Title: Nonparametric Estimation of the Trend and Its Derivatives in TS
Description: The nonparametric trend and its derivatives in equidistant time
series (TS) with short-memory stationary errors can be estimated. The
estimation is conducted via local polynomial regression using an
automatically selected bandwidth obtained by a built-in iterative plug-in
algorithm or a bandwidth fixed by the user. A Nadaraya-Watson kernel
smoother is also built-in as a comparison. With version 1.1.0, a linearity
test for the trend function, forecasting methods and backtesting
approaches are implemented as well.
The smoothing methods of the package are described in Feng, Y., Gries, T.,
and Fritz, M. (2020) <doi:10.1080/10485252.2020.1759598>.
Author: Yuanhua Feng [aut] (Paderborn University, Germany),
Sebastian Letmathe [aut] (Paderborn University, Germany),
Dominik Schulz [aut, cre] (Paderborn University, Germany),
Thomas Gries [ctb] (Paderborn University, Germany),
Marlon Fritz [ctb] (Paderborn University, Germany)
Maintainer: Dominik Schulz <schulzd@mail.uni-paderborn.de>
Diff between smoots versions 1.1.2 dated 2021-10-05 and 1.1.3 dated 2021-10-09
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 6 ++++++ R/bootCast.R | 2 +- R/rollCast.R | 2 +- 5 files changed, 15 insertions(+), 9 deletions(-)
Title: Create Interactive Web Graphics via 'plotly.js'
Description: Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.
Author: Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>),
Chris Parmer [aut],
Toby Hocking [aut],
Scott Chamberlain [aut],
Karthik Ram [aut],
Marianne Corvellec [aut] (<https://orcid.org/0000-0002-1994-3581>),
Pedro Despouy [aut],
Salim Brüggemann [ctb] (<https://orcid.org/0000-0002-5329-5987>),
Plotly Technologies Inc. [cph]
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Diff between plotly versions 4.9.4.1 dated 2021-06-18 and 4.10.0 dated 2021-10-09
plotly-4.10.0/plotly/DESCRIPTION | 18 plotly-4.10.0/plotly/MD5 | 914 ++++------ plotly-4.10.0/plotly/NAMESPACE | 4 plotly-4.10.0/plotly/NEWS.md | 25 plotly-4.10.0/plotly/R/add.R | 34 plotly-4.10.0/plotly/R/deprecated.R | 2 plotly-4.10.0/plotly/R/ggplotly.R | 74 plotly-4.10.0/plotly/R/kaleido.R |only plotly-4.10.0/plotly/R/layers2traces.R | 5 plotly-4.10.0/plotly/R/layout.R | 9 plotly-4.10.0/plotly/R/mathjax.R | 2 plotly-4.10.0/plotly/R/orca.R | 29 plotly-4.10.0/plotly/R/plotly.R | 11 plotly-4.10.0/plotly/R/subplots.R | 2 plotly-4.10.0/plotly/R/sysdata.rda |binary plotly-4.10.0/plotly/R/utils.R | 3 plotly-4.10.0/plotly/README.md | 11 plotly-4.10.0/plotly/inst/examples/shiny/event_data/tests/shinytest/mytest-expected/001.json | 12 plotly-4.10.0/plotly/inst/examples/shiny/event_data/tests/shinytest/mytest-expected/001.png |binary plotly-4.10.0/plotly/inst/examples/shiny/event_data/tests/shinytest/mytest-expected/002.json | 13 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plotly-4.10.0/plotly/man/orca.Rd | 12 plotly-4.10.0/plotly/man/plotly.Rd | 2 plotly-4.10.0/plotly/man/print.kaleidoScope.Rd |only plotly-4.10.0/plotly/man/save_image.Rd |only plotly-4.10.0/plotly/tests/testthat/Rplots.pdf |binary plotly-4.10.0/plotly/tests/testthat/_snaps |only plotly-4.10.0/plotly/tests/testthat/helper-skip.R | 32 plotly-4.10.0/plotly/tests/testthat/helper-vdiffr.R | 113 - plotly-4.10.0/plotly/tests/testthat/test-animate-highlight.R | 2 plotly-4.10.0/plotly/tests/testthat/test-api.R | 361 ++- plotly-4.10.0/plotly/tests/testthat/test-cookbook-axes.R | 2 plotly-4.10.0/plotly/tests/testthat/test-cookbook-lines.R | 2 plotly-4.10.0/plotly/tests/testthat/test-cookbook-scatterplots.R | 2 plotly-4.10.0/plotly/tests/testthat/test-geom-errorbar-flipped-aes.R | 2 plotly-4.10.0/plotly/tests/testthat/test-geom-errorbar-issue-1751.R | 1 plotly-4.10.0/plotly/tests/testthat/test-ggplot-abline.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-annotation_.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-area.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-bar.R | 4 plotly-4.10.0/plotly/tests/testthat/test-ggplot-blank.R | 1 plotly-4.10.0/plotly/tests/testthat/test-ggplot-boxplot.R | 1 plotly-4.10.0/plotly/tests/testthat/test-ggplot-col.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-contour.R | 3 plotly-4.10.0/plotly/tests/testthat/test-ggplot-coord-fixed.R | 1 plotly-4.10.0/plotly/tests/testthat/test-ggplot-crossbar.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-date.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-density.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-density2d.R | 8 plotly-4.10.0/plotly/tests/testthat/test-ggplot-device.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-dynamicTicks.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-errorbar-horizontal.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-errorbar.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-facets.R | 1 plotly-4.10.0/plotly/tests/testthat/test-ggplot-ggplotly.R | 1 plotly-4.10.0/plotly/tests/testthat/test-ggplot-heatmap.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-hex.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-histogram.R | 1 plotly-4.10.0/plotly/tests/testthat/test-ggplot-hline.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-jitter.R | 1 plotly-4.10.0/plotly/tests/testthat/test-ggplot-labels.R | 1 plotly-4.10.0/plotly/tests/testthat/test-ggplot-legend.R | 11 plotly-4.10.0/plotly/tests/testthat/test-ggplot-lines.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-map.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-path.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-point.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-polygons.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-quantile.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-rect.R | 1 plotly-4.10.0/plotly/tests/testthat/test-ggplot-resize.R | 1 plotly-4.10.0/plotly/tests/testthat/test-ggplot-ribbon.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-rug.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-segment.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-sf.R | 1 plotly-4.10.0/plotly/tests/testthat/test-ggplot-size.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-smooth.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-spoke.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-step.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-text.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-theme.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-ticks.R | 1 plotly-4.10.0/plotly/tests/testthat/test-ggplot-tooltip.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-violin.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ggplot-vline.R | 1 plotly-4.10.0/plotly/tests/testthat/test-ggplot-ylim.R | 1 plotly-4.10.0/plotly/tests/testthat/test-group2NA.R | 2 plotly-4.10.0/plotly/tests/testthat/test-icicle.R |only plotly-4.10.0/plotly/tests/testthat/test-mean-error-bars.R | 1 plotly-4.10.0/plotly/tests/testthat/test-plotly-area.R |only plotly-4.10.0/plotly/tests/testthat/test-plotly-color.R | 1 plotly-4.10.0/plotly/tests/testthat/test-plotly-colorbar.R | 2 plotly-4.10.0/plotly/tests/testthat/test-plotly-colorscale.R | 2 plotly-4.10.0/plotly/tests/testthat/test-plotly-customdata.R | 2 plotly-4.10.0/plotly/tests/testthat/test-plotly-data.R | 2 plotly-4.10.0/plotly/tests/testthat/test-plotly-group.R | 2 plotly-4.10.0/plotly/tests/testthat/test-plotly-image-trace.R | 2 plotly-4.10.0/plotly/tests/testthat/test-plotly-internals.R | 1 plotly-4.10.0/plotly/tests/testthat/test-plotly-linetype.R | 2 plotly-4.10.0/plotly/tests/testthat/test-plotly-name.R | 1 plotly-4.10.0/plotly/tests/testthat/test-plotly-partial-bundles.R | 1 plotly-4.10.0/plotly/tests/testthat/test-plotly-pie.R | 2 plotly-4.10.0/plotly/tests/testthat/test-plotly-sf.R | 2 plotly-4.10.0/plotly/tests/testthat/test-plotly-shiny.R | 63 plotly-4.10.0/plotly/tests/testthat/test-plotly-size.R | 1 plotly-4.10.0/plotly/tests/testthat/test-plotly-splom.R | 2 plotly-4.10.0/plotly/tests/testthat/test-plotly-subplot.R | 2 plotly-4.10.0/plotly/tests/testthat/test-plotly-sunburst.R | 2 plotly-4.10.0/plotly/tests/testthat/test-plotly-symbol.R | 1 plotly-4.10.0/plotly/tests/testthat/test-plotly-treemaps.R | 1 plotly-4.10.0/plotly/tests/testthat/test-plotly-waterfall.R | 1 plotly-4.10.0/plotly/tests/testthat/test-plotly.R | 1 plotly-4.10.0/plotly/tests/testthat/test-rotated-ticks.R | 1 plotly-4.10.0/plotly/tests/testthat/test-style.R | 2 plotly-4.10.0/plotly/tests/testthat/test-ticktext-linebreaks.R | 1 plotly-4.10.0/plotly/tests/testthat/test-toRGB.R | 1 plotly-4.10.0/plotly/tools |only plotly-4.9.4.1/plotly/inst/docker |only plotly-4.9.4.1/plotly/inst/plotlyjs.R |only plotly-4.9.4.1/plotly/tests/figs |only plotly-4.9.4.1/plotly/tests/testthat/test-plotly-filename.R |only plotly-4.9.4.1/plotly/tests/testthat/test-plotly-getfigure.R |only plotly-4.9.4.1/plotly/tests/testthat/test-thematic.R |only 134 files changed, 1033 insertions(+), 962 deletions(-)
Title: Tools to Format Numbers for Publication
Description: Format numbers and plots for publication; includes the removal of leading zeros,
standardization of number of digits, addition of affixes, and a p-value formatter. These
tools combine the functionality of several 'base' functions such as 'paste()',
'format()', and 'sprintf()' into specific use case functions that are named in a way
that is consistent with usage, making their names easy to remember and easy to deploy.
Author: Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between numform versions 0.6.4 dated 2020-09-27 and 0.7.0 dated 2021-10-09
DESCRIPTION | 11 ++++++----- MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 4 ++-- NEWS | 28 ++++++++++++++++++++-------- R/f_dollar.R | 11 ++++++++--- R/f_num.R | 8 +++++--- R/f_ordinal.R | 7 +++---- R/f_percent.R | 20 +++++++++++++------- R/glue-reexports.R | 4 ++-- R/round.R | 2 +- inst/CITATION | 8 ++++---- man/f_dollar.Rd | 6 +++++- man/f_num.Rd | 4 ++++ man/f_ordinal.Rd | 2 +- man/f_percent.Rd | 10 +++++++++- man/reexports.Rd | 4 ++-- man/round2.Rd | 2 +- 17 files changed, 102 insertions(+), 61 deletions(-)
Title: MCMC, Particle Filtering, and Programmable Hierarchical Modeling
Description: A system for writing hierarchical statistical models largely
compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models
and do basic R-style math, and compiling both models and nimbleFunctions via
custom-generated C++. 'NIMBLE' includes default methods for MCMC, Monte Carlo
Expectation Maximization, and some other tools. The nimbleFunction system makes
it easy to do things like implement new MCMC samplers from R, customize the
assignment of samplers to different parts of a model from R, and compile the
new samplers automatically via C++ alongside the samplers 'NIMBLE' provides.
'NIMBLE' extends the 'BUGS'/'JAGS' language by making it extensible: New
distributions and functions can be added, including as calls to external
compiled code. Although most people think of MCMC as the main goal of the
'BUGS'/'JAGS' language for writing models, one can use 'NIMBLE' for writing
arbitrary other kinds of model-generic algorithms as well. A full User Manual is
available at <https://r-nimble.org>.
Author: Perry de Valpine [aut],
Christopher Paciorek [aut, cre],
Daniel Turek [aut],
Nick Michaud [aut],
Cliff Anderson-Bergman [aut],
Fritz Obermeyer [aut],
Claudia Wehrhahn Cortes [aut] (Bayesian nonparametrics system),
Abel Rodrìguez [aut] (Bayesian nonparametrics system),
Duncan Temple Lang [aut] (packaging configuration),
Sally Paganin [aut] (reversible jump MCMC),
Joshua Hug [aut] (WAIC),
Jagadish Babu [ctb] (code for the compilation system for an early
version of NIMBLE),
Lauren Ponisio [ctb] (contributions to the cross-validation code),
Peter Sujan [ctb] (multivariate t distribution code)
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Diff between nimble versions 0.12.0 dated 2021-09-28 and 0.12.1 dated 2021-10-09
DESCRIPTION | 8 - MD5 | 83 +++++------ NAMESPACE | 268 ------------------------------------- R/BUGS_readBUGS.R | 4 R/MCMC_WAIC.R | 3 R/MCMC_conjugacy.R | 15 +- R/MCMC_samplers.R | 2 R/all_utils.R | 4 R/distributions_implementations.R | 6 R/distributions_processInputList.R | 2 R/nimble-package.r | 3 R/nimbleFunction_Rexecution.R | 6 R/nimbleFunction_core.R | 6 R/nimbleList_core.R | 2 R/nimbleProject.R | 2 R/types_modelValues.R | 6 R/types_nimbleFunctionList.R | 2 inst/CppCode/dists.cpp | 52 +++---- inst/NEWS | 16 ++ inst/include/nimble/dists.h | 11 + man/CAR-Normal.Rd | 2 man/compileNimble.Rd | 2 man/getsize.Rd | 2 man/modelValues.Rd | 2 man/modelValuesBaseClass-class.Rd | 2 man/modelValuesConf.Rd | 2 man/nfVar.Rd | 4 man/nimEigen.Rd | 2 man/nimSvd.Rd | 2 man/nimble-R-functions.Rd | 2 man/nimble-internal.Rd | 17 -- man/nimble.Rd | 2 man/nimbleFunction.Rd | 4 man/nimbleFunctionList-class.Rd | 2 man/nimbleFunctionVirtual.Rd | 2 man/nimbleModel.Rd | 4 man/nimbleType-class.Rd | 2 man/registerDistributions.Rd | 2 man/resize.Rd | 2 man/samplers.Rd | 2 man/waic.Rd | 3 tests/testthat/test-mcmc.R | 156 ++++++++++++++++++++- tests/testthat/test-newmcmcshort.R |only 43 files changed, 309 insertions(+), 412 deletions(-)
Title: R Interface for the 'H2O' Scalable Machine Learning Platform
Description: R interface for 'H2O', the scalable open source machine learning
platform that offers parallelized implementations of many supervised and
unsupervised machine learning algorithms such as Generalized Linear
Models (GLM), Gradient Boosting Machines (including XGBoost), Random Forests,
Deep Neural Networks (Deep Learning), Stacked Ensembles, Naive Bayes,
Generalized Additive Models (GAM), ANOVA GLM, Cox Proportional Hazards, K-Means, PCA, Maximum R GLM (maxrglm),
Word2Vec, as well as a fully automatic machine learning algorithm (H2O AutoML).
