0/bqror/man/ineffactorOR2.Rd |only bqror-1.5.0/bqror/man/logMargLikeOR1.Rd | 26 - bqror-1.5.0/bqror/man/logMargLikeOR2.Rd | 17 bqror-1.5.0/bqror/man/qrminfundtheorem.Rd | 11 bqror-1.5.0/bqror/man/qrnegLogLikeOR2.Rd | 14 bqror-1.5.0/bqror/man/qrnegLogLikensumOR1.Rd | 10 bqror-1.5.0/bqror/man/quantregOR1.Rd | 65 +- bqror-1.5.0/bqror/man/quantregOR2.Rd | 56 +- bqror-1.5.0/bqror/man/rndald.Rd | 2 bqror-1.5.0/bqror/man/summary.bqrorOR1.Rd |only bqror-1.5.0/bqror/man/summary.bqrorOR2.Rd |only bqror-1.5.0/bqror/tests/testthat/test-ODRI.R | 37 - bqror-1.5.0/bqror/tests/testthat/test-ODRII.R | 21 49 files changed, 735 insertions(+), 997 deletions(-)
Title: Propensity Score Matching for Unordered 3-Group Data
Description: You can use this program for 3 sets of categorical data for propensity score matching.
Assume that the data has 3 different categorical variables. You can use it to perform propensity matching of baseline indicator groupings.
The matching will make the differences in the baseline data smaller.
This method was described by Alvaro Fuentes (2022) <doi:10.1080/00273171.2021.1925521>.
Author: Qiang LIU [aut, cre]
Maintainer: Qiang LIU <dege857@163.com>
Diff between pm3 versions 0.1.2 dated 2023-03-06 and 0.1.4 dated 2023-03-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/pm3.R | 3 ++- R/pm3datalist.R | 6 +++--- man/pm3.Rd | 2 +- 5 files changed, 13 insertions(+), 12 deletions(-)
Title: Analysis and Visualisation of Benchmark Experiments
Description: Implements methods for post-hoc analysis and
visualisation of benchmark experiments, for 'mlr3' and beyond.
Author: Sonabend Raphael [aut] ,
Florian Pfisterer [aut] ,
Michel Lang [ctb] ,
Bernd Bischl [ctb] ,
Sebastian Fischer [cre, ctb]
Maintainer: Sebastian Fischer <sebf.fischer@gmail.com>
Diff between mlr3benchmark versions 0.1.4 dated 2022-10-10 and 0.1.5 dated 2023-03-14
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 5 +++++ R/BenchmarkAggr.R | 28 +++++++++++++++------------- R/autoplot.BenchmarkAggr.R | 31 ++++++++++++++++--------------- README.md | 4 +--- man/autoplot.BenchmarkAggr.Rd | 5 +++-- man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-8-2.png |binary 10 files changed, 53 insertions(+), 46 deletions(-)
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre],
Javier Luraschi [aut],
Kevin Kuo [aut] ,
RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>
Diff between mlflow versions 2.1.1 dated 2023-01-16 and 2.1.2 dated 2023-03-14
DESCRIPTION | 6 +-- MD5 | 4 +- tests/testthat/test-tracking-experiments.R | 47 ++++++++++++++++------------- 3 files changed, 32 insertions(+), 25 deletions(-)
Title: Convert Identifiers in Biological Databases
Description: Identifiers in biological databases connect different levels
of metadata, phenotype data or genotype data. This tool is designed to
easily convert identifiers within or between different biological
databases (Wang, Shixiang, et al. (2021) <DOI:10.1371/journal.pgen.1009557>).
