Title: Linear Biomarker Combination: Empirical Performance Optimization
Description: Perform two linear combination methods for biomarkers: (1) Empirical performance optimization for specificity (or sensitivity) at a controlled sensitivity (or specificity) level of Huang and Sanda (2022) <doi:10.1214/22-aos2210>, and (2) weighted maximum score estimator with empirical minimization of averaged false positive rate and false negative rate. Both adopt the algorithms of Huang and Sanda (2022) <doi:10.1214/22-aos2210>. 'MOSEK' solver is used and needs to be installed; an academic license for 'MOSEK' is free.
Author: Yijian Huang <yhuang5@emory.edu>
Maintainer: Yijian Huang <yhuang5@emory.edu>
Diff between lincom versions 1.1 dated 2023-06-21 and 1.2 dated 2024-06-30
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- NAMESPACE | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Latin Hypercube Samples
Description: Provides a number of methods for creating and augmenting Latin Hypercube Samples and Orthogonal Array Latin Hypercube Samples.
Author: Rob Carnell [aut, cre]
Maintainer: Rob Carnell <bertcarnell@gmail.com>
Diff between lhs versions 1.1.6 dated 2022-12-17 and 1.2.0 dated 2024-06-30
DESCRIPTION | 10 MD5 | 68 +-- NAMESPACE | 5 NEWS | 12 R/correlatedLHS.R |only R/createOA.R | 549 +++++++++++++-------------- R/quantile_transforms.R |only build/vignette.rds |binary inst/doc/augment_lhs.html | 125 +++--- inst/doc/correlated_lhs.R |only inst/doc/correlated_lhs.Rmd |only inst/doc/correlated_lhs.html |only inst/doc/lhs_basics.html | 177 ++++---- inst/doc/lhs_faq.R | 126 ------ inst/doc/lhs_faq.Rmd | 579 ++++++++++------------------ inst/doc/lhs_faq.html | 587 ++++++++++------------------- man/correlatedLHS.Rd |only man/createAddelKemp.Rd | 3 man/createAddelKemp3.Rd | 3 man/createBose.Rd | 3 man/createBoseBush.Rd | 3 man/createBoseBushl.Rd | 3 man/createBush.Rd | 3 man/createBusht.Rd | 3 man/quanttrans.Rd |only src/Makevars | 1 src/Makevars.win | 3 src/OACommonDefines.h | 111 ++--- src/runif.cpp | 40 - src/runif.h | 40 - tests/testthat.R | 12 tests/testthat/helper-lhs.R | 102 ++--- tests/testthat/test-correlatedLHS.R |only tests/testthat/test-createoa.R | 410 ++++++++++---------- tests/testthat/test-galois_field.R | 357 +++++++++-------- tests/testthat/test-get_library_versions.R | 16 tests/testthat/test-quantile_transforms.R |only tests/testthat/test-randomlhs.r | 2 vignettes/correlated_lhs.Rmd |only vignettes/lhs_faq.Rmd | 579 ++++++++++------------------ 40 files changed, 1748 insertions(+), 2184 deletions(-)
Title: Robust Methods for High-Dimensional Data
Description: Robust methods for high-dimensional data, in particular linear
model selection techniques based on least angle regression and sparse
regression. Specifically, the package implements robust least angle
regression (Khan, Van Aelst & Zamar, 2007; <doi:10.1198/016214507000000950>),
(robust) groupwise least angle regression (Alfons, Croux & Gelper, 2016;
<doi:10.1016/j.csda.2015.02.007>), and sparse least trimmed squares
regression (Alfons, Croux & Gelper, 2013; <doi:10.1214/12-AOAS575>).
Author: Andreas Alfons [aut, cre] ,
Dirk Eddelbuettel [ctb]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between robustHD versions 0.8.0 dated 2023-09-26 and 0.8.1 dated 2024-06-30
DESCRIPTION | 10 MD5 | 116 +++--- NAMESPACE | 264 ++++++------- NEWS | 9 R/AIC.R | 326 ++++++++--------- R/accessors.R | 410 ++++++++++----------- R/fastLasso.R | 100 ++--- R/initialSubsets.R | 100 ++--- R/nci60.R | 188 ++++----- R/perry.R | 314 ++++++++-------- R/plot.R | 4 R/print.R | 374 +++++++++---------- R/regFun.R | 114 ++--- R/robustHD-package.R | 4 R/seqModel.R | 212 +++++------ R/setupCoefPlot.R | 570 ++++++++++++++--------------- R/setupCritPlot.R | 478 ++++++++++++------------ R/standardize.R | 260 ++++++------- R/test.R | 62 +-- R/tsBlocks.R | 180 ++++----- R/utils.R | 510 +++++++++++++------------- R/weights.R | 120 +++--- build/partial.rdb |binary data/TopGear.RData |binary data/nci60.RData |binary man/AIC.seqModel.Rd | 216 +++++------ man/coef.seqModel.Rd | 230 ++++++------ man/coefPlot.Rd | 264 ++++++------- man/corHuber.Rd | 228 +++++------ man/critPlot.Rd | 246 ++++++------ man/diagnosticPlot.Rd | 400 ++++++++++---------- man/fitted.seqModel.Rd | 222 +++++------ man/getScale.Rd | 138 +++---- man/grplars.Rd | 544 ++++++++++++++-------------- man/lambda0.Rd | 230 ++++++------ man/nci60.Rd | 176 ++++----- man/partialOrder.Rd | 84 ++-- man/perry.seqModel.Rd | 286 +++++++------- man/plot.seqModel.Rd | 190 ++++----- man/predict.seqModel.Rd | 242 ++++++------ man/residuals.seqModel.Rd | 238 ++++++------ man/rlars.Rd | 478 ++++++++++++------------ man/robustHD-package.Rd | 9 man/setupCoefPlot.Rd | 312 ++++++++-------- man/setupCritPlot.Rd | 296 +++++++-------- man/setupDiagnosticPlot.Rd | 322 ++++++++-------- man/sparseLTS.Rd | 594 +++++++++++++++---------------- man/standardize.Rd | 152 +++---- man/tsBlocks.Rd | 82 ++-- man/tslars.Rd | 402 ++++++++++---------- man/tslarsP.Rd | 458 +++++++++++------------ man/weights.sparseLTS.Rd | 172 ++++---- man/winsorize.Rd | 252 ++++++------- src/fastLars.cpp | 306 ++++++++------- src/fastLars.h | 2 tests/testthat.R | 8 tests/testthat/test-fastLasso-highdim.R | 102 ++--- tests/testthat/test-fastLasso-multiple.R | 132 +++--- tests/testthat/test-fastLasso-simple.R | 124 +++--- 59 files changed, 6451 insertions(+), 6411 deletions(-)
Title: A Collection of Small Text Corpora of Interesting Data
Description: A collection of small text corpora of interesting data.
