Title: A Collection of Efficient and Extremely Fast R Functions II
Description: A collection of fast statistical and utility functions for data analysis. Functions for regression, maximum likelihood, column-wise statistics and many more have been included. C++ has been utilized to speed up the functions.
Author: Manos Papadakis, Michail Tsagris, Stefanos Fafalios and Marios Dimitriadis.
Maintainer: Manos Papadakis <rfastofficial@gmail.com>
Diff between Rfast2 versions 0.0.5 dated 2019-12-16 and 0.0.6 dated 2020-10-12
Rfast2-0.0.5/Rfast2/R/bic.regs.R |only Rfast2-0.0.5/Rfast2/R/censpois.mle.R |only Rfast2-0.0.5/Rfast2/R/censweibull.mle.R |only Rfast2-0.0.5/Rfast2/R/circ.cors1.R |only Rfast2-0.0.5/Rfast2/R/cls.R |only Rfast2-0.0.5/Rfast2/R/cluster.lm.R |only Rfast2-0.0.5/Rfast2/R/fbed.reg.R |only Rfast2-0.0.5/Rfast2/R/fipois.reg.R |only Rfast2-0.0.5/Rfast2/R/gamma_regression.R |only Rfast2-0.0.5/Rfast2/R/gammapois.mle.R |only Rfast2-0.0.5/Rfast2/R/gee.reg.R |only Rfast2-0.0.5/Rfast2/R/gumbel.reg.R |only Rfast2-0.0.5/Rfast2/R/halfcauchy.mle.R |only Rfast2-0.0.5/Rfast2/R/kumar.mle.R |only Rfast2-0.0.5/Rfast2/R/logiquant.regs.R |only Rfast2-0.0.5/Rfast2/R/mle.lda.R |only Rfast2-0.0.5/Rfast2/R/mmpc.R |only Rfast2-0.0.5/Rfast2/R/mmpc2.R |only Rfast2-0.0.5/Rfast2/R/multinom.reg.R |only Rfast2-0.0.5/Rfast2/R/negbin.reg.R |only Rfast2-0.0.5/Rfast2/R/pc.sel.R |only Rfast2-0.0.5/Rfast2/R/powerlaw.mle.R |only Rfast2-0.0.5/Rfast2/R/propols.reg.R |only Rfast2-0.0.5/Rfast2/R/purka.mle.R |only Rfast2-0.0.5/Rfast2/R/score.zipregs.R |only Rfast2-0.0.5/Rfast2/R/simplex.mle.R |only Rfast2-0.0.5/Rfast2/R/sp.logiregs.R |only Rfast2-0.0.5/Rfast2/R/trunccauchy.mle.R |only Rfast2-0.0.5/Rfast2/R/truncexpmle.R |only Rfast2-0.0.5/Rfast2/R/weib.regs.R |only Rfast2-0.0.5/Rfast2/R/zigamma.mle.R |only Rfast2-0.0.5/Rfast2/R/zil.mle.R |only Rfast2-0.0.5/Rfast2/R/ziweibull.mle.R |only Rfast2-0.0.5/Rfast2/R/ztp.reg.R |only Rfast2-0.0.6/Rfast2/DESCRIPTION | 10 Rfast2-0.0.6/Rfast2/MD5 | 165 +++++------ Rfast2-0.0.6/Rfast2/NAMESPACE | 36 +- Rfast2-0.0.6/Rfast2/NEWS.md | 4 Rfast2-0.0.6/Rfast2/R/Intersect.R | 1 Rfast2-0.0.6/Rfast2/R/Quantile.R | 1 Rfast2-0.0.6/Rfast2/R/benchmark.R | 3 Rfast2-0.0.6/Rfast2/R/big.knn.R |only Rfast2-0.0.6/Rfast2/R/boot.ttest1.R |only Rfast2-0.0.6/Rfast2/R/censweib.reg.R |only Rfast2-0.0.6/Rfast2/R/circ.cor1.R | 30 ++ Rfast2-0.0.6/Rfast2/R/circaov.R | 15 - Rfast2-0.0.6/Rfast2/R/colQuantile.R | 1 Rfast2-0.0.6/Rfast2/R/colTrimMean.R | 1 Rfast2-0.0.6/Rfast2/R/colcauchy.mle.R |only Rfast2-0.0.6/Rfast2/R/column_wise_mle.R | 16 + Rfast2-0.0.6/Rfast2/R/dcora.R |only Rfast2-0.0.6/Rfast2/R/empirical.entropy.R | 4 Rfast2-0.0.6/Rfast2/R/het.lmfit.R |only Rfast2-0.0.6/Rfast2/R/is.lower.tri.R | 1 Rfast2-0.0.6/Rfast2/R/is.skew.symmetric.R | 2 Rfast2-0.0.6/Rfast2/R/is.upper.tri.R | 1 Rfast2-0.0.6/Rfast2/R/lm.bsreg.R |only Rfast2-0.0.6/Rfast2/R/lud.R | 1 Rfast2-0.0.6/Rfast2/R/makefolds.R |only Rfast2-0.0.6/Rfast2/R/many_regression_models.R |only Rfast2-0.0.6/Rfast2/R/multinomreg.cv.R |only Rfast2-0.0.6/Rfast2/R/naive.bayes.classifiers.R | 49 +++ Rfast2-0.0.6/Rfast2/R/nb.cv.R |only Rfast2-0.0.6/Rfast2/R/pca.R | 2 Rfast2-0.0.6/Rfast2/R/pcr.R |only Rfast2-0.0.6/Rfast2/R/rbeta1.R |only Rfast2-0.0.6/Rfast2/R/refmeta.R | 2 Rfast2-0.0.6/Rfast2/R/reg.mle.lda.R | 61 ++++ Rfast2-0.0.6/Rfast2/R/regression_models.R |only Rfast2-0.0.6/Rfast2/R/regression_models_for_clustered_data.R |only Rfast2-0.0.6/Rfast2/R/rowQuantile.R | 1 Rfast2-0.0.6/Rfast2/R/rowTrimMean.R | 1 Rfast2-0.0.6/Rfast2/R/univariate.mle.R |only Rfast2-0.0.6/Rfast2/R/variable_selection_algortihms.R |only Rfast2-0.0.6/Rfast2/man/Rfast2-package.Rd | 4 Rfast2-0.0.6/Rfast2/man/big.knn.Rd |only Rfast2-0.0.6/Rfast2/man/bigknn.cv.Rd |only Rfast2-0.0.6/Rfast2/man/binom.reg.Rd |only Rfast2-0.0.6/Rfast2/man/boot.ttest1.Rd |only Rfast2-0.0.6/Rfast2/man/censweib.reg.Rd |only Rfast2-0.0.6/Rfast2/man/censweibull.mle.Rd | 1 Rfast2-0.0.6/Rfast2/man/collognorm.mle.Rd | 23 + Rfast2-0.0.6/Rfast2/man/dcora.Rd |only Rfast2-0.0.6/Rfast2/man/fbed.reg.Rd | 3 Rfast2-0.0.6/Rfast2/man/gammaregs.Rd | 2 Rfast2-0.0.6/Rfast2/man/halfcauchy.mle.Rd | 3 Rfast2-0.0.6/Rfast2/man/hellinger.countreg.Rd |only Rfast2-0.0.6/Rfast2/man/het.lmfit.Rd |only Rfast2-0.0.6/Rfast2/man/hp.reg.Rd |only Rfast2-0.0.6/Rfast2/man/lm.bsreg.Rd |only Rfast2-0.0.6/Rfast2/man/lm.drop1.Rd | 8 Rfast2-0.0.6/Rfast2/man/lm.parboot.Rd | 2 Rfast2-0.0.6/Rfast2/man/mmpc.Rd | 15 - Rfast2-0.0.6/Rfast2/man/mmpc2.Rd | 10 Rfast2-0.0.6/Rfast2/man/multinom.reg.Rd | 4 Rfast2-0.0.6/Rfast2/man/multinomreg.cv.Rd |only Rfast2-0.0.6/Rfast2/man/nb.cv.Rd |only Rfast2-0.0.6/Rfast2/man/negbin.reg.Rd | 2 Rfast2-0.0.6/Rfast2/man/omp2.Rd |only Rfast2-0.0.6/Rfast2/man/pcr.Rd |only Rfast2-0.0.6/Rfast2/man/propjs.reg.Rd |only Rfast2-0.0.6/Rfast2/man/propols.reg.Rd | 11 Rfast2-0.0.6/Rfast2/man/purka.mle.Rd | 3 Rfast2-0.0.6/Rfast2/man/rbeta1.Rd |only Rfast2-0.0.6/Rfast2/man/reg.mle.lda.Rd | 2 Rfast2-0.0.6/Rfast2/man/regmlelda.cv.Rd |only Rfast2-0.0.6/Rfast2/man/sclr.Rd |only Rfast2-0.0.6/Rfast2/man/tobit.reg.Rd |only Rfast2-0.0.6/Rfast2/man/vm.nb.Rd | 2 Rfast2-0.0.6/Rfast2/man/vmnb.pred.Rd | 2 Rfast2-0.0.6/Rfast2/man/weibull.nb.Rd | 14 Rfast2-0.0.6/Rfast2/man/weibullnb.pred.Rd | 15 - Rfast2-0.0.6/Rfast2/src/censweib_reg.cpp |only Rfast2-0.0.6/Rfast2/src/colbeta_mle.cpp |only Rfast2-0.0.6/Rfast2/src/colcauchy_mle.cpp |only Rfast2-0.0.6/Rfast2/src/fbed_reg.cpp | 4 Rfast2-0.0.6/Rfast2/src/init.c | 6 Rfast2-0.0.6/Rfast2/src/mmpc2.cpp | 4 Rfast2-0.0.6/Rfast2/src/reg_lib_helper.cpp | 68 ++-- Rfast2-0.0.6/Rfast2/src/utilities.cpp | 12 120 files changed, 413 insertions(+), 215 deletions(-)
Title: Fit Interpretable Machine Learning Models
Description: Package for training interpretable machine learning models. Historically, the most interpretable machine learning models were not very accurate, and the most accurate models were not very interpretable. Microsoft Research has developed an algorithm called the Explainable Boosting Machine (EBM) which has both high accuracy and interpretable characteristics. EBM uses machine learning techniques like bagging and boosting to breathe new life into traditional GAMs (Generalized Additive Models). This makes them as accurate as random forests and gradient boosted trees, and also enhances their intelligibility and editability. Details on the EBM algorithm can be found in the paper by Rich Caruana, Yin Lou, Johannes Gehrke, Paul Koch, Marc Sturm, and Noemie Elhadad (2015, <doi:10.1145/2783258.2788613>).
Author: Samuel Jenkins [aut],
Harsha Nori [aut],
Paul Koch [aut],
Rich Caruana [aut, cre],
Microsoft Corporation [cph]
Maintainer: Rich Caruana <interpretml@outlook.com>
Diff between interpret versions 0.1.25 dated 2019-12-12 and 0.1.26 dated 2020-10-12
interpret-0.1.25/interpret/R/interpret_core.R |only interpret-0.1.25/interpret/R/native_booster.R |only interpret-0.1.25/interpret/R/native_interactions.R |only interpret-0.1.25/interpret/man/ebm_feature.Rd |only interpret-0.1.25/interpret/man/ebm_feature_combination.Rd |only interpret-0.1.25/interpret/man/get_interaction_score.Rd |only interpret-0.1.25/interpret/man/initialize_interaction_classification.Rd |only interpret-0.1.25/interpret/man/initialize_interaction_regression.Rd |only interpret-0.1.25/interpret/src/core |only interpret-0.1.26/interpret/DESCRIPTION | 13 interpret-0.1.26/interpret/MD5 | 105 interpret-0.1.26/interpret/NAMESPACE | 9 interpret-0.1.26/interpret/R/binning.R |only interpret-0.1.26/interpret/R/booster.R |only interpret-0.1.26/interpret/R/ebm.R |only interpret-0.1.26/interpret/R/interaction_detection.R |only interpret-0.1.26/interpret/R/random_numbers.R |only interpret-0.1.26/interpret/R/sampling.R |only interpret-0.1.26/interpret/man/ebm_classify.Rd | 48 interpret-0.1.26/interpret/man/ebm_predict_proba.Rd | 23 interpret-0.1.26/interpret/man/ebm_show.Rd |only interpret-0.1.26/interpret/src/Makevars | 41 interpret-0.1.26/interpret/src/ebm_native |only interpret-0.1.26/interpret/src/interpret_R.cpp | 1223 ++++++---- 24 files changed, 961 insertions(+), 501 deletions(-)
Title: Apply Mapping Functions in Parallel using Futures
Description: Implementations of the family of map() functions
from 'purrr' that can be resolved using any 'future'-supported
backend, e.g. parallel on the local machine or distributed on a
compute cluster.
