Title: Multiple Empirical Likelihood Tests
Description: Performs multiple empirical likelihood tests. It offers an
easy-to-use interface and flexibility in specifying hypotheses and
calibration methods, extending the framework to simultaneous
inferences. The core computational routines are implemented using the
'Eigen' 'C++' library and 'RcppEigen' interface, with 'OpenMP' for
parallel computation. Details of the testing procedures are provided
in Kim, MacEachern, and Peruggia (2023)
<doi:10.1080/10485252.2023.2206919>. A companion paper by Kim,
MacEachern, and Peruggia (2024) <doi:10.18637/jss.v108.i05> is
available for further information. This work was supported by the U.S.
National Science Foundation under Grants No. SES-1921523 and
DMS-2015552.
Author: Eunseop Kim [aut, cph, cre],
Steven MacEachern [ctb, ths],
Mario Peruggia [ctb, ths],
Pierre Chausse [rev],
Alex Stringer [rev]
Maintainer: Eunseop Kim <markean@pm.me>
Diff between melt versions 1.11.1 dated 2024-03-01 and 1.11.2 dated 2024-03-20
melt-1.11.1/melt/inst/doc/usage.R |only melt-1.11.1/melt/inst/doc/usage.Rmd |only melt-1.11.1/melt/inst/doc/usage.html |only melt-1.11.1/melt/vignettes/usage.Rmd |only melt-1.11.2/melt/DESCRIPTION | 6 +-- melt-1.11.2/melt/MD5 | 46 +++++++++++++---------------- melt-1.11.2/melt/NAMESPACE | 1 melt-1.11.2/melt/NEWS.md | 5 +++ melt-1.11.2/melt/R/confint-methods.R | 4 +- melt-1.11.2/melt/R/confreg-methods.R | 2 - melt-1.11.2/melt/R/el_eval.R | 4 +- melt-1.11.2/melt/R/el_glm.R | 2 - melt-1.11.2/melt/R/el_lm.R | 4 +- melt-1.11.2/melt/R/el_mean.R | 4 +- melt-1.11.2/melt/R/el_sd.R | 4 +- melt-1.11.2/melt/R/eld-methods.R | 6 +-- melt-1.11.2/melt/R/elmt-methods.R | 2 - melt-1.11.2/melt/R/elt-methods.R | 8 ++--- melt-1.11.2/melt/R/melt-package.R | 1 melt-1.11.2/melt/build/partial.rdb |binary melt-1.11.2/melt/build/vignette.rds |binary melt-1.11.2/melt/inst/doc/article.Rnw | 9 +---- melt-1.11.2/melt/inst/doc/article.pdf |binary melt-1.11.2/melt/inst/doc/model.html | 2 - melt-1.11.2/melt/inst/doc/performance.html | 26 ++++++++-------- melt-1.11.2/melt/vignettes/article.Rnw | 9 +---- 26 files changed, 69 insertions(+), 76 deletions(-)
Title: Plotting Decision Curve Analysis with Coloured Bars
Description: Decision curve analysis is a method for evaluating and comparing prediction models that incorporates clinical consequences, requires only the data set on which the models are tested, and can be applied to models that have either continuous or dichotomous results. The 'ggscidca' package adds coloured bars of discriminant relevance to the traditional decision curve. Improved practicality and aesthetics. This method was described by Balachandran VP (2015) <doi:10.1016/S1470-2045(14)71116-7>.
Author: Qiang Liu [aut, cre]
Maintainer: Qiang Liu <dege857@163.com>
Diff between ggscidca versions 0.1.9 dated 2024-03-13 and 0.2.0 dated 2024-03-20
DESCRIPTION | 8 ++++---- MD5 | 21 +++++++++++++++------ NAMESPACE | 4 ++++ R/cmprskstdca.R |only R/df_surv.R |only R/getplot.R | 2 +- R/modeldata.R | 16 ++++++++++++++-- R/newcrr.R |only R/scidca.R | 14 +++++++++++++- R/scidcacrr.R |only data/df_surv.rda |only man/cmprskstdca.Rd |only man/df_surv.Rd |only man/newcrr.Rd |only man/scidca.Rd | 14 +++++++++++++- man/scidca.crr.Rd |only 16 files changed, 64 insertions(+), 15 deletions(-)
Title: Additional Functions for Model Tuning
Description: The ability to tune models is important. 'finetune' enhances
the 'tune' package by providing more specialized methods for finding
reasonable values of model tuning parameters. Two racing methods
described by Kuhn (2014) <arXiv:1405.6974> are included. An iterative
search method using generalized simulated annealing (Bohachevsky,
Johnson and Stein, 1986) <doi:10.1080/00401706.1986.10488128> is also
included.
Author: Max Kuhn [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between finetune versions 1.1.0 dated 2023-04-19 and 1.2.0 dated 2024-03-20
DESCRIPTION | 10 - MD5 | 70 +++---- NAMESPACE | 1 NEWS.md | 26 ++ R/control_race.R | 4 R/control_sim_anneal.R | 6 R/finetune-package.R | 4 R/plot_race.R | 23 ++ R/racing_helpers.R | 116 +++++++++++-- R/sim_anneal_helpers.R | 35 +++ R/tune_race_anova.R | 267 ++++++++++++++++++------------ R/tune_race_win_loss.R | 228 +++++++++++++++---------- R/tune_sim_anneal.R | 172 ++++++++++++++----- README.md | 11 + build/partial.rdb |binary inst/WORDLIST | 2 man/collect_predictions.Rd | 20 +- man/show_best.Rd | 28 ++- man/tune_race_anova.Rd | 21 ++ man/tune_race_win_loss.Rd | 92 ++++++---- man/tune_sim_anneal.Rd | 20 ++ tests/testthat/_snaps/anova-filter.md | 6 tests/testthat/_snaps/anova-overall.md | 4 tests/testthat/_snaps/race-control.md | 4 tests/testthat/_snaps/sa-control.md | 8 tests/testthat/_snaps/sa-misc.md | 8 tests/testthat/_snaps/sa-overall.md | 79 +++++--- tests/testthat/_snaps/win-loss-overall.md | 11 + tests/testthat/test-anova-filter.R | 2 tests/testthat/test-anova-overall.R | 18 +- tests/testthat/test-race-s3.R | 3 tests/testthat/test-sa-decision.R | 4 tests/testthat/test-sa-overall.R | 75 +++++++- tests/testthat/test-sa-perturb.R | 8 tests/testthat/test-win-loss-filter.R | 2 tests/testthat/test-win-loss-overall.R | 8 36 files changed, 972 insertions(+), 424 deletions(-)
Title: Joint Longitudinal and Survival Model for Big Data
Description: Provides analysis tools for big data where the sample size is very large. It offers
a suite of functions for fitting and predicting joint models, which allow for the simultaneous
analysis of longitudinal and time-to-event data. This statistical methodology is particularly
useful in medical research where there is often interest in understanding the relationship
between a longitudinal biomarker and a clinical outcome, such as survival or disease progression.
This can be particularly useful in a clinical setting where it is important to be able to predict
how a patient's health status may change over time. Overall, this package provides a
comprehensive set of tools for joint modeling of BIG data obtained as survival and
longitudinal outcomes with both Bayesian and non-Bayesian approaches. Its versatility
and flexibility make it a valuable resource for researchers in many different fields,
particularly in the medical and health sciences.
Author: Atanu Bhattacharjee [aut, cre, ctb],
Bhrigu Kumar Rajbongshi [aut, ctb],
Gajendra K Vishwakarma [aut, ctb]
Maintainer: Atanu Bhattacharjee <atanustat@gmail.com>
Diff between jmBIG versions 0.1.1 dated 2023-10-29 and 0.1.2 dated 2024-03-20
DESCRIPTION | 10 +- MD5 | 44 +++++---- NAMESPACE | 7 + R/jmbayesBig.R | 2 R/jmcsBig.R | 46 ---------- R/jmstanBig.R | 2 R/joineRMLBig.R | 2 R/prediction.R | 208 +++++++++++++++++++++++++++++++++++++++++----- R/print.R | 31 ++++++ man/cisurvfitJMCS.Rd |only man/jmbayesBig.Rd | 2 man/jmcsBig.Rd | 5 - man/jmstanBig.Rd | 2 man/joinRMLBig.Rd | 2 man/plot_cisurvfitJMCS.Rd |only man/postSurvfit.Rd | 2 man/postTraj.Rd | 4 man/predJMbayes.Rd | 6 - man/predJRML.Rd | 8 - man/print.jmbayesBig.Rd | 2 man/print.jmcsBig.Rd | 2 man/print.jmstanBig.Rd | 2 man/print.joinRMLBig.Rd | 2 man/survfitJMCS.Rd | 20 ++-- 24 files changed, 287 insertions(+), 124 deletions(-)
Title: 'GeoNetwork' API R Interface
Description: Provides an R interface to the 'GeoNetwork' API (<https://geonetwork-opensource.org/#api>) allowing to upload and publish metadata in a 'GeoNetwork' web-application and expose it to OGC CSW.
Author: Emmanuel Blondel [aut, cre]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between geonapi versions 0.7 dated 2023-07-10 and 0.7-1 dated 2024-03-20
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS.md | 9 +++++++-- R/GNManager.R | 1 + R/GNOpenAPIManager.R | 2 +- README.md | 3 ++- 7 files changed, 23 insertions(+), 15 deletions(-)
Title: Occurrence Data Cleaning
Description: Flags and checks occurrence data that are in Darwin Core
format. The package includes generic functions and data as well as
some that are specific to bees. This package is meant to build upon
and be complimentary to other excellent occurrence cleaning packages,
including 'bdc' and 'CoordinateCleaner'. This package uses datasets
from several sources and particularly from the Discover Life Website,
created by Ascher and Pickering (2020). For further information,
please see the original publication and package website. Publication
- Dorey et al. (2023) <doi:10.1101/2023.06.30.547152> and package
website - Dorey et al. (2023) <https://github.com/jbdorey/BeeBDC>.
Author: James B. Dorey [aut, cre, cph]
,
Robert L. O'Reilly [aut] ,
Silas Bossert [aut] ,
Erica E. Fischer [aut]
Maintainer: James B. Dorey <jbdorey@me.com>
Diff between BeeBDC versions 1.0.4 dated 2024-02-13 and 1.1.0 dated 2024-03-20
DESCRIPTION | 10 MD5 | 43 - NAMESPACE | 1 NEWS.md | 18 R/beesTaxonomy.R | 4 R/dateFindR.R | 95 ++- R/dupeSummary.R | 6 R/harmoniseR.R | 3 R/interactiveMapR.R | 21 R/plotFlagSummary.R | 8 R/taxadbToBeeBDC.R |only R/taxoDuplicator.R | 2 README.md | 29 inst/BeeBDC_fullWorkflow.R | 24 inst/doc/BeeBDC_main.Rmd | 18 inst/doc/BeeBDC_main.html | 1092 +++++++++++++++++------------------ inst/doc/basic_workflow.html | 6 man/beesTaxonomy.Rd | 5 man/dupeSummary.Rd | 5 man/harmoniseR.Rd | 4 man/taxadbToBeeBDC.Rd |only tests/testthat/test-dateFindR.R | 68 ++ tests/testthat/test-taxadbToBeeBDC.R |only vignettes/BeeBDC_main.Rmd | 18 24 files changed, 841 insertions(+), 639 deletions(-)
Title: Tune Random Forest of the 'ranger' Package
Description: Tuning random forest with one line. The package is mainly based on the packages 'ranger' and 'mlrMBO'.
