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:
2020-09-11 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-16 1.0.5
Title: The Complete R6 Probability Distributions Interface
Description: An R6 object oriented distributions package. Unified interface for 42 probability distributions and 11 kernels including functionality for multiple scientific types. Additionally functionality for composite distributions and numerical imputation. Design patterns including wrappers and decorators are described in Gamma et al. (1994, ISBN:0-201-63361-2). For quick reference of probability distributions including d/p/q/r functions and results we refer to McLaughlin, M. P. (2001). Additionally Devroye (1986, ISBN:0-387-96305-7) for sampling the Dirichlet distribution, Gentle (2009) <doi:10.1007/978-0-387-98144-4> for sampling the Multivariate Normal distribution and Michael et al. (1976) <doi:10.2307/2683801> for sampling the Wald distribution.
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>),
Franz Kiraly [aut],
Peter Ruckdeschel [ctb] (Author of distr),
Matthias Kohl [ctb] (Author of distr),
Shen Chen [ctb],
Jordan Deenichin [ctb],
Chengyang Gao [ctb],
Chloe Zhaoyuan Gu [ctb],
Yunjie He [ctb],
Xiaowen Huang [ctb],
Shuhan Liu [ctb],
Runlong Yu [ctb],
Chijing Zeng [ctb],
Qian Zhou [ctb]
Maintainer: Raphael Sonabend <raphael.sonabend.15@ucl.ac.uk>
Diff between distr6 versions 1.4.3 dated 2020-08-26 and 1.4.4 dated 2020-09-27
DESCRIPTION | 10 MD5 | 95 +-- NAMESPACE | 3 NEWS.md | 10 R/DistributionDecorator_CoreStatistics.R | 135 ++-- R/DistributionDecorator_ExoticStatistics.R | 4 R/DistributionDecorator_FunctionImputation.R | 3 R/ParameterSet.R | 26 R/ParameterSetCollection.R | 38 - R/SDistribution_WeightedDiscrete.R | 18 R/Wrapper_MixtureDistribution.R | 97 ++- R/Wrapper_ProductDistribution.R | 95 ++- R/Wrapper_VectorDistribution.R | 690 ++++++++++++++----------- R/c.Distribution.R | 3 R/lines.R | 1 R/mixturiseVector.R | 3 R/plot_multivariate.R | 2 R/zzz.R | 11 README.md | 30 - inst/doc/distr6.html | 324 ++++++----- man/CoreStatistics.Rd | 60 +- man/ExoticStatistics.Rd | 7 man/FunctionImputation.Rd | 3 man/MixtureDistribution.Rd | 19 man/ParameterSet.Rd | 60 +- man/ProductDistribution.Rd | 31 - man/VectorDistribution.Rd | 11 man/as.MixtureDistribution.Rd |only man/as.ProductDistribution.Rd |only man/as.VectorDistribution.Rd |only man/cf.Rd | 4 man/entropy.Rd | 4 man/genExp.Rd | 6 man/kthmoment.Rd | 4 man/kurtosis.Rd | 6 man/lines.Distribution.Rd | 1 man/mean.Distribution.Rd | 2 man/mgf.Rd | 4 man/mixturiseVector.Rd | 3 man/pgf.Rd | 4 man/skewness.Rd | 4 man/variance.Rd | 4 tests/testthat/Rplots.pdf |binary tests/testthat/helpers.R | 26 tests/testthat/test-VectorDistribution.R | 9 tests/testthat/test-WrappedMixture.R | 16 tests/testthat/test-WrappedProduct.R | 16 tests/testthat/test-cDistribution.R | 4 tests/testthat/test-wrapper.R | 8 tests/testthat/test_decorator_corestatistics.R | 4 50 files changed, 1165 insertions(+), 753 deletions(-)
Title: Multiway Clustering via Tensor Block Models
Description: Implements the multiway sparse clustering approach of M. Wang and Y. Zeng, "Multiway clustering via tensor block models". Advances in Neural Information Processing System 32 (NeurIPS), 715-725, 2019.
Author: Miaoyan Wang, Yuchen Zeng
Maintainer: Yuchen Zeng <yzeng58@wisc.edu>
Diff between tensorsparse versions 2.0 dated 2020-03-22 and 3.0 dated 2020-09-27
tensorsparse-2.0/tensorsparse/R/choosekrl_bic.R |only tensorsparse-2.0/tensorsparse/R/get_data.R |only tensorsparse-2.0/tensorsparse/R/get_data4.R |only tensorsparse-2.0/tensorsparse/R/tbm_clustering.R |only tensorsparse-2.0/tensorsparse/man/choosekrl_bic.Rd |only tensorsparse-2.0/tensorsparse/man/get_data.Rd |only tensorsparse-2.0/tensorsparse/man/get_data4.Rd |only tensorsparse-2.0/tensorsparse/man/tbm_clustering.Rd |only tensorsparse-3.0/tensorsparse/DESCRIPTION | 11 +- tensorsparse-3.0/tensorsparse/MD5 | 28 +++--- tensorsparse-3.0/tensorsparse/NAMESPACE | 20 ---- tensorsparse-3.0/tensorsparse/NEWS | 6 + tensorsparse-3.0/tensorsparse/R/chooseClusteringSize.R |only tensorsparse-3.0/tensorsparse/R/chooseLambda.R | 2 tensorsparse-3.0/tensorsparse/R/functions.R | 58 +++++++------- tensorsparse-3.0/tensorsparse/R/getOrder3Tensor.R |only tensorsparse-3.0/tensorsparse/R/getOrder4Tensor.R |only tensorsparse-3.0/tensorsparse/R/tbmClustering.R |only tensorsparse-3.0/tensorsparse/man/chooseClusteringSize.Rd |only tensorsparse-3.0/tensorsparse/man/chooseLambda.Rd | 2 tensorsparse-3.0/tensorsparse/man/getOrder3Tensor.Rd |only tensorsparse-3.0/tensorsparse/man/getOrder4Tensor.Rd |only tensorsparse-3.0/tensorsparse/man/tbmClustering.Rd |only 23 files changed, 61 insertions(+), 66 deletions(-)
Title: Statistical Inference in Weighted Lindley Distribution
Description: Estimate the parameters of weighted Lindley distribution, and provide some
useful results like goodness of fit or confidence interval etc.
Ghitany, M., Alqallaf, F., Al-Mutairi, D., Husain, H. (2011) <doi:10.1016/j.matcom.2010.11.005>.
Hyoung-Moon Kim. and Yu-Hyeong Jang. (2020) submitted.
Wang, M., Wang, W. (2017) <doi:10.1080/03610918.2014.970696>.
Author: Yu-Hyeong Jang, SungBum Kim, Hyun-Ju Jung and Hyoung-Moon Kim
Maintainer: SungBum Kim <kimsb0707@hanmail.net>
Diff between WLinfer versions 1.0.0 dated 2020-09-09 and 1.1.0 dated 2020-09-27
DESCRIPTION | 6 - MD5 | 8 - NAMESPACE | 2 R/WL.R | 315 +++++++++++++++++++++++++++++++++++++++----------------- man/Firth_WL.Rd | 8 + 5 files changed, 238 insertions(+), 101 deletions(-)
Title: Busy Indicator for 'Shiny' Applications
Description: Add indicators (spinner, progress bar, gif) in your 'shiny' applications to show the user that the server is busy.
Author: Fanny Meyer [aut],
Victor Perrier [aut, cre],
Silex Technologies [fnd] (https://www.silex-ip.com)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between shinybusy versions 0.2.1 dated 2020-09-10 and 0.2.2 dated 2020-09-27
DESCRIPTION | 6 ++-- MD5 | 20 +++++++------- NEWS.md | 6 ++++ R/busy-gif.R | 67 +++++++++++++++++++++++++++++++++--------------- R/busy-spinner.R | 31 +++++++++++++++------- R/dependencies.R | 9 ++++-- R/spinners-spinkit.R | 10 ++++--- inst/doc/spinners.html | 62 ++++++++++++++++++++++---------------------- man/add_busy_gif.Rd | 9 ++++-- man/add_busy_spinner.Rd | 2 - man/manual-gif.Rd | 9 ++++-- 11 files changed, 144 insertions(+), 87 deletions(-)
Title: Convert Between Bibliography Formats
Description: Converts between a number of bibliography formats,
including 'BibTeX', 'BibLaTeX' and 'Bibentry'. Includes a port of the
'bibutils' utilities by Chris Putnam
<https://sourceforge.net/projects/bibutils/>. Supports all
bibliography formats and character encodings implemented in
'bibutils'.
Author: Georgi N. Boshnakov [aut, cre] (R port, modifications to bibutils' C
code),
Chris Putman [aut] (src/*, author of the bibutils libraries,
https://sourceforge.net/projects/bibutils/),
Richard Mathar [ctb] (src/addsout.c),
Johannes Wilm [ctb] (src/biblatexin.c, src/bltypes.c)
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between rbibutils versions 1.0.3 dated 2020-07-20 and 1.1.0 dated 2020-09-27
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 9 +++++++++ TODO | 7 +++++++ build/partial.rdb |binary src/bibtexin.c | 30 +++++++++++++++++++++++++----- src/latex_parse.c | 7 +++++++ src/modsout.c | 24 +++++++++++++----------- 8 files changed, 72 insertions(+), 27 deletions(-)
Title: Bridging the Gap Between Qualitative Data and Quantitative
Analysis
Description: Automates many of the tasks associated with quantitative discourse analysis of transcripts containing discourse
including frequency counts of sentence types, words, sentences, turns of talk, syllables and other assorted
analysis tasks. The package provides parsing tools for preparing transcript data. Many functions enable the user
to aggregate data by any number of grouping variables, providing analysis and seamless integration with other R
packages that undertake higher level analysis and visualization of text. This affords the user a more efficient
and targeted analysis. 'qdap' is designed for transcript analysis, however, many functions are applicable to other
areas of Text Mining/ Natural Language Processing.
Author: Tyler Rinker [aut, cre],
Bryan Goodrich [ctb],
Dason Kurkiewicz [ctb]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between qdap versions 2.4.1 dated 2020-04-20 and 2.4.3 dated 2020-09-27
DESCRIPTION | 22 ++++---- MD5 | 118 +++++++++++++++++++++---------------------- NAMESPACE | 5 - NEWS | 8 ++ R/adjacency_matrix.R | 2 R/beg2char.R | 2 R/bracketX.R | 2 R/chaining.R | 2 R/check_spelling.R | 4 - R/cm_df.transcript.R | 2 R/cm_distance.R | 2 R/discourse_map.R | 4 - R/diversity.R | 2 R/gradient_cloud.R | 7 ++ R/igraph_params.R | 2 R/new_project.R | 8 +- R/phrase_net.R | 7 +- R/polarity.R | 4 - R/read_transcript.R | 16 ++--- R/synonyms.R | 5 - R/trans_context.R | 2 R/word_cor.R | 2 README.md | 5 - data/DATA.SPLIT.rda |binary data/DATA.rda |binary data/DATA2.rda |binary data/env.syl.rda |binary data/hamlet.rda |binary data/mraja1.rda |binary data/mraja1spl.rda |binary data/pres_debate_raw2012.rda |binary data/pres_debates2012.rda |binary data/raj.act.1.rda |binary data/raj.act.1POS.rda |binary data/raj.act.2.rda |binary data/raj.act.3.rda |binary data/raj.act.4.rda |binary data/raj.act.5.rda |binary data/raj.demographics.rda |binary data/raj.rda |binary data/rajPOS.rda |binary data/rajSPLIT.rda |binary data/raw.time.span.rda |binary data/sample.time.span.rda |binary inst/CITATION | 8 +- man/adjacency_matrix.Rd | 2 man/beg2char.Rd | 2 man/bracketX.Rd | 2 man/chain.Rd | 2 man/check_spelling.Rd | 4 - man/cm_df.transcript.Rd | 2 man/cm_distance.Rd | 2 man/discourse_map.Rd | 4 - man/diversity.Rd | 2 man/igraph_params.Rd | 2 man/new_project.Rd | 8 +- man/phrase_net.Rd | 7 +- man/polarity.Rd | 4 - man/synonyms.Rd | 5 - man/word_cor.Rd | 2 60 files changed, 147 insertions(+), 144 deletions(-)
Title: Calculate Pairwise Multiple Comparisons of Mean Rank Sums
Extended
Description: For one-way layout experiments the one-way ANOVA can
be performed as an omnibus test. All-pairs multiple comparisons
tests (Tukey-Kramer test, Scheffe test, LSD-test)
and many-to-one tests (Dunnett test) for normally distributed
residuals and equal within variance are available. Furthermore,
all-pairs tests (Games-Howell test, Tamhane's T2 test,
Dunnett T3 test, Ury-Wiggins-Hochberg test) and many-to-one
(Tamhane-Dunnett Test) for normally distributed residuals
and heterogeneous variances are provided. Van der Waerden's normal
scores test for omnibus, all-pairs and many-to-one tests is
provided for non-normally distributed residuals and homogeneous
variances. The Kruskal-Wallis, BWS and Anderson-Darling
omnibus test and all-pairs tests
(Nemenyi test, Dunn test, Conover test, Dwass-Steele-Critchlow-
Fligner test) as well as many-to-one (Nemenyi test, Dunn test,
U-test) are given for the analysis of variance by ranks.
Non-parametric trend tests (Jonckheere test, Cuzick test,
Johnson-Mehrotra test, Spearman test) are included.
In addition, a Friedman-test for one-way ANOVA with repeated
measures on ranks (CRBD) and Skillings-Mack test for unbalanced
CRBD is provided with consequent all-pairs tests (Nemenyi test,
Siegel test, Miller test, Conover test, Exact test)
and many-to-one tests (Nemenyi test, Demsar test, Exact test).
A trend can be tested with Pages's test. Durbin's test
for a two-way balanced incomplete block design (BIBD) is given
in this package as well as Gore's test for CRBD with multiple
observations per cell is given. Outlier tests, Mandel's k- and
h statistic as well as functions for Type I error and Power
analysis as well as generic summary, print and plot methods
are provided.
Author: Thorsten Pohlert [aut, cre] (<https://orcid.org/0000-0003-3855-3025>)
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between PMCMRplus versions 1.5.0 dated 2020-09-12 and 1.5.1 dated 2020-09-27
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/kwManyOneNdwTest.R | 6 ++++-- R/siegelTukeyTest.R | 2 +- inst/NEWS.Rd | 7 +++++++ inst/doc/QuickReferenceGuide.html | 4 ++-- man/siegelTukeyTest.Rd | 2 +- 7 files changed, 25 insertions(+), 16 deletions(-)
Title: Explore and Visualize Your Data Interactively
Description: A 'shiny' gadget to create 'ggplot2' charts interactively with drag-and-drop to map your variables.
You can quickly visualize your data accordingly to their type, export to 'PNG' or 'PowerPoint',
and retrieve the code to reproduce the chart.
Author: Fanny Meyer [aut],
Victor Perrier [aut, cre],
Ian Carroll [ctb] (Faceting support),
Xiangnan Dang [ctb] (Facets rows and cols, X/Y limits)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between esquisse versions 0.3.0 dated 2020-01-27 and 0.3.1 dated 2020-09-27
esquisse-0.3.0/esquisse/R/layoutAddin.R |only esquisse-0.3.1/esquisse/DESCRIPTION | 18 esquisse-0.3.1/esquisse/MD5 | 67 - esquisse-0.3.1/esquisse/NAMESPACE | 9 esquisse-0.3.1/esquisse/NEWS.md | 12 esquisse-0.3.1/esquisse/R/esquisser.R | 12 esquisse-0.3.1/esquisse/R/esquisserServer.R | 139 ++- esquisse-0.3.1/esquisse/R/esquisserUI.R | 62 - esquisse-0.3.1/esquisse/R/ggcall.R | 33 esquisse-0.3.1/esquisse/R/input-colors.R | 2 esquisse-0.3.1/esquisse/R/input-dragula.R | 230 ++++- esquisse-0.3.1/esquisse/R/input-drop.R | 1 esquisse-0.3.1/esquisse/R/mapping.R | 4 esquisse-0.3.1/esquisse/R/module-chartControls.R | 235 +++--- esquisse-0.3.1/esquisse/R/module-chooseData.R | 30 esquisse-0.3.1/esquisse/R/module-coerce.R | 14 esquisse-0.3.1/esquisse/R/module-filterDF.R | 10 esquisse-0.3.1/esquisse/R/safe_ggplot.R | 3 esquisse-0.3.1/esquisse/R/utils-shiny.R | 13 esquisse-0.3.1/esquisse/R/utils.R | 2 esquisse-0.3.1/esquisse/README.md | 7 esquisse-0.3.1/esquisse/build/vignette.rds |binary esquisse-0.3.1/esquisse/inst/assets/dragula/dragula-bindings.js | 34 esquisse-0.3.1/esquisse/inst/assets/shiny-utils.js | 85 +- esquisse-0.3.1/esquisse/inst/assets/styles-dad.css | 21 esquisse-0.3.1/esquisse/inst/assets/styles.css | 23 esquisse-0.3.1/esquisse/inst/doc/get-started.html | 52 - esquisse-0.3.1/esquisse/inst/doc/shiny-usage.html | 384 +++++----- esquisse-0.3.1/esquisse/man/dragulaInput.Rd | 99 ++ esquisse-0.3.1/esquisse/man/ggcall.Rd | 256 +++--- esquisse-0.3.1/esquisse/man/input-colors.Rd | 2 esquisse-0.3.1/esquisse/man/module-chooseData.Rd | 10 esquisse-0.3.1/esquisse/man/module-esquisse.Rd | 2 esquisse-0.3.1/esquisse/man/run_module.Rd | 46 - esquisse-0.3.1/esquisse/man/updateDragulaInput.Rd | 7 35 files changed, 1157 insertions(+), 767 deletions(-)
Title: Generalized Power Analysis for LATE
Description: An implementation of the generalized power analysis for the local average treatment effect (LATE), proposed by Bansak (2020) <doi:10.1214/19-STS732>. Power analysis is in the context of estimating the LATE (also known as the complier average causal effect, or CACE), with calculations based on a test of the null hypothesis that the LATE equals 0 with a two-sided alternative. The method uses standardized effect sizes to place a conservative bound on the power under minimal assumptions. Package allows users to recover power, sample size requirements, or minimum detectable effect sizes. Package also allows users to work with absolute effects rather than effect sizes, to specify an additional assumption to narrow the bounds, and to incorporate covariate adjustment.
Author: Kirk Bansak [aut],
Eddie Yang [aut, cre]
Maintainer: Eddie Yang <z5yang@ucsd.edu>
Diff between powerLATE versions 0.1.0 dated 2020-08-14 and 0.1.1 dated 2020-09-27
powerLATE-0.1.0/powerLATE/man/figures |only powerLATE-0.1.1/powerLATE/DESCRIPTION | 6 - powerLATE-0.1.1/powerLATE/MD5 | 9 - powerLATE-0.1.1/powerLATE/NAMESPACE | 1 powerLATE-0.1.1/powerLATE/R/onAttach.R |only powerLATE-0.1.1/powerLATE/README.md | 145 +------------------------- powerLATE-0.1.1/powerLATE/man/dot-onAttach.Rd |only 7 files changed, 20 insertions(+), 141 deletions(-)
Title: Tools to Format Numbers for Publication
Description: Format numbers and plots for publication; includes the removal of leading zeros,
standardization of number of digits, addition of affixes, and a p-value formatter. These
tools combine the functionality of several 'base' functions such as 'paste()',
'format()', and 'sprintf()' into specific use case functions that are named in a way
that is consistent with usage, making their names easy to remember and easy to deploy.
Author: Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between numform versions 0.6.0 dated 2020-04-16 and 0.6.4 dated 2020-09-27
DESCRIPTION | 11 ++++---- MD5 | 20 +++++++++------ NAMESPACE | 7 +++++ NEWS | 36 ++++++++++++++++++++++++++- R/f_pad_zero.R | 69 +++++++++++++++++++++++++++++++++++++++++++++++++---- R/round.R |only R/time_digits.R |only README.md | 4 +-- inst/CITATION | 8 +++--- man/f_pad_zero.Rd | 23 ++++++++++++++++- man/reexports.Rd | 2 - man/round2.Rd |only man/time_digits.Rd |only 13 files changed, 152 insertions(+), 28 deletions(-)
Title: Create Simple Packages Which Do not Upset R Package Checks
Description: Provides a function kitten() which creates cute little
packages which pass R package checks. This sets it apart from
package.skeleton() which it calls, and which leaves imperfect files
behind. As this is not exactly helpful for beginners, kitten() offers
an alternative. Unit test support is added if the 'tinytest' package
is present.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between pkgKitten versions 0.1.5 dated 2019-10-22 and 0.2.0 dated 2020-09-27
ChangeLog | 63 +++++++++++++++++++++++++++++++++++++- DESCRIPTION | 14 ++++---- MD5 | 15 ++++----- R/pkgKitten.R | 18 ++++++++-- README.md | 17 +++++++++- inst/NEWS.Rd | 15 +++++++-- inst/replacements/NAMESPACE |only man/kitten.Rd | 14 ++++---- man/playWithPerPackageHelpPage.Rd | 3 - 9 files changed, 129 insertions(+), 30 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 0.9.9.5 dated 2020-06-10 and 0.10.1 dated 2020-09-27
DESCRIPTION | 34 +++---- MD5 | 35 ++++--- NAMESPACE | 4 R/acs.R | 16 ++- R/census.R | 52 +++++++++-- R/fips_codes.R | 41 +++++++++ R/helpers.R | 8 + R/load_data.R | 217 ++++++++++++++++++++++++++++++++++++++++++++++++ R/moe.R | 5 + R/pums.R |only R/search_variables.R | 4 R/significance.R | 2 R/tidycensus-package.R | 2 R/zzz.r | 41 ++++++++- README.md | 38 ++------ data/pums_variables.rda |only man/get_acs.Rd | 2 man/get_pums.Rd |only man/pums_variables.Rd |only man/significance.Rd | 2 man/to_survey.Rd |only 21 files changed, 423 insertions(+), 80 deletions(-)
Title: Operations Research LOCational Analysis Models
Description: Objects and methods to handle and solve the min-sum location problem, also known as Fermat-Weber problem. The min-sum location problem search for a point such that the weighted sum of the distances to the demand points are minimized. See "The Fermat-Weber location problem revisited" by Brimberg, Mathematical Programming, 1, pg. 71-76, 1995. <DOI:10.1007/BF01592245>.
General global optimization algorithms are used to solve the problem, along with the adhoc Weiszfeld method, see "Sur le point pour lequel la Somme des distances de n points donnes est minimum", by Weiszfeld, Tohoku Mathematical Journal, First Series, 43, pg. 355-386, 1937 or "On the point for which the sum of the distances to n given points is minimum", by E. Weiszfeld and F. Plastria, Annals of Operations Research, 167, pg. 7-41, 2009. <DOI:10.1007/s10479-008-0352-z>.
Author: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Diff between orloca versions 4.9 dated 2020-03-04 and 4.10 dated 2020-09-27
ChangeLog | 3 DESCRIPTION | 14 - MD5 | 24 +- R/contour.loca.p.R | 108 ++++++----- R/distsumlp.R | 2 R/orloca-package.R | 4 R/persp.loca.p.R | 2 inst/doc/localizacionplana.html | 376 +++++++++++++++++++++------------------- inst/doc/planarlocation.html | 376 +++++++++++++++++++++------------------- man/andalusia.Rd | 6 man/contour.loca.p.Rd | 2 man/distsumlp.Rd | 2 man/persp.loca.p.Rd | 2 13 files changed, 501 insertions(+), 420 deletions(-)
Title: Ecological Metadata as Linked Data
Description: This is a utility for transforming Ecological Metadata Language
('EML') files into 'JSON-LD' and back into 'EML.' Doing so creates a
list-based representation of 'EML' in R, so that 'EML' data can easily
be manipulated using standard 'R' tools. This makes this package an
effective backend for other 'R'-based tools working with 'EML.' By
abstracting away the complexity of 'XML' Schema, developers can
build around native 'R' list objects and not have to worry about satisfying
many of the additional constraints of set by the schema (such as element
ordering, which is handled automatically). Additionally, the 'JSON-LD'
representation enables the use of developer-friendly 'JSON' parsing and
serialization that may facilitate the use of 'EML' in contexts outside of 'R,'
as well as the informatics-friendly serializations such as 'RDF' and
'SPARQL' queries.
Author: Carl Boettiger [aut, cre, cph]
(<https://orcid.org/0000-0002-1642-628X>),
Matthew B. Jones [aut, cph] (<https://orcid.org/0000-0003-0077-4738>),
Bryce Mecum [aut, cph] (<https://orcid.org/0000-0002-0381-3766>)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between emld versions 0.5.0 dated 2020-07-08 and 0.5.1 dated 2020-09-27
DESCRIPTION | 10 ++-- MD5 | 22 +++++----- NEWS.md | 7 ++- R/sysdata.rda |binary README.md | 15 ++----- build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/tutorial.R | 16 +++++-- inst/doc/tutorial.Rmd | 24 ++++++----- inst/doc/tutorial.html | 105 ++++++++++++++++++++++++++----------------------- man/emld-package.Rd | 2 vignettes/tutorial.Rmd | 24 ++++++----- 12 files changed, 125 insertions(+), 101 deletions(-)
Title: Methods for Correlation Analysis
Description: Lightweight package for computing different kinds of correlations, such as partial correlations, Bayesian correlations, multilevel correlations, polychoric correlations, biweight correlations, distance correlations and more. Relies on the easystats ecosystem (Lüdecke, Waggoner & Makowski (2019) <doi:10.21105/joss.01412>).
Author: Dominique Makowski [aut, cre] (<https://orcid.org/0000-0001-5375-9967>),
Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>),
Mattan S. Ben-Shachar [ctb] (<https://orcid.org/0000-0002-4287-4801>),
Indrajeet Patil [ctb] (<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between correlation versions 0.3.0 dated 2020-06-19 and 0.4.0 dated 2020-09-27
DESCRIPTION | 19 +++++----- MD5 | 53 +++++++++++++++++++----------- NEWS.md | 21 +++++++++++ R/cor_test.R | 59 +++++++++++++++++++++++++++------ R/cor_test_bayes.R | 23 ++++++++++++- R/cor_test_biserial.R | 28 ++++++--------- R/cor_test_blomqvist.R |only R/cor_test_freq.R | 12 +++++- R/cor_test_gamma.R |only R/cor_test_gaussian.R |only R/cor_test_hoeffding.R |only R/cor_test_percentage.R | 9 ++--- R/cor_test_polychoric.R | 6 +-- R/cor_to_ci.R | 4 +- R/correlation.R | 20 +++++++++-- README.md | 67 ++++++++++++++++++++++++++++---------- build |only inst/CITATION | 13 ++++--- inst/doc |only man/cor_test.Rd | 11 +++++- man/cor_to_p.Rd | 2 - man/correlation.Rd | 18 +++++++--- man/figures/unnamed-chunk-7-1.png |binary tests/testthat/test-cor_test.R | 39 ++++++++++++++++++++++ tests/testthat/test-correlation.R | 2 - vignettes |only 26 files changed, 304 insertions(+), 102 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-10 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-12 3.30.1.2
2020-04-09 3.30.0.1
2020-02-26 3.28.0.4
2020-01-22 3.28.0.2
2019-08-01 3.26.0.2
2019-06-21 3.24.0.5
2019-01-10 3.22.1.1
2018-09-25 3.20.0.8
2018-06-17 3.20.0.2
2018-05-24 3.18.0.11
2018-05-02 3.18.0.8
2017-12-01 3.16.0.2
2017-11-27 3.16.0.1
2017-09-27 3.14.0.3
2017-07-01 3.10.5.3
2017-06-23 3.10.5.2
2017-05-02 3.10.4.6
2017-04-17 3.10.4.4
2017-02-22 3.10.3.6
2017-02-03 3.10.3.3
2017-01-17 3.10.2.2
2016-10-14 3.10.0.8
2016-09-03 3.10.0.6
2016-07-13 3.8.3.3
2016-06-02 3.8.2.6
2016-03-15 3.8.1.3
2015-11-24 3.6.0.8
2015-09-22 3.2.0.3
2015-09-14 3.2.0.1
2015-07-22 3.0.0.30
2015-06-14 3.0.0.22
2015-02-07 2.8.4.4
2014-10-27 2.8.1.1
Title: Extract Decennial Census and American Community Survey Data
Description: Download summary files from Census Bureau <https://www2.census.gov/>
and extract data, in particular high resolution data at
block, block group, and tract level, from decennial census and
American Community Survey 1-year and 5-year estimates.
Author: Guanglai Li
Maintainer: Guanglai Li <liguanglai@gmail.com>
Diff between totalcensus versions 0.6.3 dated 2020-01-08 and 0.6.4 dated 2020-09-27
totalcensus-0.6.3/totalcensus/data/datalist |only totalcensus-0.6.4/totalcensus/DESCRIPTION | 12 totalcensus-0.6.4/totalcensus/MD5 | 147 +++++----- totalcensus-0.6.4/totalcensus/R/data_acs.R | 128 ++++---- totalcensus-0.6.4/totalcensus/R/quiet_global_variable_in_cran_check.R | 3 totalcensus-0.6.4/totalcensus/R/search_census_and_acs.R | 17 - totalcensus-0.6.4/totalcensus/data/dict_acs1_table.RData |binary totalcensus-0.6.4/totalcensus/data/lookup_acs1year_2005.RData |binary totalcensus-0.6.4/totalcensus/data/lookup_acs1year_2006.RData |binary totalcensus-0.6.4/totalcensus/data/lookup_acs1year_2007.RData |binary totalcensus-0.6.4/totalcensus/data/lookup_acs1year_2008.RData |binary totalcensus-0.6.4/totalcensus/data/lookup_acs1year_2009.RData |binary totalcensus-0.6.4/totalcensus/data/lookup_acs1year_2010.RData |binary totalcensus-0.6.4/totalcensus/data/lookup_acs1year_2011.RData |binary totalcensus-0.6.4/totalcensus/data/lookup_acs1year_2012.RData |binary totalcensus-0.6.4/totalcensus/data/lookup_acs1year_2013.RData |binary totalcensus-0.6.4/totalcensus/data/lookup_acs1year_2014.RData |binary totalcensus-0.6.4/totalcensus/data/lookup_acs1year_2015.RData |binary totalcensus-0.6.4/totalcensus/data/lookup_acs1year_2016.RData |binary totalcensus-0.6.4/totalcensus/data/lookup_acs1year_2017.RData |binary totalcensus-0.6.4/totalcensus/data/lookup_acs1year_2018.RData |binary totalcensus-0.6.4/totalcensus/data/lookup_acs1year_2019.RData |only totalcensus-0.6.4/totalcensus/data/table_content_acs1year_all_years.RData |only totalcensus-0.6.4/totalcensus/man/dict_acs1_geocomponent.Rd | 6 totalcensus-0.6.4/totalcensus/man/dict_acs1_summarylevel.Rd | 6 totalcensus-0.6.4/totalcensus/man/dict_acs1_table.Rd | 9 totalcensus-0.6.4/totalcensus/man/dict_acs5_geocomponent.Rd | 6 totalcensus-0.6.4/totalcensus/man/dict_acs5_summarylevel.Rd | 6 totalcensus-0.6.4/totalcensus/man/dict_acs5_table.Rd | 6 totalcensus-0.6.4/totalcensus/man/dict_acs_geoheader_2005_1year.Rd | 6 totalcensus-0.6.4/totalcensus/man/dict_acs_geoheader_2006_2008_1year.Rd | 6 totalcensus-0.6.4/totalcensus/man/dict_acs_geoheader_2009_1year.Rd | 6 totalcensus-0.6.4/totalcensus/man/dict_acs_geoheader_2009_5year.Rd | 6 totalcensus-0.6.4/totalcensus/man/dict_acs_geoheader_2010.Rd | 6 totalcensus-0.6.4/totalcensus/man/dict_acs_geoheader_2011_now.Rd | 6 totalcensus-0.6.4/totalcensus/man/dict_all_geocomponent_2000.Rd | 12 totalcensus-0.6.4/totalcensus/man/dict_all_geocomponent_2010.Rd | 12 totalcensus-0.6.4/totalcensus/man/dict_all_summarylevel.Rd | 6 totalcensus-0.6.4/totalcensus/man/dict_cbsa.Rd | 6 totalcensus-0.6.4/totalcensus/man/dict_decennial_geocomponent_2000.Rd | 6 totalcensus-0.6.4/totalcensus/man/dict_decennial_geocomponent_2010.Rd | 6 totalcensus-0.6.4/totalcensus/man/dict_decennial_geoheader_2000.Rd | 6 totalcensus-0.6.4/totalcensus/man/dict_decennial_geoheader_2010.Rd | 6 totalcensus-0.6.4/totalcensus/man/dict_decennial_summarylevel_2000.Rd | 6 totalcensus-0.6.4/totalcensus/man/dict_decennial_summarylevel_2010.Rd | 6 totalcensus-0.6.4/totalcensus/man/dict_decennial_table_2000.Rd | 6 totalcensus-0.6.4/totalcensus/man/dict_decennial_table_2010.Rd | 6 totalcensus-0.6.4/totalcensus/man/dict_fips.Rd | 6 totalcensus-0.6.4/totalcensus/man/lookup_acs1year_2005.Rd | 10 totalcensus-0.6.4/totalcensus/man/lookup_acs1year_2006.Rd | 10 totalcensus-0.6.4/totalcensus/man/lookup_acs1year_2007.Rd | 10 totalcensus-0.6.4/totalcensus/man/lookup_acs1year_2008.Rd | 10 totalcensus-0.6.4/totalcensus/man/lookup_acs1year_2009.Rd | 10 totalcensus-0.6.4/totalcensus/man/lookup_acs1year_2010.Rd | 10 totalcensus-0.6.4/totalcensus/man/lookup_acs1year_2011.Rd | 10 totalcensus-0.6.4/totalcensus/man/lookup_acs1year_2012.Rd | 10 totalcensus-0.6.4/totalcensus/man/lookup_acs1year_2013.Rd | 10 totalcensus-0.6.4/totalcensus/man/lookup_acs1year_2014.Rd | 10 totalcensus-0.6.4/totalcensus/man/lookup_acs1year_2015.Rd | 10 totalcensus-0.6.4/totalcensus/man/lookup_acs1year_2016.Rd | 10 totalcensus-0.6.4/totalcensus/man/lookup_acs1year_2017.Rd | 10 totalcensus-0.6.4/totalcensus/man/lookup_acs1year_2018.Rd | 10 totalcensus-0.6.4/totalcensus/man/lookup_acs1year_2019.Rd |only totalcensus-0.6.4/totalcensus/man/lookup_acs5year_2009.Rd | 6 totalcensus-0.6.4/totalcensus/man/lookup_acs5year_2010.Rd | 6 totalcensus-0.6.4/totalcensus/man/lookup_acs5year_2011.Rd | 6 totalcensus-0.6.4/totalcensus/man/lookup_acs5year_2012.Rd | 6 totalcensus-0.6.4/totalcensus/man/lookup_acs5year_2013.Rd | 6 totalcensus-0.6.4/totalcensus/man/lookup_acs5year_2014.Rd | 6 totalcensus-0.6.4/totalcensus/man/lookup_acs5year_2015.Rd | 6 totalcensus-0.6.4/totalcensus/man/lookup_acs5year_2016.Rd | 6 totalcensus-0.6.4/totalcensus/man/lookup_acs5year_2017.Rd | 6 totalcensus-0.6.4/totalcensus/man/lookup_acs5year_2018.Rd | 6 totalcensus-0.6.4/totalcensus/man/lookup_decennial_2000.Rd | 6 totalcensus-0.6.4/totalcensus/man/lookup_decennial_2010.Rd | 6 totalcensus-0.6.4/totalcensus/man/states_DC.Rd | 4 totalcensus-0.6.4/totalcensus/man/table_content_acs1year_all_years.Rd |only 77 files changed, 386 insertions(+), 302 deletions(-)
Title: Manipulate MCMC Samples
Description: Functions and classes to store, manipulate and
summarise Monte Carlo Markov Chain (MCMC) samples. For more
information see Brooks et al. (2011) <isbn:978-1-4200-7941-8>.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>),
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between mcmcr versions 0.3.0 dated 2020-07-13 and 0.4.0 dated 2020-09-27
mcmcr-0.3.0/mcmcr/R/complete-terms.R |only mcmcr-0.3.0/mcmcr/man/as.mcmc.list.mcarray.Rd |only mcmcr-0.3.0/mcmcr/man/as.mcmc.list.mcmc.Rd |only mcmcr-0.3.0/mcmcr/man/as.mcmc.list.mcmc.list.Rd |only mcmcr-0.3.0/mcmcr/man/as.mcmc.list.mcmcarray.Rd |only mcmcr-0.3.0/mcmcr/man/as.mcmc.list.mcmcr.Rd |only mcmcr-0.3.0/mcmcr/man/as_nlist.mcmc.Rd |only mcmcr-0.3.0/mcmcr/man/as_nlist.mcmc.list.Rd |only mcmcr-0.3.0/mcmcr/man/as_nlists.mcmc.Rd |only mcmcr-0.3.0/mcmcr/man/bind_iterations.Rd |only mcmcr-0.3.0/mcmcr/man/collapse_chains.default.Rd |only mcmcr-0.3.0/mcmcr/man/collapse_chains.mcmc.list.Rd |only mcmcr-0.3.0/mcmcr/man/complete_terms.mcmc.Rd |only mcmcr-0.3.0/mcmcr/man/nchains.mcmc.Rd |only mcmcr-0.3.0/mcmcr/man/nchains.mcmc.list.Rd |only mcmcr-0.3.0/mcmcr/man/niters.mcmc.Rd |only mcmcr-0.3.0/mcmcr/man/niters.mcmc.list.Rd |only mcmcr-0.3.0/mcmcr/man/npdims.mcmc.list.Rd |only mcmcr-0.3.0/mcmcr/man/nterms.mcmc.Rd |only mcmcr-0.3.0/mcmcr/man/nterms.mcmc.list.Rd |only mcmcr-0.3.0/mcmcr/man/parameters-set.Rd |only mcmcr-0.3.0/mcmcr/man/parameters.Rd |only mcmcr-0.3.0/mcmcr/man/pars.mcmc.Rd |only mcmcr-0.3.0/mcmcr/man/pars.mcmc.list.Rd |only mcmcr-0.3.0/mcmcr/man/pdims.mcmc.Rd |only mcmcr-0.3.0/mcmcr/man/pdims.mcmc.list.Rd |only mcmcr-0.3.0/mcmcr/man/set_pars.mcmc.Rd |only mcmcr-0.3.0/mcmcr/man/set_pars.mcmc.list.Rd |only mcmcr-0.3.0/mcmcr/man/tidy.mcmc.Rd |only mcmcr-0.3.0/mcmcr/man/tidy.mcmc.list.Rd |only mcmcr-0.4.0/mcmcr/DESCRIPTION | 8 - mcmcr-0.4.0/mcmcr/MD5 | 163 ++++++++------------- mcmcr-0.4.0/mcmcr/NAMESPACE | 37 ---- mcmcr-0.4.0/mcmcr/NEWS.md | 10 + mcmcr-0.4.0/mcmcr/R/as-mcmc.list.R | 17 +- mcmcr-0.4.0/mcmcr/R/as-nlist.R | 12 - mcmcr-0.4.0/mcmcr/R/as-nlists.R | 6 mcmcr-0.4.0/mcmcr/R/as-term.R | 6 mcmcr-0.4.0/mcmcr/R/bind-iterations.R | 59 ------- mcmcr-0.4.0/mcmcr/R/collapse-chains.R | 20 -- mcmcr-0.4.0/mcmcr/R/export.R | 4 mcmcr-0.4.0/mcmcr/R/nchains.R | 8 - mcmcr-0.4.0/mcmcr/R/niters.R | 8 - mcmcr-0.4.0/mcmcr/R/npdims.R | 4 mcmcr-0.4.0/mcmcr/R/nterms.R | 8 - mcmcr-0.4.0/mcmcr/R/parameters.R | 68 -------- mcmcr-0.4.0/mcmcr/R/pars.R | 41 ++--- mcmcr-0.4.0/mcmcr/R/pdims.R | 8 - mcmcr-0.4.0/mcmcr/R/set-pars.R | 33 ---- mcmcr-0.4.0/mcmcr/R/sort.R | 6 mcmcr-0.4.0/mcmcr/R/subset.R | 66 -------- mcmcr-0.4.0/mcmcr/R/tidy.R | 16 -- mcmcr-0.4.0/mcmcr/build/mcmcr.pdf |binary mcmcr-0.4.0/mcmcr/inst/WORDLIST |only mcmcr-0.4.0/mcmcr/man/as_nlist.mcmcr.Rd | 4 mcmcr-0.4.0/mcmcr/man/as_nlists.mcmc.list.Rd | 2 mcmcr-0.4.0/mcmcr/man/as_nlists.mcmcr.Rd | 2 mcmcr-0.4.0/mcmcr/man/bind_chains.mcarray.Rd | 1 mcmcr-0.4.0/mcmcr/man/bind_chains.mcmc.Rd | 1 mcmcr-0.4.0/mcmcr/man/bind_chains.mcmc.list.Rd | 1 mcmcr-0.4.0/mcmcr/man/bind_chains.mcmcarray.Rd | 1 mcmcr-0.4.0/mcmcr/man/bind_chains.mcmcr.Rd | 1 mcmcr-0.4.0/mcmcr/man/collapse_chains.mcmcr.Rd | 1 mcmcr-0.4.0/mcmcr/man/estimates.mcarray.Rd | 10 - mcmcr-0.4.0/mcmcr/man/estimates.mcmc.Rd | 10 - mcmcr-0.4.0/mcmcr/man/estimates.mcmc.list.Rd | 10 - mcmcr-0.4.0/mcmcr/man/estimates.mcmcarray.Rd | 10 - mcmcr-0.4.0/mcmcr/man/estimates.mcmcr.Rd | 1 mcmcr-0.4.0/mcmcr/man/nchains.mcarray.Rd | 10 - mcmcr-0.4.0/mcmcr/man/nchains.mcmcarray.Rd | 10 - mcmcr-0.4.0/mcmcr/man/nchains.mcmcr.Rd | 10 - mcmcr-0.4.0/mcmcr/man/nchains.mcmcrs.Rd | 10 - mcmcr-0.4.0/mcmcr/man/niters.mcarray.Rd | 8 - mcmcr-0.4.0/mcmcr/man/niters.mcmcarray.Rd | 8 - mcmcr-0.4.0/mcmcr/man/niters.mcmcr.Rd | 8 - mcmcr-0.4.0/mcmcr/man/niters.mcmcrs.Rd | 8 - mcmcr-0.4.0/mcmcr/man/npdims.mcmcarray.Rd | 8 - mcmcr-0.4.0/mcmcr/man/npdims.mcmcr.Rd | 8 - mcmcr-0.4.0/mcmcr/man/nterms.mcmcarray.Rd | 13 - mcmcr-0.4.0/mcmcr/man/nterms.mcmcr.Rd | 13 - mcmcr-0.4.0/mcmcr/man/nterms.mcmcrs.Rd | 13 - mcmcr-0.4.0/mcmcr/man/pars.mcmcr.Rd | 7 mcmcr-0.4.0/mcmcr/man/pars.mcmcrs.Rd | 7 mcmcr-0.4.0/mcmcr/man/pdims.mcarray.Rd | 8 - mcmcr-0.4.0/mcmcr/man/pdims.mcmcarray.Rd | 8 - mcmcr-0.4.0/mcmcr/man/pdims.mcmcr.Rd | 8 - mcmcr-0.4.0/mcmcr/man/reexports.Rd | 17 +- mcmcr-0.4.0/mcmcr/man/set_pars.mcmcr.Rd | 10 - mcmcr-0.4.0/mcmcr/man/set_pars.mcmcrs.Rd | 10 - mcmcr-0.4.0/mcmcr/man/split_chains.mcmcarray.Rd | 10 - mcmcr-0.4.0/mcmcr/man/split_chains.mcmcr.Rd | 10 - mcmcr-0.4.0/mcmcr/man/subset.Rd | 28 --- mcmcr-0.4.0/mcmcr/tests/testthat/test-as-nlist.R | 4 mcmcr-0.4.0/mcmcr/tests/testthat/test-as-nlists.R | 4 mcmcr-0.4.0/mcmcr/tests/testthat/test-as-term.R | 8 - mcmcr-0.4.0/mcmcr/tests/testthat/test-converged.R | 20 +- mcmcr-0.4.0/mcmcr/tests/testthat/test-ess.R | 12 - mcmcr-0.4.0/mcmcr/tests/testthat/test-tidy.R | 4 98 files changed, 180 insertions(+), 785 deletions(-)
Title: Hierarchical Bayesian Vector Autoregression
Description: Estimation of hierarchical Bayesian vector autoregressive models.