It contains all data sets from 'dariusk/corpora'. Some examples:
names of animals: birds, dinosaurs, dogs; foods: beer categories,
pizza toppings; geography: English towns, rivers, oceans;
humans: authors, US presidents, occupations; science: elements,
planets; words: adjectives, verbs, proverbs, US president quotes.
Author: Darius Kazemi, Cole Willsea, Serin Delaunay, Karl Swedberg,
Matthew Rothenberg, Greg Kennedy, Nathaniel Mitchell, Javier
Arce, Mark Sample, Parker Higgins, Allison Parrish, Matthew
Hokanson, Aaron Marriner, Casey Kolderup, Michael Paulukonis,
Neil Fr [...truncated...]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between rcorpora versions 2.0.0 dated 2018-07-17 and 2.0.1 dated 2024-06-30
rcorpora-2.0.0/rcorpora/build/rcorpora.pdf |only rcorpora-2.0.1/rcorpora/DESCRIPTION | 6 +++--- rcorpora-2.0.1/rcorpora/MD5 | 8 ++++---- rcorpora-2.0.1/rcorpora/build/stage23.rdb |only rcorpora-2.0.1/rcorpora/inst/NEWS.md | 4 ++++ rcorpora-2.0.1/rcorpora/inst/README.markdown | 2 +- 6 files changed, 12 insertions(+), 8 deletions(-)
Title: Beautiful Graph Drawing
Description: A graph visualization engine that emphasizes on
aesthetics at the same time providing default parameters that yield
out-of-the-box-nice visualizations. The package is built on top of
'The Grid Graphics Package' and seamlessly work with 'igraph' and
'network' objects.
Author: George Vega Yon [aut, cre] ,
Porter Bischoff [aut]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
Diff between netplot versions 0.2-0 dated 2023-09-18 and 0.3-0 dated 2024-06-30
netplot-0.2-0/netplot/man/figures/README-pressure-1.png |only netplot-0.2-0/netplot/man/figures/README-uk-faculty-gradient-1.png |only netplot-0.2-0/netplot/man/figures/README-unnamed-chunk-1-1.png |only netplot-0.2-0/netplot/man/figures/README-unnamed-chunk-1-2.png |only netplot-0.2-0/netplot/man/figures/README-unnamed-chunk-2-1.png |only netplot-0.2-0/netplot/man/figures/README-us-airports-1.png |only netplot-0.3-0/netplot/DESCRIPTION | 12 netplot-0.3-0/netplot/MD5 | 53 - netplot-0.3-0/netplot/NEWS.md | 34 - netplot-0.3-0/netplot/R/attribute-extraction.R | 8 netplot-0.3-0/netplot/R/color_nodes_function.R | 4 netplot-0.3-0/netplot/R/geometry.R | 2 netplot-0.3-0/netplot/R/grob_vertex.R | 9 netplot-0.3-0/netplot/R/netplot.R | 327 ++++++++-- netplot-0.3-0/netplot/R/netplot_base.R | 2 netplot-0.3-0/netplot/R/nplot_legend.R | 2 netplot-0.3-0/netplot/README.md | 66 +- netplot-0.3-0/netplot/build/vignette.rds |binary netplot-0.3-0/netplot/inst/NEWS | 4 netplot-0.3-0/netplot/inst/doc/base-and-grid.html | 6 netplot-0.3-0/netplot/inst/doc/examples.R | 2 netplot-0.3-0/netplot/inst/doc/examples.Rmd | 2 netplot-0.3-0/netplot/inst/doc/examples.html | 29 netplot-0.3-0/netplot/man/figures/README-example-1.png |binary netplot-0.3-0/netplot/man/figures/README-example-2.png |binary netplot-0.3-0/netplot/man/figures/README-example-3.png |binary netplot-0.3-0/netplot/man/figures/README-fig-uk-faculty-1.png |only netplot-0.3-0/netplot/man/figures/README-fig-uk-faculty-gradient-1.png |only netplot-0.3-0/netplot/man/figures/README-fig-us-airports-1.png |only netplot-0.3-0/netplot/man/nplot.Rd | 167 ++++- netplot-0.3-0/netplot/man/nplot_base.Rd | 28 netplot-0.3-0/netplot/vignettes/examples.Rmd | 2 32 files changed, 562 insertions(+), 197 deletions(-)
Title: Prediction Performance Metrics
Description: A compilation of more than 80 functions designed to quantitatively and visually evaluate prediction performance of regression (continuous variables) and classification (categorical variables) of point-forecast models (e.g. APSIM, DSSAT, DNDC, supervised Machine Learning). For regression, it includes functions to generate plots (scatter, tiles, density, & Bland-Altman plot), and to estimate error metrics (e.g. MBE, MAE, RMSE), error decomposition (e.g. lack of accuracy-precision), model efficiency (e.g. NSE, E1, KGE), indices of agreement (e.g. d, RAC), goodness of fit (e.g. r, R2), adjusted correlation coefficients (e.g. CCC, dcorr), symmetric regression coefficients (intercept, slope), and mean absolute scaled error (MASE) for time series predictions. For classification (binomial and multinomial), it offers functions to generate and plot confusion matrices, and to estimate performance metrics such as accuracy, precision, recall, specificity, F-score, Cohen's Kappa, G-mean, and man [...truncated...]
