Title: Interactively Explore Dimension-Reduced Embeddings
Description: A tool to interactively explore the
embeddings created by dimension reduction methods such as
Principal Components Analysis (PCA), Multidimensional Scaling (MDS),
T-distributed Stochastic Neighbour Embedding (t-SNE),
Uniform Manifold Approximation and Projection (UMAP) or any other.
Author: Svetlana Ovchinnikova [aut, cre],
Simon Anders [aut]
Maintainer: Svetlana Ovchinnikova <s.ovchinnikova@zmbh.uni-heidelberg.de>
Diff between sleepwalk versions 0.3.0 dated 2020-02-26 and 0.3.1 dated 2020-09-29
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NEWS.md | 4 ++++ R/sleepwalk.R | 4 ++-- 4 files changed, 14 insertions(+), 10 deletions(-)
Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data
sets, regression models, and more. The code to create the tables is
concise and highly customizable. Data frames can be summarized with
any function, e.g. mean(), median(), even user-written functions.
Regression models are summarized and include the reference rows for
categorical variables. Common regression models, such as logistic
regression and Cox proportional hazards regression, are automatically
identified and the tables are pre-filled with appropriate column
headers.
Author: Daniel D. Sjoberg [aut, cre] (<https://orcid.org/0000-0003-0862-2018>),
Michael Curry [aut] (<https://orcid.org/0000-0002-0261-4044>),
Margie Hannum [aut] (<https://orcid.org/0000-0002-2953-0449>),
Karissa Whiting [aut] (<https://orcid.org/0000-0002-4683-1868>),
Emily C. Zabor [aut] (<https://orcid.org/0000-0002-1402-4498>),
Esther Drill [ctb] (<https://orcid.org/0000-0002-3315-4538>),
Jessica Flynn [ctb] (<https://orcid.org/0000-0001-8310-6684>),
Joseph Larmarange [ctb] (<https://orcid.org/0000-0001-7097-700X>),
Stephanie Lobaugh [ctb],
Gustavo Zapata Wainberg [ctb] (<https://orcid.org/0000-0002-2524-3637>)
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between gtsummary versions 1.3.4 dated 2020-08-27 and 1.3.5 dated 2020-09-29
gtsummary-1.3.4/gtsummary/R/sort_p.R |only gtsummary-1.3.4/gtsummary/man/figures/sort_p_ex1.png |only gtsummary-1.3.4/gtsummary/man/sort_p.Rd |only gtsummary-1.3.5/gtsummary/DESCRIPTION | 23 gtsummary-1.3.5/gtsummary/MD5 | 276 gtsummary-1.3.5/gtsummary/NAMESPACE | 10 gtsummary-1.3.5/gtsummary/NEWS.md | 40 gtsummary-1.3.5/gtsummary/R/add_glance_source_note.R |only gtsummary-1.3.5/gtsummary/R/add_nevent.R | 3 gtsummary-1.3.5/gtsummary/R/add_overall.R | 14 gtsummary-1.3.5/gtsummary/R/add_stat_label.R | 62 gtsummary-1.3.5/gtsummary/R/as_gt.R | 14 gtsummary-1.3.5/gtsummary/R/custom_tidiers.R |only gtsummary-1.3.5/gtsummary/R/gtsummary-package.R | 2 gtsummary-1.3.5/gtsummary/R/inline_text.R | 5 gtsummary-1.3.5/gtsummary/R/modify_table_header.R |only gtsummary-1.3.5/gtsummary/R/select_helpers.R | 23 gtsummary-1.3.5/gtsummary/R/sort_filter_p.R |only gtsummary-1.3.5/gtsummary/R/style_ratio.R | 2 gtsummary-1.3.5/gtsummary/R/style_sigfig.R | 3 gtsummary-1.3.5/gtsummary/R/sysdata.rda |binary gtsummary-1.3.5/gtsummary/R/tbl_summary.R | 74 gtsummary-1.3.5/gtsummary/R/tbl_svysummary.R | 78 gtsummary-1.3.5/gtsummary/R/tbl_uvregression.R | 8 gtsummary-1.3.5/gtsummary/R/theme_gtsummary.R | 115 gtsummary-1.3.5/gtsummary/R/utils-add_p.R | 10 gtsummary-1.3.5/gtsummary/R/utils-gtsummary_core.R | 6 gtsummary-1.3.5/gtsummary/R/utils-tbl_summary.R | 186 gtsummary-1.3.5/gtsummary/README.md | 1 gtsummary-1.3.5/gtsummary/build/gtsummary.pdf |20464 +++++----- gtsummary-1.3.5/gtsummary/inst/WORDLIST | 5 gtsummary-1.3.5/gtsummary/inst/doc/gallery.R | 66 gtsummary-1.3.5/gtsummary/inst/doc/gallery.Rmd | 75 gtsummary-1.3.5/gtsummary/inst/doc/gallery.html | 1653 gtsummary-1.3.5/gtsummary/inst/doc/global_options.html | 72 gtsummary-1.3.5/gtsummary/inst/doc/inline_text.R | 32 gtsummary-1.3.5/gtsummary/inst/doc/inline_text.Rmd | 67 gtsummary-1.3.5/gtsummary/inst/doc/inline_text.html | 552 gtsummary-1.3.5/gtsummary/inst/doc/rmarkdown.R | 23 gtsummary-1.3.5/gtsummary/inst/doc/rmarkdown.Rmd | 46 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gtsummary-1.3.5/gtsummary/tests/testthat/test-add_overall.R | 41 gtsummary-1.3.5/gtsummary/tests/testthat/test-add_p.R | 49 gtsummary-1.3.5/gtsummary/tests/testthat/test-add_p.tbl_svysummary.R | 40 gtsummary-1.3.5/gtsummary/tests/testthat/test-add_stat_label.R | 40 gtsummary-1.3.5/gtsummary/tests/testthat/test-custom_tidiers.R |only gtsummary-1.3.5/gtsummary/tests/testthat/test-filter_p.R |only gtsummary-1.3.5/gtsummary/tests/testthat/test-modify_table_header.R |only gtsummary-1.3.5/gtsummary/tests/testthat/test-show_header_names.R | 2 gtsummary-1.3.5/gtsummary/tests/testthat/test-style_ratio.R |only gtsummary-1.3.5/gtsummary/tests/testthat/test-style_sigfig.R |only gtsummary-1.3.5/gtsummary/tests/testthat/test-tbl_summary.R | 54 gtsummary-1.3.5/gtsummary/tests/testthat/test-tbl_summary_input_checks.R | 4 gtsummary-1.3.5/gtsummary/tests/testthat/test-tbl_svysummary.R | 6 gtsummary-1.3.5/gtsummary/tests/testthat/test-tbl_uvregression.R | 16 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Title: Feature Selection Algorithms for Computer Aided Diagnosis
Description: Contains a set of utilities for building and testing statistical models (linear, logistic,ordinal or COX) for Computer Aided Diagnosis/Prognosis applications. Utilities include data adjustment, univariate analysis, model building, model-validation, longitudinal analysis, reporting and visualization.
Author: Jose Gerardo Tamez-Pena, Antonio Martinez-Torteya, Israel Alanis and Jorge Orozco
Maintainer: Jose Gerardo Tamez-Pena <jose.tamezpena@tec.mx>
Diff between FRESA.CAD versions 3.1.0 dated 2018-11-27 and 3.3.0 dated 2020-09-29
DESCRIPTION | 12 MD5 | 272 + NAMESPACE | 250 + NEWS | 18 R/BSWiMS.r | 278 +- R/CoxBenchmark.R |only R/EmpiricalSurvDiff.r | 478 +-- R/FRESA.Model.R | 14 R/FRESAModelingFunctions.R | 1278 ++++++++- R/FRESAScale.r | 93 R/ForwardSelection.Model.Bin.R | 20 R/ForwardSelection.Model.Res.R | 311 +- R/GMVECluster.r |only R/OrdinalBenchmark.R | 937 +++--- R/RegresionBenchmark.R | 945 +++--- R/backVarElimination.Bin.R | 300 +- R/backVarElimination.Res.R | 4 R/baggedModel.R | 157 - R/barPlotCiError.R | 38 R/binaryBenchMark.R | 867 +++--- R/bootstrapValidation.Bin.R | 10 R/bootstrapValidation.Res.R | 330 +- R/bootstrapVarElimination.Res.R | 515 +-- R/crossValidationFeatureSelection.Bin.R | 16 R/crossValidationFeatureSelection.Res.R | 1224 ++++---- R/ensemblePredict.R | 44 R/featureAdjustment.R | 66 R/getKNNpredictionFromFormula.R | 128 R/getSignature.r | 398 +- R/getVar.Bin.R | 466 +-- R/getVar.Res.R | 320 +- R/heatMaps.R | 836 +++--- R/improvedResiduals.R | 158 - R/isoData.r |only R/jaccard.r |only R/listTopCorrelatedVariables.R | 114 R/modelFitting.R | 4 R/nearestCentroid.r |only R/nearestneighborimpute.R | 165 - R/orderFeatures.r | 300 +- R/plot.FRESABenchmark.R | 487 +++ R/plot.bootstrapValidation.Bin.R | 226 - R/plot.bootstrapValidation.Res.R | 70 R/plotModels.ROC.R | 43 R/predictForFresa.R | 253 + R/predictionStats.R | 182 + R/randomCV.R | 1220 +++++--- R/randomCVFunctions.R | 90 R/reportEquivalentVariables.R | 440 +-- R/residualtForFRESA.R | 160 - R/rpredict.R |only R/signatureDistance.r | 256 - R/summary.bootstrapValidation.R | 228 - R/summary.fitFRESA.R | 347 +- R/summaryReport.R | 82 R/timeSerieAnalysis.R | 74 R/uniRankVar.R | 113 R/univariateCox.R |only R/univariateRankVariables.R | 10 R/update.uniRankVar.R | 48 R/updateModel.Res.R | 248 - inst/doc/CVMethods_totorial.pdf |only inst/doc/VignetteFRESABenchmark.pdf |binary man/BESS.Rd |only man/BSWiMS.Rd | 7 man/CV_signature.Rd | 72 man/CancerVarNames.Rd | 52 man/ClustClass.Rd |only man/EmpiricalSurvDiff.Rd | 224 - man/FRESA.CAD-package.Rd | 4 man/FRESA.Model.Rd | 466 +-- man/FRESAScale.Rd | 99 man/FilterUnivariate.Rd | 16 man/Filter_mRMR.Rd | 66 man/ForwardModel.Bin.Rd | 204 - man/ForwardModel.Res.Rd | 190 - man/GMVEBSWiMS.Rd |only man/GMVECluster.Rd |only man/HCLAS_KNN_CLASS.Rd |only man/KNN_method.Rd | 108 man/LASSO_MIN.Rd | 15 man/LM_RIDGE_MIN.Rd | 60 man/NAIVE_BAYES.Rd | 8 man/TUNED_SVM.Rd |only man/backVarElimination.Bin.Rd | 150 - man/backVarElimination.Res.Rd | 160 - man/baggedModel.Rd | 162 - man/barPlotCiError.Rd | 154 - man/benchmarking.Rd | 605 ++-- man/bootstrapValidation.Bin.Rd | 310 +- man/bootstrapValidation.Res.Rd | 238 - man/bootstrapVarElimination.Bin.Rd | 186 - man/bootstrapVarElimination.Res.Rd | 204 - man/clusterISODATA.Rd |only man/crossValidationFeatureSelection.Bin.Rd | 536 +-- man/crossValidationFeatureSelection.Res.Rd | 494 +-- man/ensemblePredict.Rd | 120 man/featureAdjustment.Rd | 98 man/filteredFit.Rd |only man/getKNNpredictionFromFormula.Rd | 98 man/getSignature.Rd | 144 - man/getVar.Bin.Rd | 146 - man/getVar.Res.Rd | 158 - man/heatMaps.Rd | 200 - man/improvedResiduals.Rd | 128 man/jaccardMatrix.Rd |only man/listTopCorrelatedVariables.Rd | 148 - man/modelFitting.Rd | 72 man/nearestCentroid.Rd |only man/nearestneighborimpute.Rd | 103 man/plot.FRESABenchmark.Rd | 80 man/plot.bootstrapValidation.Bin.Rd | 86 man/plot.bootstrapValidation.Res.Rd | 60 man/plotModels.ROC.Rd | 132 man/predict.CLUSTER_CLASS.Rd |only man/predict.FRESAKNN.Rd | 46 man/predict.FRESA_BOOST.Rd |only man/predict.FRESA_FILTERFIT.Rd |only man/predict.FRESA_LASSO.Rd | 14 man/predict.FRESA_NAIVEBAYES.Rd | 46 man/predict.FRESA_RIDGE.Rd | 46 man/predict.FRESA_SVM.Rd |only man/predict.FRESAsignature.Rd | 46 man/predict.GMVE.Rd |only man/predict.GMVE_BSWiMS.Rd |only man/predict.bess.Rd |only man/predictForFresa.Rd | 56 man/predictionStats.Rd | 208 - man/randomCV.Rd | 365 +- man/rankInverseNormalDataFrame.Rd | 128 man/reportEquivalentVariables.Rd | 150 - man/residualForFRESA.Rd | 66 man/signatureDistance.Rd | 74 man/summary.bootstrapValidation.Rd | 76 man/summary.fitFRESA.Rd | 74 man/summaryReport.Rd | 86 man/timeSeriesAnalysis.Rd | 170 - man/trajectoriesPolyFeatures.Rd |only man/uniRankVar.Rd | 266 - man/univariateRankVariables.Rd | 556 ++-- man/update.uniRankVar.Rd | 50 man/updateModel.Bin.Rd | 152 - man/updateModel.Res.Rd | 152 - src/FRESACAD_init.cpp | 141 - src/FRESAcommons.cpp | 4001 ++++++++++++++--------------- src/FRESAcommons.h | 228 - src/Makevars | 6 src/Makevars.win | 5 src/binaryFeatureSelectionCpp.cpp | 2 src/regresionFeatureSelectionCpp.cpp | 34 150 files changed, 16385 insertions(+), 13365 deletions(-)
Title: Bindings to the 'HarfBuzz' and 'Fribidi' Libraries for Text
Shaping
Description: Provides access to the text shaping functionality in the 'HarfBuzz'
library and the bidirectional algorithm in the 'Fribidi' library.
'textshaping' is a low-level utility package mainly for graphic devices that
expands upon the font tool-set provided by the 'systemfonts' package.
Author: Thomas Lin Pedersen [cre, aut]
(<https://orcid.org/0000-0002-5147-4711>),
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@rstudio.com>
Diff between textshaping versions 0.1.0 dated 2020-09-17 and 0.1.1 dated 2020-09-29
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 1 - NEWS.md | 4 ++++ R/textshaping-package.R | 1 - README.md | 10 ++++++---- man/textshaping-package.Rd | 10 +++++----- src/string_metrics.cpp | 2 +- 8 files changed, 27 insertions(+), 23 deletions(-)
Title: Advanced Statistical Methods to Model and Adjust for Bias in
Meta-Analysis
Description: The following methods are implemented to evaluate how sensitive the results of a meta-analysis are to potential bias in meta-analysis and to support Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 5 'Small-Study Effects in Meta-Analysis':
- Copas selection model described in Copas & Shi (2001) <DOI:10.1177/096228020101000402>;
- limit meta-analysis by Rücker et al. (2011) <DOI:10.1093/biostatistics/kxq046>;
- upper bound for outcome reporting bias by Copas & Jackson (2004) <DOI:10.1111/j.0006-341X.2004.00161.x>;
- imputation methods for missing binary data by Gamble & Hollis (2005) <DOI:10.1016/j.jclinepi.2004.09.013> and Higgins et al. (2008) <DOI:10.1177/1740774508091600>.