Author: Philipp Probst [aut, cre],
Simon Klau [ctb]
Maintainer: Philipp Probst <philipp_probst@gmx.de>
Diff between tuneRanger versions 0.5 dated 2019-04-16 and 0.7 dated 2024-03-20
DESCRIPTION | 13 - MD5 | 38 +-- NAMESPACE | 71 +++--- R/RLearner_classif_tuneMtryFast.R | 94 ++++---- R/RLearner_classif_tuneRanger.R | 110 ++++----- R/RLearner_regr_tuneMtryFast.R | 94 ++++---- R/RLearner_regr_tuneRanger.R | 66 ++--- R/RLearner_surv_tuneMtryFast.R | 94 ++++---- R/estimateTimeTuneRanger.R | 80 +++---- R/restartTuneRanger.R | 116 +++++----- R/tuneMtryFast.R | 178 +++++++-------- R/tuneRanger.R | 432 +++++++++++++++++++------------------- README.md | 166 +++++++------- inst/CITATION | 30 +- man/estimateTimeTuneRanger.Rd | 63 ++--- man/restartTuneRanger.Rd | 91 +++----- man/tuneMtryFast.Rd | 115 +++++----- man/tuneRanger.Rd | 172 +++++++-------- tests/testthat.R | 8 tests/testthat/test_base.R | 96 ++++---- 20 files changed, 1070 insertions(+), 1057 deletions(-)
Title: Fitting Survival Regression Models via 'Stan'
Description: Parametric survival regression models under the maximum likelihood approach via 'Stan'. Implemented regression models include accelerated failure time models, proportional hazards models, proportional odds models, accelerated hazard models, Yang and Prentice models, and extended hazard models. Available baseline survival distributions include exponential, Weibull, log-normal, log-logistic, gamma, generalized gamma, rayleigh, Gompertz and fatigue (Birnbaum-Saunders) distributions. References: Lawless (2002) <ISBN:9780471372158>; Bennett (1982) <doi:10.1002/sim.4780020223>; Chen and Wang(2000) <doi:10.1080/01621459.2000.10474236>; Demarqui and Mayrink (2021) <doi:10.1214/20-BJPS471>.
Author: Fabio Demarqui [aut, cre, cph]
,
Andrew Johnson [ctb]
Maintainer: Fabio Demarqui <fndemarqui@est.ufmg.br>
Diff between survstan versions 0.0.6.1 dated 2024-02-05 and 0.0.7 dated 2024-03-20
DESCRIPTION | 8 MD5 | 64 - NAMESPACE | 12 NEWS.md | 6 R/aftreg.R | 20 R/ahreg.R | 16 R/bootstrap.R | 17 R/cross_time.R | 29 R/dists.R | 3 R/ehreg.R | 19 R/emmeans.R | 37 R/ggprentice.R |only R/ggstacy.R |only R/gompertz.R |only R/phreg.R | 16 R/poreg.R | 16 R/summary.R | 36 R/survfit.R | 17 R/utils.R | 66 + R/ypreg.R | 20 README.md | 87 ++ build/partial.rdb |binary inst/doc/LRT.R | 8 inst/doc/LRT.Rmd | 8 inst/doc/LRT.html | 79 +- inst/doc/survstan.Rmd | 4 inst/doc/survstan.html | 7 inst/stan/chunks/baselines.stan | 73 + inst/stan/survreg.stan | 48 + man/Gompertz.Rd |only man/emmeans-survstan-helpers.Rd | 5 man/ggprentice.Rd |only man/ggstacy.Rd |only src/stanExports_survreg.h | 1558 +++++++++++++++++++++++++++------------- vignettes/LRT.Rmd | 8 vignettes/survstan.Rmd | 4 36 files changed, 1652 insertions(+), 639 deletions(-)
Title: Create Regular Expressions Easily
Description: Build regular expressions using grammar and functionality inspired
by <https://github.com/VerbalExpressions>. Usage of the %>% is encouraged to
build expressions in a chain-like fashion.
Author: Tyler Littlefield [aut, cre] ,
Dmytro Perepolkin [ctb]
Maintainer: Tyler Littlefield <tylurp1@gmail.com>
Diff between RVerbalExpressions versions 0.1.0 dated 2019-11-06 and 0.1.1 dated 2024-03-20
DESCRIPTION | 13 -- MD5 | 20 +-- NEWS.md | 5 README.md | 51 ++++---- build/vignette.rds |binary inst/doc/examples.R | 14 +- inst/doc/examples.html | 271 +++++++++++++++++++++++++------------------- man/rx_line_break.Rd | 2 man/rx_space.Rd | 2 man/rx_tab.Rd | 2 tests/testthat/test-avoid.R | 9 - 11 files changed, 218 insertions(+), 171 deletions(-)
More information about RVerbalExpressions at CRAN
Permanent link
Title: Linked Inference of Genomic Experimental Relationships
Description: Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) <doi:10.1016/j.cell.2019.05.006>, and Liu J, Gao C, Sodicoff J, et al (2020) <doi:10.1038/s41596-020-0391-8> for more details.
Author: Joshua Welch [aut],
Yichen Wang [aut, cre],
Chao Gao [aut],
Jialin Liu [aut],
Joshua Sodicoff [aut, ctb],
Velina Kozareva [aut, ctb],
Evan Macosko [aut, ctb],
Paul Hoffman [ctb],
Ilya Korsunsky [ctb],
Robert Lee [ctb],
Andrew Robbins [ctb]
Maintainer: Yichen Wang <wayichen@umich.edu>
Diff between rliger versions 1.0.1 dated 2023-11-08 and 2.0.0 dated 2024-03-20
rliger-1.0.1/rliger/R/rliger.R |only rliger-1.0.1/rliger/R/utilities.R |only rliger-1.0.1/rliger/data/ctrl.rda |only rliger-1.0.1/rliger/data/stim.rda |only rliger-1.0.1/rliger/inst/include |only rliger-1.0.1/rliger/man/calcAlignmentPerCluster.Rd |only rliger-1.0.1/rliger/man/calcGeneVars.Rd |only rliger-1.0.1/rliger/man/calcNormLoadings.Rd |only rliger-1.0.1/rliger/man/getGeneValues.Rd |only rliger-1.0.1/rliger/man/liger-demodata.Rd |only rliger-1.0.1/rliger/man/louvainCluster.Rd |only rliger-1.0.1/rliger/man/makeInteractTrack.Rd |only rliger-1.0.1/rliger/man/makeRiverplot.Rd |only rliger-1.0.1/rliger/man/online_iNMF.Rd |only rliger-1.0.1/rliger/man/optimizeALS.Rd |only rliger-1.0.1/rliger/man/plotByDatasetAndCluster.Rd |only rliger-1.0.1/rliger/man/plotClusterFactors.Rd |only rliger-1.0.1/rliger/man/plotClusterProportions.Rd |only rliger-1.0.1/rliger/man/plotFactors.Rd |only rliger-1.0.1/rliger/man/plotFeature.Rd |only rliger-1.0.1/rliger/man/plotGene.Rd |only rliger-1.0.1/rliger/man/plotGeneViolin.Rd |only rliger-1.0.1/rliger/man/plotGenes.Rd |only rliger-1.0.1/rliger/man/plotWordClouds.Rd |only rliger-1.0.1/rliger/man/quantile_norm.Rd |only rliger-1.0.1/rliger/man/removeMissingObs.Rd |only rliger-1.0.1/rliger/man/reorganizeLiger.Rd |only rliger-1.0.1/rliger/man/restoreOnlineLiger.Rd |only rliger-1.0.1/rliger/man/runWilcoxon.Rd |only rliger-1.0.1/rliger/man/seuratToLiger.Rd |only rliger-1.0.1/rliger/man/show-methods.Rd |only rliger-1.0.1/rliger/man/suggestK.Rd |only rliger-1.0.1/rliger/man/suggestLambda.Rd |only rliger-1.0.1/rliger/src/entities.h |only rliger-1.0.1/rliger/src/factorization.h |only rliger-1.0.1/rliger/src/fast_wilcox.cpp |only rliger-1.0.1/rliger/src/ls.h |only rliger-1.0.1/rliger/src/mask.h |only rliger-1.0.1/rliger/src/matrix.h |only rliger-1.0.1/rliger/src/nnls.h |only rliger-1.0.1/rliger/src/parameters.h |only rliger-1.0.1/rliger/src/run_nmf.cpp |only rliger-1.0.1/rliger/src/vector.h |only rliger-1.0.1/rliger/tests/testdata |only rliger-1.0.1/rliger/tests/testthat/test_post_factorization.R |only rliger-2.0.0/rliger/DESCRIPTION | 59 - 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Title: Estimate Ensemble Bayesian Model Averaging Forecasts using Gibbs
Sampling or EM-Algorithms
Description: Create forecasts from multiple predictions using ensemble Bayesian model averaging (EBMA). EBMA models can be estimated using an expectation maximization (EM) algorithm or as fully Bayesian models via Gibbs sampling. The methods in this package are Montgomery, Hollenbach, and Ward (2015) <doi:10.1016/j.ijforecast.2014.08.001> and Montgomery, Hollenbach, and Ward (2012) <doi:10.1093/pan/mps002>.
Author: Florian M. Hollenbach [aut, cre]
,
Jacob M. Montgomery [aut],
Michael D. Ward [aut]
Maintainer: Florian M. Hollenbach <fho.egb@cbs.dk>
Diff between EBMAforecast versions 1.0.31 dated 2023-11-10 and 1.0.32 dated 2024-03-20
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/fitEnsembleLogit.R | 4 ++-- R/fitEnsembleNormal.R | 4 ++-- build/partial.rdb |binary tests/testthat/Rplots.pdf |binary 6 files changed, 13 insertions(+), 13 deletions(-)
Title: Modern Database Engine for Multi-Modal Data via Sparse and Dense
Multidimensional Arrays
Description: The modern database 'TileDB' introduces a powerful on-disk
format for multi-modal data based on dimensional arrays. It supports
dense and sparse arrays, dataframes and key-values stores, cloud
storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression,
encryption and checksum filters, uses a fully multi-threaded
implementation, supports parallel I/O, data versioning ('time
travel'), metadata and groups. It is implemented as an embeddable
cross-platform C++ library with APIs from several languages, and
integrations.
