Title: Fit a Cosinor Model Using a Generalized Mixed Modeling Framework
Description: Allows users to fit a cosinor model using the 'glmmTMB' framework.
This extends on existing cosinor modeling packages, including 'cosinor'
and 'circacompare', by including a wide range of available link functions
and the capability to fit mixed models. The cosinor model is described by
Cornelissen (2014) <doi:10.1186/1742-4682-11-16>.
Author: Rex Parsons [aut, cre] ,
Oliver Jayasinghe [aut],
Nicole White [aut] ,
Oliver Rawashdeh [aut, fnd] ,
Prasad Chunduri [ctb, fnd] ,
Margaret Doyle [ctb],
Michael Sachs [rev] ,
Joaquin Cavieres [rev]
Maintainer: Rex Parsons <rex.parsons94@gmail.com>
Diff between GLMMcosinor versions 0.2.0 dated 2024-01-11 and 0.2.1 dated 2024-10-31
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GLMMcosinor-0.2.1/GLMMcosinor/R/print.R | 56 GLMMcosinor-0.2.1/GLMMcosinor/R/simulate_cosinor.R | 2 GLMMcosinor-0.2.1/GLMMcosinor/R/summary.R | 2 GLMMcosinor-0.2.1/GLMMcosinor/R/test_cosinor.R | 14 GLMMcosinor-0.2.1/GLMMcosinor/README.md | 71 - GLMMcosinor-0.2.1/GLMMcosinor/build/vignette.rds |binary GLMMcosinor-0.2.1/GLMMcosinor/inst/WORDLIST | 17 GLMMcosinor-0.2.1/GLMMcosinor/inst/doc/GLMMcosinor.R | 4 GLMMcosinor-0.2.1/GLMMcosinor/inst/doc/GLMMcosinor.Rmd | 38 GLMMcosinor-0.2.1/GLMMcosinor/inst/doc/GLMMcosinor.html | 151 -- GLMMcosinor-0.2.1/GLMMcosinor/inst/doc/data-simulations.Rmd | 4 GLMMcosinor-0.2.1/GLMMcosinor/inst/doc/data-simulations.html | 507 ++----- GLMMcosinor-0.2.1/GLMMcosinor/inst/doc/mixed-models.R | 2 GLMMcosinor-0.2.1/GLMMcosinor/inst/doc/mixed-models.Rmd | 4 GLMMcosinor-0.2.1/GLMMcosinor/inst/doc/mixed-models.html | 38 GLMMcosinor-0.2.1/GLMMcosinor/inst/doc/model-specification.R | 2 GLMMcosinor-0.2.1/GLMMcosinor/inst/doc/model-specification.Rmd | 18 GLMMcosinor-0.2.1/GLMMcosinor/inst/doc/model-specification.html | 403 +++--- GLMMcosinor-0.2.1/GLMMcosinor/inst/doc/model-visualizations.R |only GLMMcosinor-0.2.1/GLMMcosinor/inst/doc/model-visualizations.Rmd |only GLMMcosinor-0.2.1/GLMMcosinor/inst/doc/model-visualizations.html |only GLMMcosinor-0.2.1/GLMMcosinor/inst/doc/multiple-components.Rmd | 6 GLMMcosinor-0.2.1/GLMMcosinor/inst/doc/multiple-components.html | 18 GLMMcosinor-0.2.1/GLMMcosinor/man/GLMMcosinor-package.Rd | 5 GLMMcosinor-0.2.1/GLMMcosinor/man/autoplot.cglmm.Rd | 2 GLMMcosinor-0.2.1/GLMMcosinor/man/cosinor_mixed.Rd | 2 GLMMcosinor-0.2.1/GLMMcosinor/man/figures/README-unnamed-chunk-5-1.png |binary GLMMcosinor-0.2.1/GLMMcosinor/man/polar_plot.Rd | 266 ++-- GLMMcosinor-0.2.1/GLMMcosinor/man/polar_plot.cglmm.Rd | 264 ++-- GLMMcosinor-0.2.1/GLMMcosinor/man/reexports.Rd | 5 GLMMcosinor-0.2.1/GLMMcosinor/man/vitamind.Rd | 4 GLMMcosinor-0.2.1/GLMMcosinor/tests/testthat/_snaps/amp_acro.md |only GLMMcosinor-0.2.1/GLMMcosinor/tests/testthat/_snaps/autoplot/chceck-that-multiple-args-work.svg | 8 GLMMcosinor-0.2.1/GLMMcosinor/tests/testthat/_snaps/autoplot/check-a-simple-plot-command.svg | 66 - 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GLMMcosinor-0.2.1/GLMMcosinor/tests/testthat/test-summary.cosinor.R | 56 GLMMcosinor-0.2.1/GLMMcosinor/tests/testthat/test-test_cosinor.R | 306 ++-- GLMMcosinor-0.2.1/GLMMcosinor/tests/testthat/test-update_formula_and_data.R | 39 GLMMcosinor-0.2.1/GLMMcosinor/vignettes/GLMMcosinor.Rmd | 38 GLMMcosinor-0.2.1/GLMMcosinor/vignettes/data-simulations.Rmd | 4 GLMMcosinor-0.2.1/GLMMcosinor/vignettes/mixed-models.Rmd | 4 GLMMcosinor-0.2.1/GLMMcosinor/vignettes/model-specification.Rmd | 18 GLMMcosinor-0.2.1/GLMMcosinor/vignettes/model-visualizations.Rmd |only GLMMcosinor-0.2.1/GLMMcosinor/vignettes/multiple-components.Rmd | 6 98 files changed, 3405 insertions(+), 3592 deletions(-)
Title: File IO for Intracranial Electroencephalography
Description: Integrated toolbox supporting common file formats used for intracranial
Electroencephalography (iEEG) and deep-brain stimulation (DBS) study.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ieegio versions 0.0.1 dated 2024-09-16 and 0.0.2 dated 2024-10-31
DESCRIPTION | 14 - MD5 | 30 +- NEWS.md | 9 R/aaa-generics-volume.R | 17 + R/hdf5-class.R | 555 ++++++++++++++++++++++++++++------------ R/hdf5.R | 86 +++++- R/math.R | 2 R/mgz.R | 13 R/nifti.R | 58 ++-- R/nwb-class.R | 1 README.md | 2 inst/doc/read-ephys.html | 4 inst/doc/read-imaging-data.html | 6 man/imaging-volume.Rd | 21 + tests |only 15 files changed, 594 insertions(+), 224 deletions(-)
Title: Background Resource Logging
Description: Intense parallel workloads can be difficult to monitor.
Packages 'crew.cluster', 'clustermq', and 'future.batchtools'
distribute hundreds of worker processes over multiple computers.
If a worker process exhausts its available memory,
it may terminate silently, leaving the underlying problem difficult
to detect or troubleshoot.
Using the 'autometric' package, a worker can proactively monitor
itself in a detached background thread.
The worker process itself runs normally,
and the thread writes to a log every few seconds.
If the worker terminates unexpectedly, 'autometric' can read and
visualize the log file to reveal potential resource-related
reasons for the crash. The 'autometric' package borrows heavily from
the methods of packages 'ps' <doi:10.32614/CRAN.package.ps> and 'psutil'.
Author: William Michael Landau [aut, cre]
,
Eli Lilly and Company [cph, fnd],
Posit Software, PBC [cph] ,
Jay Loden [cph] ,
Dave Daeschler [cph] ,
Giampaolo Rodola [cph]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between autometric versions 0.1.0 dated 2024-10-30 and 0.1.1 dated 2024-10-31
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ src/version.h | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Tools Developed by the NCEAS Scientific Computing Support Team
Description: Set of tools to import, summarize, wrangle, and visualize data.
These functions were originally written based on the needs of the
various synthesis working groups that were supported by the
National Center for Ecological Analysis and Synthesis (NCEAS).
These tools are meant to be useful inside and
outside of the context for which they were designed.
Author: Angel Chen [aut, cre] ,
Nicholas J Lyon [aut] ,
Gabriel Antunes Daldegan [aut]
,
Julien Brun [aut] ,
Gabe De La Rosa [ctb] ,
Kara Koenig [aut] ,
Kendall Miller [aut],
Timothy D Nguyen [aut] ,
National Science Foundation [fnd] ,
University of Californ [...truncated...]
Maintainer: Angel Chen <angel777chen@gmail.com>
Diff between scicomptools versions 1.0.0 dated 2023-06-06 and 1.1.0 dated 2024-10-31
DESCRIPTION | 66 ++++++++++++++++++++++----------------------- MD5 | 37 +++++++++++++++++-------- NAMESPACE | 2 + NEWS.md | 6 ++++ R/issue_extract.R |only R/molec_wt.R |only R/word_clouds.R | 29 ++++++------------- README.md | 11 +++++++ build/vignette.rds |binary inst/doc/scicomptools.R | 29 +++++++++++++++++++ inst/doc/scicomptools.Rmd | 44 ++++++++++++++++++++++++++++++ inst/doc/scicomptools.html | 49 +++++++++++++++++++++++++++++++++ man/issue_extract.Rd |only man/molec_wt.Rd |only man/word_cloud_plot.Rd | 17 ----------- man/word_cloud_prep.Rd | 3 -- tests |only vignettes/scicomptools.Rmd | 44 ++++++++++++++++++++++++++++++ 18 files changed, 253 insertions(+), 84 deletions(-)
Title: Comparison of Phylogenetic Trees Using Quartet and Split
Measures
Description: Calculates the number of four-taxon subtrees consistent with a pair
of cladograms, calculating the symmetric quartet distance of Bandelt & Dress
(1986), Reconstructing the shape of a tree from observed dissimilarity data,
Advances in Applied Mathematics, 7, 309-343 <doi:10.1016/0196-8858(86)90038-2>,
and using the tqDist algorithm of Sand et al. (2014), tqDist: a library for
computing the quartet and triplet distances between binary or general trees,
Bioinformatics, 30, 2079–2080 <doi:10.1093/bioinformatics/btu157>
for pairs of binary trees.