Author: Guido Schwarzer [cre, aut] (<https://orcid.org/0000-0001-6214-9087>),
James R. Carpenter [aut] (<https://orcid.org/0000-0003-3890-6206>),
Gerta Rücker [aut] (<https://orcid.org/0000-0002-2192-2560>)
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between metasens versions 0.4-1 dated 2020-07-02 and 0.5-0 dated 2020-09-29
DESCRIPTION | 10 - MD5 | 48 +++---- NEWS.md | 32 +++++ R/copas.R | 251 +++++++++++++++++++++++++++++++---------- R/forest.orbbound.R | 4 R/limitmeta.R | 23 +-- R/metamiss.R | 4 R/orbbound.R | 4 R/plot.copas.R | 24 --- R/print.copas.R | 20 --- R/print.limitmeta.R | 2 R/print.orbbound.R | 33 ++--- R/print.summary.copas.R | 10 - R/print.summary.limitmeta.R | 24 +-- R/summary.copas.R | 124 ++++++-------------- man/copas.Rd | 42 ++++++ man/forest.orbbound.Rd | 4 man/limitmeta.Rd | 11 - man/orbbound.Rd | 4 man/plot.copas.Rd | 12 - man/print.copas.Rd | 7 - man/print.orbbound.Rd | 13 +- man/print.summary.copas.Rd | 4 man/print.summary.limitmeta.Rd | 4 man/summary.copas.Rd | 22 +-- 25 files changed, 430 insertions(+), 306 deletions(-)
Title: System Native Font Finding
Description: Provides system native access to the font catalogue. As font
handling varies between systems it is difficult to correctly locate
installed fonts across different operating systems. The 'systemfonts'
package provides bindings to the native libraries on Windows, macOS and
Linux for finding font files that can then be used further by e.g. graphic
devices. The main use is intended to be from compiled code but 'systemfonts'
also provides access from R.
Author: Thomas Lin Pedersen [aut, cre]
(<https://orcid.org/0000-0002-5147-4711>),
Jeroen Ooms [aut] (<https://orcid.org/0000-0002-4035-0289>),
Devon Govett [aut] (Author of font-manager),
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@rstudio.com>
Diff between systemfonts versions 0.3.1 dated 2020-09-08 and 0.3.2 dated 2020-09-29
DESCRIPTION | 7 +++---- MD5 | 20 ++++++++++---------- NAMESPACE | 1 - NEWS.md | 5 +++++ R/systemfonts-package.R | 1 - src/cache_store.h | 1 + src/caches.h | 1 + src/font_matching.h | 1 + src/font_metrics.h | 1 + src/string_metrics.cpp | 2 +- src/string_metrics.h | 1 + 11 files changed, 24 insertions(+), 17 deletions(-)
Title: Parameter-Free Domain-Agnostic Season Length Detection in Time
Series
Description: Spectral and Average Autocorrelation Zero Distance Density
('sazed') is a method for estimating the season length of a
seasonal time series. 'sazed' is aimed at practitioners, as it employs only
domain-agnostic preprocessing and does not depend on parameter tuning or
empirical constants. The computation of 'sazed' relies on the efficient
autocorrelation computation methods suggested by Thibauld Nion (2012, URL:
<https://etudes.tibonihoo.net/literate_musing/autocorrelations.html>) and by
Bob Carpenter (2012, URL:
<https://lingpipe-blog.com/2012/06/08/autocorrelation-fft-kiss-eigen/>).
Author: Maximilian Toller [aut],
Tiago Santos [aut, cre],
Roman Kern [aut]
Maintainer: Tiago Santos <teixeiradossantos@tugraz.at>
Diff between sazedR versions 2.0.1 dated 2019-09-16 and 2.0.2 dated 2020-09-29
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 5 +++++ R/sazed.R | 16 ++++++++-------- 4 files changed, 20 insertions(+), 15 deletions(-)
Title: Legacy 'Ryacas' (Interface to 'Yacas' Computer Algebra System)
Description: A legacy version of 'Ryacas', an interface to the 'yacas' computer algebra system (<http://www.yacas.org/>).
Author: Mikkel Meyer Andersen [aut, cre, cph],
Rob Goedman [aut, cph],
Gabor Grothendieck [aut, cph],
Søren Højsgaard [aut, cph],
Grzegorz Mazur [aut, cph],
Ayal Pinkus [aut, cph],
Nemanja Trifunovic [cph] (UTF-8 part of yacas
(src/yacas/include/yacas/utf8*))
Maintainer: Mikkel Meyer Andersen <mikl@math.aau.dk>
Diff between Ryacas0 versions 0.4.2 dated 2019-10-09 and 0.4.3 dated 2020-09-29
DESCRIPTION | 12 +- MD5 | 44 ++++---- R/ryacas-package.R | 4 R/yacas.R | 6 - README.md | 12 +- build/vignette.rds |binary inst/NEWS | 6 - inst/doc/elaborate-reference.R | 186 ++++++++++++++++++------------------ inst/doc/elaborate-reference.html | 29 ++--- inst/doc/getting-started.R | 16 +-- inst/doc/getting-started.html | 15 +- inst/doc/latent-variable-model.R | 16 +-- inst/doc/latent-variable-model.html | 15 +- inst/doc/ssm-matrix.R | 22 ++-- inst/doc/ssm-matrix.html | 15 +- inst/doc/sym-matrix-vector.R | 28 ++--- inst/doc/sym-matrix-vector.html | 35 +++--- man/Ryacas0-package.Rd | 2 man/Ryacas_options.Rd | 2 man/Sym.Rd | 2 man/stripvar.Rd | 4 man/yacasTranslations.Rd | 2 man/yacmode.Rd | 2 23 files changed, 231 insertions(+), 244 deletions(-)
Title: Graph Theory Analysis of Brain MRI Data
Description: A set of tools for performing graph theory analysis of brain MRI
data. It works with data from a Freesurfer analysis (cortical thickness,
volumes, local gyrification index, surface area), diffusion tensor
tractography data (e.g., from FSL) and resting-state fMRI data (e.g., from
DPABI). It contains a graphical user interface for graph visualization and
data exploration, along with several functions for generating useful
figures.
Author: Christopher G. Watson [aut, cre]
(<https://orcid.org/0000-0002-7082-7631>)
Maintainer: Christopher G. Watson <cgwatson@bu.edu>
Diff between brainGraph versions 2.7.3 dated 2019-11-07 and 3.0.0 dated 2020-09-29
brainGraph-2.7.3/brainGraph/R/plot_brainGraph_list.R |only brainGraph-2.7.3/brainGraph/R/plot_corr_mat.R |only brainGraph-2.7.3/brainGraph/man/aal.Rd |only brainGraph-2.7.3/brainGraph/man/args_as_list.Rd |only brainGraph-2.7.3/brainGraph/man/brainGraph_GLM_fit.Rd |only brainGraph-2.7.3/brainGraph/man/brainsuite.Rd |only brainGraph-2.7.3/brainGraph/man/check_degree.Rd |only brainGraph-2.7.3/brainGraph/man/check_strength.Rd |only brainGraph-2.7.3/brainGraph/man/check_weights.Rd |only brainGraph-2.7.3/brainGraph/man/color_vertices_edges.Rd |only brainGraph-2.7.3/brainGraph/man/corr.matrix.Rd |only brainGraph-2.7.3/brainGraph/man/craddock200.Rd |only brainGraph-2.7.3/brainGraph/man/dosenbach160.Rd |only brainGraph-2.7.3/brainGraph/man/freesurfer_atlases.Rd |only brainGraph-2.7.3/brainGraph/man/get_lm_vars.Rd |only brainGraph-2.7.3/brainGraph/man/hoa112.Rd |only brainGraph-2.7.3/brainGraph/man/is.brainGraph.Rd |only brainGraph-2.7.3/brainGraph/man/lpba40.Rd |only brainGraph-2.7.3/brainGraph/man/make_empty_brainGraph.Rd |only brainGraph-2.7.3/brainGraph/man/make_glm_brainGraph.Rd |only brainGraph-2.7.3/brainGraph/man/make_mediate_brainGraph.Rd |only brainGraph-2.7.3/brainGraph/man/make_nbs_brainGraph.Rd |only brainGraph-2.7.3/brainGraph/man/partition.Rd |only brainGraph-2.7.3/brainGraph/man/plot.brainGraph_GLM.Rd |only brainGraph-2.7.3/brainGraph/man/plot.brainGraph_NBS.Rd |only brainGraph-2.7.3/brainGraph/man/plot.brainGraph_mediate.Rd |only brainGraph-2.7.3/brainGraph/man/plot.brainGraph_mtpc.Rd |only brainGraph-2.7.3/brainGraph/man/plot_brainGraph_list.Rd |only brainGraph-2.7.3/brainGraph/man/plot_corr_mat.Rd |only brainGraph-2.7.3/brainGraph/man/rotation.Rd |only brainGraph-2.7.3/brainGraph/man/rstudent_mat.Rd |only brainGraph-2.7.3/brainGraph/man/set_brainGraph_attr.Rd |only brainGraph-2.7.3/brainGraph/man/symm_mean.Rd |only brainGraph-2.7.3/brainGraph/man/symmetrize_mats.Rd |only brainGraph-2.7.3/brainGraph/man/update_brainGraph_gui.Rd |only brainGraph-2.7.3/brainGraph/man/vec.transform.Rd |only brainGraph-2.7.3/brainGraph/man/xfm.weights.Rd |only brainGraph-3.0.0/brainGraph/DESCRIPTION | 34 brainGraph-3.0.0/brainGraph/MD5 | 301 +- brainGraph-3.0.0/brainGraph/NAMESPACE | 172 + brainGraph-3.0.0/brainGraph/NEWS.md | 38 brainGraph-3.0.0/brainGraph/R/NBS.R | 415 +-- brainGraph-3.0.0/brainGraph/R/analysis_random_graphs.R | 215 - brainGraph-3.0.0/brainGraph/R/atlas.R |only brainGraph-3.0.0/brainGraph/R/auc.R |only brainGraph-3.0.0/brainGraph/R/boot_global.R | 166 - brainGraph-3.0.0/brainGraph/R/brainGraph_GLM.R | 1320 ++++------ brainGraph-3.0.0/brainGraph/R/brainGraph_mediate.R | 619 ++-- brainGraph-3.0.0/brainGraph/R/centr_lev.R | 19 brainGraph-3.0.0/brainGraph/R/communicability.R | 32 brainGraph-3.0.0/brainGraph/R/contract_brainGraph.R | 64 brainGraph-3.0.0/brainGraph/R/corr_matrix.R | 311 ++ brainGraph-3.0.0/brainGraph/R/count_edges.R | 45 brainGraph-3.0.0/brainGraph/R/create_graphs.R | 778 ++--- brainGraph-3.0.0/brainGraph/R/create_mats.R | 477 ++- brainGraph-3.0.0/brainGraph/R/data.R | 250 + brainGraph-3.0.0/brainGraph/R/data_tables.R | 134 - brainGraph-3.0.0/brainGraph/R/distances.R |only brainGraph-3.0.0/brainGraph/R/edge_asymmetry.R | 11 brainGraph-3.0.0/brainGraph/R/get_resid.R | 672 ++--- brainGraph-3.0.0/brainGraph/R/glm_design.R |only brainGraph-3.0.0/brainGraph/R/glm_fit.R |only brainGraph-3.0.0/brainGraph/R/glm_methods.R |only brainGraph-3.0.0/brainGraph/R/glm_randomise.R |only brainGraph-3.0.0/brainGraph/R/glm_stats.R |only brainGraph-3.0.0/brainGraph/R/graph_efficiency.R | 81 brainGraph-3.0.0/brainGraph/R/hubs.R | 57 brainGraph-3.0.0/brainGraph/R/import.R | 94 brainGraph-3.0.0/brainGraph/R/individ_contrib.R | 426 +-- brainGraph-3.0.0/brainGraph/R/list.R |only brainGraph-3.0.0/brainGraph/R/method_helpers.R |only brainGraph-3.0.0/brainGraph/R/methods.R |only brainGraph-3.0.0/brainGraph/R/mtpc.R | 457 ++- brainGraph-3.0.0/brainGraph/R/permute_group.R | 540 ++-- brainGraph-3.0.0/brainGraph/R/plot_brainGraph.R | 569 ++-- brainGraph-3.0.0/brainGraph/R/plot_brainGraph_gui.R | 1126 ++++---- brainGraph-3.0.0/brainGraph/R/plot_brainGraph_multi.R | 250 + brainGraph-3.0.0/brainGraph/R/plot_global.R | 190 + brainGraph-3.0.0/brainGraph/R/plot_group_means.R | 63 brainGraph-3.0.0/brainGraph/R/plot_rich_norm.R | 164 - brainGraph-3.0.0/brainGraph/R/plot_vertex_measures.R | 78 brainGraph-3.0.0/brainGraph/R/random_graphs.R | 194 + brainGraph-3.0.0/brainGraph/R/rich_club.R | 195 - brainGraph-3.0.0/brainGraph/R/robustness.R | 125 brainGraph-3.0.0/brainGraph/R/s_core.R | 21 brainGraph-3.0.0/brainGraph/R/set_brainGraph_attributes.R | 420 ++- brainGraph-3.0.0/brainGraph/R/small_world.R | 94 brainGraph-3.0.0/brainGraph/R/spatial_dist.R | 21 brainGraph-3.0.0/brainGraph/R/sysdata.rda |binary brainGraph-3.0.0/brainGraph/R/update_brainGraph_gui.R | 291 +- brainGraph-3.0.0/brainGraph/R/utils.R | 521 ++- brainGraph-3.0.0/brainGraph/R/utils_matrix.R |only brainGraph-3.0.0/brainGraph/R/vertex_roles.R | 50 brainGraph-3.0.0/brainGraph/R/vulnerability.R | 48 brainGraph-3.0.0/brainGraph/R/write_brainnet.R | 74 brainGraph-3.0.0/brainGraph/R/zzz.R |only brainGraph-3.0.0/brainGraph/data/aal116.rda |binary brainGraph-3.0.0/brainGraph/data/aal2.120.rda |binary brainGraph-3.0.0/brainGraph/data/aal2.94.rda |binary brainGraph-3.0.0/brainGraph/data/aal90.rda |binary brainGraph-3.0.0/brainGraph/data/brainnetome.rda |only brainGraph-3.0.0/brainGraph/data/brainsuite.rda |binary brainGraph-3.0.0/brainGraph/data/craddock200.rda |binary brainGraph-3.0.0/brainGraph/data/destrieux.rda |binary brainGraph-3.0.0/brainGraph/data/destrieux.scgm.rda |binary brainGraph-3.0.0/brainGraph/data/dk.rda |binary brainGraph-3.0.0/brainGraph/data/dk.scgm.rda |binary brainGraph-3.0.0/brainGraph/data/dkt.rda |binary brainGraph-3.0.0/brainGraph/data/dkt.scgm.rda |binary brainGraph-3.0.0/brainGraph/data/dosenbach160.rda |binary brainGraph-3.0.0/brainGraph/data/gordon333.rda |only brainGraph-3.0.0/brainGraph/data/hcp_mmp1.0.rda |only brainGraph-3.0.0/brainGraph/data/hoa112.rda |binary brainGraph-3.0.0/brainGraph/data/lpba40.rda |binary brainGraph-3.0.0/brainGraph/data/power264.rda |only brainGraph-3.0.0/brainGraph/man/Bootstrapping.Rd | 36 brainGraph-3.0.0/brainGraph/man/NBS.Rd | 118 brainGraph-3.0.0/brainGraph/man/apply_thresholds.Rd | 15 brainGraph-3.0.0/brainGraph/man/atlas_helpers.Rd |only brainGraph-3.0.0/brainGraph/man/attributes.Rd |only brainGraph-3.0.0/brainGraph/man/auc_diff.Rd | 22 brainGraph-3.0.0/brainGraph/man/brainGraph-methods.Rd |only brainGraph-3.0.0/brainGraph/man/brainGraph.Rd |only brainGraph-3.0.0/brainGraph/man/brainGraphList.Rd |only brainGraph-3.0.0/brainGraph/man/brainGraph_permute.Rd | 47 brainGraph-3.0.0/brainGraph/man/brain_atlases.Rd |only brainGraph-3.0.0/brainGraph/man/centr_betw_comm.Rd | 8 brainGraph-3.0.0/brainGraph/man/centr_lev.Rd | 12 brainGraph-3.0.0/brainGraph/man/check_attributes.Rd |only brainGraph-3.0.0/brainGraph/man/choose.edges.Rd | 7 brainGraph-3.0.0/brainGraph/man/coeff_var.Rd | 25 brainGraph-3.0.0/brainGraph/man/communicability.Rd | 10 brainGraph-3.0.0/brainGraph/man/contract_brainGraph.Rd | 23 brainGraph-3.0.0/brainGraph/man/cor.diff.test.Rd | 31 brainGraph-3.0.0/brainGraph/man/correlation_matrices.Rd |only brainGraph-3.0.0/brainGraph/man/count_edges.Rd | 16 brainGraph-3.0.0/brainGraph/man/create_mats.Rd | 67 brainGraph-3.0.0/brainGraph/man/data_tables.Rd | 32 brainGraph-3.0.0/brainGraph/man/delete_all_attr.Rd | 2 brainGraph-3.0.0/brainGraph/man/dir2files.Rd |only brainGraph-3.0.0/brainGraph/man/edge_asymmetry.Rd | 5 brainGraph-3.0.0/brainGraph/man/efficiency.Rd | 33 brainGraph-3.0.0/brainGraph/man/get_rand_attrs.Rd |only brainGraph-3.0.0/brainGraph/man/glm.Rd | 256 + brainGraph-3.0.0/brainGraph/man/glm_brainGraphList.Rd |only brainGraph-3.0.0/brainGraph/man/glm_design.Rd | 105 brainGraph-3.0.0/brainGraph/man/glm_fit.Rd |only brainGraph-3.0.0/brainGraph/man/glm_graph_plots.Rd |only brainGraph-3.0.0/brainGraph/man/glm_helpers.Rd | 150 - brainGraph-3.0.0/brainGraph/man/glm_influence.Rd |only brainGraph-3.0.0/brainGraph/man/glm_info.Rd |only brainGraph-3.0.0/brainGraph/man/glm_model_select.Rd |only brainGraph-3.0.0/brainGraph/man/glm_stats.Rd |only brainGraph-3.0.0/brainGraph/man/hubness.Rd | 35 brainGraph-3.0.0/brainGraph/man/import_scn.Rd | 21 brainGraph-3.0.0/brainGraph/man/individ_contrib.Rd | 65 brainGraph-3.0.0/brainGraph/man/inverse.Rd |only brainGraph-3.0.0/brainGraph/man/make_auc_brainGraph.Rd |only brainGraph-3.0.0/brainGraph/man/make_brainGraph.Rd | 226 + brainGraph-3.0.0/brainGraph/man/make_ego_brainGraph.Rd | 10 brainGraph-3.0.0/brainGraph/man/make_intersection_brainGraph.Rd | 24 brainGraph-3.0.0/brainGraph/man/matrix_utils.Rd |only brainGraph-3.0.0/brainGraph/man/mean_distance_wt.Rd |only brainGraph-3.0.0/brainGraph/man/mediation.Rd | 154 - brainGraph-3.0.0/brainGraph/man/mtpc.Rd | 121 brainGraph-3.0.0/brainGraph/man/pad_zeros.Rd |only brainGraph-3.0.0/brainGraph/man/plot.brainGraph.Rd | 119 brainGraph-3.0.0/brainGraph/man/plot.brainGraphList.Rd |only brainGraph-3.0.0/brainGraph/man/plot_brainGraph_gui.Rd | 9 brainGraph-3.0.0/brainGraph/man/plot_brainGraph_multi.Rd | 130 brainGraph-3.0.0/brainGraph/man/plot_global.Rd | 49 brainGraph-3.0.0/brainGraph/man/plot_rich_norm.Rd | 29 brainGraph-3.0.0/brainGraph/man/plot_vertex_measures.Rd | 33 brainGraph-3.0.0/brainGraph/man/plot_volumetric.Rd | 6 brainGraph-3.0.0/brainGraph/man/random_graphs.Rd | 99 brainGraph-3.0.0/brainGraph/man/randomise.Rd | 180 + brainGraph-3.0.0/brainGraph/man/rename_levels.Rd |only brainGraph-3.0.0/brainGraph/man/residuals.Rd | 99 brainGraph-3.0.0/brainGraph/man/rich_club.Rd | 70 brainGraph-3.0.0/brainGraph/man/rich_club_attrs.Rd | 22 brainGraph-3.0.0/brainGraph/man/robustness.Rd | 25 brainGraph-3.0.0/brainGraph/man/s_core.Rd | 9 brainGraph-3.0.0/brainGraph/man/set_graph_colors.Rd |only brainGraph-3.0.0/brainGraph/man/small.world.Rd | 28 brainGraph-3.0.0/brainGraph/man/spatial_dist.Rd | 11 brainGraph-3.0.0/brainGraph/man/subset_graph.Rd | 6 brainGraph-3.0.0/brainGraph/man/update_fs_names.Rd | 2 brainGraph-3.0.0/brainGraph/man/utils.Rd |only brainGraph-3.0.0/brainGraph/man/vertex_roles.Rd | 26 brainGraph-3.0.0/brainGraph/man/vif.bg_GLM.Rd |only brainGraph-3.0.0/brainGraph/man/vulnerability.Rd | 9 brainGraph-3.0.0/brainGraph/man/write_brainnet.Rd | 38 192 files changed, 8430 insertions(+), 6467 deletions(-)
Title: Urban Water and Sanitation Survey Dataset
Description: Urban water and sanitation survey dataset collected by Water and
Sanitation for the Urban Poor (WSUP) with technical support from
Valid International. These citywide surveys have been collecting data
allowing water and sanitation service levels across the entire city to be
characterised, while also allowing more detailed data to be collected in
areas of the city of particular interest. These surveys are intended to
generate useful information for others working in the water and sanitation
sector. Current release version includes datasets collected from a survey
conducted in Dhaka, Bangladesh in March 2017. This survey in Dhaka is one of
a series of surveys to be conducted by WSUP in various
cities in which they operate including Accra, Ghana; Nakuru, Kenya;
Antananarivo, Madagascar; Maputo, Mozambique; and, Lusaka, Zambia. This
package will be updated once the surveys in other cities are completed and
datasets have been made available.
Author: Ernest Guevarra [aut, cre],
Valid International [cph],
Water and Sanitation for the Urban Poor [cph]
Maintainer: Ernest Guevarra <ernestgmd@gmail.com>
Diff between washdata versions 0.1.2 dated 2018-01-05 and 0.1.3 dated 2020-09-29
DESCRIPTION | 20 ++--- MD5 | 37 ++++++---- NAMESPACE | 3 NEWS.md | 3 R/data.R | 37 +++++++++- README.md | 36 +++++----- build/vignette.rds |binary inst/WORDLIST |only inst/_pkgdown.yml |only inst/createHexSticker.R |only inst/doc/washdata.R | 2 inst/doc/washdata.Rmd | 65 +++++++++--------- inst/doc/washdata.html | 167 ++++++++++++++++++++++++++--------------------- inst/figures |only man/figures |only man/indicatorsDataBGD.Rd | 8 +- man/popBGD.Rd | 9 +- man/ppiMatrixBGD.Rd | 8 +- man/surveyDataBGD.Rd | 10 ++ man/washdata.Rd | 23 +++++- tests |only vignettes/washdata.Rmd | 65 +++++++++--------- 22 files changed, 300 insertions(+), 193 deletions(-)
Title: Objective Bayesian Analysis for Spatial Regression Models
Description: It makes an objective Bayesian analysis of the spatial regression model using both the normal (NSR) and student-T (TSR) distributions. The functions provided give prior and posterior objective densities and allow default Bayesian estimation of the model regression parameters. Details can be found in Ordonez et al. (2020) <arXiv:2004.04341>.
Author: Alejandro Ordonez, Marcos O. Prates , Larissa A. Matos, Victor H. Lachos.
Maintainer: Alejandro Ordonez <ordonezjosealejandro@gmail.com>
Diff between OBASpatial versions 1.1 dated 2020-04-16 and 1.7 dated 2020-09-29
ChangeLog |only DESCRIPTION | 11 MD5 | 29 - NAMESPACE | 4 R/auxfunctionsnorm.R | 138 --------- R/auxfunctionst.R | 761 +++++++++++++++++++++++++++++++------------------- R/prinfunctions.R | 66 +--- man/dtsrposoba.Rd | 200 ++++++------- man/dtsrprioroba.Rd | 174 +++++------ man/intmT.Rd | 272 ++++++++--------- man/nsroba.Rd | 10 man/nsrobapred.Rd | 150 ++++----- man/summary.nsroba.Rd | 170 +++++------ man/summary.tsroba.Rd | 184 ++++++------ man/tsroba.Rd | 476 +++++++++++++++---------------- man/tsrobapred.Rd | 166 +++++----- 16 files changed, 1442 insertions(+), 1369 deletions(-)
Title: A Grammar of Clinical Data Summary
Description: A tool created to simplify the data manipulation necessary to create clinical reports.
Author: Eli Miller [aut] (<https://orcid.org/0000-0002-2127-9456>),
Mike Stackhouse [aut, cre] (<https://orcid.org/0000-0001-6030-723X>),
Ashley Tarasiewicz [aut],
Nathan Kosiba [aut] (<https://orcid.org/0000-0001-5359-4234>),
Atorus Research LLC [cph]
Maintainer: Mike Stackhouse <mike.stackhouse@atorusresearch.com>
Diff between Tplyr versions 0.1.1 dated 2020-09-10 and 0.1.2 dated 2020-09-29
DESCRIPTION | 6 MD5 | 22 +- NEWS.md | 5 R/count.R | 2 R/pop_data.R | 3 README.md | 386 ++++++--------------------------------- inst/doc/Tplyr.html | 12 - inst/doc/table.Rmd | 1 inst/doc/table.html | 13 - tests/testthat/test-count.R | 10 + tests/testthat/test-functional.R | 16 + vignettes/table.Rmd | 1 12 files changed, 121 insertions(+), 356 deletions(-)
Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015):
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from 'RevMan 5';
- prediction interval, Hartung-Knapp method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression;
- generalised linear mixed models;
- produce forest plot summarising several (subgroup) meta-analyses.
Author: Guido Schwarzer [cre, aut] (<https://orcid.org/0000-0001-6214-9087>)
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between meta versions 4.14-0 dated 2020-09-09 and 4.15-0 dated 2020-09-29
DESCRIPTION | 8 - MD5 | 82 +++++++++---------- NEWS.md | 43 ++++++++++ R/forest.R | 64 ++++++++++---- R/forest.metabind.R | 32 ++++++- R/hetcalc.R | 4 R/meta-internal.R | 3 R/meta-package.R | 2 R/metabias.R | 91 ++++++++++++--------- R/metabias.rm5.R | 2 R/metabin.R | 210 +++++++++++++++++++++++++++++-------------------- R/metacont.R | 10 ++ R/metacor.R | 10 ++ R/metacr.R | 48 ++++++++--- R/metagen.R | 52 +++++++++++- R/metainc.R | 178 ++++++++++++++++++++++++++--------------- R/metamean.R | 10 ++ R/metaprop.R | 10 ++ R/metarate.R | 10 ++ R/read.rm5-internal.R | 23 +++-- R/read.rm5.R | 2 R/settings.meta.R | 21 +++- R/summary.meta.R | 34 +++++-- R/summary.rm5.R | 2 man/forest.meta.Rd | 19 ++-- man/forest.metabind.Rd | 4 man/meta-package.Rd | 2 man/metabias.Rd | 86 ++++++++++++-------- man/metabias.rm5.Rd | 2 man/metabin.Rd | 208 +++++++++++++++++++++++++++++------------------- man/metacont.Rd | 10 ++ man/metacor.Rd | 10 ++ man/metacr.Rd | 2 man/metagen.Rd | 52 +++++++++++- man/metainc.Rd | 178 ++++++++++++++++++++++++++--------------- man/metamean.Rd | 10 ++ man/metaprop.Rd | 10 ++ man/metarate.Rd | 10 ++ man/read.rm5.Rd | 2 man/settings.meta.Rd | 2 man/summary.meta.Rd | 11 +- man/summary.rm5.Rd | 2 42 files changed, 1072 insertions(+), 499 deletions(-)
Title: Deep Time Redox Analysis of the Geobiology Ontology Network
Description: Create, visualize, manipulate, and analyze bipartite mineral-chemistry
networks for set of focal element(s) across deep-time on Earth. The method is
described in Spielman and Moore (2020) <doi:10.3389/feart.2020.585087>.
Author: Stephanie J. Spielman [aut, cre]
(<https://orcid.org/0000-0002-9090-4788>)
Maintainer: Stephanie J. Spielman <spielman@rowan.edu>
Diff between dragon versions 1.0.2 dated 2020-08-31 and 1.0.3 dated 2020-09-29
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- README.md | 17 ++++++++++------- inst/app/www/favicon.ico |binary inst/doc/dragon.html | 4 ++-- 5 files changed, 20 insertions(+), 17 deletions(-)
Title: Fast Searching for Multiple Keywords in Multiple Texts
Description: Aho-Corasick is an optimal algorithm for finding many
keywords in a text. It can locate all matches in a text in O(N+M) time; i.e.,
the time needed scales linearly with the number of keywords (N) and the size of
the text (M). Compare this to the naive approach which takes O(N*M) time to loop
through each pattern and scan for it in the text. This implementation builds the
trie (the generic name of the data structure) and runs the search in a single
function call. If you want to search multiple texts with the same trie, the
function will take a list or vector of texts and return a list of matches to
each text. By default, all 128 ASCII characters are allowed in both the keywords
and the text. A more efficient trie is possible if the alphabet size can be
reduced. For example, DNA sequences use at most 19 distinct characters and
usually only 4; protein sequences use at most 26 distinct characters and usually
only 20. UTF-8 (Unicode) matching is not currently supported.