Author: Davis Vaughan [aut, cre],
Matt Dancho [aut],
RStudio [cph]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between furrr versions 0.1.0 dated 2018-05-16 and 0.2.0 dated 2020-10-12
furrr-0.1.0/furrr/R/fold.R |only furrr-0.1.0/furrr/R/future_imap.R |only furrr-0.1.0/furrr/R/future_invoke_map.R |only furrr-0.1.0/furrr/R/future_map.R |only furrr-0.1.0/furrr/R/future_map2.R |only furrr-0.1.0/furrr/R/future_map2_template.R |only furrr-0.1.0/furrr/R/future_map_template.R |only furrr-0.1.0/furrr/R/future_modify.R |only furrr-0.1.0/furrr/R/future_options.R |only furrr-0.1.0/furrr/R/future_pmap.R |only furrr-0.1.0/furrr/R/future_pmap_template.R |only furrr-0.1.0/furrr/R/global-gatherer.R |only furrr-0.1.0/furrr/R/load-balancer.R |only furrr-0.1.0/furrr/R/random-seeds.R |only furrr-0.1.0/furrr/R/resolve.R |only furrr-0.1.0/furrr/man/figures/progress.gif |only furrr-0.1.0/furrr/man/fold.Rd |only furrr-0.1.0/furrr/tests/testthat/helper-test-setup.R |only furrr-0.1.0/furrr/tests/testthat/test-future-options.R |only furrr-0.1.0/furrr/tests/testthat/test-map.R |only furrr-0.1.0/furrr/tests/testthat/test-map2.R |only furrr-0.1.0/furrr/tests/testthat/test-pmap.R |only furrr-0.1.0/furrr/tests/testthat/test-progress.R |only furrr-0.2.0/furrr/DESCRIPTION | 46 + furrr-0.2.0/furrr/LICENSE |only furrr-0.2.0/furrr/MD5 | 90 ++- furrr-0.2.0/furrr/NAMESPACE | 39 + furrr-0.2.0/furrr/NEWS.md | 123 ++++ furrr-0.2.0/furrr/R/chunks.R |only furrr-0.2.0/furrr/R/furrr-options.R |only furrr-0.2.0/furrr/R/furrr-package.R |only furrr-0.2.0/furrr/R/future-imap.R |only furrr-0.2.0/furrr/R/future-invoke-map.R |only furrr-0.2.0/furrr/R/future-map.R |only furrr-0.2.0/furrr/R/future-map2.R |only furrr-0.2.0/furrr/R/future-modify.R |only furrr-0.2.0/furrr/R/future-pmap.R |only furrr-0.2.0/furrr/R/future-walk.R |only furrr-0.2.0/furrr/R/globals.R |only furrr-0.2.0/furrr/R/progress.R | 139 +++-- furrr-0.2.0/furrr/R/recycle.R |only furrr-0.2.0/furrr/R/seed.R |only furrr-0.2.0/furrr/R/template.R |only furrr-0.2.0/furrr/R/utils-purrr.R |only furrr-0.2.0/furrr/R/utils.R | 229 --------- furrr-0.2.0/furrr/README.md | 296 +++--------- furrr-0.2.0/furrr/man/figures/lifecycle-archived.svg |only furrr-0.2.0/furrr/man/figures/lifecycle-defunct.svg |only furrr-0.2.0/furrr/man/figures/lifecycle-deprecated.svg |only furrr-0.2.0/furrr/man/figures/lifecycle-experimental.svg |only furrr-0.2.0/furrr/man/figures/lifecycle-maturing.svg |only furrr-0.2.0/furrr/man/figures/lifecycle-questioning.svg |only furrr-0.2.0/furrr/man/figures/lifecycle-soft-deprecated.svg |only furrr-0.2.0/furrr/man/figures/lifecycle-stable.svg |only furrr-0.2.0/furrr/man/figures/lifecycle-superseded.svg |only furrr-0.2.0/furrr/man/figures/logo.png |only furrr-0.2.0/furrr/man/furrr-package.Rd |only furrr-0.2.0/furrr/man/furrr_options.Rd |only furrr-0.2.0/furrr/man/future_imap.Rd | 161 ++++-- furrr-0.2.0/furrr/man/future_invoke_map.Rd | 133 ++++- furrr-0.2.0/furrr/man/future_map.Rd | 216 +++++--- furrr-0.2.0/furrr/man/future_map2.Rd | 264 ++++++++-- furrr-0.2.0/furrr/man/future_map_if.Rd |only furrr-0.2.0/furrr/man/future_modify.Rd | 120 +++- furrr-0.2.0/furrr/man/future_options.Rd | 132 +---- furrr-0.2.0/furrr/tests/testthat/helper-deprecation.R |only furrr-0.2.0/furrr/tests/testthat/helper-eval.R |only furrr-0.2.0/furrr/tests/testthat/helper-furrr-test-that.R |only furrr-0.2.0/furrr/tests/testthat/test-chunks.R |only furrr-0.2.0/furrr/tests/testthat/test-deprecation.R |only furrr-0.2.0/furrr/tests/testthat/test-furrr-options.R |only furrr-0.2.0/furrr/tests/testthat/test-future-imap.R |only furrr-0.2.0/furrr/tests/testthat/test-future-invoke-map.R |only furrr-0.2.0/furrr/tests/testthat/test-future-map.R |only furrr-0.2.0/furrr/tests/testthat/test-future-map2.R |only furrr-0.2.0/furrr/tests/testthat/test-future-modify.R |only furrr-0.2.0/furrr/tests/testthat/test-future-pmap.R |only furrr-0.2.0/furrr/tests/testthat/test-future-walk.R |only furrr-0.2.0/furrr/tests/testthat/test-seed.R |only 79 files changed, 1108 insertions(+), 880 deletions(-)
Title: Nested and Crossed Block Designs for Factorial and Unstructured
Treatment Sets
Description: Constructs treatment and block designs for linear
treatment models with crossed or nested block factors. The treatment design can be any
feasible linear model and the block design can be any feasible combination of crossed or
nested block factors. The block design is a sum of one or more block factors
and the block design is optimized sequentially with the levels of each successive block factor optimized
conditional on all previously optimized block factors.
D-optimality is used throughout except for square or rectangular lattice block designs
which are constructed algebraically using mutually orthogonal Latin squares.
Crossed block designs with interaction effects are optimized using a weighting scheme
which allows for differential weighting of first and second-order block effects.
Outputs include a table showing the allocation of treatments to blocks and tables showing
the achieved D-efficiency factors for each block and treatment design.
Edmondson, R.N. Multi-level Block Designs for Comparative Experiments. JABES (2020).
<doi:10.1007/s13253-020-00416-0>.
Author: R. N. Edmondson.
Maintainer: Rodney Edmondson <rodney.edmondson@gmail.com>
Diff between blocksdesign versions 4.4 dated 2020-08-28 and 4.5 dated 2020-10-12
blocksdesign-4.4/blocksdesign/R/ppMOLS.R |only blocksdesign-4.4/blocksdesign/inst/doc/design_Vignette.pdf |only blocksdesign-4.4/blocksdesign/inst/doc/design_Vignette.pdf.asis |only blocksdesign-4.4/blocksdesign/vignettes/design_Vignette.pdf.asis |only blocksdesign-4.5/blocksdesign/DESCRIPTION | 33 +- blocksdesign-4.5/blocksdesign/MD5 | 30 +- blocksdesign-4.5/blocksdesign/NAMESPACE | 2 blocksdesign-4.5/blocksdesign/R/GraecoLatin.R |only blocksdesign-4.5/blocksdesign/R/MOLS.R |only blocksdesign-4.5/blocksdesign/R/blocks.r | 125 +++----- blocksdesign-4.5/blocksdesign/R/blocksdesign-package.r | 139 ++++------ blocksdesign-4.5/blocksdesign/R/design.r | 84 +++--- blocksdesign-4.5/blocksdesign/R/isPrmePower.R | 6 blocksdesign-4.5/blocksdesign/build/vignette.rds |binary blocksdesign-4.5/blocksdesign/inst/doc/blocksdesign.pdf |only blocksdesign-4.5/blocksdesign/inst/doc/blocksdesign.pdf.asis |only blocksdesign-4.5/blocksdesign/man/GraecoLatin.Rd |only blocksdesign-4.5/blocksdesign/man/MOLS.Rd | 57 ++-- blocksdesign-4.5/blocksdesign/man/blocksdesign-package.Rd | 76 ++--- blocksdesign-4.5/blocksdesign/man/design.Rd | 47 +-- blocksdesign-4.5/blocksdesign/vignettes/blocksdesign.pdf.asis |only 21 files changed, 285 insertions(+), 314 deletions(-)
Title: Allows you to Easily Interact with the Algorithmia Platform
Description: The company, Algorithmia, houses the largest marketplace of online
algorithms. This package essentially holds a bunch of REST wrappers that
make it very easy to call algorithms in the Algorithmia platform and access
files and directories in the Algorithmia data API. To learn more about the
services they offer and the algorithms in the platform visit
<http://algorithmia.com>. More information for developers can be found at
<https://algorithmia.com/developers>.
Author: James Sutton, James Athappilly, Taylor Raack
Maintainer: Robert Fulton <rfulton@algorithmia.com>
Diff between algorithmia versions 0.2.0 dated 2019-08-01 and 0.3.0 dated 2020-10-12
algorithmia-0.2.0/algorithmia/tools/build-cran-package |only algorithmia-0.3.0/algorithmia/DESCRIPTION | 16 algorithmia-0.3.0/algorithmia/LICENSE | 4 algorithmia-0.3.0/algorithmia/MD5 | 35 - algorithmia-0.3.0/algorithmia/R/AlgorithmHandler.r | 2 algorithmia-0.3.0/algorithmia/R/Client.r | 8 algorithmia-0.3.0/algorithmia/README.md | 17 algorithmia-0.3.0/algorithmia/build/vignette.rds |binary algorithmia-0.3.0/algorithmia/inst/doc/introduction-to-algorithmia.Rmd | 2 algorithmia-0.3.0/algorithmia/inst/doc/introduction-to-algorithmia.html | 324 ++++++---- algorithmia-0.3.0/algorithmia/man/AlgorithmiaAlgorithm-class.Rd | 8 algorithmia-0.3.0/algorithmia/man/AlgorithmiaClient-class.Rd | 2 algorithmia-0.3.0/algorithmia/man/ReadAcl.MY_ALGORITHMS.Rd | 4 algorithmia-0.3.0/algorithmia/man/ReadAcl.PRIVATE.Rd | 4 algorithmia-0.3.0/algorithmia/man/ReadAcl.PUBLIC.Rd | 4 algorithmia-0.3.0/algorithmia/man/getAlgorithmHandler.Rd | 9 algorithmia-0.3.0/algorithmia/man/getAlgorithmiaClient.Rd | 3 algorithmia-0.3.0/algorithmia/tools/check-rhub.r |only algorithmia-0.3.0/algorithmia/tools/test-cran-package |only algorithmia-0.3.0/algorithmia/vignettes/introduction-to-algorithmia.Rmd | 2 20 files changed, 290 insertions(+), 154 deletions(-)
Title: Stochastic Blockmodels
Description: A collection of tools and function to adjust a variety of stochastic blockmodels (SBM).