Author: Adrian A. Correndo [aut, cre, cph]
,
Luiz H. Moro Rosso [aut] ,
Rai Schwalbert [aut] ,
Carlos Hernandez [aut] ,
Leonardo M. Bastos [aut] ,
Luciana Nieto [aut] ,
Dean Holzworth [aut],
Ignacio A. Ciampitti [aut]
Maintainer: Adrian A. Correndo <acorrend@uoguelph.ca>
Diff between metrica versions 2.0.3 dated 2023-04-14 and 2.1.0 dated 2024-06-30
DESCRIPTION | 19 MD5 | 108 - NAMESPACE | 1 NEWS.md | 412 ++-- R/class_agf.R | 268 +- R/class_confusion_matrix.R | 688 +++---- R/class_p4.R |only R/metrics_summary.R | 5 R/plot_bland_altman.R | 181 +- R/plot_density.R | 405 ++-- R/plot_scatter.R | 430 ++-- R/plot_tiles.R | 406 ++-- README.md | 1679 +++++++++--------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Cheatsheet.R | 16 inst/doc/Cheatsheet.Rmd | 62 inst/doc/Cheatsheet.html | 552 +++--- inst/doc/JOSS_publication.R | 16 inst/doc/JOSS_publication.html | 570 +++--- inst/doc/Shinyapp.R | 16 inst/doc/Shinyapp.html | 556 +++--- inst/doc/apsim_open.R | 68 inst/doc/apsim_open.html | 808 ++++----- inst/doc/available_metrics_classification.R | 12 inst/doc/available_metrics_classification.Rmd | 355 ++- inst/doc/available_metrics_classification.html | 1420 ++++++++------- inst/doc/available_metrics_regression.R | 12 inst/doc/available_metrics_regression.html | 1840 ++++++++++---------- inst/doc/classification_case.R | 550 +++--- inst/doc/classification_case.Rmd | 880 ++++----- inst/doc/classification_case.html | 2241 ++++++++++++------------- inst/doc/regression_case.R | 313 +-- inst/doc/regression_case.Rmd | 557 +++--- inst/doc/regression_case.html | 1436 ++++++++-------- man/bland_altman_plot.Rd | 3 man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-14-1.png |binary man/figures/README-unnamed-chunk-15-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/cheatsheet.png |binary man/figures/land_cover_example.png |binary man/figures/maize_phenology_example.png |binary man/figures/shinyapp.png |binary man/metrica-package.Rd | 3 man/p4.Rd |only man/scatter_plot.Rd | 5 tests/testthat/examples/soybean.example.db-shm |only tests/testthat/examples/soybean.example.db-wal |only tests/testthat/test-class.R | 1707 +++++++++---------- vignettes/Cheatsheet.Rmd | 62 vignettes/available_metrics_classification.Rmd | 355 ++- vignettes/classification_case.Rmd | 880 ++++----- vignettes/regression_case.Rmd | 557 +++--- 57 files changed, 10295 insertions(+), 10159 deletions(-)
Title: Cluster-Based Permutation Analysis for Densely Sampled Time Data
Description: An implementation of fast cluster-based permutation analysis
(CPA) for densely-sampled time data developed in Maris & Oostenveld,
2007 <doi:10.1016/j.jneumeth.2007.03.024>. Supports (generalized,
mixed-effects) regression models for the calculation of timewise
statistics. Provides both a wholesale and a piecemeal interface to the
CPA procedure with an emphasis on interpretability and diagnostics.
Integrates 'Julia' libraries 'MixedModels.jl' and 'GLM.jl' for
performance improvements, with additional functionalities for
interfacing with 'Julia' from 'R' powered by the 'JuliaConnectoR'
package.