Author: Matt Chambers [aut, cre],
Tomas Petricek [aut, cph],
Vanderbilt University [cph]
Maintainer: Matt Chambers <matt.chambers42@gmail.com>
Diff between AhoCorasickTrie versions 0.1.0 dated 2016-07-29 and 0.1.2 dated 2020-09-29
DESCRIPTION | 10 +++---- MD5 | 20 +++++++++------ R/AhoCorasickTrie.R | 3 ++ R/RcppExports.R | 19 +++++++------- man/AhoCorasickSearch.Rd | 16 ++++++++---- man/AhoCorasickSearchList.Rd | 16 ++++++++---- man/AhoCorasickTrie.Rd | 6 ++-- src/AhoCorasickTrie.cpp | 56 +++++++++++++++++++++++++++++++++++-------- src/RcppExports.cpp | 39 +++++++++++++++++++---------- tests/benchmark.R |only tests/testthat |only tests/testthat.R |only 12 files changed, 127 insertions(+), 58 deletions(-)
More information about AhoCorasickTrie at CRAN
Permanent link
Title: Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for
Genome-Wide Association Study
Description: Conduct multi-locus genome-wide association study under the framework of multi-locus random-SNP-effect mixed linear model (mrMLM). First, each marker on the genome is scanned. Bonferroni correction is replaced by a less stringent selection criterion for significant test. Then, all the markers that are potentially associated with the trait are included in a multi-locus genetic model, their effects are estimated by empirical Bayes and all the nonzero effects were further identified by likelihood ratio test for true QTL. Wen YJ, Zhang H, Ni YL, Huang B, Zhang J, Feng JY, Wang SB, Dunwell JM, Zhang YM, Wu R (2018) <doi:10.1093/bib/bbw145>.
Author: Zhang Ya-Wen, Li Pei, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Diff between mrMLM versions 4.0 dated 2019-10-22 and 4.0.1 dated 2020-09-29
mrMLM-4.0.1/mrMLM/DESCRIPTION | 17 mrMLM-4.0.1/mrMLM/MD5 | 35 mrMLM-4.0.1/mrMLM/NAMESPACE | 12 mrMLM-4.0.1/mrMLM/R/FASTmrEMMA.R | 59 mrMLM-4.0.1/mrMLM/R/FASTmrMLM.R | 36 mrMLM-4.0.1/mrMLM/R/ISIS.R | 17 mrMLM-4.0.1/mrMLM/R/MultiManhattan.R |only mrMLM-4.0.1/mrMLM/R/RcppExports.R |only mrMLM-4.0.1/mrMLM/R/mrMLM.R | 651 +++++----- mrMLM-4.0.1/mrMLM/R/mrMLMFun.R | 1598 ++++++++++++-------------- mrMLM-4.0.1/mrMLM/R/pKWmEB.R | 59 mrMLM-4.0.1/mrMLM/R/pLARmEB.R | 29 mrMLM-4.0.1/mrMLM/data/ResultFinal.rda |only mrMLM-4.0.1/mrMLM/data/ResultIntermediate.rda |only mrMLM-4.0.1/mrMLM/inst/doc/Instruction.pdf |binary mrMLM-4.0.1/mrMLM/man/MultiManhattan.Rd |only mrMLM-4.0.1/mrMLM/man/ResultFinal.Rd |only mrMLM-4.0.1/mrMLM/man/ResultIntermediate.Rd |only mrMLM-4.0.1/mrMLM/man/mrMLM.Rd | 101 + mrMLM-4.0.1/mrMLM/man/multiplication_speed.Rd |only mrMLM-4.0.1/mrMLM/src |only mrMLM-4.0/mrMLM/inst/extdata/Genotype_Cha.txt |only mrMLM-4.0/mrMLM/inst/extdata/Genotype_Num.txt |only mrMLM-4.0/mrMLM/inst/extdata/Kinship.txt |only 24 files changed, 1256 insertions(+), 1358 deletions(-)
Title: Detecting Anomalies in Data
Description: Implements Collective And Point Anomaly (CAPA) <arXiv:1806.01947>, Multi-Variate Collective And Point Anomaly (MVCAPA) <arXiv:1909.01691>, Proportion Adaptive Segment Selection (PASS) <doi:10.1093/biomet/ass059>, and Bayesian Abnormal Region Detector (BARD) <doi:10.1214/16-BA998> methods for the detection of anomalies in time series data. Also includes sequential versions of CAPA and MVCAPA <arXiv:2009.06670>.
Author: Alex Fisch [aut],
Daniel Grose [aut, cre],
Lawrence Bardwell [ctb],
Idris Eckley [ths],
Paul Fearnhead [ths]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>
Diff between anomaly versions 3.0.2 dated 2020-08-07 and 4.0.0 dated 2020-09-29
anomaly-3.0.2/anomaly/R/zzz.R |only anomaly-4.0.0/anomaly/DESCRIPTION | 10 anomaly-4.0.0/anomaly/MD5 | 41 anomaly-4.0.0/anomaly/NAMESPACE | 4 anomaly-4.0.0/anomaly/R/bard.R | 33 anomaly-4.0.0/anomaly/R/capa.R | 780 ++------------ anomaly-4.0.0/anomaly/R/capa.mv.R |only anomaly-4.0.0/anomaly/R/capa.uv.R |only anomaly-4.0.0/anomaly/R/pass.R | 2 anomaly-4.0.0/anomaly/R/pass.class.R | 23 anomaly-4.0.0/anomaly/R/scapa.mv.R |only anomaly-4.0.0/anomaly/R/scapa.uv.R |only anomaly-4.0.0/anomaly/R/tierney.R |only anomaly-4.0.0/anomaly/build/partial.rdb |binary anomaly-4.0.0/anomaly/inst/REFERENCES.bib | 13 anomaly-4.0.0/anomaly/man/capa.mv.Rd | 4 anomaly-4.0.0/anomaly/man/capa.uv.Rd | 8 anomaly-4.0.0/anomaly/man/collective_anomalies-methods.Rd | 30 anomaly-4.0.0/anomaly/man/pass.Rd | 2 anomaly-4.0.0/anomaly/man/plot-methods.Rd | 28 anomaly-4.0.0/anomaly/man/point_anomaly-methods.Rd | 28 anomaly-4.0.0/anomaly/man/scapa.mv.Rd |only anomaly-4.0.0/anomaly/man/scapa.uv.Rd |only anomaly-4.0.0/anomaly/man/show-methods.Rd | 11 anomaly-4.0.0/anomaly/man/summary-methods.Rd | 14 anomaly-4.0.0/anomaly/man/tierney.Rd |only 26 files changed, 292 insertions(+), 739 deletions(-)
Title: Workflow for Open Reproducible Code in Science
Description: Create reproducible and transparent research projects in 'R', with
a minimal amount of code. This package is based on the Workflow for Open
Reproducible Code in Science (WORCS), a step-by-step procedure based on best
practices for
Open Science. It includes an 'RStudio' project template, several
convenience functions, and all dependencies required to make your project
reproducible and transparent. WORCS is explained in the tutorial paper
by Van Lissa, Brandmaier, Brinkman, Lamprecht, Struiksma, & Vreede (2020).
<doi:10.17605/OSF.IO/ZCVBS>.
Author: Caspar J. van Lissa [aut, cre]
(<https://orcid.org/0000-0002-0808-5024>),
Aaron Peikert [aut] (<https://orcid.org/0000-0001-7813-818X>),
Andreas M. Brandmaier [aut] (<https://orcid.org/0000-0001-8765-6982>)
Maintainer: Caspar J. van Lissa <c.j.vanlissa@uu.nl>
Diff between worcs versions 0.1.3 dated 2020-06-27 and 0.1.4 dated 2020-09-29
DESCRIPTION | 10 - MD5 | 43 ++++---- NAMESPACE | 2 R/descriptives.R | 7 - R/misc.R | 30 +++++ R/save_load.R | 63 ++++++++---- R/synthetic.R | 53 ++++++---- R/worcs_badge.R | 61 +++++------ R/worcs_project.R | 170 ++++++++++++++++++++++----------- build/vignette.rds |binary inst/doc/git_cloud.Rmd | 12 +- inst/doc/git_cloud.html | 12 +- inst/doc/setup.Rmd | 8 + inst/doc/setup.html | 5 man/add_manuscript.Rd |only man/closed_data.Rd | 15 +- man/load_data.Rd | 3 man/open_data.Rd | 15 +- tests/testthat/test-add_manuscript.R |only tests/testthat/test-citations.R | 6 - tests/testthat/test-synthetic.R |only tests/testthat/test-test-closed_data.R | 36 +++--- vignettes/git_cloud.Rmd | 12 +- vignettes/setup.Rmd | 8 + 24 files changed, 366 insertions(+), 205 deletions(-)
Title: Tabular Data Backed by Partitioned 'fst' Files
Description: Intended for larger-than-memory tabular data, 'prt' objects provide an interface to read row and/or column subsets into memory as data.table objects. Data queries, constructed as 'R' expressions, are evaluated using the non-standard evaluation framework provided by 'rlang' and file-backing is powered by the fast and efficient 'fst' package.
Author: Nicolas Bennett [aut, cre],
Drago Plecko [ctb]
Maintainer: Nicolas Bennett <nicolas.bennett@stat.math.ethz.ch>
Diff between prt versions 0.1.1 dated 2020-09-02 and 0.1.2 dated 2020-09-29
DESCRIPTION | 8 +++--- MD5 | 15 ++++++------ NAMESPACE | 1 NEWS.md | 4 +++ R/format.R | 2 + R/glimpse.R | 37 +++++++++++++++---------------- inst/doc/prt.html | 4 +-- tests/testthat/output/str/mtcars-len.txt |only tests/testthat/test-glimpse.R | 8 +++++- 9 files changed, 46 insertions(+), 33 deletions(-)
Title: Robust Trimmed Clustering
Description: Provides functions for robust trimmed clustering. The methods are described in Garcia-Escudero (2008) <doi:10.1214/07-AOS515>, Fritz et al. (2012) <doi:10.18637/jss.v047.i12>, Garcia-Escudero et al. (2011) <doi:10.1007/s11222-010-9194-z> and others.
Author: Agustin Mayo Iscar, Luis Angel Garcia Escudero, Heinrich Fritz
Maintainer: Valentin Todorov <valentin.todorov@chello.at>
Diff between tclust versions 1.4-1 dated 2018-05-24 and 1.4-2 dated 2020-09-29
tclust-1.4-1/tclust/man/tclust.package.Rd |only tclust-1.4-2/tclust/DESCRIPTION | 11 +++++---- tclust-1.4-2/tclust/MD5 | 35 ++++++++++++++---------------- tclust-1.4-2/tclust/R/R_tclust.R | 22 +++++++++--------- tclust-1.4-2/tclust/R/ctlcurves.R | 33 ++++++++++++++-------------- tclust-1.4-2/tclust/R/print.DiscrFact.R | 11 ++++----- tclust-1.4-2/tclust/R/print.tclust.R | 4 +++ tclust-1.4-2/tclust/R/tkmeans.R | 14 +++++++----- tclust-1.4-2/tclust/build/vignette.rds |binary tclust-1.4-2/tclust/inst/CITATION | 4 +-- tclust-1.4-2/tclust/inst/doc/tclust.pdf |binary tclust-1.4-2/tclust/man/DiscrFact.Rd | 15 +++++++----- tclust-1.4-2/tclust/man/M5data.Rd | 7 +----- tclust-1.4-2/tclust/man/geyser2.Rd | 4 --- tclust-1.4-2/tclust/man/plot.DiscrFact.Rd | 6 ++--- tclust-1.4-2/tclust/man/plot.ctlcurves.Rd | 4 +-- tclust-1.4-2/tclust/man/plot.tclust.Rd | 8 +++--- tclust-1.4-2/tclust/man/swissbank.Rd | 4 --- tclust-1.4-2/tclust/vignettes/tclust.bib | 2 - 19 files changed, 94 insertions(+), 90 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 1.0.2 dated 2020-04-13 and 1.1.0 dated 2020-09-29
ChangeLog | 8 + DESCRIPTION | 8 - MD5 | 50 +++++------ R/createOA.R | 45 +++++++--- R/improvedLHS.r | 2 R/maximinLHS.R | 2 inst/doc/augment_lhs.html | 4 inst/doc/lhs_basics.html | 4 inst/doc/lhs_faq.html | 4 man/createAddelKemp.Rd | 8 + man/createAddelKemp3.Rd | 9 +- man/createAddelKempN.Rd | 16 +++ man/createBose.Rd | 7 + man/createBoseBush.Rd | 7 + man/createBoseBushl.Rd | 10 +- man/createBush.Rd | 7 + man/createBusht.Rd | 8 + man/improvedLHS.Rd | 2 man/maximinLHS.Rd | 2 src/COrthogonalArray.cpp | 4 src/akn.cpp | 48 +++-------- src/oaLHS.h | 2 src/oaLHSUtility.h | 22 ++++- tests/testthat/helper-lhs.R | 27 ++++++ tests/testthat/test-createoa.R | 88 +++++++------------- tests/testthat/test-randomlhs.r | 172 ++++++++++++++++++++-------------------- 26 files changed, 309 insertions(+), 257 deletions(-)
Title: Routing with GTFS (General Transit Feed Specification) Data
Description: Use GTFS (General Transit Feed Specification) data
for routing from nominated start and end stations, and for extracting
isochrones from nominated start station.
Author: Mark Padgham [aut, cre],
Marcin Stepniak [aut] (<https://orcid.org/0000-0002-6489-5443>),
Alexandra Kapp [ctb]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between gtfsrouter versions 0.0.3 dated 2020-08-27 and 0.0.4 dated 2020-09-29
DESCRIPTION | 6 +++--- MD5 | 19 +++++++++++-------- NAMESPACE | 1 + NEWS.md | 12 +++++++++++- R/RcppExports.R | 12 ++++++++++++ R/route-headway.R |only R/router.R | 8 +++++++- inst/doc/gtfsrouter.html | 26 ++++++++++++-------------- man/gtfs_route_headway.Rd |only src/RcppExports.cpp | 19 +++++++++++++++++++ src/csa-matrix.cpp |only src/csa.h | 6 ++++++ 12 files changed, 82 insertions(+), 27 deletions(-)
Title: Locate Errors with Validation Rules
Description: Errors in data can be located and removed using validation rules from package 'validate'.
Author: Edwin de Jonge [aut, cre] (<https://orcid.org/0000-0002-6580-4718>),
Mark van der Loo [aut]
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between errorlocate versions 0.3.0 dated 2020-02-06 and 0.4 dated 2020-09-29
errorlocate-0.3.0/errorlocate/R/expr_simplify.R |only errorlocate-0.3.0/errorlocate/R/local_variable.R |only errorlocate-0.3.0/errorlocate/man/substitute_.Rd |only errorlocate-0.3.0/errorlocate/tests/testthat/test.mps |only errorlocate-0.4/errorlocate/DESCRIPTION | 17 -- errorlocate-0.4/errorlocate/MD5 | 42 ++--- errorlocate-0.4/errorlocate/NAMESPACE | 1 errorlocate-0.4/errorlocate/NEWS.md | 11 + errorlocate-0.4/errorlocate/R/MipRules.R | 31 +++ errorlocate-0.4/errorlocate/R/categorical.R | 4 errorlocate-0.4/errorlocate/R/dnf.R | 17 -- errorlocate-0.4/errorlocate/R/errorlocalizer.R | 82 ++++++---- errorlocate-0.4/errorlocate/R/expr_manip.R | 8 errorlocate-0.4/errorlocate/R/mip_lpsolve.R | 2 errorlocate-0.4/errorlocate/R/replace-errors.R | 18 +- errorlocate-0.4/errorlocate/R/utils.R | 60 +++---- errorlocate-0.4/errorlocate/R/values.R | 9 - errorlocate-0.4/errorlocate/man/MipRules-class.Rd | 4 errorlocate-0.4/errorlocate/man/errorlocate-package.Rd | 2 errorlocate-0.4/errorlocate/man/locate_errors.Rd | 20 -- errorlocate-0.4/errorlocate/man/replace_errors.Rd | 37 ++-- errorlocate-0.4/errorlocate/tests/testthat/test-conditional.R | 18 ++ errorlocate-0.4/errorlocate/tests/testthat/test-dnf.R | 17 ++ errorlocate-0.4/errorlocate/tests/testthat/test-locate_errors.R | 22 ++ 24 files changed, 260 insertions(+), 162 deletions(-)
Title: Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for
Genome-Wide Association Study with Graphical User Interface
Description: Conduct multi-locus genome-wide association study under the framework of multi-locus random-SNP-effect mixed linear model (mrMLM). First, each marker on the genome is scanned. Bonferroni correction is replaced by a less stringent selection criterion for significant test. Then, all the markers that are potentially associated with the trait are included in a multi-locus genetic model, their effects are estimated by empirical Bayes and all the nonzero effects were further identified by likelihood ratio test for true QTL. Wen YJ, Zhang H, Ni YL, Huang B, Zhang J, Feng JY, Wang SB, Dunwell JM, Zhang YM, Wu R (2018) <doi:10.1093/bib/bbw145>.