Implements hierarchical prior selection for conjugate priors in the fashion
of Giannone, Lenza & Primiceri (2015) <doi:10.1162/REST_a_00483>. Functions
to compute and identify impulse responses, calculate forecasts,
forecast error variance decompositions and scenarios are available.
Several methods to print, plot and summarise results facilitate analysis.
Author: Nikolas Kuschnig [aut, cre] (<https://orcid.org/0000-0002-6642-2543>),
Lukas Vashold [aut] (<https://orcid.org/0000-0002-3562-3414>),
Michael McCracken [dtc],
Serena Ng [dtc]
Maintainer: Nikolas Kuschnig <nikolas.kuschnig@wu.ac.at>
Diff between BVAR versions 1.0.0 dated 2020-05-05 and 1.0.1 dated 2020-09-27
BVAR-1.0.0/BVAR/R/22_get.R |only BVAR-1.0.0/BVAR/R/63_fevd.R |only BVAR-1.0.1/BVAR/DESCRIPTION | 14 +- BVAR-1.0.1/BVAR/MD5 | 133 ++++++++++++------------ BVAR-1.0.1/BVAR/NEWS.md | 10 + BVAR-1.0.1/BVAR/R/10_bvar.R | 32 +---- BVAR-1.0.1/BVAR/R/11_input.R | 79 +++++++++++--- BVAR-1.0.1/BVAR/R/12_aux.R | 79 +++----------- BVAR-1.0.1/BVAR/R/13_mvtnorm.R | 7 - BVAR-1.0.1/BVAR/R/15_prep_data.R | 3 BVAR-1.0.1/BVAR/R/20_ml.R | 12 +- BVAR-1.0.1/BVAR/R/21_draw.R | 9 - BVAR-1.0.1/BVAR/R/22_calc.R |only BVAR-1.0.1/BVAR/R/30_metropolis_setup.R | 1 BVAR-1.0.1/BVAR/R/35_metropolis_print.R | 5 BVAR-1.0.1/BVAR/R/40_priors_setup.R | 1 BVAR-1.0.1/BVAR/R/41_minnesota.R | 1 BVAR-1.0.1/BVAR/R/42_dummy.R | 3 BVAR-1.0.1/BVAR/R/43_sur_soc.R | 1 BVAR-1.0.1/BVAR/R/45_priors_print.R | 11 -- BVAR-1.0.1/BVAR/R/50_fcast_setup.R | 3 BVAR-1.0.1/BVAR/R/51_fcast_compute.R | 1 BVAR-1.0.1/BVAR/R/52_fcast_cond.R | 1 BVAR-1.0.1/BVAR/R/54_predict.R | 8 - BVAR-1.0.1/BVAR/R/55_fcast_print.R | 13 -- BVAR-1.0.1/BVAR/R/58_fcast_plot.R | 6 - BVAR-1.0.1/BVAR/R/60_irf_setup.R | 69 +++++++----- BVAR-1.0.1/BVAR/R/61_irf_compute.R | 29 +++-- BVAR-1.0.1/BVAR/R/62_sign_restr.R | 69 +++++++++--- BVAR-1.0.1/BVAR/R/63_fevd_compute.R |only BVAR-1.0.1/BVAR/R/64_irf_method.R | 67 ++++++------ BVAR-1.0.1/BVAR/R/65_irf_print.R | 7 - BVAR-1.0.1/BVAR/R/68_irf_plot.R | 2 BVAR-1.0.1/BVAR/R/80_coda.R | 4 BVAR-1.0.1/BVAR/R/81_parallel.R | 3 BVAR-1.0.1/BVAR/R/85_transform.R | 16 +- BVAR-1.0.1/BVAR/R/90_print.R | 3 BVAR-1.0.1/BVAR/R/91_plot.R | 7 - BVAR-1.0.1/BVAR/R/92_coef.R | 9 - BVAR-1.0.1/BVAR/R/93_density.R | 12 -- BVAR-1.0.1/BVAR/R/94_logLik.R | 24 +++- BVAR-1.0.1/BVAR/R/95_fitted.R | 17 --- BVAR-1.0.1/BVAR/R/96_summary.R | 3 BVAR-1.0.1/BVAR/R/97_companion.R | 5 BVAR-1.0.1/BVAR/R/BVAR-package.R | 10 - BVAR-1.0.1/BVAR/R/data.R | 18 +-- BVAR-1.0.1/BVAR/R/zzz.R | 1 BVAR-1.0.1/BVAR/build/vignette.rds |binary BVAR-1.0.1/BVAR/inst/CITATION | 18 +-- BVAR-1.0.1/BVAR/inst/doc/article.Rnw | 162 +++++++++++++++--------------- BVAR-1.0.1/BVAR/inst/doc/article.pdf |binary BVAR-1.0.1/BVAR/inst/fred_trans.csv | 2 BVAR-1.0.1/BVAR/inst/tinytest/internal.R | 5 BVAR-1.0.1/BVAR/inst/tinytest/test_BVAR.R | 71 +++++++++---- BVAR-1.0.1/BVAR/man/BVAR-package.Rd | 9 - BVAR-1.0.1/BVAR/man/bv_dummy.Rd | 2 BVAR-1.0.1/BVAR/man/bv_fcast.Rd | 2 BVAR-1.0.1/BVAR/man/bv_irf.Rd | 48 +++++--- BVAR-1.0.1/BVAR/man/bvar.Rd | 13 +- BVAR-1.0.1/BVAR/man/coda.Rd | 2 BVAR-1.0.1/BVAR/man/fred_qd.Rd | 17 +-- BVAR-1.0.1/BVAR/man/fred_transform.Rd | 14 +- BVAR-1.0.1/BVAR/man/irf.bvar.Rd | 3 BVAR-1.0.1/BVAR/man/logLik.bvar.Rd |only BVAR-1.0.1/BVAR/man/par_bvar.Rd | 4 BVAR-1.0.1/BVAR/man/plot.bvar.Rd | 6 - BVAR-1.0.1/BVAR/man/plot.bvar_fcast.Rd | 2 BVAR-1.0.1/BVAR/tests/tinytest.R | 5 BVAR-1.0.1/BVAR/vignettes/article.Rnw | 162 +++++++++++++++--------------- BVAR-1.0.1/BVAR/vignettes/refs.bib | 85 +++++++++++---- 70 files changed, 776 insertions(+), 664 deletions(-)
Title: Bioequivalence Study Data Analysis
Description: Analyze bioequivalence study data with industrial strength. Sample size could be determined for various crossover designs, such as 2x2 design, 2x4 design, 4x4 design, Balaam design, Two-sequence dual design, and William design.
Reference: Chow SC, Liu JP. Design and Analysis of Bioavailability and Bioequivalence Studies. 3rd ed. (2009, ISBN:978-1-58488-668-6).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between BE versions 0.1.1 dated 2018-07-19 and 0.1.2 dated 2020-09-27
DESCRIPTION | 10 +++++----- MD5 | 42 +++++++++++++++++++++--------------------- R/be2x2.R | 2 +- R/powmse.R | 6 +++--- R/test2x2.R | 9 +++++---- inst/doc/BE-manual.pdf |binary man/BE-package.Rd | 24 +++++++++++++++++++++--- man/be2x2.Rd | 4 ++-- man/ci2cv.Rd | 2 +- man/ci2mse.Rd | 2 +- man/cv2mse.Rd | 2 +- man/hodges.Rd | 2 +- man/mse2cv.Rd | 2 +- man/plot2x2.Rd | 2 +- man/pow2x2ci.Rd | 2 +- man/pow2x2mse.Rd | 2 +- man/powcv.Rd | 22 ++++++++++++---------- man/powmse.Rd | 22 ++++++++++++---------- man/ss2x2ci.Rd | 2 +- man/sscv.Rd | 22 ++++++++++++---------- man/ssmse.Rd | 24 +++++++++++++----------- man/test2x2.Rd | 6 +++--- 22 files changed, 119 insertions(+), 92 deletions(-)
Title: An Implementation of Z-Curves
Description: An implementation of z-curves - a method for estimating expected discovery
and replicability rates on the bases of test-statistics of published studies. The package
provides functions for fitting the new density and EM version
(Bartoš & Schimmack, 2020, <doi:10.31234/osf.io/urgtn>) as well as the original density
z-curve (Brunner & Schimmack, 2017, <doi:10.31219/osf.io/wr93f>). Furthermore, the package
provides summarizing and plotting functions for the fitted z-curve objects. See the
aforementioned articles for more information about the z-curves, expected discovery
and replicability rates, validation studies, and limitations.
Author: František Bartoš [aut, cre],
Ulrich Schimmack [aut]
Maintainer: František Bartoš <f.bartos96@gmail.com>
Diff between zcurve versions 1.0.0 dated 2020-03-31 and 1.0.6 dated 2020-09-26
DESCRIPTION | 8 - MD5 | 37 +++--- NAMESPACE | 15 ++ R/main.R | 80 ++++++++------ R/tools.R | 239 ++++++++++++++++++++++++++++++++++++++++-- R/zcurve_EM.R | 40 +++---- R/zcurve_density.R | 80 +++++++------- README.md | 9 + build/partial.rdb |binary inst/CITATION | 2 man/OSC.z.Rd | 4 man/control_EM.Rd | 2 man/control_density.Rd | 2 man/control_density_v1.Rd | 2 man/is.zcurve.Rd |only man/power_to_z.Rd | 9 - man/print.estimates.zcurve.Rd |only man/print.summary.zcurve.Rd | 36 +++--- man/print.zcurve.Rd | 36 +++--- man/z_to_power.Rd | 4 man/zcurve.estimates.Rd |only 21 files changed, 434 insertions(+), 171 deletions(-)
Title: Add Gate Information to Your Tibble
Description: It interactively or programmatically label points within custom gates on two dimensions.
The information is added to your tibble. It is based on the package 'gatepoints' from Wajid Jawaid.
The benefits are (i) in interactive mode you can draw your gates on extensive 'ggplot'-like scatter plots;
(ii) you can draw multiple gates; and (iii) you can save your gates and apply the programmatically.
Author: Stefano Mangiola [aut, cre],
Wajid Jawaid [ctb]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>
Diff between tidygate versions 0.2.7 dated 2020-07-06 and 0.2.8 dated 2020-09-26
DESCRIPTION | 8 +++---- MD5 | 16 +++++++-------- NAMESPACE | 3 ++ R/functions.R | 47 ++++++++++++++++++++++++++++---------------- R/methods.R | 51 ++++++++++++++++++++++++++++++------------------ build/tidygate.pdf |binary build/vignette.rds |binary man/gate-methods.Rd | 13 ++++++++---- man/gate_interactive.Rd | 3 ++ 9 files changed, 89 insertions(+), 52 deletions(-)
Title: Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)
Description: Designed to be compatible with the R package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this 'Python' 'Boto3' Software Development Kit ('SDK')
<https://boto3.amazonaws.com/v1/documentation/api/latest/index.html> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between RAthena versions 1.10.0 dated 2020-08-06 and 1.10.1 dated 2020-09-26
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 7 ++++++- R/Connection.R | 4 ++-- R/Options.R | 2 +- R/View.R | 4 ++-- inst/doc/getting_started.Rmd | 2 +- inst/doc/getting_started.html | 2 +- vignettes/getting_started.Rmd | 2 +- 9 files changed, 25 insertions(+), 20 deletions(-)
Title: Comfortable Search for R Packages on CRAN, Either Directly from
the R Console or with an R Studio Add-in
Description: Search for R packages on CRAN directly from the R console, based on the packages' titles, short and long descriptions, or other fields. Combine multiple keywords with logical operators ('and', 'or'), view detailed information on any package and keep track of the latest package contributions to CRAN. If you don't want to search from the R console, use the comfortable R Studio add-in.
Author: Joachim Zuckarelli [aut, cre] (<https://orcid.org/0000-0002-9280-3016>)
Maintainer: Joachim Zuckarelli <joachim@zuckarelli.de>
Diff between packagefinder versions 0.3.0 dated 2020-09-14 and 0.3.1 dated 2020-09-26
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ R/packagefinder.r | 10 ++++++---- README.md | 8 +++++++- 5 files changed, 29 insertions(+), 13 deletions(-)
Title: Estimation of Model-Based Predictions, Contrasts and Means
Description: Implements a general interface for model-based estimations for a wide variety of models (see support list of insight; Lüdecke, Waggoner & Makowski (2019) <doi:10.21105/joss.01412>), used in the computation of marginal means, contrast analysis and predictions.
Author: Dominique Makowski [aut, cre] (<https://orcid.org/0000-0001-5375-9967>),
Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>),
Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between modelbased versions 0.1.2 dated 2020-03-12 and 0.3.0 dated 2020-09-26
DESCRIPTION | 15 - MD5 | 93 ++++---- NAMESPACE | 14 + NEWS.md | 23 ++ R/estimate_contrasts.bayesian.R | 54 +++-- R/estimate_contrasts.frequentist.R | 36 ++- R/estimate_means.bayesian.R | 58 ++--- R/estimate_means.frequentist.R | 30 +- R/estimate_response.bayesian.R | 37 ++- R/estimate_response.frequentist.R | 19 + R/estimate_slopes.R | 81 +++++-- R/estimate_smooth.R | 19 + R/print.R | 2 R/reshape_draws.R | 2 R/signal.R | 3 R/utils.R | 11 - R/utils_clean_names.R |only R/utils_emmeans_wrapper.R | 89 ++++---- R/utils_estimate_response_init.R | 1 R/utils_guess_arguments.R |only R/utils_predict_wrapper.R | 79 +++++-- R/visualisation_matrix.R | 33 ++- README.md | 90 ++++---- inst |only man/as.numeric_ifnumeric.Rd | 41 +-- man/dot-uniroot.all.Rd | 40 +-- man/estimate_contrasts.lm.Rd | 138 ++++++------ man/estimate_contrasts.stanreg.Rd | 197 +++++++++--------- man/estimate_means.lm.Rd | 121 +++++------ man/estimate_means.stanreg.Rd | 139 ++++++------ man/estimate_response.glm.Rd | 138 ++++++------ man/estimate_response.stanreg.Rd | 268 ++++++++++++------------- man/estimate_slopes.Rd | 100 +++++---- man/estimate_slopes.lm.Rd | 86 ++++---- man/estimate_slopes.stanreg.Rd | 146 ++++++------- man/estimate_smooth.Rd | 80 +++---- man/estimate_smooth.stanreg.Rd | 106 ++++----- man/figures/unnamed-chunk-13-1.png |binary man/figures/unnamed-chunk-5-1.png |binary man/figures/unnamed-chunk-8-1.png |binary man/find_inversions.Rd | 43 +--- tests/testthat/test-attributes_visualisation.R | 3 tests/testthat/test-estimate_contrasts.R | 141 +++++++++++-- tests/testthat/test-estimate_means.R | 146 ++++++++++++- tests/testthat/test-estimate_response.R | 55 +++-- tests/testthat/test-estimate_slopes.R | 27 +- tests/testthat/test-estimate_smooth.R | 11 - tests/testthat/test-glmmTMB.R |only tests/testthat/test-mgcv.R |only tests/testthat/test-visualisation_matrix.R | 4 50 files changed, 1658 insertions(+), 1161 deletions(-)
Title: Covariate-Adaptive Randomization for Clinical Trials
Description: Provides functions and command-line user interface to generate allocation sequence by covariate-adaptive randomization for clinical trials. The package currently supports six covariate-adaptive randomization procedures. Three hypothesis testing methods that are valid and robust under covariate-adaptive randomization are also available in the package to facilitate the inference for treatment effect under the included randomization procedures. Additionally, the package provides comprehensive and efficient tools to allow one to evaluate and compare the performance of randomization procedures and tests based on various criteria.
Author: Fuyi Tu [aut],
Xiaoqing Ye [aut, cre],
Wei Ma [aut, ths],
Feifang Hu [aut, ths]
Maintainer: Xiaoqing Ye <ye_xiaoq@163.com>
Diff between carat versions 1.3 dated 2020-09-08 and 1.4 dated 2020-09-26
carat-1.3/carat/R/class_plottest.R |only carat-1.3/carat/man/print.carandom.Rd |only carat-1.3/carat/src/All.cpp |only carat-1.4/carat/DESCRIPTION | 26 - carat-1.4/carat/MD5 | 51 +- carat-1.4/carat/NAMESPACE | 10 carat-1.4/carat/R/RcppExports.R | 602 ++++++++++++++++----------------- carat-1.4/carat/R/class_plotrandtest.R |only carat-1.4/carat/R/rand_CLI.R | 14 carat-1.4/carat/R/rand_evalRand.R | 1 carat-1.4/carat/R/test_Rfunction.R | 357 +++++++++---------- carat-1.4/carat/data/pats.rda |binary carat-1.4/carat/inst/NEWS.Rd | 17 carat-1.4/carat/man/AdjBCD.sim.Rd | 3 carat-1.4/carat/man/AdjBCD.ui.Rd | 3 carat-1.4/carat/man/DoptBCD.sim.Rd | 3 carat-1.4/carat/man/DoptBCD.ui.Rd | 3 carat-1.4/carat/man/HuHuCAR.sim.Rd | 3 carat-1.4/carat/man/HuHuCAR.ui.Rd | 3 carat-1.4/carat/man/PocSimMIN.sim.Rd | 3 carat-1.4/carat/man/PocSimMIN.ui.Rd | 3 carat-1.4/carat/man/StrBCD.sim.Rd | 3 carat-1.4/carat/man/StrBCD.ui.Rd | 3 carat-1.4/carat/man/StrPBR.sim.Rd | 3 carat-1.4/carat/man/StrPBR.ui.Rd | 3 carat-1.4/carat/man/carat-package.Rd | 78 ++-- carat-1.4/carat/src/InnerFun.cpp |only carat-1.4/carat/src/Makevars | 5 carat-1.4/carat/src/RcppExports.cpp | 12 29 files changed, 609 insertions(+), 600 deletions(-)
Title: Software for Project AERO
Description: Implements methods for anticipating the emergence and eradication
of infectious diseases from surveillance time series. Also provides support
for computational experiments testing the performance of such methods.
Author: Eamon O'Dea [aut, cre]
Maintainer: Eamon O'Dea <odea35@gmail.com>
Diff between spaero versions 0.5.0 dated 2019-05-24 and 0.6.0 dated 2020-09-26
DESCRIPTION | 12 ++++---- MD5 | 16 +++++------ NEWS.md | 5 +++ R/simulation.R | 54 +++++++++------------------------------ README.md | 3 -- build/vignette.rds |binary inst/doc/spaero-introduction.pdf |binary man/create_simulator.Rd | 14 +++++----- man/get_stats.Rd | 15 +++++++--- 9 files changed, 52 insertions(+), 67 deletions(-)
Title: Methods and Measures for Semantic Network Analysis
Description: Implements several functions for the analysis of semantic networks including different network estimation algorithms, partial node bootstrapping (Kenett, Anaki, & Faust, 2014 <doi:10.3389/fnhum.2014.00407>), random walk simulation (Kenett & Austerweil, 2016 <http://alab.psych.wisc.edu/papers/files/Kenett16CreativityRW.pdf>), and a function to compute global network measures. Significance tests and plotting features are also implemented.
Author: Alexander P. Christensen [aut, cre]
(<https://orcid.org/0000-0002-9798-7037>),
Yoed N. Kenett [aut, ctb] (<https://orcid.org/0000-0003-3872-7689>)
Maintainer: Alexander P. Christensen <alexpaulchristensen@gmail.com>
Diff between SemNeT versions 1.3.0 dated 2020-06-09 and 1.4.0 dated 2020-09-26
SemNeT-1.3.0/SemNeT/build |only SemNeT-1.3.0/SemNeT/inst/doc |only SemNeT-1.3.0/SemNeT/vignettes |only SemNeT-1.4.0/SemNeT/DESCRIPTION | 20 SemNeT-1.4.0/SemNeT/MD5 | 93 - SemNeT-1.4.0/SemNeT/NAMESPACE | 14 SemNeT-1.4.0/SemNeT/NEWS | 55 SemNeT-1.4.0/SemNeT/R/ASPL.R |only SemNeT-1.4.0/SemNeT/R/CC.R |only SemNeT-1.4.0/SemNeT/R/CN.R | 17 SemNeT-1.4.0/SemNeT/R/NRW.R | 10 SemNeT-1.4.0/SemNeT/R/PF.R | 109 - SemNeT-1.4.0/SemNeT/R/Q.R |only SemNeT-1.4.0/SemNeT/R/SemNeTShiny.R | 6 SemNeT-1.4.0/SemNeT/R/TMFG.R |only SemNeT-1.4.0/SemNeT/R/bootSemNeT.R | 219 ++- SemNeT-1.4.0/SemNeT/R/compare_nets.R | 20 SemNeT-1.4.0/SemNeT/R/convert2cytoscape.R | 8 SemNeT-1.4.0/SemNeT/R/convert2igraph.R |only SemNeT-1.4.0/SemNeT/R/equate.R | 5 SemNeT-1.4.0/SemNeT/R/methods.R | 6 SemNeT-1.4.0/SemNeT/R/permSemNeT.R |only SemNeT-1.4.0/SemNeT/R/plot.bootSemNeT.R | 2 SemNeT-1.4.0/SemNeT/R/randnet.test.R | 38 SemNeT-1.4.0/SemNeT/R/randwalk.R | 121 + SemNeT-1.4.0/SemNeT/R/semnetmeas.R | 13 SemNeT-1.4.0/SemNeT/R/test.bootSemNeT.R | 300 ++-- SemNeT-1.4.0/SemNeT/R/utils-SemNeT.R | 896 +++++++------- SemNeT-1.4.0/SemNeT/R/utils-SemNeTShiny.R | 1355 ++++++++++++--------- SemNeT-1.4.0/SemNeT/R/zzz.R | 5 SemNeT-1.4.0/SemNeT/data/open.clean.RData |binary SemNeT-1.4.0/SemNeT/data/two.result.RData |binary SemNeT-1.4.0/SemNeT/inst/Shiny/server.R | 1718 ++++++++++++++++++++++++--- SemNeT-1.4.0/SemNeT/inst/Shiny/ui.R | 279 +++- SemNeT-1.4.0/SemNeT/man/ASPL.Rd |only SemNeT-1.4.0/SemNeT/man/CC.Rd |only SemNeT-1.4.0/SemNeT/man/CN.Rd | 7 SemNeT-1.4.0/SemNeT/man/NRW.Rd | 2 SemNeT-1.4.0/SemNeT/man/PF.Rd | 8 SemNeT-1.4.0/SemNeT/man/Q.Rd |only SemNeT-1.4.0/SemNeT/man/SemNeTShiny.Rd | 6 SemNeT-1.4.0/SemNeT/man/TMFG.Rd |only SemNeT-1.4.0/SemNeT/man/bootSemNeT.Rd | 22 SemNeT-1.4.0/SemNeT/man/compare_nets.Rd | 6 SemNeT-1.4.0/SemNeT/man/convert2cytoscape.Rd | 8 SemNeT-1.4.0/SemNeT/man/convert2igraph.Rd |only SemNeT-1.4.0/SemNeT/man/equate.Rd | 3 SemNeT-1.4.0/SemNeT/man/plot.animateShiny.Rd |only SemNeT-1.4.0/SemNeT/man/plot.compareShiny.Rd | 6 SemNeT-1.4.0/SemNeT/man/randnet.test.Rd | 16 SemNeT-1.4.0/SemNeT/man/randwalk.Rd | 14 SemNeT-1.4.0/SemNeT/man/semnetmeas.Rd | 4 SemNeT-1.4.0/SemNeT/man/test.bootSemNeT.Rd | 38 53 files changed, 3870 insertions(+), 1579 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-07-20 0.1.4
Title: FDR Power
Description: This is a package for calculating two differing notions of power, or deriving sample
sizes for specified requisite power in multiple testing experiments under a variety of methods for
control of the distribution of the False Discovery Proportion (FDP). More specifically, one can
choose to control the FDP distribution according to control of its (i) mean, e.g. the usual BH-FDR
procedure, or via the probability that it exceeds a given value, delta, via (ii) the Romano
procedure, or via (iii) my procedure based upon asymptotic approximation. Likewise, we can think of
the power in multiple testing experiments in terms of a summary of the distribution of the
True Positive Proportion (TPP). The package will compute power, sample size or any other missing
parameter required for power based upon (i) the mean of the TPP which is the average power
(ii) the probability that the TPP exceeds a given value, lambda, via my asymptotic approximation
procedure. The theoretical results are described in Izmirlian, G. (2020) Stat. and Prob. letters,
<doi:10.1016/j.spl.2020.108713>, and an applied paper describing the methodology with a
simulation study is in preparation.
Author: Grant Izmirlian Jr <izmirlig@mail.nih.gov>
Maintainer: Grant Izmirlian Jr <izmirlig@mail.nih.gov>
Diff between pwrFDR versions 1.95 dated 2018-08-22 and 2.8.4 dated 2020-09-26
pwrFDR-1.95/pwrFDR/man/Ch02-controlFDF.Rd |only pwrFDR-1.95/pwrFDR/man/Ch03-dists.Rd |only pwrFDR-1.95/pwrFDR/man/Ch04-detail.Rd |only pwrFDR-1.95/pwrFDR/man/Ch05-cCDF.SoM.Rd |only pwrFDR-1.95/pwrFDR/man/Ch06-cCDF.ToJ.Rd |only pwrFDR-1.95/pwrFDR/man/Ch07-CDF.Pval.Rd |only pwrFDR-1.95/pwrFDR/man/Ch08-CDF.Pval.HA.Rd |only pwrFDR-1.95/pwrFDR/man/Ch09-var.J.o.rtm.Rd |only pwrFDR-1.95/pwrFDR/man/Ch10-var.rtm.SoM.Rd |only pwrFDR-1.95/pwrFDR/man/Ch11-var.rtm.ToJ.Rd |only pwrFDR-1.95/pwrFDR/man/Ch12-logit.Rd |only pwrFDR-1.95/pwrFDR/man/Ch13-logitInv.Rd |only pwrFDR-1.95/pwrFDR/man/Ch14-over.Rd |only pwrFDR-1.95/pwrFDR/man/Ch15-concat.Rd |only pwrFDR-1.95/pwrFDR/man/Ch16-gentempfilenm.Rd |only pwrFDR-2.8.4/pwrFDR/DESCRIPTION | 25 pwrFDR-2.8.4/pwrFDR/MD5 | 54 pwrFDR-2.8.4/pwrFDR/NAMESPACE | 11 pwrFDR-2.8.4/pwrFDR/R/pwrFDR.R | 2672 ++++++++++++----------- pwrFDR-2.8.4/pwrFDR/man/Ch01-pwrFDR.Rd | 463 ++- pwrFDR-2.8.4/pwrFDR/man/Ch02-pwrFDR-grid.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch03-controlFDP.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch04-dists.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch05-detail.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch06-cCDF-Rom.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch07-cCDF-ToM.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch08-cCDF-VoR.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch09-CDF-Pval.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch10-CDF-Pval-HA.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch11-sd-rtm-Rom.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch12-sd-rtm-ToM.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch13-sd-rtm-VoR.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch14-logit.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch15-logitInv.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch16-over.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch17-concat.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch18-gentempfilenm.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch19-CDF-Pval-ua-eq-u.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch20-CDF-Pval-ar-eq-u.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch21-cc-ROC.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch22-es-ROC.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch23-criterion.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch24-arg-vals.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch25-if-0-rm.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch26-if-na-x.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch27-if-y-z.Rd |only pwrFDR-2.8.4/pwrFDR/man/Ch28-nna.Rd |only pwrFDR-2.8.4/pwrFDR/src/pwrFDRsim.c | 115 pwrFDR-2.8.4/pwrFDR/src/pwrFDRsimCS.c | 103 49 files changed, 2012 insertions(+), 1431 deletions(-)
Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for more details.
Author: Rahul Satija [aut] (<https://orcid.org/0000-0001-9448-8833>),
Andrew Butler [aut] (<https://orcid.org/0000-0003-3608-0463>),
Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>),
Tim Stuart [aut] (<https://orcid.org/0000-0002-3044-0897>),
Jeff Farrell [ctb],
Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>),
Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>),
Patrick Roelli [ctb],
Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>)
Maintainer: Paul Hoffman <nygcSatijalab@nygenome.org>
Diff between Seurat versions 3.2.1 dated 2020-09-07 and 3.2.2 dated 2020-09-26
DESCRIPTION | 10 MD5 | 44 +-- NAMESPACE | 1 NEWS.md | 8 R/clustering.R | 6 R/dimensional_reduction.R | 18 - R/generics.R | 14 - R/integration.R | 408 ++++++++++++++++++------------------ R/objects.R | 18 - R/preprocessing.R | 10 R/utilities.R | 2 R/visualization.R | 32 +- README.md | 2 man/AddModuleScore.Rd | 2 man/FindIntegrationAnchors.Rd | 36 +-- man/FindTransferAnchors.Rd | 66 ++--- man/GetTransferPredictions.Rd | 6 man/IntegrateData.Rd | 62 ++--- man/PrepSCTIntegration.Rd | 22 - man/SelectIntegrationFeatures.Rd | 12 - man/TransferData.Rd | 42 +-- tests/testthat/test_objects.R | 15 - tests/testthat/test_preprocessing.R | 16 - 23 files changed, 435 insertions(+), 417 deletions(-)
Title: Dictionaries for the 'SemNetCleaner' Package
Description: Implements dictionaries that can be used in the 'SemNetCleaner' package. Also includes several functions aimed at facilitating the text cleaning analysis in the 'SemNetCleaner' package. This package is designed to integrate and update word lists and dictionaries based on each user's individual needs by allowing users to store and save their own dictionaries. Dictionaries can be added to the 'SemNetDictionaries' package by submitting user-defined dictionaries to <https://github.com/AlexChristensen/SemNetDictionaries>.
Author: Alexander P. Christensen [aut, cre]
(<https://orcid.org/0000-0002-9798-7037>)
Maintainer: Alexander P. Christensen <alexpaulchristensen@gmail.com>
Diff between SemNetDictionaries versions 0.1.6 dated 2020-06-08 and 0.1.7 dated 2020-09-26
SemNetDictionaries-0.1.6/SemNetDictionaries/build |only SemNetDictionaries-0.1.6/SemNetDictionaries/inst/doc |only SemNetDictionaries-0.1.6/SemNetDictionaries/vignettes |only SemNetDictionaries-0.1.7/SemNetDictionaries/DESCRIPTION | 15 +++--- SemNetDictionaries-0.1.7/SemNetDictionaries/MD5 | 23 +++------- SemNetDictionaries-0.1.7/SemNetDictionaries/NEWS | 7 +++ SemNetDictionaries-0.1.7/SemNetDictionaries/R/append.dictionary.R | 18 +++---- SemNetDictionaries-0.1.7/SemNetDictionaries/R/find.dictionaries.R | 15 ++++-- SemNetDictionaries-0.1.7/SemNetDictionaries/R/load.dictionaries.R | 20 +++++--- SemNetDictionaries-0.1.7/SemNetDictionaries/R/zzz.R | 4 - SemNetDictionaries-0.1.7/SemNetDictionaries/man/find.dictionaries.Rd | 6 +- SemNetDictionaries-0.1.7/SemNetDictionaries/man/load.dictionaries.Rd | 10 +++- 12 files changed, 66 insertions(+), 52 deletions(-)
More information about SemNetDictionaries at CRAN
Permanent link
Title: Latent Variable Models
Description: A general implementation of Structural Equation Models
with latent variables (MLE, 2SLS, and composite likelihood
estimators) with both continuous, censored, and ordinal
outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>).
Mixture latent variable models and non-linear latent variable models
(Holst and Budtz-Joergensen (2019) <doi:10.1093/biostatistics/kxy082>).
The package also provides methods for graph exploration (d-separation,
back-door criterion), simulation of general non-linear latent variable
models, and estimation of influence functions for a broad range of
statistical models.