Author: June Choe [aut, cre, cph]
Maintainer: June Choe <jchoe001@gmail.com>
Diff between jlmerclusterperm versions 1.1.3 dated 2024-03-04 and 1.1.4 dated 2024-06-30
DESCRIPTION | 12 - LICENSE | 4 MD5 | 66 +++++----- NAMESPACE | 100 +++++++-------- NEWS.md | 10 + R/jlmer_spec.R | 1 R/srr-stats-standards.R | 196 +++++++++++++++--------------- R/utils.R | 70 +++++----- README.md | 11 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/jlmerclusterperm.R | 3 inst/doc/jlmerclusterperm.Rmd | 160 ++++++++++++------------ inst/doc/jlmerclusterperm.html | 5 man/figures/README-/CPA-io-dark.svg | 2 man/figures/README-/CPA-io.svg | 2 man/figures/README-/reCPA-io-dark.svg | 2 man/figures/README-/reCPA-io.svg | 2 man/figures/README-/setup-io-dark.svg | 2 man/figures/README-/setup-io.svg | 2 man/reexports.Rd | 40 +++--- tests/testthat.R | 24 +-- tests/testthat/test-aaa-a-logging.R | 18 +- tests/testthat/test-aaa-b-setup.R | 4 tests/testthat/test-clusterpermute.R | 114 ++++++++--------- tests/testthat/test-jlmer.R | 66 +++++----- tests/testthat/test-jlmer_spec.R | 26 +-- tests/testthat/test-julia_rng.R | 2 tests/testthat/test-permute.R | 116 ++++++++--------- tests/testthat/test-progress.R | 2 tests/testthat/test-singularity.R | 2 tests/testthat/test-threshold_search.R | 3 tests/testthat/test-timewise_statistics.R | 76 +++++------ vignettes/jlmerclusterperm.Rmd | 160 ++++++++++++------------ 34 files changed, 659 insertions(+), 644 deletions(-)
More information about jlmerclusterperm at CRAN
Permanent link
Title: 'NoSQL' Database Connector
Description: Simplified document database access and manipulation,
providing a common API across supported 'NoSQL' databases
'Elasticsearch', 'CouchDB', 'MongoDB' as well as
'SQLite/JSON1', 'PostgreSQL', and 'DuckDB'.
Author: Ralf Herold [aut, cre] ,
Scott Chamberlain [aut] ,
Rich FitzJohn [aut],
Jeroen Ooms [aut]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between nodbi versions 0.10.4 dated 2024-03-05 and 0.10.5 dated 2024-06-30
DESCRIPTION | 6 LICENSE | 2 MD5 | 32 +-- NEWS.md | 10 + R/delete.R | 12 - R/query.R | 49 +---- R/src_mongo.R | 8 R/update.R | 3 R/zzz.R | 5 inst/doc/nodbi-overview.R | 42 ++-- inst/doc/nodbi-overview.Rmd | 46 ++--- inst/doc/nodbi-overview.html | 371 ++++++++++++++++++++++--------------------- man/docdb_query.Rd | 6 man/docdb_update.Rd | 5 man/src_duckdb.Rd | 4 tests/testthat/core-nodbi.R | 4 vignettes/nodbi-overview.Rmd | 46 ++--- 17 files changed, 337 insertions(+), 314 deletions(-)
Title: Easily Install and Load the 'mlr3' Package Family
Description: The 'mlr3' package family is a set of packages for
machine-learning purposes built in a modular fashion. This wrapper
package is aimed to simplify the installation and loading of the core
'mlr3' packages. Get more information about the 'mlr3' project at
<https://mlr3book.mlr-org.com/>.
Author: Michel Lang [aut] ,
Patrick Schratz [aut] ,
Marc Becker [cre, aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3verse versions 0.2.8 dated 2023-04-26 and 0.3.0 dated 2024-06-30
DESCRIPTION | 47 ++++++++++++++++++++++----------------------- MD5 | 24 +++++++++++------------ NAMESPACE | 28 +++++++++++++------------- NEWS.md | 26 +++++++++++++++++------- R/mlr3verse_info.R | 2 - R/reexport_mlr3misc.R | 4 +++ R/reexports_mlr3cluster.R | 4 --- R/reexports_mlr3fselect.R | 38 +++++++++++++++++------------------- R/reexports_mlr3tuning.R | 48 +++++++++++++++++++++++----------------------- R/zzz.R | 1 man/mlr3verse-package.Rd | 3 +- man/mlr3verse_info.Rd | 2 - man/reexports.Rd | 40 +++++++++++++++++++------------------- 13 files changed, 137 insertions(+), 130 deletions(-)
Title: Retrieve and Analyze Clinical Trials in Public Registers
Description: A system for querying, retrieving and analyzing
protocol- and results-related information on clinical trials from
four public registers, the 'European Union Clinical Trials Register'
('EUCTR', <https://www.clinicaltrialsregister.eu/>),
'ClinicalTrials.gov' (<https://clinicaltrials.gov/> and also
translating queries the retired classic interface), the
'ISRCTN' (<http://www.isrctn.com/>) and the
'European Union Clinical Trials Information System'
('CTIS', <https://euclinicaltrials.eu/>).
Trial information is downloaded, converted and stored in a database
('PostgreSQL', 'SQLite', 'DuckDB' or 'MongoDB'; via package 'nodbi').
Documents in registers associated with trials can also be downloaded.
Other functions identify deduplicated records,
easily find and extract variables (fields) of interest even
from complex nested data as used by the registers,
merge variables and update queries.
The package can be used for meta-analysis and trend-analysis of
the design and cond [...truncated...]
