Title: A Library for using 'Pathling'
Description: R API for 'Pathling', a tool for querying and transforming electronic health record data that is represented using the 'Fast Healthcare Interoperability Resources' (FHIR) standard - see <https://pathling.csiro.au/docs>.
Author: Australian e-Health Research Centre, CSIRO [cph, cre],
Piotr Szul [aut],
John Grimes [aut]
Maintainer: "Australian e-Health Research Centre, CSIRO" <ontoserver-support@csiro.au>
Diff between pathling versions 6.4.1 dated 2023-12-13 and 6.4.2 dated 2023-12-20
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/datasource.R | 6 +++--- R/etc.R | 2 +- man/ds_write_delta.Rd | 2 +- man/ds_write_ndjson.Rd | 2 +- man/ds_write_parquet.Rd | 2 +- 7 files changed, 18 insertions(+), 18 deletions(-)
Title: Infrastructure for Partially Observable Markov Decision
Processes (POMDP)
Description: Provides the infrastructure to define and analyze the solutions of Partially Observable Markov Decision Process (POMDP) models. Interfaces for various exact and approximate solution algorithms are available including value iteration, point-based value iteration and SARSOP. Smallwood and Sondik (1973) <doi:10.1287/opre.21.5.1071>.
Author: Michael Hahsler [aut, cph, cre]
,
Hossein Kamalzadeh [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between pomdp versions 1.1.2 dated 2023-09-08 and 1.1.3 dated 2023-12-20
DESCRIPTION | 15 ++--- MD5 | 85 +++++++++++++++-------------- NAMESPACE | 1 NEWS.md | 14 ++++ R/AAA_shorten.R |only R/MDP.R | 8 ++ R/Maze.R | 28 +++++---- R/POMDP.R | 50 ++++++++++++++--- R/add_policy.R |only R/foreach_helper.R | 5 - R/plot_belief_space.R | 6 +- R/policy_graph.R | 15 +++-- R/regret.R | 2 R/reward.R | 47 +++++++++++----- R/simulate_MDP.R | 50 +++++++++++------ R/simulate_POMDP.R | 81 ++++++++++++++++------------ R/solve_POMDP.R | 26 ++++++--- R/value_function.R | 100 +++++++++++++++++++++++------------ README.md | 28 +++++++-- build/vignette.rds |binary data/Maze.rda |binary inst/README_files/policy_graph-1.png |binary inst/doc/POMDP.R | 10 +-- inst/doc/POMDP.html | 16 ++--- man/Maze.Rd | 28 +++++---- man/POMDP.Rd | 17 ++++- man/POMDP_accessors.Rd | 1 man/add_policy.Rd |only man/plot_belief_space.Rd | 1 man/projection.Rd | 1 man/regret.Rd | 3 - man/reward.Rd | 13 +++- man/sample_belief_space.Rd | 1 man/simulate_MDP.Rd | 23 +++++--- man/simulate_POMDP.Rd | 37 ++++++++---- man/solve_POMDP.Rd | 11 +++ man/solve_SARSOP.Rd | 1 man/transition_graph.Rd | 1 man/update_belief.Rd | 1 man/value_function.Rd | 7 +- man/write_POMDP.Rd | 1 src/model.h | 21 +++++++ src/simulate_MDP.cpp | 2 src/simulate_POMDP.cpp | 12 +++- tests/testthat/test-solve_POMDP.R | 26 +++++++++ 45 files changed, 547 insertions(+), 248 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 2.8.1 dated 2023-11-22 and 2.9.2 dated 2023-12-20
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/cli.R | 2 +- R/databricks-utils.R | 2 +- man/build_context_tags_from_databricks_job_info.Rd | 2 +- 5 files changed, 10 insertions(+), 10 deletions(-)
Title: Wrap Vectors in Markdown Formatting
Description: Ease the transition between R vectors and markdown
text. With 'gluedown' and 'rmarkdown', users can create traditional
vectors in R, glue those strings together with the markdown syntax,
and print those formatted vectors directly to the document. This
package primarily uses GitHub Flavored Markdown (GFM), an offshoot of
the unambiguous CommonMark specification by John MacFarlane (2019)
<https://spec.commonmark.org/>.
Author: Kiernan Nicholls [aut, cre]
Maintainer: Kiernan Nicholls <kiernann@protonmail.com>
Diff between gluedown versions 1.0.7 dated 2023-10-28 and 1.0.8 dated 2023-12-20
DESCRIPTION | 6 - MD5 | 10 - NEWS.md | 5 R/md-convert.R | 4 inst/doc/github-spec.html | 223 +++++++++++++++++++------------------- inst/doc/literal-programming.html | 8 - 6 files changed, 129 insertions(+), 127 deletions(-)
Title: Tools for Analyzing Climate Extremes
Description: Functions for fitting GEV and POT (via point process fitting)
models for extremes in climate data, providing return values, return
probabilities, and return periods for stationary and nonstationary models.
Also provides differences in return values and differences in log return
probabilities for contrasts of covariate values. Functions for estimating risk
ratios for event attribution analyses, including uncertainty. Under the hood,
many of the functions use functions from 'extRemes', including for fitting the
statistical models. Details are given in Paciorek, Stone, and Wehner (2018)
<doi:10.1016/j.wace.2018.01.002>.
Author: Christopher Paciorek [aut, cre],
Harinarayan Krishnan [ctb]
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Diff between climextRemes versions 0.3.0 dated 2022-08-06 and 0.3.1 dated 2023-12-20
climextRemes-0.3.0/climextRemes/inst/tests |only climextRemes-0.3.0/climextRemes/man/climextRemes.Rd |only climextRemes-0.3.1/climextRemes/DESCRIPTION | 11 climextRemes-0.3.1/climextRemes/LICENSE | 2 climextRemes-0.3.1/climextRemes/MD5 | 107 - climextRemes-0.3.1/climextRemes/NEWS | 18 climextRemes-0.3.1/climextRemes/R/climextRemes-package.R | 13 climextRemes-0.3.1/climextRemes/R/gev.R | 6 climextRemes-0.3.1/climextRemes/R/pot.R | 6 climextRemes-0.3.1/climextRemes/R/risk_ratio.R | 28 climextRemes-0.3.1/climextRemes/build |only climextRemes-0.3.1/climextRemes/inst/conda/deploy.sh | 11 climextRemes-0.3.1/climextRemes/inst/conda/noarch/meta.yaml | 2 climextRemes-0.3.1/climextRemes/inst/pip/README.md | 7 climextRemes-0.3.1/climextRemes/inst/python/climextRemes_wrapper.py | 18 climextRemes-0.3.1/climextRemes/inst/python_help/calc_riskRatio_gev_args.txt | 4 climextRemes-0.3.1/climextRemes/inst/python_help/calc_riskRatio_pot_args.txt | 4 climextRemes-0.3.1/climextRemes/inst/python_help/fit_gev_args.txt | 2 climextRemes-0.3.1/climextRemes/inst/python_help/fit_pot_args.txt | 2 climextRemes-0.3.1/climextRemes/inst/python_wrapper/COPYRIGHTS.txt | 2 climextRemes-0.3.1/climextRemes/inst/python_wrapper/LICENSE.txt | 2 climextRemes-0.3.1/climextRemes/inst/python_wrapper/README.md | 8 climextRemes-0.3.1/climextRemes/inst/python_wrapper/build/lib/climextremes/__init__.py | 9 climextRemes-0.3.1/climextRemes/inst/python_wrapper/climextremes.egg-info |only climextRemes-0.3.1/climextRemes/inst/python_wrapper/climextremes/__init__.py | 9 climextRemes-0.3.1/climextRemes/inst/python_wrapper/dist |only climextRemes-0.3.1/climextRemes/inst/python_wrapper/docs/build_sphinx_docs.sh | 2 climextRemes-0.3.1/climextRemes/inst/python_wrapper/docs/climextremesDocumentation.pdf |binary climextRemes-0.3.1/climextRemes/inst/python_wrapper/docs/html/_modules/climextRemes_wrapper.html | 940 +++++----- climextRemes-0.3.1/climextRemes/inst/python_wrapper/docs/html/_modules/climextremes.html | 246 +- climextRemes-0.3.1/climextRemes/inst/python_wrapper/docs/html/_modules/index.html | 24 climextRemes-0.3.1/climextRemes/inst/python_wrapper/docs/html/_static/alabaster.css | 4 climextRemes-0.3.1/climextRemes/inst/python_wrapper/docs/html/_static/basic.css | 73 climextRemes-0.3.1/climextRemes/inst/python_wrapper/docs/html/_static/doctools.js | 416 +--- climextRemes-0.3.1/climextRemes/inst/python_wrapper/docs/html/_static/documentation_options.js | 5 climextRemes-0.3.1/climextRemes/inst/python_wrapper/docs/html/_static/language_data.js | 102 - climextRemes-0.3.1/climextRemes/inst/python_wrapper/docs/html/_static/pygments.css | 2 climextRemes-0.3.1/climextRemes/inst/python_wrapper/docs/html/_static/searchtools.js | 845 ++++---- climextRemes-0.3.1/climextRemes/inst/python_wrapper/docs/html/_static/sphinx_highlight.js |only climextRemes-0.3.1/climextRemes/inst/python_wrapper/docs/html/genindex.html | 24 climextRemes-0.3.1/climextRemes/inst/python_wrapper/docs/html/index.html | 72 climextRemes-0.3.1/climextRemes/inst/python_wrapper/docs/html/objects.inv |binary climextRemes-0.3.1/climextRemes/inst/python_wrapper/docs/html/search.html | 22 climextRemes-0.3.1/climextRemes/inst/python_wrapper/docs/html/searchindex.js | 2 climextRemes-0.3.1/climextRemes/inst/python_wrapper/setup.py | 4 climextRemes-0.3.1/climextRemes/inst/python_wrapper/version.py | 2 climextRemes-0.3.1/climextRemes/man/calc_riskRatio_gev.Rd | 12 climextRemes-0.3.1/climextRemes/man/calc_riskRatio_pot.Rd | 18 climextRemes-0.3.1/climextRemes/man/climextRemes-package.Rd |only climextRemes-0.3.1/climextRemes/man/fit_gev.Rd | 6 climextRemes-0.3.1/climextRemes/man/fit_pot.Rd | 6 climextRemes-0.3.1/climextRemes/tests |only 52 files changed, 1460 insertions(+), 1638 deletions(-)
Title: Use 'QGIS' Processing Algorithms
Description: Provides seamless access to the 'QGIS'
(<https://qgis.org/en/site/>) processing toolbox using the standalone
'qgis_process' command-line utility. Both native and third-party
(plugin) processing providers are supported. Beside referring data
sources from file, also common objects from 'sf', 'terra' and 'stars'
are supported. The native processing algorithms are documented by QGIS.org
(2023) <https://docs.qgis.org/latest/en/docs/user_manual/processing_algs/>.
Author: Dewey Dunnington [aut] ,
Floris Vanderhaeghe [aut, cre]
),
Jan Caha [aut] ,
Jannes Muenchow [aut] ,
Antony Barja [ctb] ,
Robin Lovelace [ctb] ,
Jakub Nowosad [ctb] ,
Research Institute for Nature and Forest [cph, fnd]
Maintainer: Floris Vanderhaeghe <floris.vanderhaeghe@inbo.be>
Diff between qgisprocess versions 0.1.0 dated 2023-08-17 and 0.2.0 dated 2023-12-20
qgisprocess-0.1.0/qgisprocess/man/qgis_detect_windows_paths.Rd |only qgisprocess-0.2.0/qgisprocess/DESCRIPTION | 14 qgisprocess-0.2.0/qgisprocess/MD5 | 91 - qgisprocess-0.2.0/qgisprocess/NAMESPACE | 4 qgisprocess-0.2.0/qgisprocess/NEWS.md | 26 qgisprocess-0.2.0/qgisprocess/R/compat-sf.R | 12 qgisprocess-0.2.0/qgisprocess/R/compat-stars.R | 7 qgisprocess-0.2.0/qgisprocess/R/compat-terra.R | 178 +++ qgisprocess-0.2.0/qgisprocess/R/qgis-algorithms.R | 8 qgisprocess-0.2.0/qgisprocess/R/qgis-cache.R | 16 qgisprocess-0.2.0/qgisprocess/R/qgis-configure.R | 176 ++- qgisprocess-0.2.0/qgisprocess/R/qgis-detect.R | 60 + qgisprocess-0.2.0/qgisprocess/R/qgis-has.R | 8 qgisprocess-0.2.0/qgisprocess/R/qgis-plugins.R | 31 qgisprocess-0.2.0/qgisprocess/R/qgis-run-algorithm.R | 44 qgisprocess-0.2.0/qgisprocess/R/qgis-run.R | 15 qgisprocess-0.2.0/qgisprocess/R/qgis-state.R | 21 qgisprocess-0.2.0/qgisprocess/R/zzz.R | 22 qgisprocess-0.2.0/qgisprocess/README.md | 77 - qgisprocess-0.2.0/qgisprocess/build/vignette.rds |binary qgisprocess-0.2.0/qgisprocess/inst/CITATION | 4 qgisprocess-0.2.0/qgisprocess/inst/doc/cheatsheet_en.Rmd | 2 qgisprocess-0.2.0/qgisprocess/inst/doc/cheatsheet_en.html | 6 qgisprocess-0.2.0/qgisprocess/inst/doc/cheatsheet_es.Rmd | 4 qgisprocess-0.2.0/qgisprocess/inst/doc/cheatsheet_es.html | 8 qgisprocess-0.2.0/qgisprocess/inst/doc/qgis_expressions.R | 2 qgisprocess-0.2.0/qgisprocess/inst/doc/qgis_expressions.Rmd | 4 qgisprocess-0.2.0/qgisprocess/inst/doc/qgis_expressions.html | 3 qgisprocess-0.2.0/qgisprocess/inst/doc/qgisprocess.R | 2 qgisprocess-0.2.0/qgisprocess/inst/doc/qgisprocess.Rmd | 4 qgisprocess-0.2.0/qgisprocess/inst/doc/qgisprocess.html | 481 +++++----- qgisprocess-0.2.0/qgisprocess/man/qgis_as_terra.Rd | 29 qgisprocess-0.2.0/qgisprocess/man/qgis_delete_old_cachefiles.Rd | 15 qgisprocess-0.2.0/qgisprocess/man/qgis_detect_paths.Rd |only qgisprocess-0.2.0/qgisprocess/man/qgis_run_algorithm.Rd | 47 qgisprocess-0.2.0/qgisprocess/tests/testthat/test-compat-terra.R | 338 ++++++- qgisprocess-0.2.0/qgisprocess/tests/testthat/test-qgis-algorithms.R | 12 qgisprocess-0.2.0/qgisprocess/tests/testthat/test-qgis-configure.R | 55 - qgisprocess-0.2.0/qgisprocess/tests/testthat/test-qgis-detect.R | 57 + qgisprocess-0.2.0/qgisprocess/tests/testthat/test-qgis-has.R |only qgisprocess-0.2.0/qgisprocess/tests/testthat/test-qgis-plugins.R | 7 qgisprocess-0.2.0/qgisprocess/tests/testthat/test-qgis-run.R |only qgisprocess-0.2.0/qgisprocess/tests/testthat/test-qgis-state.R |only qgisprocess-0.2.0/qgisprocess/vignettes/cheatsheet_en.Rmd | 2 qgisprocess-0.2.0/qgisprocess/vignettes/cheatsheet_es.Rmd | 4 qgisprocess-0.2.0/qgisprocess/vignettes/img/qgisprocess_en.png |binary qgisprocess-0.2.0/qgisprocess/vignettes/img/qgisprocess_es.png |binary qgisprocess-0.2.0/qgisprocess/vignettes/qgis_expressions.Rmd | 4 qgisprocess-0.2.0/qgisprocess/vignettes/qgisprocess.Rmd | 4 49 files changed, 1413 insertions(+), 491 deletions(-)
Title: Bayesian Latent Gaussian Modelling using INLA and Extensions
Description: Facilitates spatial and general latent Gaussian modeling using
integrated nested Laplace approximation via the INLA package (<https://www.r-inla.org>).
Additionally, extends the GAM-like model class to more general nonlinear predictor
expressions, and implements a log Gaussian Cox process likelihood for
modeling univariate and spatial point processes based on ecological survey data.
Model components are specified with general inputs and mapping methods to the
latent variables, and the predictors are specified via general R expressions,
with separate expressions for each observation likelihood model in
multi-likelihood models. A prediction method based on fast Monte Carlo sampling
allows posterior prediction of general expressions of the latent variables.
Ecology-focused introduction in Bachl, Lindgren, Borchers, and Illian (2019)
<doi:10.1111/2041-210X.13168>.
Author: Finn Lindgren [aut, cre, cph] ,
Fabian E. Bachl [aut, cph] ,
David L. Borchers [ctb, dtc, cph] ,
Daniel Simpson [ctb, cph] ,
Lindesay Scott-Howard [ctb, dtc, cph] ,
Seaton Andy [ctb] ,
Suen Man Ho [ctb, cph] ,
Roudier Pierre [ctb, cph] ,
Meehan Tim [ [...truncated...]
Maintainer: Finn Lindgren <finn.lindgren@gmail.com>
Diff between inlabru versions 2.10.0 dated 2023-10-29 and 2.10.1 dated 2023-12-20
inlabru-2.10.0/inlabru/inst/doc/website_examples.R |only inlabru-2.10.0/inlabru/inst/doc/website_examples.Rmd |only inlabru-2.10.0/inlabru/inst/doc/website_examples.html |only inlabru-2.10.0/inlabru/vignettes/website_examples.Rmd |only inlabru-2.10.1/inlabru/DESCRIPTION | 15 - inlabru-2.10.1/inlabru/MD5 | 88 ++++---- inlabru-2.10.1/inlabru/NEWS.md | 31 ++ inlabru-2.10.1/inlabru/R/bru.integration.R | 23 -- inlabru-2.10.1/inlabru/R/bru.spatial.R | 3 inlabru-2.10.1/inlabru/R/data.gorillas.R | 4 inlabru-2.10.1/inlabru/R/data.mexdolphin.R | 24 -- inlabru-2.10.1/inlabru/R/data.mrsea.R | 3 inlabru-2.10.1/inlabru/R/ggplot.R | 104 ++------- inlabru-2.10.1/inlabru/R/local_testthat.R | 6 inlabru-2.10.1/inlabru/R/transformation.R | 88 +++++--- inlabru-2.10.1/inlabru/R/utils.R | 52 +++- inlabru-2.10.1/inlabru/README.md | 6 inlabru-2.10.1/inlabru/build/vignette.rds |binary inlabru-2.10.1/inlabru/inst/doc/articles.R |only inlabru-2.10.1/inlabru/inst/doc/articles.Rmd |only inlabru-2.10.1/inlabru/inst/doc/articles.html |only inlabru-2.10.1/inlabru/inst/doc/component.R | 12 - inlabru-2.10.1/inlabru/inst/doc/component.Rmd | 42 ++-- inlabru-2.10.1/inlabru/inst/doc/component.html | 105 +++++----- inlabru-2.10.1/inlabru/inst/doc/linearapprox.html | 8 inlabru-2.10.1/inlabru/inst/examples/gg.inla.mesh.R | 3 inlabru-2.10.1/inlabru/inst/examples/gg.spatial.R | 1 inlabru-2.10.1/inlabru/inst/examples/predict.bru.R | 3 inlabru-2.10.1/inlabru/man/cprod.Rd | 23 -- inlabru-2.10.1/inlabru/man/figures/README-example-1.png |binary inlabru-2.10.1/inlabru/man/gg.Rd | 3 inlabru-2.10.1/inlabru/man/gg.SpatialGridDataFrame.Rd | 1 inlabru-2.10.1/inlabru/man/gg.SpatialLines.Rd | 1 inlabru-2.10.1/inlabru/man/gg.SpatialPixelsDataFrame.Rd | 1 inlabru-2.10.1/inlabru/man/gg.SpatialPoints.Rd | 1 inlabru-2.10.1/inlabru/man/gg.SpatialPolygons.Rd | 20 - inlabru-2.10.1/inlabru/man/gg.inla.mesh.Rd | 3 inlabru-2.10.1/inlabru/man/gm.Rd | 3 inlabru-2.10.1/inlabru/man/gmap.Rd | 19 - inlabru-2.10.1/inlabru/man/gorillas.Rd | 3 inlabru-2.10.1/inlabru/man/gorillas_sf.Rd | 1 inlabru-2.10.1/inlabru/man/mexdolphin.Rd | 7 inlabru-2.10.1/inlabru/man/mexdolphin_sf.Rd | 17 - inlabru-2.10.1/inlabru/man/mrsea.Rd | 3 inlabru-2.10.1/inlabru/man/predict.bru.Rd | 3 inlabru-2.10.1/inlabru/man/spoly.Rd | 3 inlabru-2.10.1/inlabru/tests/testthat/test-latent_fixed_effects.R | 6 inlabru-2.10.1/inlabru/vignettes/articles.Rmd |only inlabru-2.10.1/inlabru/vignettes/component.Rmd | 42 ++-- 49 files changed, 381 insertions(+), 400 deletions(-)
Title: Biochemically Intuitive Generalized Loewe Model
Description: Response surface methods for drug synergy analysis. Available
methods include generalized and classical Loewe formulations as well as Highest
Single Agent methodology. Response surfaces can be plotted in an interactive
3-D plot and formal statistical tests for presence of synergistic effects are
available. Implemented methods and tests are described in the article
"BIGL: Biochemically Intuitive Generalized Loewe null model for prediction
of the expected combined effect compatible with partial agonism and antagonism"
by Koen Van der Borght, Annelies Tourny, Rytis Bagdziunas, Olivier Thas,
Maxim Nazarov, Heather Turner, Bie Verbist & Hugo Ceulemans (2017)
<doi:10.1038/s41598-017-18068-5>.