Author: Martin R. Smith [aut, cre, cph]
,
Andreas Sand [ant],
Gerth Stoelting Brodal [ant],
Rolf Fagerberg [ant],
Thomas Mailund [ant],
Christian N. S. Pedersen [ant]
,
Jens Johansen [ant],
Morten K. Holt [ant]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between Quartet versions 1.2.6 dated 2024-02-09 and 1.2.7 dated 2024-10-31
DESCRIPTION | 38 MD5 | 80 - NAMESPACE | 231 ++-- NEWS.md | 6 R/CompareQuartets.R | 14 R/Metrics.R | 770 +++++++------- R/ResolvedQuartets.R | 9 R/TernaryPoints.R | 23 R/VisualizeQuartets.R | 63 - R/tqDist.r | 1069 +++++++++----------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 156 +- inst/REFERENCES.bib | 440 ++++---- inst/WORDLIST | 118 +- inst/apa-old-doi-prefix.csl |only inst/doc/Quartet-Distance.Rmd | 2 inst/doc/Quartet-Distance.pdf |binary inst/doc/Using-Quartet.Rmd | 2 inst/doc/Using-Quartet.html | 8 man/AllQuartets.Rd | 2 man/CompareQuartets.Rd | 8 man/CompareSplits.Rd | 2 man/Distances.Rd | 16 man/PairSharedQuartetStatus.Rd | 2 man/Quartet-package.Rd | 192 +-- man/QuartetPoints.Rd | 24 man/QuartetState.Rd | 8 man/QuartetStatus.Rd | 17 man/ResolvedQuartets.Rd | 14 man/SimilarityMetrics.Rd | 388 +++---- man/SplitStatus.Rd | 2 man/TQDist.Rd | 32 man/TQFile.Rd | 40 man/VisualizeQuartets.Rd | 39 src/EdgeParser.cpp | 4 tests/testthat/_snaps/VisualizeQuartet/vq-label.svg | 106 + tests/testthat/_snaps/VisualizeQuartet/vq-size.svg | 106 + tests/testthat/test-VisualizeQuartet.R | 8 tests/testthat/test-rQuartetDist.cpp.R |only vignettes/Quartet-Distance.Rmd | 2 vignettes/Using-Quartet.Rmd | 2 42 files changed, 2156 insertions(+), 1887 deletions(-)
Title: Estimate Incidence and Prevalence using the OMOP Common Data
Model
Description: Calculate incidence and prevalence using data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model. Incidence and prevalence can be estimated for the total population in a database or for a stratification cohort.
Author: Edward Burn [aut, cre] ,
Berta Raventos [aut] ,
Marti Catala [aut] ,
Mike Du [ctb] ,
Yuchen Guo [ctb] ,
Adam Black [ctb] ,
Ger Inberg [ctb] ,
Kim Lopez [ctb]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between IncidencePrevalence versions 0.8.0 dated 2024-10-13 and 0.8.1 dated 2024-10-31
DESCRIPTION | 6 MD5 | 56 R/dateUtilities.R | 12 R/generateDenominatorCohortSet.R | 1661 +++--- R/getDenominatorCohorts.R | 41 R/getIncidence.R | 8 R/reexport-omopgenerics.R | 94 build/vignette.rds |binary inst/doc/a01_Introduction_to_IncidencePrevalence.Rmd | 252 inst/doc/a01_Introduction_to_IncidencePrevalence.html | 9 inst/doc/a02_Creating_denominator_populations.html | 26 inst/doc/a03_Creating_target_denominator_populations.Rmd | 336 - inst/doc/a03_Creating_target_denominator_populations.html | 4 inst/doc/a04_Calculating_prevalence.Rmd | 510 - inst/doc/a04_Calculating_prevalence.html | 61 inst/doc/a05_Calculating_incidence.Rmd | 516 - inst/doc/a05_Calculating_incidence.html | 59 inst/doc/a06_Plotting_options.Rmd | 180 inst/doc/a06_Plotting_options.html | 4 tests/testthat/test-dateUtilities.R | 234 tests/testthat/test-generateDenominatorCohortSet.R | 3874 +++++++------- tests/testthat/test-getStudyDays.R | 522 - tests/testthat/test-plotting.R | 506 - tests/testthat/test-tables.R | 201 vignettes/a01_Introduction_to_IncidencePrevalence.Rmd | 252 vignettes/a03_Creating_target_denominator_populations.Rmd | 336 - vignettes/a04_Calculating_prevalence.Rmd | 510 - vignettes/a05_Calculating_incidence.Rmd | 516 - vignettes/a06_Plotting_options.Rmd | 180 29 files changed, 5569 insertions(+), 5397 deletions(-)
More information about IncidencePrevalence at CRAN
Permanent link
Title: Association Among Disease Counts and Socio-Environmental Factors
Description: Estimation of association between disease or death counts (e.g. COVID-19) and socio-environmental risk factors using a zero-inflated Bayesian spatiotemporal model. Non-spatiotemporal models and/or models without zero-inflation are also included for comparison. Functions to produce corresponding maps are also included. See Chakraborty et al. (2022) <doi:10.1007/s13253-022-00487-1> for more details on the method.
Author: Suman Majumder [cre, aut, cph],
Yoon-Bae Jun [aut, cph],
Sounak Chakraborty [ctb],
Chae-Young Lim [ctb],
Tanujit Dey [ctb]
Maintainer: Suman Majumder <smajumd2@gmail.com>
Diff between BSTZINB versions 1.0.0 dated 2024-10-31 and 1.0.1 dated 2024-10-31
DESCRIPTION | 16 - MD5 | 12 - NEWS.md | 10 inst/doc/BSTZINB_vignette.R | 12 - inst/doc/BSTZINB_vignette.Rmd | 12 - inst/doc/BSTZINB_vignette.html | 490 +++++++++++++++++++---------------------- vignettes/BSTZINB_vignette.Rmd | 12 - 7 files changed, 270 insertions(+), 294 deletions(-)
Title: Utilities for Scoring and Assessing Predictions
Description: Facilitate the evaluation of forecasts in a convenient
framework based on data.table. It allows user to to check their forecasts
and diagnose issues, to visualise forecasts and missing data, to transform
data before scoring, to handle missing forecasts, to aggregate scores, and
to visualise the results of the evaluation. The package mostly focuses on
the evaluation of probabilistic forecasts and allows evaluating several
different forecast types and input formats. Find more information about the
package in the Vignettes as well as in the accompanying paper,
<doi:10.48550/arXiv.2205.07090>.
Author: Nikos Bosse [aut, cre] ,
Sam Abbott [aut] ,
Hugo Gruson [aut] ,
Johannes Bracher [ctb] ,
Toshiaki Asakura [ctb] ,
James Mba Azam [ctb] ,
Sebastian Funk [aut],
Michael Chirico [ctb]
Maintainer: Nikos Bosse <nikosbosse@gmail.com>
Diff between scoringutils versions 1.2.2 dated 2023-11-29 and 2.0.0 dated 2024-10-31
scoringutils-1.2.2/scoringutils/R/avail_forecasts.R |only scoringutils-1.2.2/scoringutils/R/bias.R |only scoringutils-1.2.2/scoringutils/R/brier_score.R |only scoringutils-1.2.2/scoringutils/R/check_forecasts.R |only scoringutils-1.2.2/scoringutils/R/convenience-functions.R |only scoringutils-1.2.2/scoringutils/R/correlations.R |only scoringutils-1.2.2/scoringutils/R/data.R |only scoringutils-1.2.2/scoringutils/R/input-check-helpers.R |only scoringutils-1.2.2/scoringutils/R/interval_score.R |only scoringutils-1.2.2/scoringutils/R/log_score.R |only scoringutils-1.2.2/scoringutils/R/metrics_point_forecasts.R |only scoringutils-1.2.2/scoringutils/R/pit.R |only scoringutils-1.2.2/scoringutils/R/plot.R |only scoringutils-1.2.2/scoringutils/R/score_binary.R |only scoringutils-1.2.2/scoringutils/R/score_continuous_integer.R |only scoringutils-1.2.2/scoringutils/R/score_quantile.R |only scoringutils-1.2.2/scoringutils/R/scoringRules_wrappers.R |only 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Title: Predictive Data Analysis System
Description: Perform a supervised data analysis on a database through a 'shiny' graphical interface. It includes methods such as K-Nearest Neighbors, Decision Trees, ADA Boosting, Extreme Gradient Boosting, Random Forest, Neural Networks, Deep Learning, Support Vector Machines and Bayesian Methods.