Support at the moment Simple and Bipartite SBM (undirected and directed) for Bernoulli, Poisson and
Gaussian emission laws of the edges as described in Léger, 2016 <arxiv:1602.07587>.
Author: Julien Chiquet [aut, cre] (<https://orcid.org/0000-0002-3629-3429>),
Sophie Donnet [aut],
großBM team [ctb],
Pierre Barbillon [aut] (<https://orcid.org/0000-0002-7766-7693>)
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Diff between sbm versions 0.2.1 dated 2020-07-17 and 0.2.2 dated 2020-10-12
DESCRIPTION | 10 - MD5 | 80 +++++++------- NEWS.md | 6 + R/R6Class-BipartiteSBM_fit.R | 11 + R/R6Class-BipartiteSBM_sampler.R | 7 - R/R6Class-SBM.R | 45 ++++--- R/R6Class-SBM_fit.R | 5 R/R6Class-SBM_sampler.R | 5 R/R6Class-SimpleSBM_fit.R | 13 +- R/R6Class-SimpleSBM_sampler.R | 7 - R/RcppExports.R | 4 R/estimate.R | 8 + R/plotMyMatrix.R | 10 - R/sample.R | 8 + R/utils.R | 4 README.md | 1 inst/WORDLIST | 5 inst/doc/SBM_fungus_tree_network.R | 25 ++-- inst/doc/SBM_fungus_tree_network.Rmd | 25 ++-- inst/doc/SBM_fungus_tree_network.html | 125 +++++++++++++++++----- man/BipartiteSBM_fit.Rd | 15 ++ man/BipartiteSBM_sampler.Rd | 5 man/SBM.Rd | 18 +-- man/SBM_fit.Rd | 4 man/SBM_sampler.Rd | 3 man/SimpleSBM_fit.Rd | 22 +++ man/SimpleSBM_sampler.Rd | 5 man/estimateBipartiteSBM.Rd | 3 man/estimateSimpleSBM.Rd | 3 man/plot.SBM.Rd | 13 -- man/plotMyMatrix.Rd | 8 - man/sampleBipartiteSBM.Rd | 3 man/sampleSimpleSBM.Rd | 3 man/sbm-package.Rd | 2 src/RcppExports.cpp | 8 - src/roundProduct.cpp | 27 +++- tests/testthat/test-BipartiteSBM_fit.R | 6 + tests/testthat/test-BipartiteSBM_fit_covariates.R | 21 ++- tests/testthat/test-SimpleSBM_fit.R | 9 + tests/testthat/test-SimpleSBM_fit_covariates.R | 69 ++++++------ vignettes/SBM_fungus_tree_network.Rmd | 25 ++-- 41 files changed, 437 insertions(+), 239 deletions(-)
Title: A Toolkit for Recursive Partytioning
Description: A toolkit with infrastructure for representing, summarizing, and
visualizing tree-structured regression and classification models. This
unified infrastructure can be used for reading/coercing tree models from
different sources ('rpart', 'RWeka', 'PMML') yielding objects that share
functionality for print()/plot()/predict() methods. Furthermore, new and improved
reimplementations of conditional inference trees (ctree()) and model-based
recursive partitioning (mob()) from the 'party' package are provided based
on the new infrastructure. A description of this package was published
by Hothorn and Zeileis (2015) <https://jmlr.org/papers/v16/hothorn15a.html>.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>),
Heidi Seibold [ctb] (<https://orcid.org/0000-0002-8960-9642>),
Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between partykit versions 1.2-9 dated 2020-07-10 and 1.2-10 dated 2020-10-12
DESCRIPTION | 12 ++--- MD5 | 34 ++++++++-------- R/modelparty.R | 16 ++++--- R/varimp.R | 4 + inst/CITATION | 4 - inst/NEWS.Rd | 14 +++++- inst/doc/constparty.pdf |binary inst/doc/ctree.pdf |binary inst/doc/mob.Rnw | 4 - inst/doc/mob.pdf |binary inst/doc/partykit.pdf |binary man/cforest.Rd | 4 - man/panelfunctions.Rd | 2 man/party-plot.Rd | 2 man/varimp.Rd | 12 ++--- vignettes/ctree.Rout.save | 94 +++++++++++++++++++++++----------------------- vignettes/mob.Rnw | 4 - vignettes/party.bib | 8 +++ 18 files changed, 119 insertions(+), 95 deletions(-)
Title: Incremental Cost-Effectiveness Inference using Two Unbiased
Samples
Description: Given two unbiased samples of patient level data on cost and effectiveness
for a pair of treatments, make head-to-head treatment comparisons by (i) generating the
bivariate bootstrap resampling distribution of ICE uncertainty for a specified value of
the shadow price of health, lambda, (ii) form the wedge-shaped ICE confidence region with
specified confidence fraction within [0.50, 0.99] that is equivariant with respect to
changes in lambda, (iii) color the bootstrap outcomes within the above confidence wedge
with economic preferences from an ICE map with specified values of lambda, beta and gamma
parameters, (iv) display VAGR and ALICE acceptability curves, and (v) illustrate variation
in ICE preferences by displaying potentially non-linear indifference(iso-preference) curves
from an ICE map with specified values of lambda, beta and either gamma or eta parameters.
Author: Bob Obenchain
Maintainer: Bob Obenchain <wizbob@att.net>
Diff between ICEinfer versions 1.2 dated 2020-08-30 and 1.3 dated 2020-10-12
DESCRIPTION | 8 ++--- MD5 | 22 ++++++------- R/ICEpref.R | 42 +++++++++++++++++++++----- R/ICEuncrt.R | 42 ++++++++++---------------- R/ICEwedge.R | 14 +++++--- data/dpunc.rda |binary data/dpwdg.rda |binary demo/00Index | 2 - demo/sepsis.R | 76 +++++++++++++++++++++++++++++++++++++++++------- man/ICEinfer-package.Rd | 25 ++++++++++----- man/ICEpref.Rd | 38 +++++++++++++----------- man/sepsis.Rd | 4 ++ 12 files changed, 181 insertions(+), 92 deletions(-)
Title: R Interface to COVID-19 Data Hub
Description: Download COVID-19 data across governmental sources at national, regional, and city level, as described in Guidotti and Ardia (2020) <doi:10.21105/joss.02376>. Includes policy measures by 'Oxford COVID-19 Government Response Tracker' <https://www.bsg.ox.ac.uk/research/research-projects/coronavirus-government-response-tracker>. Provides a seamless integration with 'World Bank Open Data' <https://data.worldbank.org/>, 'Google Mobility Reports' <https://www.google.com/covid19/mobility/>, 'Apple Mobility Reports' <https://covid19.apple.com/mobility>.
Author: Emanuele Guidotti [aut, cre] (<https://orcid.org/0000-0002-8961-6623>),
David Ardia [ctb] (<https://orcid.org/0000-0003-2823-782X>)
Maintainer: Emanuele Guidotti <emanuele.guidotti@unine.ch>
Diff between COVID19 versions 2.3.0 dated 2020-08-28 and 2.3.1 dated 2020-10-12
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ R/covid19.R | 4 ++-- R/wb.R | 3 +++ README.md | 2 +- build/partial.rdb |binary man/covid19.Rd | 4 ++-- 7 files changed, 19 insertions(+), 15 deletions(-)
Title: Visualize Species Occurrence Data
Description: Utilities for visualizing species occurrence data. Includes
functions to visualize occurrence data from 'spocc', 'rgbif',
and other packages. Mapping options included for base R plots, 'ggplot2',
'leaflet' and 'GitHub' 'gists'.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between mapr versions 0.5.0 dated 2020-07-30 and 0.5.2 dated 2020-10-12
mapr-0.5.0/mapr/build |only mapr-0.5.0/mapr/inst |only mapr-0.5.0/mapr/vignettes |only mapr-0.5.2/mapr/DESCRIPTION | 15 ++++++------ mapr-0.5.2/mapr/MD5 | 29 ++++++++++--------------- mapr-0.5.2/mapr/NEWS.md | 8 ++++++ mapr-0.5.2/mapr/R/map_gist.R | 5 ---- mapr-0.5.2/mapr/R/mapr-package.R | 2 - mapr-0.5.2/mapr/R/occ2sp.R | 3 -- mapr-0.5.2/mapr/R/util_github.r | 2 - mapr-0.5.2/mapr/README.md | 2 - mapr-0.5.2/mapr/man/map_gist.Rd | 5 ---- mapr-0.5.2/mapr/man/mapr-package.Rd | 2 - mapr-0.5.2/mapr/man/occ2sp.Rd | 3 -- mapr-0.5.2/mapr/man/style_geojson.Rd | 2 - mapr-0.5.2/mapr/tests/testthat/test-map_gist.R | 9 ++++++- 16 files changed, 43 insertions(+), 44 deletions(-)
Title: Computes & Plots Compatibility (Confidence), Surprisal, &
Likelihood Distributions
Description: Computes compatibility (confidence) distributions along with their corresponding P-values,
S-values, and likelihoods. The intervals can be plotted to form the distributions themselves.
Functions can be compared to one another to see how much they overlap. Results can be
exported to Microsoft Word, Powerpoint, and TeX documents. The package currently supports
resampling methods, computing differences, generalized linear models, mixed-effects models,
survival analysis, and meta-analysis. These methods are discussed
by Schweder T, Hjort NL. (2016, ISBN:9781316445051) and
Rafi Z, Greenland S. (2020) <doi:10.1186/s12874-020-01105-9>.