Author: Zhang Ya-Wen, Li Pei, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Diff between mrMLM.GUI versions 4.0 dated 2019-10-22 and 4.0.1 dated 2020-09-29
mrMLM.GUI-4.0.1/mrMLM.GUI/DESCRIPTION | 17 mrMLM.GUI-4.0.1/mrMLM.GUI/MD5 | 30 mrMLM.GUI-4.0.1/mrMLM.GUI/NAMESPACE | 12 mrMLM.GUI-4.0.1/mrMLM.GUI/R/FASTmrEMMA.R | 57 mrMLM.GUI-4.0.1/mrMLM.GUI/R/FASTmrMLM.R | 54 mrMLM.GUI-4.0.1/mrMLM.GUI/R/ISIS.R | 17 mrMLM.GUI-4.0.1/mrMLM.GUI/R/RcppExports.R |only mrMLM.GUI-4.0.1/mrMLM.GUI/R/mrMLM.GUI.R | 1474 +++++++++--------- mrMLM.GUI-4.0.1/mrMLM.GUI/R/mrMLMFun.R | 59 mrMLM.GUI-4.0.1/mrMLM.GUI/R/pKWmEB.R | 71 mrMLM.GUI-4.0.1/mrMLM.GUI/R/pLARmEB.R | 30 mrMLM.GUI-4.0.1/mrMLM.GUI/inst/doc/Instruction.pdf |binary mrMLM.GUI-4.0.1/mrMLM.GUI/man/mrMLM.GUI-package.Rd | 12 mrMLM.GUI-4.0.1/mrMLM.GUI/man/multiplication_speed.Rd |only mrMLM.GUI-4.0.1/mrMLM.GUI/src |only mrMLM.GUI-4.0/mrMLM.GUI/inst/extdata/Genotype_Cha.txt |only mrMLM.GUI-4.0/mrMLM.GUI/inst/extdata/Genotype_Hmp.csv |only mrMLM.GUI-4.0/mrMLM.GUI/inst/extdata/Genotype_Num.txt |only mrMLM.GUI-4.0/mrMLM.GUI/inst/extdata/Kinship.txt |only 19 files changed, 863 insertions(+), 970 deletions(-)
Title: Read 'Excel' Binary (.xlsb) Workbooks
Description: Import data from 'Excel' binary (.xlsb) workbooks into R.
Author: Michael Allen [aut, cre]
Maintainer: Michael Allen <michael@velofrog.com>
Diff between readxlsb versions 0.1.3 dated 2020-04-14 and 0.1.4 dated 2020-09-29
DESCRIPTION | 10 ++-- MD5 | 10 ++-- R/read_xlsb.R | 20 ++++++++- build/vignette.rds |binary inst/doc/read-xlsb-workbook.html | 84 +++++++++++++++++++++++---------------- man/read_xlsb.Rd | 2 6 files changed, 80 insertions(+), 46 deletions(-)
Title: Miscellaneous Functions by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>),
Wush Wu [ctb],
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brüggemann [ctb] (<https://orcid.org/0000-0002-5329-5987>)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.17 dated 2020-09-09 and 0.18 dated 2020-09-29
DESCRIPTION | 6 - MD5 | 50 ++++++---- NAMESPACE | 12 ++ NEWS.md | 32 ++++++ R/io.R | 98 ++++++++++++++++++++ R/json.R | 18 ++- R/paths.R | 220 +++++++++++++++++++++++++++++++++++++++++++++ R/session.R |only R/string.R | 37 ++++++- R/utils.R | 120 ------------------------ inst/doc/xfun.R | 13 ++ inst/doc/xfun.Rmd | 45 +++++++++ inst/doc/xfun.html | 167 +++++++++++++++++++++------------- man/bump_version.Rd |only man/do_once.Rd |only man/download_file.Rd | 8 - man/from_root.Rd |only man/github_releases.Rd |only man/grep_sub.Rd |only man/magic_path.Rd |only man/process_file.Rd |only man/proj_root.Rd |only man/relative_path.Rd |only man/session_info.Rd | 2 man/url_filename.Rd |only man/valid_syntax.Rd |only src/base64.c | 13 -- tests/testit/test-io.R | 4 tests/testit/test-json.R | 2 tests/testit/test-paths.R | 9 + tests/testit/test-string.R | 19 +++ vignettes/xfun.Rmd | 45 +++++++++ 32 files changed, 690 insertions(+), 230 deletions(-)
Title: Automatic Unobserved Components Models
Description: Comprehensive analysis and forecasting
of univariate time series using automatic
unobserved components models and algorithms.
Harvey, AC (1989) <doi:10.1017/CBO9781107049994>.
Pedregal, DJ and Young PC (2002) <doi:10.1002/9780470996430>.
Durbin J and Koopman SJ (2012) <doi:10.1093/acprof:oso/9780199641178.001.0001>.
Author: Diego J. Pedregal [aut, cre] (<https://orcid.org/0000-0003-4958-0969>)
Maintainer: Diego J. Pedregal <Diego.Pedregal@uclm.es>
Diff between UComp versions 1.1 dated 2020-07-01 and 2.0 dated 2020-09-29
UComp-1.1/UComp/build |only UComp-1.1/UComp/man/UComp-package.Rd |only UComp-2.0/UComp/DESCRIPTION | 13 UComp-2.0/UComp/MD5 | 62 ++- UComp-2.0/UComp/NAMESPACE | 40 + UComp-2.0/UComp/R/RcppExports.R | 14 UComp-2.0/UComp/R/UCS3functions.R |only UComp-2.0/UComp/R/UCcomponents.R | 186 ++++----- UComp-2.0/UComp/R/UCestim.R | 248 ++++++------ UComp-2.0/UComp/R/UCfilter.R | 323 +++++++-------- UComp-2.0/UComp/R/UCmodel.R | 673 ++++++++++++++++----------------- UComp-2.0/UComp/R/UComp-package.R |only UComp-2.0/UComp/R/UCvalidate.R | 106 ++--- UComp-2.0/UComp/R/data.R |only UComp-2.0/UComp/data |only UComp-2.0/UComp/man/Forecast.Rd |only UComp-2.0/UComp/man/OECDgdp.Rd |only UComp-2.0/UComp/man/UC.Rd | 6 UComp-2.0/UComp/man/UCcomponents.Rd | 2 UComp-2.0/UComp/man/UCdisturb.Rd | 4 UComp-2.0/UComp/man/UCestim.Rd | 2 UComp-2.0/UComp/man/UCfilter.Rd | 4 UComp-2.0/UComp/man/UCmodel.Rd | 4 UComp-2.0/UComp/man/UComp.Rd |only UComp-2.0/UComp/man/UCsetup.Rd | 4 UComp-2.0/UComp/man/UCsmooth.Rd | 4 UComp-2.0/UComp/man/UCvalidate.Rd | 62 +-- UComp-2.0/UComp/man/USgdp.Rd |only UComp-2.0/UComp/man/airpas.Rd |only UComp-2.0/UComp/man/ch4.Rd |only UComp-2.0/UComp/man/coef.UComp.Rd |only UComp-2.0/UComp/man/fitted.UComp.Rd |only UComp-2.0/UComp/man/logLik.UComp.Rd |only UComp-2.0/UComp/man/plot.UComp.Rd |only UComp-2.0/UComp/man/predict.UComp.Rd |only UComp-2.0/UComp/man/print.UComp.Rd |only UComp-2.0/UComp/man/residuals.UComp.Rd |only UComp-2.0/UComp/man/summary.UComp.Rd |only UComp-2.0/UComp/man/tsdiag.UComp.Rd |only UComp-2.0/UComp/src/BSMmodel.h | 6 UComp-2.0/UComp/src/SSpace.h | 39 + 41 files changed, 923 insertions(+), 879 deletions(-)
Title: A Tool Kit for Working with Time Series in R
Description: Easy visualization, wrangling, and feature engineering of time series data for
forecasting and machine learning prediction.
Methods discussed herein are commonplace in machine learning, and have been cited
in various literature. Refer to "Calendar Effects" in papers such as
Taieb, Souhaib Ben. "Machine learning strategies for multi-step-ahead time series
forecasting." Universit Libre de Bruxelles, Belgium (2014): 75-86.
<http://souhaib-bentaieb.com/pdf/2014_phd.pdf>.
Author: Matt Dancho [aut, cre],
Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between timetk versions 2.2.1 dated 2020-09-01 and 2.3.0 dated 2020-09-29
DESCRIPTION | 6 MD5 | 79 +++--- NAMESPACE | 17 - NEWS.md | 22 - R/augment-tk_augment_differences.R | 1 R/augment-tk_augment_fourier.R | 1 R/augment-tk_augment_lags.R | 1 R/augment-tk_augment_timeseries.R | 1 R/dplyr-pad_by_time.R | 116 ++++++---- R/recipes-step_fourier.R | 6 R/rsample-tk_time_series_cv_plan.R | 5 R/vec-diff.R | 42 --- R/vec-lag.R | 20 - R/vec-log_interval.R | 4 R/vec-normalize.R | 4 R/vec-slidify.R | 2 R/vec-smooth.R | 19 - R/vec-standardize.R | 4 R/vec-ts_clean.R | 2 R/vec-ts_impute.R | 2 README.md | 77 +++--- inst/doc/TK04_Plotting_Time_Series.R | 3 inst/doc/TK04_Plotting_Time_Series.Rmd | 22 + inst/doc/TK04_Plotting_Time_Series.html | 18 + inst/doc/TK05_Plotting_Seasonality_and_Correlation.R | 3 inst/doc/TK05_Plotting_Seasonality_and_Correlation.Rmd | 21 + inst/doc/TK05_Plotting_Seasonality_and_Correlation.html | 18 + 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/README-unnamed-chunk-8-1.png |only man/pad_by_time.Rd | 17 + vignettes/TK04_Plotting_Time_Series.Rmd | 22 + vignettes/TK05_Plotting_Seasonality_and_Correlation.Rmd | 21 + vignettes/temp_archive/TK00_Time_Series_Coercion.Rmd | 22 + vignettes/temp_archive/TK01_Working_With_Time_Series_Index.Rmd | 22 + vignettes/temp_archive/TK02_Time_Series_Date_Sequences.Rmd | 21 + vignettes/temp_archive/TK03_Forecasting_Using_Time_Series_Signature.Rmd | 23 + vignettes/temp_archive/TK06_Automatic_Frequency_And_Trend_Selection.Rmd | 21 + vignettes/temp_archive/TK07_Time_Series_Data_Wrangling.Rmd | 21 + vignettes/temp_archive/TK08_Automatic_Anomaly_Detection.Rmd | 21 + 41 files changed, 406 insertions(+), 321 deletions(-)
Title: Genome Wide Association Studies
Description: Fast single trait Genome Wide Association Studies (GWAS) following
the method described in Kang et al. (2010), <doi:10.1038/ng.548>.
One of a series of statistical genetic packages for streamlining the
analysis of typical plant breeding experiments developed by Biometris.
Author: Bart-Jan van Rossum [aut, cre],
Willem Kruijer [aut] (<https://orcid.org/0000-0001-7179-1733>),
Fred van Eeuwijk [ctb] (<https://orcid.org/0000-0003-3672-2921>),
Martin Boer [ctb],
Marcos Malosetti [ctb] (<https://orcid.org/0000-0002-8150-1397>),
Daniela Bustos-Korts [ctb] (<https://orcid.org/0000-0003-3827-6726>),
Emilie Millet [ctb] (<https://orcid.org/0000-0002-2913-4892>),
Joao Paulo [ctb] (<https://orcid.org/0000-0002-4180-0763>),
Maikel Verouden [ctb] (<https://orcid.org/0000-0002-4893-3323>),
Ron Wehrens [ctb] (<https://orcid.org/0000-0002-8798-5599>),
Choazhi Zheng [ctb] (<https://orcid.org/0000-0001-6030-3933>)
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenGWAS versions 1.0.4 dated 2020-03-02 and 1.0.5 dated 2020-09-29
statgenGWAS-1.0.4/statgenGWAS/data/datalist |only statgenGWAS-1.0.5/statgenGWAS/DESCRIPTION | 13 statgenGWAS-1.0.5/statgenGWAS/MD5 | 69 - statgenGWAS-1.0.5/statgenGWAS/NAMESPACE | 3 statgenGWAS-1.0.5/statgenGWAS/NEWS.md | 10 statgenGWAS-1.0.5/statgenGWAS/R/GWASHelp.R | 609 +++++----- statgenGWAS-1.0.5/statgenGWAS/R/RcppExports.R | 4 statgenGWAS-1.0.5/statgenGWAS/R/codeMarkers.R | 91 - statgenGWAS-1.0.5/statgenGWAS/R/createGData.R | 9 statgenGWAS-1.0.5/statgenGWAS/R/createGWAS.R | 56 statgenGWAS-1.0.5/statgenGWAS/R/data.R | 2 statgenGWAS-1.0.5/statgenGWAS/R/manhattanPlot.R | 250 ++-- statgenGWAS-1.0.5/statgenGWAS/R/qqPlot.R | 114 - statgenGWAS-1.0.5/statgenGWAS/R/qtlPlot.R | 82 - statgenGWAS-1.0.5/statgenGWAS/R/runSingleTraitGwas.R | 95 + statgenGWAS-1.0.5/statgenGWAS/README.md | 115 + statgenGWAS-1.0.5/statgenGWAS/build/vignette.rds |binary statgenGWAS-1.0.5/statgenGWAS/configure | 72 - statgenGWAS-1.0.5/statgenGWAS/configure.ac | 5 statgenGWAS-1.0.5/statgenGWAS/inst/doc/GWAS.R | 20 statgenGWAS-1.0.5/statgenGWAS/inst/doc/GWAS.Rmd | 62 - statgenGWAS-1.0.5/statgenGWAS/inst/doc/GWAS.html | 131 +- statgenGWAS-1.0.5/statgenGWAS/inst/tinytest/test_STGoptions.R | 24 statgenGWAS-1.0.5/statgenGWAS/inst/tinytest/test_plots.R | 6 statgenGWAS-1.0.5/statgenGWAS/man/dropsData.Rd | 202 +-- statgenGWAS-1.0.5/statgenGWAS/man/figures |only statgenGWAS-1.0.5/statgenGWAS/man/gData.Rd | 225 +-- statgenGWAS-1.0.5/statgenGWAS/man/plot.GWAS.Rd | 274 ++-- statgenGWAS-1.0.5/statgenGWAS/man/runSingleTraitGwas.Rd | 484 ++++--- statgenGWAS-1.0.5/statgenGWAS/man/statgenGWAS-package.Rd | 89 - statgenGWAS-1.0.5/statgenGWAS/man/summary.GWAS.Rd | 43 statgenGWAS-1.0.5/statgenGWAS/src/RcppExports.cpp | 15 statgenGWAS-1.0.5/statgenGWAS/src/codeCharMarkers.cpp |only statgenGWAS-1.0.5/statgenGWAS/src/getThr.cpp | 2 statgenGWAS-1.0.5/statgenGWAS/vignettes/GWAS.Rmd | 62 - statgenGWAS-1.0.5/statgenGWAS/vignettes/bibliography.bib | 15 36 files changed, 1816 insertions(+), 1437 deletions(-)
Title: Simulation and Prediction with Seasonal ARIMA Models
Description: Functions, classes and methods for time series modelling with ARIMA
and related models. The aim of the package is to provide consistent
interface for the user. For example, a single function autocorrelations()
computes various kinds of theoretical and sample autocorrelations. This is
work in progress, see the documentation and vignettes for the current
functionality. Function sarima() fits extended multiplicative seasonal
ARIMA models with trends, exogenous variables and arbitrary roots on the
unit circle, which can be fixed or estimated.