Author: Erin LeDell [aut, cre],
Navdeep Gill [aut],
Spencer Aiello [aut],
Anqi Fu [aut],
Arno Candel [aut],
Cliff Click [aut],
Tom Kraljevic [aut],
Tomas Nykodym [aut],
Patrick Aboyoun [aut],
Michal Kurka [aut],
Michal Malohlava [aut],
Ludi Rehak [ctb],
Eric Eckstrand [ctb],
Brandon Hill [ctb],
Sebastian Vidrio [ctb],
Surekha Jadhawani [ctb],
Amy Wang [ctb],
Raymond Peck [ctb],
Wendy Wong [ctb],
Jan Gorecki [ctb],
Matt Dowle [ctb],
Yuan Tang [ctb],
Lauren DiPerna [ctb],
Tomas Fryda [ctb],
H2O.ai [cph, fnd]
Maintainer: Erin LeDell <erin@h2o.ai>
Diff between h2o versions 3.32.1.3 dated 2021-05-23 and 3.34.0.3 dated 2021-10-09
h2o-3.32.1.3/h2o/inst/java |only h2o-3.34.0.3/h2o/DESCRIPTION | 21 - h2o-3.34.0.3/h2o/MD5 | 133 ++++--- h2o-3.34.0.3/h2o/NAMESPACE | 12 h2o-3.34.0.3/h2o/R/anovaglm.R |only h2o-3.34.0.3/h2o/R/automl.R | 43 +- h2o-3.34.0.3/h2o/R/classes.R | 104 ++++++ h2o-3.34.0.3/h2o/R/connection.R | 16 h2o-3.34.0.3/h2o/R/coxph.R | 4 h2o-3.34.0.3/h2o/R/deeplearning.R | 4 h2o-3.34.0.3/h2o/R/explain.R | 273 +++++++++++----- h2o-3.34.0.3/h2o/R/export.R | 24 + h2o-3.34.0.3/h2o/R/extendedisolationforest.R |only h2o-3.34.0.3/h2o/R/frame.R | 30 + h2o-3.34.0.3/h2o/R/gam.R | 4 h2o-3.34.0.3/h2o/R/gbm.R | 4 h2o-3.34.0.3/h2o/R/glm.R | 4 h2o-3.34.0.3/h2o/R/grid.R | 13 h2o-3.34.0.3/h2o/R/kvstore.R | 65 ++- h2o-3.34.0.3/h2o/R/maxrglm.R |only h2o-3.34.0.3/h2o/R/models.R | 123 ++++--- h2o-3.34.0.3/h2o/R/pca.R | 21 + h2o-3.34.0.3/h2o/R/permutation_varimp.R |only h2o-3.34.0.3/h2o/R/randomforest.R | 4 h2o-3.34.0.3/h2o/R/rulefit.R | 8 h2o-3.34.0.3/h2o/R/segment.R | 2 h2o-3.34.0.3/h2o/R/stackedensemble.R | 4 h2o-3.34.0.3/h2o/R/targetencoder.R | 11 h2o-3.34.0.3/h2o/R/word2vec.R | 2 h2o-3.34.0.3/h2o/R/xgboost.R | 28 + h2o-3.34.0.3/h2o/inst/branch.txt | 2 h2o-3.34.0.3/h2o/man/H2OModelMetrics-class.Rd | 3 h2o-3.34.0.3/h2o/man/as.factor.Rd | 18 - h2o-3.34.0.3/h2o/man/dot-get_domain_mapping.Rd |only h2o-3.34.0.3/h2o/man/dot-get_first_of_family.Rd | 2 h2o-3.34.0.3/h2o/man/h2o-package.Rd | 8 h2o-3.34.0.3/h2o/man/h2o.anovaglm.Rd |only h2o-3.34.0.3/h2o/man/h2o.automl.Rd | 41 +- h2o-3.34.0.3/h2o/man/h2o.connect.Rd | 1 h2o-3.34.0.3/h2o/man/h2o.coxph.Rd | 4 h2o-3.34.0.3/h2o/man/h2o.deeplearning.Rd | 4 h2o-3.34.0.3/h2o/man/h2o.download_model.Rd | 5 h2o-3.34.0.3/h2o/man/h2o.download_mojo.Rd | 11 h2o-3.34.0.3/h2o/man/h2o.explain.Rd | 3 h2o-3.34.0.3/h2o/man/h2o.explain_row.Rd | 3 h2o-3.34.0.3/h2o/man/h2o.extendedIsolationForest.Rd |only h2o-3.34.0.3/h2o/man/h2o.gam.Rd | 4 h2o-3.34.0.3/h2o/man/h2o.gbm.Rd | 4 h2o-3.34.0.3/h2o/man/h2o.getModelTree.Rd | 9 h2o-3.34.0.3/h2o/man/h2o.get_best_model.Rd | 2 h2o-3.34.0.3/h2o/man/h2o.get_best_model_predictors.Rd |only h2o-3.34.0.3/h2o/man/h2o.get_best_r2_values.Rd |only h2o-3.34.0.3/h2o/man/h2o.glm.Rd | 4 h2o-3.34.0.3/h2o/man/h2o.grid.Rd | 2 h2o-3.34.0.3/h2o/man/h2o.h.Rd |only h2o-3.34.0.3/h2o/man/h2o.init.Rd | 2 h2o-3.34.0.3/h2o/man/h2o.maxrglm.Rd |only h2o-3.34.0.3/h2o/man/h2o.model_correlation.Rd |only h2o-3.34.0.3/h2o/man/h2o.model_correlation_heatmap.Rd | 2 h2o-3.34.0.3/h2o/man/h2o.permutation_importance.Rd |only h2o-3.34.0.3/h2o/man/h2o.permutation_importance_plot.Rd |only h2o-3.34.0.3/h2o/man/h2o.randomForest.Rd | 4 h2o-3.34.0.3/h2o/man/h2o.result.Rd |only h2o-3.34.0.3/h2o/man/h2o.rulefit.Rd | 8 h2o-3.34.0.3/h2o/man/h2o.saveModel.Rd | 5 h2o-3.34.0.3/h2o/man/h2o.saveModelDetails.Rd | 4 h2o-3.34.0.3/h2o/man/h2o.save_mojo.Rd | 4 h2o-3.34.0.3/h2o/man/h2o.screeplot.Rd |only h2o-3.34.0.3/h2o/man/h2o.stackedEnsemble.Rd | 4 h2o-3.34.0.3/h2o/man/h2o.targetencoder.Rd | 11 h2o-3.34.0.3/h2o/man/h2o.train_segments.Rd | 2 h2o-3.34.0.3/h2o/man/h2o.varimp-H2OAutoML-method.Rd |only h2o-3.34.0.3/h2o/man/h2o.varimp-H2OFrame-method.Rd |only h2o-3.34.0.3/h2o/man/h2o.varimp-H2OModel-method.Rd |only h2o-3.34.0.3/h2o/man/h2o.varimp.Rd | 15 h2o-3.34.0.3/h2o/man/h2o.varimp_heatmap.Rd | 2 h2o-3.34.0.3/h2o/man/h2o.xgboost.Rd | 18 - h2o-3.34.0.3/h2o/man/predict_contributions.H2OModel.Rd | 34 + 78 files changed, 854 insertions(+), 348 deletions(-)
Title: Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
Description: Calculates the Delaunay triangulation and the Dirichlet
or Voronoi tessellation (with respect to the entire plane) of
a planar point set. Plots triangulations and tessellations in
various ways. Clips tessellations to sub-windows. Calculates
perimeters of tessellations. Summarises information about
the tiles of the tessellation. Calculates the centroidal
Voronoi (Dirichlet) tessellation using Lloyd's algorithm.
Author: Rolf Turner
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>
Diff between deldir versions 1.0-2 dated 2021-10-05 and 1.0-5 dated 2021-10-09
ChangeLog | 35 +++++++++ DESCRIPTION | 8 +- MD5 | 18 ++--- R/deldir.R | 63 ++++++++++++++--- R/plot.triang.list.R | 4 - R/prelimtlist.R | 15 ++-- R/triang.list.R | 8 +- man/deldir.Rd | 170 ++++++++++++++++++++++++++++++++++++------------ man/plot.triang.list.Rd | 30 +++++--- man/triang.list.Rd | 20 ++++- 10 files changed, 281 insertions(+), 90 deletions(-)
Title: Libraries, Data Dictionaries, and a Data Step for R
Description: Contains a set of functions to create data libraries,
generate data dictionaries, and simulate a data step.
The libname() function will load a directory of data into
a library in one line of code. The dictionary() function
will generate data dictionaries for individual
data frames or an entire library. And the datestep() function
will perform row-by-row data processing.
Author: David J. Bosak
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between libr versions 1.2.0 dated 2021-06-29 and 1.2.1 dated 2021-10-09
DESCRIPTION | 11 - MD5 | 68 +++--- NEWS.md | 7 R/datastep.R | 300 +---------------------------- R/dictionary.R | 33 ++- R/dsarray.R | 6 R/dsattr.R | 6 R/libname.R | 2 R/specs.R | 3 R/utilities.R | 54 ++--- README.md | 5 build/vignette.rds |binary inst/doc/libr-datastep.R | 3 inst/doc/libr-datastep.Rmd | 3 inst/doc/libr-datastep.html | 67 +++--- inst/doc/libr-management.R | 3 inst/doc/libr-management.Rmd | 3 inst/doc/libr-management.html | 165 ++++++++-------- man/dictionary.Rd | 6 man/dsarray.Rd | 3 man/dsattr.Rd | 232 +++++++++++----------- man/specs.Rd | 3 man/sub-.dsarray.Rd | 3 src/RcppExports.cpp | 5 tests/testthat/test-datastep.R | 4 tests/testthat/test-dictionary.R | 87 ++++++++ tests/testthat/test-dsarray.R | 284 +++++++++++++++------------ tests/testthat/test-dsattr.R | 159 +++++++++------ tests/testthat/test-libname.R | 379 ++++++++++++++++++------------------- tests/testthat/test-manipulation.R | 124 ++++++------ tests/testthat/test-performance.R | 2 tests/testthat/test-specs.R | 15 + tests/testthat/test-utilities.R | 37 +++ vignettes/libr-datastep.Rmd | 3 vignettes/libr-management.Rmd | 3 35 files changed, 1026 insertions(+), 1062 deletions(-)
Title: Generate Generative Data for a Data Source
Description: Generative Adversarial Networks are applied to generate generative data for a data source. In iterative training steps the distribution of generated data converges to that of the data source. An application of generative data is the created density value function which is used to classify data records. Reference: Goodfellow et al. (2014) <arXiv:1406.2661v1>.
Author: Werner Mueller
Maintainer: Werner Mueller <werner.mueller5@chello.at>
Diff between ganGenerativeData versions 1.1.1 dated 2021-05-24 and 1.2.0 dated 2021-10-09
ganGenerativeData-1.1.1/ganGenerativeData/man/figures/gd12d.svg |only ganGenerativeData-1.1.1/ganGenerativeData/man/figures/gd34d.svg |only ganGenerativeData-1.2.0/ganGenerativeData/DESCRIPTION | 10 ganGenerativeData-1.2.0/ganGenerativeData/MD5 | 79 +- ganGenerativeData-1.2.0/ganGenerativeData/NAMESPACE | 5 ganGenerativeData-1.2.0/ganGenerativeData/R/RcppExports.R | 85 ++ ganGenerativeData-1.2.0/ganGenerativeData/R/dsInt.R | 18 ganGenerativeData-1.2.0/ganGenerativeData/R/gdCalculateDensitiyValues.R |only ganGenerativeData-1.2.0/ganGenerativeData/R/gdGenerate.R | 54 + ganGenerativeData-1.2.0/ganGenerativeData/R/gdPlot2dProjection.R | 227 +++++-- ganGenerativeData-1.2.0/ganGenerativeData/man/dsActivateColumns.Rd | 2 ganGenerativeData-1.2.0/ganGenerativeData/man/dsCreateWithDataFrame.Rd | 6 ganGenerativeData-1.2.0/ganGenerativeData/man/dsDeactivateColumns.Rd | 2 ganGenerativeData-1.2.0/ganGenerativeData/man/dsGetActiveColumnNames.Rd | 5 ganGenerativeData-1.2.0/ganGenerativeData/man/dsGetInactiveColumnNames.Rd | 5 ganGenerativeData-1.2.0/ganGenerativeData/man/dsGetNumberOfRows.Rd | 2 ganGenerativeData-1.2.0/ganGenerativeData/man/dsGetRow.Rd | 8 ganGenerativeData-1.2.0/ganGenerativeData/man/dsRead.Rd | 2 ganGenerativeData-1.2.0/ganGenerativeData/man/dsWrite.Rd | 5 ganGenerativeData-1.2.0/ganGenerativeData/man/figures/gd12d.png |binary ganGenerativeData-1.2.0/ganGenerativeData/man/figures/gd12d_.png |only ganGenerativeData-1.2.0/ganGenerativeData/man/figures/gd12ddv.png |only ganGenerativeData-1.2.0/ganGenerativeData/man/figures/gd12ddv_.png |only ganGenerativeData-1.2.0/ganGenerativeData/man/figures/gd34d.png |binary ganGenerativeData-1.2.0/ganGenerativeData/man/figures/gd34d_.png |only ganGenerativeData-1.2.0/ganGenerativeData/man/figures/gd34ddv.png |only ganGenerativeData-1.2.0/ganGenerativeData/man/figures/gd34ddv_.png |only ganGenerativeData-1.2.0/ganGenerativeData/man/ganGenerativeData-package.Rd | 79 +- ganGenerativeData-1.2.0/ganGenerativeData/man/gdCalculateDensityValue.Rd |only ganGenerativeData-1.2.0/ganGenerativeData/man/gdCalculateDensityValueQuantile.Rd |only ganGenerativeData-1.2.0/ganGenerativeData/man/gdCalculateDensityValues.Rd |only ganGenerativeData-1.2.0/ganGenerativeData/man/gdGenerate.Rd | 18 ganGenerativeData-1.2.0/ganGenerativeData/man/gdGetRow.Rd | 6 ganGenerativeData-1.2.0/ganGenerativeData/man/gdPlot2dProjection.Rd | 29 ganGenerativeData-1.2.0/ganGenerativeData/man/gdRead.Rd | 10 ganGenerativeData-1.2.0/ganGenerativeData/src/RcppExports.cpp | 69 ++ ganGenerativeData-1.2.0/ganGenerativeData/src/column.h | 7 ganGenerativeData-1.2.0/ganGenerativeData/src/dataSource.h | 119 ++- ganGenerativeData-1.2.0/ganGenerativeData/src/density.h |only ganGenerativeData-1.2.0/ganGenerativeData/src/dsInt.cpp | 36 - ganGenerativeData-1.2.0/ganGenerativeData/src/gdInt.cpp | 304 +++++++--- ganGenerativeData-1.2.0/ganGenerativeData/src/generativeData.h | 29 ganGenerativeData-1.2.0/ganGenerativeData/src/inOut.h | 53 + ganGenerativeData-1.2.0/ganGenerativeData/src/normalizeData.h | 154 +++-- ganGenerativeData-1.2.0/ganGenerativeData/src/numberColumn.h | 21 ganGenerativeData-1.2.0/ganGenerativeData/src/progress.h |only ganGenerativeData-1.2.0/ganGenerativeData/src/stringColumn.h | 19 ganGenerativeData-1.2.0/ganGenerativeData/src/vpTree.h |only 48 files changed, 994 insertions(+), 474 deletions(-)
More information about ganGenerativeData at CRAN
Permanent link
Title: Generalized Latent Markov Models
Description: Latent Markov models for longitudinal continuous and categorical data. See Bartolucci, Pandolfi, Pennoni (2017)<doi:10.18637/jss.v081.i04>.