Author: Klaus K. Holst [aut, cre],
Brice Ozenne [ctb],
Thomas Gerds [ctb]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between lava versions 1.6.7 dated 2020-03-05 and 1.6.8 dated 2020-09-26
lava-1.6.7/lava/NEWS |only lava-1.6.7/lava/inst/doc/reference.pdf |only lava-1.6.7/lava/inst/gof1.png |only lava-1.6.7/lava/inst/lava1.png |only lava-1.6.7/lava/inst/me1.png |only lava-1.6.7/lava/inst/mediation1.png |only lava-1.6.7/lava/inst/mediation2.png |only lava-1.6.8/lava/DESCRIPTION | 25 +-- lava-1.6.8/lava/MD5 | 134 +++++++++-------- lava-1.6.8/lava/NAMESPACE | 1 lava-1.6.8/lava/NEWS.md |only lava-1.6.8/lava/R/addhook.R | 2 lava-1.6.8/lava/R/complik.R | 13 - lava-1.6.8/lava/R/constrain.R | 6 lava-1.6.8/lava/R/covariance.R | 6 lava-1.6.8/lava/R/estimate.lvm.R | 2 lava-1.6.8/lava/R/mixture.R | 54 +++--- lava-1.6.8/lava/R/mvnmix.R | 61 +++---- lava-1.6.8/lava/R/normal.R | 4 lava-1.6.8/lava/R/parameter.R | 1 lava-1.6.8/lava/R/profile.R | 5 lava-1.6.8/lava/R/twostage.R | 37 +++- lava-1.6.8/lava/R/utils.R | 6 lava-1.6.8/lava/R/wkm.R | 10 - lava-1.6.8/lava/README.md |only lava-1.6.8/lava/build |only lava-1.6.8/lava/data/bmd.rda |binary lava-1.6.8/lava/data/bmidata.rda |binary lava-1.6.8/lava/data/brisa.rda |binary lava-1.6.8/lava/data/calcium.rda |binary lava-1.6.8/lava/data/hubble.rda |binary lava-1.6.8/lava/data/hubble2.rda |binary lava-1.6.8/lava/data/indoorenv.rda |binary lava-1.6.8/lava/data/missingdata.rda |binary lava-1.6.8/lava/data/nldata.rda |binary lava-1.6.8/lava/data/nsem.rda |binary lava-1.6.8/lava/data/semdata.rda |binary lava-1.6.8/lava/data/serotonin.rda |binary lava-1.6.8/lava/data/serotonin2.rda |binary lava-1.6.8/lava/data/twindata.rda |binary lava-1.6.8/lava/inst/doc/correlation.R |only lava-1.6.8/lava/inst/doc/correlation.Rmd |only lava-1.6.8/lava/inst/doc/correlation.html |only lava-1.6.8/lava/inst/doc/gof.R |only lava-1.6.8/lava/inst/doc/gof.Rmd |only lava-1.6.8/lava/inst/doc/gof.html |only lava-1.6.8/lava/inst/doc/nonlinear.R |only lava-1.6.8/lava/inst/doc/nonlinear.Rmd |only lava-1.6.8/lava/inst/doc/nonlinear.html |only lava-1.6.8/lava/man/bmd.Rd | 4 lava-1.6.8/lava/man/bmidata.Rd | 4 lava-1.6.8/lava/man/brisa.Rd | 4 lava-1.6.8/lava/man/calcium.Rd | 6 lava-1.6.8/lava/man/complik.Rd | 4 lava-1.6.8/lava/man/figures |only lava-1.6.8/lava/man/hubble.Rd | 4 lava-1.6.8/lava/man/hubble2.Rd | 4 lava-1.6.8/lava/man/indoorenv.Rd | 4 lava-1.6.8/lava/man/missingdata.Rd | 4 lava-1.6.8/lava/man/mixture.Rd | 14 + lava-1.6.8/lava/man/nldata.Rd | 4 lava-1.6.8/lava/man/nsem.Rd | 4 lava-1.6.8/lava/man/semdata.Rd | 4 lava-1.6.8/lava/man/serotonin.Rd | 4 lava-1.6.8/lava/man/serotonin2.Rd | 4 lava-1.6.8/lava/man/twindata.Rd | 4 lava-1.6.8/lava/man/twostageCV.Rd | 11 - lava-1.6.8/lava/tests/testthat/test-constrain.R | 21 +- lava-1.6.8/lava/tests/testthat/test-estimate_default.R | 16 +- lava-1.6.8/lava/tests/testthat/test-inference.R | 82 +++++----- lava-1.6.8/lava/vignettes |only 71 files changed, 333 insertions(+), 240 deletions(-)
Title: Interactive Interface to Data Envelopment Analysis Modeling
Description: Allows the user to execute interactively radial data envelopment analysis models. The user has the ability to upload a data frame,
select the input/output variables, choose the technology assumption to adopt and decide whether to run an input or an output oriented model.
When the model is executed a set of results are displayed which include efficiency scores, peers' determination, scale efficiencies' evaluation
and slacks' calculation. Fore more information about the theoretical background of the package,
please refer to Bogetoft & Otto (2011) <doi:10.1007/978-1-4419-7961-2>.
Author: Mohamed El Fodil Ihaddaden
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>
Diff between farrell versions 0.2.0 dated 2020-06-03 and 0.2.1 dated 2020-09-26
DESCRIPTION | 8 - LICENSE | 4 MD5 | 31 +++-- NAMESPACE | 10 - NEWS.md |only R/farrell.R | 17 +-- R/globals.R | 6 - R/utils-pipe.R | 22 ++-- README.md | 254 +++++++++++++++++++++++++----------------------- build/vignette.rds |binary inst/doc/Intro.R | 5 inst/doc/Intro.Rmd | 229 ++++++++++++++++++++++++------------------- inst/doc/Intro.html | 58 +++++++++- inst/rstudio/addins.dcf | 10 - man/farrell.Rd | 42 +++---- man/pipe.Rd | 24 ++-- vignettes/Intro.Rmd | 229 ++++++++++++++++++++++++------------------- 17 files changed, 529 insertions(+), 420 deletions(-)
Title: Helper Functions for Bayesian Analyses
Description: Functions to 'numericise' 'R' objects (coerce to numeric objects)
and summarise 'MCMC' (Monte Carlo Markov Chain) samples
as well as 'R' translations of 'BUGS' (Bayesian Using Gibbs Sampling)
and 'JAGS' (Just Another Gibbs Sampler) functions.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>),
Kirill Müller [ctb] (<https://orcid.org/0000-0002-1416-3412>),
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between extras versions 0.0.1 dated 2020-06-16 and 0.1.0 dated 2020-09-26
DESCRIPTION | 15 +++++++--- MD5 | 54 +++++++++++++++++++++++++------------- NAMESPACE | 9 ++++++ NEWS.md | 7 ++++ R/as-list.R |only R/chk-index.R |only R/chk-indices.R |only R/chk-pars.R | 13 +++------ R/par-pattern.R |only R/params.R | 2 + R/pextreme.R |only R/pvalue.R | 2 - R/sextreme.R |only R/svalue.R | 2 - README.md | 4 +- inst/WORDLIST | 4 +- man/as_list_unnamed.Rd |only man/chk_index.Rd |only man/chk_indices.Rd |only man/chk_pars.Rd | 5 ++- man/extras-package.Rd | 3 +- man/ilogit.Rd | 2 - man/logit.Rd | 2 - man/par_pattern.Rd |only man/params.Rd | 3 ++ man/pextreme.Rd |only man/phi.Rd | 2 - man/pvalue.Rd | 2 - man/sextreme.Rd |only man/svalue.Rd | 2 - tests/testthat/test-as-list.R |only tests/testthat/test-chk-index.R |only tests/testthat/test-chk-indices.R |only tests/testthat/test-chk-pars.R | 15 ++-------- tests/testthat/test-par-pattern.R |only tests/testthat/test-pextreme.R |only tests/testthat/test-sextreme.R |only 37 files changed, 92 insertions(+), 56 deletions(-)
Title: Cycle Routing and Data for Cycling Advocacy
Description: An interface to the cycle routing/data services provided by 'CycleStreets',
a not-for-profit social enterprise and advocacy organisation.
The application programming interfaces (APIs) provided by 'CycleStreets' are documented at (<https://www.cyclestreets.net/api/>).
The focus of this package is the journey planning API, which aims to emulate the routes taken by a knowledgeable cyclist.
An innovative feature of the routing service of its provision of fastest, quietest and balanced profiles.
These represent routes taken to minimise time, avoid traffic and compromise between the two, respectively.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>),
Martin Lucas-Smith [aut],
Eric Krueger [ctb],
Joey Talbot [aut] (<https://orcid.org/0000-0002-6520-4560>)
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between cyclestreets versions 0.1.5 dated 2018-05-06 and 0.3.0 dated 2020-09-26
cyclestreets-0.1.5/cyclestreets/R/hello.R |only cyclestreets-0.3.0/cyclestreets/DESCRIPTION | 21 cyclestreets-0.3.0/cyclestreets/MD5 | 27 - cyclestreets-0.3.0/cyclestreets/NAMESPACE | 1 cyclestreets-0.3.0/cyclestreets/NEWS.md | 6 cyclestreets-0.3.0/cyclestreets/R/data.R |only cyclestreets-0.3.0/cyclestreets/R/journey.R | 238 +++++++++- cyclestreets-0.3.0/cyclestreets/README.md | 30 - cyclestreets-0.3.0/cyclestreets/data |only cyclestreets-0.3.0/cyclestreets/inst/extdata/journey-2018.json |only cyclestreets-0.3.0/cyclestreets/inst/extdata/journey.json | 2 cyclestreets-0.3.0/cyclestreets/inst/gradient-tests.R |only cyclestreets-0.3.0/cyclestreets/man/cyclestreets_column_names.Rd |only cyclestreets-0.3.0/cyclestreets/man/figures/README-example-1.png |binary cyclestreets-0.3.0/cyclestreets/man/figures/README-unnamed-chunk-2-1.png |binary cyclestreets-0.3.0/cyclestreets/man/journey.Rd | 55 +- cyclestreets-0.3.0/cyclestreets/man/json2sf_cs.Rd | 38 + cyclestreets-0.3.0/cyclestreets/man/smooth_with_cutoffs.Rd |only 18 files changed, 361 insertions(+), 57 deletions(-)
Title: Measuring Morphological Diversity and Evolutionary Tempo
Description: Measures morphological diversity from discrete character data and
estimates evolutionary tempo on phylogenetic trees. Imports morphological
data from #NEXUS (Maddison et al. (1997) <doi:10.1093/sysbio/46.4.590>)
format with read_nexus_matrix(), and writes to both #NEXUS and TNT format
(Goloboff et al. (2008) <doi:10.1111/j.1096-0031.2008.00217.x>). Main
functions are test_rates(), which implements AIC and likelihood
ratio tests for discrete character rates introduced across Lloyd et al.
(2012) <doi:10.1111/j.1558-5646.2011.01460.x>, Brusatte et al. (2014)
<doi:10.1016/j.cub.2014.08.034>, Close et al. (2015)
<doi:10.1016/j.cub.2015.06.047>, and Lloyd (2016) <doi:10.1111/bij.12746>,
and MatrixDistances(), which implements multiple discrete character
distance metrics from Gower (1971) <doi:10.2307/2528823>, Wills (1998)
<doi:10.1006/bijl.1998.0255>, Lloyd (2016) <doi:10.1111/bij.12746>, and
Hopkins and St John (2018) <doi:10.1098/rspb.2018.1784>. This also includes
the GED correction from Lehmann et al. (2019) <doi:10.1111/pala.12430>.
Multiple functions implement morphospace plots:
plot_chronophylomorphospace() implements Sakamoto and Ruta (2012)
<doi:10.1371/journal.pone.0039752>, plot_morphospace() implements Wills et
al. (1994) <doi:10.1017/S009483730001263X>, plot_changes_on_tree()
implements Wang and Lloyd (2016) <doi:10.1098/rspb.2016.0214>, and
plot_morphospace_stack() implements Foote (1993)
<doi:10.1017/S0094837300015864>. Other functions include
safe_taxonomic_reduction(), which implements Wilkinson (1995)
<doi:10.1093/sysbio/44.4.501>, map_dollo_changes() implements
the Dollo stochastic character mapping of Tarver et al. (2018)
<doi:10.1093/gbe/evy096>, and estimate_ancestral_states() implements
the ancestral state options of Lloyd (2018) <doi:10.1111/pala.12380>.
Author: Graeme T. Lloyd [aut, cre, cph],
Thomas Guillerme [aut, cph],
Emma Sherratt [aut, cph],
Steve C. Wang [aut, cph]
Maintainer: Graeme T. Lloyd <graemetlloyd@gmail.com>
Diff between Claddis versions 0.6.1 dated 2020-08-26 and 0.6.3 dated 2020-09-26
CHANGELOG | 21 +++++++++++ DESCRIPTION | 11 ++--- MD5 | 59 ++++++++++++++++--------------- NAMESPACE | 13 +++++- R/Claddis-package.R | 1 R/assign_taxa_to_bins.R | 2 - R/bin_character_completeness.R | 3 + R/build_cladistic_matrix.R | 10 ++++- R/calculate_morphological_distances.R | 7 ++- R/compactify_matrix.R | 9 +++- R/constructors.r |only R/estimate_ancestral_states.R | 7 ++- R/map_stochastic_changes.R | 5 ++ R/ordinate_cladistic_matrix.R | 3 + R/plot_morphospace.R | 3 - R/plot_morphospace_stack.R | 19 +++++++-- R/print.cladisticMatrix.r |only R/prune_cladistic_matrix.R | 6 +++ R/read_nexus_matrix.R | 15 +++++-- R/safe_taxonomic_reduction.R | 3 + R/test_rates.R | 9 +++- R/trim_marginal_whitespace.r |only R/write_nexus_matrix.R | 3 + R/write_tnt_matrix.R | 3 + README.md | 30 +++++++++++---- data/day_2016.RData |binary data/gauthier_1986.RData |binary data/michaux_1989.RData |binary man/calculate_morphological_distances.Rd | 2 - man/plot_morphospace.Rd | 3 - man/print.cladisticMatrix.Rd |only man/test_rates.Rd | 4 +- man/trim_marginal_whitespace.Rd |only 33 files changed, 176 insertions(+), 75 deletions(-)
Title: Obtaining Star Schemas from Flat Tables
Description: Data in multidimensional systems is obtained from
operational systems and is transformed to adapt it to the new
structure. Frequently, the operations to be performed aim to
transform a flat table into a star schema. Transformations can
be carried out using professional ETL (extract, transform and
load) tools or tools intended for data transformation for end
users. With the tools mentioned, this transformation can be
carried out, but it requires a lot of work. The main objective
this package is to define transformations that allow obtaining
star schemas from flat tables easily. In addition, it includes
basic data cleaning, dimension enrichment, incremental data
refresh and query operations, adapted to this context.
Author: Jose Samos [aut, cre, cph] (<https://orcid.org/0000-0002-4457-3439>)
Maintainer: Jose Samos <jsamos@ugr.es>
Diff between starschemar versions 1.1.0 dated 2020-09-13 and 1.2.0 dated 2020-09-25
DESCRIPTION | 6 MD5 | 73 NAMESPACE | 6 NEWS.md | 6 R/constellation_get_star_schema.R |only R/data.R | 38 R/dimensional_query_filter_dimension.R | 2 R/dimensional_query_run_query.R | 17 R/dimensional_query_select_fact.R | 4 R/multistar_as_flat_table.R | 30 R/star_schema_enrich_dimension.R | 56 README.md | 389 ++-- data/ft_london_boroughs.rda |only data/ft_usa_city_county.rda |only data/ft_usa_states.rda |only data/ms_mrs.rda |binary inst/CITATION | 2 inst/doc/starschemar.R | 414 +++- inst/doc/starschemar.Rmd | 631 ++++-- inst/doc/starschemar.html | 2023 +++++++++++++-------- man/enrich_dimension_export.Rd | 1 man/enrich_dimension_import.Rd | 3 man/enrich_dimension_import_test.Rd |only man/filter_dimension.Rd | 2 man/filter_fact_rows.Rd | 2 man/ft_london_boroughs.Rd |only man/ft_usa_city_county.Rd |only man/ft_usa_states.Rd |only man/get_star_schema.Rd |only man/get_star_schema_names.Rd |only man/incremental_refresh_constellation.Rd | 2 man/incremental_refresh_star_schema.Rd | 2 man/ms_mrs.Rd | 4 man/ms_mrs_test.Rd | 2 man/multistar_as_flat_table.Rd | 24 man/purge_dimensions_constellation.Rd | 2 man/purge_dimensions_star_schema.Rd | 2 man/run_query.Rd | 14 man/select_fact.Rd | 4 tests/testthat/test-enrich_dimension_import_test.R |only tests/testthat/test-get_star_schema.R |only tests/testthat/test-get_star_schema_names.R |only tests/testthat/test-multistar_as_flat_table.R | 7 vignettes/starschemar.Rmd | 631 ++++-- 44 files changed, 2941 insertions(+), 1458 deletions(-)
Title: Distributions for Ecological Models in 'nimble'
Description: Common ecological distributions for 'nimble' models in the form of nimbleFunction objects.
Includes Cormack-Jolly-Seber, occupancy, dynamic occupancy, hidden Markov, dynamic hidden Markov, and N-mixture models.
(Jolly (1965) <DOI: 10.2307/2333826>, Seber (1965) <DOI: 10.2307/2333827>, Turek et al. (2016) <doi:10.1007/s10651-016-0353-z>).
Author: Benjamin R. Goldstein [aut, cre],
Daniel Turek [aut],
Lauren Ponisio [aut],
Perry de Valpine [aut]
Maintainer: Benjamin R. Goldstein <ben.goldstein@berkeley.edu>
Diff between nimbleEcology versions 0.3.0 dated 2020-05-29 and 0.3.1 dated 2020-09-25
DESCRIPTION | 8 MD5 | 10 R/dNmixture.R | 222 +++++++++++---------- build/vignette.rds |binary inst/NEWS | 5 inst/doc/Introduction_to_nimbleEcology.html | 296 ++++++++++++++-------------- 6 files changed, 296 insertions(+), 245 deletions(-)
Title: Functions that Apply to Rows and Columns of Matrices (and to
Vectors)
Description: High-performing functions operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. There are also optimized vector-based methods, e.g. binMeans(), madDiff() and weightedMedian().
Author: Henrik Bengtsson [aut, cre, cph],
Hector Corrada Bravo [ctb],
Robert Gentleman [ctb],
Ola Hossjer [ctb],
Harris Jaffee [ctb],
Dongcan Jiang [ctb],
Peter Langfelder [ctb],
Peter Hickey [ctb],
Brian Montgomery [ctb],
Constantin Ahlmann-Eltze [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between matrixStats versions 0.56.0 dated 2020-03-13 and 0.57.0 dated 2020-09-25
DESCRIPTION | 14 ++-- MD5 | 50 ++++++++-------- NEWS | 25 +++++++- R/rowAlls.R | 66 ++++++++++++++-------- R/rowCollapse.R | 12 ++-- build/vignette.rds |binary inst/doc/matrixStats-methods.html | 2 man/rowAlls.Rd | 44 ++------------ man/rowAvgsPerColSet.Rd | 22 +------ man/rowCounts.Rd | 22 +------ man/rowDiffs.Rd | 22 +------ man/rowProds.Rd | 20 +----- man/rowQuantiles.Rd | 24 +------- man/rowRanks.Rd | 22 +------ man/rowSds.Rd | 46 ++------------- man/rowVars.Rd | 22 +------ man/varDiff.Rd | 113 ++++++++------------------------------ man/weightedMad.Rd | 35 ++--------- man/weightedMedian.Rd | 11 --- man/x_OP_y.Rd | 24 +------- src/rowCumprods.c | 4 - tests/anyMissing.R | 3 - tests/rowAllAnys.R | 49 ++++++++-------- tests/rowAvgsPerColSet.R | 96 ++++++++++++++++---------------- tests/rowCollapse_subset.R | 31 +++++----- tests/rowCumprods.R | 17 +++-- 26 files changed, 290 insertions(+), 506 deletions(-)
Title: Exchange Commands Between R and 'JavaScript'
Description: An 'httpuv' based bridge between R and 'JavaScript'. Provides an easy way to exchange commands and data between a web page and a currently running R session.
Author: Svetlana Ovchinnikova [aut, cre],
Simon Anders [aut]
Maintainer: Svetlana Ovchinnikova <s.ovchinnikova@zmbh.uni-heidelberg.de>
Diff between jrc versions 0.3.1 dated 2020-02-07 and 0.4.0 dated 2020-09-25
DESCRIPTION | 12 +- MD5 | 25 +++--- NAMESPACE | 2 NEWS.md | 10 ++ R/jrc.R | 187 +++++++++++++++++++++++++++++++++------------- man/App.Rd | 10 ++ man/allowDirectories.Rd |only man/allowFunctions.Rd | 3 man/allowVariables.Rd | 3 man/callFunction.Rd | 1 man/closeSession.Rd | 3 man/getSessionVariable.Rd | 3 man/limitStorage.Rd | 3 man/openPage.Rd | 7 + 14 files changed, 195 insertions(+), 74 deletions(-)
Title: Analyze Group Patterns using Graph Theory in Educational
Settings
Description: Analyzes group patterns using discourse analysis data with graph theory mathematics. Takes the order of which individuals talk and converts it to a network edge and weight list. Returns the density, centrality, centralization, and subgroup information for each group. Based on the analytical framework laid out in Chai et al. (2019) <doi:10.1187/cbe.18-11-0222>.
Author: Albert Chai [aut],
Andrew Lee [aut],
Joshua Le [aut, cre],
Katherine Ly [ctb],
Kevin Banh [ctb],
Priya Pahal [ctb],
Stanley Lo [aut]
Maintainer: Joshua Le <jpl038@ucsd.edu>
Diff between discourseGT versions 1.0.0 dated 2020-02-17 and 1.1.0 dated 2020-09-25
discourseGT-1.0.0/discourseGT/R/run_all.R |only discourseGT-1.0.0/discourseGT/man/run_all.Rd |only discourseGT-1.1.0/discourseGT/DESCRIPTION | 20 +- discourseGT-1.1.0/discourseGT/LICENSE | 4 discourseGT-1.1.0/discourseGT/MD5 | 50 +++---- discourseGT-1.1.0/discourseGT/NAMESPACE | 1 discourseGT-1.1.0/discourseGT/R/coreNetAnalysis.R | 32 +--- discourseGT-1.1.0/discourseGT/R/graphicalPlot.R | 27 ++- discourseGT-1.1.0/discourseGT/R/plotGraphs.R | 7 - discourseGT-1.1.0/discourseGT/R/plotGraphs2.R | 10 - discourseGT-1.1.0/discourseGT/R/plotNGTData.R | 98 +++++++++++--- discourseGT-1.1.0/discourseGT/R/prepareGraphs.R | 26 +-- discourseGT-1.1.0/discourseGT/R/subgroupsNetAnalysis.R | 19 -- discourseGT-1.1.0/discourseGT/R/summaryNet.R | 13 - discourseGT-1.1.0/discourseGT/R/tabulate_edges.R | 26 ++- discourseGT-1.1.0/discourseGT/R/writeData.R | 13 - discourseGT-1.1.0/discourseGT/README.md | 6 discourseGT-1.1.0/discourseGT/man/coreNetAnalysis.Rd | 5 discourseGT-1.1.0/discourseGT/man/graphicalPlot.Rd | 24 ++- discourseGT-1.1.0/discourseGT/man/plotGraphs.Rd | 5 discourseGT-1.1.0/discourseGT/man/plotGraphs2.Rd | 5 discourseGT-1.1.0/discourseGT/man/plotNGTData.Rd | 6 discourseGT-1.1.0/discourseGT/man/prepareGraphs.Rd | 19 -- discourseGT-1.1.0/discourseGT/man/subgroupsNetAnalysis.Rd | 5 discourseGT-1.1.0/discourseGT/man/summaryNet.Rd | 5 discourseGT-1.1.0/discourseGT/man/tabulate_edges.Rd | 8 - discourseGT-1.1.0/discourseGT/man/writeData.Rd | 5 27 files changed, 241 insertions(+), 198 deletions(-)
Title: RDF Library Bindings in R
Description: Provides methods to parse, query and serialize information
stored in the Resource Description Framework (RDF). RDF is described at <https://www.w3.org/TR/rdf-primer/>.
This package supports RDF by implementing an R interface to the Redland RDF C library,
described at <http://librdf.org/docs/api/index.html>. In brief, RDF provides a structured graph
consisting of Statements composed of Subject, Predicate, and Object Nodes.
Author: Matthew B. Jones [aut, cre],
Peter Slaughter [aut],
Jeroen Ooms [aut],
Carl Boettiger [aut],
Scott Chamberlain [aut],
David Beckett [cph],
University of Bristol [cph],
Regents of the University of California [cph]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>
Diff between redland versions 1.0.17-11 dated 2019-10-13 and 1.0.17-12 dated 2020-09-25
DESCRIPTION | 12 MD5 | 526 +++++++++--------- NEWS | 11 R/Node.R | 4 R/redland-package.R | 2 README.md | 30 - build/vignette.rds |binary configure | 9 inst/doc/redland_overview.R | 8 inst/doc/redland_overview.Rmd | 4 inst/doc/redland_overview.html | 105 ++- man/Model-initialize.Rd | 1 man/Node-initialize.Rd | 4 man/Parser-initialize.Rd | 10 man/Query-initialize.Rd | 11 man/QueryResults-initialize.Rd | 1 man/Serializer-initialize.Rd | 10 man/Statement-initialize.Rd | 16 man/Storage-initialize.Rd | 10 man/World-initialize.Rd | 1 man/addStatement.Rd | 1 man/executeQuery.Rd | 1 man/freeModel.Rd | 1 man/freeParser.Rd | 1 man/freeQuery.Rd | 1 man/freeQueryResults.Rd | 1 man/freeSerializer.Rd | 1 man/freeStatement.Rd | 1 man/freeStorage.Rd | 1 man/freeWorld.Rd | 1 man/getBlankNodeId.Rd | 1 man/getNodeType.Rd | 1 man/getNodeValue.Rd | 3 man/getQueryResultsLimit.Rd | 1 man/getResults.Rd | 1 man/getTermType.Rd | 1 man/librdf_copyright_string.Rd | 2 man/librdf_copyright_string_get.Rd | 2 man/librdf_digest_final.Rd | 2 man/librdf_digest_init.Rd | 2 man/librdf_digest_to_string.Rd | 2 man/librdf_digest_update.Rd | 2 man/librdf_digest_update_string.Rd | 2 man/librdf_free_digest.Rd | 2 man/librdf_free_hash.Rd | 2 man/librdf_free_iterator.Rd | 2 man/librdf_free_model.Rd | 2 man/librdf_free_node.Rd | 2 man/librdf_free_parser.Rd | 2 man/librdf_free_query.Rd | 2 man/librdf_free_query_results.Rd | 2 man/librdf_free_serializer.Rd | 2 man/librdf_free_statement.Rd | 2 man/librdf_free_storage.Rd | 2 man/librdf_free_stream.Rd | 2 man/librdf_free_uri.Rd | 2 man/librdf_free_world.Rd | 2 man/librdf_hash_to_string.Rd | 2 man/librdf_internal_test_error.Rd | 2 man/librdf_internal_test_warning.Rd | 2 man/librdf_iterator_end.Rd | 2 man/librdf_iterator_get_context.Rd | 2 man/librdf_iterator_get_object.Rd | 2 man/librdf_iterator_next.Rd | 2 man/librdf_log_message_code.Rd | 2 man/librdf_log_message_facility.Rd | 2 man/librdf_log_message_level.Rd | 2 man/librdf_log_message_locator.Rd | 2 man/librdf_log_message_message.Rd | 2 man/librdf_model_add.Rd | 2 man/librdf_model_add_statement.Rd | 2 man/librdf_model_add_statements.Rd | 2 man/librdf_model_add_string_literal_statement.Rd | 2 man/librdf_model_add_typed_literal_statement.Rd | 2 man/librdf_model_as_stream.Rd | 2 man/librdf_model_contains_context.Rd | 2 man/librdf_model_contains_statement.Rd | 2 man/librdf_model_context_add_statement.Rd | 2 man/librdf_model_context_add_statements.Rd | 2 man/librdf_model_context_as_stream.Rd | 2 man/librdf_model_context_remove_statement.Rd | 2 man/librdf_model_context_remove_statements.Rd | 2 man/librdf_model_find_statements.Rd | 2 man/librdf_model_find_statements_in_context.Rd | 2 man/librdf_model_get_arc.Rd | 2 man/librdf_model_get_arcs.Rd | 2 man/librdf_model_get_arcs_in.Rd | 2 man/librdf_model_get_arcs_out.Rd | 2 man/librdf_model_get_contexts.Rd | 2 man/librdf_model_get_feature.Rd | 2 man/librdf_model_get_source.Rd | 2 man/librdf_model_get_sources.Rd | 2 man/librdf_model_get_target.Rd | 2 man/librdf_model_get_targets.Rd | 2 man/librdf_model_has_arc_in.Rd | 2 man/librdf_model_has_arc_out.Rd | 2 man/librdf_model_load.Rd | 2 man/librdf_model_query_execute.Rd | 2 man/librdf_model_remove_statement.Rd | 2 man/librdf_model_set_feature.Rd | 2 man/librdf_model_size.Rd | 2 man/librdf_model_sync.Rd | 2 man/librdf_model_to_string.Rd | 2 man/librdf_model_transaction_commit.Rd | 2 man/librdf_model_transaction_rollback.Rd | 2 man/librdf_model_transaction_start.Rd | 2 man/librdf_new_digest.Rd | 2 man/librdf_new_hash.Rd | 2 man/librdf_new_hash_from_array_of_strings.Rd | 2 man/librdf_new_hash_from_string.Rd | 2 man/librdf_new_model.Rd | 2 man/librdf_new_model_from_model.Rd | 2 man/librdf_new_model_with_options.Rd | 2 man/librdf_new_node.Rd | 2 man/librdf_new_node_from_blank_identifier.Rd | 2 man/librdf_new_node_from_literal.Rd | 2 man/librdf_new_node_from_node.Rd | 2 man/librdf_new_node_from_normalised_uri_string.Rd | 2 man/librdf_new_node_from_typed_literal.Rd | 2 man/librdf_new_node_from_uri.Rd | 2 man/librdf_new_node_from_uri_local_name.Rd | 2 man/librdf_new_node_from_uri_string.Rd | 2 man/librdf_new_parser.Rd | 2 man/librdf_new_query.Rd | 2 man/librdf_new_query_from_query.Rd | 2 man/librdf_new_serializer.Rd | 2 man/librdf_new_statement.Rd | 2 man/librdf_new_statement_from_nodes.Rd | 2 man/librdf_new_statement_from_statement.Rd | 2 man/librdf_new_storage.Rd | 2 man/librdf_new_storage_from_storage.Rd | 2 man/librdf_new_uri.Rd | 2 man/librdf_new_uri_from_filename.Rd | 2 man/librdf_new_uri_from_uri.Rd | 2 man/librdf_new_world.Rd | 2 man/librdf_node_equals.Rd | 2 man/librdf_node_get_blank_identifier.Rd | 2 man/librdf_node_get_li_ordinal.Rd | 2 man/librdf_node_get_literal_value.Rd | 2 man/librdf_node_get_literal_value_as_latin1.Rd | 2 man/librdf_node_get_literal_value_datatype_uri.Rd | 2 man/librdf_node_get_literal_value_is_wf_xml.Rd | 2 man/librdf_node_get_literal_value_language.Rd | 2 man/librdf_node_get_type.Rd | 2 man/librdf_node_get_uri.Rd | 2 man/librdf_node_is_blank.Rd | 2 man/librdf_node_is_literal.Rd | 2 man/librdf_node_is_resource.Rd | 2 man/librdf_parser_check_name.Rd | 2 man/librdf_parser_get_accept_header.Rd | 2 man/librdf_parser_get_feature.Rd | 2 man/librdf_parser_get_namespaces_seen_count.Rd | 2 man/librdf_parser_get_namespaces_seen_prefix.Rd | 2 man/librdf_parser_get_namespaces_seen_uri.Rd | 2 man/librdf_parser_guess_name2.Rd | 2 man/librdf_parser_parse_as_stream.Rd | 2 man/librdf_parser_parse_counted_string_as_stream.Rd | 2 man/librdf_parser_parse_counted_string_into_model.Rd | 2 man/librdf_parser_parse_into_model.Rd | 2 man/librdf_parser_parse_string_as_stream.Rd | 2 man/librdf_parser_parse_string_into_model.Rd | 2 man/librdf_parser_set_feature.Rd | 2 man/librdf_query_execute.Rd | 2 man/librdf_query_get_limit.Rd | 2 man/librdf_query_get_offset.Rd | 2 man/librdf_query_results_as_stream.Rd | 2 man/librdf_query_results_finished.Rd | 2 man/librdf_query_results_get_binding_name.Rd | 2 man/librdf_query_results_get_binding_value.Rd | 2 man/librdf_query_results_get_binding_value_by_name.Rd | 2 man/librdf_query_results_get_bindings_count.Rd | 2 man/librdf_query_results_get_boolean.Rd | 2 man/librdf_query_results_get_count.Rd | 2 man/librdf_query_results_is_bindings.Rd | 2 man/librdf_query_results_is_boolean.Rd | 2 man/librdf_query_results_is_graph.Rd | 2 man/librdf_query_results_is_syntax.Rd | 2 man/librdf_query_results_next.Rd | 2 man/librdf_query_results_to_file2.Rd | 2 man/librdf_query_results_to_string2.Rd | 2 man/librdf_query_set_limit.Rd | 2 man/librdf_query_set_offset.Rd | 2 man/librdf_serializer_check_name.Rd | 2 man/librdf_serializer_get_feature.Rd | 2 man/librdf_serializer_serialize_model_to_file.Rd | 2 man/librdf_serializer_serialize_model_to_string.Rd | 2 man/librdf_serializer_serialize_stream_to_file.Rd | 2 man/librdf_serializer_serialize_stream_to_string.Rd | 2 man/librdf_serializer_set_feature.Rd | 2 man/librdf_serializer_set_namespace.Rd | 2 man/librdf_short_copyright_string.Rd | 2 man/librdf_short_copyright_string_get.Rd | 2 man/librdf_statement_equals.Rd | 2 man/librdf_statement_get_object.Rd | 2 man/librdf_statement_get_predicate.Rd | 2 man/librdf_statement_get_subject.Rd | 2 man/librdf_statement_is_complete.Rd | 2 man/librdf_statement_match.Rd | 2 man/librdf_statement_set_object.Rd | 2 man/librdf_statement_set_predicate.Rd | 2 man/librdf_statement_set_subject.Rd | 2 man/librdf_stream_end.Rd | 2 man/librdf_stream_get_object.Rd | 2 man/librdf_stream_next.Rd | 2 man/librdf_uri_compare.Rd | 2 man/librdf_uri_equals.Rd | 2 man/librdf_uri_to_string.Rd | 2 man/librdf_version_decimal.Rd | 2 man/librdf_version_decimal_get.Rd | 2 man/librdf_version_major.Rd | 2 man/librdf_version_major_get.Rd | 2 man/librdf_version_minor.Rd | 2 man/librdf_version_minor_get.Rd | 2 man/librdf_version_release.Rd | 2 man/librdf_version_release_get.Rd | 2 man/librdf_version_string.Rd | 2 man/librdf_version_string_get.Rd | 2 man/librdf_world_get_feature.Rd | 2 man/librdf_world_open.Rd | 2 man/librdf_world_set_feature.Rd | 2 man/librdf_world_set_logger.Rd | 2 man/parseFileIntoModel.Rd | 4 man/raptor_locator_byte.Rd | 2 man/raptor_locator_column.Rd | 2 man/raptor_locator_file.Rd | 2 man/raptor_locator_line.Rd | 2 man/raptor_locator_uri.Rd | 2 man/raptor_version_decimal.Rd | 2 man/raptor_version_decimal_get.Rd | 2 man/raptor_version_major.Rd | 2 man/raptor_version_major_get.Rd | 2 man/raptor_version_minor.Rd | 2 man/raptor_version_minor_get.Rd | 2 man/raptor_version_release.Rd | 2 man/raptor_version_release_get.Rd | 2 man/raptor_version_string.Rd | 2 man/raptor_version_string_get.Rd | 2 man/rasqal_version_decimal.Rd | 2 man/rasqal_version_decimal_get.Rd | 2 man/rasqal_version_major.Rd | 2 man/rasqal_version_major_get.Rd | 2 man/rasqal_version_minor.Rd | 2 man/rasqal_version_minor_get.Rd | 2 man/rasqal_version_release.Rd | 2 man/rasqal_version_release_get.Rd | 2 man/rasqal_version_string.Rd | 2 man/rasqal_version_string_get.Rd | 2 man/redland.Rd | 3 man/roclet_process.roclet_mergeNamespace.Rd | 3 man/serializeToCharacter.Rd | 4 man/serializeToFile.Rd | 4 man/setNameSpace.Rd | 4 man/setQueryResultsLimit.Rd | 1 man/writeResults.Rd | 12 tests/testthat/test.Model.R | 1 tests/testthat/test.Node.R | 1 tests/testthat/test.Parser.R | 1 tests/testthat/test.Query.R | 1 tests/testthat/test.Serializer.R | 5 tests/testthat/test.Statement.R | 1 tests/testthat/test.Storage.R | 2 tests/testthat/test.World.R | 1 tests/testthat/test.redland_base.R | 6 vignettes/redland_overview.Rmd | 4 264 files changed, 642 insertions(+), 629 deletions(-)
Title: Lists of Numeric Atomic Objects
Description: Create and manipulate numeric list ('nlist') objects.
An 'nlist' is an S3 list of uniquely named numeric objects.
An numeric object is an integer or double vector, matrix or array.
