Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-15 2.0.19
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-14 0.1.0
Title: Read RSS, Atom and RDF Feeds
Description: Retrieve data from RSS/Atom feeds.
Author: Andrew Collier [aut, cre]
Maintainer: Andrew Collier <andrew@exegetic.biz>
Diff between feedeR versions 0.0.8 dated 2020-04-19 and 0.0.10 dated 2020-09-28
feedeR-0.0.10/feedeR/DESCRIPTION | 8 ++++---- feedeR-0.0.10/feedeR/MD5 | 12 ++++++------ feedeR-0.0.10/feedeR/R/parse-rss.R | 4 ++-- feedeR-0.0.10/feedeR/README.md | 14 ++++++-------- feedeR-0.0.10/feedeR/inst/hex/logo.R |only feedeR-0.0.10/feedeR/tests/testthat/test_atom.R | 1 - feedeR-0.0.10/feedeR/tests/testthat/test_rss.R | 17 +++++++++++++++++ feedeR-0.0.8/feedeR/inst/hex/feedeR-hex.R |only 8 files changed, 35 insertions(+), 21 deletions(-)
Title: The FisherEM Algorithm to Simultaneously Cluster and Visualize
High-Dimensional Data
Description: The FisherEM algorithm, proposed by Bouveyron & Brunet (2012) <doi:10.1007/s11222-011-9249-9>,
is an efficient method for the clustering of high-dimensional data. FisherEM models and
clusters the data in a discriminative and low-dimensional latent subspace. It also provides
a low-dimensional representation of the clustered data. A sparse version of Fisher-EM
algorithm is also provided.
Author: Charles Bouveyron, Camille Brunet & Nicolas Jouvin.
Maintainer: Charles Bouveyron <charles.bouveyron@gmail.com>
Diff between FisherEM versions 1.5.2 dated 2020-07-22 and 1.6 dated 2020-09-28
DESCRIPTION | 14 +++++++++----- MD5 | 29 +++++++++++++++++++++++++---- NAMESPACE | 6 ++++++ R/bfem.R |only R/bfem.criteria.R |only R/bfem.elbo.R |only R/bfem.emp.bayes.R |only R/bfem.main.R |only R/bfem.mstep.R |only R/bfem.vestep.R |only R/fem.R | 2 +- R/plot.bfem.R |only R/simu_bfem.R |only man/bfem.Rd |only man/fem.Rd | 6 +++--- man/figures |only man/plot.bfem.Rd |only man/simu_bfem.Rd |only tests |only 19 files changed, 44 insertions(+), 13 deletions(-)
Title: Working with Audio and Video in R
Description: Bindings to 'FFmpeg' <http://www.ffmpeg.org/> AV library for working with
audio and video in R. Generates high quality video from images or R graphics with
custom audio. Also offers high performance tools for reading raw audio, creating
'spectrograms', and converting between countless audio / video formats. This package
interfaces directly to the C API and does not require any command line utilities.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between av versions 0.5.0 dated 2020-01-29 and 0.5.1 dated 2020-09-28
DESCRIPTION | 12 +++++++----- MD5 | 12 ++++++------ NAMESPACE | 4 ++++ NEWS | 4 ++++ R/fft.R | 16 +++++++++------- configure | 2 +- tests/testthat.R | 3 ++- 7 files changed, 33 insertions(+), 20 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-14 0.1.0
Title: Tensors and Neural Networks with 'GPU' Acceleration
Description: Provides functionality to define and train neural networks similar to
'PyTorch' by Paszke et al (2019) <arXiv:1912.01703> but written entirely in R
using the 'libtorch' library. Also supports low-level tensor operations and
'GPU' acceleration.
Author: Daniel Falbel [aut, cre, cph],
Javier Luraschi [aut, cph],
Dmitriy Selivanov [ctb],
Athos Damiani [ctb],
RStudio [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between torch versions 0.0.3 dated 2020-09-18 and 0.1.0 dated 2020-09-28
DESCRIPTION | 18 MD5 | 80 + NAMESPACE | 32 NEWS.md | 8 R/conditions.R | 4 R/dtype.R | 2 R/gen-namespace.R | 8 R/install.R | 2 R/nn-distance.R |only R/nn-loss.R | 1184 ++++++++++++++++++++++++++- R/nn-pooling.R | 22 R/nn.R | 42 R/nnf-loss.R | 51 - R/optim-lr_scheduler.R |only R/optim.R | 8 R/wrapers.R | 12 build/vignette.rds |binary inst/doc/serialization.R |only inst/doc/serialization.Rmd |only inst/doc/serialization.html |only man/figures/torch-full.png |only man/figures/torch.png |binary man/is_nn_buffer.Rd |only man/is_nn_module.Rd |only man/is_nn_parameter.Rd |only man/is_optimizer.Rd |only man/lr_lambda.Rd |only man/lr_multiplicative.Rd |only man/lr_one_cycle.Rd |only man/lr_scheduler.Rd |only man/lr_step.Rd |only man/nn_bce_with_logits_loss.Rd |only man/nn_buffer.Rd |only man/nn_cosine_embedding_loss.Rd |only man/nn_ctc_loss.Rd |only man/nn_fractional_max_pool2d.Rd | 6 man/nn_hinge_embedding_loss.Rd |only man/nn_kl_div_loss.Rd |only man/nn_l1_loss.Rd |only man/nn_margin_ranking_loss.Rd |only man/nn_mse_loss.Rd |only man/nn_multi_margin_loss.Rd |only man/nn_multilabel_margin_loss.Rd |only man/nn_multilabel_soft_margin_loss.Rd |only man/nn_nll_loss.Rd |only man/nn_pairwise_distance.Rd |only man/nn_parameter.Rd |only man/nn_poisson_nll_loss.Rd |only man/nn_smooth_l1_loss.Rd |only man/nn_soft_margin_loss.Rd |only man/nn_triplet_margin_loss.Rd |only man/nn_triplet_margin_with_distance_loss.Rd |only man/nnf_triplet_margin_with_distance_loss.Rd |only tests/testthat/test-nn-loss.R | 98 ++ tests/testthat/test-nn.R | 49 + tests/testthat/test-optim-lr_scheduler.R |only tests/testthat/test-wrapers.R | 15 tools/torchgen/R/r.R | 4 vignettes/model.pt |only vignettes/serialization.Rmd |only vignettes/tensor.pt |only 61 files changed, 1572 insertions(+), 73 deletions(-)
Title: Factor Big Integers with the Quadratic Sieve
Description: Features the multiple polynomial quadratic sieve (MPQS) algorithm
for factoring large integers and a vectorized factoring function that
returns the complete factorization of an integer. The MPQS is based off of
the seminal work of Carl Pomerance (1984) <doi:10.1007/3-540-39757-4_17>
along with the modification of multiple polynomials introduced by Peter
Montgomery and J. Davis as outlined by Robert D. Silverman (1987)
<doi:10.1090/S0025-5718-1987-0866119-8>. Utilizes the C library
GMP (GNU Multiple Precision Arithmetic). The Pollard's rho algorithm for
factoring smaller numbers is the same algorithm used by the factorize
function in the 'gmp' package.