Author: Francesco Bartolucci [aut, cre],
Silvia Pandolfi [aut],
Fulvia Pennoni [aut],
Alessio Farcomeni [ctb],
Alessio Serafini [ctb]
Maintainer: Francesco Bartolucci <bart@stat.unipg.it>
Diff between LMest versions 3.0.1 dated 2020-12-05 and 3.0.2 dated 2021-10-09
DESCRIPTION | 20 +-- MD5 | 22 ++-- R/lmbasic.cont.R | 3 R/lmcovlatent.R | 1 R/lmestCont.R | 233 +++++++++++++++++--------------------------- R/lmestDecoding.R | 14 +- build/vignette.rds |binary inst/doc/vignetteLMest.Rmd | 2 inst/doc/vignetteLMest.html | 233 +++++--------------------------------------- man/LMest-package.Rd | 2 man/PSIDlong.Rd | 2 vignettes/vignetteLMest.Rmd | 2 12 files changed, 161 insertions(+), 373 deletions(-)
Title: Easily Apply Formats to Data
Description: Contains a set of functions that can be used to apply
formats to data frames or vectors. The package aims to provide to
functionality similar to that of SAS® formats. Formats are assigned to
the format attribute on data frame columns. Then when the fdata()
function is called, a new data frame is created with the column data
formatted as specified. The package also contains a value() function
to create a user-defined format, similar to a SAS® user-defined format.
Author: David Bosak
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between fmtr versions 1.5.2 dated 2021-07-25 and 1.5.3 dated 2021-10-09
DESCRIPTION | 10 +++--- MD5 | 60 ++++++++++++++++++------------------ NEWS.md | 6 +++ R/descriptions.R | 32 +++++++++++++++---- R/formats.R | 31 +++++++++++++++--- R/justification.R | 32 +++++++++++++++---- R/labels.R | 34 ++++++++++++++++---- R/widths.R | 32 +++++++++++++++---- README.md | 5 +-- build/vignette.rds |binary inst/doc/fmtr-convenience.html | 4 +- inst/doc/fmtr-fapply.html | 4 +- inst/doc/fmtr-fcat.html | 4 +- inst/doc/fmtr-fdata.html | 4 +- inst/doc/fmtr-helpers.html | 4 +- man/descriptions.Rd | 9 +++++ man/formats.Rd | 9 +++++ man/justification.Rd | 10 +++++- man/labels.data.frame.Rd | 9 +++++ man/widths.Rd | 9 +++++ src/RcppExports.cpp | 5 +++ tests/testthat/test-descriptions.R | 10 +++++- tests/testthat/test-fapply.R | 14 ++++++++ tests/testthat/test-fcat.R | 22 +++++++++++++ tests/testthat/test-fdata.R | 20 ++++++++++++ tests/testthat/test-flist.R | 52 ++++++++++++++++++++++++++++++- tests/testthat/test-fmt.R | 10 ++++++ tests/testthat/test-formats.R | 14 +++++++- tests/testthat/test-justification.R | 11 ++++-- tests/testthat/test-labels.R | 22 +++++++++++++ tests/testthat/test-widths.R | 11 ++++++ 31 files changed, 411 insertions(+), 88 deletions(-)
Title: R Interface to PXWEB APIs
Description: Generic interface for the PX-Web/PC-Axis API. The PX-Web/PC-Axis
API is used by organizations such as Statistics Sweden and Statistics
Finland to disseminate data. The R package can interact with all
PX-Web/PC-Axis APIs to fetch information about the data hierarchy, extract
metadata and extract and parse statistics to R data.frame format. PX-Web is
a solution to disseminate PC-Axis data files in dynamic tables on the web.
Since 2013 PX-Web contains an API to disseminate PC-Axis files.
Author: Mans Magnusson [aut, cre],
Markus Kainu [aut],
Janne Huovari [aut],
Leo Lahti [aut] (<https://orcid.org/0000-0001-5537-637X>),
Love Hansson [ctb],
Eydun Nielsen [ctb],
Bo Werth [ctb],
Thomas Runarsson [ctb],
Torbjörn Lindquist [ctb],
Palmar Thorsteinsson [ctb],
Pyry Kantanen [ctb],
Sebastian Ankargren [ctb]
Maintainer: Mans Magnusson <mons.magnusson@gmail.com>
Diff between pxweb versions 0.11.0 dated 2021-07-08 and 0.12.0 dated 2021-10-09
DESCRIPTION | 12 +++------ MD5 | 24 +++++++++--------- NAMESPACE | 2 - R/defunct_functions.R | 25 ------------------- R/pxweb_as_data_frame.R | 4 +-- R/pxweb_interactive.R | 51 +++++++++++++++++++++++++++++----------- R/pxweb_levels.R | 11 +++++++- inst/doc/pxweb.html | 22 ++++++++--------- inst/extdata/api.json | 4 +-- man/api_catalogue.Rd | 44 +--------------------------------- man/pxe_position_choice_size.Rd | 3 ++ tests/testthat/test-defunct.R | 2 - tests/testthat/test-pxweb_get.R | 10 +++++++ 13 files changed, 94 insertions(+), 120 deletions(-)
Title: Exploratory Analysis of Genetic and Genomic Data
Description: Toolset for the exploration of genetic and genomic
data. Adegenet provides formal (S4) classes for storing and handling
various genetic data, including genetic markers with varying ploidy
and hierarchical population structure ('genind' class), alleles counts
by populations ('genpop'), and genome-wide SNP data ('genlight'). It
also implements original multivariate methods (DAPC, sPCA), graphics,
statistical tests, simulation tools, distance and similarity measures,
and several spatial methods. A range of both empirical and simulated
datasets is also provided to illustrate various methods.
Author: Thibaut Jombart [aut] (<https://orcid.org/0000-0003-2226-8692>),
Zhian N. Kamvar [aut, cre] (<https://orcid.org/0000-0003-1458-7108>),
Caitlin Collins [ctb],
Roman Lustrik [ctb],
Marie-Pauline Beugin [ctb],
Brian J. Knaus [ctb],
Peter Solymos [ctb],
Vladimir Mikryukov [ctb],
Klaus Schliep [ctb],
Tiago Maié [ctb],
Libor Morkovsky [ctb],
Ismail Ahmed [ctb],
Anne Cori [ctb],
Federico Calboli [ctb],
RJ Ewing [ctb],
Frédéric Michaud [ctb],
Rebecca DeCamp [ctb],
Alexandre Courtiol [ctb] (<https://orcid.org/0000-0003-0637-2959>)
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>
Diff between adegenet versions 2.1.4 dated 2021-07-17 and 2.1.5 dated 2021-10-09
ChangeLog | 22 +++++++++++++++ DESCRIPTION | 15 ++++------ MD5 | 51 ++++++++++++++++++------------------ NAMESPACE | 12 -------- R/chooseCN.R | 30 ++++++++++++--------- R/datasets.R | 9 ++++-- R/handling.R | 10 ++++++- R/import.R | 4 +- R/spca.R | 24 ++++++++++++---- R/spca_randtest.R | 8 ++++- build/partial.rdb |binary data/H3N2.rda |binary data/dapcIllus.rda |binary data/eHGDP.rda |binary data/hybridtoy.RData |binary data/microbov.rda |binary data/nancycats.rda |binary data/rupica.RData |binary data/sim2pop.rda |binary data/spcaIllus.rda |binary data/swallowtails.rda |binary man/fasta2genlight.Rd | 4 +- man/glPca.Rd | 6 ++-- man/read.PLINK.Rd | 2 - man/rupica.Rd | 5 ++- man/spcaIllus.Rd | 5 ++- tests/testthat/test-genind2genpop.R |only 27 files changed, 128 insertions(+), 79 deletions(-)
Title: Geographically-Weighted Models
Description: Techniques from a particular branch of spatial statistics,termed geographically-weighted (GW) models. GW models suit situations when data are not described well by some global model, but where there are spatial regions where a suitably localised calibration provides a better description. 'GWmodel' includes functions to calibrate: GW summary statistics (Brunsdon et al., 2002)<doi: 10.1016/s0198-9715(01)00009-6>, GW principal components analysis (Harris et al., 2011)<doi: 10.1080/13658816.2011.554838>, GW discriminant analysis (Brunsdon et al., 2007)<doi: 10.1111/j.1538-4632.2007.00709.x> and various forms of GW regression (Brunsdon et al., 1996)<doi: 10.1111/j.1538-4632.1996.tb00936.x>; some of which are provided in basic and robust (outlier resistant) forms.
Author: Binbin Lu[aut], Paul Harris[aut], Martin Charlton[aut], Chris Brunsdon[aut], Tomoki Nakaya[aut], Daisuke Murakami[aut],Isabella Gollini[ctb], Yigong Hu[ctb], Fiona H Evans[ctb]
Maintainer: Binbin Lu <binbinlu@whu.edu.cn>
Diff between GWmodel versions 2.2-7 dated 2021-09-07 and 2.2-8 dated 2021-10-09
DESCRIPTION | 8 ++++---- MD5 | 17 +++++++++-------- R/zzz.r | 2 +- build |only configure | 2 ++ configure.ac | 5 ++++- inst/CITATION | 8 ++++---- man/GWmodel-package.Rd | 8 ++++---- man/gwr.basic.rd | 5 +++-- src/GWmodel.cpp | 6 +++--- 10 files changed, 34 insertions(+), 27 deletions(-)
Title: Conceptual Properties Norming Studies as Parameter Estimation
Description: Implementation of conceptual properties norming studies, including estimates of CPNs parameters with their corresponding variances and estimates for the sampling process, and a sampling property function based on a modified empirical distribution from the original data.
Author: Sebastian Moreno [aut, cre],
Enrique Canessa [ths],
Sergio Chaigneau [ths],
Rodrigo Lagos [ths],
Felipe Medina [ths]
Maintainer: Sebastian Moreno <sebastian.moreno.araya@gmail.com>
Diff between CPNCoverageAnalysis versions 1.0.0 dated 2021-09-09 and 1.1.0 dated 2021-10-09
DESCRIPTION | 8 ++++---- MD5 | 6 ++++-- NAMESPACE | 4 ++++ R/property_simulator.R |only man/property_simulator.Rd |only 5 files changed, 12 insertions(+), 6 deletions(-)
More information about CPNCoverageAnalysis at CRAN
Permanent link
Title: Multi-Objective Parameter Tuning for Classifiers
Description: Generic methods for parameter tuning of classification algorithms using multiple scoring functions (Muessel et al. (2012), <doi:10.18637/jss.v046.i05>).
Author: Christoph Müssel, Ludwig Lausser, Hans Kestler
Maintainer: Hans Kestler <hans.kestler@uni-ulm.de>
Diff between TunePareto versions 2.5 dated 2018-06-08 and 2.5.1 dated 2021-10-09
DESCRIPTION | 9 ++++----- MD5 | 22 +++++++++++----------- inst/CITATION | 4 ++-- man/TunePareto-package.Rd | 5 ++--- man/createObjective.Rd | 4 +--- man/plotDominationGraph.Rd | 4 +--- man/plotObjectivePairs.Rd | 4 +--- man/plotParetoFronts2D.Rd | 4 +--- man/precalculation.Rd | 4 +--- man/predefinedClassifiers.Rd | 7 +------ man/predefinedObjectiveFunctions.Rd | 4 +--- man/tunePareto.Rd | 6 +----- 12 files changed, 27 insertions(+), 50 deletions(-)
Title: Estimation of Transition Probabilities in Multistate Models
Description: Estimation of transition probabilities for the
illness-death model and or the three-state progressive model.