An 'nlists' object is a S3 class list of 'nlist' objects with the
same names, dimensionalities and typeofs. Numeric list objects are of
interest because they are the raw data inputs for analytic engines
such as 'JAGS', 'STAN' and 'TMB'. Numeric lists objects, which are
useful for storing multiple realizations of of simulated data sets,
can be converted to coda::mcmc and coda::mcmc.list objects.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>),
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between nlist versions 0.2.0 dated 2020-06-25 and 0.3.0 dated 2020-09-25
nlist-0.2.0/nlist/man/as.mcmc.list.nlist.Rd |only nlist-0.2.0/nlist/man/as.mcmc.list.nlists.Rd |only nlist-0.2.0/nlist/man/as.mcmc.nlist.Rd |only nlist-0.2.0/nlist/man/as.mcmc.nlists.Rd |only nlist-0.3.0/nlist/DESCRIPTION | 12 - nlist-0.3.0/nlist/MD5 | 127 +++++++++------- nlist-0.3.0/nlist/NAMESPACE | 44 +++++ nlist-0.3.0/nlist/NEWS.md | 9 + nlist-0.3.0/nlist/R/as-list.R |only nlist-0.3.0/nlist/R/as-mcmc-list.R | 59 +++++-- nlist-0.3.0/nlist/R/as-mcmc.R | 56 ++++++- nlist-0.3.0/nlist/R/as-nlist.R | 29 +++ nlist-0.3.0/nlist/R/as-nlists.R | 11 + nlist-0.3.0/nlist/R/as-term-frame.R | 6 nlist-0.3.0/nlist/R/as-term.R | 13 + nlist-0.3.0/nlist/R/bind-iterations.R |only nlist-0.3.0/nlist/R/brackets.R | 5 nlist-0.3.0/nlist/R/c.R | 4 nlist-0.3.0/nlist/R/chk.R | 5 nlist-0.3.0/nlist/R/collapse-chains.R | 15 + nlist-0.3.0/nlist/R/complete-terms.R |only nlist-0.3.0/nlist/R/extras.R |only nlist-0.3.0/nlist/R/internal.R | 5 nlist-0.3.0/nlist/R/nchains.R | 8 + nlist-0.3.0/nlist/R/niters.R | 8 + nlist-0.3.0/nlist/R/npdims.R | 4 nlist-0.3.0/nlist/R/nterms.R | 8 + nlist-0.3.0/nlist/R/params.R | 2 nlist-0.3.0/nlist/R/pars.R | 28 +++ nlist-0.3.0/nlist/R/pdims.R | 8 + nlist-0.3.0/nlist/R/set-pars.R | 30 +++ nlist-0.3.0/nlist/R/sort.R |only nlist-0.3.0/nlist/R/split-chains.R | 6 nlist-0.3.0/nlist/R/subset.R | 91 +++++++++++ nlist-0.3.0/nlist/R/tidy.R | 16 ++ nlist-0.3.0/nlist/R/utils.R |only nlist-0.3.0/nlist/R/vld.R | 2 nlist-0.3.0/nlist/build/nlist.pdf |binary nlist-0.3.0/nlist/man/as_mcmc.Rd |only nlist-0.3.0/nlist/man/as_mcmc_list.Rd |only nlist-0.3.0/nlist/man/as_nlist.Rd | 10 + nlist-0.3.0/nlist/man/as_nlists.Rd | 5 nlist-0.3.0/nlist/man/as_term.mcmc.Rd |only nlist-0.3.0/nlist/man/bind_iterations.mcmc.Rd |only nlist-0.3.0/nlist/man/bind_iterations.mcmc.list.Rd |only nlist-0.3.0/nlist/man/collapse_chains.mcmc.Rd |only nlist-0.3.0/nlist/man/collapse_chains.mcmc.list.Rd |only nlist-0.3.0/nlist/man/collapse_chains.nlist.Rd | 1 nlist-0.3.0/nlist/man/collapse_chains.nlists.Rd | 1 nlist-0.3.0/nlist/man/complete_terms.mcmc.Rd |only nlist-0.3.0/nlist/man/estimates.nlist.Rd | 1 nlist-0.3.0/nlist/man/estimates.nlists.Rd | 1 nlist-0.3.0/nlist/man/nchains.mcmc.Rd |only nlist-0.3.0/nlist/man/nchains.mcmc.list.Rd |only nlist-0.3.0/nlist/man/niters.mcmc.Rd |only nlist-0.3.0/nlist/man/niters.mcmc.list.Rd |only nlist-0.3.0/nlist/man/npdims.mcmc.list.Rd |only nlist-0.3.0/nlist/man/nterms.mcmc.Rd |only nlist-0.3.0/nlist/man/nterms.mcmc.list.Rd |only nlist-0.3.0/nlist/man/params.Rd | 4 nlist-0.3.0/nlist/man/pars.mcmc.Rd |only nlist-0.3.0/nlist/man/pars.mcmc.list.Rd |only nlist-0.3.0/nlist/man/pdims.mcmc.Rd |only nlist-0.3.0/nlist/man/pdims.mcmc.list.Rd |only nlist-0.3.0/nlist/man/reexports.Rd | 16 +- nlist-0.3.0/nlist/man/set_pars.mcmc.Rd |only nlist-0.3.0/nlist/man/set_pars.mcmc.list.Rd |only nlist-0.3.0/nlist/man/set_pars.nlist.Rd | 8 - nlist-0.3.0/nlist/man/set_pars.nlists.Rd | 8 - nlist-0.3.0/nlist/man/split_chains.nlists.Rd | 8 - nlist-0.3.0/nlist/man/subset.mcmc.Rd |only nlist-0.3.0/nlist/man/subset.mcmc.list.Rd |only nlist-0.3.0/nlist/man/tidy.mcmc.Rd |only nlist-0.3.0/nlist/man/tidy.mcmc.list.Rd |only nlist-0.3.0/nlist/tests/testthat/test-as-list.R |only nlist-0.3.0/nlist/tests/testthat/test-as-mcmc-list.R | 133 ++++++++++++++++- nlist-0.3.0/nlist/tests/testthat/test-as-mcmc.R | 124 +++++++++++++++ nlist-0.3.0/nlist/tests/testthat/test-as-nlist.R | 20 ++ nlist-0.3.0/nlist/tests/testthat/test-as-nlists.R | 16 ++ nlist-0.3.0/nlist/tests/testthat/test-c.R | 4 nlist-0.3.0/nlist/tests/testthat/test-complete-terms.R |only nlist-0.3.0/nlist/tests/testthat/test-split-chains.R | 3 nlist-0.3.0/nlist/tests/testthat/test-subset.R | 41 +++++ 83 files changed, 892 insertions(+), 123 deletions(-)
Title: Sparklyr Extension for 'Flint'
Description: This sparklyr extension makes 'Flint' time series library
functionalities (<https://github.com/twosigma/flint>) easily accessible
through R.
Author: Yitao Li [aut, cre] (<https://orcid.org/0000-0002-1261-905X>)
Maintainer: Yitao Li <yitao@rstudio.com>
Diff between sparklyr.flint versions 0.1.1 dated 2020-08-24 and 0.2.0 dated 2020-09-25
sparklyr.flint-0.1.1/sparklyr.flint/man/fromRDD.Rd |only sparklyr.flint-0.1.1/sparklyr.flint/man/fromSDF.Rd |only sparklyr.flint-0.2.0/sparklyr.flint/DESCRIPTION | 15 sparklyr.flint-0.2.0/sparklyr.flint/MD5 | 81 + sparklyr.flint-0.2.0/sparklyr.flint/NAMESPACE | 22 sparklyr.flint-0.2.0/sparklyr.flint/NEWS.md | 14 sparklyr.flint-0.2.0/sparklyr.flint/R/asof_join.R |only sparklyr.flint-0.2.0/sparklyr.flint/R/ols_regression.R |only sparklyr.flint-0.2.0/sparklyr.flint/R/reexports.R |only sparklyr.flint-0.2.0/sparklyr.flint/R/sdf_utils.R | 176 +++- sparklyr.flint-0.2.0/sparklyr.flint/R/summarizers.R | 408 ++++++++-- sparklyr.flint-0.2.0/sparklyr.flint/R/window_exprs.R | 14 sparklyr.flint-0.2.0/sparklyr.flint/man/asof_future_left_join.Rd |only sparklyr.flint-0.2.0/sparklyr.flint/man/asof_join.Rd |only sparklyr.flint-0.2.0/sparklyr.flint/man/asof_left_join.Rd |only sparklyr.flint-0.2.0/sparklyr.flint/man/collect.ts_rdd.Rd | 13 sparklyr.flint-0.2.0/sparklyr.flint/man/from_rdd.Rd |only sparklyr.flint-0.2.0/sparklyr.flint/man/from_sdf.Rd |only sparklyr.flint-0.2.0/sparklyr.flint/man/ols_regression.Rd |only sparklyr.flint-0.2.0/sparklyr.flint/man/spark_connection.Rd |only sparklyr.flint-0.2.0/sparklyr.flint/man/spark_connection.ts_rdd.Rd |only sparklyr.flint-0.2.0/sparklyr.flint/man/spark_dataframe.Rd |only sparklyr.flint-0.2.0/sparklyr.flint/man/spark_dataframe.ts_rdd.Rd |only sparklyr.flint-0.2.0/sparklyr.flint/man/spark_jobj.Rd |only sparklyr.flint-0.2.0/sparklyr.flint/man/spark_jobj.ts_rdd.Rd |only sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_avg.Rd | 24 sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_corr.Rd | 34 sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_corr2.Rd | 40 sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_count.Rd | 32 sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_covar.Rd | 26 sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_dot_product.Rd | 26 sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_ema_half_life.Rd |only sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_ewma.Rd |only sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_geometric_mean.Rd |only sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_kurtosis.Rd |only sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_max.Rd | 26 sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_min.Rd | 26 sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_nth_central_moment.Rd | 40 sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_nth_moment.Rd | 40 sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_product.Rd | 24 sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_quantile.Rd | 26 sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_skewness.Rd |only sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_stddev.Rd | 26 sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_sum.Rd | 24 sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_var.Rd | 26 sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_weighted_avg.Rd | 24 sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_weighted_corr.Rd | 35 sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_weighted_covar.Rd | 26 sparklyr.flint-0.2.0/sparklyr.flint/man/summarize_z_score.Rd | 43 - sparklyr.flint-0.2.0/sparklyr.flint/man/summarizers.Rd | 30 sparklyr.flint-0.2.0/sparklyr.flint/man/to_sdf.Rd |only sparklyr.flint-0.2.0/sparklyr.flint/man/ts_rdd_builder.Rd | 11 sparklyr.flint-0.2.0/sparklyr.flint/man/window_exprs.Rd | 13 53 files changed, 1070 insertions(+), 295 deletions(-)
More information about sparklyr.flint at CRAN
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Title: Measuring Disparity
Description: A modular package for measuring disparity (multidimensional space occupancy). Disparity can be calculated from any matrix defining a multidimensional space. The package provides a set of implemented metrics to measure properties of the space and allows users to provide and test their own metrics (Guillerme (2018) <doi:10.1111/2041-210X.13022>). The package also provides functions for looking at disparity in a serial way (e.g. disparity through time - Guillerme and Cooper (2018) <doi:10.1111/pala.12364>) or per groups as well as visualising the results. Finally, this package provides several statistical tests for disparity analysis.
Author: Thomas Guillerme [aut, cre, cph],
Mark N Puttick [aut, cph]
Maintainer: Thomas Guillerme <guillert@tcd.ie>
Diff between dispRity versions 1.4.2 dated 2020-09-04 and 1.5.0 dated 2020-09-25
dispRity-1.4.2/dispRity/R/sequential.test.R |only dispRity-1.4.2/dispRity/R/sequential.test_fun.R |only dispRity-1.5.0/dispRity/DESCRIPTION | 13 dispRity-1.5.0/dispRity/MD5 | 97 dispRity-1.5.0/dispRity/NAMESPACE | 14 dispRity-1.5.0/dispRity/NEWS.md | 28 dispRity-1.5.0/dispRity/R/Claddis.ordination.R | 13 dispRity-1.5.0/dispRity/R/Claddis.ordination_fun.R | 2 dispRity-1.5.0/dispRity/R/char.diff.R | 13 dispRity-1.5.0/dispRity/R/char.diff_fun.R | 8 dispRity-1.5.0/dispRity/R/chrono.subsets.R | 3 dispRity-1.5.0/dispRity/R/chrono.subsets_fun.R | 13 dispRity-1.5.0/dispRity/R/dispRity-package.R | 4 dispRity-1.5.0/dispRity/R/dispRity.R | 108 dispRity-1.5.0/dispRity/R/dispRity.metric.R | 171 - dispRity-1.5.0/dispRity/R/dispRity.utilities.R | 12 dispRity-1.5.0/dispRity/R/dispRity.utilities_fun.R | 52 dispRity-1.5.0/dispRity/R/dispRity_fun.R | 129 dispRity-1.5.0/dispRity/R/dtt.dispRity.R | 10 dispRity-1.5.0/dispRity/R/fit.ace.model.R |only dispRity-1.5.0/dispRity/R/make.demo.data.R | 4 dispRity-1.5.0/dispRity/R/make.metric.R | 60 dispRity-1.5.0/dispRity/R/model.test.R | 9 dispRity-1.5.0/dispRity/R/model.test.sim.R | 3 dispRity-1.5.0/dispRity/R/model.test.wrapper.R | 7 dispRity-1.5.0/dispRity/R/model.test_fun.R | 20 dispRity-1.5.0/dispRity/R/multi.ace.R |only dispRity-1.5.0/dispRity/R/multi.ace_fun.R |only dispRity-1.5.0/dispRity/R/plot.dispRity.R | 595 +-- dispRity-1.5.0/dispRity/R/plot.dispRity_fun.R | 1564 ++++++---- dispRity-1.5.0/dispRity/R/print.dispRity.R | 40 dispRity-1.5.0/dispRity/R/reduce.space.R |only dispRity-1.5.0/dispRity/R/reduce.space_fun.R |only dispRity-1.5.0/dispRity/R/sanitizing.R | 7 dispRity-1.5.0/dispRity/R/summary.dispRity.R | 112 dispRity-1.5.0/dispRity/R/summary.dispRity_fun.R | 31 dispRity-1.5.0/dispRity/R/test.metric.R |only dispRity-1.5.0/dispRity/R/test.metric_fun.R |only dispRity-1.5.0/dispRity/R/zzz.R | 2 dispRity-1.5.0/dispRity/data/BeckLee_disparity.rda |binary dispRity-1.5.0/dispRity/data/disparity.rda |binary dispRity-1.5.0/dispRity/inst/References.bib | 26 dispRity-1.5.0/dispRity/inst/vignettes/dispRity_workhop_code.Rmd |only dispRity-1.5.0/dispRity/man/BeckLee.Rd | 2 dispRity-1.5.0/dispRity/man/dispRity.Rd | 20 dispRity-1.5.0/dispRity/man/dispRity.metric.Rd | 76 dispRity-1.5.0/dispRity/man/dtt.dispRity.Rd | 3 dispRity-1.5.0/dispRity/man/make.metric.Rd | 17 dispRity-1.5.0/dispRity/man/model.test.Rd | 3 dispRity-1.5.0/dispRity/man/model.test.sim.Rd | 2 dispRity-1.5.0/dispRity/man/model.test.wrapper.Rd | 2 dispRity-1.5.0/dispRity/man/multi.ace.Rd |only dispRity-1.5.0/dispRity/man/plot.dispRity.Rd | 71 dispRity-1.5.0/dispRity/man/reduce.space.Rd |only dispRity-1.5.0/dispRity/man/rescale.dispRity.Rd | 2 dispRity-1.5.0/dispRity/man/test.metric.Rd |only 56 files changed, 2082 insertions(+), 1286 deletions(-)
Title: Create, Manipulate and Query Parameter Terms
Description: Creates, manipulates, queries and repairs vectors
of parameter terms. Parameter terms are the labels used to reference
values in vectors, matrices and arrays. They represent the names in
coefficient tables and the column names in 'mcmc' and 'mcmc.list'
objects.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>),
Kirill Müller [aut] (<https://orcid.org/0000-0002-1416-3412>),
Ayla Pearson [ctb] (<https://orcid.org/0000-0001-7388-1222>),
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between term versions 0.2.0 dated 2020-06-20 and 0.3.0 dated 2020-09-25
term-0.2.0/term/R/FIXME.R |only term-0.2.0/term/R/npdims-terms.R |only term-0.2.0/term/R/sys.R |only term-0.2.0/term/R/vec-cast.R |only term-0.2.0/term/man/vec_cast.term.Rd |only term-0.2.0/term/man/vec_ptype2.term.Rd |only term-0.2.0/term/tests/testthat/out/print.txt |only term-0.2.0/term/tests/testthat/test-base.R |only term-0.2.0/term/tests/testthat/test-in-inconsistent-terms.R |only term-0.2.0/term/tests/testthat/test-npdims-terms.R |only term-0.3.0/term/DESCRIPTION | 15 term-0.3.0/term/MD5 | 204 +++++++----- term-0.3.0/term/NAMESPACE | 67 +++ term-0.3.0/term/NEWS.md | 29 + term-0.3.0/term/R/anyNA.R |only term-0.3.0/term/R/anyduplicated.R |only term-0.3.0/term/R/as-character.R |only term-0.3.0/term/R/as-data-frame.R |only term-0.3.0/term/R/as-term-rcrd.R |only term-0.3.0/term/R/as-term.R | 35 +- term-0.3.0/term/R/chk.R | 31 + term-0.3.0/term/R/complete-terms.R | 29 + term-0.3.0/term/R/consistent-term.R | 7 term-0.3.0/term/R/deprecated.R | 4 term-0.3.0/term/R/dims.R | 10 term-0.3.0/term/R/extras.R |only term-0.3.0/term/R/format.R | 6 term-0.3.0/term/R/internal.R | 88 +++++ term-0.3.0/term/R/is-incomplete-terms.R | 3 term-0.3.0/term/R/is-inconsistent-terms.R | 10 term-0.3.0/term/R/is.R | 18 + term-0.3.0/term/R/is.na.R |only term-0.3.0/term/R/levels.R |only term-0.3.0/term/R/namespace.R | 7 term-0.3.0/term/R/new-term-rcrd.R |only term-0.3.0/term/R/normalize-terms.R |only term-0.3.0/term/R/npdims.R | 14 term-0.3.0/term/R/nterms.R | 36 +- term-0.3.0/term/R/params.R | 4 term-0.3.0/term/R/pars-terms.R | 22 - term-0.3.0/term/R/pars.R | 45 +- term-0.3.0/term/R/pdims.R | 19 - term-0.3.0/term/R/print.R |only term-0.3.0/term/R/rep.R | 4 term-0.3.0/term/R/repair-terms.R | 32 - term-0.3.0/term/R/scalar-term.R |only term-0.3.0/term/R/set-pars.R | 9 term-0.3.0/term/R/subset.R | 40 ++ term-0.3.0/term/R/summary.R |only term-0.3.0/term/R/term-rcrd.R |only term-0.3.0/term/R/term.R | 28 - term-0.3.0/term/R/tindex.R | 22 - term-0.3.0/term/R/unique.R |only term-0.3.0/term/R/valid-term.R | 22 - term-0.3.0/term/R/vec-cast-character.R |only term-0.3.0/term/R/vec-cast-term-rcrd.R |only term-0.3.0/term/R/vec-cast-term.R |only term-0.3.0/term/R/vec-proxy-compare.R | 5 term-0.3.0/term/R/vec-ptype2.R | 15 term-0.3.0/term/R/vld.R | 40 ++ term-0.3.0/term/README.md | 2 term-0.3.0/term/build |only term-0.3.0/term/man/NA_term_rcrd_.Rd |only term-0.3.0/term/man/as_term.Rd | 6 term-0.3.0/term/man/as_term_rcrd.Rd |only term-0.3.0/term/man/chk_term.Rd | 19 + term-0.3.0/term/man/complete_terms.Rd | 12 term-0.3.0/term/man/dims.term_rcrd.Rd |only term-0.3.0/term/man/figures/lifecycle-superseded.svg |only term-0.3.0/term/man/is_inconsistent_terms.Rd | 1 term-0.3.0/term/man/is_term_rcrd.Rd |only term-0.3.0/term/man/new_term_rcrd.Rd |only term-0.3.0/term/man/normalize_terms.Rd |only term-0.3.0/term/man/npdims.term.Rd | 23 - term-0.3.0/term/man/nterms.default.Rd |only term-0.3.0/term/man/nterms.term.Rd | 7 term-0.3.0/term/man/nterms.term_rcrd.Rd |only term-0.3.0/term/man/params.Rd | 5 term-0.3.0/term/man/pars.default.Rd | 5 term-0.3.0/term/man/pars.term.Rd | 1 term-0.3.0/term/man/pars.term_rcrd.Rd |only term-0.3.0/term/man/pars_terms.Rd | 3 term-0.3.0/term/man/pdims.term.Rd | 2 term-0.3.0/term/man/pdims.term_rcrd.Rd |only term-0.3.0/term/man/reexports.Rd | 2 term-0.3.0/term/man/repair_terms.Rd | 13 term-0.3.0/term/man/scalar_term.Rd |only term-0.3.0/term/man/set_pars.term.Rd | 6 term-0.3.0/term/man/subset.term.Rd | 3 term-0.3.0/term/man/subset.term_rcrd.Rd |only term-0.3.0/term/man/term_rcrd.Rd |only term-0.3.0/term/man/tindex.Rd | 2 term-0.3.0/term/man/valid_term.Rd | 4 term-0.3.0/term/man/vld_term.Rd | 19 - term-0.3.0/term/tests/testthat/out/print-term-rcrd.txt |only term-0.3.0/term/tests/testthat/out/print-term.txt |only term-0.3.0/term/tests/testthat/test-anyduplicated.R |only term-0.3.0/term/tests/testthat/test-as-data-frame.R |only term-0.3.0/term/tests/testthat/test-as-term-rcrd.R |only term-0.3.0/term/tests/testthat/test-as-term.R | 13 term-0.3.0/term/tests/testthat/test-chk.R | 13 term-0.3.0/term/tests/testthat/test-complete-terms.R | 30 + term-0.3.0/term/tests/testthat/test-consistent-term.R | 20 + term-0.3.0/term/tests/testthat/test-deprecated.R | 10 term-0.3.0/term/tests/testthat/test-dims.R | 7 term-0.3.0/term/tests/testthat/test-inconsistent-terms.R |only term-0.3.0/term/tests/testthat/test-internal.R | 18 + term-0.3.0/term/tests/testthat/test-is-incomplete-terms.R | 2 term-0.3.0/term/tests/testthat/test-is-na.R |only term-0.3.0/term/tests/testthat/test-is.R | 6 term-0.3.0/term/tests/testthat/test-levels.R |only term-0.3.0/term/tests/testthat/test-new-term-rcrd.R |only term-0.3.0/term/tests/testthat/test-normalize-terms.R |only term-0.3.0/term/tests/testthat/test-npars.R | 20 - term-0.3.0/term/tests/testthat/test-npdims.R | 22 - term-0.3.0/term/tests/testthat/test-nterms.R | 15 term-0.3.0/term/tests/testthat/test-pars-terms.R | 23 - term-0.3.0/term/tests/testthat/test-pars.R | 49 +- term-0.3.0/term/tests/testthat/test-pdims.R | 15 term-0.3.0/term/tests/testthat/test-print.R | 8 term-0.3.0/term/tests/testthat/test-rep.R | 8 term-0.3.0/term/tests/testthat/test-repair-terms.R | 19 + term-0.3.0/term/tests/testthat/test-scalar-term.R | 23 + term-0.3.0/term/tests/testthat/test-subset.R | 43 ++ term-0.3.0/term/tests/testthat/test-summary.R |only term-0.3.0/term/tests/testthat/test-term-rcrd.R |only term-0.3.0/term/tests/testthat/test-tindex.R | 8 term-0.3.0/term/tests/testthat/test-unique.R | 14 term-0.3.0/term/tests/testthat/test-valid-term.R | 34 +- term-0.3.0/term/tests/testthat/test-vec-cast.R |only term-0.3.0/term/tests/testthat/test-vld.R | 32 + 131 files changed, 1052 insertions(+), 455 deletions(-)
Title: Maximum Likelihood Estimates of Gaussian Processes
Description: Maximum likelihood Gaussian process modeling for
univariate and multi-dimensional outputs with diagnostic plots
following Santner et al (2003) <doi:10.1007/978-1-4757-3799-8>.
Contact the maintainer for a package version that includes
sensitivity analysis.
Author: Garrett M. Dancik
Maintainer: Garrett M. Dancik <dancikg@easternct.edu>
Diff between mlegp versions 3.1.7 dated 2018-04-14 and 3.1.8 dated 2020-09-25
CHANGES | 5 +++ DESCRIPTION | 8 +++--- MD5 | 54 +++++++++++++++++++++--------------------- R/createGP.R | 3 +- R/mlegp.R | 1 R/mlegp2.R | 17 +++++++------ R/summary.gp.list.R | 2 - man/CV.Rd | 2 - man/createGP.Rd | 2 - man/createWindow.Rd | 2 - man/gp.list.Rd | 2 - man/is.gp.Rd | 2 - man/mlegp-internal.Rd | 2 - man/mlegp-naming-functions.Rd | 2 - man/mlegp-package.Rd | 2 - man/mlegp-svd-functions.Rd | 2 - man/mlegp.Rd | 5 +++ man/nugget.Rd | 2 - man/paramLookup.Rd | 2 - man/plot.gp.Rd | 2 - man/plot.gp.list.Rd | 2 - man/plotObservedEffects.Rd | 2 - man/predict.gp.Rd | 2 - man/print.gp.Rd | 2 - man/print.gp.list.Rd | 2 - man/summary.gp.Rd | 2 - man/summary.gp.list.Rd | 2 - man/uniqueSummary.Rd | 2 - 28 files changed, 72 insertions(+), 63 deletions(-)
Title: "Eating the Liver of Data Science"
Description: Provides a collection of helper functions that make various techniques from data science more user-friendly for non-experts. In this way, our aim is to allow non-experts to become familiar with the techniques with only a minimal level of coding knowledge. Indeed, following an ancient Persian idiom, we refer to this as "eating the liver of data science" which could be interpreted as "getting intimately close with data science". Examples of procedures we include are: data partitioning for out-of-sample testing, computing Mean Squared Error (MSE) for quantifying prediction accuracy, and data transformation (z-score and min-max). Besides such helper functions, the package also includes several interesting datasets that are useful for multivariate analysis.
Author: Reza Mohammadi [aut, cre] (<https://orcid.org/0000-0001-9538-0648>),
Kevin Burke [aut]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between liver versions 1.1 dated 2020-09-10 and 1.2 dated 2020-09-25
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++++-------- NAMESPACE | 9 +++++++-- NEWS.md | 5 +++++ R/kNN.R |only R/mse.R | 3 +++ data/bank.RData |only man/adult.Rd | 2 +- man/bank.Rd |only man/churn.Rd | 2 +- man/churnTel.Rd | 2 +- man/classifyRisk.Rd | 2 +- man/kNN.Rd |only 13 files changed, 35 insertions(+), 18 deletions(-)
Title: Phylogenetic Ridge Regression Methods for Comparative Studies
Description: Functions for phylogenetic analysis (Castiglione et al, 2018 <doi:10.1111/2041-210X.12954>). The functions perform the estimation of phenotypic evolutionary rates, identification of phenotypic evolutionary rate shifts, quantification of direction and size of evolutionary change in multivariate traits, the computation of ontogenetic shape vectors and test for morphological convergence.
Author: Pasquale Raia, Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Marina Melchionna, Mirko Di Febbraro, Antonio Profico, Francesco Carotenuto
Maintainer: Pasquale Raia <pasquale.raia@unina.it>
Diff between RRphylo versions 2.4.7 dated 2020-07-13 and 2.4.11 dated 2020-09-25
RRphylo-2.4.11/RRphylo/DESCRIPTION | 14 RRphylo-2.4.11/RRphylo/MD5 | 107 ++- RRphylo-2.4.11/RRphylo/NAMESPACE | 6 RRphylo-2.4.11/RRphylo/R/DataSimians.R |only RRphylo-2.4.11/RRphylo/R/PGLS_fossil.R | 8 RRphylo-2.4.11/RRphylo/R/RRphylo.R | 183 ++++-- RRphylo-2.4.11/RRphylo/R/StableTraitsR.R | 7 RRphylo-2.4.11/RRphylo/R/conv.map.R |only RRphylo-2.4.11/RRphylo/R/cutPhylo.R | 37 + RRphylo-2.4.11/RRphylo/R/distNodes.R | 7 RRphylo-2.4.11/RRphylo/R/getMommy.R | 8 RRphylo-2.4.11/RRphylo/R/getSis.R | 9 RRphylo-2.4.11/RRphylo/R/makeFossil.R | 8 RRphylo-2.4.11/RRphylo/R/makeL.R | 7 RRphylo-2.4.11/RRphylo/R/makeL1.R | 7 RRphylo-2.4.11/RRphylo/R/overfitRR.R | 22 RRphylo-2.4.11/RRphylo/R/phyloclust.R | 8 RRphylo-2.4.11/RRphylo/R/plotRates.R | 1 RRphylo-2.4.11/RRphylo/R/random.evolvability.test.R |only RRphylo-2.4.11/RRphylo/R/scaleTree.R | 8 RRphylo-2.4.11/RRphylo/R/search.conv.R | 9 RRphylo-2.4.11/RRphylo/R/search.shift.R | 1 RRphylo-2.4.11/RRphylo/R/search.trend.R | 465 +++++++++-------- RRphylo-2.4.11/RRphylo/R/setBM.R | 8 RRphylo-2.4.11/RRphylo/R/sizedsubtree.R | 11 RRphylo-2.4.11/RRphylo/R/swap.phylo.R | 7 RRphylo-2.4.11/RRphylo/R/swapONE.R | 9 RRphylo-2.4.11/RRphylo/build/vignette.rds |binary RRphylo-2.4.11/RRphylo/data/DataSimians.rda |only RRphylo-2.4.11/RRphylo/inst/doc/RRphylo.R | 136 +++- RRphylo-2.4.11/RRphylo/inst/doc/RRphylo.Rmd | 47 + RRphylo-2.4.11/RRphylo/inst/doc/RRphylo.html | 120 ++-- RRphylo-2.4.11/RRphylo/inst/doc/Tree-Manipulation.R |only RRphylo-2.4.11/RRphylo/inst/doc/Tree-Manipulation.Rmd |only RRphylo-2.4.11/RRphylo/inst/doc/Tree-Manipulation.html |only RRphylo-2.4.11/RRphylo/inst/doc/overfitRR.R | 10 RRphylo-2.4.11/RRphylo/inst/doc/overfitRR.Rmd | 10 RRphylo-2.4.11/RRphylo/inst/doc/overfitRR.html | 96 +-- RRphylo-2.4.11/RRphylo/inst/doc/search.trend.R | 39 + RRphylo-2.4.11/RRphylo/inst/doc/search.trend.Rmd | 45 + RRphylo-2.4.11/RRphylo/inst/doc/search.trend.html | 119 ++-- RRphylo-2.4.11/RRphylo/man/DataSimians.Rd |only RRphylo-2.4.11/RRphylo/man/PGLS_fossil.Rd | 3 RRphylo-2.4.11/RRphylo/man/RRphylo.Rd | 54 + RRphylo-2.4.11/RRphylo/man/conv.map.Rd |only RRphylo-2.4.11/RRphylo/man/cutPhylo.Rd | 20 RRphylo-2.4.11/RRphylo/man/overfitRR.Rd | 16 RRphylo-2.4.11/RRphylo/man/plotRates.Rd | 3 RRphylo-2.4.11/RRphylo/man/random.evolvability.test.Rd |only RRphylo-2.4.11/RRphylo/man/scaleTree.Rd | 3 RRphylo-2.4.11/RRphylo/man/search.conv.Rd | 3 RRphylo-2.4.11/RRphylo/man/search.shift.Rd | 3 RRphylo-2.4.11/RRphylo/man/search.trend.Rd | 70 +- RRphylo-2.4.11/RRphylo/man/swapONE.Rd | 2 RRphylo-2.4.11/RRphylo/vignettes/RRphylo.Rmd | 47 + RRphylo-2.4.11/RRphylo/vignettes/Tree-Manipulation.Rmd |only RRphylo-2.4.11/RRphylo/vignettes/overfitRR.Rmd | 10 RRphylo-2.4.11/RRphylo/vignettes/search.trend.Rmd | 45 + RRphylo-2.4.7/RRphylo/inst/doc/scaleTree.R |only RRphylo-2.4.7/RRphylo/inst/doc/scaleTree.Rmd |only RRphylo-2.4.7/RRphylo/inst/doc/scaleTree.html |only RRphylo-2.4.7/RRphylo/vignettes/scaleTree.Rmd |only 62 files changed, 1265 insertions(+), 593 deletions(-)
Title: Confirmatory Adaptive Clinical Trial Design and Analysis
Description: Design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints according to the methods described in the monograph by Wassmer and Brannath (2016) <doi:10.1007/978-3-319-32562-0>. This includes classical group sequential as well as multi-stage adaptive hypotheses tests that are based on the combination testing principle.
Author: Gernot Wassmer [aut],
Friedrich Pahlke [aut, cre]
Maintainer: Friedrich Pahlke <friedrich.pahlke@rpact.com>
Diff between rpact versions 3.0.0 dated 2020-09-07 and 3.0.1 dated 2020-09-25
DESCRIPTION | 11 MD5 | 93 - NEWS.md | 24 R/class_analysis_results.R | 8 R/class_core_parameter_set.R | 47 R/class_simulation_results.R | 138 +- R/class_summary.R | 479 +++++---- R/f_analysis_multiarm_means.R | 6 R/f_analysis_multiarm_rates.R | 6 R/f_analysis_multiarm_survival.R | 7 R/f_core_assertions.R | 40 R/f_core_constants.R | 7 R/f_core_output_formats.R | 27 R/f_core_plot.R | 44 R/f_core_utilities.R | 103 + R/f_design_fisher_combination_test.R | 10 R/f_design_group_sequential.R | 12 R/f_design_sample_size_calculator.R | 12 R/f_design_utilities.R | 9 R/f_simulation_base_means.R | 11 R/f_simulation_base_rates.R | 13 R/f_simulation_multiarm.R | 34 R/f_simulation_multiarm_means.R | 78 - R/f_simulation_multiarm_rates.R | 113 +- R/f_simulation_multiarm_survival.R | 179 +-- R/parameter_descriptions.R | 10 R/pkgname.R | 4 README.md | 65 + build |only inst/doc |only inst/tests/testthat/test-f_simulation_base_rates.R | 9 inst/tests/testthat/test-f_simulation_multiarm_means.R | 122 +- inst/tests/testthat/test-f_simulation_multiarm_rates.R | 724 +++++++------- inst/tests/testthat/test-f_simulation_multiarm_survival.R | 512 ++++----- man/AnalysisResults_summary.Rd | 1 man/ParameterSet_summary.Rd | 1 man/Trial_Design_Set_summary.Rd | 1 man/getSimulationMultiArmMeans.Rd | 8 man/getSimulationMultiArmRates.Rd | 30 man/getSimulationMultiArmSurvival.Rd | 4 man/param_rValue.Rd | 2 man/param_typeOfSelection.Rd | 2 man/utilitiesForPiecewiseExponentialDistribution.Rd | 2 tests/testthat/test-f_simulation_base_rates.R | 7 tests/testthat/test-f_simulation_multiarm_means.R | 122 +- tests/testthat/test-f_simulation_multiarm_rates.R | 724 +++++++------- tests/testthat/test-f_simulation_multiarm_survival.R | 512 ++++----- vignettes |only 48 files changed, 2453 insertions(+), 1920 deletions(-)
Title: Rapid Realistic Routing with 'R5'
Description: Rapid realistic routing on multimodal transport networks (walk,
bike, public transport and car) using 'R5', the Rapid Realistic
Routing on Real-world and Reimagined networks
<https://github.com/conveyal/r5>. The package allows users to
generate detailed routing analysis or calculate travel time matrices
using seamless parallel computing on top of the R5 Java machine.
Author: Marcus Saraiva [aut] (<https://orcid.org/0000-0001-6218-2338>),
Rafael H. M. Pereira [aut, cre]
(<https://orcid.org/0000-0003-2125-7465>),
Daniel Herszenhut [aut] (<https://orcid.org/0000-0001-8066-1105>),
Carlos Kaue Vieira Braga [aut]
(<https://orcid.org/0000-0002-6104-7297>),
Ipea - Institue for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between r5r versions 0.1.0 dated 2020-09-18 and 0.1-1 dated 2020-09-25
DESCRIPTION | 12 MD5 | 49 - NEWS.md |only R/detailed_itineraries.R | 3 R/download_r5.R | 18 R/setup_r5.R | 228 ++++---- R/street_network_to_sf.R | 94 +-- R/travel_time_matrix.R | 9 R/utils.R | 6 build/vignette.rds |binary inst/doc/intro_to_r5r.R | 6 inst/doc/intro_to_r5r.Rmd | 436 ++++++++-------- inst/doc/intro_to_r5r.html | 762 ++++++++++++----------------- inst/extdata/network.dat |binary inst/extdata/poa_osm.pbf.mapdb |binary inst/extdata/poa_osm.pbf.mapdb.p |binary man/detailed_itineraries.Rd | 3 man/travel_time_matrix.Rd | 9 tests/testthat/test-detailed_itineraries.R | 3 tests/testthat/test-download_r5.R | 2 tests/testthat/test-setup_r5.R | 1 tests/testthat/test-stop_r5.R | 88 +-- tests/testthat/test-street_network_to_sf.R | 51 - tests/testthat/test-travel_time_matrix.R | 423 ++++++++-------- tests/testthat/test-utils.R | 304 +++++------ vignettes/intro_to_r5r.Rmd | 436 ++++++++-------- 26 files changed, 1419 insertions(+), 1524 deletions(-)
Title: Robust Tests for Equal Correlation
Description: There are 6 novel robust tests for equal correlation. They are all based on logistic regressions. The score statistic U is proportion to difference of two correlations based on different types of correlation in 6 methods. The ST1() is based on Pearson correlation. ST2() improved ST1() by using median absolute deviation. ST3() utilized type M correlation and ST4() used Spearman correlation. ST5() and ST6() used two different ways to combine ST3() and ST4(). We highly recommend ST5() according to the article titled ''New Statistical Methods for Constructing Robust Differential Correlation Networks to characterize the interactions among microRNAs'' published in Scientific Reports. Please see the reference: Yu et al. (2019) <doi:10.1038/s41598-019-40167-8>.