Author: TileDB, Inc. [aut, cph],
Dirk Eddelbuettel [cre]
Maintainer: Dirk Eddelbuettel <dirk@tiledb.com>
Diff between tiledb versions 0.24.0 dated 2024-02-22 and 0.25.0 dated 2024-03-20
DESCRIPTION | 10 MD5 | 101 +++--- NAMESPACE | 3 NEWS.md | 31 + R/Array.R | 17 - R/ArrowIO.R | 18 - R/Attribute.R | 11 R/Object.R | 34 +- R/Query.R | 4 R/RcppExports.R | 4 R/TileDBArray.R | 12 README.md | 2 build/vignette.rds |binary inst/include/tiledb.h | 2 inst/tinytest/test_arrayschema.R | 37 -- inst/tinytest/test_arrayschemaevolution.R | 1 inst/tinytest/test_arrowio.R | 3 inst/tinytest/test_attr.R | 38 +- inst/tinytest/test_ctx.R | 3 inst/tinytest/test_dataframe.R | 3 inst/tinytest/test_datetime.R | 3 inst/tinytest/test_dim.R | 3 inst/tinytest/test_dimsubset.R | 3 inst/tinytest/test_domain.R | 3 inst/tinytest/test_filestore.R | 3 inst/tinytest/test_filterlist.R | 3 inst/tinytest/test_fragmentinfo.R | 2 inst/tinytest/test_group.R | 20 + inst/tinytest/test_libtiledb.R | 3 inst/tinytest/test_matrix.R | 3 inst/tinytest/test_metadata.R | 3 inst/tinytest/test_misc.R | 3 inst/tinytest/test_query.R | 22 + inst/tinytest/test_querycondition.R | 13 inst/tinytest/test_sparsematrix.R | 3 inst/tinytest/test_tiledbarray.R | 18 - inst/tinytest/test_timetravel.R | 7 inst/tinytest/test_vfs.R | 3 man/tiledb-package.Rd | 1 man/tiledb_array_upgrade_version.Rd |only man/tiledb_object_walk.Rd | 8 man/tiledb_query_get_range.Rd | 11 man/tiledb_query_get_range_var.Rd |only src/Makevars.win | 2 src/RcppExports.cpp | 16 src/arrowio.cpp | 131 ++++---- src/libtiledb.cpp | 69 ++-- src/libtiledb.h | 1 src/nanoarrow.c | 170 +++++----- src/nanoarrow.h | 491 +++++++++++++++++++++--------- src/nanoarrow.hpp |only tools/ci/valgrind/installDependencies.sh | 2 tools/tiledbVersion.txt | 4 53 files changed, 830 insertions(+), 528 deletions(-)
Title: Visualize Simon's Two-Stage Design
Description: To visualize the probabilities of early
termination, fail and success of Simon's two-stage
design. To evaluate and visualize the operating
characteristics of Simon's two-stage design.
Author: Tingting Zhan [aut, cre, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between VisualizeSimon2Stage versions 0.1.2 dated 2023-10-19 and 0.1.3 dated 2024-03-20
VisualizeSimon2Stage-0.1.2/VisualizeSimon2Stage/R/VisualizeSimon2Stage_info.R |only VisualizeSimon2Stage-0.1.2/VisualizeSimon2Stage/man/Simon_oc-class.Rd |only VisualizeSimon2Stage-0.1.2/VisualizeSimon2Stage/man/Simon_pr-class.Rd |only VisualizeSimon2Stage-0.1.3/VisualizeSimon2Stage/DESCRIPTION | 30 +++++----- VisualizeSimon2Stage-0.1.3/VisualizeSimon2Stage/MD5 | 29 ++++----- VisualizeSimon2Stage-0.1.3/VisualizeSimon2Stage/NAMESPACE | 11 +++ VisualizeSimon2Stage-0.1.3/VisualizeSimon2Stage/NEWS.md | 2 VisualizeSimon2Stage-0.1.3/VisualizeSimon2Stage/R/0info.R |only VisualizeSimon2Stage-0.1.3/VisualizeSimon2Stage/R/Simon_oc.R | 26 ++++++-- VisualizeSimon2Stage-0.1.3/VisualizeSimon2Stage/R/Simon_pr.R | 21 ++++--- VisualizeSimon2Stage-0.1.3/VisualizeSimon2Stage/R/ph2simon_etc.R | 22 +++++-- VisualizeSimon2Stage-0.1.3/VisualizeSimon2Stage/build/partial.rdb |binary VisualizeSimon2Stage-0.1.3/VisualizeSimon2Stage/inst |only VisualizeSimon2Stage-0.1.3/VisualizeSimon2Stage/man/Simon_oc.Rd | 19 +++++- VisualizeSimon2Stage-0.1.3/VisualizeSimon2Stage/man/Simon_pr.Rd | 16 +++++ VisualizeSimon2Stage-0.1.3/VisualizeSimon2Stage/man/Sprintf.ph2simon.Rd | 2 VisualizeSimon2Stage-0.1.3/VisualizeSimon2Stage/man/VisualizeSimon2Stage-package.Rd | 6 +- VisualizeSimon2Stage-0.1.3/VisualizeSimon2Stage/man/summary.ph2simon.Rd | 2 18 files changed, 125 insertions(+), 61 deletions(-)
More information about VisualizeSimon2Stage at CRAN
Permanent link
Title: Tidy Tuning Tools
Description: The ability to tune models is important. 'tune' contains
functions and classes to be used in conjunction with other
'tidymodels' packages for finding reasonable values of
hyper-parameters in models, pre-processing methods, and
post-processing steps.
Author: Max Kuhn [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between tune versions 1.1.2 dated 2023-08-23 and 1.2.0 dated 2024-03-20
DESCRIPTION | 28 MD5 | 209 +++-- NAMESPACE | 32 NEWS.md | 59 + R/0_imports.R | 78 -- R/augment.R | 58 - R/checks.R | 89 +- R/collect.R | 221 ++++- R/compat-dplyr.R | 18 R/compat-vctrs-helpers.R | 6 R/compute_metrics.R |only R/conf_mat_resampled.R | 4 R/control.R | 13 R/fit_best.R | 43 - R/grid_code_paths.R | 186 +++- R/grid_helpers.R | 110 ++ R/grid_performance.R | 89 ++ R/int_pctl.R |only R/iteration_results.R | 35 R/last_fit.R | 95 ++ R/load_ns.R | 9 R/logging.R | 15 R/merge.R | 1 R/metric-selection.R |only R/parallel.R | 11 R/plots.R | 163 +++- R/predict.R |only R/pull.R | 24 R/reexports.R | 4 R/resample.R | 22 R/resample_results.R | 32 R/select_best.R | 258 ++---- R/standalone-survival.R |only R/tune_bayes.R | 187 +++- R/tune_grid.R | 44 - R/tune_results.R | 33 R/utils.R | 55 + R/zzz.R | 8 README.md | 2 inst/WORDLIST | 45 - inst/event_time_analysis.Rmd |only inst/event_time_analysis.pdf |only inst/test_objects.R | 56 + inst/test_objects.Rout | 773 +++++--------------- man/augment.tune_results.Rd | 10 man/autoplot.tune_results.Rd | 11 man/choose_metric.Rd |only man/collect_predictions.Rd | 62 + man/compute_metrics.Rd |only man/conf_mat_resampled.Rd | 4 man/control_bayes.Rd | 27 man/control_grid.Rd | 19 man/empty_ellipses.Rd | 26 man/fit_best.Rd | 58 + man/fit_resamples.Rd | 75 + man/get_metric_time.Rd |only man/int_pctl.tune_results.Rd |only man/last_fit.Rd | 98 ++ man/load_pkgs.Rd | 2 man/reexports.Rd | 8 man/show_best.Rd | 28 man/tune_accessor.Rd | 9 man/tune_bayes.Rd | 94 ++ man/tune_grid.Rd | 85 ++ tests/testthat/Rplots.pdf |only tests/testthat/_snaps/augment.md | 14 tests/testthat/_snaps/autoplot.md | 22 tests/testthat/_snaps/bayes.md | 78 +- tests/testthat/_snaps/censored-reg.md |only tests/testthat/_snaps/checks.md | 11 tests/testthat/_snaps/collect.md | 92 +- tests/testthat/_snaps/compute_metrics.md |only tests/testthat/_snaps/conf-mat-resampled.md | 9 tests/testthat/_snaps/eval-time-args.md |only tests/testthat/_snaps/eval-time-single-selection.md |only tests/testthat/_snaps/finalization.md | 2 tests/testthat/_snaps/fit_best.md | 24 tests/testthat/_snaps/int_pctl.md |only tests/testthat/_snaps/last-fit.md | 17 tests/testthat/_snaps/metric-args.md |only tests/testthat/_snaps/metric-single-selection.md |only tests/testthat/_snaps/notes.md | 59 - tests/testthat/_snaps/predict.md |only tests/testthat/_snaps/resample.md | 4 tests/testthat/_snaps/select_best.md | 663 +++++++++++++++-- tests/testthat/data/knn_gp.rds |binary tests/testthat/data/knn_grid.rds |binary tests/testthat/data/knn_results.rds |binary tests/testthat/data/knn_set.rds |binary tests/testthat/data/lm_bayes.rds |binary tests/testthat/data/lm_resamples.rds |binary tests/testthat/data/rcv_results.rds |binary tests/testthat/data/surv_boost_tree_res.rds |only tests/testthat/data/svm_reg_results.rds |binary tests/testthat/data/svm_results.rds |binary tests/testthat/data/test_objects.RData |binary tests/testthat/test-GP.R | 12 tests/testthat/test-augment.R | 43 + tests/testthat/test-autoplot.R | 145 +++ tests/testthat/test-bayes.R | 59 + tests/testthat/test-censored-reg.R |only tests/testthat/test-checks.R | 44 - tests/testthat/test-collect.R | 137 +++ tests/testthat/test-compute_metrics.R |only tests/testthat/test-conf-mat-resampled.R | 8 tests/testthat/test-estimate.R | 36 tests/testthat/test-eval-time-args.R |only tests/testthat/test-eval-time-single-selection.R |only tests/testthat/test-extract.R | 19 tests/testthat/test-fit_best.R | 21 tests/testthat/test-grid.R | 220 +++++ tests/testthat/test-int_pctl.R |only tests/testthat/test-last-fit.R | 19 tests/testthat/test-metric-args.R |only tests/testthat/test-metric-single-selection.R |only tests/testthat/test-misc.R | 6 tests/testthat/test-notes.R | 16 tests/testthat/test-predict.R |only tests/testthat/test-resample.R | 4 tests/testthat/test-select_best.R | 264 +++++- 120 files changed, 4138 insertions(+), 1641 deletions(-)
Title: Warping Landmark Configurations
Description: Compute bending energies, principal warps, partial warp scores, and the non-affine component of shape variation for 2D landmark configurations, as well as Mardia-Dryden distributions and self-similar distributions of landmarks, as described in Mitteroecker et al. (2020) <doi:10.1093/sysbio/syaa007>. Working examples to decompose shape variation into small-scale and large-scale components, and to decompose the total shape variation into outline and residual shape components are provided. Two landmark datasets are provided, that quantify skull morphology in humans and papionin primates, respectively from Mitteroecker et al. (2020) <doi:10.5061/dryad.j6q573n8s> and Grunstra et al. (2020) <doi:10.5061/dryad.zkh189373>.