Author: Artur Araujo [aut, cre] (<https://orcid.org/0000-0003-1419-4208>),
Javier Roca-Pardinas [aut] (<https://orcid.org/0000-0003-3107-4515>),
Luis Meira-Machado [aut] (<https://orcid.org/0000-0002-8577-7665>)
Maintainer: Artur Araujo <artur.stat@gmail.com>
Diff between TPmsm versions 1.2.2 dated 2019-08-04 and 1.2.4 dated 2021-10-09
DESCRIPTION | 49 ++++++-- LICENSE |only MD5 | 158 ++++++++++++++------------ NAMESPACE | 42 +++---- R/BtoTPCmsm.R | 6 - R/BtoTPmsm.R | 22 +-- R/Clean.R | 6 - R/OutTPmsm.R | 6 - R/Outetm.R | 46 +++---- R/Outp3state.R | 6 - R/TPmsmOut.R | 38 +++--- R/Trans.R | 86 +++++++------- R/TransBoot.R | 120 ++++++++++---------- R/TransCheck.R | 258 ++++++++++++++++++++++---------------------- R/TransMatrix.R | 82 ++++++------- R/TransMethod.R | 40 +++--- R/TransPROB.R | 90 +++++++-------- R/TransWidth.R | 30 ++--- R/addlegend.R | 30 ++--- R/as.data.frame.survTP.R | 14 +- R/contour.TPCmsm.R | 122 ++++++++++---------- R/corrTP.R | 58 ++++----- R/csample.int.R | 8 - R/dgpTP.R | 20 +-- R/image.TPCmsm.R | 190 ++++++++++++++++---------------- R/lines.TPCmsm.R | 150 ++++++++++++------------- R/lines.TPmsm.R | 62 +++++----- R/methods.R | 62 +++++----- R/object.R | 14 +- R/plot.TPCmsm.R | 170 ++++++++++++++-------------- R/plot.TPmsm.R | 68 +++++------ R/print.TPCmsm.R | 46 +++---- R/print.TPmsm.R | 52 ++++---- R/setPackageSeedTP.R | 26 ++-- R/setSeedTP.R | 50 ++++---- R/setThreadsTP.R | 16 +- R/survTP.R | 88 +++++++-------- R/toTPCmsm.R | 6 - R/toTPmsm.R | 22 +-- R/transAJ.R | 18 +-- R/transIPCW.R | 30 ++--- R/transKMPW.R | 24 ++-- R/transKMW.R | 24 ++-- R/transLIN.R | 32 ++--- R/transLS.R | 28 ++-- R/transPAJ.R | 18 +-- R/uniqueTP.R | 14 +- R/zzz.R | 6 - README.md |only build |only inst/CITATION | 64 +++++++--- inst/NEWS.Rd | 218 +++++++++++++++++-------------------- inst/doc |only man/TPmsm-package.Rd | 168 +++++++++++++++------------- man/TPmsmOut.Rd | 11 + man/as.data.frame.survTP.Rd | 11 + man/bladderTP.Rd | 10 - man/colonTP.Rd | 26 ++-- man/contour.TPCmsm.Rd | 27 ++-- man/corrTP.Rd | 9 + man/dgpTP.Rd | 13 +- man/heartTP.Rd | 8 - man/image.TPCmsm.Rd | 29 ++-- man/lines.TPCmsm.Rd | 15 +- man/lines.TPmsm.Rd | 15 +- man/plot.TPCmsm.Rd | 15 +- man/plot.TPmsm.Rd | 15 +- man/setPackageSeedTP.Rd | 55 ++++----- man/setSeedTP.Rd | 47 ++++---- man/setThreadsTP.Rd | 36 +++--- man/survTP.Rd | 15 +- man/transAJ.Rd | 45 ++++--- man/transIPCW.Rd | 111 +++++++++--------- man/transKMPW.Rd | 85 +++++++------- man/transKMW.Rd | 85 +++++++------- man/transLIN.Rd | 87 +++++++------- man/transLS.Rd | 49 ++++---- man/transPAJ.Rd | 45 ++++--- src/TPmsm-win.def | 8 - vignettes |only 80 files changed, 2005 insertions(+), 1870 deletions(-)
Title: Read Text Documents into R
Description: A small collection of convenience tools for reading text documents into R.
Author: Tyler Rinker [aut, cre],
Bryan Goodrich [ctb],
Dason Kurkiewicz [ctb]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between textreadr versions 1.0.2 dated 2020-06-17 and 1.2.0 dated 2021-10-09
DESCRIPTION | 10 MD5 | 36 +- NAMESPACE | 1 NEWS | 13 + R/browse.R | 2 R/read_document.R | 1 R/read_docx.R | 17 - R/read_html.R | 2 R/read_odt.R |only R/read_pdf.R | 2 R/read_transcript.R | 60 ++++ README.md | 467 ++++++++++++++++++++----------------- data/presidential_debates_2012.rda |binary inst/CITATION | 12 inst/docs/Hello_World.odt |only inst/docs/trans8.odt |only man/browse.Rd | 2 man/read_html.Rd | 2 man/read_odt.Rd |only man/read_pdf.Rd | 2 man/read_transcript.Rd | 9 21 files changed, 380 insertions(+), 258 deletions(-)
Title: Linear Model Evaluation with Randomized Residuals in a
Permutation Procedure
Description: Linear model calculations are made for many random versions of data.
Using residual randomization in a permutation procedure, sums of squares are
calculated over many permutations to generate empirical probability distributions
for evaluating model effects. This packaged is described by
Collyer & Adams (2018) <doi:10.1111/2041-210X.13029>. Additionally, coefficients, statistics, fitted values, and residuals generated over many
permutations can be used for various procedures including pairwise tests, prediction, classification, and
model comparison. This package should provide most tools one could need for the analysis of
high-dimensional data, especially in ecology and evolutionary biology, but certainly other fields, as well.
Author: Michael Collyer [aut, cre] (<https://orcid.org/0000-0003-0238-2201>),
Dean Adams [aut] (<https://orcid.org/0000-0001-9172-7894>)
Maintainer: Michael Collyer <mlcollyer@gmail.com>
Diff between RRPP versions 1.0.0 dated 2021-03-30 and 1.1.0 dated 2021-10-09
RRPP-1.0.0/RRPP/R/RcppExports.R |only RRPP-1.1.0/RRPP/DESCRIPTION | 10 RRPP-1.1.0/RRPP/MD5 | 47 RRPP-1.1.0/RRPP/NAMESPACE | 5 RRPP-1.1.0/RRPP/NEWS.md | 17 RRPP-1.1.0/RRPP/R/RRPP.support.code.r | 1416 +++++++------------------ RRPP-1.1.0/RRPP/R/RRPP.utils.r | 228 +++- RRPP-1.1.0/RRPP/R/add.tree.r | 5 RRPP-1.1.0/RRPP/R/anova.lm.rrpp.r | 3 RRPP-1.1.0/RRPP/R/coef.lm.rrpp.r | 24 RRPP-1.1.0/RRPP/R/lm.rrpp.r | 111 - RRPP-1.1.0/RRPP/R/looCV.r |only RRPP-1.1.0/RRPP/R/ordinate.r | 37 RRPP-1.1.0/RRPP/R/pairwise.r | 4 RRPP-1.1.0/RRPP/R/predict.lm.rrpp.r | 2 RRPP-1.1.0/RRPP/R/trajectory.analysis.r | 3 RRPP-1.1.0/RRPP/build/vignette.rds |binary RRPP-1.1.0/RRPP/inst/doc/ANOVA.vs.MANOVA.html | 4 RRPP-1.1.0/RRPP/inst/doc/Using.RRPP.Rmd | 4 RRPP-1.1.0/RRPP/inst/doc/Using.RRPP.html | 30 RRPP-1.1.0/RRPP/man/anova.lm.rrpp.Rd | 3 RRPP-1.1.0/RRPP/man/coef.lm.rrpp.Rd | 22 RRPP-1.1.0/RRPP/man/looCV.Rd |only RRPP-1.1.0/RRPP/man/na.omit.rrpp.data.frame.Rd |only RRPP-1.1.0/RRPP/man/plot.looCV.Rd |only RRPP-1.1.0/RRPP/man/print.looCV.Rd |only RRPP-1.1.0/RRPP/man/summary.looCV.Rd |only RRPP-1.1.0/RRPP/vignettes/Using.RRPP.Rmd | 4 28 files changed, 868 insertions(+), 1111 deletions(-)
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and
regression models.
Author: Max Kuhn [aut, cre],
Jed Wing [ctb],
Steve Weston [ctb],
Andre Williams [ctb],
Chris Keefer [ctb],
Allan Engelhardt [ctb],
Tony Cooper [ctb],
Zachary Mayer [ctb],
Brenton Kenkel [ctb],
R Core Team [ctb],
Michael Benesty [ctb],
Reynald Lescarbeau [ctb],
Andrew Ziem [ctb],
Luca Scrucca [ctb],
Yuan Tang [ctb],
Can Candan [ctb],
Tyler Hunt [ctb]
Maintainer: Max Kuhn <mxkuhn@gmail.com>
Diff between caret versions 6.0-89 dated 2021-09-28 and 6.0-90 dated 2021-10-09
caret-6.0-89/caret/vignettes/train_algo.png |only caret-6.0-90/caret/DESCRIPTION | 6 - caret-6.0-90/caret/MD5 | 77 ++++++++++++------------ caret-6.0-90/caret/R/confusionMatrix.R | 2 caret-6.0-90/caret/R/misc.R | 6 + caret-6.0-90/caret/R/plot.train.R | 2 caret-6.0-90/caret/R/preProcess.R | 2 caret-6.0-90/caret/R/prec_rec.R | 2 caret-6.0-90/caret/R/predict.train.R | 2 caret-6.0-90/caret/R/rfe.R | 2 caret-6.0-90/caret/R/sensitivity.R | 2 caret-6.0-90/caret/R/train.default.R | 11 +++ caret-6.0-90/caret/build/partial.rdb |only caret-6.0-90/caret/data/BloodBrain.RData |binary caret-6.0-90/caret/data/GermanCredit.RData |binary caret-6.0-90/caret/data/Sacramento.RData |binary caret-6.0-90/caret/data/cars.RData |binary caret-6.0-90/caret/data/cox2.RData |binary caret-6.0-90/caret/data/dhfr.RData |binary caret-6.0-90/caret/data/mdrr.RData |binary caret-6.0-90/caret/data/oil.RData |binary caret-6.0-90/caret/data/pottery.RData |binary caret-6.0-90/caret/data/scat.RData |binary caret-6.0-90/caret/data/segmentationData.RData |binary caret-6.0-90/caret/data/tecator.RData |binary caret-6.0-90/caret/inst/NEWS.Rd | 6 + caret-6.0-90/caret/inst/doc/caret.R | 3 caret-6.0-90/caret/inst/doc/caret.Rmd | 6 - caret-6.0-90/caret/inst/doc/caret.html | 3 caret-6.0-90/caret/inst/models/models.RData |binary caret-6.0-90/caret/inst/models/sampling.RData |binary caret-6.0-90/caret/man/confusionMatrix.Rd | 2 caret-6.0-90/caret/man/plot.rfe.Rd | 2 caret-6.0-90/caret/man/plot.train.Rd | 2 caret-6.0-90/caret/man/preProcess.Rd | 2 caret-6.0-90/caret/man/predict.train.Rd | 2 caret-6.0-90/caret/man/recall.Rd | 2 caret-6.0-90/caret/man/sensitivity.Rd | 2 caret-6.0-90/caret/man/train.Rd | 2 caret-6.0-90/caret/tests/testthat/test_ptypes.R |only caret-6.0-90/caret/vignettes/caret.Rmd | 6 - 41 files changed, 82 insertions(+), 72 deletions(-)
Title: Zero-Truncated Poisson Lognormal Distribution
Description: Functions for obtaining the density, random variates
and maximum likelihood estimates of the Zero-truncated Poisson lognormal
distribution and their mixture distribution.
Author: Masatoshi Katabuchi
Maintainer: Masatoshi Katabuchi <mattocci27@gmail.com>
Diff between ztpln versions 0.1.1 dated 2020-07-27 and 0.1.2 dated 2021-10-09
DESCRIPTION | 13 -- MD5 | 16 +- build/vignette.rds |binary inst/doc/ztpln.R | 6 inst/doc/ztpln.html | 330 ++++++++++++---------------------------------------- inst/doc/ztpln.rmd | 18 +- src/Makevars |only src/Makevars.win |only src/RcppExports.cpp | 5 vignettes/ztpln.rmd | 18 +- 10 files changed, 119 insertions(+), 287 deletions(-)
Title: Spatial Analysis on Network
Description: Perform spatial analysis on network.
Implement several methods for spatial analysis on network: Network Kernel Density estimation,
building of spatial matrices based on network distance ('listw' objects from 'spdep' package), K functions estimation
for point pattern analysis on network, k nearest neighbours on network, reachable area calculation, and graph generation
References: Okabe et al (2019) <doi:10.1080/13658810802475491>;
Okabe et al (2012, ISBN:978-0470770818);Baddeley el al (2015, ISBN:9781482210200).