Author: Danyang Yu, Weiliang Qiu, Zeyu Zhang, Kimberly Glass, Jessica Su, Dawn L. DeMeo, Kelan Tantisira, Scott T. Weiss
Maintainer: Danyang Yu <dyu33@jhu.edu>
Diff between corTest versions 1.0.4 dated 2020-07-19 and 1.0.7 dated 2020-09-25
DESCRIPTION | 12 +- MD5 | 18 ++- NAMESPACE | 37 ++++++ NEWS |only R/corTest.R | 249 +++++++++++++++++++++++++++++++++++++++++++++++ R/data.R |only R/genEset.R |only R/plotDiffCor.R |only data |only man/construct_network.Rd |only man/es.Rd |only man/genEset.Rd |only man/generate_data.Rd |only man/plotDiffCor.Rd |only man/st6.Rd | 108 ++++++++++---------- 15 files changed, 360 insertions(+), 64 deletions(-)
Title: Connect to 'AWS Athena' using R 'AWS SDK' 'paws' ('DBI'
Interface)
Description: Designed to be compatible with the 'R' package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this the 'R' 'AWS' Software Development Kit ('SDK') 'paws'
<https://github.com/paws-r/paws> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between noctua versions 1.8.0 dated 2020-08-10 and 1.8.1 dated 2020-09-25
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 6 ++++++ R/Connection.R | 4 ++-- R/Options.R | 2 +- R/Result.R | 10 ++++++---- R/View.R | 4 ++-- tests/testthat/test-dplyr-compute.R | 6 ++++++ 8 files changed, 34 insertions(+), 20 deletions(-)
Title: Recommended Learners for 'mlr3'
Description: Recommended Learners for 'mlr3'. Extends 'mlr3' and 'mlr3proba'
with interfaces to essential machine learning packages on CRAN. This
includes, but is not limited to: (penalized) linear and logistic
regression, linear and quadratic discriminant analysis, k-nearest
neighbors, naive Bayes, support vector machines, and gradient
boosting.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Quay Au [aut] (<https://orcid.org/0000-0002-5252-8902>),
Stefan Coors [aut] (<https://orcid.org/0000-0002-7465-2146>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3learners versions 0.3.0 dated 2020-08-29 and 0.4.0 dated 2020-09-25
DESCRIPTION | 10 ++-- MD5 | 66 ++++++++++++++++---------------- NEWS.md | 7 +++ R/LearnerClassifCVGlmnet.R | 13 +++--- R/LearnerClassifGlmnet.R | 11 ++--- R/LearnerClassifKKNN.R | 4 - R/LearnerClassifLDA.R | 4 - R/LearnerClassifLogReg.R | 4 - R/LearnerClassifMultinom.R | 4 - R/LearnerClassifNaiveBayes.R | 4 - R/LearnerClassifQDA.R | 4 - R/LearnerClassifRanger.R | 4 - R/LearnerClassifSVM.R | 3 - R/LearnerClassifXgboost.R | 7 +-- R/LearnerRegrCVGlmnet.R | 4 - R/LearnerRegrGlmnet.R | 4 - R/LearnerRegrKKNN.R | 2 R/LearnerRegrKM.R | 8 +-- R/LearnerRegrLM.R | 7 +-- R/LearnerRegrRanger.R | 2 R/LearnerRegrSVM.R | 2 R/LearnerRegrXgboost.R | 2 R/LearnerSurvCVGlmnet.R | 4 - R/LearnerSurvGlmnet.R | 4 - R/LearnerSurvRanger.R | 5 +- R/LearnerSurvXgboost.R | 6 +- R/helpers.R | 13 ++++++ build/partial.rdb |binary man/mlr_learners_regr.km.Rd | 5 +- tests/testthat/test_classif_cv_glmnet.R | 17 +++++++- tests/testthat/test_classif_glmnet.R | 17 +++++++- tests/testthat/test_regr_km.R | 2 tests/testthat/test_surv_cv_glmnet.R | 2 tests/testthat/test_surv_glmnet.R | 2 34 files changed, 153 insertions(+), 100 deletions(-)
Title: Tufte's Styles for R Markdown Documents
Description: Provides R Markdown output formats to use Tufte styles for PDF and HTML output.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
JJ Allaire [aut],
Andrzej Oles [ctb],
Dave Liepmann [ctb] (Tufte CSS in
inst/rmarkdown/templates/tufte_html/resources),
RStudio, PBC [cph]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tufte versions 0.6 dated 2020-05-08 and 0.7 dated 2020-09-25
DESCRIPTION | 10 ++++---- MD5 | 12 +++++----- R/handout.R | 2 - README.md | 2 - inst/rmarkdown/templates/tufte_handout/resources/tufte-handout.tex | 9 +++++++ inst/rmarkdown/templates/tufte_html/skeleton/skeleton.Rmd | 12 +++++----- man/tufte_handout.Rd | 2 - 7 files changed, 29 insertions(+), 20 deletions(-)
Title: Multidimensional Penalized Splines for Survival and Net Survival
Models
Description: Fits hazard and excess hazard models with multidimensional penalized splines allowing for
time-dependent effects, non-linear effects and interactions between several continuous covariates. In survival and net survival analysis, in addition to modelling the effect of time (via the baseline hazard), one has often to deal with several continuous covariates and model their functional forms, their time-dependent effects, and their interactions. Model specification becomes therefore a complex problem and penalized regression splines represent an appealing solution to that problem as splines offer the required flexibility while penalization limits overfitting issues. Current implementations of penalized survival models can be slow or unstable and sometimes lack some key features like taking into account expected mortality to provide net survival and excess hazard estimates. In contrast, survPen provides an automated, fast, and stable implementation (thanks to explicit calculation of the derivatives of the likelihood) and offers a unified framework for
multidimensional penalized hazard and excess hazard models. survPen may be of interest to those who 1) analyse any kind of time-to-event data: mortality, disease relapse, machinery breakdown, unemployment, etc 2) wish to describe the associated hazard and to understand which predictors impact its dynamics.
See Fauvernier et al. (2019a) <doi:10.21105/joss.01434> for an overview of the package and Fauvernier et al. (2019b) <doi:10.1111/rssc.12368> for the method.
Author: Mathieu Fauvernier [aut, cre], Laurent Roche [aut], Laurent Remontet [aut], Zoe Uhry [ctb], Nadine Bossard [ctb]
Maintainer: Mathieu Fauvernier <mathieu.fauvernier@gmail.com>
Diff between survPen versions 1.5.0 dated 2020-05-25 and 1.5.1 dated 2020-09-25
survPen-1.5.0/survPen/R/survPenV1_50.r |only survPen-1.5.1/survPen/DESCRIPTION | 8 survPen-1.5.1/survPen/MD5 | 76 +- survPen-1.5.1/survPen/NAMESPACE | 1 survPen-1.5.1/survPen/NEWS | 55 + survPen-1.5.1/survPen/R/survPenV1_51.r |only survPen-1.5.1/survPen/build/vignette.rds |binary survPen-1.5.1/survPen/inst/doc/survival_analysis_with_survPen.html | 374 ++-------- survPen-1.5.1/survPen/man/NR.beta.Rd | 2 survPen-1.5.1/survPen/man/NR.rho.Rd | 2 survPen-1.5.1/survPen/man/constraint.Rd | 2 survPen-1.5.1/survPen/man/cor.var.Rd | 2 survPen-1.5.1/survPen/man/crs.FP.Rd | 2 survPen-1.5.1/survPen/man/crs.Rd | 2 survPen-1.5.1/survPen/man/datCancer.Rd | 2 survPen-1.5.1/survPen/man/design.matrix.Rd | 2 survPen-1.5.1/survPen/man/instr.Rd | 2 survPen-1.5.1/survPen/man/inv.repam.Rd | 2 survPen-1.5.1/survPen/man/model.cons.Rd | 2 survPen-1.5.1/survPen/man/predict.survPen.Rd | 2 survPen-1.5.1/survPen/man/print.summary.survPen.Rd | 13 survPen-1.5.1/survPen/man/rd.Rd | 2 survPen-1.5.1/survPen/man/repam.Rd | 2 survPen-1.5.1/survPen/man/smf.Rd | 2 survPen-1.5.1/survPen/man/smooth.cons.Rd | 2 survPen-1.5.1/survPen/man/smooth.cons.integral.Rd | 2 survPen-1.5.1/survPen/man/smooth.spec.Rd | 2 survPen-1.5.1/survPen/man/summary.survPen.Rd | 2 survPen-1.5.1/survPen/man/survPen.Rd | 2 survPen-1.5.1/survPen/man/survPen.fit.Rd | 2 survPen-1.5.1/survPen/man/survPenObject.Rd | 2 survPen-1.5.1/survPen/man/tensor.in.Rd | 2 survPen-1.5.1/survPen/man/tensor.prod.S.Rd | 2 survPen-1.5.1/survPen/man/tensor.prod.X.Rd | 2 survPen-1.5.1/survPen/src/Makevars | 4 survPen-1.5.1/survPen/src/Makevars.win | 3 survPen-1.5.1/survPen/tests/compar_LAML_LCV.pdf |only survPen-1.5.1/survPen/tests/compar_several_mods.pdf |only survPen-1.5.1/survPen/tests/compar_tensor_tint.pdf |only survPen-1.5.1/survPen/tests/compar_total_excess.pdf |only survPen-1.5.1/survPen/tests/compar_total_excess_CI.pdf |only survPen-1.5.1/survPen/tests/compar_unpen_pen.pdf |only survPen-1.5.1/survPen/tests/output_tests_survPen.lis |only survPen-1.5.1/survPen/tests/test_survPen.r |only 44 files changed, 249 insertions(+), 335 deletions(-)
Title: Visualizations for 'mlr3'
Description: Provides visualizations for 'mlr3' objects such as
tasks, predictions, resample results or benchmark results via the
autoplot() generic of 'ggplot2'. The returned 'ggplot' objects are
intended to provide sensible defaults, yet can easily be customized to
create camera-ready figures. Visualizations include barplots,
boxplots, histograms, ROC curves, and Precision-Recall curves.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>),
Raphael Sonabend [aut] (<https://orcid.org/0000-0001-9225-4654>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3viz versions 0.2.0 dated 2020-08-07 and 0.3.0 dated 2020-09-25
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/BenchmarkResult.R | 8 ++++---- R/LearnerClasssifRpart.R | 10 +++++++++- R/LearnerRegrRpart.R | 3 ++- R/as_precrec.R | 3 ++- man/autoplot.BenchmarkResult.Rd | 4 ++-- man/autoplot.LearnerClassifRpart.Rd | 7 +++++++ tests/testthat/test_BenchmarkResult.R | 4 ++-- 10 files changed, 46 insertions(+), 25 deletions(-)
Title: Identification and Classification of the Most Influential Nodes
Description: Contains functions for the classification and ranking of top candidate features, reconstruction of networks from
adjacency matrices and data frames, analysis of the topology of the network
and calculation of centrality measures, and identification of the most
influential nodes. Also, a function is provided for running SIRIR model, which
is the combination of leave-one-out cross validation technique and the conventional SIR model, on a network to unsupervisedly rank the true influence of vertices. Additionally, some functions have been provided for the assessment
of dependence and correlation of two network centrality measures as well as
the conditional probability of deviation from their corresponding means in opposite direction.
Fred Viole and David Nawrocki (2013, ISBN:1490523995).
Csardi G, Nepusz T (2006). "The igraph software package for complex network research." InterJournal, Complex Systems, 1695.
Adopted algorithms and sources are referenced in function document.
Author: Adrian (Abbas) Salavaty [aut, cre], Mirana Ramialison [ths], Peter D. Currie [ths]
Maintainer: Adrian Salavaty <abbas.salavaty@gmail.com>
Diff between influential versions 1.1.2 dated 2020-06-26 and 2.0.0 dated 2020-09-25
DESCRIPTION | 14 MD5 | 72 - NAMESPACE | 4 NEWS.md | 40 R/data.R | 6 R/functions.R | 1748 ++++++++++++++++++++++++---- README.md | 53 build/vignette.rds |binary inst/CITATION | 2 inst/doc/Vignettes.R | 458 +++++-- inst/doc/Vignettes.Rmd | 664 ++++++++-- inst/doc/Vignettes.html | 2277 +++++++++++++++++++++---------------- man/betweenness.Rd | 7 man/cent_network.vis.Rd |only man/centrality.measures.Rd | 2 man/clusterRank.Rd | 6 man/coexpression.adjacency.Rd | 2 man/coexpression.data.Rd | 2 man/collective.influence.Rd | 6 man/degree.Rd | 7 man/exir.Rd | 48 man/exir.vis.Rd |only man/figures |only man/graph_from_adjacency_matrix.Rd | 6 man/graph_from_data_frame.Rd | 6 man/graph_from_incidence_matrix.Rd |only man/h_index.Rd | 6 man/hubness.score.Rd | 2 man/influential-package.Rd | 10 man/ivi.Rd | 3 man/ivi.from.indices.Rd | 3 man/lh_index.Rd | 6 man/neighborhood.connectivity.Rd | 6 man/sif2igraph.Rd | 8 man/sirir.Rd | 18 man/spreading.score.Rd | 2 vignettes/Sample_SIF.sif |only vignettes/Vignettes.Rmd | 664 ++++++++-- vignettes/influentialVignette.css |only 39 files changed, 4442 insertions(+), 1716 deletions(-)
Title: Calculation and Visualization of the Impact Effect Size Measure
Description: A non-parametric effect size measure capturing changes in central tendency or shape of data distributions. The package provides the necessary functions to calculate and plot the Impact effect size measure between two groups.
Author: Jorn Lotsch[aut,cre], Alfred Ultsch[aut]
Maintainer: Jorn Lotsch <j.loetsch@em.uni-frankfurt.de>
Diff between ImpactEffectsize versions 0.6.0 dated 2020-07-18 and 0.6.1 dated 2020-09-25
DESCRIPTION | 7 ++++--- MD5 | 3 ++- inst |only 3 files changed, 6 insertions(+), 4 deletions(-)
More information about ImpactEffectsize at CRAN
Permanent link
Title: Functional Time Series Analysis
Description: Functions for visualizing, modeling, forecasting and hypothesis testing of functional time series.
Author: Rob Hyndman [aut] (<https://orcid.org/0000-0002-2140-5352>),
Han Lin Shang [aut, cre, cph] (<https://orcid.org/0000-0003-1769-6430>)
Maintainer: Han Lin Shang <hanlin.shang@mq.edu.au>
Diff between ftsa versions 5.8 dated 2020-06-15 and 5.9 dated 2020-09-25
ChangeLog | 7 DESCRIPTION | 8 MD5 | 11 - R/dmfpca.R | 3 R/dynamic_FLR.R | 516 +++++++++++++++++++++++++++----------------------------- R/plsPI_var.R |only man/pm_10_GR.Rd | 2 7 files changed, 276 insertions(+), 271 deletions(-)
Title: High-Throughput Toxicokinetics
Description: Generic models and chemical-specific data for simulation and
statistical analysis of chemical toxicokinetics ("TK") as
described by Pearce et al. (2017) <doi:10.18637/jss.v079.i04>.
Chemical-specific in vitro data have been obtained from relatively
high throughput experiments. Both physiologically-based ("PBTK")
and empirical (for example, one compartment) "TK" models can be
parameterized with the data provided for thousands of chemicals,
multiple exposure routes, and various species. The models consist
of systems of ordinary differential equations which are solved
using compiled (C-based) code for speed. A Monte Carlo sampler is
included, which allows for simulating human biological variability
(Ring et al., 2017 <doi:10.1016/j.envint.2017.06.004>)
and propagating parameter uncertainty. Calibrated methods are
included for predicting tissue:plasma partition coefficients and
volume of distribution
(Pearce et al., 2017 <doi:10.1007/s10928-017-9548-7>).
These functions and data provide a set of tools for
in vitro-in vivo extrapolation ("IVIVE") of high throughput
screening data (for example, Tox21, ToxCast) to real-world
exposures via reverse dosimetry (also known as "RTK")
(Wetmore et al., 2015 <doi:10.1093/toxsci/kfv171>).
Author: John Wambaugh [aut, cre] (<https://orcid.org/0000-0002-4024-534X>),
Robert Pearce [aut] (<https://orcid.org/0000-0003-3168-4049>),
Caroline Ring [aut] (<https://orcid.org/0000-0002-0463-1251>),
Greg Honda [aut] (<https://orcid.org/0000-0001-7713-9850>),
Mark Sfeir [aut],
Matt Linakis [aut] (<https://orcid.org/0000-0003-0526-2395>),
Jimena Davis [ctb],
James Sluka [ctb] (<https://orcid.org/0000-0002-5901-1404>),
Nisha Sipes [ctb] (<https://orcid.org/0000-0003-4203-6426>),
Barbara Wetmore [ctb] (<https://orcid.org/0000-0002-6878-5348>),
Woodrow Setzer [ctb] (<https://orcid.org/0000-0002-6709-9186>)
Maintainer: John Wambaugh <wambaugh.john@epa.gov>
Diff between httk versions 2.0.2 dated 2020-07-19 and 2.0.3 dated 2020-09-25
httk-2.0.2/httk/R/calc_stats.R |only httk-2.0.2/httk/R/vLiverPBPKfetus_inits.R |only httk-2.0.2/httk/tests/solve_gas_crude_test.R |only httk-2.0.2/httk/tests/solve_gas_crude_test.Rout.save |only httk-2.0.3/httk/DESCRIPTION | 50 httk-2.0.3/httk/MD5 | 357 httk-2.0.3/httk/NAMESPACE | 1 httk-2.0.3/httk/NEWS | 20 httk-2.0.3/httk/R/Parameterize_gas_PBTK.R | 750 httk-2.0.3/httk/R/add_chemtable.R | 249 httk-2.0.3/httk/R/armitage.R | 744 httk-2.0.3/httk/R/available_rblood2plasma.R | 246 httk-2.0.3/httk/R/calc_analytic_css.R | 536 httk-2.0.3/httk/R/calc_analytic_css_1comp.R | 292 httk-2.0.3/httk/R/calc_analytic_css_3comp.R | 354 httk-2.0.3/httk/R/calc_analytic_css_3compss.R | 436 httk-2.0.3/httk/R/calc_analytic_css_pbtk.R | 388 httk-2.0.3/httk/R/calc_css.R | 576 httk-2.0.3/httk/R/calc_elimination_rate.R | 306 httk-2.0.3/httk/R/calc_hep_bioavailability.R | 172 httk-2.0.3/httk/R/calc_hep_clearance.R | 683 httk-2.0.3/httk/R/calc_hep_fu.R | 170 httk-2.0.3/httk/R/calc_mc_css.R | 680 httk-2.0.3/httk/R/calc_mc_oral_equiv.R | 359 httk-2.0.3/httk/R/calc_mc_tk.R | 472 httk-2.0.3/httk/R/calc_rblood2plasma.R | 326 httk-2.0.3/httk/R/calc_tkstats.R |only httk-2.0.3/httk/R/calc_total_clearance.R | 178 httk-2.0.3/httk/R/calc_volume_of_distribution.R | 404 httk-2.0.3/httk/R/create_mc_samples.R | 824 httk-2.0.3/httk/R/data.R | 2902 - httk-2.0.3/httk/R/export_pbtk_sbml.R | 1116 httk-2.0.3/httk/R/get_chem_id.R | 286 httk-2.0.3/httk/R/get_cheminfo.R | 206 httk-2.0.3/httk/R/get_invitroPK_param.R | 168 httk-2.0.3/httk/R/get_physchem_param.R | 322 httk-2.0.3/httk/R/get_rblood2plasma.R | 160 httk-2.0.3/httk/R/get_weight_class.R | 268 httk-2.0.3/httk/R/honda.ivive.R | 198 httk-2.0.3/httk/R/httk-package.R | 172 httk-2.0.3/httk/R/in.list.R | 422 httk-2.0.3/httk/R/invitro_mc.R | 25 httk-2.0.3/httk/R/ionization_functions.R | 532 httk-2.0.3/httk/R/parameterize_1comp.R | 418 httk-2.0.3/httk/R/parameterize_3comp.R | 230 httk-2.0.3/httk/R/parameterize_pbtk.R | 688 httk-2.0.3/httk/R/parameterize_schmitt.R | 547 httk-2.0.3/httk/R/parameterize_steadystate.R | 670 httk-2.0.3/httk/R/predict_partitioning_schmitt.R | 616 httk-2.0.3/httk/R/solve_1comp.R | 314 httk-2.0.3/httk/R/solve_3comp.R | 326 httk-2.0.3/httk/R/solve_gas_pbtk.R | 660 httk-2.0.3/httk/R/solve_model.R | 1108 httk-2.0.3/httk/R/solve_pbtk.R | 376 httk-2.0.3/httk/R/sysdata.rda |binary httk-2.0.3/httk/build/httk.pdf |22982 +++++----- httk-2.0.3/httk/build/vignette.rds |binary httk-2.0.3/httk/data/Frank2018.RData |binary httk-2.0.3/httk/data/Linakis2020.RData |binary httk-2.0.3/httk/data/Tables.RData |binary httk-2.0.3/httk/data/armitage_input.RData |binary httk-2.0.3/httk/data/httkpop.RData |binary httk-2.0.3/httk/data/vignettes.RData |binary httk-2.0.3/httk/data/wambaugh2019.RData |binary httk-2.0.3/httk/data/well_param.RData |binary httk-2.0.3/httk/inst/doc/Frank2018.html | 184 httk-2.0.3/httk/inst/doc/Honda2019.html | 2 httk-2.0.3/httk/inst/doc/Linakis2020.html | 2149 httk-2.0.3/httk/inst/doc/Pearce2017.html | 84 httk-2.0.3/httk/inst/doc/Ring_2017_vignette01_subpopulations.html | 4 httk-2.0.3/httk/inst/doc/Ring_2017_vignette02_evalmodelsubpop.html | 4 httk-2.0.3/httk/inst/doc/Ring_2017_vignette03_paper_fig2.html | 4 httk-2.0.3/httk/inst/doc/Ring_2017_vignette04_paper_fig3.html | 4 httk-2.0.3/httk/inst/doc/Ring_2017_vignette05b_plothowgatejohnson.html | 4 httk-2.0.3/httk/inst/doc/Ring_2017_vignette06_aerplotting.Rmd | 2 httk-2.0.3/httk/inst/doc/Ring_2017_vignette06_aerplotting.html | 6 httk-2.0.3/httk/inst/doc/Ring_2017_vignette_05a_virtualstudypops.html | 4 httk-2.0.3/httk/inst/doc/Wambaugh2018.html | 210 httk-2.0.3/httk/inst/doc/Wambaugh2019.html | 4 httk-2.0.3/httk/man/EPA.ref.Rd | 48 httk-2.0.3/httk/man/Frank2018invivo.Rd | 64 httk-2.0.3/httk/man/Obach2008.Rd | 44 httk-2.0.3/httk/man/Tables.Rdata.stamp.Rd | 42 httk-2.0.3/httk/man/Wetmore.data.Rd | 94 httk-2.0.3/httk/man/Wetmore2012.Rd | 52 httk-2.0.3/httk/man/add_chemtable.Rd | 14 httk-2.0.3/httk/man/age_dist_smooth.Rd | 60 httk-2.0.3/httk/man/armitage_eval.Rd | 208 httk-2.0.3/httk/man/armitage_input.Rd | 76 httk-2.0.3/httk/man/augment.table.Rd |only httk-2.0.3/httk/man/available_rblood2plasma.Rd | 126 httk-2.0.3/httk/man/bmiage.Rd | 90 httk-2.0.3/httk/man/calc_analytic_css.Rd | 2 httk-2.0.3/httk/man/calc_analytic_css_1comp.Rd | 2 httk-2.0.3/httk/man/calc_analytic_css_3comp.Rd | 2 httk-2.0.3/httk/man/calc_analytic_css_3compss.Rd | 2 httk-2.0.3/httk/man/calc_analytic_css_pbtk.Rd | 2 httk-2.0.3/httk/man/calc_css.Rd | 334 httk-2.0.3/httk/man/calc_elimination_rate.Rd | 184 httk-2.0.3/httk/man/calc_hep_bioavailability.Rd | 110 httk-2.0.3/httk/man/calc_hep_clearance.Rd | 164 httk-2.0.3/httk/man/calc_hep_fu.Rd | 112 httk-2.0.3/httk/man/calc_hepatic_clearance.Rd | 168 httk-2.0.3/httk/man/calc_ionization.Rd | 156 httk-2.0.3/httk/man/calc_mc_css.Rd | 2 httk-2.0.3/httk/man/calc_mc_oral_equiv.Rd | 2 httk-2.0.3/httk/man/calc_mc_tk.Rd | 2 httk-2.0.3/httk/man/calc_rblood2plasma.Rd | 180 httk-2.0.3/httk/man/calc_stats.Rd | 250 httk-2.0.3/httk/man/calc_tkstats.Rd |only httk-2.0.3/httk/man/calc_total_clearance.Rd | 150 httk-2.0.3/httk/man/calc_vdist.Rd | 172 httk-2.0.3/httk/man/chem.invivo.PK.aggregate.data.Rd | 52 httk-2.0.3/httk/man/chem.invivo.PK.data.Rd | 416 httk-2.0.3/httk/man/chem.invivo.PK.summary.data.Rd | 414 httk-2.0.3/httk/man/chem.lists.Rd | 80 httk-2.0.3/httk/man/chem.physical_and_invitro.data.Rd | 260 httk-2.0.3/httk/man/concentration_data_Linakis2020.Rd | 50 httk-2.0.3/httk/man/create_mc_samples.Rd | 2 httk-2.0.3/httk/man/get_chem_id.Rd | 50 httk-2.0.3/httk/man/get_invitroPK_param.Rd | 78 httk-2.0.3/httk/man/get_lit_cheminfo.Rd | 126 httk-2.0.3/httk/man/get_lit_css.Rd | 168 httk-2.0.3/httk/man/get_lit_oral_equiv.Rd | 194 httk-2.0.3/httk/man/get_physchem_param.Rd | 70 httk-2.0.3/httk/man/get_rblood2plasma.Rd | 98 httk-2.0.3/httk/man/honda.ivive.Rd | 110 httk-2.0.3/httk/man/howgate.Rd | 48 httk-2.0.3/httk/man/httk-package.Rd | 112 httk-2.0.3/httk/man/in.list.Rd | 220 httk-2.0.3/httk/man/is.httk.Rd | 210 httk-2.0.3/httk/man/johnson.Rd | 50 httk-2.0.3/httk/man/mcnally_dt.Rd | 80 httk-2.0.3/httk/man/metabolism_data_Linakis2020.Rd | 50 httk-2.0.3/httk/man/monte_carlo.Rd | 306 httk-2.0.3/httk/man/nhanes_mec_svy.Rd | 80 httk-2.0.3/httk/man/onlyp.Rd | 48 httk-2.0.3/httk/man/parameterize_1comp.Rd | 2 httk-2.0.3/httk/man/parameterize_3comp.Rd | 226 httk-2.0.3/httk/man/parameterize_gas_pbtk.Rd | 364 httk-2.0.3/httk/man/parameterize_pbtk.Rd | 2 httk-2.0.3/httk/man/parameterize_schmitt.Rd | 184 httk-2.0.3/httk/man/parameterize_steadystate.Rd | 2 httk-2.0.3/httk/man/pc.data.Rd | 132 httk-2.0.3/httk/man/pharma.Rd | 54 httk-2.0.3/httk/man/physiology.data.Rd | 72 httk-2.0.3/httk/man/predict_partitioning_schmitt.Rd | 222 httk-2.0.3/httk/man/scale_dosing.Rd | 74 httk-2.0.3/httk/man/set_httk_precision.Rd | 58 httk-2.0.3/httk/man/sipes2017.Rd | 66 httk-2.0.3/httk/man/solve_1comp.Rd | 2 httk-2.0.3/httk/man/solve_3comp.Rd | 2 httk-2.0.3/httk/man/solve_gas_pbtk.Rd | 9 httk-2.0.3/httk/man/solve_model.Rd | 346 httk-2.0.3/httk/man/solve_pbtk.Rd | 2 httk-2.0.3/httk/man/spline_heightweight.Rd | 72 httk-2.0.3/httk/man/spline_hematocrit.Rd | 66 httk-2.0.3/httk/man/spline_serumcreat.Rd | 74 httk-2.0.3/httk/man/supptab1_Linakis2020.Rd | 50 httk-2.0.3/httk/man/supptab2_Linakis2020.Rd | 50 httk-2.0.3/httk/man/tissue.data.Rd | 96 httk-2.0.3/httk/man/wambaugh2019.Rd | 124 httk-2.0.3/httk/man/wambaugh2019.nhanes.Rd | 84 httk-2.0.3/httk/man/wambaugh2019.raw.Rd | 200 httk-2.0.3/httk/man/wambaugh2019.seem3.Rd | 68 httk-2.0.3/httk/man/wambaugh2019.tox21.Rd | 102 httk-2.0.3/httk/man/well_param.Rd | 81 httk-2.0.3/httk/man/wfl.Rd | 80 httk-2.0.3/httk/src/init.c | 7 httk-2.0.3/httk/tests/1comp_test.Rout.save | 256 httk-2.0.3/httk/tests/3comp_test.Rout.save | 346 httk-2.0.3/httk/tests/3compss_test.Rout.save | 120 httk-2.0.3/httk/tests/adddata_test.Rout.save | 156 httk-2.0.3/httk/tests/cheminfo_test.R | 9 httk-2.0.3/httk/tests/cheminfo_test.Rout.save | 119 httk-2.0.3/httk/tests/httk2.0_test.Rout.save | 744 httk-2.0.3/httk/tests/ivive_test.R | 136 httk-2.0.3/httk/tests/ivive_test.Rout.save | 156 httk-2.0.3/httk/tests/montecarlo_tests.Rout.save | 402 httk-2.0.3/httk/tests/other_tests.Rout.save | 40 httk-2.0.3/httk/tests/pbtk_test.Rout.save | 242 httk-2.0.3/httk/tests/solve_gas_test.R |only httk-2.0.3/httk/tests/solve_gas_test.Rout.save |only httk-2.0.3/httk/vignettes/Ring_2017_vignette06_aerplotting.Rmd | 2 184 files changed, 30472 insertions(+), 29465 deletions(-)
Title: The 'Monaco' Editor in 'Shiny'
Description: A 'Shiny' app including the 'Monaco' editor. The 'Monaco' editor is the code editor which powers 'VS Code'. It is particularly well developed for 'JavaScript'. In addition to the 'Monaco' editor features, the app provides prettifiers and minifiers for multiple languages, 'SCSS' and 'TypeScript' compilers, code checking for 'C' and 'C++' (requires 'cppcheck').
Author: Stéphane Laurent [aut, cre],
Microsoft Corporation [ctb, cph] (Monaco Editor),
Brijesh Brittu [ctb, cph] (monaco-ace-tokenizer),
James Long and contributors [ctb, cph] (Prettier),
Leandro Vital [ctb, cph] (Bootstrap Flash Alert),
Daniel Eden [ctb, cph] (animate.css),
Adam Schwartz [ctb, cph] (chrome-tabs),
David DeSandro [ctb, cph] (Draggabilly),
JakubPawlowicz.com [ctb, cph] (clean-css),
Mihai Bazon [ctb, cph] (terser),
Juriy "kangax" Zaytsev [ctb, cph] (HTMLMinifier),
Rodney Rehm [ctb, cph] (Sass.js),
Rich Harris [ctb, cph] (svg-parser),
Lionel Tzatzkin [ctb, cph] (scale-that-svg),
Andrei Kashcha [ctb, cph] (panzoom),
Vitaly Puzrin [ctb, cph] (markdown-it),
Alex Kocharin [ctb, cph] (markdown-it),
John Schlinkert [ctb, cph] (word-wrap),
Terence Eden [ctb, cph] (SuperTinyIcons),
www.jeasyui.com [ctb, cph] (EasyUI)
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Diff between shinyMonacoEditor versions 0.1.0 dated 2020-09-09 and 1.0.0 dated 2020-09-25
DESCRIPTION | 24 LICENSE.note | 79 MD5 | 66 NEWS.md | 11 README.md | 5 inst/shinyApp/server.R | 193 inst/shinyApp/ui.R | 67 inst/shinyApp/www/chrome-tabs/chrome-tabs.css | 4 inst/shinyApp/www/chrome-tabs/mock-browser.css | 7 inst/shinyApp/www/css/shinyMonacoEditor.css | 148 inst/shinyApp/www/icons/freeicons/freeicon.eot |only inst/shinyApp/www/icons/freeicons/freeicon.ttf |only inst/shinyApp/www/icons/freeicons/freeicon.woff |only inst/shinyApp/www/icons/freeicons/freeicons.css |only inst/shinyApp/www/icons/freeicons/wifi-off.svg |only inst/shinyApp/www/jQuery-simple-slider |only inst/shinyApp/www/jquery-easyui |only inst/shinyApp/www/js/chromeTabs.js | 10 inst/shinyApp/www/js/customMessageHandlers.js | 290 inst/shinyApp/www/js/docReady.js | 172 inst/shinyApp/www/js/functions.js | 69 inst/shinyApp/www/js/globalVariables.js | 5 inst/shinyApp/www/js/shinyMonacoEditor.js | 537 inst/shinyApp/www/panzoom |only inst/shinyApp/www/prettier/parser-babel.js | 2 inst/shinyApp/www/prettier/parser-html.js | 30 inst/shinyApp/www/prettier/parser-markdown.js | 8 inst/shinyApp/www/prettier/parser-postcss.js | 4 inst/shinyApp/www/prettier/parser-typescript.js | 6 inst/shinyApp/www/prettier/parser-yaml.js | 25 inst/shinyApp/www/prettier/standalone.js |32938 ------------------------ inst/shinyApp/www/scale-that-svg |only 32 files changed, 1514 insertions(+), 33186 deletions(-)
More information about shinyMonacoEditor at CRAN
Permanent link
Title: Interactive Graphics for QTL Experiments
Description: Web-based interactive charts (using D3.js) for the analysis of
experimental crosses to identify genetic loci (quantitative trait
loci, QTL) contributing to variation in quantitative traits.
Broman (2015) <doi:10.1534/genetics.114.172742>.
Author: Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>),
Michael Bostock [ctb, cph] (d3.js library in htmlwidgets/lib,
https://d3js.org),
jQuery Foundation [cph] (jQuery library in htmlwidgets/lib,
https://jquery.com),
jQuery contributors [ctb] (jQuery library in htmlwidgets/lib; see
https://github.com/jquery/jquery/blob/master/AUTHORS.txt),
jQuery UI contributors [ctb] (jQuery UI library in htmlwidgets/lib; see
https://jqueryui.com/about/)
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtlcharts versions 0.11-6 dated 2019-02-05 and 0.12-10 dated 2020-09-25
qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/colorbrewer |only qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/d3-tip |only qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/d3panels/License.md |only qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/d3panels/ReadMe.md |only qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/animated-overlay.gif |only qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-bg_flat_0_aaaaaa_40x100.png |only qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/jquery-ui/themes/smoothness/images/ui-bg_flat_75_ffffff_40x100.png |only qtlcharts-0.11-6/qtlcharts/inst/htmlwidgets/lib/jquery/MIT-LICENSE.txt |only qtlcharts-0.12-10/qtlcharts/DESCRIPTION | 38 - qtlcharts-0.12-10/qtlcharts/LICENSE | 78 -- qtlcharts-0.12-10/qtlcharts/MD5 | 311 ++++------ qtlcharts-0.12-10/qtlcharts/NEWS.md | 50 + qtlcharts-0.12-10/qtlcharts/R/convert4crosstab.R | 24 qtlcharts-0.12-10/qtlcharts/R/convert_pxg.R | 20 qtlcharts-0.12-10/qtlcharts/R/estQTLeffects.R | 32 - qtlcharts-0.12-10/qtlcharts/R/geneExpr-data.R | 4 qtlcharts-0.12-10/qtlcharts/R/grav-data.R | 6 qtlcharts-0.12-10/qtlcharts/R/iboxplot.R | 6 qtlcharts-0.12-10/qtlcharts/R/idotplot.R | 4 qtlcharts-0.12-10/qtlcharts/R/iheatmap.R | 10 qtlcharts-0.12-10/qtlcharts/R/ipleiotropy.R | 30 qtlcharts-0.12-10/qtlcharts/R/iplot.R | 6 qtlcharts-0.12-10/qtlcharts/R/iplotCorr.R | 26 qtlcharts-0.12-10/qtlcharts/R/iplotCurves.R | 4 qtlcharts-0.12-10/qtlcharts/R/iplotMScanone.R | 31 qtlcharts-0.12-10/qtlcharts/R/iplotMap.R | 12 qtlcharts-0.12-10/qtlcharts/R/iplotPXG.R | 22 qtlcharts-0.12-10/qtlcharts/R/iplotRF.R | 24 qtlcharts-0.12-10/qtlcharts/R/iplotScanone.R | 36 - qtlcharts-0.12-10/qtlcharts/R/iplotScantwo.R | 46 - qtlcharts-0.12-10/qtlcharts/R/itriplot.R | 8 qtlcharts-0.12-10/qtlcharts/R/qtlcharts.R | 30 qtlcharts-0.12-10/qtlcharts/R/scat2scat.R | 10 qtlcharts-0.12-10/qtlcharts/R/setScreenSize.R | 4 qtlcharts-0.12-10/qtlcharts/R/util.R | 20 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qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotMap.yaml | 13 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotRF.coffee | 2 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotRF.js | 8 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotRF.yaml | 11 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotScanone.coffee | 2 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotScanone.js | 9 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotScanone.yaml | 11 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotScantwo.coffee | 2 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotScantwo.js | 10 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/iplotScantwo.yaml | 17 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/itriplot.coffee | 2 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/itriplot.js | 8 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/itriplot.yaml | 17 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/lib/d3/d3.min.js | 4 qtlcharts-0.12-10/qtlcharts/inst/htmlwidgets/lib/d3panels/LICENSE.md |only 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Title: Magnetic Resonance Binning, Integration and Normalization
Description: Nuclear Magnetic Resonance is widely used in Life Science
research. The package (<http://www.kleinomicslab.com/software>) converts 1D or 2D data into a matrix of values
suitable for further data analysis and performs basic processing steps in a
reproducible way. Negative values, a common issue in such data, are replaced
by positive values. All used parameters are stored in a readable text file
and can be restored from that file to enable exact reproduction of the data
at a later time.
Author: Matthias Klein [aut, cre] (<https://orcid.org/0000-0001-7455-5381>)
Maintainer: Matthias Klein <klein.663@osu.edu>
Diff between mrbin versions 1.4.2 dated 2020-06-01 and 1.4.3 dated 2020-09-25
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/mrbin.R | 26 ++++++++++++++------------ inst/doc/mrbin.Rnw | 2 +- inst/doc/mrbin.pdf |binary vignettes/mrbin.Rnw | 2 +- 7 files changed, 30 insertions(+), 23 deletions(-)
Title: Easily Process a Batch of Cox Models
Description: A tool to operate a batch of univariate or multivariate
Cox models and return tidy result.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>)
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between ezcox versions 0.7.0 dated 2020-07-01 and 0.8.0 dated 2020-09-25
DESCRIPTION | 6 MD5 | 66 +- NEWS.md | 118 ++-- R/clean_model_dir.R | 36 - R/cox_panel.R | 72 +- R/ezcox.R | 474 ++++++++--------- R/ezcox_parallel.R | 246 ++++----- R/ezgrp.R | 226 ++++---- R/filter_ezcox.R | 114 ++-- R/get_models.R | 128 ++-- R/show_forest.R | 157 +++-- R/show_models.R | 170 +++--- R/utils.R | 16 R/zzz.R | 30 - README.md | 308 +++++------ build/vignette.rds |binary inst/CITATION | 32 - inst/doc/ezcox.R | 96 +-- inst/doc/ezcox.Rmd | 226 ++++---- inst/doc/ezcox.html | 1065 +++++++++++++++++++-------------------- inst/doc/ezforest.R | 46 - inst/doc/ezforest.Rmd | 70 +- inst/doc/ezforest.html | 770 +++++++++++++--------------- inst/doc/ezgroup.R | 30 - inst/doc/ezgroup.Rmd | 56 +- inst/doc/ezgroup.html | 824 ++++++++++++++++-------------- man/ezcox.Rd | 158 ++--- man/ezcox_group.Rd | 124 ++-- man/show_forest.Rd | 166 +++--- man/show_models.Rd | 100 +-- tests/testthat/test-test_ezcox.R | 108 +-- vignettes/ezcox.Rmd | 226 ++++---- vignettes/ezforest.Rmd | 70 +- vignettes/ezgroup.Rmd | 56 +- 34 files changed, 3245 insertions(+), 3145 deletions(-)
Title: Interactive Conditional Visualization for Supervised and
Unsupervised Models in Shiny
Description: Constructs a shiny app function with interactive displays for conditional visualization of models,
data and density functions. An extended version of package 'condvis'.