Author: Ralf Herold [aut, cre]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 1.18.0 dated 2024-05-13 and 1.19.0 dated 2024-06-30
ctrdata-1.18.0/ctrdata/R/ctrLoadQueryIntoDbCtgov.R |only ctrdata-1.18.0/ctrdata/R/utils.R |only ctrdata-1.18.0/ctrdata/inst/tinytest/more_test_ctrdata_duckdb_ctgov.R |only ctrdata-1.18.0/ctrdata/inst/tinytest/more_test_ctrdata_postgres_ctgov.R |only ctrdata-1.18.0/ctrdata/inst/tinytest/test_ctrdata_duckdb_ctis.R |only ctrdata-1.18.0/ctrdata/inst/tinytest/test_ctrdata_mongo_local_ctgov.R |only ctrdata-1.18.0/ctrdata/vignettes/ctgovnested.png |only ctrdata-1.19.0/ctrdata/DESCRIPTION | 13 ctrdata-1.19.0/ctrdata/MD5 | 107 - ctrdata-1.19.0/ctrdata/NAMESPACE | 3 ctrdata-1.19.0/ctrdata/NEWS.md | 29 ctrdata-1.19.0/ctrdata/R/ctrFindActiveSubstanceSynonyms.R | 95 - ctrdata-1.19.0/ctrdata/R/ctrGetQueryUrl.R | 98 - ctrdata-1.19.0/ctrdata/R/ctrLoadQueryIntoDb.R | 32 ctrdata-1.19.0/ctrdata/R/ctrLoadQueryIntoDbCtgov2.R | 47 ctrdata-1.19.0/ctrdata/R/ctrLoadQueryIntoDbCtis.R | 794 ++------- ctrdata-1.19.0/ctrdata/R/ctrLoadQueryIntoDbEuctr.R | 4 ctrdata-1.19.0/ctrdata/R/ctrLoadQueryIntoDbIsrctn.R | 9 ctrdata-1.19.0/ctrdata/R/ctrOpenSearchPagesInBrowser.R | 49 ctrdata-1.19.0/ctrdata/R/ctrdata-registers.R | 102 - ctrdata-1.19.0/ctrdata/R/dbFindFields.R | 10 ctrdata-1.19.0/ctrdata/R/util_fields.R |only ctrdata-1.19.0/ctrdata/R/util_functions.R |only ctrdata-1.19.0/ctrdata/R/zzz.R | 4 ctrdata-1.19.0/ctrdata/README.md | 443 ++--- ctrdata-1.19.0/ctrdata/inst/WORDLIST | 15 ctrdata-1.19.0/ctrdata/inst/doc/ctrdata_install.pdf |binary ctrdata-1.19.0/ctrdata/inst/doc/ctrdata_retrieve.pdf |binary ctrdata-1.19.0/ctrdata/inst/doc/ctrdata_summarise.pdf |binary ctrdata-1.19.0/ctrdata/inst/extdata/demo.sqlite |binary ctrdata-1.19.0/ctrdata/inst/tinytest/ctrdata_ctgov.R | 120 - ctrdata-1.19.0/ctrdata/inst/tinytest/ctrdata_ctgov2.R | 14 ctrdata-1.19.0/ctrdata/inst/tinytest/ctrdata_ctis.R | 105 - ctrdata-1.19.0/ctrdata/inst/tinytest/ctrdata_isrctn.R | 2 ctrdata-1.19.0/ctrdata/inst/tinytest/more_test_ctrdata_duckdb_ctis.R |only ctrdata-1.19.0/ctrdata/inst/tinytest/more_test_ctrdata_mongo_local_ctis.R | 9 ctrdata-1.19.0/ctrdata/inst/tinytest/more_test_ctrdata_param_checks.R | 109 - ctrdata-1.19.0/ctrdata/inst/tinytest/more_test_ctrdata_postgres_ctis.R | 11 ctrdata-1.19.0/ctrdata/inst/tinytest/test_ctrdata_ctrfindactivesubstance.R | 10 ctrdata-1.19.0/ctrdata/inst/tinytest/test_ctrdata_other_functions.R | 10 ctrdata-1.19.0/ctrdata/inst/tinytest/test_ctrdata_sqlite_ctis.R | 2 ctrdata-1.19.0/ctrdata/man/ctrDb.Rd | 2 ctrdata-1.19.0/ctrdata/man/ctrFindActiveSubstanceSynonyms.Rd | 19 ctrdata-1.19.0/ctrdata/man/ctrGetQueryUrl.Rd | 11 ctrdata-1.19.0/ctrdata/man/ctrLoadQueryIntoDb.Rd | 29 ctrdata-1.19.0/ctrdata/man/ctrOpenSearchPagesInBrowser.Rd | 8 ctrdata-1.19.0/ctrdata/man/ctrdata-registers.Rd | 106 - ctrdata-1.19.0/ctrdata/man/figures/README-ctrdata_across_registers.png |binary ctrdata-1.19.0/ctrdata/man/figures/README-ctrdata_results_neuroblastoma.png |binary ctrdata-1.19.0/ctrdata/vignettes/boxpep.png |binary ctrdata-1.19.0/ctrdata/vignettes/ctgov2nestedresults.png |only ctrdata-1.19.0/ctrdata/vignettes/ctgovnestedresults.png |only ctrdata-1.19.0/ctrdata/vignettes/ctisnested.png |only ctrdata-1.19.0/ctrdata/vignettes/ctrdata_retrieve.Rmd | 109 - ctrdata-1.19.0/ctrdata/vignettes/ctrdata_summarise.Rmd | 839 ++++++---- ctrdata-1.19.0/ctrdata/vignettes/nb1.png |binary ctrdata-1.19.0/ctrdata/vignettes/nb2.png |binary ctrdata-1.19.0/ctrdata/vignettes/nbtrials.png |binary ctrdata-1.19.0/ctrdata/vignettes/phase23_paed_p_values.png |binary ctrdata-1.19.0/ctrdata/vignettes/phase23_paed_p_values_participants.png |binary ctrdata-1.19.0/ctrdata/vignettes/samplesizechanges.png |binary 61 files changed, 1717 insertions(+), 1652 deletions(-)
Title: Drift Adaptable Models
Description: By analyzing streaming datasets, it is possible to observe significant changes in the data distribution or models' accuracy during their prediction (concept drift). The goal of 'heimdall' is to measure when concept drift occurs. The package makes available several state-of-the-art methods. It also tackles how to adapt models in a nonstationary context. Some concept drifts methods are described in Tavares (2022) <doi:10.1007/s12530-021-09415-z>.