Author: Heather Turner, Annelies Tourny, Olivier Thas, Maxim Nazarov, Rytis Bagdziunas, Stijn Hawinkel, Javier Franco Perez, Kathy Mutambanengwe
Maintainer: Kathy Mutambanengwe <kathy.mutambanengwe@openanalytics.eu>
Diff between BIGL versions 1.8.0 dated 2023-06-13 and 1.9.0 dated 2023-12-20
DESCRIPTION | 15 MD5 | 249 - NAMESPACE | 234 - NEWS.md | 289 - R/Blissindependence.R | 76 R/MarginalFit-methods.R | 496 +- R/ResponseSurface-methods.R | 463 +- R/bootConfInt.R | 284 - R/bootstrap.R | 471 +- R/confInt-functions.R | 308 - R/data.R | 72 R/effectSize-functions.R | 288 - R/fitMarginals.R | 832 ++-- R/fitSurface.R | 607 +-- R/generalizedLoewe.R | 172 R/getd1d2.R | 10 R/harbronLoewe.R | 210 - R/helper.R | 48 R/hsa.R | 64 R/initialMarginal.R | 298 - R/isobologram.R | 189 R/maxR-functions.R | 408 +- R/maxR.R | 234 - R/meanR-functions.R | 104 R/meanR.R | 168 R/modelVar.R | 24 R/plotMeanVarFit.R | 56 R/plotReponseSurface.R | 953 ++-- R/predictOffAxis.R | 98 R/predictResponseSurface.R | 44 R/runBIGL.R | 32 R/scaleResids.R | 145 R/splitPlot.R | 332 - R/statistics.R | 90 R/transformations.R | 390 - build/vignette.rds |binary inst/doc/analysis.R | 555 +- inst/doc/analysis.Rmd | 1113 ++--- inst/doc/analysis.html | 6923 +++++++++++++++++------------------ inst/doc/methodology.Rmd | 736 +-- inst/doc/methodology.html | 1363 ++---- inst/ui/server.R | 356 - inst/ui/ui.R | 278 - man/Blissindependence.Rd | 44 man/GetStartGuess.Rd | 42 man/L4.Rd | 44 man/addResids.Rd | 32 man/backscaleResids.Rd | 32 man/bootConfInt.Rd | 242 - man/boxcox.transformation.Rd | 44 man/coef.MarginalFit.Rd | 32 man/col2hex.Rd | 32 man/constructFormula.Rd | 88 man/contour.ResponseSurface.Rd | 53 man/df.residual.MarginalFit.Rd | 32 man/directAntivirals.Rd | 40 man/directAntivirals_ALL.Rd | 46 man/fitMarginals.Rd | 200 - man/fitSurface.Rd | 390 + man/fitted.MarginalFit.Rd | 32 man/fitted.ResponseSurface.Rd | 32 man/generalizedLoewe.Rd | 78 man/generateData.Rd | 232 - man/get.abs_tval.Rd | 44 man/get.summ.data.Rd | 32 man/getCP.Rd | 64 man/getR.Rd | 48 man/getTransformations.Rd | 138 man/getd1d2.Rd | 34 man/harbronLoewe.Rd | 74 man/hsa.Rd | 44 man/initialMarginal.Rd | 92 man/isobologram.Rd | 55 man/marginalNLS.Rd | 68 man/marginalOptim.Rd | 86 man/maxR.Rd | 278 - man/meanR.Rd | 250 - man/modelVar.Rd | 38 man/optim.boxcox.Rd | 56 man/outsidePoints.Rd | 70 man/plot.BIGLconfInt.Rd | 70 man/plot.MarginalFit.Rd | 66 man/plot.ResponseSurface.Rd | 72 man/plot.effect-size.Rd | 105 man/plot.maxR.Rd | 113 man/plot.meanR.Rd | 32 man/plotConfInt.Rd | 32 man/plotMeanVarFit.Rd | 70 man/plotResponseSurface.Rd | 297 - man/predict.MarginalFit.Rd | 42 man/predictOffAxis.Rd | 128 man/predictResponseSurface.Rd | 88 man/predictVar.Rd | 36 man/print.summary.BIGLconfInt.Rd | 32 man/print.summary.MarginalFit.Rd | 32 man/print.summary.ResponseSurface.Rd | 32 man/print.summary.maxR.Rd | 32 man/print.summary.meanR.Rd | 32 man/residuals.MarginalFit.Rd | 32 man/runBIGL.Rd | 38 man/sampleResids.Rd | 74 man/scaleResids.Rd | 40 man/simulateNull.Rd | 128 man/summary.BIGLconfInt.Rd | 32 man/summary.MarginalFit.Rd | 32 man/summary.ResponseSurface.Rd | 32 man/summary.maxR.Rd | 32 man/summary.meanR.Rd | 32 man/synergy_plot_bycomp.Rd | 86 man/vcov.MarginalFit.Rd | 32 man/wildbootAddResids.Rd |only tests/testthat.R | 10 tests/testthat/helper_calls.R | 106 tests/testthat/helper_marginals.R | 46 tests/testthat/helper_statistics.R | 42 tests/testthat/test_calls.R | 348 - tests/testthat/test_confint.R | 50 tests/testthat/test_logistic.R | 32 tests/testthat/test_marginals.R | 524 +- tests/testthat/test_maxR.R | 44 tests/testthat/test_meanR.R | 58 tests/testthat/test_plotMeanVarFit.R | 16 tests/testthat/test_splitPlot.R | 60 tests/testthat/test_wrapper.R | 160 vignettes/analysis.Rmd | 1113 ++--- vignettes/methodology.Rmd | 736 +-- 126 files changed, 14373 insertions(+), 14188 deletions(-)
Title: Binary Expansion Testing
Description: Nonparametric detection of nonuniformity and dependence with Binary Expansion Testing (BET). See Kai Zhang (2019) BET on Independence, Journal of the American Statistical Association, 114:528, 1620-1637, <DOI:10.1080/01621459.2018.1537921>, Kai Zhang, Zhigen Zhai, and Wen Zhou. (2021). BEAUTY Powered BEAST, <arXiv:2103.00674> and Wan Zhang, Zhigen Zhao, Michael Baiocchi, Yao Li, Kai Zhang. SorBET: A Fast and Powerful Algorithm to Test Dependence of Variables, Techinical report, 2023.
Author: Wan Zhang [aut, cre],
Zhigen Zhao [aut],
Michael Baiocchi [aut],
Kai Zhang [aut]
Maintainer: Wan Zhang <wanz63@live.unc.edu>
Diff between BET versions 0.5.2 dated 2023-07-21 and 0.5.3 dated 2023-12-20
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- build/partial.rdb |binary man/BET_package.Rd | 4 ++-- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Retrieving Oral Opioid Information
Description: Provides details such as Morphine Equivalent Dose (MED),
brand name and opioid content which are calculated of all oral opioids
authorized for sale by Health Canada and the FDA based on their Drug Identification Number (DIN) or National Drug Code (NDC).
MEDs are calculated based on recommendations by Canadian Institute for Health Information (CIHI) and Von Korff et al (2008)
and information obtained from Health Canada's Drug Product Database's monthly data dump or FDA Daily database for Canadian and US databases respectively.
Please note in no way should output from this package be a substitute for medical advise.
All medications should only be consumed on prescription from a licensed healthcare provider.
Author: Ankona Banerjee [aut, cre] ,
Erik Stricker [aut]
Maintainer: Ankona Banerjee <asb426@mail.usask.ca>
Diff between OralOpioids versions 1.2.0 dated 2023-08-23 and 2.0.0 dated 2023-12-20
OralOpioids-1.2.0/OralOpioids/R/utils-pipe.R |only OralOpioids-1.2.0/OralOpioids/inst/download/2023-04-03_HealthCanada_Opioid_Table.xlsx |only OralOpioids-1.2.0/OralOpioids/man/pipe.Rd |only OralOpioids-2.0.0/OralOpioids/DESCRIPTION | 19 OralOpioids-2.0.0/OralOpioids/MD5 | 39 OralOpioids-2.0.0/OralOpioids/NAMESPACE | 53 OralOpioids-2.0.0/OralOpioids/NEWS.md | 28 OralOpioids-2.0.0/OralOpioids/R/OralOpioids.R | 2417 ++++++---- OralOpioids-2.0.0/OralOpioids/README.md | 132 OralOpioids-2.0.0/OralOpioids/inst/doc/OralOpioid.Rmd | 168 OralOpioids-2.0.0/OralOpioids/inst/doc/OralOpioid.html | 152 OralOpioids-2.0.0/OralOpioids/inst/download/2023-12-01_HealthCanada_Opioid_Table.xlsx |only OralOpioids-2.0.0/OralOpioids/inst/download/2023-12-20_FDA_Opioid_Table.xlsx |only OralOpioids-2.0.0/OralOpioids/inst/extdata/old_data.csv | 369 + OralOpioids-2.0.0/OralOpioids/man/Brand.Rd | 53 OralOpioids-2.0.0/OralOpioids/man/MED.Rd | 52 OralOpioids-2.0.0/OralOpioids/man/MED_50.Rd | 54 OralOpioids-2.0.0/OralOpioids/man/MED_90.Rd | 52 OralOpioids-2.0.0/OralOpioids/man/Opioid.Rd | 53 OralOpioids-2.0.0/OralOpioids/man/OralOpioids.Rd | 24 OralOpioids-2.0.0/OralOpioids/man/load_FDA_Opioid_Table.Rd |only OralOpioids-2.0.0/OralOpioids/man/load_HealthCanada_Opioid_Table.Rd | 70 OralOpioids-2.0.0/OralOpioids/man/load_Opioid_Table.Rd |only OralOpioids-2.0.0/OralOpioids/vignettes/OralOpioid.Rmd | 168 24 files changed, 2608 insertions(+), 1295 deletions(-)
Title: Mixed GAM Computation Vehicle with Automatic Smoothness
Estimation
Description: Generalized additive (mixed) models, some of their extensions and
other generalized ridge regression with multiple smoothing
parameter estimation by (Restricted) Marginal Likelihood,
Generalized Cross Validation and similar, or using iterated
nested Laplace approximation for fully Bayesian inference. See
Wood (2017) <doi:10.1201/9781315370279> for an overview.
Includes a gam() function, a wide variety of smoothers, 'JAGS'
support and distributions beyond the exponential family.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between mgcv versions 1.9-0 dated 2023-07-11 and 1.9-1 dated 2023-12-20
mgcv-1.9-0/mgcv/inst/po/it |only mgcv-1.9-0/mgcv/po/R-it.po |only mgcv-1.9-0/mgcv/po/it.po |only mgcv-1.9-1/mgcv/ChangeLog | 23 mgcv-1.9-1/mgcv/DESCRIPTION | 6 mgcv-1.9-1/mgcv/MD5 | 62 +- mgcv-1.9-1/mgcv/R/bam.r | 33 - mgcv-1.9-1/mgcv/R/gam.fit4.r | 50 - mgcv-1.9-1/mgcv/R/gamlss.r | 2 mgcv-1.9-1/mgcv/R/gfam.r | 21 mgcv-1.9-1/mgcv/R/inla.r | 24 mgcv-1.9-1/mgcv/R/mgcv.r | 5 mgcv-1.9-1/mgcv/R/misc.r | 164 +++--- mgcv-1.9-1/mgcv/R/mvam.r | 36 - mgcv-1.9-1/mgcv/R/smooth.r | 6 mgcv-1.9-1/mgcv/build/partial.rdb |binary mgcv-1.9-1/mgcv/man/XWXd.Rd | 2 mgcv-1.9-1/mgcv/man/bam.Rd | 5 mgcv-1.9-1/mgcv/man/blas.thread.test.Rd | 2 mgcv-1.9-1/mgcv/man/gam.Rd | 2 mgcv-1.9-1/mgcv/man/gam.mh.Rd | 2 mgcv-1.9-1/mgcv/man/ginla.Rd | 18 mgcv-1.9-1/mgcv/man/smooth.construct.so.smooth.spec.Rd | 4 mgcv-1.9-1/mgcv/man/smooth.terms.Rd | 2 mgcv-1.9-1/mgcv/man/trind.generator.Rd | 2 mgcv-1.9-1/mgcv/man/ziplss.Rd | 6 mgcv-1.9-1/mgcv/src/discrete.c | 439 +++++++---------- mgcv-1.9-1/mgcv/src/init.c | 11 mgcv-1.9-1/mgcv/src/mat.c | 110 ++++ mgcv-1.9-1/mgcv/src/matrix.c | 2 mgcv-1.9-1/mgcv/src/mgcv.h | 27 - mgcv-1.9-1/mgcv/src/misc.c | 2 mgcv-1.9-1/mgcv/src/mvn.c | 30 + 33 files changed, 628 insertions(+), 470 deletions(-)
Title: Australian Tax Policy Analysis
Description: Utilities to cost and evaluate Australian tax policy, including fast
projections of personal income tax collections, high-performance tax and
transfer calculators, and an interface to common indices from the Australian
Bureau of Statistics. Written to support Grattan Institute's Australian
Perspectives program, and related projects. Access to the Australian Taxation
Office's sample files of personal income tax returns is assumed.
Author: Hugh Parsonage [aut, cre],
Tim Cameron [aut],
Brendan Coates [aut],
Matthew Katzen [aut],
William Young [aut],
Ittima Cherastidtham [dtc],
W. Karsten [ctb],
M. Enrique Garcia [ctb],
Matt Cowgill [aut]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between grattan versions 2023.1.2 dated 2023-12-08 and 2024.0.0 dated 2023-12-20
DESCRIPTION | 8 ++++---- MD5 | 27 ++++++++++++++------------- NEWS.md | 6 ++++++ R/income_tax.R | 12 ++++++++---- man/apply_super_caps_and_div293.Rd | 2 +- man/income_tax.Rd | 2 +- man/inverse_average_rate.Rd | 2 +- man/model_new_caps_and_div293.Rd | 4 ++-- src/2024.c |only src/Cincome_tax.c | 23 ++++++++++++++++++++++- src/Crebate_income.c | 5 +++++ src/Offset.c | 2 +- src/grattan.h | 1 + src/init.c | 4 ++-- src/tax-system.c | 4 +++- 15 files changed, 71 insertions(+), 31 deletions(-)
Title: Estimating and Displaying Population Attributable Fractions
Description: Estimation and display of various types of population attributable fraction and impact fractions. As well as the usual calculations of attributable fractions and impact fractions, functions are provided for attributable fraction nomograms and fan plots, continuous exposures, for pathway specific population attributable fractions, and for joint, average and sequential population attributable fractions.
Author: John Ferguson [aut, cre]
Maintainer: John Ferguson <john.ferguson@universityofgalway.ie>
Diff between graphPAF versions 1.0.2 dated 2023-02-09 and 2.0.0 dated 2023-12-20
DESCRIPTION | 10 - MD5 | 61 ++++----- NAMESPACE | 6 R/Levin.R |only R/PAF_calc_continuous.R | 39 +++++ R/PAF_calc_discrete.R | 9 - R/data.R | 2 R/data_clean.R | 5 R/fanplot.R | 269 ++++++++++++++++++++++------------------- R/graphPAF.R | 4 R/impact_fraction.R | 64 ++++++++- R/joint_PAF.R | 107 +++++++++++++--- R/plot_PAF_continuous.R | 9 - R/plot_sequential_PAF.R | 12 + R/pspaf.R | 27 +++- build/vignette.rds |binary inst/doc/graphPAF_vignette.pdf |binary man/PAF_calc_continuous.Rd | 5 man/PAF_calc_discrete.Rd | 9 + man/average_paf.Rd | 5 man/data_clean.Rd | 4 man/graphPAF.Rd | 4 man/impact_fraction.Rd | 7 - man/joint_paf.Rd | 7 - man/paf_levin.Rd |only man/paf_miettinen.Rd |only man/plot.SAF_summary.Rd | 20 ++- man/plot.rf.data.frame.Rd | 45 ++++++ man/print.PAF_q.Rd | 2 man/ps_paf.Rd | 7 - man/rf_summary.Rd | 11 + man/seq_paf.Rd | 7 - man/stroke_reduced.Rd | 2 33 files changed, 531 insertions(+), 228 deletions(-)
Title: Model Diagnostics for Accelerated Failure Time Models
Description: A collection of model checking methods for semiparametric accelerated
failure time (AFT) models under the rank-based approach. For the (computational)
efficiency, Gehan's weight is used. It provides functions to verify whether the
observed data fit the specific model assumptions such as a functional form of
each covariate, a link function, and an omnibus test. The p-value offered in this
package is based on the Kolmogorov-type supremum test and the variance of the
proposed test statistics is estimated through the re-sampling method. Furthermore,
a graphical technique to compare the shape of the observed residual to a number of
the approximated realizations is provided.
Author: Woojung Bae [aut, cre] ,
Dongrak Choi [aut] ,
Jun Yan [aut] ,
Sangwook Kang [aut]
Maintainer: Woojung Bae <matt.woojung@gmail.com>
Diff between afttest versions 4.3.2 dated 2023-12-06 and 4.3.2.1 dated 2023-12-20
DESCRIPTION | 16 MD5 | 30 NAMESPACE | 56 - R/RcppExports.R | 14 R/afttest.R | 470 +++++------ R/afttestplot.R | 534 ++++++------ R/generic.R | 126 +- README.md | 94 +- inst/CITATION | 86 +- inst/bib/afttest.bib | 40 inst/examples/ex_afttest.R | 40 inst/examples/ex_afttestplot.R | 38 man/afttest.Rd | 14 src/afttest.cpp | 1612 ++++++++++++++++++++++---------------- tests/testthat/test-afttest.R | 63 - tests/testthat/test-afttestplot.R | 61 - 16 files changed, 1780 insertions(+), 1514 deletions(-)
Title: Scientific Analysis of Trial Errors (SATE)
Description: Bundles functions used to analyze the harmfulness of trial errors in criminal trials.