Author: Joseph Wood [aut, cre],
Free Software Foundation, Inc. [cph],
Mike Tryczak [ctb]
Maintainer: Joseph Wood <jwood000@gmail.com>
Diff between RcppBigIntAlgos versions 0.2.4 dated 2020-06-22 and 0.3.1 dated 2020-09-28
RcppBigIntAlgos-0.2.4/RcppBigIntAlgos/inst/include/GrowMPZArray.h |only RcppBigIntAlgos-0.2.4/RcppBigIntAlgos/src/CleanConvert.cc |only RcppBigIntAlgos-0.2.4/RcppBigIntAlgos/src/FactorUtils.cc |only RcppBigIntAlgos-0.2.4/RcppBigIntAlgos/src/Factorization.cc |only RcppBigIntAlgos-0.2.4/RcppBigIntAlgos/src/GrowMPZArray.cc |only RcppBigIntAlgos-0.2.4/RcppBigIntAlgos/src/ImportExportMPZ.cc |only RcppBigIntAlgos-0.2.4/RcppBigIntAlgos/src/PollardRho.cc |only RcppBigIntAlgos-0.2.4/RcppBigIntAlgos/src/QuadraticSieve.cc |only RcppBigIntAlgos-0.2.4/RcppBigIntAlgos/src/RSAFactorUtils.cc |only RcppBigIntAlgos-0.2.4/RcppBigIntAlgos/src/RSAFactorize.cc |only RcppBigIntAlgos-0.2.4/RcppBigIntAlgos/src/ReduceMatrix.cc |only RcppBigIntAlgos-0.2.4/RcppBigIntAlgos/src/SieveUtils.cc |only RcppBigIntAlgos-0.2.4/RcppBigIntAlgos/src/SolutionSearch.cc |only RcppBigIntAlgos-0.2.4/RcppBigIntAlgos/src/TonelliShanks.cc |only RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/DESCRIPTION | 6 RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/MD5 | 70 +-- RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/NAMESPACE | 3 RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/NEWS | 13 RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/R/IntegerFactorization.R | 6 RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/R/RcppExports.R | 4 RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/README.md | 195 ++++++++-- RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/inst/include/FactorUtils.h | 4 RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/inst/include/GmpxxCopy.h |only RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/inst/include/ImportExportMPZ.h | 9 RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/inst/include/PollardRho.h | 9 RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/inst/include/Polynomial.h |only RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/inst/include/Primes.h | 2 RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/inst/include/QuadraticSieve.h | 4 RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/inst/include/RSAFactorUtils.h | 8 RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/inst/include/ReduceMatrix.h | 9 RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/inst/include/SieveUtils.h | 68 +-- RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/inst/include/SolutionSearch.h | 9 RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/inst/include/StatsUtils.h | 54 +- RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/inst/include/TonelliShanks.h | 4 RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/man/quadraticSieve.Rd | 6 RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/man/stdThreadMax.Rd |only RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/src/CleanConvert.cpp |only RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/src/FactorUtils.cpp |only RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/src/Factorization.cpp |only RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/src/ImportExportMPZ.cpp |only RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/src/PollardRho.cpp |only RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/src/Polynomial.cpp |only RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/src/QuadraticSieve.cpp |only RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/src/RSAFactorUtils.cpp |only RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/src/RSAFactorize.cpp |only RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/src/RcppExports.cpp | 9 RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/src/ReduceMatrix.cpp |only RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/src/SieveUtils.cpp |only RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/src/SolutionSearch.cpp |only RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/src/TonelliShanks.cpp |only RcppBigIntAlgos-0.3.1/RcppBigIntAlgos/tests/testthat/testQuadraticSieve.R | 32 + 51 files changed, 363 insertions(+), 161 deletions(-)
More information about RcppBigIntAlgos at CRAN
Permanent link
Title: MArginal ePIstasis Test for Regions
Description: A genetic analysis tool and variance component
model for identifying marginal epistasis between pathways
and the rest of the genome. 'MAPITR' uses as input a matrix
of genotypes, a vector of phenotypes, and a list of
pathways. 'MAPITR' then iteratively tests each pathway for
epistasis between any variants within the pathway versus
any variants remaining in the rest of the genome. 'MAPITR'
returns results in the form of p-values for every pathway
indicating whether the null model of there being no
epistatic interactions between a pathway and the rest of
the genome can be rejected.
Author: Michael Turchin [aut, cre] (<https://orcid.org/0000-0003-3569-1529>),
Gregory Darnell [aut, ctb] (<https://orcid.org/0000-0003-0425-940X>),
Lorin Crawford [aut, ctb] (<https://orcid.org/0000-0003-0178-8242>),
Sohini Ramachandran [aut] (<https://orcid.org/0000-0002-9588-7964>),
Peter Carbonetto [ctb] (<https://orcid.org/0000-0003-1144-6780>)
Maintainer: Michael Turchin <michael_turchin@brown.edu>
Diff between MAPITR versions 1.1.1 dated 2020-09-23 and 1.1.2 dated 2020-09-28
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/MAPITR.R | 15 ++++++++++----- README.md | 2 +- inst/doc/MAPITR.Intro.SimulatedData.html | 20 ++++++++++---------- man/MAPITR.Rd | 12 ++++++++---- 6 files changed, 38 insertions(+), 29 deletions(-)
Title: Tools for Highfrequency Data Analysis
Description: Provide functionality to manage, clean and match highfrequency
trades and quotes data, calculate various liquidity measures, estimate and
forecast volatility, detect price jumps and investigate microstructure noise and intraday
periodicity.
Author: Kris Boudt [aut, cre] (<https://orcid.org/0000-0002-1000-5142>),
Jonathan Cornelissen [aut],
Scott Payseur [aut],
Giang Nguyen [ctb],
Onno Kleen [aut] (<https://orcid.org/0000-0003-4731-4640>),
Emil Sjoerup [aut]
Maintainer: Kris Boudt
<kris.boudt@ugent.be>
Diff between highfrequency versions 0.7.0 dated 2020-09-15 and 0.7.0.1 dated 2020-09-28
DESCRIPTION | 8 +++--- MD5 | 26 ++++++++++---------- NAMESPACE | 1 R/data_handling.R | 3 -- R/internal.R | 39 ------------------------------ R/internal_data_handling.R | 35 ++++++++++++++++++++++++++ tests/testthat/Rplots.pdf |binary tests/testthat/tests_data_handling.R | 6 ++-- tests/testthat/tests_jump_tests.R | 8 +++--- tests/testthat/tests_leadLag.R | 13 ++++------ tests/testthat/tests_liquidity_measures.R | 4 +-- tests/testthat/tests_models.R | 4 +-- tests/testthat/tests_realized_measures.R | 23 +++++++++-------- tests/testthat/tests_spotvol_and_drift.R | 4 +-- 14 files changed, 85 insertions(+), 89 deletions(-)
Title: Inhomogeneous K- And Pair Correlation Functions Using Global
Estimators
Description: Second-order summary statistics K- and pair-correlation functions describe
interactions in point pattern data. This package provides computations to estimate those
statistics on inhomogeneous point processes, using the methods of
in T Shaw, J Møller, R Waagepetersen, 2020 <arXiv:2004.00527>.
Author: Thomas Shaw [aut, cre],
Ege Rubak [ctb],
Adrian Baddeley [ctb],
Rolf Turner [ctb]
Maintainer: Thomas Shaw <shawtr@umich.edu>
Diff between globalKinhom versions 0.1.1 dated 2020-09-25 and 0.1.2 dated 2020-09-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- build/partial.rdb |binary src/rho_rho_excess.c | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Dynamic Time Warping Algorithms
Description: A comprehensive implementation of dynamic time warping
(DTW) algorithms in R. DTW computes the optimal (least cumulative
distance) alignment between points of two time series. Common DTW
variants covered include local (slope) and global (window)
constraints, subsequence matches, arbitrary distance definitions,
normalizations, minimum variance matching, and so on. Provides
cumulative distances, alignments, specialized plot styles, etc.,
as described in Giorgino (2009) <doi:10.18637/jss.v031.i07>.