Author: Lucas Tavares [aut],
Leonardo Carvalho [aut],
Diego Carvalho [aut],
Esther Pacitti [aut],
Fabio Porto [aut],
Eduardo Ogasawara [aut, ths, cre]
,
Federal Center for Technological Education of Rio de Janeiro
[cph]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between heimdall versions 1.0.707 dated 2024-06-22 and 1.0.717 dated 2024-06-30
heimdall-1.0.707/heimdall/R/dfr_cumsum.R |only heimdall-1.0.707/heimdall/data/st_real_examples.RData |only heimdall-1.0.707/heimdall/man/dfr_cumsum.Rd |only heimdall-1.0.707/heimdall/man/inactive.Rd |only heimdall-1.0.707/heimdall/man/passive.Rd |only heimdall-1.0.707/heimdall/man/st_real_examples.Rd |only heimdall-1.0.717/heimdall/DESCRIPTION | 9 +- heimdall-1.0.717/heimdall/MD5 | 60 ++++++++--------- heimdall-1.0.717/heimdall/NAMESPACE | 16 ++-- heimdall-1.0.717/heimdall/R/ac_drifter.R | 12 +-- heimdall-1.0.717/heimdall/R/ac_metrics.R | 2 heimdall-1.0.717/heimdall/R/data.R | 18 ----- heimdall-1.0.717/heimdall/R/dfr_adwin.R | 12 +-- heimdall-1.0.717/heimdall/R/dfr_cusum.R |only heimdall-1.0.717/heimdall/R/dfr_ddm.R | 25 +++---- heimdall-1.0.717/heimdall/R/dfr_ecdd.R | 19 ++--- heimdall-1.0.717/heimdall/R/dfr_eddm.R | 29 +++----- heimdall-1.0.717/heimdall/R/dfr_hddm.R | 19 ++--- heimdall-1.0.717/heimdall/R/dfr_kldist.R | 21 ++--- heimdall-1.0.717/heimdall/R/dfr_kswin.R | 21 ++--- heimdall-1.0.717/heimdall/R/dfr_mcdd.R | 21 ++--- heimdall-1.0.717/heimdall/R/dfr_page_hinkley.R | 14 +-- heimdall-1.0.717/heimdall/README.md | 12 ++- heimdall-1.0.717/heimdall/data/st_drift_examples.RData |binary heimdall-1.0.717/heimdall/inst |only heimdall-1.0.717/heimdall/man/dfr_cusum.Rd |only heimdall-1.0.717/heimdall/man/dfr_ddm.Rd | 17 ++-- heimdall-1.0.717/heimdall/man/dfr_ecdd.Rd | 13 +-- heimdall-1.0.717/heimdall/man/dfr_eddm.Rd | 17 ++-- heimdall-1.0.717/heimdall/man/dfr_hddm.Rd | 17 ++-- heimdall-1.0.717/heimdall/man/dfr_inactive.Rd |only heimdall-1.0.717/heimdall/man/dfr_kldist.Rd | 13 +-- heimdall-1.0.717/heimdall/man/dfr_kswin.Rd | 13 +-- heimdall-1.0.717/heimdall/man/dfr_mcdd.Rd | 13 +-- heimdall-1.0.717/heimdall/man/dfr_page_hinkley.Rd | 6 - heimdall-1.0.717/heimdall/man/dfr_passive.Rd |only 36 files changed, 187 insertions(+), 232 deletions(-)
Title: Check Arguments and Generate Readable Error Messages
Description: Provides several validator functions for checking if arguments
passed by users have valid types, lengths, etc. and for generating
informative and well-formatted error messages in a consistent style. Also
provides tools for users to create their own validator functions. The
error message style used is adopted from
<https://style.tidyverse.org/error-messages.html>.
Author: Renfei Mao
Maintainer: Renfei Mao <renfeimao@gmail.com>
Diff between erify versions 0.4.0 dated 2022-10-04 and 0.6.0 dated 2024-06-30
DESCRIPTION | 8 MD5 | 38 ++-- NAMESPACE | 3 NEWS.md | 11 + R/check-classes.R | 6 R/check-content.R | 5 R/check-interval.R |only R/check-intervals.R |only R/check-length.R | 4 R/check-lengths.R | 2 R/check-n.R | 20 +- R/check-string.R | 7 R/check-type.R | 3 R/utils.R | 13 - build/vignette.rds |binary inst/doc/erify.R | 2 inst/doc/erify.html | 401 ++++++++++++++++++++++++------------------------- man/check_interval.Rd |only man/check_intervals.Rd |only man/check_n.Rd | 4 man/check_string.Rd | 3 man/check_type.Rd | 3 22 files changed, 275 insertions(+), 258 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 0.7.1 dated 2024-03-07 and 0.8.0 dated 2024-06-30
DESCRIPTION | 11 ++++--- MD5 | 29 ++++++++++--------- NAMESPACE | 2 + R/help.R | 1 R/humann2meco.R | 6 ++-- R/mpa2meco.R | 65 +++++++++++++++++++++++++++++++------------- R/ncyc2meco.R | 8 ++--- R/physeq2meco.R | 75 +++++++++++++++++++++++++-------------------------- R/tse2meco.R |only man/file2meco.Rd | 1 man/humann2meco.Rd | 6 ++-- man/meco2phyloseq.Rd | 8 ++--- man/meco2tse.Rd |only man/mpa2meco.Rd | 8 ++++- man/ncyc2meco.Rd | 8 ++--- man/phyloseq2meco.Rd | 2 - man/tse2meco.Rd |only 17 files changed, 136 insertions(+), 94 deletions(-)
Title: Posterior Predictive (PoP) Design for Phase I Clinical Trials
Description: The primary goal of phase I clinical trials is to find the maximum tolerated dose (MTD). To reach this objective, we introduce a new design for phase I clinical trials, the posterior predictive (PoP) design. The PoP design is an innovative model-assisted design that is as simply as the conventional algorithmic designs as its decision rules can be pre-tabulated prior to the onset of trial, but is of more flexibility of selecting diverse target toxicity rates and cohort sizes. The PoP design has desirable properties, such as coherence and consistency. Moreover, the PoP design provides better empirical performance than the BOIN and Keyboard design with respect to high average probabilities of choosing the MTD and slightly lower risk of treating patients at subtherapeutic or overly toxic doses.