Author: Zad Rafi [aut, cre] (<https://orcid.org/0000-0003-1545-8199>),
Andrew D. Vigotsky [aut] (<https://orcid.org/0000-0003-3166-0688>),
Aaron Caldwell [ctb] (<https://orcid.org/0000-0002-4541-6283>)
Maintainer: Zad Rafi <zad@lesslikely.com>
Diff between concurve versions 2.5.0 dated 2020-04-20 and 2.7.7 dated 2020-10-12
concurve-2.5.0/concurve/README.md |only concurve-2.5.0/concurve/build |only concurve-2.5.0/concurve/inst/doc |only concurve-2.5.0/concurve/vignettes |only concurve-2.7.7/concurve/DESCRIPTION | 73 +-- concurve-2.7.7/concurve/MD5 | 129 ++--- concurve-2.7.7/concurve/NAMESPACE | 7 concurve-2.7.7/concurve/NEWS.md | 43 + concurve-2.7.7/concurve/R/concurve-package.R | 76 ++- concurve-2.7.7/concurve/R/curve_boot.R | 48 +- concurve-2.7.7/concurve/R/curve_compare.R | 3 concurve-2.7.7/concurve/R/curve_corr.R | 9 concurve-2.7.7/concurve/R/curve_gen.R | 98 +++- concurve-2.7.7/concurve/R/curve_lik.R | 1 concurve-2.7.7/concurve/R/curve_lmer.R | 10 concurve-2.7.7/concurve/R/curve_mean.R | 16 concurve-2.7.7/concurve/R/curve_meta.R | 49 +- concurve-2.7.7/concurve/R/curve_rev.R | 163 +++++-- concurve-2.7.7/concurve/R/curve_surv.R | 10 concurve-2.7.7/concurve/R/curve_table.R | 3 concurve-2.7.7/concurve/R/ggcurve.R | 232 ++++------ concurve-2.7.7/concurve/R/misc.R |only concurve-2.7.7/concurve/R/plot_compare.R | 99 ++-- concurve-2.7.7/concurve/R/utils-tidy-eval.R |only concurve-2.7.7/concurve/inst/CITATION | 16 concurve-2.7.7/concurve/inst/WORDLIST | 50 +- concurve-2.7.7/concurve/inst/assets |only concurve-2.7.7/concurve/inst/templates |only concurve-2.7.7/concurve/man/RobustMax.Rd |only concurve-2.7.7/concurve/man/RobustMin.Rd |only concurve-2.7.7/concurve/man/concurve-package.Rd | 115 +++- concurve-2.7.7/concurve/man/curve_boot.Rd | 8 concurve-2.7.7/concurve/man/curve_compare.Rd | 3 concurve-2.7.7/concurve/man/curve_corr.Rd | 9 concurve-2.7.7/concurve/man/curve_gen.Rd | 40 + concurve-2.7.7/concurve/man/curve_lik.Rd | 1 concurve-2.7.7/concurve/man/curve_lmer.Rd | 10 concurve-2.7.7/concurve/man/curve_mean.Rd | 12 concurve-2.7.7/concurve/man/curve_meta.Rd | 15 concurve-2.7.7/concurve/man/curve_rev.Rd | 29 - concurve-2.7.7/concurve/man/curve_surv.Rd | 10 concurve-2.7.7/concurve/man/curve_table.Rd | 3 concurve-2.7.7/concurve/man/figures/checkmark.png |only concurve-2.7.7/concurve/man/figures/crossmark.jpg |only concurve-2.7.7/concurve/man/figures/lifecycle-defunct.svg |only concurve-2.7.7/concurve/man/figures/lifecycle-deprecated.svg |only concurve-2.7.7/concurve/man/figures/lifecycle-experimental.svg |only concurve-2.7.7/concurve/man/figures/lifecycle-maturing.svg |only concurve-2.7.7/concurve/man/figures/lifecycle-stable.svg |only concurve-2.7.7/concurve/man/figures/logo.png |only concurve-2.7.7/concurve/man/ggcurve.Rd | 33 - concurve-2.7.7/concurve/man/plot_compare.Rd | 26 - concurve-2.7.7/concurve/man/tidyeval.Rd |only concurve-2.7.7/concurve/tests/spelling.R | 9 concurve-2.7.7/concurve/tests/testthat/test-name.R |only 55 files changed, 934 insertions(+), 524 deletions(-)
Title: Storage Management in 'Azure'
Description: Manage storage in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/services/storage/>. On the admin side, 'AzureStor' includes features to create, modify and delete storage accounts. On the client side, it includes an interface to blob storage, file storage, and 'Azure Data Lake Storage Gen2': upload and download files and blobs; list containers and files/blobs; create containers; and so on. Authenticated access to storage is supported, via either a shared access key or a shared access signature (SAS). Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi73@gmail.com>
Diff between AzureStor versions 3.2.3 dated 2020-08-07 and 3.3.0 dated 2020-10-12
DESCRIPTION | 12 +- MD5 | 56 ++++++------ NEWS.md | 13 ++ R/add_methods.R | 2 R/adls_client_funcs.R | 32 ++++--- R/adls_transfer_internal.R | 54 ++++------- R/azcopy.R | 31 ++++-- R/blob_client_funcs.R | 103 ++++++++++++++++------ R/blob_transfer_internal.R | 89 +++---------------- R/blob_upload_internal.R |only R/client_endpoint.R | 18 +++ R/download_dest.R |only R/file_client_funcs.R | 29 +++--- R/file_transfer_internal.R | 46 +++------- R/sas.R | 2 R/sign_request.R | 4 R/storage_utils.R | 31 +++++- R/transfer_utils.R | 31 +++++- README.md | 16 +++ inst/doc/intro.html | 164 +++++++++++++++++++----------------- inst/doc/intro.rmd | 14 +++ man/adls.Rd | 14 +-- man/blob.Rd | 37 ++++++-- man/create_storage_account.Rd | 152 ++++++++++++++++----------------- man/file.Rd | 16 ++- man/storage_endpoint.Rd | 20 ++++ tests/testthat/test02a_blobext.R | 2 tests/testthat/test02c_blobappend.R |only tests/testthat/test12_azurite.R |only tests/testthat/test13_md5.R |only tests/testthat/test13a_azcopy_md5.R |only vignettes/intro.rmd | 14 +++ 32 files changed, 576 insertions(+), 426 deletions(-)
Title: Phonetic Spelling Algorithms
Description: Provides a collection of phonetic algorithms including
Soundex, Metaphone, NYSIIS, Caverphone, and others. The package is
documented in <doi:10.18637/jss.v095.i08>.
Author: James Howard [aut, cre] (<https://orcid.org/0000-0003-4530-1547>),
Kyle Haynes [ctb],
Amanda Hood [ctb],
Os Keyes [ctb]
Maintainer: James Howard <jh@jameshoward.us>
Diff between phonics versions 1.3.8 dated 2020-10-01 and 1.3.9 dated 2020-10-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- README.md | 10 +++------- inst/doc/phonics.html | 4 ++-- 4 files changed, 12 insertions(+), 16 deletions(-)
Title: Composite-Based Structural Equation Modeling
Description: Estimate, assess, test, and study linear, nonlinear, hierarchical
and multigroup structural equation models using composite-based approaches
and procedures, including estimation techniques such as partial least squares
path modeling (PLS-PM) and its derivatives (PLSc, ordPLSc, robustPLSc),
generalized structured component analysis (GSCA), generalized structured
component analysis with uniqueness terms (GSCAm), generalized canonical
correlation analysis (GCCA), principal component analysis (PCA),
factor score regression (FSR) using sum score, regression or
bartlett scores (including bias correction using Croon’s approach),
as well as several tests and typical postestimation procedures
(e.g., verify admissibility of the estimates, assess the model fit,
test the model fit etc.).
Author: Manuel E. Rademaker [aut, cre]
(<https://orcid.org/0000-0002-8902-3561>),
Florian Schuberth [aut] (<https://orcid.org/0000-0002-2110-9086>),
Tamara Schamberger [ctb] (<https://orcid.org/0000-0002-7845-784X>),
Michael Klesel [ctb] (<https://orcid.org/0000-0002-2884-1819>),
Theo K. Dijkstra [ctb],
Jörg Henseler [ctb] (<https://orcid.org/0000-0002-9736-3048>)
Maintainer: Manuel E. Rademaker <manuel.rademaker@uni-wuerzburg.de>
Diff between cSEM versions 0.2.0 dated 2020-03-29 and 0.3.0 dated 2020-10-12
cSEM-0.2.0/cSEM/R/plot.cSEMFloodlight.R |only cSEM-0.2.0/cSEM/R/plot.cSEMSurface.R |only cSEM-0.2.0/cSEM/R/postestimate_doFloodlightAnalysis.R |only cSEM-0.2.0/cSEM/R/postestimate_doSurfaceAnalysis.R |only cSEM-0.2.0/cSEM/man/args_csem_dotdotdot.Rd |only cSEM-0.2.0/cSEM/man/doFloodlightAnalysis.Rd |only cSEM-0.2.0/cSEM/man/doSurfaceAnalysis.Rd |only cSEM-0.2.0/cSEM/man/figures/api_02.svg |only cSEM-0.2.0/cSEM/man/figures/api_old.png |only cSEM-0.2.0/cSEM/man/plot.cSEMFloodlight.Rd |only cSEM-0.2.0/cSEM/man/plot.cSEMSurface.Rd |only cSEM-0.3.0/cSEM/DESCRIPTION | 26 cSEM-0.3.0/cSEM/MD5 | 255 +- cSEM-0.3.0/cSEM/NAMESPACE | 16 cSEM-0.3.0/cSEM/R/00_csem.R | 104 cSEM-0.3.0/cSEM/R/csem_fit.R | 11 cSEM-0.3.0/cSEM/R/csem_resample.R | 543 ++-- cSEM-0.3.0/cSEM/R/helper_assess.R | 397 +++ cSEM-0.3.0/cSEM/R/helper_doNonlinearEffectsAnalysis.R |only cSEM-0.3.0/cSEM/R/helper_estimators_paths.R | 5 cSEM-0.3.0/cSEM/R/helper_infer.R | 56 cSEM-0.3.0/cSEM/R/helper_resample.R | 28 cSEM-0.3.0/cSEM/R/helper_summarize.R | 7 cSEM-0.3.0/cSEM/R/helper_test_MGD.R | 303 ++ cSEM-0.3.0/cSEM/R/plot.cSEMIPMA.R |only cSEM-0.3.0/cSEM/R/plot.cSEMNonlinearEffects.R |only cSEM-0.3.0/cSEM/R/plot.cSEMPredict.R | 4 cSEM-0.3.0/cSEM/R/postestimate_assess.R | 247 +- cSEM-0.3.0/cSEM/R/postestimate_doIPMA.R |only cSEM-0.3.0/cSEM/R/postestimate_doNonlinearEffectsAnalysis.R |only cSEM-0.3.0/cSEM/R/postestimate_doRedundancyAnalysis.R | 4 cSEM-0.3.0/cSEM/R/postestimate_getConstructScores.R | 46 cSEM-0.3.0/cSEM/R/postestimate_infer.R | 120 cSEM-0.3.0/cSEM/R/postestimate_predict.R | 2 cSEM-0.3.0/cSEM/R/postestimate_summarize.R | 95 cSEM-0.3.0/cSEM/R/postestimate_test_MGD.R | 247 +- cSEM-0.3.0/cSEM/R/postestimate_test_MICOM.R | 242 + cSEM-0.3.0/cSEM/R/postestimate_test_OMF.R | 135 - 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cSEM-0.3.0/cSEM/man/calculateModelSelectionCriteria.Rd |only cSEM-0.3.0/cSEM/man/calculatePr.Rd | 50 cSEM-0.3.0/cSEM/man/calculateVIFModeB.Rd | 74 cSEM-0.3.0/cSEM/man/calculatef2.Rd | 49 cSEM-0.3.0/cSEM/man/csem.Rd | 1212 +++++----- cSEM-0.3.0/cSEM/man/csem_arguments.Rd | 843 +++--- cSEM-0.3.0/cSEM/man/csem_results.Rd | 118 cSEM-0.3.0/cSEM/man/csem_summary.Rd | 32 cSEM-0.3.0/cSEM/man/dgp_2ndorder_cf_of_c.Rd | 82 cSEM-0.3.0/cSEM/man/distance_measures.Rd | 134 - cSEM-0.3.0/cSEM/man/doIPMA.Rd |only cSEM-0.3.0/cSEM/man/doNonlinearEffectsAnalysis.Rd |only cSEM-0.3.0/cSEM/man/doRedundancyAnalysis.Rd | 98 cSEM-0.3.0/cSEM/man/estimatePath.Rd | 98 cSEM-0.3.0/cSEM/man/figures/api.png |binary cSEM-0.3.0/cSEM/man/figures/lifecycle-archived.svg |only cSEM-0.3.0/cSEM/man/figures/lifecycle-defunct.svg |only cSEM-0.3.0/cSEM/man/figures/lifecycle-deprecated.svg |only cSEM-0.3.0/cSEM/man/figures/lifecycle-experimental.svg |only cSEM-0.3.0/cSEM/man/figures/lifecycle-maturing.svg |only cSEM-0.3.0/cSEM/man/figures/lifecycle-questioning.svg |only cSEM-0.3.0/cSEM/man/figures/lifecycle-soft-deprecated.svg |only cSEM-0.3.0/cSEM/man/figures/lifecycle-stable.svg |only cSEM-0.3.0/cSEM/man/figures/lifecycle-superseded.svg |only cSEM-0.3.0/cSEM/man/fit.Rd | 84 cSEM-0.3.0/cSEM/man/fit_measures.Rd | 195 - cSEM-0.3.0/cSEM/man/getConstructScores.Rd | 56 cSEM-0.3.0/cSEM/man/getRelevantParameters.Rd | 60 cSEM-0.3.0/cSEM/man/getValuesFloodlight.Rd |only cSEM-0.3.0/cSEM/man/infer.Rd | 373 +-- cSEM-0.3.0/cSEM/man/inference_helper.Rd |only cSEM-0.3.0/cSEM/man/moments.Rd | 185 - cSEM-0.3.0/cSEM/man/plot.cSEMIPMA.Rd |only cSEM-0.3.0/cSEM/man/plot.cSEMNonlinearEffects.Rd |only cSEM-0.3.0/cSEM/man/predict.Rd | 330 +- cSEM-0.3.0/cSEM/man/print.cSEMAssess.Rd | 28 cSEM-0.3.0/cSEM/man/print.cSEMNonlinearEffects.Rd |only cSEM-0.3.0/cSEM/man/print.cSEMPredict.Rd | 28 cSEM-0.3.0/cSEM/man/print.cSEMResults.Rd | 28 cSEM-0.3.0/cSEM/man/print.cSEMSummarize.Rd | 38 cSEM-0.3.0/cSEM/man/print.cSEMTestHausman.Rd | 28 cSEM-0.3.0/cSEM/man/print.cSEMTestMGD.Rd | 52 cSEM-0.3.0/cSEM/man/print.cSEMTestMICOM.Rd | 28 cSEM-0.3.0/cSEM/man/print.cSEMTestOMF.Rd | 28 cSEM-0.3.0/cSEM/man/print.cSEMVerify.Rd | 28 cSEM-0.3.0/cSEM/man/reliability.Rd | 194 - cSEM-0.3.0/cSEM/man/resamplecSEMResults.Rd | 544 ++-- cSEM-0.3.0/cSEM/man/satisfaction.Rd | 118 cSEM-0.3.0/cSEM/man/satisfaction_gender.Rd | 118 cSEM-0.3.0/cSEM/man/structureTestMGDDecisions.Rd |only cSEM-0.3.0/cSEM/man/summarize.Rd | 178 - cSEM-0.3.0/cSEM/man/testHausman.Rd | 230 - cSEM-0.3.0/cSEM/man/testMGD.Rd | 640 ++--- cSEM-0.3.0/cSEM/man/testMICOM.Rd | 264 +- cSEM-0.3.0/cSEM/man/testOMF.Rd | 234 - cSEM-0.3.0/cSEM/man/threecommonfactors.Rd | 100 cSEM-0.3.0/cSEM/man/verify.Rd | 200 - cSEM-0.3.0/cSEM/tests/other_tests |only cSEM-0.3.0/cSEM/tests/testthat/test-assess.R | 28 cSEM-0.3.0/cSEM/tests/testthat/test-csem.r | 7 cSEM-0.3.0/cSEM/tests/testthat/test-infer.R |only cSEM-0.3.0/cSEM/tests/testthat/test-summarize.R | 3 cSEM-0.3.0/cSEM/tests/testthat/test-testMGD.R | 15 cSEM-0.3.0/cSEM/tests/testthat/test-testOMF.R | 6 cSEM-0.3.0/cSEM/vignettes/Using-assess.Rmd | 223 - cSEM-0.3.0/cSEM/vignettes/cSEM.Rmd | 39 150 files changed, 8136 insertions(+), 6583 deletions(-)
Title: R Bindings to 'PyTorch'
Description: 'R' implementation and interface of the Machine Learning platform
'PyTorch' <https://pytorch.org/> developed in 'Python'. It requires a 'conda'
environment with 'torch' and 'torchvision' Python packages to provide
'PyTorch' functions, methods and classes. The key object in 'PyTorch' is the
tensor which is in essence a multidimensional array. These tensors are fairly
flexible in performing calculations in CPUs as well as 'GPUs' to accelerate
tensor operations.