Functions in the Scientific Analysis of Trial Errors ('SATE') package help users estimate the
probability that a jury will find a defendant guilty given jurors' preferences for a guilty
verdict and the uncertainty of that estimate. Users can also compare actual and hypothetical
trial conditions to conduct harmful error analysis. The relationship between individual jurors'
verdict preferences and the probability that a jury returns a guilty verdict has been studied
by Davis (1973) <doi:10.1037/h0033951>; MacCoun & Kerr (1988) <doi:10.1037/0022-3514.54.1.21>,
and Devine et el. (2001) <doi:10.1037/1076-8971.7.3.622>, among others.
Author: Barry Edwards, J.D., Ph.D.
Maintainer: Barry Edwards <barry.edwards@ucf.edu>
Diff between sate versions 1.1.0 dated 2020-03-24 and 2.1.0 dated 2023-12-20
sate-1.1.0/sate/R/CI90.r |only sate-1.1.0/sate/R/as.jury.stat.r |only sate-1.1.0/sate/R/se.prop.r |only sate-1.1.0/sate/man/CI90.Rd |only sate-1.1.0/sate/man/as.jury.stat.Rd |only sate-1.1.0/sate/man/se.prop.Rd |only sate-2.1.0/sate/DESCRIPTION | 11 +-- sate-2.1.0/sate/MD5 | 37 +++++++---- sate-2.1.0/sate/NAMESPACE | 30 ++++++++- sate-2.1.0/sate/NEWS.md | 17 +++++ sate-2.1.0/sate/R/as.jury.point.r | 35 ++++++++--- sate-2.1.0/sate/R/as.jury.stats.r |only sate-2.1.0/sate/R/compare.jury.stats.r | 82 +++++++++++--------------- sate-2.1.0/sate/R/deliberate.civil.r |only sate-2.1.0/sate/R/deliberate.r |only sate-2.1.0/sate/R/graph.effect.defendant.r |only sate-2.1.0/sate/R/graph.estimate.r |only sate-2.1.0/sate/R/helper.functions.r |only sate-2.1.0/sate/R/select.with.strikes.r |only sate-2.1.0/sate/R/sim.as.jury.stats.r |only sate-2.1.0/sate/R/sim.compare.jury.stats.r |only sate-2.1.0/sate/man/as.jury.point.Rd | 28 ++++++-- sate-2.1.0/sate/man/as.jury.stats.Rd |only sate-2.1.0/sate/man/compare.jury.stats.Rd | 22 +++++- sate-2.1.0/sate/man/deliberate.Rd |only sate-2.1.0/sate/man/deliberate.civil.Rd |only sate-2.1.0/sate/man/graph.effect.defendant.Rd |only sate-2.1.0/sate/man/graph.estimate.Rd |only sate-2.1.0/sate/man/select.with.strikes.Rd |only sate-2.1.0/sate/man/sim.as.jury.stats.Rd |only sate-2.1.0/sate/man/sim.compare.jury.stats.Rd |only 31 files changed, 172 insertions(+), 90 deletions(-)
Title: Get Silhouettes of Organisms from PhyloPic
Description: Work with the PhyloPic Web Service (<http://api-docs.phylopic.org/v2/>)
to fetch silhouette images of organisms. Includes functions for adding
silhouettes to both base R plots and ggplot2 plots.
Author: William Gearty [aut, cre] ,
Lewis A. Jones [aut] ,
Scott Chamberlain [aut] ,
David Miller [ctb]
Maintainer: William Gearty <willgearty@gmail.com>
Diff between rphylopic versions 1.2.2 dated 2023-10-28 and 1.3.0 dated 2023-12-20
DESCRIPTION | 12 MD5 | 150 ++--- NAMESPACE | 6 NEWS.md | 10 R/add_phylopic.r | 17 R/add_phylopic_base.r | 26 R/browse_phylopic.R | 3 R/geom_phylopic.R | 49 + R/get_attribution.R | 9 R/get_phylopic.R | 53 + R/get_uuid.R | 11 R/pick_phylopic.R | 19 R/resolve_phylopic.R |only R/save_phylopic.R | 3 R/zzz.r | 30 - README.md | 8 build/vignette.rds |binary inst/CITATION | 13 inst/doc/a-getting-started.Rmd | 30 - inst/doc/a-getting-started.html | 45 - inst/doc/b-advanced-ggplot.Rmd | 63 +- inst/doc/b-advanced-ggplot.html | 207 ++++--- inst/doc/c-advanced-base.Rmd | 16 inst/doc/c-advanced-base.html | 32 - man/add_phylopic.Rd | 18 man/add_phylopic_base.Rd | 18 man/browse_phylopic.Rd | 2 man/geom_phylopic.Rd | 27 - man/get_attribution.Rd | 3 man/get_phylopic.Rd | 2 man/get_uuid.Rd | 2 man/pick_phylopic.Rd | 19 man/resolve_phylopic.Rd |only man/rphylopic-package.Rd | 4 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/add_phylopic/phylopic-in-background.svg | 38 - tests/testthat/_snaps/add_phylopic/phylopic-png-in-background.svg | 2 tests/testthat/_snaps/add_phylopic/phylopics-on-top-of-plot.svg | 252 ++++----- tests/testthat/_snaps/add_phylopic_base/phylopic-in-background.svg | 12 tests/testthat/_snaps/add_phylopic_base/phylopic-png-in-background.svg | 2 tests/testthat/_snaps/add_phylopic_base/phylopics-on-top-of-plot.svg | 266 +++++----- tests/testthat/_snaps/geom_phylopic/geom-phylopic-with-png.svg | 8 tests/testthat/_snaps/geom_phylopic/geom-phylopic.svg | 46 - tests/testthat/_snaps/geom_phylopic/phylopic-key-glyph-with-img.svg | 32 - tests/testthat/_snaps/geom_phylopic/phylopic-key-glyph-with-larger-glyphs.svg | 34 - tests/testthat/_snaps/geom_phylopic/phylopic-key-glyph-with-uuid.svg | 38 - tests/testthat/_snaps/geom_phylopic/phylopic-key-glyph.svg | 36 - tests/testthat/_snaps/phylopic_utils/plot-array.svg | 2 tests/testthat/_snaps/phylopic_utils/plot-picture.svg | 10 tests/testthat/test-add_phylopic.R | 5 tests/testthat/test-add_phylopic_base.R | 7 tests/testthat/test-geom_phylopic.R | 12 tests/testthat/test-get_phylopic.R | 1 tests/testthat/test-resolve_phylopic.R |only vignettes/a-getting-started.Rmd | 30 - vignettes/b-advanced-ggplot.Rmd | 63 +- vignettes/base-geog-plot-1-1.png |binary vignettes/base-geog-plot-2-1.png |binary vignettes/base-penguin-plot-2-1.png |binary vignettes/base-penguin-plot-3-1.png |binary vignettes/base-penguin-plot-4-1.png |binary vignettes/base-penguin-plot-5-1.png |binary vignettes/base-phylo-plot-3-1.png |binary vignettes/base-phylo-plot-4-1.png |binary vignettes/c-advanced-base.Rmd | 16 vignettes/ggplot-geog-plot-1-1.png |binary vignettes/ggplot-geog-plot-2-1.png |binary vignettes/ggplot-geog-plot-3-1.png |only vignettes/ggplot-penguin-plot-2-1.png |binary vignettes/ggplot-penguin-plot-3-1.png |binary vignettes/ggplot-penguin-plot-4-1.png |binary vignettes/ggplot-penguin-plot-5-1.png |binary vignettes/ggplot-penguin-plot-6-1.png |binary vignettes/ggplot-phylo-plot-3-1.png |binary vignettes/ggplot-phylo-plot-4-1.png |binary vignettes/intro-base-plot-1.png |binary vignettes/intro-ggplot-plot-1.png |binary vignettes/intro-transform-plot-1.png |binary 78 files changed, 1001 insertions(+), 818 deletions(-)
Title: Plotting Linkage and Association Results
Description: Provides routines for plotting
linkage and association results along a chromosome,
with marker names displayed along the top border.
There are also routines for generating BED and BedGraph
custom tracks for viewing in the UCSC genome browser.
The data reformatting program Mega2 uses this
package to plot output from a variety of
programs.
Author: Robert V Baron <rvb5@pitt.edu>, Nandita Mukhopadhyay,
Xinyu Tang, Daniel E. Weeks <weeks@pitt.edu>
Maintainer: Daniel E. Weeks <weeks@pitt.edu>
Diff between nplplot versions 4.6 dated 2022-05-18 and 4.7 dated 2023-12-20
nplplot-4.6/nplplot/tests/Rallegro.07.Rout |only nplplot-4.7/nplplot/DESCRIPTION | 8 ++++---- nplplot-4.7/nplplot/MD5 | 6 +++--- nplplot-4.7/nplplot/man/prepareplot.Rd | 4 ++-- nplplot-4.7/nplplot/tests/Rallegro.07.Rout.save |only 5 files changed, 9 insertions(+), 9 deletions(-)
Title: Statistical Methods for Psychologists
Description: Implements confidence interval and sample size methods that are especially useful in psychological research. The methods can be applied in 1-group, 2-group, paired-samples, and multiple-group designs and to a variety of parameters including means, medians, proportions, slopes, standardized mean differences, standardized linear contrasts of means, plus several measures of correlation and association. The confidence intervals and sample size functions are applicable to single parameters as well as differences, ratios, and linear contrasts of parameters. The sample size functions can be used to approximate the sample size needed to estimate a parameter or function of parameters with desired confidence interval precision or to perform a variety of hypothesis tests (directional two-sided, equivalence, superiority, noninferiority) with desired power. For details see: Statistical Methods for Psychologists, Volumes 1 – 4, <https://dgbonett.sites.ucsc.edu/>.
Author: Douglas G. Bonett [aut, cre],
Robert J. Calin-Jageman [ctb]
Maintainer: Douglas G. Bonett <dgbonett@ucsc.edu>
Diff between statpsych versions 1.4.0 dated 2023-06-14 and 1.5.0 dated 2023-12-20
statpsych-1.4.0/statpsych/man/ci.mape.Rd |only statpsych-1.5.0/statpsych/DESCRIPTION | 6 statpsych-1.5.0/statpsych/MD5 | 349 +- statpsych-1.5.0/statpsych/NAMESPACE | 13 statpsych-1.5.0/statpsych/NEWS.md | 34 statpsych-1.5.0/statpsych/R/statpsych1.R | 1643 ++++++++++--- statpsych-1.5.0/statpsych/R/statpsych2.R | 436 ++- statpsych-1.5.0/statpsych/R/statpsych3.R | 402 ++- statpsych-1.5.0/statpsych/build/partial.rdb |binary statpsych-1.5.0/statpsych/inst/REFERENCES.bib | 150 - statpsych-1.5.0/statpsych/man/ci.2x2.mean.bs.Rd | 8 statpsych-1.5.0/statpsych/man/ci.2x2.mean.mixed.Rd | 16 statpsych-1.5.0/statpsych/man/ci.2x2.mean.ws.Rd | 8 statpsych-1.5.0/statpsych/man/ci.2x2.median.bs.Rd | 8 statpsych-1.5.0/statpsych/man/ci.2x2.median.mixed.Rd |only statpsych-1.5.0/statpsych/man/ci.2x2.median.ws.Rd |only statpsych-1.5.0/statpsych/man/ci.2x2.prop.bs.Rd | 17 statpsych-1.5.0/statpsych/man/ci.2x2.prop.mixed.Rd | 4 statpsych-1.5.0/statpsych/man/ci.2x2.stdmean.bs.Rd | 27 statpsych-1.5.0/statpsych/man/ci.2x2.stdmean.mixed.Rd |only statpsych-1.5.0/statpsych/man/ci.2x2.stdmean.ws.Rd |only statpsych-1.5.0/statpsych/man/ci.agree.3rater.Rd | 12 statpsych-1.5.0/statpsych/man/ci.agree.Rd | 4 statpsych-1.5.0/statpsych/man/ci.bayes.normal.Rd | 12 statpsych-1.5.0/statpsych/man/ci.bayes.prop1.Rd | 4 statpsych-1.5.0/statpsych/man/ci.biphi.Rd | 4 statpsych-1.5.0/statpsych/man/ci.cod1.Rd | 4 statpsych-1.5.0/statpsych/man/ci.cod2.Rd | 12 statpsych-1.5.0/statpsych/man/ci.condslope.Rd | 4 statpsych-1.5.0/statpsych/man/ci.condslope.log.Rd | 6 statpsych-1.5.0/statpsych/man/ci.cor.Rd | 4 statpsych-1.5.0/statpsych/man/ci.cor.dep.Rd | 4 statpsych-1.5.0/statpsych/man/ci.cor2.Rd | 4 statpsych-1.5.0/statpsych/man/ci.cor2.gen.Rd | 4 statpsych-1.5.0/statpsych/man/ci.cqv1.Rd | 4 statpsych-1.5.0/statpsych/man/ci.cramer.Rd | 6 statpsych-1.5.0/statpsych/man/ci.cronbach.Rd | 6 statpsych-1.5.0/statpsych/man/ci.cronbach2.Rd | 4 statpsych-1.5.0/statpsych/man/ci.cv1.Rd |only statpsych-1.5.0/statpsych/man/ci.etasqr.Rd | 6 statpsych-1.5.0/statpsych/man/ci.fisher.Rd | 23 statpsych-1.5.0/statpsych/man/ci.indirect.Rd | 4 statpsych-1.5.0/statpsych/man/ci.lc.gen.bs.Rd | 4 statpsych-1.5.0/statpsych/man/ci.lc.glm.Rd | 4 statpsych-1.5.0/statpsych/man/ci.lc.median.bs.Rd | 4 statpsych-1.5.0/statpsych/man/ci.lc.prop.bs.Rd | 6 statpsych-1.5.0/statpsych/man/ci.lc.reg.Rd | 4 statpsych-1.5.0/statpsych/man/ci.lc.stdmean.bs.Rd | 11 statpsych-1.5.0/statpsych/man/ci.lc.stdmean.ws.Rd | 9 statpsych-1.5.0/statpsych/man/ci.mad1.Rd | 4 statpsych-1.5.0/statpsych/man/ci.mann.Rd | 6 statpsych-1.5.0/statpsych/man/ci.mape1.Rd |only statpsych-1.5.0/statpsych/man/ci.mape2.Rd | 9 statpsych-1.5.0/statpsych/man/ci.mean.ps.Rd | 4 statpsych-1.5.0/statpsych/man/ci.mean1.Rd | 4 statpsych-1.5.0/statpsych/man/ci.median.ps.Rd | 12 statpsych-1.5.0/statpsych/man/ci.median1.Rd | 4 statpsych-1.5.0/statpsych/man/ci.median2.Rd | 4 statpsych-1.5.0/statpsych/man/ci.pairs.prop.bs.Rd | 3 statpsych-1.5.0/statpsych/man/ci.pairs.prop1.Rd | 3 statpsych-1.5.0/statpsych/man/ci.pbcor.Rd | 2 statpsych-1.5.0/statpsych/man/ci.phi.Rd | 4 statpsych-1.5.0/statpsych/man/ci.popsize.Rd | 4 statpsych-1.5.0/statpsych/man/ci.prop.ps.Rd | 4 statpsych-1.5.0/statpsych/man/ci.prop1.inv.Rd | 6 statpsych-1.5.0/statpsych/man/ci.prop2.Rd | 4 statpsych-1.5.0/statpsych/man/ci.prop2.inv.Rd | 8 statpsych-1.5.0/statpsych/man/ci.pv.Rd |only statpsych-1.5.0/statpsych/man/ci.ratio.cv2.Rd |only statpsych-1.5.0/statpsych/man/ci.ratio.mad.ps.Rd | 6 statpsych-1.5.0/statpsych/man/ci.ratio.mad2.Rd | 4 statpsych-1.5.0/statpsych/man/ci.ratio.mean.ps.Rd | 6 statpsych-1.5.0/statpsych/man/ci.ratio.mean2.Rd | 4 statpsych-1.5.0/statpsych/man/ci.ratio.median.ps.Rd | 6 statpsych-1.5.0/statpsych/man/ci.ratio.median2.Rd | 4 statpsych-1.5.0/statpsych/man/ci.ratio.prop.ps.Rd | 4 statpsych-1.5.0/statpsych/man/ci.ratio.prop2.Rd | 4 statpsych-1.5.0/statpsych/man/ci.ratio.sd2.Rd | 4 statpsych-1.5.0/statpsych/man/ci.rel2.Rd | 4 statpsych-1.5.0/statpsych/man/ci.reliability.Rd | 4 statpsych-1.5.0/statpsych/man/ci.rsqr.Rd | 4 statpsych-1.5.0/statpsych/man/ci.sign1.Rd | 4 statpsych-1.5.0/statpsych/man/ci.slope.prop.bs.Rd | 4 statpsych-1.5.0/statpsych/man/ci.spcor.Rd | 4 statpsych-1.5.0/statpsych/man/ci.spear.Rd | 4 statpsych-1.5.0/statpsych/man/ci.spear2.Rd | 4 statpsych-1.5.0/statpsych/man/ci.stdmean.ps.Rd | 11 statpsych-1.5.0/statpsych/man/ci.stdmean.strat.Rd | 13 statpsych-1.5.0/statpsych/man/ci.stdmean1.Rd | 7 statpsych-1.5.0/statpsych/man/ci.stdmean2.Rd | 13 statpsych-1.5.0/statpsych/man/ci.tetra.Rd | 4 statpsych-1.5.0/statpsych/man/ci.theil.Rd | 4 statpsych-1.5.0/statpsych/man/ci.var.upper.Rd | 4 statpsych-1.5.0/statpsych/man/ci.yule.Rd | 1 statpsych-1.5.0/statpsych/man/etasqr.adj.Rd | 4 statpsych-1.5.0/statpsych/man/iqv.Rd | 4 statpsych-1.5.0/statpsych/man/pi.score.ps.Rd | 4 statpsych-1.5.0/statpsych/man/pi.score1.Rd | 4 statpsych-1.5.0/statpsych/man/pi.var.upper.Rd | 4 statpsych-1.5.0/statpsych/man/power.cor1.Rd | 4 statpsych-1.5.0/statpsych/man/power.cor2.Rd | 4 statpsych-1.5.0/statpsych/man/power.lc.mean.bs.Rd | 6 statpsych-1.5.0/statpsych/man/power.mean.ps.Rd | 4 statpsych-1.5.0/statpsych/man/power.mean1.Rd | 4 statpsych-1.5.0/statpsych/man/power.mean2.Rd | 4 statpsych-1.5.0/statpsych/man/power.prop.ps.Rd | 4 statpsych-1.5.0/statpsych/man/power.prop1.Rd | 4 statpsych-1.5.0/statpsych/man/power.prop2.Rd | 4 statpsych-1.5.0/statpsych/man/random.sample.Rd | 2 statpsych-1.5.0/statpsych/man/random.y.Rd | 2 statpsych-1.5.0/statpsych/man/sim.ci.mean.ps.Rd | 4 statpsych-1.5.0/statpsych/man/sim.ci.mean1.Rd | 4 statpsych-1.5.0/statpsych/man/sim.ci.median.ps.Rd | 4 statpsych-1.5.0/statpsych/man/sim.ci.median1.Rd | 4 statpsych-1.5.0/statpsych/man/sim.ci.median2.Rd | 4 statpsych-1.5.0/statpsych/man/size.ci.agree.Rd | 4 statpsych-1.5.0/statpsych/man/size.ci.condmean.Rd | 4 statpsych-1.5.0/statpsych/man/size.ci.cor.Rd | 4 statpsych-1.5.0/statpsych/man/size.ci.cronbach.Rd | 4 statpsych-1.5.0/statpsych/man/size.ci.cronbach2.Rd | 6 statpsych-1.5.0/statpsych/man/size.ci.etasqr.Rd | 10 statpsych-1.5.0/statpsych/man/size.ci.indirect.Rd | 14 statpsych-1.5.0/statpsych/man/size.ci.lc.ancova.Rd | 6 statpsych-1.5.0/statpsych/man/size.ci.lc.mean.bs.Rd | 4 statpsych-1.5.0/statpsych/man/size.ci.lc.mean.ws.Rd | 4 statpsych-1.5.0/statpsych/man/size.ci.lc.prop.bs.Rd | 6 statpsych-1.5.0/statpsych/man/size.ci.mape1.Rd |only statpsych-1.5.0/statpsych/man/size.ci.mean.ps.Rd | 4 statpsych-1.5.0/statpsych/man/size.ci.mean1.Rd | 4 statpsych-1.5.0/statpsych/man/size.ci.mean2.Rd | 4 statpsych-1.5.0/statpsych/man/size.ci.pbcor.Rd |only statpsych-1.5.0/statpsych/man/size.ci.prop.ps.Rd | 4 statpsych-1.5.0/statpsych/man/size.ci.prop1.Rd | 4 statpsych-1.5.0/statpsych/man/size.ci.prop2.Rd | 6 statpsych-1.5.0/statpsych/man/size.ci.ratio.mean.ps.Rd | 4 statpsych-1.5.0/statpsych/man/size.ci.ratio.mean2.Rd | 4 statpsych-1.5.0/statpsych/man/size.ci.ratio.prop.ps.Rd | 8 statpsych-1.5.0/statpsych/man/size.ci.ratio.prop2.Rd | 6 statpsych-1.5.0/statpsych/man/size.ci.rsqr.Rd | 6 statpsych-1.5.0/statpsych/man/size.ci.second.Rd | 4 statpsych-1.5.0/statpsych/man/size.ci.slope.Rd | 4 statpsych-1.5.0/statpsych/man/size.ci.spear.Rd |only statpsych-1.5.0/statpsych/man/size.ci.stdmean2.Rd | 2 statpsych-1.5.0/statpsych/man/size.equiv.mean.ps.Rd | 4 statpsych-1.5.0/statpsych/man/size.equiv.mean2.Rd | 6 statpsych-1.5.0/statpsych/man/size.equiv.prop.ps.Rd | 6 statpsych-1.5.0/statpsych/man/size.equiv.prop2.Rd | 6 statpsych-1.5.0/statpsych/man/size.interval.cor.Rd | 4 statpsych-1.5.0/statpsych/man/size.supinf.mean.ps.Rd | 4 statpsych-1.5.0/statpsych/man/size.supinf.mean2.Rd | 6 statpsych-1.5.0/statpsych/man/size.supinf.prop.ps.Rd | 4 statpsych-1.5.0/statpsych/man/size.supinf.prop2.Rd | 6 statpsych-1.5.0/statpsych/man/size.test.cor.Rd | 4 statpsych-1.5.0/statpsych/man/size.test.cor2.Rd | 6 statpsych-1.5.0/statpsych/man/size.test.cronbach.Rd | 4 statpsych-1.5.0/statpsych/man/size.test.cronbach2.Rd | 6 statpsych-1.5.0/statpsych/man/size.test.lc.ancova.Rd | 6 statpsych-1.5.0/statpsych/man/size.test.lc.mean.bs.Rd | 6 statpsych-1.5.0/statpsych/man/size.test.lc.mean.ws.Rd | 4 statpsych-1.5.0/statpsych/man/size.test.lc.prop.bs.Rd | 6 statpsych-1.5.0/statpsych/man/size.test.mann.Rd | 6 statpsych-1.5.0/statpsych/man/size.test.mean.ps.Rd | 4 statpsych-1.5.0/statpsych/man/size.test.mean1.Rd | 4 statpsych-1.5.0/statpsych/man/size.test.mean2.Rd | 6 statpsych-1.5.0/statpsych/man/size.test.prop.ps.Rd | 6 statpsych-1.5.0/statpsych/man/size.test.prop1.Rd | 4 statpsych-1.5.0/statpsych/man/size.test.prop2.Rd | 6 statpsych-1.5.0/statpsych/man/size.test.sign.ps.Rd | 4 statpsych-1.5.0/statpsych/man/size.test.sign1.Rd | 4 statpsych-1.5.0/statpsych/man/size.test.slope.Rd | 4 statpsych-1.5.0/statpsych/man/spearmanbrown.Rd |only statpsych-1.5.0/statpsych/man/test.anova1.bs.Rd | 8 statpsych-1.5.0/statpsych/man/test.kurtosis.Rd | 4 statpsych-1.5.0/statpsych/man/test.prop.bs.Rd | 4 statpsych-1.5.0/statpsych/man/test.prop.ps.Rd | 4 statpsych-1.5.0/statpsych/man/test.prop1.Rd | 4 statpsych-1.5.0/statpsych/man/test.prop2.Rd | 4 statpsych-1.5.0/statpsych/man/test.skew.Rd | 4 statpsych-1.5.0/statpsych/tests/testthat/test_statpsych1.R | 143 - statpsych-1.5.0/statpsych/tests/testthat/test_statpsych2.R | 51 statpsych-1.5.0/statpsych/tests/testthat/test_statpsych3.R | 12 statpsych-1.5.0/statpsych/tests/testthat/test_statpsych4.R | 2 182 files changed, 2848 insertions(+), 1250 deletions(-)
Title: Semi-Supervised Algorithm for Document Scaling
Description: A word embeddings-based semi-supervised model for document scaling Watanabe (2020) <doi:10.1080/19312458.2020.1832976>.