Author: Chenqi Fu [aut],
Xinying Fang [aut, cre],
Shouhao Zhou [aut]
Maintainer: Xinying Fang <xf.research@outlook.com>
Diff between PoPdesign versions 1.0.4 dated 2023-12-10 and 1.1.0 dated 2024-06-30
PoPdesign-1.0.4/PoPdesign/inst/temp_results |only PoPdesign-1.1.0/PoPdesign/DESCRIPTION | 11 PoPdesign-1.1.0/PoPdesign/MD5 | 33 PoPdesign-1.1.0/PoPdesign/R/bound.R | 15 PoPdesign-1.1.0/PoPdesign/R/get.boundary.pop.R | 23 PoPdesign-1.1.0/PoPdesign/R/get.oc.pop.R | 413 ++-------- PoPdesign-1.1.0/PoPdesign/R/prbf01.R | 2 PoPdesign-1.1.0/PoPdesign/R/select.mtd.pop.R | 73 - PoPdesign-1.1.0/PoPdesign/R/summary.pop.R | 4 PoPdesign-1.1.0/PoPdesign/build/vignette.rds |binary PoPdesign-1.1.0/PoPdesign/inst/doc/vignette_for_PoP_design.R | 30 PoPdesign-1.1.0/PoPdesign/inst/doc/vignette_for_PoP_design.Rmd | 42 - PoPdesign-1.1.0/PoPdesign/inst/doc/vignette_for_PoP_design.html | 155 +-- PoPdesign-1.1.0/PoPdesign/man/get.boundary.pop.Rd | 6 PoPdesign-1.1.0/PoPdesign/man/get.oc.pop.Rd | 6 PoPdesign-1.1.0/PoPdesign/man/summary.pop.Rd | 4 PoPdesign-1.1.0/PoPdesign/vignettes/vignette_for_PoP_design.Rmd | 42 - 17 files changed, 284 insertions(+), 575 deletions(-)
Title: Estimate Bayesian Multilevel Models for Compositional Data
Description: Implement Bayesian Multilevel Modelling for compositional data
in a multilevel framework. Compute multilevel compositional data and
Isometric log ratio (ILR) at between and within-person levels,
fit Bayesian multilevel models for compositional predictors and outcomes,
and run post-hoc analyses such as isotemporal substitution models.
Author: Flora Le [aut, cre] ,
Joshua F. Wiley [aut]
Maintainer: Flora Le <13florale@gmail.com>
Diff between multilevelcoda versions 1.3.0 dated 2024-06-11 and 1.3.0.1 dated 2024-06-30
DESCRIPTION | 8 ++-- MD5 | 68 ++++++++++++++++++++-------------------- R/brmcoda-methods.R | 2 - R/brmcoda.R | 4 +- R/plot.R | 22 ++++++------ R/posterior.R | 32 +++++++----------- R/shiny.R | 3 + R/substitution-helpers.R | 2 - R/substitution.R | 2 - R/summary.R | 2 - R/update.R | 5 +- man/VarCorr.brmcoda.Rd | 2 - man/bayes_factor.brmcoda.Rd | 2 - man/brmcoda.Rd | 4 +- man/bsub.Rd | 2 - man/bsubmargins.Rd | 2 - man/coef.brmcoda.Rd | 2 - man/fitted.brmcoda.Rd | 2 - man/fixef.brmcoda.Rd | 2 - man/launch_shinystan.brmcoda.Rd | 3 + man/mcmc_plot.brmcoda.Rd | 6 +-- man/pairs.brmcoda.Rd | 8 ++-- man/plot.brmcoda.Rd | 6 +-- man/plot.substitution.Rd | 2 - man/predict.brmcoda.Rd | 2 - man/ranef.brmcoda.Rd | 2 - man/residuals.brmcoda.Rd | 2 - man/sub.Rd | 2 - man/submargins.Rd | 2 - man/substitution.Rd | 2 - man/summary.brmcoda.Rd | 2 - man/update.brmcoda.Rd | 5 +- man/vcov.brmcoda.Rd | 2 - man/wsub.Rd | 2 - man/wsubmargins.Rd | 2 - 35 files changed, 108 insertions(+), 110 deletions(-)
More information about multilevelcoda at CRAN
Permanent link
Title: Tidyverse-Friendly Introductory Linear Regression
Description: Datasets and wrapper functions for tidyverse-friendly introductory linear regression, used in "Statistical Inference via Data Science: A ModernDive into R and the Tidyverse" available at <https://moderndive.com/>.