Author: Alfonso R. Reyes [aut, cre, cph]
Maintainer: Alfonso R. Reyes <alfonso.reyes@oilgainsanalytics.com>
Diff between rTorch versions 0.4.0 dated 2020-10-09 and 0.4.2 dated 2020-10-12
rTorch-0.4.0/rTorch/inst/not-used/rhub-tests.R |only rTorch-0.4.2/rTorch/DESCRIPTION | 22 rTorch-0.4.2/rTorch/MD5 | 14 rTorch-0.4.2/rTorch/NEWS.md | 62 +- rTorch-0.4.2/rTorch/README.md | 233 +++++----- rTorch-0.4.2/rTorch/inst/rhub-tests.R |only rTorch-0.4.2/rTorch/tests/testthat/test-install_rtorch_dryrun.R | 3 rTorch-0.4.2/rTorch/tests/testthat/test_r_torch_share_objects.R | 3 rTorch-0.4.2/rTorch/tests/testthat/test_types.R | 9 9 files changed, 188 insertions(+), 158 deletions(-)
Title: R to Solr Interface
Description: A comprehensive R API for querying Apache Solr databases.
A Solr core is represented as a data frame or list that
supports Solr-side filtering, sorting,
transformation and aggregation, all through the familiar
base R API. Queries are processed
lazily, i.e., a query is only sent to the database when
the data are required.
Author: Michael Lawrence, Gabe Becker, Jan Vogel
Maintainer: Michael Lawrence <michafla@gene.com>
Diff between rsolr versions 0.0.9 dated 2018-08-21 and 0.0.10 dated 2020-10-12
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/Facets-class.R | 2 +- R/SolrPromise-class.R | 4 ++-- build/vignette.rds |binary inst/doc/intro.pdf |binary inst/unitTests/test_SolrFrame.R | 2 +- 7 files changed, 13 insertions(+), 13 deletions(-)
Title: Helpers for Developing Command Line Interfaces
Description: A suite of tools to build attractive command line interfaces
('CLIs'), from semantic elements: headings, lists, alerts, paragraphs,
etc. Supports custom themes via a 'CSS'-like language. It also contains a
number of lower level 'CLI' elements: rules, boxes, trees, and
'Unicode' symbols with 'ASCII' alternatives. It integrates with the
'crayon' package to support 'ANSI' terminal colors.
Author: Gábor Csárdi [aut, cre],
Hadley Wickham [ctb],
Kirill Müller [ctb]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between cli versions 2.0.2 dated 2020-02-28 and 2.1.0 dated 2020-10-12
cli-2.0.2/cli/build |only cli-2.0.2/cli/inst/doc |only cli-2.0.2/cli/vignettes |only cli-2.1.0/cli/DESCRIPTION | 13 +- cli-2.1.0/cli/MD5 | 77 ++++++------- cli-2.1.0/cli/NAMESPACE | 2 cli-2.1.0/cli/NEWS.md | 43 +++++++ cli-2.1.0/cli/R/cli.R | 4 cli-2.1.0/cli/R/cliapp.R | 2 cli-2.1.0/cli/R/format.R | 30 +++++ cli-2.1.0/cli/R/inline.R | 53 ++++++--- cli-2.1.0/cli/R/internals.R | 7 + cli-2.1.0/cli/R/pluralize.R | 80 +++++++++++++ cli-2.1.0/cli/R/simple-theme.R | 30 ++--- cli-2.1.0/cli/R/spinner.R | 38 ++++-- cli-2.1.0/cli/R/themes.R | 16 ++ cli-2.1.0/cli/R/tty.R | 36 ++++-- cli-2.1.0/cli/R/utils.R | 12 ++ cli-2.1.0/cli/R/width.R | 98 ++++++++++++++--- cli-2.1.0/cli/README.md | 12 +- cli-2.1.0/cli/man/ansi_hide_cursor.Rd | 11 + cli-2.1.0/cli/man/chunks/pluralization.Rmd | 17 +- cli-2.1.0/cli/man/cli_format.Rd | 3 cli-2.1.0/cli/man/cli_vec.Rd |only cli-2.1.0/cli/man/console_width.Rd | 34 +++++ cli-2.1.0/cli/man/is_ansi_tty.Rd | 7 - cli-2.1.0/cli/man/is_dynamic_tty.Rd | 9 - cli-2.1.0/cli/man/make_spinner.Rd | 8 + cli-2.1.0/cli/man/pluralization-helpers.Rd | 3 cli-2.1.0/cli/man/pluralization.Rd | 38 +++--- cli-2.1.0/cli/man/pluralize.Rd |only cli-2.1.0/cli/man/symbol.Rd | 4 cli-2.1.0/cli/tests/testthat/test-cliapp-output.R | 68 +++++++++++ cli-2.1.0/cli/tests/testthat/test-code.R |only cli-2.1.0/cli/tests/testthat/test-collapsing.R | 36 ++++++ cli-2.1.0/cli/tests/testthat/test-crayon.R | 11 + cli-2.1.0/cli/tests/testthat/test-inline.R | 28 ++++ cli-2.1.0/cli/tests/testthat/test-non-breaking-space.R | 2 cli-2.1.0/cli/tests/testthat/test-pluralization.R | 23 +++ cli-2.1.0/cli/tests/testthat/test-rules.R | 9 - cli-2.1.0/cli/tests/testthat/test-suppress.R |only cli-2.1.0/cli/tests/testthat/test-verbatim.R |only 42 files changed, 686 insertions(+), 178 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-23 0.3.3
Title: Bayesian and Classical Audit Sampling
Description: Implements the audit sampling workflow as discussed in Derks et al. (2019) <doi:10.31234/osf.io/9f6ub>. The package makes it easy for an auditor to plan an audit sample, sample from the population, and evaluating that sample using various confidence bounds according to the International Standards on Auditing. Furthermore, the package implements Bayesian equivalents of these methods.
Author: Koen Derks [aut, cre]
Maintainer: Koen Derks <k.derks@nyenrode.nl>
Diff between jfa versions 0.3.0 dated 2020-09-15 and 0.3.1 dated 2020-10-12
DESCRIPTION | 6 +++--- MD5 | 13 ++++++++----- NEWS.md | 11 ++++++++--- R/planning.R | 6 +++--- R/sampling.R | 8 ++++++-- README.md | 4 ++-- man/manual/jfa_0.3.1.pdf |only tests/testthat/test-attribute-sample-sizes-and-bound.R |only tests/testthat/test-monetary-unit-sample-sizes-and-bound.R |only 9 files changed, 30 insertions(+), 18 deletions(-)
Title: Explore Correlations Between Variables in a Machine Learning
Model
Description: When exploring data or models we often examine variables one by one.
This analysis is incomplete if the relationship between these variables is
not taken into account. The 'corrgrapher' package facilitates simultaneous
exploration of the Partial Dependence Profiles and the correlation between
variables in the model.
The package 'corrgrapher' is a part of the 'DrWhy.AI' universe.
Author: Pawel Morgen [aut, cre],
Przemyslaw Biecek [aut]
Maintainer: Pawel Morgen <seriousmorgen@protonmail.com>
Diff between corrgrapher versions 1.0.2 dated 2020-06-04 and 1.0.3 dated 2020-10-12
corrgrapher-1.0.2/corrgrapher/tests/testthat/test_knit_print.R |only corrgrapher-1.0.3/corrgrapher/DESCRIPTION | 13 +- corrgrapher-1.0.3/corrgrapher/MD5 | 16 +-- corrgrapher-1.0.3/corrgrapher/NEWS.md | 6 - corrgrapher-1.0.3/corrgrapher/R/print_corrgrapher.R | 2 corrgrapher-1.0.3/corrgrapher/R/save_to_html.R | 1 corrgrapher-1.0.3/corrgrapher/R/utils.R | 52 +--------- corrgrapher-1.0.3/corrgrapher/README.md | 2 corrgrapher-1.0.3/corrgrapher/tests/testthat/test_print.R |only corrgrapher-1.0.3/corrgrapher/tests/testthat/test_utils.R | 29 ----- 10 files changed, 27 insertions(+), 94 deletions(-)
Title: Analyses of Phylogenetic Treeshape
Description: Simulation and analysis
of phylogenetic tree topologies using statistical indices. It
is a companion library of the 'ape' package. It provides
additional functions for reading, plotting, manipulating
phylogenetic trees. It also offers convenient web-access to
public databases, and enables testing null models of
macroevolution using corrected test statistics. Trees of class
"phylo" (from 'ape' package) can be converted easily.
Implements methods described in Bortolussi et al. (2005)
<doi:10.1093/bioinformatics/bti798> and Maliet et al. (2017)
<doi:10.1101/224295>.