Author: Jeremy Gelb [aut, cre] (<https://orcid.org/0000-0002-7114-2714>),
Philippe Apparicio [ctb] (<https://orcid.org/0000-0001-6466-9342>)
Maintainer: Jeremy Gelb <jeremy.gelb@ucs.inrs.ca>
Diff between spNetwork versions 0.1.1 dated 2021-01-21 and 0.2.0 dated 2021-10-09
spNetwork-0.1.1/spNetwork/man/add_center_lines.mc.Rd |only spNetwork-0.1.1/spNetwork/man/add_vertices.Rd |only spNetwork-0.1.1/spNetwork/man/continuousWorker_int.Rd |only spNetwork-0.1.1/spNetwork/man/find_vertices.Rd |only spNetwork-0.1.1/spNetwork/man/nearest.Rd |only spNetwork-0.1.1/spNetwork/src/code.cpp |only spNetwork-0.1.1/spNetwork/tests/testthat/test_error_env.RData |only spNetwork-0.2.0/spNetwork/DESCRIPTION | 47 spNetwork-0.2.0/spNetwork/MD5 | 268 +- spNetwork-0.2.0/spNetwork/NAMESPACE | 22 spNetwork-0.2.0/spNetwork/NEWS.md | 38 spNetwork-0.2.0/spNetwork/R/RcppExports.R | 488 +++- spNetwork-0.2.0/spNetwork/R/bandwidth_selection_cv.R |only spNetwork-0.2.0/spNetwork/R/bandwidth_selection_cvl.R |only spNetwork-0.2.0/spNetwork/R/border_correction.R | 17 spNetwork-0.2.0/spNetwork/R/geometrical_functions.R | 900 +++++++-- spNetwork-0.2.0/spNetwork/R/graph_functions.R | 262 +- spNetwork-0.2.0/spNetwork/R/isochrones.R |only spNetwork-0.2.0/spNetwork/R/k_functions.R | 260 -- spNetwork-0.2.0/spNetwork/R/knn.R |only spNetwork-0.2.0/spNetwork/R/neighbouring.R | 55 spNetwork-0.2.0/spNetwork/R/nkde_execution_functions.R | 208 -- spNetwork-0.2.0/spNetwork/R/spatial_indexing.R | 36 spNetwork-0.2.0/spNetwork/README.md | 242 +- spNetwork-0.2.0/spNetwork/build/partial.rdb |only spNetwork-0.2.0/spNetwork/build/vignette.rds |binary spNetwork-0.2.0/spNetwork/inst/REFERENCES.bib |only spNetwork-0.2.0/spNetwork/inst/doc/Isochrones.R |only spNetwork-0.2.0/spNetwork/inst/doc/Isochrones.Rmd |only spNetwork-0.2.0/spNetwork/inst/doc/Isochrones.html |only spNetwork-0.2.0/spNetwork/inst/doc/KNetworkFunctions.R | 85 spNetwork-0.2.0/spNetwork/inst/doc/KNetworkFunctions.Rmd | 107 - spNetwork-0.2.0/spNetwork/inst/doc/KNetworkFunctions.html | 402 +--- spNetwork-0.2.0/spNetwork/inst/doc/NKDE.R | 60 spNetwork-0.2.0/spNetwork/inst/doc/NKDE.Rmd | 114 - spNetwork-0.2.0/spNetwork/inst/doc/NKDE.html | 988 ++++------ spNetwork-0.2.0/spNetwork/inst/doc/NKDEdetailed.R | 295 +- spNetwork-0.2.0/spNetwork/inst/doc/NKDEdetailed.Rmd | 329 +-- spNetwork-0.2.0/spNetwork/inst/doc/NKDEdetailed.html | 546 +---- spNetwork-0.2.0/spNetwork/inst/doc/NetworkBuilding.R |only spNetwork-0.2.0/spNetwork/inst/doc/NetworkBuilding.Rmd |only spNetwork-0.2.0/spNetwork/inst/doc/NetworkBuilding.html |only spNetwork-0.2.0/spNetwork/inst/doc/SpatialWeightMatrices.Rmd | 11 spNetwork-0.2.0/spNetwork/inst/doc/SpatialWeightMatrices.html | 421 ---- spNetwork-0.2.0/spNetwork/inst/extdata/networks.gpkg |binary spNetwork-0.2.0/spNetwork/inst/extdata/results_vignette_kfunc.rda |binary spNetwork-0.2.0/spNetwork/inst/extdata/results_vignette_nkde.rda |binary spNetwork-0.2.0/spNetwork/inst/extdata/results_vignette_wmat.rda |binary spNetwork-0.2.0/spNetwork/man/add_vertices_lines.Rd | 2 spNetwork-0.2.0/spNetwork/man/aggregate_points.Rd | 58 spNetwork-0.2.0/spNetwork/man/build_graph.Rd | 22 spNetwork-0.2.0/spNetwork/man/build_graph_directed.Rd | 37 spNetwork-0.2.0/spNetwork/man/build_grid.Rd | 48 spNetwork-0.2.0/spNetwork/man/build_quadtree.Rd | 43 spNetwork-0.2.0/spNetwork/man/bw_cv_likelihood_calc.Rd |only spNetwork-0.2.0/spNetwork/man/bw_cv_likelihood_calc.mc.Rd |only spNetwork-0.2.0/spNetwork/man/bw_cvl_calc.Rd |only spNetwork-0.2.0/spNetwork/man/bw_cvl_calc.mc.Rd |only spNetwork-0.2.0/spNetwork/man/calc_isochrones.Rd |only spNetwork-0.2.0/spNetwork/man/clean_events.Rd | 2 spNetwork-0.2.0/spNetwork/man/closest_points.Rd | 8 spNetwork-0.2.0/spNetwork/man/continuousWorker.Rd |only spNetwork-0.2.0/spNetwork/man/continuousWorker_sparse.Rd | 9 spNetwork-0.2.0/spNetwork/man/continuousfunction.Rd | 3 spNetwork-0.2.0/spNetwork/man/corrfactor_continuous.Rd | 1 spNetwork-0.2.0/spNetwork/man/corrfactor_continuous_sparse.Rd | 1 spNetwork-0.2.0/spNetwork/man/corrfactor_discontinuous.Rd | 4 spNetwork-0.2.0/spNetwork/man/corrfactor_discontinuous_sparse.Rd | 1 spNetwork-0.2.0/spNetwork/man/cosine_kernel_cpp.Rd |only spNetwork-0.2.0/spNetwork/man/cosine_kernelos.Rd |only spNetwork-0.2.0/spNetwork/man/cross_gfun.Rd | 78 spNetwork-0.2.0/spNetwork/man/cross_kfunc.Rd | 74 spNetwork-0.2.0/spNetwork/man/cross_kfunctions.Rd | 223 +- spNetwork-0.2.0/spNetwork/man/cross_kfunctions.mc.Rd | 188 - spNetwork-0.2.0/spNetwork/man/cut_lines_at_distance.Rd |only spNetwork-0.2.0/spNetwork/man/discontinuousWorker_int.Rd | 1 spNetwork-0.2.0/spNetwork/man/discontinuousWorker_sparse.Rd | 1 spNetwork-0.2.0/spNetwork/man/discontinuousfunction.Rd | 1 spNetwork-0.2.0/spNetwork/man/dist_mat_dupl.Rd | 50 spNetwork-0.2.0/spNetwork/man/epanechnikov_kernel_cpp.Rd |only spNetwork-0.2.0/spNetwork/man/epanechnikov_kernelos.Rd |only spNetwork-0.2.0/spNetwork/man/esc_kernel_loo.Rd |only spNetwork-0.2.0/spNetwork/man/esd_kernel_loo.Rd |only spNetwork-0.2.0/spNetwork/man/figures/unnamed-chunk-4-1.png |only spNetwork-0.2.0/spNetwork/man/figures/unnamed-chunk-5-1.png |only spNetwork-0.2.0/spNetwork/man/figures/unnamed-chunk-6-1.png |only spNetwork-0.2.0/spNetwork/man/gaussian_kernel_cpp.Rd |only spNetwork-0.2.0/spNetwork/man/gaussian_kernel_scaled.Rd | 44 spNetwork-0.2.0/spNetwork/man/gaussian_kernel_scaled_cpp.Rd |only spNetwork-0.2.0/spNetwork/man/gaussian_kernel_scaledos.Rd |only spNetwork-0.2.0/spNetwork/man/gaussian_kernelos.Rd |only spNetwork-0.2.0/spNetwork/man/get_loo_values_continuous.Rd |only spNetwork-0.2.0/spNetwork/man/get_loo_values_discontinuous.Rd |only spNetwork-0.2.0/spNetwork/man/get_loo_values_simple.Rd |only spNetwork-0.2.0/spNetwork/man/gfunc.Rd | 70 spNetwork-0.2.0/spNetwork/man/graph_checking.Rd | 79 spNetwork-0.2.0/spNetwork/man/heal_edges.Rd |only spNetwork-0.2.0/spNetwork/man/kfunc.Rd | 66 spNetwork-0.2.0/spNetwork/man/kfunctions.Rd | 204 +- spNetwork-0.2.0/spNetwork/man/kfunctions.mc.Rd | 186 - spNetwork-0.2.0/spNetwork/man/lines_center.Rd | 8 spNetwork-0.2.0/spNetwork/man/lines_direction.Rd | 16 spNetwork-0.2.0/spNetwork/man/lines_extremities.Rd | 44 spNetwork-0.2.0/spNetwork/man/lines_points_along.Rd | 52 spNetwork-0.2.0/spNetwork/man/lixelize_lines.Rd | 8 spNetwork-0.2.0/spNetwork/man/lixelize_lines.mc.Rd | 4 spNetwork-0.2.0/spNetwork/man/nearestPointOnLine.Rd | 46 spNetwork-0.2.0/spNetwork/man/nearestPointOnSegment.Rd | 46 spNetwork-0.2.0/spNetwork/man/nearest_lines.Rd |only spNetwork-0.2.0/spNetwork/man/network_knn.Rd |only spNetwork-0.2.0/spNetwork/man/network_knn.mc.Rd |only spNetwork-0.2.0/spNetwork/man/network_knn_worker.Rd |only spNetwork-0.2.0/spNetwork/man/network_listw.Rd | 6 spNetwork-0.2.0/spNetwork/man/network_listw.mc.Rd | 6 spNetwork-0.2.0/spNetwork/man/network_listw_worker.Rd | 2 spNetwork-0.2.0/spNetwork/man/nkde.Rd | 84 spNetwork-0.2.0/spNetwork/man/nkde.mc.Rd | 63 spNetwork-0.2.0/spNetwork/man/nkde_worker.Rd | 2 spNetwork-0.2.0/spNetwork/man/nkde_worker_bw_sel.Rd |only spNetwork-0.2.0/spNetwork/man/nkde_worker_bw_sel_cvl.Rd |only spNetwork-0.2.0/spNetwork/man/plot_graph.Rd | 36 spNetwork-0.2.0/spNetwork/man/quartic_kernel_cpp.Rd |only spNetwork-0.2.0/spNetwork/man/quartic_kernelos.Rd |only spNetwork-0.2.0/spNetwork/man/randomize_distmatrix.Rd | 56 spNetwork-0.2.0/spNetwork/man/randomize_distmatrix2.Rd | 64 spNetwork-0.2.0/spNetwork/man/remove_loop_lines.Rd | 50 spNetwork-0.2.0/spNetwork/man/remove_mirror_edges.Rd |only spNetwork-0.2.0/spNetwork/man/reverse_lines.Rd |only spNetwork-0.2.0/spNetwork/man/sanity_check_knn.Rd |only spNetwork-0.2.0/spNetwork/man/simplify_network.Rd |only spNetwork-0.2.0/spNetwork/man/snapPointsToLines2.Rd | 70 spNetwork-0.2.0/spNetwork/man/sp_char_index.Rd | 48 spNetwork-0.2.0/spNetwork/man/spatial_request.Rd | 49 spNetwork-0.2.0/spNetwork/man/split_by_grid.Rd | 5 spNetwork-0.2.0/spNetwork/man/split_by_grid.mc.Rd | 71 spNetwork-0.2.0/spNetwork/man/split_by_grid_abw.Rd | 66 spNetwork-0.2.0/spNetwork/man/split_by_grid_abw.mc.Rd | 66 spNetwork-0.2.0/spNetwork/man/split_graph_components.Rd |only spNetwork-0.2.0/spNetwork/man/split_lines_at_vertex.Rd |only spNetwork-0.2.0/spNetwork/man/triangle_kernel_cpp.Rd |only spNetwork-0.2.0/spNetwork/man/triangle_kernelos.Rd |only spNetwork-0.2.0/spNetwork/man/tricube_kernel_cpp.Rd |only spNetwork-0.2.0/spNetwork/man/tricube_kernelos.Rd |only spNetwork-0.2.0/spNetwork/man/triweight_kernel_cpp.Rd |only spNetwork-0.2.0/spNetwork/man/triweight_kernelos.Rd |only spNetwork-0.2.0/spNetwork/man/uniform_kernel.Rd | 44 spNetwork-0.2.0/spNetwork/man/uniform_kernel_cpp.Rd |only spNetwork-0.2.0/spNetwork/man/uniform_kernelos.Rd |only spNetwork-0.2.0/spNetwork/src/RcppExports.cpp | 491 ++++ spNetwork-0.2.0/spNetwork/src/base_kernel_funtions.cpp |only spNetwork-0.2.0/spNetwork/src/base_kernel_funtions.h |only spNetwork-0.2.0/spNetwork/src/border_correction.cpp |only spNetwork-0.2.0/spNetwork/src/bw_selection.cpp |only spNetwork-0.2.0/spNetwork/src/geometrical_functions.cpp |only spNetwork-0.2.0/spNetwork/src/matrices_functions.cpp |only spNetwork-0.2.0/spNetwork/src/matrices_functions.h |only spNetwork-0.2.0/spNetwork/src/nkde_continuous.cpp |only spNetwork-0.2.0/spNetwork/src/nkde_discontinuous.cpp |only spNetwork-0.2.0/spNetwork/src/spNetwork.h |only spNetwork-0.2.0/spNetwork/tests/testthat/test_adaptive_bw.R |only spNetwork-0.2.0/spNetwork/tests/testthat/test_base_kernels.R |only spNetwork-0.2.0/spNetwork/tests/testthat/test_basics_listw.R |only spNetwork-0.2.0/spNetwork/tests/testthat/test_border_correction.R |only spNetwork-0.2.0/spNetwork/tests/testthat/test_bw_selection.R |only spNetwork-0.2.0/spNetwork/tests/testthat/test_geometrical_functions.R |only spNetwork-0.2.0/spNetwork/tests/testthat/test_graph_functions.R |only spNetwork-0.2.0/spNetwork/tests/testthat/test_isochrone.R |only spNetwork-0.2.0/spNetwork/tests/testthat/test_k_functions.R |only spNetwork-0.2.0/spNetwork/tests/testthat/test_kernels.R | 167 + spNetwork-0.2.0/spNetwork/tests/testthat/test_knn.R |only spNetwork-0.2.0/spNetwork/tests/testthat/test_listw_symetry.R | 1 spNetwork-0.2.0/spNetwork/tests/testthat/test_nkde_execution_functions.R |only spNetwork-0.2.0/spNetwork/vignettes/Isochrones.Rmd |only spNetwork-0.2.0/spNetwork/vignettes/KNetworkFunctions.Rmd | 107 - spNetwork-0.2.0/spNetwork/vignettes/NKDE.Rmd | 114 - spNetwork-0.2.0/spNetwork/vignettes/NKDEdetailed.Rmd | 329 +-- spNetwork-0.2.0/spNetwork/vignettes/NetworkBuilding.Rmd |only spNetwork-0.2.0/spNetwork/vignettes/SpatialWeightMatrices.Rmd | 11 spNetwork-0.2.0/spNetwork/vignettes/spnetwork_bilbio.bibtex | 13 179 files changed, 5618 insertions(+), 4332 deletions(-)
Title: Tools to Create Gene Sets
Description: A set of functions to create SQL tables of gene and SNP information and compose them into a SNP Set, for example to export to a PLINK set.
Author: Chanhee Yi, Alexander Sibley, and Kouros Owzar
Maintainer: Alexander Sibley <dcibioinformatics@duke.edu>
Diff between snplist versions 0.18.1 dated 2017-12-11 and 0.18.2 dated 2021-10-09
DESCRIPTION | 12 ++++++------ MD5 | 20 ++++++++++---------- NEWS | 6 ++++++ build/vignette.rds |binary inst/doc/snplist.R | 26 ++++++++++++++++++++------ inst/doc/snplist.Rnw | 25 ++++++++++++++++++------- inst/doc/snplist.pdf |binary man/setGeneTable.Rd | 2 ++ man/setSNPTable.Rd | 2 ++ man/snplist-package.Rd | 2 ++ vignettes/snplist.Rnw | 25 ++++++++++++++++++------- 11 files changed, 84 insertions(+), 36 deletions(-)
Title: Exact or Asymptotic Permutation Tests
Description: Perform Exact or Asymptotic permutation tests [see Fay and Shaw <doi:10.18637/jss.v036.i02>].