Author: Anne Le Maitre [aut, cre] ,
Silvester Bartsch [aut],
Nicole Grunstra [aut],
Philipp Mitteroecker [aut]
Maintainer: Anne Le Maitre <anne.le.maitre@univie.ac.at>
Diff between prWarp versions 1.0.0 dated 2020-11-02 and 1.0.1 dated 2024-03-20
DESCRIPTION | 10 MD5 | 35 - NEWS |only R/HomoMidSag-dataset.R | 4 R/papionin-dataset.R | 21 R/tps.all.R | 6 build/vignette.rds |binary inst/CITATION | 19 inst/doc/prWarp-homo-example.R | 8 inst/doc/prWarp-homo-example.Rmd | 14 inst/doc/prWarp-homo-example.html | 492 +++++++++++---- inst/doc/prWarp-papionin-example.R | 18 inst/doc/prWarp-papionin-example.Rmd | 22 inst/doc/prWarp-papionin-example.html | 1093 +++++++++++++++++++++------------- man/HomoMidSag.Rd | 4 man/papionin.Rd | 21 man/tps.all.Rd | 6 vignettes/prWarp-homo-example.Rmd | 14 vignettes/prWarp-papionin-example.Rmd | 22 19 files changed, 1195 insertions(+), 614 deletions(-)
Title: Load US Census Boundary and Attribute Data as 'tidyverse' and
'sf'-Ready Data Frames
Description: An integrated R interface to several United States Census Bureau
APIs (<https://www.census.gov/data/developers/data-sets.html>) and the US Census Bureau's
geographic boundary files. Allows R users to return Census and ACS data as
tidyverse-ready data frames, and optionally returns a list-column with feature geometry for mapping
and spatial analysis.
Author: Kyle Walker [aut, cre],
Matt Herman [aut],
Kris Eberwein [ctb]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between tidycensus versions 1.6.2 dated 2024-03-05 and 1.6.3 dated 2024-03-20
DESCRIPTION | 8 +- MD5 | 10 +-- NEWS.md | 4 + R/estimates.R | 144 ++++++++++++++++++++++++++++++++++----------------- R/zzz.r | 1 man/get_estimates.Rd | 19 ++++-- 6 files changed, 122 insertions(+), 64 deletions(-)
Title: Tidy Dataframes and Expressions with Statistical Details
Description: Utilities for producing dataframes with rich details for the
most common types of statistical approaches and tests: parametric,
nonparametric, robust, and Bayesian t-test, one-way ANOVA, correlation
analyses, contingency table analyses, and meta-analyses. The
functions are pipe-friendly and provide a consistent syntax to work
with tidy data. These dataframes additionally contain expressions with
statistical details, and can be used in graphing packages. This
package also forms the statistical processing backend for
'ggstatsplot'. References: Patil (2021) <doi:10.21105/joss.03236>.
Author: Indrajeet Patil [cre, aut, cph]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between statsExpressions versions 1.5.3 dated 2024-01-13 and 1.5.4 dated 2024-03-20
DESCRIPTION | 20 +- MD5 | 97 +++++------ NAMESPACE | 3 NEWS.md | 17 + R/add-expression-col.R | 28 +-- R/centrality-description.R | 4 R/contingency-table.R | 74 +------- R/corr-test.R | 4 R/globals.R | 5 R/meta-analysis.R | 4 R/one-sample-test.R | 5 R/oneway-anova.R | 20 +- R/pairwise-comparisons.R | 8 R/reexports.R | 46 ++--- R/statsExpressions-package.R | 59 +++--- R/tidy-model-expressions.R | 4 R/two-sample-test.R | 14 - README.md | 2 build/vignette.rds |binary inst/WORDLIST | 1 man/add_expression_col.Rd | 15 - man/centrality_description.Rd | 10 - man/contingency_table.Rd | 146 ++++++++++------ man/corr_test.Rd | 10 - man/examples/examples-contingency-table.R |only man/figures/README-anova_parametric2-1.png |binary man/figures/README-centrality-1.png |binary man/figures/README-gof-1.png |binary man/meta_analysis.Rd | 10 - man/one_sample_test.Rd | 10 - man/oneway_anova.Rd | 10 - man/pairwise_comparisons.Rd | 10 - man/reexports.Rd | 3 man/tidy_model_expressions.Rd | 10 - man/two_sample_test.Rd | 10 - tests/testthat/_snaps/contingency-table.md | 24 +- tests/testthat/helper.R | 1 tests/testthat/test-centrality-description.R | 4 tests/testthat/test-contingency-table.R | 12 - tests/testthat/test-corr-test.R | 10 - tests/testthat/test-meta-random-bayes.R | 2 tests/testthat/test-one-sample.R | 14 - tests/testthat/test-oneway-anova-parametric.R | 8 tests/testthat/test-oneway-anova-robust.R | 6 tests/testthat/test-pairwise-comparisons.R | 16 - tests/testthat/test-tidy-model-expressions.R | 216 ++++++++++++------------- tests/testthat/test-two-sample-nonparametric.R | 4 tests/testthat/test-two-sample-parametric.R | 8 tests/testthat/test-two-sample-robust.R | 8 vignettes/web_only/dataframe_outputs.Rmd | 71 -------- 50 files changed, 517 insertions(+), 546 deletions(-)
More information about statsExpressions at CRAN
Permanent link
Title: Rendering Parameterized SQL and Translation to Dialects
Description: A rendering tool for parameterized SQL that also translates into
different SQL dialects. These dialects include 'Microsoft SQL Server', 'Oracle',
'PostgreSql', 'Amazon RedShift', 'Apache Impala', 'IBM Netezza', 'Google BigQuery', 'Microsoft PDW', 'Snowflake',
'Azure Synapse Analytics Dedicated', 'Apache Spark', and 'SQLite'.
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between SqlRender versions 1.16.1 dated 2023-10-07 and 1.17.0 dated 2024-03-20
DESCRIPTION | 8 MD5 | 154 NAMESPACE | 62 NEWS.md | 1146 +++--- R/HelperFunctions.R | 1222 +++--- R/RenderSql.R | 664 +-- R/ShinyApps.R | 112 R/SparkSql.R | 76 R/SqlRender.R | 86 README.md | 314 - build/vignette.rds |binary inst/csv/jarChecksum.txt | 2 inst/csv/replacementPatterns.csv | 2713 +++++++------- inst/csv/supportedDialects.csv | 32 inst/doc/UsingSqlRender.R | 228 - inst/doc/UsingSqlRender.Rmd | 914 ++-- inst/doc/UsingSqlRender.pdf |binary inst/shinyApps/SqlDeveloper/server.R | 148 inst/shinyApps/SqlDeveloper/ui.R | 90 inst/shinyApps/SqlDeveloper/widgets.R | 78 inst/sql/oracle/test.sql | 6 inst/sql/sql_server/test.sql | 6 inst/sql/test2.sql | 6 java/SqlRender.jardesc | 34 java/org/ohdsi/sql/BigQuerySparkTranslate.java | 1262 +++--- java/org/ohdsi/sql/JarChecksum.java | 122 java/org/ohdsi/sql/MainClass.java | 270 - java/org/ohdsi/sql/SqlRender.java | 792 ++-- java/org/ohdsi/sql/SqlSplit.java | 148 java/org/ohdsi/sql/SqlTranslate.java | 1306 +++---- java/org/ohdsi/sql/StringUtils.java | 538 +- java/org/ohdsi/sql/TestSqlRender.java | 68 man/SqlRender-package.Rd | 58 man/camelCaseToSnakeCase.Rd | 42 man/camelCaseToSnakeCaseNames.Rd | 44 man/camelCaseToTitleCase.Rd | 42 man/createRWrapperForSql.Rd | 80 man/getTempTablePrefix.Rd | 38 man/launchSqlRenderDeveloper.Rd | 38 man/listSupportedDialects.Rd | 36 man/loadRenderTranslateSql.Rd | 118 man/readSql.Rd | 50 man/render.Rd | 110 man/renderSql.Rd | 50 man/renderSqlFile.Rd | 72 man/snakeCaseToCamelCase.Rd | 42 man/snakeCaseToCamelCaseNames.Rd | 44 man/sparkHandleInsert.Rd | 40 man/splitSql.Rd | 48 man/supportsJava8.Rd | 34 man/translate.Rd | 82 man/translateSingleStatement.Rd | 80 man/translateSql.Rd | 50 man/translateSqlFile.Rd | 84 man/writeSql.Rd | 50 tests/testthat.R | 8 tests/testthat/setup.R | 10 tests/testthat/test-helperFunctions.R | 264 - tests/testthat/test-renderSql.R | 346 - tests/testthat/test-replacement-patterns-file-format.R | 16 tests/testthat/test-splitSql.R | 122 tests/testthat/test-translate-bigquery.R | 1102 ++--- tests/testthat/test-translate-duckdb.R | 462 +- tests/testthat/test-translate-hive.R | 1202 +++--- tests/testthat/test-translate-impala.R | 562 +-- tests/testthat/test-translate-netezza.R | 516 +- tests/testthat/test-translate-oracle.R | 1092 +++-- tests/testthat/test-translate-pdw.R | 500 +- tests/testthat/test-translate-postgresql.R | 555 +-- tests/testthat/test-translate-redshift.R | 3138 ++++++++--------- tests/testthat/test-translate-snowflake.R | 424 +- tests/testthat/test-translate-spark.R | 915 ++-- tests/testthat/test-translate-sql_server.R | 64 tests/testthat/test-translate-sqlite-extended.R | 248 - tests/testthat/test-translate-sqlite.R | 548 +- tests/testthat/test-translate-synapse.R | 106 tests/testthat/test-translateSql.R | 52 vignettes/UsingSqlRender.Rmd | 914 ++-- 78 files changed, 13658 insertions(+), 13447 deletions(-)
Title: Ensemble Sampler for Affine-Invariant MCMC
Description: Provides ensemble samplers for
affine-invariant Monte Carlo Markov Chain, which allow a faster
convergence for badly scaled estimation problems. Two samplers are
proposed: the 'differential.evolution' sampler from ter Braak and
Vrugt (2008) <doi:10.1007/s11222-008-9104-9> and the 'stretch' sampler
from Goodman and Weare (2010) <doi:10.2140/camcos.2010.5.65>.