Author: Nicolas Bortolussi, Michael Blum, Eric Durand, Olivier Francois, Odile Maliet
Maintainer: Michael Blum <michael.blum@univ-grenoble-alpes.fr>
Diff between apTreeshape versions 1.5-0 dated 2018-04-04 and 1.5-0.1 dated 2020-10-12
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/maxlik.betasplit.R | 4 ++-- data/carnivora.treeshape.rda |binary data/cytochromc.rda |binary data/hivtree.treeshape.rda |binary data/primates.rda |binary data/rhodopsin.rda |binary data/universal.treeshape.rda |binary man/carnivora.treeshape.Rd | 2 +- 10 files changed, 16 insertions(+), 16 deletions(-)
Title: Phylogenetics for the Environmental Sciences
Description: Eco-phylogenetic and community phylogenetic analyses.
Keeps community ecological and phylogenetic data matched up and
comparable using 'comparative.comm' objects. Wrappers for common
community phylogenetic indices ('pez.shape', 'pez.evenness',
'pez.dispersion', and 'pez.dissimilarity' metrics). Implementation
of Cavender-Bares (2004) correlation of phylogenetic and
ecological matrices ('fingerprint.regression'). Phylogenetic
Generalised Linear Mixed Models (PGLMMs; 'pglmm') following Ives &
Helmus (2011) and Rafferty & Ives (2013). Simulation of null
assemblages, traits, and phylogenies ('scape', 'sim.meta.comm').
Author: William D. Pearse, Marc W. Cadotte, Jeannine Cavender-Bares,
Anthony R. Ives, Caroline Tucker, Steve C. Walker, Matthew R. Helmus
Maintainer: William D. Pearse <will.pearse@gmail.com>
Diff between pez versions 1.2-1 dated 2020-07-26 and 1.2-2 dated 2020-10-12
DESCRIPTION | 14 +++--- MD5 | 60 ++++++++++++++-------------- NAMESPACE | 4 - NEWS | 4 + R/laja.R | 2 R/metrics.R | 30 +------------- R/shape.R | 25 ++++------- build/vignette.rds |binary inst/doc/pez-intro.pdf |binary inst/doc/pez-pglmm-overview.pdf |binary man/ConDivSim.Rd | 3 - man/cc.manip.Rd | 9 +++- man/comparative.comm.Rd | 10 +++- man/dist.xxx.Rd | 3 - man/eco.scape.Rd | 18 ++++++-- man/eco.xxx.regression.Rd | 44 +++++++++++++++----- man/fibre.plot.Rd | 15 +++++-- man/fingerprint.regression.Rd | 26 ++++++++---- man/generic.metrics.Rd | 24 ++++++++--- man/laja.Rd | 7 +-- man/pez.dispersion.Rd | 17 +++++--- man/pez.dissimilarity.Rd | 15 +++++-- man/pez.evenness.Rd | 11 ++++- man/pez.metrics.Rd | 85 ++++++++++++++++++++++++++-------------- man/pez.shape.Rd | 28 +++++++------ man/pglmm.Rd | 80 +++++++++++++++++++++++++++---------- man/plot.comparative.comm.Rd | 15 +++++-- man/scape.Rd | 26 +++++++++--- man/sim.meta.Rd | 24 ++++++++--- man/sim.phy.Rd | 13 ++++-- man/trait.asm.Rd | 10 +++- 31 files changed, 403 insertions(+), 219 deletions(-)
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 0.9.7 dated 2020-09-12 and 0.9.8 dated 2020-10-12
DESCRIPTION | 8 +-- MD5 | 14 +++--- NEWS.md | 6 ++ R/CreateTableOneJS.R | 37 ++++++++-------- R/svyCreateTableOneJS.R | 36 +++++++++------- inst/doc/jstable.html | 102 +++++++++++++++++++++++++++++++++++++++------- man/CreateTableOne2.Rd | 5 +- man/svyCreateTableOne2.Rd | 5 +- 8 files changed, 151 insertions(+), 62 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 1.1.1 dated 2020-08-28 and 1.1.2 dated 2020-10-12
DESCRIPTION | 8 ++--- MD5 | 10 +++--- NEWS.md | 7 ++++ R/FilePsInput.R | 42 ++++++++++++++++----------- R/jsPropensityGadget.R | 28 ++++++++++-------- inst/doc/jsmodule.html | 76 +++++++++++++++++++++++++++++++++++++++++++++++-- 6 files changed, 133 insertions(+), 38 deletions(-)
Title: Small Area Estimation with Measurement Error
Description: A set of functions and datasets implementation of small area estimation when auxiliary variable is measured with error. These functions provide a empirical best linear unbiased prediction (EBLUP) estimator and mean squared error (MSE) estimator of the EBLUP. These models were developed by Ybarra and Lohr (2008) <doi:10.1093/biomet/asn048>.
Author: Muhammad Rifqi Mubarak [aut, cre],
Azka Ubaidillah [aut]
Maintainer: Muhammad Rifqi Mubarak <16.9304@stis.ac.id>
Diff between saeME versions 1.2.2 dated 2020-10-01 and 1.2.3 dated 2020-10-12
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/FHme_nonsamples.R | 39 +++++++++++++++++++++------------------ R/mse_FHme.R | 29 +++++++++++++---------------- man/FHme_nonsamples.Rd | 2 +- man/mse_FHme.Rd | 14 +------------- 6 files changed, 44 insertions(+), 56 deletions(-)
Title: Revisiting Base Rapply
Description: The 'rrapply'-package contains a single function rrapply(), providing an extended implementation of 'R'-base rapply() by allowing to recursively apply a function to elements of a nested list based on a general condition function and including the possibility to prune or aggregate nested list elements from the result. In addition, special arguments can be supplied to access the name, location, parents and siblings in the nested list of the element under evaluation. The rrapply() function is implemented in 'R''s 'C' interface and requires no other package dependencies.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>
Diff between rrapply versions 1.1.0 dated 2020-07-05 and 1.2.0 dated 2020-10-12
DESCRIPTION | 12 MD5 | 27 +- NEWS.md | 10 R/rrapply.R | 219 +++++++++++------ README.md | 275 +++++++++++++++++---- build/vignette.rds |binary inst/doc/rrapply.R | 175 ++++++++++++- inst/doc/rrapply.Rnw | 212 ++++++++++++++-- inst/doc/rrapply.pdf |binary inst/unit_tests/unit_test_rrapply.R | 257 ++++++++++++++++++-- man/rrapply.Rd | 153 ++++++++---- src/init.c | 2 src/rrapply.c | 457 ++++++++++++++++++++++++++---------- src/unmelt.c |only vignettes/rrapply.Rnw | 212 ++++++++++++++-- 15 files changed, 1596 insertions(+), 415 deletions(-)
Title: Mixtures of von Mises-Fisher Distributions
Description: Fit and simulate mixtures of von Mises-Fisher distributions.
Author: Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>),
Bettina Grün [aut] (<https://orcid.org/0000-0001-7265-4773>)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between movMF versions 0.2-4 dated 2018-09-26 and 0.2-5 dated 2020-10-12
DESCRIPTION | 10 MD5 | 30 + NAMESPACE | 3 R/FLXMCvMF.R |only R/movMF.R | 146 +++++---- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 9 inst/doc/movMF.R | 47 +- inst/doc/movMF.Rnw | 19 - inst/doc/movMF.pdf |binary man/FLXMCvMF.Rd |only man/movMF.Rd | 2 man/movMF_distribution.Rd | 4 src/rW.c | 2 vignettes/movMF.Rnw | 19 - vignettes/vMF.bib | 731 +++++++++++++++++++++++++--------------------- 17 files changed, 570 insertions(+), 452 deletions(-)
Title: Simple Data Frames
Description: Provides a 'tbl_df' class (the 'tibble') that
provides stricter checking and better formatting than the traditional
data frame.
Author: Kirill Müller [aut, cre],
Hadley Wickham [aut],
Romain Francois [ctb],
Jennifer Bryan [ctb],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between tibble versions 3.0.3 dated 2020-07-10 and 3.0.4 dated 2020-10-12
tibble-3.0.3/tibble/man/print.tbl_df.Rd |only tibble-3.0.4/tibble/DESCRIPTION | 8 tibble-3.0.4/tibble/MD5 | 88 tibble-3.0.4/tibble/NAMESPACE | 3 tibble-3.0.4/tibble/NEWS.md | 21 tibble-3.0.4/tibble/R/aaa-pillar.R | 22 tibble-3.0.4/tibble/R/add.R | 8 tibble-3.0.4/tibble/R/class-tbl_df.R | 8 tibble-3.0.4/tibble/R/compat-lifecycle.R | 6 tibble-3.0.4/tibble/R/print.R | 32 tibble-3.0.4/tibble/R/subsetting.R | 66 tibble-3.0.4/tibble/R/tbl_sum.R | 11 tibble-3.0.4/tibble/R/tibble-package.R | 12 tibble-3.0.4/tibble/R/utils-tick.R | 2 tibble-3.0.4/tibble/R/zzz.R | 17 tibble-3.0.4/tibble/README.md | 163 - tibble-3.0.4/tibble/inst/doc/invariants.R | 6 tibble-3.0.4/tibble/inst/doc/invariants.Rmd | 7 tibble-3.0.4/tibble/inst/doc/invariants.html | 925 +++++----- tibble-3.0.4/tibble/inst/doc/tibble.html | 116 - tibble-3.0.4/tibble/inst/doc/types.R | 3 tibble-3.0.4/tibble/inst/doc/types.Rmd | 7 tibble-3.0.4/tibble/inst/doc/types.html | 76 tibble-3.0.4/tibble/man/formatting.Rd | 10 tibble-3.0.4/tibble/man/subsetting.Rd | 4 tibble-3.0.4/tibble/man/tbl_df-class.Rd | 8 tibble-3.0.4/tibble/man/tbl_sum.Rd | 2 tibble-3.0.4/tibble/man/tibble-package.Rd | 14 tibble-3.0.4/tibble/tests/testthat/helper-pillar.R |only tibble-3.0.4/tibble/tests/testthat/helper-zzz.R | 4 tibble-3.0.4/tibble/tests/testthat/msg.txt | 32 tibble-3.0.4/tibble/tests/testthat/subsetting.txt | 12 tibble-3.0.4/tibble/tests/testthat/tbl_sum.txt | 4 tibble-3.0.4/tibble/tests/testthat/test-add.R | 19 tibble-3.0.4/tibble/tests/testthat/test-class-tbl_df.R | 18 tibble-3.0.4/tibble/tests/testthat/test-msg.R | 12 tibble-3.0.4/tibble/tests/testthat/test-print.R | 15 tibble-3.0.4/tibble/tests/testthat/test-tbl_sum.R | 1 tibble-3.0.4/tibble/tests/testthat/test-zzz-glimpse.R | 4 tibble-3.0.4/tibble/tests/testthat/test-zzz-options.R | 2 tibble-3.0.4/tibble/tests/testthat/test-zzz-syntactic-names.R | 2 tibble-3.0.4/tibble/tests/testthat/test-zzz-tribble.R | 3 tibble-3.0.4/tibble/tests/testthat/test-zzz-trunc-mat.R | 20 tibble-3.0.4/tibble/tests/testthat/trunc_mat.txt | 6 tibble-3.0.4/tibble/vignettes/invariants.Rmd | 7 tibble-3.0.4/tibble/vignettes/types.Rmd | 7 46 files changed, 921 insertions(+), 892 deletions(-)
Title: Summarize Text by Ranking Sentences and Finding Keywords
Description: The 'textrank' algorithm is an extension of the 'Pagerank' algorithm for text. The algorithm allows to summarize text by calculating how sentences are related to one another. This is done by looking at overlapping terminology used in sentences in order to set up links between sentences. The resulting sentence network is next plugged into the 'Pagerank' algorithm which identifies the most important sentences in your text and ranks them.
In a similar way 'textrank' can also be used to extract keywords. A word network is constructed by looking if words are following one another. On top of that network the 'Pagerank' algorithm is applied to extract relevant words after which relevant words which are following one another are combined to get keywords.
More information can be found in the paper from Mihalcea, Rada & Tarau, Paul (2004) <https://www.aclweb.org/anthology/W04-3252/>.