Author: Georgi N. Boshnakov [aut, cre],
Jamie Halliday [aut]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between sarima versions 0.8.2 dated 2020-03-02 and 0.8.4 dated 2020-09-29
DESCRIPTION | 8 ++++---- MD5 | 21 +++++++++++---------- NEWS.md | 5 +++++ build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 12 +++++++++++- inst/auto |only inst/doc/garch_tests_example.pdf |binary inst/doc/white_noise_tests.pdf |binary man/arma_Q0Gardner.Rd | 2 +- man/arma_Q0gnb.Rd | 2 +- man/sarima.Rd | 2 +- 12 files changed, 34 insertions(+), 18 deletions(-)
More information about prettifyAddins at CRAN
Permanent link
Title: Summary Tables and Plots for Statistical Models and Data:
Beautiful, Customizable, and Publication-Ready
Description: Create beautiful and customizable tables to summarize several
statistical models side-by-side. Draw coefficient plots, multi-level
cross-tabs, dataset summaries, balance tables (a.k.a. "Table 1s"), and
correlation matrices. This package supports dozens of statistical models,
and it can produce tables in HTML, LaTeX, Word, Markdown, PDF, PowerPoint,
Excel, RTF, JPG, or PNG. Tables can easily be embedded in 'Rmarkdown' or
'knitr' dynamic documents.
Author: Vincent Arel-Bundock [aut, cre]
(<https://orcid.org/0000-0003-2042-7063>)
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between modelsummary versions 0.6.1 dated 2020-09-04 and 0.6.2 dated 2020-09-29
modelsummary-0.6.1/modelsummary/man/override_statistic.Rd |only modelsummary-0.6.1/modelsummary/man/override_statistic.character.Rd |only modelsummary-0.6.1/modelsummary/man/override_statistic.function.Rd |only modelsummary-0.6.1/modelsummary/man/override_statistic.matrix.Rd |only modelsummary-0.6.1/modelsummary/man/override_statistic.numeric.Rd |only modelsummary-0.6.2/modelsummary/DESCRIPTION | 15 modelsummary-0.6.2/modelsummary/MD5 | 130 +-- modelsummary-0.6.2/modelsummary/NAMESPACE | 17 modelsummary-0.6.2/modelsummary/NEWS.md | 13 modelsummary-0.6.2/modelsummary/R/convenience.R | 30 modelsummary-0.6.2/modelsummary/R/datasummary.R | 174 ++-- modelsummary-0.6.2/modelsummary/R/datasummary_balance.R | 428 +++++----- modelsummary-0.6.2/modelsummary/R/datasummary_correlation.R | 66 - modelsummary-0.6.2/modelsummary/R/datasummary_df.R |only modelsummary-0.6.2/modelsummary/R/datasummary_extract.R | 253 ++--- modelsummary-0.6.2/modelsummary/R/datasummary_functions.R | 189 +--- modelsummary-0.6.2/modelsummary/R/datasummary_skim.R | 281 +++++- modelsummary-0.6.2/modelsummary/R/extract_estimates.R | 197 ++-- modelsummary-0.6.2/modelsummary/R/extract_gof.R | 125 +- modelsummary-0.6.2/modelsummary/R/extract_models.R | 245 +++-- modelsummary-0.6.2/modelsummary/R/extract_statistic_override.R | 142 --- modelsummary-0.6.2/modelsummary/R/factory.R | 279 +++--- modelsummary-0.6.2/modelsummary/R/factory_dataframe.R | 18 modelsummary-0.6.2/modelsummary/R/factory_flextable.R | 70 - modelsummary-0.6.2/modelsummary/R/factory_gt.R | 120 +- modelsummary-0.6.2/modelsummary/R/factory_huxtable.R | 106 +- modelsummary-0.6.2/modelsummary/R/factory_kableExtra.R | 111 +- modelsummary-0.6.2/modelsummary/R/glance_custom.R | 16 modelsummary-0.6.2/modelsummary/R/gof_map.R | 71 + modelsummary-0.6.2/modelsummary/R/modelplot.R | 225 ++--- modelsummary-0.6.2/modelsummary/R/modelsummary.R | 214 ++--- modelsummary-0.6.2/modelsummary/R/parse_output_arg.R | 166 +-- modelsummary-0.6.2/modelsummary/R/sanity_checks.R | 97 +- modelsummary-0.6.2/modelsummary/R/stars.R | 50 - modelsummary-0.6.2/modelsummary/R/tidy_custom.R | 6 modelsummary-0.6.2/modelsummary/R/utils_pad.R | 27 modelsummary-0.6.2/modelsummary/R/utils_pipe.R | 4 modelsummary-0.6.2/modelsummary/R/utils_rounding.R | 14 modelsummary-0.6.2/modelsummary/README.md | 47 - modelsummary-0.6.2/modelsummary/build/modelsummary.pdf |binary modelsummary-0.6.2/modelsummary/man/DinM.Rd | 8 modelsummary-0.6.2/modelsummary/man/PercentMissing.Rd | 2 modelsummary-0.6.2/modelsummary/man/assert_dependency.Rd |only modelsummary-0.6.2/modelsummary/man/datasummary.Rd | 7 modelsummary-0.6.2/modelsummary/man/datasummary_balance.Rd | 16 modelsummary-0.6.2/modelsummary/man/datasummary_correlation.Rd | 4 modelsummary-0.6.2/modelsummary/man/datasummary_df.Rd |only modelsummary-0.6.2/modelsummary/man/datasummary_skim.Rd | 44 - modelsummary-0.6.2/modelsummary/man/extract_estimates.Rd | 8 modelsummary-0.6.2/modelsummary/man/extract_gof.Rd | 8 modelsummary-0.6.2/modelsummary/man/extract_models.Rd | 23 modelsummary-0.6.2/modelsummary/man/extract_statistic_override.Rd | 8 modelsummary-0.6.2/modelsummary/man/factory.Rd | 10 modelsummary-0.6.2/modelsummary/man/factory_dataframe.Rd | 6 modelsummary-0.6.2/modelsummary/man/factory_flextable.Rd | 6 modelsummary-0.6.2/modelsummary/man/factory_gt.Rd | 6 modelsummary-0.6.2/modelsummary/man/factory_huxtable.Rd | 6 modelsummary-0.6.2/modelsummary/man/factory_kableExtra.Rd | 6 modelsummary-0.6.2/modelsummary/man/glance_custom.Rd | 2 modelsummary-0.6.2/modelsummary/man/glance_custom.default.Rd | 2 modelsummary-0.6.2/modelsummary/man/glance_custom.fixest.Rd | 2 modelsummary-0.6.2/modelsummary/man/gof_map.Rd | 2 modelsummary-0.6.2/modelsummary/man/gof_map_build.Rd |only modelsummary-0.6.2/modelsummary/man/make_stars.Rd |only modelsummary-0.6.2/modelsummary/man/modelplot.Rd | 49 - modelsummary-0.6.2/modelsummary/man/modelsummary.Rd | 68 - modelsummary-0.6.2/modelsummary/man/msummary.Rd | 68 - modelsummary-0.6.2/modelsummary/man/reexports.Rd | 2 modelsummary-0.6.2/modelsummary/man/sanity_ds_right_handed_formula.Rd | 4 modelsummary-0.6.2/modelsummary/man/tidy_custom.Rd | 8 modelsummary-0.6.2/modelsummary/man/tidy_custom.default.Rd | 8 71 files changed, 2289 insertions(+), 2040 deletions(-)
Title: Health-Economic Simulation Modeling and Decision Analysis
Description: A modular and computationally efficient R package for
parameterizing, simulating, and analyzing health-economic simulation
models. The package supports cohort discrete time state transition models
(Briggs et al. 1998) <doi:10.2165/00019053-199813040-00003>,
N-state partitioned survival models (Glasziou et al. 1990)
<doi:10.1002/sim.4780091106>, and individual-level continuous
time state transition models (Siebert et al. 2012) <doi:10.1016/j.jval.2012.06.014>,
encompassing both Markov (time-homogeneous and time-inhomogeneous) and
semi-Markov processes. Decision uncertainty from a cost-effectiveness analysis is
quantified with standard graphical and tabular summaries of a probabilistic
sensitivity analysis (Claxton et al. 2005, Barton et al. 2008) <doi:10.1002/hec.985>,
<doi:10.1111/j.1524-4733.2008.00358.x>. Use of C++ and data.table
make individual-patient simulation, probabilistic sensitivity analysis,
and incorporation of patient heterogeneity fast.
Author: Devin Incerti [aut, cre],
Jeroen P. Jansen [aut],
R Core Team [ctb] (hesim uses some slightly modified C functions from
base R)
Maintainer: Devin Incerti <devin.incerti@gmail.com>
Diff between hesim versions 0.3.1 dated 2020-06-02 and 0.4.0 dated 2020-09-29
hesim-0.3.1/hesim/inst/doc/getting-started.R |only hesim-0.3.1/hesim/inst/doc/getting-started.Rmd |only hesim-0.3.1/hesim/inst/doc/getting-started.html |only hesim-0.3.1/hesim/inst/doc/icea.R |only hesim-0.3.1/hesim/inst/doc/icea.Rmd |only hesim-0.3.1/hesim/inst/doc/icea.html |only hesim-0.3.1/hesim/inst/doc/markov-inhomogeneous.R |only hesim-0.3.1/hesim/inst/doc/markov-inhomogeneous.Rmd |only hesim-0.3.1/hesim/inst/doc/markov-inhomogeneous.html |only hesim-0.3.1/hesim/vignettes/getting-started.Rmd |only hesim-0.3.1/hesim/vignettes/getting-started.png |only hesim-0.3.1/hesim/vignettes/icea.Rmd |only hesim-0.3.1/hesim/vignettes/markov-inhomogeneous.Rmd |only hesim-0.4.0/hesim/DESCRIPTION | 9 hesim-0.4.0/hesim/MD5 | 167 +++--- hesim-0.4.0/hesim/NAMESPACE | 13 hesim-0.4.0/hesim/R/RcppExports.R | 4 hesim-0.4.0/hesim/R/cea.R | 99 ++- hesim-0.4.0/hesim/R/ctstm.R | 113 +++- hesim-0.4.0/hesim/R/dtstm.R | 4 hesim-0.4.0/hesim/R/hesim_data.R | 4 hesim-0.4.0/hesim/R/model_def.R | 97 ++- hesim-0.4.0/hesim/R/outcomes.R | 2 hesim-0.4.0/hesim/R/params.R | 118 +++- hesim-0.4.0/hesim/R/psm.R | 7 hesim-0.4.0/hesim/R/statevals.R | 54 +- hesim-0.4.0/hesim/R/utils.R | 4 hesim-0.4.0/hesim/README.md | 2 hesim-0.4.0/hesim/build/vignette.rds |binary hesim-0.4.0/hesim/inst/doc/cea.R |only hesim-0.4.0/hesim/inst/doc/cea.Rmd |only hesim-0.4.0/hesim/inst/doc/cea.html |only hesim-0.4.0/hesim/inst/doc/expected-values.Rmd | 2 hesim-0.4.0/hesim/inst/doc/expected-values.html | 4 hesim-0.4.0/hesim/inst/doc/intro.R | 6 hesim-0.4.0/hesim/inst/doc/intro.Rmd | 10 hesim-0.4.0/hesim/inst/doc/intro.html | 142 ++--- hesim-0.4.0/hesim/inst/doc/markov-cohort.R |only hesim-0.4.0/hesim/inst/doc/markov-cohort.Rmd |only hesim-0.4.0/hesim/inst/doc/markov-cohort.html |only hesim-0.4.0/hesim/inst/doc/markov-inhomogeneous-cohort.R |only hesim-0.4.0/hesim/inst/doc/markov-inhomogeneous-cohort.Rmd |only hesim-0.4.0/hesim/inst/doc/markov-inhomogeneous-cohort.html |only hesim-0.4.0/hesim/inst/doc/markov-inhomogeneous-indiv.R |only hesim-0.4.0/hesim/inst/doc/markov-inhomogeneous-indiv.Rmd |only hesim-0.4.0/hesim/inst/doc/markov-inhomogeneous-indiv.html |only hesim-0.4.0/hesim/inst/doc/mlogit.R | 4 hesim-0.4.0/hesim/inst/doc/mlogit.Rmd | 6 hesim-0.4.0/hesim/inst/doc/mlogit.html | 26 hesim-0.4.0/hesim/inst/doc/mstate.R | 4 hesim-0.4.0/hesim/inst/doc/mstate.Rmd | 27 - hesim-0.4.0/hesim/inst/doc/mstate.html | 88 +-- hesim-0.4.0/hesim/inst/doc/psm.R | 4 hesim-0.4.0/hesim/inst/doc/psm.Rmd | 6 hesim-0.4.0/hesim/inst/doc/psm.html | 24 hesim-0.4.0/hesim/inst/include/hesim/math/composite.h | 1 hesim-0.4.0/hesim/inst/include/hesim/statevals.h | 66 +- hesim-0.4.0/hesim/inst/include/hesim/statmods/params.h | 26 hesim-0.4.0/hesim/inst/include/hesim/statmods/statmods.h | 14 hesim-0.4.0/hesim/inst/include/hesim/stats/distributions.h | 321 +++++++++--- hesim-0.4.0/hesim/man/CohortDtstm.Rd | 2 hesim-0.4.0/hesim/man/IndivCtstm.Rd | 17 hesim-0.4.0/hesim/man/IndivCtstmTrans.Rd | 51 + hesim-0.4.0/hesim/man/Psm.Rd | 2 hesim-0.4.0/hesim/man/cea.Rd |only hesim-0.4.0/hesim/man/create_IndivCtstmTrans.Rd | 10 hesim-0.4.0/hesim/man/define_model.Rd | 27 - hesim-0.4.0/hesim/man/define_rng.Rd | 7 hesim-0.4.0/hesim/man/disprog.Rd |only hesim-0.4.0/hesim/man/expand.hesim_data.Rd | 2 hesim-0.4.0/hesim/man/icea.Rd | 125 ---- hesim-0.4.0/hesim/man/icer_tbl.Rd | 6 hesim-0.4.0/hesim/man/params_surv.Rd | 50 + hesim-0.4.0/hesim/man/sim_ev.Rd | 14 hesim-0.4.0/hesim/man/summarize_ce.Rd | 2 hesim-0.4.0/hesim/man/time_intervals.Rd | 2 hesim-0.4.0/hesim/man/tparams_transprobs.Rd | 14 hesim-0.4.0/hesim/man/tpmatrix.Rd | 5 hesim-0.4.0/hesim/man/tpmatrix_id.Rd |only hesim-0.4.0/hesim/src/RcppExports.cpp | 20 hesim-0.4.0/hesim/src/cea.cpp | 8 hesim-0.4.0/hesim/src/distributions.cpp | 40 + hesim-0.4.0/hesim/src/statevals.cpp | 55 +- hesim-0.4.0/hesim/tests/testthat/test-cea.R | 92 +-- hesim-0.4.0/hesim/tests/testthat/test-cpp-distributions.R | 117 ++++ hesim-0.4.0/hesim/tests/testthat/test-ctstm.R | 28 - hesim-0.4.0/hesim/tests/testthat/test-dtstm.R | 30 - hesim-0.4.0/hesim/tests/testthat/test-model_def.R | 43 + hesim-0.4.0/hesim/tests/testthat/test-params.R | 16 hesim-0.4.0/hesim/tests/testthat/test-psm.R | 69 +- hesim-0.4.0/hesim/tests/testthat/test-statevals.R | 211 +++++-- hesim-0.4.0/hesim/vignettes/cea.Rmd |only hesim-0.4.0/hesim/vignettes/expected-values.Rmd | 2 hesim-0.4.0/hesim/vignettes/intro.Rmd | 10 hesim-0.4.0/hesim/vignettes/markov-cohort.Rmd |only hesim-0.4.0/hesim/vignettes/markov-cohort.png |only hesim-0.4.0/hesim/vignettes/markov-inhomogeneous-cohort.Rmd |only hesim-0.4.0/hesim/vignettes/markov-inhomogeneous-indiv.Rmd |only hesim-0.4.0/hesim/vignettes/mlogit.Rmd | 6 hesim-0.4.0/hesim/vignettes/mstate.Rmd | 27 - hesim-0.4.0/hesim/vignettes/psm.Rmd | 6 101 files changed, 1693 insertions(+), 901 deletions(-)
Title: Effect Estimates from All Models
Description: Estimates and plots effect estimates from models with all possible
combinations of a list of variables. It can be used for assessing treatment
effects in clinical trials or risk factors in bio-medical and epidemiological
research. Like Stata command 'confall' (Wang Z (2007) <doi:10.1177/1536867X0700700203> ),
'allestimates' calculates and stores all effect estimates, and plots them against p values or
Akaike information criterion (AIC) values. It currently has functions for linear
regression: all_lm(), logistic and Poisson regression: all_glm() and all_speedglm(),
and Cox proportional hazards regression: all_cox().