Author: Hugo Gruson [cre, aut, cph] ,
Sanda Dejanic [aut, cph],
Andreas Scheidegger [aut, cph]
Maintainer: Hugo Gruson <hugo.gruson+R@normalesup.org>
Diff between mcmcensemble versions 3.0.0 dated 2021-04-28 and 3.1.0 dated 2024-03-20
DESCRIPTION | 13 MD5 | 34 - NEWS.md | 10 R/MCMCEnsemble.R | 7 README.md | 37 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/diagnostic-pkgs.R | 6 inst/doc/diagnostic-pkgs.html | 535 ++++++++++++++++++------- inst/doc/faq.R | 12 inst/doc/faq.Rmd | 2 inst/doc/faq.html | 656 ++++++++++++++++++++----------- man/MCMCEnsemble.Rd | 3 man/figures/README-example-de-1.svg | 97 ++-- man/figures/README-example-stretch-1.svg | 97 ++-- man/mcmcensemble-package.Rd | 2 tests/testthat/test-MCMCEnsemble.R | 9 vignettes/faq.Rmd | 2 18 files changed, 1000 insertions(+), 522 deletions(-)
Title: Generalized Linear Mixed Models using Template Model Builder
Description: Fit linear and generalized linear mixed models with various
extensions, including zero-inflation. The models are fitted using maximum
likelihood estimation via 'TMB' (Template Model Builder). Random effects are
assumed to be Gaussian on the scale of the linear predictor and are integrated
out using the Laplace approximation. Gradients are calculated using automatic
differentiation.
Author: Mollie Brooks [aut, cre] ,
Ben Bolker [aut] ,
Kasper Kristensen [aut],
Martin Maechler [aut] ,
Arni Magnusson [aut] ,
Maeve McGillycuddy [ctb],
Hans Skaug [aut] ,
Anders Nielsen [aut] ,
Casper Berg [aut] ,
Koen van Bentham [aut],
Nafis Sadat [ctb] ,
[...truncated...]
Maintainer: Mollie Brooks <mollieebrooks@gmail.com>
Diff between glmmTMB versions 1.1.8 dated 2023-10-07 and 1.1.9 dated 2024-03-20
DESCRIPTION | 13 +- MD5 | 134 ++++++++++++++++-------------- NAMESPACE | 22 +---- R/Anova.R | 9 -- R/VarCorr.R | 17 +-- R/effects.R | 6 - R/enum.R | 16 +++ R/family.R | 59 +++++++++---- R/glmmTMB.R | 139 +++++++++++++++++++------------- R/methods.R | 19 ++-- R/predict.R | 4 R/priors.R |only R/reformulas.R | 59 +++++++++---- R/utils.R | 135 ++++++++++++++++++++++++++----- R/zzz.R | 4 build/partial.rdb |binary build/vignette.rds |binary inst/Matrix-version | 2 inst/NEWS.Rd | 52 +++++++++++ inst/TMB-version | 2 inst/doc/covstruct.html | 12 +- inst/doc/glmmTMB.pdf |binary inst/doc/hacking.html | 4 inst/doc/mcmc.html | 6 - inst/doc/mcmc.rmd | 4 inst/doc/miscEx.html | 4 inst/doc/model_evaluation.pdf |binary inst/doc/parallel.html | 4 inst/doc/priors.R |only inst/doc/priors.html |only inst/doc/priors.rmd |only inst/doc/sim.html | 11 +- inst/doc/troubleshooting.html | 6 - inst/test_data/make_ex.R | 9 -- inst/test_data/models.rda |binary inst/vignette_data/cs_profile_plot.png |binary inst/vignette_data/culcita.rds |only inst/vignette_data/gophertortoise.rds |only inst/vignette_data/model_evaluation.rda |binary inst/vignette_data/us_profile_plot.png |binary inst/vignette_data/volcano_data.png |binary inst/vignette_data/volcano_results.png |binary man/formfuns.Rd | 4 man/glmmTMB.Rd | 7 + man/glmmTMBControl.Rd | 2 man/gt_load.Rd | 8 + man/mkTMBStruc.Rd | 12 +- man/nbinom2.Rd | 4 man/omp_check.Rd | 2 man/priors.Rd |only man/sigma.glmmTMB.Rd | 10 +- man/simulate_new.Rd | 3 man/startParams.Rd | 2 man/sub_specials.Rd | 10 +- src/cordistrib.h |only src/distrib.h | 11 ++ src/glmmTMB.cpp | 138 +++++++++++++++++++++++++++---- tests/testthat/setup_makeex.R | 5 - tests/testthat/test-VarCorr.R | 5 - tests/testthat/test-basics.R | 57 +++++++++---- tests/testthat/test-checkRank.R | 18 ++-- tests/testthat/test-disp.R | 2 tests/testthat/test-families.R | 68 ++++++++++----- tests/testthat/test-methods.R | 93 ++++++++++++++------- tests/testthat/test-offset.R | 4 tests/testthat/test-predict.R | 46 ++++++++-- tests/testthat/test-priors.R |only tests/testthat/test-smooths.R | 2 tests/testthat/test-sparseX.R | 3 tests/testthat/test-varstruc.R | 15 +-- vignettes/glmmTMB.bib | 54 ++++++++++++ vignettes/mcmc.rmd | 4 vignettes/priors.rmd |only 73 files changed, 940 insertions(+), 401 deletions(-)
Title: Simple and Configurable Tables in 'HTML', 'LaTeX', 'Markdown',
'Word', 'PNG', 'PDF', and 'Typst' Formats
Description: Create highly customized tables with this simple and dependency-free package. Data frames can be converted to 'HTML', 'LaTeX', 'Markdown', 'Word', 'PNG', 'PDF', or 'Typst' tables. The user interface is minimalist and easy to learn. The syntax concise. 'HTML' tables can be customized using the flexible 'Bootstrap' framework, and 'LaTeX' code with the 'tabularray' package.
Author: Vincent Arel-Bundock [aut, cre]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinytable versions 0.1.0 dated 2024-03-11 and 0.2.0 dated 2024-03-20
DESCRIPTION | 12 MD5 | 65 ++-- NAMESPACE | 2 NEWS.md | 19 + R/build_tt.R | 20 + R/class.R | 26 + R/plot_tt.R | 7 R/print.R | 15 - R/rbind2.R |only R/sanity.R | 3 R/save_tt.R | 4 R/style_grid.R | 132 +++++----- R/style_grid_dataframe.R |only R/style_tt.R | 6 R/theme_tt.R | 17 - R/tt_grid.R | 18 + R/tt_typst.R | 4 R/utils.R | 4 README.md | 4 build/partial.rdb |binary inst/tinytest/_tinysnapshot/theme-placement_options_no_doubling.txt | 2 inst/tinytest/_tinysnapshot/typst-formatting.txt | 6 inst/tinytest/test-format_tt.R | 4 inst/tinytest/test-html.R | 9 inst/tinytest/test-theme.R | 7 inst/tinytest/test-typst.R | 11 man/colnames-set-tinytable-method.Rd |only man/finalize-tinytable_dataframe-method.Rd |only man/group_eval-tinytable_dataframe-method.Rd |only man/plot_tt.Rd | 3 man/print.tinytable.Rd | 4 man/rbind2-tinytable-ANY-method.Rd |only man/style_eval-tinytable_dataframe-method.Rd |only man/style_eval-tinytable_grid-method.Rd |only man/style_grid_internal.Rd |only man/style_tt.Rd | 7 man/theme_tt.Rd | 1 man/tt.Rd | 1 38 files changed, 264 insertions(+), 149 deletions(-)
Title: Analysis of Complex Survey Samples
Description: Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase subsampling designs. Graphics. PPS sampling without replacement. Small-area estimation.
Author: Thomas Lumley, Peter Gao, Ben Schneider
Maintainer: "Thomas Lumley" <t.lumley@auckland.ac.nz>
Diff between survey versions 4.4-1 dated 2024-03-08 and 4.4-2 dated 2024-03-20
DESCRIPTION | 8 +- MD5 | 20 +++---- inst/NEWS | 4 + inst/doc/domain.pdf |binary inst/doc/epi.pdf |binary inst/doc/pps.pdf |binary inst/doc/precalibrated.pdf |binary inst/doc/qrule.pdf |binary inst/doc/survey-sae.html | 121 ++++++++++++++++++++++----------------------- inst/doc/survey.pdf |binary src/arma_multistage.cpp | 6 -- 11 files changed, 80 insertions(+), 79 deletions(-)
Title: Data Visualisation on 'Lifemap' Tree
Description: Allow to visualise data on the NCBI phylogenetic tree as presented in Lifemap '<http://lifemap.univ-lyon1.fr/>'. It takes as input a dataframe with at least a "taxid" column containing NCBI format TaxIds and allows to draw multiple layers with different visualisation tools.
Author: Cassandra Bompard [aut],
Damien M. de Vienne [aut],
Aurelie Siberchicot [ctb, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between LifemapR versions 1.0.4 dated 2023-08-24 and 1.1.1 dated 2024-03-20
LifemapR-1.0.4/LifemapR/man/get_direct_ancestor.Rd |only LifemapR-1.0.4/LifemapR/man/request_database.Rd |only LifemapR-1.0.4/LifemapR/man/url_verification.Rd |only LifemapR-1.1.1/LifemapR/DESCRIPTION | 12 LifemapR-1.1.1/LifemapR/MD5 | 32 - LifemapR-1.1.1/LifemapR/NAMESPACE | 11 LifemapR-1.1.1/LifemapR/R/build_Lifemap.R | 340 ++++++--------------- LifemapR-1.1.1/LifemapR/R/create_matrix.R | 170 +++++----- LifemapR-1.1.1/LifemapR/R/display_map.R | 69 ++-- LifemapR-1.1.1/LifemapR/R/draw_Lifemap.R | 20 - LifemapR-1.1.1/LifemapR/README.md | 4 LifemapR-1.1.1/LifemapR/build/vignette.rds |binary LifemapR-1.1.1/LifemapR/inst/WORDLIST |only LifemapR-1.1.1/LifemapR/inst/doc/runLifemapR.R | 56 +-- LifemapR-1.1.1/LifemapR/inst/doc/runLifemapR.Rmd | 6 LifemapR-1.1.1/LifemapR/inst/doc/runLifemapR.html | 133 +++----- LifemapR-1.1.1/LifemapR/man/build_Lifemap.Rd | 30 + LifemapR-1.1.1/LifemapR/man/display_map.Rd | 2 LifemapR-1.1.1/LifemapR/vignettes/runLifemapR.Rmd | 6 19 files changed, 398 insertions(+), 493 deletions(-)
Title: Miscellaneous Functions for Environmental Analyses
Description: Small toolbox for data analyses in environmental chemistry and
ecotoxicology. Provides, for example, calibration() to calculate calibration
curves and corresponding limits of detection (LODs) and limits of
quantification (LOQs) according to German DIN 32645 (2008). texture() makes
it easy to estimate soil particle size distributions from hydrometer
measurements (ASTM D422-63, 2007).