LSS allows users to analyze large and complex corpora on arbitrary dimensions with seed words exploiting efficiency of word embeddings (SVD, Glove).
It can generate word vectors on a users-provided corpus or incorporate a pre-trained word vectors.
Author: Kohei Watanabe [aut, cre, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between LSX versions 1.3.1 dated 2023-02-25 and 1.3.2 dated 2023-12-20
DESCRIPTION | 6 MD5 | 89 +- NAMESPACE | 173 ++-- NEWS.md | 194 ++--- R/as.textmodel.R | 202 ++--- R/bootstrap.R | 108 +-- R/data.R | 70 - R/predict.R | 226 +++--- R/textmodel-methods.R | 322 ++++----- R/textmodel.R | 863 ++++++++++++------------ R/textplot.R | 335 ++++----- R/textstat.R | 150 ++-- R/utils.R | 384 +++++----- build/partial.rdb |binary man/as.coefficients_textmodel.Rd | 34 man/as.seedwords.Rd | 46 - man/as.statistics_textmodel.Rd | 32 man/as.summary.textmodel.Rd | 30 man/as.textmodel_lss.Rd | 66 - man/bootstrap_lss.Rd | 74 +- man/coef.textmodel_lss.Rd | 40 - man/cohesion.Rd | 34 man/data_dictionary_ideology.Rd | 24 man/data_dictionary_sentiment.Rd | 34 man/data_textmodel_lss_russianprotests.Rd | 42 - man/diagnosys.Rd | 34 man/predict.textmodel_lss.Rd | 106 +- man/print.coefficients_textmodel.Rd | 46 - man/print.statistics_textmodel.Rd | 42 - man/print.summary.textmodel.Rd | 42 - man/seedwords.Rd | 46 - man/smooth_lss.Rd | 76 +- man/textmodel_lss.Rd | 258 +++---- man/textplot_components.Rd | 52 - man/textplot_simil.Rd | 28 man/textplot_terms.Rd | 46 - man/textstat_context.Rd | 148 ++-- man/weight_seeds.Rd | 24 tests/testthat.R | 7 tests/testthat/Rplots.pdf |only tests/testthat/test-as.textmodel.R | 334 ++++----- tests/testthat/test-bootstrap.R | 116 +-- tests/testthat/test-textmodel.R | 1066 +++++++++++++++--------------- tests/testthat/test-textplot.R | 189 ++--- tests/testthat/test-textstat.R | 106 +- tests/testthat/test-utils.R | 140 +-- 46 files changed, 3256 insertions(+), 3228 deletions(-)
Title: Sequential Quadratic Programming for Fast Maximum-Likelihood
Estimation of Mixture Proportions
Description: Provides an optimization method based on sequential
quadratic programming (SQP) for maximum likelihood estimation of
the mixture proportions in a finite mixture model where the
component densities are known. The algorithm is expected to obtain
solutions that are at least as accurate as the state-of-the-art
MOSEK interior-point solver (called by function "KWDual" in the
'REBayes' package), and they are expected to arrive at solutions
more quickly when the number of samples is large and the number of
mixture components is not too large. This implements the "mix-SQP"
algorithm, with some improvements, described in Y. Kim,
P. Carbonetto, M. Stephens & M. Anitescu (2020)
<DOI:10.1080/10618600.2019.1689985>.
Author: Youngseok Kim [aut],
Peter Carbonetto [aut, cre],
Mihai Anitescu [aut],
Matthew Stephens [aut],
Jason Willwerscheid [ctb],
Jean Morrison [ctb]
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>
Diff between mixsqp versions 0.3-48 dated 2022-11-16 and 0.3-54 dated 2023-12-20
mixsqp-0.3-48/mixsqp/R/rebayes.R |only mixsqp-0.3-48/mixsqp/man/mixkwdual.Rd |only mixsqp-0.3-54/mixsqp/DESCRIPTION | 10 - mixsqp-0.3-54/mixsqp/MD5 | 32 ++-- mixsqp-0.3-54/mixsqp/NAMESPACE | 1 mixsqp-0.3-54/mixsqp/R/mixsqp.R | 15 -- mixsqp-0.3-54/mixsqp/R/tacks.R | 6 mixsqp-0.3-54/mixsqp/build/partial.rdb |binary mixsqp-0.3-54/mixsqp/inst/CITATION | 10 - mixsqp-0.3-54/mixsqp/inst/doc/mixsqp-intro.R | 32 ---- mixsqp-0.3-54/mixsqp/inst/doc/mixsqp-intro.Rmd | 74 ---------- mixsqp-0.3-54/mixsqp/inst/doc/mixsqp-intro.html | 153 +++++----------------- mixsqp-0.3-54/mixsqp/man/mixsqp.Rd | 11 - mixsqp-0.3-54/mixsqp/man/tacks.Rd | 6 mixsqp-0.3-54/mixsqp/src/Makevars | 1 mixsqp-0.3-54/mixsqp/src/Makevars.win | 1 mixsqp-0.3-54/mixsqp/tests/testthat/test_mixsqp.R | 6 mixsqp-0.3-54/mixsqp/vignettes/mixsqp-intro.Rmd | 74 ---------- 18 files changed, 80 insertions(+), 352 deletions(-)
Title: Triangle Meshes and Related Geometry Tools
Description: Generate planar and spherical triangle meshes,
compute finite element calculations for 1- and 2-dimensional flat and curved
manifolds with associated basis function spaces, methods for lines and
polygons, and transparent handling of coordinate reference systems and
coordinate transformation, including 'sf' and 'sp' geometries. The core
'fmesher' library code was originally part of the 'INLA' package, and
implements parts of "Triangulations and Applications" by
Hjelle and Daehlen (2006) <doi:10.1007/3-540-33261-8>.
Author: Finn Lindgren [aut, cre, cph] ,
Seaton Andy [ctb] ,
Suen Man Ho [ctb] ,
Fabian E. Bachl [ctb]
Maintainer: Finn Lindgren <finn.lindgren@gmail.com>
Diff between fmesher versions 0.1.4 dated 2023-10-28 and 0.1.5 dated 2023-12-20
DESCRIPTION | 6 +++--- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 9 +++++++++ R/evaluator.R | 28 ++++++++++++++++++++-------- R/matern.R | 9 +++++---- R/mesh.R | 29 ++++++++++++++++++++++------- R/mesh_2d.R | 2 +- R/plot.R | 4 ++++ R/segm.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/basic_use.html | 24 ++++++++++++------------ inst/doc/inla_conversion.html | 8 ++++---- man/figures/README-example1-plot-1.png |binary man/figures/README-example2-plot-1.png |binary man/fm_gmrf.Rd | 3 ++- man/fm_rcdt_2d.Rd | 2 +- 17 files changed, 100 insertions(+), 58 deletions(-)
Title: Tools to Accompany the 'psych' Package for Psychological
Research
Description: Support functions, data sets, and vignettes for the 'psych' package. Contains several of the biggest data sets for the 'psych' package as well as four vignettes. A few helper functions for file manipulation are included as well. For more information, see the <https://personality-project.org/r/> web page.
Author: William Revelle [aut, cre]
Maintainer: William Revelle <revelle@northwestern.edu>
Diff between psychTools versions 2.3.9 dated 2023-09-26 and 2.3.12 dated 2023-12-20
DESCRIPTION | 8 +-- MD5 | 36 +++++++------- R/df2latex.R | 2 build/partial.rdb |binary build/vignette.rds |binary data/salary.rda |only inst/CITATION | 2 inst/NEWS.Rd | 13 ++++- inst/doc/factor.R | 60 ++++++++++++------------ inst/doc/factor.Rnw | 9 ++- inst/doc/factor.pdf |binary inst/doc/mediation.R | 118 ++++++++++++++++++++++++++++++------------------ inst/doc/mediation.pdf |binary inst/doc/mediation.rnw | 89 +++++++++++++++++++++++++++++------- inst/doc/omega.pdf |binary inst/doc/overview.pdf |binary man/read.clipboard.Rd | 22 ++++---- man/salary.Rd |only vignettes/factor.Rnw | 9 ++- vignettes/mediation.rnw | 89 +++++++++++++++++++++++++++++------- 20 files changed, 307 insertions(+), 150 deletions(-)
Title: Recreates Some 'SAS®' Procedures in 'R'
Description: Contains functions to simulate the most commonly used
'SAS®' procedures. Specifically, the package aims to
simulate the functionality of 'proc freq', 'proc means', 'proc ttest',
'proc transpose', 'proc sort', and 'proc print'.
The simulation will include recreating
all statistics with the highest fidelity possible.
Author: David Bosak [aut, cre],
Kevin Kramer [ctb],
Brian Varney [ctb],
Duong Tran [ctb],
Yifei Chen [ctb]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between procs versions 1.0.3 dated 2023-09-05 and 1.0.4 dated 2023-12-20
DESCRIPTION | 10 - MD5 | 72 ++++--- NAMESPACE | 2 NEWS.md | 9 R/plots.R |only R/proc_freq.R | 22 +- R/proc_means.R | 33 ++- R/proc_sort.R | 18 + R/proc_transpose.R | 30 ++- R/proc_ttest.R |only R/statistics.R | 36 +++ R/supplements.R | 4 R/utilities.R | 358 +++++++++++++++++++++++++++++++++------ README.md | 4 build/vignette.rds |binary inst/doc/procs-dm.R | 76 ++++++++ inst/doc/procs-dm.Rmd | 101 ++++++++++- inst/doc/procs-dm.html | 85 ++++++++- inst/doc/procs-ttest.R |only inst/doc/procs-ttest.Rmd |only inst/doc/procs-ttest.html |only inst/doc/procs.R | 38 ++++ inst/doc/procs.Rmd | 62 ++++++ inst/doc/procs.html | 189 +++++++++++++------- man/images/ttest.png |only man/images/ttest1.png |only man/images/ttest2.png |only man/images/ttest3.png |only man/images/ttest4.png |only man/proc_means.Rd | 11 - man/proc_sort.Rd | 16 + man/proc_transpose.Rd | 5 man/proc_ttest.Rd |only tests/testthat/data/CLASS.dbf |only tests/testthat/log |only tests/testthat/test-freq.R | 38 +++- tests/testthat/test-sort.R | 38 ++++ tests/testthat/test-statistics.R | 25 ++ tests/testthat/test-transpose.R | 11 + tests/testthat/test-ttest.R |only tests/testthat/test-utilities.R | 131 ++++++++------ vignettes/procs-dm.Rmd | 101 ++++++++++- vignettes/procs-ttest.Rmd |only vignettes/procs.Rmd | 62 ++++++ 44 files changed, 1336 insertions(+), 251 deletions(-)
Title: Test for Finiteness of Moments in a Distribution
Description: The purpose of this package is to tests whether a given
moment of the distribution of a given sample is finite or not. For
heavy-tailed distributions with tail exponent b, only moments of
order smaller than b are finite. Tail exponent and heavy-
tailedness are notoriously difficult to ascertain. But the
finiteness of moments (including fractional moments) can be tested
directly. This package does that following the test suggested by
Trapani (2016) <doi:10.1016/j.jeconom.2015.08.006>.
Author: Torsten Heinrich [aut, cre],
Julian Winkler [aut]
Maintainer: Torsten Heinrich <torsten.heinrich@posteo.net>
Diff between finity versions 0.1.4.1 dated 2020-04-23 and 0.1.5 dated 2023-12-20
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- build/partial.rdb |binary src/RcppExports.cpp | 5 +++++ src/finite_moment_test.cpp | 10 ++++------ 5 files changed, 18 insertions(+), 15 deletions(-)
Title: Generate Machine- And Human-Readable Plot Labels for Experiments
Description: A no-frills open-source solution for designing plot labels affixed with QR
codes. It features 'EasyQrlabelr', a 'BrAPI-compliant' 'shiny' app that
simplifies the process of plot label design for non-R users. It builds on the
methods described by Wu 'et al.' (2020) <doi:10.1111/2041-210X.13405>.
Author: Alexander Wireko Kena [aut, cre]
,
Ebenezer Ogoe [aut],
Clara Cruet Burgos [aut],
Geoffrey Preston Morris [aut],
Rubi Raymundo-Carhuapoma [aut],
Yihan Wu [ctb] ,
Robert Colautti [ctb] ,
Colorado State University [cph],
Kwame Nkrumah University of Sci [...truncated...]
Maintainer: Alexander Wireko Kena <alex.kena24@gmail.com>
Diff between qrlabelr versions 0.1.1 dated 2023-10-26 and 0.2.0 dated 2023-12-20
DESCRIPTION | 32 MD5 | 18 NAMESPACE | 1 NEWS.md | 10 R/qrlabelr.R | 1 README.md | 23 inst/doc/qrlabelr.Rmd | 27 inst/doc/qrlabelr.html | 240 ++-- inst/shinyapps/qrlabelr/app.R | 2184 +++++++++++++++++++++++------------------- vignettes/qrlabelr.Rmd | 27 10 files changed, 1432 insertions(+), 1131 deletions(-)
Title: Advanced Graphics and Image-Processing in R
Description: Bindings to 'ImageMagick': the most comprehensive open-source image
processing library available. Supports many common formats (png, jpeg, tiff,
pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc).
All operations are vectorized via the Magick++ STL meaning they operate either
on a single frame or a series of frames for working with layers, collages,
or animation. In RStudio images are automatically previewed when printed to
the console, resulting in an interactive editing environment. The latest
version of the package includes a native graphics device for creating
in-memory graphics or drawing onto images using pixel coordinates.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between magick versions 2.8.1 dated 2023-10-22 and 2.8.2 dated 2023-12-20
DESCRIPTION | 6 +- MD5 | 38 ++++++++------- NEWS | 5 ++ R/RcppExports.R | 4 - R/composite.R | 4 - R/device.R | 2 R/edit.R | 4 - R/paint.R | 7 ++ R/utils.R | 54 ++++++---------------- build/vignette.rds |binary cleanup | 1 configure | 5 ++ inst/doc/intro.html | 108 ++++++++++++++++++++++---------------------- man/composite.Rd | 4 - man/editing.Rd | 4 - man/painting.Rd | 3 + src/RcppExports.cpp | 9 ++- src/options.cpp | 2 src/transformations.cpp | 5 +- tests/imagemagick.R |only tests/imagemagick.Rout.save |only 21 files changed, 133 insertions(+), 132 deletions(-)
Title: An R Interface to the JBrowse 2 Genome Browser
Description: Provides an R interface to the JBrowse 2 genome browser.
Enables embedding a JB2 genome browser in a Shiny app or R Markdown
document. The browser can also be launched from an interactive R console.
The browser can be loaded with a variety of common genomics data types,
and can be used with a custom theme.