Author: Michael Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between perm versions 1.0-0.0 dated 2010-07-29 and 1.0-0.2 dated 2021-10-09
DESCRIPTION | 15 ++++++++------- MD5 |only NAMESPACE | 4 ++++ NEWS | 6 ++++++ build |only inst/CITATION | 4 ++-- man/calcPvalsMC.Rd | 2 +- man/perm-internal.Rd | 9 ++++++--- man/perm-package.Rd | 6 +++--- man/perm.Rd | 20 +++++++++++++------- 10 files changed, 43 insertions(+), 23 deletions(-)
Title: Light Gradient Boosting Machine
Description: Tree based algorithms can be improved by introducing boosting frameworks.
'LightGBM' is one such framework, based on Ke, Guolin et al. (2017) <https://papers.nips.cc/paper/6907-lightgbm-a-highly-efficient-gradient-boosting-decision>.
This package offers an R interface to work with it.
It is designed to be distributed and efficient with the following advantages:
1. Faster training speed and higher efficiency.
2. Lower memory usage.
3. Better accuracy.
4. Parallel learning supported.
5. Capable of handling large-scale data.
In recognition of these advantages, 'LightGBM' has been widely-used in many winning solutions of machine learning competitions.
Comparison experiments on public datasets suggest that 'LightGBM' can outperform existing boosting frameworks on both efficiency and accuracy, with significantly lower memory consumption. In addition, parallel experiments suggest that in certain circumstances, 'LightGBM' can achieve a linear speed-up in training time by using multiple machines.
Author: Yu Shi [aut, cre],
Guolin Ke [aut],
Damien Soukhavong [aut],
James Lamb [aut],
Qi Meng [aut],
Thomas Finley [aut],
Taifeng Wang [aut],
Wei Chen [aut],
Weidong Ma [aut],
Qiwei Ye [aut],
Tie-Yan Liu [aut],
Nikita Titov [aut],
Yachen Yan [ctb],
Microsoft Corporation [cph],
Dropbox, Inc. [cph],
Jay Loden [cph],
Dave Daeschler [cph],
Giampaolo Rodola [cph],
Alberto Ferreira [ctb],
Daniel Lemire [ctb],
Victor Zverovich [cph],
IBM Corporation [ctb],
David Cortes [ctb]
Maintainer: Yu Shi <yushi2@microsoft.com>
Diff between lightgbm versions 3.2.1 dated 2021-04-13 and 3.3.0 dated 2021-10-09
lightgbm-3.2.1/lightgbm/src/R_object_helper.h |only lightgbm-3.3.0/lightgbm/DESCRIPTION | 26 lightgbm-3.3.0/lightgbm/MD5 | 244 +- lightgbm-3.3.0/lightgbm/NAMESPACE | 5 lightgbm-3.3.0/lightgbm/R/aliases.R | 14 lightgbm-3.3.0/lightgbm/R/callback.R | 17 lightgbm-3.3.0/lightgbm/R/lgb.Booster.R | 347 +-- lightgbm-3.3.0/lightgbm/R/lgb.Dataset.R | 708 +++++-- lightgbm-3.3.0/lightgbm/R/lgb.Predictor.R | 58 lightgbm-3.3.0/lightgbm/R/lgb.convert_with_rules.R | 6 lightgbm-3.3.0/lightgbm/R/lgb.cv.R | 98 lightgbm-3.3.0/lightgbm/R/lgb.importance.R | 4 lightgbm-3.3.0/lightgbm/R/lgb.interprete.R | 12 lightgbm-3.3.0/lightgbm/R/lgb.model.dt.tree.R | 6 lightgbm-3.3.0/lightgbm/R/lgb.plot.interpretation.R | 8 lightgbm-3.3.0/lightgbm/R/lgb.train.R | 47 lightgbm-3.3.0/lightgbm/R/lgb.unloader.R | 9 lightgbm-3.3.0/lightgbm/R/lightgbm.R | 19 lightgbm-3.3.0/lightgbm/R/readRDS.lgb.Booster.R | 9 lightgbm-3.3.0/lightgbm/R/saveRDS.lgb.Booster.R | 11 lightgbm-3.3.0/lightgbm/R/utils.R | 160 - lightgbm-3.3.0/lightgbm/README.md | 15 lightgbm-3.3.0/lightgbm/configure | 67 lightgbm-3.3.0/lightgbm/configure.ac | 31 lightgbm-3.3.0/lightgbm/configure.win | 15 lightgbm-3.3.0/lightgbm/demo/basic_walkthrough.R | 53 lightgbm-3.3.0/lightgbm/demo/boost_from_prediction.R | 4 lightgbm-3.3.0/lightgbm/demo/categorical_features_rules.R | 1 lightgbm-3.3.0/lightgbm/demo/cross_validation.R | 4 lightgbm-3.3.0/lightgbm/demo/early_stopping.R | 6 lightgbm-3.3.0/lightgbm/demo/leaf_stability.R | 31 lightgbm-3.3.0/lightgbm/demo/multiclass.R | 24 lightgbm-3.3.0/lightgbm/demo/multiclass_custom_objective.R | 32 lightgbm-3.3.0/lightgbm/demo/weight_param.R | 12 lightgbm-3.3.0/lightgbm/man/dim.Rd | 2 lightgbm-3.3.0/lightgbm/man/get_field.Rd |only lightgbm-3.3.0/lightgbm/man/getinfo.Rd | 2 lightgbm-3.3.0/lightgbm/man/lgb.Dataset.Rd | 52 lightgbm-3.3.0/lightgbm/man/lgb.Dataset.create.valid.Rd | 77 lightgbm-3.3.0/lightgbm/man/lgb.Dataset.set.reference.Rd | 5 lightgbm-3.3.0/lightgbm/man/lgb.cv.Rd | 35 lightgbm-3.3.0/lightgbm/man/lgb.dump.Rd | 9 lightgbm-3.3.0/lightgbm/man/lgb.get.eval.result.Rd | 9 lightgbm-3.3.0/lightgbm/man/lgb.interprete.Rd | 6 lightgbm-3.3.0/lightgbm/man/lgb.load.Rd | 11 lightgbm-3.3.0/lightgbm/man/lgb.plot.interpretation.Rd | 6 lightgbm-3.3.0/lightgbm/man/lgb.save.Rd | 9 lightgbm-3.3.0/lightgbm/man/lgb.train.Rd | 44 lightgbm-3.3.0/lightgbm/man/lgb.unloader.Rd | 9 lightgbm-3.3.0/lightgbm/man/lgb_shared_dataset_params.Rd |only lightgbm-3.3.0/lightgbm/man/lgb_shared_params.Rd | 12 lightgbm-3.3.0/lightgbm/man/lightgbm.Rd | 19 lightgbm-3.3.0/lightgbm/man/predict.lgb.Booster.Rd | 30 lightgbm-3.3.0/lightgbm/man/readRDS.lgb.Booster.Rd | 9 lightgbm-3.3.0/lightgbm/man/saveRDS.lgb.Booster.Rd | 11 lightgbm-3.3.0/lightgbm/man/set_field.Rd |only lightgbm-3.3.0/lightgbm/man/setinfo.Rd | 2 lightgbm-3.3.0/lightgbm/man/slice.Rd | 2 lightgbm-3.3.0/lightgbm/src/application/predictor.hpp | 7 lightgbm-3.3.0/lightgbm/src/boosting/gbdt.cpp | 4 lightgbm-3.3.0/lightgbm/src/boosting/gbdt.h | 6 lightgbm-3.3.0/lightgbm/src/c_api.cpp | 79 lightgbm-3.3.0/lightgbm/src/include/LightGBM/bin.h | 7 lightgbm-3.3.0/lightgbm/src/include/LightGBM/c_api.h | 65 lightgbm-3.3.0/lightgbm/src/include/LightGBM/config.h | 50 lightgbm-3.3.0/lightgbm/src/include/LightGBM/dataset.h | 15 lightgbm-3.3.0/lightgbm/src/include/LightGBM/metric.h | 15 lightgbm-3.3.0/lightgbm/src/include/LightGBM/network.h | 24 lightgbm-3.3.0/lightgbm/src/include/LightGBM/tree.h | 17 lightgbm-3.3.0/lightgbm/src/include/LightGBM/utils/array_args.h | 4 lightgbm-3.3.0/lightgbm/src/include/LightGBM/utils/common.h | 40 lightgbm-3.3.0/lightgbm/src/include/LightGBM/utils/log.h | 6 lightgbm-3.3.0/lightgbm/src/include/LightGBM/utils/openmp_wrapper.h | 2 lightgbm-3.3.0/lightgbm/src/include/LightGBM/utils/random.h | 2 lightgbm-3.3.0/lightgbm/src/include/LightGBM/utils/text_reader.h | 8 lightgbm-3.3.0/lightgbm/src/io/bin.cpp | 17 lightgbm-3.3.0/lightgbm/src/io/config.cpp | 2 lightgbm-3.3.0/lightgbm/src/io/config_auto.cpp | 23 lightgbm-3.3.0/lightgbm/src/io/dataset.cpp | 7 lightgbm-3.3.0/lightgbm/src/io/dataset_loader.cpp | 10 lightgbm-3.3.0/lightgbm/src/io/parser.cpp | 21 lightgbm-3.3.0/lightgbm/src/io/parser.hpp | 21 lightgbm-3.3.0/lightgbm/src/io/tree.cpp | 38 lightgbm-3.3.0/lightgbm/src/lightgbm-win.def |only lightgbm-3.3.0/lightgbm/src/lightgbm_R.cpp | 981 +++++----- lightgbm-3.3.0/lightgbm/src/lightgbm_R.h | 712 +++---- lightgbm-3.3.0/lightgbm/src/metric/binary_metric.hpp | 18 lightgbm-3.3.0/lightgbm/src/metric/dcg_calculator.cpp | 21 lightgbm-3.3.0/lightgbm/src/metric/multiclass_metric.hpp | 4 lightgbm-3.3.0/lightgbm/src/metric/rank_metric.hpp | 4 lightgbm-3.3.0/lightgbm/src/metric/regression_metric.hpp | 4 lightgbm-3.3.0/lightgbm/src/metric/xentropy_metric.hpp | 4 lightgbm-3.3.0/lightgbm/src/network/linker_topo.cpp | 6 lightgbm-3.3.0/lightgbm/src/network/linkers.h | 2 lightgbm-3.3.0/lightgbm/src/network/network.cpp | 8 lightgbm-3.3.0/lightgbm/src/network/socket_wrapper.hpp | 21 lightgbm-3.3.0/lightgbm/src/objective/binary_objective.hpp | 4 lightgbm-3.3.0/lightgbm/src/objective/rank_objective.hpp | 12 lightgbm-3.3.0/lightgbm/src/objective/regression_objective.hpp | 10 lightgbm-3.3.0/lightgbm/src/objective/xentropy_objective.hpp | 16 lightgbm-3.3.0/lightgbm/src/treelearner/cuda_kernel_launcher.cu | 32 lightgbm-3.3.0/lightgbm/src/treelearner/cuda_tree_learner.h | 4 lightgbm-3.3.0/lightgbm/src/treelearner/data_parallel_tree_learner.cpp | 16 lightgbm-3.3.0/lightgbm/src/treelearner/feature_histogram.hpp | 10 lightgbm-3.3.0/lightgbm/src/treelearner/gpu_tree_learner.cpp | 30 lightgbm-3.3.0/lightgbm/src/treelearner/gpu_tree_learner.h | 8 lightgbm-3.3.0/lightgbm/src/treelearner/kernels/histogram_16_64_256.cu | 26 lightgbm-3.3.0/lightgbm/src/treelearner/leaf_splits.hpp | 6 lightgbm-3.3.0/lightgbm/src/treelearner/monotone_constraints.hpp | 2 lightgbm-3.3.0/lightgbm/src/treelearner/ocl/histogram16.cl | 54 lightgbm-3.3.0/lightgbm/src/treelearner/ocl/histogram256.cl | 34 lightgbm-3.3.0/lightgbm/src/treelearner/ocl/histogram64.cl | 36 lightgbm-3.3.0/lightgbm/src/treelearner/parallel_tree_learner.h | 2 lightgbm-3.3.0/lightgbm/src/treelearner/serial_tree_learner.h | 2 lightgbm-3.3.0/lightgbm/src/treelearner/split_info.hpp | 50 lightgbm-3.3.0/lightgbm/src/treelearner/voting_parallel_tree_learner.cpp | 42 lightgbm-3.3.0/lightgbm/tests/testthat.R | 1 lightgbm-3.3.0/lightgbm/tests/testthat/test_Predictor.R | 26 lightgbm-3.3.0/lightgbm/tests/testthat/test_basic.R | 246 ++ lightgbm-3.3.0/lightgbm/tests/testthat/test_custom_objective.R | 4 lightgbm-3.3.0/lightgbm/tests/testthat/test_dataset.R | 327 +++ lightgbm-3.3.0/lightgbm/tests/testthat/test_lgb.Booster.R | 230 ++ lightgbm-3.3.0/lightgbm/tests/testthat/test_lgb.interprete.R | 6 lightgbm-3.3.0/lightgbm/tests/testthat/test_lgb.plot.interpretation.R | 6 lightgbm-3.3.0/lightgbm/tests/testthat/test_utils.R | 64 lightgbm-3.3.0/lightgbm/tests/testthat/test_weighted_loss.R |only 126 files changed, 3767 insertions(+), 2278 deletions(-)
Title: Analyzing High-Throughput Single Cell Sequencing Data
Description: A toolkit that allows scientists to work with data from single cell sequencing technologies such as scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST). Single (i) Cell R package ('iCellR') provides unprecedented flexibility at every step of the analysis pipeline, including normalization, clustering, dimensionality reduction, imputation, visualization, and so on. Users can design both unsupervised and supervised models to best suit their research. In addition, the toolkit provides 2D and 3D interactive visualizations, differential expression analysis, filters based on cells, genes and clusters, data merging, normalizing for dropouts, data imputation methods, correcting for batch differences, pathway analysis, tools to find marker genes for clusters and conditions, predict cell types and pseudotime analysis. See Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.05.05.078550> and Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.03.31.019109> for more details.