Author: Zacharias Steinmetz [aut, cre]
,
Julius Albert [ctb] ,
Kilian Kenngott [ctb]
Maintainer: Zacharias Steinmetz <z.steinmetz@rptu.de>
Diff between envalysis versions 0.6.0 dated 2023-09-20 and 0.7.0 dated 2024-03-20
DESCRIPTION | 10 +++++----- MD5 | 26 +++++++++++++------------- NAMESPACE | 1 + NEWS.md | 7 +++++++ R/calibration.R | 36 +++++++++++++++++++++++++++--------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/calibration.R | 10 ++++++++-- inst/doc/calibration.Rmd | 10 ++++++++++ inst/doc/calibration.html | 39 ++++++++++++++++++++++++++++++--------- inst/doc/texture.html | 4 ++-- inst/doc/theme_publish.html | 4 ++-- man/calibration.Rd | 11 +++++++++++ vignettes/calibration.Rmd | 10 ++++++++++ 14 files changed, 126 insertions(+), 42 deletions(-)
Title: Information Analysis for Test and Rating Scale Data
Description: Develop, evaluate, and score multiple choice examinations,
psychological scales, questionnaires, and similar types of data involving
sequences of choices among one or more sets of answers.
This version of the package should be considered as brand new. Almost all
of the functions have been changed, including their argument list.
See the file NEWS.Rd in the Inst folder for more information.
Using the package does not require any formal statistical knowledge
beyond what would be provided by a first course in statistics in a
social science department. There the user would encounter the concept
of probability and how it is used to model data and make decisions,
and would become familiar with basic mathematical and statistical notation.
Most of the output is in graphical form.
Author: James Ramsay [aut, cre],
Juan Li [ctb],
Marie Wiberg [ctb],
Joakim Wallmark [ctb],
Spencer Graves [ctb]
Maintainer: James Ramsay <james.ramsay@mcgill.ca>
Diff between TestGardener versions 3.3.2 dated 2024-01-17 and 3.3.3 dated 2024-03-20
DESCRIPTION | 8 - MD5 | 12 +- R/Analyze.R | 160 ++++++++++++++------------- R/TG_analysis.R | 84 +++----------- R/make_dataList.R | 312 ++++++++++++++++------------------------------------- man/Analyze.Rd | 6 - man/TG_analysis.Rd | 29 ++-- 7 files changed, 235 insertions(+), 376 deletions(-)
Title: Aid Querying 'nomis' and 'Office for National Statistics Open
Geography' APIs
Description: Facilitates extraction of geospatial data from the 'Office for National Statistics Open Geography' and 'nomis' Application Programming Interfaces (APIs). Simplifies process of querying 'nomis' datasets <https://www.nomisweb.co.uk/> and extracting desired datasets in dataframe format. Extracts area shapefiles at chosen resolution from 'Office for National Statistics Open Geography' <https://geoportal.statistics.gov.uk/>.
Author: Andrew Christy [aut, cre],
James Macpherson [aut],
Hadyn Jenkins [aut],
Crown Copyright
[cph]
Maintainer: Andrew Christy <OR_Hub@defra.gov.uk>
Diff between sgapi versions 1.0.0 dated 2024-03-18 and 1.0.1 dated 2024-03-20
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/get_boundaries.R | 1 + R/get_boundaries_areaname.R | 17 +++++++++++------ R/get_table_link_lookup.R | 2 ++ man/get_table_link_lookup.Rd | 2 ++ tests/testthat/test-get_boundaries.R | 15 +++++++++++---- tests/testthat/test-get_table.R | 10 ++++++++++ 8 files changed, 47 insertions(+), 20 deletions(-)
Title: Pre-Compiled 'CmdStan' Models in R Packages
Description: Similar to 'rstantools' for 'rstan',
the 'instantiate' package builds pre-compiled
'CmdStan' models into CRAN-ready statistical modeling R packages.
The models compile once during installation,
the executables live inside the file systems of their respective packages,
and users have the full power and convenience of
'cmdstanr' without any additional compilation after package installation.
This approach saves time and helps R package developers
migrate from 'rstan' to the more modern 'cmdstanr'.
Packages 'rstantools', 'cmdstanr', 'stannis', and
'stanapi' are similar Stan clients with different objectives.
Author: William Michael Landau [aut, cre]
,
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between instantiate versions 0.2.1 dated 2024-02-06 and 0.2.2 dated 2024-03-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/stan_package_compile.R | 5 ++++- 4 files changed, 14 insertions(+), 7 deletions(-)
Title: Watch the CRAN Incoming Directories
Description: Directory reads and summaries are provided for one or more of the subdirectories
of the <https://cran.r-project.org/incoming/> directory, and a compact summary object is returned.
The package name is a contraption of 'CRAN Incoming Watcher'.
Author: Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between ciw versions 0.0.1 dated 2024-03-13 and 0.0.2 dated 2024-03-20
ChangeLog | 31 +++++++++++++++++++++++++++++++ DESCRIPTION | 10 ++++++---- MD5 | 17 +++++++++-------- NAMESPACE | 1 + R/incoming.R | 34 ++++++++++++++++++++++++---------- README.md | 12 ++++++------ build/partial.rdb |binary inst |only man/ciw-package.Rd | 1 - man/incoming.Rd | 23 ++++++++++++++++++----- 10 files changed, 95 insertions(+), 34 deletions(-)
Title: Bayesian Regression Models using 'Stan'
Description: Fit Bayesian generalized (non-)linear multivariate multilevel models
using 'Stan' for full Bayesian inference. A wide range of distributions
and link functions are supported, allowing users to fit -- among others --
linear, robust linear, count data, survival, response times, ordinal,
zero-inflated, hurdle, and even self-defined mixture models all in a
multilevel context. Further modeling options include both theory-driven and
data-driven non-linear terms, auto-correlation structures, censoring and
truncation, meta-analytic standard errors, and quite a few more.
In addition, all parameters of the response distribution can be predicted
in order to perform distributional regression. Prior specifications are
flexible and explicitly encourage users to apply prior distributions that
actually reflect their prior knowledge. Models can easily be evaluated and
compared using several methods assessing posterior or prior predictions.
References: Bürkner (2017) <doi:10.18637/jss.v080.i01>;
B [...truncated...]
Author: Paul-Christian Buerkner [aut, cre],
Jonah Gabry [ctb],
Sebastian Weber [ctb],
Andrew Johnson [ctb],
Martin Modrak [ctb],
Hamada S. Badr [ctb],
Frank Weber [ctb],
Aki Vehtari [ctb],
Mattan S. Ben-Shachar [ctb],
Hayden Rabel [ctb],
Simon C. Mills [ctb], [...truncated...]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between brms versions 2.20.4 dated 2023-09-25 and 2.21.0 dated 2024-03-20
brms-2.20.4/brms/R/make_stancode.R |only brms-2.20.4/brms/R/make_standata.R |only brms-2.20.4/brms/man/get_prior.Rd |only brms-2.20.4/brms/man/make_stancode.Rd |only brms-2.20.4/brms/man/make_standata.Rd |only brms-2.20.4/brms/tests/testthat/tests.make_stancode.R |only brms-2.20.4/brms/tests/testthat/tests.make_standata.R |only brms-2.21.0/brms/DESCRIPTION | 34 - brms-2.21.0/brms/MD5 | 259 +++++----- brms-2.21.0/brms/NAMESPACE | 18 brms-2.21.0/brms/NEWS.md | 43 + brms-2.21.0/brms/R/backends.R | 235 +++++---- brms-2.21.0/brms/R/bayes_R2.R | 7 brms-2.21.0/brms/R/brm.R | 35 - brms-2.21.0/brms/R/brm_multiple.R | 30 - brms-2.21.0/brms/R/brms-package.R | 7 brms-2.21.0/brms/R/brmsfit-helpers.R | 4 brms-2.21.0/brms/R/brmsfit-methods.R | 15 brms-2.21.0/brms/R/data-helpers.R | 7 brms-2.21.0/brms/R/data-predictor.R | 11 brms-2.21.0/brms/R/data-response.R | 20 brms-2.21.0/brms/R/distributions.R | 12 brms-2.21.0/brms/R/exclude_pars.R | 5 brms-2.21.0/brms/R/families.R | 13 brms-2.21.0/brms/R/family-lists.R | 26 - 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Title: Mixed Effect Excess Hazard Models
Description: Fit flexible (excess) hazard regression models with the possibility of including non-proportional effects of covariables and of adding a random effect at the cluster level (corresponding to a shared frailty). A detailed description of the package functionalities is provided in Charvat and Belot (2021) <doi: 10.18637/jss.v098.i14>.
Author: Hadrien Charvat, Aurelien Belot
Maintainer: Hadrien Charvat <h.charvat.ef@juntendo.ac.jp>
Diff between mexhaz versions 2.4 dated 2022-10-31 and 2.5 dated 2024-03-20
mexhaz-2.4/mexhaz/man/vcov.Rd |only mexhaz-2.5/mexhaz/DESCRIPTION | 8 mexhaz-2.5/mexhaz/MD5 | 38 ++-- mexhaz-2.5/mexhaz/NAMESPACE | 2 mexhaz-2.5/mexhaz/NEWS | 12 + mexhaz-2.5/mexhaz/R/adjsurv.R | 25 -- mexhaz-2.5/mexhaz/R/mexhaz.R | 10 - mexhaz-2.5/mexhaz/R/mexhazEgh.R | 32 ++- mexhaz-2.5/mexhaz/R/mexhazStd.R | 37 ++- mexhaz-2.5/mexhaz/R/predict.mexhaz.R | 271 ++++++++++++++++++----------- mexhaz-2.5/mexhaz/R/print.summary.mexhaz.R | 4 mexhaz-2.5/mexhaz/R/riskfunc.R | 25 +- mexhaz-2.5/mexhaz/R/summary.mexhaz.R | 4 mexhaz-2.5/mexhaz/R/vcov.mexhaz.R | 2 mexhaz-2.5/mexhaz/man/adjsurv.Rd | 69 ++++--- mexhaz-2.5/mexhaz/man/mexhaz-package.Rd | 16 - mexhaz-2.5/mexhaz/man/mexhaz.Rd | 11 + mexhaz-2.5/mexhaz/man/predict.mexhaz.Rd | 89 +++++---- mexhaz-2.5/mexhaz/man/riskfunc.Rd | 64 ++++-- mexhaz-2.5/mexhaz/src/HGHAggr_Pois.c |only mexhaz-2.5/mexhaz/src/init.c | 2 21 files changed, 449 insertions(+), 272 deletions(-)
Title: Feature Stores for the 'diseasy' Framework
Description: Simple feature stores and tools for creating personalised feature stores.