Author: Oldemar Rodriguez [aut, cre],
Diego Jimenez [ctb, prg],
Andres Navarro [ctb, prg]
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Diff between predictoR versions 3.0.10 dated 2024-05-15 and 4.1.1 dated 2024-10-31
predictoR-3.0.10/predictoR/R/mod_bayes.R |only predictoR-3.0.10/predictoR/R/mod_boosting.R |only predictoR-3.0.10/predictoR/R/mod_boosting_fct.R |only predictoR-3.0.10/predictoR/R/mod_boosting_utils.R |only predictoR-3.0.10/predictoR/R/mod_comparacion.R |only predictoR-3.0.10/predictoR/R/mod_comparacion_utils.R |only predictoR-3.0.10/predictoR/R/mod_cross_validation.R |only predictoR-3.0.10/predictoR/R/mod_cv_bayes.R |only predictoR-3.0.10/predictoR/R/mod_cv_boosting.R |only predictoR-3.0.10/predictoR/R/mod_cv_dt.R |only predictoR-3.0.10/predictoR/R/mod_cv_knn.R |only predictoR-3.0.10/predictoR/R/mod_cv_lda.R |only predictoR-3.0.10/predictoR/R/mod_cv_qda.R |only predictoR-3.0.10/predictoR/R/mod_cv_rf.R |only predictoR-3.0.10/predictoR/R/mod_cv_rl.R |only predictoR-3.0.10/predictoR/R/mod_cv_rlr.R |only predictoR-3.0.10/predictoR/R/mod_cv_svm.R |only predictoR-3.0.10/predictoR/R/mod_cv_xgb.R |only predictoR-3.0.10/predictoR/R/mod_d_tree.R |only predictoR-3.0.10/predictoR/R/mod_d_tree_fct.R |only predictoR-3.0.10/predictoR/R/mod_knn.R |only predictoR-3.0.10/predictoR/R/mod_l_regression.R |only predictoR-3.0.10/predictoR/R/mod_lda.R |only predictoR-3.0.10/predictoR/R/mod_neural_net.R |only predictoR-3.0.10/predictoR/R/mod_penalized_l_r.R |only predictoR-3.0.10/predictoR/R/mod_penalized_l_r_utils.R |only predictoR-3.0.10/predictoR/R/mod_qda.R |only predictoR-3.0.10/predictoR/R/mod_r_forest.R |only predictoR-3.0.10/predictoR/R/mod_r_forest_fct.R |only predictoR-3.0.10/predictoR/R/mod_r_forest_utils.R |only predictoR-3.0.10/predictoR/R/mod_svm.R |only predictoR-3.0.10/predictoR/R/mod_varerr.R |only predictoR-3.0.10/predictoR/R/mod_xgboosting.R |only predictoR-3.0.10/predictoR/man/e_coeff_landa.Rd |only predictoR-3.0.10/predictoR/man/prob.values.Rd |only predictoR-4.1.1/predictoR/DESCRIPTION | 17 predictoR-4.1.1/predictoR/MD5 | 95 +- predictoR-4.1.1/predictoR/NAMESPACE | 20 predictoR-4.1.1/predictoR/R/app_server.R | 206 ++--- predictoR-4.1.1/predictoR/R/app_ui.R | 202 +---- predictoR-4.1.1/predictoR/R/generate_code_utils.R | 3 predictoR-4.1.1/predictoR/R/golem_utils_server.R | 4 predictoR-4.1.1/predictoR/R/mod_acercade.R | 2 predictoR-4.1.1/predictoR/R/mod_cross_val.R |only predictoR-4.1.1/predictoR/R/mod_cross_val_utils.R |only predictoR-4.1.1/predictoR/R/mod_evaluacion.R |only predictoR-4.1.1/predictoR/R/mod_model_boost_fct.R |only predictoR-4.1.1/predictoR/R/mod_model_boost_utils.R |only predictoR-4.1.1/predictoR/R/mod_model_lda_utils.R |only predictoR-4.1.1/predictoR/R/mod_model_nnet_utils.R |only predictoR-4.1.1/predictoR/R/mod_model_regp_utils.R |only predictoR-4.1.1/predictoR/R/mod_model_rndf_fct.R |only predictoR-4.1.1/predictoR/R/mod_model_rndf_utils.R |only predictoR-4.1.1/predictoR/R/mod_model_svm_utils.R |only predictoR-4.1.1/predictoR/R/mod_model_tree_fct.R |only predictoR-4.1.1/predictoR/R/mod_model_tree_utils.R |only predictoR-4.1.1/predictoR/R/mod_model_xgb_utils.R |only predictoR-4.1.1/predictoR/R/mod_models_utils.R |only predictoR-4.1.1/predictoR/R/mod_train_test.R |only predictoR-4.1.1/predictoR/R/predictoR.R | 13 predictoR-4.1.1/predictoR/R/run_app.R | 1 predictoR-4.1.1/predictoR/R/utils_global.R | 131 +++ predictoR-4.1.1/predictoR/inst/app/lang/diccionario.csv | 414 ++++++------ predictoR-4.1.1/predictoR/inst/app/lang/translation.bin |binary predictoR-4.1.1/predictoR/inst/app/www/predictor_inputs.css | 2 predictoR-4.1.1/predictoR/inst/golem-config.yml | 2 predictoR-4.1.1/predictoR/man/contr.dummy.Rd |only predictoR-4.1.1/predictoR/man/contr.metric.Rd |only predictoR-4.1.1/predictoR/man/contr.ordinal.Rd |only predictoR-4.1.1/predictoR/man/data.frame.dummy.Rd |only predictoR-4.1.1/predictoR/man/e_ada_evol_error.Rd |only predictoR-4.1.1/predictoR/man/e_boost_importance.Rd |only predictoR-4.1.1/predictoR/man/e_coeff_lambda.Rd |only predictoR-4.1.1/predictoR/man/e_posib_lambda.Rd | 3 predictoR-4.1.1/predictoR/man/e_rf_error.Rd | 2 predictoR-4.1.1/predictoR/man/e_rndf_importance.Rd |only predictoR-4.1.1/predictoR/man/e_xgb_importance.Rd |only predictoR-4.1.1/predictoR/man/predictoR.Rd | 5 predictoR-4.1.1/predictoR/man/voronoi_svm_plot.Rd |only 79 files changed, 565 insertions(+), 557 deletions(-)
Title: Collection of Helper Functions
Description: Provides a collection of lightweight helper functions (imps) both
for interactive use and for inclusion within other packages. These include
functions for minimal input assertions, visualising colour palettes,
quoting user input, searching rows of a data frame and capturing string
tokens.
Author: Tim Taylor [aut, cre, cph] ,
R Core Team [cph] ,
Toby Hocking [cph]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between ympes versions 1.5.0 dated 2024-08-28 and 1.6.0 dated 2024-10-31
DESCRIPTION | 9 MD5 | 27 + NAMESPACE | 18 + NEWS.md | 72 +++- R/assert.R | 590 ++++++++++++++++++++++++++++------------ R/greprows.R | 11 R/new_name.R |only build/vignette.rds |binary inst/doc/ympes.R | 29 + inst/doc/ympes.Rmd | 109 +++++++ inst/doc/ympes.html | 141 ++++++++- inst/tinytest/test_assertions.R | 69 ++-- inst/tinytest/test_new_name.R |only man/assertions.Rd | 218 +++++++++++--- man/new_name.Rd |only vignettes/ympes.Rmd | 109 +++++++ 16 files changed, 1076 insertions(+), 326 deletions(-)
Title: Supporting Functions for Packages Maintained by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] ,
Wush Wu [ctb],
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brueggemann [ctb] ,
Christophe Dervieux [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.48 dated 2024-10-03 and 0.49 dated 2024-10-31
DESCRIPTION | 11 ++--- MD5 | 31 +++++++-------- NEWS.md | 16 +++++++ R/app.R | 9 +++- R/io.R | 17 +++++--- R/markdown.R | 82 ++++++++++++++++++++++++++-------------- R/packages.R | 9 ---- R/record.R | 9 +++- R/string.R | 8 ++- inst/doc/xfun.html | 78 +++++++++++++++++++------------------- man/embed_file.Rd | 4 - man/fenced_block.Rd | 6 ++ man/html_tag.Rd | 4 - man/protect_math.Rd | 17 +++++--- man/read_all.Rd | 8 +-- tests/test-cran/test-markdown.R | 12 +++++ tests/test-cran/test-record.R |only 17 files changed, 200 insertions(+), 121 deletions(-)
Title: Optimal Binning of Data
Description: Defines thresholds for breaking data into a number of
discrete levels, minimizing the (mean) squared error within all bins.
Author: Greg Kreider [aut, cre]
Maintainer: Greg Kreider <support@primachvis.com>
Diff between optbin versions 1.3 dated 2023-12-04 and 1.4 dated 2024-10-31
ChangeLog | 1 + DESCRIPTION | 12 +++++++----- MD5 | 8 ++++---- src/optbin.c | 6 +++--- src/optbin.h | 4 ++++ 5 files changed, 19 insertions(+), 12 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 2.16.2 dated 2024-09-24 and 2.17.2 dated 2024-10-31
DESCRIPTION | 6 +++--- MD5 | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)
Title: Exporting 'flextable' to 'xlsx' Files
Description: Exports 'flextable' objects to 'xlsx' files,
utilizing functionalities provided by 'flextable' and 'openxlsx2'.