Author: Toni Giorgino [aut, cre]
Maintainer: Toni Giorgino <toni.giorgino@gmail.com>
Diff between dtw versions 1.21-3 dated 2019-09-01 and 1.22-3 dated 2020-09-28
dtw-1.21-3/dtw/src/computeCM.c |only dtw-1.21-3/dtw/src/dtw.h |only dtw-1.21-3/dtw/src/init.c |only dtw-1.21-3/dtw/src/triangleFixing.c |only dtw-1.22-3/dtw/DESCRIPTION | 24 +++++++--- dtw-1.22-3/dtw/MD5 | 62 ++++++++++++++-------------- dtw-1.22-3/dtw/R/dtw-package.R | 11 ++-- dtw-1.22-3/dtw/R/dtw.R | 39 ++++++++--------- dtw-1.22-3/dtw/R/dtwDist.R | 13 ----- dtw-1.22-3/dtw/R/mvm.R | 2 dtw-1.22-3/dtw/R/stepPattern.R | 22 ++++----- dtw-1.22-3/dtw/R/window.R | 8 +-- dtw-1.22-3/dtw/build/partial.rdb |only dtw-1.22-3/dtw/build/vignette.rds |binary dtw-1.22-3/dtw/inst/CITATION | 5 +- dtw-1.22-3/dtw/inst/ChangeLog | 9 ++++ dtw-1.22-3/dtw/inst/doc/dtw.R | 1 dtw-1.22-3/dtw/inst/doc/dtw.pdf |binary dtw-1.22-3/dtw/man/aami.Rd | 4 + dtw-1.22-3/dtw/man/dtw-package.Rd | 11 ++-- dtw-1.22-3/dtw/man/dtw.Rd | 56 +++++++++++++------------ dtw-1.22-3/dtw/man/dtwDist.Rd | 9 ---- dtw-1.22-3/dtw/man/dtwPlot.Rd | 16 ++++--- dtw-1.22-3/dtw/man/dtwPlotDensity.Rd | 15 ++++-- dtw-1.22-3/dtw/man/dtwPlotThreeWay.Rd | 25 ++++++++--- dtw-1.22-3/dtw/man/dtwPlotTwoWay.Rd | 23 ++++++++-- dtw-1.22-3/dtw/man/dtwWindowingFunctions.Rd | 12 ++--- dtw-1.22-3/dtw/man/mvm.Rd | 2 dtw-1.22-3/dtw/man/stepPattern.Rd | 32 ++++++-------- dtw-1.22-3/dtw/src/Makevars | 6 +- dtw-1.22-3/dtw/src/Makevars.win | 2 dtw-1.22-3/dtw/src/dtw_R.c |only dtw-1.22-3/dtw/src/dtw_core.c |only dtw-1.22-3/dtw/src/dtw_core.h |only dtw-1.22-3/dtw/tests/dtw_test.R | 13 ++++- dtw-1.22-3/dtw/tests/dtw_test.Rout.save | 26 ++++++++--- 36 files changed, 252 insertions(+), 196 deletions(-)
Title: Load US Census Boundary and Attribute Data as 'tidyverse' and
'sf'-Ready Data Frames
Description: An integrated R interface to the decennial US Census and American Community Survey APIs and
the US Census Bureau's geographic boundary files. Allows R users to return Census and ACS data as
tidyverse-ready data frames, and optionally returns a list-column with feature geometry for all Census
geographies.
Author: Kyle Walker [aut, cre],
Matt Herman [aut],
Kris Eberwein [ctb]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between tidycensus versions 0.10.1 dated 2020-09-27 and 0.10.2 dated 2020-09-28
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/load_data.R | 28 +++++++++++++++++----------- R/search_variables.R | 8 ++++++++ README.md | 5 +++-- 5 files changed, 36 insertions(+), 21 deletions(-)
Title: The Tidymodels Extension for Time Series Modeling
Description: The time series forecasting framework for use with the 'tidymodels' ecosystem.
Models include ARIMA, Exponential Smoothing, and additional time series models
from the 'forecast' and 'prophet' packages. Refer to "Forecasting Principles & Practice, Second edition"
(<https://otexts.com/fpp2/>).
Refer to "Prophet: forecasting at scale"
(<https://research.fb.com/blog/2017/02/prophet-forecasting-at-scale/>.).
Author: Matt Dancho [aut, cre],
Business Science [cph]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between modeltime versions 0.1.0 dated 2020-09-02 and 0.2.0 dated 2020-09-28
DESCRIPTION | 6 MD5 | 87 +++++++----- NAMESPACE | 6 NEWS.md | 34 ++++ R/data.R | 110 +++++++++++++++ R/dev-model_descriptions.R | 28 +-- R/helpers-modeltime_residuals.R |only R/helpers-modeltime_table.R |only R/modeltime-calibrate.R | 2 R/modeltime-forecast-plot.R | 4 R/modeltime-forecast.R | 5 R/modeltime-refit.R | 101 ++++---------- R/modeltime-residuals.R | 41 ----- R/modeltime-table.R | 115 ---------------- R/parsnip-arima_boost.R | 21 +- R/parsnip-arima_reg.R | 4 R/parsnip-exp_smoothing.R | 6 R/parsnip-nnetar_reg.R | 12 - R/parsnip-prophet_boost.R | 33 ++-- R/parsnip-prophet_reg.R | 44 +++++- R/utils-checks-validations.R | 4 R/utils-parsnip-helpers.R | 98 +++++++++++++ README.md | 86 ++++++++--- data/m750.rda |only data/m750_models.rda |only data/m750_splits.rda |only data/m750_training_resamples.rda |only inst/doc/extending-modeltime.html | 2 inst/doc/getting-started-with-modeltime.R | 12 - inst/doc/getting-started-with-modeltime.Rmd | 33 ++-- inst/doc/getting-started-with-modeltime.html | 103 +++++++------- man/add_modeltime_model.Rd |only man/arima_boost.Rd | 19 +- man/arima_reg.Rd | 4 man/combine_modeltime_tables.Rd | 2 man/exp_smoothing.Rd | 4 man/figures/logo.png |only man/m750.Rd |only man/m750_models.Rd |only man/m750_splits.Rd |only man/m750_training_resamples.Rd |only man/nnetar_reg.Rd | 12 - man/pluck_modeltime_model.Rd |only man/prophet_boost.Rd | 37 ++--- man/prophet_fit_impl.Rd | 15 ++ man/prophet_reg.Rd | 32 +++- man/pull_modeltime_residuals.Rd | 2 man/pull_parsnip_preprocessor.Rd |only man/update_model_description.Rd | 8 - tests/testthat/test-helpers-pull_parsnip_preprocessor.R |only tests/testthat/test-helpers-update-modeltime-tables.R | 24 ++- vignettes/getting-started-with-modeltime.Rmd | 33 ++-- 52 files changed, 702 insertions(+), 487 deletions(-)
More information about ConcordanceTest at CRAN
Permanent link
Title: 'Rcpp' Interface to 'PostgreSQL'
Description: Fully 'DBI'-compliant 'Rcpp'-backed interface to
'PostgreSQL' <https://www.postgresql.org/>, an open-source relational
database.
Author: Hadley Wickham [aut],
Jeroen Ooms [aut],
Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
RStudio [cph],
R Consortium [fnd],
Tomoaki Nishiyama [ctb] (Code for encoding vectors into strings derived
from RPostgreSQL)
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between RPostgres versions 1.2.0 dated 2019-12-18 and 1.2.1 dated 2020-09-28
RPostgres-1.2.0/RPostgres/man/dbConnect-PqDriver-method.Rd |only RPostgres-1.2.1/RPostgres/DESCRIPTION | 14 +- RPostgres-1.2.1/RPostgres/MD5 | 24 ++- RPostgres-1.2.1/RPostgres/NAMESPACE | 3 RPostgres-1.2.1/RPostgres/NEWS.md | 9 + RPostgres-1.2.1/RPostgres/R/PqConnection.R | 25 ++-- RPostgres-1.2.1/RPostgres/R/PqDriver.R | 6 RPostgres-1.2.1/RPostgres/R/PqResult.R | 2 RPostgres-1.2.1/RPostgres/R/Redshift.R |only RPostgres-1.2.1/RPostgres/man/Postgres.Rd | 79 ++++++++++++- RPostgres-1.2.1/RPostgres/man/Redshift.Rd |only RPostgres-1.2.1/RPostgres/man/postgresHasDefault.Rd | 2 RPostgres-1.2.1/RPostgres/src/Makevars.win | 4 RPostgres-1.2.1/RPostgres/tests/testthat/helper-DBItest.R | 3 RPostgres-1.2.1/RPostgres/tests/testthat/test-Redshift.R |only 15 files changed, 129 insertions(+), 42 deletions(-)
Title: A Collection of Disease Outbreak Data
Description: Empirical or simulated disease outbreak data, provided either as
RData or as text files.