Mark O'Connell, Catherine B. Hurley, Katarina Domijan (2017) <doi:10.18637/jss.v081.i05>.
Author: Catherine Hurley [aut, cre],
Mark OConnell [aut],
Katarina Domijan [aut]
Maintainer: Catherine Hurley <catherine.hurley@mu.ie>
Diff between condvis2 versions 0.1.0 dated 2019-06-28 and 0.1.1 dated 2020-09-25
condvis2-0.1.0/condvis2/man/condtour.Rd |only condvis2-0.1.1/condvis2/DESCRIPTION | 19 condvis2-0.1.1/condvis2/MD5 | 96 +- condvis2-0.1.1/condvis2/NAMESPACE | 16 condvis2-0.1.1/condvis2/NEWS.md |only condvis2-0.1.1/condvis2/R/CVpredict.R | 314 +++++- condvis2-0.1.1/condvis2/R/arrangeC.R | 47 - condvis2-0.1.1/condvis2/R/cluspath.R |only condvis2-0.1.1/condvis2/R/colours.R |only condvis2-0.1.1/condvis2/R/conditionplots.R | 81 + condvis2-0.1.1/condvis2/R/condpath.R | 341 +------ condvis2-0.1.1/condvis2/R/createServer.R | 163 ++- condvis2-0.1.1/condvis2/R/createUI.R | 92 +- condvis2-0.1.1/condvis2/R/diagnostics.R | 7 condvis2-0.1.1/condvis2/R/fitpath.R |only condvis2-0.1.1/condvis2/R/helper.R | 157 +-- condvis2-0.1.1/condvis2/R/sectionplot3dprobs.R | 375 +++++--- condvis2-0.1.1/condvis2/R/sectionplots.R | 642 ++++++++------ condvis2-0.1.1/condvis2/R/similarityweight.R | 217 +++- condvis2-0.1.1/condvis2/build/vignette.rds |binary condvis2-0.1.1/condvis2/inst/doc/Keras.R | 63 - condvis2-0.1.1/condvis2/inst/doc/Keras.Rmd | 34 condvis2-0.1.1/condvis2/inst/doc/Keras.html | 346 ++++--- condvis2-0.1.1/condvis2/inst/doc/introduction.R | 38 condvis2-0.1.1/condvis2/inst/doc/introduction.Rmd | 23 condvis2-0.1.1/condvis2/inst/doc/introduction.html | 150 +-- condvis2-0.1.1/condvis2/inst/doc/mclust.R | 46 - condvis2-0.1.1/condvis2/inst/doc/mclust.Rmd | 21 condvis2-0.1.1/condvis2/inst/doc/mclust.html | 195 ++-- condvis2-0.1.1/condvis2/inst/doc/mlr.R |only condvis2-0.1.1/condvis2/inst/doc/mlr.Rmd |only condvis2-0.1.1/condvis2/inst/doc/mlr.html |only condvis2-0.1.1/condvis2/inst/doc/parsnip.R |only condvis2-0.1.1/condvis2/inst/doc/parsnip.Rmd |only condvis2-0.1.1/condvis2/inst/doc/parsnip.html |only condvis2-0.1.1/condvis2/man/CVpredict.Rd | 414 +++++++-- condvis2-0.1.1/condvis2/man/clusPath.Rd |only condvis2-0.1.1/condvis2/man/conditionPlot.Rd | 11 condvis2-0.1.1/condvis2/man/condvis.Rd | 39 condvis2-0.1.1/condvis2/man/createCVServer.Rd | 43 condvis2-0.1.1/condvis2/man/createCVUI.Rd | 23 condvis2-0.1.1/condvis2/man/fitPath.Rd |only condvis2-0.1.1/condvis2/man/medoid.Rd |only condvis2-0.1.1/condvis2/man/plotTourDiagnostics.Rd | 10 condvis2-0.1.1/condvis2/man/sectionPlot.Rd | 46 - condvis2-0.1.1/condvis2/man/similarityweight.Rd | 15 condvis2-0.1.1/condvis2/man/tours.Rd |only condvis2-0.1.1/condvis2/man/weightcolor.Rd | 2 condvis2-0.1.1/condvis2/tests |only condvis2-0.1.1/condvis2/vignettes/Keras.Rmd | 34 condvis2-0.1.1/condvis2/vignettes/introduction.Rmd | 23 condvis2-0.1.1/condvis2/vignettes/mclust.Rmd | 21 condvis2-0.1.1/condvis2/vignettes/mlr.Rmd |only condvis2-0.1.1/condvis2/vignettes/parsnip.Rmd |only condvis2-0.1.1/condvis2/vignettes/vignettefigs/Boston.png |binary condvis2-0.1.1/condvis2/vignettes/vignettefigs/Pima.png |binary 56 files changed, 2642 insertions(+), 1522 deletions(-)
Title: Critical Line Algorithm in Pure R
Description: Implements 'Markowitz' Critical Line Algorithm ('CLA') for classical
mean-variance portfolio optimization, see Markowitz (1952) <doi:10.2307/2975974>.
Care has been taken for correctness in light of previous buggy implementations.
Author: Yanhao Shi <syhelena@163.com>,
Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between CLA versions 0.96-0 dated 2020-09-07 and 0.96-1 dated 2020-09-25
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- build/partial.rdb |binary tests/SP500-ex.R | 14 ++++++++------ 4 files changed, 15 insertions(+), 13 deletions(-)
Title: Subset Partitioning via Anticlustering
Description: The method of anticlustering partitions a pool of
elements into groups (i.e., anticlusters) in such a way that the
between-group similarity is maximized and -- at the same time -- the
within-group heterogeneity is maximized. This reverses the logic of
cluster analysis that strives for high within-group homogeneity and
low similarity of the different groups. Computationally,
anticlustering is accomplished by maximizing instead of minimizing a
clustering objective function, such as the intra-cluster variance
(used in k-means clustering) or the sum of pairwise distances within
clusters. The function anticlustering() implements exact and
heuristic anticlustering algorithms as described in Papenberg and Klau
(2020; <doi:10.1037/met0000301>). The exact approach requires that the
GNU linear programming kit
(<https://www.gnu.org/software/glpk/glpk.html>) is available and the R
package 'Rglpk' (<https://cran.R-project.org/package=Rglpk>) is
installed. Some other functions are available to solve classical
clustering problems. The function balanced_clustering() applies a
cluster analysis under size constraints, i.e., creates equal-sized
clusters. The function matching() can be used for (unrestricted,
bipartite, or K-partite) matching. The function wce() can be used
optimally solve the (weighted) cluster editing problem, also known as
correlation clustering, clique partitioning problem or transitivity
clustering.
Author: Martin Papenberg [aut, cre] (<https://orcid.org/0000-0002-9900-4268>),
Meik Michalke [ctb] (centroid based clustering algorithm),
Gunnar W. Klau [ths],
Juliane V. Tkotz [ctb] (package logo)
Maintainer: Martin Papenberg <martin.papenberg@hhu.de>
Diff between anticlust versions 0.5.0 dated 2020-06-29 and 0.5.3 dated 2020-09-25
DESCRIPTION | 14 +- MD5 | 40 ++++-- NAMESPACE | 1 R/categorical-variable-handling.R | 2 R/exact-anticlustering.R | 2 R/exchange-method-generic.R | 5 R/exchange-method-kmeans-anticlustering.R | 6 R/input-validation.R | 59 ++++++--- R/objective-kplus.R |only R/repeated-exchange.R |only R/sample-by-category.R | 49 ++++++- R/wrapper-anticlustering.R | 176 +++++++++++++++++++--------- R/wrapper-clustering.R | 2 build |only inst/doc |only man/anticlustering.Rd | 134 ++++++++++++++------- man/categorical_sampling.Rd | 12 + man/kplus_objective.Rd |only man/schaper2019.Rd | 6 tests/testthat/test-argument-K.R |only tests/testthat/test-exchange-method.R | 18 ++ tests/testthat/test-kplus-criterion.R |only tests/testthat/test-local-updating-kmeans.R |only tests/testthat/test-repeated-exchange.R |only vignettes |only 25 files changed, 371 insertions(+), 155 deletions(-)
Title: Fitting Point Process Models via the Palm Likelihood
Description: Functions to fit point process models using the Palm likelihood. First proposed by Tanaka, Ogata, and Stoyan (2008) <DOI:10.1002/bimj.200610339>, maximisation of the Palm likelihood can provide computationally efficient parameter estimation for point process models in situations where the full likelihood is intractable. This package is chiefly focused on Neyman-Scott point processes, but can also fit the void processes proposed by Jones-Todd et al. (2019) <DOI:10.1002/sim.8046>. The development of this package was motivated by the analysis of capture-recapture surveys on which individuals cannot be identified---the data from which can conceptually be seen as a clustered point process (Stevenson, Borchers, and Fewster, 2019 <DOI:10.1111/biom.12983>). As such, some of the functions in this package are specifically for the estimation of cetacean density from two-camera aerial surveys.
Author: Ben Stevenson <ben.stevenson@auckland.ac.nz>
Maintainer: Ben Stevenson <ben.stevenson@auckland.ac.nz>
Diff between palm versions 1.1.3 dated 2018-12-08 and 1.1.4 dated 2020-09-25
palm-1.1.3/palm/src/palm_init.c |only palm-1.1.4/palm/DESCRIPTION | 14 ++++----- palm-1.1.4/palm/MD5 | 44 +++++++++++++++---------------- palm-1.1.4/palm/NAMESPACE | 7 ---- palm-1.1.4/palm/NEWS | 14 +++++++-- palm-1.1.4/palm/R/RcppExports.R | 4 ++ palm-1.1.4/palm/R/fit-ns.r | 18 +++++------- palm-1.1.4/palm/R/methods.r | 1 palm-1.1.4/palm/R/palm.r | 16 +++++------ palm-1.1.4/palm/R/refclass.r | 24 +++++++++------- palm-1.1.4/palm/man/coef.palm.Rd | 3 -- palm-1.1.4/palm/man/confint.palm.Rd | 3 -- palm-1.1.4/palm/man/example.1D.Rd | 4 ++ palm-1.1.4/palm/man/example.2D.Rd | 4 ++ palm-1.1.4/palm/man/example.twocamera.Rd | 4 ++ palm-1.1.4/palm/man/fit.ns.Rd | 33 +++++++++++++++-------- palm-1.1.4/palm/man/fit.twocamera.Rd | 21 +++++++++++--- palm-1.1.4/palm/man/fit.void.Rd | 16 ++++++++--- palm-1.1.4/palm/man/palm.Rd | 14 ++++----- palm-1.1.4/palm/man/plot.palm.Rd | 3 -- palm-1.1.4/palm/man/porpoise.data.Rd | 4 ++ palm-1.1.4/palm/man/sim.ns.Rd | 14 +++++++-- palm-1.1.4/palm/src/RcppExports.cpp | 26 ++++++++++++++++++ palm-1.1.4/palm/src/euc_distances.cpp |only 24 files changed, 182 insertions(+), 109 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-21 0.1.2
2019-12-02 0.1.1
2019-11-25 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-25 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-25 0.1.1
2020-03-15 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-06-28 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-13 3.1.11
2018-04-12 3.1.10
2018-03-30 3.1.9
2016-08-23 3.1.7
2016-06-25 3.1.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-03-03 2.0.1
2014-07-16 2.0
2013-10-29 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-15 0.1.8
2020-09-11 0.1.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-23 1.5.2
2020-09-18 1.5.1
2020-09-11 1.5.0
Title: A Simple Package for Testing R Packages
Description: Provides two convenience functions assert() and test_pkg() to
facilitate testing R packages.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Steven Mortimer [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between testit versions 0.11 dated 2019-11-12 and 0.12 dated 2020-09-25
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ NEWS | 6 ++++++ R/testit.R | 25 ++++++++++++++++++++++++- R/utils.R | 10 ++++++++-- R/zzz.R |only README.md | 2 +- man/assert.Rd | 2 +- 8 files changed, 51 insertions(+), 15 deletions(-)
Title: Extra String Manipulation Functions
Description: There are some things that I wish were easier with
the 'stringr' or 'stringi' packages. The foremost of these is the
extraction of numbers from strings. 'stringr' and 'stringi' make you
figure out the regular expression for yourself; 'strex' takes care of
this for you. There are many other handy functionalities in 'strex'.
Contributions to this package are encouraged: it is intended as a
miscellany of string manipulation functions that cannot be found in
'stringi' or 'stringr'.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between strex versions 1.2.0 dated 2019-09-13 and 1.3.0 dated 2020-09-25
strex-1.2.0/strex/R/RcppExports.R |only strex-1.2.0/strex/R/all-equal.R |only strex-1.2.0/strex/configure |only strex-1.2.0/strex/configure.win |only strex-1.2.0/strex/src/RcppExports.cpp |only strex-1.2.0/strex/src/arg-match.cpp |only strex-1.2.0/strex/src/interleave.cpp |only strex-1.2.0/strex/src/list-utils.cpp |only strex-1.2.0/strex/src/mymath.h |only strex-1.2.0/strex/src/split-by-nums.cpp |only strex-1.2.0/strex/src/stod.cpp |only strex-1.2.0/strex/src/stod.h |only strex-1.2.0/strex/src/substrs.cpp |only strex-1.2.0/strex/src/substrs.h |only strex-1.2.0/strex/tests/testthat/test-RcppExports.R |only strex-1.2.0/strex/tools |only strex-1.3.0/strex/DESCRIPTION | 17 -- strex-1.3.0/strex/MD5 | 145 ++++++++---------- strex-1.3.0/strex/NAMESPACE | 4 strex-1.3.0/strex/R/after.R | 2 strex-1.3.0/strex/R/alphord.R | 16 +- strex-1.3.0/strex/R/arg-match.R | 78 +++++---- strex-1.3.0/strex/R/c-wrappers.R |only strex-1.3.0/strex/R/currency.R | 20 +- strex-1.3.0/strex/R/extract-non-nums.R | 8 - strex-1.3.0/strex/R/extract-nums.R | 13 - strex-1.3.0/strex/R/locate.R | 26 +-- strex-1.3.0/strex/R/split-by-nums.R | 5 strex-1.3.0/strex/R/strex-package.R | 9 - strex-1.3.0/strex/R/trim.R | 73 +++++++-- strex-1.3.0/strex/R/utils.R | 151 +++++++++---------- strex-1.3.0/strex/README.md | 6 strex-1.3.0/strex/build/partial.rdb |binary strex-1.3.0/strex/build/vignette.rds |binary strex-1.3.0/strex/inst/WORDLIST | 2 strex-1.3.0/strex/inst/doc/alphordering-numbers.R | 10 - strex-1.3.0/strex/inst/doc/alphordering-numbers.Rmd | 2 strex-1.3.0/strex/inst/doc/alphordering-numbers.html | 17 -- strex-1.3.0/strex/inst/doc/argument-matching.R | 18 +- strex-1.3.0/strex/inst/doc/argument-matching.html | 33 +--- strex-1.3.0/strex/inst/doc/before-and-after.R | 12 - strex-1.3.0/strex/inst/doc/before-and-after.html | 15 - strex-1.3.0/strex/inst/doc/important-miscellany.R | 30 +-- strex-1.3.0/strex/inst/doc/important-miscellany.html | 62 +++---- strex-1.3.0/strex/inst/doc/numbers-in-strings.R | 32 ++-- strex-1.3.0/strex/inst/doc/numbers-in-strings.Rmd | 10 - strex-1.3.0/strex/inst/doc/numbers-in-strings.html | 127 +++++++-------- strex-1.3.0/strex/man/before-and-after.Rd | 7 strex-1.3.0/strex/man/currency.Rd | 8 - strex-1.3.0/strex/man/str_before_last_dot.Rd | 3 strex-1.3.0/strex/man/str_elem.Rd | 5 strex-1.3.0/strex/man/str_elems.Rd | 5 strex-1.3.0/strex/man/str_extract_non_numerics.Rd | 14 + strex-1.3.0/strex/man/str_extract_numbers.Rd | 23 +- strex-1.3.0/strex/man/str_locate_braces.Rd | 13 - strex-1.3.0/strex/man/str_locate_nth.Rd | 7 strex-1.3.0/strex/man/str_match_arg.Rd | 18 +- strex-1.3.0/strex/man/str_nth_non_numeric.Rd | 41 +++-- strex-1.3.0/strex/man/str_nth_number.Rd | 48 ++++-- strex-1.3.0/strex/man/str_nth_number_after_mth.Rd | 150 +++++++++++++----- strex-1.3.0/strex/man/str_nth_number_before_mth.Rd | 150 +++++++++++++----- strex-1.3.0/strex/man/str_paste_elems.Rd | 5 strex-1.3.0/strex/man/str_remove_quoted.Rd | 7 strex-1.3.0/strex/man/str_singleize.Rd | 9 - strex-1.3.0/strex/man/str_split_by_numbers.Rd | 14 + strex-1.3.0/strex/man/str_split_camel_case.Rd | 3 strex-1.3.0/strex/man/str_trim_anything.Rd | 9 - strex-1.3.0/strex/src/arg-match.c |only strex-1.3.0/strex/src/fullocate.c |only strex-1.3.0/strex/src/init.c |only strex-1.3.0/strex/src/interleave.c |only strex-1.3.0/strex/src/list-utils.c |only strex-1.3.0/strex/src/list-utils.h |only strex-1.3.0/strex/src/matrix-utils.c |only strex-1.3.0/strex/src/pairlist-utils.c |only strex-1.3.0/strex/src/pairlist-utils.h |only strex-1.3.0/strex/src/stringi-imports.h |only strex-1.3.0/strex/src/vec-utils.c |only strex-1.3.0/strex/tests/testthat/test-arg-match.R | 2 strex-1.3.0/strex/tests/testthat/test-c-wrappers.R |only strex-1.3.0/strex/tests/testthat/test-currency.R | 52 ++---- strex-1.3.0/strex/tests/testthat/test-extract-nums.R | 6 strex-1.3.0/strex/tests/testthat/test-trim.R | 11 + strex-1.3.0/strex/tests/testthat/test-utils.R | 48 ++---- strex-1.3.0/strex/vignettes/alphordering-numbers.Rmd | 2 strex-1.3.0/strex/vignettes/numbers-in-strings.Rmd | 10 - 86 files changed, 919 insertions(+), 694 deletions(-)
Title: Utilities for Working with NEON Data
Description: NEON data packages can be accessed through the NEON Data Portal <https://data.neonscience.org/home>
or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from
the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files
can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting
data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and
converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.
Author: Claire Lunch [aut, cre, ctb],
Christine Laney [aut, ctb],
Nathan Mietkiewicz [aut, ctb],
Eric Sokol [aut, ctb],
Kaelin Cawley [aut, ctb],
NEON (National Ecological Observatory Network) [aut]
Maintainer: Claire Lunch <clunch@battelleecology.org>
Diff between neonUtilities versions 1.3.6 dated 2020-07-26 and 1.3.7 dated 2020-09-25
neonUtilities-1.3.6/neonUtilities/R/getFilesize.R |only neonUtilities-1.3.6/neonUtilities/man/getFilesize.Rd |only neonUtilities-1.3.7/neonUtilities/DESCRIPTION | 14 ++-- neonUtilities-1.3.7/neonUtilities/MD5 | 32 +++++------ neonUtilities-1.3.7/neonUtilities/NAMESPACE | 4 - neonUtilities-1.3.7/neonUtilities/R/byFileAOP.R | 6 +- neonUtilities-1.3.7/neonUtilities/R/byTileAOP.R | 6 +- neonUtilities-1.3.7/neonUtilities/R/convByteSize.R |only neonUtilities-1.3.7/neonUtilities/R/getAvg.R | 2 neonUtilities-1.3.7/neonUtilities/R/getRecentPublication.R | 2 neonUtilities-1.3.7/neonUtilities/R/getTimeIndex.R |only neonUtilities-1.3.7/neonUtilities/R/loadByProduct.R | 9 ++- neonUtilities-1.3.7/neonUtilities/R/stackDataFilesParallel.R | 4 + neonUtilities-1.3.7/neonUtilities/R/zipsByProduct.R | 21 +++++-- neonUtilities-1.3.7/neonUtilities/R/zipsByURI.R | 2 neonUtilities-1.3.7/neonUtilities/README.md | 10 +++ neonUtilities-1.3.7/neonUtilities/man/convByteSize.Rd |only neonUtilities-1.3.7/neonUtilities/man/getTimeIndex.Rd |only neonUtilities-1.3.7/neonUtilities/man/loadByProduct.Rd | 9 ++- neonUtilities-1.3.7/neonUtilities/man/zipsByProduct.Rd | 10 ++- 20 files changed, 82 insertions(+), 49 deletions(-)
Title: Syntax Highlighting and Automatic Linking
Description: Syntax highlighting of R code, specifically designed
for the needs of 'RMarkdown' packages like 'pkgdown', 'hugodown', and
'bookdown'. It includes linking of function calls to their documentation
on the web, and automatic translation of ANSI escapes in output to the
equivalent HTML.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between downlit versions 0.1.0 dated 2020-09-01 and 0.2.0 dated 2020-09-25
DESCRIPTION | 8 +- MD5 | 43 ++++++------- NEWS.md |only R/downlit-html.R | 33 ++++++++- R/downlit-md.R | 19 ++++- R/highlight.R | 109 ++++++++++++++++++++++++++------- R/link.R | 5 + R/metadata.R | 24 ++++++- R/utils.R | 16 ++++ README.md | 14 +++- man/downlit-package.Rd | 1 man/downlit_html_path.Rd | 9 ++ man/downlit_md_path.Rd | 2 tests/testthat/test-downlit-html.R | 14 ++++ tests/testthat/test-downlit-html.txt | 3 tests/testthat/test-downlit-md-v20.txt | 3 tests/testthat/test-downlit-md-v21.txt | 3 tests/testthat/test-downlit-md.R | 14 ++++ tests/testthat/test-evaluate.txt | 10 +-- tests/testthat/test-highlight.R | 25 ++++++- tests/testthat/test-highlight.txt | 20 +++--- tests/testthat/test-link.R | 6 - tests/testthat/test-metadata.R | 2 23 files changed, 295 insertions(+), 88 deletions(-)
Title: An Interface for Content-Based Identifiers
Description: An interface for creating, registering, and resolving content-based
identifiers for data management. Content-based identifiers rely on
the 'cryptographic' hashes to refer to the files they identify, thus,
anyone possessing the file can compute the identifier using a
well-known standard algorithm, such as 'SHA256'. By registering
a URL at which the content is accessible to a public archive, such
as <https://hash-archive.org>, the content identifier can serve
many functions typically associated with A Digital Object Identifier
('DOI'). Unlike location-based identifiers like 'DOIs', content-based
identifiers permit the same content to be registered in many locations.
Author: Carl Boettiger [aut, cre] (<https://orcid.org/0000-0002-1642-628X>),
Jorrit Poelen [aut] (<https://orcid.org/0000-0003-3138-4118>),
NSF OAC 1839201 [fnd]
(https://www.nsf.gov/awardsearch/showAward?AWD_ID=1839201)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between contentid versions 0.0.7 dated 2020-09-08 and 0.0.8 dated 2020-09-25
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/query_sources.R | 31 +++++++++++++++++-------------- R/tsv_registry.R | 8 ++++---- build/vignette.rds |binary inst/doc/intro.Rmd | 2 +- inst/doc/intro.html | 2 +- vignettes/intro.Rmd | 2 +- vignettes/intro.Rmd-source | 2 +- 10 files changed, 41 insertions(+), 34 deletions(-)
Title: Bindings to 'OpenCV' Computer Vision Library
Description: Experimenting with computer vision and machine learning in R. This
package exposes some of the available 'OpenCV' <https://opencv.org/> algorithms,
such as edge, body or face detection. These can either be applied to analyze
static images, or to filter live video footage from a camera device.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Jan Wijffels [aut]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between opencv versions 0.1 dated 2019-04-01 and 0.2.0 dated 2020-09-24
DESCRIPTION | 31 ++++--- MD5 | 44 +++++++---- NAMESPACE | 8 ++ NEWS |only R/RcppExports.R | 60 +++++++++++++++ R/areas.R |only R/init.R | 45 ++++++++++- R/keypoints.R |only R/opencv.R | 33 +++++++- R/utils.R |only cleanup |only configure | 28 ++++--- man/ocv_keypoints.Rd |only man/opencv-area.Rd |only man/opencv.Rd | 18 +++- man/reexports.Rd | 2 src/Makevars.win | 12 +-- src/RcppExports.cpp | 198 +++++++++++++++++++++++++++++++++++++++++++++++++++ src/areas.cpp |only src/base.cpp | 45 ++++++++++- src/color.cpp |only src/effects.cpp | 8 ++ src/enums.cpp |only src/face.cpp | 8 ++ src/features.cpp |only src/hog.cpp | 6 + src/util.cpp | 31 ------- src/util.hpp | 1 src/version.cpp |only 29 files changed, 484 insertions(+), 94 deletions(-)
Title: Labelled Data Utility Functions
Description: Collection of functions dealing with labelled data, like reading and
writing data between R and other statistical software packages like 'SPSS',
'SAS' or 'Stata', and working with labelled data. This includes easy ways
to get, set or change value and variable label attributes, to convert
labelled vectors into factors or numeric (and vice versa), or to deal with
multiple declared missing values.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
David Ranzolin [ctb]
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjlabelled versions 1.1.6 dated 2020-06-25 and 1.1.7 dated 2020-09-24
DESCRIPTION | 10 +++--- MD5 | 20 ++++++------- NEWS.md | 10 ++++++ R/set_labels.R | 6 ++-- R/utils_get_dots.R | 40 +++++++++++++++++++++++++++ R/write.R | 18 ++++++++---- README.md | 4 +- inst/doc/intro_sjlabelled.html | 52 +++++++++++++++++------------------ inst/doc/labelleddata.html | 4 +- inst/doc/quasiquotation.html | 60 ++++++++++++++++++++--------------------- man/write_spss.Rd | 5 ++- 11 files changed, 143 insertions(+), 86 deletions(-)
Title: Eigenvalues and Singular Values and Vectors from Large Matrices
Description: R interface to 'PRIMME' <http://www.cs.wm.edu/~andreas/software/>, a C library for computing a few
eigenvalues and their corresponding eigenvectors of a real symmetric or complex
Hermitian matrix, or generalized Hermitian eigenproblem. It can also compute
singular values and vectors of a square or rectangular matrix. 'PRIMME' finds
largest, smallest, or interior singular/eigenvalues and can use preconditioning
to accelerate convergence. General description of the methods are provided in the papers
Stathopoulos (2010, <doi:10.1145/1731022.1731031>) and Wu (2017, <doi:10.1137/16M1082214>).
See 'citation("PRIMME")' for details.
Author: Eloy Romero [aut, cre],
Andreas Stathopoulos [aut],
Lingfei Wu [aut],
College of William & Mary [cph]
Maintainer: Eloy Romero <eloy@cs.wm.edu>
Diff between PRIMME versions 3.1-1 dated 2020-05-26 and 3.1-2 dated 2020-09-24
DESCRIPTION | 16 +- MD5 | 20 +-- inst/include/primme_eigs.h | 3 inst/include/primme_svds.h | 2 src/primme/eigs/main_iter.c | 198 ++++++++++++++++++++++++++----- src/primme/eigs/main_iter.h | 201 ++++++++++++++++++++++++++------ src/primme/eigs/primme_c.c | 16 +- src/primme/eigs/primme_interface.c | 130 ++++++++++++++++++++ src/primme/eigs/solve_projection.c | 3 src/primme/eigs/solve_projection.h | 101 ++++++++++++++-- src/primme/svds/primme_svds_interface.c | 73 +++++++++++ 11 files changed, 663 insertions(+), 100 deletions(-)
Title: Functions to Efficiently Access NFL Play by Play Data
Description: A set of functions to access National Football League play-by-play
data from <https://www.nfl.com/>.
Author: Sebastian Carl [aut],
Ben Baldwin [cre, aut],
Lee Sharpe [ctb],
Maksim Horowitz [ctb],
Ron Yurko [ctb],
Samuel Ventura [ctb]
Maintainer: Ben Baldwin <bbaldwin206@gmail.com>
Diff between nflfastR versions 2.2.1 dated 2020-09-01 and 3.0.0 dated 2020-09-24
nflfastR-2.2.1/nflfastR/R/helper_add_roster_mutations.R |only nflfastR-2.2.1/nflfastR/R/helper_scrape_roster.R |only nflfastR-2.2.1/nflfastR/R/helper_scrape_schedule.R |only nflfastR-3.0.0/nflfastR/DESCRIPTION | 8 nflfastR-3.0.0/nflfastR/MD5 | 43 - nflfastR-3.0.0/nflfastR/NAMESPACE | 8 nflfastR-3.0.0/nflfastR/NEWS.md | 26 nflfastR-3.0.0/nflfastR/R/helper_add_cp_cpoe.R | 2 nflfastR-3.0.0/nflfastR/R/helper_add_fixed_drives.R | 6 nflfastR-3.0.0/nflfastR/R/helper_add_game_data.R | 59 + nflfastR-3.0.0/nflfastR/R/helper_add_nflscrapr_mutations.R | 5 nflfastR-3.0.0/nflfastR/R/helper_add_xyac.R | 282 ++++---- nflfastR-3.0.0/nflfastR/R/helper_additional_functions.R | 412 ++++++------- nflfastR-3.0.0/nflfastR/R/helper_database_functions.R | 66 +- nflfastR-3.0.0/nflfastR/R/helper_decode_player_ids.R |only nflfastR-3.0.0/nflfastR/R/helper_get_scheds_and_rosters.R |only nflfastR-3.0.0/nflfastR/R/helper_scrape_cdns.R |only nflfastR-3.0.0/nflfastR/R/helper_tidy_play_stats.R | 113 +-- nflfastR-3.0.0/nflfastR/R/top-level_scraper.R | 183 ++--- nflfastR-3.0.0/nflfastR/README.md | 25 nflfastR-3.0.0/nflfastR/man/decode_player_ids.Rd |only nflfastR-3.0.0/nflfastR/man/fast_scraper.Rd | 14 nflfastR-3.0.0/nflfastR/man/fast_scraper_roster.Rd |only nflfastR-3.0.0/nflfastR/man/update_db.Rd | 11 nflfastR-3.0.0/nflfastR/tests |only 25 files changed, 671 insertions(+), 592 deletions(-)
Title: Model and Analyse Interval Data
Description: Implements methodologies for modelling interval data by Normal
and Skew-Normal distributions, considering appropriate parameterizations of
the variance-covariance matrix that takes into account the intrinsic nature of
interval data, and lead to four different possible configuration structures.
The Skew-Normal parameters can be estimated by maximum likelihood, while Normal
parameters may be estimated by maximum likelihood or robust trimmed maximum
likelihood methods.
Author: Pedro Duarte Silva <psilva@porto.ucp.pt>, Paula Brito
<mpbrito.fep.up.pt>
Maintainer: Pedro Duarte Silva <psilva@porto.ucp.pt>
Diff between MAINT.Data versions 2.4.0 dated 2020-06-25 and 2.5.0 dated 2020-09-24
MAINT.Data-2.4.0/MAINT.Data/R/Azzalini_sn_code.R |only MAINT.Data-2.4.0/MAINT.Data/man/InfCrt-methods.Rd |only MAINT.Data-2.4.0/MAINT.Data/man/logLik-methods.Rd |only MAINT.Data-2.5.0/MAINT.Data/CHANGELOG | 70 ++ MAINT.Data-2.5.0/MAINT.Data/DESCRIPTION | 14 MAINT.Data-2.5.0/MAINT.Data/MD5 | 168 +++--- MAINT.Data-2.5.0/MAINT.Data/NAMESPACE | 16 MAINT.Data-2.5.0/MAINT.Data/R/AgrMcDt.R | 7 MAINT.Data-2.5.0/MAINT.Data/R/CPMaxLik.R | 13 MAINT.Data-2.5.0/MAINT.Data/R/ClasGenMetDef.R | 28 - MAINT.Data-2.5.0/MAINT.Data/R/Conversions.R | 11 MAINT.Data-2.5.0/MAINT.Data/R/CorrHetSNSol.R | 77 +- MAINT.Data-2.5.0/MAINT.Data/R/CorrSNSol.R | 33 - MAINT.Data-2.5.0/MAINT.Data/R/DACrossVal.R | 2 MAINT.Data-2.5.0/MAINT.Data/R/IData.R | 279 ++++++---- MAINT.Data-2.5.0/MAINT.Data/R/IdtMaxLikN.R | 11 MAINT.Data-2.5.0/MAINT.Data/R/IdtMaxLikSN.R | 229 +++++--- MAINT.Data-2.5.0/MAINT.Data/R/IdtMclust_methods.R | 145 +++-- MAINT.Data-2.5.0/MAINT.Data/R/IdtOutl_methods.R | 8 MAINT.Data-2.5.0/MAINT.Data/R/RepLOptim.R | 14 MAINT.Data-2.5.0/MAINT.Data/R/RestCPMaxLik.R | 76 +- MAINT.Data-2.5.0/MAINT.Data/R/Rfasttle.R | 3 MAINT.Data-2.5.0/MAINT.Data/R/RobMxtDEst.R | 15 MAINT.Data-2.5.0/MAINT.Data/R/Robldaqda.R | 17 MAINT.Data-2.5.0/MAINT.Data/R/SNmle.R | 67 +- MAINT.Data-2.5.0/MAINT.Data/R/fasttle.R | 9 MAINT.Data-2.5.0/MAINT.Data/R/fulltle.R | 6 MAINT.Data-2.5.0/MAINT.Data/R/lqda.R | 12 MAINT.Data-2.5.0/MAINT.Data/R/mle.R | 129 ++++ MAINT.Data-2.5.0/MAINT.Data/R/msnCP.dev.R | 7 MAINT.Data-2.5.0/MAINT.Data/R/msnCP.dev.grad.R | 10 MAINT.Data-2.5.0/MAINT.Data/R/msnCP.dev.grad.out.prod.R |only MAINT.Data-2.5.0/MAINT.Data/R/sknda.R | 49 - MAINT.Data-2.5.0/MAINT.Data/man/Abalone.Rd | 4 MAINT.Data-2.5.0/MAINT.Data/man/AgrMcDt.Rd | 37 + MAINT.Data-2.5.0/MAINT.Data/man/BestModel-methods.Rd | 2 MAINT.Data-2.5.0/MAINT.Data/man/Cars.Rd | 2 MAINT.Data-2.5.0/MAINT.Data/man/ChinaTemp.Rd | 4 MAINT.Data-2.5.0/MAINT.Data/man/ConfTests-class.Rd | 2 MAINT.Data-2.5.0/MAINT.Data/man/EMControl.Rd | 4 MAINT.Data-2.5.0/MAINT.Data/man/IData-class.Rd | 7 MAINT.Data-2.5.0/MAINT.Data/man/IData.Rd | 90 +-- MAINT.Data-2.5.0/MAINT.Data/man/IDtOutl-class.Rd | 2 MAINT.Data-2.5.0/MAINT.Data/man/IdtE-class.Rd | 6 MAINT.Data-2.5.0/MAINT.Data/man/IdtMANOVA-class.Rd | 10 MAINT.Data-2.5.0/MAINT.Data/man/IdtMclust-class.Rd | 6 MAINT.Data-2.5.0/MAINT.Data/man/IdtMxSNDE-class.Rd | 2 MAINT.Data-2.5.0/MAINT.Data/man/IdtMxtNDE-class.Rd | 2 MAINT.Data-2.5.0/MAINT.Data/man/IdtNandSNDE-class.Rd | 2 MAINT.Data-2.5.0/MAINT.Data/man/IdtOutl-methods.Rd | 6 MAINT.Data-2.5.0/MAINT.Data/man/IdtSNgenda-class.Rd | 4 MAINT.Data-2.5.0/MAINT.Data/man/IdtSNlocda-class.Rd | 4 MAINT.Data-2.5.0/MAINT.Data/man/Idtmclust-methods.Rd | 31 - MAINT.Data-2.5.0/MAINT.Data/man/MAINT.Data-internal.Rd | 20 MAINT.Data-2.5.0/MAINT.Data/man/MAINT.Data-package.Rd | 367 ++++++-------- MAINT.Data-2.5.0/MAINT.Data/man/MANOVA-methods.Rd | 18 MAINT.Data-2.5.0/MAINT.Data/man/MANOVAPermTest.Rd | 48 + MAINT.Data-2.5.0/MAINT.Data/man/RepLOptim.Rd | 6 MAINT.Data-2.5.0/MAINT.Data/man/RobEstControl-class.Rd | 6 MAINT.Data-2.5.0/MAINT.Data/man/RobMxtDEst-methods.Rd | 23 MAINT.Data-2.5.0/MAINT.Data/man/Robda-methods.Rd | 6 MAINT.Data-2.5.0/MAINT.Data/man/coef-methods.Rd | 31 + MAINT.Data-2.5.0/MAINT.Data/man/cor-methods.Rd | 16 MAINT.Data-2.5.0/MAINT.Data/man/fasttle-methods.Rd | 6 MAINT.Data-2.5.0/MAINT.Data/man/fulltle-methods.Rd | 28 - MAINT.Data-2.5.0/MAINT.Data/man/getIdtOutl.Rd | 37 + MAINT.Data-2.5.0/MAINT.Data/man/lda-methods.Rd | 2 MAINT.Data-2.5.0/MAINT.Data/man/mle-methods.Rd | 5 MAINT.Data-2.5.0/MAINT.Data/man/nycflights.Rd | 2 MAINT.Data-2.5.0/MAINT.Data/man/pcoordplot-methos.Rd | 30 + MAINT.Data-2.5.0/MAINT.Data/man/plot-methods.Rd | 45 + MAINT.Data-2.5.0/MAINT.Data/man/plotInfCrt-methos.Rd | 37 + MAINT.Data-2.5.0/MAINT.Data/man/snda-methods.Rd | 12 MAINT.Data-2.5.0/MAINT.Data/man/summary-methods.Rd | 9 MAINT.Data-2.5.0/MAINT.Data/man/testMod-methods.Rd | 4 MAINT.Data-2.5.0/MAINT.Data/src/AuxFoo.cpp | 41 + MAINT.Data-2.5.0/MAINT.Data/src/AuxFoo.h | 3 MAINT.Data-2.5.0/MAINT.Data/src/CEMGauss.cpp | 72 -- MAINT.Data-2.5.0/MAINT.Data/src/MDataGaussLogLik.cpp | 6 MAINT.Data-2.5.0/MAINT.Data/src/MDataGaussLogLik.h | 4 MAINT.Data-2.5.0/MAINT.Data/src/RestCovGrad.cpp | 3 MAINT.Data-2.5.0/MAINT.Data/src/msnCP_dev.cpp | 9 MAINT.Data-2.5.0/MAINT.Data/src/msnCP_dev.h | 7 MAINT.Data-2.5.0/MAINT.Data/src/msnCP_dev_RIntf.cpp | 21 MAINT.Data-2.5.0/MAINT.Data/src/msnCP_dev_grad.cpp | 44 + MAINT.Data-2.5.0/MAINT.Data/src/msnCP_dev_grad.h | 6 MAINT.Data-2.5.0/MAINT.Data/src/registerDynamicSimbol.cpp | 12 87 files changed, 1693 insertions(+), 1045 deletions(-)
Title: Geo-Processing Helper Functions
Description: Helper tools for facilitating basic geo-processing tasks, such as reading/writing
Shapefiles, merging polygons or generating terrain contours.