Author: Zhiqiang Wang [aut, cre]
Maintainer: Zhiqiang Wang <zhiqiang.wang@menzies.edu.au>
Diff between allestimates versions 0.1.8 dated 2020-07-12 and 0.1.9 dated 2020-09-29
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/all_speedglm.R | 8 ++++++-- inst/doc/allestimates-vignette.html | 10 ++++------ man/all_speedglm.Rd | 1 + 6 files changed, 23 insertions(+), 16 deletions(-)
Title: Finds the Critical Sequential Point of Stability for a Pearson
Correlation
Description: Finds the critical sample size ("critical point of stability") for a
correlation to stabilize in Schoenbrodt and Perugini's definition of
sequential stability (see <doi:10.1016/j.jrp.2013.05.009>).
Author: Johannes Titz [aut, cre, cph]
Maintainer: Johannes Titz <johannes.titz@gmail.com>
Diff between fastpos versions 0.4.0 dated 2020-08-10 and 0.4.1 dated 2020-09-29
DESCRIPTION | 8 - MD5 | 18 +- NEWS.md | 7 + R/fastpos.R | 5 README.md | 271 +++++++++++++++++++----------------------- inst/doc/fastpos.Rmd | 2 inst/doc/fastpos.html | 32 +--- src/rcpparma.cpp | 13 +- tests/testthat/test-fastpos.R | 26 ++-- vignettes/fastpos.Rmd | 2 10 files changed, 182 insertions(+), 202 deletions(-)
Title: Bayesian Optimal INterval (BOIN) Design for Single-Agent and
Drug- Combination Phase I Clinical Trials
Description: The Bayesian optimal interval (BOIN) design is a novel phase I
clinical trial design for finding the maximum tolerated dose (MTD). It can be
used to design both single-agent and drug-combination trials. The BOIN design
is motivated by the top priority and concern of clinicians when testing a new
drug, which is to effectively treat patients and minimize the chance of exposing
them to subtherapeutic or overly toxic doses. The prominent advantage of the
BOIN design is that it achieves simplicity and superior performance at the same
time. The BOIN design is algorithm-based and can be implemented in a simple
way similar to the traditional 3+3 design. The BOIN design yields an average
performance that is comparable to that of the continual reassessment method
(CRM, one of the best model-based designs) in terms of selecting the MTD, but
has a substantially lower risk of assigning patients to subtherapeutic or overly
toxic doses. For tutorial, please check Yan et al. (2020) <doi:10.18637/jss.v094.i13>.
Author: Ying Yuan and Suyu Liu
Maintainer: Ying Yuan <yyuan@mdanderson.org>
Diff between BOIN versions 2.6.9 dated 2020-09-01 and 2.7.0 dated 2020-09-29
DESCRIPTION | 8 - MD5 | 8 - R/select.mtd.R | 9 - R/select.mtd.comb.R | 413 ++++++++++++++++++++++++++-------------------------- R/summary.boin.R | 11 - 5 files changed, 230 insertions(+), 219 deletions(-)
Title: Leland Wilkinson's Algorithm for Detecting Multidimensional
Outliers
Description: An implementation of an algorithm for outlier detection that can handle a) data with a mixed categorical and continuous variables, b) many columns of data, c) many rows of data, d) outliers that mask other outliers, and e) both unidimensional and multidimensional datasets. Unlike ad hoc methods found in many machine learning papers, HDoutliers is based on a distributional model that uses probabilities to determine outliers.
Author: Chris Fraley [aut, cre],
Leland Wilkinson [ctb]
Maintainer: Chris Fraley <cfraley@tableau.com>
Diff between HDoutliers versions 1.0.2 dated 2020-07-10 and 1.0.3 dated 2020-09-29
CHANGELOG | 5 +++-- DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/dataTrans.R | 1 - 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Companion to Applied Regression
Description: Functions to Accompany J. Fox and S. Weisberg,
An R Companion to Applied Regression, Third Edition, Sage, 2019.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Brad Price [aut],
Daniel Adler [ctb],
Douglas Bates [ctb],
Gabriel Baud-Bovy [ctb],
Ben Bolker [ctb],
Steve Ellison [ctb],
David Firth [ctb],
Michael Friendly [ctb],
Gregor Gorjanc [ctb],
Spencer Graves [ctb],
Richard Heiberger [ctb],
Pavel Krivitsky [ctb],
Rafael Laboissiere [ctb],
Martin Maechler [ctb],
Georges Monette [ctb],
Duncan Murdoch [ctb],
Henric Nilsson [ctb],
Derek Ogle [ctb],
Brian Ripley [ctb],
William Venables [ctb],
Steve Walker [ctb],
David Winsemius [ctb],
Achim Zeileis [ctb],
R-Core [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between car versions 3.0-9 dated 2020-08-11 and 3.0-10 dated 2020-09-29
DESCRIPTION | 12 MD5 | 14 NEWS | 1788 +++++++++++++++++++++++------------------------ R/Boot.R | 126 ++- R/deltaMethod.R | 356 ++++----- R/scatterplotSmoothers.R | 10 inst/doc/embedding.pdf |binary man/Boot.Rd | 4 8 files changed, 1178 insertions(+), 1132 deletions(-)
Title: VPC Percentiles and Prediction Intervals
Description: Perform a Visual Predictive Check (VPC), while accounting for
stratification, censoring, and prediction correction. Using piping from
'magrittr', the intuitive syntax gives users a flexible and powerful method
to generate VPCs using both traditional binning and a new binless approach
Jamsen et al. (2018) <doi:10.1002/psp4.12319> with Additive Quantile
Regression (AQR) and Locally Estimated Scatterplot Smoothing (LOESS)
prediction correction.
Author: Olivier Barriere [aut],
Benjamin Rich [aut],
James Craig [aut, cre],
Samer Mouksassi [aut],
Kris Jamsen [ctb]
Maintainer: James Craig <jameswbcraig@gmail.com>
Diff between tidyvpc versions 1.0.0 dated 2020-03-26 and 1.1.0 dated 2020-09-29
DESCRIPTION | 20 - MD5 | 59 ++-- NAMESPACE | 3 R/vpcstats.R | 174 +++++++----- README.md | 18 - build/vignette.rds |binary inst/doc/tidyvpc.R | 8 inst/doc/tidyvpc.Rmd | 21 + inst/doc/tidyvpc.html | 648 ++++++++++++++++++++++++---------------------- inst/img/logo_tidyvpc.png |only man/bininfo.Rd | 96 +++--- man/binless.Rd | 181 ++++++------ man/binning.Rd | 174 ++++++------ man/binningfunctions.Rd | 116 ++++---- man/censoring.Rd | 126 ++++---- man/check_order.Rd | 80 ++--- man/generics.Rd | 30 +- man/nopredcorrect.Rd | 44 +-- man/obs_data.Rd | 58 ++-- man/observed.Rd | 117 ++++---- man/plot.Rd | 122 ++++---- man/predcorrect.Rd | 130 ++++----- man/print.tidyvpcobj.Rd | 38 +- man/runShinyVPC.Rd | 34 +- man/sim_data.Rd | 60 ++-- man/simulated.Rd | 78 ++--- man/stratify.Rd | 98 +++--- man/vpcstats.Rd | 98 +++--- tests |only vignettes/tidyvpc.Rmd | 21 + 30 files changed, 1404 insertions(+), 1248 deletions(-)
Title: Authentication and Administration for 'shiny' Apps
Description: Easily add modern authentication and user administration to your 'shiny' apps.
Customize user sign in and registration pages to match your brand. Control who can
access one or more of your 'shiny' apps.
Author: Andy Merlino [aut, cre],
Patrick Howard [aut]
Maintainer: Andy Merlino <andy.merlino@tychobra.com>
Diff between polished versions 0.1.0 dated 2020-07-01 and 0.2.0 dated 2020-09-29
polished-0.1.0/polished/R/dashboard_module.R |only polished-0.1.0/polished/R/sign_in_no_invite_module.R |only polished-0.1.0/polished/inst/assets/js/auth_all.js |only polished-0.1.0/polished/inst/assets/js/auth_all_no_invite.js |only polished-0.1.0/polished/inst/assets/js/verify_email_module.js |only polished-0.1.0/polished/inst/examples/polished_example_01/example_config.yml |only polished-0.1.0/polished/inst/examples/polished_example_02/example_config.yml |only polished-0.1.0/polished/man/sign_in_no_invite_module.Rd |only polished-0.1.0/polished/man/sign_in_no_invite_module_ui.Rd |only polished-0.2.0/polished/DESCRIPTION | 19 polished-0.2.0/polished/MD5 | 100 +- polished-0.2.0/polished/NAMESPACE | 45 - polished-0.2.0/polished/NEWS.md | 18 polished-0.2.0/polished/R/Sessions.R | 262 +++--- polished-0.2.0/polished/R/admin_button.R | 17 polished-0.2.0/polished/R/admin_module.R | 29 polished-0.2.0/polished/R/email_input.R | 12 polished-0.2.0/polished/R/global_sessions_config.R | 64 + polished-0.2.0/polished/R/password_input.R |only polished-0.2.0/polished/R/profile_module.R | 13 polished-0.2.0/polished/R/providers_ui.R | 136 ++- polished-0.2.0/polished/R/secure_server.R | 201 +++- polished-0.2.0/polished/R/secure_static.R | 39 polished-0.2.0/polished/R/secure_ui.R | 96 +- polished-0.2.0/polished/R/send_password_reset_email_module.R |only polished-0.2.0/polished/R/sign_in_components.R |only polished-0.2.0/polished/R/sign_in_module.R | 410 ++++------ polished-0.2.0/polished/R/sign_in_module_2.R |only polished-0.2.0/polished/R/sign_in_ui_default.R | 88 +- polished-0.2.0/polished/R/user_access_module.R | 48 - polished-0.2.0/polished/R/user_edit_module.R | 84 +- polished-0.2.0/polished/R/utils.R | 53 + polished-0.2.0/polished/R/verify_email_module.R | 141 ++- polished-0.2.0/polished/README.md | 12 polished-0.2.0/polished/build |only polished-0.2.0/polished/inst/assets/js/auth_firebase.js | 81 - polished-0.2.0/polished/inst/assets/js/auth_keypress.js |only polished-0.2.0/polished/inst/assets/js/auth_main.js |only polished-0.2.0/polished/inst/assets/js/router.js |only polished-0.2.0/polished/inst/assets/js/set_password_module.js |only polished-0.2.0/polished/inst/doc |only polished-0.2.0/polished/inst/examples/polished_example_01/config.yml | 13 polished-0.2.0/polished/inst/examples/polished_example_01/global.R | 6 polished-0.2.0/polished/inst/examples/polished_example_02/global.R | 4 polished-0.2.0/polished/inst/examples/polished_example_02/server.R | 5 polished-0.2.0/polished/inst/examples/polished_example_02/ui.R | 2 polished-0.2.0/polished/man/Sessions.Rd | 36 polished-0.2.0/polished/man/email_input.Rd | 8 polished-0.2.0/polished/man/global_sessions_config.Rd | 8 polished-0.2.0/polished/man/password_input.Rd |only polished-0.2.0/polished/man/providers_ui.Rd | 13 polished-0.2.0/polished/man/remove_query_string.Rd |only polished-0.2.0/polished/man/secure_server.Rd | 10 polished-0.2.0/polished/man/secure_static.Rd | 9 polished-0.2.0/polished/man/secure_ui.Rd | 13 polished-0.2.0/polished/man/send_password_reset_email_module.Rd |only polished-0.2.0/polished/man/send_password_reset_email_module_ui.Rd |only polished-0.2.0/polished/man/sign_in_check_jwt.Rd |only polished-0.2.0/polished/man/sign_in_js.Rd |only polished-0.2.0/polished/man/sign_in_module_2.Rd |only polished-0.2.0/polished/man/sign_in_module_2_ui.Rd |only polished-0.2.0/polished/man/sign_in_module_ui.Rd | 3 polished-0.2.0/polished/man/sign_in_ui_default.Rd | 18 polished-0.2.0/polished/vignettes |only 64 files changed, 1302 insertions(+), 814 deletions(-)
Title: Management Strategy Evaluation Toolkit
Description: Simulation tools for management strategy evaluation are provided for the 'DLMtool' operating model to inform data-rich fisheries.
'MSEtool' provides complementary assessment models of varying complexity with standardized reporting, diagnostic tools for evaluating
assessment models within closed-loop simulation, and helper functions for building more complex operating models and model-based management procedures.