Author: Elliot Hershberg [aut] ,
Colin Diesh [aut, cre] ,
the JBrowse 2 Team [aut]
Maintainer: Colin Diesh <colin.diesh@gmail.com>
Diff between JBrowseR versions 0.10.0 dated 2023-06-08 and 0.10.2 dated 2023-12-20
DESCRIPTION | 16 +-- MD5 | 48 +++++------ NEWS.md | 30 ++++--- R/alignments.R | 2 R/assembly.R | 2 R/text-index.R | 4 README.md | 95 +++++++++++++++++------ build/vignette.rds |binary inst/doc/JBrowseR.R | 2 inst/doc/JBrowseR.html | 124 ++++++++++++++++-------------- inst/doc/creating-urls.R | 2 inst/doc/creating-urls.html | 124 ++++++++++++++++-------------- inst/doc/custom-browser-tutorial.R | 2 inst/doc/custom-browser-tutorial.Rmd | 2 inst/doc/custom-browser-tutorial.html | 126 ++++++++++++++++--------------- inst/doc/json-tutorial.R | 2 inst/doc/json-tutorial.Rmd | 2 inst/doc/json-tutorial.html | 126 ++++++++++++++++--------------- inst/htmlwidgets/JBrowseR.js | 2 inst/htmlwidgets/JBrowseR.js.LICENSE.txt | 74 +++++++----------- man/assembly.Rd | 2 man/text_index.Rd | 4 man/track_alignments.Rd | 2 vignettes/custom-browser-tutorial.Rmd | 2 vignettes/json-tutorial.Rmd | 2 25 files changed, 431 insertions(+), 366 deletions(-)
Title: Additive Information & Details of Evidence Synthesis
Description: A supportive collection of functions for pooled analysis of aggregate data. The current version supports users to test assumptions before relevant analysis of bias from study size and sequential analysis such as mentioned by Wetterslev, J., Jakobsen, J. C., & Gluud, C. (2017) <doi:10.1186/s12874-017-0315-7>.
Author: Enoch Kang [aut, cre]
Maintainer: Enoch Kang <y.enoch.kang@gmail.com>
Diff between aides versions 1.2.0 dated 2023-10-25 and 1.3.0 dated 2023-12-20
DESCRIPTION | 8 MD5 | 45 ++--- NAMESPACE | 5 NEWS.md | 44 ++++ R/aides-package.R | 8 R/do_observed_sequential_analysis.R | 192 +++++++++++++-------- R/do_sequential_analysis.R | 78 ++++---- R/plot_disparity.R | 2 R/plot_distribution_of_study_sizes.R | 49 ++++- R/plot_observed_sequential_analysis.R | 121 +++++++++---- R/plot_power.R |only R/test_disparity.R | 91 +++++++--- README.md | 18 +- inst/doc/An_overview_on_pakcage_aides.R | 193 ++++++++++----------- inst/doc/An_overview_on_pakcage_aides.Rmd | 215 ++++++++++++------------ inst/doc/An_overview_on_pakcage_aides.html | 257 +++++++++++++++-------------- man/DoOSA.Rd | 33 +-- man/DoSA.Rd | 36 ++-- man/PlotDistrSS.Rd | 5 man/PlotOSA.Rd | 21 +- man/PlotPower.Rd |only man/TestDisparity.Rd | 26 ++ man/aides-package.Rd | 4 tests/testthat/test-PlotPower.R |only vignettes/An_overview_on_pakcage_aides.Rmd | 215 ++++++++++++------------ 25 files changed, 969 insertions(+), 697 deletions(-)
Title: Time Series Forecasting Using Nearest Neighbors
Description: Allows forecasting time series using nearest neighbors regression
Francisco Martinez, Maria P. Frias, Maria D. Perez-Godoy and Antonio J.
Rivera (2019) <doi:10.1007/s10462-017-9593-z>. When the forecasting horizon
is higher than 1, two multi-step ahead forecasting strategies can be used.
The model built is autoregressive, that is, it is only based on the
observations of the time series. The nearest neighbors used in a prediction
can be consulted and plotted.
Author: Francisco Martinez [aut, cre]
Maintainer: Francisco Martinez <fmartin@ujaen.es>
Diff between tsfknn versions 0.5.2 dated 2023-09-04 and 0.6.0 dated 2023-12-20
DESCRIPTION | 11 + MD5 | 38 +++--- NEWS.md | 9 + R/forecasting.R | 10 + R/knn.R | 3 build/partial.rdb |binary build/vignette.rds |binary inst/doc/tsfknn.R | 17 ++ inst/doc/tsfknn.Rmd | 106 ++++++++++++----- inst/doc/tsfknn.html | 180 ++++++++++++++++++++++-------- man/tsfknn-package.Rd | 2 tests/testthat.R | 16 ++ tests/testthat/test_build_examples.R | 72 ++++++++---- tests/testthat/test_knn_forecasting.R | 14 +- tests/testthat/test_knn_model.R | 12 -- tests/testthat/test_n_training_examples.R | 2 tests/testthat/test_predict.R | 2 tests/testthat/test_regression.R | 2 tests/testthat/test_rolling_origin.R | 2 vignettes/tsfknn.Rmd | 106 ++++++++++++----- 20 files changed, 417 insertions(+), 187 deletions(-)
Title: Econometric Models for Spatial Panel Data
Description: ML and GM estimation and diagnostic testing of econometric models for spatial panel data.
Author: Giovanni Millo [aut, cre],
Gianfranco Piras [aut],
Roger Bivand [ctb]
Maintainer: Giovanni Millo <giovanni.millo@deams.units.it>
Diff between splm versions 1.6-3 dated 2023-07-20 and 1.6-5 dated 2023-12-20
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NAMESPACE | 1 - R/bsktest.R | 16 ++++++++++++++++ R/impacts.splm.R | 6 +++--- man/spml.Rd | 25 +++++++++++++++++++++++++ 6 files changed, 55 insertions(+), 15 deletions(-)
Title: Article Formats for R Markdown
Description: A suite of custom R Markdown formats and templates for
authoring journal articles and conference submissions.
Author: JJ Allaire [aut],
Yihui Xie [aut] ,
Christophe Dervieux [aut, cre]
,
Posit Software, PBC [cph, fnd],
R Foundation [aut, cph],
Hadley Wickham [aut],
Journal of Statistical Software [aut, cph],
Ramnath Vaidyanathan [aut, cph],
Association for Computing [...truncated...]
Maintainer: Christophe Dervieux <cderv@posit.co>
Diff between rticles versions 0.25 dated 2023-05-15 and 0.26 dated 2023-12-20
rticles-0.25/rticles/inst/rmarkdown/templates/copernicus/resources/README_copernicus_package_7_3.txt |only rticles-0.25/rticles/inst/rmarkdown/templates/sim/skeleton/WileyNJD-v2.cls |only rticles-0.25/rticles/inst/rmarkdown/templates/springer/skeleton/skeleton.pdf |only rticles-0.25/rticles/inst/rmarkdown/templates/springer/skeleton/skeleton.tex |only rticles-0.25/rticles/inst/rmarkdown/templates/springer/skeleton/skeleton_files |only rticles-0.26/rticles/DESCRIPTION | 8 rticles-0.26/rticles/MD5 | 180 rticles-0.26/rticles/NEWS.md | 23 rticles-0.26/rticles/R/article.R | 27 rticles-0.26/rticles/R/copernicus_article.R | 2 rticles-0.26/rticles/R/ieee_article.R | 2 rticles-0.26/rticles/R/utils.R | 21 rticles-0.26/rticles/inst/rmarkdown/templates/acm/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/acs/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/aea/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/agu/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/agu/skeleton/skeleton.Rmd | 3 rticles-0.26/rticles/inst/rmarkdown/templates/ajs/skeleton/ajs-template.bib |only rticles-0.26/rticles/inst/rmarkdown/templates/ajs/skeleton/ajs.bst | 2198 ++++----- rticles-0.26/rticles/inst/rmarkdown/templates/ajs/skeleton/ajs.cls | 18 rticles-0.26/rticles/inst/rmarkdown/templates/ajs/skeleton/skeleton.Rmd | 1 rticles-0.26/rticles/inst/rmarkdown/templates/amq/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/ams/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/ams/skeleton/skeleton.log |only rticles-0.26/rticles/inst/rmarkdown/templates/arxiv/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/asa/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/bioinformatics/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/biometrics/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/copernicus/resources/README_copernicus_package_7_5.txt |only rticles-0.26/rticles/inst/rmarkdown/templates/copernicus/resources/template.tex | 69 rticles-0.26/rticles/inst/rmarkdown/templates/copernicus/skeleton/copernicus.bst | 105 rticles-0.26/rticles/inst/rmarkdown/templates/copernicus/skeleton/copernicus.cls | 120 rticles-0.26/rticles/inst/rmarkdown/templates/copernicus/skeleton/skeleton.log |only rticles-0.26/rticles/inst/rmarkdown/templates/elsevier/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/elsevier/skeleton/skeleton.Rmd | 8 rticles-0.26/rticles/inst/rmarkdown/templates/frontiers/resources/template.tex | 89 rticles-0.26/rticles/inst/rmarkdown/templates/frontiers/skeleton/Frontiers-Harvard.bst |only rticles-0.26/rticles/inst/rmarkdown/templates/frontiers/skeleton/Frontiers-Vancouver.bst |only rticles-0.26/rticles/inst/rmarkdown/templates/frontiers/skeleton/FrontiersinHarvard.cls |only rticles-0.26/rticles/inst/rmarkdown/templates/frontiers/skeleton/FrontiersinVancouver.cls |only rticles-0.26/rticles/inst/rmarkdown/templates/frontiers/skeleton/frontiersinFPHY_FAMS.cls |only rticles-0.26/rticles/inst/rmarkdown/templates/frontiers/skeleton/logo1.eps |only rticles-0.26/rticles/inst/rmarkdown/templates/frontiers/skeleton/skeleton.Rmd | 50 rticles-0.26/rticles/inst/rmarkdown/templates/frontiers/skeleton/skeleton.log |only rticles-0.26/rticles/inst/rmarkdown/templates/glossa/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/ieee/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/ims/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/informs/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/iop/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/iop/skeleton/iopart.cls | 2214 +++++----- rticles-0.26/rticles/inst/rmarkdown/templates/iop/skeleton/skeleton.Rmd | 7 rticles-0.26/rticles/inst/rmarkdown/templates/isba/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/jasa/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/jedm/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/joss/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/jss/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/lipics/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/lncs/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/lncs/skeleton/skeleton.Rmd | 5 rticles-0.26/rticles/inst/rmarkdown/templates/mdpi/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/mnras/resources/template.tex | 70 rticles-0.26/rticles/inst/rmarkdown/templates/mnras/skeleton/skeleton.Rmd | 14 rticles-0.26/rticles/inst/rmarkdown/templates/oup_v0/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/oup_v1/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/peerj/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/pihph/resources/template.tex | 57 rticles-0.26/rticles/inst/rmarkdown/templates/plos/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/pnas/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/rjournal/resources/RJwrapper.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/rsos/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/rss/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/sage/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/sage/skeleton/skeleton.Rmd | 2 rticles-0.26/rticles/inst/rmarkdown/templates/sim/resources/template.tex | 87 rticles-0.26/rticles/inst/rmarkdown/templates/sim/skeleton/Fonts |only rticles-0.26/rticles/inst/rmarkdown/templates/sim/skeleton/LETTERSP.STY |only rticles-0.26/rticles/inst/rmarkdown/templates/sim/skeleton/WileyNJD-AMA.bst | 33 rticles-0.26/rticles/inst/rmarkdown/templates/sim/skeleton/WileyNJD-v5.cls |only rticles-0.26/rticles/inst/rmarkdown/templates/sim/skeleton/skeleton.Rmd | 8 rticles-0.26/rticles/inst/rmarkdown/templates/sim/skeleton/skeleton.log |only rticles-0.26/rticles/inst/rmarkdown/templates/springer/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/tf/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/tf/skeleton/skeleton.Rmd | 2 rticles-0.26/rticles/inst/rmarkdown/templates/trb/resources/template.tex | 55 rticles-0.26/rticles/inst/rmarkdown/templates/trb/skeleton/skeleton.Rmd | 2 rticles-0.26/rticles/inst/rmarkdown/templates/wellcomeor/resources/template.tex | 78 rticles-0.26/rticles/man/ajs_article.Rd | 6 rticles-0.26/rticles/man/article.Rd | 24 rticles-0.26/rticles/man/copernicus_article.Rd | 8 rticles-0.26/rticles/man/ieee_article.Rd | 8 rticles-0.26/rticles/man/jss_article.Rd | 6 rticles-0.26/rticles/man/oup_article.Rd | 6 rticles-0.26/rticles/man/rjournal_article.Rd | 6 rticles-0.26/rticles/man/rsos_article.Rd | 6 rticles-0.26/rticles/man/rss_article.Rd | 6 rticles-0.26/rticles/tests/testit/test-formats.R | 3 rticles-0.26/rticles/tests/testit/test-utils.R | 7 rticles-0.26/rticles/tests/testthat/_snaps/rjournal_article.md | 3 rticles-0.26/rticles/tests/testthat/test-check-template.R | 1 99 files changed, 5101 insertions(+), 2472 deletions(-)
Title: Comparative 'Phylogenetic' Analyses of Diversification
Description: Contains a number of comparative 'phylogenetic' methods,
mostly focusing on analysing diversification and character
evolution. Contains implementations of 'BiSSE' (Binary State
'Speciation' and Extinction) and its unresolved tree extensions,
'MuSSE' (Multiple State 'Speciation' and Extinction), 'QuaSSE',
'GeoSSE', and 'BiSSE-ness' Other included methods include Markov
models of discrete and continuous trait evolution and constant rate
'speciation' and extinction.
Author: Richard G. FitzJohn [aut, cre],
Emma Goldberg [aut],
Karen Magnuson-Ford [aut],
Roger Sidje [aut]
Maintainer: Richard G. FitzJohn <rich.fitzjohn@gmail.com>
Diff between diversitree versions 0.9-20 dated 2023-09-06 and 0.10-0 dated 2023-12-20
diversitree-0.10-0/diversitree/DESCRIPTION | 6 diversitree-0.10-0/diversitree/MD5 | 47 +--- diversitree-0.10-0/diversitree/R/expm.R | 68 ------ diversitree-0.10-0/diversitree/R/model-bisse-unresolved.R | 63 ------ diversitree-0.10-0/diversitree/R/model-bisseness-unresolved.R | 71 ------ diversitree-0.10-0/diversitree/R/model-mkn.R | 2 diversitree-0.10-0/diversitree/README.md | 4 diversitree-0.10-0/diversitree/build/partial.rdb |binary diversitree-0.10-0/diversitree/man/make.bisse.Rd | 102 ---------- diversitree-0.10-0/diversitree/man/make.bisse.split.Rd | 17 - diversitree-0.10-0/diversitree/man/make.bisseness.Rd | 80 ------- diversitree-0.10-0/diversitree/man/make.mkn.Rd | 4 diversitree-0.10-0/diversitree/man/simulate.Rd | 2 diversitree-0.10-0/diversitree/src/GslOdeBase.cpp | 6 diversitree-0.10-0/diversitree/src/TimeMachine.cpp | 2 diversitree-0.10-0/diversitree/src/zzz.c | 18 - diversitree-0.10-0/diversitree/src/zzz.h | 86 -------- diversitree-0.9-20/diversitree/R/model-mkn-expokit.R |only diversitree-0.9-20/diversitree/inst/tests/test-expm.R |only diversitree-0.9-20/diversitree/src/bucexp.f |only diversitree-0.9-20/diversitree/src/dgcoov.f |only diversitree-0.9-20/diversitree/src/dgexpvi.f |only diversitree-0.9-20/diversitree/src/dgpadm.f |only diversitree-0.9-20/diversitree/src/dmexpv.f |only diversitree-0.9-20/diversitree/src/dnchbv.f |only diversitree-0.9-20/diversitree/src/dsexpv.f |only diversitree-0.9-20/diversitree/src/dsexpvi.f |only diversitree-0.9-20/diversitree/src/expm.f |only diversitree-0.9-20/diversitree/src/hyperg.f |only diversitree-0.9-20/diversitree/src/mkn-expokit.c |only diversitree-0.9-20/diversitree/src/mkn-expokit.h |only diversitree-0.9-20/diversitree/src/nucexp.f |only 32 files changed, 42 insertions(+), 536 deletions(-)
Title: R-Squared Measures for Multilevel Models
Description: Generates both total- and level-specific R-squared measures from
Rights and Sterba’s (2019) <doi:10.1037/met0000184> framework of R-squared measures for multilevel
models with random intercepts and/or slopes, which is based on a complete
decomposition of variance. Additionally generates graphical
representations of these R-squared measures to allow visualizing and
interpreting all measures in the framework together as an integrated set.
This framework subsumes 10 previously-developed R-squared measures for
multilevel models as special cases of 5 measures from the framework, and it
also includes several newly-developed measures. Measures in the framework
can be used to compute R-squared differences when comparing multilevel
models (following procedures in Rights & Sterba (2020) <doi:10.1080/00273171.2019.1660605>).
Bootstrapped confidence intervals can also be calculated. To use the
confidence interval functionality, download bootmlm from <https://github.com/marklhc/b [...truncated...]
Author: Mairead Shaw [aut, cre],
Jason Rights [aut],
Sonya Sterba [aut],
Jessica Flake [aut]
Maintainer: Mairead Shaw <mairead.shaw@mail.mcgill.ca>
Diff between r2mlm versions 0.3.5 dated 2023-07-20 and 0.3.7 dated 2023-12-20
DESCRIPTION | 10 ++++++---- MD5 | 24 +++++++++++++----------- NAMESPACE | 2 ++ NEWS.md | 15 +++++++++++++++ R/r2mlm_ci.R |only R/r2mlm_comp_manual.R | 27 ++++++++++++++++++--------- R/r2mlm_manual.R | 17 ++++++++++++----- inst/CITATION | 20 +++++++++++--------- man/r2mlm.Rd | 1 + man/r2mlm3_manual.Rd | 1 + man/r2mlm_ci.Rd |only man/r2mlm_comp_manual.Rd | 27 ++++++++++++++++++--------- man/r2mlm_long_manual.Rd | 1 + man/r2mlm_manual.Rd | 18 +++++++++++++----- 14 files changed, 111 insertions(+), 52 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] ,
Luc De Wilde [aut],
Daniel Oberski [ctb],
Jarrett Byrnes [ctb],
Leonard Vanbrabant [ctb],
Victoria Savalei [ctb],
Ed Merkle [ctb],
Michael Hallquist [ctb],
Mijke Rhemtulla [ctb],
Myrsini Katsika [...truncated...]