Author: Thibaut Jombart [aut],
Simon Frost [aut],
Pierre Nouvellet [aut],
Finlay Campbell [aut, cre],
Bertrand Sudre [aut],
Sang Woo Park [ctb],
Juliet R.C. Pulliam [ctb],
Jakob Schumacher [ctb],
Eric Brown [ctb]
Maintainer: Finlay Campbell <finlaycampbell93@gmail.com>
Diff between outbreaks versions 1.5.0 dated 2019-01-21 and 1.9.0 dated 2020-09-28
DESCRIPTION | 20 +-- MD5 | 68 ++++++---- NEWS.md | 44 ++++++ R/covid19_england_nhscalls_2020.R |only R/dengue_fais_2011.R | 2 R/dengue_yap_2011.R | 2 R/ebola_sierraleone_2014.R |only R/fluH7N9_china_2013.R | 2 R/influenza_england_1978_school.R | 2 R/norovirus_derbyshire_2001_school.R | 2 R/sarscov2_who_2019.R |only R/varicella_sim_berlin.R |only R/zika_girardot_2015.R | 6 R/zika_sanandres_2015.R | 4 R/zika_yap_2007.R | 2 README.md | 202 ++++++++++++++++--------------- data/covid19_england_nhscalls_2020.RData |only data/ebola_sierraleone_2014.RData |only data/sarscov2_who_2019.RData |only data/varicella_sim_berlin.RData |only man/covid19_england_nhscalls_2020.Rd |only man/dengue_fais_2011.Rd | 8 - man/dengue_yap_2011.Rd | 8 - man/ebola_kikwit_1995.Rd | 6 man/ebola_sierraleone_2014.Rd |only man/ebola_sim.Rd | 6 man/fluH7N9_china_2013.Rd | 6 man/influenza_england_1978_school.Rd | 8 - man/measles_hagelloch_1861.Rd | 6 man/mers_korea_2015.Rd | 6 man/nipah_malaysia.Rd | 6 man/norovirus_derbyshire_2001_school.Rd | 8 - man/rabies_car_2003.Rd | 6 man/s_enteritidis_pt59.Rd | 4 man/sars_canada_2003.Rd | 6 man/sarscov2_who_2019.Rd |only man/smallpox_abakaliki_1967.Rd | 6 man/varicella_sim_berlin.Rd |only man/zika_girardot_2015.Rd | 12 + man/zika_sanandres_2015.Rd | 10 - man/zika_yap_2007.Rd | 8 - 41 files changed, 289 insertions(+), 187 deletions(-)
Title: Loading NONMEM Output Files with Functions for Visual Predictive
Checks (VPC) and Goodness of Fit (GOF) Plots
Description: Loading NONMEM (NONlinear Mixed-Effect Modeling, <http://www.iconplc.com/innovation/nonmem/>) and PSN (Perl-speaks-NONMEM, <https://uupharmacometrics.github.io/PsN/>) output files to extract parameter estimates, provide visual predictive check (VPC) and goodness of fit (GOF) plots, and simulate with parameter uncertainty.
Author: Magnus Astrand
Maintainer: Magnus Astrand <magnus.astrand@astrazeneca.com>
Diff between nonmem2R versions 0.2.1 dated 2019-02-18 and 0.2.2 dated 2020-09-28
nonmem2R-0.2.1/nonmem2R/R/vpcfig2.R |only nonmem2R-0.2.2/nonmem2R/DESCRIPTION | 8 +-- nonmem2R-0.2.2/nonmem2R/MD5 | 30 +++++++----- nonmem2R-0.2.2/nonmem2R/NAMESPACE | 4 + nonmem2R-0.2.2/nonmem2R/NEWS | 17 ++++++ nonmem2R-0.2.2/nonmem2R/R/04_GOFs.R | 54 ++++++++++++++++++---- nonmem2R-0.2.2/nonmem2R/R/GOF.control.R | 2 nonmem2R-0.2.2/nonmem2R/R/LoadNonmemOutput.R | 19 ++++++- nonmem2R-0.2.2/nonmem2R/R/vpcfig2_v2.R |only nonmem2R-0.2.2/nonmem2R/build/vignette.rds |binary nonmem2R-0.2.2/nonmem2R/inst/doc/GOFvignette.html | 42 +++++++++-------- nonmem2R-0.2.2/nonmem2R/inst/doc/VPCvignette.R |only nonmem2R-0.2.2/nonmem2R/inst/doc/VPCvignette.Rmd |only nonmem2R-0.2.2/nonmem2R/inst/doc/VPCvignette.html |only nonmem2R-0.2.2/nonmem2R/inst/extdata/vpc001 |only nonmem2R-0.2.2/nonmem2R/man/basic.eta.GOF.Rd | 8 ++- nonmem2R-0.2.2/nonmem2R/man/eta.cov.GOF.Rd | 32 ++++++------- nonmem2R-0.2.2/nonmem2R/man/vpcfig2.Rd | 12 ++++ nonmem2R-0.2.2/nonmem2R/vignettes/VPCvignette.Rmd |only 19 files changed, 162 insertions(+), 66 deletions(-)
Title: Build MultiClass Pair-Based Classifiers using TSPs or RF
Description: A toolbox to train a single sample classifier that uses in-sample feature relationships. The relationships are represented as feature1 < feature2 (e.g. gene1 < gene2). We provide two options to go with. First is based on 'switchBox' package which uses Top-score pairs algorithm. Second is a novel implementation based on random forest algorithm. For simple problems we recommend to use one-vs-rest using TSP option due to its simplicity and for being easy to interpret. For complex problems RF performs better. Both lines filter the features first then combine the filtered features to make the list of all the possible rules (i.e. rule1: feature1 < feature2, rule2: feature1 < feature3, etc...). Then the list of rules will be filtered and the most important and informative rules will be kept. The informative rules will be assembled in an one-vs-rest model or in an RF model. We provide a detailed description with each function in this package to explain the filtration and training methodology in each line.
Author: Nour-al-dain Marzouka
Maintainer: Nour-al-dain Marzouka <Nour-al-dain.Marzouka@med.lu.se>
Diff between multiclassPairs versions 0.1.6 dated 2020-09-10 and 0.2.0 dated 2020-09-28
DESCRIPTION | 13 MD5 | 27 - NAMESPACE | 4 NEWS.md |only R/functions.R | 866 ++++++++++++++++++++++++++++++++++++----- man/filter_genes_TSP.Rd | 48 +- man/optimize_RF.Rd |only man/plot_binary_RF.Rd | 154 +++++-- man/plot_binary_TSP.Rd | 31 - man/predict_RF.Rd | 129 ++++-- man/predict_one_vs_rest_TSP.Rd | 46 +- man/sort_genes_RF.Rd | 109 ++++- man/sort_rules_RF.Rd | 120 ++++- man/summary_genes_RF.Rd |only man/train_RF.Rd | 124 ++++- man/train_one_vs_rest_TSP.Rd | 46 +- 16 files changed, 1362 insertions(+), 355 deletions(-)
More information about multiclassPairs at CRAN
Permanent link
Title: ICES Vocabularies Database Web Services
Description: R interface to access the RECO POX web services of the ICES
(International Council for the Exploration of the Sea) Vocabularies database
<https://vocab.ices.dk/services/POX.aspx>.
Author: Colin Millar [aut, cre],
Arni Magnusson [aut]
Maintainer: Colin Millar <colin.millar@ices.dk>
Diff between icesVocab versions 1.1.7 dated 2020-09-18 and 1.1.8 dated 2020-09-28
DESCRIPTION | 10 +-- MD5 | 16 ++-- NAMESPACE | 9 -- NEWS.md | 3 R/findAphia.R | 15 ++-- R/getCodeDetail.R | 8 +- R/getCodeList.R | 8 +- R/getCodeTypeList.R | 4 - R/utilities.R | 171 +++++++++++++++++++--------------------------------- 9 files changed, 103 insertions(+), 141 deletions(-)
Title: Mock the Unix Make Utility
Description: Use R as a minimal build system. This might come in
handy if you are developing R packages and can not use a proper build
system. Stay away if you can (use a proper build system).
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between fakemake versions 1.7.2 dated 2020-09-24 and 1.8.0 dated 2020-09-28
fakemake-1.7.2/fakemake/man/check_archive.Rd |only fakemake-1.7.2/fakemake/man/check_archive_as_cran.Rd |only fakemake-1.7.2/fakemake/man/get_pkg_archive_path.Rd |only fakemake-1.8.0/fakemake/DESCRIPTION | 10 fakemake-1.8.0/fakemake/MD5 | 41 +-- fakemake-1.8.0/fakemake/NAMESPACE | 3 fakemake-1.8.0/fakemake/NEWS.md | 6 fakemake-1.8.0/fakemake/R/main.R | 9 fakemake-1.8.0/fakemake/R/package_makelist.R | 5 fakemake-1.8.0/fakemake/R/tools.R | 81 ------- fakemake-1.8.0/fakemake/inst/doc/An_Introduction_to_fakemake.Rmd | 4 fakemake-1.8.0/fakemake/inst/doc/An_Introduction_to_fakemake.html | 34 +- fakemake-1.8.0/fakemake/inst/doc/Building_Packages.R | 2 fakemake-1.8.0/fakemake/inst/doc/Building_Packages.Rmd | 6 fakemake-1.8.0/fakemake/inst/doc/Building_Packages.html | 115 +++------- fakemake-1.8.0/fakemake/inst/runit_tests/runit-check_makelist.R | 3 fakemake-1.8.0/fakemake/inst/runit_tests/runit-makelists.R | 10 fakemake-1.8.0/fakemake/inst/runit_tests/runit-misc.R | 10 fakemake-1.8.0/fakemake/inst/runit_tests/runit-xmake.R | 7 fakemake-1.8.0/fakemake/man/provide_make_list.Rd | 2 fakemake-1.8.0/fakemake/tests/runit.R | 1 fakemake-1.8.0/fakemake/vignettes/An_Introduction_to_fakemake.Rmd | 4 fakemake-1.8.0/fakemake/vignettes/Building_Packages.Rmd | 6 23 files changed, 124 insertions(+), 235 deletions(-)
Title: Comprehensive Science Mapping Analysis
Description: Tool for quantitative research in scientometrics and bibliometrics.