Author: Tobias Heidler [aut, cre, cph]
Maintainer: Tobias Heidler <tobias.heidler@googlemail.com>
Diff between flexlsx versions 0.2.1 dated 2024-05-07 and 0.3.0 dated 2024-10-31
flexlsx-0.2.1/flexlsx/R/wb_apply.R |only flexlsx-0.2.1/flexlsx/tests/testthat/test-wb_apply.R |only flexlsx-0.3.0/flexlsx/DESCRIPTION | 8 flexlsx-0.3.0/flexlsx/LICENSE | 4 flexlsx-0.3.0/flexlsx/MD5 | 80 flexlsx-0.3.0/flexlsx/NAMESPACE | 74 flexlsx-0.3.0/flexlsx/NEWS.md | 65 flexlsx-0.3.0/flexlsx/R/dim_ranges.R | 319 flexlsx-0.3.0/flexlsx/R/flexlsx-package.R | 14 flexlsx-0.3.0/flexlsx/R/ft_to_style.R | 270 flexlsx-0.3.0/flexlsx/R/helpers.R |only flexlsx-0.3.0/flexlsx/R/wb_add_caption.R |only flexlsx-0.3.0/flexlsx/R/wb_add_flextable.R |only flexlsx-0.3.0/flexlsx/R/wb_apply_border.R |only flexlsx-0.3.0/flexlsx/R/wb_apply_cell_styles.R |only flexlsx-0.3.0/flexlsx/R/wb_apply_content.R |only flexlsx-0.3.0/flexlsx/R/wb_apply_merge.R |only flexlsx-0.3.0/flexlsx/R/wb_apply_text_styles.R |only flexlsx-0.3.0/flexlsx/R/wb_change_height_width.R |only flexlsx-0.3.0/flexlsx/README.md | 102 flexlsx-0.3.0/flexlsx/inst/CITATION | 20 flexlsx-0.3.0/flexlsx/man/flexlsx-package.Rd | 50 flexlsx-0.3.0/flexlsx/man/ft_to_style_tibble.Rd | 56 flexlsx-0.3.0/flexlsx/man/ft_to_xlsx_border_width.Rd | 34 flexlsx-0.3.0/flexlsx/man/ftpart_to_style_tibble.Rd | 42 flexlsx-0.3.0/flexlsx/man/get_dim_colwise.Rd | 34 flexlsx-0.3.0/flexlsx/man/get_dim_ranges.Rd | 34 flexlsx-0.3.0/flexlsx/man/get_dim_rowwise.Rd | 42 flexlsx-0.3.0/flexlsx/man/handle_null_border.Rd | 34 flexlsx-0.3.0/flexlsx/man/prepare_color.Rd | 36 flexlsx-0.3.0/flexlsx/man/style_to_hash.Rd | 40 flexlsx-0.3.0/flexlsx/man/wb_add_caption.Rd | 56 flexlsx-0.3.0/flexlsx/man/wb_add_flextable.Rd | 110 flexlsx-0.3.0/flexlsx/man/wb_apply_border.Rd | 36 flexlsx-0.3.0/flexlsx/man/wb_apply_cell_styles.Rd | 36 flexlsx-0.3.0/flexlsx/man/wb_apply_content.Rd | 36 flexlsx-0.3.0/flexlsx/man/wb_apply_merge.Rd | 42 flexlsx-0.3.0/flexlsx/man/wb_apply_text_styles.Rd | 36 flexlsx-0.3.0/flexlsx/man/wb_change_cell_width.Rd | 40 flexlsx-0.3.0/flexlsx/man/wb_change_row_height.Rd | 36 flexlsx-0.3.0/flexlsx/tests/testthat.R | 24 flexlsx-0.3.0/flexlsx/tests/testthat/_snaps/ft_to_style.md |160072 +++++----- flexlsx-0.3.0/flexlsx/tests/testthat/test-dim_ranges.R | 274 flexlsx-0.3.0/flexlsx/tests/testthat/test-ft_to_style.R | 62 flexlsx-0.3.0/flexlsx/tests/testthat/test-string_num.R |only flexlsx-0.3.0/flexlsx/tests/testthat/test-wb_add_caption.R |only flexlsx-0.3.0/flexlsx/tests/testthat/test-wb_add_flextable.R |only flexlsx-0.3.0/flexlsx/tests/testthat/test-wb_apply_cell_styles.R |only flexlsx-0.3.0/flexlsx/tests/testthat/test-wb_apply_merge.R |only 49 files changed, 81122 insertions(+), 81096 deletions(-)
Title: Import Data from EDC Software
Description: A convenient toolbox to import data exported from Electronic Data Capture (EDC) software 'TrialMaster'.
Author: Dan Chaltiel [aut, cre]
Maintainer: Dan Chaltiel <dan.chaltiel@gmail.com>
Diff between EDCimport versions 0.5.0 dated 2024-10-24 and 0.5.1 dated 2024-10-31
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ tests/testthat/_snaps/trialmaster-simple.md | 8 +++----- tests/testthat/helper-init.R | 16 ++++++++++------ tests/testthat/test-trialmaster-simple.R | 1 + 6 files changed, 26 insertions(+), 19 deletions(-)
Title: Win Time Methods for Time-to-Event Data in Clinical Trials
Description: Performs an analysis of time-to-event clinical trial data using various "win time" methods,
including 'ewt', 'ewtr', 'rmt', 'max', 'wtr', 'rwtr', and 'pwt'. These methods are used to calculate and compare
treatment effects on ordered composite endpoints. The package handles event times, event indicators, and treatment
arm indicators and supports calculations on observed and resampled data. Detailed explanations of each method and
usage examples are provided in "Use of win time for ordered composite endpoints in clinical trials," by Troendle et al.
(2024)<https://pubmed.ncbi.nlm.nih.gov/38417455/>. For more information, see the package documentation or the vignette titled "Introduction to wintime."
Author: James Troendle [aut, cre],
Samuel Lawrence [aut]
Maintainer: James Troendle <james.troendle@nih.gov>
Diff between wintime versions 0.2.0 dated 2024-09-20 and 0.3.0 dated 2024-10-31
DESCRIPTION | 6 ++-- MD5 | 18 ++++++------ NAMESPACE | 2 - R/bootstrap.R | 4 +- R/comp.R | 7 +++- R/perm.R | 2 - R/wintime.R | 2 - build/vignette.rds |binary inst/doc/wintime_vignette.html | 2 - man/COMP.Rd | 58 ++++++++++++++++++++--------------------- 10 files changed, 52 insertions(+), 49 deletions(-)
Title: Nonlinear Time Series Models with Regime Switching
Description: Implements nonlinear autoregressive (AR) time series models. For univariate series, a non-parametric approach is available through additive nonlinear AR. Parametric modeling and testing for regime switching dynamics is available when the transition is either direct (TAR: threshold AR) or smooth (STAR: smooth transition AR, LSTAR). For multivariate series, one can estimate a range of TVAR or threshold cointegration TVECM models with two or three regimes. Tests can be conducted for TVAR as well as for TVECM (Hansen and Seo 2002 and Seo 2006).
Author: Antonio Fabio Di Narzo [aut] ,
Jose Luis Aznarte [ctb] ,
Matthieu Stigler [aut, cre]
Maintainer: Matthieu Stigler <Matthieu.Stigler@gmail.com>
Diff between tsDyn versions 11.0.4.1 dated 2024-02-01 and 11.0.5.2 dated 2024-10-31
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Title: Missing Data and Measurement Error Modelling in INLA
Description: Facilitates fitting measurement error and missing data imputation models using integrated nested Laplace approximations, according to the method described in Skarstein, Martino and Muff (2023) <doi:10.1002/bimj.202300078>. See Skarstein and Muff (2024) <doi:10.48550/arXiv.2406.08172> for details on using the package.
Author: Emma Skarstein [cre, aut, cph]
,
Stefanie Muff [aut]
Maintainer: Emma Skarstein <emma@skarstein.no>
Diff between inlamemi versions 1.0.0 dated 2024-06-24 and 1.1.0 dated 2024-10-31
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Title: Machine Learning Time Series Forecasting
Description: Compute static, onestep and multistep time series forecasts for machine learning models.
Author: Ho Tsung-wu [aut, cre]
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>
Diff between iForecast versions 1.0.8 dated 2024-09-14 and 1.0.9 dated 2024-10-31
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/ttsCaret.R | 3 ++- 3 files changed, 8 insertions(+), 7 deletions(-)
Title: Compute Krippendorff's Alpha
Description: Provides functions to compute and plot Krippendorff's inter-coder
reliability coefficient alpha and bootstrapped uncertainty estimates
(Krippendorff 2004, ISBN:0761915443). The bootstrap routines are set up to
make use of parallel threads where supported.
Author: Alexander Staudt [aut, cre],
Pierre L'Ecuyer [ctb] ,
Chung-hong Chan [ctb]
Maintainer: Alexander Staudt <staudtlex@live.de>
Diff between icr versions 0.6.5 dated 2024-03-03 and 0.6.6 dated 2024-10-31
DESCRIPTION | 27 ++++++++++++++++++++------- MD5 | 34 ++++++++++++++++++++++++++++++++-- R/krippalpha.R | 2 +- inst |only tests |only 5 files changed, 53 insertions(+), 10 deletions(-)
Title: Bayesian Mode Inference
Description: A two-step Bayesian approach for mode inference following
Cross, Hoogerheide, Labonne and van Dijk (2024) <doi:10.1016/j.econlet.2024.111579>).
First, a mixture distribution is fitted on the data using a sparse finite
mixture (SFM) Markov chain Monte Carlo (MCMC) algorithm. The number of
mixture components does not have to be known; the size of the mixture is
estimated endogenously through the SFM approach. Second, the modes of the
estimated mixture at each MCMC draw are retrieved using algorithms
specifically tailored for mode detection. These estimates are then used to
construct posterior probabilities for the number of modes, their locations
and uncertainties, providing a powerful tool for mode inference.
Author: Nalan Bastuerk [aut],
Jamie Cross [aut],
Peter de Knijff [aut],
Lennart Hoogerheide [aut],
Paul Labonne [aut, cre],
Herman van Dijk [aut]
Maintainer: Paul Labonne <labonnepaul@gmail.com>
Diff between BayesMultiMode versions 0.7.2 dated 2024-10-25 and 0.7.3 dated 2024-10-31
DESCRIPTION | 6 +++--- MD5 | 6 +++--- build/partial.rdb |binary tests/testthat/test-bayes_mode.R | 1 + 4 files changed, 7 insertions(+), 6 deletions(-)
More information about BayesMultiMode at CRAN
Permanent link
Title: Estimate Real-Time Case Counts and Time-Varying Epidemiological
Parameters
Description: Estimates the time-varying reproduction number,
rate of spread, and doubling time using a range of open-source tools
(Abbott et al. (2020) <doi:10.12688/wellcomeopenres.16006.1>), and
current best practices (Gostic et al. (2020)
<doi:10.1101/2020.06.18.20134858>). It aims to help users avoid some
of the limitations of naive implementations in a framework that is
informed by community feedback and is actively supported.