Author: Alireza Khodadadi-Jamayran [aut, cre]
(<https://orcid.org/0000-0003-2495-7504>),
Joseph Pucella [aut, ctb] (<https://orcid.org/0000-0003-0875-8046>),
Hua Zhou [aut, ctb] (<https://orcid.org/0000-0003-1822-1306>),
Nicole Doudican [aut, ctb] (<https://orcid.org/0000-0003-3827-9644>),
John Carucci [aut, ctb] (<https://orcid.org/0000-0001-6817-9439>),
Adriana Heguy [aut, ctb],
Boris Reizis [aut, ctb] (<https://orcid.org/0000-0003-1140-7853>),
Aristotelis Tsirigos [aut, ctb]
(<https://orcid.org/0000-0002-7512-8477>)
Maintainer: Alireza Khodadadi-Jamayran <alireza.khodadadi.j@gmail.com>
Diff between iCellR versions 1.6.4 dated 2021-04-27 and 1.6.5 dated 2021-10-09
iCellR-1.6.4/iCellR/R/F001.R |only iCellR-1.6.4/iCellR/R/F00100.R |only iCellR-1.6.4/iCellR/R/F002.R |only iCellR-1.6.4/iCellR/R/F003.R |only iCellR-1.6.4/iCellR/R/F004.R |only iCellR-1.6.4/iCellR/R/F005.R |only iCellR-1.6.4/iCellR/R/F006.R |only iCellR-1.6.4/iCellR/R/F007.R |only iCellR-1.6.4/iCellR/R/F0072.R |only iCellR-1.6.4/iCellR/R/F008.R |only iCellR-1.6.4/iCellR/R/F009.R |only iCellR-1.6.4/iCellR/data/demo.obj.rda |only iCellR-1.6.4/iCellR/man/demo.obj.Rd |only iCellR-1.6.5/iCellR/DESCRIPTION | 8 - iCellR-1.6.5/iCellR/MD5 | 155 +++++++++++++--------------- iCellR-1.6.5/iCellR/R/F0001.R |only iCellR-1.6.5/iCellR/R/F0002.R |only iCellR-1.6.5/iCellR/R/F0003.R |only iCellR-1.6.5/iCellR/R/F0004.R |only iCellR-1.6.5/iCellR/R/F0005.R |only iCellR-1.6.5/iCellR/R/F0006.R |only iCellR-1.6.5/iCellR/R/F0007.R |only iCellR-1.6.5/iCellR/R/F0008.R |only iCellR-1.6.5/iCellR/R/F0009.R |only iCellR-1.6.5/iCellR/R/F0010.R | 4 iCellR-1.6.5/iCellR/R/F0011.R | 20 --- iCellR-1.6.5/iCellR/R/F0012.R | 5 iCellR-1.6.5/iCellR/R/F0013.R | 3 iCellR-1.6.5/iCellR/R/F0014.R | 6 - iCellR-1.6.5/iCellR/R/F0015.R | 11 - iCellR-1.6.5/iCellR/R/F0017.R | 5 iCellR-1.6.5/iCellR/R/F0018.R | 4 iCellR-1.6.5/iCellR/R/F0020.R | 12 -- iCellR-1.6.5/iCellR/R/F0025.R | 9 - iCellR-1.6.5/iCellR/R/F0027.R | 5 iCellR-1.6.5/iCellR/R/F0029.R | 3 iCellR-1.6.5/iCellR/R/F0030.R | 10 - iCellR-1.6.5/iCellR/R/F0031.R | 15 -- iCellR-1.6.5/iCellR/R/F0032.R | 10 - iCellR-1.6.5/iCellR/R/F0034.R | 5 iCellR-1.6.5/iCellR/R/F0035.R | 16 -- iCellR-1.6.5/iCellR/R/F0039.R | 11 - iCellR-1.6.5/iCellR/R/F0040.R | 13 -- iCellR-1.6.5/iCellR/R/F0042.R | 13 -- iCellR-1.6.5/iCellR/R/F0043.R | 5 iCellR-1.6.5/iCellR/R/F0044.R | 1 iCellR-1.6.5/iCellR/R/F0049.R | 2 iCellR-1.6.5/iCellR/R/F0051.R | 2 iCellR-1.6.5/iCellR/R/F0052.R | 31 ++++- iCellR-1.6.5/iCellR/R/F0053.R | 2 iCellR-1.6.5/iCellR/R/F0057.R | 11 - iCellR-1.6.5/iCellR/R/F0058.R | 21 ++- iCellR-1.6.5/iCellR/R/F0071.R | 2 iCellR-1.6.5/iCellR/R/F0100.R |only iCellR-1.6.5/iCellR/man/add.vdj.Rd | 14 -- iCellR-1.6.5/iCellR/man/cell.cycle.Rd | 2 iCellR-1.6.5/iCellR/man/cell.filter.Rd | 14 -- iCellR-1.6.5/iCellR/man/change.clust.Rd | 10 - iCellR-1.6.5/iCellR/man/clust.stats.plot.Rd | 6 - iCellR-1.6.5/iCellR/man/cluster.plot.Rd | 13 -- iCellR-1.6.5/iCellR/man/data.aggregation.Rd | 2 iCellR-1.6.5/iCellR/man/data.scale.Rd | 8 - iCellR-1.6.5/iCellR/man/down.sample.Rd | 8 - iCellR-1.6.5/iCellR/man/find.dim.genes.Rd | 7 - iCellR-1.6.5/iCellR/man/g2m.phase.Rd | 2 iCellR-1.6.5/iCellR/man/gene.plot.Rd | 16 -- iCellR-1.6.5/iCellR/man/gene.stats.Rd | 5 iCellR-1.6.5/iCellR/man/heatmap.gg.plot.Rd | 11 - iCellR-1.6.5/iCellR/man/hto.anno.Rd | 12 -- iCellR-1.6.5/iCellR/man/i.score.Rd | 2 iCellR-1.6.5/iCellR/man/load10x.Rd | 2 iCellR-1.6.5/iCellR/man/make.bed.Rd | 2 iCellR-1.6.5/iCellR/man/make.gene.model.Rd | 21 --- iCellR-1.6.5/iCellR/man/make.obj.Rd | 2 iCellR-1.6.5/iCellR/man/norm.data.Rd | 7 - iCellR-1.6.5/iCellR/man/opt.pcs.plot.Rd | 4 iCellR-1.6.5/iCellR/man/prep.vdj.Rd | 12 -- iCellR-1.6.5/iCellR/man/pseudotime.tree.Rd | 11 - iCellR-1.6.5/iCellR/man/qc.stats.Rd | 6 - iCellR-1.6.5/iCellR/man/run.clustering.Rd | 12 -- iCellR-1.6.5/iCellR/man/run.diff.exp.Rd | 6 - iCellR-1.6.5/iCellR/man/run.pc.tsne.Rd | 6 - iCellR-1.6.5/iCellR/man/run.pca.Rd | 6 - iCellR-1.6.5/iCellR/man/run.tsne.Rd | 6 - iCellR-1.6.5/iCellR/man/run.umap.Rd | 5 iCellR-1.6.5/iCellR/man/s.phase.Rd | 2 iCellR-1.6.5/iCellR/man/stats.plot.Rd | 13 -- iCellR-1.6.5/iCellR/man/top.markers.Rd | 4 iCellR-1.6.5/iCellR/man/vdj.stats.Rd | 14 -- iCellR-1.6.5/iCellR/man/volcano.ma.plot.Rd | 17 --- 90 files changed, 139 insertions(+), 571 deletions(-)
Title: Enabling Hierarchical Multiple Testing
Description: Implementation of hierarchical inference based on Renaux and
Bühlmann (2021) 'Efficient Multiple Testing Adjustment for Hierarchical
Inference' <arXiv:2104.15028>.
The R-package 'hierbase' offers tools to perform hierarchical inference
for one or multiple data sets based on ready-to-use (group) test functions
or alternatively a user specified (group) test function. The procedure
is based on an efficient hierarchical multiple testing correction and
controls the family-wise error rate (FWER). The functions can easily
be run in parallel.
Hierarchical inference can be applied to (low- or) high-dimensional
data sets to find significant groups or single variables (depending on
the signal strength and correlation structure) in a data-driven and
automated procedure. Possible applications can for example be found
in statistical genetics and statistical genomics.
Author: Claude Renaux [aut, cre],
Peter Bühlmann [ths]
Maintainer: Claude Renaux <renaux@stat.math.ethz.ch>
Diff between hierbase versions 0.0.4 dated 2021-10-03 and 0.1.0 dated 2021-10-09
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/advance_hierarchy.R | 4 +++- R/test-functions.R | 24 ++++++++++++++++++------ inst/doc/vignette-hierbase.pdf |binary 5 files changed, 29 insertions(+), 15 deletions(-)
Title: Interactive Cluster Heat Maps Using 'plotly' and 'ggplot2'
Description: Create interactive cluster 'heatmaps' that can be saved as a stand-
alone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app, and
available in the 'RStudio' viewer pane. Hover the mouse pointer over a cell to
show details or drag a rectangle to zoom. A 'heatmap' is a popular graphical
method for visualizing high-dimensional data, in which a table of numbers
are encoded as a grid of colored cells. The rows and columns of the matrix
are ordered to highlight patterns and are often accompanied by 'dendrograms'.
'Heatmaps' are used in many fields for visualizing observations, correlations,
missing values patterns, and more. Interactive 'heatmaps' allow the inspection
of specific value by hovering the mouse over a cell, as well as zooming into
a region of the 'heatmap' by dragging a rectangle around the relevant area.
This work is based on the 'ggplot2' and 'plotly.js' engine. It produces
similar 'heatmaps' to 'heatmap.2' with the advantage of speed
('plotly.js' is able to handle larger size matrix), the ability to zoom from
the 'dendrogram' panes, and the placing of factor variables in the sides of the
'heatmap'.
Author: Tal Galili [aut, cre, cph] (https://www.r-statistics.com),
Alan O'Callaghan [aut] (https://github.com/Alanocallaghan),
Jonathan Sidi [ctb] (https://github.com/yonicd),
Jaehyun Joo [ctb] (https://github.com/jaehyunjoo),
Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between heatmaply versions 1.2.1 dated 2021-02-02 and 1.3.0 dated 2021-10-09
ChangeLog | 187 +++++++++++++++++++++++++++++++++++++ DESCRIPTION | 13 +- MD5 | 20 ++-- NEWS | 17 +++ NEWS.md | 38 +++++++ R/ggheatmap.R | 41 +++++--- R/plots.R | 28 +++-- R/zzz.R | 4 README.md | 18 +-- inst/doc/heatmaply.html | 238 +++++++++++++++++++++++++++--------------------- man/ggheatmap.Rd | 15 ++- 11 files changed, 464 insertions(+), 155 deletions(-)
Title: Change Point Detection in High-Dimensional Time Series Networks
Description: Implementation of the Factorized Binary Search (FaBiSearch) methodology for the estimation of the number and the location of multiple change points in the network (or clustering) structure of multivariate high-dimensional time series. The method is motivated by the detection of change points in functional connectivity networks for functional magnetic resonance imaging (fMRI) data. FaBiSearch uses non-negative matrix factorization (NMF), an unsupervised dimension reduction technique, and a new binary search algorithm to identify multiple change points. It requires minimal assumptions. Lastly, we provide interactive, 3-dimensional, brain-specific network visualization capability in a flexible, stand-alone function. This function can be conveniently used with any node coordinate atlas, and nodes can be color coded according to community membership, if applicable. The output is an elegantly displayed network laid over a cortical surface, which can berotated in the 3-dimensional space. The main routines of the package are detect.cps(), for multiple change point detection, est.net(), for estimating a network between stationary multivariate time series, net.3dplot(), for plotting the estimated functional connectivity networks, and opt.rank(), for finding the optimal rank in NMF for a given data set. The functions have been extensively tested on simulated multivariate high-dimensional time series data and fMRI data. For details on the FaBiSearch methodology, please see Ondrus et al. (2021) <arXiv:2103.06347>. For a more detailed explanation and applied examples of the fabisearch package, please see Ondrus and Cribben (2021), preprint.
Author: Martin Ondrus [aut, cre],
Ivor Cribben [aut]
Maintainer: Martin Ondrus <mondrus@ualberta.ca>
Diff between fabisearch versions 0.0.2.4 dated 2021-02-24 and 0.0.3.6 dated 2021-10-09
fabisearch-0.0.2.4/fabisearch/data/fmridata.rda |only fabisearch-0.0.2.4/fabisearch/man/fmridata.Rd |only fabisearch-0.0.3.6/fabisearch/DESCRIPTION | 10 - fabisearch-0.0.3.6/fabisearch/MD5 | 48 ++++-- fabisearch-0.0.3.6/fabisearch/NAMESPACE | 4 fabisearch-0.0.3.6/fabisearch/NEWS.md |only fabisearch-0.0.3.6/fabisearch/R/data.R | 60 +++++++- fabisearch-0.0.3.6/fabisearch/R/detect.cps.R | 28 ++-- fabisearch-0.0.3.6/fabisearch/R/est.net.R | 161 +++++++++++++++++------ fabisearch-0.0.3.6/fabisearch/R/net.3dplot.R | 79 ++++++----- fabisearch-0.0.3.6/fabisearch/R/opt.rank.R | 4 fabisearch-0.0.3.6/fabisearch/R/perm_distr.R | 7 - fabisearch-0.0.3.6/fabisearch/R/refit_splits.R | 6 fabisearch-0.0.3.6/fabisearch/R/sign_splits.R | 39 ++++- fabisearch-0.0.3.6/fabisearch/R/sysdata.rda |binary fabisearch-0.0.3.6/fabisearch/build |only fabisearch-0.0.3.6/fabisearch/data/AALatlas.rda |only fabisearch-0.0.3.6/fabisearch/data/AALfmri.rda |only fabisearch-0.0.3.6/fabisearch/data/gordatlas.rda |only fabisearch-0.0.3.6/fabisearch/data/gordfmri.rda |only fabisearch-0.0.3.6/fabisearch/data/logSP500.rda |only fabisearch-0.0.3.6/fabisearch/man/AALatlas.Rd |only fabisearch-0.0.3.6/fabisearch/man/AALfmri.Rd |only fabisearch-0.0.3.6/fabisearch/man/adjmatrix.Rd | 4 fabisearch-0.0.3.6/fabisearch/man/detect.cps.Rd | 4 fabisearch-0.0.3.6/fabisearch/man/est.net.Rd | 35 +++-- fabisearch-0.0.3.6/fabisearch/man/fabisearch.Rd | 4 fabisearch-0.0.3.6/fabisearch/man/gordatlas.Rd |only fabisearch-0.0.3.6/fabisearch/man/gordfmri.Rd |only fabisearch-0.0.3.6/fabisearch/man/logSP500.Rd |only fabisearch-0.0.3.6/fabisearch/man/net.3dplot.Rd | 25 ++- fabisearch-0.0.3.6/fabisearch/man/opt.rank.Rd | 4 32 files changed, 369 insertions(+), 153 deletions(-)
Title: Pulling Clean Data from Covid19india.org
Description: Pull raw and pre-cleaned versions of national and state-level
COVID-19 time-series data from covid19india.org <https://www.covid19india.org>.