It provides various routines for importing bibliographic data from 'SCOPUS' (<https://scopus.com>),
'Clarivate Analytics Web of Science' (<https://www.webofknowledge.com/>), 'Digital Science Dimensions'
(<https://www.dimensions.ai/>), 'Cochrane Library' (<https://www.cochranelibrary.com/>)
and 'PubMed' (<https://pubmed.ncbi.nlm.nih.gov/>) databases, performing bibliometric analysis
and building networks for co-citation, coupling, scientific collaboration and co-word analysis.
Author: Massimo Aria [cre, aut],
Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between bibliometrix versions 3.0.2 dated 2020-06-17 and 3.0.3 dated 2020-09-28
DESCRIPTION | 15 MD5 | 94 ++--- NEWS | 12 R/biblio.R | 24 - R/biblioAnalysis.R | 459 ++++++++++++++-------------- R/biblio_df.R | 58 +-- R/bradford.R | 2 R/cocMatrix.R | 354 ++++++++++----------- R/convert2df.R | 4 R/garfield.R | 52 +-- R/histNetwork.R | 9 R/histPlot.R | 321 ++++++++++--------- R/isiCollection.R | 56 +-- R/management.R | 154 ++++----- R/metaTagExtraction.R | 11 R/net2VOSviewer.R | 128 +++---- R/plot.bibliometrix.R | 388 +++++++++++------------ R/readFiles.R | 84 ++--- R/rpys.R | 13 R/scientometrics.R | 58 +-- R/scientometrics_text.R | 24 - R/scopusCollection.R | 54 +-- build/partial.rdb |binary inst/biblioshiny/server.R | 112 ++++-- inst/biblioshiny/ui.R | 62 +-- inst/doc/Data-Importing-and-Converting.Rmd | 4 inst/doc/Data-Importing-and-Converting.html | 8 inst/doc/bibliometrix-vignette.Rmd | 22 - inst/doc/bibliometrix-vignette.html | 297 ++++++++---------- man/biblio.Rd | 4 man/biblioAnalysis.Rd | 4 man/biblio_df.Rd | 4 man/bibliometrix-package.Rd | 384 +++++++++++------------ man/bradford.Rd | 2 man/cocMatrix.Rd | 2 man/convert2df.Rd | 2 man/garfield.Rd | 4 man/histPlot.Rd | 15 man/isiCollection.Rd | 4 man/management.Rd | 4 man/metaTagExtraction.Rd | 4 man/net2VOSviewer.Rd | 4 man/readFiles.Rd | 2 man/scientometrics.Rd | 4 man/scientometrics_text.Rd | 4 man/scopusCollection.Rd | 4 vignettes/Data-Importing-and-Converting.Rmd | 4 vignettes/bibliometrix-vignette.Rmd | 22 - 48 files changed, 1700 insertions(+), 1656 deletions(-)
Title: Create, Build and Maintain Packages
Description: Helper functions for package creation, building and
maintenance. Designed to work with a build system such as 'GNU make' or
package 'fakemake' to help you to conditionally work through the stages of
package development (such as spell checking, linting, testing, before
building and checking a package).
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between packager versions 1.4.0 dated 2020-08-24 and 1.5.0 dated 2020-09-28
DESCRIPTION | 6 - MD5 | 26 ++-- NEWS.md | 9 + R/checks.R | 4 R/cran_comments.R | 2 R/gitlab.R | 2 R/makelist.R | 4 R/rcmdcheck.R | 11 + inst/doc/An_Introduction_to_packager.html | 179 ++++++++++++++---------------- inst/templates/dot_gitlab-ci.yml | 34 ++++- man/check_archive.Rd | 4 man/get_package_makelist.Rd | 2 man/provide_cran_comments.Rd | 2 man/rcmdcheck_and_log.Rd | 5 14 files changed, 157 insertions(+), 133 deletions(-)
Title: Design Experiments for Batches
Description: Distributes samples in batches while making batches homogeneous
according to their description. Allows for an arbitrary number of variables,
both numeric and categorical. For quality control it provides functions to
subset a representative sample.
Author: Lluís Revilla Sancho [aut, cre]
(<https://orcid.org/0000-0001-9747-2570>)
Maintainer: Lluís Revilla Sancho <lluis.revilla@gmail.com>
Diff between experDesign versions 0.0.2 dated 2020-09-08 and 0.0.4 dated 2020-09-28
DESCRIPTION | 9 MD5 | 82 ++--- NAMESPACE | 1 NEWS.md | 7 R/QC.R | 14 R/designer.R | 27 + R/entropy.R | 4 R/evaluate.R | 22 - R/evaluate_category.R | 20 - R/evaluate_num.R | 22 + R/experDesign-package.R | 4 R/indexing.R | 35 +- R/optimum.R | 12 R/reporting.R | 29 + R/spatial.R |only R/utils.R | 34 +- README.md | 53 +-- build/vignette.rds |binary inst/doc/experdesign.R | 20 - inst/doc/experdesign.Rmd | 53 ++- inst/doc/experdesign.html | 531 +++------------------------------ man/batch_names.Rd | 4 man/check_index.Rd | 16 man/create_subset.Rd | 15 man/design.Rd | 21 - man/distribution.Rd | 19 - man/evaluate_entropy.Rd | 7 man/evaluate_independence.Rd | 15 man/evaluate_index.Rd | 14 man/evaluate_mad.Rd | 11 man/evaluate_mean.Rd | 7 man/evaluate_orig.Rd | 4 man/evaluate_sd.Rd | 7 man/experDesign-package.Rd | 4 man/extreme_cases.Rd | 6 man/inspect.Rd | 12 man/optimum.Rd | 12 man/replicates.Rd | 11 man/spatial.Rd |only man/use_index.Rd | 4 tests/testthat/test-distribution.R |only tests/testthat/test-evaluate_entropy.R |only tests/testthat/test-inspect.R |only tests/testthat/test-spatial.R |only vignettes/experdesign.Rmd | 53 ++- 45 files changed, 517 insertions(+), 704 deletions(-)
Title: Optimum Threshold Estimation
Description: Functions that provide point and interval estimations of optimum thresholds for continuous diagnostic tests. The methodology used is based on minimizing an overall cost function in the two- and three-state settings. The package also provides functions for sample size determination and estimation of diagnostic accuracy measures. It also includes graphical tools.