Author: Sam Abbott [aut] ,
Joel Hellewell [aut] ,
Katharine Sherratt [aut],
Katelyn Gostic [aut],
Joe Hickson [aut],
Hamada S. Badr [aut] ,
Michael DeWitt [aut] ,
James M. Azam [aut] ,
Robin Thompson [ctb],
Sophie Meakin [ctb],
James Munday [ctb],
Nikos Boss [...truncated...]
Maintainer: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Diff between EpiNow2 versions 1.6.0 dated 2024-10-02 and 1.6.1 dated 2024-10-31
DESCRIPTION | 6 MD5 | 85 NEWS.md | 13 R/checks.R | 92 R/estimate_infections.R | 10 R/estimate_secondary.R | 15 R/opts.R | 23 README.md | 44 inst/doc/EpiNow2.Rmd | 27 inst/doc/EpiNow2.html | 404 +- inst/doc/case-studies.html | 14 inst/doc/epinow.html | 355 - inst/doc/estimate_infections.html | 68 inst/doc/estimate_infections_options.html | 922 ++-- inst/doc/estimate_infections_workflow.html | 366 - inst/doc/estimate_secondary.html | 16 inst/doc/estimate_truncation.html | 14 inst/doc/gaussian_process_implementation_details.Rmd | 42 inst/doc/gaussian_process_implementation_details.html | 109 inst/stan/functions/gaussian_process.stan | 51 man/check_generation_time.Rd | 3 man/check_na_setting_against_data.Rd |only man/gp_opts.Rd | 15 man/test_data_complete.Rd |only src/stanExports_dist_fit.cc | 34 src/stanExports_dist_fit.h | 216 - src/stanExports_estimate_infections.cc | 34 src/stanExports_estimate_infections.h | 3438 +++++++----------- src/stanExports_estimate_secondary.cc | 34 src/stanExports_estimate_secondary.h | 943 +--- src/stanExports_estimate_truncation.cc | 34 src/stanExports_estimate_truncation.h | 823 +--- src/stanExports_simulate_infections.cc | 34 src/stanExports_simulate_infections.h | 2823 ++++++-------- src/stanExports_simulate_secondary.cc | 34 src/stanExports_simulate_secondary.h | 759 +-- tests/testthat/test-checks.R | 91 tests/testthat/test-create_gp_data.R | 2 tests/testthat/test-delays.R | 4 tests/testthat/test-gp_opts.R | 2 tests/testthat/test-obs_opts.R |only tests/testthat/test-stan-guassian-process.R | 40 vignettes/EpiNow2.Rmd | 27 vignettes/EpiNow2.Rmd.orig | 1 vignettes/gaussian_process_implementation_details.Rmd | 42 45 files changed, 5033 insertions(+), 7076 deletions(-)
More information about dsTidyverseClient at CRAN
Permanent link
Title: Preprocessing Tools for Clinical Trial Data
Description: A collection of functions to preprocess data and organize
them in a format amenable to use by chevron.
Author: Liming Li [aut, cre],
Benoit Falquet [aut],
Xiaoli Duan [ctb],
Pawel Rucki [ctb],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Liming Li <liming.li@roche.com>
Diff between dunlin versions 0.1.7 dated 2023-12-13 and 0.1.8 dated 2024-10-31
DESCRIPTION | 12 - MD5 | 53 ++--- NAMESPACE | 3 NEWS.md | 5 R/assertions.R | 6 R/explicit_na.R | 1 R/filter.R | 8 R/reformat.R | 37 ++- R/rules.R | 101 +++++++++- R/utils.R | 38 +++ README.md | 10 - build/vignette.rds |binary inst/doc/Reformatting.Rmd | 2 inst/doc/Reformatting.html | 379 ++++++++++++++++++++------------------ man/combine_list_rules.Rd |only man/combine_rules.Rd |only man/get_arg.Rd |only man/h_expand_all_datasets.Rd | 4 man/log_filter.Rd | 3 man/ls_explicit_na.Rd | 1 man/reformat.Rd | 16 + tests/testthat/_snaps/filter.md |only tests/testthat/_snaps/rules.md | 21 +- tests/testthat/setup-options.R |only tests/testthat/test-filter.R | 12 + tests/testthat/test-reformat.R | 60 ++++++ tests/testthat/test-render_safe.R | 4 tests/testthat/test-rules.R | 114 +++++++++++ tests/testthat/test-utils.R | 32 +++ vignettes/Reformatting.Rmd | 2 30 files changed, 681 insertions(+), 243 deletions(-)
Title: High-Dimensional Temporal Disaggregation
Description: Provides tools for temporal disaggregation, including:
(1) High-dimensional and low-dimensional series generation for simulation studies;
(2) A toolkit for temporal disaggregation and benchmarking using low-dimensional indicator series
as proposed by Dagum and Cholette (2006, ISBN:978-0-387-35439-2);
(3) Novel techniques by Mosley, Gibberd, and Eckley (2022, <doi:10.1111/rssa.12952>)
for disaggregating low-frequency series in the presence of high-dimensional indicator matrices.
Author: Kaveh Salehzadeh Nobari [aut, cre],
Luke Mosley [aut]
Maintainer: Kaveh Salehzadeh Nobari <k.salehzadeh-nobari@imperial.ac.uk>
Diff between DisaggregateTS versions 3.0.0 dated 2024-10-29 and 3.0.1 dated 2024-10-31
DisaggregateTS-3.0.0/DisaggregateTS/data/combined_data.rda |only DisaggregateTS-3.0.0/DisaggregateTS/data/data.R |only DisaggregateTS-3.0.0/DisaggregateTS/man/combined_data.Rd |only DisaggregateTS-3.0.1/DisaggregateTS/DESCRIPTION | 6 DisaggregateTS-3.0.1/DisaggregateTS/MD5 | 23 +- DisaggregateTS-3.0.1/DisaggregateTS/R/data.R | 10 - DisaggregateTS-3.0.1/DisaggregateTS/R/disaggregate.R | 4 DisaggregateTS-3.0.1/DisaggregateTS/build/partial.rdb |binary DisaggregateTS-3.0.1/DisaggregateTS/data/Data.rda |only DisaggregateTS-3.0.1/DisaggregateTS/inst/doc/High_Dimensional_Temporal_Disaggregation.R | 77 ++++----- DisaggregateTS-3.0.1/DisaggregateTS/inst/doc/High_Dimensional_Temporal_Disaggregation.Rmd | 77 ++++----- DisaggregateTS-3.0.1/DisaggregateTS/inst/doc/High_Dimensional_Temporal_Disaggregation.html | 80 +++++----- DisaggregateTS-3.0.1/DisaggregateTS/man/Data.Rd |only DisaggregateTS-3.0.1/DisaggregateTS/man/disaggregate.Rd | 2 DisaggregateTS-3.0.1/DisaggregateTS/vignettes/High_Dimensional_Temporal_Disaggregation.Rmd | 77 ++++----- 15 files changed, 169 insertions(+), 187 deletions(-)
More information about DisaggregateTS at CRAN
Permanent link
Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015):
- common effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- three-level meta-analysis model;
- generalised linear mixed model;
- Hartung-Knapp method for random effects model;
- Kenward-Roger method for random effects model;
- prediction interval;
- statistical tests for funnel plot asymmetry;
- trim-and-fill method to evaluate bias in meta-analysis;
- meta-regression;
- cumulative meta-analysis and leave-one-out meta-analysis;
- import data from 'RevMan 5';
- produce forest plot summarising several (subgroup) meta-analyses.
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer <guido.schwarzer@uniklinik-freiburg.de>
Diff between meta versions 7.0-0 dated 2024-01-12 and 8.0-1 dated 2024-10-31
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Title: Visual Regression Testing and Graphical Diffing
Description: An extension to the 'testthat' package that makes it easy to
add graphical unit tests. It provides a Shiny application to manage
the test cases.
Author: Lionel Henry [cre, aut],
Thomas Lin Pedersen [aut] ,
Posit Software, PBC [cph, fnd],
T Jake Luciani [aut] ,
Matthieu Decorde [aut] ,
Vaudor Lise [aut] ,
Tony Plate [ctb] ,
David Gohel [ctb] ,
Yixuan Qiu [ctb] ,
Hakon Malmedal [ctb]
Maintainer: Lionel Henry <lionel@posit.co>
Diff between vdiffr versions 1.0.7 dated 2023-09-22 and 1.0.8 dated 2024-10-31
vdiffr-1.0.7/vdiffr/tests/testthat/_snaps/expect-doppelganger/stale-snapshots-are-skipped.svg |only vdiffr-1.0.8/vdiffr/DESCRIPTION | 57 +++++---- vdiffr-1.0.8/vdiffr/LICENSE | 2 vdiffr-1.0.8/vdiffr/MD5 | 31 ++--- vdiffr-1.0.8/vdiffr/NEWS.md | 7 + vdiffr-1.0.8/vdiffr/R/expect-doppelganger.R | 15 ++ vdiffr-1.0.8/vdiffr/README.md | 35 +++++ vdiffr-1.0.8/vdiffr/man/expect_doppelganger.Rd | 12 +- vdiffr-1.0.8/vdiffr/man/vdiffr-package.Rd | 6 - vdiffr-1.0.8/vdiffr/src/Makevars.ucrt | 5 vdiffr-1.0.8/vdiffr/tests/testthat.R | 8 - vdiffr-1.0.8/vdiffr/tests/testthat/_snaps/bar |only vdiffr-1.0.8/vdiffr/tests/testthat/_snaps/expect-doppelganger/myplot.svg | 60 +++++----- vdiffr-1.0.8/vdiffr/tests/testthat/_snaps/expect-doppelganger/page-error1.svg | 12 +- vdiffr-1.0.8/vdiffr/tests/testthat/_snaps/expect-doppelganger/page-error2.svg | 12 +- vdiffr-1.0.8/vdiffr/tests/testthat/_snaps/foo |only vdiffr-1.0.8/vdiffr/tests/testthat/test-expect-doppelganger.R | 38 +----- vdiffr-1.0.8/vdiffr/tests/testthat/test-log.R | 2 18 files changed, 169 insertions(+), 133 deletions(-)
Title: Tropical Fisheries Analysis
Description: A compilation of fish stock assessment methods for the
analysis of length-frequency data in the context of data-poor
fisheries. Includes methods and examples included in the FAO
Manual by P. Sparre and S.C. Venema (1998), "Introduction to tropical fish
stock assessment" (<https://openknowledge.fao.org/server/api/core/bitstreams/bc7c37b6-30df-49c0-b5b4-8367a872c97e/content>),
as well as other more recent methods.