Author: Jan Wijffels [aut, cre, cph],
BNOSAC [cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between textrank versions 0.3.0 dated 2019-01-17 and 0.3.1 dated 2020-10-12
DESCRIPTION | 12 MD5 | 26 NEWS.md | 4 R/textrank.R | 6 build/vignette.rds |binary inst/doc/textrank.R | 2 inst/doc/textrank.Rmd | 2 inst/doc/textrank.html | 1400 ++++++++++++++++++++++++++++++++++++-- man/summary.textrank_sentences.Rd | 3 man/textrank_candidates_all.Rd | 2 man/textrank_candidates_lsh.Rd | 2 man/textrank_keywords.Rd | 9 man/textrank_sentences.Rd | 12 vignettes/textrank.Rmd | 2 14 files changed, 1389 insertions(+), 93 deletions(-)
Title: Cluster-Robust (Sandwich) Variance Estimators with Small-Sample
Corrections
Description: Provides several cluster-robust variance estimators (i.e.,
sandwich estimators) for ordinary and weighted least squares linear regression
models, including the bias-reduced linearization estimator introduced by Bell
and McCaffrey (2002)
<https://www150.statcan.gc.ca/n1/pub/12-001-x/2002002/article/9058-eng.pdf> and
developed further by Pustejovsky and Tipton (2017)
<DOI:10.1080/07350015.2016.1247004>. The package includes functions for estimating
the variance- covariance matrix and for testing single- and multiple-
contrast hypotheses based on Wald test statistics. Tests of single regression
coefficients use Satterthwaite or saddle-point corrections. Tests of multiple-
contrast hypotheses use an approximation to Hotelling's T-squared distribution.
Methods are provided for a variety of fitted models, including lm() and mlm
objects, glm(), ivreg() (from package 'AER'), plm() (from package 'plm'), gls()
and lme() (from 'nlme'), lmer() (from `lme4`), robu() (from 'robumeta'), and
rma.uni() and rma.mv() (from 'metafor').
Author: James Pustejovsky [aut, cre] (<https://orcid.org/0000-0003-0591-9465>)
Maintainer: James Pustejovsky <jepusto@gmail.com>
Diff between clubSandwich versions 0.5.0 dated 2020-09-01 and 0.5.1 dated 2020-10-12
DESCRIPTION | 11 MD5 | 28 - NAMESPACE | 1 NEWS | 10 R/rma-mv.R | 416 +++++++++++++++++++++++-- build/clubSandwich.pdf |only build/partial.rdb |binary inst/doc/Wald-tests-in-clubSandwich.html | 4 inst/doc/meta-analysis-with-CRVE.html | 4 inst/doc/panel-data-CRVE.Rmd | 2 inst/doc/panel-data-CRVE.html | 6 man/impute_covariance_matrix.Rd | 93 ++++- man/pattern_covariance_matrix.Rd |only tests/testthat/test_impute_covariance_matrix.R | 266 +++++++++++++++ tests/testthat/test_rma-mv.R | 112 ++++++ vignettes/panel-data-CRVE.Rmd | 2 16 files changed, 881 insertions(+), 74 deletions(-)
Title: Key and Secret Management in 'Azure'
Description: Manage keys, certificates, secrets, and storage accounts in Microsoft's 'Key Vault' service: <https://azure.microsoft.com/services/key-vault/>. Provides facilities to store and retrieve secrets, use keys to encrypt, decrypt, sign and verify data, and manage certificates. Integrates with the 'AzureAuth' package to enable authentication with a certificate, and with the 'openssl' package for importing and exporting cryptographic objects. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi73@gmail.com>
Diff between AzureKeyVault versions 1.0.3 dated 2020-01-15 and 1.0.4 dated 2020-10-12
DESCRIPTION | 14 +++++++------- MD5 | 14 +++++++------- NEWS.md | 5 ++++- README.md | 2 +- build/vignette.rds |binary inst/doc/intro.Rmd | 2 +- inst/doc/intro.html | 24 ++++++++++++++---------- vignettes/intro.Rmd | 2 +- 8 files changed, 35 insertions(+), 28 deletions(-)
Title: Simple Interface to 'Microsoft Graph'
Description: A simple interface to the 'Microsoft Graph' API <https://docs.microsoft.com/en-us/graph/overview>. 'Graph' is a comprehensive framework for accessing data in various online Microsoft services. Currently, this package aims to provide an R interface only to the 'Azure Active Directory' part, with a view to supporting interoperability of R and 'Azure': users, groups, registered apps and service principals. However it can be easily extended to cover other services. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi73@gmail.com>
Diff between AzureGraph versions 1.1.1 dated 2020-05-25 and 1.1.2 dated 2020-10-12
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NEWS.md | 4 ++++ README.md | 2 +- build/vignette.rds |binary 5 files changed, 15 insertions(+), 11 deletions(-)
Title: Authentication Services for Azure Active Directory
Description: Provides Azure Active Directory (AAD) authentication functionality for R users of Microsoft's 'Azure' cloud <https://azure.microsoft.com/>. Use this package to obtain 'OAuth' 2.0 tokens for services including Azure Resource Manager, Azure Storage and others. It supports both AAD v1.0 and v2.0, as well as multiple authentication methods, including device code and resource owner grant. Tokens are cached in a user-specific directory obtained using the 'rappdirs' package. The interface is based on the 'OAuth' framework in the 'httr' package, but customised and streamlined for Azure. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
httr development team [ctb] (Original OAuth listener code),
Scott Holden [ctb] (Advice on AAD authentication),
Chris Stone [ctb] (Advice on AAD authentication),
Microsoft [cph]
Maintainer: Hong Ooi <hongooi73@gmail.com>
Diff between AzureAuth versions 1.2.4 dated 2020-05-23 and 1.2.5 dated 2020-10-12
DESCRIPTION | 13 +++++++------ MD5 | 8 ++++---- NEWS.md | 4 ++++ README.md | 2 +- build/vignette.rds |binary 5 files changed, 16 insertions(+), 11 deletions(-)
Title: Simple Key Value Stores
Description: Creates and manages simple key-value stores. These can
use a variety of approaches for storing the data. This package
implements the base methods and support for file system, in-memory
and DBI-based database stores.
Author: Rich FitzJohn [aut, cre],
William Michael Landau [ctb] (<https://orcid.org/0000-0003-1878-3253>)
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Diff between storr versions 1.2.1 dated 2018-10-18 and 1.2.4 dated 2020-10-12
DESCRIPTION | 24 + MD5 | 45 +-- NAMESPACE | 1 NEWS.md | 8 R/driver_rds.R | 13 - R/spec.R | 15 + R/storr.R | 2 R/utils.R | 14 + README.md | 6 build/vignette.rds |binary inst/doc/external.R | 40 +-- inst/doc/external.Rmd | 6 inst/doc/external.html | 500 ++++++++++++++++++++++++++++----------- inst/doc/storr.R | 78 +++--- inst/doc/storr.html | 486 ++++++++++++++++++++++++++++--------- inst/spec/test-external.R | 3 inst/spec/test-storr.R | 21 + man/storr_rds.Rd | 5 src |only tests/testthat/helper-remote.R | 3 tests/testthat/test-defunct.R | 10 tests/testthat/test-driver-rds.R | 15 - tests/testthat/test-util.R | 55 ++++ vignettes/external.Rmd | 6 24 files changed, 976 insertions(+), 380 deletions(-)
Title: Flexible Mixture Modeling
Description: A general framework for finite mixtures of regression
models using the EM algorithm is implemented. The E-step and all
data handling are provided, while the M-step can be supplied by the
user to easily define new models. Existing drivers implement
mixtures of standard linear models, generalized linear models and
model-based clustering.
Author: Bettina Gruen [aut, cre] (<https://orcid.org/0000-0001-7265-4773>),
Friedrich Leisch [aut] (<https://orcid.org/0000-0001-7278-1983>),
Deepayan Sarkar [ctb] (<https://orcid.org/0000-0003-4107-1553>),
Frederic Mortier [ctb],
Nicolas Picard [ctb] (<https://orcid.org/0000-0001-5548-9171>)
Maintainer: Bettina Gruen <Bettina.Gruen@R-project.org>
Diff between flexmix versions 2.3-15 dated 2019-02-18 and 2.3-17 dated 2020-10-12
DESCRIPTION | 10 ++-- MD5 | 87 +++++++++++++++++++------------------- NAMESPACE | 2 R/allClasses.R | 16 +++--- R/flexmix.R | 6 +- R/flxmcsparse.R |only R/lmm.R | 11 +++- build/vignette.rds |binary data/BregFix.RData |binary data/Mehta.RData |binary data/NPreg.RData |binary data/Nclus.RData |binary data/NregFix.RData |binary data/betablocker.RData |binary data/bioChemists.RData |binary data/candy.RData |binary data/dmft.RData |binary data/fabricfault.RData |binary data/patent.RData |binary data/seizure.RData |binary data/tribolium.RData |binary data/trypanosome.RData |binary data/whiskey.RData |binary inst/CITATION | 4 - inst/NEWS.Rd | 21 ++++++++- inst/doc/bootstrapping.R | 75 ++++++++++++++++++++------------ inst/doc/bootstrapping.Rnw | 65 +++++++++++++++------------- inst/doc/bootstrapping.pdf |binary inst/doc/flexmix-intro.R | 4 - inst/doc/flexmix-intro.Rnw | 6 +- inst/doc/flexmix-intro.pdf |binary inst/doc/mixture-regressions.R | 9 ++- inst/doc/mixture-regressions.Rnw | 18 +++---- inst/doc/mixture-regressions.pdf |binary inst/doc/regression-examples.R | 1 inst/doc/regression-examples.Rnw | 16 +++--- inst/doc/regression-examples.pdf |binary man/FLXMCdist1.Rd | 6 +- man/FLXmodel-class.Rd | 3 - man/bioChemists.Rd | 4 - man/flexmix-internal.Rd | 3 - vignettes/bootstrapping.Rnw | 65 +++++++++++++++------------- vignettes/flexmix-intro.Rnw | 6 +- vignettes/mixture-regressions.Rnw | 18 +++---- vignettes/regression-examples.Rnw | 16 +++--- 45 files changed, 270 insertions(+), 202 deletions(-)
Title: Benthic Multi-Metric Index
Description: Analysis tool for evaluating benthic multimetric indices (BENMMIs).
It generates reproducible reports on the analysis of benthic data, e.g.,
validation and correction of species names, sample pooling, automatic
conversion of genus to species names, outlier detection, benthic
indicator calculation, optimization of single and
multimetric indicators against a pressure gradient, and spatial aggregation
of benthic indicators. One of its use cases was the development of a common
benthic indicator for <https://www.ospar.org> (publication accepted by
Ecological Indicators). See Van Loon et al. (2018) <doi:10.1016/j.ecolind.2017.09.029> for details.
Author: Dennis Walvoort [aut, cre],
Willem van Loon [aut, cph]
Maintainer: Dennis Walvoort <dennis.Walvoort@wur.nl>
Diff between BENMMI versions 4.3-6 dated 2019-01-25 and 4.3-7 dated 2020-10-12
DESCRIPTION | 11 MD5 | 29 R/benmmi-main.R | 2098 +++++++++++++++++++--------------------- build |only inst/NEWS.Rd | 27 inst/doc/BENMMI_User_Manual.R |only inst/doc/BENMMI_User_Manual.Rnw |only inst/doc/BENMMI_User_Manual.pdf |binary inst/doc/FAQ.Rnw |only inst/doc/FAQ.pdf |binary man/benmmi-main.Rd | 3 man/benmmi-pkg.Rd | 1 vignettes |only 13 files changed, 1094 insertions(+), 1075 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-09 0.0.1.2
2020-07-08 0.0.1.1
2020-07-03 0.0.1
Title: D-Vine Quantile Regression
Description: Implements D-vine quantile regression models with
parametric or nonparametric pair-copulas. See
Kraus and Czado (2017) <doi:10.1016/j.csda.2016.12.009> and
Schallhorn et al. (2017) <arXiv:1705.08310>.