Author: Sara Perez-Jaume, Natalia Pallares, Konstantina Skaltsa
Maintainer: Sara Perez-Jaume <spjaume@gmail.com>
Diff between ThresholdROC versions 2.8.2 dated 2020-03-03 and 2.8.3 dated 2020-09-28
ThresholdROC-2.8.2/ThresholdROC/data/AD.txt.gz |only ThresholdROC-2.8.2/ThresholdROC/data/chemo.txt.gz |only ThresholdROC-2.8.3/ThresholdROC/DESCRIPTION | 8 ++++---- ThresholdROC-2.8.3/ThresholdROC/MD5 | 10 +++++----- ThresholdROC-2.8.3/ThresholdROC/data/AD.txt |only ThresholdROC-2.8.3/ThresholdROC/data/chemo.txt |only ThresholdROC-2.8.3/ThresholdROC/man/SS.Rd | 4 ++-- ThresholdROC-2.8.3/ThresholdROC/man/ThresholdROC-package.Rd | 4 ++-- 8 files changed, 13 insertions(+), 13 deletions(-)
Title: Survival Analysis
Description: Contains the core survival analysis routines, including
definition of Surv objects,
Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models,
and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre],
Thomas Lumley [ctb, trl] (original S->R port and R maintainer until
2009),
Atkinson Elizabeth [ctb],
Crowson Cynthia [ctb]
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>
Diff between survival versions 3.2-3 dated 2020-06-13 and 3.2-7 dated 2020-09-28
survival-3.2-3/survival/src/dcount.c |only survival-3.2-3/survival/tests/dcount.R |only survival-3.2-3/survival/tests/nafld.R |only survival-3.2-3/survival/tests/tmerge.Rout.save.orig |only survival-3.2-7/survival/DESCRIPTION | 9 survival-3.2-7/survival/MD5 | 181 +- survival-3.2-7/survival/NAMESPACE | 2 survival-3.2-7/survival/R/cch.R | 4 survival-3.2-7/survival/R/concordance.R | 5 survival-3.2-7/survival/R/coxph.R | 4 survival-3.2-7/survival/R/coxph.detail.R | 16 survival-3.2-7/survival/R/finegray.R | 13 survival-3.2-7/survival/R/model.matrix.coxph.R | 4 survival-3.2-7/survival/R/predict.coxph.R | 12 survival-3.2-7/survival/R/predict.coxphms.R |only survival-3.2-7/survival/R/print.survcheck.R | 4 survival-3.2-7/survival/R/print.survfit.R | 2 survival-3.2-7/survival/R/residuals.coxph.R | 2 survival-3.2-7/survival/R/royston.R |only survival-3.2-7/survival/R/rttright.R |only survival-3.2-7/survival/R/summary.coxph.penal.R | 3 survival-3.2-7/survival/R/survcheck.R | 2 survival-3.2-7/survival/R/survexpm.R | 5 survival-3.2-7/survival/R/survfit.R | 276 +-- survival-3.2-7/survival/R/survfit.coxph.R | 6 survival-3.2-7/survival/R/survfit.coxphms.R | 10 survival-3.2-7/survival/R/survfitCI.R | 1 survival-3.2-7/survival/R/survfitms.R | 12 survival-3.2-7/survival/R/xtras.R | 4 survival-3.2-7/survival/R/yates.R | 50 survival-3.2-7/survival/data/gbsg.rda |only survival-3.2-7/survival/data/rotterdam.rda |only survival-3.2-7/survival/inst/NEWS.Rd | 47 survival-3.2-7/survival/inst/doc/adjcurve.pdf |binary survival-3.2-7/survival/inst/doc/approximate.pdf |binary survival-3.2-7/survival/inst/doc/compete.pdf |binary survival-3.2-7/survival/inst/doc/concordance.pdf |binary survival-3.2-7/survival/inst/doc/multi.pdf |binary survival-3.2-7/survival/inst/doc/other.pdf |binary survival-3.2-7/survival/inst/doc/population.pdf |binary survival-3.2-7/survival/inst/doc/splines.pdf |binary survival-3.2-7/survival/inst/doc/survival.pdf |binary survival-3.2-7/survival/inst/doc/tiedtimes.pdf |binary survival-3.2-7/survival/inst/doc/timedep.pdf |binary survival-3.2-7/survival/inst/doc/validate.pdf |binary survival-3.2-7/survival/man/Surv.Rd | 2 survival-3.2-7/survival/man/cch.Rd | 2 survival-3.2-7/survival/man/coxph.detail.Rd | 12 survival-3.2-7/survival/man/finegray.Rd | 8 survival-3.2-7/survival/man/gbsg.Rd |only survival-3.2-7/survival/man/heart.Rd | 4 survival-3.2-7/survival/man/logan.Rd | 2 survival-3.2-7/survival/man/predict.coxph.Rd | 26 survival-3.2-7/survival/man/residuals.coxph.Rd | 4 survival-3.2-7/survival/man/rotterdam.Rd |only survival-3.2-7/survival/man/royston.Rd |only survival-3.2-7/survival/man/rttright.Rd |only survival-3.2-7/survival/man/summary.survfit.Rd | 1 survival-3.2-7/survival/man/survfit.formula.Rd | 7 survival-3.2-7/survival/noweb/Makefile | 2 survival-3.2-7/survival/noweb/agreg.Rnw | 68 survival-3.2-7/survival/noweb/cch.Rnw |only survival-3.2-7/survival/noweb/code.nw | 1483 +++++++++++++++--- survival-3.2-7/survival/noweb/code.toc | 42 survival-3.2-7/survival/noweb/concordance.Rnw | 9 survival-3.2-7/survival/noweb/coxph.Rnw | 4 survival-3.2-7/survival/noweb/coxph.Rnw.orig |only survival-3.2-7/survival/noweb/coxsurv.Rnw | 6 survival-3.2-7/survival/noweb/coxsurv2.Rnw | 17 survival-3.2-7/survival/noweb/coxsurv3.Rnw | 10 survival-3.2-7/survival/noweb/finegray.Rnw | 13 survival-3.2-7/survival/noweb/finegray.old |only survival-3.2-7/survival/noweb/finegray.xxx |only survival-3.2-7/survival/noweb/msurv.nw | 28 survival-3.2-7/survival/noweb/msurv.nw.orig |only survival-3.2-7/survival/noweb/msurvnew |only survival-3.2-7/survival/noweb/predict.coxph.Rnw | 51 survival-3.2-7/survival/noweb/residuals.survfit.2 |only survival-3.2-7/survival/noweb/residuals.survfit.Rnw |only survival-3.2-7/survival/noweb/survexpm.Rnw | 5 survival-3.2-7/survival/noweb/survfit.Rnw | 207 +- survival-3.2-7/survival/noweb/survfitCI.Rnw | 1 survival-3.2-7/survival/noweb/survfitKM.Rnw | 4 survival-3.2-7/survival/noweb/survfitms.Rnw | 6 survival-3.2-7/survival/noweb/tmerge.Rnw.orig |only survival-3.2-7/survival/noweb/yates.Rnw | 27 survival-3.2-7/survival/noweb/yates2.Rnw | 26 survival-3.2-7/survival/src/agfit4.c | 189 -- survival-3.2-7/survival/src/collapse.c |only survival-3.2-7/survival/src/init.c | 2 survival-3.2-7/survival/src/survfitci.c | 14 survival-3.2-7/survival/src/survfitresid.c |only survival-3.2-7/survival/src/survproto.h | 6 survival-3.2-7/survival/src/zph2.c | 46 survival-3.2-7/survival/tests/coxsurv2.Rout.save.orig |only survival-3.2-7/survival/tests/fr_kidney.Rout.save | 8 survival-3.2-7/survival/tests/mstate.R | 26 survival-3.2-7/survival/tests/mstate.Rout.save | 34 survival-3.2-7/survival/tests/plot1.pdf |only survival-3.2-7/survival/tests/pspline.R | 11 survival-3.2-7/survival/tests/pspline.Rout.save | 17 survival-3.2-7/survival/tests/residsf.Rout.save |only survival-3.2-7/survival/tests/royston.R |only survival-3.2-7/survival/tests/royston.Rout.save |only survival-3.2-7/survival/tests/rttright.R |only survival-3.2-7/survival/tests/rttright.Rout.save |only survival-3.2-7/survival/tests/survfit1.Rout.save | 16 survival-3.2-7/survival/vignettes/.install_extras |only 108 files changed, 2128 insertions(+), 992 deletions(-)
Title: Quantile Regression
Description: Estimation and inference methods for models of conditional quantiles:
Linear and nonlinear parametric and non-parametric (total variation penalized) models
for conditional quantiles of a univariate response and several methods for handling
censored survival data. Portfolio selection methods based on expected shortfall
risk are also now included.
Author: Roger Koenker [cre, aut],
Stephen Portnoy [ctb] (Contributions to Censored QR code),
Pin Tian Ng [ctb] (Contributions to Sparse QR code),
Blaise Melly [ctb] (Contributions to preprocessing code),
Achim Zeileis [ctb] (Contributions to dynrq code essentially identical
to his dynlm code),
Philip Grosjean [ctb] (Contributions to nlrq code),
Cleve Moler [ctb] (author of several linpack routines),
Brian D Ripley [trl, ctb] (Initial (2001) R port from S (to my
everlasting shame -- how could I have been so slow to adopt R!) and
for numerous other suggestions and useful advice)
Maintainer: Roger Koenker <rkoenker@illinois.edu>
Diff between quantreg versions 5.67 dated 2020-09-09 and 5.70 dated 2020-09-28
DESCRIPTION | 6 +- MD5 | 17 +++--- NAMESPACE | 2 R/rqss.R | 153 +++++++++++++++++++++++++++++++++++-------------------- demo/00Index | 1 demo/rqsslasso.R | 2 demo/subset.R |only inst/ChangeLog | 16 +++++ man/qss.Rd | 17 +++++- man/rqss.Rd | 10 +++ 10 files changed, 153 insertions(+), 71 deletions(-)
Title: Data Base Backend for 'mlr3'
Description: Extends the 'mlr3' package with a backend to
transparently work with data bases. Internally relies on the
abstraction of package 'dbplyr' to interact with one of the many
supported data base management systems (DBMS).