Maintainer: Yves Rosseel <Yves.Rosseel@UGent.be>
Diff between lavaan versions 0.6-16 dated 2023-07-19 and 0.6-17 dated 2023-12-20
DESCRIPTION | 30 MD5 | 142 ++- NAMESPACE | 2 R/00class.R | 477 ++++++------- R/ctr_informative_testing.R | 3 R/ctr_pml_doubly_robust_utils.R | 794 ++++++++++----------- R/lav_cor.R | 1 R/lav_data_update.R | 4 R/lav_export_mplus.R | 2 R/lav_fit_cfi.R | 9 R/lav_fit_measures.R | 5 R/lav_fit_rmsea.R | 5 R/lav_lavaanList_methods.R | 2 R/lav_matrix.R | 73 +- R/lav_model.R | 16 R/lav_model_compute.R | 29 R/lav_model_estimate.R | 14 R/lav_model_gradient.R | 2 R/lav_model_gradient_pml.R | 24 R/lav_model_h1_information.R | 19 R/lav_model_information.R | 40 - R/lav_model_objective.R | 2 R/lav_modification.R | 6 R/lav_mvnorm_cluster.R | 5 R/lav_object_generate.R | 3 R/lav_object_inspect.R | 116 ++- R/lav_object_methods.R | 92 +- R/lav_object_summary.R | 26 R/lav_objective.R | 15 R/lav_optim_gn.R | 5 R/lav_optim_noniter.R | 4 R/lav_options.R | 116 ++- R/lav_partable_bounds.R | 29 R/lav_partable_complete.R | 17 R/lav_partable_labels.R | 6 R/lav_partable_subset.R | 19 R/lav_predict.R | 289 ++++++- R/lav_predict_y.R | 2 R/lav_print.R | 30 R/lav_representation_lisrel.R | 32 R/lav_residuals.R | 2 R/lav_residuals_casewise.R | 4 R/lav_sam_step1.R | 98 ++ R/lav_samplestats.R | 32 R/lav_samplestats_robust.R |only R/lav_sem_miiv.R |only R/lav_start.R | 8 R/lav_syntax.R | 29 R/lav_syntax_parser.R |only R/lav_tables.R | 15 R/lav_test_LRT.R | 17 R/lav_test_Wald.R | 3 R/lav_utils.R | 123 +++ R/lav_uvord.R | 6 R/lav_uvreg.R | 7 R/xxx_efa.R | 9 R/xxx_lavaan.R | 1236 ++++++++++++++++++---------------- R/xxx_sam.R | 8 build/partial.rdb |binary inst/understanding_lavaan_internals.R |only man/cfa.Rd | 4 man/growth.Rd | 4 man/lavInspect.Rd | 10 man/lavOptions.Rd | 8 man/lavPredict.Rd | 14 man/lavTestLRT.Rd | 4 man/lav_model.Rd | 2 man/lav_partable.Rd | 4 man/lavaan-class.Rd | 4 man/lavaan.Rd | 4 man/model.syntax.Rd | 114 ++- man/parameterEstimates.Rd | 9 man/sem.Rd | 4 man/simulateData.Rd | 4 74 files changed, 2709 insertions(+), 1584 deletions(-)
Title: Read Data from 'LimeSurvey'
Description: Read data from 'LimeSurvey'
(<https://www.limesurvey.org/>)
in a comfortable way.
Heavily inspired by 'limer'
(<https://github.com/cloudyr/limer/>),
which lacked a few comfort features for me.
Author: Maximilian Hagspiel [aut, cre, cph]
Maintainer: Maximilian Hagspiel <maxhag@mailbox.org>
Diff between ipanema versions 0.4.1 dated 2023-12-05 and 0.6.5 dated 2023-12-20
DESCRIPTION | 6 +++--- MD5 | 12 +++++++----- NAMESPACE | 1 + R/get_sql_varname.R | 21 ++++++++++++++------- R/get_survey_data.R | 17 ++++++++++------- R/wipe_survey_data.R |only man/get_sql_varname.Rd | 8 +++++--- man/wipe_survey_data.Rd |only 8 files changed, 40 insertions(+), 25 deletions(-)
Title: Enhanced Wrapper to Show Which Functions Call What
Description: Enhances the functionality of the mvbutils::foodweb() program. The matrix-format output of the original program contains identical row names and column names, each name representing a retrieved function. This format is enhanced by using the find_funs() program [see Sebastian (2017) <https://sebastiansauer.github.io/finds_funs/>] to concatenate the package name to the function name. Each package is assigned a unique color, that is used to color code the text naming the packages and the functions. This color coding is extended to the entries of value "1" within the matrix, indicating the pattern of ancestor and descendent functions.
Author: Barry Zeeberg [aut, cre]
Maintainer: Barry Zeeberg <barryz2013@gmail.com>
Diff between foodwebWrapper versions 1.0 dated 2023-07-18 and 1.1.0 dated 2023-12-20
foodwebWrapper-1.0/foodwebWrapper/man/find_funs.Rd |only foodwebWrapper-1.0/foodwebWrapper/man/leftJustifyHack.Rd |only foodwebWrapper-1.1.0/foodwebWrapper/DESCRIPTION | 10 foodwebWrapper-1.1.0/foodwebWrapper/MD5 | 82 + foodwebWrapper-1.1.0/foodwebWrapper/NAMESPACE | 5 foodwebWrapper-1.1.0/foodwebWrapper/R/data.R | 80 + foodwebWrapper-1.1.0/foodwebWrapper/R/foodweb.R | 457 ++++------ foodwebWrapper-1.1.0/foodwebWrapper/data/x_colorMap.RData |only foodwebWrapper-1.1.0/foodwebWrapper/data/x_f.RData |only foodwebWrapper-1.1.0/foodwebWrapper/data/x_funs.RData |only foodwebWrapper-1.1.0/foodwebWrapper/data/x_m.RData |only foodwebWrapper-1.1.0/foodwebWrapper/data/x_m2.RData |only foodwebWrapper-1.1.0/foodwebWrapper/data/x_m3.RData |only foodwebWrapper-1.1.0/foodwebWrapper/data/x_m4.RData |only foodwebWrapper-1.1.0/foodwebWrapper/data/x_m5.RData |only foodwebWrapper-1.1.0/foodwebWrapper/data/x_packages.RData |only foodwebWrapper-1.1.0/foodwebWrapper/data/x_v.RData |only foodwebWrapper-1.1.0/foodwebWrapper/data/x_v2.RData |only foodwebWrapper-1.1.0/foodwebWrapper/data/x_where.RData |only foodwebWrapper-1.1.0/foodwebWrapper/data/x_x.RData |only foodwebWrapper-1.1.0/foodwebWrapper/data/x_x2.RData |only foodwebWrapper-1.1.0/foodwebWrapper/data/x_x3.RData |only foodwebWrapper-1.1.0/foodwebWrapper/data/x_y.RData |only foodwebWrapper-1.1.0/foodwebWrapper/inst/doc/foodwebWrapper.Rmd | 5 foodwebWrapper-1.1.0/foodwebWrapper/inst/doc/foodwebWrapper.html | 34 foodwebWrapper-1.1.0/foodwebWrapper/man/addStyle.Rd | 23 foodwebWrapper-1.1.0/foodwebWrapper/man/attachedFunctions.Rd | 5 foodwebWrapper-1.1.0/foodwebWrapper/man/attachedFunctionsBatch.Rd |only foodwebWrapper-1.1.0/foodwebWrapper/man/attachedPackages.Rd | 4 foodwebWrapper-1.1.0/foodwebWrapper/man/colorTag.Rd | 39 foodwebWrapper-1.1.0/foodwebWrapper/man/concatPackFunc2.Rd | 12 foodwebWrapper-1.1.0/foodwebWrapper/man/consolidate.Rd | 11 foodwebWrapper-1.1.0/foodwebWrapper/man/find_funz.Rd |only foodwebWrapper-1.1.0/foodwebWrapper/man/foodwebWrapper.Rd | 28 foodwebWrapper-1.1.0/foodwebWrapper/man/mapFunctionsColors.Rd | 17 foodwebWrapper-1.1.0/foodwebWrapper/man/rearrangeM.Rd | 13 foodwebWrapper-1.1.0/foodwebWrapper/man/removeZeroRowsCols.Rd | 14 foodwebWrapper-1.1.0/foodwebWrapper/man/replaceRotTag.Rd | 25 foodwebWrapper-1.1.0/foodwebWrapper/man/rotStyle.Rd | 1 foodwebWrapper-1.1.0/foodwebWrapper/man/rotTag.Rd | 16 foodwebWrapper-1.1.0/foodwebWrapper/man/spanTag.Rd | 20 foodwebWrapper-1.1.0/foodwebWrapper/man/x_colorMap.Rd |only foodwebWrapper-1.1.0/foodwebWrapper/man/x_f.Rd |only foodwebWrapper-1.1.0/foodwebWrapper/man/x_funs.Rd |only foodwebWrapper-1.1.0/foodwebWrapper/man/x_m.Rd |only foodwebWrapper-1.1.0/foodwebWrapper/man/x_m2.Rd |only foodwebWrapper-1.1.0/foodwebWrapper/man/x_m3.Rd |only foodwebWrapper-1.1.0/foodwebWrapper/man/x_m4.Rd |only foodwebWrapper-1.1.0/foodwebWrapper/man/x_m5.Rd |only foodwebWrapper-1.1.0/foodwebWrapper/man/x_packages.Rd |only foodwebWrapper-1.1.0/foodwebWrapper/man/x_v.Rd |only foodwebWrapper-1.1.0/foodwebWrapper/man/x_v2.Rd |only foodwebWrapper-1.1.0/foodwebWrapper/man/x_where.Rd |only foodwebWrapper-1.1.0/foodwebWrapper/man/x_x.Rd |only foodwebWrapper-1.1.0/foodwebWrapper/man/x_x2.Rd |only foodwebWrapper-1.1.0/foodwebWrapper/man/x_x3.Rd |only foodwebWrapper-1.1.0/foodwebWrapper/man/x_y.Rd |only foodwebWrapper-1.1.0/foodwebWrapper/vignettes/console.jpg |binary foodwebWrapper-1.1.0/foodwebWrapper/vignettes/foodwebWrapper.Rmd | 5 foodwebWrapper-1.1.0/foodwebWrapper/vignettes/html.jpg |binary 60 files changed, 401 insertions(+), 505 deletions(-)
More information about foodwebWrapper at CRAN
Permanent link
Title: Occurrence Data Cleaning
Description: Flags and checks occurrence data that are in Darwin Core
format. The package includes generic functions and data as well as
some that are specific to bees. This package is meant to build upon
and be complimentary to other excellent occurrence cleaning packages,
including 'bdc' and 'CoordinateCleaner'. This package uses datasets
from several sources and particularly from the Discover Life Website,
created by Ascher and Pickering (2020). For further information,
please see the original publication and package website. Publication
- Dorey et al. (2023) <doi:10.1101/2023.06.30.547152> and package
website - Dorey et al. (2023) <https://github.com/jbdorey/BeeBDC>.
Author: James B. Dorey [aut, cre, cph]
,
Robert L. O'Reilly [aut] ,
Silas Bossert [aut] ,
Erica E. Fischer [aut]
Maintainer: James B. Dorey <jbdorey@me.com>
Diff between BeeBDC versions 1.0.2 dated 2023-11-30 and 1.0.3 dated 2023-12-20
DESCRIPTION | 6 MD5 | 14 NEWS.md | 5 R/jbd_correct_coordinates.R | 2 inst/CITATION | 4 inst/doc/BeeBDC_main.Rmd | 32 inst/doc/BeeBDC_main.html | 1619 ++++++++++++++++++++++---------------------- vignettes/BeeBDC_main.Rmd | 32 8 files changed, 869 insertions(+), 845 deletions(-)
Title: Augments 'ASReml-R' in Fitting Mixed Models and Packages
Generally in Exploring Prediction Differences
Description: Assists in automating the selection of terms to include in mixed models when
'asreml' is used to fit the models. Also used to display, in tables and graphs, predictions
obtained using any model fitting function and to explore differences between predictions.
The content falls into the following natural groupings: (i) Data, (ii) Object manipulation
functions, (iii) Model modification functions, (iv) Model selection functions, (v) Model
diagnostics and simulation functions, (vi) Prediction production and presentation
functions, (vii) Response transformation functions, and (viii) Miscellaneous functions
(for further details see 'asremlPlus-package' in help). A history of the fitting of a
sequence of models is kept in a data frame. Procedures are available for choosing models
that conform to the hierarchy or marginality principle, for fitting and choosing between
two-dimensional spatial models using correlation, natural cubic smoothing spline and
P-spline models, for displaying prediction [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between asremlPlus versions 4.4.21 dated 2023-11-05 and 4.4.24 dated 2023-12-20
asremlPlus-4.4.21/asremlPlus/R/spatial.funcs.v7.r |only asremlPlus-4.4.24/asremlPlus/DESCRIPTION | 12 asremlPlus-4.4.24/asremlPlus/MD5 | 81 +- asremlPlus-4.4.24/asremlPlus/NAMESPACE | 8 asremlPlus-4.4.24/asremlPlus/R/S3methodsDeprecations.r | 1 asremlPlus-4.4.24/asremlPlus/R/alldiffs.v2.r | 17 asremlPlus-4.4.24/asremlPlus/R/asremlPlusUtilities.r | 120 ++- asremlPlus-4.4.24/asremlPlus/R/plotLSDs.r | 25 asremlPlus-4.4.24/asremlPlus/R/psplineUtilities.v2.R | 232 ++++-- asremlPlus-4.4.24/asremlPlus/R/reml4.v10.r | 8 asremlPlus-4.4.24/asremlPlus/R/spatial.funcs.v8.r |only asremlPlus-4.4.24/asremlPlus/build/partial.rdb |binary asremlPlus-4.4.24/asremlPlus/inst/NEWS.Rd | 20 asremlPlus-4.4.24/asremlPlus/inst/doc/Ladybird.asreml.pdf |binary asremlPlus-4.4.24/asremlPlus/inst/doc/Ladybird.lm.pdf |binary asremlPlus-4.4.24/asremlPlus/inst/doc/Wheat.analysis.pdf |binary asremlPlus-4.4.24/asremlPlus/inst/doc/Wheat.infoCriteria.pdf |binary asremlPlus-4.4.24/asremlPlus/inst/doc/WheatSpatialModels.pdf |binary asremlPlus-4.4.24/asremlPlus/inst/doc/asremlPlus-manual.pdf |binary asremlPlus-4.4.24/asremlPlus/man/Wheat.dat.Rd | 4 asremlPlus-4.4.24/asremlPlus/man/addSpatialModel.asrtests.Rd | 90 +- asremlPlus-4.4.24/asremlPlus/man/addSpatialModelOnIC.asrtests.Rd | 88 +- asremlPlus-4.4.24/asremlPlus/man/allDifferences.data.frame.Rd | 20 asremlPlus-4.4.24/asremlPlus/man/asremlPlus-package.Rd | 5 asremlPlus-4.4.24/asremlPlus/man/chooseSpatialModelOnIC.asrtests.Rd | 88 +- asremlPlus-4.4.24/asremlPlus/man/convAsremlobj.asreml.Rd | 2 asremlPlus-4.4.24/asremlPlus/man/convEffectNames2DataFrame.asreml.Rd |only asremlPlus-4.4.24/asremlPlus/man/estimateV.asreml.Rd | 4 asremlPlus-4.4.24/asremlPlus/man/getFormulae.asreml.Rd | 4 asremlPlus-4.4.24/asremlPlus/man/linTransform.alldiffs.Rd | 13 asremlPlus-4.4.24/asremlPlus/man/makeTPPSplineMats.data.frame.Rd | 2 asremlPlus-4.4.24/asremlPlus/man/newfit.asreml.Rd | 2 asremlPlus-4.4.24/asremlPlus/man/pickLSDstatistics.alldiffs.Rd | 9 asremlPlus-4.4.24/asremlPlus/man/plotPredictions.data.frame.Rd | 8 asremlPlus-4.4.24/asremlPlus/man/predictPlus.asreml.Rd | 17 asremlPlus-4.4.24/asremlPlus/man/predictPresent.asreml.Rd | 22 asremlPlus-4.4.24/asremlPlus/man/setvarianceterms.call.Rd | 2 asremlPlus-4.4.24/asremlPlus/tests/testthat.R | 4 asremlPlus-4.4.24/asremlPlus/tests/testthat/test42PredictionsPresentation.r | 107 +++ asremlPlus-4.4.24/asremlPlus/tests/testthat/test42Selection.r | 2 asremlPlus-4.4.24/asremlPlus/tests/testthat/test42SpatialModels.r | 344 +++++++--- asremlPlus-4.4.24/asremlPlus/tests/testthat/test42WheatSpatialVignette.r | 16 asremlPlus-4.4.24/asremlPlus/tests/testthat/test42WheatVignette.r | 8 43 files changed, 952 insertions(+), 433 deletions(-)
Title: Localization Microscopy Data Analysis
Description: Read, register and compare point sets from single molecule localization microscopy.
Author: Jean-Karim Heriche [cre, aut]
Maintainer: Jean-Karim Heriche <heriche@embl.de>
Diff between LOMAR versions 0.2.1 dated 2022-03-16 and 0.4.0 dated 2023-12-20
DESCRIPTION | 12 +- MD5 | 44 ++++++---- NAMESPACE | 8 + R/TDA.R | 11 +- R/alpha_shape.R |only R/data_input.R | 12 +- R/utils.R | 160 +++++++++++++++++++++++++++++++++---- README.md | 10 ++ man/crop_point_set.Rd | 9 +- man/denoise.Rd |only man/dist_to_boundary.Rd |only man/dist_to_line.Rd |only man/get_kernel_matrix.Rd | 5 - man/get_persistence_diagrams.Rd | 5 - man/get_shape.Rd |only man/get_surface_area.Rd |only man/group_events.Rd |only man/scale_alpha_shape.Rd |only man/shape_features_3d.Rd |only src/Makevars | 2 src/topology/dynamic-persistence.h | 18 ++-- src/topology/lsvineyard.h | 2 src/topology/lsvineyard.hpp | 6 - src/topology/static-persistence.h | 18 +++- src/utilities/circular_list.h | 23 ++--- tests/testthat/test-TDA.R | 8 + tests/testthat/test-alphashape.R |only tests/testthat/test-utils.R | 8 + 28 files changed, 278 insertions(+), 83 deletions(-)
Title: Mixed-Effect Models, with or without Spatial Random Effects
Description: Inference based on models with or without spatially-correlated random effects, multivariate responses, or non-Gaussian random effects (e.g., Beta). Variation in residual variance (heteroscedasticity) can itself be represented by a mixed-effect model. Both classical geostatistical models (Rousset and Ferdy 2014 <doi:10.1111/ecog.00566>), and Markov random field models on irregular grids (as considered in the 'INLA' package, <https://www.r-inla.org>), can be fitted, with distinct computational procedures exploiting the sparse matrix representations for the latter case and other autoregressive models. Laplace approximations are used for likelihood or restricted likelihood. Penalized quasi-likelihood and other variants discussed in the h-likelihood literature (Lee and Nelder 2001 <doi:10.1093/biomet/88.4.987>) are also implemented.
Author: Francois Rousset [aut, cre, cph]
,
Jean-Baptiste Ferdy [aut, cph],
Alexandre Courtiol [aut]
Maintainer: Francois Rousset <francois.rousset@umontpellier.fr>
Diff between spaMM versions 4.4.0 dated 2023-08-29 and 4.4.16 dated 2023-12-20
DESCRIPTION | 8 - MD5 | 91 +++++++------- NAMESPACE | 5 R/HLfit_Internals.R | 2 R/HLframes.R | 2 R/LMLTslots.R | 2 R/LR.R | 2 R/combinepar.R | 7 - R/confint.R | 2 R/correlationFns.R | 18 +- R/cov_new_fix.R | 29 ++-- R/fitmecorrHLfit_body_internals.R | 6 R/mapMM.R | 34 +++-- R/plot_effects.R | 17 +- R/postfit_internals.R | 15 +- R/predict.R | 230 +++++++++++++++++++++++++++++++++---- R/predict_mv.R | 36 ++++- R/preprocess.R | 18 ++ R/preprocess_MV.R | 4 R/preprocess_internals.R | 57 ++++++--- R/profile.R | 12 - R/sXaug_sparsePrecisions.R | 6 R/safe_opt.R | 10 + R/spaMM.data.R | 1 R/spaMM_boot.R | 129 ++++++++++++++++++++ R/utils.R | 4 inst/NEWS.Rd | 25 +++- man/IMRF.Rd | 3 man/Leuca.Rd | 2 man/autoregressive.Rd | 2 man/corrMatrix.Rd | 2 man/diallel_fixed.Rd | 6 man/drop1.HLfit.Rd | 4 man/fixed.Rd | 2 man/libraries.Rd | 1 man/mapMM.Rd | 10 - man/options.Rd | 2 man/predict.Rd | 28 +++- man/resid.model.Rd | 2 man/spaMM-conventions.Rd | 2 man/spaMM.Rd | 2 man/spaMM.filled.contour.Rd | 5 man/update.Rd | 4 tests/testthat/test-IsoriX-new.R | 8 - tests/testthat/test-LLM.R | 5 tests/testthat/test-more-predict.R | 19 ++- tests/testthat/test-pdep-effects.R |only 47 files changed, 678 insertions(+), 203 deletions(-)
Title: A Framework for Data-Driven Stochastic Disease Spread
Simulations
Description: Provides an efficient and very flexible framework to
conduct data-driven epidemiological modeling in realistic large
scale disease spread simulations. The framework integrates
infection dynamics in subpopulations as continuous-time Markov
chains using the Gillespie stochastic simulation algorithm and
incorporates available data such as births, deaths and movements
as scheduled events at predefined time-points. Using C code for
the numerical solvers and 'OpenMP' (if available) to divide work
over multiple processors ensures high performance when simulating
a sample outcome. One of our design goals was to make the package
extendable and enable usage of the numerical solvers from other R
extension packages in order to facilitate complex epidemiological
research. The package contains template models and can be extended
with user-defined models. For more details see the paper by
Widgren, Bauer, Eriksson and Engblom (2019)
<doi:10.18637/jss.v091.i12>. The package also provides
function [...truncated...]