Author: Tobias K. Mildenberger [aut, cre]
,
Marc H. Taylor [aut],
Matthias Wolff [aut]
Maintainer: Tobias K. Mildenberger <t.k.mildenberger@gmail.com>
Diff between TropFishR versions 1.6.4 dated 2024-03-01 and 1.6.5 dated 2024-10-31
DESCRIPTION | 30 + MD5 | 66 +-- R/Bhattacharya.R | 7 R/ELEFAN.R | 4 R/ELEFAN_SA.R | 4 R/alba.R | 2 R/catchCurve.R | 3 R/growth_length_age.R | 2 R/plot.catchCurve.R | 2 R/powell_wetherall.R | 2 R/synLFQ1.R | 1 R/synLFQ2.R | 1 R/synLFQ3.R | 1 R/synLFQ4.R | 1 R/synLFQ5.R | 1 R/synLFQ6.R | 1 R/synLFQ7.R | 1 R/synLFQ8.R | 1 R/ypr_sel.R | 52 +- README.md | 25 - build/vignette.rds |binary inst/CITATION | 5 inst/doc/Using_TropFishR_ELEFAN_functions.R | 13 inst/doc/Using_TropFishR_ELEFAN_functions.Rmd | 17 inst/doc/Using_TropFishR_ELEFAN_functions.html | 512 ++++++++++++------------ inst/doc/lfqData.Rmd | 13 inst/doc/lfqData.html | 215 +++++----- inst/doc/tutorial.html | 517 ++++++++++++------------- man/growth_length_age.Rd | 2 man/plot.catchCurve.Rd | 2 man/ypr_sel.Rd | 46 -- vignettes/TropFishR.bib | 104 ++--- vignettes/Using_TropFishR_ELEFAN_functions.Rmd | 17 vignettes/lfqData.Rmd | 13 34 files changed, 842 insertions(+), 841 deletions(-)
Title: Deconvolution of Spatial Transcriptomics Data Based on Neural
Networks
Description: Deconvolution of spatial transcriptomics data based on neural networks and single-cell RNA-seq data. SpatialDDLS implements a workflow to create neural network models able to make accurate estimates of cell composition of spots from spatial transcriptomics data using deep learning and the meaningful information provided by single-cell RNA-seq data. See Torroja and Sanchez-Cabo (2019) <doi:10.3389/fgene.2019.00978> and Mañanes et al. (2024) <doi:10.1093/bioinformatics/btae072> to get an overview of the method and see some examples of its performance.
Author: Diego Mananes [aut, cre] ,
Carlos Torroja [aut] ,
Fatima Sanchez-Cabo [aut]
Maintainer: Diego Mananes <dmananesc@cnic.es>
Diff between SpatialDDLS versions 1.0.2 dated 2024-04-26 and 1.0.3 dated 2024-10-31
DESCRIPTION | 8 MD5 | 95 +-- NAMESPACE | 8 NEWS.md | 4 R/AllClasses.R | 49 +- R/AllGenerics.R | 95 ++- R/SpatialDDLS.R | 6 R/dnnModel.R | 1 R/interGradientsDL.R | 1 R/loadData.R | 66 +- R/plotSpatialCoor.R | 8 R/simMixedSpots.R | 5 R/simSingleCell.R | 4 R/spatialClustering.R | 4 R/utils.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/realModelExample.html | 824 +++++++++++++++++++++------------- man/SpatialDDLS-Rpackage.Rd | 1 man/SpatialDDLS-class.Rd | 36 - man/SpatialDDLS-package.Rd |only man/ZinbParametersModel-class.Rd | 8 man/createSpatialDDLSobject.Rd | 45 - man/deconv.spots.Rd | 6 man/installTFpython.Rd | 18 man/loadSTProfiles.Rd | 21 man/mixed.profiles.Rd | 16 man/plotSpatialClustering.Rd | 2 man/plotSpatialGeneExpr.Rd | 2 man/plotSpatialProp.Rd | 2 man/plotSpatialPropAll.Rd | 2 man/prob.cell.types.Rd | 6 man/project.Rd | 10 man/saveRDS.Rd | 32 - man/simMixedProfiles.Rd | 5 man/simSCProfiles.Rd | 4 man/single.cell.real.Rd | 10 man/single.cell.simul.Rd | 10 man/spatial.experiments.Rd | 9 man/spatialPropClustering.Rd | 2 man/trained.model.Rd | 6 man/zinb.params.Rd | 8 man/zinbwave.model.Rd | 4 tests/testthat/test_dnnModel.R | 4 tests/testthat/test_evalMetrics.R | 2 tests/testthat/test_loadData.R | 54 +- tests/testthat/test_plotSpatialCoor.R | 2 tests/testthat/test_simSingleCell.R | 23 tests/testthat/test_utils.R | 2 49 files changed, 890 insertions(+), 642 deletions(-)
Title: Preparation, Checking and Post-Processing Data for PK/PD
Modeling
Description: Efficient tools for preparation, checking and post-processing of data in PK/PD (pharmacokinetics/pharmacodynamics) modeling, with focus on use of Nonmem. Attention is paid to ensure consistency, traceability, and Nonmem compatibility of Data. Rigorously checks final Nonmem datasets. Implemented in 'data.table', but easily integrated with 'base' and 'tidyverse'.
Author: Philip Delff [aut, cre],
Eric Anderson [ctb],
Matthew Fidler [ctb]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMdata versions 0.1.7 dated 2024-08-26 and 0.1.8 dated 2024-10-31
NMdata-0.1.7/NMdata/inst/examples/data/xgxr2covs.csv |only NMdata-0.1.7/NMdata/inst/examples/data/xgxr2covs.rds |only NMdata-0.1.7/NMdata/inst/examples/data/xgxr2covs_meta.txt |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134.coi |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134.cor |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134.cov |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134.ext |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134.lst |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134.mod |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134.msf |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134.phi |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134.shk |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134.xml |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134_ETAS.msf |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134_etas.txt |only NMdata-0.1.7/NMdata/inst/examples/nonmem/xgxr134_res.txt |only NMdata-0.1.7/NMdata/tests/testthat/testReference/NMscanData_18.rds |only NMdata-0.1.7/NMdata/tests/testthat/test_flagsCount.R |only NMdata-0.1.8/NMdata/DESCRIPTION | 10 NMdata-0.1.8/NMdata/MD5 | 165 ++++------ NMdata-0.1.8/NMdata/NEWS.md | 37 ++ NMdata-0.1.8/NMdata/R/NMapplyFilters.R | 26 + NMdata-0.1.8/NMdata/R/NMcheckData.R | 51 +-- NMdata-0.1.8/NMdata/R/NMgenText.R | 15 NMdata-0.1.8/NMdata/R/NMreadExt.R | 2 NMdata-0.1.8/NMdata/R/NMreadParsText.R | 45 +- NMdata-0.1.8/NMdata/R/NMreadPhi.R | 19 - NMdata-0.1.8/NMdata/R/NMreadSection.R | 4 NMdata-0.1.8/NMdata/R/NMrelate.R | 1 NMdata-0.1.8/NMdata/R/NMscanData.R | 16 NMdata-0.1.8/NMdata/R/NMscanMultiple.R | 5 NMdata-0.1.8/NMdata/R/NMscanTables.R | 44 ++ NMdata-0.1.8/NMdata/R/NMwriteData.R | 35 +- NMdata-0.1.8/NMdata/R/cleanSpaces.R | 1 NMdata-0.1.8/NMdata/R/colLabels.R | 1 NMdata-0.1.8/NMdata/R/dt2mat.R | 15 NMdata-0.1.8/NMdata/R/editCharCols.R | 1 NMdata-0.1.8/NMdata/R/mergeCheck.R | 3 NMdata-0.1.8/NMdata/R/uniquePresent.R | 3 NMdata-0.1.8/NMdata/R/zzz.R | 2 NMdata-0.1.8/NMdata/README.md | 65 ++- NMdata-0.1.8/NMdata/man/NMcheckData.Rd | 19 - NMdata-0.1.8/NMdata/man/NMreadParsText.Rd | 3 NMdata-0.1.8/NMdata/man/NMreadPhi.Rd | 18 - NMdata-0.1.8/NMdata/man/NMreadSection.Rd | 4 NMdata-0.1.8/NMdata/man/NMrelate.Rd | 3 NMdata-0.1.8/NMdata/man/NMscanTables.Rd | 29 + NMdata-0.1.8/NMdata/man/cleanSpaces.Rd | 3 NMdata-0.1.8/NMdata/man/colLabels.Rd | 3 NMdata-0.1.8/NMdata/man/dt2mat.Rd | 7 NMdata-0.1.8/NMdata/man/editCharCols.Rd | 3 NMdata-0.1.8/NMdata/man/figures/README-NMscanMultiple-plot-1.png |only NMdata-0.1.8/NMdata/man/figures/README-unnamed-chunk-2-1.png |binary NMdata-0.1.8/NMdata/man/figures/README-unnamed-chunk-3-1.png |only NMdata-0.1.8/NMdata/man/mergeCheck.Rd | 3 NMdata-0.1.8/NMdata/man/uniquePresent.Rd | 3 NMdata-0.1.8/NMdata/tests/testthat/testData/R |only NMdata-0.1.8/NMdata/tests/testthat/testData/data/xgxr12.csv |only NMdata-0.1.8/NMdata/tests/testthat/testData/data/xgxr12.rds |only NMdata-0.1.8/NMdata/tests/testthat/testData/data/xgxr12_meta.txt |only NMdata-0.1.8/NMdata/tests/testthat/testData/nonmem/xgxr043.mod |only NMdata-0.1.8/NMdata/tests/testthat/testReference/NMcheckData_19.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMcheckData_21.rds |only NMdata-0.1.8/NMdata/tests/testthat/testReference/NMdataConf_03.rds |only NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanData1.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanData4.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanData_03.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanData_11.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanData_13.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanData_14.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanData_15b.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanData_16.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanData_17.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanData_20.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanData_22.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanData_22b.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanData_23.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanData_24.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanData_25.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanData_27.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanData_28.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanData_28b.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanData_30.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanData_31.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanTables1.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanTables2.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanTables3.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanTables4.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanTables_05.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanTables_06.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/NMscanTables_07.rds |binary NMdata-0.1.8/NMdata/tests/testthat/testReference/dt2mat_1.rds |only NMdata-0.1.8/NMdata/tests/testthat/testReference/mat2dt_1.rds |only NMdata-0.1.8/NMdata/tests/testthat/test_NMcheckData.R | 49 +- NMdata-0.1.8/NMdata/tests/testthat/test_NMdataConf.R | 17 + NMdata-0.1.8/NMdata/tests/testthat/test_NMscanData.R | 4 NMdata-0.1.8/NMdata/tests/testthat/test_NMscanTables.R | 3 NMdata-0.1.8/NMdata/tests/testthat/test_dt2mat.R |only NMdata-0.1.8/NMdata/tests/testthat/test_mat2dt.R |only 99 files changed, 463 insertions(+), 274 deletions(-)
Title: Survival Distributions with Piece-Wise Constant Hazards
Description: Density, distribution function, ... hazard function, cumulative
hazard function, survival function for survival distributions with
piece-wise constant hazards and multiple states and methods to plot and
summarise those distributions.