'diseasystore' powers feature stores which can automatically link and aggregate features to a given stratification
level. These feature stores are automatically time-versioned (powered by the 'SCDB' package) and allows you to easily
and dynamically compute features as part of your continuous integration.
Author: Rasmus Skytte Randloev [aut, cre]
,
Marcus Munch Gruenewald [ctb] ,
Kaare Graesboell [rev] ,
Kasper Schou Telkamp [rev] ,
Lasse Engbo Christiansen [rev]
,
Sofia Myrup Otero [rev],
Statens Serum Institut, SSI [cph, fnd]
Maintainer: Rasmus Skytte Randloev <rske@ssi.dk>
Diff between diseasystore versions 0.1.1 dated 2024-01-18 and 0.2.0 dated 2024-03-20
diseasystore-0.1.1/diseasystore/R/feature_store_helpers.R |only diseasystore-0.1.1/diseasystore/tests/testthat/test-SCDB_messages.R |only diseasystore-0.2.0/diseasystore/DESCRIPTION | 35 diseasystore-0.2.0/diseasystore/MD5 | 101 + diseasystore-0.2.0/diseasystore/NAMESPACE | 6 diseasystore-0.2.0/diseasystore/NEWS.md | 22 diseasystore-0.2.0/diseasystore/R/0_R6_utils.R | 23 diseasystore-0.2.0/diseasystore/R/0_documentation.R | 25 diseasystore-0.2.0/diseasystore/R/0_locks.R | 38 diseasystore-0.2.0/diseasystore/R/2_FeatureHandler.R | 2 diseasystore-0.2.0/diseasystore/R/3_feature_store_helpers.R |only diseasystore-0.2.0/diseasystore/R/DiseasystoreBase.R | 135 +- diseasystore-0.2.0/diseasystore/R/DiseasystoreEcdcRespiratoryViruses.R |only diseasystore-0.2.0/diseasystore/R/DiseasystoreGoogleCovid19.R | 37 diseasystore-0.2.0/diseasystore/R/drop_diseasystore.R | 169 ++- diseasystore-0.2.0/diseasystore/R/source_conn_helpers.R |only diseasystore-0.2.0/diseasystore/R/test_diseasystore.R |only diseasystore-0.2.0/diseasystore/R/truncate_interlace.R | 26 diseasystore-0.2.0/diseasystore/README.md | 4 diseasystore-0.2.0/diseasystore/build/vignette.rds |binary diseasystore-0.2.0/diseasystore/inst/WORDLIST | 14 diseasystore-0.2.0/diseasystore/inst/doc/diseasystore-ecdc-respiratory-viruses.R |only diseasystore-0.2.0/diseasystore/inst/doc/diseasystore-ecdc-respiratory-viruses.Rmd |only diseasystore-0.2.0/diseasystore/inst/doc/diseasystore-ecdc-respiratory-viruses.html |only diseasystore-0.2.0/diseasystore/inst/doc/diseasystore-google-covid-19.R | 96 - diseasystore-0.2.0/diseasystore/inst/doc/diseasystore-google-covid-19.Rmd | 19 diseasystore-0.2.0/diseasystore/inst/doc/diseasystore-google-covid-19.html | 104 +- diseasystore-0.2.0/diseasystore/inst/doc/diseasystore.R | 103 + diseasystore-0.2.0/diseasystore/inst/doc/diseasystore.Rmd | 7 diseasystore-0.2.0/diseasystore/inst/doc/diseasystore.html | 209 ++-- diseasystore-0.2.0/diseasystore/inst/doc/extending-diseasystore.Rmd | 416 ++++---- diseasystore-0.2.0/diseasystore/inst/doc/extending-diseasystore.html | 43 diseasystore-0.2.0/diseasystore/man/DiseasystoreBase.Rd | 2 diseasystore-0.2.0/diseasystore/man/DiseasystoreEcdcRespiratoryViruses.Rd |only diseasystore-0.2.0/diseasystore/man/DiseasystoreGoogleCovid19.Rd | 10 diseasystore-0.2.0/diseasystore/man/FeatureHandler.Rd | 2 diseasystore-0.2.0/diseasystore/man/age_labels.Rd | 2 diseasystore-0.2.0/diseasystore/man/available_diseasystores.Rd | 2 diseasystore-0.2.0/diseasystore/man/diseasyoption.Rd | 18 diseasystore-0.2.0/diseasystore/man/diseasystore-package.Rd | 9 diseasystore-0.2.0/diseasystore/man/diseasystore_exists.Rd | 2 diseasystore-0.2.0/diseasystore/man/drop_diseasystore.Rd | 2 diseasystore-0.2.0/diseasystore/man/get_diseasystore.Rd | 2 diseasystore-0.2.0/diseasystore/man/source_conn_helpers.Rd |only diseasystore-0.2.0/diseasystore/man/test_diseasystore.Rd |only diseasystore-0.2.0/diseasystore/man/to_diseasystore_case.Rd | 2 diseasystore-0.2.0/diseasystore/tests/testthat/helper-setup.R |only diseasystore-0.2.0/diseasystore/tests/testthat/setup.R | 119 -- diseasystore-0.2.0/diseasystore/tests/testthat/test-0_R6_utils.R | 18 diseasystore-0.2.0/diseasystore/tests/testthat/test-DiseasystoreBase.R | 520 +++++----- diseasystore-0.2.0/diseasystore/tests/testthat/test-DiseasystoreEcdcRespitoryViruses.R |only diseasystore-0.2.0/diseasystore/tests/testthat/test-DiseasystoreGoogleCovid19.R | 408 ------- diseasystore-0.2.0/diseasystore/tests/testthat/test-drop_diseasystore.R | 142 +- diseasystore-0.2.0/diseasystore/tests/testthat/test-truncate_interlace.R | 200 +-- diseasystore-0.2.0/diseasystore/tests/testthat/test_data/data |only diseasystore-0.2.0/diseasystore/vignettes/diseasystore-ecdc-respiratory-viruses.Rmd |only diseasystore-0.2.0/diseasystore/vignettes/diseasystore-google-covid-19.Rmd | 19 diseasystore-0.2.0/diseasystore/vignettes/diseasystore.Rmd | 7 diseasystore-0.2.0/diseasystore/vignettes/extending-diseasystore.Rmd | 416 ++++---- diseasystore-0.2.0/diseasystore/vignettes/vignette_data/data |only 60 files changed, 1736 insertions(+), 1800 deletions(-)
Title: 'Rcpp' Tic-Toc Timer with 'OpenMP' Support
Description: Provides 'Rcpp' bindings for 'cpptimer', a simple tic-toc timer class for benchmarking 'C++' code <https://github.com/BerriJ/cpptimer>. It's not just simple, it's blazing fast! This sleek tic-toc timer class supports overlapping timers as well as 'OpenMP' parallelism <https://www.openmp.org/>. It boasts a microsecond-level time resolution. We did not find any overhead of the timer itself at this resolution. Results (with summary statistics) are automatically passed back to 'R' as a data frame.
Author: Jonathan Berrisch [aut, cre]
Maintainer: Jonathan Berrisch <Jonathan@Berrisch.biz>
Diff between rcpptimer versions 1.0.0 dated 2024-03-05 and 1.1.0 dated 2024-03-20
DESCRIPTION | 11 ++-- MD5 | 18 ++++--- NEWS.md | 31 ++++++++++-- README.md | 28 +++++++++++ build |only inst/doc |only inst/include/chameleon.h |only inst/include/cpptimer/cpptimer.h | 94 ++++++++++++++++++++++++++++++++++----- inst/include/rcpptimer.h | 10 ++++ src/fibonacci.cpp | 19 ++++--- vignettes |only 11 files changed, 176 insertions(+), 35 deletions(-)
Title: Add Logging to Functions
Description: Decorate functions to make them return enhanced output. The enhanced output consists in an object of type
'chronicle' containing the result of the function applied to its arguments, as well as a log detailing when the function
was run, what were its inputs, what were the errors (if the function failed to run) and other useful information.
Tools to handle decorated functions are included, such as a forward pipe operator that makes chaining decorated functions possible.
Author: Bruno Rodrigues [aut, cre, cph]
Maintainer: Bruno Rodrigues <bruno@brodrigues.co>
Diff between chronicler versions 0.2.1 dated 2023-02-03 and 0.2.2 dated 2024-03-20
DESCRIPTION | 8 MD5 | 42 +-- NEWS.md | 6 build/vignette.rds |binary inst/doc/advanced-topics.R | 4 inst/doc/advanced-topics.html | 406 +++++++++++++++++----------------- inst/doc/maybe-monad.R | 2 inst/doc/maybe-monad.html | 86 +++---- inst/doc/real-world-example.R | 2 inst/doc/real-world-example.html | 236 +++++++++---------- man/avia.Rd | 2 man/check_diff.Rd | 4 man/check_g.Rd | 4 man/flatten_record.Rd | 2 man/fmap_record.Rd | 4 man/make_log_df.Rd | 2 man/pick.Rd | 2 man/print.chronicle.Rd | 16 - man/purely.Rd | 8 man/record.Rd | 22 - man/record_many.Rd | 6 tests/testthat/test-test_chronicler.R | 4 22 files changed, 435 insertions(+), 433 deletions(-)
Title: Generalized Additive Models for Location Scale and Shape
Description: Functions for fitting the Generalized Additive Models for Location Scale and Shape introduced by Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The models use a distributional regression approach where all the parameters of the conditional distribution of the response variable are modelled using explanatory variables.