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3db versions 0.1.5 dated 2020-02-19 and 0.2.0 dated 2020-09-28
DESCRIPTION | 10 - MD5 | 26 +- NAMESPACE | 1 NEWS.md | 6 R/DataBackendDplyr.R | 160 +++++++++++------ R/as_sqlite_backend.R | 20 +- R/zzz.R | 6 README.md | 13 - man/DataBackendDplyr.Rd | 285 +++++++++++++++++++++++++------- tests/testthat/helper.R | 21 ++ tests/testthat/test_as_sqlite_backend.R | 9 + tests/testthat/test_basic_ops.R | 4 tests/testthat/test_reconnect.R | 15 - tests/testthat/test_train_predict.R | 5 14 files changed, 421 insertions(+), 160 deletions(-)
Title: Cox Regression with Firth's Penalized Likelihood
Description: Implements Firth's penalized maximum likelihood bias reduction method for Cox regression
which has been shown to provide a solution in case of monotone likelihood (nonconvergence of likelihood function), see
Heinze and Schemper (2001) and Heinze and Dunkler (2008).
The program fits profile penalized likelihood confidence intervals which were proved to outperform
Wald confidence intervals.
Author: Georg Heinze [aut, cre],
Meinhard Ploner [aut],
Lena Jiricka [aut]
Maintainer: Georg Heinze <georg.heinze@meduniwien.ac.at>
Diff between coxphf versions 1.13 dated 2018-03-03 and 1.13.1 dated 2020-09-28
DESCRIPTION | 23 + MD5 | 27 +- NAMESPACE | 44 ++- R/breast.R |only R/coxphf-package.R |only R/coxphf.R | 668 ++++++++++++++++----------------------------------- R/coxphfplot.R |only R/coxphftest.R |only R/data.R |only R/decomposeSurv.r | 3 R/print.coxphf.R |only R/print.coxphftest.R |only R/summary.coxphf.R |only README.md |only man/breast.Rd | 41 +-- man/coxphf.rd | 247 ++++++++++-------- man/coxphfplot.Rd | 140 +++++----- man/coxphftest.Rd | 126 ++++----- src/coxphf.f90 | 4 19 files changed, 583 insertions(+), 740 deletions(-)
Title: Australian Government Bureau of Meteorology ('BOM') Data Client
Description: Provides functions to interface with Australian Government Bureau
of Meteorology ('BOM') data, fetching data and returning a data frame of
precis forecasts, historical and current weather data from stations,
agriculture bulletin data, 'BOM' 0900 or 1500 weather bulletins and
downloading and importing radar and satellite imagery files. Data (c)
Australian Government Bureau of Meteorology Creative Commons (CC)
Attribution 3.0 licence or Public Access Licence (PAL) as appropriate. See
<http://www.bom.gov.au/other/copyright.shtml> for further details.
Author: Adam H. Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>),
Jonathan Carroll [aut] (<https://orcid.org/0000-0002-1404-5264>),
James Goldie [aut] (<https://orcid.org/0000-0002-5024-6207>),
Dean Marchiori [aut],
Paul Melloy [aut] (<https://orcid.org/0000-0003-4253-7167>),
Mark Padgham [aut, rev] (<https://orcid.org/0000-0003-2172-5265>),
Hugh Parsonage [aut] (<https://orcid.org/0000-0003-4055-0835>),
Keith Pembleton [aut] (<https://orcid.org/0000-0002-1896-4516>),
James Balamuta [ctb] (<https://orcid.org/0000-0003-2826-8458>),
Brooke Anderson [rev] (<https://orcid.org/0000-0002-5012-9035>)
Maintainer: Adam H. Sparks <adamhsparks@gmail.com>
Diff between bomrang versions 0.7.0 dated 2020-01-20 and 0.7.1 dated 2020-09-28
bomrang-0.7.0/bomrang/R/bomrang.r |only bomrang-0.7.0/bomrang/R/get_historical.R |only bomrang-0.7.0/bomrang/man/bomrang.Rd |only bomrang-0.7.0/bomrang/man/get_historical.Rd |only bomrang-0.7.1/bomrang/DESCRIPTION | 92 bomrang-0.7.1/bomrang/MD5 | 142 bomrang-0.7.1/bomrang/NAMESPACE | 2 bomrang-0.7.1/bomrang/NEWS.md | 326 - bomrang-0.7.1/bomrang/R/bomrang-package.R |only bomrang-0.7.1/bomrang/R/bomrang_tbl.R | 2 bomrang-0.7.1/bomrang/R/dplyr.R | 27 bomrang-0.7.1/bomrang/R/get_ag_bulletin.R | 175 bomrang-0.7.1/bomrang/R/get_coastal_forecast.R | 266 bomrang-0.7.1/bomrang/R/get_current_weather.R | 26 bomrang-0.7.1/bomrang/R/get_historical_weather.R |only bomrang-0.7.1/bomrang/R/get_precis_forecast.R | 277 bomrang-0.7.1/bomrang/R/get_radar_imagery.R | 8 bomrang-0.7.1/bomrang/R/get_satellite_imagery.R | 6 bomrang-0.7.1/bomrang/R/get_weather_bulletins.R | 13 bomrang-0.7.1/bomrang/R/internal_functions.R | 709 -- bomrang-0.7.1/bomrang/R/manage_cached_files.R | 8 bomrang-0.7.1/bomrang/R/parse_ag_bulletin.R | 11 bomrang-0.7.1/bomrang/R/parse_coastal_forecast.R | 12 bomrang-0.7.1/bomrang/R/parse_precis_forecast.R | 12 bomrang-0.7.1/bomrang/R/sweep_for_forecast_towns.R | 6 bomrang-0.7.1/bomrang/R/sweep_for_stations.R | 12 bomrang-0.7.1/bomrang/R/update_forecast_towns.R | 20 bomrang-0.7.1/bomrang/R/update_station_locations.R | 16 bomrang-0.7.1/bomrang/R/zzz.R | 5 bomrang-0.7.1/bomrang/README.md | 58 bomrang-0.7.1/bomrang/build/vignette.rds |binary bomrang-0.7.1/bomrang/inst/doc/bomrang.Rmd | 2289 +++----- bomrang-0.7.1/bomrang/inst/doc/bomrang.html | 2848 ++++------ bomrang-0.7.1/bomrang/inst/doc/use_case.html | 172 bomrang-0.7.1/bomrang/inst/extdata/AAC_codes.rda |binary bomrang-0.7.1/bomrang/inst/extdata/JSONurl_site_list.rda |binary bomrang-0.7.1/bomrang/inst/extdata/current_stations_site_list.rda |binary bomrang-0.7.1/bomrang/inst/extdata/marine_AAC_codes.rda |binary bomrang-0.7.1/bomrang/inst/extdata/radar_locations.rda |binary bomrang-0.7.1/bomrang/inst/extdata/stations_site_list.rda |binary bomrang-0.7.1/bomrang/man/bomrang-package.Rd |only bomrang-0.7.1/bomrang/man/get_ag_bulletin.Rd | 32 bomrang-0.7.1/bomrang/man/get_available_imagery.Rd | 2 bomrang-0.7.1/bomrang/man/get_available_radar.Rd | 2 bomrang-0.7.1/bomrang/man/get_coastal_forecast.Rd | 29 bomrang-0.7.1/bomrang/man/get_current_weather.Rd | 11 bomrang-0.7.1/bomrang/man/get_historical_weather.Rd |only bomrang-0.7.1/bomrang/man/get_precis_forecast.Rd | 32 bomrang-0.7.1/bomrang/man/get_radar_imagery.Rd | 4 bomrang-0.7.1/bomrang/man/get_satellite_imagery.Rd | 10 bomrang-0.7.1/bomrang/man/get_weather_bulletin.Rd | 26 bomrang-0.7.1/bomrang/man/manage_cache.Rd | 22 bomrang-0.7.1/bomrang/man/parse_ag_bulletin.Rd | 34 bomrang-0.7.1/bomrang/man/parse_coastal_forecast.Rd | 32 bomrang-0.7.1/bomrang/man/parse_precis_forecast.Rd | 34 bomrang-0.7.1/bomrang/man/sweep_for_forecast_towns.Rd | 2 bomrang-0.7.1/bomrang/man/update_forecast_towns.Rd | 4 bomrang-0.7.1/bomrang/man/update_station_locations.Rd | 14 bomrang-0.7.1/bomrang/tests/testthat/test-bomrang_tbl.R | 5 bomrang-0.7.1/bomrang/tests/testthat/test-file_caching.R | 8 bomrang-0.7.1/bomrang/tests/testthat/test-get_ag_bulletin.R | 2 