Author: Andrew Plowright
Maintainer: Andrew Plowright <andrew.plowright@alumni.ubc.ca>
Diff between APfun versions 0.1.4 dated 2019-08-19 and 0.1.6 dated 2020-09-24
DESCRIPTION | 12 +++--- MD5 | 26 +++++++-------- NEWS.md | 28 +++++++++------- R/APcontours.R | 2 - R/APpolygonize.R | 44 ++++++++++++------------- README.md | 14 +++++--- man/APSHPsave.Rd | 50 ++++++++++++++-------------- man/APcontours.Rd | 38 ++++++++++----------- man/APpolyMerge.Rd | 40 +++++++++++------------ man/APpolygonize.Rd | 83 +++++++++++++++++++++++++----------------------- man/AProunder.Rd | 52 +++++++++++++++--------------- man/APtimer.Rd | 42 ++++++++++++------------ man/SHPextensions.Rd | 4 +- man/rasterExtensions.Rd | 4 +- 14 files changed, 229 insertions(+), 210 deletions(-)
Title: Shape Constrained Additive Models
Description: Routines for generalized additive modelling under shape
constraints on the component functions of the linear predictor
(Pya and Wood, 2015) <doi:10.1007/s11222-013-9448-7>.
Models can contain multiple shape constrained (univariate
and/or bivariate) and unconstrained terms. The routines of gam()
in package 'mgcv' are used for setting up the model matrix,
printing and plotting the results. Penalized likelihood
maximization based on Newton-Raphson method is used to fit a
model with multiple smoothing parameter selection by GCV or
UBRE/AIC.
Author: Natalya Pya <nat.pya@gmail.com>
Maintainer: Natalya Pya <nat.pya@gmail.com>
Diff between scam versions 1.2-6 dated 2020-06-10 and 1.2-7 dated 2020-09-24
ChangeLog | 8 +++++ DESCRIPTION | 8 ++--- MD5 | 14 ++++----- R/bfgs.r | 10 +++--- R/predict.scam.R | 80 +++++++++++++++++++++++++++++++++++++----------------- R/scam.r | 36 ++++++++++++++---------- build/partial.rdb |binary man/scam.Rd | 7 ++++ 8 files changed, 108 insertions(+), 55 deletions(-)
Title: An Automated Cleaning Tool for Semantic and Linguistic Data
Description: Implements several functions that automates the cleaning and spell-checking of text data. Also converges, finalizes, removes plurals and continuous strings, and puts text data in binary format for semantic network analysis. Uses the 'SemNetDictionaries' package to make the cleaning process more accurate, efficient, and reproducible.
Author: Alexander P. Christensen [aut, cre]
(<https://orcid.org/0000-0002-9798-7037>)
Maintainer: Alexander P. Christensen <alexpaulchristensen@gmail.com>
Diff between SemNetCleaner versions 1.2.0 dated 2020-06-09 and 1.3.0 dated 2020-09-24
SemNetCleaner-1.2.0/SemNetCleaner/build |only SemNetCleaner-1.2.0/SemNetCleaner/inst/doc |only SemNetCleaner-1.2.0/SemNetCleaner/vignettes |only SemNetCleaner-1.3.0/SemNetCleaner/DESCRIPTION | 16 SemNetCleaner-1.3.0/SemNetCleaner/MD5 | 34 SemNetCleaner-1.3.0/SemNetCleaner/NAMESPACE | 3 SemNetCleaner-1.3.0/SemNetCleaner/NEWS | 17 SemNetCleaner-1.3.0/SemNetCleaner/R/convert2snafu.R |only SemNetCleaner-1.3.0/SemNetCleaner/R/correct.changes.R | 264 +++--- SemNetCleaner-1.3.0/SemNetCleaner/R/open.clean.R |only SemNetCleaner-1.3.0/SemNetCleaner/R/textcleaner.R | 88 +- SemNetCleaner-1.3.0/SemNetCleaner/R/utils-SemNetCleaner.R | 592 +++++++++----- SemNetCleaner-1.3.0/SemNetCleaner/R/zzz.R | 4 SemNetCleaner-1.3.0/SemNetCleaner/data/open.clean.RData |only SemNetCleaner-1.3.0/SemNetCleaner/man/convert2snafu.Rd |only SemNetCleaner-1.3.0/SemNetCleaner/man/correct.changes.Rd | 9 SemNetCleaner-1.3.0/SemNetCleaner/man/open.clean.Rd |only SemNetCleaner-1.3.0/SemNetCleaner/man/textcleaner.Rd | 20 18 files changed, 688 insertions(+), 359 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-07 0.1.13
2017-09-01 0.1.11
2017-08-21 0.1.10
2015-09-04 0.1.9
2014-08-04 0.1.8
2012-10-12 0.1.7
2012-01-04 0.1.5
2011-02-17 0.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-07 0.1.5
2018-04-23 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-16 1.0
Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data
visualization. Results of various statistical analyses (that are commonly used
in social sciences) can be visualized using this package, including simple and
cross tabulated frequencies, histograms, box plots, (generalized) linear models,
mixed effects models, principal component analysis and correlation matrices,
cluster analyses, scatter plots, stacked scales, effects plots of regression
models (including interaction terms) and much more. This package supports
labelled data.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Alexander Bartel [ctb] (<https://orcid.org/0000-0002-1280-6138>),
Carsten Schwemmer [ctb],
Chuck Powell [ctb] (<https://orcid.org/0000-0002-3606-2188>),
Amir Djalovski [ctb],
Johannes Titz [ctb] (<https://orcid.org/0000-0002-1102-5719>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjPlot versions 2.8.4 dated 2020-05-24 and 2.8.5 dated 2020-09-24
DESCRIPTION | 15 MD5 | 130 ++++---- NAMESPACE | 4 NEWS.md | 17 + R/html_print.R | 14 R/plot_grpfrq.R | 10 R/plot_model.R | 5 R/plot_models.R | 16 R/plot_stackfrq.R | 27 - R/plot_type_int.R | 12 R/sjPlotPearsonsChi2Test.R | 2 R/tab_itemscale.R | 2 R/tab_model.R | 148 ++++++--- R/tidiers.R | 11 README.md | 4 build/vignette.rds |binary inst/doc/blackwhitefigures.html | 136 +++++--- inst/doc/custplot.Rmd | 2 inst/doc/custplot.html | 304 ++++++++++-------- inst/doc/plot_interactions.Rmd | 2 inst/doc/plot_interactions.html | 124 +++++-- inst/doc/plot_likert_scales.html | 172 ++++++---- inst/doc/plot_marginal_effects.Rmd | 2 inst/doc/plot_marginal_effects.html | 142 +++++--- inst/doc/plot_model_estimates.Rmd | 2 inst/doc/plot_model_estimates.html | 298 ++++++++++-------- inst/doc/sjtitemanalysis.html | 82 +++-- inst/doc/tab_bayes.html | 284 +++++++++-------- inst/doc/tab_mixed.html | 129 ++++--- inst/doc/tab_model_estimates.html | 318 ++++++++++--------- inst/doc/tab_model_robust.html | 284 +++++++++++------ inst/doc/table_css.html | 272 +++++++++------- man/dist_chisq.Rd | 130 ++++---- man/dist_f.Rd | 122 +++---- man/dist_norm.Rd | 120 +++---- man/dist_t.Rd | 116 +++---- man/plot_frq.Rd | 4 man/plot_gpt.Rd | 286 ++++++++--------- man/plot_grid.Rd | 118 +++---- man/plot_grpfrq.Rd | 528 ++++++++++++++++---------------- man/plot_kfold_cv.Rd | 118 +++---- man/plot_model.Rd | 2 man/plot_residuals.Rd | 140 ++++---- man/plot_scatter.Rd | 308 +++++++++---------- man/plot_stackfrq.Rd | 278 ++++++++--------- man/plot_xtab.Rd | 462 ++++++++++++++-------------- man/save_plot.Rd | 124 +++---- man/set_theme.Rd | 582 ++++++++++++++++++------------------ man/sjPlot-package.Rd | 10 man/sjPlot-themes.Rd | 304 +++++++++--------- man/sjp.aov1.Rd | 234 +++++++------- man/sjp.chi2.Rd | 125 +++---- man/sjp.poly.Rd | 278 ++++++++--------- man/sjplot.Rd | 162 +++++----- man/tab_corr.Rd | 308 +++++++++---------- man/tab_df.Rd | 310 +++++++++---------- man/tab_fa.Rd | 268 ++++++++-------- man/tab_itemscale.Rd | 2 man/tab_model.Rd | 25 - man/tab_pca.Rd | 266 ++++++++-------- man/tab_xtab.Rd | 4 man/view_df.Rd | 298 +++++++++--------- vignettes/custplot.Rmd | 2 vignettes/plot_interactions.Rmd | 2 vignettes/plot_marginal_effects.Rmd | 2 vignettes/plot_model_estimates.Rmd | 2 66 files changed, 4758 insertions(+), 4252 deletions(-)
Title: Prediction Model Selection and Performance Evaluation in
Multiple Imputed Datasets
Description: Pooling, backward and forward selection of logistic and Cox regression models in
multiply imputed datasets. Backward and forward selection can be done
from the pooled model using Rubin's Rules (RR), the D1, D2, D3 and
the median p-values method. This is also possible for Mixed models.
The models can contain continuous, dichotomous, categorical and restricted
cubic spline predictors and interaction terms between all these type of predictors.
The stability of the models can be evaluated using bootstrapping and cluster
bootstrapping. The package further contains functions to pool the model performance
as ROC/AUC, R-squares, scaled Brier score and calibration plots for logistic
regression models. Internal validation can be done with cross-validation or bootstrapping.
The adjusted intercept after shrinkage of pooled regression coefficients can be obtained.
Backward and forward selection as part of internal validation is possible.
Also a function to externally validate logistic prediction models in multiple imputed
datasets is available.
Eekhout (2017) <doi:10.1186/s12874-017-0404-7>.
Wiel (2009) <doi:10.1093/biostatistics/kxp011>.
Marshall (2009) <doi:10.1186/1471-2288-9-57>.
Author: Martijn Heymans [cre, aut] (<https://orcid.org/0000-0002-3889-0921>),
Iris Eekhout [ctb]
Maintainer: Martijn Heymans <mw.heymans@amsterdamumc.nl>
Diff between psfmi versions 0.2.0 dated 2020-02-03 and 0.5.0 dated 2020-09-24
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psfmi-0.5.0/psfmi/inst/doc/psfmi_mice.R |only psfmi-0.5.0/psfmi/inst/doc/psfmi_mice.Rmd |only psfmi-0.5.0/psfmi/inst/doc/psfmi_mice.html |only psfmi-0.5.0/psfmi/inst/doc/psfmi_valext.R |only psfmi-0.5.0/psfmi/inst/doc/psfmi_valext.Rmd |only psfmi-0.5.0/psfmi/inst/doc/psfmi_valext.html |only psfmi-0.5.0/psfmi/man/MI_boot.Rd |only psfmi-0.5.0/psfmi/man/MI_cv_naive.Rd |only psfmi-0.5.0/psfmi/man/boot_MI.Rd |only psfmi-0.5.0/psfmi/man/bw_single.Rd |only psfmi-0.5.0/psfmi/man/clean_P.Rd |only psfmi-0.5.0/psfmi/man/cv_MI.Rd |only psfmi-0.5.0/psfmi/man/cv_MI_RR.Rd |only psfmi-0.5.0/psfmi/man/figures |only psfmi-0.5.0/psfmi/man/lbpmi_extval.Rd |only psfmi-0.5.0/psfmi/man/mean_auc_log.Rd |only psfmi-0.5.0/psfmi/man/miceImp.Rd |only psfmi-0.5.0/psfmi/man/mivalext_lr.Rd | 19 psfmi-0.5.0/psfmi/man/pool_auc.Rd |only psfmi-0.5.0/psfmi/man/pool_intadj.Rd | 2 psfmi-0.5.0/psfmi/man/pool_performance.Rd | 10 psfmi-0.5.0/psfmi/man/psfmi_coxr.Rd | 169 +- psfmi-0.5.0/psfmi/man/psfmi_coxr_bw.Rd |only psfmi-0.5.0/psfmi/man/psfmi_coxr_fw.Rd |only psfmi-0.5.0/psfmi/man/psfmi_lr.Rd | 130 +- psfmi-0.5.0/psfmi/man/psfmi_lr_bw.Rd |only psfmi-0.5.0/psfmi/man/psfmi_lr_fw.Rd |only psfmi-0.5.0/psfmi/man/psfmi_mm.Rd | 4 psfmi-0.5.0/psfmi/man/psfmi_perform.Rd | 176 +-- psfmi-0.5.0/psfmi/man/psfmi_stab.Rd | 50 psfmi-0.5.0/psfmi/man/rsq_nagel.Rd |only psfmi-0.5.0/psfmi/man/scaled_brier.Rd |only psfmi-0.5.0/psfmi/vignettes/MI_boot.Rmd |only psfmi-0.5.0/psfmi/vignettes/MI_boot.png |only psfmi-0.5.0/psfmi/vignettes/MI_cv_naive.Rmd |only psfmi-0.5.0/psfmi/vignettes/MI_cv_naive.png |only psfmi-0.5.0/psfmi/vignettes/boot_MI.Rmd |only psfmi-0.5.0/psfmi/vignettes/boot_MI.png |only psfmi-0.5.0/psfmi/vignettes/cv_MI.Rmd |only psfmi-0.5.0/psfmi/vignettes/cv_MI.png |only psfmi-0.5.0/psfmi/vignettes/cv_MI_RR.Rmd |only psfmi-0.5.0/psfmi/vignettes/cv_mi_RR.png |only psfmi-0.5.0/psfmi/vignettes/psfmi_CoxModels.Rmd |only psfmi-0.5.0/psfmi/vignettes/psfmi_LogisticModels.Rmd |only psfmi-0.5.0/psfmi/vignettes/psfmi_StabilityAnalysis.Rmd |only psfmi-0.5.0/psfmi/vignettes/psfmi_mice.Rmd |only psfmi-0.5.0/psfmi/vignettes/psfmi_valext.Rmd |only 113 files changed, 1802 insertions(+), 2350 deletions(-)
Title: An Import Mechanism for R
Description: Alternative mechanism for importing objects from packages
and R modules. The syntax allows for importing multiple objects with a single
command in an expressive way. The import package bridges some of the gap
between using library (or require) and direct (single-object) imports.
Furthermore the imported objects are not placed in the current environment.
Author: Stefan Milton Bache [aut],
Magnus Thor Torfason [aut, cre]
Maintainer: Magnus Thor Torfason <m@zulutime.net>
Diff between import versions 1.1.0 dated 2015-06-21 and 1.2.0 dated 2020-09-24
import-1.1.0/import/NEWS |only import-1.1.0/import/README |only import-1.1.0/import/man/make_import_call.Rd |only import-1.1.0/import/man/symbol_as_character.Rd |only import-1.1.0/import/man/symbol_list.Rd |only import-1.1.0/import/vignettes/import.md |only import-1.2.0/import/DESCRIPTION | 40 - import-1.2.0/import/LICENSE | 4 import-1.2.0/import/MD5 | 81 +- import-1.2.0/import/NAMESPACE | 10 import-1.2.0/import/NEWS.md |only import-1.2.0/import/R/detect_bad_recursion.R |only import-1.2.0/import/R/file_path.R |only import-1.2.0/import/R/from.R | 392 ++++++++---- import-1.2.0/import/R/here.R | 44 - import-1.2.0/import/R/import.R | 48 - import-1.2.0/import/R/import_aliases.R |only import-1.2.0/import/R/into.R | 42 - import-1.2.0/import/R/is_script.R | 33 - import-1.2.0/import/R/make_import_call.R | 45 - import-1.2.0/import/R/modified.R | 76 +- import-1.2.0/import/R/package_specs.R |only import-1.2.0/import/R/safe_assign.R |only import-1.2.0/import/R/scripts.R | 16 import-1.2.0/import/R/suppress_output.R | 2 import-1.2.0/import/R/symbol_as_character.R | 32 - import-1.2.0/import/R/symbol_list.R | 52 + import-1.2.0/import/R/zzz.R | 24 import-1.2.0/import/build/vignette.rds |binary import-1.2.0/import/inst/doc/import.R | 255 +++++-- import-1.2.0/import/inst/doc/import.Rmd | 792 +++++++++++++++++------- import-1.2.0/import/inst/doc/import.html | 800 ++++++++++++++++++------- import-1.2.0/import/man/examples |only import-1.2.0/import/man/import.Rd | 67 +- import-1.2.0/import/man/importfunctions.Rd | 221 ++++-- import-1.2.0/import/tests |only import-1.2.0/import/vignettes/import.Rmd | 792 +++++++++++++++++------- 37 files changed, 2631 insertions(+), 1237 deletions(-)
Title: Interpretable Machine Learning
Description: Interpretability methods to analyze the behavior
and predictions of any machine learning model. Implemented methods
are: Feature importance described by Fisher et al. (2018)
<arXiv:1801.01489>, accumulated local effects plots described by Apley
(2018) <arXiv:1612.08468>, partial dependence plots described by
Friedman (2001) <www.jstor.org/stable/2699986>, individual
conditional expectation ('ice') plots described by Goldstein et al.
(2013) <doi:10.1080/10618600.2014.907095>, local models (variant of
'lime') described by Ribeiro et. al (2016) <arXiv:1602.04938>, the
Shapley Value described by Strumbelj et. al (2014)
<doi:10.1007/s10115-013-0679-x>, feature interactions described by
Friedman et. al <doi:10.1214/07-AOAS148> and tree surrogate models.
Author: Christoph Molnar [aut, cre],
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>)
Maintainer: Christoph Molnar <christoph.molnar@gmail.com>
Diff between iml versions 0.10.0 dated 2020-03-26 and 0.10.1 dated 2020-09-24
DESCRIPTION | 20 MD5 | 31 - NAMESPACE | 2 NEWS.md | 30 - R/FeatureEffects.R | 2 R/FeatureImp.R | 4 R/Predictor.R | 5 R/iml.R | 4 build/vignette.rds |binary inst/CITATION | 2 inst/doc/intro.html | 807 +++++++++++++++++++--------------------- inst/doc/parallel.html | 609 ++++++++++++------------------ tests/testthat/Rplots.pdf |binary tests/testthat/check-mlr3.R |only tests/testthat/helper.R | 6 tests/testthat/setup.R | 25 - tests/testthat/test-Predictor.R | 10 17 files changed, 743 insertions(+), 814 deletions(-)
Title: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models
Description: Manipulation of genetic data (SNPs). Computation of GRM and dominance matrix, LD, heritability with efficient algorithms for linear mixed model (AIREML). Dandine et al <doi:10.1159/000488519>.
Author: Hervé Perdry [cre, aut, cph],
Claire Dandine-Roulland [aut, cph],
Deepak Bandyopadhyay [cph] (C++ gzstream class),
Lutz Kettner [cph] (C++ gzstream class)
Maintainer: Hervé Perdry <herve.perdry@u-psud.fr>
Diff between gaston versions 1.5.6 dated 2020-02-26 and 1.5.7 dated 2020-09-24
gaston-1.5.6/gaston/src/Parallel.h |only gaston-1.5.6/gaston/src/ai-reml-1k-covar.h |only gaston-1.5.6/gaston/src/ai-reml-1k.h |only gaston-1.5.6/gaston/src/ai-reml-logit-1k-covar.h |only gaston-1.5.6/gaston/src/ai-reml-logit-1k.h |only gaston-1.5.6/gaston/src/ai-reml-logit-nk-covar.h |only gaston-1.5.6/gaston/src/ai-reml-logit-nk.h |only gaston-1.5.6/gaston/src/ai-reml-nk-covar.h |only gaston-1.5.6/gaston/src/ai-reml-nk.h |only gaston-1.5.6/gaston/src/any.h |only gaston-1.5.6/gaston/src/diago2.h |only gaston-1.5.6/gaston/src/diago2_full.h |only gaston-1.5.6/gaston/src/diago2_full_nocovar.h |only gaston-1.5.6/gaston/src/diago2_nocovar.h |only gaston-1.5.6/gaston/src/flip_strand.h |only gaston-1.5.6/gaston/src/gzstream.h |only gaston-1.5.6/gaston/src/lmm_diago_min_max_h2.h |only gaston-1.5.6/gaston/src/logit_model.h |only gaston-1.5.6/gaston/src/loubar.h |only gaston-1.5.6/gaston/src/m4_kinship_type.h |only gaston-1.5.6/gaston/src/m4_ld.h |only gaston-1.5.6/gaston/src/matrix-varia.h |only gaston-1.5.6/gaston/src/matrix4.h |only gaston-1.5.6/gaston/src/optimize_2.h |only gaston-1.5.6/gaston/src/snp_hash.h |only gaston-1.5.7/gaston/DESCRIPTION | 8 gaston-1.5.7/gaston/MD5 | 81 +-- gaston-1.5.7/gaston/NEWS | 3 gaston-1.5.7/gaston/R/ld_plot.r | 2 gaston-1.5.7/gaston/R/logistic_mm_aireml.r | 16 gaston-1.5.7/gaston/TODO | 11 gaston-1.5.7/gaston/build/vignette.rds |binary gaston-1.5.7/gaston/inst/doc/gaston-faq.pdf |binary gaston-1.5.7/gaston/inst/doc/gaston.pdf |binary gaston-1.5.7/gaston/inst/include/gaston/Parallel.h |only gaston-1.5.7/gaston/inst/include/gaston/ai-reml-1k-covar.h | 3 gaston-1.5.7/gaston/inst/include/gaston/ai-reml-logit-1k-covar.h | 28 - gaston-1.5.7/gaston/inst/include/gaston/ai-reml-logit-1k.h | 32 + gaston-1.5.7/gaston/inst/include/gaston/ai-reml-logit-nk-covar.h | 49 +- gaston-1.5.7/gaston/inst/include/gaston/ai-reml-logit-nk.h | 48 +- gaston-1.5.7/gaston/inst/include/gaston/any_nan.h |only gaston-1.5.7/gaston/inst/include/gaston/flip_strand.h |only gaston-1.5.7/gaston/inst/include/gaston/gzstream.h |only gaston-1.5.7/gaston/inst/include/gaston/gzstream0.h |only gaston-1.5.7/gaston/inst/include/gaston/logit_model.h | 1 gaston-1.5.7/gaston/inst/include/gaston/loubar.h |only gaston-1.5.7/gaston/inst/include/gaston/m4_ld.h |only gaston-1.5.7/gaston/inst/include/gaston/snp_hash.h | 128 ++--- gaston-1.5.7/gaston/inst/include/gaston/string_equal.h |only gaston-1.5.7/gaston/man/logistic.mm.aireml.Rd | 11 gaston-1.5.7/gaston/src/Makevars | 2 gaston-1.5.7/gaston/src/export-aireml-logit-1k.cpp | 33 - gaston-1.5.7/gaston/src/export-aireml-logit-nk.cpp | 91 ++-- gaston-1.5.7/gaston/src/gaston_init.c | 218 ++++------ gaston-1.5.7/gaston/src/gwas_lmm_diago_lrt.cpp | 2 gaston-1.5.7/gaston/src/gwas_lmm_diago_wald.cpp | 2 gaston-1.5.7/gaston/src/gzstream.cpp | 167 ------- gaston-1.5.7/gaston/src/snp_match.cpp | 16 58 files changed, 423 insertions(+), 529 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-18 0.1.1
2018-06-12 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-07 0.2.4
2019-12-17 0.2.3
2019-06-05 0.2.2
2017-09-25 0.2.1
2017-07-17 0.2.0
2017-03-16 0.1.0
Title: Shrinkage t Statistic and Correlation-Adjusted t-Score
Description: Implements the "shrinkage t" statistic
introduced in Opgen-Rhein and Strimmer (2007) <DOI:10.2202/1544-6115.1252> and
a shrinkage estimate of the "correlation-adjusted t-score" (CAT score) described
in Zuber and Strimmer (2009) <DOI:10.1093/bioinformatics/btp460>.
It also offers a convenient interface to a number of other regularized
t-statistics commonly employed in high-dimensional case-control studies.
Author: Rainer Opgen-Rhein, Verena Zuber, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>
Diff between st versions 1.2.5 dated 2015-07-08 and 1.2.6 dated 2020-09-24
DESCRIPTION | 24 ++++++++++++------------ MD5 | 22 +++++++++++----------- NEWS | 5 +++++ R/modt.R | 4 ++-- man/cst.stat.Rd | 4 ++-- man/diffmean.stat.Rd | 2 +- man/lait.stat.Rd | 2 +- man/regularizedt.Rd | 4 ++-- man/shrinkcat.stat.Rd | 4 ++-- man/shrinkt.stat.Rd | 4 ++-- man/st.package.Rd | 4 ++-- man/studentt.stat.Rd | 2 +- 12 files changed, 43 insertions(+), 38 deletions(-)
Title: Functions for Working with 'Eprime' Text Files
Description: 'Eprime' is a set of programs for administering
psychological experiments by computer. This package provides functions
for loading, parsing, filtering and exporting data in the text files
produced by 'Eprime' experiments.
Author: Tristan Mahr [aut, cre] (<https://orcid.org/0000-0002-8890-5116>)
Maintainer: Tristan Mahr <tristan.mahr@wisc.edu>
Diff between rprime versions 0.1.0 dated 2015-05-29 and 0.1.2 dated 2020-09-24
rprime-0.1.0/rprime/LICENSE |only rprime-0.1.0/rprime/R/rprime.R |only rprime-0.1.0/rprime/man/count_tabs.Rd |only rprime-0.1.0/rprime/man/make_filter.Rd |only rprime-0.1.0/rprime/man/make_ranges.Rd |only rprime-0.1.0/rprime/man/parse_chunks.Rd |only rprime-0.1.0/rprime/man/tidy.Rd |only rprime-0.1.2/rprime/DESCRIPTION | 36 rprime-0.1.2/rprime/MD5 | 73 - rprime-0.1.2/rprime/NAMESPACE | 7 rprime-0.1.2/rprime/NEWS.md |only rprime-0.1.2/rprime/R/extract.R | 10 rprime-0.1.2/rprime/R/filter.R | 5 rprime-0.1.2/rprime/R/frames.R | 11 rprime-0.1.2/rprime/R/load.R | 10 rprime-0.1.2/rprime/R/patterns.R | 1 rprime-0.1.2/rprime/R/rprime-package.R |only rprime-0.1.2/rprime/build/vignette.rds |binary rprime-0.1.2/rprime/inst/doc/multiple-files.R | 10 rprime-0.1.2/rprime/inst/doc/multiple-files.html | 462 ++++++++-- rprime-0.1.2/rprime/inst/doc/parsing-summary.R | 14 rprime-0.1.2/rprime/inst/doc/parsing-summary.Rmd | 10 rprime-0.1.2/rprime/inst/doc/parsing-summary.html | 484 ++++++++--- rprime-0.1.2/rprime/inst/doc/quick-start-demo.R | 30 rprime-0.1.2/rprime/inst/doc/quick-start-demo.Rmd | 41 rprime-0.1.2/rprime/inst/doc/quick-start-demo.html | 902 +++++++++++++-------- rprime-0.1.2/rprime/man/EprimeFrame.Rd | 3 rprime-0.1.2/rprime/man/FrameList.Rd | 35 rprime-0.1.2/rprime/man/as.EprimeFrame.Rd | 3 rprime-0.1.2/rprime/man/as.FrameList.Rd | 3 rprime-0.1.2/rprime/man/extract_chunks.Rd | 7 rprime-0.1.2/rprime/man/filter_in.Rd | 5 rprime-0.1.2/rprime/man/keep_levels.Rd | 5 rprime-0.1.2/rprime/man/list_functions.Rd | 7 rprime-0.1.2/rprime/man/listify.Rd | 3 rprime-0.1.2/rprime/man/preview_eprime.Rd | 5 rprime-0.1.2/rprime/man/read_eprime.Rd | 3 rprime-0.1.2/rprime/man/rprime.Rd | 21 rprime-0.1.2/rprime/man/to_data_frame.Rd | 3 rprime-0.1.2/rprime/tests/testthat/test-load.R | 4 rprime-0.1.2/rprime/vignettes/parsing-summary.Rmd | 10 rprime-0.1.2/rprime/vignettes/quick-start-demo.Rmd | 41 42 files changed, 1563 insertions(+), 701 deletions(-)
Title: Sampling from Order Statistics of New Families of Distributions
Description: Set of tools to generate samples of order statistics and others quantities of interest from new families of distributions.
The main references for this package are: Gentle, J. (2009), Computational Statistics, Springer-Verlag;
Naradajah, S. and Rocha, R. (2016), <DOI:10.18637/jss.v069.i10> and
Stasinopoulos, M. and Rigby, R. (2015), <DOI:10.1111/j.1467-9876.2005.00510.x>.
The families of distributions are: Marshall Olkin G distributions, exponentiated G distributions, beta G distributions, gamma G distributions, Kumaraswamy G distributions, generalized beta G distributions,
beta extended G distributions, gamma G distributions, gamma uniform G distributions, beta exponential G distributions, Weibull G distributions, log gamma G I distributions, log gamma G II distributions,
exponentiated generalized G distributions, exponentiated Kumaraswamy G distributions, geometric exponential Poisson G distributions, truncated-exponential skew-symmetric G distributions, modified beta G distributions,
and exponentiated exponential Poisson G distributions, Poisson-inverse gaussian distribution, Skew normal type 1 distributions, Skew student t distribution, Sinh-Arcsinh distribution, Sichel distribution and Zero inflated Poisson.
Author: Carlos Alberto Cardozo Delgado
Maintainer: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com>
Diff between orders versions 0.1.3 dated 2019-05-16 and 0.1.4 dated 2020-09-24
DESCRIPTION | 19 +++--- MD5 | 16 +++++ NAMESPACE | 130 ++++++++++++++++++++++++++--------------------- R/order_pig.R |only R/order_sichel.R |only R/order_sinharcsinh.R |only R/order_snormal1.R |only R/order_sstudentt.R |only R/order_zip.R |only man/order_pig.Rd |only man/order_sichel.Rd |only man/order_sinharcsinh.Rd |only man/order_snormal1.Rd |only man/order_sstudentt.Rd |only man/order_zip.Rd |only 15 files changed, 97 insertions(+), 68 deletions(-)
Title: Prioritization of Candidate Cancer Subtype Specific Drugs
Description: A systematic biology tool was developed to prioritize cancer subtype-specific drugs by integrating genetic perturbation, drug action, biological pathway, and cancer subtype.
The capabilities of this tool include inferring patient-specific subpathway activity profiles in the context of gene expression profiles with subtype labels, calculating differentially
expressed subpathways based on cultured human cells treated with drugs in the 'cMap' (connectivity map) database, prioritizing cancer subtype specific drugs according to drug-disease
reverse association score based on subpathway, and visualization of results (Castelo (2013) <doi:10.1186/1471-2105-14-7>; Han et al (2019) <doi:10.1093/bioinformatics/btz894>; Lamb and Justin (2006) <DOI:10.1126/science.1132939>).
Author: Xudong Han,
Junwei Han,
Chonghui Liu
Maintainer: Junwei Han <hanjunwei1981@163.com>
Diff between SubtypeDrug versions 0.1.1 dated 2020-06-26 and 0.1.2 dated 2020-09-24
SubtypeDrug-0.1.1/SubtypeDrug/R/OCSSD.R |only SubtypeDrug-0.1.1/SubtypeDrug/R/plotDrugStructure.R |only SubtypeDrug-0.1.1/SubtypeDrug/man/OCSSD.Rd |only SubtypeDrug-0.1.1/SubtypeDrug/man/plotDrugStructure.Rd |only SubtypeDrug-0.1.2/SubtypeDrug/DESCRIPTION | 6 SubtypeDrug-0.1.2/SubtypeDrug/MD5 | 48 ++--- SubtypeDrug-0.1.2/SubtypeDrug/NAMESPACE | 4 SubtypeDrug-0.1.2/SubtypeDrug/R/AccumulateNormal.R | 2 SubtypeDrug-0.1.2/SubtypeDrug/R/Disease_drugs.R | 4 SubtypeDrug-0.1.2/SubtypeDrug/R/PrioSubtypeDrug.R |only SubtypeDrug-0.1.2/SubtypeDrug/R/getDrugSpw.R | 4 SubtypeDrug-0.1.2/SubtypeDrug/R/getDrugStructure.R |only SubtypeDrug-0.1.2/SubtypeDrug/R/plotDScoreHeatmap.R | 39 ++-- SubtypeDrug-0.1.2/SubtypeDrug/R/plotDSpwHeatmap.R | 25 +-- SubtypeDrug-0.1.2/SubtypeDrug/R/plotGlobalGraph.R | 19 +- SubtypeDrug-0.1.2/SubtypeDrug/build/vignette.rds |binary SubtypeDrug-0.1.2/SubtypeDrug/data/Colork.rda |binary SubtypeDrug-0.1.2/SubtypeDrug/inst/doc/vignette.R | 5 SubtypeDrug-0.1.2/SubtypeDrug/inst/doc/vignette.Rmd | 110 ++++++------- SubtypeDrug-0.1.2/SubtypeDrug/inst/doc/vignette.html | 139 ++++++++--------- SubtypeDrug-0.1.2/SubtypeDrug/man/AccumulateNormal.Rd | 2 SubtypeDrug-0.1.2/SubtypeDrug/man/Disease_drugs.Rd | 4 SubtypeDrug-0.1.2/SubtypeDrug/man/PrioSubtypeDrug.Rd |only SubtypeDrug-0.1.2/SubtypeDrug/man/getDrugStructure.Rd |only SubtypeDrug-0.1.2/SubtypeDrug/man/plotDScoreHeatmap.Rd | 39 ++-- SubtypeDrug-0.1.2/SubtypeDrug/man/plotDSpwHeatmap.Rd | 6 SubtypeDrug-0.1.2/SubtypeDrug/man/plotGlobalGraph.Rd | 4 SubtypeDrug-0.1.2/SubtypeDrug/vignettes/references.bib | 33 ++++ SubtypeDrug-0.1.2/SubtypeDrug/vignettes/vignette.Rmd | 110 ++++++------- 29 files changed, 317 insertions(+), 286 deletions(-)
Title: R Script Visualization in Cytoscape
Description: Displays the content of a R script into the 'Cytoscape' network-visualization app <https://cytoscape.org/>.
Author: Raphael Bonnet [aut, cre], Marion Guernoté [ctb], Terry Gouin [ctb], Maxime Laurens [ctb], Thibault Meekel [ctb], Jean-François Peyron[aut,ths]
Maintainer: Raphaël Bonnet <raphael.bonnet@univ-cotedazur.fr>
Diff between ScriptMapR versions 0.0.2 dated 2020-09-21 and 0.0.3 dated 2020-09-24
DESCRIPTION | 8 MD5 | 6 R/scriptmapr.R | 3613 ++++++++++++++++++++++++------------------------ README.md |only inst/extdata/parsed.RDS |only 5 files changed, 1842 insertions(+), 1785 deletions(-)
Title: Random Chuck Norris Facts
Description: R functions for generating and/or displaying random Chuck Norris
facts. Based on data from the 'Internet Chuck Norris database' ('ICNDb').
Author: Brandon Greenwell [aut, cre]
Maintainer: Brandon Greenwell <greenwell.brandon@gmail.com>
Diff between roundhouse versions 0.0.1 dated 2018-09-16 and 0.0.2 dated 2020-09-24
roundhouse-0.0.1/roundhouse/man/fetch_categories.Rd |only roundhouse-0.0.1/roundhouse/tests/testthat |only roundhouse-0.0.1/roundhouse/tests/testthat.R |only roundhouse-0.0.2/roundhouse/DESCRIPTION | 19 +-- roundhouse-0.0.2/roundhouse/MD5 | 29 +++-- roundhouse-0.0.2/roundhouse/NAMESPACE | 4 roundhouse-0.0.2/roundhouse/NEWS.md | 20 +++ roundhouse-0.0.2/roundhouse/R/facts.R |only roundhouse-0.0.2/roundhouse/R/kick.R | 6 - roundhouse-0.0.2/roundhouse/R/punch.R |only roundhouse-0.0.2/roundhouse/R/random_fact.R | 114 ++++---------------- roundhouse-0.0.2/roundhouse/R/suggest_new_fact.R |only roundhouse-0.0.2/roundhouse/data |only roundhouse-0.0.2/roundhouse/inst |only roundhouse-0.0.2/roundhouse/man/facts.Rd |only roundhouse-0.0.2/roundhouse/man/figures |only roundhouse-0.0.2/roundhouse/man/kick.Rd | 12 +- roundhouse-0.0.2/roundhouse/man/punch.Rd |only roundhouse-0.0.2/roundhouse/man/random_fact.Rd | 16 ++ roundhouse-0.0.2/roundhouse/man/suggest_new_fact.Rd |only roundhouse-0.0.2/roundhouse/tests/tinytest.R |only 21 files changed, 102 insertions(+), 118 deletions(-)
Title: The Lorentz Transform in Relativistic Physics
Description: The Lorentz transform in special relativity; also the gyrogroup structure of three-velocities. Includes active and passive transforms and the ability to use units in which the speed of light is not one. For general relativity, see the
'schwarzschild' package.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between lorentz versions 1.0-2 dated 2019-03-21 and 1.0-5 dated 2020-09-24
lorentz-1.0-2/lorentz/tests/aaa.R |only lorentz-1.0-2/lorentz/tests/aab.R |only lorentz-1.0-5/lorentz/DESCRIPTION | 15 - lorentz-1.0-5/lorentz/MD5 | 71 ++++--- lorentz-1.0-5/lorentz/NAMESPACE | 10 - lorentz-1.0-5/lorentz/R/gyrogroup.R | 191 +++++++++++++------- lorentz-1.0-5/lorentz/R/nullvector.R | 10 - lorentz-1.0-5/lorentz/README.md |only lorentz-1.0-5/lorentz/build/partial.rdb |binary lorentz-1.0-5/lorentz/build/vignette.rds |binary lorentz-1.0-5/lorentz/inst/JOC |only lorentz-1.0-5/lorentz/inst/distributive_search.R | 40 +++- lorentz-1.0-5/lorentz/inst/doc/lorentz.R | 218 ++++++++++++++--------- lorentz-1.0-5/lorentz/inst/doc/lorentz.Rnw | 175 +++++++++++++----- lorentz-1.0-5/lorentz/inst/doc/lorentz.pdf |binary lorentz-1.0-5/lorentz/inst/mobius.Rmd |only lorentz-1.0-5/lorentz/man/3vel.Rd | 3 lorentz-1.0-5/lorentz/man/4mom.Rd | 36 ++- lorentz-1.0-5/lorentz/man/4vel.Rd | 28 +- lorentz-1.0-5/lorentz/man/Extract.Rd | 5 lorentz-1.0-5/lorentz/man/as.matrix.Rd |only lorentz-1.0-5/lorentz/man/boost.Rd | 55 +++-- lorentz-1.0-5/lorentz/man/c.Rd | 9 lorentz-1.0-5/lorentz/man/comm_fail.Rd | 12 - lorentz-1.0-5/lorentz/man/cosines.Rd |only lorentz-1.0-5/lorentz/man/galileo.Rd |only lorentz-1.0-5/lorentz/man/gam.Rd | 9 lorentz-1.0-5/lorentz/man/gyr.Rd | 5 lorentz-1.0-5/lorentz/man/r3vel.Rd | 28 ++ lorentz-1.0-5/lorentz/man/reflect.Rd | 30 ++- lorentz-1.0-5/lorentz/man/seq.Rd | 2 lorentz-1.0-5/lorentz/man/set.Rd | 13 - lorentz-1.0-5/lorentz/man/sol.Rd | 25 +- lorentz-1.0-5/lorentz/tests/testthat |only lorentz-1.0-5/lorentz/tests/testthat.R |only lorentz-1.0-5/lorentz/vignettes/f-002.pdf |only lorentz-1.0-5/lorentz/vignettes/lorentz.Rnw | 175 +++++++++++++----- lorentz-1.0-5/lorentz/vignettes/lorentz.bib | 5 38 files changed, 789 insertions(+), 381 deletions(-)
Title: Weighted Logrank Tests and NPMLE for Interval Censored Data
Description: Functions to fit nonparametric survival curves, plot them, and perform logrank or Wilcoxon type tests.