Author: Mikis Stasinopoulos [aut, cre, cph]
,
Robert Rigby [aut] ,
Vlasios Voudouris [ctb],
Calliope Akantziliotou [ctb],
Marco Enea [ctb],
Daniil Kiose [ctb] ,
Achim Zeileis [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@gre.ac.uk>
Diff between gamlss versions 5.4-20 dated 2023-10-04 and 5.4-22 dated 2024-03-20
gamlss-5.4-20/gamlss/R/centilesPlot.R |only gamlss-5.4-20/gamlss/R/random.r |only gamlss-5.4-20/gamlss/inst/doc |only gamlss-5.4-22/gamlss/DESCRIPTION | 12 - gamlss-5.4-22/gamlss/MD5 | 33 +-- gamlss-5.4-22/gamlss/NEWS.md | 41 +++ gamlss-5.4-22/gamlss/R/DropAddStepGAIC-Parallel.R | 199 +++++++++--------- gamlss-5.4-22/gamlss/R/centilesPLOT.R |only gamlss-5.4-22/gamlss/R/predict.gamlss_23_12_21.R | 2 gamlss-5.4-22/gamlss/R/random.R |only gamlss-5.4-22/gamlss/R/stepGAIC-03-10-13..R | 239 ++-------------------- gamlss-5.4-22/gamlss/R/stepGAICAll-A-parallel.R | 16 - gamlss-5.4-22/gamlss/README.md | 2 gamlss-5.4-22/gamlss/build/partial.rdb |binary gamlss-5.4-22/gamlss/man/VC.test.Rd | 6 gamlss-5.4-22/gamlss/man/fitDist.Rd | 14 - gamlss-5.4-22/gamlss/man/histDist.Rd | 7 gamlss-5.4-22/gamlss/man/histSmo.Rd | 2 gamlss-5.4-22/gamlss/man/lms.Rd | 2 gamlss-5.4-22/gamlss/man/ri.Rd | 2 20 files changed, 218 insertions(+), 359 deletions(-)
Title: Rarefaction-Based Species Richness Estimator
Description: Calculate rarefaction-based alpha- and beta-diversity. Offer parametric extrapolation to estimate the total expected species in a single community and the total expected shared species between two communities. Visualize the curve-fitting for these estimators.
Author: Peng Zhao [aut, cre] ,
Yi Zou [aut]
Maintainer: Peng Zhao <pengzhao20@outlook.com>
Diff between rarestR versions 0.1.0 dated 2023-10-06 and 1.0.0 dated 2024-03-20
rarestR-0.1.0/rarestR/R/ES.R |only rarestR-1.0.0/rarestR/DESCRIPTION | 11 +-- rarestR-1.0.0/rarestR/MD5 | 28 ++++---- rarestR-1.0.0/rarestR/NAMESPACE | 1 rarestR-1.0.0/rarestR/R/es.R |only rarestR-1.0.0/rarestR/R/ess.R | 85 +++++++++++++------------ rarestR-1.0.0/rarestR/R/plot.TES.R | 24 +++---- rarestR-1.0.0/rarestR/R/plot.TESS.R | 7 -- rarestR-1.0.0/rarestR/R/tes.R | 82 +++++++++++++----------- rarestR-1.0.0/rarestR/R/tess.R | 99 +++++++++++++++--------------- rarestR-1.0.0/rarestR/build |only rarestR-1.0.0/rarestR/inst/CITATION | 80 ++++++++++++++++++++---- rarestR-1.0.0/rarestR/inst/REFERENCES.bib |only rarestR-1.0.0/rarestR/man/es.Rd | 5 + rarestR-1.0.0/rarestR/man/ess.Rd | 3 rarestR-1.0.0/rarestR/man/tes.Rd | 3 rarestR-1.0.0/rarestR/man/tess.Rd | 3 17 files changed, 257 insertions(+), 174 deletions(-)
Title: Trellis Graphics for R
Description: A powerful and elegant high-level data visualization
system inspired by Trellis graphics, with an emphasis on
multivariate data. Lattice is sufficient for typical graphics needs,
and is also flexible enough to handle most nonstandard requirements.
See ?Lattice for an introduction.
Author: Deepayan Sarkar [aut, cre] ,
Felix Andrews [ctb],
Kevin Wright [ctb] ,
Neil Klepeis [ctb],
Johan Larsson [ctb] ,
Zhijian Wen [cph] ,
Paul Murrell [ctb],
Stefan Eng [ctb] ,
Achim Zeileis [ctb] ,
Alexandre Courtiol [ctb]
Maintainer: Deepayan Sarkar <deepayan.sarkar@r-project.org>
Diff between lattice versions 0.22-5 dated 2023-10-24 and 0.22-6 dated 2024-03-20
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/shingle.R | 8 +++++++- inst/doc/grid.pdf |binary 4 files changed, 14 insertions(+), 8 deletions(-)
Title: Extra Recipes for Encoding Predictors
Description: Predictors can be converted to one or more numeric
representations using a variety of methods. Effect encodings using
simple generalized linear models <arXiv:1611.09477> or nonlinear
models <arXiv:1604.06737> can be used. There are also functions for
dimension reduction and other approaches.
Author: Emil Hvitfeldt [aut, cre] ,
Max Kuhn [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between embed versions 1.1.3 dated 2023-10-28 and 1.1.4 dated 2024-03-20
embed-1.1.3/embed/R/tidy.R |only embed-1.1.3/embed/man/tidy.recipe.Rd |only embed-1.1.4/embed/DESCRIPTION | 20 +- embed-1.1.4/embed/MD5 | 100 +++++------- embed-1.1.4/embed/NAMESPACE | 11 - embed-1.1.4/embed/NEWS.md | 12 + embed-1.1.4/embed/R/collapse_cart.R | 19 +- embed-1.1.4/embed/R/collapse_stringdist.R | 18 +- embed-1.1.4/embed/R/discretize_cart.R | 16 + embed-1.1.4/embed/R/discretize_xgb.R | 16 + embed-1.1.4/embed/R/embed-package.R | 11 - embed-1.1.4/embed/R/embed.R | 50 +++--- embed-1.1.4/embed/R/feature_hash.R | 19 +- embed-1.1.4/embed/R/lencode_bayes.R | 27 ++- embed-1.1.4/embed/R/lencode_glm.R | 17 +- embed-1.1.4/embed/R/lencode_mixed.R | 15 + embed-1.1.4/embed/R/pca_sparse.R | 15 + embed-1.1.4/embed/R/pca_sparse_bayes.R | 15 + embed-1.1.4/embed/R/pca_truncated.R | 29 ++- embed-1.1.4/embed/R/umap.R | 45 ++++- embed-1.1.4/embed/R/woe.R | 23 ++ embed-1.1.4/embed/man/step_collapse_cart.Rd | 14 + embed-1.1.4/embed/man/step_collapse_stringdist.Rd | 13 + embed-1.1.4/embed/man/step_discretize_cart.Rd | 11 + embed-1.1.4/embed/man/step_discretize_xgb.Rd | 11 + embed-1.1.4/embed/man/step_embed.Rd | 19 +- embed-1.1.4/embed/man/step_feature_hash.Rd | 12 + embed-1.1.4/embed/man/step_lencode_bayes.Rd | 20 +- embed-1.1.4/embed/man/step_lencode_glm.Rd | 12 + embed-1.1.4/embed/man/step_lencode_mixed.Rd | 12 + embed-1.1.4/embed/man/step_pca_sparse.Rd | 12 + embed-1.1.4/embed/man/step_pca_sparse_bayes.Rd | 12 + embed-1.1.4/embed/man/step_pca_truncated.Rd | 24 ++ embed-1.1.4/embed/man/step_umap.Rd | 24 ++ embed-1.1.4/embed/man/step_woe.Rd | 20 ++ embed-1.1.4/embed/tests/testthat/_snaps/collapse_cart.md | 2 embed-1.1.4/embed/tests/testthat/_snaps/discretize_cart.md | 5 embed-1.1.4/embed/tests/testthat/_snaps/discretize_xgb.md | 55 +++--- embed-1.1.4/embed/tests/testthat/_snaps/embed.md | 23 +- embed-1.1.4/embed/tests/testthat/_snaps/feature_hash.md | 14 - embed-1.1.4/embed/tests/testthat/_snaps/lencode_bayes.md | 18 +- embed-1.1.4/embed/tests/testthat/_snaps/lencode_glm.md | 15 - embed-1.1.4/embed/tests/testthat/_snaps/lencode_mixed.md | 15 - embed-1.1.4/embed/tests/testthat/_snaps/pca_sparse.md | 12 - embed-1.1.4/embed/tests/testthat/_snaps/pca_sparse_bayes.md | 12 - embed-1.1.4/embed/tests/testthat/_snaps/pca_truncated.md | 10 - embed-1.1.4/embed/tests/testthat/_snaps/umap.md | 8 embed-1.1.4/embed/tests/testthat/_snaps/woe.md | 13 - embed-1.1.4/embed/tests/testthat/test-embed.R | 15 + embed-1.1.4/embed/tests/testthat/test-lencode_bayes.R | 11 + embed-1.1.4/embed/tests/testthat/test-lencode_mixed.R | 29 ++- embed-1.1.4/embed/tests/testthat/test-umap.R | 39 ++++ 52 files changed, 661 insertions(+), 329 deletions(-)
Title: Normalize Gene Expression Data using Evaluated Methods
Description: It provides a framework and a fast and simple way for researchers to evaluate methods (particularly some data-driven methods or their own methods) and then select a best one for data normalization in the gene expression analysis, based on the consistency of metrics and the consistency of datasets.
Zhenfeng Wu, Weixiang Liu, Xiufeng Jin, Deshui Yu, Hua Wang, Gustavo Glusman, Max Robinson, Lin Liu, Jishou Ruan and Shan Gao (2018) <doi:10.1101/251140>.
Author: Zhenfeng Wu , Shan Gao
Maintainer: Shan Gao <gao_shan@mail.nankai.edu.cn>
Diff between NormExpression versions 0.1.0 dated 2018-03-05 and 0.1.1 dated 2024-03-20
DESCRIPTION | 6 +-- MD5 | 62 ++++++++++++++++++------------------ man/CV2AUCVC.Rd | 8 +--- man/calcFactorRLE.Rd | 8 +--- man/calcFactorUpperquartile.Rd | 10 +---- man/calcFactorWeighted.Rd | 20 ++++------- man/change_colours.Rd | 10 +---- man/estimateSizeFactorsForMatrix.Rd | 8 +--- man/filteredZero.Rd | 8 +--- man/findGenes.Rd | 12 ++---- man/gatherCVs.Rd | 34 ++++++++----------- man/gatherCVs4Matrices.Rd | 14 ++------ man/gatherCors.Rd | 38 +++++++++------------- man/gatherCors4Matrices.Rd | 18 ++++------ man/gatherFactors.Rd | 28 ++++++---------- man/getAUCVC.Rd | 12 ++---- man/getAUCVCs.Rd | 12 ++---- man/getArea.Rd | 8 +--- man/getCV.Rd | 8 +--- man/getCor.Rd | 10 +---- man/getCorMedians.Rd | 6 --- man/getFactors.Rd | 18 ++++------ man/getNormMatrix.Rd | 8 +--- man/gridAUCVC.Rd | 36 +++++++++----------- man/gridAUCVC4Matrices.Rd | 12 ++---- man/identifyUbq.Rd | 14 ++------ man/identifyUbqRepeat.Rd | 12 ++---- man/nonzeroRatio2AUCVC.Rd | 36 +++++++++----------- man/optTU.Rd | 24 +++++-------- man/plotCVs.Rd | 10 +---- man/plotCors.Rd | 10 +---- man/plotHC.Rd | 10 +---- 32 files changed, 205 insertions(+), 325 deletions(-)
More information about NormExpression at CRAN
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