A derivation of the used algorithms can be found in my masters thesis
<doi:10.25365/thesis.76098>.
Author: Tobias Fellinger [aut, cre] ,
Florian Klinglmueller [aut]
Maintainer: Tobias Fellinger <tobias.fellinger@ages.at>
Diff between miniPCH versions 0.3.2 dated 2024-03-06 and 0.4.0 dated 2024-10-31
DESCRIPTION | 17 +++++++++++------ MD5 | 21 +++++++++++++-------- NAMESPACE | 9 +++++++++ NEWS.md | 4 ++++ R/miniPCH-pacakge.R | 10 +++++++++- R/pch_functions.R | 2 +- R/s3methods.R |only README.md | 1 + man/miniPCH.class.Rd |only man/pch_functions.Rd | 2 +- tests/testthat.R | 24 ++++++++++++------------ tests/testthat/test-autoplot.R |only tests/testthat/test-plotting.R |only tests/testthat/test-print.R |only 14 files changed, 61 insertions(+), 29 deletions(-)
Title: Process and Report 'GreenFeed' Data
Description: Provides tools for downloading, processing, and reporting daily and finalized 'GreenFeed' data.
Author: Guillermo Martinez-Boggio [cre, aut, cph]
,
Meredith Harrison [ctb],
Patrick Lutz [ctb]
Maintainer: Guillermo Martinez-Boggio <guillermo.martinezboggio@wisc.edu>
Diff between greenfeedr versions 1.0.0 dated 2024-10-21 and 1.0.1 dated 2024-10-31
DESCRIPTION | 15 ++++----------- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 6 ++++-- R/get_gfdata.R | 2 +- R/process_gfdata.R | 2 +- R/report_gfdata.R | 11 +++++------ R/utils.R | 1 - README.md | 9 +++++---- inst/DailyReportsGF.Rmd | 40 ++++++++++++++++++++++++++-------------- inst/FinalReportsGF.Rmd | 4 ++-- inst/doc/greenfeedr.R | 1 + inst/doc/greenfeedr.Rmd | 1 + inst/doc/greenfeedr.html | 5 +++-- man/get_gfdata.Rd | 2 +- man/process_gfdata.Rd | 2 +- man/report_gfdata.Rd | 11 +++++------ vignettes/greenfeedr.Rmd | 1 + 17 files changed, 77 insertions(+), 68 deletions(-)
Title: Linguistic Typology and Mapping
Description: Provides R with the Glottolog database <https://glottolog.org/> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <https://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://docs.ropensci.org/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching. In addition, package provides an ability to download data from typological databases such as WALS, AUTOTYP and some others and to create your own database website.
Author: George Moroz [aut, cre] ,
Kirill Koncha [ctb] ,
Mikhail Leonov [ctb],
Anna Smirnova [ctb],
Ekaterina Zalivina [ctb]
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between lingtypology versions 1.1.19 dated 2024-09-20 and 1.1.20 dated 2024-10-31
DESCRIPTION | 8 +++--- MD5 | 30 ++++++++++++------------- NEWS | 3 ++ R/glottolog.R | 6 ++--- R/zzz.r | 2 - data/glottolog.RData |binary inst/doc/lingtypology_creating_maps.html | 6 ++--- inst/doc/lingtypology_db_API.html | 6 ++--- inst/doc/lingtypology_dplyr.html | 8 +++--- inst/doc/lingtypology_glottolog_functions.html | 18 +++++++-------- inst/doc/lingtypology_intro.Rmd | 2 - inst/doc/lingtypology_intro.html | 8 +++--- man/glottolog.Rd | 6 ++--- tests/testthat/test-glottolog-database.R | 2 - tests/testthat/test-lang-aff.R | 8 +++--- vignettes/lingtypology_intro.Rmd | 2 - 16 files changed, 59 insertions(+), 56 deletions(-)
Title: Oblique Classification Trees with Uncorrelated Linear
Discriminant Analysis Splits
Description: A classification tree method that uses Uncorrelated Linear Discriminant Analysis (ULDA) for variable selection, split determination, and model fitting in terminal nodes. It automatically handles missing values and offers visualization tools. For more details, see Wang (2024) <doi:10.48550/arXiv.2410.23147>.
Author: Siyu Wang [aut, cre, cph]
Maintainer: Siyu Wang <iamwangsiyu@gmail.com>
Diff between LDATree versions 0.1.2 dated 2023-08-25 and 0.2.0 dated 2024-10-31
LDATree-0.1.2/LDATree/R/ldaGSVD.R |only LDATree-0.1.2/LDATree/man/figures/lifecycle-archived.svg |only LDATree-0.1.2/LDATree/man/figures/lifecycle-defunct.svg |only LDATree-0.1.2/LDATree/man/figures/lifecycle-deprecated.svg |only LDATree-0.1.2/LDATree/man/figures/lifecycle-experimental.svg |only LDATree-0.1.2/LDATree/man/figures/lifecycle-maturing.svg |only LDATree-0.1.2/LDATree/man/figures/lifecycle-questioning.svg |only LDATree-0.1.2/LDATree/man/figures/lifecycle-soft-deprecated.svg |only LDATree-0.1.2/LDATree/man/figures/lifecycle-stable.svg |only LDATree-0.1.2/LDATree/man/figures/lifecycle-superseded.svg |only LDATree-0.1.2/LDATree/man/ldaGSVD.Rd |only LDATree-0.1.2/LDATree/man/predict.ldaGSVD.Rd |only LDATree-0.2.0/LDATree/DESCRIPTION | 28 LDATree-0.2.0/LDATree/MD5 | 70 -- LDATree-0.2.0/LDATree/NAMESPACE | 15 LDATree-0.2.0/LDATree/NEWS.md | 10 LDATree-0.2.0/LDATree/R/LDATree-package.R | 9 LDATree-0.2.0/LDATree/R/Treee.R | 260 +++---- LDATree-0.2.0/LDATree/R/new_SingleTreee.R | 186 ++--- LDATree-0.2.0/LDATree/R/new_TreeeNode.R | 114 ++- LDATree-0.2.0/LDATree/R/plot.R | 207 ++---- LDATree-0.2.0/LDATree/R/predict.R | 137 ++- LDATree-0.2.0/LDATree/R/print.R | 12 LDATree-0.2.0/LDATree/R/prune.R | 248 ++++--- LDATree-0.2.0/LDATree/R/split.R |only LDATree-0.2.0/LDATree/R/utils.R | 344 +--------- LDATree-0.2.0/LDATree/README.md | 116 ++- LDATree-0.2.0/LDATree/build/partial.rdb |only LDATree-0.2.0/LDATree/build/vignette.rds |binary LDATree-0.2.0/LDATree/inst/doc/LDATree.R | 74 -- LDATree-0.2.0/LDATree/inst/doc/LDATree.Rmd | 114 +-- LDATree-0.2.0/LDATree/inst/doc/LDATree.html | 196 ++--- LDATree-0.2.0/LDATree/man/LDATree-package.Rd | 6 LDATree-0.2.0/LDATree/man/Treee.Rd | 192 +++-- LDATree-0.2.0/LDATree/man/figures/README-plot1-1.png |binary LDATree-0.2.0/LDATree/man/figures/README-plot2-1.png |binary LDATree-0.2.0/LDATree/man/figures/README-plot2-2.png |binary LDATree-0.2.0/LDATree/man/plot.Treee.Rd | 69 -- LDATree-0.2.0/LDATree/man/predict.Treee.Rd | 56 - LDATree-0.2.0/LDATree/tests/testthat/test-Treee.R | 15 LDATree-0.2.0/LDATree/tests/testthat/test-utils.R |only LDATree-0.2.0/LDATree/vignettes/LDATree.Rmd | 114 +-- LDATree-0.2.0/LDATree/vignettes/README-plot1-1.png |only LDATree-0.2.0/LDATree/vignettes/README-plot2-1.png |only LDATree-0.2.0/LDATree/vignettes/README-plot2-2.png |only 45 files changed, 1244 insertions(+), 1348 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrology and Water Quality
Data
Description: Collection of functions to help retrieve U.S. Geological Survey
and U.S. Environmental Protection Agency water quality and
hydrology data from web services. Data are discovered from
National Water Information System <https://waterservices.usgs.gov/> and <https://waterdata.usgs.gov/nwis>.