Author: Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between interval versions 1.1-0.1 dated 2014-01-22 and 1.1-0.7 dated 2020-09-24
DESCRIPTION | 10 ++--- MD5 | 25 +++++++------- NAMESPACE | 7 +++- NEWS | 12 ++++++ R/onLoad.R |only build/vignette.rds |binary inst/CITATION | 4 +- inst/doc/intervalCensoring.R | 70 ++++++++++++++++++++-------------------- inst/doc/intervalCensoring.Rnw | 1 inst/doc/intervalCensoring.pdf |binary man/icfit.Rd | 9 ++--- man/ictest.Rd | 6 +-- man/interval-package.Rd | 6 +-- vignettes/intervalCensoring.Rnw | 1 14 files changed, 84 insertions(+), 67 deletions(-)
Title: Graph-Based Change-Point Detection (g-Segmentation)
Description: Using an approach based on similarity graph to estimate change-point(s) and the corresponding p-values. Can be applied to any type of data (high-dimensional, non-Euclidean, etc.) as long as a reasonable similarity measure is available.
Author: Hao Chen, Nancy R. Zhang, Lynna Chu, and Hoseung Song
Maintainer: Hao Chen <hxchen@ucdavis.edu>
Diff between gSeg versions 0.7 dated 2020-04-12 and 1.0 dated 2020-09-24
DESCRIPTION | 10 +++++----- MD5 | 15 ++++++++++----- NAMESPACE | 2 +- R/NNL.R |only R/gSeg_discrete.R |only man/gSeg-package.Rd | 34 ++++++++++++++++++++++++++++++---- man/gseg1.Rd | 4 +--- man/gseg1_discrete.Rd |only man/gseg2.Rd | 4 +--- man/gseg2_discrete.Rd |only man/nnl.Rd |only 11 files changed, 48 insertions(+), 21 deletions(-)
Title: S3 Generics for Bayesian Analyses
Description: Provides S3 generic methods and some default implementations
for Bayesian analyses that generate Markov Chain Monte Carlo (MCMC) samples.
The purpose of 'universals' is to reduce package dependencies and conflicts.
The 'nlist' package implements many of the methods for its 'nlist' class.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>),
Kirill Müller [ctb] (<https://orcid.org/0000-0002-1416-3412>),
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between universals versions 0.0.3 dated 2020-07-08 and 0.0.4 dated 2020-09-24
DESCRIPTION | 11 +++--- MD5 | 62 +++++++++++++++++----------------- NAMESPACE | 2 + NEWS.md | 4 ++ R/bind-iterations.R |only R/collapse-chains.R | 15 ++++++++ R/estimates.R | 6 --- R/nchains.R | 7 --- R/ndims.R | 1 R/niters.R | 5 -- R/npdims.R | 5 -- R/nsams.R | 9 ---- R/nsims.R | 5 -- R/nterms.R | 10 ----- R/pars.R | 4 -- R/pdims.R | 5 -- R/set-pars.R | 7 --- R/split-chains.R | 6 --- man/bind_chains.Rd | 1 man/bind_iterations.Rd |only man/collapse_chains.Rd | 4 ++ man/estimates.Rd | 10 ----- man/nchains.Rd | 10 ----- man/niters.Rd | 8 ---- man/npdims.Rd | 8 ---- man/nsams.Rd | 12 ------ man/nsims.Rd | 8 ---- man/nterms.Rd | 13 ------- man/pars.Rd | 7 --- man/pdims.Rd | 8 ---- man/set_pars.Rd | 10 ----- man/split_chains.Rd | 10 ----- tests/testthat/test-collapse-chains.R | 1 33 files changed, 67 insertions(+), 207 deletions(-)
Title: Time Series, Analysis and Application
Description: Accompanies the book Rainer Schlittgen and Cristina Sattarhoff (2020) <https://www.degruyter.com/view/title/575978> "Angewandte Zeitreihenanalyse mit R, 4. Auflage" . The package contains the time series and functions used therein. It was developed over many years teaching courses about time series analysis.
Author: Rainer Schlittgen
Maintainer: Rainer Schlittgen <R.Schlittgen@t-online.de>
Diff between tsapp versions 1.0.1 dated 2020-09-21 and 1.0.2 dated 2020-09-24
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/specialfun.r | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Score Optimal Probabilistic Forecast Reconciliation
Description: Training of reconciliation weights for probabilistic forecasts to optimise total energy (or variogram) score using Stochastic Gradient Descent with automatically differentiated gradients. See Panagiotelis, Gamakumara, Athanasopoulos and Hyndman, (2020) <https://www.monash.edu/business/ebs/research/publications/ebs/wp26-2020.pdf> for a description of the methods.
Author: Anastasios Panagiotelis [aut, cre]
(<https://orcid.org/0000-0001-8678-7294>)
Maintainer: Anastasios Panagiotelis <anastasios.panagiotelis@sydney.edu.au>
Diff between ProbReco versions 0.1.0 dated 2020-08-18 and 0.1.0.1 dated 2020-09-24
DESCRIPTION | 13 MD5 | 22 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/ProbReco-with-fable.html | 575 +++++++++++++++++++++++++++----------- inst/doc/ProbReco.html | 472 ++++++++++++++++++++++--------- man/ProbReco-package.Rd | 2 man/inscoreopt.Rd | 22 + man/scoreopt.Rd | 19 - man/scoreopt.control.Rd | 16 - man/sim_hierarchy.Rd | 6 man/total_score.Rd | 9 12 files changed, 836 insertions(+), 320 deletions(-)
Title: Tools for Inference in the Presence of a Monotone Likelihood
Description: Proportional hazards estimation in the presence of a partially monotone likelihood has difficulties, in that finite estimators do not exist. These difficulties are related to those arising from logistic and multinomial regression. References for methods are given in the separate function documents.
Author: John E. Kolassa and Juan Zhang
Maintainer: John E. Kolassa <kolassa@stat.rutgers.edu>
Diff between PHInfiniteEstimates versions 1.3 dated 2020-03-29 and 1.5 dated 2020-09-24
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NAMESPACE | 4 +--- R/convertmtol.R | 1 + R/testp.R | 8 ++++++-- R/voter.ml.R | 1 + build/partial.rdb |binary inst/REFERENCES.bib | 2 +- man/convertmtol.Rd | 1 + man/voter.ml.Rd | 1 + 10 files changed, 26 insertions(+), 20 deletions(-)
More information about PHInfiniteEstimates at CRAN
Permanent link
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 1.7.1 dated 2020-04-12 and 1.7.2 dated 2020-09-24
DESCRIPTION | 8 MD5 | 14 NEWS.md | 5 R/tools.R | 2 build/vignette.rds |binary inst/doc/An_Introduction_to_fakemake.html | 421 ++++++++++++++++++++++-------- inst/doc/Building_Packages.html | 371 ++++++++++++++++++++------ man/check_archive.Rd | 2 8 files changed, 625 insertions(+), 198 deletions(-)
Title: Extract Subsequences from GenBank Annotations
Description: Extraction of subsequences into FASTA files from GenBank annotations where gene names may vary among accessions. Borstein & O'Meara (2018) <doi:10.7717/peerj.5179>.
Author: Samuel R. Borstein <sam@borstein.com>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Samuel R. Borstein <sam@borstein.com>
Diff between AnnotationBustR versions 1.2 dated 2018-04-09 and 1.3.0 dated 2020-09-24
DESCRIPTION | 14 - MD5 | 37 +-- NEWS.md | 8 R/AnnotationBust.R | 36 ++- R/FindLongestSeq.R | 2 build/vignette.rds |binary inst/CITATION |only inst/doc/AnnotationBustR-vignette.R | 2 inst/doc/AnnotationBustR-vignette.Rmd | 29 ++ inst/doc/AnnotationBustR-vignette.html | 345 +++++++++++++++++++++++++++++---- man/AnnotationBust.Rd | 22 +- man/AnnotationBustR.Rd | 1 man/FindLongestSeq.Rd | 2 man/cpDNAterms.Rd | 6 man/mtDNAterms.Rd | 6 man/mtDNAtermsPlants.Rd | 6 man/rDNAterms.Rd | 6 tests/testthat/test_AnnotationBust.R | 11 - tests/testthat/test_FindLongestSeq.R | 18 + vignettes/AnnotationBustR-vignette.Rmd | 29 ++ 20 files changed, 465 insertions(+), 115 deletions(-)
More information about AnnotationBustR at CRAN
Permanent link
Title: Presentation Ninja
Description: Create HTML5 slides with R Markdown and the JavaScript library
'remark.js' (<https://remarkjs.com>).
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Alessandro Gasparini [ctb] (<https://orcid.org/0000-0002-8319-7624>),
Benjie Gillam [ctb],
Claus Thorn Ekstrøm [ctb],
Daniel Anderson [ctb],
Dawei Lang [ctb],
Emi Tanaka [ctb],
Garrick Aden-Buie [ctb] (<https://orcid.org/0000-0002-7111-0077>),
Iñaki Ucar [ctb] (<https://orcid.org/0000-0001-6403-5550>),
John Little [ctb],
Joselyn Chávez [ctb] (<https://orcid.org/0000-0002-4974-4591>),
Joseph Casillas [ctb],
Lucy D'Agostino McGowan [ctb] (<https://orcid.org/0000-0001-7297-9359>),
Malcolm Barrett [ctb] (<https://orcid.org/0000-0003-0299-5825>),
Matthew Mark Strasiotto [ctb] (mstr3336),
Michael Wayne Kearney [ctb],
Nan-Hung Hsieh [ctb],
Ole Petter Bang [ctb] (CSS in
rmarkdown/templates/xaringan/resources/default.css),
Patrick Schratz [ctb],
Paul Klemm [ctb] (<https://orcid.org/0000-0002-5985-1737>),
Paul Lemmens [ctb],
Sean Lopp [ctb],
Yongfu Liao [ctb],
Yue Jiang [ctb] (<https://orcid.org/0000-0002-9798-5517>)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xaringan versions 0.16 dated 2020-03-31 and 0.17 dated 2020-09-24
DESCRIPTION | 12 MD5 | 38 +- R/render.R | 39 +- README.md | 8 build/vignette.rds |binary inst/examples/ki-demo.Rmd | 2 inst/examples/uol-demo.Rmd | 2 inst/rmarkdown/templates/xaringan/resources/default.css | 2 inst/rmarkdown/templates/xaringan/resources/fc.css | 10 inst/rmarkdown/templates/xaringan/resources/ki-fonts.css | 2 inst/rmarkdown/templates/xaringan/resources/ki.css | 154 +++++----- inst/rmarkdown/templates/xaringan/resources/middlebury.css | 6 inst/rmarkdown/templates/xaringan/resources/robot.css | 2 inst/rmarkdown/templates/xaringan/resources/rutgers.css | 2 inst/rmarkdown/templates/xaringan/resources/uol.css | 2 inst/rmarkdown/templates/xaringan/resources/useR-fonts.css |only inst/rmarkdown/templates/xaringan/resources/useR.css |only inst/rmarkdown/templates/xaringan/skeleton/skeleton.Rmd | 45 +- inst/rmarkdown/templates/xaringan_zh-CN/skeleton/skeleton.Rmd | 16 - man/inf_mr.Rd | 2 man/moon_reader.Rd | 19 - 21 files changed, 192 insertions(+), 171 deletions(-)
Title: An R Package for Text Analysis
Description: A set of tools to analyze texts. Includes, amongst others, functions for automatic language detection, hyphenation, several indices of lexical diversity (e.g., type
token ratio, HD-D/vocd-D, MTLD) and readability (e.g., Flesch, SMOG, LIX, Dale-Chall). Basic import functions for language corpora are also provided, to enable
frequency analyses (supports Celex and Leipzig Corpora Collection file formats) and measures like tf-idf. Note: For full functionality a local installation of
TreeTagger is recommended. It is also recommended to not load this package directly, but by loading one of the available language support packages from the
'l10n' repository <https://undocumeantit.github.io/repos/l10n/>. 'koRpus' also includes a plugin for the R GUI and IDE RKWard, providing graphical dialogs for
its basic features. The respective R package 'rkward' cannot be installed directly from a repository, as it is a part of RKWard. To make full use of this
feature, please install RKWard from <https://rkward.kde.org> (plugins are detected automatically). Due to some restrictions on CRAN, the full package sources
are only available from the project homepage. To ask for help, report bugs, request features, or discuss the development of the package, please subscribe to
the koRpus-dev mailing list (<https://korpusml.reaktanz.de>).
Author: Meik Michalke [aut, cre],
Earl Brown [ctb],
Alberto Mirisola [ctb],
Alexandre Brulet [ctb],
Laura Hauser [ctb]
Maintainer: Meik Michalke <meik.michalke@hhu.de>
Diff between koRpus versions 0.13-1 dated 2020-09-21 and 0.13-2 dated 2020-09-24
ChangeLog | 7 +++++++ DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/02_method_readTagged.R | 2 +- R/koRpus-package.R | 4 ++-- build/partial.rdb |binary inst/CITATION | 4 ++-- inst/doc/koRpus_vignette.html | 4 ++-- man/koRpus-package.Rd | 4 ++-- man/readTagged-methods.Rd | 2 +- tests/testthat/test_tokenizing_POS_tagging.R | 21 ++++++++++++++++----- 11 files changed, 47 insertions(+), 29 deletions(-)
Title: A Universal Foreach Parallel Adapter using the Future API of the
'future' Package
Description: Provides a '%dopar%' adapter such that any type of futures can
be used as backends for the 'foreach' framework.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between doFuture versions 0.9.0 dated 2020-01-11 and 0.10.0 dated 2020-09-24
doFuture-0.10.0/doFuture/DESCRIPTION | 14 - doFuture-0.10.0/doFuture/MD5 | 73 +++++----- doFuture-0.10.0/doFuture/NEWS | 23 ++- doFuture-0.10.0/doFuture/R/doFuture-package.R | 4 doFuture-0.10.0/doFuture/R/doFuture.R | 3 doFuture-0.10.0/doFuture/R/makeChunks.R |only doFuture-0.10.0/doFuture/R/registerDoFuture.R | 15 ++ doFuture-0.10.0/doFuture/R/utils.R | 23 +-- doFuture-0.10.0/doFuture/build/vignette.rds |binary doFuture-0.10.0/doFuture/inst/CITATION |only doFuture-0.10.0/doFuture/inst/doc/doFuture.html | 12 - doFuture-0.10.0/doFuture/inst/doc/doFuture.md.rsp | 12 - doFuture-0.10.0/doFuture/inst/tests2/NMF/manual.R | 2 doFuture-0.10.0/doFuture/inst/tests2/caret/examples.R | 2 doFuture-0.10.0/doFuture/inst/tests2/glmnet/examples.R | 2 doFuture-0.10.0/doFuture/inst/tests2/incl/utils.R | 30 ++-- doFuture-0.10.0/doFuture/man/doFuture.Rd | 17 +- doFuture-0.10.0/doFuture/man/makeChunks.Rd | 2 doFuture-0.10.0/doFuture/tests/DEPRECATED.R | 4 doFuture-0.10.0/doFuture/tests/doRNG,dorng.R | 5 doFuture-0.10.0/doFuture/tests/foreach,errors.R | 2 doFuture-0.10.0/doFuture/tests/foreach,globals.R | 2 doFuture-0.10.0/doFuture/tests/foreach.R | 45 ------ doFuture-0.10.0/doFuture/tests/incl/end.R | 3 doFuture-0.10.0/doFuture/tests/incl/start,load-only.R | 2 doFuture-0.10.0/doFuture/tests/makeChunks.R |only doFuture-0.10.0/doFuture/tests/registerDoFuture.R | 2 doFuture-0.10.0/doFuture/tests/times.R | 2 doFuture-0.10.0/doFuture/tests/utils.R |only doFuture-0.10.0/doFuture/tests/zzz,BiocParallel.R |only doFuture-0.10.0/doFuture/tests/zzz_opt-in,NMF,examples.R |only doFuture-0.10.0/doFuture/tests/zzz_opt-in,TSP,examples.R |only doFuture-0.10.0/doFuture/tests/zzz_opt-in,caret,examples.R |only doFuture-0.10.0/doFuture/tests/zzz_opt-in,foreach,examples.R |only doFuture-0.10.0/doFuture/tests/zzz_opt-in,future.BatchJobs.R |only doFuture-0.10.0/doFuture/tests/zzz_opt-in,future.batchtools.R |only doFuture-0.10.0/doFuture/tests/zzz_opt-in,glmnet,examples.R |only doFuture-0.10.0/doFuture/tests/zzz_opt-in,plyr,examples.R |only doFuture-0.10.0/doFuture/tests/zzz_opt-in,plyr.R | 55 +++++-- doFuture-0.10.0/doFuture/vignettes/doFuture.md.rsp | 12 - doFuture-0.9.0/doFuture/R/chunks.R |only doFuture-0.9.0/doFuture/tests/future.BatchJobs.R |only doFuture-0.9.0/doFuture/tests/future.batchtools.R |only doFuture-0.9.0/doFuture/tests/zzz_opt-in,NMF.R |only doFuture-0.9.0/doFuture/tests/zzz_opt-in,TSP.R |only doFuture-0.9.0/doFuture/tests/zzz_opt-in,caret.R |only doFuture-0.9.0/doFuture/tests/zzz_opt-in,foreach.R |only doFuture-0.9.0/doFuture/tests/zzz_opt-in,glmnet.R |only 48 files changed, 191 insertions(+), 177 deletions(-)
Title: Apply Functions to All Combinations of List Elements
Description: Provides an extension to the 'purrr' family of
mapping functions to apply a function to each combination of elements
in a list of inputs. Also includes functions for automatically
detecting output type in mapping functions, finding every combination
of elements of lists or rows of data frames, and applying multiple
models to multiple subsets of a dataset.
Author: Alexander Rossell Hayes [aut, cre, cph]
(<https://orcid.org/0000-0001-9412-0457>)
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>
Diff between crossmap versions 0.1.0 dated 2020-09-10 and 0.2.0 dated 2020-09-24
DESCRIPTION | 11 ++--- MD5 | 17 ++++---- NEWS.md |only R/cross_fit.R | 55 ++++++++++++++++++++++---- R/isFALSE.R | 12 ++--- README.md | 84 ++++++++++++++++++++-------------------- man/cross_fit.Rd | 11 ++++- man/cross_join.Rd | 4 - man/crossmap-package.Rd | 1 tests/testthat/test-cross_fit.R | 71 ++++++++++++++++++++++++++++----- 10 files changed, 185 insertions(+), 81 deletions(-)
Title: Reading and Saving DICOM Image Files
Description: This function provides an interface between 'Matlab' and 'R' in facilitating fast processing for reading and saving DICOM images.
Author: Shu Jiang [aut, cre] (<https://orcid.org/0000-0003-1464-4838>)
Maintainer: Shu Jiang <jiang.shu@wustl.edu>
Diff between DICOMread versions 0.0.0.1 dated 2020-09-01 and 0.0.0.2 dated 2020-09-24
DICOMread-0.0.0.1/DICOMread/R/save_mat.R |only DICOMread-0.0.0.1/DICOMread/man/form_mat_fun.Rd |only DICOMread-0.0.0.2/DICOMread/DESCRIPTION | 6 +++--- DICOMread-0.0.0.2/DICOMread/MD5 | 6 ++---- DICOMread-0.0.0.2/DICOMread/NAMESPACE | 1 - 5 files changed, 5 insertions(+), 8 deletions(-)
Title: An Extension of the Taylor Diagram to Two-Dimensional Vector
Data
Description: A new diagram for the verification of vector variables (wind, current, etc) generated by multiple models against a set of observations is presented in this package. It has been designed as a generalization of the Taylor diagram to two dimensional quantities. It is based on the analysis of the two-dimensional structure of the mean squared error matrix between model and observations. The matrix is divided into the part corresponding to the relative rotation and the bias of the empirical orthogonal functions of the data. The full set of diagnostics produced by the analysis of the errors between model and observational vector datasets comprises the errors in the means, the analysis of the total variance of both datasets, the rotation matrix corresponding to the principal components in observation and model, the angle of rotation of model-derived empirical orthogonal functions respect to the ones from observations, the standard deviation of model and observations, the root mean squared error between both datasets and the squared two-dimensional correlation coefficient. See the output of function UVError() in this package.
Author: Jon Sáenz [aut, cph] (<https://orcid.org/0000-0002-5920-7570>),
Sheila Carreno-Madinabeitia [aut, cph]
(<https://orcid.org/0000-0003-4625-6178>),
Santos J. González-Rojí [aut, cre, cph]
(<https://orcid.org/0000-0003-4737-0984>),
Ganix Esnaola [ctb, cph] (<https://orcid.org/0000-0001-9058-043X>),
Gabriel Ibarra-Berastegi [ctb, cph]
(<https://orcid.org/0000-0001-8681-3755>),
Alain Ulazia [ctb, cph] (<https://orcid.org/0000-0002-4124-2853>)
Maintainer: Santos J. González-Rojí <santosjose.gonzalez@ehu.eus>
Diff between SailoR versions 1.1.2 dated 2020-07-16 and 1.2 dated 2020-09-23
DESCRIPTION | 8 - MD5 | 6 NEWS.md | 5 R/UVError.R | 397 ++++++++++++++++++++++++++++++------------------------------ 4 files changed, 215 insertions(+), 201 deletions(-)
Title: Crawler and Data Scraper for Open Journal System ('OJS')
Description: Crawler for 'OJS' pages and scraper for meta-data from articles.
You can crawl 'OJS' archives, issues, articles, galleys, and search results.
You can scrape articles metadata from their head tag in html,
or from Open Archives Initiative ('OAI') records.
Most of these functions rely on 'OJS' routing conventions
(<https://docs.pkp.sfu.ca/dev/documentation/en/architecture-routes>).
Author: Gaston Becerra [aut, cre] (<https://orcid.org/0000-0001-9432-8848>)
Maintainer: Gaston Becerra <gaston.becerra@gmail.com>
Diff between ojsr versions 0.1.1 dated 2020-07-01 and 0.1.2 dated 2020-09-23
DESCRIPTION | 14 - MD5 | 34 +-- NEWS.md | 11 + R/ojsr.R | 7 R/scrapers.R | 201 +++++++++++--------- R/url_parsers.R | 4 README.md | 35 ++- inst/doc/ojsr-vignette.R | 79 ++++++- inst/doc/ojsr-vignette.Rmd | 195 +++++++++++-------- inst/doc/ojsr-vignette.html | 377 ++++++++++++++++++++------------------ man/get_articles_from_issue.Rd | 4 man/get_articles_from_search.Rd | 6 man/get_galleys_from_article.Rd | 4 man/get_html_meta_from_article.Rd | 4 man/get_issues_from_archive.Rd | 4 man/get_oai_meta_from_article.Rd | 4 man/ojsr.Rd | 7 vignettes/ojsr-vignette.Rmd | 195 +++++++++++-------- 18 files changed, 700 insertions(+), 485 deletions(-)
Title: Learning Causal or Non-Causal Graphical Models Using Information
Theory
Description: We report an information-theoretic method which learns a large
class of causal or non-causal graphical models from purely observational
data, while including the effects of unobserved latent variables, commonly
found in many datasets. Starting from a complete graph, the method
iteratively removes dispensable edges, by uncovering significant information
contributions from indirect paths, and assesses edge-specific confidences
from randomization of available data. The remaining edges are then oriented
based on the signature of causality in observational data. This approach can
be applied on a wide range of datasets and provide new biological insights
on regulatory networks from single cell expression data, genomic alterations
during tumor development and co-evolving residues in protein structures.
For more information you can refer to:
Cabeli et al. PLoS Comp. Bio. 2020 <doi:10.1371/journal.pcbi.1007866>,
Verny et al. PLoS Comp. Bio. 2017 <doi:10.1371/journal.pcbi.1005662>.
Author: Vincent Cabeli [aut, cre],
Honghao Li [aut],
Marcel Ribeiro Dantas [aut],
Nadir Sella [aut],
Louis Verny [aut],
Severine Affeldt [aut],
Hervé Isambert [aut]
Maintainer: Vincent Cabeli <vincent.cabeli@curie.fr>
Diff between miic versions 1.5.1 dated 2020-09-18 and 1.5.2 dated 2020-09-23
DESCRIPTION | 6 MD5 | 34 R/miic.R | 2 man/miic.Rd | 2 src/computation_continuous.cpp | 1839 ++++++++++++++--------------------------- src/computation_continuous.h | 7 src/computation_discrete.cpp | 551 ++++-------- src/confidence_cut.cpp | 6 src/environment.h | 1 src/get_information.cpp | 8 src/linear_allocator.cpp | 19 src/linear_allocator.h | 6 src/mdl_pair_discretize.cpp | 48 - src/mutual_information.cpp | 294 ++---- src/mutual_information.h | 166 +-- src/skeleton.cpp | 14 src/structure.h | 22 src/utilities.cpp | 25 18 files changed, 1135 insertions(+), 1915 deletions(-)
Title: Animal Social Network Inference and Permutations for Ecologists
Description: Implements several tools that are used in animal social network analysis, as described in Whitehead (2007) Analyzing Animal Societies <University of Chicago Press> and Farine & Whitehead (2015) <doi: 10.1111/1365-2656.12418>. In particular, this package provides the tools to infer groups and generate networks from observation data, perform permutation tests on the data, calculate lagged association rates, and performed multiple regression analysis on social network data.
Author: Damien R. Farine <dfarine@ab.mpg.de>
Maintainer: Damien R. Farine <dfarine@ab.mpg.de>
Diff between asnipe versions 1.1.12 dated 2019-08-19 and 1.1.13 dated 2020-09-23
DESCRIPTION | 10 ++++----- MD5 | 17 ++++++++------- R/network_permutation.R | 50 ++++++++++++++++++++++++++++++++------------- R/network_swap.R | 48 ++++++++++++++++++++++++++++++++----------- inst |only man/asnipe-package.Rd | 4 +-- man/mrqap.custom.null.Rd | 4 +-- man/mrqap.dsp.Rd | 4 +-- man/network_permutation.Rd | 10 ++++++++- man/network_swap.Rd | 13 ++++++++++- 10 files changed, 113 insertions(+), 47 deletions(-)
Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting including the introduced here Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, color themes, Trellis graphics and a built-in help system. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, and generation and rendering of R markdown instructions for interpretative output.
Author: David Gerbing, The School of Business, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 3.9.6 dated 2020-06-11 and 3.9.7 dated 2020-09-23
lessR-3.9.6/lessR/R/corFA.Rmd.R |only lessR-3.9.7/lessR/DESCRIPTION | 8 lessR-3.9.7/lessR/MD5 | 115 +++++---- lessR-3.9.7/lessR/NAMESPACE | 2 lessR-3.9.7/lessR/NEWS | 58 ++++- lessR-3.9.7/lessR/R/ANOVA.R | 3 lessR-3.9.7/lessR/R/ANOVAz2.R | 93 +++++--- lessR-3.9.7/lessR/R/BarChart.R | 18 - lessR-3.9.7/lessR/R/Logit.R | 2 lessR-3.9.7/lessR/R/Plot.R | 11 lessR-3.9.7/lessR/R/Read.R | 22 + lessR-3.9.7/lessR/R/Regression.R | 290 +++++++++++++------------ lessR-3.9.7/lessR/R/Rescale.R |only lessR-3.9.7/lessR/R/corCFA.R | 27 +- lessR-3.9.7/lessR/R/corEFA.R | 23 + lessR-3.9.7/lessR/R/corFA_Rmd.R |only lessR-3.9.7/lessR/R/corProp.R | 19 - lessR-3.9.7/lessR/R/corReflect.R | 20 - lessR-3.9.7/lessR/R/corReorder.R | 104 +++++++- lessR-3.9.7/lessR/R/corScree.R | 37 ++- lessR-3.9.7/lessR/R/factors.R | 2 lessR-3.9.7/lessR/R/plt.zadd.R | 21 + lessR-3.9.7/lessR/R/plt.zbubble.R |only lessR-3.9.7/lessR/R/plt.zmain.R | 215 ++++++------------ lessR-3.9.7/lessR/R/reg.z1modelBasic.R | 3 lessR-3.9.7/lessR/R/reg.zKfold.R | 45 ++- lessR-3.9.7/lessR/R/style.R | 5 lessR-3.9.7/lessR/R/style.zshow.R | 2 lessR-3.9.7/lessR/R/zzz.R | 67 +++-- lessR-3.9.7/lessR/build/vignette.rds |binary lessR-3.9.7/lessR/inst/doc/BarChart.html | 78 +++--- lessR-3.9.7/lessR/inst/doc/Customize.html | 17 + lessR-3.9.7/lessR/inst/doc/Extract.html | 32 ++ lessR-3.9.7/lessR/inst/doc/FactorAnalysis.R |only lessR-3.9.7/lessR/inst/doc/FactorAnalysis.Rmd |only lessR-3.9.7/lessR/inst/doc/FactorAnalysis.html |only lessR-3.9.7/lessR/inst/doc/Histogram.html | 16 + lessR-3.9.7/lessR/inst/doc/Means.R | 21 + lessR-3.9.7/lessR/inst/doc/Means.Rmd | 65 +++-- lessR-3.9.7/lessR/inst/doc/Means.html | 210 +++++++++++------- lessR-3.9.7/lessR/inst/doc/Plot.R | 13 + lessR-3.9.7/lessR/inst/doc/Plot.Rmd | 24 +- lessR-3.9.7/lessR/inst/doc/Plot.html | 100 +++++++- lessR-3.9.7/lessR/inst/doc/Read.html | 16 + lessR-3.9.7/lessR/inst/doc/Regression.R | 5 lessR-3.9.7/lessR/inst/doc/Regression.Rmd | 11 lessR-3.9.7/lessR/inst/doc/Regression.html | 108 ++++++++- lessR-3.9.7/lessR/inst/doc/pivot.html | 16 + lessR-3.9.7/lessR/man/ANOVA.Rd | 7 lessR-3.9.7/lessR/man/Plot.Rd | 46 ++- lessR-3.9.7/lessR/man/Regression.Rd | 60 +++-- lessR-3.9.7/lessR/man/Rescale.Rd |only lessR-3.9.7/lessR/man/corCFA.Rd | 6 lessR-3.9.7/lessR/man/corEFA.Rd | 6 lessR-3.9.7/lessR/man/corProp.Rd | 2 lessR-3.9.7/lessR/man/corReflect.Rd | 2 lessR-3.9.7/lessR/man/corReorder.Rd | 23 + lessR-3.9.7/lessR/man/corScree.Rd | 4 lessR-3.9.7/lessR/man/style.Rd | 2 lessR-3.9.7/lessR/vignettes/FactorAnalysis.Rmd |only lessR-3.9.7/lessR/vignettes/Means.Rmd | 65 +++-- lessR-3.9.7/lessR/vignettes/Plot.Rmd | 24 +- lessR-3.9.7/lessR/vignettes/Regression.Rmd | 11 63 files changed, 1430 insertions(+), 772 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and
individual-level relations in time series data from within a structural
equation modeling framework.
Author: Stephanie Lane [aut, trl],
Kathleen Gates [aut, cre],
Zachary Fisher [aut],
Cara Arizmendi [aut],
Peter Molenaar [aut],
Michael Hallquist [ctb],
Hallie Pike [ctb],
Teague Henry [ctb],
Kelly Duffy [ctb],
Lan Luo [ctb],
Adriene Beltz [csp]
Maintainer: KM Gates <gateskm@email.unc.edu>
Diff between gimme versions 0.7-2 dated 2020-09-03 and 0.7-3 dated 2020-09-23
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/final.org.R | 6 +++--- inst/doc/gimme_vignette.html | 4 ++-- 4 files changed, 13 insertions(+), 13 deletions(-)
Title: Tests for Right and Interval-Censored Survival Data Based on the
Fleming-Harrington Class
Description: Functions to compare two or more survival curves with:
a) The Fleming-Harrington test for right-censored data based on permutations and on counting processes.
b) An extension of the Fleming-Harrington test for interval-censored data based on a permutation distribution and on a score vector distribution.
Author: Ramon Oller, Klaus Langohr
Maintainer: Ramon Oller <ramon.oller@uvic.cat>
Diff between FHtest versions 1.4 dated 2017-11-08 and 1.5 dated 2020-09-23
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- R/rcc.R | 2 +- R/rcp.R | 2 +- man/FHtest-package.Rd | 4 ++-- man/FHtesticp.Rd | 16 ++++++++-------- man/FHtestics.Rd | 10 +++++----- man/FHtestrcc.Rd | 8 ++++---- man/FHtestrcp.Rd | 14 +++++++------- man/illust3.Rd | 2 +- 10 files changed, 44 insertions(+), 44 deletions(-)
Title: General Resampling Infrastructure
Description: Classes and functions to create and summarize different types of resampling objects (e.g. bootstrap, cross-validation).
Author: Max Kuhn [aut, cre],
Fanny Chow [aut],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between rsample versions 0.0.7 dated 2020-06-04 and 0.0.8 dated 2020-09-23
DESCRIPTION | 13 - MD5 | 116 +++++++------ NAMESPACE | 63 +++++++ NEWS.md | 8 R/apparent.R | 2 R/boot.R | 20 +- R/bootci.R | 20 +- R/compat-vctrs-helpers.R | 14 + R/compat-vctrs.R | 208 +++++++++++++++++++++++++ R/complement.R | 37 +++- R/data.R | 2 R/form_pred.R | 4 R/groups.R | 4 R/initial_split.R | 2 R/lables.R | 37 +++- R/loo.R | 2 R/manual.R |only R/mc.R | 22 +- R/misc.R | 4 R/nest.R | 2 R/pkg.R | 2 R/rolling_origin.R | 7 R/rset.R | 12 + R/rsplit.R | 4 R/slide.R |only R/validation_split.R | 4 R/vfold.R | 24 +- build/vignette.rds |binary inst/doc/Basics.html | 16 + inst/doc/Working_with_rsets.html | 68 +++++--- man/add_resample_id.Rd | 2 man/apparent.Rd | 2 man/bootstraps.Rd | 20 +- man/complement.Rd | 2 man/form_pred.Rd | 4 man/group_vfold_cv.Rd | 2 man/initial_split.Rd | 2 man/int_pctl.Rd | 9 - man/labels.rset.Rd | 2 man/manual_rset.Rd |only man/mc_cv.Rd | 20 +- man/nested_cv.Rd | 2 man/populate.Rd | 4 man/pretty.vfold_cv.Rd | 16 + man/rolling_origin.Rd | 8 man/rsample.Rd | 2 man/slide-resampling.Rd |only man/two_class_dat.Rd | 2 man/validation_split.Rd | 2 man/vfold_cv.Rd | 22 +- tests/testthat/test-manual.R |only tests/testthat/test-print-groups.txt | 10 - tests/testthat/test-slide.R |only tests/testthat/test_boot.R | 27 +-- tests/testthat/test_bootci.R | 35 +++- tests/testthat/test_for_pred.R | 8 tests/testthat/test_group.R | 44 ++--- tests/testthat/test_mc.R | 17 -- tests/testthat/test_rset.R | 4 tests/testthat/test_validation.R | 19 +- tests/testthat/test_vfold.R | 15 - vignettes/Applications/Recipes_and_rsample.Rmd | 2 62 files changed, 734 insertions(+), 287 deletions(-)
Title: Novel Statistical Test for Aberration Enrichment
Description: Testing for heterogeneous effects in a case-control setting.
The aim here to discover an association that is beyond a mean difference
between all cases and all controls. Instead, the signal of interest here
is present in only a proportion of the cases. This test should be more
powerful than a t-test or Wilcoxon test in this heterogeneous setting.
Please cite the corresponding paper: Mezlini et al. (2020)
<doi:10.1101/2020.03.23.002972>.
Author: Aziz M. Mezlini [aut,cre,cph]
Maintainer: Aziz M. Mezlini <mmezlini@mgh.harvard.edu>
Diff between aziztest versions 0.1.0 dated 2020-04-01 and 0.2.0 dated 2020-09-23
DESCRIPTION | 6 +-- MD5 | 22 ++++++------ NAMESPACE | 2 + R/aziztest_description.R | 4 +- R/main.R | 77 +++++++++++++++++++++++++++++------------- R/post_analysis.R | 11 +++--- inst/CITATION | 4 +- man/aziz.test.Rd | 27 ++++++++++++-- man/aziztest.Rd | 4 +- man/calibrate_test.Rd | 21 +++++++++-- man/get_calibrated_pvalues.Rd | 12 ++++-- man/which_aberrant.Rd | 2 - 12 files changed, 134 insertions(+), 58 deletions(-)