bomrang-0.7.1/bomrang/tests/testthat/test-get_coastal_forecast.R | 69 bomrang-0.7.1/bomrang/tests/testthat/test-get_current_weather.R | 23 bomrang-0.7.1/bomrang/tests/testthat/test-get_historical.R | 96 bomrang-0.7.1/bomrang/tests/testthat/test-get_precis_forecast.R | 4 bomrang-0.7.1/bomrang/tests/testthat/test-get_radar_imagery.R | 10 bomrang-0.7.1/bomrang/tests/testthat/test-sweep_for_forecast_towns.R | 2 bomrang-0.7.1/bomrang/tests/testthat/test-update_forecast_towns.R | 2 bomrang-0.7.1/bomrang/tests/testthat/test-update_station_locations.R | 16 bomrang-0.7.1/bomrang/vignettes/bomrang.Rmd | 2289 +++----- bomrang-0.7.1/bomrang/vignettes/bomrang.Rmd.orig | 475 - bomrang-0.7.1/bomrang/vignettes/completeness_map-1.png |binary bomrang-0.7.1/bomrang/vignettes/get_radar_imagery-1.png |binary bomrang-0.7.1/bomrang/vignettes/get_satellite_imagery-1.png |binary bomrang-0.7.1/bomrang/vignettes/station-locations-map-1.png |binary bomrang-0.7.1/bomrang/vignettes/years_available-1.png |binary 76 files changed, 5187 insertions(+), 5644 deletions(-)
Title: Extract, Analyze and Visualize Signatures for Genomic Variations
Description: Genomic alterations including single nucleotide
substitution, copy number alteration, etc. are the major force for
cancer initialization and development. Due to the specificity of
molecular lesions caused by genomic alterations, we can generate
characteristic alteration spectra, called 'signature' (Wang, Shixiang,
et al. (2020) <DOI:10.1101/2020.04.27.20082404> & Alexandrov, Ludmil
B., et al. (2020) <DOI:10.1038/s41586-020-1943-3> & Macintyre, Geoff,
et al. (2018) <DOI:10.1038/s41588-018-0179-8>). This package helps
users to extract, analyze and visualize signatures from genomic
alteration records, thus providing new insight into cancer study.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Xue-Song Liu [aut, ctb] (<https://orcid.org/0000-0002-7736-0077>),
Tao Wu [aut, ctb],
Ziyu Tao [aut, ctb],
Geoffrey Macintyre [ctb],
Anand Mayakonda [ctb]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between sigminer versions 1.0.16 dated 2020-09-12 and 1.0.19 dated 2020-09-28
DESCRIPTION | 16 ++--- MD5 | 54 +++++++++-------- NAMESPACE | 1 NEWS.md | 22 +++++++ R/add_labels.R | 6 + R/get_sig_exposure.R | 4 + R/get_sig_similarity.R | 94 ++++++++++++++++++++++++------- R/output.R | 62 +++++++++++++++++++- R/show_cor.R |only R/show_cosmic_signatures.R | 6 + R/show_group_distribution.R | 33 ++++++++-- R/show_sig_bootstrap.R | 2 R/show_sig_feature_corrplot.R | 17 ++++- R/sig_convert.R | 3 R/sig_fit.R | 40 ++++++------- R/sig_fit_bootstrap.R | 16 ++--- inst/extdata/DBS_signatures_list.rds |only inst/extdata/SBS_signatures_list.rds |only man/add_labels.Rd | 5 + man/figures/README-unnamed-chunk-7-1.png |binary man/get_sig_db.Rd | 11 ++- man/get_sig_similarity.Rd | 28 +++++++-- man/show_cor.Rd |only man/show_cosmic_sig_profile.Rd | 6 + man/show_group_distribution.Rd | 19 +++++- man/show_sig_bootstrap.Rd | 2 man/show_sig_feature_corrplot.Rd | 3 man/sig_convert.Rd | 2 man/sig_fit.Rd | 23 +------ man/sig_fit_bootstrap.Rd | 15 +--- 30 files changed, 349 insertions(+), 141 deletions(-)
Title: Hypothesis Matrix Translation
Description: Translation between experimental null hypotheses, hypothesis matrices, and contrast matrices as used in linear regression models. The package is based on the method described in Schad, Vasishth, Hohenstein, and Kliegl (2019) <doi:10.1016/j.jml.2019.104038> and Rabe, Vasishth, Hohenstein, Kliegl, and Schad (2020) <doi:10.21105/joss.02134>.
Author: Maximilian M. Rabe [aut, cre] (<https://orcid.org/0000-0002-2556-5644>),
Shravan Vasishth [aut] (<https://orcid.org/0000-0003-2027-1994>),
Sven Hohenstein [aut] (<https://orcid.org/0000-0002-9708-1593>),
Reinhold Kliegl [aut] (<https://orcid.org/0000-0002-0180-8488>),
Daniel J. Schad [aut] (<https://orcid.org/0000-0003-2586-6823>)
Maintainer: Maximilian M. Rabe <maximilian.rabe@uni-potsdam.de>
Diff between hypr versions 0.1.10 dated 2020-09-08 and 0.1.11 dated 2020-09-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/hypr.R | 6 +++--- inst/CITATION | 3 +++ 4 files changed, 12 insertions(+), 9 deletions(-)
Title: Build Graphs for Landscape Genetics Analysis
Description: Build graphs for landscape genetics analysis. This set of
functions can be used to import and convert spatial and genetic data
initially in different formats, import landscape graphs created with
'GRAPHAB' software (Foltete et al., 2012) <doi:10.1016/j.envsoft.2012.07.002>,
make diagnosis plots of isolation by distance relationships in order to
choose how to build genetic graphs, create graphs with a large range of
pruning methods, weight their links with several genetic distances, plot
and analyse graphs, compare them with other graphs. It uses functions from
other packages such as 'adegenet'
(Jombart, 2008) <doi:10.1093/bioinformatics/btn129> and 'igraph' (Csardi
et Nepusz, 2006) <https://igraph.org/>. It also implements methods
commonly used in landscape genetics to create graphs, described by Dyer et
Nason (2004) <doi:10.1111/j.1365-294X.2004.02177.x> and Greenbaum et
Fefferman (2017) <doi:10.1111/mec.14059>, and to analyse distance data
(van Strien et al., 2015) <doi:10.1038/hdy.2014.62>.
Author: Paul Savary
Maintainer: Paul Savary <savarypaul660@gmail.com>
Diff between graph4lg versions 1.0.0 dated 2020-07-22 and 1.0.1 dated 2020-09-28
DESCRIPTION | 18 +++++------ MD5 | 48 +++++++++++++++---------------- NEWS.md | 11 +++++++ R/g_percol.R | 15 ++++----- R/genepop_to_genind.R | 2 - R/genind_to_genepop.R | 6 +-- R/graph_to_shp.R | 52 ++++++++++++++++++++++++++-------- R/graphab_metric.R | 21 +++++++------ R/mat_cost_dist.R | 21 ++++++++++++- R/mat_pw_d_jost.R | 2 - R/mat_pw_dps.R | 2 - R/mat_pw_fst.R | 2 - R/mat_pw_gst.R | 2 - build/partial.rdb |binary inst/doc/genetic_graph_2.html | 22 +++++++------- inst/doc/input_data_processing_1.Rmd | 2 - inst/doc/input_data_processing_1.html | 10 +++--- man/genepop_to_genind.Rd | 2 - man/genind_to_genepop.Rd | 2 - man/mat_cost_dist.Rd | 8 ++++- man/mat_pw_d_j.Rd | 2 - man/mat_pw_dps.Rd | 2 - man/mat_pw_fst.Rd | 2 - man/mat_pw_gst.Rd | 2 - vignettes/input_data_processing_1.Rmd | 2 - 25 files changed, 160 insertions(+), 98 deletions(-)
More information about covid19.analytics at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-16 1.0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-11 0.1.0