Author: Thomas Nagler [aut, cre],
Dani Kraus [ctb]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between vinereg versions 0.7.0 dated 2019-12-02 and 0.7.1 dated 2020-10-12
DESCRIPTION | 10 MD5 | 16 NEWS.md | 13 R/tools.R | 3 build/vignette.rds |binary inst/doc/abalone-example.R | 32 - inst/doc/abalone-example.html | 824 +++++++++++++++++++++--------------------- inst/doc/bike-rental.R | 40 +- inst/doc/bike-rental.html | 808 ++++++++++++++++++++++------------------- 9 files changed, 938 insertions(+), 808 deletions(-)
Title: Filter Methods for Parameter Estimation in Linear and Non Linear
Regression Models
Description: We present a method based on filtering algorithms to estimate the parameters of linear, i.e. the coefficients and the variance of the error term. The proposed algorithms make use of Particle Filters following Ristic, B., Arulampalam, S., Gordon, N. (2004, ISBN: 158053631X) resampling methods. Parameters of logistic regression models are also estimated using an evolutionary particle filter method.
Author: Christian Llano Robayo [aut, cre],
Nazrul Shaikh [aut]
Maintainer: Christian Llano Robayo <cxl985@miami.edu>
Diff between LMfilteR versions 0.1.2 dated 2018-08-14 and 0.1.3 dated 2020-10-12
DESCRIPTION | 18 - MD5 | 19 + NAMESPACE | 10 - NEWS.md | 31 ++- R/EPF_L_compl.R |only R/EPF_logist_compl.R |only R/PF_lm.R | 461 +++++++++++++++++++++++------------------------- R/PF_lm_ss.R | 429 ++++++++++++++++++++++---------------------- R/utils.R |only man/EPF_L_compl.Rd |only man/EPF_logist_compl.Rd |only man/PF_lm.Rd | 249 ++++++++++++------------- man/PF_lm_ss.Rd | 249 +++++++++++++------------ 13 files changed, 740 insertions(+), 726 deletions(-)
Title: Parallel Chain Tools for Bayesian Kernel Machine Regression
Description: Bayesian kernel machine regression (from the 'bkmr'
package) is a Bayesian semi-parametric generalized linear model
approach under identity and probit links. There are a number of
functions in this package that extend Bayesian kernel machine
regression fits to allow multiple-chain inference and diagnostics,
which leverage functions from the 'future', 'rstan', and 'coda'
packages. Reference: Bobb, J. F., Henn, B. C., Valeri, L., & Coull,
B. A. (2018). Statistical software for analyzing the health effects of
multiple concurrent exposures via Bayesian kernel machine regression.
; <doi:10.1186/s12940-018-0413-y>.
Author: Alexander Keil [aut, cre]
Maintainer: Alexander Keil <akeil@unc.edu>
Diff between bkmrhat versions 0.1.16 dated 2020-09-16 and 1.0.0 dated 2020-10-12
bkmrhat-0.1.16/bkmrhat/man/comb_bkmrfits.Rd |only bkmrhat-0.1.16/bkmrhat/man/kmbayes_diag.Rd |only bkmrhat-1.0.0/bkmrhat/DESCRIPTION | 8 bkmrhat-1.0.0/bkmrhat/MD5 | 49 bkmrhat-1.0.0/bkmrhat/NAMESPACE | 6 bkmrhat-1.0.0/bkmrhat/NEWS.md | 11 bkmrhat-1.0.0/bkmrhat/R/coda_funs.R | 10 bkmrhat-1.0.0/bkmrhat/R/continue_funs.R |only bkmrhat-1.0.0/bkmrhat/R/diag_funs.R | 70 - bkmrhat-1.0.0/bkmrhat/R/experimental_funs.R |only bkmrhat-1.0.0/bkmrhat/R/invisible_funs.R | 4 bkmrhat-1.0.0/bkmrhat/R/modelchecking_funs.R | 1 bkmrhat-1.0.0/bkmrhat/R/parallel_funs.R | 22 bkmrhat-1.0.0/bkmrhat/R/prediction_funs.R | 4 bkmrhat-1.0.0/bkmrhat/inst/doc/bkmrhat-vignette.R | 46 bkmrhat-1.0.0/bkmrhat/inst/doc/bkmrhat-vignette.Rmd | 65 + bkmrhat-1.0.0/bkmrhat/inst/doc/bkmrhat-vignette.html | 843 +++++++++++------ bkmrhat-1.0.0/bkmrhat/man/as.mcmc.bkmrfit.Rd | 4 bkmrhat-1.0.0/bkmrhat/man/as.mcmc.list.bkmrfit.list.Rd | 6 bkmrhat-1.0.0/bkmrhat/man/kmbayes_combine.Rd |only bkmrhat-1.0.0/bkmrhat/man/kmbayes_continue.Rd |only bkmrhat-1.0.0/bkmrhat/man/kmbayes_diagnose.Rd |only bkmrhat-1.0.0/bkmrhat/man/kmbayes_parallel.Rd | 5 bkmrhat-1.0.0/bkmrhat/man/kmbayes_parallel_continue.Rd |only bkmrhat-1.0.0/bkmrhat/man/predict.bkmrfit.Rd | 4 bkmrhat-1.0.0/bkmrhat/tests |only bkmrhat-1.0.0/bkmrhat/vignettes/bkmrhat-vignette.Rmd | 65 + 27 files changed, 848 insertions(+), 375 deletions(-)
Title: Tokenization, Parts of Speech Tagging, Lemmatization and
Dependency Parsing with the 'UDPipe' 'NLP' Toolkit
Description: This natural language processing toolkit provides language-agnostic
'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency
parsing' of raw text. Next to text parsing, the package also allows you to train
annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided
at <https://universaldependencies.org/format.html>. The techniques are explained
in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0
with UDPipe', available at <doi:10.18653/v1/K17-3009>.
The toolkit also contains functionalities for commonly used data manipulations on texts
which are enriched with the output of the parser. Namely functionalities and algorithms
for collocations, token co-occurrence, document term matrix handling,
term frequency inverse document frequency calculations,
information retrieval metrics (Okapi BM25), handling of multi-word expressions,
keyword detection (Rapid Automatic Keyword Extraction, noun phrase extraction, syntactical patterns)
sentiment scoring and semantic similarity analysis.
Author: Jan Wijffels [aut, cre, cph],
BNOSAC [cph],
Institute of Formal and Applied Linguistics, Faculty of Mathematics and
Physics, Charles University in Prague, Czech Republic [cph],
Milan Straka [ctb, cph],
Jana Straková [ctb, cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between udpipe versions 0.8.4 dated 2020-10-10 and 0.8.4-1 dated 2020-10-12
DESCRIPTION | 8 ++-- MD5 | 32 +++++++++--------- NEWS.md | 4 ++ R/topicmodels.R | 2 + build/vignette.rds |binary inst/doc/udpipe-annotation.html | 15 +------- inst/doc/udpipe-parallel.html | 15 +------- inst/doc/udpipe-train.html | 25 ++++---------- inst/doc/udpipe-tryitout.html | 13 +------ inst/doc/udpipe-universe.html | 13 +------ inst/doc/udpipe-usecase-postagging-lemmatisation.html | 25 ++++---------- inst/doc/udpipe-usecase-topicmodelling.R | 2 - inst/doc/udpipe-usecase-topicmodelling.Rmd | 2 - inst/doc/udpipe-usecase-topicmodelling.html | 13 +------ man/predict.LDA.Rd | 2 + src/udpipe.cpp | 14 +++++-- vignettes/udpipe-usecase-topicmodelling.Rmd | 2 - 17 files changed, 68 insertions(+), 119 deletions(-)
Title: QTL Genome-Wide Composite Interval Mapping with Graphical User
Interface
Description: Conduct multiple quantitative trait loci (QTL) mapping under the framework of random-QTL-effect linear mixed model. First, each position on the genome is detected in order to obtain a negative logarithm P-value curve against genome position. Then, all the peaks on each effect (additive or dominant) curve are viewed as potential QTL, all the effects of the potential QTL are included in a multi-QTL model, their effects are estimated by empirical Bayes in doubled haploid population or by adaptive lasso in F2 population, and true QTL are identified by likelihood radio test. See Wen et al. (2018) <doi:10.1093/bib/bby058>.
Author: Zhang Ya-Wen, Wen Yang-Jun, Wang Shi-Bo, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Diff between QTL.gCIMapping.GUI versions 2.1 dated 2020-05-01 and 2.1.1 dated 2020-10-12
DESCRIPTION | 8 MD5 | 10 - NAMESPACE | 10 - R/QTL.gCIMapping.GUI.R | 414 ++++++++++++++++++++++------------------------ inst/doc/Instruction.pdf |binary man/QTL.gCIMapping.GUI.Rd | 6 6 files changed, 220 insertions(+), 228 deletions(-)
More information about QTL.gCIMapping.GUI at CRAN
Permanent link
Title: QTL Genome-Wide Composite Interval Mapping
Description: Conduct multiple quantitative trait loci (QTL) mapping under the framework of random-QTL-effect linear mixed model. First, each position on the genome is detected in order to obtain a negative logarithm P-value curve against genome position. Then, all the peaks on each effect (additive or dominant) curve are viewed as potential QTL, all the effects of the potential QTL are included in a multi-QTL model, their effects are estimated by empirical Bayes in doubled haploid population or by adaptive lasso in F2 population, and true QTL are identified by likelihood radio test. See Wen et al. (2018) <doi:10.1093/bib/bby058>.
Author: Zhang Ya-Wen, Wen Yang-Jun, Wang Shi-Bo, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Diff between QTL.gCIMapping versions 3.3 dated 2020-05-01 and 3.3.1 dated 2020-10-12
DESCRIPTION | 8 - MD5 | 10 +- NAMESPACE | 8 - R/QTL.gCIMapping.R | 233 ++++++++++++++++++++++++++++++----------------- inst/doc/instruction.pdf |binary man/QTL.gCIMapping.Rd | 32 ++++-- 6 files changed, 182 insertions(+), 109 deletions(-)
More information about QTL.gCIMapping at CRAN
Permanent link
Title: Bias Reduction in Binomial-Response Generalized Linear Models
Description: Fit generalized linear models with binomial responses using either an adjusted-score approach to bias reduction or maximum penalized likelihood where penalization is by Jeffreys invariant prior. These procedures return estimates with improved frequentist properties (bias, mean squared error) that are always finite even in cases where the maximum likelihood estimates are infinite (data separation). Fitting takes place by fitting generalized linear models on iteratively updated pseudo-data. The interface is essentially the same as 'glm'. More flexibility is provided by the fact that custom pseudo-data representations can be specified and used for model fitting. Functions are provided for the construction of confidence intervals for the reduced-bias estimates.
Author: Ioannis Kosmidis [aut, cre] (<https://orcid.org/0000-0003-1556-0302>)
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between brglm versions 0.6.2 dated 2019-04-02 and 0.7.1 dated 2020-10-12
DESCRIPTION | 7 +++---- MD5 | 28 +++++++++++++++------------- inst/CHANGES | 29 +++++++++++++++++------------ inst/CITATION | 15 ++++++++++----- inst/Jeffreys_power.R |only inst/WORDLIST |only man/brglm.Rd | 39 +++++++++++++++++---------------------- man/brglm.control.Rd | 6 +++++- man/confint.brglm.Rd | 8 ++++++-- man/gethats.Rd | 2 +- man/glm.control1.Rd | 6 +++--- man/modifications.Rd | 39 ++++++++++++++++++++++++++++++++++----- man/plot.profile.brglm.Rd | 2 +- man/profile.brglm.Rd | 4 ++-- man/profileObjectives.Rd | 8 ++++++-- man/separation.detection.Rd | 14 ++++++++++---- 16 files changed, 130 insertions(+), 77 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-28 1.1.8
2020-09-18 1.1.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-15 1.0.3