Water quality data are obtained from the Water Quality Portal <https://www.waterqualitydata.us/>.
Author: Laura DeCicco [aut, cre] ,
Robert Hirsch [aut] ,
David Lorenz [aut],
Jordan Read [ctb],
Jordan Walker [ctb],
Lindsay Platt [ctb],
David Watkins [aut] ,
David Blodgett [aut] ,
Mike Johnson [aut] ,
Aliesha Krall [ctb] ,
Lee Stanish [ctb]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between dataRetrieval versions 2.7.16 dated 2024-07-30 and 2.7.17 dated 2024-10-31
dataRetrieval-2.7.16/dataRetrieval/R/readNWISqw.R |only dataRetrieval-2.7.16/dataRetrieval/man/readNWISqw.Rd |only dataRetrieval-2.7.17/dataRetrieval/DESCRIPTION | 26 dataRetrieval-2.7.17/dataRetrieval/MD5 | 121 - dataRetrieval-2.7.17/dataRetrieval/NAMESPACE | 3 dataRetrieval-2.7.17/dataRetrieval/NEWS | 14 dataRetrieval-2.7.17/dataRetrieval/R/AAA.R | 33 dataRetrieval-2.7.17/dataRetrieval/R/addWaterYear.R | 9 dataRetrieval-2.7.17/dataRetrieval/R/constructNWISURL.R | 188 -- dataRetrieval-2.7.17/dataRetrieval/R/dataRetrievals-package.R | 9 dataRetrieval-2.7.17/dataRetrieval/R/findNLDI.R | 106 - dataRetrieval-2.7.17/dataRetrieval/R/getWebServiceData.R | 113 - dataRetrieval-2.7.17/dataRetrieval/R/importRDB1.R | 16 dataRetrieval-2.7.17/dataRetrieval/R/importWQP.R | 409 ++--- dataRetrieval-2.7.17/dataRetrieval/R/importWaterML1.R | 11 dataRetrieval-2.7.17/dataRetrieval/R/pcode_to_name.R | 2 dataRetrieval-2.7.17/dataRetrieval/R/readNGWMNdata.R | 6 dataRetrieval-2.7.17/dataRetrieval/R/readNWISdata.R | 3 dataRetrieval-2.7.17/dataRetrieval/R/readNWISdv.R | 15 dataRetrieval-2.7.17/dataRetrieval/R/readNWISunit.R | 117 - dataRetrieval-2.7.17/dataRetrieval/R/readWQPdata.R | 315 ++- dataRetrieval-2.7.17/dataRetrieval/R/readWQPdots.R | 69 dataRetrieval-2.7.17/dataRetrieval/R/readWQPqw.R | 92 - dataRetrieval-2.7.17/dataRetrieval/R/setAccess.R | 8 dataRetrieval-2.7.17/dataRetrieval/R/sysdata.rda |binary dataRetrieval-2.7.17/dataRetrieval/R/whatNWISdata.R | 8 dataRetrieval-2.7.17/dataRetrieval/R/whatNWISsites.R | 45 dataRetrieval-2.7.17/dataRetrieval/R/whatWQPdata.R | 99 - dataRetrieval-2.7.17/dataRetrieval/R/whatWQPsites.R | 84 - dataRetrieval-2.7.17/dataRetrieval/inst/CITATION | 11 dataRetrieval-2.7.17/dataRetrieval/inst/doc/dataRetrieval.Rmd | 4 dataRetrieval-2.7.17/dataRetrieval/inst/doc/dataRetrieval.html | 20 dataRetrieval-2.7.17/dataRetrieval/inst/doc/qwdata_changes.R | 138 - dataRetrieval-2.7.17/dataRetrieval/inst/doc/qwdata_changes.Rmd | 245 -- dataRetrieval-2.7.17/dataRetrieval/inst/doc/qwdata_changes.html | 818 +++++----- dataRetrieval-2.7.17/dataRetrieval/man/addWaterYear.Rd | 2 dataRetrieval-2.7.17/dataRetrieval/man/constructNWISURL.Rd | 15 dataRetrieval-2.7.17/dataRetrieval/man/constructWQPURL.Rd | 17 dataRetrieval-2.7.17/dataRetrieval/man/importRDB1.Rd | 8 dataRetrieval-2.7.17/dataRetrieval/man/importWQP.Rd | 9 dataRetrieval-2.7.17/dataRetrieval/man/parameterCdFile.Rd | 2 dataRetrieval-2.7.17/dataRetrieval/man/parse_WQP.Rd |only dataRetrieval-2.7.17/dataRetrieval/man/readNGWMNdata.Rd | 2 dataRetrieval-2.7.17/dataRetrieval/man/readNGWMNlevels.Rd | 4 dataRetrieval-2.7.17/dataRetrieval/man/readNGWMNsites.Rd | 4 dataRetrieval-2.7.17/dataRetrieval/man/readNWISdv.Rd | 16 dataRetrieval-2.7.17/dataRetrieval/man/readNWISgwl.Rd | 5 dataRetrieval-2.7.17/dataRetrieval/man/readWQPdata.Rd | 169 +- dataRetrieval-2.7.17/dataRetrieval/man/readWQPdots.Rd | 2 dataRetrieval-2.7.17/dataRetrieval/man/readWQPqw.Rd | 21 dataRetrieval-2.7.17/dataRetrieval/man/readWQPsummary.Rd | 35 dataRetrieval-2.7.17/dataRetrieval/man/whatNWISdata.Rd | 5 dataRetrieval-2.7.17/dataRetrieval/man/whatWQPdata.Rd | 5 dataRetrieval-2.7.17/dataRetrieval/man/wqpSpecials.Rd | 9 dataRetrieval-2.7.17/dataRetrieval/man/wqp_check_status.Rd |only dataRetrieval-2.7.17/dataRetrieval/tests/testthat/tests_general.R | 292 ++- dataRetrieval-2.7.17/dataRetrieval/tests/testthat/tests_imports.R | 37 dataRetrieval-2.7.17/dataRetrieval/tests/testthat/tests_nldi.R | 9 dataRetrieval-2.7.17/dataRetrieval/tests/testthat/tests_userFriendly_fxns.R | 97 - dataRetrieval-2.7.17/dataRetrieval/vignettes/dataRetrieval.Rmd | 4 dataRetrieval-2.7.17/dataRetrieval/vignettes/nwisData.rds |binary dataRetrieval-2.7.17/dataRetrieval/vignettes/qwdata_changes.Rmd | 245 -- dataRetrieval-2.7.17/dataRetrieval/vignettes/wi_phos_data.rds |only dataRetrieval-2.7.17/dataRetrieval/vignettes/wqpData.rds |binary 64 files changed, 1992 insertions(+), 2179 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-10-17 0.2.1
Title: Draw Sectors
Description: Some useful functions that can use 'grid' and 'ggplot2' to plot sectors and interact with 'Seurat' to plot gene expression percentages. Also, there are some examples of how to draw sectors in 'ComplexHeatmap'.
Author: Pengdong Yan [aut, cre, cph]
Maintainer: Pengdong Yan <yanpd01@gmail.com>
Diff between ggsector versions 1.6.5 dated 2022-12-05 and 1.7.0 dated 2024-10-31
DESCRIPTION | 13 MD5 | 18 R/sector_df.R | 1 R/seurat.R | 90 +- build/vignette.rds |binary inst/doc/ggsector.R | 955 +++++++++++++-------------- inst/doc/ggsector.Rmd | 29 inst/doc/ggsector.html | 1704 ++++++++++++++++++++++++------------------------- man/geom_sector.Rd | 71 +- vignettes/ggsector.Rmd | 29 10 files changed, 1517 insertions(+), 1393 deletions(-)
Title: Transform Files to 'microtable' Object with 'microeco' Package
Description: Transform output files of some tools to the 'microtable' object of 'microtable' class in 'microeco' package. The 'microtable' class is the basic class in 'microeco' package and is necessary for the downstream microbial community data analysis.
Author: Chi Liu [aut, cre]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between file2meco versions 0.8.0 dated 2024-06-30 and 0.9.0 dated 2024-10-31
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- R/mpa2meco.R | 10 +++++++--- R/qiime1meco.R | 9 +++++---- data/MetaCyc_pathway_map.RData |binary data/ncyc_map.RData |binary man/mpa2meco.Rd | 3 +++ man/qiime1meco.Rd | 3 +++ 8 files changed, 31 insertions(+), 20 deletions(-)