Easily obtain and merge case count data, testing data, and vaccine data.
Also assists in calculating the time-varying effective reproduction number
with sensible parameters for COVID-19.
Author: Max Salvatore [aut, cre],
Michael Kleinsasser [aut]
Maintainer: Max Salvatore <mmsalva@umich.edu>
Diff between covid19india versions 0.1.3 dated 2021-07-28 and 0.1.4 dated 2021-10-09
DESCRIPTION | 12 +- MD5 | 58 ++++----- NAMESPACE | 14 -- R/check_for_data_correction.R | 15 +- R/extract_latest.R | 23 +-- R/get_all_data.R | 82 ++++++------- R/get_cfr.R | 45 ++----- R/get_district_counts.R | 49 ++++---- R/get_metrics_tables.R | 232 +++++++++++++++++---------------------- R/get_nat_counts.R | 55 ++++----- R/get_nat_tests.R | 49 +++----- R/get_r0.R | 113 +++++------------- R/get_r_est.R | 23 +-- R/get_state_counts.R | 90 +++++---------- R/get_state_tests.R | 46 +++---- R/get_state_vax.R | 63 ++++------ R/globalVariables.R | 5 README.md | 17 +- data/pop.rda |binary man/check_for_data_correction.Rd | 6 - man/estR0_out.Rd | 11 - man/extract_latest.Rd | 10 - man/get_cfr.Rd | 6 - man/get_metrics_tables.Rd | 3 man/get_nat_counts.Rd | 2 man/get_nat_tests.Rd | 5 man/get_r0.Rd | 11 - man/get_r_est.Rd | 6 - man/get_state_tests.Rd | 2 man/get_state_vax.Rd | 2 30 files changed, 441 insertions(+), 614 deletions(-)
Title: Search and Download Data from the Swiss Federal Statistical
Office (BFS)
Description: Search and download data from the Swiss Federal Statistical Office <https://www.bfs.admin.ch/>.
Author: Felix Luginbuhl [aut, cre]
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>
Diff between BFS versions 0.4.0 dated 2021-10-06 and 0.4.1 dated 2021-10-09
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- R/bfs_get_catalog.R | 2 +- R/bfs_get_catalog_data.R | 2 +- R/bfs_get_catalog_tables.R | 2 +- R/bfs_get_data.R | 6 +++--- README.md | 40 ++++++++++++++++++++-------------------- man/bfs_get_catalog.Rd | 5 +---- man/bfs_get_catalog_data.Rd | 2 +- man/bfs_get_catalog_tables.Rd | 2 +- 10 files changed, 41 insertions(+), 44 deletions(-)
Title: MareFrame DB Querying Library
Description: Creates and manages a PostgreSQL database suitable for storing fisheries data
and aggregating ready for use within a Gadget <https://gadget-framework.github.io/gadget2/> model.
See <https://mareframe.github.io/mfdb/> for more information.
Author: Jamie Lentin [aut, cre, cph],
Bjarki Thor Elvarsson [aut]
Maintainer: Jamie Lentin <lentinj@shuttlethread.com>
Diff between mfdb versions 7.1-0 dated 2021-08-18 and 7.1-1 dated 2021-10-09
ChangeLog | 5 +++++ DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- inst/doc/tow_data.R | 10 ++++++---- inst/doc/tow_data.Rmd | 10 ++++++---- inst/doc/tow_data.html | 16 ++++++++-------- inst/doc/trip.R | 7 ++++--- inst/doc/trip.Rmd | 7 ++++--- inst/doc/trip.html | 7 ++++--- vignettes/tow_data.Rmd | 10 ++++++---- vignettes/trip.Rmd | 7 ++++--- 11 files changed, 61 insertions(+), 46 deletions(-)
Title: Supporting Functions for Packages Maintained by 'YuLab-SMU'
Description: Miscellaneous functions commonly used by 'YuLab-SMU'.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between yulab.utils versions 0.0.2 dated 2021-08-16 and 0.0.4 dated 2021-10-09
DESCRIPTION | 8 ++++---- MD5 | 10 +++++++--- NAMESPACE | 3 +++ R/read.R |only R/str-wrap.R |only R/utilities.R | 2 ++ man/read.cb.Rd |only man/str_wrap.Rd |only 8 files changed, 16 insertions(+), 7 deletions(-)
Title: Geometrical Functionality of the 'spatstat' Family
Description: Defines types of spatial data such as point patterns,
mainly in two dimensions, but also in higher dimensions.
Provides class support, and functions for geometrical operations
on spatial data, used in the 'spatstat' family of packages.
Excludes spatial data on a linear network, which are covered by
the separate package 'spatstat.linnet'.
Author: Adrian Baddeley [aut, cre],
Rolf Turner [aut],
Ege Rubak [aut],
Tilman Davies [ctb],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Sebastian Meyer [ctb],
Suman Rakshit [ctb],
Dominic Schuhmacher [ctb],
Rasmus Waagepetersen [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.geom versions 2.2-2 dated 2021-07-12 and 2.3-0 dated 2021-10-09
DESCRIPTION | 14 +- MD5 | 85 ++++++++------- NAMESPACE | 19 +++ NEWS | 103 ++++++++++++++++++ R/convexdist.R |only R/deldir.R | 30 ----- R/disc.R | 9 + R/distancemetrics.R |only R/distances.R | 24 +++- R/distanxD.R | 12 -- R/distmap.R | 22 +++ R/ewcdf.R | 17 ++- R/images.R | 17 ++- R/nncross.R | 14 ++ R/nndist.R | 18 ++- R/nnutils.R |only R/psp.R | 2 R/randombasic.R | 24 +++- R/randomseg.R | 2 R/window.R | 22 +++ R/wingeom.R | 72 ++++++------ inst/CITATION | 8 - inst/doc/packagesizes.txt | 2 man/convexmetric.Rd |only man/crossdist.ppp.Rd | 9 + man/disc.Rd | 22 ++- man/distmap.owin.Rd | 7 + man/distmap.ppp.Rd | 7 + man/distmap.psp.Rd | 7 + man/ewcdf.Rd | 20 ++- man/invoke.metric.Rd |only man/mean.ewcdf.Rd |only man/metric.object.Rd |only man/nncross.Rd | 8 + man/nndist.Rd | 6 - man/nnwhich.Rd | 6 - man/pairdist.ppp.Rd | 7 + man/persp.im.Rd | 8 - man/quadscheme.Rd | 35 ++++++ man/rjitter.Rd | 25 ++-- man/spatstat.geom-deprecated.Rd | 3 man/spatstat.geom-internal.Rd | 14 ++ man/transformquantiles.Rd |only src/init.c | 1 src/metricPdist.c | 43 +++++++ src/metricPdist.h | 222 +++++++++++++++++++++------------------- src/proto.h | 2 tests/testsR.R |only 48 files changed, 674 insertions(+), 294 deletions(-)
Title: Set Axis Break for 'ggplot2'
Description: An implementation of scale functions for setting axis breaks of a 'gg' plot.
Author: Guangchuang Yu [aut, cre, cph]
(<https://orcid.org/0000-0002-6485-8781>),
Shuangbin Xu [aut] (<https://orcid.org/0000-0003-3513-5362>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggbreak versions 0.0.5 dated 2021-09-06 and 0.0.6 dated 2021-10-09
DESCRIPTION | 9 MD5 | 20 - NAMESPACE | 2 NEWS.md | 9 R/grid-draw-utilities.R | 10 R/method-ggplot-add.R | 21 +- R/method-grid-draw.R | 33 +-- R/utilities.R | 24 +- inst/doc/ggbreak.Rmd | 486 ++++++++++++++++++++++++------------------------ inst/doc/ggbreak.html | 46 ++-- vignettes/ggbreak.Rmd | 486 ++++++++++++++++++++++++------------------------ 11 files changed, 590 insertions(+), 556 deletions(-)
Title: Read and Process 'Pamguard' Binary Data
Description: Functions for easily reading and processing binary data files created by
'Pamguard' (<https://www.pamguard.org/>). All functions for directly reading the
binary data files are based on 'MATLAB' code written by Michael Oswald.
Author: Taiki Sakai [aut, cre],
Michael Oswald [aut],
Douglas Gillespie [ctb]
Maintainer: Taiki Sakai <taiki.sakai@noaa.gov>
Diff between PamBinaries versions 1.4.0 dated 2020-09-02 and 1.6.0 dated 2021-10-09
DESCRIPTION | 16 ++-- MD5 | 89 +++++++++++++---------- NAMESPACE | 8 ++ R/convertPgDate.R | 6 + R/loadBackgroundNoise.R |only R/loadPamguardBinaryFile.R | 21 +++++ R/pamBinRead.R | 6 + R/pbToDf.R | 3 R/readClickBackground.R |only R/readClickData.R | 2 R/readClipData.R | 4 + R/readGPLDetections.R |only R/readPamData.R | 86 ++++++++++++++++------- R/readSpectralBackground.R |only README.md | 2 inst/extdata/GPL.pgdf |only inst/extdata/GPL.pgnf |only inst/extdata/NoiseMonitor.pgdf |only inst/extdata/README.txt | 7 + man/contourToFreq.Rd | 76 ++++++++++---------- man/convertPgDate.Rd | 62 ++++++++-------- man/countChannels.Rd | 52 ++++++------- man/dateNumToMillis.Rd | 48 ++++++------ man/loadBackgroundNoise.Rd |only man/loadPamguardBinaryFile.Rd | 138 ++++++++++++++++++------------------- man/millisToDateNum.Rd | 52 ++++++------- man/pamBinRead.Rd | 77 ++++++++++---------- man/pbToDf.Rd | 100 +++++++++++++------------- man/plotWMD.Rd | 70 +++++++++--------- man/readAISData.Rd | 58 +++++++-------- man/readClickBackground.Rd |only man/readClickClsfrAnnotation.Rd | 48 ++++++------ man/readClickData.Rd | 82 ++++++++++----------- man/readClickFooter.Rd | 44 +++++------ man/readClickTriggerData.Rd | 58 +++++++-------- man/readClipData.Rd | 58 +++++++-------- man/readDbHtData.Rd | 58 +++++++-------- man/readDifarData.Rd | 58 +++++++-------- man/readFileFooterInfo.Rd | 48 ++++++------ man/readGPLDetections.Rd |only man/readLTSAData.Rd | 58 +++++++-------- man/readMatchClsfrAnnotation.Rd | 62 ++++++++-------- man/readNoiseBandData.Rd | 58 +++++++-------- man/readNoiseMonData.Rd | 58 +++++++-------- man/readPamData.Rd | 70 +++++++++--------- man/readRWEDetectorData.Rd | 58 +++++++-------- man/readSpectralBackground.Rd |only man/readStdModuleFooter.Rd | 44 +++++------ man/readStdModuleHeader.Rd | 44 +++++------ man/readWMDData.Rd | 58 +++++++-------- tests/testthat/test-dfConversion.R | 11 ++ 51 files changed, 1034 insertions(+), 924 deletions(-)
Title: Utility Functions for Production R Code
Description: A suite of utility functions providing functionality commonly
needed for production level projects such as logging, error handling,
cache management and date-time parsing. Functions for date-time parsing and
formatting require that time zones be specified explicitly, avoiding a common
source of error when working with environmental time series.
Author: Jonathan Callahan [aut, cre],
Eli Grosman [aut],
Spencer Pease [aut],
Thomas Bergamaschi [aut]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between MazamaCoreUtils versions 0.4.8 dated 2021-08-18 and 0.4.9 dated 2021-10-09
DESCRIPTION | 14 MD5 | 51 +- NAMESPACE | 3 NEWS.md | 8 R/cacheManagement.R | 2 R/dateRange.R | 10 R/dateSequence.R | 2 R/functionArgument_linting.R | 12 R/initializeLogging.R | 52 +- R/loadDataFile.R | 8 R/parseDatetime.R | 12 R/setIfNull.R | 6 R/stopIfNull.R | 2 R/timeRange.R | 2 R/timeStamp.R | 8 R/utils-location.R |only README.md | 19 build/vignette.rds |binary inst/doc/cache-management.html | 611 ++++++++++++++++------------ inst/doc/date-parsing.html | 443 +++++++++++--------- inst/doc/error-handling.html | 671 ++++++++++++++++++------------- inst/doc/logging.html | 772 +++++++++++++++++++----------------- man/createLocationID.Rd |only man/initializeLogging.Rd | 10 man/timeStamp.Rd | 2 man/validateLonLat.Rd |only man/validateLonsLats.Rd |only tests/testthat/test-locationUtils.R |only tests/testthat/test-parseDatetime.R | 11 29 files changed, 1556 insertions(+), 1175 deletions(-)
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Title: Multivariate and Propensity Score Matching with Balance
Optimization
Description: Provides functions for multivariate and propensity score matching
and for finding optimal balance based on a genetic search algorithm.
A variety of univariate and multivariate metrics to
determine if balance has been obtained are also provided. For
details, see the paper by Jasjeet Sekhon
(2007, <doi:10.18637/jss.v042.i07>).
Author: Jasjeet Singh Sekhon <jas.sekhon@yale.edu>
Maintainer: Jasjeet Singh Sekhon <jas.sekhon@yale.edu>
Diff between Matching versions 4.9-9 dated 2021-04-13 and 4.9-10 dated 2021-10-09
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- build |only inst/CITATION | 4 ++-- man/GenMatch.Rd | 2 +- man/Match.Rd | 2 +- man/MatchBalance.Rd | 2 +- man/Matchby.Rd | 2 +- man/balanceUV.Rd | 2 +- man/ks.boot.Rd | 2 +- man/qqstats.Rd | 2 +- 11 files changed, 23 insertions(+), 22 deletions(-)
Title: Tests of Randomness and Tests of Independence
Description: Functions for testing randomness for a univariate time series with arbitrary distribution (discrete, continuous, mixture of both types) and for testing independence between random variables with arbitrary distributions. The test statistics are based on the multilinear empirical copula and multipliers are used to compute P-values. The test of independence between random variables appeared in <doi:10.1093/biomet/asy059>.
Author: Bouchra R. Nasri [aut, cre, cph],
Bruno N Remillard [aut],
Johanna G Neslehova [aut],
Christian Genest [aut]
Maintainer: Bouchra R. Nasri <bouchra.nasri@umontreal.ca>
Diff between MixedIndTests versions 0.1.4 dated 2021-08-02 and 0.1.5 dated 2021-10-09
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/TestIndCopula.R | 10 ++++++++-- R/TestIndSerCopula.R | 10 ++++++++-- 4 files changed, 22 insertions(+), 10 deletions(-)