Author: Stefan Widgren [aut, cre] ,
Robin Eriksson [aut] ,
Stefan Engblom [aut] ,
Pavol Bauer [aut] ,
Thomas Rosendal [ctb] ,
Ivana Rodriguez Ewerloef [ctb] ,
Attractive Chaos [cph]
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between SimInf versions 9.5.0 dated 2023-01-23 and 9.6.0 dated 2023-12-20
SimInf-9.5.0/SimInf/src/misc/SimInf_clean_raw_events.c |only SimInf-9.5.0/SimInf/tests/clean_raw_events.R |only SimInf-9.6.0/SimInf/DESCRIPTION | 21 SimInf-9.6.0/SimInf/MD5 | 154 +-- SimInf-9.6.0/SimInf/NAMESPACE | 7 SimInf-9.6.0/SimInf/NEWS.md | 9 SimInf-9.6.0/SimInf/R/C-generator.R | 4 SimInf-9.6.0/SimInf/R/SEIR.R | 48 - SimInf-9.6.0/SimInf/R/SIR.R | 51 - SimInf-9.6.0/SimInf/R/SIS.R | 46 - SimInf-9.6.0/SimInf/R/SISe.R | 46 - SimInf-9.6.0/SimInf/R/SISe3.R | 53 - SimInf-9.6.0/SimInf/R/SISe3_sp.R | 34 SimInf-9.6.0/SimInf/R/SISe_sp.R | 30 SimInf-9.6.0/SimInf/R/SimInf-package.R |only SimInf-9.6.0/SimInf/R/SimInf.R | 9 SimInf-9.6.0/SimInf/R/SimInf_events.R | 92 -- SimInf-9.6.0/SimInf/R/SimInf_indiv_events.R |only SimInf-9.6.0/SimInf/R/SimInf_model.R | 33 SimInf-9.6.0/SimInf/R/abc.R | 77 - SimInf-9.6.0/SimInf/R/check_arguments.R | 84 - SimInf-9.6.0/SimInf/R/classes.R | 4 SimInf-9.6.0/SimInf/R/degree.R | 8 SimInf-9.6.0/SimInf/R/density_ratio.R | 6 SimInf-9.6.0/SimInf/R/distance.R | 3 SimInf-9.6.0/SimInf/R/distributions.R | 8 SimInf-9.6.0/SimInf/R/edge_properties.R |only SimInf-9.6.0/SimInf/R/init.R | 12 SimInf-9.6.0/SimInf/R/match_compartments.R | 2 SimInf-9.6.0/SimInf/R/mparse.R | 3 SimInf-9.6.0/SimInf/R/package_skeleton.R | 19 SimInf-9.6.0/SimInf/R/pfilter.R | 42 SimInf-9.6.0/SimInf/R/plot.R | 57 - SimInf-9.6.0/SimInf/R/print.R | 14 SimInf-9.6.0/SimInf/R/punchcard.R | 27 SimInf-9.6.0/SimInf/R/run.R | 39 SimInf-9.6.0/SimInf/R/trajectory.R | 3 SimInf-9.6.0/SimInf/R/u0.R | 80 + SimInf-9.6.0/SimInf/R/v0.R | 4 SimInf-9.6.0/SimInf/build/partial.rdb |binary SimInf-9.6.0/SimInf/build/vignette.rds |binary SimInf-9.6.0/SimInf/inst/doc/SimInf.pdf |binary SimInf-9.6.0/SimInf/inst/doc/scheduled-events.R | 4 SimInf-9.6.0/SimInf/inst/doc/scheduled-events.html | 433 +++++++--- SimInf-9.6.0/SimInf/inst/include/SimInf.h | 8 SimInf-9.6.0/SimInf/man/SimInf.Rd | 1 SimInf-9.6.0/SimInf/man/SimInf_indiv_events-class.Rd |only SimInf-9.6.0/SimInf/man/abc.Rd | 2 SimInf-9.6.0/SimInf/man/as.data.frame.SimInf_indiv_events.Rd |only SimInf-9.6.0/SimInf/man/continue.Rd | 2 SimInf-9.6.0/SimInf/man/edge_properties_to_matrix.Rd |only SimInf-9.6.0/SimInf/man/events.Rd | 30 SimInf-9.6.0/SimInf/man/events_SEIR.Rd | 6 SimInf-9.6.0/SimInf/man/events_SIR.Rd | 6 SimInf-9.6.0/SimInf/man/events_SIS.Rd | 6 SimInf-9.6.0/SimInf/man/events_SISe.Rd | 6 SimInf-9.6.0/SimInf/man/events_SISe3.Rd | 10 SimInf-9.6.0/SimInf/man/get_individuals.Rd |only SimInf-9.6.0/SimInf/man/individual_events.Rd |only SimInf-9.6.0/SimInf/man/nodes.Rd | 8 SimInf-9.6.0/SimInf/man/pairs-SimInf_model-method.Rd | 6 SimInf-9.6.0/SimInf/man/plot-SimInf_indiv_events-method.Rd |only SimInf-9.6.0/SimInf/man/plot.Rd | 8 SimInf-9.6.0/SimInf/man/punchcard-set.Rd | 6 SimInf-9.6.0/SimInf/man/run.Rd | 6 SimInf-9.6.0/SimInf/man/show-SimInf_indiv_events-method.Rd |only SimInf-9.6.0/SimInf/man/summary-SimInf_indiv_events-method.Rd |only SimInf-9.6.0/SimInf/man/u0.Rd | 23 SimInf-9.6.0/SimInf/man/u0_SEIR.Rd | 8 SimInf-9.6.0/SimInf/man/u0_SIR.Rd | 8 SimInf-9.6.0/SimInf/man/u0_SIS.Rd | 8 SimInf-9.6.0/SimInf/man/u0_SISe.Rd | 8 SimInf-9.6.0/SimInf/man/u0_SISe3.Rd | 8 SimInf-9.6.0/SimInf/src/SimInf.c | 94 +- SimInf-9.6.0/SimInf/src/init.c | 8 SimInf-9.6.0/SimInf/src/misc/SimInf_abc.c | 5 SimInf-9.6.0/SimInf/src/misc/SimInf_arg.c | 6 SimInf-9.6.0/SimInf/src/misc/SimInf_arg.h | 4 SimInf-9.6.0/SimInf/src/misc/SimInf_clean_indiv_events.c |only SimInf-9.6.0/SimInf/src/misc/SimInf_distance_matrix.c | 21 SimInf-9.6.0/SimInf/src/misc/SimInf_ldata.c | 14 SimInf-9.6.0/SimInf/src/misc/SimInf_openmp.c | 4 SimInf-9.6.0/SimInf/src/misc/SimInf_particle_filter.c | 4 SimInf-9.6.0/SimInf/src/misc/SimInf_trajectory.c | 26 SimInf-9.6.0/SimInf/tests/edge_properties.R |only SimInf-9.6.0/SimInf/tests/indiv_events.R |only 86 files changed, 1214 insertions(+), 712 deletions(-)
Title: REDCap Castellated Data Handling
Description: Originally forked from the R part of 'REDCapRITS' by Paul Egeler.
See <https://github.com/pegeler/REDCapRITS>.
Handles castellated datasets from 'REDCap' projects with repeating instruments.
Assists in casting tidy tables from raw 'REDCap' data exports for each
repeated instrument. Keeps a focused data export approach, by allowing to
only export required data from the database.
'REDCap' (Research Electronic Data Capture) is a secure, web-based software
platform designed to support data capture for research studies, providing
1) an intuitive interface for validated data capture; 2) audit trails for
tracking data manipulation and export procedures; 3) automated export
procedures for seamless data downloads to common statistical packages; and
4) procedures for data integration and interoperability with external sources
(Harris et al (2009) <doi:10.1016/j.jbi.2008.08.010>;
Harris et al (2019) <doi:10.1016/j.jbi.2019.103208>).
Author: Andreas Gammelgaard Damsbo [aut, cre]
,
Paul Egeler [aut]
Maintainer: Andreas Gammelgaard Damsbo <agdamsbo@clin.au.dk>
Diff between REDCapCAST versions 23.6.2 dated 2023-07-04 and 23.12.1 dated 2023-12-20
DESCRIPTION | 20 ++-- MD5 | 22 ++-- NAMESPACE | 7 + NEWS.md | 10 ++ R/easy_redcap.R |only R/read_redcap_tables.R | 2 R/utils.r | 2 README.md | 8 + inst/WORDLIST | 4 inst/doc/Introduction.R | 2 inst/doc/Introduction.html | 212 ++++++++++++++++++++++----------------------- man/easy_redcap.Rd |only man/get_api_key.Rd |only tests/spelling.Rout.save |only 14 files changed, 160 insertions(+), 129 deletions(-)
Title: Phylogenetic Structural Equation Model
Description: Applies phylogenetic comparative methods (PCM) and phylogenetic trait imputation using
structural equation models (SEM), extending methods from Thorson et al. (2023) <doi:10.1111/2041-210X.14076>.
This implementation includes a minimal set of features, to
allow users to easily read all of the documentation and source code. PCM using SEM
includes phylogenetic linear models and structural equation models as nested submodels,
but also allows imputation of missing values. Features and comparison with other packages
are described in Thorson and van der Bijl (2023) <doi:10.1111/jeb.14234>.
Author: James Thorson [aut, cre] ,
Wouter van der Bijl [ctb]
Maintainer: James Thorson <James.Thorson@noaa.gov>
Diff between phylosem versions 1.1.1 dated 2023-11-26 and 1.1.2 dated 2023-12-20
phylosem-1.1.1/phylosem/inst/doc/comparison.html |only phylosem-1.1.1/phylosem/inst/doc/phylopath.html |only phylosem-1.1.2/phylosem/DESCRIPTION | 15 - phylosem-1.1.2/phylosem/MD5 | 60 +++-- phylosem-1.1.2/phylosem/NAMESPACE | 92 ++++---- phylosem-1.1.2/phylosem/NEWS.md | 4 phylosem-1.1.2/phylosem/R/utils.R |only phylosem-1.1.2/phylosem/R/zzz.R |only phylosem-1.1.2/phylosem/README.md | 24 +- phylosem-1.1.2/phylosem/build/partial.rdb |binary phylosem-1.1.2/phylosem/build/vignette.rds |binary phylosem-1.1.2/phylosem/inst/CITATION | 13 - phylosem-1.1.2/phylosem/inst/Matrix-version |only phylosem-1.1.2/phylosem/inst/TMB-version |only phylosem-1.1.2/phylosem/inst/brms/pdat.RDS |only phylosem-1.1.2/phylosem/inst/doc/comparison.R | 22 + phylosem-1.1.2/phylosem/inst/doc/comparison.Rmd | 25 +- phylosem-1.1.2/phylosem/inst/doc/comparison.pdf |only phylosem-1.1.2/phylosem/inst/doc/demonstration.R | 4 phylosem-1.1.2/phylosem/inst/doc/demonstration.Rmd | 4 phylosem-1.1.2/phylosem/inst/doc/demonstration.html | 206 ++++++++---------- phylosem-1.1.2/phylosem/inst/doc/fisheries.R | 4 phylosem-1.1.2/phylosem/inst/doc/fisheries.Rmd | 9 phylosem-1.1.2/phylosem/inst/doc/phylopath.R | 8 phylosem-1.1.2/phylosem/inst/doc/phylopath.Rmd | 12 - phylosem-1.1.2/phylosem/inst/doc/phylopath.pdf |only phylosem-1.1.2/phylosem/man/Mlifehist_ver1_0.Rd | 32 +- phylosem-1.1.2/phylosem/man/checkDepPackageVersion.Rd |only phylosem-1.1.2/phylosem/man/coef.phylosem.Rd | 42 +-- phylosem-1.1.2/phylosem/man/reinstalling.Rd |only phylosem-1.1.2/phylosem/man/vcov.phylosem.Rd | 36 +-- phylosem-1.1.2/phylosem/src/Makevars |only phylosem-1.1.2/phylosem/vignettes/comparison.Rmd | 25 +- phylosem-1.1.2/phylosem/vignettes/comparison.html |only phylosem-1.1.2/phylosem/vignettes/demonstration.Rmd | 4 phylosem-1.1.2/phylosem/vignettes/fisheries.Rmd | 9 phylosem-1.1.2/phylosem/vignettes/phylopath.Rmd | 12 - phylosem-1.1.2/phylosem/vignettes/phylopath.html |only 38 files changed, 380 insertions(+), 282 deletions(-)
Title: Publication Bias Tests for Meta-Analysis of Diagnostic Accuracy
Test
Description: Generalized Egger tests for detecting publication bias in meta-analysis for diagnostic accuracy test (Noma (2020) <doi:10.1111/biom.13343>, Noma (2022) <doi:10.48550/arXiv.2209.07270>). These publication bias tests are generally more powerful compared with the conventional univariate publication bias tests and can incorporate correlation information between the outcome variables.
Author: Hisashi Noma [aut, cre]
Maintainer: Hisashi Noma <noma@ism.ac.jp>
Diff between MVPBT versions 1.1-1 dated 2023-05-29 and 1.2-1 dated 2023-12-20
DESCRIPTION | 8 ++++---- MD5 | 10 +++++++--- NAMESPACE | 3 +++ NEWS.md | 4 ++++ R/bifunnel.r |only R/sdta.r |only man/bifunnel.Rd |only man/sdta.Rd |only 8 files changed, 18 insertions(+), 7 deletions(-)
Title: A Future API for Parallel and Distributed Processing using
'batchtools'
Description: Implementation of the Future API on top of the 'batchtools' package.
This allows you to process futures, as defined by the 'future' package,
in parallel out of the box, not only on your local machine or ad-hoc
cluster of machines, but also via high-performance compute ('HPC') job
schedulers such as 'LSF', 'OpenLava', 'Slurm', 'SGE', and 'TORQUE' / 'PBS',
e.g. 'y <- future.apply::future_lapply(files, FUN = process)'.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.batchtools versions 0.12.0 dated 2023-02-24 and 0.12.1 dated 2023-12-20
DESCRIPTION | 15 +- MD5 | 24 +-- NEWS.md | 19 ++ R/BatchtoolsFuture-class.R | 5 R/batchtools_multicore.R | 6 R/nbrOfWorkers.R | 2 R/temp_registry.R | 4 R/waitForWorker.R | 3 build/vignette.rds |binary inst/doc/future.batchtools.html | 273 ++++++++++++++++++++++--------------- inst/doc/future.batchtools.md.rsp | 119 ++++++++++------ man/loggedOutput.Rd | 3 vignettes/future.batchtools.md.rsp | 119 ++++++++++------ 13 files changed, 377 insertions(+), 215 deletions(-)
More information about future.batchtools at CRAN
Permanent link
Title: Use Foreach to Parallelize via the Future Framework
Description: The 'future' package provides a unifying parallelization framework for R that supports many parallel and distributed backends. The 'foreach' package provides a powerful API for iterating over an R expression in parallel. The 'doFuture' package brings the best of the two together. There are two alternative ways to use this package. The recommended approach is to use 'y <- foreach(...) %dofuture% { ... }', which does not require using 'registerDoFuture()' and has many advantages over '%dopar%'. The alternative is the traditional 'foreach' approach by registering the 'foreach' adapter 'registerDoFuture()' and so that 'y <- foreach(...) %dopar% { ... }' runs in parallelizes with the 'future' framework.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between doFuture versions 1.0.0 dated 2023-03-24 and 1.0.1 dated 2023-12-20
DESCRIPTION | 15 +- MD5 | 33 ++--- NEWS.md | 10 + R/doFuture-package.R | 54 ++++---- R/doFuture.R | 7 - R/dofuture_OP.R | 30 +++- R/registerDoFuture.R | 21 +++ build/vignette.rds |binary inst/doc/doFuture-1-overview.html | 231 ++++++++++++++++++++--------------- inst/doc/doFuture-1-overview.md.rsp | 76 +++++------ inst/doc/doFuture-2-dopar.html | 177 ++++++++++++++++---------- inst/doc/doFuture-3-dofuture.html | 171 +++++++++++++++---------- man/doFuture.Rd | 50 +++---- man/grapes-dofuture-grapes.Rd | 23 +++ man/registerDoFuture.Rd | 23 +++ tests/incl/start,load-only.R | 16 +- tests/options,nested.R |only vignettes/doFuture-1-overview.md.rsp | 76 +++++------ 18 files changed, 622 insertions(+), 391 deletions(-)
Title: USGS ScienceBase Tools
Description: Tools for interacting with U.S. Geological Survey ScienceBase
<https://www.sciencebase.gov> interfaces. ScienceBase is a data cataloging and
collaborative data management platform. Functions included for querying
ScienceBase, and creating and fetching datasets.