Author: Quang Huynh [aut],
Tom Carruthers [aut, cre],
Adrian Hordyk [aut],
Chris Grandin [ctb] (iSCAM functions)
Maintainer: Tom Carruthers <t.carruthers@oceans.ubc.ca>
Diff between MSEtool versions 2.0.0 dated 2020-08-06 and 2.0.1 dated 2020-09-29
DESCRIPTION | 12 MD5 | 163 +++++------ NAMESPACE | 2 NEWS.md | 5 R/Ancillary_Indicators.R | 13 R/MSEtool-package.R | 2 R/Misc_fun.R | 38 ++ R/SRA_scope.R | 34 +- R/SRA_scope_data.R | 6 R/SS2Data.R | 17 - R/SS2MOM.R |only R/SS2OM.R | 469 -------------------------------- R/SSinternal.R |only R/VPA2OM.R |only R/define_S4_class_SRA.R | 14 R/define_S4_generic_SRA_scope.R | 4 R/report_DD_TMB.R | 19 - R/report_SCA.R | 15 - R/report_SCA_Pope.R | 15 - R/report_SP.R | 21 - R/report_VPA.R | 5 R/report_cDD.R | 20 - R/report_spict.R | 13 README.md | 4 build/vignette.rds |binary inst/doc/Delay_difference.html | 20 + inst/doc/MSEtool.Rmd | 6 inst/doc/MSEtool.html | 24 + inst/doc/SCA.html | 20 + inst/doc/SRA_scope.Rmd | 2 inst/doc/SRA_scope.html | 20 + inst/doc/SRA_scope_eq.html | 20 + inst/doc/SRA_scope_sel.html | 20 + inst/doc/Surplus_production.html | 20 + inst/doc/VPA.html | 20 + inst/doc/multiMSE.Rmd | 4 inst/doc/multiMSE.html | 38 +- man/Awatea2OM.Rd | 74 ++--- man/CASAL2OM.Rd | 168 +++++------ man/HCR_ramp.Rd | 228 +++++++-------- man/HistMICE.Rd | 136 ++++----- man/MSEtool-package.Rd | 140 ++++----- man/Model-based-MP.Rd | 192 ++++++------- man/PRBcalc.Rd | 108 +++---- man/Probs.Rd | 68 ++-- man/SCA.Rd | 564 +++++++++++++++++++-------------------- man/SRA_scope.Rd | 4 man/SS2MOM.Rd |only man/VPA2OM.Rd |only man/diagnostic_AM.Rd | 92 +++--- man/getinds.Rd | 74 ++--- man/getq_multi.Rd | 180 ++++++------ man/getq_multi_MICE.Rd | 144 ++++----- man/iSCAM2Data.Rd | 70 ++-- man/iSCAM2OM.Rd | 90 +++--- man/multiMSE.Rd | 162 +++++------ man/multidebug.Rd | 54 +-- man/optQ_multi.Rd | 198 ++++++------- man/plot.Assessment.Rd | 136 ++++----- man/plot.MMSE.Rd | 76 ++--- man/plot.MOM.Rd | 44 +-- man/plot.SRA.Rd | 182 ++++++------ man/plot.prof.Rd | 46 +-- man/plot.retro.Rd | 74 ++--- man/plot_SR.Rd | 94 +++--- man/plot_composition.Rd | 158 +++++----- man/plot_crosscorr.Rd | 74 ++--- man/plot_lognormalvar.Rd | 90 +++--- man/plot_residuals.Rd | 98 +++--- man/plot_steepness.Rd | 102 +++---- man/plot_timeseries.Rd | 116 ++++---- man/plotquant.Rd | 74 ++--- man/popdynMICE.Rd | 232 ++++++++-------- man/popdynOneMICE.Rd | 214 +++++++------- man/projection.Rd | 102 +++---- man/qestMICE.Rd | 248 ++++++++--------- man/read.control.file.Rd | 58 ++-- man/retrospective.Rd | 96 +++--- man/retrospective_AM.Rd | 110 +++---- man/simmov.Rd | 140 ++++----- man/summary.Assessment.Rd | 44 +-- man/tinyErr.Rd | 58 ++-- vignettes/MSEtool.Rmd | 6 vignettes/SRA_scope.Rmd | 2 vignettes/multiMSE.Rmd | 4 85 files changed, 3099 insertions(+), 3430 deletions(-)
Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors, each of which may have a shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The ShapeSelect routine chooses a subset of predictor variables and describes the component relationships with the response. For each predictor, the user needs only specify a set of possible shape or order restrictions. A model selection method chooses the shapes and orderings of the relationships as well as the variables. The cone information criterion (CIC) is used to select the best combination of variables and shapes. A genetic algorithm may be used when the set of possible models is large. In addition, the cgam routine implements a two-dimensional isotonic regression using warped-plane splines without additivity assumptions. It can also fit a convex or concave regression surface with triangle splines without additivity assumptions. See Liao X, Meyer MC (2019)<doi: 10.18637/jss.v089.i05> for more details.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao <liaoxiyue2011@gmail.com>
Diff between cgam versions 1.15 dated 2019-10-13 and 1.16 dated 2020-09-29
DESCRIPTION | 9 MD5 | 18 NAMESPACE | 2 R/cgam.R | 2575 +++++++++++++++++++++++++++++++---------------------- man/cgam.Rd | 16 man/plotpersp.Rd | 2 man/s.decr.decr.Rd | 4 man/s.decr.incr.Rd | 2 man/s.incr.decr.Rd | 2 man/s.incr.incr.Rd | 2 10 files changed, 1559 insertions(+), 1073 deletions(-)
Title: Access to VK API via R
Description: Provides an interface to the VK API <https://vk.com/dev/methods>.
VK <https://vk.com/> is the largest European online social networking
service, based in Russia.
Author: Dmitriy Sorokin [aut, cre],
Anton Antonov [ctb]
Maintainer: Dmitriy Sorokin <dementiy@yandex.ru>
Diff between vkR versions 0.1 dated 2016-12-02 and 0.2 dated 2020-09-29
vkR-0.1/vkR/man/getNetwork.Rd |only vkR-0.2/vkR/DESCRIPTION | 22 +- vkR-0.2/vkR/MD5 | 203 ++++++++++++++++----------- vkR-0.2/vkR/NAMESPACE | 33 ++++ vkR-0.2/vkR/R/auth.R | 12 - vkR-0.2/vkR/R/board.R |only vkR-0.2/vkR/R/friends.R | 85 ++++++++++- vkR-0.2/vkR/R/groups.R | 160 +++++++++++++++++---- vkR-0.2/vkR/R/likes.R | 5 vkR-0.2/vkR/R/messages.R | 55 +++++++ vkR-0.2/vkR/R/mongo_connection.R |only vkR-0.2/vkR/R/network.R | 6 vkR-0.2/vkR/R/newsfeed.R |only vkR-0.2/vkR/R/queries.R | 175 +++++++++++++++-------- vkR-0.2/vkR/R/users.R | 114 +++++++++++++-- vkR-0.2/vkR/R/utils.R | 14 + vkR-0.2/vkR/R/vkR.R | 17 +- vkR-0.2/vkR/R/wall.R | 28 +++ vkR-0.2/vkR/README.md | 70 +++++++++ vkR-0.2/vkR/man/age_predict.Rd | 1 vkR-0.2/vkR/man/areFriends.Rd | 1 vkR-0.2/vkR/man/boardGetComments.Rd |only vkR-0.2/vkR/man/boardGetCommentsExecute.Rd |only vkR-0.2/vkR/man/boardGetCommentsList.Rd |only vkR-0.2/vkR/man/clear_text.Rd | 1 vkR-0.2/vkR/man/collection_exists.Rd |only vkR-0.2/vkR/man/create_empty_collection.Rd |only vkR-0.2/vkR/man/databaseGetChairs.Rd | 9 - vkR-0.2/vkR/man/databaseGetCities.Rd | 12 + vkR-0.2/vkR/man/databaseGetCitiesById.Rd | 1 vkR-0.2/vkR/man/databaseGetCountries.Rd | 10 - vkR-0.2/vkR/man/databaseGetCountriesById.Rd | 1 vkR-0.2/vkR/man/databaseGetFaculties.Rd | 9 - vkR-0.2/vkR/man/databaseGetRegions.Rd | 10 - vkR-0.2/vkR/man/databaseGetSchoolClasses.Rd | 1 vkR-0.2/vkR/man/databaseGetSchools.Rd | 10 - vkR-0.2/vkR/man/databaseGetStreetsById.Rd | 1 vkR-0.2/vkR/man/databaseGetUniversities.Rd | 11 + vkR-0.2/vkR/man/db_drop.Rd |only vkR-0.2/vkR/man/db_drop_collection.Rd |only vkR-0.2/vkR/man/db_getActive.Rd |only vkR-0.2/vkR/man/db_getName.Rd |only vkR-0.2/vkR/man/db_get_collection.Rd |only vkR-0.2/vkR/man/db_get_connection.Rd |only vkR-0.2/vkR/man/db_init.Rd |only vkR-0.2/vkR/man/db_insert.Rd |only vkR-0.2/vkR/man/db_load.Rd |only vkR-0.2/vkR/man/db_load_collection.Rd |only vkR-0.2/vkR/man/db_metaConnection.Rd |only vkR-0.2/vkR/man/db_save.Rd |only vkR-0.2/vkR/man/db_update.Rd |only vkR-0.2/vkR/man/execute.Rd | 1 vkR-0.2/vkR/man/filterAttachments.Rd | 1 vkR-0.2/vkR/man/getAccessToken.Rd | 1 vkR-0.2/vkR/man/getArbitraryNetwork.Rd | 1 vkR-0.2/vkR/man/getCountryByCityId.Rd | 1 vkR-0.2/vkR/man/getEgoNetwork.Rd |only vkR-0.2/vkR/man/getFriends.Rd | 15 + vkR-0.2/vkR/man/getFriendsBy25.Rd | 1 vkR-0.2/vkR/man/getFriendsFor.Rd | 1 vkR-0.2/vkR/man/getGroups.Rd | 12 + vkR-0.2/vkR/man/getGroupsById.Rd |only vkR-0.2/vkR/man/getGroupsForUsers.Rd | 11 + vkR-0.2/vkR/man/getGroupsMembers.Rd | 12 + vkR-0.2/vkR/man/getGroupsMembersExecute.Rd | 19 +- vkR-0.2/vkR/man/getMutual.Rd | 14 + vkR-0.2/vkR/man/getMutualExecute.Rd |only vkR-0.2/vkR/man/getPaths.Rd | 1 vkR-0.2/vkR/man/getStatus.Rd | 9 - vkR-0.2/vkR/man/getTopics.Rd |only vkR-0.2/vkR/man/getTopicsExecute.Rd |only vkR-0.2/vkR/man/getURLs.Rd | 1 vkR-0.2/vkR/man/getUsers.Rd | 10 - vkR-0.2/vkR/man/getUsersExecute.Rd | 18 +- vkR-0.2/vkR/man/getWall.Rd | 13 + vkR-0.2/vkR/man/getWallExecute.Rd | 21 ++ vkR-0.2/vkR/man/get_stop_words.Rd | 1 vkR-0.2/vkR/man/groupsSearch.Rd |only vkR-0.2/vkR/man/handle_captcha.Rd |only vkR-0.2/vkR/man/handle_validation.Rd |only vkR-0.2/vkR/man/has_error.Rd | 1 vkR-0.2/vkR/man/likesGetList.Rd | 17 +- vkR-0.2/vkR/man/likesGetListForObjects.Rd | 14 + vkR-0.2/vkR/man/me.Rd | 1 vkR-0.2/vkR/man/messagesGet.Rd | 14 + vkR-0.2/vkR/man/messagesGetHistory.Rd | 12 + vkR-0.2/vkR/man/messagesGetHistoryAll.Rd | 4 vkR-0.2/vkR/man/messagesGetHistoryExecute.Rd | 14 + vkR-0.2/vkR/man/messagesSend.Rd |only vkR-0.2/vkR/man/messagesSplitByDate.Rd | 1 vkR-0.2/vkR/man/newsfeedSearch.Rd |only vkR-0.2/vkR/man/or.Rd |only vkR-0.2/vkR/man/postGetComments.Rd | 18 +- vkR-0.2/vkR/man/profile_fields.Rd |only vkR-0.2/vkR/man/queryBuilder.Rd | 1 vkR-0.2/vkR/man/repeat_last_query.Rd | 1 vkR-0.2/vkR/man/request_delay.Rd | 1 vkR-0.2/vkR/man/saveAsGEXF.Rd | 1 vkR-0.2/vkR/man/search.getHints.Rd | 10 - vkR-0.2/vkR/man/setAPIVersion.Rd | 1 vkR-0.2/vkR/man/setAccessToken.Rd | 1 vkR-0.2/vkR/man/setRepeats.Rd |only vkR-0.2/vkR/man/setTimeout.Rd |only vkR-0.2/vkR/man/show_collections.Rd |only vkR-0.2/vkR/man/show_dbs.Rd |only vkR-0.2/vkR/man/tag2Id.Rd | 1 vkR-0.2/vkR/man/try_handle_error.Rd | 1 vkR-0.2/vkR/man/try_handle_network_error.Rd |only vkR-0.2/vkR/man/use_db.Rd |only vkR-0.2/vkR/man/usersGetFollowers.Rd | 15 + vkR-0.2/vkR/man/usersGetSubscriptions.Rd | 14 + vkR-0.2/vkR/man/usersSearch.Rd | 47 ++++-- vkR-0.2/vkR/man/vkApply.Rd | 1 vkR-0.2/vkR/man/vkOAuth.Rd | 1 vkR-0.2/vkR/man/vkOAuthWeb.Rd | 1 vkR-0.2/vkR/man/vkPost.Rd | 1 vkR-0.2/vkR/man/vkR.Rd | 8 - vkR-0.2/vkR/man/vk_stop.Rd |only vkR-0.2/vkR/man/wallGetById.Rd | 10 - vkR-0.2/vkR/man/wallGetComments.Rd | 16 +- vkR-0.2/vkR/man/wallGetCommentsList.Rd | 1 vkR-0.2/vkR/man/wallGetReposts.Rd | 10 - vkR-0.2/vkR/man/wallSearch.Rd | 15 + 123 files changed, 1120 insertions(+), 375 deletions(-)
Title: Graphical User Interface ('Shiny' App) for Package 'brms'
Description: A graphical user interface (GUI) for fitting Bayesian
regression models using the package 'brms' which in turn relies on
'Stan' (<https://mc-stan.org/>). The 'shinybrms' GUI is a 'Shiny'
(<https://shiny.rstudio.com/>) app.
Author: Frank Weber [aut, cre] (<https://orcid.org/0000-0002-4842-7922>),
Thomas Park [ctb, cph] ('Bootswatch' theme "United"),
Twitter, Inc. [ctb, cph] ('Bootstrap' (basis for the 'Bootswatch' theme
"United")),
Google, LLC [ctb, cph] ("Open Sans" font)
Maintainer: Frank Weber <fweber144@protonmail.com>
Diff between shinybrms versions 1.4.0 dated 2020-09-13 and 1.4.1 dated 2020-09-29
DESCRIPTION | 34 ++++++++++++++++++++++++---------- MD5 | 6 +++--- NEWS.md | 8 ++++++++ inst/shinybrms_app/app.R | 8 ++++---- 4 files changed, 39 insertions(+), 17 deletions(-)
Title: Gene Set Uncertainty in Enrichment Analysis
Description: Toolbox for various enrichment analysis methods and quantification of uncertainty of gene sets (Schmid et al. (2016) <doi:10.1093/bioinformatics/btw030>).
Author: Florian Schmid, Christoph Muessel, Johann M. Kraus, Hans A. Kestler
Maintainer: Hans Kestler <hans.kestler@uni-ulm.de>
Diff between GiANT versions 1.3 dated 2020-05-04 and 1.3.1 dated 2020-09-29
DESCRIPTION | 10 ++++---- MD5 | 16 ++++++------- R/gls.R | 41 ++++++++++++++++++----------------- build/vignette.rds |binary inst/doc/giant_package_vignette.R | 2 - inst/doc/giant_package_vignette.Snw | 2 - inst/doc/giant_package_vignette.pdf |binary man/gls.Rd | 10 ++++---- vignettes/giant_package_vignette.Snw | 2 - 9 files changed, 43 insertions(+), 40 deletions(-)