Author: Shixiang Wang [aut, cre]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between IDConverter versions 0.3.3 dated 2022-08-15 and 0.3.4 dated 2023-03-14
DESCRIPTION | 8 +- MD5 | 24 +++---- NEWS.md | 4 + R/common_human_and_mouse_ids.R | 5 + R/convert_icgc.R | 2 R/convert_pcawg.R | 2 R/convert_tcga.R | 2 R/load_data.R | 16 ++-- README.md | 45 +++++++------- build/partial.rdb |binary tests/testthat/test-roxytest-testexamples-convert_icgc.R | 12 +-- tests/testthat/test-roxytest-testexamples-convert_pcawg.R | 16 ++-- tests/testthat/test-roxytest-testexamples-convert_tcga.R | 10 +-- 13 files changed, 81 insertions(+), 65 deletions(-)
Title: Running 'MLwiN' from Within R
Description: An R command interface to the 'MLwiN' multilevel
modelling software package.
Author: Zhengzheng Zhang [aut, cre],
Chris Charlton [aut],
Richard Parker [aut],
George Leckie [aut],
William Browne [aut]
Maintainer: Zhengzheng Zhang <zhengzheng236@gmail.com>
Diff between R2MLwiN versions 0.8-7 dated 2020-06-27 and 0.8-8 dated 2023-03-14
DESCRIPTION | 10 +-- MD5 | 56 ++++++++++++++------- NEWS | 35 +++++++++++++ R/Formula.translate.R | 35 +++++++------ R/caterpillarR.R | 2 R/data-alevchem.R |only R/data-bang.R |only R/data-bang1.R |only R/data-bes83.R |only R/data-cvd_data.R |only R/data-diag1.R |only R/data-gcsecomp1.R |only R/data-gcsemv1.R |only R/data-height.R |only R/data-hungary1.R |only R/data-jspmix1.R |only R/data-lips1.R |only R/data-mmmec.R |only R/data-rats.R |only R/data-reading1.R |only R/data-tutorial.R |only R/data-wage1.R |only R/data-xc.R |only R/data-xc1.R |only R/init.R | 4 - R/mlwinfitIGLS.R | 30 ++++++++--- R/mlwinfitMCMC.R | 22 ++++++-- R/prior2macro.R | 2 R/runMLwiN.R | 109 +++++++++++++++++++++++++++++++++++++---- R/trajectories.R | 2 R/write.IGLS.R | 9 --- demo/MCMCGuide11.R | 3 - demo/MCMCGuide23.R | 2 demo/MCMCGuide25.R | 2 demo/UserGuide07.R | 4 - demo/UserGuide12.R | 2 man/getSummary.mlwinfitMCMC.Rd | 2 man/logLik.mlwinfitIGLS.Rd |only man/runMLwiN.Rd | 5 + 39 files changed, 249 insertions(+), 87 deletions(-)
Title: Tidy Data and 'Geoms' for Bayesian Models
Description: Compose data for and extract, manipulate, and visualize posterior draws from Bayesian models
('JAGS', 'Stan', 'rstanarm', 'brms', 'MCMCglmm', 'coda', ...) in a tidy data format. Functions are provided
to help extract tidy data frames of draws from Bayesian models and that generate point
summaries and intervals in a tidy format. In addition, 'ggplot2' 'geoms' and 'stats' are provided for
common visualization primitives like points with multiple uncertainty intervals, eye plots (intervals plus
densities), and fit curves with multiple, arbitrary uncertainty bands.
Author: Matthew Kay [aut, cre],
Timothy Mastny [ctb]
Maintainer: Matthew Kay <mjskay@northwestern.edu>
Diff between tidybayes versions 3.0.3 dated 2023-02-04 and 3.0.4 dated 2023-03-14
DESCRIPTION | 6 - MD5 | 16 ++-- NEWS.md | 8 ++ inst/doc/tidy-brms.html | 110 ++++++++++++++++---------------- inst/doc/tidy-posterior.html | 6 - inst/doc/tidy-rstanarm.html | 108 ++++++++++++++++---------------- inst/doc/tidybayes-residuals.html | 4 - inst/doc/tidybayes.html | 114 +++++++++++++++++----------------- tests/testthat/test.summarise_draws.R | 1 9 files changed, 191 insertions(+), 182 deletions(-)