Author: Albert Y. Kim [aut, cre] ,
Chester Ismay [aut] ,
Andrew Bray [ctb] ,
Delaney Moran [ctb],
Evgeni Chasnovski [ctb] ,
Will Hopper [ctb] ,
Benjamin S. Baumer [ctb] ,
Marium Tapal [ctb] ,
Wayne Ndlovu [ctb],
Catherine Peppers [ctb],
Annah Mutaya [ctb],
A [...truncated...]
Maintainer: Albert Y. Kim <albert.ys.kim@gmail.com>
Diff between moderndive versions 0.5.5 dated 2022-12-01 and 0.6.1 dated 2024-06-30
DESCRIPTION | 14 - MD5 | 50 ++- NAMESPACE | 2 NEWS.md | 149 ++++------- R/datasets.R | 71 +++++ R/geom_categorical_model.R | 7 R/geom_parallel_slopes.R | 4 R/moderndive.R | 2 R/rep_sample_n.R | 4 build/partial.rdb |binary build/vignette.rds |binary data/almonds_bowl.rda |only data/almonds_sample_100.rda |only data/early_january_2023_weather.rda |only data/early_january_weather.rda |binary data/envoy_flights.rda |only inst/CITATION | 29 +- inst/doc/moderndive.R | 22 - inst/doc/moderndive.html | 470 +++++++++++++++++------------------- inst/doc/paper.R | 4 man/almonds_bowl.Rd |only man/almonds_sample_100.Rd |only man/early_january_2023_weather.Rd |only man/early_january_weather.Rd | 2 man/envoy_flights.Rd |only man/geom_categorical_model.Rd | 56 +++- man/geom_parallel_slopes.Rd | 53 +++- man/moderndive.Rd | 64 ++++ man/reexports.Rd | 3 vignettes/paper.html | 18 - 30 files changed, 604 insertions(+), 420 deletions(-)
Title: Bayesian Seemingly Unrelated Regression Models in
High-Dimensional Settings
Description: Bayesian seemingly unrelated regression with general variable selection and dense/sparse covariance matrix. The sparse seemingly unrelated regression is described in Bottolo et al. (2021) <doi:10.1111/rssc.12490>, the software paper is in Zhao et al. (2021) <doi:10.18637/jss.v100.i11>, and the model with random effects is described in Zhao et al. (2024) <doi:10.1093/jrsssc/qlad102>.
Author: Marco Banterle [aut],
Zhi Zhao [aut, cre],
Leonardo Bottolo [ctb],
Sylvia Richardson [ctb],
Waldir Leoncio [ctb],
Alex Lewin [aut],
Manuela Zucknick [aut]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Diff between BayesSUR versions 2.2-0 dated 2024-06-13 and 2.2-1 dated 2024-06-30
DESCRIPTION | 10 ++--- MD5 | 16 ++++---- NEWS.md | 5 ++ R/BayesSUR.R | 1 README.md | 7 ++- build/vignette.rds |binary data/exampleGDSC.rda |binary inst/CITATION | 20 ++++++++++ src/SUR_Chain.cpp | 102 ++++++++++++++++++++++++++++----------------------- 9 files changed, 100 insertions(+), 61 deletions(-)
Title: Fitting the Metastatistical Extreme Value Distribution MEVD
Description: Extreme value analysis with the metastatistical extreme value distribution MEVD (Marani and Ignaccolo, 2015, <doi:10.1016/j.advwatres.2015.03.001>) and some of its variants. In particular, analysis can be performed with the simplified metastatistical extreme value distribution SMEV (Marra et al., 2019, <doi:10.1016/j.advwatres.2019.04.002>) and the temporal metastatistical extreme value distribution TMEV (Falkensteiner et al., 2023, <doi:10.1016/j.wace.2023.100601>). Parameters can be estimated with probability weighted moments, maximum likelihood and least squares. The data can also be left-censored prior to a fit. Density, distribution function, quantile function and random generation for the MEVD, SMEV and TMEV are included. In addition, functions for the calculation of return levels including confidence intervals are provided. For a description of use cases please see the provided references.
Author: Harald Schellander [aut, cre] ,
Alexander Lieb [ctb] ,
Marc-Andre Falkensteiner [ctb]
Maintainer: Harald Schellander <harald.schellander@geosphere.at>
Diff between mevr versions 1.0.0 dated 2024-06-15 and 1.1.1 dated 2024-06-30
DESCRIPTION | 10 - MD5 | 35 ++-- NAMESPACE | 6 NEWS |only R/mevr.R | 259 +++++++++++++++++++++----------- R/weibull_tail_test.R |only README.md |only man/censored_weibull_fit.Rd |only man/fmev.Rd | 2 man/fsmev.Rd | 38 ++++ man/ftmev.Rd | 2 man/pp.weibull.Rd | 2 man/predict.mevr.Rd | 2 man/weibull_tail_test.Rd |only tests/testthat.R | 24 +- tests/testthat/test-dtmev.R |only tests/testthat/test-fmev.R | 9 - tests/testthat/test-fsmev.R | 31 ++- tests/testthat/test-ftmev.R | 23 ++ tests/testthat/test-pp-weibull.R |only tests/testthat/test-print-mevr.R |only tests/testthat/test-qtmev.R |only tests/testthat/test-return-levels-mev.R |only tests/testthat/test-weibull-tail-test.R |only 24 files changed, 307 insertions(+), 136 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-05 0.0.9
2023-10-03 0.0.8
2023-08-11 0.0.5
2023-08-10 0.0.4