Author: David Blodgett [cre],
Luke Winslow [aut],
Scott Chamberlain [ctb],
Alison Appling [ctb],
Jordan Read [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between sbtools versions 1.2.0 dated 2023-04-30 and 1.3.0 dated 2023-12-20
sbtools-1.2.0/sbtools/R/folder_create.R |only sbtools-1.2.0/sbtools/R/is_logged_in.R |only sbtools-1.2.0/sbtools/R/item_exists.R |only sbtools-1.2.0/sbtools/R/item_get_fields.R |only sbtools-1.2.0/sbtools/R/item_get_parent.R |only sbtools-1.2.0/sbtools/R/item_rm_recursive.R |only sbtools-1.2.0/sbtools/R/items_create.R |only sbtools-1.2.0/sbtools/R/items_rm.R |only sbtools-1.2.0/sbtools/R/items_update.R |only sbtools-1.2.0/sbtools/R/items_upsert.R |only sbtools-1.2.0/sbtools/R/query_item_identifier.R |only sbtools-1.2.0/sbtools/R/query_item_in_folder.R |only sbtools-1.2.0/sbtools/R/query_sb_datatype.R |only sbtools-1.2.0/sbtools/R/query_sb_date.R |only sbtools-1.2.0/sbtools/R/query_sb_doi.R |only sbtools-1.2.0/sbtools/R/query_sb_spatial.R |only sbtools-1.2.0/sbtools/R/query_sb_text.R |only sbtools-1.2.0/sbtools/R/sb_ping.R |only sbtools-1.2.0/sbtools/R/session_age.R |only sbtools-1.2.0/sbtools/R/session_age_reset.R |only sbtools-1.2.0/sbtools/R/session_details.R |only sbtools-1.2.0/sbtools/R/session_logout.R |only sbtools-1.2.0/sbtools/R/session_renew.R |only sbtools-1.2.0/sbtools/R/session_set.R |only sbtools-1.2.0/sbtools/R/session_validate.R |only sbtools-1.2.0/sbtools/R/set_endpoint.R |only sbtools-1.2.0/sbtools/R/user_id.R |only sbtools-1.2.0/sbtools/man/items_rm.Rd |only sbtools-1.2.0/sbtools/man/sbtools_DELETE.Rd |only sbtools-1.2.0/sbtools/man/session_age_reset.Rd |only sbtools-1.2.0/sbtools/man/session_logout.Rd |only sbtools-1.2.0/sbtools/man/session_set.Rd |only sbtools-1.2.0/sbtools/man/set_expiration.Rd |only sbtools-1.2.0/sbtools/tests/testthat/test-eg.R |only sbtools-1.2.0/sbtools/tests/testthat/test-expiration.R |only sbtools-1.3.0/sbtools/DESCRIPTION | 13 sbtools-1.3.0/sbtools/MD5 | 208 +++---- sbtools-1.3.0/sbtools/NAMESPACE | 7 sbtools-1.3.0/sbtools/NEWS.md | 19 sbtools-1.3.0/sbtools/R/AAA.R | 143 ++++- sbtools-1.3.0/sbtools/R/REST_helpers.R | 83 +-- sbtools-1.3.0/sbtools/R/authenticate_sb.R | 180 +++++- sbtools-1.3.0/sbtools/R/current_session.R | 209 +++++++ sbtools-1.3.0/sbtools/R/gql_helpers.R | 23 sbtools-1.3.0/sbtools/R/identifier_exists.R | 56 +- sbtools-1.3.0/sbtools/R/item_create.R | 108 +++ sbtools-1.3.0/sbtools/R/item_file_download.R | 10 sbtools-1.3.0/sbtools/R/item_get.R | 147 +++-- sbtools-1.3.0/sbtools/R/item_list_children.R | 9 sbtools-1.3.0/sbtools/R/item_list_files.R | 327 +++++------- sbtools-1.3.0/sbtools/R/item_move.R | 4 sbtools-1.3.0/sbtools/R/item_rename_files.R | 8 sbtools-1.3.0/sbtools/R/item_replace_files.R | 10 sbtools-1.3.0/sbtools/R/item_rm.R | 63 ++ sbtools-1.3.0/sbtools/R/item_rm_files.R | 7 sbtools-1.3.0/sbtools/R/item_update.R | 57 ++ sbtools-1.3.0/sbtools/R/item_update_identifier.R | 176 +++--- sbtools-1.3.0/sbtools/R/item_upload_files.R | 28 - sbtools-1.3.0/sbtools/R/item_upsert.R | 69 ++ sbtools-1.3.0/sbtools/R/query_items.R | 104 +++ sbtools-1.3.0/sbtools/R/query_sb.R | 232 ++++++++ sbtools-1.3.0/sbtools/R/sb_item.R | 140 ++--- sbtools-1.3.0/sbtools/README.md | 232 +++----- sbtools-1.3.0/sbtools/build |only sbtools-1.3.0/sbtools/inst/doc |only sbtools-1.3.0/sbtools/man/current_session.Rd | 2 sbtools-1.3.0/sbtools/man/folder_create.Rd | 9 sbtools-1.3.0/sbtools/man/identifier_exists.Rd | 67 +- sbtools-1.3.0/sbtools/man/initialize_sciencebase_session.Rd |only sbtools-1.3.0/sbtools/man/is_logged_in.Rd | 9 sbtools-1.3.0/sbtools/man/item_append_files.Rd | 13 sbtools-1.3.0/sbtools/man/item_create.Rd | 13 sbtools-1.3.0/sbtools/man/item_exists.Rd | 6 sbtools-1.3.0/sbtools/man/item_file_download.Rd | 6 sbtools-1.3.0/sbtools/man/item_get.Rd | 79 +- sbtools-1.3.0/sbtools/man/item_get_fields.Rd | 15 sbtools-1.3.0/sbtools/man/item_get_parent.Rd | 59 +- sbtools-1.3.0/sbtools/man/item_list_children.Rd | 13 sbtools-1.3.0/sbtools/man/item_list_files.Rd | 139 ++--- sbtools-1.3.0/sbtools/man/item_move.Rd | 7 sbtools-1.3.0/sbtools/man/item_publish_cloud.Rd | 7 sbtools-1.3.0/sbtools/man/item_rename_files.Rd | 7 sbtools-1.3.0/sbtools/man/item_replace_files.Rd | 14 sbtools-1.3.0/sbtools/man/item_rm.Rd | 13 sbtools-1.3.0/sbtools/man/item_rm_files.Rd | 7 sbtools-1.3.0/sbtools/man/item_rm_recursive.Rd | 13 sbtools-1.3.0/sbtools/man/item_update.Rd | 7 sbtools-1.3.0/sbtools/man/item_update_identifier.Rd | 18 sbtools-1.3.0/sbtools/man/item_upload_cloud.Rd | 13 sbtools-1.3.0/sbtools/man/item_upload_create.Rd | 13 sbtools-1.3.0/sbtools/man/item_upsert.Rd | 13 sbtools-1.3.0/sbtools/man/items_create.Rd | 15 sbtools-1.3.0/sbtools/man/items_update.Rd | 7 sbtools-1.3.0/sbtools/man/items_upsert.Rd | 15 sbtools-1.3.0/sbtools/man/query_item_identifier.Rd | 14 sbtools-1.3.0/sbtools/man/query_item_in_folder.Rd | 13 sbtools-1.3.0/sbtools/man/query_items.Rd | 4 sbtools-1.3.0/sbtools/man/query_sb.Rd | 4 sbtools-1.3.0/sbtools/man/query_sb_datatype.Rd | 6 sbtools-1.3.0/sbtools/man/query_sb_date.Rd | 7 sbtools-1.3.0/sbtools/man/query_sb_doi.Rd | 6 sbtools-1.3.0/sbtools/man/query_sb_spatial.Rd | 16 sbtools-1.3.0/sbtools/man/query_sb_text.Rd | 6 sbtools-1.3.0/sbtools/man/sb_datatypes.Rd | 6 sbtools-1.3.0/sbtools/man/sb_ping.Rd | 2 sbtools-1.3.0/sbtools/man/sbitem.Rd | 90 +-- sbtools-1.3.0/sbtools/man/sbtools_GET.Rd | 4 sbtools-1.3.0/sbtools/man/sbtools_POST.Rd | 4 sbtools-1.3.0/sbtools/man/sbtools_PUT.Rd | 4 sbtools-1.3.0/sbtools/man/session_age.Rd | 16 sbtools-1.3.0/sbtools/man/session_details.Rd | 38 - sbtools-1.3.0/sbtools/man/session_expired.Rd | 13 sbtools-1.3.0/sbtools/man/session_renew.Rd | 7 sbtools-1.3.0/sbtools/man/session_validate.Rd | 23 sbtools-1.3.0/sbtools/man/set_endpoint.Rd | 2 sbtools-1.3.0/sbtools/man/user_id.Rd | 6 sbtools-1.3.0/sbtools/tests/testthat/set_env.R |only sbtools-1.3.0/sbtools/tests/testthat/test-REST-helpers.R |only sbtools-1.3.0/sbtools/tests/testthat/test-REST.R | 63 -- sbtools-1.3.0/sbtools/tests/testthat/test-auth-item.R |only sbtools-1.3.0/sbtools/tests/testthat/test-auth-item2.R |only sbtools-1.3.0/sbtools/tests/testthat/test-auth-rm.R |only sbtools-1.3.0/sbtools/tests/testthat/test-auth.R | 207 +------ sbtools-1.3.0/sbtools/tests/testthat/test-list_files.R | 4 sbtools-1.3.0/sbtools/tests/testthat/test_examples.R | 24 sbtools-1.3.0/sbtools/vignettes |only 126 files changed, 2195 insertions(+), 1665 deletions(-)
Title: Estimation and Additional Tools for Quantile Generalized Beta
Regression Model
Description: Provide estimation and data generation tools for the quantile generalized beta
regression model. For details, see Bourguignon, Gallardo and Saulo <arXiv:2110.04428>
The package also provides tools to perform covariates selection.
Author: Diego Gallardo [aut, cre],
Marcelo Bourguignon [aut]
Maintainer: Diego Gallardo <dgallardo@ubiobio.cl>
Diff between RBE3 versions 1.0 dated 2023-05-24 and 1.1 dated 2023-12-20
RBE3-1.0/RBE3/man/BE3.backward.Rd |only RBE3-1.1/RBE3/DESCRIPTION | 12 +-- RBE3-1.1/RBE3/MD5 | 21 +++--- RBE3-1.1/RBE3/NAMESPACE | 2 RBE3-1.1/RBE3/NEWS.md |only RBE3-1.1/RBE3/R/BE3.backward.crit.R | 8 +- RBE3-1.1/RBE3/R/ML.BE3.R | 114 ++++++--------------------------- RBE3-1.1/RBE3/R/llike.BE3.R | 2 RBE3-1.1/RBE3/R/qBE3.R | 2 RBE3-1.1/RBE3/man/BE3.Rd | 2 RBE3-1.1/RBE3/man/BE3.backward.crit.Rd |only RBE3-1.1/RBE3/man/ML.BE3.Rd | 19 +---- RBE3-1.1/RBE3/man/gumbel2.Rd | 1 13 files changed, 52 insertions(+), 131 deletions(-)
Title: Procedures for Psychological, Psychometric, and Personality
Research
Description: A general purpose toolbox developed originally for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Validation and cross validation of scales developed using basic machine learning algorithms are provided, as are functions for simulating and testing particular item and test structures. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, including mediation models, factor analysis and structural equation models are created using basic graphics. Some of the fu [...truncated...]
Author: William Revelle [aut, cre]
Maintainer: William Revelle <revelle@northwestern.edu>
Diff between psych versions 2.3.9 dated 2023-09-25 and 2.3.12 dated 2023-12-20
psych-2.3.12/psych/DESCRIPTION | 8 psych-2.3.12/psych/MD5 | 148 ++++--- psych-2.3.12/psych/NAMESPACE | 10 psych-2.3.12/psych/R/ICLUST.diagram.R | 2 psych-2.3.12/psych/R/alpha.R | 4 psych-2.3.12/psych/R/anova.psych.R | 4 psych-2.3.12/psych/R/corr.test.R | 2 psych-2.3.12/psych/R/crossValidation.r | 8 psych-2.3.12/psych/R/diagram.R | 16 psych-2.3.12/psych/R/error.bars.by.R | 11 psych-2.3.12/psych/R/esem.R | 3 psych-2.3.12/psych/R/esem.diagram.R | 55 ++ psych-2.3.12/psych/R/fa.extension.R | 14 psych-2.3.12/psych/R/faReg.R | 2 psych-2.3.12/psych/R/lavaan.diagram.R | 70 ++- psych-2.3.12/psych/R/lmCor.R |only psych-2.3.12/psych/R/manhattan.R | 4 psych-2.3.12/psych/R/mat.regress.R | 4 psych-2.3.12/psych/R/misc.R | 46 ++ psych-2.3.12/psych/R/partial.r.R | 9 psych-2.3.12/psych/R/predict.principal.R | 31 + psych-2.3.12/psych/R/print.psych.R | 2 psych-2.3.12/psych/R/reliability.R | 14 psych-2.3.12/psych/R/sim.structural.R | 36 + psych-2.3.12/psych/R/splitHalf.R | 6 psych-2.3.12/psych/R/structure.diagram.R | 429 ++++++++++++++++++++++- psych-2.3.12/psych/R/summary.psych.R | 8 psych-2.3.12/psych/R/unidim.r | 15 psych-2.3.12/psych/build/partial.rdb |binary psych-2.3.12/psych/build/vignette.rds |binary psych-2.3.12/psych/inst/CITATION | 2 psych-2.3.12/psych/inst/NEWS.Rd |only psych-2.3.12/psych/inst/doc/intro.R | 47 ++ psych-2.3.12/psych/inst/doc/intro.Rnw | 97 ++++- psych-2.3.12/psych/inst/doc/intro.pdf |binary psych-2.3.12/psych/inst/doc/scoring.pdf |binary psych-2.3.12/psych/man/00.psych-package.Rd | 4 psych-2.3.12/psych/man/Garcia.Rd | 4 psych-2.3.12/psych/man/KMO.Rd | 6 psych-2.3.12/psych/man/alpha.Rd | 7 psych-2.3.12/psych/man/anova.psych.Rd | 6 psych-2.3.12/psych/man/bassAckward.Rd | 4 psych-2.3.12/psych/man/biplot.psych.Rd | 2 psych-2.3.12/psych/man/cor.plot.Rd | 14 psych-2.3.12/psych/man/corr.test.Rd | 9 psych-2.3.12/psych/man/cortest.mat.Rd | 2 psych-2.3.12/psych/man/deprecated.Rd | 107 ----- psych-2.3.12/psych/man/esem.Rd | 32 + psych-2.3.12/psych/man/fa.Rd | 2 psych-2.3.12/psych/man/fa.extension.Rd | 3 psych-2.3.12/psych/man/fa.lookup.Rd | 6 psych-2.3.12/psych/man/fparse.Rd | 4 psych-2.3.12/psych/man/guttman.Rd | 2 psych-2.3.12/psych/man/lmCor.Rd |only psych-2.3.12/psych/man/mediate.Rd | 2 psych-2.3.12/psych/man/misc.Rd | 14 psych-2.3.12/psych/man/multilevel.reliability.Rd | 2 psych-2.3.12/psych/man/omega.Rd | 2 psych-2.3.12/psych/man/omega.graph.Rd | 2 psych-2.3.12/psych/man/partial.r.Rd | 10 psych-2.3.12/psych/man/predicted.validity.Rd | 2 psych-2.3.12/psych/man/r.test.Rd | 2 psych-2.3.12/psych/man/reliability.Rd | 5 psych-2.3.12/psych/man/scatter.hist.Rd | 2 psych-2.3.12/psych/man/scoreWtd.Rd | 8 psych-2.3.12/psych/man/sim.Rd | 15 psych-2.3.12/psych/man/sim.anova.Rd | 14 psych-2.3.12/psych/man/skew.Rd | 2 psych-2.3.12/psych/man/structure.diagram.Rd | 24 + psych-2.3.12/psych/tests |only psych-2.3.12/psych/vignettes/intro.Rnw | 97 ++++- psych-2.3.9/psych/R/set.cor.R |only psych-2.3.9/psych/inst/News.Rd |only psych-2.3.9/psych/man/set.cor.Rd |only 74 files changed, 1123 insertions(+), 401 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>).
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],
Vinh Nguyen [aut],
Olga Starostecka [ctb],
Uwe Bader [ctb],
Karl Kennedy [ctb],
Edo [...truncated...]
Maintainer: Stefan Bundfuss <stefan.bundfuss@roche.com>
Diff between admiralonco versions 0.5.0 dated 2023-09-14 and 1.0.0 dated 2023-12-20
admiralonco-0.5.0/admiralonco/R/utils.R |only admiralonco-0.5.0/admiralonco/man/call_aval_fun.Rd |only admiralonco-0.5.0/admiralonco/tests/testthat/test-utils.R |only admiralonco-1.0.0/admiralonco/DESCRIPTION | 24 admiralonco-1.0.0/admiralonco/MD5 | 110 +- admiralonco-1.0.0/admiralonco/NAMESPACE | 2 admiralonco-1.0.0/admiralonco/NEWS.md | 34 admiralonco-1.0.0/admiralonco/R/admiralonco-package.R | 6 admiralonco-1.0.0/admiralonco/R/check_crpr.R | 8 admiralonco-1.0.0/admiralonco/R/derive_param_bor.R | 9 admiralonco-1.0.0/admiralonco/R/derive_param_clinbenefit.R | 9 admiralonco-1.0.0/admiralonco/R/derive_param_confirmed_bor.R | 33 admiralonco-1.0.0/admiralonco/R/derive_param_confirmed_resp.R | 33 admiralonco-1.0.0/admiralonco/R/derive_param_response.R | 10 admiralonco-1.0.0/admiralonco/R/filter_pd.R | 8 admiralonco-1.0.0/admiralonco/R/response_sources.R | 14 admiralonco-1.0.0/admiralonco/README.md | 38 admiralonco-1.0.0/admiralonco/build/vignette.rds |binary admiralonco-1.0.0/admiralonco/inst/WORDLIST | 11 admiralonco-1.0.0/admiralonco/inst/doc/admiralonco.R | 27 admiralonco-1.0.0/admiralonco/inst/doc/admiralonco.Rmd | 50 admiralonco-1.0.0/admiralonco/inst/doc/admiralonco.html | 14 admiralonco-1.0.0/admiralonco/inst/doc/adrs.R | 129 +- admiralonco-1.0.0/admiralonco/inst/doc/adrs.Rmd | 134 +- admiralonco-1.0.0/admiralonco/inst/doc/adrs.html | 439 ++++---- admiralonco-1.0.0/admiralonco/inst/doc/adrs_basic.R | 78 - admiralonco-1.0.0/admiralonco/inst/doc/adrs_basic.Rmd | 85 - admiralonco-1.0.0/admiralonco/inst/doc/adrs_basic.html | 180 +-- admiralonco-1.0.0/admiralonco/inst/doc/adtr.R | 91 - admiralonco-1.0.0/admiralonco/inst/doc/adtr.Rmd | 114 -- admiralonco-1.0.0/admiralonco/inst/doc/adtr.html | 528 +++------- admiralonco-1.0.0/admiralonco/inst/doc/adtte.R | 36 admiralonco-1.0.0/admiralonco/inst/doc/adtte.Rmd | 46 admiralonco-1.0.0/admiralonco/inst/doc/adtte.html | 18 admiralonco-1.0.0/admiralonco/inst/doc/irecist.R |only admiralonco-1.0.0/admiralonco/inst/doc/irecist.Rmd |only admiralonco-1.0.0/admiralonco/inst/doc/irecist.html |only admiralonco-1.0.0/admiralonco/inst/doc/nactdt.R | 78 - admiralonco-1.0.0/admiralonco/inst/doc/nactdt.Rmd | 101 - admiralonco-1.0.0/admiralonco/inst/doc/nactdt.html | 153 +- admiralonco-1.0.0/admiralonco/inst/templates/ad_adrs.R | 81 + admiralonco-1.0.0/admiralonco/inst/templates/ad_adrs_basic.R | 58 - admiralonco-1.0.0/admiralonco/inst/templates/ad_adtr.R | 59 - admiralonco-1.0.0/admiralonco/inst/templates/ad_adtte.R | 19 admiralonco-1.0.0/admiralonco/man/admiralonco-package.Rd | 5 admiralonco-1.0.0/admiralonco/man/derive_param_bor.Rd | 12 admiralonco-1.0.0/admiralonco/man/derive_param_clinbenefit.Rd | 12 admiralonco-1.0.0/admiralonco/man/derive_param_confirmed_bor.Rd | 12 admiralonco-1.0.0/admiralonco/man/derive_param_confirmed_resp.Rd | 12 admiralonco-1.0.0/admiralonco/man/derive_param_response.Rd | 12 admiralonco-1.0.0/admiralonco/man/filter_pd.Rd | 15 admiralonco-1.0.0/admiralonco/man/get_crpr_dataset.Rd | 2 admiralonco-1.0.0/admiralonco/vignettes/admiralonco.Rmd | 50 admiralonco-1.0.0/admiralonco/vignettes/adrs.Rmd | 134 +- admiralonco-1.0.0/admiralonco/vignettes/adrs_basic.Rmd | 85 - admiralonco-1.0.0/admiralonco/vignettes/adtr.Rmd | 114 -- admiralonco-1.0.0/admiralonco/vignettes/adtte.Rmd | 46 admiralonco-1.0.0/admiralonco/vignettes/articles |only admiralonco-1.0.0/admiralonco/vignettes/irecist.Rmd |only admiralonco-1.0.0/admiralonco/vignettes/nactdt.Rmd | 101 - 60 files changed, 1521 insertions(+), 1958 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-10-07 1.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-10-11 2.1.5